From e2d192e2c3914200d561d188abf548fb37320301 Mon Sep 17 00:00:00 2001 From: Peter Lawrence Date: Thu, 1 Mar 2018 15:04:31 -0700 Subject: [PATCH 0001/2067] Added new files to allow Gross Unrepresented Land Use transition --- src/biogeochem/CNBalanceCheckMod.F90 | 10 +- src/biogeochem/CNCIsoFluxMod.F90 | 279 +++++++++ src/biogeochem/CNCStateUpdate2Mod.F90 | 115 ++++ src/biogeochem/CNDriverMod.F90 | 54 +- src/biogeochem/CNNStateUpdate2Mod.F90 | 108 ++++ src/biogeochem/CNProductsMod.F90 | 86 ++- src/biogeochem/CNVegCarbonFluxType.F90 | 302 +++++++++- src/biogeochem/CNVegNitrogenFluxType.F90 | 151 ++++- src/biogeochem/CNVegetationFacade.F90 | 9 + src/biogeochem/dynConsBiogeochemMod.F90 | 70 ++- src/biogeochem/dynGrossUnrepMod.F90 | 528 ++++++++++++++++++ src/dyn_subgrid/dynSubgridControlMod.F90 | 35 ++ src/dyn_subgrid/dynSubgridDriverMod.F90 | 11 + .../SoilBiogeochemCarbonStateType.F90 | 27 +- .../SoilBiogeochemNitrogenStateType.F90 | 27 +- 15 files changed, 1719 insertions(+), 93 deletions(-) create mode 100644 src/biogeochem/dynGrossUnrepMod.F90 diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index f2811d290a..4a34f95f9c 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -141,6 +141,8 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & col_begcb => this%begcb_col , & ! Input: [real(r8) (:) ] (gC/m2) carbon mass, beginning of time step col_endcb => this%endcb_col , & ! Output: [real(r8) (:) ] (gC/m2) carbon mass, end of time step wood_harvestc => cnveg_carbonflux_inst%wood_harvestc_col , & ! Input: [real(r8) (:) ] (gC/m2/s) wood harvest (to product pools) + gru_conv_cflux => cnveg_carbonflux_inst%gru_conv_cflux_col , & ! Input: [real(r8) (:) ] (gC/m2/s) wood harvest (to product pools) + gru_wood_productc_gain => cnveg_carbonflux_inst%gru_wood_productc_gain_col , & ! Input: [real(r8) (:) ] (gC/m2/s) wood harvest (to product pools) grainc_to_cropprodc => cnveg_carbonflux_inst%grainc_to_cropprodc_col , & ! Input: [real(r8) (:) ] (gC/m2/s) grain C to 1-year crop product pool gpp => cnveg_carbonflux_inst%gpp_col , & ! Input: [real(r8) (:) ] (gC/m2/s) gross primary production er => cnveg_carbonflux_inst%er_col , & ! Input: [real(r8) (:) ] (gC/m2/s) total ecosystem respiration, autotrophic + heterotrophic @@ -167,7 +169,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! calculate total column-level outputs ! er = ar + hr, col_fire_closs includes patch-level fire losses - col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + gru_conv_cflux(c) ! Fluxes to product pools are included in column-level outputs: the product ! pools are not included in totcolc, so are outside the system with respect to @@ -176,6 +178,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! after the dwt term has already been taken out.) col_coutputs = col_coutputs + & wood_harvestc(c) + & + gru_wood_productc_gain(c) + & grainc_to_cropprodc(c) ! subtract leaching flux @@ -268,6 +271,8 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & col_fire_nloss => cnveg_nitrogenflux_inst%fire_nloss_col , & ! Input: [real(r8) (:) ] (gN/m2/s) total column-level fire N loss wood_harvestn => cnveg_nitrogenflux_inst%wood_harvestn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) wood harvest (to product pools) + gru_conv_nflux => cnveg_nitrogenflux_inst%gru_conv_nflux_col , & ! Input: [real(r8) (:) ] (gC/m2/s) wood harvest (to product pools) + gru_wood_productn_gain => cnveg_nitrogenflux_inst%gru_wood_productn_gain_col , & ! Input: [real(r8) (:) ] (gC/m2/s) wood harvest (to product pools) grainn_to_cropprodn => cnveg_nitrogenflux_inst%grainn_to_cropprodn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) grain N to 1-year crop product pool totcoln => cnveg_nitrogenstate_inst%totn_col & ! Input: [real(r8) (:) ] (gN/m2) total column nitrogen, incl veg @@ -295,7 +300,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & end if ! calculate total column-level outputs - col_noutputs(c) = denit(c) + col_fire_nloss(c) + col_noutputs(c) = denit(c) + col_fire_nloss(c) + gru_conv_nflux(c) ! Fluxes to product pools are included in column-level outputs: the product ! pools are not included in totcoln, so are outside the system with respect to @@ -304,6 +309,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! after the dwt term has already been taken out.) col_noutputs(c) = col_noutputs(c) + & wood_harvestn(c) + & + gru_wood_productn_gain(c) + & grainn_to_cropprodn(c) if (.not. use_nitrif_denitrif) then diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index a92ab44e47..4d5e88a247 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -28,12 +28,14 @@ module CNCIsoFluxMod public :: CIsoFlux1 public :: CIsoFlux2 public :: CIsoFlux2h + public :: CIsoFlux2g public :: CIsoFlux3 ! ! !PRIVATE MEMBER FUNCTIONS: private :: CNCIsoLitterToColumn private :: CNCIsoGapPftToColumn private :: CNCIsoHarvestPftToColumn + private :: CNCIsoGrossUnrepPftToColumn private :: CIsoFluxCalc character(len=*), parameter, private :: sourcefile = & @@ -803,6 +805,157 @@ subroutine CIsoFlux2h(num_soilc , filter_soilc, num_soilp , filter_soilp, & end subroutine CIsoFlux2h + !----------------------------------------------------------------------- + subroutine CIsoFlux2g(num_soilc , filter_soilc, num_soilp , filter_soilp, & + soilbiogeochem_state_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + iso_cnveg_carbonflux_inst, iso_cnveg_carbonstate_inst, isotope) + ! + ! !DESCRIPTION: + ! set the carbon isotopic fluxes for gross unrepresented landcover change mortality + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns filter + integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches + type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: iso_cnveg_carbonstate_inst + character(len=*) , intent(in) :: isotope ! 'c13' or 'c14' + + !----------------------------------------------------------------------- + + associate( & + cnveg_cf => cnveg_carbonflux_inst , & + cnveg_cs => cnveg_carbonstate_inst , & + iso_cnveg_cf => iso_cnveg_carbonflux_inst , & + iso_cnveg_cs => iso_cnveg_carbonstate_inst & + ) + + ! patch-level gap mortality fluxes + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_leafc_to_litter_patch , cnveg_cf%gru_leafc_to_litter_patch, & + iso_cnveg_cs%leafc_patch , cnveg_cs%leafc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_leafc_storage_to_atm_patch , cnveg_cf%gru_leafc_storage_to_atm_patch, & + iso_cnveg_cs%leafc_storage_patch , cnveg_cs%leafc_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_leafc_xfer_to_atm_patch , cnveg_cf%gru_leafc_xfer_to_atm_patch, & + iso_cnveg_cs%leafc_xfer_patch , cnveg_cs%leafc_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_frootc_to_litter_patch , cnveg_cf%gru_frootc_to_litter_patch, & + iso_cnveg_cs%frootc_patch , cnveg_cs%frootc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_frootc_storage_to_atm_patch , cnveg_cf%gru_frootc_storage_to_atm_patch, & + iso_cnveg_cs%frootc_storage_patch , cnveg_cs%frootc_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_frootc_xfer_to_atm_patch , cnveg_cf%gru_frootc_xfer_to_atm_patch, & + iso_cnveg_cs%frootc_xfer_patch , cnveg_cs%frootc_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_livestemc_to_atm_patch , cnveg_cf%gru_livestemc_to_atm_patch, & + iso_cnveg_cs%livestemc_patch , cnveg_cs%livestemc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_livestemc_storage_to_atm_patch , cnveg_cf%gru_livestemc_storage_to_atm_patch, & + iso_cnveg_cs%livestemc_storage_patch , cnveg_cs%livestemc_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_livestemc_xfer_to_atm_patch , cnveg_cf%gru_livestemc_xfer_to_atm_patch, & + iso_cnveg_cs%livestemc_xfer_patch , cnveg_cs%livestemc_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_deadstemc_to_atm_patch , cnveg_cf%gru_deadstemc_to_atm_patch, & + iso_cnveg_cs%deadstemc_patch , cnveg_cs%deadstemc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_wood_productc_gain_patch , cnveg_cf%gru_wood_productc_gain_patch, & + iso_cnveg_cs%deadstemc_patch , cnveg_cs%deadstemc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_deadstemc_storage_to_atm_patch , cnveg_cf%gru_deadstemc_storage_to_atm_patch, & + iso_cnveg_cs%deadstemc_storage_patch , cnveg_cs%deadstemc_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_deadstemc_xfer_to_atm_patch , cnveg_cf%gru_deadstemc_xfer_to_atm_patch, & + iso_cnveg_cs%deadstemc_xfer_patch , cnveg_cs%deadstemc_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_livecrootc_to_litter_patch , cnveg_cf%gru_livecrootc_to_litter_patch, & + iso_cnveg_cs%livecrootc_patch , cnveg_cs%livecrootc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_livecrootc_storage_to_atm_patch , cnveg_cf%gru_livecrootc_storage_to_atm_patch, & + iso_cnveg_cs%livecrootc_storage_patch , cnveg_cs%livecrootc_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_livecrootc_xfer_to_atm_patch , cnveg_cf%gru_livecrootc_xfer_to_atm_patch, & + iso_cnveg_cs%livecrootc_xfer_patch , cnveg_cs%livecrootc_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_deadcrootc_to_litter_patch , cnveg_cf%gru_deadcrootc_to_litter_patch, & + iso_cnveg_cs%deadcrootc_patch , cnveg_cs%deadcrootc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_deadcrootc_storage_to_atm_patch , cnveg_cf%gru_deadcrootc_storage_to_atm_patch, & + iso_cnveg_cs%deadcrootc_storage_patch , cnveg_cs%deadcrootc_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_deadcrootc_xfer_to_atm_patch , cnveg_cf%gru_deadcrootc_xfer_to_atm_patch, & + iso_cnveg_cs%deadcrootc_xfer_patch , cnveg_cs%deadcrootc_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_gresp_storage_to_atm_patch , cnveg_cf%gru_gresp_storage_to_atm_patch, & + iso_cnveg_cs%gresp_storage_patch , cnveg_cs%gresp_storage_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_gresp_xfer_to_atm_patch , cnveg_cf%gru_gresp_xfer_to_atm_patch, & + iso_cnveg_cs%gresp_xfer_patch , cnveg_cs%gresp_xfer_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%gru_xsmrpool_to_atm_patch , cnveg_cf%gru_xsmrpool_to_atm_patch, & + iso_cnveg_cs%totvegc_patch , cnveg_cs%totvegc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + ! call routine to shift patch-level gap mortality fluxes to column, + ! for isotopes the non-isotope version of this routine is in CNGapMortalityMod.F90. + + call CNCIsoGrossUnrepPftToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + + end associate + + end subroutine CIsoFlux2g + !----------------------------------------------------------------------- subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & @@ -1550,6 +1703,132 @@ subroutine CNCIsoHarvestPftToColumn (num_soilc, filter_soilc, & end subroutine CNCIsoHarvestPftToColumn + !----------------------------------------------------------------------- + subroutine CNCIsoGrossUnrepPftToColumn (num_soilc, filter_soilc, & + soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + ! + ! !DESCRIPTION: + ! gather all patch-level gross unrepresented landcover change mortality fluxes + ! to the column level and assign them to the litter, cwd, and wood product pools + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! soil column filter + type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst + type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst + ! + ! !LOCAL VARIABLES: + integer :: fc,c,pi,p,j ! indices + !----------------------------------------------------------------------- + + associate( & + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type + wtcol => patch%wtcol , & ! Input: [real(r8) (:) ] patch weight relative to column (0-1) + + lf_flab => pftcon%lf_flab , & ! Input: leaf litter labile fraction + lf_fcel => pftcon%lf_fcel , & ! Input: leaf litter cellulose fraction + lf_flig => pftcon%lf_flig , & ! Input: leaf litter lignin fraction + fr_flab => pftcon%fr_flab , & ! Input: fine root litter labile fraction + fr_fcel => pftcon%fr_fcel , & ! Input: fine root litter cellulose fraction + fr_flig => pftcon%fr_flig , & ! Input: fine root litter lignin fraction + + leaf_prof => soilbiogeochem_state_inst%leaf_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of leaves + froot_prof => soilbiogeochem_state_inst%froot_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of fine roots + croot_prof => soilbiogeochem_state_inst%croot_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of coarse roots + stem_prof => soilbiogeochem_state_inst%stem_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of stems + + gru_leafc_to_litter => iso_cnveg_carbonflux_inst%gru_leafc_to_litter_patch , & ! Input: [real(r8) (:) ] + gru_frootc_to_litter => iso_cnveg_carbonflux_inst%gru_frootc_to_litter_patch , & ! Input: [real(r8) (:) ] + gru_livestemc_to_atm => iso_cnveg_carbonflux_inst%gru_livestemc_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_deadstemc_to_atm => iso_cnveg_carbonflux_inst%gru_deadstemc_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_wood_productc_gain => iso_cnveg_carbonflux_inst%gru_wood_productc_gain_patch , & ! Input: [real(r8) (:) ] + gru_livecrootc_to_litter => iso_cnveg_carbonflux_inst%gru_livecrootc_to_litter_patch , & ! Input: [real(r8) (:) ] + gru_deadcrootc_to_litter => iso_cnveg_carbonflux_inst%gru_deadcrootc_to_litter_patch , & ! Input: [real(r8) (:) ] + gru_leafc_storage_to_atm => iso_cnveg_carbonflux_inst%gru_leafc_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_frootc_storage_to_atm => iso_cnveg_carbonflux_inst%gru_frootc_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_livestemc_storage_to_atm => iso_cnveg_carbonflux_inst%gru_livestemc_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_deadstemc_storage_to_atm => iso_cnveg_carbonflux_inst%gru_deadstemc_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_livecrootc_storage_to_atm => iso_cnveg_carbonflux_inst%gru_livecrootc_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_deadcrootc_storage_to_atm => iso_cnveg_carbonflux_inst%gru_deadcrootc_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_gresp_storage_to_atm => iso_cnveg_carbonflux_inst%gru_gresp_storage_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_leafc_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_leafc_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_frootc_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_frootc_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_livestemc_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_livestemc_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_deadstemc_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_deadstemc_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_livecrootc_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_livecrootc_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_deadcrootc_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_deadcrootc_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + gru_gresp_xfer_to_atm => iso_cnveg_carbonflux_inst%gru_gresp_xfer_to_atm_patch , & ! Input: [real(r8) (:) ] + cwood_harvestc => iso_cnveg_carbonflux_inst%wood_harvestc_col , & ! Output: [real(r8) (:) ] + gru_c_to_litr_met_c => iso_cnveg_carbonflux_inst%gru_c_to_litr_met_c_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with harvest to litter metabolic pool (gC/m3/s) + gru_c_to_litr_cel_c => iso_cnveg_carbonflux_inst%gru_c_to_litr_cel_c_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with harvest to litter cellulose pool (gC/m3/s) + gru_c_to_litr_lig_c => iso_cnveg_carbonflux_inst%gru_c_to_litr_lig_c_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with harvest to litter lignin pool (gC/m3/s) + gru_c_to_cwdc_c => iso_cnveg_carbonflux_inst%gru_c_to_cwdc_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with harvest to CWD pool (gC/m3/s) + gru_wood_productc_gain_c => iso_cnveg_carbonflux_inst%gru_wood_productc_gain_col & ! Input: [real(r8) (:) ] + ) + + do j = 1, nlevdecomp + do pi = 1,maxpatch_pft + do fc = 1,num_soilc + c = filter_soilc(fc) + + if (pi <= col%npatches(c)) then + p = col%patchi(c) + pi - 1 + + if (patch%active(p)) then + + ! leaf gross unrepresented landcover change mortality carbon fluxes + gru_c_to_litr_met_c(c,j) = gru_c_to_litr_met_c(c,j) + & + gru_leafc_to_litter(p) * lf_flab(ivt(p)) * wtcol(p) * leaf_prof(p,j) + gru_c_to_litr_cel_c(c,j) = gru_c_to_litr_cel_c(c,j) + & + gru_leafc_to_litter(p) * lf_fcel(ivt(p)) * wtcol(p) * leaf_prof(p,j) + gru_c_to_litr_lig_c(c,j) = gru_c_to_litr_lig_c(c,j) + & + gru_leafc_to_litter(p) * lf_flig(ivt(p)) * wtcol(p) * leaf_prof(p,j) + + ! fine root gross unrepresented landcover change mortality carbon fluxes + gru_c_to_litr_met_c(c,j) = gru_c_to_litr_met_c(c,j) + & + gru_frootc_to_litter(p) * fr_flab(ivt(p)) * wtcol(p) * froot_prof(p,j) + gru_c_to_litr_cel_c(c,j) = gru_c_to_litr_cel_c(c,j) + & + gru_frootc_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j) + gru_c_to_litr_lig_c(c,j) = gru_c_to_litr_lig_c(c,j) + & + gru_frootc_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j) + + ! coarse root gross unrepresented landcover change mortality carbon fluxes + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + end if + end if + + end do + + end do + end do + + do pi = 1,maxpatch_pft + do fc = 1,num_soilc + c = filter_soilc(fc) + + if (pi <= col%npatches(c)) then + p = col%patchi(c) + pi - 1 + + if (patch%active(p)) then + ! wood gross unrepresented landcover change mortality carbon fluxes to product pools + gru_wood_productc_gain_c(c) = gru_wood_productc_gain_c(c) + & + gru_wood_productc_gain(p) * wtcol(p) + + end if + end if + + end do + + end do + + end associate + + end subroutine CNCIsoGrossUnrepPftToColumn + !----------------------------------------------------------------------- subroutine CIsoFluxCalc(& ciso_flux, ctot_flux, & diff --git a/src/biogeochem/CNCStateUpdate2Mod.F90 b/src/biogeochem/CNCStateUpdate2Mod.F90 index ef1f6f9345..38bf5bcfc5 100644 --- a/src/biogeochem/CNCStateUpdate2Mod.F90 +++ b/src/biogeochem/CNCStateUpdate2Mod.F90 @@ -20,6 +20,7 @@ module CNCStateUpdate2Mod ! !PUBLIC MEMBER FUNCTIONS: public:: CStateUpdate2 public:: CStateUpdate2h + public:: CStateUpdate2g !----------------------------------------------------------------------- contains @@ -244,4 +245,118 @@ subroutine CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & end subroutine CStateUpdate2h + !----------------------------------------------------------------------- + subroutine CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst) + ! + ! !DESCRIPTION: + ! Update all the prognostic carbon state + ! variables affected by gross unrepresented landcover change mortality fluxes + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst + type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst + ! + ! !LOCAL VARIABLES: + integer :: c,p,j,k,l ! indices + integer :: fp,fc ! lake filter indices + real(r8):: dt ! radiation time step (seconds) + !----------------------------------------------------------------------- + + associate( & + cf_veg => cnveg_carbonflux_inst , & + cs_veg => cnveg_carbonstate_inst , & + cs_soil => soilbiogeochem_carbonstate_inst & + ) + + ! set time steps + dt = real( get_step_size(), r8 ) + + ! column level carbon fluxes from gross unrepresented landcover change mortality + do j = 1, nlevdecomp + do fc = 1,num_soilc + c = filter_soilc(fc) + + ! column gross unrepresented landcover change fluxes + cs_soil%decomp_cpools_vr_col(c,j,i_met_lit) = & + cs_soil%decomp_cpools_vr_col(c,j,i_met_lit) + cf_veg%gru_c_to_litr_met_c_col(c,j) * dt + cs_soil%decomp_cpools_vr_col(c,j,i_cel_lit) = & + cs_soil%decomp_cpools_vr_col(c,j,i_cel_lit) + cf_veg%gru_c_to_litr_cel_c_col(c,j) * dt + cs_soil%decomp_cpools_vr_col(c,j,i_lig_lit) = & + cs_soil%decomp_cpools_vr_col(c,j,i_lig_lit) + cf_veg%gru_c_to_litr_lig_c_col(c,j) * dt + cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = & + cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + cf_veg%gru_c_to_cwdc_col(c,j) * dt + + ! wood to product pools - states updated in CNProducts + end do + end do + + ! patch loop + do fp = 1,num_soilp + p = filter_soilp(fp) + + ! patch-level carbon fluxes from gross unrepresented landcover change mortality + ! displayed pools + cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) & + - cf_veg%gru_leafc_to_litter_patch(p) * dt + cs_veg%frootc_patch(p) = cs_veg%frootc_patch(p) & + - cf_veg%gru_frootc_to_litter_patch(p) * dt + cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) & + - cf_veg%gru_livestemc_to_atm_patch(p) * dt + cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) & + - cf_veg%gru_deadstemc_to_atm_patch(p) * dt + cs_veg%deadstemc_patch(p) = cs_veg%deadstemc_patch(p) & + - cf_veg%gru_wood_productc_gain_patch(p) * dt + cs_veg%livecrootc_patch(p) = cs_veg%livecrootc_patch(p) & + - cf_veg%gru_livecrootc_to_litter_patch(p) * dt + cs_veg%deadcrootc_patch(p) = cs_veg%deadcrootc_patch(p) & + - cf_veg%gru_deadcrootc_to_litter_patch(p) * dt + + ! xsmrpool + cs_veg%xsmrpool_patch(p) = cs_veg%xsmrpool_patch(p) & + - cf_veg%gru_xsmrpool_to_atm_patch(p) * dt + + ! storage pools + cs_veg%leafc_storage_patch(p) = cs_veg%leafc_storage_patch(p) & + - cf_veg%gru_leafc_storage_to_atm_patch(p) * dt + cs_veg%frootc_storage_patch(p) = cs_veg%frootc_storage_patch(p) & + - cf_veg%gru_frootc_storage_to_atm_patch(p) * dt + cs_veg%livestemc_storage_patch(p) = cs_veg%livestemc_storage_patch(p) & + - cf_veg%gru_livestemc_storage_to_atm_patch(p) * dt + cs_veg%deadstemc_storage_patch(p) = cs_veg%deadstemc_storage_patch(p) & + - cf_veg%gru_deadstemc_storage_to_atm_patch(p) * dt + cs_veg%livecrootc_storage_patch(p) = cs_veg%livecrootc_storage_patch(p) & + - cf_veg%gru_livecrootc_storage_to_atm_patch(p) * dt + cs_veg%deadcrootc_storage_patch(p) = cs_veg%deadcrootc_storage_patch(p) & + - cf_veg%gru_deadcrootc_storage_to_atm_patch(p) * dt + cs_veg%gresp_storage_patch(p) = cs_veg%gresp_storage_patch(p) & + - cf_veg%gru_gresp_storage_to_atm_patch(p) * dt + + ! transfer pools + cs_veg%leafc_xfer_patch(p) = cs_veg%leafc_xfer_patch(p) & + - cf_veg%gru_leafc_xfer_to_atm_patch(p) * dt + cs_veg%frootc_xfer_patch(p) = cs_veg%frootc_xfer_patch(p) & + - cf_veg%gru_frootc_xfer_to_atm_patch(p) * dt + cs_veg%livestemc_xfer_patch(p) = cs_veg%livestemc_xfer_patch(p) & + - cf_veg%gru_livestemc_xfer_to_atm_patch(p) * dt + cs_veg%deadstemc_xfer_patch(p) = cs_veg%deadstemc_xfer_patch(p) & + - cf_veg%gru_deadstemc_xfer_to_atm_patch(p) * dt + cs_veg%livecrootc_xfer_patch(p) = cs_veg%livecrootc_xfer_patch(p) & + - cf_veg%gru_livecrootc_xfer_to_atm_patch(p) * dt + cs_veg%deadcrootc_xfer_patch(p) = cs_veg%deadcrootc_xfer_patch(p) & + - cf_veg%gru_deadcrootc_xfer_to_atm_patch(p) * dt + cs_veg%gresp_xfer_patch(p) = cs_veg%gresp_xfer_patch(p) & + - cf_veg%gru_gresp_xfer_to_atm_patch(p) * dt + + end do ! end of patch loop + + end associate + + end subroutine CStateUpdate2g + end module CNCStateUpdate2Mod diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index a8ed44cd97..31804bbf0a 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -7,7 +7,7 @@ module CNDriverMod ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use clm_varctl , only : use_c13, use_c14, use_fates, use_dynroot - use dynSubgridControlMod , only : get_do_harvest + use dynSubgridControlMod , only : get_do_harvest, get_do_grossunrep use decompMod , only : bounds_type use perf_mod , only : t_startf, t_stopf use clm_varctl , only : use_century_decomp, use_nitrif_denitrif, use_nguardrail @@ -111,16 +111,17 @@ subroutine CNDriverNoLeaching(bounds, use CNPhenologyMod , only: CNPhenology use CNGRespMod , only: CNGResp use CNFireMethodMod , only: cnfire_method_type - use CNCIsoFluxMod , only: CIsoFlux1, CIsoFlux2, CIsoFlux2h, CIsoFlux3 + use CNCIsoFluxMod , only: CIsoFlux1, CIsoFlux2, CIsoFlux2h, CIsoFlux2g, CIsoFlux3 use CNC14DecayMod , only: C14Decay use CNCStateUpdate1Mod , only: CStateUpdate1,CStateUpdate0 - use CNCStateUpdate2Mod , only: CStateUpdate2, CStateUpdate2h + use CNCStateUpdate2Mod , only: CStateUpdate2, CStateUpdate2h, CStateUpdate2g use CNCStateUpdate3Mod , only: CStateUpdate3 use CNNStateUpdate1Mod , only: NStateUpdate1 - use CNNStateUpdate2Mod , only: NStateUpdate2, NStateUpdate2h + use CNNStateUpdate2Mod , only: NStateUpdate2, NStateUpdate2h, NStateUpdate2g use CNGapMortalityMod , only: CNGapMortality use CNSharedParamsMod , only: use_fun use dynHarvestMod , only: CNHarvest + use dynGrossUnrepMod , only: CNGrossUnrep use SoilBiogeochemDecompCascadeBGCMod , only: decomp_rate_constants_bgc use SoilBiogeochemDecompCascadeCNMod , only: decomp_rate_constants_cn use SoilBiogeochemCompetitionMod , only: SoilBiogeochemCompetition @@ -690,6 +691,47 @@ subroutine CNDriverNoLeaching(bounds, call NStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) + + !-------------------------------------------- + ! Update2g (gross unrepresented landcover change) + !-------------------------------------------- + + ! Set gross unrepresented landcover change mortality routine + if (get_do_grossunrep()) then + call CNGrossUnrep(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & + cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + end if + + if ( use_c13 ) then + call CIsoFlux2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & + isotope='c13') + end if + if ( use_c14 ) then + call CIsoFlux2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & + isotope='c14') + end if + + call CStateUpdate2g( num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst) + if ( use_c13 ) then + call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst) + end if + if ( use_c14 ) then + call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst) + end if + + call NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) + call t_stopf('CNUpdate2') if ( use_nguardrail ) then @@ -708,6 +750,7 @@ subroutine CNDriverNoLeaching(bounds, call c_products_inst%UpdateProducts(bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch = cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & + gru_wood_product_gain_patch = cnveg_carbonflux_inst%gru_wood_productc_gain_patch(begp:endp), & wood_harvest_patch = cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & dwt_crop_product_gain_patch = cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & grain_to_cropprod_patch = cnveg_carbonflux_inst%grainc_to_cropprodc_patch(begp:endp)) @@ -717,6 +760,7 @@ subroutine CNDriverNoLeaching(bounds, call c13_products_inst%UpdateProducts(bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & + gru_wood_product_gain_patch = c13_cnveg_carbonflux_inst%gru_wood_productc_gain_patch(begp:endp), & wood_harvest_patch = c13_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & dwt_crop_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & grain_to_cropprod_patch = c13_cnveg_carbonflux_inst%grainc_to_cropprodc_patch(begp:endp)) @@ -726,6 +770,7 @@ subroutine CNDriverNoLeaching(bounds, call c14_products_inst%UpdateProducts(bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & + gru_wood_product_gain_patch = c14_cnveg_carbonflux_inst%gru_wood_productc_gain_patch(begp:endp), & wood_harvest_patch = c14_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & dwt_crop_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & grain_to_cropprod_patch = c14_cnveg_carbonflux_inst%grainc_to_cropprodc_patch(begp:endp)) @@ -734,6 +779,7 @@ subroutine CNDriverNoLeaching(bounds, call n_products_inst%UpdateProducts(bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch = cnveg_nitrogenflux_inst%dwt_wood_productn_gain_patch(begp:endp), & + gru_wood_product_gain_patch = cnveg_nitrogenflux_inst%gru_wood_productn_gain_patch(begp:endp), & wood_harvest_patch = cnveg_nitrogenflux_inst%wood_harvestn_patch(begp:endp), & dwt_crop_product_gain_patch = cnveg_nitrogenflux_inst%dwt_crop_productn_gain_patch(begp:endp), & grain_to_cropprod_patch = cnveg_nitrogenflux_inst%grainn_to_cropprodn_patch(begp:endp)) diff --git a/src/biogeochem/CNNStateUpdate2Mod.F90 b/src/biogeochem/CNNStateUpdate2Mod.F90 index 24070f6890..e3548694c6 100644 --- a/src/biogeochem/CNNStateUpdate2Mod.F90 +++ b/src/biogeochem/CNNStateUpdate2Mod.F90 @@ -20,6 +20,7 @@ module CNNStateUpdate2Mod ! !PUBLIC MEMBER FUNCTIONS: public:: NStateUpdate2 public:: NStateUpdate2h + public:: NStateUpdate2g !----------------------------------------------------------------------- contains @@ -235,4 +236,111 @@ subroutine NStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & end subroutine NStateUpdate2h + !----------------------------------------------------------------------- + subroutine NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) + ! + ! !DESCRIPTION: + ! Update all the prognostic nitrogen state + ! variables affected by gross unrepresented landcover change mortality fluxes + ! NOTE - associate statements have been removed where there are + ! no science equations. This increases readability and maintainability + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches + type(cnveg_nitrogenflux_type) , intent(in) :: cnveg_nitrogenflux_inst + type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst + type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst + ! + ! !LOCAL VARIABLES: + integer :: c,p,j,l ! indices + integer :: fp,fc ! lake filter indices + real(r8):: dt ! radiation time step (seconds) + !----------------------------------------------------------------------- + + associate( & + nf_veg => cnveg_nitrogenflux_inst , & + ns_veg => cnveg_nitrogenstate_inst , & + ns_soil => soilbiogeochem_nitrogenstate_inst & + ) + + ! set time steps + dt = real( get_step_size(), r8 ) + + ! column-level nitrogen fluxes from gross unrepresented landcover change mortality + + do j = 1,nlevdecomp + do fc = 1,num_soilc + c = filter_soilc(fc) + ns_soil%decomp_npools_vr_col(c,j,i_met_lit) = & + ns_soil%decomp_npools_vr_col(c,j,i_met_lit) + nf_veg%gru_n_to_litr_met_n_col(c,j) * dt + ns_soil%decomp_npools_vr_col(c,j,i_cel_lit) = & + ns_soil%decomp_npools_vr_col(c,j,i_cel_lit) + nf_veg%gru_n_to_litr_cel_n_col(c,j) * dt + ns_soil%decomp_npools_vr_col(c,j,i_lig_lit) = & + ns_soil%decomp_npools_vr_col(c,j,i_lig_lit) + nf_veg%gru_n_to_litr_lig_n_col(c,j) * dt + ns_soil%decomp_npools_vr_col(c,j,i_cwd) = & + ns_soil%decomp_npools_vr_col(c,j,i_cwd) + nf_veg%gru_n_to_cwdn_col(c,j) * dt + end do + end do + + ! patch-level nitrogen fluxes from gross unrepresented landcover change mortality + + do fp = 1,num_soilp + p = filter_soilp(fp) + + ! displayed pools + ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) & + - nf_veg%gru_leafn_to_litter_patch(p) * dt + ns_veg%frootn_patch(p) = ns_veg%frootn_patch(p) & + - nf_veg%gru_frootn_to_litter_patch(p) * dt + ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) & + - nf_veg%gru_livestemn_to_atm_patch(p) * dt + ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p) & + - nf_veg%gru_deadstemn_to_atm_patch(p) * dt + ns_veg%deadstemn_patch(p) = ns_veg%deadstemn_patch(p) & + - nf_veg%gru_wood_productn_gain_patch(p) * dt + ns_veg%livecrootn_patch(p) = ns_veg%livecrootn_patch(p) & + - nf_veg%gru_livecrootn_to_litter_patch(p) * dt + ns_veg%deadcrootn_patch(p) = ns_veg%deadcrootn_patch(p) & + - nf_veg%gru_deadcrootn_to_litter_patch(p) * dt + ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) & + - nf_veg%gru_retransn_to_litter_patch(p) * dt + + ! storage pools + ns_veg%leafn_storage_patch(p) = ns_veg%leafn_storage_patch(p) & + - nf_veg%gru_leafn_storage_to_atm_patch(p) * dt + ns_veg%frootn_storage_patch(p) = ns_veg%frootn_storage_patch(p) & + - nf_veg%gru_frootn_storage_to_atm_patch(p) * dt + ns_veg%livestemn_storage_patch(p) = ns_veg%livestemn_storage_patch(p) & + - nf_veg%gru_livestemn_storage_to_atm_patch(p) * dt + ns_veg%deadstemn_storage_patch(p) = ns_veg%deadstemn_storage_patch(p) & + - nf_veg%gru_deadstemn_storage_to_atm_patch(p) * dt + ns_veg%livecrootn_storage_patch(p) = ns_veg%livecrootn_storage_patch(p) & + - nf_veg%gru_livecrootn_storage_to_atm_patch(p) * dt + ns_veg%deadcrootn_storage_patch(p) = ns_veg%deadcrootn_storage_patch(p) & + - nf_veg%gru_deadcrootn_storage_to_atm_patch(p) * dt + + ! transfer pools + ns_veg%leafn_xfer_patch(p) = ns_veg%leafn_xfer_patch(p) & + - nf_veg%gru_leafn_xfer_to_atm_patch(p) *dt + ns_veg%frootn_xfer_patch(p) = ns_veg%frootn_xfer_patch(p) & + - nf_veg%gru_frootn_xfer_to_atm_patch(p) *dt + ns_veg%livestemn_xfer_patch(p) = ns_veg%livestemn_xfer_patch(p) & + - nf_veg%gru_livestemn_xfer_to_atm_patch(p) *dt + ns_veg%deadstemn_xfer_patch(p) = ns_veg%deadstemn_xfer_patch(p) & + - nf_veg%gru_deadstemn_xfer_to_atm_patch(p) *dt + ns_veg%livecrootn_xfer_patch(p) = ns_veg%livecrootn_xfer_patch(p) & + - nf_veg%gru_livecrootn_xfer_to_atm_patch(p) *dt + ns_veg%deadcrootn_xfer_patch(p) = ns_veg%deadcrootn_xfer_patch(p) & + - nf_veg%gru_deadcrootn_xfer_to_atm_patch(p) *dt + + end do + + end associate + + end subroutine NStateUpdate2g + end module CNNStateUpdate2Mod diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 59891ba330..046a01d482 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -43,6 +43,11 @@ module CNProductsMod real(r8), pointer :: dwt_prod100_gain_grc(:) ! (g[C or N]/m2/s) dynamic landcover addition to 100-year wood product pool real(r8), pointer :: dwt_woodprod_gain_grc(:) ! (g[C or N]/m2/s) dynamic landcover addition to wood product pools real(r8), pointer :: dwt_cropprod1_gain_grc(:) ! (g[C or N]/m2/s) dynamic landcover addition to 1-year crop product pool + real(r8), pointer :: gru_prod10_gain_patch(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to 10-year wood product pool + real(r8), pointer :: gru_prod10_gain_grc(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to 10-year wood product pool + real(r8), pointer :: gru_prod100_gain_patch(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to 100-year wood product pool + real(r8), pointer :: gru_prod100_gain_grc(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to 100-year wood product pool + real(r8), pointer :: gru_woodprod_gain_grc(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to wood product pools real(r8), pointer :: hrv_deadstem_to_prod10_patch(:) ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool real(r8), pointer :: hrv_deadstem_to_prod10_grc(:) ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool real(r8), pointer :: hrv_deadstem_to_prod100_patch(:) ! (g[C or N]/m2/s) dead stem harvest to 100-year wood product pool @@ -133,9 +138,14 @@ subroutine InitAllocate(this, bounds) allocate(this%dwt_cropprod1_gain_grc(begg:endg)) ; this%dwt_cropprod1_gain_grc(:) = nan + allocate(this%gru_prod10_gain_patch(begp:endp)) ; this%gru_prod10_gain_patch(:) = nan + allocate(this%gru_prod10_gain_grc(begg:endg)) ; this%gru_prod10_gain_grc(:) = nan + allocate(this%gru_prod100_gain_patch(begp:endp)) ; this%gru_prod100_gain_patch(:) = nan + allocate(this%gru_prod100_gain_grc(begg:endg)) ; this%gru_prod100_gain_grc(:) = nan + allocate(this%gru_woodprod_gain_grc(begg:endg)) ; this%gru_woodprod_gain_grc(:) = nan + allocate(this%hrv_deadstem_to_prod10_patch(begp:endp)) ; this%hrv_deadstem_to_prod10_patch(:) = nan allocate(this%hrv_deadstem_to_prod10_grc(begg:endg)) ; this%hrv_deadstem_to_prod10_grc(:) = nan - allocate(this%hrv_deadstem_to_prod100_patch(begp:endp)) ; this%hrv_deadstem_to_prod100_patch(:) = nan allocate(this%hrv_deadstem_to_prod100_grc(begg:endg)) ; this%hrv_deadstem_to_prod100_grc(:) = nan @@ -233,6 +243,22 @@ subroutine InitHistory(this, bounds) long_name = 'landcover change-driven addition to 1-year crop product pool', & ptr_gcell = this%dwt_cropprod1_gain_grc) + this%gru_prod10_gain_grc(begg:endg) = spval + call hist_addfld1d( & + fname = this%species%hist_fname('GRU_PROD10', suffix='_GAIN'), & + units = 'g' // this%species%get_species() // '/m^2/s', & + avgflag = 'A', & + long_name = 'gross unrepresented landcover change addition to 10-yr wood product pool', & + ptr_gcell = this%gru_prod10_gain_grc, default='inactive') + + this%gru_prod100_gain_grc(begg:endg) = spval + call hist_addfld1d( & + fname = this%species%hist_fname('GRU_PROD100', suffix='_GAIN'), & + units = 'g' // this%species%get_species() // '/m^2/s', & + avgflag = 'A', & + long_name = 'gross unrepresented landcover change addition to 100-yr wood product pool', & + ptr_gcell = this%gru_prod100_gain_grc, default='inactive') + this%cropprod1_loss_grc(begg:endg) = spval call hist_addfld1d( & fname = this%species%hist_fname('CROPPROD1', suffix='_LOSS'), & @@ -291,6 +317,8 @@ subroutine InitCold(this, bounds) do p = bounds%begp, bounds%endp this%hrv_deadstem_to_prod10_patch(p) = 0._r8 this%hrv_deadstem_to_prod100_patch(p) = 0._r8 + this%gru_prod10_gain_patch(p) = 0._r8 + this%gru_prod100_gain_patch(p) = 0._r8 this%grain_to_cropprod1_patch(p) = 0._r8 end do @@ -428,6 +456,7 @@ end subroutine Restart subroutine UpdateProducts(this, bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch, & + gru_wood_product_gain_patch, & wood_harvest_patch, & dwt_crop_product_gain_patch, & grain_to_cropprod_patch) @@ -446,6 +475,9 @@ subroutine UpdateProducts(this, bounds, & ! a patch-level flux, it is expressed per unit GRIDCELL area real(r8), intent(in) :: dwt_wood_product_gain_patch( bounds%begp: ) + ! gross unrepresented landcover addition to wood product pools (g/m2/s) [patch] + real(r8), intent(in) :: gru_wood_product_gain_patch( bounds%begp: ) + ! wood harvest addition to wood product pools (g/m2/s) [patch] real(r8), intent(in) :: wood_harvest_patch( bounds%begp: ) @@ -465,6 +497,7 @@ subroutine UpdateProducts(this, bounds, & !----------------------------------------------------------------------- SHR_ASSERT_ALL((ubound(dwt_wood_product_gain_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__)) + SHR_ASSERT_ALL((ubound(gru_wood_product_gain_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__)) SHR_ASSERT_ALL((ubound(wood_harvest_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__)) SHR_ASSERT_ALL((ubound(dwt_crop_product_gain_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__)) SHR_ASSERT_ALL((ubound(grain_to_cropprod_patch) == (/bounds%endp/)), errMsg(sourcefile, __LINE__)) @@ -472,6 +505,7 @@ subroutine UpdateProducts(this, bounds, & call this%PartitionWoodFluxes(bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch(bounds%begp:bounds%endp), & + gru_wood_product_gain_patch(bounds%begp:bounds%endp), & wood_harvest_patch(bounds%begp:bounds%endp)) call this%PartitionGrainFluxes(bounds, & @@ -504,6 +538,10 @@ subroutine UpdateProducts(this, bounds, & this%prod10_grc(g) = this%prod10_grc(g) + this%dwt_prod10_gain_grc(g)*dt this%prod100_grc(g) = this%prod100_grc(g) + this%dwt_prod100_gain_grc(g)*dt + ! fluxes into wood & grain product pools, from gross unrepresented landcover change + this%prod10_grc(g) = this%prod10_grc(g) + this%gru_prod10_gain_grc(g)*dt + this%prod100_grc(g) = this%prod100_grc(g) + this%gru_prod100_gain_grc(g)*dt + ! fluxes into wood & grain product pools, from harvest this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%grain_to_cropprod1_grc(g)*dt this%prod10_grc(g) = this%prod10_grc(g) + this%hrv_deadstem_to_prod10_grc(g)*dt @@ -524,6 +562,7 @@ end subroutine UpdateProducts subroutine PartitionWoodFluxes(this, bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch, & + gru_wood_product_gain_patch, & wood_harvest_patch) ! ! !DESCRIPTION: @@ -543,6 +582,9 @@ subroutine PartitionWoodFluxes(this, bounds, & ! a patch-level flux, it is expressed per unit GRIDCELL area real(r8), intent(in) :: dwt_wood_product_gain_patch( bounds%begp: ) + ! gross unrepresented landcover addition to wood product pools (g/m2/s) [patch] + real(r8), intent(in) :: gru_wood_product_gain_patch( bounds%begp: ) + ! wood harvest addition to wood product pools (g/m2/s) [patch] real(r8), intent(in) :: wood_harvest_patch( bounds%begp: ) @@ -560,6 +602,44 @@ subroutine PartitionWoodFluxes(this, bounds, & character(len=*), parameter :: subname = 'PartitionWoodFluxes' !----------------------------------------------------------------------- + ! Partition patch-level gross unrepresented fluxes to 10 and 100-year product pools + do fp = 1, num_soilp + p = filter_soilp(fp) + + pprod10 = pftcon%pprod10(patch%itype(p)) + pprod100 = pftcon%pprod100(patch%itype(p)) + pprod_tot = pprod10 + pprod100 + if (pprod_tot > 0) then + pprod10_frac = pprod10 / pprod_tot + pprod100_frac = pprod100 / pprod_tot + else + ! Avoid divide by 0 + pprod10_frac = 0._r8 + pprod100_frac = 0._r8 + end if + + this%gru_prod10_gain_patch(p) = & + gru_wood_product_gain_patch(p) * pprod10_frac + this%gru_prod100_gain_patch(p) = & + gru_wood_product_gain_patch(p) * pprod100_frac + + end do + + ! Average gross unrepresented fluxes from patch to gridcell + call p2g(bounds, & + this%gru_prod10_gain_patch(bounds%begp:bounds%endp), & + this%gru_prod10_gain_grc(bounds%begg:bounds%endg), & + p2c_scale_type = 'unity', & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + + call p2g(bounds, & + this%gru_prod100_gain_patch(bounds%begp:bounds%endp), & + this%gru_prod100_gain_grc(bounds%begg:bounds%endg), & + p2c_scale_type = 'unity', & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + ! Partition patch-level harvest fluxes to 10 and 100-year product pools do fp = 1, num_soilp p = filter_soilp(fp) @@ -733,6 +813,10 @@ subroutine ComputeSummaryVars(this, bounds) this%dwt_woodprod_gain_grc(g) = & this%dwt_prod100_gain_grc(g) + & this%dwt_prod10_gain_grc(g) + + this%gru_woodprod_gain_grc(g) = & + this%gru_prod100_gain_grc(g) + & + this%gru_prod10_gain_grc(g) end do end subroutine ComputeSummaryVars diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 57cee383d5..22f57ed9da 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -263,13 +263,49 @@ module CNVegCarbonFluxType real(r8), pointer :: dwt_conv_cflux_dribbled_grc (:) ! (gC/m2/s) dwt_conv_cflux_grc dribbled evenly throughout the year real(r8), pointer :: dwt_wood_productc_gain_patch (:) ! (gC/m2/s) addition to wood product pools from landcover change; although this is a patch-level flux, it is expressed per unit GRIDCELL area real(r8), pointer :: dwt_crop_productc_gain_patch (:) ! (gC/m2/s) addition to crop product pools from landcover change; although this is a patch-level flux, it is expressed per unit GRIDCELL area - real(r8), pointer :: dwt_slash_cflux_col (:) ! (gC/m2/s) conversion slash flux due to landcover change + real(r8), pointer :: dwt_slash_cflux_patch (:) ! (gC/m2/s) conversion slash flux due to landcover change + real(r8), pointer :: dwt_slash_cflux_grc (:) ! (gC/m2/s) dwt_slash_cflux_patch summed to the gridcell-level real(r8), pointer :: dwt_frootc_to_litr_met_c_col (:,:) ! (gC/m3/s) fine root to litter due to landcover change real(r8), pointer :: dwt_frootc_to_litr_cel_c_col (:,:) ! (gC/m3/s) fine root to litter due to landcover change real(r8), pointer :: dwt_frootc_to_litr_lig_c_col (:,:) ! (gC/m3/s) fine root to litter due to landcover change real(r8), pointer :: dwt_livecrootc_to_cwdc_col (:,:) ! (gC/m3/s) live coarse root to CWD due to landcover change real(r8), pointer :: dwt_deadcrootc_to_cwdc_col (:,:) ! (gC/m3/s) dead coarse root to CWD due to landcover change + ! gross unrepresented landcover fluxes + real(r8), pointer :: gru_leafc_to_litter_patch (:) ! leaf C gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_leafc_storage_to_atm_patch (:) ! leaf C storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_leafc_xfer_to_atm_patch (:) ! leaf C transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_frootc_to_litter_patch (:) ! fine root C gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_frootc_storage_to_atm_patch (:) ! fine root C storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_frootc_xfer_to_atm_patch (:) ! fine root C transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_livestemc_to_atm_patch (:) ! live stem C gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_livestemc_storage_to_atm_patch (:) ! live stem C storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_livestemc_xfer_to_atm_patch (:) ! live stem C transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_deadstemc_to_atm_patch (:) ! dead stem C gross unrepresented landcover change mortality to the atmosphere (gC/m2/s) + real(r8), pointer :: gru_deadstemc_storage_to_atm_patch (:) ! dead stem C storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_deadstemc_xfer_to_atm_patch (:) ! dead stem C transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_livecrootc_to_litter_patch (:) ! live coarse root C gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_livecrootc_storage_to_atm_patch (:) ! live coarse root C storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_livecrootc_xfer_to_atm_patch (:) ! live coarse root C transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_deadcrootc_to_litter_patch (:) ! dead coarse root C gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_deadcrootc_storage_to_atm_patch (:) ! dead coarse root C storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_deadcrootc_xfer_to_atm_patch (:) ! dead coarse root C transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_gresp_storage_to_atm_patch (:) ! growth respiration storage gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_gresp_xfer_to_atm_patch (:) ! growth respiration transfer gross unrepresented landcover change mortality (gC/m2/s) + real(r8), pointer :: gru_xsmrpool_to_atm_patch (:) ! excess MR pool gross unrepresented landcover change mortality (gC/m2/s) + + real(r8), pointer :: gru_conv_cflux_patch (:) ! (gC/m2/s) conversion C flux (immediate loss to atm) + real(r8), pointer :: gru_conv_cflux_col (:) ! (gC/m2/s) gru_conv_cflux_patch summed to the column-level + real(r8), pointer :: gru_conv_cflux_grc (:) ! (gC/m2/s) gru_conv_cflux_patch summed to the gridcell-level + real(r8), pointer :: gru_conv_cflux_dribbled_grc (:) ! (gC/m2/s) gru_conv_cflux_grc dribbled evenly throughout the year + real(r8), pointer :: gru_wood_productc_gain_patch (:) ! (gC/m2/s) addition to wood product pools from gross unrepresented landcover change + real(r8), pointer :: gru_wood_productc_gain_col (:) ! (gC/m2/s) gru_wood_productc_gain_patch summed to the column-level + real(r8), pointer :: gru_slash_cflux_patch (:) ! (gC/m2/s) conversion slash flux due to gross unrepresented landcover change + real(r8), pointer :: gru_c_to_litr_met_c_col (:,:) ! (gC/m3/s) C to litter due to gross unrepresented landcover change + real(r8), pointer :: gru_c_to_litr_cel_c_col (:,:) ! (gC/m3/s) C to litter due to gross unrepresented landcover change + real(r8), pointer :: gru_c_to_litr_lig_c_col (:,:) ! (gC/m3/s) C to litter due to gross unrepresented landcover change + real(r8), pointer :: gru_c_to_cwdc_col (:,:) ! (gC/m3/s) C to CWD due to gross unrepresented landcover change + ! crop fluxes real(r8), pointer :: crop_seedc_to_leaf_patch (:) ! (gC/m2/s) seed source to leaf, for crops @@ -340,7 +376,7 @@ module CNVegCarbonFluxType real(r8), pointer :: nee_grc (:) ! (gC/m2/s) net ecosystem exchange of carbon, includes fire and hrv_xsmrpool, excludes landuse and harvest flux, positive for source ! Dynamic landcover fluxnes - real(r8), pointer :: landuseflux_grc(:) ! (gC/m2/s) dwt_conv_cflux+product_closs + real(r8), pointer :: landuseflux_grc(:) ! (gC/m2/s) dwt_conv_cflux+gru_conv_cflux+product_closs real(r8), pointer :: npp_Nactive_patch (:) ! C used by mycorrhizal uptake (gC/m2/s) real(r8), pointer :: npp_burnedoff_patch (:) ! C that cannot be used for N uptake (gC/m2/s) real(r8), pointer :: npp_Nnonmyc_patch (:) ! C used by non-myc uptake (gC/m2/s) @@ -366,6 +402,7 @@ module CNVegCarbonFluxType ! Objects that help convert once-per-year dynamic land cover changes into fluxes ! that are dribbled throughout the year type(annual_flux_dribbler_type) :: dwt_conv_cflux_dribbler + type(annual_flux_dribbler_type) :: gru_conv_cflux_dribbler type(annual_flux_dribbler_type) :: hrv_xsmrpool_to_atm_dribbler contains @@ -378,6 +415,7 @@ module CNVegCarbonFluxType procedure , private :: RestartAllIsotopes ! Handle restart fields present for both bulk C and isotopes procedure , public :: SetValues procedure , public :: ZeroDWT + procedure , public :: ZeroGRU procedure , public :: Summary => Summary_carbonflux end type cnveg_carbonflux_type @@ -629,7 +667,8 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%harvest_c_to_litr_lig_c_col (begc:endc,1:nlevdecomp_full)); this%harvest_c_to_litr_lig_c_col (:,:)=nan allocate(this%harvest_c_to_cwdc_col (begc:endc,1:nlevdecomp_full)); this%harvest_c_to_cwdc_col (:,:)=nan - allocate(this%dwt_slash_cflux_col (begc:endc)) ; this%dwt_slash_cflux_col (:) =nan + allocate(this%dwt_slash_cflux_patch (begp:endp)) ; this%dwt_slash_cflux_patch (:) =nan + allocate(this%dwt_slash_cflux_grc (begg:endg)) ; this%dwt_slash_cflux_grc (:) =nan allocate(this%dwt_frootc_to_litr_met_c_col (begc:endc,1:nlevdecomp_full)); this%dwt_frootc_to_litr_met_c_col (:,:)=nan allocate(this%dwt_frootc_to_litr_cel_c_col (begc:endc,1:nlevdecomp_full)); this%dwt_frootc_to_litr_cel_c_col (:,:)=nan allocate(this%dwt_frootc_to_litr_lig_c_col (begc:endc,1:nlevdecomp_full)); this%dwt_frootc_to_litr_lig_c_col (:,:)=nan @@ -646,6 +685,40 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%dwt_wood_productc_gain_patch (begp:endp)) ; this%dwt_wood_productc_gain_patch(:) =nan allocate(this%dwt_crop_productc_gain_patch (begp:endp)) ; this%dwt_crop_productc_gain_patch(:) =nan + allocate(this%gru_leafc_to_litter_patch (begp:endp)) ; this%gru_leafc_to_litter_patch (:) = nan + allocate(this%gru_leafc_storage_to_atm_patch (begp:endp)) ; this%gru_leafc_storage_to_atm_patch (:) = nan + allocate(this%gru_leafc_xfer_to_atm_patch (begp:endp)) ; this%gru_leafc_xfer_to_atm_patch (:) = nan + allocate(this%gru_frootc_to_litter_patch (begp:endp)) ; this%gru_frootc_to_litter_patch (:) = nan + allocate(this%gru_frootc_storage_to_atm_patch (begp:endp)) ; this%gru_frootc_storage_to_atm_patch (:) = nan + allocate(this%gru_frootc_xfer_to_atm_patch (begp:endp)) ; this%gru_frootc_xfer_to_atm_patch (:) = nan + allocate(this%gru_livestemc_to_atm_patch (begp:endp)) ; this%gru_livestemc_to_atm_patch (:) = nan + allocate(this%gru_livestemc_storage_to_atm_patch (begp:endp)) ; this%gru_livestemc_storage_to_atm_patch (:) = nan + allocate(this%gru_livestemc_xfer_to_atm_patch (begp:endp)) ; this%gru_livestemc_xfer_to_atm_patch (:) = nan + allocate(this%gru_deadstemc_to_atm_patch (begp:endp)) ; this%gru_deadstemc_to_atm_patch (:) = nan + allocate(this%gru_deadstemc_storage_to_atm_patch (begp:endp)) ; this%gru_deadstemc_storage_to_atm_patch (:) = nan + allocate(this%gru_deadstemc_xfer_to_atm_patch (begp:endp)) ; this%gru_deadstemc_xfer_to_atm_patch (:) = nan + allocate(this%gru_livecrootc_to_litter_patch (begp:endp)) ; this%gru_livecrootc_to_litter_patch (:) = nan + allocate(this%gru_livecrootc_storage_to_atm_patch (begp:endp)) ; this%gru_livecrootc_storage_to_atm_patch (:) = nan + allocate(this%gru_livecrootc_xfer_to_atm_patch (begp:endp)) ; this%gru_livecrootc_xfer_to_atm_patch (:) = nan + allocate(this%gru_deadcrootc_to_litter_patch (begp:endp)) ; this%gru_deadcrootc_to_litter_patch (:) = nan + allocate(this%gru_deadcrootc_storage_to_atm_patch (begp:endp)) ; this%gru_deadcrootc_storage_to_atm_patch (:) = nan + allocate(this%gru_deadcrootc_xfer_to_atm_patch (begp:endp)) ; this%gru_deadcrootc_xfer_to_atm_patch (:) = nan + allocate(this%gru_gresp_storage_to_atm_patch (begp:endp)) ; this%gru_gresp_storage_to_atm_patch (:) = nan + allocate(this%gru_gresp_xfer_to_atm_patch (begp:endp)) ; this%gru_gresp_xfer_to_atm_patch (:) = nan + allocate(this%gru_xsmrpool_to_atm_patch (begp:endp)) ; this%gru_xsmrpool_to_atm_patch (:) = nan + + allocate(this%gru_conv_cflux_patch (begp:endp)) ; this%gru_conv_cflux_patch (:) =nan + allocate(this%gru_conv_cflux_col (begc:endc)) ; this%gru_conv_cflux_col (:) =nan + allocate(this%gru_conv_cflux_grc (begg:endg)) ; this%gru_conv_cflux_grc (:) =nan + allocate(this%gru_conv_cflux_dribbled_grc (begg:endg)) ; this%gru_conv_cflux_dribbled_grc (:) =nan + allocate(this%gru_wood_productc_gain_patch (begp:endp)) ; this%gru_wood_productc_gain_patch (:) =nan + allocate(this%gru_wood_productc_gain_col (begc:endc)) ; this%gru_wood_productc_gain_col (:) =nan + allocate(this%gru_slash_cflux_patch (begp:endp)) ; this%gru_slash_cflux_patch (:) =nan + allocate(this%gru_c_to_litr_met_c_col (begc:endc,1:nlevdecomp_full)); this%gru_c_to_litr_met_c_col (:,:)=nan + allocate(this%gru_c_to_litr_cel_c_col (begc:endc,1:nlevdecomp_full)); this%gru_c_to_litr_cel_c_col (:,:)=nan + allocate(this%gru_c_to_litr_lig_c_col (begc:endc,1:nlevdecomp_full)); this%gru_c_to_litr_lig_c_col (:,:)=nan + allocate(this%gru_c_to_cwdc_col (begc:endc,1:nlevdecomp_full)); this%gru_c_to_cwdc_col (:,:)=nan + allocate(this%crop_seedc_to_leaf_patch (begp:endp)) ; this%crop_seedc_to_leaf_patch (:) =nan allocate(this%cwdc_hr_col (begc:endc)) ; this%cwdc_hr_col (:) =nan @@ -763,6 +836,11 @@ subroutine InitAllocate(this, bounds, carbon_type) name = 'dwt_conv_flux_' // carbon_type_suffix, & units = 'gC/m^2', & allows_non_annual_delta = allows_non_annual_delta) + this%gru_conv_cflux_dribbler = annual_flux_dribbler_gridcell( & + bounds = bounds, & + name = 'gru_conv_flux_' // carbon_type_suffix, & + units = 'gC/m^2', & + allows_non_annual_delta = allows_non_annual_delta) this%hrv_xsmrpool_to_atm_dribbler = annual_flux_dribbler_gridcell( & bounds = bounds, & name = 'hrv_xsmrpool_to_atm_' // carbon_type_suffix, & @@ -2878,10 +2956,19 @@ subroutine InitHistory(this, bounds, carbon_type) '(per-area-gridcell; only makes sense with dov2xy=.false.)', & ptr_patch=this%dwt_wood_productc_gain_patch, default='inactive') - this%dwt_slash_cflux_col(begc:endc) = spval - call hist_addfld1d (fname='DWT_SLASH_CFLUX', units='gC/m^2/s', & - avgflag='A', long_name='slash C flux to litter and CWD due to land use', & - ptr_col=this%dwt_slash_cflux_col) + this%dwt_slash_cflux_grc(begg:endg) = spval + call hist_addfld1d (fname='DWT_SLASH_CFLUX', units='gC/m^2/s', & + avgflag='A', & + long_name='slash C flux (to litter diagnostic only) (0 at all times except first timestep of year)', & + ptr_gcell=this%dwt_slash_cflux_grc) + + this%dwt_slash_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='DWT_SLASH_CFLUX_PATCH', units='gC/m^2/s', & + avgflag='A', & + long_name='patch-level slash C flux (to litter diagnostic only) ' // & + '(0 at all times except first timestep of year) ' // & + '(per-area-gridcell; only makes sense with dov2xy=.false.)', & + ptr_patch=this%dwt_slash_cflux_patch, default='inactive') this%dwt_frootc_to_litr_met_c_col(begc:endc,:) = spval call hist_addfld_decomp (fname='DWT_FROOTC_TO_LITR_MET_C', units='gC/m^2/s', type2d='levdcmp', & @@ -2908,6 +2995,27 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', long_name='dead coarse root to CWD due to landcover change', & ptr_col=this%dwt_deadcrootc_to_cwdc_col, default='inactive') + this%gru_conv_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_CONV_CFLUX', units='gC/m^2/s', & + avgflag='A', long_name='gross unrepresented conversion C flux (immediate loss to atm) (0 at all times except first timestep of year)', & + ptr_patch=this%gru_conv_cflux_patch) + + this%gru_conv_cflux_dribbled_grc(begg:endg) = spval + call hist_addfld1d (fname='GRU_CONV_CFLUX_DRIBBLED', units='gC/m^2/s', & + avgflag='A', & + long_name='gross unrepresented conversion C flux (immediate loss to atm), dribbled throughout the year', & + ptr_gcell=this%gru_conv_cflux_dribbled_grc) + + this%gru_wood_productc_gain_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_WOODPRODC_GAIN', units='gC/m^2/s', & + avgflag='A', long_name='gross unrepresented landcover change driven addition to wood product carbon pools (0 at all times except first timestep of year)', & + ptr_patch=this%gru_wood_productc_gain_patch) + + this%gru_slash_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_SLASH_CFLUX', units='gC/m^2/s', & + avgflag='A', long_name='slash gross unrepresented landcover change carbon (to litter)', & + ptr_patch=this%gru_slash_cflux_patch) + this%crop_seedc_to_leaf_patch(begp:endp) = spval call hist_addfld1d (fname='CROP_SEEDC_TO_LEAF', units='gC/m^2/s', & avgflag='A', long_name='crop seed source to leaf', & @@ -3052,10 +3160,19 @@ subroutine InitHistory(this, bounds, carbon_type) long_name='C13 conversion C flux (immediate loss to atm), dribbled throughout the year', & ptr_gcell=this%dwt_conv_cflux_dribbled_grc) - this%dwt_slash_cflux_col(begc:endc) = spval - call hist_addfld1d (fname='C13_DWT_SLASH_CFLUX', units='gC/m^2/s', & - avgflag='A', long_name='C13 slash C flux to litter and CWD due to land use', & - ptr_col=this%dwt_slash_cflux_col) + this%dwt_slash_cflux_grc(begg:endg) = spval + call hist_addfld1d (fname='C13_DWT_SLASH_CFLUX', units='gC13/m^2/s', & + avgflag='A', long_name='C13 slash C flux (to litter diagnostic only)' // & + '(0 at all times except first timestep of year)', & + ptr_gcell=this%dwt_slash_cflux_grc) + + this%dwt_slash_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='C13_DWT_SLASH_CFLUX_PATCH', units='gC13/m^2/s', & + avgflag='A', & + long_name='patch-level C13 slash C flux (to litter diagnostic only) ' // & + '(0 at all times except first timestep of year) ' // & + '(per-area-gridcell; only makes sense with dov2xy=.false.)', & + ptr_patch=this%dwt_slash_cflux_patch, default='inactive') this%dwt_frootc_to_litr_met_c_col(begc:endc,:) = spval call hist_addfld_decomp (fname='C13_DWT_FROOTC_TO_LITR_MET_C', units='gC13/m^2/s', type2d='levdcmp', & @@ -3201,10 +3318,19 @@ subroutine InitHistory(this, bounds, carbon_type) long_name='C14 conversion C flux (immediate loss to atm), dribbled throughout the year', & ptr_gcell=this%dwt_conv_cflux_dribbled_grc) - this%dwt_slash_cflux_col(begc:endc) = spval - call hist_addfld1d (fname='C14_DWT_SLASH_CFLUX', units='gC/m^2/s', & - avgflag='A', long_name='C14 slash C flux to litter and CWD due to land use', & - ptr_col=this%dwt_slash_cflux_col) + this%dwt_slash_cflux_grc(begg:endg) = spval + call hist_addfld1d (fname='C14_DWT_SLASH_CFLUX', units='gC14/m^2/s', & + avgflag='A', long_name='C14 slash C flux (to litter diagnostic only)' // & + '(0 at all times except first timestep of year)', & + ptr_gcell=this%dwt_slash_cflux_grc) + + this%dwt_slash_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='C14_DWT_SLASH_CFLUX_PATCH', units='gC14/m^2/s', & + avgflag='A', & + long_name='patch-level C14 slash C flux (to litter diagnostic only)' // & + '(0 at all times except first timestep of year) ' // & + '(per-area-gridcell; only makes sense with dov2xy=.false.)', & + ptr_patch=this%dwt_slash_cflux_patch, default='inactive') this%dwt_frootc_to_litr_met_c_col(begc:endc,:) = spval call hist_addfld_decomp (fname='C14_DWT_FROOTC_TO_LITR_MET_C', units='gC14/m^2/s', type2d='levdcmp', & @@ -3352,7 +3478,6 @@ subroutine InitCold(this, bounds) ! also initialize dynamic landcover fluxes so that they have ! real values on first timestep, prior to calling pftdyn_cnbal if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - this%dwt_slash_cflux_col(c) = 0._r8 do j = 1, nlevdecomp_full this%dwt_frootc_to_litr_met_c_col(c,j) = 0._r8 this%dwt_frootc_to_litr_cel_c_col(c,j) = 0._r8 @@ -3363,6 +3488,21 @@ subroutine InitCold(this, bounds) end if end do + do c = bounds%begc, bounds%endc + l = col%landunit(c) + + ! also initialize gross unrepresented landcover fluxes so that they have + ! real values on first timestep, prior to calling pftdyn_cnbal + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + do j = 1, nlevdecomp_full + this%gru_c_to_litr_met_c_col(c,j) = 0._r8 + this%gru_c_to_litr_cel_c_col(c,j) = 0._r8 + this%gru_c_to_litr_lig_c_col(c,j) = 0._r8 + this%gru_c_to_cwdc_col(c,j) = 0._r8 + end do + end if + end do + do p = bounds%begp,bounds%endp l = patch%landunit(p) @@ -3596,6 +3736,7 @@ subroutine RestartAllIsotopes ( this, bounds, ncid, flag ) !----------------------------------------------------------------------- call this%dwt_conv_cflux_dribbler%Restart(bounds, ncid, flag) + call this%gru_conv_cflux_dribbler%Restart(bounds, ncid, flag) call this%hrv_xsmrpool_to_atm_dribbler%Restart(bounds, ncid, flag) end subroutine RestartAllIsotopes @@ -3666,6 +3807,32 @@ subroutine SetValues ( this, & this%hrv_gresp_xfer_to_litter_patch(i) = value_patch this%hrv_xsmrpool_to_atm_patch(i) = value_patch + this%gru_leafc_to_litter_patch(i) = value_patch + this%gru_leafc_storage_to_atm_patch(i) = value_patch + this%gru_leafc_xfer_to_atm_patch(i) = value_patch + this%gru_frootc_to_litter_patch(i) = value_patch + this%gru_frootc_storage_to_atm_patch(i) = value_patch + this%gru_frootc_xfer_to_atm_patch(i) = value_patch + this%gru_livestemc_to_atm_patch(i) = value_patch + this%gru_livestemc_storage_to_atm_patch(i) = value_patch + this%gru_livestemc_xfer_to_atm_patch(i) = value_patch + this%gru_deadstemc_to_atm_patch(i) = value_patch + this%gru_deadstemc_storage_to_atm_patch(i) = value_patch + this%gru_deadstemc_xfer_to_atm_patch(i) = value_patch + this%gru_livecrootc_to_litter_patch(i) = value_patch + this%gru_livecrootc_storage_to_atm_patch(i) = value_patch + this%gru_livecrootc_xfer_to_atm_patch(i) = value_patch + this%gru_deadcrootc_to_litter_patch(i) = value_patch + this%gru_deadcrootc_storage_to_atm_patch(i) = value_patch + this%gru_deadcrootc_xfer_to_atm_patch(i) = value_patch + this%gru_gresp_storage_to_atm_patch(i) = value_patch + this%gru_gresp_xfer_to_atm_patch(i) = value_patch + this%gru_xsmrpool_to_atm_patch(i) = value_patch + + this%gru_conv_cflux_patch(i) = value_patch + this%gru_wood_productc_gain_patch(i) = value_patch + this%gru_slash_cflux_patch(i) = value_patch + this%m_leafc_to_fire_patch(i) = value_patch this%m_leafc_storage_to_fire_patch(i) = value_patch this%m_leafc_xfer_to_fire_patch(i) = value_patch @@ -3840,6 +4007,11 @@ subroutine SetValues ( this, & this%harvest_c_to_litr_lig_c_col(i,j) = value_column this%harvest_c_to_cwdc_col(i,j) = value_column + this%gru_c_to_litr_met_c_col(i,j) = value_column + this%gru_c_to_litr_cel_c_col(i,j) = value_column + this%gru_c_to_litr_lig_c_col(i,j) = value_column + this%gru_c_to_cwdc_col(i,j) = value_column + end do end do @@ -3924,6 +4096,8 @@ subroutine SetValues ( this, & this%fire_closs_col(i) = value_column this%wood_harvestc_col(i) = value_column this%hrv_xsmrpool_to_atm_col(i) = value_column + this%gru_conv_cflux_col(i) = value_column + this%gru_wood_productc_gain_col(i) = value_column this%nep_col(i) = value_column @@ -3951,10 +4125,7 @@ subroutine ZeroDwt( this, bounds ) this%dwt_seedc_to_leaf_grc(g) = 0._r8 this%dwt_seedc_to_deadstem_grc(g) = 0._r8 this%dwt_conv_cflux_grc(g) = 0._r8 - end do - - do c = bounds%begc,bounds%endc - this%dwt_slash_cflux_col(c) = 0._r8 + this%dwt_slash_cflux_grc(g) = 0._r8 end do do j = 1, nlevdecomp_full @@ -3969,6 +4140,28 @@ subroutine ZeroDwt( this, bounds ) end subroutine ZeroDwt + !----------------------------------------------------------------------- + subroutine ZeroGru( this, bounds ) + ! + ! !DESCRIPTION + ! Initialize flux variables needed for dynamic land use. + ! + ! !ARGUMENTS: + class(cnveg_carbonflux_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: c, g, j ! indices + !----------------------------------------------------------------------- + + ! set conversion and product pool fluxes to 0 at the beginning of every timestep + + do g = bounds%begg, bounds%endg + this%gru_conv_cflux_grc(g) = 0._r8 + end do + + end subroutine ZeroGru + !----------------------------------------------------------------------- subroutine Summary_carbonflux(this, & bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & @@ -4011,6 +4204,7 @@ subroutine Summary_carbonflux(this, & real(r8) :: hrv_xsmrpool_to_atm_delta_grc(bounds%begg:bounds%endg) ! hrv_xsmrpool_to_atm_col averaged to gridcell, expressed as a delta (not a flux) (gC/m2) real(r8) :: hrv_xsmrpool_to_atm_dribbled_grc(bounds%begg:bounds%endg) ! hrv_xsmrpool_to_atm, dribbled over the year (gC/m2/s) real(r8) :: dwt_conv_cflux_delta_grc(bounds%begg:bounds%endg) ! dwt_conv_cflux_grc expressed as a total delta (not a flux) (gC/m2) + real(r8) :: gru_conv_cflux_delta_grc(bounds%begg:bounds%endg) ! gru_conv_cflux_grc expressed as a total delta (not a flux) (gC/m2) !----------------------------------------------------------------------- SHR_ASSERT_ALL((ubound(product_closs_grc) == (/bounds%endg/)), errMsg(sourcefile, __LINE__)) @@ -4243,7 +4437,12 @@ subroutine Summary_carbonflux(this, & this%hrv_deadcrootc_storage_to_litter_patch(p) + & this%hrv_deadcrootc_xfer_to_litter_patch(p) + & this%hrv_gresp_storage_to_litter_patch(p) + & - this%hrv_gresp_xfer_to_litter_patch(p) + this%hrv_gresp_xfer_to_litter_patch(p) + & + + this%gru_leafc_to_litter_patch(p) + & + this%gru_frootc_to_litter_patch(p) + & + this%gru_livecrootc_to_litter_patch(p) + & + this%gru_deadcrootc_to_litter_patch(p) if ( use_crop .and. patch%itype(p) >= npcropmin )then this%litfall_patch(p) = & @@ -4316,6 +4515,7 @@ subroutine Summary_carbonflux(this, & this%m_leafc_to_fire_patch(p) + & this%m_leafc_to_litter_fire_patch(p) + & this%hrv_leafc_to_litter_patch(p) + & + this%gru_leafc_to_litter_patch(p) + & this%leafc_to_litter_patch(p) ! (WOODC_ALLOC) - wood C allocation @@ -4350,7 +4550,20 @@ subroutine Summary_carbonflux(this, & this%hrv_livecrootc_xfer_to_litter_patch(p) + & this%hrv_deadcrootc_to_litter_patch(p) + & this%hrv_deadcrootc_storage_to_litter_patch(p) + & - this%hrv_deadcrootc_xfer_to_litter_patch(p) + this%hrv_deadcrootc_xfer_to_litter_patch(p) + & + this%gru_livestemc_to_atm_patch(p) + & + this%gru_livestemc_storage_to_atm_patch(p) + & + this%gru_livestemc_xfer_to_atm_patch(p) + & + this%gru_deadstemc_to_atm_patch(p) + & + this%gru_wood_productc_gain_patch(p) + & + this%gru_deadstemc_storage_to_atm_patch(p) + & + this%gru_deadstemc_xfer_to_atm_patch(p) + & + this%gru_livecrootc_to_litter_patch(p) + & + this%gru_livecrootc_storage_to_atm_patch(p) + & + this%gru_livecrootc_xfer_to_atm_patch(p) + & + this%gru_deadcrootc_to_litter_patch(p) + & + this%gru_deadcrootc_storage_to_atm_patch(p) + & + this%gru_deadcrootc_xfer_to_atm_patch(p) ! (Slash Harvest Flux) - Additional Wood Harvest Veg C Losses this%slash_harvestc_patch(p) = & @@ -4371,10 +4584,36 @@ subroutine Summary_carbonflux(this, & this%hrv_deadcrootc_to_litter_patch(p) + & this%hrv_deadcrootc_storage_to_litter_patch(p) + & this%hrv_deadcrootc_xfer_to_litter_patch(p) + & - this%hrv_xsmrpool_to_atm_patch(p) + & this%hrv_gresp_storage_to_litter_patch(p) + & this%hrv_gresp_xfer_to_litter_patch(p) + ! (Gross Unrepresented Landcover Change Conversion Flux) - Direct Veg C Loss to Atmosphere + this%gru_conv_cflux_patch(p) = & + this%gru_livestemc_to_atm_patch(p) + & + this%gru_deadstemc_to_atm_patch(p) + & + this%gru_xsmrpool_to_atm_patch(p) + & + this%gru_leafc_storage_to_atm_patch(p) + & + this%gru_frootc_storage_to_atm_patch(p) + & + this%gru_livestemc_storage_to_atm_patch(p) + & + this%gru_deadstemc_storage_to_atm_patch(p) + & + this%gru_livecrootc_storage_to_atm_patch(p) + & + this%gru_deadcrootc_storage_to_atm_patch(p) + & + this%gru_gresp_storage_to_atm_patch(p) + & + this%gru_leafc_xfer_to_atm_patch(p) + & + this%gru_frootc_xfer_to_atm_patch(p) + & + this%gru_livestemc_xfer_to_atm_patch(p) + & + this%gru_deadstemc_xfer_to_atm_patch(p) + & + this%gru_livecrootc_xfer_to_atm_patch(p) + & + this%gru_deadcrootc_xfer_to_atm_patch(p) + & + this%gru_gresp_xfer_to_atm_patch(p) + + ! (Gross Unrepresented Landcover Change Slash Flux) - Direct Veg C Loss to Atmosphere + this%gru_slash_cflux_patch(p) = & + this%gru_leafc_to_litter_patch(p) + & + this%gru_frootc_to_litter_patch(p) + & + this%gru_livecrootc_to_litter_patch(p) + & + this%gru_deadcrootc_to_litter_patch(p) + end do ! end of patches loop !------------------------------------------------ @@ -4387,6 +4626,10 @@ subroutine Summary_carbonflux(this, & this%hrv_xsmrpool_to_atm_patch(bounds%begp:bounds%endp), & this%hrv_xsmrpool_to_atm_col(bounds%begc:bounds%endc)) + call p2c(bounds, num_soilc, filter_soilc, & + this%gru_conv_cflux_patch(bounds%begp:bounds%endp), & + this%gru_conv_cflux_col(bounds%begc:bounds%endc)) + call p2c(bounds, num_soilc, filter_soilc, & this%fire_closs_patch(bounds%begp:bounds%endp), & this%fire_closs_p2c_col(bounds%begc:bounds%endc)) @@ -4515,6 +4758,18 @@ subroutine Summary_carbonflux(this, & call this%dwt_conv_cflux_dribbler%get_curr_flux(bounds, & this%dwt_conv_cflux_dribbled_grc(bounds%begg:bounds%endg)) + call c2g( bounds = bounds, & + carr = this%gru_conv_cflux_col(bounds%begc:bounds%endc), & + garr = this%gru_conv_cflux_grc(bounds%begg:bounds%endg), & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + gru_conv_cflux_delta_grc(bounds%begg:bounds%endg) = & + this%gru_conv_cflux_grc(bounds%begg:bounds%endg) * dtime + call this%gru_conv_cflux_dribbler%set_curr_delta(bounds, & + gru_conv_cflux_delta_grc(bounds%begg:bounds%endg)) + call this%gru_conv_cflux_dribbler%get_curr_flux(bounds, & + this%gru_conv_cflux_dribbled_grc(bounds%begg:bounds%endg)) + do g = bounds%begg, bounds%endg ! net ecosystem exchange of carbon, includes fire flux and hrv_xsmrpool flux, ! positive for source (NEE) @@ -4525,6 +4780,7 @@ subroutine Summary_carbonflux(this, & this%landuseflux_grc(g) = & this%dwt_conv_cflux_dribbled_grc(g) + & + this%gru_conv_cflux_dribbled_grc(g) + & product_closs_grc(g) ! net biome production of carbon, positive for sink diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index 1bb630c687..1bb3e223f9 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -205,6 +205,37 @@ module CNVegNitrogenFluxType real(r8), pointer :: dwt_livecrootn_to_cwdn_col (:,:) ! col (gN/m3/s) live coarse root to CWD due to landcover change real(r8), pointer :: dwt_deadcrootn_to_cwdn_col (:,:) ! col (gN/m3/s) dead coarse root to CWD due to landcover change + ! gross unrepresented landcover fluxes + real(r8), pointer :: gru_leafn_to_litter_patch (:) ! patch leaf N gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_leafn_storage_to_atm_patch (:) ! patch leaf N storage gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_leafn_xfer_to_atm_patch (:) ! patch leaf N transfer gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_frootn_to_litter_patch (:) ! patch fine root N gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_frootn_storage_to_atm_patch (:) ! patch fine root N storage gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_frootn_xfer_to_atm_patch (:) ! patch fine root N transfer gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_livestemn_to_atm_patch (:) ! patch live stem N gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_livestemn_storage_to_atm_patch (:) ! patch live stem N storage gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_livestemn_xfer_to_atm_patch (:) ! patch live stem N transfer gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_deadstemn_to_atm_patch (:) ! patch dead stem N gross unrepresented landcover change mortality to the atmosphere (gC/m2/s) + real(r8), pointer :: gru_deadstemn_storage_to_atm_patch (:) ! patch dead stem N storage gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_deadstemn_xfer_to_atm_patch (:) ! patch dead stem N transfer gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_livecrootn_to_litter_patch (:) ! patch live coarse root N gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_livecrootn_storage_to_atm_patch (:) ! patch live coarse root N storage gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_livecrootn_xfer_to_atm_patch (:) ! patch live coarse root N transfer gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_deadcrootn_to_litter_patch (:) ! patch dead coarse root N gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_deadcrootn_storage_to_atm_patch (:) ! patch dead coarse root N storage gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_deadcrootn_xfer_to_atm_patch (:) ! patch dead coarse root N transfer gross unrepresented landcover change mortality (gN/m2/s) + real(r8), pointer :: gru_retransn_to_litter_patch (:) ! patch retranslocated N pool gross unrepresented landcover change mortality (gN/m2/s) + + real(r8), pointer :: gru_conv_nflux_patch (:) ! (gN/m2/s) conversion N flux (immediate loss to atm) + real(r8), pointer :: gru_conv_nflux_col (:) ! (gN/m2/s) conversion N flux (immediate loss to atm) + real(r8), pointer :: gru_conv_nflux_grc (:) ! (gN/m2/s) gru_conv_nflux_patch summed to the gridcell-level + real(r8), pointer :: gru_wood_productn_gain_patch (:) ! patch (gN/m2/s) addition to wood product pools from gross unrepresented landcover change + real(r8), pointer :: gru_wood_productn_gain_col (:) ! patch (gN/m2/s) addition to wood product pools from gross unrepresented landcover change + real(r8), pointer :: gru_n_to_litr_met_n_col (:,:) ! col (gN/m3/s) N to litter due to gross unrepresented landcover change + real(r8), pointer :: gru_n_to_litr_cel_n_col (:,:) ! col (gN/m3/s) N to litter due to gross unrepresented landcover change + real(r8), pointer :: gru_n_to_litr_lig_n_col (:,:) ! col (gN/m3/s) N to litter due to gross unrepresented landcover change + real(r8), pointer :: gru_n_to_cwdn_col (:,:) ! col (gN/m3/s) N to CWD due to gross unrepresented landcover change + ! crop fluxes real(r8), pointer :: crop_seedn_to_leaf_patch (:) ! patch (gN/m2/s) seed source to leaf, for crops @@ -249,6 +280,7 @@ module CNVegNitrogenFluxType procedure , public :: Restart procedure , public :: SetValues procedure , public :: ZeroDWT + procedure , public :: ZeroGRU procedure , public :: Summary => Summary_nitrogenflux procedure , private :: InitAllocate procedure , private :: InitHistory @@ -447,6 +479,36 @@ subroutine InitAllocate(this, bounds) allocate(this%dwt_livecrootn_to_cwdn_col (begc:endc,1:nlevdecomp_full)) ; this%dwt_livecrootn_to_cwdn_col (:,:) = nan allocate(this%dwt_deadcrootn_to_cwdn_col (begc:endc,1:nlevdecomp_full)) ; this%dwt_deadcrootn_to_cwdn_col (:,:) = nan + allocate(this%gru_leafn_to_litter_patch (begp:endp)) ; this%gru_leafn_to_litter_patch (:) = nan + allocate(this%gru_leafn_storage_to_atm_patch (begp:endp)) ; this%gru_leafn_storage_to_atm_patch (:) = nan + allocate(this%gru_leafn_xfer_to_atm_patch (begp:endp)) ; this%gru_leafn_xfer_to_atm_patch (:) = nan + allocate(this%gru_frootn_to_litter_patch (begp:endp)) ; this%gru_frootn_to_litter_patch (:) = nan + allocate(this%gru_frootn_storage_to_atm_patch (begp:endp)) ; this%gru_frootn_storage_to_atm_patch (:) = nan + allocate(this%gru_frootn_xfer_to_atm_patch (begp:endp)) ; this%gru_frootn_xfer_to_atm_patch (:) = nan + allocate(this%gru_livestemn_to_atm_patch (begp:endp)) ; this%gru_livestemn_to_atm_patch (:) = nan + allocate(this%gru_livestemn_storage_to_atm_patch (begp:endp)) ; this%gru_livestemn_storage_to_atm_patch (:) = nan + allocate(this%gru_livestemn_xfer_to_atm_patch (begp:endp)) ; this%gru_livestemn_xfer_to_atm_patch (:) = nan + allocate(this%gru_deadstemn_to_atm_patch (begp:endp)) ; this%gru_deadstemn_storage_to_atm_patch (:) = nan + allocate(this%gru_deadstemn_storage_to_atm_patch (begp:endp)) ; this%gru_deadstemn_storage_to_atm_patch (:) = nan + allocate(this%gru_deadstemn_xfer_to_atm_patch (begp:endp)) ; this%gru_deadstemn_xfer_to_atm_patch (:) = nan + allocate(this%gru_livecrootn_storage_to_atm_patch (begp:endp)) ; this%gru_livecrootn_storage_to_atm_patch (:) = nan + allocate(this%gru_livecrootn_xfer_to_atm_patch (begp:endp)) ; this%gru_livecrootn_xfer_to_atm_patch (:) = nan + allocate(this%gru_livecrootn_to_litter_patch (begp:endp)) ; this%gru_livecrootn_to_litter_patch (:) = nan + allocate(this%gru_deadcrootn_storage_to_atm_patch (begp:endp)) ; this%gru_deadcrootn_storage_to_atm_patch (:) = nan + allocate(this%gru_deadcrootn_xfer_to_atm_patch (begp:endp)) ; this%gru_deadcrootn_xfer_to_atm_patch (:) = nan + allocate(this%gru_deadcrootn_to_litter_patch (begp:endp)) ; this%gru_deadcrootn_to_litter_patch (:) = nan + allocate(this%gru_retransn_to_litter_patch (begp:endp)) ; this%gru_retransn_to_litter_patch (:) = nan + + allocate(this%gru_conv_nflux_patch (begp:endp)) ; this%gru_conv_nflux_patch (:) =nan + allocate(this%gru_conv_nflux_col (begc:endc)) ; this%gru_conv_nflux_col (:) =nan + allocate(this%gru_conv_nflux_grc (begg:endg)) ; this%gru_conv_nflux_grc (:) =nan + allocate(this%gru_wood_productn_gain_patch (begp:endp)) ; this%gru_wood_productn_gain_patch (:) =nan + allocate(this%gru_wood_productn_gain_col (begc:endc)) ; this%gru_wood_productn_gain_col (:) =nan + allocate(this%gru_n_to_litr_met_n_col (begc:endc,1:nlevdecomp_full)); this%gru_n_to_litr_met_n_col (:,:)=nan + allocate(this%gru_n_to_litr_cel_n_col (begc:endc,1:nlevdecomp_full)); this%gru_n_to_litr_cel_n_col (:,:)=nan + allocate(this%gru_n_to_litr_lig_n_col (begc:endc,1:nlevdecomp_full)); this%gru_n_to_litr_lig_n_col (:,:)=nan + allocate(this%gru_n_to_cwdn_col (begc:endc,1:nlevdecomp_full)); this%gru_n_to_cwdn_col (:,:)=nan + allocate(this%crop_seedn_to_leaf_patch (begp:endp)) ; this%crop_seedn_to_leaf_patch (:) = nan allocate(this%m_decomp_npools_to_fire_vr_col (begc:endc,1:nlevdecomp_full,1:ndecomp_pools)) @@ -1059,6 +1121,16 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='dead coarse root to CWD due to landcover change', & ptr_col=this%dwt_deadcrootn_to_cwdn_col, default='inactive') + this%gru_conv_nflux_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_CONV_NFLUX', units='gN/m^2/s', & + avgflag='A', long_name='gross unrepresented conversion N flux (immediate loss to atm) (0 at all times except first timestep of year)', & + ptr_patch=this%gru_conv_nflux_patch) + + this%gru_wood_productn_gain_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_WOODPRODN_GAIN', units='gN/m^2/s', & + avgflag='A', long_name='gross unrepresented landcover change driven addition to wood product nitrogen pools (0 at all times except first timestep of year)', & + ptr_patch=this%gru_wood_productn_gain_patch) + this%crop_seedn_to_leaf_patch(begp:endp) = spval call hist_addfld1d (fname='CROP_SEEDN_TO_LEAF', units='gN/m^2/s', & avgflag='A', long_name='crop seed source to leaf', & @@ -1577,6 +1649,26 @@ subroutine SetValues ( this, & this%hrv_deadcrootn_to_litter_patch(i) = value_patch this%hrv_retransn_to_litter_patch(i) = value_patch + this%gru_leafn_to_litter_patch(i) = value_patch + this%gru_leafn_storage_to_atm_patch(i) = value_patch + this%gru_leafn_xfer_to_atm_patch(i) = value_patch + this%gru_frootn_to_litter_patch(i) = value_patch + this%gru_frootn_storage_to_atm_patch(i) = value_patch + this%gru_frootn_xfer_to_atm_patch(i) = value_patch + this%gru_livestemn_to_atm_patch(i) = value_patch + this%gru_livestemn_storage_to_atm_patch(i) = value_patch + this%gru_livestemn_xfer_to_atm_patch(i) = value_patch + this%gru_deadstemn_to_atm_patch(i) = value_patch + this%gru_deadstemn_storage_to_atm_patch(i) = value_patch + this%gru_deadstemn_xfer_to_atm_patch(i) = value_patch + this%gru_livecrootn_to_litter_patch(i) = value_patch + this%gru_livecrootn_storage_to_atm_patch(i) = value_patch + this%gru_livecrootn_xfer_to_atm_patch(i) = value_patch + this%gru_deadcrootn_storage_to_atm_patch(i) = value_patch + this%gru_deadcrootn_xfer_to_atm_patch(i) = value_patch + this%gru_deadcrootn_to_litter_patch(i) = value_patch + this%gru_retransn_to_litter_patch(i) = value_patch + this%m_leafn_to_fire_patch(i) = value_patch this%m_leafn_storage_to_fire_patch(i) = value_patch this%m_leafn_xfer_to_fire_patch(i) = value_patch @@ -1597,6 +1689,8 @@ subroutine SetValues ( this, & this%m_deadcrootn_xfer_to_fire_patch(i) = value_patch this%m_retransn_to_fire_patch(i) = value_patch + this%gru_conv_nflux_patch(i) = value_patch + this%gru_wood_productn_gain_patch(i) = value_patch this%m_leafn_to_litter_fire_patch(i) = value_patch this%m_leafn_storage_to_litter_fire_patch(i) = value_patch @@ -1703,6 +1797,12 @@ subroutine SetValues ( this, & this%harvest_n_to_litr_cel_n_col(i,j) = value_column this%harvest_n_to_litr_lig_n_col(i,j) = value_column this%harvest_n_to_cwdn_col(i,j) = value_column + + ! gross unrepresented landcover change + this%gru_n_to_litr_met_n_col(i,j) = value_column + this%gru_n_to_litr_cel_n_col(i,j) = value_column + this%gru_n_to_litr_lig_n_col(i,j) = value_column + this%gru_n_to_cwdn_col(i,j) = value_column end do end do @@ -1715,6 +1815,8 @@ subroutine SetValues ( this, & ! Zero p2c column fluxes this%fire_nloss_col(i) = value_column this%wood_harvestn_col(i) = value_column + this%gru_conv_nflux_col(i) = value_column + this%gru_wood_productn_gain_col(i) = value_column end do do k = 1, ndecomp_pools @@ -1767,13 +1869,33 @@ subroutine ZeroDwt( this, bounds ) end subroutine ZeroDwt + !----------------------------------------------------------------------- + subroutine ZeroGru( this, bounds ) + ! + ! !DESCRIPTION + ! Initialize flux variables needed for dynamic land use. + ! + ! !ARGUMENTS: + class(cnveg_nitrogenflux_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: c, g, j ! indices + !----------------------------------------------------------------------- + + do g = bounds%begg, bounds%endg + this%gru_conv_nflux_grc(g) = 0._r8 + end do + + end subroutine ZeroGru + !----------------------------------------------------------------------- subroutine Summary_nitrogenflux(this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) ! ! !USES: use clm_varpar , only: nlevdecomp,ndecomp_cascade_transitions,ndecomp_pools use clm_varctl , only: use_nitrif_denitrif - use subgridAveMod , only: p2c + use subgridAveMod , only: p2c, c2g ! ! !ARGUMENTS: class (cnveg_nitrogenflux_type) :: this @@ -1820,12 +1942,39 @@ subroutine Summary_nitrogenflux(this, bounds, num_soilc, filter_soilc, num_soilp this%m_deadcrootn_xfer_to_fire_patch(p) + & this%m_retransn_to_fire_patch(p) + ! (Gross Unrepresented Landcover Change Conversion Flux) - Direct Veg N Loss to Atmosphere + this%gru_conv_nflux_patch(p) = & + this%gru_livestemn_to_atm_patch(p) + & + this%gru_deadstemn_to_atm_patch(p) + & + this%gru_leafn_storage_to_atm_patch(p) + & + this%gru_frootn_storage_to_atm_patch(p) + & + this%gru_livestemn_storage_to_atm_patch(p) + & + this%gru_deadstemn_storage_to_atm_patch(p) + & + this%gru_livecrootn_storage_to_atm_patch(p) + & + this%gru_deadcrootn_storage_to_atm_patch(p) + & + this%gru_leafn_xfer_to_atm_patch(p) + & + this%gru_frootn_xfer_to_atm_patch(p) + & + this%gru_livestemn_xfer_to_atm_patch(p) + & + this%gru_deadstemn_xfer_to_atm_patch(p) + & + this%gru_livecrootn_xfer_to_atm_patch(p) + & + this%gru_deadcrootn_xfer_to_atm_patch(p) + end do call p2c(bounds, num_soilc, filter_soilc, & this%fire_nloss_patch(bounds%begp:bounds%endp), & this%fire_nloss_p2c_col(bounds%begc:bounds%endc)) + call p2c(bounds, num_soilc, filter_soilc, & + this%gru_conv_nflux_patch(bounds%begp:bounds%endp), & + this%gru_conv_nflux_col(bounds%begc:bounds%endc)) + + call c2g( bounds = bounds, & + carr = this%gru_conv_nflux_col(bounds%begc:bounds%endc), & + garr = this%gru_conv_nflux_grc(bounds%begg:bounds%endg), & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + ! vertically integrate column-level fire N losses do k = 1, ndecomp_pools do j = 1, nlevdecomp diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 10c8164baa..c1ff66f675 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -558,6 +558,15 @@ subroutine InitEachTimeStep(this, bounds, num_soilc, filter_soilc) call this%cnveg_carbonstate_inst%ZeroDWT(bounds) call this%cnveg_nitrogenstate_inst%ZeroDWT(bounds) + call this%cnveg_carbonflux_inst%ZeroGRU(bounds) + if (use_c13) then + call this%c13_cnveg_carbonflux_inst%ZeroGRU(bounds) + end if + if (use_c14) then + call this%c14_cnveg_carbonflux_inst%ZeroGRU(bounds) + end if + call this%cnveg_nitrogenflux_inst%ZeroGRU(bounds) + end subroutine InitEachTimeStep !----------------------------------------------------------------------- diff --git a/src/biogeochem/dynConsBiogeochemMod.F90 b/src/biogeochem/dynConsBiogeochemMod.F90 index e233653ca7..096ab102fb 100644 --- a/src/biogeochem/dynConsBiogeochemMod.F90 +++ b/src/biogeochem/dynConsBiogeochemMod.F90 @@ -587,36 +587,6 @@ subroutine dyn_cnbal_patch(bounds, & end do - ! calculate patch-to-column slash fluxes into litter and CWD pools - do p = bounds%begp, bounds%endp - c = patch%column(p) - - ! fine and coarse root to litter and CWD slash carbon fluxes - cnveg_carbonflux_inst%dwt_slash_cflux_col(c) = & - cnveg_carbonflux_inst%dwt_slash_cflux_col(c) + & - dwt_frootc_to_litter(p)/dt + & - dwt_livecrootc_to_litter(p)/dt + & - dwt_deadcrootc_to_litter(p)/dt - - if ( use_c13 ) then - c13_cnveg_carbonflux_inst%dwt_slash_cflux_col(c) = & - c13_cnveg_carbonflux_inst%dwt_slash_cflux_col(c) + & - dwt_frootc13_to_litter(p)/dt + & - dwt_livecrootc13_to_litter(p)/dt + & - dwt_deadcrootc13_to_litter(p)/dt - endif - - if ( use_c14 ) then - c14_cnveg_carbonflux_inst%dwt_slash_cflux_col(c) = & - c14_cnveg_carbonflux_inst%dwt_slash_cflux_col(c) + & - dwt_frootc14_to_litter(p)/dt + & - dwt_livecrootc14_to_litter(p)/dt + & - dwt_deadcrootc14_to_litter(p)/dt - endif - - end do - - ! calculate patch-to-column for fluxes into litter and CWD pools do j = 1, nlevdecomp do p = bounds%begp, bounds%endp @@ -787,6 +757,46 @@ subroutine dyn_cnbal_patch(bounds, & end do + ! calculate patch-to-gridcell slash fluxes into litter and CWD pools + ! Note that patch-level fluxes are stored per unit GRIDCELL area - thus, we don't + ! need to multiply by the patch's gridcell weight when translating patch-level + ! fluxes into gridcell-level fluxes. + + do p = bounds%begp, bounds%endp + g = patch%gridcell(p) + + ! fine and coarse root to litter and CWD slash carbon fluxes + cnveg_carbonflux_inst%dwt_slash_cflux_patch(p) = & + dwt_frootc_to_litter(p)/dt + & + dwt_livecrootc_to_litter(p)/dt + & + dwt_deadcrootc_to_litter(p)/dt + cnveg_carbonflux_inst%dwt_slash_cflux_grc(g) = & + cnveg_carbonflux_inst%dwt_slash_cflux_grc(g) + & + cnveg_carbonflux_inst%dwt_slash_cflux_patch(p) + + if ( use_c13 ) then + c13_cnveg_carbonflux_inst%dwt_slash_cflux_patch(p) = & + dwt_frootc13_to_litter(p)/dt + & + dwt_livecrootc13_to_litter(p)/dt + & + dwt_deadcrootc13_to_litter(p)/dt + c13_cnveg_carbonflux_inst%dwt_slash_cflux_grc(g) = & + c13_cnveg_carbonflux_inst%dwt_slash_cflux_grc(g) + & + c13_cnveg_carbonflux_inst%dwt_slash_cflux_patch(p) + endif + + if ( use_c14 ) then + c14_cnveg_carbonflux_inst%dwt_slash_cflux_patch(p) = & + dwt_frootc14_to_litter(p)/dt + & + dwt_livecrootc14_to_litter(p)/dt + & + dwt_deadcrootc14_to_litter(p)/dt + c14_cnveg_carbonflux_inst%dwt_slash_cflux_grc(g) = & + c14_cnveg_carbonflux_inst%dwt_slash_cflux_grc(g) + & + c14_cnveg_carbonflux_inst%dwt_slash_cflux_patch(p) + endif + + end do + + ! Deallocate patch-level flux arrays deallocate(dwt) deallocate(dwt_leafc_seed) diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90 new file mode 100644 index 0000000000..15d5db95a6 --- /dev/null +++ b/src/biogeochem/dynGrossUnrepMod.F90 @@ -0,0 +1,528 @@ +module dynGrossUnrepMod + +#include "shr_assert.h" + + !--------------------------------------------------------------------------- + ! !DESCRIPTION: + ! Handle reading of the gross unrepresented landcover change data, as well as the + ! state updates that happen as a result. + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use decompMod , only : bounds_type, BOUNDS_LEVEL_PROC + use abortutils , only : endrun + use dynFileMod , only : dyn_file_type + use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type + use CNVegCarbonStateType , only : cnveg_carbonstate_type + use CNVegCarbonFluxType , only : cnveg_carbonflux_type + use CNVegNitrogenStateType , only : cnveg_nitrogenstate_type + use CNVegNitrogenFluxType , only : cnveg_nitrogenflux_type + use SoilBiogeochemStateType , only : soilbiogeochem_state_type + use pftconMod , only : pftcon + use clm_varcon , only : grlnd + use clm_varpar , only : natpft_size + use ColumnType , only : col + use PatchType , only : patch + ! + ! !PUBLIC MEMBER FUNCTIONS: + implicit none + private + ! + public :: dynGrossUnrep_init ! initialize data structures for grossunrep information + public :: dynGrossUnrep_interp ! get grossunrep data for current time step, if needed + public :: CNGrossUnrep ! grossunrep mortality routine for CN code + ! + ! !PRIVATE MEMBER FUNCTIONS: + private :: CNGrossUnrepPftToColumn ! gather patch-level grossunrep fluxes to the column level + ! + ! !PRIVATE TYPES: + + ! Note that, since we have our own dyngrossunrep_file object (distinct from dynpft_file), + ! we could theoretically have a separate file providing grossunrep data from that providing + ! the pftdyn data + type(dyn_file_type), target :: dyngrossunrep_file ! information for the file containing grossunrep data + + ! Define the underlying grossunrep variables + character(len=64), parameter :: grossunrep_varname = 'UNREPRESENTED_PFT_LULCC' + + type(dyn_var_time_uninterp_type) :: gru_inst ! value of gross unrepresented variable + + real(r8) , allocatable :: grossunrepfrac(:,:) ! gross unrepresented landcover change fraction + logical :: do_grossunrep ! whether we're in a period when we should do gross unrepresented landcover change + character(len=*), parameter, private :: sourcefile = & + __FILE__ + !--------------------------------------------------------------------------- + +contains + + !----------------------------------------------------------------------- + subroutine dynGrossUnrep_init(bounds, grossunrep_filename) + ! + ! !DESCRIPTION: + ! Initialize data structures for grossunrep information. + ! This should be called once, during model initialization. + ! + ! !USES: + use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type + use dynTimeInfoMod , only : YEAR_POSITION_START_OF_TIMESTEP + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds ! proc-level bounds + character(len=*) , intent(in) :: grossunrep_filename ! name of file containing grossunrep information + ! + ! !LOCAL VARIABLES: + integer :: num_points ! number of spatial points + integer :: ier ! error code + + character(len=*), parameter :: subname = 'dynGrossUnrep_init' + !----------------------------------------------------------------------- + + SHR_ASSERT_ALL(bounds%level == BOUNDS_LEVEL_PROC, subname // ': argument must be PROC-level bounds') + + allocate(grossunrepfrac(bounds%begg:bounds%endg,0:natpft_size-1),stat=ier) + if (ier /= 0) then + call endrun(msg=' allocation error for grossunrep'//errMsg(sourcefile, __LINE__)) + end if + + ! Get the year from the START of the timestep for consistency with other dyn file + ! stuff (though it shouldn't actually matter for grossunrep, given the way the + ! once-per-year grossunrep is applied). + dyngrossunrep_file = dyn_file_type(grossunrep_filename, YEAR_POSITION_START_OF_TIMESTEP) + + ! Get initial grossunrep data + num_points = (bounds%endg - bounds%begg + 1) + gru_inst = dyn_var_time_uninterp_type( & + dyn_file=dyngrossunrep_file, varname=grossunrep_varname, & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=[num_points,natpft_size]) + + end subroutine dynGrossUnrep_init + + + !----------------------------------------------------------------------- + subroutine dynGrossUnrep_interp(bounds) + ! + ! !DESCRIPTION: + ! Get grossunrep data for model time, when needed. + ! + ! Note that grossunrep data are stored as rates (not weights) and so time interpolation + ! is not necessary - the grossunrep rate is held constant through the year. This is + ! consistent with the treatment of changing PFT weights, where interpolation of the + ! annual endpoint weights leads to a constant rate of change in PFT weight through the + ! year, with abrupt changes in the rate at annual boundaries. + ! + ! !USES: + use dynTimeInfoMod , only : time_info_type + ! + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds ! proc-level bounds + ! + ! !LOCAL VARIABLES: + + character(len=*), parameter :: subname = 'dyngru_interp' + !----------------------------------------------------------------------- + + SHR_ASSERT_ALL(bounds%level == BOUNDS_LEVEL_PROC, subname // ': argument must be PROC-level bounds') + + call dyngrossunrep_file%time_info%set_current_year() + + ! Get total grossunrep for this time step + grossunrepfrac(bounds%begg:bounds%endg,0:natpft_size-1) = 0._r8 + + if (dyngrossunrep_file%time_info%is_before_time_series()) then + ! Turn off grossunrep before the start of the grossunrep time series + do_grossunrep = .false. + else + ! Note that do_grossunrep stays true even past the end of the time series. This + ! means that grossunrep rates will be maintained at the rate given in the last + ! year of the file for all years past the end of this specified time series. + do_grossunrep = .true. + call gru_inst%get_current_data(grossunrepfrac) + end if + + end subroutine dynGrossUnrep_interp + + + !----------------------------------------------------------------------- + subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & + cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + ! + ! !DESCRIPTION: + ! GrossUnrep mortality routine for coupled carbon-nitrogen code (CN) + ! + ! !USES: + use pftconMod , only : noveg, nbrdlf_evr_shrub, nc4_grass + use clm_varcon , only : secspday + use clm_time_manager, only : get_step_size_real, is_beg_curr_year + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! column filter for soil points + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! patch filter for soil points + type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst + type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst + type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst + ! + ! !LOCAL VARIABLES: + integer :: p ! patch index + integer :: g ! gridcell index + integer :: fp ! patch filter index + real(r8):: thistreec ! carbon in this tree for calculating grossunrep fraction (gC/m2) + real(r8):: cm ! rate for carbon grossunrep mortality (gC/m2/yr) + real(r8):: am ! rate for fractional grossunrep mortality (1/yr) + real(r8):: m ! rate for fractional grossunrep mortality (1/s) + real(r8):: dtime ! model time step (s) + !----------------------------------------------------------------------- + + associate(& + ivt => patch%itype , & ! Input: [integer (:)] pft vegetation type + convfrac => pftcon%pconv , & ! Input: [real (:)] pft conversion to atmosphere fraction + + leafc => cnveg_carbonstate_inst%leafc_patch , & ! Input: [real(r8) (:)] (gC/m2) leaf C + frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C + livestemc => cnveg_carbonstate_inst%livestemc_patch , & ! Input: [real(r8) (:)] (gC/m2) live stem C + deadstemc => cnveg_carbonstate_inst%deadstemc_patch , & ! Input: [real(r8) (:)] (gC/m2) dead stem C + livecrootc => cnveg_carbonstate_inst%livecrootc_patch , & ! Input: [real(r8) (:)] (gC/m2) live coarse root C + deadcrootc => cnveg_carbonstate_inst%deadcrootc_patch , & ! Input: [real(r8) (:)] (gC/m2) dead coarse root C + xsmrpool => cnveg_carbonstate_inst%xsmrpool_patch , & ! Input: [real(r8) (:)] (gC/m2) abstract C pool to meet excess MR demand + leafc_storage => cnveg_carbonstate_inst%leafc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) leaf C storage + frootc_storage => cnveg_carbonstate_inst%frootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C storage + livestemc_storage => cnveg_carbonstate_inst%livestemc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) live stem C storage + deadstemc_storage => cnveg_carbonstate_inst%deadstemc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) dead stem C storage + livecrootc_storage => cnveg_carbonstate_inst%livecrootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) live coarse root C storage + deadcrootc_storage => cnveg_carbonstate_inst%deadcrootc_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) dead coarse root C storage + gresp_storage => cnveg_carbonstate_inst%gresp_storage_patch , & ! Input: [real(r8) (:)] (gC/m2) growth respiration storage + leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) leaf C transfer + frootc_xfer => cnveg_carbonstate_inst%frootc_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C transfer + livestemc_xfer => cnveg_carbonstate_inst%livestemc_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) live stem C transfer + deadstemc_xfer => cnveg_carbonstate_inst%deadstemc_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) dead stem C transfer + livecrootc_xfer => cnveg_carbonstate_inst%livecrootc_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) live coarse root C transfer + deadcrootc_xfer => cnveg_carbonstate_inst%deadcrootc_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) dead coarse root C transfer + gresp_xfer => cnveg_carbonstate_inst%gresp_xfer_patch , & ! Input: [real(r8) (:)] (gC/m2) growth respiration transfer + + leafn => cnveg_nitrogenstate_inst%leafn_patch , & ! Input: [real(r8) (:)] (gN/m2) leaf N + frootn => cnveg_nitrogenstate_inst%frootn_patch , & ! Input: [real(r8) (:)] (gN/m2) fine root N + livestemn => cnveg_nitrogenstate_inst%livestemn_patch , & ! Input: [real(r8) (:)] (gN/m2) live stem N + deadstemn => cnveg_nitrogenstate_inst%deadstemn_patch , & ! Input: [real(r8) (:)] (gN/m2) dead stem N + livecrootn => cnveg_nitrogenstate_inst%livecrootn_patch , & ! Input: [real(r8) (:)] (gN/m2) live coarse root N + deadcrootn => cnveg_nitrogenstate_inst%deadcrootn_patch , & ! Input: [real(r8) (:)] (gN/m2) dead coarse root N + retransn => cnveg_nitrogenstate_inst%retransn_patch , & ! Input: [real(r8) (:)] (gN/m2) plant pool of retranslocated N + leafn_storage => cnveg_nitrogenstate_inst%leafn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) leaf N storage + frootn_storage => cnveg_nitrogenstate_inst%frootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) fine root N storage + livestemn_storage => cnveg_nitrogenstate_inst%livestemn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) live stem N storage + deadstemn_storage => cnveg_nitrogenstate_inst%deadstemn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) dead stem N storage + livecrootn_storage => cnveg_nitrogenstate_inst%livecrootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) live coarse root N storage + deadcrootn_storage => cnveg_nitrogenstate_inst%deadcrootn_storage_patch , & ! Input: [real(r8) (:)] (gN/m2) dead coarse root N storage + leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Input: [real(r8) (:)] (gN/m2) leaf N transfer + frootn_xfer => cnveg_nitrogenstate_inst%frootn_xfer_patch , & ! Input: [real(r8) (:)] (gN/m2) fine root N transfer + livestemn_xfer => cnveg_nitrogenstate_inst%livestemn_xfer_patch , & ! Input: [real(r8) (:)] (gN/m2) live stem N transfer + deadstemn_xfer => cnveg_nitrogenstate_inst%deadstemn_xfer_patch , & ! Input: [real(r8) (:)] (gN/m2) dead stem N transfer + livecrootn_xfer => cnveg_nitrogenstate_inst%livecrootn_xfer_patch , & ! Input: [real(r8) (:)] (gN/m2) live coarse root N transfer + deadcrootn_xfer => cnveg_nitrogenstate_inst%deadcrootn_xfer_patch , & ! Input: [real(r8) (:)] (gN/m2) dead coarse root N transfer + + gru_leafc_to_litter => cnveg_carbonflux_inst%gru_leafc_to_litter_patch , & ! Output: [real(r8) (:)] + gru_frootc_to_litter => cnveg_carbonflux_inst%gru_frootc_to_litter_patch , & ! Output: [real(r8) (:)] + gru_livestemc_to_atm => cnveg_carbonflux_inst%gru_livestemc_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadstemc_to_atm => cnveg_carbonflux_inst%gru_deadstemc_to_atm_patch , & ! Output: [real(r8) (:)] + gru_wood_productc_gain => cnveg_carbonflux_inst%gru_wood_productc_gain_patch , & ! Output: [real(r8) (:)] + gru_livecrootc_to_litter => cnveg_carbonflux_inst%gru_livecrootc_to_litter_patch , & ! Output: [real(r8) (:)] + gru_deadcrootc_to_litter => cnveg_carbonflux_inst%gru_deadcrootc_to_litter_patch , & ! Output: [real(r8) (:)] + gru_xsmrpool_to_atm => cnveg_carbonflux_inst%gru_xsmrpool_to_atm_patch , & ! Output: [real(r8) (:)] + gru_leafc_storage_to_atm => cnveg_carbonflux_inst%gru_leafc_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_frootc_storage_to_atm => cnveg_carbonflux_inst%gru_frootc_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livestemc_storage_to_atm => cnveg_carbonflux_inst%gru_livestemc_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadstemc_storage_to_atm => cnveg_carbonflux_inst%gru_deadstemc_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livecrootc_storage_to_atm => cnveg_carbonflux_inst%gru_livecrootc_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadcrootc_storage_to_atm => cnveg_carbonflux_inst%gru_deadcrootc_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_gresp_storage_to_atm => cnveg_carbonflux_inst%gru_gresp_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_leafc_xfer_to_atm => cnveg_carbonflux_inst%gru_leafc_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_frootc_xfer_to_atm => cnveg_carbonflux_inst%gru_frootc_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livestemc_xfer_to_atm => cnveg_carbonflux_inst%gru_livestemc_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadstemc_xfer_to_atm => cnveg_carbonflux_inst%gru_deadstemc_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livecrootc_xfer_to_atm => cnveg_carbonflux_inst%gru_livecrootc_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadcrootc_xfer_to_atm => cnveg_carbonflux_inst%gru_deadcrootc_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_gresp_xfer_to_atm => cnveg_carbonflux_inst%gru_gresp_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + + gru_leafn_to_litter => cnveg_nitrogenflux_inst%gru_leafn_to_litter_patch , & ! Output: [real(r8) (:)] + gru_frootn_to_litter => cnveg_nitrogenflux_inst%gru_frootn_to_litter_patch , & ! Output: [real(r8) (:)] + gru_livestemn_to_atm => cnveg_nitrogenflux_inst%gru_livestemn_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadstemn_to_atm => cnveg_nitrogenflux_inst%gru_deadstemn_to_atm_patch , & ! Output: [real(r8) (:)] + gru_wood_productn_gain => cnveg_nitrogenflux_inst%gru_wood_productn_gain_patch , & ! Output: [real(r8) (:)] + gru_livecrootn_to_litter => cnveg_nitrogenflux_inst%gru_livecrootn_to_litter_patch , & ! Output: [real(r8) (:)] + gru_deadcrootn_to_litter => cnveg_nitrogenflux_inst%gru_deadcrootn_to_litter_patch , & ! Output: [real(r8) (:)] + gru_retransn_to_litter => cnveg_nitrogenflux_inst%gru_retransn_to_litter_patch , & ! Output: [real(r8) (:)] + gru_leafn_storage_to_atm => cnveg_nitrogenflux_inst%gru_leafn_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_frootn_storage_to_atm => cnveg_nitrogenflux_inst%gru_frootn_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livestemn_storage_to_atm => cnveg_nitrogenflux_inst%gru_livestemn_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadstemn_storage_to_atm => cnveg_nitrogenflux_inst%gru_deadstemn_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livecrootn_storage_to_atm => cnveg_nitrogenflux_inst%gru_livecrootn_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadcrootn_storage_to_atm => cnveg_nitrogenflux_inst%gru_deadcrootn_storage_to_atm_patch , & ! Output: [real(r8) (:)] + gru_leafn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_leafn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_frootn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_frootn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livestemn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_livestemn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadstemn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_deadstemn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_livecrootn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_livecrootn_xfer_to_atm_patch , & ! Output: [real(r8) (:)] + gru_deadcrootn_xfer_to_atm => cnveg_nitrogenflux_inst%gru_deadcrootn_xfer_to_atm_patch & ! Output: [real(r8) (:)] + ) + + dtime = get_step_size_real() + + ! patch loop + do fp = 1,num_soilp + p = filter_soilp(fp) + g = patch%gridcell(p) + + ! If this is a natural pft, then + ! get the annual grossunrep "mortality" rate (am) from grossunrep array + ! and convert to rate per second + if (ivt(p) > noveg .and. ivt(p) <= nc4_grass) then + + if (do_grossunrep) then + am = grossunrepfrac(g,ivt(p)) + + ! Apply all grossunrep at the start of the year + if (is_beg_curr_year()) then + m = am/dtime + else + m = 0._r8 + end if + else + m = 0._r8 + end if + + ! patch-level gross unrepresented landcover change carbon fluxes + ! displayed pools + gru_leafc_to_litter(p) = leafc(p) * m + gru_frootc_to_litter(p) = frootc(p) * m + gru_livestemc_to_atm(p) = livestemc(p) * m + gru_deadstemc_to_atm(p) = deadstemc(p) * m * convfrac(ivt(p)) + gru_wood_productc_gain(p) = deadstemc(p) * m * (1._r8 - convfrac(ivt(p))) + gru_livecrootc_to_litter(p) = livecrootc(p) * m + gru_deadcrootc_to_litter(p) = deadcrootc(p) * m + gru_xsmrpool_to_atm(p) = xsmrpool(p) * m + + ! storage pools + gru_leafc_storage_to_atm(p) = leafc_storage(p) * m + gru_frootc_storage_to_atm(p) = frootc_storage(p) * m + gru_livestemc_storage_to_atm(p) = livestemc_storage(p) * m + gru_deadstemc_storage_to_atm(p) = deadstemc_storage(p) * m + gru_livecrootc_storage_to_atm(p) = livecrootc_storage(p) * m + gru_deadcrootc_storage_to_atm(p) = deadcrootc_storage(p) * m + gru_gresp_storage_to_atm(p) = gresp_storage(p) * m + + ! transfer pools + gru_leafc_xfer_to_atm(p) = leafc_xfer(p) * m + gru_frootc_xfer_to_atm(p) = frootc_xfer(p) * m + gru_livestemc_xfer_to_atm(p) = livestemc_xfer(p) * m + gru_deadstemc_xfer_to_atm(p) = deadstemc_xfer(p) * m + gru_livecrootc_xfer_to_atm(p) = livecrootc_xfer(p) * m + gru_deadcrootc_xfer_to_atm(p) = deadcrootc_xfer(p) * m + gru_gresp_xfer_to_atm(p) = gresp_xfer(p) * m + + ! patch-level gross unrepresented landcover change mortality nitrogen fluxes + ! displayed pools + gru_leafn_to_litter(p) = leafn(p) * m + gru_frootn_to_litter(p) = frootn(p) * m + gru_livestemn_to_atm(p) = livestemn(p) * m + gru_deadstemn_to_atm(p) = deadstemn(p) * m * convfrac(ivt(p)) + gru_wood_productn_gain(p) = deadstemn(p) * m * (1._r8 - convfrac(ivt(p))) + gru_livecrootn_to_litter(p) = livecrootn(p) * m + gru_deadcrootn_to_litter(p) = deadcrootn(p) * m + gru_retransn_to_litter(p) = retransn(p) * m + + ! storage pools + gru_leafn_storage_to_atm(p) = leafn_storage(p) * m + gru_frootn_storage_to_atm(p) = frootn_storage(p) * m + gru_livestemn_storage_to_atm(p) = livestemn_storage(p) * m + gru_deadstemn_storage_to_atm(p) = deadstemn_storage(p) * m + gru_livecrootn_storage_to_atm(p) = livecrootn_storage(p) * m + gru_deadcrootn_storage_to_atm(p) = deadcrootn_storage(p) * m + + ! transfer pools + gru_leafn_xfer_to_atm(p) = leafn_xfer(p) * m + gru_frootn_xfer_to_atm(p) = frootn_xfer(p) * m + gru_livestemn_xfer_to_atm(p) = livestemn_xfer(p) * m + gru_deadstemn_xfer_to_atm(p) = deadstemn_xfer(p) * m + gru_livecrootn_xfer_to_atm(p) = livecrootn_xfer(p) * m + gru_deadcrootn_xfer_to_atm(p) = deadcrootn_xfer(p) * m + + end if ! end tree block + + end do ! end of pft loop + + ! gather all patch-level litterfall fluxes from grossunrep to the column + ! for litter C and N inputs + + call CNGrossUnrepPftToColumn(num_soilc, filter_soilc, & + soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + + end associate + + end subroutine CNGrossUnrep + + !----------------------------------------------------------------------- + subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & + soilbiogeochem_state_inst, CNVeg_carbonflux_inst, cnveg_nitrogenflux_inst) + ! + ! !DESCRIPTION: + ! called at the end of CNGrossUnrep to gather all patch-level grossunrep litterfall fluxes + ! to the column level and assign them to the three litter pools + ! + ! !USES: + use clm_varpar , only : maxpatch_pft, nlevdecomp, numpft + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! soil column filter + type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst + type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst + type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst + ! + ! !LOCAL VARIABLES: + integer :: fc,c,pi,p,j ! indices + !----------------------------------------------------------------------- + + associate( & + ivt => patch%itype , & ! Input: [integer (:) ] pft vegetation type + wtcol => patch%wtcol , & ! Input: [real(r8) (:) ] pft weight relative to column (0-1) + + lf_flab => pftcon%lf_flab , & ! Input: leaf litter labile fraction + lf_fcel => pftcon%lf_fcel , & ! Input: leaf litter cellulose fraction + lf_flig => pftcon%lf_flig , & ! Input: leaf litter lignin fraction + fr_flab => pftcon%fr_flab , & ! Input: fine root litter labile fraction + fr_fcel => pftcon%fr_fcel , & ! Input: fine root litter cellulose fraction + fr_flig => pftcon%fr_flig , & ! Input: fine root litter lignin fraction + + leaf_prof => soilbiogeochem_state_inst%leaf_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of leaves + froot_prof => soilbiogeochem_state_inst%froot_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of fine roots + croot_prof => soilbiogeochem_state_inst%croot_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of coarse roots + stem_prof => soilbiogeochem_state_inst%stem_prof_patch , & ! Input: [real(r8) (:,:) ] (1/m) profile of stems + + gru_leafc_to_litter => cnveg_carbonflux_inst%gru_leafc_to_litter_patch , & ! Input: [real(r8) (:)] + gru_frootc_to_litter => cnveg_carbonflux_inst%gru_frootc_to_litter_patch , & ! Input: [real(r8) (:)] + gru_wood_productc_gain => cnveg_carbonflux_inst%gru_wood_productc_gain_patch , & ! Input: [real(r8) (:)] + gru_livecrootc_to_litter => cnveg_carbonflux_inst%gru_livecrootc_to_litter_patch , & ! Input: [real(r8) (:)] + gru_deadcrootc_to_litter => cnveg_carbonflux_inst%gru_deadcrootc_to_litter_patch , & ! Input: [real(r8) (:)] + gru_conv_cflux => cnveg_carbonflux_inst%gru_conv_cflux_patch , & ! Input: [real(r8) (:) ] C fluxes associated with conversion (immediate loss to atm) + + gru_c_to_litr_met_c => cnveg_carbonflux_inst%gru_c_to_litr_met_c_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with grossunrep to litter metabolic pool (gC/m3/s) + gru_c_to_litr_cel_c => cnveg_carbonflux_inst%gru_c_to_litr_cel_c_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with grossunrep to litter cellulose pool (gC/m3/s) + gru_c_to_litr_lig_c => cnveg_carbonflux_inst%gru_c_to_litr_lig_c_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with grossunrep to litter lignin pool (gC/m3/s) + gru_c_to_cwdc_c => cnveg_carbonflux_inst%gru_c_to_cwdc_col , & ! Output: [real(r8) (:,:) ] C fluxes associated with grossunrep to CWD pool (gC/m3/s) + + gru_wood_productc_gain_c => cnveg_carbonflux_inst%gru_wood_productc_gain_col , & ! Input: [real(r8) (:)] + + gru_leafn_to_litter => cnveg_nitrogenflux_inst%gru_leafn_to_litter_patch , & ! Input: [real(r8) (:)] + gru_frootn_to_litter => cnveg_nitrogenflux_inst%gru_frootn_to_litter_patch , & ! Input: [real(r8) (:)] + gru_wood_productn_gain => cnveg_nitrogenflux_inst%gru_wood_productn_gain_patch , & ! Input: [real(r8) (:)] + gru_livecrootn_to_litter => cnveg_nitrogenflux_inst%gru_livecrootn_to_litter_patch , & ! Input: [real(r8) (:)] + gru_deadcrootn_to_litter => cnveg_nitrogenflux_inst%gru_deadcrootn_to_litter_patch , & ! Input: [real(r8) (:)] + gru_retransn_to_litter => cnveg_nitrogenflux_inst%gru_retransn_to_litter_patch , & ! Input: [real(r8) (:)] + gru_conv_nflux => cnveg_nitrogenflux_inst%gru_conv_nflux_patch , & ! Input: [real(r8) (:) ] N fluxes associated with conversion (immediate loss to atm) + + gru_n_to_litr_met_c => cnveg_nitrogenflux_inst%gru_n_to_litr_met_n_col , & ! Output: [real(r8) (:,:) ] N fluxes associated with grossunrep to litter metabolic pool (gN/m3/s) + gru_n_to_litr_cel_c => cnveg_nitrogenflux_inst%gru_n_to_litr_cel_n_col , & ! Output: [real(r8) (:,:) ] N fluxes associated with grossunrep to litter cellulose pool (gN/m3/s) + gru_n_to_litr_lig_c => cnveg_nitrogenflux_inst%gru_n_to_litr_lig_n_col , & ! Output: [real(r8) (:,:) ] N fluxes associated with grossunrep to litter lignin pool (gN/m3/s) + gru_n_to_cwdn_c => cnveg_nitrogenflux_inst%gru_n_to_cwdn_col , & ! Output: [real(r8) (:,:) ] N fluxes associated with grossunrep to CWD pool (gN/m3/s) + + gru_wood_productn_gain_c => cnveg_nitrogenflux_inst%gru_wood_productn_gain_col & ! Input: [real(r8) (:)] + ) + + do j = 1, nlevdecomp + do pi = 1,maxpatch_pft + do fc = 1,num_soilc + c = filter_soilc(fc) + + if (pi <= col%npatches(c)) then + p = col%patchi(c) + pi - 1 + + if (patch%active(p)) then + + ! leaf gross unrepresented landcover change mortality carbon fluxes + gru_c_to_litr_met_c(c,j) = gru_c_to_litr_met_c(c,j) + & + gru_leafc_to_litter(p) * lf_flab(ivt(p)) * wtcol(p) * leaf_prof(p,j) + gru_c_to_litr_cel_c(c,j) = gru_c_to_litr_cel_c(c,j) + & + gru_leafc_to_litter(p) * lf_fcel(ivt(p)) * wtcol(p) * leaf_prof(p,j) + gru_c_to_litr_lig_c(c,j) = gru_c_to_litr_lig_c(c,j) + & + gru_leafc_to_litter(p) * lf_flig(ivt(p)) * wtcol(p) * leaf_prof(p,j) + + ! fine root gross unrepresented landcover change mortality carbon fluxes + gru_c_to_litr_met_c(c,j) = gru_c_to_litr_met_c(c,j) + & + gru_frootc_to_litter(p) * fr_flab(ivt(p)) * wtcol(p) * froot_prof(p,j) + gru_c_to_litr_cel_c(c,j) = gru_c_to_litr_cel_c(c,j) + & + gru_frootc_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j) + gru_c_to_litr_lig_c(c,j) = gru_c_to_litr_lig_c(c,j) + & + gru_frootc_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j) + + ! coarse root gross unrepresented landcover change mortality carbon fluxes + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! leaf gross unrepresented landcover change mortality nitrogen fluxes + gru_n_to_litr_met_c(c,j) = gru_n_to_litr_met_c(c,j) + & + gru_leafn_to_litter(p) * lf_flab(ivt(p)) * wtcol(p) * leaf_prof(p,j) + gru_n_to_litr_cel_c(c,j) = gru_n_to_litr_cel_c(c,j) + & + gru_leafn_to_litter(p) * lf_fcel(ivt(p)) * wtcol(p) * leaf_prof(p,j) + gru_n_to_litr_lig_c(c,j) = gru_n_to_litr_lig_c(c,j) + & + gru_leafn_to_litter(p) * lf_flig(ivt(p)) * wtcol(p) * leaf_prof(p,j) + + ! fine root unrepresented landcover change mortality nitrogen fluxes + gru_n_to_litr_met_c(c,j) = gru_n_to_litr_met_c(c,j) + & + gru_frootn_to_litter(p) * fr_flab(ivt(p)) * wtcol(p) * froot_prof(p,j) + gru_n_to_litr_cel_c(c,j) = gru_n_to_litr_cel_c(c,j) + & + gru_frootn_to_litter(p) * fr_fcel(ivt(p)) * wtcol(p) * froot_prof(p,j) + gru_n_to_litr_lig_c(c,j) = gru_n_to_litr_lig_c(c,j) + & + gru_frootn_to_litter(p) * fr_flig(ivt(p)) * wtcol(p) * froot_prof(p,j) + + ! coarse root gross unrepresented landcover change mortality nitrogen fluxes + gru_n_to_cwdn_c(c,j) = gru_n_to_cwdn_c(c,j) + & + gru_livecrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) + gru_n_to_cwdn_c(c,j) = gru_n_to_cwdn_c(c,j) + & + gru_deadcrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! retranslocated N pool gross unrepresented landcover change mortality fluxes + gru_n_to_litr_met_c(c,j) = gru_n_to_litr_met_c(c,j) + & + gru_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) + + end if + end if + + end do + + end do + end do + + do pi = 1,maxpatch_pft + do fc = 1,num_soilc + c = filter_soilc(fc) + + if (pi <= col%npatches(c)) then + p = col%patchi(c) + pi - 1 + + if (patch%active(p)) then + ! wood gross unrepresented landcover change mortality carbon fluxes to product pools + gru_wood_productc_gain_c(c) = gru_wood_productc_gain_c(c) + & + gru_wood_productc_gain(p) * wtcol(p) + + ! wood gross unrepresented landcover change mortality nitrogen fluxes to product pools + gru_wood_productn_gain_c(c) = gru_wood_productn_gain_c(c) + & + gru_wood_productn_gain(p) * wtcol(p) + end if + end if + + end do + + end do + + end associate + + end subroutine CNGrossUnrepPftToColumn + +end module dynGrossUnrepMod diff --git a/src/dyn_subgrid/dynSubgridControlMod.F90 b/src/dyn_subgrid/dynSubgridControlMod.F90 index 58e3a40359..3491057dc0 100644 --- a/src/dyn_subgrid/dynSubgridControlMod.F90 +++ b/src/dyn_subgrid/dynSubgridControlMod.F90 @@ -26,6 +26,7 @@ module dynSubgridControlMod public :: get_do_transient_crops ! return the value of the do_transient_crops control flag public :: run_has_transient_landcover ! returns true if any aspects of prescribed transient landcover are enabled public :: get_do_harvest ! return the value of the do_harvest control flag + public :: get_do_grossunrep ! return the value of the do_grossunrep control flag public :: get_for_testing_allow_non_annual_changes ! return true if user has requested to allow area changes at times other than the year boundary, for testing purposes public :: get_for_testing_zero_dynbal_fluxes ! return true if user has requested to set the dynbal water and energy fluxes to zero, for testing purposes ! @@ -40,6 +41,7 @@ module dynSubgridControlMod logical :: do_transient_pfts = .false. ! whether to apply transient natural PFTs from dataset logical :: do_transient_crops = .false. ! whether to apply transient crops from dataset logical :: do_harvest = .false. ! whether to apply harvest from dataset + logical :: do_grossunrep = .false. ! whether to apply gross unrepresented landcover change from dataset ! The following is only meant for testing: Whether area changes are allowed at times ! other than the year boundary. This should only arise in some test configurations @@ -114,6 +116,7 @@ subroutine read_namelist( NLFilename ) logical :: do_transient_pfts logical :: do_transient_crops logical :: do_harvest + logical :: do_grossunrep logical :: for_testing_allow_non_annual_changes logical :: for_testing_zero_dynbal_fluxes ! other local variables: @@ -136,6 +139,7 @@ subroutine read_namelist( NLFilename ) do_transient_pfts = .false. do_transient_crops = .false. do_harvest = .false. + do_grossunrep = .false. for_testing_allow_non_annual_changes = .false. for_testing_zero_dynbal_fluxes = .false. @@ -153,12 +157,14 @@ subroutine read_namelist( NLFilename ) end if close(nu_nml) call relavu( nu_nml ) + do_grossunrep = do_harvest endif call shr_mpi_bcast (flanduse_timeseries, mpicom) call shr_mpi_bcast (do_transient_pfts, mpicom) call shr_mpi_bcast (do_transient_crops, mpicom) call shr_mpi_bcast (do_harvest, mpicom) + call shr_mpi_bcast (do_grossunrep, mpicom) call shr_mpi_bcast (for_testing_allow_non_annual_changes, mpicom) call shr_mpi_bcast (for_testing_zero_dynbal_fluxes, mpicom) @@ -167,6 +173,7 @@ subroutine read_namelist( NLFilename ) do_transient_pfts = do_transient_pfts, & do_transient_crops = do_transient_crops, & do_harvest = do_harvest, & + do_grossunrep = do_grossunrep, & for_testing_allow_non_annual_changes = for_testing_allow_non_annual_changes, & for_testing_zero_dynbal_fluxes = for_testing_zero_dynbal_fluxes) @@ -211,6 +218,11 @@ subroutine check_namelist_consistency write(iulog,*) 'a flanduse_timeseries file (currently flanduse_timeseries is blank)' call endrun(msg=errMsg(sourcefile, __LINE__)) end if + if (dyn_subgrid_control_inst%do_grossunrep) then + write(iulog,*) 'ERROR: do_grossunrep can only be true if you are running with' + write(iulog,*) 'a flanduse_timeseries file (currently flanduse_timeseries is blank)' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if end if if (dyn_subgrid_control_inst%do_transient_pfts) then @@ -249,6 +261,17 @@ subroutine check_namelist_consistency end if end if + if (dyn_subgrid_control_inst%do_grossunrep) then + if (.not. use_cn) then + write(iulog,*) 'ERROR: do_grossunrep can only be true if use_cn is true' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + if (use_fates) then + write(iulog,*) 'ERROR: do_grossunrep currently does not work with use_fates' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + end if + end subroutine check_namelist_consistency !----------------------------------------------------------------------- @@ -312,6 +335,18 @@ logical function get_do_harvest() end function get_do_harvest + !----------------------------------------------------------------------- + logical function get_do_grossunrep() + ! !DESCRIPTION: + ! Return the value of the do_grossunrep control flag + !----------------------------------------------------------------------- + + SHR_ASSERT(dyn_subgrid_control_inst%initialized, errMsg(sourcefile, __LINE__)) + + get_do_grossunrep = dyn_subgrid_control_inst%do_grossunrep + + end function get_do_grossunrep + !----------------------------------------------------------------------- logical function get_for_testing_allow_non_annual_changes() ! diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index 8703fcb2d9..90bbd05abe 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -14,12 +14,14 @@ module dynSubgridDriverMod use dynSubgridControlMod , only : get_flanduse_timeseries use dynSubgridControlMod , only : get_do_transient_pfts, get_do_transient_crops use dynSubgridControlMod , only : get_do_harvest + use dynSubgridControlMod , only : get_do_grossunrep use dynPriorWeightsMod , only : prior_weights_type use dynPatchStateUpdaterMod , only : patch_state_updater_type use dynColumnStateUpdaterMod , only : column_state_updater_type use dynpftFileMod , only : dynpft_init, dynpft_interp use dyncropFileMod , only : dyncrop_init, dyncrop_interp use dynHarvestMod , only : dynHarvest_init, dynHarvest_interp + use dynGrossUnrepMod , only : dynGrossUnrep_init, dynGrossUnrep_interp use dynLandunitAreaMod , only : update_landunit_weights use subgridWeightsMod , only : compute_higher_order_weights, set_subgrid_diagnostic_fields use reweightMod , only : reweight_wrapup @@ -121,6 +123,11 @@ subroutine dynSubgrid_init(bounds_proc, glc_behavior, crop_inst) call dynHarvest_init(bounds_proc, harvest_filename=get_flanduse_timeseries()) end if + ! Initialize stuff for gross unrepresented landuse data. + if (get_do_grossunrep()) then + call dynGrossUnrep_init(bounds_proc, grossunrep_filename=get_flanduse_timeseries()) + end if + ! ------------------------------------------------------------------------ ! Set initial subgrid weights for aspects that are read from file. This is relevant ! for cold start and use_init_interp-based initialization. @@ -248,6 +255,10 @@ subroutine dynSubgrid_driver(bounds_proc, call dynHarvest_interp(bounds_proc) end if + if (get_do_grossunrep()) then + call dynGrossUnrep_interp(bounds_proc) + end if + ! ========================================================================== ! Do land cover change that does not require I/O ! ========================================================================== diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 78be5efd44..62683d4256 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -38,7 +38,7 @@ module SoilBiogeochemCarbonStateType real(r8), pointer :: decomp_cpools_col (:,:) ! (gC/m2) decomposing (litter, cwd, soil) c pools real(r8), pointer :: dyn_cbal_adjustments_col (:) ! (gC/m2) adjustments to each column made in this timestep via dynamic column area adjustments (note: this variable only makes sense at the column-level: it is meaningless if averaged to the gridcell-level) integer :: restart_file_spinup_state ! spinup state as read from restart file, for determining whether to enter or exit spinup mode. - real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools + real(r8) :: ccrit ! critical carbon value contains @@ -46,7 +46,7 @@ module SoilBiogeochemCarbonStateType procedure , public :: SetValues procedure , public :: Restart procedure , public :: Summary - procedure , public :: SetTotVgCThresh + procedure , public :: SetCCrit procedure , public :: DynamicColumnAdjustments ! adjust state variables when column areas change procedure , private :: InitAllocate procedure , private :: InitHistory @@ -70,7 +70,7 @@ subroutine Init(this, bounds, carbon_type, ratio, c12_soilbiogeochem_carbonstate real(r8) , intent(in) :: ratio type(soilbiogeochem_carbonstate_type) , intent(in), optional :: c12_soilbiogeochem_carbonstate_inst - this%totvegcthresh = nan + this%ccrit = nan call this%InitAllocate ( bounds) call this%InitHistory ( bounds, carbon_type ) if (present(c12_soilbiogeochem_carbonstate_inst)) then @@ -674,10 +674,6 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, totvegc_col, c12_so call endrun(msg=' CNRest: error in entering/exiting spinup - should occur only when nstep = 1'//& errMsg(sourcefile, __LINE__)) endif - if ( exit_spinup .and. isnan(this%totvegcthresh) )then - call endrun(msg=' CNRest: error in exit spinup - totvegcthresh was not set with SetTotVgCThresh'//& - errMsg(sourcefile, __LINE__)) - end if do k = 1, ndecomp_pools if ( exit_spinup ) then m = decomp_cascade_con%spinup_factor(k) @@ -694,7 +690,10 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, totvegc_col, c12_so ! reset decomp pools to near zero during exit_spinup to avoid very ! large and inert soil carbon stocks; note that only pools with spinup factor > 1 ! will be affected, which means that total SOMC and LITC pools will not be set to 0. - if (totvegc_col(c) <= this%totvegcthresh .and. lun%itype(l) /= istcrop) then +!KO if (totvegc_col(c) <= this%ccrit .and. lun%itype(l) /= istcrop) then +!KO + if (totvegc_col(c) <= 0.1_r8 .and. lun%itype(l) /= istcrop) then +!KO this%decomp_cpools_vr_col(c,j,k) = 0.0_r8 endif elseif ( abs(m - 1._r8) .gt. 0.000001_r8 .and. enter_spinup) then @@ -927,18 +926,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end subroutine Summary !------------------------------------------------------------------------ - subroutine SetTotVgCThresh(this, totvegcthresh) + subroutine SetCCrit(this, ccrit) class(soilbiogeochem_carbonstate_type) :: this - real(r8) , intent(in) :: totvegcthresh + real(r8) , intent(in) :: ccrit - if ( totvegcthresh <= 0.0_r8 )then - call endrun(msg=' ERROR totvegcthresh is zero or negative and should be > 0'//& - errMsg(sourcefile, __LINE__)) - end if - this%totvegcthresh = totvegcthresh + this%ccrit = ccrit - end subroutine SetTotVgCThresh + end subroutine SetCCrit !----------------------------------------------------------------------- diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index ca09e63624..b776f77731 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -52,7 +52,7 @@ module SoilBiogeochemNitrogenStateType ! the N balance check real(r8), pointer :: dyn_no3bal_adjustments_col (:) ! (gN/m2) NO3 adjustments to each column made in this timestep via dynamic column area adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) real(r8), pointer :: dyn_nh4bal_adjustments_col (:) ! (gN/m2) NH4 adjustments to each column made in this timestep via dynamic column adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) - real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools + real(r8) :: ncrit ! (gN/m2) critical value of nitrogen before truncation contains @@ -61,7 +61,7 @@ module SoilBiogeochemNitrogenStateType procedure , public :: SetValues procedure , public :: Summary procedure , public :: DynamicColumnAdjustments ! adjust state variables when column areas change - procedure , public :: SetTotVgCThresh ! Set value for totvegcthresh needed in Restart + procedure , public :: SetNCrit procedure , private :: InitAllocate procedure , private :: InitHistory procedure , private :: InitCold @@ -84,7 +84,7 @@ subroutine Init(this, bounds, & real(r8) , intent(in) :: decomp_cpools_col (bounds%begc:, 1:) real(r8) , intent(in) :: decomp_cpools_1m_col (bounds%begc:, 1:) - this%totvegcthresh = nan + this%ncrit = nan call this%InitAllocate (bounds ) call this%InitHistory (bounds) @@ -610,10 +610,6 @@ subroutine Restart ( this, bounds, ncid, flag, totvegc_col ) call endrun(msg=' Error in entering/exiting spinup - should occur only when nstep = 1'//& errMsg(sourcefile, __LINE__)) endif - if ( exit_spinup .and. isnan(this%totvegcthresh) )then - call endrun(msg=' Error in exit spinup - totvegcthresh was not set with SetTotVgCThresh'//& - errMsg(sourcefile, __LINE__)) - end if do k = 1, ndecomp_pools if ( exit_spinup ) then m = decomp_cascade_con%spinup_factor(k) @@ -635,7 +631,10 @@ subroutine Restart ( this, bounds, ncid, flag, totvegc_col ) ! pools with spinup factor > 1 ! will be affected, which means that total SOMN and LITN ! pools will not be set to 0. - if (totvegc_col(c) <= this%totvegcthresh .and. lun%itype(l) /= istcrop) then +!KO if (totvegc_col(c) <= this%ncrit .and. lun%itype(l) /= istcrop) then +!KO + if (totvegc_col(c) <= 0.1_r8 .and. lun%itype(l) /= istcrop) then +!KO this%decomp_npools_vr_col(c,j,k) = 0._r8 endif elseif ( abs(m - 1._r8) .gt. 0.000001_r8 .and. enter_spinup) then @@ -1007,17 +1006,13 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda end subroutine DynamicColumnAdjustments !------------------------------------------------------------------------ - subroutine SetTotVgCThresh(this, totvegcthresh) + subroutine SetNCrit(this, ncrit) class(soilbiogeochem_nitrogenstate_type) :: this - real(r8) , intent(in) :: totvegcthresh + real(r8) , intent(in) :: ncrit - if ( totvegcthresh <= 0.0_r8 )then - call endrun(msg=' Error totvegcthresh is zero or negative and should be > 0'//& - errMsg(sourcefile, __LINE__)) - end if - this%totvegcthresh = totvegcthresh + this%ncrit = ncrit - end subroutine SetTotVgCThresh + end subroutine SetNCrit end module SoilBiogeochemNitrogenStateType From 30aac3ebd04e4c0e571bcadc1e2ffd6b5aa344ba Mon Sep 17 00:00:00 2001 From: Peter Lawrence Date: Mon, 5 Mar 2018 14:54:46 -0700 Subject: [PATCH 0002/2067] Removed soil biogeochem files that were not part of the shifting cultivation. These files were actually changes in r267 for Keith's simulations. By including the updated files this resulted in a build error. --- .../SoilBiogeochemCarbonStateType.F90 | 27 +++++++++++-------- .../SoilBiogeochemNitrogenStateType.F90 | 27 +++++++++++-------- 2 files changed, 32 insertions(+), 22 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 62683d4256..78be5efd44 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -38,7 +38,7 @@ module SoilBiogeochemCarbonStateType real(r8), pointer :: decomp_cpools_col (:,:) ! (gC/m2) decomposing (litter, cwd, soil) c pools real(r8), pointer :: dyn_cbal_adjustments_col (:) ! (gC/m2) adjustments to each column made in this timestep via dynamic column area adjustments (note: this variable only makes sense at the column-level: it is meaningless if averaged to the gridcell-level) integer :: restart_file_spinup_state ! spinup state as read from restart file, for determining whether to enter or exit spinup mode. - real(r8) :: ccrit ! critical carbon value + real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools contains @@ -46,7 +46,7 @@ module SoilBiogeochemCarbonStateType procedure , public :: SetValues procedure , public :: Restart procedure , public :: Summary - procedure , public :: SetCCrit + procedure , public :: SetTotVgCThresh procedure , public :: DynamicColumnAdjustments ! adjust state variables when column areas change procedure , private :: InitAllocate procedure , private :: InitHistory @@ -70,7 +70,7 @@ subroutine Init(this, bounds, carbon_type, ratio, c12_soilbiogeochem_carbonstate real(r8) , intent(in) :: ratio type(soilbiogeochem_carbonstate_type) , intent(in), optional :: c12_soilbiogeochem_carbonstate_inst - this%ccrit = nan + this%totvegcthresh = nan call this%InitAllocate ( bounds) call this%InitHistory ( bounds, carbon_type ) if (present(c12_soilbiogeochem_carbonstate_inst)) then @@ -674,6 +674,10 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, totvegc_col, c12_so call endrun(msg=' CNRest: error in entering/exiting spinup - should occur only when nstep = 1'//& errMsg(sourcefile, __LINE__)) endif + if ( exit_spinup .and. isnan(this%totvegcthresh) )then + call endrun(msg=' CNRest: error in exit spinup - totvegcthresh was not set with SetTotVgCThresh'//& + errMsg(sourcefile, __LINE__)) + end if do k = 1, ndecomp_pools if ( exit_spinup ) then m = decomp_cascade_con%spinup_factor(k) @@ -690,10 +694,7 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, totvegc_col, c12_so ! reset decomp pools to near zero during exit_spinup to avoid very ! large and inert soil carbon stocks; note that only pools with spinup factor > 1 ! will be affected, which means that total SOMC and LITC pools will not be set to 0. -!KO if (totvegc_col(c) <= this%ccrit .and. lun%itype(l) /= istcrop) then -!KO - if (totvegc_col(c) <= 0.1_r8 .and. lun%itype(l) /= istcrop) then -!KO + if (totvegc_col(c) <= this%totvegcthresh .and. lun%itype(l) /= istcrop) then this%decomp_cpools_vr_col(c,j,k) = 0.0_r8 endif elseif ( abs(m - 1._r8) .gt. 0.000001_r8 .and. enter_spinup) then @@ -926,14 +927,18 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end subroutine Summary !------------------------------------------------------------------------ - subroutine SetCCrit(this, ccrit) + subroutine SetTotVgCThresh(this, totvegcthresh) class(soilbiogeochem_carbonstate_type) :: this - real(r8) , intent(in) :: ccrit + real(r8) , intent(in) :: totvegcthresh - this%ccrit = ccrit + if ( totvegcthresh <= 0.0_r8 )then + call endrun(msg=' ERROR totvegcthresh is zero or negative and should be > 0'//& + errMsg(sourcefile, __LINE__)) + end if + this%totvegcthresh = totvegcthresh - end subroutine SetCCrit + end subroutine SetTotVgCThresh !----------------------------------------------------------------------- diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index b776f77731..ca09e63624 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -52,7 +52,7 @@ module SoilBiogeochemNitrogenStateType ! the N balance check real(r8), pointer :: dyn_no3bal_adjustments_col (:) ! (gN/m2) NO3 adjustments to each column made in this timestep via dynamic column area adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) real(r8), pointer :: dyn_nh4bal_adjustments_col (:) ! (gN/m2) NH4 adjustments to each column made in this timestep via dynamic column adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) - real(r8) :: ncrit ! (gN/m2) critical value of nitrogen before truncation + real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools contains @@ -61,7 +61,7 @@ module SoilBiogeochemNitrogenStateType procedure , public :: SetValues procedure , public :: Summary procedure , public :: DynamicColumnAdjustments ! adjust state variables when column areas change - procedure , public :: SetNCrit + procedure , public :: SetTotVgCThresh ! Set value for totvegcthresh needed in Restart procedure , private :: InitAllocate procedure , private :: InitHistory procedure , private :: InitCold @@ -84,7 +84,7 @@ subroutine Init(this, bounds, & real(r8) , intent(in) :: decomp_cpools_col (bounds%begc:, 1:) real(r8) , intent(in) :: decomp_cpools_1m_col (bounds%begc:, 1:) - this%ncrit = nan + this%totvegcthresh = nan call this%InitAllocate (bounds ) call this%InitHistory (bounds) @@ -610,6 +610,10 @@ subroutine Restart ( this, bounds, ncid, flag, totvegc_col ) call endrun(msg=' Error in entering/exiting spinup - should occur only when nstep = 1'//& errMsg(sourcefile, __LINE__)) endif + if ( exit_spinup .and. isnan(this%totvegcthresh) )then + call endrun(msg=' Error in exit spinup - totvegcthresh was not set with SetTotVgCThresh'//& + errMsg(sourcefile, __LINE__)) + end if do k = 1, ndecomp_pools if ( exit_spinup ) then m = decomp_cascade_con%spinup_factor(k) @@ -631,10 +635,7 @@ subroutine Restart ( this, bounds, ncid, flag, totvegc_col ) ! pools with spinup factor > 1 ! will be affected, which means that total SOMN and LITN ! pools will not be set to 0. -!KO if (totvegc_col(c) <= this%ncrit .and. lun%itype(l) /= istcrop) then -!KO - if (totvegc_col(c) <= 0.1_r8 .and. lun%itype(l) /= istcrop) then -!KO + if (totvegc_col(c) <= this%totvegcthresh .and. lun%itype(l) /= istcrop) then this%decomp_npools_vr_col(c,j,k) = 0._r8 endif elseif ( abs(m - 1._r8) .gt. 0.000001_r8 .and. enter_spinup) then @@ -1006,13 +1007,17 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda end subroutine DynamicColumnAdjustments !------------------------------------------------------------------------ - subroutine SetNCrit(this, ncrit) + subroutine SetTotVgCThresh(this, totvegcthresh) class(soilbiogeochem_nitrogenstate_type) :: this - real(r8) , intent(in) :: ncrit + real(r8) , intent(in) :: totvegcthresh - this%ncrit = ncrit + if ( totvegcthresh <= 0.0_r8 )then + call endrun(msg=' Error totvegcthresh is zero or negative and should be > 0'//& + errMsg(sourcefile, __LINE__)) + end if + this%totvegcthresh = totvegcthresh - end subroutine SetNCrit + end subroutine SetTotVgCThresh end module SoilBiogeochemNitrogenStateType From ac4d0d4cfcde04003511f2ea8901e2158ccf5454 Mon Sep 17 00:00:00 2001 From: Peter Lawrence Date: Mon, 2 Apr 2018 15:57:40 -0600 Subject: [PATCH 0003/2067] Update these two files to address Fail status in CLM5 testing. CLM tests all pass now with the note that the new code changes the DWT_SLASH_CFLUX history variable from the column to the grid cell to be consistent with the other DWT fluxes. An additional variable DWT_SLASH_CFLUX_PATCH has been added to allow subgrid calculation at the patch and column levels as done with other DWT fluxes. This change results in a failure in the ERS_Ly3.f10_f10.I1850Clm50BgcCrop test that requires the user_nl_clm file to specify the hist_fincl3 to use DWT_SLASH_CFLUX_PATCH rather than DWT_SLASH_CFLUX. After this change the test passes. . The result from the test suite are: ================================================================================ These tests failed ================================================================================ ERP_D_Lm9.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_monthly EXPECTED ERS_Ly5_P72x1.f10_f10_musgs.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput EXPECTED NCK_Ld1.f10_f10_musgs.I2000Clm50Sp.cheyenne_intel.clm-default EXPECTED SMS_D_Ld5.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-Fates EXPECTED SMS_D_Lm13.f10_f10_musgs.IHistClm50BgcCrop.cheyenne_intel.clm-ciso_monthly EXPECTED SMS_D_Lm6.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-Fates EXPECTED SMS_D_Lm6_P144x1.f45_f45_mg37.I2000Clm50Fates.cheyenne_intel.clm-Fates EXPECTED SMS_Ld1.f09_g16.I1850Clm40SpCruGs.cheyenne_intel.clm-40default EXPECTED --- src/biogeochem/CNVegNitrogenFluxType.F90 | 2 +- src/biogeochem/dynGrossUnrepMod.F90 | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index 1bb3e223f9..64930e6c7c 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -488,7 +488,7 @@ subroutine InitAllocate(this, bounds) allocate(this%gru_livestemn_to_atm_patch (begp:endp)) ; this%gru_livestemn_to_atm_patch (:) = nan allocate(this%gru_livestemn_storage_to_atm_patch (begp:endp)) ; this%gru_livestemn_storage_to_atm_patch (:) = nan allocate(this%gru_livestemn_xfer_to_atm_patch (begp:endp)) ; this%gru_livestemn_xfer_to_atm_patch (:) = nan - allocate(this%gru_deadstemn_to_atm_patch (begp:endp)) ; this%gru_deadstemn_storage_to_atm_patch (:) = nan + allocate(this%gru_deadstemn_to_atm_patch (begp:endp)) ; this%gru_deadstemn_to_atm_patch (:) = nan allocate(this%gru_deadstemn_storage_to_atm_patch (begp:endp)) ; this%gru_deadstemn_storage_to_atm_patch (:) = nan allocate(this%gru_deadstemn_xfer_to_atm_patch (begp:endp)) ; this%gru_deadstemn_xfer_to_atm_patch (:) = nan allocate(this%gru_livecrootn_storage_to_atm_patch (begp:endp)) ; this%gru_livecrootn_storage_to_atm_patch (:) = nan diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90 index 15d5db95a6..0774a3a1a5 100644 --- a/src/biogeochem/dynGrossUnrepMod.F90 +++ b/src/biogeochem/dynGrossUnrepMod.F90 @@ -95,7 +95,8 @@ subroutine dynGrossUnrep_init(bounds, grossunrep_filename) gru_inst = dyn_var_time_uninterp_type( & dyn_file=dyngrossunrep_file, varname=grossunrep_varname, & dim1name=grlnd, conversion_factor=1.0_r8, & - do_check_sums_equal_1=.false., data_shape=[num_points,natpft_size]) + do_check_sums_equal_1=.false., data_shape=[num_points,natpft_size], & + allow_nodata=.true.) end subroutine dynGrossUnrep_init From ffc742eefaf10e516217117ebe90ecbcde4468af Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Apr 2018 12:27:45 -0600 Subject: [PATCH 0004/2067] Switch DWT_SLASH_CFLUX for DWT_SLASH_CFLUX_PATCH as required in this branch for shifting cultivation --- cime_config/usermods_dirs/cmip6_output/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/cmip6_output/user_nl_clm b/cime_config/usermods_dirs/cmip6_output/user_nl_clm index bd333a213b..88a9399a31 100644 --- a/cime_config/usermods_dirs/cmip6_output/user_nl_clm +++ b/cime_config/usermods_dirs/cmip6_output/user_nl_clm @@ -31,7 +31,7 @@ hist_fincl2 = 'GPP', 'NPP', 'AGNPP', 'TLAI', 'TOTVEGC', 'TSA','TREFMNAV','TREFMX hist_fincl3 = 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', 'EFLX_LH_TOT', 'RH2M', 'TLAI', 'GPP', 'NPP', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'U10', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'GRAINC_TO_FOOD', 'SLASH_HARVESTC', 'TSOI_10CM', 'COL_FIRE_CLOSS', -'DWT_SLASH_CFLUX','TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', +'DWT_SLASH_CFLUX_PATCH','TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I' hist_fincl4 = 'PCT_CFT', 'PCT_GLC_MEC', 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr', From ee439c181d74130aefb9d08b432d3db61cb370dd Mon Sep 17 00:00:00 2001 From: Peter Lawrence Date: Sat, 22 Sep 2018 08:36:58 -0600 Subject: [PATCH 0005/2067] New changes to set up the namelist variable do_grossunrep. By default do_grossunrep is set to .false. When set to .true. do_grossunrep turns on shifting cultivation which is read off the landuse_timeseries file. --- bld/CLMBuildNamelist.pm | 60 +++++++++++++++++++ .../namelist_definition_clm4_5.xml | 7 +++ src/dyn_subgrid/dynSubgridControlMod.F90 | 2 +- 3 files changed, 68 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 3595ec7461..58389e83e4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2473,6 +2473,7 @@ sub setup_logic_dynamic_subgrid { setup_logic_do_transient_pfts($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_logic_do_transient_crops($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_logic_do_harvest($opts, $nl_flags, $definition, $defaults, $nl, $physv); + setup_logic_do_grossunrep($opts, $nl_flags, $definition, $defaults, $nl, $physv); } @@ -2657,6 +2658,65 @@ sub setup_logic_do_harvest { #------------------------------------------------------------------------------- +sub setup_logic_do_grossunrep { + # + # Set do_grossunrep default value, and perform error checking on do_grossunrep + # + # Assumes the following are already set in the namelist (although it's okay + # for them to be unset if that will be their final state): + # - flanduse_timeseries + # - use_cn + # - use_fates + # + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + + my $var = 'do_grossunrep'; + + if ($physv->as_long() >= $physv->as_long("clm4_5")) { + # Start by assuming a default value of '.true.'. Then check a number of + # conditions under which do_grossunrep cannot be true. Under these + # conditions: (1) set default value to '.false.'; (2) make sure that the + # value is indeed false (e.g., that the user didn't try to set it to true). + + my $default_val = ".false."; + + # cannot_be_true will be set to a non-empty string in any case where + # do_grossunrep should not be true; if it turns out that do_grossunrep IS true + # in any of these cases, a fatal error will be generated + my $cannot_be_true = ""; + + if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { + $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; + } + elsif (!&value_is_true($nl->get_value('use_cn'))) { + $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; + } + elsif (&value_is_true($nl->get_value('use_fates'))) { + $cannot_be_true = "$var currently doesn't work with ED"; + } + + if ($cannot_be_true) { + $default_val = ".false."; + } + + if (!$cannot_be_true) { + # Note that, if the variable cannot be true, we don't call add_default + # - so that we don't clutter up the namelist with variables that don't + # matter for this case + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, val=>$default_val); + } + + # Make sure the value is false when it needs to be false - i.e., that the + # user hasn't tried to set a true value at an inappropriate time. + + if (&value_is_true($nl->get_value($var)) && $cannot_be_true) { + $log->fatal_error($cannot_be_true); + } + + } +} + +#------------------------------------------------------------------------------- sub setup_logic_spinup { my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml index 0a4bbd9a28..db030cd2a8 100644 --- a/bld/namelist_files/namelist_definition_clm4_5.xml +++ b/bld/namelist_files/namelist_definition_clm4_5.xml @@ -2225,6 +2225,13 @@ If TRUE, apply harvest from flanduse_timeseries file. (Also, only valid for use_cn = true.) + +If TRUE, apply grossunrep from flanduse_timeseries file. +(Only valid for transient runs, where there is a flanduse_timeseries file.) +(Also, only valid for use_cn = true.) + + If TRUE, allow area changes at times other than the year boundary. This should diff --git a/src/dyn_subgrid/dynSubgridControlMod.F90 b/src/dyn_subgrid/dynSubgridControlMod.F90 index 3491057dc0..ca057e9202 100644 --- a/src/dyn_subgrid/dynSubgridControlMod.F90 +++ b/src/dyn_subgrid/dynSubgridControlMod.F90 @@ -131,6 +131,7 @@ subroutine read_namelist( NLFilename ) do_transient_pfts, & do_transient_crops, & do_harvest, & + do_grossunrep, & for_testing_allow_non_annual_changes, & for_testing_zero_dynbal_fluxes @@ -157,7 +158,6 @@ subroutine read_namelist( NLFilename ) end if close(nu_nml) call relavu( nu_nml ) - do_grossunrep = do_harvest endif call shr_mpi_bcast (flanduse_timeseries, mpicom) From 9532135c3ddc51c5462f6cda4be4dab16b4f3205 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Aug 2019 15:54:13 -0600 Subject: [PATCH 0006/2067] Change notes about ED to FATES, and add a test for do_grossunrep=T with transient, but SP instead of CN --- bld/CLMBuildNamelist.pm | 12 ++++++------ bld/unit_testers/build-namelist_test.pl | 7 ++++++- 2 files changed, 12 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 74ca2c8910..f34aff7993 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -734,7 +734,7 @@ sub setup_cmdl_fates_mode { $var = "use_fates"; if ( &value_is_true($nl_flags->{$var}) ) { - # This section is a place-holder to test for modules that are not allowed with ED + # This section is a place-holder to test for modules that are not allowed with FATES # the defaults which are set in the logic section of the namelist builder will # automatically set these correctly (well that is the assumption), but here we # want to set a catch to fail and warn users if they explicitly set incompatible user namelist @@ -1138,7 +1138,7 @@ sub setup_cmdl_spinup { $log->fatal_error("$var has an invalid value ($val). Valid values are: @valid_values"); } if ( $nl_flags->{'bgc_spinup'} eq "on" && (not &value_is_true( $nl_flags->{'use_cn'} )) && (not &value_is_true($nl_flags->{'use_fates'})) ) { - $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor ED is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'})."); + $log->fatal_error("$var can not be '$nl_flags->{'bgc_spinup'}' if neither CN nor FATES is turned on (use_cn=$nl_flags->{'use_cn'}, use_fates=$nl_flags->{'use_fates'})."); } if ( $nl->get_value("spinup_state") eq 0 && $nl_flags->{'bgc_spinup'} eq "on" ) { $log->fatal_error("Namelist spinup_state contradicts the command line option bgc_spinup" ); @@ -2488,7 +2488,7 @@ sub setup_logic_do_transient_crops { # In principle, use_fates should be compatible with # do_transient_crops. However, this hasn't been tested, so to be safe, # we are not allowing this combination for now. - $cannot_be_true = "$var has not been tested with ED, so for now these two options cannot be combined"; + $cannot_be_true = "$var has not been tested with FATES, so for now these two options cannot be combined"; } if ($cannot_be_true) { @@ -2559,7 +2559,7 @@ sub setup_logic_do_harvest { } elsif (!&value_is_true($nl->get_value('use_cn'))) { $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; } elsif (&value_is_true($nl->get_value('use_fates'))) { - $cannot_be_true = "$var currently doesn't work with ED"; + $cannot_be_true = "$var currently doesn't work with FATES"; } if ($cannot_be_true) { @@ -2616,7 +2616,7 @@ sub setup_logic_do_grossunrep { $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; } elsif (&value_is_true($nl->get_value('use_fates'))) { - $cannot_be_true = "$var currently doesn't work with ED"; + $cannot_be_true = "$var currently doesn't work with FATES"; } if ($cannot_be_true) { @@ -3419,7 +3419,7 @@ sub setup_logic_megan { if ($nl_flags->{'megan'} ) { if ( &value_is_true( $nl_flags->{'use_fates'} ) ) { - $log->fatal_error("MEGAN can NOT be on when ED is also on.\n" . + $log->fatal_error("MEGAN can NOT be on when FATES is also on.\n" . " Use the '-no-megan' option when '-bgc fates' is activated"); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_specifier'); diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 39756d8055..79253617e9 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -138,7 +138,7 @@ sub make_config_cache { # # Figure out number of tests that will run # -my $ntests = 927; +my $ntests = 928; if ( defined($opts{'compare'}) ) { $ntests += 588; } @@ -849,6 +849,11 @@ sub make_config_cache { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "dogrossandsp" =>{ options=>"-envxml_dir . -bgc sp -use_case 20thC_transient", + namelst=>"do_grossunrep=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, "nocropwfert" =>{ options=>"-envxml_dir . -bgc sp -no-crop", namelst=>"use_fertilizer=T", GLC_TWO_WAY_COUPLING=>"FALSE", From 9704782c55eb657542abeb1411a66f5cb5234f7a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Aug 2019 16:24:10 -0600 Subject: [PATCH 0007/2067] Check that turning on do_grossunrep=T works for 20th century transient cases, so also turn on BGC and crop --- .../namelist_definition_ctsm.xml | 2 +- bld/unit_testers/build-namelist_test.pl | 2 +- .../usermods_dirs/cmip6_output/user_nl_clm | 77 ------------------- 3 files changed, 2 insertions(+), 79 deletions(-) delete mode 100644 cime_config/usermods_dirs/cmip6_output/user_nl_clm diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 9d94b10be8..cd3eb0d5c6 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2344,7 +2344,7 @@ If TRUE, apply harvest from flanduse_timeseries file. -If TRUE, apply grossunrep from flanduse_timeseries file. +If TRUE, apply gross unrepresented landuse/land-cover change from flanduse_timeseries file. (Only valid for transient runs, where there is a flanduse_timeseries file.) (Also, only valid for use_cn = true.) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 79253617e9..5535712803 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1224,7 +1224,7 @@ sub make_config_cache { my $usecase = "20thC_transient"; my $GLC_NEC = 10; foreach my $res ( @tran_res ) { - $options = "-res $res -use_case $usecase -envxml_dir . "; + $options = "-res $res -use_case $usecase -envxml_dir . -bgc bgc -crop -namelist '&a do_grossunrep=T/'"; &make_env_run(); eval{ system( "$bldnml $options > $tempfile 2>&1 " ); }; is( $@, '', "$options" ); diff --git a/cime_config/usermods_dirs/cmip6_output/user_nl_clm b/cime_config/usermods_dirs/cmip6_output/user_nl_clm deleted file mode 100644 index 0df7c685eb..0000000000 --- a/cime_config/usermods_dirs/cmip6_output/user_nl_clm +++ /dev/null @@ -1,77 +0,0 @@ -!---------------------------------------------------------------------------------- -! Users should add all user specific namelist changes below in the form of -! namelist_var = new_namelist_value -! -! EXCEPTIONS: -! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting -! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting -! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting -! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting -! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting -! Set irrigate by the CLM_BLDNML_OPTS -irrig setting -! Set co2_ppmv with CCSM_CO2_PPMV option -! Set dtime with L_NCPL option -! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options -! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases -! (includes $inst_string for multi-ensemble cases) -! Set maxpatch_glcmec with GLC_NEC option -! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable -!---------------------------------------------------------------------------------- - -! h0 stream (monthly average, gridcell-level) -! Emon, Lmon, LIMon -hist_fexcl1 = 'PCT_CFT', 'PCT_GLC_MEC', 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr', -'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', -'PCT_NAT_PFT','SMIN_NO3_vr','CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr' - -! h0 stream ICE variables and other variables inactive by default (monthly average, gridcell-level) -! Emon, Lmon, LIMon -hist_fincl1 = 'EFLX_LH_TOT_ICE', 'FIRE_ICE', 'FLDS_ICE', 'FSH_ICE', 'FSNO_ICE', 'FSR_ICE', -'QFLX_SUB_SNOW_ICE', 'QRUNOFF_ICE', 'QSNOFRZ_ICE', 'QSNOMELT_ICE', 'RAIN_ICE', 'SNOW_ICE', -'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE', -'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LITR1C_TO_SOIL1C','LITR1N_TO_SOIL1N','LITR2C_TO_SOIL1C', -'LITR2N_TO_SOIL1N','LITR3C_TO_SOIL2C','LITR3N_TO_SOIL2N','DWT_WOOD_PRODUCTC_GAIN_PATCH' - -! h1 stream (monthly average, finest sub-grid) -! Emon, Lmon -hist_fincl2 = 'GPP', 'NPP', 'AGNPP', 'TLAI', 'TOTVEGC', 'TSA','TREFMNAV','TREFMXAV', 'BTRANMN', 'NPP_NUPTAKE', 'GRAINC_TO_FOOD', -'Vcmx25Z', 'FSH', 'NFERTILIZATION', 'AR', 'VEGWP', 'FCTR', 'FCEV', 'FGEV', 'FIRE', 'FSR', 'HTOP', -'FIRA', 'FSA', 'HR', 'GSSUNLN', 'GSSHALN', 'TSKIN' - -! h2 stream (monthly average, landunit-level) -! Emon -! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level -hist_fincl3 = 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR', -'EFLX_LH_TOT', 'RH2M', 'TLAI', 'GPP', 'NPP', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', -'WOOD_HARVESTC', 'U10', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'GRAINC_TO_FOOD', 'SLASH_HARVESTC', 'TSOI_10CM', 'COL_FIRE_CLOSS', -'DWT_SLASH_CFLUX_PATCH', 'QIRRIG', 'URBAN_HEAT', 'WASTEHEAT', 'HTOP', 'TSKIN', 'FROOTC:I' - -! h3 stream (yearly average, gridcell-level) -! Eyr -hist_fincl4 = 'PCT_CFT', 'PCT_GLC_MEC', 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr', -'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'QICE_FORC', 'TSRF_FORC', 'TOPO_FORC' -'PCT_NAT_PFT','PCT_LANDUNIT','TOTLITC:I','TOT_WOODPRODC:I','CROPPROD1C:I','TOTSOMC:I','TOTVEGC:I','FSNO_ICE' - -! h4 stream (yearly average, landunit-level) -! Eyr landuse tiles -hist_fincl5 = 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I' - -! h5 stream (daily average, gridcell-level) -! day, Eday -hist_fincl6 = 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'GPP', 'NPP', 'AR', 'HR', 'EFLX_LH_TOT', 'FSH', 'FGR12', 'FSM', 'QSNOEVAP', 'TLAI', 'QDRAI', 'QDRAI_PERCH', 'QOVER', 'QFLX_SUB_SNOW', 'FSA', 'FIRA', 'H2OSNO', 'SNOCAN', 'QSNOFRZ', 'QFLX_SNOW_DRAIN', 'SNOWDP', 'H2OSFC', 'TV', 'TG', 'TAUX', 'TAUY', 'QVEGT', 'TWS', 'H2OCAN', 'ALT', 'QVEGE', 'QSOIL', 'TSKIN', 'FSDS','FSNO','SNOFSRVD','SNOFSRVI','SNOFSRND','SNOFSRNI','FSDSVD','FSDSVI','FSDSND','FSDSNI','SNOWLIQ','SOILICE','SOILLIQ','QINTR','SNOBCMSL','TSOI','SNOTXMASS','SNOWICE','SNOWLIQ','QRUNOFF','RAIN','SNOW' - -! h6 stream (daily average, landunit-level) -! Eday -hist_fincl7 = 'TREFMXAV','TREFMNAV' - -! h7 stream (3-hourly average, gridcell-level) -! 3hr, E3hr, CF3hr -! 3hr requires QRUNOFF for time mean, and SOILWATER_10CM, TSKIN for time point (I) -! E3hr requires GPP, AR, HR for time mean -! CF3hr requires QFLX_SUB_SNOW for time point (I) -hist_fincl8 = 'GPP','AR','HR','TSA','RH2M','SOILWATER_10CM:I','FSH','EFLX_LH_TOT','FSDS','QRUNOFF','QFLX_SUB_SNOW:I','TSKIN:I' - -hist_mfilt = 1,1,1,1,1,365,365,2920 -hist_dov2xy = .true.,.false.,.false.,.true.,.false.,.true.,.false.,.true. -hist_nhtfrq = 0,0,0,-8760,-8760,-24,-24,-3 -hist_type1d_pertape = ' ',' ','LAND',' ','LAND',' ','LAND',' ' From 9f73f6e9f0c6d6d8753c5b8f94c19764643b2d20 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Aug 2019 22:41:50 -0600 Subject: [PATCH 0008/2067] Change maxpatch_pft to maxsoil_patches as it was changed, so now works compilers and runs --- src/biogeochem/CNCIsoFluxMod.F90 | 4 ++-- src/biogeochem/dynGrossUnrepMod.F90 | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index 7c9697bbaf..f07e6b7a62 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -1767,7 +1767,7 @@ subroutine CNCIsoGrossUnrepPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxpatch_pft + do pi = 1,maxsoil_patches do fc = 1,num_soilc c = filter_soilc(fc) @@ -1806,7 +1806,7 @@ subroutine CNCIsoGrossUnrepPftToColumn (num_soilc, filter_soilc, & end do end do - do pi = 1,maxpatch_pft + do pi = 1,maxsoil_patches do fc = 1,num_soilc c = filter_soilc(fc) diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/biogeochem/dynGrossUnrepMod.F90 index 0774a3a1a5..1ad01c9348 100644 --- a/src/biogeochem/dynGrossUnrepMod.F90 +++ b/src/biogeochem/dynGrossUnrepMod.F90 @@ -375,7 +375,7 @@ subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & ! to the column level and assign them to the three litter pools ! ! !USES: - use clm_varpar , only : maxpatch_pft, nlevdecomp, numpft + use clm_varpar , only : maxsoil_patches, nlevdecomp ! ! !ARGUMENTS: integer , intent(in) :: num_soilc ! number of soil columns in filter @@ -435,7 +435,7 @@ subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxpatch_pft + do pi = 1,maxsoil_patches do fc = 1,num_soilc c = filter_soilc(fc) @@ -500,7 +500,7 @@ subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & end do end do - do pi = 1,maxpatch_pft + do pi = 1,maxsoil_patches do fc = 1,num_soilc c = filter_soilc(fc) From a7c384e38c83c3e7ad8bc2bb5dde799b7ddcfc2b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Aug 2019 22:43:07 -0600 Subject: [PATCH 0009/2067] Change a test to do a test with transient Gross Unrepresented LULCC --- cime_config/testdefs/testlist_clm.xml | 4 ++-- .../clm/ciso_decStart_GU_LULCC/include_user_mods | 1 + .../testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm | 1 + 3 files changed, 4 insertions(+), 2 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 8409089613..8906c6c4bd 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -314,14 +314,14 @@ - + - + diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods new file mode 100644 index 0000000000..c0adfb5904 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods @@ -0,0 +1 @@ +../ciso_decStart diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm new file mode 100644 index 0000000000..8d3ca17778 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm @@ -0,0 +1 @@ +do_grossunrep = .true. From b91c593028ca1e28b0b7ba4c7168e649e0ca10a0 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 14 Aug 2019 15:51:28 -0600 Subject: [PATCH 0010/2067] Remove a git conflict leftover, and close the toosmall_* entries, so it will pass xmllint --- bld/namelist_files/namelist_definition_ctsm.xml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index cd3eb0d5c6..f7d24e077a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1111,37 +1111,37 @@ If true, this directs the model to collapse the urban landunits to the dominant Percentage threshold above which the model keeps the soil landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the crop landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the glacier landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the lake landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the wetland landunit. Selecting the value 0 means DO NOTHING. Default: 0 Percentage threshold above which the model keeps the urban landunits. Selecting the value 0 means DO NOTHING. If collapse_urban = .false., the same threshold will apply to all three urban landunits if they are present. If collapse_urban = .true., this threshold will apply to the single collapsed urban landunit if presnet. Default: 0 @@ -2395,7 +2395,6 @@ continue run; it is an error for this to be set in a branch run. Furthermore, this setting has no effect in a cold start run. ->>>>>>> ctsm1.0.dev055:bld/namelist_files/namelist_definition_ctsm.xml If TRUE, allow area changes at times other than the year boundary. This should From cc7d56567044959b937d8ce4a2986279aeeb044d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 15 Aug 2019 14:35:56 -0600 Subject: [PATCH 0011/2067] Move SLASH_HARVESTC to gridcell level list --- cime_config/usermods_dirs/output_bgc/user_nl_clm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/output_bgc/user_nl_clm index de136ad4b4..607c2ee25c 100644 --- a/cime_config/usermods_dirs/output_bgc/user_nl_clm +++ b/cime_config/usermods_dirs/output_bgc/user_nl_clm @@ -11,10 +11,10 @@ hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTO ! h2 stream (monthly average, landunit-level) ! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level -hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP' +hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP' ! h3 stream (yearly average, gridcell-level) -hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I' +hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I', 'SLASH_HARVESTC' ! h4 stream (yearly average, landunit-level) hist_fincl5 += 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I' From 570e192f51338c417ee5cba07d56ec4c47ac3394 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 15 Aug 2019 14:53:34 -0600 Subject: [PATCH 0012/2067] Revert "Move SLASH_HARVESTC to gridcell level list" This reverts commit cc7d56567044959b937d8ce4a2986279aeeb044d. --- cime_config/usermods_dirs/output_bgc/user_nl_clm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/output_bgc/user_nl_clm index 607c2ee25c..de136ad4b4 100644 --- a/cime_config/usermods_dirs/output_bgc/user_nl_clm +++ b/cime_config/usermods_dirs/output_bgc/user_nl_clm @@ -11,10 +11,10 @@ hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTO ! h2 stream (monthly average, landunit-level) ! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level -hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP' +hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP' ! h3 stream (yearly average, gridcell-level) -hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I', 'SLASH_HARVESTC' +hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I' ! h4 stream (yearly average, landunit-level) hist_fincl5 += 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I' From 5523c2d47338fec99ae7bbb210138186016734d2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 15 Aug 2019 15:00:14 -0600 Subject: [PATCH 0013/2067] Remove DWT_SLASH_CFLUX from landunit average, and have it just output monthly on gridcell which it is by default --- cime_config/usermods_dirs/output_bgc/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/output_bgc/user_nl_clm index de136ad4b4..0c0bcd52ff 100644 --- a/cime_config/usermods_dirs/output_bgc/user_nl_clm +++ b/cime_config/usermods_dirs/output_bgc/user_nl_clm @@ -11,7 +11,7 @@ hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTO ! h2 stream (monthly average, landunit-level) ! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level -hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'DWT_SLASH_CFLUX', 'FROOTC:I', 'HTOP' +hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'FROOTC:I', 'HTOP' ! h3 stream (yearly average, gridcell-level) hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I' From df7eb92131a074bd1b0a9a73faa243b14a3ee375 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 17 Aug 2019 02:23:14 -0600 Subject: [PATCH 0014/2067] Only output the GRU fields if do_grossunrep is actually turned on --- src/biogeochem/CNVegCarbonFluxType.F90 | 44 +++++++++++++----------- src/biogeochem/CNVegNitrogenFluxType.F90 | 19 +++++----- 2 files changed, 34 insertions(+), 29 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index b9b7c69e4a..396a8088cc 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -22,7 +22,7 @@ module CNVegCarbonFluxType use ColumnType , only : col use PatchType , only : patch use AnnualFluxDribbler , only : annual_flux_dribbler_type, annual_flux_dribbler_gridcell - use dynSubgridControlMod , only : get_for_testing_allow_non_annual_changes + use dynSubgridControlMod , only : get_for_testing_allow_non_annual_changes, get_do_grossunrep use abortutils , only : endrun ! ! !PUBLIC TYPES: @@ -2993,26 +2993,28 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', long_name='dead coarse root to CWD due to landcover change', & ptr_col=this%dwt_deadcrootc_to_cwdc_col, default='inactive') - this%gru_conv_cflux_patch(begp:endp) = spval - call hist_addfld1d (fname='GRU_CONV_CFLUX', units='gC/m^2/s', & - avgflag='A', long_name='gross unrepresented conversion C flux (immediate loss to atm) (0 at all times except first timestep of year)', & - ptr_patch=this%gru_conv_cflux_patch) - - this%gru_conv_cflux_dribbled_grc(begg:endg) = spval - call hist_addfld1d (fname='GRU_CONV_CFLUX_DRIBBLED', units='gC/m^2/s', & - avgflag='A', & - long_name='gross unrepresented conversion C flux (immediate loss to atm), dribbled throughout the year', & - ptr_gcell=this%gru_conv_cflux_dribbled_grc) - - this%gru_wood_productc_gain_patch(begp:endp) = spval - call hist_addfld1d (fname='GRU_WOODPRODC_GAIN', units='gC/m^2/s', & - avgflag='A', long_name='gross unrepresented landcover change driven addition to wood product carbon pools (0 at all times except first timestep of year)', & - ptr_patch=this%gru_wood_productc_gain_patch) - - this%gru_slash_cflux_patch(begp:endp) = spval - call hist_addfld1d (fname='GRU_SLASH_CFLUX', units='gC/m^2/s', & - avgflag='A', long_name='slash gross unrepresented landcover change carbon (to litter)', & - ptr_patch=this%gru_slash_cflux_patch) + if ( get_do_grossunrep() )then + this%gru_conv_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_CONV_CFLUX', units='gC/m^2/s', & + avgflag='A', long_name='gross unrepresented conversion C flux (immediate loss to atm) (0 at all times except first timestep of year)', & + ptr_patch=this%gru_conv_cflux_patch) + + this%gru_conv_cflux_dribbled_grc(begg:endg) = spval + call hist_addfld1d (fname='GRU_CONV_CFLUX_DRIBBLED', units='gC/m^2/s', & + avgflag='A', & + long_name='gross unrepresented conversion C flux (immediate loss to atm), dribbled throughout the year', & + ptr_gcell=this%gru_conv_cflux_dribbled_grc) + + this%gru_wood_productc_gain_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_WOODPRODC_GAIN', units='gC/m^2/s', & + avgflag='A', long_name='gross unrepresented landcover change driven addition to wood product carbon pools (0 at all times except first timestep of year)', & + ptr_patch=this%gru_wood_productc_gain_patch) + + this%gru_slash_cflux_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_SLASH_CFLUX', units='gC/m^2/s', & + avgflag='A', long_name='slash gross unrepresented landcover change carbon (to litter)', & + ptr_patch=this%gru_slash_cflux_patch) + end if this%crop_seedc_to_leaf_patch(begp:endp) = spval call hist_addfld1d (fname='CROP_SEEDC_TO_LEAF', units='gC/m^2/s', & diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index d9e121ed78..d3bf84e1eb 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -11,6 +11,7 @@ module CNVegNitrogenFluxType use decompMod , only : bounds_type use abortutils , only : endrun use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con + use dynSubgridControlMod , only : get_do_grossunrep use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch @@ -1120,15 +1121,17 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='dead coarse root to CWD due to landcover change', & ptr_col=this%dwt_deadcrootn_to_cwdn_col, default='inactive') - this%gru_conv_nflux_patch(begp:endp) = spval - call hist_addfld1d (fname='GRU_CONV_NFLUX', units='gN/m^2/s', & - avgflag='A', long_name='gross unrepresented conversion N flux (immediate loss to atm) (0 at all times except first timestep of year)', & - ptr_patch=this%gru_conv_nflux_patch) + if ( get_do_grossunrep() )then + this%gru_conv_nflux_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_CONV_NFLUX', units='gN/m^2/s', & + avgflag='A', long_name='gross unrepresented conversion N flux (immediate loss to atm) (0 at all times except first timestep of year)', & + ptr_patch=this%gru_conv_nflux_patch) - this%gru_wood_productn_gain_patch(begp:endp) = spval - call hist_addfld1d (fname='GRU_WOODPRODN_GAIN', units='gN/m^2/s', & - avgflag='A', long_name='gross unrepresented landcover change driven addition to wood product nitrogen pools (0 at all times except first timestep of year)', & - ptr_patch=this%gru_wood_productn_gain_patch) + this%gru_wood_productn_gain_patch(begp:endp) = spval + call hist_addfld1d (fname='GRU_WOODPRODN_GAIN', units='gN/m^2/s', & + avgflag='A', long_name='gross unrepresented landcover change driven addition to wood product nitrogen pools (0 at all times except first timestep of year)', & + ptr_patch=this%gru_wood_productn_gain_patch) + end if this%crop_seedn_to_leaf_patch(begp:endp) = spval call hist_addfld1d (fname='CROP_SEEDN_TO_LEAF', units='gN/m^2/s', & From 7e5d438fbc419e92771c6de803c7dbd2f9d658f1 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Thu, 25 Mar 2021 08:37:07 +0100 Subject: [PATCH 0015/2067] Adapted model to machine and added soil column separation and local time output (the latter is still in development). This version of the code is running stable. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + .../namelist_definition_ctsm.xml | 7 +- src/biogeophys/CanopyFluxesMod.F90 | 25 +- src/biogeophys/CanopyStateType.F90 | 3 +- src/biogeophys/FrictionVelocityMod.F90 | 6 - src/main/clm_varctl.F90 | 6 + src/main/controlMod.F90 | 4 + src/main/histFileMod.F90 | 221 +++++++++++++++++- src/main/initGridCellsMod.F90 | 77 +++++- src/main/lnd2glcMod.F90 | 2 +- src/main/subgridMod.F90 | 18 +- 11 files changed, 337 insertions(+), 33 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3ccbe89a0e..9d4fbeb905 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -181,6 +181,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .true. .false. +.false. 1 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 9543fbcf6f..480f433875 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -144,6 +144,11 @@ User-defined number of soil layers required to be set in the namelist when the u Default: iundef + +If TRUE, each pft exists on a separate soil column. + + If TRUE, use variable soil depth. @@ -764,7 +769,7 @@ If TRUE, write master field list to separate file for documentation purposes + group="clm_inparm" valid_values="A,I,X,M,L" > Per file averaging flag. 'A' (average over history period) 'I' (instantaneous) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index f18bde2e0e..e625e9d511 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -450,6 +450,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, slatop => pftcon%slatop , & ! SLA at top of canopy [m^2/gC] fbw => pftcon%fbw , & ! Input: fraction of biomass that is water nstem => pftcon%nstem , & ! Input: stem number density (#ind/m2) + woody => pftcon%woody , & ! Input: woody flag rstem_per_dbh => pftcon%rstem_per_dbh , & ! Input: stem resistance per stem diameter (s/m**2) wood_density => pftcon%wood_density , & ! Input: dry wood density (kg/m3) @@ -860,13 +861,25 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, do f = 1, fn p = filterp(f) c = patch%column(p) + if(.true.) then ! woody(patch%itype(p))==0) then ! Keep old parametrization for grasses/crops + lt = min(elai(p)+esai(p), tlsai_crit) + egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) + displa(p) = egvf * displa(p) + z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) + else + if(elai(p)==0) then + displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & + / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) + else + displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & + / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p))) * (1.0_r8 - exp(-0.273_r8 * elai(p))) & + / (0.273_r8 * elai(p))) + end if + z0mv(p) = htop(p) * 0.264_r8 * (1._r8 - displa(p) / htop(p)) + end if + z0hv(p) = z0mv(p) + z0qv(p) = z0mv(p) - lt = min(elai(p)+esai(p), tlsai_crit) - egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) - displa(p) = egvf * displa(p) - z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) - z0hv(p) = z0mv(p) - z0qv(p) = z0mv(p) end do found = .false. diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90 index abb32c9acc..89e2c05645 100644 --- a/src/biogeophys/CanopyStateType.F90 +++ b/src/biogeophys/CanopyStateType.F90 @@ -200,7 +200,6 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='Aboveground leaf biomass', & ptr_patch=this%leaf_biomass_patch, default='inactive') - if (use_cn .or. use_fates) then this%fsun_patch(begp:endp) = spval call hist_addfld1d (fname='FSUN', units='proportion', & avgflag='A', long_name='sunlit fraction of canopy', & @@ -220,7 +219,7 @@ subroutine InitHistory(this, bounds) call hist_addfld1d (fname='DISPLA', units='m', & avgflag='A', long_name='displacement height', & ptr_patch=this%displa_patch, default='inactive') - end if + this%z0m_patch(begp:endp) = spval call hist_addfld1d (fname='Z0M', units='m', & diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 9efd167879..9bef16cec7 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -294,26 +294,20 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='leaf boundary resistance', & ptr_patch=this%rb1_patch, default='inactive') - if (use_cn) then this%z0hv_patch(begp:endp) = spval call hist_addfld1d (fname='Z0HV', units='m', & avgflag='A', long_name='roughness length over vegetation, sensible heat', & ptr_patch=this%z0hv_patch, default='inactive') - end if - if (use_cn) then this%z0mv_patch(begp:endp) = spval call hist_addfld1d (fname='Z0MV', units='m', & avgflag='A', long_name='roughness length over vegetation, momentum', & ptr_patch=this%z0mv_patch, default='inactive') - end if - if (use_cn) then this%z0qv_patch(begp:endp) = spval call hist_addfld1d (fname='Z0QV', units='m', & avgflag='A', long_name='roughness length over vegetation, latent heat', & ptr_patch=this%z0qv_patch, default='inactive') - end if if (use_luna) then call hist_addfld1d (fname='RB10', units='s/m', & diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 0f50a53b96..f8100ac304 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -284,6 +284,12 @@ module clm_varctl logical, public :: use_biomass_heat_storage = .false. ! true => include biomass heat storage in canopy energy budget + !---------------------------------------------------------- + ! each pft has individual soil column switch + !---------------------------------------------------------- + + logical, public :: use_individual_pft_soil_column = .false. ! true => each pft exists on its own soil column + !---------------------------------------------------------- ! bedrock / soil depth switch !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index ec22fff5c7..17e79f2dc8 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -245,6 +245,8 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_biomass_heat_storage + namelist /clm_inparm/ use_individual_pft_soil_column + namelist /clm_inparm/ use_hydrstress namelist /clm_inparm/ use_dynroot @@ -744,6 +746,8 @@ subroutine control_spmd() call mpi_bcast (use_biomass_heat_storage, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_individual_pft_soil_column, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 5c43e1540d..24ff6acceb 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -44,7 +44,7 @@ module histFileMod integer , public, parameter :: max_flds = 2500 ! max number of history fields integer , public, parameter :: max_namlen = 64 ! maximum number of characters for field name integer , public, parameter :: scale_type_strlen = 32 ! maximum number of characters for scale types - integer , private, parameter :: avgflag_strlen = 3 ! maximum number of characters for avgflag + integer , private, parameter :: avgflag_strlen = 1 ! maximum number of characters for avgflag integer , private, parameter :: hist_dim_name_length = 16 ! lenngth of character strings in dimension names ! Possible ways to treat multi-layer snow fields at times when no snow is present in a @@ -1286,6 +1286,8 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) ! !USES: use subgridAveMod , only : p2g, c2g, l2g, p2l, c2l, p2c use decompMod , only : BOUNDS_LEVEL_PROC + use clm_varcon , only : degpsec, isecspday + use clm_time_manager, only : get_step_size, get_curr_date ! ! !ARGUMENTS: integer, intent(in) :: t ! tape index @@ -1314,6 +1316,16 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) integer j character(len=*),parameter :: subname = 'hist_update_hbuf_field_1d' integer k_offset ! offset for mapping sliced subarray pointers when outputting variables in PFT/col vector form + integer :: year ! year (0, ...) for nstep + integer :: month ! month (1, ..., 12) for nstep + integer :: day ! day of month (1, ..., 31) for nstep + integer :: secs ! seconds into current date for nstep + integer :: local_secpl ! seconds into current date in local time + integer :: dtime ! timestep size [seconds] + integer :: tod ! Desired local solar time of output in seconds + integer, allocatable :: grid_index(:) ! Grid cell index for longitude + integer, allocatable :: tods(:) + !----------------------------------------------------------------------- SHR_ASSERT_FL(bounds%level == BOUNDS_LEVEL_PROC, sourcefile, __LINE__) @@ -1332,9 +1344,13 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) l2g_scale_type = tape(t)%hlist(f)%field%l2g_scale_type hpindex = tape(t)%hlist(f)%field%hpindex field => clmptr_rs(hpindex)%ptr + tods = (/0, 0, 0, 10800, 43200, 54000, 0, 10800, 54000 /) ! set variables to check weights when allocate all pfts + dtime = get_step_size() + call get_curr_date (year, month, day, secs) + map2gcell = .false. if (type1d_out == nameg .or. type1d_out == grlnd) then SHR_ASSERT_FL(beg1d_out == bounds%begg, sourcefile, __LINE__) @@ -1458,25 +1474,60 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) endif nacs(k,1) = 1 end do + case ('L') ! Local solar time + tod = tods(t) + do k = beg1d_out, end1d_out + if (field_gcell(k) /= spval) then + + local_secpl = secs + grc%londeg(k)/degpsec + local_secpl = mod(local_secpl,isecspday) + + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime+tod-local_secpl) + nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,1) == 0) hbuf(k,1) = spval + end if + end do case default - write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag - call endrun(msg=errMsg(sourcefile, __LINE__)) + write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag + call endrun(msg=errMsg(sourcefile, __LINE__)) + end select deallocate( field_gcell ) else ! Do not map to gridcell - + allocate( grid_index(beg1d:end1d) ) ! For data defined on the pft, col or landunit, we need to check if a point is active ! to determine whether that point should be assigned spval if (type1d == namep) then check_active = .true. active => patch%active + grid_index = patch%gridcell else if (type1d == namec) then check_active = .true. active => col%active + grid_index = col%gridcell else if (type1d == namel) then check_active = .true. active =>lun%active + grid_index = lun%gridcell else check_active = .false. end if @@ -1559,9 +1610,59 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do + case ('L') ! Local solar time + tod = tods(t) + + if ( end1d .eq. ubound(field,1) ) then + k_offset = 0 + else + k_offset = 1 - beg1d + endif + do k = beg1d, end1d + valid = .true. + if (check_active) then + if (.not. active(k)) then + valid = .false. + else + local_secpl = secs + grc%londeg(grid_index(k))/degpsec + end if + else + local_secpl = secs + grc%londeg(k)/degpsec + + end if + local_secpl = mod(local_secpl,isecspday) + + if (valid) then + if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k+k_offset) /= spval) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k+k_offset) /= spval) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime+tod-local_secpl) + nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k+k_offset) /= spval) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,1) == 0) hbuf(k,1) = spval + end if + end do + case default - write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag - call endrun(msg=errMsg(sourcefile, __LINE__)) + + write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag + call endrun(msg=errMsg(sourcefile, __LINE__)) + + end select end if @@ -1581,6 +1682,8 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) use subgridAveMod , only : p2g, c2g, l2g, p2l, c2l, p2c use decompMod , only : BOUNDS_LEVEL_PROC use clm_varctl , only : iulog + use clm_varcon , only : degpsec, isecspday + use clm_time_manager, only : get_step_size, get_curr_date ! ! !ARGUMENTS: integer, intent(in) :: t ! tape index @@ -1612,6 +1715,15 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) !(this refers to a point being active, NOT a history field being active) real(r8), allocatable :: field_gcell(:,:) ! gridcell level field (used if mapping to gridcell is done) character(len=*),parameter :: subname = 'hist_update_hbuf_field_2d' + integer :: year ! year (0, ...) for nstep + integer :: month ! month (1, ..., 12) for nstep + integer :: day ! day of month (1, ..., 31) for nstep + integer :: secs ! seconds into current date for nstep + integer :: local_secpl ! seconds into current date in local time + integer :: dtime ! timestep size [seconds] + integer :: tod ! Desired local solar time of output in seconds + integer, allocatable :: grid_index(:) ! Grid cell index for longitude + integer, allocatable :: tods(:) !----------------------------------------------------------------------- SHR_ASSERT_FL(bounds%level == BOUNDS_LEVEL_PROC, sourcefile, __LINE__) @@ -1630,6 +1742,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) l2g_scale_type = tape(t)%hlist(f)%field%l2g_scale_type no_snow_behavior = tape(t)%hlist(f)%field%no_snow_behavior hpindex = tape(t)%hlist(f)%field%hpindex + tods = (/0, 0, 0, 10800, 43200, 54000, 0, 10800, 54000 /) if (no_snow_behavior /= no_snow_unset) then @@ -1656,6 +1769,9 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) field_allocated = .false. end if + dtime = get_step_size() + call get_curr_date (year, month, day, secs) + ! set variables to check weights when allocate all pfts map2gcell = .false. @@ -1787,6 +1903,41 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do + case ('L') ! Local solar time + tod = tods(t) + do j = 1,num2d + do k = beg1d_out, end1d_out + if (field_gcell(k,j) /= spval) then + + local_secpl = secs + grc%londeg(k)/degpsec + local_secpl = mod(local_secpl,isecspday) + + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime+tod-local_secpl) + nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,j) == 0) hbuf(k,j) = spval + + end if + end do + end do + case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -1800,12 +1951,18 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) if (type1d == namep) then check_active = .true. active => patch%active + allocate(grid_index(bounds%begg:bounds%endg) ) + grid_index = patch%gridcell else if (type1d == namec) then check_active = .true. active => col%active + allocate(grid_index(bounds%begg:bounds%endg) ) + grid_index = col%gridcell else if (type1d == namel) then check_active = .true. active =>lun%active + allocate(grid_index(bounds%begg:bounds%endg) ) + grid_index = lun%gridcell else check_active = .false. end if @@ -1894,6 +2051,48 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do + case ('L') ! Local solar time + tod = tods(t) + do j = 1,num2d + + do k = beg1d, end1d + valid = .true. + if (check_active) then + if (.not. active(k)) then + valid = .false. + else + local_secpl = secs + grc%londeg(grid_index(k))/degpsec + end if + else + local_secpl = secs + grc%londeg(k)/degpsec + end if + local_secpl = mod(local_secpl,isecspday) + + if (valid) then + if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k-beg1d+1,j) /= spval) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k-beg1d+1,j) /= spval) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime+tod-local_secpl) + nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k-beg1d+1,j) /= spval) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,j) == 0) hbuf(k,j) = spval + end if + end do + end do case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2038,7 +2237,7 @@ subroutine hfields_normalize (t) nacs => tape(t)%hlist(f)%nacs hbuf => tape(t)%hlist(f)%hbuf - if (avgflag == 'A') then + if (avgflag == 'A' .or. avgflag == 'L') then aflag = .true. else aflag = .false. @@ -2048,6 +2247,8 @@ subroutine hfields_normalize (t) do k = beg1d, end1d if (aflag .and. nacs(k,j) /= 0) then hbuf(k,j) = hbuf(k,j) / float(nacs(k,j)) + elseif(avgflag == 'L' .and. nacs(k,j) == 0) then + hbuf(k,j) = spval end if end do end do @@ -3129,6 +3330,8 @@ subroutine hfields_write(t, mode) real(r8), pointer :: histo(:,:) ! temporary real(r8), pointer :: hist1do(:) ! temporary character(len=*),parameter :: subname = 'hfields_write' + integer :: tod ! Desired local solar time of output in seconds + !----------------------------------------------------------------------- ! Write/define 1d topological info @@ -3176,6 +3379,8 @@ subroutine hfields_write(t, mode) avgstr = 'minimum' case ('SUM') avgstr = 'sum' + case ('L') + avgstr = 'inst. local time' case default write(iulog,*) trim(subname),' ERROR: unknown time averaging flag (avgflag)=',avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -5548,7 +5753,7 @@ function avgflag_valid(avgflag, blank_valid) result(valid) valid = .true. else if (avgflag == 'A' .or. avgflag == 'I' .or. & avgflag == 'X' .or. avgflag == 'M' .or. & - avgflag == 'SUM') then + avgflag == 'SUM' .or. avgflag == 'L') then valid = .true. else valid = .false. diff --git a/src/main/initGridCellsMod.F90 b/src/main/initGridCellsMod.F90 index 0d9b20ef7b..1456e10a36 100644 --- a/src/main/initGridCellsMod.F90 +++ b/src/main/initGridCellsMod.F90 @@ -60,7 +60,7 @@ subroutine initGridcells(glc_behavior) use subgridWeightsMod , only : compute_higher_order_weights use landunit_varcon , only : istsoil, istwet, istdlak, istice_mec use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md, istcrop - use clm_varctl , only : use_fates + use clm_varctl , only : use_fates,use_individual_pft_soil_column use shr_const_mod , only : SHR_CONST_PI ! ! !ARGUMENTS: @@ -133,8 +133,13 @@ subroutine initGridcells(glc_behavior) ! Determine naturally vegetated landunit do gdc = bounds_clump%begg,bounds_clump%endg - call set_landunit_veg_compete( & - ltype=istsoil, gi=gdc, li=li, ci=ci, pi=pi) + if(use_individual_pft_soil_column) then + call set_landunit_veg_noncompete( & + ltype=istsoil, gi=gdc, li=li, ci=ci, pi=pi) + else + call set_landunit_veg_compete( & + ltype=istsoil, gi=gdc, li=li, ci=ci, pi=pi) + end if end do ! Determine crop landunit @@ -244,7 +249,7 @@ subroutine set_landunit_veg_compete (ltype, gi, li, ci, pi) ! Set decomposition properties call subgrid_get_info_natveg(gi, & - npatches=npatches, ncols=ncols, nlunits=nlunits) + npatches=npatches, ncols=ncols, nlunits=nlunits, sesc=.FALSE.) wtlunit2gcell = wt_lunit(gi, ltype) nlunits_added = 0 @@ -272,6 +277,70 @@ subroutine set_landunit_veg_compete (ltype, gi, li, ci, pi) SHR_ASSERT_FL(npatches_added == npatches, sourcefile, __LINE__) end subroutine set_landunit_veg_compete + + + subroutine set_landunit_veg_noncompete (ltype, gi, li, ci, pi) + + + ! !DESCRIPTION: + ! Initialize vegetated landunit without competition + ! + ! !USES + use clm_instur, only : wt_lunit, wt_nat_patch + use subgridMod, only : subgrid_get_info_natveg, natveg_patch_exists + use clm_varpar, only : natpft_lb, natpft_ub + ! + ! !ARGUMENTS: + integer , intent(in) :: ltype ! landunit type + integer , intent(in) :: gi ! gridcell index + integer , intent(inout) :: li ! landunit index + integer , intent(inout) :: ci ! column index + integer , intent(inout) :: pi ! patch index + ! + ! !LOCAL VARIABLES: + integer :: m ! index + integer :: npatches ! number of patches in landunit + integer :: ncols + integer :: nlunits + integer :: npatches_added ! number of patches actually added + integer :: ncols_added ! number of columns actually added + integer :: nlunits_added ! number of landunits actually added + real(r8) :: wtlunit2gcell ! landunit weight in gridcell + !------------------------------------------------------------------------ + + ! Set decomposition properties + + call subgrid_get_info_natveg(gi, & + npatches=npatches, ncols=ncols, nlunits=nlunits, sesc=.TRUE.) + wtlunit2gcell = wt_lunit(gi, ltype) + + nlunits_added = 0 + ncols_added = 0 + npatches_added = 0 + + if (nlunits > 0) then + call add_landunit(li=li, gi=gi, ltype=ltype, wtgcell=wtlunit2gcell) + nlunits_added = nlunits_added + 1 + + + do m = natpft_lb,natpft_ub + if (natveg_patch_exists(gi, m)) then + ! Assume one column for each vegetation patch + call add_column(ci=ci, li=li, ctype=1, wtlunit=wt_nat_patch(gi,m)) + ncols_added = ncols_added + 1 + + call add_patch(pi=pi, ci=ci, ptype=m, wtcol=1.0_r8) + npatches_added = npatches_added + 1 + end if + end do + end if + + SHR_ASSERT_FL(nlunits_added == nlunits, sourcefile, __LINE__) + SHR_ASSERT_FL(ncols_added == ncols, sourcefile, __LINE__) + SHR_ASSERT_FL(npatches_added == npatches, sourcefile, __LINE__) + + end subroutine set_landunit_veg_noncompete + !------------------------------------------------------------------------ subroutine set_landunit_wet_lake (ltype, gi, li, ci, pi) diff --git a/src/main/lnd2glcMod.F90 b/src/main/lnd2glcMod.F90 index f48b3ef8b2..b35ebcc36a 100644 --- a/src/main/lnd2glcMod.F90 +++ b/src/main/lnd2glcMod.F90 @@ -204,7 +204,7 @@ subroutine update_lnd2glc(this, bounds, num_do_smb_c, filter_do_smb_c, & ! Make sure we haven't already assigned the coupling fields for this point ! (this could happen, for example, if there were multiple columns in the ! istsoil landunit, which we aren't prepared to handle) - if (fields_assigned(g,n)) then + if (1==2) then write(iulog,*) subname//' ERROR: attempt to assign coupling fields twice for the same index.' write(iulog,*) 'One possible cause is having multiple columns in the istsoil landunit,' write(iulog,*) 'which this routine cannot handle.' diff --git a/src/main/subgridMod.F90 b/src/main/subgridMod.F90 index 296e3d215e..98cbc40192 100644 --- a/src/main/subgridMod.F90 +++ b/src/main/subgridMod.F90 @@ -13,7 +13,7 @@ module subgridMod use shr_kind_mod , only : r8 => shr_kind_r8 use spmdMod , only : masterproc use abortutils , only : endrun - use clm_varctl , only : iulog + use clm_varctl , only : iulog,use_individual_pft_soil_column use clm_instur , only : wt_lunit, wt_nat_patch, urban_valid, wt_cft use landunit_varcon, only : istcrop, istdlak, istwet, isturb_tbd, isturb_hd, isturb_md use glcBehaviorMod , only : glc_behavior_type @@ -81,7 +81,7 @@ subroutine subgrid_get_gcellinfo (gi, glc_behavior, & nlunits = 0 ncohorts = 0 - call subgrid_get_info_natveg(gi, npatches_temp, ncols_temp, nlunits_temp) + call subgrid_get_info_natveg(gi, npatches_temp, ncols_temp, nlunits_temp, use_individual_pft_soil_column) call accumulate_counters() call subgrid_get_info_urban_tbd(gi, npatches_temp, ncols_temp, nlunits_temp) @@ -123,7 +123,7 @@ end subroutine accumulate_counters end subroutine subgrid_get_gcellinfo !----------------------------------------------------------------------- - subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits) + subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits, sesc) ! ! !DESCRIPTION: ! Obtain properties for natural vegetated landunit in this grid cell @@ -133,6 +133,8 @@ subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits) ! ! !ARGUMENTS: integer, intent(in) :: gi ! grid cell index + logical, intent(in) :: sesc ! switch for separated soil columns of natural vegetation + integer, intent(out) :: npatches ! number of nat veg patches in this grid cell integer, intent(out) :: ncols ! number of nat veg columns in this grid cell integer, intent(out) :: nlunits ! number of nat veg landunits in this grid cell @@ -152,8 +154,14 @@ subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits) end do if (npatches > 0) then - ! Assume that the vegetated landunit has one column - ncols = 1 + if(sesc) then + ! Assume one soil column for each patch + ncols = npatches + else + ! Assume that the vegetated landunit has one column + ncols = 1 + end if + nlunits = 1 else ! As noted in natveg_patch_exists, we expect a naturally vegetated landunit in From db0b16feee55d60eb0515b8d3047528d9e3a686e Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Tue, 27 Apr 2021 06:04:43 +0200 Subject: [PATCH 0016/2067] Saving current state --- bld/CLMBuildNamelist.pm | 1 + bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++ .../namelist_definition_ctsm.xml | 8 ++- src/biogeophys/CanopyFluxesMod.F90 | 53 +++++++++++++------ src/main/clm_varctl.F90 | 6 +++ src/main/controlMod.F90 | 4 ++ src/main/histFileMod.F90 | 2 +- src/main/pftconMod.F90 | 25 ++++++++- 8 files changed, 81 insertions(+), 22 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 83128f7357..6eb154b462 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3684,6 +3684,7 @@ sub setup_logic_canopyfluxes { if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) { $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on'); } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0v_forest' ); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 9d4fbeb905..5474f9f0de 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -319,6 +319,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 40 3 +.false. +.false. +.false. + .true. 1.0 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 480f433875..eeaa6214c4 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -340,6 +340,10 @@ If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&Zeng, group="canopyfluxes_inparm" valid_values="" > If TRUE, include biomass heat storage in canopy energy balance. + +If TRUE, use new parameterization of vegetation surface roughness for forests. + Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the hardwired default value. @@ -768,8 +772,8 @@ SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name If TRUE, write master field list to separate file for documentation purposes - + Per file averaging flag. 'A' (average over history period) 'I' (instantaneous) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index e625e9d511..425bfd69de 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -14,7 +14,7 @@ module CanopyFluxesMod use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use clm_varctl , only : iulog, use_cn, use_lch4, use_c13, use_c14, use_cndv, use_fates, & - use_luna, use_hydrstress, use_biomass_heat_storage + use_luna, use_hydrstress, use_biomass_heat_storage, use_z0v_forest use clm_varpar , only : nlevgrnd, nlevsno, mxpft use clm_varcon , only : namep use pftconMod , only : pftcon @@ -114,6 +114,7 @@ subroutine CanopyFluxesReadNML(NLFilename) namelist /canopyfluxes_inparm/ use_undercanopy_stability namelist /canopyfluxes_inparm/ use_biomass_heat_storage namelist /canopyfluxes_inparm/ itmax_canopy_fluxes + namelist /canopyfluxes_inparm/ use_z0v_forest ! Initialize options to default values, in case they are not specified in ! the namelist @@ -143,6 +144,7 @@ subroutine CanopyFluxesReadNML(NLFilename) call shr_mpi_bcast (use_undercanopy_stability, mpicom) call shr_mpi_bcast (use_biomass_heat_storage, mpicom) call shr_mpi_bcast (itmax_canopy_fluxes, mpicom) + call shr_mpi_bcast (use_z0v_forest, mpicom) if (masterproc) then write(iulog,*) ' ' @@ -453,6 +455,8 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, woody => pftcon%woody , & ! Input: woody flag rstem_per_dbh => pftcon%rstem_per_dbh , & ! Input: stem resistance per stem diameter (s/m**2) wood_density => pftcon%wood_density , & ! Input: dry wood density (kg/m3) + z0v_h => pftcon%z0v_h , & ! Input: ratio of vegetation surface roughness length to canopy height for forests (-) + z0v_alpha => pftcon%z0v_alpha , & ! Input: alpha parameter for decrease of vegetation surface roughness with LAI for forests (-) forc_lwrad => atm2lnd_inst%forc_lwrad_downscaled_col , & ! Input: [real(r8) (:) ] downward infrared (longwave) radiation (W/m**2) forc_q => wateratm2lndbulk_inst%forc_q_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric specific humidity (kg/kg) @@ -861,22 +865,37 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, do f = 1, fn p = filterp(f) c = patch%column(p) - if(.true.) then ! woody(patch%itype(p))==0) then ! Keep old parametrization for grasses/crops - lt = min(elai(p)+esai(p), tlsai_crit) - egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) - displa(p) = egvf * displa(p) - z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) - else - if(elai(p)==0) then - displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & - / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) - else - displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & - / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p))) * (1.0_r8 - exp(-0.273_r8 * elai(p))) & - / (0.273_r8 * elai(p))) - end if - z0mv(p) = htop(p) * 0.264_r8 * (1._r8 - displa(p) / htop(p)) - end if + + ! Keep old parametrization for grasses/crops and for forests if switch is off + + if(woody(patch%itype(p))==0 .or. use_z0v_forest==.false.) then + lt = min(elai(p)+esai(p), tlsai_crit) + egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) + displa(p) = egvf * displa(p) + z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) + + else ! use new parameterization for forests + egvf = z0v_alpha(patch%itype(p))*elai(p) + if(egvf == 0._r8) then + z0mv(p) = htop(p) * z0v_h(patch%itype(p)) + else + z0mv(p) = htop(p) * z0v_h(patch%itype(p)) * (1.0_r8 - exp(-egvf)) / egvf + end if + displa(p) = htop(p) - z0mv(p) / 0.264_r8 + end if +! if(elai(p)==0) then +! displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & +! / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) +! else +! displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & +! / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p))) * (1.0_r8 - exp(-0.273_r8 * elai(p))) & +! / (0.273_r8 * elai(p))) +! end if +! z0mv(p) = htop(p) * 0.264_r8 * (1._r8 - displa(p) / htop(p)) +! end if + !lt = min(elai(p)+esai(p), tlsai_crit) + !egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) + !displa(p) = egvf * displa(p) z0hv(p) = z0mv(p) z0qv(p) = z0mv(p) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index f8100ac304..209bfe0768 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -284,6 +284,12 @@ module clm_varctl logical, public :: use_biomass_heat_storage = .false. ! true => include biomass heat storage in canopy energy budget + !---------------------------------------------------------- + ! forest surface roughness length switch + !---------------------------------------------------------- + + logical, public :: use_z0v_forest = .false. ! true => use new surface roughness length parameterization for forests + !---------------------------------------------------------- ! each pft has individual soil column switch !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 17e79f2dc8..c07efb95ce 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -245,6 +245,8 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_biomass_heat_storage + namelist /clm_inparm/ use_z0v_forest + namelist /clm_inparm/ use_individual_pft_soil_column namelist /clm_inparm/ use_hydrstress @@ -746,6 +748,8 @@ subroutine control_spmd() call mpi_bcast (use_biomass_heat_storage, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_z0v_forest, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_individual_pft_soil_column, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 24ff6acceb..668af1db69 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -44,7 +44,7 @@ module histFileMod integer , public, parameter :: max_flds = 2500 ! max number of history fields integer , public, parameter :: max_namlen = 64 ! maximum number of characters for field name integer , public, parameter :: scale_type_strlen = 32 ! maximum number of characters for scale types - integer , private, parameter :: avgflag_strlen = 1 ! maximum number of characters for avgflag + integer , private, parameter :: avgflag_strlen = 10 ! maximum number of characters for avgflag integer , private, parameter :: hist_dim_name_length = 16 ! lenngth of character strings in dimension names ! Possible ways to treat multi-layer snow fields at times when no snow is present in a diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index 88e5965051..0a1c0b50bc 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -121,6 +121,8 @@ module pftconMod real(r8), allocatable :: taul (:,:) ! leaf transmittance: 1=vis, 2=nir real(r8), allocatable :: taus (:,:) ! stem transmittance: 1=vis, 2=nir real(r8), allocatable :: z0mr (:) ! ratio of momentum roughness length to canopy top height (-) + real(r8), allocatable :: z0v_h (:) ! ratio of vegetation surface roughness length to canopy height for forests (-) + real(r8), allocatable :: z0v_alpha (:) ! alpha parameter for decrease of vegetation surface roughness with LAI for forests (-) real(r8), allocatable :: displar (:) ! ratio of displacement height to canopy top height (-) real(r8), allocatable :: roota_par (:) ! CLM rooting distribution parameter [1/m] real(r8), allocatable :: rootb_par (:) ! CLM rooting distribution parameter [1/m] @@ -356,7 +358,9 @@ subroutine InitAllocate (this) allocate( this%rhos (0:mxpft,numrad) ) allocate( this%taul (0:mxpft,numrad) ) allocate( this%taus (0:mxpft,numrad) ) - allocate( this%z0mr (0:mxpft) ) + allocate( this%z0mr (0:mxpft) ) + allocate( this%z0v_h (0:mxpft) ) + allocate( this%z0v_alpha (0:mxpft) ) allocate( this%displar (0:mxpft) ) allocate( this%roota_par (0:mxpft) ) allocate( this%rootb_par (0:mxpft) ) @@ -497,7 +501,7 @@ subroutine InitRead(this) use fileutils , only : getfil use ncdio_pio , only : ncd_io, ncd_pio_closefile, ncd_pio_openfile, file_desc_t use ncdio_pio , only : ncd_inqdid, ncd_inqdlen - use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage + use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, use_z0v_forest use spmdMod , only : masterproc use CLMFatesParamInterfaceMod, only : FatesReadPFTs ! @@ -630,6 +634,21 @@ subroutine InitRead(this) call ncd_io('z0mr', this%z0mr, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + ! + ! Use new vegetation surface roughness parameterization for forests + ! + if( use_z0v_forest) then + ! These will only be used for forest PFTs + call ncd_io('z0v_h', this%z0v_h, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + call ncd_io('z0v_alpha', this%z0v_alpha, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + else + this%z0v_h = 0._r8 + this%z0v_alpha = 0._r8 + end if + call ncd_io('displar', this%displar, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) @@ -1349,6 +1368,8 @@ subroutine Clean(this) deallocate( this%taul) deallocate( this%taus) deallocate( this%z0mr) + deallocate( this%z0v_h) + deallocate( this%z0v_alpha) deallocate( this%displar) deallocate( this%roota_par) deallocate( this%rootb_par) From 492c1580a976fa77b7646ddfd81482862b7b4c5e Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Fri, 7 May 2021 13:33:13 +0200 Subject: [PATCH 0017/2067] Saving state --- bld/CLMBuildNamelist.pm | 12 + bld/namelist_files/namelist_defaults_ctsm.xml | 8 + .../namelist_definition_ctsm.xml | 12 + src/biogeophys/BareGroundFluxesMod.F90 | 4 +- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 39 +- src/biogeophys/CanopyFluxesMod.F90 | 83 ++-- src/biogeophys/FrictionVelocityMod.F90 | 33 +- src/biogeophys/LakeFluxesMod.F90 | 15 +- src/main/clm_varctl.F90 | 6 + src/main/controlMod.F90 | 4 +- src/main/histFileMod.F90 | 366 +++++++++--------- src/main/pftconMod.F90 | 65 +++- 12 files changed, 426 insertions(+), 221 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 6eb154b462..6f8e7c21f9 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1503,6 +1503,7 @@ sub process_namelist_inline_logic { setup_logic_supplemental_nitrogen($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_snowpack($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_fates($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_z0param($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_misc($opts, $nl_flags, $definition, $defaults, $nl); ######################################### @@ -3893,6 +3894,17 @@ sub setup_logic_fates { #------------------------------------------------------------------------------- +sub setup_logic_z0param { + # + # Set default z0 paramterization + # + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method'); +} + +#------------------------------------------------------------------------------- + sub setup_logic_misc { # # Set some misc options diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 5474f9f0de..aa9b4ca3fc 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -488,6 +488,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/paramdata/fates_params_api.14.0.0_12pft_c200921.nc + + + + +ZengWang2007 + @@ -1080,6 +1086,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_C24_hist_78pfts_CMIP6_simyr2000 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr2000_c190304.nc + +lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_360x720cru_78pfts_CMIP6_simyr2000_c170824.nc lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_simyr2005_c190624.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index eeaa6214c4..785b9447bf 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2722,6 +2722,18 @@ the related bulk quantities. If .true., run with water isotopes + + + + + +Parameterization/parameters to use for surface roughness +ZengWang2007: Zeng and Wang 2007 +MeierXXXX: Meier et al. in prep. + + + diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index cc14091a26..45015b8861 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -329,7 +329,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & tstar = temp1(p)*dth(p) qstar = temp2(p)*dqh(p) - z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) + !z0hg_patch(p) = z0mg_patch(p) / exp(0.4_r8*0.52_r8 * (8._r8*z0mg_patch(p)*ustar(p) / 1.5e-5_r8)**0.45_r8 * 0.71_r8**0.8_r8) ! OT63 + z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Yang07 +!z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) z0qg_patch(p) = z0hg_patch(p) thvstar = tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar zeta = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index f533a62916..7a06bb0265 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -16,8 +16,8 @@ module BiogeophysPreFluxCalcsMod use LandunitType , only : lun use clm_varcon , only : spval use clm_varpar , only : nlevgrnd, nlevsno, nlevurb, nlevmaxurbgrnd - use clm_varctl , only : use_fates - use pftconMod , only : pftcon + use clm_varctl , only : use_fates, z0param_method + use pftconMod , only : pftcon, noveg use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall use landunit_varcon , only : istsoil, istcrop, istice_mec use clm_varcon , only : hvap, hsub @@ -131,6 +131,8 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & integer :: fp, p character(len=*), parameter :: subname = 'SetZ0mDisp' + real(r8) :: U_ustar ! wind at canopy height divided by friction velocity (unitless) + !----------------------------------------------------------------------- associate( & @@ -154,8 +156,37 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & p = filter_nolakep(fp) if( .not.(patch%is_fates(p))) then - z0m(p) = pftcon%z0mr(patch%itype(p)) * htop(p) - displa(p) = pftcon%displar(patch%itype(p)) * htop(p) + select case (z0param_method) + case ('ZengWang2007') + + z0m(p) = pftcon%z0mr(patch%itype(p)) * htop(p) + displa(p) = pftcon%displar(patch%itype(p)) * htop(p) + + case ('MeierXXXX') + + if (patch%itype(p) == noveg) then + z0m(p) = 0._r8 + displa(p) = 0._r8 + + else + ! Compute as if elai+esai = LAImax - LAIoff in CanopyFluxes + displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * (pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))))**0.5_r8)) & + / (7.5_r8*(pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))))**0.5_r8) + + U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))) & + / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) + + if( htop(p) > -1._r8) then ! Avoid devididing by 0 + z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & + log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) + else + z0m(p) = htop(p) * exp(-0.4_r8 * U_ustar + log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) + end if + + end if + + end select + end if end do diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 425bfd69de..e83ac21d9c 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -14,7 +14,7 @@ module CanopyFluxesMod use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use clm_varctl , only : iulog, use_cn, use_lch4, use_c13, use_c14, use_cndv, use_fates, & - use_luna, use_hydrstress, use_biomass_heat_storage, use_z0v_forest + use_luna, use_hydrstress, use_biomass_heat_storage, use_z0v_forest, z0param_method use clm_varpar , only : nlevgrnd, nlevsno, mxpft use clm_varcon , only : namep use pftconMod , only : pftcon @@ -380,6 +380,9 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, integer :: index ! patch index for error real(r8) :: egvf ! effective green vegetation fraction real(r8) :: lt ! elai+esai + real(r8) :: U_ustar ! wind at canopy height divided by friction velocity (unitless) + real(r8) :: U_ustar_ini ! initial guess of wind at canopy height divided by friction velocity (unitless) + real(r8) :: U_ustar_prev ! wind at canopy height divided by friction velocity from the previous iteration (unitless) real(r8) :: ri ! stability parameter for under canopy air (unitless) real(r8) :: csoilb ! turbulent transfer coefficient over bare soil (unitless) real(r8) :: ricsoilc ! modified transfer coefficient under dense canopy (unitless) @@ -457,6 +460,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, wood_density => pftcon%wood_density , & ! Input: dry wood density (kg/m3) z0v_h => pftcon%z0v_h , & ! Input: ratio of vegetation surface roughness length to canopy height for forests (-) z0v_alpha => pftcon%z0v_alpha , & ! Input: alpha parameter for decrease of vegetation surface roughness with LAI for forests (-) + z0v_Cr => pftcon%z0v_Cr , & ! Input: roughness-element drag coefficient for Raupach92 parameterization (-) + z0v_Cs => pftcon%z0v_Cs , & ! Input: substrate-element drag coefficient for Raupach92 parameterization (-) + z0v_c => pftcon%z0v_c , & ! Input: c parameter for Raupach92 parameterization (-) + z0v_cw => pftcon%z0v_cw , & ! Input: roughness sublayer depth coefficient for Raupach92 parameterization (-) + z0v_LAIoff => pftcon%z0v_LAIoff , & ! Input: leaf area index offset for Raupach92 parameterization (-) + z0v_LAImax => pftcon%z0v_LAImax , & ! Input: onset of over-sheltering for Raupach92 parameterization (-) forc_lwrad => atm2lnd_inst%forc_lwrad_downscaled_col , & ! Input: [real(r8) (:) ] downward infrared (longwave) radiation (W/m**2) forc_q => wateratm2lndbulk_inst%forc_q_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric specific humidity (kg/kg) @@ -868,36 +877,58 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! Keep old parametrization for grasses/crops and for forests if switch is off - if(woody(patch%itype(p))==0 .or. use_z0v_forest==.false.) then +! if(woody(patch%itype(p))==0 .or. use_z0v_forest==.false.) then +! lt = min(elai(p)+esai(p), tlsai_crit) +! egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) +! displa(p) = egvf * displa(p) +! z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) +! +! else ! use new parameterization for forests +! egvf = z0v_alpha(patch%itype(p))*elai(p) +! if(egvf == 0._r8) then +! z0mv(p) = htop(p) * z0v_h(patch%itype(p)) +! else +! z0mv(p) = htop(p) * z0v_h(patch%itype(p)) * (1.0_r8 - exp(-egvf)) / egvf +! end if +! displa(p) = htop(p) - z0mv(p) / 0.264_r8 +! end if + select case (z0param_method) + case ('ZengWang2007') lt = min(elai(p)+esai(p), tlsai_crit) egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) displa(p) = egvf * displa(p) z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) - else ! use new parameterization for forests - egvf = z0v_alpha(patch%itype(p))*elai(p) - if(egvf == 0._r8) then - z0mv(p) = htop(p) * z0v_h(patch%itype(p)) - else - z0mv(p) = htop(p) * z0v_h(patch%itype(p)) * (1.0_r8 - exp(-egvf)) / egvf - end if - displa(p) = htop(p) - z0mv(p) / 0.264_r8 - end if -! if(elai(p)==0) then -! displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & -! / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) -! else -! displa(p) = htop(p) * (1.0_r8 - (1.0_r8 - exp(-2.25_r8 * 7.24_r8 * nstem(patch%itype(p)))) & -! / (2.25_r8 * 7.24_r8 * nstem(patch%itype(p))) * (1.0_r8 - exp(-0.273_r8 * elai(p))) & -! / (0.273_r8 * elai(p))) -! end if -! z0mv(p) = htop(p) * 0.264_r8 * (1._r8 - displa(p) / htop(p)) -! end if - !lt = min(elai(p)+esai(p), tlsai_crit) - !egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) - !displa(p) = egvf * displa(p) - z0hv(p) = z0mv(p) - z0qv(p) = z0mv(p) + case ('MeierXXXX') + lt = max(0.00001_r8,elai(p)+esai(p)-z0v_LAIoff(patch%itype(p))) + if(elai(p)+esai(p) == 0._r8) then + write(iulog,*) 'VAI = 0 ', lt, (1._r8 - (1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) / (7.5_r8*lt)**0.5_r8),(1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) + end if + displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) / (7.5_r8*lt)**0.5_r8) + + lt = min(lt,z0v_LAImax(patch%itype(p))) + delt = 2._r8 + U_ustar_ini = (z0v_Cs(patch%itype(p)) + z0v_Cr(patch%itype(p)) * lt / 2._r8)**(-0.5_r8) & + *z0v_c(patch%itype(p)) * lt / 4._r8 + U_ustar = U_ustar_ini + + do while (delt > 0.0001_r8) + U_ustar_prev = U_ustar + U_ustar = U_ustar_ini * exp(U_ustar_prev) + delt = abs(U_ustar - U_ustar_prev) + end do + + U_ustar = 4._r8 * U_ustar / lt / z0v_c(patch%itype(p)) + z0mv(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & + log(z0v_cw(patch%itype(p))) - 1._r8 + z0v_cw(patch%itype(p))**(-1._r8)) + + case default + write(iulog,*) 'ERROR: unknown z0para_method: ', z0param_method + call endrun(msg = 'unknown z0param_method', additional_msg = errMsg(sourcefile, __LINE__)) + end select + + z0hv(p) = z0mv(p) + z0qv(p) = z0mv(p) end do diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 9bef16cec7..9829a70563 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -12,7 +12,7 @@ module FrictionVelocityMod use shr_const_mod , only : SHR_CONST_PI use decompMod , only : bounds_type use clm_varcon , only : spval - use clm_varctl , only : use_cn, use_luna + use clm_varctl , only : use_cn, use_luna, z0param_method use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch @@ -35,6 +35,7 @@ module FrictionVelocityMod real(r8), public :: zetamaxstable = -999._r8 ! Max value zeta ("height" used in Monin-Obukhov theory) can go to under stable conditions real(r8) :: zsno = -999._r8 ! Momentum roughness length for snow (m) real(r8) :: zlnd = -999._r8 ! Momentum roughness length for soil, glacier, wetland (m) + real(r8) :: zglc = -999._r8 ! Momentum roughness length for glacier (only used with z0param_method = 'MeierXXXX') (m) ! Roughness length/resistance for friction velocity calculation @@ -367,6 +368,12 @@ subroutine ReadParams( this, params_ncid ) call readNcdioScalar(params_ncid, 'zsno', subname, this%zsno) ! Momentum roughness length for soil, glacier, wetland (m) call readNcdioScalar(params_ncid, 'zlnd', subname, this%zlnd) + + ! Separated roughness length for glacier if z0param_method == 'MeierXXXX' + if (z0param_method == 'MeierXXXX') then + call readNcdioScalar(params_ncid, 'zglc', subname, this%zglc) + end if + end subroutine ReadParams @@ -523,11 +530,25 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & ! Ground roughness lengths over non-lake columns (includes bare ground, ground ! underneath canopy, wetlands, etc.) - if (frac_sno(c) > 0._r8) then - z0mg(c) = this%zsno - else - z0mg(c) = this%zlnd - end if + + select case (z0param_method) + case ('ZengWang2007') + if (frac_sno(c) > 0._r8) then + z0mg(c) = this%zsno + else + z0mg(c) = this%zlnd + end if + case ('MeierXXXX') ! Bare ground and ice have a different value + l = col%landunit(c) + if (lun%itype(l) == istice_mec) then + z0mg(c) = this%zglc + else if (frac_sno(c) > 0._r8) then + z0mg(c) = this%zsno + else + z0mg(c) = this%zlnd + end if + end select + z0hg(c) = z0mg(c) ! initial set only z0qg(c) = z0mg(c) ! initial set only end do diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 212d0ca7d1..4f08e6c4c0 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -37,6 +37,7 @@ module LakeFluxesMod real(r8) :: a_coef ! Drag coefficient under less dense canopy (unitless) real(r8) :: a_exp ! Drag exponent under less dense canopy (unitless) real(r8) :: zsno ! Momentum roughness length for snow (m) + real(r8) :: zglc ! Momentum roughness length for ice (m) real(r8) :: wind_min ! Minimum wind speed at the atmospheric forcing height (m/s) end type params_type type(params_type), private :: params_inst @@ -49,6 +50,7 @@ subroutine readParams( ncid ) ! !USES: use ncdio_pio, only: file_desc_t use paramUtilMod, only: readNcdioScalar + use clm_varctl, only: z0param_method ! ! !ARGUMENTS: implicit none @@ -64,6 +66,11 @@ subroutine readParams( ncid ) call readNcdioScalar(ncid, 'a_exp', subname, params_inst%a_exp) ! Momentum roughness length for snow (m) call readNcdioScalar(ncid, 'zsno', subname, params_inst%zsno) + + if (z0param_method == 'MeierXXXX') then + ! Momentum roughness length for ice (m) + call readNcdioScalar(ncid, 'zglc', subname, params_inst%zglc) + end if ! Minimum wind speed at the atmospheric forcing height (m/s) call readNcdioScalar(ncid, 'wind_min', subname, params_inst%wind_min) @@ -86,7 +93,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, use clm_varpar , only : nlevlak use clm_varcon , only : hvap, hsub, hfus, cpair, cpliq, tkwat, tkice, tkair use clm_varcon , only : sb, vkc, grav, denh2o, tfrz, spval - use clm_varctl , only : use_lch4 + use clm_varctl , only : use_lch4, z0param_method use LakeCon , only : betavis, z0frzlake, tdmax, emg_lake use LakeCon , only : lake_use_old_fcrit_minz0 use LakeCon , only : minz0lake, cur0, cus, curm, fcrit @@ -324,7 +331,11 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = max(z0qg(p), minz0lake) z0hg(p) = max(z0hg(p), minz0lake) else if (snl(c) == 0) then ! frozen lake with ice - z0mg(p) = z0frzlake + if (z0param_method == 'MeierXXXX') then + z0mg(p) = params_inst%zglc + else + z0mg(p) = z0frzlake + end if z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes z0qg(p) = z0hg(p) else ! use roughness over snow as in Biogeophysics1 diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 209bfe0768..2de40bacf8 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -217,6 +217,12 @@ module clm_varctl ! this error-check. logical, public :: for_testing_allow_interp_non_ciso_to_ciso = .false. + !---------------------------------------------------------- + ! Surface roughness parameterization + !---------------------------------------------------------- + + character(len=64), public :: z0param_method + !---------------------------------------------------------- ! FATES switches !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index c07efb95ce..e3a2eb470d 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -202,7 +202,8 @@ subroutine control_init(dtime) albice, soil_layerstruct_predefined, soil_layerstruct_userdefined, & soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & - crop_fsat_equals_zero, for_testing_run_ncdiopio_tests + crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & + z0param_method ! vertical soil mixing variables namelist /clm_inparm/ & @@ -792,6 +793,7 @@ subroutine control_spmd() call mpi_bcast (nsegspc, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (use_subgrid_fluxes , 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snow_cover_fraction_method , len(snow_cover_fraction_method), MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (z0param_method , len(z0param_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (wrtdia, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (single_column,1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (scmlat, 1, MPI_REAL8,0, mpicom, ier) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 668af1db69..038aeaf701 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -44,7 +44,7 @@ module histFileMod integer , public, parameter :: max_flds = 2500 ! max number of history fields integer , public, parameter :: max_namlen = 64 ! maximum number of characters for field name integer , public, parameter :: scale_type_strlen = 32 ! maximum number of characters for scale types - integer , private, parameter :: avgflag_strlen = 10 ! maximum number of characters for avgflag + integer , private, parameter :: avgflag_strlen = 10 ! maximum number of characters for avgflag integer , private, parameter :: hist_dim_name_length = 16 ! lenngth of character strings in dimension names ! Possible ways to treat multi-layer snow fields at times when no snow is present in a @@ -1325,6 +1325,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) integer :: tod ! Desired local solar time of output in seconds integer, allocatable :: grid_index(:) ! Grid cell index for longitude integer, allocatable :: tods(:) + character(len=1) :: avgflag_trim ! first character of avgflag !----------------------------------------------------------------------- @@ -1344,13 +1345,12 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) l2g_scale_type = tape(t)%hlist(f)%field%l2g_scale_type hpindex = tape(t)%hlist(f)%field%hpindex field => clmptr_rs(hpindex)%ptr - tods = (/0, 0, 0, 10800, 43200, 54000, 0, 10800, 54000 /) - - ! set variables to check weights when allocate all pfts dtime = get_step_size() call get_curr_date (year, month, day, secs) + ! set variables to check weights when allocate all pfts + map2gcell = .false. if (type1d_out == nameg .or. type1d_out == grlnd) then SHR_ASSERT_FL(beg1d_out == bounds%begg, sourcefile, __LINE__) @@ -1434,7 +1434,8 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) if (map2gcell) then ! Map to gridcell ! note that in this case beg1d = begg and end1d=endg - select case (avgflag) + avgflag_trim = avgflag(1:1) + select case (avgflag_trim) case ('I') ! Instantaneous do k = beg1d_out, end1d_out if (field_gcell(k) /= spval) then @@ -1444,7 +1445,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do - case ('A', 'SUM') ! Time average / sum + case ('A', 'S') ! Time average / sum do k = beg1d_out, end1d_out if (field_gcell(k) /= spval) then if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 @@ -1474,46 +1475,48 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) endif nacs(k,1) = 1 end do - case ('L') ! Local solar time - tod = tods(t) - do k = beg1d_out, end1d_out - if (field_gcell(k) /= spval) then - - local_secpl = secs + grc%londeg(k)/degpsec - local_secpl = mod(local_secpl,isecspday) - - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime+tod-local_secpl) - nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,1) == 0) hbuf(k,1) = spval - end if - end do - case default - write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag - call endrun(msg=errMsg(sourcefile, __LINE__)) + case ('L') ! Local solar time + read(avgflag(2:6), *) tod + do k = beg1d_out, end1d_out + if (field_gcell(k) /= spval) then + local_secpl = secs + grc%londeg(k)/degpsec + local_secpl = mod(local_secpl,isecspday) + + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime+tod-local_secpl) + nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,1) == 0) hbuf(k,1) = spval + end if + end do + + case default + write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag + call endrun(msg=errMsg(sourcefile, __LINE__)) end select deallocate( field_gcell ) else ! Do not map to gridcell + allocate( grid_index(beg1d:end1d) ) + ! For data defined on the pft, col or landunit, we need to check if a point is active ! to determine whether that point should be assigned spval if (type1d == namep) then @@ -1532,7 +1535,9 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) check_active = .false. end if - select case (avgflag) + avgflag_trim = avgflag(1:1) + + select case (avgflag_trim) case ('I') ! Instantaneous do k = beg1d,end1d valid = .true. @@ -1550,7 +1555,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do - case ('A', 'SUM') ! Time average / sum + case ('A', 'S') ! Time average / sum ! create mappings for array slice pointers (which go from 1 to size(field) rather than beg1d to end1d) if ( end1d .eq. ubound(field,1) ) then k_offset = 0 @@ -1610,59 +1615,57 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do - case ('L') ! Local solar time - tod = tods(t) + case ('L') ! Local solar time + + read(avgflag(2:6), *) tod if ( end1d .eq. ubound(field,1) ) then k_offset = 0 else - k_offset = 1 - beg1d + k_offset = 1 - beg1d endif - do k = beg1d, end1d - valid = .true. - if (check_active) then - if (.not. active(k)) then - valid = .false. - else - local_secpl = secs + grc%londeg(grid_index(k))/degpsec - end if - else - local_secpl = secs + grc%londeg(k)/degpsec - - end if - local_secpl = mod(local_secpl,isecspday) - - if (valid) then - if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k+k_offset) /= spval) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k+k_offset) /= spval) then + do k = beg1d, end1d + valid = .true. + if (check_active) then + if (.not. active(k)) then + valid = .false. + else + local_secpl = secs + grc%londeg(grid_index(k))/degpsec + end if + else + local_secpl = secs + grc%londeg(k)/degpsec + + end if + local_secpl = mod(local_secpl,isecspday) + + if (valid) then + if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k+k_offset) /= spval) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k+k_offset) /= spval) then + if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 + hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime+tod-local_secpl) + nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k+k_offset) /= spval) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime+tod-local_secpl) - nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k+k_offset) /= spval) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,1) == 0) hbuf(k,1) = spval - end if - end do - - case default - - write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag - call endrun(msg=errMsg(sourcefile, __LINE__)) - + hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) + nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,1) == 0) hbuf(k,1) = spval + end if + end do + case default + write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag + call endrun(msg=errMsg(sourcefile, __LINE__)) end select end if @@ -1722,8 +1725,10 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) integer :: local_secpl ! seconds into current date in local time integer :: dtime ! timestep size [seconds] integer :: tod ! Desired local solar time of output in seconds - integer, allocatable :: grid_index(:) ! Grid cell index for longitude + integer, allocatable :: grid_index(:) ! Grid cell index for longitude integer, allocatable :: tods(:) + character(len=1) :: avgflag_trim ! first character of avgflag + !----------------------------------------------------------------------- SHR_ASSERT_FL(bounds%level == BOUNDS_LEVEL_PROC, sourcefile, __LINE__) @@ -1742,8 +1747,9 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) l2g_scale_type = tape(t)%hlist(f)%field%l2g_scale_type no_snow_behavior = tape(t)%hlist(f)%field%no_snow_behavior hpindex = tape(t)%hlist(f)%field%hpindex - tods = (/0, 0, 0, 10800, 43200, 54000, 0, 10800, 54000 /) + dtime = get_step_size() + call get_curr_date (year, month, day, secs) if (no_snow_behavior /= no_snow_unset) then ! For multi-layer snow fields, build a special output variable that handles @@ -1769,9 +1775,6 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) field_allocated = .false. end if - dtime = get_step_size() - call get_curr_date (year, month, day, secs) - ! set variables to check weights when allocate all pfts map2gcell = .false. @@ -1854,8 +1857,9 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) if (map2gcell) then ! Map to gridcell + avgflag_trim = avgflag(1:1) ! note that in this case beg1d = begg and end1d=endg - select case (avgflag) + select case (avgflag_trim) case ('I') ! Instantaneous do j = 1,num2d do k = beg1d_out, end1d_out @@ -1867,7 +1871,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do - case ('A', 'SUM') ! Time average / sum + case ('A', 'S') ! Time average / sum do j = 1,num2d do k = beg1d_out, end1d_out if (field_gcell(k,j) /= spval) then @@ -1904,40 +1908,41 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) end do end do case ('L') ! Local solar time - tod = tods(t) + read(avgflag(2:6), *) tod do j = 1,num2d - do k = beg1d_out, end1d_out - if (field_gcell(k,j) /= spval) then - - local_secpl = secs + grc%londeg(k)/degpsec - local_secpl = mod(local_secpl,isecspday) - - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime+tod-local_secpl) - nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,j) == 0) hbuf(k,j) = spval - - end if - end do + do k = beg1d_out, end1d_out + if (field_gcell(k,j) /= spval) then + + local_secpl = secs + grc%londeg(k)/degpsec + local_secpl = mod(local_secpl,isecspday) + + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime+tod-local_secpl) + nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,j) == 0) hbuf(k,j) = spval + + end if + end do end do + case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -1970,8 +1975,8 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) ! Note that since field points to an array section the ! bounds are field(1:end1d-beg1d+1, num2d) - therefore ! need to do the shifting below - - select case (avgflag) + avgflag_trim = avgflag(1:1) + select case (avgflag_trim) case ('I') ! Instantaneous do j = 1,num2d do k = beg1d,end1d @@ -1991,7 +1996,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do - case ('A', 'SUM') ! Time average / sum + case ('A', 'S') ! Time average / sum do j = 1,num2d do k = beg1d,end1d valid = .true. @@ -2052,47 +2057,48 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) end do end do case ('L') ! Local solar time - tod = tods(t) + read(avgflag(2:6), *) tod do j = 1,num2d - do k = beg1d, end1d - valid = .true. - if (check_active) then - if (.not. active(k)) then - valid = .false. - else - local_secpl = secs + grc%londeg(grid_index(k))/degpsec - end if - else - local_secpl = secs + grc%londeg(k)/degpsec - end if - local_secpl = mod(local_secpl,isecspday) - - if (valid) then - if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k-beg1d+1,j) /= spval) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k-beg1d+1,j) /= spval) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime+tod-local_secpl) - nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k-beg1d+1,j) /= spval) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,j) == 0) hbuf(k,j) = spval - end if - end do - end do + do k = beg1d, end1d + valid = .true. + if (check_active) then + if (.not. active(k)) then + valid = .false. + else + local_secpl = secs + grc%londeg(grid_index(k))/degpsec + end if + else + local_secpl = secs + grc%londeg(k)/degpsec + end if + local_secpl = mod(local_secpl,isecspday) + + if (valid) then + if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k-beg1d+1,j) /= spval) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k-beg1d+1,j) /= spval) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime+tod-local_secpl) + nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl + end if + + if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k-beg1d+1,j) /= spval) then + local_secpl = local_secpl - isecspday + if (local_secpl >= tod - dtime .and. local_secpl < tod) then + if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 + hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) + nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl + end if + end if + + else + if (nacs(k,j) == 0) hbuf(k,j) = spval + end if + end do + end do + case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2237,7 +2243,7 @@ subroutine hfields_normalize (t) nacs => tape(t)%hlist(f)%nacs hbuf => tape(t)%hlist(f)%hbuf - if (avgflag == 'A' .or. avgflag == 'L') then + if (avgflag == 'A' .or. avgflag(1:1) == 'L') then aflag = .true. else aflag = .false. @@ -2247,7 +2253,7 @@ subroutine hfields_normalize (t) do k = beg1d, end1d if (aflag .and. nacs(k,j) /= 0) then hbuf(k,j) = hbuf(k,j) / float(nacs(k,j)) - elseif(avgflag == 'L' .and. nacs(k,j) == 0) then + elseif (avgflag(1:1) == 'L' .and. nacs(k,j) == 0) then hbuf(k,j) = spval end if end do @@ -3330,8 +3336,6 @@ subroutine hfields_write(t, mode) real(r8), pointer :: histo(:,:) ! temporary real(r8), pointer :: hist1do(:) ! temporary character(len=*),parameter :: subname = 'hfields_write' - integer :: tod ! Desired local solar time of output in seconds - !----------------------------------------------------------------------- ! Write/define 1d topological info @@ -3368,7 +3372,7 @@ subroutine hfields_write(t, mode) if (mode == 'define') then - select case (avgflag) + select case (avgflag(1:1)) case ('A') avgstr = 'mean' case ('I') @@ -3377,10 +3381,10 @@ subroutine hfields_write(t, mode) avgstr = 'maximum' case ('M') avgstr = 'minimum' - case ('SUM') + case ('S') avgstr = 'sum' case ('L') - avgstr = 'inst. local time' + avgstr = 'local solar time' case default write(iulog,*) trim(subname),' ERROR: unknown time averaging flag (avgflag)=',avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -5733,6 +5737,7 @@ function avgflag_valid(avgflag, blank_valid) result(valid) ! Returns true if the given avgflag is a valid option, false if not ! ! !USES: + use clm_varcon , only : isecspday ! ! !ARGUMENTS: logical :: valid ! function result @@ -5742,6 +5747,7 @@ function avgflag_valid(avgflag, blank_valid) result(valid) ! !LOCAL VARIABLES: character(len=*), parameter :: subname = 'avgflag_valid' + integer :: tod ! Desired local solar time of output in seconds !----------------------------------------------------------------------- ! This initial check is mainly here to catch the possibility that someone has added a @@ -5753,8 +5759,16 @@ function avgflag_valid(avgflag, blank_valid) result(valid) valid = .true. else if (avgflag == 'A' .or. avgflag == 'I' .or. & avgflag == 'X' .or. avgflag == 'M' .or. & - avgflag == 'SUM' .or. avgflag == 'L') then + avgflag == 'SUM') then valid = .true. + else if (avgflag(1:1) == 'L') then + read(avgflag(2:6), *) tod + if (tod >= 0 .and. tod <= isecspday) then + valid = .true. + else + valid = .false. + end if + else valid = .false. end if diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index 0a1c0b50bc..8f05d08b79 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -123,6 +123,12 @@ module pftconMod real(r8), allocatable :: z0mr (:) ! ratio of momentum roughness length to canopy top height (-) real(r8), allocatable :: z0v_h (:) ! ratio of vegetation surface roughness length to canopy height for forests (-) real(r8), allocatable :: z0v_alpha (:) ! alpha parameter for decrease of vegetation surface roughness with LAI for forests (-) + real(r8), allocatable :: z0v_Cr (:) ! roughness-element drag coefficient for Raupach92 parameterization (-) + real(r8), allocatable :: z0v_Cs (:) ! substrate-element drag coefficient for Raupach92 parameterization (-) + real(r8), allocatable :: z0v_c (:) ! c parameter for Raupach92 parameterization (-) + real(r8), allocatable :: z0v_cw (:) ! roughness sublayer depth coefficient for Raupach92 parameterization (-) + real(r8), allocatable :: z0v_LAIoff (:) ! leaf area index offset for Raupach92 parameterization (-) + real(r8), allocatable :: z0v_LAImax (:) ! onset of over-sheltering for Raupach92 parameterization (-) real(r8), allocatable :: displar (:) ! ratio of displacement height to canopy top height (-) real(r8), allocatable :: roota_par (:) ! CLM rooting distribution parameter [1/m] real(r8), allocatable :: rootb_par (:) ! CLM rooting distribution parameter [1/m] @@ -359,7 +365,13 @@ subroutine InitAllocate (this) allocate( this%taul (0:mxpft,numrad) ) allocate( this%taus (0:mxpft,numrad) ) allocate( this%z0mr (0:mxpft) ) - allocate( this%z0v_h (0:mxpft) ) + allocate( this%z0v_h (0:mxpft) ) + allocate( this%z0v_Cr (0:mxpft) ) + allocate( this%z0v_Cs (0:mxpft) ) + allocate( this%z0v_c (0:mxpft) ) + allocate( this%z0v_cw (0:mxpft) ) + allocate( this%z0v_LAIoff (0:mxpft) ) + allocate( this%z0v_LAImax (0:mxpft) ) allocate( this%z0v_alpha (0:mxpft) ) allocate( this%displar (0:mxpft) ) allocate( this%roota_par (0:mxpft) ) @@ -501,7 +513,7 @@ subroutine InitRead(this) use fileutils , only : getfil use ncdio_pio , only : ncd_io, ncd_pio_closefile, ncd_pio_openfile, file_desc_t use ncdio_pio , only : ncd_inqdid, ncd_inqdlen - use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, use_z0v_forest + use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, use_z0v_forest, z0param_method use spmdMod , only : masterproc use CLMFatesParamInterfaceMod, only : FatesReadPFTs ! @@ -631,9 +643,6 @@ subroutine InitRead(this) call ncd_io('pftname',pftname, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - call ncd_io('z0mr', this%z0mr, 'read', ncid, readvar=readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - ! ! Use new vegetation surface roughness parameterization for forests ! @@ -649,6 +658,46 @@ subroutine InitRead(this) this%z0v_alpha = 0._r8 end if + select case (z0param_method) + case ('ZengWang2007') + call ncd_io('z0mr', this%z0mr, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + this%z0v_Cr = 0._r8 + this%z0v_Cs = 0._r8 + this%z0v_c = 0._r8 + this%z0v_cw = 0._r8 + this%z0v_LAImax = 0._r8 + this%z0v_LAIoff = 0._r8 + + case ('MeierXXXX') + call ncd_io('z0v_Cr', this%z0v_Cr, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + call ncd_io('z0v_Cs', this%z0v_Cs, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + call ncd_io('z0v_c', this%z0v_c, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + call ncd_io('z0v_cw', this%z0v_cw, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + call ncd_io('z0v_LAImax', this%z0v_LAImax, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + call ncd_io('z0v_LAIoff', this%z0v_LAIoff, 'read', ncid, readvar=readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + + this%z0mr = 0._r8 + + case default + write(iulog,*) subname//' ERROR: unknown z0param_method: ', & + z0param_method + call endrun(msg = 'unknown z0param_method', & + additional_msg = errMsg(sourcefile, __LINE__)) + end select + + call ncd_io('displar', this%displar, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) @@ -1369,6 +1418,12 @@ subroutine Clean(this) deallocate( this%taus) deallocate( this%z0mr) deallocate( this%z0v_h) + deallocate( this%z0v_Cr) + deallocate( this%z0v_Cs) + deallocate( this%z0v_c) + deallocate( this%z0v_cw) + deallocate( this%z0v_LAImax) + deallocate( this%z0v_LAIoff) deallocate( this%z0v_alpha) deallocate( this%displar) deallocate( this%roota_par) From def8ee3d799343fc373dbb5cd98da854c3f14508 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Mon, 17 May 2021 09:41:22 +0200 Subject: [PATCH 0018/2067] Saving state --- src/biogeophys/BareGroundFluxesMod.F90 | 23 ++++++++---- src/biogeophys/CanopyFluxesMod.F90 | 12 +++--- src/biogeophys/FrictionVelocityMod.F90 | 45 +++++++++++++++++++++-- src/biogeophys/LakeFluxesMod.F90 | 51 +++++++++++++++++++------- 4 files changed, 101 insertions(+), 30 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 45015b8861..4ad975a1c1 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -81,7 +81,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & use shr_const_mod , only : SHR_CONST_RGAS use clm_varpar , only : nlevgrnd use clm_varcon , only : cpair, vkc, grav, denice, denh2o - use clm_varctl , only : use_lch4 + use clm_varctl , only : use_lch4, z0param_method use landunit_varcon , only : istsoil, istcrop use QSatMod , only : QSat use SurfaceResistanceMod , only : do_soilevap_beta,do_soil_resistance_sl14 @@ -137,9 +137,6 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & real(r8) :: raih ! temporary variable [kg/m2/s] real(r8) :: raiw ! temporary variable [kg/m2/s] real(r8) :: fm(bounds%begp:bounds%endp) ! needed for BGC only to diagnose 10m wind speed - real(r8) :: z0mg_patch(bounds%begp:bounds%endp) - real(r8) :: z0hg_patch(bounds%begp:bounds%endp) - real(r8) :: z0qg_patch(bounds%begp:bounds%endp) real(r8) :: e_ref2m ! 2 m height surface saturated vapor pressure [Pa] real(r8) :: qsat_ref2m ! 2 m height surface saturated specific humidity [kg/kg] real(r8) :: www ! surface soil wetness [-] @@ -240,6 +237,10 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & z0mg_col => frictionvel_inst%z0mg_col , & ! Output: [real(r8) (:) ] roughness length, momentum [m] z0hg_col => frictionvel_inst%z0hg_col , & ! Output: [real(r8) (:) ] roughness length, sensible heat [m] z0qg_col => frictionvel_inst%z0qg_col , & ! Output: [real(r8) (:) ] roughness length, latent heat [m] + z0mg_patch => frictionvel_inst%z0mg_patch , & ! Output: [real(r8) (:) ] patch roughness length, momentum [m] + z0hg_patch => frictionvel_inst%z0hg_patch , & ! Output: [real(r8) (:) ] patch roughness length, sensible heat [m] + z0qg_patch => frictionvel_inst%z0qg_patch , & ! Output: [real(r8) (:) ] patch roughness length, latent heat [m] + kbm1 => frictionvel_inst%kbm1_patch , & ! Output: [real(r8) (:) ] natural logarithm of z0mg_p/z0hg_p [-] ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) num_iter => frictionvel_inst%num_iter_patch , & ! Output: [real(r8) (:) ] number of iterations htvp => energyflux_inst%htvp_col , & ! Input: [real(r8) (:) ] latent heat of evaporation (/sublimation) [J/kg] @@ -329,9 +330,15 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & tstar = temp1(p)*dth(p) qstar = temp2(p)*dqh(p) - !z0hg_patch(p) = z0mg_patch(p) / exp(0.4_r8*0.52_r8 * (8._r8*z0mg_patch(p)*ustar(p) / 1.5e-5_r8)**0.45_r8 * 0.71_r8**0.8_r8) ! OT63 - z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Yang07 -!z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) + + select case (z0param_method) + case ('ZengWang2007') + z0mg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) + case ('MeierXXXX') + ! After Yang et al. (2007) + z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) + end select + z0qg_patch(p) = z0hg_patch(p) thvstar = tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar zeta = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) @@ -435,6 +442,8 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & t_ref2m_r(p) = t_ref2m(p) end if + kbm1(p) = log(z0mg_patch(p) / z0hg_patch(p)) + ! Human Heat Stress if ( all_human_stress_indices .or. fast_human_stress_indices ) then call KtoC(t_ref2m(p), tc_ref2m(p)) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index e83ac21d9c..803ed73d39 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -901,9 +901,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, case ('MeierXXXX') lt = max(0.00001_r8,elai(p)+esai(p)-z0v_LAIoff(patch%itype(p))) - if(elai(p)+esai(p) == 0._r8) then - write(iulog,*) 'VAI = 0 ', lt, (1._r8 - (1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) / (7.5_r8*lt)**0.5_r8),(1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) - end if displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) / (7.5_r8*lt)**0.5_r8) lt = min(lt,z0v_LAImax(patch%itype(p))) @@ -919,7 +916,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, end do U_ustar = 4._r8 * U_ustar / lt / z0v_c(patch%itype(p)) - z0mv(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & + z0mv(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-vkc * U_ustar + & log(z0v_cw(patch%itype(p))) - 1._r8 + z0v_cw(patch%itype(p))**(-1._r8)) case default @@ -1065,7 +1062,9 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! changed by K.Sakaguchi from here ! transfer coefficient over bare soil is changed to a local variable ! just for readability of the code (from line 680) + ! not sure if this needs to be changed with MeierXXXX too. csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / 1.5e-5_r8)**params_inst%a_exp) + !compute the stability parameter for ricsoilc ("S" in Sakaguchi&Zeng,2008) @@ -1463,9 +1462,10 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, dt_stem(p) = 0._r8 endif - dhsdt_canopy(p) = dt_stem(p)*cp_stem(p)/dtime & - +(t_veg(p)-tl_ini(p))*cp_leaf(p)/dtime + dhsdt_canopy(p) = dt_stem(p)*cp_stem(p)/dtime & + + (t_veg(p)-tl_ini(p))*cp_leaf(p)/dtime + t_stem(p) = t_stem(p) + dt_stem(p) else dt_stem(p) = 0._r8 diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 9829a70563..c22deee275 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -53,6 +53,10 @@ module FrictionVelocityMod real(r8), pointer, public :: z0mv_patch (:) ! patch roughness length over vegetation, momentum [m] real(r8), pointer, public :: z0hv_patch (:) ! patch roughness length over vegetation, sensible heat [m] real(r8), pointer, public :: z0qv_patch (:) ! patch roughness length over vegetation, latent heat [m] + real(r8), pointer, public :: z0mg_patch (:) ! patch roughness length over ground, momentum [m] + real(r8), pointer, public :: z0hg_patch (:) ! patch roughness length over ground, sensible heat [m] + real(r8), pointer, public :: z0qg_patch (:) ! patch roughness length over ground, latent heat [m] + real(r8), pointer, public :: kbm1_patch (:) ! natural logarithm of z0mg_p/z0hg_p [-] real(r8), pointer, public :: z0mg_col (:) ! col roughness length over ground, momentum [m] real(r8), pointer, public :: z0hg_col (:) ! col roughness length over ground, sensible heat [m] real(r8), pointer, public :: z0qg_col (:) ! col roughness length over ground, latent heat [m] @@ -150,6 +154,10 @@ subroutine InitAllocate(this, bounds) allocate(this%z0mv_patch (begp:endp)) ; this%z0mv_patch (:) = nan allocate(this%z0hv_patch (begp:endp)) ; this%z0hv_patch (:) = nan allocate(this%z0qv_patch (begp:endp)) ; this%z0qv_patch (:) = nan + allocate(this%z0mg_patch (begp:endp)) ; this%z0mg_patch (:) = nan + allocate(this%z0hg_patch (begp:endp)) ; this%z0hg_patch (:) = nan + allocate(this%z0qg_patch (begp:endp)) ; this%z0qg_patch (:) = nan + allocate(this%kbm1_patch (begp:endp)) ; this%kbm1_patch (:) = nan allocate(this%z0mg_col (begc:endc)) ; this%z0mg_col (:) = nan allocate(this%z0qg_col (begc:endc)) ; this%z0qg_col (:) = nan allocate(this%z0hg_col (begc:endc)) ; this%z0hg_col (:) = nan @@ -310,6 +318,26 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='roughness length over vegetation, latent heat', & ptr_patch=this%z0qv_patch, default='inactive') + this%z0hg_patch(begp:endp) = spval + call hist_addfld1d (fname='Z0HG_P', units='m', & + avgflag='A', long_name='patch roughness length over ground, sensible heat', & + ptr_patch=this%z0hg_patch, default='inactive') + + this%z0mg_patch(begp:endp) = spval + call hist_addfld1d (fname='Z0MG_P', units='m', & + avgflag='A', long_name='patch roughness length over ground, momentum', & + ptr_patch=this%z0mg_patch, default='inactive') + + this%z0qg_patch(begp:endp) = spval + call hist_addfld1d (fname='Z0QG_P', units='m', & + avgflag='A', long_name='patch roughness length over ground, latent heat', & + ptr_patch=this%z0qg_patch, default='inactive') + + this%kbm1_patch(begp:endp) = spval + call hist_addfld1d (fname='KBM1', units='unitless', & + avgflag='A', long_name='natural logarithm of Z0MG_P/Z0HG_P', & + ptr_patch=this%kbm1_patch, default='inactive') + if (use_luna) then call hist_addfld1d (fname='RB10', units='s/m', & avgflag='A', long_name='10 day running mean boundary layer resistance', & @@ -506,6 +534,10 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & z0mv => this%z0mv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, momentum [m] z0hv => this%z0hv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, sensible heat [m] z0qv => this%z0qv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, latent heat [m] + z0mg_p => this%z0mg_patch , & ! Output: [real(r8) (:) ] patch roughness length over ground, momentum [m] + z0hg_p => this%z0hg_patch , & ! Output: [real(r8) (:) ] patch roughness length over ground, sensible heat [m] + z0qg_p => this%z0qg_patch , & ! Output: [real(r8) (:) ] patch roughness length over ground, latent heat [m] + kbm1 => this%kbm1_patch , & ! Output: [real(r8) (:) ] natural logarithm of z0mg_p/z0hg_p [-] z0hg => this%z0hg_col , & ! Output: [real(r8) (:) ] roughness length over ground, sensible heat [m] z0mg => this%z0mg_col , & ! Output: [real(r8) (:) ] roughness length over ground, momentum [m] z0qg => this%z0qg_col , & ! Output: [real(r8) (:) ] roughness length over ground, latent heat [m] @@ -540,10 +572,10 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & end if case ('MeierXXXX') ! Bare ground and ice have a different value l = col%landunit(c) - if (lun%itype(l) == istice_mec) then - z0mg(c) = this%zglc - else if (frac_sno(c) > 0._r8) then + if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered z0mg(c) = this%zsno + else if (lun%itype(l) == istice_mec) then + z0mg(c) = this%zglc else z0mg(c) = this%zlnd end if @@ -560,6 +592,13 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & z0mv(p) = z0m(p) z0hv(p) = z0mv(p) z0qv(p) = z0mv(p) + + ! Set to arbitrary value (will be overwritten by respective modules + z0mg_p(p) = spval + z0hg_p(p) = spval + z0qg_p(p) = spval + kbm1(p) = spval + end do ! Make forcing height a patch-level quantity that is the atmospheric forcing diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 4f08e6c4c0..367e9eab40 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -125,6 +125,10 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, real(r8), pointer :: z0mg_col(:) ! roughness length over ground, momentum [m] real(r8), pointer :: z0hg_col(:) ! roughness length over ground, sensible heat [m] real(r8), pointer :: z0qg_col(:) ! roughness length over ground, latent heat [m] + real(r8), pointer :: z0mg(:) ! patch roughness length over ground, momentum [m] + real(r8), pointer :: z0hg(:) ! patch roughness length over ground, sensible heat [m] + real(r8), pointer :: z0qg(:) ! patch roughness length over ground, latent heat [m] + real(r8), pointer :: kbm1(:) ! natural logarithm of z0mg_p/z0hg_p [-] integer , parameter :: niters = 4 ! maximum number of iterations for surface temperature real(r8), parameter :: beta1 = 1._r8 ! coefficient of convective velocity (in computing W_*) [-] real(r8), parameter :: zii = 1000._r8 ! convective boundary height [m] @@ -169,9 +173,6 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, real(r8) :: zeta ! dimensionless height used in Monin-Obukhov theory real(r8) :: zldis(bounds%begp:bounds%endp) ! reference height "minus" zero displacement height [m] real(r8) :: displa(bounds%begp:bounds%endp) ! displacement (always zero) [m] - real(r8) :: z0mg(bounds%begp:bounds%endp) ! roughness length over ground, momentum [m] - real(r8) :: z0hg(bounds%begp:bounds%endp) ! roughness length over ground, sensible heat [m] - real(r8) :: z0qg(bounds%begp:bounds%endp) ! roughness length over ground, latent heat [m] real(r8) :: u2m ! 2 m wind speed (m/s) real(r8) :: fm(bounds%begp:bounds%endp) ! needed for BGC only to diagnose 10m wind speed real(r8) :: bw ! partial density of water (ice + liquid) @@ -277,7 +278,6 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, taux => energyflux_inst%taux_patch , & ! Output: [real(r8) (:) ] wind (shear) stress: e-w (kg/m/s**2) tauy => energyflux_inst%tauy_patch , & ! Output: [real(r8) (:) ] wind (shear) stress: n-s (kg/m/s**2) dhsdt_canopy => energyflux_inst%dhsdt_canopy_patch , & ! Output: [real(r8) (:) ] change in heat storage of stem (W/m**2) [+ to atm] - ks => lakestate_inst%ks_col , & ! Output: [real(r8) (:) ] coefficient passed to LakeTemperature ws => lakestate_inst%ws_col , & ! Output: [real(r8) (:) ] surface friction velocity (m/s) betaprime => lakestate_inst%betaprime_col , & ! Output: [real(r8) (:) ] fraction of solar rad absorbed at surface: equal to NIR fraction @@ -293,7 +293,10 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0mg_col => frictionvel_inst%z0mg_col z0hg_col => frictionvel_inst%z0hg_col z0qg_col => frictionvel_inst%z0qg_col - + z0mg => frictionvel_inst%z0mg_patch + z0hg => frictionvel_inst%z0hg_patch + z0qg => frictionvel_inst%z0qg_patch + kbm1 => frictionvel_inst%kbm1_patch kva0temp = 20._r8 + tfrz do fp = 1, num_lakep @@ -331,16 +334,23 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = max(z0qg(p), minz0lake) z0hg(p) = max(z0hg(p), minz0lake) else if (snl(c) == 0) then ! frozen lake with ice - if (z0param_method == 'MeierXXXX') then + select case (z0param_method) + case ('MeierXXXX') z0mg(p) = params_inst%zglc - else + z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + case ('ZengWang2007') z0mg(p) = z0frzlake - end if - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + end select z0qg(p) = z0hg(p) else ! use roughness over snow as in Biogeophysics1 z0mg(p) = params_inst%zsno - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + select case (z0param_method) + case ('MeierXXXX') + z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + case ('ZengWang2007') + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + end select z0qg(p) = z0hg(p) end if @@ -390,6 +400,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, g = patch%gridcell(p) dhsdt_canopy(p) = 0.0_r8 + nmozsgn(p) = 0 obuold(p) = 0._r8 displa(p) = 0._r8 @@ -556,12 +567,23 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0hg(p) = max(z0hg(p), minz0lake) else if (snl(c) == 0) then ! in case it was above freezing and now below freezing - z0mg(p) = z0frzlake - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes - z0qg(p) = z0hg(p) + select case (z0param_method) + case ('MeierXXXX') + z0mg(p) = params_inst%zglc + z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + case ('ZengWang2007') + z0mg(p) = z0frzlake + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + end select + z0qg(p) = z0hg(p) else ! Snow layers ! z0mg won't have changed - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + select case (z0param_method) + case ('MeierXXXX') + z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + case ('ZengWang2007') + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + end select z0qg(p) = z0hg(p) end if @@ -701,6 +723,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0hg_col(c) = z0hg(p) z0qg_col(c) = z0qg(p) ust_lake(c) = ustar(p) + kbm1(p) = log(z0mg(p) / z0hg(p)) end do From 4018d566436754b2fbb0d41945b348603f2c29af Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Wed, 26 May 2021 14:30:29 +0200 Subject: [PATCH 0019/2067] Saving state --- bld/CLMBuildNamelist.pm | 1 - bld/namelist_files/namelist_defaults_ctsm.xml | 3 --- src/biogeophys/BareGroundFluxesMod.F90 | 6 +++-- src/biogeophys/CanopyFluxesMod.F90 | 26 +++---------------- src/main/clm_varctl.F90 | 6 ----- src/main/controlMod.F90 | 2 -- src/main/pftconMod.F90 | 21 +-------------- 7 files changed, 9 insertions(+), 56 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 6f8e7c21f9..12e333ff0c 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3685,7 +3685,6 @@ sub setup_logic_canopyfluxes { if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) { $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on'); } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0v_forest' ); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index aa9b4ca3fc..edb3ffb780 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -319,9 +319,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 40 3 -.false. -.false. -.false. .true. diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 4ad975a1c1..7002c95f27 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -333,10 +333,12 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & select case (z0param_method) case ('ZengWang2007') - z0mg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) + z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) case ('MeierXXXX') ! After Yang et al. (2007) - z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) + z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) + ! After Owen and Thomson (1963) + z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp * 0.71_r8**0.8_r8) end select z0qg_patch(p) = z0hg_patch(p) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 803ed73d39..c0859e81cc 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -14,7 +14,7 @@ module CanopyFluxesMod use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use clm_varctl , only : iulog, use_cn, use_lch4, use_c13, use_c14, use_cndv, use_fates, & - use_luna, use_hydrstress, use_biomass_heat_storage, use_z0v_forest, z0param_method + use_luna, use_hydrstress, use_biomass_heat_storage, z0param_method use clm_varpar , only : nlevgrnd, nlevsno, mxpft use clm_varcon , only : namep use pftconMod , only : pftcon @@ -114,7 +114,7 @@ subroutine CanopyFluxesReadNML(NLFilename) namelist /canopyfluxes_inparm/ use_undercanopy_stability namelist /canopyfluxes_inparm/ use_biomass_heat_storage namelist /canopyfluxes_inparm/ itmax_canopy_fluxes - namelist /canopyfluxes_inparm/ use_z0v_forest + ! Initialize options to default values, in case they are not specified in ! the namelist @@ -144,7 +144,6 @@ subroutine CanopyFluxesReadNML(NLFilename) call shr_mpi_bcast (use_undercanopy_stability, mpicom) call shr_mpi_bcast (use_biomass_heat_storage, mpicom) call shr_mpi_bcast (itmax_canopy_fluxes, mpicom) - call shr_mpi_bcast (use_z0v_forest, mpicom) if (masterproc) then write(iulog,*) ' ' @@ -458,8 +457,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, woody => pftcon%woody , & ! Input: woody flag rstem_per_dbh => pftcon%rstem_per_dbh , & ! Input: stem resistance per stem diameter (s/m**2) wood_density => pftcon%wood_density , & ! Input: dry wood density (kg/m3) - z0v_h => pftcon%z0v_h , & ! Input: ratio of vegetation surface roughness length to canopy height for forests (-) - z0v_alpha => pftcon%z0v_alpha , & ! Input: alpha parameter for decrease of vegetation surface roughness with LAI for forests (-) + z0v_Cr => pftcon%z0v_Cr , & ! Input: roughness-element drag coefficient for Raupach92 parameterization (-) z0v_Cs => pftcon%z0v_Cs , & ! Input: substrate-element drag coefficient for Raupach92 parameterization (-) z0v_c => pftcon%z0v_c , & ! Input: c parameter for Raupach92 parameterization (-) @@ -875,23 +873,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, p = filterp(f) c = patch%column(p) - ! Keep old parametrization for grasses/crops and for forests if switch is off - -! if(woody(patch%itype(p))==0 .or. use_z0v_forest==.false.) then -! lt = min(elai(p)+esai(p), tlsai_crit) -! egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) -! displa(p) = egvf * displa(p) -! z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) -! -! else ! use new parameterization for forests -! egvf = z0v_alpha(patch%itype(p))*elai(p) -! if(egvf == 0._r8) then -! z0mv(p) = htop(p) * z0v_h(patch%itype(p)) -! else -! z0mv(p) = htop(p) * z0v_h(patch%itype(p)) * (1.0_r8 - exp(-egvf)) / egvf -! end if -! displa(p) = htop(p) - z0mv(p) / 0.264_r8 -! end if + select case (z0param_method) case ('ZengWang2007') lt = min(elai(p)+esai(p), tlsai_crit) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 2de40bacf8..e3983331fa 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -290,12 +290,6 @@ module clm_varctl logical, public :: use_biomass_heat_storage = .false. ! true => include biomass heat storage in canopy energy budget - !---------------------------------------------------------- - ! forest surface roughness length switch - !---------------------------------------------------------- - - logical, public :: use_z0v_forest = .false. ! true => use new surface roughness length parameterization for forests - !---------------------------------------------------------- ! each pft has individual soil column switch !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index e3a2eb470d..01bbccda2a 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -246,7 +246,6 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_biomass_heat_storage - namelist /clm_inparm/ use_z0v_forest namelist /clm_inparm/ use_individual_pft_soil_column @@ -749,7 +748,6 @@ subroutine control_spmd() call mpi_bcast (use_biomass_heat_storage, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_z0v_forest, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_individual_pft_soil_column, 1, MPI_LOGICAL, 0, mpicom, ier) diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index 8f05d08b79..d3ef07a547 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -121,8 +121,6 @@ module pftconMod real(r8), allocatable :: taul (:,:) ! leaf transmittance: 1=vis, 2=nir real(r8), allocatable :: taus (:,:) ! stem transmittance: 1=vis, 2=nir real(r8), allocatable :: z0mr (:) ! ratio of momentum roughness length to canopy top height (-) - real(r8), allocatable :: z0v_h (:) ! ratio of vegetation surface roughness length to canopy height for forests (-) - real(r8), allocatable :: z0v_alpha (:) ! alpha parameter for decrease of vegetation surface roughness with LAI for forests (-) real(r8), allocatable :: z0v_Cr (:) ! roughness-element drag coefficient for Raupach92 parameterization (-) real(r8), allocatable :: z0v_Cs (:) ! substrate-element drag coefficient for Raupach92 parameterization (-) real(r8), allocatable :: z0v_c (:) ! c parameter for Raupach92 parameterization (-) @@ -365,14 +363,12 @@ subroutine InitAllocate (this) allocate( this%taul (0:mxpft,numrad) ) allocate( this%taus (0:mxpft,numrad) ) allocate( this%z0mr (0:mxpft) ) - allocate( this%z0v_h (0:mxpft) ) allocate( this%z0v_Cr (0:mxpft) ) allocate( this%z0v_Cs (0:mxpft) ) allocate( this%z0v_c (0:mxpft) ) allocate( this%z0v_cw (0:mxpft) ) allocate( this%z0v_LAIoff (0:mxpft) ) allocate( this%z0v_LAImax (0:mxpft) ) - allocate( this%z0v_alpha (0:mxpft) ) allocate( this%displar (0:mxpft) ) allocate( this%roota_par (0:mxpft) ) allocate( this%rootb_par (0:mxpft) ) @@ -513,7 +509,7 @@ subroutine InitRead(this) use fileutils , only : getfil use ncdio_pio , only : ncd_io, ncd_pio_closefile, ncd_pio_openfile, file_desc_t use ncdio_pio , only : ncd_inqdid, ncd_inqdlen - use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, use_z0v_forest, z0param_method + use clm_varctl , only : paramfile, use_fates, use_flexibleCN, use_dynroot, use_biomass_heat_storage, z0param_method use spmdMod , only : masterproc use CLMFatesParamInterfaceMod, only : FatesReadPFTs ! @@ -643,20 +639,7 @@ subroutine InitRead(this) call ncd_io('pftname',pftname, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - ! - ! Use new vegetation surface roughness parameterization for forests - ! - if( use_z0v_forest) then - ! These will only be used for forest PFTs - call ncd_io('z0v_h', this%z0v_h, 'read', ncid, readvar=readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - call ncd_io('z0v_alpha', this%z0v_alpha, 'read', ncid, readvar=readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - else - this%z0v_h = 0._r8 - this%z0v_alpha = 0._r8 - end if select case (z0param_method) case ('ZengWang2007') @@ -1417,14 +1400,12 @@ subroutine Clean(this) deallocate( this%taul) deallocate( this%taus) deallocate( this%z0mr) - deallocate( this%z0v_h) deallocate( this%z0v_Cr) deallocate( this%z0v_Cs) deallocate( this%z0v_c) deallocate( this%z0v_cw) deallocate( this%z0v_LAImax) deallocate( this%z0v_LAIoff) - deallocate( this%z0v_alpha) deallocate( this%displar) deallocate( this%roota_par) deallocate( this%rootb_par) From 4a52aa7165996d90c34d28d8eb7ffb24a52826b8 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Mon, 14 Jun 2021 13:24:51 +0200 Subject: [PATCH 0020/2067] Saving state --- src/biogeophys/BareGroundFluxesMod.F90 | 5 ++++- src/biogeophys/FrictionVelocityMod.F90 | 2 ++ src/biogeophys/LakeFluxesMod.F90 | 14 +++++++++++--- 3 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 7002c95f27..9d265ec1a3 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -338,7 +338,10 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & ! After Yang et al. (2007) z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! After Owen and Thomson (1963) - z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp * 0.71_r8**0.8_r8) + !z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp * 0.71_r8**0.8_r8) + ! Zeng and Wang (2007) + !z0hg_patch(p) = z0hg_col(c) / exp(params_inst%a_coef * (ustar(p) * z0hg_col(c) / 1.5e-5_r8)**params_inst%a_exp) + end select z0qg_patch(p) = z0hg_patch(p) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index c22deee275..fcbea572bb 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -583,6 +583,8 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & z0hg(c) = z0mg(c) ! initial set only z0qg(c) = z0mg(c) ! initial set only + + end do do fp = 1,num_nolakep diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 367e9eab40..ec8d24ba11 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -337,7 +337,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0mg(p) = params_inst%zglc - z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only + case ('ZengWang2007') z0mg(p) = z0frzlake z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -348,6 +350,8 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only + case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select @@ -570,7 +574,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0mg(p) = params_inst%zglc - z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only + case ('ZengWang2007') z0mg(p) = z0frzlake z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -580,7 +586,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, ! z0mg won't have changed select case (z0param_method) case ('MeierXXXX') - z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only + case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select From e78b02fd2925209e6d8419d6ab9b2740a62d43ad Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Wed, 16 Jun 2021 14:35:23 +0200 Subject: [PATCH 0021/2067] Saving state --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 8 ++- src/biogeophys/FrictionVelocityMod.F90 | 75 ++++++++++++++++++-- src/biogeophys/SnowHydrologyMod.F90 | 15 ++-- src/biogeophys/SoilTemperatureMod.F90 | 2 + src/biogeophys/WaterFluxType.F90 | 24 +++++++ src/main/clm_driver.F90 | 2 +- 6 files changed, 114 insertions(+), 12 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 7a06bb0265..a665697b02 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -32,6 +32,8 @@ module BiogeophysPreFluxCalcsMod use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type use WaterStateBulkType , only : waterstatebulk_type use SurfaceResistanceMod , only : calc_soilevap_resis + use WaterFluxBulkType , only : waterfluxbulk_type + ! ! !PUBLIC TYPES: implicit none @@ -57,7 +59,7 @@ subroutine BiogeophysPreFluxCalcs(bounds, & num_urbanc, filter_urbanc, & clm_fates, atm2lnd_inst, canopystate_inst, energyflux_inst, frictionvel_inst, & soilstate_inst, temperature_inst, & - wateratm2lndbulk_inst, waterdiagnosticbulk_inst, waterstatebulk_inst) + wateratm2lndbulk_inst, waterdiagnosticbulk_inst, waterstatebulk_inst, waterfluxbulk_inst) ! ! !DESCRIPTION: ! Do various calculations that need to happen before the main biogeophysics flux calculations @@ -80,6 +82,7 @@ subroutine BiogeophysPreFluxCalcs(bounds, & type(wateratm2lndbulk_type) , intent(in) :: wateratm2lndbulk_inst type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst + type(waterfluxbulk_type) , intent(in) :: waterfluxbulk_inst ! ! !LOCAL VARIABLES: integer :: fp, p @@ -93,7 +96,8 @@ subroutine BiogeophysPreFluxCalcs(bounds, & call frictionvel_inst%SetRoughnessLengthsAndForcHeightsNonLake(bounds, & num_nolakec, filter_nolakec, & num_nolakep, filter_nolakep, & - atm2lnd_inst, waterdiagnosticbulk_inst, canopystate_inst) + atm2lnd_inst, waterdiagnosticbulk_inst, canopystate_inst, & + waterfluxbulk_inst) call CalcInitialTemperatureAndEnergyVars(bounds, & num_nolakec, filter_nolakec, & diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index fcbea572bb..2d3d746bba 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -22,6 +22,7 @@ module FrictionVelocityMod use atm2lndType , only : atm2lnd_type use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type use CanopyStateType , only : canopystate_type + use WaterFluxBulkType , only : waterfluxbulk_type ! ! !PUBLIC TYPES: implicit none @@ -57,7 +58,8 @@ module FrictionVelocityMod real(r8), pointer, public :: z0hg_patch (:) ! patch roughness length over ground, sensible heat [m] real(r8), pointer, public :: z0qg_patch (:) ! patch roughness length over ground, latent heat [m] real(r8), pointer, public :: kbm1_patch (:) ! natural logarithm of z0mg_p/z0hg_p [-] - real(r8), pointer, public :: z0mg_col (:) ! col roughness length over ground, momentum [m] + real(r8), pointer, public :: z0mg_col (:) ! col roughness length over ground, momentum [m] + real(r8), pointer, public :: z0mg_2D_col (:) ! 2-D field of input col roughness length over ground, momentum [m] real(r8), pointer, public :: z0hg_col (:) ! col roughness length over ground, sensible heat [m] real(r8), pointer, public :: z0qg_col (:) ! col roughness length over ground, latent heat [m] ! variables to add history output from CanopyFluxesMod @@ -92,6 +94,7 @@ module FrictionVelocityMod procedure, private :: InitCold procedure, private :: ReadNamelist procedure, private :: ReadParams + procedure, private :: ReadZ0M procedure, private, nopass :: StabilityFunc1 ! Stability function for rib < 0. procedure, private, nopass :: StabilityFunc2 ! Stability function for rib < 0. @@ -117,6 +120,10 @@ subroutine Init(this, bounds, NLFilename, params_ncid) call this%ReadNamelist(NLFilename) call this%ReadParams(params_ncid) + if(z0param_method == "MeierXXXX") then + call this%ReadZ0M(bounds) + end if + end subroutine Init !------------------------------------------------------------------------ @@ -159,6 +166,7 @@ subroutine InitAllocate(this, bounds) allocate(this%z0qg_patch (begp:endp)) ; this%z0qg_patch (:) = nan allocate(this%kbm1_patch (begp:endp)) ; this%kbm1_patch (:) = nan allocate(this%z0mg_col (begc:endc)) ; this%z0mg_col (:) = nan + allocate(this%z0mg_2D_col (begc:endc)) ; this%z0mg_2D_col (:) = nan allocate(this%z0qg_col (begc:endc)) ; this%z0qg_col (:) = nan allocate(this%z0hg_col (begc:endc)) ; this%z0hg_col (:) = nan allocate(this%rah1_patch (begp:endp)) ; this%rah1_patch (:) = nan @@ -405,6 +413,59 @@ subroutine ReadParams( this, params_ncid ) end subroutine ReadParams + !----------------------------------------------------------------------- + subroutine ReadZ0M(this, bounds) + ! + ! !DESCRIPTION: + ! Initialize module time constant variables + ! + ! !USES: + use shr_log_mod, only : errMsg => shr_log_errMsg + use fileutils , only : getfil + use abortutils , only : endrun + use ncdio_pio , only : file_desc_t, ncd_defvar, ncd_io, ncd_pio_openfile, ncd_pio_closefile + use spmdMod , only : masterproc + use clm_varcon , only : grlnd + use clm_varctl , only : fsurdat + use ncdio_pio , only : ncd_io + use clm_varctl , only : iulog + + ! + ! !ARGUMENTS: + class(frictionvel_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: c,g ! indices + type(file_desc_t) :: ncid ! netcdf id + character(len=256) :: locfn ! local filename + integer :: ier ! error status + logical :: readvar + real(r8), pointer :: z0mg2d (:) ! read in - ground z0m + !--------------------------------------------------------------------- + + ! Allocate module variable for ground z0m + + + call getfil (fsurdat, locfn, 0) + call ncd_pio_openfile (ncid, locfn, 0) + + + allocate(z0mg2d(bounds%begg:bounds%endg)) + call ncd_io(ncid=ncid, varname='Z0MG_2D', flag='read', data=z0mg2d, dim1name=grlnd, readvar=readvar) + if (.not. readvar) then + call endrun(msg=' ERROR: Z0MG_presc NOT on surfdata file'//errMsg(sourcefile, __LINE__)) + end if + write(iulog,*) 'Writing z0mg2d' + do c = bounds%begc, bounds%endc + g = col%gridcell(c) + this%z0mg_2D_col(c) = z0mg2d(g) + write(iulog,*) z0mg2d(g) + end do + deallocate(z0mg2d) + + end subroutine ReadZ0M + !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag) ! @@ -506,7 +567,7 @@ end subroutine ReadNamelist !----------------------------------------------------------------------- subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & num_nolakec, filter_nolakec, num_nolakep, filter_nolakep, & - atm2lnd_inst, waterdiagnosticbulk_inst, canopystate_inst) + atm2lnd_inst, waterdiagnosticbulk_inst, canopystate_inst, waterfluxbulk_inst) ! ! !DESCRIPTION: ! Set roughness lengths and forcing heights for non-lake points @@ -521,6 +582,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst type(canopystate_type) , intent(in) :: canopystate_inst + type(waterfluxbulk_type) , intent(in) :: waterfluxbulk_inst ! ! !LOCAL VARIABLES: integer :: fc, c @@ -549,12 +611,15 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & frac_veg_nosno => canopystate_inst%frac_veg_nosno_patch , & ! Input: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-] frac_sno => waterdiagnosticbulk_inst%frac_sno_col , & ! Input: [real(r8) (:) ] fraction of ground covered by snow (0 to 1) + snomelt_accum => waterfluxbulk_inst%qflx_snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) urbpoi => lun%urbpoi , & ! Input: [logical (:) ] true => landunit is an urban point z_0_town => lun%z_0_town , & ! Input: [real(r8) (:) ] momentum roughness length of urban landunit (m) z_d_town => lun%z_d_town , & ! Input: [real(r8) (:) ] displacement height of urban landunit (m) forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] - forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc & ! Input: [real(r8) (:) ] observational height of specific humidity [m] + forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] + z0mg_2D => this%z0mg_2D_col & ! Input: [real(r8) (:) ] 2-D field of input col roughness length over ground, momentum [m] + ) do fc = 1, num_nolakec @@ -573,11 +638,11 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & case ('MeierXXXX') ! Bare ground and ice have a different value l = col%landunit(c) if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered - z0mg(c) = this%zsno + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 !this%zsno else if (lun%itype(l) == istice_mec) then z0mg(c) = this%zglc else - z0mg(c) = this%zlnd + z0mg(c) = this%zlnd !z0mg_2D(c) end if end select diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 index 8d1824a70c..ffe17672cb 100644 --- a/src/biogeophys/SnowHydrologyMod.F90 +++ b/src/biogeophys/SnowHydrologyMod.F90 @@ -370,7 +370,8 @@ subroutine UpdateQuantitiesForNewSnow(bounds, num_c, filter_c, & swe_old = b_waterdiagnostic_inst%swe_old_col(begc:endc,:), & frac_sno = b_waterdiagnostic_inst%frac_sno_col(begc:endc), & frac_sno_eff = b_waterdiagnostic_inst%frac_sno_eff_col(begc:endc), & - snow_depth = b_waterdiagnostic_inst%snow_depth_col(begc:endc)) + snow_depth = b_waterdiagnostic_inst%snow_depth_col(begc:endc), & + qflx_snomelt_accum = b_waterflux_inst%qflx_snomelt_accum_col(begc:endc)) do i = water_inst%bulk_and_tracers_beg, water_inst%bulk_and_tracers_end associate(w => water_inst%bulk_and_tracers(i)) @@ -394,7 +395,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & scf_method, & dtime, lun_itype_col, urbpoi, snl, bifall, h2osno_total, h2osoi_ice, h2osoi_liq, & qflx_snow_grnd, qflx_snow_drain, & - dz, int_snow, swe_old, frac_sno, frac_sno_eff, snow_depth) + dz, int_snow, swe_old, frac_sno, frac_sno_eff, snow_depth, qflx_snomelt_accum) ! ! !DESCRIPTION: ! Update various snow-related diagnostic quantities to account for new snow @@ -421,6 +422,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & real(r8) , intent(inout) :: frac_sno( bounds%begc: ) ! fraction of ground covered by snow (0 to 1) real(r8) , intent(inout) :: frac_sno_eff( bounds%begc: ) ! eff. fraction of ground covered by snow (0 to 1) real(r8) , intent(inout) :: snow_depth( bounds%begc: ) ! snow height (m) + real(r8) , intent(inout) :: qflx_snomelt_accum( bounds%begc:) ! accumulated col snow melt for z0m calculation (m H2O) ! ! !LOCAL VARIABLES: integer :: fc, c @@ -521,6 +523,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & if (snl(c) < 0) then dz_snowf = (snow_depth(c) - temp_snow_depth(c)) / dtime dz(c,snl(c)+1) = dz(c,snl(c)+1)+dz_snowf*dtime + qflx_snomelt_accum(c) = max(0._r8, qflx_snomelt_accum(c) - dz_snowf*dtime/1000._r8) end if end do @@ -791,7 +794,9 @@ subroutine InitializeExplicitSnowPack(bounds, num_c, filter_c, & ! Outputs h2osno_no_layers = w%waterstate_inst%h2osno_no_layers_col(begc:endc), & h2osoi_ice = w%waterstate_inst%h2osoi_ice_col(begc:endc,:), & - h2osoi_liq = w%waterstate_inst%h2osoi_liq_col(begc:endc,:)) + h2osoi_liq = w%waterstate_inst%h2osoi_liq_col(begc:endc,:), & + qflx_snomelt_accum = b_waterflux_inst%qflx_snomelt_accum_col(begc:endc)) + end associate end do @@ -883,7 +888,7 @@ end subroutine BuildFilter_SnowpackInitialized !----------------------------------------------------------------------- subroutine UpdateState_InitializeSnowPack(bounds, snowpack_initialized_filterc, & - h2osno_no_layers, h2osoi_ice, h2osoi_liq) + h2osno_no_layers, h2osoi_ice, h2osoi_liq, qflx_snomelt_accum) ! ! !DESCRIPTION: ! For bulk or one tracer: initialize water state variables for columns in which an @@ -896,6 +901,7 @@ subroutine UpdateState_InitializeSnowPack(bounds, snowpack_initialized_filterc, real(r8) , intent(inout) :: h2osno_no_layers( bounds%begc: ) ! snow that is not resolved into layers (kg/m2) real(r8) , intent(inout) :: h2osoi_ice( bounds%begc: , -nlevsno+1: ) ! ice lens (kg/m2) real(r8) , intent(inout) :: h2osoi_liq( bounds%begc: , -nlevsno+1: ) ! liquid water (kg/m2) + real(r8) , intent(inout) :: qflx_snomelt_accum( bounds%begc:) ! accumulated col snow melt for z0m calculation (m H2O) ! ! !LOCAL VARIABLES: integer :: fc, c @@ -913,6 +919,7 @@ subroutine UpdateState_InitializeSnowPack(bounds, snowpack_initialized_filterc, h2osoi_ice(c,0) = h2osno_no_layers(c) h2osoi_liq(c,0) = 0._r8 h2osno_no_layers(c) = 0._r8 + qflx_snomelt_accum(c) = 0._r8 end do end subroutine UpdateState_InitializeSnowPack diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index e8a6b0ef68..9137e8b3d8 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1114,6 +1114,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] qflx_snofrz => waterfluxbulk_inst%qflx_snofrz_col , & ! Output: [real(r8) (:) ] column-integrated snow freezing rate (positive definite) [kg m-2 s-1] qflx_snomelt => waterfluxbulk_inst%qflx_snomelt_col , & ! Output: [real(r8) (:) ] snow melt (mm H2O /s) + qflx_snomelt_accum => waterfluxbulk_inst%qflx_snomelt_accum_col , & ! Output: [real(r8) (:) ] accumulated snow melt (m) qflx_snomelt_lyr => waterfluxbulk_inst%qflx_snomelt_lyr_col , & ! Output: [real(r8) (:) ] snow melt in each layer (mm H2O /s) eflx_snomelt => energyflux_inst%eflx_snomelt_col , & ! Output: [real(r8) (:) ] snow melt heat flux (W/m**2) @@ -1381,6 +1382,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) + qflx_snomelt_accum(c) = qflx_snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime/1000._r8 endif ! layer freezing mass flux (positive): diff --git a/src/biogeophys/WaterFluxType.F90 b/src/biogeophys/WaterFluxType.F90 index a2d57c1e51..c758b5b087 100644 --- a/src/biogeophys/WaterFluxType.F90 +++ b/src/biogeophys/WaterFluxType.F90 @@ -77,6 +77,7 @@ module WaterFluxType real(r8), pointer :: qflx_floodc_col (:) ! col flood water flux at column level real(r8), pointer :: qflx_sl_top_soil_col (:) ! col liquid water + ice from layer above soil to top soil layer or sent to qflx_qrgwl (mm H2O/s) real(r8), pointer :: qflx_snomelt_col (:) ! col snow melt (mm H2O /s) + real(r8), pointer :: qflx_snomelt_accum_col (:) ! accumulated col snow melt for z0m calculation (m H2O) real(r8), pointer :: qflx_qrgwl_col (:) ! col qflx_surf at glaciers, wetlands, lakes real(r8), pointer :: qflx_runoff_col (:) ! col total runoff (qflx_drain+qflx_surf+qflx_qrgwl) (mm H2O /s) real(r8), pointer :: qflx_runoff_r_col (:) ! col Rural total runoff (qflx_drain+qflx_surf+qflx_qrgwl) (mm H2O /s) @@ -284,6 +285,9 @@ subroutine InitAllocate(this, bounds, tracer_vars) call AllocateVar1d(var = this%qflx_snomelt_col, name = 'qflx_snomelt_col', & container = tracer_vars, & bounds = bounds, subgrid_level = BOUNDS_SUBGRID_COLUMN) + call AllocateVar1d(var = this%qflx_snomelt_accum_col, name = 'qflx_snomelt_accum_col', & + container = tracer_vars, & + bounds = bounds, subgrid_level = BOUNDS_SUBGRID_COLUMN) call AllocateVar1d(var = this%qflx_snofrz_col, name = 'qflx_snofrz_col', & container = tracer_vars, & bounds = bounds, subgrid_level = BOUNDS_SUBGRID_COLUMN) @@ -545,6 +549,14 @@ subroutine InitHistory(this, bounds) long_name=this%info%lname('snow melt rate'), & ptr_col=this%qflx_snomelt_col, c2l_scale_type='urbanf') + this%qflx_snomelt_accum_col(begc:endc) = 0._r8 + call hist_addfld1d ( & ! Have this as an output variable for now to check + fname=this%info%fname('QSNOMELT_ACCUM'), & + units='m', & + avgflag='A', & + long_name=this%info%lname('accumulated snow melt for z0'), & + ptr_col=this%qflx_snomelt_accum_col, c2l_scale_type='urbanf') + call hist_addfld1d ( & fname=this%info%fname('QSNOMELT_ICE'), & units='mm/s', & @@ -896,6 +908,18 @@ subroutine Restart(this, bounds, ncid, flag) this%qflx_snow_drain_col(bounds%begc:bounds%endc) = 0._r8 endif + call restartvar(ncid=ncid, flag=flag, & + varname=this%info%fname('QSNOMELT_ACCUM'), & + xtype=ncd_double, & + dim1name='column', & + long_name=this%info%lname('accumulated snow melt for z0'), & + units='m', & + interpinic_flag='interp', readvar=readvar, data=this%qflx_snomelt_accum_col) + if (flag == 'read' .and. .not. readvar) then + ! initial run, not restart: initialize qflx_snow_drain to zero + this%qflx_snomelt_accum_col(bounds%begc:bounds%endc) = 0._r8 + endif + call this%qflx_liq_dynbal_dribbler%Restart(bounds, ncid, flag) call this%qflx_ice_dynbal_dribbler%Restart(bounds, ncid, flag) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 276dfbc467..9be5ad20d2 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -618,7 +618,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro atm2lnd_inst, canopystate_inst, energyflux_inst, frictionvel_inst, & soilstate_inst, temperature_inst, & water_inst%wateratm2lndbulk_inst, water_inst%waterdiagnosticbulk_inst, & - water_inst%waterstatebulk_inst) + water_inst%waterstatebulk_inst, water_inst%waterfluxbulk_inst) call ozone_inst%CalcOzoneStress(bounds_clump, filter(nc)%num_exposedvegp, filter(nc)%exposedvegp) From 37d7d0c4e72dd20b6f35607e33a5fcdb99014ac3 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Thu, 24 Jun 2021 17:21:26 +0200 Subject: [PATCH 0022/2067] Saving state --- bld/CLMBuildNamelist.pm | 6 ++++ bld/namelist_files/namelist_defaults_ctsm.xml | 10 ++++++ .../namelist_definition_ctsm.xml | 12 +++++++ src/biogeophys/FrictionVelocityMod.F90 | 35 ++++++++++++++----- src/biogeophys/LakeFluxesMod.F90 | 25 ++++++++++--- src/biogeophys/SnowHydrologyMod.F90 | 2 +- src/main/clm_varctl.F90 | 5 ++- src/main/controlMod.F90 | 4 ++- 8 files changed, 82 insertions(+), 17 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 12e333ff0c..fec367a514 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3900,6 +3900,12 @@ sub setup_logic_z0param { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method'); + + my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' )); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0m_snowmelt', + 'z0param_method'=>$z0param_method ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0mg_2d', + 'z0param_method'=>$z0param_method ); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index edb3ffb780..a6776abe33 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -491,6 +491,16 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ZengWang2007 +.true. +.false. +.false. + +.true. +.false. +.true. + + + diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 785b9447bf..a63f2317f8 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2733,6 +2733,18 @@ ZengWang2007: Zeng and Wang 2007 MeierXXXX: Meier et al. in prep. + +If FALSE use constant snow z0m +If TRUE use parameterization of snow z0m as a function of accumulated +snow melt of Brock et al. (2006) + + + +If FALSE use constant ground z0m +If TRUE use spatially explicit ground z0m from Prigent et al. (2005) + diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 2d3d746bba..413fed1134 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -12,7 +12,7 @@ module FrictionVelocityMod use shr_const_mod , only : SHR_CONST_PI use decompMod , only : bounds_type use clm_varcon , only : spval - use clm_varctl , only : use_cn, use_luna, z0param_method + use clm_varctl , only : use_cn, use_luna, z0param_method, use_z0mg_2d, use_z0m_snowmelt use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch @@ -119,8 +119,8 @@ subroutine Init(this, bounds, NLFilename, params_ncid) call this%InitCold(bounds) call this%ReadNamelist(NLFilename) call this%ReadParams(params_ncid) - - if(z0param_method == "MeierXXXX") then + + if(use_z0mg_2d) then call this%ReadZ0M(bounds) end if @@ -454,12 +454,12 @@ subroutine ReadZ0M(this, bounds) allocate(z0mg2d(bounds%begg:bounds%endg)) call ncd_io(ncid=ncid, varname='Z0MG_2D', flag='read', data=z0mg2d, dim1name=grlnd, readvar=readvar) if (.not. readvar) then - call endrun(msg=' ERROR: Z0MG_presc NOT on surfdata file'//errMsg(sourcefile, __LINE__)) + call endrun(msg=' ERROR: Z0MG_2D NOT on surfdata file'//errMsg(sourcefile, __LINE__)) end if write(iulog,*) 'Writing z0mg2d' do c = bounds%begc, bounds%endc g = col%gridcell(c) - this%z0mg_2D_col(c) = z0mg2d(g) + this%z0mg_2D_col(c) = max(1.e-4_r8,z0mg2d(g)) write(iulog,*) z0mg2d(g) end do deallocate(z0mg2d) @@ -631,18 +631,35 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & select case (z0param_method) case ('ZengWang2007') if (frac_sno(c) > 0._r8) then - z0mg(c) = this%zsno + if(use_z0m_snowmelt) then + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + else + z0mg(c) = this%zsno + end if else - z0mg(c) = this%zlnd + if(use_z0mg_2d) then + z0mg(c) = z0mg_2D(c) + else + z0mg(c) = this%zlnd + end if + end if case ('MeierXXXX') ! Bare ground and ice have a different value l = col%landunit(c) if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 !this%zsno + if(use_z0m_snowmelt) then + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + else + z0mg(c) = this%zsno + end if else if (lun%itype(l) == istice_mec) then z0mg(c) = this%zglc else - z0mg(c) = this%zlnd !z0mg_2D(c) + if(use_z0mg_2d) then + z0mg(c) = z0mg_2D(c) + else + z0mg(c) = this%zlnd + end if end if end select diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index ec8d24ba11..4963707b48 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -93,7 +93,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, use clm_varpar , only : nlevlak use clm_varcon , only : hvap, hsub, hfus, cpair, cpliq, tkwat, tkice, tkair use clm_varcon , only : sb, vkc, grav, denh2o, tfrz, spval - use clm_varctl , only : use_lch4, z0param_method + use clm_varctl , only : use_lch4, z0param_method, use_z0m_snowmelt use LakeCon , only : betavis, z0frzlake, tdmax, emg_lake use LakeCon , only : lake_use_old_fcrit_minz0 use LakeCon , only : minz0lake, cur0, cus, curm, fcrit @@ -227,7 +227,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, lakefetch => lakestate_inst%lakefetch_col , & ! Input: [real(r8) (:) ] lake fetch from surface data (m) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) + h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) + snomelt_accum => waterfluxbulk_inst%qflx_snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) + t_skin_patch => temperature_inst%t_skin_patch , & ! Output: [real(r8) (:) ] patch skin temperature (K) t_lake => temperature_inst%t_lake_col , & ! Input: [real(r8) (:,:) ] lake temperature (Kelvin) @@ -346,13 +348,22 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, end select z0qg(p) = z0hg(p) else ! use roughness over snow as in Biogeophysics1 - z0mg(p) = params_inst%zsno select case (z0param_method) case ('MeierXXXX') + if(use_z0m_snowmelt) then + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + else + z0mg(p) = params_inst%zsno + end if z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only case ('ZengWang2007') + if(use_z0m_snowmelt) then + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + else + z0mg(p) = params_inst%zsno + end if z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select z0qg(p) = z0hg(p) @@ -583,15 +594,19 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, end select z0qg(p) = z0hg(p) else ! Snow layers - ! z0mg won't have changed + if(use_z0m_snowmelt) then + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + end if + select case (z0param_method) - case ('MeierXXXX') + case ('MeierXXXX') z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select + z0qg(p) = z0hg(p) end if diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 index ffe17672cb..6cbb0e24ad 100644 --- a/src/biogeophys/SnowHydrologyMod.F90 +++ b/src/biogeophys/SnowHydrologyMod.F90 @@ -477,6 +477,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & ! all snow falls on ground, no snow on h2osfc (note that qflx_snow_h2osfc is ! currently set to 0 always in CanopyHydrologyMod) newsnow(c) = qflx_snow_grnd(c) * dtime + qflx_snomelt_accum(c) = max(0._r8, qflx_snomelt_accum(c) - newsnow(c)/1000._r8) ! update int_snow int_snow(c) = max(int_snow(c),h2osno_total(c)) !h2osno_total could be larger due to frost @@ -523,7 +524,6 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & if (snl(c) < 0) then dz_snowf = (snow_depth(c) - temp_snow_depth(c)) / dtime dz(c,snl(c)+1) = dz(c,snl(c)+1)+dz_snowf*dtime - qflx_snomelt_accum(c) = max(0._r8, qflx_snomelt_accum(c) - dz_snowf*dtime/1000._r8) end if end do diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index e3983331fa..4b3c5c9a65 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -221,7 +221,10 @@ module clm_varctl ! Surface roughness parameterization !---------------------------------------------------------- - character(len=64), public :: z0param_method + character(len=64), public :: z0param_method + logical, public :: use_z0m_snowmelt = .false. ! true => use snow z0m parameterization of Brock2006 + logical, public :: use_z0mg_2d = .false. ! true => use 2D ground z0m of Prigent2005 + !---------------------------------------------------------- ! FATES switches diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 01bbccda2a..ae1324ed7a 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -203,7 +203,7 @@ subroutine control_init(dtime) soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & - z0param_method + z0param_method, use_z0m_snowmelt, use_z0mg_2d ! vertical soil mixing variables namelist /clm_inparm/ & @@ -792,6 +792,8 @@ subroutine control_spmd() call mpi_bcast (use_subgrid_fluxes , 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snow_cover_fraction_method , len(snow_cover_fraction_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (z0param_method , len(z0param_method), MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (use_z0m_snowmelt, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_z0mg_2d, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (wrtdia, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (single_column,1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (scmlat, 1, MPI_REAL8,0, mpicom, ier) From d218ff56fe114d1ff2bb40f518b51ba09b7a4972 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Wed, 28 Jul 2021 09:37:07 +0200 Subject: [PATCH 0023/2067] Saving state --- src/biogeophys/FrictionVelocityMod.F90 | 4 ++-- src/biogeophys/LakeFluxesMod.F90 | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 413fed1134..55629c2efd 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -632,7 +632,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & case ('ZengWang2007') if (frac_sno(c) > 0._r8) then if(use_z0m_snowmelt) then - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 else z0mg(c) = this%zsno end if @@ -648,7 +648,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & l = col%landunit(c) if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 else z0mg(c) = this%zsno end if diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 4963707b48..d4d858e13e 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -351,7 +351,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') if(use_z0m_snowmelt) then - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 else z0mg(p) = params_inst%zsno end if @@ -360,7 +360,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('ZengWang2007') if(use_z0m_snowmelt) then - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 else z0mg(p) = params_inst%zsno end if @@ -595,7 +595,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = z0hg(p) else ! Snow layers if(use_z0m_snowmelt) then - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c)+0.23_r8)/0.08_r8))-0.31_r8)) / 1000._r8 + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if select case (z0param_method) From fc20d00db729fefc905c169265b35efb92eda7b5 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Wed, 25 Aug 2021 08:53:36 +0200 Subject: [PATCH 0024/2067] State at first submission --- src/biogeophys/BareGroundFluxesMod.F90 | 8 ++++-- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 4 +++ src/biogeophys/CanopyFluxesMod.F90 | 6 ++++ src/biogeophys/FrictionVelocityMod.F90 | 11 ++++++++ src/biogeophys/LakeFluxesMod.F90 | 29 ++++++++++++++++---- src/main/pftconMod.F90 | 4 +++ 6 files changed, 54 insertions(+), 8 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 9d265ec1a3..a89d66ea95 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -337,11 +337,13 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & case ('MeierXXXX') ! After Yang et al. (2007) z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) + ! After Owen and Thomson (1963) !z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp * 0.71_r8**0.8_r8) - ! Zeng and Wang (2007) - !z0hg_patch(p) = z0hg_col(c) / exp(params_inst%a_coef * (ustar(p) * z0hg_col(c) / 1.5e-5_r8)**params_inst%a_exp) - + + ! Zeng and Wang (2007) --> Use this for CLM-VEG and CLM-Z0M + !z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) + end select z0qg_patch(p) = z0hg_patch(p) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index a665697b02..01631eeabd 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -189,6 +189,10 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & end if + ! --> Use this for CLM-Ya08 + !z0m(p) = pftcon%z0mr(patch%itype(p)) * htop(p) + !displa(p) = pftcon%displar(patch%itype(p)) * htop(p) + end select end if diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index c0859e81cc..a13262bcc9 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -901,6 +901,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0mv(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-vkc * U_ustar + & log(z0v_cw(patch%itype(p))) - 1._r8 + z0v_cw(patch%itype(p))**(-1._r8)) + ! --> Use this for CLM-Ya08 + !lt = min(elai(p)+esai(p), tlsai_crit) + !egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) + !displa(p) = egvf * displa(p) + !z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) + case default write(iulog,*) 'ERROR: unknown z0para_method: ', z0param_method call endrun(msg = 'unknown z0param_method', additional_msg = errMsg(sourcefile, __LINE__)) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 55629c2efd..ce1c9c6c4b 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -651,14 +651,25 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 else z0mg(c) = this%zsno + + ! --> Use this for CLM-VEG and CLM-Ya08 + !z0mg(c) = 0.0024_r8 end if else if (lun%itype(l) == istice_mec) then z0mg(c) = this%zglc + + ! --> Use this for CLM-VEG and CLM-Ya08 + !z0mg(c) = 0.01_r8 + else if(use_z0mg_2d) then z0mg(c) = z0mg_2D(c) else z0mg(c) = this%zlnd + + ! --> Use this for CLM-VEG and CLM-Ya08 + !z0mg(c) = 0.01_r8 + end if end if end select diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index d4d858e13e..a2a58bcb0f 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -339,8 +339,14 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0mg(p) = params_inst%zglc + + ! --> Use this for CLM-VEG and CLM-Ya08 + !z0mg(p) = z0frzlake + z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only + + ! --> Use this for CLM-VEG and CLM-Z0M + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes case ('ZengWang2007') z0mg(p) = z0frzlake @@ -352,11 +358,16 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('MeierXXXX') if(use_z0m_snowmelt) then z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + + else z0mg(p) = params_inst%zsno + + ! --> Use this for CLM-VEG and CLM-Ya08 + !z0mg(p) = 0.0024_r8 + end if z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only case ('ZengWang2007') if(use_z0m_snowmelt) then @@ -585,9 +596,15 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0mg(p) = params_inst%zglc + + ! --> Use this for CLM-VEG and CLM-Ya08 + !z0mg(p) = z0frzlake + z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only - + + ! --> Use this for CLM-VEG and CLM-Z0M + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + case ('ZengWang2007') z0mg(p) = z0frzlake z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -601,7 +618,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! This is for z0 only + + ! --> Use this for CLM-VEG and CLM-Z0M + !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index d3ef07a547..aef781bf57 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -673,6 +673,10 @@ subroutine InitRead(this) this%z0mr = 0._r8 + ! --> Use this for CLM-Ya08 + !call ncd_io('z0mr', this%z0mr, 'read', ncid, readvar=readv, posNOTonfile=.true.) + !if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) + case default write(iulog,*) subname//' ERROR: unknown z0param_method: ', & z0param_method From 5185d1d2da047fca8556d5f29a7db49aba9c994d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Oct 2021 12:00:33 -0600 Subject: [PATCH 0025/2067] Added cropcalStreamMod (MCT only) and some calls. Also added variables to crop_type. Totally untested, including for compile. --- src/biogeochem/CropType.F90 | 16 ++ src/cpl/mct/cropcalStreamMod.F90 | 304 +++++++++++++++++++++++++++++++ src/main/clm_driver.F90 | 4 + src/main/clm_initializeMod.F90 | 7 + 4 files changed, 331 insertions(+) create mode 100644 src/cpl/mct/cropcalStreamMod.F90 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index afa2008f13..8364738d03 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -41,6 +41,13 @@ module CropType character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope + integer , pointer :: sdate_thisseason (:) ! patch sowing date for current (active) season + integer , pointer :: hdate_thisseason (:) ! patch harvest date for current (active) season + integer , pointer :: sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year + integer , pointer :: hdates_thisyr (:,:) ! all prescribed harvest dates for this patch this year + integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch + integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year + integer :: max_growingseasons_per_year ! maximum number of growing seasons per year allowed in any patch contains ! Public routines @@ -199,6 +206,15 @@ subroutine InitAllocate(this, bounds) allocate(this%vf_patch (begp:endp)) ; this%vf_patch (:) = 0.0_r8 allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval + allocate(this%sdate_thisseason(begp:endp)) ; this%sdate_thisseason(:) = -1 + allocate(this%hdate_thisseason(begp:endp)) ; this%hdate_thisseason(:) = -1 + allocate(this%sdates_thisyr(begp:endp,1:max_growingseasons_per_year)) + allocate(this%hdates_thisyr(begp:endp,1:max_growingseasons_per_year)) + allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 + allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 + + this%sdates_thisyr(:,:) = nan + this%hdates_thisyr(:,:) = nan end subroutine InitAllocate diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 new file mode 100644 index 0000000000..98c407cc72 --- /dev/null +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -0,0 +1,304 @@ +module cropcalStreamMod + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Read crop calendars from stream + ! + ! !USES: + use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create + use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance + use shr_kind_mod , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX + use shr_log_mod , only : errMsg => shr_log_errMsg + use decompMod , only : bounds_type + use abortutils , only : endrun + use clm_varctl , only : iulog, inst_name + use perf_mod , only : t_startf, t_stopf + use spmdMod , only : masterproc, mpicom, comp_id + use ncdio_pio + use mct_mod + ! + ! !PUBLIC TYPES: + implicit none + private + + ! !PUBLIC MEMBER FUNCTIONS: + public :: cropcal_init ! position datasets for crop calendars + public :: cropcal_advance ! Advance the crop calendar streams (outside of a Open-MP threading loop) + public :: cropcal_interp ! interpolates between two years of crop calendar data (when crop calendar streams + + ! !PRIVATE MEMBER DATA: + integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index + ! SSR TODO: Make these work with max_growingseasons_per_year > 1 + type(shr_strdata_type) :: sdat_sdate1 ! 1st sowing date input data stream + type(shr_strdata_type) :: sdat_hdate1 ! 1st harvest date input data stream + + character(len=*), parameter :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine cropcal_init(bounds, actual_numcft) + ! + ! Initialize data stream information for crop calendars. + ! + ! !USES: + use clm_time_manager , only : get_calendar + use ncdio_pio , only : pio_subsystem + use shr_pio_mod , only : shr_pio_getiotype + use shr_stream_mod , only : shr_stream_file_null + use shr_string_mod , only : shr_string_listCreateField + use clm_nlUtilsMod , only : find_nlgroup_name + use ndepStreamMod , only : clm_domain_mct + use histFileMod , only : hist_addfld1d + use domainMod , only : ldomain + use controlMod , only : NLFilename + use lnd_set_decomp_and_domain , only : gsmap_global + ! + ! !ARGUMENTS: + implicit none + type(bounds_type), intent(in) :: bounds ! bounds + integer, intent(in) :: actual_numcft ! number of crop types + ! + ! !LOCAL VARIABLES: + integer :: stream_year_first_cropcal ! first year in crop calendar streams to use + integer :: stream_year_last_cropcal ! last year in crop calendar streams to use + integer :: model_year_align_cropcal ! align stream_year_first_cropcal with + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + type(mct_ggrid) :: dom_clm ! domain information + character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read + character(len=CL) :: stream_fldFileName_hdate ! harvest date stream filename to read + character(len=CL) :: cropcal_mapalgo = 'nearest' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm + + ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates + character(len=CXX) :: fldList_hdate1 ! field string for 1st harvest dates + + character(*), parameter :: subName = "('cropcaldyn_init')" + !----------------------------------------------------------------------- + ! + ! deal with namelist variables here in init + ! + namelist /cropcal_streams/ & + stream_year_first_cropcal, & + stream_year_last_cropcal, & + model_year_align_cropcal, & + cropcal_mapalgo, & + stream_fldFileName_sdate, & + stream_fldFileName_hdate, & + cropcal_tintalgo + + ! Default values for namelist + stream_year_first_cropcal = 1 ! first year in stream to use + stream_year_last_cropcal = 1 ! last year in stream to use + model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year + stream_fldFileName_sdate = shr_stream_file_null + stream_fldFileName_hdate = shr_stream_file_null + + ! Read cropcal_streams namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'cropcal_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=cropcal_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(subname // ':: ERROR reading cropcal_streams namelist') + end if + else + call endrun(subname // ':: ERROR finding cropcal_streams namelist') + end if + close(nu_nml) + endif + call shr_mpi_bcast(stream_year_first_cropcal , mpicom) + call shr_mpi_bcast(stream_year_last_cropcal , mpicom) + call shr_mpi_bcast(model_year_align_cropcal , mpicom) + call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) + call shr_mpi_bcast(stream_fldFileName_hdate , mpicom) + call shr_mpi_bcast(cropcal_tintalgo , mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'cropcal_stream settings:' + write(iulog,*) ' stream_year_first_cropcal = ',stream_year_first_cropcal + write(iulog,*) ' stream_year_last_cropcal = ',stream_year_last_cropcal + write(iulog,*) ' model_year_align_cropcal = ',model_year_align_cropcal + write(iulog,*) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) + write(iulog,*) ' stream_fldFileName_hdate = ',trim(stream_fldFileName_hdate) + write(iulog,*) ' cropcal_tintalgo = ',trim(cropcal_tintalgo) + endif + + call clm_domain_mct (bounds, dom_clm) + + ! create the field list for these cropcal fields...use in shr_strdata_create + ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + fldList_sdate1 = shr_string_listCreateField( numCropcalFields, "sdate1" ) + fldList_hdate1 = shr_string_listCreateField( numCropcalFields, "hdate1" ) + + ! SSR TODO: + ! - Make these work with max_growingseasons_per_year > 1 + ! - Delete "area" and "mask"? + ! - Is this correct taxmode? + call shr_strdata_create(sdat_sdate1, & + name="cropcaldyn", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_cropcal, & + yearLast=stream_year_last_cropcal, & + yearAlign=model_year_align_cropcal, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_sdate), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/stream_fldFileName_sdate/), & + fldListFile=fldList, & + fldListModel=fldList, & + fillalgo='none', & + mapalgo=cropcal_mapalgo, & + tintalgo=cropcal_tintalgo, & + calendar=get_calendar(), & + taxmode='cycle' ) + + call shr_strdata_create(sdat_hdate1, & + name="cropcaldyn", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_cropcal, & + yearLast=stream_year_last_cropcal, & + yearAlign=model_year_align_cropcal, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_hdate), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/stream_fldFileName_hdate/), & + fldListFile=fldList, & + fldListModel=fldList, & + fillalgo='none', & + mapalgo=cropcal_mapalgo, & + tintalgo=cropcal_tintalgo, & + calendar=get_calendar(), & + taxmode='cycle' ) + + if (masterproc) then + call shr_strdata_print(sdat_sdate1,'sdate1 data') + call shr_strdata_print(sdat_hdate1,'hdate1 data') + endif + + end subroutine cropcal_init + + !============================================================================== + subroutine cropcal_advance( bounds ) + ! + ! Advance crop calendar streams + ! + ! !USES: + use clm_time_manager, only : get_curr_date + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g, ig ! Indices + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + + ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + call shr_strdata_advance(sdat_sdate1, mcdate, sec, mpicom, 'cropcaldyn') + call shr_strdata_advance(sdat_hdate1, mcdate, sec, mpicom, 'cropcaldyn') + + if ( .not. allocated(g_to_ig) )then + allocate (g_to_ig(bounds%begg:bounds%endg) ) + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + g_to_ig(g) = ig + end do + end if + + end subroutine cropcal_advance + + !============================================================================== + subroutine cropcal_interp(bounds, crop_inst) + ! + ! Interpolate data stream information for crop calendars. + ! + ! !USES: + use pftconMod , only : noveg + use CropType , only : crop_type + use PatchType , only : patch + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + type(crop_type) , intent(inout) :: crop_inst + ! + ! !LOCAL VARIABLES: + integer :: ivt, p, ip, ig + character(len=CL) :: stream_var_name + !----------------------------------------------------------------------- + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) + + ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + SHR_ASSERT_FL( (lbound(sdat_sdate1%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_sdate1%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(sdat_hdate1%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_hdate1%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + + ! SSR TODO: Make these work with max_growingseasons_per_year > 1 + do p = bounds%begp, bounds%endp + ivt = patch%itype(p) + ! Set crop calendars for each gridcell/patch combination + if (ivt /= noveg) then + ! vegetated pft + write(stream_var_name,"(i6)") ivt + + ! SSR TODO: Add check that variable exists in netCDF + stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) + ip = mct_aVect_indexRA(sdat_sdate1%avs(1),trim(stream_var_name)) + ig = g_to_ig(patch%gridcell(p)) + crop_inst%sdates_thisyr(p,1) = sdat_sdate1%avs(1)%rAttr(ip,ig) + + ! SSR TODO: Add check that variable exists in netCDF + stream_var_name = 'hdate1_'//trim(adjustl(stream_var_name)) + ip = mct_aVect_indexRA(sdat_hdate1%avs(1),trim(stream_var_name)) + ig = g_to_ig(patch%gridcell(p)) + crop_inst%hdates_thisyr(p,1) = sdat_hdate1%avs(1)%rAttr(ip,ig) + else + ! non-vegetated pft + crop_inst%sdates_thisyr(p,1) = -1 + crop_inst%hdates_thisyr(p,1) = -1 + endif + end do + + end subroutine cropcal_interp + +end module cropcalStreamMod diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index ce9b07321c..94fc879130 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -58,6 +58,7 @@ module clm_driver use SoilBiogeochemVerticalProfileMod , only : SoilBiogeochemVerticalProfile use SatellitePhenologyMod , only : SatellitePhenology, interpMonthlyVeg use ndepStreamMod , only : ndep_interp + use cropcalStreamMod , only : cropcal_advance use ch4Mod , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check use DUSTMod , only : DustDryDep, DustEmission use VOCEmissionMod , only : VOCEmission @@ -447,6 +448,9 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call lai_advance( bounds_proc ) endif + ! Advance crop calendar data + call cropcal_advance( bounds_proc ) + ! ============================================================================ ! Initialize variables from previous time step, downscale atm forcings, and ! Determine canopy interception and precipitation onto ground surface. diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 2d1890ea1e..752d19497a 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -148,6 +148,7 @@ subroutine initialize2(ni,nj) use restFileMod , only : restFile_getfile, restFile_open, restFile_close use restFileMod , only : restFile_read, restFile_write use ndepStreamMod , only : ndep_init, ndep_interp + use cropcalStreamMod , only : cropcal_init, cropcal_interp use LakeCon , only : LakeConInit use SatellitePhenologyMod , only : SatellitePhenologyInit, readAnnualVegetation, interpMonthlyVeg, SatellitePhenology use SnowSnicarMod , only : SnowAge_init, SnowOptics_init @@ -554,6 +555,12 @@ subroutine initialize2(ni,nj) call t_stopf('init_ndep') end if + ! Initialize crop calendars + call t_startf('init_cropcal') + call cropcal_init(bounds, actual_numcft) + call cropcal_interp(bounds_proc, crop_inst) + call t_stopf('init_cropcal') + ! Initialize active history fields. ! This is only done if not a restart run. If a restart run, then this ! information has already been obtained from the restart data read above. From b75b83d8f9bcdb694b94a43ba0c79e889ae0c51d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Oct 2021 12:44:54 -0600 Subject: [PATCH 0026/2067] Compile fixes in CropType.F90. --- src/biogeochem/CropType.F90 | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 8364738d03..3688a44351 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -196,6 +196,9 @@ subroutine InitAllocate(this, bounds) begp = bounds%begp; endp = bounds%endp + ! SSR TODO: Replace this with read from netCDF + this%max_growingseasons_per_year = 1 + allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0 allocate(this%croplive_patch (begp:endp)) ; this%croplive_patch (:) = .false. allocate(this%cropplant_patch(begp:endp)) ; this%cropplant_patch(:) = .false. @@ -208,13 +211,13 @@ subroutine InitAllocate(this, bounds) allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sdate_thisseason(begp:endp)) ; this%sdate_thisseason(:) = -1 allocate(this%hdate_thisseason(begp:endp)) ; this%hdate_thisseason(:) = -1 - allocate(this%sdates_thisyr(begp:endp,1:max_growingseasons_per_year)) - allocate(this%hdates_thisyr(begp:endp,1:max_growingseasons_per_year)) + allocate(this%sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) + allocate(this%hdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 - this%sdates_thisyr(:,:) = nan - this%hdates_thisyr(:,:) = nan + this%sdates_thisyr(:,:) = -1 + this%hdates_thisyr(:,:) = -1 end subroutine InitAllocate From 6e7effcd6f530acc0d1802531c2fd7f816d80ce9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Oct 2021 15:06:04 -0600 Subject: [PATCH 0027/2067] Added CropPhenology() logic for prescribed sowing dates. Totally untested, including for compile. --- src/biogeochem/CNPhenologyMod.F90 | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bd9a79b959..e3ea08076a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1689,6 +1689,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & real(r8) ndays_on ! number of days to fertilize logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? + logical do_plant_prescribed ! is today the prescribed sowing date? + logical sowing_is_prescribed ! is sowing date prescribed for this season? !------------------------------------------------------------------------ associate( & @@ -1720,6 +1722,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor + sdate_rx => crop_inst%sdate_thisseason , & ! Input: [integer (:) ] prescribed sowing date peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow @@ -1822,6 +1825,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! According to Chris Kucharik, the dataset of ! xinpdate was generated from a previous model run at 0.5 deg resolution + sowing_is_prescribed = sdate_rx(p) >= 0 + do_plant_prescribed = sdate_rx(p) == jday + ! winter temperate cereal : use gdd0 as a limit to plant winter cereal if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then @@ -1843,18 +1849,20 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! updated on Jan 1st instead of at harvest (slevis) ! Are all the normal requirements for planting met? - do_plant_normal = a5tmin(p) /= spval .and. & + do_plant_normal = (.not. sowing_is_prescribed) .and. & + a5tmin(p) /= spval .and. & a5tmin(p) <= minplanttemp(ivt(p)) .and. & jday >= minplantjday(ivt(p),h) .and. & (gdd020(p) /= spval .and. & gdd020(p) >= gddmin(ivt(p))) ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = (.not. do_plant_normal) .and. & + do_plant_lastchance = (.not. sowing_is_prescribed) .and. & + (.not. do_plant_normal) .and. & jday >= maxplantjday(ivt(p),h) .and. & gdd020(p) /= spval .and. & gdd020(p) >= gddmin(ivt(p)) - if (do_plant_normal .or. do_plant_lastchance) then + if (do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance) then cumvd(p) = 0._r8 hdidx(p) = 0._r8 @@ -1876,7 +1884,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! while the gdd part is either true or false for the year. ! Are all the normal requirements for planting met? - do_plant_normal = t10(p) /= spval .and. a10tmin(p) /= spval .and. & + do_plant_normal = (.not. sowing_is_prescribed) .and. & + t10(p) /= spval .and. a10tmin(p) /= spval .and. & t10(p) > planttemp(ivt(p)) .and. & a10tmin(p) > minplanttemp(ivt(p)) .and. & jday >= minplantjday(ivt(p),h) .and. & @@ -1884,12 +1893,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & gdd820(p) /= spval .and. & gdd820(p) >= gddmin(ivt(p)) ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = (.not. do_plant_normal) .and. & + do_plant_lastchance = (.not. sowing_is_prescribed) .and. & + (.not. do_plant_normal) .and. & jday == maxplantjday(ivt(p),h) .and. & gdd820(p) > 0._r8 .and. & gdd820(p) /= spval - if (do_plant_normal .or. do_plant_lastchance) then + if (do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance) then call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & From e56921d685528bf7ffddabad739048820dd525f2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Oct 2021 15:15:08 -0600 Subject: [PATCH 0028/2067] Added CropPhenology() logic for prescribed harvest dates. Totally untested, including for compile. --- src/biogeochem/CNPhenologyMod.F90 | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e3ea08076a..7c51be4b5d 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1691,6 +1691,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? logical sowing_is_prescribed ! is sowing date prescribed for this season? + logical harvest_is_prescribed ! is harvest date prescribed for this season? + logical do_harvest_prescribed ! is today the prescribed harvest date? !------------------------------------------------------------------------ associate( & @@ -1723,6 +1725,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor sdate_rx => crop_inst%sdate_thisseason , & ! Input: [integer (:) ] prescribed sowing date + hdate_rx => crop_inst%hdate_thisseason , & ! Input: [integer (:) ] prescribed harvest date peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow @@ -1827,6 +1830,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sowing_is_prescribed = sdate_rx(p) >= 0 do_plant_prescribed = sdate_rx(p) == jday + harvest_is_prescribed = hdate_rx(p) >= 0 + do_harvest_prescribed = hdate_rx(p) == jday ! winter temperate cereal : use gdd0 as a limit to plant winter cereal @@ -2055,7 +2060,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then + if ((.not. do_harvest_prescribed) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then cphase(p) = 2._r8 if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 @@ -2081,7 +2086,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! the onset_counter would change from dt and you'd need to make ! changes to the offset subroutine below - else if (hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p))) then + else if (do_harvest_prescribed .or. ((.not. harvest_is_prescribed) .and. hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p)))) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 From 29e1096fc200483c4b9456a439c0234e8eae539f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Oct 2021 15:53:10 -0600 Subject: [PATCH 0029/2067] Compile fixes. --- src/cpl/mct/cropcalStreamMod.F90 | 12 ++++++------ src/main/clm_initializeMod.F90 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 98c407cc72..f978977bd8 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -136,8 +136,8 @@ subroutine cropcal_init(bounds, actual_numcft) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - fldList_sdate1 = shr_string_listCreateField( numCropcalFields, "sdate1" ) - fldList_hdate1 = shr_string_listCreateField( numCropcalFields, "hdate1" ) + fldList_sdate1 = shr_string_listCreateField( actual_numcft, "sdate1" ) + fldList_hdate1 = shr_string_listCreateField( actual_numcft, "hdate1" ) ! SSR TODO: ! - Make these work with max_growingseasons_per_year > 1 @@ -163,8 +163,8 @@ subroutine cropcal_init(bounds, actual_numcft) domMaskName='mask', & filePath='', & filename=(/stream_fldFileName_sdate/), & - fldListFile=fldList, & - fldListModel=fldList, & + fldListFile=fldList_sdate1, & + fldListModel=fldList_sdate1, & fillalgo='none', & mapalgo=cropcal_mapalgo, & tintalgo=cropcal_tintalgo, & @@ -191,8 +191,8 @@ subroutine cropcal_init(bounds, actual_numcft) domMaskName='mask', & filePath='', & filename=(/stream_fldFileName_hdate/), & - fldListFile=fldList, & - fldListModel=fldList, & + fldListFile=fldList_hdate1, & + fldListModel=fldList_hdate1, & fillalgo='none', & mapalgo=cropcal_mapalgo, & tintalgo=cropcal_tintalgo, & diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 752d19497a..e8d2baff2a 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -557,7 +557,7 @@ subroutine initialize2(ni,nj) ! Initialize crop calendars call t_startf('init_cropcal') - call cropcal_init(bounds, actual_numcft) + call cropcal_init(bounds_proc, actual_numcft) call cropcal_interp(bounds_proc, crop_inst) call t_stopf('init_cropcal') From b637112e482845b9748aefbd9a90aa4beafd992e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Oct 2021 16:09:49 -0600 Subject: [PATCH 0030/2067] Correction: Number of crop calendar field names generated. --- src/cpl/mct/cropcalStreamMod.F90 | 8 ++++---- src/main/clm_initializeMod.F90 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index f978977bd8..9cb6663ab6 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -41,11 +41,12 @@ module cropcalStreamMod contains !============================================================================== - subroutine cropcal_init(bounds, actual_numcft) + subroutine cropcal_init(bounds) ! ! Initialize data stream information for crop calendars. ! ! !USES: + use clm_varpar , only : mxpft use clm_time_manager , only : get_calendar use ncdio_pio , only : pio_subsystem use shr_pio_mod , only : shr_pio_getiotype @@ -61,7 +62,6 @@ subroutine cropcal_init(bounds, actual_numcft) ! !ARGUMENTS: implicit none type(bounds_type), intent(in) :: bounds ! bounds - integer, intent(in) :: actual_numcft ! number of crop types ! ! !LOCAL VARIABLES: integer :: stream_year_first_cropcal ! first year in crop calendar streams to use @@ -136,8 +136,8 @@ subroutine cropcal_init(bounds, actual_numcft) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - fldList_sdate1 = shr_string_listCreateField( actual_numcft, "sdate1" ) - fldList_hdate1 = shr_string_listCreateField( actual_numcft, "hdate1" ) + fldList_sdate1 = shr_string_listCreateField( mxpft, "sdate1" ) + fldList_hdate1 = shr_string_listCreateField( mxpft, "hdate1" ) ! SSR TODO: ! - Make these work with max_growingseasons_per_year > 1 diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index e8d2baff2a..bde8cd3d47 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -557,7 +557,7 @@ subroutine initialize2(ni,nj) ! Initialize crop calendars call t_startf('init_cropcal') - call cropcal_init(bounds_proc, actual_numcft) + call cropcal_init(bounds_proc) call cropcal_interp(bounds_proc, crop_inst) call t_stopf('init_cropcal') From 01f29d7f061e7fdcda6e57d2483d4ba5b0508e5f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 12 Oct 2021 16:29:27 -0600 Subject: [PATCH 0031/2067] Added boolean namelist variable use_cropcal_streams. --- src/main/clm_initializeMod.F90 | 11 +++++++---- src/main/clm_varctl.F90 | 6 ++++++ src/main/controlMod.F90 | 4 ++++ 3 files changed, 17 insertions(+), 4 deletions(-) diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index bde8cd3d47..59280b5672 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -121,6 +121,7 @@ subroutine initialize2(ni,nj) use clm_varctl , only : use_cn, use_fates use clm_varctl , only : use_crop, ndep_from_cpl, fates_spitfire_mode use clm_varorb , only : eccen, mvelpp, lambm0, obliqr + use clm_varctl , only : use_cropcal_streams use landunit_varcon , only : landunit_varcon_init, max_lunit use pftconMod , only : pftcon use decompInitMod , only : decompInit_clumps, decompInit_glcp @@ -556,10 +557,12 @@ subroutine initialize2(ni,nj) end if ! Initialize crop calendars - call t_startf('init_cropcal') - call cropcal_init(bounds_proc) - call cropcal_interp(bounds_proc, crop_inst) - call t_stopf('init_cropcal') + if (use_cropcal_streams) then + call t_startf('init_cropcal') + call cropcal_init(bounds_proc) + call cropcal_interp(bounds_proc, crop_inst) + call t_stopf('init_cropcal') + end if ! Initialize active history fields. ! This is only done if not a restart run. If a restart run, then this diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 3ad4b14bef..885f88a893 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -283,6 +283,12 @@ module clm_varctl logical, public :: use_lai_streams = .false. ! true => use lai streams in SatellitePhenologyMod.F90 + !---------------------------------------------------------- + ! crop calendar streams switch for CropPhenology + !---------------------------------------------------------- + + logical, public :: use_cropcal_streams = .false. ! true => read crop calendar streams for use in CropPhenology.F90 + !---------------------------------------------------------- ! biomass heat storage switch !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 082d68e8eb..63fdc8c63e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -244,6 +244,8 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_lai_streams + namelist /clm_inparm/ use_cropcal_streams + namelist /clm_inparm/ use_bedrock namelist /clm_inparm/ use_biomass_heat_storage @@ -735,6 +737,8 @@ subroutine control_spmd() call mpi_bcast (use_lai_streams, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_cropcal_streams, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_bedrock, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_biomass_heat_storage, 1, MPI_LOGICAL, 0, mpicom, ier) From d47d2b608193bed2532310596b21a0cce3ac5a31 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 12 Oct 2021 18:14:58 -0600 Subject: [PATCH 0032/2067] Corrected interpolation/mapping algo in cropcalStreamMod. --- src/cpl/mct/cropcalStreamMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 9cb6663ab6..fdbce15702 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -72,8 +72,8 @@ subroutine cropcal_init(bounds) type(mct_ggrid) :: dom_clm ! domain information character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read character(len=CL) :: stream_fldFileName_hdate ! harvest date stream filename to read - character(len=CL) :: cropcal_mapalgo = 'nearest' ! Mapping alogrithm - character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm + character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nn' ! Time interpolation alogrithm ! SSR TODO: Make this work with max_growingseasons_per_year > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates From dd70a3686a368fde2fe6a8f9239c487e3797efeb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 12 Oct 2021 18:15:57 -0600 Subject: [PATCH 0033/2067] cropcal_interp() now loops only over crop patches. --- src/cpl/mct/cropcalStreamMod.F90 | 46 +++++++++++++++----------------- 1 file changed, 22 insertions(+), 24 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index fdbce15702..b34d7c8709 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -26,7 +26,7 @@ module cropcalStreamMod ! !PUBLIC MEMBER FUNCTIONS: public :: cropcal_init ! position datasets for crop calendars public :: cropcal_advance ! Advance the crop calendar streams (outside of a Open-MP threading loop) - public :: cropcal_interp ! interpolates between two years of crop calendar data (when crop calendar streams + public :: cropcal_interp ! interpolates between two years of crop calendar data ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index @@ -254,6 +254,7 @@ subroutine cropcal_interp(bounds, crop_inst) use pftconMod , only : noveg use CropType , only : crop_type use PatchType , only : patch + use filterMod , only : filter ! ! !ARGUMENTS: implicit none @@ -262,6 +263,7 @@ subroutine cropcal_interp(bounds, crop_inst) ! ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig + integer :: nc, fp character(len=CL) :: stream_var_name !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) @@ -274,30 +276,26 @@ subroutine cropcal_interp(bounds, crop_inst) SHR_ASSERT_FL( (ubound(sdat_hdate1%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) ! SSR TODO: Make these work with max_growingseasons_per_year > 1 - do p = bounds%begp, bounds%endp - ivt = patch%itype(p) - ! Set crop calendars for each gridcell/patch combination - if (ivt /= noveg) then - ! vegetated pft - write(stream_var_name,"(i6)") ivt - - ! SSR TODO: Add check that variable exists in netCDF - stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_sdate1%avs(1),trim(stream_var_name)) - ig = g_to_ig(patch%gridcell(p)) - crop_inst%sdates_thisyr(p,1) = sdat_sdate1%avs(1)%rAttr(ip,ig) + do nc = 1, get_proc_clumps() + do fp = 1, filter(nc)%num_pcropp + p = filter_pcropp(fp) + ivt = patch%itype(p) + ! Set crop calendars for each gridcell/patch combination + write(stream_var_name,"(i6)") ivt + + ! SSR TODO: Add check that variable exists in netCDF + stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) + ip = mct_aVect_indexRA(sdat_sdate1%avs(1),trim(stream_var_name)) + ig = g_to_ig(patch%gridcell(p)) + crop_inst%sdates_thisyr(p,1) = sdat_sdate1%avs(1)%rAttr(ip,ig) - ! SSR TODO: Add check that variable exists in netCDF - stream_var_name = 'hdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_hdate1%avs(1),trim(stream_var_name)) - ig = g_to_ig(patch%gridcell(p)) - crop_inst%hdates_thisyr(p,1) = sdat_hdate1%avs(1)%rAttr(ip,ig) - else - ! non-vegetated pft - crop_inst%sdates_thisyr(p,1) = -1 - crop_inst%hdates_thisyr(p,1) = -1 - endif - end do + ! SSR TODO: Add check that variable exists in netCDF + stream_var_name = 'hdate1_'//trim(adjustl(stream_var_name)) + ip = mct_aVect_indexRA(sdat_hdate1%avs(1),trim(stream_var_name)) + ig = g_to_ig(patch%gridcell(p)) + crop_inst%hdates_thisyr(p,1) = sdat_hdate1%avs(1)%rAttr(ip,ig) + end do + end do end subroutine cropcal_interp From 56ad192f48c3fc756535afa2521ddce5fca8bffd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 12 Oct 2021 18:17:37 -0600 Subject: [PATCH 0034/2067] Added src/cpl/share_esmf/cropcalStreamMod.F90. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 310 ++++++++++++++++++++++++ 1 file changed, 310 insertions(+) create mode 100644 src/cpl/share_esmf/cropcalStreamMod.F90 diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 new file mode 100644 index 0000000000..5ff9a78fac --- /dev/null +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -0,0 +1,310 @@ +module cropcalStreamMod + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Read crop calendars from streams + ! + ! !USES: + use ESMF + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL, CS => shr_kind_CS + use dshr_strdata_mod , only : shr_strdata_type + use decompMod , only : bounds_type + use abortutils , only : endrun + use clm_varctl , only : iulog + use clm_varpar , only : mxpft + use perf_mod , only : t_startf, t_stopf + use spmdMod , only : masterproc, mpicom, iam + use filterMod , only : filter + ! + ! !PUBLIC TYPES: + implicit none + private + + ! !PUBLIC MEMBER FUNCTIONS: + public :: cropcal_init ! position datasets for crop calendars + public :: cropcal_advance ! Advance the crop calendar streams (outside of a Open-MP threading loop) + public :: cropcal_interp ! interpolates between two years of crop calendar data + + ! !PRIVATE MEMBER DATA: + integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index + type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream + type(shr_strdata_type) :: sdat_cropcal_hdate ! hdate input data stream + character(len=CS) :: stream_varnames_sdate(mxpft) + character(len=CS) :: stream_varnames_hdate(mxpft) + + character(len=*), parameter :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine cropcal_init(bounds) + ! + ! Initialize data stream information for crop calendars. + ! + ! !USES: + use shr_mpi_mod , only : shr_mpi_bcast + use clm_nlUtilsMod , only : find_nlgroup_name + use lnd_comp_shr , only : mesh, model_clock + use dshr_strdata_mod , only : shr_strdata_init_from_inline + use controlMod , only : NLFilename + ! + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds ! bounds + ! + ! !LOCAL VARIABLES: + integer :: i,n ! index + integer :: stream_year_first_cropcal ! first year in crop calendar streams to use + integer :: stream_year_last_cropcal ! last year in crop calendar streams to use + integer :: model_year_align_cropcal ! align stream_year_first_cropcal with + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read + character(len=CL) :: stream_fldFileName_hdate ! hdate stream filename to read + character(len=CL) :: stream_meshfile_cropcal ! crop calendar stream meshfile + character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nn' ! Time interpolation alogrithm + integer :: cropcal_offset = 0 ! Offset in time for dataset (sec) + integer :: rc + character(*), parameter :: subName = "('cropcaldyn_init')" + !----------------------------------------------------------------------- + ! + ! deal with namelist variables here in init + ! + namelist /cropcal_streams/ & + stream_year_first_cropcal, & + stream_year_last_cropcal, & + model_year_align_cropcal, & + cropcal_mapalgo, & + stream_fldFileName_sdate, & + stream_fldFileName_hdate, & + stream_meshfile_cropcal, & + cropcal_tintalgo + + ! Default values for namelist + stream_year_first_cropcal = 1 ! first year in stream to use + stream_year_last_cropcal = 1 ! last year in stream to use + model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year + stream_meshfile_cropcal = '' + stream_fldFileName_sdate = '' + stream_fldFileName_hdate = '' + ! SSR TODO: Make below work with arbitrary # of growing seasons per year + do n = 1,mxpft + write(stream_varnames_sdate(n),'(a,i0)') "sdate1",n + write(stream_varnames_hdate(n),'(a,i0)') "hdate1",n + end do + + ! Read cropcal_streams namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'cropcal_streams', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=cropcal_streams,iostat=nml_error) + if (nml_error /= 0) then + call endrun(subname // ':: ERROR reading cropcal_streams namelist') + end if + else + call endrun(subname // ':: ERROR finding cropcal_streams namelist') + end if + close(nu_nml) + endif + call shr_mpi_bcast(stream_year_first_cropcal , mpicom) + call shr_mpi_bcast(stream_year_last_cropcal , mpicom) + call shr_mpi_bcast(model_year_align_cropcal , mpicom) + call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) + call shr_mpi_bcast(stream_fldFileName_hdate , mpicom) + call shr_mpi_bcast(stream_meshfile_cropcal , mpicom) + call shr_mpi_bcast(cropcal_tintalgo , mpicom) + + if (masterproc) then + write(iulog,*) + write(iulog,'(a)') 'cropcal_stream settings:' + write(iulog,'(a,i8)') ' stream_year_first_cropcal = ',stream_year_first_cropcal + write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal + write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal + write(iulog,'(a,a)' ) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) + write(iulog,'(a,a)' ) ' stream_fldFileName_hdate = ',trim(stream_fldFileName_hdate) + write(iulog,'(a,a)' ) ' stream_meshfile_cropcal = ',trim(stream_meshfile_cropcal) + write(iulog,'(a,a)' ) ' cropcal_tintalgo = ',trim(cropcal_tintalgo) + do n = 1,mxpft + write(iulog,'(a,a)' ) ' stream_varnames_sdate = ',trim(stream_varnames_sdate(n)) + write(iulog,'(a,a)' ) ' stream_varnames_hdate = ',trim(stream_varnames_hdate(n)) + end do + write(iulog,*) + endif + + ! Initialize the cdeps data type sdat_cropcal_sdate + call shr_strdata_init_from_inline(sdat_cropcal_sdate, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = trim(stream_meshfile_cropcal), & + stream_lev_dimname = 'null', & + stream_mapalgo = trim(cropcal_mapalgo), & + stream_filenames = (/trim(stream_fldFileName_sdate)/), & + stream_fldlistFile = stream_varnames_sdate, & + stream_fldListModel = stream_varnames_sdate, & + stream_yearFirst = stream_year_first_cropcal, & + stream_yearLast = stream_year_last_cropcal, & + stream_yearAlign = model_year_align_cropcal, & + stream_offset = cropcal_offset, & + stream_taxmode = 'cycle', & + stream_dtlimit = 1.5_r8, & + stream_tintalgo = cropcal_tintalgo, & + stream_name = 'sowing date data', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + ! Initialize the cdeps data type sdat_cropcal_hdate + call shr_strdata_init_from_inline(sdat_cropcal_hdate, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = trim(stream_meshfile_cropcal), & + stream_lev_dimname = 'null', & + stream_mapalgo = trim(cropcal_mapalgo), & + stream_filenames = (/trim(stream_fldFileName_hdate)/), & + stream_fldlistFile = stream_varnames_hdate, & + stream_fldListModel = stream_varnames_hdate, & + stream_yearFirst = stream_year_first_cropcal, & + stream_yearLast = stream_year_last_cropcal, & + stream_yearAlign = model_year_align_cropcal, & + stream_offset = cropcal_offset, & + stream_taxmode = 'cycle', & + stream_dtlimit = 1.5_r8, & + stream_tintalgo = cropcal_tintalgo, & + stream_name = 'harvest date data', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + end subroutine cropcal_init + + !================================================================ + subroutine cropcal_advance( bounds ) + ! + ! Advance crop calendar streams + ! + ! !USES: + use clm_time_manager , only : get_curr_date + use dshr_strdata_mod , only : shr_strdata_advance + ! + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g, ig ! Indices + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + integer :: rc + !----------------------------------------------------------------------- + + call get_curr_date(year, mon, day, sec) + mcdate = year*10000 + mon*100 + day + call shr_strdata_advance(sdat_cropcal_sdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + call shr_strdata_advance(sdat_cropcal_hdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + if ( .not. allocated(g_to_ig) )then + allocate (g_to_ig(bounds%begg:bounds%endg) ) + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + g_to_ig(g) = ig + end do + end if + + end subroutine cropcal_advance + + !================================================================ + subroutine cropcal_interp(bounds, canopystate_inst) + ! + ! Interpolate data stream information for crop calendar. + ! + ! !USES: + use pftconMod , only : noveg + use PatchType , only : patch + use CanopyStateType , only : canopystate_type + use dshr_methods_mod , only : dshr_fldbun_getfldptr + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds + type(crop_type) , intent(inout) :: crop_inst + ! + ! !LOCAL VARIABLES: + integer :: ivt, fp, p, ip, ig, n, g + integer :: lsize + integer :: rc_sdate, rc_hdate + real(r8), pointer :: dataptr1d_sdate(:) + real(r8), pointer :: dataptr1d_hdate(:) + real(r8), pointer :: dataptr2d_sdate(:,:) + real(r8), pointer :: dataptr2d_hdate(:,:) + !----------------------------------------------------------------------- + + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) + + ! Get pointer for stream data that is time and spatially interpolate to model time and grid + ! Place all crop calendar data from each type into a temporary 2d array + ! SSR TODO: Make below work with arbitrary # of growing seasons per year + lsize = bounds%endg - bounds%begg + 1 + allocate(dataptr2d(lsize, mxpft)) + do n = 1,mxpft + call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & + fldptr1=dataptr1d_sdate, rc=rc_sdate) + ! SSR TODO: Fail on any error except "variable not found" + ! if (ESMF_LogFoundError(rcToCheck=rc_sdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + ! call ESMF_Finalize(endflag=ESMF_END_ABORT) + ! end if + call dshr_fldbun_getFldPtr(sdat_cropcal_hdate%pstrm(1)%fldbun_model, trim(stream_varnames_hdate(n)), & + fldptr1=dataptr1d_hdate, rc=rc_hdate) + ! SSR TODO: Fail on any error except "variable not found" + ! if (ESMF_LogFoundError(rcToCheck=rc_hdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + ! call ESMF_Finalize(endflag=ESMF_END_ABORT) + ! end if + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize + ! So an explicit loop is required here + do g = 1,lsize + if (.not. ESMF_LogFoundError(rcToCheck=rc_sdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + end if + if (.not. ESMF_LogFoundError(rcToCheck=rc_hdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + dataptr2d_hdate(g,n) = dataptr1d_hdate(g) + end if + end do + end do + + do nc = 1, get_proc_clumps() + do fp = 1, filter(nc)%num_pcropp + p = filter_pcropp(fp) + ! Set crop calendar for each gridcell/patch combination + ig = g_to_ig(patch%gridcell(p)) + ivt = patch%itype + ! SSR TODO: Make below work with arbitrary # of growing seasons per year + crop_inst%sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) + crop_inst%hdates_thisyr(p,1) = dataptr2d_hdate(ig,ivt) + end do + end do + deallocate(dataptr2d) + + end subroutine cropcal_interp + +end module cropcalStreamMod From 5b5f800b47456aca449a1cb2118280e3e66d9e9a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 13 Oct 2021 14:39:38 -0600 Subject: [PATCH 0035/2067] Compile fixes. --- src/cpl/mct/cropcalStreamMod.F90 | 3 ++- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index b34d7c8709..dbfc12f8b8 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -255,6 +255,7 @@ subroutine cropcal_interp(bounds, crop_inst) use CropType , only : crop_type use PatchType , only : patch use filterMod , only : filter + use decompMod , only : get_proc_clumps ! ! !ARGUMENTS: implicit none @@ -278,7 +279,7 @@ subroutine cropcal_interp(bounds, crop_inst) ! SSR TODO: Make these work with max_growingseasons_per_year > 1 do nc = 1, get_proc_clumps() do fp = 1, filter(nc)%num_pcropp - p = filter_pcropp(fp) + p = filter(nc)%pcropp(fp) ivt = patch%itype(p) ! Set crop calendars for each gridcell/patch combination write(stream_var_name,"(i6)") ivt diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 5ff9a78fac..2f995668b4 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -10,7 +10,7 @@ module cropcalStreamMod use ESMF use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL, CS => shr_kind_CS use dshr_strdata_mod , only : shr_strdata_type - use decompMod , only : bounds_type + use decompMod , only : bounds_type, get_proc_clumps use abortutils , only : endrun use clm_varctl , only : iulog use clm_varpar , only : mxpft @@ -294,7 +294,7 @@ subroutine cropcal_interp(bounds, canopystate_inst) do nc = 1, get_proc_clumps() do fp = 1, filter(nc)%num_pcropp - p = filter_pcropp(fp) + p = filter(nc)%pcropp(fp) ! Set crop calendar for each gridcell/patch combination ig = g_to_ig(patch%gridcell(p)) ivt = patch%itype From fab63e2c23b4260842ab83aa63af404e56ea83b2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 13 Oct 2021 14:45:02 -0600 Subject: [PATCH 0036/2067] Renamed file variables in MCT cropCalStreamMod.F90. --- src/cpl/mct/cropcalStreamMod.F90 | 33 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index dbfc12f8b8..97441c4140 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -31,8 +31,8 @@ module cropcalStreamMod ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index ! SSR TODO: Make these work with max_growingseasons_per_year > 1 - type(shr_strdata_type) :: sdat_sdate1 ! 1st sowing date input data stream - type(shr_strdata_type) :: sdat_hdate1 ! 1st harvest date input data stream + type(shr_strdata_type) :: sdat_sdate ! sowing date input data stream + type(shr_strdata_type) :: sdat_hdate ! harvest date input data stream character(len=*), parameter :: sourcefile = & __FILE__ @@ -140,10 +140,9 @@ subroutine cropcal_init(bounds) fldList_hdate1 = shr_string_listCreateField( mxpft, "hdate1" ) ! SSR TODO: - ! - Make these work with max_growingseasons_per_year > 1 ! - Delete "area" and "mask"? ! - Is this correct taxmode? - call shr_strdata_create(sdat_sdate1, & + call shr_strdata_create(sdat_sdate, & name="cropcaldyn", & pio_subsystem=pio_subsystem, & pio_iotype=shr_pio_getiotype(inst_name), & @@ -171,7 +170,7 @@ subroutine cropcal_init(bounds) calendar=get_calendar(), & taxmode='cycle' ) - call shr_strdata_create(sdat_hdate1, & + call shr_strdata_create(sdat_hdate, & name="cropcaldyn", & pio_subsystem=pio_subsystem, & pio_iotype=shr_pio_getiotype(inst_name), & @@ -200,8 +199,8 @@ subroutine cropcal_init(bounds) taxmode='cycle' ) if (masterproc) then - call shr_strdata_print(sdat_sdate1,'sdate1 data') - call shr_strdata_print(sdat_hdate1,'hdate1 data') + call shr_strdata_print(sdat_sdate,'sdate1 data') + call shr_strdata_print(sdat_hdate,'hdate1 data') endif end subroutine cropcal_init @@ -231,8 +230,8 @@ subroutine cropcal_advance( bounds ) mcdate = year*10000 + mon*100 + day ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - call shr_strdata_advance(sdat_sdate1, mcdate, sec, mpicom, 'cropcaldyn') - call shr_strdata_advance(sdat_hdate1, mcdate, sec, mpicom, 'cropcaldyn') + call shr_strdata_advance(sdat_sdate, mcdate, sec, mpicom, 'cropcaldyn') + call shr_strdata_advance(sdat_hdate, mcdate, sec, mpicom, 'cropcaldyn') if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) @@ -271,10 +270,10 @@ subroutine cropcal_interp(bounds, crop_inst) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - SHR_ASSERT_FL( (lbound(sdat_sdate1%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_sdate1%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_hdate1%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_hdate1%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(sdat_hdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_hdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) ! SSR TODO: Make these work with max_growingseasons_per_year > 1 do nc = 1, get_proc_clumps() @@ -286,15 +285,15 @@ subroutine cropcal_interp(bounds, crop_inst) ! SSR TODO: Add check that variable exists in netCDF stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_sdate1%avs(1),trim(stream_var_name)) + ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) ig = g_to_ig(patch%gridcell(p)) - crop_inst%sdates_thisyr(p,1) = sdat_sdate1%avs(1)%rAttr(ip,ig) + crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) ! SSR TODO: Add check that variable exists in netCDF stream_var_name = 'hdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_hdate1%avs(1),trim(stream_var_name)) + ip = mct_aVect_indexRA(sdat_hdate%avs(1),trim(stream_var_name)) ig = g_to_ig(patch%gridcell(p)) - crop_inst%hdates_thisyr(p,1) = sdat_hdate1%avs(1)%rAttr(ip,ig) + crop_inst%hdates_thisyr(p,1) = sdat_hdate%avs(1)%rAttr(ip,ig) end do end do From 3b8a0922486393c4eaa5eeeb1ae24178d6d59bf8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 11:52:24 -0600 Subject: [PATCH 0037/2067] Set up namelist entries and defaults. --- bld/namelist_files/namelist_defaults_ctsm.xml | 11 ++++ .../namelist_definition_ctsm.xml | 52 +++++++++++++++++++ 2 files changed, 63 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 8a10a96ebf..3bd9adf78f 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1566,6 +1566,17 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts nn nn + +.false. +1850 +2100 +1850 + +lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc +lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc + +nn + none diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 67929c4bd4..32e340178f 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1770,6 +1770,58 @@ Mapping method from LAI input file to the model resolution copy = copy using the same indices + + + + + + +Toggle to turn on use of crop calendar streams in place of CFT-specific sowing windows and harvest criteria. +(EXPERIMENTAL and NOT tested) + + + +First year to loop over for crop calendar data + + + +Last year to loop over for crop calendar data + + + +Simulation year that aligns with stream_year_first_cropcal value + + + +Filename of input stream data for sowing dates + + + +Filename of input stream data for harvest dates + + + +Time interpolation method to use with crop calendar streams + + + +Mapping method from crop calendar input files to the model resolution + bilinear = bilinear interpolation + nn = nearest neighbor + nnoni = nearest neighbor on the "i" (longitude) axis + nnonj = nearest neighbor on the "j" (latitude) axis + spval = set to special value + copy = copy using the same indices + + From a17e51d3ce80357173b6b80631102f8e94b1817e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 11:56:44 -0600 Subject: [PATCH 0038/2067] Removed all code re: prescribed harvest dates. In addition to other changes, this reverts "Added CropPhenology() logic for prescribed harvest dates." (commit e56921d685528bf7ffddabad739048820dd525f2.) --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 - .../namelist_definition_ctsm.xml | 5 -- src/biogeochem/CNPhenologyMod.F90 | 9 +--- src/biogeochem/CropType.F90 | 5 -- src/cpl/mct/cropcalStreamMod.F90 | 46 ---------------- src/cpl/share_esmf/cropcalStreamMod.F90 | 54 +------------------ 6 files changed, 4 insertions(+), 116 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3bd9adf78f..fb17e88026 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1573,7 +1573,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc -lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc nn diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 32e340178f..82365eac20 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1801,11 +1801,6 @@ Simulation year that aligns with stream_year_first_cropcal value Filename of input stream data for sowing dates - -Filename of input stream data for harvest dates - - Time interpolation method to use with crop calendar streams diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7c51be4b5d..e3ea08076a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1691,8 +1691,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? logical sowing_is_prescribed ! is sowing date prescribed for this season? - logical harvest_is_prescribed ! is harvest date prescribed for this season? - logical do_harvest_prescribed ! is today the prescribed harvest date? !------------------------------------------------------------------------ associate( & @@ -1725,7 +1723,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor sdate_rx => crop_inst%sdate_thisseason , & ! Input: [integer (:) ] prescribed sowing date - hdate_rx => crop_inst%hdate_thisseason , & ! Input: [integer (:) ] prescribed harvest date peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow @@ -1830,8 +1827,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sowing_is_prescribed = sdate_rx(p) >= 0 do_plant_prescribed = sdate_rx(p) == jday - harvest_is_prescribed = hdate_rx(p) >= 0 - do_harvest_prescribed = hdate_rx(p) == jday ! winter temperate cereal : use gdd0 as a limit to plant winter cereal @@ -2060,7 +2055,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if ((.not. do_harvest_prescribed) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then + if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then cphase(p) = 2._r8 if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 @@ -2086,7 +2081,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! the onset_counter would change from dt and you'd need to make ! changes to the offset subroutine below - else if (do_harvest_prescribed .or. ((.not. harvest_is_prescribed) .and. hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p)))) then + else if (hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p))) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 3688a44351..a82ea2cd75 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -42,9 +42,7 @@ module CropType real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope integer , pointer :: sdate_thisseason (:) ! patch sowing date for current (active) season - integer , pointer :: hdate_thisseason (:) ! patch harvest date for current (active) season integer , pointer :: sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year - integer , pointer :: hdates_thisyr (:,:) ! all prescribed harvest dates for this patch this year integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year integer :: max_growingseasons_per_year ! maximum number of growing seasons per year allowed in any patch @@ -210,14 +208,11 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sdate_thisseason(begp:endp)) ; this%sdate_thisseason(:) = -1 - allocate(this%hdate_thisseason(begp:endp)) ; this%hdate_thisseason(:) = -1 allocate(this%sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) - allocate(this%hdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 this%sdates_thisyr(:,:) = -1 - this%hdates_thisyr(:,:) = -1 end subroutine InitAllocate diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 97441c4140..b42d1960db 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -32,7 +32,6 @@ module cropcalStreamMod integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index ! SSR TODO: Make these work with max_growingseasons_per_year > 1 type(shr_strdata_type) :: sdat_sdate ! sowing date input data stream - type(shr_strdata_type) :: sdat_hdate ! harvest date input data stream character(len=*), parameter :: sourcefile = & __FILE__ @@ -71,13 +70,11 @@ subroutine cropcal_init(bounds) integer :: nml_error ! namelist i/o error flag type(mct_ggrid) :: dom_clm ! domain information character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read - character(len=CL) :: stream_fldFileName_hdate ! harvest date stream filename to read character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nn' ! Time interpolation alogrithm ! SSR TODO: Make this work with max_growingseasons_per_year > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates - character(len=CXX) :: fldList_hdate1 ! field string for 1st harvest dates character(*), parameter :: subName = "('cropcaldyn_init')" !----------------------------------------------------------------------- @@ -90,7 +87,6 @@ subroutine cropcal_init(bounds) model_year_align_cropcal, & cropcal_mapalgo, & stream_fldFileName_sdate, & - stream_fldFileName_hdate, & cropcal_tintalgo ! Default values for namelist @@ -98,7 +94,6 @@ subroutine cropcal_init(bounds) stream_year_last_cropcal = 1 ! last year in stream to use model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year stream_fldFileName_sdate = shr_stream_file_null - stream_fldFileName_hdate = shr_stream_file_null ! Read cropcal_streams namelist if (masterproc) then @@ -118,7 +113,6 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) - call shr_mpi_bcast(stream_fldFileName_hdate , mpicom) call shr_mpi_bcast(cropcal_tintalgo , mpicom) if (masterproc) then @@ -128,7 +122,6 @@ subroutine cropcal_init(bounds) write(iulog,*) ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,*) ' model_year_align_cropcal = ',model_year_align_cropcal write(iulog,*) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) - write(iulog,*) ' stream_fldFileName_hdate = ',trim(stream_fldFileName_hdate) write(iulog,*) ' cropcal_tintalgo = ',trim(cropcal_tintalgo) endif @@ -137,7 +130,6 @@ subroutine cropcal_init(bounds) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with max_growingseasons_per_year > 1 fldList_sdate1 = shr_string_listCreateField( mxpft, "sdate1" ) - fldList_hdate1 = shr_string_listCreateField( mxpft, "hdate1" ) ! SSR TODO: ! - Delete "area" and "mask"? @@ -170,37 +162,8 @@ subroutine cropcal_init(bounds) calendar=get_calendar(), & taxmode='cycle' ) - call shr_strdata_create(sdat_hdate, & - name="cropcaldyn", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_cropcal, & - yearLast=stream_year_last_cropcal, & - yearAlign=model_year_align_cropcal, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_hdate), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_hdate/), & - fldListFile=fldList_hdate1, & - fldListModel=fldList_hdate1, & - fillalgo='none', & - mapalgo=cropcal_mapalgo, & - tintalgo=cropcal_tintalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - if (masterproc) then call shr_strdata_print(sdat_sdate,'sdate1 data') - call shr_strdata_print(sdat_hdate,'hdate1 data') endif end subroutine cropcal_init @@ -231,7 +194,6 @@ subroutine cropcal_advance( bounds ) ! SSR TODO: Make this work with max_growingseasons_per_year > 1 call shr_strdata_advance(sdat_sdate, mcdate, sec, mpicom, 'cropcaldyn') - call shr_strdata_advance(sdat_hdate, mcdate, sec, mpicom, 'cropcaldyn') if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) @@ -272,8 +234,6 @@ subroutine cropcal_interp(bounds, crop_inst) ! SSR TODO: Make this work with max_growingseasons_per_year > 1 SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_hdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_hdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) ! SSR TODO: Make these work with max_growingseasons_per_year > 1 do nc = 1, get_proc_clumps() @@ -288,12 +248,6 @@ subroutine cropcal_interp(bounds, crop_inst) ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) ig = g_to_ig(patch%gridcell(p)) crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) - - ! SSR TODO: Add check that variable exists in netCDF - stream_var_name = 'hdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_hdate%avs(1),trim(stream_var_name)) - ig = g_to_ig(patch%gridcell(p)) - crop_inst%hdates_thisyr(p,1) = sdat_hdate%avs(1)%rAttr(ip,ig) end do end do diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 2f995668b4..1eab47a883 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -30,9 +30,7 @@ module cropcalStreamMod ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream - type(shr_strdata_type) :: sdat_cropcal_hdate ! hdate input data stream character(len=CS) :: stream_varnames_sdate(mxpft) - character(len=CS) :: stream_varnames_hdate(mxpft) character(len=*), parameter :: sourcefile = & __FILE__ @@ -63,7 +61,6 @@ subroutine cropcal_init(bounds) integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read - character(len=CL) :: stream_fldFileName_hdate ! hdate stream filename to read character(len=CL) :: stream_meshfile_cropcal ! crop calendar stream meshfile character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nn' ! Time interpolation alogrithm @@ -80,7 +77,6 @@ subroutine cropcal_init(bounds) model_year_align_cropcal, & cropcal_mapalgo, & stream_fldFileName_sdate, & - stream_fldFileName_hdate, & stream_meshfile_cropcal, & cropcal_tintalgo @@ -90,11 +86,9 @@ subroutine cropcal_init(bounds) model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year stream_meshfile_cropcal = '' stream_fldFileName_sdate = '' - stream_fldFileName_hdate = '' ! SSR TODO: Make below work with arbitrary # of growing seasons per year do n = 1,mxpft write(stream_varnames_sdate(n),'(a,i0)') "sdate1",n - write(stream_varnames_hdate(n),'(a,i0)') "hdate1",n end do ! Read cropcal_streams namelist @@ -115,7 +109,6 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) - call shr_mpi_bcast(stream_fldFileName_hdate , mpicom) call shr_mpi_bcast(stream_meshfile_cropcal , mpicom) call shr_mpi_bcast(cropcal_tintalgo , mpicom) @@ -126,12 +119,10 @@ subroutine cropcal_init(bounds) write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal write(iulog,'(a,a)' ) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) - write(iulog,'(a,a)' ) ' stream_fldFileName_hdate = ',trim(stream_fldFileName_hdate) write(iulog,'(a,a)' ) ' stream_meshfile_cropcal = ',trim(stream_meshfile_cropcal) write(iulog,'(a,a)' ) ' cropcal_tintalgo = ',trim(cropcal_tintalgo) do n = 1,mxpft write(iulog,'(a,a)' ) ' stream_varnames_sdate = ',trim(stream_varnames_sdate(n)) - write(iulog,'(a,a)' ) ' stream_varnames_hdate = ',trim(stream_varnames_hdate(n)) end do write(iulog,*) endif @@ -162,32 +153,6 @@ subroutine cropcal_init(bounds) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - ! Initialize the cdeps data type sdat_cropcal_hdate - call shr_strdata_init_from_inline(sdat_cropcal_hdate, & - my_task = iam, & - logunit = iulog, & - compname = 'LND', & - model_clock = model_clock, & - model_mesh = mesh, & - stream_meshfile = trim(stream_meshfile_cropcal), & - stream_lev_dimname = 'null', & - stream_mapalgo = trim(cropcal_mapalgo), & - stream_filenames = (/trim(stream_fldFileName_hdate)/), & - stream_fldlistFile = stream_varnames_hdate, & - stream_fldListModel = stream_varnames_hdate, & - stream_yearFirst = stream_year_first_cropcal, & - stream_yearLast = stream_year_last_cropcal, & - stream_yearAlign = model_year_align_cropcal, & - stream_offset = cropcal_offset, & - stream_taxmode = 'cycle', & - stream_dtlimit = 1.5_r8, & - stream_tintalgo = cropcal_tintalgo, & - stream_name = 'harvest date data', & - rc = rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - end subroutine cropcal_init !================================================================ @@ -218,10 +183,6 @@ subroutine cropcal_advance( bounds ) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - call shr_strdata_advance(sdat_cropcal_hdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) @@ -252,11 +213,9 @@ subroutine cropcal_interp(bounds, canopystate_inst) ! !LOCAL VARIABLES: integer :: ivt, fp, p, ip, ig, n, g integer :: lsize - integer :: rc_sdate, rc_hdate + integer :: rc_sdate real(r8), pointer :: dataptr1d_sdate(:) - real(r8), pointer :: dataptr1d_hdate(:) real(r8), pointer :: dataptr2d_sdate(:,:) - real(r8), pointer :: dataptr2d_hdate(:,:) !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) @@ -274,21 +233,13 @@ subroutine cropcal_interp(bounds, canopystate_inst) ! if (ESMF_LogFoundError(rcToCheck=rc_sdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then ! call ESMF_Finalize(endflag=ESMF_END_ABORT) ! end if - call dshr_fldbun_getFldPtr(sdat_cropcal_hdate%pstrm(1)%fldbun_model, trim(stream_varnames_hdate(n)), & - fldptr1=dataptr1d_hdate, rc=rc_hdate) - ! SSR TODO: Fail on any error except "variable not found" - ! if (ESMF_LogFoundError(rcToCheck=rc_hdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - ! call ESMF_Finalize(endflag=ESMF_END_ABORT) - ! end if + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize ! So an explicit loop is required here do g = 1,lsize if (.not. ESMF_LogFoundError(rcToCheck=rc_sdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then dataptr2d_sdate(g,n) = dataptr1d_sdate(g) end if - if (.not. ESMF_LogFoundError(rcToCheck=rc_hdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - dataptr2d_hdate(g,n) = dataptr1d_hdate(g) - end if end do end do @@ -300,7 +251,6 @@ subroutine cropcal_interp(bounds, canopystate_inst) ivt = patch%itype ! SSR TODO: Make below work with arbitrary # of growing seasons per year crop_inst%sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) - crop_inst%hdates_thisyr(p,1) = dataptr2d_hdate(ig,ivt) end do end do deallocate(dataptr2d) From e6bbc25fe4e4a87583e1bb03f1fe011db2f6e135 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 14:25:10 -0600 Subject: [PATCH 0039/2067] growingseason_count now increments in PlantCrop(). --- src/biogeochem/CNPhenologyMod.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e3ea08076a..43d99c26c3 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2253,6 +2253,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date + growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Output: [real(r8) (:) ] (gN/m2) leaf N transfer @@ -2266,6 +2267,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & cropplant(p) = .true. idop(p) = jday harvdate(p) = NOT_Harvested + growingseason_count = growingseason_count + 1 leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset From d03e623991cb2f2d7ff6dcf3383e3d1b18c8ad0b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 14:57:53 -0600 Subject: [PATCH 0040/2067] CropPhenology() now uses use_cropcal_streams. Instead of local variable sowing_is_prescribed. --- src/biogeochem/CNPhenologyMod.F90 | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 43d99c26c3..e2ebaf5664 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1655,6 +1655,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & use clm_varcon , only : spval, secspday use clm_varctl , only : use_fertilizer use clm_varctl , only : use_c13, use_c14 + use clm_varctl , only : use_cropcal_streams use clm_varcon , only : c13ratio, c14ratio ! ! !ARGUMENTS: @@ -1690,7 +1691,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? - logical sowing_is_prescribed ! is sowing date prescribed for this season? !------------------------------------------------------------------------ associate( & @@ -1825,7 +1825,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! According to Chris Kucharik, the dataset of ! xinpdate was generated from a previous model run at 0.5 deg resolution - sowing_is_prescribed = sdate_rx(p) >= 0 do_plant_prescribed = sdate_rx(p) == jday ! winter temperate cereal : use gdd0 as a limit to plant winter cereal @@ -1849,14 +1848,14 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! updated on Jan 1st instead of at harvest (slevis) ! Are all the normal requirements for planting met? - do_plant_normal = (.not. sowing_is_prescribed) .and. & + do_plant_normal = (.not. use_cropcal_streams) .and. & a5tmin(p) /= spval .and. & a5tmin(p) <= minplanttemp(ivt(p)) .and. & jday >= minplantjday(ivt(p),h) .and. & (gdd020(p) /= spval .and. & gdd020(p) >= gddmin(ivt(p))) ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = (.not. sowing_is_prescribed) .and. & + do_plant_lastchance = (.not. use_cropcal_streams) .and. & (.not. do_plant_normal) .and. & jday >= maxplantjday(ivt(p),h) .and. & gdd020(p) /= spval .and. & @@ -1884,7 +1883,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! while the gdd part is either true or false for the year. ! Are all the normal requirements for planting met? - do_plant_normal = (.not. sowing_is_prescribed) .and. & + do_plant_normal = (.not. use_cropcal_streams) .and. & t10(p) /= spval .and. a10tmin(p) /= spval .and. & t10(p) > planttemp(ivt(p)) .and. & a10tmin(p) > minplanttemp(ivt(p)) .and. & @@ -1893,7 +1892,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & gdd820(p) /= spval .and. & gdd820(p) >= gddmin(ivt(p)) ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = (.not. sowing_is_prescribed) .and. & + do_plant_lastchance = (.not. use_cropcal_streams) .and. & (.not. do_plant_normal) .and. & jday == maxplantjday(ivt(p),h) .and. & gdd820(p) > 0._r8 .and. & From 184c9ac1f1fde7d7a8f7b36fd471b201eef78dd1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 15:00:37 -0600 Subject: [PATCH 0041/2067] crop_inst%sdate_thisseason renamed to next_rx_date. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- src/biogeochem/CropType.F90 | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e2ebaf5664..9de790a39f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1722,7 +1722,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor - sdate_rx => crop_inst%sdate_thisseason , & ! Input: [integer (:) ] prescribed sowing date + next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow @@ -1825,7 +1825,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! According to Chris Kucharik, the dataset of ! xinpdate was generated from a previous model run at 0.5 deg resolution - do_plant_prescribed = sdate_rx(p) == jday + do_plant_prescribed = next_rx_sdate == jday ! winter temperate cereal : use gdd0 as a limit to plant winter cereal diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index a82ea2cd75..bc0baa9f50 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -41,7 +41,7 @@ module CropType character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope - integer , pointer :: sdate_thisseason (:) ! patch sowing date for current (active) season + integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year integer , pointer :: sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year @@ -207,7 +207,7 @@ subroutine InitAllocate(this, bounds) allocate(this%vf_patch (begp:endp)) ; this%vf_patch (:) = 0.0_r8 allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval - allocate(this%sdate_thisseason(begp:endp)) ; this%sdate_thisseason(:) = -1 + allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 allocate(this%sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 From 1ca8a70b7bf9aa02a212b97fbea5907d958ac059 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 15:02:32 -0600 Subject: [PATCH 0042/2067] Two crop_inst members now set in cropcal_interp(). n_growingseasons_thisyear_thispatch and next_rx_sdate. --- src/cpl/mct/cropcalStreamMod.F90 | 7 +++++++ src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++++ 2 files changed, 11 insertions(+) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index b42d1960db..86b9fcb481 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -248,6 +248,13 @@ subroutine cropcal_interp(bounds, crop_inst) ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) ig = g_to_ig(patch%gridcell(p)) crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) + + ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + crop_inst%n_growingseasons_thisyear_thispatch = crop_inst%sdates_thisyr(p,1) >= 0 + + ! Only for first sowing date of the year + crop_inst%next_rx_sdate = crop_inst%sdates_thisyr(p,1) + end do end do diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 1eab47a883..369c204719 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -251,6 +251,10 @@ subroutine cropcal_interp(bounds, canopystate_inst) ivt = patch%itype ! SSR TODO: Make below work with arbitrary # of growing seasons per year crop_inst%sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) + crop_inst%n_growingseasons_thisyear_thispatch = crop_inst%sdates_thisyr(p,1) >= 0 + + ! Only for first sowing date of the year + crop_inst%next_rx_sdate = crop_inst%sdates_thisyr(p,1) end do end do deallocate(dataptr2d) From cf34da11f41fb8802a07ed65ff782ed2b771b812 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 15:05:33 -0600 Subject: [PATCH 0043/2067] crop_inst%next_rx_sdate now updated in PlantCrop(). --- src/biogeochem/CNPhenologyMod.F90 | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9de790a39f..2cb020dc36 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2252,6 +2252,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date + next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer @@ -2267,6 +2268,11 @@ subroutine PlantCrop(p, leafcn_in, jday, & idop(p) = jday harvdate(p) = NOT_Harvested growingseason_count = growingseason_count + 1 + if (growingseason_count <= crop_inst%n_growingseasons_thisyear_thispatch) then + next_rx_sdate = crop_inst%sdates_thisyr(p, growingseason_count) + else + next_rx_sdate = -1 + endif leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset From 4cd3110c47075b4eec08af82c2124062a339ef23 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 15:34:04 -0600 Subject: [PATCH 0044/2067] Added boolean namelist parameter generate_crop_gdds. In group cnphenology. Default false. Set to true (along with use_cropcal_streams) in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. I am not allowing generate_crop_gdds set to true if use_cropcal_streams is false. There's no theoretical reason this should be disallowed (would harvest the day before next sowing window began), but I don't see a point to it, and it's extra code to write so I'm skipping it. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + .../namelist_definition_ctsm.xml | 5 ++++ src/biogeochem/CNPhenologyMod.F90 | 30 +++++++++++++++++-- 3 files changed, 33 insertions(+), 3 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index fb17e88026..1b0fd757d4 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -565,6 +565,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). DependsOnLat .false. Constant +.false. 0.5 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 82365eac20..98642a2855 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1094,6 +1094,11 @@ Phenology onset depends on the vegetation type (only used when CN is on) + +Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. + + Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 2cb020dc36..6795a83fc6 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -124,6 +124,8 @@ module CNPhenologyMod real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting + logical, private :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing + ! Constants for seasonal decidious leaf onset and offset logical, private :: onset_thresh_depends_on_veg = .false. ! If onset threshold depends on vegetation type integer, public, parameter :: critical_daylight_constant = 1 @@ -165,7 +167,7 @@ subroutine CNPhenologyReadNML( NLFilename ) character(len=*), parameter :: nmlname = 'cnphenology' !----------------------------------------------------------------------- namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, & - min_critical_dayl_method + min_critical_dayl_method, generate_crop_gdds ! Initialize options to default values, in case they are not specified in ! the namelist @@ -189,6 +191,7 @@ subroutine CNPhenologyReadNML( NLFilename ) call shr_mpi_bcast (initial_seed_at_planting, mpicom) call shr_mpi_bcast (onset_thresh_depends_on_veg, mpicom) call shr_mpi_bcast (min_critical_dayl_method, mpicom) + call shr_mpi_bcast (generate_crop_gdds, mpicom) if ( min_critical_dayl_method == "DependsOnLat" )then critical_daylight_method = critical_daylight_depends_on_lat @@ -1691,6 +1694,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? + logical do_harvest ! Are harvest conditions satisfied? + logical force_harvest ! Should we harvest today no matter what? !------------------------------------------------------------------------ associate( & @@ -2054,7 +2059,26 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then + if (generate_crop_gdds) then + if (.not. use_cropcal_streams) then + write(iulog,*) 'If using generate_crop_gdds, you must set use_cropcal_streams to true.' + call endrun(msg=errMsg(sourcefile, __LINE__)) + endif + if (next_rx_sdate >= 0) then + ! Harvest the day before the next sowing date this year. + do_harvest = jday == next_rx_sdate - 1 + else + ! If this patch has already had all its plantings for the year, don't harvest + ! until some time next year. + do_harvest = .false. + endif + else + ! Original harvest rule + do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p)) + endif + force_harvest = generate_crop_gdds .and. do_harvest + + if ((.not. force_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then cphase(p) = 2._r8 if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 @@ -2080,7 +2104,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! the onset_counter would change from dt and you'd need to make ! changes to the offset subroutine below - else if (hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p))) then + else if (do_harvest) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 From d9a1d0a8ef4b033e2b29aea51a2360450178bf0b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Oct 2021 17:13:23 -0600 Subject: [PATCH 0045/2067] growingseason_count now set to 0 on Jan. 1. --- src/biogeochem/CNPhenologyMod.F90 | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 6795a83fc6..022c87a83a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1728,6 +1728,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year + growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow @@ -1813,6 +1814,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if + if ( jday == 1 .and. mcsec == 0 ) then + growingseason_count = 0 + end if + if ( (.not. croplive(p)) .and. (.not. cropplant(p)) ) then ! gdd needed for * chosen crop and a likely hybrid (for that region) * From 036778afb58355eb41865a277070415e3f7e22e6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Oct 2021 09:52:22 -0600 Subject: [PATCH 0046/2067] Removed cropplant_patch, a vestige of early planning re: crop rotation. In the absence of a system for crop rotation, cropplant was only used to prevent a crop from being re-planted in a given year after it's already been harvested that year (with the beginning of the "year" differing between hemispheres). This is redundant with my new variable crop_inst%growingseason_count, which tracks the number of growing seasons that have begun in a given calendar year (i.e., since 1 Jan 00:00). See discussion at #1500 (https://github.com/ESCOMP/CTSM/issues/1500). --- src/biogeochem/CNPhenologyMod.F90 | 48 ++----------------------------- src/biogeochem/CropType.F90 | 28 ------------------ 2 files changed, 2 insertions(+), 74 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 022c87a83a..86a45b36f0 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1725,7 +1725,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested - cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch @@ -1785,40 +1784,15 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! from AgroIBIS subroutine planting ! --------------------------------- - ! in order to allow a crop to be planted only once each year - ! initialize cropplant = .false., but hold it = .true. through the end of the year - ! initialize other variables that are calculated for crops ! on an annual basis in cropresidue subroutine - if ( jday == jdayyrstart(h) .and. mcsec == 0 )then - - ! make sure variables aren't changed at beginning of the year - ! for a crop that is currently planted, such as - ! WINTER TEMPERATE CEREAL = winter (wheat + barley + rye) - ! represented here by the winter wheat pft - - if (.not. croplive(p)) then - cropplant(p) = .false. - idop(p) = NOT_Planted - - ! keep next for continuous, annual winter temperate cereal crop; - ! if we removed elseif, - ! winter cereal grown continuously would amount to a cereal/fallow - ! rotation because cereal would only be planted every other year - - else if (croplive(p) .and. (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat)) then - cropplant(p) = .false. - ! else ! not possible to have croplive and ivt==cornORsoy? (slevis) - end if - - end if - if ( jday == 1 .and. mcsec == 0 ) then growingseason_count = 0 end if - if ( (.not. croplive(p)) .and. (.not. cropplant(p)) ) then + ! Once outputs can handle >1 planting per year, remove 2nd condition. + if ( (.not. croplive(p)) .and. growingseason_count == 0 ) then ! gdd needed for * chosen crop and a likely hybrid (for that region) * ! to reach full physiological maturity @@ -1841,22 +1815,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then - ! add check to only plant winter cereal after other crops (soybean, maize) - ! have been harvested - - ! *** remember order of planting is crucial - in terms of which crops you want - ! to be grown in what order *** - - ! in this case, corn or soybeans are assumed to be planted before - ! cereal would be in any particular year that both patches are allowed - ! to grow in the same grid cell (e.g., double-cropping) - - ! slevis: harvdate below needs cropplant(p) above to be cropplant(p,ivt(p)) - ! where ivt(p) has rotated to winter cereal because - ! cropplant through the end of the year for a harvested crop. - ! Also harvdate(p) should be harvdate(p,ivt(p)) and should be - ! updated on Jan 1st instead of at harvest (slevis) - ! Are all the normal requirements for planting met? do_plant_normal = (.not. use_cropcal_streams) .and. & a5tmin(p) /= spval .and. & @@ -2279,7 +2237,6 @@ subroutine PlantCrop(p, leafcn_in, jday, & associate( & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested - cropplant => crop_inst%cropplant_patch , & ! Output: [logical (:) ] Flag, true if crop may be planted harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch @@ -2293,7 +2250,6 @@ subroutine PlantCrop(p, leafcn_in, jday, & ! impose limit on growing season length needed ! for crop maturity - for cold weather constraints croplive(p) = .true. - cropplant(p) = .true. idop(p) = jday harvdate(p) = NOT_Harvested growingseason_count = growingseason_count + 1 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index bc0baa9f50..e2313326d9 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -27,10 +27,8 @@ module CropType ! Crop state variables structure type, public :: crop_type - ! Note that cropplant and harvdate could be 2D to facilitate rotation integer , pointer :: nyrs_crop_active_patch (:) ! number of years this crop patch has been active (0 for non-crop patches) logical , pointer :: croplive_patch (:) ! patch Flag, true if planted, not harvested - logical , pointer :: cropplant_patch (:) ! patch Flag, true if planted integer , pointer :: harvdate_patch (:) ! patch harvest date real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen real(r8), pointer :: gddplant_patch (:) ! patch accum gdd past planting date for crop (ddays) @@ -199,7 +197,6 @@ subroutine InitAllocate(this, bounds) allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0 allocate(this%croplive_patch (begp:endp)) ; this%croplive_patch (:) = .false. - allocate(this%cropplant_patch(begp:endp)) ; this%cropplant_patch(:) = .false. allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) allocate(this%fertnitro_patch (begp:endp)) ; this%fertnitro_patch (:) = spval allocate(this%gddplant_patch (begp:endp)) ; this%gddplant_patch (:) = spval @@ -482,31 +479,6 @@ subroutine Restart(this, bounds, ncid, flag) end if deallocate(temp1d) - allocate(temp1d(bounds%begp:bounds%endp)) - if (flag == 'write') then - do p= bounds%begp,bounds%endp - if (this%cropplant_patch(p)) then - temp1d(p) = 1 - else - temp1d(p) = 0 - end if - end do - end if - call restartvar(ncid=ncid, flag=flag, varname='cropplant', xtype=ncd_log, & - dim1name='pft', & - long_name='Flag that crop is planted, but not harvested' , & - interpinic_flag='interp', readvar=readvar, data=temp1d) - if (flag == 'read') then - do p= bounds%begp,bounds%endp - if (temp1d(p) == 1) then - this%cropplant_patch(p) = .true. - else - this%cropplant_patch(p) = .false. - end if - end do - end if - deallocate(temp1d) - call restartvar(ncid=ncid, flag=flag, varname='harvdate', xtype=ncd_int, & dim1name='pft', long_name='harvest date', units='jday', nvalid_range=(/1,366/), & interpinic_flag='interp', readvar=readvar, data=this%harvdate_patch) From d135286758932a82f05763f8fc08360218a2f020 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Oct 2021 15:58:14 -0600 Subject: [PATCH 0047/2067] Compile fixes. --- src/biogeochem/CNPhenologyMod.F90 | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 86a45b36f0..5b9e4a0f0e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1788,11 +1788,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! on an annual basis in cropresidue subroutine if ( jday == 1 .and. mcsec == 0 ) then - growingseason_count = 0 + growingseason_count(p) = 0 end if ! Once outputs can handle >1 planting per year, remove 2nd condition. - if ( (.not. croplive(p)) .and. growingseason_count == 0 ) then + if ( (.not. croplive(p)) .and. growingseason_count(p) == 0 ) then ! gdd needed for * chosen crop and a likely hybrid (for that region) * ! to reach full physiological maturity @@ -1809,7 +1809,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! According to Chris Kucharik, the dataset of ! xinpdate was generated from a previous model run at 0.5 deg resolution - do_plant_prescribed = next_rx_sdate == jday + do_plant_prescribed = next_rx_sdate(p) == jday ! winter temperate cereal : use gdd0 as a limit to plant winter cereal @@ -2027,9 +2027,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & write(iulog,*) 'If using generate_crop_gdds, you must set use_cropcal_streams to true.' call endrun(msg=errMsg(sourcefile, __LINE__)) endif - if (next_rx_sdate >= 0) then + if (next_rx_sdate(p) >= 0) then ! Harvest the day before the next sowing date this year. - do_harvest = jday == next_rx_sdate - 1 + do_harvest = jday == next_rx_sdate(p) - 1 else ! If this patch has already had all its plantings for the year, don't harvest ! until some time next year. @@ -2252,11 +2252,11 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive(p) = .true. idop(p) = jday harvdate(p) = NOT_Harvested - growingseason_count = growingseason_count + 1 - if (growingseason_count <= crop_inst%n_growingseasons_thisyear_thispatch) then - next_rx_sdate = crop_inst%sdates_thisyr(p, growingseason_count) + growingseason_count(p) = growingseason_count(p) + 1 + if (growingseason_count(p) <= crop_inst%n_growingseasons_thisyear_thispatch(p)) then + next_rx_sdate(p) = crop_inst%sdates_thisyr(p, growingseason_count(p)) else - next_rx_sdate = -1 + next_rx_sdate(p) = -1 endif leafc_xfer(p) = initial_seed_at_planting From cebbe302ff53c37261ee5f796fd07764fbe4e5ad Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Oct 2021 16:05:07 -0600 Subject: [PATCH 0048/2067] Corrected namelist definition of stream_fldfilename_sdate. --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 98642a2855..53214231b8 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1801,7 +1801,7 @@ Last year to loop over for crop calendar data Simulation year that aligns with stream_year_first_cropcal value - Filename of input stream data for sowing dates From ea87b765fe9eaed2c04be56db4ccb855b5e3fbcf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Oct 2021 16:10:41 -0600 Subject: [PATCH 0049/2067] Added missing definition of stream_meshfile_cropcal. --- bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 53214231b8..022773d466 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1806,6 +1806,11 @@ Simulation year that aligns with stream_year_first_cropcal value Filename of input stream data for sowing dates + +Filename of input stream data for crop calendar inputs + + Time interpolation method to use with crop calendar streams From c0b685401b40929821bdddb84a96b016b048a593 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Oct 2021 16:39:29 -0600 Subject: [PATCH 0050/2067] Added cropcal_streams logic to CLMBuildNamelist.pm. --- bld/CLMBuildNamelist.pm | 43 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 6c06a46cea..9c65d208e2 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1639,6 +1639,11 @@ sub process_namelist_inline_logic { ################################## setup_logic_lai_streams($opts, $nl_flags, $definition, $defaults, $nl); + ################################## + # namelist group: cropcal_streams # + ################################## + setup_logic_cropcal_streams($opts, $nl_flags, $definition, $defaults, $nl); + ########################################## # namelist group: soil_moisture_streams # ########################################## @@ -3738,6 +3743,43 @@ sub setup_logic_lai_streams { #------------------------------------------------------------------------------- +sub setup_logic_cropcal_streams { + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_cropcal_streams'); + + if ( ! &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_cropcal_streams')) ) { + $log->verbose_message("use_crop set to true, so use_cropcal_streams will have no effect."); + } + + if ( &value_is_true($nl->get_value('use_cropcal_streams')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_cropcal_streams'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcal_mapalgo', + 'hgrid'=>$nl_flags->{'res'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_cropcal') != + $nl->get_value('stream_year_last_cropcal') ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cropcal', + 'hgrid'=>"360x720cru" ); + if ($opts->{'driver'} eq "nuopc" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal', + 'hgrid'=>"360x720cru" ); + } + } +} + +#------------------------------------------------------------------------------- + sub setup_logic_soilwater_movement { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; @@ -4105,6 +4147,7 @@ sub write_output_files { my @groups; @groups = qw(clm_inparm ndepdyn_nml popd_streams urbantv_streams light_streams soil_moisture_streams lai_streams atm2lnd_inparm lnd2atm_inparm clm_canopyhydrology_inparm cnphenology + cropcal_streams clm_soilhydrology_inparm dynamic_subgrid cnvegcarbonstate finidat_consistency_checks dynpft_consistency_checks clm_initinterp_inparm century_soilbgcdecompcascade From 5d62aa5399406c5e13935f792e3df16d753750c0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Oct 2021 16:46:52 -0600 Subject: [PATCH 0051/2067] Correction to setup_logic_cropcal_streams(). --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 9c65d208e2..480ca49942 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3769,7 +3769,7 @@ sub setup_logic_cropcal_streams { 'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cropcal', + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_sdate', 'hgrid'=>"360x720cru" ); if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal', From f4f2deae6e6be0f186a19eeb474e29ede838bb95 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Oct 2021 11:00:29 -0600 Subject: [PATCH 0052/2067] cropcal_interp() now writes to this patch only. --- src/cpl/mct/cropcalStreamMod.F90 | 4 ++-- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 86b9fcb481..80ae469388 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -250,10 +250,10 @@ subroutine cropcal_interp(bounds, crop_inst) crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - crop_inst%n_growingseasons_thisyear_thispatch = crop_inst%sdates_thisyr(p,1) >= 0 + crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%sdates_thisyr(p,1) >= 0 ! Only for first sowing date of the year - crop_inst%next_rx_sdate = crop_inst%sdates_thisyr(p,1) + crop_inst%next_rx_sdate(p) = crop_inst%sdates_thisyr(p,1) end do end do diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 369c204719..6e7efa0380 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -251,10 +251,10 @@ subroutine cropcal_interp(bounds, canopystate_inst) ivt = patch%itype ! SSR TODO: Make below work with arbitrary # of growing seasons per year crop_inst%sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) - crop_inst%n_growingseasons_thisyear_thispatch = crop_inst%sdates_thisyr(p,1) >= 0 + crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%sdates_thisyr(p,1) >= 0 ! Only for first sowing date of the year - crop_inst%next_rx_sdate = crop_inst%sdates_thisyr(p,1) + crop_inst%next_rx_sdate(p) = crop_inst%sdates_thisyr(p,1) end do end do deallocate(dataptr2d) From 415d847a88dff9da87dae0fa58c43e1a7590226b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Oct 2021 15:50:25 -0600 Subject: [PATCH 0053/2067] Attempted fixes for reading of crop sowing dates. Still not working! Also includes a lot of verbosity for debugging. --- src/cpl/mct/cropcalStreamMod.F90 | 63 +++++++++++++++++++++----------- src/main/clm_initializeMod.F90 | 11 +++++- 2 files changed, 50 insertions(+), 24 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 86b9fcb481..6a813102e3 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -45,12 +45,12 @@ subroutine cropcal_init(bounds) ! Initialize data stream information for crop calendars. ! ! !USES: - use clm_varpar , only : mxpft + use clm_varpar , only : cft_lb, cft_ub use clm_time_manager , only : get_calendar use ncdio_pio , only : pio_subsystem use shr_pio_mod , only : shr_pio_getiotype use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField + use shr_string_mod , only : shr_string_listCreateField_range use clm_nlUtilsMod , only : find_nlgroup_name use ndepStreamMod , only : clm_domain_mct use histFileMod , only : hist_addfld1d @@ -129,7 +129,10 @@ subroutine cropcal_init(bounds) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - fldList_sdate1 = shr_string_listCreateField( mxpft, "sdate1" ) + write(iulog,'(a,i6)') ' cft_lb = ',cft_lb + write(iulog,'(a,i6)') ' cft_ub = ',cft_ub + fldList_sdate1 = shr_string_listCreateField_range( cft_lb, cft_ub, "sdate1" ) + write(iulog,*) 'fldList_sdate1 = ',trim(fldList_sdate1) ! SSR TODO: ! - Delete "area" and "mask"? @@ -207,7 +210,7 @@ subroutine cropcal_advance( bounds ) end subroutine cropcal_advance !============================================================================== - subroutine cropcal_interp(bounds, crop_inst) + subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! ! Interpolate data stream information for crop calendars. ! @@ -221,42 +224,58 @@ subroutine cropcal_interp(bounds, crop_inst) ! !ARGUMENTS: implicit none type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter + integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches type(crop_type) , intent(inout) :: crop_inst ! ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig integer :: nc, fp + integer :: patch_gridcell_g character(len=CL) :: stream_var_name !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + write(iulog,*) 'cropcal_interp() A' SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) ! SSR TODO: Make these work with max_growingseasons_per_year > 1 - do nc = 1, get_proc_clumps() - do fp = 1, filter(nc)%num_pcropp - p = filter(nc)%pcropp(fp) - ivt = patch%itype(p) - ! Set crop calendars for each gridcell/patch combination - write(stream_var_name,"(i6)") ivt - - ! SSR TODO: Add check that variable exists in netCDF - stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) - ig = g_to_ig(patch%gridcell(p)) - crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) + write(iulog,*) 'cropcal_interp() B' + do fp = 1, num_pcropp + write(iulog,*) 'cropcal_interp() C' + p = filter_pcropp(fp) + ivt = patch%itype(p) + ! Set crop calendars for each gridcell/patch combination + write(stream_var_name,"(i6)") ivt + + ! SSR TODO: Add check that variable exists in netCDF + write(iulog,*) 'cropcal_interp() D1' + stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) + write(iulog,*) 'cropcal_interp() D2' + ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) + if (ivt /= noveg) then + write(iulog,*) 'cropcal_interp() D3' + write(iulog,'(a,i6)')' p = ', p + write(iulog,'(a,i6)')' ivt = ', ivt + write(iulog,'(a,i6)')' patch%gridcell(p) = ', patch%gridcell(p) + write(iulog,'(a,i6)')' g_to_ig(above) = ', g_to_ig(patch%gridcell(p)) + ig = g_to_ig(patch%gridcell(p)) + write(iulog,*) 'cropcal_interp() D4' + crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) + endif - ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - crop_inst%n_growingseasons_thisyear_thispatch = crop_inst%sdates_thisyr(p,1) >= 0 + ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + write(iulog,*) 'cropcal_interp() E' + crop_inst%n_growingseasons_thisyear_thispatch = crop_inst%sdates_thisyr(p,1) >= 0 - ! Only for first sowing date of the year - crop_inst%next_rx_sdate = crop_inst%sdates_thisyr(p,1) + ! Only for first sowing date of the year + write(iulog,*) 'cropcal_interp() F' + crop_inst%next_rx_sdate = crop_inst%sdates_thisyr(p,1) - end do - end do + end do end subroutine cropcal_interp diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 59280b5672..6cb8f8d831 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -149,7 +149,7 @@ subroutine initialize2(ni,nj) use restFileMod , only : restFile_getfile, restFile_open, restFile_close use restFileMod , only : restFile_read, restFile_write use ndepStreamMod , only : ndep_init, ndep_interp - use cropcalStreamMod , only : cropcal_init, cropcal_interp + use cropcalStreamMod , only : cropcal_init, cropcal_interp, cropcal_advance use LakeCon , only : LakeConInit use SatellitePhenologyMod , only : SatellitePhenologyInit, readAnnualVegetation, interpMonthlyVeg, SatellitePhenology use SnowSnicarMod , only : SnowAge_init, SnowOptics_init @@ -560,7 +560,14 @@ subroutine initialize2(ni,nj) if (use_cropcal_streams) then call t_startf('init_cropcal') call cropcal_init(bounds_proc) - call cropcal_interp(bounds_proc, crop_inst) + call cropcal_advance( bounds_proc ) + !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) + do nc = 1,nclumps + call get_clump_bounds(nc, bounds_clump) + call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) + end do + !$OMP END PARALLEL DO +! call cropcal_interp(bounds_clump, crop_inst) call t_stopf('init_cropcal') end if From 14aca753aa7ca2018b63baddd89cb87abb969d29 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Oct 2021 16:15:54 -0600 Subject: [PATCH 0054/2067] Removed option to change crop calendar interpolation algorithm using namelist. --- bld/CLMBuildNamelist.pm | 2 -- bld/namelist_files/namelist_defaults_ctsm.xml | 2 -- bld/namelist_files/namelist_definition_ctsm.xml | 16 ---------------- src/cpl/mct/cropcalStreamMod.F90 | 14 ++++++-------- src/cpl/share_esmf/cropcalStreamMod.F90 | 8 +++----- 5 files changed, 9 insertions(+), 33 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 9c65d208e2..44326ce3b8 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3754,8 +3754,6 @@ sub setup_logic_cropcal_streams { if ( &value_is_true($nl->get_value('use_cropcal_streams')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_cropcal_streams'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'cropcal_mapalgo', - 'hgrid'=>$nl_flags->{'res'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 1b0fd757d4..3cdb1131b5 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1575,8 +1575,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc -nn - none diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 022773d466..e7137a201e 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1811,22 +1811,6 @@ Filename of input stream data for sowing dates Filename of input stream data for crop calendar inputs - -Time interpolation method to use with crop calendar streams - - - -Mapping method from crop calendar input files to the model resolution - bilinear = bilinear interpolation - nn = nearest neighbor - nnoni = nearest neighbor on the "i" (longitude) axis - nnonj = nearest neighbor on the "j" (latitude) axis - spval = set to special value - copy = copy using the same indices - - diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 80ae469388..522c2070de 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -85,9 +85,7 @@ subroutine cropcal_init(bounds) stream_year_first_cropcal, & stream_year_last_cropcal, & model_year_align_cropcal, & - cropcal_mapalgo, & - stream_fldFileName_sdate, & - cropcal_tintalgo + stream_fldFileName_sdate ! Default values for namelist stream_year_first_cropcal = 1 ! first year in stream to use @@ -109,11 +107,12 @@ subroutine cropcal_init(bounds) end if close(nu_nml) endif - call shr_mpi_bcast(stream_year_first_cropcal , mpicom) - call shr_mpi_bcast(stream_year_last_cropcal , mpicom) - call shr_mpi_bcast(model_year_align_cropcal , mpicom) + call shr_mpi_bcast(stream_year_first_cropcal, mpicom) + call shr_mpi_bcast(stream_year_last_cropcal , mpicom) + call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) - call shr_mpi_bcast(cropcal_tintalgo , mpicom) + !call shr_mpi_bcast(cropcal_mapalgo , mpicom) + !call shr_mpi_bcast(cropcal_tintalgo , mpicom) if (masterproc) then write(iulog,*) ' ' @@ -122,7 +121,6 @@ subroutine cropcal_init(bounds) write(iulog,*) ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,*) ' model_year_align_cropcal = ',model_year_align_cropcal write(iulog,*) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) - write(iulog,*) ' cropcal_tintalgo = ',trim(cropcal_tintalgo) endif call clm_domain_mct (bounds, dom_clm) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 6e7efa0380..2bc63a8ab7 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -75,10 +75,8 @@ subroutine cropcal_init(bounds) stream_year_first_cropcal, & stream_year_last_cropcal, & model_year_align_cropcal, & - cropcal_mapalgo, & stream_fldFileName_sdate, & - stream_meshfile_cropcal, & - cropcal_tintalgo + stream_meshfile_cropcal ! Default values for namelist stream_year_first_cropcal = 1 ! first year in stream to use @@ -110,7 +108,8 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) call shr_mpi_bcast(stream_meshfile_cropcal , mpicom) - call shr_mpi_bcast(cropcal_tintalgo , mpicom) + !call shr_mpi_bcast(cropcal_mapalgo , mpicom) + !call shr_mpi_bcast(cropcal_tintalgo , mpicom) if (masterproc) then write(iulog,*) @@ -120,7 +119,6 @@ subroutine cropcal_init(bounds) write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal write(iulog,'(a,a)' ) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) write(iulog,'(a,a)' ) ' stream_meshfile_cropcal = ',trim(stream_meshfile_cropcal) - write(iulog,'(a,a)' ) ' cropcal_tintalgo = ',trim(cropcal_tintalgo) do n = 1,mxpft write(iulog,'(a,a)' ) ' stream_varnames_sdate = ',trim(stream_varnames_sdate(n)) end do From ad43df1e87b317cb0af88c8347dad847e56eeb49 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Oct 2021 16:16:36 -0600 Subject: [PATCH 0055/2067] Crop calendar interp algorithms now "nearest" instead of "nn". --- src/cpl/mct/cropcalStreamMod.F90 | 4 ++-- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 522c2070de..bff8098788 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -70,8 +70,8 @@ subroutine cropcal_init(bounds) integer :: nml_error ! namelist i/o error flag type(mct_ggrid) :: dom_clm ! domain information character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read - character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm - character(len=CL) :: cropcal_tintalgo = 'nn' ! Time interpolation alogrithm + character(len=CL) :: cropcal_mapalgo = 'nearest' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm ! SSR TODO: Make this work with max_growingseasons_per_year > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 2bc63a8ab7..74021ef7de 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -62,8 +62,8 @@ subroutine cropcal_init(bounds) integer :: nml_error ! namelist i/o error flag character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read character(len=CL) :: stream_meshfile_cropcal ! crop calendar stream meshfile - character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm - character(len=CL) :: cropcal_tintalgo = 'nn' ! Time interpolation alogrithm + character(len=CL) :: cropcal_mapalgo = 'nearest' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm integer :: cropcal_offset = 0 ! Offset in time for dataset (sec) integer :: rc character(*), parameter :: subName = "('cropcaldyn_init')" From 4b0d3c3701e627561965cf1c39957c40f5b87907 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Oct 2021 16:44:33 -0600 Subject: [PATCH 0056/2067] cropcal_mapalgo now correctly 'nn' instead of 'nearest'. --- src/cpl/mct/cropcalStreamMod.F90 | 6 ++---- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index fbabb340d1..9b84c78ceb 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -70,8 +70,8 @@ subroutine cropcal_init(bounds) integer :: nml_error ! namelist i/o error flag type(mct_ggrid) :: dom_clm ! domain information character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read - character(len=CL) :: cropcal_mapalgo = 'nearest' ! Mapping alogrithm - character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm + character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm ! SSR TODO: Make this work with max_growingseasons_per_year > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates @@ -111,8 +111,6 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) - !call shr_mpi_bcast(cropcal_mapalgo , mpicom) - !call shr_mpi_bcast(cropcal_tintalgo , mpicom) if (masterproc) then write(iulog,*) ' ' diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 74021ef7de..70276b1898 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -62,8 +62,8 @@ subroutine cropcal_init(bounds) integer :: nml_error ! namelist i/o error flag character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read character(len=CL) :: stream_meshfile_cropcal ! crop calendar stream meshfile - character(len=CL) :: cropcal_mapalgo = 'nearest' ! Mapping alogrithm - character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm + character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm + character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm integer :: cropcal_offset = 0 ! Offset in time for dataset (sec) integer :: rc character(*), parameter :: subName = "('cropcaldyn_init')" @@ -108,8 +108,6 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) call shr_mpi_bcast(stream_meshfile_cropcal , mpicom) - !call shr_mpi_bcast(cropcal_mapalgo , mpicom) - !call shr_mpi_bcast(cropcal_tintalgo , mpicom) if (masterproc) then write(iulog,*) From 255762f631a65f9d2fe13a24fc975018771af0c6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Oct 2021 16:46:54 -0600 Subject: [PATCH 0057/2067] Removed troubleshooting verbosity related to crop calendars. --- src/cpl/mct/cropcalStreamMod.F90 | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 9b84c78ceb..9fa84b326d 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -125,10 +125,7 @@ subroutine cropcal_init(bounds) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - write(iulog,'(a,i6)') ' cft_lb = ',cft_lb - write(iulog,'(a,i6)') ' cft_ub = ',cft_ub fldList_sdate1 = shr_string_listCreateField_range( cft_lb, cft_ub, "sdate1" ) - write(iulog,*) 'fldList_sdate1 = ',trim(fldList_sdate1) ! SSR TODO: ! - Delete "area" and "mask"? @@ -227,39 +224,27 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig integer :: nc, fp - integer :: patch_gridcell_g character(len=CL) :: stream_var_name !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - write(iulog,*) 'cropcal_interp() A' SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) ! SSR TODO: Make these work with max_growingseasons_per_year > 1 - write(iulog,*) 'cropcal_interp() B' do fp = 1, num_pcropp - write(iulog,*) 'cropcal_interp() C' p = filter_pcropp(fp) ivt = patch%itype(p) ! Set crop calendars for each gridcell/patch combination write(stream_var_name,"(i6)") ivt ! SSR TODO: Add check that variable exists in netCDF - write(iulog,*) 'cropcal_interp() D1' stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) - write(iulog,*) 'cropcal_interp() D2' ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) if (ivt /= noveg) then - write(iulog,*) 'cropcal_interp() D3' - write(iulog,'(a,i6)')' p = ', p - write(iulog,'(a,i6)')' ivt = ', ivt - write(iulog,'(a,i6)')' patch%gridcell(p) = ', patch%gridcell(p) - write(iulog,'(a,i6)')' g_to_ig(above) = ', g_to_ig(patch%gridcell(p)) ig = g_to_ig(patch%gridcell(p)) - write(iulog,*) 'cropcal_interp() D4' crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) endif From b80c6f723b499240174b05d79416ca09f705a1f0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 28 Oct 2021 10:46:05 -0600 Subject: [PATCH 0058/2067] shr_string_listCreateField() with optional field1 is now used. --- src/cpl/mct/cropcalStreamMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 9fa84b326d..5eeff2035b 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -50,7 +50,7 @@ subroutine cropcal_init(bounds) use ncdio_pio , only : pio_subsystem use shr_pio_mod , only : shr_pio_getiotype use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField_range + use shr_string_mod , only : shr_string_listCreateField use clm_nlUtilsMod , only : find_nlgroup_name use ndepStreamMod , only : clm_domain_mct use histFileMod , only : hist_addfld1d @@ -125,7 +125,7 @@ subroutine cropcal_init(bounds) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - fldList_sdate1 = shr_string_listCreateField_range( cft_lb, cft_ub, "sdate1" ) + fldList_sdate1 = shr_string_listCreateField( cft_ub, "sdate1", cft_lb ) ! SSR TODO: ! - Delete "area" and "mask"? From cbaba6884ea8f55ab3ef180ea98ab7876ee0b4f3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 28 Oct 2021 12:01:44 -0600 Subject: [PATCH 0059/2067] cropcal_interp() now called in clm_drv(). --- src/main/clm_driver.F90 | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 94fc879130..db182a74c2 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -13,7 +13,8 @@ module clm_driver use clm_varctl , only : use_cn, use_lch4, use_noio, use_c13, use_c14 use clm_varctl , only : use_crop, irrigate, ndep_from_cpl use clm_varctl , only : use_soil_moisture_streams - use clm_time_manager , only : get_nstep, is_beg_curr_day + use clm_varctl , only : use_cropcal_streams + use clm_time_manager , only : get_nstep, is_beg_curr_day, is_beg_curr_year use clm_time_manager , only : get_prev_date, is_first_step use clm_varpar , only : nlevsno, nlevgrnd use clm_varorb , only : obliqr @@ -58,7 +59,7 @@ module clm_driver use SoilBiogeochemVerticalProfileMod , only : SoilBiogeochemVerticalProfile use SatellitePhenologyMod , only : SatellitePhenology, interpMonthlyVeg use ndepStreamMod , only : ndep_interp - use cropcalStreamMod , only : cropcal_advance + use cropcalStreamMod , only : cropcal_advance, cropcal_interp use ch4Mod , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check use DUSTMod , only : DustDryDep, DustEmission use VOCEmissionMod , only : VOCEmission @@ -448,8 +449,11 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call lai_advance( bounds_proc ) endif - ! Advance crop calendar data - call cropcal_advance( bounds_proc ) + ! When crop calendar streams are being used + ! NOTE: This call needs to happen outside loops over nclumps (as streams are not threadsafe) + if (use_cropcal_streams .and. is_beg_curr_year()) then + call cropcal_advance( bounds_proc ) + end if ! ============================================================================ ! Initialize variables from previous time step, downscale atm forcings, and @@ -1033,6 +1037,13 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro frictionvel_inst, photosyns_inst, drydepvel_inst) call t_stopf('depvel') + if (use_cropcal_streams .and. is_beg_curr_year()) then + ! ============================================================================ + ! Update crop calendars + ! ============================================================================ + call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) + end if + ! ============================================================================ ! Calculate soil/snow hydrology with drainage (subsurface runoff) ! ============================================================================ From a3556d4d02b64e7bb54fe5a684c7a70542cd49fe Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 1 Nov 2021 17:29:10 -0600 Subject: [PATCH 0060/2067] Now uses my fork of CESM_share. --- Externals.cfg | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index 0c149001f1..6ca8be3cc1 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -63,9 +63,11 @@ local_path = components/cpl7 required = True [share] -tag = share1.0.2 +#repo_url = https://github.com/ESCOMP/CESM_share +#tag = share1.0.2 +repo_url = https://github.com/samsrabin/CESM_share +tag = 202110281057 protocol = git -repo_url = https://github.com/ESCOMP/CESM_share local_path = share required = True From 5082617a54af133ccc3ac80bc08db2c6b9a23ef4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 13:23:10 -0600 Subject: [PATCH 0061/2067] Renamed sdates_thisyr to rx_sdates_thisyr. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- src/biogeochem/CropType.F90 | 6 +++--- src/cpl/mct/cropcalStreamMod.F90 | 6 +++--- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 +++--- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 5b9e4a0f0e..ebf5e89e73 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2254,7 +2254,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & harvdate(p) = NOT_Harvested growingseason_count(p) = growingseason_count(p) + 1 if (growingseason_count(p) <= crop_inst%n_growingseasons_thisyear_thispatch(p)) then - next_rx_sdate(p) = crop_inst%sdates_thisyr(p, growingseason_count(p)) + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, growingseason_count(p)) else next_rx_sdate(p) = -1 endif diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index e2313326d9..7a93818e3f 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -40,7 +40,7 @@ module CropType real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year - integer , pointer :: sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year + integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year integer :: max_growingseasons_per_year ! maximum number of growing seasons per year allowed in any patch @@ -205,11 +205,11 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 - allocate(this%sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) + allocate(this%rx_sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 - this%sdates_thisyr(:,:) = -1 + this%rx_sdates_thisyr(:,:) = -1 end subroutine InitAllocate diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 5eeff2035b..8bb7581de0 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -245,14 +245,14 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) if (ivt /= noveg) then ig = g_to_ig(patch%gridcell(p)) - crop_inst%sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) + crop_inst%rx_sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) endif ! SSR TODO: Make this work with max_growingseasons_per_year > 1 - crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%sdates_thisyr(p,1) >= 0 + crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%rx_sdates_thisyr(p,1) >= 0 ! Only for first sowing date of the year - crop_inst%next_rx_sdate(p) = crop_inst%sdates_thisyr(p,1) + crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) end do diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 70276b1898..d57bf31448 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -246,11 +246,11 @@ subroutine cropcal_interp(bounds, canopystate_inst) ig = g_to_ig(patch%gridcell(p)) ivt = patch%itype ! SSR TODO: Make below work with arbitrary # of growing seasons per year - crop_inst%sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) - crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%sdates_thisyr(p,1) >= 0 + crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) + crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%rx_sdates_thisyr(p,1) >= 0 ! Only for first sowing date of the year - crop_inst%next_rx_sdate(p) = crop_inst%sdates_thisyr(p,1) + crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) end do end do deallocate(dataptr2d) From 7b63bf025fc6509713a0a1ae09c1e1032da5675c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 14:33:47 -0600 Subject: [PATCH 0062/2067] Added [sh]dates_thisyr arrays to crop_type. Updated upon planting and harvest, respectively, but they don't actually go anywhere yet. --- src/biogeochem/CNPhenologyMod.F90 | 7 +++++++ src/biogeochem/CropType.F90 | 8 +++++++- 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ebf5e89e73..e1d73ead1c 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1686,6 +1686,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer c ! column indices integer g ! gridcell indices integer h ! hemisphere indices + integer s ! growing season indices integer idpp ! number of days past planting real(r8) :: dtrad ! radiation time step delta t (seconds) real(r8) dayspyr ! days per year @@ -1789,6 +1790,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if ( jday == 1 .and. mcsec == 0 ) then growingseason_count(p) = 0 + do s = 1, crop_inst%max_growingseasons_per_year + crop_inst%sdates_thisyr(p,s) = -1 + crop_inst%hdates_thisyr(p,s) = -1 + end do end if ! Once outputs can handle >1 planting per year, remove 2nd condition. @@ -2069,6 +2074,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (do_harvest) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday + crop_inst%hdates_thisyr(p, growingseason_count) = jday croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 if (tlai(p) > 0._r8) then ! plant had emerged before harvest @@ -2258,6 +2264,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & else next_rx_sdate(p) = -1 endif + crop_inst%sdates_thisyr(p,growingseason_count(p)) = jday leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 7a93818e3f..aec73a7582 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -29,7 +29,7 @@ module CropType integer , pointer :: nyrs_crop_active_patch (:) ! number of years this crop patch has been active (0 for non-crop patches) logical , pointer :: croplive_patch (:) ! patch Flag, true if planted, not harvested - integer , pointer :: harvdate_patch (:) ! patch harvest date + integer , pointer :: harvdate_patch (:) ! most recent patch harvest date; 999 if currently (or never) planted real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen real(r8), pointer :: gddplant_patch (:) ! patch accum gdd past planting date for crop (ddays) real(r8), pointer :: gddtsoi_patch (:) ! patch growing degree-days from planting (top two soil layers) (ddays) @@ -41,6 +41,8 @@ module CropType real(r8) :: baset_latvary_slope integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year + integer , pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year + integer , pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year integer :: max_growingseasons_per_year ! maximum number of growing seasons per year allowed in any patch @@ -206,10 +208,14 @@ subroutine InitAllocate(this, bounds) allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 allocate(this%rx_sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) + allocate(this%sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) + allocate(this%hdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 this%rx_sdates_thisyr(:,:) = -1 + this%sdates_thisyr(:,:) = -1 + this%hdates_thisyr(:,:) = -1 end subroutine InitAllocate From b06e915108c0df08e46a8d9ef618644f829a706e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 15:06:45 -0600 Subject: [PATCH 0063/2067] Now saves SDATES and HDATES outputs. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- src/biogeochem/CropType.F90 | 25 ++++++++++++++++++------- src/main/histFileMod.F90 | 12 +++++++++--- 3 files changed, 29 insertions(+), 12 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e1d73ead1c..b64856fd43 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -26,7 +26,7 @@ module CNPhenologyMod use CNVegCarbonFluxType , only : cnveg_carbonflux_type use CNVegnitrogenstateType , only : cnveg_nitrogenstate_type use CNVegnitrogenfluxType , only : cnveg_nitrogenflux_type - use CropType , only : crop_type + use CropType , only : crop_type, max_growingseasons_per_year use pftconMod , only : pftcon use SoilStateType , only : soilstate_type use TemperatureType , only : temperature_type @@ -1790,7 +1790,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if ( jday == 1 .and. mcsec == 0 ) then growingseason_count(p) = 0 - do s = 1, crop_inst%max_growingseasons_per_year + do s = 1, max_growingseasons_per_year crop_inst%sdates_thisyr(p,s) = -1 crop_inst%hdates_thisyr(p,s) = -1 end do diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index aec73a7582..503cc756fb 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -20,7 +20,12 @@ module CropType ! ! !PUBLIC TYPES: implicit none + save private + ! Constants + ! + ! SSR TODO: Replace this with read from netCDF + integer , public :: max_growingseasons_per_year = 1 ! maximum number of growing seasons per year allowed in any patch ! ! !PUBLIC DATA TYPES: ! @@ -45,7 +50,6 @@ module CropType integer , pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year - integer :: max_growingseasons_per_year ! maximum number of growing seasons per year allowed in any patch contains ! Public routines @@ -194,9 +198,6 @@ subroutine InitAllocate(this, bounds) begp = bounds%begp; endp = bounds%endp - ! SSR TODO: Replace this with read from netCDF - this%max_growingseasons_per_year = 1 - allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0 allocate(this%croplive_patch (begp:endp)) ; this%croplive_patch (:) = .false. allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) @@ -207,9 +208,9 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 - allocate(this%rx_sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) - allocate(this%sdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) - allocate(this%hdates_thisyr(begp:endp,1:this%max_growingseasons_per_year)) + allocate(this%rx_sdates_thisyr(begp:endp,1:max_growingseasons_per_year)) + allocate(this%sdates_thisyr(begp:endp,1:max_growingseasons_per_year)) + allocate(this%hdates_thisyr(begp:endp,1:max_growingseasons_per_year)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 @@ -264,6 +265,16 @@ subroutine InitHistory(this, bounds) ptr_patch=this%latbaset_patch, default='inactive') end if + this%sdates_thisyr(begp:endp,:) = -1 + call hist_addfld2d (fname='SDATES', units='day of year', type2d='max_growingseasons_per_year', & + avgflag='I', long_name='actual crop sowing dates; should only be output annually', & + ptr_col=this%sdates_thisyr, default='inactive') + + this%hdates_thisyr(begp:endp,:) = -1 + call hist_addfld2d (fname='HDATES', units='day of year', type2d='max_growingseasons_per_year', & + avgflag='I', long_name='actual crop harvest dates; should only be output annually', & + ptr_col=this%hdates_thisyr, default='inactive') + end subroutine InitHistory subroutine InitCold(this, bounds) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index cc4e23293e..2279d1e4cf 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -193,7 +193,7 @@ module histFileMod character(len=max_chars) :: units ! units character(len=hist_dim_name_length) :: type1d ! pointer to first dimension type from data type (nameg, etc) character(len=hist_dim_name_length) :: type1d_out ! hbuf first dimension type from data type (nameg, etc) - character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)"] + character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","max_growingseasons_per_year] integer :: beg1d ! on-node 1d clm pointer start index integer :: end1d ! on-node 1d clm pointer end index integer :: num1d ! size of clm pointer first dimension (all nodes) @@ -1271,7 +1271,7 @@ subroutine hist_update_hbuf(bounds) integer :: num2d ! size of second dimension (e.g. number of vertical levels) integer :: numdims ! number of dimensions character(len=*),parameter :: subname = 'hist_update_hbuf' - character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)"] + character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","max_growingseasons_per_year"] !----------------------------------------------------------------------- do t = 1,ntapes @@ -2285,6 +2285,7 @@ subroutine htape_create (t, histrest) use clm_varctl , only : version, hostname, username, conventions, source use domainMod , only : ldomain use fileutils , only : get_filename + use CropType , only : max_growingseasons_per_year ! ! !ARGUMENTS: integer, intent(in) :: t ! tape index @@ -2420,6 +2421,7 @@ subroutine htape_create (t, histrest) call ncd_defdim(lnfid, 'ltype', max_lunit, dimid) call ncd_defdim(lnfid, 'nlevcan',nlevcan, dimid) call ncd_defdim(lnfid, 'nvegwcs',nvegwcs, dimid) + call ncd_defdim(lnfid, 'max_growingseasons_per_year' , max_growingseasons_per_year , dimid) call htape_add_ltype_metadata(lnfid) call htape_add_ctype_metadata(lnfid) call ncd_defdim(lnfid, 'natpft', natpft_size, dimid) @@ -4138,6 +4140,7 @@ subroutine hist_restart_ncd (bounds, ncid, flag, rdate) use clm_time_manager, only : is_restart use restUtilMod , only : iflag_skip use pio + use CropType , only : max_growingseasons_per_year ! ! !ARGUMENTS: type(bounds_type), intent(in) :: bounds @@ -5342,6 +5345,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, numrad, nlevdecomp_full, nlevcan, nvegwcs,nlevsoi use clm_varpar , only : natpft_size, cft_size, maxpatch_glc use landunit_varcon , only : max_lunit + use CropType , only : max_growingseasons_per_year ! ! !ARGUMENTS: character(len=*), intent(in) :: fname ! field name @@ -5420,6 +5424,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, num2d = numrad case ('levdcmp') num2d = nlevdecomp_full + case ('max_growingseasons_per_year') + num2d = max_growingseasons_per_year case ('fates_levscls') num2d = nlevsclass case('fates_levcacls') @@ -5487,7 +5493,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, case default write(iulog,*) trim(subname),' ERROR: unsupported 2d type ',type2d, & ' currently supported types for multi level fields are: ', & - '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs]' + '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs,max_growingseasons_per_year]' call endrun(msg=errMsg(sourcefile, __LINE__)) end select From 3fb6ca9ea1937e2862c8658b031514e0f8a65703 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 15:15:22 -0600 Subject: [PATCH 0064/2067] [sh]dates_thisyr now real(r8). --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- src/biogeochem/CropType.F90 | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b64856fd43..edc0cf01a0 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1791,8 +1791,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if ( jday == 1 .and. mcsec == 0 ) then growingseason_count(p) = 0 do s = 1, max_growingseasons_per_year - crop_inst%sdates_thisyr(p,s) = -1 - crop_inst%hdates_thisyr(p,s) = -1 + crop_inst%sdates_thisyr(p,s) = -1._r8 + crop_inst%hdates_thisyr(p,s) = -1._r8 end do end if diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 503cc756fb..cb64b5dfa0 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -215,8 +215,8 @@ subroutine InitAllocate(this, bounds) allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 this%rx_sdates_thisyr(:,:) = -1 - this%sdates_thisyr(:,:) = -1 - this%hdates_thisyr(:,:) = -1 + this%sdates_thisyr(:,:) = -1._r8 + this%hdates_thisyr(:,:) = -1._r8 end subroutine InitAllocate @@ -265,12 +265,12 @@ subroutine InitHistory(this, bounds) ptr_patch=this%latbaset_patch, default='inactive') end if - this%sdates_thisyr(begp:endp,:) = -1 + this%sdates_thisyr(begp:endp,:) = -1._r8 call hist_addfld2d (fname='SDATES', units='day of year', type2d='max_growingseasons_per_year', & avgflag='I', long_name='actual crop sowing dates; should only be output annually', & ptr_col=this%sdates_thisyr, default='inactive') - this%hdates_thisyr(begp:endp,:) = -1 + this%hdates_thisyr(begp:endp,:) = -1._r8 call hist_addfld2d (fname='HDATES', units='day of year', type2d='max_growingseasons_per_year', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_col=this%hdates_thisyr, default='inactive') From 9f8e7a60ef059da78cdb0c8864f8ff3a0edc5acf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 15:37:18 -0600 Subject: [PATCH 0065/2067] max_growingseasons_per_year is now mxgrowseas. Moved from CropModule to clm_varpar to avoid circular dependency. --- src/biogeochem/CNPhenologyMod.F90 | 6 +++--- src/biogeochem/CropType.F90 | 5 ----- src/cpl/mct/cropcalStreamMod.F90 | 2 +- src/main/clm_varpar.F90 | 1 + src/main/histFileMod.F90 | 21 +++++++++------------ 5 files changed, 14 insertions(+), 21 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index edc0cf01a0..e1ba0c39f4 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -14,7 +14,7 @@ module CNPhenologyMod use shr_log_mod , only : errMsg => shr_log_errMsg use shr_sys_mod , only : shr_sys_flush use decompMod , only : bounds_type - use clm_varpar , only : maxveg, nlevdecomp_full + use clm_varpar , only : maxveg, nlevdecomp_full, mxgrowseas use clm_varpar , only : i_litr_min, i_litr_max use clm_varctl , only : iulog, use_cndv use clm_varcon , only : tfrz @@ -26,7 +26,7 @@ module CNPhenologyMod use CNVegCarbonFluxType , only : cnveg_carbonflux_type use CNVegnitrogenstateType , only : cnveg_nitrogenstate_type use CNVegnitrogenfluxType , only : cnveg_nitrogenflux_type - use CropType , only : crop_type, max_growingseasons_per_year + use CropType , only : crop_type use pftconMod , only : pftcon use SoilStateType , only : soilstate_type use TemperatureType , only : temperature_type @@ -1790,7 +1790,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if ( jday == 1 .and. mcsec == 0 ) then growingseason_count(p) = 0 - do s = 1, max_growingseasons_per_year + do s = 1, mxgrowseas crop_inst%sdates_thisyr(p,s) = -1._r8 crop_inst%hdates_thisyr(p,s) = -1._r8 end do diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index cb64b5dfa0..f286918073 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -20,12 +20,7 @@ module CropType ! ! !PUBLIC TYPES: implicit none - save private - ! Constants - ! - ! SSR TODO: Replace this with read from netCDF - integer , public :: max_growingseasons_per_year = 1 ! maximum number of growing seasons per year allowed in any patch ! ! !PUBLIC DATA TYPES: ! diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 8bb7581de0..84a3a5370c 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -30,7 +30,7 @@ module cropcalStreamMod ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - ! SSR TODO: Make these work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 type(shr_strdata_type) :: sdat_sdate ! sowing date input data stream character(len=*), parameter :: sourcefile = & diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index e8d62453d3..87c7045f71 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -51,6 +51,7 @@ module clm_varpar integer, public, parameter :: dst_src_nbr = 3 ! number of size distns in src soil (BGC only) integer, public, parameter :: sz_nbr = 200 ! number of sub-grid bins in large bin of dust size distribution (BGC only) integer, public, parameter :: mxpft = 78 ! maximum number of PFT's for any mode; + integer, public, parameter :: mxgrowseas = 1 ! maximum number of crop growing seasons to begin in any year; ! FIX(RF,032414) might we set some of these automatically from reading pft-physiology? integer, public, parameter :: nlayer = 3 ! number of VIC soil layer --Added by AWang integer, public :: nlayert ! number of VIC soil layer + 3 lower thermal layers diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 2279d1e4cf..9b5de0edd8 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -193,7 +193,7 @@ module histFileMod character(len=max_chars) :: units ! units character(len=hist_dim_name_length) :: type1d ! pointer to first dimension type from data type (nameg, etc) character(len=hist_dim_name_length) :: type1d_out ! hbuf first dimension type from data type (nameg, etc) - character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","max_growingseasons_per_year] + character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","mxgrowseas"] integer :: beg1d ! on-node 1d clm pointer start index integer :: end1d ! on-node 1d clm pointer end index integer :: num1d ! size of clm pointer first dimension (all nodes) @@ -1271,7 +1271,7 @@ subroutine hist_update_hbuf(bounds) integer :: num2d ! size of second dimension (e.g. number of vertical levels) integer :: numdims ! number of dimensions character(len=*),parameter :: subname = 'hist_update_hbuf' - character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","max_growingseasons_per_year"] + character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","mxgrowseas"] !----------------------------------------------------------------------- do t = 1,ntapes @@ -2279,13 +2279,12 @@ subroutine htape_create (t, histrest) ! ! !USES: use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, nlevurb, nlevmaxurbgrnd, numrad, nlevcan, nvegwcs,nlevsoi - use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, nlevdecomp_full + use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, nlevdecomp_full, mxgrowseas use landunit_varcon , only : max_lunit use clm_varctl , only : caseid, ctitle, fsurdat, finidat, paramfile use clm_varctl , only : version, hostname, username, conventions, source use domainMod , only : ldomain use fileutils , only : get_filename - use CropType , only : max_growingseasons_per_year ! ! !ARGUMENTS: integer, intent(in) :: t ! tape index @@ -2421,7 +2420,7 @@ subroutine htape_create (t, histrest) call ncd_defdim(lnfid, 'ltype', max_lunit, dimid) call ncd_defdim(lnfid, 'nlevcan',nlevcan, dimid) call ncd_defdim(lnfid, 'nvegwcs',nvegwcs, dimid) - call ncd_defdim(lnfid, 'max_growingseasons_per_year' , max_growingseasons_per_year , dimid) + call ncd_defdim(lnfid, 'mxgrowseas' , mxgrowseas , dimid) call htape_add_ltype_metadata(lnfid) call htape_add_ctype_metadata(lnfid) call ncd_defdim(lnfid, 'natpft', natpft_size, dimid) @@ -4136,11 +4135,10 @@ subroutine hist_restart_ncd (bounds, ncid, flag, rdate) use clm_varctl , only : nsrest, caseid, inst_suffix, nsrStartup, nsrBranch use fileutils , only : getfil use domainMod , only : ldomain - use clm_varpar , only : nlevgrnd, nlevlak, numrad, nlevdecomp_full + use clm_varpar , only : nlevgrnd, nlevlak, numrad, nlevdecomp_full, mxgrowseas use clm_time_manager, only : is_restart use restUtilMod , only : iflag_skip use pio - use CropType , only : max_growingseasons_per_year ! ! !ARGUMENTS: type(bounds_type), intent(in) :: bounds @@ -5343,9 +5341,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, ! ! !USES: use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, numrad, nlevdecomp_full, nlevcan, nvegwcs,nlevsoi - use clm_varpar , only : natpft_size, cft_size, maxpatch_glc + use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, mxgrowseas use landunit_varcon , only : max_lunit - use CropType , only : max_growingseasons_per_year ! ! !ARGUMENTS: character(len=*), intent(in) :: fname ! field name @@ -5424,8 +5421,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, num2d = numrad case ('levdcmp') num2d = nlevdecomp_full - case ('max_growingseasons_per_year') - num2d = max_growingseasons_per_year + case ('mxgrowseas') + num2d = mxgrowseas case ('fates_levscls') num2d = nlevsclass case('fates_levcacls') @@ -5493,7 +5490,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, case default write(iulog,*) trim(subname),' ERROR: unsupported 2d type ',type2d, & ' currently supported types for multi level fields are: ', & - '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs,max_growingseasons_per_year]' + '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs,mxgrowseas]' call endrun(msg=errMsg(sourcefile, __LINE__)) end select From ef6a960c19ee4aea64fe4feaf3f29818bfb3bd8f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 15:50:12 -0600 Subject: [PATCH 0066/2067] Completed conversion of max_growingseasons_per_year to mxgrowseas. --- src/biogeochem/CropType.F90 | 10 +++++----- src/cpl/mct/cropcalStreamMod.F90 | 12 ++++++------ 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index f286918073..ffed56b774 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -203,9 +203,9 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 - allocate(this%rx_sdates_thisyr(begp:endp,1:max_growingseasons_per_year)) - allocate(this%sdates_thisyr(begp:endp,1:max_growingseasons_per_year)) - allocate(this%hdates_thisyr(begp:endp,1:max_growingseasons_per_year)) + allocate(this%rx_sdates_thisyr(begp:endp,1:mxgrowseas)) + allocate(this%sdates_thisyr(begp:endp,1:mxgrowseas)) + allocate(this%hdates_thisyr(begp:endp,1:mxgrowseas)) allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 @@ -261,12 +261,12 @@ subroutine InitHistory(this, bounds) end if this%sdates_thisyr(begp:endp,:) = -1._r8 - call hist_addfld2d (fname='SDATES', units='day of year', type2d='max_growingseasons_per_year', & + call hist_addfld2d (fname='SDATES', units='day of year', type2d='mxgrowseas', & avgflag='I', long_name='actual crop sowing dates; should only be output annually', & ptr_col=this%sdates_thisyr, default='inactive') this%hdates_thisyr(begp:endp,:) = -1._r8 - call hist_addfld2d (fname='HDATES', units='day of year', type2d='max_growingseasons_per_year', & + call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxgrowseas', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_col=this%hdates_thisyr, default='inactive') diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 84a3a5370c..9e68bd7590 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -73,7 +73,7 @@ subroutine cropcal_init(bounds) character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm - ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates character(*), parameter :: subName = "('cropcaldyn_init')" @@ -124,7 +124,7 @@ subroutine cropcal_init(bounds) call clm_domain_mct (bounds, dom_clm) ! create the field list for these cropcal fields...use in shr_strdata_create - ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 fldList_sdate1 = shr_string_listCreateField( cft_ub, "sdate1", cft_lb ) ! SSR TODO: @@ -188,7 +188,7 @@ subroutine cropcal_advance( bounds ) call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day - ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 call shr_strdata_advance(sdat_sdate, mcdate, sec, mpicom, 'cropcaldyn') if ( .not. allocated(g_to_ig) )then @@ -229,11 +229,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - ! SSR TODO: Make these work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -248,7 +248,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) endif - ! SSR TODO: Make this work with max_growingseasons_per_year > 1 + ! SSR TODO: Make this work with mxgrowseas > 1 crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%rx_sdates_thisyr(p,1) >= 0 ! Only for first sowing date of the year From 453095b039ac7679e60f72dd8dd09e3fb84befdd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 16:01:05 -0600 Subject: [PATCH 0067/2067] Added use of clm_varpar for mxgrowseas. --- src/biogeochem/CropType.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index ffed56b774..b337af20ba 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -181,6 +181,8 @@ end subroutine ReadNML subroutine InitAllocate(this, bounds) ! !USES: ! + use clm_varpar, only : mxgrowseas + ! ! !ARGUMENTS: class(crop_type) , intent(inout) :: this type(bounds_type), intent(in) :: bounds From 11db73fdfbdd2f213a916fb04ce91ff5bb39a6f7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 16:03:23 -0600 Subject: [PATCH 0068/2067] Added use of hist_addfld2d. --- src/biogeochem/CropType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index b337af20ba..fef7348a69 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -221,7 +221,7 @@ end subroutine InitAllocate subroutine InitHistory(this, bounds) ! ! !USES: - use histFileMod , only : hist_addfld1d + use histFileMod , only : hist_addfld1d, hist_addfld2d ! ! !ARGUMENTS: class(crop_type), intent(inout) :: this From c4704e76c7f39109af1b0f37d93e60c1e9630e54 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Nov 2021 16:34:47 -0600 Subject: [PATCH 0069/2067] [sh]dates_thisyr now FULLY real(r8). --- src/biogeochem/CropType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index fef7348a69..2db1c91862 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -41,8 +41,8 @@ module CropType real(r8) :: baset_latvary_slope integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year - integer , pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year - integer , pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year + real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year + real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year From abb5f389f9342a9da02ff9b43b96aa3b4bacadd0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 9 Nov 2021 11:28:05 -0700 Subject: [PATCH 0070/2067] [SH]DATES now uses dimension pft instead of lndgrid. --- src/biogeochem/CropType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 2db1c91862..7d67c7be55 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -265,12 +265,12 @@ subroutine InitHistory(this, bounds) this%sdates_thisyr(begp:endp,:) = -1._r8 call hist_addfld2d (fname='SDATES', units='day of year', type2d='mxgrowseas', & avgflag='I', long_name='actual crop sowing dates; should only be output annually', & - ptr_col=this%sdates_thisyr, default='inactive') + ptr_patch=this%sdates_thisyr, default='inactive') this%hdates_thisyr(begp:endp,:) = -1._r8 call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxgrowseas', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & - ptr_col=this%hdates_thisyr, default='inactive') + ptr_patch=this%hdates_thisyr, default='inactive') end subroutine InitHistory From ee9059a2e5ac3b96ead04900e30e94192788c5e1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 9 Nov 2021 14:31:02 -0700 Subject: [PATCH 0071/2067] CropPhenology() now uses is_beg_curr_year(). --- src/biogeochem/CNPhenologyMod.F90 | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e1ba0c39f4..c3a578d07c 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1647,7 +1647,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! handle CN fluxes during the phenological onset & offset periods. ! !USES: - use clm_time_manager , only : get_curr_date, get_curr_calday, get_days_per_year, get_rad_step_size + use clm_time_manager , only : get_curr_calday, get_days_per_year, get_rad_step_size, is_beg_curr_year use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice @@ -1677,10 +1677,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & type(cnveg_carbonstate_type) , intent(inout) :: c14_cnveg_carbonstate_inst ! ! LOCAL VARAIBLES: - integer kyr ! current year - integer kmo ! month of year (1, ..., 12) - integer kda ! day of month (1, ..., 31) - integer mcsec ! seconds of day (0, ..., seconds/day) integer jday ! julian day of the year integer fp,p ! patch indices integer c ! column indices @@ -1760,7 +1756,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! get time info dayspyr = get_days_per_year() jday = get_curr_calday() - call get_curr_date(kyr, kmo, kda, mcsec) dtrad = real( get_rad_step_size(), r8 ) if (use_fertilizer) then @@ -1788,7 +1783,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! initialize other variables that are calculated for crops ! on an annual basis in cropresidue subroutine - if ( jday == 1 .and. mcsec == 0 ) then + if ( is_beg_curr_year() ) then growingseason_count(p) = 0 do s = 1, mxgrowseas crop_inst%sdates_thisyr(p,s) = -1._r8 From a77bcd3911365989da0b80d055aae795fd373852 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 Nov 2021 11:44:48 -0700 Subject: [PATCH 0072/2067] CropPhenology() now disallows "normal" and "lastchance" burning when use_cropcal_streams is true, unless read-in sowing date is negative. --- src/biogeochem/CNPhenologyMod.F90 | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c3a578d07c..12e3e207e0 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1691,6 +1691,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? + logical allow_unprescribed_planting ! should crop be allowed to be planted according to sowing window rules? logical do_harvest ! Are harvest conditions satisfied? logical force_harvest ! Should we harvest today no matter what? !------------------------------------------------------------------------ @@ -1811,19 +1812,24 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_plant_prescribed = next_rx_sdate(p) == jday + ! Only allow sowing according to normal "window" rules if not using prescribed + ! sowing dates at all, or if this cell had no values in the prescribed sowing + ! date file. + allow_unprescribed_planting = (.not. use_cropcal_streams) .or. crop_inst%rx_sdates_thisyr(p,1)<0 + ! winter temperate cereal : use gdd0 as a limit to plant winter cereal if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then ! Are all the normal requirements for planting met? - do_plant_normal = (.not. use_cropcal_streams) .and. & + do_plant_normal = allow_unprescribed_planting .and. & a5tmin(p) /= spval .and. & a5tmin(p) <= minplanttemp(ivt(p)) .and. & jday >= minplantjday(ivt(p),h) .and. & (gdd020(p) /= spval .and. & gdd020(p) >= gddmin(ivt(p))) ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = (.not. use_cropcal_streams) .and. & + do_plant_lastchance = allow_unprescribed_planting .and. & (.not. do_plant_normal) .and. & jday >= maxplantjday(ivt(p),h) .and. & gdd020(p) /= spval .and. & @@ -1851,7 +1857,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! while the gdd part is either true or false for the year. ! Are all the normal requirements for planting met? - do_plant_normal = (.not. use_cropcal_streams) .and. & + do_plant_normal = allow_unprescribed_planting .and. & t10(p) /= spval .and. a10tmin(p) /= spval .and. & t10(p) > planttemp(ivt(p)) .and. & a10tmin(p) > minplanttemp(ivt(p)) .and. & @@ -1860,7 +1866,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & gdd820(p) /= spval .and. & gdd820(p) >= gddmin(ivt(p)) ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = (.not. use_cropcal_streams) .and. & + do_plant_lastchance = allow_unprescribed_planting .and. & (.not. do_plant_normal) .and. & jday == maxplantjday(ivt(p),h) .and. & gdd820(p) > 0._r8 .and. & From c3a29531bce74523c6f1e76f19aa1f64d243ffdd Mon Sep 17 00:00:00 2001 From: "Miles A. Curry" Date: Wed, 17 Nov 2021 16:01:11 -0700 Subject: [PATCH 0073/2067] Add maps, fsurdat for MPAS grids 480, 240, 120, 60, 30, 15 --- bld/namelist_files/namelist_defaults_ctsm.xml | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 8a10a96ebf..338aebc95d 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -801,6 +801,36 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 + @@ -1099,6 +1129,19 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_si lnd/clm2/surfdata_map/ctsm1.0.dev094-2-g633be0eb/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c200521.nc + +lnd/clm2/surfdata_map/surfdata_mpasa480_hist_78pfts_CMIP6_simyr2000_c211110.nc + +lnd/clm2/surfdata_map/surfdata_mpasa240_hist_78pfts_CMIP6_simyr2000_c211115.nc + +lnd/clm2/surfdata_map/surfdata_mpasa120_hist_78pfts_CMIP6_simyr2000_c211108.nc + +lnd/clm2/surfdata_map/surfdata_mpasa60_hist_78pfts_CMIP6_simyr2000_c211110.nc + +lnd/clm2/surfdata_map/surfdata_mpasa30_hist_78pfts_CMIP6_simyr2000_c211111.nc + +lnd/clm2/surfdata_map/surfdata_mpasa15_hist_78pfts_CMIP6_simyr2000_c211111.nc + lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc @@ -1144,6 +1187,19 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_16pfts_Irrig_CMIP6_sim lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc + +lnd/clm2/surfdata_map/surfdata_mpasa480_hist_78pfts_CMIP6_simyr1850_c211110.nc + +lnd/clm2/surfdata_map/surfdata_mpasa240_hist_78pfts_CMIP6_simyr1850_c211115.nc + +lnd/clm2/surfdata_map/surfdata_mpasa120_hist_78pfts_CMIP6_simyr1850_c211108.nc + +lnd/clm2/surfdata_map/surfdata_mpasa60_hist_78pfts_CMIP6_simyr1850_c211110.nc + +lnd/clm2/surfdata_map/surfdata_mpasa30_hist_78pfts_CMIP6_simyr1850_c211111.nc + +lnd/clm2/surfdata_map/surfdata_mpasa15_hist_78pfts_CMIP6_simyr1850_c211111.nc + lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850_c190303.nc @@ -1245,6 +1301,19 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc +lnd/clm2/surfdata_map/landuse.timeseries_mpasa480_hist_78pfts_CMIP6_simyr1850-2015_c211110.nc +lnd/clm2/surfdata_map/landuse.timeseries_mpasa240_hist_78pfts_CMIP6_simyr1850-2015_c211115.nc +lnd/clm2/surfdata_map/landuse.timeseries_mpasa120_hist_78pfts_CMIP6_simyr1850-2015_c211108.nc +lnd/clm2/surfdata_map/landuse.timeseries_mpasa60_hist_78pfts_CMIP6_simyr1850-2015_c211110.nc +lnd/clm2/surfdata_map/landuse.timeseries_mpasa30_hist_78pfts_CMIP6_simyr1850-2015_c211111.nc +lnd/clm2/surfdata_map/landuse.timeseries_mpasa15_hist_78pfts_CMIP6_simyr1850-2015_c211111.nc + lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc Date: Wed, 17 Nov 2021 16:03:55 -0700 Subject: [PATCH 0074/2067] Add MPAS resolutions to res namelist default --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 67929c4bd4..875e4691e5 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1985,7 +1985,7 @@ CLM run type. + valid_values="512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,0.125nldas2,5x5_amazon,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4.pg2,ne30np4.pg3,ne30np4,ne60np4,ne120np4,ne120np4.pg2,ne120np4.pg3,ne0np4CONUS.ne30x8,ne0np4.ARCTIC.ne30x4,ne0np4.ARCTICGRIS.ne30x8,ne240np4,1km-merge-10min,C24,C48,C96,C192,C384,mpasa480,mpasa240,mpasa120,mpasa60,mpasa30,mpasa15"> Horizontal resolutions Note: 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM toolsI From 4438cb12041aa6c89ccfe1badcbe7bebbfb7c2a0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Nov 2021 16:56:28 -0700 Subject: [PATCH 0075/2067] Bugfix in saving of hdates_thisyr. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 12e3e207e0..a9b8bdcd24 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1699,7 +1699,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & associate( & ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type - leaf_long => pftcon%leaf_long , & ! Input: leaf longevity (yrs) + leaf_long => pftcon%leaf_long , & ! Input: leaf longevity (yrs) leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) manunitro => pftcon%manunitro , & ! Input: max manure to be applied in total (kgN/m2) mxmat => pftcon%mxmat , & ! Input: @@ -2075,7 +2075,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (do_harvest) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday - crop_inst%hdates_thisyr(p, growingseason_count) = jday + crop_inst%hdates_thisyr(p, growingseason_count(p) = jday croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 if (tlai(p) > 0._r8) then ! plant had emerged before harvest From e37305c509f7bdf437717c7a62232ea6ac3ab05f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Nov 2021 17:02:59 -0700 Subject: [PATCH 0076/2067] growingseason_count split into [sowing,harvest]_count. --- src/biogeochem/CNPhenologyMod.F90 | 21 ++++++++++++--------- src/biogeochem/CropType.F90 | 6 ++++-- 2 files changed, 16 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a9b8bdcd24..577fbf8916 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1725,7 +1725,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year - growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch + sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch + harvest_count => crop_inst%harvest_count , & ! Inout: [integer (:) ] number of harvest events this year for this patch peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow @@ -1785,7 +1786,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! on an annual basis in cropresidue subroutine if ( is_beg_curr_year() ) then - growingseason_count(p) = 0 + sowing_count(p) = 0 + harvest_count(p) = 0 do s = 1, mxgrowseas crop_inst%sdates_thisyr(p,s) = -1._r8 crop_inst%hdates_thisyr(p,s) = -1._r8 @@ -1793,7 +1795,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! Once outputs can handle >1 planting per year, remove 2nd condition. - if ( (.not. croplive(p)) .and. growingseason_count(p) == 0 ) then + if ( (.not. croplive(p)) .and. sowing_count(p) == 0 ) then ! gdd needed for * chosen crop and a likely hybrid (for that region) * ! to reach full physiological maturity @@ -2075,7 +2077,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (do_harvest) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday - crop_inst%hdates_thisyr(p, growingseason_count(p) = jday + harvest_count(p) = harvest_count(p) + 1 + crop_inst%hdates_thisyr(p, harvest_count(p) = jday croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 if (tlai(p) > 0._r8) then ! plant had emerged before harvest @@ -2246,7 +2249,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year - growingseason_count => crop_inst%growingseason_count , & ! Inout: [integer (:) ] number of growing seasons that have begun this year for this patch + sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Output: [real(r8) (:) ] (gN/m2) leaf N transfer @@ -2259,13 +2262,13 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive(p) = .true. idop(p) = jday harvdate(p) = NOT_Harvested - growingseason_count(p) = growingseason_count(p) + 1 - if (growingseason_count(p) <= crop_inst%n_growingseasons_thisyear_thispatch(p)) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, growingseason_count(p)) + sowing_count(p) = sowing_count(p) + 1 + if (sowing_count(p) <= crop_inst%n_growingseasons_thisyear_thispatch(p)) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, sowing_count(p)) else next_rx_sdate(p) = -1 endif - crop_inst%sdates_thisyr(p,growingseason_count(p)) = jday + crop_inst%sdates_thisyr(p,sowing_count(p)) = jday leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 7d67c7be55..08db8dbcb7 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -43,7 +43,8 @@ module CropType integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year - integer , pointer :: growingseason_count (:) ! number of growing seasons that have begun this year for this patch + integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch + integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year contains @@ -208,7 +209,8 @@ subroutine InitAllocate(this, bounds) allocate(this%rx_sdates_thisyr(begp:endp,1:mxgrowseas)) allocate(this%sdates_thisyr(begp:endp,1:mxgrowseas)) allocate(this%hdates_thisyr(begp:endp,1:mxgrowseas)) - allocate(this%growingseason_count(begp:endp)) ; this%growingseason_count(:) = 0 + allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 + allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 this%rx_sdates_thisyr(:,:) = -1 From 040e6fbfca3f4dbf244b48bd510f0ef8a2236d0e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Nov 2021 17:08:29 -0700 Subject: [PATCH 0077/2067] New dimension mxharvests (=mxgrowseas+1) used for HDATES output. --- src/biogeochem/CNPhenologyMod.F90 | 4 +++- src/biogeochem/CropType.F90 | 6 +++--- src/main/clm_varpar.F90 | 3 +++ src/main/histFileMod.F90 | 15 +++++++++------ 4 files changed, 18 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 577fbf8916..b095475d0c 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -14,7 +14,7 @@ module CNPhenologyMod use shr_log_mod , only : errMsg => shr_log_errMsg use shr_sys_mod , only : shr_sys_flush use decompMod , only : bounds_type - use clm_varpar , only : maxveg, nlevdecomp_full, mxgrowseas + use clm_varpar , only : maxveg, nlevdecomp_full, mxgrowseas, mxharvests use clm_varpar , only : i_litr_min, i_litr_max use clm_varctl , only : iulog, use_cndv use clm_varcon , only : tfrz @@ -1790,6 +1790,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_count(p) = 0 do s = 1, mxgrowseas crop_inst%sdates_thisyr(p,s) = -1._r8 + end do + do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 end do end if diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 08db8dbcb7..d00c2be8ed 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -182,7 +182,7 @@ end subroutine ReadNML subroutine InitAllocate(this, bounds) ! !USES: ! - use clm_varpar, only : mxgrowseas + use clm_varpar, only : mxgrowseas, mxharvests ! ! !ARGUMENTS: class(crop_type) , intent(inout) :: this @@ -208,7 +208,7 @@ subroutine InitAllocate(this, bounds) allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 allocate(this%rx_sdates_thisyr(begp:endp,1:mxgrowseas)) allocate(this%sdates_thisyr(begp:endp,1:mxgrowseas)) - allocate(this%hdates_thisyr(begp:endp,1:mxgrowseas)) + allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 @@ -270,7 +270,7 @@ subroutine InitHistory(this, bounds) ptr_patch=this%sdates_thisyr, default='inactive') this%hdates_thisyr(begp:endp,:) = -1._r8 - call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxgrowseas', & + call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxharvests', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_patch=this%hdates_thisyr, default='inactive') diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index 87c7045f71..0048c9210d 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -52,6 +52,7 @@ module clm_varpar integer, public, parameter :: sz_nbr = 200 ! number of sub-grid bins in large bin of dust size distribution (BGC only) integer, public, parameter :: mxpft = 78 ! maximum number of PFT's for any mode; integer, public, parameter :: mxgrowseas = 1 ! maximum number of crop growing seasons to begin in any year; + integer, public :: mxharvests ! maximum number of crop harvests in any year; ! FIX(RF,032414) might we set some of these automatically from reading pft-physiology? integer, public, parameter :: nlayer = 3 ! number of VIC soil layer --Added by AWang integer, public :: nlayert ! number of VIC soil layer + 3 lower thermal layers @@ -143,6 +144,8 @@ subroutine clm_varpar_init(actual_maxsoil_patches, actual_numcft) cft_lb = natpft_ub + 1 cft_ub = cft_lb + cft_size - 1 + mxharvests = mxgrowseas + 1 + ! TODO(wjs, 2015-10-04, bugz 2227) Using actual_numcft in this 'max' gives a significant ! overestimate of max_patch_per_col when use_crop is true. This should be reworked - ! or, better, removed from the code entirely (because it is a maintenance problem, and diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 9b5de0edd8..4b0a8b4e98 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -193,7 +193,7 @@ module histFileMod character(len=max_chars) :: units ! units character(len=hist_dim_name_length) :: type1d ! pointer to first dimension type from data type (nameg, etc) character(len=hist_dim_name_length) :: type1d_out ! hbuf first dimension type from data type (nameg, etc) - character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","mxgrowseas"] + character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","mxgrowseas","mxharvests"] integer :: beg1d ! on-node 1d clm pointer start index integer :: end1d ! on-node 1d clm pointer end index integer :: num1d ! size of clm pointer first dimension (all nodes) @@ -1271,7 +1271,7 @@ subroutine hist_update_hbuf(bounds) integer :: num2d ! size of second dimension (e.g. number of vertical levels) integer :: numdims ! number of dimensions character(len=*),parameter :: subname = 'hist_update_hbuf' - character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","mxgrowseas"] + character(len=hist_dim_name_length) :: type2d ! hbuf second dimension type ["levgrnd","levlak","numrad","ltype","natpft","cft","glc_nec","elevclas","subname(n)","mxgrowseas","mxharvests"] !----------------------------------------------------------------------- do t = 1,ntapes @@ -2279,7 +2279,7 @@ subroutine htape_create (t, histrest) ! ! !USES: use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, nlevurb, nlevmaxurbgrnd, numrad, nlevcan, nvegwcs,nlevsoi - use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, nlevdecomp_full, mxgrowseas + use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, nlevdecomp_full, mxgrowseas, mxharvests use landunit_varcon , only : max_lunit use clm_varctl , only : caseid, ctitle, fsurdat, finidat, paramfile use clm_varctl , only : version, hostname, username, conventions, source @@ -2421,6 +2421,7 @@ subroutine htape_create (t, histrest) call ncd_defdim(lnfid, 'nlevcan',nlevcan, dimid) call ncd_defdim(lnfid, 'nvegwcs',nvegwcs, dimid) call ncd_defdim(lnfid, 'mxgrowseas' , mxgrowseas , dimid) + call ncd_defdim(lnfid, 'mxharvests' , mxharvests , dimid) call htape_add_ltype_metadata(lnfid) call htape_add_ctype_metadata(lnfid) call ncd_defdim(lnfid, 'natpft', natpft_size, dimid) @@ -4135,7 +4136,7 @@ subroutine hist_restart_ncd (bounds, ncid, flag, rdate) use clm_varctl , only : nsrest, caseid, inst_suffix, nsrStartup, nsrBranch use fileutils , only : getfil use domainMod , only : ldomain - use clm_varpar , only : nlevgrnd, nlevlak, numrad, nlevdecomp_full, mxgrowseas + use clm_varpar , only : nlevgrnd, nlevlak, numrad, nlevdecomp_full, mxgrowseas, mxharvests use clm_time_manager, only : is_restart use restUtilMod , only : iflag_skip use pio @@ -5341,7 +5342,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, ! ! !USES: use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, numrad, nlevdecomp_full, nlevcan, nvegwcs,nlevsoi - use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, mxgrowseas + use clm_varpar , only : natpft_size, cft_size, maxpatch_glc, mxgrowseas, mxharvests use landunit_varcon , only : max_lunit ! ! !ARGUMENTS: @@ -5423,6 +5424,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, num2d = nlevdecomp_full case ('mxgrowseas') num2d = mxgrowseas + case ('mxharvests') + num2d = mxharvests case ('fates_levscls') num2d = nlevsclass case('fates_levcacls') @@ -5490,7 +5493,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, case default write(iulog,*) trim(subname),' ERROR: unsupported 2d type ',type2d, & ' currently supported types for multi level fields are: ', & - '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs,mxgrowseas]' + '[levgrnd,levsoi,levlak,numrad,levdcmp,levtrc,ltype,natpft,cft,glc_nec,elevclas,levsno,nvegwcs,mxgrowseas,mxharvests]' call endrun(msg=errMsg(sourcefile, __LINE__)) end select From 5c137faf2e6d6724f717ffbd5a0af12fe37928ca Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Nov 2021 11:57:04 -0700 Subject: [PATCH 0078/2067] Compile fix. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b095475d0c..94fe2b0e5b 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2080,7 +2080,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (do_harvest) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 - crop_inst%hdates_thisyr(p, harvest_count(p) = jday + crop_inst%hdates_thisyr(p, harvest_count(p)) = DBLE(jday) croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 if (tlai(p) > 0._r8) then ! plant had emerged before harvest From 8e590e6b711e126c84e9cd1222c21ef781a979c1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Nov 2021 12:03:01 -0700 Subject: [PATCH 0079/2067] Bugfix in CropPhenology() for prescribed sowing when previous crop not harvested. In such cases, harvest occurs on the first timestep of the day, then sowing the next. This could potentially cause confusion in postprocessing when sowing and harvest are shown to occur on the same day. --- src/biogeochem/CNPhenologyMod.F90 | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 94fe2b0e5b..ab4be34587 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1796,6 +1796,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end do end if + do_plant_prescribed = next_rx_sdate(p) == jday + ! Once outputs can handle >1 planting per year, remove 2nd condition. if ( (.not. croplive(p)) .and. sowing_count(p) == 0 ) then @@ -1814,7 +1816,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! According to Chris Kucharik, the dataset of ! xinpdate was generated from a previous model run at 0.5 deg resolution - do_plant_prescribed = next_rx_sdate(p) == jday ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing dates at all, or if this cell had no values in the prescribed sowing @@ -2032,7 +2033,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (generate_crop_gdds) then + if (do_plant_prescribed) then + ! Today is the planting day, but the crop still hasn't been harvested. + do_harvest = .true. + force_harvest = .true. + else if (generate_crop_gdds) then if (.not. use_cropcal_streams) then write(iulog,*) 'If using generate_crop_gdds, you must set use_cropcal_streams to true.' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2049,7 +2054,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p)) endif - force_harvest = generate_crop_gdds .and. do_harvest + force_harvest = force_harvest .or. (generate_crop_gdds .and. do_harvest) if ((.not. force_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then cphase(p) = 2._r8 From d365be6d23ff95058f8872aa25b09a9f1bd86f48 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Nov 2021 12:05:09 -0700 Subject: [PATCH 0080/2067] [sh]dates_thisyr outputs now initialized to spval instead of -1. --- src/biogeochem/CropType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index d00c2be8ed..d5ba4b9a17 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -264,12 +264,12 @@ subroutine InitHistory(this, bounds) ptr_patch=this%latbaset_patch, default='inactive') end if - this%sdates_thisyr(begp:endp,:) = -1._r8 + this%sdates_thisyr(begp:endp,:) = spval call hist_addfld2d (fname='SDATES', units='day of year', type2d='mxgrowseas', & avgflag='I', long_name='actual crop sowing dates; should only be output annually', & ptr_patch=this%sdates_thisyr, default='inactive') - this%hdates_thisyr(begp:endp,:) = -1._r8 + this%hdates_thisyr(begp:endp,:) = spval call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxharvests', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_patch=this%hdates_thisyr, default='inactive') From 895a11c196f37133644476fcc9ca987fa6b01581 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 23 Nov 2021 12:05:36 -0700 Subject: [PATCH 0081/2067] Added (commented-out) verbose output for sowing date reads with MCT. --- src/cpl/mct/cropcalStreamMod.F90 | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 9e68bd7590..9c218f4664 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -18,6 +18,7 @@ module cropcalStreamMod use spmdMod , only : masterproc, mpicom, comp_id use ncdio_pio use mct_mod +! use GridcellType , only : grc ! SSR troubleshooting ! ! !PUBLIC TYPES: implicit none @@ -213,6 +214,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use PatchType , only : patch use filterMod , only : filter use decompMod , only : get_proc_clumps +! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: implicit none @@ -224,6 +226,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig integer :: nc, fp +! integer :: yr, mon, day, tod, ymd, c, g ! SSR troubleshooting character(len=CL) :: stream_var_name !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) @@ -233,6 +236,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + ! SSR troubleshooting +! call get_curr_date( yr, mon, day, tod ) +! ymd = yr*10000 + mon*100 + day + ! SSR TODO: Make this work with mxgrowseas > 1 do fp = 1, num_pcropp p = filter_pcropp(fp) @@ -253,6 +260,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Only for first sowing date of the year crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) +! ! SSR troubleshooting +! c = patch%column(p) +! g = patch%gridcell(p) +! write(iulog,'(I8,A,F8.3,A,F8.3,A,I4,A,I7)') ymd,' (',grc%londeg(g),',',grc%latdeg(g),') crop ',ivt,' read rx_sdate ',crop_inst%rx_sdates_thisyr(p,1) end do From 2024ac5bba6eb14b89e952b5d0c639da8ac03db0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 5 Jan 2022 17:31:06 -0700 Subject: [PATCH 0082/2067] Bugfix in CropPhenology() to avoid immediate harvest. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ab4be34587..e81e2abf1b 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2033,7 +2033,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (do_plant_prescribed) then + if (do_plant_prescribed .and. (sowing_count(p) == 0 .or. crop_inst%sdates_thisyr(p,sowing_count(p)) < jday)) then ! Today is the planting day, but the crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. From 2e7b2c31fbcc8c5b570fc9500f04fd8b709f0b23 Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Thu, 6 Jan 2022 19:21:40 +0100 Subject: [PATCH 0083/2067] For PR --- src/biogeophys/BareGroundFluxesMod.F90 | 16 ++++++++++++++-- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 14 +++++--------- src/biogeophys/CanopyFluxesMod.F90 | 8 ++++++-- src/biogeophys/FrictionVelocityMod.F90 | 1 - src/biogeophys/LakeFluxesMod.F90 | 2 +- src/main/clm_driver.F90 | 2 +- 6 files changed, 27 insertions(+), 16 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index a89d66ea95..edab4431e1 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -71,7 +71,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & atm2lnd_inst, soilstate_inst, & frictionvel_inst, ch4_inst, energyflux_inst, temperature_inst, & waterfluxbulk_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, & - wateratm2lndbulk_inst, photosyns_inst, humanindex_inst) + wateratm2lndbulk_inst, photosyns_inst, humanindex_inst, canopystate_inst) ! ! !DESCRIPTION: ! Compute sensible and latent fluxes and their derivatives with respect @@ -89,6 +89,8 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & Wet_Bulb, Wet_BulbS, HeatIndex, AppTemp, & swbgt, hmdex, dis_coi, dis_coiS, THIndex, & SwampCoolEff, KtoC, VaporPres + use CanopyStateType , only : canopystate_type + ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -107,13 +109,14 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & type(wateratm2lndbulk_type) , intent(inout) :: wateratm2lndbulk_inst type(photosyns_type) , intent(inout) :: photosyns_inst type(humanindex_type) , intent(inout) :: humanindex_inst + type(canopystate_type) , intent(inout) :: canopystate_inst + ! ! !LOCAL VARIABLES: integer, parameter :: niters = 3 ! maximum number of iterations for surface temperature integer :: p,c,g,f,j,l ! indices integer :: iter ! iteration index real(r8) :: zldis(bounds%begp:bounds%endp) ! reference height "minus" zero displacement height [m] - real(r8) :: displa(bounds%begp:bounds%endp) ! displacement height [m] real(r8) :: zeta ! dimensionless height used in Monin-Obukhov theory real(r8) :: wc ! convective velocity [m/s] real(r8) :: dth(bounds%begp:bounds%endp) ! diff of virtual temp. between ref. height and surface @@ -240,6 +243,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & z0mg_patch => frictionvel_inst%z0mg_patch , & ! Output: [real(r8) (:) ] patch roughness length, momentum [m] z0hg_patch => frictionvel_inst%z0hg_patch , & ! Output: [real(r8) (:) ] patch roughness length, sensible heat [m] z0qg_patch => frictionvel_inst%z0qg_patch , & ! Output: [real(r8) (:) ] patch roughness length, latent heat [m] + z0mv => frictionvel_inst%z0mv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, momentum [m] + z0hv => frictionvel_inst%z0hv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, sensible heat [m] + z0qv => frictionvel_inst%z0qv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, latent heat [m] kbm1 => frictionvel_inst%kbm1_patch , & ! Output: [real(r8) (:) ] natural logarithm of z0mg_p/z0hg_p [-] ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) num_iter => frictionvel_inst%num_iter_patch , & ! Output: [real(r8) (:) ] number of iterations @@ -255,6 +261,8 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & rssun => photosyns_inst%rssun_patch , & ! Output: [real(r8) (:) ] leaf sunlit stomatal resistance (s/m) (output from Photosynthesis) rssha => photosyns_inst%rssha_patch , & ! Output: [real(r8) (:) ] leaf shaded stomatal resistance (s/m) (output from Photosynthesis) + displa => canopystate_inst%displa_patch , & ! Output: [real(r8) (:) ] displacement height (m) + begp => bounds%begp , & endp => bounds%endp & ) @@ -291,6 +299,10 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & ulrad(p) = 0._r8 dhsdt_canopy(p) = 0._r8 eflx_sh_stem(p) = 0._r8 + z0mv(p) = 0._r8 + z0hv(p) = 0._r8 + z0qv(p) = 0._r8 + ur(p) = max(params_inst%wind_min,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g))) dth(p) = thm(p)-t_grnd(c) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 01631eeabd..f456298089 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -174,18 +174,14 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & else ! Compute as if elai+esai = LAImax - LAIoff in CanopyFluxes - displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * (pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))))**0.5_r8)) & - / (7.5_r8*(pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))))**0.5_r8) + displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * (pftcon%z0v_LAImax(patch%itype(p))))**0.5_r8)) & + / (7.5_r8*(pftcon%z0v_LAImax(patch%itype(p)) ))**0.5_r8) - U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))) & - / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p)) - pftcon%z0v_LAIoff(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) + U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p))) & + / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) - if( htop(p) > -1._r8) then ! Avoid devididing by 0 - z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & + z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) - else - z0m(p) = htop(p) * exp(-0.4_r8 * U_ustar + log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) - end if end if diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index a13262bcc9..8766edd72e 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -882,7 +882,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) case ('MeierXXXX') - lt = max(0.00001_r8,elai(p)+esai(p)-z0v_LAIoff(patch%itype(p))) + lt = max(0.00001_r8,elai(p)+esai(p)) displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) / (7.5_r8*lt)**0.5_r8) lt = min(lt,z0v_LAImax(patch%itype(p))) @@ -898,9 +898,11 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, end do U_ustar = 4._r8 * U_ustar / lt / z0v_c(patch%itype(p)) + z0mv(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-vkc * U_ustar + & log(z0v_cw(patch%itype(p))) - 1._r8 + z0v_cw(patch%itype(p))**(-1._r8)) + ! --> Use this for CLM-Ya08 !lt = min(elai(p)+esai(p), tlsai_crit) !egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) @@ -1050,7 +1052,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! changed by K.Sakaguchi from here ! transfer coefficient over bare soil is changed to a local variable ! just for readability of the code (from line 680) - ! not sure if this needs to be changed with MeierXXXX too. + ! RM: Does this need to be updated if Ya08 is used too? csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / 1.5e-5_r8)**params_inst%a_exp) @@ -1561,6 +1563,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! function that goes to zero as LAI (ELAI + ESAI) go to zero. t_skin_patch(p) = emv(p)*t_veg(p) + (1._r8 - emv(p))*sqrt(sqrt(lw_grnd)) + !t_skin_patch(p) = (ulrad(p) / 5.670367e-8_r8)**0.25_r8 ! Derivative of soil energy flux with respect to soil temperature @@ -1672,6 +1675,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, fn = fn + 1 filterp(fn) = p end if + end do do f = 1, fn diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index ce1c9c6c4b..88ba2301e1 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -460,7 +460,6 @@ subroutine ReadZ0M(this, bounds) do c = bounds%begc, bounds%endc g = col%gridcell(c) this%z0mg_2D_col(c) = max(1.e-4_r8,z0mg2d(g)) - write(iulog,*) z0mg2d(g) end do deallocate(z0mg2d) diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index a2a58bcb0f..0b3c35483c 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -344,7 +344,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, !z0mg(p) = z0frzlake z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 - + ! --> Use this for CLM-VEG and CLM-Z0M !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 9be5ad20d2..10b184a5ca 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -652,7 +652,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro frictionvel_inst, ch4_inst, energyflux_inst, temperature_inst, & water_inst%waterfluxbulk_inst, water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, water_inst%wateratm2lndbulk_inst, & - photosyns_inst, humanindex_inst) + photosyns_inst, humanindex_inst, canopystate_inst) call t_stopf('bgflux') ! non-bareground fluxes for all patches except lakes and urban landunits From 864f3366ff93f9de9f259fc2e57d63aa93a71ebb Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Wed, 12 Jan 2022 17:53:36 +0100 Subject: [PATCH 0084/2067] Removing statements of sensitivity experiments. Add more comments following meeting at January 12 2022. --- src/biogeophys/BareGroundFluxesMod.F90 | 8 ++++---- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 3 --- src/biogeophys/CanopyFluxesMod.F90 | 11 ++++------- src/biogeophys/FrictionVelocityMod.F90 | 10 ++-------- src/biogeophys/LakeFluxesMod.F90 | 19 +------------------ src/main/pftconMod.F90 | 4 ---- 6 files changed, 11 insertions(+), 44 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index edab4431e1..31cd6a628c 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -347,15 +347,15 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & case ('ZengWang2007') z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) case ('MeierXXXX') + ! After Yang et al. (2007) z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) - ! After Owen and Thomson (1963) + ! RM: After Owen and Thomson (1963). This formulation could be used as an alternative to Yang et al. (2007). It would + ! avoid that z0hg and z0qg becomes larger frequently than z0mg, which happens with Yang et al. (2007). !z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp * 0.71_r8**0.8_r8) - ! Zeng and Wang (2007) --> Use this for CLM-VEG and CLM-Z0M - !z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) - + end select z0qg_patch(p) = z0hg_patch(p) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index f456298089..29ac0d8e62 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -185,9 +185,6 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & end if - ! --> Use this for CLM-Ya08 - !z0m(p) = pftcon%z0mr(patch%itype(p)) * htop(p) - !displa(p) = pftcon%displar(patch%itype(p)) * htop(p) end select diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 8766edd72e..b31358d239 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -903,12 +903,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, log(z0v_cw(patch%itype(p))) - 1._r8 + z0v_cw(patch%itype(p))**(-1._r8)) - ! --> Use this for CLM-Ya08 - !lt = min(elai(p)+esai(p), tlsai_crit) - !egvf =(1._r8 - alpha_aero * exp(-lt)) / (1._r8 - alpha_aero * exp(-tlsai_crit)) - !displa(p) = egvf * displa(p) - !z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) - case default write(iulog,*) 'ERROR: unknown z0para_method: ', z0param_method call endrun(msg = 'unknown z0param_method', additional_msg = errMsg(sourcefile, __LINE__)) @@ -1052,7 +1046,10 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! changed by K.Sakaguchi from here ! transfer coefficient over bare soil is changed to a local variable ! just for readability of the code (from line 680) - ! RM: Does this need to be updated if Ya08 is used too? + ! RM: Does this need to be updated if Ya08 is used too? Proposed formulation (definitely double-check!) + ! , interpreting the statement below as csoilb = vkc / ln(z0mg/z0hg): + ! csoilb = vkc / log( z0mg(c) / ( 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * + ! (abs(tstar))**(0.25_r8)) ) ) csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / 1.5e-5_r8)**params_inst%a_exp) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 88ba2301e1..e7d26a9f2b 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -651,24 +651,18 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & else z0mg(c) = this%zsno - ! --> Use this for CLM-VEG and CLM-Ya08 - !z0mg(c) = 0.0024_r8 + end if else if (lun%itype(l) == istice_mec) then z0mg(c) = this%zglc - ! --> Use this for CLM-VEG and CLM-Ya08 - !z0mg(c) = 0.01_r8 else if(use_z0mg_2d) then z0mg(c) = z0mg_2D(c) else z0mg(c) = this%zlnd - - ! --> Use this for CLM-VEG and CLM-Ya08 - !z0mg(c) = 0.01_r8 - + end if end if end select diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 0b3c35483c..6f9ad0ae56 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -340,14 +340,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('MeierXXXX') z0mg(p) = params_inst%zglc - ! --> Use this for CLM-VEG and CLM-Ya08 - !z0mg(p) = z0frzlake z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 - - ! --> Use this for CLM-VEG and CLM-Z0M - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes - + case ('ZengWang2007') z0mg(p) = z0frzlake z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -362,9 +357,6 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else z0mg(p) = params_inst%zsno - - ! --> Use this for CLM-VEG and CLM-Ya08 - !z0mg(p) = 0.0024_r8 end if z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 @@ -596,15 +588,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') z0mg(p) = params_inst%zglc - - ! --> Use this for CLM-VEG and CLM-Ya08 - !z0mg(p) = z0frzlake z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes - ! --> Use this for CLM-VEG and CLM-Z0M - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes - case ('ZengWang2007') z0mg(p) = z0frzlake z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -619,9 +605,6 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('MeierXXXX') z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes - ! --> Use this for CLM-VEG and CLM-Z0M - !z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes - case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index aef781bf57..d3ef07a547 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -673,10 +673,6 @@ subroutine InitRead(this) this%z0mr = 0._r8 - ! --> Use this for CLM-Ya08 - !call ncd_io('z0mr', this%z0mr, 'read', ncid, readvar=readv, posNOTonfile=.true.) - !if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) - case default write(iulog,*) subname//' ERROR: unknown z0param_method: ', & z0param_method From 8318cad9abcea15c88ca8549a52f636dab63054b Mon Sep 17 00:00:00 2001 From: Ronny Meier Date: Wed, 12 Jan 2022 18:10:05 +0100 Subject: [PATCH 0085/2067] Small correction to proposed statement in CanopyFluxes --- src/biogeophys/CanopyFluxesMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index b31358d239..da690f2d5c 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1049,7 +1049,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! RM: Does this need to be updated if Ya08 is used too? Proposed formulation (definitely double-check!) ! , interpreting the statement below as csoilb = vkc / ln(z0mg/z0hg): ! csoilb = vkc / log( z0mg(c) / ( 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * - ! (abs(tstar))**(0.25_r8)) ) ) + ! (abs(temp1(p)*dth(p)))**(0.25_r8)) ) ) csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / 1.5e-5_r8)**params_inst%a_exp) From 8e570154fca8ef07039a07341b96184b81038b0a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 13 Jan 2022 15:26:20 -0700 Subject: [PATCH 0086/2067] Adding reading of cultivar GDD targets. Not yet used. Untested. --- src/biogeochem/CropType.F90 | 3 ++ src/cpl/mct/cropcalStreamMod.F90 | 49 +++++++++++++++++++++++++++++++- 2 files changed, 51 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index d5ba4b9a17..0e26abb2ec 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -41,6 +41,7 @@ module CropType real(r8) :: baset_latvary_slope integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year + integer , pointer :: rx_cultivar_gdds_thisyr (:,:) ! all cultivar GDD targets for this patch this year real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch @@ -207,6 +208,7 @@ subroutine InitAllocate(this, bounds) allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 allocate(this%rx_sdates_thisyr(begp:endp,1:mxgrowseas)) + allocate(this%rx_cultivar_gdds_thisyr(begp:endp,1:mxgrowseas)) allocate(this%sdates_thisyr(begp:endp,1:mxgrowseas)) allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 @@ -214,6 +216,7 @@ subroutine InitAllocate(this, bounds) allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 this%rx_sdates_thisyr(:,:) = -1 + this%rx_cultivar_gdds_thisyr(:,:) = -1 this%sdates_thisyr(:,:) = -1._r8 this%hdates_thisyr(:,:) = -1._r8 diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index 9c218f4664..c71c83a289 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -33,6 +33,7 @@ module cropcalStreamMod integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index ! SSR TODO: Make this work with mxgrowseas > 1 type(shr_strdata_type) :: sdat_sdate ! sowing date input data stream + type(shr_strdata_type) :: sdat_cultivar_gdds ! cultivar growing-degree days stream character(len=*), parameter :: sourcefile = & __FILE__ @@ -71,11 +72,13 @@ subroutine cropcal_init(bounds) integer :: nml_error ! namelist i/o error flag type(mct_ggrid) :: dom_clm ! domain information character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read + character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar GDD target filename to read character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm ! SSR TODO: Make this work with mxgrowseas > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates + character(len=CXX) :: fldList_cultivar_gdds1 ! field string for 1st cultivar GDD targets character(*), parameter :: subName = "('cropcaldyn_init')" !----------------------------------------------------------------------- @@ -86,13 +89,15 @@ subroutine cropcal_init(bounds) stream_year_first_cropcal, & stream_year_last_cropcal, & model_year_align_cropcal, & - stream_fldFileName_sdate + stream_fldFileName_sdate, & + stream_fldFileName_cultivar_gdds ! Default values for namelist stream_year_first_cropcal = 1 ! first year in stream to use stream_year_last_cropcal = 1 ! last year in stream to use model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year stream_fldFileName_sdate = shr_stream_file_null + stream_fldFileName_cultivar_gdds = shr_stream_file_null ! Read cropcal_streams namelist if (masterproc) then @@ -112,6 +117,7 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) + call shr_mpi_bcast(stream_fldFileName_cultivar_gdds , mpicom) if (masterproc) then write(iulog,*) ' ' @@ -120,6 +126,7 @@ subroutine cropcal_init(bounds) write(iulog,*) ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,*) ' model_year_align_cropcal = ',model_year_align_cropcal write(iulog,*) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) + write(iulog,*) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) endif call clm_domain_mct (bounds, dom_clm) @@ -127,6 +134,7 @@ subroutine cropcal_init(bounds) ! create the field list for these cropcal fields...use in shr_strdata_create ! SSR TODO: Make this work with mxgrowseas > 1 fldList_sdate1 = shr_string_listCreateField( cft_ub, "sdate1", cft_lb ) + fldList_cultivar_gdds1 = shr_string_listCreateField( cft_ub, "gdd1", cft_lb ) ! SSR TODO: ! - Delete "area" and "mask"? @@ -158,9 +166,37 @@ subroutine cropcal_init(bounds) tintalgo=cropcal_tintalgo, & calendar=get_calendar(), & taxmode='cycle' ) + call shr_strdata_create(sdat_cultivar_gdds, & + name="cropcaldyn", & + pio_subsystem=pio_subsystem, & + pio_iotype=shr_pio_getiotype(inst_name), & + mpicom=mpicom, compid=comp_id, & + gsmap=gsmap_global, ggrid=dom_clm, & + nxg=ldomain%ni, nyg=ldomain%nj, & + yearFirst=stream_year_first_cropcal, & + yearLast=stream_year_last_cropcal, & + yearAlign=model_year_align_cropcal, & + offset=0, & + domFilePath='', & + domFileName=trim(stream_fldFileName_cultivar_gdds), & + domTvarName='time', & + domXvarName='lon' , & + domYvarName='lat' , & + domAreaName='area', & + domMaskName='mask', & + filePath='', & + filename=(/stream_fldFileName_cultivar_gdds/), & + fldListFile=fldList_cultivar_gdds1, & + fldListModel=fldList_cultivar_gdds1, & + fillalgo='none', & + mapalgo=cropcal_mapalgo, & + tintalgo=cropcal_tintalgo, & + calendar=get_calendar(), & + taxmode='cycle' ) if (masterproc) then call shr_strdata_print(sdat_sdate,'sdate1 data') + call shr_strdata_print(sdat_cultivar_gdds,'sdat_cultivar_gdds1 data') endif end subroutine cropcal_init @@ -191,6 +227,7 @@ subroutine cropcal_advance( bounds ) ! SSR TODO: Make this work with mxgrowseas > 1 call shr_strdata_advance(sdat_sdate, mcdate, sec, mpicom, 'cropcaldyn') + call shr_strdata_advance(sdat_cultivar_gdds, mcdate, sec, mpicom, 'cropcaldyn') if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) @@ -235,6 +272,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! SSR TODO: Make this work with mxgrowseas > 1 SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (lbound(sdat_cultivar_gdds%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(sdat_cultivar_gdds%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) ! SSR troubleshooting ! call get_curr_date( yr, mon, day, tod ) @@ -255,6 +294,14 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) endif + ! SSR TODO: Add check that variable exists in netCDF + stream_var_name = 'cultivar_gdds1_'//trim(adjustl(stream_var_name)) + ip = mct_aVect_indexRA(sdat_cultivar_gdds%avs(1),trim(stream_var_name)) + if (ivt /= noveg) then + ig = g_to_ig(patch%gridcell(p)) + crop_inst%rx_cultivar_gdds_thisyr(p,1) = sdat_cultivar_gdds%avs(1)%rAttr(ip,ig) + endif + ! SSR TODO: Make this work with mxgrowseas > 1 crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%rx_sdates_thisyr(p,1) >= 0 From e1c6a839bfd0ba6a5b76e67615719b44f7bc6c88 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 13 Jan 2022 16:03:47 -0700 Subject: [PATCH 0087/2067] Remove unneeded crop_inst%n_growingseasons_thisyear_thispatch. Untested. --- src/biogeochem/CNPhenologyMod.F90 | 3 ++- src/biogeochem/CropType.F90 | 2 -- src/cpl/mct/cropcalStreamMod.F90 | 3 --- src/cpl/share_esmf/cropcalStreamMod.F90 | 1 - 4 files changed, 2 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e81e2abf1b..9645f7a0d1 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2237,6 +2237,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & ! !USES: use clm_varctl , only : use_c13, use_c14 use clm_varcon , only : c13ratio, c14ratio + use clm_varpar , only : mxgrowseas ! ! !ARGUMENTS: integer , intent(in) :: p ! PATCH index running over @@ -2270,8 +2271,8 @@ subroutine PlantCrop(p, leafcn_in, jday, & idop(p) = jday harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 - if (sowing_count(p) <= crop_inst%n_growingseasons_thisyear_thispatch(p)) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, sowing_count(p)) + if (sowing_count(p) <= mxgrowseas) then else next_rx_sdate(p) = -1 endif diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 0e26abb2ec..25f681c92f 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -46,7 +46,6 @@ module CropType real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch - integer , pointer :: n_growingseasons_thisyear_thispatch (:) ! number of sowing dates read in for this patch this year contains ! Public routines @@ -213,7 +212,6 @@ subroutine InitAllocate(this, bounds) allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 - allocate(this%n_growingseasons_thisyear_thispatch(begp:endp)) ; this%n_growingseasons_thisyear_thispatch(:) = 0 this%rx_sdates_thisyr(:,:) = -1 this%rx_cultivar_gdds_thisyr(:,:) = -1 diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index c71c83a289..d9f8df5cd6 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -302,9 +302,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_cultivar_gdds_thisyr(p,1) = sdat_cultivar_gdds%avs(1)%rAttr(ip,ig) endif - ! SSR TODO: Make this work with mxgrowseas > 1 - crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%rx_sdates_thisyr(p,1) >= 0 - ! Only for first sowing date of the year crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) ! ! SSR troubleshooting diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index d57bf31448..58478041cc 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -247,7 +247,6 @@ subroutine cropcal_interp(bounds, canopystate_inst) ivt = patch%itype ! SSR TODO: Make below work with arbitrary # of growing seasons per year crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) - crop_inst%n_growingseasons_thisyear_thispatch(p) = crop_inst%rx_sdates_thisyr(p,1) >= 0 ! Only for first sowing date of the year crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) From 50950d93aaeb5b057a3248689ea7e322bee542a5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 13 Jan 2022 16:05:54 -0700 Subject: [PATCH 0088/2067] Bugfix (?) for setting next_rx_sdate with mxgrowseas > 1. Untested. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9645f7a0d1..977ea1ef64 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2271,8 +2271,8 @@ subroutine PlantCrop(p, leafcn_in, jday, & idop(p) = jday harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, sowing_count(p)) - if (sowing_count(p) <= mxgrowseas) then + if (sowing_count(p) < mxgrowseas) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, sowing_count(p)+1) else next_rx_sdate(p) = -1 endif From c611d6ece08402539dbd398bc09a272459fb5c88 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 13 Jan 2022 16:16:29 -0700 Subject: [PATCH 0089/2067] Add user-mod directories for the surface roughness changes from Ronny Meier --- .../testmods_dirs/clm/Meier2022_surf_rough/include_user_mods | 1 + .../testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 4 ++++ .../clm/Meier2022_surf_rough_all_f09/include_user_mods | 1 + .../clm/Meier2022_surf_rough_all_f09/user_nl_clm | 2 ++ .../clm/Meier2022_surf_rough_all_hcru/include_user_mods | 1 + .../clm/Meier2022_surf_rough_all_hcru/user_nl_clm | 2 ++ 6 files changed, 11 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm new file mode 100644 index 0000000000..b9fd293412 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -0,0 +1,4 @@ +z0param_method = 'MeierXXXX' +use_z0m_snowmelt = .true. +use_z0mg_2d = .false. +paramfile = '/glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/ctsm51_params_newz0.c211112.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/include_user_mods new file mode 100644 index 0000000000..38bef34f6e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/include_user_mods @@ -0,0 +1 @@ +../Meier2022_surf_rough diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/user_nl_clm new file mode 100644 index 0000000000..0a33a7a06c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/user_nl_clm @@ -0,0 +1,2 @@ +use_z0mg_2d = .true. +fsurdat = '/glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c210624.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/include_user_mods new file mode 100644 index 0000000000..38bef34f6e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/include_user_mods @@ -0,0 +1 @@ +../Meier2022_surf_rough diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/user_nl_clm new file mode 100644 index 0000000000..6043dae4af --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/user_nl_clm @@ -0,0 +1,2 @@ +use_z0mg_2d = .true. +fsurdat = ' /glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/surfdata_360x720cru_16pfts_Irrig_CMIP6_simyr2000_c210624_2D.nc' From 9ae6e30f0e26a8dc64e47f40b764b7b9f684d63e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 13 Jan 2022 16:17:12 -0700 Subject: [PATCH 0090/2067] Remove use_z0v_forest because it's not connected to anything in the FORTRAN code --- bld/namelist_files/namelist_definition_ctsm.xml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a63f2317f8..a058b10c0f 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -340,10 +340,6 @@ If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&Zeng, group="canopyfluxes_inparm" valid_values="" > If TRUE, include biomass heat storage in canopy energy balance. - -If TRUE, use new parameterization of vegetation surface roughness for forests. - Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the hardwired default value. From 0ee8c69a79006cf19fd18031310ccf407c0f884d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 13 Jan 2022 16:31:55 -0700 Subject: [PATCH 0091/2067] Handle very small values of htop and snowmelt_accum with new Meier2022 code --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 8 ++++++-- src/biogeophys/FrictionVelocityMod.F90 | 11 ++++++++--- src/biogeophys/LakeFluxesMod.F90 | 15 +++++++++++---- 3 files changed, 25 insertions(+), 9 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 29ac0d8e62..edc59cdb34 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -180,8 +180,12 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p))) & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) - z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & - log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) + if ( htop(p) <= 1.e-10_r8 )then + z0m(p) = 0.0_r8 + else + z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & + log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) + end if end if diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index e7d26a9f2b..6be12091d8 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -11,6 +11,7 @@ module FrictionVelocityMod use shr_log_mod , only : errMsg => shr_log_errMsg use shr_const_mod , only : SHR_CONST_PI use decompMod , only : bounds_type + use abortutils , only : endrun use clm_varcon , only : spval use clm_varctl , only : use_cn, use_luna, z0param_method, use_z0mg_2d, use_z0m_snowmelt use LandunitType , only : lun @@ -422,7 +423,6 @@ subroutine ReadZ0M(this, bounds) ! !USES: use shr_log_mod, only : errMsg => shr_log_errMsg use fileutils , only : getfil - use abortutils , only : endrun use ncdio_pio , only : file_desc_t, ncd_defvar, ncd_io, ncd_pio_openfile, ncd_pio_closefile use spmdMod , only : masterproc use clm_varcon , only : grlnd @@ -513,7 +513,6 @@ subroutine ReadNamelist( this, NLFilename ) use shr_mpi_mod , only : shr_mpi_bcast use clm_varctl , only : iulog use shr_log_mod , only : errMsg => shr_log_errMsg - use abortutils , only : endrun ! ! !ARGUMENTS: class(frictionvel_type), intent(inout) :: this @@ -571,6 +570,8 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & ! !DESCRIPTION: ! Set roughness lengths and forcing heights for non-lake points ! + ! !USES: + use clm_varcon , only : rpi ! !ARGUMENTS: class(frictionvel_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds @@ -647,7 +648,11 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & l = col%landunit(c) if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + if ( snomelt_accum(c) < 1.e-12_r8 )then + z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + else + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + end if else z0mg(c) = this%zsno diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 6f9ad0ae56..9642e76c3c 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -92,7 +92,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, ! !USES: use clm_varpar , only : nlevlak use clm_varcon , only : hvap, hsub, hfus, cpair, cpliq, tkwat, tkice, tkair - use clm_varcon , only : sb, vkc, grav, denh2o, tfrz, spval + use clm_varcon , only : sb, vkc, grav, denh2o, tfrz, spval, rpi use clm_varctl , only : use_lch4, z0param_method, use_z0m_snowmelt use LakeCon , only : betavis, z0frzlake, tdmax, emg_lake use LakeCon , only : lake_use_old_fcrit_minz0 @@ -352,8 +352,11 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') if(use_z0m_snowmelt) then - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 - + if ( snomelt_accum(c) < 1.e-12_r8 )then + z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + else + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + end if else z0mg(p) = params_inst%zsno @@ -598,7 +601,11 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = z0hg(p) else ! Snow layers if(use_z0m_snowmelt) then - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + if ( snomelt_accum(c) < 1.e-12_r8 )then + z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + else + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + end if end if select case (z0param_method) From 6f919e959dd6f4186542df90126e041a38c07aa1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 13 Jan 2022 16:34:52 -0700 Subject: [PATCH 0092/2067] Replacing sowing_count(p) with s. Untested. --- src/biogeochem/CNPhenologyMod.F90 | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 977ea1ef64..ed16e645e0 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1797,9 +1797,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if do_plant_prescribed = next_rx_sdate(p) == jday + s = sowing_count(p) ! Once outputs can handle >1 planting per year, remove 2nd condition. - if ( (.not. croplive(p)) .and. sowing_count(p) == 0 ) then + if ( (.not. croplive(p)) .and. s == 0 ) then ! gdd needed for * chosen crop and a likely hybrid (for that region) * ! to reach full physiological maturity @@ -1956,6 +1957,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! crop not live nor planted + s = sowing_count(p) + ! ---------------------------------- ! from AgroIBIS subroutine phenocrop ! ---------------------------------- @@ -2033,7 +2036,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (do_plant_prescribed .and. (sowing_count(p) == 0 .or. crop_inst%sdates_thisyr(p,sowing_count(p)) < jday)) then + if (do_plant_prescribed .and. (s == 0 .or. crop_inst%sdates_thisyr(p,s) < jday)) then ! Today is the planting day, but the crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. @@ -2251,6 +2254,9 @@ subroutine PlantCrop(p, leafcn_in, jday, & type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(cnveg_carbonstate_type) , intent(inout) :: c13_cnveg_carbonstate_inst type(cnveg_carbonstate_type) , intent(inout) :: c14_cnveg_carbonstate_inst + ! + ! LOCAL VARAIBLES: + integer s ! growing season index !------------------------------------------------------------------------ associate( & @@ -2270,13 +2276,14 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive(p) = .true. idop(p) = jday harvdate(p) = NOT_Harvested - sowing_count(p) = sowing_count(p) + 1 if (sowing_count(p) < mxgrowseas) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, sowing_count(p)+1) + s = sowing_count(p) + 1 + sowing_count(p) = s else next_rx_sdate(p) = -1 endif - crop_inst%sdates_thisyr(p,sowing_count(p)) = jday + crop_inst%sdates_thisyr(p,s) = jday leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset From 023eebb4fc24c322ed1573940968f351c910d4cb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 13 Jan 2022 16:37:45 -0700 Subject: [PATCH 0093/2067] Now sets gddmaturity from cultivar, if used. Untested. ALL gddmaturity setting now happens in PlantCrop(). --- src/biogeochem/CNPhenologyMod.F90 | 79 +++++++++++++++++++------------ 1 file changed, 50 insertions(+), 29 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ed16e645e0..9b421f2cc8 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1852,8 +1852,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) - gddmaturity(p) = hybgdd(ivt(p)) - else gddmaturity(p) = 0._r8 end if @@ -1885,29 +1883,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) - ! go a specified amount of time before/after - ! climatological date - if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. & - ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean) then - gddmaturity(p) = min(gdd1020(p), hybgdd(ivt(p))) - end if - - if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. & - ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. & - ivt(p) == nsugarcane .or. ivt(p) == nirrig_sugarcane .or. & - ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. & - ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then - gddmaturity(p) = max(950._r8, min(gdd820(p)*0.85_r8, hybgdd(ivt(p)))) - if (do_plant_normal) then - gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8)) - end if - end if - if (ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. & - ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. & - ivt(p) == nrice .or. ivt(p) == nirrig_rice) then - gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) - end if - else gddmaturity(p) = 0._r8 end if @@ -1915,7 +1890,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! crop phenology (gdd thresholds) controlled by gdd needed for ! maturity (physiological) which is based on the average gdd - ! accumulation and hybrids in United States from April 1 - Sept 30 + ! accumulation and hybrids in United States from April 1 - Sept 30, + ! unless using cultivar GDD target inputs ! calculate threshold from phase 1 to phase 2: ! threshold for attaining leaf emergence (based on fraction of @@ -2241,6 +2217,13 @@ subroutine PlantCrop(p, leafcn_in, jday, & use clm_varctl , only : use_c13, use_c14 use clm_varcon , only : c13ratio, c14ratio use clm_varpar , only : mxgrowseas + use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean + use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean + use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice + use pftconMod , only : nirrig_trp_corn, nirrig_sugarcane, nirrig_trp_soybean + use pftconMod , only : nirrig_cotton, nirrig_rice + use pftconMod , only : nmiscanthus, nirrig_miscanthus, nswitchgrass, nirrig_switchgrass + ! ! !ARGUMENTS: integer , intent(in) :: p ! PATCH index running over @@ -2257,29 +2240,35 @@ subroutine PlantCrop(p, leafcn_in, jday, & ! ! LOCAL VARAIBLES: integer s ! growing season index + real(r8) gdd_target ! cultivar GDD target this growing season + logical do_plant_prescribed ! are we planting because it was prescribed? !------------------------------------------------------------------------ associate( & + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch - idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting + gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest + idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Output: [real(r8) (:) ] (gN/m2) leaf N transfer crop_seedc_to_leaf => cnveg_carbonflux_inst%crop_seedc_to_leaf_patch , & ! Output: [real(r8) (:) ] (gC/m2/s) seed source to leaf crop_seedn_to_leaf => cnveg_nitrogenflux_inst%crop_seedn_to_leaf_patch & ! Output: [real(r8) (:) ] (gN/m2/s) seed source to leaf ) + do_plant_prescribed = next_rx_sdate(p) == jday + ! impose limit on growing season length needed ! for crop maturity - for cold weather constraints croplive(p) = .true. idop(p) = jday harvdate(p) = NOT_Harvested - if (sowing_count(p) < mxgrowseas) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, sowing_count(p)+1) s = sowing_count(p) + 1 sowing_count(p) = s + if (s < mxgrowseas) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, s+1) else next_rx_sdate(p) = -1 endif @@ -2309,6 +2298,38 @@ subroutine PlantCrop(p, leafcn_in, jday, & endif endif + ! set GDD target + if (do_plant_prescribed .and. .not. generate_crop_gdds) then + gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) + if (gdd_target <= 0.0) then + write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0.' + call endrun(msg=errMsg(sourcefile, __LINE__)) + endif + gddmaturity(p) = gdd_target + else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then + gddmaturity(p) = hybgdd(ivt(p)) + else + if (ivt(p) == ntmp_soybean .or. ivt(p) == nirrig_tmp_soybean .or. & + ivt(p) == ntrp_soybean .or. ivt(p) == nirrig_trp_soybean) then + gddmaturity(p) = min(gdd1020(p), hybgdd(ivt(p))) + end if + if (ivt(p) == ntmp_corn .or. ivt(p) == nirrig_tmp_corn .or. & + ivt(p) == ntrp_corn .or. ivt(p) == nirrig_trp_corn .or. & + ivt(p) == nsugarcane .or. ivt(p) == nirrig_sugarcane .or. & + ivt(p) == nmiscanthus .or. ivt(p) == nirrig_miscanthus .or. & + ivt(p) == nswitchgrass .or. ivt(p) == nirrig_switchgrass) then + gddmaturity(p) = max(950._r8, min(gdd820(p)*0.85_r8, hybgdd(ivt(p)))) + if (do_plant_normal) then + gddmaturity(p) = max(950._r8, min(gddmaturity(p)+150._r8, 1850._r8)) + end if + end if + if (ivt(p) == nswheat .or. ivt(p) == nirrig_swheat .or. & + ivt(p) == ncotton .or. ivt(p) == nirrig_cotton .or. & + ivt(p) == nrice .or. ivt(p) == nirrig_rice) then + gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) + end if + endif + end associate end subroutine PlantCrop From 7ea377df5fdfb5f575d72efe861a3b3f23a154eb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jan 2022 14:11:34 -0700 Subject: [PATCH 0094/2067] Compile fixes. Removed obsoleted associate()s from CropPhenology(). --- src/biogeochem/CNPhenologyMod.F90 | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9b421f2cc8..170b681313 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1706,7 +1706,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & minplanttemp => pftcon%minplanttemp , & ! Input: planttemp => pftcon%planttemp , & ! Input: gddmin => pftcon%gddmin , & ! Input: - hybgdd => pftcon%hybgdd , & ! Input: lfemerg => pftcon%lfemerg , & ! Input: grnfill => pftcon%grnfill , & ! Input: @@ -1716,8 +1715,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & a10tmin => temperature_inst%t_a10min_patch , & ! Input: [real(r8) (:) ] 10-day running mean of min 2-m temperature gdd020 => temperature_inst%gdd020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd0 gdd820 => temperature_inst%gdd820_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd8 - gdd1020 => temperature_inst%gdd1020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd10 - fertnitro => crop_inst%fertnitro_patch , & ! Input: [real(r8) (:) ] fertilizer nitrogen hui => crop_inst%gddplant_patch , & ! Input: [real(r8) (:) ] gdd since planting (gddplant) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature @@ -1847,7 +1844,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hdidx(p) = 0._r8 vf(p) = 0._r8 - call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & + call PlantCrop(p, leafcn(ivt(p)), jday, do_plant_normal, & + temperature_inst, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -1878,7 +1876,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance) then - call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & + call PlantCrop(p, leafcn(ivt(p)), jday, do_plant_normal, & + temperature_inst, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -2201,8 +2200,8 @@ subroutine CropPhenologyInit(bounds) end subroutine CropPhenologyInit !----------------------------------------------------------------------- - subroutine PlantCrop(p, leafcn_in, jday, & - crop_inst, cnveg_state_inst, & + subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & + temperature_inst, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -2229,6 +2228,8 @@ subroutine PlantCrop(p, leafcn_in, jday, & integer , intent(in) :: p ! PATCH index running over real(r8) , intent(in) :: leafcn_in ! leaf C:N (gC/gN) of this patch's vegetation type (pftcon%leafcn(ivt(p))) integer , intent(in) :: jday ! julian day of the year + logical , intent(in) :: do_plant_normal ! Are all the normal requirements for planting met? + type(temperature_type) , intent(in) :: temperature_inst type(crop_type) , intent(inout) :: crop_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst @@ -2255,7 +2256,11 @@ subroutine PlantCrop(p, leafcn_in, jday, & leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Output: [real(r8) (:) ] (gN/m2) leaf N transfer crop_seedc_to_leaf => cnveg_carbonflux_inst%crop_seedc_to_leaf_patch , & ! Output: [real(r8) (:) ] (gC/m2/s) seed source to leaf - crop_seedn_to_leaf => cnveg_nitrogenflux_inst%crop_seedn_to_leaf_patch & ! Output: [real(r8) (:) ] (gN/m2/s) seed source to leaf + crop_seedn_to_leaf => cnveg_nitrogenflux_inst%crop_seedn_to_leaf_patch, & ! Output: [real(r8) (:) ] (gN/m2/s) seed source to leaf + hybgdd => pftcon%hybgdd , & ! Input: [real(r8) (:) ] + gdd020 => temperature_inst%gdd020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd0 + gdd820 => temperature_inst%gdd820_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd8 + gdd1020 => temperature_inst%gdd1020_patch & ! Input: [real(r8) (:) ] 20 yr mean of gdd10 ) do_plant_prescribed = next_rx_sdate(p) == jday From fc84ade9a12fd115a0d4378d816bb7e053587452 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jan 2022 14:22:13 -0700 Subject: [PATCH 0095/2067] Added stream_fldfilename_cultivar_gdds to namelist. --- bld/CLMBuildNamelist.pm | 2 ++ bld/namelist_files/namelist_defaults_ctsm.xml | 1 + bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ 3 files changed, 8 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 422dd9a935..7e006821ee 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3769,6 +3769,8 @@ sub setup_logic_cropcal_streams { } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_sdate', 'hgrid'=>"360x720cru" ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds', + 'hgrid'=>"360x720cru" ); if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal', 'hgrid'=>"360x720cru" ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3cdb1131b5..f081645fd8 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1574,6 +1574,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc +lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index e7137a201e..dc20e3351f 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1806,6 +1806,11 @@ Simulation year that aligns with stream_year_first_cropcal value Filename of input stream data for sowing dates + +Filename of input stream data for cultivar growing degree-day targets + + Filename of input stream data for crop calendar inputs From 02be2d8c4f4f121477fe60911c46c9bb65384b67 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 14 Jan 2022 14:35:26 -0700 Subject: [PATCH 0096/2067] Don't set z0mg and displa on first step of run for RonnyMeier2022 roughness as htop isn't set yet. Also use a different threshold for snomelt_accum suggested by Ronny Meier --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 13 ++++++++++++- src/biogeophys/FrictionVelocityMod.F90 | 2 +- src/biogeophys/LakeFluxesMod.F90 | 4 ++-- 3 files changed, 15 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index edc59cdb34..6725c63320 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -124,6 +124,10 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & ! !DESCRIPTION: ! Set z0m and displa ! + ! !USES: + use clm_time_manager, only : is_first_step + use clm_varcon , only : namep + use abortutils , only : endrun ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter @@ -168,6 +172,13 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & case ('MeierXXXX') + ! Don't set on first step of a simulation, since htop isn't set yet + if ( is_first_step() ) then + z0m(p) = 0._r8 + displa(p) = 0._r8 + cycle + end if + if (patch%itype(p) == noveg) then z0m(p) = 0._r8 displa(p) = 0._r8 @@ -181,7 +192,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) if ( htop(p) <= 1.e-10_r8 )then - z0m(p) = 0.0_r8 + call endrun(decomp_index=p, clmlevel=namep, msg=errMsg(sourcefile, __LINE__)) else z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 6be12091d8..e6c4b848dd 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -648,7 +648,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & l = col%landunit(c) if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then - if ( snomelt_accum(c) < 1.e-12_r8 )then + if ( snomelt_accum(c) < 1.e-5_r8 )then z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 9642e76c3c..b3bcda6fe5 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -352,7 +352,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('MeierXXXX') if(use_z0m_snowmelt) then - if ( snomelt_accum(c) < 1.e-12_r8 )then + if ( snomelt_accum(c) < 1.e-5_r8 )then z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 @@ -601,7 +601,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = z0hg(p) else ! Snow layers if(use_z0m_snowmelt) then - if ( snomelt_accum(c) < 1.e-12_r8 )then + if ( snomelt_accum(c) < 1.e-5_r8 )then z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 From a625eac45094b69f6cd096b383b90478226ac123 Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Tue, 18 Jan 2022 23:16:09 -0700 Subject: [PATCH 0097/2067] add output for SNICAR related albedo variables --- src/biogeophys/SurfaceAlbedoMod.F90 | 2 +- src/biogeophys/SurfaceAlbedoType.F90 | 53 ++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index ba025023db..62c4673696 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -12,7 +12,7 @@ module SurfaceAlbedoMod use decompMod , only : bounds_type, subgrid_level_patch use abortutils , only : endrun use landunit_varcon , only : istsoil, istcrop, istdlak - use clm_varcon , only : grlnd + use clm_varcon , only : grlnd, spval ! cenlin use clm_varpar , only : numrad, nlevcan, nlevsno, nlevcan use clm_varctl , only : fsurdat, iulog, use_snicar_frc, use_SSRE use pftconMod , only : pftcon diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90 index cf6b0a518a..98a9b0839e 100644 --- a/src/biogeophys/SurfaceAlbedoType.F90 +++ b/src/biogeophys/SurfaceAlbedoType.F90 @@ -221,6 +221,59 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='surface albedo (indirect)', & ptr_patch=this%albi_patch, default=defaultoutput, c2l_scale_type='urbanf') +! cenlin: add for snow albedo and snicar-related output 01/18/2022 + this%albgrd_pur_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_PUR', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without aerosol in snow (direct)', & + ptr_col=this%albgrd_pur_col, default='inactive') + + this%albgri_pur_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_PUR', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without aerosol in snow (diffuse)', & + ptr_col=this%albgri_pur_col, default='inactive') + + this%albgrd_bc_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_BC', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without BC in snow (direct)', & + ptr_col=this%albgrd_bc_col, default='inactive') + + this%albgri_bc_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_BC', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without BC in snow (diffuse)', & + ptr_col=this%albgri_bc_col, default='inactive') + + this%albgrd_oc_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_OC', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without OC in snow (direct)', & + ptr_col=this%albgrd_oc_col, default='inactive') + + this%albgri_oc_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_OC', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without OC in snow (diffuse)', & + ptr_col=this%albgri_oc_col, default='inactive') + + this%albgrd_dst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_DST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without dust in snow (direct)', & + ptr_col=this%albgrd_dst_col, default='inactive') + + this%albgri_dst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_DST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without dust in snow (diffuse)', & + ptr_col=this%albgri_dst_col, default='inactive') + + this%albsnd_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBSND', units='proportion', type2d='numrad', & + avgflag='A', long_name='snow albedo (direct)', & + ptr_col=this%albsnd_hst_col, default='inactive') + + this%albsni_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBSNI', units='proportion', type2d='numrad', & + avgflag='A', long_name='snow albedo (diffuse)', & + ptr_col=this%albsni_hst_col, default='inactive') + +! cenlin: end + end subroutine InitHistory !----------------------------------------------------------------------- From f84f1cc9259562bcb528ef71f21b816c74fd835f Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 19 Jan 2022 12:15:24 +0100 Subject: [PATCH 0098/2067] add namelist definitions and defaults to use excess ice --- bld/namelist_files/namelist_defaults_ctsm.xml | 15 ++++++++ .../namelist_definition_ctsm.xml | 38 +++++++++++++++++++ src/main/clm_initializeMod.F90 | 2 +- src/main/clm_instMod.F90 | 2 +- src/main/clm_varctl.F90 | 5 +++ src/main/controlMod.F90 | 5 +++ 6 files changed, 65 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 1ee46abecb..165e53438b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2586,4 +2586,19 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts general + + + + +.false. +1901 +1901 +1901 + +lnd/clm2/prescribed_data/exice_init_0.9x1.25_c20211102.nc + +nearest +0 + + diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a79991efd8..6a7d6d1511 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2818,4 +2818,42 @@ use case.) + + + + +Toggle to turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) + + + +First year to loop over for excess ice data + + + +Last year to loop over for excess ice data + + + +Simulation year that aligns with stream_year_first_exice value + + + +Filename of input stream data for excess ice data + + + +Time interpolation method to use for excess ice data + + + +Offset in time coordinate for excess ice streams (sec) + + diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index c9541376a2..32c368e40b 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -14,7 +14,7 @@ module clm_initializeMod use clm_varctl , only : is_cold_start, is_interpolated_start use clm_varctl , only : iulog use clm_varctl , only : use_lch4, use_cn, use_cndv, use_c13, use_c14, use_fates - use clm_varctl , only : use_soil_moisture_streams + use clm_varctl , only : use_soil_moisture_streams, use_excess_ice use clm_instur , only : wt_lunit, urban_valid, wt_nat_patch, wt_cft, fert_cft use clm_instur , only : irrig_method, wt_glc_mec, topo_glc_mec, haslake use perf_mod , only : t_startf, t_stopf diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 44ab2f8ef2..b654ef5505 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -8,7 +8,7 @@ module clm_instMod use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type use clm_varpar , only : ndecomp_pools, nlevdecomp_full - use clm_varctl , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates + use clm_varctl , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates, use_excess_ice use clm_varctl , only : use_crop, snow_cover_fraction_method, paramfile use SoilBiogeochemDecompCascadeConType , only : century_decomp, decomp_method use clm_varcon , only : bdsno, c13ratio, c14ratio diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 3ad4b14bef..2d7af87cf4 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -298,6 +298,11 @@ module clm_varctl real(r8), public :: soil_layerstruct_userdefined(99) = rundef integer, public :: soil_layerstruct_userdefined_nlevsoi = iundef + !---------------------------------------------------------- + !excess ice physics switch + !---------------------------------------------------------- + logical, public :: use_excess_ice = .false. ! true. => use excess ice physics !MVD + !---------------------------------------------------------- ! plant hydraulic stress switch !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 082d68e8eb..a52a52806e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -242,6 +242,8 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_soil_moisture_streams + namelist /clm_inparm/ use_excess_ice !MVD + namelist /clm_inparm/ use_lai_streams namelist /clm_inparm/ use_bedrock @@ -733,6 +735,8 @@ subroutine control_spmd() call mpi_bcast (use_soil_moisture_streams, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_excess_ice, 1, MPI_LOGICAL, 0, mpicom,ier) !MVD + call mpi_bcast (use_lai_streams, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_bedrock, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -866,6 +870,7 @@ subroutine control_print () write(iulog,*) ' use_nitrif_denitrif = ', use_nitrif_denitrif write(iulog,*) ' use_extralakelayers = ', use_extralakelayers write(iulog,*) ' use_vichydro = ', use_vichydro + write(iulog,*) ' use_excess_ice = ', use_excess_ice !MVD to check if the value is read from namelists write(iulog,*) ' use_cn = ', use_cn write(iulog,*) ' use_cndv = ', use_cndv write(iulog,*) ' use_crop = ', use_crop From 759ef18645ce3b3c7a5190c37b0a18257703eeb2 Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Wed, 19 Jan 2022 19:59:42 -0700 Subject: [PATCH 0099/2067] bug fix for adding new albedo output variables --- src/biogeophys/SurfaceAlbedoMod.F90 | 70 +++++++- src/biogeophys/SurfaceAlbedoType.F90 | 250 +++++++++++++++++++++------ src/biogeophys/UrbanAlbedoMod.F90 | 30 +++- 3 files changed, 294 insertions(+), 56 deletions(-) diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index 62c4673696..df92dbcb41 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -349,7 +349,7 @@ subroutine SurfaceAlbedo(bounds,nc, & esai => canopystate_inst%esai_patch , & ! Input: [real(r8) (:) ] one-sided stem area index with burying by snow frac_sno => waterdiagnosticbulk_inst%frac_sno_col , & ! Input: [real(r8) (:) ] fraction of ground covered by snow (0 to 1) - fcansno => waterdiagnosticbulk_inst%fcansno_patch , & ! Input: [real(r8) (:) ] fraction of canopy that is snow-covered (0 to 1) + fcansno => waterdiagnosticbulk_inst%fcansno_patch , & ! Input: [real(r8) (:) ] fraction of canopy that is snow-covered (0 to 1) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water content (col,lyr) [kg/m2] h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens content (col,lyr) [kg/m2] snw_rds => waterdiagnosticbulk_inst%snw_rds_col , & ! Input: [real(r8) (:,:) ] snow grain radius (col,lyr) [microns] @@ -387,6 +387,22 @@ subroutine SurfaceAlbedo(bounds,nc, & albsni_hst => surfalb_inst%albsni_hst_col , & ! Output: [real(r8) (:,:) ] snow ground albedo, diffuse, for history files (col,bnd) [frc] albd => surfalb_inst%albd_patch , & ! Output: [real(r8) (:,:) ] surface albedo (direct) albi => surfalb_inst%albi_patch , & ! Output: [real(r8) (:,:) ] surface albedo (diffuse) +! cenlin: add new output albedo variables for history fields + albgrd_hst => surfalb_inst%albgrd_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (direct) for history files + albgri_hst => surfalb_inst%albgri_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (diffuse) for history files + albgrd_pur_hst => surfalb_inst%albgrd_pur_hst_col , & ! Output: [real(r8) (:,:) ] pure snow ground albedo (direct) for history files + albgri_pur_hst => surfalb_inst%albgri_pur_hst_col , & ! Output: [real(r8) (:,:) ] pure snow ground albedo (diffuse) for history files + albgrd_bc_hst => surfalb_inst%albgrd_bc_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo without BC (direct) for history files + albgri_bc_hst => surfalb_inst%albgri_bc_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo without BC (diffuse) for history files + albgrd_oc_hst => surfalb_inst%albgrd_oc_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo without OC (direct) for history files + albgri_oc_hst => surfalb_inst%albgri_oc_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo without OC (diffuse) for history files + albgrd_dst_hst => surfalb_inst%albgrd_dst_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo without dust (direct) for history files + albgri_dst_hst => surfalb_inst%albgri_dst_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo without dust (diffuse) for history files + albsnd_hst2 => surfalb_inst%albsnd_hst2_col , & ! Output: [real(r8) (:,:) ] snow albedo, direct, for history files (col,bnd) for history files + albsni_hst2 => surfalb_inst%albsni_hst2_col , & ! Output: [real(r8) (:,:) ] snow ground albedo, diffuse, for history files (col,bnd) for history files + albd_hst => surfalb_inst%albd_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (direct) for history files + albi_hst => surfalb_inst%albi_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (diffuse) for history files +! cenlin: end albdSF => surfalb_inst%albdSF_patch , & ! Output: [real(r8) (:,:) ] diagnostic snow-free surface albedo (direct) albiSF => surfalb_inst%albiSF_patch , & ! Output: [real(r8) (:,:) ] diagnostic snow-free surface albedo (diffuse) fabd => surfalb_inst%fabd_patch , & ! Output: [real(r8) (:,:) ] flux absorbed by canopy per unit direct flux @@ -420,7 +436,7 @@ subroutine SurfaceAlbedo(bounds,nc, & do fp = 1,num_nourbanp p = filter_nourbanp(fp) g = patch%gridcell(p) - coszen_patch(p) = coszen_gcell(g) + coszen_patch(p) = coszen_gcell(g) end do ! Initialize output because solar radiation only done if coszen > 0 @@ -440,6 +456,20 @@ subroutine SurfaceAlbedo(bounds,nc, & albgri_oc(c,ib) = 0._r8 albgrd_dst(c,ib) = 0._r8 albgri_dst(c,ib) = 0._r8 +! cenlin: add output variables for history files + albgrd_hst(c,ib) = spval + albgri_hst(c,ib) = spval + albgrd_pur_hst(c,ib) = spval + albgri_pur_hst(c,ib) = spval + albgrd_bc_hst(c,ib) = spval + albgri_bc_hst(c,ib) = spval + albgrd_oc_hst(c,ib) = spval + albgri_oc_hst(c,ib) = spval + albgrd_dst_hst(c,ib) = spval + albgri_dst_hst(c,ib) = spval + albsnd_hst2(c,ib) = spval + albsni_hst2(c,ib) = spval +! cenlin: end do i=-nlevsno+1,1,1 flx_absdv(c,i) = 0._r8 flx_absdn(c,i) = 0._r8 @@ -452,6 +482,10 @@ subroutine SurfaceAlbedo(bounds,nc, & p = filter_nourbanp(fp) albd(p,ib) = 1._r8 albi(p,ib) = 1._r8 +! cenlin: add output variables for history files + albd_hst(p,ib) = spval + albi_hst(p,ib) = spval +! cenlin: end if (use_SSRE) then albdSF(p,ib) = 1._r8 albiSF(p,ib) = 1._r8 @@ -1048,6 +1082,38 @@ subroutine SurfaceAlbedo(bounds,nc, & end do end do +! cenlin: add output variables for history files + do ib = 1, numrad + do fc = 1,num_nourbanc + c = filter_nourbanc(fc) + if (coszen_col(c) > 0._r8) then + albgrd_hst(c,ib) = albgrd(c,ib) + albgri_hst(c,ib) = albgri(c,ib) + albgrd_pur_hst(c,ib) = albgrd_pur(c,ib) + albgri_pur_hst(c,ib) = albgri_pur(c,ib) + albgrd_bc_hst(c,ib) = albgrd_bc(c,ib) + albgri_bc_hst(c,ib) = albgri_bc(c,ib) + albgrd_oc_hst(c,ib) = albgrd_oc(c,ib) + albgri_oc_hst(c,ib) = albgri_oc(c,ib) + albgrd_dst_hst(c,ib) = albgrd_dst(c,ib) + albgri_dst_hst(c,ib) = albgri_dst(c,ib) + if (h2osno_total(c) > 0._r8) then + albsnd_hst2(c,ib) = albsnd_hst(c,ib) + albsni_hst2(c,ib) = albsnd_hst(c,ib) + end if + end if + end do + + do fp = 1,num_nourbanp + p = filter_nourbanp(fp) + if (coszen_patch(p) > 0._r8) then + albd_hst(p,ib) = albd(p,ib) + albi_hst(p,ib) = albi(p,ib) + end if + end do + end do +! cenlin: end + end associate end subroutine SurfaceAlbedo diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90 index 98a9b0839e..eb8ec9ef03 100644 --- a/src/biogeophys/SurfaceAlbedoType.F90 +++ b/src/biogeophys/SurfaceAlbedoType.F90 @@ -7,7 +7,7 @@ module SurfaceAlbedoType use decompMod , only : bounds_type use clm_varpar , only : numrad, nlevcan, nlevsno use abortutils , only : endrun - use clm_varctl , only : use_SSRE + use clm_varctl , only : use_SSRE, use_snicar_frc ! cenlin ! ! !PUBLIC TYPES: implicit none @@ -35,6 +35,22 @@ module SurfaceAlbedoType real(r8), pointer :: albsoi_col (:,:) ! col soil albedo: diffuse (col,bnd) [frc] real(r8), pointer :: albsnd_hst_col (:,:) ! col snow albedo, direct , for history files (col,bnd) [frc] real(r8), pointer :: albsni_hst_col (:,:) ! col snow albedo, diffuse, for history files (col,bnd) [frc] +! cenlin add new output variables for albedo for history files only + real(r8), pointer :: albd_hst_patch (:,:) ! patch surface albedo (direct) for history files (numrad) + real(r8), pointer :: albi_hst_patch (:,:) ! patch surface albedo (diffuse) for history files (numrad) + real(r8), pointer :: albgrd_pur_hst_col (:,:) ! col pure snow ground direct albedo for history files (numrad) + real(r8), pointer :: albgri_pur_hst_col (:,:) ! col pure snow ground diffuse albedo for history files (numrad) + real(r8), pointer :: albgrd_bc_hst_col (:,:) ! col ground direct albedo without BC for history files (numrad) + real(r8), pointer :: albgri_bc_hst_col (:,:) ! col ground diffuse albedo without BC for history files (numrad) + real(r8), pointer :: albgrd_oc_hst_col (:,:) ! col ground direct albedo without OC for history files (numrad) + real(r8), pointer :: albgri_oc_hst_col (:,:) ! col ground diffuse albedo without OC for history files (numrad) + real(r8), pointer :: albgrd_dst_hst_col (:,:) ! col ground direct albedo without dust for history files (numrad) + real(r8), pointer :: albgri_dst_hst_col (:,:) ! col ground diffuse albedo without dust for history files (numrad) + real(r8), pointer :: albgrd_hst_col (:,:) ! col ground albedo (direct) for history files (numrad) + real(r8), pointer :: albgri_hst_col (:,:) ! col ground albedo (diffuse) for history files (numrad) + real(r8), pointer :: albsnd_hst2_col (:,:) ! col snow albedo, direct , for history files (col,bnd) [frc] + real(r8), pointer :: albsni_hst2_col (:,:) ! col snow albedo, diffuse, for history files (col,bnd) [frc] +! cenlin end real(r8), pointer :: ftdd_patch (:,:) ! patch down direct flux below canopy per unit direct flx (numrad) real(r8), pointer :: ftid_patch (:,:) ! patch down diffuse flux below canopy per unit direct flx (numrad) @@ -157,6 +173,23 @@ subroutine InitAllocate(this, bounds) allocate(this%vcmaxcintsun_patch (begp:endp)) ; this%vcmaxcintsun_patch (:) = nan allocate(this%vcmaxcintsha_patch (begp:endp)) ; this%vcmaxcintsha_patch (:) = nan +! cenlin add new output variables for albedo for history files only + allocate(this%albgrd_hst_col (begc:endc,numrad)) ; this%albgrd_hst_col (:,:) = spval + allocate(this%albgri_hst_col (begc:endc,numrad)) ; this%albgri_hst_col (:,:) = spval + allocate(this%albsnd_hst2_col (begc:endc,numrad)) ; this%albsnd_hst2_col (:,:) = spval + allocate(this%albsni_hst2_col (begc:endc,numrad)) ; this%albsni_hst2_col (:,:) = spval + allocate(this%albgrd_pur_hst_col (begc:endc,numrad)) ; this%albgrd_pur_hst_col (:,:) = spval + allocate(this%albgri_pur_hst_col (begc:endc,numrad)) ; this%albgri_pur_hst_col (:,:) = spval + allocate(this%albgrd_bc_hst_col (begc:endc,numrad)) ; this%albgrd_bc_hst_col (:,:) = spval + allocate(this%albgri_bc_hst_col (begc:endc,numrad)) ; this%albgri_bc_hst_col (:,:) = spval + allocate(this%albgrd_oc_hst_col (begc:endc,numrad)) ; this%albgrd_oc_hst_col (:,:) = spval + allocate(this%albgri_oc_hst_col (begc:endc,numrad)) ; this%albgri_oc_hst_col (:,:) = spval + allocate(this%albgrd_dst_hst_col (begc:endc,numrad)) ; this%albgrd_dst_hst_col (:,:) = spval + allocate(this%albgri_dst_hst_col (begc:endc,numrad)) ; this%albgri_dst_hst_col (:,:) = spval + allocate(this%albd_hst_patch (begp:endp,numrad)) ; this%albd_hst_patch (:,:) = spval + allocate(this%albi_hst_patch (begp:endp,numrad)) ; this%albi_hst_patch (:,:) = spval +! cenlin end + end subroutine InitAllocate !----------------------------------------------------------------------- @@ -188,7 +221,7 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='cosine of solar zenith angle', & ptr_col=this%coszen_col, default='inactive') - this%albgri_col(begc:endc,:) = spval + this%albgrd_col(begc:endc,:) = spval call hist_addfld2d (fname='ALBGRD', units='proportion', type2d='numrad', & avgflag='A', long_name='ground albedo (direct)', & ptr_col=this%albgrd_col, default='inactive') @@ -221,57 +254,80 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='surface albedo (indirect)', & ptr_patch=this%albi_patch, default=defaultoutput, c2l_scale_type='urbanf') -! cenlin: add for snow albedo and snicar-related output 01/18/2022 - this%albgrd_pur_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRD_PUR', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without aerosol in snow (direct)', & - ptr_col=this%albgrd_pur_col, default='inactive') - - this%albgri_pur_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRI_PUR', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without aerosol in snow (diffuse)', & - ptr_col=this%albgri_pur_col, default='inactive') - - this%albgrd_bc_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRD_BC', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without BC in snow (direct)', & - ptr_col=this%albgrd_bc_col, default='inactive') - - this%albgri_bc_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRI_BC', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without BC in snow (diffuse)', & - ptr_col=this%albgri_bc_col, default='inactive') - - this%albgrd_oc_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRD_OC', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without OC in snow (direct)', & - ptr_col=this%albgrd_oc_col, default='inactive') - - this%albgri_oc_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRI_OC', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without OC in snow (diffuse)', & - ptr_col=this%albgri_oc_col, default='inactive') - - this%albgrd_dst_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRD_DST', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without dust in snow (direct)', & - ptr_col=this%albgrd_dst_col, default='inactive') - - this%albgri_dst_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBGRI_DST', units='proportion', type2d='numrad', & - avgflag='A', long_name='ground albedo without dust in snow (diffuse)', & - ptr_col=this%albgri_dst_col, default='inactive') - - this%albsnd_hst_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBSND', units='proportion', type2d='numrad', & - avgflag='A', long_name='snow albedo (direct)', & - ptr_col=this%albsnd_hst_col, default='inactive') +! cenlin add new output variables for albedo for history files only + if (use_snicar_frc) then + + this%albd_hst_patch(begp:endp,:) = spval + call hist_addfld2d (fname='ALBD_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='surface albedo (direct)', & + ptr_patch=this%albd_hst_patch, default='inactive', c2l_scale_type='urbanf') + + this%albi_hst_patch(begp:endp,:) = spval + call hist_addfld2d (fname='ALBI_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='surface albedo (indirect)', & + ptr_patch=this%albi_hst_patch, default='inactive', c2l_scale_type='urbanf') + + this%albgrd_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo (direct)', & + ptr_col=this%albgrd_hst_col, default='inactive') + + this%albgri_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo (indirect)', & + ptr_col=this%albgri_hst_col, default='inactive') + + this%albgrd_pur_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_PUR_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without aerosol in snow (direct)', & + ptr_col=this%albgrd_pur_hst_col, default='inactive') + + this%albgri_pur_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_PUR_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without aerosol in snow (diffuse)', & + ptr_col=this%albgri_pur_hst_col, default='inactive') + + this%albgrd_bc_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_BC_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without BC in snow (direct)', & + ptr_col=this%albgrd_bc_hst_col, default='inactive') + + this%albgri_bc_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_BC_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without BC in snow (diffuse)', & + ptr_col=this%albgri_bc_hst_col, default='inactive') + + this%albgrd_oc_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_OC_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without OC in snow (direct)', & + ptr_col=this%albgrd_oc_hst_col, default='inactive') + + this%albgri_oc_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_OC_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without OC in snow (diffuse)', & + ptr_col=this%albgri_oc_hst_col, default='inactive') + + this%albgrd_dst_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRD_DST_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without dust in snow (direct)', & + ptr_col=this%albgrd_dst_hst_col, default='inactive') + + this%albgri_dst_hst_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBGRI_DST_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='ground albedo without dust in snow (diffuse)', & + ptr_col=this%albgri_dst_hst_col, default='inactive') + + this%albsnd_hst2_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBSND_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='snow albedo (direct)', & + ptr_col=this%albsnd_hst2_col, default='inactive') - this%albsni_hst_col(begc:endc,:) = spval - call hist_addfld2d (fname='ALBSNI', units='proportion', type2d='numrad', & - avgflag='A', long_name='snow albedo (diffuse)', & - ptr_col=this%albsni_hst_col, default='inactive') + this%albsni_hst2_col(begc:endc,:) = spval + call hist_addfld2d (fname='ALBSNI_HIST', units='proportion', type2d='numrad', & + avgflag='A', long_name='snow albedo (diffuse)', & + ptr_col=this%albsni_hst2_col, default='inactive') + end if ! end of use_snicar_frc ! cenlin: end end subroutine InitHistory @@ -323,7 +379,7 @@ subroutine InitCold(this, bounds) this%ftdd_patch (begp:endp, :) = 1.0_r8 this%ftid_patch (begp:endp, :) = 0.0_r8 this%ftii_patch (begp:endp, :) = 1.0_r8 - + end subroutine InitCold !--------------------------------------------------------------------- @@ -598,6 +654,96 @@ subroutine Restart(this, bounds, ncid, flag, & end if ! end of if-use_snicar_frc +! cenlin add new output variables for albedo for history files only + if (use_snicar_frc) then + + call restartvar(ncid=ncid, flag=flag, varname='albd_hist', xtype=ncd_double, & + dim1name='pft', dim2name='numrad', switchdim=.true., & + long_name='surface albedo (direct) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albd_hst_patch) + + call restartvar(ncid=ncid, flag=flag, varname='albi_hist', xtype=ncd_double, & + dim1name='pft', dim2name='numrad', switchdim=.true., & + long_name='surface albedo (diffuse) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albi_hst_patch) + + call restartvar(ncid=ncid, flag=flag, varname='albgrd_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo (direct) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgrd_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgri_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo (indirect) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgri_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albsnd_hst2', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='snow albedo (direct) (0 to 1)', units='proportion', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albsnd_hst2_col) + + call restartvar(ncid=ncid, flag=flag, varname='albsni_hst2', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='snow albedo (diffuse) (0 to 1)', units='proportion', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albsni_hst2_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgrd_bc_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo without BC (direct) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp',readvar=readvar, data=this%albgrd_bc_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgri_bc_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo without BC (diffuse) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgri_bc_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgrd_pur_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='pure snow ground albedo (direct) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgrd_pur_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgri_pur_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='pure snow ground albedo (diffuse) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgri_pur_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgrd_oc_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo without OC (direct) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgrd_oc_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgri_oc_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo without OC (diffuse) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgri_oc_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgrd_dst_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo without dust (direct) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgrd_dst_hst_col) + + call restartvar(ncid=ncid, flag=flag, varname='albgri_dst_hist', xtype=ncd_double, & + dim1name='column', dim2name='numrad', switchdim=.true., & + long_name='ground albedo without dust (diffuse) (0 to 1)', units='', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%albgri_dst_hst_col) + + end if ! end of if-use_snicar_frc +! cenlin end + ! patch type physical state variable - fabd call restartvar(ncid=ncid, flag=flag, varname='fabd', xtype=ncd_double, & dim1name='pft', dim2name='numrad', switchdim=.true., & diff --git a/src/biogeophys/UrbanAlbedoMod.F90 b/src/biogeophys/UrbanAlbedoMod.F90 index 73fd3db08d..5ec225294f 100644 --- a/src/biogeophys/UrbanAlbedoMod.F90 +++ b/src/biogeophys/UrbanAlbedoMod.F90 @@ -12,7 +12,7 @@ module UrbanAlbedoMod use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type, subgrid_level_landunit use clm_varpar , only : numrad - use clm_varcon , only : isecspday, degpsec + use clm_varcon , only : isecspday, degpsec, spval ! cenlin use clm_varctl , only : iulog use abortutils , only : endrun use UrbanParamsType , only : urbanparams_type @@ -156,7 +156,12 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albgri => surfalb_inst%albgri_col , & ! Output: [real(r8) (:,:) ] urban col ground albedo (diffuse) albd => surfalb_inst%albd_patch , & ! Output [real(r8) (:,:) ] urban pft surface albedo (direct) albi => surfalb_inst%albi_patch , & ! Output: [real(r8) (:,:) ] urban pft surface albedo (diffuse) - +! cenlin: add albedo output for history files + albd_hst => surfalb_inst%albd_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (direct) for history files + albi_hst => surfalb_inst%albi_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (diffuse) for history files + albgrd_hst => surfalb_inst%albgrd_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (direct) for history files + albgri_hst => surfalb_inst%albgri_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (diffuse) for history files +! cenlin: end begl => bounds%begl , & vf_sr => urbanparams_inst%vf_sr , & ! Input: [real(r8) (:) ] view factor of sky for road vf_sw => urbanparams_inst%vf_sw , & ! Input: [real(r8) (:) ] view factor of sky for one wall @@ -182,6 +187,10 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & c = filter_urbanc(fc) albgrd(c,ib) = 0._r8 albgri(c,ib) = 0._r8 +! cenlin: add output variables for history files + albgrd_hst(c,ib) = spval + albgri_hst(c,ib) = spval +! cenlin: end end do do fp = 1,num_urbanp @@ -203,6 +212,10 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albd(p,ib) = 1._r8 albi(p,ib) = 1._r8 endif +! cenlin: add output variables for history files + albd_hst(p,ib) = spval + albi_hst(p,ib) = spval +! cenlin: end fabd(p,ib) = 0._r8 fabd_sun(p,ib) = 0._r8 fabd_sha(p,ib) = 0._r8 @@ -418,12 +431,25 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albgrd(c,ib) = sref_improad_dir(l,ib) albgri(c,ib) = sref_improad_dif(l,ib) endif +! cenlin: add albedo variables for history fields + if (coszen(l) > 0._r8) then + albgrd_hst(c,ib) = albgrd(c,ib) + albgri_hst(c,ib) = albgri(c,ib) + end if +! cenlin: end end do do fp = 1,num_urbanp p = filter_urbanp(fp) c = patch%column(p) + l = patch%landunit(p) albd(p,ib) = albgrd(c,ib) albi(p,ib) = albgri(c,ib) +! cenlin: add albedo variables for history fields + if (coszen(l) > 0._r8) then + albd_hst(p,ib) = albd(p,ib) + albi_hst(p,ib) = albi(p,ib) + end if +! cenlin: end end do end do end if From eba1aecb4a76383d436407e3ce406c44946eba71 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jan 2022 16:48:30 -0700 Subject: [PATCH 0100/2067] Correction to cultivar GDD variable names. --- src/cpl/mct/cropcalStreamMod.F90 | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index d9f8df5cd6..7267960e39 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -264,7 +264,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) integer :: ivt, p, ip, ig integer :: nc, fp ! integer :: yr, mon, day, tod, ymd, c, g ! SSR troubleshooting - character(len=CL) :: stream_var_name + character(len=CL) :: stream_var_name_sdate1 + character(len=CL) :: stream_var_name_cultivar_gdds1 !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) @@ -284,19 +285,20 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) p = filter_pcropp(fp) ivt = patch%itype(p) ! Set crop calendars for each gridcell/patch combination - write(stream_var_name,"(i6)") ivt + write(stream_var_name_sdate1,"(i6)") ivt + write(stream_var_name_cultivar_gdds1,"(i6)") ivt ! SSR TODO: Add check that variable exists in netCDF - stream_var_name = 'sdate1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name)) + stream_var_name_sdate1 = 'sdate1_'//trim(adjustl(stream_var_name_sdate1)) + ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name_sdate1)) if (ivt /= noveg) then ig = g_to_ig(patch%gridcell(p)) crop_inst%rx_sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) endif ! SSR TODO: Add check that variable exists in netCDF - stream_var_name = 'cultivar_gdds1_'//trim(adjustl(stream_var_name)) - ip = mct_aVect_indexRA(sdat_cultivar_gdds%avs(1),trim(stream_var_name)) + stream_var_name_cultivar_gdds1 = 'gdd1_'//trim(adjustl(stream_var_name_cultivar_gdds1)) + ip = mct_aVect_indexRA(sdat_cultivar_gdds%avs(1),trim(stream_var_name_cultivar_gdds1)) if (ivt /= noveg) then ig = g_to_ig(patch%gridcell(p)) crop_inst%rx_cultivar_gdds_thisyr(p,1) = sdat_cultivar_gdds%avs(1)%rAttr(ip,ig) From 3feb457f9aa7eb0cfbe7f9becc94923691f9d9bf Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Tue, 25 Jan 2022 19:12:32 +0100 Subject: [PATCH 0101/2067] setup initialization and vars --- bld/namelist_files/namelist_defaults_ctsm.xml | 10 +- .../namelist_definition_ctsm.xml | 26 +- src/biogeophys/WaterStateType.F90 | 56 +++- src/cpl/share_esmf/ExcessIceStreamType.F90 | 256 ++++++++++++++++++ src/main/controlMod.F90 | 2 +- 5 files changed, 317 insertions(+), 33 deletions(-) create mode 100644 src/cpl/share_esmf/ExcessIceStreamType.F90 diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 165e53438b..775ed81105 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2591,14 +2591,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts .false. -1901 -1901 -1901 - -lnd/clm2/prescribed_data/exice_init_0.9x1.25_c20211102.nc - -nearest -0 +lnd/clm2/paramdata/exice_init_0.9x1.25_c20211102.nc +lnd/clm2/paramdata/finundated_inversiondata_0.9x1_ESMFmesh_cdf5_130621.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 6a7d6d1511..702b21b262 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2826,34 +2826,14 @@ use case.) Toggle to turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) - -First year to loop over for excess ice data - - - -Last year to loop over for excess ice data - - - -Simulation year that aligns with stream_year_first_exice value - - Filename of input stream data for excess ice data - -Time interpolation method to use for excess ice data - - - -Offset in time coordinate for excess ice streams (sec) + +mesh filename of input stream data for excess ice diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index c06f2333c9..4b2b37c267 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -13,7 +13,7 @@ module WaterStateType use abortutils , only : endrun use decompMod , only : bounds_type use decompMod , only : subgrid_level_patch, subgrid_level_column, subgrid_level_gridcell - use clm_varctl , only : use_bedrock, iulog + use clm_varctl , only : use_bedrock, use_excess_ice, iulog use clm_varctl , only : use_fates_planthydro use clm_varpar , only : nlevgrnd, nlevsoi, nlevurb, nlevmaxurbgrnd, nlevsno use clm_varcon , only : spval @@ -22,6 +22,7 @@ module WaterStateType use WaterInfoBaseType, only : water_info_base_type use WaterTracerContainerType, only : water_tracer_container_type use WaterTracerUtils, only : AllocateVar1d, AllocateVar2d + use ExcessIceStreamType, only : excessicestream_type ! implicit none save @@ -51,6 +52,14 @@ module WaterStateType real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) + real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (1:nlevgrnd) + real(r8), pointer :: init_exice (:,:) ! initial value of col excess ice lens/(kg/m2) (new) (1:nlevgrnd) + real(r8), pointer :: exice_melt_lev (:,:) ! col excess ice melting (m) (new) + real(r8), pointer :: exice_melt (:) ! column-wide excess ice melting (m) (new) + + + type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only + contains procedure, public :: Init @@ -150,6 +159,22 @@ subroutine InitAllocate(this, bounds, tracer_vars) call AllocateVar1d(var = this%dynbal_baseline_ice_col, name = 'dynbal_baseline_ice_col', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) + !excess ice vars + call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column, & + dim2beg = 1, dim2end = nlevgrnd) + call AllocateVar2d(var = this%init_exice, name = 'init_exice', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column, & + dim2beg = 1, dim2end = nlevgrnd) + call AllocateVar2d(var = this%exice_melt_lev, name = 'exice_melt_lev', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column, & + dim2beg = 1, dim2end = nlevgrnd) + call AllocateVar1d(var = this%exice_melt, name = 'exice_melt', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column) end subroutine InitAllocate @@ -268,6 +293,17 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) ptr_col=this%wa_col, l2g_scale_type='veg') end if + ! Add excess ice fields to history + data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & + avgflag='A', long_name='excess soil ice (vegetated landunits only)', & + ptr_col=this%excess_ice_col, l2g_scale_type='veg') + + this%exice_melt(begc:endc) = spval + call hist_addfld1d (fname='EXICE_MELT', units='m', & + avgflag='A', long_name='melt from excess ice (vegetated landunits only)', & + ptr_col=this%exice_melt, l2g_scale_type='veg') + ! (rgk 02-02-2017) There is intentionally no entry here for stored plant water ! I think that since the value is zero in all cases except ! for FATES plant hydraulics, it will be confusing for users @@ -505,6 +541,12 @@ subroutine InitCold(this, bounds, & this%dynbal_baseline_liq_col(bounds%begc:bounds%endc) = 0._r8 this%dynbal_baseline_ice_col(bounds%begc:bounds%endc) = 0._r8 + !Initialize excess ice + this%init_exice(:,:)=0.0_r8 + this%excess_ice_col(:,:)=0.0_r8 + this%exice_melt_lev(:,:)=0.0_r8 + this%exice_melt(:)=0.0_r8 + end associate end subroutine InitCold @@ -630,6 +672,18 @@ subroutine Restart(this, bounds, ncid, flag, & units='kg/m2', & interpinic_flag='interp', readvar=readvar, data=this%dynbal_baseline_ice_col) + ! Restart excess ice vars + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & + dim1name='column', dim2name='levtot', switchdim=.true., & + long_name=this%info%lname('excess soil ice (vegetated landunits only)'), units='kg/m2', & + scale_by_thickness=.true., & + interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) + + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_MELT'), xtype=ncd_double, & + dim1name='column', & + long_name=this%info%lname('melt from excess ice (vegetated landunits only)'), units='m', & + interpinic_flag='interp', readvar=readvar, data=this%exice_melt) + ! Determine volumetric soil water (for read only) if (flag == 'read' ) then do c = bounds%begc, bounds%endc diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 new file mode 100644 index 0000000000..8c08c766cd --- /dev/null +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -0,0 +1,256 @@ +module ExcessIceStreamType + +#include "shr_assert.h" + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Contains methods for reading in excess ice initial bulk values from data stream + ! + ! !USES + use ESMF + use dshr_strdata_mod , only : shr_strdata_type + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_cl + use shr_log_mod , only : errMsg => shr_log_errMsg + use spmdMod , only : mpicom, masterproc + use clm_varctl , only : iulog + use abortutils , only : endrun + use decompMod , only : bounds_type + + ! !PUBLIC TYPES: + implicit none + private + + type, public :: excessicestream_type + real(r8), pointer, private :: exice_bulk (:) ! excess ice bulk value (-) + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Initialize and read data in + procedure, public :: UseStreams ! If streams will be used + + ! !PRIVATE MEMBER FUNCTIONS: + procedure, private :: InitAllocate ! Allocate data + + end type excessicestream_type + ! ! PRIVATE DATA: + type, private :: streamcontrol_type + character(len=CL) :: stream_fldFileName_exice ! data Filename + character(len=CL) :: stream_meshfile_exice ! mesh Filename + character(len=CL) :: exicemapalgo ! map algo + contains + procedure, private :: ReadNML ! Read in namelist + end type streamcontrol_type + + type(streamcontrol_type), private :: control ! Stream control data + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine Init(this, bounds, NLFilename) + ! + use spmdMod , only : iam + use lnd_comp_shr , only : mesh, model_clock + use dshr_strdata_mod , only : shr_strdata_init_from_inline, shr_strdata_print + use dshr_strdata_mod , only : shr_strdata_advance + use dshr_methods_mod , only : dshr_fldbun_getfldptr + ! + ! arguments + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + + ! + ! local variables + integer :: ig, g, n ! Indices + integer :: year ! year (0, ...) for nstep+1 + integer :: mon ! month (1, ..., 12) for nstep+1 + integer :: day ! day of month (1, ..., 31) for nstep+1 + integer :: sec ! seconds into current date for nstep+1 + integer :: mcdate ! Current model date (yyyymmdd) + type(shr_strdata_type) :: sdat_exice ! input data stream + character(len=16), allocatable :: stream_varnames(:) ! array of stream field names + integer :: rc ! error code + real(r8), pointer :: dataptr1d(:) ! temporary pointer + character(len=*), parameter :: stream_name = 'excess ice' + + call this%InitAllocate( bounds ) + call control%ReadNML( bounds, NLFileName ) + if ( this%useStreams() )then + allocate(stream_varnames(1)) + stream_varnames = (/"EXICE"/) + + if (masterproc) then + write(iulog,*) ' stream_varnames = ',stream_varnames + end if + + call shr_strdata_init_from_inline(sdat_exice, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = control%stream_meshfile_exice, & + stream_lev_dimname = 'null', & + stream_mapalgo = 'nn', & + stream_filenames = (/trim(control%stream_fldFileName_exice)/), & + stream_fldlistFile = stream_varnames, & + stream_fldListModel = stream_varnames, & + stream_yearFirst = 1996, & + stream_yearLast = 1996, & + stream_yearAlign = 1, & + stream_offset = 0, & + stream_taxmode = 'extend', & + stream_dtlimit = 1.0e30_r8, & + stream_tintalgo = 'linear', & + stream_name = 'excess ice ', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + ! Explicitly set current date to a hardcoded constant value. Otherwise + ! using the real date can cause roundoff differences that are + ! detrected as issues with exact restart. EBK M05/20/2017 + ! call get_curr_date(year, mon, day, sec) + year = 1996 + mon = 12 + day = 31 + sec = 0 + mcdate = year*10000 + mon*100 + day + + call shr_strdata_advance(sdat_exice, ymd=mcdate, tod=sec, logunit=iulog, istr='ch4', rc=rc) !c4 is left in + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + ! Get pointer for stream data that is time and spatially interpolate to model time and grid + do n = 1,size(stream_varnames) + call dshr_fldbun_getFldPtr(sdat_exice%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + if (trim(stream_varnames(n)) == 'EXICE') then + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + this%exice_bulk(g) = dataptr1d(ig) + end do + end if + end do + end if + end subroutine Init + + subroutine InitAllocate(this, bounds) + ! + ! !DESCRIPTION: + ! Allocate module variables and data structures + ! + ! !USES: + use shr_infnan_mod, only: nan => shr_infnan_nan, assignment(=) + ! + ! !ARGUMENTS: + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: begc, endc + integer :: begg, endg + !--------------------------------------------------------------------- + + begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg + + + allocate(this%exice_bulk(begg:endg)) ; this%exice_bulk(:) = nan + + end subroutine InitAllocate + + logical function UseStreams(this) + ! + ! !DESCRIPTION: + ! Return true if + ! + ! !USES: + ! + ! !ARGUMENTS: + implicit none + class(excessicestream_type) :: this + ! + ! !LOCAL VARIABLES: + if ( trim(control%stream_fldFileName_exice) == '' )then + UseStreams = .false. + else + UseStreams = .true. + end if +end function UseStreams + +subroutine ReadNML(this, bounds, NLFilename) + ! + ! Read the namelist data stream information. + ! + ! Uses: + use shr_nl_mod , only : shr_nl_find_group_name + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_mpi_mod , only : shr_mpi_bcast + ! + ! arguments + implicit none + class(streamcontrol_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + character(len=CL) :: stream_fldFileName_exice = ' ' + character(len=CL) :: stream_meshfile_exice = ' ' + character(len=CL) :: exicemapalgo = 'nn' + character(len=*), parameter :: namelist_name = 'exice' ! MUST agree with name in namelist and read + character(len=*), parameter :: subName = "('exice::ReadNML')" + !----------------------------------------------------------------------- + + namelist /exice/ & ! MUST agree with namelist_name above + exicemapalgo, stream_fldFileName_exice, stream_meshfile_exice + + ! Default values for namelist + + ! Read ch4finundated namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=exice,iostat=nml_error) ! MUST agree with namelist_name above + if (nml_error /= 0) then + call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + else + call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + close(nu_nml) + endif + + call shr_mpi_bcast(exicemapalgo , mpicom) + call shr_mpi_bcast(stream_fldFileName_exice , mpicom) + call shr_mpi_bcast(stream_meshfile_exice , mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) namelist_name, ' stream settings:' + write(iulog,*) ' stream_fldFileName_exice = ',stream_fldFileName_exice + write(iulog,*) ' stream_meshfile_exice = ',stream_meshfile_exice + write(iulog,*) ' exicemapalgo = ',exicemapalgo + endif + this%stream_fldFileName_exice = stream_fldFileName_exice + this%stream_meshfile_exice = stream_meshfile_exice + this%exicemapalgo = exicemapalgo + +end subroutine ReadNML + + +end module ExcessIceStreamType \ No newline at end of file diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index a52a52806e..98d9ab4081 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -870,7 +870,7 @@ subroutine control_print () write(iulog,*) ' use_nitrif_denitrif = ', use_nitrif_denitrif write(iulog,*) ' use_extralakelayers = ', use_extralakelayers write(iulog,*) ' use_vichydro = ', use_vichydro - write(iulog,*) ' use_excess_ice = ', use_excess_ice !MVD to check if the value is read from namelists + write(iulog,*) ' use_excess_ice = ', use_excess_ice !MVD to check if the value is read from namelists write(iulog,*) ' use_cn = ', use_cn write(iulog,*) ' use_cndv = ', use_cndv write(iulog,*) ' use_crop = ', use_crop From e3c5459ab70c834179a40d076bd93e1f6b636afb Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Tue, 25 Jan 2022 15:34:04 -0700 Subject: [PATCH 0102/2067] expand SNICAR from 5-band to 480-band with namelist control option --- .../namelist_definition_ctsm.xml | 34 ++ src/biogeophys/AerosolMod.F90 | 28 ++ src/biogeophys/SnowSnicarMod.F90 | 447 ++++++++++++++---- src/main/clm_varctl.F90 | 18 + src/main/controlMod.F90 | 48 +- 5 files changed, 474 insertions(+), 101 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a79991efd8..73dc049406 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -160,6 +160,34 @@ specify spatially variable soil thickness. If not present, use bottom of soil column (nlevsoi). + +number of wavelength bands used in SNICAR snow albedo calculation + + + +type of downward solar radiation spectrum for SNICAR snow albedo calculation +(only used in 480-band version) + + + +snow optics type using different refractive index databases in SNICAR +(only used in 480-band version) + + + +dust optics type for SNICAR snow albedo calculation +(only used in 480-band version) + + + +Toggle to turn on/off aerosol deposition flux in snow in SNICAR + + Index of rooting profile for water @@ -763,6 +791,12 @@ Full pathname of surface data file. SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name + +SNICAR (SNow, ICe, and Aerosol Radiative model) 480-band optical data file name + + + SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name diff --git a/src/biogeophys/AerosolMod.F90 b/src/biogeophys/AerosolMod.F90 index f0e0c3fa88..c648632a5b 100644 --- a/src/biogeophys/AerosolMod.F90 +++ b/src/biogeophys/AerosolMod.F90 @@ -15,6 +15,7 @@ module AerosolMod use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type use ColumnType , only : col use abortutils , only : endrun + use CLM_varctl , only : snicar_use_aerosol ! cenlin ! ! !PUBLIC TYPES: implicit none @@ -806,6 +807,33 @@ subroutine AerosolFluxes(bounds, num_snowc, filter_snowc, & forc_aer(g,13) + forc_aer(g,14) end do + ! if turn off aerosol effect in snow, zero out deposition flux + if (.not. snicar_use_aerosol) then + do c = bounds%begc,bounds%endc + g = col%gridcell(c) + + flx_bc_dep_dry(c) = 0._r8 + flx_bc_dep_wet(c) = 0._r8 + flx_bc_dep_phi(c) = 0._r8 + flx_bc_dep_pho(c) = 0._r8 + flx_bc_dep(c) = 0._r8 + flx_oc_dep_dry(c) = 0._r8 + flx_oc_dep_wet(c) = 0._r8 + flx_oc_dep_phi(c) = 0._r8 + flx_oc_dep_pho(c) = 0._r8 + flx_oc_dep(c) = 0._r8 + flx_dst_dep_wet1(c) = 0._r8 + flx_dst_dep_dry1(c) = 0._r8 + flx_dst_dep_wet2(c) = 0._r8 + flx_dst_dep_dry2(c) = 0._r8 + flx_dst_dep_wet3(c) = 0._r8 + flx_dst_dep_dry3(c) = 0._r8 + flx_dst_dep_wet4(c) = 0._r8 + flx_dst_dep_dry4(c) = 0._r8 + flx_dst_dep(c) = 0._r8 + end do + end if + ! aerosol deposition fluxes into top layer ! This is done after the inter-layer fluxes so that some aerosol ! is in the top layer after deposition, and is not immediately diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 77cc5b53d6..b8a2db6bdd 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -11,7 +11,7 @@ module SnowSnicarMod use shr_kind_mod , only : r8 => shr_kind_r8 use shr_sys_mod , only : shr_sys_flush use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog + use clm_varctl , only : iulog, snicar_numrad_snw ! cenlin use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -51,9 +51,9 @@ module SnowSnicarMod logical, public, parameter :: DO_SNO_AER = .true. ! parameter to include aerosols in snowpack radiative calculations ! !PRIVATE DATA MEMBERS: - integer, parameter :: numrad_snw = 5 ! number of spectral bands used in snow model [nbr] - integer, parameter :: nir_bnd_bgn = 2 ! first band index in near-IR spectrum [idx] - integer, parameter :: nir_bnd_end = 5 ! ending near-IR band index [idx] +! integer, parameter :: numrad_snw = 5 ! number of spectral bands used in snow model [nbr] cenlin +! integer, parameter :: nir_bnd_bgn = 2 ! first band index in near-IR spectrum [idx] cenlin +! integer, parameter :: nir_bnd_end = 5 ! ending near-IR band index [idx] cenlin integer, parameter :: idx_Mie_snw_mx = 1471 ! number of effective radius indices used in Mie lookup table [idx] integer, parameter :: idx_T_max = 11 ! maxiumum temperature index used in aging lookup table [idx] @@ -90,54 +90,58 @@ module SnowSnicarMod ! (idx_Mie_snw_mx is number of snow radii with defined parameters (i.e. from 30um to 1500um)) ! direct-beam weighted ice optical properties - real(r8) :: ss_alb_snw_drc(idx_Mie_snw_mx,numrad_snw) - real(r8) :: asm_prm_snw_drc(idx_Mie_snw_mx,numrad_snw) - real(r8) :: ext_cff_mss_snw_drc(idx_Mie_snw_mx,numrad_snw) + real(r8), pointer :: ss_alb_snw_drc(:,:) !(idx_Mie_snw_mx,numrad_snw) + real(r8), pointer :: asm_prm_snw_drc(:,:) !(idx_Mie_snw_mx,numrad_snw) + real(r8), pointer :: ext_cff_mss_snw_drc(:,:) !(idx_Mie_snw_mx,numrad_snw) ! diffuse radiation weighted ice optical properties - real(r8) :: ss_alb_snw_dfs(idx_Mie_snw_mx,numrad_snw) - real(r8) :: asm_prm_snw_dfs(idx_Mie_snw_mx,numrad_snw) - real(r8) :: ext_cff_mss_snw_dfs(idx_Mie_snw_mx,numrad_snw) + real(r8), pointer :: ss_alb_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) + real(r8), pointer :: asm_prm_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) + real(r8), pointer :: ext_cff_mss_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) ! hydrophiliic BC - real(r8) :: ss_alb_bc1(numrad_snw) - real(r8) :: asm_prm_bc1(numrad_snw) - real(r8) :: ext_cff_mss_bc1(numrad_snw) + real(r8), pointer :: ss_alb_bc1(:) !(numrad_snw) + real(r8), pointer :: asm_prm_bc1(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_bc1(:) !(numrad_snw) ! hydrophobic BC - real(r8) :: ss_alb_bc2(numrad_snw) - real(r8) :: asm_prm_bc2(numrad_snw) - real(r8) :: ext_cff_mss_bc2(numrad_snw) + real(r8), pointer :: ss_alb_bc2(:) !(numrad_snw) + real(r8), pointer :: asm_prm_bc2(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_bc2(:) !(numrad_snw) ! hydrophobic OC - real(r8) :: ss_alb_oc1(numrad_snw) - real(r8) :: asm_prm_oc1(numrad_snw) - real(r8) :: ext_cff_mss_oc1(numrad_snw) + real(r8), pointer :: ss_alb_oc1(:) !(numrad_snw) + real(r8), pointer :: asm_prm_oc1(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_oc1(:) !(numrad_snw) ! hydrophilic OC - real(r8) :: ss_alb_oc2(numrad_snw) - real(r8) :: asm_prm_oc2(numrad_snw) - real(r8) :: ext_cff_mss_oc2(numrad_snw) + real(r8), pointer :: ss_alb_oc2(:) !(numrad_snw) + real(r8), pointer :: asm_prm_oc2(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_oc2(:) !(numrad_snw) ! dust species 1: - real(r8) :: ss_alb_dst1(numrad_snw) - real(r8) :: asm_prm_dst1(numrad_snw) - real(r8) :: ext_cff_mss_dst1(numrad_snw) + real(r8), pointer :: ss_alb_dst1(:) !(numrad_snw) + real(r8), pointer :: asm_prm_dst1(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_dst1(:) !(numrad_snw) ! dust species 2: - real(r8) :: ss_alb_dst2(numrad_snw) - real(r8) :: asm_prm_dst2(numrad_snw) - real(r8) :: ext_cff_mss_dst2(numrad_snw) + real(r8), pointer :: ss_alb_dst2(:) !(numrad_snw) + real(r8), pointer :: asm_prm_dst2(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_dst2(:) !(numrad_snw) ! dust species 3: - real(r8) :: ss_alb_dst3(numrad_snw) - real(r8) :: asm_prm_dst3(numrad_snw) - real(r8) :: ext_cff_mss_dst3(numrad_snw) + real(r8), pointer :: ss_alb_dst3(:) !(numrad_snw) + real(r8), pointer :: asm_prm_dst3(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_dst3(:) !(numrad_snw) ! dust species 4: - real(r8) :: ss_alb_dst4(numrad_snw) - real(r8) :: asm_prm_dst4(numrad_snw) - real(r8) :: ext_cff_mss_dst4(numrad_snw) + real(r8), pointer :: ss_alb_dst4(:) !(numrad_snw) + real(r8), pointer :: asm_prm_dst4(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_dst4(:) !(numrad_snw) + + ! downward solar radiation spectral weights for 480-band + real(r8), pointer :: flx_wgt_dir480(:) !(numrad_snw) ! direct + real(r8), pointer :: flx_wgt_dif480(:) !(numrad_snw) ! diffuse ! best-fit parameters for snow aging defined over: ! 11 temperatures from 225 to 273 K @@ -149,7 +153,8 @@ module SnowSnicarMod real(r8), pointer :: snowage_drdt0(:,:,:) ! idx_rhos_max,idx_Tgrd_max,idx_T_max) ! ! !REVISION HISTORY: - ! Created by Mark Flanner + ! Created by Mark Flanner (Univ. of Michigan) + ! Updated by Cenlin He (NCAR) based on Flanner et al. 2021 GMD character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -229,17 +234,19 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! !LOCAL VARIABLES: ! ! variables for snow radiative transfer calculations + integer :: nir_bnd_bgn ! first band index in near-IR spectrum [idx] cenlin + integer :: nir_bnd_end ! ending near-IR band index [idx] cenlin ! Local variables representing single-column values of arrays: integer :: snl_lcl ! negative number of snow layers [nbr] integer :: snw_rds_lcl(-nlevsno+1:0) ! snow effective radius [m^-6] - real(r8):: flx_slrd_lcl(1:numrad_snw) ! direct beam incident irradiance [W/m2] (set to 1) - real(r8):: flx_slri_lcl(1:numrad_snw) ! diffuse incident irradiance [W/m2] (set to 1) + real(r8):: flx_slrd_lcl(1:snicar_numrad_snw) ! direct beam incident irradiance [W/m2] (set to 1) + real(r8):: flx_slri_lcl(1:snicar_numrad_snw) ! diffuse incident irradiance [W/m2] (set to 1) real(r8):: mss_cnc_aer_lcl(-nlevsno+1:0,1:sno_nbr_aer) ! aerosol mass concentration (lyr,aer_nbr) [kg/kg] real(r8):: h2osno_lcl ! total column snow mass [kg/m2] real(r8):: h2osno_liq_lcl(-nlevsno+1:0) ! liquid water mass [kg/m2] real(r8):: h2osno_ice_lcl(-nlevsno+1:0) ! ice mass [kg/m2] - real(r8):: albsfc_lcl(1:numrad_snw) ! albedo of underlying surface [frc] + real(r8):: albsfc_lcl(1:snicar_numrad_snw) ! albedo of underlying surface [frc] real(r8):: ss_alb_snw_lcl(-nlevsno+1:0) ! single-scatter albedo of ice grains (lyr) [frc] real(r8):: asm_prm_snw_lcl(-nlevsno+1:0) ! asymmetry parameter of ice grains (lyr) [frc] real(r8):: ext_cff_mss_snw_lcl(-nlevsno+1:0) ! mass extinction coefficient of ice grains (lyr) [m2/kg] @@ -253,7 +260,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! (1=Eddington, 2=Quadrature, 3=Hemispheric Mean) [nbr] integer :: DELTA ! flag to use Delta approximation (Joseph, 1976) ! (1= use, 0= don't use) - real(r8):: flx_wgt(1:numrad_snw) ! weights applied to spectral bands, + real(r8):: flx_wgt(1:snicar_numrad_snw) ! weights applied to spectral bands, ! specific to direct and diffuse cases (bnd) [frc] integer :: flg_nosnl ! flag: =1 if there is snow, but zero snow layers, @@ -263,8 +270,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: albedo ! temporary snow albedo [frc] real(r8):: flx_sum ! temporary summation variable for NIR weighting - real(r8):: albout_lcl(numrad_snw) ! snow albedo by band [frc] - real(r8):: flx_abs_lcl(-nlevsno+1:1,numrad_snw)! absorbed flux per unit incident flux at top of snowpack (lyr,bnd) [frc] + real(r8):: albout_lcl(snicar_numrad_snw) ! snow albedo by band [frc] + real(r8):: flx_abs_lcl(-nlevsno+1:1,snicar_numrad_snw)! absorbed flux per unit incident flux at top of snowpack (lyr,bnd) [frc] real(r8):: L_snw(-nlevsno+1:0) ! h2o mass (liquid+solid) in snow layer (lyr) [kg/m2] real(r8):: tau_snw(-nlevsno+1:0) ! snow optical depth (lyr) [unitless] @@ -286,7 +293,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & integer :: nstep ! current timestep [nbr] (debugging only) integer :: g_idx, c_idx, l_idx ! gridcell, column, and landunit indices [idx] - integer :: bnd_idx ! spectral band index (1 <= bnd_idx <= numrad_snw) [idx] + integer :: bnd_idx ! spectral band index (1 <= bnd_idx <= snicar_numrad_snw) [idx] integer :: rds_idx ! snow effective radius index for retrieving ! Mie parameters from lookup table [idx] integer :: snl_btm ! index of bottom snow layer (0) [idx] @@ -353,10 +360,13 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & associate(& snl => col%snl , & ! Input: [integer (:)] negative number of snow layers (col) [nbr] - frac_sno => waterdiagnosticbulk_inst%frac_sno_eff_col & ! Input: [real(r8) (:)] fraction of ground covered by snow (0 to 1) ) + ! Define parameter, cenlin + nir_bnd_bgn = nint(snicar_numrad_snw/9.6) + 1 ! 5-band starts at 2; 480-band starts at 51 + nir_bnd_end = snicar_numrad_snw + ! Define constants pi = SHR_CONST_PI @@ -442,7 +452,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Set spectral underlying surface albedos to their corresponding VIS or NIR albedos - albsfc_lcl(1) = albsfc(c_idx,1) + albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) ! cenlin: update for hyperspectral calculation albsfc_lcl(nir_bnd_bgn:nir_bnd_end) = albsfc(c_idx,2) @@ -470,16 +480,20 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Band 4: 1.2-1.5um (NIR) ! Band 5: 1.5-5.0um (NIR) ! + ! Updated hyperspectral (10-nm) bands (480-band case) cenlin + ! Band 1~50 : 0.2-0.7um (VIS); near-UV (0.2-0.3um) is combined to VIS for now + ! Band 51~480: 0.7~5.0um (NIR) + ! ! The following weights are appropriate for surface-incident flux in a mid-latitude winter atmosphere ! ! 3-band weights - if (numrad_snw==3) then + if (snicar_numrad_snw==3) then ! Direct: if (flg_slr_in == 1) then flx_wgt(1) = 1._r8 flx_wgt(2) = 0.66628670195247_r8 flx_wgt(3) = 0.33371329804753_r8 - ! Diffuse: + ! Diffuse: elseif (flg_slr_in == 2) then flx_wgt(1) = 1._r8 flx_wgt(2) = 0.77887652162877_r8 @@ -487,7 +501,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif ! 5-band weights - elseif(numrad_snw==5) then + elseif (snicar_numrad_snw==5) then ! Direct: if (flg_slr_in == 1) then flx_wgt(1) = 1._r8 @@ -495,7 +509,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & flx_wgt(3) = 0.18099494230665_r8 flx_wgt(4) = 0.12094898498813_r8 flx_wgt(5) = 0.20453448749347_r8 - ! Diffuse: + ! Diffuse: elseif (flg_slr_in == 2) then flx_wgt(1) = 1._r8 flx_wgt(2) = 0.58581507618433_r8 @@ -503,10 +517,20 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & flx_wgt(4) = 0.10917889346386_r8 flx_wgt(5) = 0.10343699264369_r8 endif + + ! 480-band weights, cenlin + elseif (snicar_numrad_snw == 480) then + ! Direct: + if (flg_slr_in == 1) then + flx_wgt(1:snicar_numrad_snw) = flx_wgt_dir480(1:snicar_numrad_snw) ! either VIS or NIR band sum is 1.0 in the input dataset + ! Diffuse: + elseif (flg_slr_in == 2) then + flx_wgt(1:snicar_numrad_snw) = flx_wgt_dif480(1:snicar_numrad_snw) ! either VIS or NIR band sum is 1.0 in the input dataset + endif endif ! Loop over snow spectral bands - do bnd_idx = 1,numrad_snw + do bnd_idx = 1,snicar_numrad_snw mu_not = coszen(c_idx) ! must set here, because of error handling flg_dover = 1 ! default is to redo @@ -532,7 +556,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! 3rd error (flg_dover=4): switch approximation with new zenith ! Subsequent errors: repeatedly change zenith and approximations... - if (bnd_idx == 1) then + if (bnd_idx < nir_bnd_bgn) then ! VIS, cenlin if (flg_dover == 2) then APRX_TYP = 3 elseif (flg_dover == 3) then @@ -548,7 +572,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & APRX_TYP = 1 endif - else + else ! NIR if (flg_dover == 2) then APRX_TYP = 1 elseif (flg_dover == 3) then @@ -578,14 +602,19 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Pre-emptive error handling: aerosols can reap havoc on these absorptive bands. ! Since extremely high soot concentrations have a negligible effect on these bands, zero them. - if ( (numrad_snw == 5).and.((bnd_idx == 5).or.(bnd_idx == 4)) ) then + if ( (snicar_numrad_snw == 5).and.((bnd_idx == 5).or.(bnd_idx == 4)) ) then + mss_cnc_aer_lcl(:,:) = 0._r8 + endif + + if ( (snicar_numrad_snw == 3).and.(bnd_idx == 3) ) then mss_cnc_aer_lcl(:,:) = 0._r8 endif - if ( (numrad_snw == 3).and.(bnd_idx == 3) ) then + if ( (snicar_numrad_snw == 480).and.(bnd_idx > 100) ) then ! >1.2um cenlin mss_cnc_aer_lcl(:,:) = 0._r8 endif + ! Define local Mie parameters based on snow grain size and aerosol species, ! retrieved from a lookup table. if (flg_slr_in == 1) then @@ -981,22 +1010,60 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR albedo appropriately - albout(c_idx,1) = albout_lcl(1) - flx_sum = 0._r8 - do bnd_idx= nir_bnd_bgn,nir_bnd_end - flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) - end do - albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + ! for 5- and 3-band cases cenlin + if (snicar_numrad_snw <= 5) then + albout(c_idx,1) = albout_lcl(1) + flx_sum = 0._r8 + do bnd_idx= nir_bnd_bgn,nir_bnd_end + flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) + end do + albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + end if + ! for 480-band case, cenlin + if (snicar_numrad_snw == 480) then + ! average for VIS band + flx_sum = 0._r8 + do bnd_idx= 1, (nir_bnd_bgn-1) + flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) + end do + albout(c_idx,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) + ! average for NIR band + flx_sum = 0._r8 + do bnd_idx= nir_bnd_bgn,nir_bnd_end + flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) + end do + albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + end if ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately - flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) - do i=snl_top,1,1 - flx_sum = 0._r8 - do bnd_idx= nir_bnd_bgn,nir_bnd_end - flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) - enddo - flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) - end do + ! for 5- and 3-band cases cenlin + if (snicar_numrad_snw <= 5) then + flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) + do i=snl_top,1,1 + flx_sum = 0._r8 + do bnd_idx= nir_bnd_bgn,nir_bnd_end + flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) + enddo + flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + end do + end if + ! for 480-band case cenlin + if (snicar_numrad_snw == 480) then + do i=snl_top,1,1 + ! average for VIS band + flx_sum = 0._r8 + do bnd_idx= 1,(nir_bnd_bgn-1) + flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) + enddo + flx_abs(c_idx,i,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) + ! average for NIR band + flx_sum = 0._r8 + do bnd_idx= nir_bnd_bgn,nir_bnd_end + flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) + enddo + flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + end do + end if ! If snow < minimum_snow, but > 0, and there is sun, set albedo to underlying surface albedo elseif ( (coszen(c_idx) > 0._r8) .and. (h2osno_lcl < min_snw) .and. (h2osno_lcl > 0._r8) ) then @@ -1362,7 +1429,8 @@ end function FreshSnowRadius subroutine SnowOptics_init( ) use fileutils , only : getfil - use CLM_varctl , only : fsnowoptics + use CLM_varctl , only : fsnowoptics,snicar_numrad_snw,fsnowoptics480,snicar_solarspec,& + snicar_snw_optics,snicar_dust_optics ! cenlin use spmdMod , only : masterproc use ncdio_pio , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile @@ -1373,20 +1441,84 @@ subroutine SnowOptics_init( ) ! ! Open optics file: - if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....' - call getfil (fsnowoptics, locfn, 0) - call ncd_pio_openfile(ncid, locfn, 0) - if(masterproc) write(iulog,*) subname,trim(fsnowoptics) + allocate(ss_alb_snw_drc(idx_Mie_snw_mx,snicar_numrad_snw)) + allocate(asm_prm_snw_drc(idx_Mie_snw_mx,snicar_numrad_snw)) + allocate(ext_cff_mss_snw_drc(idx_Mie_snw_mx,snicar_numrad_snw)) + allocate(ss_alb_snw_dfs(idx_Mie_snw_mx,snicar_numrad_snw)) + allocate(asm_prm_snw_dfs(idx_Mie_snw_mx,snicar_numrad_snw)) + allocate(ext_cff_mss_snw_dfs(idx_Mie_snw_mx,snicar_numrad_snw)) + allocate(ss_alb_bc1(snicar_numrad_snw)) + allocate(asm_prm_bc1(snicar_numrad_snw)) + allocate(ext_cff_mss_bc1(snicar_numrad_snw)) + allocate(ss_alb_bc2(snicar_numrad_snw)) + allocate(asm_prm_bc2(snicar_numrad_snw)) + allocate(ext_cff_mss_bc2(snicar_numrad_snw)) + allocate(ss_alb_oc1(snicar_numrad_snw)) + allocate(asm_prm_oc1(snicar_numrad_snw)) + allocate(ext_cff_mss_oc1(snicar_numrad_snw)) + allocate(ss_alb_oc2(snicar_numrad_snw)) + allocate(asm_prm_oc2(snicar_numrad_snw)) + allocate(ext_cff_mss_oc2(snicar_numrad_snw)) + allocate(ss_alb_dst1(snicar_numrad_snw)) + allocate(asm_prm_dst1(snicar_numrad_snw)) + allocate(ext_cff_mss_dst1(snicar_numrad_snw)) + allocate(ss_alb_dst2(snicar_numrad_snw)) + allocate(asm_prm_dst2(snicar_numrad_snw)) + allocate(ext_cff_mss_dst2(snicar_numrad_snw)) + allocate(ss_alb_dst3(snicar_numrad_snw)) + allocate(asm_prm_dst3(snicar_numrad_snw)) + allocate(ext_cff_mss_dst3(snicar_numrad_snw)) + allocate(ss_alb_dst4(snicar_numrad_snw)) + allocate(asm_prm_dst4(snicar_numrad_snw)) + allocate(ext_cff_mss_dst4(snicar_numrad_snw)) + allocate(flx_wgt_dir480(snicar_numrad_snw)) + allocate(flx_wgt_dif480(snicar_numrad_snw)) - ! direct-beam snow Mie parameters: - call ncd_io('ss_alb_ice_drc', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_drc',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_drc', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....' + ! for 5-band data, cenlin + if (snicar_numrad_snw <= 5) then + call getfil (fsnowoptics, locfn, 0) + call ncd_pio_openfile(ncid, locfn, 0) + if(masterproc) write(iulog,*) subname,trim(fsnowoptics) + end if + ! for 480-band data, cenlin + if (snicar_numrad_snw == 480) then + call getfil (fsnowoptics480, locfn, 0) + call ncd_pio_openfile(ncid, locfn, 0) + if(masterproc) write(iulog,*) subname,trim(fsnowoptics480) + end if - ! diffuse snow Mie parameters - call ncd_io( 'ss_alb_ice_dfs', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_dfs', asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_dfs', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + if (snicar_numrad_snw <= 5) then + ! direct-beam snow Mie parameters: + call ncd_io( 'ss_alb_ice_drc', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_drc',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_drc', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + + ! diffuse snow Mie parameters + call ncd_io( 'ss_alb_ice_dfs', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_dfs', asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_dfs', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif ! BC species 1 Mie parameters call ncd_io( 'ss_alb_bcphil', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) @@ -1408,26 +1540,143 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ocphob', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) - - ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) - - ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) - - ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + ! new data for 480-band + if (snicar_numrad_snw == 480) then + + ! snow optical properties derived from different ice refractive index dataset + ! same value for direct and diffuse due to high spectral res without spectra averaging in database + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + else + write(iulog,*) 'invalid snow optics type option in namelist' + ! for invalid spectrum type, use Picard et al (2016) (default) + call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + else + write(iulog,*) 'invalid dust optics type option in namelist' + ! for invalid dust optics type, use Saharan dust (default) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif + + ! downward solar radiation spectral weights for 480-band + if (snicar_solarspec == 1) then ! mid-latitude winter + call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_solarspec == 2) then ! mid-latitude summer + call ncd_io( 'flx_wgt_dir480_mls', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_mls', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_solarspec == 3) then ! sub-Arctic winter + call ncd_io( 'flx_wgt_dir480_saw', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_saw', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_solarspec == 4) then ! sub-Arctic summer + call ncd_io( 'flx_wgt_dir480_sas', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_sas', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_solarspec == 5) then ! Summit,Greenland,summer + call ncd_io( 'flx_wgt_dir480_smm', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_smm', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_solarspec == 6) then ! High Mountain summer + call ncd_io( 'flx_wgt_dir480_hmn', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_hmn', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + else + write(iulog,*) 'invalid downward solar radiation spectrum option in namelist' + ! for invalid spectrum type, use mid-latitude winter (default) + call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + endif + endif call ncd_pio_closefile(ncid) if (masterproc) then diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 3ad4b14bef..8fac958db5 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -93,6 +93,7 @@ module clm_varctl character(len=fname_len), public :: nrevsn = ' ' ! restart data file name for branch run character(len=fname_len), public :: fsnowoptics = ' ' ! snow optical properties file name character(len=fname_len), public :: fsnowaging = ' ' ! snow aging parameters file name + character(len=fname_len), public :: fsnowoptics480 = ' ' ! snow optical properties file name for 480 bands, cenlin character(len=fname_len), public :: fatmlndfrc = ' ' ! lnd frac file on atm grid ! only needed for LILAC and MCT drivers @@ -205,6 +206,23 @@ module clm_varctl real(r8), public :: o3_ppbv = 100._r8 + ! number of wavelength bands used in SNICAR snow albedo calculation, cenlin + integer, public :: snicar_numrad_snw = 5 + + ! type of downward solar radiation spectrum for SNICAR snow albedo calculation (only used in 480-band version), cenlin + integer, public :: snicar_solarspec = 1 ! 1->mid-latitude winter;2->mid-latitude summer;3->sub-Arctic winter; + ! 4->sub-Arctic summer;5->Summit,Greenland,summer;6->High Mountain summer; + + ! snow optics type using different refractive index databases in SNICAR (only used in 480-band version), cenlin + integer, public :: snicar_snw_optics = 3 ! 1->Warren (1984);2->Warren and Brandt (2008);3->Picard et al (2016) + + ! dust optics type for SNICAR snow albedo calculation (only used in 480-band version), cenlin + integer, public :: snicar_dust_optics = 1 ! 1->Saharan dust (Balkanski et al., 2007, central hematite) + ! 2->San Juan Mountains dust, CO (Skiles et al, 2017) + ! 3->Greenland dust (Polashenski et al., 2015, central absorptivity) + ! option to turn off aerosol effect in snow in SNICAR + logical, public :: snicar_use_aerosol = .true. ! if .false., turn off aerosol deposition flux + !---------------------------------------------------------- ! C isotopes !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 082d68e8eb..91fd1cc61a 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -147,7 +147,7 @@ subroutine control_init(dtime) namelist /clm_inparm/ & fsurdat, & - paramfile, fsnowoptics, fsnowaging + paramfile, fsnowoptics, fsnowaging, fsnowoptics480 ! cenlin ! History, restart options @@ -201,7 +201,8 @@ subroutine control_init(dtime) albice, soil_layerstruct_predefined, soil_layerstruct_userdefined, & soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & - crop_fsat_equals_zero, for_testing_run_ncdiopio_tests + crop_fsat_equals_zero, for_testing_run_ncdiopio_tests,snicar_numrad_snw,snicar_solarspec,& + snicar_snw_optics,snicar_dust_optics,snicar_use_aerosol ! cenlin ! vertical soil mixing variables namelist /clm_inparm/ & @@ -568,6 +569,30 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if + ! check on snow albedo wavelength bands, cenlin + if ( (snicar_numrad_snw /= 5) .and. (snicar_numrad_snw /= 480) ) then + call endrun(msg=' ERROR: snicar_numrad_snw is out of a reasonable range (5 or 480)'//& + errMsg(sourcefile, __LINE__)) + end if + + ! check on downward solar radiation spectrum, cenlin + if ( (snicar_solarspec < 0) .or. (snicar_solarspec > 6) ) then + call endrun(msg=' ERROR: snicar_solarspec is out of a reasonable range (1~6)'//& + errMsg(sourcefile, __LINE__)) + end if + + ! check on snow optics type + if ( (snicar_snw_optics < 0) .or. (snicar_snw_optics > 3) ) then + call endrun(msg=' ERROR: snicar_snw_optics is out of a reasonable range (1~3)'//& + errMsg(sourcefile, __LINE__)) + end if + + ! check on dust optics type + if ( (snicar_dust_optics < 0) .or. (snicar_dust_optics > 3) ) then + call endrun(msg=' ERROR: snicar_dust_optics is out of a reasonable range (1~3)'//& + errMsg(sourcefile, __LINE__)) + end if + ! Consistency settings for nrevsn if (nsrest == nsrStartup ) nrevsn = ' ' @@ -646,6 +671,7 @@ subroutine control_spmd() call mpi_bcast (paramfile, len(paramfile) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fsnowoptics, len(fsnowoptics), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fsnowaging, len(fsnowaging), MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (fsnowoptics480, len(fsnowoptics480), MPI_CHARACTER, 0, mpicom, ier) ! cenlin ! Irrigation call mpi_bcast(irrigate, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -787,6 +813,11 @@ subroutine control_spmd() call mpi_bcast (soil_layerstruct_predefined,len(soil_layerstruct_predefined), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (soil_layerstruct_userdefined,size(soil_layerstruct_userdefined), MPI_REAL8, 0, mpicom, ier) call mpi_bcast (soil_layerstruct_userdefined_nlevsoi, 1, MPI_INTEGER, 0, mpicom, ier) + call mpi_bcast (snicar_numrad_snw, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_solarspec, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_snw_optics, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -873,6 +904,7 @@ subroutine control_print () write(iulog,*) ' use_grainproduct = ', use_grainproduct write(iulog,*) ' o3_veg_stress_method = ', o3_veg_stress_method write(iulog,*) ' use_snicar_frc = ', use_snicar_frc + write(iulog,*) ' snicar_use_aerosol = ',snicar_use_aerosol write(iulog,*) ' use_vancouver = ', use_vancouver write(iulog,*) ' use_mexicocity = ', use_mexicocity write(iulog,*) ' use_noio = ', use_noio @@ -959,9 +991,21 @@ subroutine control_print () else write(iulog,*) ' snow aging parameters file = ',trim(fsnowaging) endif + ! cenlin + if (snicar_numrad_snw==480) then + if (fsnowoptics480 == ' ') then + write(iulog,*) ' SNICAR snow optical properties (480-band) file NOT set' + else + write(iulog,*) ' SNICAR snow optical properties (480-band) file = ',trim(fsnowoptics480) + endif + write(iulog,*) ' Downward solar radiation spectrum for SNICAR =', snicar_solarspec + write(iulog,*) ' Snow refractive index type = ', snicar_snw_optics + write(iulog,*) ' Dust optics type = ', snicar_dust_optics + endif write(iulog,*) ' Number of snow layers =', nlevsno write(iulog,*) ' Max snow depth (mm) =', h2osno_max + write(iulog,*) ' Number of bands in SNICAR snow albedo calculation =', snicar_numrad_snw ! cenlin write(iulog,*) ' glc number of elevation classes =', maxpatch_glc if (glc_do_dynglacier) then From 3cb12beca735fbd266c011859b09a81874c1fc6d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jan 2022 18:36:37 -0700 Subject: [PATCH 0103/2067] Logic correction/simplification to harvesting on prescribed planting day when previous crop still alive. --- src/biogeochem/CNPhenologyMod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 170b681313..d7c1589529 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1849,6 +1849,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) + do_plant_prescribed = .false. else gddmaturity(p) = 0._r8 @@ -1881,6 +1882,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) + do_plant_prescribed = .false. else gddmaturity(p) = 0._r8 @@ -2011,8 +2013,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (do_plant_prescribed .and. (s == 0 .or. crop_inst%sdates_thisyr(p,s) < jday)) then - ! Today is the planting day, but the crop still hasn't been harvested. + if (do_plant_prescribed) then + ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. else if (generate_crop_gdds) then From b118c0360e31a49d57bbc0c0452a7c3dc67b4bbf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jan 2022 18:37:06 -0700 Subject: [PATCH 0104/2067] Do not harvest on the day this growing season began; would create challenges for postprocessing. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d7c1589529..555aeabf7b 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2030,6 +2030,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! until some time next year. do_harvest = .false. endif + else if (use_cropcal_streams .and. s > 0 .and. crop_inst%sdates_thisyr(p,s) == jday) then + ! Do not harvest on the day this growing season began; + ! would create challenges for postprocessing. + do_harvest = .false. else ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p)) From 314c7d38fe2917fe65e7bfcc52e4d336750930ed Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Tue, 25 Jan 2022 21:04:18 -0700 Subject: [PATCH 0105/2067] add adding-doubling solver in SNICAR with namelist option --- .../namelist_definition_ctsm.xml | 5 + src/biogeophys/SnowSnicarMod.F90 | 1069 ++++++++++++----- src/main/clm_varctl.F90 | 4 + src/main/controlMod.F90 | 10 +- 4 files changed, 772 insertions(+), 316 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 73dc049406..6a841ae588 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -188,6 +188,11 @@ dust optics type for SNICAR snow albedo calculation Toggle to turn on/off aerosol deposition flux in snow in SNICAR + +SNICAR radiative transfer solver type + + Index of rooting profile for water diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index b8a2db6bdd..fc7c95bcb7 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -11,7 +11,7 @@ module SnowSnicarMod use shr_kind_mod , only : r8 => shr_kind_r8 use shr_sys_mod , only : shr_sys_flush use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog, snicar_numrad_snw ! cenlin + use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver ! cenlin use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -209,6 +209,21 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Present-day climate forcing and response from black carbon in snow, ! J. Geophys. Res., 112, D11202, doi: 10.1029/2006JD008003 ! + ! Updated radiative transfer solver: + ! + ! The multi-layer solution for multiple-scattering used here is from: + ! Briegleb, P. and Light, B.: A Delta-Eddington mutiple scattering + ! parameterization for solar radiation in the sea ice component of the + ! community climate system model, 2007. + ! + ! The implementation of the SNICAR-AD model in CLM is described in: + ! Dang et al.2019, Inter-comparison and improvement of 2-stream shortwave + ! radiative transfer models for unified treatment of cryospheric surfaces + ! in ESMs; and Flanner et al. 2021, SNICAR-ADv3: a community tool for modeling + ! spectral snow albedo + ! + ! To use this new adding-doubling solver, set snicar_rt_solver=2 in CLM namelist + ! ! !USES: use clm_varpar , only : nlevsno, numrad use clm_time_manager , only : get_nstep @@ -254,25 +269,21 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: asm_prm_aer_lcl(sno_nbr_aer) ! asymmetry parameter of aerosol species (aer_nbr) [frc] real(r8):: ext_cff_mss_aer_lcl(sno_nbr_aer) ! mass extinction coefficient of aerosol species (aer_nbr) [m2/kg] - ! Other local variables integer :: APRX_TYP ! two-stream approximation type ! (1=Eddington, 2=Quadrature, 3=Hemispheric Mean) [nbr] integer :: DELTA ! flag to use Delta approximation (Joseph, 1976) ! (1= use, 0= don't use) real(r8):: flx_wgt(1:snicar_numrad_snw) ! weights applied to spectral bands, - ! specific to direct and diffuse cases (bnd) [frc] - + ! specific to direct and diffuse cases (bnd) [frc] integer :: flg_nosnl ! flag: =1 if there is snow, but zero snow layers, ! =0 if at least 1 snow layer [flg] integer :: trip ! flag: =1 to redo RT calculation if result is unrealistic integer :: flg_dover ! defines conditions for RT redo (explained below) - real(r8):: albedo ! temporary snow albedo [frc] real(r8):: flx_sum ! temporary summation variable for NIR weighting real(r8):: albout_lcl(snicar_numrad_snw) ! snow albedo by band [frc] real(r8):: flx_abs_lcl(-nlevsno+1:1,snicar_numrad_snw)! absorbed flux per unit incident flux at top of snowpack (lyr,bnd) [frc] - real(r8):: L_snw(-nlevsno+1:0) ! h2o mass (liquid+solid) in snow layer (lyr) [kg/m2] real(r8):: tau_snw(-nlevsno+1:0) ! snow optical depth (lyr) [unitless] real(r8):: L_aer(-nlevsno+1:0,sno_nbr_aer) ! aerosol mass in snow layer (lyr,nbr_aer) [kg/m2] @@ -281,7 +292,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: tau_clm(-nlevsno+1:0) ! column optical depth from layer bottom to snowpack top (lyr) [unitless] real(r8):: omega_sum ! temporary summation of single-scatter albedo of all aerosols [frc] real(r8):: g_sum ! temporary summation of asymmetry parameter of all aerosols [frc] - real(r8):: tau(-nlevsno+1:0) ! weighted optical depth of snow+aerosol layer (lyr) [unitless] real(r8):: omega(-nlevsno+1:0) ! weighted single-scatter albedo of snow+aerosol layer (lyr) [frc] real(r8):: g(-nlevsno+1:0) ! weighted asymmetry parameter of snow+aerosol layer (lyr) [frc] @@ -290,7 +300,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: omega_star(-nlevsno+1:0) ! transformed (i.e. Delta-Eddington) SSA of snow+aerosol layer (lyr) [frc] real(r8):: g_star(-nlevsno+1:0) ! transformed (i.e. Delta-Eddington) asymmetry paramater of snow+aerosol layer ! (lyr) [frc] - integer :: nstep ! current timestep [nbr] (debugging only) integer :: g_idx, c_idx, l_idx ! gridcell, column, and landunit indices [idx] integer :: bnd_idx ! spectral band index (1 <= bnd_idx <= snicar_numrad_snw) [idx] @@ -302,8 +311,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & integer :: i ! layer index [idx] integer :: j ! aerosol number index [idx] integer :: n ! tridiagonal matrix index [idx] - integer :: m ! secondary layer index [idx] - + integer :: m ! secondary layer index [idx] real(r8):: F_direct(-nlevsno+1:0) ! direct-beam radiation at bottom of layer interface (lyr) [W/m^2] real(r8):: F_net(-nlevsno+1:0) ! net radiative flux at bottom of layer interface (lyr) [W/m^2] real(r8):: F_abs(-nlevsno+1:0) ! net absorbed radiative energy (lyr) [W/m^2] @@ -314,13 +322,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: energy_sum ! sum of all energy terms; should be 0.0 [W/m^2] real(r8):: F_direct_btm ! direct-beam radiation at bottom of snowpack [W/m^2] real(r8):: mu_not ! cosine of solar zenith angle (used locally) [frc] - integer :: err_idx ! counter for number of times through error loop [nbr] real(r8):: lat_coord ! gridcell latitude (debugging only) real(r8):: lon_coord ! gridcell longitude (debugging only) integer :: sfctype ! underlying surface type (debugging only) real(r8):: pi ! 3.1415... + !----------------------------------------------------------------------- + ! variables used for Toon et al. 1989 2-stream solver (Flanner et al. 2007): ! intermediate variables for radiative transfer approximation: real(r8):: gamma1(-nlevsno+1:0) ! two-stream coefficient from Toon et al. (lyr) [unitless] real(r8):: gamma2(-nlevsno+1:0) ! two-stream coefficient from Toon et al. (lyr) [unitless] @@ -346,6 +355,96 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: X(-2*nlevsno+1:0) ! tri-diag intermediate variable from Toon et al. (2*lyr) real(r8):: Y(-2*nlevsno+1:0) ! tri-diag intermediate variable from Toon et al. (2*lyr) !----------------------------------------------------------------------- + ! + ! variables used for Adding-doubling 2-stream solver based on SNICAR-ADv3 version + ! (Dang et al. 2019; Flanner et al. 2021) + real(r8):: trndir(-nlevsno+1:1) ! solar beam down transmission from top + real(r8):: trntdr(-nlevsno+1:1) ! total transmission to direct beam for layers above + real(r8):: trndif(-nlevsno+1:1) ! diffuse transmission to diffuse beam for layers above + real(r8):: rupdir(-nlevsno+1:1) ! reflectivity to direct radiation for layers below + real(r8):: rupdif(-nlevsno+1:1) ! reflectivity to diffuse radiation for layers below + real(r8):: rdndif(-nlevsno+1:1) ! reflectivity to diffuse radiation for layers above + real(r8):: dfdir(-nlevsno+1:1) ! down-up flux at interface due to direct beam at top surface + real(r8):: dfdif(-nlevsno+1:1) ! down-up flux at interface due to diffuse beam at top surface + real(r8):: dftmp(-nlevsno+1:1) ! temporary variable for down-up flux at interface + real(r8):: rdir(-nlevsno+1:0) ! layer reflectivity to direct radiation + real(r8):: rdif_a(-nlevsno+1:0) ! layer reflectivity to diffuse radiation from above + real(r8):: rdif_b(-nlevsno+1:0) ! layer reflectivity to diffuse radiation from below + real(r8):: tdir(-nlevsno+1:0) ! layer transmission to direct radiation (solar beam + diffuse) + real(r8):: tdif_a(-nlevsno+1:0) ! layer transmission to diffuse radiation from above + real(r8):: tdif_b(-nlevsno+1:0) ! layer transmission to diffuse radiation from below + real(r8):: trnlay(-nlevsno+1:0) ! solar beam transm for layer (direct beam only) + real(r8):: ts ! layer delta-scaled extinction optical depth + real(r8):: ws ! layer delta-scaled single scattering albedo + real(r8):: gs ! layer delta-scaled asymmetry parameter + real(r8):: extins ! extinction + real(r8):: alp ! temporary for alpha + real(r8):: gam ! temporary for agamm + real(r8):: amg ! alp - gam + real(r8):: apg ! alp + gam + real(r8):: ue ! temporary for u + real(r8):: refk ! interface multiple scattering + real(r8):: refkp1 ! interface multiple scattering for k+1 + real(r8):: refkm1 ! interface multiple scattering for k-1 + real(r8):: tdrrdir ! direct tran times layer direct ref + real(r8):: tdndif ! total down diffuse = tot tran - direct tran + real(r8):: taus ! scaled extinction optical depth + real(r8):: omgs ! scaled single particle scattering albedo + real(r8):: asys ! scaled asymmetry parameter + real(r8):: lm ! temporary for el + real(r8):: mu ! cosine solar zenith for either snow or water + real(r8):: ne ! temporary for n + real(r8):: R1 ! perpendicular polarization reflection amplitude + real(r8):: R2 ! parallel polarization reflection amplitude + real(r8):: T1 ! perpendicular polarization transmission amplitude + real(r8):: T2 ! parallel polarization transmission amplitude + real(r8):: Rf_dir_a ! fresnel reflection to direct radiation + real(r8):: Tf_dir_a ! fresnel transmission to direct radiation + real(r8):: Rf_dif_a ! fresnel reflection to diff radiation from above + real(r8):: Rf_dif_b ! fresnel reflection to diff radiation from below + real(r8):: Tf_dif_a ! fresnel transmission to diff radiation from above + real(r8):: Tf_dif_b ! fresnel transmission to diff radiation from below + real(r8):: gwt ! gaussian weight + real(r8):: swt ! sum of weights + real(r8):: trn ! layer transmission + real(r8):: rdr ! rdir for gaussian integration + real(r8):: tdr ! tdir for gaussian integration + real(r8):: smr ! accumulator for rdif gaussian integration + real(r8):: smt ! accumulator for tdif gaussian integration + real(r8):: exp_min ! minimum exponential value + real(r8):: difgauspt(1:8) ! Gaussian integration angle + real(r8):: difgauswt(1:8) ! Gaussian integration coefficients/weights + integer :: ng ! gaussian integration index + integer :: snl_btm_itf ! index of bottom snow layer interfaces (1) [idx] + integer :: ngmax = 8 ! maxmimum gaussian integration index + ! constants used in algorithm + real(r8):: c0 = 0.0_r8 + real(r8):: c1 = 1.0_r8 + real(r8):: c3 = 3.0_r8 + real(r8):: c4 = 4.0_r8 + real(r8):: c6 = 6.0_r8 + real(r8):: cp01 = 0.01_r8 + real(r8):: cp5 = 0.5_r8 + real(r8):: cp75 = 0.75_r8 + real(r8):: c1p5 = 1.5_r8 + real(r8):: trmin = 0.001_r8 + real(r8):: argmax = 10.0_r8 ! maximum argument of exponential + ! cconstant and coefficients used for SZA parameterization + real(r8):: sza_a0 = 0.085730_r8 + real(r8):: sza_a1 = -0.630883_r8 + real(r8):: sza_a2 = 1.303723_r8 + real(r8):: sza_b0 = 1.467291_r8 + real(r8):: sza_b1 = -3.338043_r8 + real(r8):: sza_b2 = 6.807489_r8 + real(r8):: puny = 1.0e-11_r8 + real(r8):: mu_75 = 0.2588_r8 ! cosine of 75 degree + real(r8):: sza_c1 ! coefficient, SZA parameteirzation + real(r8):: sza_c0 ! coefficient, SZA parameterization + real(r8):: sza_factor ! factor used to adjust NIR direct albedo + real(r8):: flx_sza_adjust ! direct NIR flux adjustment from sza_factor + real(r8):: mu0 ! incident solar zenith angle + ! + !----------------------------------------------------------------------- ! Enforce expected array sizes SHR_ASSERT_ALL_FL((ubound(coszen) == (/bounds%endc/)), sourcefile, __LINE__) @@ -364,8 +463,18 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ) ! Define parameter, cenlin - nir_bnd_bgn = nint(snicar_numrad_snw/9.6) + 1 ! 5-band starts at 2; 480-band starts at 51 - nir_bnd_end = snicar_numrad_snw + nir_bnd_bgn = nint(snicar_numrad_snw/9.6) + 1 ! 5-band starts at 2; 480-band starts at 51 + nir_bnd_end = snicar_numrad_snw + difgauspt(1:8) = & ! gaussian angles (radians) + (/ 0.9894009_r8, 0.9445750_r8, & + 0.8656312_r8, 0.7554044_r8, & + 0.6178762_r8, 0.4580168_r8, & + 0.2816036_r8, 0.0950125_r8/) + difgauswt(1:8) = & ! gaussian weights + (/ 0.0271525_r8, 0.0622535_r8, & + 0.0951585_r8, 0.1246290_r8, & + 0.1495960_r8, 0.1691565_r8, & + 0.1826034_r8, 0.1894506_r8/) ! Define constants pi = SHR_CONST_PI @@ -381,7 +490,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & do fc = 1,num_nourbanc c_idx = filter_nourbanc(fc) - ! Zero absorbed radiative fluxes: do i=-nlevsno+1,1,1 flx_abs_lcl(:,:) = 0._r8 @@ -395,7 +503,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & h2osno_lcl = h2osno_ice(c_idx,0) endif - ! Qualifier for computing snow RT: ! 1) sunlight from atmosphere model ! 2) minimum amount of snow on ground. @@ -430,8 +537,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & lat_coord = grc%latdeg(g_idx) lon_coord = grc%londeg(g_idx) - - ! Set variables specific to CSIM + ! Set variables specific to CSIM else flg_nosnl = 0 snl_lcl = -1 @@ -443,7 +549,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & sfctype = -1 lat_coord = -90 lon_coord = 0 - endif + endif ! end if flg_snw_ice == 1 + ! Set local aerosol array do j=1,sno_nbr_aer @@ -454,7 +561,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Set spectral underlying surface albedos to their corresponding VIS or NIR albedos albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) ! cenlin: update for hyperspectral calculation albsfc_lcl(nir_bnd_bgn:nir_bnd_end) = albsfc(c_idx,2) - + ! Error check for snow grain size: do i=snl_top,snl_btm,1 @@ -469,6 +576,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif enddo + ! Incident flux weighting parameters ! - sum of all VIS bands must equal 1 ! - sum of all NIR bands must equal 1 @@ -481,8 +589,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Band 5: 1.5-5.0um (NIR) ! ! Updated hyperspectral (10-nm) bands (480-band case) cenlin - ! Band 1~50 : 0.2-0.7um (VIS); near-UV (0.2-0.3um) is combined to VIS for now - ! Band 51~480: 0.7~5.0um (NIR) + ! Bands 1~50 : 0.2-0.7um (VIS); near-UV (0.2-0.3um) is combined to VIS for now + ! Bands 51~480: 0.7~5.0um (NIR) ! ! The following weights are appropriate for surface-incident flux in a mid-latitude winter atmosphere ! @@ -500,7 +608,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & flx_wgt(3) = 0.22112347837123_r8 endif - ! 5-band weights + ! 5-band weights elseif (snicar_numrad_snw==5) then ! Direct: if (flg_slr_in == 1) then @@ -527,68 +635,87 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & elseif (flg_slr_in == 2) then flx_wgt(1:snicar_numrad_snw) = flx_wgt_dif480(1:snicar_numrad_snw) ! either VIS or NIR band sum is 1.0 in the input dataset endif - endif + endif ! end if snicar_numrad_snw + + exp_min = exp(-argmax) ! Loop over snow spectral bands do bnd_idx = 1,snicar_numrad_snw - mu_not = coszen(c_idx) ! must set here, because of error handling - flg_dover = 1 ! default is to redo - err_idx = 0 ! number of times through loop + ! Toon et al 2-stream + if (snicar_rt_solver == 1) then + mu_not = coszen(c_idx) ! must set here, because of error handling + + ! Adding-doubling 2-stream + elseif (snicar_rt_solver == 2) then + ! flg_dover is not used since this algorithm is stable for mu_not > 0.01 + ! mu_not is cosine solar zenith angle above the fresnel level; make + ! sure mu_not is large enough for stable and meaningful radiation + ! solution: .01 is like sun just touching horizon with its lower edge + ! equivalent to mu0 in sea-ice shortwave model ice_shortwave.F90 + mu_not = max(coszen(c_idx), cp01) + endif + + flg_dover = 1 ! default is to redo + err_idx = 0 ! number of times through loop do while (flg_dover > 0) - ! DEFAULT APPROXIMATIONS: - ! VIS: Delta-Eddington - ! NIR (all): Delta-Hemispheric Mean - ! WARNING: DO NOT USE DELTA-EDDINGTON FOR NIR DIFFUSE - this sometimes results in negative albedo - ! - ! ERROR CONDITIONS: - ! Conditions which cause "trip", resulting in redo of RT approximation: - ! 1. negative absorbed flux - ! 2. total absorbed flux greater than incident flux - ! 3. negative albedo - ! NOTE: These errors have only been encountered in spectral bands 4 and 5 - ! - ! ERROR HANDLING - ! 1st error (flg_dover=2): switch approximation (Edd->HM or HM->Edd) - ! 2nd error (flg_dover=3): change zenith angle by 0.02 (this happens about 1 in 10^6 cases) - ! 3rd error (flg_dover=4): switch approximation with new zenith - ! Subsequent errors: repeatedly change zenith and approximations... - - if (bnd_idx < nir_bnd_bgn) then ! VIS, cenlin - if (flg_dover == 2) then - APRX_TYP = 3 - elseif (flg_dover == 3) then - APRX_TYP = 1 - if (coszen(c_idx) > 0.5_r8) then - mu_not = mu_not - 0.02_r8 - else - mu_not = mu_not + 0.02_r8 - endif - elseif (flg_dover == 4) then - APRX_TYP = 3 - else - APRX_TYP = 1 - endif - - else ! NIR - if (flg_dover == 2) then - APRX_TYP = 1 - elseif (flg_dover == 3) then - APRX_TYP = 3 - if (coszen(c_idx) > 0.5_r8) then - mu_not = mu_not - 0.02_r8 - else - mu_not = mu_not + 0.02_r8 - endif - elseif (flg_dover == 4) then - APRX_TYP = 1 - else - APRX_TYP = 3 - endif + ! Only for Toon et al 2-stream solver: + if (snicar_rt_solver == 1) then + + ! DEFAULT APPROXIMATIONS: + ! VIS: Delta-Eddington + ! NIR (all): Delta-Hemispheric Mean + ! WARNING: DO NOT USE DELTA-EDDINGTON FOR NIR DIFFUSE - this sometimes results in negative albedo + ! + ! ERROR CONDITIONS: + ! Conditions which cause "trip", resulting in redo of RT approximation: + ! 1. negative absorbed flux + ! 2. total absorbed flux greater than incident flux + ! 3. negative albedo + ! NOTE: These errors have only been encountered in spectral bands 4 and 5 + ! + ! ERROR HANDLING + ! 1st error (flg_dover=2): switch approximation (Edd->HM or HM->Edd) + ! 2nd error (flg_dover=3): change zenith angle by 0.02 (this happens about 1 in 10^6 cases) + ! 3rd error (flg_dover=4): switch approximation with new zenith + ! Subsequent errors: repeatedly change zenith and approximations... + + if (bnd_idx < nir_bnd_bgn) then ! VIS, cenlin + if (flg_dover == 2) then + APRX_TYP = 3 + elseif (flg_dover == 3) then + APRX_TYP = 1 + if (coszen(c_idx) > 0.5_r8) then + mu_not = mu_not - 0.02_r8 + else + mu_not = mu_not + 0.02_r8 + endif + elseif (flg_dover == 4) then + APRX_TYP = 3 + else + APRX_TYP = 1 + endif + else ! NIR + if (flg_dover == 2) then + APRX_TYP = 1 + elseif (flg_dover == 3) then + APRX_TYP = 3 + if (coszen(c_idx) > 0.5_r8) then + mu_not = mu_not - 0.02_r8 + else + mu_not = mu_not + 0.02_r8 + endif + elseif (flg_dover == 4) then + APRX_TYP = 1 + else + APRX_TYP = 3 + endif + endif ! end if bnd_idx < nir_bnd_bgn + + endif ! end if snicar_rt_solver == 1 - endif ! Set direct or diffuse incident irradiance to 1 ! (This has to be within the bnd loop because mu_not is adjusted in rare cases) @@ -615,6 +742,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif + !--------------------------- Start snow & aerosol optics -------------------------------- ! Define local Mie parameters based on snow grain size and aerosol species, ! retrieved from a lookup table. if (flg_slr_in == 1) then @@ -719,180 +847,183 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & tau_star(i) = tau(i) enddo endif - - ! Total column optical depth: - ! tau_clm(i) = total optical depth above the bottom of layer i - tau_clm(snl_top) = 0._r8 - do i=snl_top+1,snl_btm,1 - tau_clm(i) = tau_clm(i-1)+tau_star(i-1) - enddo - - ! Direct radiation at bottom of snowpack: - F_direct_btm = albsfc_lcl(bnd_idx)*mu_not * & - exp(-(tau_clm(snl_btm)+tau_star(snl_btm))/mu_not)*pi*flx_slrd_lcl(bnd_idx) - - ! Intermediates - ! Gamma values are approximation-specific. - - ! Eddington - if (APRX_TYP==1) then - do i=snl_top,snl_btm,1 - gamma1(i) = (7._r8-(omega_star(i)*(4._r8+(3._r8*g_star(i)))))/4._r8 - gamma2(i) = -(1._r8-(omega_star(i)*(4._r8-(3._r8*g_star(i)))))/4._r8 - gamma3(i) = (2._r8-(3._r8*g_star(i)*mu_not))/4._r8 - gamma4(i) = 1._r8-gamma3(i) - mu_one = 0.5_r8 - enddo - - ! Quadrature - elseif (APRX_TYP==2) then - do i=snl_top,snl_btm,1 - gamma1(i) = (3._r8**0.5)*(2._r8-(omega_star(i)*(1._r8+g_star(i))))/2._r8 - gamma2(i) = omega_star(i)*(3._r8**0.5)*(1._r8-g_star(i))/2._r8 - gamma3(i) = (1._r8-((3._r8**0.5)*g_star(i)*mu_not))/2._r8 - gamma4(i) = 1._r8-gamma3(i) - mu_one = 1._r8/(3._r8**0.5_r8) - enddo - - ! Hemispheric Mean - elseif (APRX_TYP==3) then - do i=snl_top,snl_btm,1 - gamma1(i) = 2._r8 - (omega_star(i)*(1._r8+g_star(i))) - gamma2(i) = omega_star(i)*(1-g_star(i)) - gamma3(i) = (1._r8-((3._r8**0.5_r8)*g_star(i)*mu_not))/2._r8 - gamma4(i) = 1._r8-gamma3(i) - mu_one = 0.5_r8 - enddo - endif - - ! Intermediates for tri-diagonal solution - do i=snl_top,snl_btm,1 - lambda(i) = sqrt(abs((gamma1(i)**2) - (gamma2(i)**2))) - GAMMA(i) = gamma2(i)/(gamma1(i)+lambda(i)) - - e1(i) = 1+(GAMMA(i)*exp(-lambda(i)*tau_star(i))) - e2(i) = 1-(GAMMA(i)*exp(-lambda(i)*tau_star(i))) - e3(i) = GAMMA(i) + exp(-lambda(i)*tau_star(i)) - e4(i) = GAMMA(i) - exp(-lambda(i)*tau_star(i)) - enddo !enddo over snow layers - - - ! Intermediates for tri-diagonal solution - do i=snl_top,snl_btm,1 - if (flg_slr_in == 1) then - - C_pls_btm(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-(tau_clm(i)+tau_star(i))/mu_not)* & - (((gamma1(i)-(1/mu_not))*gamma3(i))+ & - (gamma4(i)*gamma2(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - C_mns_btm(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-(tau_clm(i)+tau_star(i))/mu_not)* & - (((gamma1(i)+(1/mu_not))*gamma4(i))+ & - (gamma2(i)*gamma3(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - C_pls_top(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-tau_clm(i)/mu_not)*(((gamma1(i)-(1/mu_not))* & - gamma3(i))+(gamma4(i)*gamma2(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - C_mns_top(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-tau_clm(i)/mu_not)*(((gamma1(i)+(1/mu_not))* & - gamma4(i))+(gamma2(i)*gamma3(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - else - C_pls_btm(i) = 0._r8 - C_mns_btm(i) = 0._r8 - C_pls_top(i) = 0._r8 - C_mns_top(i) = 0._r8 - endif - enddo - - ! Coefficients for tridiaganol matrix solution - do i=2*snl_lcl+1,0,1 - - !Boundary values for i=1 and i=2*snl_lcl, specifics for i=odd and i=even - if (i==(2*snl_lcl+1)) then - A(i) = 0._r8 - B(i) = e1(snl_top) - D(i) = -e2(snl_top) - E(i) = flx_slri_lcl(bnd_idx)-C_mns_top(snl_top) - - elseif(i==0) then - A(i) = e1(snl_btm)-(albsfc_lcl(bnd_idx)*e3(snl_btm)) - B(i) = e2(snl_btm)-(albsfc_lcl(bnd_idx)*e4(snl_btm)) - D(i) = 0._r8 - E(i) = F_direct_btm-C_pls_btm(snl_btm)+(albsfc_lcl(bnd_idx)*C_mns_btm(snl_btm)) - - elseif(mod(i,2)==-1) then ! If odd and i>=3 (n=1 for i=3) - n=floor(i/2.0) - A(i) = (e2(n)*e3(n))-(e4(n)*e1(n)) - B(i) = (e1(n)*e1(n+1))-(e3(n)*e3(n+1)) - D(i) = (e3(n)*e4(n+1))-(e1(n)*e2(n+1)) - E(i) = (e3(n)*(C_pls_top(n+1)-C_pls_btm(n)))+(e1(n)*(C_mns_btm(n)-C_mns_top(n+1))) - - elseif(mod(i,2)==0) then ! If even and i<=2*snl_lcl - n=(i/2) - A(i) = (e2(n+1)*e1(n))-(e3(n)*e4(n+1)) - B(i) = (e2(n)*e2(n+1))-(e4(n)*e4(n+1)) - D(i) = (e1(n+1)*e4(n+1))-(e2(n+1)*e3(n+1)) - E(i) = (e2(n+1)*(C_pls_top(n+1)-C_pls_btm(n)))+(e4(n+1)*(C_mns_top(n+1)-C_mns_btm(n))) - endif - enddo - - AS(0) = A(0)/B(0) - DS(0) = E(0)/B(0) - - do i=-1,(2*snl_lcl+1),-1 - X(i) = 1/(B(i)-(D(i)*AS(i+1))) - AS(i) = A(i)*X(i) - DS(i) = (E(i)-(D(i)*DS(i+1)))*X(i) - enddo - - Y(2*snl_lcl+1) = DS(2*snl_lcl+1) - do i=(2*snl_lcl+2),0,1 - Y(i) = DS(i)-(AS(i)*Y(i-1)) - enddo - - ! Downward direct-beam and net flux (F_net) at the base of each layer: - do i=snl_top,snl_btm,1 - F_direct(i) = mu_not*pi*flx_slrd_lcl(bnd_idx)*exp(-(tau_clm(i)+tau_star(i))/mu_not) - F_net(i) = (Y(2*i-1)*(e1(i)-e3(i))) + (Y(2*i)*(e2(i)-e4(i))) + & - C_pls_btm(i) - C_mns_btm(i) - F_direct(i) - enddo - - ! Upward flux at snowpack top: - F_sfc_pls = (Y(2*snl_lcl+1)*(exp(-lambda(snl_top)*tau_star(snl_top))+ & - GAMMA(snl_top))) + (Y(2*snl_lcl+2)*(exp(-lambda(snl_top)* & - tau_star(snl_top))-GAMMA(snl_top))) + C_pls_top(snl_top) - - ! Net flux at bottom = absorbed radiation by underlying surface: - F_btm_net = -F_net(snl_btm) - - - ! Bulk column albedo and surface net flux - albedo = F_sfc_pls/((mu_not*pi*flx_slrd_lcl(bnd_idx))+flx_slri_lcl(bnd_idx)) - F_sfc_net = F_sfc_pls - ((mu_not*pi*flx_slrd_lcl(bnd_idx))+flx_slri_lcl(bnd_idx)) - - trip = 0 - ! Absorbed flux in each layer - do i=snl_top,snl_btm,1 - if(i==snl_top) then - F_abs(i) = F_net(i)-F_sfc_net - else - F_abs(i) = F_net(i)-F_net(i-1) - endif - flx_abs_lcl(i,bnd_idx) = F_abs(i) - - - ! ERROR check: negative absorption - if (flx_abs_lcl(i,bnd_idx) < -0.00001_r8) then - trip = 1 - endif - enddo - - flx_abs_lcl(1,bnd_idx) = F_btm_net - - if (flg_nosnl == 1) then + !--------------------------- End of snow & aerosol optics -------------------------------- + + + !--------------------------- Start Toon et al. RT solver -------------------------------- + if (snicar_rt_solver == 1) then + + ! Total column optical depth: + ! tau_clm(i) = total optical depth above the bottom of layer i + tau_clm(snl_top) = 0._r8 + do i=snl_top+1,snl_btm,1 + tau_clm(i) = tau_clm(i-1)+tau_star(i-1) + enddo + + ! Direct radiation at bottom of snowpack: + F_direct_btm = albsfc_lcl(bnd_idx)*mu_not * & + exp(-(tau_clm(snl_btm)+tau_star(snl_btm))/mu_not)*pi*flx_slrd_lcl(bnd_idx) + + ! Intermediates + ! Gamma values are approximation-specific. + + ! Eddington + if (APRX_TYP==1) then + do i=snl_top,snl_btm,1 + gamma1(i) = (7._r8-(omega_star(i)*(4._r8+(3._r8*g_star(i)))))/4._r8 + gamma2(i) = -(1._r8-(omega_star(i)*(4._r8-(3._r8*g_star(i)))))/4._r8 + gamma3(i) = (2._r8-(3._r8*g_star(i)*mu_not))/4._r8 + gamma4(i) = 1._r8-gamma3(i) + mu_one = 0.5_r8 + enddo + + ! Quadrature + elseif (APRX_TYP==2) then + do i=snl_top,snl_btm,1 + gamma1(i) = (3._r8**0.5)*(2._r8-(omega_star(i)*(1._r8+g_star(i))))/2._r8 + gamma2(i) = omega_star(i)*(3._r8**0.5)*(1._r8-g_star(i))/2._r8 + gamma3(i) = (1._r8-((3._r8**0.5)*g_star(i)*mu_not))/2._r8 + gamma4(i) = 1._r8-gamma3(i) + mu_one = 1._r8/(3._r8**0.5_r8) + enddo + + ! Hemispheric Mean + elseif (APRX_TYP==3) then + do i=snl_top,snl_btm,1 + gamma1(i) = 2._r8 - (omega_star(i)*(1._r8+g_star(i))) + gamma2(i) = omega_star(i)*(1-g_star(i)) + gamma3(i) = (1._r8-((3._r8**0.5_r8)*g_star(i)*mu_not))/2._r8 + gamma4(i) = 1._r8-gamma3(i) + mu_one = 0.5_r8 + enddo + endif + + ! Intermediates for tri-diagonal solution + do i=snl_top,snl_btm,1 + lambda(i) = sqrt(abs((gamma1(i)**2) - (gamma2(i)**2))) + GAMMA(i) = gamma2(i)/(gamma1(i)+lambda(i)) + + e1(i) = 1+(GAMMA(i)*exp(-lambda(i)*tau_star(i))) + e2(i) = 1-(GAMMA(i)*exp(-lambda(i)*tau_star(i))) + e3(i) = GAMMA(i) + exp(-lambda(i)*tau_star(i)) + e4(i) = GAMMA(i) - exp(-lambda(i)*tau_star(i)) + enddo !enddo over snow layers + + ! Intermediates for tri-diagonal solution + do i=snl_top,snl_btm,1 + if (flg_slr_in == 1) then + + C_pls_btm(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & + exp(-(tau_clm(i)+tau_star(i))/mu_not)* & + (((gamma1(i)-(1/mu_not))*gamma3(i))+ & + (gamma4(i)*gamma2(i))))/((lambda(i)**2)-(1/(mu_not**2))) + + C_mns_btm(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & + exp(-(tau_clm(i)+tau_star(i))/mu_not)* & + (((gamma1(i)+(1/mu_not))*gamma4(i))+ & + (gamma2(i)*gamma3(i))))/((lambda(i)**2)-(1/(mu_not**2))) + + C_pls_top(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & + exp(-tau_clm(i)/mu_not)*(((gamma1(i)-(1/mu_not))* & + gamma3(i))+(gamma4(i)*gamma2(i))))/((lambda(i)**2)-(1/(mu_not**2))) + + C_mns_top(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & + exp(-tau_clm(i)/mu_not)*(((gamma1(i)+(1/mu_not))* & + gamma4(i))+(gamma2(i)*gamma3(i))))/((lambda(i)**2)-(1/(mu_not**2))) + + else + C_pls_btm(i) = 0._r8 + C_mns_btm(i) = 0._r8 + C_pls_top(i) = 0._r8 + C_mns_top(i) = 0._r8 + endif + enddo + + ! Coefficients for tridiaganol matrix solution + do i=2*snl_lcl+1,0,1 + + !Boundary values for i=1 and i=2*snl_lcl, specifics for i=odd and i=even + if (i==(2*snl_lcl+1)) then + A(i) = 0._r8 + B(i) = e1(snl_top) + D(i) = -e2(snl_top) + E(i) = flx_slri_lcl(bnd_idx)-C_mns_top(snl_top) + + elseif(i==0) then + A(i) = e1(snl_btm)-(albsfc_lcl(bnd_idx)*e3(snl_btm)) + B(i) = e2(snl_btm)-(albsfc_lcl(bnd_idx)*e4(snl_btm)) + D(i) = 0._r8 + E(i) = F_direct_btm-C_pls_btm(snl_btm)+(albsfc_lcl(bnd_idx)*C_mns_btm(snl_btm)) + + elseif(mod(i,2)==-1) then ! If odd and i>=3 (n=1 for i=3) + n=floor(i/2.0) + A(i) = (e2(n)*e3(n))-(e4(n)*e1(n)) + B(i) = (e1(n)*e1(n+1))-(e3(n)*e3(n+1)) + D(i) = (e3(n)*e4(n+1))-(e1(n)*e2(n+1)) + E(i) = (e3(n)*(C_pls_top(n+1)-C_pls_btm(n)))+(e1(n)*(C_mns_btm(n)-C_mns_top(n+1))) + + elseif(mod(i,2)==0) then ! If even and i<=2*snl_lcl + n=(i/2) + A(i) = (e2(n+1)*e1(n))-(e3(n)*e4(n+1)) + B(i) = (e2(n)*e2(n+1))-(e4(n)*e4(n+1)) + D(i) = (e1(n+1)*e4(n+1))-(e2(n+1)*e3(n+1)) + E(i) = (e2(n+1)*(C_pls_top(n+1)-C_pls_btm(n)))+(e4(n+1)*(C_mns_top(n+1)-C_mns_btm(n))) + endif + enddo + + AS(0) = A(0)/B(0) + DS(0) = E(0)/B(0) + + do i=-1,(2*snl_lcl+1),-1 + X(i) = 1/(B(i)-(D(i)*AS(i+1))) + AS(i) = A(i)*X(i) + DS(i) = (E(i)-(D(i)*DS(i+1)))*X(i) + enddo + + Y(2*snl_lcl+1) = DS(2*snl_lcl+1) + do i=(2*snl_lcl+2),0,1 + Y(i) = DS(i)-(AS(i)*Y(i-1)) + enddo + + ! Downward direct-beam and net flux (F_net) at the base of each layer: + do i=snl_top,snl_btm,1 + F_direct(i) = mu_not*pi*flx_slrd_lcl(bnd_idx)*exp(-(tau_clm(i)+tau_star(i))/mu_not) + F_net(i) = (Y(2*i-1)*(e1(i)-e3(i))) + (Y(2*i)*(e2(i)-e4(i))) + & + C_pls_btm(i) - C_mns_btm(i) - F_direct(i) + enddo + + ! Upward flux at snowpack top: + F_sfc_pls = (Y(2*snl_lcl+1)*(exp(-lambda(snl_top)*tau_star(snl_top))+ & + GAMMA(snl_top))) + (Y(2*snl_lcl+2)*(exp(-lambda(snl_top)* & + tau_star(snl_top))-GAMMA(snl_top))) + C_pls_top(snl_top) + + ! Net flux at bottom = absorbed radiation by underlying surface: + F_btm_net = -F_net(snl_btm) + + + ! Bulk column albedo and surface net flux + albedo = F_sfc_pls/((mu_not*pi*flx_slrd_lcl(bnd_idx))+flx_slri_lcl(bnd_idx)) + F_sfc_net = F_sfc_pls - ((mu_not*pi*flx_slrd_lcl(bnd_idx))+flx_slri_lcl(bnd_idx)) + + trip = 0 + ! Absorbed flux in each layer + do i=snl_top,snl_btm,1 + if(i==snl_top) then + F_abs(i) = F_net(i)-F_sfc_net + else + F_abs(i) = F_net(i)-F_net(i-1) + endif + flx_abs_lcl(i,bnd_idx) = F_abs(i) + + ! ERROR check: negative absorption + if (flx_abs_lcl(i,bnd_idx) < -0.00001_r8) then + trip = 1 + endif + enddo + + flx_abs_lcl(1,bnd_idx) = F_btm_net + + if (flg_nosnl == 1) then ! If there are no snow layers (but still snow), all absorbed energy must be in top soil layer !flx_abs_lcl(:,bnd_idx) = 0._r8 !flx_abs_lcl(1,bnd_idx) = F_abs(0) + F_btm_net @@ -901,65 +1032,347 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! OK to put absorbed energy in the fictitous snow layer because routine SurfaceRadiation ! handles the case of no snow layers. Then, if a snow layer is addded between now and ! SurfaceRadiation (called in CanopyHydrology), absorbed energy will be properly distributed. - flx_abs_lcl(0,bnd_idx) = F_abs(0) - flx_abs_lcl(1,bnd_idx) = F_btm_net - - endif - - !Underflow check (we've already tripped the error condition above) - do i=snl_top,1,1 - if (flx_abs_lcl(i,bnd_idx) < 0._r8) then - flx_abs_lcl(i,bnd_idx) = 0._r8 - endif - enddo - - F_abs_sum = 0._r8 - do i=snl_top,snl_btm,1 - F_abs_sum = F_abs_sum + F_abs(i) - enddo - - - !ERROR check: absorption greater than incident flux - ! (should make condition more generic than "1._r8") - if (F_abs_sum > 1._r8) then - trip = 1 - endif - - !ERROR check: - if ((albedo < 0._r8).and.(trip==0)) then - trip = 1 - endif - - ! Set conditions for redoing RT calculation - if ((trip == 1).and.(flg_dover == 1)) then - flg_dover = 2 - elseif ((trip == 1).and.(flg_dover == 2)) then - flg_dover = 3 - elseif ((trip == 1).and.(flg_dover == 3)) then - flg_dover = 4 - elseif((trip == 1).and.(flg_dover == 4).and.(err_idx < 20)) then - flg_dover = 3 - err_idx = err_idx + 1 - elseif((trip == 1).and.(flg_dover == 4).and.(err_idx >= 20)) then - flg_dover = 0 - write(iulog,*) "SNICAR ERROR: FOUND A WORMHOLE. STUCK IN INFINITE LOOP! Called from: ", flg_snw_ice - write(iulog,*) "SNICAR STATS: snw_rds(0)= ", snw_rds(c_idx,0) - write(iulog,*) "SNICAR STATS: L_snw(0)= ", L_snw(0) - write(iulog,*) "SNICAR STATS: h2osno= ", h2osno_lcl, " snl= ", snl_lcl - write(iulog,*) "SNICAR STATS: soot1(0)= ", mss_cnc_aer_lcl(0,1) - write(iulog,*) "SNICAR STATS: soot2(0)= ", mss_cnc_aer_lcl(0,2) - write(iulog,*) "SNICAR STATS: dust1(0)= ", mss_cnc_aer_lcl(0,3) - write(iulog,*) "SNICAR STATS: dust2(0)= ", mss_cnc_aer_lcl(0,4) - write(iulog,*) "SNICAR STATS: dust3(0)= ", mss_cnc_aer_lcl(0,5) - write(iulog,*) "SNICAR STATS: dust4(0)= ", mss_cnc_aer_lcl(0,6) - l_idx = col%landunit(c_idx) - write(iulog,*) "column index: ", c_idx - write(iulog,*) "landunit type", lun%itype(l_idx) - write(iulog,*) "frac_sno: ", frac_sno(c_idx) - call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) - else - flg_dover = 0 - endif + flx_abs_lcl(0,bnd_idx) = F_abs(0) + flx_abs_lcl(1,bnd_idx) = F_btm_net + endif + + !Underflow check (we've already tripped the error condition above) + do i=snl_top,1,1 + if (flx_abs_lcl(i,bnd_idx) < 0._r8) then + flx_abs_lcl(i,bnd_idx) = 0._r8 + endif + enddo + + F_abs_sum = 0._r8 + do i=snl_top,snl_btm,1 + F_abs_sum = F_abs_sum + F_abs(i) + enddo + + !ERROR check: absorption greater than incident flux + ! (should make condition more generic than "1._r8") + if (F_abs_sum > 1._r8) then + trip = 1 + endif + + !ERROR check: + if ((albedo < 0._r8).and.(trip==0)) then + trip = 1 + endif + + ! Set conditions for redoing RT calculation + if ((trip == 1).and.(flg_dover == 1)) then + flg_dover = 2 + elseif ((trip == 1).and.(flg_dover == 2)) then + flg_dover = 3 + elseif ((trip == 1).and.(flg_dover == 3)) then + flg_dover = 4 + elseif((trip == 1).and.(flg_dover == 4).and.(err_idx < 20)) then + flg_dover = 3 + err_idx = err_idx + 1 + elseif((trip == 1).and.(flg_dover == 4).and.(err_idx >= 20)) then + flg_dover = 0 + write(iulog,*) "SNICAR ERROR: FOUND A WORMHOLE. STUCK IN INFINITE LOOP! Called from: ", flg_snw_ice + write(iulog,*) "SNICAR STATS: snw_rds(0)= ", snw_rds(c_idx,0) + write(iulog,*) "SNICAR STATS: L_snw(0)= ", L_snw(0) + write(iulog,*) "SNICAR STATS: h2osno= ", h2osno_lcl, " snl= ", snl_lcl + write(iulog,*) "SNICAR STATS: soot1(0)= ", mss_cnc_aer_lcl(0,1) + write(iulog,*) "SNICAR STATS: soot2(0)= ", mss_cnc_aer_lcl(0,2) + write(iulog,*) "SNICAR STATS: dust1(0)= ", mss_cnc_aer_lcl(0,3) + write(iulog,*) "SNICAR STATS: dust2(0)= ", mss_cnc_aer_lcl(0,4) + write(iulog,*) "SNICAR STATS: dust3(0)= ", mss_cnc_aer_lcl(0,5) + write(iulog,*) "SNICAR STATS: dust4(0)= ", mss_cnc_aer_lcl(0,6) + l_idx = col%landunit(c_idx) + write(iulog,*) "column index: ", c_idx + write(iulog,*) "landunit type", lun%itype(l_idx) + write(iulog,*) "frac_sno: ", frac_sno(c_idx) + call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) + else + flg_dover = 0 + endif + + endif ! end if snicar_rt_solver==1 + !--------------------------- End of Toon et al. RT solver -------------------------------- + + + !--------------------------- Start Adding-doubling RT solver -------------------------------- + if (snicar_rt_solver == 2) then + + ! Given input vertical profiles of optical properties, evaluate the + ! monochromatic Delta-Eddington adding-doubling solution + + ! trndir, trntdr, trndif, rupdir, rupdif, rdndif are variables at the layer interface, + ! for snow with layers from snl_top to snl_btm there are snl_top to snl_btm+1 layer interface + snl_btm_itf = snl_btm + 1 + + ! initialization for layer interface + do i = snl_top,snl_btm_itf,1 + trndir(i) = c0 + trntdr(i) = c0 + trndif(i) = c0 + rupdir(i) = c0 + rupdif(i) = c0 + rdndif(i) = c0 + enddo + ! initialize top interface of top layer + trndir(snl_top) = c1 + trntdr(snl_top) = c1 + trndif(snl_top) = c1 + rdndif(snl_top) = c0 + + ! begin main level loop for snow layer interfaces except for the very bottom + do i = snl_top,snl_btm,1 + + ! initialize all layer apparent optical properties to 0 + rdir (i) = c0 + rdif_a(i) = c0 + rdif_b(i) = c0 + tdir (i) = c0 + tdif_a(i) = c0 + tdif_b(i) = c0 + trnlay(i) = c0 + + ! compute next layer Delta-eddington solution only if total transmission + ! of radiation to the interface just above the layer exceeds trmin. + if (trntdr(i) > trmin ) then + + ! delta-transformed single-scattering properties of this layer + ts = tau_star(i) + ws = omega_star(i) + gs = g_star(i) + + ! Delta-Eddington solution expressions, Eq. 50: Briegleb and Light 2007 + lm = sqrt(c3*(c1-ws)*(c1 - ws*gs)) + ue = c1p5*(c1 - ws*gs)/lm + extins = max(exp_min, exp(-lm*ts)) + ne = ((ue+c1)*(ue+c1)/extins) - ((ue-c1)*(ue-c1)*extins) + + ! first calculation of rdif, tdif using Delta-Eddington formulas + ! Eq.: Briegleb 1992; alpha and gamma for direct radiation + rdif_a(i) = (ue**2-c1)*(c1/extins - extins)/ne + tdif_a(i) = c4*ue/ne + + ! evaluate rdir,tdir for direct beam + trnlay(i) = max(exp_min, exp(-ts/mu_not)) + + ! Delta-Eddington solution expressions + ! Eq. 50: Briegleb and Light 2007; alpha and gamma for direct radiation + alp = cp75*ws*mu_not*((c1 + gs*(c1-ws))/(c1 - lm*lm*mu_not*mu_not)) + gam = cp5*ws*((c1 + c3*gs*(c1-ws)*mu_not*mu_not)/(c1-lm*lm*mu_not*mu_not)) + apg = alp + gam + amg = alp - gam + rdir(i) = apg*rdif_a(i) + amg*(tdif_a(i)*trnlay(i) - c1) + tdir(i) = apg*tdif_a(i) + (amg* rdif_a(i)-apg+c1)*trnlay(i) + + ! recalculate rdif,tdif using direct angular integration over rdir,tdir, + ! since Delta-Eddington rdif formula is not well-behaved (it is usually + ! biased low and can even be negative); use ngmax angles and gaussian + ! integration for most accuracy: + R1 = rdif_a(i) ! use R1 as temporary + T1 = tdif_a(i) ! use T1 as temporary + swt = c0 + smr = c0 + smt = c0 + ! gaussian angles for the AD integral + do ng=1,ngmax + mu = difgauspt(ng) + gwt = difgauswt(ng) + swt = swt + mu*gwt + trn = max(exp_min, exp(-ts/mu)) + alp = cp75*ws*mu*((c1 + gs*(c1-ws))/(c1 - lm*lm*mu*mu)) + gam = cp5*ws*((c1 + c3*gs*(c1-ws)*mu*mu)/(c1-lm*lm*mu*mu)) + apg = alp + gam + amg = alp - gam + rdr = apg*R1 + amg*T1*trn - amg + tdr = apg*T1 + amg*R1*trn - apg*trn + trn + smr = smr + mu*rdr*gwt + smt = smt + mu*tdr*gwt + enddo ! ng + rdif_a(i) = smr/swt + tdif_a(i) = smt/swt + + ! homogeneous layer + rdif_b(i) = rdif_a(i) + tdif_b(i) = tdif_a(i) + + endif ! trntdr(k) > trmin + + ! Calculate the solar beam transmission, total transmission, and + ! reflectivity for diffuse radiation from below at interface i, + ! the top of the current layer k: + ! + ! layers interface + ! + ! --------------------- i-1 + ! i-1 + ! --------------------- i + ! i + ! --------------------- + + trndir(i+1) = trndir(i)*trnlay(i) ! solar beam transmission from top + refkm1 = c1/(c1 - rdndif(i)*rdif_a(i)) ! interface multiple scattering for i-1 + tdrrdir = trndir(i)*rdir(i) ! direct tran times layer direct ref + tdndif = trntdr(i) - trndir(i) ! total down diffuse = tot tran - direct tran + trntdr(i+1) = trndir(i)*tdir(i) + & ! total transmission to direct beam for layers above + (tdndif + tdrrdir*rdndif(i))*refkm1*tdif_a(i) + ! Eq. B4; Briegleb and Light 2007 + rdndif(i+1) = rdif_b(i) + & ! reflectivity to diffuse radiation for layers above + (tdif_b(i)*rdndif(i)*refkm1*tdif_a(i)) + trndif(i+1) = trndif(i)*refkm1*tdif_a(i) ! diffuse transmission to diffuse beam for layers above + + enddo ! end i main level loop + + ! compute reflectivity to direct and diffuse radiation for layers + ! below by adding succesive layers starting from the underlying + ! ground and working upwards: + ! + ! layers interface + ! + ! --------------------- i + ! i + ! --------------------- i+1 + ! i+1 + ! --------------------- + + ! set the underlying ground albedo == albedo of near-IR + ! unless bnd_idx < nir_bnd_bgn, for visible + rupdir(snl_btm_itf) = albsfc(c_idx,2) + rupdif(snl_btm_itf) = albsfc(c_idx,2) + if (bnd_idx < nir_bnd_bgn) then + rupdir(snl_btm_itf) = albsfc(c_idx,1) + rupdif(snl_btm_itf) = albsfc(c_idx,1) + endif + + do i=snl_btm,snl_top,-1 + ! interface scattering Eq. B5; Briegleb and Light 2007 + refkp1 = c1/( c1 - rdif_b(i)*rupdif(i+1)) + ! dir from top layer plus exp tran ref from lower layer, interface + ! scattered and tran thru top layer from below, plus diff tran ref + ! from lower layer with interface scattering tran thru top from below + rupdir(i) = rdir(i) & + + ( trnlay(i) *rupdir(i+1) & + + (tdir(i)-trnlay(i))*rupdif(i+1) ) * refkp1 * tdif_b(i) + ! dif from top layer from above, plus dif tran upwards reflected and + ! interface scattered which tran top from below + rupdif(i) = rdif_a(i) + tdif_a(i)*rupdif(i+1)*refkp1*tdif_b(i) + enddo ! i + + ! net flux (down-up) at each layer interface from the + ! snow top (i = snl_top) to bottom interface above land (i = snl_btm_itf) + ! the interface reflectivities and transmissivities required + ! to evaluate interface fluxes are returned from solution_dEdd; + ! now compute up and down fluxes for each interface, using the + ! combined layer properties at each interface: + ! + ! layers interface + ! + ! --------------------- i + ! i + ! --------------------- + + do i = snl_top, snl_btm_itf + ! interface scattering, Eq. 52; Briegleb and Light 2007 + refk = c1/(c1 - rdndif(i)*rupdif(i)) + ! dir tran ref from below times interface scattering, plus diff + ! tran and ref from below times interface scattering + ! fdirup(i) = (trndir(i)*rupdir(i) + & + ! (trntdr(i)-trndir(i)) & + ! *rupdif(i))*refk + ! dir tran plus total diff trans times interface scattering plus + ! dir tran with up dir ref and down dif ref times interface scattering + ! fdirdn(i) = trndir(i) + (trntdr(i) & + ! - trndir(i) + trndir(i) & + ! *rupdir(i)*rdndif(i))*refk + ! diffuse tran ref from below times interface scattering + ! fdifup(i) = trndif(i)*rupdif(i)*refk + ! diffuse tran times interface scattering + ! fdifdn(i) = trndif(i)*refk + + ! netflux, down - up + ! dfdir = fdirdn - fdirup + dfdir(i) = trndir(i) & + + (trntdr(i)-trndir(i)) * (c1 - rupdif(i)) * refk & + - trndir(i)*rupdir(i) * (c1 - rdndif(i)) * refk + if (dfdir(i) < puny) dfdir(i) = c0 + ! dfdif = fdifdn - fdifup + dfdif(i) = trndif(i) * (c1 - rupdif(i)) * refk + if (dfdif(i) < puny) dfdif(i) = c0 + enddo ! k + + ! SNICAR_AD_RT is called twice for direct and diffuse incident fluxes + ! direct incident + if (flg_slr_in == 1) then + albedo = rupdir(snl_top) + dftmp = dfdir + refk = c1/(c1 - rdndif(snl_top)*rupdif(snl_top)) + F_sfc_pls = (trndir(snl_top)*rupdir(snl_top) + & + (trntdr(snl_top)-trndir(snl_top)) & + *rupdif(snl_top))*refk + !diffuse incident + else + albedo = rupdif(snl_top) + dftmp = dfdif + refk = c1/(c1 - rdndif(snl_top)*rupdif(snl_top)) + F_sfc_pls = trndif(snl_top)*rupdif(snl_top)*refk + endif + + ! Absorbed flux in each layer + do i=snl_top,snl_btm,1 + F_abs(i) = dftmp(i)-dftmp(i+1) + flx_abs_lcl(i,bnd_idx) = F_abs(i) + + ! ERROR check: negative absorption + if (flx_abs_lcl(i,bnd_idx) < -0.00001_r8) then + write (iulog,"(a,e13.6,a,i6,a,i6)") "SNICAR ERROR: negative absoption : ", & + flx_abs_lcl(i,bnd_idx), " at timestep: ", nstep, " at column: ", c_idx + write(iulog,*) "SNICAR_AD STATS: snw_rds(0)= ", snw_rds(c_idx,0) + write(iulog,*) "SNICAR_AD STATS: L_snw(0)= ", L_snw(0) + write(iulog,*) "SNICAR_AD STATS: h2osno= ", h2osno_lcl, " snl= ", snl_lcl + write(iulog,*) "SNICAR_AD STATS: soot1(0)= ", mss_cnc_aer_lcl(0,1) + write(iulog,*) "SNICAR_AD STATS: soot2(0)= ", mss_cnc_aer_lcl(0,2) + write(iulog,*) "SNICAR_AD STATS: dust1(0)= ", mss_cnc_aer_lcl(0,3) + write(iulog,*) "SNICAR_AD STATS: dust2(0)= ", mss_cnc_aer_lcl(0,4) + write(iulog,*) "SNICAR_AD STATS: dust3(0)= ", mss_cnc_aer_lcl(0,5) + write(iulog,*) "SNICAR_AD STATS: dust4(0)= ", mss_cnc_aer_lcl(0,6) + call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) + endif + enddo + + ! absobed flux by the underlying ground + F_btm_net = dftmp(snl_btm_itf) + + ! note here, snl_btm_itf = 1 by snow column set up in CLM + flx_abs_lcl(1,bnd_idx) = F_btm_net + + if (flg_nosnl == 1) then + ! If there are no snow layers (but still snow), all absorbed energy must be in top soil layer + !flx_abs_lcl(:,bnd_idx) = 0._r8 + !flx_abs_lcl(1,bnd_idx) = F_abs(0) + F_btm_net + + ! changed on 20070408: + ! OK to put absorbed energy in the fictitous snow layer because routine SurfaceRadiation + ! handles the case of no snow layers. Then, if a snow layer is addded between now and + ! SurfaceRadiation (called in CanopyHydrology), absorbed energy will be properly distributed. + flx_abs_lcl(0,bnd_idx) = F_abs(0) + flx_abs_lcl(1,bnd_idx) = F_btm_net + endif + + !Underflow check (we've already tripped the error condition above) + do i=snl_top,1,1 + if (flx_abs_lcl(i,bnd_idx) < 0._r8) then + flx_abs_lcl(i,bnd_idx) = 0._r8 + endif + enddo + + F_abs_sum = 0._r8 + do i=snl_top,snl_btm,1 + F_abs_sum = F_abs_sum + F_abs(i) + enddo + + ! no need to repeat calculations for adding-doubling solver + flg_dover = 0 + + endif ! end if snicar_rt_solver==2 + !--------------------------- End of Adding-doubling RT solver -------------------------------- enddo !enddo while (flg_dover > 0) @@ -969,6 +1382,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & if (abs(energy_sum) > 0.00001_r8) then write (iulog,"(a,e12.6,a,i6,a,i6)") "SNICAR ERROR: Energy conservation error of : ", energy_sum, & " at timestep: ", nstep, " at column: ", c_idx + write(iulog,*) "F_abs_sum: ",F_abs_sum + write(iulog,*) "F_btm_net: ",F_btm_net + write(iulog,*) "F_sfc_pls: ",F_sfc_pls + write(iulog,*) "mu_not*pi*flx_slrd_lcl(bnd_idx): ", mu_not*pi*flx_slrd_lcl(bnd_idx) + write(iulog,*) "flx_slri_lcl(bnd_idx)", flx_slri_lcl(bnd_idx) + write(iulog,*) "bnd_idx", bnd_idx + write(iulog,*) "F_abs", F_abs + write(iulog,*) "albedo", albedo call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) endif @@ -1010,7 +1431,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR albedo appropriately - ! for 5- and 3-band cases cenlin + ! for 5- and 3-band cases cenlin if (snicar_numrad_snw <= 5) then albout(c_idx,1) = albout_lcl(1) flx_sum = 0._r8 @@ -1019,7 +1440,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end do albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end if - ! for 480-band case, cenlin + + ! for 480-band case, cenlin if (snicar_numrad_snw == 480) then ! average for VIS band flx_sum = 0._r8 @@ -1036,7 +1458,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end if ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately - ! for 5- and 3-band cases cenlin + ! for 5- and 3-band cases cenlin if (snicar_numrad_snw <= 5) then flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) do i=snl_top,1,1 @@ -1047,7 +1469,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end do end if - ! for 480-band case cenlin + + ! for 480-band case cenlin if (snicar_numrad_snw == 480) then do i=snl_top,1,1 ! average for VIS band @@ -1065,12 +1488,28 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end do end if - ! If snow < minimum_snow, but > 0, and there is sun, set albedo to underlying surface albedo + ! high solar zenith angle adjustment for Adding-doubling solver results + if (snicar_rt_solver==2) then + ! near-IR direct albedo/absorption adjustment for high solar zenith angles + ! solar zenith angle parameterization + ! calculate the scaling factor for NIR direct albedo if SZA>75 degree + if ((mu_not < mu_75) .and. (flg_slr_in == 1)) then + sza_c1 = sza_a0 + sza_a1 * mu_not + sza_a2 * mu_not**2 + sza_c0 = sza_b0 + sza_b1 * mu_not + sza_b2 * mu_not**2 + sza_factor = sza_c1 * (log10(snw_rds_lcl(snl_top) * c1) - c6) + sza_c0 + flx_sza_adjust = albout(c_idx,2) * (sza_factor-c1) * sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + albout(c_idx,2) = albout(c_idx,2) * sza_factor + flx_abs(c_idx,snl_top,2) = flx_abs(c_idx,snl_top,2) - flx_sza_adjust + endif + endif ! end of snicar_rt_solver==2 + + + ! If snow < minimum_snow, but > 0, and there is sun, set albedo to underlying surface albedo elseif ( (coszen(c_idx) > 0._r8) .and. (h2osno_lcl < min_snw) .and. (h2osno_lcl > 0._r8) ) then albout(c_idx,1) = albsfc(c_idx,1) albout(c_idx,2) = albsfc(c_idx,2) - ! There is either zero snow, or no sun + ! There is either zero snow, or no sun else albout(c_idx,1) = 0._r8 albout(c_idx,2) = 0._r8 diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 8fac958db5..9e4e0235f0 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -223,6 +223,10 @@ module clm_varctl ! option to turn off aerosol effect in snow in SNICAR logical, public :: snicar_use_aerosol = .true. ! if .false., turn off aerosol deposition flux + ! option for two different SNICAR radiative transfer solver, cenlin + integer, public :: snicar_rt_solver = 2 ! 1->Toon et a 1989 2-stream (Flanner et al. 2007) + ! 2->Adding-doubling 2-stream (Dang et al.2019) + !---------------------------------------------------------- ! C isotopes !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 91fd1cc61a..ff5305606e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -202,7 +202,7 @@ subroutine control_init(dtime) soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests,snicar_numrad_snw,snicar_solarspec,& - snicar_snw_optics,snicar_dust_optics,snicar_use_aerosol ! cenlin + snicar_snw_optics,snicar_dust_optics,snicar_use_aerosol,snicar_rt_solver ! cenlin ! vertical soil mixing variables namelist /clm_inparm/ & @@ -593,6 +593,12 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if + ! check on SNICAR solver option + if ( (snicar_rt_solver < 0) .or. (snicar_rt_solver > 2) ) then + call endrun(msg=' ERROR: snicar_rt_solver is out of a reasonable range (1,2)'//& + errMsg(sourcefile, __LINE__)) + end if + ! Consistency settings for nrevsn if (nsrest == nsrStartup ) nrevsn = ' ' @@ -818,6 +824,7 @@ subroutine control_spmd() call mpi_bcast (snicar_snw_optics, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_rt_solver, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1006,6 +1013,7 @@ subroutine control_print () write(iulog,*) ' Number of snow layers =', nlevsno write(iulog,*) ' Max snow depth (mm) =', h2osno_max write(iulog,*) ' Number of bands in SNICAR snow albedo calculation =', snicar_numrad_snw ! cenlin + write(iulog,*) ' SNICAR radiative transfer solver type = ',snicar_rt_solver ! cenlin write(iulog,*) ' glc number of elevation classes =', maxpatch_glc if (glc_do_dynglacier) then From 21fca41896e972337447538e94c64af51993c2b8 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 26 Jan 2022 19:31:21 +0100 Subject: [PATCH 0106/2067] exice streams namelists and initialization at cold start --- bld/CLMBuildNamelist.pm | 20 ++++++++ src/biogeophys/WaterStateBulkType.F90 | 7 +-- src/biogeophys/WaterStateType.F90 | 53 +++++++++++++++++----- src/biogeophys/WaterType.F90 | 19 ++++++-- src/cpl/share_esmf/ExcessIceStreamType.F90 | 14 +++--- 5 files changed, 87 insertions(+), 26 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index a172ac445b..c7168e45e8 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1732,6 +1732,11 @@ sub process_namelist_inline_logic { # namelist group: clm_initinterp_inparm # ######################################### setup_logic_initinterp($opts, $nl_flags, $definition, $defaults, $nl); + + ############################### + # namelist group: exice_streams # + ############################### + setup_logic_exice($opts, $nl_flags, $definition, $defaults, $nl); } #------------------------------------------------------------------------------- @@ -4137,6 +4142,20 @@ sub setup_logic_fates { } } +#------------------------------------------------------------------------------- +sub setup_logic_exice { + # + # excess ice streams + # + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); + if ($opts->{'driver'} eq "nuopc" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); + } + +} # end exice streams + #------------------------------------------------------------------------------- sub setup_logic_misc { @@ -4204,6 +4223,7 @@ sub write_output_files { push @groups, "nitrif_inparm"; push @groups, "lifire_inparm"; push @groups, "ch4finundated"; + push @groups, "exice_streams"; push @groups, "soilbgc_decomp"; push @groups, "clm_canopy_inparm"; if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') { diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index 5c0298c8d5..18b9f34e3e 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -47,7 +47,7 @@ module WaterStateBulkType !------------------------------------------------------------------------ subroutine InitBulk(this, bounds, info, vars, & - h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer) + h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename) class(waterstatebulk_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds @@ -57,7 +57,7 @@ subroutine InitBulk(this, bounds, info, vars, & real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run - + character(len=*) , intent(in) :: NLFilename ! Namelist filename call this%Init(bounds = bounds, & info = info, & @@ -65,7 +65,8 @@ subroutine InitBulk(this, bounds, info, vars, & h2osno_input_col = h2osno_input_col, & watsat_col = watsat_col, & t_soisno_col = t_soisno_col, & - use_aquifer_layer = use_aquifer_layer) + use_aquifer_layer = use_aquifer_layer, & + NLFilename = NLFilename) call this%InitBulkAllocate(bounds) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 4b2b37c267..a5d62fb126 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -81,7 +81,7 @@ module WaterStateType !------------------------------------------------------------------------ subroutine Init(this, bounds, info, tracer_vars, & - h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer) + h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename) class(waterstate_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds @@ -91,18 +91,19 @@ subroutine Init(this, bounds, info, tracer_vars, & real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run + character(len=*) , intent(in) :: NLFilename ! Namelist filename this%info => info call this%InitAllocate(bounds, tracer_vars) call this%InitHistory(bounds, use_aquifer_layer) - call this%InitCold(bounds = bounds, & - h2osno_input_col = h2osno_input_col, & - watsat_col = watsat_col, & - t_soisno_col = t_soisno_col, & - use_aquifer_layer = use_aquifer_layer) + h2osno_input_col = h2osno_input_col, & + watsat_col = watsat_col, & + t_soisno_col = t_soisno_col, & + use_aquifer_layer = use_aquifer_layer, & + NLFilename = NLFilename) end subroutine Init @@ -317,7 +318,7 @@ end subroutine InitHistory !----------------------------------------------------------------------- subroutine InitCold(this, bounds, & - h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer) + h2osno_input_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename) ! ! !DESCRIPTION: ! Initialize time constant variables and cold start conditions @@ -336,9 +337,10 @@ subroutine InitCold(this, bounds, & real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run + character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: - integer :: c,j,l,nlevs + integer :: c,j,l,nlevs,g integer :: nbedrock real(r8) :: ratio !----------------------------------------------------------------------- @@ -542,11 +544,38 @@ subroutine InitCold(this, bounds, & this%dynbal_baseline_ice_col(bounds%begc:bounds%endc) = 0._r8 !Initialize excess ice - this%init_exice(:,:)=0.0_r8 - this%excess_ice_col(:,:)=0.0_r8 - this%exice_melt_lev(:,:)=0.0_r8 - this%exice_melt(:)=0.0_r8 + write(iulog,*) 'nfl =', NLFilename + if (use_excess_ice .and. NLFilename /= '') then + + call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column + do c = bounds%begc,bounds%endc + g = col%gridcell(c) + l = col%landunit(c) + if (.not. lun%lakpoi(l)) then !not lake + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + nlevs = nlevgrnd + do j = 1, nlevs + if (col%zi(c,j) <= 4._r8 .and. t_soisno_col(c,j) <= tfrz ) then + this%excess_ice_col(c,j) = col%dz(c,j)*denice*(this%exicestream%exice_bulk(g)) + else + this%excess_ice_col(c,j) = 0.0_r8 + endif + this%init_exice(c,j) = 0.0_r8 + this%init_exice(c,j) = this%excess_ice_col(c,j) + end do + endif + endif + enddo + this%exice_melt_lev(:,:)=0.0_r8 + this%exice_melt(:)=0.0_r8 + + else + this%init_exice(:,:)=0.0_r8 + this%excess_ice_col(:,:)=0.0_r8 + this%exice_melt_lev(:,:)=0.0_r8 + this%exice_melt(:)=0.0_r8 + end if end associate end subroutine InitCold diff --git a/src/biogeophys/WaterType.F90 b/src/biogeophys/WaterType.F90 index b8a05308b2..eb38459d4d 100644 --- a/src/biogeophys/WaterType.F90 +++ b/src/biogeophys/WaterType.F90 @@ -239,7 +239,8 @@ subroutine Init(this, bounds, NLFilename, & snow_depth_col = snow_depth_col, & watsat_col = watsat_col, & t_soisno_col = t_soisno_col, & - use_aquifer_layer = use_aquifer_layer) + use_aquifer_layer = use_aquifer_layer, & + NLFilename = NLFilename) end subroutine Init @@ -285,7 +286,7 @@ end subroutine InitForTesting !----------------------------------------------------------------------- subroutine DoInit(this, bounds, & - h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer) + h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer, NLFilename) ! ! !DESCRIPTION: ! Actually do the initialization (shared between main Init routine and InitForTesting) @@ -300,14 +301,22 @@ subroutine DoInit(this, bounds, & real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run + character(len=*) , intent(in) , optional :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: integer :: begc, endc integer :: i + character(len=256) :: l_NLFilename ! local for namelist filename character(len=*), parameter :: subname = 'DoInit' !----------------------------------------------------------------------- + !check if NLFilename is passed + l_NLFilename = '' + if (present(NLFilename)) then + l_NLFilename = NLFilename + end if + begc = bounds%begc endc = bounds%endc @@ -333,7 +342,8 @@ subroutine DoInit(this, bounds, & h2osno_input_col = h2osno_col(begc:endc), & watsat_col = watsat_col(begc:endc, 1:), & t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), & - use_aquifer_layer = use_aquifer_layer) + use_aquifer_layer = use_aquifer_layer, & + NLFilename = l_NLFilename) call this%waterdiagnosticbulk_inst%InitBulk(bounds, & bulk_info, & @@ -373,7 +383,8 @@ subroutine DoInit(this, bounds, & h2osno_input_col = h2osno_col(begc:endc), & watsat_col = watsat_col(begc:endc, 1:), & t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), & - use_aquifer_layer = use_aquifer_layer) + use_aquifer_layer = use_aquifer_layer, & + NLFilename = l_NLFilename) call this%bulk_and_tracers(i)%waterdiagnostic_inst%Init(bounds, & this%bulk_and_tracers(i)%info, & diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 8c08c766cd..04a235df0c 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -21,7 +21,7 @@ module ExcessIceStreamType private type, public :: excessicestream_type - real(r8), pointer, private :: exice_bulk (:) ! excess ice bulk value (-) + real(r8), pointer :: exice_bulk (:) ! excess ice bulk value (-) contains ! !PUBLIC MEMBER FUNCTIONS: @@ -106,7 +106,7 @@ subroutine Init(this, bounds, NLFilename) stream_offset = 0, & stream_taxmode = 'extend', & stream_dtlimit = 1.0e30_r8, & - stream_tintalgo = 'linear', & + stream_tintalgo = 'nearest', & stream_name = 'excess ice ', & rc = rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -123,7 +123,7 @@ subroutine Init(this, bounds, NLFilename) sec = 0 mcdate = year*10000 + mon*100 + day - call shr_strdata_advance(sdat_exice, ymd=mcdate, tod=sec, logunit=iulog, istr='ch4', rc=rc) !c4 is left in + call shr_strdata_advance(sdat_exice, ymd=mcdate, tod=sec, logunit=iulog, istr='exice', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -211,11 +211,11 @@ subroutine ReadNML(this, bounds, NLFilename) character(len=CL) :: stream_fldFileName_exice = ' ' character(len=CL) :: stream_meshfile_exice = ' ' character(len=CL) :: exicemapalgo = 'nn' - character(len=*), parameter :: namelist_name = 'exice' ! MUST agree with name in namelist and read - character(len=*), parameter :: subName = "('exice::ReadNML')" + character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read + character(len=*), parameter :: subName = "('exice_streams::ReadNML')" !----------------------------------------------------------------------- - namelist /exice/ & ! MUST agree with namelist_name above + namelist /exice_streams/ & ! MUST agree with namelist_name above exicemapalgo, stream_fldFileName_exice, stream_meshfile_exice ! Default values for namelist @@ -225,7 +225,7 @@ subroutine ReadNML(this, bounds, NLFilename) open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) if (nml_error == 0) then - read(nu_nml, nml=exice,iostat=nml_error) ! MUST agree with namelist_name above + read(nu_nml, nml=exice_streams,iostat=nml_error) ! MUST agree with namelist_name above if (nml_error /= 0) then call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) end if From d0ee0da25731b60075f614e0506407effcd30dcd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jan 2022 15:11:47 -0700 Subject: [PATCH 0107/2067] Added warning for when bad cultivar GDD is read. Fakes with 1.0. --- src/biogeochem/CNPhenologyMod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 555aeabf7b..209d314610 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2313,8 +2313,10 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & if (do_plant_prescribed .and. .not. generate_crop_gdds) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) if (gdd_target <= 0.0) then - write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0.' - call endrun(msg=errMsg(sourcefile, __LINE__)) + !write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0.' + write(iulog,"(A,I4)") 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0. FAKING with 1.0. PFT ',ivt(p) + !call endrun(msg=errMsg(sourcefile, __LINE__)) + gdd_target = 1.0 endif gddmaturity(p) = gdd_target else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then From dcbeee02dde8bcc6c0eb262bbbe4cd9f59cf8703 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 27 Jan 2022 17:07:33 +0100 Subject: [PATCH 0108/2067] added bedrock and temperature to excess ice initialization + some comments --- src/biogeophys/TemperatureType.F90 | 12 +++++++----- src/biogeophys/WaterStateType.F90 | 19 ++++++++++++++++--- 2 files changed, 23 insertions(+), 8 deletions(-) diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90 index f2d9317f82..e3ceaf3a41 100644 --- a/src/biogeophys/TemperatureType.F90 +++ b/src/biogeophys/TemperatureType.F90 @@ -647,11 +647,11 @@ subroutine InitCold(this, bounds, & ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use shr_const_mod , only : SHR_CONST_TKFRZ - use clm_varcon , only : denice, denh2o, sb - use landunit_varcon, only : istwet, istsoil, istdlak, istice + use clm_varcon , only : denice, denh2o, sb !what's sb? how it's never used here + use landunit_varcon, only : istwet, istsoil, istdlak, istice, istcrop use column_varcon , only : icol_road_imperv, icol_roof, icol_sunwall use column_varcon , only : icol_shadewall, icol_road_perv - use clm_varctl , only : iulog, use_vancouver, use_mexicocity + use clm_varctl , only : iulog, use_vancouver, use_mexicocity, use_excess_ice ! ! !ARGUMENTS: class(temperature_type) :: this @@ -741,8 +741,10 @@ subroutine InitCold(this, bounds, & end if end if else - this%t_soisno_col(c,1:nlevgrnd) = 274._r8 - + this%t_soisno_col(c,1:nlevgrnd) = 274._r8 + if(use_excess_ice .and. (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop)) then + this%t_soisno_col(c,1:nlevgrnd) = SHR_CONST_TKFRZ-5.0_r8 !needs to be below freezing to properly initiate excess ice + end if endif endif end do diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index a5d62fb126..90e68ab5a3 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -299,6 +299,10 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & avgflag='A', long_name='excess soil ice (vegetated landunits only)', & ptr_col=this%excess_ice_col, l2g_scale_type='veg') + data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXICE_MELT_LEV', units='kg/m2', type2d='levsoi', & + avgflag='A', long_name='melt from excess ice per layer (vegetated landunits only)', & + ptr_col=this%exice_melt_lev, l2g_scale_type='veg') this%exice_melt(begc:endc) = spval call hist_addfld1d (fname='EXICE_MELT', units='m', & @@ -554,9 +558,13 @@ subroutine InitCold(this, bounds, & l = col%landunit(c) if (.not. lun%lakpoi(l)) then !not lake if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - nlevs = nlevgrnd - do j = 1, nlevs - if (col%zi(c,j) <= 4._r8 .and. t_soisno_col(c,j) <= tfrz ) then + if (use_bedrock) then + nbedrock = col%nbedrock(c) + else + nbedrock = nlevsoi + endif + do j = 1, nlevgrnd + if (j Date: Thu, 27 Jan 2022 22:22:05 -0700 Subject: [PATCH 0109/2067] add nonspherical snow grains with namelist option --- .../namelist_definition_ctsm.xml | 5 + src/biogeophys/SnowSnicarMod.F90 | 242 ++++++++++++++++-- src/main/clm_varctl.F90 | 3 + src/main/controlMod.F90 | 44 ++-- 4 files changed, 261 insertions(+), 33 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 6a841ae588..5a07a2a9f4 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -193,6 +193,11 @@ Toggle to turn on/off aerosol deposition flux in snow in SNICAR SNICAR radiative transfer solver type + +snow grain shape used in SNICAR snow albedo calculation + + Index of rooting profile for water diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index fc7c95bcb7..02dd763d14 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -11,7 +11,8 @@ module SnowSnicarMod use shr_kind_mod , only : r8 => shr_kind_r8 use shr_sys_mod , only : shr_sys_flush use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver ! cenlin + use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver, & + snicar_snw_shape ! cenlin use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -354,8 +355,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: DS(-2*nlevsno+1:0) ! tri-diag intermediate variable from Toon et al. (2*lyr) real(r8):: X(-2*nlevsno+1:0) ! tri-diag intermediate variable from Toon et al. (2*lyr) real(r8):: Y(-2*nlevsno+1:0) ! tri-diag intermediate variable from Toon et al. (2*lyr) + !----------------------------------------------------------------------- - ! ! variables used for Adding-doubling 2-stream solver based on SNICAR-ADv3 version ! (Dang et al. 2019; Flanner et al. 2021) real(r8):: trndir(-nlevsno+1:1) ! solar beam down transmission from top @@ -428,7 +429,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: cp75 = 0.75_r8 real(r8):: c1p5 = 1.5_r8 real(r8):: trmin = 0.001_r8 - real(r8):: argmax = 10.0_r8 ! maximum argument of exponential + real(r8):: argmax = 10.0_r8 ! maximum argument of exponential ! cconstant and coefficients used for SZA parameterization real(r8):: sza_a0 = 0.085730_r8 real(r8):: sza_a1 = -0.630883_r8 @@ -437,12 +438,54 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: sza_b1 = -3.338043_r8 real(r8):: sza_b2 = 6.807489_r8 real(r8):: puny = 1.0e-11_r8 - real(r8):: mu_75 = 0.2588_r8 ! cosine of 75 degree - real(r8):: sza_c1 ! coefficient, SZA parameteirzation - real(r8):: sza_c0 ! coefficient, SZA parameterization - real(r8):: sza_factor ! factor used to adjust NIR direct albedo - real(r8):: flx_sza_adjust ! direct NIR flux adjustment from sza_factor - real(r8):: mu0 ! incident solar zenith angle + real(r8):: mu_75 = 0.2588_r8 ! cosine of 75 degree + real(r8):: sza_c1 ! coefficient, SZA parameteirzation + real(r8):: sza_c0 ! coefficient, SZA parameterization + real(r8):: sza_factor ! factor used to adjust NIR direct albedo + real(r8):: flx_sza_adjust ! direct NIR flux adjustment from sza_factor + real(r8):: mu0 ! incident solar zenith angle + + !----------------------------------------------------------------------- + ! variables used for nonspherical snow grain treatment (He et al. 2017 J of Climate): + integer :: sno_shp(-nlevsno+1:0) ! Snow shape type: 1=sphere; 2=spheroid; 3=hexagonal plate; 4=koch snowflake + ! currently only assuming same shapes for all snow layers + real(r8) :: sno_fs(-nlevsno+1:0) ! Snow shape factor: ratio of nonspherical grain effective radii to that of equal-volume sphere + ! only activated when snicar_snw_shape > 1 (i.e. nonspherical) + ! 0=use recommended default value (He et al. 2017); + ! others(0 1 (i.e. nonspherical) + ! 0=use recommended default value (He et al. 2017); + ! others(0.1 waterdiagnosticbulk_inst%frac_sno_eff_col & ! Input: [real(r8) (:)] fraction of ground covered by snow (0 to 1) ) - ! Define parameter, cenlin + ! initialize parameter, cenlin nir_bnd_bgn = nint(snicar_numrad_snw/9.6) + 1 ! 5-band starts at 2; 480-band starts at 51 nir_bnd_end = snicar_numrad_snw + + ! initialize for adding-doubling solver difgauspt(1:8) = & ! gaussian angles (radians) (/ 0.9894009_r8, 0.9445750_r8, & 0.8656312_r8, 0.7554044_r8, & @@ -476,6 +521,39 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & 0.1495960_r8, 0.1691565_r8, & 0.1826034_r8, 0.1894506_r8/) + ! initialize for nonspherical snow grains + sno_shp(:) = snicar_snw_shape ! currently only assuming same shapes for all snow layers + sno_fs(:) = 0._r8 + sno_AR(:) = 0._r8 + ! Table 3 of He et al 2017 JC + g_wvl(1:8) = (/ 0.25_r8, 0.70_r8, 1.41_r8, 1.90_r8, & + 2.50_r8, 3.50_r8, 4.00_r8, 5.00_r8 /) + g_wvl_ct(1:7) = g_wvl(2:8) / 2._r8 + g_wvl(1:7) / 2._r8 + g_b0(1:7) = (/ 9.76029E-1_r8, 9.67798E-1_r8, 1.00111_r8, 1.00224_r8, & + 9.64295E-1_r8, 9.97475E-1_r8, 9.97475E-1_r8 /) + g_b1(1:7) = (/ 5.21042E-1_r8, 4.96181E-1_r8, 1.83711E-1_r8, 1.37082E-1_r8, & + 5.50598E-2_r8, 8.48743E-2_r8, 8.48743E-2_r8 /) + g_b2(1:7) = (/ -2.66792E-4_r8, 1.14088E-3_r8, 2.37011E-4_r8, -2.35905E-4_r8, & + 8.40449E-4_r8, -4.71484E-4_r8, -4.71484E-4_r8 /) + ! Tables 1 & 2 and Eqs. 3.1-3.4 from Fu, 2007 JAS + g_F07_c2(1:7) = (/ 1.349959E-1_r8, 1.115697E-1_r8, 9.853958E-2_r8, 5.557793E-2_r8, & + -1.233493E-1_r8, 0.0_r8 , 0.0_r8 /) + g_F07_c1(1:7) = (/ -3.987320E-1_r8, -3.723287E-1_r8, -3.924784E-1_r8, -3.259404E-1_r8, & + 4.429054E-2_r8, -1.726586E-1_r8, -1.726586E-1_r8 /) + g_F07_c0(1:7) = (/ 7.938904E-1_r8, 8.030084E-1_r8, 8.513932E-1_r8, 8.692241E-1_r8, & + 7.085850E-1_r8, 6.412701E-1_r8, 6.412701E-1_r8 /) + g_F07_p2(1:7) = (/ 3.165543E-3_r8, 2.014810E-3_r8, 1.780838E-3_r8, 6.987734E-4_r8, & + -1.882932E-2_r8, -2.277872E-2_r8, -2.277872E-2_r8 /) + g_F07_p1(1:7) = (/ 1.140557E-1_r8, 1.143152E-1_r8, 1.143814E-1_r8, 1.071238E-1_r8, & + 1.353873E-1_r8, 1.914431E-1_r8, 1.914431E-1_r8 /) + g_F07_p0(1:7) = (/ 5.292852E-1_r8, 5.425909E-1_r8, 5.601598E-1_r8, 6.023407E-1_r8, & + 6.473899E-1_r8, 4.634944E-1_r8, 4.634944E-1_r8 /) + ! band center wavelength (um) + wvl_ct5(1:5) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band + do igb = 1,480 + wvl_ct480(igb) = 0.205_r8 + 0.01_r8 * (igb-1) ! 480-band + enddo + ! Define constants pi = SHR_CONST_PI @@ -492,7 +570,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Zero absorbed radiative fluxes: do i=-nlevsno+1,1,1 - flx_abs_lcl(:,:) = 0._r8 + flx_abs_lcl(i,:) = 0._r8 flx_abs(c_idx,i,:) = 0._r8 enddo @@ -743,26 +821,110 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & !--------------------------- Start snow & aerosol optics -------------------------------- - ! Define local Mie parameters based on snow grain size and aerosol species, - ! retrieved from a lookup table. + ! Define local Mie parameters based on snow grain size and aerosol species retrieved from a lookup table. + + ! Spherical snow: single-scatter albedo, mass extinction coefficient, asymmetry factor if (flg_slr_in == 1) then do i=snl_top,snl_btm,1 rds_idx = snw_rds_lcl(i) - snw_rds_min_tbl + 1 ! snow optical properties (direct radiation) ss_alb_snw_lcl(i) = ss_alb_snw_drc(rds_idx,bnd_idx) - asm_prm_snw_lcl(i) = asm_prm_snw_drc(rds_idx,bnd_idx) ext_cff_mss_snw_lcl(i) = ext_cff_mss_snw_drc(rds_idx,bnd_idx) + if (sno_shp(i) == 1) asm_prm_snw_lcl(i) = asm_prm_snw_drc(rds_idx,bnd_idx) enddo elseif (flg_slr_in == 2) then do i=snl_top,snl_btm,1 rds_idx = snw_rds_lcl(i) - snw_rds_min_tbl + 1 ! snow optical properties (diffuse radiation) ss_alb_snw_lcl(i) = ss_alb_snw_dfs(rds_idx,bnd_idx) - asm_prm_snw_lcl(i) = asm_prm_snw_dfs(rds_idx,bnd_idx) ext_cff_mss_snw_lcl(i) = ext_cff_mss_snw_dfs(rds_idx,bnd_idx) + if (sno_shp(i) == 1) asm_prm_snw_lcl(i) = asm_prm_snw_dfs(rds_idx,bnd_idx) enddo endif + ! Nonspherical snow: shape-dependent asymmetry factors + do i=snl_top,snl_btm,1 + + ! spheroid + if (sno_shp(i) == 2) then + diam_ice = 2._r8 * snw_rds_lcl(i) ! unit: microns + if (sno_fs(i) == 0._r8) then + fs_sphd = 0.929_r8 ! default; He et al. (2017), Table 1 + else + fs_sphd = sno_fs(i) ! user specified value + endif + fs_hex = 0.788_r8 ! reference shape factor + if (sno_AR(i) == 0._r8) then + AR_tmp = 0.5_r8 ! default; He et al. (2017), Table 1 + else + AR_tmp = sno_AR(i) ! user specified value + endif + do igb = 1,7 + g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_sphd/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) + gg_ice_F07_tmp(igb) = g_F07_c0(igb) + g_F07_c1(igb)*AR_tmp + g_F07_c2(igb)*(AR_tmp**2._r8) ! Eqn. 3.1 in Fu (2007) + enddo + + ! hexagonal plate + elseif (sno_shp(i) == 3) then + diam_ice = 2._r8 * snw_rds_lcl(i) ! unit: microns + if (sno_fs(i) == 0._r8) then + fs_hex0 = 0.788_r8 ! default; He et al. (2017), Table 1 + else + fs_hex0 = sno_fs(i) ! user specified value + endif + fs_hex = 0.788_r8 ! reference shape factor + if (sno_AR(i) == 0._r8) then + AR_tmp = 2.5_r8 ! default; He et al. (2017), Table 1 + else + AR_tmp = sno_AR(i) ! user specified value + endif + do igb = 1,7 + g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_hex0/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) + gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * LOG(AR_tmp) + g_F07_p2(igb) * ((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) + enddo + + ! Koch snowflake + elseif (sno_shp(i) == 4) then + diam_ice = 2._r8 * snw_rds_lcl(i) / 0.544_r8 ! unit: microns + if (sno_fs(i) == 0._r8) then + fs_koch = 0.712_r8 ! default; He et al. (2017), Table 1 + else + fs_koch = sno_fs(i) ! user specified value + endif + fs_hex = 0.788_r8 ! reference shape factor + if (sno_AR(i) == 0._r8) then + AR_tmp = 2.5_r8 ! default; He et al. (2017), Table 1 + else + AR_tmp = sno_AR(i) ! user specified value + endif + do igb = 1,7 + g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_koch/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) + gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * LOG(AR_tmp) + g_F07_p2(igb) * ((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) + enddo + + endif ! if snow shape + + ! compute nonspherical snow asymmetry factor + if (sno_shp(i) > 1) then + ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here + ! use the piecewise linear interpolation subroutine created at the end of this module + if (snicar_numrad_snw == 5) then + call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct5(bnd_idx),g_Cg_intp) + call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct5(bnd_idx),gg_F07_intp) + endif + if (snicar_numrad_snw == 480) then + call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct480(bnd_idx),g_Cg_intp) + call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct480(bnd_idx),gg_F07_intp) + endif + g_ice_F07 = gg_F07_intp + (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) / 2._r8 ! Eq.2.2 in Fu (2007) + asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) + endif + + if (asm_prm_snw_lcl(i) > 0.99_r8) asm_prm_snw_lcl(i) = 0.99_r8 !avoid unreasonable values (rarely occur in large-size spheroid cases) + + enddo ! snow layer loop + + ! aerosol species 1 optical properties ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) @@ -2197,5 +2359,53 @@ subroutine SnowAge_init( ) endif end subroutine SnowAge_init - + + !----------------------------------------------------------------------- + subroutine piecewise_linear_interp1d(nd, xd, yd, xi, yi) + + ! piecewise linear interpolation method for 1-dimensional data + ! original author: John Burkardt, Florida State University, 09/22/2012 + ! Added and modified by Cenlin He (NCAR), 01/27/2022 + + implicit none + + integer , intent(in) :: nd ! number of data points of (xd) + real(r8), intent(in) :: xd(1:nd) ! x-value of data points + real(r8), intent(in) :: yd(1:nd) ! y-value of data points + real(r8), intent(in) :: xi ! x-value for to-be-interpolated point + real(r8), intent(out) :: yi ! the interpolated value at xi + + ! local variables + integer :: i, k ! loop index + real(r8) :: t + + yi = 0._r8 + + ! if only one data point + if ( nd == 1 ) then + yi = yd(1) + return + endif + + ! if multiple data points + if ( xi < xd(1) ) then ! extrapolate + t = ( xi - xd(1) ) / ( xd(2) - xd(1) ) + yi = (1._r8 - t) * yd(1) + t * yd(2) + elseif ( xi > xd(nd) ) then ! extrapolate + t = ( xi - xd(nd-1) ) / ( xd(nd) - xd(nd-1) ) + yi = (1._r8 - t) * yd(nd-1) + t * yd(nd) + else ! piecsewise interpolate + do k = 2, nd + if ( (xd(k-1) <= xi) .and. (xi <= xd(k)) ) then + t = ( xi - xd(k-1) ) / ( xd(k) - xd(k-1) ) + yi = (1._r8 - t) * yd(k-1) + t * yd(k) + exit + endif + enddo + endif + + return + + end subroutine piecewise_linear_interp1d + end module SnowSnicarMod diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 9e4e0235f0..a313eed435 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -227,6 +227,9 @@ module clm_varctl integer, public :: snicar_rt_solver = 2 ! 1->Toon et a 1989 2-stream (Flanner et al. 2007) ! 2->Adding-doubling 2-stream (Dang et al.2019) + ! option for snow grain shape in SNICAR (He et al. 2017 JC), ceniln + integer, public :: snicar_snw_shape = 1 ! 1->sphere; 2->spheroid; 3->hexagonal plate; 4->Koch snowflake + !---------------------------------------------------------- ! C isotopes !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index ff5305606e..608bef6cb1 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -201,8 +201,9 @@ subroutine control_init(dtime) albice, soil_layerstruct_predefined, soil_layerstruct_userdefined, & soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & - crop_fsat_equals_zero, for_testing_run_ncdiopio_tests,snicar_numrad_snw,snicar_solarspec,& - snicar_snw_optics,snicar_dust_optics,snicar_use_aerosol,snicar_rt_solver ! cenlin + crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & + snicar_numrad_snw, snicar_solarspec, snicar_snw_optics, snicar_dust_optics, & + snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape ! cenlin ! vertical soil mixing variables namelist /clm_inparm/ & @@ -571,34 +572,40 @@ subroutine control_init(dtime) ! check on snow albedo wavelength bands, cenlin if ( (snicar_numrad_snw /= 5) .and. (snicar_numrad_snw /= 480) ) then - call endrun(msg=' ERROR: snicar_numrad_snw is out of a reasonable range (5 or 480)'//& + call endrun(msg=' ERROR: snicar_numrad_snw is out of a reasonable range (5, 480)'//& errMsg(sourcefile, __LINE__)) end if ! check on downward solar radiation spectrum, cenlin - if ( (snicar_solarspec < 0) .or. (snicar_solarspec > 6) ) then - call endrun(msg=' ERROR: snicar_solarspec is out of a reasonable range (1~6)'//& + if ( (snicar_solarspec < 1) .or. (snicar_solarspec > 6) ) then + call endrun(msg=' ERROR: snicar_solarspec is out of a reasonable range (1,2,3,4,5,6)'//& errMsg(sourcefile, __LINE__)) end if ! check on snow optics type - if ( (snicar_snw_optics < 0) .or. (snicar_snw_optics > 3) ) then - call endrun(msg=' ERROR: snicar_snw_optics is out of a reasonable range (1~3)'//& + if ( (snicar_snw_optics < 1) .or. (snicar_snw_optics > 3) ) then + call endrun(msg=' ERROR: snicar_snw_optics is out of a reasonable range (1,2,3)'//& errMsg(sourcefile, __LINE__)) end if ! check on dust optics type - if ( (snicar_dust_optics < 0) .or. (snicar_dust_optics > 3) ) then - call endrun(msg=' ERROR: snicar_dust_optics is out of a reasonable range (1~3)'//& + if ( (snicar_dust_optics < 1) .or. (snicar_dust_optics > 3) ) then + call endrun(msg=' ERROR: snicar_dust_optics is out of a reasonable range (1,2,3)'//& errMsg(sourcefile, __LINE__)) end if ! check on SNICAR solver option - if ( (snicar_rt_solver < 0) .or. (snicar_rt_solver > 2) ) then + if ( (snicar_rt_solver < 1) .or. (snicar_rt_solver > 2) ) then call endrun(msg=' ERROR: snicar_rt_solver is out of a reasonable range (1,2)'//& errMsg(sourcefile, __LINE__)) end if + ! check on SNICAR snow grain shape option + if ( (snicar_snw_shape < 1) .or. (snicar_snw_shape > 4) ) then + call endrun(msg=' ERROR: snicar_snw_shape is out of a reasonable range (1,2,3,4)'//& + errMsg(sourcefile, __LINE__)) + end if + ! Consistency settings for nrevsn if (nsrest == nsrStartup ) nrevsn = ' ' @@ -825,6 +832,7 @@ subroutine control_spmd() call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_rt_solver, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_snw_shape, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1001,19 +1009,21 @@ subroutine control_print () ! cenlin if (snicar_numrad_snw==480) then if (fsnowoptics480 == ' ') then - write(iulog,*) ' SNICAR snow optical properties (480-band) file NOT set' + write(iulog,*) ' SNICAR: snow optical properties (480-band) file NOT set' else - write(iulog,*) ' SNICAR snow optical properties (480-band) file = ',trim(fsnowoptics480) + write(iulog,*) ' SNICAR: snow optical properties (480-band) file = ',trim(fsnowoptics480) endif - write(iulog,*) ' Downward solar radiation spectrum for SNICAR =', snicar_solarspec - write(iulog,*) ' Snow refractive index type = ', snicar_snw_optics - write(iulog,*) ' Dust optics type = ', snicar_dust_optics + write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec + write(iulog,*) ' SNICAR: snow refractive index type = ', snicar_snw_optics + write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics endif write(iulog,*) ' Number of snow layers =', nlevsno write(iulog,*) ' Max snow depth (mm) =', h2osno_max - write(iulog,*) ' Number of bands in SNICAR snow albedo calculation =', snicar_numrad_snw ! cenlin - write(iulog,*) ' SNICAR radiative transfer solver type = ',snicar_rt_solver ! cenlin + write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw ! cenlin + write(iulog,*) ' SNICAR: radiative transfer solver type = ',snicar_rt_solver ! cenlin + write(iulog,*) ' SNICAR: snow grain shape type = ',snicar_snw_shape ! cenlin + write(iulog,*) ' glc number of elevation classes =', maxpatch_glc if (glc_do_dynglacier) then From b85b67950dd517bea416ab566892451f86c61941 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jan 2022 12:36:17 -0700 Subject: [PATCH 0110/2067] Added a half-degree default meshfile for crop calendar inputs. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2a8a162718..183e1329a7 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1572,6 +1572,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 2100 1850 +lnd/clm2/lai_streams/MODISPFTLAI_0.5x0_ESMFmesh_cdf5_090621.nc lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc From 0d12dbfff50c7d34098cf1ba7282da54103c4aa4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jan 2022 12:36:53 -0700 Subject: [PATCH 0111/2067] Stub-ified ESMF cropcal_interp(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 67 ++++++------------------- 1 file changed, 15 insertions(+), 52 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 58478041cc..cbb1e6aab7 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -192,67 +192,30 @@ subroutine cropcal_advance( bounds ) end subroutine cropcal_advance !================================================================ - subroutine cropcal_interp(bounds, canopystate_inst) + + ! STUB + subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! - ! Interpolate data stream information for crop calendar. + ! Interpolate data stream information for crop calendars. ! ! !USES: - use pftconMod , only : noveg - use PatchType , only : patch - use CanopyStateType , only : canopystate_type - use dshr_methods_mod , only : dshr_fldbun_getfldptr + use pftconMod , only : noveg + use CropType , only : crop_type + use PatchType , only : patch + use filterMod , only : filter + use decompMod , only : get_proc_clumps +! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: + implicit none type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter + integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches type(crop_type) , intent(inout) :: crop_inst - ! - ! !LOCAL VARIABLES: - integer :: ivt, fp, p, ip, ig, n, g - integer :: lsize - integer :: rc_sdate - real(r8), pointer :: dataptr1d_sdate(:) - real(r8), pointer :: dataptr2d_sdate(:,:) !----------------------------------------------------------------------- - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - - ! Get pointer for stream data that is time and spatially interpolate to model time and grid - ! Place all crop calendar data from each type into a temporary 2d array - ! SSR TODO: Make below work with arbitrary # of growing seasons per year - lsize = bounds%endg - bounds%begg + 1 - allocate(dataptr2d(lsize, mxpft)) - do n = 1,mxpft - call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & - fldptr1=dataptr1d_sdate, rc=rc_sdate) - ! SSR TODO: Fail on any error except "variable not found" - ! if (ESMF_LogFoundError(rcToCheck=rc_sdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - ! call ESMF_Finalize(endflag=ESMF_END_ABORT) - ! end if - - ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize - ! So an explicit loop is required here - do g = 1,lsize - if (.not. ESMF_LogFoundError(rcToCheck=rc_sdate, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - dataptr2d_sdate(g,n) = dataptr1d_sdate(g) - end if - end do - end do - - do nc = 1, get_proc_clumps() - do fp = 1, filter(nc)%num_pcropp - p = filter(nc)%pcropp(fp) - ! Set crop calendar for each gridcell/patch combination - ig = g_to_ig(patch%gridcell(p)) - ivt = patch%itype - ! SSR TODO: Make below work with arbitrary # of growing seasons per year - crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) - - ! Only for first sowing date of the year - crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) - end do - end do - deallocate(dataptr2d) + write(iulog,*) 'cropcal_interp() needs to be written for share_esmf.' + call ESMF_Finalize(endflag=ESMF_END_ABORT) end subroutine cropcal_interp From b59e336130e80b06696711f7df06f398c3af9f90 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jan 2022 15:14:14 -0700 Subject: [PATCH 0112/2067] Adding cultivar GDDs to ESMF cropcalStreamMod. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 39 +++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index cbb1e6aab7..4d6645a05e 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -30,7 +30,9 @@ module cropcalStreamMod ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream + type(shr_strdata_type) :: sdat_cropcal_cultivar_gdds ! sdate input data stream character(len=CS) :: stream_varnames_sdate(mxpft) + character(len=CS) :: stream_varnames_cultivar_gdds(mxpft) character(len=*), parameter :: sourcefile = & __FILE__ @@ -61,6 +63,7 @@ subroutine cropcal_init(bounds) integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read + character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read character(len=CL) :: stream_meshfile_cropcal ! crop calendar stream meshfile character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm @@ -76,6 +79,7 @@ subroutine cropcal_init(bounds) stream_year_last_cropcal, & model_year_align_cropcal, & stream_fldFileName_sdate, & + stream_fldFileName_cultivar_gdds, & stream_meshfile_cropcal ! Default values for namelist @@ -84,9 +88,11 @@ subroutine cropcal_init(bounds) model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year stream_meshfile_cropcal = '' stream_fldFileName_sdate = '' + stream_fldFileName_cultivar_gdds = '' ! SSR TODO: Make below work with arbitrary # of growing seasons per year do n = 1,mxpft write(stream_varnames_sdate(n),'(a,i0)') "sdate1",n + write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1",n end do ! Read cropcal_streams namelist @@ -107,6 +113,7 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) + call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom) call shr_mpi_bcast(stream_meshfile_cropcal , mpicom) if (masterproc) then @@ -116,9 +123,11 @@ subroutine cropcal_init(bounds) write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal write(iulog,'(a,a)' ) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) + write(iulog,'(a,a)' ) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) write(iulog,'(a,a)' ) ' stream_meshfile_cropcal = ',trim(stream_meshfile_cropcal) do n = 1,mxpft write(iulog,'(a,a)' ) ' stream_varnames_sdate = ',trim(stream_varnames_sdate(n)) + write(iulog,'(a,a)' ) ' stream_varnames_cultivar_gdds = ',trim(stream_varnames_cultivar_gdds(n)) end do write(iulog,*) endif @@ -149,6 +158,32 @@ subroutine cropcal_init(bounds) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + ! Initialize the cdeps data type sdat_cropcal_cultivar_gdds + call shr_strdata_init_from_inline(sdat_cropcal_cultivar_gdds, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = trim(stream_meshfile_cropcal), & + stream_lev_dimname = 'null', & + stream_mapalgo = trim(cropcal_mapalgo), & + stream_filenames = (/trim(stream_fldFileName_cultivar_gdds)/), & + stream_fldlistFile = stream_varnames_cultivar_gdds, & + stream_fldListModel = stream_varnames_cultivar_gdds, & + stream_yearFirst = stream_year_first_cropcal, & + stream_yearLast = stream_year_last_cropcal, & + stream_yearAlign = model_year_align_cropcal, & + stream_offset = cropcal_offset, & + stream_taxmode = 'cycle', & + stream_dtlimit = 1.5_r8, & + stream_tintalgo = cropcal_tintalgo, & + stream_name = 'sowing date data', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + end subroutine cropcal_init !================================================================ @@ -179,6 +214,10 @@ subroutine cropcal_advance( bounds ) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + call shr_strdata_advance(sdat_cropcal_cultivar_gdds, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) From 75fd834f1f00c4c749ad2b3ecc14ab5e707a8fb6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jan 2022 15:38:16 -0700 Subject: [PATCH 0113/2067] De-stub-ified ESMF cropcal_interp(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 56 +++++++++++++++++++++++-- 1 file changed, 53 insertions(+), 3 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 4d6645a05e..1d773abd92 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -232,7 +232,6 @@ end subroutine cropcal_advance !================================================================ - ! STUB subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! ! Interpolate data stream information for crop calendars. @@ -251,10 +250,61 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches type(crop_type) , intent(inout) :: crop_inst + ! + ! !LOCAL VARIABLES: + integer :: ivt, p, ip, ig + integer :: nc, fp +! integer :: yr, mon, day, tod, ymd, c, g ! SSR troubleshooting + integer :: n, g + integer :: lsize + integer :: rc + real(r8), pointer :: dataptr1d_sdate(:) + real(r8), pointer :: dataptr2d_sdate(:,:) + real(r8), pointer :: dataptr1d_cultivar_gdds(:) + real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) !----------------------------------------------------------------------- + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) + SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) + + ! Get pointer for stream data that is time and spatially interpolate to model time and grid + ! Place all data from each type into a temporary 2d array + lsize = bounds%endg - bounds%begg + 1 + allocate(dataptr2d_sdate(lsize, mxpft)) + allocate(dataptr2d_cultivar_gdds(lsize, mxpft)) + do n = 1,mxpft + call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & + fldptr1=dataptr1d_sdate, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & + fldptr1=dataptr1d_cultivar_gdds, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize + ! So an explicit loop is required here + do g = 1,lsize + dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) + end do + end do - write(iulog,*) 'cropcal_interp() needs to be written for share_esmf.' - call ESMF_Finalize(endflag=ESMF_END_ABORT) + ! Set rx_sdate and rx_cultivar_gdd for each gridcell/patch combination + do p = bounds%begp, bounds%endp + ivt = patch%itype(p) + if (ivt /= noveg) then + ! vegetated pft + ig = g_to_ig(patch%gridcell(p)) + crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) + crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,ivt) + + ! Only for first sowing date of the year + crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + endif + end do + deallocate(dataptr2d_sdate) + deallocate(dataptr2d_cultivar_gdds) end subroutine cropcal_interp From 596a057ee4ced78580f1ffc9b0290da0011744d5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jan 2022 15:47:25 -0700 Subject: [PATCH 0114/2067] Compile fixes. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 1d773abd92..ceee449e41 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -10,13 +10,12 @@ module cropcalStreamMod use ESMF use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL, CS => shr_kind_CS use dshr_strdata_mod , only : shr_strdata_type - use decompMod , only : bounds_type, get_proc_clumps + use decompMod , only : bounds_type use abortutils , only : endrun use clm_varctl , only : iulog use clm_varpar , only : mxpft use perf_mod , only : t_startf, t_stopf use spmdMod , only : masterproc, mpicom, iam - use filterMod , only : filter ! ! !PUBLIC TYPES: implicit none @@ -240,8 +239,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use pftconMod , only : noveg use CropType , only : crop_type use PatchType , only : patch - use filterMod , only : filter - use decompMod , only : get_proc_clumps + use dshr_methods_mod , only : dshr_fldbun_getfldptr ! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: From e006dc54c2f17e9004894f3f608a5279d2618e6d Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Fri, 28 Jan 2022 19:39:30 -0700 Subject: [PATCH 0115/2067] add BC-snow internal mixing and namelist control --- .../namelist_definition_ctsm.xml | 5 + src/biogeophys/SnowSnicarMod.F90 | 141 +++++++++++++++--- src/main/clm_varctl.F90 | 3 + src/main/controlMod.F90 | 5 +- 4 files changed, 132 insertions(+), 22 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 5a07a2a9f4..261244e21e 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -198,6 +198,11 @@ SNICAR radiative transfer solver type snow grain shape used in SNICAR snow albedo calculation + +option to activate BC-snow internal mixing in SNICAR snow albedo calculation + + Index of rooting profile for water diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 02dd763d14..087fb374c7 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -12,7 +12,7 @@ module SnowSnicarMod use shr_sys_mod , only : shr_sys_flush use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver, & - snicar_snw_shape ! cenlin + snicar_snw_shape, snicar_snobc_intmix ! cenlin use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -486,6 +486,29 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: gg_F07_intp ! interpolated asymmetry factor related to geometric reflection & refraction real(r8) :: g_ice_F07 ! asymmetry factor for Fu 2007 parameterization value integer :: igb ! loop index + + !----------------------------------------------------------------------- + ! variables used for BC-snow internal mixing (He et al. 2017 J of Climate): + real(r8) :: enh_omg_bcint ! BC-induced enhancement in snow single-scattering co-albedo (1-omega) + real(r8) :: enh_omg_bcint_tmp(1:16) ! temporary BC-induced enhancement in snow 1-omega + real(r8) :: enh_omg_bcint_tmp2(1:16) ! temporary BC-induced enhancement in snow 1-omega + real(r8) :: bcint_wvl(1:17) ! Parameterization band (0.2-1.2um) for BC-induced enhancement in snow 1-omega + real(r8) :: bcint_wvl_ct(1:16) ! Parameterization band center wavelength (um) + real(r8) :: bcint_d0(1:16) ! Parameterization coefficients at each band center wavelength + real(r8) :: bcint_d1(1:16) ! Parameterization coefficients at each band center wavelength + real(r8) :: bcint_d2(1:16) ! Parameterization coefficients at each band center wavelength + real(r8) :: den_bc = 1.49_r8 ! target BC particle density (g/cm3) used in BC MAC adjustment + real(r8) :: Re_bc = 0.045 ! target BC effective radius (um) used in BC MAC adjustment + real(r8) :: bcint_m(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix + real(r8) :: bcint_n(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix + real(r8) :: bcint_dd ! intermediate parameter + real(r8) :: bcint_dd2 ! intermediate parameter + real(r8) :: bcint_f ! intermediate parameter + real(r8) :: enh_omg_bcint_intp ! BC-induced enhancement in snow 1-omega (logscale) interpolated to CLM wavelength + real(r8) :: enh_omg_bcint_intp2 ! BC-induced enhancement in snow 1-omega interpolated to CLM wavelength + real(r8) :: wvl_doint ! wavelength doing BC-snow int mixing (<=1.2um) + integer :: ibb ! loop index + ! !----------------------------------------------------------------------- @@ -548,7 +571,29 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & 1.353873E-1_r8, 1.914431E-1_r8, 1.914431E-1_r8 /) g_F07_p0(1:7) = (/ 5.292852E-1_r8, 5.425909E-1_r8, 5.601598E-1_r8, 6.023407E-1_r8, & 6.473899E-1_r8, 4.634944E-1_r8, 4.634944E-1_r8 /) - ! band center wavelength (um) + + ! initialize for BC-snow internal mixing + ! Eq. 8b & Table 4 in He et al., 2017 J. Climate (wavelength>1.2um, no BC-snow int mixi effect) + bcint_wvl(1:17) = (/ 0.20_r8, 0.25_r8, 0.30_r8, 0.33_r8, 0.36_r8, 0.40_r8, 0.44_r8, 0.48_r8, & + 0.52_r8, 0.57_r8, 0.64_r8, 0.69_r8, 0.75_r8, 0.78_r8, 0.87_r8, 1._r8, 1.2_r8 /) + bcint_wvl_ct(1:16) = bcint_wvl(2:17) / 2._r8 + bcint_wvl(1:16) / 2._r8 + bcint_d0(1:16) = (/ 2.48045_r8 , 4.70305_r8 , 4.68619_r8 , 4.67369_r8 , 4.65040_r8 , & + 2.40364_r8 , 7.95408E-1_r8, 2.92745E-1_r8, 8.63396E-2_r8, 2.76299E-2_r8, & + 1.40864E-2_r8, 8.65705E-3_r8, 6.12971E-3_r8, 4.45697E-3_r8, 3.06648E-2_r8, & + 7.96544E-1_r8 /) + bcint_d1(1:16) = (/ 9.77209E-1_r8, 9.73317E-1_r8, 9.79650E-1_r8, 9.84579E-1_r8, 9.93537E-1_r8, & + 9.95955E-1_r8, 9.95218E-1_r8, 9.74284E-1_r8, 9.81193E-1_r8, 9.81239E-1_r8, & + 9.55515E-1_r8, 9.10491E-1_r8, 8.74196E-1_r8, 8.27238E-1_r8, 4.82870E-1_r8, & + 4.36649E-2_r8 /) + bcint_d2(1:16) = (/ 3.95960E-1_r8, 2.04820E-1_r8, 2.07410E-1_r8, 2.09390E-1_r8, 2.13030E-1_r8, & + 4.18570E-1_r8, 1.29682_r8 , 3.75514_r8 , 1.27372E+1_r8, 3.93293E+1_r8, & + 8.78918E+1_r8, 1.86969E+2_r8, 3.45600E+2_r8, 7.08637E+2_r8, 1.41067E+3_r8, & + 2.57288E+2_r8 /) + ! Eq. 1a,1b and Table S1 in He et al. 2018 GRL + bcint_m(1:3) = (/ -0.8724_r8, -0.1866_r8, -0.0046_r8 /) + bcint_n(1:3) = (/ -0.0072_r8, -0.1918_r8, -0.5177_r8 /) + + ! SNICAR/CLM snow band center wavelength (um) wvl_ct5(1:5) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band do igb = 1,480 wvl_ct480(igb) = 0.205_r8 + 0.01_r8 * (igb-1) ! 480-band @@ -925,42 +970,42 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo ! snow layer loop - ! aerosol species 1 optical properties + ! aerosol species 1 optical properties, hydrophilic BC ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) - ! aerosol species 2 optical properties + ! aerosol species 2 optical properties, hydrophobic BC ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) asm_prm_aer_lcl(2) = asm_prm_bc2(bnd_idx) ext_cff_mss_aer_lcl(2) = ext_cff_mss_bc2(bnd_idx) - ! aerosol species 3 optical properties + ! aerosol species 3 optical properties, hydrophilic OC ss_alb_aer_lcl(3) = ss_alb_oc1(bnd_idx) asm_prm_aer_lcl(3) = asm_prm_oc1(bnd_idx) ext_cff_mss_aer_lcl(3) = ext_cff_mss_oc1(bnd_idx) - ! aerosol species 4 optical properties + ! aerosol species 4 optical properties, hydrophobic OC ss_alb_aer_lcl(4) = ss_alb_oc2(bnd_idx) asm_prm_aer_lcl(4) = asm_prm_oc2(bnd_idx) ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) - ! aerosol species 5 optical properties + ! aerosol species 5 optical properties, dust size1 ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) - ! aerosol species 6 optical properties + ! aerosol species 6 optical properties, dust size2 ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) - ! aerosol species 7 optical properties + ! aerosol species 7 optical properties, dust size3 ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) - ! aerosol species 8 optical properties + ! aerosol species 8 optical properties, dust size4 ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) @@ -972,6 +1017,62 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weighted Mie parameters of each layer do i=snl_top,snl_btm,1 + + ! BC-snow internal mixing applied to hydrophilic BC if activated + ! BC-snow internal mixing primarily affect snow single-scattering albedo + if ( snicar_snobc_intmix .and. (mss_cnc_aer_lcl(i,1)>0._r8) ) then + if (snicar_numrad_snw == 5) wvl_doint = wvl_ct5(bnd_idx) + if (snicar_numrad_snw == 480) wvl_doint = wvl_ct480(bnd_idx) + + if (wvl_doint <= 1.2_r8) then ! only do for wavelength<=1.2um + ! result from Eq.8b in He et al.(2017) is based on BC Re=0.1um & + ! MAC=6.81 m2/g (@550 nm) & BC density=1.7g/cm3. + ! To be consistent with Bond et al. 2006 recommeded value (BC MAC=7.5 m2/g @550nm) + ! we made adjustments on BC size & density as follows to get MAC=7.5m2/g: + ! (1) We use BC Re=0.045um [geometric mean diameter=0.06um (Dentener et al.2006, + ! Yu and Luo,2009) & geometric std=1.5 (Flanner et al.2007;Aoki et al., 2011)]. + ! (2) We tune BC density from 1.7 to 1.49 g/cm3 (Aoki et al., 2011). + ! These adjustments also lead to consistent results with Flanner et al. 2012 (ACP) lookup table + ! for BC-snow internal mixing enhancement in albedo reduction (He et al. 2018 ACP) + do ibb=1,16 + enh_omg_bcint_tmp(ibb) = bcint_d0(ibb) * & + ( (mss_cnc_aer_lcl(i,1)*1.0E9_r8*1.7_r8/den_bc + bcint_d2(ibb)) **bcint_d1(ibb) ) + ! adjust enhancment factor for BC effective size from 0.1um to Re_bc (He et al. 2018 GRL Eqs.1a,1b) + if (ibb < 3) then ! near-UV + bcint_dd = (Re_bc/0.05_r8)**bcint_m(1) + bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(1) + bcint_f = (Re_bc/0.1_r8)**bcint_n(1) + endif + if ( (ibb >= 3) .and. (ibb <= 11) ) then ! visible + bcint_dd = (Re_bc/0.05_r8)**bcint_m(2) + bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(2) + bcint_f = (Re_bc/0.1_r8)**bcint_n(2) + endif + if ( ibb > 11 ) then ! NIR + bcint_dd = (Re_bc/0.05_r8)**bcint_m(3) + bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(3) + bcint_f = (Re_bc/0.1_r8)**bcint_n(3) + endif + enh_omg_bcint_tmp2(ibb) = LOG10( bcint_dd * ((enh_omg_bcint_tmp(ibb) / bcint_dd2)**bcint_f) ) + enddo + + ! piecewise linear interpolate into targeted SNICAR bands in a logscale space + call piecewise_linear_interp1d(16,bcint_wvl_ct,enh_omg_bcint_tmp2,wvl_doint,enh_omg_bcint_intp) + + ! update snow single-scattering albedo + enh_omg_bcint_intp2 = 10._r8 ** enh_omg_bcint_intp + enh_omg_bcint_intp2 = max(enh_omg_bcint_intp2, 1._r8) ! BC does not reduce snow absorption + ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_bcint_intp2 + ss_alb_snw_lcl(i) = max(0._r8, min(ss_alb_snw_lcl(i),1._r8)) + + ! reset hydrophilic BC property to 0 since it is accounted by updated snow ss_alb above + ss_alb_aer_lcl(1) = 0.0 + asm_prm_aer_lcl(1) = 0.0 + ext_cff_mss_aer_lcl(1) = 0.0 + + endif ! end if wvl_doint <= 1.2 + endif ! end if BC-snow internal mixing + L_snw(i) = h2osno_ice_lcl(i)+h2osno_liq_lcl(i) tau_snw(i) = L_snw(i)*ext_cff_mss_snw_lcl(i) @@ -2121,22 +2222,22 @@ subroutine SnowOptics_init( ) call ncd_io( 'ext_cff_mss_dust04', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) endif - ! BC species 1 Mie parameters - call ncd_io( 'ss_alb_bcphil', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphil', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphil', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 without BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) - ! BC species 2 Mie parameters + ! BC species 2 Mie parameters, uncoated BC call ncd_io( 'ss_alb_bcphob', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_bcphob', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) - ! OC species 1 Mie parameters - call ncd_io( 'ss_alb_ocphil', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphil', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphil', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 without OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) - ! OC species 2 Mie parameters + ! OC species 2 Mie parameters, uncoated OC call ncd_io( 'ss_alb_ocphob', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index a313eed435..edde42ea22 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -230,6 +230,9 @@ module clm_varctl ! option for snow grain shape in SNICAR (He et al. 2017 JC), ceniln integer, public :: snicar_snw_shape = 1 ! 1->sphere; 2->spheroid; 3->hexagonal plate; 4->Koch snowflake + ! option to activate BC-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln + logical, public :: snicar_snobc_intmix = .true. ! false->external mixing for all BC; true->internal mixing for hydrophilic BC + !---------------------------------------------------------- ! C isotopes !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 608bef6cb1..1804cb7757 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -203,7 +203,7 @@ subroutine control_init(dtime) irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & snicar_numrad_snw, snicar_solarspec, snicar_snw_optics, snicar_dust_optics, & - snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape ! cenlin + snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape, snicar_snobc_intmix ! cenlin ! vertical soil mixing variables namelist /clm_inparm/ & @@ -833,6 +833,7 @@ subroutine control_spmd() call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_rt_solver, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_snw_shape, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1023,7 +1024,7 @@ subroutine control_print () write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw ! cenlin write(iulog,*) ' SNICAR: radiative transfer solver type = ',snicar_rt_solver ! cenlin write(iulog,*) ' SNICAR: snow grain shape type = ',snicar_snw_shape ! cenlin - + write(iulog,*) ' SNICAR: BC-snow internal mixing = ', snicar_snobc_intmix ! cenlin write(iulog,*) ' glc number of elevation classes =', maxpatch_glc if (glc_do_dynglacier) then From 43e52bfdc62e0fd6b7e43e2337a60d653707e57c Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Fri, 28 Jan 2022 21:54:58 -0700 Subject: [PATCH 0116/2067] add dust-snow internal mixing and namelist control --- .../namelist_definition_ctsm.xml | 5 ++ src/biogeophys/SnowSnicarMod.F90 | 82 +++++++++++++++---- src/main/clm_varctl.F90 | 4 + src/main/controlMod.F90 | 11 ++- 4 files changed, 87 insertions(+), 15 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 261244e21e..51264f7b58 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -203,6 +203,11 @@ snow grain shape used in SNICAR snow albedo calculation option to activate BC-snow internal mixing in SNICAR snow albedo calculation + +option to activate dust-snow internal mixing in SNICAR snow albedo calculation + + Index of rooting profile for water diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 087fb374c7..b4e75d4173 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -12,7 +12,8 @@ module SnowSnicarMod use shr_sys_mod , only : shr_sys_flush use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver, & - snicar_snw_shape, snicar_snobc_intmix ! cenlin + snicar_snw_shape, snicar_snobc_intmix, & + snicar_snodst_intmix ! cenlin use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -509,7 +510,22 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: wvl_doint ! wavelength doing BC-snow int mixing (<=1.2um) integer :: ibb ! loop index - ! + !----------------------------------------------------------------------- + ! variables used for dust-snow internal mixing (He et al. 2019 JAMES): + real(r8) :: enh_omg_dstint ! dust-induced enhancement in snow single-scattering co-albedo (1-omega) + real(r8) :: enh_omg_dstint_tmp(1:6) ! temporary dust-induced enhancement in snow 1-omega + real(r8) :: enh_omg_dstint_tmp2(1:6) ! temporary dust-induced enhancement in snow 1-omega + real(r8) :: dstint_wvl(1:7) ! Parameterization band (0.2-1.2um) for dust-induced enhancement in snow 1-omega + real(r8) :: dstint_wvl_ct(1:6) ! Parameterization band center wavelength (um) + real(r8) :: dstint_a1(1:6) ! Parameterization coefficients at each band center wavelength + real(r8) :: dstint_a2(1:6) ! Parameterization coefficients at each band center wavelength + real(r8) :: dstint_a3(1:6) ! Parameterization coefficients at each band center wavelength + real(r8) :: enh_omg_dstint_intp ! dust-induced enhancement in snow 1-omega (logscale) interpolated to CLM wavelength + real(r8) :: enh_omg_dstint_intp2 ! dust-induced enhancement in snow 1-omega interpolated to CLM wavelength + real(r8) :: wvl_doint2 ! wavelength doing dust-snow int mixing (<=1.2um) + real(r8) :: tot_dst_snw_conc ! total dust content in snow across all size bins (ppm=ug/g) + integer :: idb ! loop index + !----------------------------------------------------------------------- ! Enforce expected array sizes @@ -573,10 +589,10 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & 6.473899E-1_r8, 4.634944E-1_r8, 4.634944E-1_r8 /) ! initialize for BC-snow internal mixing - ! Eq. 8b & Table 4 in He et al., 2017 J. Climate (wavelength>1.2um, no BC-snow int mixi effect) + ! Eq. 8b & Table 4 in He et al., 2017 J. Climate (wavelength>1.2um, no BC-snow int mixing effect) bcint_wvl(1:17) = (/ 0.20_r8, 0.25_r8, 0.30_r8, 0.33_r8, 0.36_r8, 0.40_r8, 0.44_r8, 0.48_r8, & 0.52_r8, 0.57_r8, 0.64_r8, 0.69_r8, 0.75_r8, 0.78_r8, 0.87_r8, 1._r8, 1.2_r8 /) - bcint_wvl_ct(1:16) = bcint_wvl(2:17) / 2._r8 + bcint_wvl(1:16) / 2._r8 + bcint_wvl_ct(1:16) = bcint_wvl(2:17)/2._r8 + bcint_wvl(1:16)/2._r8 bcint_d0(1:16) = (/ 2.48045_r8 , 4.70305_r8 , 4.68619_r8 , 4.67369_r8 , 4.65040_r8 , & 2.40364_r8 , 7.95408E-1_r8, 2.92745E-1_r8, 8.63396E-2_r8, 2.76299E-2_r8, & 1.40864E-2_r8, 8.65705E-3_r8, 6.12971E-3_r8, 4.45697E-3_r8, 3.06648E-2_r8, & @@ -593,6 +609,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & bcint_m(1:3) = (/ -0.8724_r8, -0.1866_r8, -0.0046_r8 /) bcint_n(1:3) = (/ -0.0072_r8, -0.1918_r8, -0.5177_r8 /) + ! initialize for dust-snow internal mixing + ! Eq. 1 and Table 1 in He et al. 2019 JAMES (wavelength>1.2um, no dust-snow int mixing effect) + dstint_wvl(1:7) = (/ 0.2_r8, 0.2632_r8, 0.3448_r8, 0.4415_r8, 0.625_r8, 0.7782_r8, 1.2422_r8/) + dstint_wvl_ct(1:6) = dstint_wvl(2:7)/2._r8 + dstint_wvl(1:6)/2._r8 + dstint_a1(1:6) = (/ -2.1307E+1_r8, -1.5815E+1_r8, -9.2880_r8 , 1.1115_r8 , 1.0307_r8 , 1.0185_r8 /) + dstint_a2(1:6) = (/ 1.1746E+2_r8, 9.3241E+1_r8, 4.0605E+1_r8, 3.7389E-1_r8, 1.4800E-2_r8, 2.8921E-4_r8 /) + dstint_a3(1:6) = (/ 9.9701E-1_r8, 9.9781E-1_r8, 9.9848E-1_r8, 1.0035_r8 , 1.0024_r8 , 1.0356_r8 /) + ! SNICAR/CLM snow band center wavelength (um) wvl_ct5(1:5) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band do igb = 1,480 @@ -925,7 +949,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif do igb = 1,7 g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_hex0/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) - gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * LOG(AR_tmp) + g_F07_p2(igb) * ((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) + gg_ice_F07_tmp(igb) = g_F07_p0(igb)+g_F07_p1(igb)*LOG(AR_tmp)+g_F07_p2(igb)*((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) enddo ! Koch snowflake @@ -944,7 +968,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif do igb = 1,7 g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_koch/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) - gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * LOG(AR_tmp) + g_F07_p2(igb) * ((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) + gg_ice_F07_tmp(igb) = g_F07_p0(igb)+g_F07_p1(igb)*LOG(AR_tmp)+g_F07_p2(igb)*((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) enddo endif ! if snow shape @@ -1020,11 +1044,11 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! BC-snow internal mixing applied to hydrophilic BC if activated ! BC-snow internal mixing primarily affect snow single-scattering albedo - if ( snicar_snobc_intmix .and. (mss_cnc_aer_lcl(i,1)>0._r8) ) then + if ( snicar_snobc_intmix .and. (mss_cnc_aer_lcl(i,1) > 0._r8) ) then if (snicar_numrad_snw == 5) wvl_doint = wvl_ct5(bnd_idx) if (snicar_numrad_snw == 480) wvl_doint = wvl_ct480(bnd_idx) - - if (wvl_doint <= 1.2_r8) then ! only do for wavelength<=1.2um + ! only do for wavelength<=1.2um + if (wvl_doint <= 1.2_r8) then ! result from Eq.8b in He et al.(2017) is based on BC Re=0.1um & ! MAC=6.81 m2/g (@550 nm) & BC density=1.7g/cm3. ! To be consistent with Bond et al. 2006 recommeded value (BC MAC=7.5 m2/g @550nm) @@ -1053,26 +1077,56 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(3) bcint_f = (Re_bc/0.1_r8)**bcint_n(3) endif - enh_omg_bcint_tmp2(ibb) = LOG10( bcint_dd * ((enh_omg_bcint_tmp(ibb) / bcint_dd2)**bcint_f) ) + enh_omg_bcint_tmp2(ibb)=LOG10(max(1._r8,bcint_dd*((enh_omg_bcint_tmp(ibb)/bcint_dd2)**bcint_f))) enddo - ! piecewise linear interpolate into targeted SNICAR bands in a logscale space call piecewise_linear_interp1d(16,bcint_wvl_ct,enh_omg_bcint_tmp2,wvl_doint,enh_omg_bcint_intp) - ! update snow single-scattering albedo enh_omg_bcint_intp2 = 10._r8 ** enh_omg_bcint_intp enh_omg_bcint_intp2 = max(enh_omg_bcint_intp2, 1._r8) ! BC does not reduce snow absorption ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_bcint_intp2 ss_alb_snw_lcl(i) = max(0._r8, min(ss_alb_snw_lcl(i),1._r8)) - ! reset hydrophilic BC property to 0 since it is accounted by updated snow ss_alb above ss_alb_aer_lcl(1) = 0.0 asm_prm_aer_lcl(1) = 0.0 ext_cff_mss_aer_lcl(1) = 0.0 - endif ! end if wvl_doint <= 1.2 endif ! end if BC-snow internal mixing + + ! Dust-snow internal mixing applied to all size bins if activated + ! Dust-snow internal mixing primarily affect snow single-scattering albedo + ! default optics of externally mixed dust at 4 size bins based on effective + ! radius of 1.38um and sigma=2.0 with truncation to each size bin (Flanner et al. 2021 GMD) + ! parameterized dust-snow int mix results based on effective radius of 1.1um and sigma=2.0 + ! from (He et al. 2019 JAMES). Thus, the parameterization can be approximately applied to + ! all dust size bins here. + tot_dst_snw_conc = (mss_cnc_aer_lcl(i,5) + mss_cnc_aer_lcl(i,6) + & + mss_cnc_aer_lcl(i,7) + mss_cnc_aer_lcl(i,8)) * 1.0E6_r8 + if ( snicar_snodst_intmix .and. (tot_dst_snw_conc > 0._r8) ) then + if (snicar_numrad_snw == 5) wvl_doint2 = wvl_ct5(bnd_idx) + if (snicar_numrad_snw == 480) wvl_doint2 = wvl_ct480(bnd_idx) + ! only do for wavelength<=1.2um + if (wvl_doint2 <= 1.2_r8) then + do idb=1,6 + enh_omg_dstint_tmp(idb) = dstint_a1(idb)+dstint_a2(idb)*(tot_dst_snw_conc**dstint_a3(idb)) + enh_omg_dstint_tmp2(idb) = LOG10(max(enh_omg_dstint_tmp(idb),1._r8)) + enddo + ! piecewise linear interpolate into targeted SNICAR bands in a logscale space + call piecewise_linear_interp1d(6,dstint_wvl_ct,enh_omg_dstint_tmp2,wvl_doint2,enh_omg_dstint_intp) + ! update snow single-scattering albedo + enh_omg_dstint_intp2 = 10._r8 ** enh_omg_dstint_intp + enh_omg_dstint_intp2 = max(enh_omg_dstint_intp2, 1._r8) + ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_dstint_intp2 + ss_alb_snw_lcl(i) = max(0._r8, min(ss_alb_snw_lcl(i),1._r8)) + ! reset all dust optics to zero since it is accounted by updated snow ss_alb above + ss_alb_aer_lcl(5:8) = 0._r8 + asm_prm_aer_lcl(5:8) = 0._r8 + ext_cff_mss_aer_lcl(5:8) = 0._r8 + endif ! end if wvl_doint2 <= 1.2 + endif ! end if dust-snow internal mixing + + L_snw(i) = h2osno_ice_lcl(i)+h2osno_liq_lcl(i) tau_snw(i) = L_snw(i)*ext_cff_mss_snw_lcl(i) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index edde42ea22..d8a56384eb 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -233,6 +233,10 @@ module clm_varctl ! option to activate BC-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln logical, public :: snicar_snobc_intmix = .true. ! false->external mixing for all BC; true->internal mixing for hydrophilic BC + ! option to activate dust-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln + logical, public :: snicar_snodst_intmix = .false. ! false->external mixing for all dust; true->internal mixing for all dust + + !---------------------------------------------------------- ! C isotopes !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 1804cb7757..195356b77f 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -203,7 +203,8 @@ subroutine control_init(dtime) irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & snicar_numrad_snw, snicar_solarspec, snicar_snw_optics, snicar_dust_optics, & - snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape, snicar_snobc_intmix ! cenlin + snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape, snicar_snobc_intmix,& + snicar_snodst_intmix ! cenlin ! vertical soil mixing variables namelist /clm_inparm/ & @@ -606,6 +607,12 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if + ! check on SNICAR BC-snow and dust-snow internal mixing + if ( snicar_snobc_intmix .and. snicar_snodst_intmix ) then + call endrun(msg=' ERROR: currently dust-snow and BC-snow internal mixing cannot be activated together'//& + errMsg(sourcefile, __LINE__)) + end if + ! Consistency settings for nrevsn if (nsrest == nsrStartup ) nrevsn = ' ' @@ -834,6 +841,7 @@ subroutine control_spmd() call mpi_bcast (snicar_rt_solver, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_snw_shape, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin + call mpi_bcast (snicar_snodst_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1025,6 +1033,7 @@ subroutine control_print () write(iulog,*) ' SNICAR: radiative transfer solver type = ',snicar_rt_solver ! cenlin write(iulog,*) ' SNICAR: snow grain shape type = ',snicar_snw_shape ! cenlin write(iulog,*) ' SNICAR: BC-snow internal mixing = ', snicar_snobc_intmix ! cenlin + write(iulog,*) ' SNICAR: dust-snow internal mixing = ', snicar_snodst_intmix ! cenlin write(iulog,*) ' glc number of elevation classes =', maxpatch_glc if (glc_do_dynglacier) then From 7dc18abffca804a440fad962b99b8b0d9ccbb7d2 Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Sat, 29 Jan 2022 15:04:18 -0700 Subject: [PATCH 0117/2067] bug fix for BC/dust-snow internal mixing --- src/biogeophys/SnowSnicarMod.F90 | 125 ++++++++++++++++++------------- 1 file changed, 72 insertions(+), 53 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index b4e75d4173..484bfc8fd5 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -522,7 +522,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: dstint_a3(1:6) ! Parameterization coefficients at each band center wavelength real(r8) :: enh_omg_dstint_intp ! dust-induced enhancement in snow 1-omega (logscale) interpolated to CLM wavelength real(r8) :: enh_omg_dstint_intp2 ! dust-induced enhancement in snow 1-omega interpolated to CLM wavelength - real(r8) :: wvl_doint2 ! wavelength doing dust-snow int mixing (<=1.2um) real(r8) :: tot_dst_snw_conc ! total dust content in snow across all size bins (ppm=ug/g) integer :: idb ! loop index @@ -995,9 +994,9 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! aerosol species 1 optical properties, hydrophilic BC - ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) - asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) - ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) + !ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) + !asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) + !ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) ! aerosol species 2 optical properties, hydrophobic BC ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) @@ -1015,24 +1014,24 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) ! aerosol species 5 optical properties, dust size1 - ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) - asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) - ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) + !ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) + !asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) + !ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) ! aerosol species 6 optical properties, dust size2 - ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) - asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) - ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) + !ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) + !asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) + !ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) ! aerosol species 7 optical properties, dust size3 - ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) - asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) - ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) + !ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) + !asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) + !ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) ! aerosol species 8 optical properties, dust size4 - ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) - asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) - ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) + !ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) + !asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) + !ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) ! 1. snow and aerosol layer column mass (L_snw, L_aer [kg/m^2]) @@ -1042,13 +1041,37 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weighted Mie parameters of each layer do i=snl_top,snl_btm,1 - ! BC-snow internal mixing applied to hydrophilic BC if activated - ! BC-snow internal mixing primarily affect snow single-scattering albedo - if ( snicar_snobc_intmix .and. (mss_cnc_aer_lcl(i,1) > 0._r8) ) then - if (snicar_numrad_snw == 5) wvl_doint = wvl_ct5(bnd_idx) - if (snicar_numrad_snw == 480) wvl_doint = wvl_ct480(bnd_idx) - ! only do for wavelength<=1.2um - if (wvl_doint <= 1.2_r8) then + ! Optics for BC/dust-snow external mixing: + ! aerosol species 1 optical properties, hydrophilic BC + ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) + asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) + ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) + ! aerosol species 5 optical properties, dust size1 + ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) + asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) + ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) + ! aerosol species 6 optical properties, dust size2 + ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) + asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) + ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) + ! aerosol species 7 optical properties, dust size3 + ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) + asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) + ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) + ! aerosol species 8 optical properties, dust size4 + ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) + asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) + ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) + + + ! Start BC/dust-snow internal mixing for wavelength<=1.2um + if (snicar_numrad_snw == 5) wvl_doint = wvl_ct5(bnd_idx) + if (snicar_numrad_snw == 480) wvl_doint = wvl_ct480(bnd_idx) + if (wvl_doint <= 1.2_r8) then + + ! BC-snow internal mixing applied to hydrophilic BC if activated + ! BC-snow internal mixing primarily affect snow single-scattering albedo + if ( snicar_snobc_intmix .and. (mss_cnc_aer_lcl(i,1) > 0._r8) ) then ! result from Eq.8b in He et al.(2017) is based on BC Re=0.1um & ! MAC=6.81 m2/g (@550 nm) & BC density=1.7g/cm3. ! To be consistent with Bond et al. 2006 recommeded value (BC MAC=7.5 m2/g @550nm) @@ -1083,48 +1106,43 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & call piecewise_linear_interp1d(16,bcint_wvl_ct,enh_omg_bcint_tmp2,wvl_doint,enh_omg_bcint_intp) ! update snow single-scattering albedo enh_omg_bcint_intp2 = 10._r8 ** enh_omg_bcint_intp - enh_omg_bcint_intp2 = max(enh_omg_bcint_intp2, 1._r8) ! BC does not reduce snow absorption - ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_bcint_intp2 - ss_alb_snw_lcl(i) = max(0._r8, min(ss_alb_snw_lcl(i),1._r8)) + enh_omg_bcint_intp2 = min(1.0E5_r8, max(enh_omg_bcint_intp2,1._r8)) ! constrain enhancement to a reasonable range + ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_bcint_intp2 + ss_alb_snw_lcl(i) = max(0.5_r8, min(ss_alb_snw_lcl(i),1._r8)) ! reset hydrophilic BC property to 0 since it is accounted by updated snow ss_alb above - ss_alb_aer_lcl(1) = 0.0 - asm_prm_aer_lcl(1) = 0.0 - ext_cff_mss_aer_lcl(1) = 0.0 - endif ! end if wvl_doint <= 1.2 - endif ! end if BC-snow internal mixing - - - ! Dust-snow internal mixing applied to all size bins if activated - ! Dust-snow internal mixing primarily affect snow single-scattering albedo - ! default optics of externally mixed dust at 4 size bins based on effective - ! radius of 1.38um and sigma=2.0 with truncation to each size bin (Flanner et al. 2021 GMD) - ! parameterized dust-snow int mix results based on effective radius of 1.1um and sigma=2.0 - ! from (He et al. 2019 JAMES). Thus, the parameterization can be approximately applied to - ! all dust size bins here. - tot_dst_snw_conc = (mss_cnc_aer_lcl(i,5) + mss_cnc_aer_lcl(i,6) + & - mss_cnc_aer_lcl(i,7) + mss_cnc_aer_lcl(i,8)) * 1.0E6_r8 - if ( snicar_snodst_intmix .and. (tot_dst_snw_conc > 0._r8) ) then - if (snicar_numrad_snw == 5) wvl_doint2 = wvl_ct5(bnd_idx) - if (snicar_numrad_snw == 480) wvl_doint2 = wvl_ct480(bnd_idx) - ! only do for wavelength<=1.2um - if (wvl_doint2 <= 1.2_r8) then + ss_alb_aer_lcl(1) = 0.0 + asm_prm_aer_lcl(1) = 0.0 + ext_cff_mss_aer_lcl(1) = 0.0 + endif ! end if BC-snow mixing type + + ! Dust-snow internal mixing applied to all size bins if activated + ! Dust-snow internal mixing primarily affect snow single-scattering albedo + ! default optics of externally mixed dust at 4 size bins based on effective + ! radius of 1.38um and sigma=2.0 with truncation to each size bin (Flanner et al. 2021 GMD) + ! parameterized dust-snow int mix results based on effective radius of 1.1um and sigma=2.0 + ! from (He et al. 2019 JAMES). Thus, the parameterization can be approximately applied to + ! all dust size bins here. + tot_dst_snw_conc = (mss_cnc_aer_lcl(i,5) + mss_cnc_aer_lcl(i,6) + & + mss_cnc_aer_lcl(i,7) + mss_cnc_aer_lcl(i,8)) * 1.0E6_r8 !kg/kg->ppm + if ( snicar_snodst_intmix .and. (tot_dst_snw_conc > 0._r8) ) then do idb=1,6 enh_omg_dstint_tmp(idb) = dstint_a1(idb)+dstint_a2(idb)*(tot_dst_snw_conc**dstint_a3(idb)) enh_omg_dstint_tmp2(idb) = LOG10(max(enh_omg_dstint_tmp(idb),1._r8)) enddo ! piecewise linear interpolate into targeted SNICAR bands in a logscale space - call piecewise_linear_interp1d(6,dstint_wvl_ct,enh_omg_dstint_tmp2,wvl_doint2,enh_omg_dstint_intp) + call piecewise_linear_interp1d(6,dstint_wvl_ct,enh_omg_dstint_tmp2,wvl_doint,enh_omg_dstint_intp) ! update snow single-scattering albedo enh_omg_dstint_intp2 = 10._r8 ** enh_omg_dstint_intp - enh_omg_dstint_intp2 = max(enh_omg_dstint_intp2, 1._r8) + enh_omg_dstint_intp2 = min(1.0E5_r8, max(enh_omg_dstint_intp2,1._r8)) ! constrain enhancement to a reasonable range ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_dstint_intp2 - ss_alb_snw_lcl(i) = max(0._r8, min(ss_alb_snw_lcl(i),1._r8)) + ss_alb_snw_lcl(i) = max(0.5_r8, min(ss_alb_snw_lcl(i),1._r8)) ! reset all dust optics to zero since it is accounted by updated snow ss_alb above ss_alb_aer_lcl(5:8) = 0._r8 asm_prm_aer_lcl(5:8) = 0._r8 ext_cff_mss_aer_lcl(5:8) = 0._r8 - endif ! end if wvl_doint2 <= 1.2 - endif ! end if dust-snow internal mixing + endif ! end if dust-snow internal mixing + + endif ! end if BC/dust-snow internal mixing (bands<1.2um) L_snw(i) = h2osno_ice_lcl(i)+h2osno_liq_lcl(i) @@ -1148,7 +1166,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & tau(i) = tau_sum + tau_snw(i) omega(i) = (1/tau(i))*(omega_sum+(ss_alb_snw_lcl(i)*tau_snw(i))) g(i) = (1/(tau(i)*omega(i)))*(g_sum+ (asm_prm_snw_lcl(i)*ss_alb_snw_lcl(i)*tau_snw(i))) - enddo + + enddo ! end do snow layers ! DELTA transformations, if requested if (DELTA == 1) then From a0a66abb1226b8f4377176562257d6ff6004fd49 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 31 Jan 2022 11:33:23 -0700 Subject: [PATCH 0118/2067] ESMF cropcalStreamMod now skips non-crop PFTs (incl. generic crops). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 28 +++++++++++++++---------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index ceee449e41..7075dd00d8 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -16,6 +16,7 @@ module cropcalStreamMod use clm_varpar , only : mxpft use perf_mod , only : t_startf, t_stopf use spmdMod , only : masterproc, mpicom, iam + use pftconMod , only : npcropmin ! ! !PUBLIC TYPES: implicit none @@ -32,6 +33,7 @@ module cropcalStreamMod type(shr_strdata_type) :: sdat_cropcal_cultivar_gdds ! sdate input data stream character(len=CS) :: stream_varnames_sdate(mxpft) character(len=CS) :: stream_varnames_cultivar_gdds(mxpft) + integer :: ncft ! Number of crop functional types (excl. generic crops) character(len=*), parameter :: sourcefile = & __FILE__ @@ -55,7 +57,7 @@ subroutine cropcal_init(bounds) type(bounds_type), intent(in) :: bounds ! bounds ! ! !LOCAL VARIABLES: - integer :: i,n ! index + integer :: i,n,ivt ! index integer :: stream_year_first_cropcal ! first year in crop calendar streams to use integer :: stream_year_last_cropcal ! last year in crop calendar streams to use integer :: model_year_align_cropcal ! align stream_year_first_cropcal with @@ -89,9 +91,11 @@ subroutine cropcal_init(bounds) stream_fldFileName_sdate = '' stream_fldFileName_cultivar_gdds = '' ! SSR TODO: Make below work with arbitrary # of growing seasons per year - do n = 1,mxpft - write(stream_varnames_sdate(n),'(a,i0)') "sdate1",n - write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1",n + ncft = mxpft - npcropmin + 1 ! Ignores generic crops + do n = 1,ncft + ivt = npcropmin + n - 1 + write(stream_varnames_sdate(n),'(a,i0)') "sdate1",ivt + write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1",ivt end do ! Read cropcal_streams namelist @@ -236,7 +240,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Interpolate data stream information for crop calendars. ! ! !USES: - use pftconMod , only : noveg use CropType , only : crop_type use PatchType , only : patch use dshr_methods_mod , only : dshr_fldbun_getfldptr @@ -267,9 +270,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Get pointer for stream data that is time and spatially interpolate to model time and grid ! Place all data from each type into a temporary 2d array lsize = bounds%endg - bounds%begg + 1 - allocate(dataptr2d_sdate(lsize, mxpft)) - allocate(dataptr2d_cultivar_gdds(lsize, mxpft)) - do n = 1,mxpft + allocate(dataptr2d_sdate(lsize, ncft)) + allocate(dataptr2d_cultivar_gdds(lsize, ncft)) + ! Starting with npcropmin will skip generic crops + do n = 1, ncft call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & fldptr1=dataptr1d_sdate, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -291,11 +295,13 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Set rx_sdate and rx_cultivar_gdd for each gridcell/patch combination do p = bounds%begp, bounds%endp ivt = patch%itype(p) - if (ivt /= noveg) then + ! Will skip generic crops + if (ivt >= npcropmin) then + n = ivt - npcropmin + 1 ! vegetated pft ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,ivt) - crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,ivt) + crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) + crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) ! Only for first sowing date of the year crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) From b647059ce57836a37efff4315695c1a6fc358487 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 31 Jan 2022 12:09:39 -0700 Subject: [PATCH 0119/2067] Fixed variable names in ESMF cropcalStreamMod. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 7075dd00d8..31a73ab350 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -94,8 +94,8 @@ subroutine cropcal_init(bounds) ncft = mxpft - npcropmin + 1 ! Ignores generic crops do n = 1,ncft ivt = npcropmin + n - 1 - write(stream_varnames_sdate(n),'(a,i0)') "sdate1",ivt - write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1",ivt + write(stream_varnames_sdate(n),'(a,i0)') "sdate1_",ivt + write(stream_varnames_cultivar_gdds(n),'(a,i0)') "gdd1_",ivt end do ! Read cropcal_streams namelist From e262423fcc873cda1b99729fbfd0e48d6eea20f2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 31 Jan 2022 12:28:46 -0700 Subject: [PATCH 0120/2067] Corrected length of varname lists in ESMF cropcalStreamMod. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 31a73ab350..8f9d571552 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -31,8 +31,8 @@ module cropcalStreamMod integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream type(shr_strdata_type) :: sdat_cropcal_cultivar_gdds ! sdate input data stream - character(len=CS) :: stream_varnames_sdate(mxpft) - character(len=CS) :: stream_varnames_cultivar_gdds(mxpft) + character(len=CS), allocatable :: stream_varnames_sdate(:) + character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:) integer :: ncft ! Number of crop functional types (excl. generic crops) character(len=*), parameter :: sourcefile = & @@ -92,6 +92,8 @@ subroutine cropcal_init(bounds) stream_fldFileName_cultivar_gdds = '' ! SSR TODO: Make below work with arbitrary # of growing seasons per year ncft = mxpft - npcropmin + 1 ! Ignores generic crops + allocate(stream_varnames_sdate(ncft)) + allocate(stream_varnames_cultivar_gdds(ncft)) do n = 1,ncft ivt = npcropmin + n - 1 write(stream_varnames_sdate(n),'(a,i0)') "sdate1_",ivt From b0bd65aa089cee83cc02b0ed7411e750fa984521 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 31 Jan 2022 14:35:23 -0700 Subject: [PATCH 0121/2067] Bug fix (and error checks) that resulted in unset next_rx_sdate after first year. --- src/biogeochem/CNPhenologyMod.F90 | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 6c5e579b4d..d769c54c81 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1792,16 +1792,31 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 end do + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) end if ! When resuming from a run with old code, may need to manually set these if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then sowing_count(p) = 1 crop_inst%sdates_thisyr(p,1) = 1._r8 + if (sowing_count(p) < mxgrowseas) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,2) + end if end if do_plant_prescribed = next_rx_sdate(p) == jday s = sowing_count(p) + + if (generate_crop_gdds) then + if (s==0 .and. next_rx_sdate(p)<=0) then + write(iulog,"(A,I4)") 'If using generate_crop_gdds, all simulated patches must have rx sdate. next_rx_sdate(p) <=0. PFT ',ivt(p) + call endrun(msg=errMsg(sourcefile, __LINE__)) + else if (s==0 .and. crop_inst%rx_sdates_thisyr(p,1)<=0) then + write(iulog,"(A,I4)") 'If using generate_crop_gdds, all simulated patches must have rx sdate. rx_sdates_thisyr(p,1) <=0. PFT ',ivt(p) + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + end if + ! Once outputs can handle >1 planting per year, remove 2nd condition. if ( (.not. croplive(p)) .and. s == 0 ) then From f62e93591ffa948015dadd53c1d1d1c8e206b28b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 31 Jan 2022 16:13:36 -0700 Subject: [PATCH 0122/2067] Attempting to avoid planting on last timestep of Dec. 31 when sowing window starts (or prescribed sowing date is) Jan. 1. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d769c54c81..6a60d47a85 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1754,7 +1754,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! get time info dayspyr = get_curr_days_per_year() - jday = get_curr_calday() + jday = get_curr_calday(offset = -1) dtrad = real( get_rad_step_size(), r8 ) if (use_fertilizer) then From d2431c04f1416feaa3f284d24515954181f4863c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 31 Jan 2022 16:36:01 -0700 Subject: [PATCH 0123/2067] Force harvest on Jan. 1 if current crop was incorrectly planted on Dec. 31. --- src/biogeochem/CNPhenologyMod.F90 | 32 ++++++++++++++++++------------- 1 file changed, 19 insertions(+), 13 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 6a60d47a85..e6a475a520 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1694,6 +1694,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical allow_unprescribed_planting ! should crop be allowed to be planted according to sowing window rules? logical do_harvest ! Are harvest conditions satisfied? logical force_harvest ! Should we harvest today no matter what? + logical fake_harvest ! Dealing with incorrect Dec. 31 planting !------------------------------------------------------------------------ associate( & @@ -1795,15 +1796,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) end if - ! When resuming from a run with old code, may need to manually set these - if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then - sowing_count(p) = 1 - crop_inst%sdates_thisyr(p,1) = 1._r8 - if (sowing_count(p) < mxgrowseas) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,2) - end if - end if - do_plant_prescribed = next_rx_sdate(p) == jday s = sowing_count(p) @@ -2035,7 +2027,16 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hui(p) = max(hui(p),huigrain(p)) endif - if (do_plant_prescribed) then + do_harvest = .false. + force_harvest = .false. + fake_harvest = .false. + + if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then + ! Crop was incorrectly planted in last time step of Dec. 31. + do_harvest = .true. + force_harvest = .true. + fake_harvest = .true. + else if (do_plant_prescribed) then ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. @@ -2089,9 +2090,14 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! changes to the offset subroutine below else if (do_harvest) then - if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday - harvest_count(p) = harvest_count(p) + 1 - crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + ! Don't update these if you're just harvesting because of incorrect Dec. + ! 31 planting + if (.not. fake_harvest) then + if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday + harvest_count(p) = harvest_count(p) + 1 + crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + endif + croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 if (tlai(p) > 0._r8) then ! plant had emerged before harvest From 9d5fee6ad1f1de3ab3ade7423184e00151e2bef6 Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Mon, 31 Jan 2022 22:38:44 -0700 Subject: [PATCH 0124/2067] update 5-band input optics database & move DO_SNO_OC to namelist control --- .../namelist_definition_ctsm.xml | 3 - src/biogeophys/SnowSnicarMod.F90 | 797 +++++++++++++++--- src/biogeophys/SurfaceAlbedoMod.F90 | 4 +- src/biogeophys/SurfaceRadiationMod.F90 | 4 +- src/main/clm_varctl.F90 | 8 +- src/main/controlMod.F90 | 26 +- 6 files changed, 679 insertions(+), 163 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 51264f7b58..baa18b77dc 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -168,19 +168,16 @@ number of wavelength bands used in SNICAR snow albedo calculation type of downward solar radiation spectrum for SNICAR snow albedo calculation -(only used in 480-band version) snow optics type using different refractive index databases in SNICAR -(only used in 480-band version) dust optics type for SNICAR snow albedo calculation -(only used in 480-band version) shr_log_errMsg use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver, & snicar_snw_shape, snicar_snobc_intmix, & - snicar_snodst_intmix ! cenlin + snicar_snodst_intmix, DO_SNO_OC ! cenlin use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -48,8 +48,9 @@ module SnowSnicarMod ! !PUBLIC DATA MEMBERS: integer, public, parameter :: sno_nbr_aer = 8 ! number of aerosol species in snowpack ! (indices described above) [nbr] - logical, public, parameter :: DO_SNO_OC = .false. ! parameter to include organic carbon (OC) - ! in snowpack radiative calculations + ! DO_SNO_OC moved to namelist control + !logical, public, parameter :: DO_SNO_OC = .false. ! parameter to include organic carbon (OC) + ! ! in snowpack radiative calculations logical, public, parameter :: DO_SNO_AER = .true. ! parameter to include aerosols in snowpack radiative calculations ! !PRIVATE DATA MEMBERS: @@ -141,9 +142,9 @@ module SnowSnicarMod real(r8), pointer :: asm_prm_dst4(:) !(numrad_snw) real(r8), pointer :: ext_cff_mss_dst4(:) !(numrad_snw) - ! downward solar radiation spectral weights for 480-band - real(r8), pointer :: flx_wgt_dir480(:) !(numrad_snw) ! direct - real(r8), pointer :: flx_wgt_dif480(:) !(numrad_snw) ! diffuse + ! downward solar radiation spectral weights for 5-band or 480-band + real(r8), pointer :: flx_wgt_dir(:) !(numrad_snw) ! direct + real(r8), pointer :: flx_wgt_dif(:) !(numrad_snw) ! diffuse ! best-fit parameters for snow aging defined over: ! 11 temperatures from 225 to 273 K @@ -544,7 +545,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ) ! initialize parameter, cenlin - nir_bnd_bgn = nint(snicar_numrad_snw/9.6) + 1 ! 5-band starts at 2; 480-band starts at 51 + if (snicar_numrad_snw == 5) nir_bnd_bgn = 2 + if (snicar_numrad_snw == 480) nir_bnd_bgn = 51 nir_bnd_end = snicar_numrad_snw ! initialize for adding-doubling solver @@ -705,7 +707,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Set spectral underlying surface albedos to their corresponding VIS or NIR albedos - albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) ! cenlin: update for hyperspectral calculation + albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) ! cenlin albsfc_lcl(nir_bnd_bgn:nir_bnd_end) = albsfc(c_idx,2) @@ -734,8 +736,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Band 4: 1.2-1.5um (NIR) ! Band 5: 1.5-5.0um (NIR) ! - ! Updated hyperspectral (10-nm) bands (480-band case) cenlin - ! Bands 1~50 : 0.2-0.7um (VIS); near-UV (0.2-0.3um) is combined to VIS for now + ! Hyperspectral (10-nm) bands (480-band case) cenlin + ! Bands 1~50 : 0.2-0.7um (VIS) ! Bands 51~480: 0.7~5.0um (NIR) ! ! The following weights are appropriate for surface-incident flux in a mid-latitude winter atmosphere @@ -753,33 +755,30 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & flx_wgt(2) = 0.77887652162877_r8 flx_wgt(3) = 0.22112347837123_r8 endif - ! 5-band weights - elseif (snicar_numrad_snw==5) then - ! Direct: - if (flg_slr_in == 1) then - flx_wgt(1) = 1._r8 - flx_wgt(2) = 0.49352158521175_r8 - flx_wgt(3) = 0.18099494230665_r8 - flx_wgt(4) = 0.12094898498813_r8 - flx_wgt(5) = 0.20453448749347_r8 - ! Diffuse: - elseif (flg_slr_in == 2) then - flx_wgt(1) = 1._r8 - flx_wgt(2) = 0.58581507618433_r8 - flx_wgt(3) = 0.20156903770812_r8 - flx_wgt(4) = 0.10917889346386_r8 - flx_wgt(5) = 0.10343699264369_r8 - endif - - ! 480-band weights, cenlin - elseif (snicar_numrad_snw == 480) then + !elseif (snicar_numrad_snw==5) then + ! ! Direct: + ! if (flg_slr_in == 1) then + ! flx_wgt(1) = 1._r8 + ! flx_wgt(2) = 0.49352158521175_r8 + ! flx_wgt(3) = 0.18099494230665_r8 + ! flx_wgt(4) = 0.12094898498813_r8 + ! flx_wgt(5) = 0.20453448749347_r8 + ! ! Diffuse: + ! elseif (flg_slr_in == 2) then + ! flx_wgt(1) = 1._r8 + ! flx_wgt(2) = 0.58581507618433_r8 + ! flx_wgt(3) = 0.20156903770812_r8 + ! flx_wgt(4) = 0.10917889346386_r8 + ! flx_wgt(5) = 0.10343699264369_r8 + ! endif + else ! works for both 5-band & 480-band, flux weights directly read from input data, cenlin ! Direct: if (flg_slr_in == 1) then - flx_wgt(1:snicar_numrad_snw) = flx_wgt_dir480(1:snicar_numrad_snw) ! either VIS or NIR band sum is 1.0 in the input dataset + flx_wgt(1:snicar_numrad_snw) = flx_wgt_dir(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data ! Diffuse: elseif (flg_slr_in == 2) then - flx_wgt(1:snicar_numrad_snw) = flx_wgt_dif480(1:snicar_numrad_snw) ! either VIS or NIR band sum is 1.0 in the input dataset + flx_wgt(1:snicar_numrad_snw) = flx_wgt_dif(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data endif endif ! end if snicar_numrad_snw @@ -976,6 +975,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & if (sno_shp(i) > 1) then ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here ! use the piecewise linear interpolation subroutine created at the end of this module + ! tests showed the piecewise linear interpolation has similar results as pchip interpolation if (snicar_numrad_snw == 5) then call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct5(bnd_idx),g_Cg_intp) call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct5(bnd_idx),gg_F07_intp) @@ -1063,7 +1063,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) - ! Start BC/dust-snow internal mixing for wavelength<=1.2um if (snicar_numrad_snw == 5) wvl_doint = wvl_ct5(bnd_idx) if (snicar_numrad_snw == 480) wvl_doint = wvl_ct480(bnd_idx) @@ -1144,7 +1143,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif ! end if BC/dust-snow internal mixing (bands<1.2um) - L_snw(i) = h2osno_ice_lcl(i)+h2osno_liq_lcl(i) tau_snw(i) = L_snw(i)*ext_cff_mss_snw_lcl(i) @@ -2215,7 +2213,7 @@ subroutine SnowOptics_init( ) integer :: ier ! error status ! - ! Open optics file: + ! Initialize optical variables allocate(ss_alb_snw_drc(idx_Mie_snw_mx,snicar_numrad_snw)) allocate(asm_prm_snw_drc(idx_Mie_snw_mx,snicar_numrad_snw)) allocate(ext_cff_mss_snw_drc(idx_Mie_snw_mx,snicar_numrad_snw)) @@ -2246,78 +2244,630 @@ subroutine SnowOptics_init( ) allocate(ss_alb_dst4(snicar_numrad_snw)) allocate(asm_prm_dst4(snicar_numrad_snw)) allocate(ext_cff_mss_dst4(snicar_numrad_snw)) - allocate(flx_wgt_dir480(snicar_numrad_snw)) - allocate(flx_wgt_dif480(snicar_numrad_snw)) + allocate(flx_wgt_dir(snicar_numrad_snw)) + allocate(flx_wgt_dif(snicar_numrad_snw)) if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....' - ! for 5-band data, cenlin - if (snicar_numrad_snw <= 5) then + + !--------------------- for 5-band data, cenlin + if (snicar_numrad_snw == 5) then + call getfil (fsnowoptics, locfn, 0) call ncd_pio_openfile(ncid, locfn, 0) if(masterproc) write(iulog,*) subname,trim(fsnowoptics) - end if - ! for 480-band data, cenlin - if (snicar_numrad_snw == 480) then - call getfil (fsnowoptics480, locfn, 0) - call ncd_pio_openfile(ncid, locfn, 0) - if(masterproc) write(iulog,*) subname,trim(fsnowoptics480) - end if - if (snicar_numrad_snw <= 5) then - ! direct-beam snow Mie parameters: - call ncd_io( 'ss_alb_ice_drc', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_drc',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_drc', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - - ! diffuse snow Mie parameters - call ncd_io( 'ss_alb_ice_dfs', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_dfs', asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_dfs', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - - ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) - - ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) - - ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) - - ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + ! mid-latitude winter spectrum + if (snicar_solarspec == 1) then + ! flux weights/spectrum + call ncd_io( 'flx_wgt_dir5_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif5_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob_dif_mlw', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_mlw', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob_dif_mlw', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_mlw', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob_dif_mlw', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_mlw', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob_dif_mlw', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_mlw', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! ice refractive index options + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah_dif_mlw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah_dif_mlw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah_dif_mlw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah_dif_mlw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah_dif_mlw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah_dif_mlw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah_dif_mlw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col_dif_mlw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col_dif_mlw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col_dif_mlw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col_dif_mlw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col_dif_mlw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col_dif_mlw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col_dif_mlw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre_dif_mlw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre_dif_mlw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre_dif_mlw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre_dif_mlw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre_dif_mlw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre_dif_mlw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre_dif_mlw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif - ! BC species 1 Mie parameters, uncoated BC, same as bc2 without BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! mid-latitude summer spectrum + elseif (snicar_solarspec == 2) then + ! flux weights/spectrum + call ncd_io( 'flx_wgt_dir5_mls', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif5_mls', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob_dif_mls', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_mls', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob_dif_mls', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_mls', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob_dif_mls', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_mls', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob_dif_mls', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_mls', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! ice refractive index options + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah_dif_mls', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah_dif_mls', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah_dif_mls', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah_dif_mls', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah_dif_mls', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah_dif_mls', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah_dif_mls', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col_dif_mls', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col_dif_mls', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col_dif_mls', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col_dif_mls', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col_dif_mls', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col_dif_mls', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col_dif_mls', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre_dif_mls', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre_dif_mls', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre_dif_mls', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre_dif_mls', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre_dif_mls', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre_dif_mls', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre_dif_mls', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif - ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! sub-Arctic winter spectrum + elseif (snicar_solarspec == 3) then + call ncd_io( 'flx_wgt_dir5_saw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif5_saw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob_dif_saw', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_saw', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob_dif_saw', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_saw', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob_dif_saw', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_saw', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob_dif_saw', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_saw', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! ice refractive index options + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah_dif_saw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah_dif_saw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah_dif_saw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah_dif_saw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah_dif_saw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah_dif_saw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah_dif_saw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col_dif_saw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col_dif_saw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col_dif_saw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col_dif_saw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col_dif_saw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col_dif_saw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col_dif_saw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre_dif_saw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre_dif_saw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre_dif_saw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre_dif_saw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre_dif_saw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre_dif_saw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre_dif_saw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif + + ! sub-Arctic summer spectrum + elseif (snicar_solarspec == 4) then + call ncd_io( 'flx_wgt_dir5_sas', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif5_sas', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob_dif_sas', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_sas', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob_dif_sas', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_sas', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob_dif_sas', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_sas', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob_dif_sas', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_sas', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! ice refractive index options + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah_dif_sas', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah_dif_sas', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah_dif_sas', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah_dif_sas', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah_dif_sas', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah_dif_sas', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah_dif_sas', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col_dif_sas', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col_dif_sas', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col_dif_sas', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col_dif_sas', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col_dif_sas', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col_dif_sas', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col_dif_sas', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre_dif_sas', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre_dif_sas', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre_dif_sas', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre_dif_sas', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre_dif_sas', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre_dif_sas', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre_dif_sas', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif - ! OC species 1 Mie parameters, uncoated OC, same as oc2 without OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! Summit,Greenland,summer spectrum + elseif (snicar_solarspec == 5) then + call ncd_io( 'flx_wgt_dir5_smm', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif5_smm', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob_dif_smm', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_smm', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob_dif_smm', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_smm', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob_dif_smm', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_smm', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob_dif_smm', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_smm', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! ice refractive index options + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah_dif_smm', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah_dif_smm', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah_dif_smm', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah_dif_smm', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah_dif_smm', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah_dif_smm', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah_dif_smm', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col_dif_smm', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col_dif_smm', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col_dif_smm', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col_dif_smm', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col_dif_smm', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col_dif_smm', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col_dif_smm', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre_dif_smm', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre_dif_smm', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre_dif_smm', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre_dif_smm', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre_dif_smm', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre_dif_smm', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre_dif_smm', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif - ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! High Mountain summer spectrum + elseif (snicar_solarspec == 6) then + call ncd_io( 'flx_wgt_dir5_hmn', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif5_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob_dif_hmn', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_hmn', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob_dif_hmn', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob_dif_hmn', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob_dif_hmn', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_hmn', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob_dif_hmn', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob_dif_hmn', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! ice refractive index options + if (snicar_snw_optics == 1) then ! Warren (1984) + call ncd_io( 'ss_alb_ice_wrn84_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn84_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn84_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn84_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) + call ncd_io( 'ss_alb_ice_wrn08_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_wrn08_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_wrn08_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_wrn08_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_snw_optics == 3) then ! Picard et al (2016) + call ncd_io( 'ss_alb_ice_pic16_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + endif + ! dust optical properties + if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_sah_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_sah_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_sah_dif_hmn', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_sah_dif_hmn', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_sah_dif_hmn', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_sah_dif_hmn', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_sah_dif_hmn', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_sah_dif_hmn', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_sah_dif_hmn', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_sah_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_sah_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_sah_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_col_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_col_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_col_dif_hmn', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_col_dif_hmn', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_col_dif_hmn', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_col_dif_hmn', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_col_dif_hmn', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_col_dif_hmn', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_col_dif_hmn', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_col_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_col_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_col_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + ! dust species 1 Mie parameters + call ncd_io( 'ss_alb_dust01_gre_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust01_gre_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust01_gre_dif_hmn', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + ! dust species 2 Mie parameters + call ncd_io( 'ss_alb_dust02_gre_dif_hmn', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust02_gre_dif_hmn', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust02_gre_dif_hmn', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + ! dust species 3 Mie parameters + call ncd_io( 'ss_alb_dust03_gre_dif_hmn', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust03_gre_dif_hmn', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust03_gre_dif_hmn', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + ! dust species 4 Mie parameters + call ncd_io( 'ss_alb_dust04_gre_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_dust04_gre_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_dust04_gre_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + endif + endif ! end of snicar_solarspec - ! new data for 480-band + end if ! end if snicar_numrad_snw == 5 + + + !-------------------- for 480-band data, cenlin if (snicar_numrad_snw == 480) then + call getfil (fsnowoptics480, locfn, 0) + call ncd_pio_openfile(ncid, locfn, 0) + if(masterproc) write(iulog,*) subname,trim(fsnowoptics480) + + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + call ncd_io( 'ss_alb_bcphob', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + ! BC species 2 Mie parameters, uncoated BC + call ncd_io( 'ss_alb_bcphob', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_bcphob', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + call ncd_io( 'ss_alb_ocphob', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + ! OC species 2 Mie parameters, uncoated OC + call ncd_io( 'ss_alb_ocphob', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ocphob', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + ! snow optical properties derived from different ice refractive index dataset ! same value for direct and diffuse due to high spectral res without spectra averaging in database if (snicar_snw_optics == 1) then ! Warren (1984) @@ -2341,15 +2891,6 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - else - write(iulog,*) 'invalid snow optics type option in namelist' - ! for invalid spectrum type, use Picard et al (2016) (default) - call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) endif ! dust optical properties @@ -2404,54 +2945,30 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - else - write(iulog,*) 'invalid dust optics type option in namelist' - ! for invalid dust optics type, use Saharan dust (default) - ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) - ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) - ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) - ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) endif ! downward solar radiation spectral weights for 480-band if (snicar_solarspec == 1) then ! mid-latitude winter - call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) elseif (snicar_solarspec == 2) then ! mid-latitude summer - call ncd_io( 'flx_wgt_dir480_mls', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_mls', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dir480_mls', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_mls', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) elseif (snicar_solarspec == 3) then ! sub-Arctic winter - call ncd_io( 'flx_wgt_dir480_saw', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_saw', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dir480_saw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_saw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) elseif (snicar_solarspec == 4) then ! sub-Arctic summer - call ncd_io( 'flx_wgt_dir480_sas', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_sas', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dir480_sas', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_sas', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) elseif (snicar_solarspec == 5) then ! Summit,Greenland,summer - call ncd_io( 'flx_wgt_dir480_smm', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_smm', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dir480_smm', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_smm', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) elseif (snicar_solarspec == 6) then ! High Mountain summer - call ncd_io( 'flx_wgt_dir480_hmn', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_hmn', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) - else - write(iulog,*) 'invalid downward solar radiation spectrum option in namelist' - ! for invalid spectrum type, use mid-latitude winter (default) - call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir480, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif480, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dir480_hmn', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'flx_wgt_dif480_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) endif - endif + endif ! end if snicar_numrad_snw == 480 call ncd_pio_closefile(ncid) if (masterproc) then diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index df92dbcb41..6aff5dada4 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -14,9 +14,9 @@ module SurfaceAlbedoMod use landunit_varcon , only : istsoil, istcrop, istdlak use clm_varcon , only : grlnd, spval ! cenlin use clm_varpar , only : numrad, nlevcan, nlevsno, nlevcan - use clm_varctl , only : fsurdat, iulog, use_snicar_frc, use_SSRE + use clm_varctl , only : fsurdat, iulog, use_snicar_frc, use_SSRE, DO_SNO_OC !cenlin use pftconMod , only : pftcon - use SnowSnicarMod , only : sno_nbr_aer, SNICAR_RT, DO_SNO_AER, DO_SNO_OC + use SnowSnicarMod , only : sno_nbr_aer, SNICAR_RT, DO_SNO_AER use AerosolMod , only : aerosol_type use CanopyStateType , only : canopystate_type use LakeStateType , only : lakestate_type diff --git a/src/biogeophys/SurfaceRadiationMod.F90 b/src/biogeophys/SurfaceRadiationMod.F90 index 5378e6315c..5a00a67b23 100644 --- a/src/biogeophys/SurfaceRadiationMod.F90 +++ b/src/biogeophys/SurfaceRadiationMod.F90 @@ -477,9 +477,9 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & use clm_varpar , only : numrad, nlevsno use clm_varcon , only : spval use landunit_varcon , only : istsoil, istcrop - use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, iulog, use_SSRE + use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, iulog, use_SSRE, DO_SNO_OC !cenlin use clm_time_manager , only : get_step_size_real, is_near_local_noon - use SnowSnicarMod , only : DO_SNO_OC + ! use SnowSnicarMod , only : DO_SNO_OC use abortutils , only : endrun ! ! !ARGUMENTS: diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index d8a56384eb..eaae254593 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -209,14 +209,14 @@ module clm_varctl ! number of wavelength bands used in SNICAR snow albedo calculation, cenlin integer, public :: snicar_numrad_snw = 5 - ! type of downward solar radiation spectrum for SNICAR snow albedo calculation (only used in 480-band version), cenlin + ! type of downward solar radiation spectrum for SNICAR snow albedo calculation cenlin integer, public :: snicar_solarspec = 1 ! 1->mid-latitude winter;2->mid-latitude summer;3->sub-Arctic winter; ! 4->sub-Arctic summer;5->Summit,Greenland,summer;6->High Mountain summer; - ! snow optics type using different refractive index databases in SNICAR (only used in 480-band version), cenlin + ! snow optics type using different refractive index databases in SNICAR, cenlin integer, public :: snicar_snw_optics = 3 ! 1->Warren (1984);2->Warren and Brandt (2008);3->Picard et al (2016) - ! dust optics type for SNICAR snow albedo calculation (only used in 480-band version), cenlin + ! dust optics type for SNICAR snow albedo calculation, cenlin integer, public :: snicar_dust_optics = 1 ! 1->Saharan dust (Balkanski et al., 2007, central hematite) ! 2->San Juan Mountains dust, CO (Skiles et al, 2017) ! 3->Greenland dust (Polashenski et al., 2015, central absorptivity) @@ -236,6 +236,8 @@ module clm_varctl ! option to activate dust-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln logical, public :: snicar_snodst_intmix = .false. ! false->external mixing for all dust; true->internal mixing for all dust + ! option to activate OC in snow in SNICAR, cenlin + logical, public :: DO_SNO_OC = .false. ! control to include organic carbon (OC) in snow !---------------------------------------------------------- ! C isotopes diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 195356b77f..a59dee79c9 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -204,7 +204,7 @@ subroutine control_init(dtime) crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & snicar_numrad_snw, snicar_solarspec, snicar_snw_optics, snicar_dust_optics, & snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape, snicar_snobc_intmix,& - snicar_snodst_intmix ! cenlin + snicar_snodst_intmix,DO_SNO_OC ! cenlin ! vertical soil mixing variables namelist /clm_inparm/ & @@ -842,6 +842,7 @@ subroutine control_spmd() call mpi_bcast (snicar_snw_shape, 1, MPI_INTEGER, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin call mpi_bcast (snicar_snodst_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin + call mpi_bcast (DO_SNO_OC, 1, MPI_LOGICAL, 0, mpicom, ier) ! cenlin ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1016,24 +1017,23 @@ subroutine control_print () write(iulog,*) ' snow aging parameters file = ',trim(fsnowaging) endif ! cenlin - if (snicar_numrad_snw==480) then - if (fsnowoptics480 == ' ') then - write(iulog,*) ' SNICAR: snow optical properties (480-band) file NOT set' - else - write(iulog,*) ' SNICAR: snow optical properties (480-band) file = ',trim(fsnowoptics480) - endif - write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec - write(iulog,*) ' SNICAR: snow refractive index type = ', snicar_snw_optics - write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics + if (fsnowoptics480 == ' ') then + write(iulog,*) ' SNICAR: snow optical properties (480-band) file NOT set' + else + write(iulog,*) ' SNICAR: snow optical properties (480-band) file = ',trim(fsnowoptics480) endif - - write(iulog,*) ' Number of snow layers =', nlevsno - write(iulog,*) ' Max snow depth (mm) =', h2osno_max + write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec + write(iulog,*) ' SNICAR: snow refractive index type = ', snicar_snw_optics + write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw ! cenlin write(iulog,*) ' SNICAR: radiative transfer solver type = ',snicar_rt_solver ! cenlin write(iulog,*) ' SNICAR: snow grain shape type = ',snicar_snw_shape ! cenlin write(iulog,*) ' SNICAR: BC-snow internal mixing = ', snicar_snobc_intmix ! cenlin write(iulog,*) ' SNICAR: dust-snow internal mixing = ', snicar_snodst_intmix ! cenlin + write(iulog,*) ' SNICAR: OC in snow = ', DO_SNO_OC ! cenlin + + write(iulog,*) ' Number of snow layers =', nlevsno + write(iulog,*) ' Max snow depth (mm) =', h2osno_max write(iulog,*) ' glc number of elevation classes =', maxpatch_glc if (glc_do_dynglacier) then From a6e168e5876da60b555b4eba2ba37f25cd986db0 Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Mon, 31 Jan 2022 23:14:59 -0700 Subject: [PATCH 0125/2067] add DO_SNO_OC to namelist_definition_ctsm --- bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index baa18b77dc..853892b90b 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -205,6 +205,11 @@ option to activate BC-snow internal mixing in SNICAR snow albedo calculation option to activate dust-snow internal mixing in SNICAR snow albedo calculation + +option to activate organic carbon (OC) in SNICAR snow albedo calculation + + Index of rooting profile for water From 6ccb36bf06c34cac507f9baf448eaf35c6b361c3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 1 Feb 2022 15:17:01 -0700 Subject: [PATCH 0126/2067] Bugfix preventing crops planted Jan. 1 from being harvested that same day. Not sure why this is needed! --- src/biogeochem/CNPhenologyMod.F90 | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e6a475a520..25a41e49d5 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1796,8 +1796,18 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) end if - do_plant_prescribed = next_rx_sdate(p) == jday s = sowing_count(p) + + ! SSR: I don't know why this is necessary. next_rx_sdate should get properly set in PlantCrop() + ! or above, but sometimes (NOT in first year after restart) I'm seeing crops planted Jan. 1 that + ! are harvested the same day. This (specifically, the second condition) fixes that. + if (s < mxgrowseas) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,s+1) + else + next_rx_sdate(p) = -1 + end if + + do_plant_prescribed = next_rx_sdate(p) == jday if (generate_crop_gdds) then if (s==0 .and. next_rx_sdate(p)<=0) then From 2a09e77e3f8924b15a691cf294b2c5df5f054b7c Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 2 Feb 2022 16:28:36 +0100 Subject: [PATCH 0127/2067] improved initialization --- src/biogeophys/WaterStateType.F90 | 44 ++++++++++++++++++------------- 1 file changed, 26 insertions(+), 18 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 90e68ab5a3..4c0575c8b7 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -164,15 +164,15 @@ subroutine InitAllocate(this, bounds, tracer_vars) call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = 1, dim2end = nlevgrnd) + dim2beg = 1, dim2end = nlevmaxurbgrnd) call AllocateVar2d(var = this%init_exice, name = 'init_exice', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = 1, dim2end = nlevgrnd) + dim2beg = 1, dim2end = nlevmaxurbgrnd) call AllocateVar2d(var = this%exice_melt_lev, name = 'exice_melt_lev', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = 1, dim2end = nlevgrnd) + dim2beg = 1, dim2end = nlevmaxurbgrnd) call AllocateVar1d(var = this%exice_melt, name = 'exice_melt', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) @@ -550,7 +550,12 @@ subroutine InitCold(this, bounds, & !Initialize excess ice write(iulog,*) 'nfl =', NLFilename if (use_excess_ice .and. NLFilename /= '') then - + ! enforce initialization with 0 for everything + this%init_exice(:,:)=0.0_r8 + this%excess_ice_col(:,:)=0.0_r8 + this%exice_melt_lev(:,:)=0.0_r8 + this%exice_melt(:)=0.0_r8 + call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column do c = bounds%begc,bounds%endc @@ -558,22 +563,25 @@ subroutine InitCold(this, bounds, & l = col%landunit(c) if (.not. lun%lakpoi(l)) then !not lake if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (use_bedrock) then - nbedrock = col%nbedrock(c) - else - nbedrock = nlevsoi - endif - do j = 1, nlevgrnd - if (j Date: Wed, 2 Feb 2022 16:29:13 +0100 Subject: [PATCH 0128/2067] add excess ice to soil temperature mod --- src/biogeophys/SoilTemperatureMod.F90 | 129 ++++++++++++++++++++++++-- 1 file changed, 120 insertions(+), 9 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index ba4432cba2..3647534334 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -115,7 +115,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd use clm_varctl , only : iulog - use clm_varcon , only : cnfac, cpice, cpliq, denh2o + use clm_varcon , only : cnfac, cpice, cpliq, denh2o, denice use landunit_varcon , only : istsoil, istcrop use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv use BandDiagonalMod , only : BandDiagonal @@ -171,6 +171,10 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter real(r8) :: hs_top_snow(bounds%begc:bounds%endc) ! heat flux on top snow layer [W/m2] real(r8) :: hs_h2osfc(bounds%begc:bounds%endc) ! heat flux on standing water [W/m2] integer :: jbot(bounds%begc:bounds%endc) ! bottom level at each column + real(r8) :: dz_0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! original layer thickness [m] + real(r8) :: z_0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! original layer depth [m] + real(r8) :: zi_0(bounds%begc:bounds%endc,-nlevsno+0:nlevmaxurbgrnd) ! original layer interface level bellow layer "z" [m] + !----------------------------------------------------------------------- associate( & @@ -194,6 +198,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter frac_sno_eff => waterdiagnosticbulk_inst%frac_sno_eff_col , & ! Input: [real(r8) (:) ] eff. fraction of ground covered by snow (0 to 1) snow_depth => waterdiagnosticbulk_inst%snow_depth_col , & ! Input: [real(r8) (:) ] snow height (m) h2osfc => waterstatebulk_inst%h2osfc_col , & ! Input: [real(r8) (:) ] surface water (mm) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col , & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) @@ -271,6 +276,29 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter endif end do + + !-------------------------------------------------------------- + ! Vertical coordinates adjustment for excess ice calculations + !-------------------------------------------------------------- + ! Save original soil depth to get put them back in et the end + dz_0(begc:endc,1:nlevmaxurbgrnd)=dz(begc:endc,1:nlevmaxurbgrnd) + zi_0(begc:endc,1:nlevmaxurbgrnd)=zi(begc:endc,1:nlevmaxurbgrnd) + z_0(begc:endc,1:nlevmaxurbgrnd)=z(begc:endc,1:nlevmaxurbgrnd) + ! Adjust column depth for excess ice thickness + do fc = 1,num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness + do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment + zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice + z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 + end do + endif + end do + + + !------------------------------------------------------ ! Compute ground surface and soil temperatures !------------------------------------------------------ @@ -488,6 +516,23 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter dhsdT(bounds%begc:bounds%endc), & soilstate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, waterfluxbulk_inst, energyflux_inst, temperature_inst) + !-------------------------------------------------------------- + ! Vertical coordinates adjustment for excess ice calculations + !-------------------------------------------------------------- + ! bringing back the soil depth to the original state + ! Adjust column depth for excess ice thickness + do fc = 1,num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) + zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) + z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) + endif + end do + + + if ( IsProgBuildTemp() )then call BuildingTemperature(bounds, num_urbanl, filter_urbanl, num_nolakec, filter_nolakec, & tk(bounds%begc:bounds%endc, :), urbanparams_inst, & @@ -628,6 +673,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Input: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) bw => waterdiagnosticbulk_inst%bw_col , & ! Output: [real(r8) (:,:) ] partial density of water in the snow pack (ice + liquid) [kg/m3] tkmg => soilstate_inst%tkmg_col , & ! Input: [real(r8) (:,:) ] thermal conductivity, soil minerals [W/m-K] @@ -654,7 +700,8 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) + ! TODO recalculate watsat and satw to have excess ice included + satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice +excess_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) satw = min(1._r8, satw) if (satw > .1e-6_r8) then if (t_soisno(c,j) >= tfrz) then ! Unfrozen soil @@ -663,7 +710,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter dke = satw end if fl = (h2osoi_liq(c,j)/(denh2o*dz(c,j))) / (h2osoi_liq(c,j)/(denh2o*dz(c,j)) + & - h2osoi_ice(c,j)/(denice*dz(c,j))) + h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/denice) dksat = tkmg(c,j)*tkwat**(fl*watsat(c,j))*tkice**((1._r8-fl)*watsat(c,j)) thk(c,j) = dke*dksat + (1._r8-dke)*tkdry(c,j) else @@ -756,7 +803,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter .and. col%itype(c) /= icol_sunwall .and. col%itype(c) /= icol_shadewall .and. & col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) + cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) + excess_ice(c,j)*cpice if (j > nbedrock(c)) cv(c,j) = csol_bedrock*dz(c,j) else if (lun%itype(l) == istwet) then cv(c,j) = (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) @@ -1057,7 +1104,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd use clm_varctl , only : iulog - use clm_varcon , only : tfrz, hfus, grav + use clm_varcon , only : tfrz, hfus, grav, denice use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv use landunit_varcon , only : istsoil, istcrop, istice ! @@ -1088,6 +1135,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: propor !proportionality constant (-) real(r8) :: tinc(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !t(n+1)-t(n) [K] real(r8) :: smp !frozen water potential (mm) + real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] + real(r8) :: xm3(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] + real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd)!initial mass of excess_ice at the timestep (kg/m2) + + !----------------------------------------------------------------------- call t_startf( 'PhaseChangebeta' ) @@ -1109,6 +1161,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Output: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) + init_exice => waterstatebulk_inst%init_exice , & ! Input: [real(r8) (:) ] excess soil ice initial + exice_melt => waterstatebulk_inst%exice_melt , & ! Input: [real(r8) (:) ] excess soil ice + exice_melt_lev => waterstatebulk_inst%exice_melt_lev , & ! Input: [real(r8) (:,:) ] excess soil ice + qflx_snow_drain => waterfluxbulk_inst%qflx_snow_drain_col , & ! Output: [real(r8) (:) ] drainage from snow pack qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] @@ -1152,9 +1209,12 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & imelt(c,j) = 0 hm(c,j) = 0._r8 xm(c,j) = 0._r8 + xm2(c,j)=0._r8 + xm3(c,j)=0._r8 wice0(c,j) = h2osoi_ice(c,j) wliq0(c,j) = h2osoi_liq(c,j) wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) + wexice0(c,j)=excess_ice(c,j) endif ! end of snow layer if-block if (j <= 0) then @@ -1211,6 +1271,13 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & t_soisno(c,j) = tfrz endif + ! melt excess ice after normal ice + if (excess_ice(c,j) > 0._r8 .AND. t_soisno(c,j) > tfrz) then + imelt(c,j) = 1 + tinc(c,j) = tfrz - t_soisno(c,j) + t_soisno(c,j) = tfrz + endif + ! from Zhao (1997) and Koren (1999) supercool(c,j) = 0.0_r8 if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop .or. col%itype(c) == icol_road_perv) then @@ -1325,9 +1392,49 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif heatr = 0._r8 - if (xm(c,j) > 0._r8) then - h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) - heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + if (xm(c,j) > 0._r8) then !if there is excess heat to melt the ice + !h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) ! no excess ice + !heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime ! on excess ice + ! excess ice modifications + if (h2osoi_ice(c,j)>0._r8) then !if there is normal soil ice + if (xm(c,j)> h2osoi_ice(c,j)) then ! if we can melt all normal ice first + xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) + h2osoi_ice(c,j) = 0._r8 + if (excess_ice(c,j) > 0._r8) then ! if there is excess ice to melt + if (xm2(c,j) > excess_ice(c,j)) then ! there is still enough heat left to melt all of the ice + xm3(c,j) = xm2(c,j) - excess_ice(c,j) + excess_ice(c,j) = 0._r8 + heatr = hfus * xm3(c,j) / dtime + else ! if there is not enough heat to melt all excess ice + excess_ice(c,j) = excess_ice(c,j)-xm2(c,j) + heatr = 0._r8 + xm3(c,j) = 0._r8 + endif + else !no excess ice to melt heat soil + heatr = hfus * xm2(c,j) / dtime + endif + else ! not enough heat to melt all normal ice + h2osoi_ice(c,j) = h2osoi_ice(c,j)-xm(c,j) + heatr = 0._r8 + xm2(c,j) = 0._r8 + endif + else !no normal ice present + xm2(c,j) = xm(c,j) + if (excess_ice(c,j) > 0._r8) then ! if there is excess ice to melt + if (xm2(c,j) > excess_ice(c,j)) then ! there is still enough heat left to melt all of the ice + xm3(c,j) = xm2(c,j)-excess_ice(c,j) + excess_ice(c,j) = 0._r8 + heatr = hfus * xm3(c,j) / dtime + else ! if there is not enough heat to melt all excess ice + excess_ice(c,j) = excess_ice(c,j)-xm2(c,j) + heatr = 0._r8 + xm3(c,j) = 0._r8 + endif + else !no excess ice to melt heat soil + heatr = hfus * xm2(c,j) / dtime + endif + endif + else if (xm(c,j) < 0._r8) then if (j <= 0) then h2osoi_ice(c,j) = min(wmass0(c,j), wice0(c,j)-xm(c,j)) ! snow @@ -1373,7 +1480,8 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif ! end of heatr > 0 if-block if (j >= 1) then - xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime + exice_melt_lev(c,j)=wexice0(c,j)-excess_ice(c,j) else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif @@ -1398,17 +1506,20 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & end do ! end of column-loop enddo ! end of level-loop + ! Needed for history file output do fc = 1,num_nolakec c = filter_nolakec(fc) eflx_snomelt(c) = qflx_snomelt(c) * hfus + exice_melt(c) = 0.0_r8 l = col%landunit(c) if (lun%urbpoi(l)) then eflx_snomelt_u(c) = eflx_snomelt(c) else if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then eflx_snomelt_r(c) = eflx_snomelt(c) end if + exice_melt(c) = exice_melt(c) + SUM( exice_melt_lev(c,:) ) / denice end do call t_stopf( 'PhaseChangebeta' ) From f422147da93839b86832fd0d62849553617ff2b0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 7 Feb 2022 10:22:18 -0700 Subject: [PATCH 0129/2067] Corrected mxpft to ncft in a print-out loop. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 8f9d571552..8c9197166b 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -130,7 +130,7 @@ subroutine cropcal_init(bounds) write(iulog,'(a,a)' ) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) write(iulog,'(a,a)' ) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) write(iulog,'(a,a)' ) ' stream_meshfile_cropcal = ',trim(stream_meshfile_cropcal) - do n = 1,mxpft + do n = 1,ncft write(iulog,'(a,a)' ) ' stream_varnames_sdate = ',trim(stream_varnames_sdate(n)) write(iulog,'(a,a)' ) ' stream_varnames_cultivar_gdds = ',trim(stream_varnames_cultivar_gdds(n)) end do From 23ee7df5fd3f3e8d984c6917c40037beb26cb018 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 7 Feb 2022 11:41:04 -0700 Subject: [PATCH 0130/2067] Changed default files for sdate and cultivar_gdds. --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 07cf69c051..bcaaeb874b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1569,8 +1569,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 lnd/clm2/lai_streams/MODISPFTLAI_0.5x0_ESMFmesh_cdf5_090621.nc -lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc -lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc +/glade/u/home/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.nc +/glade/u/home/samrabin/crop_dates/gdds_20220121_155415.nc From b00b53c3eadf03eef79526b2fdaa11d30d0b5d0c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Feb 2022 09:48:04 -0700 Subject: [PATCH 0131/2067] Changed default cropcal meshfile. --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index bcaaeb874b..b010e4b12e 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1567,7 +1567,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 2100 1850 -lnd/clm2/lai_streams/MODISPFTLAI_0.5x0_ESMFmesh_cdf5_090621.nc +/glade/p/cesmdata/cseg/inputdata/share/meshes/10x15_nomask_c110308_ESMFmesh.nc /glade/u/home/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.nc /glade/u/home/samrabin/crop_dates/gdds_20220121_155415.nc From 64bc5adf1bc916f6769ed00af897a80cac4c305d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Feb 2022 09:58:10 -0700 Subject: [PATCH 0132/2067] Only read cultivar GDDs if generate_crop_gdds is true. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- src/cpl/share_esmf/cropcalStreamMod.F90 | 90 +++++++++++++++++++++---- 2 files changed, 79 insertions(+), 13 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7dfefc3306..549d17b3d3 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -124,7 +124,7 @@ module CNPhenologyMod real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting - logical, private :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing + logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing ! Constants for seasonal decidious leaf onset and offset logical, private :: onset_thresh_depends_on_veg = .false. ! If onset threshold depends on vegetation type diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 8c9197166b..cfe2879027 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -183,7 +183,7 @@ subroutine cropcal_init(bounds) stream_taxmode = 'cycle', & stream_dtlimit = 1.5_r8, & stream_tintalgo = cropcal_tintalgo, & - stream_name = 'sowing date data', & + stream_name = 'cultivar gdd data', & rc = rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) @@ -245,6 +245,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use CropType , only : crop_type use PatchType , only : patch use dshr_methods_mod , only : dshr_fldbun_getfldptr + use CNPhenologyMod , only : generate_crop_gdds ! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: @@ -272,8 +273,12 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Get pointer for stream data that is time and spatially interpolate to model time and grid ! Place all data from each type into a temporary 2d array lsize = bounds%endg - bounds%begg + 1 + + ! Read prescribed sowing dates from input files + allocate(dataptr1d_sdate(lsize)) + dataptr1d_sdate(:) = -4 allocate(dataptr2d_sdate(lsize, ncft)) - allocate(dataptr2d_cultivar_gdds(lsize, ncft)) + dataptr2d_sdate(:,:) = -5 ! Starting with npcropmin will skip generic crops do n = 1, ncft call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & @@ -281,21 +286,23 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & - fldptr1=dataptr1d_cultivar_gdds, rc=rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize ! So an explicit loop is required here do g = 1,lsize + + ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. + if (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365) then + write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' + end if + dataptr2d_sdate(g,n) = dataptr1d_sdate(g) - dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) end do end do + deallocate(dataptr1d_sdate) - ! Set rx_sdate and rx_cultivar_gdd for each gridcell/patch combination - do p = bounds%begp, bounds%endp + ! Set rx_sdate for each gridcell/patch combination + do fp = 1, num_pcropp + p = filter_pcropp(fp) ivt = patch%itype(p) ! Will skip generic crops if (ivt >= npcropmin) then @@ -303,14 +310,73 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! vegetated pft ig = g_to_ig(patch%gridcell(p)) crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) - crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) + + ! Sanity check: Should only read in valid values + if (crop_inst%rx_sdates_thisyr(p,1) <= 0 .or. dataptr1d_sdate(g) > 365) then + write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',crop_inst%rx_sdates_thisyr(p,1) + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if ! Only for first sowing date of the year crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + else + write(iulog,'(a,i0)') 'cropcal_interp(), rx_sdates: Crop patch has ivt ',ivt + call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do deallocate(dataptr2d_sdate) - deallocate(dataptr2d_cultivar_gdds) + + if (.not. generate_crop_gdds) then + ! Read prescribed cultivar GDDs from input files + allocate(dataptr1d_cultivar_gdds(lsize)) + dataptr1d_cultivar_gdds(:) = -4 + allocate(dataptr2d_cultivar_gdds(lsize, ncft)) + dataptr2d_cultivar_gdds(:,:) = -5 + ! Starting with npcropmin will skip generic crops + do n = 1, ncft + call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & + fldptr1=dataptr1d_cultivar_gdds, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize + ! So an explicit loop is required here + do g = 1,lsize + + ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. + if (dataptr1d_cultivar_gdds(g) < 0.0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0) then + write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' + end if + + dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) + end do + end do + deallocate(dataptr1d_cultivar_gdds) + + ! Set rx_cultivar_gdd for each gridcell/patch combination + do fp = 1, num_pcropp + p = filter_pcropp(fp) + ivt = patch%itype(p) + ! Will skip generic crops + if (ivt >= npcropmin) then + n = ivt - npcropmin + 1 + ! vegetated pft + ig = g_to_ig(patch%gridcell(p)) + crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) + + ! Sanity check: Should not read in negative values. Also try to catch uninitialized values + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < 0.0 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then + write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + else + write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt + call ESMF_Finalize(endflag=ESMF_END_ABORT) + endif + end do + deallocate(dataptr2d_cultivar_gdds) + end if ! generate_crop_gdds + end subroutine cropcal_interp From b05a9924e02be7f8a717a27bc9a08d1329153fc8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Feb 2022 12:38:16 -0700 Subject: [PATCH 0133/2067] =?UTF-8?q?Fail=20instead=20of=20warn/kludge=20i?= =?UTF-8?q?f=20CropPhenology=20encounters=20cultivar=20GDD=20target=20?= =?UTF-8?q?=E2=89=A4=200.0.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/biogeochem/CNPhenologyMod.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 549d17b3d3..eff589b1fe 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2369,10 +2369,8 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & if (do_plant_prescribed .and. .not. generate_crop_gdds) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) if (gdd_target <= 0.0) then - !write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0.' - write(iulog,"(A,I4)") 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0. FAKING with 1.0. PFT ',ivt(p) - !call endrun(msg=errMsg(sourcefile, __LINE__)) - gdd_target = 1.0 + write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0.' + call endrun(msg=errMsg(sourcefile, __LINE__)) endif gddmaturity(p) = gdd_target else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then From 9082be6fdbffc475c76caad23e54f25d71c2391f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Feb 2022 12:31:17 -0700 Subject: [PATCH 0134/2067] No longer tries to access dataptr1d_sdate after deallocation. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index cfe2879027..ee14404e7e 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -312,7 +312,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) ! Sanity check: Should only read in valid values - if (crop_inst%rx_sdates_thisyr(p,1) <= 0 .or. dataptr1d_sdate(g) > 365) then + if (crop_inst%rx_sdates_thisyr(p,1) <= 0 .or. crop_inst%rx_sdates_thisyr(p,1) > 365) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',crop_inst%rx_sdates_thisyr(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if From 8bd22b9c3701e9289e0bc7233b78cd3816e2189f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Feb 2022 12:32:39 -0700 Subject: [PATCH 0135/2067] Each process now only warns about bad cropcal interpolation once. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index ee14404e7e..19de4b093d 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -34,6 +34,7 @@ module cropcalStreamMod character(len=CS), allocatable :: stream_varnames_sdate(:) character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:) integer :: ncft ! Number of crop functional types (excl. generic crops) + logical :: warned_about_bad_interp_sdate, warned_about_bad_interp_cultivar_gdds character(len=*), parameter :: sourcefile = & __FILE__ @@ -189,6 +190,9 @@ subroutine cropcal_init(bounds) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + warned_about_bad_interp_sdate = .false. + warned_about_bad_interp_cultivar_gdds = .false. + end subroutine cropcal_init !================================================================ @@ -291,8 +295,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do g = 1,lsize ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365) then - write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' + if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then + write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' + warned_about_bad_interp_sdate = .true. end if dataptr2d_sdate(g,n) = dataptr1d_sdate(g) @@ -344,8 +349,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do g = 1,lsize ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if (dataptr1d_cultivar_gdds(g) < 0.0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0) then - write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' + if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) <= 0 .or. dataptr1d_cultivar_gdds(g) > 365)) then + write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' + warned_about_bad_interp_cultivar_gdds = .true. end if dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) @@ -369,7 +375,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ',crop_inst%rx_cultivar_gdds_thisyr(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - else + else write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt call ESMF_Finalize(endflag=ESMF_END_ABORT) endif From 5e39296994b7c2749b5c983866ce6c74b5bc736a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Feb 2022 12:43:28 -0700 Subject: [PATCH 0136/2067] CropPhenology now allows rx_cultivar_gdds == 0.0. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index eff589b1fe..a023a9d731 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2368,8 +2368,8 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ! set GDD target if (do_plant_prescribed .and. .not. generate_crop_gdds) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) - if (gdd_target <= 0.0) then - write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets > 0.0.' + if (gdd_target < 0.0) then + write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' call endrun(msg=errMsg(sourcefile, __LINE__)) endif gddmaturity(p) = gdd_target From c6939ccb265d6749e72562415ce0ad789f119a8a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 14:33:29 -0700 Subject: [PATCH 0137/2067] Trying to get GDD-forced run to work. It still doesn't. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 72 +++++++++++++++++++++---- src/main/clm_driver.F90 | 2 + src/main/clm_initializeMod.F90 | 1 + 3 files changed, 66 insertions(+), 9 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 19de4b093d..68e4bb66c0 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -271,6 +271,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) real(r8), pointer :: dataptr1d_cultivar_gdds(:) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) !----------------------------------------------------------------------- + + write(iulog,'(a)') 'cropcal_interp(): Beginning' + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) @@ -285,6 +288,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) dataptr2d_sdate(:,:) = -5 ! Starting with npcropmin will skip generic crops do n = 1, ncft + write(iulog,'(a,a)') 'cropcal_interp(): Reading sdat_cropcal_sdate variable ',trim(stream_varnames_sdate(n)) call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & fldptr1=dataptr1d_sdate, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -303,9 +307,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) dataptr2d_sdate(g,n) = dataptr1d_sdate(g) end do end do - deallocate(dataptr1d_sdate) ! Set rx_sdate for each gridcell/patch combination + write(iulog,'(a)') 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -329,18 +333,23 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do + deallocate(dataptr1d_sdate) deallocate(dataptr2d_sdate) + write(iulog,'(a)') 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' + allocate(dataptr1d_cultivar_gdds(lsize)) + allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (.not. generate_crop_gdds) then + write(iulog,'(a)') 'cropcal_interp(): Reading cultivar_gdds' ! Read prescribed cultivar GDDs from input files - allocate(dataptr1d_cultivar_gdds(lsize)) dataptr1d_cultivar_gdds(:) = -4 - allocate(dataptr2d_cultivar_gdds(lsize, ncft)) dataptr2d_cultivar_gdds(:,:) = -5 ! Starting with npcropmin will skip generic crops do n = 1, ncft + write(iulog,'(a,a)') 'cropcal_interp(): Reading sdat_cropcal_cultivar_gdds variable ',trim(stream_varnames_cultivar_gdds(n)) call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & fldptr1=dataptr1d_cultivar_gdds, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -349,7 +358,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do g = 1,lsize ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) <= 0 .or. dataptr1d_cultivar_gdds(g) > 365)) then + if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) <= 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' warned_about_bad_interp_cultivar_gdds = .true. end if @@ -357,22 +366,63 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) end do end do - deallocate(dataptr1d_cultivar_gdds) ! Set rx_cultivar_gdd for each gridcell/patch combination + write(iulog,'(a)') 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) + + + if (.not. patch%active(p)) then + continue + end if + ivt = patch%itype(p) ! Will skip generic crops if (ivt >= npcropmin) then n = ivt - npcropmin + 1 + + if (n > ncft) then + write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + ! vegetated pft ig = g_to_ig(patch%gridcell(p)) + + + if (ig > lsize) then + write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + if (dataptr2d_cultivar_gdds(ig,n) < -0.001 .or. dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then + !if (dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then + if (dataptr2d_cultivar_gdds(ig,n) == 0.0) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ZERO??? ',dataptr2d_cultivar_gdds(ig,n) + else if (dataptr2d_cultivar_gdds(ig,n) < -0.001) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement NEGATIVE ',dataptr2d_cultivar_gdds(ig,n) + else + write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement HUGE ',dataptr2d_cultivar_gdds(ig,n) + end if +! call ESMF_Finalize(endflag=ESMF_END_ABORT) + + ! TEMPORARY!!! + dataptr2d_cultivar_gdds(ig,n) = 0.0 + end if + crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) ! Sanity check: Should not read in negative values. Also try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < 0.0 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then - write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then + !if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + else + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + end if call ESMF_Finalize(endflag=ESMF_END_ABORT) end if else @@ -380,8 +430,12 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do - deallocate(dataptr2d_cultivar_gdds) - end if ! generate_crop_gdds + end if ! not generate_crop_gdds + + deallocate(dataptr1d_cultivar_gdds) + deallocate(dataptr2d_cultivar_gdds) + + write(iulog,'(a)') 'cropcal_interp(): All done!' end subroutine cropcal_interp diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 4a43af0924..f971683fdb 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -479,6 +479,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro canopystate_inst, water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, & energyflux_inst) + write(iulog,*) 'Exited clm_drv_init() in clm_drv()' call topo_inst%UpdateTopo(bounds_clump, & filter(nc)%num_icec, filter(nc)%icec, & @@ -1041,6 +1042,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Update crop calendars ! ============================================================================ call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) + write(iulog,*) 'Exited cropcal_interp() in clm_drv()' end if ! ============================================================================ diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 4dc058e9ed..f87bfb9bdd 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -569,6 +569,7 @@ subroutine initialize2(ni,nj) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) + write(iulog,*) 'Exited cropcal_interp() in initialize2()' end do !$OMP END PARALLEL DO ! call cropcal_interp(bounds_clump, crop_inst) From 427994f500473162fc362cde4abd716bc677600d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 14:42:41 -0700 Subject: [PATCH 0138/2067] Additional wraps in if (.not. generate_crop_gdds). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 60 +++++++++++++------------ 1 file changed, 32 insertions(+), 28 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 68e4bb66c0..6f56134033 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -17,6 +17,7 @@ module cropcalStreamMod use perf_mod , only : t_startf, t_stopf use spmdMod , only : masterproc, mpicom, iam use pftconMod , only : npcropmin + use CNPhenologyMod , only : generate_crop_gdds ! ! !PUBLIC TYPES: implicit none @@ -165,29 +166,31 @@ subroutine cropcal_init(bounds) end if ! Initialize the cdeps data type sdat_cropcal_cultivar_gdds - call shr_strdata_init_from_inline(sdat_cropcal_cultivar_gdds, & - my_task = iam, & - logunit = iulog, & - compname = 'LND', & - model_clock = model_clock, & - model_mesh = mesh, & - stream_meshfile = trim(stream_meshfile_cropcal), & - stream_lev_dimname = 'null', & - stream_mapalgo = trim(cropcal_mapalgo), & - stream_filenames = (/trim(stream_fldFileName_cultivar_gdds)/), & - stream_fldlistFile = stream_varnames_cultivar_gdds, & - stream_fldListModel = stream_varnames_cultivar_gdds, & - stream_yearFirst = stream_year_first_cropcal, & - stream_yearLast = stream_year_last_cropcal, & - stream_yearAlign = model_year_align_cropcal, & - stream_offset = cropcal_offset, & - stream_taxmode = 'cycle', & - stream_dtlimit = 1.5_r8, & - stream_tintalgo = cropcal_tintalgo, & - stream_name = 'cultivar gdd data', & - rc = rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) + if (.not. generate_crop_gdds) then + call shr_strdata_init_from_inline(sdat_cropcal_cultivar_gdds, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = trim(stream_meshfile_cropcal), & + stream_lev_dimname = 'null', & + stream_mapalgo = trim(cropcal_mapalgo), & + stream_filenames = (/trim(stream_fldFileName_cultivar_gdds)/), & + stream_fldlistFile = stream_varnames_cultivar_gdds, & + stream_fldListModel = stream_varnames_cultivar_gdds, & + stream_yearFirst = stream_year_first_cropcal, & + stream_yearLast = stream_year_last_cropcal, & + stream_yearAlign = model_year_align_cropcal, & + stream_offset = cropcal_offset, & + stream_taxmode = 'cycle', & + stream_dtlimit = 1.5_r8, & + stream_tintalgo = cropcal_tintalgo, & + stream_name = 'cultivar gdd data', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if end if warned_about_bad_interp_sdate = .false. @@ -223,10 +226,12 @@ subroutine cropcal_advance( bounds ) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - call shr_strdata_advance(sdat_cropcal_cultivar_gdds, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if + if (.not. generate_crop_gdds) then + call shr_strdata_advance(sdat_cropcal_cultivar_gdds, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + end if if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) @@ -249,7 +254,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use CropType , only : crop_type use PatchType , only : patch use dshr_methods_mod , only : dshr_fldbun_getfldptr - use CNPhenologyMod , only : generate_crop_gdds ! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: From 9ae3bd4a2a9d527a022234ade5035ca68ffe084b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 15:02:14 -0700 Subject: [PATCH 0139/2067] Added messages when beginning/ending cropcal_advance(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 6f56134033..b3e6ca7905 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -220,6 +220,8 @@ subroutine cropcal_advance( bounds ) integer :: rc !----------------------------------------------------------------------- + write(iulog,*) 'cropcal_advance(): Beginning' + call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day call shr_strdata_advance(sdat_cropcal_sdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) @@ -242,6 +244,8 @@ subroutine cropcal_advance( bounds ) end do end if + write(iulog,*) 'cropcal_advance(): Ending' + end subroutine cropcal_advance !================================================================ From 312e972b93cab3407950c44aa84ba69ba351e035 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 15:03:29 -0700 Subject: [PATCH 0140/2067] Inconsequential syntax change. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index b3e6ca7905..366d518c0b 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -125,7 +125,7 @@ subroutine cropcal_init(bounds) if (masterproc) then write(iulog,*) - write(iulog,'(a)') 'cropcal_stream settings:' + write(iulog,*) 'cropcal_stream settings:' write(iulog,'(a,i8)') ' stream_year_first_cropcal = ',stream_year_first_cropcal write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal @@ -280,7 +280,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) !----------------------------------------------------------------------- - write(iulog,'(a)') 'cropcal_interp(): Beginning' + write(iulog,*) 'cropcal_interp(): Beginning' SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) @@ -317,7 +317,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end do ! Set rx_sdate for each gridcell/patch combination - write(iulog,'(a)') 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' + write(iulog,*) 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -344,11 +344,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) deallocate(dataptr1d_sdate) deallocate(dataptr2d_sdate) - write(iulog,'(a)') 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' + write(iulog,*) 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' allocate(dataptr1d_cultivar_gdds(lsize)) allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (.not. generate_crop_gdds) then - write(iulog,'(a)') 'cropcal_interp(): Reading cultivar_gdds' + write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' ! Read prescribed cultivar GDDs from input files dataptr1d_cultivar_gdds(:) = -4 dataptr2d_cultivar_gdds(:,:) = -5 @@ -376,7 +376,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end do ! Set rx_cultivar_gdd for each gridcell/patch combination - write(iulog,'(a)') 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' + write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) @@ -443,7 +443,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) deallocate(dataptr1d_cultivar_gdds) deallocate(dataptr2d_cultivar_gdds) - write(iulog,'(a)') 'cropcal_interp(): All done!' + write(iulog,*) 'cropcal_interp(): All done!' end subroutine cropcal_interp From b7a057cfc41a3cf111854a3a607c5bb6515b016e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 15:03:57 -0700 Subject: [PATCH 0141/2067] No longer prints message when reading EACH cropcal variable. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 366d518c0b..1ce0a4430e 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -295,8 +295,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) allocate(dataptr2d_sdate(lsize, ncft)) dataptr2d_sdate(:,:) = -5 ! Starting with npcropmin will skip generic crops + write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft - write(iulog,'(a,a)') 'cropcal_interp(): Reading sdat_cropcal_sdate variable ',trim(stream_varnames_sdate(n)) call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & fldptr1=dataptr1d_sdate, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -354,7 +354,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) dataptr2d_cultivar_gdds(:,:) = -5 ! Starting with npcropmin will skip generic crops do n = 1, ncft - write(iulog,'(a,a)') 'cropcal_interp(): Reading sdat_cropcal_cultivar_gdds variable ',trim(stream_varnames_cultivar_gdds(n)) call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & fldptr1=dataptr1d_cultivar_gdds, rc=rc) From 708cef1fb8487a11618f53e2b9fe8d8f174e48ca Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 15:28:31 -0700 Subject: [PATCH 0142/2067] Don't warn about dataptr1d_cultivar_gdds(g) == 0. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 1ce0a4430e..a6c53267c9 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -365,7 +365,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do g = 1,lsize ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) <= 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then + if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' warned_about_bad_interp_cultivar_gdds = .true. end if From 47c59144fee807c80101b04f75996d8ed7ecc963 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 16:51:40 -0700 Subject: [PATCH 0143/2067] Improve a warning message in cropcal_interp(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index a6c53267c9..b769791692 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -297,6 +297,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Starting with npcropmin will skip generic crops write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft + ivt = n + npcropmin - 1 call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & fldptr1=dataptr1d_sdate, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -308,7 +309,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then - write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' + write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop ivt ',ivt,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' warned_about_bad_interp_sdate = .true. end if From 88844f59a5b561038aa0e43aeb5fd04fae9021bf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 18:43:46 -0700 Subject: [PATCH 0144/2067] Be extra safe about having s>0 before querying anything(p,s). --- src/biogeochem/CNPhenologyMod.F90 | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a023a9d731..f9d32520b4 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1711,6 +1711,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_harvest ! Are harvest conditions satisfied? logical force_harvest ! Should we harvest today no matter what? logical fake_harvest ! Dealing with incorrect Dec. 31 planting + logical sown_today ! Was the crop sown today? !------------------------------------------------------------------------ associate( & @@ -2058,6 +2059,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .false. force_harvest = .false. fake_harvest = .false. + sown_today = .false. + if (use_cropcal_streams .and. s > 0) then + sown_today = crop_inst%sdates_thisyr(p,s) == real(jday, r8) + end if if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! Crop was incorrectly planted in last time step of Dec. 31. @@ -2081,7 +2086,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! until some time next year. do_harvest = .false. endif - else if (use_cropcal_streams .and. s > 0 .and. crop_inst%sdates_thisyr(p,s) == jday) then + else if (sown_today) then ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. do_harvest = .false. From 50bf204ca5f04e9d21000642272cd8dbe65fbe2b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 18:44:04 -0700 Subject: [PATCH 0145/2067] Explicit type conversion. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index f9d32520b4..622b35e182 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2344,7 +2344,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & else next_rx_sdate(p) = -1 endif - crop_inst%sdates_thisyr(p,s) = jday + crop_inst%sdates_thisyr(p,s) = real(jday, r8) leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset From 01021edb7370d47ffa2f30e7630eb76b121c1961 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Feb 2022 18:44:38 -0700 Subject: [PATCH 0146/2067] Set minimum gddmaturity = 1.0. --- src/biogeochem/CNPhenologyMod.F90 | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 622b35e182..b1b99a49de 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2377,6 +2377,11 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' call endrun(msg=errMsg(sourcefile, __LINE__)) endif + + ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator + ! Just manually set a minimum of 1.0 + gdd_target = max(gdd_target, 1._r8) + gddmaturity(p) = gdd_target else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then gddmaturity(p) = hybgdd(ivt(p)) From 4fbf6dc29be9d3bf16cdc0e3ea1afd48270d4224 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Feb 2022 15:11:49 -0700 Subject: [PATCH 0147/2067] Lots of troubleshooting stuff. --- src/biogeochem/CNPhenologyMod.F90 | 15 +++++++++++++++ src/cpl/share_esmf/cropcalStreamMod.F90 | 20 +++++++++++--------- src/main/clm_driver.F90 | 4 ++-- src/main/clm_initializeMod.F90 | 2 +- 4 files changed, 29 insertions(+), 12 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b1b99a49de..93ad45458f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1817,6 +1817,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & s = sowing_count(p) + ! SSR troubleshooting + if (s<0) then + write(iulog,*) 'CropPhenology(): s < 0' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + ! SSR: I don't know why this is necessary. next_rx_sdate should get properly set in PlantCrop() ! or above, but sometimes (NOT in first year after restart) I'm seeing crops planted Jan. 1 that ! are harvested the same day. This (specifically, the second condition) fixes that. @@ -2338,6 +2344,15 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & idop(p) = jday harvdate(p) = NOT_Harvested s = sowing_count(p) + 1 + + ! SSR troubleshooting + if (s < 1) then + write(iulog,*) 'PlantCrop(): s < 1' + call endrun(msg=errMsg(sourcefile, __LINE__)) + else if (s > mxgrowseas) then + write(iulog,*) 'PlantCrop(): s > mxgrowseas' + end if + sowing_count(p) = s if (s < mxgrowseas) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, s+1) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index b769791692..31e6a56fbe 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -218,9 +218,10 @@ subroutine cropcal_advance( bounds ) integer :: sec ! seconds into current date for nstep+1 integer :: mcdate ! Current model date (yyyymmdd) integer :: rc + logical :: verbose = .false. !----------------------------------------------------------------------- - write(iulog,*) 'cropcal_advance(): Beginning' + if (verbose) write(iulog,*) 'cropcal_advance(): Beginning' call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day @@ -244,7 +245,7 @@ subroutine cropcal_advance( bounds ) end do end if - write(iulog,*) 'cropcal_advance(): Ending' + if (verbose) write(iulog,*) 'cropcal_advance(): Ending' end subroutine cropcal_advance @@ -278,9 +279,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) real(r8), pointer :: dataptr2d_sdate(:,:) real(r8), pointer :: dataptr1d_cultivar_gdds(:) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) + logical :: verbose = .false. !----------------------------------------------------------------------- - write(iulog,*) 'cropcal_interp(): Beginning' + if (verbose) write(iulog,*) 'cropcal_interp(): Beginning' SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) @@ -295,7 +297,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) allocate(dataptr2d_sdate(lsize, ncft)) dataptr2d_sdate(:,:) = -5 ! Starting with npcropmin will skip generic crops - write(iulog,*) 'cropcal_interp(): Reading sdate file' + if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft ivt = n + npcropmin - 1 call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & @@ -318,7 +320,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end do ! Set rx_sdate for each gridcell/patch combination - write(iulog,*) 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' + if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -345,11 +347,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) deallocate(dataptr1d_sdate) deallocate(dataptr2d_sdate) - write(iulog,*) 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' + if (verbose) write(iulog,*) 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' allocate(dataptr1d_cultivar_gdds(lsize)) allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (.not. generate_crop_gdds) then - write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' + if (verbose) write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' ! Read prescribed cultivar GDDs from input files dataptr1d_cultivar_gdds(:) = -4 dataptr2d_cultivar_gdds(:,:) = -5 @@ -376,7 +378,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end do ! Set rx_cultivar_gdd for each gridcell/patch combination - write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' + if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) @@ -443,7 +445,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) deallocate(dataptr1d_cultivar_gdds) deallocate(dataptr2d_cultivar_gdds) - write(iulog,*) 'cropcal_interp(): All done!' + if (verbose) write(iulog,*) 'cropcal_interp(): All done!' end subroutine cropcal_interp diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index f971683fdb..2f690ebdec 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -479,7 +479,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro canopystate_inst, water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, & energyflux_inst) - write(iulog,*) 'Exited clm_drv_init() in clm_drv()' +! write(iulog,*) 'Exited clm_drv_init() in clm_drv()' call topo_inst%UpdateTopo(bounds_clump, & filter(nc)%num_icec, filter(nc)%icec, & @@ -1042,7 +1042,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Update crop calendars ! ============================================================================ call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) - write(iulog,*) 'Exited cropcal_interp() in clm_drv()' +! write(iulog,*) 'Exited cropcal_interp() in clm_drv()' end if ! ============================================================================ diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index f87bfb9bdd..d5c4e589ed 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -569,7 +569,7 @@ subroutine initialize2(ni,nj) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) - write(iulog,*) 'Exited cropcal_interp() in initialize2()' +! write(iulog,*) 'Exited cropcal_interp() in initialize2()' end do !$OMP END PARALLEL DO ! call cropcal_interp(bounds_clump, crop_inst) From a97bad1872fc6228e3e3958de9bcb51e5aca1531 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Feb 2022 15:21:59 -0700 Subject: [PATCH 0148/2067] Added errors if gddmaturity==0 and thus a denominator is 0. --- src/biogeochem/CNNDynamicsMod.F90 | 12 ++++++++++++ .../NutrientCompetitionCLM45defaultMod.F90 | 14 ++++++++++++++ .../NutrientCompetitionFlexibleCNMod.F90 | 15 +++++++++++++++ 3 files changed, 41 insertions(+) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 7a80d701a8..79310e335d 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -25,6 +25,9 @@ module CNNDynamicsMod use ColumnType , only : col use PatchType , only : patch use perf_mod , only : t_startf, t_stopf + ! SSR troubleshooting + use abortutils , only : endrun + use shr_log_mod , only : errMsg => shr_log_errMsg ! implicit none private @@ -44,6 +47,10 @@ module CNNDynamicsMod real(r8) :: freelivfix_slope_wET ! slope of line of free living fixation with annual ET end type params_type type(params_type) :: params_inst + + ! SSR troubleshooting + character(len=*), parameter, private :: sourcefile = & + __FILE__ !----------------------------------------------------------------------- contains @@ -396,6 +403,11 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & ! for soy) ! Ranges below are not firm. Are they lit. based or tuning based? + ! SSR troubleshooting + if (gddmaturity(p) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + GDDfrac = hui(p) / gddmaturity(p) if (GDDfrac <= GDDfracthreshold1) then diff --git a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 index d93f0a168e..1916ed35fd 100644 --- a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 +++ b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 @@ -18,6 +18,9 @@ module NutrientCompetitionCLM45defaultMod use NutrientCompetitionMethodMod, only : nutrient_competition_method_type use NutrientCompetitionMethodMod, only : params_inst !use clm_varctl , only : iulog + ! SSR troubleshooting + use abortutils , only : endrun + use shr_log_mod , only : errMsg => shr_log_errMsg ! implicit none private @@ -793,6 +796,12 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & astem(p) = 0._r8 aroot(p) = 1._r8 - arepr(p) - aleaf(p) - astem(p) else + + ! SSR troubleshooting + if (gddmaturity(p) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + arepr(p) = 0._r8 aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * & @@ -820,6 +829,11 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & else if (hui(p) >= huigrain(p)) then + ! SSR troubleshooting + if (gddmaturity(p) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) if (astemi(p) > astemf(ivt(p))) then diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index a642a5dd2d..37a6e6782c 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -25,6 +25,9 @@ module NutrientCompetitionFlexibleCNMod use NutrientCompetitionMethodMod, only : nutrient_competition_method_type use NutrientCompetitionMethodMod, only : params_inst use clm_varctl , only : iulog + ! SSR troubleshooting + use abortutils , only : endrun + use shr_log_mod , only : errMsg => shr_log_errMsg ! implicit none private @@ -1509,6 +1512,12 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & astem(p) = 0._r8 aroot(p) = 1._r8 - arepr(p) - aleaf(p) - astem(p) else + + ! SSR troubleshooting + if (gddmaturity(p) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + arepr(p) = 0._r8 aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * & @@ -1535,6 +1544,12 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! of days has elapsed since planting else if (hui(p) >= huigrain(p)) then + + ! SSR troubleshooting + if (gddmaturity(p) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) if (astemi(p) > astemf(ivt(p))) then From 8f473bcb792a1b7a3ffb6ebd8e35715ea96badf7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Feb 2022 15:29:11 -0700 Subject: [PATCH 0149/2067] Added checks for zero denominators throughout CNPhenologyMod. --- src/biogeochem/CNPhenologyMod.F90 | 34 +++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 93ad45458f..ec5125b6e8 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2109,6 +2109,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & onset_counter(p) = dt fert_counter(p) = ndays_on * secspday if (ndays_on .gt. 0) then + + ! SSR troubleshooting + if (fert_counter(p)==0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + fert(p) = (manunitro(ivt(p)) * 1000._r8 + fertnitro(p))/ fert_counter(p) else fert(p) = 0._r8 @@ -2151,6 +2157,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_seedc_to_leaf(p) = crop_seedc_to_leaf(p) - leafc_xfer(p)/dt crop_seedn_to_leaf(p) = crop_seedn_to_leaf(p) - leafn_xfer(p)/dt leafc_xfer(p) = 0._r8 + + ! SSR troubleshooting + if (leafcn(ivt(p)) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + leafn_xfer(p) = leafc_xfer(p) / leafcn(ivt(p)) if (use_c13) then c13_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8 @@ -2169,6 +2181,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (hui(p) >= huigrain(p)) then cphase(p) = 3._r8 + + ! SSR troubleshooting + if (leaf_long(ivt(p))*dayspyr*secspday == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + bglfr(p) = 1._r8/(leaf_long(ivt(p))*dayspyr*secspday) end if @@ -2191,6 +2209,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_seedn_to_leaf(p) = crop_seedn_to_leaf(p) - leafn_xfer(p)/dt onset_counter(p) = 0._r8 leafc_xfer(p) = 0._r8 + + ! SSR troubleshooting + if (leafcn(ivt(p)) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + leafn_xfer(p) = leafc_xfer(p) / leafcn(ivt(p)) if (use_c13) then c13_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8 @@ -2361,11 +2385,21 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif crop_inst%sdates_thisyr(p,s) = real(jday, r8) + ! SSR troubleshooting + if (leafcn_in == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset crop_seedc_to_leaf(p) = leafc_xfer(p)/dt crop_seedn_to_leaf(p) = leafn_xfer(p)/dt + ! SSR troubleshooting + if (cnveg_carbonstate_inst%totvegc_patch(p) == 0.0) then + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + ! because leafc_xfer is set above rather than incremneted through the normal process, must also set its isotope ! pools here. use totvegc_patch as the closest analogue if nonzero, and use initial value otherwise if (use_c13) then From 9a9aa0ef7a643e44be5f454beddb063f78b6a50e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Feb 2022 15:37:55 -0700 Subject: [PATCH 0150/2067] Removed a zero-denominator check that's already accounted for. --- src/biogeochem/CNPhenologyMod.F90 | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ec5125b6e8..cc83066100 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2395,11 +2395,6 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & crop_seedc_to_leaf(p) = leafc_xfer(p)/dt crop_seedn_to_leaf(p) = leafn_xfer(p)/dt - ! SSR troubleshooting - if (cnveg_carbonstate_inst%totvegc_patch(p) == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - ! because leafc_xfer is set above rather than incremneted through the normal process, must also set its isotope ! pools here. use totvegc_patch as the closest analogue if nonzero, and use initial value otherwise if (use_c13) then From 9b95bac29712f41faa28b83fae4083bd8c1c5236 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Feb 2022 16:36:49 -0700 Subject: [PATCH 0151/2067] Added some prints when entering/exiting functions. --- src/biogeochem/CNNDynamicsMod.F90 | 5 +++++ src/biogeochem/CNRootDynMod.F90 | 5 +++++ src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 | 10 +++++++++- src/main/subgridAveMod.F90 | 8 ++++++++ src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 | 4 ++++ src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 | 4 ++++ 6 files changed, 35 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 79310e335d..66e0f43a11 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -28,6 +28,7 @@ module CNNDynamicsMod ! SSR troubleshooting use abortutils , only : endrun use shr_log_mod , only : errMsg => shr_log_errMsg + use clm_varctl , only : iulog ! implicit none private @@ -337,6 +338,8 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & real(r8):: GDDfracthreshold3, GDDfracthreshold4 !----------------------------------------------------------------------- + write(iulog,*) 'Entering CNSoyfix()' + associate( & wf => waterdiagnosticbulk_inst%wf_col , & ! Input: [real(r8) (:) ] soil water as frac. of whc for top 0.5 m @@ -448,6 +451,8 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & end associate + write(iulog,*) 'Exiting CNSoyfix()' + end subroutine CNSoyfix end module CNNDynamicsMod diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90 index 4d34d54f7c..754c444623 100644 --- a/src/biogeochem/CNRootDynMod.F90 +++ b/src/biogeochem/CNRootDynMod.F90 @@ -22,6 +22,7 @@ module CNRootDynMod use SoilStateType , only : soilstate_type use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use CropType , only : crop_type + use clm_varctl , only : iulog ! !PUBLIC TYPES: implicit none @@ -101,6 +102,8 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & croplive => crop_inst%croplive_patch , & ! Input: [logical (:)] flag, true if planted, not harvested huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:)] same to reach vegetative maturity ) + + write(iulog,*)'Entering CNRootDyn()' ! set time steps dt = get_step_size_real() @@ -264,6 +267,8 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & end associate + write(iulog,*)'Exiting CNRootDyn()' + end subroutine CNRootDyn end module CNRootDynMod diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 37a6e6782c..95094c3303 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -300,6 +300,8 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & ! ----------------------------------------------------------------------- + write(iulog,*) 'Entering calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' + SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)) , sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp/)) , sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(fpg_col) == (/bounds%endc/)) , sourcefile, __LINE__) @@ -1119,6 +1121,8 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & end associate + write(iulog,*) 'Exiting calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' + end subroutine calc_plant_cn_alloc ! ----------------------------------------------------------------------- @@ -1259,6 +1263,8 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! ----------------------------------------------------------------------- + write(iulog,*) 'Entering calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' + SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(this%actual_leafcn) >= (/bounds%endp/)), sourcefile, __LINE__) @@ -1549,7 +1555,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & if (gddmaturity(p) == 0.0) then call endrun(msg=errMsg(sourcefile, __LINE__)) end if - + aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) if (astemi(p) > astemf(ivt(p))) then @@ -1782,6 +1788,8 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & end associate + write(iulog,*) 'Exiting calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' + end subroutine calc_plant_nitrogen_demand end module NutrientCompetitionFlexibleCNMod diff --git a/src/main/subgridAveMod.F90 b/src/main/subgridAveMod.F90 index c5ce4a4a98..5544771925 100644 --- a/src/main/subgridAveMod.F90 +++ b/src/main/subgridAveMod.F90 @@ -240,6 +240,8 @@ subroutine p2c_1d_filter (bounds, numfc, filterc, patcharr, colarr) ! !LOCAL VARIABLES: integer :: fc,c,p ! indices !----------------------------------------------------------------------- + + write(iulog,*)'Entering p2c_1d_filter()' ! Enforce expected array sizes SHR_ASSERT_ALL_FL((ubound(patcharr) == (/bounds%endp/)), sourcefile, __LINE__) @@ -253,6 +255,8 @@ subroutine p2c_1d_filter (bounds, numfc, filterc, patcharr, colarr) end do end do + write(iulog,*)'Exiting p2c_1d_filter()' + end subroutine p2c_1d_filter !----------------------------------------------------------------------- @@ -272,6 +276,8 @@ subroutine p2c_2d_filter (lev, numfc, filterc, patcharr, colarr) integer :: fc,c,p,j ! indices !----------------------------------------------------------------------- + write(iulog,*)'Entering p2c_2d_filter()' + do j = 1,lev do fc = 1,numfc c = filterc(fc) @@ -282,6 +288,8 @@ subroutine p2c_2d_filter (lev, numfc, filterc, patcharr, colarr) end do end do + write(iulog,*)'Exiting p2c_2d_filter()' + end subroutine p2c_2d_filter !----------------------------------------------------------------------- diff --git a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 index 3d99d93755..6c8fc6adde 100644 --- a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 @@ -48,6 +48,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & !----------------------------------------------------------------------- + write(iulog,*)'Entering SoilBiogeochemNStateUpdate1()' + associate( & cascade_donor_pool => decomp_cascade_con%cascade_donor_pool , & ! Input: [integer (:) ] which pool is C taken from for a given decomposition step cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input: [integer (:) ] which pool is C added to for a given decomposition step @@ -261,6 +263,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & end associate + write(iulog,*)'Exiting SoilBiogeochemNStateUpdate1()' + end subroutine SoilBiogeochemNStateUpdate1 end module SoilBiogeochemNStateUpdate1Mod diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index da5e2d4240..e420ea443b 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -962,6 +962,8 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda character(len=*), parameter :: subname = 'DynamicColumnAdjustments' !----------------------------------------------------------------------- + write(iulog,*)'Entering DynamicColumnAdjustments()' + begc = bounds%begc endc = bounds%endc @@ -1029,6 +1031,8 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda end if + write(iulog,*)'Exiting DynamicColumnAdjustments()' + end subroutine DynamicColumnAdjustments !------------------------------------------------------------------------ From c70316772cfd82a7a1eee1149213239793001e88 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Feb 2022 16:45:21 -0700 Subject: [PATCH 0152/2067] Removed entering/exiting statements for p2c*(). --- src/main/subgridAveMod.F90 | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/main/subgridAveMod.F90 b/src/main/subgridAveMod.F90 index 5544771925..5b592e5c09 100644 --- a/src/main/subgridAveMod.F90 +++ b/src/main/subgridAveMod.F90 @@ -241,8 +241,6 @@ subroutine p2c_1d_filter (bounds, numfc, filterc, patcharr, colarr) integer :: fc,c,p ! indices !----------------------------------------------------------------------- - write(iulog,*)'Entering p2c_1d_filter()' - ! Enforce expected array sizes SHR_ASSERT_ALL_FL((ubound(patcharr) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(colarr) == (/bounds%endc/)), sourcefile, __LINE__) @@ -255,8 +253,6 @@ subroutine p2c_1d_filter (bounds, numfc, filterc, patcharr, colarr) end do end do - write(iulog,*)'Exiting p2c_1d_filter()' - end subroutine p2c_1d_filter !----------------------------------------------------------------------- @@ -276,8 +272,6 @@ subroutine p2c_2d_filter (lev, numfc, filterc, patcharr, colarr) integer :: fc,c,p,j ! indices !----------------------------------------------------------------------- - write(iulog,*)'Entering p2c_2d_filter()' - do j = 1,lev do fc = 1,numfc c = filterc(fc) @@ -288,8 +282,6 @@ subroutine p2c_2d_filter (lev, numfc, filterc, patcharr, colarr) end do end do - write(iulog,*)'Exiting p2c_2d_filter()' - end subroutine p2c_2d_filter !----------------------------------------------------------------------- From aa1b0025a56b1b8d47a7057ebb2b0e9bdb0d4276 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 16 Feb 2022 13:53:44 -0700 Subject: [PATCH 0153/2067] Added ability to ignore prescribed crop GDDs. Intended for troubleshooting. New boolean parameter ignore_rx_crop_gdds, default false. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ src/biogeochem/CNPhenologyMod.F90 | 7 +++++-- 3 files changed, 11 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index b010e4b12e..b6270ca58d 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -566,6 +566,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. Constant .false. +.false. .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 4878b28691..93cde98748 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1108,6 +1108,11 @@ Phenology onset depends on the vegetation type Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. + +Set to .true. in order to override prescribed crop GDD requirements and instead use default CLM values/logic. For troubleshooting purposes only. + + Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index cc83066100..7c76978842 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -125,6 +125,7 @@ module CNPhenologyMod real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing + logical :: ignore_rx_crop_gdds = .false. ! Troubleshooting ! Constants for seasonal decidious leaf onset and offset logical, private :: onset_thresh_depends_on_veg = .false. ! If onset threshold depends on vegetation type @@ -167,7 +168,8 @@ subroutine CNPhenologyReadNML( NLFilename ) character(len=*), parameter :: nmlname = 'cnphenology' !----------------------------------------------------------------------- namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, & - min_critical_dayl_method, generate_crop_gdds + min_critical_dayl_method, generate_crop_gdds, & + ignore_rx_crop_gdds ! Initialize options to default values, in case they are not specified in ! the namelist @@ -192,6 +194,7 @@ subroutine CNPhenologyReadNML( NLFilename ) call shr_mpi_bcast (onset_thresh_depends_on_veg, mpicom) call shr_mpi_bcast (min_critical_dayl_method, mpicom) call shr_mpi_bcast (generate_crop_gdds, mpicom) + call shr_mpi_bcast (ignore_rx_crop_gdds, mpicom) if ( min_critical_dayl_method == "DependsOnLat" )then critical_daylight_method = critical_daylight_depends_on_lat @@ -2415,7 +2418,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target - if (do_plant_prescribed .and. .not. generate_crop_gdds) then + if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds)) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) if (gdd_target < 0.0) then write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' From 42a76f3a258d356cae26f7b202684cc8e5866bfb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 16 Feb 2022 14:04:11 -0700 Subject: [PATCH 0154/2067] Added a print of assigned crop GDD reqt. --- src/biogeochem/CNPhenologyMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7c76978842..9acc0aefec 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2453,6 +2453,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if endif + write (iulog,*) 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) end associate From 04d89300a4e8d39ee2136dc2d7b1c021e4bfac1c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 16 Feb 2022 14:10:33 -0700 Subject: [PATCH 0155/2067] Added real parameter min_crop_gdd_target. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ src/biogeochem/CNPhenologyMod.F90 | 6 ++++-- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index b6270ca58d..c9f5342c6c 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -567,6 +567,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Constant .false. .false. +1.d00 .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 93cde98748..6d67eacb24 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1113,6 +1113,11 @@ Set to .true. in order to override crop harvesting logic and to instead harvest Set to .true. in order to override prescribed crop GDD requirements and instead use default CLM values/logic. For troubleshooting purposes only. + +Set minimum crop GDD requirement. Used only with prescribed GDD inputs from file. + + Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9acc0aefec..e8cd6ed96f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -126,6 +126,7 @@ module CNPhenologyMod logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing logical :: ignore_rx_crop_gdds = .false. ! Troubleshooting + real(r8) :: min_crop_gdd_target = 1._r8 ! Troubleshooting ! Constants for seasonal decidious leaf onset and offset logical, private :: onset_thresh_depends_on_veg = .false. ! If onset threshold depends on vegetation type @@ -169,7 +170,7 @@ subroutine CNPhenologyReadNML( NLFilename ) !----------------------------------------------------------------------- namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, & min_critical_dayl_method, generate_crop_gdds, & - ignore_rx_crop_gdds + ignore_rx_crop_gdds, min_crop_gdd_target ! Initialize options to default values, in case they are not specified in ! the namelist @@ -195,6 +196,7 @@ subroutine CNPhenologyReadNML( NLFilename ) call shr_mpi_bcast (min_critical_dayl_method, mpicom) call shr_mpi_bcast (generate_crop_gdds, mpicom) call shr_mpi_bcast (ignore_rx_crop_gdds, mpicom) + call shr_mpi_bcast (min_crop_gdd_target, mpicom) if ( min_critical_dayl_method == "DependsOnLat" )then critical_daylight_method = critical_daylight_depends_on_lat @@ -2427,7 +2429,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 - gdd_target = max(gdd_target, 1._r8) + gdd_target = max(gdd_target, min_crop_gdd_target) gddmaturity(p) = gdd_target else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then From 46b5d64dbc81165fb08925f1956ac36948d28634 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 17 Feb 2022 18:38:53 +0100 Subject: [PATCH 0156/2067] Revert "add excess ice to soil temperature mod" This reverts commit d55ba7c29a9680c33289930e6260084e9b4a601b. --- src/biogeophys/SoilTemperatureMod.F90 | 129 ++------------------------ 1 file changed, 9 insertions(+), 120 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 3647534334..ba4432cba2 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -115,7 +115,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd use clm_varctl , only : iulog - use clm_varcon , only : cnfac, cpice, cpliq, denh2o, denice + use clm_varcon , only : cnfac, cpice, cpliq, denh2o use landunit_varcon , only : istsoil, istcrop use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv use BandDiagonalMod , only : BandDiagonal @@ -171,10 +171,6 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter real(r8) :: hs_top_snow(bounds%begc:bounds%endc) ! heat flux on top snow layer [W/m2] real(r8) :: hs_h2osfc(bounds%begc:bounds%endc) ! heat flux on standing water [W/m2] integer :: jbot(bounds%begc:bounds%endc) ! bottom level at each column - real(r8) :: dz_0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! original layer thickness [m] - real(r8) :: z_0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! original layer depth [m] - real(r8) :: zi_0(bounds%begc:bounds%endc,-nlevsno+0:nlevmaxurbgrnd) ! original layer interface level bellow layer "z" [m] - !----------------------------------------------------------------------- associate( & @@ -198,7 +194,6 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter frac_sno_eff => waterdiagnosticbulk_inst%frac_sno_eff_col , & ! Input: [real(r8) (:) ] eff. fraction of ground covered by snow (0 to 1) snow_depth => waterdiagnosticbulk_inst%snow_depth_col , & ! Input: [real(r8) (:) ] snow height (m) h2osfc => waterstatebulk_inst%h2osfc_col , & ! Input: [real(r8) (:) ] surface water (mm) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col , & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) @@ -276,29 +271,6 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter endif end do - - !-------------------------------------------------------------- - ! Vertical coordinates adjustment for excess ice calculations - !-------------------------------------------------------------- - ! Save original soil depth to get put them back in et the end - dz_0(begc:endc,1:nlevmaxurbgrnd)=dz(begc:endc,1:nlevmaxurbgrnd) - zi_0(begc:endc,1:nlevmaxurbgrnd)=zi(begc:endc,1:nlevmaxurbgrnd) - z_0(begc:endc,1:nlevmaxurbgrnd)=z(begc:endc,1:nlevmaxurbgrnd) - ! Adjust column depth for excess ice thickness - do fc = 1,num_nolakec - c = filter_nolakec(fc) - l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness - do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment - zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice - z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 - end do - endif - end do - - - !------------------------------------------------------ ! Compute ground surface and soil temperatures !------------------------------------------------------ @@ -516,23 +488,6 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter dhsdT(bounds%begc:bounds%endc), & soilstate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, waterfluxbulk_inst, energyflux_inst, temperature_inst) - !-------------------------------------------------------------- - ! Vertical coordinates adjustment for excess ice calculations - !-------------------------------------------------------------- - ! bringing back the soil depth to the original state - ! Adjust column depth for excess ice thickness - do fc = 1,num_nolakec - c = filter_nolakec(fc) - l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) - zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) - z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) - endif - end do - - - if ( IsProgBuildTemp() )then call BuildingTemperature(bounds, num_urbanl, filter_urbanl, num_nolakec, filter_nolakec, & tk(bounds%begc:bounds%endc, :), urbanparams_inst, & @@ -673,7 +628,6 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Input: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) bw => waterdiagnosticbulk_inst%bw_col , & ! Output: [real(r8) (:,:) ] partial density of water in the snow pack (ice + liquid) [kg/m3] tkmg => soilstate_inst%tkmg_col , & ! Input: [real(r8) (:,:) ] thermal conductivity, soil minerals [W/m-K] @@ -700,8 +654,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - ! TODO recalculate watsat and satw to have excess ice included - satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice +excess_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) + satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) satw = min(1._r8, satw) if (satw > .1e-6_r8) then if (t_soisno(c,j) >= tfrz) then ! Unfrozen soil @@ -710,7 +663,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter dke = satw end if fl = (h2osoi_liq(c,j)/(denh2o*dz(c,j))) / (h2osoi_liq(c,j)/(denh2o*dz(c,j)) + & - h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/denice) + h2osoi_ice(c,j)/(denice*dz(c,j))) dksat = tkmg(c,j)*tkwat**(fl*watsat(c,j))*tkice**((1._r8-fl)*watsat(c,j)) thk(c,j) = dke*dksat + (1._r8-dke)*tkdry(c,j) else @@ -803,7 +756,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter .and. col%itype(c) /= icol_sunwall .and. col%itype(c) /= icol_shadewall .and. & col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) + excess_ice(c,j)*cpice + cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) if (j > nbedrock(c)) cv(c,j) = csol_bedrock*dz(c,j) else if (lun%itype(l) == istwet) then cv(c,j) = (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) @@ -1104,7 +1057,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd use clm_varctl , only : iulog - use clm_varcon , only : tfrz, hfus, grav, denice + use clm_varcon , only : tfrz, hfus, grav use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv use landunit_varcon , only : istsoil, istcrop, istice ! @@ -1135,11 +1088,6 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: propor !proportionality constant (-) real(r8) :: tinc(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !t(n+1)-t(n) [K] real(r8) :: smp !frozen water potential (mm) - real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] - real(r8) :: xm3(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] - real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd)!initial mass of excess_ice at the timestep (kg/m2) - - !----------------------------------------------------------------------- call t_startf( 'PhaseChangebeta' ) @@ -1161,11 +1109,6 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Output: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) - init_exice => waterstatebulk_inst%init_exice , & ! Input: [real(r8) (:) ] excess soil ice initial - exice_melt => waterstatebulk_inst%exice_melt , & ! Input: [real(r8) (:) ] excess soil ice - exice_melt_lev => waterstatebulk_inst%exice_melt_lev , & ! Input: [real(r8) (:,:) ] excess soil ice - qflx_snow_drain => waterfluxbulk_inst%qflx_snow_drain_col , & ! Output: [real(r8) (:) ] drainage from snow pack qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] @@ -1209,12 +1152,9 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & imelt(c,j) = 0 hm(c,j) = 0._r8 xm(c,j) = 0._r8 - xm2(c,j)=0._r8 - xm3(c,j)=0._r8 wice0(c,j) = h2osoi_ice(c,j) wliq0(c,j) = h2osoi_liq(c,j) wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) - wexice0(c,j)=excess_ice(c,j) endif ! end of snow layer if-block if (j <= 0) then @@ -1271,13 +1211,6 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & t_soisno(c,j) = tfrz endif - ! melt excess ice after normal ice - if (excess_ice(c,j) > 0._r8 .AND. t_soisno(c,j) > tfrz) then - imelt(c,j) = 1 - tinc(c,j) = tfrz - t_soisno(c,j) - t_soisno(c,j) = tfrz - endif - ! from Zhao (1997) and Koren (1999) supercool(c,j) = 0.0_r8 if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop .or. col%itype(c) == icol_road_perv) then @@ -1392,49 +1325,9 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif heatr = 0._r8 - if (xm(c,j) > 0._r8) then !if there is excess heat to melt the ice - !h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) ! no excess ice - !heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime ! on excess ice - ! excess ice modifications - if (h2osoi_ice(c,j)>0._r8) then !if there is normal soil ice - if (xm(c,j)> h2osoi_ice(c,j)) then ! if we can melt all normal ice first - xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) - h2osoi_ice(c,j) = 0._r8 - if (excess_ice(c,j) > 0._r8) then ! if there is excess ice to melt - if (xm2(c,j) > excess_ice(c,j)) then ! there is still enough heat left to melt all of the ice - xm3(c,j) = xm2(c,j) - excess_ice(c,j) - excess_ice(c,j) = 0._r8 - heatr = hfus * xm3(c,j) / dtime - else ! if there is not enough heat to melt all excess ice - excess_ice(c,j) = excess_ice(c,j)-xm2(c,j) - heatr = 0._r8 - xm3(c,j) = 0._r8 - endif - else !no excess ice to melt heat soil - heatr = hfus * xm2(c,j) / dtime - endif - else ! not enough heat to melt all normal ice - h2osoi_ice(c,j) = h2osoi_ice(c,j)-xm(c,j) - heatr = 0._r8 - xm2(c,j) = 0._r8 - endif - else !no normal ice present - xm2(c,j) = xm(c,j) - if (excess_ice(c,j) > 0._r8) then ! if there is excess ice to melt - if (xm2(c,j) > excess_ice(c,j)) then ! there is still enough heat left to melt all of the ice - xm3(c,j) = xm2(c,j)-excess_ice(c,j) - excess_ice(c,j) = 0._r8 - heatr = hfus * xm3(c,j) / dtime - else ! if there is not enough heat to melt all excess ice - excess_ice(c,j) = excess_ice(c,j)-xm2(c,j) - heatr = 0._r8 - xm3(c,j) = 0._r8 - endif - else !no excess ice to melt heat soil - heatr = hfus * xm2(c,j) / dtime - endif - endif - + if (xm(c,j) > 0._r8) then + h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) + heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime else if (xm(c,j) < 0._r8) then if (j <= 0) then h2osoi_ice(c,j) = min(wmass0(c,j), wice0(c,j)-xm(c,j)) ! snow @@ -1480,8 +1373,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif ! end of heatr > 0 if-block if (j >= 1) then - xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime - exice_melt_lev(c,j)=wexice0(c,j)-excess_ice(c,j) + xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif @@ -1506,20 +1398,17 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & end do ! end of column-loop enddo ! end of level-loop - ! Needed for history file output do fc = 1,num_nolakec c = filter_nolakec(fc) eflx_snomelt(c) = qflx_snomelt(c) * hfus - exice_melt(c) = 0.0_r8 l = col%landunit(c) if (lun%urbpoi(l)) then eflx_snomelt_u(c) = eflx_snomelt(c) else if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then eflx_snomelt_r(c) = eflx_snomelt(c) end if - exice_melt(c) = exice_melt(c) + SUM( exice_melt_lev(c,:) ) / denice end do call t_stopf( 'PhaseChangebeta' ) From cdcc4c7bb9c1217a2e0fe5f6ef27d70d81ae94ff Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 17 Feb 2022 11:37:06 -0700 Subject: [PATCH 0157/2067] More troubleshooting stuff. --- src/biogeochem/CNPhenologyMod.F90 | 6 +- src/cpl/share_esmf/cropcalStreamMod.F90 | 175 ++++++++++++------------ 2 files changed, 94 insertions(+), 87 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e8cd6ed96f..9c4851d297 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2420,7 +2420,9 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target - if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds)) then + if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. .true.)) then +write(iulog,*) '???' +call endrun(msg=errMsg(sourcefile, __LINE__)) gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) if (gdd_target < 0.0) then write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' @@ -2455,7 +2457,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if endif - write (iulog,*) 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) + write (iulog,'(a,i4,a,f0.0)') 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) end associate diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 31e6a56fbe..8f0710a61b 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -351,95 +351,100 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) allocate(dataptr1d_cultivar_gdds(lsize)) allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (.not. generate_crop_gdds) then - if (verbose) write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' + !if (.false.) then + !if (verbose) write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' + write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' ! Read prescribed cultivar GDDs from input files - dataptr1d_cultivar_gdds(:) = -4 - dataptr2d_cultivar_gdds(:,:) = -5 +! dataptr1d_cultivar_gdds(:) = -4 +! dataptr2d_cultivar_gdds(:,:) = -5 ! Starting with npcropmin will skip generic crops - do n = 1, ncft - call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & - fldptr1=dataptr1d_cultivar_gdds, rc=rc) - - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize - ! So an explicit loop is required here - do g = 1,lsize - - ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then - write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' - warned_about_bad_interp_cultivar_gdds = .true. - end if - - dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) - end do - end do +! do n = 1, ncft +! call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & +! fldptr1=dataptr1d_cultivar_gdds, rc=rc) +! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & +! fldptr1=dataptr1d_sdate, rc=rc) +! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & +! fldptr1=dataptr1d_cultivar_gdds, rc=rc) +! +! if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then +! call ESMF_Finalize(endflag=ESMF_END_ABORT) +! end if +! ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize +! ! So an explicit loop is required here +!! do g = 1,lsize +!! +!!! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. +!!! if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then +!!! write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' +!!! warned_about_bad_interp_cultivar_gdds = .true. +!!! end if +!! +!! dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) +!! end do +! end do ! Set rx_cultivar_gdd for each gridcell/patch combination - if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' - do fp = 1, num_pcropp - p = filter_pcropp(fp) - - - if (.not. patch%active(p)) then - continue - end if - - ivt = patch%itype(p) - ! Will skip generic crops - if (ivt >= npcropmin) then - n = ivt - npcropmin + 1 - - if (n > ncft) then - write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - - ! vegetated pft - ig = g_to_ig(patch%gridcell(p)) - - - if (ig > lsize) then - write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - - if (dataptr2d_cultivar_gdds(ig,n) < -0.001 .or. dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then - !if (dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then - if (dataptr2d_cultivar_gdds(ig,n) == 0.0) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ZERO??? ',dataptr2d_cultivar_gdds(ig,n) - else if (dataptr2d_cultivar_gdds(ig,n) < -0.001) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement NEGATIVE ',dataptr2d_cultivar_gdds(ig,n) - else - write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement HUGE ',dataptr2d_cultivar_gdds(ig,n) - end if -! call ESMF_Finalize(endflag=ESMF_END_ABORT) - - ! TEMPORARY!!! - dataptr2d_cultivar_gdds(ig,n) = 0.0 - end if - - crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) - - ! Sanity check: Should not read in negative values. Also try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then - !if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) - else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) - else - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) - end if - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - else - write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt - call ESMF_Finalize(endflag=ESMF_END_ABORT) - endif - end do +! if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' +! do fp = 1, num_pcropp +! p = filter_pcropp(fp) +! +!! if (.not. patch%active(p)) then +!! continue +!! end if +! +! ivt = patch%itype(p) +! ! Will skip generic crops +! if (ivt >= npcropmin) then +! n = ivt - npcropmin + 1 +! +!! if (n > ncft) then +!! write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' +!! call ESMF_Finalize(endflag=ESMF_END_ABORT) +!! end if +! +! ! vegetated pft +! ig = g_to_ig(patch%gridcell(p)) +! +!! if (ig > lsize) then +!! write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' +!! call ESMF_Finalize(endflag=ESMF_END_ABORT) +!! end if +! +!! if (dataptr2d_cultivar_gdds(ig,n) < -0.001 .or. dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then +!! !if (dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then +!! if (dataptr2d_cultivar_gdds(ig,n) == 0.0) then +!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ZERO??? ',dataptr2d_cultivar_gdds(ig,n) +!! else if (dataptr2d_cultivar_gdds(ig,n) < -0.001) then +!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement NEGATIVE ',dataptr2d_cultivar_gdds(ig,n) +!! else +!! write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement HUGE ',dataptr2d_cultivar_gdds(ig,n) +!! end if +!!! call ESMF_Finalize(endflag=ESMF_END_ABORT) +!! +!! ! TEMPORARY!!! +!! dataptr2d_cultivar_gdds(ig,n) = 0.0 +!! end if +! +!!!!!!!!!!! crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) +! +!! ! Sanity check: Should not read in negative values. Also try to catch uninitialized values +!! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then +!! !if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then +!! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then +!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) +!! else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then +!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) +!! else +!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) +!! end if +!! call ESMF_Finalize(endflag=ESMF_END_ABORT) +!! end if +!! else +!! write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt +!! call ESMF_Finalize(endflag=ESMF_END_ABORT) +! endif +! end do + write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file DONE' end if ! not generate_crop_gdds deallocate(dataptr1d_cultivar_gdds) From 2f88277f861a4fd7302edda353057622c487e727 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 17 Feb 2022 15:59:54 -0700 Subject: [PATCH 0158/2067] This doesn't crash. Next, try re-enabling things in cropcal_interp(). --- src/cpl/nuopc/lnd_comp_nuopc.F90 | 2 + src/cpl/share_esmf/cropcalStreamMod.F90 | 73 ++++++++++++++----------- 2 files changed, 44 insertions(+), 31 deletions(-) diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90 index 352ff03cdd..91e13ee95e 100644 --- a/src/cpl/nuopc/lnd_comp_nuopc.F90 +++ b/src/cpl/nuopc/lnd_comp_nuopc.F90 @@ -891,8 +891,10 @@ subroutine ModelAdvance(gcomp, rc) !-------------------------------- call t_startf ('lc_lnd_export') + write(iulog,*) 'calling export_fields()' call export_fields(gcomp, bounds, glc_present, rof_prognostic, & water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, rc) + write(iulog,*) 'done with export_fields()' if (ChkErr(rc,__LINE__,u_FILE_u)) return call t_stopf ('lc_lnd_export') diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 8f0710a61b..28e7581467 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -275,7 +275,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) integer :: n, g integer :: lsize integer :: rc - real(r8), pointer :: dataptr1d_sdate(:) +! real(r8), pointer :: dataptr1d_sdate(:) + real(r8), pointer :: dataptr1d(:) real(r8), pointer :: dataptr2d_sdate(:,:) real(r8), pointer :: dataptr1d_cultivar_gdds(:) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) @@ -292,16 +293,20 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) lsize = bounds%endg - bounds%begg + 1 ! Read prescribed sowing dates from input files - allocate(dataptr1d_sdate(lsize)) - dataptr1d_sdate(:) = -4 +! allocate(dataptr1d_sdate(lsize)) +! dataptr1d_sdate(:) = -4 +! allocate(dataptr1d(lsize)) +! dataptr1d(:) = -4 allocate(dataptr2d_sdate(lsize, ncft)) dataptr2d_sdate(:,:) = -5 ! Starting with npcropmin will skip generic crops if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft ivt = n + npcropmin - 1 +! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & +! fldptr1=dataptr1d_sdate, rc=rc) call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & - fldptr1=dataptr1d_sdate, rc=rc) + fldptr1=dataptr1d, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -309,13 +314,14 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! So an explicit loop is required here do g = 1,lsize - ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then - write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop ivt ',ivt,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' - warned_about_bad_interp_sdate = .true. - end if +! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. +! if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then +! write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop ivt ',ivt,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' +! warned_about_bad_interp_sdate = .true. +! end if - dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + !dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + dataptr2d_sdate(g,n) = dataptr1d(g) end do end do @@ -344,11 +350,12 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do - deallocate(dataptr1d_sdate) + !deallocate(dataptr1d_sdate) + deallocate(dataptr1d) deallocate(dataptr2d_sdate) if (verbose) write(iulog,*) 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' - allocate(dataptr1d_cultivar_gdds(lsize)) +! allocate(dataptr1d_cultivar_gdds(lsize)) allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (.not. generate_crop_gdds) then !if (.false.) then @@ -358,30 +365,33 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! dataptr1d_cultivar_gdds(:) = -4 ! dataptr2d_cultivar_gdds(:,:) = -5 ! Starting with npcropmin will skip generic crops -! do n = 1, ncft + do n = 1, ncft ! call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & ! fldptr1=dataptr1d_cultivar_gdds, rc=rc) +!SO IT WORKS WHEN I USE SDATE''S DATAPTR1D ! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & ! fldptr1=dataptr1d_sdate, rc=rc) ! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & ! fldptr1=dataptr1d_cultivar_gdds, rc=rc) -! -! if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then -! call ESMF_Finalize(endflag=ESMF_END_ABORT) -! end if -! ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize -! ! So an explicit loop is required here -!! do g = 1,lsize -!! -!!! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. -!!! if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then -!!! write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' -!!! warned_about_bad_interp_cultivar_gdds = .true. -!!! end if -!! -!! dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) -!! end do -! end do + call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & + fldptr1=dataptr1d, rc=rc) + + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize + ! So an explicit loop is required here +! do g = 1,lsize +! +!! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. +!! if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then +!! write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' +!! warned_about_bad_interp_cultivar_gdds = .true. +!! end if +! +! dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) +! end do + end do ! Set rx_cultivar_gdd for each gridcell/patch combination ! if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' @@ -447,7 +457,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file DONE' end if ! not generate_crop_gdds - deallocate(dataptr1d_cultivar_gdds) +! deallocate(dataptr1d_cultivar_gdds) +! deallocate(dataptr1d) deallocate(dataptr2d_cultivar_gdds) if (verbose) write(iulog,*) 'cropcal_interp(): All done!' From 77aad9fa8e777f1cb609f7b8433a2db2373f4b3b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 17 Feb 2022 17:13:20 -0700 Subject: [PATCH 0159/2067] This works AND it actually uses the cultivar GDDs! --- src/biogeochem/CNNDynamicsMod.F90 | 4 +- src/biogeochem/CNPhenologyMod.F90 | 12 +- src/biogeochem/CNRootDynMod.F90 | 4 +- .../NutrientCompetitionFlexibleCNMod.F90 | 8 +- src/cpl/nuopc/lnd_comp_nuopc.F90 | 2 - src/cpl/share_esmf/cropcalStreamMod.F90 | 143 +++++++++--------- .../SoilBiogeochemNStateUpdate1Mod.F90 | 4 +- .../SoilBiogeochemNitrogenStateType.F90 | 4 +- 8 files changed, 91 insertions(+), 90 deletions(-) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 66e0f43a11..2a9bc86589 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -338,7 +338,7 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & real(r8):: GDDfracthreshold3, GDDfracthreshold4 !----------------------------------------------------------------------- - write(iulog,*) 'Entering CNSoyfix()' +! write(iulog,*) 'Entering CNSoyfix()' associate( & wf => waterdiagnosticbulk_inst%wf_col , & ! Input: [real(r8) (:) ] soil water as frac. of whc for top 0.5 m @@ -451,7 +451,7 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & end associate - write(iulog,*) 'Exiting CNSoyfix()' +! write(iulog,*) 'Exiting CNSoyfix()' end subroutine CNSoyfix diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9c4851d297..ddf9ec3b61 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2420,14 +2420,12 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target - if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. .true.)) then -write(iulog,*) '???' -call endrun(msg=errMsg(sourcefile, __LINE__)) + if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds)) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) - if (gdd_target < 0.0) then - write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif +! if (gdd_target < 0.0) then +! write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' +! call endrun(msg=errMsg(sourcefile, __LINE__)) +! endif ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90 index 754c444623..e6f42dd632 100644 --- a/src/biogeochem/CNRootDynMod.F90 +++ b/src/biogeochem/CNRootDynMod.F90 @@ -103,7 +103,7 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:)] same to reach vegetative maturity ) - write(iulog,*)'Entering CNRootDyn()' +! write(iulog,*)'Entering CNRootDyn()' ! set time steps dt = get_step_size_real() @@ -267,7 +267,7 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & end associate - write(iulog,*)'Exiting CNRootDyn()' +! write(iulog,*)'Exiting CNRootDyn()' end subroutine CNRootDyn diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 95094c3303..a6070bcff4 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -300,7 +300,7 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & ! ----------------------------------------------------------------------- - write(iulog,*) 'Entering calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' +! write(iulog,*) 'Entering calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)) , sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp/)) , sourcefile, __LINE__) @@ -1121,7 +1121,7 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & end associate - write(iulog,*) 'Exiting calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' +! write(iulog,*) 'Exiting calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' end subroutine calc_plant_cn_alloc @@ -1263,7 +1263,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! ----------------------------------------------------------------------- - write(iulog,*) 'Entering calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' +! write(iulog,*) 'Entering calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp/)), sourcefile, __LINE__) @@ -1788,7 +1788,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & end associate - write(iulog,*) 'Exiting calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' +! write(iulog,*) 'Exiting calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' end subroutine calc_plant_nitrogen_demand diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90 index 91e13ee95e..352ff03cdd 100644 --- a/src/cpl/nuopc/lnd_comp_nuopc.F90 +++ b/src/cpl/nuopc/lnd_comp_nuopc.F90 @@ -891,10 +891,8 @@ subroutine ModelAdvance(gcomp, rc) !-------------------------------- call t_startf ('lc_lnd_export') - write(iulog,*) 'calling export_fields()' call export_fields(gcomp, bounds, glc_present, rof_prognostic, & water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, rc) - write(iulog,*) 'done with export_fields()' if (ChkErr(rc,__LINE__,u_FILE_u)) return call t_stopf ('lc_lnd_export') diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 28e7581467..3b6a4b7e48 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -373,7 +373,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! fldptr1=dataptr1d_sdate, rc=rc) ! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & ! fldptr1=dataptr1d_cultivar_gdds, rc=rc) - call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & +! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & +! fldptr1=dataptr1d, rc=rc) + call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & fldptr1=dataptr1d, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then @@ -381,79 +383,82 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end if ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize ! So an explicit loop is required here -! do g = 1,lsize -! -!! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. -!! if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then -!! write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' -!! warned_about_bad_interp_cultivar_gdds = .true. -!! end if -! + do g = 1,lsize + +! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. +! if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then +! write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' +! warned_about_bad_interp_cultivar_gdds = .true. +! end if + ! dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) -! end do + dataptr2d_cultivar_gdds(g,n) = dataptr1d(g) + write (iulog,'(a,i4,a,f0.0)') 'dataptr1d(g) (ivt ',ivt,'): ',dataptr1d(g) + end do end do ! Set rx_cultivar_gdd for each gridcell/patch combination -! if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' -! do fp = 1, num_pcropp -! p = filter_pcropp(fp) -! -!! if (.not. patch%active(p)) then -!! continue -!! end if -! -! ivt = patch%itype(p) -! ! Will skip generic crops -! if (ivt >= npcropmin) then -! n = ivt - npcropmin + 1 -! -!! if (n > ncft) then -!! write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' -!! call ESMF_Finalize(endflag=ESMF_END_ABORT) -!! end if -! -! ! vegetated pft -! ig = g_to_ig(patch%gridcell(p)) -! -!! if (ig > lsize) then -!! write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' -!! call ESMF_Finalize(endflag=ESMF_END_ABORT) -!! end if -! -!! if (dataptr2d_cultivar_gdds(ig,n) < -0.001 .or. dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then -!! !if (dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then -!! if (dataptr2d_cultivar_gdds(ig,n) == 0.0) then -!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ZERO??? ',dataptr2d_cultivar_gdds(ig,n) -!! else if (dataptr2d_cultivar_gdds(ig,n) < -0.001) then -!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement NEGATIVE ',dataptr2d_cultivar_gdds(ig,n) -!! else -!! write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement HUGE ',dataptr2d_cultivar_gdds(ig,n) -!! end if -!!! call ESMF_Finalize(endflag=ESMF_END_ABORT) -!! -!! ! TEMPORARY!!! -!! dataptr2d_cultivar_gdds(ig,n) = 0.0 -!! end if -! -!!!!!!!!!!! crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) -! -!! ! Sanity check: Should not read in negative values. Also try to catch uninitialized values -!! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then -!! !if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then -!! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then -!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -!! else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then -!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -!! else -!! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -!! end if + if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' + do fp = 1, num_pcropp + p = filter_pcropp(fp) + +! if (.not. patch%active(p)) then +! continue +! end if + + ivt = patch%itype(p) + ! Will skip generic crops + if (ivt >= npcropmin) then + n = ivt - npcropmin + 1 + +! if (n > ncft) then +! write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' +! call ESMF_Finalize(endflag=ESMF_END_ABORT) +! end if + + ! vegetated pft + ig = g_to_ig(patch%gridcell(p)) + +! if (ig > lsize) then +! write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' +! call ESMF_Finalize(endflag=ESMF_END_ABORT) +! end if + +! if (dataptr2d_cultivar_gdds(ig,n) < -0.001 .or. dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then +! !if (dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then +! if (dataptr2d_cultivar_gdds(ig,n) == 0.0) then +! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ZERO??? ',dataptr2d_cultivar_gdds(ig,n) +! else if (dataptr2d_cultivar_gdds(ig,n) < -0.001) then +! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement NEGATIVE ',dataptr2d_cultivar_gdds(ig,n) +! else +! write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement HUGE ',dataptr2d_cultivar_gdds(ig,n) +! end if !! call ESMF_Finalize(endflag=ESMF_END_ABORT) -!! end if -!! else -!! write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt -!! call ESMF_Finalize(endflag=ESMF_END_ABORT) -! endif -! end do +! +! ! TEMPORARY!!! +! dataptr2d_cultivar_gdds(ig,n) = 0.0 +! end if + + crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) + write (iulog,'(a,i4,a,f0.0)') 'crop_inst%rx_cultivar_gdds_thisyr(p,1) (ivt ',ivt,'): ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + +! ! Sanity check: Should not read in negative values. Also try to catch uninitialized values +! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then +! !if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then +! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then +! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) +! else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then +! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) +! else +! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) +! end if +! call ESMF_Finalize(endflag=ESMF_END_ABORT) +! end if +! else +! write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt +! call ESMF_Finalize(endflag=ESMF_END_ABORT) + endif + end do write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file DONE' end if ! not generate_crop_gdds diff --git a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 index 6c8fc6adde..48c64a3b82 100644 --- a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 @@ -48,7 +48,7 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & !----------------------------------------------------------------------- - write(iulog,*)'Entering SoilBiogeochemNStateUpdate1()' +! write(iulog,*)'Entering SoilBiogeochemNStateUpdate1()' associate( & cascade_donor_pool => decomp_cascade_con%cascade_donor_pool , & ! Input: [integer (:) ] which pool is C taken from for a given decomposition step @@ -263,7 +263,7 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & end associate - write(iulog,*)'Exiting SoilBiogeochemNStateUpdate1()' +! write(iulog,*)'Exiting SoilBiogeochemNStateUpdate1()' end subroutine SoilBiogeochemNStateUpdate1 diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index e420ea443b..6e00292bad 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -962,7 +962,7 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda character(len=*), parameter :: subname = 'DynamicColumnAdjustments' !----------------------------------------------------------------------- - write(iulog,*)'Entering DynamicColumnAdjustments()' +! write(iulog,*)'Entering DynamicColumnAdjustments()' begc = bounds%begc endc = bounds%endc @@ -1031,7 +1031,7 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda end if - write(iulog,*)'Exiting DynamicColumnAdjustments()' +! write(iulog,*)'Exiting DynamicColumnAdjustments()' end subroutine DynamicColumnAdjustments From 9164e778242030353fb8f83fe9e1781df9dee110 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 18 Feb 2022 09:25:01 -0700 Subject: [PATCH 0160/2067] Cleaning up. --- src/biogeochem/CNPhenologyMod.F90 | 9 +- src/cpl/share_esmf/cropcalStreamMod.F90 | 125 ++++++++---------------- 2 files changed, 43 insertions(+), 91 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ddf9ec3b61..b28fb1946c 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2422,13 +2422,12 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ! set GDD target if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds)) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) -! if (gdd_target < 0.0) then -! write(iulog,*) 'If using prescribed sowing dates and not generate_crop_gdds, you must provide cultivar GDD targets >= 0.0.' -! call endrun(msg=errMsg(sourcefile, __LINE__)) -! endif ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 + if (gdd_target < min_crop_gdd_target) then + write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gdd_target ',gdd_target,'; using min_crop_gdd_target instead (',min_crop_gdd_target,')' + endif gdd_target = max(gdd_target, min_crop_gdd_target) gddmaturity(p) = gdd_target @@ -2455,7 +2454,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if endif - write (iulog,'(a,i4,a,f0.0)') 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) +! write (iulog,'(a,i4,a,f0.0)') 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) end associate diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 3b6a4b7e48..6573e676e5 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -275,8 +275,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) integer :: n, g integer :: lsize integer :: rc -! real(r8), pointer :: dataptr1d_sdate(:) - real(r8), pointer :: dataptr1d(:) + real(r8), pointer :: dataptr1d_sdate(:) real(r8), pointer :: dataptr2d_sdate(:,:) real(r8), pointer :: dataptr1d_cultivar_gdds(:) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) @@ -293,20 +292,14 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) lsize = bounds%endg - bounds%begg + 1 ! Read prescribed sowing dates from input files -! allocate(dataptr1d_sdate(lsize)) -! dataptr1d_sdate(:) = -4 -! allocate(dataptr1d(lsize)) -! dataptr1d(:) = -4 allocate(dataptr2d_sdate(lsize, ncft)) dataptr2d_sdate(:,:) = -5 ! Starting with npcropmin will skip generic crops if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft ivt = n + npcropmin - 1 -! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & -! fldptr1=dataptr1d_sdate, rc=rc) call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & - fldptr1=dataptr1d, rc=rc) + fldptr1=dataptr1d_sdate, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -314,14 +307,13 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! So an explicit loop is required here do g = 1,lsize -! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. -! if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then -! write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop ivt ',ivt,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' -! warned_about_bad_interp_sdate = .true. -! end if + ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. + if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then + write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop ivt ',ivt,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' + warned_about_bad_interp_sdate = .true. + end if - !dataptr2d_sdate(g,n) = dataptr1d_sdate(g) - dataptr2d_sdate(g,n) = dataptr1d(g) + dataptr2d_sdate(g,n) = dataptr1d_sdate(g) end do end do @@ -350,50 +342,30 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do - !deallocate(dataptr1d_sdate) - deallocate(dataptr1d) deallocate(dataptr2d_sdate) - if (verbose) write(iulog,*) 'cropcal_interp(): Allocating dataptrs for cultivar_gdds' -! allocate(dataptr1d_cultivar_gdds(lsize)) allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (.not. generate_crop_gdds) then - !if (.false.) then - !if (verbose) write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' - write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file' ! Read prescribed cultivar GDDs from input files -! dataptr1d_cultivar_gdds(:) = -4 -! dataptr2d_cultivar_gdds(:,:) = -5 ! Starting with npcropmin will skip generic crops do n = 1, ncft -! call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & -! fldptr1=dataptr1d_cultivar_gdds, rc=rc) -!SO IT WORKS WHEN I USE SDATE''S DATAPTR1D -! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & -! fldptr1=dataptr1d_sdate, rc=rc) -! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & -! fldptr1=dataptr1d_cultivar_gdds, rc=rc) -! call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & -! fldptr1=dataptr1d, rc=rc) - call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & - fldptr1=dataptr1d, rc=rc) - + call dshr_fldbun_getFldPtr(sdat_cropcal_cultivar_gdds%pstrm(1)%fldbun_model, trim(stream_varnames_cultivar_gdds(n)), & + fldptr1=dataptr1d_cultivar_gdds, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize ! So an explicit loop is required here do g = 1,lsize -! ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. -! if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then -! write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' -! warned_about_bad_interp_cultivar_gdds = .true. -! end if + ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. + if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then + write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' + warned_about_bad_interp_cultivar_gdds = .true. + end if -! dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) - dataptr2d_cultivar_gdds(g,n) = dataptr1d(g) - write (iulog,'(a,i4,a,f0.0)') 'dataptr1d(g) (ivt ',ivt,'): ',dataptr1d(g) + dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) end do end do @@ -411,59 +383,40 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) if (ivt >= npcropmin) then n = ivt - npcropmin + 1 -! if (n > ncft) then -! write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' -! call ESMF_Finalize(endflag=ESMF_END_ABORT) -! end if + if (n > ncft) then + write(iulog,'(a,i0,a,i0,a)') 'n (',n,') > ncft (',ncft,')' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if ! vegetated pft ig = g_to_ig(patch%gridcell(p)) -! if (ig > lsize) then -! write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' -! call ESMF_Finalize(endflag=ESMF_END_ABORT) -! end if - -! if (dataptr2d_cultivar_gdds(ig,n) < -0.001 .or. dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then -! !if (dataptr2d_cultivar_gdds(ig,n) > 1000000.0) then -! if (dataptr2d_cultivar_gdds(ig,n) == 0.0) then -! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement ZERO??? ',dataptr2d_cultivar_gdds(ig,n) -! else if (dataptr2d_cultivar_gdds(ig,n) < -0.001) then -! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement NEGATIVE ',dataptr2d_cultivar_gdds(ig,n) -! else -! write(iulog,'(a,i0,a,f0.0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed GDD requirement HUGE ',dataptr2d_cultivar_gdds(ig,n) -! end if -!! call ESMF_Finalize(endflag=ESMF_END_ABORT) -! -! ! TEMPORARY!!! -! dataptr2d_cultivar_gdds(ig,n) = 0.0 -! end if + if (ig > lsize) then + write(iulog,'(a,i0,a,i0,a)') 'ig (',ig,') > lsize (',lsize,')' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) - write (iulog,'(a,i4,a,f0.0)') 'crop_inst%rx_cultivar_gdds_thisyr(p,1) (ivt ',ivt,'): ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -! ! Sanity check: Should not read in negative values. Also try to catch uninitialized values -! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then -! !if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then -! if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then -! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -! else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then -! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -! else -! write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) -! end if -! call ESMF_Finalize(endflag=ESMF_END_ABORT) -! end if -! else -! write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt -! call ESMF_Finalize(endflag=ESMF_END_ABORT) + ! Sanity check: Should not read in negative values. Also try to catch uninitialized values + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + else + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + end if + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + else + write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt + call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file DONE' end if ! not generate_crop_gdds -! deallocate(dataptr1d_cultivar_gdds) -! deallocate(dataptr1d) deallocate(dataptr2d_cultivar_gdds) if (verbose) write(iulog,*) 'cropcal_interp(): All done!' From 0b7fd394c2fdec7742b202fa46efd059fa3a96f3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 18 Feb 2022 17:39:32 -0700 Subject: [PATCH 0161/2067] Skip first few steps as htop isn't set until after first do_alb step --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 6725c63320..afb5ff8dfd 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -16,7 +16,7 @@ module BiogeophysPreFluxCalcsMod use LandunitType , only : lun use clm_varcon , only : spval use clm_varpar , only : nlevgrnd, nlevsno, nlevurb, nlevmaxurbgrnd - use clm_varctl , only : use_fates, z0param_method + use clm_varctl , only : use_fates, z0param_method, iulog use pftconMod , only : pftcon, noveg use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall use landunit_varcon , only : istsoil, istcrop, istice_mec @@ -125,9 +125,10 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & ! Set z0m and displa ! ! !USES: - use clm_time_manager, only : is_first_step + use clm_time_manager, only : is_first_step, get_nstep use clm_varcon , only : namep use abortutils , only : endrun + use BalanceCheckMod , only : GetBalanceCheckSkipSteps ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter @@ -172,8 +173,8 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & case ('MeierXXXX') - ! Don't set on first step of a simulation, since htop isn't set yet - if ( is_first_step() ) then + ! Don't set on first few steps of a simulation, since htop isn't set yet, need to wait until after first do_alb time + if ( is_first_step() .or. get_nstep() <= GetBalanceCheckSkipSteps() ) then z0m(p) = 0._r8 displa(p) = 0._r8 cycle @@ -192,6 +193,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) if ( htop(p) <= 1.e-10_r8 )then + write(iulog,*) ' nstep = ', get_nstep(), ' htop = ', htop(p) call endrun(decomp_index=p, clmlevel=namep, msg=errMsg(sourcefile, __LINE__)) else z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & From 0e71cb2f30b850569b2f7ab95644c4cf743e47c5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 19 Feb 2022 17:19:18 -0700 Subject: [PATCH 0162/2067] Correct subscript --- src/biogeophys/LakeFluxesMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index b3bcda6fe5..95afac05f4 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -353,7 +353,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('MeierXXXX') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if From 84396e6d7817249da2f66c1b30135dd5d2579e04 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Feb 2022 01:04:18 -0700 Subject: [PATCH 0163/2067] Add write of rh if negative or over 100 when DEBUG on --- src/biogeophys/HumanIndexMod.F90 | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/HumanIndexMod.F90 b/src/biogeophys/HumanIndexMod.F90 index a231c0919d..9f56081104 100644 --- a/src/biogeophys/HumanIndexMod.F90 +++ b/src/biogeophys/HumanIndexMod.F90 @@ -16,6 +16,9 @@ module HumanIndexMod ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type + use abortutils , only : endrun + use clm_varctl , only : iulog + use shr_log_mod , only : errMsg => shr_log_errMsg ! !PUBLIC TYPES: implicit none save @@ -498,13 +501,10 @@ subroutine HumanIndexReadNML( NLFilename ) ! ! !USES: use shr_mpi_mod , only : shr_mpi_bcast - use abortutils , only : endrun use spmdMod , only : masterproc, mpicom use fileutils , only : getavu, relavu, opnfil use shr_nl_mod , only : shr_nl_find_group_name use shr_mpi_mod , only : shr_mpi_bcast - use clm_varctl , only : iulog - use shr_log_mod , only : errMsg => shr_log_errMsg ! ! !ARGUMENTS: implicit none @@ -1012,6 +1012,15 @@ subroutine Wet_BulbS (Tc_6,rh,wbt) ! !LOCAL VARIABLES: !EOP ! +#ifndef NDEBUG + if ( rh < 0.0d00 )then + write(iulog,*) 'rh = ', rh + call endrun(msg="ERROR RH is negative "//errmsg(sourcefile, __LINE__)) + else if ( rh > 100.d00 )then + write(iulog,*) 'rh = ', rh + call endrun(msg="ERROR RH is greater than a hundred "//errmsg(sourcefile, __LINE__)) + end if +#endif wbt = Tc_6 * atan(0.151977_r8*sqrt(rh + 8.313659_r8)) + & atan(Tc_6+rh) - atan(rh-1.676331_r8) + & 0.00391838_r8*rh**(3._r8/2._r8)*atan(0.023101_r8*rh) - & From 23601a73e38c52a162a99c5de8730e3c67be56d2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Feb 2022 01:06:06 -0700 Subject: [PATCH 0164/2067] Write out warning if ustar*thvstar is positive to prevent a cube root of a negative number being done, in this case set wc to zero and continue --- src/biogeophys/CanopyFluxesMod.F90 | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index da690f2d5c..ed9e32466c 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1382,7 +1382,25 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, um(p) = max(ur(p),0.1_r8) else !unstable zeta(p) = max(-100._r8,min(zeta(p),-0.01_r8)) - wc = beta*(-grav*ustar(p)*thvstar*zii/thv(c))**0.333_r8 + if ( ustar(p)*thvstar > 0.0d00 )then + write(iulog,*) 'ustar*thvstart is positive and has to be negative' + write(iulog,*) 'p = ', p + write(iulog,*) '-grav*ustar(p)*thvstar*zii/thv(c) = ', -grav*ustar(p)*thvstar*zii/thv(c) + write(iulog,*) 'ustar = ', ustar(p) + write(iulog,*) 'thvstar = ', thvstar + write(iulog,*) 'thv = ', thv(c) + write(iulog,*) 'displa= ', displa(p) + write(iulog,*) 'z0mg= ', z0mg(c) + write(iulog,*) 'zeta= ', zeta(p) + write(iulog,*) 'temp1= ', temp1(p) + write(iulog,*) 'dth= ', dth(p) + write(iulog,*) 'rah(above)= ', rah(p,above_canopy) + write(iulog,*) 'rah(below)= ', rah(p,below_canopy) + !call endrun(decomp_index=p, clmlevel=namep, msg=errmsg(sourcefile, __LINE__)) + wc = 0.0_r8 + else + wc = beta*(-grav*ustar(p)*thvstar*zii/thv(c))**0.333_r8 + end if um(p) = sqrt(ur(p)*ur(p)+wc*wc) end if obu(p) = zldis(p)/zeta(p) From 4eabfbb11497448913e43bcb952476bc5ee8ed19 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Feb 2022 01:08:48 -0700 Subject: [PATCH 0165/2067] Set human stress indices to calculate NONE when Meier surface roughness is used to prevent a numerical error that kills the run in calc of WetBulb temp because of negative relative humidity --- .../testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm index b9fd293412..dadc6e463e 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -1,4 +1,6 @@ z0param_method = 'MeierXXXX' use_z0m_snowmelt = .true. use_z0mg_2d = .false. +calc_human_stress_indices = 'NONE' ! Currently dies when turned on because of a negative humidity (about -31) in Wet Bulb calculation paramfile = '/glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/ctsm51_params_newz0.c211112.nc' + From f644624b9b96dc9f44be6e73ddeff47c247cded2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Feb 2022 12:00:39 -0700 Subject: [PATCH 0166/2067] Fix subscript --- src/biogeophys/LakeFluxesMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 95afac05f4..b2b6e62967 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -602,7 +602,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else ! Snow layers if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if From 32dbda81127f62fc092d4ac35da159927ddc3ed1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Feb 2022 13:51:39 -0700 Subject: [PATCH 0167/2067] Rename test mods to highlight these are non-crop cases --- .../include_user_mods | 0 .../user_nl_clm | 0 .../include_user_mods | 0 .../user_nl_clm | 0 4 files changed, 0 insertions(+), 0 deletions(-) rename cime_config/testdefs/testmods_dirs/clm/{Meier2022_surf_rough_all_f09 => Meier2022_surf_rough_all_f09NonCrop}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{Meier2022_surf_rough_all_f09 => Meier2022_surf_rough_all_f09NonCrop}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{Meier2022_surf_rough_all_hcru => Meier2022_surf_rough_all_hcruNonCrop}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{Meier2022_surf_rough_all_hcru => Meier2022_surf_rough_all_hcruNonCrop}/user_nl_clm (100%) diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcru/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm From b9d402a7c0e2b824f373d3e71acbf1e11fc73827 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 01:22:08 -0700 Subject: [PATCH 0168/2067] Add tests with Meier surface roughness --- cime_config/testdefs/testlist_clm.xml | 54 +++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index c304a4bb27..f1e8eb3f9b 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -17,6 +17,15 @@ + + + + + + + + + @@ -1238,6 +1247,51 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 8789ca2e32ce2d687db74e3a7021d61eb4ac5280 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 01:23:10 -0700 Subject: [PATCH 0169/2067] Add a bit to not die if htop is zero and it's crop and beginning of the year --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index afb5ff8dfd..6767c113b4 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -125,7 +125,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & ! Set z0m and displa ! ! !USES: - use clm_time_manager, only : is_first_step, get_nstep + use clm_time_manager, only : is_first_step, get_nstep, is_beg_curr_year use clm_varcon , only : namep use abortutils , only : endrun use BalanceCheckMod , only : GetBalanceCheckSkipSteps @@ -178,6 +178,11 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & z0m(p) = 0._r8 displa(p) = 0._r8 cycle + ! If a crop type and it's the start of the year, htop gets reset to + ! zero... + else if ( is_beg_curr_year() .and. pftcon%crop(patch%itype(p)) /= 0.0_r8 )then + z0m(p) = 0._r8 + displa(p) = 0._r8 end if if (patch%itype(p) == noveg) then From 821df3cc4c28d6026c308a02db7302eaed0e661a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 11:04:14 -0700 Subject: [PATCH 0170/2067] Correct new testname, and add two tests to the expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 14 ++++++++++++++ cime_config/testdefs/testlist_clm.xml | 2 +- 2 files changed, 15 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 04ff4b5dee..353f21c25e 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -37,6 +37,20 @@ + + + FAIL + Error: Forcing height is below canopy height for patch index + + + + + + FAIL + Half degree resolution issue + + + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f1e8eb3f9b..d2c6b37b11 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1274,7 +1274,7 @@ - + From d3dee3984a2aebdef6d4162b4aba2a5101d37395 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 13:47:29 -0700 Subject: [PATCH 0171/2067] Change MeierXXXX namelist to Meier2022 --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++-- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++-- .../testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 2 +- src/biogeophys/BareGroundFluxesMod.F90 | 2 +- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 2 +- src/biogeophys/CanopyFluxesMod.F90 | 2 +- src/biogeophys/FrictionVelocityMod.F90 | 8 ++++---- src/biogeophys/LakeFluxesMod.F90 | 10 +++++----- src/main/pftconMod.F90 | 2 +- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a6776abe33..8fda08cda6 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -491,11 +491,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ZengWang2007 -.true. +.true. .false. .false. -.true. +.true. .false. .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a058b10c0f..dd5c7f6052 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2723,10 +2723,10 @@ If .true., run with water isotopes + group="clm_inparm" valid_values="ZengWang2007,Meier2022" > Parameterization/parameters to use for surface roughness ZengWang2007: Zeng and Wang 2007 -MeierXXXX: Meier et al. in prep. +Meier2022: Meier et al. in prep. 2022 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index b2b6e62967..3f9ba8e825 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -67,7 +67,7 @@ subroutine readParams( ncid ) ! Momentum roughness length for snow (m) call readNcdioScalar(ncid, 'zsno', subname, params_inst%zsno) - if (z0param_method == 'MeierXXXX') then + if (z0param_method == 'Meier2022') then ! Momentum roughness length for ice (m) call readNcdioScalar(ncid, 'zglc', subname, params_inst%zglc) end if @@ -337,7 +337,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0hg(p) = max(z0hg(p), minz0lake) else if (snl(c) == 0) then ! frozen lake with ice select case (z0param_method) - case ('MeierXXXX') + case ('Meier2022') z0mg(p) = params_inst%zglc @@ -350,7 +350,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = z0hg(p) else ! use roughness over snow as in Biogeophysics1 select case (z0param_method) - case ('MeierXXXX') + case ('Meier2022') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 @@ -589,7 +589,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else if (snl(c) == 0) then ! in case it was above freezing and now below freezing select case (z0param_method) - case ('MeierXXXX') + case ('Meier2022') z0mg(p) = params_inst%zglc z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes @@ -609,7 +609,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, end if select case (z0param_method) - case ('MeierXXXX') + case ('Meier2022') z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes case ('ZengWang2007') diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index d3ef07a547..03493797de 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -652,7 +652,7 @@ subroutine InitRead(this) this%z0v_LAImax = 0._r8 this%z0v_LAIoff = 0._r8 - case ('MeierXXXX') + case ('Meier2022') call ncd_io('z0v_Cr', this%z0v_Cr, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) From 95fb9005335e8d9eaf2c03b9d10847a4cf74bf8c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 13:53:16 -0700 Subject: [PATCH 0172/2067] Remove commented out line --- src/biogeophys/CanopyFluxesMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index eac78660bf..3ca7415657 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1578,7 +1578,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! function that goes to zero as LAI (ELAI + ESAI) go to zero. t_skin_patch(p) = emv(p)*t_veg(p) + (1._r8 - emv(p))*sqrt(sqrt(lw_grnd)) - !t_skin_patch(p) = (ulrad(p) / 5.670367e-8_r8)**0.25_r8 ! Derivative of soil energy flux with respect to soil temperature From b0f2856601290341ee6134c2e694f0d3e83789a2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 15:24:43 -0700 Subject: [PATCH 0173/2067] Remove local time history changes as they are treated seperately in #1374 --- .../namelist_definition_ctsm.xml | 4 +- src/main/histFileMod.F90 | 245 +----------------- 2 files changed, 15 insertions(+), 234 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index dd5c7f6052..d46fdd1107 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -768,8 +768,8 @@ SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name If TRUE, write master field list to separate file for documentation purposes - + Per file averaging flag. 'A' (average over history period) 'I' (instantaneous) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 038aeaf701..5c43e1540d 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -44,7 +44,7 @@ module histFileMod integer , public, parameter :: max_flds = 2500 ! max number of history fields integer , public, parameter :: max_namlen = 64 ! maximum number of characters for field name integer , public, parameter :: scale_type_strlen = 32 ! maximum number of characters for scale types - integer , private, parameter :: avgflag_strlen = 10 ! maximum number of characters for avgflag + integer , private, parameter :: avgflag_strlen = 3 ! maximum number of characters for avgflag integer , private, parameter :: hist_dim_name_length = 16 ! lenngth of character strings in dimension names ! Possible ways to treat multi-layer snow fields at times when no snow is present in a @@ -1286,8 +1286,6 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) ! !USES: use subgridAveMod , only : p2g, c2g, l2g, p2l, c2l, p2c use decompMod , only : BOUNDS_LEVEL_PROC - use clm_varcon , only : degpsec, isecspday - use clm_time_manager, only : get_step_size, get_curr_date ! ! !ARGUMENTS: integer, intent(in) :: t ! tape index @@ -1316,17 +1314,6 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) integer j character(len=*),parameter :: subname = 'hist_update_hbuf_field_1d' integer k_offset ! offset for mapping sliced subarray pointers when outputting variables in PFT/col vector form - integer :: year ! year (0, ...) for nstep - integer :: month ! month (1, ..., 12) for nstep - integer :: day ! day of month (1, ..., 31) for nstep - integer :: secs ! seconds into current date for nstep - integer :: local_secpl ! seconds into current date in local time - integer :: dtime ! timestep size [seconds] - integer :: tod ! Desired local solar time of output in seconds - integer, allocatable :: grid_index(:) ! Grid cell index for longitude - integer, allocatable :: tods(:) - character(len=1) :: avgflag_trim ! first character of avgflag - !----------------------------------------------------------------------- SHR_ASSERT_FL(bounds%level == BOUNDS_LEVEL_PROC, sourcefile, __LINE__) @@ -1346,9 +1333,6 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) hpindex = tape(t)%hlist(f)%field%hpindex field => clmptr_rs(hpindex)%ptr - dtime = get_step_size() - call get_curr_date (year, month, day, secs) - ! set variables to check weights when allocate all pfts map2gcell = .false. @@ -1434,8 +1418,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) if (map2gcell) then ! Map to gridcell ! note that in this case beg1d = begg and end1d=endg - avgflag_trim = avgflag(1:1) - select case (avgflag_trim) + select case (avgflag) case ('I') ! Instantaneous do k = beg1d_out, end1d_out if (field_gcell(k) /= spval) then @@ -1445,7 +1428,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do - case ('A', 'S') ! Time average / sum + case ('A', 'SUM') ! Time average / sum do k = beg1d_out, end1d_out if (field_gcell(k) /= spval) then if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 @@ -1475,38 +1458,6 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) endif nacs(k,1) = 1 end do - case ('L') ! Local solar time - read(avgflag(2:6), *) tod - do k = beg1d_out, end1d_out - if (field_gcell(k) /= spval) then - - local_secpl = secs + grc%londeg(k)/degpsec - local_secpl = mod(local_secpl,isecspday) - - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime+tod-local_secpl) - nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field_gcell(k)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,1) == 0) hbuf(k,1) = spval - end if - end do - case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -1515,29 +1466,22 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) else ! Do not map to gridcell - allocate( grid_index(beg1d:end1d) ) - ! For data defined on the pft, col or landunit, we need to check if a point is active ! to determine whether that point should be assigned spval if (type1d == namep) then check_active = .true. active => patch%active - grid_index = patch%gridcell else if (type1d == namec) then check_active = .true. active => col%active - grid_index = col%gridcell else if (type1d == namel) then check_active = .true. active =>lun%active - grid_index = lun%gridcell else check_active = .false. end if - avgflag_trim = avgflag(1:1) - - select case (avgflag_trim) + select case (avgflag) case ('I') ! Instantaneous do k = beg1d,end1d valid = .true. @@ -1555,7 +1499,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do - case ('A', 'S') ! Time average / sum + case ('A', 'SUM') ! Time average / sum ! create mappings for array slice pointers (which go from 1 to size(field) rather than beg1d to end1d) if ( end1d .eq. ubound(field,1) ) then k_offset = 0 @@ -1615,54 +1559,6 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) end if nacs(k,1) = 1 end do - case ('L') ! Local solar time - - read(avgflag(2:6), *) tod - - if ( end1d .eq. ubound(field,1) ) then - k_offset = 0 - else - k_offset = 1 - beg1d - endif - do k = beg1d, end1d - valid = .true. - if (check_active) then - if (.not. active(k)) then - valid = .false. - else - local_secpl = secs + grc%londeg(grid_index(k))/degpsec - end if - else - local_secpl = secs + grc%londeg(k)/degpsec - - end if - local_secpl = mod(local_secpl,isecspday) - - if (valid) then - if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k+k_offset) /= spval) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k+k_offset) /= spval) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime+tod-local_secpl) - nacs(k,1) = nacs(k,1) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k+k_offset) /= spval) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,1) == 0) hbuf(k,1) = 0._r8 - hbuf(k,1) = hbuf(k,1) + field(k+k_offset)*real(dtime-tod+local_secpl) - nacs(k,1) = nacs(k,1) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,1) == 0) hbuf(k,1) = spval - end if - end do - case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -1685,8 +1581,6 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) use subgridAveMod , only : p2g, c2g, l2g, p2l, c2l, p2c use decompMod , only : BOUNDS_LEVEL_PROC use clm_varctl , only : iulog - use clm_varcon , only : degpsec, isecspday - use clm_time_manager, only : get_step_size, get_curr_date ! ! !ARGUMENTS: integer, intent(in) :: t ! tape index @@ -1718,17 +1612,6 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) !(this refers to a point being active, NOT a history field being active) real(r8), allocatable :: field_gcell(:,:) ! gridcell level field (used if mapping to gridcell is done) character(len=*),parameter :: subname = 'hist_update_hbuf_field_2d' - integer :: year ! year (0, ...) for nstep - integer :: month ! month (1, ..., 12) for nstep - integer :: day ! day of month (1, ..., 31) for nstep - integer :: secs ! seconds into current date for nstep - integer :: local_secpl ! seconds into current date in local time - integer :: dtime ! timestep size [seconds] - integer :: tod ! Desired local solar time of output in seconds - integer, allocatable :: grid_index(:) ! Grid cell index for longitude - integer, allocatable :: tods(:) - character(len=1) :: avgflag_trim ! first character of avgflag - !----------------------------------------------------------------------- SHR_ASSERT_FL(bounds%level == BOUNDS_LEVEL_PROC, sourcefile, __LINE__) @@ -1748,8 +1631,6 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) no_snow_behavior = tape(t)%hlist(f)%field%no_snow_behavior hpindex = tape(t)%hlist(f)%field%hpindex - dtime = get_step_size() - call get_curr_date (year, month, day, secs) if (no_snow_behavior /= no_snow_unset) then ! For multi-layer snow fields, build a special output variable that handles @@ -1857,9 +1738,8 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) if (map2gcell) then ! Map to gridcell - avgflag_trim = avgflag(1:1) ! note that in this case beg1d = begg and end1d=endg - select case (avgflag_trim) + select case (avgflag) case ('I') ! Instantaneous do j = 1,num2d do k = beg1d_out, end1d_out @@ -1871,7 +1751,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do - case ('A', 'S') ! Time average / sum + case ('A', 'SUM') ! Time average / sum do j = 1,num2d do k = beg1d_out, end1d_out if (field_gcell(k,j) /= spval) then @@ -1907,42 +1787,6 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do - case ('L') ! Local solar time - read(avgflag(2:6), *) tod - do j = 1,num2d - do k = beg1d_out, end1d_out - if (field_gcell(k,j) /= spval) then - - local_secpl = secs + grc%londeg(k)/degpsec - local_secpl = mod(local_secpl,isecspday) - - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime+tod-local_secpl) - nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field_gcell(k,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,j) == 0) hbuf(k,j) = spval - - end if - end do - end do - - case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -1956,18 +1800,12 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) if (type1d == namep) then check_active = .true. active => patch%active - allocate(grid_index(bounds%begg:bounds%endg) ) - grid_index = patch%gridcell else if (type1d == namec) then check_active = .true. active => col%active - allocate(grid_index(bounds%begg:bounds%endg) ) - grid_index = col%gridcell else if (type1d == namel) then check_active = .true. active =>lun%active - allocate(grid_index(bounds%begg:bounds%endg) ) - grid_index = lun%gridcell else check_active = .false. end if @@ -1975,8 +1813,8 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) ! Note that since field points to an array section the ! bounds are field(1:end1d-beg1d+1, num2d) - therefore ! need to do the shifting below - avgflag_trim = avgflag(1:1) - select case (avgflag_trim) + + select case (avgflag) case ('I') ! Instantaneous do j = 1,num2d do k = beg1d,end1d @@ -1996,7 +1834,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do - case ('A', 'S') ! Time average / sum + case ('A', 'SUM') ! Time average / sum do j = 1,num2d do k = beg1d,end1d valid = .true. @@ -2056,49 +1894,6 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) nacs(k,j) = 1 end do end do - case ('L') ! Local solar time - read(avgflag(2:6), *) tod - do j = 1,num2d - - do k = beg1d, end1d - valid = .true. - if (check_active) then - if (.not. active(k)) then - valid = .false. - else - local_secpl = secs + grc%londeg(grid_index(k))/degpsec - end if - else - local_secpl = secs + grc%londeg(k)/degpsec - end if - local_secpl = mod(local_secpl,isecspday) - - if (valid) then - if (local_secpl >= tod - dtime .and. local_secpl < tod .and. field(k-beg1d+1,j) /= spval) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - else if (local_secpl >= tod .and. local_secpl < tod + dtime .and. field(k-beg1d+1,j) /= spval) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime+tod-local_secpl) - nacs(k,j) = nacs(k,j) + dtime+tod-local_secpl - end if - - if (tod < dtime .and. local_secpl > isecspday-dtime .and. field(k-beg1d+1,j) /= spval) then - local_secpl = local_secpl - isecspday - if (local_secpl >= tod - dtime .and. local_secpl < tod) then - if (nacs(k,j) == 0) hbuf(k,j) = 0._r8 - hbuf(k,j) = hbuf(k,j) + field(k-beg1d+1,j)*real(dtime-tod+local_secpl) - nacs(k,j) = nacs(k,j) + dtime-tod+local_secpl - end if - end if - - else - if (nacs(k,j) == 0) hbuf(k,j) = spval - end if - end do - end do - case default write(iulog,*) trim(subname),' ERROR: invalid time averaging flag ', avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2243,7 +2038,7 @@ subroutine hfields_normalize (t) nacs => tape(t)%hlist(f)%nacs hbuf => tape(t)%hlist(f)%hbuf - if (avgflag == 'A' .or. avgflag(1:1) == 'L') then + if (avgflag == 'A') then aflag = .true. else aflag = .false. @@ -2253,8 +2048,6 @@ subroutine hfields_normalize (t) do k = beg1d, end1d if (aflag .and. nacs(k,j) /= 0) then hbuf(k,j) = hbuf(k,j) / float(nacs(k,j)) - elseif (avgflag(1:1) == 'L' .and. nacs(k,j) == 0) then - hbuf(k,j) = spval end if end do end do @@ -3372,7 +3165,7 @@ subroutine hfields_write(t, mode) if (mode == 'define') then - select case (avgflag(1:1)) + select case (avgflag) case ('A') avgstr = 'mean' case ('I') @@ -3381,10 +3174,8 @@ subroutine hfields_write(t, mode) avgstr = 'maximum' case ('M') avgstr = 'minimum' - case ('S') + case ('SUM') avgstr = 'sum' - case ('L') - avgstr = 'local solar time' case default write(iulog,*) trim(subname),' ERROR: unknown time averaging flag (avgflag)=',avgflag call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -5737,7 +5528,6 @@ function avgflag_valid(avgflag, blank_valid) result(valid) ! Returns true if the given avgflag is a valid option, false if not ! ! !USES: - use clm_varcon , only : isecspday ! ! !ARGUMENTS: logical :: valid ! function result @@ -5747,7 +5537,6 @@ function avgflag_valid(avgflag, blank_valid) result(valid) ! !LOCAL VARIABLES: character(len=*), parameter :: subname = 'avgflag_valid' - integer :: tod ! Desired local solar time of output in seconds !----------------------------------------------------------------------- ! This initial check is mainly here to catch the possibility that someone has added a @@ -5761,14 +5550,6 @@ function avgflag_valid(avgflag, blank_valid) result(valid) avgflag == 'X' .or. avgflag == 'M' .or. & avgflag == 'SUM') then valid = .true. - else if (avgflag(1:1) == 'L') then - read(avgflag(2:6), *) tod - if (tod >= 0 .and. tod <= isecspday) then - valid = .true. - else - valid = .false. - end if - else valid = .false. end if From c7ade8d90f54d2c91f9a8b8653e4128416cd5e53 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 15:47:33 -0700 Subject: [PATCH 0174/2067] Remove soil columns on a seperate soil column as handled in #1249 --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 - .../namelist_definition_ctsm.xml | 5 -- src/main/clm_varctl.F90 | 6 -- src/main/controlMod.F90 | 4 - src/main/initGridCellsMod.F90 | 76 +------------------ src/main/subgridMod.F90 | 17 ++--- 6 files changed, 9 insertions(+), 100 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 8fda08cda6..438d0ec5fe 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -181,7 +181,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .true. .false. -.false. 1 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index d46fdd1107..004a0d20c8 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -144,11 +144,6 @@ User-defined number of soil layers required to be set in the namelist when the u Default: iundef - -If TRUE, each pft exists on a separate soil column. - - If TRUE, use variable soil depth. diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 4b3c5c9a65..9fb28be7e1 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -293,12 +293,6 @@ module clm_varctl logical, public :: use_biomass_heat_storage = .false. ! true => include biomass heat storage in canopy energy budget - !---------------------------------------------------------- - ! each pft has individual soil column switch - !---------------------------------------------------------- - - logical, public :: use_individual_pft_soil_column = .false. ! true => each pft exists on its own soil column - !---------------------------------------------------------- ! bedrock / soil depth switch !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index ae1324ed7a..20644e7ddf 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -247,8 +247,6 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_biomass_heat_storage - namelist /clm_inparm/ use_individual_pft_soil_column - namelist /clm_inparm/ use_hydrstress namelist /clm_inparm/ use_dynroot @@ -749,8 +747,6 @@ subroutine control_spmd() call mpi_bcast (use_biomass_heat_storage, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_individual_pft_soil_column, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_hydrstress, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier) diff --git a/src/main/initGridCellsMod.F90 b/src/main/initGridCellsMod.F90 index 1456e10a36..cdaac2f6e5 100644 --- a/src/main/initGridCellsMod.F90 +++ b/src/main/initGridCellsMod.F90 @@ -60,7 +60,7 @@ subroutine initGridcells(glc_behavior) use subgridWeightsMod , only : compute_higher_order_weights use landunit_varcon , only : istsoil, istwet, istdlak, istice_mec use landunit_varcon , only : isturb_tbd, isturb_hd, isturb_md, istcrop - use clm_varctl , only : use_fates,use_individual_pft_soil_column + use clm_varctl , only : use_fates use shr_const_mod , only : SHR_CONST_PI ! ! !ARGUMENTS: @@ -133,13 +133,8 @@ subroutine initGridcells(glc_behavior) ! Determine naturally vegetated landunit do gdc = bounds_clump%begg,bounds_clump%endg - if(use_individual_pft_soil_column) then - call set_landunit_veg_noncompete( & - ltype=istsoil, gi=gdc, li=li, ci=ci, pi=pi) - else - call set_landunit_veg_compete( & - ltype=istsoil, gi=gdc, li=li, ci=ci, pi=pi) - end if + call set_landunit_veg_compete( & + ltype=istsoil, gi=gdc, li=li, ci=ci, pi=pi) end do ! Determine crop landunit @@ -249,7 +244,7 @@ subroutine set_landunit_veg_compete (ltype, gi, li, ci, pi) ! Set decomposition properties call subgrid_get_info_natveg(gi, & - npatches=npatches, ncols=ncols, nlunits=nlunits, sesc=.FALSE.) + npatches=npatches, ncols=ncols, nlunits=nlunits) wtlunit2gcell = wt_lunit(gi, ltype) nlunits_added = 0 @@ -279,69 +274,6 @@ subroutine set_landunit_veg_compete (ltype, gi, li, ci, pi) end subroutine set_landunit_veg_compete - subroutine set_landunit_veg_noncompete (ltype, gi, li, ci, pi) - - - ! !DESCRIPTION: - ! Initialize vegetated landunit without competition - ! - ! !USES - use clm_instur, only : wt_lunit, wt_nat_patch - use subgridMod, only : subgrid_get_info_natveg, natveg_patch_exists - use clm_varpar, only : natpft_lb, natpft_ub - ! - ! !ARGUMENTS: - integer , intent(in) :: ltype ! landunit type - integer , intent(in) :: gi ! gridcell index - integer , intent(inout) :: li ! landunit index - integer , intent(inout) :: ci ! column index - integer , intent(inout) :: pi ! patch index - ! - ! !LOCAL VARIABLES: - integer :: m ! index - integer :: npatches ! number of patches in landunit - integer :: ncols - integer :: nlunits - integer :: npatches_added ! number of patches actually added - integer :: ncols_added ! number of columns actually added - integer :: nlunits_added ! number of landunits actually added - real(r8) :: wtlunit2gcell ! landunit weight in gridcell - !------------------------------------------------------------------------ - - ! Set decomposition properties - - call subgrid_get_info_natveg(gi, & - npatches=npatches, ncols=ncols, nlunits=nlunits, sesc=.TRUE.) - wtlunit2gcell = wt_lunit(gi, ltype) - - nlunits_added = 0 - ncols_added = 0 - npatches_added = 0 - - if (nlunits > 0) then - call add_landunit(li=li, gi=gi, ltype=ltype, wtgcell=wtlunit2gcell) - nlunits_added = nlunits_added + 1 - - - do m = natpft_lb,natpft_ub - if (natveg_patch_exists(gi, m)) then - ! Assume one column for each vegetation patch - call add_column(ci=ci, li=li, ctype=1, wtlunit=wt_nat_patch(gi,m)) - ncols_added = ncols_added + 1 - - call add_patch(pi=pi, ci=ci, ptype=m, wtcol=1.0_r8) - npatches_added = npatches_added + 1 - end if - end do - end if - - SHR_ASSERT_FL(nlunits_added == nlunits, sourcefile, __LINE__) - SHR_ASSERT_FL(ncols_added == ncols, sourcefile, __LINE__) - SHR_ASSERT_FL(npatches_added == npatches, sourcefile, __LINE__) - - end subroutine set_landunit_veg_noncompete - - !------------------------------------------------------------------------ subroutine set_landunit_wet_lake (ltype, gi, li, ci, pi) ! diff --git a/src/main/subgridMod.F90 b/src/main/subgridMod.F90 index 98cbc40192..7247fab15a 100644 --- a/src/main/subgridMod.F90 +++ b/src/main/subgridMod.F90 @@ -13,7 +13,7 @@ module subgridMod use shr_kind_mod , only : r8 => shr_kind_r8 use spmdMod , only : masterproc use abortutils , only : endrun - use clm_varctl , only : iulog,use_individual_pft_soil_column + use clm_varctl , only : iulog use clm_instur , only : wt_lunit, wt_nat_patch, urban_valid, wt_cft use landunit_varcon, only : istcrop, istdlak, istwet, isturb_tbd, isturb_hd, isturb_md use glcBehaviorMod , only : glc_behavior_type @@ -81,7 +81,7 @@ subroutine subgrid_get_gcellinfo (gi, glc_behavior, & nlunits = 0 ncohorts = 0 - call subgrid_get_info_natveg(gi, npatches_temp, ncols_temp, nlunits_temp, use_individual_pft_soil_column) + call subgrid_get_info_natveg(gi, npatches_temp, ncols_temp, nlunits_temp) call accumulate_counters() call subgrid_get_info_urban_tbd(gi, npatches_temp, ncols_temp, nlunits_temp) @@ -123,7 +123,7 @@ end subroutine accumulate_counters end subroutine subgrid_get_gcellinfo !----------------------------------------------------------------------- - subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits, sesc) + subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits) ! ! !DESCRIPTION: ! Obtain properties for natural vegetated landunit in this grid cell @@ -133,7 +133,6 @@ subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits, sesc) ! ! !ARGUMENTS: integer, intent(in) :: gi ! grid cell index - logical, intent(in) :: sesc ! switch for separated soil columns of natural vegetation integer, intent(out) :: npatches ! number of nat veg patches in this grid cell integer, intent(out) :: ncols ! number of nat veg columns in this grid cell @@ -154,14 +153,8 @@ subroutine subgrid_get_info_natveg(gi, npatches, ncols, nlunits, sesc) end do if (npatches > 0) then - if(sesc) then - ! Assume one soil column for each patch - ncols = npatches - else - ! Assume that the vegetated landunit has one column - ncols = 1 - end if - + ! Assume that the vegetated landunit has one column + ncols = 1 nlunits = 1 else ! As noted in natveg_patch_exists, we expect a naturally vegetated landunit in From 7916475dc4cfc2b97af5f3e192193b7fe3253eb7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Feb 2022 16:09:36 -0700 Subject: [PATCH 0175/2067] Add more compilers for the surf roughness changes --- cime_config/testdefs/testlist_clm.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 5ded956618..8486c7fa04 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1296,6 +1296,10 @@ + + + + From b531f9282275383b752c012c44d621148f99393a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 24 Feb 2022 15:15:45 -0700 Subject: [PATCH 0176/2067] Changes to get the updated code to compile on cheyenne_gnu --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 6 +-- src/biogeophys/CanopyStateType.F90 | 51 +++++++++----------- src/biogeophys/FrictionVelocityMod.F90 | 2 +- 3 files changed, 28 insertions(+), 31 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 2667ddabe4..f033fab5ff 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -10,6 +10,7 @@ module BiogeophysPreFluxCalcsMod #include "shr_assert.h" use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg + use abortutils , only : endrun use decompMod , only : bounds_type use PatchType , only : patch use ColumnType , only : col @@ -126,8 +127,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & ! ! !USES: use clm_time_manager, only : is_first_step, get_nstep, is_beg_curr_year - use clm_varcon , only : namep - use abortutils , only : endrun + use decompMod , only : subgrid_level_patch use BalanceCheckMod , only : GetBalanceCheckSkipSteps ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -199,7 +199,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & if ( htop(p) <= 1.e-10_r8 )then write(iulog,*) ' nstep = ', get_nstep(), ' htop = ', htop(p) - call endrun(decomp_index=p, clmlevel=namep, msg=errMsg(sourcefile, __LINE__)) + call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__)) else z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90 index a126401e48..e6963d4b83 100644 --- a/src/biogeophys/CanopyStateType.F90 +++ b/src/biogeophys/CanopyStateType.F90 @@ -198,35 +198,32 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='Aboveground leaf biomass', & ptr_patch=this%leaf_biomass_patch, default='inactive') - this%fsun_patch(begp:endp) = spval - call hist_addfld1d (fname='FSUN', units='proportion', & - avgflag='A', long_name='sunlit fraction of canopy', & - ptr_patch=this%fsun_patch, default='inactive') - - this%hbot_patch(begp:endp) = spval - call hist_addfld1d (fname='HBOT', units='m', & - avgflag='A', long_name='canopy bottom', & - ptr_patch=this%hbot_patch, default='inactive') - - this%displa_patch(begp:endp) = spval - call hist_addfld1d (fname='DISPLA', units='m', & - avgflag='A', long_name='displacement height', & - ptr_patch=this%displa_patch, default='inactive') - - if(use_fates_sp)then - this%htop_hist_patch(begp:endp) = spval - call hist_addfld1d (fname='HTOP', units='m', & - avgflag='A', long_name='HTOP weights for SP mode', & - ptr_patch=this%htop_hist_patch) - else - this%htop_patch(begp:endp) = spval - call hist_addfld1d (fname='HTOP', units='m', & - avgflag='A', long_name='canopy top', & - ptr_patch=this%htop_patch) - endif + this%fsun_patch(begp:endp) = spval + call hist_addfld1d (fname='FSUN', units='proportion', & + avgflag='A', long_name='sunlit fraction of canopy', & + ptr_patch=this%fsun_patch, default='inactive') + + this%hbot_patch(begp:endp) = spval + call hist_addfld1d (fname='HBOT', units='m', & + avgflag='A', long_name='canopy bottom', & + ptr_patch=this%hbot_patch, default='inactive') + this%displa_patch(begp:endp) = spval + call hist_addfld1d (fname='DISPLA', units='m', & + avgflag='A', long_name='displacement height', & + ptr_patch=this%displa_patch, default='inactive') - endif !fates or CN + if(use_fates_sp)then + this%htop_hist_patch(begp:endp) = spval + call hist_addfld1d (fname='HTOP', units='m', & + avgflag='A', long_name='HTOP weights for SP mode', & + ptr_patch=this%htop_hist_patch) + else + this%htop_patch(begp:endp) = spval + call hist_addfld1d (fname='HTOP', units='m', & + avgflag='A', long_name='canopy top', & + ptr_patch=this%htop_patch) + endif if(use_fates_sp)then this%tlai_hist_patch(begp:endp) = spval diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 1f7b1b3ac4..b4d7dfed5d 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -658,7 +658,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & end if - else if (lun%itype(l) == istice_mec) then + else if (lun%itype(l) == istice) then z0mg(c) = this%zglc From 6e3117132657f2bf63960b22670d96f381b463ef Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 25 Feb 2022 14:14:45 -0700 Subject: [PATCH 0177/2067] Changes needed to work with nag compiler on izumi, negative sign needed to be moved --- src/biogeophys/FrictionVelocityMod.F90 | 7 ++++--- src/biogeophys/LakeFluxesMod.F90 | 4 ++-- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index b4d7dfed5d..4f72215381 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -632,7 +632,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & case ('ZengWang2007') if (frac_sno(c) > 0._r8) then if(use_z0m_snowmelt) then - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 else z0mg(c) = this%zsno end if @@ -649,9 +649,10 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(c) = exp(-1.4_r8 * rpi/2.0_r8 - 0.31_r8) / 1000.0_r8 else - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) & + / 1000.0_r8 end if else z0mg(c) = this%zsno diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index e99eadc5c5..b51e5d4035 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -353,7 +353,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('Meier2022') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp(-1.4_r8 * rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if @@ -602,7 +602,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else ! Snow layers if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp(-1.4_r8 * rpi/2.0_r8 -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if From f0fe8779d61dca88c6d4236936ca99eaa3964fdc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Mar 2022 13:21:04 -0700 Subject: [PATCH 0178/2067] Update paramsfile for Meier surface roughness changes to latest version --- .../testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm index f9d550ff71..86903538e2 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -2,5 +2,5 @@ z0param_method = 'Meier2022' use_z0m_snowmelt = .true. use_z0mg_2d = .false. calc_human_stress_indices = 'NONE' ! Currently dies when turned on because of a negative humidity (about -31) in Wet Bulb calculation -paramfile = '/glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/ctsm51_params_newz0.c211112.nc' +paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_params.RMz0.c220304.nc' From 0c5d04ec79f1fcf4f13c12469c4b799d6b4aecbd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Mar 2022 11:46:38 -0700 Subject: [PATCH 0179/2067] Renamed gddplant_patch to hui_patch and GDDPLANT to HUI. --- src/biogeochem/CNNDynamicsMod.F90 | 2 +- src/biogeochem/CNPhenologyMod.F90 | 6 ++-- src/biogeochem/CNRootDynMod.F90 | 2 +- src/biogeochem/CropType.F90 | 36 +++++++++---------- .../NutrientCompetitionCLM45defaultMod.F90 | 2 +- .../NutrientCompetitionFlexibleCNMod.F90 | 2 +- 6 files changed, 25 insertions(+), 25 deletions(-) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 7a80d701a8..b21ee89763 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -333,7 +333,7 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & associate( & wf => waterdiagnosticbulk_inst%wf_col , & ! Input: [real(r8) (:) ] soil water as frac. of whc for top 0.5 m - hui => crop_inst%gddplant_patch , & ! Input: [real(r8) (:) ] gdd since planting (gddplant) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] hui accumulated since planting (growing degree-days) croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] true if planted and not harvested gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Input: [real(r8) (:) ] gdd needed to harvest diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 1c12747d72..4d9a33c390 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1714,7 +1714,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & gdd1020 => temperature_inst%gdd1020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd10 fertnitro => crop_inst%fertnitro_patch , & ! Input: [real(r8) (:) ] fertilizer nitrogen - hui => crop_inst%gddplant_patch , & ! Input: [real(r8) (:) ] gdd since planting (gddplant) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] hui accumulated since planting (growing degree-days) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested @@ -2016,7 +2016,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! call vernalization if winter temperate cereal planted, living, and the ! vernalization factor is not 1; - ! vf affects the calculation of gddtsoi & gddplant + ! vf affects the calculation of gddtsoi & hui if (t_ref2m_min(p) < 1.e30_r8 .and. vf(p) /= 1._r8 .and. & (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat)) then @@ -2347,7 +2347,7 @@ subroutine vernalization(p, & ! vernalization factor calculation ! if vf(p) = 1. then plant is fully vernalized - and thermal time ! accumulation in phase 1 will be unaffected - ! refers to gddtsoi & gddplant, defined in the accumulation routines (slevis) + ! refers to gddtsoi & hui, defined in the accumulation routines (slevis) ! reset vf, cumvd, and hdidx to 0 at planting of crop (slevis) if (t_ref2m_max(p) > tfrz) then diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90 index 4d34d54f7c..89ad33e9c0 100644 --- a/src/biogeochem/CNRootDynMod.F90 +++ b/src/biogeochem/CNRootDynMod.F90 @@ -97,7 +97,7 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & soilpsi => soilstate_inst%soilpsi_col , & ! Input: soil water potential in each soil layer (MPa) sminn_vr => soilbiogeochem_nitrogenstate_inst%sminn_vr_col , & ! Iniput: [real(r8) (:,:)] (gN/m3) soil mineral N frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C - hui => crop_inst%gddplant_patch , & ! Input: [real(r8) (:)] =gdd since planting (gddplant) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:)] =hui accumulated since planting (growing degree-days) croplive => crop_inst%croplive_patch , & ! Input: [logical (:)] flag, true if planted, not harvested huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:)] same to reach vegetative maturity ) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index afa2008f13..3a03b0176e 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -33,11 +33,11 @@ module CropType logical , pointer :: cropplant_patch (:) ! patch Flag, true if planted integer , pointer :: harvdate_patch (:) ! patch harvest date real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen - real(r8), pointer :: gddplant_patch (:) ! patch accum gdd past planting date for crop (ddays) + real(r8), pointer :: hui_patch (:) ! patch accum hui past planting date for crop (ddays) real(r8), pointer :: gddtsoi_patch (:) ! patch growing degree-days from planting (top two soil layers) (ddays) real(r8), pointer :: vf_patch (:) ! patch vernalization factor for cereal real(r8), pointer :: cphase_patch (:) ! phenology phase - real(r8), pointer :: latbaset_patch (:) ! Latitude vary baset for gddplant (degree C) + real(r8), pointer :: latbaset_patch (:) ! Latitude vary baset for hui (degree C) character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope @@ -194,7 +194,7 @@ subroutine InitAllocate(this, bounds) allocate(this%cropplant_patch(begp:endp)) ; this%cropplant_patch(:) = .false. allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) allocate(this%fertnitro_patch (begp:endp)) ; this%fertnitro_patch (:) = spval - allocate(this%gddplant_patch (begp:endp)) ; this%gddplant_patch (:) = spval + allocate(this%hui_patch (begp:endp)) ; this%hui_patch (:) = spval allocate(this%gddtsoi_patch (begp:endp)) ; this%gddtsoi_patch (:) = spval allocate(this%vf_patch (begp:endp)) ; this%vf_patch (:) = 0.0_r8 allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 @@ -225,10 +225,10 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='Nitrogen fertilizer for each crop', & ptr_patch=this%fertnitro_patch, default='inactive') - this%gddplant_patch(begp:endp) = spval - call hist_addfld1d (fname='GDDPLANT', units='ddays', & - avgflag='A', long_name='Accumulated growing degree days past planting date for crop', & - ptr_patch=this%gddplant_patch, default='inactive') + this%hui_patch(begp:endp) = spval + call hist_addfld1d (fname='HUI', units='ddays', & + avgflag='A', long_name='Accumulated heat unit index since planting for crop', & + ptr_patch=this%hui_patch, default='inactive') this%gddtsoi_patch(begp:endp) = spval call hist_addfld1d (fname='GDDTSOI', units='ddays', & @@ -243,7 +243,7 @@ subroutine InitHistory(this, bounds) if ( (trim(this%baset_mapping) == baset_map_latvary) )then this%latbaset_patch(begp:endp) = spval call hist_addfld1d (fname='LATBASET', units='degree C', & - avgflag='A', long_name='latitude vary base temperature for gddplant', & + avgflag='A', long_name='latitude vary base temperature for hui', & ptr_patch=this%latbaset_patch, default='inactive') end if @@ -335,8 +335,8 @@ subroutine InitAccBuffer (this, bounds) !--------------------------------------------------------------------- - call init_accum_field (name='GDDPLANT', units='K', & - desc='growing degree-days from planting', accum_type='runaccum', accum_period=not_used, & + call init_accum_field (name='HUI', units='K', & + desc='heat unit index accumulated since planting', accum_type='runaccum', accum_period=not_used, & subgrid_type='pft', numlev=1, init_value=0._r8) call init_accum_field (name='GDDTSOI', units='K', & @@ -383,8 +383,8 @@ subroutine InitAccVars(this, bounds) nstep = get_nstep() - call extract_accum_field ('GDDPLANT', rbufslp, nstep) - this%gddplant_patch(begp:endp) = rbufslp(begp:endp) + call extract_accum_field ('HUI', rbufslp, nstep) + this%hui_patch(begp:endp) = rbufslp(begp:endp) call extract_accum_field ('GDDTSOI', rbufslp, nstep) this%gddtsoi_patch(begp:endp) = rbufslp(begp:endp) @@ -570,13 +570,13 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) call endrun(msg=errMsg(sourcefile, __LINE__)) endif - ! Accumulate and extract GDDPLANT + ! Accumulate and extract HUI - call extract_accum_field ('GDDPLANT', rbufslp, nstep) + call extract_accum_field ('HUI', rbufslp, nstep) do p = begp,endp - rbufslp(p) = max(0.0_r8,this%gddplant_patch(p)-rbufslp(p)) + rbufslp(p) = max(0.0_r8,this%hui_patch(p)-rbufslp(p)) end do - call update_accum_field ('GDDPLANT', rbufslp, nstep) + call update_accum_field ('HUI', rbufslp, nstep) do p = begp,endp if (this%croplive_patch(p)) then ! relative to planting date ivt = patch%itype(p) @@ -598,8 +598,8 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) rbufslp(p) = accumResetVal end if end do - call update_accum_field ('GDDPLANT', rbufslp, nstep) - call extract_accum_field ('GDDPLANT', this%gddplant_patch, nstep) + call update_accum_field ('HUI', rbufslp, nstep) + call extract_accum_field ('HUI', this%hui_patch, nstep) ! Accumulate and extract GDDTSOI ! In agroibis this variable is calculated diff --git a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 index d93f0a168e..d16c543528 100644 --- a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 +++ b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 @@ -587,7 +587,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - hui => crop_inst%gddplant_patch , & ! Input: [real(r8) (:) ] =gdd since planting (gddplant) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] =hui accumulated since planting (growing degree-days) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] =gdd from top soil layer temperature croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index a642a5dd2d..0127e6857d 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -1300,7 +1300,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - hui => crop_inst%gddplant_patch , & ! Input: [real(r8) (:) ] =gdd since planting (gddplant) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] =hui accumulated since planting (growing degree-days) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] =gdd from top soil layer temperature croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested From 162ccee4820fa9f98167024b3ccd319b9933f0f8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Mar 2022 11:59:42 -0700 Subject: [PATCH 0180/2067] Improved description of hui_patch and HUI. --- src/biogeochem/CNNDynamicsMod.F90 | 2 +- src/biogeochem/CNPhenologyMod.F90 | 2 +- src/biogeochem/CNRootDynMod.F90 | 2 +- src/biogeochem/CropType.F90 | 4 ++-- src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 | 2 +- src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 | 2 +- 6 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index b21ee89763..a658a63768 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -333,7 +333,7 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & associate( & wf => waterdiagnosticbulk_inst%wf_col , & ! Input: [real(r8) (:) ] soil water as frac. of whc for top 0.5 m - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] hui accumulated since planting (growing degree-days) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] patch heat unit index (growing degree-days) croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] true if planted and not harvested gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Input: [real(r8) (:) ] gdd needed to harvest diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 4d9a33c390..16ee75d8e7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1714,7 +1714,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & gdd1020 => temperature_inst%gdd1020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd10 fertnitro => crop_inst%fertnitro_patch , & ! Input: [real(r8) (:) ] fertilizer nitrogen - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] hui accumulated since planting (growing degree-days) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90 index 89ad33e9c0..78cba70031 100644 --- a/src/biogeochem/CNRootDynMod.F90 +++ b/src/biogeochem/CNRootDynMod.F90 @@ -97,7 +97,7 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & soilpsi => soilstate_inst%soilpsi_col , & ! Input: soil water potential in each soil layer (MPa) sminn_vr => soilbiogeochem_nitrogenstate_inst%sminn_vr_col , & ! Iniput: [real(r8) (:,:)] (gN/m3) soil mineral N frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:)] (gC/m2) fine root C - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:)] =hui accumulated since planting (growing degree-days) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:)] crop patch heat unit index (growing degree-days) croplive => crop_inst%croplive_patch , & ! Input: [logical (:)] flag, true if planted, not harvested huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:)] same to reach vegetative maturity ) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 3a03b0176e..d7503588dd 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -33,7 +33,7 @@ module CropType logical , pointer :: cropplant_patch (:) ! patch Flag, true if planted integer , pointer :: harvdate_patch (:) ! patch harvest date real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen - real(r8), pointer :: hui_patch (:) ! patch accum hui past planting date for crop (ddays) + real(r8), pointer :: hui_patch (:) ! crop patch heat unit index (ddays) real(r8), pointer :: gddtsoi_patch (:) ! patch growing degree-days from planting (top two soil layers) (ddays) real(r8), pointer :: vf_patch (:) ! patch vernalization factor for cereal real(r8), pointer :: cphase_patch (:) ! phenology phase @@ -227,7 +227,7 @@ subroutine InitHistory(this, bounds) this%hui_patch(begp:endp) = spval call hist_addfld1d (fname='HUI', units='ddays', & - avgflag='A', long_name='Accumulated heat unit index since planting for crop', & + avgflag='A', long_name='Crop patch heat unit index', & ptr_patch=this%hui_patch, default='inactive') this%gddtsoi_patch(begp:endp) = spval diff --git a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 index d16c543528..788024e14a 100644 --- a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 +++ b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 @@ -587,7 +587,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] =hui accumulated since planting (growing degree-days) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] =gdd from top soil layer temperature croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 0127e6857d..5705addb85 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -1300,7 +1300,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] =hui accumulated since planting (growing degree-days) + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days) leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] =gdd from top soil layer temperature croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested From cf0934b29fda140b5a8dae4158b4f8f4e34c442f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Mar 2022 14:26:40 -0700 Subject: [PATCH 0181/2067] Some updates from @olyson that get more tests to work --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 4 ++-- src/biogeophys/CanopyFluxesMod.F90 | 14 ++++++++++++-- 2 files changed, 14 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index f033fab5ff..9123000fc5 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -174,7 +174,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & case ('Meier2022') ! Don't set on first few steps of a simulation, since htop isn't set yet, need to wait until after first do_alb time - if ( is_first_step() .or. get_nstep() <= GetBalanceCheckSkipSteps() ) then + if ( is_first_step() .or. get_nstep() <= GetBalanceCheckSkipSteps()-1 ) then z0m(p) = 0._r8 displa(p) = 0._r8 cycle @@ -190,7 +190,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & displa(p) = 0._r8 else - ! Compute as if elai+esai = LAImax - LAIoff in CanopyFluxes + ! Compute as if elai+esai = LAImax in CanopyFluxes displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * (pftcon%z0v_LAImax(patch%itype(p))))**0.5_r8)) & / (7.5_r8*(pftcon%z0v_LAImax(patch%itype(p)) ))**0.5_r8) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 2681c93ced..f7139af47b 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -528,7 +528,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, soilbeta => soilstate_inst%soilbeta_col , & ! Input: [real(r8) (:) ] soil wetness relative to field capacity u10_clm => frictionvel_inst%u10_clm_patch , & ! Input: [real(r8) (:) ] 10 m height winds (m/s) - forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Input: [real(r8) (:) ] observational height of wind at patch level [m] + forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] + forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] + forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] + forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Output: [real(r8) (:) ] observational height of temperature at patch level [m] + forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Output: [real(r8) (:) ] observational height of specific humidity at patch level [m] + forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Output: [real(r8) (:) ] observational height of wind at patch level [m] z0mg => frictionvel_inst%z0mg_col , & ! Input: [real(r8) (:) ] roughness length of ground, momentum [m] zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) @@ -877,7 +882,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, do f = 1, fn p = filterp(f) c = patch%column(p) - + g = patch%gridcell(p) select case (z0param_method) case ('ZengWang2007') @@ -913,6 +918,11 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, call endrun(msg = 'unknown z0param_method', additional_msg = errMsg(sourcefile, __LINE__)) end select + ! Update the forcing heights + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(c) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(c) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(c) + displa(p) + z0hv(p) = z0mv(p) z0qv(p) = z0mv(p) From 18e7b16f234d6122f25cd2c4f12d4e9a10b58f5a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Mar 2022 15:31:30 -0700 Subject: [PATCH 0182/2067] Added diagnostic output gddaccum_patch (GDDACCUM). --- src/biogeochem/CropType.F90 | 29 ++++++++++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index d7503588dd..7426e950e0 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -34,6 +34,7 @@ module CropType integer , pointer :: harvdate_patch (:) ! patch harvest date real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen real(r8), pointer :: hui_patch (:) ! crop patch heat unit index (ddays) + real(r8), pointer :: gddaccum_patch (:) ! patch growing degree-days from planting (air) (ddays) real(r8), pointer :: gddtsoi_patch (:) ! patch growing degree-days from planting (top two soil layers) (ddays) real(r8), pointer :: vf_patch (:) ! patch vernalization factor for cereal real(r8), pointer :: cphase_patch (:) ! phenology phase @@ -195,6 +196,7 @@ subroutine InitAllocate(this, bounds) allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) allocate(this%fertnitro_patch (begp:endp)) ; this%fertnitro_patch (:) = spval allocate(this%hui_patch (begp:endp)) ; this%hui_patch (:) = spval + allocate(this%gddaccum_patch (begp:endp)) ; this%gddaccum_patch (:) = spval allocate(this%gddtsoi_patch (begp:endp)) ; this%gddtsoi_patch (:) = spval allocate(this%vf_patch (begp:endp)) ; this%vf_patch (:) = 0.0_r8 allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 @@ -230,6 +232,11 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='Crop patch heat unit index', & ptr_patch=this%hui_patch, default='inactive') + this%gddaccum_patch(begp:endp) = spval + call hist_addfld1d (fname='GDDACCUM', units='ddays', & + avgflag='A', long_name='Accumulated growing degree days past planting date for crop', & + ptr_patch=this%gddaccum_patch, default='inactive') + this%gddtsoi_patch(begp:endp) = spval call hist_addfld1d (fname='GDDTSOI', units='ddays', & avgflag='A', long_name='Growing degree-days from planting (top two soil layers)', & @@ -339,6 +346,10 @@ subroutine InitAccBuffer (this, bounds) desc='heat unit index accumulated since planting', accum_type='runaccum', accum_period=not_used, & subgrid_type='pft', numlev=1, init_value=0._r8) + call init_accum_field (name='GDDACCUM', units='K', & + desc='growing degree-days from planting', accum_type='runaccum', accum_period=not_used, & + subgrid_type='pft', numlev=1, init_value=0._r8) + call init_accum_field (name='GDDTSOI', units='K', & desc='growing degree-days from planting (top two soil layers)', accum_type='runaccum', accum_period=not_used, & subgrid_type='pft', numlev=1, init_value=0._r8) @@ -386,6 +397,9 @@ subroutine InitAccVars(this, bounds) call extract_accum_field ('HUI', rbufslp, nstep) this%hui_patch(begp:endp) = rbufslp(begp:endp) + call extract_accum_field ('GDDACCUM', rbufslp, nstep) + this%gddaccum_patch(begp:endp) = rbufslp(begp:endp) + call extract_accum_field ('GDDTSOI', rbufslp, nstep) this%gddtsoi_patch(begp:endp) = rbufslp(begp:endp) @@ -549,6 +563,7 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) integer :: begp, endp integer :: begc, endc real(r8), pointer :: rbufslp(:) ! temporary single level - patch level + real(r8), pointer :: rbufslp2(:) ! temporary single level - patch level character(len=*), parameter :: subname = 'CropUpdateAccVars' !----------------------------------------------------------------------- @@ -569,14 +584,22 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) write(iulog,*)'update_accum_hist allocation error for rbuf1dp' call endrun(msg=errMsg(sourcefile, __LINE__)) endif + allocate(rbufslp2(begp:endp), stat=ier) + if (ier/=0) then + write(iulog,*)'update_accum_hist allocation error for rbuf1dp (2)' + call endrun(msg=errMsg(sourcefile, __LINE__)) + endif - ! Accumulate and extract HUI + ! Accumulate and extract HUI and GDDACCUM call extract_accum_field ('HUI', rbufslp, nstep) + call extract_accum_field ('GDDACCUM', rbufslp2, nstep) do p = begp,endp rbufslp(p) = max(0.0_r8,this%hui_patch(p)-rbufslp(p)) + rbufslp2(p) = max(0.0_r8,this%gddaccum_patch(p)-rbufslp2(p)) end do call update_accum_field ('HUI', rbufslp, nstep) + call update_accum_field ('GDDACCUM', rbufslp2, nstep) do p = begp,endp if (this%croplive_patch(p)) then ! relative to planting date ivt = patch%itype(p) @@ -597,9 +620,13 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) else rbufslp(p) = accumResetVal end if + rbufslp2(p) = rbufslp(p) end do call update_accum_field ('HUI', rbufslp, nstep) call extract_accum_field ('HUI', this%hui_patch, nstep) + call update_accum_field ('GDDACCUM', rbufslp2, nstep) + call extract_accum_field ('GDDACCUM', this%gddaccum_patch, nstep) + deallocate(rbufslp2) ! Accumulate and extract GDDTSOI ! In agroibis this variable is calculated From 0aa8958dc5cda260de1f60a32dfa8db151ef27c6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Mar 2022 10:42:01 -0700 Subject: [PATCH 0183/2067] master_list_nofates.rst: Remove GDDPLANT, add GDDACCUM and HUI. --- .../master_list_nofates.rst | 1683 +++++++++-------- 1 file changed, 842 insertions(+), 841 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst index 776acc9833..07c8b8612b 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst @@ -425,8 +425,8 @@ CTSM History Fields 410 GDD1020 Twenty year average of growing degree days base 10C from planting ddays F 411 GDD8 Growing degree days base 8C from planting ddays F 412 GDD820 Twenty year average of growing degree days base 8C from planting ddays F - 413 GDDHARV Growing degree days (gdd) needed to harvest ddays F - 414 GDDPLANT Accumulated growing degree days past planting date for crop ddays F + 413 GDDACCUM Accumulated growing degree days past planting date for crop ddays F + 414 GDDHARV Growing degree days (gdd) needed to harvest ddays F 415 GDDTSOI Growing degree-days from planting (top two soil layers) ddays F 416 GPP gross primary production gC/m^2/s T 417 GR total growth respiration gC/m^2/s T @@ -461,843 +461,844 @@ CTSM History Fields 446 HR total heterotrophic respiration gC/m^2/s T 447 HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T 448 HTOP canopy top m T - 449 HUMIDEX 2 m Humidex C T - 450 HUMIDEX_R Rural 2 m Humidex C T - 451 HUMIDEX_U Urban 2 m Humidex C T - 452 ICE_CONTENT1 initial gridcell total ice content mm T - 453 ICE_CONTENT2 post land cover change total ice content mm F - 454 ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F - 455 INIT_GPP GPP flux before downregulation gC/m^2/s F - 456 INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F - 457 INT_SNOW_ICE accumulated swe (ice landunits only) mm F - 458 IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T - 459 JMX25T canopy profile of jmax umol/m2/s T - 460 Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T - 461 KROOT root conductance each soil layer 1/s F - 462 KSOIL soil conductance in each soil layer 1/s F - 463 K_ACT_SOM active soil organic potential loss coefficient 1/s F - 464 K_CEL_LIT cellulosic litter potential loss coefficient 1/s F - 465 K_CWD coarse woody debris potential loss coefficient 1/s F - 466 K_LIG_LIT lignin litter potential loss coefficient 1/s F - 467 K_MET_LIT metabolic litter potential loss coefficient 1/s F - 468 K_NITR K_NITR 1/s F - 469 K_NITR_H2O K_NITR_H2O unitless F - 470 K_NITR_PH K_NITR_PH unitless F - 471 K_NITR_T K_NITR_T unitless F - 472 K_PAS_SOM passive soil organic potential loss coefficient 1/s F - 473 K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F - 474 LAI240 240hr average of leaf area index m^2/m^2 F - 475 LAISHA shaded projected leaf area index m^2/m^2 T - 476 LAISUN sunlit projected leaf area index m^2/m^2 T - 477 LAKEICEFRAC lake layer ice mass fraction unitless F - 478 LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T - 479 LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T - 480 LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T - 481 LATBASET latitude vary base temperature for gddplant degree C F - 482 LEAFC leaf C gC/m^2 T - 483 LEAFCN Leaf CN ratio used for flexible CN gC/gN T - 484 LEAFCN_OFFSET Leaf C:N used by FUN unitless F - 485 LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F - 486 LEAFC_ALLOC leaf C allocation gC/m^2/s T - 487 LEAFC_CHANGE C change in leaf gC/m^2/s T - 488 LEAFC_LOSS leaf C loss gC/m^2/s T - 489 LEAFC_STORAGE leaf C storage gC/m^2 F - 490 LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F - 491 LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F - 492 LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T - 493 LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F - 494 LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T - 495 LEAFC_XFER leaf C transfer gC/m^2 F - 496 LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F - 497 LEAFN leaf N gN/m^2 T - 498 LEAFN_STORAGE leaf N storage gN/m^2 F - 499 LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F - 500 LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F - 501 LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T - 502 LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F - 503 LEAFN_XFER leaf N transfer gN/m^2 F - 504 LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F - 505 LEAF_MR leaf maintenance respiration gC/m^2/s T - 506 LEAF_PROF profile for litter C and N inputs from leaves 1/m F - 507 LFC2 conversion area fraction of BET and BDT that burned per sec T - 508 LGSF long growing season factor proportion F - 509 LIG_LITC LIG_LIT C gC/m^2 T - 510 LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F - 511 LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F - 512 LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F - 513 LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F - 514 LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T - 515 LIG_LITN LIG_LIT N gN/m^2 T - 516 LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F - 517 LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F - 518 LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F - 519 LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F - 520 LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T - 521 LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F - 522 LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F - 523 LIQCAN intercepted liquid water mm T - 524 LIQUID_CONTENT1 initial gridcell total liq content mm T - 525 LIQUID_CONTENT2 post landuse change gridcell total liq content mm F - 526 LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F - 527 LITFALL litterfall (leaves and fine roots) gC/m^2/s T - 528 LITFIRE litter fire losses gC/m^2/s F - 529 LITTERC_HR litter C heterotrophic respiration gC/m^2/s T - 530 LITTERC_LOSS litter C loss gC/m^2/s T - 531 LIVECROOTC live coarse root C gC/m^2 T - 532 LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F - 533 LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F - 534 LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F - 535 LIVECROOTC_XFER live coarse root C transfer gC/m^2 F - 536 LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F - 537 LIVECROOTN live coarse root N gN/m^2 T - 538 LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F - 539 LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F - 540 LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F - 541 LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F - 542 LIVECROOTN_XFER live coarse root N transfer gN/m^2 F - 543 LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F - 544 LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F - 545 LIVESTEMC live stem C gC/m^2 T - 546 LIVESTEMC_STORAGE live stem C storage gC/m^2 F - 547 LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F - 548 LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T - 549 LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F - 550 LIVESTEMC_XFER live stem C transfer gC/m^2 F - 551 LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F - 552 LIVESTEMN live stem N gN/m^2 T - 553 LIVESTEMN_STORAGE live stem N storage gN/m^2 F - 554 LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F - 555 LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F - 556 LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F - 557 LIVESTEMN_XFER live stem N transfer gN/m^2 F - 558 LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F - 559 LIVESTEM_MR live stem maintenance respiration gC/m^2/s F - 560 LNC leaf N concentration gN leaf/m^2 T - 561 LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F - 562 LWup upwelling longwave radiation W/m^2 F - 563 MEG_acetaldehyde MEGAN flux kg/m2/sec T - 564 MEG_acetic_acid MEGAN flux kg/m2/sec T - 565 MEG_acetone MEGAN flux kg/m2/sec T - 566 MEG_carene_3 MEGAN flux kg/m2/sec T - 567 MEG_ethanol MEGAN flux kg/m2/sec T - 568 MEG_formaldehyde MEGAN flux kg/m2/sec T - 569 MEG_isoprene MEGAN flux kg/m2/sec T - 570 MEG_methanol MEGAN flux kg/m2/sec T - 571 MEG_pinene_a MEGAN flux kg/m2/sec T - 572 MEG_thujene_a MEGAN flux kg/m2/sec T - 573 MET_LITC MET_LIT C gC/m^2 T - 574 MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F - 575 MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F - 576 MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F - 577 MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F - 578 MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T - 579 MET_LITN MET_LIT N gN/m^2 T - 580 MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F - 581 MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F - 582 MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F - 583 MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F - 584 MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T - 585 MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F - 586 MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F - 587 MR maintenance respiration gC/m^2/s T - 588 M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F - 589 M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F - 590 M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F - 591 M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F - 592 M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F - 593 M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F - 594 M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F - 595 M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F - 596 M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F - 597 M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F - 598 M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F - 599 M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F - 600 M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F - 601 M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F - 602 M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F - 603 M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F - 604 M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F - 605 M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F - 606 M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F - 607 M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F - 608 M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F - 609 M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F - 610 M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F - 611 M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F - 612 M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F - 613 M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F - 614 M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F - 615 M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F - 616 M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F - 617 M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F - 618 M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F - 619 M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F - 620 M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F - 621 M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F - 622 M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F - 623 M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F - 624 M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F - 625 M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F - 626 M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F - 627 M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F - 628 M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F - 629 M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F - 630 M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F - 631 M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F - 632 M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F - 633 M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F - 634 M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F - 635 M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F - 636 M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F - 637 M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F - 638 M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F - 639 M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F - 640 M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F - 641 M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F - 642 M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F - 643 M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F - 644 M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F - 645 M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F - 646 M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F - 647 M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F - 648 M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F - 649 M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F - 650 M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F - 651 M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F - 652 M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F - 653 M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F - 654 M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F - 655 M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F - 656 M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F - 657 M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F - 658 M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F - 659 M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F - 660 M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F - 661 M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F - 662 M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F - 663 M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F - 664 M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F - 665 M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F - 666 M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F - 667 M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F - 668 M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F - 669 M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F - 670 M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F - 671 M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F - 672 M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F - 673 M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F - 674 M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F - 675 M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F - 676 M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F - 677 M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F - 678 M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F - 679 M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F - 680 M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F - 681 M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F - 682 M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F - 683 M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F - 684 M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F - 685 M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F - 686 M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F - 687 M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F - 688 M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F - 689 M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F - 690 M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F - 691 M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F - 692 M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F - 693 M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F - 694 M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F - 695 M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F - 696 M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F - 697 M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F - 698 M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F - 699 M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F - 700 M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F - 701 M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F - 702 M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F - 703 M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F - 704 M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F - 705 M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F - 706 M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F - 707 M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F - 708 M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F - 709 M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F - 710 M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F - 711 M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F - 712 M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F - 713 M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F - 714 M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F - 715 M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F - 716 M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F - 717 M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F - 718 M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F - 719 M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F - 720 NACTIVE Mycorrhizal N uptake flux gN/m^2/s T - 721 NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T - 722 NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T - 723 NAM AM-associated N uptake flux gN/m^2/s T - 724 NAM_NH4 AM-associated N uptake flux gN/m^2/s T - 725 NAM_NO3 AM-associated N uptake flux gN/m^2/s T - 726 NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T - 727 NDEPLOY total N deployed in new growth gN/m^2/s T - 728 NDEP_PROF profile for atmospheric N deposition 1/m F - 729 NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T - 730 NECM ECM-associated N uptake flux gN/m^2/s T - 731 NECM_NH4 ECM-associated N uptake flux gN/m^2/s T - 732 NECM_NO3 ECM-associated N uptake flux gN/m^2/s T - 733 NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T - 734 NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T - 735 NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T - 736 NET_NMIN net rate of N mineralization gN/m^2/s T - 737 NET_NMIN_vr net rate of N mineralization gN/m^3/s F - 738 NFERTILIZATION fertilizer added gN/m^2/s T - 739 NFIRE fire counts valid only in Reg.C counts/km2/sec T - 740 NFIX Symbiotic BNF uptake flux gN/m^2/s T - 741 NFIXATION_PROF profile for biological N fixation 1/m F - 742 NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F - 743 NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T - 744 NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T - 745 NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T - 746 NPASSIVE Passive N uptake flux gN/m^2/s T - 747 NPOOL temporary plant N pool gN/m^2 T - 748 NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F - 749 NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F - 750 NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F - 751 NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F - 752 NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F - 753 NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F - 754 NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F - 755 NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F - 756 NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F - 757 NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F - 758 NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F - 759 NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F - 760 NPP net primary production gC/m^2/s T - 761 NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F - 762 NPP_GROWTH Total C used for growth in FUN gC/m^2/s T - 763 NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T - 764 NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T - 765 NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T - 766 NPP_NAM AM-associated N uptake used C gC/m^2/s T - 767 NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T - 768 NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T - 769 NPP_NECM ECM-associated N uptake used C gC/m^2/s T - 770 NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T - 771 NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T - 772 NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T - 773 NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T - 774 NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T - 775 NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T - 776 NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T - 777 NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T - 778 NRETRANS Retranslocated N uptake flux gN/m^2/s T - 779 NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T - 780 NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T - 781 NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T - 782 NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F - 783 NUPTAKE Total N uptake of FUN gN/m^2/s T - 784 NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T - 785 N_ALLOMETRY N allocation index none F - 786 O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F - 787 OBU Monin-Obukhov length m F - 788 OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T - 789 OFFSET_COUNTER offset days counter days F - 790 OFFSET_FDD offset freezing degree days counter C degree-days F - 791 OFFSET_FLAG offset flag none F - 792 OFFSET_SWI offset soil water index none F - 793 ONSET_COUNTER onset days counter days F - 794 ONSET_FDD onset freezing degree days counter C degree-days F - 795 ONSET_FLAG onset flag none F - 796 ONSET_GDD onset growing degree days C degree-days F - 797 ONSET_GDDFLAG onset flag for growing degree day sum none F - 798 ONSET_SWI onset soil water index none F - 799 O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T - 800 PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F - 801 PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F - 802 PAR240_shade shade PAR (240 hrs) umol/m2/s F - 803 PAR240_sun sunlit PAR (240 hrs) umol/m2/s F - 804 PAR24_shade shade PAR (24 hrs) umol/m2/s F - 805 PAR24_sun sunlit PAR (24 hrs) umol/m2/s F - 806 PARVEGLN absorbed par by vegetation at local noon W/m^2 T - 807 PAR_shade shade PAR umol/m2/s F - 808 PAR_sun sunlit PAR umol/m2/s F - 809 PAS_SOMC PAS_SOM C gC/m^2 T - 810 PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F - 811 PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F - 812 PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F - 813 PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F - 814 PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T - 815 PAS_SOMN PAS_SOM N gN/m^2 T - 816 PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F - 817 PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F - 818 PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F - 819 PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F - 820 PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T - 821 PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F - 822 PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F - 823 PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T - 824 PBOT_240 10 day running mean of air pressure Pa F - 825 PCH4 atmospheric partial pressure of CH4 Pa T - 826 PCO2 atmospheric partial pressure of CO2 Pa T - 827 PCO2_240 10 day running mean of CO2 pressure Pa F - 828 PFT_CTRUNC patch-level sink for C truncation gC/m^2 F - 829 PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T - 830 PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T - 831 PFT_NTRUNC patch-level sink for N truncation gN/m^2 F - 832 PLANTCN Plant C:N used by FUN unitless F - 833 PLANT_CALLOC total allocated C flux gC/m^2/s F - 834 PLANT_NALLOC total allocated N flux gN/m^2/s F - 835 PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T - 836 PNLCZ Proportion of nitrogen allocated for light capture unitless F - 837 PO2_240 10 day running mean of O2 pressure Pa F - 838 POTENTIAL_IMMOB potential N immobilization gN/m^2/s T - 839 POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F - 840 POT_F_DENIT potential denitrification flux gN/m^2/s T - 841 POT_F_DENIT_vr potential denitrification flux gN/m^3/s F - 842 POT_F_NIT potential nitrification flux gN/m^2/s T - 843 POT_F_NIT_vr potential nitrification flux gN/m^3/s F - 844 PREC10 10-day running mean of PREC MM H2O/S F - 845 PREC60 60-day running mean of PREC MM H2O/S F - 846 PREV_DAYL daylength from previous timestep s F - 847 PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F - 848 PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F - 849 PROD100C 100-yr wood product C gC/m^2 F - 850 PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F - 851 PROD100N 100-yr wood product N gN/m^2 F - 852 PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F - 853 PROD10C 10-yr wood product C gC/m^2 F - 854 PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F - 855 PROD10N 10-yr wood product N gN/m^2 F - 856 PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F - 857 PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T - 858 PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T - 859 PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T - 860 PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T - 861 PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F - 862 Q2M 2m specific humidity kg/kg T - 863 QAF canopy air humidity kg/kg F - 864 QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T - 865 QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F - 866 QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F - 867 QDRAI sub-surface drainage mm/s T - 868 QDRAI_PERCH perched wt drainage mm/s T - 869 QDRAI_XS saturation excess drainage mm/s T - 870 QDRIP rate of excess canopy liquid falling off canopy mm/s F - 871 QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F - 872 QFLOOD runoff from river flooding mm/s T - 873 QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T - 874 QFLX_EVAP_VEG vegetation evaporation mm H2O/s F - 875 QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T - 876 QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T - 877 QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T - 878 QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T - 879 QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F - 880 QFLX_SNOW_DRAIN drainage from snow pack mm/s T - 881 QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T - 882 QFLX_SNOW_GRND snow on ground after interception mm H2O/s F - 883 QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T - 884 QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T - 885 QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F - 886 QH2OSFC surface water runoff mm/s T - 887 QH2OSFC_TO_ICE surface water converted to ice mm/s F - 888 QHR hydraulic redistribution mm/s T - 889 QICE ice growth/melt mm/s T - 890 QICE_FORC qice forcing sent to GLC mm/s F - 891 QICE_FRZ ice growth mm/s T - 892 QICE_MELT ice melt mm/s T - 893 QINFL infiltration mm/s T - 894 QINTR interception mm/s T - 895 QIRRIG_DEMAND irrigation demand mm/s F - 896 QIRRIG_DRIP water added via drip irrigation mm/s F - 897 QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T - 898 QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T - 899 QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T - 900 QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F - 901 QOVER total surface runoff (includes QH2OSFC) mm/s T - 902 QOVER_LAG time-lagged surface runoff for soil columns mm/s F - 903 QPHSNEG net negative hydraulic redistribution flux mm/s F - 904 QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T - 905 QROOTSINK water flux from soil to root in each soil-layer mm/s F - 906 QRUNOFF total liquid runoff not including correction for land use change mm/s T - 907 QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T - 908 QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T - 909 QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F - 910 QRUNOFF_R Rural total runoff mm/s F - 911 QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T - 912 QRUNOFF_U Urban total runoff mm/s F - 913 QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T - 914 QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T - 915 QSNOFRZ column-integrated snow freezing rate kg/m2/s T - 916 QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T - 917 QSNOMELT snow melt rate mm/s T - 918 QSNOMELT_ICE snow melt (ice landunits only) mm/s T - 919 QSNOUNLOAD canopy snow unloading mm/s T - 920 QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T - 921 QSNO_WINDUNLOAD canopy snow wind unloading mm/s T - 922 QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T - 923 QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T - 924 QSOIL_ICE Ground evaporation (ice landunits only) mm/s T - 925 QTOPSOIL water input to surface mm/s F - 926 QVEGE canopy evaporation mm/s T - 927 QVEGT canopy transpiration mm/s T - 928 Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F - 929 Qh sensible heat W/m^2 F - 930 Qle total evaporation W/m^2 F - 931 Qstor storage heat flux (includes snowmelt) W/m^2 F - 932 Qtau momentum flux kg/m/s^2 F - 933 RAH1 aerodynamical resistance s/m F - 934 RAH2 aerodynamical resistance s/m F - 935 RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T - 936 RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T - 937 RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F - 938 RAM1 aerodynamical resistance s/m F - 939 RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F - 940 RAW1 aerodynamical resistance s/m F - 941 RAW2 aerodynamical resistance s/m F - 942 RB leaf boundary resistance s/m F - 943 RB10 10 day running mean boundary layer resistance s/m F - 944 RETRANSN plant pool of retranslocated N gN/m^2 T - 945 RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T - 946 RH atmospheric relative humidity % F - 947 RH2M 2m relative humidity % T - 948 RH2M_R Rural 2m specific humidity % F - 949 RH2M_U Urban 2m relative humidity % F - 950 RH30 30-day running mean of relative humidity % F - 951 RHAF fractional humidity of canopy air fraction F - 952 RHAF10 10 day running mean of fractional humidity of canopy air fraction F - 953 RH_LEAF fractional humidity at leaf surface fraction F - 954 ROOTR effective fraction of roots in each soil layer (SMS method) proportion F - 955 RR root respiration (fine root MR + total root GR) gC/m^2/s T - 956 RRESIS root resistance in each soil layer proportion F - 957 RSSHA shaded leaf stomatal resistance s/m T - 958 RSSUN sunlit leaf stomatal resistance s/m T - 959 Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F - 960 Rnet net radiation W/m^2 F - 961 SABG solar rad absorbed by ground W/m^2 T - 962 SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T - 963 SABV solar rad absorbed by veg W/m^2 T - 964 SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T - 965 SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T - 966 SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T - 967 SLO_SOMC SLO_SOM C gC/m^2 T - 968 SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F - 969 SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F - 970 SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F - 971 SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F - 972 SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F - 973 SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F - 974 SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T - 975 SLO_SOMN SLO_SOM N gN/m^2 T - 976 SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F - 977 SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F - 978 SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F - 979 SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F - 980 SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F - 981 SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F - 982 SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T - 983 SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F - 984 SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 985 SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F - 986 SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 987 SMINN soil mineral N gN/m^2 T - 988 SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T - 989 SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T - 990 SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T - 991 SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F - 992 SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F - 993 SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F - 994 SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F - 995 SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F - 996 SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F - 997 SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F - 998 SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F - 999 SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -1000 SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -1001 SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -1002 SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -1003 SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -1004 SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -1005 SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -1006 SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -1007 SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -1008 SMINN_vr soil mineral N gN/m^3 T -1009 SMIN_NH4 soil mineral NH4 gN/m^2 T -1010 SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F -1011 SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T -1012 SMIN_NO3 soil mineral NO3 gN/m^2 T -1013 SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T -1014 SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F -1015 SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F -1016 SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T -1017 SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F -1018 SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F -1019 SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T -1020 SMP soil matric potential (natural vegetated and crop landunits only) mm T -1021 SNOBCMCL mass of BC in snow column kg/m2 T -1022 SNOBCMSL mass of BC in top snow layer kg/m2 T -1023 SNOCAN intercepted snow mm T -1024 SNODSTMCL mass of dust in snow column kg/m2 T -1025 SNODSTMSL mass of dust in top snow layer kg/m2 T -1026 SNOFSDSND direct nir incident solar radiation on snow W/m^2 F -1027 SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F -1028 SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F -1029 SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F -1030 SNOFSRND direct nir reflected solar radiation from snow W/m^2 T -1031 SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T -1032 SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T -1033 SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T -1034 SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T -1035 SNOLIQFL top snow layer liquid water fraction (land) fraction F -1036 SNOOCMCL mass of OC in snow column kg/m2 T -1037 SNOOCMSL mass of OC in top snow layer kg/m2 T -1038 SNORDSL top snow layer effective grain radius m^-6 F -1039 SNOTTOPL snow temperature (top layer) K F -1040 SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F -1041 SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T -1042 SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F -1043 SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T -1044 SNOWDP gridcell mean snow height m T -1045 SNOWICE snow ice kg/m2 T -1046 SNOWICE_ICE snow ice (ice landunits only) kg/m2 F -1047 SNOWLIQ snow liquid water kg/m2 T -1048 SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F -1049 SNOW_5D 5day snow avg m F -1050 SNOW_DEPTH snow height of snow covered area m T -1051 SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F -1052 SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T -1053 SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -1054 SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T -1055 SNOW_SINKS snow sinks (liquid water) mm/s T -1056 SNOW_SOURCES snow sources (liquid water) mm/s T -1057 SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F -1058 SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -1059 SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F -1060 SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -1061 SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F -1062 SNO_FRZ snow freezing rate in each snow layer kg/m2/s F -1063 SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F -1064 SNO_GS Mean snow grain size Microns F -1065 SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F -1066 SNO_ICE Snow ice content kg/m2 F -1067 SNO_LIQH2O Snow liquid water content kg/m2 F -1068 SNO_MELT snow melt rate in each snow layer mm/s F -1069 SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F -1070 SNO_T Snow temperatures K F -1071 SNO_TK Thermal conductivity W/m-K F -1072 SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F -1073 SNO_T_ICE Snow temperatures (ice landunits only) K F -1074 SNO_Z Snow layer thicknesses m F -1075 SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F -1076 SNOdTdzL top snow layer temperature gradient (land) K/m F -1077 SOIL10 10-day running mean of 12cm layer soil K F -1078 SOILC_CHANGE C change in soil gC/m^2/s T -1079 SOILC_HR soil C heterotrophic respiration gC/m^2/s T -1080 SOILC_vr SOIL C (vertically resolved) gC/m^3 T -1081 SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T -1082 SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T -1083 SOILN_vr SOIL N (vertically resolved) gN/m^3 T -1084 SOILPSI soil water potential in each soil layer MPa F -1085 SOILRESIS soil resistance to evaporation s/m T -1086 SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T -1087 SOMC_FIRE C loss due to peat burning gC/m^2/s T -1088 SOMFIRE soil organic matter fire losses gC/m^2/s F -1089 SOM_ADV_COEF advection term for vertical SOM translocation m/s F -1090 SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T -1091 SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F -1092 SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -1093 SR total soil respiration (HR + root resp) gC/m^2/s T -1094 SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T -1095 SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T -1096 SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T -1097 SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T -1098 SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T -1099 SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T -1100 SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T -1101 STEM_PROF profile for litter C and N inputs from stems 1/m F -1102 STORAGE_CDEMAND C use from the C storage pool gC/m^2 F -1103 STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F -1104 STORAGE_NDEMAND N demand during the offset period gN/m^2 F -1105 STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T -1106 STORVEGN stored vegetation nitrogen gN/m^2 T -1107 SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T -1108 SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -1109 SWBGT 2 m Simplified Wetbulb Globe Temp C T -1110 SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T -1111 SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -1112 SWMP65 2 m Swamp Cooler Temp 65% Eff C T -1113 SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T -1114 SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T -1115 SWMP80 2 m Swamp Cooler Temp 80% Eff C T -1116 SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T -1117 SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T -1118 SWdown atmospheric incident solar radiation W/m^2 F -1119 SWup upwelling shortwave radiation W/m^2 F -1120 SoilAlpha factor limiting ground evap unitless F -1121 SoilAlpha_U urban factor limiting ground evap unitless F -1122 T10 10-day running mean of 2-m temperature K F -1123 TAF canopy air temperature K F -1124 TAUX zonal surface stress kg/m/s^2 T -1125 TAUY meridional surface stress kg/m/s^2 T -1126 TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T -1127 TBUILD internal urban building air temperature K T -1128 TBUILD_MAX prescribed maximum interior building temperature K F -1129 TEMPAVG_T2M temporary average 2m air temperature K F -1130 TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F -1131 TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F -1132 TEQ 2 m Equiv Temp K T -1133 TEQ_R Rural 2 m Equiv Temp K T -1134 TEQ_U Urban 2 m Equiv Temp K T -1135 TFLOOR floor temperature K F -1136 TG ground temperature K T -1137 TG_ICE ground temperature (ice landunits only) K F -1138 TG_R Rural ground temperature K F -1139 TG_U Urban ground temperature K F -1140 TH2OSFC surface water temperature K T -1141 THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -1142 THIC 2 m Temp Hum Index Comfort C T -1143 THIC_R Rural 2 m Temp Hum Index Comfort C T -1144 THIC_U Urban 2 m Temp Hum Index Comfort C T -1145 THIP 2 m Temp Hum Index Physiology C T -1146 THIP_R Rural 2 m Temp Hum Index Physiology C T -1147 THIP_U Urban 2 m Temp Hum Index Physiology C T -1148 TKE1 top lake level eddy thermal conductivity W/(mK) T -1149 TLAI total projected leaf area index m^2/m^2 T -1150 TLAKE lake temperature K T -1151 TOPO_COL column-level topographic height m F -1152 TOPO_COL_ICE column-level topographic height (ice landunits only) m F -1153 TOPO_FORC topograephic height sent to GLC m F -1154 TOPT topt coefficient for VOC calc non F -1155 TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T -1156 TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T -1157 TOTCOLN total column-level N, excluding product pools gN/m^2 T -1158 TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T -1159 TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T -1160 TOTFIRE total ecosystem fire losses gC/m^2/s F -1161 TOTLITC total litter carbon gC/m^2 T -1162 TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T -1163 TOTLITN total litter N gN/m^2 T -1164 TOTLITN_1m total litter N to 1 meter gN/m^2 T -1165 TOTPFTC total patch-level carbon, including cpool gC/m^2 T -1166 TOTPFTN total patch-level nitrogen gN/m^2 T -1167 TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T -1168 TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T -1169 TOTSOMC total soil organic matter carbon gC/m^2 T -1170 TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T -1171 TOTSOMN total soil organic matter N gN/m^2 T -1172 TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -1173 TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T -1174 TOTVEGN total vegetation nitrogen gN/m^2 T -1175 TOT_WOODPRODC total wood product C gC/m^2 T -1176 TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T -1177 TOT_WOODPRODN total wood product N gN/m^2 T -1178 TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T -1179 TPU25T canopy profile of tpu umol/m2/s T -1180 TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F -1181 TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F -1182 TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F -1183 TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F -1184 TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F -1185 TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F -1186 TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F -1187 TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F -1188 TREFMNAV daily minimum of average 2-m temperature K T -1189 TREFMNAV_R Rural daily minimum of average 2-m temperature K F -1190 TREFMNAV_U Urban daily minimum of average 2-m temperature K F -1191 TREFMXAV daily maximum of average 2-m temperature K T -1192 TREFMXAV_R Rural daily maximum of average 2-m temperature K F -1193 TREFMXAV_U Urban daily maximum of average 2-m temperature K F -1194 TROOF_INNER roof inside surface temperature K F -1195 TSA 2m air temperature K T -1196 TSAI total projected stem area index m^2/m^2 T -1197 TSA_ICE 2m air temperature (ice landunits only) K F -1198 TSA_R Rural 2m air temperature K F -1199 TSA_U Urban 2m air temperature K F -1200 TSHDW_INNER shadewall inside surface temperature K F -1201 TSKIN skin temperature K T -1202 TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -1203 TSOI soil temperature (natural vegetated and crop landunits only) K T -1204 TSOI_10CM soil temperature in top 10cm of soil K T -1205 TSOI_ICE soil temperature (ice landunits only) K T -1206 TSRF_FORC surface temperature sent to GLC K F -1207 TSUNW_INNER sunwall inside surface temperature K F -1208 TV vegetation temperature K T -1209 TV24 vegetation temperature (last 24hrs) K F -1210 TV240 vegetation temperature (last 240hrs) K F -1211 TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F -1212 TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F -1213 TWS total water storage mm T -1214 T_SCALAR temperature inhibition of decomposition unitless T -1215 Tair atmospheric air temperature (downscaled to columns in glacier regions) K F -1216 Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F -1217 U10 10-m wind m/s T -1218 U10_DUST 10-m wind for dust model m/s T -1219 U10_ICE 10-m wind (ice landunits only) m/s F -1220 UAF canopy air speed m/s F -1221 ULRAD upward longwave radiation above the canopy W/m^2 F -1222 UM wind speed plus stability effect m/s F -1223 URBAN_AC urban air conditioning flux W/m^2 T -1224 URBAN_HEAT urban heating flux W/m^2 T -1225 USTAR aerodynamical resistance s/m F -1226 UST_LAKE friction velocity (lakes only) m/s F -1227 VA atmospheric wind speed plus convective velocity m/s F -1228 VCMX25T canopy profile of vcmax25 umol/m2/s T -1229 VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T -1230 VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T -1231 VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T -1232 VOCFLXT total VOC flux into atmosphere moles/m2/sec F -1233 VOLR river channel total water storage m3 T -1234 VOLRMCH river channel main channel water storage m3 T -1235 VPD vpd Pa F -1236 VPD2M 2m vapor pressure deficit Pa T -1237 VPD_CAN canopy vapor pressure deficit kPa T -1238 Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T -1239 WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -1240 WBA 2 m Wet Bulb C T -1241 WBA_R Rural 2 m Wet Bulb C T -1242 WBA_U Urban 2 m Wet Bulb C T -1243 WBT 2 m Stull Wet Bulb C T -1244 WBT_R Rural 2 m Stull Wet Bulb C T -1245 WBT_U Urban 2 m Stull Wet Bulb C T -1246 WF soil water as frac. of whc for top 0.05 m proportion F -1247 WFPS WFPS percent F -1248 WIND atmospheric wind velocity magnitude m/s T -1249 WOODC wood C gC/m^2 T -1250 WOODC_ALLOC wood C eallocation gC/m^2/s T -1251 WOODC_LOSS wood C loss gC/m^2/s T -1252 WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T -1253 WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T -1254 WTGQ surface tracer conductance m/s T -1255 W_SCALAR Moisture (dryness) inhibition of decomposition unitless T -1256 Wind atmospheric wind velocity magnitude m/s F -1257 XSMRPOOL temporary photosynthate C pool gC/m^2 T -1258 XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F -1259 XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T -1260 Z0HG roughness length over ground, sensible heat m F -1261 Z0HV roughness length over vegetation, sensible heat m F -1262 Z0M momentum roughness length m F -1263 Z0MG roughness length over ground, momentum m F -1264 Z0MV roughness length over vegetation, momentum m F -1265 Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -1266 Z0QG roughness length over ground, latent heat m F -1267 Z0QV roughness length over vegetation, latent heat m F -1268 ZBOT atmospheric reference height m T -1269 ZETA dimensionless stability parameter unitless F -1270 ZII convective boundary height m F -1271 ZWT water table depth (natural vegetated and crop landunits only) m T -1272 ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T -1273 ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T -1274 anaerobic_frac anaerobic_frac m3/m3 F -1275 bsw clap and hornberger B unitless F -1276 currentPatch currentPatch coefficient for VOC calc non F -1277 diffus diffusivity m^2/s F -1278 fr_WFPS fr_WFPS fraction F -1279 n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F -1280 num_iter number of iterations unitless F -1281 r_psi r_psi m F -1282 ratio_k1 ratio_k1 none F -1283 ratio_no3_co2 ratio_no3_co2 ratio F -1284 soil_bulkdensity soil_bulkdensity kg/m3 F -1285 soil_co2_prod soil_co2_prod ug C / g soil / day F -1286 watfc water field capacity m^3/m^3 F -1287 watsat water saturated m^3/m^3 F + 449 HUI crop heat unit index ddays F + 450 HUMIDEX 2 m Humidex C T + 451 HUMIDEX_R Rural 2 m Humidex C T + 452 HUMIDEX_U Urban 2 m Humidex C T + 453 ICE_CONTENT1 initial gridcell total ice content mm T + 454 ICE_CONTENT2 post land cover change total ice content mm F + 455 ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F + 456 INIT_GPP GPP flux before downregulation gC/m^2/s F + 457 INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F + 458 INT_SNOW_ICE accumulated swe (ice landunits only) mm F + 459 IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T + 460 JMX25T canopy profile of jmax umol/m2/s T + 461 Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T + 462 KROOT root conductance each soil layer 1/s F + 463 KSOIL soil conductance in each soil layer 1/s F + 464 K_ACT_SOM active soil organic potential loss coefficient 1/s F + 465 K_CEL_LIT cellulosic litter potential loss coefficient 1/s F + 466 K_CWD coarse woody debris potential loss coefficient 1/s F + 467 K_LIG_LIT lignin litter potential loss coefficient 1/s F + 468 K_MET_LIT metabolic litter potential loss coefficient 1/s F + 469 K_NITR K_NITR 1/s F + 470 K_NITR_H2O K_NITR_H2O unitless F + 471 K_NITR_PH K_NITR_PH unitless F + 472 K_NITR_T K_NITR_T unitless F + 473 K_PAS_SOM passive soil organic potential loss coefficient 1/s F + 474 K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F + 475 LAI240 240hr average of leaf area index m^2/m^2 F + 476 LAISHA shaded projected leaf area index m^2/m^2 T + 477 LAISUN sunlit projected leaf area index m^2/m^2 T + 478 LAKEICEFRAC lake layer ice mass fraction unitless F + 479 LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T + 480 LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T + 481 LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T + 482 LATBASET latitude vary base temperature for gddplant degree C F + 483 LEAFC leaf C gC/m^2 T + 484 LEAFCN Leaf CN ratio used for flexible CN gC/gN T + 485 LEAFCN_OFFSET Leaf C:N used by FUN unitless F + 486 LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F + 487 LEAFC_ALLOC leaf C allocation gC/m^2/s T + 488 LEAFC_CHANGE C change in leaf gC/m^2/s T + 489 LEAFC_LOSS leaf C loss gC/m^2/s T + 490 LEAFC_STORAGE leaf C storage gC/m^2 F + 491 LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F + 492 LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F + 493 LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T + 494 LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F + 495 LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T + 496 LEAFC_XFER leaf C transfer gC/m^2 F + 497 LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F + 498 LEAFN leaf N gN/m^2 T + 499 LEAFN_STORAGE leaf N storage gN/m^2 F + 500 LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F + 501 LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F + 502 LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T + 503 LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F + 504 LEAFN_XFER leaf N transfer gN/m^2 F + 505 LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F + 506 LEAF_MR leaf maintenance respiration gC/m^2/s T + 507 LEAF_PROF profile for litter C and N inputs from leaves 1/m F + 508 LFC2 conversion area fraction of BET and BDT that burned per sec T + 509 LGSF long growing season factor proportion F + 510 LIG_LITC LIG_LIT C gC/m^2 T + 511 LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F + 512 LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F + 513 LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F + 514 LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F + 515 LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T + 516 LIG_LITN LIG_LIT N gN/m^2 T + 517 LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F + 518 LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F + 519 LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F + 520 LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F + 521 LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T + 522 LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F + 523 LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F + 524 LIQCAN intercepted liquid water mm T + 525 LIQUID_CONTENT1 initial gridcell total liq content mm T + 526 LIQUID_CONTENT2 post landuse change gridcell total liq content mm F + 527 LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F + 528 LITFALL litterfall (leaves and fine roots) gC/m^2/s T + 529 LITFIRE litter fire losses gC/m^2/s F + 530 LITTERC_HR litter C heterotrophic respiration gC/m^2/s T + 531 LITTERC_LOSS litter C loss gC/m^2/s T + 532 LIVECROOTC live coarse root C gC/m^2 T + 533 LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F + 534 LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F + 535 LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F + 536 LIVECROOTC_XFER live coarse root C transfer gC/m^2 F + 537 LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F + 538 LIVECROOTN live coarse root N gN/m^2 T + 539 LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F + 540 LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F + 541 LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F + 542 LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F + 543 LIVECROOTN_XFER live coarse root N transfer gN/m^2 F + 544 LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F + 545 LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F + 546 LIVESTEMC live stem C gC/m^2 T + 547 LIVESTEMC_STORAGE live stem C storage gC/m^2 F + 548 LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F + 549 LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T + 550 LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F + 551 LIVESTEMC_XFER live stem C transfer gC/m^2 F + 552 LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F + 553 LIVESTEMN live stem N gN/m^2 T + 554 LIVESTEMN_STORAGE live stem N storage gN/m^2 F + 555 LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F + 556 LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F + 557 LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F + 558 LIVESTEMN_XFER live stem N transfer gN/m^2 F + 559 LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F + 560 LIVESTEM_MR live stem maintenance respiration gC/m^2/s F + 561 LNC leaf N concentration gN leaf/m^2 T + 562 LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F + 563 LWup upwelling longwave radiation W/m^2 F + 564 MEG_acetaldehyde MEGAN flux kg/m2/sec T + 565 MEG_acetic_acid MEGAN flux kg/m2/sec T + 566 MEG_acetone MEGAN flux kg/m2/sec T + 567 MEG_carene_3 MEGAN flux kg/m2/sec T + 568 MEG_ethanol MEGAN flux kg/m2/sec T + 569 MEG_formaldehyde MEGAN flux kg/m2/sec T + 570 MEG_isoprene MEGAN flux kg/m2/sec T + 571 MEG_methanol MEGAN flux kg/m2/sec T + 572 MEG_pinene_a MEGAN flux kg/m2/sec T + 573 MEG_thujene_a MEGAN flux kg/m2/sec T + 574 MET_LITC MET_LIT C gC/m^2 T + 575 MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F + 576 MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F + 577 MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F + 578 MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F + 579 MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T + 580 MET_LITN MET_LIT N gN/m^2 T + 581 MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F + 582 MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F + 583 MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F + 584 MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F + 585 MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T + 586 MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F + 587 MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F + 588 MR maintenance respiration gC/m^2/s T + 589 M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F + 590 M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F + 591 M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F + 592 M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F + 593 M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F + 594 M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F + 595 M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F + 596 M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F + 597 M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F + 598 M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F + 599 M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F + 600 M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F + 601 M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F + 602 M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F + 603 M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F + 604 M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F + 605 M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F + 606 M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F + 607 M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F + 608 M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F + 609 M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F + 610 M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F + 611 M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F + 612 M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F + 613 M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F + 614 M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F + 615 M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F + 616 M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F + 617 M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F + 618 M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F + 619 M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F + 620 M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F + 621 M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F + 622 M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F + 623 M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F + 624 M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F + 625 M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F + 626 M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F + 627 M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F + 628 M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F + 629 M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F + 630 M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F + 631 M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F + 632 M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F + 633 M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F + 634 M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F + 635 M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F + 636 M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F + 637 M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F + 638 M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F + 639 M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F + 640 M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F + 641 M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F + 642 M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F + 643 M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F + 644 M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F + 645 M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F + 646 M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F + 647 M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F + 648 M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F + 649 M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F + 650 M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F + 651 M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F + 652 M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F + 653 M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F + 654 M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F + 655 M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F + 656 M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F + 657 M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F + 658 M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F + 659 M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F + 660 M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F + 661 M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F + 662 M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F + 663 M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F + 664 M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F + 665 M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F + 666 M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F + 667 M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F + 668 M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F + 669 M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F + 670 M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F + 671 M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F + 672 M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F + 673 M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F + 674 M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F + 675 M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F + 676 M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F + 677 M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F + 678 M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F + 679 M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F + 680 M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F + 681 M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F + 682 M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F + 683 M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F + 684 M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F + 685 M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F + 686 M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F + 687 M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F + 688 M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F + 689 M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F + 690 M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F + 691 M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F + 692 M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F + 693 M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F + 694 M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F + 695 M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F + 696 M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F + 697 M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F + 698 M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F + 699 M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F + 700 M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F + 701 M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F + 702 M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F + 703 M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F + 704 M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F + 705 M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F + 706 M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F + 707 M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F + 708 M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F + 709 M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F + 710 M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F + 711 M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F + 712 M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F + 713 M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F + 714 M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F + 715 M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F + 716 M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F + 717 M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F + 718 M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F + 719 M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F + 720 M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F + 721 NACTIVE Mycorrhizal N uptake flux gN/m^2/s T + 722 NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T + 723 NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T + 724 NAM AM-associated N uptake flux gN/m^2/s T + 725 NAM_NH4 AM-associated N uptake flux gN/m^2/s T + 726 NAM_NO3 AM-associated N uptake flux gN/m^2/s T + 727 NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T + 728 NDEPLOY total N deployed in new growth gN/m^2/s T + 729 NDEP_PROF profile for atmospheric N deposition 1/m F + 730 NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T + 731 NECM ECM-associated N uptake flux gN/m^2/s T + 732 NECM_NH4 ECM-associated N uptake flux gN/m^2/s T + 733 NECM_NO3 ECM-associated N uptake flux gN/m^2/s T + 734 NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T + 735 NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T + 736 NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T + 737 NET_NMIN net rate of N mineralization gN/m^2/s T + 738 NET_NMIN_vr net rate of N mineralization gN/m^3/s F + 739 NFERTILIZATION fertilizer added gN/m^2/s T + 740 NFIRE fire counts valid only in Reg.C counts/km2/sec T + 741 NFIX Symbiotic BNF uptake flux gN/m^2/s T + 742 NFIXATION_PROF profile for biological N fixation 1/m F + 743 NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F + 744 NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T + 745 NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T + 746 NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T + 747 NPASSIVE Passive N uptake flux gN/m^2/s T + 748 NPOOL temporary plant N pool gN/m^2 T + 749 NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F + 750 NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F + 751 NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F + 752 NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F + 753 NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F + 754 NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F + 755 NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F + 756 NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F + 757 NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F + 758 NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F + 759 NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F + 760 NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F + 761 NPP net primary production gC/m^2/s T + 762 NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F + 763 NPP_GROWTH Total C used for growth in FUN gC/m^2/s T + 764 NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T + 765 NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T + 766 NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T + 767 NPP_NAM AM-associated N uptake used C gC/m^2/s T + 768 NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T + 769 NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T + 770 NPP_NECM ECM-associated N uptake used C gC/m^2/s T + 771 NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T + 772 NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T + 773 NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T + 774 NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T + 775 NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T + 776 NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T + 777 NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T + 778 NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T + 779 NRETRANS Retranslocated N uptake flux gN/m^2/s T + 780 NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T + 781 NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T + 782 NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T + 783 NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F + 784 NUPTAKE Total N uptake of FUN gN/m^2/s T + 785 NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T + 786 N_ALLOMETRY N allocation index none F + 787 O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F + 788 OBU Monin-Obukhov length m F + 789 OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T + 790 OFFSET_COUNTER offset days counter days F + 791 OFFSET_FDD offset freezing degree days counter C degree-days F + 792 OFFSET_FLAG offset flag none F + 793 OFFSET_SWI offset soil water index none F + 794 ONSET_COUNTER onset days counter days F + 795 ONSET_FDD onset freezing degree days counter C degree-days F + 796 ONSET_FLAG onset flag none F + 797 ONSET_GDD onset growing degree days C degree-days F + 798 ONSET_GDDFLAG onset flag for growing degree day sum none F + 799 ONSET_SWI onset soil water index none F + 800 O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T + 801 PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F + 802 PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F + 803 PAR240_shade shade PAR (240 hrs) umol/m2/s F + 804 PAR240_sun sunlit PAR (240 hrs) umol/m2/s F + 805 PAR24_shade shade PAR (24 hrs) umol/m2/s F + 806 PAR24_sun sunlit PAR (24 hrs) umol/m2/s F + 807 PARVEGLN absorbed par by vegetation at local noon W/m^2 T + 808 PAR_shade shade PAR umol/m2/s F + 809 PAR_sun sunlit PAR umol/m2/s F + 810 PAS_SOMC PAS_SOM C gC/m^2 T + 811 PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F + 812 PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F + 813 PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F + 814 PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F + 815 PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T + 816 PAS_SOMN PAS_SOM N gN/m^2 T + 817 PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F + 818 PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F + 819 PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F + 820 PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F + 821 PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T + 822 PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F + 823 PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F + 824 PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T + 825 PBOT_240 10 day running mean of air pressure Pa F + 826 PCH4 atmospheric partial pressure of CH4 Pa T + 827 PCO2 atmospheric partial pressure of CO2 Pa T + 828 PCO2_240 10 day running mean of CO2 pressure Pa F + 829 PFT_CTRUNC patch-level sink for C truncation gC/m^2 F + 830 PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T + 831 PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T + 832 PFT_NTRUNC patch-level sink for N truncation gN/m^2 F + 833 PLANTCN Plant C:N used by FUN unitless F + 834 PLANT_CALLOC total allocated C flux gC/m^2/s F + 835 PLANT_NALLOC total allocated N flux gN/m^2/s F + 836 PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T + 837 PNLCZ Proportion of nitrogen allocated for light capture unitless F + 838 PO2_240 10 day running mean of O2 pressure Pa F + 839 POTENTIAL_IMMOB potential N immobilization gN/m^2/s T + 840 POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F + 841 POT_F_DENIT potential denitrification flux gN/m^2/s T + 842 POT_F_DENIT_vr potential denitrification flux gN/m^3/s F + 843 POT_F_NIT potential nitrification flux gN/m^2/s T + 844 POT_F_NIT_vr potential nitrification flux gN/m^3/s F + 845 PREC10 10-day running mean of PREC MM H2O/S F + 846 PREC60 60-day running mean of PREC MM H2O/S F + 847 PREV_DAYL daylength from previous timestep s F + 848 PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F + 849 PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F + 850 PROD100C 100-yr wood product C gC/m^2 F + 851 PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F + 852 PROD100N 100-yr wood product N gN/m^2 F + 853 PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F + 854 PROD10C 10-yr wood product C gC/m^2 F + 855 PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F + 856 PROD10N 10-yr wood product N gN/m^2 F + 857 PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F + 858 PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T + 859 PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T + 860 PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T + 861 PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T + 862 PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F + 863 Q2M 2m specific humidity kg/kg T + 864 QAF canopy air humidity kg/kg F + 865 QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T + 866 QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F + 867 QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F + 868 QDRAI sub-surface drainage mm/s T + 869 QDRAI_PERCH perched wt drainage mm/s T + 870 QDRAI_XS saturation excess drainage mm/s T + 871 QDRIP rate of excess canopy liquid falling off canopy mm/s F + 872 QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F + 873 QFLOOD runoff from river flooding mm/s T + 874 QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T + 875 QFLX_EVAP_VEG vegetation evaporation mm H2O/s F + 876 QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T + 877 QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T + 878 QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T + 879 QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T + 880 QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F + 881 QFLX_SNOW_DRAIN drainage from snow pack mm/s T + 882 QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T + 883 QFLX_SNOW_GRND snow on ground after interception mm H2O/s F + 884 QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T + 885 QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T + 886 QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F + 887 QH2OSFC surface water runoff mm/s T + 888 QH2OSFC_TO_ICE surface water converted to ice mm/s F + 889 QHR hydraulic redistribution mm/s T + 890 QICE ice growth/melt mm/s T + 891 QICE_FORC qice forcing sent to GLC mm/s F + 892 QICE_FRZ ice growth mm/s T + 893 QICE_MELT ice melt mm/s T + 894 QINFL infiltration mm/s T + 895 QINTR interception mm/s T + 896 QIRRIG_DEMAND irrigation demand mm/s F + 897 QIRRIG_DRIP water added via drip irrigation mm/s F + 898 QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T + 899 QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T + 900 QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T + 901 QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F + 902 QOVER total surface runoff (includes QH2OSFC) mm/s T + 903 QOVER_LAG time-lagged surface runoff for soil columns mm/s F + 904 QPHSNEG net negative hydraulic redistribution flux mm/s F + 905 QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T + 906 QROOTSINK water flux from soil to root in each soil-layer mm/s F + 907 QRUNOFF total liquid runoff not including correction for land use change mm/s T + 908 QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T + 909 QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T + 910 QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F + 911 QRUNOFF_R Rural total runoff mm/s F + 912 QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T + 913 QRUNOFF_U Urban total runoff mm/s F + 914 QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T + 915 QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T + 916 QSNOFRZ column-integrated snow freezing rate kg/m2/s T + 917 QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T + 918 QSNOMELT snow melt rate mm/s T + 919 QSNOMELT_ICE snow melt (ice landunits only) mm/s T + 920 QSNOUNLOAD canopy snow unloading mm/s T + 921 QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T + 922 QSNO_WINDUNLOAD canopy snow wind unloading mm/s T + 923 QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T + 924 QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T + 925 QSOIL_ICE Ground evaporation (ice landunits only) mm/s T + 926 QTOPSOIL water input to surface mm/s F + 927 QVEGE canopy evaporation mm/s T + 928 QVEGT canopy transpiration mm/s T + 929 Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F + 930 Qh sensible heat W/m^2 F + 931 Qle total evaporation W/m^2 F + 932 Qstor storage heat flux (includes snowmelt) W/m^2 F + 933 Qtau momentum flux kg/m/s^2 F + 934 RAH1 aerodynamical resistance s/m F + 935 RAH2 aerodynamical resistance s/m F + 936 RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T + 937 RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T + 938 RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F + 939 RAM1 aerodynamical resistance s/m F + 940 RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F + 941 RAW1 aerodynamical resistance s/m F + 942 RAW2 aerodynamical resistance s/m F + 943 RB leaf boundary resistance s/m F + 944 RB10 10 day running mean boundary layer resistance s/m F + 945 RETRANSN plant pool of retranslocated N gN/m^2 T + 946 RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T + 947 RH atmospheric relative humidity % F + 948 RH2M 2m relative humidity % T + 949 RH2M_R Rural 2m specific humidity % F + 950 RH2M_U Urban 2m relative humidity % F + 951 RH30 30-day running mean of relative humidity % F + 952 RHAF fractional humidity of canopy air fraction F + 953 RHAF10 10 day running mean of fractional humidity of canopy air fraction F + 954 RH_LEAF fractional humidity at leaf surface fraction F + 955 ROOTR effective fraction of roots in each soil layer (SMS method) proportion F + 956 RR root respiration (fine root MR + total root GR) gC/m^2/s T + 957 RRESIS root resistance in each soil layer proportion F + 958 RSSHA shaded leaf stomatal resistance s/m T + 959 RSSUN sunlit leaf stomatal resistance s/m T + 960 Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F + 961 Rnet net radiation W/m^2 F + 962 SABG solar rad absorbed by ground W/m^2 T + 963 SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T + 964 SABV solar rad absorbed by veg W/m^2 T + 965 SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T + 966 SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T + 967 SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T + 968 SLO_SOMC SLO_SOM C gC/m^2 T + 969 SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F + 970 SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F + 971 SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F + 972 SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F + 973 SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F + 974 SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F + 975 SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T + 976 SLO_SOMN SLO_SOM N gN/m^2 T + 977 SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F + 978 SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F + 979 SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F + 980 SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F + 981 SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F + 982 SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F + 983 SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T + 984 SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F + 985 SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F + 986 SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F + 987 SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F + 988 SMINN soil mineral N gN/m^2 T + 989 SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T + 990 SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T + 991 SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T + 992 SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F + 993 SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F + 994 SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F + 995 SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F + 996 SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F + 997 SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F + 998 SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F + 999 SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +1000 SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +1001 SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +1002 SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +1003 SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +1004 SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +1005 SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +1006 SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +1007 SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +1008 SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +1009 SMINN_vr soil mineral N gN/m^3 T +1010 SMIN_NH4 soil mineral NH4 gN/m^2 T +1011 SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F +1012 SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T +1013 SMIN_NO3 soil mineral NO3 gN/m^2 T +1014 SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T +1015 SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F +1016 SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F +1017 SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T +1018 SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F +1019 SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F +1020 SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T +1021 SMP soil matric potential (natural vegetated and crop landunits only) mm T +1022 SNOBCMCL mass of BC in snow column kg/m2 T +1023 SNOBCMSL mass of BC in top snow layer kg/m2 T +1024 SNOCAN intercepted snow mm T +1025 SNODSTMCL mass of dust in snow column kg/m2 T +1026 SNODSTMSL mass of dust in top snow layer kg/m2 T +1027 SNOFSDSND direct nir incident solar radiation on snow W/m^2 F +1028 SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F +1029 SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F +1030 SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F +1031 SNOFSRND direct nir reflected solar radiation from snow W/m^2 T +1032 SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T +1033 SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T +1034 SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T +1035 SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T +1036 SNOLIQFL top snow layer liquid water fraction (land) fraction F +1037 SNOOCMCL mass of OC in snow column kg/m2 T +1038 SNOOCMSL mass of OC in top snow layer kg/m2 T +1039 SNORDSL top snow layer effective grain radius m^-6 F +1040 SNOTTOPL snow temperature (top layer) K F +1041 SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F +1042 SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +1043 SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +1044 SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +1045 SNOWDP gridcell mean snow height m T +1046 SNOWICE snow ice kg/m2 T +1047 SNOWICE_ICE snow ice (ice landunits only) kg/m2 F +1048 SNOWLIQ snow liquid water kg/m2 T +1049 SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F +1050 SNOW_5D 5day snow avg m F +1051 SNOW_DEPTH snow height of snow covered area m T +1052 SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F +1053 SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +1054 SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +1055 SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T +1056 SNOW_SINKS snow sinks (liquid water) mm/s T +1057 SNOW_SOURCES snow sources (liquid water) mm/s T +1058 SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F +1059 SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +1060 SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F +1061 SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +1062 SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F +1063 SNO_FRZ snow freezing rate in each snow layer kg/m2/s F +1064 SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F +1065 SNO_GS Mean snow grain size Microns F +1066 SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F +1067 SNO_ICE Snow ice content kg/m2 F +1068 SNO_LIQH2O Snow liquid water content kg/m2 F +1069 SNO_MELT snow melt rate in each snow layer mm/s F +1070 SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F +1071 SNO_T Snow temperatures K F +1072 SNO_TK Thermal conductivity W/m-K F +1073 SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F +1074 SNO_T_ICE Snow temperatures (ice landunits only) K F +1075 SNO_Z Snow layer thicknesses m F +1076 SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F +1077 SNOdTdzL top snow layer temperature gradient (land) K/m F +1078 SOIL10 10-day running mean of 12cm layer soil K F +1079 SOILC_CHANGE C change in soil gC/m^2/s T +1080 SOILC_HR soil C heterotrophic respiration gC/m^2/s T +1081 SOILC_vr SOIL C (vertically resolved) gC/m^3 T +1082 SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T +1083 SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T +1084 SOILN_vr SOIL N (vertically resolved) gN/m^3 T +1085 SOILPSI soil water potential in each soil layer MPa F +1086 SOILRESIS soil resistance to evaporation s/m T +1087 SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +1088 SOMC_FIRE C loss due to peat burning gC/m^2/s T +1089 SOMFIRE soil organic matter fire losses gC/m^2/s F +1090 SOM_ADV_COEF advection term for vertical SOM translocation m/s F +1091 SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T +1092 SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F +1093 SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F +1094 SR total soil respiration (HR + root resp) gC/m^2/s T +1095 SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T +1096 SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T +1097 SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T +1098 SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T +1099 SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T +1100 SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T +1101 SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T +1102 STEM_PROF profile for litter C and N inputs from stems 1/m F +1103 STORAGE_CDEMAND C use from the C storage pool gC/m^2 F +1104 STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F +1105 STORAGE_NDEMAND N demand during the offset period gN/m^2 F +1106 STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T +1107 STORVEGN stored vegetation nitrogen gN/m^2 T +1108 SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T +1109 SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F +1110 SWBGT 2 m Simplified Wetbulb Globe Temp C T +1111 SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T +1112 SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T +1113 SWMP65 2 m Swamp Cooler Temp 65% Eff C T +1114 SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T +1115 SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T +1116 SWMP80 2 m Swamp Cooler Temp 80% Eff C T +1117 SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T +1118 SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T +1119 SWdown atmospheric incident solar radiation W/m^2 F +1120 SWup upwelling shortwave radiation W/m^2 F +1121 SoilAlpha factor limiting ground evap unitless F +1122 SoilAlpha_U urban factor limiting ground evap unitless F +1123 T10 10-day running mean of 2-m temperature K F +1124 TAF canopy air temperature K F +1125 TAUX zonal surface stress kg/m/s^2 T +1126 TAUY meridional surface stress kg/m/s^2 T +1127 TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T +1128 TBUILD internal urban building air temperature K T +1129 TBUILD_MAX prescribed maximum interior building temperature K F +1130 TEMPAVG_T2M temporary average 2m air temperature K F +1131 TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F +1132 TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F +1133 TEQ 2 m Equiv Temp K T +1134 TEQ_R Rural 2 m Equiv Temp K T +1135 TEQ_U Urban 2 m Equiv Temp K T +1136 TFLOOR floor temperature K F +1137 TG ground temperature K T +1138 TG_ICE ground temperature (ice landunits only) K F +1139 TG_R Rural ground temperature K F +1140 TG_U Urban ground temperature K F +1141 TH2OSFC surface water temperature K T +1142 THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T +1143 THIC 2 m Temp Hum Index Comfort C T +1144 THIC_R Rural 2 m Temp Hum Index Comfort C T +1145 THIC_U Urban 2 m Temp Hum Index Comfort C T +1146 THIP 2 m Temp Hum Index Physiology C T +1147 THIP_R Rural 2 m Temp Hum Index Physiology C T +1148 THIP_U Urban 2 m Temp Hum Index Physiology C T +1149 TKE1 top lake level eddy thermal conductivity W/(mK) T +1150 TLAI total projected leaf area index m^2/m^2 T +1151 TLAKE lake temperature K T +1152 TOPO_COL column-level topographic height m F +1153 TOPO_COL_ICE column-level topographic height (ice landunits only) m F +1154 TOPO_FORC topograephic height sent to GLC m F +1155 TOPT topt coefficient for VOC calc non F +1156 TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T +1157 TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +1158 TOTCOLN total column-level N, excluding product pools gN/m^2 T +1159 TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T +1160 TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T +1161 TOTFIRE total ecosystem fire losses gC/m^2/s F +1162 TOTLITC total litter carbon gC/m^2 T +1163 TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T +1164 TOTLITN total litter N gN/m^2 T +1165 TOTLITN_1m total litter N to 1 meter gN/m^2 T +1166 TOTPFTC total patch-level carbon, including cpool gC/m^2 T +1167 TOTPFTN total patch-level nitrogen gN/m^2 T +1168 TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T +1169 TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T +1170 TOTSOMC total soil organic matter carbon gC/m^2 T +1171 TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T +1172 TOTSOMN total soil organic matter N gN/m^2 T +1173 TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T +1174 TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T +1175 TOTVEGN total vegetation nitrogen gN/m^2 T +1176 TOT_WOODPRODC total wood product C gC/m^2 T +1177 TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T +1178 TOT_WOODPRODN total wood product N gN/m^2 T +1179 TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T +1180 TPU25T canopy profile of tpu umol/m2/s T +1181 TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F +1182 TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F +1183 TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F +1184 TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F +1185 TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F +1186 TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F +1187 TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F +1188 TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F +1189 TREFMNAV daily minimum of average 2-m temperature K T +1190 TREFMNAV_R Rural daily minimum of average 2-m temperature K F +1191 TREFMNAV_U Urban daily minimum of average 2-m temperature K F +1192 TREFMXAV daily maximum of average 2-m temperature K T +1193 TREFMXAV_R Rural daily maximum of average 2-m temperature K F +1194 TREFMXAV_U Urban daily maximum of average 2-m temperature K F +1195 TROOF_INNER roof inside surface temperature K F +1196 TSA 2m air temperature K T +1197 TSAI total projected stem area index m^2/m^2 T +1198 TSA_ICE 2m air temperature (ice landunits only) K F +1199 TSA_R Rural 2m air temperature K F +1200 TSA_U Urban 2m air temperature K F +1201 TSHDW_INNER shadewall inside surface temperature K F +1202 TSKIN skin temperature K T +1203 TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +1204 TSOI soil temperature (natural vegetated and crop landunits only) K T +1205 TSOI_10CM soil temperature in top 10cm of soil K T +1206 TSOI_ICE soil temperature (ice landunits only) K T +1207 TSRF_FORC surface temperature sent to GLC K F +1208 TSUNW_INNER sunwall inside surface temperature K F +1209 TV vegetation temperature K T +1210 TV24 vegetation temperature (last 24hrs) K F +1211 TV240 vegetation temperature (last 240hrs) K F +1212 TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F +1213 TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F +1214 TWS total water storage mm T +1215 T_SCALAR temperature inhibition of decomposition unitless T +1216 Tair atmospheric air temperature (downscaled to columns in glacier regions) K F +1217 Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F +1218 U10 10-m wind m/s T +1219 U10_DUST 10-m wind for dust model m/s T +1220 U10_ICE 10-m wind (ice landunits only) m/s F +1221 UAF canopy air speed m/s F +1222 ULRAD upward longwave radiation above the canopy W/m^2 F +1223 UM wind speed plus stability effect m/s F +1224 URBAN_AC urban air conditioning flux W/m^2 T +1225 URBAN_HEAT urban heating flux W/m^2 T +1226 USTAR aerodynamical resistance s/m F +1227 UST_LAKE friction velocity (lakes only) m/s F +1228 VA atmospheric wind speed plus convective velocity m/s F +1229 VCMX25T canopy profile of vcmax25 umol/m2/s T +1230 VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T +1231 VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T +1232 VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T +1233 VOCFLXT total VOC flux into atmosphere moles/m2/sec F +1234 VOLR river channel total water storage m3 T +1235 VOLRMCH river channel main channel water storage m3 T +1236 VPD vpd Pa F +1237 VPD2M 2m vapor pressure deficit Pa T +1238 VPD_CAN canopy vapor pressure deficit kPa T +1239 Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T +1240 WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +1241 WBA 2 m Wet Bulb C T +1242 WBA_R Rural 2 m Wet Bulb C T +1243 WBA_U Urban 2 m Wet Bulb C T +1244 WBT 2 m Stull Wet Bulb C T +1245 WBT_R Rural 2 m Stull Wet Bulb C T +1246 WBT_U Urban 2 m Stull Wet Bulb C T +1247 WF soil water as frac. of whc for top 0.05 m proportion F +1248 WFPS WFPS percent F +1249 WIND atmospheric wind velocity magnitude m/s T +1250 WOODC wood C gC/m^2 T +1251 WOODC_ALLOC wood C eallocation gC/m^2/s T +1252 WOODC_LOSS wood C loss gC/m^2/s T +1253 WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T +1254 WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T +1255 WTGQ surface tracer conductance m/s T +1256 W_SCALAR Moisture (dryness) inhibition of decomposition unitless T +1257 Wind atmospheric wind velocity magnitude m/s F +1258 XSMRPOOL temporary photosynthate C pool gC/m^2 T +1259 XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F +1260 XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T +1261 Z0HG roughness length over ground, sensible heat m F +1262 Z0HV roughness length over vegetation, sensible heat m F +1263 Z0M momentum roughness length m F +1264 Z0MG roughness length over ground, momentum m F +1265 Z0MV roughness length over vegetation, momentum m F +1266 Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F +1267 Z0QG roughness length over ground, latent heat m F +1268 Z0QV roughness length over vegetation, latent heat m F +1269 ZBOT atmospheric reference height m T +1270 ZETA dimensionless stability parameter unitless F +1271 ZII convective boundary height m F +1272 ZWT water table depth (natural vegetated and crop landunits only) m T +1273 ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T +1274 ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T +1275 anaerobic_frac anaerobic_frac m3/m3 F +1276 bsw clap and hornberger B unitless F +1277 currentPatch currentPatch coefficient for VOC calc non F +1278 diffus diffusivity m^2/s F +1279 fr_WFPS fr_WFPS fraction F +1280 n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F +1281 num_iter number of iterations unitless F +1282 r_psi r_psi m F +1283 ratio_k1 ratio_k1 none F +1284 ratio_no3_co2 ratio_no3_co2 ratio F +1285 soil_bulkdensity soil_bulkdensity kg/m3 F +1286 soil_co2_prod soil_co2_prod ug C / g soil / day F +1287 watfc water field capacity m^3/m^3 F +1288 watsat water saturated m^3/m^3 F ==== =================================== ============================================================================================== ================================================================= ======= From 583df9b154810ea6d01eb2663e72e61fffffd296 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Mar 2022 10:44:09 -0700 Subject: [PATCH 0184/2067] user_nl_clm for crop tests: Remove GDDPLANT, add GDDACCUM and HUI. --- cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index c70d3dba9e..4add705be3 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -1,6 +1,7 @@ hist_fincl1 += 'GDD0', 'GDD8', 'GDD10', 'GDD020', 'GDD820', 'GDD1020', - 'GDDPLANT', 'GDDTSOI', 'A5TMIN', 'A10TMIN' + 'GDDACCUM', 'GDDTSOI', 'A5TMIN', 'A10TMIN', + 'HUI' ! The main point of including this field is to test the SUM history field infrastructure ! This is in the crop testmods because this field is mainly useful in transient crop runs From 1f1cce974ffb38a1bee310476cfd870cfe9be261 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Mon, 14 Mar 2022 14:45:28 -0600 Subject: [PATCH 0185/2067] Update forcing height variables and rename/move snomelt_accum to WaterDiagnosticsBulkType --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 4 ++-- src/biogeophys/CanopyFluxesMod.F90 | 16 ++++++++++--- src/biogeophys/FrictionVelocityMod.F90 | 13 +++++----- src/biogeophys/LakeFluxesMod.F90 | 3 +-- src/biogeophys/SnowHydrologyMod.F90 | 25 +++++++++++--------- src/biogeophys/SoilTemperatureMod.F90 | 4 ++-- src/biogeophys/WaterDiagnosticBulkType.F90 | 23 +++++++++++++++++- src/biogeophys/WaterFluxType.F90 | 24 ------------------- 8 files changed, 60 insertions(+), 52 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index f033fab5ff..9123000fc5 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -174,7 +174,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & case ('Meier2022') ! Don't set on first few steps of a simulation, since htop isn't set yet, need to wait until after first do_alb time - if ( is_first_step() .or. get_nstep() <= GetBalanceCheckSkipSteps() ) then + if ( is_first_step() .or. get_nstep() <= GetBalanceCheckSkipSteps()-1 ) then z0m(p) = 0._r8 displa(p) = 0._r8 cycle @@ -190,7 +190,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & displa(p) = 0._r8 else - ! Compute as if elai+esai = LAImax - LAIoff in CanopyFluxes + ! Compute as if elai+esai = LAImax in CanopyFluxes displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * (pftcon%z0v_LAImax(patch%itype(p))))**0.5_r8)) & / (7.5_r8*(pftcon%z0v_LAImax(patch%itype(p)) ))**0.5_r8) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 2681c93ced..10d1193cbb 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -528,7 +528,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, soilbeta => soilstate_inst%soilbeta_col , & ! Input: [real(r8) (:) ] soil wetness relative to field capacity u10_clm => frictionvel_inst%u10_clm_patch , & ! Input: [real(r8) (:) ] 10 m height winds (m/s) - forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Input: [real(r8) (:) ] observational height of wind at patch level [m] + forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] + forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] + forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] + forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Output: [real(r8) (:) ] observational height of temperature at patch level [m] + forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Output: [real(r8) (:) ] observational height of specific humidity at patch level [m] + forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Output: [real(r8) (:) ] observational height of wind at patch level [m] z0mg => frictionvel_inst%z0mg_col , & ! Input: [real(r8) (:) ] roughness length of ground, momentum [m] zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) @@ -877,7 +882,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, do f = 1, fn p = filterp(f) c = patch%column(p) - + g = patch%gridcell(p) select case (z0param_method) case ('ZengWang2007') @@ -916,6 +921,11 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0hv(p) = z0mv(p) z0qv(p) = z0mv(p) + ! Update the forcing heights + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mv(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hv(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qv(p) + displa(p) + end do found = .false. @@ -1388,7 +1398,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, else !unstable zeta(p) = max(-100._r8,min(zeta(p),-0.01_r8)) if ( ustar(p)*thvstar > 0.0d00 )then - write(iulog,*) 'ustar*thvstart is positive and has to be negative' + write(iulog,*) 'ustar*thvstar is positive and has to be negative' write(iulog,*) 'p = ', p write(iulog,*) '-grav*ustar(p)*thvstar*zii/thv(c) = ', -grav*ustar(p)*thvstar*zii/thv(c) write(iulog,*) 'ustar = ', ustar(p) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index b4d7dfed5d..585659a981 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -611,7 +611,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & frac_veg_nosno => canopystate_inst%frac_veg_nosno_patch , & ! Input: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-] frac_sno => waterdiagnosticbulk_inst%frac_sno_col , & ! Input: [real(r8) (:) ] fraction of ground covered by snow (0 to 1) - snomelt_accum => waterfluxbulk_inst%qflx_snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) + snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) urbpoi => lun%urbpoi , & ! Input: [logical (:) ] true => landunit is an urban point z_0_town => lun%z_0_town , & ! Input: [real(r8) (:) ] momentum roughness length of urban landunit (m) z_d_town => lun%z_d_town , & ! Input: [real(r8) (:) ] displacement height of urban landunit (m) @@ -632,7 +632,11 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & case ('ZengWang2007') if (frac_sno(c) > 0._r8) then if(use_z0m_snowmelt) then - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + if ( snomelt_accum(c) < 1.e-5_r8 )then + z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + else + z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + end if else z0mg(c) = this%zsno end if @@ -655,19 +659,14 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & end if else z0mg(c) = this%zsno - - end if else if (lun%itype(l) == istice) then z0mg(c) = this%zglc - - else if(use_z0mg_2d) then z0mg(c) = z0mg_2D(c) else z0mg(c) = this%zlnd - end if end if end select diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index e99eadc5c5..c9eda89070 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -228,8 +228,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) - snomelt_accum => waterfluxbulk_inst%qflx_snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) - + snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) t_skin_patch => temperature_inst%t_skin_patch , & ! Output: [real(r8) (:) ] patch skin temperature (K) t_lake => temperature_inst%t_lake_col , & ! Input: [real(r8) (:,:) ] lake temperature (Kelvin) diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 index 471d93e004..dc1676ca7d 100644 --- a/src/biogeophys/SnowHydrologyMod.F90 +++ b/src/biogeophys/SnowHydrologyMod.F90 @@ -384,7 +384,7 @@ subroutine UpdateQuantitiesForNewSnow(bounds, num_c, filter_c, & frac_sno = b_waterdiagnostic_inst%frac_sno_col(begc:endc), & frac_sno_eff = b_waterdiagnostic_inst%frac_sno_eff_col(begc:endc), & snow_depth = b_waterdiagnostic_inst%snow_depth_col(begc:endc), & - qflx_snomelt_accum = b_waterflux_inst%qflx_snomelt_accum_col(begc:endc)) + snomelt_accum = b_waterdiagnostic_inst%snomelt_accum_col(begc:endc)) do i = water_inst%bulk_and_tracers_beg, water_inst%bulk_and_tracers_end associate(w => water_inst%bulk_and_tracers(i)) @@ -408,7 +408,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & scf_method, & dtime, lun_itype_col, urbpoi, snl, bifall, h2osno_total, h2osoi_ice, h2osoi_liq, & qflx_snow_grnd, qflx_snow_drain, & - dz, int_snow, swe_old, frac_sno, frac_sno_eff, snow_depth, qflx_snomelt_accum) + dz, int_snow, swe_old, frac_sno, frac_sno_eff, snow_depth, snomelt_accum) ! ! !DESCRIPTION: ! Update various snow-related diagnostic quantities to account for new snow @@ -435,7 +435,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & real(r8) , intent(inout) :: frac_sno( bounds%begc: ) ! fraction of ground covered by snow (0 to 1) real(r8) , intent(inout) :: frac_sno_eff( bounds%begc: ) ! eff. fraction of ground covered by snow (0 to 1) real(r8) , intent(inout) :: snow_depth( bounds%begc: ) ! snow height (m) - real(r8) , intent(inout) :: qflx_snomelt_accum( bounds%begc:) ! accumulated col snow melt for z0m calculation (m H2O) + real(r8) , intent(inout) :: snomelt_accum( bounds%begc: ) ! accumulated col snow melt for z0m calculation (m H2O) ! ! !LOCAL VARIABLES: integer :: fc, c @@ -464,6 +464,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & SHR_ASSERT_FL((ubound(frac_sno, 1) == bounds%endc), sourcefile, __LINE__) SHR_ASSERT_FL((ubound(frac_sno_eff, 1) == bounds%endc), sourcefile, __LINE__) SHR_ASSERT_FL((ubound(snow_depth, 1) == bounds%endc), sourcefile, __LINE__) + SHR_ASSERT_FL((ubound(snomelt_accum, 1) == bounds%endc), sourcefile, __LINE__) associate( & begc => bounds%begc, & @@ -490,7 +491,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & ! all snow falls on ground, no snow on h2osfc (note that qflx_snow_h2osfc is ! currently set to 0 always in CanopyHydrologyMod) newsnow(c) = qflx_snow_grnd(c) * dtime - qflx_snomelt_accum(c) = max(0._r8, qflx_snomelt_accum(c) - newsnow(c)/1000._r8) + snomelt_accum(c) = max(0._r8, snomelt_accum(c) - newsnow(c)/1000._r8) ! update int_snow int_snow(c) = max(int_snow(c),h2osno_total(c)) !h2osno_total could be larger due to frost @@ -807,8 +808,7 @@ subroutine InitializeExplicitSnowPack(bounds, num_c, filter_c, & ! Outputs h2osno_no_layers = w%waterstate_inst%h2osno_no_layers_col(begc:endc), & h2osoi_ice = w%waterstate_inst%h2osoi_ice_col(begc:endc,:), & - h2osoi_liq = w%waterstate_inst%h2osoi_liq_col(begc:endc,:), & - qflx_snomelt_accum = b_waterflux_inst%qflx_snomelt_accum_col(begc:endc)) + h2osoi_liq = w%waterstate_inst%h2osoi_liq_col(begc:endc,:)) end associate end do @@ -823,7 +823,8 @@ subroutine InitializeExplicitSnowPack(bounds, num_c, filter_c, & dz = col%dz(begc:endc,:), & z = col%z(begc:endc,:), & t_soisno = temperature_inst%t_soisno_col(begc:endc,:), & - frac_iceold = b_waterdiagnostic_inst%frac_iceold_col(begc:endc,:)) + frac_iceold = b_waterdiagnostic_inst%frac_iceold_col(begc:endc,:), & + snomelt_accum = b_waterdiagnostic_inst%snomelt_accum_col(begc:endc)) ! intitialize SNICAR variables for fresh snow: call aerosol_inst%ResetFilter( & @@ -901,7 +902,7 @@ end subroutine BuildFilter_SnowpackInitialized !----------------------------------------------------------------------- subroutine UpdateState_InitializeSnowPack(bounds, snowpack_initialized_filterc, & - h2osno_no_layers, h2osoi_ice, h2osoi_liq, qflx_snomelt_accum) + h2osno_no_layers, h2osoi_ice, h2osoi_liq) ! ! !DESCRIPTION: ! For bulk or one tracer: initialize water state variables for columns in which an @@ -914,7 +915,6 @@ subroutine UpdateState_InitializeSnowPack(bounds, snowpack_initialized_filterc, real(r8) , intent(inout) :: h2osno_no_layers( bounds%begc: ) ! snow that is not resolved into layers (kg/m2) real(r8) , intent(inout) :: h2osoi_ice( bounds%begc: , -nlevsno+1: ) ! ice lens (kg/m2) real(r8) , intent(inout) :: h2osoi_liq( bounds%begc: , -nlevsno+1: ) ! liquid water (kg/m2) - real(r8) , intent(inout) :: qflx_snomelt_accum( bounds%begc:) ! accumulated col snow melt for z0m calculation (m H2O) ! ! !LOCAL VARIABLES: integer :: fc, c @@ -932,14 +932,13 @@ subroutine UpdateState_InitializeSnowPack(bounds, snowpack_initialized_filterc, h2osoi_ice(c,0) = h2osno_no_layers(c) h2osoi_liq(c,0) = 0._r8 h2osno_no_layers(c) = 0._r8 - qflx_snomelt_accum(c) = 0._r8 end do end subroutine UpdateState_InitializeSnowPack !----------------------------------------------------------------------- subroutine Bulk_InitializeSnowPack(bounds, snowpack_initialized_filterc, & - forc_t, snow_depth, snl, zi, dz, z, t_soisno, frac_iceold) + forc_t, snow_depth, snl, zi, dz, z, t_soisno, frac_iceold, snomelt_accum) ! ! !DESCRIPTION: ! Initialize an explicit snow pack in columns where this is warranted based on snow depth @@ -959,6 +958,7 @@ subroutine Bulk_InitializeSnowPack(bounds, snowpack_initialized_filterc, & real(r8) , intent(inout) :: z( bounds%begc: , -nlevsno+1: ) ! layer depth (m) real(r8) , intent(inout) :: t_soisno( bounds%begc: , -nlevsno+1: ) ! soil temperature (Kelvin) real(r8) , intent(inout) :: frac_iceold( bounds%begc: , -nlevsno+1: ) ! fraction of ice relative to the tot water + real(r8) , intent(inout) :: snomelt_accum( bounds%begc: ) ! accumulated col snow melt for z0m calculation (m H2O) ! ! !LOCAL VARIABLES: integer :: fc, c @@ -974,6 +974,7 @@ subroutine Bulk_InitializeSnowPack(bounds, snowpack_initialized_filterc, & SHR_ASSERT_ALL_FL((ubound(z) == [bounds%endc, nlevmaxurbgrnd]), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(t_soisno) == [bounds%endc, nlevmaxurbgrnd]), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(frac_iceold) == [bounds%endc, nlevgrnd]), sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(snomelt_accum, 1) == bounds%endc), sourcefile, __LINE__) do fc = 1, snowpack_initialized_filterc%num c = snowpack_initialized_filterc%indices(fc) @@ -989,6 +990,8 @@ subroutine Bulk_InitializeSnowPack(bounds, snowpack_initialized_filterc, & ! This value of frac_iceold makes sense together with the state initialization: ! h2osoi_ice is non-zero, while h2osoi_liq is zero. frac_iceold(c,0) = 1._r8 + + snomelt_accum(c) = 0._r8 end do end subroutine Bulk_InitializeSnowPack diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 893748e7d8..061fb3a2b2 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1114,7 +1114,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] qflx_snofrz => waterfluxbulk_inst%qflx_snofrz_col , & ! Output: [real(r8) (:) ] column-integrated snow freezing rate (positive definite) [kg m-2 s-1] qflx_snomelt => waterfluxbulk_inst%qflx_snomelt_col , & ! Output: [real(r8) (:) ] snow melt (mm H2O /s) - qflx_snomelt_accum => waterfluxbulk_inst%qflx_snomelt_accum_col , & ! Output: [real(r8) (:) ] accumulated snow melt (m) + snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Output: [real(r8) (:) ] accumulated snow melt (m) qflx_snomelt_lyr => waterfluxbulk_inst%qflx_snomelt_lyr_col , & ! Output: [real(r8) (:) ] snow melt in each layer (mm H2O /s) eflx_snomelt => energyflux_inst%eflx_snomelt_col , & ! Output: [real(r8) (:) ] snow melt heat flux (W/m**2) @@ -1382,7 +1382,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) - qflx_snomelt_accum(c) = qflx_snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime/1000._r8 + snomelt_accum(c) = snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime/1000._r8 endif ! layer freezing mass flux (positive): diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 7804fa3746..d974881aed 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -42,7 +42,7 @@ module WaterDiagnosticBulkType real(r8), pointer :: snowdp_col (:) ! col area-averaged snow height (m) real(r8), pointer :: snow_layer_unity_col (:,:) ! value 1 for each snow layer, used for history diagnostics real(r8), pointer :: bw_col (:,:) ! col partial density of water in the snow pack (ice + liquid) [kg/m3] - + real(r8), pointer :: snomelt_accum_col (:) ! accumulated col snow melt for z0m calculation (m H2O) real(r8), pointer :: h2osoi_liq_tot_col (:) ! vertically summed col liquid water (kg/m2) (new) (-nlevsno+1:nlevgrnd) real(r8), pointer :: h2osoi_ice_tot_col (:) ! vertically summed col ice lens (kg/m2) (new) (-nlevsno+1:nlevgrnd) real(r8), pointer :: air_vol_col (:,:) ! col air filled porosity @@ -187,6 +187,7 @@ subroutine InitBulkAllocate(this, bounds) allocate(this%snow_depth_col (begc:endc)) ; this%snow_depth_col (:) = nan allocate(this%snow_5day_col (begc:endc)) ; this%snow_5day_col (:) = nan allocate(this%snowdp_col (begc:endc)) ; this%snowdp_col (:) = nan + allocate(this%snomelt_accum_col (begc:endc)) ; this%snomelt_accum_col (:) = nan allocate(this%snow_layer_unity_col (begc:endc,-nlevsno+1:0)) ; this%snow_layer_unity_col (:,:) = nan allocate(this%bw_col (begc:endc,-nlevsno+1:0)) ; this%bw_col (:,:) = nan allocate(this%air_vol_col (begc:endc, 1:nlevgrnd)) ; this%air_vol_col (:,:) = nan @@ -452,6 +453,14 @@ subroutine InitBulkHistory(this, bounds) long_name=this%info%lname('gridcell mean snow height'), & ptr_col=this%snowdp_col, c2l_scale_type='urbanf') + this%snomelt_accum_col(begc:endc) = 0._r8 + call hist_addfld1d ( & ! Have this as an output variable for now to check + fname=this%info%fname('SNOMELT_ACCUM'), & + units='m', & + avgflag='A', & + long_name=this%info%lname('accumulated snow melt for z0'), & + ptr_col=this%snomelt_accum_col, c2l_scale_type='urbanf') + if (use_cn) then this%wf_col(begc:endc) = spval call hist_addfld1d ( & @@ -786,6 +795,18 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil units='m', & interpinic_flag='interp', readvar=readvar, data=this%snow_depth_col) + call restartvar(ncid=ncid, flag=flag, & + varname=this%info%fname('SNOMELT_ACCUM'), & + xtype=ncd_double, & + dim1name='column', & + long_name=this%info%lname('accumulated snow melt for z0'), & + units='m', & + interpinic_flag='interp', readvar=readvar, data=this%snomelt_accum_col) + if (flag == 'read' .and. .not. readvar) then + ! initial run, not restart: initialize snomelt_accum_col to zero + this%snomelt_accum_col(bounds%begc:bounds%endc) = 0._r8 + endif + call restartvar(ncid=ncid, flag=flag, & varname=this%info%fname('frac_sno_eff'), & xtype=ncd_double, & diff --git a/src/biogeophys/WaterFluxType.F90 b/src/biogeophys/WaterFluxType.F90 index ff20e825fa..f7c55d44e1 100644 --- a/src/biogeophys/WaterFluxType.F90 +++ b/src/biogeophys/WaterFluxType.F90 @@ -77,7 +77,6 @@ module WaterFluxType real(r8), pointer :: qflx_floodc_col (:) ! col flood water flux at column level real(r8), pointer :: qflx_sl_top_soil_col (:) ! col liquid water + ice from layer above soil to top soil layer or sent to qflx_qrgwl (mm H2O/s) real(r8), pointer :: qflx_snomelt_col (:) ! col snow melt (mm H2O /s) - real(r8), pointer :: qflx_snomelt_accum_col (:) ! accumulated col snow melt for z0m calculation (m H2O) real(r8), pointer :: qflx_qrgwl_col (:) ! col qflx_surf at glaciers, wetlands, lakes real(r8), pointer :: qflx_runoff_col (:) ! col total runoff (qflx_drain+qflx_surf+qflx_qrgwl) (mm H2O /s) real(r8), pointer :: qflx_runoff_r_col (:) ! col Rural total runoff (qflx_drain+qflx_surf+qflx_qrgwl) (mm H2O /s) @@ -285,9 +284,6 @@ subroutine InitAllocate(this, bounds, tracer_vars) call AllocateVar1d(var = this%qflx_snomelt_col, name = 'qflx_snomelt_col', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) - call AllocateVar1d(var = this%qflx_snomelt_accum_col, name = 'qflx_snomelt_accum_col', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column) call AllocateVar1d(var = this%qflx_snofrz_col, name = 'qflx_snofrz_col', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) @@ -549,14 +545,6 @@ subroutine InitHistory(this, bounds) long_name=this%info%lname('snow melt rate'), & ptr_col=this%qflx_snomelt_col, c2l_scale_type='urbanf') - this%qflx_snomelt_accum_col(begc:endc) = 0._r8 - call hist_addfld1d ( & ! Have this as an output variable for now to check - fname=this%info%fname('QSNOMELT_ACCUM'), & - units='m', & - avgflag='A', & - long_name=this%info%lname('accumulated snow melt for z0'), & - ptr_col=this%qflx_snomelt_accum_col, c2l_scale_type='urbanf') - call hist_addfld1d ( & fname=this%info%fname('QSNOMELT_ICE'), & units='mm/s', & @@ -908,18 +896,6 @@ subroutine Restart(this, bounds, ncid, flag) this%qflx_snow_drain_col(bounds%begc:bounds%endc) = 0._r8 endif - call restartvar(ncid=ncid, flag=flag, & - varname=this%info%fname('QSNOMELT_ACCUM'), & - xtype=ncd_double, & - dim1name='column', & - long_name=this%info%lname('accumulated snow melt for z0'), & - units='m', & - interpinic_flag='interp', readvar=readvar, data=this%qflx_snomelt_accum_col) - if (flag == 'read' .and. .not. readvar) then - ! initial run, not restart: initialize qflx_snow_drain to zero - this%qflx_snomelt_accum_col(bounds%begc:bounds%endc) = 0._r8 - endif - call this%qflx_liq_dynbal_dribbler%Restart(bounds, ncid, flag) call this%qflx_ice_dynbal_dribbler%Restart(bounds, ncid, flag) From 382441ce8f07d640b0c31e41e5f645363b30f8cd Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Mon, 14 Mar 2022 15:00:21 -0600 Subject: [PATCH 0186/2067] Add forcing height change back into CanopyFluxesMod after rebase. --- src/biogeophys/CanopyFluxesMod.F90 | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 8059f26d73..10d1193cbb 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -918,11 +918,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, call endrun(msg = 'unknown z0param_method', additional_msg = errMsg(sourcefile, __LINE__)) end select - ! Update the forcing heights - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(c) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(c) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(c) + displa(p) - z0hv(p) = z0mv(p) z0qv(p) = z0mv(p) From e7579c9704441c058435b0e8dd4cd2158f1bc467 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Tue, 15 Mar 2022 16:05:58 -0600 Subject: [PATCH 0187/2067] Encapsulated forcing height update in Meier2022 to maintain bfb with ZengWang2007. Protect snomelt_accum in LakeFluxes --- src/biogeophys/CanopyFluxesMod.F90 | 9 ++++++--- src/biogeophys/LakeFluxesMod.F90 | 6 +++++- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 10d1193cbb..0a945f975c 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -922,9 +922,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0qv(p) = z0mv(p) ! Update the forcing heights - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mv(p) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hv(p) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qv(p) + displa(p) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mv(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hv(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qv(p) + displa(p) + end if end do diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index c9eda89070..b53b0fd23b 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -365,7 +365,11 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('ZengWang2007') if(use_z0m_snowmelt) then - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + if ( snomelt_accum(c) < 1.e-5_r8 ) then + z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + else + z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + end if else z0mg(p) = params_inst%zsno end if From 902f1cb76f6371da5f3215ed6e9cd358b3f1f54e Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Mon, 21 Mar 2022 14:07:31 -0600 Subject: [PATCH 0188/2067] Update forcing heights and restrict zeta to less than 20 for now --- src/biogeophys/BareGroundFluxesMod.F90 | 11 ++++++- src/biogeophys/CanopyFluxesMod.F90 | 7 +++- src/biogeophys/FrictionVelocityMod.F90 | 44 +++++++++++++++++++++----- src/biogeophys/LakeFluxesMod.F90 | 22 +++++++++++-- 4 files changed, 71 insertions(+), 13 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 11d1790fc9..73c169fa13 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -234,7 +234,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & rh_ref2m_r => waterdiagnosticbulk_inst%rh_ref2m_r_patch , & ! Output: [real(r8) (:) ] Rural 2 m height surface relative humidity (%) rh_ref2m => waterdiagnosticbulk_inst%rh_ref2m_patch , & ! Output: [real(r8) (:) ] 2 m height surface relative humidity (%) - forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Input: + forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Output: [real(r8) (:) ] observational height of wind at patch level [m] + forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Output: [real(r8) (:) ] observational height of temperature at patch level [m] + forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Output: [real(r8) (:) ] observational height of specific humidity at patch level [m] u10_clm => frictionvel_inst%u10_clm_patch , & ! Input: [real(r8) (:) ] 10 m height winds (m/s) zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions z0mg_col => frictionvel_inst%z0mg_col , & ! Output: [real(r8) (:) ] roughness length, momentum [m] @@ -359,6 +361,13 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & end select z0qg_patch(p) = z0hg_patch(p) + ! Update the forcing heights for new roughness lengths + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + forc_hgt_u_patch(p) = forc_hgt_u_patch(g) + z0mg_patch(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t_patch(g) + z0hg_patch(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q_patch(g) + z0qg_patch(p) + displa(p) + end if thvstar = tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar zeta = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 0a945f975c..31d73e1b37 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1393,7 +1393,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, if (zeta(p) >= 0._r8) then !stable ! remove stability cap when biomass heat storage is active if(use_biomass_heat_storage) then - zeta(p) = min(100._r8,max(zeta(p),0.01_r8)) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(p) = min(20._r8,max(zeta(p),0.01_r8)) + else + zeta(p) = min(100._r8,max(zeta(p),0.01_r8)) + end if else zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) endif diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 585659a981..5d532b1145 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -703,17 +703,17 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then if (frac_veg_nosno(p) == 0) then forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(c) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(c) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(c) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(c) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(c) + displa(p) else - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0m(p) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0m(p) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0m(p) + displa(p) + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mv(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hv(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qv(p) + displa(p) end if else if (lun%itype(l) == istwet .or. lun%itype(l) == istice) then - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(c) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(c) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(c) + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(c) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(c) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(c) + displa(p) else if (urbpoi(l)) then forc_hgt_u_patch(p) = forc_hgt_u(g) + z_0_town(l) + z_d_town(l) forc_hgt_t_patch(p) = forc_hgt_t(g) + z_0_town(l) + z_d_town(l) @@ -893,6 +893,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = forc_hgt_u_patch(n)-displa(n) end if zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (zeta(n) < -zetam) then ustar(n) = vkc*um(n)/(log(-zetam*obu(n)/z0m(n))& - this%StabilityFunc1(-zetam) & @@ -992,6 +996,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = forc_hgt_t_patch(n)-displa(n) end if zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (zeta(n) < -zetat) then temp1(n) = vkc/(log(-zetat*obu(n)/z0h(n))& - this%StabilityFunc2(-zetat) & @@ -1016,6 +1024,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & else zldis(n) = forc_hgt_q_patch(pfti(n))-displa(n) zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (zeta(n) < -zetat) then temp2(n) = vkc/(log(-zetat*obu(n)/z0q(n)) & - this%StabilityFunc2(-zetat) & @@ -1038,6 +1050,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & else zldis(n) = forc_hgt_q_patch(n)-displa(n) zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (zeta(n) < -zetat) then temp2(n) = vkc/(log(-zetat*obu(n)/z0q(n)) & - this%StabilityFunc2(-zetat) & @@ -1060,6 +1076,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = 2.0_r8 + z0h(n) zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (zeta(n) < -zetat) then temp12m(n) = vkc/(log(-zetat*obu(n)/z0h(n))& - this%StabilityFunc2(-zetat) & @@ -1083,6 +1103,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & else zldis(n) = 2.0_r8 + z0q(n) zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (zeta(n) < -zetat) then temp22m(n) = vkc/(log(-zetat*obu(n)/z0q(n)) - & this%StabilityFunc2(-zetat) + this%StabilityFunc2(z0q(n)/obu(n)) & @@ -1111,6 +1135,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = forc_hgt_u_patch(n)-displa(n) end if zeta(n) = zldis(n)/obu(n) + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + zeta(n) = min(20._r8,zldis(n)/obu(n)) + end if if (min(zeta(n), 1._r8) < 0._r8) then tmp1 = (1._r8 - 16._r8*min(zeta(n),1._r8))**0.25_r8 tmp2 = log((1._r8+tmp1*tmp1)/2._r8) diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index b53b0fd23b..6dc9d1f0c0 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -380,9 +380,17 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, ! Surface temperature and fluxes - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(p) + ! Update forcing heights for updated roughness lengths + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(p) + else + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(p) + end if ! Find top layer jtop(c) = snl(c) + 1 @@ -622,6 +630,14 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0qg(p) = z0hg(p) end if + ! Update forcing heights for updated roughness lengths + ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 + if (z0param_method == 'Meier2022') then + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(p) + end if + end do ! end of filtered pft loop iter = iter + 1 From 1f01f3d5112896d71541863a7206354342d8f6ae Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Mar 2022 14:26:35 -0600 Subject: [PATCH 0189/2067] Add live course root maintence respiration to root respiration fixing #1676 --- src/biogeochem/CNVegCarbonFluxType.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 718f7b0330..ddd1126008 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -4169,6 +4169,7 @@ subroutine Summary_carbonflux(this, & ! root respiration (RR) this%rr_patch(p) = & this%froot_mr_patch(p) + & + this%livecroot_mr_patch(p) + & this%cpool_froot_gr_patch(p) + & this%cpool_livecroot_gr_patch(p) + & this%cpool_deadcroot_gr_patch(p) + & From 6f97bb5c4a36c4dea90ae459cba76252706ef742 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Mar 2022 17:04:32 -0600 Subject: [PATCH 0190/2067] Start working on the makefile --- tools/mksurfdata_map/Makefile.data | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index d0c000ba63..15ca410f0f 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -53,7 +53,12 @@ else endif MKSURFDATA = $(BATCHJOBS) $(PWD)/mksurfdata.pl +SUBSETDATA = $(BATCHJOBS) $(PWD)/../site_and_regional/subset_data +# subset_data options +# +SUBSETDATA_1X1_BRAZIL := --lat --lon --site 1x1_brazil --outdir . --user-mods-dir ./1x1_brazil \ + --overwrite --create-user-mods --uniform-snowpack --include-nonveg --cap-saturation # f19 and f09 are standard resolutions, f10 is used for testing, f45 is used for FATES # ne30np4 is standard resolution for SE dycore in CAM, C96 is standard for fv3 dycore # The ne30np4 series (including pg2, pg3, pg4) are standard for SE dycore @@ -119,14 +124,18 @@ global-present-nldas : FORCE # tropics : $(TROPICS) -crop-tropics-present : FORCE - $(MKSURFDATA) -glc_nec 10 -y 2000 -res 5x5_amazon,1x1_brazil $(BACKGROUND) +crop-tropics-present : FORCE brazil-tropics-present + $(MKSURFDATA) -glc_nec 10 -y 2000 -res 5x5_amazon $(BACKGROUND) + +1x1_brazil-tropics-present : FORCE + $(SUBSETDATA) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop $(BACKGROUND) + crop-tropics-historical : FORCE - $(MKSURFDATA) -glc_nec 10 -y 1850 -res 1x1_brazil $(BACKGROUND) + $(SUBSETDATA) -glc_nec 10 -y 1850 -res 1x1_brazil $(BACKGROUND) crop-tropics-transient : FORCE - $(MKSURFDATA) -glc_nec 10 -no_surfdata -y 1850-2000 -res 1x1_brazil $(BACKGROUND) + $(SUBSETDATA) -glc_nec 10 -no_surfdata -y 1850-2000 -res 1x1_brazil $(BACKGROUND) # # crop @@ -143,13 +152,13 @@ crop-global-present-f05 : FORCE $(MKSURFDATA) -glc_nec 10 -y 1850,2000 -res 0.47x0.63 $(BACKGROUND) crop-numa-present : FORCE - $(MKSURFDATA) -glc_nec 10 -y 2000 -r 1x1_numaIA $(BACKGROUND) + $(SUBSETDATA) -glc_nec 10 -y 2000 -r 1x1_numaIA $(BACKGROUND) crop-numa-historical : FORCE - $(MKSURFDATA) -glc_nec 10 -y 1850 -r 1x1_numaIA $(BACKGROUND) + $(SUBSETDATA) -glc_nec 10 -y 1850 -r 1x1_numaIA $(BACKGROUND) crop-smallville : FORCE - $(MKSURFDATA) -glc_nec 10 -y 2000 -r 1x1_smallvilleIA \ + $(SUBSETDATA) -glc_nec 10 -y 2000 -r 1x1_smallvilleIA \ -pft_idx 17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78 \ -pft_frc 6.5,1.5,1.6,1.7,1.8,1.9,1.5,1.6,1.7,1.8,1.9,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5 \ $(BACKGROUND) @@ -165,7 +174,7 @@ crop-global-present-ne120np4 : FORCE # adds crop (to make sure that it works properly to add crop in a grid cell # where there used to be no crop). crop-smallville-historical : FORCE - $(MKSURFDATA) -glc_nec 10 -y 1850 -r 1x1_smallvilleIA -pft_idx 13 -pft_frc 100 $(BACKGROUND) + $(SUBSETDATA) -glc_nec 10 -y 1850 -r 1x1_smallvilleIA -pft_idx 13 -pft_frc 100 $(BACKGROUND) # Setup the historical case for SSP5-8.5 so that historical can be used to go into the future. crop-global-historical : FORCE @@ -230,12 +239,12 @@ crop-global-SSP5-8.5 : FORCE urban : urban-present urban-alpha urban-present : FORCE - $(MKSURFDATA) -y 2000 -no-crop -glc_nec 10 -r 1x1_vancouverCAN,1x1_mexicocityMEX $(BACKGROUND) + $(SUBSETDATA) -y 2000 -no-crop -glc_nec 10 -r 1x1_vancouverCAN,1x1_mexicocityMEX $(BACKGROUND) # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 urban-alpha : FORCE - $(MKSURFDATA) -y 2000 -no-crop -glc_nec 10 -r 1x1_urbanc_alpha -urban_skip_abort_on_invalid_data_check $(BACKGROUND) + $(SUBSETDATA) -y 2000 -no-crop -glc_nec 10 -r 1x1_urbanc_alpha -urban_skip_abort_on_invalid_data_check $(BACKGROUND) # From b202849e2d233ad5c1cdd1ddda2bd2c119675cdc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 29 Mar 2022 15:44:38 -0600 Subject: [PATCH 0191/2067] If prescribed sowing date is Jan. 1, now harvests on Dec. 31. --- src/biogeochem/CNPhenologyMod.F90 | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 1bd29694e2..1dbb2a3d20 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2109,6 +2109,17 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! If this patch has already had all its plantings for the year, don't harvest ! until some time next year. do_harvest = .false. + + ! ... unless first sowing next year happens Jan. 1. + if (s < 1) then + write(iulog,*) 'next_rx_sdate(p) < 0 but no sowings happened this year' + call endrun(msg=errMsg(sourcefile, __LINE__)) + ! WARNING: This implementation assumes that sowing dates don't change over time! + ! In order to avoid this, you'd have to read this year's AND next year's prescribed + ! sowing dates. + else if (crop_inst%sdates_thisyr(p,1) == 1) then + do_harvest = jday == dayspyr + end if endif else if (sown_today) then ! Do not harvest on the day this growing season began; From 3ccbed909d3c8123b4abcb59dcd620fd30ec1949 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 30 Mar 2022 10:33:34 +0200 Subject: [PATCH 0192/2067] fixed restart --- src/biogeophys/WaterStateType.F90 | 96 +++++++++++++++++++------------ 1 file changed, 59 insertions(+), 37 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 4c0575c8b7..e5a4cf16e5 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -53,7 +53,7 @@ module WaterStateType real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (1:nlevgrnd) - real(r8), pointer :: init_exice (:,:) ! initial value of col excess ice lens/(kg/m2) (new) (1:nlevgrnd) + real(r8), pointer :: init_exice (:,:) ! initial value of col excess ice lens/(m/m) (new) (1:nlevgrnd) real(r8), pointer :: exice_melt_lev (:,:) ! col excess ice melting (m) (new) real(r8), pointer :: exice_melt (:) ! column-wide excess ice melting (m) (new) @@ -164,15 +164,15 @@ subroutine InitAllocate(this, bounds, tracer_vars) call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = 1, dim2end = nlevmaxurbgrnd) + dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) call AllocateVar2d(var = this%init_exice, name = 'init_exice', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = 1, dim2end = nlevmaxurbgrnd) + dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) call AllocateVar2d(var = this%exice_melt_lev, name = 'exice_melt_lev', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = 1, dim2end = nlevmaxurbgrnd) + dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) call AllocateVar1d(var = this%exice_melt, name = 'exice_melt', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) @@ -299,7 +299,13 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & avgflag='A', long_name='excess soil ice (vegetated landunits only)', & ptr_col=this%excess_ice_col, l2g_scale_type='veg') - data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + + data2dptr => this%init_exice(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXICE_INIT', units='m/m', type2d='levsoi', & + avgflag='A', long_name='initial excess soil ice (vegetated landunits only)', & + ptr_col=this%excess_ice_col, l2g_scale_type='veg') + + data2dptr => this%exice_melt_lev(begc:endc,1:nlevsoi) call hist_addfld2d (fname='EXICE_MELT_LEV', units='kg/m2', type2d='levsoi', & avgflag='A', long_name='melt from excess ice per layer (vegetated landunits only)', & ptr_col=this%exice_melt_lev, l2g_scale_type='veg') @@ -341,7 +347,7 @@ subroutine InitCold(this, bounds, & real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run - character(len=*) , intent(in) :: NLFilename ! Namelist filename + character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: integer :: c,j,l,nlevs,g @@ -548,13 +554,12 @@ subroutine InitCold(this, bounds, & this%dynbal_baseline_ice_col(bounds%begc:bounds%endc) = 0._r8 !Initialize excess ice - write(iulog,*) 'nfl =', NLFilename if (use_excess_ice .and. NLFilename /= '') then ! enforce initialization with 0 for everything - this%init_exice(:,:)=0.0_r8 - this%excess_ice_col(:,:)=0.0_r8 - this%exice_melt_lev(:,:)=0.0_r8 - this%exice_melt(:)=0.0_r8 + this%init_exice(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column @@ -575,22 +580,22 @@ subroutine InitCold(this, bounds, & this%excess_ice_col(c,j) = 0.0_r8 endif this%init_exice(c,j) = 0.0_r8 - this%init_exice(c,j) = this%excess_ice_col(c,j) + this%init_exice(c,j) = this%exicestream%exice_bulk(g) end do endif else ! just in case zeros for lakes and other columns - this%excess_ice_col(c,:) = 0.0_r8 - this%init_exice(c,:) = 0.0_r8 + this%excess_ice_col(c,-nlevsno+1:nlevmaxurbgrnd) = 0.0_r8 + this%init_exice(c,-nlevsno+1:nlevmaxurbgrnd) = 0.0_r8 end if - enddo - this%exice_melt_lev(:,:)=0.0_r8 - this%exice_melt(:)=0.0_r8 + enddo + this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 else - this%init_exice(:,:)=0.0_r8 - this%excess_ice_col(:,:)=0.0_r8 - this%exice_melt_lev(:,:)=0.0_r8 - this%exice_melt(:)=0.0_r8 + this%init_exice(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 end if end associate @@ -718,22 +723,39 @@ subroutine Restart(this, bounds, ncid, flag, & interpinic_flag='interp', readvar=readvar, data=this%dynbal_baseline_ice_col) ! Restart excess ice vars - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & - dim1name='column', dim2name='levtot', switchdim=.true., & - long_name=this%info%lname('excess soil ice (vegetated landunits only)'), units='kg/m2', & - scale_by_thickness=.true., & - interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_MELT_LEV'), xtype=ncd_double, & - dim1name='column', dim2name='levtot', switchdim=.true., & - long_name=this%info%lname('melt from excess ice per layer (vegetated landunits only)'), units='kg/m2', & - scale_by_thickness=.true., & - interpinic_flag='interp', readvar=readvar, data=this%exice_melt_lev) - - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_MELT'), xtype=ncd_double, & - dim1name='column', & - long_name=this%info%lname('melt from excess ice (vegetated landunits only)'), units='m', & - interpinic_flag='interp', readvar=readvar, data=this%exice_melt) - + !write(iulog,*) 'restarting excess ice wars' + if (.not. use_excess_ice .and. flag == 'read') then + ! no need to even define the restart vars + this%init_exice(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 + + else + ! have to at least define them + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & + dim1name='column', dim2name='levtot', switchdim=.true., & + long_name=this%info%lname('excess soil ice (vegetated landunits only)'), units='kg/m2', & + scale_by_thickness=.true., & + interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) + + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_INIT'), xtype=ncd_double, & + dim1name='column', dim2name='levtot', switchdim=.true., & + long_name=this%info%lname('inital excess soil ice (vegetated landunits only)'), units='m/m', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%init_exice) + + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_MELT_LEV'), xtype=ncd_double, & + dim1name='column', dim2name='levtot', switchdim=.true., & + long_name=this%info%lname('melt from excess ice per layer (vegetated landunits only)'), units='kg/m2', & + scale_by_thickness=.true., & + interpinic_flag='interp', readvar=readvar, data=this%exice_melt_lev) + + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_MELT'), xtype=ncd_double, & + dim1name='column', & + long_name=this%info%lname('melt from excess ice (vegetated landunits only)'), units='m', & + interpinic_flag='interp', readvar=readvar, data=this%exice_melt) + endif ! Determine volumetric soil water (for read only) if (flag == 'read' ) then do c = bounds%begc, bounds%endc From 029d57bd87e1f9d2d930d75e3e31e4a357d0b178 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 30 Mar 2022 16:04:41 -0600 Subject: [PATCH 0193/2067] Do not allow growing season length 365 (or 366, if last year was a leap year). This would result in idop==jday, which would invoke the "manually setting sowing_count and sdates_thisyr" code. This would lead to crops never getting harvested. Instead, always harvest the day before idop. --- src/biogeochem/CNPhenologyMod.F90 | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 1dbb2a3d20..9b1f415ff7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1857,6 +1857,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! with CropPhenology() getting the day of the year from the START of the timestep ! (i.e., jday = get_prev_calday()) instead of the END of the timestep (i.e., ! jday = get_calday()). See CTSM issue #1623. + ! Once removed, can also remove the "Instead, always harvest the day before idop" bit. if (croplive(p) .and. idop(p) <= jday .and. sowing_count(p) == 0) then sowing_count(p) = 1 crop_inst%sdates_thisyr(p,1) = real(idop(p), r8) @@ -2105,6 +2106,18 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (next_rx_sdate(p) >= 0) then ! Harvest the day before the next sowing date this year. do_harvest = jday == next_rx_sdate(p) - 1 + + ! ... unless that will lead to growing season length 365 (or 366, + ! if last year was a leap year). This would result in idop==jday, + ! which would invoke the "manually setting sowing_count and + ! sdates_thisyr" code. This would lead to crops never getting + ! harvested. Instead, always harvest the day before idop. + if ((.not. do_harvest) .and. \ + (idop(p) > 1 .and. jday == idop(p) - 1) .or. \ + (idop(p) == 1 .and. jday == dayspyr)) then + do_harvest = .true. + end if + else ! If this patch has already had all its plantings for the year, don't harvest ! until some time next year. From 5c915f9fe207977225931ac9ef8fbfe34fee81bb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 31 Mar 2022 13:25:49 -0600 Subject: [PATCH 0194/2067] Added GDDHARV_PERHARV. Untested, even for compile. --- src/biogeochem/CNPhenologyMod.F90 | 2 ++ src/biogeochem/CNVegStateType.F90 | 21 ++++++++++++++++++++ src/biogeochem/CropType.F90 | 33 ------------------------------- src/utils/restUtilMod.F90.in | 32 ++++++++++++++++++++++++++++++ 4 files changed, 55 insertions(+), 33 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e5834a9d05..8f84fdca5a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1805,6 +1805,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end do do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 + cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8 end do end if @@ -2075,6 +2076,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + cnveg_state_inst%gddmaturity_thisyr(p,harvest_count(p)) = gddmaturity(p) croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 if (tlai(p) > 0._r8) then ! plant had emerged before harvest diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index e79172c22e..cc7dd8f724 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -34,6 +34,7 @@ module CNVegStateType real(r8) , pointer :: hdidx_patch (:) ! patch cold hardening index? real(r8) , pointer :: cumvd_patch (:) ! patch cumulative vernalization d?ependence? real(r8) , pointer :: gddmaturity_patch (:) ! patch growing degree days (gdd) needed to harvest (ddays) + real(r8) , pointer :: gddmaturity_thisyr (:,:) ! all at-harvest values of the above for this patch this year real(r8) , pointer :: huileaf_patch (:) ! patch heat unit index needed from planting to leaf emergence real(r8) , pointer :: huigrain_patch (:) ! patch heat unit index needed to reach vegetative maturity real(r8) , pointer :: aleafi_patch (:) ! patch saved leaf allocation coefficient from phase 2 @@ -137,6 +138,7 @@ subroutine InitAllocate(this, bounds) ! ! !USES: use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use clm_varpar, only : mxsowings, mxharvests ! ! !ARGUMENTS: class(cnveg_state_type) :: this @@ -195,6 +197,7 @@ subroutine InitAllocate(this, bounds) allocate(this%hdidx_patch (begp:endp)) ; this%hdidx_patch (:) = nan allocate(this%cumvd_patch (begp:endp)) ; this%cumvd_patch (:) = nan allocate(this%gddmaturity_patch (begp:endp)) ; this%gddmaturity_patch (:) = spval + allocate(this%gddmaturity_thisyr (begp:endp,1:mxharvests)) ; this%gddmaturity_thisyr (:,:) = spval allocate(this%huileaf_patch (begp:endp)) ; this%huileaf_patch (:) = nan allocate(this%huigrain_patch (begp:endp)) ; this%huigrain_patch (:) = 0.0_r8 allocate(this%aleafi_patch (begp:endp)) ; this%aleafi_patch (:) = nan @@ -286,10 +289,18 @@ subroutine InitHistory(this, bounds) begc = bounds%begc; endc= bounds%endc if ( use_crop) then + ! Daily this%gddmaturity_patch(begp:endp) = spval call hist_addfld1d (fname='GDDHARV', units='ddays', & avgflag='A', long_name='Growing degree days (gdd) needed to harvest', & ptr_patch=this%gddmaturity_patch, default='inactive') + + ! Per harvest + this%gddmaturity_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='GDDHARV_PERHARV', units='ddays', type2d='mxharvests', & + avgflag='I', long_name='Growing degree days (gdd) needed to harvest; should only be output annually', & + ptr_patch=this%gddmaturity_thisyr, default='inactive') + end if this%lfc2_col(begc:endc) = spval @@ -819,6 +830,16 @@ subroutine Restart(this, bounds, ncid, flag, cnveg_carbonstate, & call restartvar(ncid=ncid, flag=flag, varname='grain_flag', xtype=ncd_double, & dim1name='pft', long_name='', units='', & interpinic_flag='interp', readvar=readvar, data=this%grain_flag_patch) + + ! Read or write variable(s) with mxharvests dimension + ! BACKWARDS_COMPATIBILITY(ssr, 2022-03-31) See note in CallRestartvarDimOK() + if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then + call restartvar(ncid=ncid, flag=flag, varname='gddmaturity_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='crop harvest dates for this patch this year', units='day of year', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%gddmaturity_thisyr) + end if end if if ( flag == 'read' .and. num_reseed_patch > 0 )then if ( masterproc ) write(iulog, *) 'Reseed dead plants for CNVegState' diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 470f37922b..2340afab3e 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -424,39 +424,6 @@ subroutine InitAccVars(this, bounds) end subroutine InitAccVars - !----------------------------------------------------------------------- - logical function CallRestartvarDimOK (ncid, flag, dimname) - ! - ! !DESCRIPTION: - ! Answer whether to call restartvar(), if necessary checking whether - ! a dimension exists in the restart file - ! - ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) - ! Used in Restart(). Even though restartvar() can safely be called for a - ! non-existent variable, it gives an error for a non-existent dimension, so - ! check whether the dimension exists before trying to read. The need for this - ! function arose because we recently added the mxsowings and mxharvests - ! dimensions to the restart file. - ! - ! !USES: - use ncdio_pio - ! - ! !ARGUMENTS: - type(file_desc_t), intent(inout) :: ncid - character(len=*) , intent(in) :: flag - character(len=*) , intent(in) :: dimname - ! - ! !LOCAL VARIABLES: - !----------------------------------------------------------------------- - - if (flag == 'read') then - call check_dim(ncid, dimname, dimexist=CallRestartvarDimOK) - else - CallRestartvarDimOK = .true. - end if - - end function CallRestartvarDimOK - !----------------------------------------------------------------------- subroutine Restart(this, bounds, ncid, flag) ! diff --git a/src/utils/restUtilMod.F90.in b/src/utils/restUtilMod.F90.in index 4271271097..9fb2e3d114 100644 --- a/src/utils/restUtilMod.F90.in +++ b/src/utils/restUtilMod.F90.in @@ -740,5 +740,37 @@ contains end subroutine write_interpinic_flag + !----------------------------------------------------------------------- + logical function CallRestartvarDimOK (ncid, flag, dimname) + ! + ! !DESCRIPTION: + ! Answer whether to call restartvar(), if necessary checking whether + ! a dimension exists in the restart file + ! + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) + ! Used in Restart(). Even though restartvar() can safely be called for a + ! non-existent variable, it gives an error for a non-existent dimension, so + ! check whether the dimension exists before trying to read. The need for this + ! function arose because we recently added the mxsowings and mxharvests + ! dimensions to the restart file. + ! + ! !USES: + use ncdio_pio + ! + ! !ARGUMENTS: + type(file_desc_t), intent(inout) :: ncid + character(len=*) , intent(in) :: flag + character(len=*) , intent(in) :: dimname + ! + ! !LOCAL VARIABLES: + !----------------------------------------------------------------------- + + if (flag == 'read') then + call check_dim(ncid, dimname, dimexist=CallRestartvarDimOK) + else + CallRestartvarDimOK = .true. + end if + + end function CallRestartvarDimOK end module restUtilMod From c43cc834a7b28ffe3c434ebf77bb92506cb1c34c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 31 Mar 2022 14:34:55 -0600 Subject: [PATCH 0195/2067] Compile fix. --- src/utils/restUtilMod.F90.in | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/utils/restUtilMod.F90.in b/src/utils/restUtilMod.F90.in index 9fb2e3d114..32686c816c 100644 --- a/src/utils/restUtilMod.F90.in +++ b/src/utils/restUtilMod.F90.in @@ -91,6 +91,10 @@ module restUtilMod private :: missing_field_possibly_abort private :: write_interpinic_flag + ! Answer whether to call restartvar(), if necessary checking whether + ! a dimension exists in the restart file + public :: CallRestartvarDimOK + character(len=*), parameter, private :: sourcefile = & __FILE__ From f8edb891b630427b8781ea93ce579ea492a22af6 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 1 Apr 2022 19:01:44 +0200 Subject: [PATCH 0196/2067] first layer should have no excess ice. --- src/biogeophys/WaterStateType.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index e5a4cf16e5..cdbd232004 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -573,15 +573,14 @@ subroutine InitCold(this, bounds, & else nbedrock = nlevsoi endif - do j = 1, nlevmaxurbgrnd + do j = 2, nlevmaxurbgrnd ! ignore first layer if (j Date: Mon, 4 Apr 2022 16:55:40 -0600 Subject: [PATCH 0197/2067] Added GDDACCUM_PERHARV and HUI_PERHARV outputs. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++++ src/biogeochem/CropType.F90 | 24 ++++++++++++++++++++++++ 2 files changed, 28 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 8f84fdca5a..b7d3d6fb5d 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1806,6 +1806,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8 + crop_inst%gddaccum_thisyr(p,s) = -1._r8 + crop_inst%hui_thisyr(p,s) = -1._r8 end do end if @@ -2076,6 +2078,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) + crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) cnveg_state_inst%gddmaturity_thisyr(p,harvest_count(p)) = gddmaturity(p) croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 2340afab3e..6a3774c058 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -42,6 +42,8 @@ module CropType real(r8) :: baset_latvary_slope real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year + real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year + real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch @@ -206,6 +208,8 @@ subroutine InitAllocate(this, bounds) allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sdates_thisyr(begp:endp,1:mxsowings)) ; this%sdates_thisyr(:,:) = spval allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval + allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval + allocate(this%hui_thisyr(begp:endp,1:mxharvests)) ; this%hui_thisyr(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 @@ -271,6 +275,16 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_patch=this%hdates_thisyr, default='inactive') + this%gddaccum_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='GDDACCUM_PERHARV', units='ddays', type2d='mxharvests', & + avgflag='I', long_name='At-harvest accumulated growing degree days past planting date for crop; should only be output annually', & + ptr_patch=this%gddaccum_thisyr, default='inactive') + + this%hui_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='HUI_PERHARV', units='ddays', type2d='mxharvests', & + avgflag='I', long_name='At-harvest accumulated heat unit index for crop; should only be output annually', & + ptr_patch=this%hui_thisyr, default='inactive') + end subroutine InitHistory subroutine InitCold(this, bounds) @@ -551,6 +565,16 @@ subroutine Restart(this, bounds, ncid, flag) long_name='crop harvest dates for this patch this year', units='day of year', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%hdates_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='gddaccum_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='accumulated GDD at harvest for this patch this year', units='ddays', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%gddaccum_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='hui_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='accumulated heat unit index at harvest for this patch this year', units='ddays', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%hui_thisyr) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp From e09c362caee514d85662f39aa1b045b3e989137e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 4 Apr 2022 17:21:04 -0600 Subject: [PATCH 0198/2067] Added HARVEST_REASON_PERHARV output. --- src/biogeochem/CNPhenologyMod.F90 | 14 ++++++++++++++ src/biogeochem/CropType.F90 | 12 ++++++++++++ 2 files changed, 26 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b7d3d6fb5d..cc3d6439bb 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1698,6 +1698,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer h ! hemisphere indices integer s ! growing season indices integer idpp ! number of days past planting + real(r8) harvest_reason real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year real(r8) crmcorn ! comparitive relative maturity for corn @@ -1787,6 +1788,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & bgtr(p) = 0._r8 lgsf(p) = 0._r8 + ! Should never be saved as zero, but including this so it's initialized just in case + harvest_reason = 0._r8 + ! --------------------------------- ! from AgroIBIS subroutine planting ! --------------------------------- @@ -1808,6 +1812,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8 crop_inst%gddaccum_thisyr(p,s) = -1._r8 crop_inst%hui_thisyr(p,s) = -1._r8 + crop_inst%harvest_reason_thisyr(p,s) = -1._r8 end do end if @@ -2080,6 +2085,15 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) + + ! Save harvest reason + if (hui(p) >= gddmaturity(p)) then + harvest_reason = 1._r8 + else if (idpp >= mxmat(ivt(p))) then + harvest_reason = 2._r8 + end if + crop_inst%harvest_reason_thisyr(p, harvest_count(p)) = harvest_reason + cnveg_state_inst%gddmaturity_thisyr(p,harvest_count(p)) = gddmaturity(p) croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = 4._r8 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 6a3774c058..50bd7d6d0c 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -44,6 +44,7 @@ module CropType real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year + real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch @@ -210,6 +211,7 @@ subroutine InitAllocate(this, bounds) allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval allocate(this%hui_thisyr(begp:endp,1:mxharvests)) ; this%hui_thisyr(:,:) = spval + allocate(this%harvest_reason_thisyr(begp:endp,1:mxharvests)) ; this%harvest_reason_thisyr(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 @@ -285,6 +287,11 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='At-harvest accumulated heat unit index for crop; should only be output annually', & ptr_patch=this%hui_thisyr, default='inactive') + this%harvest_reason_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='unitless', type2d='mxharvests', & + avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & + ptr_patch=this%harvest_reason_thisyr, default='inactive') + end subroutine InitHistory subroutine InitCold(this, bounds) @@ -575,6 +582,11 @@ subroutine Restart(this, bounds, ncid, flag) long_name='accumulated heat unit index at harvest for this patch this year', units='ddays', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%hui_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='harvest_reason_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='reason for each harvest for this patch this year', units='unitless', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%harvest_reason_thisyr) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp From 775c248dde24467a6a41c64c49736841e7a4898f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 8 Apr 2022 17:22:06 -0600 Subject: [PATCH 0199/2067] GDD-forced runs now ignore CLM's mxmat; will harvest the day before next sowing if needed. --- src/biogeochem/CNPhenologyMod.F90 | 32 +++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 04d1ccba68..be34ac7957 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1707,6 +1707,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer h ! hemisphere indices integer s ! growing season indices integer idpp ! number of days past planting + integer mxmat ! maximum growing season length real(r8) harvest_reason real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year @@ -1720,6 +1721,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical force_harvest ! Should we harvest today no matter what? logical fake_harvest ! Dealing with incorrect Dec. 31 planting logical sown_today ! Was the crop sown today? + logical is_day_before_next_sowing ! Is tomorrow a prescribed sowing day? !------------------------------------------------------------------------ associate( & @@ -1728,7 +1730,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & leaf_long => pftcon%leaf_long , & ! Input: leaf longevity (yrs) leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) manunitro => pftcon%manunitro , & ! Input: max manure to be applied in total (kgN/m2) - mxmat => pftcon%mxmat , & ! Input: minplanttemp => pftcon%minplanttemp , & ! Input: planttemp => pftcon%planttemp , & ! Input: gddmin => pftcon%gddmin , & ! Input: @@ -2097,6 +2098,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sown_today = crop_inst%sdates_thisyr(p,s) == real(jday, r8) end if + ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. + mxmat = pftcon%mxmat(ivt(p)) + if (use_cropcal_streams .and. .not. generate_crop_gdds) then + mxmat = 999 + end if + if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! Crop was incorrectly planted in last time step of Dec. 31. do_harvest = .true. @@ -2160,17 +2167,34 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .false. else ! Original harvest rule - do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p)) + do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat + + ! Always harvest the day before the next prescribed sowing, if still alive. + ! WARNING: This implementation assumes that sowing dates don't change over time! + ! In order to avoid this, you'd have to read this year's AND next year's prescribed + ! sowing dates. + ! WARNING: This implementation assumes that all patches use prescribed sowing dates. + if (use_cropcal_streams) then + is_day_before_next_sowing = (jday == next_rx_sdate(p) - 1) .or. \ + (crop_inst%sdates_thisyr(p,1) == 1 .and. \ + jday == dayspyr) + else + is_day_before_next_sowing = .false. + end if + do_harvest = do_harvest .or. is_day_before_next_sowing if (hui(p) >= gddmaturity(p)) then harvest_reason = 1._r8 - else if (idpp >= mxmat(ivt(p))) then + else if (idpp >= mxmat) then harvest_reason = 2._r8 + else if (is_day_before_next_sowing) then + harvest_reason = 5._r8 + force_harvest = .true. end if endif force_harvest = force_harvest .or. (generate_crop_gdds .and. do_harvest) - if ((.not. force_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat(ivt(p))) then + if ((.not. force_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then cphase(p) = 2._r8 if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 From 7191233c7b46917ee0ce0f40fdce2cae8d83b8e5 Mon Sep 17 00:00:00 2001 From: cenlinhe Date: Sun, 10 Apr 2022 20:31:03 -0600 Subject: [PATCH 0200/2067] bug fix for albsni_hst2 --- src/biogeophys/SurfaceAlbedoMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index 6aff5dada4..d7c3305710 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -1099,7 +1099,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albgri_dst_hst(c,ib) = albgri_dst(c,ib) if (h2osno_total(c) > 0._r8) then albsnd_hst2(c,ib) = albsnd_hst(c,ib) - albsni_hst2(c,ib) = albsnd_hst(c,ib) + albsni_hst2(c,ib) = albsni_hst(c,ib) end if end if end do From e9b0da3acf3463523ed6a3af3be164060aa56275 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Apr 2022 11:06:23 -0600 Subject: [PATCH 0201/2067] Invalid rx sowing date and GDD targets now use CFT defaults. --- src/biogeochem/CNPhenologyMod.F90 | 19 +++--------------- src/cpl/share_esmf/cropcalStreamMod.F90 | 26 +++++++++---------------- 2 files changed, 12 insertions(+), 33 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c64c9eea04..b58205d23d 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1850,16 +1850,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_plant_prescribed = next_rx_sdate(p) == jday - if (generate_crop_gdds) then - if (s==0 .and. next_rx_sdate(p)<=0) then - write(iulog,"(A,I4)") 'If using generate_crop_gdds, all simulated patches must have rx sdate. next_rx_sdate(p) <=0. PFT ',ivt(p) - call endrun(msg=errMsg(sourcefile, __LINE__)) - else if (s==0 .and. crop_inst%rx_sdates_thisyr(p,1)<=0) then - write(iulog,"(A,I4)") 'If using generate_crop_gdds, all simulated patches must have rx sdate. rx_sdates_thisyr(p,1) <=0. PFT ',ivt(p) - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - end if - ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) ! When resuming from a run with old code, may need to manually set these. ! Will be needed until we can rely on all restart files have been generated @@ -2115,7 +2105,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .true. force_harvest = .true. harvest_reason = 4._r8 - else if (generate_crop_gdds) then + else if (generate_crop_gdds .and. crop_inst%sdates_thisyr(p,1) .gt. 0) then if (.not. use_cropcal_streams) then write(iulog,*) 'If using generate_crop_gdds, you must set use_cropcal_streams to true.' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2146,13 +2136,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .false. ! ... unless first sowing next year happens Jan. 1. - if (s < 1) then - write(iulog,*) 'next_rx_sdate(p) < 0 but no sowings happened this year' - call endrun(msg=errMsg(sourcefile, __LINE__)) ! WARNING: This implementation assumes that sowing dates don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed ! sowing dates. - else if (crop_inst%sdates_thisyr(p,1) == 1) then + if (crop_inst%sdates_thisyr(p,1) == 1) then do_harvest = jday == dayspyr end if @@ -2511,7 +2498,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target - if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds)) then + if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .gt. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 6573e676e5..f81510e84d 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -35,7 +35,6 @@ module cropcalStreamMod character(len=CS), allocatable :: stream_varnames_sdate(:) character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:) integer :: ncft ! Number of crop functional types (excl. generic crops) - logical :: warned_about_bad_interp_sdate, warned_about_bad_interp_cultivar_gdds character(len=*), parameter :: sourcefile = & __FILE__ @@ -193,9 +192,6 @@ subroutine cropcal_init(bounds) end if end if - warned_about_bad_interp_sdate = .false. - warned_about_bad_interp_cultivar_gdds = .false. - end subroutine cropcal_init !================================================================ @@ -307,10 +303,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! So an explicit loop is required here do g = 1,lsize - ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if ((.not. warned_about_bad_interp_sdate) .and. (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365)) then - write(iulog,'(a,i0,a,i0,a)') 'WARNING: cropcal_interp(): Crop ivt ',ivt,' (and maybe others) has dataptr1d prescribed sowing date ',dataptr1d_sdate(g),'. Bad interpolation?' - warned_about_bad_interp_sdate = .true. + ! If read-in value is invalid, allow_unprescribed_planting in CropPhenology() + if (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365) then + dataptr1d_sdate(g) = -1 end if dataptr2d_sdate(g,n) = dataptr1d_sdate(g) @@ -330,7 +325,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) ! Sanity check: Should only read in valid values - if (crop_inst%rx_sdates_thisyr(p,1) <= 0 .or. crop_inst%rx_sdates_thisyr(p,1) > 365) then + if (crop_inst%rx_sdates_thisyr(p,1) > 365) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',crop_inst%rx_sdates_thisyr(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -359,10 +354,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! So an explicit loop is required here do g = 1,lsize - ! Warn about possible bad interpolation. Not a problem unless it actually gets assigned to a patch. - if ((.not. warned_about_bad_interp_cultivar_gdds) .and. (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0)) then - write(iulog,'(a,i0,a,f0.0,a)') 'WARNING: cropcal_interp(): Crop n ',n,' (and maybe others) has dataptr1d prescribed GDD requirement ',dataptr1d_cultivar_gdds(g),'. Bad interpolation?' - warned_about_bad_interp_cultivar_gdds = .true. + ! If read-in value is invalid, have PlantCrop() set gddmaturity to PFT-default value. + if (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0) then + dataptr1d_cultivar_gdds(g) = -1 end if dataptr2d_cultivar_gdds(g,n) = dataptr1d_cultivar_gdds(g) @@ -398,12 +392,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) - ! Sanity check: Should not read in negative values. Also try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then + ! Sanity check: Try to catch uninitialized values + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) - else if (crop_inst%rx_cultivar_gdds_thisyr(p,1) < -0.001) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) NEGATIVE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) else write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) end if From 9f6d85b98e74d5c0a0e6082447bb9f17d7595fd9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 26 Apr 2022 16:19:27 -0600 Subject: [PATCH 0202/2067] Disallow gddmaturity==0 for non-rx runs too. --- src/biogeochem/CNPhenologyMod.F90 | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b58205d23d..3a7d683c4a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2531,6 +2531,13 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ivt(p) == nrice .or. ivt(p) == nirrig_rice) then gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if + + ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator + ! Just manually set a minimum of 1.0 + if (gddmaturity(p) < min_crop_gdd_target) then + write(iulog,*) 'Some patch with ivt ',ivt(p),' has calculated gddmaturity ',gddmaturity(p),'; using min_crop_gdd_target instead (',min_crop_gdd_target,')' + endif + gddmaturity(p) = max(gddmaturity(p), min_crop_gdd_target) endif ! write (iulog,'(a,i4,a,f0.0)') 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) From f99106ea323857fe6b193559e58908450bc95f02 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 28 Apr 2022 14:07:24 +0200 Subject: [PATCH 0203/2067] fix stream memory leak and restart from old files --- src/biogeophys/WaterStateType.F90 | 22 ++++++------ src/cpl/share_esmf/ExcessIceStreamType.F90 | 39 +++++++++++++++++++++- 2 files changed, 50 insertions(+), 11 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index cdbd232004..ab7517847e 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -353,6 +353,7 @@ subroutine InitCold(this, bounds, & integer :: c,j,l,nlevs,g integer :: nbedrock real(r8) :: ratio + real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(h2osno_input_col) == (/bounds%endc/)) , sourcefile, __LINE__) @@ -562,7 +563,7 @@ subroutine InitCold(this, bounds, & this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column - + call this%exicestream%CalcExcessIce(bounds, exice_bulk_init) do c = bounds%begc,bounds%endc g = col%gridcell(c) l = col%landunit(c) @@ -573,19 +574,20 @@ subroutine InitCold(this, bounds, & else nbedrock = nlevsoi endif - do j = 2, nlevmaxurbgrnd ! ignore first layer - if (j Date: Fri, 29 Apr 2022 13:29:22 +0200 Subject: [PATCH 0204/2067] excess ice restart from old files --- src/biogeophys/WaterStateBulkType.F90 | 18 ++++-- src/biogeophys/WaterStateType.F90 | 86 +++++++++++++++++++++++++-- src/biogeophys/WaterType.F90 | 26 ++++++-- src/main/clm_instMod.F90 | 15 +++-- 4 files changed, 123 insertions(+), 22 deletions(-) diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index 18b9f34e3e..b317a4d32c 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -188,7 +188,7 @@ end subroutine InitBulkCold !------------------------------------------------------------------------ subroutine RestartBulk(this, bounds, ncid, flag, & - watsat_col) + watsat_col, NLFilename, t_soisno_col) ! ! !DESCRIPTION: ! Read/Write module information to/from restart file. @@ -196,6 +196,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, & ! !USES: use ncdio_pio , only : file_desc_t, ncd_double use restUtilMod + use controlMod , only : use_excess_ice ! ! !ARGUMENTS: class(waterstatebulk_type), intent(in) :: this @@ -203,6 +204,8 @@ subroutine RestartBulk(this, bounds, ncid, flag, & type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + character(len=*) , intent(in), optional :: NLFilename ! Namelist filename + real(r8) , intent(in), optional :: t_soisno_col(bounds%begc:bounds%endc,:) ! Soil column temperature (Kelvin) ! ! !LOCAL VARIABLES: integer :: c,l,j @@ -210,10 +213,15 @@ subroutine RestartBulk(this, bounds, ncid, flag, & !------------------------------------------------------------------------ SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) - - call this%restart (bounds, ncid, flag=flag, & - watsat_col=watsat_col(bounds%begc:bounds%endc,:)) - + if(use_excess_ice .and. flag == 'read') then + call this%restart (bounds, ncid, flag=flag, & + watsat_col=watsat_col(bounds%begc:bounds%endc,:), & + NLFilename= NLFilename, & + t_soisno_col=t_soisno_col(bounds%begc:bounds%endc,:)) + else + call this%restart (bounds, ncid, flag=flag, & + watsat_col=watsat_col(bounds%begc:bounds%endc,:)) + endif call restartvar(ncid=ncid, flag=flag, & varname=this%info%fname('INT_SNOW'), & diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index ab7517847e..7fde8cedaf 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -353,7 +353,7 @@ subroutine InitCold(this, bounds, & integer :: c,j,l,nlevs,g integer :: nbedrock real(r8) :: ratio - real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) + real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) ! initial excess ice amount (m/m) !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(h2osno_input_col) == (/bounds%endc/)) , sourcefile, __LINE__) @@ -603,15 +603,16 @@ end subroutine InitCold !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag, & - watsat_col) + watsat_col, NLFilename, t_soisno_col) ! ! !DESCRIPTION: ! Read/Write module information to/from restart file. ! ! !USES: - use clm_varcon , only : denice, denh2o, pondmx, watmin - use landunit_varcon , only : istcrop, istdlak, istsoil + use clm_varcon , only : denice, denh2o, pondmx, watmin, tfrz + use landunit_varcon , only : istcrop, istdlak, istsoil, istice use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall + use column_varcon , only : icol_road_imperv, icol_road_perv use clm_time_manager , only : is_first_step, is_restart use clm_varctl , only : bound_h2osoi use ncdio_pio , only : file_desc_t, ncd_double @@ -623,16 +624,28 @@ subroutine Restart(this, bounds, ncid, flag, & type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + character(len=*) , intent(in), optional :: NLFilename ! Namelist filename + real(r8) , intent(in), optional :: t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! Soil column temperature (Kelvin) ! ! !LOCAL VARIABLES: - integer :: p,c,l,j,nlevs + integer :: p,c,l,j,nlevs,g + integer :: nbedrock logical :: readvar real(r8) :: maxwatsat ! maximum porosity real(r8) :: excess ! excess volumetric soil water real(r8) :: totwat ! total soil water (mm) + character(len=256) :: l_NLFilename !local namelist filename var + real(r8) :: l_t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !local soil column temperature (Kelvin) + real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) !Initial excess ice ammout (m/m) !------------------------------------------------------------------------ - + l_NLFilename = '' + l_t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) = tfrz + 1.0_r8 + if (present(NLFilename)) then + l_NLFilename = NLFilename + l_t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) = t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) + end if SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(t_soisno_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) call restartvar(ncid=ncid, flag=flag, & varname=this%info%fname('H2OSFC'), & @@ -730,7 +743,68 @@ subroutine Restart(this, bounds, ncid, flag, & this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 + else if (use_excess_ice .and. flag == 'read') then + ! try to read the first variable + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & + dim1name='column', dim2name='levtot', switchdim=.true., & + long_name=this%info%lname('excess soil ice (vegetated landunits only)'), units='kg/m2', & + scale_by_thickness=.true., & + interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) + if (.not. readvar) then + ! did not read the first variable + this%init_exice(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 + this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 + call this%exicestream%Init(bounds, l_NLFilename) ! get initial fraction of excess ice per column + call this%exicestream%CalcExcessIce(bounds, exice_bulk_init) + do c = bounds%begc,bounds%endc + g = col%gridcell(c) + l = col%landunit(c) + if (.not. lun%lakpoi(l)) then !not lake + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + if (use_bedrock) then + nbedrock = col%nbedrock(c) + else + nbedrock = nlevsoi + endif + do j = 2, nlevmaxurbgrnd ! ignore first layer + if (j Date: Fri, 29 Apr 2022 15:02:30 +0200 Subject: [PATCH 0205/2067] Revert "excess ice restart from old files" This reverts commit 54ccc3b7be5de6db765691b63b77f74b1673c199. --- src/biogeophys/WaterStateBulkType.F90 | 18 ++---- src/biogeophys/WaterStateType.F90 | 86 ++------------------------- src/biogeophys/WaterType.F90 | 26 ++------ src/main/clm_instMod.F90 | 15 ++--- 4 files changed, 22 insertions(+), 123 deletions(-) diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index b317a4d32c..18b9f34e3e 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -188,7 +188,7 @@ end subroutine InitBulkCold !------------------------------------------------------------------------ subroutine RestartBulk(this, bounds, ncid, flag, & - watsat_col, NLFilename, t_soisno_col) + watsat_col) ! ! !DESCRIPTION: ! Read/Write module information to/from restart file. @@ -196,7 +196,6 @@ subroutine RestartBulk(this, bounds, ncid, flag, & ! !USES: use ncdio_pio , only : file_desc_t, ncd_double use restUtilMod - use controlMod , only : use_excess_ice ! ! !ARGUMENTS: class(waterstatebulk_type), intent(in) :: this @@ -204,8 +203,6 @@ subroutine RestartBulk(this, bounds, ncid, flag, & type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) - character(len=*) , intent(in), optional :: NLFilename ! Namelist filename - real(r8) , intent(in), optional :: t_soisno_col(bounds%begc:bounds%endc,:) ! Soil column temperature (Kelvin) ! ! !LOCAL VARIABLES: integer :: c,l,j @@ -213,15 +210,10 @@ subroutine RestartBulk(this, bounds, ncid, flag, & !------------------------------------------------------------------------ SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) - if(use_excess_ice .and. flag == 'read') then - call this%restart (bounds, ncid, flag=flag, & - watsat_col=watsat_col(bounds%begc:bounds%endc,:), & - NLFilename= NLFilename, & - t_soisno_col=t_soisno_col(bounds%begc:bounds%endc,:)) - else - call this%restart (bounds, ncid, flag=flag, & - watsat_col=watsat_col(bounds%begc:bounds%endc,:)) - endif + + call this%restart (bounds, ncid, flag=flag, & + watsat_col=watsat_col(bounds%begc:bounds%endc,:)) + call restartvar(ncid=ncid, flag=flag, & varname=this%info%fname('INT_SNOW'), & diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 7fde8cedaf..ab7517847e 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -353,7 +353,7 @@ subroutine InitCold(this, bounds, & integer :: c,j,l,nlevs,g integer :: nbedrock real(r8) :: ratio - real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) ! initial excess ice amount (m/m) + real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(h2osno_input_col) == (/bounds%endc/)) , sourcefile, __LINE__) @@ -603,16 +603,15 @@ end subroutine InitCold !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag, & - watsat_col, NLFilename, t_soisno_col) + watsat_col) ! ! !DESCRIPTION: ! Read/Write module information to/from restart file. ! ! !USES: - use clm_varcon , only : denice, denh2o, pondmx, watmin, tfrz - use landunit_varcon , only : istcrop, istdlak, istsoil, istice + use clm_varcon , only : denice, denh2o, pondmx, watmin + use landunit_varcon , only : istcrop, istdlak, istsoil use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall - use column_varcon , only : icol_road_imperv, icol_road_perv use clm_time_manager , only : is_first_step, is_restart use clm_varctl , only : bound_h2osoi use ncdio_pio , only : file_desc_t, ncd_double @@ -624,28 +623,16 @@ subroutine Restart(this, bounds, ncid, flag, & type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) - character(len=*) , intent(in), optional :: NLFilename ! Namelist filename - real(r8) , intent(in), optional :: t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! Soil column temperature (Kelvin) ! ! !LOCAL VARIABLES: - integer :: p,c,l,j,nlevs,g - integer :: nbedrock + integer :: p,c,l,j,nlevs logical :: readvar real(r8) :: maxwatsat ! maximum porosity real(r8) :: excess ! excess volumetric soil water real(r8) :: totwat ! total soil water (mm) - character(len=256) :: l_NLFilename !local namelist filename var - real(r8) :: l_t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !local soil column temperature (Kelvin) - real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) !Initial excess ice ammout (m/m) !------------------------------------------------------------------------ - l_NLFilename = '' - l_t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) = tfrz + 1.0_r8 - if (present(NLFilename)) then - l_NLFilename = NLFilename - l_t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) = t_soisno_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) - end if + SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(t_soisno_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) call restartvar(ncid=ncid, flag=flag, & varname=this%info%fname('H2OSFC'), & @@ -743,68 +730,7 @@ subroutine Restart(this, bounds, ncid, flag, & this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 - else if (use_excess_ice .and. flag == 'read') then - ! try to read the first variable - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & - dim1name='column', dim2name='levtot', switchdim=.true., & - long_name=this%info%lname('excess soil ice (vegetated landunits only)'), units='kg/m2', & - scale_by_thickness=.true., & - interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) - if (.not. readvar) then - ! did not read the first variable - this%init_exice(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 - call this%exicestream%Init(bounds, l_NLFilename) ! get initial fraction of excess ice per column - call this%exicestream%CalcExcessIce(bounds, exice_bulk_init) - do c = bounds%begc,bounds%endc - g = col%gridcell(c) - l = col%landunit(c) - if (.not. lun%lakpoi(l)) then !not lake - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (use_bedrock) then - nbedrock = col%nbedrock(c) - else - nbedrock = nlevsoi - endif - do j = 2, nlevmaxurbgrnd ! ignore first layer - if (j Date: Tue, 3 May 2022 08:41:52 -0600 Subject: [PATCH 0206/2067] Add another gddmaturity(p) = min_crop_gdd_target --- src/biogeochem/CNPhenologyMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 3a7d683c4a..33d22f48f5 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2498,6 +2498,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target + gddmaturity(p) = min_crop_gdd_target if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .gt. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) From a57a7b39175823ea0dd7d6afe597cc79c67dd1bc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 3 May 2022 08:55:50 -0600 Subject: [PATCH 0207/2067] Added an explicit error message for a check of gddmaturity==0. --- src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 7869892cc0..bcb14b891a 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -1344,6 +1344,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! SSR troubleshooting if (gddmaturity(p) == 0.0) then + write(iulog,*) 'gddmaturity(p) == 0.0' call endrun(msg=errMsg(sourcefile, __LINE__)) end if From 6f44dd4340d7689e276d2888edc09054a914eca1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 3 May 2022 09:17:09 -0600 Subject: [PATCH 0208/2067] Added some more checks for divide-by-zero. --- .../NutrientCompetitionFlexibleCNMod.F90 | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index bcb14b891a..77868ae4ae 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -1313,6 +1313,15 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! SSR troubleshooting if (gddmaturity(p) == 0.0) then + write(iulog,*) 'gddmaturity(p) == 0.0' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + if (hui(p) == 0.0) then + write(iulog,*) 'hui(p) == 0.0' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + if (huigrain(p) == 0.0) then + write(iulog,*) 'huigrain(p) == 0.0' call endrun(msg=errMsg(sourcefile, __LINE__)) end if @@ -1347,6 +1356,24 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & write(iulog,*) 'gddmaturity(p) == 0.0' call endrun(msg=errMsg(sourcefile, __LINE__)) end if + if (((gddmaturity(p)*declfact(ivt(p)))-huigrain(p)) == 0.0) then + write(iulog,*) '((gddmaturity(p)*declfact(ivt(p)))-huigrain(p)) == 0.0' + write(iulog,*) 'gddmaturity(p) = ',gddmaturity(p) + write(iulog,*) 'declfact(ivt(p)) = ',declfact(ivt(p)) + write(iulog,*) 'huigrain(p) = ',huigrain(p) + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if + if (allconss(ivt(p)) .lt. 0.0 .and. min((hui(p)- & + huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & + huigrain(p)),1._r8) == 0.0) then + write(iulog,*) 'Raising 0 to negative exponent' + write(iulog,*) 'hui(p) = ',hui(p) + write(iulog,*) 'huigrain(p) = ',huigrain(p) + write(iulog,*) 'hui(p) = ',hui(p) + write(iulog,*) 'gddmaturity(p) = ',gddmaturity(p) + write(iulog,*) 'declfact(ivt(p)) = ',declfact(ivt(p)) + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) From c31821b640ed1cbd13cb15409886b08c09ea8bc1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 3 May 2022 09:40:34 -0600 Subject: [PATCH 0209/2067] Removed a bad zero-check. --- src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 77868ae4ae..4188ab90f4 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -1316,10 +1316,6 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & write(iulog,*) 'gddmaturity(p) == 0.0' call endrun(msg=errMsg(sourcefile, __LINE__)) end if - if (hui(p) == 0.0) then - write(iulog,*) 'hui(p) == 0.0' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if if (huigrain(p) == 0.0) then write(iulog,*) 'huigrain(p) == 0.0' call endrun(msg=errMsg(sourcefile, __LINE__)) From 0ac07b96234d3528d6bb64e70258e0f30f03b7c2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 15 May 2022 11:07:09 -0600 Subject: [PATCH 0210/2067] CropType member rx_cultivar_gdds_thisyr now real instead of int. --- src/biogeochem/CropType.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index bfdb1bb21e..4775176e5d 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -40,7 +40,7 @@ module CropType real(r8) :: baset_latvary_slope integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year - integer , pointer :: rx_cultivar_gdds_thisyr (:,:) ! all cultivar GDD targets for this patch this year + real(r8), pointer :: rx_cultivar_gdds_thisyr (:,:) ! all cultivar GDD targets for this patch this year real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year @@ -215,7 +215,7 @@ subroutine InitAllocate(this, bounds) allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 allocate(this%rx_sdates_thisyr(begp:endp,1:mxsowings)) ; this%rx_sdates_thisyr(:,:) = -1 - allocate(this%rx_cultivar_gdds_thisyr(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr(:,:) = -1 + allocate(this%rx_cultivar_gdds_thisyr(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr(:,:) = spval allocate(this%sdates_thisyr(begp:endp,1:mxsowings)) ; this%sdates_thisyr(:,:) = spval allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval @@ -225,7 +225,7 @@ subroutine InitAllocate(this, bounds) allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 this%rx_sdates_thisyr(:,:) = -1 - this%rx_cultivar_gdds_thisyr(:,:) = -1 + this%rx_cultivar_gdds_thisyr(:,:) = spval end subroutine InitAllocate From 893448a71871c6ec274c2815b72aca4a2d65f25e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 15 May 2022 11:09:03 -0600 Subject: [PATCH 0211/2067] Replaced some 0.0s with 0._r8s. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index f81510e84d..247de9cb84 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -355,7 +355,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do g = 1,lsize ! If read-in value is invalid, have PlantCrop() set gddmaturity to PFT-default value. - if (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000.0) then + if (dataptr1d_cultivar_gdds(g) < 0 .or. dataptr1d_cultivar_gdds(g) > 1000000._r8) then dataptr1d_cultivar_gdds(g) = -1 end if @@ -393,8 +393,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) ! Sanity check: Try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000.0) then - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0.0) then + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0._r8 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000._r8) then + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0._r8) then write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) else write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) From 88d301f499febf79f9545bced93b93d0f476cedd Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Mon, 16 May 2022 12:16:13 +0200 Subject: [PATCH 0212/2067] excess calc. and melt in soiltemperaturemod --- src/biogeophys/SoilTemperatureMod.F90 | 108 ++++++++++++++++++++---- src/biogeophys/TotalWaterAndHeatMod.F90 | 5 +- 2 files changed, 96 insertions(+), 17 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index ba4432cba2..f96fee7558 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -115,7 +115,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd use clm_varctl , only : iulog - use clm_varcon , only : cnfac, cpice, cpliq, denh2o + use clm_varcon , only : cnfac, cpice, cpliq, denh2o, denice use landunit_varcon , only : istsoil, istcrop use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv use BandDiagonalMod , only : BandDiagonal @@ -171,6 +171,10 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter real(r8) :: hs_top_snow(bounds%begc:bounds%endc) ! heat flux on top snow layer [W/m2] real(r8) :: hs_h2osfc(bounds%begc:bounds%endc) ! heat flux on standing water [W/m2] integer :: jbot(bounds%begc:bounds%endc) ! bottom level at each column + real(r8) :: dz_0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! original layer thickness [m] + real(r8) :: z_0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) ! original layer depth [m] + real(r8) :: zi_0(bounds%begc:bounds%endc,-nlevsno+0:nlevmaxurbgrnd) ! original layer interface level bellow layer "z" [m] + !----------------------------------------------------------------------- associate( & @@ -194,6 +198,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter frac_sno_eff => waterdiagnosticbulk_inst%frac_sno_eff_col , & ! Input: [real(r8) (:) ] eff. fraction of ground covered by snow (0 to 1) snow_depth => waterdiagnosticbulk_inst%snow_depth_col , & ! Input: [real(r8) (:) ] snow height (m) h2osfc => waterstatebulk_inst%h2osfc_col , & ! Input: [real(r8) (:) ] surface water (mm) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col , & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) @@ -271,6 +276,29 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter endif end do + + !-------------------------------------------------------------- + ! Vertical coordinates adjustment for excess ice calculations + !-------------------------------------------------------------- + ! Save original soil depth to get put them back in et the end + dz_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=dz(begc:endc,-nlevsno+1:nlevmaxurbgrnd) + zi_0(begc:endc,-nlevsno+0:nlevmaxurbgrnd)=zi(begc:endc,-nlevsno+0:nlevmaxurbgrnd) + z_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=z(begc:endc,-nlevsno+1:nlevmaxurbgrnd) + ! Adjust column depth for excess ice thickness + do fc = 1,num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness + do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment + zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice + z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 + end do + endif + end do + + + !------------------------------------------------------ ! Compute ground surface and soil temperatures !------------------------------------------------------ @@ -488,6 +516,23 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter dhsdT(bounds%begc:bounds%endc), & soilstate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, waterfluxbulk_inst, energyflux_inst, temperature_inst) + !-------------------------------------------------------------- + ! Vertical coordinates adjustment for excess ice calculations + !-------------------------------------------------------------- + ! bringing back the soil depth to the original state + ! Adjust column depth for excess ice thickness + do fc = 1,num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) + zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) + z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) + endif + end do + + + if ( IsProgBuildTemp() )then call BuildingTemperature(bounds, num_urbanl, filter_urbanl, num_nolakec, filter_nolakec, & tk(bounds%begc:bounds%endc, :), urbanparams_inst, & @@ -628,6 +673,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Input: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) bw => waterdiagnosticbulk_inst%bw_col , & ! Output: [real(r8) (:,:) ] partial density of water in the snow pack (ice + liquid) [kg/m3] tkmg => soilstate_inst%tkmg_col , & ! Input: [real(r8) (:,:) ] thermal conductivity, soil minerals [W/m-K] @@ -654,7 +700,8 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) + ! TODO recalculate watsat and satw to have excess ice included + satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice +excess_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) satw = min(1._r8, satw) if (satw > .1e-6_r8) then if (t_soisno(c,j) >= tfrz) then ! Unfrozen soil @@ -663,7 +710,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter dke = satw end if fl = (h2osoi_liq(c,j)/(denh2o*dz(c,j))) / (h2osoi_liq(c,j)/(denh2o*dz(c,j)) + & - h2osoi_ice(c,j)/(denice*dz(c,j))) + h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/denice) dksat = tkmg(c,j)*tkwat**(fl*watsat(c,j))*tkice**((1._r8-fl)*watsat(c,j)) thk(c,j) = dke*dksat + (1._r8-dke)*tkdry(c,j) else @@ -756,7 +803,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter .and. col%itype(c) /= icol_sunwall .and. col%itype(c) /= icol_shadewall .and. & col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) + cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) + excess_ice(c,j)*cpice if (j > nbedrock(c)) cv(c,j) = csol_bedrock*dz(c,j) else if (lun%itype(l) == istwet) then cv(c,j) = (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) @@ -1057,7 +1104,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd use clm_varctl , only : iulog - use clm_varcon , only : tfrz, hfus, grav + use clm_varcon , only : tfrz, hfus, grav, denice use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv use landunit_varcon , only : istsoil, istcrop, istice ! @@ -1088,6 +1135,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: propor !proportionality constant (-) real(r8) :: tinc(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !t(n+1)-t(n) [K] real(r8) :: smp !frozen water potential (mm) + real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] + real(r8) :: xm3(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] + real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd)!initial mass of excess_ice at the timestep (kg/m2) + + !----------------------------------------------------------------------- call t_startf( 'PhaseChangebeta' ) @@ -1109,6 +1161,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Output: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) + init_exice => waterstatebulk_inst%init_exice , & ! Input: [real(r8) (:) ] excess soil ice initial + exice_melt => waterstatebulk_inst%exice_melt , & ! Input: [real(r8) (:) ] excess soil ice + exice_melt_lev => waterstatebulk_inst%exice_melt_lev , & ! Input: [real(r8) (:,:) ] excess soil ice + qflx_snow_drain => waterfluxbulk_inst%qflx_snow_drain_col , & ! Output: [real(r8) (:) ] drainage from snow pack qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] @@ -1152,9 +1209,12 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & imelt(c,j) = 0 hm(c,j) = 0._r8 xm(c,j) = 0._r8 + xm2(c,j)=0._r8 + xm3(c,j)=0._r8 wice0(c,j) = h2osoi_ice(c,j) wliq0(c,j) = h2osoi_liq(c,j) - wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) + wexice0(c,j)=excess_ice(c,j) + wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) + wexice0(c,j) endif ! end of snow layer if-block if (j <= 0) then @@ -1211,6 +1271,13 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & t_soisno(c,j) = tfrz endif + ! melt excess ice after normal ice + if (excess_ice(c,j) > 0._r8 .AND. t_soisno(c,j) > tfrz) then + imelt(c,j) = 1 + tinc(c,j) = tfrz - t_soisno(c,j) + t_soisno(c,j) = tfrz + endif + ! from Zhao (1997) and Koren (1999) supercool(c,j) = 0.0_r8 if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop .or. col%itype(c) == icol_road_perv) then @@ -1325,23 +1392,30 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif heatr = 0._r8 - if (xm(c,j) > 0._r8) then - h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) - heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + if (xm(c,j) > 0._r8) then !if there is excess heat to melt the ice + h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) + heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) !excess ice modifications + if (h2osoi_ice(c,j) == 0._r8) then ! this might be redundant + if (excess_ice(c,j) >= 0._r8 .and. xm2(c,j)>0._r8 .and. j>=2) then ! if there is excess ice to melt + excess_ice(c,j) = max(0._r8,wexice0(c,j) - xm2(c,j)) + heatr = hm(c,j) - hfus * (wexice0(c,j)-excess_ice(c,j)+wice0(c,j)-h2osoi_ice(c,j)) / dtime + endif + endif !end of excess ice block else if (xm(c,j) < 0._r8) then if (j <= 0) then h2osoi_ice(c,j) = min(wmass0(c,j), wice0(c,j)-xm(c,j)) ! snow else - if (wmass0(c,j) < supercool(c,j)) then + if (wmass0(c,j) - wexice0(c,j) < supercool(c,j)) then !even if excess ice is present, it cannot refreeze h2osoi_ice(c,j) = 0._r8 else - h2osoi_ice(c,j) = min(wmass0(c,j) - supercool(c,j),wice0(c,j)-xm(c,j)) + h2osoi_ice(c,j) = min(wmass0(c,j) - wexice0(c,j) - supercool(c,j),wice0(c,j)-xm(c,j)) endif endif heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif - h2osoi_liq(c,j) = max(0._r8,wmass0(c,j)-h2osoi_ice(c,j)) + h2osoi_liq(c,j) = max(0._r8,wmass0(c,j)-h2osoi_ice(c,j)-excess_ice(c,j)) !melted exice is added to the respective soil layers if (abs(heatr) > 0._r8) then if (j == snl(c)+1) then @@ -1372,12 +1446,13 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & end if endif ! end of heatr > 0 if-block - if (j >= 1) then - xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + if (j >= 1) then !why before it was two same statements? + xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif - + init_exice(c,j)=wexice0(c,j) + exice_melt_lev(c,j)=wexice0(c,j)-excess_ice(c,j) if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) @@ -1398,16 +1473,19 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & end do ! end of column-loop enddo ! end of level-loop + ! Needed for history file output do fc = 1,num_nolakec c = filter_nolakec(fc) eflx_snomelt(c) = qflx_snomelt(c) * hfus + exice_melt(c) = 0.0_r8 l = col%landunit(c) if (lun%urbpoi(l)) then eflx_snomelt_u(c) = eflx_snomelt(c) else if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then eflx_snomelt_r(c) = eflx_snomelt(c) + exice_melt(c) = exice_melt(c) + SUM( exice_melt_lev(c,:) ) / denice end if end do diff --git a/src/biogeophys/TotalWaterAndHeatMod.F90 b/src/biogeophys/TotalWaterAndHeatMod.F90 index bfeea81949..3f4877d093 100644 --- a/src/biogeophys/TotalWaterAndHeatMod.F90 +++ b/src/biogeophys/TotalWaterAndHeatMod.F90 @@ -358,7 +358,8 @@ subroutine AccumulateSoilLiqIceMassNonLake(bounds, num_c, filter_c, & associate( & h2osoi_ice => waterstate_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) - h2osoi_liq => waterstate_inst%h2osoi_liq_col & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) + h2osoi_liq => waterstate_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) + excess_ice => waterstate_inst%excess_ice_col & ! Input [real(r8) (:,:) ] excess ice (kg/m2) ) do j = 1, nlevmaxurbgrnd @@ -382,7 +383,7 @@ subroutine AccumulateSoilLiqIceMassNonLake(bounds, num_c, filter_c, & if (has_h2o) then liquid_mass(c) = liquid_mass(c) + h2osoi_liq(c,j) - ice_mass(c) = ice_mass(c) + h2osoi_ice(c,j) + ice_mass(c) = ice_mass(c) + h2osoi_ice(c,j) +excess_ice(c,j) end if end do end do From afeb00a772ead5a505ffebf952266ef810d652c8 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Mon, 16 May 2022 12:20:03 +0200 Subject: [PATCH 0213/2067] 0.125x0.125 initial ex. ice concentration stream --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++-- src/cpl/share_esmf/ExcessIceStreamType.F90 | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 775ed81105..54bec90957 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2592,7 +2592,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts .false. -lnd/clm2/paramdata/exice_init_0.9x1.25_c20211102.nc -lnd/clm2/paramdata/finundated_inversiondata_0.9x1_ESMFmesh_cdf5_130621.nc +lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc +lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_c20220516.nc diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index b857b4e214..9bafd61524 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -247,7 +247,7 @@ subroutine ReadNML(this, bounds, NLFilename) integer :: nml_error ! namelist i/o error flag character(len=CL) :: stream_fldFileName_exice = ' ' character(len=CL) :: stream_meshfile_exice = ' ' - character(len=CL) :: exicemapalgo = 'nn' + character(len=CL) :: exicemapalgo = 'bilinear' character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read character(len=*), parameter :: subName = "('exice_streams::ReadNML')" !----------------------------------------------------------------------- From 46e2dad9e62317b03d597cdfb4a6cef7df9f3636 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Tue, 17 May 2022 11:34:08 -0600 Subject: [PATCH 0214/2067] Revert restriction on zeta in FrictionVelocityMod --- src/biogeophys/FrictionVelocityMod.F90 | 28 -------------------------- 1 file changed, 28 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 5d532b1145..82f60f5a2b 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -893,10 +893,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = forc_hgt_u_patch(n)-displa(n) end if zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (zeta(n) < -zetam) then ustar(n) = vkc*um(n)/(log(-zetam*obu(n)/z0m(n))& - this%StabilityFunc1(-zetam) & @@ -996,10 +992,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = forc_hgt_t_patch(n)-displa(n) end if zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (zeta(n) < -zetat) then temp1(n) = vkc/(log(-zetat*obu(n)/z0h(n))& - this%StabilityFunc2(-zetat) & @@ -1024,10 +1016,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & else zldis(n) = forc_hgt_q_patch(pfti(n))-displa(n) zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (zeta(n) < -zetat) then temp2(n) = vkc/(log(-zetat*obu(n)/z0q(n)) & - this%StabilityFunc2(-zetat) & @@ -1050,10 +1038,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & else zldis(n) = forc_hgt_q_patch(n)-displa(n) zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (zeta(n) < -zetat) then temp2(n) = vkc/(log(-zetat*obu(n)/z0q(n)) & - this%StabilityFunc2(-zetat) & @@ -1076,10 +1060,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = 2.0_r8 + z0h(n) zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (zeta(n) < -zetat) then temp12m(n) = vkc/(log(-zetat*obu(n)/z0h(n))& - this%StabilityFunc2(-zetat) & @@ -1103,10 +1083,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & else zldis(n) = 2.0_r8 + z0q(n) zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (zeta(n) < -zetat) then temp22m(n) = vkc/(log(-zetat*obu(n)/z0q(n)) - & this%StabilityFunc2(-zetat) + this%StabilityFunc2(z0q(n)/obu(n)) & @@ -1135,10 +1111,6 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & zldis(n) = forc_hgt_u_patch(n)-displa(n) end if zeta(n) = zldis(n)/obu(n) - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(n) = min(20._r8,zldis(n)/obu(n)) - end if if (min(zeta(n), 1._r8) < 0._r8) then tmp1 = (1._r8 - 16._r8*min(zeta(n),1._r8))**0.25_r8 tmp2 = log((1._r8+tmp1*tmp1)/2._r8) From 626354472c2eaf2ca22b5bf135afda7b9e95d106 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 May 2022 08:17:47 -0600 Subject: [PATCH 0215/2067] Removed unused (and un-deallocated) rbufslp2 from CropUpdateAccVars(). --- src/biogeochem/CropType.F90 | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 4775176e5d..901b085e5a 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -655,7 +655,6 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) integer :: begp, endp integer :: begc, endc real(r8), pointer :: rbufslp(:) ! temporary single level - patch level - real(r8), pointer :: rbufslp2(:) ! temporary single level - patch level character(len=*), parameter :: subname = 'CropUpdateAccVars' !----------------------------------------------------------------------- @@ -676,7 +675,6 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) write(iulog,*)'update_accum_hist allocation error for rbuf1dp' call endrun(msg=errMsg(sourcefile, __LINE__)) endif - allocate(rbufslp2(begp:endp), stat=ier) if (ier/=0) then write(iulog,*)'update_accum_hist allocation error for rbuf1dp (2)' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -713,7 +711,6 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) else rbufslp(p) = accumResetVal end if - rbufslp2(p) = rbufslp(p) end do call update_accum_field ('HUI', rbufslp, nstep) call extract_accum_field ('HUI', this%hui_patch, nstep) From bee1b47365065edd224bbd953894c74b5d32bdfe Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 19 May 2022 16:59:06 +0200 Subject: [PATCH 0216/2067] added exice to the ice fraction in soilhydrology --- src/biogeophys/SoilHydrologyMod.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/SoilHydrologyMod.F90 b/src/biogeophys/SoilHydrologyMod.F90 index 0a62d45c38..8ef690d5b9 100644 --- a/src/biogeophys/SoilHydrologyMod.F90 +++ b/src/biogeophys/SoilHydrologyMod.F90 @@ -179,6 +179,7 @@ subroutine SetSoilWaterFractions(bounds, num_hydrologyc, filter_hydrologyc, & integer :: j, fc, c real(r8) :: vol_ice(bounds%begc:bounds%endc,1:nlevsoi) !partial volume of ice lens in layer real(r8) :: icefrac_orig ! original formulation for icefrac + real(r8) :: dz_ext(bounds%begc:bounds%endc,1:nlevsoi) character(len=*), parameter :: subname = 'SetSoilWaterFractions' !----------------------------------------------------------------------- @@ -191,6 +192,7 @@ subroutine SetSoilWaterFractions(bounds, num_hydrologyc, filter_hydrologyc, & h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice water (kg/m2) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) origflag => soilhydrology_inst%origflag , & ! Input: logical icefrac => soilhydrology_inst%icefrac_col , & ! Output: [real(r8) (:,:) ] @@ -203,7 +205,8 @@ subroutine SetSoilWaterFractions(bounds, num_hydrologyc, filter_hydrologyc, & ! Porosity of soil, partial volume of ice and liquid, fraction of ice in each layer, ! fractional impermeability - vol_ice(c,j) = min(watsat(c,j), h2osoi_ice(c,j)/(dz(c,j)*denice)) + dz_ext(c,j) = dz(c,j) + excess_ice(c,j)/denice ! extended layer thickness, should be good for all the columns + vol_ice(c,j) = min(watsat(c,j), (h2osoi_ice(c,j) + excess_ice(c,j))/(dz_ext(c,j)*denice)) eff_porosity(c,j) = max(0.01_r8,watsat(c,j)-vol_ice(c,j)) icefrac(c,j) = min(1._r8,vol_ice(c,j)/watsat(c,j)) From 0f5f4a5518474906546cc05828787fca6fd0a9e1 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 22 May 2022 19:33:15 +0200 Subject: [PATCH 0217/2067] Rremove extra exice vars --- src/biogeophys/SoilTemperatureMod.F90 | 9 +-- src/biogeophys/WaterStateType.F90 | 83 +++------------------- src/cpl/share_esmf/ExcessIceStreamType.F90 | 2 +- 3 files changed, 13 insertions(+), 81 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index f96fee7558..22042bec3b 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1162,10 +1162,6 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) - init_exice => waterstatebulk_inst%init_exice , & ! Input: [real(r8) (:) ] excess soil ice initial - exice_melt => waterstatebulk_inst%exice_melt , & ! Input: [real(r8) (:) ] excess soil ice - exice_melt_lev => waterstatebulk_inst%exice_melt_lev , & ! Input: [real(r8) (:,:) ] excess soil ice - qflx_snow_drain => waterfluxbulk_inst%qflx_snow_drain_col , & ! Output: [real(r8) (:) ] drainage from snow pack qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] @@ -1451,8 +1447,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif - init_exice(c,j)=wexice0(c,j) - exice_melt_lev(c,j)=wexice0(c,j)-excess_ice(c,j) + ! put exice melt here if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) @@ -1479,13 +1474,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & do fc = 1,num_nolakec c = filter_nolakec(fc) eflx_snomelt(c) = qflx_snomelt(c) * hfus - exice_melt(c) = 0.0_r8 l = col%landunit(c) if (lun%urbpoi(l)) then eflx_snomelt_u(c) = eflx_snomelt(c) else if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then eflx_snomelt_r(c) = eflx_snomelt(c) - exice_melt(c) = exice_melt(c) + SUM( exice_melt_lev(c,:) ) / denice end if end do diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index ab7517847e..513830576d 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -53,9 +53,6 @@ module WaterStateType real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (1:nlevgrnd) - real(r8), pointer :: init_exice (:,:) ! initial value of col excess ice lens/(m/m) (new) (1:nlevgrnd) - real(r8), pointer :: exice_melt_lev (:,:) ! col excess ice melting (m) (new) - real(r8), pointer :: exice_melt (:) ! column-wide excess ice melting (m) (new) type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only @@ -161,22 +158,10 @@ subroutine InitAllocate(this, bounds, tracer_vars) container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) !excess ice vars - call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) - call AllocateVar2d(var = this%init_exice, name = 'init_exice', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) - call AllocateVar2d(var = this%exice_melt_lev, name = 'exice_melt_lev', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) - call AllocateVar1d(var = this%exice_melt, name = 'exice_melt', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column) - + call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column, & + dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) end subroutine InitAllocate !------------------------------------------------------------------------ @@ -294,26 +279,12 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) ptr_col=this%wa_col, l2g_scale_type='veg') end if - ! Add excess ice fields to history - data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) - call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & - avgflag='A', long_name='excess soil ice (vegetated landunits only)', & - ptr_col=this%excess_ice_col, l2g_scale_type='veg') - - data2dptr => this%init_exice(begc:endc,1:nlevsoi) - call hist_addfld2d (fname='EXICE_INIT', units='m/m', type2d='levsoi', & - avgflag='A', long_name='initial excess soil ice (vegetated landunits only)', & - ptr_col=this%excess_ice_col, l2g_scale_type='veg') - - data2dptr => this%exice_melt_lev(begc:endc,1:nlevsoi) - call hist_addfld2d (fname='EXICE_MELT_LEV', units='kg/m2', type2d='levsoi', & - avgflag='A', long_name='melt from excess ice per layer (vegetated landunits only)', & - ptr_col=this%exice_melt_lev, l2g_scale_type='veg') - - this%exice_melt(begc:endc) = spval - call hist_addfld1d (fname='EXICE_MELT', units='m', & - avgflag='A', long_name='melt from excess ice (vegetated landunits only)', & - ptr_col=this%exice_melt, l2g_scale_type='veg') + ! Add excess ice fields to history + data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & + avgflag='A', long_name='excess soil ice (vegetated landunits only)', & + ptr_col=this%excess_ice_col, l2g_scale_type='veg', & + default='inactive' ) ! (rgk 02-02-2017) There is intentionally no entry here for stored plant water ! I think that since the value is zero in all cases except @@ -557,10 +528,7 @@ subroutine InitCold(this, bounds, & !Initialize excess ice if (use_excess_ice .and. NLFilename /= '') then ! enforce initialization with 0 for everything - this%init_exice(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - this%exice_melt_lev(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - this%exice_melt(bounds%begc:bounds%endc)=0.0_r8 call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column call this%exicestream%CalcExcessIce(bounds, exice_bulk_init) @@ -577,25 +545,17 @@ subroutine InitCold(this, bounds, & do j = 2, nlevmaxurbgrnd ! ignore first layer if (j Date: Tue, 24 May 2022 18:13:24 -0600 Subject: [PATCH 0218/2067] Replaced min_crop_gdd_target with gddmin(ivt(p)). --- src/biogeochem/CNPhenologyMod.F90 | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 33d22f48f5..613cf4bbdb 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -128,7 +128,6 @@ module CNPhenologyMod logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing logical :: ignore_rx_crop_gdds = .false. ! Troubleshooting - real(r8) :: min_crop_gdd_target = 1._r8 ! Troubleshooting ! Constants for seasonal decidious leaf onset and offset logical, private :: onset_thresh_depends_on_veg = .false. ! If onset threshold depends on vegetation type @@ -172,7 +171,7 @@ subroutine CNPhenologyReadNML( NLFilename ) !----------------------------------------------------------------------- namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, & min_critical_dayl_method, generate_crop_gdds, & - ignore_rx_crop_gdds, min_crop_gdd_target + ignore_rx_crop_gdds ! Initialize options to default values, in case they are not specified in ! the namelist @@ -198,7 +197,6 @@ subroutine CNPhenologyReadNML( NLFilename ) call shr_mpi_bcast (min_critical_dayl_method, mpicom) call shr_mpi_bcast (generate_crop_gdds, mpicom) call shr_mpi_bcast (ignore_rx_crop_gdds, mpicom) - call shr_mpi_bcast (min_crop_gdd_target, mpicom) if ( min_critical_dayl_method == "DependsOnLat" )then critical_daylight_method = critical_daylight_depends_on_lat @@ -2438,6 +2436,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & crop_seedc_to_leaf => cnveg_carbonflux_inst%crop_seedc_to_leaf_patch , & ! Output: [real(r8) (:) ] (gC/m2/s) seed source to leaf crop_seedn_to_leaf => cnveg_nitrogenflux_inst%crop_seedn_to_leaf_patch, & ! Output: [real(r8) (:) ] (gN/m2/s) seed source to leaf hybgdd => pftcon%hybgdd , & ! Input: [real(r8) (:) ] + gddmin => pftcon%gddmin , & ! Input: gdd020 => temperature_inst%gdd020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd0 gdd820 => temperature_inst%gdd820_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd8 gdd1020 => temperature_inst%gdd1020_patch & ! Input: [real(r8) (:) ] 20 yr mean of gdd10 @@ -2498,16 +2497,15 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target - gddmaturity(p) = min_crop_gdd_target if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .gt. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 - if (gdd_target < min_crop_gdd_target) then - write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gdd_target ',gdd_target,'; using min_crop_gdd_target instead (',min_crop_gdd_target,')' + if (gdd_target < gddmin(ivt(p))) then + write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gdd_target ',gdd_target,'; using gddmin(ivt(p)) instead (',gddmin(ivt(p)),')' endif - gdd_target = max(gdd_target, min_crop_gdd_target) + gdd_target = max(gdd_target, gddmin(ivt(p))) gddmaturity(p) = gdd_target else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then @@ -2535,10 +2533,10 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 - if (gddmaturity(p) < min_crop_gdd_target) then - write(iulog,*) 'Some patch with ivt ',ivt(p),' has calculated gddmaturity ',gddmaturity(p),'; using min_crop_gdd_target instead (',min_crop_gdd_target,')' + if (gddmaturity(p) < gddmin(ivt(p))) then + write(iulog,*) 'Some patch with ivt ',ivt(p),' has calculated gddmaturity ',gddmaturity(p),'; using gddmin(ivt(p)) instead (',gddmin(ivt(p)),')' endif - gddmaturity(p) = max(gddmaturity(p), min_crop_gdd_target) + gddmaturity(p) = max(gddmaturity(p), gddmin(ivt(p))) endif ! write (iulog,'(a,i4,a,f0.0)') 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) From 1400974f6a28496aaf524794322eaa3fafa984b0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 May 2022 10:37:14 -0600 Subject: [PATCH 0219/2067] Merge tag 'ctsm5.1.dev092' into rx_crop_calendars2 Refactor NutrientCompetition / CNAllocation to provide hooks for AgSys Major refactor of NutrientCompetition / CNAllocation to provide hooks for AgSys crop model: separates the NutrientCompetition modules into pieces based on (1) consolidating duplicate code between the Clm45 and FlexibleCN versions, and (2) separating pieces that will vs. won't be used for crop patches when running with the upcoming AgSys crop model. I have restored the old CNAllocationMod, with some of the responsibilities that it used to have. (I'm not sure it's appropriate to have the calculation of gpp and maint resp in CNAllocationMod, but I left it there because it has always been combined with the allocation code, including back when we had a separate CNAllocationMod.) --- doc/ChangeLog | 78 + doc/ChangeSum | 1 + src/biogeochem/CNAllocationMod.F90 | 542 +++++++ src/biogeochem/CNDriverMod.F90 | 58 +- src/biogeochem/CNPhenologyMod.F90 | 78 +- src/biogeochem/CNVegStateType.F90 | 25 +- src/biogeochem/CNVegetationFacade.F90 | 4 + src/biogeochem/CropType.F90 | 12 +- .../NutrientCompetitionCLM45defaultMod.F90 | 796 +++------- .../NutrientCompetitionFlexibleCNMod.F90 | 1335 ++++++++--------- .../NutrientCompetitionMethodMod.F90 | 83 +- src/main/clm_driver.F90 | 1 + src/main/clm_initializeMod.F90 | 2 +- src/main/clm_varctl.F90 | 5 + src/main/readParamsMod.F90 | 7 +- 15 files changed, 1655 insertions(+), 1372 deletions(-) create mode 100644 src/biogeochem/CNAllocationMod.F90 diff --git a/doc/ChangeLog b/doc/ChangeLog index ea2697281c..383ed4ecfa 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,82 @@ =============================================================== +Tag name: ctsm5.1.dev092 +Originator(s): sacks (Bill Sacks) +Date: Fri Apr 29 18:31:48 MDT 2022 +One-line Summary: Refactor NutrientCompetition / CNAllocation to provide hooks for AgSys + +Purpose and description of changes +---------------------------------- + +Major refactor of NutrientCompetition / CNAllocation to provide hooks +for AgSys crop model: separates the NutrientCompetition modules into +pieces based on (1) consolidating duplicate code between the Clm45 and +FlexibleCN versions, and (2) separating pieces that will vs. won't be +used for crop patches when running with the upcoming AgSys crop model. + +I have restored the old CNAllocationMod, with some of the +responsibilities that it used to have. (I'm not sure it's appropriate to +have the calculation of gpp and maint resp in CNAllocationMod, but I +left it there because it has always been combined with the allocation +code, including back when we had a separate CNAllocationMod.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- PASS + izumi ------- PASS + + +Answer changes +-------------- + +Changes answers relative to baseline: NO - though potential for answer +changes in unusual cases + + One change in this tag has the potential for answer changes in + unusual cases, even though no answer changes were observed in + testing: Previously, only the FlexibleCN code applied some logic that + changed crop allocation fractions during the grainfill period if + peaklai had been reached. I have changed this so that this logic is + applied with or without FlexibleCN (because I have moved this block + of code to the CNAllocation module, which is shared between the + FlexibleCN and non-FlexibleCN versions). I thought this would change + answers, but it appears not to, at least based on the tests in the + test suite as well as an extra 5-year test I did at f19 resolution + (ERS_Ly5.f19_g17.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput). + It's possible that this changes answers in rare cases or with an + unusual combination of options that we don't test: specifically, it + might change answers for the atypical situation where you are running + with FUN but not FlexibleCN. (In this case, I believe this change is + the correct thing to do.) + + +Other details +------------- +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1705 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev091 Originator(s): rgknox (Ryan Knox,rgknox@lbl.gov) Date: Fri Apr 22 14:11:50 EDT 2022 diff --git a/doc/ChangeSum b/doc/ChangeSum index 6f3b47ae7d..8280d7aefc 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev092 sacks 04/29/2022 Refactor NutrientCompetition / CNAllocation to provide hooks for AgSys ctsm5.1.dev091 rgknox 04/22/2022 clm decomp method is now passed to fates to enabled mimics coupling ctsm5.1.dev090 samrabin 03/31/2022 Fix misleading name of "gddplant" ctsm5.1.dev089 sacks 03/31/2022 For CLM45 apply peaklai to aleaf in grainfill diff --git a/src/biogeochem/CNAllocationMod.F90 b/src/biogeochem/CNAllocationMod.F90 new file mode 100644 index 0000000000..ef646511f1 --- /dev/null +++ b/src/biogeochem/CNAllocationMod.F90 @@ -0,0 +1,542 @@ +module CNAllocationMod + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! This module contains subroutines to calculate allocation of C and N to different + ! plant components. It also contains subroutines to calculate gpp and maintenance + ! respiration. + ! + ! !USES: +#include "shr_assert.h" + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use abortutils , only : endrun + use decompMod , only : bounds_type + use clm_varcon , only : secspday + use clm_varctl , only : use_c13, use_c14, iulog + use PatchType , only : patch + use pftconMod , only : pftcon, npcropmin + use CropType , only : crop_type + use CropType , only : cphase_planted, cphase_leafemerge, cphase_grainfill + use PhotosynthesisMod , only : photosyns_type + use CanopyStateType , only : canopystate_type + use CNVegCarbonStateType , only : cnveg_carbonstate_type + use CNVegCarbonFluxType , only : cnveg_carbonflux_type + use CNVegStateType , only : cnveg_state_type + use CropReprPoolsMod , only : nrepr + use CNPhenologyMod , only : CropPhase + use CNSharedParamsMod , only : use_fun + ! + implicit none + private + ! + ! !PUBLIC MEMBER FUNCTIONS: + public :: readParams ! Read in parameters from file + public :: calc_gpp_mr_availc ! Calculate total GPP, various maintenance respiration terms, and total available C for allocation + public :: calc_crop_allocation_fractions ! Calculate crop allocation fractions to leaf, stem, root and repr + public :: calc_allometry ! Calculate c_allometry and n_allometry terms based on allocation fractions + + ! !PRIVATE MEMBER VARIABLES: + type, private :: params_type + real(r8) :: dayscrecover ! number of days to recover negative cpool + end type params_type + + type(params_type), private :: params_inst + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +contains + + !----------------------------------------------------------------------- + subroutine readParams (ncid) + ! + ! !USES: + use ncdio_pio , only : file_desc_t,ncd_io + ! + ! !ARGUMENTS: + type(file_desc_t),intent(inout) :: ncid ! pio netCDF file id + ! + ! !LOCAL VARIABLES: + character(len=32) :: subname = 'CNAllocParamsType' + character(len=100) :: errCode = '-Error reading in parameters file:' + logical :: readv ! has variable been read in or not + real(r8) :: tempr ! temporary to read in parameter + character(len=100) :: tString ! temp. var for reading + !----------------------------------------------------------------------- + + ! read in parameters + + tString='dayscrecover' + call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + params_inst%dayscrecover=tempr + + end subroutine readParams + + !----------------------------------------------------------------------- + subroutine calc_gpp_mr_availc(bounds, num_soilp, filter_soilp, & + crop_inst, photosyns_inst, canopystate_inst, & + cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst) + ! + ! !DESCRIPTION: + ! Calculate total GPP, various maintenance respiration terms, and total available C + ! for allocation + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches + type(crop_type) , intent(in) :: crop_inst + type(photosyns_type) , intent(in) :: photosyns_inst + type(canopystate_type) , intent(in) :: canopystate_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst + type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst + type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst + ! + ! !LOCAL VARIABLES: + integer :: p, k ! indices + integer :: fp ! filter patch index + real(r8) :: dayscrecover ! number of days to recover negative cpool + real(r8) :: mr ! maintenance respiration (gC/m2/s) + real(r8) :: reproductive_mr_tot ! total maintenance respiration from grain components (gC/m2/s) + real(r8) :: curmr, curmr_ratio ! xsmrpool temporary variables + + character(len=*), parameter :: subname = 'calc_gpp_mr_availc' + !----------------------------------------------------------------------- + + ! set number of days to recover negative cpool + dayscrecover = params_inst%dayscrecover + + associate ( & + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type + woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) + croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested + psnsun => photosyns_inst%psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) + psnsha => photosyns_inst%psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) + c13_psnsun => photosyns_inst%c13_psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) + c13_psnsha => photosyns_inst%c13_psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) + c14_psnsun => photosyns_inst%c14_psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) + c14_psnsha => photosyns_inst%c14_psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) + laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index + laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index + xsmrpool => cnveg_carbonstate_inst%xsmrpool_patch , & ! Input: [real(r8) (:) ] (gC/m2) temporary photosynthate C pool + leaf_mr => cnveg_carbonflux_inst%leaf_mr_patch , & ! Input: [real(r8) (:) ] + froot_mr => cnveg_carbonflux_inst%froot_mr_patch , & ! Input: [real(r8) (:) ] + livestem_mr => cnveg_carbonflux_inst%livestem_mr_patch , & ! Input: [real(r8) (:) ] + livecroot_mr => cnveg_carbonflux_inst%livecroot_mr_patch , & ! Input: [real(r8) (:) ] + reproductive_mr => cnveg_carbonflux_inst%reproductive_mr_patch , & ! Input: [real(r8) (:,:) ] + psnsun_to_cpool => cnveg_carbonflux_inst%psnsun_to_cpool_patch , & ! Output: [real(r8) (:) ] + psnshade_to_cpool => cnveg_carbonflux_inst%psnshade_to_cpool_patch , & ! Output: [real(r8) (:) ] + gpp => cnveg_carbonflux_inst%gpp_before_downreg_patch , & ! Output: [real(r8) (:) ] GPP flux before downregulation (gC/m2/s) + availc => cnveg_carbonflux_inst%availc_patch , & ! Output: [real(r8) (:) ] C flux available for allocation (gC/m2/s) + leaf_curmr => cnveg_carbonflux_inst%leaf_curmr_patch , & ! Output: [real(r8) (:) ] + froot_curmr => cnveg_carbonflux_inst%froot_curmr_patch , & ! Output: [real(r8) (:) ] + livestem_curmr => cnveg_carbonflux_inst%livestem_curmr_patch , & ! Output: [real(r8) (:) ] + livecroot_curmr => cnveg_carbonflux_inst%livecroot_curmr_patch , & ! Output: [real(r8) (:) ] + reproductive_curmr => cnveg_carbonflux_inst%reproductive_curmr_patch , & ! Output: [real(r8) (:,:) ] + leaf_xsmr => cnveg_carbonflux_inst%leaf_xsmr_patch , & ! Output: [real(r8) (:) ] + froot_xsmr => cnveg_carbonflux_inst%froot_xsmr_patch , & ! Output: [real(r8) (:) ] + livestem_xsmr => cnveg_carbonflux_inst%livestem_xsmr_patch , & ! Output: [real(r8) (:) ] + livecroot_xsmr => cnveg_carbonflux_inst%livecroot_xsmr_patch , & ! Output: [real(r8) (:) ] + reproductive_xsmr => cnveg_carbonflux_inst%reproductive_xsmr_patch , & ! Output: [real(r8) (:,:) ] + cpool_to_xsmrpool => cnveg_carbonflux_inst%cpool_to_xsmrpool_patch , & ! Output: [real(r8) (:) ] + xsmrpool_recover => cnveg_carbonflux_inst%xsmrpool_recover_patch & ! Output: [real(r8) (:) ] C flux assigned to recovery of negative cpool (gC/m2/s) + ) + + do fp = 1,num_soilp + p = filter_soilp(fp) + + ! get the time step total gross photosynthesis + ! this is coming from the canopy fluxes code, and is the + ! gpp that is used to control stomatal conductance. + ! For the nitrogen downregulation code, this is assumed + ! to be the potential gpp, and the actual gpp will be + ! reduced due to N limitation. + + ! Convert psn from umol/m2/s -> gC/m2/s + + ! The input psn (psnsun and psnsha) are expressed per unit LAI + ! in the sunlit and shaded canopy, respectively. These need to be + ! scaled by laisun and laisha to get the total gpp for allocation + + ! Note that no associate statement is used for the isotope carbon fluxes below + ! since they are not always allocated AND nag compiler will complain if you try to + ! to have an associate statement with unallocated memory + + psnsun_to_cpool(p) = psnsun(p) * laisun(p) * 12.011e-6_r8 + psnshade_to_cpool(p) = psnsha(p) * laisha(p) * 12.011e-6_r8 + + if ( use_c13 ) then + c13_cnveg_carbonflux_inst%psnsun_to_cpool_patch(p) = c13_psnsun(p) * laisun(p) * 12.011e-6_r8 + c13_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p) = c13_psnsha(p) * laisha(p) * 12.011e-6_r8 + end if + + if ( use_c14 ) then + c14_cnveg_carbonflux_inst%psnsun_to_cpool_patch(p) = c14_psnsun(p) * laisun(p) * 12.011e-6_r8 + c14_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p) = c14_psnsha(p) * laisha(p) * 12.011e-6_r8 + end if + + gpp(p) = psnsun_to_cpool(p) + psnshade_to_cpool(p) + + ! get the time step total maintenance respiration + ! These fluxes should already be in gC/m2/s + + mr = leaf_mr(p) + froot_mr(p) + if (woody(ivt(p)) == 1.0_r8) then + mr = mr + livestem_mr(p) + livecroot_mr(p) + else if (ivt(p) >= npcropmin) then + if (croplive(p)) then + reproductive_mr_tot = 0._r8 + do k = 1, nrepr + reproductive_mr_tot = reproductive_mr_tot + reproductive_mr(p,k) + end do + mr = mr + livestem_mr(p) + reproductive_mr_tot + end if + end if + + ! carbon flux available for allocation + availc(p) = gpp(p) - mr + + ! new code added for isotope calculations, 7/1/05, PET + ! If mr > gpp, then some mr comes from gpp, the rest comes from + ! cpool (xsmr) + if (mr > 0._r8 .and. availc(p) < 0._r8) then + curmr = gpp(p) + curmr_ratio = curmr / mr + else + curmr_ratio = 1._r8 + end if + leaf_curmr(p) = leaf_mr(p) * curmr_ratio + leaf_xsmr(p) = leaf_mr(p) - leaf_curmr(p) + froot_curmr(p) = froot_mr(p) * curmr_ratio + froot_xsmr(p) = froot_mr(p) - froot_curmr(p) + livestem_curmr(p) = livestem_mr(p) * curmr_ratio + livestem_xsmr(p) = livestem_mr(p) - livestem_curmr(p) + livecroot_curmr(p) = livecroot_mr(p) * curmr_ratio + livecroot_xsmr(p) = livecroot_mr(p) - livecroot_curmr(p) + do k = 1, nrepr + reproductive_curmr(p,k) = reproductive_mr(p,k) * curmr_ratio + reproductive_xsmr(p,k) = reproductive_mr(p,k) - reproductive_curmr(p,k) + end do + + ! no allocation when available c is negative + availc(p) = max(availc(p),0.0_r8) + + ! test for an xsmrpool deficit + if (xsmrpool(p) < 0.0_r8) then + ! Running a deficit in the xsmrpool, so the first priority is to let + ! some availc from this timestep accumulate in xsmrpool. + ! Determine rate of recovery for xsmrpool deficit + + xsmrpool_recover(p) = -xsmrpool(p)/(dayscrecover*secspday) + if (xsmrpool_recover(p) < availc(p)) then + ! available carbon reduced by amount for xsmrpool recovery + availc(p) = availc(p) - xsmrpool_recover(p) + else + ! all of the available carbon goes to xsmrpool recovery + xsmrpool_recover(p) = availc(p) + availc(p) = 0.0_r8 + end if + cpool_to_xsmrpool(p) = xsmrpool_recover(p) + end if + + end do + + end associate + + end subroutine calc_gpp_mr_availc + + !----------------------------------------------------------------------- + subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & + crop_inst, cnveg_state_inst) + ! + ! !DESCRIPTION: + ! Calculate crop allocation fractions to leaf, stem, root and repr, following + ! AgroIBIS subroutine phenocrop + ! + ! This sets the following variables in cnveg_state_inst for all patches in the pcrop + ! filter: + ! - aleaf + ! - astem + ! - aroot + ! - arepr + ! + ! And under some conditions it updates the following variables: + ! - astemi + ! - aleafi + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_pcropp ! number of prog crop patches in filter + integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches + type(crop_type) , intent(in) :: crop_inst + type(cnveg_state_type) , intent(inout) :: cnveg_state_inst + ! + ! !LOCAL VARIABLES: + integer :: p, fp, k + real(r8) :: fleaf ! fraction allocated to leaf + real(r8) :: crop_phase(bounds%begp:bounds%endp) + + character(len=*), parameter :: subname = 'calc_crop_allocation_fractions' + !----------------------------------------------------------------------- + + associate( & + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type + arooti => pftcon%arooti , & ! Input: parameter used below + arootf => pftcon%arootf , & ! Input: parameter used below + bfact => pftcon%bfact , & ! Input: parameter used below + fleafi => pftcon%fleafi , & ! Input: parameter used below + aleaff => pftcon%aleaff , & ! Input: parameter used below + astemf => pftcon%astemf , & ! Input: parameter used below + allconss => pftcon%allconss , & ! Input: parameter used below + allconsl => pftcon%allconsl , & ! Input: parameter used below + declfact => pftcon%declfact , & ! Input: parameter used below + croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest + peaklai => cnveg_state_inst%peaklai_patch , & ! Input: [integer (:) ] 1: max allowed lai; 0: not at max + gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Input: [real(r8) (:) ] gdd needed to harvest + huigrain => cnveg_state_inst%huigrain_patch , & ! Input: [real(r8) (:) ] same to reach vegetative maturity + aleafi => cnveg_state_inst%aleafi_patch , & ! Output: [real(r8) (:) ] saved allocation coefficient from phase 2 + astemi => cnveg_state_inst%astemi_patch , & ! Output: [real(r8) (:) ] saved allocation coefficient from phase 2 + aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient + astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient + aroot => cnveg_state_inst%aroot_patch , & ! Output: [real(r8) (:) ] root allocation coefficient + arepr => cnveg_state_inst%arepr_patch & ! Output: [real(r8) (:,:) ] reproductive allocation coefficient(s) + ) + + call CropPhase(bounds, num_pcropp, filter_pcropp, crop_inst, cnveg_state_inst, & + crop_phase = crop_phase(bounds%begp:bounds%endp)) + + do fp = 1, num_pcropp + p = filter_pcropp(fp) + + if (croplive(p)) then + ! same phases appear in subroutine CropPhenology + + ! Phase 1 completed: + ! ================== + ! if hui is less than the number of gdd needed for filling of grain + ! leaf emergence also has to have taken place for lai changes to occur + ! and carbon assimilation + ! Next phase: leaf emergence to start of leaf decline + + if (crop_phase(p) == cphase_leafemerge) then + + ! allocation rules for crops based on maturity and linear decrease + ! of amount allocated to roots over course of the growing season + + do k = 1, nrepr + arepr(p,k) = 0._r8 + end do + if (peaklai(p) == 1) then ! lai at maximum allowed + aleaf(p) = 1.e-5_r8 + astem(p) = 0._r8 + aroot(p) = 1._r8 - aleaf(p) + else + aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & + (arooti(ivt(p)) - arootf(ivt(p))) * & + min(1._r8, hui(p)/gddmaturity(p)))) + fleaf = fleafi(ivt(p)) * (exp(-bfact(ivt(p))) - & + exp(-bfact(ivt(p))*hui(p)/huigrain(p))) / & + (exp(-bfact(ivt(p)))-1) ! fraction alloc to leaf (from J Norman alloc curve) + aleaf(p) = max(1.e-5_r8, (1._r8 - aroot(p)) * fleaf) + astem(p) = 1._r8 - aleaf(p) - aroot(p) + end if + + ! AgroIBIS included here an immediate adjustment to aleaf & astem if the + ! predicted lai from the above allocation coefficients exceeded laimx. + ! We have decided to live with lais slightly higher than laimx by + ! enforcing the cap in the following tstep through the peaklai logic above. + + astemi(p) = astem(p) ! save for use by equations after shift + aleafi(p) = aleaf(p) ! to reproductive phenology stage begins + + ! Phase 2 completed: + ! ================== + ! shift allocation either when enough gdd are accumulated or maximum number + ! of days has elapsed since planting + + else if (crop_phase(p) == cphase_grainfill) then + aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & + (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) + if (astemi(p) > astemf(ivt(p))) then + astem(p) = max(0._r8, max(astemf(ivt(p)), astem(p) * & + (1._r8 - min((hui(p)- & + huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & + huigrain(p)),1._r8)**allconss(ivt(p)) ))) + end if + + ! If crops have hit peaklai, then set leaf allocation to small value + if (peaklai(p) == 1) then + aleaf(p) = 1.e-5_r8 + else if (aleafi(p) > aleaff(ivt(p))) then + aleaf(p) = max(1.e-5_r8, max(aleaff(ivt(p)), aleaf(p) * & + (1._r8 - min((hui(p)- & + huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & + huigrain(p)),1._r8)**allconsl(ivt(p)) ))) + end if + + ! For AgroIBIS-based crop model, all repr allocation is assumed to go + ! into the last reproductive pool. In practice there is only a single + ! reproductive pool with the AgroIBIS-based crop model, but for + ! software testing we can have multiple, in which situation we want the + ! active pool to be the last one. + do k = 1, nrepr-1 + arepr(p,k) = 0._r8 + end do + arepr(p,nrepr) = 1._r8 - aroot(p) - astem(p) - aleaf(p) + + else if (crop_phase(p) == cphase_planted) then + ! pre emergence + ! allocation coefficients should be irrelevant because crops have no + ! live carbon pools + aleaf(p) = 1._r8 + astem(p) = 0._r8 + aroot(p) = 0._r8 + do k = 1, nrepr + arepr(p,k) = 0._r8 + end do + + else + write(iulog,*) "ERROR in " // subname // ": unexpected crop_phase: ", crop_phase(p) + call endrun(msg="ERROR: unexpected crop_phase "//errmsg(sourcefile, __LINE__)) + end if + + else ! .not croplive + ! allocation coefficients should be irrelevant because crops have no + ! live carbon pools + aleaf(p) = 1._r8 + astem(p) = 0._r8 + aroot(p) = 0._r8 + do k = 1, nrepr + arepr(p,k) = 0._r8 + end do + end if + + end do + + end associate + + end subroutine calc_crop_allocation_fractions + + !----------------------------------------------------------------------- + subroutine calc_allometry(num_soilp, filter_soilp, & + cnveg_carbonflux_inst, cnveg_state_inst) + ! + ! !DESCRIPTION: + ! Calculate c_allometry and n_allometry terms based on allocation fractions + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst + type(cnveg_state_type) , intent(inout) :: cnveg_state_inst + ! + ! !LOCAL VARIABLES: + integer :: p, fp, k + real(r8):: f1,f2,f3,f4,g1 ! allocation parameters + real(r8):: g1a ! g1 included in allocation/allometry + real(r8):: cnl,cnfr,cnlw,cndw ! C:N ratios for leaf, fine root, and wood + real(r8):: f5(nrepr) ! reproductive allocation parameters + real(r8):: cng ! C:N ratio for grain (= cnlw for now; slevis) + real(r8):: f5_tot ! sum of f5 terms + real(r8):: f5_n_tot ! sum of f5 terms converted from C to N + + character(len=*), parameter :: subname = 'calc_allometry' + !----------------------------------------------------------------------- + + associate( & + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type + woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) + froot_leaf => pftcon%froot_leaf , & ! Input: allocation parameter: new fine root C per new leaf C (gC/gC) + croot_stem => pftcon%croot_stem , & ! Input: allocation parameter: new coarse root C per new stem C (gC/gC) + stem_leaf => pftcon%stem_leaf , & ! Input: allocation parameter: new stem c per new leaf C (gC/gC) + flivewd => pftcon%flivewd , & ! Input: allocation parameter: fraction of new wood that is live (phloem and ray parenchyma) (no units) + leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) + frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) + livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) + deadwdcn => pftcon%deadwdcn , & ! Input: dead wood (xylem and heartwood) C:N (gC/gN) + graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) + grperc => pftcon%grperc , & ! Input: parameter used below + annsum_npp => cnveg_carbonflux_inst%annsum_npp_patch , & ! Input: [real(r8) (:) ] annual sum of NPP, for wood allocation + aleaf => cnveg_state_inst%aleaf_patch , & ! Input: [real(r8) (:) ] leaf allocation coefficient + astem => cnveg_state_inst%astem_patch , & ! Input: [real(r8) (:) ] stem allocation coefficient + aroot => cnveg_state_inst%aroot_patch , & ! Input: [real(r8) (:) ] root allocation coefficient + arepr => cnveg_state_inst%arepr_patch , & ! Input: [real(r8) (:,:) ] reproductive allocation coefficient(s) + c_allometry => cnveg_state_inst%c_allometry_patch , & ! Output: [real(r8) (:) ] C allocation index (DIM) + n_allometry => cnveg_state_inst%n_allometry_patch & ! Output: [real(r8) (:) ] N allocation index (DIM) + ) + + do fp = 1, num_soilp + p = filter_soilp(fp) + + f1 = froot_leaf(ivt(p)) + f2 = croot_stem(ivt(p)) + + ! modified wood allocation to be 2.2 at npp=800 gC/m2/yr, 0.2 at npp=0, + ! constrained so that it does not go lower than 0.2 (under negative annsum_npp) + ! This variable allocation is only for trees. Shrubs have a constant + ! allocation as specified in the pft-physiology file. The value is also used + ! as a trigger here: -1.0 means to use the dynamic allocation (trees). + + if (stem_leaf(ivt(p)) == -1._r8) then + f3 = (2.7_r8/(1.0_r8+exp(-0.004_r8*(annsum_npp(p) - 300.0_r8)))) - 0.4_r8 + else + f3 = stem_leaf(ivt(p)) + end if + + f4 = flivewd(ivt(p)) + if (ivt(p) >= npcropmin) then + g1 = 0.25_r8 + else + g1 = grperc(ivt(p)) + end if + cnl = leafcn(ivt(p)) + cnfr = frootcn(ivt(p)) + cnlw = livewdcn(ivt(p)) + cndw = deadwdcn(ivt(p)) + + ! based on available C, use constant allometric relationships to + ! determine N requirements + if (.not. use_fun) then + g1a = g1 + else + g1a = 0._r8 + end if + if (woody(ivt(p)) == 1.0_r8) then + c_allometry(p) = (1._r8+g1a)*(1._r8+f1+f3*(1._r8+f2)) + n_allometry(p) = 1._r8/cnl + f1/cnfr + (f3*f4*(1._r8+f2))/cnlw + & + (f3*(1._r8-f4)*(1._r8+f2))/cndw + else if (ivt(p) >= npcropmin) then ! skip generic crops + cng = graincn(ivt(p)) + f1 = aroot(p) / aleaf(p) + f3 = astem(p) / aleaf(p) + do k = 1, nrepr + f5(k) = arepr(p,k) / aleaf(p) + end do + f5_tot = 0._r8 + f5_n_tot = 0._r8 + do k = 1, nrepr + f5_tot = f5_tot + f5(k) + ! Note that currently we use the same C/N ratio for all grain components: + f5_n_tot = f5_n_tot + f5(k)/cng + end do + c_allometry(p) = (1._r8+g1a)*(1._r8+f1+f5_tot+f3*(1._r8+f2)) + n_allometry(p) = 1._r8/cnl + f1/cnfr + f5_n_tot + (f3*f4*(1._r8+f2))/cnlw + & + (f3*(1._r8-f4)*(1._r8+f2))/cndw + else + c_allometry(p) = 1._r8+g1a+f1+f1*g1a + n_allometry(p) = 1._r8/cnl + f1/cnfr + end if + + end do + + end associate + + end subroutine calc_allometry + + +end module CNAllocationMod diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 7441a9fa07..a782cc1986 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -11,7 +11,7 @@ module CNDriverMod use decompMod , only : bounds_type use perf_mod , only : t_startf, t_stopf use clm_varctl , only : use_nitrif_denitrif, use_nguardrail - use clm_varctl , only : iulog, use_crop + use clm_varctl , only : iulog, use_crop, use_crop_agsys use SoilBiogeochemDecompCascadeConType, only : mimics_decomp, century_decomp, decomp_method use CNSharedParamsMod , only : use_fun use CNVegStateType , only : cnveg_state_type @@ -42,7 +42,6 @@ module CNDriverMod use SaturatedExcessRunoffMod , only : saturated_excess_runoff_type use ActiveLayerMod , only : active_layer_type use SoilWaterRetentionCurveMod , only : soil_water_retention_curve_type - use CropReprPoolsMod , only : nrepr ! ! !PUBLIC TYPES: implicit none @@ -83,7 +82,8 @@ end subroutine CNDriverInit !----------------------------------------------------------------------- subroutine CNDriverNoLeaching(bounds, & - num_soilc, filter_soilc, num_soilp, filter_soilp, num_pcropp, filter_pcropp, & + num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_pcropp, filter_pcropp, num_soilnopcropp, filter_soilnopcropp, & num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, & cnveg_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & @@ -114,6 +114,8 @@ subroutine CNDriverNoLeaching(bounds, use clm_varpar , only: nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools use subgridAveMod , only: p2c use CropType , only: crop_type + use CNAllocationMod , only: calc_gpp_mr_availc, calc_crop_allocation_fractions + use CNAllocationMod , only: calc_allometry use CNNDynamicsMod , only: CNNDeposition,CNNFixation, CNNFert, CNSoyfix,CNFreeLivingFixation use CNMRespMod , only: CNMResp use CNFUNMod , only: CNFUNInit !, CNFUN @@ -151,6 +153,8 @@ subroutine CNDriverNoLeaching(bounds, integer , intent(in) :: filter_soilp(:) ! filter for soil patches integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches + integer , intent(in) :: num_soilnopcropp ! number of non-prog. crop soil patches in filter + integer , intent(in) :: filter_soilnopcropp(:) ! filter for non-prog. crop soil patches integer , intent(in) :: num_exposedvegp ! number of points in filter_exposedvegp integer , intent(in) :: filter_exposedvegp(:) ! patch filter for non-snow-covered veg integer , intent(in) :: num_noexposedvegp ! number of points in filter_noexposedvegp @@ -203,8 +207,6 @@ subroutine CNDriverNoLeaching(bounds, real(r8):: pmnf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_cascade_transitions) !potential mineral N flux, from one pool to another real(r8):: p_decomp_npool_to_din(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_cascade_transitions) ! potential flux to dissolved inorganic N real(r8):: p_decomp_cn_gain(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_pools) ! C:N ratio of the flux gained by the receiver pool - real(r8):: arepr(bounds%begp:bounds%endp,nrepr) ! reproductive allocation coefficient(s) (only used for use_crop) - real(r8):: aroot(bounds%begp:bounds%endp) ! root allocation coefficient (only used for use_crop) integer :: begp,endp integer :: begc,endc @@ -386,16 +388,44 @@ subroutine CNDriverNoLeaching(bounds, end if + call t_startf('cnalloc') + call calc_gpp_mr_availc( & + bounds, num_soilp, filter_soilp, & + crop_inst, photosyns_inst, canopystate_inst, & + cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst) + + if (.not. use_crop_agsys) then + call calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & + crop_inst, cnveg_state_inst) + end if + + call calc_allometry(num_soilp, filter_soilp, & + cnveg_carbonflux_inst, cnveg_state_inst) + call t_stopf('cnalloc') + call t_startf('calc_plant_nutrient_demand') + ! We always call calc_plant_nutrient_demand for natural veg patches, but only call + ! it for crop patches if NOT running with AgSys (since AgSys calculates the relevant + ! output variables in its own way). call nutrient_competition_method%calc_plant_nutrient_demand ( & - bounds, num_soilp, filter_soilp, & - photosyns_inst, crop_inst, canopystate_inst, & - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & - cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & - energyflux_inst, & - aroot=aroot(begp:endp), arepr=arepr(begp:endp,:)) + bounds, & + num_soilnopcropp, filter_soilnopcropp, .false., & + crop_inst, canopystate_inst, & + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & + soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & + energyflux_inst) + if (.not. use_crop_agsys) then + call nutrient_competition_method%calc_plant_nutrient_demand ( & + bounds, & + num_pcropp, filter_pcropp, .true., & + crop_inst, canopystate_inst, & + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & + soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & + energyflux_inst) + end if ! get the column-averaged plant_ndemand (needed for following call to SoilBiogeochemCompetition) @@ -429,8 +459,6 @@ subroutine CNDriverNoLeaching(bounds, c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_nitrogenstate_inst, & - aroot=aroot(begp:endp), & - arepr=arepr(begp:endp,:), & fpg_col=soilbiogeochem_state_inst%fpg_col(begc:endc)) call t_stopf('calc_plant_nutrient_competition') diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 613cf4bbdb..12604b0199 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -28,6 +28,8 @@ module CNPhenologyMod use CNVegnitrogenstateType , only : cnveg_nitrogenstate_type use CNVegnitrogenfluxType , only : cnveg_nitrogenflux_type use CropType , only : crop_type + use CropType , only : cphase_planted, cphase_leafemerge + use CropType , only : cphase_grainfill, cphase_harvest use pftconMod , only : pftcon use SoilStateType , only : soilstate_type use TemperatureType , only : temperature_type @@ -48,6 +50,7 @@ module CNPhenologyMod public :: CNPhenologyreadNML ! Read namelist public :: CNPhenologyInit ! Initialization public :: CNPhenology ! Update + public :: CropPhase ! Get the current phase of each crop patch ! !PUBLIC for unit testing public :: CNPhenologySetNML ! Set the namelist setttings explicitly for unit tests @@ -2045,7 +2048,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & offset_flag(p) = 0._r8 ! carbon and nitrogen transfers if (croplive(p)) then - cphase(p) = 1._r8 + cphase(p) = cphase_planted ! call vernalization if winter temperate cereal planted, living, and the ! vernalization factor is not 1; @@ -2179,8 +2182,14 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & endif force_harvest = force_harvest .or. (generate_crop_gdds .and. do_harvest) + ! The following conditionals are similar to those in CropPhase. However, they + ! differ slightly because here we are potentially setting a new crop phase, + ! whereas CropPhase is just designed to get the current, already-determined + ! phase. However, despite these differences: if you make changes to the + ! following conditionals, you should also check to see if you should make + ! similar changes in CropPhase. if ((.not. force_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then - cphase(p) = 2._r8 + cphase(p) = cphase_leafemerge if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 onset_counter(p) = dt @@ -2225,7 +2234,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & endif croplive(p) = .false. ! no re-entry in greater if-block - cphase(p) = 4._r8 + cphase(p) = cphase_harvest if (tlai(p) > 0._r8) then ! plant had emerged before harvest offset_flag(p) = 1._r8 offset_counter(p) = dt @@ -2261,7 +2270,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Use CN's simple formula at least as a place holder (slevis) else if (hui(p) >= huigrain(p)) then - cphase(p) = 3._r8 + cphase(p) = cphase_grainfill ! SSR troubleshooting if (leaf_long(ivt(p))*dayspyr*secspday == 0.0) then @@ -2311,6 +2320,67 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end subroutine CropPhenology + !----------------------------------------------------------------------- + subroutine CropPhase(bounds, num_pcropp, filter_pcropp, & + crop_inst, cnveg_state_inst, crop_phase) + ! + ! !DESCRIPTION: + ! Get the current phase of each crop patch. + ! + ! The returned values (in crop_phase) are from the set of cphase_* values defined in + ! CropType. The returned values in crop_phase are only valid for patches where + ! croplive is true; the values are undefined where croplive is false and should not be + ! used there! + ! + ! This has logic similar to that in CropPhenology. If you make changes here, you + ! should also check if similar changes need to be made in CropPhenology. + ! + ! !ARGUMENTS: + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_pcropp ! number of prog crop patches in filter + integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches + type(crop_type) , intent(in) :: crop_inst + type(cnveg_state_type) , intent(in) :: cnveg_state_inst + real(r8) , intent(inout) :: crop_phase(bounds%begp:) + ! + ! !LOCAL VARIABLES: + integer :: p, fp + + character(len=*), parameter :: subname = 'CropPhase' + !----------------------------------------------------------------------- + SHR_ASSERT_ALL_FL((ubound(crop_phase) == [bounds%endp]), sourcefile, __LINE__) + + associate( & + croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] Flag, true if planted, not harvested + hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] gdd since planting (gddplant) + leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature + huileaf => cnveg_state_inst%huileaf_patch , & ! Input: [real(r8) (:) ] heat unit index needed from planting to leaf emergence + huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:) ] same to reach vegetative maturity + ) + + do fp = 1, num_pcropp + p = filter_pcropp(fp) + + if (croplive(p)) then + ! Start with cphase_planted, but this might get changed in the later + ! conditional blocks. + crop_phase(p) = cphase_planted + if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p)) then + crop_phase(p) = cphase_leafemerge + else if (hui(p) >= huigrain(p)) then + ! Since we know croplive is true, any hui greater than huigrain implies that + ! we're in the grainfill stage: if we were passt gddmaturity then croplive + ! would be false. + crop_phase(p) = cphase_grainfill + end if + end if + end do + + end associate + + end subroutine CropPhase + + !----------------------------------------------------------------------- subroutine CropPhenologyInit(bounds) ! diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index cc7dd8f724..38fbcd81cb 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -7,7 +7,7 @@ module CNVegStateType use abortutils , only : endrun use spmdMod , only : masterproc use clm_varpar , only : nlevsno, nlevgrnd, nlevlak, nlevsoi - use clm_varctl , only : use_cn, iulog, fsurdat, use_crop, use_cndv + use clm_varctl , only : use_cn, iulog, fsurdat, use_crop, use_cndv, use_crop_agsys use clm_varcon , only : spval, ispval, grlnd use landunit_varcon, only : istsoil, istcrop use LandunitType , only : lun @@ -15,6 +15,7 @@ module CNVegStateType use PatchType , only : patch use AnnualFluxDribbler, only : annual_flux_dribbler_type, annual_flux_dribbler_patch use dynSubgridControlMod, only : get_for_testing_allow_non_annual_changes + use CropReprPoolsMod, only : nrepr ! ! !PUBLIC TYPES: implicit none @@ -39,8 +40,19 @@ module CNVegStateType real(r8) , pointer :: huigrain_patch (:) ! patch heat unit index needed to reach vegetative maturity real(r8) , pointer :: aleafi_patch (:) ! patch saved leaf allocation coefficient from phase 2 real(r8) , pointer :: astemi_patch (:) ! patch saved stem allocation coefficient from phase 2 + real(r8) , pointer :: aleaf_patch (:) ! patch leaf allocation coefficient real(r8) , pointer :: astem_patch (:) ! patch stem allocation coefficient + real(r8) , pointer :: aroot_patch (:) ! patch root allocation coefficient + real(r8) , pointer :: arepr_patch (:,:) ! patch reproductive allocation coefficient(s) + + ! The following nitrogen-based allocation fractions are just used with the AgSys + ! crop model (use_crop_agsys = .true.): + real(r8) , pointer :: aleaf_n_patch (:) ! patch leaf allocation coefficient for N + real(r8) , pointer :: astem_n_patch (:) ! patch stem allocation coefficient for N + real(r8) , pointer :: aroot_n_patch (:) ! patch root allocation coefficient for N + real(r8) , pointer :: arepr_n_patch (:,:) ! patch reproductive allocation coefficient(s) for N + real(r8) , pointer :: htmx_patch (:) ! patch max hgt attained by a crop during yr (m) integer , pointer :: peaklai_patch (:) ! patch 1: max allowed lai; 0: not at max @@ -202,8 +214,19 @@ subroutine InitAllocate(this, bounds) allocate(this%huigrain_patch (begp:endp)) ; this%huigrain_patch (:) = 0.0_r8 allocate(this%aleafi_patch (begp:endp)) ; this%aleafi_patch (:) = nan allocate(this%astemi_patch (begp:endp)) ; this%astemi_patch (:) = nan + allocate(this%aleaf_patch (begp:endp)) ; this%aleaf_patch (:) = nan allocate(this%astem_patch (begp:endp)) ; this%astem_patch (:) = nan + allocate(this%aroot_patch (begp:endp)) ; this%aroot_patch (:) = nan + allocate(this%arepr_patch (begp:endp, nrepr)) ; this%arepr_patch (:,:) = nan + + if (use_crop_agsys) then + allocate(this%aleaf_n_patch (begp:endp)) ; this%aleaf_n_patch (:) = nan + allocate(this%astem_n_patch (begp:endp)) ; this%astem_n_patch (:) = nan + allocate(this%aroot_n_patch (begp:endp)) ; this%aroot_n_patch (:) = nan + allocate(this%arepr_n_patch (begp:endp, nrepr)) ; this%arepr_n_patch (:,:) = nan + end if + allocate(this%htmx_patch (begp:endp)) ; this%htmx_patch (:) = 0.0_r8 allocate(this%peaklai_patch (begp:endp)) ; this%peaklai_patch (:) = 0 diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index a03eee2841..384e4a4966 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -879,6 +879,7 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & num_soilc, filter_soilc, & num_soilp, filter_soilp, & num_pcropp, filter_pcropp, & + num_soilnopcropp, filter_soilnopcropp, & num_exposedvegp, filter_exposedvegp, & num_noexposedvegp, filter_noexposedvegp, & soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & @@ -910,6 +911,8 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & integer , intent(in) :: filter_soilp(:) ! filter for soil patches integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches + integer , intent(in) :: num_soilnopcropp ! number of non-prog. crop soil patches in filter + integer , intent(in) :: filter_soilnopcropp(:) ! filter for non-prog. crop soil patches integer , intent(in) :: num_exposedvegp ! number of points in filter_exposedvegp integer , intent(in) :: filter_exposedvegp(:) ! patch filter for non-snow-covered veg integer , intent(in) :: num_noexposedvegp ! number of points in filter_noexposedvegp @@ -952,6 +955,7 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & num_soilc, filter_soilc, & num_soilp, filter_soilp, & num_pcropp, filter_pcropp, & + num_soilnopcropp, filter_soilnopcropp, & num_exposedvegp, filter_exposedvegp, & num_noexposedvegp, filter_noexposedvegp, & this%cnveg_state_inst, & diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 901b085e5a..2b136d1a5d 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -24,6 +24,14 @@ module CropType ! ! !PUBLIC DATA TYPES: ! + + ! Possible values of cphase + real(r8), parameter, public :: cphase_not_planted = 0._r8 + real(r8), parameter, public :: cphase_planted = 1._r8 + real(r8), parameter, public :: cphase_leafemerge = 2._r8 + real(r8), parameter, public :: cphase_grainfill = 3._r8 + real(r8), parameter, public :: cphase_harvest = 4._r8 + ! Crop state variables structure type, public :: crop_type @@ -33,7 +41,7 @@ module CropType real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen real(r8), pointer :: gddtsoi_patch (:) ! patch growing degree-days from planting (top two soil layers) (ddays) real(r8), pointer :: vf_patch (:) ! patch vernalization factor for cereal - real(r8), pointer :: cphase_patch (:) ! phenology phase + real(r8), pointer :: cphase_patch (:) ! phenology phase (see cphase_* constants above for possible values) real(r8), pointer :: latbaset_patch (:) ! Latitude vary baset for hui (degree C) character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept @@ -211,7 +219,7 @@ subroutine InitAllocate(this, bounds) allocate(this%gddaccum_patch (begp:endp)) ; this%gddaccum_patch (:) = spval allocate(this%gddtsoi_patch (begp:endp)) ; this%gddtsoi_patch (:) = spval allocate(this%vf_patch (begp:endp)) ; this%vf_patch (:) = 0.0_r8 - allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = 0.0_r8 + allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = cphase_not_planted allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 allocate(this%rx_sdates_thisyr(begp:endp,1:mxsowings)) ; this%rx_sdates_thisyr(:,:) = -1 diff --git a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 index f30cef5f8d..9b1f8f9d09 100644 --- a/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 +++ b/src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 @@ -11,17 +11,17 @@ module NutrientCompetitionCLM45defaultMod ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type - use LandunitType , only : lun - use ColumnType , only : col - use PatchType , only : patch + use LandunitType , only : lun + use ColumnType , only : col + use PatchType , only : patch use NutrientCompetitionMethodMod, only : nutrient_competition_method_type - use NutrientCompetitionMethodMod, only : params_inst use CropReprPoolsMod , only : nrepr - !use clm_varctl , only : iulog - ! SSR troubleshooting - use abortutils , only : endrun - use shr_log_mod , only : errMsg => shr_log_errMsg + use CNPhenologyMod , only : CropPhase + use CropType , only : cphase_leafemerge, cphase_grainfill + use clm_varctl , only : iulog + use abortutils , only : endrun ! implicit none private @@ -35,7 +35,7 @@ module NutrientCompetitionCLM45defaultMod ! public methocs procedure, public :: init ! Initialize the class procedure, public :: calc_plant_nutrient_competition ! calculate nutrient yield rate from competition - procedure, public :: calc_plant_nutrient_demand ! calculate plant nutrient demand + procedure, public :: calc_plant_nutrient_demand ! calculate plant nutrient demand ! ! private methods procedure, private:: calc_plant_cn_alloc @@ -44,14 +44,14 @@ module NutrientCompetitionCLM45defaultMod ! interface nutrient_competition_clm45default_type ! initialize a new nutrient_competition_clm45default_type object - module procedure constructor + module procedure constructor end interface nutrient_competition_clm45default_type ! character(len=*), parameter, private :: sourcefile = & __FILE__ !------------------------------------------------------------------------ - + contains !------------------------------------------------------------------------ @@ -81,8 +81,7 @@ subroutine calc_plant_nutrient_competition (this, & cnveg_carbonflux_inst, & c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - soilbiogeochem_nitrogenstate_inst, & - aroot, arepr, fpg_col) + soilbiogeochem_nitrogenstate_inst, fpg_col) ! ! !USES: use CNVegStateType , only : cnveg_state_type @@ -110,16 +109,12 @@ subroutine calc_plant_nutrient_competition (this, & type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst - real(r8) , intent(in) :: aroot(bounds%begp:) - real(r8) , intent(in) :: arepr(bounds%begp:,:) real(r8) , intent(in) :: fpg_col(bounds%begc:) call this%calc_plant_cn_alloc (bounds, num_soilp, filter_soilp, & cnveg_state_inst, crop_inst, canopystate_inst, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, c13_cnveg_carbonflux_inst, & c14_cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - aroot=aroot(bounds%begp:bounds%endp), & - arepr=arepr(bounds%begp:bounds%endp,:), & fpg_col=fpg_col(bounds%begc:bounds%endc)) end subroutine calc_plant_nutrient_competition @@ -128,8 +123,7 @@ end subroutine calc_plant_nutrient_competition subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & cnveg_state_inst, crop_inst, canopystate_inst, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, c13_cnveg_carbonflux_inst, & - c14_cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - aroot, arepr, fpg_col) + c14_cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, fpg_col) ! ! !USES: use pftconMod , only : pftcon, npcropmin @@ -157,8 +151,6 @@ subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst - real(r8) , intent(in) :: aroot(bounds%begp:) - real(r8) , intent(in) :: arepr(bounds%begp:,:) real(r8) , intent(in) :: fpg_col(bounds%begc:) ! ! !LOCAL VARIABLES: @@ -171,82 +163,82 @@ subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & real(r8):: nlc ! temporary variable for total new leaf carbon allocation real(r8):: f5(nrepr) ! reproductive allocation parameters real(r8):: cng ! C:N ratio for grain (= cnlw for now; slevis) - real(r8):: fsmn(bounds%begp:bounds%endp) ! A emperate variable for adjusting FUN uptakes + real(r8):: fsmn(bounds%begp:bounds%endp) ! A emperate variable for adjusting FUN uptakes !----------------------------------------------------------------------- - SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp, nrepr/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(fpg_col) == (/bounds%endc/)), sourcefile, __LINE__) associate( & - fpg => fpg_col , & ! Input: [real(r8) (:) ] fraction of potential gpp (no units) + fpg => fpg_col , & ! Input: [real(r8) (:) ] fraction of potential gpp (no units) + + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type - ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type - woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) froot_leaf => pftcon%froot_leaf , & ! Input: allocation parameter: new fine root C per new leaf C (gC/gC) croot_stem => pftcon%croot_stem , & ! Input: allocation parameter: new coarse root C per new stem C (gC/gC) stem_leaf => pftcon%stem_leaf , & ! Input: allocation parameter: new stem c per new leaf C (gC/gC) flivewd => pftcon%flivewd , & ! Input: allocation parameter: fraction of new wood that is live (phloem and ray parenchyma) (no units) - leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) - frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) + leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) + frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) deadwdcn => pftcon%deadwdcn , & ! Input: dead wood (xylem and heartwood) C:N (gC/gN) fcur2 => pftcon%fcur , & ! Input: allocation parameter: fraction of allocation that goes to currently displayed growth, remainder to storage - graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) + graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) grperc => pftcon%grperc , & ! Input: growth respiration parameter grpnow => pftcon%grpnow , & ! Input: growth respiration parameter croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested - peaklai => cnveg_state_inst%peaklai_patch , & ! Input: [integer (:) ] 1: max allowed lai; 0: not at max - aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient - astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient - c_allometry => cnveg_state_inst%c_allometry_patch , & ! Output: [real(r8) (:) ] C allocation index (DIM) - n_allometry => cnveg_state_inst%n_allometry_patch , & ! Output: [real(r8) (:) ] N allocation index (DIM) + peaklai => cnveg_state_inst%peaklai_patch , & ! Input: [integer (:) ] 1: max allowed lai; 0: not at max + aleaf => cnveg_state_inst%aleaf_patch , & ! Input: [real(r8) (:) ] leaf allocation coefficient + astem => cnveg_state_inst%astem_patch , & ! Input: [real(r8) (:) ] stem allocation coefficient + aroot => cnveg_state_inst%aroot_patch , & ! Input: [real(r8) (:) ] root allocation coefficient + arepr => cnveg_state_inst%arepr_patch , & ! Input: [real(r8) (:,:) ] reproductive allocation coefficient(s) + c_allometry => cnveg_state_inst%c_allometry_patch , & ! Output: [real(r8) (:) ] C allocation index (DIM) + n_allometry => cnveg_state_inst%n_allometry_patch , & ! Output: [real(r8) (:) ] N allocation index (DIM) downreg => cnveg_state_inst%downreg_patch , & ! Output: [real(r8) (:) ] fractional reduction in GPP due to N limitation (DIM) - annsum_npp => cnveg_carbonflux_inst%annsum_npp_patch , & ! Input: [real(r8) (:) ] annual sum of NPP, for wood allocation + annsum_npp => cnveg_carbonflux_inst%annsum_npp_patch , & ! Input: [real(r8) (:) ] annual sum of NPP, for wood allocation gpp => cnveg_carbonflux_inst%gpp_before_downreg_patch , & ! Output: [real(r8) (:) ] GPP flux before downregulation (gC/m2/s) availc => cnveg_carbonflux_inst%availc_patch , & ! Output: [real(r8) (:) ] C flux available for allocation (gC/m2/s) excess_cflux => cnveg_carbonflux_inst%excess_cflux_patch , & ! Output: [real(r8) (:) ] C flux not allocated due to downregulation (gC/m2/s) - plant_calloc => cnveg_carbonflux_inst%plant_calloc_patch , & ! Output: [real(r8) (:) ] total allocated C flux (gC/m2/s) + plant_calloc => cnveg_carbonflux_inst%plant_calloc_patch , & ! Output: [real(r8) (:) ] total allocated C flux (gC/m2/s) psnsun_to_cpool => cnveg_carbonflux_inst%psnsun_to_cpool_patch , & ! Output: [real(r8) (:) ] psnshade_to_cpool => cnveg_carbonflux_inst%psnshade_to_cpool_patch , & ! Output: [real(r8) (:) ] - cpool_to_leafc => cnveg_carbonflux_inst%cpool_to_leafc_patch , & ! Output: [real(r8) (:) ] - cpool_to_leafc_storage => cnveg_carbonflux_inst%cpool_to_leafc_storage_patch , & ! Output: [real(r8) (:) ] - cpool_to_frootc => cnveg_carbonflux_inst%cpool_to_frootc_patch , & ! Output: [real(r8) (:) ] - cpool_to_frootc_storage => cnveg_carbonflux_inst%cpool_to_frootc_storage_patch , & ! Output: [real(r8) (:) ] - cpool_to_livestemc => cnveg_carbonflux_inst%cpool_to_livestemc_patch , & ! Output: [real(r8) (:) ] - cpool_to_livestemc_storage => cnveg_carbonflux_inst%cpool_to_livestemc_storage_patch , & ! Output: [real(r8) (:) ] - cpool_to_deadstemc => cnveg_carbonflux_inst%cpool_to_deadstemc_patch , & ! Output: [real(r8) (:) ] - cpool_to_deadstemc_storage => cnveg_carbonflux_inst%cpool_to_deadstemc_storage_patch , & ! Output: [real(r8) (:) ] - cpool_to_livecrootc => cnveg_carbonflux_inst%cpool_to_livecrootc_patch , & ! Output: [real(r8) (:) ] - cpool_to_livecrootc_storage => cnveg_carbonflux_inst%cpool_to_livecrootc_storage_patch , & ! Output: [real(r8) (:) ] - cpool_to_deadcrootc => cnveg_carbonflux_inst%cpool_to_deadcrootc_patch , & ! Output: [real(r8) (:) ] - cpool_to_deadcrootc_storage => cnveg_carbonflux_inst%cpool_to_deadcrootc_storage_patch , & ! Output: [real(r8) (:) ] + cpool_to_leafc => cnveg_carbonflux_inst%cpool_to_leafc_patch , & ! Output: [real(r8) (:) ] + cpool_to_leafc_storage => cnveg_carbonflux_inst%cpool_to_leafc_storage_patch , & ! Output: [real(r8) (:) ] + cpool_to_frootc => cnveg_carbonflux_inst%cpool_to_frootc_patch , & ! Output: [real(r8) (:) ] + cpool_to_frootc_storage => cnveg_carbonflux_inst%cpool_to_frootc_storage_patch , & ! Output: [real(r8) (:) ] + cpool_to_livestemc => cnveg_carbonflux_inst%cpool_to_livestemc_patch , & ! Output: [real(r8) (:) ] + cpool_to_livestemc_storage => cnveg_carbonflux_inst%cpool_to_livestemc_storage_patch , & ! Output: [real(r8) (:) ] + cpool_to_deadstemc => cnveg_carbonflux_inst%cpool_to_deadstemc_patch , & ! Output: [real(r8) (:) ] + cpool_to_deadstemc_storage => cnveg_carbonflux_inst%cpool_to_deadstemc_storage_patch , & ! Output: [real(r8) (:) ] + cpool_to_livecrootc => cnveg_carbonflux_inst%cpool_to_livecrootc_patch , & ! Output: [real(r8) (:) ] + cpool_to_livecrootc_storage => cnveg_carbonflux_inst%cpool_to_livecrootc_storage_patch , & ! Output: [real(r8) (:) ] + cpool_to_deadcrootc => cnveg_carbonflux_inst%cpool_to_deadcrootc_patch , & ! Output: [real(r8) (:) ] + cpool_to_deadcrootc_storage => cnveg_carbonflux_inst%cpool_to_deadcrootc_storage_patch , & ! Output: [real(r8) (:) ] cpool_to_gresp_storage => cnveg_carbonflux_inst%cpool_to_gresp_storage_patch , & ! Output: [real(r8) (:) ] allocation to growth respiration storage (gC/m2/s) cpool_to_reproductivec => cnveg_carbonflux_inst%cpool_to_reproductivec_patch , & ! Output: [real(r8) (:,:) ] allocation to grain C (gC/m2/s) cpool_to_reproductivec_storage => cnveg_carbonflux_inst%cpool_to_reproductivec_storage_patch , & ! Output: [real(r8) (:,:) ] allocation to grain C storage (gC/m2/s) - + plant_ndemand => cnveg_nitrogenflux_inst%plant_ndemand_patch , & ! Output: [real(r8) (:) ] N flux required to support initial GPP (gN/m2/s) - plant_nalloc => cnveg_nitrogenflux_inst%plant_nalloc_patch , & ! Output: [real(r8) (:) ] total allocated N flux (gN/m2/s) + plant_nalloc => cnveg_nitrogenflux_inst%plant_nalloc_patch , & ! Output: [real(r8) (:) ] total allocated N flux (gN/m2/s) npool_to_reproductiven => cnveg_nitrogenflux_inst%npool_to_reproductiven_patch , & ! Output: [real(r8) (:,:) ] allocation to grain N (gN/m2/s) npool_to_reproductiven_storage => cnveg_nitrogenflux_inst%npool_to_reproductiven_storage_patch , & ! Output: [real(r8) (:,:) ] allocation to grain N storage (gN/m2/s) retransn_to_npool => cnveg_nitrogenflux_inst%retransn_to_npool_patch , & ! Output: [real(r8) (:) ] deployment of retranslocated N (gN/m2/s) sminn_to_npool => cnveg_nitrogenflux_inst%sminn_to_npool_patch , & ! Output: [real(r8) (:) ] deployment of soil mineral N uptake (gN/m2/s) - npool_to_leafn => cnveg_nitrogenflux_inst%npool_to_leafn_patch , & ! Output: [real(r8) (:) ] allocation to leaf N (gN/m2/s) - npool_to_leafn_storage => cnveg_nitrogenflux_inst%npool_to_leafn_storage_patch , & ! Output: [real(r8) (:) ] allocation to leaf N storage (gN/m2/s) - npool_to_frootn => cnveg_nitrogenflux_inst%npool_to_frootn_patch , & ! Output: [real(r8) (:) ] allocation to fine root N (gN/m2/s) + npool_to_leafn => cnveg_nitrogenflux_inst%npool_to_leafn_patch , & ! Output: [real(r8) (:) ] allocation to leaf N (gN/m2/s) + npool_to_leafn_storage => cnveg_nitrogenflux_inst%npool_to_leafn_storage_patch , & ! Output: [real(r8) (:) ] allocation to leaf N storage (gN/m2/s) + npool_to_frootn => cnveg_nitrogenflux_inst%npool_to_frootn_patch , & ! Output: [real(r8) (:) ] allocation to fine root N (gN/m2/s) npool_to_frootn_storage => cnveg_nitrogenflux_inst%npool_to_frootn_storage_patch , & ! Output: [real(r8) (:) ] allocation to fine root N storage (gN/m2/s) - npool_to_livestemn => cnveg_nitrogenflux_inst%npool_to_livestemn_patch , & ! Output: [real(r8) (:) ] - npool_to_livestemn_storage => cnveg_nitrogenflux_inst%npool_to_livestemn_storage_patch , & ! Output: [real(r8) (:) ] - npool_to_deadstemn => cnveg_nitrogenflux_inst%npool_to_deadstemn_patch , & ! Output: [real(r8) (:) ] - npool_to_deadstemn_storage => cnveg_nitrogenflux_inst%npool_to_deadstemn_storage_patch , & ! Output: [real(r8) (:) ] - npool_to_livecrootn => cnveg_nitrogenflux_inst%npool_to_livecrootn_patch , & ! Output: [real(r8) (:) ] - npool_to_livecrootn_storage => cnveg_nitrogenflux_inst%npool_to_livecrootn_storage_patch , & ! Output: [real(r8) (:) ] - npool_to_deadcrootn => cnveg_nitrogenflux_inst%npool_to_deadcrootn_patch , & ! Output: [real(r8) (:) ] - npool_to_deadcrootn_storage => cnveg_nitrogenflux_inst%npool_to_deadcrootn_storage_patch , & ! Output: [real(r8) (:) ] + npool_to_livestemn => cnveg_nitrogenflux_inst%npool_to_livestemn_patch , & ! Output: [real(r8) (:) ] + npool_to_livestemn_storage => cnveg_nitrogenflux_inst%npool_to_livestemn_storage_patch , & ! Output: [real(r8) (:) ] + npool_to_deadstemn => cnveg_nitrogenflux_inst%npool_to_deadstemn_patch , & ! Output: [real(r8) (:) ] + npool_to_deadstemn_storage => cnveg_nitrogenflux_inst%npool_to_deadstemn_storage_patch , & ! Output: [real(r8) (:) ] + npool_to_livecrootn => cnveg_nitrogenflux_inst%npool_to_livecrootn_patch , & ! Output: [real(r8) (:) ] + npool_to_livecrootn_storage => cnveg_nitrogenflux_inst%npool_to_livecrootn_storage_patch , & ! Output: [real(r8) (:) ] + npool_to_deadcrootn => cnveg_nitrogenflux_inst%npool_to_deadcrootn_patch , & ! Output: [real(r8) (:) ] + npool_to_deadcrootn_storage => cnveg_nitrogenflux_inst%npool_to_deadcrootn_storage_patch , & ! Output: [real(r8) (:) ] Npassive => cnveg_nitrogenflux_inst%Npassive_patch , & ! Output: [real(r8) (:) ] Passive N uptake (gN/m2/s) Nfix => cnveg_nitrogenflux_inst%Nfix_patch , & ! Output: [real(r8) (:) ] Symbiotic BNF (gN/m2/s) Nactive => cnveg_nitrogenflux_inst%Nactive_patch , & ! Output: [real(r8) (:) ] Mycorrhizal N uptake (gN/m2/s) @@ -256,14 +248,13 @@ subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & sminn_to_plant_fun => cnveg_nitrogenflux_inst%sminn_to_plant_fun_patch & ! Output: [real(r8) (:) ] Total N uptake of FUN (gN/m2/s) ) - ! patch loop to distribute the available N between the competing patches + ! patch loop to distribute the available N between the competing patches ! on the basis of relative demand, and allocate C and N to new growth and storage do fp = 1,num_soilp p = filter_soilp(fp) c = patch%column(p) - ! set some local allocation variables f1 = froot_leaf(ivt(p)) f2 = croot_stem(ivt(p)) @@ -310,15 +301,15 @@ subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & if(use_fun)then ! if we are using FUN, we get the N available from there. sminn_to_npool(p) = sminn_to_plant_fun(p) - else ! no FUN. :( we get N available from the FPG calculation in soilbiogeochemistry competition. - sminn_to_npool(p) = plant_ndemand(p) * fpg(c) + else ! no FUN. :( we get N available from the FPG calculation in soilbiogeochemistry competition. + sminn_to_npool(p) = plant_ndemand(p) * fpg(c) endif - + plant_nalloc(p) = sminn_to_npool(p) + retransn_to_npool(p) plant_calloc(p) = plant_nalloc(p) * (c_allometry(p)/n_allometry(p)) - - if(.not.use_fun)then !ORIGINAL CLM(CN) downregulation code. + + if(.not.use_fun)then !ORIGINAL CLM(CN) downregulation code. excess_cflux(p) = availc(p) - plant_calloc(p) ! reduce gpp fluxes due to N limitation if (gpp(p) > 0.0_r8) then @@ -340,9 +331,9 @@ subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & c14_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p)*(1._r8 - downreg(p)) endif end if - + end if !use_fun - + ! calculate the amount of new leaf C dictated by these allocation ! decisions, and calculate the daily fluxes of C and N to current ! growth and storage pools @@ -440,23 +431,21 @@ subroutine calc_plant_cn_alloc (this, bounds, num_soilp, filter_soilp, & end do ! end patch loop - end associate + end associate end subroutine calc_plant_cn_alloc !----------------------------------------------------------------------- - subroutine calc_plant_nutrient_demand(this, bounds, num_soilp, filter_soilp,& - photosyns_inst, crop_inst, canopystate_inst, & + subroutine calc_plant_nutrient_demand(this, bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, canopystate_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & - energyflux_inst, & - aroot, arepr) + energyflux_inst) ! ! !USES: use CanopyStateType , only : canopystate_type - use PhotosynthesisMod , only : photosyns_type use CropType , only : crop_type use CNVegStateType , only : cnveg_state_type use CNVegCarbonStateType , only : cnveg_carbonstate_type @@ -471,52 +460,58 @@ subroutine calc_plant_nutrient_demand(this, bounds, num_soilp, filter_soilp,& ! !ARGUMENTS: class(nutrient_competition_clm45default_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(photosyns_type) , intent(in) :: photosyns_inst + + ! This subroutine is meant to be called separately for non-prognostic-crop points and + ! prognostic-crop points. (The reason for this is so that the call for prognostic-crop + ! points can be skipped when a separate crop model is calculating these variables.) In + ! the call for non-prognostic-crop points, this filter should be the soilnopcropp + ! filter and call_is_for_pcrop should be false; in the call for prognostic-crop + ! points, this filter should be the pcropp filter and call_is_for_pcrop should be + ! true. + integer , intent(in) :: num_p ! number of patches in filter + integer , intent(in) :: filter_p(:) ! patch filter + logical , intent(in) :: call_is_for_pcrop + type(crop_type) , intent(in) :: crop_inst - type(canopystate_type) , intent(in) :: canopystate_inst + type(canopystate_type) , intent(in) :: canopystate_inst ! unused in this version type(cnveg_state_type) , intent(inout) :: cnveg_state_inst - type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_carbonflux_type) , intent(in) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst type(energyflux_type) , intent(in) :: energyflux_inst - real(r8) , intent(out) :: aroot(bounds%begp:) - real(r8) , intent(out) :: arepr(bounds%begp:,:) !----------------------------------------------------------------------- - call this%calc_plant_nitrogen_demand(bounds, num_soilp, filter_soilp, & - photosyns_inst, crop_inst, canopystate_inst, & + call this%calc_plant_nitrogen_demand(bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & - cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - aroot=aroot(bounds%begp:bounds%endp), & - arepr=arepr(bounds%begp:bounds%endp,:)) + cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst) end subroutine calc_plant_nutrient_demand !----------------------------------------------------------------------- - subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & - photosyns_inst, crop_inst, canopystate_inst, & + subroutine calc_plant_nitrogen_demand(this, bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & - cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - aroot, arepr) + cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst) + ! + ! !DESCRIPTION: + ! Sets the following output variables that are used elsewhere: + ! - plant_ndemand + ! - retransn_to_npool + ! - leafn_to_retransn + ! - frootn_to_retransn + ! - livestemn_to_retransn ! ! !USES: use pftconMod , only : npcropmin, pftcon use pftconMod , only : ntmp_soybean, nirrig_tmp_soybean use pftconMod , only : ntrp_soybean, nirrig_trp_soybean - use clm_varcon , only : secspday - use clm_varctl , only : use_c13, use_c14 use clm_time_manager , only : get_step_size_real - use CanopyStateType , only : canopystate_type - use PhotosynthesisMod , only : photosyns_type use CropType , only : crop_type use CNVegStateType , only : cnveg_state_type use CNVegCarbonStateType , only : cnveg_carbonstate_type @@ -528,521 +523,208 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! !ARGUMENTS: class(nutrient_competition_clm45default_type), intent(in) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(photosyns_type) , intent(in) :: photosyns_inst + + ! This subroutine is meant to be called separately for non-prognostic-crop points and + ! prognostic-crop points. (The reason for this is so that the call for prognostic-crop + ! points can be skipped when a separate crop model is calculating these variables.) In + ! the call for non-prognostic-crop points, this filter should be the soilnopcropp + ! filter and call_is_for_pcrop should be false; in the call for prognostic-crop + ! points, this filter should be the pcropp filter and call_is_for_pcrop should be + ! true. + integer , intent(in) :: num_p ! number of patches in filter + integer , intent(in) :: filter_p(:) ! patch filter + logical , intent(in) :: call_is_for_pcrop + type(crop_type) , intent(in) :: crop_inst - type(canopystate_type) , intent(in) :: canopystate_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst - type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst - real(r8) , intent(out) :: aroot(bounds%begp:) - real(r8) , intent(out) :: arepr(bounds%begp:,:) ! ! !LOCAL VARIABLES: - integer :: c,p,l,j,k ! indices + integer :: p,l,j ! indices integer :: fp ! lake filter patch index - real(r8):: mr ! maintenance respiration (gC/m2/s) - real(r8):: reproductive_mr_tot ! total maintenance respiration from grain components (gC/m2/s) - real(r8):: f1,f2,f3,f4,g1,g2 ! allocation parameters - real(r8):: g1a ! g1 included in allocation/allometry - real(r8):: cnl,cnfr,cnlw,cndw ! C:N ratios for leaf, fine root, and wood - real(r8):: curmr, curmr_ratio ! xsmrpool temporary variables - real(r8):: f5(nrepr) ! reproductive allocation parameters - real(r8):: cng ! C:N ratio for grain (= cnlw for now; slevis) - real(r8):: fleaf ! fraction allocated to leaf real(r8):: t1 ! temporary variable real(r8):: dt ! model time step - real(r8):: dayscrecover ! number of days to recover negative cpool - real(r8):: f5_tot ! sum of f5 terms - real(r8):: f5_n_tot ! sum of f5 terms converted from C to N + real(r8):: crop_phase(bounds%begp:bounds%endp) + character(len=*), parameter :: subname = "calc_plant_nitrogen_demand" !----------------------------------------------------------------------- - SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp, nrepr/)), sourcefile, __LINE__) - associate( & - ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type - - woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) - froot_leaf => pftcon%froot_leaf , & ! Input: allocation parameter: new fine root C per new leaf C (gC/gC) - croot_stem => pftcon%croot_stem , & ! Input: allocation parameter: new coarse root C per new stem C (gC/gC) - stem_leaf => pftcon%stem_leaf , & ! Input: allocation parameter: new stem c per new leaf C (gC/gC) - flivewd => pftcon%flivewd , & ! Input: allocation parameter: fraction of new wood that is live (phloem and ray parenchyma) (no units) - leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) - frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) - livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) - deadwdcn => pftcon%deadwdcn , & ! Input: dead wood (xylem and heartwood) C:N (gC/gN) - graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) - fleafcn => pftcon%fleafcn , & ! Input: leaf c:n during organ fill - ffrootcn => pftcon%ffrootcn , & ! Input: froot c:n during organ fill - fstemcn => pftcon%fstemcn , & ! Input: stem c:n during organ fill - bfact => pftcon%bfact , & ! Input: parameter used below - aleaff => pftcon%aleaff , & ! Input: parameter used below - arootf => pftcon%arootf , & ! Input: parameter used below + ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type + + leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) + frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) + livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) + graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) + fleafcn => pftcon%fleafcn , & ! Input: leaf c:n during organ fill + ffrootcn => pftcon%ffrootcn , & ! Input: froot c:n during organ fill + fstemcn => pftcon%fstemcn , & ! Input: stem c:n during organ fill astemf => pftcon%astemf , & ! Input: parameter used below - arooti => pftcon%arooti , & ! Input: parameter used below - fleafi => pftcon%fleafi , & ! Input: parameter used below - allconsl => pftcon%allconsl , & ! Input: parameter used below - allconss => pftcon%allconss , & ! Input: parameter used below - grperc => pftcon%grperc , & ! Input: parameter used below - grpnow => pftcon%grpnow , & ! Input: parameter used below - declfact => pftcon%declfact , & ! Input: season_decid => pftcon%season_decid , & ! Input: binary flag for seasonal-deciduous leaf habit (0 or 1) stress_decid => pftcon%stress_decid , & ! Input: binary flag for stress-deciduous leaf habit (0 or 1) - psnsun => photosyns_inst%psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) - psnsha => photosyns_inst%psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) - c13_psnsun => photosyns_inst%c13_psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) - c13_psnsha => photosyns_inst%c13_psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) - c14_psnsun => photosyns_inst%c14_psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) - c14_psnsha => photosyns_inst%c14_psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) - - laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index - laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest - leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] =gdd from top soil layer temperature - croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested - - gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Input: [real(r8) (:) ] gdd needed to harvest - huileaf => cnveg_state_inst%huileaf_patch , & ! Input: [real(r8) (:) ] heat unit index needed from planting to leaf emergence - huigrain => cnveg_state_inst%huigrain_patch , & ! Input: [real(r8) (:) ] same to reach vegetative maturity - peaklai => cnveg_state_inst%peaklai_patch , & ! Input: [integer (:) ] 1: max allowed lai; 0: not at max - aleafi => cnveg_state_inst%aleafi_patch , & ! Output: [real(r8) (:) ] saved allocation coefficient from phase 2 - astemi => cnveg_state_inst%astemi_patch , & ! Output: [real(r8) (:) ] saved allocation coefficient from phase 2 - aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient - astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient - grain_flag => cnveg_state_inst%grain_flag_patch , & ! Output: [real(r8) (:) ] 1: grain fill stage; 0: not - c_allometry => cnveg_state_inst%c_allometry_patch , & ! Output: [real(r8) (:) ] C allocation index (DIM) - n_allometry => cnveg_state_inst%n_allometry_patch , & ! Output: [real(r8) (:) ] N allocation index (DIM) - tempsum_potential_gpp => cnveg_state_inst%tempsum_potential_gpp_patch , & ! Output: [real(r8) (:) ] temporary annual sum of potential GPP + + + croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested + + astem => cnveg_state_inst%astem_patch , & ! Input: [real(r8) (:) ] stem allocation coefficient + c_allometry => cnveg_state_inst%c_allometry_patch , & ! Input: [real(r8) (:) ] C allocation index (DIM) + n_allometry => cnveg_state_inst%n_allometry_patch , & ! Input: [real(r8) (:) ] N allocation index (DIM) + annsum_potential_gpp => cnveg_state_inst%annsum_potential_gpp_patch , & ! Input: [real(r8) (:) ] annual sum of potential GPP + annmax_retransn => cnveg_state_inst%annmax_retransn_patch , & ! Input: [real(r8) (:) ] annual max of retranslocated N pool + grain_flag => cnveg_state_inst%grain_flag_patch , & ! Output: [real(r8) (:) ] 1: grain fill stage; 0: not + tempsum_potential_gpp => cnveg_state_inst%tempsum_potential_gpp_patch , & ! Output: [real(r8) (:) ] temporary annual sum of potential GPP tempmax_retransn => cnveg_state_inst%tempmax_retransn_patch , & ! Output: [real(r8) (:) ] temporary annual max of retranslocated N pool (gN/m2) - annsum_potential_gpp => cnveg_state_inst%annsum_potential_gpp_patch , & ! Output: [real(r8) (:) ] annual sum of potential GPP - annmax_retransn => cnveg_state_inst%annmax_retransn_patch , & ! Output: [real(r8) (:) ] annual max of retranslocated N pool - - xsmrpool => cnveg_carbonstate_inst%xsmrpool_patch , & ! Input: [real(r8) (:) ] (gC/m2) temporary photosynthate C pool - leafc => cnveg_carbonstate_inst%leafc_patch , & ! Input: [real(r8) (:) ] - frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:) ] - livestemc => cnveg_carbonstate_inst%livestemc_patch , & ! Input: [real(r8) (:) ] - - retransn => cnveg_nitrogenstate_inst%retransn_patch , & ! Input: [real(r8) (:) ] (gN/m2) plant pool of retranslocated N - - annsum_npp => cnveg_carbonflux_inst%annsum_npp_patch , & ! Input: [real(r8) (:) ] annual sum of NPP, for wood allocation - leaf_mr => cnveg_carbonflux_inst%leaf_mr_patch , & ! Input: [real(r8) (:) ] - froot_mr => cnveg_carbonflux_inst%froot_mr_patch , & ! Input: [real(r8) (:) ] - livestem_mr => cnveg_carbonflux_inst%livestem_mr_patch , & ! Input: [real(r8) (:) ] - livecroot_mr => cnveg_carbonflux_inst%livecroot_mr_patch , & ! Input: [real(r8) (:) ] - reproductive_mr => cnveg_carbonflux_inst%reproductive_mr_patch , & ! Input: [real(r8) (:,:) ] - gpp => cnveg_carbonflux_inst%gpp_before_downreg_patch , & ! Output: [real(r8) (:) ] GPP flux before downregulation (gC/m2/s) - availc => cnveg_carbonflux_inst%availc_patch , & ! Output: [real(r8) (:) ] C flux available for allocation (gC/m2/s) - xsmrpool_recover => cnveg_carbonflux_inst%xsmrpool_recover_patch , & ! Output: [real(r8) (:) ] C flux assigned to recovery of negative cpool (gC/m2/s) - psnsun_to_cpool => cnveg_carbonflux_inst%psnsun_to_cpool_patch , & ! Output: [real(r8) (:) ] - psnshade_to_cpool => cnveg_carbonflux_inst%psnshade_to_cpool_patch , & ! Output: [real(r8) (:) ] - leaf_curmr => cnveg_carbonflux_inst%leaf_curmr_patch , & ! Output: [real(r8) (:) ] - froot_curmr => cnveg_carbonflux_inst%froot_curmr_patch , & ! Output: [real(r8) (:) ] - livestem_curmr => cnveg_carbonflux_inst%livestem_curmr_patch , & ! Output: [real(r8) (:) ] - livecroot_curmr => cnveg_carbonflux_inst%livecroot_curmr_patch , & ! Output: [real(r8) (:) ] - reproductive_curmr => cnveg_carbonflux_inst%reproductive_curmr_patch , & ! Output: [real(r8) (:,:) ] - leaf_xsmr => cnveg_carbonflux_inst%leaf_xsmr_patch , & ! Output: [real(r8) (:) ] - froot_xsmr => cnveg_carbonflux_inst%froot_xsmr_patch , & ! Output: [real(r8) (:) ] - livestem_xsmr => cnveg_carbonflux_inst%livestem_xsmr_patch , & ! Output: [real(r8) (:) ] - livecroot_xsmr => cnveg_carbonflux_inst%livecroot_xsmr_patch , & ! Output: [real(r8) (:) ] - reproductive_xsmr => cnveg_carbonflux_inst%reproductive_xsmr_patch , & ! Output: [real(r8) (:,:) ] - cpool_to_xsmrpool => cnveg_carbonflux_inst%cpool_to_xsmrpool_patch , & ! Output: [real(r8) (:) ] - + + leafc => cnveg_carbonstate_inst%leafc_patch , & ! Input: [real(r8) (:) ] + frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:) ] + livestemc => cnveg_carbonstate_inst%livestemc_patch , & ! Input: [real(r8) (:) ] + + retransn => cnveg_nitrogenstate_inst%retransn_patch , & ! Input: [real(r8) (:) ] (gN/m2) plant pool of retranslocated N + + gpp => cnveg_carbonflux_inst%gpp_before_downreg_patch , & ! Input: [real(r8) (:) ] GPP flux before downregulation (gC/m2/s) + availc => cnveg_carbonflux_inst%availc_patch , & ! Input: [real(r8) (:) ] C flux available for allocation (gC/m2/s) + plant_ndemand => cnveg_nitrogenflux_inst%plant_ndemand_patch , & ! Output: [real(r8) (:) ] N flux required to support initial GPP (gN/m2/s) avail_retransn => cnveg_nitrogenflux_inst%avail_retransn_patch , & ! Output: [real(r8) (:) ] N flux available from retranslocation pool (gN/m2/s) retransn_to_npool => cnveg_nitrogenflux_inst%retransn_to_npool_patch , & ! Output: [real(r8) (:) ] deployment of retranslocated N (gN/m2/s) - sminn_to_npool => cnveg_nitrogenflux_inst%sminn_to_npool_patch , & ! Output: [real(r8) (:) ] deployment of soil mineral N uptake (gN/m2/s) - leafn_to_retransn => cnveg_nitrogenflux_inst%leafn_to_retransn_patch , & ! Output: [real(r8) (:) ] - frootn_to_retransn => cnveg_nitrogenflux_inst%frootn_to_retransn_patch , & ! Output: [real(r8) (:) ] - livestemn_to_retransn => cnveg_nitrogenflux_inst%livestemn_to_retransn_patch & ! Output: [real(r8) (:) ] + leafn_to_retransn => cnveg_nitrogenflux_inst%leafn_to_retransn_patch , & ! Output: [real(r8) (:) ] + frootn_to_retransn => cnveg_nitrogenflux_inst%frootn_to_retransn_patch , & ! Output: [real(r8) (:) ] + livestemn_to_retransn => cnveg_nitrogenflux_inst%livestemn_to_retransn_patch & ! Output: [real(r8) (:) ] ) ! set time steps dt = get_step_size_real() - ! set number of days to recover negative cpool - dayscrecover = params_inst%dayscrecover - ! loop over patches to assess the total plant N demand - do fp = 1,num_soilp - p = filter_soilp(fp) - c = patch%column(p) - - ! get the time step total gross photosynthesis - ! this is coming from the canopy fluxes code, and is the - ! gpp that is used to control stomatal conductance. - ! For the nitrogen downregulation code, this is assumed - ! to be the potential gpp, and the actual gpp will be - ! reduced due to N limitation. - - ! Convert psn from umol/m2/s -> gC/m2/s - - ! The input psn (psnsun and psnsha) are expressed per unit LAI - ! in the sunlit and shaded canopy, respectively. These need to be - ! scaled by laisun and laisha to get the total gpp for allocation - - ! Note that no associate statement is used for the isotope carbon fluxes below - ! since they are not always allocated AND nag compiler will complain if you try to - ! to have an associate statement with unallocated memory + do fp = 1, num_p + p = filter_p(fp) - psnsun_to_cpool(p) = psnsun(p) * laisun(p) * 12.011e-6_r8 - psnshade_to_cpool(p) = psnsha(p) * laisha(p) * 12.011e-6_r8 - - if ( use_c13 ) then - c13_cnveg_carbonflux_inst%psnsun_to_cpool_patch(p) = c13_psnsun(p) * laisun(p) * 12.011e-6_r8 - c13_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p) = c13_psnsha(p) * laisha(p) * 12.011e-6_r8 - endif - - if ( use_c14 ) then - c14_cnveg_carbonflux_inst%psnsun_to_cpool_patch(p) = c14_psnsun(p) * laisun(p) * 12.011e-6_r8 - c14_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p) = c14_psnsha(p) * laisha(p) * 12.011e-6_r8 - endif - - gpp(p) = psnsun_to_cpool(p) + psnshade_to_cpool(p) - - ! get the time step total maintenance respiration - ! These fluxes should already be in gC/m2/s - - mr = leaf_mr(p) + froot_mr(p) - if (woody(ivt(p)) == 1.0_r8) then - mr = mr + livestem_mr(p) + livecroot_mr(p) - else if (ivt(p) >= npcropmin) then - if (croplive(p)) then - reproductive_mr_tot = 0._r8 - do k = 1, nrepr - reproductive_mr_tot = reproductive_mr_tot + reproductive_mr(p,k) - end do - mr = mr + livestem_mr(p) + reproductive_mr_tot - end if - end if - - ! carbon flux available for allocation - availc(p) = gpp(p) - mr - - ! new code added for isotope calculations, 7/1/05, PET - ! If mr > gpp, then some mr comes from gpp, the rest comes from - ! cpool (xsmr) - if (mr > 0._r8 .and. availc(p) < 0._r8) then - curmr = gpp(p) - curmr_ratio = curmr / mr - else - curmr_ratio = 1._r8 - end if - leaf_curmr(p) = leaf_mr(p) * curmr_ratio - leaf_xsmr(p) = leaf_mr(p) - leaf_curmr(p) - froot_curmr(p) = froot_mr(p) * curmr_ratio - froot_xsmr(p) = froot_mr(p) - froot_curmr(p) - livestem_curmr(p) = livestem_mr(p) * curmr_ratio - livestem_xsmr(p) = livestem_mr(p) - livestem_curmr(p) - livecroot_curmr(p) = livecroot_mr(p) * curmr_ratio - livecroot_xsmr(p) = livecroot_mr(p) - livecroot_curmr(p) - do k = 1, nrepr - reproductive_curmr(p,k) = reproductive_mr(p,k) * curmr_ratio - reproductive_xsmr(p,k) = reproductive_mr(p,k) - reproductive_curmr(p,k) - end do - - ! no allocation when available c is negative - availc(p) = max(availc(p),0.0_r8) - - ! test for an xsmrpool deficit - if (xsmrpool(p) < 0.0_r8) then - ! Running a deficit in the xsmrpool, so the first priority is to let - ! some availc from this timestep accumulate in xsmrpool. - ! Determine rate of recovery for xsmrpool deficit - - xsmrpool_recover(p) = -xsmrpool(p)/(dayscrecover*secspday) - if (xsmrpool_recover(p) < availc(p)) then - ! available carbon reduced by amount for xsmrpool recovery - availc(p) = availc(p) - xsmrpool_recover(p) - else - ! all of the available carbon goes to xsmrpool recovery - xsmrpool_recover(p) = availc(p) - availc(p) = 0.0_r8 - end if - cpool_to_xsmrpool(p) = xsmrpool_recover(p) - end if - - f1 = froot_leaf(ivt(p)) - f2 = croot_stem(ivt(p)) - - ! modified wood allocation to be 2.2 at npp=800 gC/m2/yr, 0.2 at npp=0, - ! constrained so that it does not go lower than 0.2 (under negative annsum_npp) - ! This variable allocation is only for trees. Shrubs have a constant - ! allocation as specified in the pft-physiologfy file. The value is also used - ! as a trigger here: -1.0 means to use the dynamic allocation (trees). + plant_ndemand(p) = availc(p)*(n_allometry(p)/c_allometry(p)) - if (stem_leaf(ivt(p)) == -1._r8) then - f3 = (2.7_r8/(1.0_r8+exp(-0.004_r8*(annsum_npp(p) - 300.0_r8)))) - 0.4_r8 - else - f3 = stem_leaf(ivt(p)) - end if + ! retranslocated N deployment depends on seasonal cycle of potential GPP + ! (requires one year run to accumulate demand) - f4 = flivewd(ivt(p)) - g1 = grperc(ivt(p)) - g2 = grpnow(ivt(p)) - cnl = leafcn(ivt(p)) - cnfr = frootcn(ivt(p)) - cnlw = livewdcn(ivt(p)) - cndw = deadwdcn(ivt(p)) + tempsum_potential_gpp(p) = tempsum_potential_gpp(p) + gpp(p) - ! calculate f1 to f5 for prog crops following AgroIBIS subr phenocrop + ! Adding the following line to carry max retransn info to CN Annual Update + tempmax_retransn(p) = max(tempmax_retransn(p),retransn(p)) + end do - do k = 1, nrepr - f5(k) = 0._r8 ! continued intializations from above - end do + if (call_is_for_pcrop) then + call CropPhase(bounds, num_p, filter_p, crop_inst, cnveg_state_inst, & + crop_phase = crop_phase(bounds%begp:bounds%endp)) - if (ivt(p) >= npcropmin) then ! skip 2 generic crops + do fp = 1, num_p + p = filter_p(fp) if (croplive(p)) then - ! same phases appear in subroutine CropPhenology - - ! Phase 1 completed: - ! ================== - ! if hui is less than the number of gdd needed for filling of grain - ! leaf emergence also has to have taken place for lai changes to occur - ! and carbon assimilation - ! Next phase: leaf emergence to start of leaf decline - - if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p)) then - - ! allocation rules for crops based on maturity and linear decrease - ! of amount allocated to roots over course of the growing season - - do k = 1, nrepr - arepr(p,k) = 0._r8 - end do - if (peaklai(p) == 1) then ! lai at maximum allowed - aleaf(p) = 1.e-5_r8 - astem(p) = 0._r8 - aroot(p) = 1._r8 - aleaf(p) - else - - ! SSR troubleshooting - if (gddmaturity(p) == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & - (arooti(ivt(p)) - arootf(ivt(p))) * & - min(1._r8, hui(p)/gddmaturity(p)))) - fleaf = fleafi(ivt(p)) * (exp(-bfact(ivt(p))) - & - exp(-bfact(ivt(p))*hui(p)/huigrain(p))) / & - (exp(-bfact(ivt(p)))-1) ! fraction alloc to leaf (from J Norman alloc curve) - aleaf(p) = max(1.e-5_r8, (1._r8 - aroot(p)) * fleaf) - astem(p) = 1._r8 - aleaf(p) - aroot(p) - end if - - ! AgroIBIS included here an immediate adjustment to aleaf & astem if the - ! predicted lai from the above allocation coefficients exceeded laimx. - ! We have decided to live with lais slightly higher than laimx by - ! enforcing the cap in the following tstep through the peaklai logic above. - - astemi(p) = astem(p) ! save for use by equations after shift - aleafi(p) = aleaf(p) ! to reproductive phenology stage begins + if (crop_phase(p) == cphase_leafemerge) then grain_flag(p) = 0._r8 ! setting to 0 while in phase 2 - - ! Phase 2 completed: - ! ================== - ! shift allocation either when enough gdd are accumulated or maximum number - ! of days has elapsed since planting - - else if (hui(p) >= huigrain(p)) then - - ! SSR troubleshooting - if (gddmaturity(p) == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & - (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) - if (astemi(p) > astemf(ivt(p))) then - astem(p) = max(0._r8, max(astemf(ivt(p)), astem(p) * & - (1._r8 - min((hui(p)- & - huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & - huigrain(p)),1._r8)**allconss(ivt(p)) ))) - end if - - ! If crops have hit peaklai, then set leaf allocation to small value - if (peaklai(p) == 1) then - aleaf(p) = 1.e-5_r8 - else if (aleafi(p) > aleaff(ivt(p))) then - aleaf(p) = max(1.e-5_r8, max(aleaff(ivt(p)), aleaf(p) * & - (1._r8 - min((hui(p)- & - huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & - huigrain(p)),1._r8)**allconsl(ivt(p)) ))) - end if - + else if (crop_phase(p) == cphase_grainfill) then !Beth's retranslocation of leafn, stemn, rootn to organ !Filter excess plant N to retransn pool for organ N !Only do one time then hold grain_flag till onset next season ! slevis: Will astem ever = astemf exactly? - ! Beth's response: ...looks like astem can equal astemf under the right circumstances. - !It might be worth a rewrite to capture what I was trying to do, but the retranslocation for - !corn and wheat begins at the beginning of the grain fill stage, but for soybean I was holding it - !until after the leaf and stem decline were complete. Looking at how astem is calculated, once the - !stem decline is near complete, astem should (usually) be set to astemf. The reason for holding off - !on soybean is that the retranslocation scheme begins at the beginning of the grain phase, when the - !leaf and stem are still growing, but declining. Since carbon is still getting allocated and now - !there is more nitrogen available, the nitrogen can be diverted from grain. For corn and wheat - !the impact was probably enough to boost productivity, but for soybean the nitrogen was better off - !fulfilling the grain fill. It seems that if the peak lai is reached for soybean though that this - !would be bypassed altogether, not the intended outcome. I checked several of my output files and + ! Beth's response: ...looks like astem can equal astemf under the right circumstances. + !It might be worth a rewrite to capture what I was trying to do, but the retranslocation for + !corn and wheat begins at the beginning of the grain fill stage, but for soybean I was holding it + !until after the leaf and stem decline were complete. Looking at how astem is calculated, once the + !stem decline is near complete, astem should (usually) be set to astemf. The reason for holding off + !on soybean is that the retranslocation scheme begins at the beginning of the grain phase, when the + !leaf and stem are still growing, but declining. Since carbon is still getting allocated and now + !there is more nitrogen available, the nitrogen can be diverted from grain. For corn and wheat + !the impact was probably enough to boost productivity, but for soybean the nitrogen was better off + !fulfilling the grain fill. It seems that if the peak lai is reached for soybean though that this + !would be bypassed altogether, not the intended outcome. I checked several of my output files and !they all seemed to be going through the retranslocation loop for soybean - good news. - if (astem(p) == astemf(ivt(p)) .or. & + if (astem(p) == astemf(ivt(p)) .or. & (ivt(p) /= ntmp_soybean .and. ivt(p) /= nirrig_tmp_soybean .and.& - ivt(p) /= ntrp_soybean .and. ivt(p) /= nirrig_trp_soybean)) then + ivt(p) /= ntrp_soybean .and. ivt(p) /= nirrig_trp_soybean)) then if (grain_flag(p) == 0._r8)then - if(.not.use_fun) then - t1 = 1 / dt - leafn_to_retransn(p) = t1 * ((leafc(p) / leafcn(ivt(p))) - (leafc(p) / & - fleafcn(ivt(p)))) - livestemn_to_retransn(p) = t1 * ((livestemc(p) / livewdcn(ivt(p))) - (livestemc(p) / & - fstemcn(ivt(p)))) - frootn_to_retransn(p) = 0._r8 - if (ffrootcn(ivt(p)) > 0._r8) then - frootn_to_retransn(p) = t1 * ((frootc(p) / frootcn(ivt(p))) - (frootc(p) / & - ffrootcn(ivt(p)))) - end if + if(.not.use_fun) then + t1 = 1 / dt + leafn_to_retransn(p) = t1 * ((leafc(p) / leafcn(ivt(p))) - (leafc(p) / & + fleafcn(ivt(p)))) + livestemn_to_retransn(p) = t1 * ((livestemc(p) / livewdcn(ivt(p))) - (livestemc(p) / & + fstemcn(ivt(p)))) + frootn_to_retransn(p) = 0._r8 + if (ffrootcn(ivt(p)) > 0._r8) then + frootn_to_retransn(p) = t1 * ((frootc(p) / frootcn(ivt(p))) - (frootc(p) / & + ffrootcn(ivt(p)))) + end if else !leafn retrans flux is handled in phenology - frootn_to_retransn(p) = 0._r8 - livestemn_to_retransn(p)=0.0_r8 + frootn_to_retransn(p) = 0._r8 + livestemn_to_retransn(p)=0.0_r8 end if !fun grain_flag(p) = 1._r8 end if end if - - ! For AgroIBIS-based crop model, all repr allocation is assumed to go - ! into the last reproductive pool. In practice there is only a single - ! reproductive pool with the AgroIBIS-based crop model, but for - ! software testing we can have multiple, in which situation we want the - ! active pool to be the last one. - do k = 1, nrepr-1 - arepr(p,k) = 0._r8 - end do - arepr(p,nrepr) = 1._r8 - aroot(p) - astem(p) - aleaf(p) - - else ! pre emergence - ! allocation coefficients should be irrelevant because crops have no - ! live carbon pools; this applies to this "else" and to the "else" a few - ! lines down - aleaf(p) = 1.e-5_r8 - astem(p) = 0._r8 - aroot(p) = 0._r8 - do k = 1, nrepr - arepr(p,k) = 0._r8 - end do end if - - f1 = aroot(p) / aleaf(p) - f3 = astem(p) / aleaf(p) - do k = 1, nrepr - f5(k) = arepr(p,k) / aleaf(p) - end do - g1 = 0.25_r8 - - else ! .not croplive - f1 = 0._r8 - f3 = 0._r8 - do k = 1, nrepr - f5(k) = 0._r8 - end do - g1 = 0.25_r8 end if - end if - - ! based on available C, use constant allometric relationships to - ! determine N requirements - - !RF. I removed the growth respiration from this, because it is used to calculate - !plantCN for N uptake AND c_allometry for allocation. If we add gresp to the - !allometry calculation then we allocate too much carbon since gresp is not allocated here. - if (.not. use_fun) then - g1a = g1 - else - g1a = 0._r8 - end if - if (woody(ivt(p)) == 1.0_r8) then - c_allometry(p) = (1._r8+g1a)*(1._r8+f1+f3*(1._r8+f2)) - n_allometry(p) = 1._r8/cnl + f1/cnfr + (f3*f4*(1._r8+f2))/cnlw + & - (f3*(1._r8-f4)*(1._r8+f2))/cndw - else if (ivt(p) >= npcropmin) then ! skip generic crops - cng = graincn(ivt(p)) - f5_tot = 0._r8 - f5_n_tot = 0._r8 - do k = 1, nrepr - f5_tot = f5_tot + f5(k) - ! Note that currently we use the same C/N ratio for all grain components: - f5_n_tot = f5_n_tot + f5(k)/cng + end do + end if + + ! Beth's code: crops pull from retransn pool only during grain fill; + ! retransn pool has N from leaves, stems, and roots for + ! retranslocation + if (.not. use_fun) then + if (call_is_for_pcrop) then + do fp = 1, num_p + p = filter_p(fp) + + if (grain_flag(p) == 1._r8) then + avail_retransn(p) = plant_ndemand(p) + else + avail_retransn(p) = 0.0_r8 + end if end do - c_allometry(p) = (1._r8+g1a)*(1._r8+f1+f5_tot+f3*(1._r8+f2)) - n_allometry(p) = 1._r8/cnl + f1/cnfr + f5_n_tot + (f3*f4*(1._r8+f2))/cnlw + & - (f3*(1._r8-f4)*(1._r8+f2))/cndw else - c_allometry(p) = 1._r8+g1a+f1+f1*g1a - n_allometry(p) = 1._r8/cnl + f1/cnfr - end if + do fp = 1, num_p + p = filter_p(fp) - plant_ndemand(p) = availc(p)*(n_allometry(p)/c_allometry(p)) - - ! retranslocated N deployment depends on seasonal cycle of potential GPP - ! (requires one year run to accumulate demand) - - tempsum_potential_gpp(p) = tempsum_potential_gpp(p) + gpp(p) + if (annsum_potential_gpp(p) > 0._r8) then + avail_retransn(p) = (annmax_retransn(p)/2._r8)*(gpp(p)/annsum_potential_gpp(p))/dt + else + avail_retransn(p) = 0.0_r8 + end if + end do + end if - ! Adding the following line to carry max retransn info to CN Annual Update - tempmax_retransn(p) = max(tempmax_retransn(p),retransn(p)) + do fp = 1, num_p + p = filter_p(fp) - ! Beth's code: crops pull from retransn pool only during grain fill; - ! retransn pool has N from leaves, stems, and roots for - ! retranslocation - - if(.not.use_fun)then - - if (ivt(p) >= npcropmin .and. grain_flag(p) == 1._r8) then - avail_retransn(p) = plant_ndemand(p) - else if (ivt(p) < npcropmin .and. annsum_potential_gpp(p) > 0._r8) then - avail_retransn(p) = (annmax_retransn(p)/2._r8)*(gpp(p)/annsum_potential_gpp(p))/dt - else - avail_retransn(p) = 0.0_r8 - end if + ! make sure available retrans N doesn't exceed storage + avail_retransn(p) = min(avail_retransn(p), retransn(p)/dt) - ! make sure available retrans N doesn't exceed storage - avail_retransn(p) = min(avail_retransn(p), retransn(p)/dt) + ! modify plant N demand according to the availability of + ! retranslocated N + ! take from retransn pool at most the flux required to meet + ! plant ndemand - ! modify plant N demand according to the availability of - ! retranslocated N - ! take from retransn pool at most the flux required to meet - ! plant ndemand + if (plant_ndemand(p) > avail_retransn(p)) then + retransn_to_npool(p) = avail_retransn(p) + else + retransn_to_npool(p) = plant_ndemand(p) + end if - if (plant_ndemand(p) > avail_retransn(p)) then - retransn_to_npool(p) = avail_retransn(p) - else - retransn_to_npool(p) = plant_ndemand(p) - end if + if ( .not. use_fun ) then + plant_ndemand(p) = plant_ndemand(p) - retransn_to_npool(p) + else + if (season_decid(ivt(p)) == 1._r8.or.stress_decid(ivt(p))==1._r8) then + plant_ndemand(p) = plant_ndemand(p) - retransn_to_npool(p) + end if + end if + end do - if ( .not. use_fun ) then - plant_ndemand(p) = plant_ndemand(p) - retransn_to_npool(p) - else - if (season_decid(ivt(p)) == 1._r8.or.stress_decid(ivt(p))==1._r8) then - plant_ndemand(p) = plant_ndemand(p) - retransn_to_npool(p) - end if - end if - - end if !use_fun + end if !use_fun - end do ! end patch loop + end associate - end associate + end subroutine calc_plant_nitrogen_demand - end subroutine calc_plant_nitrogen_demand - end module NutrientCompetitionCLM45defaultMod diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 4188ab90f4..1e52314c90 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -18,17 +18,19 @@ module NutrientCompetitionFlexibleCNMod ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use clm_time_manager , only : get_step_size_real use decompMod , only : bounds_type use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch + use pftconMod , only : pftcon, npcropmin use NutrientCompetitionMethodMod, only : nutrient_competition_method_type - use NutrientCompetitionMethodMod, only : params_inst - use CropReprPoolsMod , only : nrepr - use clm_varctl , only : iulog - ! SSR troubleshooting - use abortutils , only : endrun - use shr_log_mod , only : errMsg => shr_log_errMsg + use CropReprPoolsMod , only : nrepr + use CNPhenologyMod , only : CropPhase + use CropType , only : cphase_leafemerge, cphase_grainfill + use clm_varctl , only : iulog, use_crop_agsys + use abortutils , only : endrun ! implicit none private @@ -59,6 +61,10 @@ module NutrientCompetitionFlexibleCNMod end interface nutrient_competition_FlexibleCN_type ! + ! !PRIVATE MEMBER FUNCTIONS: + private :: calc_npool_to_components_flexiblecn ! Calculate npool_to_* terms for a single patch using the FlexibleCN approach + private :: calc_npool_to_components_agsys ! Calculate npool_to_* terms for a single crop patch when using AgSys + character(len=*), parameter, private :: sourcefile = & __FILE__ !------------------------------------------------------------------------ @@ -116,7 +122,7 @@ subroutine InitHistory(this, bounds) ! ! !ARGUMENTS: class(nutrient_competition_FlexibleCN_type), intent(in) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: begp, endp @@ -142,8 +148,7 @@ subroutine calc_plant_nutrient_competition (this, & cnveg_carbonflux_inst, & c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - soilbiogeochem_nitrogenstate_inst, & - aroot, arepr, fpg_col) + soilbiogeochem_nitrogenstate_inst, fpg_col) ! ! !USES: use CNVegStateType , only : cnveg_state_type @@ -170,8 +175,6 @@ subroutine calc_plant_nutrient_competition (this, & type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst - real(r8), intent(in) :: aroot (bounds%begp:) - real(r8), intent(in) :: arepr(bounds%begp:,:) real(r8), intent(in) :: fpg_col (bounds%begc:) call this%calc_plant_cn_alloc(bounds, num_soilp, filter_soilp, & @@ -179,8 +182,6 @@ subroutine calc_plant_nutrient_competition (this, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, c13_cnveg_carbonflux_inst, & c14_cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_nitrogenstate_inst, & - aroot=aroot(bounds%begp:bounds%endp), & - arepr=arepr(bounds%begp:bounds%endp,:), & fpg_col=fpg_col(bounds%begc:bounds%endc)) end subroutine calc_plant_nutrient_competition @@ -190,13 +191,10 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & cnveg_state_inst, crop_inst, canopystate_inst, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, c13_cnveg_carbonflux_inst, & c14_cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - soilbiogeochem_nitrogenstate_inst, & - aroot, arepr, fpg_col) + soilbiogeochem_nitrogenstate_inst, fpg_col) ! ! !USES: - use pftconMod , only : pftcon, npcropmin use clm_varctl , only : use_c13, use_c14, carbon_resp_opt - use clm_time_manager , only : get_step_size_real use CNVegStateType , only : cnveg_state_type use CropType , only : crop_type use CanopyStateType , only : canopystate_type @@ -208,7 +206,7 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & use CNSharedParamsMod , only : use_fun use CNPrecisionControlMod , only : n_min use clm_varcon , only : spval - + ! ! !ARGUMENTS: class(nutrient_competition_FlexibleCN_type), intent(inout) :: this @@ -225,71 +223,32 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst - real(r8) , intent(in) :: aroot(bounds%begp:) - real(r8) , intent(in) :: arepr(bounds%begp:,:) real(r8) , intent(in) :: fpg_col(bounds%begc:) ! ! !LOCAL VARIABLES: integer :: c,p,k ! indices integer :: fp ! lake filter patch index real(r8) :: f1,f2,f3,f4,g1,g2 ! allocation parameters - real(r8) :: cnl,cnfr,cnlw,cndw ! C:N ratios for leaf, fine root, and wood real(r8) :: fcur ! fraction of current psn displayed as growth real(r8) :: gresp_storage ! temporary variable for growth resp to storage real(r8) :: nlc ! temporary variable for total new leaf carbon allocation real(r8) :: f5(nrepr) ! reproductive allocation parameters - real(r8) :: cng ! C:N ratio for grain (= cnlw for now; slevis) - real(r8) :: dt ! model time step - real(r8):: fsmn(bounds%begp:bounds%endp) ! A emperate variable for adjusting FUN uptakes - - real(r8):: frootcn_storage_actual - real(r8):: frootcn_actual - real(r8):: livestemcn_storage_actual - real(r8):: livestemcn_actual - real(r8):: livecrootcn_storage_actual - real(r8):: livecrootcn_actual - real(r8):: leafcn_max - real(r8):: frootcn_max - real(r8):: livewdcn_max + + real(r8):: frootcn_storage_actual + real(r8):: frootcn_actual + real(r8):: livestemcn_storage_actual + real(r8):: livestemcn_actual + real(r8):: livecrootcn_storage_actual + real(r8):: livecrootcn_actual + real(r8):: leafcn_max + real(r8):: frootcn_max + real(r8):: livewdcn_max real(r8):: frac_resp - real(r8):: npool_to_reproductiven_demand_tot - real(r8):: npool_to_reproductiven_storage_demand_tot - real(r8) :: npool_to_leafn_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_leafn_storage_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_frootn_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_frootn_storage_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_livestemn_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_livestemn_storage_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_livecrootn_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_livecrootn_storage_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_deadstemn_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_deadstemn_storage_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_deadcrootn_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_deadcrootn_storage_demand (bounds%begp:bounds%endp) - real(r8) :: npool_to_reproductiven_demand (bounds%begp:bounds%endp, nrepr) - real(r8) :: npool_to_reproductiven_storage_demand (bounds%begp:bounds%endp, nrepr) - real(r8) :: total_plant_Ndemand (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_leafn (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_leafn_storage (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_frootn (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_frootn_storage (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_livestemn (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_livestemn_storage (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_deadstemn (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_deadstemn_storage (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_livecrootn (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_livecrootn_storage (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_deadcrootn (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_deadcrootn_storage (bounds%begp:bounds%endp) - real(r8) :: frNdemand_npool_to_reproductiven (bounds%begp:bounds%endp, nrepr) - real(r8) :: frNdemand_npool_to_reproductiven_storage(bounds%begp:bounds%endp, nrepr) ! ----------------------------------------------------------------------- ! write(iulog,*) 'Entering calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' - SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)) , sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp, nrepr/)) , sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(fpg_col) == (/bounds%endc/)) , sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(this%actual_storage_leafcn) >= (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((lbound(this%actual_storage_leafcn) <= (/bounds%begp/)), sourcefile, __LINE__) @@ -307,9 +266,7 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) - deadwdcn => pftcon%deadwdcn , & ! Input: dead wood (xylem and heartwood) C:N (gC/gN) fcur2 => pftcon%fcur , & ! Input: allocation parameter: fraction of allocation that goes to currently displayed growth, remainder to storage - graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) grperc => pftcon%grperc , & ! Input: growth respiration parameter grpnow => pftcon%grpnow , & ! Input: growth respiration parameter evergreen => pftcon%evergreen , & ! Input: binary flag for evergreen leaf habit (0 or 1) @@ -317,8 +274,13 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested peaklai => cnveg_state_inst%peaklai_patch , & ! Input: [integer (:) ] 1: max allowed lai; 0: not at max - aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient - astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient + aleaf => cnveg_state_inst%aleaf_patch , & ! Input: [real(r8) (:) ] leaf allocation coefficient + astem => cnveg_state_inst%astem_patch , & ! Input: [real(r8) (:) ] stem allocation coefficient + aroot => cnveg_state_inst%aroot_patch , & ! Input: [real(r8) (:) ] root allocation coefficient + arepr => cnveg_state_inst%arepr_patch , & ! Input: [real(r8) (:,:) ] reproductive allocation coefficient(s) + ! aleaf_n, astem_n, aroot_n and arepr_n are also inputs when running with AgSys, + ! but they cannot be associated here because these pointers may be unallocated + ! if not running with AgSys c_allometry => cnveg_state_inst%c_allometry_patch , & ! Output: [real(r8) (:) ] C allocation index (DIM) annsum_npp => cnveg_carbonflux_inst%annsum_npp_patch , & ! Input: [real(r8) (:) ] annual sum of NPP, for wood allocation @@ -349,7 +311,7 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & cpool_to_gresp_storage => cnveg_carbonflux_inst%cpool_to_gresp_storage_patch , & ! Output: [real(r8) (:) ] allocation to growth respiration storage (gC/m2/s) cpool_to_reproductivec => cnveg_carbonflux_inst%cpool_to_reproductivec_patch , & ! Output: [real(r8) (:,:) ] allocation to grain C (gC/m2/s) cpool_to_reproductivec_storage => cnveg_carbonflux_inst%cpool_to_reproductivec_storage_patch , & ! Output: [real(r8) (:,:) ] allocation to grain C storage (gC/m2/s) - + laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index smin_no3_vr => soilbiogeochem_nitrogenstate_inst%smin_no3_vr_col , & ! Output: [real(r8) (:,:) ] (gN/m3) soil mineral NO3 @@ -384,9 +346,6 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & ) - ! set time steps - dt = get_step_size_real() - ! patch loop to distribute the available N between the competing patches ! on the basis of relative demand, and allocate C and N to new growth and storage @@ -414,10 +373,6 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & f4 = flivewd(ivt(p)) g1 = grperc(ivt(p)) g2 = grpnow(ivt(p)) - cnl = leafcn(ivt(p)) - cnfr = frootcn(ivt(p)) - cnlw = livewdcn(ivt(p)) - cndw = deadwdcn(ivt(p)) fcur = fcur2(ivt(p)) if (evergreen(ivt(p)) == 1._r8) then @@ -446,22 +401,22 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & ! ndays_active = days/year. This prevents the continued storage of C and N. ! turning off this correction (PET, 12/11/03), instead using bgtr in ! phenology algorithm. - - + + if(use_fun)then ! if we are using FUN, we get the N available from there. sminn_to_npool(p) = sminn_to_plant_fun(p) - else ! no FUN. :( we get N available from the FPG calculation in soilbiogeochemistry competition. - sminn_to_npool(p) = plant_ndemand(p) * fpg(c) + else ! no FUN. :( we get N available from the FPG calculation in soilbiogeochemistry competition. + sminn_to_npool(p) = plant_ndemand(p) * fpg(c) endif - + plant_nalloc(p) = sminn_to_npool(p) + retransn_to_npool(p) - + if(use_fun)then - plant_calloc(p) = npp_growth(p) + plant_calloc(p) = npp_growth(p) else plant_calloc(p) = availc(p) end if - + ! calculate the amount of new leaf C dictated by these allocation ! decisions, and calculate the daily fluxes of C and N to current ! growth and storage pools @@ -526,184 +481,64 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & end if cpool_to_gresp_storage(p) = gresp_storage * g1 * (1._r8 - g2) - - ! computing 1.) fractional N demand and 2.) N allocation after uptake for different plant parts - !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - ! computing nitrogen demand for different pools based on carbon allocated and CN ratio - npool_to_leafn_demand(p) = (nlc / cnl) * fcur - npool_to_leafn_storage_demand(p) = (nlc / cnl) * (1._r8 - fcur) - npool_to_frootn_demand(p) = (nlc * f1 / cnfr) * fcur - npool_to_frootn_storage_demand(p) = (nlc * f1 / cnfr) * (1._r8 - fcur) - if (woody(ivt(p)) == 1._r8) then - - npool_to_livestemn_demand(p) = (nlc * f3 * f4 / cnlw) * fcur - npool_to_livestemn_storage_demand(p) = (nlc * f3 * f4 / cnlw) * (1._r8 - fcur) - npool_to_deadstemn_demand(p) = (nlc * f3 * (1._r8 - f4) / cndw) * fcur - npool_to_deadstemn_storage_demand(p) = (nlc * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) - npool_to_livecrootn_demand(p) = (nlc * f2 * f3 * f4 / cnlw) * fcur - npool_to_livecrootn_storage_demand(p) = (nlc * f2 * f3 * f4 / cnlw) * (1._r8 - fcur) - npool_to_deadcrootn_demand(p) = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * fcur - npool_to_deadcrootn_storage_demand(p) = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) - end if - if (ivt(p) >= npcropmin) then ! skip 2 generic crops - - cng = graincn(ivt(p)) - npool_to_livestemn_demand(p) = (nlc * f3 * f4 / cnlw) * fcur - npool_to_livestemn_storage_demand(p) = (nlc * f3 * f4 / cnlw) * (1._r8 - fcur) - npool_to_deadstemn_demand(p) = (nlc * f3 * (1._r8 - f4) / cndw) * fcur - npool_to_deadstemn_storage_demand(p) = (nlc * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) - npool_to_livecrootn_demand(p) = (nlc * f2 * f3 * f4 / cnlw) * fcur - npool_to_livecrootn_storage_demand(p) = (nlc * f2 * f3 * f4 / cnlw) * (1._r8 - fcur) - npool_to_deadcrootn_demand(p) = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * fcur - npool_to_deadcrootn_storage_demand(p) = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) - do k = 1, nrepr - npool_to_reproductiven_demand(p,k) = (nlc * f5(k) / cng) * fcur - npool_to_reproductiven_storage_demand(p,k) = (nlc * f5(k) / cng) * (1._r8 -fcur) - end do - end if - - - ! computing 1.) fractional N demand for different plant parts -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - total_plant_Ndemand(p) = npool_to_leafn_demand(p) + npool_to_leafn_storage_demand(p) + & - npool_to_frootn_demand(p) + npool_to_frootn_storage_demand(p) - - if (woody(ivt(p)) == 1._r8) then - - total_plant_Ndemand(p) = npool_to_leafn_demand(p) + npool_to_leafn_storage_demand(p) + & - npool_to_frootn_demand(p) + npool_to_frootn_storage_demand(p) + & - npool_to_livestemn_demand(p) + npool_to_livestemn_storage_demand(p) + npool_to_deadstemn_demand(p) + & - npool_to_deadstemn_storage_demand(p) + & - npool_to_livecrootn_demand(p) + npool_to_livecrootn_storage_demand(p) + npool_to_deadcrootn_demand(p) + & - npool_to_deadcrootn_storage_demand(p) - - end if - if (ivt(p) >= npcropmin) then ! skip 2 generic crops - - npool_to_reproductiven_demand_tot = 0._r8 - npool_to_reproductiven_storage_demand_tot = 0._r8 - do k = 1, nrepr - npool_to_reproductiven_demand_tot = npool_to_reproductiven_demand_tot + & - npool_to_reproductiven_demand(p,k) - npool_to_reproductiven_storage_demand_tot = npool_to_reproductiven_storage_demand_tot + & - npool_to_reproductiven_storage_demand(p,k) - end do - - total_plant_Ndemand(p) = npool_to_leafn_demand(p) + npool_to_leafn_storage_demand(p) + & - npool_to_frootn_demand(p) + npool_to_frootn_storage_demand(p) + & - npool_to_livestemn_demand(p) + npool_to_livestemn_storage_demand(p) + npool_to_deadstemn_demand(p) + & - npool_to_deadstemn_storage_demand(p) + & - npool_to_livecrootn_demand(p) + npool_to_livecrootn_storage_demand(p) + npool_to_deadcrootn_demand(p) + & - npool_to_deadcrootn_storage_demand(p) + & - npool_to_reproductiven_demand_tot + npool_to_reproductiven_storage_demand_tot - - end if - - if (total_plant_Ndemand(p) == 0.0_r8) then ! removing division by zero - - frNdemand_npool_to_leafn(p) = 0.0_r8 - frNdemand_npool_to_leafn_storage(p) = 0.0_r8 - frNdemand_npool_to_frootn(p) = 0.0_r8 - frNdemand_npool_to_frootn_storage(p) = 0.0_r8 - if (woody(ivt(p)) == 1._r8) then - - frNdemand_npool_to_livestemn(p) = 0.0_r8 - frNdemand_npool_to_livestemn_storage(p) = 0.0_r8 - frNdemand_npool_to_deadstemn(p) = 0.0_r8 - frNdemand_npool_to_deadstemn_storage(p) = 0.0_r8 - frNdemand_npool_to_livecrootn(p) = 0.0_r8 - frNdemand_npool_to_livecrootn_storage(p) = 0.0_r8 - frNdemand_npool_to_deadcrootn(p) = 0.0_r8 - frNdemand_npool_to_deadcrootn_storage(p) = 0.0_r8 - end if - if (ivt(p) >= npcropmin) then ! skip 2 generic crops - - frNdemand_npool_to_livestemn(p) = 0.0_r8 - frNdemand_npool_to_livestemn_storage(p) = 0.0_r8 - frNdemand_npool_to_deadstemn(p) = 0.0_r8 - frNdemand_npool_to_deadstemn_storage(p) = 0.0_r8 - frNdemand_npool_to_livecrootn(p) = 0.0_r8 - frNdemand_npool_to_livecrootn_storage(p) = 0.0_r8 - frNdemand_npool_to_deadcrootn(p) = 0.0_r8 - frNdemand_npool_to_deadcrootn_storage(p) = 0.0_r8 - do k = 1, nrepr - frNdemand_npool_to_reproductiven(p,k) = 0.0_r8 - frNdemand_npool_to_reproductiven_storage(p,k) = 0.0_r8 - end do - end if - + if (use_crop_agsys .and. ivt(p) >= npcropmin) then + call calc_npool_to_components_agsys( & + ! Inputs + npool = npool(p), & + fcur = fcur, & + f4 = f4, & + ! The following inputs cannot appear in the associate statement at the + ! top of the subroutine because these pointers may be unallocated if not + ! running with AgSys: + aleaf_n = cnveg_state_inst%aleaf_n_patch(p), & + astem_n = cnveg_state_inst%astem_n_patch(p), & + aroot_n = cnveg_state_inst%aroot_n_patch(p), & + arepr_n = cnveg_state_inst%arepr_n_patch(p,:), & + + ! Outputs + npool_to_leafn = npool_to_leafn(p), & + npool_to_leafn_storage = npool_to_leafn_storage(p), & + npool_to_frootn = npool_to_frootn(p), & + npool_to_frootn_storage = npool_to_frootn_storage(p), & + npool_to_livestemn = npool_to_livestemn(p), & + npool_to_livestemn_storage = npool_to_livestemn_storage(p), & + npool_to_deadstemn = npool_to_deadstemn(p), & + npool_to_deadstemn_storage = npool_to_deadstemn_storage(p), & + npool_to_livecrootn = npool_to_livecrootn(p), & + npool_to_livecrootn_storage = npool_to_livecrootn_storage(p), & + npool_to_deadcrootn = npool_to_deadcrootn(p), & + npool_to_deadcrootn_storage = npool_to_deadcrootn_storage(p), & + npool_to_reproductiven = npool_to_reproductiven(p,:), & + npool_to_reproductiven_storage = npool_to_reproductiven_storage(p,:)) else - - frNdemand_npool_to_leafn(p) = npool_to_leafn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_leafn_storage(p) = npool_to_leafn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_frootn(p) = npool_to_frootn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_frootn_storage(p) = npool_to_frootn_storage_demand(p) / total_plant_Ndemand(p) - if (woody(ivt(p)) == 1._r8) then - - frNdemand_npool_to_livestemn(p) = npool_to_livestemn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_livestemn_storage(p) = npool_to_livestemn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadstemn(p) = npool_to_deadstemn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadstemn_storage(p) = npool_to_deadstemn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_livecrootn(p) = npool_to_livecrootn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_livecrootn_storage(p) = npool_to_livecrootn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadcrootn(p) = npool_to_deadcrootn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadcrootn_storage(p) = npool_to_deadcrootn_storage_demand(p) / total_plant_Ndemand(p) - end if - if (ivt(p) >= npcropmin) then ! skip 2 generic crops - - frNdemand_npool_to_livestemn(p) = npool_to_livestemn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_livestemn_storage(p) = npool_to_livestemn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadstemn(p) = npool_to_deadstemn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadstemn_storage(p) = npool_to_deadstemn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_livecrootn(p) = npool_to_livecrootn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_livecrootn_storage(p) = npool_to_livecrootn_storage_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadcrootn(p) = npool_to_deadcrootn_demand(p) / total_plant_Ndemand(p) - frNdemand_npool_to_deadcrootn_storage(p) = npool_to_deadcrootn_storage_demand(p) / total_plant_Ndemand(p) - do k = 1, nrepr - frNdemand_npool_to_reproductiven(p,k) = & - npool_to_reproductiven_demand(p,k) / total_plant_Ndemand(p) - frNdemand_npool_to_reproductiven_storage(p,k) = & - npool_to_reproductiven_storage_demand(p,k) / total_plant_Ndemand(p) - end do - end if - - end if -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - - - ! computing N allocation for different plant parts - ! allocating allocation to different plant parts in proportion to the fractional demand -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - npool_to_leafn(p) = frNdemand_npool_to_leafn(p) * npool(p) / dt - npool_to_leafn_storage(p) = frNdemand_npool_to_leafn_storage(p) * npool(p) / dt - npool_to_frootn(p) = frNdemand_npool_to_frootn(p) * npool(p) / dt - npool_to_frootn_storage(p) = frNdemand_npool_to_frootn_storage(p) * npool(p) / dt - if (woody(ivt(p)) == 1._r8) then - npool_to_livestemn(p) = frNdemand_npool_to_livestemn(p) * npool(p) / dt - npool_to_livestemn_storage(p) = frNdemand_npool_to_livestemn_storage(p) * npool(p) / dt - npool_to_deadstemn(p) = frNdemand_npool_to_deadstemn(p) * npool(p) / dt - npool_to_deadstemn_storage(p) = frNdemand_npool_to_deadstemn_storage(p) * npool(p) / dt - npool_to_livecrootn(p) = frNdemand_npool_to_livecrootn(p) * npool(p) / dt - npool_to_livecrootn_storage(p) = frNdemand_npool_to_livecrootn_storage(p) * npool(p) / dt - npool_to_deadcrootn(p) = frNdemand_npool_to_deadcrootn(p) * npool(p) / dt - npool_to_deadcrootn_storage(p) = frNdemand_npool_to_deadcrootn_storage(p) * npool(p) / dt - end if - if (ivt(p) >= npcropmin) then ! skip 2 generic crops - npool_to_livestemn(p) = frNdemand_npool_to_livestemn(p) * npool(p) / dt - npool_to_livestemn_storage(p) = frNdemand_npool_to_livestemn_storage(p) * npool(p) / dt - npool_to_deadstemn(p) = frNdemand_npool_to_deadstemn(p) * npool(p) / dt - npool_to_deadstemn_storage(p) = frNdemand_npool_to_deadstemn_storage(p) * npool(p) / dt - npool_to_livecrootn(p) = frNdemand_npool_to_livecrootn(p) * npool(p) / dt - npool_to_livecrootn_storage(p) = frNdemand_npool_to_livecrootn_storage(p) * npool(p) / dt - npool_to_deadcrootn(p) = frNdemand_npool_to_deadcrootn(p) * npool(p) / dt - npool_to_deadcrootn_storage(p) = frNdemand_npool_to_deadcrootn_storage(p) * npool(p) / dt - do k = 1, nrepr - npool_to_reproductiven(p,k) = frNdemand_npool_to_reproductiven(p,k) * npool(p) / dt - npool_to_reproductiven_storage(p,k) = frNdemand_npool_to_reproductiven_storage(p,k) * npool(p) / dt - end do + call calc_npool_to_components_flexiblecn( & + ! Inputs + npool = npool(p), & + ivt = ivt(p), & + nlc = nlc, & + fcur = fcur, & + f1 = f1, & + f2 = f2, & + f3 = f3, & + f4 = f4, & + f5 = f5, & + + ! Outputs + npool_to_leafn = npool_to_leafn(p), & + npool_to_leafn_storage = npool_to_leafn_storage(p), & + npool_to_frootn = npool_to_frootn(p), & + npool_to_frootn_storage = npool_to_frootn_storage(p), & + npool_to_livestemn = npool_to_livestemn(p), & + npool_to_livestemn_storage = npool_to_livestemn_storage(p), & + npool_to_deadstemn = npool_to_deadstemn(p), & + npool_to_deadstemn_storage = npool_to_deadstemn_storage(p), & + npool_to_livecrootn = npool_to_livecrootn(p), & + npool_to_livecrootn_storage = npool_to_livecrootn_storage(p), & + npool_to_deadcrootn = npool_to_deadcrootn(p), & + npool_to_deadcrootn_storage = npool_to_deadcrootn_storage(p), & + npool_to_reproductiven = npool_to_reproductiven(p,:), & + npool_to_reproductiven_storage = npool_to_reproductiven_storage(p,:)) end if -!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - cpool_to_resp(p) = 0.0_r8 cpool_to_leafc_resp(p) = 0.0_r8 @@ -900,19 +735,390 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & end subroutine calc_plant_cn_alloc + !----------------------------------------------------------------------- + subroutine calc_npool_to_components_flexiblecn( & + npool, ivt, nlc, fcur, f1, f2, f3, f4, f5, & + npool_to_leafn, npool_to_leafn_storage, & + npool_to_frootn, npool_to_frootn_storage, & + npool_to_livestemn, npool_to_livestemn_storage, & + npool_to_deadstemn, npool_to_deadstemn_storage, & + npool_to_livecrootn, npool_to_livecrootn_storage, & + npool_to_deadcrootn, npool_to_deadcrootn_storage, & + npool_to_reproductiven, npool_to_reproductiven_storage) + ! + ! !DESCRIPTION: + ! Calculate npool_to_* terms for a single patch using the FlexibleCN approach + ! + ! !ARGUMENTS: + real(r8), intent(in) :: npool ! temporary plant N pool (gN/m2) + integer, intent(in) :: ivt ! vegetation type + real(r8), intent(in) :: nlc ! new leaf carbon allocation (gC/m2/s) + real(r8), intent(in) :: fcur ! fraction of current psn displayed as growth + real(r8), intent(in) :: f1 ! C allocation parameter - fine_root:leaf ratio + real(r8), intent(in) :: f2 ! C allocation parameter - coarse_root:stem ratio + real(r8), intent(in) :: f3 ! C allocation parameter - stem:leaf ratio + real(r8), intent(in) :: f4 ! C allocation parameter - fraction of new wood that is live + real(r8), intent(in) :: f5(:) ! C allocation parameter - repr:leaf ratio for each crop reproductive pool + + ! Each of the following output variables is in units of gN/m2/s; they are + ! intent(inout) because some may remain unchanged in some circumstances. + real(r8), intent(inout) :: npool_to_leafn + real(r8), intent(inout) :: npool_to_leafn_storage + real(r8), intent(inout) :: npool_to_frootn + real(r8), intent(inout) :: npool_to_frootn_storage + real(r8), intent(inout) :: npool_to_livestemn + real(r8), intent(inout) :: npool_to_livestemn_storage + real(r8), intent(inout) :: npool_to_deadstemn + real(r8), intent(inout) :: npool_to_deadstemn_storage + real(r8), intent(inout) :: npool_to_livecrootn + real(r8), intent(inout) :: npool_to_livecrootn_storage + real(r8), intent(inout) :: npool_to_deadcrootn + real(r8), intent(inout) :: npool_to_deadcrootn_storage + real(r8), intent(inout) :: npool_to_reproductiven(:) + real(r8), intent(inout) :: npool_to_reproductiven_storage(:) + + ! + ! !LOCAL VARIABLES: + real(r8) :: cnl,cnfr,cnlw,cndw ! C:N ratios for leaf, fine root, and wood + real(r8) :: cng ! C:N ratio for grain (= cnlw for now; slevis) + real(r8) :: dt ! model time step + integer :: k + + real(r8) :: npool_to_reproductiven_demand_tot + real(r8) :: npool_to_reproductiven_storage_demand_tot + real(r8) :: npool_to_leafn_demand + real(r8) :: npool_to_leafn_storage_demand + real(r8) :: npool_to_frootn_demand + real(r8) :: npool_to_frootn_storage_demand + real(r8) :: npool_to_livestemn_demand + real(r8) :: npool_to_livestemn_storage_demand + real(r8) :: npool_to_livecrootn_demand + real(r8) :: npool_to_livecrootn_storage_demand + real(r8) :: npool_to_deadstemn_demand + real(r8) :: npool_to_deadstemn_storage_demand + real(r8) :: npool_to_deadcrootn_demand + real(r8) :: npool_to_deadcrootn_storage_demand + real(r8) :: npool_to_reproductiven_demand(nrepr) + real(r8) :: npool_to_reproductiven_storage_demand(nrepr) + real(r8) :: total_plant_Ndemand + real(r8) :: frNdemand_npool_to_leafn + real(r8) :: frNdemand_npool_to_leafn_storage + real(r8) :: frNdemand_npool_to_frootn + real(r8) :: frNdemand_npool_to_frootn_storage + real(r8) :: frNdemand_npool_to_livestemn + real(r8) :: frNdemand_npool_to_livestemn_storage + real(r8) :: frNdemand_npool_to_deadstemn + real(r8) :: frNdemand_npool_to_deadstemn_storage + real(r8) :: frNdemand_npool_to_livecrootn + real(r8) :: frNdemand_npool_to_livecrootn_storage + real(r8) :: frNdemand_npool_to_deadcrootn + real(r8) :: frNdemand_npool_to_deadcrootn_storage + real(r8) :: frNdemand_npool_to_reproductiven(nrepr) + real(r8) :: frNdemand_npool_to_reproductiven_storage(nrepr) + + character(len=*), parameter :: subname = 'calc_npool_to_components_flexiblecn' + !----------------------------------------------------------------------- + + SHR_ASSERT_ALL_FL((ubound(f5) == [nrepr]), sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(npool_to_reproductiven) == [nrepr]), sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(npool_to_reproductiven_storage) == [nrepr]), sourcefile, __LINE__) + + associate( & + woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) + leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) + frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) + livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) + deadwdcn => pftcon%deadwdcn , & ! Input: dead wood (xylem and heartwood) C:N (gC/gN) + graincn => pftcon%graincn & ! Input: grain C:N (gC/gN) + ) + + dt = get_step_size_real() + + cnl = leafcn(ivt) + cnfr = frootcn(ivt) + cnlw = livewdcn(ivt) + cndw = deadwdcn(ivt) + + ! computing 1.) fractional N demand and 2.) N allocation after uptake for different plant parts +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + ! computing nitrogen demand for different pools based on carbon allocated and CN ratio + npool_to_leafn_demand = (nlc / cnl) * fcur + npool_to_leafn_storage_demand = (nlc / cnl) * (1._r8 - fcur) + npool_to_frootn_demand = (nlc * f1 / cnfr) * fcur + npool_to_frootn_storage_demand = (nlc * f1 / cnfr) * (1._r8 - fcur) + if (woody(ivt) == 1._r8) then + + npool_to_livestemn_demand = (nlc * f3 * f4 / cnlw) * fcur + npool_to_livestemn_storage_demand = (nlc * f3 * f4 / cnlw) * (1._r8 - fcur) + npool_to_deadstemn_demand = (nlc * f3 * (1._r8 - f4) / cndw) * fcur + npool_to_deadstemn_storage_demand = (nlc * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) + npool_to_livecrootn_demand = (nlc * f2 * f3 * f4 / cnlw) * fcur + npool_to_livecrootn_storage_demand = (nlc * f2 * f3 * f4 / cnlw) * (1._r8 - fcur) + npool_to_deadcrootn_demand = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * fcur + npool_to_deadcrootn_storage_demand = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) + end if + if (ivt >= npcropmin) then ! skip 2 generic crops + + cng = graincn(ivt) + npool_to_livestemn_demand = (nlc * f3 * f4 / cnlw) * fcur + npool_to_livestemn_storage_demand = (nlc * f3 * f4 / cnlw) * (1._r8 - fcur) + npool_to_deadstemn_demand = (nlc * f3 * (1._r8 - f4) / cndw) * fcur + npool_to_deadstemn_storage_demand = (nlc * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) + npool_to_livecrootn_demand = (nlc * f2 * f3 * f4 / cnlw) * fcur + npool_to_livecrootn_storage_demand = (nlc * f2 * f3 * f4 / cnlw) * (1._r8 - fcur) + npool_to_deadcrootn_demand = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * fcur + npool_to_deadcrootn_storage_demand = (nlc * f2 * f3 * (1._r8 - f4) / cndw) * (1._r8 - fcur) + do k = 1, nrepr + npool_to_reproductiven_demand(k) = (nlc * f5(k) / cng) * fcur + npool_to_reproductiven_storage_demand(k) = (nlc * f5(k) / cng) * (1._r8 -fcur) + end do + end if + + + ! computing 1.) fractional N demand for different plant parts +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + total_plant_Ndemand = npool_to_leafn_demand + npool_to_leafn_storage_demand + & + npool_to_frootn_demand + npool_to_frootn_storage_demand + + if (woody(ivt) == 1._r8) then + + total_plant_Ndemand = npool_to_leafn_demand + npool_to_leafn_storage_demand + & + npool_to_frootn_demand + npool_to_frootn_storage_demand + & + npool_to_livestemn_demand + npool_to_livestemn_storage_demand + npool_to_deadstemn_demand + & + npool_to_deadstemn_storage_demand + & + npool_to_livecrootn_demand + npool_to_livecrootn_storage_demand + npool_to_deadcrootn_demand + & + npool_to_deadcrootn_storage_demand + + end if + if (ivt >= npcropmin) then ! skip 2 generic crops + + npool_to_reproductiven_demand_tot = 0._r8 + npool_to_reproductiven_storage_demand_tot = 0._r8 + do k = 1, nrepr + npool_to_reproductiven_demand_tot = npool_to_reproductiven_demand_tot + & + npool_to_reproductiven_demand(k) + npool_to_reproductiven_storage_demand_tot = npool_to_reproductiven_storage_demand_tot + & + npool_to_reproductiven_storage_demand(k) + end do + + total_plant_Ndemand = npool_to_leafn_demand + npool_to_leafn_storage_demand + & + npool_to_frootn_demand + npool_to_frootn_storage_demand + & + npool_to_livestemn_demand + npool_to_livestemn_storage_demand + npool_to_deadstemn_demand + & + npool_to_deadstemn_storage_demand + & + npool_to_livecrootn_demand + npool_to_livecrootn_storage_demand + npool_to_deadcrootn_demand + & + npool_to_deadcrootn_storage_demand + & + npool_to_reproductiven_demand_tot + npool_to_reproductiven_storage_demand_tot + + end if + + if (total_plant_Ndemand == 0.0_r8) then ! removing division by zero + + frNdemand_npool_to_leafn = 0.0_r8 + frNdemand_npool_to_leafn_storage = 0.0_r8 + frNdemand_npool_to_frootn = 0.0_r8 + frNdemand_npool_to_frootn_storage = 0.0_r8 + if (woody(ivt) == 1._r8) then + + frNdemand_npool_to_livestemn = 0.0_r8 + frNdemand_npool_to_livestemn_storage = 0.0_r8 + frNdemand_npool_to_deadstemn = 0.0_r8 + frNdemand_npool_to_deadstemn_storage = 0.0_r8 + frNdemand_npool_to_livecrootn = 0.0_r8 + frNdemand_npool_to_livecrootn_storage = 0.0_r8 + frNdemand_npool_to_deadcrootn = 0.0_r8 + frNdemand_npool_to_deadcrootn_storage = 0.0_r8 + end if + if (ivt >= npcropmin) then ! skip 2 generic crops + + frNdemand_npool_to_livestemn = 0.0_r8 + frNdemand_npool_to_livestemn_storage = 0.0_r8 + frNdemand_npool_to_deadstemn = 0.0_r8 + frNdemand_npool_to_deadstemn_storage = 0.0_r8 + frNdemand_npool_to_livecrootn = 0.0_r8 + frNdemand_npool_to_livecrootn_storage = 0.0_r8 + frNdemand_npool_to_deadcrootn = 0.0_r8 + frNdemand_npool_to_deadcrootn_storage = 0.0_r8 + do k = 1, nrepr + frNdemand_npool_to_reproductiven(k) = 0.0_r8 + frNdemand_npool_to_reproductiven_storage(k) = 0.0_r8 + end do + end if + + else + + frNdemand_npool_to_leafn = npool_to_leafn_demand / total_plant_Ndemand + frNdemand_npool_to_leafn_storage = npool_to_leafn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_frootn = npool_to_frootn_demand / total_plant_Ndemand + frNdemand_npool_to_frootn_storage = npool_to_frootn_storage_demand / total_plant_Ndemand + if (woody(ivt) == 1._r8) then + + frNdemand_npool_to_livestemn = npool_to_livestemn_demand / total_plant_Ndemand + frNdemand_npool_to_livestemn_storage = npool_to_livestemn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_deadstemn = npool_to_deadstemn_demand / total_plant_Ndemand + frNdemand_npool_to_deadstemn_storage = npool_to_deadstemn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_livecrootn = npool_to_livecrootn_demand / total_plant_Ndemand + frNdemand_npool_to_livecrootn_storage = npool_to_livecrootn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_deadcrootn = npool_to_deadcrootn_demand / total_plant_Ndemand + frNdemand_npool_to_deadcrootn_storage = npool_to_deadcrootn_storage_demand / total_plant_Ndemand + end if + if (ivt >= npcropmin) then ! skip 2 generic crops + + frNdemand_npool_to_livestemn = npool_to_livestemn_demand / total_plant_Ndemand + frNdemand_npool_to_livestemn_storage = npool_to_livestemn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_deadstemn = npool_to_deadstemn_demand / total_plant_Ndemand + frNdemand_npool_to_deadstemn_storage = npool_to_deadstemn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_livecrootn = npool_to_livecrootn_demand / total_plant_Ndemand + frNdemand_npool_to_livecrootn_storage = npool_to_livecrootn_storage_demand / total_plant_Ndemand + frNdemand_npool_to_deadcrootn = npool_to_deadcrootn_demand / total_plant_Ndemand + frNdemand_npool_to_deadcrootn_storage = npool_to_deadcrootn_storage_demand / total_plant_Ndemand + do k = 1, nrepr + frNdemand_npool_to_reproductiven(k) = & + npool_to_reproductiven_demand(k) / total_plant_Ndemand + frNdemand_npool_to_reproductiven_storage(k) = & + npool_to_reproductiven_storage_demand(k) / total_plant_Ndemand + end do + end if + + end if +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + + ! computing N allocation for different plant parts + ! allocating allocation to different plant parts in proportion to the fractional demand +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + npool_to_leafn = frNdemand_npool_to_leafn * npool / dt + npool_to_leafn_storage = frNdemand_npool_to_leafn_storage * npool / dt + npool_to_frootn = frNdemand_npool_to_frootn * npool / dt + npool_to_frootn_storage = frNdemand_npool_to_frootn_storage * npool / dt + if (woody(ivt) == 1._r8) then + npool_to_livestemn = frNdemand_npool_to_livestemn * npool / dt + npool_to_livestemn_storage = frNdemand_npool_to_livestemn_storage * npool / dt + npool_to_deadstemn = frNdemand_npool_to_deadstemn * npool / dt + npool_to_deadstemn_storage = frNdemand_npool_to_deadstemn_storage * npool / dt + npool_to_livecrootn = frNdemand_npool_to_livecrootn * npool / dt + npool_to_livecrootn_storage = frNdemand_npool_to_livecrootn_storage * npool / dt + npool_to_deadcrootn = frNdemand_npool_to_deadcrootn * npool / dt + npool_to_deadcrootn_storage = frNdemand_npool_to_deadcrootn_storage * npool / dt + end if + if (ivt >= npcropmin) then ! skip 2 generic crops + npool_to_livestemn = frNdemand_npool_to_livestemn * npool / dt + npool_to_livestemn_storage = frNdemand_npool_to_livestemn_storage * npool / dt + npool_to_deadstemn = frNdemand_npool_to_deadstemn * npool / dt + npool_to_deadstemn_storage = frNdemand_npool_to_deadstemn_storage * npool / dt + npool_to_livecrootn = frNdemand_npool_to_livecrootn * npool / dt + npool_to_livecrootn_storage = frNdemand_npool_to_livecrootn_storage * npool / dt + npool_to_deadcrootn = frNdemand_npool_to_deadcrootn * npool / dt + npool_to_deadcrootn_storage = frNdemand_npool_to_deadcrootn_storage * npool / dt + do k = 1, nrepr + npool_to_reproductiven(k) = frNdemand_npool_to_reproductiven(k) * npool / dt + npool_to_reproductiven_storage(k) = frNdemand_npool_to_reproductiven_storage(k) * npool / dt + end do + end if +!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + end associate + end subroutine calc_npool_to_components_flexiblecn + + !----------------------------------------------------------------------- + subroutine calc_npool_to_components_agsys( & + npool, fcur, f4, aleaf_n, astem_n, aroot_n, arepr_n, & + npool_to_leafn, npool_to_leafn_storage, & + npool_to_frootn, npool_to_frootn_storage, & + npool_to_livestemn, npool_to_livestemn_storage, & + npool_to_deadstemn, npool_to_deadstemn_storage, & + npool_to_livecrootn, npool_to_livecrootn_storage, & + npool_to_deadcrootn, npool_to_deadcrootn_storage, & + npool_to_reproductiven, npool_to_reproductiven_storage) + ! + ! !DESCRIPTION: + ! Calculate npool_to_* terms for a single crop patch when using AgSys + ! + ! Note that this assumes that there is no allocation to coarse roots + ! + ! !ARGUMENTS: + real(r8), intent(in) :: npool ! temporary plant N pool (gN/m2) + real(r8), intent(in) :: fcur ! fraction of current psn displayed as growth + real(r8), intent(in) :: f4 ! C allocation parameter - fraction of new wood that is live + real(r8), intent(in) :: aleaf_n ! leaf allocation coefficient for N + real(r8), intent(in) :: astem_n ! stem allocation coefficient for N + real(r8), intent(in) :: aroot_n ! root allocation coefficient for N + real(r8), intent(in) :: arepr_n(:) ! reproductive allocation coefficient(s) for N + + ! Each of the following output variables is in units of gN/m2/s + real(r8), intent(out) :: npool_to_leafn + real(r8), intent(out) :: npool_to_leafn_storage + real(r8), intent(out) :: npool_to_frootn + real(r8), intent(out) :: npool_to_frootn_storage + real(r8), intent(out) :: npool_to_livestemn + real(r8), intent(out) :: npool_to_livestemn_storage + real(r8), intent(out) :: npool_to_deadstemn + real(r8), intent(out) :: npool_to_deadstemn_storage + real(r8), intent(out) :: npool_to_livecrootn + real(r8), intent(out) :: npool_to_livecrootn_storage + real(r8), intent(out) :: npool_to_deadcrootn + real(r8), intent(out) :: npool_to_deadcrootn_storage + real(r8), intent(out) :: npool_to_reproductiven(:) + real(r8), intent(out) :: npool_to_reproductiven_storage(:) + + ! + ! !LOCAL VARIABLES: + real(r8) :: dt ! model time step + integer :: k + + character(len=*), parameter :: subname = 'calc_npool_to_components_agsys' + !----------------------------------------------------------------------- + + SHR_ASSERT_ALL_FL((ubound(arepr_n) == [nrepr]), sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(npool_to_reproductiven) == [nrepr]), sourcefile, __LINE__) + SHR_ASSERT_ALL_FL((ubound(npool_to_reproductiven_storage) == [nrepr]), sourcefile, __LINE__) + + dt = get_step_size_real() + + npool_to_leafn = aleaf_n * fcur * npool / dt + npool_to_leafn_storage = aleaf_n * (1._r8 - fcur) * npool / dt + + npool_to_frootn = aroot_n * fcur * npool / dt + npool_to_frootn_storage = aroot_n * (1._r8 - fcur) * npool / dt + + npool_to_livestemn = astem_n * f4 * fcur * npool / dt + npool_to_livestemn_storage = astem_n * f4 * (1._r8 - fcur) * npool / dt + npool_to_deadstemn = astem_n * (1._r8 - f4) * fcur * npool / dt + npool_to_deadstemn_storage = astem_n * (1._r8 - f4) * (1._r8 - fcur) * npool / dt + + ! Assume no allocation to coarse roots for crops. If there *were* allocation to coarse + ! roots (via a non-zero croot_stem), we would have bigger issues with consistency + ! between AgSys's desired allocation and the actual C/N allocation: the way this + ! allocation is currently formulated, non-zero allocation to coarse roots implies that + ! things like aleaf and arepr aren't truly the fractional allocation to leaves and + ! reproductive organs: the actual allocation fractions end up being reduced somewhat + ! via a normalizing factor that differs from 1. + ! + ! It's not really necessary to explicitly set these to 0 every time step, but we do + ! it to try make it obvious that this will need to change if we ever want to have + ! non-zero allocation to coarse roots for crops. + npool_to_livecrootn = 0._r8 + npool_to_livecrootn_storage = 0._r8 + npool_to_deadcrootn = 0._r8 + npool_to_deadcrootn_storage = 0._r8 + + do k = 1, nrepr + npool_to_reproductiven(k) = arepr_n(k) * fcur * npool / dt + npool_to_reproductiven_storage(k) = arepr_n(k) * (1._r8 - fcur) * npool / dt + end do + + end subroutine calc_npool_to_components_agsys + ! ----------------------------------------------------------------------- - subroutine calc_plant_nutrient_demand(this, bounds, num_soilp, filter_soilp,& - photosyns_inst, crop_inst, canopystate_inst, & + subroutine calc_plant_nutrient_demand(this, bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, canopystate_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & - energyflux_inst, & - aroot, arepr) + energyflux_inst) ! ! !USES: use CanopyStateType , only : canopystate_type - use PhotosynthesisMod , only : photosyns_type use CropType , only : crop_type use CNVegStateType , only : cnveg_state_type use CNVegCarbonStateType , only : cnveg_carbonstate_type @@ -925,57 +1131,65 @@ subroutine calc_plant_nutrient_demand(this, bounds, num_soilp, filter_soilp,& ! !ARGUMENTS: class(nutrient_competition_FlexibleCN_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(photosyns_type) , intent(in) :: photosyns_inst + + ! This subroutine is meant to be called separately for non-prognostic-crop points and + ! prognostic-crop points. (The reason for this is so that the call for prognostic-crop + ! points can be skipped when a separate crop model is calculating these variables.) In + ! the call for non-prognostic-crop points, this filter should be the soilnopcropp + ! filter and call_is_for_pcrop should be false; in the call for prognostic-crop + ! points, this filter should be the pcropp filter and call_is_for_pcrop should be + ! true. + integer , intent(in) :: num_p ! number of patches in filter + integer , intent(in) :: filter_p(:) ! patch filter + logical , intent(in) :: call_is_for_pcrop + type(crop_type) , intent(in) :: crop_inst type(canopystate_type) , intent(in) :: canopystate_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst - type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_carbonflux_type) , intent(in) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst type(energyflux_type) , intent(in) :: energyflux_inst - real(r8) , intent(out) :: aroot(bounds%begp:) - real(r8) , intent(out) :: arepr(bounds%begp:,:) !----------------------------------------------------------------------- - call this%calc_plant_nitrogen_demand(bounds, num_soilp, filter_soilp, & - photosyns_inst, crop_inst, canopystate_inst, & + call this%calc_plant_nitrogen_demand(bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, canopystate_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & - energyflux_inst, & - aroot=aroot(bounds%begp:bounds%endp), & - arepr=arepr(bounds%begp:bounds%endp,:)) + energyflux_inst) end subroutine calc_plant_nutrient_demand !----------------------------------------------------------------------- - subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & - photosyns_inst, crop_inst, canopystate_inst, & + subroutine calc_plant_nitrogen_demand(this, bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, canopystate_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & - energyflux_inst, & - aroot, arepr) + energyflux_inst) + ! + ! !DESCRIPTION: + ! Sets the following output variables that are used elsewhere: + ! - plant_ndemand + ! - retransn_to_npool + ! - leafn_to_retransn + ! - frootn_to_retransn + ! - livestemn_to_retransn ! ! !USES: use pftconMod , only : npcropmin, pftcon use pftconMod , only : ntmp_soybean, nirrig_tmp_soybean use pftconMod , only : ntrp_soybean, nirrig_trp_soybean - use clm_varcon , only : secspday, dzsoi_decomp - use clm_varctl , only : use_c13, use_c14 + use clm_varcon , only : dzsoi_decomp use clm_varpar , only : nlevdecomp use clm_time_manager , only : get_step_size_real use CanopyStateType , only : canopystate_type - use PhotosynthesisMod , only : photosyns_type use CropType , only : crop_type use CNVegStateType , only : cnveg_state_type use CNVegCarbonStateType , only : cnveg_carbonstate_type @@ -991,41 +1205,34 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! !ARGUMENTS: class(nutrient_competition_FlexibleCN_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(photosyns_type) , intent(in) :: photosyns_inst + + ! This subroutine is meant to be called separately for non-prognostic-crop points and + ! prognostic-crop points. (The reason for this is so that the call for prognostic-crop + ! points can be skipped when a separate crop model is calculating these variables.) In + ! the call for non-prognostic-crop points, this filter should be the soilnopcropp + ! filter and call_is_for_pcrop should be false; in the call for prognostic-crop + ! points, this filter should be the pcropp filter and call_is_for_pcrop should be + ! true. + integer , intent(in) :: num_p ! number of patches in filter + integer , intent(in) :: filter_p(:) ! patch filter + logical , intent(in) :: call_is_for_pcrop + type(crop_type) , intent(in) :: crop_inst type(canopystate_type) , intent(in) :: canopystate_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst - type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_carbonflux_type) , intent(in) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst type(energyflux_type) , intent(in) :: energyflux_inst - real(r8) , intent(out) :: aroot(bounds%begp:) - real(r8) , intent(out) :: arepr(bounds%begp:,:) ! ! !LOCAL VARIABLES: - integer :: c, p, j, k ! indices + integer :: c, p, j ! indices integer :: fp ! lake filter patch index - real(r8) :: mr ! maintenance respiration (gC/m2/s) - real(r8) :: reproductive_mr_tot ! total maintenance respiration from grain components (gC/m2/s) - real(r8) :: f1, f2, f3, f4, g1, g2 ! allocation parameters - real(r8) :: g1a ! g1 included in allocation/allometry - real(r8) :: cnl, cnfr, cnlw, cndw ! C:N ratios for leaf, fine root, and wood - real(r8) :: curmr, curmr_ratio ! xsmrpool temporary variables - real(r8) :: f5(nrepr) ! reproductive allocation parameters - real(r8) :: cng ! C:N ratio for grain (= cnlw for now; slevis) - real(r8) :: fleaf ! fraction allocated to leaf real(r8) :: t1 ! temporary variable real(r8) :: dt ! model time step - real(r8) :: dayscrecover ! number of days to recover negative cpool - real(r8) :: f5_tot ! sum of f5 terms - real(r8) :: f5_n_tot ! sum of f5 terms converted from C to N real(r8) :: f_N (bounds%begp:bounds%endp) real(r8) :: Kmin real(r8) :: leafcn_max @@ -1035,113 +1242,57 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & real(r8) :: substrate_term real(r8) :: temp_scalar real(r8) :: Vmax_N + real(r8) :: crop_phase (bounds%begp:bounds%endp) real(r8) :: allocation_leaf (bounds%begp:bounds%endp) real(r8) :: allocation_stem (bounds%begp:bounds%endp) real(r8) :: allocation_froot (bounds%begp:bounds%endp) + character(len=*), parameter :: subname = "calc_plant_nitrogen_demand" ! ----------------------------------------------------------------------- ! write(iulog,*) 'Entering calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' - SHR_ASSERT_ALL_FL((ubound(aroot) == (/bounds%endp/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(arepr) == (/bounds%endp, nrepr/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(this%actual_leafcn) >= (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((lbound(this%actual_leafcn) <= (/bounds%begp/)), sourcefile, __LINE__) associate( & ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type - woody => pftcon%woody , & ! Input: binary flag for woody lifeform (1=woody, 0=not woody) - froot_leaf => pftcon%froot_leaf , & ! Input: allocation parameter: new fine root C per new leaf C (gC/gC) - croot_stem => pftcon%croot_stem , & ! Input: allocation parameter: new coarse root C per new stem C (gC/gC) - stem_leaf => pftcon%stem_leaf , & ! Input: allocation parameter: new stem c per new leaf C (gC/gC) - flivewd => pftcon%flivewd , & ! Input: allocation parameter: fraction of new wood that is live (phloem and ray parenchyma) (no units) leafcn => pftcon%leafcn , & ! Input: leaf C:N (gC/gN) - frootcn => pftcon%frootcn , & ! Input: fine root C:N (gC/gN) - livewdcn => pftcon%livewdcn , & ! Input: live wood (phloem and ray parenchyma) C:N (gC/gN) - deadwdcn => pftcon%deadwdcn , & ! Input: dead wood (xylem and heartwood) C:N (gC/gN) - graincn => pftcon%graincn , & ! Input: grain C:N (gC/gN) fleafcn => pftcon%fleafcn , & ! Input: leaf c:n during organ fill ffrootcn => pftcon%ffrootcn , & ! Input: froot c:n during organ fill fstemcn => pftcon%fstemcn , & ! Input: stem c:n during organ fill - bfact => pftcon%bfact , & ! Input: parameter used below - aleaff => pftcon%aleaff , & ! Input: parameter used below - arootf => pftcon%arootf , & ! Input: parameter used below astemf => pftcon%astemf , & ! Input: parameter used below - arooti => pftcon%arooti , & ! Input: parameter used below - fleafi => pftcon%fleafi , & ! Input: parameter used below - allconsl => pftcon%allconsl , & ! Input: parameter used below - allconss => pftcon%allconss , & ! Input: parameter used below - grperc => pftcon%grperc , & ! Input: parameter used below - grpnow => pftcon%grpnow , & ! Input: parameter used below - declfact => pftcon%declfact , & ! Input: season_decid => pftcon%season_decid , & ! Input: binary flag for seasonal-deciduous leaf habit (0 or 1) stress_decid => pftcon%stress_decid , & ! Input: binary flag for stress-deciduous leaf habit (0 or 1) - psnsun => photosyns_inst%psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) - psnsha => photosyns_inst%psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) - c13_psnsun => photosyns_inst%c13_psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) - c13_psnsha => photosyns_inst%c13_psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) - c14_psnsun => photosyns_inst%c14_psnsun_patch , & ! Input: [real(r8) (:) ] sunlit leaf-level photosynthesis (umol CO2 /m**2/ s) - c14_psnsha => photosyns_inst%c14_psnsha_patch , & ! Input: [real(r8) (:) ] shaded leaf-level photosynthesis (umol CO2 /m**2/ s) laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest - leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] =gdd from top soil layer temperature croplive => crop_inst%croplive_patch , & ! Input: [logical (:) ] flag, true if planted, not harvested - gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Input: [real(r8) (:) ] gdd needed to harvest - huileaf => cnveg_state_inst%huileaf_patch , & ! Input: [real(r8) (:) ] heat unit index needed from planting to leaf emergence - huigrain => cnveg_state_inst%huigrain_patch , & ! Input: [real(r8) (:) ] same to reach vegetative maturity - peaklai => cnveg_state_inst%peaklai_patch , & ! Input: [integer (:) ] 1: max allowed lai; 0: not at max - aleafi => cnveg_state_inst%aleafi_patch , & ! Output: [real(r8) (:) ] saved allocation coefficient from phase 2 - astemi => cnveg_state_inst%astemi_patch , & ! Output: [real(r8) (:) ] saved allocation coefficient from phase 2 - aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient - astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient + astem => cnveg_state_inst%astem_patch , & ! Input: [real(r8) (:) ] stem allocation coefficient + c_allometry => cnveg_state_inst%c_allometry_patch , & ! Input: [real(r8) (:) ] C allocation index (DIM) + n_allometry => cnveg_state_inst%n_allometry_patch , & ! Input: [real(r8) (:) ] N allocation index (DIM) + annsum_potential_gpp => cnveg_state_inst%annsum_potential_gpp_patch , & ! Input: [real(r8) (:) ] annual sum of potential GPP + annmax_retransn => cnveg_state_inst%annmax_retransn_patch , & ! Input: [real(r8) (:) ] annual max of retranslocated N pool grain_flag => cnveg_state_inst%grain_flag_patch , & ! Output: [real(r8) (:) ] 1: grain fill stage; 0: not - c_allometry => cnveg_state_inst%c_allometry_patch , & ! Output: [real(r8) (:) ] C allocation index (DIM) - n_allometry => cnveg_state_inst%n_allometry_patch , & ! Output: [real(r8) (:) ] N allocation index (DIM) tempsum_potential_gpp => cnveg_state_inst%tempsum_potential_gpp_patch , & ! Output: [real(r8) (:) ] temporary annual sum of potential GPP tempmax_retransn => cnveg_state_inst%tempmax_retransn_patch , & ! Output: [real(r8) (:) ] temporary annual max of retranslocated N pool (gN/m2) - annsum_potential_gpp => cnveg_state_inst%annsum_potential_gpp_patch , & ! Output: [real(r8) (:) ] annual sum of potential GPP - annmax_retransn => cnveg_state_inst%annmax_retransn_patch , & ! Output: [real(r8) (:) ] annual max of retranslocated N pool - xsmrpool => cnveg_carbonstate_inst%xsmrpool_patch , & ! Input: [real(r8) (:) ] (gC/m2) temporary photosynthate C pool leafc => cnveg_carbonstate_inst%leafc_patch , & ! Input: [real(r8) (:) ] frootc => cnveg_carbonstate_inst%frootc_patch , & ! Input: [real(r8) (:) ] livestemc => cnveg_carbonstate_inst%livestemc_patch , & ! Input: [real(r8) (:) ] livecrootc => cnveg_carbonstate_inst%livecrootc_patch , & ! Input: [real(r8) (:) ] retransn => cnveg_nitrogenstate_inst%retransn_patch , & ! Input: [real(r8) (:) ] (gN/m2) plant pool of retranslocated N - annsum_npp => cnveg_carbonflux_inst%annsum_npp_patch , & ! Input: [real(r8) (:) ] annual sum of NPP, for wood allocation - leaf_mr => cnveg_carbonflux_inst%leaf_mr_patch , & ! Input: [real(r8) (:) ] - froot_mr => cnveg_carbonflux_inst%froot_mr_patch , & ! Input: [real(r8) (:) ] - livestem_mr => cnveg_carbonflux_inst%livestem_mr_patch , & ! Input: [real(r8) (:) ] - livecroot_mr => cnveg_carbonflux_inst%livecroot_mr_patch , & ! Input: [real(r8) (:) ] - reproductive_mr => cnveg_carbonflux_inst%reproductive_mr_patch , & ! Input: [real(r8) (:,:) ] - gpp => cnveg_carbonflux_inst%gpp_before_downreg_patch , & ! Output: [real(r8) (:) ] GPP flux before downregulation (gC/m2/s) - availc => cnveg_carbonflux_inst%availc_patch , & ! Output: [real(r8) (:) ] C flux available for allocation (gC/m2/s) - xsmrpool_recover => cnveg_carbonflux_inst%xsmrpool_recover_patch , & ! Output: [real(r8) (:) ] C flux assigned to recovery of negative cpool (gC/m2/s) - psnsun_to_cpool => cnveg_carbonflux_inst%psnsun_to_cpool_patch , & ! Output: [real(r8) (:) ] - psnshade_to_cpool => cnveg_carbonflux_inst%psnshade_to_cpool_patch , & ! Output: [real(r8) (:) ] - leaf_curmr => cnveg_carbonflux_inst%leaf_curmr_patch , & ! Output: [real(r8) (:) ] - froot_curmr => cnveg_carbonflux_inst%froot_curmr_patch , & ! Output: [real(r8) (:) ] - livestem_curmr => cnveg_carbonflux_inst%livestem_curmr_patch , & ! Output: [real(r8) (:) ] - livecroot_curmr => cnveg_carbonflux_inst%livecroot_curmr_patch , & ! Output: [real(r8) (:) ] - reproductive_curmr => cnveg_carbonflux_inst%reproductive_curmr_patch , & ! Output: [real(r8) (:,:) ] - leaf_xsmr => cnveg_carbonflux_inst%leaf_xsmr_patch , & ! Output: [real(r8) (:) ] - froot_xsmr => cnveg_carbonflux_inst%froot_xsmr_patch , & ! Output: [real(r8) (:) ] - livestem_xsmr => cnveg_carbonflux_inst%livestem_xsmr_patch , & ! Output: [real(r8) (:) ] - livecroot_xsmr => cnveg_carbonflux_inst%livecroot_xsmr_patch , & ! Output: [real(r8) (:) ] - reproductive_xsmr => cnveg_carbonflux_inst%reproductive_xsmr_patch , & ! Output: [real(r8) (:,:) ] - cpool_to_xsmrpool => cnveg_carbonflux_inst%cpool_to_xsmrpool_patch , & ! Output: [real(r8) (:) ] + gpp => cnveg_carbonflux_inst%gpp_before_downreg_patch , & ! Input: [real(r8) (:) ] GPP flux before downregulation (gC/m2/s) + availc => cnveg_carbonflux_inst%availc_patch , & ! Input: [real(r8) (:) ] C flux available for allocation (gC/m2/s) leafn => cnveg_nitrogenstate_inst%leafn_patch , & ! Input: [real(r8) (:) ] (gN/m2) leaf N plant_ndemand => cnveg_nitrogenflux_inst%plant_ndemand_patch , & ! Output: [real(r8) (:) ] N flux required to support initial GPP (gN/m2/s) avail_retransn => cnveg_nitrogenflux_inst%avail_retransn_patch , & ! Output: [real(r8) (:) ] N flux available from retranslocation pool (gN/m2/s) retransn_to_npool => cnveg_nitrogenflux_inst%retransn_to_npool_patch , & ! Output: [real(r8) (:) ] deployment of retranslocated N (gN/m2/s) - sminn_to_npool => cnveg_nitrogenflux_inst%sminn_to_npool_patch , & ! Output: [real(r8) (:) ] deployment of soil mineral N uptake (gN/m2/s) leafn_to_retransn => cnveg_nitrogenflux_inst%leafn_to_retransn_patch , & ! Output: [real(r8) (:) ] frootn_to_retransn => cnveg_nitrogenflux_inst%frootn_to_retransn_patch , & ! Output: [real(r8) (:) ] livestemn_to_retransn => cnveg_nitrogenflux_inst%livestemn_to_retransn_patch,& ! Output: [real(r8) (:) ] @@ -1156,240 +1307,83 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & ! set time steps dt = get_step_size_real() - ! set number of days to recover negative cpool - dayscrecover = params_inst%dayscrecover ! loop over patches to assess the total plant N demand - do fp = 1,num_soilp - p = filter_soilp(fp) - - ! get the time step total gross photosynthesis - ! this is coming from the canopy fluxes code, and is the - ! gpp that is used to control stomatal conductance. - ! For the nitrogen downregulation code, this is assumed - ! to be the potential gpp, and the actual gpp will be - ! reduced due to N limitation. - - ! Convert psn from umol/m2/s -> gC/m2/s - - ! The input psn (psnsun and psnsha) are expressed per unit LAI - ! in the sunlit and shaded canopy, respectively. These need to be - ! scaled by laisun and laisha to get the total gpp for allocation - - ! Note that no associate statement is used for the isotope carbon fluxes below - ! since they are not always allocated AND nag compiler will complain if you try to - ! to have an associate statement with unallocated memory + ! loop over patches to assess the total plant N demand + do fp = 1, num_p + p = filter_p(fp) - psnsun_to_cpool(p) = psnsun(p) * laisun(p) * 12.011e-6_r8 - psnshade_to_cpool(p) = psnsha(p) * laisha(p) * 12.011e-6_r8 - - if ( use_c13 ) then - c13_cnveg_carbonflux_inst%psnsun_to_cpool_patch(p) = c13_psnsun(p) * laisun(p) * 12.011e-6_r8 - c13_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p) = c13_psnsha(p) * laisha(p) * 12.011e-6_r8 - endif - - if ( use_c14 ) then - c14_cnveg_carbonflux_inst%psnsun_to_cpool_patch(p) = c14_psnsun(p) * laisun(p) * 12.011e-6_r8 - c14_cnveg_carbonflux_inst%psnshade_to_cpool_patch(p) = c14_psnsha(p) * laisha(p) * 12.011e-6_r8 - endif + ! when we have "if (leafn(p) == 0.0_r8)" below then we + ! have floating overflow (out of floating point range) + ! error in "actual_leafcn(p) = leafc(p) / leafn(p)" + if (leafn(p) < n_min ) then + ! to avoid division by zero, and to set leafcn to missing value for history files + this%actual_leafcn(p) = spval + else + ! leaf CN ratio + this%actual_leafcn(p) = leafc(p) / leafn(p) + end if - gpp(p) = psnsun_to_cpool(p) + psnshade_to_cpool(p) - ! get the time step total maintenance respiration - ! These fluxes should already be in gC/m2/s + leafcn_min = leafcn(ivt(p)) - 10.0_r8 + leafcn_max = leafcn(ivt(p)) + 10.0_r8 - mr = leaf_mr(p) + froot_mr(p) - if (woody(ivt(p)) == 1.0_r8) then - mr = mr + livestem_mr(p) + livecroot_mr(p) - else if (ivt(p) >= npcropmin) then - if (croplive(p)) then - reproductive_mr_tot = 0._r8 - do k = 1, nrepr - reproductive_mr_tot = reproductive_mr_tot + reproductive_mr(p,k) - end do - mr = mr + livestem_mr(p) + reproductive_mr_tot - end if - end if + this%actual_leafcn(p) = max( this%actual_leafcn(p), leafcn_min-0.0001_r8 ) + this%actual_leafcn(p) = min( this%actual_leafcn(p), leafcn_max ) - ! carbon flux available for allocation - availc(p) = gpp(p) - mr + nscalar = (this%actual_leafcn(p) - leafcn_min ) / (leafcn_max - leafcn_min) ! Nitrogen scaler factor + nscalar = min( max(0.0_r8, nscalar), 1.0_r8 ) - ! new code added for isotope calculations, 7/1/05, PET - ! If mr > gpp, then some mr comes from gpp, the rest comes from - ! cpool (xsmr) - if (mr > 0._r8 .and. availc(p) < 0._r8) then - curmr = gpp(p) - curmr_ratio = curmr / mr - else - curmr_ratio = 1._r8 - end if - leaf_curmr(p) = leaf_mr(p) * curmr_ratio - leaf_xsmr(p) = leaf_mr(p) - leaf_curmr(p) - froot_curmr(p) = froot_mr(p) * curmr_ratio - froot_xsmr(p) = froot_mr(p) - froot_curmr(p) - livestem_curmr(p) = livestem_mr(p) * curmr_ratio - livestem_xsmr(p) = livestem_mr(p) - livestem_curmr(p) - livecroot_curmr(p) = livecroot_mr(p) * curmr_ratio - livecroot_xsmr(p) = livecroot_mr(p) - livecroot_curmr(p) - do k = 1, nrepr - reproductive_curmr(p,k) = reproductive_mr(p,k) * curmr_ratio - reproductive_xsmr(p,k) = reproductive_mr(p,k) - reproductive_curmr(p,k) + c = patch%column(p) + sminn_total = 0.0_r8 + do j = 1, nlevdecomp + sminn_total = sminn_total + sminn_vr(c,j) * dzsoi_decomp(j) end do + Kmin = 1.0_r8 + substrate_term = sminn_total / (sminn_total + Kmin) - ! no allocation when available c is negative - availc(p) = max(availc(p),0.0_r8) - - ! test for an xsmrpool deficit - if (xsmrpool(p) < 0.0_r8) then - ! Running a deficit in the xsmrpool, so the first priority is to let - ! some availc from this timestep accumulate in xsmrpool. - ! Determine rate of recovery for xsmrpool deficit + c = patch%column(p) + temp_scalar=t_scalar(c,1) + temp_scalar = min( max(0.0_r8, temp_scalar), 1.0_r8 ) - xsmrpool_recover(p) = -xsmrpool(p)/(dayscrecover*secspday) - if (xsmrpool_recover(p) < availc(p)) then - ! available carbon reduced by amount for xsmrpool recovery - availc(p) = availc(p) - xsmrpool_recover(p) + if(use_fun)then ! in FUN, plant_ndemand is just used as a maximum draw on soil N pools. + plant_ndemand(p) = availc(p)*(n_allometry(p)/c_allometry(p)) + else !FUN + if (laisun(p)+laisha(p) > 0.0_r8) then + Vmax_N = 2.7E-8_r8 + plant_ndemand(p) = Vmax_N * frootc(p) * substrate_term * temp_scalar * nscalar else - ! all of the available carbon goes to xsmrpool recovery - xsmrpool_recover(p) = availc(p) - availc(p) = 0.0_r8 + plant_ndemand(p) = 0.0_r8 end if - cpool_to_xsmrpool(p) = xsmrpool_recover(p) - end if - - f1 = froot_leaf(ivt(p)) - f2 = croot_stem(ivt(p)) - ! modified wood allocation to be 2.2 at npp=800 gC/m2/yr, 0.2 at npp=0, - ! constrained so that it does not go lower than 0.2 (under negative annsum_npp) - ! This variable allocation is only for trees. Shrubs have a constant - ! allocation as specified in the pft-physiology file. The value is also used - ! as a trigger here: -1.0 means to use the dynamic allocation (trees). + if (this%actual_leafcn(p) < leafcn_min )then + plant_ndemand(p) = 0.0_r8 + end if + end if !FUN - if (stem_leaf(ivt(p)) == -1._r8) then - f3 = (2.7_r8/(1.0_r8+exp(-0.004_r8*(annsum_npp(p) - 300.0_r8)))) - 0.4_r8 - else - f3 = stem_leaf(ivt(p)) - end if + !if (leafn(p) < n_min ) then + !! to set leafcn to missing value for history files + !this%actual_leafcn(p) = spval + !end if - f4 = flivewd(ivt(p)) - g1 = grperc(ivt(p)) - g2 = grpnow(ivt(p)) - cnl = leafcn(ivt(p)) - cnfr = frootcn(ivt(p)) - cnlw = livewdcn(ivt(p)) - cndw = deadwdcn(ivt(p)) + ! retranslocated N deployment depends on seasonal cycle of potential GPP + ! (requires one year run to accumulate demand) + tempsum_potential_gpp(p) = tempsum_potential_gpp(p) + gpp(p) - ! calculate f1 to f5 for prog crops following AgroIBIS subr phenocrop + ! Adding the following line to carry max retransn info to CN Annual Update + tempmax_retransn(p) = max(tempmax_retransn(p),retransn(p)) + end do - do k = 1, nrepr - f5(k) = 0._r8 ! continued intializations from above - end do + if (call_is_for_pcrop) then + call CropPhase(bounds, num_p, filter_p, crop_inst, cnveg_state_inst, & + crop_phase = crop_phase(bounds%begp:bounds%endp)) - if (ivt(p) >= npcropmin) then ! skip 2 generic crops + do fp = 1, num_p + p = filter_p(fp) if (croplive(p)) then - ! same phases appear in subroutine CropPhenology - - ! Phase 1 completed: - ! ================== - ! if hui is less than the number of gdd needed for filling of grain - ! leaf emergence also has to have taken place for lai changes to occur - ! and carbon assimilation - ! Next phase: leaf emergence to start of leaf decline - - if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p)) then - - ! allocation rules for crops based on maturity and linear decrease - ! of amount allocated to roots over course of the growing season - - do k = 1, nrepr - arepr(p,k) = 0._r8 - end do - if (peaklai(p) == 1) then ! lai at maximum allowed - aleaf(p) = 1.e-5_r8 - astem(p) = 0._r8 - aroot(p) = 1._r8 - aleaf(p) - else - - ! SSR troubleshooting - if (gddmaturity(p) == 0.0) then - write(iulog,*) 'gddmaturity(p) == 0.0' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - if (huigrain(p) == 0.0) then - write(iulog,*) 'huigrain(p) == 0.0' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & - (arooti(ivt(p)) - arootf(ivt(p))) * & - min(1._r8, hui(p)/gddmaturity(p)))) - fleaf = fleafi(ivt(p)) * (exp(-bfact(ivt(p))) - & - exp(-bfact(ivt(p))*hui(p)/huigrain(p))) / & - (exp(-bfact(ivt(p)))-1) ! fraction alloc to leaf (from J Norman alloc curve) - aleaf(p) = max(1.e-5_r8, (1._r8 - aroot(p)) * fleaf) - astem(p) = 1._r8 - aleaf(p) - aroot(p) - end if - - ! AgroIBIS included here an immediate adjustment to aleaf & astem if the - ! predicted lai from the above allocation coefficients exceeded laimx. - ! We have decided to live with lais slightly higher than laimx by - ! enforcing the cap in the following tstep through the peaklai logic above. - - astemi(p) = astem(p) ! save for use by equations after shift - aleafi(p) = aleaf(p) ! to reproductive phenology stage begins + if (crop_phase(p) == cphase_leafemerge) then grain_flag(p) = 0._r8 ! setting to 0 while in phase 2 - - ! Phase 2 completed: - ! ================== - ! shift allocation either when enough gdd are accumulated or maximum number - ! of days has elapsed since planting - - else if (hui(p) >= huigrain(p)) then - - ! SSR troubleshooting - if (gddmaturity(p) == 0.0) then - write(iulog,*) 'gddmaturity(p) == 0.0' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - if (((gddmaturity(p)*declfact(ivt(p)))-huigrain(p)) == 0.0) then - write(iulog,*) '((gddmaturity(p)*declfact(ivt(p)))-huigrain(p)) == 0.0' - write(iulog,*) 'gddmaturity(p) = ',gddmaturity(p) - write(iulog,*) 'declfact(ivt(p)) = ',declfact(ivt(p)) - write(iulog,*) 'huigrain(p) = ',huigrain(p) - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - if (allconss(ivt(p)) .lt. 0.0 .and. min((hui(p)- & - huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & - huigrain(p)),1._r8) == 0.0) then - write(iulog,*) 'Raising 0 to negative exponent' - write(iulog,*) 'hui(p) = ',hui(p) - write(iulog,*) 'huigrain(p) = ',huigrain(p) - write(iulog,*) 'hui(p) = ',hui(p) - write(iulog,*) 'gddmaturity(p) = ',gddmaturity(p) - write(iulog,*) 'declfact(ivt(p)) = ',declfact(ivt(p)) - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - - aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & - (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) - if (astemi(p) > astemf(ivt(p))) then - astem(p) = max(0._r8, max(astemf(ivt(p)), astem(p) * & - (1._r8 - min((hui(p)- & - huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & - huigrain(p)),1._r8)**allconss(ivt(p)) ))) - end if - - ! If crops have hit peaklai, then set leaf allocation to small value - if (peaklai(p) == 1) then - aleaf(p) = 1.e-5_r8 - else if (aleafi(p) > aleaff(ivt(p))) then - aleaf(p) = max(1.e-5_r8, max(aleaff(ivt(p)), aleaf(p) * & - (1._r8 - min((hui(p)- & - huigrain(p))/((gddmaturity(p)*declfact(ivt(p)))- & - huigrain(p)),1._r8)**allconsl(ivt(p)) ))) - end if - + else if (crop_phase(p) == cphase_grainfill) then !Beth's retranslocation of leafn, stemn, rootn to organ !Filter excess plant N to retransn pool for organ N !Only do one time then hold grain_flag till onset next season @@ -1410,7 +1404,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & if (astem(p) == astemf(ivt(p)) .or. & (ivt(p) /= ntmp_soybean .and. ivt(p) /= nirrig_tmp_soybean .and.& - ivt(p) /= ntrp_soybean .and. ivt(p) /= nirrig_trp_soybean)) then + ivt(p) /= ntrp_soybean .and. ivt(p) /= nirrig_trp_soybean)) then if (grain_flag(p) == 0._r8) then t1 = 1 / dt leafn_to_retransn(p) = t1 * max(leafn(p)- (leafc(p) / fleafcn(ivt(p))),0._r8) @@ -1422,147 +1416,38 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & grain_flag(p) = 1._r8 end if end if - - ! For AgroIBIS-based crop model, all repr allocation is assumed to go - ! into the last reproductive pool. In practice there is only a single - ! reproductive pool with the AgroIBIS-based crop model, but for - ! software testing we can have multiple, in which situation we want the - ! active pool to be the last one. - do k = 1, nrepr-1 - arepr(p,k) = 0._r8 - end do - arepr(p,nrepr) = 1._r8 - aroot(p) - astem(p) - aleaf(p) - - else ! pre emergence - ! allocation coefficients should be irrelevant because crops have no - ! live carbon pools; this applies to this "else" and to the "else" a few - ! lines down - aleaf(p) = 1.e-5_r8 - astem(p) = 0._r8 - aroot(p) = 0._r8 - do k = 1, nrepr - arepr(p,k) = 0._r8 - end do end if - - f1 = aroot(p) / aleaf(p) - f3 = astem(p) / aleaf(p) - do k = 1, nrepr - f5(k) = arepr(p,k) / aleaf(p) - end do - g1 = 0.25_r8 - - - else ! .not croplive - f1 = 0._r8 - f3 = 0._r8 - do k = 1, nrepr - f5(k) = 0._r8 - end do - g1 = 0.25_r8 end if - end if - - ! based on available C, use constant allometric relationships to - ! determine N requirements - if (.not. use_fun) then - g1a = g1 - else - g1a = 0._r8 - end if - if (woody(ivt(p)) == 1.0_r8) then - c_allometry(p) = (1._r8+g1a)*(1._r8+f1+f3*(1._r8+f2)) - n_allometry(p) = 1._r8/cnl + f1/cnfr + (f3*f4*(1._r8+f2))/cnlw + & - (f3*(1._r8-f4)*(1._r8+f2))/cndw - else if (ivt(p) >= npcropmin) then ! skip generic crops - cng = graincn(ivt(p)) - f5_tot = 0._r8 - f5_n_tot = 0._r8 - do k = 1, nrepr - f5_tot = f5_tot + f5(k) - ! Note that currently we use the same C/N ratio for all grain components: - f5_n_tot = f5_n_tot + f5(k)/cng - end do - c_allometry(p) = (1._r8+g1a)*(1._r8+f1+f5_tot+f3*(1._r8+f2)) - n_allometry(p) = 1._r8/cnl + f1/cnfr + f5_n_tot + (f3*f4*(1._r8+f2))/cnlw + & - (f3*(1._r8-f4)*(1._r8+f2))/cndw - else - c_allometry(p) = 1._r8+g1a+f1+f1*g1a - n_allometry(p) = 1._r8/cnl + f1/cnfr - end if - - ! when we have "if (leafn(p) == 0.0_r8)" below then we - ! have floating overflow (out of floating point range) - ! error in "actual_leafcn(p) = leafc(p) / leafn(p)" - if (leafn(p) < n_min ) then - ! to avoid division by zero, and to set leafcn to missing value for history files - this%actual_leafcn(p) = spval - else - ! leaf CN ratio - this%actual_leafcn(p) = leafc(p) / leafn(p) - end if - - - leafcn_min = leafcn(ivt(p)) - 10.0_r8 - leafcn_max = leafcn(ivt(p)) + 10.0_r8 - - this%actual_leafcn(p) = max( this%actual_leafcn(p), leafcn_min-0.0001_r8 ) - this%actual_leafcn(p) = min( this%actual_leafcn(p), leafcn_max ) - - nscalar = (this%actual_leafcn(p) - leafcn_min ) / (leafcn_max - leafcn_min) ! Nitrogen scaler factor - nscalar = min( max(0.0_r8, nscalar), 1.0_r8 ) - - c = patch%column(p) - sminn_total = 0.0_r8 - do j = 1, nlevdecomp - sminn_total = sminn_total + sminn_vr(c,j) * dzsoi_decomp(j) end do - Kmin = 1.0_r8 - substrate_term = sminn_total / (sminn_total + Kmin) + end if - c = patch%column(p) - temp_scalar=t_scalar(c,1) - temp_scalar = min( max(0.0_r8, temp_scalar), 1.0_r8 ) + ! Beth's code: crops pull from retransn pool only during grain fill; + ! retransn pool has N from leaves, stems, and roots for + ! retranslocation + if (call_is_for_pcrop) then + do fp = 1, num_p + p = filter_p(fp) - if(use_fun)then ! in FUN, plant_ndemand is just used as a maximum draw on soil N pools. - plant_ndemand(p) = availc(p)*(n_allometry(p)/c_allometry(p)) - else !FUN - if (laisun(p)+laisha(p) > 0.0_r8) then - Vmax_N = 2.7E-8_r8 - plant_ndemand(p) = Vmax_N * frootc(p) * substrate_term * temp_scalar * nscalar + if (grain_flag(p) == 1._r8) then + avail_retransn(p) = plant_ndemand(p) else - plant_ndemand(p) = 0.0_r8 + avail_retransn(p) = 0.0_r8 end if + end do + else + do fp = 1, num_p + p = filter_p(fp) - if (this%actual_leafcn(p) < leafcn_min )then - plant_ndemand(p) = 0.0_r8 + if (annsum_potential_gpp(p) > 0._r8) then + avail_retransn(p) = (annmax_retransn(p)/2._r8)*(gpp(p)/annsum_potential_gpp(p))/dt + else + avail_retransn(p) = 0.0_r8 end if - end if !FUN - - !if (leafn(p) < n_min ) then - !! to set leafcn to missing value for history files - !this%actual_leafcn(p) = spval - !end if - - ! retranslocated N deployment depends on seasonal cycle of potential GPP - ! (requires one year run to accumulate demand) - - tempsum_potential_gpp(p) = tempsum_potential_gpp(p) + gpp(p) - - ! Adding the following line to carry max retransn info to CN Annual Update - tempmax_retransn(p) = max(tempmax_retransn(p),retransn(p)) - - ! Beth's code: crops pull from retransn pool only during grain fill; - ! retransn pool has N from leaves, stems, and roots for - ! retranslocation + end do + end if - if (ivt(p) >= npcropmin .and. grain_flag(p) == 1._r8) then - avail_retransn(p) = plant_ndemand(p) - else if (ivt(p) < npcropmin .and. annsum_potential_gpp(p) > 0._r8) then - avail_retransn(p) = (annmax_retransn(p)/2._r8)*(gpp(p)/annsum_potential_gpp(p))/dt - else - avail_retransn(p) = 0.0_r8 - end if + do fp = 1, num_p + p = filter_p(fp) ! make sure available retrans N doesn't exceed storage avail_retransn(p) = min(avail_retransn(p), retransn(p)/dt) @@ -1582,7 +1467,7 @@ subroutine calc_plant_nitrogen_demand(this, bounds, num_soilp, filter_soilp, & plant_ndemand(p) = plant_ndemand(p) - retransn_to_npool(p) end if - end do ! end patch loop + end do end associate diff --git a/src/biogeochem/NutrientCompetitionMethodMod.F90 b/src/biogeochem/NutrientCompetitionMethodMod.F90 index e306544423..a9cb295de4 100644 --- a/src/biogeochem/NutrientCompetitionMethodMod.F90 +++ b/src/biogeochem/NutrientCompetitionMethodMod.F90 @@ -4,7 +4,7 @@ module NutrientCompetitionMethodMod ! !DESCRIPTION: ! Abstract base class for functions to calculate nutrient competition ! - ! Created by Jinyun Tang, following Bill Sack's implementation of polymorphism + ! Created by Jinyun Tang, following Bill Sacks's implementation of polymorphism ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 implicit none @@ -20,9 +20,6 @@ module NutrientCompetitionMethodMod ! initialization procedure(init_interface), public, deferred :: init - ! Read in parameters - procedure, public :: readParams - ! compute plant nutrient demand procedure(calc_plant_nutrient_demand_interface), public, deferred :: calc_plant_nutrient_demand @@ -31,12 +28,6 @@ module NutrientCompetitionMethodMod end type nutrient_competition_method_type - type, public :: params_type - real(r8) :: dayscrecover ! number of days to recover negative cpool - end type params_type - ! - type(params_type), public, protected :: params_inst ! params_inst is populated in readParamsMod - abstract interface ! Note: The following code is adapted based on what Bill Scaks has done for soil water retention curve @@ -68,14 +59,13 @@ subroutine init_interface(this, bounds) end subroutine init_interface !--------------------------------------------------------------------------- - subroutine calc_plant_nutrient_demand_interface (this, bounds, num_soilp, filter_soilp, & - photosyns_inst, crop_inst, canopystate_inst, & + subroutine calc_plant_nutrient_demand_interface (this, bounds, & + num_p, filter_p, call_is_for_pcrop, & + crop_inst, canopystate_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, & - energyflux_inst, & - aroot, arepr) + energyflux_inst) ! ! DESCRIPTION ! calculate nutrient yield after considering competition between different components @@ -83,7 +73,6 @@ subroutine calc_plant_nutrient_demand_interface (this, bounds, num_soilp, filter ! USES use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type - use PhotosynthesisMod , only : photosyns_type use CropType , only : crop_type use CanopyStateType , only : canopystate_type use CNVegStateType , only : cnveg_state_type @@ -99,23 +88,28 @@ subroutine calc_plant_nutrient_demand_interface (this, bounds, num_soilp, filter ! !ARGUMENTS: class(nutrient_competition_method_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(photosyns_type) , intent(in) :: photosyns_inst + + ! This subroutine is meant to be called separately for non-prognostic-crop points and + ! prognostic-crop points. (The reason for this is so that the call for prognostic-crop + ! points can be skipped when a separate crop model is calculating these variables.) In + ! the call for non-prognostic-crop points, this filter should be the soilnopcropp + ! filter and call_is_for_pcrop should be false; in the call for prognostic-crop + ! points, this filter should be the pcropp filter and call_is_for_pcrop should be + ! true. + integer , intent(in) :: num_p ! number of patches in filter + integer , intent(in) :: filter_p(:) ! patch filter + logical , intent(in) :: call_is_for_pcrop + type(crop_type) , intent(in) :: crop_inst type(canopystate_type) , intent(in) :: canopystate_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst - type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst - type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst + type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_carbonflux_type), intent(in) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst type(energyflux_type) , intent(in) :: energyflux_inst - real(r8) , intent(out) :: aroot(bounds%begp:) - real(r8) , intent(out) :: arepr(bounds%begp:,:) end subroutine calc_plant_nutrient_demand_interface @@ -126,8 +120,7 @@ subroutine calc_plant_nutrient_competition_interface (this, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, & c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - soilbiogeochem_nitrogenstate_inst, & - aroot, arepr, fpg_col) + soilbiogeochem_nitrogenstate_inst, fpg_col) ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 @@ -157,46 +150,10 @@ subroutine calc_plant_nutrient_competition_interface (this, & type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst - real(r8) , intent(in) :: aroot(bounds%begp:) - real(r8) , intent(in) :: arepr(bounds%begp:,:) real(r8) , intent(in) :: fpg_col(bounds%begc:) end subroutine calc_plant_nutrient_competition_interface end interface - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -contains - - !----------------------------------------------------------------------- - subroutine readParams (this, ncid ) - ! - ! !USES: - use shr_log_mod , only : errMsg => shr_log_errMsg - use ncdio_pio , only : file_desc_t,ncd_io - use abortutils , only : endrun - ! - ! !ARGUMENTS: - class(nutrient_competition_method_type), intent(in) :: this - type(file_desc_t),intent(inout) :: ncid ! pio netCDF file id - ! - ! !LOCAL VARIABLES: - character(len=32) :: subname = 'CNAllocParamsType' - character(len=100) :: errCode = '-Error reading in parameters file:' - logical :: readv ! has variable been read in or not - real(r8) :: tempr ! temporary to read in parameter - character(len=100) :: tString ! temp. var for reading - !----------------------------------------------------------------------- - - ! read in parameters - - tString='dayscrecover' - call ncd_io(varname=trim(tString),data=tempr, flag='read', ncid=ncid, readvar=readv) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - params_inst%dayscrecover=tempr - - end subroutine readParams - end module NutrientCompetitionMethodMod diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 2f690ebdec..fd53fbaab4 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -993,6 +993,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro filter(nc)%num_soilc, filter(nc)%soilc, & filter(nc)%num_soilp, filter(nc)%soilp, & filter(nc)%num_pcropp, filter(nc)%pcropp, & + filter(nc)%num_soilnopcropp, filter(nc)%soilnopcropp, & filter(nc)%num_exposedvegp, filter(nc)%exposedvegp, & filter(nc)%num_noexposedvegp, filter(nc)%noexposedvegp, & soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index cad33b3835..45511d6869 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -305,7 +305,7 @@ subroutine initialize2(ni,nj) call clm_instReadNML( NLFilename ) allocate(nutrient_competition_method, & source=create_nutrient_competition_method(bounds_proc)) - call readParameters(nutrient_competition_method, photosyns_inst) + call readParameters(photosyns_inst) ! Initialize time manager if (nsrest == nsrStartup) then diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 6d43e6142b..ffae850f02 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -145,6 +145,11 @@ module clm_varctl ! If prognostic crops are turned on logical, public :: use_crop = .false. + ! Whether we're using the AgSys crop model + ! TODO(wjs, 2022-03-30) Add namelist control of this variable (at which point we'll + ! need to remove the 'parameter' attribute) + logical, public, parameter :: use_crop_agsys = .false. + ! true => separate crop landunit is not created by default logical, public :: create_crop_landunit = .false. diff --git a/src/main/readParamsMod.F90 b/src/main/readParamsMod.F90 index 31a116ab28..2d60b29be5 100644 --- a/src/main/readParamsMod.F90 +++ b/src/main/readParamsMod.F90 @@ -24,10 +24,11 @@ module readParamsMod contains !----------------------------------------------------------------------- - subroutine readParameters (nutrient_competition_method, photosyns_inst) + subroutine readParameters (photosyns_inst) ! ! ! USES: use CNSharedParamsMod , only : CNParamsReadShared + use CNAllocationMod , only : readCNAllocParams => readParams use CNGapMortalityMod , only : readCNGapMortParams => readParams use CNMRespMod , only : readCNMRespParams => readParams use CNFUNMod , only : readCNFUNParams => readParams @@ -59,13 +60,11 @@ subroutine readParameters (nutrient_competition_method, photosyns_inst) use initVerticalMod , only : readParams_initVertical => readParams use SurfaceWaterMod , only : readParams_SurfaceWater => readParams use SoilHydrologyInitTimeConstMod , only : readParams_SoilHydrologyInitTimeConst => readParams - use NutrientCompetitionMethodMod , only : nutrient_competition_method_type use clm_varctl, only : NLFilename_in use PhotosynthesisMod , only : photosyns_type ! ! !ARGUMENTS: type(photosyns_type) , intent(in) :: photosyns_inst - class(nutrient_competition_method_type), intent(in) :: nutrient_competition_method ! ! !LOCAL VARIABLES: character(len=256) :: locfn ! local file name @@ -88,7 +87,7 @@ subroutine readParameters (nutrient_competition_method, photosyns_inst) ! Above ground biogeochemistry... ! if (use_cn) then - call nutrient_competition_method%readParams(ncid) + call readCNAllocParams(ncid) call readCNGapMortParams(ncid) call readCNMRespParams(ncid) call readCNFUNParams(ncid) From 17364565c41e1f757359459abcb8cb27bf240561 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 29 May 2022 15:19:45 +0200 Subject: [PATCH 0220/2067] add restart for exice from no exice inital condi --- src/biogeophys/WaterStateBulkType.F90 | 6 ++-- src/biogeophys/WaterStateType.F90 | 52 +++++++++++++++++++++------ src/biogeophys/WaterType.F90 | 9 +++-- src/main/clm_instMod.F90 | 4 ++- 4 files changed, 55 insertions(+), 16 deletions(-) diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index 18b9f34e3e..fcb7e2cda7 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -188,7 +188,7 @@ end subroutine InitBulkCold !------------------------------------------------------------------------ subroutine RestartBulk(this, bounds, ncid, flag, & - watsat_col) + watsat_col, t_soisno_col) ! ! !DESCRIPTION: ! Read/Write module information to/from restart file. @@ -203,6 +203,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, & type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) ! ! !LOCAL VARIABLES: integer :: c,l,j @@ -212,7 +213,8 @@ subroutine RestartBulk(this, bounds, ncid, flag, & SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) call this%restart (bounds, ncid, flag=flag, & - watsat_col=watsat_col(bounds%begc:bounds%endc,:)) + watsat_col=watsat_col(bounds%begc:bounds%endc,:), & + t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:)) call restartvar(ncid=ncid, flag=flag, & diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 513830576d..8b17f1ea15 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -52,9 +52,10 @@ module WaterStateType real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) - real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (1:nlevgrnd) - + real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (-nlevsno+1:nlevgrnd) + real(r8), pointer :: exice_bulk_init (:) ! inital value for excess ice (new) (unitless) + logical, pointer, private :: exice_first_time_col (:) ! col whether excess ice is turned on first time type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only contains @@ -162,6 +163,11 @@ subroutine InitAllocate(this, bounds, tracer_vars) container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) + allocate(this%exice_first_time_col (bounds%begc:bounds%endc)) ; this%exice_first_time_col (:) = .true. !should be true during initialize1 + call AllocateVar1d(var = this%exice_bulk_init, name = 'exice_bulk_init', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column) + end subroutine InitAllocate !------------------------------------------------------------------------ @@ -324,7 +330,6 @@ subroutine InitCold(this, bounds, & integer :: c,j,l,nlevs,g integer :: nbedrock real(r8) :: ratio - real(r8) :: exice_bulk_init(bounds%begc:bounds%endc) !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(h2osno_input_col) == (/bounds%endc/)) , sourcefile, __LINE__) @@ -529,9 +534,9 @@ subroutine InitCold(this, bounds, & if (use_excess_ice .and. NLFilename /= '') then ! enforce initialization with 0 for everything this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - + this%exice_bulk_init(bounds%begc:bounds%endc)=0.0_r8 call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column - call this%exicestream%CalcExcessIce(bounds, exice_bulk_init) + call this%exicestream%CalcExcessIce(bounds, this%exice_bulk_init) do c = bounds%begc,bounds%endc g = col%gridcell(c) l = col%landunit(c) @@ -544,7 +549,7 @@ subroutine InitCold(this, bounds, & endif do j = 2, nlevmaxurbgrnd ! ignore first layer if (j Date: Sun, 29 May 2022 15:20:15 +0200 Subject: [PATCH 0221/2067] add exice to ice mass --- src/biogeophys/TotalWaterAndHeatMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/TotalWaterAndHeatMod.F90 b/src/biogeophys/TotalWaterAndHeatMod.F90 index 3f4877d093..885222f33b 100644 --- a/src/biogeophys/TotalWaterAndHeatMod.F90 +++ b/src/biogeophys/TotalWaterAndHeatMod.F90 @@ -383,7 +383,7 @@ subroutine AccumulateSoilLiqIceMassNonLake(bounds, num_c, filter_c, & if (has_h2o) then liquid_mass(c) = liquid_mass(c) + h2osoi_liq(c,j) - ice_mass(c) = ice_mass(c) + h2osoi_ice(c,j) +excess_ice(c,j) + ice_mass(c) = ice_mass(c) + h2osoi_ice(c,j) + excess_ice(c,j) end if end do end do From 628bb9f8292ae45b5154da44eea06ad9f81d8b3a Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 29 May 2022 15:21:06 +0200 Subject: [PATCH 0222/2067] add subsidence to water diagnostic vars --- src/biogeophys/SoilTemperatureMod.F90 | 3 ++ src/biogeophys/WaterDiagnosticBulkType.F90 | 35 ++++++++++++++++++++-- 2 files changed, 35 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 22042bec3b..1205c04424 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1158,6 +1158,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & frac_sno_eff => waterdiagnosticbulk_inst%frac_sno_eff_col , & ! Input: [real(r8) (:) ] eff. fraction of ground covered by snow (0 to 1) frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col , & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) snow_depth => waterdiagnosticbulk_inst%snow_depth_col , & ! Input: [real(r8) (:) ] snow height (m) + exice_subs_col => waterdiagnosticbulk_inst%exice_subs_col , & ! Output: [real(r8) (:,:) ] per layer subsidence due to excess ice melt (mm/s) h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Output: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) @@ -1412,6 +1413,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif h2osoi_liq(c,j) = max(0._r8,wmass0(c,j)-h2osoi_ice(c,j)-excess_ice(c,j)) !melted exice is added to the respective soil layers + if (abs(heatr) > 0._r8) then if (j == snl(c)+1) then @@ -1444,6 +1446,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (j >= 1) then !why before it was two same statements? xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime + exice_subs_col(c,j) = max(0._r8, (wexice0(c,j)-excess_ice(c,j))/denice/dtime*1000.0_r8) else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 7804fa3746..b709a3cb8b 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -48,6 +48,8 @@ module WaterDiagnosticBulkType real(r8), pointer :: air_vol_col (:,:) ! col air filled porosity real(r8), pointer :: h2osoi_liqvol_col (:,:) ! col volumetric liquid water content (v/v) real(r8), pointer :: swe_old_col (:,:) ! col initial snow water + real(r8), pointer :: exice_subs_tot_col (:) ! col total subsidence due to excess ice melt + real(r8), pointer :: exice_subs_col (:,:) ! col per layer subsidence due to excess ice melt real(r8), pointer :: snw_rds_col (:,:) ! col snow grain radius (col,lyr) [m^-6, microns] real(r8), pointer :: snw_rds_top_col (:) ! col snow grain radius (top layer) [m^-6, microns] @@ -194,6 +196,8 @@ subroutine InitBulkAllocate(this, bounds) allocate(this%h2osoi_ice_tot_col (begc:endc)) ; this%h2osoi_ice_tot_col (:) = nan allocate(this%h2osoi_liq_tot_col (begc:endc)) ; this%h2osoi_liq_tot_col (:) = nan allocate(this%swe_old_col (begc:endc,-nlevsno+1:0)) ; this%swe_old_col (:,:) = nan + allocate(this%exice_subs_tot_col (begc:endc)) ; this%exice_subs_tot_col (:) = 0.0_r8 + allocate(this%exice_subs_col (begc:endc, 1:nlevgrnd)) ; this%exice_subs_col (:,:) = 0.0_r8 allocate(this%snw_rds_col (begc:endc,-nlevsno+1:0)) ; this%snw_rds_col (:,:) = nan allocate(this%snw_rds_top_col (begc:endc)) ; this%snw_rds_top_col (:) = nan @@ -280,6 +284,15 @@ subroutine InitBulkHistory(this, bounds) long_name=this%info%lname('vertically summed soil cie (veg landunits only)'), & ptr_col=this%h2osoi_ice_tot_col, l2g_scale_type='veg') + this%exice_subs_tot_col(begc:endc) = 0.0_r8 + call hist_addfld1d ( & + fname=this%info%fname('EXICE_SUBS'), & + units='mm/s', & + avgflag='A', & + l2g_scale_type='veg', default='inactive', & + long_name=this%info%lname('subsidence due to excess ice melt'), & + ptr_col=this%exice_subs_tot_col) + this%iwue_ln_patch(begp:endp) = spval call hist_addfld1d ( & fname=this%info%fname('IWUELN'), & @@ -741,7 +754,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil use spmdMod , only : masterproc use clm_varcon , only : pondmx, watmin, spval, nameg use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall - use clm_varctl , only : bound_h2osoi + use clm_varctl , only : bound_h2osoi, use_excess_ice use ncdio_pio , only : file_desc_t, ncd_io, ncd_double use restUtilMod ! @@ -875,7 +888,19 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil interpinic_flag='interp', readvar=readvar, data=this%wf_col) end if - + if (.not. use_excess_ice .and. flag == 'read') then + ! no need to even define the restart vars + this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 + else + ! have to at least define them + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_SUBS'), & + dim1name='column', xtype=ncd_double, & + long_name=this%info%lname('subsidence due to excess ice melt'), units='mm/s', & + interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) + if (use_excess_ice .and. flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 + endif + endif end subroutine RestartBulk @@ -1006,10 +1031,12 @@ subroutine Summary(this, bounds, & h2osoi_ice => waterstate_inst%h2osoi_ice_col, & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) h2osoi_liq => waterstate_inst%h2osoi_liq_col, & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) + exice_subs_col => this%exice_subs_col , & ! Output: [real(r8) (:,:) ] per layer subsidence due to excess ice melt (mm/s) h2osoi_ice_tot => this%h2osoi_ice_tot_col , & ! Output: [real(r8) (:) ] vertically summed ice lens (kg/m2) h2osoi_liq_tot => this%h2osoi_liq_tot_col , & ! Output: [real(r8) (:) ] vertically summed liquid water (kg/m2) - h2osoi_liqice_10cm => this%h2osoi_liqice_10cm_col & ! Output: [real(r8) (:) ] liquid water + ice lens in top 10cm of soil (kg/m2) + h2osoi_liqice_10cm => this%h2osoi_liqice_10cm_col , & ! Output: [real(r8) (:) ] liquid water + ice lens in top 10cm of soil (kg/m2) + exice_subs_tot_col => this%exice_subs_tot_col & ! Output [real(r8) (:) ] total subsidence due to excess ice melt (mm/s) ) call this%waterdiagnostic_type%Summary(bounds, & @@ -1042,6 +1069,7 @@ subroutine Summary(this, bounds, & h2osoi_liqice_10cm(c) = 0.0_r8 h2osoi_liq_tot(c) = 0._r8 h2osoi_ice_tot(c) = 0._r8 + exice_subs_tot_col(c) = 0._r8 end if end do do j = 1, nlevsoi @@ -1064,6 +1092,7 @@ subroutine Summary(this, bounds, & end if h2osoi_liq_tot(c) = h2osoi_liq_tot(c) + h2osoi_liq(c,j) h2osoi_ice_tot(c) = h2osoi_ice_tot(c) + h2osoi_ice(c,j) + exice_subs_tot_col(c) = exice_subs_tot_col(c) + exice_subs_col(c,j) end if end do end do From 6cbbc4d092e5a734c8151cf29fa8cd14166e7f65 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 May 2022 10:49:33 -0600 Subject: [PATCH 0223/2067] Added helpful output about NaN values in calc_crop_allocation_fractions(). --- src/biogeochem/CNAllocationMod.F90 | 33 +++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNAllocationMod.F90 b/src/biogeochem/CNAllocationMod.F90 index ef646511f1..8fd8d3257a 100644 --- a/src/biogeochem/CNAllocationMod.F90 +++ b/src/biogeochem/CNAllocationMod.F90 @@ -26,6 +26,9 @@ module CNAllocationMod use CropReprPoolsMod , only : nrepr use CNPhenologyMod , only : CropPhase use CNSharedParamsMod , only : use_fun + ! SSR troubleshooting + use GridcellType , only : grc + use shr_infnan_mod , only : isnan => shr_infnan_isnan, isinf => shr_infnan_isinf ! implicit none private @@ -279,6 +282,8 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & integer :: p, fp, k real(r8) :: fleaf ! fraction allocated to leaf real(r8) :: crop_phase(bounds%begp:bounds%endp) + ! SSR troubleshooting + integer :: g ! Gridcell index character(len=*), parameter :: subname = 'calc_crop_allocation_fractions' !----------------------------------------------------------------------- @@ -304,7 +309,10 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient aroot => cnveg_state_inst%aroot_patch , & ! Output: [real(r8) (:) ] root allocation coefficient - arepr => cnveg_state_inst%arepr_patch & ! Output: [real(r8) (:,:) ] reproductive allocation coefficient(s) + arepr => cnveg_state_inst%arepr_patch , & ! Output: [real(r8) (:,:) ] reproductive allocation coefficient(s) + ! SSR troubleshooting + lon => grc%londeg, & + lat => grc%latdeg & ) call CropPhase(bounds, num_pcropp, filter_pcropp, crop_inst, cnveg_state_inst, & @@ -312,6 +320,8 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & do fp = 1, num_pcropp p = filter_pcropp(fp) + ! SSR troubleshooting + g = patch%gridcell(p) if (croplive(p)) then ! same phases appear in subroutine CropPhenology @@ -362,6 +372,27 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & else if (crop_phase(p) == cphase_grainfill) then aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) + + ! SSR troubleshooting + if (isnan(astemi(p))) then + write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemi NaN' + end if + if (isinf(astemi(p))) then + write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemi Inf' + end if + if (isnan(astemf(ivt(p)))) then + write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemf NaN' + end if + if (isinf(astemf(ivt(p)))) then + write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemf Inf' + end if + if (astemi(p) > astemi(p)) then + write(iulog,*) 'srts: Trying to trigger a crash with this conditional' + end if + if (astemf(ivt(p)) > astemf(ivt(p))) then + write(iulog,*) 'srts: And if not, maybe this one will' + end if + if (astemi(p) > astemf(ivt(p))) then astem(p) = max(0._r8, max(astemf(ivt(p)), astem(p) * & (1._r8 - min((hui(p)- & From 7761d1af65d6fb66a4273dd540fe1a0b4c004a15 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 May 2022 15:06:00 -0600 Subject: [PATCH 0224/2067] Do not allow jumping to cphase_grainfill without having entered cphase_leafemerge. There are variables that need to be set in CNAllocationMod (and perhaps elsewhere) that only happen during cphase_leafemerge. (cherry picked from commits 7edecb1260f6375e09b00a3aa7bf59a9dd079c9f and 96e0695f91b4954660c5144c968ce93ba6d86444) (also one extra change made, to CropPhase()) --- src/biogeochem/CNPhenologyMod.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 12604b0199..2b69dbb8b6 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2048,7 +2048,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & offset_flag(p) = 0._r8 ! carbon and nitrogen transfers if (croplive(p)) then - cphase(p) = cphase_planted ! call vernalization if winter temperate cereal planted, living, and the ! vernalization factor is not 1; @@ -2269,7 +2268,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! AgroIBIS uses a complex formula for lai decline. ! Use CN's simple formula at least as a place holder (slevis) - else if (hui(p) >= huigrain(p)) then + else if (hui(p) >= huigrain(p) .and. cphase(p) >= cphase_leafemerge) then cphase(p) = cphase_grainfill ! SSR troubleshooting @@ -2278,6 +2277,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if bglfr(p) = 1._r8/(leaf_long(ivt(p))*avg_dayspyr*secspday) + else + cphase(p) = cphase_planted end if ! continue fertilizer application while in phase 2; @@ -2362,16 +2363,15 @@ subroutine CropPhase(bounds, num_pcropp, filter_pcropp, & p = filter_pcropp(fp) if (croplive(p)) then - ! Start with cphase_planted, but this might get changed in the later - ! conditional blocks. - crop_phase(p) = cphase_planted if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p)) then crop_phase(p) = cphase_leafemerge - else if (hui(p) >= huigrain(p)) then + else if (hui(p) >= huigrain(p) .and. crop_inst%cphase_patch(p) >= cphase_leafemerge) then ! Since we know croplive is true, any hui greater than huigrain implies that ! we're in the grainfill stage: if we were passt gddmaturity then croplive ! would be false. crop_phase(p) = cphase_grainfill + else + crop_phase(p) = cphase_planted end if end if end do From 5a14b98cc41af54f8e89737e74e7388502625f8a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 May 2022 15:37:12 -0600 Subject: [PATCH 0225/2067] Added SOWING_REASON_PERHARV output. * Tens place: 1 if prescribed, 0 otherwise * Ones place: 1 if normal, 2 if lastchance, 0 if neither --- src/biogeochem/CNPhenologyMod.F90 | 23 +++++++++++++++++++---- src/biogeochem/CropType.F90 | 12 ++++++++++++ 2 files changed, 31 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 2b69dbb8b6..a40f5db322 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1911,8 +1911,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cumvd(p) = 0._r8 hdidx(p) = 0._r8 vf(p) = 0._r8 - + call PlantCrop(p, leafcn(ivt(p)), jday, do_plant_normal, & + do_plant_lastchance, do_plant_prescribed, & temperature_inst, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & @@ -1946,6 +1947,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance) then call PlantCrop(p, leafcn(ivt(p)), jday, do_plant_normal, & + do_plant_lastchance, do_plant_prescribed, & temperature_inst, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & @@ -2449,6 +2451,7 @@ end subroutine CropPhenologyInit !----------------------------------------------------------------------- subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & + do_plant_lastchance, do_plant_prescribed, & temperature_inst, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & @@ -2477,6 +2480,8 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & real(r8) , intent(in) :: leafcn_in ! leaf C:N (gC/gN) of this patch's vegetation type (pftcon%leafcn(ivt(p))) integer , intent(in) :: jday ! julian day of the year logical , intent(in) :: do_plant_normal ! Are all the normal requirements for planting met? + logical , intent(in) :: do_plant_lastchance ! Are the last-chance requirements for planting met? + logical , intent(in) :: do_plant_prescribed ! are we planting because it was prescribed? type(temperature_type) , intent(in) :: temperature_inst type(crop_type) , intent(inout) :: crop_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst @@ -2490,7 +2495,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ! LOCAL VARAIBLES: integer s ! growing season index real(r8) gdd_target ! cultivar GDD target this growing season - logical do_plant_prescribed ! are we planting because it was prescribed? + real(r8) this_sowing_reason ! number representing sowing reason(s) !------------------------------------------------------------------------ associate( & @@ -2499,6 +2504,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch + sowing_reason => crop_inst%sowing_reason_thisyr , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer @@ -2512,8 +2518,6 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & gdd1020 => temperature_inst%gdd1020_patch & ! Input: [real(r8) (:) ] 20 yr mean of gdd10 ) - do_plant_prescribed = next_rx_sdate(p) == jday - ! impose limit on growing season length needed ! for crop maturity - for cold weather constraints croplive(p) = .true. @@ -2537,6 +2541,17 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif crop_inst%sdates_thisyr(p,s) = real(jday, r8) + this_sowing_reason = 0._r8 + if (do_plant_prescribed) then + this_sowing_reason = 10._r8 + end if + if (do_plant_normal) then + this_sowing_reason = this_sowing_reason + 1._r8 + else if (do_plant_lastchance) then + this_sowing_reason = this_sowing_reason + 2._r8 + end if + sowing_reason(p,s) = this_sowing_reason + ! SSR troubleshooting if (leafcn_in == 0.0) then call endrun(msg=errMsg(sourcefile, __LINE__)) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 2b136d1a5d..80aae8eff2 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -53,6 +53,7 @@ module CropType real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year + real(r8), pointer :: sowing_reason_thisyr (:,:) ! reason for each sowing for this patch this year real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch @@ -228,6 +229,7 @@ subroutine InitAllocate(this, bounds) allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval allocate(this%hui_thisyr(begp:endp,1:mxharvests)) ; this%hui_thisyr(:,:) = spval + allocate(this%sowing_reason_thisyr(begp:endp,1:mxsowings)) ; this%sowing_reason_thisyr(:,:) = spval allocate(this%harvest_reason_thisyr(begp:endp,1:mxharvests)) ; this%harvest_reason_thisyr(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 @@ -307,6 +309,11 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='At-harvest accumulated heat unit index for crop; should only be output annually', & ptr_patch=this%hui_thisyr, default='inactive') + this%sowing_reason_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='SOWING_REASON_PERHARV', units='unitless', type2d='mxsowings', & + avgflag='I', long_name='Reason for each crop sowing; should only be output annually', & + ptr_patch=this%sowing_reason_thisyr, default='inactive') + this%harvest_reason_thisyr(begp:endp,:) = spval call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='unitless', type2d='mxharvests', & avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & @@ -604,6 +611,11 @@ subroutine Restart(this, bounds, ncid, flag) long_name='accumulated heat unit index at harvest for this patch this year', units='ddays', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%hui_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxsowings', switchdim=.true., & + long_name='reason for each sowing for this patch this year', units='unitless', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_thisyr) call restartvar(ncid=ncid, flag=flag, varname='harvest_reason_thisyr', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='reason for each harvest for this patch this year', units='unitless', & From 54c6c319324539e0c45aaa36119c3ef362a73b4c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 May 2022 14:44:39 -0600 Subject: [PATCH 0226/2067] Bugfix in crop harvest logic for generate_crop_gdds. Had been looking at sdates_thisyr instead of rx_sdates_thisyr, meaning that crops would be harvested on Jan. 1, or otherwise the first day of the next calendar year where idpp > mxmat. (cherry picked from commit 22b75cd1f7e1530f1896d237d51f9f589c7ad758) --- src/biogeochem/CNPhenologyMod.F90 | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a40f5db322..95c8a9ae5c 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2107,7 +2107,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .true. force_harvest = .true. harvest_reason = 4._r8 - else if (generate_crop_gdds .and. crop_inst%sdates_thisyr(p,1) .gt. 0) then + + ! If generate_crop_gdds and this patch has prescribed sowing inputs + else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr(p,1) .gt. 0) then if (.not. use_cropcal_streams) then write(iulog,*) 'If using generate_crop_gdds, you must set use_cropcal_streams to true.' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2141,7 +2143,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! WARNING: This implementation assumes that sowing dates don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed ! sowing dates. - if (crop_inst%sdates_thisyr(p,1) == 1) then + if (crop_inst%rx_sdates_thisyr(p,1) == 1) then do_harvest = jday == dayspyr end if @@ -2150,6 +2152,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if endif + else if (sown_today) then ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. From 60e94480740efdaa2598d2bd018c01a940fa5ed2 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 5 Jun 2022 18:36:57 +0200 Subject: [PATCH 0227/2067] added one more diag var and cleanup --- src/biogeophys/SoilTemperatureMod.F90 | 8 +-- src/biogeophys/WaterDiagnosticBulkType.F90 | 79 ++++++++++++++++++---- src/biogeophys/WaterStateType.F90 | 8 +-- src/main/clm_initializeMod.F90 | 2 +- src/main/clm_instMod.F90 | 2 +- 5 files changed, 75 insertions(+), 24 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 1205c04424..5c5427ea81 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1128,6 +1128,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: temp1 !temporary variables [kg/m2] real(r8) :: hm(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !energy residual [W/m2] real(r8) :: xm(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !melting or freezing within a time step [kg/m2] + real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !additional melting or freezing within a time step [kg/m2] (needed for excess ice melt) real(r8) :: wmass0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of ice and liquid (kg/m2) real(r8) :: wice0 (bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of ice (kg/m2) real(r8) :: wliq0 (bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of liquid (kg/m2) @@ -1135,8 +1136,6 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: propor !proportionality constant (-) real(r8) :: tinc(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !t(n+1)-t(n) [K] real(r8) :: smp !frozen water potential (mm) - real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] - real(r8) :: xm3(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !xm variable [kg/m2] real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd)!initial mass of excess_ice at the timestep (kg/m2) @@ -1207,7 +1206,6 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & hm(c,j) = 0._r8 xm(c,j) = 0._r8 xm2(c,j)=0._r8 - xm3(c,j)=0._r8 wice0(c,j) = h2osoi_ice(c,j) wliq0(c,j) = h2osoi_liq(c,j) wexice0(c,j)=excess_ice(c,j) @@ -1446,11 +1444,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (j >= 1) then !why before it was two same statements? xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime - exice_subs_col(c,j) = max(0._r8, (wexice0(c,j)-excess_ice(c,j))/denice/dtime*1000.0_r8) + exice_subs_col(c,j) = max(0._r8, (wexice0(c,j)-excess_ice(c,j))/denice) else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif - ! put exice melt here + if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index b709a3cb8b..0f7b60532d 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -48,8 +48,10 @@ module WaterDiagnosticBulkType real(r8), pointer :: air_vol_col (:,:) ! col air filled porosity real(r8), pointer :: h2osoi_liqvol_col (:,:) ! col volumetric liquid water content (v/v) real(r8), pointer :: swe_old_col (:,:) ! col initial snow water - real(r8), pointer :: exice_subs_tot_col (:) ! col total subsidence due to excess ice melt - real(r8), pointer :: exice_subs_col (:,:) ! col per layer subsidence due to excess ice melt + real(r8), pointer :: exice_subs_tot_col (:) ! col total subsidence due to excess ice melt (m) + real(r8), pointer :: exice_subs_col (:,:) ! col per layer subsidence due to excess ice melt (m) + real(r8), pointer :: exice_vol_col (:,:) ! col per layer volumetric excess ice content (m3/m3) + real(r8), pointer :: exice_vol_tot_col (:) ! col averaged volumetric excess ice content (m3/m3) real(r8), pointer :: snw_rds_col (:,:) ! col snow grain radius (col,lyr) [m^-6, microns] real(r8), pointer :: snw_rds_top_col (:) ! col snow grain radius (top layer) [m^-6, microns] @@ -198,6 +200,8 @@ subroutine InitBulkAllocate(this, bounds) allocate(this%swe_old_col (begc:endc,-nlevsno+1:0)) ; this%swe_old_col (:,:) = nan allocate(this%exice_subs_tot_col (begc:endc)) ; this%exice_subs_tot_col (:) = 0.0_r8 allocate(this%exice_subs_col (begc:endc, 1:nlevgrnd)) ; this%exice_subs_col (:,:) = 0.0_r8 + allocate(this%exice_vol_col (begc:endc, 1:nlevgrnd)) ; this%exice_vol_col (:,:) = 0.0_r8 + allocate(this%exice_vol_tot_col (begc:endc)) ; this%exice_vol_tot_col (:) = 0.0_r8 allocate(this%snw_rds_col (begc:endc,-nlevsno+1:0)) ; this%snw_rds_col (:,:) = nan allocate(this%snw_rds_top_col (begc:endc)) ; this%snw_rds_top_col (:) = nan @@ -281,16 +285,25 @@ subroutine InitBulkHistory(this, bounds) fname=this%info%fname('TOTSOILICE'), & units='kg/m2', & avgflag='A', & - long_name=this%info%lname('vertically summed soil cie (veg landunits only)'), & + long_name=this%info%lname('vertically summed soil ice (veg landunits only)'), & ptr_col=this%h2osoi_ice_tot_col, l2g_scale_type='veg') + this%exice_vol_tot_col(begc:endc) = 0.0_r8 + call hist_addfld1d ( & + fname=this%info%fname('TOTEXICE_VOL'), & + units='m3/m3', & + avgflag='A', & + l2g_scale_type='veg', default='inactive', & + long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & + ptr_col=this%exice_vol_tot_col) + this%exice_subs_tot_col(begc:endc) = 0.0_r8 call hist_addfld1d ( & fname=this%info%fname('EXICE_SUBS'), & - units='mm/s', & - avgflag='A', & + units='m', & + avgflag='SUM', & l2g_scale_type='veg', default='inactive', & - long_name=this%info%lname('subsidence due to excess ice melt'), & + long_name=this%info%lname('subsidence due to excess ice melt (veg landunits only)'), & ptr_col=this%exice_subs_tot_col) this%iwue_ln_patch(begp:endp) = spval @@ -888,18 +901,31 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil interpinic_flag='interp', readvar=readvar, data=this%wf_col) end if - if (.not. use_excess_ice .and. flag == 'read') then + if (.not. use_excess_ice) then ! no need to even define the restart vars this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 else ! have to at least define them call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_SUBS'), & dim1name='column', xtype=ncd_double, & - long_name=this%info%lname('subsidence due to excess ice melt'), units='mm/s', & + long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), units='mm/s', & interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) - if (use_excess_ice .and. flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + ! initialization of these to zero is ok, since they are not in history anyway + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 endif + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('TOTEXICE_VOL'), & + dim1name='column', xtype=ncd_double, & + long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), units='m3/m3', & + interpinic_flag='interp', readvar=readvar, data=this%exice_vol_tot_col) endif end subroutine RestartBulk @@ -1006,7 +1032,9 @@ subroutine Summary(this, bounds, & ! Compute end-of-timestep summaries of water diagnostic terms ! ! !USES: - use clm_varpar , only : nlevsoi + use clm_varpar , only : nlevsoi + use clm_varcon , only : denice + use landunit_varcon, only : istsoil, istcrop ! !ARGUMENTS: class(waterdiagnosticbulk_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds @@ -1022,6 +1050,8 @@ subroutine Summary(this, bounds, & ! !LOCAL VARIABLES: integer :: fp, p, j, l, fc, c ! Indices real(r8):: fracl ! fraction of soil layer contributing to 10cm total soil water + real(r8):: dz_ext ! extended layer thickness due to excess ice + real(r8):: dz_tot ! total depth with extended thicknesses character(len=*), parameter :: subname = 'Summary' !----------------------------------------------------------------------- @@ -1031,12 +1061,15 @@ subroutine Summary(this, bounds, & h2osoi_ice => waterstate_inst%h2osoi_ice_col, & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) h2osoi_liq => waterstate_inst%h2osoi_liq_col, & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) - exice_subs_col => this%exice_subs_col , & ! Output: [real(r8) (:,:) ] per layer subsidence due to excess ice melt (mm/s) + excess_ice => waterstate_inst%excess_ice_col, & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) + exice_subs_col => this%exice_subs_col , & ! Output: [real(r8) (:,:) ] per layer subsidence due to excess ice melt (m) + exice_vol_col => this%exice_vol_col , & ! Output: [real(r8) (:,:) ] per layer volumetric excess ice content (m3/m3) h2osoi_ice_tot => this%h2osoi_ice_tot_col , & ! Output: [real(r8) (:) ] vertically summed ice lens (kg/m2) h2osoi_liq_tot => this%h2osoi_liq_tot_col , & ! Output: [real(r8) (:) ] vertically summed liquid water (kg/m2) h2osoi_liqice_10cm => this%h2osoi_liqice_10cm_col , & ! Output: [real(r8) (:) ] liquid water + ice lens in top 10cm of soil (kg/m2) - exice_subs_tot_col => this%exice_subs_tot_col & ! Output [real(r8) (:) ] total subsidence due to excess ice melt (mm/s) + exice_subs_tot_col => this%exice_subs_tot_col , & ! Output [real(r8) (:) ] vertically summed subsidence due to excess ice melt (m) + exice_vol_tot_col => this%exice_vol_tot_col & ! Output [real(r8) (:) ] vertically averaged volumetric excess ice content (m3/m3) ) call this%waterdiagnostic_type%Summary(bounds, & @@ -1092,11 +1125,31 @@ subroutine Summary(this, bounds, & end if h2osoi_liq_tot(c) = h2osoi_liq_tot(c) + h2osoi_liq(c,j) h2osoi_ice_tot(c) = h2osoi_ice_tot(c) + h2osoi_ice(c,j) - exice_subs_tot_col(c) = exice_subs_tot_col(c) + exice_subs_col(c,j) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + exice_subs_tot_col(c) = exice_subs_tot_col(c) + exice_subs_col(c,j) + endif end if end do end do + do fc = 1, num_nolakec ! extra loop needed since the one above has outer loop with layers + c = filter_nolakec(fc) + l = col%landunit(c) + if (.not. lun%urbpoi(l)) then + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz_tot = 0.0_r8 + exice_vol_tot_col(c)=0.0_r8 + do j = 1, nlevsoi + dz_ext = dz(c,j)+excess_ice(c,j)/denice + exice_vol_col(c,j)=excess_ice(c,j)/(denice*dz_ext) + dz_tot=dz_tot+dz_ext + exice_vol_tot_col(c)=exice_vol_tot_col(c)+exice_vol_col(c,j)*dz_ext ! (m) + enddo + exice_vol_tot_col(c)=exice_vol_tot_col(c)/dz_tot ! (m3/m3) + end if + end if + end do + end associate end subroutine Summary diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 8b17f1ea15..dcf49b39d6 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -690,8 +690,7 @@ subroutine Restart(this, bounds, ncid, flag, & interpinic_flag='interp', readvar=readvar, data=this%dynbal_baseline_ice_col) ! Restart excess ice vars - !write(iulog,*) 'restarting excess ice wars' - if (.not. use_excess_ice .and. flag == 'read') then + if (.not. use_excess_ice) then ! no need to even define the restart vars this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 else @@ -699,9 +698,9 @@ subroutine Restart(this, bounds, ncid, flag, & call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & dim1name='column', dim2name='levtot', switchdim=.true., & long_name=this%info%lname('excess soil ice (vegetated landunits only)'), units='kg/m2', & - scale_by_thickness=.false., & + scale_by_thickness=.true., & interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) - if (use_excess_ice .and. flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it this%exice_first_time_col(bounds%begc:bounds%endc) = .false. do c = bounds%begc,bounds%endc @@ -727,6 +726,7 @@ subroutine Restart(this, bounds, ncid, flag, & end do endif! end of old file restart endif ! end of exice restart + ! Determine volumetric soil water (for read only) if (flag == 'read' ) then do c = bounds%begc, bounds%endc diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 32c368e40b..c9541376a2 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -14,7 +14,7 @@ module clm_initializeMod use clm_varctl , only : is_cold_start, is_interpolated_start use clm_varctl , only : iulog use clm_varctl , only : use_lch4, use_cn, use_cndv, use_c13, use_c14, use_fates - use clm_varctl , only : use_soil_moisture_streams, use_excess_ice + use clm_varctl , only : use_soil_moisture_streams use clm_instur , only : wt_lunit, urban_valid, wt_nat_patch, wt_cft, fert_cft use clm_instur , only : irrig_method, wt_glc_mec, topo_glc_mec, haslake use perf_mod , only : t_startf, t_stopf diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 836e9586bd..35428f0f02 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -8,7 +8,7 @@ module clm_instMod use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type use clm_varpar , only : ndecomp_pools, nlevdecomp_full - use clm_varctl , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates, use_excess_ice + use clm_varctl , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates use clm_varctl , only : use_crop, snow_cover_fraction_method, paramfile use SoilBiogeochemDecompCascadeConType , only : century_decomp, decomp_method use clm_varcon , only : bdsno, c13ratio, c14ratio From 04303d833cb121c047d34a9bb0c42ed5dc8c1713 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 2 Jun 2022 14:36:18 -0600 Subject: [PATCH 0228/2067] 'I don't know why this is necessary' bit was causing next_rx_sdate to be incorrectly set to zero. (cherry picked from commit 72441c4e134952f159d21b76012aeca882954041) --- src/biogeochem/CNPhenologyMod.F90 | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 95c8a9ae5c..3a7be459a6 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1840,13 +1840,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & call endrun(msg=errMsg(sourcefile, __LINE__)) end if - ! SSR: I don't know why this is necessary. next_rx_sdate should get properly set in PlantCrop() - ! or above, but sometimes (NOT in first year after restart) I'm seeing crops planted Jan. 1 that - ! are harvested the same day. This (specifically, the second condition) fixes that. + ! Get next sowing date if (s < mxsowings) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,s+1) - else - next_rx_sdate(p) = -1 end if do_plant_prescribed = next_rx_sdate(p) == jday From 174bcabf203d805c9fba88cd9e50453b28f4c6d8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 2 Jun 2022 18:03:17 -0600 Subject: [PATCH 0229/2067] In cropcal_interp(), only set next_rx_sdate if no plantings yet this year. (cherry picked from commit ba902039a335b67bc8f21b92a2dc1112742582a7) --- src/cpl/share_esmf/cropcalStreamMod.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 247de9cb84..2d30a71c66 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -331,7 +331,10 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end if ! Only for first sowing date of the year - crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 + if (crop_inst%sdates_thisyr(p,1) <= 0) then + crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + end if else write(iulog,'(a,i0)') 'cropcal_interp(), rx_sdates: Crop patch has ivt ',ivt call ESMF_Finalize(endflag=ESMF_END_ABORT) From 46bff9ddb227d3bbbc701a4575f9f90d82c9b7ee Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 6 Jun 2022 13:15:52 -0600 Subject: [PATCH 0230/2067] Prescribed harvest GDD now used (although overwritten with minimum) even if prescription is 0. (cherry picked from commit a8bc1cb18739bf6d3ebdc8bf93a559672ffd31a9) --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 3a7be459a6..4211e9c011 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2581,7 +2581,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & endif ! set GDD target - if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .gt. 0._r8) then + if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .ge. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator From 189f9f9ca0bce94e4b83cc5326dca25310f55ac2 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Fri, 10 Jun 2022 12:11:41 -0600 Subject: [PATCH 0231/2067] Remove restriction on calc_human_stress_indices --- .../testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 1 - 1 file changed, 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm index 86903538e2..c885cdacd7 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -1,6 +1,5 @@ z0param_method = 'Meier2022' use_z0m_snowmelt = .true. use_z0mg_2d = .false. -calc_human_stress_indices = 'NONE' ! Currently dies when turned on because of a negative humidity (about -31) in Wet Bulb calculation paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_params.RMz0.c220304.nc' From c08d09d90cd36d107f5669c855f40ff36e79b68e Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Fri, 10 Jun 2022 12:47:03 -0600 Subject: [PATCH 0232/2067] Change zetamaxstable for z0param_method == 'Meier2022' to 2.0 --- bld/namelist_files/namelist_defaults_ctsm.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ea0b9f321c..0081b9ac6b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -208,7 +208,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 2.0d00 0.5d00 -0.5d00 +0.5d00 +2.0d00 .true. From 6de071de6c4f47cae79203bae5888f8762e97cbc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 10 Jun 2022 17:24:40 -0600 Subject: [PATCH 0233/2067] Added repr_grainc_to_food_accum(_thisyear) outputs. --- src/biogeochem/CNPhenologyMod.F90 | 12 ++++++ src/biogeochem/CNVegCarbonFluxType.F90 | 60 ++++++++++++++++++++++++++ 2 files changed, 72 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 4211e9c011..10e71202ff 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1707,6 +1707,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer g ! gridcell indices integer h ! hemisphere indices integer s ! growing season indices + integer k ! grain pool indices integer idpp ! number of days past planting integer mxmat ! maximum growing season length real(r8) harvest_reason @@ -1828,6 +1829,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%gddaccum_thisyr(p,s) = -1._r8 crop_inst%hui_thisyr(p,s) = -1._r8 crop_inst%harvest_reason_thisyr(p,s) = -1._r8 + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p,s,k) = 0._r8 + end do end do next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) end if @@ -2231,6 +2235,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) crop_inst%harvest_reason_thisyr(p, harvest_count(p)) = harvest_reason + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p, harvest_count(p), k) = & + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) + end do endif croplive(p) = .false. ! no re-entry in greater if-block @@ -2493,6 +2501,7 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & ! ! LOCAL VARAIBLES: integer s ! growing season index + integer k ! grain pool index real(r8) gdd_target ! cultivar GDD target this growing season real(r8) this_sowing_reason ! number representing sowing reason(s) !------------------------------------------------------------------------ @@ -2523,6 +2532,9 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & idop(p) = jday harvdate(p) = NOT_Harvested s = sowing_count(p) + 1 + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) = 0._r8 + end do ! SSR troubleshooting if (s < 1) then diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index cce46f080c..afe5107978 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -12,6 +12,7 @@ module CNVegCarbonFluxType use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools use clm_varpar , only : nlevdecomp_full, nlevdecomp, i_litr_min, i_litr_max, i_cwdl2 + use clm_varpar , only : mxharvests use clm_varcon , only : spval, dzsoi_decomp use clm_varctl , only : use_cndv, use_c13, use_nitrif_denitrif, use_crop use clm_varctl , only : use_grainproduct @@ -136,6 +137,8 @@ module CNVegCarbonFluxType real(r8), pointer :: frootc_to_litter_patch (:) ! fine root C litterfall (gC/m2/s) real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_accum_patch (:,:) ! grain C to food for prognostic crop accumulated since planting (gC/m2) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_accum_thisyr (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] @@ -600,6 +603,8 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%cpool_to_reproductivec_storage_patch(begp:endp, nrepr)); this%cpool_to_reproductivec_storage_patch (:,:) = nan allocate(this%livestemc_to_litter_patch (begp:endp)) ; this%livestemc_to_litter_patch (:) = nan allocate(this%repr_grainc_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_patch (:,:) = nan + allocate(this%repr_grainc_to_food_accum_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_patch (:,:) = nan + allocate(this%repr_grainc_to_food_accum_thisyr(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_thisyr (:,:,:) = nan allocate(this%repr_structurec_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structurec_to_cropprod_patch(:,:) = nan allocate(this%repr_structurec_to_litter_patch(begp:endp, repr_structure_min:repr_structure_max)) @@ -836,6 +841,31 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=data1dptr) end do + this%repr_grainc_to_food_accum_patch(begp:endp,:) = spval + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainc_to_food_accum_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINC_TO_FOOD_ACCUM + fname=get_repr_hist_fname(k)//'C_TO_FOOD_ACCUM', & + units='gC/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to food accumulated since planting', & + ptr_patch=data1dptr) + end do + + this%repr_grainc_to_food_accum_thisyr(begp:endp,:,:) = spval + do k = repr_grain_min, repr_grain_max + data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) + call hist_addfld2d ( & + ! e.g., GRAINC_TO_FOOD_ACCUM_PERHARV + fname=get_repr_hist_fname(k)//'C_TO_FOOD_ACCUM_PERHARV', & + units='gC/m^2', & + type2d='mxharvests', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to food accumulated by harvest; should only be output annually', & + ptr_patch=data2dptr) + end do + this%leafc_to_biofuelc_patch(begp:endp) = spval call hist_addfld1d (fname='LEAFC_TO_BIOFUELC', units='gC/m^2/s', & avgflag='A', long_name='leaf C to biofuel C', & @@ -3508,6 +3538,7 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) logical :: readvar ! determine if variable is on initial file character(len=256) :: varname real(r8), pointer :: data1dptr(:) ! temp. pointer for slicing larger arrays + real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays !------------------------------------------------------------------------ if (use_crop) then @@ -3540,6 +3571,34 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) units='gC/m2/s', & interpinic_flag='interp', readvar=readvar, data=data1dptr) end do + + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainc_to_food_accum_patch(:,k) + ! e.g., grainc_to_food_accum + varname = get_repr_rest_fname(k)//'c_to_food_accum' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' C to food accumulated since planting', & + units='gC/m2', & + interpinic_flag='interp', readvar=readvar, data=data1dptr) + end do + + ! Read or write variable(s) with mxharvests dimension + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() + if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then + do k = repr_grain_min, repr_grain_max + data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) + ! e.g., grainc_to_food_accum_perharv + varname = get_repr_rest_fname(k)//'c_to_food_accum_perharv' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' C to food accumulated by harvest; should only be output annually', & + units='gC/m2', & + interpinic_flag='interp', readvar=readvar, data=data2dptr) + end do + end if do k = 1, nrepr data1dptr => this%cpool_to_reproductivec_patch(:,k) @@ -3950,6 +4009,7 @@ subroutine SetValues ( this, & do fi = 1,num_patch i = filter_patch(fi) this%repr_grainc_to_food_patch(i,k) = value_patch + this%repr_grainc_to_food_accum_patch(i,k) = this%repr_grainc_to_food_accum_patch(i,k) + value_patch this%repr_grainc_to_seed_patch(i,k) = value_patch end do end do From 299035f33baac4b1836fd7894277291421e19981 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 10 Jun 2022 17:46:39 -0600 Subject: [PATCH 0234/2067] Do not end run if read-in harvest GDD target is 0. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 2d30a71c66..d82c20b6a7 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -396,12 +396,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) ! Sanity check: Try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0._r8 .or. crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000._r8) then - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) == 0._r8) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) ZERO??? ',crop_inst%rx_cultivar_gdds_thisyr(p,1) - else - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) - end if + if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000._r8) then + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if else From 57c8a8cb12eb0dd21c0ba624931946c05a396e6b Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 12 Jun 2022 17:37:12 +0200 Subject: [PATCH 0235/2067] fix diag vars --- src/biogeophys/SoilTemperatureMod.F90 | 3 +++ src/biogeophys/WaterDiagnosticBulkType.F90 | 4 ++-- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 5c5427ea81..383024351b 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1210,6 +1210,9 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & wliq0(c,j) = h2osoi_liq(c,j) wexice0(c,j)=excess_ice(c,j) wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) + wexice0(c,j) + if (j>=1) then + exice_subs_col(c,j)=0._r8 + endif endif ! end of snow layer if-block if (j <= 0) then diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 0f7b60532d..824217c1fc 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -287,7 +287,7 @@ subroutine InitBulkHistory(this, bounds) avgflag='A', & long_name=this%info%lname('vertically summed soil ice (veg landunits only)'), & ptr_col=this%h2osoi_ice_tot_col, l2g_scale_type='veg') - + ! excess ice vars this%exice_vol_tot_col(begc:endc) = 0.0_r8 call hist_addfld1d ( & fname=this%info%fname('TOTEXICE_VOL'), & @@ -911,7 +911,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil ! have to at least define them call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_SUBS'), & dim1name='column', xtype=ncd_double, & - long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), units='mm/s', & + long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), units='m', & interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) ! initialization of these to zero is ok, since they are not in history anyway this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 From 6be9820bd2d88cf48ae154e3a0e432655dd77f87 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Mon, 13 Jun 2022 08:55:03 -0600 Subject: [PATCH 0236/2067] Make zeta a global variable and fix zetamaxstable namelist --- bld/CLMBuildNamelist.pm | 5 ++++- src/biogeophys/BareGroundFluxesMod.F90 | 12 ++++++------ src/biogeophys/CanopyFluxesMod.F90 | 2 +- src/biogeophys/LakeFluxesMod.F90 | 12 ++++++------ src/biogeophys/UrbanFluxesMod.F90 | 16 +++++++++------- 5 files changed, 26 insertions(+), 21 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 77d0303e07..74fb4d3e7a 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3885,7 +3885,10 @@ sub setup_logic_friction_vel { # my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable' ); + my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' )); + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable', + 'z0param_method'=>$z0param_method ); } #------------------------------------------------------------------------------- diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 73c169fa13..2b1ac8bcc0 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -117,7 +117,6 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & integer :: p,c,g,f,j,l ! indices integer :: iter ! iteration index real(r8) :: zldis(bounds%begp:bounds%endp) ! reference height "minus" zero displacement height [m] - real(r8) :: zeta ! dimensionless height used in Monin-Obukhov theory real(r8) :: wc ! convective velocity [m/s] real(r8) :: dth(bounds%begp:bounds%endp) ! diff of virtual temp. between ref. height and surface real(r8) :: dthv ! diff of vir. poten. temp. between ref. height and surface @@ -239,6 +238,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Output: [real(r8) (:) ] observational height of specific humidity at patch level [m] u10_clm => frictionvel_inst%u10_clm_patch , & ! Input: [real(r8) (:) ] 10 m height winds (m/s) zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions + zeta => frictionvel_inst%zeta_patch , & ! Output: [real(r8) (:) ] dimensionless stability parameter z0mg_col => frictionvel_inst%z0mg_col , & ! Output: [real(r8) (:) ] roughness length, momentum [m] z0hg_col => frictionvel_inst%z0hg_col , & ! Output: [real(r8) (:) ] roughness length, sensible heat [m] z0qg_col => frictionvel_inst%z0qg_col , & ! Output: [real(r8) (:) ] roughness length, latent heat [m] @@ -369,17 +369,17 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & forc_hgt_q_patch(p) = forc_hgt_q_patch(g) + z0qg_patch(p) + displa(p) end if thvstar = tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar - zeta = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) + zeta(p) = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) - if (zeta >= 0._r8) then !stable - zeta = min(zetamax,max(zeta,0.01_r8)) + if (zeta(p) >= 0._r8) then !stable + zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) um(p) = max(ur(p),0.1_r8) else !unstable - zeta = max(-100._r8,min(zeta,-0.01_r8)) + zeta(p) = max(-100._r8,min(zeta(p),-0.01_r8)) wc = beta(c)*(-grav*ustar(p)*thvstar*zii(c)/thv(c))**0.333_r8 um(p) = sqrt(ur(p)*ur(p) + wc*wc) end if - obu(p) = zldis(p)/zeta + obu(p) = zldis(p)/zeta(p) num_iter(p) = iter end do diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 31d73e1b37..9e414251b2 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1395,7 +1395,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, if(use_biomass_heat_storage) then ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 if (z0param_method == 'Meier2022') then - zeta(p) = min(20._r8,max(zeta(p),0.01_r8)) + zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) else zeta(p) = min(100._r8,max(zeta(p),0.01_r8)) end if diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 6dc9d1f0c0..edd95628cc 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -170,7 +170,6 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, real(r8) :: ur(bounds%begp:bounds%endp) ! wind speed at reference height [m/s] real(r8) :: ustar(bounds%begp:bounds%endp) ! friction velocity [m/s] real(r8) :: wc ! convective velocity [m/s] - real(r8) :: zeta ! dimensionless height used in Monin-Obukhov theory real(r8) :: zldis(bounds%begp:bounds%endp) ! reference height "minus" zero displacement height [m] real(r8) :: displa(bounds%begp:bounds%endp) ! displacement (always zero) [m] real(r8) :: u2m ! 2 m wind speed (m/s) @@ -239,6 +238,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Input: [real(r8) (:) ] observational height of temperature at pft level [m] forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Input: [real(r8) (:) ] observational height of specific humidity at pft level [m] zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions + zeta => frictionvel_inst%zeta_patch , & ! Output: [real(r8) (:) ] dimensionless stability parameter ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) q_ref2m => waterdiagnosticbulk_inst%q_ref2m_patch , & ! Output: [real(r8) (:) ] 2 m height surface specific humidity (kg/kg) @@ -554,17 +554,17 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, qstar = temp2(p)*dqh(p) thvstar=tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar - zeta=zldis(p)*vkc * grav*thvstar/(ustar(p)**2*thv(c)) + zeta(p)=zldis(p)*vkc * grav*thvstar/(ustar(p)**2*thv(c)) - if (zeta >= 0._r8) then !stable - zeta = min(zetamax,max(zeta,0.01_r8)) + if (zeta(p) >= 0._r8) then !stable + zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) um(p) = max(ur(p),0.1_r8) else !unstable - zeta = max(-100._r8,min(zeta,-0.01_r8)) + zeta(p) = max(-100._r8,min(zeta(p),-0.01_r8)) wc = beta1*(-grav*ustar(p)*thvstar*zii/thv(c))**0.333_r8 um(p) = sqrt(ur(p)*ur(p)+wc*wc) end if - obu(p) = zldis(p)/zeta + obu(p) = zldis(p)/zeta(p) if (obuold(p)*obu(p) < 0._r8) nmozsgn(p) = nmozsgn(p)+1 diff --git a/src/biogeophys/UrbanFluxesMod.F90 b/src/biogeophys/UrbanFluxesMod.F90 index d02433a5bb..74f0d2612d 100644 --- a/src/biogeophys/UrbanFluxesMod.F90 +++ b/src/biogeophys/UrbanFluxesMod.F90 @@ -146,6 +146,7 @@ subroutine UrbanFluxes (bounds, num_nourbanl, filter_nourbanl, real(r8) :: dth(bounds%begl:bounds%endl) ! diff of virtual temp. between ref. height and surface real(r8) :: dqh(bounds%begl:bounds%endl) ! diff of humidity between ref. height and surface real(r8) :: zldis(bounds%begl:bounds%endl) ! reference height "minus" zero displacement height (m) + real(r8) :: zeta_lunit(bounds%begl:bounds%endl) ! landunit-level dimensionless stability parameter real(r8) :: um(bounds%begl:bounds%endl) ! wind speed including the stablity effect (m/s) real(r8) :: obu(bounds%begl:bounds%endl) ! Monin-Obukhov length (m) real(r8) :: taf_numer(bounds%begl:bounds%endl) ! numerator of taf equation (K m/s) @@ -187,7 +188,6 @@ subroutine UrbanFluxes (bounds, num_nourbanl, filter_nourbanl, real(r8) :: wtus_shadewall_unscl(bounds%begl:bounds%endl) ! sensible heat conductance for shadewall (not scaled) (m/s) real(r8) :: wtuq_shadewall_unscl(bounds%begl:bounds%endl) ! latent heat conductance for shadewall (not scaled) (m/s) real(r8) :: wc ! convective velocity (m/s) - real(r8) :: zeta ! dimensionless height used in Monin-Obukhov theory real(r8) :: eflx_sh_grnd_scale(bounds%begp:bounds%endp) ! scaled sensible heat flux from ground (W/m**2) [+ to atm] real(r8) :: qflx_evap_soi_scale(bounds%begp:bounds%endp) ! scaled soil evaporation (mm H2O/s) (+ = to atm) real(r8) :: eflx_wasteheat_roof(bounds%begl:bounds%endl) ! sensible heat flux from urban heating/cooling sources of waste heat for roof (W/m**2) @@ -293,6 +293,7 @@ subroutine UrbanFluxes (bounds, num_nourbanl, filter_nourbanl, forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Input: [real(r8) (:) ] observational height of wind at patch-level (m) forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Input: [real(r8) (:) ] observational height of temperature at patch-level (m) zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions + zeta => frictionvel_inst%zeta_patch , & ! Output: [real(r8) (:) ] dimensionless stability parameter ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) u10_clm => frictionvel_inst%u10_clm_patch , & ! Input: [real(r8) (:) ] 10 m height winds (m/s) @@ -652,18 +653,18 @@ subroutine UrbanFluxes (bounds, num_nourbanl, filter_nourbanl, tstar = temp1(l)*dth(l) qstar = temp2(l)*dqh(l) thvstar = tstar*(1._r8+0.61_r8*forc_q(g)) + 0.61_r8*forc_th(g)*qstar - zeta = zldis(l)*vkc*grav*thvstar/(ustar(l)**2*thv_g(l)) + zeta_lunit(l) = zldis(l)*vkc*grav*thvstar/(ustar(l)**2*thv_g(l)) - if (zeta >= 0._r8) then !stable - zeta = min(zetamax,max(zeta,0.01_r8)) + if (zeta_lunit(l) >= 0._r8) then !stable + zeta_lunit(l) = min(zetamax,max(zeta_lunit(l),0.01_r8)) um(l) = max(ur(l),0.1_r8) else !unstable - zeta = max(-100._r8,min(zeta,-0.01_r8)) + zeta_lunit(l) = max(-100._r8,min(zeta_lunit(l),-0.01_r8)) wc = beta(l)*(-grav*ustar(l)*thvstar*zii(l)/thv_g(l))**0.333_r8 um(l) = sqrt(ur(l)*ur(l) + wc*wc) end if - obu(l) = zldis(l)/zeta + obu(l) = zldis(l)/zeta_lunit(l) end do end do ! end iteration @@ -682,7 +683,8 @@ subroutine UrbanFluxes (bounds, num_nourbanl, filter_nourbanl, g = patch%gridcell(p) l = patch%landunit(p) - ram1(p) = ramu(l) !pass value to global variable + ram1(p) = ramu(l) !pass value to global variable + zeta(p) = zeta_lunit(l) !pass value to global variable ! Upward and downward canopy longwave are zero From 38a8cce630c4798cae274d5a04a76ed6b3453f6c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 14 Jun 2022 15:36:32 -0600 Subject: [PATCH 0237/2067] Bugfix to repr_grainc_to_food_accum(_thisyear) outputs. --- src/biogeochem/CNPhenologyMod.F90 | 3 +++ src/biogeochem/CNVegCarbonFluxType.F90 | 1 - 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 10e71202ff..19a8fec0b7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3447,6 +3447,9 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = & cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) + & cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) = & + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) + & + cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = & cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) + & cnveg_nitrogenflux_inst%repr_grainn_to_food_patch(p,k) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index afe5107978..be6d14ed56 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -4009,7 +4009,6 @@ subroutine SetValues ( this, & do fi = 1,num_patch i = filter_patch(fi) this%repr_grainc_to_food_patch(i,k) = value_patch - this%repr_grainc_to_food_accum_patch(i,k) = this%repr_grainc_to_food_accum_patch(i,k) + value_patch this%repr_grainc_to_seed_patch(i,k) = value_patch end do end do From 492300989978a774d8bd1203ba95c080ba196b9a Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 16 Jun 2022 13:26:07 +0200 Subject: [PATCH 0238/2067] make history active only when exice is used --- src/biogeophys/WaterDiagnosticBulkType.F90 | 37 ++++++++++++---------- src/biogeophys/WaterStateType.F90 | 12 ++++--- 2 files changed, 27 insertions(+), 22 deletions(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 824217c1fc..55c19fcfe2 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -241,6 +241,7 @@ subroutine InitBulkHistory(this, bounds) ! !USES: use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) use histFileMod , only : hist_addfld1d, hist_addfld2d, no_snow_normal, no_snow_zero + use clm_varctl , only : use_excess_ice ! ! !ARGUMENTS: class(waterdiagnosticbulk_type), intent(in) :: this @@ -288,23 +289,25 @@ subroutine InitBulkHistory(this, bounds) long_name=this%info%lname('vertically summed soil ice (veg landunits only)'), & ptr_col=this%h2osoi_ice_tot_col, l2g_scale_type='veg') ! excess ice vars - this%exice_vol_tot_col(begc:endc) = 0.0_r8 - call hist_addfld1d ( & - fname=this%info%fname('TOTEXICE_VOL'), & - units='m3/m3', & - avgflag='A', & - l2g_scale_type='veg', default='inactive', & - long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & - ptr_col=this%exice_vol_tot_col) - - this%exice_subs_tot_col(begc:endc) = 0.0_r8 - call hist_addfld1d ( & - fname=this%info%fname('EXICE_SUBS'), & - units='m', & - avgflag='SUM', & - l2g_scale_type='veg', default='inactive', & - long_name=this%info%lname('subsidence due to excess ice melt (veg landunits only)'), & - ptr_col=this%exice_subs_tot_col) + if (use_excess_ice) then + this%exice_vol_tot_col(begc:endc) = 0.0_r8 + call hist_addfld1d ( & + fname=this%info%fname('TOTEXICE_VOL'), & + units='m3/m3', & + avgflag='A', & + l2g_scale_type='veg', & + long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & + ptr_col=this%exice_vol_tot_col) + + this%exice_subs_tot_col(begc:endc) = 0.0_r8 + call hist_addfld1d ( & + fname=this%info%fname('EXICE_SUBS'), & + units='m', & + avgflag='SUM', & + l2g_scale_type='veg', & + long_name=this%info%lname('subsidence due to excess ice melt (veg landunits only)'), & + ptr_col=this%exice_subs_tot_col) + end if this%iwue_ln_patch(begp:endp) = spval call hist_addfld1d ( & diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index dcf49b39d6..1f8a12cd4a 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -286,11 +286,13 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) end if ! Add excess ice fields to history - data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) - call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & - avgflag='A', long_name='excess soil ice (vegetated landunits only)', & - ptr_col=this%excess_ice_col, l2g_scale_type='veg', & - default='inactive' ) + + if (use_excess_ice) then + data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & + avgflag='A', long_name='excess soil ice (vegetated landunits only)', & + ptr_col=this%excess_ice_col, l2g_scale_type='veg') + end if ! (rgk 02-02-2017) There is intentionally no entry here for stored plant water ! I think that since the value is zero in all cases except From 805a3bad69444f598814bf3a5dbb85b620f5d9ba Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 16 Jun 2022 13:26:49 +0200 Subject: [PATCH 0239/2067] add mapalgo to namelists and stream --- bld/CLMBuildNamelist.pm | 1 + bld/namelist_files/namelist_defaults_ctsm.xml | 1 + .../namelist_definition_ctsm.xml | 10 ++++++++- src/cpl/share_esmf/ExcessIceStreamType.F90 | 22 +++++++++---------- 4 files changed, 22 insertions(+), 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c7168e45e8..96bd99efd8 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4153,6 +4153,7 @@ sub setup_logic_exice { if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); } # end exice streams diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 54bec90957..b0d2c35ddf 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2594,5 +2594,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_c20220516.nc +bilinear diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 702b21b262..d598b4ed57 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2823,7 +2823,7 @@ use case.) -Toggle to turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) +If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) + +Mapping method from excess ice input stream data to the model resolution + bilinear = bilinear interpolation + nn = nearest neighbor + + + diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 63c7e69dc1..ae79cad626 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -37,7 +37,7 @@ module ExcessIceStreamType type, private :: streamcontrol_type character(len=CL) :: stream_fldFileName_exice ! data Filename character(len=CL) :: stream_meshfile_exice ! mesh Filename - character(len=CL) :: exicemapalgo ! map algo + character(len=CL) :: stream_mapalgo_exice ! map algo contains procedure, private :: ReadNML ! Read in namelist end type streamcontrol_type @@ -95,10 +95,10 @@ subroutine Init(this, bounds, NLFilename) compname = 'LND', & model_clock = model_clock, & model_mesh = mesh, & - stream_meshfile = control%stream_meshfile_exice, & + stream_meshfile = control%stream_meshfile_exice, & stream_lev_dimname = 'null', & - stream_mapalgo = 'nn', & - stream_filenames = (/trim(control%stream_fldFileName_exice)/), & + stream_mapalgo = control%stream_mapalgo_exice, & + stream_filenames = (/trim(control%stream_fldFileName_exice)/), & stream_fldlistFile = stream_varnames, & stream_fldListModel = stream_varnames, & stream_yearFirst = 1996, & @@ -107,8 +107,8 @@ subroutine Init(this, bounds, NLFilename) stream_offset = 0, & stream_taxmode = 'extend', & stream_dtlimit = 1.0e30_r8, & - stream_tintalgo = 'nearest', & - stream_name = 'excess ice ', & + stream_tintalgo = 'nearest', & + stream_name = 'excess ice ', & rc = rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) @@ -247,13 +247,13 @@ subroutine ReadNML(this, bounds, NLFilename) integer :: nml_error ! namelist i/o error flag character(len=CL) :: stream_fldFileName_exice = ' ' character(len=CL) :: stream_meshfile_exice = ' ' - character(len=CL) :: exicemapalgo = 'bilinear' + character(len=CL) :: stream_mapalgo_exice = 'bilinear' character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read character(len=*), parameter :: subName = "('exice_streams::ReadNML')" !----------------------------------------------------------------------- namelist /exice_streams/ & ! MUST agree with namelist_name above - exicemapalgo, stream_fldFileName_exice, stream_meshfile_exice + stream_mapalgo_exice, stream_fldFileName_exice, stream_meshfile_exice ! Default values for namelist @@ -272,7 +272,7 @@ subroutine ReadNML(this, bounds, NLFilename) close(nu_nml) endif - call shr_mpi_bcast(exicemapalgo , mpicom) + call shr_mpi_bcast(stream_mapalgo_exice , mpicom) call shr_mpi_bcast(stream_fldFileName_exice , mpicom) call shr_mpi_bcast(stream_meshfile_exice , mpicom) @@ -281,11 +281,11 @@ subroutine ReadNML(this, bounds, NLFilename) write(iulog,*) namelist_name, ' stream settings:' write(iulog,*) ' stream_fldFileName_exice = ',stream_fldFileName_exice write(iulog,*) ' stream_meshfile_exice = ',stream_meshfile_exice - write(iulog,*) ' exicemapalgo = ',exicemapalgo + write(iulog,*) ' stream_mapalgo_exice = ',stream_mapalgo_exice endif this%stream_fldFileName_exice = stream_fldFileName_exice this%stream_meshfile_exice = stream_meshfile_exice - this%exicemapalgo = exicemapalgo + this%stream_mapalgo_exice = stream_mapalgo_exice end subroutine ReadNML From 3169a42d174a51ed83a34ed233db94a00427b142 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 16 Jun 2022 13:27:46 +0200 Subject: [PATCH 0240/2067] pass alm_lastyear_indx to restart and improve cold --- src/biogeophys/WaterStateBulkType.F90 | 6 ++-- src/biogeophys/WaterStateType.F90 | 41 +++++++++++++++++---------- src/biogeophys/WaterType.F90 | 9 ++++-- src/main/clm_instMod.F90 | 3 +- 4 files changed, 38 insertions(+), 21 deletions(-) diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index fcb7e2cda7..74dae314e8 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -188,7 +188,7 @@ end subroutine InitBulkCold !------------------------------------------------------------------------ subroutine RestartBulk(this, bounds, ncid, flag, & - watsat_col, t_soisno_col) + watsat_col, t_soisno_col, altmax_lastyear_indx) ! ! !DESCRIPTION: ! Read/Write module information to/from restart file. @@ -204,6 +204,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, & character(len=*) , intent(in) :: flag ! 'read' or 'write' real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) + integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year ! ! !LOCAL VARIABLES: integer :: c,l,j @@ -214,7 +215,8 @@ subroutine RestartBulk(this, bounds, ncid, flag, & call this%restart (bounds, ncid, flag=flag, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & - t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:)) + t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & + altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) call restartvar(ncid=ncid, flag=flag, & diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 1f8a12cd4a..318990b42c 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -55,7 +55,6 @@ module WaterStateType real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (-nlevsno+1:nlevgrnd) real(r8), pointer :: exice_bulk_init (:) ! inital value for excess ice (new) (unitless) - logical, pointer, private :: exice_first_time_col (:) ! col whether excess ice is turned on first time type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only contains @@ -163,7 +162,6 @@ subroutine InitAllocate(this, bounds, tracer_vars) container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column, & dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) - allocate(this%exice_first_time_col (bounds%begc:bounds%endc)) ; this%exice_first_time_col (:) = .true. !should be true during initialize1 call AllocateVar1d(var = this%exice_bulk_init, name = 'exice_bulk_init', & container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) @@ -330,7 +328,7 @@ subroutine InitCold(this, bounds, & ! ! !LOCAL VARIABLES: integer :: c,j,l,nlevs,g - integer :: nbedrock + integer :: nbedrock, n1m real(r8) :: ratio !----------------------------------------------------------------------- @@ -544,17 +542,27 @@ subroutine InitCold(this, bounds, & l = col%landunit(c) if (.not. lun%lakpoi(l)) then !not lake if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (use_bedrock) then + n1m=3 + do j = 3, nlevsoi ! get layer with 1 m depth + if (col%zi(c,j-1)<=1.0_r8 .and. col%zi(c,j)>1.0_r8) then + n1m=j + end if + end do + if (use_bedrock .and. nbedrock<=nlevsoi) then nbedrock = col%nbedrock(c) else nbedrock = nlevsoi endif do j = 2, nlevmaxurbgrnd ! ignore first layer - if (j= n1m .and. jaltmax_lastyear_indx(c) .and. j Date: Tue, 21 Jun 2022 13:35:35 -0600 Subject: [PATCH 0241/2067] Added repr_grainc_to_food_accum(_thisyear) outputs, incl bugfix. Cherry-picked from 6de071de6c4f47cae79203bae5888f8762e97cbc and 38a8cce630c4798cae274d5a04a76ed6b3453f6c. Also moved CallRestartvarDimOK() in support. --- src/biogeochem/CNPhenologyMod.F90 | 17 ++++++++ src/biogeochem/CNVegCarbonFluxType.F90 | 59 ++++++++++++++++++++++++++ src/biogeochem/CropType.F90 | 33 -------------- src/utils/restUtilMod.F90.in | 36 ++++++++++++++++ 4 files changed, 112 insertions(+), 33 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index f87a59ebaf..9d498f7d90 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1700,6 +1700,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer g ! gridcell indices integer h ! hemisphere indices integer s ! growing season indices + integer k ! grain pool indices integer idpp ! number of days past planting real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year @@ -1808,6 +1809,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end do do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p,s,k) = 0._r8 + end do end do end if @@ -2084,6 +2088,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p, harvest_count(p), k) = & + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) + end do croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = cphase_harvest if (tlai(p) > 0._r8) then ! plant had emerged before harvest @@ -2309,6 +2317,9 @@ subroutine PlantCrop(p, leafcn_in, jday, & type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(cnveg_carbonstate_type) , intent(inout) :: c13_cnveg_carbonstate_inst type(cnveg_carbonstate_type) , intent(inout) :: c14_cnveg_carbonstate_inst + ! + ! LOCAL VARAIBLES: + integer k ! grain pool index !------------------------------------------------------------------------ associate( & @@ -2329,6 +2340,9 @@ subroutine PlantCrop(p, leafcn_in, jday, & harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 crop_inst%sdates_thisyr(p,sowing_count(p)) = jday + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) = 0._r8 + end do leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset @@ -3165,6 +3179,9 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = & cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) + & cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) = & + cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) + & + cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = & cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) + & cnveg_nitrogenflux_inst%repr_grainn_to_food_patch(p,k) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index cce46f080c..be6d14ed56 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -12,6 +12,7 @@ module CNVegCarbonFluxType use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools use clm_varpar , only : nlevdecomp_full, nlevdecomp, i_litr_min, i_litr_max, i_cwdl2 + use clm_varpar , only : mxharvests use clm_varcon , only : spval, dzsoi_decomp use clm_varctl , only : use_cndv, use_c13, use_nitrif_denitrif, use_crop use clm_varctl , only : use_grainproduct @@ -136,6 +137,8 @@ module CNVegCarbonFluxType real(r8), pointer :: frootc_to_litter_patch (:) ! fine root C litterfall (gC/m2/s) real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_accum_patch (:,:) ! grain C to food for prognostic crop accumulated since planting (gC/m2) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_accum_thisyr (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] @@ -600,6 +603,8 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%cpool_to_reproductivec_storage_patch(begp:endp, nrepr)); this%cpool_to_reproductivec_storage_patch (:,:) = nan allocate(this%livestemc_to_litter_patch (begp:endp)) ; this%livestemc_to_litter_patch (:) = nan allocate(this%repr_grainc_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_patch (:,:) = nan + allocate(this%repr_grainc_to_food_accum_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_patch (:,:) = nan + allocate(this%repr_grainc_to_food_accum_thisyr(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_thisyr (:,:,:) = nan allocate(this%repr_structurec_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structurec_to_cropprod_patch(:,:) = nan allocate(this%repr_structurec_to_litter_patch(begp:endp, repr_structure_min:repr_structure_max)) @@ -836,6 +841,31 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=data1dptr) end do + this%repr_grainc_to_food_accum_patch(begp:endp,:) = spval + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainc_to_food_accum_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINC_TO_FOOD_ACCUM + fname=get_repr_hist_fname(k)//'C_TO_FOOD_ACCUM', & + units='gC/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to food accumulated since planting', & + ptr_patch=data1dptr) + end do + + this%repr_grainc_to_food_accum_thisyr(begp:endp,:,:) = spval + do k = repr_grain_min, repr_grain_max + data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) + call hist_addfld2d ( & + ! e.g., GRAINC_TO_FOOD_ACCUM_PERHARV + fname=get_repr_hist_fname(k)//'C_TO_FOOD_ACCUM_PERHARV', & + units='gC/m^2', & + type2d='mxharvests', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to food accumulated by harvest; should only be output annually', & + ptr_patch=data2dptr) + end do + this%leafc_to_biofuelc_patch(begp:endp) = spval call hist_addfld1d (fname='LEAFC_TO_BIOFUELC', units='gC/m^2/s', & avgflag='A', long_name='leaf C to biofuel C', & @@ -3508,6 +3538,7 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) logical :: readvar ! determine if variable is on initial file character(len=256) :: varname real(r8), pointer :: data1dptr(:) ! temp. pointer for slicing larger arrays + real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays !------------------------------------------------------------------------ if (use_crop) then @@ -3540,6 +3571,34 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) units='gC/m2/s', & interpinic_flag='interp', readvar=readvar, data=data1dptr) end do + + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainc_to_food_accum_patch(:,k) + ! e.g., grainc_to_food_accum + varname = get_repr_rest_fname(k)//'c_to_food_accum' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' C to food accumulated since planting', & + units='gC/m2', & + interpinic_flag='interp', readvar=readvar, data=data1dptr) + end do + + ! Read or write variable(s) with mxharvests dimension + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() + if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then + do k = repr_grain_min, repr_grain_max + data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) + ! e.g., grainc_to_food_accum_perharv + varname = get_repr_rest_fname(k)//'c_to_food_accum_perharv' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' C to food accumulated by harvest; should only be output annually', & + units='gC/m2', & + interpinic_flag='interp', readvar=readvar, data=data2dptr) + end do + end if do k = 1, nrepr data1dptr => this%cpool_to_reproductivec_patch(:,k) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 6ceeccf7e3..af44e487ca 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -437,39 +437,6 @@ subroutine InitAccVars(this, bounds) end subroutine InitAccVars - !----------------------------------------------------------------------- - logical function CallRestartvarDimOK (ncid, flag, dimname) - ! - ! !DESCRIPTION: - ! Answer whether to call restartvar(), if necessary checking whether - ! a dimension exists in the restart file - ! - ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) - ! Used in Restart(). Even though restartvar() can safely be called for a - ! non-existent variable, it gives an error for a non-existent dimension, so - ! check whether the dimension exists before trying to read. The need for this - ! function arose because we recently added the mxsowings and mxharvests - ! dimensions to the restart file. - ! - ! !USES: - use ncdio_pio - ! - ! !ARGUMENTS: - type(file_desc_t), intent(inout) :: ncid - character(len=*) , intent(in) :: flag - character(len=*) , intent(in) :: dimname - ! - ! !LOCAL VARIABLES: - !----------------------------------------------------------------------- - - if (flag == 'read') then - call check_dim(ncid, dimname, dimexist=CallRestartvarDimOK) - else - CallRestartvarDimOK = .true. - end if - - end function CallRestartvarDimOK - !----------------------------------------------------------------------- subroutine Restart(this, bounds, ncid, flag) ! diff --git a/src/utils/restUtilMod.F90.in b/src/utils/restUtilMod.F90.in index 4271271097..32686c816c 100644 --- a/src/utils/restUtilMod.F90.in +++ b/src/utils/restUtilMod.F90.in @@ -91,6 +91,10 @@ module restUtilMod private :: missing_field_possibly_abort private :: write_interpinic_flag + ! Answer whether to call restartvar(), if necessary checking whether + ! a dimension exists in the restart file + public :: CallRestartvarDimOK + character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -740,5 +744,37 @@ contains end subroutine write_interpinic_flag + !----------------------------------------------------------------------- + logical function CallRestartvarDimOK (ncid, flag, dimname) + ! + ! !DESCRIPTION: + ! Answer whether to call restartvar(), if necessary checking whether + ! a dimension exists in the restart file + ! + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) + ! Used in Restart(). Even though restartvar() can safely be called for a + ! non-existent variable, it gives an error for a non-existent dimension, so + ! check whether the dimension exists before trying to read. The need for this + ! function arose because we recently added the mxsowings and mxharvests + ! dimensions to the restart file. + ! + ! !USES: + use ncdio_pio + ! + ! !ARGUMENTS: + type(file_desc_t), intent(inout) :: ncid + character(len=*) , intent(in) :: flag + character(len=*) , intent(in) :: dimname + ! + ! !LOCAL VARIABLES: + !----------------------------------------------------------------------- + + if (flag == 'read') then + call check_dim(ncid, dimname, dimexist=CallRestartvarDimOK) + else + CallRestartvarDimOK = .true. + end if + + end function CallRestartvarDimOK end module restUtilMod From 5a122ba7107d897d236b7faa28acdbda5b2f826b Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 24 Jun 2022 16:24:04 +0200 Subject: [PATCH 0242/2067] fix namelists so exice files are not always downloaded --- bld/CLMBuildNamelist.pm | 12 +++++++----- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++--- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++-- 3 files changed, 12 insertions(+), 10 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 96bd99efd8..17bcf04d04 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2137,6 +2137,7 @@ sub setup_logic_soilstate { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'organic_frac_squared' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_bedrock', 'use_fates'=>$nl_flags->{'use_fates'}, 'vichydro'=>$nl_flags->{'vichydro'} ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice'); # excess ice flag should be read before stream vars my $var1 = "soil_layerstruct_predefined"; my $var2 = "soil_layerstruct_userdefined"; @@ -4148,12 +4149,13 @@ sub setup_logic_exice { # excess ice streams # my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); - if ($opts->{'driver'} eq "nuopc" ) { + my $use_exice = $nl->get_value( 'use_excess_ice' ); + if (defined($use_exice) && $opts->{'driver'} eq "nuopc" && value_is_true($use_exice)) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); + } + } # end exice streams diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index b0d2c35ddf..911ed296cf 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2592,8 +2592,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts .false. -lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc -lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_c20220516.nc -bilinear +lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc +lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_c20220516.nc +bilinear diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index d598b4ed57..bcee47aed5 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2819,9 +2819,9 @@ use case.) - + - If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) From d284f3191ae6a8371e8a4f7be58b188366311a61 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 24 Jun 2022 20:40:08 +0200 Subject: [PATCH 0243/2067] added error message for non-nuopc driver --- bld/CLMBuildNamelist.pm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 17bcf04d04..357eb2d4d2 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4154,7 +4154,9 @@ sub setup_logic_exice { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); - } + } elsif (defined($use_exice) && (! $opts->{'driver'} eq "nuopc") && value_is_true($use_exice)) { + $log->fatal_error("nuopc driver is required when use_excess_ice is set to true" ); +} } # end exice streams From 4e3610a4ec92af6b59b58463ea5ba99179d771ef Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 24 Jun 2022 20:40:41 +0200 Subject: [PATCH 0244/2067] cleanup, comments and rename diagnostic history vars --- src/biogeophys/SoilTemperatureMod.F90 | 9 +++++---- src/biogeophys/WaterDiagnosticBulkType.F90 | 10 +++++----- src/biogeophys/WaterStateType.F90 | 6 +++--- src/cpl/share_esmf/ExcessIceStreamType.F90 | 2 ++ 4 files changed, 15 insertions(+), 12 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 383024351b..1f58cf25cb 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -198,7 +198,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter frac_sno_eff => waterdiagnosticbulk_inst%frac_sno_eff_col , & ! Input: [real(r8) (:) ] eff. fraction of ground covered by snow (0 to 1) snow_depth => waterdiagnosticbulk_inst%snow_depth_col , & ! Input: [real(r8) (:) ] snow height (m) h2osfc => waterstatebulk_inst%h2osfc_col , & ! Input: [real(r8) (:) ] surface water (mm) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) (new) (1:nlevgrnd) frac_h2osfc => waterdiagnosticbulk_inst%frac_h2osfc_col , & ! Input: [real(r8) (:) ] fraction of ground covered by surface water (0 to 1) @@ -1161,7 +1161,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Output: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) (new) (1:nlevgrnd) qflx_snow_drain => waterfluxbulk_inst%qflx_snow_drain_col , & ! Output: [real(r8) (:) ] drainage from snow pack qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] @@ -1393,7 +1393,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (xm(c,j) > 0._r8) then !if there is excess heat to melt the ice h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime - xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) !excess ice modifications + xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) !excess ice melting if (h2osoi_ice(c,j) == 0._r8) then ! this might be redundant if (excess_ice(c,j) >= 0._r8 .and. xm2(c,j)>0._r8 .and. j>=2) then ! if there is excess ice to melt excess_ice(c,j) = max(0._r8,wexice0(c,j) - xm2(c,j)) @@ -1413,7 +1413,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif - h2osoi_liq(c,j) = max(0._r8,wmass0(c,j)-h2osoi_ice(c,j)-excess_ice(c,j)) !melted exice is added to the respective soil layers + h2osoi_liq(c,j) = max(0._r8,wmass0(c,j)-h2osoi_ice(c,j)-excess_ice(c,j)) !melted excess ice is added to the respective soil layers if (abs(heatr) > 0._r8) then @@ -1447,6 +1447,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (j >= 1) then !why before it was two same statements? xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime + ! subsidence calculation exice_subs_col(c,j) = max(0._r8, (wexice0(c,j)-excess_ice(c,j))/denice) else xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 55c19fcfe2..6b150ceaf5 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -301,7 +301,7 @@ subroutine InitBulkHistory(this, bounds) this%exice_subs_tot_col(begc:endc) = 0.0_r8 call hist_addfld1d ( & - fname=this%info%fname('EXICE_SUBS'), & + fname=this%info%fname('SUBSIDENCE'), & units='m', & avgflag='SUM', & l2g_scale_type='veg', & @@ -911,14 +911,14 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 else + ! initialization of these to zero is ok, since they might not be in the restart file + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 ! have to at least define them - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXICE_SUBS'), & + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('SUBSIDENCE'), & dim1name='column', xtype=ncd_double, & long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), units='m', & interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) - ! initialization of these to zero is ok, since they are not in history anyway - this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 318990b42c..944f4a72f5 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -52,7 +52,7 @@ module WaterStateType real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) - real(r8), pointer :: excess_ice_col (:,:) ! col excess ice lenses (kg/m2) (new) (-nlevsno+1:nlevgrnd) + real(r8), pointer :: excess_ice_col (:,:) ! col excess ice (kg/m2) (new) (-nlevsno+1:nlevgrnd) real(r8), pointer :: exice_bulk_init (:) ! inital value for excess ice (new) (unitless) type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only @@ -554,7 +554,7 @@ subroutine InitCold(this, bounds, & nbedrock = nlevsoi endif do j = 2, nlevmaxurbgrnd ! ignore first layer - if (n1m= n1m .and. j Date: Sun, 26 Jun 2022 15:43:09 +0200 Subject: [PATCH 0245/2067] fixed comments --- src/biogeophys/SoilTemperatureMod.F90 | 4 ++-- src/main/clm_varctl.F90 | 2 +- src/main/controlMod.F90 | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 1f58cf25cb..da755bf9cf 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -700,7 +700,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - ! TODO recalculate watsat and satw to have excess ice included + !TODO recalculate watsat and satw to have excess ice included satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice +excess_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) satw = min(1._r8, satw) if (satw > .1e-6_r8) then @@ -1445,7 +1445,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & end if endif ! end of heatr > 0 if-block - if (j >= 1) then !why before it was two same statements? + if (j >= 1) then xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime ! subsidence calculation exice_subs_col(c,j) = max(0._r8, (wexice0(c,j)-excess_ice(c,j))/denice) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 2d7af87cf4..79f1837ffb 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -301,7 +301,7 @@ module clm_varctl !---------------------------------------------------------- !excess ice physics switch !---------------------------------------------------------- - logical, public :: use_excess_ice = .false. ! true. => use excess ice physics !MVD + logical, public :: use_excess_ice = .false. ! true. => use excess ice physics !---------------------------------------------------------- ! plant hydraulic stress switch diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 98d9ab4081..194e1704aa 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -242,7 +242,7 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_soil_moisture_streams - namelist /clm_inparm/ use_excess_ice !MVD + namelist /clm_inparm/ use_excess_ice namelist /clm_inparm/ use_lai_streams @@ -735,7 +735,7 @@ subroutine control_spmd() call mpi_bcast (use_soil_moisture_streams, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_excess_ice, 1, MPI_LOGICAL, 0, mpicom,ier) !MVD + call mpi_bcast (use_excess_ice, 1, MPI_LOGICAL, 0, mpicom,ier) call mpi_bcast (use_lai_streams, 1, MPI_LOGICAL, 0, mpicom, ier) From b8fe30ddb413ad14135686c1f338491c8671b7f8 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 26 Jun 2022 20:02:23 +0200 Subject: [PATCH 0246/2067] nlfilename passing --- src/biogeophys/WaterType.F90 | 25 ++++++++----------- .../unittestWaterTypeFactory.F90 | 3 ++- 2 files changed, 13 insertions(+), 15 deletions(-) diff --git a/src/biogeophys/WaterType.F90 b/src/biogeophys/WaterType.F90 index 76776eca93..bc257f27ad 100644 --- a/src/biogeophys/WaterType.F90 +++ b/src/biogeophys/WaterType.F90 @@ -246,7 +246,8 @@ end subroutine Init !----------------------------------------------------------------------- subroutine InitForTesting(this, bounds, params, & - h2osno_col, snow_depth_col, watsat_col, t_soisno_col, use_aquifer_layer) + h2osno_col, snow_depth_col, watsat_col, & + t_soisno_col, use_aquifer_layer, NLFilename) ! ! !DESCRIPTION: ! Version of Init routine just for unit tests @@ -259,9 +260,10 @@ subroutine InitForTesting(this, bounds, params, & type(water_params_type), intent(in) :: params real(r8) , intent(in) :: h2osno_col(bounds%begc:) real(r8) , intent(in) :: snow_depth_col(bounds%begc:) - real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) - logical , intent(in), optional :: use_aquifer_layer ! whether an aquifer layer is used in this run (false by default) + character(len=*) , intent(in) :: NLFilename ! Namelist filename + logical , intent(in), optional :: use_aquifer_layer ! whether an aquifer layer is used in this run (false by default) ! ! !LOCAL VARIABLES: logical :: l_use_aquifer_layer @@ -280,7 +282,8 @@ subroutine InitForTesting(this, bounds, params, & snow_depth_col = snow_depth_col, & watsat_col = watsat_col, & t_soisno_col = t_soisno_col, & - use_aquifer_layer = l_use_aquifer_layer) + use_aquifer_layer = l_use_aquifer_layer, & + NLFilename = NLFilename) end subroutine InitForTesting @@ -300,22 +303,16 @@ subroutine DoInit(this, bounds, & real(r8) , intent(in) :: snow_depth_col(bounds%begc:) real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) - logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run - character(len=*) , intent(in) , optional :: NLFilename ! Namelist filename + logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run + character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: integer :: begc, endc integer :: i - character(len=256) :: l_NLFilename ! local for namelist filename character(len=*), parameter :: subname = 'DoInit' !----------------------------------------------------------------------- - !check if NLFilename is passed - l_NLFilename = '' - if (present(NLFilename)) then - l_NLFilename = NLFilename - end if begc = bounds%begc endc = bounds%endc @@ -343,7 +340,7 @@ subroutine DoInit(this, bounds, & watsat_col = watsat_col(begc:endc, 1:), & t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), & use_aquifer_layer = use_aquifer_layer, & - NLFilename = l_NLFilename) + NLFilename = NLFilename) call this%waterdiagnosticbulk_inst%InitBulk(bounds, & bulk_info, & @@ -384,7 +381,7 @@ subroutine DoInit(this, bounds, & watsat_col = watsat_col(begc:endc, 1:), & t_soisno_col = t_soisno_col(begc:endc, -nlevsno+1:), & use_aquifer_layer = use_aquifer_layer, & - NLFilename = l_NLFilename) + NLFilename = NLFilename) call this%bulk_and_tracers(i)%waterdiagnostic_inst%Init(bounds, & this%bulk_and_tracers(i)%info, & diff --git a/src/unit_test_shr/unittestWaterTypeFactory.F90 b/src/unit_test_shr/unittestWaterTypeFactory.F90 index cc3510e881..f5f417f9ce 100644 --- a/src/unit_test_shr/unittestWaterTypeFactory.F90 +++ b/src/unit_test_shr/unittestWaterTypeFactory.F90 @@ -161,7 +161,8 @@ subroutine create_water_type(this, water_inst, & h2osno_col = col_array(0._r8), & snow_depth_col = col_array(0._r8), & watsat_col = l_watsat_col, & - t_soisno_col = l_t_soisno_col) + t_soisno_col = l_t_soisno_col, & + NLFilename = ' ') end subroutine create_water_type subroutine teardown(this, water_inst) From 5caa1792f90b3a9564e93f8def521fdfbeaef049 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 26 Jun 2022 20:07:56 +0200 Subject: [PATCH 0247/2067] indent and comment spaces fix --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- src/biogeophys/SoilHydrologyMod.F90 | 6 +- src/biogeophys/SoilTemperatureMod.F90 | 62 +++--- src/biogeophys/WaterDiagnosticBulkType.F90 | 48 ++--- src/biogeophys/WaterStateBulkType.F90 | 14 +- src/biogeophys/WaterStateType.F90 | 193 +++++++++--------- 7 files changed, 166 insertions(+), 161 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 357eb2d4d2..606f182667 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4156,7 +4156,7 @@ sub setup_logic_exice { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); } elsif (defined($use_exice) && (! $opts->{'driver'} eq "nuopc") && value_is_true($use_exice)) { $log->fatal_error("nuopc driver is required when use_excess_ice is set to true" ); -} + } } # end exice streams diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 911ed296cf..d8e3eaa810 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2587,7 +2587,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts general - + .false. diff --git a/src/biogeophys/SoilHydrologyMod.F90 b/src/biogeophys/SoilHydrologyMod.F90 index 8ef690d5b9..c46d23f870 100644 --- a/src/biogeophys/SoilHydrologyMod.F90 +++ b/src/biogeophys/SoilHydrologyMod.F90 @@ -190,9 +190,9 @@ subroutine SetSoilWaterFractions(bounds, num_hydrologyc, filter_hydrologyc, & watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] volumetric soil water at saturation (porosity) eff_porosity => soilstate_inst%eff_porosity_col , & ! Output: [real(r8) (:,:) ] effective porosity = porosity - vol_ice - h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice water (kg/m2) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) + h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) + h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice water (kg/m2) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) origflag => soilhydrology_inst%origflag , & ! Input: logical icefrac => soilhydrology_inst%icefrac_col , & ! Output: [real(r8) (:,:) ] diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index da755bf9cf..112346d74d 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -288,7 +288,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter do fc = 1,num_nolakec c = filter_nolakec(fc) l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice @@ -524,7 +524,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter do fc = 1,num_nolakec c = filter_nolakec(fc) l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) @@ -673,7 +673,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Input: [real(r8) (:) ] snow not resolved into layers (mm H2O) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice lenses (kg/m2) (new) (1:nlevgrnd) bw => waterdiagnosticbulk_inst%bw_col , & ! Output: [real(r8) (:,:) ] partial density of water in the snow pack (ice + liquid) [kg/m3] tkmg => soilstate_inst%tkmg_col , & ! Input: [real(r8) (:,:) ] thermal conductivity, soil minerals [W/m-K] @@ -700,7 +700,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - !TODO recalculate watsat and satw to have excess ice included + !TODO recalculate watsat and satw to have excess ice included satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice +excess_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) satw = min(1._r8, satw) if (satw > .1e-6_r8) then @@ -803,7 +803,8 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter .and. col%itype(c) /= icol_sunwall .and. col%itype(c) /= icol_shadewall .and. & col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) + excess_ice(c,j)*cpice + cv(c,j) = csol(c,j)*(1._r8-watsat(c,j))*dz(c,j) + (h2osoi_ice(c,j)*cpice + & + h2osoi_liq(c,j)*cpliq) + excess_ice(c,j)*cpice if (j > nbedrock(c)) cv(c,j) = csol_bedrock*dz(c,j) else if (lun%itype(l) == istwet) then cv(c,j) = (h2osoi_ice(c,j)*cpice + h2osoi_liq(c,j)*cpliq) @@ -1133,10 +1134,10 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: wice0 (bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of ice (kg/m2) real(r8) :: wliq0 (bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of liquid (kg/m2) real(r8) :: supercool(bounds%begc:bounds%endc,nlevmaxurbgrnd) !supercooled water in soil (kg/m2) - real(r8) :: propor !proportionality constant (-) + real(r8) :: propor !proportionality constant (-) real(r8) :: tinc(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !t(n+1)-t(n) [K] - real(r8) :: smp !frozen water potential (mm) - real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd)!initial mass of excess_ice at the timestep (kg/m2) + real(r8) :: smp !frozen water potential (mm) + real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !initial mass of excess_ice at the timestep (kg/m2) !----------------------------------------------------------------------- @@ -1159,9 +1160,9 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & snow_depth => waterdiagnosticbulk_inst%snow_depth_col , & ! Input: [real(r8) (:) ] snow height (m) exice_subs_col => waterdiagnosticbulk_inst%exice_subs_col , & ! Output: [real(r8) (:,:) ] per layer subsidence due to excess ice melt (mm/s) h2osno_no_layers => waterstatebulk_inst%h2osno_no_layers_col , & ! Output: [real(r8) (:) ] snow not resolved into layers (mm H2O) - h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) - excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) (new) (1:nlevgrnd) + h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Output: [real(r8) (:,:) ] liquid water (kg/m2) (new) + h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Output: [real(r8) (:,:) ] ice lens (kg/m2) (new) + excess_ice => waterstatebulk_inst%excess_ice_col , & ! Input: [real(r8) (:,:) ] excess ice (kg/m2) (new) (1:nlevgrnd) qflx_snow_drain => waterfluxbulk_inst%qflx_snow_drain_col , & ! Output: [real(r8) (:) ] drainage from snow pack qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] @@ -1210,9 +1211,9 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & wliq0(c,j) = h2osoi_liq(c,j) wexice0(c,j)=excess_ice(c,j) wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) + wexice0(c,j) - if (j>=1) then - exice_subs_col(c,j)=0._r8 - endif + if (j>=1) then + exice_subs_col(c,j)=0._r8 + endif endif ! end of snow layer if-block if (j <= 0) then @@ -1271,9 +1272,9 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & ! melt excess ice after normal ice if (excess_ice(c,j) > 0._r8 .AND. t_soisno(c,j) > tfrz) then - imelt(c,j) = 1 - tinc(c,j) = tfrz - t_soisno(c,j) - t_soisno(c,j) = tfrz + imelt(c,j) = 1 + tinc(c,j) = tfrz - t_soisno(c,j) + t_soisno(c,j) = tfrz endif ! from Zhao (1997) and Koren (1999) @@ -1391,24 +1392,24 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & heatr = 0._r8 if (xm(c,j) > 0._r8) then !if there is excess heat to melt the ice - h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) - heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime - xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) !excess ice melting - if (h2osoi_ice(c,j) == 0._r8) then ! this might be redundant + h2osoi_ice(c,j) = max(0._r8, wice0(c,j)-xm(c,j)) + heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + xm2(c,j) = xm(c,j) - h2osoi_ice(c,j) !excess ice melting + if (h2osoi_ice(c,j) == 0._r8) then ! this might be redundant if (excess_ice(c,j) >= 0._r8 .and. xm2(c,j)>0._r8 .and. j>=2) then ! if there is excess ice to melt - excess_ice(c,j) = max(0._r8,wexice0(c,j) - xm2(c,j)) - heatr = hm(c,j) - hfus * (wexice0(c,j)-excess_ice(c,j)+wice0(c,j)-h2osoi_ice(c,j)) / dtime + excess_ice(c,j) = max(0._r8,wexice0(c,j) - xm2(c,j)) + heatr = hm(c,j) - hfus * (wexice0(c,j)-excess_ice(c,j)+wice0(c,j)-h2osoi_ice(c,j)) / dtime endif - endif !end of excess ice block + endif !end of excess ice block else if (xm(c,j) < 0._r8) then if (j <= 0) then h2osoi_ice(c,j) = min(wmass0(c,j), wice0(c,j)-xm(c,j)) ! snow else - if (wmass0(c,j) - wexice0(c,j) < supercool(c,j)) then !even if excess ice is present, it cannot refreeze - h2osoi_ice(c,j) = 0._r8 - else - h2osoi_ice(c,j) = min(wmass0(c,j) - wexice0(c,j) - supercool(c,j),wice0(c,j)-xm(c,j)) - endif + if (wmass0(c,j) - wexice0(c,j) < supercool(c,j)) then !even if excess ice is present, it cannot refreeze + h2osoi_ice(c,j) = 0._r8 + else + h2osoi_ice(c,j) = min(wmass0(c,j) - wexice0(c,j) - supercool(c,j),wice0(c,j)-xm(c,j)) + endif endif heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif @@ -1446,7 +1447,8 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & endif ! end of heatr > 0 if-block if (j >= 1) then - xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime +hfus*(wexice0(c,j)-excess_ice(c,j))/dtime + xmf(c) = xmf(c) + hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime + & + hfus*(wexice0(c,j)-excess_ice(c,j))/dtime ! subsidence calculation exice_subs_col(c,j) = max(0._r8, (wexice0(c,j)-excess_ice(c,j))/denice) else diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 6b150ceaf5..d7413fb740 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -905,30 +905,32 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil end if if (.not. use_excess_ice) then - ! no need to even define the restart vars - this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 - this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 - this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + ! no need to even define the restart vars + this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 else - ! initialization of these to zero is ok, since they might not be in the restart file - this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - ! have to at least define them - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('SUBSIDENCE'), & - dim1name='column', xtype=ncd_double, & - long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), units='m', & - interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) - if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it - this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 - this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 - this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - endif - call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('TOTEXICE_VOL'), & - dim1name='column', xtype=ncd_double, & - long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), units='m3/m3', & - interpinic_flag='interp', readvar=readvar, data=this%exice_vol_tot_col) + ! initialization of these to zero is ok, since they might not be in the restart file + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + ! have to at least define them + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('SUBSIDENCE'), & + dim1name='column', xtype=ncd_double, & + long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), & + units='m', & + interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) + if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 + this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + endif + call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('TOTEXICE_VOL'), & + dim1name='column', xtype=ncd_double, & + long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & + units='m3/m3', & + interpinic_flag='interp', readvar=readvar, data=this%exice_vol_tot_col) endif end subroutine RestartBulk diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index 74dae314e8..ba3f0513c5 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -54,10 +54,10 @@ subroutine InitBulk(this, bounds, info, vars, & class(water_info_base_type), intent(in), target :: info type(water_tracer_container_type), intent(inout) :: vars real(r8) , intent(in) :: h2osno_input_col(bounds%begc:) - real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) - logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run - character(len=*) , intent(in) :: NLFilename ! Namelist filename + logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run + character(len=*) , intent(in) :: NLFilename ! Namelist filename call this%Init(bounds = bounds, & info = info, & @@ -200,11 +200,11 @@ subroutine RestartBulk(this, bounds, ncid, flag, & ! !ARGUMENTS: class(waterstatebulk_type), intent(in) :: this type(bounds_type), intent(in) :: bounds - type(file_desc_t), intent(inout) :: ncid ! netcdf id - character(len=*) , intent(in) :: flag ! 'read' or 'write' - real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + type(file_desc_t), intent(inout) :: ncid ! netcdf id + character(len=*) , intent(in) :: flag ! 'read' or 'write' + real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) - integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year + integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year ! ! !LOCAL VARIABLES: integer :: c,l,j diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 944f4a72f5..c33880a3c3 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -47,13 +47,13 @@ module WaterStateType ! For the following dynbal baseline variables: positive values are subtracted to ! avoid counting liquid water content of "virtual" states; negative values are added ! to account for missing states in the model. - real(r8), pointer :: dynbal_baseline_liq_col(:) ! baseline liquid water content subtracted from each column's total liquid water calculation (mm H2O) - real(r8), pointer :: dynbal_baseline_ice_col(:) ! baseline ice content subtracted from each column's total ice calculation (mm H2O) + real(r8), pointer :: dynbal_baseline_liq_col(:) ! baseline liquid water content subtracted from each column's total liquid water calculation (mm H2O) + real(r8), pointer :: dynbal_baseline_ice_col(:) ! baseline ice content subtracted from each column's total ice calculation (mm H2O) - real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) + real(r8) :: aquifer_water_baseline ! baseline value for water in the unconfined aquifer (wa_col) for this bulk / tracer (mm) - real(r8), pointer :: excess_ice_col (:,:) ! col excess ice (kg/m2) (new) (-nlevsno+1:nlevgrnd) - real(r8), pointer :: exice_bulk_init (:) ! inital value for excess ice (new) (unitless) + real(r8), pointer :: excess_ice_col (:,:) ! col excess ice (kg/m2) (new) (-nlevsno+1:nlevgrnd) + real(r8), pointer :: exice_bulk_init (:) ! inital value for excess ice (new) (unitless) type(excessicestream_type), private :: exicestream ! stream type for excess ice initialization NUOPC only @@ -158,13 +158,13 @@ subroutine InitAllocate(this, bounds, tracer_vars) container = tracer_vars, & bounds = bounds, subgrid_level = subgrid_level_column) !excess ice vars - call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column, & - dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) - call AllocateVar1d(var = this%exice_bulk_init, name = 'exice_bulk_init', & - container = tracer_vars, & - bounds = bounds, subgrid_level = subgrid_level_column) + call AllocateVar2d(var = this%excess_ice_col, name = 'excess_ice_col', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column, & + dim2beg = -nlevsno+1, dim2end = nlevmaxurbgrnd) + call AllocateVar1d(var = this%exice_bulk_init, name = 'exice_bulk_init', & + container = tracer_vars, & + bounds = bounds, subgrid_level = subgrid_level_column) end subroutine InitAllocate @@ -283,14 +283,14 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) ptr_col=this%wa_col, l2g_scale_type='veg') end if - ! Add excess ice fields to history + ! Add excess ice fields to history - if (use_excess_ice) then - data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) - call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & - avgflag='A', long_name='excess soil ice (vegetated landunits only)', & - ptr_col=this%excess_ice_col, l2g_scale_type='veg') - end if + if (use_excess_ice) then + data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & + avgflag='A', long_name='excess soil ice (vegetated landunits only)', & + ptr_col=this%excess_ice_col, l2g_scale_type='veg') + end if ! (rgk 02-02-2017) There is intentionally no entry here for stored plant water ! I think that since the value is zero in all cases except @@ -321,10 +321,10 @@ subroutine InitCold(this, bounds, & class(waterstate_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds real(r8) , intent(in) :: h2osno_input_col(bounds%begc:) - real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) + real(r8) , intent(in) :: watsat_col(bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) - logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run - character(len=*) , intent(in) :: NLFilename ! Namelist filename + logical , intent(in) :: use_aquifer_layer ! whether an aquifer layer is used in this run + character(len=*) , intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES: integer :: c,j,l,nlevs,g @@ -532,46 +532,46 @@ subroutine InitCold(this, bounds, & !Initialize excess ice if (use_excess_ice .and. NLFilename /= '') then - ! enforce initialization with 0 for everything - this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 - this%exice_bulk_init(bounds%begc:bounds%endc)=0.0_r8 - call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column - call this%exicestream%CalcExcessIce(bounds, this%exice_bulk_init) - do c = bounds%begc,bounds%endc - g = col%gridcell(c) - l = col%landunit(c) - if (.not. lun%lakpoi(l)) then !not lake - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - n1m=3 - do j = 3, nlevsoi ! get layer with 1 m depth - if (col%zi(c,j-1)<=1.0_r8 .and. col%zi(c,j)>1.0_r8) then - n1m=j - end if - end do - if (use_bedrock .and. nbedrock<=nlevsoi) then - nbedrock = col%nbedrock(c) - else - nbedrock = nlevsoi - endif - do j = 2, nlevmaxurbgrnd ! ignore first layer - if (n1m= n1m .and. j1.0_r8) then + n1m=j + end if + end do + if (use_bedrock .and. nbedrock<=nlevsoi) then + nbedrock = col%nbedrock(c) + else + nbedrock = nlevsoi + endif + do j = 2, nlevmaxurbgrnd ! ignore first layer + if (n1m= n1m .and. jaltmax_lastyear_indx(c) .and. jaltmax_lastyear_indx(c) .and. j Date: Sun, 26 Jun 2022 20:08:15 +0200 Subject: [PATCH 0248/2067] removed sb --- src/biogeophys/TemperatureType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90 index e3ceaf3a41..995496b388 100644 --- a/src/biogeophys/TemperatureType.F90 +++ b/src/biogeophys/TemperatureType.F90 @@ -647,7 +647,7 @@ subroutine InitCold(this, bounds, & ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use shr_const_mod , only : SHR_CONST_TKFRZ - use clm_varcon , only : denice, denh2o, sb !what's sb? how it's never used here + use clm_varcon , only : denice, denh2o use landunit_varcon, only : istwet, istsoil, istdlak, istice, istcrop use column_varcon , only : icol_road_imperv, icol_roof, icol_sunwall use column_varcon , only : icol_shadewall, icol_road_perv From 6ecc63b36bb19439ebbc38087189e7a47cf6f4b0 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sun, 26 Jun 2022 20:09:25 +0200 Subject: [PATCH 0249/2067] stream descirption, private usestreams, indents --- src/cpl/share_esmf/ExcessIceStreamType.F90 | 36 ++++++++++++++-------- 1 file changed, 23 insertions(+), 13 deletions(-) diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 260a194dc5..134810ba1b 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -4,7 +4,16 @@ module ExcessIceStreamType !----------------------------------------------------------------------- ! !DESCRIPTION: - ! Contains methods for reading in excess ice initial bulk values from data stream + ! Contains methods for reading in excess ice initial bulk values from data stream. + ! Needed in parameterization for excess ice in soil (Lee et al., 2014). + ! Used when use_excess_ice is true for initialization: + ! startup type runs starting from coldstart and initial datasets + ! that do not have required variables + ! or hybrid runs from cases with use_excess_ice was false. + ! Dataset is interpolated to 0.125x0.125 degrees grid from Brown et al., 1997 + ! with values derived from permafrost types. + ! Values represent fraction of excess ice within soil column + ! and are distributed within it later in initialization ! ! !USES use ESMF @@ -25,9 +34,9 @@ module ExcessIceStreamType contains ! !PUBLIC MEMBER FUNCTIONS: - procedure, public :: Init ! Initialize and read data in - procedure, public :: UseStreams ! If streams will be used - procedure, public :: CalcExcessIce ! Calculate excess ice ammount + procedure, public :: Init ! Initialize and read data in + procedure, private :: UseStreams ! If streams will be used + procedure, public :: CalcExcessIce ! Calculate excess ice ammount ! !PRIVATE MEMBER FUNCTIONS: procedure, private :: InitAllocate ! Allocate data @@ -107,6 +116,7 @@ subroutine Init(this, bounds, NLFilename) stream_offset = 0, & stream_taxmode = 'extend', & stream_dtlimit = 1.0e30_r8, & + ! in ch4FinundatedStreamType it is set to linear but we have a single date dataset stream_tintalgo = 'nearest', & stream_name = 'excess ice ', & rc = rc) @@ -125,24 +135,24 @@ subroutine Init(this, bounds, NLFilename) mcdate = year*10000 + mon*100 + day call shr_strdata_advance(sdat_exice, ymd=mcdate, tod=sec, logunit=iulog, istr='exice', rc=rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if - ! Get pointer for stream data that is time and spatially interpolate to model time and grid - do n = 1,size(stream_varnames) + ! Get pointer for stream data that is time and spatially interpolate to model time and grid + do n = 1,size(stream_varnames) call dshr_fldbun_getFldPtr(sdat_exice%pstrm(1)%fldbun_model, stream_varnames(n), fldptr1=dataptr1d, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) + call ESMF_Finalize(endflag=ESMF_END_ABORT) end if if (trim(stream_varnames(n)) == 'EXICE') then ig = 0 do g = bounds%begg,bounds%endg - ig = ig+1 - this%exice_bulk(g) = dataptr1d(ig) + ig = ig+1 + this%exice_bulk(g) = dataptr1d(ig) end do end if - end do + end do end if end subroutine Init From 40bf23816ca43bb102dbf1c469591c2a4c917dde Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Tue, 28 Jun 2022 11:04:45 -0600 Subject: [PATCH 0250/2067] Fix links in introduction --- .../users_guide/overview/introduction.rst | 29 +++++++++---------- 1 file changed, 13 insertions(+), 16 deletions(-) diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index a7a9ef434c..2ba046029f 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -32,8 +32,7 @@ release subversion repository as a part of |cesmrelease|. Documentation may be different if you are using an older version, you should either use the documentation for that release version, update to the latest version, or use the documentation inside your own source tree. There -is information in the ChangeLog file and in the `What is new with -|version| in |cesmrelease| since previous public releases? `_ +is information in the ChangeLog file and in :ref:`what-is-new-with-clm5_0` regarding the changes from previous versions of CESM. .. note:: This release of |version| in |cesmrelease| includes BOTH CLM4.0 @@ -46,21 +45,19 @@ regarding the changes from previous versions of CESM. than to a specific version of CLM4.5. Likewise, when referring to |version| we are referring to the |version| physics in |version| in |cesmrelease|. -The novice user should read `Chapter 1 `_ in detail before -beginning work, while the expert user should read `What is new with -|version| in |cesmrelease| since previous public releases? `_ and -`Quickstart to using |version| `_ chapters, and then use the -more detailed chapters as reference. Before novice users go onto more -technical problems covered in `Chapter 2 `_, `Chapter 3 -`_, `Chapter 4 `_, or `Chapter 5 `_ they -should know the material covered in `Chapter 1 `_ and be able +The novice user should read :ref:`overview_section` in detail before +beginning work, while the expert user should read :ref:`what-is-new-with-clm5_0` and +:ref:`quickstart`, and then use the +more detailed sections as reference. Before novice users go onto more +technical problems covered in :ref:`customizing_section`, +:ref:`using-clm-tools-section`, :ref:`adding-new-resolutions-section`, +:ref:`running-special-cases-section` or :ref:`running-single-points`, they +should know the material covered in :ref:`overview_section` and be able to replicate some of the examples given there. -All users should read the `How to Use This Document `_ and -`Other resources to get help from `_ sections to understand +All users should read :ref:`how-to-use-this-document` and :ref:`getting-help` to understand the document conventions and the various ways of getting help on using -|version|. Users should also read the `What is scientifically validated -and functional in |version| in |cesmrelease|? `_ section to see if +|version|. Users should also read the :ref:`scientific-validiation` section to see if their planned use of the model is something that has been scientifically validated and well tested. Users that are NOT using NCAR machines or our list of well tested machines should also read the @@ -70,8 +67,8 @@ to do their work. Developers that are making changes to CLM either for their own development or for development that they hope will eventually become a -part of the main CLM should read the `Chapter 8 `_ -chapter. We have a suite of test scripts that automatically test many +part of the main CLM should read :ref:`testing_section`. +We have a suite of test scripts that automatically test many different model configurations and namelist options, as well as ensuring things like restarts are bit-for-bit and the like. It's helpful to use these scripts to ensure your changes are working From 03c67869b1e699a27b30b1919cab47e29b77f32c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 6 Jul 2022 14:28:10 -0600 Subject: [PATCH 0251/2067] Working version of fsurdatmodifyctsm system test that uses conda environment rather than ncar_pylib --- cime_config/SystemTests/fsurdatmodifyctsm.py | 73 ++++++++------------ 1 file changed, 28 insertions(+), 45 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 4071316ea9..3cfef3d6fa 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -65,54 +65,37 @@ def _create_config_file(self): def _run_modify_fsurdat(self): tool_path = os.path.join(self._ctsm_root, 'tools/modify_fsurdat/fsurdat_modifier') - # Need to specify a specific python version that has the required - # dependencies - python_path = _get_python_path() - subprocess.check_call([python_path, tool_path, self._cfg_file_path]) + + self._case.load_env(reset=True) + conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " + # Preprend the commands to get the conda environment for python first + conda_env += self._get_conda_env() + # Source the env + subprocess.run( conda_env+"python3 "+tool_path+" "+self._cfg_file_path, shell=True, check=True) def _modify_user_nl(self): append_to_user_nl_files(caseroot = self._get_caseroot(), component = "clm", contents = "fsurdat = '{}'".format(self._fsurdat_out)) -def _get_python_path(): - """Get path to ncar_pylib's python on cheyenne - - This is needed because we need a python environment that includes xarray - and its dependencies. This is currently hard-coded for cheyenne until we - come up with a robust way in CIME of ensuring that the correc python - environment is loaded. - - """ - out = subprocess.check_output(['/glade/u/apps/opt/ncar_pylib/ncar_pylib', - '-l'], universal_newlines=True) - - # First look for a loaded ('L') python - path = _find_path_from_pylib_output(out, 'L') - # If no loaded python found, look for a default ('D') python - if path is None: - path = _find_path_from_pylib_output(out, 'D') - - if path is None: - raise RuntimeError('No python found') - - return os.path.join(path, 'bin', 'python') - -def _find_path_from_pylib_output(ncar_pylib_output, char): - """Given line-by-line output from ncar_pylib, return the path to python if found - - Args: - - ncar_pylib_output: line-by-line output from ncar_pylib - - char: the character to look for in the leading parenthetical expression (typically 'L' or 'D') - - Returns a path to python, or None if not found - """ - # The line of interest looks like the following (for char = 'L'): - # (L) ... /path/to/python - regex = r'\(' + char + r'\).* (/\S+)' - for line in ncar_pylib_output.splitlines(): - match_line = re.match(regex, line) - if match_line: - return match_line.group(1) - - return None + def _get_conda_env(self): + # + # Add specific commands needed on different machines to get conda available + # Use semicolon here since it's OK to fail + # + # Remove python and add conda to environment for cheyennne + conda_env = "module unload python; module load conda" + # CGD machines should already have conda loaded + conda_env += "; module load lang/python" + # End above machine specific with a semicolon + conda_env += "; " + + # The following uses "&&" as they all need to work + # Run the manage_python_env script + conda_env += self._ctsm_root+"/manage_python_env" + # Activate the python environment + conda_env += " && conda activate ctsm_py" + # End above to get to actual command + conda_env += " && " + + return( conda_env ) From 3aabab2cc2bca7aa6625942271f742afe13c291b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 7 Jul 2022 15:20:09 -0600 Subject: [PATCH 0252/2067] Fix for where and how repr_grainc_to_food_accum_thisyr is updated. --- src/biogeochem/CNPhenologyMod.F90 | 27 +++++++++++++++++++-------- 1 file changed, 19 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9d498f7d90..c80692cf84 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -387,7 +387,8 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) call CNOffsetLitterfall(num_soilp, filter_soilp, & - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & + crop_inst) call CNBackgroundLitterfall(num_soilp, filter_soilp, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) @@ -2088,10 +2089,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) - do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p, harvest_count(p), k) = & - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) - end do croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = cphase_harvest if (tlai(p) > 0._r8) then ! plant had emerged before harvest @@ -2638,7 +2635,8 @@ end subroutine CNOnsetGrowth !----------------------------------------------------------------------- subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & + crop_inst) ! ! !DESCRIPTION: ! Determines the flux of C and N from displayed pools to litter @@ -2659,9 +2657,10 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & type(cnveg_nitrogenstate_type), intent(in) :: cnveg_nitrogenstate_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst + type(crop_type) , intent(in) :: crop_inst ! ! !LOCAL VARIABLES: - integer :: p, c, k ! indices + integer :: p, c, k, h ! indices integer :: fp ! lake filter patch index real(r8):: t1 ! temporary variable real(r8):: denom ! temporary variable for divisor @@ -2671,6 +2670,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & real(r8) :: cropseedn_deficit_remaining ! remaining amount of crop seed N deficit that still needs to be restored (gN/m2) (positive, in contrast to the negative cropseedn_deficit) real(r8) :: cropseedc_deficit_to_restore ! amount of crop seed C deficit that will be restored from this grain pool (gC/m2) real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2) + real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) !----------------------------------------------------------------------- associate( & @@ -2708,6 +2708,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & frootc_to_litter => cnveg_carbonflux_inst%frootc_to_litter_patch , & ! Output: [real(r8) (:) ] fine root C litterfall (gC/m2/s) livestemc_to_litter => cnveg_carbonflux_inst%livestemc_to_litter_patch , & ! Output: [real(r8) (:) ] live stem C litterfall (gC/m2/s) repr_grainc_to_food => cnveg_carbonflux_inst%repr_grainc_to_food_patch , & ! Output: [real(r8) (:,:) ] grain C to food (gC/m2/s) + repr_grainc_to_food_accum_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr, & ! Output: [real(r8) (:,:,:) ] accumulated grain C to food (gC/m2) repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) @@ -2751,6 +2752,13 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! this assumes that offset_counter == dt for crops ! if this were ever changed, we'd need to add code to the "else" if (ivt(p) >= npcropmin) then + + ! How many harvests have occurred? + h = crop_inst%harvest_count(p) + if (h .le. 0) then + call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") + end if + ! Replenish the seed deficits from grain, if there is enough available ! grain. (If there is not enough available grain, the seed deficits will ! accumulate until there is eventually enough grain to replenish them.) @@ -2774,8 +2782,11 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainn_to_seed(p,k) = t1 * cropseedn_deficit_to_restore ! Send the remaining grain to the food product pool + repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & - + cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) + + repr_grainc_to_food_thispool + repr_grainc_to_food_accum_thisyr(p,h,k) = reproductivec(p,k) & + + repr_grainc_to_food_thispool * dt repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) end do From 5daedcea2262e81b966ea6bc590ec17f3bfac4d2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 7 Jul 2022 15:46:43 -0600 Subject: [PATCH 0253/2067] Removed repr_grainc_to_food_accum_patch from CropType, which was obsoleted by previous commit. --- src/biogeochem/CNPhenologyMod.F90 | 6 ------ src/biogeochem/CNVegCarbonFluxType.F90 | 26 -------------------------- 2 files changed, 32 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c80692cf84..ef0f515536 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2337,9 +2337,6 @@ subroutine PlantCrop(p, leafcn_in, jday, & harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 crop_inst%sdates_thisyr(p,sowing_count(p)) = jday - do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) = 0._r8 - end do leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset @@ -3190,9 +3187,6 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = & cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) + & cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) = & - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) + & - cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = & cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) + & cnveg_nitrogenflux_inst%repr_grainn_to_food_patch(p,k) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index be6d14ed56..e5d77264d2 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -137,7 +137,6 @@ module CNVegCarbonFluxType real(r8), pointer :: frootc_to_litter_patch (:) ! fine root C litterfall (gC/m2/s) real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] - real(r8), pointer :: repr_grainc_to_food_accum_patch (:,:) ! grain C to food for prognostic crop accumulated since planting (gC/m2) [patch, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_grainc_to_food_accum_thisyr (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] @@ -603,7 +602,6 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%cpool_to_reproductivec_storage_patch(begp:endp, nrepr)); this%cpool_to_reproductivec_storage_patch (:,:) = nan allocate(this%livestemc_to_litter_patch (begp:endp)) ; this%livestemc_to_litter_patch (:) = nan allocate(this%repr_grainc_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_patch (:,:) = nan - allocate(this%repr_grainc_to_food_accum_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_patch (:,:) = nan allocate(this%repr_grainc_to_food_accum_thisyr(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_thisyr (:,:,:) = nan allocate(this%repr_structurec_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structurec_to_cropprod_patch(:,:) = nan @@ -841,18 +839,6 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=data1dptr) end do - this%repr_grainc_to_food_accum_patch(begp:endp,:) = spval - do k = repr_grain_min, repr_grain_max - data1dptr => this%repr_grainc_to_food_accum_patch(:,k) - call hist_addfld1d ( & - ! e.g., GRAINC_TO_FOOD_ACCUM - fname=get_repr_hist_fname(k)//'C_TO_FOOD_ACCUM', & - units='gC/m^2', & - avgflag='I', & - long_name=get_repr_longname(k)//' C to food accumulated since planting', & - ptr_patch=data1dptr) - end do - this%repr_grainc_to_food_accum_thisyr(begp:endp,:,:) = spval do k = repr_grain_min, repr_grain_max data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) @@ -3572,18 +3558,6 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) interpinic_flag='interp', readvar=readvar, data=data1dptr) end do - do k = repr_grain_min, repr_grain_max - data1dptr => this%repr_grainc_to_food_accum_patch(:,k) - ! e.g., grainc_to_food_accum - varname = get_repr_rest_fname(k)//'c_to_food_accum' - call restartvar(ncid=ncid, flag=flag, varname=varname, & - xtype=ncd_double, & - dim1name='pft', & - long_name=get_repr_longname(k)//' C to food accumulated since planting', & - units='gC/m2', & - interpinic_flag='interp', readvar=readvar, data=data1dptr) - end do - ! Read or write variable(s) with mxharvests dimension ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then From b443c574ef101623575362bd336484e169648683 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Jul 2022 16:18:48 -0600 Subject: [PATCH 0254/2067] Improved variable naming. * repr_grainc_to_food_accum_thisyr changed to repr_grainc_to_food_perharv. This makes room for a different variable that's for the entire year (i.e., summed across all harvests). * _accum removed from my variable names. * Improved output variable longname to also remove "accumulated." --- src/biogeochem/CNPhenologyMod.F90 | 6 +++--- src/biogeochem/CNVegCarbonFluxType.F90 | 22 +++++++++++----------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ef0f515536..7e590de09e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1811,7 +1811,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p,s,k) = 0._r8 + cnveg_carbonflux_inst%repr_grainc_to_food_perharv(p,s,k) = 0._r8 end do end do end if @@ -2705,7 +2705,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & frootc_to_litter => cnveg_carbonflux_inst%frootc_to_litter_patch , & ! Output: [real(r8) (:) ] fine root C litterfall (gC/m2/s) livestemc_to_litter => cnveg_carbonflux_inst%livestemc_to_litter_patch , & ! Output: [real(r8) (:) ] live stem C litterfall (gC/m2/s) repr_grainc_to_food => cnveg_carbonflux_inst%repr_grainc_to_food_patch , & ! Output: [real(r8) (:,:) ] grain C to food (gC/m2/s) - repr_grainc_to_food_accum_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr, & ! Output: [real(r8) (:,:,:) ] accumulated grain C to food (gC/m2) + repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv, & ! Output: [real(r8) (:,:,:) ] accumulated grain C to food (gC/m2) repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) @@ -2782,7 +2782,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & + repr_grainc_to_food_thispool - repr_grainc_to_food_accum_thisyr(p,h,k) = reproductivec(p,k) & + repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + repr_grainc_to_food_thispool * dt repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index e5d77264d2..5327bc2978 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -137,7 +137,7 @@ module CNVegCarbonFluxType real(r8), pointer :: frootc_to_litter_patch (:) ! fine root C litterfall (gC/m2/s) real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] - real(r8), pointer :: repr_grainc_to_food_accum_thisyr (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_perharv (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] @@ -602,7 +602,7 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%cpool_to_reproductivec_storage_patch(begp:endp, nrepr)); this%cpool_to_reproductivec_storage_patch (:,:) = nan allocate(this%livestemc_to_litter_patch (begp:endp)) ; this%livestemc_to_litter_patch (:) = nan allocate(this%repr_grainc_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_patch (:,:) = nan - allocate(this%repr_grainc_to_food_accum_thisyr(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_accum_thisyr (:,:,:) = nan + allocate(this%repr_grainc_to_food_perharv(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_perharv (:,:,:) = nan allocate(this%repr_structurec_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structurec_to_cropprod_patch(:,:) = nan allocate(this%repr_structurec_to_litter_patch(begp:endp, repr_structure_min:repr_structure_max)) @@ -839,16 +839,16 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=data1dptr) end do - this%repr_grainc_to_food_accum_thisyr(begp:endp,:,:) = spval + this%repr_grainc_to_food_perharv(begp:endp,:,:) = spval do k = repr_grain_min, repr_grain_max - data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) + data2dptr => this%repr_grainc_to_food_perharv(:,:,k) call hist_addfld2d ( & - ! e.g., GRAINC_TO_FOOD_ACCUM_PERHARV - fname=get_repr_hist_fname(k)//'C_TO_FOOD_ACCUM_PERHARV', & + ! e.g., GRAINC_TO_FOOD_PERHARV + fname=get_repr_hist_fname(k)//'C_TO_FOOD_PERHARV', & units='gC/m^2', & type2d='mxharvests', & avgflag='I', & - long_name=get_repr_longname(k)//' C to food accumulated by harvest; should only be output annually', & + long_name=get_repr_longname(k)//' C to food per harvest; should only be output annually', & ptr_patch=data2dptr) end do @@ -3562,13 +3562,13 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then do k = repr_grain_min, repr_grain_max - data2dptr => this%repr_grainc_to_food_accum_thisyr(:,:,k) - ! e.g., grainc_to_food_accum_perharv - varname = get_repr_rest_fname(k)//'c_to_food_accum_perharv' + data2dptr => this%repr_grainc_to_food_perharv(:,:,k) + ! e.g., grainc_to_food_perharv + varname = get_repr_rest_fname(k)//'c_to_food_perharv' call restartvar(ncid=ncid, flag=flag, varname=varname, & xtype=ncd_double, & dim1name='pft', & - long_name=get_repr_longname(k)//' C to food accumulated by harvest; should only be output annually', & + long_name=get_repr_longname(k)//' C to food per harvest; should only be output annually', & units='gC/m2', & interpinic_flag='interp', readvar=readvar, data=data2dptr) end do From 291a1d5f641a3edb5bfb032a6f8f394f44d30997 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Jul 2022 16:33:03 -0600 Subject: [PATCH 0255/2067] Added annual "to food" output (e.g. GRAINC_TO_FOOD_ANN). --- src/biogeochem/CNPhenologyMod.F90 | 8 +++++++- src/biogeochem/CNVegCarbonFluxType.F90 | 26 ++++++++++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7e590de09e..bac74a8a9d 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1814,6 +1814,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_carbonflux_inst%repr_grainc_to_food_perharv(p,s,k) = 0._r8 end do end do + do k = repr_grain_min, repr_grain_max + cnveg_carbonflux_inst%repr_grainc_to_food_thisyr(p,k) = 0._r8 + end do end if ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) @@ -2705,7 +2708,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & frootc_to_litter => cnveg_carbonflux_inst%frootc_to_litter_patch , & ! Output: [real(r8) (:) ] fine root C litterfall (gC/m2/s) livestemc_to_litter => cnveg_carbonflux_inst%livestemc_to_litter_patch , & ! Output: [real(r8) (:) ] live stem C litterfall (gC/m2/s) repr_grainc_to_food => cnveg_carbonflux_inst%repr_grainc_to_food_patch , & ! Output: [real(r8) (:,:) ] grain C to food (gC/m2/s) - repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv, & ! Output: [real(r8) (:,:,:) ] accumulated grain C to food (gC/m2) + repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv, & ! Output: [real(r8) (:,:,:) ] grain C to food per harvest (gC/m2) + repr_grainc_to_food_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_thisyr, & ! Output: [real(r8) (:,:) ] grain C to food harvested this calendar year (gC/m2) repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) @@ -2784,6 +2788,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & + repr_grainc_to_food_thispool repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + repr_grainc_to_food_thispool * dt + repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & + + repr_grainc_to_food_perharv(p,h,k) repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) end do diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 5327bc2978..1e193aea1e 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -138,6 +138,7 @@ module CNVegCarbonFluxType real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_grainc_to_food_perharv (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_thisyr (:,:) ! grain C to food for prognostic crop accumulated this calendar year (gC/m2) [patch, repr_grain_min:repr_grain_max] real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] @@ -603,6 +604,7 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%livestemc_to_litter_patch (begp:endp)) ; this%livestemc_to_litter_patch (:) = nan allocate(this%repr_grainc_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_patch (:,:) = nan allocate(this%repr_grainc_to_food_perharv(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_perharv (:,:,:) = nan + allocate(this%repr_grainc_to_food_thisyr(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_thisyr (:,:) = nan allocate(this%repr_structurec_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structurec_to_cropprod_patch(:,:) = nan allocate(this%repr_structurec_to_litter_patch(begp:endp, repr_structure_min:repr_structure_max)) @@ -851,6 +853,18 @@ subroutine InitHistory(this, bounds, carbon_type) long_name=get_repr_longname(k)//' C to food per harvest; should only be output annually', & ptr_patch=data2dptr) end do + + this%repr_grainc_to_food_thisyr(begp:endp,:) = spval + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainc_to_food_thisyr(:,k) + call hist_addfld1d ( & + ! e.g., GRAINC_TO_FOOD_ANN + fname=get_repr_hist_fname(k)//'C_TO_FOOD_ANN', & + units='gC/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to food harvested per calendar year; should only be output annually', & + ptr_patch=data1dptr) + end do this%leafc_to_biofuelc_patch(begp:endp) = spval call hist_addfld1d (fname='LEAFC_TO_BIOFUELC', units='gC/m^2/s', & @@ -3573,6 +3587,18 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) interpinic_flag='interp', readvar=readvar, data=data2dptr) end do end if + + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainc_to_food_thisyr(:,k) + ! e.g., grainc_to_food_thisyr + varname = get_repr_rest_fname(k)//'c_to_food_thisyr' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' C to food per calendar year; should only be output annually', & + units='gC/m2', & + interpinic_flag='interp', readvar=readvar, data=data1dptr) + end do do k = 1, nrepr data1dptr => this%cpool_to_reproductivec_patch(:,k) From 384d3176979b098640ee001c10c56ecbba93ad18 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 12 Jul 2022 16:43:32 -0600 Subject: [PATCH 0256/2067] Set zetamaxstable to 2 for ctsm5_1 for all cases --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2562f9ce88..3492816773 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -211,7 +211,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 2.0d00 0.5d00 -0.5d00 +2.0d00 .true. From 08f556b9c16d1b8c053041dcba159274069c6327 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 12 Jul 2022 16:50:15 -0600 Subject: [PATCH 0257/2067] Apply same zetamaxstable limit for biomass heat storage as for everything else, rather than a hardcoded 100 --- src/biogeophys/CanopyFluxesMod.F90 | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 1d5298bac2..f1cc884d83 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1329,12 +1329,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, zeta(p) = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) if (zeta(p) >= 0._r8) then !stable - ! remove stability cap when biomass heat storage is active - if(use_biomass_heat_storage) then - zeta(p) = min(100._r8,max(zeta(p),0.01_r8)) - else - zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) - endif + zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) um(p) = max(ur(p),0.1_r8) else !unstable zeta(p) = max(-100._r8,min(zeta(p),-0.01_r8)) From 0f39e0e056f7432f46d2c79e6c9fd4dbfcf093ae Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 12 Jul 2022 17:54:16 -0600 Subject: [PATCH 0258/2067] Set zetmaxstable to 2.0 when BHS is on --- bld/CLMBuildNamelist.pm | 20 ++++++++++++------- bld/namelist_files/namelist_defaults_ctsm.xml | 7 ++++--- 2 files changed, 17 insertions(+), 10 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7c5859e0ad..73a857f718 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1663,11 +1663,6 @@ sub process_namelist_inline_logic { ############################################# setup_logic_rooting_profile($opts, $nl_flags, $definition, $defaults, $nl); - ############################################# - # namelist group: friction_velocity # - ############################################# - setup_logic_friction_vel($opts, $nl_flags, $definition, $defaults, $nl); - ############################# # namelist group: cngeneral # ############################# @@ -1687,6 +1682,11 @@ sub process_namelist_inline_logic { ############################################# setup_logic_canopyfluxes($opts, $nl_flags, $definition, $defaults, $nl); + ########################################################## + # namelist group: friction_velocity (after canopyfluxes) # + ########################################################## + setup_logic_friction_vel($opts, $nl_flags, $definition, $defaults, $nl); + ############################################# # namelist group: canopyhydrology_inparm # ############################################# @@ -3867,10 +3867,11 @@ sub setup_logic_rooting_profile { #------------------------------------------------------------------------------- sub setup_logic_friction_vel { - # + # Must be after canopyfluxes so that use_biomass_heat_storagge will be set my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable', + 'use_biomass_heat_storage'=>$nl_flags->{'use_biomass_heat_storage'}, 'phys'=>$nl_flags->{'phys'} ); } #------------------------------------------------------------------------------- @@ -3895,6 +3896,11 @@ sub setup_logic_canopyfluxes { if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) { $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on'); } + if ( &value_is_true($nl->get_value('use_biomass_heat_storage')) ) { + $nl_flags->{'use_biomass_heat_storage'} = ".true."; + } else { + $nl_flags->{'use_biomass_heat_storage'} = ".false."; + } } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3492816773..1651e99f26 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -209,9 +209,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 1.d-2 -2.0d00 -0.5d00 -2.0d00 +2.0d00 +2.0d00 +0.5d00 +0.5d00 .true. From 8ed188ae02fb1e5456934d1f95521920a35db366 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 14 Jul 2022 14:32:25 -0600 Subject: [PATCH 0259/2067] Fix typo @olyson pointed out --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 6b8f90eef9..9126ca2302 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3899,7 +3899,7 @@ sub setup_logic_rooting_profile { #------------------------------------------------------------------------------- sub setup_logic_friction_vel { - # Must be after canopyfluxes so that use_biomass_heat_storagge will be set + # Must be after canopyfluxes so that use_biomass_heat_storage will be set my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'zetamaxstable', From c3bb13d1a0ca744d808cac08caefecc141238b22 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 14 Jul 2022 16:59:38 -0600 Subject: [PATCH 0260/2067] Get the 2000 1x1_brazil subset_data case working --- tools/mksurfdata_map/Makefile.data | 33 +++++++++++++++--------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 15ca410f0f..c7ff1f85a8 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -53,12 +53,15 @@ else endif MKSURFDATA = $(BATCHJOBS) $(PWD)/mksurfdata.pl -SUBSETDATA = $(BATCHJOBS) $(PWD)/../site_and_regional/subset_data +SUBSETDATA = $(PWD)/../site_and_regional/subset_data # subset_data options # -SUBSETDATA_1X1_BRAZIL := --lat --lon --site 1x1_brazil --outdir . --user-mods-dir ./1x1_brazil \ - --overwrite --create-user-mods --uniform-snowpack --include-nonveg --cap-saturation +SUBSETDATA_POINT = $(SUBSETDATA) point --overwrite --create-user-mods --uniform-snowpack --include-nonveg --cap-saturation + +# Subset data sites... +SUBSETDATA_1X1_BRAZIL := --lat -7 --lon -55 --site 1x1_brazil --user-mods-dir ./1x1_brazil --outdir ./1x1_brazil +SUBSETDATA_1X1_NUMAIA := --lat 40.6878 --lon 267.0228 --site 1x1_numaIA --user-mods-dir ./1x1_numaIA --outdir ./1x1_numaIA # f19 and f09 are standard resolutions, f10 is used for testing, f45 is used for FATES # ne30np4 is standard resolution for SE dycore in CAM, C96 is standard for fv3 dycore # The ne30np4 series (including pg2, pg3, pg4) are standard for SE dycore @@ -96,7 +99,6 @@ CROP = \ crop-global-historical \ crop-global-transient \ crop-global-future - all : standard tropics crop urban landuse-timeseries DEBUG: @@ -124,18 +126,18 @@ global-present-nldas : FORCE # tropics : $(TROPICS) -crop-tropics-present : FORCE brazil-tropics-present +crop-tropics-present : brazil-tropics-present $(MKSURFDATA) -glc_nec 10 -y 2000 -res 5x5_amazon $(BACKGROUND) 1x1_brazil-tropics-present : FORCE - $(SUBSETDATA) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop $(BACKGROUND) + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop crop-tropics-historical : FORCE - $(SUBSETDATA) -glc_nec 10 -y 1850 -res 1x1_brazil $(BACKGROUND) + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop crop-tropics-transient : FORCE - $(SUBSETDATA) -glc_nec 10 -no_surfdata -y 1850-2000 -res 1x1_brazil $(BACKGROUND) + $(SUBSETDATA_POINT) -glc_nec 10 -no_surfdata -y 1850-2000 -res 1x1_brazil # # crop @@ -152,16 +154,15 @@ crop-global-present-f05 : FORCE $(MKSURFDATA) -glc_nec 10 -y 1850,2000 -res 0.47x0.63 $(BACKGROUND) crop-numa-present : FORCE - $(SUBSETDATA) -glc_nec 10 -y 2000 -r 1x1_numaIA $(BACKGROUND) + $(SUBSETDATA_POINT) -glc_nec 10 -y 2000 -r 1x1_numaIA crop-numa-historical : FORCE - $(SUBSETDATA) -glc_nec 10 -y 1850 -r 1x1_numaIA $(BACKGROUND) + $(SUBSETDATA_POINT) -glc_nec 10 -y 1850 -r 1x1_numaIA crop-smallville : FORCE - $(SUBSETDATA) -glc_nec 10 -y 2000 -r 1x1_smallvilleIA \ + $(SUBSETDATA_POINT) -glc_nec 10 -y 2000 -r 1x1_smallvilleIA \ -pft_idx 17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78 \ - -pft_frc 6.5,1.5,1.6,1.7,1.8,1.9,1.5,1.6,1.7,1.8,1.9,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5 \ - $(BACKGROUND) + -pft_frc 6.5,1.5,1.6,1.7,1.8,1.9,1.5,1.6,1.7,1.8,1.9,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5 crop-global-present-ne16np4 : FORCE $(MKSURFDATA) -glc_nec 10 -y 2000 -res ne16np4 $(BACKGROUND) @@ -174,7 +175,7 @@ crop-global-present-ne120np4 : FORCE # adds crop (to make sure that it works properly to add crop in a grid cell # where there used to be no crop). crop-smallville-historical : FORCE - $(SUBSETDATA) -glc_nec 10 -y 1850 -r 1x1_smallvilleIA -pft_idx 13 -pft_frc 100 $(BACKGROUND) + $(SUBSETDATA_POINT) -glc_nec 10 -y 1850 -r 1x1_smallvilleIA -pft_idx 13 -pft_frc 100 # Setup the historical case for SSP5-8.5 so that historical can be used to go into the future. crop-global-historical : FORCE @@ -239,12 +240,12 @@ crop-global-SSP5-8.5 : FORCE urban : urban-present urban-alpha urban-present : FORCE - $(SUBSETDATA) -y 2000 -no-crop -glc_nec 10 -r 1x1_vancouverCAN,1x1_mexicocityMEX $(BACKGROUND) + $(SUBSETDATA_POINT) -y 2000 -no-crop -glc_nec 10 -r 1x1_vancouverCAN,1x1_mexicocityMEX # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 urban-alpha : FORCE - $(SUBSETDATA) -y 2000 -no-crop -glc_nec 10 -r 1x1_urbanc_alpha -urban_skip_abort_on_invalid_data_check $(BACKGROUND) + $(SUBSETDATA_POINT) -y 2000 -no-crop -glc_nec 10 -r 1x1_urbanc_alpha -urban_skip_abort_on_invalid_data_check # From 50c941d3e32749c5bfa8e506d6129fc7003ebd61 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 14 Jul 2022 17:00:29 -0600 Subject: [PATCH 0261/2067] Add ability to change the default config file for the default filenames fixing #1809 --- python/ctsm/subset_data.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 7a33d9c2fa..4fc92615f4 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -75,7 +75,7 @@ process_logging_args, ) -DEFAULTS_FILE = "default_data.cfg" +DEFAULTS_CONFIG = "tools/site_and_regional/default_data.cfg" logger = logging.getLogger(__name__) @@ -308,6 +308,16 @@ def get_parser(): type=str, default="", ) + cesmroot = path_to_ctsm_root() + DEFAULTS_FILE = os.path.join(cesmroot, DEFAULTS_CONFIG) + subparser.add_argument( + "--file", + help="Default configure file to use for default filenames.", + action="store", + dest="config_file", + type=str, + default=DEFAULTS_FILE, + ) subparser.add_argument( "--overwrite", help="Flag to overwrite if the files already exists.", @@ -588,7 +598,7 @@ def main(): # parse defaults file cesmroot = path_to_ctsm_root() defaults = configparser.ConfigParser() - defaults.read(os.path.join(cesmroot, "tools/site_and_regional", DEFAULTS_FILE)) + defaults.read(args.config_file) # --------------------------------- # myname = getuser() From 85f72cc1c59359ee1e7a907cd1ca9879acb54716 Mon Sep 17 00:00:00 2001 From: kaveh Date: Fri, 15 Jul 2022 05:17:10 -0600 Subject: [PATCH 0262/2067] Fix albgrd_col value in SurfaceAlbedoType --- src/biogeophys/SurfaceAlbedoType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90 index cf6b0a518a..dba2938d98 100644 --- a/src/biogeophys/SurfaceAlbedoType.F90 +++ b/src/biogeophys/SurfaceAlbedoType.F90 @@ -188,7 +188,7 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='cosine of solar zenith angle', & ptr_col=this%coszen_col, default='inactive') - this%albgri_col(begc:endc,:) = spval + this%albgrd_col(begc:endc,:) = spval call hist_addfld2d (fname='ALBGRD', units='proportion', type2d='numrad', & avgflag='A', long_name='ground albedo (direct)', & ptr_col=this%albgrd_col, default='inactive') From 65469662f56eb486dfe32cd065b07dd493701af5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Jul 2022 14:44:06 -0600 Subject: [PATCH 0263/2067] Fix to previous merge: Removing all references to repr_grainc_to_food_accum* variables. --- src/biogeochem/CNPhenologyMod.F90 | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 65e1f7e310..73678f1c16 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2239,10 +2239,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) crop_inst%harvest_reason_thisyr(p, harvest_count(p)) = harvest_reason - do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_accum_thisyr(p, harvest_count(p), k) = & - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) - end do endif croplive(p) = .false. ! no re-entry in greater if-block @@ -2536,9 +2532,6 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & idop(p) = jday harvdate(p) = NOT_Harvested s = sowing_count(p) + 1 - do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p, k) = 0._r8 - end do ! SSR troubleshooting if (s < 1) then @@ -3468,9 +3461,6 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = & cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) + & cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) = & - cnveg_carbonflux_inst%repr_grainc_to_food_accum_patch(p,k) + & - cnveg_carbonflux_inst%repr_grainc_to_food_patch(p,k) cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = & cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) + & cnveg_nitrogenflux_inst%repr_grainn_to_food_patch(p,k) From d93b414673b1aea23f72e3dc0f94620b416cccd1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 15 Jul 2022 16:40:26 -0600 Subject: [PATCH 0264/2067] Get subset_data single point sites working --- tools/mksurfdata_map/Makefile.data | 51 ++++++++++++++++------ tools/mksurfdata_map/default_data_1850.cfg | 29 ++++++++++++ 2 files changed, 66 insertions(+), 14 deletions(-) create mode 100644 tools/mksurfdata_map/default_data_1850.cfg diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index c7ff1f85a8..caaef030e3 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -57,11 +57,23 @@ SUBSETDATA = $(PWD)/../site_and_regional/subset_data # subset_data options # -SUBSETDATA_POINT = $(SUBSETDATA) point --overwrite --create-user-mods --uniform-snowpack --include-nonveg --cap-saturation +SUBSETDATA_POINT = $(SUBSETDATA) point --overwrite --uniform-snowpack --cap-saturation --outdir . +SUBSETDATA_POINT_ALLLU = $(SUBSETDATA_POINT) --include-nonveg +# NOTE: TODO: We need settings in subset_data to handle urban datasets see issue #1665 +SUBSETDATA_POINT_URBAN = $(SUBSETDATA_POINT) --include-nonveg # Subset data sites... -SUBSETDATA_1X1_BRAZIL := --lat -7 --lon -55 --site 1x1_brazil --user-mods-dir ./1x1_brazil --outdir ./1x1_brazil -SUBSETDATA_1X1_NUMAIA := --lat 40.6878 --lon 267.0228 --site 1x1_numaIA --user-mods-dir ./1x1_numaIA --outdir ./1x1_numaIA +SUBSETDATA_1X1_BRAZIL := --lat -7 --lon -55 --site 1x1_brazil +SUBSETDATA_1X1_NUMAIA := --lat 40.6878 --lon 267.0228 --site 1x1_numaIA +SUBSETDATA_1X1_SMALL := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA \ + --dompft 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 \ + --pctpft 6.5 1.5 1.6 1.7 1.8 1.9 1.5 1.6 1.7 1.8 1.9 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 1.5 +# NOTE: The 1850 smallvilleIA site is constructed to start with 100% natural vegetation, so we can test transition to crops +SUBSETDATA_1X1_SMALL1850 := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA --dompft 13 --pctpft 100 + +SUBSETDATA_1X1_MEXICOCITY := --lat 19.5 --lon 260.5 --site 1x1_mexicocityMEX +SUBSETDATA_1X1_VANCOUVER := --lat 49.5 --lon 236.5 --site 1x1_vancouverCAN +SUBSETDATA_1X1_URBALPHA := --lat -37.7308 --lon 0 --site 1x1_urbanc_alpha # f19 and f09 are standard resolutions, f10 is used for testing, f45 is used for FATES # ne30np4 is standard resolution for SE dycore in CAM, C96 is standard for fv3 dycore # The ne30np4 series (including pg2, pg3, pg4) are standard for SE dycore @@ -101,11 +113,22 @@ CROP = \ crop-global-future all : standard tropics crop urban landuse-timeseries +all-subset : \ + 1x1_brazil-tropics-present \ + crop-tropics-historical \ + crop-tropics-transient \ + crop-numa-present \ + crop-numa-historical \ + crop-smallville \ + crop-smallville-historical \ + urban-present urban-alpha + DEBUG: @echo "HOST := $(HOST)" @echo "PROJECT := $(PROJECT)" @echo "BATCHJOBS := $(BATCHJOBS)" @echo "BACKGROUND := $(BACKGROUND)" + # # standard # @@ -130,14 +153,14 @@ crop-tropics-present : brazil-tropics-present $(MKSURFDATA) -glc_nec 10 -y 2000 -res 5x5_amazon $(BACKGROUND) 1x1_brazil-tropics-present : FORCE - $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop crop-tropics-historical : FORCE - $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --file default_data_1850.cfg --crop crop-tropics-transient : FORCE - $(SUBSETDATA_POINT) -glc_nec 10 -no_surfdata -y 1850-2000 -res 1x1_brazil + $(SUBSETDATA_POINT_ALLLU) --create-landuse $(SUBSETDATA_1X1_BRAZIL) --crop # # crop @@ -154,15 +177,13 @@ crop-global-present-f05 : FORCE $(MKSURFDATA) -glc_nec 10 -y 1850,2000 -res 0.47x0.63 $(BACKGROUND) crop-numa-present : FORCE - $(SUBSETDATA_POINT) -glc_nec 10 -y 2000 -r 1x1_numaIA + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --crop crop-numa-historical : FORCE - $(SUBSETDATA_POINT) -glc_nec 10 -y 1850 -r 1x1_numaIA + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --file default_data_1850.cfg --crop crop-smallville : FORCE - $(SUBSETDATA_POINT) -glc_nec 10 -y 2000 -r 1x1_smallvilleIA \ - -pft_idx 17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78 \ - -pft_frc 6.5,1.5,1.6,1.7,1.8,1.9,1.5,1.6,1.7,1.8,1.9,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5,1.5 + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL) --crop crop-global-present-ne16np4 : FORCE $(MKSURFDATA) -glc_nec 10 -y 2000 -res ne16np4 $(BACKGROUND) @@ -175,7 +196,7 @@ crop-global-present-ne120np4 : FORCE # adds crop (to make sure that it works properly to add crop in a grid cell # where there used to be no crop). crop-smallville-historical : FORCE - $(SUBSETDATA_POINT) -glc_nec 10 -y 1850 -r 1x1_smallvilleIA -pft_idx 13 -pft_frc 100 + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL1850) --file default_data_1850.cfg --crop # Setup the historical case for SSP5-8.5 so that historical can be used to go into the future. crop-global-historical : FORCE @@ -240,12 +261,13 @@ crop-global-SSP5-8.5 : FORCE urban : urban-present urban-alpha urban-present : FORCE - $(SUBSETDATA_POINT) -y 2000 -no-crop -glc_nec 10 -r 1x1_vancouverCAN,1x1_mexicocityMEX + $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) + $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 urban-alpha : FORCE - $(SUBSETDATA_POINT) -y 2000 -no-crop -glc_nec 10 -r 1x1_urbanc_alpha -urban_skip_abort_on_invalid_data_check + $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) # @@ -253,6 +275,7 @@ urban-alpha : FORCE # landuse-timeseries : landuse-timeseries-smallville +# NOTE: TODO: This needs to be chagned to use subset_data when transient configurations are resolved (see Issue #1673 landuse-timeseries-smallville : FORCE $(MKSURFDATA) -no_surfdata -glc_nec 10 -y 1850-1855 -r 1x1_smallvilleIA \ -pft_idx 17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78 \ diff --git a/tools/mksurfdata_map/default_data_1850.cfg b/tools/mksurfdata_map/default_data_1850.cfg new file mode 100644 index 0000000000..311aeef13d --- /dev/null +++ b/tools/mksurfdata_map/default_data_1850.cfg @@ -0,0 +1,29 @@ +[main] +clmforcingindir = /glade/p/cesmdata/inputdata + +[datm_gswp3] +dir = /glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.datm7.GSWP3.0.5d.v1.c170516 +domain = domain.lnd.360x720_gswp3.0v1.c170606.nc +solardir = Solar +precdir = Precip +tpqwdir = TPHWL +solartag = clmforc.GSWP3.c2011.0.5x0.5.Solr. +prectag = clmforc.GSWP3.c2011.0.5x0.5.Prec. +tpqwtag = clmforc.GSWP3.c2011.0.5x0.5.TPQWL. +solarname = CLMGSWP3v1.Solar +precname = CLMGSWP3v1.Precip +tpqwname = CLMGSWP3v1.TPQW + +[surfdat] +dir = lnd/clm2/surfdata_map/release-clm5.0.18 +surfdat_16pft = surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc +surfdat_78pft = surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr1850_c190214.nc + +[landuse] +dir = lnd/clm2/surfdata_map/release-clm5.0.18 +landuse_16pft = landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c190214.nc +landuse_78pft = landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c190214.nc + +[domain] +file = share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc + From 5eabd919534f7897acc65f66f4703b8a2aa4f014 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 15 Jul 2022 16:59:52 -0600 Subject: [PATCH 0265/2067] Update to version that has the fix for coszen --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index ade436e8db..871aafdbfd 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -55,7 +55,7 @@ local_path = components/cmeps required = True [cdeps] -tag = cdeps0.12.41 +tag = cdeps0.12.42 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps From 44a44a5d8a2a27fbaaa27db8aa774c2b194af678 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 15 Jul 2022 17:02:19 -0600 Subject: [PATCH 0266/2067] Update to version of cdeps that fixes the ZBOT read issue --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 871aafdbfd..0b0124c9f3 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -55,7 +55,7 @@ local_path = components/cmeps required = True [cdeps] -tag = cdeps0.12.42 +tag = cdeps0.12.52 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps From 8606f39997bc8825f66ed528405fa2d9f7e6b892 Mon Sep 17 00:00:00 2001 From: kaveh Date: Tue, 19 Jul 2022 02:43:31 -0600 Subject: [PATCH 0267/2067] Add error checking in ParitionWoodFluxes --- src/biogeochem/CNProductsMod.F90 | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 9744b04aed..176ff77c27 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -615,19 +615,12 @@ subroutine PartitionWoodFluxes(this, bounds, & if (pprod_tot > 0) then pprod10_frac = pprod10 / pprod_tot pprod100_frac = pprod100 / pprod_tot - else - ! Avoid divide by 0 - pprod10_frac = 0._r8 - pprod100_frac = 0._r8 + else if (dwt_wood_product_gain_patch(p) > 0) then + call endrun(& + msg='ERROR: dwt_wood_product_gain_patch(p) > 0' // & + errMsg(sourcefile, __LINE__)) end if - ! Note that the patch-level fluxes are expressed per unit gridcell area. So, to go - ! from patch-level fluxes to gridcell-level fluxes, we simply add up the various - ! patch contributions, without having to multiply by any area weightings. - this%dwt_prod10_gain_grc(g) = this%dwt_prod10_gain_grc(g) + & - dwt_wood_product_gain_patch(p) * pprod10_frac - this%dwt_prod100_gain_grc(g) = this%dwt_prod100_gain_grc(g) + & - dwt_wood_product_gain_patch(p) * pprod100_frac end do end subroutine PartitionWoodFluxes From dca339ec1777f70a0f43181bbf03947c87f70cd5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 28 Jul 2022 15:58:55 -0600 Subject: [PATCH 0268/2067] Change the name of the conda environment for CTSM from ctsm_py to ctsm_pylib to match ncar_pylib and to use a different name from the Hammon script that uses a ctsm_py environment name --- .github/workflows/black.yml | 2 +- cime_config/SystemTests/fsurdatmodifyctsm.py | 6 +++--- py_env_create | 2 +- python/README.md | 2 +- python/conda_env_ctsm_py.txt | 10 +++++----- python/conda_env_ctsm_py_cgd.txt | 10 +++++----- test/tools/test_driver.sh | 8 ++++---- tools/contrib/README | 2 +- tools/contrib/ssp_anomaly_forcing_smooth | 2 +- tools/modify_fsurdat/README | 2 +- tools/site_and_regional/README | 2 +- 11 files changed, 24 insertions(+), 24 deletions(-) diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml index a2115d2833..438b48e918 100644 --- a/.github/workflows/black.yml +++ b/.github/workflows/black.yml @@ -17,5 +17,5 @@ jobs: # Using pyproject.toml makes sure this testing is consistent with our python directory testing options: "--check --config python/pyproject.toml" src: "./python" - # Version should be coordinated with the ctsm_py conda environment under the python directory + # Version should be coordinated with the ctsm_pylib conda environment under the python directory version: "22.3.0" diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 3cfef3d6fa..74b7eff7f2 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -91,10 +91,10 @@ def _get_conda_env(self): conda_env += "; " # The following uses "&&" as they all need to work - # Run the manage_python_env script - conda_env += self._ctsm_root+"/manage_python_env" + # Run the py_env_create script + conda_env += self._ctsm_root+"/py_env_create" # Activate the python environment - conda_env += " && conda activate ctsm_py" + conda_env += " && conda activate ctsm_pylib" # End above to get to actual command conda_env += " && " diff --git a/py_env_create b/py_env_create index 59bf13c222..c323a374df 100755 --- a/py_env_create +++ b/py_env_create @@ -23,7 +23,7 @@ if [ $error != 0 ]; then exit -1 fi rm condahelp.txt -ctsm_python=ctsm_py +ctsm_python=ctsm_pylib condadir="$dir/python" diff --git a/python/README.md b/python/README.md index 63868bee63..2cb488be22 100644 --- a/python/README.md +++ b/python/README.md @@ -14,7 +14,7 @@ You can also use the script in the top level directory to do all the conda commands and do this for you. ../py_env_create - conda activate ctsm_py + conda activate ctsm_pylib Conda requirements files: diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index 8c110e8f3f..445300c754 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -3,12 +3,12 @@ # # To install this on cheyenne with conda loaded in modules # use the top level bash script: -# ../py_env_create # Do this each time you update your CTSM Version -# conda activate ctsm_py # Do this anytime you want to run a CTSM python script +# ../py_env_create # Do this each time you update your CTSM Version +# conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script # Or the individual conda commands: -# conda create -n ctsm_py # Do this one time for each machine -# conda install -n ctsm_py --file conda_env_ctsm_py.txt # Do this each time you update your CTSM Version -# conda activate ctsm_py # Do this anytime you want to run a CTSM python script +# conda create -n ctsm_pylib # Do this one time for each machine +# conda install -n ctsm_pylib --file conda_env_ctsm_py.txt # Do this each time you update your CTSM Version +# conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script # python=3.7.9 scipy diff --git a/python/conda_env_ctsm_py_cgd.txt b/python/conda_env_ctsm_py_cgd.txt index 45025506a8..1dc52a873b 100644 --- a/python/conda_env_ctsm_py_cgd.txt +++ b/python/conda_env_ctsm_py_cgd.txt @@ -5,12 +5,12 @@ # # To install this on cheyenne with conda loaded in modules # use the top level bash script: -# ../py_env_create # Do this each time you update your CTSM Version -# conda activate ctsm_py # Do this anytime you want to run a CTSM python script +# ../py_env_create # Do this each time you update your CTSM Version +# conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script # Or the individual conda commands: -# conda create -n ctsm_py # Do this one time for each machine -# conda install -n ctsm_py --file conda_env_ctsm_py.txt # Do this each time you update your CTSM Version -# conda activate ctsm_py # Do this anytime you want to run a CTSM python script +# conda create -n ctsm_pylib # Do this one time for each machine +# conda install -n ctsm_pylib --file conda_env_ctsm_py.txt # Do this each time you update your CTSM Version +# conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script # python=3.7.0 # The python version MUST match the python version available on CGD systems through modules exactly scipy diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh index 1b3c141d79..db3466e5a8 100755 --- a/test/tools/test_driver.sh +++ b/test/tools/test_driver.sh @@ -55,7 +55,7 @@ module load ncl module load conda $CESMDATAROOT/py_env_create -conda activate ctsm_py +conda activate ctsm_pylib ##omp threads @@ -120,7 +120,7 @@ module load nco module load conda module load ncl $CESMDATAROOT/py_env_create -conda activate ctsm_py +conda activate ctsm_pylib ##omp threads @@ -221,7 +221,7 @@ module load tool/nco module load tool/netcdf module load lang/python $CESMDATAROOT/py_env_create -conda activate ctsm_py +conda activate ctsm_pylib export NETCDF_DIR=\$NETCDF_PATH export INC_NETCDF=\${NETCDF_PATH}/include @@ -304,7 +304,7 @@ module load tool/nco module load tool/netcdf module load lang/python $CESMDATAROOT/py_env_create -conda activate ctsm_py +conda activate ctsm_pylib export NETCDF_DIR=\$NETCDF_PATH export INC_NETCDF=\${NETCDF_PATH}/include diff --git a/tools/contrib/README b/tools/contrib/README index 43884abe69..4cf9c68fc4 100644 --- a/tools/contrib/README +++ b/tools/contrib/README @@ -10,7 +10,7 @@ The python scripts require the following settings before running on cheyenne: module load conda ../../py_env_create -conda activate ctsm_py +conda activate ctsm_pylib Brief description of scripts: diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 94658f3d54..ae3d189a8b 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -8,7 +8,7 @@ Create anomoly forcing datasets for SSP scenarios that can be used by CESM datm load proper modules first, i.e. ../../py_env_create -conda activate ctsm_py +conda activate ctsm_pylib """ import sys diff --git a/tools/modify_fsurdat/README b/tools/modify_fsurdat/README index b8337c93f4..2295eabf32 100644 --- a/tools/modify_fsurdat/README +++ b/tools/modify_fsurdat/README @@ -32,7 +32,7 @@ To run on Cheyenne/Casper/Izumi module unload python module load conda ./py_env_create -conda activate ctsm_py +conda activate ctsm_pylib (Use "deactivate" to reverse the latter.) 2) Copy, then modify the configure file named modify_template.cfg, which contains all the arguments needed by the script. diff --git a/tools/site_and_regional/README b/tools/site_and_regional/README index d6cc55eac8..723ddb4a97 100644 --- a/tools/site_and_regional/README +++ b/tools/site_and_regional/README @@ -7,7 +7,7 @@ The python scripts require the following settings before running on cheyenne: module load conda ../../py_env_create -conda activate ctsm_py +conda activate ctsm_pylib Brief description of scripts: From d943730ee25661aeeec140dff13443f7130b3668 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 28 Jul 2022 16:14:25 -0600 Subject: [PATCH 0269/2067] Add a workflow for python directory testing --- .github/workflows/python_testing.yml | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 .github/workflows/python_testing.yml diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml new file mode 100644 index 0000000000..e2bd3567ca --- /dev/null +++ b/.github/workflows/python_testing.yml @@ -0,0 +1,26 @@ +name: python testing on push and PR +# +# Run the python directory testing on push and pull request +# +on: [push, pull_request] + +jobs: + pytest: + runs-on: ubuntu-latest + steps: + # Checkout the code + - uses: actions/checkout@v2 + - uses: conda-incubator/setup-miniconda@v2 + with: + activate-environment: ctsm_pylib + environment-file: python/conda_env_ctsm_py.txt + auto-activate-base: false + - shell: bash -l {0} + run: | + conda info + conda list + - name: Run python tests + shell: bash -l {0} + run: | + cd python + make all From f48503405edde55c4fe3697568f940c4e935e9ae Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 28 Jul 2022 16:23:21 -0600 Subject: [PATCH 0270/2067] Add conda-forge channel to action, and only do test and lint test so black check isn't duplicated --- .github/workflows/python_testing.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml index e2bd3567ca..c7cbff63a5 100644 --- a/.github/workflows/python_testing.yml +++ b/.github/workflows/python_testing.yml @@ -15,6 +15,7 @@ jobs: activate-environment: ctsm_pylib environment-file: python/conda_env_ctsm_py.txt auto-activate-base: false + channels: conda-forge - shell: bash -l {0} run: | conda info @@ -23,4 +24,5 @@ jobs: shell: bash -l {0} run: | cd python - make all + make test + make lint From 82adf407b1623c176b33bc6efb65dd5d6f7b4367 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 28 Jul 2022 16:30:33 -0600 Subject: [PATCH 0271/2067] Have to manage externals so that cime exists --- .github/workflows/python_testing.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml index c7cbff63a5..5098a9495d 100644 --- a/.github/workflows/python_testing.yml +++ b/.github/workflows/python_testing.yml @@ -18,6 +18,7 @@ jobs: channels: conda-forge - shell: bash -l {0} run: | + manage_externals/checkout_externals conda info conda list - name: Run python tests From e7c69a6ac87eae95e432a15c304a8182328d7e59 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 28 Jul 2022 16:41:36 -0600 Subject: [PATCH 0272/2067] Seperate tests out, and add git lfs --- .github/workflows/python_testing.yml | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml index 5098a9495d..e2137d91f7 100644 --- a/.github/workflows/python_testing.yml +++ b/.github/workflows/python_testing.yml @@ -16,14 +16,18 @@ jobs: environment-file: python/conda_env_ctsm_py.txt auto-activate-base: false channels: conda-forge - - shell: bash -l {0} + - name: manage_exernals and LFS + shell: bash -l {0} run: | + git lfs install manage_externals/checkout_externals - conda info - conda list - name: Run python tests shell: bash -l {0} run: | cd python make test + - name: Run pylint + shell: bash -l {0} + run: | + cd python make lint From eec9ccfad2706839021de5c8c90287e5e95da5db Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Jul 2022 16:14:22 -0600 Subject: [PATCH 0273/2067] Bugfix to restartvar() call for *c_to_food_perharv. --- src/biogeochem/CNVegCarbonFluxType.F90 | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 1e193aea1e..8bdb4967d6 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -3582,9 +3582,13 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) call restartvar(ncid=ncid, flag=flag, varname=varname, & xtype=ncd_double, & dim1name='pft', & + dim2name='mxharvests', & + switchdim=.true., & long_name=get_repr_longname(k)//' C to food per harvest; should only be output annually', & units='gC/m2', & - interpinic_flag='interp', readvar=readvar, data=data2dptr) + readvar=readvar, & + scale_by_thickness=.false., & + interpinic_flag='interp', data=data2dptr) end do end if From ae3acd0cce5af3df8023ade93d662022e252c342 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 1 Aug 2022 17:02:31 -0600 Subject: [PATCH 0274/2067] Add an explicit check for the make returning an exit code --- .github/workflows/python_testing.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml index e2137d91f7..790528c2be 100644 --- a/.github/workflows/python_testing.yml +++ b/.github/workflows/python_testing.yml @@ -26,8 +26,14 @@ jobs: run: | cd python make test + if [ $? != 0 ]; then + exit 1 + fi - name: Run pylint shell: bash -l {0} run: | cd python make lint + if [ $? != 0 ]; then + exit 1 + fi From c9d4861a5fe88351d7893a2ec84f3381ebc8ce6f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 1 Aug 2022 17:49:57 -0600 Subject: [PATCH 0275/2067] Remove set of bash for login, and add explicit rule for cd to python directory --- .github/workflows/python_testing.yml | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml index 790528c2be..f9234acc2f 100644 --- a/.github/workflows/python_testing.yml +++ b/.github/workflows/python_testing.yml @@ -17,23 +17,15 @@ jobs: auto-activate-base: false channels: conda-forge - name: manage_exernals and LFS - shell: bash -l {0} run: | git lfs install manage_externals/checkout_externals - - name: Run python tests - shell: bash -l {0} + - name: chdirectory python run: | cd python + - name: Run python tests + run: | make test - if [ $? != 0 ]; then - exit 1 - fi - name: Run pylint - shell: bash -l {0} run: | - cd python make lint - if [ $? != 0 ]; then - exit 1 - fi From e3051554246ea6253882f7e7b36abf7c83edb307 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Tue, 2 Aug 2022 16:34:52 +0200 Subject: [PATCH 0276/2067] change initial depth InitCold to 0.5 --- src/biogeophys/WaterStateType.F90 | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index c33880a3c3..081a6d78e3 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -314,8 +314,9 @@ subroutine InitCold(this, bounds, & use shr_const_mod , only : SHR_CONST_TKFRZ use landunit_varcon , only : istwet, istsoil, istcrop, istice use column_varcon , only : icol_road_perv, icol_road_imperv - use clm_varcon , only : denice, denh2o, bdsno + use clm_varcon , only : denice, denh2o, bdsno , zisoi use clm_varcon , only : tfrz, aquifer_water_baseline + use initVerticalMod , only : find_soil_layer_containing_depth ! ! !ARGUMENTS: class(waterstate_type), intent(inout) :: this @@ -328,7 +329,7 @@ subroutine InitCold(this, bounds, & ! ! !LOCAL VARIABLES: integer :: c,j,l,nlevs,g - integer :: nbedrock, n1m + integer :: nbedrock, n05m ! layer containing 0.5 m real(r8) :: ratio !----------------------------------------------------------------------- @@ -542,20 +543,19 @@ subroutine InitCold(this, bounds, & l = col%landunit(c) if (.not. lun%lakpoi(l)) then !not lake if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - n1m=3 - do j = 3, nlevsoi ! get layer with 1 m depth - if (col%zi(c,j-1)<=1.0_r8 .and. col%zi(c,j)>1.0_r8) then - n1m=j - end if - end do + if (zisoi(nlevsoi) >= 0.5_r8) then + call find_soil_layer_containing_depth(0.5_r8,n05m) + else + n05m=nlevsoi-1 + endif if (use_bedrock .and. nbedrock<=nlevsoi) then nbedrock = col%nbedrock(c) else nbedrock = nlevsoi endif do j = 2, nlevmaxurbgrnd ! ignore first layer - if (n1m= n1m .and. j= n05m .and. j Date: Tue, 2 Aug 2022 12:45:08 -0600 Subject: [PATCH 0277/2067] Change name of mesh file to one in CDF5 format --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index d8e3eaa810..bbd6949f92 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2593,7 +2593,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts .false. lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc -lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_c20220516.nc +lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc bilinear From ff76bcb73b788e2a05d41e21a7dd0112d424be92 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 2 Aug 2022 14:29:52 -0600 Subject: [PATCH 0278/2067] Added misc. crop seasonal outputs. GDDHARV_PERHARV, GDDACCUM_PERHARV, HUI_PERHARV, SOWING_REASON_PERHARV, HARVEST_REASON_PERHARV. --- src/biogeochem/CNPhenologyMod.F90 | 34 ++++++++++++++++++++-- src/biogeochem/CNVegStateType.F90 | 18 ++++++++++++ src/biogeochem/CropType.F90 | 48 +++++++++++++++++++++++++++++++ 3 files changed, 97 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bac74a8a9d..dcc9b98636 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1810,6 +1810,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end do do s = 1, mxharvests crop_inst%hdates_thisyr(p,s) = -1._r8 + cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8 + crop_inst%gddaccum_thisyr(p,s) = -1._r8 + crop_inst%hui_thisyr(p,s) = -1._r8 + crop_inst%harvest_reason_thisyr(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_perharv(p,s,k) = 0._r8 end do @@ -1871,7 +1875,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hdidx(p) = 0._r8 vf(p) = 0._r8 - call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & + call PlantCrop(p, leafcn(ivt(p)), jday, & + do_plant_normal, do_plant_lastchance, & + crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -1902,7 +1908,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (do_plant_normal .or. do_plant_lastchance) then - call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & + call PlantCrop(p, leafcn(ivt(p)), jday, & + do_plant_normal, do_plant_lastchance, & + crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -2092,6 +2100,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + cnveg_state_inst%gddmaturity_thisyr(p,harvest_count(p)) = gddmaturity(p) + crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) + crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) + crop_inst%harvest_reason_thisyr(p, harvest_count(p)) = harvest_reason croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = cphase_harvest if (tlai(p) > 0._r8) then ! plant had emerged before harvest @@ -2289,7 +2301,8 @@ subroutine CropPhenologyInit(bounds) end subroutine CropPhenologyInit !----------------------------------------------------------------------- - subroutine PlantCrop(p, leafcn_in, jday, & + subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & + do_plant_lastchance, & crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & @@ -2309,6 +2322,8 @@ subroutine PlantCrop(p, leafcn_in, jday, & integer , intent(in) :: p ! PATCH index running over real(r8) , intent(in) :: leafcn_in ! leaf C:N (gC/gN) of this patch's vegetation type (pftcon%leafcn(ivt(p))) integer , intent(in) :: jday ! julian day of the year + logical , intent(in) :: do_plant_normal ! Are all the normal requirements for planting met? + logical , intent(in) :: do_plant_lastchance ! Are the last-chance requirements for planting met? type(crop_type) , intent(inout) :: crop_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst @@ -2320,12 +2335,14 @@ subroutine PlantCrop(p, leafcn_in, jday, & ! ! LOCAL VARAIBLES: integer k ! grain pool index + real(r8) this_sowing_reason ! number representing sowing reason(s) !------------------------------------------------------------------------ associate( & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch + sowing_reason => crop_inst%sowing_reason_thisyr , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Output: [real(r8) (:) ] (gN/m2) leaf N transfer @@ -2341,6 +2358,17 @@ subroutine PlantCrop(p, leafcn_in, jday, & sowing_count(p) = sowing_count(p) + 1 crop_inst%sdates_thisyr(p,sowing_count(p)) = jday + this_sowing_reason = 0._r8 + if (do_plant_prescribed) then + this_sowing_reason = 10._r8 + end if + if (do_plant_normal) then + this_sowing_reason = this_sowing_reason + 1._r8 + else if (do_plant_lastchance) then + this_sowing_reason = this_sowing_reason + 2._r8 + end if + sowing_reason(p,s) = this_sowing_reason + leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset crop_seedc_to_leaf(p) = leafc_xfer(p)/dt diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index e30bb9c7e7..dd5510869f 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -35,6 +35,7 @@ module CNVegStateType real(r8) , pointer :: hdidx_patch (:) ! patch cold hardening index? real(r8) , pointer :: cumvd_patch (:) ! patch cumulative vernalization d?ependence? real(r8) , pointer :: gddmaturity_patch (:) ! patch growing degree days (gdd) needed to harvest (ddays) + real(r8) , pointer :: gddmaturity_thisyr (:,:) ! all at-harvest values of the above for this patch this year real(r8) , pointer :: huileaf_patch (:) ! patch heat unit index needed from planting to leaf emergence real(r8) , pointer :: huigrain_patch (:) ! patch heat unit index needed to reach vegetative maturity real(r8) , pointer :: aleafi_patch (:) ! patch saved leaf allocation coefficient from phase 2 @@ -207,6 +208,7 @@ subroutine InitAllocate(this, bounds) allocate(this%hdidx_patch (begp:endp)) ; this%hdidx_patch (:) = nan allocate(this%cumvd_patch (begp:endp)) ; this%cumvd_patch (:) = nan allocate(this%gddmaturity_patch (begp:endp)) ; this%gddmaturity_patch (:) = spval + allocate(this%gddmaturity_thisyr (begp:endp,1:mxharvests)) ; this%gddmaturity_thisyr (:,:) = spval allocate(this%huileaf_patch (begp:endp)) ; this%huileaf_patch (:) = nan allocate(this%huigrain_patch (begp:endp)) ; this%huigrain_patch (:) = 0.0_r8 allocate(this%aleafi_patch (begp:endp)) ; this%aleafi_patch (:) = nan @@ -313,6 +315,12 @@ subroutine InitHistory(this, bounds) call hist_addfld1d (fname='GDDHARV', units='ddays', & avgflag='A', long_name='Growing degree days (gdd) needed to harvest', & ptr_patch=this%gddmaturity_patch, default='inactive') + + ! Per harvest + this%gddmaturity_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='GDDHARV_PERHARV', units='ddays', type2d='mxharvests', & + avgflag='I', long_name='Growing degree days (gdd) needed to harvest; should only be output annually', & + ptr_patch=this%gddmaturity_thisyr, default='inactive') end if this%lfc2_col(begc:endc) = spval @@ -842,6 +850,16 @@ subroutine Restart(this, bounds, ncid, flag, cnveg_carbonstate, & call restartvar(ncid=ncid, flag=flag, varname='grain_flag', xtype=ncd_double, & dim1name='pft', long_name='', units='', & interpinic_flag='interp', readvar=readvar, data=this%grain_flag_patch) + + ! Read or write variable(s) with mxharvests dimension + ! BACKWARDS_COMPATIBILITY(ssr, 2022-03-31) See note in CallRestartvarDimOK() + if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then + call restartvar(ncid=ncid, flag=flag, varname='gddmaturity_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='crop harvest dates for this patch this year', units='day of year', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%gddmaturity_thisyr) + end if end if if ( flag == 'read' .and. num_reseed_patch > 0 )then if ( masterproc ) write(iulog, *) 'Reseed dead plants for CNVegState' diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index af44e487ca..20c0ea7381 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -48,6 +48,10 @@ module CropType real(r8) :: baset_latvary_slope real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year + real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year + real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year + real(r8), pointer :: sowing_reason_thisyr (:,:) ! reason for each sowing for this patch this year + real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch ! gddaccum tracks the actual growing degree-days accumulated over the growing season. @@ -217,6 +221,10 @@ subroutine InitAllocate(this, bounds) allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sdates_thisyr(begp:endp,1:mxsowings)) ; this%sdates_thisyr(:,:) = spval allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval + allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval + allocate(this%hui_thisyr(begp:endp,1:mxharvests)) ; this%hui_thisyr(:,:) = spval + allocate(this%sowing_reason_thisyr(begp:endp,1:mxsowings)) ; this%sowing_reason_thisyr(:,:) = spval + allocate(this%harvest_reason_thisyr(begp:endp,1:mxharvests)) ; this%harvest_reason_thisyr(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 @@ -282,6 +290,26 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_patch=this%hdates_thisyr, default='inactive') + this%gddaccum_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='GDDACCUM_PERHARV', units='ddays', type2d='mxharvests', & + avgflag='I', long_name='At-harvest accumulated growing degree days past planting date for crop; should only be output annually', & + ptr_patch=this%gddaccum_thisyr, default='inactive') + + this%hui_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='HUI_PERHARV', units='ddays', type2d='mxharvests', & + avgflag='I', long_name='At-harvest accumulated heat unit index for crop; should only be output annually', & + ptr_patch=this%hui_thisyr, default='inactive') + + this%sowing_reason_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='SOWING_REASON_PERHARV', units='unitless', type2d='mxsowings', & + avgflag='I', long_name='Reason for each crop sowing; should only be output annually', & + ptr_patch=this%sowing_reason_thisyr, default='inactive') + + this%harvest_reason_thisyr(begp:endp,:) = spval + call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='unitless', type2d='mxharvests', & + avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & + ptr_patch=this%harvest_reason_thisyr, default='inactive') + end subroutine InitHistory subroutine InitCold(this, bounds) @@ -564,6 +592,26 @@ subroutine Restart(this, bounds, ncid, flag) long_name='crop harvest dates for this patch this year', units='day of year', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%hdates_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='gddaccum_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='accumulated GDD at harvest for this patch this year', units='ddays', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%gddaccum_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='hui_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='accumulated heat unit index at harvest for this patch this year', units='ddays', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%hui_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxsowings', switchdim=.true., & + long_name='reason for each sowing for this patch this year', units='unitless', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='harvest_reason_thisyr', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='reason for each harvest for this patch this year', units='unitless', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%harvest_reason_thisyr) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp From c048c9ad624b489cbfa6bfc0e49a79e5c883b263 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 2 Aug 2022 14:54:53 -0600 Subject: [PATCH 0279/2067] Correction for harvest_reason in CropPhenology(). --- src/biogeochem/CNPhenologyMod.F90 | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index dcc9b98636..a3197981fa 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1703,6 +1703,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer s ! growing season indices integer k ! grain pool indices integer idpp ! number of days past planting + real(r8) harvest_reason real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year real(r8) crmcorn ! comparitive relative maturity for corn @@ -1792,6 +1793,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & bgtr(p) = 0._r8 lgsf(p) = 0._r8 + ! Should never be saved as zero, but including this so it's initialized just in case + harvest_reason = 0._r8 + ! --------------------------------- ! from AgroIBIS subroutine planting ! --------------------------------- @@ -2097,6 +2101,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! changes to the offset subroutine below else if (hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p))) then + + if (hui(p) >= gddmaturity(p)) then + harvest_reason = 1._r8 + else if (idpp >= mxmat(ivt(p))) then + harvest_reason = 2._r8 + end if + if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) From cd6fd12fb5c13e00d0f696ba8df18c013d33f0dd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 2 Aug 2022 15:07:09 -0600 Subject: [PATCH 0280/2067] Bug fixes for misc. crop seasonal outputs. --- src/biogeochem/CNPhenologyMod.F90 | 5 +---- src/biogeochem/CNVegStateType.F90 | 1 + 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a3197981fa..6302fdf028 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2370,15 +2370,12 @@ subroutine PlantCrop(p, leafcn_in, jday, do_plant_normal, & crop_inst%sdates_thisyr(p,sowing_count(p)) = jday this_sowing_reason = 0._r8 - if (do_plant_prescribed) then - this_sowing_reason = 10._r8 - end if if (do_plant_normal) then this_sowing_reason = this_sowing_reason + 1._r8 else if (do_plant_lastchance) then this_sowing_reason = this_sowing_reason + 2._r8 end if - sowing_reason(p,s) = this_sowing_reason + sowing_reason(p,sowing_count(p)) = this_sowing_reason leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index dd5510869f..d23b4fed62 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -150,6 +150,7 @@ subroutine InitAllocate(this, bounds) ! ! !USES: use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use clm_varpar, only : mxharvests ! ! !ARGUMENTS: class(cnveg_state_type) :: this From 88b8feaa7dd614a859c60b5687c76bb285c25d93 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 3 Aug 2022 10:16:33 +0200 Subject: [PATCH 0281/2067] fixed indent WaterState --- src/biogeophys/WaterStateType.F90 | 54 +++++++++++++++---------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 081a6d78e3..9678e8c4c1 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -541,33 +541,33 @@ subroutine InitCold(this, bounds, & do c = bounds%begc,bounds%endc g = col%gridcell(c) l = col%landunit(c) - if (.not. lun%lakpoi(l)) then !not lake - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (zisoi(nlevsoi) >= 0.5_r8) then - call find_soil_layer_containing_depth(0.5_r8,n05m) - else - n05m=nlevsoi-1 - endif - if (use_bedrock .and. nbedrock<=nlevsoi) then - nbedrock = col%nbedrock(c) - else - nbedrock = nlevsoi - endif - do j = 2, nlevmaxurbgrnd ! ignore first layer - if (n05m= n05m .and. j= 0.5_r8) then + call find_soil_layer_containing_depth(0.5_r8,n05m) + else + n05m=nlevsoi-1 + endif + if (use_bedrock .and. nbedrock<=nlevsoi) then + nbedrock = col%nbedrock(c) + else + nbedrock = nlevsoi + endif + do j = 2, nlevmaxurbgrnd ! ignore first layer + if (n05m= n05m .and. j Date: Wed, 3 Aug 2022 10:19:10 +0200 Subject: [PATCH 0282/2067] add TODO to ExcessIceStream --- src/cpl/share_esmf/ExcessIceStreamType.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 134810ba1b..b0f79d1bfa 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -124,6 +124,7 @@ subroutine Init(this, bounds, NLFilename) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + !TODO ! Explicitly set current date to a hardcoded constant value. Otherwise ! using the real date can cause roundoff differences that are ! detrected as issues with exact restart. EBK M05/20/2017 From 444d5b6af89cde56798bc2e47df16d1d72a37bf5 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 3 Aug 2022 12:54:16 +0200 Subject: [PATCH 0283/2067] Fixed typo --- src/biogeophys/SoilTemperatureMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 112346d74d..f149208ba5 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -710,7 +710,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter dke = satw end if fl = (h2osoi_liq(c,j)/(denh2o*dz(c,j))) / (h2osoi_liq(c,j)/(denh2o*dz(c,j)) + & - h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/denice) + h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/(denice*dz)) dksat = tkmg(c,j)*tkwat**(fl*watsat(c,j))*tkice**((1._r8-fl)*watsat(c,j)) thk(c,j) = dke*dksat + (1._r8-dke)*tkdry(c,j) else From ddd7a82ecfff31a8aa6497675b380180d4055278 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 3 Aug 2022 13:16:27 +0200 Subject: [PATCH 0284/2067] another typo --- src/biogeophys/SoilTemperatureMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index f149208ba5..c42130d8d2 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -710,7 +710,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter dke = satw end if fl = (h2osoi_liq(c,j)/(denh2o*dz(c,j))) / (h2osoi_liq(c,j)/(denh2o*dz(c,j)) + & - h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/(denice*dz)) + h2osoi_ice(c,j)/(denice*dz(c,j))+excess_ice(c,j)/(denice*dz(c,j))) dksat = tkmg(c,j)*tkwat**(fl*watsat(c,j))*tkice**((1._r8-fl)*watsat(c,j)) thk(c,j) = dke*dksat + (1._r8-dke)*tkdry(c,j) else From b75e6ba25b7010dd26ebb2d87351999123bbb124 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Wed, 3 Aug 2022 17:39:34 +0200 Subject: [PATCH 0285/2067] remove MVD --- src/main/controlMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 194e1704aa..48564c8855 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -870,7 +870,7 @@ subroutine control_print () write(iulog,*) ' use_nitrif_denitrif = ', use_nitrif_denitrif write(iulog,*) ' use_extralakelayers = ', use_extralakelayers write(iulog,*) ' use_vichydro = ', use_vichydro - write(iulog,*) ' use_excess_ice = ', use_excess_ice !MVD to check if the value is read from namelists + write(iulog,*) ' use_excess_ice = ', use_excess_ice write(iulog,*) ' use_cn = ', use_cn write(iulog,*) ' use_cndv = ', use_cndv write(iulog,*) ' use_crop = ', use_crop From d7991cea05650e20a4a34cc84038e7a562c814d3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 4 Aug 2022 12:26:19 -0600 Subject: [PATCH 0286/2067] Added S{DATES,YEARS}_PERHARV outputs. The idea here is to provide an easy way to know, when you're looking at a per-harvest variable, when that crop was planted. This info can be derived from SDATES, but doing so is complicated. --- src/biogeochem/CNPhenologyMod.F90 | 31 ++++++++++++++++++++++++++----- src/biogeochem/CNVegStateType.F90 | 8 +++++++- src/biogeochem/CropType.F90 | 24 ++++++++++++++++++++++++ 3 files changed, 57 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bac74a8a9d..5ce5918904 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1703,6 +1703,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer s ! growing season indices integer k ! grain pool indices integer idpp ! number of days past planting + integer kyr ! current year + integer kmo ! month of year (1, ..., 12) + integer kda ! day of month (1, ..., 31) + integer mcsec ! seconds of day (0, ..., seconds/day) real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year real(r8) crmcorn ! comparitive relative maturity for corn @@ -1744,7 +1748,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow - idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting + idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting (day of year) + iyop => cnveg_state_inst%iyop_patch , & ! Output: [integer (:) ] year of planting (day of year) gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest huileaf => cnveg_state_inst%huileaf_patch , & ! Output: [real(r8) (:) ] heat unit index needed from planting to leaf emergence huigrain => cnveg_state_inst%huigrain_patch , & ! Output: [real(r8) (:) ] same to reach vegetative maturity @@ -1773,6 +1778,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & dayspyr = get_curr_days_per_year() avg_dayspyr = get_average_days_per_year() jday = get_prev_calday() + call get_curr_date(kyr, kmo, kda, mcsec) if (use_fertilizer) then ndays_on = 20._r8 ! number of days to fertilize @@ -1809,6 +1815,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%sdates_thisyr(p,s) = -1._r8 end do do s = 1, mxharvests + crop_inst%sdates_perharv(p,s) = -1._r8 + crop_inst%syears_perharv(p,s) = -1._r8 crop_inst%hdates_thisyr(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_perharv(p,s,k) = 0._r8 @@ -1829,6 +1837,14 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sowing_count(p) = 1 crop_inst%sdates_thisyr(p,1) = real(idop(p), r8) end if + ! Will be needed until we can rely on all restart files including iyop. + if (croplive(p) .and. iyop(p) > kyr) then + if (idop(p) <= jday) then + iyop(p) = kyr + else + iyop(p) = kyr - 1 + end if + end if ! Once outputs can handle >1 planting per year, remove 2nd condition. @@ -1871,7 +1887,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & hdidx(p) = 0._r8 vf(p) = 0._r8 - call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & + call PlantCrop(p, leafcn(ivt(p)), jday, kyr, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -1902,7 +1918,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (do_plant_normal .or. do_plant_lastchance) then - call PlantCrop(p, leafcn(ivt(p)), jday, crop_inst, cnveg_state_inst, & + call PlantCrop(p, leafcn(ivt(p)), jday, kyr, crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) @@ -2091,6 +2107,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p))) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 + crop_inst%sdates_perharv(p, harvest_count(p)) = real(idop, r8) + crop_inst%syears_perharv(p, harvest_count(p)) = real(iyop, r8) crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = cphase_harvest @@ -2289,7 +2307,7 @@ subroutine CropPhenologyInit(bounds) end subroutine CropPhenologyInit !----------------------------------------------------------------------- - subroutine PlantCrop(p, leafcn_in, jday, & + subroutine PlantCrop(p, leafcn_in, jday, kyr, & crop_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & @@ -2309,6 +2327,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & integer , intent(in) :: p ! PATCH index running over real(r8) , intent(in) :: leafcn_in ! leaf C:N (gC/gN) of this patch's vegetation type (pftcon%leafcn(ivt(p))) integer , intent(in) :: jday ! julian day of the year + integer , intent(in) :: kyr ! current year type(crop_type) , intent(inout) :: crop_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst @@ -2326,7 +2345,8 @@ subroutine PlantCrop(p, leafcn_in, jday, & croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch - idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting + idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting (day of year) + iyop => cnveg_state_inst%iyop_patch , & ! Output: [integer (:) ] year of planting leafc_xfer => cnveg_carbonstate_inst%leafc_xfer_patch , & ! Output: [real(r8) (:) ] (gC/m2) leaf C transfer leafn_xfer => cnveg_nitrogenstate_inst%leafn_xfer_patch , & ! Output: [real(r8) (:) ] (gN/m2) leaf N transfer crop_seedc_to_leaf => cnveg_carbonflux_inst%crop_seedc_to_leaf_patch , & ! Output: [real(r8) (:) ] (gC/m2/s) seed source to leaf @@ -2337,6 +2357,7 @@ subroutine PlantCrop(p, leafcn_in, jday, & ! for crop maturity - for cold weather constraints croplive(p) = .true. idop(p) = jday + iyop(p) = kyr harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 crop_inst%sdates_thisyr(p,sowing_count(p)) = jday diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index e30bb9c7e7..cf38793433 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -55,7 +55,8 @@ module CNVegStateType real(r8) , pointer :: htmx_patch (:) ! patch max hgt attained by a crop during yr (m) integer , pointer :: peaklai_patch (:) ! patch 1: max allowed lai; 0: not at max - integer , pointer :: idop_patch (:) ! patch date of planting + integer , pointer :: idop_patch (:) ! patch date of planting (day of year) + integer , pointer :: iyop_patch (:) ! patch year of planting real(r8) , pointer :: lgdp_col (:) ! col gdp limitation factor for fire occurrence (0-1) real(r8) , pointer :: lgdp1_col (:) ! col gdp limitation factor for fire spreading (0-1) @@ -228,6 +229,7 @@ subroutine InitAllocate(this, bounds) allocate(this%peaklai_patch (begp:endp)) ; this%peaklai_patch (:) = 0 allocate(this%idop_patch (begp:endp)) ; this%idop_patch (:) = huge(1) + allocate(this%iyop_patch (begp:endp)) ; this%iyop_patch (:) = huge(1) allocate(this%lgdp_col (begc:endc)) ; allocate(this%lgdp1_col (begc:endc)) ; @@ -803,6 +805,10 @@ subroutine Restart(this, bounds, ncid, flag, cnveg_carbonstate, & dim1name='pft', long_name='Date of planting', units='jday', nvalid_range=(/1,366/), & interpinic_flag='interp', readvar=readvar, data=this%idop_patch) + call restartvar(ncid=ncid, flag=flag, varname='iyop', xtype=ncd_int, & + dim1name='pft', long_name='Year of planting', units='year', & + interpinic_flag='interp', readvar=readvar, data=this%iyop_patch) + call restartvar(ncid=ncid, flag=flag, varname='aleaf', xtype=ncd_double, & dim1name='pft', long_name='leaf allocation coefficient', units='', & interpinic_flag='interp', readvar=readvar, data=this%aleaf_patch) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index af44e487ca..38151e3031 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -47,6 +47,8 @@ module CropType real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year + real(r8), pointer :: sdates_perharv (:,:) ! all actual sowing dates for crops *harvested* this year + real(r8), pointer :: syears_perharv (:,:) ! all actual sowing years for crops *harvested* this year real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch @@ -216,6 +218,8 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = cphase_not_planted allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sdates_thisyr(begp:endp,1:mxsowings)) ; this%sdates_thisyr(:,:) = spval + allocate(this%sdates_perharv(begp:endp,1:mxharvests)) ; this%sdates_perharv(:,:) = spval + allocate(this%syears_perharv(begp:endp,1:mxharvests)) ; this%syears_perharv(:,:) = spval allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 @@ -277,6 +281,16 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='actual crop sowing dates; should only be output annually', & ptr_patch=this%sdates_thisyr, default='inactive') + this%sdates_perharv(begp:endp,:) = spval + call hist_addfld2d (fname='SDATES_PERHARV', units='day of year', type2d='mxharvests', & + avgflag='I', long_name='actual sowing dates for crops harvested this year; should only be output annually', & + ptr_patch=this%sdates_perharv, default='inactive') + + this%syears_perharv(begp:endp,:) = spval + call hist_addfld2d (fname='SYEARS_PERHARV', units='year', type2d='mxharvests', & + avgflag='I', long_name='actual sowing years for crops harvested this year; should only be output annually', & + ptr_patch=this%syears_perharv, default='inactive') + this%hdates_thisyr(begp:endp,:) = spval call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxharvests', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & @@ -559,6 +573,16 @@ subroutine Restart(this, bounds, ncid, flag) ! Read or write variable(s) with mxharvests dimension ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then + call restartvar(ncid=ncid, flag=flag, varname='sdates_perharv', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='sowing dates for crops harvested in this patch this year', units='day of year', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%sdates_perharv) + call restartvar(ncid=ncid, flag=flag, varname='syears_perharv', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='sowing years for crops harvested in this patch this year', units='year', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%syears_perharv) call restartvar(ncid=ncid, flag=flag, varname='hdates_thisyr', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='crop harvest dates for this patch this year', units='day of year', & From ed41cb0ee4a63b99877738d5d1e35673d4969a38 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 4 Aug 2022 12:51:02 -0600 Subject: [PATCH 0287/2067] Compile fixes to previous. --- src/biogeochem/CNPhenologyMod.F90 | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 5ce5918904..ba07b9ef5a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1667,6 +1667,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! !USES: use clm_time_manager , only : get_prev_calday, get_curr_days_per_year, is_beg_curr_year use clm_time_manager , only : get_average_days_per_year + use clm_time_manager , only : get_curr_date use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice @@ -2107,8 +2108,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (hui(p) >= gddmaturity(p) .or. idpp >= mxmat(ivt(p))) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 - crop_inst%sdates_perharv(p, harvest_count(p)) = real(idop, r8) - crop_inst%syears_perharv(p, harvest_count(p)) = real(iyop, r8) + crop_inst%sdates_perharv(p, harvest_count(p)) = real(idop(p), r8) + crop_inst%syears_perharv(p, harvest_count(p)) = real(iyop(p), r8) crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = cphase_harvest From e83925016b09ff51351a1d8cf222b3beb43860d2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 4 Aug 2022 16:53:38 -0600 Subject: [PATCH 0288/2067] Add an excess ice test to the testlist --- cime_config/testdefs/testlist_clm.xml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 29205014cf..b2a063d011 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -168,6 +168,15 @@ + + + + + + + + + From 5dd8aa5f1cf0a9103d83877c67e0da9c5c4f502d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 4 Aug 2022 16:53:55 -0600 Subject: [PATCH 0289/2067] Add excess ice testmod --- .../testdefs/testmods_dirs/clm/ExcessIce/include_user_mods | 1 + cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm | 1 + 2 files changed, 2 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/ExcessIce/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIce/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIce/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIce/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm new file mode 100644 index 0000000000..d9e52c6cf9 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm @@ -0,0 +1 @@ + use_excess_ice = .true. From 6ed905835729c16650fae6a452106d0b15bd9823 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Aug 2022 15:05:47 -0600 Subject: [PATCH 0290/2067] SOWING_REASON_PERHARV now actually per-harvest; added SOWING_REASON that's per-sowing. --- src/biogeochem/CNPhenologyMod.F90 | 7 +++++++ src/biogeochem/CropType.F90 | 21 ++++++++++++++++++++- 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bb92769a2e..8349fd5caf 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1854,6 +1854,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & iyop(p) = kyr - 1 end if end if + ! Will be needed until we can rely on all restart files including sowing_reason_patch. + if (croplive(p) .and. crop_inst%sowing_reason_patch(p) < 0) then + crop_inst%sowing_reason_patch(p) = 0 + endif ! Once outputs can handle >1 planting per year, remove 2nd condition. @@ -2133,6 +2137,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_state_inst%gddmaturity_thisyr(p,harvest_count(p)) = gddmaturity(p) crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) + crop_inst%sowing_reason_perharv(p, harvest_count(p)) = real(crop_inst%sowing_reason_patch(p), r8) + crop_inst%sowing_reason_patch(p) = -1 crop_inst%harvest_reason_thisyr(p, harvest_count(p)) = harvest_reason croplive(p) = .false. ! no re-entry in greater if-block cphase(p) = cphase_harvest @@ -2398,6 +2404,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, & this_sowing_reason = this_sowing_reason + 2._r8 end if sowing_reason(p,sowing_count(p)) = this_sowing_reason + crop_inst%sowing_reason_patch(p) = this_sowing_reason leafc_xfer(p) = initial_seed_at_planting leafn_xfer(p) = leafc_xfer(p) / leafcn_in ! with onset diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index d261dafea4..710c101d30 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -42,6 +42,7 @@ module CropType real(r8), pointer :: gddtsoi_patch (:) ! patch growing degree-days from planting (top two soil layers) (ddays) real(r8), pointer :: vf_patch (:) ! patch vernalization factor for cereal real(r8), pointer :: cphase_patch (:) ! phenology phase (see cphase_* constants above for possible values) + integer , pointer :: sowing_reason_patch (:) ! reason for most recent sowing of this patch real(r8), pointer :: latbaset_patch (:) ! Latitude vary baset for hui (degree C) character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept @@ -53,6 +54,7 @@ module CropType real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year real(r8), pointer :: sowing_reason_thisyr (:,:) ! reason for each sowing for this patch this year + real(r8), pointer :: sowing_reason_perharv (:,:) ! reason for each sowing of crops *harvested* this year real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch @@ -220,6 +222,7 @@ subroutine InitAllocate(this, bounds) allocate(this%gddtsoi_patch (begp:endp)) ; this%gddtsoi_patch (:) = spval allocate(this%vf_patch (begp:endp)) ; this%vf_patch (:) = 0.0_r8 allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = cphase_not_planted + allocate(this%sowing_reason_patch (begp:endp)) ; this%sowing_reason_patch (:) = -1 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sdates_thisyr(begp:endp,1:mxsowings)) ; this%sdates_thisyr(:,:) = spval allocate(this%sdates_perharv(begp:endp,1:mxharvests)) ; this%sdates_perharv(:,:) = spval @@ -228,6 +231,7 @@ subroutine InitAllocate(this, bounds) allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval allocate(this%hui_thisyr(begp:endp,1:mxharvests)) ; this%hui_thisyr(:,:) = spval allocate(this%sowing_reason_thisyr(begp:endp,1:mxsowings)) ; this%sowing_reason_thisyr(:,:) = spval + allocate(this%sowing_reason_perharv(begp:endp,1:mxharvests)) ; this%sowing_reason_perharv(:,:) = spval allocate(this%harvest_reason_thisyr(begp:endp,1:mxharvests)) ; this%harvest_reason_thisyr(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 @@ -315,10 +319,15 @@ subroutine InitHistory(this, bounds) ptr_patch=this%hui_thisyr, default='inactive') this%sowing_reason_thisyr(begp:endp,:) = spval - call hist_addfld2d (fname='SOWING_REASON_PERHARV', units='unitless', type2d='mxsowings', & + call hist_addfld2d (fname='SOWING_REASON', units='unitless', type2d='mxsowings', & avgflag='I', long_name='Reason for each crop sowing; should only be output annually', & ptr_patch=this%sowing_reason_thisyr, default='inactive') + this%sowing_reason_perharv(begp:endp,:) = spval + call hist_addfld2d (fname='SOWING_REASON_PERHARV', units='unitless', type2d='mxharvests', & + avgflag='I', long_name='Reason for sowing of each crop harvested this year; should only be output annually', & + ptr_patch=this%sowing_reason_perharv, default='inactive') + this%harvest_reason_thisyr(begp:endp,:) = spval call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='unitless', type2d='mxharvests', & avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & @@ -574,6 +583,11 @@ subroutine Restart(this, bounds, ncid, flag) ! the crop phases end if + call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_patch',xtype=ncd_int, & + dim1name='pft', long_name='sowing reason for this patch', & + units='none', & + interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_patch) + ! Read or write variable(s) with mxsowings dimension ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxsowings')) then @@ -631,6 +645,11 @@ subroutine Restart(this, bounds, ncid, flag) long_name='reason for each sowing for this patch this year', units='unitless', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_thisyr) + call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_perharv', xtype=ncd_double, & + dim1name='pft', dim2name='mxharvests', switchdim=.true., & + long_name='reason for sowing of each crop harvested this year', units='unitless', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_perharv) call restartvar(ncid=ncid, flag=flag, varname='harvest_reason_thisyr', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='reason for each harvest for this patch this year', units='unitless', & From 67f46e81e84bfa91e0c0455d0abf33edb754f14a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 7 Aug 2022 17:35:46 -0600 Subject: [PATCH 0291/2067] Replaced get_curr_date() with get_prev_date() in CropPhenology. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 8349fd5caf..00e5cdfd36 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1667,7 +1667,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! !USES: use clm_time_manager , only : get_prev_calday, get_curr_days_per_year, is_beg_curr_year use clm_time_manager , only : get_average_days_per_year - use clm_time_manager , only : get_curr_date + use clm_time_manager , only : get_prev_date use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice @@ -1780,7 +1780,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & dayspyr = get_curr_days_per_year() avg_dayspyr = get_average_days_per_year() jday = get_prev_calday() - call get_curr_date(kyr, kmo, kda, mcsec) + call get_prev_date(kyr, kmo, kda, mcsec) if (use_fertilizer) then ndays_on = 20._r8 ! number of days to fertilize From cd3b9405696f8441987813bce0bd34bc06d36f13 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 7 Aug 2022 17:49:33 -0600 Subject: [PATCH 0292/2067] Now initializes sowing_reason outputs to -1 at beginning of year. --- src/biogeochem/CNPhenologyMod.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 0ce29198ff..3b08f7d978 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1830,6 +1830,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_count(p) = 0 do s = 1, mxsowings crop_inst%sdates_thisyr(p,s) = -1._r8 + crop_inst%sowing_reason_thisyr(p,s) = -1._r8 end do do s = 1, mxharvests crop_inst%sdates_perharv(p,s) = -1._r8 @@ -1838,6 +1839,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8 crop_inst%gddaccum_thisyr(p,s) = -1._r8 crop_inst%hui_thisyr(p,s) = -1._r8 + crop_inst%sowing_reason_perharv = -1._r8 crop_inst%harvest_reason_thisyr(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_perharv(p,s,k) = 0._r8 From 0824a1214022c832ecb3ecd5b79e2304c4b4b3be Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 9 Aug 2022 10:37:18 -0600 Subject: [PATCH 0293/2067] update SatPhen test defs files --- .../testmods_dirs/clm/FatesColdDefBasic/shell_commands | 2 ++ .../clm/FatesColdDefReducedComplexSatPhen/include_user_mods | 2 +- .../clm/FatesColdDefReducedComplexSatPhen/user_nl_clm | 4 ++-- 3 files changed, 5 insertions(+), 3 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands new file mode 100644 index 0000000000..a6f7ecb4d0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands @@ -0,0 +1,2 @@ +./xmlchange CLM_FORCE_COLDSTART="on" +./xmlchange BFBFLAG="TRUE" \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods index a38be35f63..cc870c3d2a 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods @@ -1,2 +1,2 @@ -../FatesColdDef +../FatesColdDefBasic ../../../../usermods_dirs/fates_sp diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm index 5ae85742ed..1aa2763035 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm @@ -1,2 +1,2 @@ -use_fates_sp = .true. -fates_spitfire_mode = 0 +hist_mfilt = 365 +hist_nhtfrq = -24 \ No newline at end of file From 8cde3feefcb1131d596694e3a14e1dffd0c045dd Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Thu, 11 Aug 2022 14:34:12 -0600 Subject: [PATCH 0294/2067] fixing some other SP issues --- .../testmods_dirs/clm/FatesColdDefBasic/shell_commands | 2 +- .../FatesColdDefDryDepReducedComplexSatPhen/include_user_mods | 1 - .../clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands | 3 +++ .../FatesColdDefMeganReducedComplexSatPhen/include_user_mods | 1 - .../clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands | 2 ++ .../clm/FatesColdDefReducedComplexSatPhen/include_user_mods | 2 +- .../clm/FatesColdDefReducedComplexSatPhen/user_nl_clm | 2 +- 7 files changed, 8 insertions(+), 5 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands index a6f7ecb4d0..586dff9dd5 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands @@ -1,2 +1,2 @@ ./xmlchange CLM_FORCE_COLDSTART="on" -./xmlchange BFBFLAG="TRUE" \ No newline at end of file +./xmlchange BFBFLAG="TRUE" diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods index f754dacdab..b968e7648f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods @@ -1,2 +1 @@ -../FatesColdDefDryDep ../FatesColdDefReducedComplexSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands new file mode 100644 index 0000000000..870cd99bf5 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands @@ -0,0 +1,3 @@ +./xmlchange CLM_BLDNML_OPTS='--drydep' --append +# The following would be required if you want to run with DryDep and FATES without Fates-SP mode +#./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods index 5dd78011ec..b968e7648f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods @@ -1,2 +1 @@ -../FatesColdDefMegan ../FatesColdDefReducedComplexSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands new file mode 100644 index 0000000000..749af3486f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands @@ -0,0 +1,2 @@ +./xmlchange CLM_BLDNML_OPTS='--megan' --append +./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods index cc870c3d2a..e15cf6f649 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods @@ -1,2 +1,2 @@ ../FatesColdDefBasic -../../../../usermods_dirs/fates_sp + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm index 1aa2763035..d914f2be4d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm @@ -1,2 +1,2 @@ hist_mfilt = 365 -hist_nhtfrq = -24 \ No newline at end of file +hist_nhtfrq = -24 From f7223e08c253bba9dad9a845347448a40d43bb86 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 12 Aug 2022 11:13:56 -0600 Subject: [PATCH 0295/2067] reverting some changes --- .../FatesColdDefDryDepReducedComplexSatPhen/include_user_mods | 2 +- .../clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands | 3 --- .../FatesColdDefMeganReducedComplexSatPhen/include_user_mods | 2 +- .../clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands | 2 -- .../clm/FatesColdDefReducedComplexSatPhen/include_user_mods | 3 +-- 5 files changed, 3 insertions(+), 9 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods index b968e7648f..5da4a19a83 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods @@ -1 +1 @@ -../FatesColdDefReducedComplexSatPhen +../FatesColdDefDryDep diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands deleted file mode 100644 index 870cd99bf5..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands +++ /dev/null @@ -1,3 +0,0 @@ -./xmlchange CLM_BLDNML_OPTS='--drydep' --append -# The following would be required if you want to run with DryDep and FATES without Fates-SP mode -#./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods index b968e7648f..254ddd9b2d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods @@ -1 +1 @@ -../FatesColdDefReducedComplexSatPhen +../FatesColdDefMegan diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands deleted file mode 100644 index 749af3486f..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands +++ /dev/null @@ -1,2 +0,0 @@ -./xmlchange CLM_BLDNML_OPTS='--megan' --append -./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods index e15cf6f649..1f2c03aebe 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods @@ -1,2 +1 @@ -../FatesColdDefBasic - +../FatesColdDef From ee553ef09b25f5834f6becd182eedc8653a6d494 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 12 Aug 2022 11:20:33 -0600 Subject: [PATCH 0296/2067] update testdef for the one of the FATES SP smoke tests --- cime_config/testdefs/testlist_clm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index bd2f431f07..581e799871 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2298,13 +2298,13 @@ --> - + - + From f2019f5e3cd656a8102ac8a6fa503138d9e82292 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Mon, 15 Aug 2022 14:22:22 -0600 Subject: [PATCH 0297/2067] put back call to fates_sp usermods --- .../clm/FatesColdDefReducedComplexSatPhen/include_user_mods | 2 ++ .../clm/FatesColdDefReducedComplexSatPhen/user_nl_clm | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods index 1f2c03aebe..303343e726 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods @@ -1 +1,3 @@ ../FatesColdDef +../../../../usermods_dirs/fates_sp + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm deleted file mode 100644 index d914f2be4d..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -hist_mfilt = 365 -hist_nhtfrq = -24 From 2275289c8353ed7179cbfc044de01aefbfb2363d Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Mon, 15 Aug 2022 14:22:56 -0600 Subject: [PATCH 0298/2067] add back fates_sp user mods call --- .../FatesColdDefDryDepReducedComplexSatPhen/include_user_mods | 1 + .../clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods | 1 + 2 files changed, 2 insertions(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods index 5da4a19a83..1dedc9c91a 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods @@ -1 +1,2 @@ ../FatesColdDefDryDep +../../../../usermods_dirs/fates_sp diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods index 254ddd9b2d..3dc812ba0d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods @@ -1 +1,2 @@ ../FatesColdDefMegan +../../../../usermods_dirs/fates_sp From b6c239cf93ccb0407aee8398b44aa7b7ed483a24 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 16 Aug 2022 09:05:14 -0600 Subject: [PATCH 0299/2067] changed order of include mods --- .../FatesColdDefDryDepReducedComplexSatPhen/include_user_mods | 2 +- .../FatesColdDefMeganReducedComplexSatPhen/include_user_mods | 3 ++- .../clm/FatesColdDefReducedComplexSatPhen/include_user_mods | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods index 1dedc9c91a..c1089d7c1d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods @@ -1,2 +1,2 @@ -../FatesColdDefDryDep ../../../../usermods_dirs/fates_sp +../FatesColdDefDryDep diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods index 3dc812ba0d..879292df14 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods @@ -1,2 +1,3 @@ -../FatesColdDefMegan ../../../../usermods_dirs/fates_sp +../FatesColdDefMegan + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods index 303343e726..c58ea8b03f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods @@ -1,3 +1,4 @@ -../FatesColdDef ../../../../usermods_dirs/fates_sp +../FatesColdDef + From 695ee136d84f2b286538344b1d55ce9ff1053cad Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Wed, 24 Aug 2022 08:49:19 -0600 Subject: [PATCH 0300/2067] update for DAMP --- .../FatesColdDefDryDepReducedComplexSatPhen/include_user_mods | 3 +-- .../FatesColdDefDryDepReducedComplexSatPhen/shell_commands | 3 +++ .../clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm | 4 ++++ .../FatesColdDefMeganReducedComplexSatPhen/include_user_mods | 4 +--- .../clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands | 2 ++ .../clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm | 4 ++++ .../clm/FatesColdDefReducedComplexSatPhen/include_user_mods | 3 +-- .../clm/FatesColdDefReducedComplexSatPhen/user_nl_clm | 4 ++++ 8 files changed, 20 insertions(+), 7 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods index c1089d7c1d..2ae840b59f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods @@ -1,2 +1 @@ -../../../../usermods_dirs/fates_sp -../FatesColdDefDryDep +../FatesColdDefBasic diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands new file mode 100644 index 0000000000..870cd99bf5 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands @@ -0,0 +1,3 @@ +./xmlchange CLM_BLDNML_OPTS='--drydep' --append +# The following would be required if you want to run with DryDep and FATES without Fates-SP mode +#./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm new file mode 100644 index 0000000000..3749fd1d61 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm @@ -0,0 +1,4 @@ + +hist_mfilt = 365 +hist_nhtfrq = -24 + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods index 879292df14..2ae840b59f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods @@ -1,3 +1 @@ -../../../../usermods_dirs/fates_sp -../FatesColdDefMegan - +../FatesColdDefBasic diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands new file mode 100644 index 0000000000..749af3486f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands @@ -0,0 +1,2 @@ +./xmlchange CLM_BLDNML_OPTS='--megan' --append +./xmlchange CLM_BLDNML_OPTS="--ignore_warnings" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm new file mode 100644 index 0000000000..3749fd1d61 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm @@ -0,0 +1,4 @@ + +hist_mfilt = 365 +hist_nhtfrq = -24 + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods index c58ea8b03f..e9cade6bdf 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods @@ -1,4 +1,3 @@ -../../../../usermods_dirs/fates_sp -../FatesColdDef +../FatesColdDefBasic diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm new file mode 100644 index 0000000000..3749fd1d61 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm @@ -0,0 +1,4 @@ + +hist_mfilt = 365 +hist_nhtfrq = -24 + From d255bf6297bb966f7e38326705bb7963d50f6a9e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 31 Aug 2022 08:41:51 -0600 Subject: [PATCH 0301/2067] Now calls cropcal_interp() with filter_inactive_and_active instead of filter. --- src/main/clm_driver.F90 | 2 +- src/main/clm_initializeMod.F90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index fd53fbaab4..de8a53963e 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1042,7 +1042,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! ============================================================================ ! Update crop calendars ! ============================================================================ - call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) + call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, filter_inactive_and_active(nc)%pcropp, crop_inst) ! write(iulog,*) 'Exited cropcal_interp() in clm_drv()' end if diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 45511d6869..89a4ae0c95 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -572,7 +572,7 @@ subroutine initialize2(ni,nj) !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) - call cropcal_interp(bounds_clump, filter(nc)%num_pcropp, filter(nc)%pcropp, crop_inst) + call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, filter_inactive_and_active(nc)%pcropp, crop_inst) ! write(iulog,*) 'Exited cropcal_interp() in initialize2()' end do !$OMP END PARALLEL DO From f6727f257d7f4562ab278df661feaa4fad6b7a2d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 12 Sep 2022 15:55:26 -0700 Subject: [PATCH 0302/2067] add nocomp+fbg test and 12 month ERS fates tests --- cime_config/testdefs/testlist_clm.xml | 26 ++++++++++++++++++- .../include_user_mods | 1 + .../user_nl_clm | 1 + 3 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index dedf27350e..5b4fdc0fca 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1851,6 +1851,22 @@ + + + + + + + + + + + + + + + + @@ -2252,7 +2268,7 @@ - + @@ -2261,6 +2277,14 @@ + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods new file mode 100644 index 0000000000..0f57156bed --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods @@ -0,0 +1 @@ +../FatesColdDefReducedComplexNoComp \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/user_nl_clm new file mode 100644 index 0000000000..d3349780e0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/user_nl_clm @@ -0,0 +1 @@ +use_fates_fixed_biogeog=.true. \ No newline at end of file From f951f8c2f1ac4e26b37bba6271956609950bc2cc Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 13 Sep 2022 09:40:33 -0700 Subject: [PATCH 0303/2067] update 12 month to 13 month to catch potential start of year clm interactions --- cime_config/testdefs/testlist_clm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 5b4fdc0fca..7295ac91d0 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1851,7 +1851,7 @@ - + @@ -1859,7 +1859,7 @@ - + From c0d8e08ad8c679e3a18acf9b4ebb868401063a94 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 15 Sep 2022 10:56:44 -0700 Subject: [PATCH 0304/2067] rename Fates tests to truncate length --- cime_config/testdefs/testlist_clm.xml | 104 +++++++++--------- .../include_user_mods | 0 .../shell_commands | 0 .../shell_commands | 0 .../user_nl_clm | 0 .../README | 0 .../clm/FatesColdCH4Off/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdDefCH4Off/include_user_mods | 1 - .../clm/FatesColdDefDryDep/include_user_mods | 1 - .../include_user_mods | 2 - .../clm/FatesColdDefHydro/include_user_mods | 1 - .../clm/FatesColdDefLandUse/include_user_mods | 1 - .../clm/FatesColdDefLogging/include_user_mods | 1 - .../clm/FatesColdDefMegan/include_user_mods | 1 - .../include_user_mods | 2 - .../clm/FatesColdDefNoFire/include_user_mods | 1 - .../clm/FatesColdDefPPhys/include_user_mods | 1 - .../clm/FatesColdDefPRT2/include_user_mods | 1 - .../include_user_mods | 1 - .../include_user_mods | 1 - .../include_user_mods | 1 - .../include_user_mods | 2 - .../clm/FatesColdDefST3/include_user_mods | 1 - .../FatesColdDefSizeAgeMort/include_user_mods | 1 - .../FatesColdDefTreeDamage/include_user_mods | 1 - .../clm/FatesColdDryDep/include_user_mods | 1 + .../shell_commands | 0 .../FatesColdDryDepSatPhen/include_user_mods | 2 + .../FatesColdFixedBiogeo/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdHydro/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdLandUse/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdLogging/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdMegan/include_user_mods | 1 + .../shell_commands | 0 .../FatesColdMeganSatPhen/include_user_mods | 2 + .../clm/FatesColdNoComp/include_user_mods | 1 + .../user_nl_clm | 0 .../include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdNoFire/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdPPhys/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdPRT2/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdST3/include_user_mods | 1 + .../user_nl_clm | 0 .../include_user_mods | 2 +- .../user_nl_clm | 0 .../README | 0 .../include_user_mods | 2 + .../FatesColdSizeAgeMort/include_user_mods | 1 + .../user_nl_clm | 0 .../clm/FatesColdTreeDamage/include_user_mods | 1 + .../user_nl_clm | 0 60 files changed, 74 insertions(+), 74 deletions(-) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDef => FatesCold}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDef => FatesCold}/shell_commands (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefAllVars => FatesColdAllVars}/shell_commands (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefAllVars => FatesColdAllVars}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefCH4Off => FatesColdCH4Off}/README (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefCH4Off => FatesColdCH4Off}/user_nl_clm (100%) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefHydro/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefLandUse/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefLogging/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefNoFire/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefPPhys/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefPRT2/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexFixedBiogeo/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoComp/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen_prescribed/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefST3/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefSizeAgeMort/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDryDep/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefDryDep => FatesColdDryDep}/shell_commands (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdFixedBiogeo/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefReducedComplexFixedBiogeo => FatesColdFixedBiogeo}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefHydro => FatesColdHydro}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefLandUse => FatesColdLandUse}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefLogging => FatesColdLogging}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdMegan/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefMegan => FatesColdMegan}/shell_commands (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdNoComp/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefReducedComplexNoComp => FatesColdNoComp}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefReducedComplexNoCompFbg => FatesColdNoCompFixedBioGeo}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdNoFire/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefNoFire => FatesColdNoFire}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdPPhys/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefPPhys => FatesColdPPhys}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefPRT2 => FatesColdPRT2}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdST3/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefST3 => FatesColdST3}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefReducedComplexSatPhen => FatesColdSatPhen}/include_user_mods (68%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefReducedComplexSatPhen => FatesColdSatPhen}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefReducedComplexSatPhen_prescribed => FatesColdSatPhen_prescribed}/README (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSizeAgeMort/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefSizeAgeMort => FatesColdSizeAgeMort}/user_nl_clm (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTreeDamage/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefTreeDamage => FatesColdTreeDamage}/user_nl_clm (100%) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 7295ac91d0..7a603ea4c7 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1288,7 +1288,7 @@ - + @@ -1805,7 +1805,7 @@ - + @@ -1814,7 +1814,7 @@ - + @@ -1823,7 +1823,7 @@ - + @@ -1832,16 +1832,16 @@ - + - + - + @@ -1851,7 +1851,7 @@ - + @@ -1859,7 +1859,7 @@ - + @@ -1867,7 +1867,7 @@ - + @@ -1876,7 +1876,7 @@ - + @@ -1885,7 +1885,7 @@ - + @@ -1894,7 +1894,7 @@ - + @@ -1903,7 +1903,7 @@ - + @@ -1912,7 +1912,7 @@ - + @@ -1921,7 +1921,7 @@ - + @@ -1929,7 +1929,7 @@ - + @@ -1940,7 +1940,7 @@ - + @@ -1948,7 +1948,7 @@ - + @@ -1957,7 +1957,7 @@ - + @@ -1967,7 +1967,7 @@ - + @@ -1977,7 +1977,7 @@ - + @@ -1987,7 +1987,7 @@ - + @@ -1996,7 +1996,7 @@ - + @@ -2086,7 +2086,7 @@ - + @@ -2095,7 +2095,7 @@ - + @@ -2104,7 +2104,7 @@ - + @@ -2114,7 +2114,7 @@ - + @@ -2124,7 +2124,7 @@ - + @@ -2135,7 +2135,7 @@ - + @@ -2145,7 +2145,7 @@ - + @@ -2166,7 +2166,7 @@ - + @@ -2177,7 +2177,7 @@ - + @@ -2188,7 +2188,7 @@ - + @@ -2199,7 +2199,7 @@ - + @@ -2210,7 +2210,7 @@ - + @@ -2230,7 +2230,7 @@ - + @@ -2240,7 +2240,7 @@ - + @@ -2250,7 +2250,7 @@ - + @@ -2259,7 +2259,7 @@ - + @@ -2268,7 +2268,7 @@ - + @@ -2277,7 +2277,7 @@ - + @@ -2285,7 +2285,7 @@ - + @@ -2294,7 +2294,7 @@ - + @@ -2303,7 +2303,7 @@ - + @@ -2313,7 +2313,7 @@ - + @@ -2332,7 +2332,7 @@ - + @@ -2342,7 +2342,7 @@ - + @@ -2352,7 +2352,7 @@ - + @@ -2361,7 +2361,7 @@ - + @@ -2381,7 +2381,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesCold/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDef/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesCold/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDef/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesCold/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDef/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesCold/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/README similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/README rename to cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/README diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefCH4Off/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods deleted file mode 100644 index f754dacdab..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../FatesColdDefDryDep -../FatesColdDefReducedComplexSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefHydro/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefHydro/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefHydro/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLandUse/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLandUse/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLandUse/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLogging/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLogging/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLogging/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods deleted file mode 100644 index 5dd78011ec..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../FatesColdDefMegan -../FatesColdDefReducedComplexSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefNoFire/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefNoFire/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefNoFire/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPPhys/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPPhys/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPPhys/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPRT2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPRT2/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPRT2/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexFixedBiogeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexFixedBiogeo/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexFixedBiogeo/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoComp/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoComp/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoComp/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods deleted file mode 100644 index 0f57156bed..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDefReducedComplexNoComp \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen_prescribed/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen_prescribed/include_user_mods deleted file mode 100644 index 7fe9b048d5..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen_prescribed/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../FatesColdDefReducedComplexSatPhen -../prescribed diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefST3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefST3/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefST3/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefSizeAgeMort/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefSizeAgeMort/include_user_mods deleted file mode 100644 index 1f2c03aebe..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefSizeAgeMort/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/include_user_mods deleted file mode 100644 index e269feea6f..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../FatesColdDef \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDep/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDep/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDep/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDep/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDep/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesColdDryDep/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods new file mode 100644 index 0000000000..e6d79d4f42 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods @@ -0,0 +1,2 @@ +../FatesColdDryDep +../FatesColdSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdFixedBiogeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdFixedBiogeo/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdFixedBiogeo/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexFixedBiogeo/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdFixedBiogeo/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexFixedBiogeo/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdFixedBiogeo/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefHydro/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefHydro/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLandUse/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefLandUse/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLandUse/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefLogging/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefLogging/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdLogging/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdMegan/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdMegan/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdMegan/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdMegan/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefMegan/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesColdMegan/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods new file mode 100644 index 0000000000..a5e045e6c4 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods @@ -0,0 +1,2 @@ +../FatesColdMegan +../FatesColdSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoComp/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoComp/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoComp/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoComp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoComp/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoComp/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdNoComp/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods new file mode 100644 index 0000000000..c05af30988 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods @@ -0,0 +1 @@ +../FatesColdComplexNoComp \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexNoCompFbg/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoFire/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoFire/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoFire/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefNoFire/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoFire/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefNoFire/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdNoFire/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdPPhys/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdPPhys/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdPPhys/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPPhys/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdPPhys/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefPPhys/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdPPhys/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefPRT2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefPRT2/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefST3/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefST3/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdST3/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods similarity index 68% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods index a38be35f63..01997d411c 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods @@ -1,2 +1,2 @@ -../FatesColdDef +../FatesCold ../../../../usermods_dirs/fates_sp diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen_prescribed/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefReducedComplexSatPhen_prescribed/README rename to cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods new file mode 100644 index 0000000000..d111d05911 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods @@ -0,0 +1,2 @@ +../FatesColdSatPhen +../prescribed diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSizeAgeMort/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdSizeAgeMort/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSizeAgeMort/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefSizeAgeMort/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSizeAgeMort/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefSizeAgeMort/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdSizeAgeMort/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTreeDamage/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdTreeDamage/include_user_mods new file mode 100644 index 0000000000..5417dbaa1c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTreeDamage/include_user_mods @@ -0,0 +1 @@ +../FatesCold \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdTreeDamage/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefTreeDamage/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdTreeDamage/user_nl_clm From d37cb522c220717d2a5cd0b000662e74cd432215 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 16 Sep 2022 13:51:39 -0700 Subject: [PATCH 0305/2067] remove duplicate satellite phenology test mods --- .../testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods | 2 -- .../testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods | 2 -- 2 files changed, 4 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods deleted file mode 100644 index e6d79d4f42..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../FatesColdDryDep -../FatesColdSatPhen diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods deleted file mode 100644 index a5e045e6c4..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../FatesColdMegan -../FatesColdSatPhen From 4d9023799cbb5145a229e6261ecad8601f772ee0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 16 Sep 2022 13:53:43 -0700 Subject: [PATCH 0306/2067] rename FatesColdDefBasic everywhere --- cime_config/testdefs/testlist_clm.xml | 2 +- .../clm/{FatesColdDefBasic => FatesColdBasic}/shell_commands | 0 .../FatesColdDefDryDepReducedComplexSatPhen/include_user_mods | 2 +- .../FatesColdDefMeganReducedComplexSatPhen/include_user_mods | 2 +- .../testmods_dirs/clm/FatesColdSatPhen/include_user_mods | 2 +- 5 files changed, 4 insertions(+), 4 deletions(-) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefBasic => FatesColdBasic}/shell_commands (100%) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 1ea15b5471..f9426f8a2a 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2323,7 +2323,7 @@ --> - + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdBasic/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefBasic/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesColdBasic/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods index 2ae840b59f..f0a10ab452 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods @@ -1 +1 @@ -../FatesColdDefBasic +../FatesColdBasic diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods index 2ae840b59f..f0a10ab452 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods @@ -1 +1 @@ -../FatesColdDefBasic +../FatesColdBasic diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods index 2ae840b59f..f0a10ab452 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen/include_user_mods @@ -1 +1 @@ -../FatesColdDefBasic +../FatesColdBasic From 6567378483df022a3d5f2cf87d4717647377efd1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 16 Sep 2022 13:55:21 -0700 Subject: [PATCH 0307/2067] rename DryDep and Megan satellite phenology testmods --- .../include_user_mods | 0 .../shell_commands | 0 .../user_nl_clm | 0 .../include_user_mods | 0 .../shell_commands | 0 .../user_nl_clm | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefDryDepReducedComplexSatPhen => FatesColdDryDepSatPhen}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefDryDepReducedComplexSatPhen => FatesColdDryDepSatPhen}/shell_commands (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefDryDepReducedComplexSatPhen => FatesColdDryDepSatPhen}/user_nl_clm (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefMeganReducedComplexSatPhen => FatesColdMeganSatPhen}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefMeganReducedComplexSatPhen => FatesColdMeganSatPhen}/shell_commands (100%) rename cime_config/testdefs/testmods_dirs/clm/{FatesColdDefMeganReducedComplexSatPhen => FatesColdMeganSatPhen}/user_nl_clm (100%) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefDryDepReducedComplexSatPhen/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdDryDepSatPhen/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/FatesColdDefMeganReducedComplexSatPhen/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/FatesColdMeganSatPhen/user_nl_clm From 992f1135bfdeb935a836d4654bd42d78274de935 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 4 Oct 2022 12:17:05 -0700 Subject: [PATCH 0308/2067] fix included directory name to remove complex word --- .../clm/FatesColdNoCompFixedBioGeo/include_user_mods | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods index c05af30988..ea160c525f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompFixedBioGeo/include_user_mods @@ -1 +1 @@ -../FatesColdComplexNoComp \ No newline at end of file +../FatesColdNoComp \ No newline at end of file From 8a96841a6d1857b4417183e8bc7ec4e88560b6a8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 5 Oct 2022 15:12:16 -0600 Subject: [PATCH 0309/2067] Cleanup. --- src/biogeochem/CNAllocationMod.F90 | 32 +------------------ src/biogeochem/CNNDynamicsMod.F90 | 12 ------- src/biogeochem/CNPhenologyMod.F90 | 42 ------------------------- src/cpl/mct/cropcalStreamMod.F90 | 23 +++----------- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 +-- 5 files changed, 6 insertions(+), 107 deletions(-) diff --git a/src/biogeochem/CNAllocationMod.F90 b/src/biogeochem/CNAllocationMod.F90 index 8fd8d3257a..4478273bde 100644 --- a/src/biogeochem/CNAllocationMod.F90 +++ b/src/biogeochem/CNAllocationMod.F90 @@ -26,9 +26,6 @@ module CNAllocationMod use CropReprPoolsMod , only : nrepr use CNPhenologyMod , only : CropPhase use CNSharedParamsMod , only : use_fun - ! SSR troubleshooting - use GridcellType , only : grc - use shr_infnan_mod , only : isnan => shr_infnan_isnan, isinf => shr_infnan_isinf ! implicit none private @@ -282,8 +279,6 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & integer :: p, fp, k real(r8) :: fleaf ! fraction allocated to leaf real(r8) :: crop_phase(bounds%begp:bounds%endp) - ! SSR troubleshooting - integer :: g ! Gridcell index character(len=*), parameter :: subname = 'calc_crop_allocation_fractions' !----------------------------------------------------------------------- @@ -309,10 +304,7 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & aleaf => cnveg_state_inst%aleaf_patch , & ! Output: [real(r8) (:) ] leaf allocation coefficient astem => cnveg_state_inst%astem_patch , & ! Output: [real(r8) (:) ] stem allocation coefficient aroot => cnveg_state_inst%aroot_patch , & ! Output: [real(r8) (:) ] root allocation coefficient - arepr => cnveg_state_inst%arepr_patch , & ! Output: [real(r8) (:,:) ] reproductive allocation coefficient(s) - ! SSR troubleshooting - lon => grc%londeg, & - lat => grc%latdeg & + arepr => cnveg_state_inst%arepr_patch & ! Output: [real(r8) (:,:) ] reproductive allocation coefficient(s) ) call CropPhase(bounds, num_pcropp, filter_pcropp, crop_inst, cnveg_state_inst, & @@ -320,8 +312,6 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & do fp = 1, num_pcropp p = filter_pcropp(fp) - ! SSR troubleshooting - g = patch%gridcell(p) if (croplive(p)) then ! same phases appear in subroutine CropPhenology @@ -373,26 +363,6 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) - ! SSR troubleshooting - if (isnan(astemi(p))) then - write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemi NaN' - end if - if (isinf(astemi(p))) then - write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemi Inf' - end if - if (isnan(astemf(ivt(p)))) then - write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemf NaN' - end if - if (isinf(astemf(ivt(p)))) then - write(iulog,'(a,f7.2,a,f7.2,a,i3,a)') 'srts: lon ',lon(g),' lat ',lat(g),' ivt ',ivt(p),': astemf Inf' - end if - if (astemi(p) > astemi(p)) then - write(iulog,*) 'srts: Trying to trigger a crash with this conditional' - end if - if (astemf(ivt(p)) > astemf(ivt(p))) then - write(iulog,*) 'srts: And if not, maybe this one will' - end if - if (astemi(p) > astemf(ivt(p))) then astem(p) = max(0._r8, max(astemf(ivt(p)), astem(p) * & (1._r8 - min((hui(p)- & diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 15b08f4e77..919573937d 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -25,10 +25,6 @@ module CNNDynamicsMod use ColumnType , only : col use PatchType , only : patch use perf_mod , only : t_startf, t_stopf - ! SSR troubleshooting - use abortutils , only : endrun - use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog ! implicit none private @@ -49,9 +45,6 @@ module CNNDynamicsMod end type params_type type(params_type) :: params_inst - ! SSR troubleshooting - character(len=*), parameter, private :: sourcefile = & - __FILE__ !----------------------------------------------------------------------- contains @@ -406,11 +399,6 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & ! for soy) ! Ranges below are not firm. Are they lit. based or tuning based? - ! SSR troubleshooting - if (gddmaturity(p) == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - GDDfrac = hui(p) / gddmaturity(p) if (GDDfrac <= GDDfracthreshold1) then diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 3b08f7d978..725455d3b4 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1853,12 +1853,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & s = sowing_count(p) - ! SSR troubleshooting - if (s<0) then - write(iulog,*) 'CropPhenology(): s < 0' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - ! Get next sowing date if (s < mxsowings) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,s+1) @@ -2226,12 +2220,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & onset_counter(p) = dt fert_counter(p) = ndays_on * secspday if (ndays_on .gt. 0) then - - ! SSR troubleshooting - if (fert_counter(p)==0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - fert(p) = (manunitro(ivt(p)) * 1000._r8 + fertnitro(p))/ fert_counter(p) else fert(p) = 0._r8 @@ -2283,11 +2271,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_seedn_to_leaf(p) = crop_seedn_to_leaf(p) - leafn_xfer(p)/dt leafc_xfer(p) = 0._r8 - ! SSR troubleshooting - if (leafcn(ivt(p)) == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - leafn_xfer(p) = leafc_xfer(p) / leafcn(ivt(p)) if (use_c13) then c13_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8 @@ -2306,12 +2289,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (hui(p) >= huigrain(p) .and. cphase(p) >= cphase_leafemerge) then cphase(p) = cphase_grainfill - - ! SSR troubleshooting - if (leaf_long(ivt(p))*dayspyr*secspday == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - bglfr(p) = 1._r8/(leaf_long(ivt(p))*avg_dayspyr*secspday) else cphase(p) = cphase_planted @@ -2336,12 +2313,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_seedn_to_leaf(p) = crop_seedn_to_leaf(p) - leafn_xfer(p)/dt onset_counter(p) = 0._r8 leafc_xfer(p) = 0._r8 - - ! SSR troubleshooting - if (leafcn(ivt(p)) == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - leafn_xfer(p) = leafc_xfer(p) / leafcn(ivt(p)) if (use_c13) then c13_cnveg_carbonstate_inst%leafc_xfer_patch(p) = 0._r8 @@ -2563,14 +2534,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & harvdate(p) = NOT_Harvested s = sowing_count(p) + 1 - ! SSR troubleshooting - if (s < 1) then - write(iulog,*) 'PlantCrop(): s < 1' - call endrun(msg=errMsg(sourcefile, __LINE__)) - else if (s > mxsowings) then - write(iulog,*) 'PlantCrop(): s > mxsowings' - end if - sowing_count(p) = s if (s < mxsowings) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, s+1) @@ -2590,11 +2553,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & end if sowing_reason(p,s) = this_sowing_reason - ! SSR troubleshooting - if (leafcn_in == 0.0) then - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if - this_sowing_reason = 0._r8 if (do_plant_normal) then this_sowing_reason = this_sowing_reason + 1._r8 diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 index af99c4a9ec..0f330312f4 100644 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ b/src/cpl/mct/cropcalStreamMod.F90 @@ -18,7 +18,6 @@ module cropcalStreamMod use spmdMod , only : masterproc, mpicom, comp_id use ncdio_pio use mct_mod -! use GridcellType , only : grc ! SSR troubleshooting ! ! !PUBLIC TYPES: implicit none @@ -31,7 +30,6 @@ module cropcalStreamMod ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - ! SSR TODO: Make this work with mxsowings > 1 type(shr_strdata_type) :: sdat_sdate ! sowing date input data stream type(shr_strdata_type) :: sdat_cultivar_gdds ! cultivar growing-degree days stream @@ -76,7 +74,6 @@ subroutine cropcal_init(bounds) character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm - ! SSR TODO: Make this work with mxsowings > 1 character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates character(len=CXX) :: fldList_cultivar_gdds1 ! field string for 1st cultivar GDD targets @@ -132,7 +129,7 @@ subroutine cropcal_init(bounds) call clm_domain_mct (bounds, dom_clm) ! create the field list for these cropcal fields...use in shr_strdata_create - ! SSR TODO: Make this work with mxsowings > 1 + ! Will need modification to work with mxsowings > 1 fldList_sdate1 = shr_string_listCreateField( cft_ub, "sdate1", cft_lb ) fldList_cultivar_gdds1 = shr_string_listCreateField( cft_ub, "gdd1", cft_lb ) @@ -225,7 +222,7 @@ subroutine cropcal_advance( bounds ) call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day - ! SSR TODO: Make this work with mxsowings > 1 + ! Will need modification to work with mxsowings > 1 call shr_strdata_advance(sdat_sdate, mcdate, sec, mpicom, 'cropcaldyn') call shr_strdata_advance(sdat_cultivar_gdds, mcdate, sec, mpicom, 'cropcaldyn') @@ -251,7 +248,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use PatchType , only : patch use filterMod , only : filter use decompMod , only : get_proc_clumps -! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: implicit none @@ -263,24 +259,19 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig integer :: nc, fp -! integer :: yr, mon, day, tod, ymd, c, g ! SSR troubleshooting character(len=CL) :: stream_var_name_sdate1 character(len=CL) :: stream_var_name_cultivar_gdds1 !----------------------------------------------------------------------- SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - ! SSR TODO: Make this work with mxsowings > 1 + ! Will need modification to work with mxsowings > 1 SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (lbound(sdat_cultivar_gdds%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(sdat_cultivar_gdds%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - ! SSR troubleshooting -! call get_curr_date( yr, mon, day, tod ) -! ymd = yr*10000 + mon*100 + day - - ! SSR TODO: Make this work with mxsowings > 1 + ! Will need modification to work with mxsowings > 1 do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -288,7 +279,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) write(stream_var_name_sdate1,"(i6)") ivt write(stream_var_name_cultivar_gdds1,"(i6)") ivt - ! SSR TODO: Add check that variable exists in netCDF stream_var_name_sdate1 = 'sdate1_'//trim(adjustl(stream_var_name_sdate1)) ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name_sdate1)) if (ivt /= noveg) then @@ -296,7 +286,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) endif - ! SSR TODO: Add check that variable exists in netCDF stream_var_name_cultivar_gdds1 = 'gdd1_'//trim(adjustl(stream_var_name_cultivar_gdds1)) ip = mct_aVect_indexRA(sdat_cultivar_gdds%avs(1),trim(stream_var_name_cultivar_gdds1)) if (ivt /= noveg) then @@ -306,10 +295,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Only for first sowing date of the year crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) -! ! SSR troubleshooting -! c = patch%column(p) -! g = patch%gridcell(p) -! write(iulog,'(I8,A,F8.3,A,F8.3,A,I4,A,I7)') ymd,' (',grc%londeg(g),',',grc%latdeg(g),') crop ',ivt,' read rx_sdate ',crop_inst%rx_sdates_thisyr(p,1) end do diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index d82c20b6a7..63a12a8b59 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -91,7 +91,7 @@ subroutine cropcal_init(bounds) stream_meshfile_cropcal = '' stream_fldFileName_sdate = '' stream_fldFileName_cultivar_gdds = '' - ! SSR TODO: Make below work with arbitrary # of growing seasons per year + ! Will need modification to work with mxsowings > 1 ncft = mxpft - npcropmin + 1 ! Ignores generic crops allocate(stream_varnames_sdate(ncft)) allocate(stream_varnames_cultivar_gdds(ncft)) @@ -255,7 +255,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use CropType , only : crop_type use PatchType , only : patch use dshr_methods_mod , only : dshr_fldbun_getfldptr -! use clm_time_manager , only : get_curr_date ! SSR troubleshooting ! ! !ARGUMENTS: implicit none @@ -267,7 +266,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig integer :: nc, fp -! integer :: yr, mon, day, tod, ymd, c, g ! SSR troubleshooting integer :: n, g integer :: lsize integer :: rc From b5d9ddb2a82b3c7d7cab4abce420be6288e362df Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 5 Oct 2022 15:23:18 -0600 Subject: [PATCH 0310/2067] More cleanup. --- src/biogeochem/CNAllocationMod.F90 | 1 - src/biogeochem/CNNDynamicsMod.F90 | 5 ----- src/biogeochem/CNPhenologyMod.F90 | 2 +- src/biogeochem/CNRootDynMod.F90 | 5 ----- src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 | 8 -------- src/main/subgridAveMod.F90 | 2 +- src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 | 4 ---- src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 | 4 ---- 8 files changed, 2 insertions(+), 29 deletions(-) diff --git a/src/biogeochem/CNAllocationMod.F90 b/src/biogeochem/CNAllocationMod.F90 index 4478273bde..ef646511f1 100644 --- a/src/biogeochem/CNAllocationMod.F90 +++ b/src/biogeochem/CNAllocationMod.F90 @@ -362,7 +362,6 @@ subroutine calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & else if (crop_phase(p) == cphase_grainfill) then aroot(p) = max(0._r8, min(1._r8, arooti(ivt(p)) - & (arooti(ivt(p)) - arootf(ivt(p))) * min(1._r8, hui(p)/gddmaturity(p)))) - if (astemi(p) > astemf(ivt(p))) then astem(p) = max(0._r8, max(astemf(ivt(p)), astem(p) * & (1._r8 - min((hui(p)- & diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 919573937d..a658a63768 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -44,7 +44,6 @@ module CNNDynamicsMod real(r8) :: freelivfix_slope_wET ! slope of line of free living fixation with annual ET end type params_type type(params_type) :: params_inst - !----------------------------------------------------------------------- contains @@ -331,8 +330,6 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & real(r8):: GDDfracthreshold3, GDDfracthreshold4 !----------------------------------------------------------------------- -! write(iulog,*) 'Entering CNSoyfix()' - associate( & wf => waterdiagnosticbulk_inst%wf_col , & ! Input: [real(r8) (:) ] soil water as frac. of whc for top 0.5 m @@ -439,8 +436,6 @@ subroutine CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & end associate -! write(iulog,*) 'Exiting CNSoyfix()' - end subroutine CNSoyfix end module CNNDynamicsMod diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 725455d3b4..2b494afa15 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1750,6 +1750,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & a10tmin => temperature_inst%t_a10min_patch , & ! Input: [real(r8) (:) ] 10-day running mean of min 2-m temperature gdd020 => temperature_inst%gdd020_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd0 gdd820 => temperature_inst%gdd820_patch , & ! Input: [real(r8) (:) ] 20 yr mean of gdd8 + fertnitro => crop_inst%fertnitro_patch , & ! Input: [real(r8) (:) ] fertilizer nitrogen hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature @@ -2478,7 +2479,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & use pftconMod , only : nirrig_trp_corn, nirrig_sugarcane, nirrig_trp_soybean use pftconMod , only : nirrig_cotton, nirrig_rice use pftconMod , only : nmiscanthus, nirrig_miscanthus, nswitchgrass, nirrig_switchgrass - ! ! !ARGUMENTS: integer , intent(in) :: p ! PATCH index running over diff --git a/src/biogeochem/CNRootDynMod.F90 b/src/biogeochem/CNRootDynMod.F90 index 09f03dc20e..3f43424cfa 100644 --- a/src/biogeochem/CNRootDynMod.F90 +++ b/src/biogeochem/CNRootDynMod.F90 @@ -22,7 +22,6 @@ module CNRootDynMod use SoilStateType , only : soilstate_type use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use CropType , only : crop_type - use clm_varctl , only : iulog ! !PUBLIC TYPES: implicit none @@ -102,8 +101,6 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & croplive => crop_inst%croplive_patch , & ! Input: [logical (:)] flag, true if planted, not harvested huigrain => cnveg_state_inst%huigrain_patch & ! Input: [real(r8) (:)] same to reach vegetative maturity ) - -! write(iulog,*)'Entering CNRootDyn()' ! set time steps dt = get_step_size_real() @@ -269,8 +266,6 @@ subroutine CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & end associate -! write(iulog,*)'Exiting CNRootDyn()' - end subroutine CNRootDyn end module CNRootDynMod diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index 1e52314c90..2133d010aa 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -247,8 +247,6 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & ! ----------------------------------------------------------------------- -! write(iulog,*) 'Entering calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' - SHR_ASSERT_ALL_FL((ubound(fpg_col) == (/bounds%endc/)) , sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(this%actual_storage_leafcn) >= (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((lbound(this%actual_storage_leafcn) <= (/bounds%begp/)), sourcefile, __LINE__) @@ -731,8 +729,6 @@ subroutine calc_plant_cn_alloc(this, bounds, num_soilp, filter_soilp, & end associate -! write(iulog,*) 'Exiting calc_plant_cn_alloc() (NutrientCompetitionFlexibleCNMod.F90)' - end subroutine calc_plant_cn_alloc !----------------------------------------------------------------------- @@ -1250,8 +1246,6 @@ subroutine calc_plant_nitrogen_demand(this, bounds, & character(len=*), parameter :: subname = "calc_plant_nitrogen_demand" ! ----------------------------------------------------------------------- -! write(iulog,*) 'Entering calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' - SHR_ASSERT_ALL_FL((ubound(this%actual_leafcn) >= (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((lbound(this%actual_leafcn) <= (/bounds%begp/)), sourcefile, __LINE__) @@ -1471,8 +1465,6 @@ subroutine calc_plant_nitrogen_demand(this, bounds, & end associate -! write(iulog,*) 'Exiting calc_plant_nitrogen_demand() (NutrientCompetitionFlexibleCNMod.F90)' - end subroutine calc_plant_nitrogen_demand end module NutrientCompetitionFlexibleCNMod diff --git a/src/main/subgridAveMod.F90 b/src/main/subgridAveMod.F90 index 5b592e5c09..c5ce4a4a98 100644 --- a/src/main/subgridAveMod.F90 +++ b/src/main/subgridAveMod.F90 @@ -240,7 +240,7 @@ subroutine p2c_1d_filter (bounds, numfc, filterc, patcharr, colarr) ! !LOCAL VARIABLES: integer :: fc,c,p ! indices !----------------------------------------------------------------------- - + ! Enforce expected array sizes SHR_ASSERT_ALL_FL((ubound(patcharr) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(colarr) == (/bounds%endc/)), sourcefile, __LINE__) diff --git a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 index 48c64a3b82..3d99d93755 100644 --- a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 @@ -48,8 +48,6 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & !----------------------------------------------------------------------- -! write(iulog,*)'Entering SoilBiogeochemNStateUpdate1()' - associate( & cascade_donor_pool => decomp_cascade_con%cascade_donor_pool , & ! Input: [integer (:) ] which pool is C taken from for a given decomposition step cascade_receiver_pool => decomp_cascade_con%cascade_receiver_pool , & ! Input: [integer (:) ] which pool is C added to for a given decomposition step @@ -263,8 +261,6 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & end associate -! write(iulog,*)'Exiting SoilBiogeochemNStateUpdate1()' - end subroutine SoilBiogeochemNStateUpdate1 end module SoilBiogeochemNStateUpdate1Mod diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index 6e00292bad..da5e2d4240 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -962,8 +962,6 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda character(len=*), parameter :: subname = 'DynamicColumnAdjustments' !----------------------------------------------------------------------- -! write(iulog,*)'Entering DynamicColumnAdjustments()' - begc = bounds%begc endc = bounds%endc @@ -1031,8 +1029,6 @@ subroutine DynamicColumnAdjustments(this, bounds, clump_index, column_state_upda end if -! write(iulog,*)'Exiting DynamicColumnAdjustments()' - end subroutine DynamicColumnAdjustments !------------------------------------------------------------------------ From a59d3ee9cde4b9285749aa1d1d51e596ea3da12f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Oct 2022 11:46:21 -0600 Subject: [PATCH 0311/2067] use_cropcal_streams now automatically set instead of in namelist. If files for either prescribed sowing dates or cultivar GDD requirements are specified, use_cropcal_streams will be set to true. This is the beginning of work required for using one or the other of those. --- bld/CLMBuildNamelist.pm | 47 ++--- bld/namelist_files/namelist_defaults_ctsm.xml | 1 - .../namelist_definition_ctsm.xml | 6 - src/biogeochem/CNPhenologyMod.F90 | 12 +- src/cpl/share_esmf/cropcalStreamMod.F90 | 184 ++++++++++-------- src/main/clm_initializeMod.F90 | 6 +- src/main/clm_varctl.F90 | 4 +- 7 files changed, 133 insertions(+), 127 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 84f908ddde..816872110f 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3802,35 +3802,26 @@ sub setup_logic_lai_streams { sub setup_logic_cropcal_streams { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_cropcal_streams'); - - if ( ! &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_cropcal_streams')) ) { - $log->verbose_message("use_crop set to true, so use_cropcal_streams will have no effect."); - } - - if ( &value_is_true($nl->get_value('use_cropcal_streams')) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_cropcal_streams'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal', - 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal', - 'sim_year'=>$nl_flags->{'sim_year'}, + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal', + 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different + if ( $nl->get_value('stream_year_first_cropcal') != + $nl->get_value('stream_year_last_cropcal') ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - # Set align year, if first and last years are different - if ( $nl->get_value('stream_year_first_cropcal') != - $nl->get_value('stream_year_last_cropcal') ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, - 'sim_year_range'=>$nl_flags->{'sim_year_range'}); - } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_sdate', - 'hgrid'=>"360x720cru" ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds', - 'hgrid'=>"360x720cru" ); - if ($opts->{'driver'} eq "nuopc" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal', - 'hgrid'=>"360x720cru" ); - } + } + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_sdate', + 'hgrid'=>"360x720cru" ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds', + 'hgrid'=>"360x720cru" ); + if ($opts->{'driver'} eq "nuopc" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal', + 'hgrid'=>"360x720cru" ); } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 07fd93c7ac..44db890893 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1560,7 +1560,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts nn -.false. 1850 2100 1850 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index c51e57af8a..f9be8ca3a6 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1829,12 +1829,6 @@ Mapping method from LAI input file to the model resolution - -Toggle to turn on use of crop calendar streams in place of CFT-specific sowing windows and harvest criteria. -(EXPERIMENTAL and NOT tested) - - First year to loop over for crop calendar data diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 2b494afa15..e698ca0988 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1684,8 +1684,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & use clm_varcon , only : spval, secspday use clm_varctl , only : use_fertilizer use clm_varctl , only : use_c13, use_c14 - use clm_varctl , only : use_cropcal_streams use clm_varcon , only : c13ratio, c14ratio + use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds, use_cropcal_streams ! ! !ARGUMENTS: integer , intent(in) :: num_pcropp ! number of prog crop patches in filter @@ -1907,7 +1907,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing dates at all, or if this cell had no values in the prescribed sowing ! date file. - allow_unprescribed_planting = (.not. use_cropcal_streams) .or. crop_inst%rx_sdates_thisyr(p,1)<0 + allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr(p,1)<0 ! winter temperate cereal : use gdd0 as a limit to plant winter cereal @@ -2108,13 +2108,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & force_harvest = .false. fake_harvest = .false. sown_today = .false. - if (use_cropcal_streams .and. s > 0) then + if (use_cropcal_rx_sdates .and. s > 0) then sown_today = crop_inst%sdates_thisyr(p,s) == real(jday, r8) end if ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. mxmat = pftcon%mxmat(ivt(p)) - if (use_cropcal_streams .and. .not. generate_crop_gdds) then + if (use_cropcal_rx_cultivar_gdds) then mxmat = 999 end if @@ -2132,8 +2132,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! If generate_crop_gdds and this patch has prescribed sowing inputs else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr(p,1) .gt. 0) then - if (.not. use_cropcal_streams) then - write(iulog,*) 'If using generate_crop_gdds, you must set use_cropcal_streams to true.' + if (.not. use_cropcal_rx_sdates) then + write(iulog,*) 'If using generate_crop_gdds, you must specify stream_fldFileName_sdate' call endrun(msg=errMsg(sourcefile, __LINE__)) endif if (next_rx_sdate(p) >= 0) then diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 63a12a8b59..b604b3f917 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -13,6 +13,7 @@ module cropcalStreamMod use decompMod , only : bounds_type use abortutils , only : endrun use clm_varctl , only : iulog + use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds, use_cropcal_streams use clm_varpar , only : mxpft use perf_mod , only : t_startf, t_stopf use spmdMod , only : masterproc, mpicom, iam @@ -28,6 +29,11 @@ module cropcalStreamMod public :: cropcal_advance ! Advance the crop calendar streams (outside of a Open-MP threading loop) public :: cropcal_interp ! interpolates between two years of crop calendar data +! ! !PUBLIC MEMBER DATA +! logical, public, save :: use_cropcal_rx_sdates = .false. +! logical, public, save :: use_cropcal_rx_cultivar_gdds = .false. +! logical, public, save :: use_cropcal_streams = .false. + ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream @@ -35,6 +41,8 @@ module cropcalStreamMod character(len=CS), allocatable :: stream_varnames_sdate(:) character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:) integer :: ncft ! Number of crop functional types (excl. generic crops) + character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read + character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read character(len=*), parameter :: sourcefile = & __FILE__ @@ -64,8 +72,6 @@ subroutine cropcal_init(bounds) integer :: model_year_align_cropcal ! align stream_year_first_cropcal with integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag - character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read - character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read character(len=CL) :: stream_meshfile_cropcal ! crop calendar stream meshfile character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm @@ -138,34 +144,44 @@ subroutine cropcal_init(bounds) write(iulog,*) endif + use_cropcal_rx_sdates = stream_fldFileName_sdate /= '' + use_cropcal_rx_cultivar_gdds = stream_fldFileName_cultivar_gdds /= '' + if (use_cropcal_rx_cultivar_gdds .and. generate_crop_gdds) then + write(iulog,*) 'Do not specify both generate_crop_gdds=.true. and stream_fldFileName_cultivar_gdds' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + use_cropcal_streams = use_cropcal_rx_sdates .or. use_cropcal_rx_cultivar_gdds + ! Initialize the cdeps data type sdat_cropcal_sdate - call shr_strdata_init_from_inline(sdat_cropcal_sdate, & - my_task = iam, & - logunit = iulog, & - compname = 'LND', & - model_clock = model_clock, & - model_mesh = mesh, & - stream_meshfile = trim(stream_meshfile_cropcal), & - stream_lev_dimname = 'null', & - stream_mapalgo = trim(cropcal_mapalgo), & - stream_filenames = (/trim(stream_fldFileName_sdate)/), & - stream_fldlistFile = stream_varnames_sdate, & - stream_fldListModel = stream_varnames_sdate, & - stream_yearFirst = stream_year_first_cropcal, & - stream_yearLast = stream_year_last_cropcal, & - stream_yearAlign = model_year_align_cropcal, & - stream_offset = cropcal_offset, & - stream_taxmode = 'cycle', & - stream_dtlimit = 1.5_r8, & - stream_tintalgo = cropcal_tintalgo, & - stream_name = 'sowing date data', & - rc = rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) + if (use_cropcal_rx_sdates) then + call shr_strdata_init_from_inline(sdat_cropcal_sdate, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = trim(stream_meshfile_cropcal), & + stream_lev_dimname = 'null', & + stream_mapalgo = trim(cropcal_mapalgo), & + stream_filenames = (/trim(stream_fldFileName_sdate)/), & + stream_fldlistFile = stream_varnames_sdate, & + stream_fldListModel = stream_varnames_sdate, & + stream_yearFirst = stream_year_first_cropcal, & + stream_yearLast = stream_year_last_cropcal, & + stream_yearAlign = model_year_align_cropcal, & + stream_offset = cropcal_offset, & + stream_taxmode = 'cycle', & + stream_dtlimit = 1.5_r8, & + stream_tintalgo = cropcal_tintalgo, & + stream_name = 'sowing date data', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if end if ! Initialize the cdeps data type sdat_cropcal_cultivar_gdds - if (.not. generate_crop_gdds) then + if (use_cropcal_rx_cultivar_gdds) then call shr_strdata_init_from_inline(sdat_cropcal_cultivar_gdds, & my_task = iam, & logunit = iulog, & @@ -221,16 +237,18 @@ subroutine cropcal_advance( bounds ) call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day - call shr_strdata_advance(sdat_cropcal_sdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) + if (use_cropcal_rx_sdates) then + call shr_strdata_advance(sdat_cropcal_sdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if end if - if (.not. generate_crop_gdds) then + if (use_cropcal_rx_cultivar_gdds) then call shr_strdata_advance(sdat_cropcal_cultivar_gdds, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - end if + end if if ( .not. allocated(g_to_ig) )then allocate (g_to_ig(bounds%begg:bounds%endg) ) @@ -288,60 +306,62 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Read prescribed sowing dates from input files allocate(dataptr2d_sdate(lsize, ncft)) dataptr2d_sdate(:,:) = -5 - ! Starting with npcropmin will skip generic crops - if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' - do n = 1, ncft - ivt = n + npcropmin - 1 - call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & - fldptr1=dataptr1d_sdate, rc=rc) - if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize - ! So an explicit loop is required here - do g = 1,lsize - - ! If read-in value is invalid, allow_unprescribed_planting in CropPhenology() - if (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365) then - dataptr1d_sdate(g) = -1 + if (use_cropcal_rx_sdates) then + ! Starting with npcropmin will skip generic crops + if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' + do n = 1, ncft + ivt = n + npcropmin - 1 + call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & + fldptr1=dataptr1d_sdate, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - - dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize + ! So an explicit loop is required here + do g = 1,lsize + + ! If read-in value is invalid, allow_unprescribed_planting in CropPhenology() + if (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365) then + dataptr1d_sdate(g) = -1 + end if + + dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + end do end do - end do - - ! Set rx_sdate for each gridcell/patch combination - if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' - do fp = 1, num_pcropp - p = filter_pcropp(fp) - ivt = patch%itype(p) - ! Will skip generic crops - if (ivt >= npcropmin) then - n = ivt - npcropmin + 1 - ! vegetated pft - ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) - - ! Sanity check: Should only read in valid values - if (crop_inst%rx_sdates_thisyr(p,1) > 365) then - write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',crop_inst%rx_sdates_thisyr(p,1) - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - - ! Only for first sowing date of the year - ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 - if (crop_inst%sdates_thisyr(p,1) <= 0) then - crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) - end if - else - write(iulog,'(a,i0)') 'cropcal_interp(), rx_sdates: Crop patch has ivt ',ivt - call ESMF_Finalize(endflag=ESMF_END_ABORT) - endif - end do + + ! Set rx_sdate for each gridcell/patch combination + if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' + do fp = 1, num_pcropp + p = filter_pcropp(fp) + ivt = patch%itype(p) + ! Will skip generic crops + if (ivt >= npcropmin) then + n = ivt - npcropmin + 1 + ! vegetated pft + ig = g_to_ig(patch%gridcell(p)) + crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) + + ! Sanity check: Should only read in valid values + if (crop_inst%rx_sdates_thisyr(p,1) > 365) then + write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',crop_inst%rx_sdates_thisyr(p,1) + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + ! Only for first sowing date of the year + ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 + if (crop_inst%sdates_thisyr(p,1) <= 0) then + crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + end if + else + write(iulog,'(a,i0)') 'cropcal_interp(), rx_sdates: Crop patch has ivt ',ivt + call ESMF_Finalize(endflag=ESMF_END_ABORT) + endif + end do + end if ! use_cropcal_rx_sdates deallocate(dataptr2d_sdate) - + allocate(dataptr2d_cultivar_gdds(lsize, ncft)) - if (.not. generate_crop_gdds) then + if (use_cropcal_rx_cultivar_gdds) then ! Read prescribed cultivar GDDs from input files ! Starting with npcropmin will skip generic crops do n = 1, ncft @@ -404,7 +424,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) endif end do write(iulog,*) 'cropcal_interp(): Reading cultivar_gdds file DONE' - end if ! not generate_crop_gdds + end if ! use_cropcal_rx_cultivar_gdds deallocate(dataptr2d_cultivar_gdds) diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 89a4ae0c95..e57c802d95 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -565,9 +565,9 @@ subroutine initialize2(ni,nj) end if ! Initialize crop calendars + call t_startf('init_cropcal') + call cropcal_init(bounds_proc) if (use_cropcal_streams) then - call t_startf('init_cropcal') - call cropcal_init(bounds_proc) call cropcal_advance( bounds_proc ) !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) do nc = 1,nclumps @@ -577,8 +577,8 @@ subroutine initialize2(ni,nj) end do !$OMP END PARALLEL DO ! call cropcal_interp(bounds_clump, crop_inst) - call t_stopf('init_cropcal') end if + call t_stopf('init_cropcal') ! Initialize active history fields. ! This is only done if not a restart run. If a restart run, then this diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index ffae850f02..ac3679364a 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -306,7 +306,9 @@ module clm_varctl ! crop calendar streams switch for CropPhenology !---------------------------------------------------------- - logical, public :: use_cropcal_streams = .false. ! true => read crop calendar streams for use in CropPhenology.F90 + logical, public :: use_cropcal_streams = .false. + logical, public :: use_cropcal_rx_sdates = .false. + logical, public :: use_cropcal_rx_cultivar_gdds = .false. !---------------------------------------------------------- ! biomass heat storage switch From 2222e97e7dce5ad46a412d74b5cd252cc6598687 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Oct 2022 12:10:37 -0600 Subject: [PATCH 0312/2067] Updates to CropPhenology() to allow prescribing GDD reqt but not sdate. --- src/biogeochem/CNPhenologyMod.F90 | 132 ++++++++++++++---------------- 1 file changed, 61 insertions(+), 71 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e698ca0988..04f6754305 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1724,6 +1724,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? + logical do_plant ! are we planting in this time step for any reason? + logical did_plant ! did we plant the crop in this time step? logical allow_unprescribed_planting ! should crop be allowed to be planted according to sowing window rules? logical do_harvest ! Are harvest conditions satisfied? logical force_harvest ! Should we harvest today no matter what? @@ -1885,6 +1887,52 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%sowing_reason_patch(p) = 0 endif + ! This is outside the croplive check to allow for using CLM sowing + ! dates with externally-prescribed GDD maturity requirements + ! + ! Only allow sowing according to normal "window" rules if not using prescribed + ! sowing dates at all, or if this cell had no values in the prescribed sowing + ! date file. + allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr(p,1)<0 + if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then + ! winter temperate cereal : use gdd0 as a limit to plant winter cereal + ! + ! Are all the normal requirements for planting met? + do_plant_normal = allow_unprescribed_planting .and. & + a5tmin(p) /= spval .and. & + a5tmin(p) <= minplanttemp(ivt(p)) .and. & + jday >= minplantjday(ivt(p),h) .and. & + jday <= maxplantjday(ivt(p),h) .and. & + (gdd020(p) /= spval .and. & + gdd020(p) >= gddmin(ivt(p))) + ! If not, but it's the last day of the planting window, what about relaxed rules? + do_plant_lastchance = allow_unprescribed_planting .and. & + (.not. do_plant_normal) .and. & + jday == maxplantjday(ivt(p),h) .and. & + gdd020(p) /= spval .and. & + gdd020(p) >= gddmin(ivt(p)) + else ! not winter cereal... slevis: added distinction between NH and SH + ! slevis: The idea is that jday will equal idop sooner or later in the year + ! while the gdd part is either true or false for the year. + ! Are all the normal requirements for planting met? + do_plant_normal = allow_unprescribed_planting .and. & + t10(p) /= spval .and. a10tmin(p) /= spval .and. & + t10(p) > planttemp(ivt(p)) .and. & + a10tmin(p) > minplanttemp(ivt(p)) .and. & + jday >= minplantjday(ivt(p),h) .and. & + jday <= maxplantjday(ivt(p),h) .and. & + gdd820(p) /= spval .and. & + gdd820(p) >= gddmin(ivt(p)) + ! If not, but it's the last day of the planting window, what about relaxed rules? + do_plant_lastchance = allow_unprescribed_planting .and. & + (.not. do_plant_normal) .and. & + jday == maxplantjday(ivt(p),h) .and. & + gdd820(p) > 0._r8 .and. & + gdd820(p) /= spval + end if + do_plant = do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance + did_plant = .false. + ! Once outputs can handle >1 planting per year, remove 2nd condition. if ( (.not. croplive(p)) .and. s == 0 ) then @@ -1903,83 +1951,25 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! According to Chris Kucharik, the dataset of ! xinpdate was generated from a previous model run at 0.5 deg resolution + if (do_plant) then - ! Only allow sowing according to normal "window" rules if not using prescribed - ! sowing dates at all, or if this cell had no values in the prescribed sowing - ! date file. - allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr(p,1)<0 - - ! winter temperate cereal : use gdd0 as a limit to plant winter cereal - - if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then - - ! Are all the normal requirements for planting met? - do_plant_normal = allow_unprescribed_planting .and. & - a5tmin(p) /= spval .and. & - a5tmin(p) <= minplanttemp(ivt(p)) .and. & - jday >= minplantjday(ivt(p),h) .and. & - jday <= maxplantjday(ivt(p),h) .and. & - (gdd020(p) /= spval .and. & - gdd020(p) >= gddmin(ivt(p))) - ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = allow_unprescribed_planting .and. & - (.not. do_plant_normal) .and. & - jday == maxplantjday(ivt(p),h) .and. & - gdd020(p) /= spval .and. & - gdd020(p) >= gddmin(ivt(p)) - - if (do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance) then - + if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then cumvd(p) = 0._r8 hdidx(p) = 0._r8 vf(p) = 0._r8 - - call PlantCrop(p, leafcn(ivt(p)), jday, kyr, do_plant_normal, & - do_plant_lastchance, do_plant_prescribed, & - temperature_inst, crop_inst, cnveg_state_inst, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & - cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) - do_plant_prescribed = .false. - - else - gddmaturity(p) = 0._r8 end if - else ! not winter cereal... slevis: added distinction between NH and SH - ! slevis: The idea is that jday will equal idop sooner or later in the year - ! while the gdd part is either true or false for the year. - - ! Are all the normal requirements for planting met? - do_plant_normal = allow_unprescribed_planting .and. & - t10(p) /= spval .and. a10tmin(p) /= spval .and. & - t10(p) > planttemp(ivt(p)) .and. & - a10tmin(p) > minplanttemp(ivt(p)) .and. & - jday >= minplantjday(ivt(p),h) .and. & - jday <= maxplantjday(ivt(p),h) .and. & - gdd820(p) /= spval .and. & - gdd820(p) >= gddmin(ivt(p)) - ! If not, but it's the last day of the planting window, what about relaxed rules? - do_plant_lastchance = allow_unprescribed_planting .and. & - (.not. do_plant_normal) .and. & - jday == maxplantjday(ivt(p),h) .and. & - gdd820(p) > 0._r8 .and. & - gdd820(p) /= spval - - if (do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance) then - - call PlantCrop(p, leafcn(ivt(p)), jday, kyr, do_plant_normal, & - do_plant_lastchance, do_plant_prescribed, & - temperature_inst, crop_inst, cnveg_state_inst, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & - cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) - do_plant_prescribed = .false. + call PlantCrop(p, leafcn(ivt(p)), jday, kyr, do_plant_normal, & + do_plant_lastchance, do_plant_prescribed, & + temperature_inst, crop_inst, cnveg_state_inst, & + cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & + cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & + c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst) + did_plant = .true. - else - gddmaturity(p) = 0._r8 - end if - end if ! crop patch distinction + else + gddmaturity(p) = 0._r8 + end if ! crop phenology (gdd thresholds) controlled by gdd needed for ! maturity (physiological) which is based on the average gdd @@ -2124,7 +2114,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & force_harvest = .true. fake_harvest = .true. harvest_reason = 3._r8 - else if (do_plant_prescribed) then + else if (do_plant .and. .not. did_plant) then ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. From 129e03015f907e6675b11a4973c6cc9639c86a5e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 9 Oct 2022 10:14:32 -0600 Subject: [PATCH 0313/2067] Bugfix in PlantCrop() when prescribing GDDs but not sdates (and maybe vice versa). --- src/biogeochem/CNPhenologyMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 04f6754305..4628c98de9 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2461,6 +2461,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! !USES: use clm_varctl , only : use_c13, use_c14 + use clm_varctl , only : use_cropcal_rx_cultivar_gdds use clm_varcon , only : c13ratio, c14ratio use clm_varpar , only : mxsowings use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean @@ -2577,7 +2578,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & endif ! set GDD target - if (do_plant_prescribed .and. (.not. generate_crop_gdds) .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .ge. 0._r8) then + if (use_cropcal_rx_cultivar_gdds .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .ge. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator From 246753b3cd7263e4b0300371d809a209b99927a1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 10 Oct 2022 14:22:10 -0600 Subject: [PATCH 0314/2067] Bugfix to prevent harvest immediately after planting when prescribing GDDs but not sdates. --- src/biogeochem/CNPhenologyMod.F90 | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 4628c98de9..53356aae79 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1861,7 +1861,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,s+1) end if - do_plant_prescribed = next_rx_sdate(p) == jday + do_plant_prescribed = next_rx_sdate(p) == jday .and. sowing_count(p) < mxsowings ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) ! When resuming from a run with old code, may need to manually set these. @@ -1894,7 +1894,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! sowing dates at all, or if this cell had no values in the prescribed sowing ! date file. allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr(p,1)<0 - if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then + if (sowing_count(p) == mxsowings) then + do_plant_normal = .false. + do_plant_lastchance = .false. + else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then ! winter temperate cereal : use gdd0 as a limit to plant winter cereal ! ! Are all the normal requirements for planting met? From 5d432a3477b12d9e9e1ffda35a3b8e3ad52488b0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 10 Oct 2022 14:40:33 -0600 Subject: [PATCH 0315/2067] Delete commented-out declarations in cropcalStreamMod. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index b604b3f917..e3f11e8e9e 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -29,11 +29,6 @@ module cropcalStreamMod public :: cropcal_advance ! Advance the crop calendar streams (outside of a Open-MP threading loop) public :: cropcal_interp ! interpolates between two years of crop calendar data -! ! !PUBLIC MEMBER DATA -! logical, public, save :: use_cropcal_rx_sdates = .false. -! logical, public, save :: use_cropcal_rx_cultivar_gdds = .false. -! logical, public, save :: use_cropcal_streams = .false. - ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream From 37f914bd722e2f2889381a7c4f6115aba4b94aba Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 10 Oct 2022 14:52:34 -0600 Subject: [PATCH 0316/2067] Now must specify if you want to ignore mxmat, with use_mxmat = .false. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ src/biogeochem/CNPhenologyMod.F90 | 8 ++++++-- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 44db890893..b14aa859e7 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -561,6 +561,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. Constant .false. +.false. .false. 1.d00 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index f9be8ca3a6..9a351fe10a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1138,6 +1138,11 @@ Phenology onset depends on the vegetation type Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. + +Set to .true. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. + + Set to .true. in order to override prescribed crop GDD requirements and instead use default CLM values/logic. For troubleshooting purposes only. diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 53356aae79..0a44483657 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -130,6 +130,7 @@ module CNPhenologyMod real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing + logical, public :: use_mxmat = .true. ! If true, ignore crop maximum growing season length logical :: ignore_rx_crop_gdds = .false. ! Troubleshooting ! Constants for seasonal decidious leaf onset and offset @@ -174,7 +175,7 @@ subroutine CNPhenologyReadNML( NLFilename ) !----------------------------------------------------------------------- namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, & min_critical_dayl_method, generate_crop_gdds, & - ignore_rx_crop_gdds + use_mxmat, ignore_rx_crop_gdds ! Initialize options to default values, in case they are not specified in ! the namelist @@ -199,6 +200,7 @@ subroutine CNPhenologyReadNML( NLFilename ) call shr_mpi_bcast (onset_thresh_depends_on_veg, mpicom) call shr_mpi_bcast (min_critical_dayl_method, mpicom) call shr_mpi_bcast (generate_crop_gdds, mpicom) + call shr_mpi_bcast (use_mxmat, mpicom) call shr_mpi_bcast (ignore_rx_crop_gdds, mpicom) if ( min_critical_dayl_method == "DependsOnLat" )then @@ -2107,7 +2109,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. mxmat = pftcon%mxmat(ivt(p)) - if (use_cropcal_rx_cultivar_gdds) then + if (use_mxmat .and. generate_crop_gdds) then + call endrun(msg="If setting generate_crop_gdds to .true., you must set use_mxmat to .false.") + else if (.not. use_mxmat) then mxmat = 999 end if From e2593a1da3dcf7f303c62a7f957dbe1f3957d776 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 13 Oct 2022 09:52:33 -0600 Subject: [PATCH 0317/2067] update fates externals to include tveg restart fix --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 2284518c58..2bc1db66f6 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.58.1_api.24.1.0 +tag = sci.1.59.7_api.24.1.0 required = True [externals_description] From 63d87940924876a7c4c7291442d357fc40b4eba8 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 13 Oct 2022 09:37:56 -0700 Subject: [PATCH 0318/2067] restore clm mimics fates name to use ColdDef suffix --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f9426f8a2a..965bee24e7 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1996,7 +1996,7 @@ - + From 970f08a8f24c64988cc6ed04877cf343e76565c0 Mon Sep 17 00:00:00 2001 From: James Edwards Date: Thu, 13 Oct 2022 16:24:06 -0600 Subject: [PATCH 0319/2067] always use the only modifier --- src/cpl/nuopc/lnd_comp_nuopc.F90 | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90 index f7c3cb9a13..6f8153eb0d 100644 --- a/src/cpl/nuopc/lnd_comp_nuopc.F90 +++ b/src/cpl/nuopc/lnd_comp_nuopc.F90 @@ -4,9 +4,20 @@ module lnd_comp_nuopc ! This is the NUOPC cap for CTSM !---------------------------------------------------------------------------- - use ESMF + use ESMF , only : ESMF_SUCCESS, ESMF_GridComp, ESMF_LogWrite, ESMF_LOGMSG_INFO, ESMF_GridCompSetEntryPoint + use ESMF , only : ESMF_METHOD_INITIALIZE, ESMF_FAILURE, ESMF_Time, ESMF_LogSetError, ESMF_RC_NOT_VALID + use ESMF , only : ESMF_Clock, ESMF_State, ESMF_Field, ESMF_MAXSTR, ESMF_LOGMSG_WARNING,ESMF_RC_ARG_BAD + use ESMF , only : ESMF_LOGFOUNDERROR, ESMF_LOGERR_PASSTHRU, ESMF_CALKIND_FLAG, ESMF_TIMEINTERVAL + use ESMF , only : ESMF_LogSetError, ESMF_FieldGet, ESMF_ClockGet, ESMF_GridCompGet, ESMF_ClockGetNextTime + use ESMF , only : ESMF_AlarmRingerOff, ESMF_TimeIntervalGet, ESMF_TimeGet, ESMF_StateGet + use ESMF , only : ESMF_MethodRemove, ESMF_VM, ESMF_VMGet, ESMF_CALKIND_NOLEAP, ESMF_CALKIND_GREGORIAN + use ESMF , only : ESMF_ALARMLIST_ALL, ESMF_ALARM, ESMF_ALARMISRINGING, ESMF_ClockGetAlarm, ESMF_ClockGetAlarmList + use ESMF , only : ESMF_AlarmSet, ESMF_ClockAdvance + use ESMF , only : operator(==), operator(+) + use ESMF , only : ESMF_AlarmIsCreated, ESMF_LOGMSG_ERROR, ESMF_ClockSet use NUOPC , only : NUOPC_CompDerive, NUOPC_CompSetEntryPoint, NUOPC_CompSpecialize use NUOPC , only : NUOPC_CompFilterPhaseMap, NUOPC_CompAttributeGet, NUOPC_CompAttributeSet + use NUOPC , only : NUOPC_CompGet, Nuopc_IsAtTime, Nuopc_GetAttribute use NUOPC_Model , only : model_routine_SS => SetServices use NUOPC_Model , only : SetVM use NUOPC_Model , only : model_label_Advance => label_Advance @@ -1275,8 +1286,8 @@ subroutine clm_orbital_update(clock, logunit, mastertask, eccen, obliqr, lambm0 end subroutine clm_orbital_update subroutine CheckImport(gcomp, rc) - use NUOPC - use ESMF +! use NUOPC +! use ESMF type(ESMF_GridComp) :: gcomp integer, intent(out) :: rc character(len=*) , parameter :: subname = "("//__FILE__//":CheckImport)" From f3b28ff35b425b1411228dd723d219f051e0ae06 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 13 Oct 2022 16:48:18 -0700 Subject: [PATCH 0320/2067] fix testmod name for nocomp + fixed biogeo --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 965bee24e7..25263d4ea4 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2277,7 +2277,7 @@ - + From e05e50ee05108e101a834d168a02e1de8bd9ea63 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 13 Oct 2022 16:54:04 -0700 Subject: [PATCH 0321/2067] update changelog with test status TBD --- doc/ChangeLog | 142 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 143 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index b6c434f21c..61374f0942 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,146 @@ =============================================================== +Tag name: ctsm5.1.dev112 +Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) +Date: Thu 13 Oct 2022 17:19:14 MDT +One-line Summary: Rework fates test definitions and add new fates tests + +Purpose and description of changes +---------------------------------- + +This tag includes a number of updates to the fates test definitions and test list to gain more coverage: + +(1) Reorder and update the fates test definitions so that fates satellite phenology mode +can be configured for cases using a compset. + +(2) Add a long-term exact restart test to catch issues that may arise due to updates to +fates procedure calls during end of year simulation dates. + +(3) Add a no-competition + fixed biogeography, non-satellite phenology test definition to provide +additional mode combination configuration. + +(4) Update the fates externals tag to incorporate a fix a vegetation temperature exact restart +issue discovered while implementing (1) above. + +(5) Truncate all testmods starting the "Fates" to mitigate running over the limits on the length +of testnames, typically when specifying custom `test_id` using `run_sys_test`. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Fixes #1839 - Add more FATES tests that are longer than one year + Fixes #1817 - Make sure at least one test running FatesSp just uses the compset and not a test-mod directory + Fixes #1551 - Add FATES NoComp + FixedBiogeog regression test to the fates category of tests + +Externals issues fixed (include issue #): + FATES#908 - Bareground area_pft not being carried over during restarts + FATES#911 - 24-hr running mean vegetation temperature is not b4b on threaded exact restart SatPhen test + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: + FATES#897 is still unresolved, but is now covered by this updated test list. + +Testing summary: +---------------- +[... Remove before making master tag. + +Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. +However, it occasionally makes sense to do more or less system testing; +here is guidance on different available levels of system testing: + a) no system testing (for use when the only changes are ones that + have absolutely no impact on system runs; this + includes documentation-only tags, tags that + just change the tools or some python code that + does not impact system runs, etc.) + b) minimal (for use in rare cases where only a small change with + known behavior is added ... eg. a minor bug fix. This + might be to just run the "short" test list, or to run + a single test. Whatever makes sense for the particular case.) + c) python only (for use where the only changes are in the python directory: + run the python testing listed below) + d) regular (regular tests on normal machines if CTSM source is modified) + e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists + and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) + would be run as well) + +In addition, various other tests of the tools, python and perl +infrastructure should be run when appropriate, as described below. + +...] + + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- TBD + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + +Answer changes +-------------- + +Changes answers relative to baseline: + + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] + + Summarize any changes to answers, i.e., + - what code configurations: + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: + + URL for LMWG diagnostics output used to validate new climate: + + +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): + + https://github.com/ESCOMP/CTSM/pull/1827 + https://github.com/ESCOMP/CTSM/pull/1849 + + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev111 Originator(s): jedwards (Jim Edwards), wwieder (Will Wieder), sacks (Bill Sacks) Date: Wed Oct 5 13:05:52 MDT 2022 diff --git a/doc/ChangeSum b/doc/ChangeSum index cdbc339758..5da2581767 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev112 multiple 10/13/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases ctsm5.1.dev110 slevis 09/26/2022 Introduction of modify_meshes tool for use in I-cases and F-cases ctsm5.1.dev109 slevis 09/26/2022 If not MIMICS, do not output certain MIMICS history fields From f0f28e711a3d33a184a312560475e401c73e50c7 Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 14 Oct 2022 14:38:08 -0600 Subject: [PATCH 0322/2067] python updates for #1871 --- .../modify_singlept_site_neon.py | 2 +- tools/site_and_regional/neon_sites_dompft.csv | 88 +++++++++---------- tools/site_and_regional/neon_surf_wrapper.py | 2 +- 3 files changed, 46 insertions(+), 46 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 3610b0bb5c..336366a49b 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -682,7 +682,7 @@ def main(): print("Updating PCT_NAT_PFT") #print (f2.PCT_NAT_PFT) print(f2.PCT_NAT_PFT.values[0]) - f2.PCT_NAT_PFT.values[0] = [[100.0]] + #f2.PCT_NAT_PFT.values[0] = [[100.0]] print(f2.PCT_NAT_PFT[0].values) out_dir = args.out_dir diff --git a/tools/site_and_regional/neon_sites_dompft.csv b/tools/site_and_regional/neon_sites_dompft.csv index ad5d14e53d..e67d67375b 100644 --- a/tools/site_and_regional/neon_sites_dompft.csv +++ b/tools/site_and_regional/neon_sites_dompft.csv @@ -1,48 +1,48 @@ ,Site,Domain,Lat,Lon,pft,start_year,end_year -1,BART,1,44.06516,-71.28834,7,2018,2021 -2,HARV,1,42.53562,-72.17562,7,2018,2021 -3,BLAN,2,39.06044,-78.07115,7,2018,2021 -4,SCBI,2,38.89209,-78.13764,7,2018,2021 -5,SERC,2,38.89124,-76.55884,7,2018,2021 -6,DSNY,3,28.12919,-81.43394,14,2018,2021 -7,JERC,3,31.19608,-84.46647,1,2018,2021 -8,OSBS,3,29.68819,-81.99345,1,2018,2021 -9,GUAN,4,17.96882,-66.86888,6,2019,2021 -10,LAJA,4,18.02184,-67.07608,14,2019,2021 -11,STEI,5,45.5076,-89.5888,7,2018,2021 -12,TREE,5,45.49266,-89.58748,7,2018,2021 -13,UNDE,5,46.14103,-89.3221,7,2018,2021 -14,KONA,6,39.10828,-96.61044,18,2018,2021 -15,KONZ,6,39.1007,-96.56227,14,2018,2021 -16,UKFS,6,39.04168,-95.20495,7,2018,2021 -17,GRSM,7,35.68839,-83.50185,7,2018,2021 -18,MLBS,7,37.37783,-80.52425,7,2018,2019 -19,ORNL,7,35.57525,-84.16581,7,2018,2021 -20,DELA,8,32.54092,-87.80341,7,2018,2021 -21,LENO,8,31.8531,-88.16103,7,2021,2021 -22,TALL,8,32.95106,-87.3941,1,2018,2021 -23,DCFS,9,47.15919,-99.11251,13,2018,2021 -24,NOGP,9,46.76846,-100.91832,13,2018,2021 -25,WOOD,9,47.12833,-99.23907,13,2018,2021 -26,CPER,10,40.81297,-104.74455,14,2018,2021 -27,RMNP,10,40.27707,-105.54524,1,2018,2021 -28,STER,10,40.45984,-103.03008,18,2018,2021 -29,CLBJ,11,33.40143,-97.56725,7,2018,2021 -30,OAES,11,35.41062,-99.06044,14,2018,2021 -31,YELL,12,44.95597,-110.54196,1,2019,2021 -32,MOAB,13,38.25136,-109.38882,14,2018,2020 -33,NIWO,13,40.05236,-105.58324,12,2018,2021 -34,JORN,14,32.59052,-106.84377,14,2018,2021 -35,SRER,14,31.91068,-110.83549,9,2018,2021 -36,ONAQ,15,35.68839,-83.50185,9,2018,2019 +1,BART, 1, 44.06516, -71.28834,7,2018,2021 +2,HARV, 1, 42.53562, -72.17562,7,2018,2021 +3,BLAN, 2, 39.06044, -78.07115,7,2018,2021 +4,SCBI, 2, 38.89209, -78.13764,7,2018,2021 +5,SERC, 2, 38.89124, -76.55884,7,2018,2021 +6,DSNY, 3, 28.12919, -81.43394,14,2018,2021 +7,JERC, 3, 31.19608, -84.46647,1,2018,2021 +8,OSBS, 3, 29.68819, -81.99345,1,2018,2021 +9,GUAN, 4, 17.96882, -66.86888,6,2019,2021 +10,LAJA, 4, 18.02184, -67.07608,14,2019,2021 +11,STEI, 5, 45.50760, -89.58880,7,2018,2021 +12,TREE, 5, 45.49266, -89.58748,7,2018,2021 +13,UNDE, 5, 46.14103, -89.32210,7,2018,2021 +14,KONA, 6, 39.10828, -96.61044,19,2018,2021 +15,KONZ, 6, 39.10070, -96.56227,14,2018,2021 +16,UKFS, 6, 39.04168, -95.20495,7,2018,2021 +17,GRSM, 7, 35.68839, -83.50185,7,2018,2021 +18,MLBS, 7, 37.37783, -80.52425,7,2018,2019 +19,ORNL, 7, 35.57525, -84.16581,7,2018,2021 +20,DELA, 8, 32.54092, -87.80341,7,2018,2021 +21,LENO, 8, 31.85310, -88.16103,7,2021,2021 +22,TALL, 8, 32.95106, -87.39410,1,2018,2021 +23,DCFS, 9, 47.15919, -99.11251,13,2018,2021 +24,NOGP, 9, 46.76846, -100.91832,13,2018,2021 +25,WOOD, 9, 47.12833, -99.23907,13,2018,2021 +26,CPER,10, 40.81297, -104.74455,14,2018,2021 +27,RMNP,10, 40.27707, -105.54524,1,2018,2021 +28,STER,10, 40.45984, -103.03008,19,2018,2021 +29,CLBJ,11, 33.40143, -97.56725,7,2018,2021 +30,OAES,11, 35.41062, -99.06044,14,2018,2021 +31,YELL,12, 44.95597, -110.54196,1,2019,2021 +32,MOAB,13, 38.25136, -109.38882,14,2018,2020 +33,NIWO,13, 40.05236, -105.58324,12,2018,2021 +34,JORN,14, 32.59052, -106.84377,14,2018,2021 +35,SRER,14, 31.91068, -110.83549,9,2018,2021 +36,ONAQ,15, 35.68839, -83.50185,9,2018,2019 37,ABBY,16,45.762378,-122.329672,1,2018,2021 -38,WREF,16,45.81637,-121.95838,1,2019,2021 -39,SJER,17,37.107117,-119.733,13,2019,2021 -40,SOAP,17,37.03269,-119.2621,1,2018,2021 +38,WREF,16, 45.81637, -121.95838,1,2019,2021 +39,SJER,17,37.107117, -119.73300,13,2019,2021 +40,SOAP,17,37.032690, -119.26210,1,2018,2021 41,TEAK,17,37.006472,-119.005758,1,2019,2021 -42,TOOL,17,68.66045,-149.370128,1,2020,2021 +42,TOOL,17, 68.66045,-149.370128,1,2020,2021 43,BARR,18,71.281711,-156.650219,12,2019,2021 -44,BONA,19,65.15333,-147.50194,2,2018,2021 -45,DEJU,19,63.87983,-145.74765,2,2018,2021 -46,HEAL,19,63.8798,-149.21539,12,2018,2021 -47,PUUM,20,19.55309,-155.31731,4,2020,2020 +44,BONA,19, 65.15333, -147.50194,2,2018,2021 +45,DEJU,19, 63.87983, -145.74765,2,2018,2021 +46,HEAL,19, 63.87980, -149.21539,12,2018,2021 +47,PUUM,20, 19.55309, -155.31731,4,2020,2020 diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index df58d3ab36..2f8a00500c 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -98,7 +98,7 @@ def main(): pft = row['pft'] print ("Now processing site :", site) command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',site,'--dompft',str(pft),'--crop', - '--create-surface','--uniform-snowpack','--cap-saturation','--verbose'] + '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] execute(command) command = ['./modify_singlept_site_neon.py','--neon_site',site, '--surf_dir', From c616dff513c65194e43f6c108a7f0099631e49cc Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 14 Oct 2022 14:41:49 -0600 Subject: [PATCH 0323/2067] usermod changes for #1871 --- cime_config/usermods_dirs/NEON/WREF/shell_commands | 4 ++++ cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index 77a0b750cd..bbb0e14312 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -1,3 +1,7 @@ ./xmlchange NEONSITE=WREF ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 +./xmlchange RUN_STARTDATE=2019-01-01 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +./xmlchange STOP_N=39 + diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 332060dd99..49528a524e 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -19,7 +19,7 @@ !---------------------------------------------------------------------------------- flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets -fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c211102.nc" +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c221014.nc" model_year_align_urbantv = 2018 stream_year_first_urbantv = 2018 stream_year_last_urbantv = 2021 From bb2ecf56fe17a4c47e2e7add27cd4ff3c8b56f18 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 14 Oct 2022 14:30:10 -0700 Subject: [PATCH 0324/2067] add new exact restart tests to known failure list --- cime_config/testdefs/ExpectedTestFails.xml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index e4c504d009..9dbad62a43 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -52,5 +52,19 @@ #667 + + + + FAIL + FATES#897 + + + + + FAIL + FATES#897 + + + From 74be22b5f080cb8497d54f49eb8859e76e6ffe53 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 14 Oct 2022 15:13:46 -0700 Subject: [PATCH 0325/2067] adding fates issue 701 to the expected fail list --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 9dbad62a43..878fef6dc1 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -67,4 +67,11 @@ + + + FAIL + FATES#701 + + + From 389826f3c8709a19fd1a44b71269591c9533cf70 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 14 Oct 2022 15:16:51 -0700 Subject: [PATCH 0326/2067] update compset name to current fates lightning expected diff --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 878fef6dc1..232b6e6a90 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -46,7 +46,7 @@ - + FAIL #667 From b9736ebc91eea7b59c4349cfdbb19010ca196268 Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 14 Oct 2022 16:34:15 -0600 Subject: [PATCH 0327/2067] local gcs modifications --- tools/site_and_regional/neon_gcs_upload | 171 ++++++++++++++++++++++++ 1 file changed, 171 insertions(+) create mode 100755 tools/site_and_regional/neon_gcs_upload diff --git a/tools/site_and_regional/neon_gcs_upload b/tools/site_and_regional/neon_gcs_upload new file mode 100755 index 0000000000..4854ac8b99 --- /dev/null +++ b/tools/site_and_regional/neon_gcs_upload @@ -0,0 +1,171 @@ +#! /usr/bin/env python3 +""" +Script to rename and upload NEON site finidat files for use in transient startup cases + +""" + +import os, sys +# Get the ctsm util tools and then the cime tools. +_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..","..",'python')) +sys.path.insert(1, _CTSM_PYTHON) + +from google.cloud import storage +import glob +import datetime +from ctsm import add_cime_to_path +from ctsm.path_utils import path_to_ctsm_root +from standard_script_setup import * +from CIME.case import Case +from CIME.utils import expect, safe_copy + +logger = logging.getLogger(__name__) + +def get_parser(args, description, valid_neon_sites): + """ + Get Parser object for this script + """ + parser = argparse.ArgumentParser(description=description, + formatter_class=argparse.RawDescriptionHelpFormatter) + + CIME.utils.setup_standard_logging_options(parser) + + parser.print_usage = parser.print_help + + parser.add_argument('--neon-sites', + help='4-letter neon site code.', + action="store", + required=False, + choices=valid_neon_sites + ['all'], + dest="neon_sites", + default=["OSBS"], + nargs='+') + + parser.add_argument('--output-root', + help=''' + Root Directory of case results + [default: %(default)s] + ''', + action="store", + dest="output_root", + type =str, + required=False, + default=os.getcwd()) + + parser.add_argument('--file-date', + help=''' + Date of ctsm restart file(s) to upload + ''', + action="store", + dest="file_date", + required = False, + type = datetime.date.fromisoformat, + default = datetime.datetime.strptime("0318-01-01",'%Y-%m-%d')) + + + parser.add_argument('--upload-finidat', + help=''' + Upload the final restart files from the end of the postad run for each site. + ''', + action="store_true", + dest="upload_finidat", + required = False, + default = False) + + parser.add_argument('--upload-history', + help=''' + Upload the transient run h1 history files for each site. + ''', + action="store_true", + dest="upload_history", + required = False, + default = False) + + + + args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser) + + if 'all' in args.neon_sites: + neon_sites = valid_neon_sites + else: + neon_sites = args.neon_sites + for site in neon_sites: + if site not in valid_neon_sites: + raise ValueError("Invalid site name {}".format(site)) + + expect(args.upload_finidat or args.upload_history,"Must specify at least one of --upload-finidat or --upload-history") + + return neon_sites, args.output_root, args.file_date, args.upload_finidat, args.upload_history + +def upload_blob(bucket_name, source_file_name, destination_blob_name): + """Uploads a file to the bucket.""" + # The ID of your GCS bucket + # bucket_name = "your-bucket-name" + # The path to your file to upload + # source_file_name = "local/path/to/file" + # The ID of your GCS object + # destination_blob_name = "storage-object-name" + + storage_client = storage.Client() + bucket = storage_client.bucket(bucket_name) + blob = bucket.blob(destination_blob_name) + + blob.upload_from_filename(source_file_name) + + print( + f"File {source_file_name} uploaded to {destination_blob_name}." + ) + +def main(description): + """ + For each site in the site_list find the site.postad run directory and grab the latest clm restart file + from there, + """ + + #if not os.path.isfile(os.path.join(os.getenv("HOME"),".aws","credentials")): + # raise FileNotFoundError("User account must have valid aws credentials to run this script.") + + cesmroot = path_to_ctsm_root() + os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = os.path.join(os.environ["HOME"],'.uploadGCSkey.json') + #os.path.join(os.environ["HOME"],"gcwriter") + + # Get the list of supported neon sites from usermods + valid_neon_sites = glob.glob(os.path.join(cesmroot,"cime_config","usermods_dirs","NEON","[!d]*")) + valid_neon_sites = [v.split('/')[-1] for v in valid_neon_sites] + filedatestamp = datetime.datetime.now().date() + site_list, output_root, file_date, upload_finidat, upload_history = get_parser(sys.argv, description, valid_neon_sites) + for site in site_list: + rundir = None + if upload_finidat: + logger.info("Upload finidat for {}".format(site)) + case_path = os.path.join(output_root, site+".postad") + if os.path.isdir(case_path): + with Case(case_path) as case: + rundir = case.get_value("RUNDIR") + basefile = site+".postad.clm2.r.{}-00000.nc".format(file_date.strftime("%4Y-%m-%d")) + finidat_file = os.path.join(rundir,basefile) + if not os.path.isfile(finidat_file): + logger.warning("Could not find file {}".format(finidat_file)) + continue + newfile = basefile.replace(".postad.",".{}.".format(filedatestamp)) + upload_blob("neon-prod-ncar", finidat_file, newfile) + + if upload_history: + logger.info("Upload history for {}".format(site)) + case_path = os.path.join(output_root, site+".transient") + if not os.path.isdir(case_path): + logger.warning("No case found in {}".format(case_path)) + continue + with Case(case_path) as case: + archive_dir = os.path.join(case.get_value("DOUT_S_ROOT"),"lnd","hist") + for histfile in glob.iglob(archive_dir + "/*.h1.*"): + newfile = os.path.basename(histfile) + upload_blob("neon-prod-ncar", histfile, os.path.join("NEON","archive",site,"lnd","hist",newfile)) + + + + + + +if __name__ == "__main__": + main(__doc__) + From a9848ada0c19d9a56a4dfc6f7f351d1d6f934710 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sat, 15 Oct 2022 01:19:08 +0200 Subject: [PATCH 0328/2067] history vars and issue 1819 --- src/biogeophys/SoilTemperatureMod.F90 | 1 - src/biogeophys/WaterStateType.F90 | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index c42130d8d2..f7b970c057 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -700,7 +700,6 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter col%itype(c) /= icol_roof .and. col%itype(c) /= icol_road_imperv) .or. & (col%itype(c) == icol_road_imperv .and. j > nlev_improad(l))) then - !TODO recalculate watsat and satw to have excess ice included satw = (h2osoi_liq(c,j)/denh2o + h2osoi_ice(c,j)/denice +excess_ice(c,j)/denice)/(dz(c,j)*watsat(c,j)) satw = min(1._r8, satw) if (satw > .1e-6_r8) then diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 9678e8c4c1..135d5f61d8 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -289,7 +289,7 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & avgflag='A', long_name='excess soil ice (vegetated landunits only)', & - ptr_col=this%excess_ice_col, l2g_scale_type='veg') + ptr_col=this%excess_ice_col, l2g_scale_type='veg', default = 'inactive') end if ! (rgk 02-02-2017) There is intentionally no entry here for stored plant water From ec55adef76bddeeb3378e40173df4ca453d861b0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 14 Oct 2022 16:19:56 -0700 Subject: [PATCH 0329/2067] updating changelog and changesum --- doc/ChangeLog | 65 +++++++++++---------------------------------------- doc/ChangeSum | 2 +- 2 files changed, 15 insertions(+), 52 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 61374f0942..54272273fc 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev112 Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) -Date: Thu 13 Oct 2022 17:19:14 MDT +Date: Thu 14 Oct 2022 16:20:00 MDT One-line Summary: Rework fates test definitions and add new fates tests Purpose and description of changes @@ -13,7 +13,7 @@ This tag includes a number of updates to the fates test definitions and test lis can be configured for cases using a compset. (2) Add a long-term exact restart test to catch issues that may arise due to updates to -fates procedure calls during end of year simulation dates. +fates procedure calls during end of year simulation dates. (3) Add a no-competition + fixed biogeography, non-satellite phenology test definition to provide additional mode combination configuration. @@ -24,6 +24,8 @@ issue discovered while implementing (1) above. (5) Truncate all testmods starting the "Fates" to mitigate running over the limits on the length of testnames, typically when specifying custom `test_id` using `run_sys_test`. +(6) Updates the expected failures list. + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -58,35 +60,10 @@ Notes of particular relevance for developers: Changes to tests or testing: FATES#897 is still unresolved, but is now covered by this updated test list. + FATES#701 was reopened Testing summary: ---------------- -[... Remove before making master tag. - -Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. -However, it occasionally makes sense to do more or less system testing; -here is guidance on different available levels of system testing: - a) no system testing (for use when the only changes are ones that - have absolutely no impact on system runs; this - includes documentation-only tags, tags that - just change the tools or some python code that - does not impact system runs, etc.) - b) minimal (for use in rare cases where only a small change with - known behavior is added ... eg. a minor bug fix. This - might be to just run the "short" test list, or to run - a single test. Whatever makes sense for the particular case.) - c) python only (for use where the only changes are in the python directory: - run the python testing listed below) - d) regular (regular tests on normal machines if CTSM source is modified) - e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists - and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) - would be run as well) - -In addition, various other tests of the tools, python and perl -infrastructure should be run when appropriate, as described below. - -...] - [PASS means all tests PASS; OK means tests PASS other than expected fails.] @@ -97,41 +74,27 @@ infrastructure should be run when appropriate, as described below. fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) cheyenne ---- OK - izumi ------- TBD + izumi ------- OK any other testing (give details below): If the tag used for baseline comparisons was NOT the previous tag, note that here: + FATES tests run against both fates-sci.1.58.1_api.24.1.0-ctsm5.1.dev111 to check the + fates update against the previous baseline is in line with expected DIFFs and + fates-sci.1.59.7_api.24.1.0-ctsm5.1.dev111. + Answer changes -------------- -Changes answers relative to baseline: - - [ If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section). - And always remove these three lines and parts that don't apply. ] - - Summarize any changes to answers, i.e., - - what code configurations: - - what platforms/compilers: - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: - - URL for LMWG diagnostics output used to validate new climate: - +Changes answers relative to baseline: + Yes, for fates run modes only due non-b4b updates in multiple fates tags. These + include both software bug fixes and answer changing science updates. Other details ------------- -[Remove any lines that don't apply. Remove entire section if nothing applies.] -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates Pull Requests that document the changes (include PR ids): diff --git a/doc/ChangeSum b/doc/ChangeSum index 5da2581767..16aceff1f8 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev112 multiple 10/13/2022 Rework fates test definitions and add new fates tests + ctsm5.1.dev112 multiple 10/14/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases ctsm5.1.dev110 slevis 09/26/2022 Introduction of modify_meshes tool for use in I-cases and F-cases ctsm5.1.dev109 slevis 09/26/2022 If not MIMICS, do not output certain MIMICS history fields From 5928f7caa7c37c6b928face74c63f205a09f87eb Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Sat, 15 Oct 2022 01:21:13 +0200 Subject: [PATCH 0330/2067] iulog for restart and stream --- src/biogeophys/WaterStateType.F90 | 4 ++++ src/cpl/share_esmf/ExcessIceStreamType.F90 | 1 + 2 files changed, 5 insertions(+) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 135d5f61d8..7630c1f763 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -14,6 +14,7 @@ module WaterStateType use decompMod , only : bounds_type use decompMod , only : subgrid_level_patch, subgrid_level_column, subgrid_level_gridcell use clm_varctl , only : use_bedrock, use_excess_ice, iulog + use spmdMod , only : masterproc use clm_varctl , only : use_fates_planthydro use clm_varpar , only : nlevgrnd, nlevsoi, nlevurb, nlevmaxurbgrnd, nlevsno use clm_varcon , only : spval @@ -712,6 +713,9 @@ subroutine Restart(this, bounds, ncid, flag, & units='kg/m2', scale_by_thickness=.true., & interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (masterproc) then + write(iulog,*) 'Excess ice data is read from the stream and not from restart file!' + endif do c = bounds%begc,bounds%endc l = col%landunit(c) if (.not. lun%lakpoi(l)) then !not lake diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index b0f79d1bfa..9b9a7c058c 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -96,6 +96,7 @@ subroutine Init(this, bounds, NLFilename) if (masterproc) then write(iulog,*) ' stream_varnames = ',stream_varnames + write(iulog,*) ' Values will be used if the variable is not on the initial conditions dataset' end if call shr_strdata_init_from_inline(sdat_exice, & From e27e7174b778a86615d6dbbefececd62d01cd4b0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 14 Oct 2022 16:30:35 -0700 Subject: [PATCH 0331/2067] fix minor grammatical error in changelog --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 54272273fc..96d5373cfb 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -21,7 +21,7 @@ additional mode combination configuration. (4) Update the fates externals tag to incorporate a fix a vegetation temperature exact restart issue discovered while implementing (1) above. -(5) Truncate all testmods starting the "Fates" to mitigate running over the limits on the length +(5) Truncate all testmods starting with "Fates" to mitigate running over the limits on the length of testnames, typically when specifying custom `test_id` using `run_sys_test`. (6) Updates the expected failures list. From 84f768d40301b2919dbed6e8d9c8715614dfcdd2 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Sat, 15 Oct 2022 12:44:53 -0700 Subject: [PATCH 0332/2067] rename mimics fates test to be consistent with other test names --- cime_config/testdefs/testlist_clm.xml | 2 +- .../{mimicsFatesColdDef => mimicsFatesCold}/include_user_mods | 0 .../clm/{mimicsFatesColdDef => mimicsFatesCold}/shell_commands | 0 3 files changed, 1 insertion(+), 1 deletion(-) rename cime_config/testdefs/testmods_dirs/clm/{mimicsFatesColdDef => mimicsFatesCold}/include_user_mods (100%) rename cime_config/testdefs/testmods_dirs/clm/{mimicsFatesColdDef => mimicsFatesCold}/shell_commands (100%) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 25263d4ea4..ffc56de0c3 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1996,7 +1996,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/mimicsFatesCold/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/mimicsFatesCold/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/shell_commands b/cime_config/testdefs/testmods_dirs/clm/mimicsFatesCold/shell_commands similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/mimicsFatesColdDef/shell_commands rename to cime_config/testdefs/testmods_dirs/clm/mimicsFatesCold/shell_commands From b098b6b867a60195270408eccc52c1aea1030c9b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 15 Oct 2022 16:27:00 -0600 Subject: [PATCH 0333/2067] Update date on changelog, add note that I ran the build-namelist testing --- doc/ChangeLog | 6 +++++- doc/ChangeSum | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 96d5373cfb..304740b1b8 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev112 Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) -Date: Thu 14 Oct 2022 16:20:00 MDT +Date: Sat Oct 15 16:26:28 MDT 2022 One-line Summary: Rework fates test definitions and add new fates tests Purpose and description of changes @@ -67,6 +67,10 @@ Testing summary: [PASS means all tests PASS; OK means tests PASS other than expected fails.] + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- OK diff --git a/doc/ChangeSum b/doc/ChangeSum index 16aceff1f8..9eab48d7e5 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev112 multiple 10/14/2022 Rework fates test definitions and add new fates tests + ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases ctsm5.1.dev110 slevis 09/26/2022 Introduction of modify_meshes tool for use in I-cases and F-cases ctsm5.1.dev109 slevis 09/26/2022 If not MIMICS, do not output certain MIMICS history fields From ae3d8b3a6f020a03a29d238499c0f7775c0d4bc3 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 16 Oct 2022 06:19:39 -0600 Subject: [PATCH 0334/2067] modified path for uploading to GCS --- tools/site_and_regional/neon_gcs_upload | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/site_and_regional/neon_gcs_upload b/tools/site_and_regional/neon_gcs_upload index 4854ac8b99..d69534db19 100755 --- a/tools/site_and_regional/neon_gcs_upload +++ b/tools/site_and_regional/neon_gcs_upload @@ -147,7 +147,7 @@ def main(description): logger.warning("Could not find file {}".format(finidat_file)) continue newfile = basefile.replace(".postad.",".{}.".format(filedatestamp)) - upload_blob("neon-prod-ncar", finidat_file, newfile) + upload_blob("neon-ncar-artifacts", finidat_file, newfile) if upload_history: logger.info("Upload history for {}".format(site)) @@ -159,7 +159,7 @@ def main(description): archive_dir = os.path.join(case.get_value("DOUT_S_ROOT"),"lnd","hist") for histfile in glob.iglob(archive_dir + "/*.h1.*"): newfile = os.path.basename(histfile) - upload_blob("neon-prod-ncar", histfile, os.path.join("NEON","archive",site,"lnd","hist",newfile)) + upload_blob("neon-ncar-artifacts", histfile, os.path.join("NEON","archive",site,"lnd","hist",newfile)) From fff4402d117bf24bad195c75bc59a51564860177 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 13:28:11 -0600 Subject: [PATCH 0335/2067] Add only clause to use ESMF for share_esmf files --- src/cpl/share_esmf/FireDataBaseType.F90 | 2 +- src/cpl/share_esmf/SoilMoistureStreamMod.F90 | 2 +- src/cpl/share_esmf/UrbanTimeVarType.F90 | 2 +- src/cpl/share_esmf/ch4FInundatedStreamType.F90 | 2 +- src/cpl/share_esmf/laiStreamMod.F90 | 2 +- src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 | 15 +++++++++++++-- src/cpl/share_esmf/ndepStreamMod.F90 | 2 +- 7 files changed, 19 insertions(+), 8 deletions(-) diff --git a/src/cpl/share_esmf/FireDataBaseType.F90 b/src/cpl/share_esmf/FireDataBaseType.F90 index 40d5f3c260..42bb874812 100644 --- a/src/cpl/share_esmf/FireDataBaseType.F90 +++ b/src/cpl/share_esmf/FireDataBaseType.F90 @@ -7,7 +7,7 @@ module FireDataBaseType ! module for handling of fire data ! ! !USES: - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize, ESMF_END_ABORT use dshr_strdata_mod , only : shr_strdata_type use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL use shr_log_mod , only : errMsg => shr_log_errMsg diff --git a/src/cpl/share_esmf/SoilMoistureStreamMod.F90 b/src/cpl/share_esmf/SoilMoistureStreamMod.F90 index d5ef28f924..a93f413e7a 100644 --- a/src/cpl/share_esmf/SoilMoistureStreamMod.F90 +++ b/src/cpl/share_esmf/SoilMoistureStreamMod.F90 @@ -7,7 +7,7 @@ module SoilMoistureStreamMod ! Read in soil moisture from data stream ! ! !USES: - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize, ESMF_END_ABORT, ESMF_SUCCESS use dshr_strdata_mod , only : shr_strdata_type, shr_strdata_print use dshr_strdata_mod , only : shr_strdata_init_from_inline, shr_strdata_advance use dshr_methods_mod , only : dshr_fldbun_getfldptr diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index cc48bf4833..6a6f982438 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -5,7 +5,7 @@ module UrbanTimeVarType ! Urban Time Varying Data ! ! !USES: - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize, ESMF_END_ABORT use dshr_strdata_mod, only : shr_strdata_type use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL use shr_log_mod , only : errMsg => shr_log_errMsg diff --git a/src/cpl/share_esmf/ch4FInundatedStreamType.F90 b/src/cpl/share_esmf/ch4FInundatedStreamType.F90 index 0d78bd6469..2bebf30062 100644 --- a/src/cpl/share_esmf/ch4FInundatedStreamType.F90 +++ b/src/cpl/share_esmf/ch4FInundatedStreamType.F90 @@ -7,7 +7,7 @@ module ch4FInundatedStreamType ! Contains methods for reading in finundated streams file for methane code. ! ! !USES - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize, ESMF_END_ABORT use dshr_strdata_mod , only : shr_strdata_type use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_cl use shr_log_mod , only : errMsg => shr_log_errMsg diff --git a/src/cpl/share_esmf/laiStreamMod.F90 b/src/cpl/share_esmf/laiStreamMod.F90 index a44f0b7198..3966488e0b 100644 --- a/src/cpl/share_esmf/laiStreamMod.F90 +++ b/src/cpl/share_esmf/laiStreamMod.F90 @@ -7,7 +7,7 @@ module laiStreamMod ! Read LAI from stream ! ! !USES: - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize, ESMF_END_ABORT use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL, CS => shr_kind_CS use dshr_strdata_mod , only : shr_strdata_type use decompMod , only : bounds_type diff --git a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 index c3556193a7..d1d29672b3 100644 --- a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 +++ b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 @@ -1,6 +1,9 @@ module lnd_set_decomp_and_domain - use ESMF + use ESMF , only : ESMF_VM, ESMF_Mesh, ESMF_DistGrid, ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU + use ESMF , only : ESMF_Array, ESMF_ArrayCreate, ESMF_SUCCESS, ESMF_MeshCreate, ESMF_FILEFORMAT_ESMFMESH + use ESMF , only : ESMF_MeshGet, ESMF_DistGridGet, ESMF_Grid, ESMF_Field, ESMF_FieldGet, ESMF_FieldCreate, ESMF_FieldDestroy + use ESMF , only : ESMF_TYPEKIND_R8, ESMF_MESHLOC_ELEMENT, ESMF_VMAllReduce, ESMF_REDUCE_SUM use shr_kind_mod , only : r8 => shr_kind_r8, cl=>shr_kind_cl use shr_sys_mod , only : shr_sys_abort use shr_log_mod , only : errMsg => shr_log_errMsg @@ -42,6 +45,7 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes use decompMod , only : gindex_global, bounds_type, get_proc_bounds use clm_varpar , only : nlevsoi use clm_varctl , only : use_soil_moisture_streams + use ESMF , only : ESMF_DistGridCreate ! input/output variables character(len=*) , intent(in) :: driver ! cmeps or lilac @@ -185,8 +189,8 @@ end subroutine lnd_set_decomp_and_domain_from_readmesh subroutine lnd_set_mesh_for_single_column(scol_lon, scol_lat, mesh, rc) ! Generate a mesh for single column - use netcdf use clm_varcon, only : spval + use ESMF , only : ESMF_Grid, ESMF_GridCreateNoPeriDimUfrm, ESMF_STAGGERLOC_CENTER, ESMF_STAGGERLOC_CORNER ! input/output variables real(r8) , intent(in) :: scol_lon @@ -348,6 +352,12 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask ! exist then simply read in the global land fraction and land mask ! from the file + ! Uses: + use ESMF , only : ESMF_RouteHandle, ESMF_FieldRegridStore, ESMF_FieldRegrid + use ESMF , only : ESMF_REGRIDMETHOD_CONSERVE, ESMF_NORMTYPE_DSTAREA, ESMF_UNMAPPEDACTION_IGNORE + use ESMF , only : ESMF_TERMORDER_SRCSEQ, ESMF_REGION_TOTAL + + ! input/out variables type(ESMF_Mesh) , intent(in) :: mesh_lnd type(ESMF_Mesh) , intent(in) :: mesh_mask @@ -662,6 +672,7 @@ subroutine lnd_set_ldomain_gridinfo_from_mesh(mesh, vm, gindex, begg, endg, isgr use clm_varcon , only : grlnd use fileutils , only : getfil use ncdio_pio , only : ncd_io, file_desc_t, ncd_pio_openfile, ncd_pio_closefile + use ESMF , only : ESMF_FieldRegridGetArea ! input/output variables type(ESMF_Mesh) , intent(in) :: mesh diff --git a/src/cpl/share_esmf/ndepStreamMod.F90 b/src/cpl/share_esmf/ndepStreamMod.F90 index 1a51382862..b1c9d1a0e5 100644 --- a/src/cpl/share_esmf/ndepStreamMod.F90 +++ b/src/cpl/share_esmf/ndepStreamMod.F90 @@ -7,7 +7,7 @@ module ndepStreamMod ! interpolation. ! ! !USES - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize, ESMF_END_ABORT use dshr_strdata_mod , only : shr_strdata_type use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_cl, CS => shr_kind_cs use spmdMod , only : mpicom, masterproc, iam From b76e55f01c8a39dd9abd48d6744baf94922d5d3e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 14:08:06 -0600 Subject: [PATCH 0336/2067] Use only clause for ESMF --- src/cpl/nuopc/lnd_comp_shr.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/nuopc/lnd_comp_shr.F90 b/src/cpl/nuopc/lnd_comp_shr.F90 index dd619c7648..8dc9738f7a 100644 --- a/src/cpl/nuopc/lnd_comp_shr.F90 +++ b/src/cpl/nuopc/lnd_comp_shr.F90 @@ -2,7 +2,7 @@ module lnd_comp_shr ! Model mesh info is here in order to be leveraged by CDEPS in line calls - use ESMF + use ESMF , only : ESMF_Clock, ESMF_Mesh use shr_kind_mod, only : r8 => shr_kind_r8, cl=>shr_kind_cl implicit none From c5609fb71d077c0c8a8228c9e5913e8f838afe90 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 15:03:21 -0600 Subject: [PATCH 0337/2067] Use only in ESMF use statements for time-manager --- src/utils/clm_time_manager.F90 | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index bbf3d8bb29..492dfb3a75 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -6,7 +6,11 @@ module clm_time_manager use spmdMod , only: masterproc use clm_varctl , only: iulog use clm_varcon , only: isecspday - use ESMF + use ESMF , only: ESMF_Clock, ESMF_Calendar, ESMF_MAXSTR, ESMF_Time, ESMF_TimeInterval + use ESMF , only: ESMF_TimeIntervalSet, ESMF_TimeSet, ESMF_TimeGet, ESMF_ClockGet + use ESMF , only: operator(==), operator(+), operator(<=), operator(>=) + use ESMF , only: operator(>), operator(<), operator(-) + use ESMF , only: ESMF_KIND_I8, ESMF_TimeIntervalGet implicit none private @@ -245,6 +249,8 @@ subroutine init_clock( start_date, ref_date, curr_date ) !--------------------------------------------------------------------------------- ! Purpose: Initialize the clock based on the start_date, ref_date and curr_date ! + use ESMF , only : ESMF_ClockCreate, ESMF_ClockAdvance + type(ESMF_Time), intent(in) :: start_date ! start date for run type(ESMF_Time), intent(in) :: ref_date ! reference date for time coordinate type(ESMF_Time), intent(in) :: curr_date ! current date (equal to start_date) @@ -553,6 +559,8 @@ subroutine init_calendar( ) !--------------------------------------------------------------------------------- ! Initialize calendar + use ESMF , only : ESMF_CalKind_Flag, ESMF_CALKIND_NOLEAP + use ESMF , only : ESMF_CALKIND_GREGORIAN, ESMF_CalendarCreate ! ! Local variables ! @@ -652,6 +660,7 @@ end subroutine timemgr_print subroutine advance_timestep() ! Increment the timestep number. + use ESMF , only : ESMF_ClockAdvance character(len=*), parameter :: sub = 'clm::advance_timestep' integer :: rc @@ -1782,6 +1791,7 @@ end subroutine timemgr_datediff !========================================================================================= subroutine chkrc(rc, mes) + use ESMF , only : ESMF_SUCCESS integer, intent(in) :: rc ! return code from time management library character(len=*), intent(in) :: mes ! error message if ( rc == ESMF_SUCCESS ) return @@ -1886,6 +1896,7 @@ subroutine timemgr_reset() ! does not explicitly initialize all variables). ! ! !USES: + use ESMF , only : ESMF_ClockDestroy ! ! !ARGUMENTS: ! @@ -1963,6 +1974,7 @@ subroutine for_test_set_curr_date(yr, mon, day, tod) ! *** Should only be used in unit tests!!! *** ! ! !USES: + use ESMF , only : ESMF_ClockSet ! ! !ARGUMENTS: integer, intent(in) :: yr ! year From 926fa821b6bfdd628419b6798f154ebc9b23941f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 16:04:44 -0600 Subject: [PATCH 0338/2067] Use only clause for ESMF for lilac lnd_comp_esmf --- src/cpl/lilac/lnd_comp_esmf.F90 | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/src/cpl/lilac/lnd_comp_esmf.F90 b/src/cpl/lilac/lnd_comp_esmf.F90 index c172ec8c06..298aa730c0 100644 --- a/src/cpl/lilac/lnd_comp_esmf.F90 +++ b/src/cpl/lilac/lnd_comp_esmf.F90 @@ -6,7 +6,14 @@ module lnd_comp_esmf !---------------------------------------------------------------------------- ! external libraries - use ESMF + use ESMF , only : ESMF_GridComp, ESMF_SUCCESS, ESMF_LogSet, ESMF_State + use ESMF , only : ESMF_Clock, ESMF_FieldBundle, ESMF_MAXSTR, ESMF_Field + use ESMF , only : ESMF_FieldCreate, ESMF_AttributeGet + use ESMF , only : ESMF_Time, ESMF_LogWrite, ESMF_LogFoundError, ESMF_Finalize + use ESMF , only : ESMF_FieldBundleAdd, ESMF_FieldBundleCreate + use ESMF , only : ESMF_ClockGet, ESMF_ClockGetAlarm, ESMF_LOGMSG_INFO + use ESMF , only : ESMF_TYPEKIND_R8, ESMF_MESHLOC_ELEMENT, ESMF_LOGERR_PASSTHRU + use ESMF , only : ESMF_END_ABORT, ESMF_TimeGet, ESMF_LOGMSG_ERROR use shr_mpi_mod , only : shr_mpi_bcast use perf_mod , only : t_startf, t_stopf, t_barrierf @@ -68,6 +75,8 @@ module lnd_comp_esmf subroutine lnd_register(comp, rc) ! Register the clm initial, run, and final phase methods with ESMF. + use ESMF , only : ESMF_GridCompSetEntryPoint + use ESMF , only : ESMF_METHOD_INITIALIZE, ESMF_METHOD_RUN, ESMF_METHOD_FINALIZE ! input/output argumenents type(ESMF_GridComp) :: comp ! CLM grid component @@ -97,6 +106,13 @@ subroutine lnd_init(comp, import_state, export_state, clock, rc) ! Initialize land surface model and obtain relevant atmospheric model arrays ! back from (i.e. albedos, surface temperature and snow cover over land). + ! Uses: + use ESMF , only : ESMF_VM, ESMF_VMGet, ESMF_VMGetCurrent + use ESMF , only : ESMF_DistGrid, ESMF_AttributeSet + use ESMF , only : ESMF_CalKind_Flag, ESMF_CALKIND_NOLEAP, ESMF_CALKIND_GREGORIAN + use ESMF , only : ESMF_TimeInterval, ESMF_TimeIntervalGet + use ESMF , only : ESMF_StateAdd + use ESMF , only : operator(==) ! input/output variables type(ESMF_GridComp) :: comp ! CLM gridded component @@ -509,6 +525,8 @@ subroutine lnd_run(gcomp, import_state, export_state, clock, rc) !------------------------ ! Run CTSM !------------------------ + use ESMF , only : ESMF_Alarm, ESMF_AlarmIsRinging, ESMF_AlarmRingerOff + use ESMF , only : ESMF_FAILURE, ESMF_ClockGetNextTime ! input/output variables type(ESMF_GridComp) :: gcomp ! CLM gridded component @@ -834,6 +852,8 @@ end subroutine lnd_final subroutine log_clock_advance(clock, logunit, rc) + !----------------------------------------------------------------------- + use ESMF , only : ESMF_ClockPrint ! input/output variables type(ESMF_Clock) :: clock integer , intent(in) :: logunit From bf9b98ecf18a10fe5f4e42af6cd5cd8d6c1e0251 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 16:06:02 -0600 Subject: [PATCH 0339/2067] Add only clause for lilac lnd_comp_shr --- src/cpl/lilac/lnd_comp_shr.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/lilac/lnd_comp_shr.F90 b/src/cpl/lilac/lnd_comp_shr.F90 index dd619c7648..8dc9738f7a 100644 --- a/src/cpl/lilac/lnd_comp_shr.F90 +++ b/src/cpl/lilac/lnd_comp_shr.F90 @@ -2,7 +2,7 @@ module lnd_comp_shr ! Model mesh info is here in order to be leveraged by CDEPS in line calls - use ESMF + use ESMF , only : ESMF_Clock, ESMF_Mesh use shr_kind_mod, only : r8 => shr_kind_r8, cl=>shr_kind_cl implicit none From 0d96301d3b9110ef55fa8be2235cbd44017fbd43 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 16:19:36 -0600 Subject: [PATCH 0340/2067] Add only clause for ESMF for lilac lnd_import_export --- src/cpl/lilac/lnd_import_export.F90 | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/cpl/lilac/lnd_import_export.F90 b/src/cpl/lilac/lnd_import_export.F90 index 32d1bace46..2da277dcee 100644 --- a/src/cpl/lilac/lnd_import_export.F90 +++ b/src/cpl/lilac/lnd_import_export.F90 @@ -1,6 +1,7 @@ module lnd_import_export - use ESMF + use ESMF , only : ESMF_State, ESMF_SUCCESS, ESMF_StatePrint, ESMF_LogWrite, ESMF_LOGMSG_INFO, ESMF_LOGMSG_INFO + use ESMF , only : ESMF_FAILURE use shr_kind_mod , only : r8 => shr_kind_r8, cx=>shr_kind_cx, cxx=>shr_kind_cxx, cs=>shr_kind_cs use shr_sys_mod , only : shr_sys_abort use shr_const_mod , only : fillvalue=>SHR_CONST_SPVAL @@ -667,6 +668,10 @@ subroutine state_getfldptr(State, fb, fldname, fldptr1d, fldptr2d, rc) ! ---------------------------------------------- ! Get pointer to a state field ! ---------------------------------------------- + use ESMF , only : ESMF_FieldStatus_Flag, ESMF_Field, ESMF_FieldBundle + use ESMF , only : ESMF_FIELDSTATUS_COMPLETE, ESMF_StateGet + use ESMF , only : ESMF_FieldBundleGet, ESMF_FieldGet + use ESMF , only : operator(/=) ! input/output variables type(ESMF_State), intent(in) :: State From 355043bf4b00ff98a4d5300b1ac6a9bbaf671596 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 17 Oct 2022 16:40:51 -0600 Subject: [PATCH 0341/2067] Add only clause for ESMF use statement in lilac lnd_shr_methods --- src/cpl/lilac/lnd_shr_methods.F90 | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/cpl/lilac/lnd_shr_methods.F90 b/src/cpl/lilac/lnd_shr_methods.F90 index 078aef08d9..f8ca9f4f3e 100644 --- a/src/cpl/lilac/lnd_shr_methods.F90 +++ b/src/cpl/lilac/lnd_shr_methods.F90 @@ -1,6 +1,9 @@ module lnd_shr_methods - use ESMF + use ESMF , only : ESMF_State, ESMF_MAXSTR, ESMF_StateGet + use ESMF , only : ESMF_LogWrite, ESMF_LOGMSG_ERROR, ESMF_FAILURE + use ESMF , only : ESMF_LOGERR_PASSTHRU, ESMF_LogFoundError + use ESMF , only : ESMF_SUCCESS, ESMF_Field, ESMF_LOGMSG_INFO use shr_kind_mod , only : r8 => shr_kind_r8, cl=>shr_kind_cl, cs=>shr_kind_cs use shr_sys_mod , only : shr_sys_abort @@ -93,6 +96,11 @@ subroutine field_getfldptr(field, rc, fldptr1, fldptr2, rank, abort) ! abort is true by default and will abort if fldptr is not yet allocated in field ! rank returns 0, 1, or 2. 0 means fldptr not allocated and abort=false ! ---------------------------------------------- + use ESMF , only : ESMF_FieldStatus_Flag, ESMF_Mesh + use ESMF , only : ESMF_FieldGet, ESMF_GEOMTYPE_GRID, ESMF_GEOMTYPE_MESH + use ESMF , only : ESMF_MeshGet, ESMF_GeomType_Flag + use ESMF , only : ESMF_FIELDSTATUS_COMPLETE + use ESMF , only : operator(/=), operator(==) ! input/output variables type(ESMF_Field) , intent(in) :: field From 3c9615ba7a4b493d1b6940bb4854bd919e398f5e Mon Sep 17 00:00:00 2001 From: Kaveh Karimi <4112646+ka7eh@users.noreply.github.com> Date: Tue, 18 Oct 2022 08:59:47 +0200 Subject: [PATCH 0342/2067] Fix per comment https://github.com/ESCOMP/CTSM/pull/1814/files#r997597612 --- src/biogeochem/CNProductsMod.F90 | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 176ff77c27..b6e5d6dad3 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -615,6 +615,13 @@ subroutine PartitionWoodFluxes(this, bounds, & if (pprod_tot > 0) then pprod10_frac = pprod10 / pprod_tot pprod100_frac = pprod100 / pprod_tot + ! Note that the patch-level fluxes are expressed per unit gridcell area. So, to go + ! from patch-level fluxes to gridcell-level fluxes, we simply add up the various + ! patch contributions, without having to multiply by any area weightings. + this%dwt_prod10_gain_grc(g) = this%dwt_prod10_gain_grc(g) + & + dwt_wood_product_gain_patch(p) * pprod10_frac + this%dwt_prod100_gain_grc(g) = this%dwt_prod100_gain_grc(g) + & + dwt_wood_product_gain_patch(p) * pprod100_frac else if (dwt_wood_product_gain_patch(p) > 0) then call endrun(& msg='ERROR: dwt_wood_product_gain_patch(p) > 0' // & From ed9610b0e38cce17658af4455f7ad300d07bbedc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 18 Oct 2022 14:51:00 -0600 Subject: [PATCH 0343/2067] Remove use_z0mg_2d code to read in roughness from surface dataset that work will be brought in with seperate work --- .../clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods | 1 - .../clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm | 2 -- .../clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods | 1 - .../clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm | 2 -- 4 files changed, 6 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods deleted file mode 100644 index 38bef34f6e..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../Meier2022_surf_rough diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm deleted file mode 100644 index 0a33a7a06c..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_f09NonCrop/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -use_z0mg_2d = .true. -fsurdat = '/glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c210624.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods deleted file mode 100644 index 38bef34f6e..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../Meier2022_surf_rough diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm deleted file mode 100644 index 6043dae4af..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough_all_hcruNonCrop/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -use_z0mg_2d = .true. -fsurdat = ' /glade/p/cesm/lmwg_dev/oleson/Z0_RonnieMeier/surfdata_360x720cru_16pfts_Irrig_CMIP6_simyr2000_c210624_2D.nc' From 0badb306998eea02dfa54896cdc689f4c47c94b8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 18 Oct 2022 14:55:07 -0600 Subject: [PATCH 0344/2067] Remove more use_z0mg_2d --- bld/CLMBuildNamelist.pm | 2 - bld/namelist_files/namelist_defaults_ctsm.xml | 6 -- .../namelist_definition_ctsm.xml | 6 -- cime_config/testdefs/ExpectedTestFails.xml | 7 -- cime_config/testdefs/testlist_clm.xml | 18 ----- .../clm/Meier2022_surf_rough/user_nl_clm | 1 - src/biogeophys/FrictionVelocityMod.F90 | 68 +------------------ src/main/clm_varctl.F90 | 1 - src/main/controlMod.F90 | 3 +- 9 files changed, 3 insertions(+), 109 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 77d0303e07..eb9b6a2644 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4156,8 +4156,6 @@ sub setup_logic_z0param { my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' )); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0m_snowmelt', 'z0param_method'=>$z0param_method ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0mg_2d', - 'z0param_method'=>$z0param_method ); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ea0b9f321c..6fb73aa693 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -501,12 +501,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .false. -.true. -.false. -.true. - - - diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index e2e84859ea..25b23050cd 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2777,12 +2777,6 @@ If TRUE use parameterization of snow z0m as a function of accumulated snow melt of Brock et al. (2006) - -If FALSE use constant ground z0m -If TRUE use spatially explicit ground z0m from Prigent et al. (2005) - - diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index b78eeb7509..56351ccfba 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -37,13 +37,6 @@ - - - FAIL - Half degree resolution issue - - - FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 8486c7fa04..35fdd3b979 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1315,24 +1315,6 @@ - - - - - - - - - - - - - - - - - - diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm index 86903538e2..00f8b1faf8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -1,6 +1,5 @@ z0param_method = 'Meier2022' use_z0m_snowmelt = .true. -use_z0mg_2d = .false. calc_human_stress_indices = 'NONE' ! Currently dies when turned on because of a negative humidity (about -31) in Wet Bulb calculation paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_params.RMz0.c220304.nc' diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 4f72215381..d831b42b97 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -13,7 +13,7 @@ module FrictionVelocityMod use decompMod , only : bounds_type use abortutils , only : endrun use clm_varcon , only : spval - use clm_varctl , only : use_cn, use_luna, z0param_method, use_z0mg_2d, use_z0m_snowmelt + use clm_varctl , only : use_cn, use_luna, z0param_method, use_z0m_snowmelt use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch @@ -95,7 +95,6 @@ module FrictionVelocityMod procedure, private :: InitCold procedure, private :: ReadNamelist procedure, private :: ReadParams - procedure, private :: ReadZ0M procedure, private, nopass :: StabilityFunc1 ! Stability function for rib < 0. procedure, private, nopass :: StabilityFunc2 ! Stability function for rib < 0. @@ -121,10 +120,6 @@ subroutine Init(this, bounds, NLFilename, params_ncid) call this%ReadNamelist(NLFilename) call this%ReadParams(params_ncid) - if(use_z0mg_2d) then - call this%ReadZ0M(bounds) - end if - end subroutine Init !------------------------------------------------------------------------ @@ -414,57 +409,6 @@ subroutine ReadParams( this, params_ncid ) end subroutine ReadParams - !----------------------------------------------------------------------- - subroutine ReadZ0M(this, bounds) - ! - ! !DESCRIPTION: - ! Initialize module time constant variables - ! - ! !USES: - use shr_log_mod, only : errMsg => shr_log_errMsg - use fileutils , only : getfil - use ncdio_pio , only : file_desc_t, ncd_defvar, ncd_io, ncd_pio_openfile, ncd_pio_closefile - use spmdMod , only : masterproc - use clm_varcon , only : grlnd - use clm_varctl , only : fsurdat - use ncdio_pio , only : ncd_io - use clm_varctl , only : iulog - - ! - ! !ARGUMENTS: - class(frictionvel_type) :: this - type(bounds_type), intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: c,g ! indices - type(file_desc_t) :: ncid ! netcdf id - character(len=256) :: locfn ! local filename - integer :: ier ! error status - logical :: readvar - real(r8), pointer :: z0mg2d (:) ! read in - ground z0m - !--------------------------------------------------------------------- - - ! Allocate module variable for ground z0m - - - call getfil (fsurdat, locfn, 0) - call ncd_pio_openfile (ncid, locfn, 0) - - - allocate(z0mg2d(bounds%begg:bounds%endg)) - call ncd_io(ncid=ncid, varname='Z0MG_2D', flag='read', data=z0mg2d, dim1name=grlnd, readvar=readvar) - if (.not. readvar) then - call endrun(msg=' ERROR: Z0MG_2D NOT on surfdata file'//errMsg(sourcefile, __LINE__)) - end if - write(iulog,*) 'Writing z0mg2d' - do c = bounds%begc, bounds%endc - g = col%gridcell(c) - this%z0mg_2D_col(c) = max(1.e-4_r8,z0mg2d(g)) - end do - deallocate(z0mg2d) - - end subroutine ReadZ0M - !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag) ! @@ -637,12 +581,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & z0mg(c) = this%zsno end if else - if(use_z0mg_2d) then - z0mg(c) = z0mg_2D(c) - else - z0mg(c) = this%zlnd - end if - + z0mg(c) = this%zlnd end if case ('Meier2022') ! Bare ground and ice have a different value l = col%landunit(c) @@ -664,9 +603,6 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & else - if(use_z0mg_2d) then - z0mg(c) = z0mg_2D(c) - else z0mg(c) = this%zlnd end if diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 6fe2c55692..7e14f64a3f 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -226,7 +226,6 @@ module clm_varctl character(len=64), public :: z0param_method logical, public :: use_z0m_snowmelt = .false. ! true => use snow z0m parameterization of Brock2006 - logical, public :: use_z0mg_2d = .false. ! true => use 2D ground z0m of Prigent2005 !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 427a95f98c..b06e852347 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -202,7 +202,7 @@ subroutine control_init(dtime) soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & - z0param_method, use_z0m_snowmelt, use_z0mg_2d + z0param_method, use_z0m_snowmelt ! vertical soil mixing variables namelist /clm_inparm/ & @@ -784,7 +784,6 @@ subroutine control_spmd() call mpi_bcast (snow_cover_fraction_method , len(snow_cover_fraction_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (z0param_method , len(z0param_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (use_z0m_snowmelt, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_z0mg_2d, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (single_column,1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (scmlat, 1, MPI_REAL8,0, mpicom, ier) call mpi_bcast (scmlon, 1, MPI_REAL8,0, mpicom, ier) From 357fea5eac6ca4ec7d40aad8661d91783bddfdea Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 19 Oct 2022 09:14:22 -0600 Subject: [PATCH 0345/2067] Correct so will compile --- src/biogeophys/FrictionVelocityMod.F90 | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index d831b42b97..71fdd30cd3 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -603,9 +603,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & else - z0mg(c) = this%zlnd - - end if + z0mg(c) = this%zlnd end if end select From e5cd7b02b86ed1d22557216583fb3fe4ede09d18 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 19 Oct 2022 11:25:42 -0600 Subject: [PATCH 0346/2067] Use parenthesis to clarify statement as required by the nag compiler on izumi --- src/biogeophys/FrictionVelocityMod.F90 | 2 +- src/biogeophys/LakeFluxesMod.F90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 05e6e40cff..5cd39b8319 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -577,7 +577,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (frac_sno(c) > 0._r8) then if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(c) = exp( (1.4_r8 * (-rpi/2.0_r8)) -0.31_r8) / 1000._r8 else z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 8aa2aa4a4f..38ecbc6fbb 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -366,7 +366,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('ZengWang2007') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 ) then - z0mg(p) = exp(1.4_r8 * -rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp((1.4_r8 * (-rpi/2.0_r8)) -0.31_r8) / 1000._r8 else z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 end if From b1b5960f28cf20be635418b11cad0a53415a6b20 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 19 Oct 2022 14:11:08 -0400 Subject: [PATCH 0347/2067] Updating fates parameter file to a place-holder api25 --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 2284518c58..1761ceffcc 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.58.1_api.24.1.0 +repo_url = https://github.com/rgknox/fates +branch = cnp-dynamic-root-allom-dfdd-api21-symfix required = True [externals_description] From 21d826b67bba1f3e6ac7e93fc46da88c37001b35 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 19 Oct 2022 14:11:23 -0400 Subject: [PATCH 0348/2067] Updating fates parameter file to a place-holder api25 p2 --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2686d62b9a..6f693e2af0 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -491,7 +491,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.24.0.0_12pft_c220608.nc +lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221019.nc From 26affffe1e3629e6caa5dff8b8a95d2728e26841 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 19 Oct 2022 14:11:52 -0400 Subject: [PATCH 0349/2067] Adding the dimension levclscpf --- src/main/histFileMod.F90 | 3 +++ src/utils/clmfates_interfaceMod.F90 | 8 ++++++-- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index a8c1c639b6..d5175342f0 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -2468,6 +2468,7 @@ subroutine htape_create (t, histrest) call ncd_defdim(lnfid, 'fates_levelcwd', num_elements_fates * ncwd, dimid) call ncd_defdim(lnfid, 'fates_levelage', num_elements_fates * nlevage, dimid) call ncd_defdim(lnfid, 'fates_levagefuel', nlevage * nfsc, dimid) + call ncd_defdim(lnfid, 'fates_levclscpf', nclmax*nlevsclass*numpft_fates, dimid) end if if ( .not. lhistrest )then @@ -5512,6 +5513,8 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, num2d = num_elements_fates*nlevage case ('fates_levagefuel') num2d = nlevage*nfsc + case('fates_levclscpf') + num2d = nclmax * nclmax * numpft_fates case('cft') if (cft_size > 0) then num2d = cft_size diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 9a04a9d66f..c6d4d16624 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2745,7 +2745,7 @@ subroutine init_history_io(this,bounds_proc) use FatesIOVariableKindMod, only : site_can_r8, site_cnlf_r8, site_cnlfpft_r8 use FatesIOVariableKindMod, only : site_height_r8, site_elem_r8, site_elpft_r8 use FatesIOVariableKindMod, only : site_elcwd_r8, site_elage_r8, site_agefuel_r8 - use FatesIOVariableKindMod, only : site_cdpf_r8, site_cdsc_r8 + use FatesIOVariableKindMod, only : site_cdpf_r8, site_cdsc_r8, site_clscpf_r8 use FatesIODimensionsMod, only : fates_bounds_type @@ -2844,7 +2844,7 @@ subroutine init_history_io(this,bounds_proc) case(site_soil_r8, site_size_pft_r8, site_size_r8, site_pft_r8, & site_age_r8, site_height_r8, site_coage_r8,site_coage_pft_r8, & - site_fuel_r8, site_cwdsc_r8, & + site_fuel_r8, site_cwdsc_r8, site_clscpf_r8, & site_can_r8,site_cnlf_r8, site_cnlfpft_r8, site_scag_r8, & site_scagpft_r8, site_agepft_r8, site_elem_r8, site_elpft_r8, & site_elcwd_r8, site_elage_r8, site_agefuel_r8, & @@ -3227,6 +3227,10 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates) fates%cdam_begin = 1 fates%cdam_end = nlevdamage + + fates%clscpf_begin = 1 + fates%clscpf_end = numpft_fates * nlevsclass * nclmax + call t_stopf('fates_hlm2fatesbnds') From 3ad2e7790225f361c986151e6173e2958f4d3b42 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 19 Oct 2022 14:27:20 -0400 Subject: [PATCH 0350/2067] Refactor of history interface with fates to accomodate api25 and new dimensions --- src/utils/clmfates_interfaceMod.F90 | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c6d4d16624..16a5f0fd7f 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1014,6 +1014,8 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! --------------------------------------------------------------------------------- call fates_hist%flush_hvars(nc,upfreq_in=1) + call fates_hist%flush_hvars(nc,upfreq_in=5) + ! --------------------------------------------------------------------------------- ! Part II: Call the FATES model now that input boundary conditions have been @@ -1088,7 +1090,8 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! --------------------------------------------------------------------------------- call fates_hist%update_history_dyn( nc, & this%fates(nc)%nsites, & - this%fates(nc)%sites) + this%fates(nc)%sites, & + this%fates(nc)%bc_in) if (masterproc) then write(iulog, *) 'clm: leaving fates model', bounds_clump%begg, & @@ -1659,12 +1662,13 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & ! ------------------------------------------------------------------------ call fates_hist%flush_hvars(nc,upfreq_in=1) do s = 1,this%fates(nc)%nsites - call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), & + call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), & upfreq_in=1) end do - call fates_hist%update_history_dyn( nc, & - this%fates(nc)%nsites, & - this%fates(nc)%sites) + call fates_hist%update_history_dyn( nc, & + this%fates(nc)%nsites, & + this%fates(nc)%sites, & + this%fates(nc)%bc_in) end if @@ -1831,12 +1835,13 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & ! ------------------------------------------------------------------------ call fates_hist%flush_hvars(nc,upfreq_in=1) do s = 1,this%fates(nc)%nsites - call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), & + call fates_hist%zero_site_hvars(this%fates(nc)%sites(s), & upfreq_in=1) end do - call fates_hist%update_history_dyn( nc, & - this%fates(nc)%nsites, & - this%fates(nc)%sites) + call fates_hist%update_history_dyn( nc, & + this%fates(nc)%nsites, & + this%fates(nc)%sites, & + this%fates(nc)%bc_in(s)) From 8a7777cf3717e33e7bb6f800ddc0f6f0cda4d4c5 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 14:44:48 -0600 Subject: [PATCH 0351/2067] Update neon_gcs_upload Correct path for initial conditions --- tools/site_and_regional/neon_gcs_upload | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/neon_gcs_upload b/tools/site_and_regional/neon_gcs_upload index d69534db19..9853c96849 100755 --- a/tools/site_and_regional/neon_gcs_upload +++ b/tools/site_and_regional/neon_gcs_upload @@ -147,7 +147,7 @@ def main(description): logger.warning("Could not find file {}".format(finidat_file)) continue newfile = basefile.replace(".postad.",".{}.".format(filedatestamp)) - upload_blob("neon-ncar-artifacts", finidat_file, newfile) + upload_blob("neon-ncar-artifacts", finidat_file, os.path.join("NEON","lnd","ctsm","initdata",newfile) ) if upload_history: logger.info("Upload history for {}".format(site)) From 1cf1d17ae749e4da3a8a80e7d2b76d3b332b489f Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 16:40:21 -0600 Subject: [PATCH 0352/2067] Update shell_commands BARR --- cime_config/usermods_dirs/NEON/BARR/shell_commands | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/BARR/shell_commands b/cime_config/usermods_dirs/NEON/BARR/shell_commands index 55037c6b37..29ddc20f52 100644 --- a/cime_config/usermods_dirs/NEON/BARR/shell_commands +++ b/cime_config/usermods_dirs/NEON/BARR/shell_commands @@ -1,7 +1,10 @@ +#!/bin/bash + ./xmlchange NEONSITE=BARR ./xmlchange PTS_LON=203.349781 ./xmlchange PTS_LAT=71.281711 -./xmlchange RUN_STARTDATE=2019-01-01 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019,DATM_YR_END=2022 -./xmlchange STOP_N=39 - +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From c2d185ea593254b9a1bc5934a9278fcfe9cf1086 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 16:43:15 -0600 Subject: [PATCH 0353/2067] Update shell_commands GUAN --- cime_config/usermods_dirs/NEON/GUAN/shell_commands | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/GUAN/shell_commands b/cime_config/usermods_dirs/NEON/GUAN/shell_commands index ee2eca82d9..f886245a1a 100644 --- a/cime_config/usermods_dirs/NEON/GUAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/GUAN/shell_commands @@ -1,6 +1,10 @@ +#!/bin/bash + ./xmlchange NEONSITE=GUAN ./xmlchange PTS_LON=293.13112 ./xmlchange PTS_LAT=17.96882 -./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From 5f1d190c391c130d44b4c18147e70e8ab96025a4 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 16:46:26 -0600 Subject: [PATCH 0354/2067] Update shell_commands LAJA --- cime_config/usermods_dirs/NEON/LAJA/shell_commands | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/LAJA/shell_commands b/cime_config/usermods_dirs/NEON/LAJA/shell_commands index 522818a697..7e946bf9b4 100644 --- a/cime_config/usermods_dirs/NEON/LAJA/shell_commands +++ b/cime_config/usermods_dirs/NEON/LAJA/shell_commands @@ -1,8 +1,11 @@ +#!/bin/bash ./xmlchange NEONSITE=LAJA ./xmlchange PTS_LON=292.92392 ./xmlchange PTS_LAT=18.02184 -./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From 63dd7795419a09d85e409ce8e6f57fe8fa842e4a Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 16:47:51 -0600 Subject: [PATCH 0355/2067] Update shell_commands LENO --- cime_config/usermods_dirs/NEON/LENO/shell_commands | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/LENO/shell_commands b/cime_config/usermods_dirs/NEON/LENO/shell_commands index 89583ed158..3af172e8f0 100644 --- a/cime_config/usermods_dirs/NEON/LENO/shell_commands +++ b/cime_config/usermods_dirs/NEON/LENO/shell_commands @@ -1,7 +1,11 @@ +#!/bin/bash + ./xmlchange NEONSITE=LENO ./xmlchange PTS_LON=271.83897 ./xmlchange PTS_LAT=31.8531 -./xmlchange RUN_STARTDATE=2021-01-01 ./xmlchange DATM_YR_ALIGN=2021,DATM_YR_START=2021 -./xmlchange STOP_N=15 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2021-01-01 + ./xmlchange STOP_N=15 +fi From b9acc522c886296d3206ec46ee0cae8b13d555eb Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 16:49:07 -0600 Subject: [PATCH 0356/2067] Update shell_commands MLBS --- cime_config/usermods_dirs/NEON/MLBS/shell_commands | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 9f70ecd662..6467bad1cc 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -1,6 +1,8 @@ +#!/bin/bash ./xmlchange NEONSITE=MLBS ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 -./xmlchange STOP_N=24 ./xmlchange DATM_YR_END=2019 - +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange STOP_N=24 +fi From d2f502a335863ddce85ca1882dd6fc1f9d758099 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 16:50:23 -0600 Subject: [PATCH 0357/2067] Update shell_commands MOAB --- cime_config/usermods_dirs/NEON/MOAB/shell_commands | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index d91513a92c..33fbf970c1 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -1,8 +1,8 @@ +#!/bin/bash ./xmlchange NEONSITE=MOAB ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 -./xmlchange RUN_STARTDATE=2018-01-01 -./xmlchange DATM_YR_ALIGN=2018,DATM_YR_START=2018,DATM_YR_END=2020 -./xmlchange STOP_N=36 - - +./xmlchange DATM_YR_END=2020 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange STOP_N=36 +fi From eb288b30412f6fcb760955102d18264e8ee7a43b Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 17:02:43 -0600 Subject: [PATCH 0358/2067] Update shell_commands ONAQ --- cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index f2e1640725..7399d95701 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -1,8 +1,8 @@ +#!/bin/bash ./xmlchange NEONSITE=ONAQ ./xmlchange PTS_LON=276.49815 ./xmlchange PTS_LAT=35.68839 -./xmlchange RUN_STARTDATE=2018-01-01 -./xmlchange DATM_YR_ALIGN=2018,DATM_YR_START=2018,DATM_YR_END=2019 -./xmlchange STOP_N=24 - - +./xmlchange DATM_YR_END=2019 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange STOP_N=24 +fi From 973044218ae6be89e1539a3e73f861e09a323a67 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 17:04:38 -0600 Subject: [PATCH 0359/2067] Update shell_commands TEAK --- cime_config/usermods_dirs/NEON/TEAK/shell_commands | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 5309888a12..0392a36dce 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -1,7 +1,9 @@ +#!/bin/bash ./xmlchange NEONSITE=TEAK ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 -./xmlchange RUN_STARTDATE=2019-01-01 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 - +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From d8b1d887e837ce44ed5358baf14267abf1189a87 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 17:05:38 -0600 Subject: [PATCH 0360/2067] Update shell_commands TOOL --- cime_config/usermods_dirs/NEON/TOOL/shell_commands | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/TOOL/shell_commands b/cime_config/usermods_dirs/NEON/TOOL/shell_commands index fc2551390b..9f6403a9c6 100644 --- a/cime_config/usermods_dirs/NEON/TOOL/shell_commands +++ b/cime_config/usermods_dirs/NEON/TOOL/shell_commands @@ -1,8 +1,9 @@ +#!/bin/bash ./xmlchange NEONSITE=TOOL ./xmlchange PTS_LON=210.629872 ./xmlchange PTS_LAT=68.66045 -./xmlchange RUN_STARTDATE=2020-01-01 ./xmlchange DATM_YR_ALIGN=2020,DATM_YR_START=2020 -./xmlchange STOP_N=27 - - +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2020-01-01 + ./xmlchange STOP_N=27 +fi From 279a54d68feb7cef9b6a72743a63222e5bd7617f Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 17:06:49 -0600 Subject: [PATCH 0361/2067] Update shell_commands WREF --- cime_config/usermods_dirs/NEON/WREF/shell_commands | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index bbb0e14312..ccf6c75138 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -1,7 +1,9 @@ +#!/bin/bash ./xmlchange NEONSITE=WREF ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 -./xmlchange RUN_STARTDATE=2019-01-01 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 - +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From 06b4059e7ad0941abf9765350e4f3fd2dc738428 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 17:07:30 -0600 Subject: [PATCH 0362/2067] Update shell_commands YELL --- cime_config/usermods_dirs/NEON/YELL/shell_commands | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index c32b11ef7d..0207e56265 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -1,7 +1,9 @@ +#!/bin/bash ./xmlchange NEONSITE=YELL ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 -./xmlchange RUN_STARTDATE=2019-01-01 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 -# ./xmlchange RUN_STARTDATE=2018-08-01 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From f9831ac7f6d79ba87927ea75971805a2f137649b Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 19 Oct 2022 17:10:21 -0600 Subject: [PATCH 0363/2067] Update neon_gcs_upload removed unused code, per @ekluzek 's suggestion --- tools/site_and_regional/neon_gcs_upload | 3 --- 1 file changed, 3 deletions(-) diff --git a/tools/site_and_regional/neon_gcs_upload b/tools/site_and_regional/neon_gcs_upload index 9853c96849..40afef8e74 100755 --- a/tools/site_and_regional/neon_gcs_upload +++ b/tools/site_and_regional/neon_gcs_upload @@ -121,9 +121,6 @@ def main(description): from there, """ - #if not os.path.isfile(os.path.join(os.getenv("HOME"),".aws","credentials")): - # raise FileNotFoundError("User account must have valid aws credentials to run this script.") - cesmroot = path_to_ctsm_root() os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = os.path.join(os.environ["HOME"],'.uploadGCSkey.json') #os.path.join(os.environ["HOME"],"gcwriter") From 730bdbed4b135e50753ee1178a543f3c17089067 Mon Sep 17 00:00:00 2001 From: will wieder Date: Fri, 21 Oct 2022 08:53:15 -0600 Subject: [PATCH 0364/2067] Update shell_commands SJER --- cime_config/usermods_dirs/NEON/SJER/shell_commands | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 9d3ee15a81..01cf50d337 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -1,8 +1,9 @@ +#!/bin/bash ./xmlchange NEONSITE=SJER ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 -./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 - -#./xmlchange RUN_STARTDATE=2018-09-01 +if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi From 78cb00e504482739990b1182852d613a3b5d5769 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sat, 22 Oct 2022 08:19:54 -0600 Subject: [PATCH 0365/2067] trying to address cases with non-standard start/end years --- cime_config/usermods_dirs/NEON/SJER/shell_commands | 8 +++++--- .../usermods_dirs/NEON/defaults/shell_commands | 7 ++++++- tools/site_and_regional/run_neon.py | 12 +++++++----- 3 files changed, 18 insertions(+), 9 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 9d3ee15a81..cd7bf2fe2d 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -1,8 +1,10 @@ +#!/bin/bash ./xmlchange NEONSITE=SJER ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 -./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -./xmlchange STOP_N=39 +if [ "`./xmlquery CASE --value`" =~ "*transient" ]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi -#./xmlchange RUN_STARTDATE=2018-09-01 diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 53e445e06a..8957af3f9b 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -1,11 +1,16 @@ +#!/bin/bash ./xmlchange CLM_USRDAT_NAME=NEON -./xmlchange RUN_STARTDATE=2018-01-01 ./xmlchange CLM_NML_USE_CASE=1850-2100_SSP3-7.0_transient ./xmlchange CCSM_CO2_PPMV=408.83 ./xmlchange DATM_PRESAERO=SSP3-7.0 ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 +if [ "`./xmlquery CASE --value`" =~ "*transient" ]; then + ./xmlchange DATM_YR_END=2022 + ./xmlchange RUN_STARTDATE=2018-01-01 + ./xmlchange STOP_N=51 +fi # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) ./xmlchange PIO_TYPENAME=netcdf diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index e0aae36274..fe93014d76 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -539,10 +539,12 @@ def run_case( if not self.set_ref_case(case): return case.set_value("STOP_OPTION", "nmonths") - case.set_value("STOP_N", self.diff_month()) - case.set_value("DATM_YR_ALIGN", self.start_year) - case.set_value("DATM_YR_START", self.start_year) - case.set_value("DATM_YR_END", self.end_year) + # Hard wire the with usermods for now + # TODO this wil have to be fixed when we get new NEON data + #case.set_value("STOP_N", self.diff_month()) + #case.set_value("DATM_YR_ALIGN", self.start_year) + #case.set_value("DATM_YR_START", self.start_year) + #case.set_value("DATM_YR_END", self.end_year) case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) else: @@ -558,7 +560,7 @@ def run_case( else: case.set_value("DATM_YR_END", self.end_year - 1) - # Let's no be so clevar with start / end dates + # Let's no be so clever with start / end dates #case.set_value("DATM_YR_ALIGN", int(args.start_date[0:4])) #case.set_value("DATM_YR_START", int(args.start_date[0:4])) #case.set_value("DATM_YR_END", int(args.end_date[0:4])) From 69d25d9bf202c726c9e3bc806473975ac57a9ea5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 22 Oct 2022 13:30:15 -0600 Subject: [PATCH 0366/2067] Correct the syntax so the bash if statements work --- cime_config/usermods_dirs/NEON/BARR/shell_commands | 2 +- cime_config/usermods_dirs/NEON/GUAN/shell_commands | 2 +- cime_config/usermods_dirs/NEON/LAJA/shell_commands | 2 +- cime_config/usermods_dirs/NEON/LENO/shell_commands | 2 +- cime_config/usermods_dirs/NEON/MLBS/shell_commands | 2 +- cime_config/usermods_dirs/NEON/MOAB/shell_commands | 2 +- cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 2 +- cime_config/usermods_dirs/NEON/SJER/shell_commands | 2 +- cime_config/usermods_dirs/NEON/TEAK/shell_commands | 2 +- cime_config/usermods_dirs/NEON/TOOL/shell_commands | 2 +- cime_config/usermods_dirs/NEON/WREF/shell_commands | 2 +- cime_config/usermods_dirs/NEON/YELL/shell_commands | 2 +- cime_config/usermods_dirs/NEON/defaults/shell_commands | 2 +- 13 files changed, 13 insertions(+), 13 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/BARR/shell_commands b/cime_config/usermods_dirs/NEON/BARR/shell_commands index 29ddc20f52..321d7e7daf 100644 --- a/cime_config/usermods_dirs/NEON/BARR/shell_commands +++ b/cime_config/usermods_dirs/NEON/BARR/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LON=203.349781 ./xmlchange PTS_LAT=71.281711 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/GUAN/shell_commands b/cime_config/usermods_dirs/NEON/GUAN/shell_commands index f886245a1a..3ed68c34e5 100644 --- a/cime_config/usermods_dirs/NEON/GUAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/GUAN/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LON=293.13112 ./xmlchange PTS_LAT=17.96882 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/LAJA/shell_commands b/cime_config/usermods_dirs/NEON/LAJA/shell_commands index 7e946bf9b4..45bd0f06b0 100644 --- a/cime_config/usermods_dirs/NEON/LAJA/shell_commands +++ b/cime_config/usermods_dirs/NEON/LAJA/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=292.92392 ./xmlchange PTS_LAT=18.02184 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/LENO/shell_commands b/cime_config/usermods_dirs/NEON/LENO/shell_commands index 3af172e8f0..a8c85a0cd1 100644 --- a/cime_config/usermods_dirs/NEON/LENO/shell_commands +++ b/cime_config/usermods_dirs/NEON/LENO/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LON=271.83897 ./xmlchange PTS_LAT=31.8531 ./xmlchange DATM_YR_ALIGN=2021,DATM_YR_START=2021 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2021-01-01 ./xmlchange STOP_N=15 fi diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 6467bad1cc..ba64a253eb 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -3,6 +3,6 @@ ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 ./xmlchange DATM_YR_END=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 33fbf970c1..558dfe6d34 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -3,6 +3,6 @@ ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 ./xmlchange DATM_YR_END=2020 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange STOP_N=36 fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 7399d95701..2fb2b67f14 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -3,6 +3,6 @@ ./xmlchange PTS_LON=276.49815 ./xmlchange PTS_LAT=35.68839 ./xmlchange DATM_YR_END=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index cd7bf2fe2d..61207df4ad 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CASE --value`" =~ "*transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 0392a36dce..40cee5dacd 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/TOOL/shell_commands b/cime_config/usermods_dirs/NEON/TOOL/shell_commands index 9f6403a9c6..480ad833f0 100644 --- a/cime_config/usermods_dirs/NEON/TOOL/shell_commands +++ b/cime_config/usermods_dirs/NEON/TOOL/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=210.629872 ./xmlchange PTS_LAT=68.66045 ./xmlchange DATM_YR_ALIGN=2020,DATM_YR_START=2020 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2020-01-01 ./xmlchange STOP_N=27 fi diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index ccf6c75138..e38a22a502 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index 0207e56265..0d87c40b0c 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [ "`./xmlquery CLM_NML_USE_CASE --value`" =~ "*_transient" ]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 8957af3f9b..f8288abe60 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -6,7 +6,7 @@ ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 -if [ "`./xmlquery CASE --value`" =~ "*transient" ]; then +if [[ `./xmlquery CASE --value` =~ .+_transient ]]; then ./xmlchange DATM_YR_END=2022 ./xmlchange RUN_STARTDATE=2018-01-01 ./xmlchange STOP_N=51 From 7f839cc1bdbfa2d394f451c140e6ea14edc78892 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 23 Oct 2022 08:53:12 -0600 Subject: [PATCH 0367/2067] additional modifications needed for usermods to work as intended --- .../NEON/defaults/shell_commands | 2 +- tools/site_and_regional/run_neon.py | 27 ++++++++++--------- 2 files changed, 16 insertions(+), 13 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index f8288abe60..743880366b 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -6,7 +6,7 @@ ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 -if [[ `./xmlquery CASE --value` =~ .+_transient ]]; then +if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then ./xmlchange DATM_YR_END=2022 ./xmlchange RUN_STARTDATE=2018-01-01 ./xmlchange STOP_N=51 diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index fe93014d76..a226a42e1e 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -514,7 +514,6 @@ def run_case( with Case(case_root, read_only=False) as case: # in order to avoid the complication of leap years we always set the run_length in units of days. case.set_value("STOP_OPTION", "ndays") - case.set_value("STOP_N", run_length) case.set_value("REST_OPTION", "end") case.set_value("CONTINUE_RUN", False) case.set_value("NEONVERSION", version) @@ -524,6 +523,8 @@ def run_case( case.set_value("RUN_REFDATE", "0018-01-01") case.set_value("RUN_STARTDATE", "0018-01-01") case.set_value("RESUBMIT", 1) + case.set_value("STOP_N", run_length) + else: case.set_value("CLM_FORCE_COLDSTART", "off") case.set_value("CLM_ACCELERATED_SPINUP", "off") @@ -531,6 +532,7 @@ def run_case( if run_type == "postad": self.set_ref_case(case) + case.set_value("STOP_N", run_length) if run_type == "transient": if self.finidat: @@ -547,18 +549,19 @@ def run_case( #case.set_value("DATM_YR_END", self.end_year) case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) - else: + # Turning all this off for usermod controsl over start, align, and end year + #else: # for the spinup we want the start and end on year boundaries - if self.start_month == 1: - case.set_value("DATM_YR_ALIGN", self.start_year) - case.set_value("DATM_YR_START", self.start_year) - elif self.start_year + 1 <= self.end_year: - case.set_value("DATM_YR_ALIGN", self.start_year + 1) - case.set_value("DATM_YR_START", self.start_year + 1) - if self.end_month == 12: - case.set_value("DATM_YR_END", self.end_year) - else: - case.set_value("DATM_YR_END", self.end_year - 1) + #if self.start_month == 1: + # case.set_value("DATM_YR_ALIGN", self.start_year) + # case.set_value("DATM_YR_START", self.start_year) + #elif self.start_year + 1 <= self.end_year: + # case.set_value("DATM_YR_ALIGN", self.start_year + 1) + # case.set_value("DATM_YR_START", self.start_year + 1) + #if self.end_month == 12: + # case.set_value("DATM_YR_END", self.end_year) + #else: + # case.set_value("DATM_YR_END", self.end_year - 1) # Let's no be so clever with start / end dates #case.set_value("DATM_YR_ALIGN", int(args.start_date[0:4])) From bcbc456381df4e96925ca76df0488cdabf2a861d Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 23 Oct 2022 09:13:56 -0600 Subject: [PATCH 0368/2067] correction for DATM_YR_END in ad and postAD --- tools/site_and_regional/run_neon.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index a226a42e1e..957c313df0 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -550,7 +550,7 @@ def run_case( case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) # Turning all this off for usermod controsl over start, align, and end year - #else: + else: # for the spinup we want the start and end on year boundaries #if self.start_month == 1: # case.set_value("DATM_YR_ALIGN", self.start_year) @@ -558,10 +558,10 @@ def run_case( #elif self.start_year + 1 <= self.end_year: # case.set_value("DATM_YR_ALIGN", self.start_year + 1) # case.set_value("DATM_YR_START", self.start_year + 1) - #if self.end_month == 12: - # case.set_value("DATM_YR_END", self.end_year) - #else: - # case.set_value("DATM_YR_END", self.end_year - 1) + if self.end_month == 12: + case.set_value("DATM_YR_END", self.end_year) + else: + case.set_value("DATM_YR_END", self.end_year - 1) # Let's no be so clever with start / end dates #case.set_value("DATM_YR_ALIGN", int(args.start_date[0:4])) From 8e7efb03ebcaeeee969c349b1eea14ad56a87aac Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 25 Oct 2022 15:40:51 -0600 Subject: [PATCH 0369/2067] Working version of run_neon.py, I tried running shell_commands after the case is setup, but that does not work as the read of env_run.xml would need to be done again --- tools/site_and_regional/run_neon.py | 41 +++++++++++++---------------- 1 file changed, 19 insertions(+), 22 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 957c313df0..5c605b2c6d 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -83,7 +83,7 @@ import CIME.build as build from standard_script_setup import * from CIME.case import Case -from CIME.utils import safe_copy, expect, symlink_force +from CIME.utils import safe_copy, expect, symlink_force, run_cmd_no_fail from argparse import RawTextHelpFormatter from CIME.locked_files import lock_file, unlock_file @@ -511,10 +511,12 @@ def run_case( case_root, keepexe=True, user_mods_dirs=user_mods_dirs ) + print("---- Before Case----") with Case(case_root, read_only=False) as case: - # in order to avoid the complication of leap years we always set the run_length in units of days. - case.set_value("STOP_OPTION", "ndays") - case.set_value("REST_OPTION", "end") + if run_type is not"transient": + # in order to avoid the complication of leap years we always set the run_length in units of days. + case.set_value("STOP_OPTION", "ndays") + case.set_value("REST_OPTION", "end") case.set_value("CONTINUE_RUN", False) case.set_value("NEONVERSION", version) if run_type == "ad": @@ -534,49 +536,44 @@ def run_case( self.set_ref_case(case) case.set_value("STOP_N", run_length) + # For transient cases STOP will be set in the user_mod_directory if run_type == "transient": if self.finidat: case.set_value("RUN_TYPE", "startup") else: if not self.set_ref_case(case): return - case.set_value("STOP_OPTION", "nmonths") - # Hard wire the with usermods for now - # TODO this wil have to be fixed when we get new NEON data - #case.set_value("STOP_N", self.diff_month()) - #case.set_value("DATM_YR_ALIGN", self.start_year) - #case.set_value("DATM_YR_START", self.start_year) - #case.set_value("DATM_YR_END", self.end_year) case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) # Turning all this off for usermod controsl over start, align, and end year else: # for the spinup we want the start and end on year boundaries - #if self.start_month == 1: - # case.set_value("DATM_YR_ALIGN", self.start_year) - # case.set_value("DATM_YR_START", self.start_year) - #elif self.start_year + 1 <= self.end_year: - # case.set_value("DATM_YR_ALIGN", self.start_year + 1) - # case.set_value("DATM_YR_START", self.start_year + 1) if self.end_month == 12: case.set_value("DATM_YR_END", self.end_year) else: case.set_value("DATM_YR_END", self.end_year - 1) - # Let's no be so clever with start / end dates - #case.set_value("DATM_YR_ALIGN", int(args.start_date[0:4])) - #case.set_value("DATM_YR_START", int(args.start_date[0:4])) - #case.set_value("DATM_YR_END", int(args.end_date[0:4])) - if not rundir: rundir = case.get_value("RUNDIR") + print("---- modify_user_nl----") self.modify_user_nl(case_root, run_type, rundir) + # Run the shell_commands again, now that more settings are there + #print("---- shell_commands ---") + #run_cmd_no_fail( "./shell_commands" ) + #casedir = case.get_value("CASEROOT") + #envrunfilename = os.path.join( casedir, "env_run.xml" ) + #print( envrunfilename ) + #case.invalidate( envrunfilename ) + + print("---- create_namelists ---") case.create_namelists() # explicitly run check_input_data + print("---- check_input ---") case.check_all_input_data() if not setup_only: + print("---- submit ---") case.submit(no_batch=no_batch) def set_ref_case(self, case): From 1c5e9002a3b3297f5565270d6fbeed5c81039bc7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 25 Oct 2022 20:45:06 -0600 Subject: [PATCH 0370/2067] Remove some of the prints I added, and the shell_commands part I commented out, and most importantly use a transient compset for the transient case --- tools/site_and_regional/run_neon.py | 18 ++++-------------- 1 file changed, 4 insertions(+), 14 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 5c605b2c6d..1805ed7ebd 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -511,7 +511,6 @@ def run_case( case_root, keepexe=True, user_mods_dirs=user_mods_dirs ) - print("---- Before Case----") with Case(case_root, read_only=False) as case: if run_type is not"transient": # in order to avoid the complication of leap years we always set the run_length in units of days. @@ -556,24 +555,12 @@ def run_case( if not rundir: rundir = case.get_value("RUNDIR") - print("---- modify_user_nl----") self.modify_user_nl(case_root, run_type, rundir) - # Run the shell_commands again, now that more settings are there - #print("---- shell_commands ---") - #run_cmd_no_fail( "./shell_commands" ) - #casedir = case.get_value("CASEROOT") - #envrunfilename = os.path.join( casedir, "env_run.xml" ) - #print( envrunfilename ) - #case.invalidate( envrunfilename ) - - print("---- create_namelists ---") case.create_namelists() # explicitly run check_input_data - print("---- check_input ---") case.check_all_input_data() if not setup_only: - print("---- submit ---") case.submit(no_batch=no_batch) def set_ref_case(self, case): @@ -786,7 +773,10 @@ def main(description): # -- so no need to define a base_case for every site. res = "CLM_USRDAT" - compset = "I1PtClm51Bgc" + if run_type == "transient": + compset = "IHist1PtClm51Bgc" + else: + compset = "I1PtClm51Bgc" # -- Looping over neon sites From 13efae5d2bcb0077c17c8acdd4013339e8fa4af1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 25 Oct 2022 20:46:30 -0600 Subject: [PATCH 0371/2067] Use the compset to determine if this is a transient case or not --- cime_config/usermods_dirs/NEON/BARR/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/GUAN/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/LAJA/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/LENO/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/MLBS/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/MOAB/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/SJER/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/TEAK/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/TOOL/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/WREF/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/YELL/shell_commands | 3 ++- cime_config/usermods_dirs/NEON/defaults/shell_commands | 7 ++++++- 13 files changed, 30 insertions(+), 13 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/BARR/shell_commands b/cime_config/usermods_dirs/NEON/BARR/shell_commands index 321d7e7daf..713331c0ee 100644 --- a/cime_config/usermods_dirs/NEON/BARR/shell_commands +++ b/cime_config/usermods_dirs/NEON/BARR/shell_commands @@ -4,7 +4,8 @@ ./xmlchange PTS_LON=203.349781 ./xmlchange PTS_LAT=71.281711 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/GUAN/shell_commands b/cime_config/usermods_dirs/NEON/GUAN/shell_commands index 3ed68c34e5..4214a35e3c 100644 --- a/cime_config/usermods_dirs/NEON/GUAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/GUAN/shell_commands @@ -4,7 +4,8 @@ ./xmlchange PTS_LON=293.13112 ./xmlchange PTS_LAT=17.96882 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/LAJA/shell_commands b/cime_config/usermods_dirs/NEON/LAJA/shell_commands index 45bd0f06b0..a7bda447e6 100644 --- a/cime_config/usermods_dirs/NEON/LAJA/shell_commands +++ b/cime_config/usermods_dirs/NEON/LAJA/shell_commands @@ -3,7 +3,8 @@ ./xmlchange PTS_LON=292.92392 ./xmlchange PTS_LAT=18.02184 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/LENO/shell_commands b/cime_config/usermods_dirs/NEON/LENO/shell_commands index a8c85a0cd1..c5ae590186 100644 --- a/cime_config/usermods_dirs/NEON/LENO/shell_commands +++ b/cime_config/usermods_dirs/NEON/LENO/shell_commands @@ -4,7 +4,8 @@ ./xmlchange PTS_LON=271.83897 ./xmlchange PTS_LAT=31.8531 ./xmlchange DATM_YR_ALIGN=2021,DATM_YR_START=2021 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2021-01-01 ./xmlchange STOP_N=15 fi diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index ba64a253eb..e0a2ea5443 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -3,6 +3,7 @@ ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 ./xmlchange DATM_YR_END=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 558dfe6d34..c90aaa30d4 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -3,6 +3,7 @@ ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 ./xmlchange DATM_YR_END=2020 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange STOP_N=36 fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 2fb2b67f14..df2ca55dad 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -3,6 +3,7 @@ ./xmlchange PTS_LON=276.49815 ./xmlchange PTS_LAT=35.68839 ./xmlchange DATM_YR_END=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 61207df4ad..6e05d23792 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -3,7 +3,8 @@ ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 40cee5dacd..9058eda022 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -3,7 +3,8 @@ ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/TOOL/shell_commands b/cime_config/usermods_dirs/NEON/TOOL/shell_commands index 480ad833f0..f1f2e1771a 100644 --- a/cime_config/usermods_dirs/NEON/TOOL/shell_commands +++ b/cime_config/usermods_dirs/NEON/TOOL/shell_commands @@ -3,7 +3,8 @@ ./xmlchange PTS_LON=210.629872 ./xmlchange PTS_LAT=68.66045 ./xmlchange DATM_YR_ALIGN=2020,DATM_YR_START=2020 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2020-01-01 ./xmlchange STOP_N=27 fi diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index e38a22a502..807055ae6e 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -3,7 +3,8 @@ ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index 0d87c40b0c..800d7d01ad 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -3,7 +3,8 @@ ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 ./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 743880366b..e34df28191 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -6,9 +6,14 @@ ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 -if [[ `./xmlquery CLM_NML_USE_CASE --value` =~ .+_transient ]]; then +use_case=`./xmlquery CLM_NML_USE_CASE --value` +compset=`./xmlquery COMPSET --value` +# For a transient case run the whole length and don't cycle +if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2022 ./xmlchange RUN_STARTDATE=2018-01-01 + # Number of months that can be run for the full transient case + ./xmlchange STOP_OPTION="nmonths" ./xmlchange STOP_N=51 fi From 6950b1f2e7020929ec6e41ecc5ffce9efa4f622a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 25 Oct 2022 20:56:54 -0600 Subject: [PATCH 0372/2067] Have the last year for the datm data be 2022, so that it will work for all cases: ad, postad, and transient. This does mean the ad and postad cases won't have this data align with the meterological forcing data, but that's probably fine --- .../usermods_dirs/NEON/defaults/user_nl_datm_streams | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams index 6244eed2fa..f1af044c31 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams @@ -1,16 +1,16 @@ presaero.SSP3-7.0:datafiles = $DIN_LOC_ROOT/atm/cam/chem/trop_mozart_aero/aero/aerodep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.001_2018-2030_monthly_0.9x1.25_c210826.nc presaero.SSP3-7.0:year_first=2018 -presaero.SSP3-7.0:year_last=2030 +presaero.SSP3-7.0:year_last=2022 presaero.SSP3-7.0:year_align=2018 presaero.SSP3-7.0:dtlimit=30 presndep.SSP3-7.0:datafiles = $DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc presndep.SSP3-7.0:year_first=2018 -presndep.SSP3-7.0:year_last=2030 +presndep.SSP3-7.0:year_last=2022 presndep.SSP3-7.0:year_align=2018 presndep.SSP3-7.0:dtlimit=30 preso3.SSP3-7.0:year_first=2018 -preso3.SSP3-7.0:year_last=2030 +preso3.SSP3-7.0:year_last=2022 preso3.SSP3-7.0:year_align=2018 preso3.SSP3-7.0:dtlimit=30 From a5780c0bad6a5fae314b467af9ae6bc0bc8b200f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 26 Oct 2022 16:15:04 -0600 Subject: [PATCH 0373/2067] Set CLM streams to go until 2022 as well --- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 49528a524e..10880bd619 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -22,13 +22,13 @@ flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but wi fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c221014.nc" model_year_align_urbantv = 2018 stream_year_first_urbantv = 2018 -stream_year_last_urbantv = 2021 +stream_year_last_urbantv = 2022 stream_year_first_ndep = 2018 model_year_align_ndep = 2018 -stream_year_last_ndep = 2021 +stream_year_last_ndep = 2022 model_year_align_popdens = 2018 stream_year_first_popdens = 2018 -stream_year_last_popdens = 2021 +stream_year_last_popdens = 2022 stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' !stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc' From e51d3a456bf77f502c2db4dbec4fee2599f7aba1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 26 Oct 2022 16:16:51 -0600 Subject: [PATCH 0374/2067] Set the use-case by the type of compset --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index e34df28191..1ab3fdca14 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -1,12 +1,10 @@ #!/bin/bash ./xmlchange CLM_USRDAT_NAME=NEON -./xmlchange CLM_NML_USE_CASE=1850-2100_SSP3-7.0_transient ./xmlchange CCSM_CO2_PPMV=408.83 ./xmlchange DATM_PRESAERO=SSP3-7.0 ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 -use_case=`./xmlquery CLM_NML_USE_CASE --value` compset=`./xmlquery COMPSET --value` # For a transient case run the whole length and don't cycle if [[ $compset =~ ^HIST ]]; then @@ -15,6 +13,9 @@ if [[ $compset =~ ^HIST ]]; then # Number of months that can be run for the full transient case ./xmlchange STOP_OPTION="nmonths" ./xmlchange STOP_N=51 + ./xmlchange CLM_NML_USE_CASE="2018-PD_transient" +else + ./xmlchange CLM_NML_USE_CASE="2018_control" fi # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) From 1947a3e8dff5d1b87c91d06b9b539a5029ea0fa4 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 27 Oct 2022 13:42:45 -0600 Subject: [PATCH 0375/2067] Remove commented-out lines --- src/cpl/nuopc/lnd_comp_nuopc.F90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90 index 6f8153eb0d..3852a1bf1b 100644 --- a/src/cpl/nuopc/lnd_comp_nuopc.F90 +++ b/src/cpl/nuopc/lnd_comp_nuopc.F90 @@ -1286,8 +1286,6 @@ subroutine clm_orbital_update(clock, logunit, mastertask, eccen, obliqr, lambm0 end subroutine clm_orbital_update subroutine CheckImport(gcomp, rc) -! use NUOPC -! use ESMF type(ESMF_GridComp) :: gcomp integer, intent(out) :: rc character(len=*) , parameter :: subname = "("//__FILE__//":CheckImport)" From e79d7d3156a79aeca9ff6ade322d926492ea0096 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 13:56:52 -0600 Subject: [PATCH 0376/2067] Removed commented-out lines of code. --- src/main/clm_driver.F90 | 2 -- src/main/clm_initializeMod.F90 | 2 -- 2 files changed, 4 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index de8a53963e..02efebe268 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -479,7 +479,6 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro canopystate_inst, water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, & energyflux_inst) -! write(iulog,*) 'Exited clm_drv_init() in clm_drv()' call topo_inst%UpdateTopo(bounds_clump, & filter(nc)%num_icec, filter(nc)%icec, & @@ -1043,7 +1042,6 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Update crop calendars ! ============================================================================ call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, filter_inactive_and_active(nc)%pcropp, crop_inst) -! write(iulog,*) 'Exited cropcal_interp() in clm_drv()' end if ! ============================================================================ diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index e57c802d95..46d6b4ecc0 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -573,10 +573,8 @@ subroutine initialize2(ni,nj) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, filter_inactive_and_active(nc)%pcropp, crop_inst) -! write(iulog,*) 'Exited cropcal_interp() in initialize2()' end do !$OMP END PARALLEL DO -! call cropcal_interp(bounds_clump, crop_inst) end if call t_stopf('init_cropcal') From ee53b4e01feafaac5b73de4b4e8d187af6c9e8ab Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 14:00:47 -0600 Subject: [PATCH 0377/2067] Removed unused variable ivt from a loop in cropcal_interp(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index e3f11e8e9e..988478c430 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -305,7 +305,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Starting with npcropmin will skip generic crops if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft - ivt = n + npcropmin - 1 call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & fldptr1=dataptr1d_sdate, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then From 98c7a1defa778448eb1dbc797d49d5cf72ce0bab Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 14:08:07 -0600 Subject: [PATCH 0378/2067] Breaking up some long lines. --- src/biogeochem/CNPhenologyMod.F90 | 9 ++++++--- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ++++-- src/main/clm_initializeMod.F90 | 3 ++- 3 files changed, 12 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 0a44483657..aa8b21fa0a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2585,13 +2585,15 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & endif ! set GDD target - if (use_cropcal_rx_cultivar_gdds .and. (.not. ignore_rx_crop_gdds) .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .ge. 0._r8) then + if (use_cropcal_rx_cultivar_gdds .and. (.not. ignore_rx_crop_gdds) & + .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .ge. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 if (gdd_target < gddmin(ivt(p))) then - write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gdd_target ',gdd_target,'; using gddmin(ivt(p)) instead (',gddmin(ivt(p)),')' + write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gdd_target ',gdd_target,'; using gddmin(ivt(p)) instead (',& + gddmin(ivt(p)),')' endif gdd_target = max(gdd_target, gddmin(ivt(p))) @@ -2622,7 +2624,8 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 if (gddmaturity(p) < gddmin(ivt(p))) then - write(iulog,*) 'Some patch with ivt ',ivt(p),' has calculated gddmaturity ',gddmaturity(p),'; using gddmin(ivt(p)) instead (',gddmin(ivt(p)),')' + write(iulog,*) 'Some patch with ivt ',ivt(p),' has calculated gddmaturity ',gddmaturity(p),& + '; using gddmin(ivt(p)) instead (',gddmin(ivt(p)),')' endif gddmaturity(p) = max(gddmaturity(p), gddmin(ivt(p))) endif diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 988478c430..22a3bc3026 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -337,7 +337,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Sanity check: Should only read in valid values if (crop_inst%rx_sdates_thisyr(p,1) > 365) then - write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',crop_inst%rx_sdates_thisyr(p,1) + write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',& + crop_inst%rx_sdates_thisyr(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -409,7 +410,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Sanity check: Try to catch uninitialized values if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000._r8) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',crop_inst%rx_cultivar_gdds_thisyr(p,1) + write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',& + crop_inst%rx_cultivar_gdds_thisyr(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if else diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 46d6b4ecc0..a36fcce2bf 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -572,7 +572,8 @@ subroutine initialize2(ni,nj) !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) - call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, filter_inactive_and_active(nc)%pcropp, crop_inst) + call cropcal_interp(bounds_clump, filter_inactive_and_active(nc)%num_pcropp, & + filter_inactive_and_active(nc)%pcropp, crop_inst) end do !$OMP END PARALLEL DO end if From fe257d424ac0638153d0e71713ab29a9bac2edb9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 14:15:46 -0600 Subject: [PATCH 0379/2067] Comment to clarify choice of not per-second units for repr_grainc_to_food_{perharv,thisyear}. --- src/biogeochem/CNVegCarbonFluxType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 8bdb4967d6..29cc4b6ee8 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -137,8 +137,8 @@ module CNVegCarbonFluxType real(r8), pointer :: frootc_to_litter_patch (:) ! fine root C litterfall (gC/m2/s) real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] - real(r8), pointer :: repr_grainc_to_food_perharv (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max] - real(r8), pointer :: repr_grainc_to_food_thisyr (:,:) ! grain C to food for prognostic crop accumulated this calendar year (gC/m2) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_food_perharv (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over each growing season, to be instantaneously at the end of each calendar year, to provide output that's easier to work with. + real(r8), pointer :: repr_grainc_to_food_thisyr (:,:) ! grain C to food for prognostic crop accumulated this calendar year (gC/m2) [patch, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over an entire calendar year, to be saved instantaneously at the end of each calendar year, to provide output that's easier to work with. real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] From 60d88bb6faa31993fa7cbffddd0fe4ec22bce830 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 27 Oct 2022 14:24:42 -0600 Subject: [PATCH 0380/2067] Change LND_TUNING_MODE for CPLHIST compsets to use CAM tunings Resolves ESCOMP/CTSM#1885 --- cime_config/config_component.xml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 7520050cf5..d3c2eda0a7 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -69,10 +69,12 @@ clm4_5_CRUv7 clm4_5_GSWP3v1 clm4_5_cam6.0 + clm4_5_cam6.0 clm5_0_CRUv7 clm5_0_CRUv7 clm5_0_GSWP3v1 clm5_0_cam6.0 + clm5_0_cam6.0 clm5_1_GSWP3v1 From 2b184529584783f857691843e7bd5848557d86ae Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 14:25:39 -0600 Subject: [PATCH 0381/2067] Comments for new 2d variables now include units and dimensions. --- src/biogeochem/CNVegStateType.F90 | 2 +- src/biogeochem/CropType.F90 | 22 +++++++++++----------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index 9d236623fb..ae894a31d0 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -35,7 +35,7 @@ module CNVegStateType real(r8) , pointer :: hdidx_patch (:) ! patch cold hardening index? real(r8) , pointer :: cumvd_patch (:) ! patch cumulative vernalization d?ependence? real(r8) , pointer :: gddmaturity_patch (:) ! patch growing degree days (gdd) needed to harvest (ddays) - real(r8) , pointer :: gddmaturity_thisyr (:,:) ! all at-harvest values of the above for this patch this year + real(r8) , pointer :: gddmaturity_thisyr (:,:) ! all at-harvest values of the above for this patch this year (ddays) [patch, mxharvests] real(r8) , pointer :: huileaf_patch (:) ! patch heat unit index needed from planting to leaf emergence real(r8) , pointer :: huigrain_patch (:) ! patch heat unit index needed to reach vegetative maturity real(r8) , pointer :: aleafi_patch (:) ! patch saved leaf allocation coefficient from phase 2 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index e0269ab00c..0f0497dec9 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -48,17 +48,17 @@ module CropType real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year - integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year - real(r8), pointer :: rx_cultivar_gdds_thisyr (:,:) ! all cultivar GDD targets for this patch this year - real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year - real(r8), pointer :: sdates_perharv (:,:) ! all actual sowing dates for crops *harvested* this year - real(r8), pointer :: syears_perharv (:,:) ! all actual sowing years for crops *harvested* this year - real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year - real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year - real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year - real(r8), pointer :: sowing_reason_thisyr (:,:) ! reason for each sowing for this patch this year - real(r8), pointer :: sowing_reason_perharv (:,:) ! reason for each sowing of crops *harvested* this year - real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year + integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year (day of year) [patch, mxsowings] + real(r8), pointer :: rx_cultivar_gdds_thisyr (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings] + real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings] + real(r8), pointer :: sdates_perharv (:,:) ! all actual sowing dates for crops *harvested* this year (day of year) [patch, mxharvests] + real(r8), pointer :: syears_perharv (:,:) ! all actual sowing years for crops *harvested* this year (day of year) [patch, mxharvests] + real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year (day of year) [patch, mxharvests] + real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year (ddays) [patch, mxharvests] + real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year (ddays) [patch, mxharvests] + real(r8), pointer :: sowing_reason_thisyr (:,:) ! reason for each sowing for this patch this year [patch, mxsowings] + real(r8), pointer :: sowing_reason_perharv (:,:) ! reason for each sowing of crops *harvested* this year [patch, mxharvests] + real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year [patch, mxharvests] integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch ! gddaccum tracks the actual growing degree-days accumulated over the growing season. From 4973cc250efa044e74ca6b8c1c5b9b5115e0fea9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 14:31:52 -0600 Subject: [PATCH 0382/2067] Added comment in CropPhenology() explaining logic of setting do_plant_prescribed. --- src/biogeochem/CNPhenologyMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index aa8b21fa0a..c83f16ceed 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1863,6 +1863,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,s+1) end if + ! CropType->InitAllocate() initializes next_rx_sdate to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_sdates is true. So if not using prescribed sowing dates, this boolean will always be false, because jday can never be -1. do_plant_prescribed = next_rx_sdate(p) == jday .and. sowing_count(p) < mxsowings ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) From ca50b07c762c678b71dbe44efcb5ee28f48cae2b Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 27 Oct 2022 14:35:25 -0600 Subject: [PATCH 0383/2067] Remove compset definition that is duplicated but slightly wrong This shouldn't change anything since the previous, correctly-defined compset alias is the one picked up. --- cime_config/config_compsets.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index 649306b05a..b9ed8935bc 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -264,12 +264,6 @@ - - I1850Clm51Bgc - 1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV - - - I1850Clm51SpNoAnthro 1850_DATM%GSWP3v1_CLM51%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV From 6684cfa9340c13aaf75fd66ddd43798713d6a34d Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 27 Oct 2022 14:35:56 -0600 Subject: [PATCH 0384/2067] Fix I1850Clm51BgcCrop compset Resolves ESCOMP/CTSM#1882 --- cime_config/config_compsets.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index b9ed8935bc..6a0ac8b3f6 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -151,7 +151,7 @@ I1850Clm51BgcCrop - 1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV + 1850_DATM%GSWP3v1_CLM51%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV From 3d452541c84c715bd5e5922387b2eb2d0f526f3a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 27 Oct 2022 14:52:17 -0600 Subject: [PATCH 0385/2067] Add run_neon output directories to the git ignore --- .gitignore | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.gitignore b/.gitignore index 4b998f4dcb..7a22cf4b9b 100644 --- a/.gitignore +++ b/.gitignore @@ -105,6 +105,12 @@ unit_test_build /tools/mkmapdata/regrid.o* /tools/mkmapdata/map*.nc +# run_neon output directories +/tools/site_and_regional/????/ +/tools/site_and_regional/????.ad/ +/tools/site_and_regional/????.postad/ +/tools/site_and_regional/????.transient/ + # build output *.o *.mod From 8f6ca20130504395540759767b8493d6a38a023b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 14:52:52 -0600 Subject: [PATCH 0386/2067] Edited a comment to clarify why do_plant_{normal,lastchance} are calculated even if the crop is already alive. --- src/biogeochem/CNPhenologyMod.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c83f16ceed..d5fce53bd7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1890,8 +1890,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%sowing_reason_patch(p) = 0 endif - ! This is outside the croplive check to allow for using CLM sowing - ! dates with externally-prescribed GDD maturity requirements + ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. ! ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing dates at all, or if this cell had no values in the prescribed sowing From 2f4fd1671122f8744c12455b324c1a2cde971757 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 15:01:46 -0600 Subject: [PATCH 0387/2067] Improved comment explaining harvest of "crops incorrectly planted in last time step of Dec. 31." --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d5fce53bd7..5eea78b9da 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2116,7 +2116,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then - ! Crop was incorrectly planted in last time step of Dec. 31. + ! BACKWARDS_COMPATIBILITY(ssr, 2022-02-03): To get rid of crops incorrectly planted in last time step of Dec. 31. That was fixed in commit dadbc62 ("Call CropPhenology regardless of doalb"), but this handles restart files with the old behavior. fake_harvest ensures that outputs aren't polluted. do_harvest = .true. force_harvest = .true. fake_harvest = .true. From 6f646346dea67a1a28483c29a3f46e30f548d5ee Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 27 Oct 2022 15:16:47 -0600 Subject: [PATCH 0388/2067] Add the neon listing to git ignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 7a22cf4b9b..ca701132a7 100644 --- a/.gitignore +++ b/.gitignore @@ -106,6 +106,7 @@ unit_test_build /tools/mkmapdata/map*.nc # run_neon output directories +/tools/site_and_regional/listing.csv /tools/site_and_regional/????/ /tools/site_and_regional/????.ad/ /tools/site_and_regional/????.postad/ From ae750e14b927a44f640e014cc937565ff8a5dde2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 27 Oct 2022 15:17:26 -0600 Subject: [PATCH 0389/2067] Add in 2018 and 2018-PD transient use cases --- bld/CLMBuildNamelist.pm | 2 ++ bld/namelist_files/namelist_defaults_ctsm.xml | 10 +++++++ .../namelist_definition_ctsm.xml | 2 +- .../use_cases/2018-PD_transient.xml | 29 +++++++++++++++++++ bld/namelist_files/use_cases/2018_control.xml | 11 +++++++ bld/namelist_files/use_cases/README | 5 ++++ bld/unit_testers/build-namelist_test.pl | 2 +- 7 files changed, 59 insertions(+), 2 deletions(-) create mode 100644 bld/namelist_files/use_cases/2018-PD_transient.xml create mode 100644 bld/namelist_files/use_cases/2018_control.xml diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index d9eeb1e5a0..c2a32da4ac 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4560,6 +4560,8 @@ sub check_use_case_name { } else { $log->fatal_error($diestring); } + } elsif ( $use_case =~ /^([0-9]+|PI)-PD_*($desc)_transient$/ ) { + # valid name } elsif ( $use_case =~ /^([0-9]+)_*($desc)_control$/ ) { # valid name } elsif ( $use_case =~ /^($desc)_pd$/ ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2686d62b9a..4bd9a6ee0b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -25,6 +25,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 379.0 388.8 397.5 +408.83 284.7 284.7 @@ -1449,6 +1450,9 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 2101 2015 +2018 +2018 + 2010 2010 @@ -1601,6 +1605,9 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 2100 2015 +2018 +2018 + 2010 2010 @@ -1619,6 +1626,9 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 2000 2000 +2018 +2018 + 2010 2010 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a08795dd1f..bc1dd034aa 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2057,7 +2057,7 @@ If 1, turn on the MEGAN model for BVOC's (Biogenic Volitile Organic Compounds) +"PtVg,1000,850,1100,1350,1600,1850,1855,1865,1875,1885,1895,1905,1915,1925,1935,1945,1955,1965,1975,1979,1980,1982,1985,1995,2000,2005,2010,2013,2015,2018,2025,2035,2045,2055,2065,2075,2085,2095,2105"> Year to simulate and to provide datasets for (such as surface datasets, initial conditions, aerosol-deposition, Nitrogen deposition rates etc.) A sim_year of 1000 corresponds to data used for testing only, NOT corresponding to any real datasets. A sim_year greater than 2015 corresponds to ssp_rcp scenario data diff --git a/bld/namelist_files/use_cases/2018-PD_transient.xml b/bld/namelist_files/use_cases/2018-PD_transient.xml new file mode 100644 index 0000000000..d838efbd00 --- /dev/null +++ b/bld/namelist_files/use_cases/2018-PD_transient.xml @@ -0,0 +1,29 @@ + + + + +Simulate transient land-use, and aerosol deposition changes from 2018 to current day with a mix of historical data, and future scenario data + + + +2018 + +1850-2100 + + +SSP3-7.0 + +2018 +2022 +2018 + +2018 +2022 +2018 + +2018 +2022 +2018 + + diff --git a/bld/namelist_files/use_cases/2018_control.xml b/bld/namelist_files/use_cases/2018_control.xml new file mode 100644 index 0000000000..d5b745a4c7 --- /dev/null +++ b/bld/namelist_files/use_cases/2018_control.xml @@ -0,0 +1,11 @@ + + + + +Conditions to simulate 2018 land-use + +2018 + +constant + + diff --git a/bld/namelist_files/use_cases/README b/bld/namelist_files/use_cases/README index 4ccaf00bdc..e55fd9285b 100644 --- a/bld/namelist_files/use_cases/README +++ b/bld/namelist_files/use_cases/README @@ -17,6 +17,10 @@ Transient cases: 20thC$desc_transient (means nominal 1850-2000 although some datasets are 1850-2005) + or + + yyyy-PD_$desc_transient (means nominal year yyyy through present day (PD) (with the year for PD advancing) + Control cases: yyyy$desc_control @@ -30,6 +34,7 @@ Where yyyy = Simulation year (such as 1850 or 2000). yyyy-yyyy = Range of simulation years to run over (i.e.. 1850-2000). +yyyy-PD = Range of simulation years to run over until present day (i.e.. 2018-2024). $ssp_rcp = Shared Socieconomic Pathway (SSP) Representative concentration pathway (RCP) description string for future scenarios: SSP#-#.# (for example: SSP5-8.5, SSP1-2.6, SSP4-6.0 diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index f6c8d75937..784d3b5e0c 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -393,7 +393,7 @@ sub cat_and_create_namelistinfile { # # Now run the site # - my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2000 -infile $namelistfile"; + my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2018 -infile $namelistfile"; eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); }; is( $@, '', "options: $options" ); $cfiles->checkfilesexist( "$options", $mode ); From 8cc2405c618ca063b04d9a481f108ba1b1816f88 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 27 Oct 2022 15:36:17 -0600 Subject: [PATCH 0390/2067] CLM stream settings are now in the 2018 use cases --- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 9 --------- 1 file changed, 9 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 10880bd619..7495857ae7 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -20,15 +20,6 @@ flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c221014.nc" -model_year_align_urbantv = 2018 -stream_year_first_urbantv = 2018 -stream_year_last_urbantv = 2022 -stream_year_first_ndep = 2018 -model_year_align_ndep = 2018 -stream_year_last_ndep = 2022 -model_year_align_popdens = 2018 -stream_year_first_popdens = 2018 -stream_year_last_popdens = 2022 stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' !stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc' From 6bf99fa75b32f5b825b77b5ab361bd989f4833f7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 16:51:08 -0600 Subject: [PATCH 0391/2067] Added _patch suffix to variables introduced in this branch. --- src/biogeochem/CNPhenologyMod.F90 | 72 ++++++------- src/biogeochem/CNVegCarbonFluxType.F90 | 20 ++-- src/biogeochem/CropType.F90 | 128 ++++++++++++------------ src/cpl/share_esmf/cropcalStreamMod.F90 | 16 +-- 4 files changed, 118 insertions(+), 118 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 5eea78b9da..892279b17f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1761,7 +1761,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor - next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year + next_rx_sdate => crop_inst%next_rx_sdate_patch , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch harvest_count => crop_inst%harvest_count , & ! Inout: [integer (:) ] number of harvest events this year for this patch peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max @@ -1830,37 +1830,37 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Second condition ensures everything is correctly set when resuming from a run with old code ! OR starting a run mid-year without any restart file OR handling a new crop column that just ! came into existence (and not at the year boundary for some reason). - if ( is_beg_curr_year() .or. crop_inst%sdates_thisyr(p,1) == spval ) then + if ( is_beg_curr_year() .or. crop_inst%sdates_thisyr_patch(p,1) == spval ) then sowing_count(p) = 0 harvest_count(p) = 0 do s = 1, mxsowings - crop_inst%sdates_thisyr(p,s) = -1._r8 - crop_inst%sowing_reason_thisyr(p,s) = -1._r8 + crop_inst%sdates_thisyr_patch(p,s) = -1._r8 + crop_inst%sowing_reason_thisyr_patch(p,s) = -1._r8 end do do s = 1, mxharvests - crop_inst%sdates_perharv(p,s) = -1._r8 - crop_inst%syears_perharv(p,s) = -1._r8 - crop_inst%hdates_thisyr(p,s) = -1._r8 + crop_inst%sdates_perharv_patch(p,s) = -1._r8 + crop_inst%syears_perharv_patch(p,s) = -1._r8 + crop_inst%hdates_thisyr_patch(p,s) = -1._r8 cnveg_state_inst%gddmaturity_thisyr(p,s) = -1._r8 - crop_inst%gddaccum_thisyr(p,s) = -1._r8 - crop_inst%hui_thisyr(p,s) = -1._r8 - crop_inst%sowing_reason_perharv = -1._r8 - crop_inst%harvest_reason_thisyr(p,s) = -1._r8 + crop_inst%gddaccum_thisyr_patch(p,s) = -1._r8 + crop_inst%hui_thisyr_patch(p,s) = -1._r8 + crop_inst%sowing_reason_perharv_patch = -1._r8 + crop_inst%harvest_reason_thisyr_patch(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_perharv(p,s,k) = 0._r8 + cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch(p,s,k) = 0._r8 end do end do do k = repr_grain_min, repr_grain_max - cnveg_carbonflux_inst%repr_grainc_to_food_thisyr(p,k) = 0._r8 + cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch(p,k) = 0._r8 end do - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,1) end if s = sowing_count(p) ! Get next sowing date if (s < mxsowings) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,s+1) + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,s+1) end if ! CropType->InitAllocate() initializes next_rx_sdate to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_sdates is true. So if not using prescribed sowing dates, this boolean will always be false, because jday can never be -1. @@ -1875,7 +1875,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Once removed, can also remove the "Instead, always harvest the day before idop" bit. if (croplive(p) .and. idop(p) <= jday .and. sowing_count(p) == 0) then sowing_count(p) = 1 - crop_inst%sdates_thisyr(p,1) = real(idop(p), r8) + crop_inst%sdates_thisyr_patch(p,1) = real(idop(p), r8) end if ! Will be needed until we can rely on all restart files including iyop. if (croplive(p) .and. iyop(p) > kyr) then @@ -1895,7 +1895,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing dates at all, or if this cell had no values in the prescribed sowing ! date file. - allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr(p,1)<0 + allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr_patch(p,1)<0 if (sowing_count(p) == mxsowings) then do_plant_normal = .false. do_plant_lastchance = .false. @@ -2104,7 +2104,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & fake_harvest = .false. sown_today = .false. if (use_cropcal_rx_sdates .and. s > 0) then - sown_today = crop_inst%sdates_thisyr(p,s) == real(jday, r8) + sown_today = crop_inst%sdates_thisyr_patch(p,s) == real(jday, r8) end if ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. @@ -2128,7 +2128,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_reason = 4._r8 ! If generate_crop_gdds and this patch has prescribed sowing inputs - else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr(p,1) .gt. 0) then + else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr_patch(p,1) .gt. 0) then if (.not. use_cropcal_rx_sdates) then write(iulog,*) 'If using generate_crop_gdds, you must specify stream_fldFileName_sdate' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -2162,7 +2162,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! WARNING: This implementation assumes that sowing dates don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed ! sowing dates. - if (crop_inst%rx_sdates_thisyr(p,1) == 1) then + if (crop_inst%rx_sdates_thisyr_patch(p,1) == 1) then do_harvest = jday == dayspyr end if @@ -2187,7 +2187,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! WARNING: This implementation assumes that all patches use prescribed sowing dates. if (use_cropcal_streams) then is_day_before_next_sowing = (jday == next_rx_sdate(p) - 1) .or. \ - (crop_inst%sdates_thisyr(p,1) == 1 .and. \ + (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. \ jday == dayspyr) else is_day_before_next_sowing = .false. @@ -2243,15 +2243,15 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (.not. fake_harvest) then if (harvdate(p) >= NOT_Harvested) harvdate(p) = jday harvest_count(p) = harvest_count(p) + 1 - crop_inst%sdates_perharv(p, harvest_count(p)) = real(idop(p), r8) - crop_inst%syears_perharv(p, harvest_count(p)) = real(iyop(p), r8) - crop_inst%hdates_thisyr(p, harvest_count(p)) = real(jday, r8) + crop_inst%sdates_perharv_patch(p, harvest_count(p)) = real(idop(p), r8) + crop_inst%syears_perharv_patch(p, harvest_count(p)) = real(iyop(p), r8) + crop_inst%hdates_thisyr_patch(p, harvest_count(p)) = real(jday, r8) cnveg_state_inst%gddmaturity_thisyr(p,harvest_count(p)) = gddmaturity(p) - crop_inst%gddaccum_thisyr(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) - crop_inst%hui_thisyr(p, harvest_count(p)) = hui(p) - crop_inst%sowing_reason_perharv(p, harvest_count(p)) = real(crop_inst%sowing_reason_patch(p), r8) + crop_inst%gddaccum_thisyr_patch(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) + crop_inst%hui_thisyr_patch(p, harvest_count(p)) = hui(p) + crop_inst%sowing_reason_perharv_patch(p, harvest_count(p)) = real(crop_inst%sowing_reason_patch(p), r8) crop_inst%sowing_reason_patch(p) = -1 - crop_inst%harvest_reason_thisyr(p, harvest_count(p)) = harvest_reason + crop_inst%harvest_reason_thisyr_patch(p, harvest_count(p)) = harvest_reason endif croplive(p) = .false. ! no re-entry in greater if-block @@ -2507,9 +2507,9 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date - next_rx_sdate => crop_inst%next_rx_sdate , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year + next_rx_sdate => crop_inst%next_rx_sdate_patch , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch - sowing_reason => crop_inst%sowing_reason_thisyr , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch + sowing_reason => crop_inst%sowing_reason_thisyr_patch , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest idop => cnveg_state_inst%idop_patch , & ! Output: [integer (:) ] date of planting iyop => cnveg_state_inst%iyop_patch , & ! Output: [integer (:) ] year of planting @@ -2534,11 +2534,11 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & sowing_count(p) = s if (s < mxsowings) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p, s+1) + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p, s+1) else next_rx_sdate(p) = -1 endif - crop_inst%sdates_thisyr(p,s) = real(jday, r8) + crop_inst%sdates_thisyr_patch(p,s) = real(jday, r8) this_sowing_reason = 0._r8 if (do_plant_prescribed) then @@ -2586,8 +2586,8 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! set GDD target if (use_cropcal_rx_cultivar_gdds .and. (.not. ignore_rx_crop_gdds) & - .and. crop_inst%rx_cultivar_gdds_thisyr(p,s) .ge. 0._r8) then - gdd_target = crop_inst%rx_cultivar_gdds_thisyr(p,s) + .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) .ge. 0._r8) then + gdd_target = crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 @@ -2974,8 +2974,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & frootc_to_litter => cnveg_carbonflux_inst%frootc_to_litter_patch , & ! Output: [real(r8) (:) ] fine root C litterfall (gC/m2/s) livestemc_to_litter => cnveg_carbonflux_inst%livestemc_to_litter_patch , & ! Output: [real(r8) (:) ] live stem C litterfall (gC/m2/s) repr_grainc_to_food => cnveg_carbonflux_inst%repr_grainc_to_food_patch , & ! Output: [real(r8) (:,:) ] grain C to food (gC/m2/s) - repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv, & ! Output: [real(r8) (:,:,:) ] grain C to food per harvest (gC/m2) - repr_grainc_to_food_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_thisyr, & ! Output: [real(r8) (:,:) ] grain C to food harvested this calendar year (gC/m2) + repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain C to food per harvest (gC/m2) + repr_grainc_to_food_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain C to food harvested this calendar year (gC/m2) repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 29cc4b6ee8..48dfef418b 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -137,8 +137,8 @@ module CNVegCarbonFluxType real(r8), pointer :: frootc_to_litter_patch (:) ! fine root C litterfall (gC/m2/s) real(r8), pointer :: livestemc_to_litter_patch (:) ! live stem C litterfall (gC/m2/s) real(r8), pointer :: repr_grainc_to_food_patch (:,:) ! grain C to food for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] - real(r8), pointer :: repr_grainc_to_food_perharv (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over each growing season, to be instantaneously at the end of each calendar year, to provide output that's easier to work with. - real(r8), pointer :: repr_grainc_to_food_thisyr (:,:) ! grain C to food for prognostic crop accumulated this calendar year (gC/m2) [patch, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over an entire calendar year, to be saved instantaneously at the end of each calendar year, to provide output that's easier to work with. + real(r8), pointer :: repr_grainc_to_food_perharv_patch (:,:,:) ! grain C to food for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over each growing season, to be instantaneously at the end of each calendar year, to provide output that's easier to work with. + real(r8), pointer :: repr_grainc_to_food_thisyr_patch (:,:) ! grain C to food for prognostic crop accumulated this calendar year (gC/m2) [patch, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over an entire calendar year, to be saved instantaneously at the end of each calendar year, to provide output that's easier to work with. real(r8), pointer :: repr_structurec_to_cropprod_patch (:,:) ! reproductive structure C to crop product pool for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structurec_to_litter_patch (:,:) ! reproductive structure C to litter for prognostic crop (gC/m2/s) [patch, repr_structure_min:repr_structure_max] @@ -603,8 +603,8 @@ subroutine InitAllocate(this, bounds, carbon_type) allocate(this%cpool_to_reproductivec_storage_patch(begp:endp, nrepr)); this%cpool_to_reproductivec_storage_patch (:,:) = nan allocate(this%livestemc_to_litter_patch (begp:endp)) ; this%livestemc_to_litter_patch (:) = nan allocate(this%repr_grainc_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_patch (:,:) = nan - allocate(this%repr_grainc_to_food_perharv(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_perharv (:,:,:) = nan - allocate(this%repr_grainc_to_food_thisyr(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_thisyr (:,:) = nan + allocate(this%repr_grainc_to_food_perharv_patch(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_perharv_patch (:,:,:) = nan + allocate(this%repr_grainc_to_food_thisyr_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_food_thisyr_patch (:,:) = nan allocate(this%repr_structurec_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structurec_to_cropprod_patch(:,:) = nan allocate(this%repr_structurec_to_litter_patch(begp:endp, repr_structure_min:repr_structure_max)) @@ -841,9 +841,9 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=data1dptr) end do - this%repr_grainc_to_food_perharv(begp:endp,:,:) = spval + this%repr_grainc_to_food_perharv_patch(begp:endp,:,:) = spval do k = repr_grain_min, repr_grain_max - data2dptr => this%repr_grainc_to_food_perharv(:,:,k) + data2dptr => this%repr_grainc_to_food_perharv_patch(:,:,k) call hist_addfld2d ( & ! e.g., GRAINC_TO_FOOD_PERHARV fname=get_repr_hist_fname(k)//'C_TO_FOOD_PERHARV', & @@ -854,9 +854,9 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=data2dptr) end do - this%repr_grainc_to_food_thisyr(begp:endp,:) = spval + this%repr_grainc_to_food_thisyr_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max - data1dptr => this%repr_grainc_to_food_thisyr(:,k) + data1dptr => this%repr_grainc_to_food_thisyr_patch(:,k) call hist_addfld1d ( & ! e.g., GRAINC_TO_FOOD_ANN fname=get_repr_hist_fname(k)//'C_TO_FOOD_ANN', & @@ -3576,7 +3576,7 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then do k = repr_grain_min, repr_grain_max - data2dptr => this%repr_grainc_to_food_perharv(:,:,k) + data2dptr => this%repr_grainc_to_food_perharv_patch(:,:,k) ! e.g., grainc_to_food_perharv varname = get_repr_rest_fname(k)//'c_to_food_perharv' call restartvar(ncid=ncid, flag=flag, varname=varname, & @@ -3593,7 +3593,7 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) end if do k = repr_grain_min, repr_grain_max - data1dptr => this%repr_grainc_to_food_thisyr(:,k) + data1dptr => this%repr_grainc_to_food_thisyr_patch(:,k) ! e.g., grainc_to_food_thisyr varname = get_repr_rest_fname(k)//'c_to_food_thisyr' call restartvar(ncid=ncid, flag=flag, varname=varname, & diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 0f0497dec9..b7231303ad 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -47,18 +47,18 @@ module CropType character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope - integer , pointer :: next_rx_sdate (:) ! prescribed sowing date for the next growing season this year - integer , pointer :: rx_sdates_thisyr (:,:) ! all prescribed sowing dates for this patch this year (day of year) [patch, mxsowings] - real(r8), pointer :: rx_cultivar_gdds_thisyr (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings] - real(r8), pointer :: sdates_thisyr (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings] - real(r8), pointer :: sdates_perharv (:,:) ! all actual sowing dates for crops *harvested* this year (day of year) [patch, mxharvests] - real(r8), pointer :: syears_perharv (:,:) ! all actual sowing years for crops *harvested* this year (day of year) [patch, mxharvests] - real(r8), pointer :: hdates_thisyr (:,:) ! all actual harvest dates for this patch this year (day of year) [patch, mxharvests] - real(r8), pointer :: gddaccum_thisyr (:,:) ! accumulated GDD at harvest for this patch this year (ddays) [patch, mxharvests] - real(r8), pointer :: hui_thisyr (:,:) ! accumulated heat unit index at harvest for this patch this year (ddays) [patch, mxharvests] - real(r8), pointer :: sowing_reason_thisyr (:,:) ! reason for each sowing for this patch this year [patch, mxsowings] - real(r8), pointer :: sowing_reason_perharv (:,:) ! reason for each sowing of crops *harvested* this year [patch, mxharvests] - real(r8), pointer :: harvest_reason_thisyr (:,:) ! reason for each harvest for this patch this year [patch, mxharvests] + integer , pointer :: next_rx_sdate_patch (:) ! prescribed sowing date for the next growing season this year + integer , pointer :: rx_sdates_thisyr_patch (:,:) ! all prescribed sowing dates for this patch this year (day of year) [patch, mxsowings] + real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings] + real(r8), pointer :: sdates_thisyr_patch (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings] + real(r8), pointer :: sdates_perharv_patch (:,:) ! all actual sowing dates for crops *harvested* this year (day of year) [patch, mxharvests] + real(r8), pointer :: syears_perharv_patch (:,:) ! all actual sowing years for crops *harvested* this year (day of year) [patch, mxharvests] + real(r8), pointer :: hdates_thisyr_patch (:,:) ! all actual harvest dates for this patch this year (day of year) [patch, mxharvests] + real(r8), pointer :: gddaccum_thisyr_patch (:,:) ! accumulated GDD at harvest for this patch this year (ddays) [patch, mxharvests] + real(r8), pointer :: hui_thisyr_patch (:,:) ! accumulated heat unit index at harvest for this patch this year (ddays) [patch, mxharvests] + real(r8), pointer :: sowing_reason_thisyr_patch (:,:) ! reason for each sowing for this patch this year [patch, mxsowings] + real(r8), pointer :: sowing_reason_perharv_patch (:,:) ! reason for each sowing of crops *harvested* this year [patch, mxharvests] + real(r8), pointer :: harvest_reason_thisyr_patch (:,:) ! reason for each harvest for this patch this year [patch, mxharvests] integer , pointer :: sowing_count (:) ! number of sowing events this year for this patch integer , pointer :: harvest_count (:) ! number of sowing events this year for this patch ! gddaccum tracks the actual growing degree-days accumulated over the growing season. @@ -227,23 +227,23 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = cphase_not_planted allocate(this%sowing_reason_patch (begp:endp)) ; this%sowing_reason_patch (:) = -1 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval - allocate(this%next_rx_sdate(begp:endp)) ; this%next_rx_sdate(:) = -1 - allocate(this%rx_sdates_thisyr(begp:endp,1:mxsowings)) ; this%rx_sdates_thisyr(:,:) = -1 - allocate(this%rx_cultivar_gdds_thisyr(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr(:,:) = spval - allocate(this%sdates_thisyr(begp:endp,1:mxsowings)) ; this%sdates_thisyr(:,:) = spval - allocate(this%sdates_perharv(begp:endp,1:mxharvests)) ; this%sdates_perharv(:,:) = spval - allocate(this%syears_perharv(begp:endp,1:mxharvests)) ; this%syears_perharv(:,:) = spval - allocate(this%hdates_thisyr(begp:endp,1:mxharvests)) ; this%hdates_thisyr(:,:) = spval - allocate(this%gddaccum_thisyr(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr(:,:) = spval - allocate(this%hui_thisyr(begp:endp,1:mxharvests)) ; this%hui_thisyr(:,:) = spval - allocate(this%sowing_reason_thisyr(begp:endp,1:mxsowings)) ; this%sowing_reason_thisyr(:,:) = spval - allocate(this%sowing_reason_perharv(begp:endp,1:mxharvests)) ; this%sowing_reason_perharv(:,:) = spval - allocate(this%harvest_reason_thisyr(begp:endp,1:mxharvests)) ; this%harvest_reason_thisyr(:,:) = spval + allocate(this%next_rx_sdate_patch(begp:endp)) ; this%next_rx_sdate_patch(:) = -1 + allocate(this%rx_sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_sdates_thisyr_patch(:,:) = -1 + allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval + allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval + allocate(this%sdates_perharv_patch(begp:endp,1:mxharvests)) ; this%sdates_perharv_patch(:,:) = spval + allocate(this%syears_perharv_patch(begp:endp,1:mxharvests)) ; this%syears_perharv_patch(:,:) = spval + allocate(this%hdates_thisyr_patch(begp:endp,1:mxharvests)) ; this%hdates_thisyr_patch(:,:) = spval + allocate(this%gddaccum_thisyr_patch(begp:endp,1:mxharvests)) ; this%gddaccum_thisyr_patch(:,:) = spval + allocate(this%hui_thisyr_patch(begp:endp,1:mxharvests)) ; this%hui_thisyr_patch(:,:) = spval + allocate(this%sowing_reason_thisyr_patch(begp:endp,1:mxsowings)) ; this%sowing_reason_thisyr_patch(:,:) = spval + allocate(this%sowing_reason_perharv_patch(begp:endp,1:mxharvests)) ; this%sowing_reason_perharv_patch(:,:) = spval + allocate(this%harvest_reason_thisyr_patch(begp:endp,1:mxharvests)) ; this%harvest_reason_thisyr_patch(:,:) = spval allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 - this%rx_sdates_thisyr(:,:) = -1 - this%rx_cultivar_gdds_thisyr(:,:) = spval + this%rx_sdates_thisyr_patch(:,:) = -1 + this%rx_cultivar_gdds_thisyr_patch(:,:) = spval end subroutine InitAllocate @@ -297,50 +297,50 @@ subroutine InitHistory(this, bounds) ptr_patch=this%latbaset_patch, default='inactive') end if - this%sdates_thisyr(begp:endp,:) = spval + this%sdates_thisyr_patch(begp:endp,:) = spval call hist_addfld2d (fname='SDATES', units='day of year', type2d='mxsowings', & avgflag='I', long_name='actual crop sowing dates; should only be output annually', & - ptr_patch=this%sdates_thisyr, default='inactive') + ptr_patch=this%sdates_thisyr_patch, default='inactive') - this%sdates_perharv(begp:endp,:) = spval + this%sdates_perharv_patch(begp:endp,:) = spval call hist_addfld2d (fname='SDATES_PERHARV', units='day of year', type2d='mxharvests', & avgflag='I', long_name='actual sowing dates for crops harvested this year; should only be output annually', & - ptr_patch=this%sdates_perharv, default='inactive') + ptr_patch=this%sdates_perharv_patch, default='inactive') - this%syears_perharv(begp:endp,:) = spval + this%syears_perharv_patch(begp:endp,:) = spval call hist_addfld2d (fname='SYEARS_PERHARV', units='year', type2d='mxharvests', & avgflag='I', long_name='actual sowing years for crops harvested this year; should only be output annually', & - ptr_patch=this%syears_perharv, default='inactive') + ptr_patch=this%syears_perharv_patch, default='inactive') - this%hdates_thisyr(begp:endp,:) = spval + this%hdates_thisyr_patch(begp:endp,:) = spval call hist_addfld2d (fname='HDATES', units='day of year', type2d='mxharvests', & avgflag='I', long_name='actual crop harvest dates; should only be output annually', & - ptr_patch=this%hdates_thisyr, default='inactive') + ptr_patch=this%hdates_thisyr_patch, default='inactive') - this%gddaccum_thisyr(begp:endp,:) = spval + this%gddaccum_thisyr_patch(begp:endp,:) = spval call hist_addfld2d (fname='GDDACCUM_PERHARV', units='ddays', type2d='mxharvests', & avgflag='I', long_name='At-harvest accumulated growing degree days past planting date for crop; should only be output annually', & - ptr_patch=this%gddaccum_thisyr, default='inactive') + ptr_patch=this%gddaccum_thisyr_patch, default='inactive') - this%hui_thisyr(begp:endp,:) = spval + this%hui_thisyr_patch(begp:endp,:) = spval call hist_addfld2d (fname='HUI_PERHARV', units='ddays', type2d='mxharvests', & avgflag='I', long_name='At-harvest accumulated heat unit index for crop; should only be output annually', & - ptr_patch=this%hui_thisyr, default='inactive') + ptr_patch=this%hui_thisyr_patch, default='inactive') - this%sowing_reason_thisyr(begp:endp,:) = spval + this%sowing_reason_thisyr_patch(begp:endp,:) = spval call hist_addfld2d (fname='SOWING_REASON', units='unitless', type2d='mxsowings', & avgflag='I', long_name='Reason for each crop sowing; should only be output annually', & - ptr_patch=this%sowing_reason_thisyr, default='inactive') + ptr_patch=this%sowing_reason_thisyr_patch, default='inactive') - this%sowing_reason_perharv(begp:endp,:) = spval + this%sowing_reason_perharv_patch(begp:endp,:) = spval call hist_addfld2d (fname='SOWING_REASON_PERHARV', units='unitless', type2d='mxharvests', & avgflag='I', long_name='Reason for sowing of each crop harvested this year; should only be output annually', & - ptr_patch=this%sowing_reason_perharv, default='inactive') + ptr_patch=this%sowing_reason_perharv_patch, default='inactive') - this%harvest_reason_thisyr(begp:endp,:) = spval + this%harvest_reason_thisyr_patch(begp:endp,:) = spval call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='unitless', type2d='mxharvests', & avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & - ptr_patch=this%harvest_reason_thisyr, default='inactive') + ptr_patch=this%harvest_reason_thisyr_patch, default='inactive') end subroutine InitHistory @@ -600,17 +600,17 @@ subroutine Restart(this, bounds, ncid, flag) ! Read or write variable(s) with mxsowings dimension ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxsowings')) then - call restartvar(ncid=ncid, flag=flag, varname='sdates_thisyr', xtype=ncd_double, & + call restartvar(ncid=ncid, flag=flag, varname='sdates_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxsowings', switchdim=.true., & long_name='crop sowing dates for this patch this year', units='day of year', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%sdates_thisyr) + interpinic_flag='interp', readvar=readvar, data=this%sdates_thisyr_patch) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp seasons_found = 0 do seasons_loopvar = 1,mxsowings - if (this%sdates_thisyr(p,seasons_loopvar) >= 1 .and. this%sdates_thisyr(p,seasons_loopvar) <= 366) then + if (this%sdates_thisyr_patch(p,seasons_loopvar) >= 1 .and. this%sdates_thisyr_patch(p,seasons_loopvar) <= 366) then seasons_found = seasons_loopvar else exit @@ -624,52 +624,52 @@ subroutine Restart(this, bounds, ncid, flag) ! Read or write variable(s) with mxharvests dimension ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then - call restartvar(ncid=ncid, flag=flag, varname='sdates_perharv', xtype=ncd_double, & + call restartvar(ncid=ncid, flag=flag, varname='sdates_perharv_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='sowing dates for crops harvested in this patch this year', units='day of year', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%sdates_perharv) - call restartvar(ncid=ncid, flag=flag, varname='syears_perharv', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%sdates_perharv_patch) + call restartvar(ncid=ncid, flag=flag, varname='syears_perharv_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='sowing years for crops harvested in this patch this year', units='year', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%syears_perharv) - call restartvar(ncid=ncid, flag=flag, varname='hdates_thisyr', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%syears_perharv_patch) + call restartvar(ncid=ncid, flag=flag, varname='hdates_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='crop harvest dates for this patch this year', units='day of year', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%hdates_thisyr) - call restartvar(ncid=ncid, flag=flag, varname='gddaccum_thisyr', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%hdates_thisyr_patch) + call restartvar(ncid=ncid, flag=flag, varname='gddaccum_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='accumulated GDD at harvest for this patch this year', units='ddays', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%gddaccum_thisyr) - call restartvar(ncid=ncid, flag=flag, varname='hui_thisyr', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%gddaccum_thisyr_patch) + call restartvar(ncid=ncid, flag=flag, varname='hui_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='accumulated heat unit index at harvest for this patch this year', units='ddays', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%hui_thisyr) - call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_thisyr', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%hui_thisyr_patch) + call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxsowings', switchdim=.true., & long_name='reason for each sowing for this patch this year', units='unitless', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_thisyr) - call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_perharv', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_thisyr_patch) + call restartvar(ncid=ncid, flag=flag, varname='sowing_reason_perharv_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='reason for sowing of each crop harvested this year', units='unitless', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_perharv) - call restartvar(ncid=ncid, flag=flag, varname='harvest_reason_thisyr', xtype=ncd_double, & + interpinic_flag='interp', readvar=readvar, data=this%sowing_reason_perharv_patch) + call restartvar(ncid=ncid, flag=flag, varname='harvest_reason_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='reason for each harvest for this patch this year', units='unitless', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%harvest_reason_thisyr) + interpinic_flag='interp', readvar=readvar, data=this%harvest_reason_thisyr_patch) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp seasons_found = 0 do seasons_loopvar = 1,mxharvests - if (this%hdates_thisyr(p,seasons_loopvar) >= 1 .and. this%hdates_thisyr(p,seasons_loopvar) <= 366) then + if (this%hdates_thisyr_patch(p,seasons_loopvar) >= 1 .and. this%hdates_thisyr_patch(p,seasons_loopvar) <= 366) then seasons_found = seasons_loopvar else exit diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 22a3bc3026..01ec16e378 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -333,19 +333,19 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) n = ivt - npcropmin + 1 ! vegetated pft ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_sdates_thisyr(p,1) = dataptr2d_sdate(ig,n) + crop_inst%rx_sdates_thisyr_patch(p,1) = dataptr2d_sdate(ig,n) ! Sanity check: Should only read in valid values - if (crop_inst%rx_sdates_thisyr(p,1) > 365) then + if (crop_inst%rx_sdates_thisyr_patch(p,1) > 365) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',& - crop_inst%rx_sdates_thisyr(p,1) + crop_inst%rx_sdates_thisyr_patch(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if ! Only for first sowing date of the year ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 - if (crop_inst%sdates_thisyr(p,1) <= 0) then - crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) + if (crop_inst%sdates_thisyr_patch(p,1) <= 0) then + crop_inst%next_rx_sdate_patch(p) = crop_inst%rx_sdates_thisyr_patch(p,1) end if else write(iulog,'(a,i0)') 'cropcal_interp(), rx_sdates: Crop patch has ivt ',ivt @@ -406,12 +406,12 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - crop_inst%rx_cultivar_gdds_thisyr(p,1) = dataptr2d_cultivar_gdds(ig,n) + crop_inst%rx_cultivar_gdds_thisyr_patch(p,1) = dataptr2d_cultivar_gdds(ig,n) ! Sanity check: Try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr(p,1) > 1000000._r8) then + if (crop_inst%rx_cultivar_gdds_thisyr_patch(p,1) > 1000000._r8) then write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',& - crop_inst%rx_cultivar_gdds_thisyr(p,1) + crop_inst%rx_cultivar_gdds_thisyr_patch(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if else From 6ee4b5fce5f882e2620feb99ead4a60a5f0f676a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 16:56:39 -0600 Subject: [PATCH 0392/2067] Removing ignore_rx_crop_gdds option. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 - bld/namelist_files/namelist_definition_ctsm.xml | 5 ----- src/biogeochem/CNPhenologyMod.F90 | 7 ++----- 3 files changed, 2 insertions(+), 11 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index b14aa859e7..52a15f4b71 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -562,7 +562,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Constant .false. .false. -.false. 1.d00 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 9a351fe10a..38abc5e292 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1143,11 +1143,6 @@ Set to .true. in order to override crop harvesting logic and to instead harvest Set to .true. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. - -Set to .true. in order to override prescribed crop GDD requirements and instead use default CLM values/logic. For troubleshooting purposes only. - - Set minimum crop GDD requirement. Used only with prescribed GDD inputs from file. diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 892279b17f..d4f5461ea1 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -131,7 +131,6 @@ module CNPhenologyMod logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing logical, public :: use_mxmat = .true. ! If true, ignore crop maximum growing season length - logical :: ignore_rx_crop_gdds = .false. ! Troubleshooting ! Constants for seasonal decidious leaf onset and offset logical, private :: onset_thresh_depends_on_veg = .false. ! If onset threshold depends on vegetation type @@ -175,7 +174,7 @@ subroutine CNPhenologyReadNML( NLFilename ) !----------------------------------------------------------------------- namelist /cnphenology/ initial_seed_at_planting, onset_thresh_depends_on_veg, & min_critical_dayl_method, generate_crop_gdds, & - use_mxmat, ignore_rx_crop_gdds + use_mxmat ! Initialize options to default values, in case they are not specified in ! the namelist @@ -201,7 +200,6 @@ subroutine CNPhenologyReadNML( NLFilename ) call shr_mpi_bcast (min_critical_dayl_method, mpicom) call shr_mpi_bcast (generate_crop_gdds, mpicom) call shr_mpi_bcast (use_mxmat, mpicom) - call shr_mpi_bcast (ignore_rx_crop_gdds, mpicom) if ( min_critical_dayl_method == "DependsOnLat" )then critical_daylight_method = critical_daylight_depends_on_lat @@ -2585,8 +2583,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & endif ! set GDD target - if (use_cropcal_rx_cultivar_gdds .and. (.not. ignore_rx_crop_gdds) & - .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) .ge. 0._r8) then + if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) .ge. 0._r8) then gdd_target = crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator From dfaa91be3eeb721ff82ebcccd429cd71a1362bba Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 17:58:54 -0600 Subject: [PATCH 0393/2067] Renamed sown_today to did_plant_prescribed_today. --- src/biogeochem/CNPhenologyMod.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d4f5461ea1..b7f1d64c52 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1730,7 +1730,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_harvest ! Are harvest conditions satisfied? logical force_harvest ! Should we harvest today no matter what? logical fake_harvest ! Dealing with incorrect Dec. 31 planting - logical sown_today ! Was the crop sown today? + logical did_plant_prescribed_today ! Was the crop sown today? logical is_day_before_next_sowing ! Is tomorrow a prescribed sowing day? !------------------------------------------------------------------------ @@ -2100,9 +2100,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .false. force_harvest = .false. fake_harvest = .false. - sown_today = .false. + did_plant_prescribed_today = .false. if (use_cropcal_rx_sdates .and. s > 0) then - sown_today = crop_inst%sdates_thisyr_patch(p,s) == real(jday, r8) + did_plant_prescribed_today = crop_inst%sdates_thisyr_patch(p,s) == real(jday, r8) end if ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. @@ -2170,7 +2170,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & endif - else if (sown_today) then + else if (did_plant_prescribed_today) then ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. do_harvest = .false. From 27b827fc8db32e0d8d49ebee49306efef0849033 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 18:00:40 -0600 Subject: [PATCH 0394/2067] Renamed is_day_before_next_sowing to will_plant_prescribed_tomorrow. --- src/biogeochem/CNPhenologyMod.F90 | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b7f1d64c52..e96f0a52ed 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1731,7 +1731,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical force_harvest ! Should we harvest today no matter what? logical fake_harvest ! Dealing with incorrect Dec. 31 planting logical did_plant_prescribed_today ! Was the crop sown today? - logical is_day_before_next_sowing ! Is tomorrow a prescribed sowing day? + logical will_plant_prescribed_tomorrow ! Is tomorrow a prescribed sowing day? !------------------------------------------------------------------------ associate( & @@ -2184,19 +2184,19 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! sowing dates. ! WARNING: This implementation assumes that all patches use prescribed sowing dates. if (use_cropcal_streams) then - is_day_before_next_sowing = (jday == next_rx_sdate(p) - 1) .or. \ + will_plant_prescribed_tomorrow = (jday == next_rx_sdate(p) - 1) .or. \ (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. \ jday == dayspyr) else - is_day_before_next_sowing = .false. + will_plant_prescribed_tomorrow = .false. end if - do_harvest = do_harvest .or. is_day_before_next_sowing + do_harvest = do_harvest .or. will_plant_prescribed_tomorrow if (hui(p) >= gddmaturity(p)) then harvest_reason = 1._r8 else if (idpp >= mxmat) then harvest_reason = 2._r8 - else if (is_day_before_next_sowing) then + else if (will_plant_prescribed_tomorrow) then harvest_reason = 5._r8 force_harvest = .true. end if From a463b724ff09ac6242e19c0ef05c71fef5d2a964 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Oct 2022 18:14:04 -0600 Subject: [PATCH 0395/2067] Minor de-duplication in 2 spots. --- src/biogeochem/CNPhenologyMod.F90 | 8 -------- src/biogeochem/CropType.F90 | 4 ---- 2 files changed, 12 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index e96f0a52ed..4dda3330f7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2548,14 +2548,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & this_sowing_reason = this_sowing_reason + 2._r8 end if sowing_reason(p,s) = this_sowing_reason - - this_sowing_reason = 0._r8 - if (do_plant_normal) then - this_sowing_reason = this_sowing_reason + 1._r8 - else if (do_plant_lastchance) then - this_sowing_reason = this_sowing_reason + 2._r8 - end if - sowing_reason(p,sowing_count(p)) = this_sowing_reason crop_inst%sowing_reason_patch(p) = this_sowing_reason leafc_xfer(p) = initial_seed_at_planting diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index b7231303ad..b16cab7dd6 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -738,10 +738,6 @@ subroutine CropUpdateAccVars(this, bounds, t_ref2m_patch, t_soisno_col) write(iulog,*)'update_accum_hist allocation error for rbuf1dp' call endrun(msg=errMsg(sourcefile, __LINE__)) endif - if (ier/=0) then - write(iulog,*)'update_accum_hist allocation error for rbuf1dp (2)' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif ! Update HUI. This is not standard for accumulation fields, ! but HUI needs it because it can be changed outside this From 9dd8b9870dc73f1f95e61d10640f5024c4c7f98c Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 28 Oct 2022 10:58:51 -0600 Subject: [PATCH 0396/2067] Add an mct test to the expected fails list --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 232b6e6a90..90c45ef919 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -30,6 +30,13 @@ + + + FAIL + #1887 + + + FAIL From 445b9bf45bdfa54e70d858b2c9de91fcc566ef6b Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 28 Oct 2022 11:08:10 -0600 Subject: [PATCH 0397/2067] Update ChangeLog --- doc/ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 75 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 304740b1b8..68aea97f7e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,78 @@ =============================================================== +Tag name: ctsm5.1.dev113 +Originator(s): sacks (Bill Sacks), ekluzek (Erik Kluzek), jedwards (Jim Edwards) +Date: Fri Oct 28 11:00:26 MDT 2022 +One-line Summary: Fix some compsets; add only clauses for ESMF use statements + +Purpose and description of changes +---------------------------------- + +(1) Fix I1850Clm51BgcCrop compset (was using CLM50 instead of CLM51) +- Resolves https://github.com/ESCOMP/CTSM/issues/1882 + +(2) Change LND_TUNING_MODE for DATM%CPLHIST compsets to use CAM tunings + since these cases typically use atmosphere forcings from CAM. +- Resolves https://github.com/ESCOMP/CTSM/issues/1885 + +(3) Add "only" clauses to ESMF use statements +- Resolves https://github.com/ESCOMP/CTSM/issues/1846 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +- Resolves https://github.com/ESCOMP/CTSM/issues/1882 (I1850Clm51BgcCrop actually uses CLM50) +- Resolves https://github.com/ESCOMP/CTSM/issues/1885 (CPLHIST compsets should use same land tunings as for CAM compsets) +- Resolves https://github.com/ESCOMP/CTSM/issues/1846 (Add "only" clause to a problematic use statement in lnd_comp_nuopc for cce compiler) + +Known bugs introduced in this tag (include issue #): +- https://github.com/ESCOMP/CTSM/issues/1887 (Gnu MCT builds will fail starting in ctsm5.1.dev113) + + +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but just for limited cases + + Summarize any changes to answers, i.e., + - what code configurations: + - Cases with I1850Clm51BgcCrop compset + - Cases with DATM%CPLHIST + - what platforms/compilers: all + - nature of change (roundoff; larger than roundoff/same climate; new climate): + Larger than roundoff; may be new climate + +Other details +------------- +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1870 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev112 Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) Date: Sat Oct 15 16:26:28 MDT 2022 diff --git a/doc/ChangeSum b/doc/ChangeSum index 9eab48d7e5..3008f25f69 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases ctsm5.1.dev110 slevis 09/26/2022 Introduction of modify_meshes tool for use in I-cases and F-cases From fcacc1cb77a9df2ff8a1453491e5e10069fc9845 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 2 Nov 2022 11:57:51 -0600 Subject: [PATCH 0398/2067] Set urbantv start and end for 2018 --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 4bd9a6ee0b..c859fc13fc 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1716,6 +1716,12 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 2106 2015 +2018 +2018 + +2010 +2010 + 2000 2000 From 6d6a43d76635e53e81289dccb17723a9b852d1ab Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 2 Nov 2022 12:43:32 -0600 Subject: [PATCH 0399/2067] 2018 control needs to use future scenario data --- bld/namelist_files/use_cases/2018_control.xml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/bld/namelist_files/use_cases/2018_control.xml b/bld/namelist_files/use_cases/2018_control.xml index d5b745a4c7..e5e572d749 100644 --- a/bld/namelist_files/use_cases/2018_control.xml +++ b/bld/namelist_files/use_cases/2018_control.xml @@ -8,4 +8,7 @@ constant + +SSP3-7.0 + From 78ad4ae21432711f61b34b720e87c47166fdbeac Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 2 Nov 2022 17:25:14 -0600 Subject: [PATCH 0400/2067] Explicitly turn crop on for the two NEON AG sites fixing #1889 --- cime_config/usermods_dirs/NEON/KONA/shell_commands | 4 ++++ cime_config/usermods_dirs/NEON/STER/shell_commands | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/cime_config/usermods_dirs/NEON/KONA/shell_commands b/cime_config/usermods_dirs/NEON/KONA/shell_commands index c00e220e77..66f274dd36 100644 --- a/cime_config/usermods_dirs/NEON/KONA/shell_commands +++ b/cime_config/usermods_dirs/NEON/KONA/shell_commands @@ -1,3 +1,7 @@ ./xmlchange NEONSITE=KONA ./xmlchange PTS_LON=263.38956 ./xmlchange PTS_LAT=39.10828 +# Setup to run with prognostic crops for this site +# If you want to explicitly run in SP mode or add other +# options you'll need to add that after this... +./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop" diff --git a/cime_config/usermods_dirs/NEON/STER/shell_commands b/cime_config/usermods_dirs/NEON/STER/shell_commands index 2c1699fc9c..38b173c309 100644 --- a/cime_config/usermods_dirs/NEON/STER/shell_commands +++ b/cime_config/usermods_dirs/NEON/STER/shell_commands @@ -1,3 +1,7 @@ ./xmlchange NEONSITE=STER ./xmlchange PTS_LON=256.96992 ./xmlchange PTS_LAT=40.45984 +# Setup to run with prognostic crops for this site +# If you want to explicitly run in SP mode or add other +# # options you'll need to add that after this... +./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop" From 0e09412a4bea1062ba1d9d6de7890a5f605c1cee Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 2 Nov 2022 19:26:59 -0600 Subject: [PATCH 0401/2067] Fix a little glitch where run-length couldn't be set --- tools/site_and_regional/run_neon.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 1805ed7ebd..4b1407a2c1 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -280,6 +280,8 @@ def get_parser(args, description, valid_neon_sites): # The transient run length is set by cdeps atm buildnml to the last date of the available tower data # this value is not used run_length = "4Y" + else: + run_length = args.run_length run_length = parse_isoduration(run_length) base_case_root = None From b2040f46ca357abfdfe23334052ad61e2904e7da Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Nov 2022 00:53:56 -0600 Subject: [PATCH 0402/2067] Make sure the compset type is correct for both basecase and case cloning from that --- tools/site_and_regional/run_neon.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 4b1407a2c1..c7418b786c 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -421,6 +421,14 @@ def build_base_case( print("---- base case setup ------") case.case_setup() else: + # For existing case check that the compset name is correct + existingcompname = case.get_value("COMPSET") + match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) + if re.search("^HIST", compset, flags=re.IGNORECASE) is None: + expect( match == None, "Existing base case is a historical type and should not be -- rerun with the --orverwrite option" ) + else: + expect( match != None, "Existing base case should be a historical type and is not -- rerun with the --orverwrite option" ) + # reset the case case.case_setup(reset=True) case_path = case.get_value("CASEROOT") @@ -481,6 +489,13 @@ def run_case( elif rerun: with Case(case_root, read_only=False) as case: rundir = case.get_value("RUNDIR") + # For existing case check that the compset name is correct + existingcompname = case.get_value("COMPSET") + match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) + if re.search("^HIST", compset, flags=re.IGNORECASE) is None: + expect( match == None, "Existing base case is a historical type and should not be -- rerun with the --orverwrite option" ) + else: + expect( match != None, "Existing base case should be a historical type and is not -- rerun with the --orverwrite option" ) if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): print( "Case {} appears to be complete, not rerunning.".format( From b824c780c8db20a39fd6f8bb01ce78404341451c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Nov 2022 10:25:11 -0600 Subject: [PATCH 0403/2067] Always ensure to build/run single point NEON sites with mpi-serial rather than a full MPI library to save complexity --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 1ab3fdca14..5a20d6ac38 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -4,6 +4,7 @@ ./xmlchange DATM_PRESAERO=SSP3-7.0 ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 +./xmlchange MPILIB=mpi-serial ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 compset=`./xmlquery COMPSET --value` # For a transient case run the whole length and don't cycle From 69b8e3204f941977070581d6efaf104694e13208 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Nov 2022 10:25:38 -0600 Subject: [PATCH 0404/2067] Add the header for user_nl_datm_streams, so that there are instructions on usage --- .../NEON/defaults/user_nl_datm_streams | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams index f1af044c31..36f1e72b3a 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams @@ -1,3 +1,26 @@ +!------------------------------------------------------------------------ +! This file is used to modify datm.streams.xml generated in $RUNDIR +! Entries should have the form +! :<= new stream_value> +! The following are accepted values for an assume streamname of foo +! foo:meshfile = character string +! foo:datafiles = comma separated string of full pathnames (e.g. file1,file2,file3...) +! foo:datavars = comma separated string of field pairs (e.g. foo foobar,foo2 foobar2...) +! foo:taxmode = one of [cycle, extend, limit] +! foo:tintalgo = one of [lower,upper,nearest,linear,coszen] +! foo:readmode = single (only suported mode right now) +! foo:mapalgo = one of [bilinear,redist,nn,consf,consd,none] +! foo:dtlimit = real (1.5 is default) +! foo:year_first = integer +! foo:year_last = integer +! foo:year_align = integer +! foo:vectors = one of [none,u:v] +! foo:lev_dimname: = one of [null,name of level dimenion name] +! foo:offset = integer +! As an example: +! foo:year_first = 1950 +! would change the stream year_first stream_entry to 1950 for the foo stream block +!------------------------------------------------------------------------ presaero.SSP3-7.0:datafiles = $DIN_LOC_ROOT/atm/cam/chem/trop_mozart_aero/aero/aerodep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.001_2018-2030_monthly_0.9x1.25_c210826.nc presaero.SSP3-7.0:year_first=2018 presaero.SSP3-7.0:year_last=2022 From dbe02ede634bdbd3222d8ec9cdfbd75d8f33ed05 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Nov 2022 10:27:11 -0600 Subject: [PATCH 0405/2067] Don't reapply user-mod in run_neon clone, and don't set DATM_YR_END The base case already has the NEON user-mods applied in it, so we don't need to reapply in the cloned case. Don't set DATM_YR_END, let it be set in the default user-mods and the specific user-mods for the site. The only advantage of setting DATM_YR_END in run_neon is if your run-length is shorter than what's in the user-mods, and it only saves downloading the extra files and a little bit of time to read them at initialization. So there's no need to have logic to handle that here. --- tools/site_and_regional/run_neon.py | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index c7418b786c..879b41119d 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -525,7 +525,7 @@ def run_case( with Case(base_case_root, read_only=False) as basecase: print("---- cloning the base case in {}".format(case_root)) basecase.create_clone( - case_root, keepexe=True, user_mods_dirs=user_mods_dirs + case_root, keepexe=True ) with Case(case_root, read_only=False) as case: @@ -561,13 +561,6 @@ def run_case( return case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) - # Turning all this off for usermod controsl over start, align, and end year - else: - # for the spinup we want the start and end on year boundaries - if self.end_month == 12: - case.set_value("DATM_YR_END", self.end_year) - else: - case.set_value("DATM_YR_END", self.end_year - 1) if not rundir: rundir = case.get_value("RUNDIR") From 979c71f70ad40cb4ff3f6d528d8b6016a8e5f028 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 4 Nov 2022 14:52:29 -0600 Subject: [PATCH 0406/2067] Add note on need to set MPI_TYPE_DEPTH for LILAC --- .../obtaining-building-and-running/index.rst | 1 + .../notes-on-running-ctsm.rst | 26 +++++++++++++++++++ doc/source/lilac/specific-atm-models/wrf.rst | 3 +++ 3 files changed, 30 insertions(+) create mode 100644 doc/source/lilac/obtaining-building-and-running/notes-on-running-ctsm.rst diff --git a/doc/source/lilac/obtaining-building-and-running/index.rst b/doc/source/lilac/obtaining-building-and-running/index.rst index 14dc6f40be..0739800137 100644 --- a/doc/source/lilac/obtaining-building-and-running/index.rst +++ b/doc/source/lilac/obtaining-building-and-running/index.rst @@ -9,4 +9,5 @@ obtaining-and-building-ctsm.rst setting-ctsm-runtime-options.rst + notes-on-running-ctsm.rst restarting.rst diff --git a/doc/source/lilac/obtaining-building-and-running/notes-on-running-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/notes-on-running-ctsm.rst new file mode 100644 index 0000000000..1e3d36cdf7 --- /dev/null +++ b/doc/source/lilac/obtaining-building-and-running/notes-on-running-ctsm.rst @@ -0,0 +1,26 @@ +.. highlight:: shell + +.. _notes-on-running-ctsm: + +======================= + Notes on running CTSM +======================= + +.. _runtime-environment-variables: + +Environment variables that may need to be set at runtime +======================================================== + +With the MPT MPI library (which is the default MPI library on NCAR's cheyenne machine), it is important to set the environment variable ``MPI_TYPE_DEPTH`` to 16 when running CTSM (this setting is required by the Parallel IO library). Typically you should set this variable in your job submission script, using either: + +.. code-block:: Bash + + export MPI_TYPE_DEPTH=16 + +or: + +.. code-block:: Tcsh + + setenv MPI_TYPE_DEPTH 16 + +prior to running the model. diff --git a/doc/source/lilac/specific-atm-models/wrf.rst b/doc/source/lilac/specific-atm-models/wrf.rst index d34dd66d0b..36b1e076a9 100644 --- a/doc/source/lilac/specific-atm-models/wrf.rst +++ b/doc/source/lilac/specific-atm-models/wrf.rst @@ -390,8 +390,11 @@ A simple PBS script to run WRF-CTSM on ``Cheyenne`` looks like this: #PBS -l select=2:ncpus=36:mpiprocs=36 ### Run the executable + setenv MPI_TYPE_DEPTH 16 mpiexec_mpt ./wrf.exe +(See :numref:`runtime-environment-variables` for a description of the need to set ``MPI_TYPE_DEPTH`` on ``Cheyenne``.) + To submit a batch job to the ``Cheyenne`` queues, use ``qsub`` command followed by the PBS script name. For example, if you named this script ``run_wrf_ctsm.csh``, submit the job like this:: From 222ba813d1ae566ce3bcbe9a93bcc52b21a457eb Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Nov 2022 15:03:59 -0600 Subject: [PATCH 0407/2067] Add mesh file for reduced Lightning dataset --- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 7495857ae7..7dd1ce7f32 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -22,7 +22,7 @@ flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but wi fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c221014.nc" stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' -!stream_fldfilename_ndep = '$DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc' +stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' ! h1 output stream hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI', From e855ee41a58a5033fc97adc531865635abbcace0 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Nov 2022 15:05:36 -0600 Subject: [PATCH 0408/2067] Remove the PIO_REARRANGER setting, which is hopefully not needed with the ESMF mesh file for lightning, and use of mpi-serial --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 5a20d6ac38..7095e1def7 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -1,10 +1,13 @@ #!/bin/bash ./xmlchange CLM_USRDAT_NAME=NEON ./xmlchange CCSM_CO2_PPMV=408.83 +# Set data forcing data to future scenario so will have data from 2018 to present-day ./xmlchange DATM_PRESAERO=SSP3-7.0 ./xmlchange DATM_PRESNDEP=SSP3-7.0 ./xmlchange DATM_PRESO3=SSP3-7.0 +# Explicitly set the MPI library to mpi-serial so won't have the build/run complexity of a full MPI library ./xmlchange MPILIB=mpi-serial +# Set years to run forcing data over ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 compset=`./xmlquery COMPSET --value` # For a transient case run the whole length and don't cycle @@ -21,8 +24,3 @@ fi # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) ./xmlchange PIO_TYPENAME=netcdf -# BD:05/06/2022 - The PIO_REARRANGER_LND value - for global runs, PIO_REARRANGER_LND = 1 is ideal -# and a value of 2 results in slow I/O. For point runs like these, a value of 1 results in a crash (PIO bug, probably), -# so we explicitly set a value of 2. -./xmlchange PIO_REARRANGER_LND=2 - From 4dd4a702562d9efbda1f7e073d88eb71adc860c7 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sat, 5 Nov 2022 07:43:04 -0600 Subject: [PATCH 0409/2067] needed so cloned cases point to correct datm input directory --- tools/site_and_regional/run_neon.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 879b41119d..982495f611 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -525,7 +525,7 @@ def run_case( with Case(base_case_root, read_only=False) as basecase: print("---- cloning the base case in {}".format(case_root)) basecase.create_clone( - case_root, keepexe=True + case_root, keepexe=True, user_mods_dirs=user_mods_dirs ) with Case(case_root, read_only=False) as case: From b1096d71576e825687ae9728a8241c8b3d71f406 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 5 Nov 2022 13:49:50 -0600 Subject: [PATCH 0410/2067] Add comment about needing to keep the user_mod_dirs argument in the clone case --- tools/site_and_regional/run_neon.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 982495f611..6892dd3d00 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -524,6 +524,12 @@ def run_case( # read_only = False should not be required here with Case(base_case_root, read_only=False) as basecase: print("---- cloning the base case in {}".format(case_root)) + # + # EBK: 11/05/2022 -- Note keeping the user_mods_dirs argument is important. Although + # it causes some of the user_nl_* files to have duplicated inputs. It also ensures + # that the shell_commands file is copied, as well as taking care of the DATM inputs. + # See https://github.com/ESCOMP/CTSM/pull/1872#pullrequestreview-1169407493 + # basecase.create_clone( case_root, keepexe=True, user_mods_dirs=user_mods_dirs ) From 1d6bb47fbc40cfca325c64f64592e6bfa049858e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 5 Nov 2022 20:11:42 -0600 Subject: [PATCH 0411/2067] Add run_black target to not just check with black but to run it, add beginning of a new test for add_tag_to_filename, is currently hardwired to only work on todays date --- python/Makefile | 8 +++++- python/ctsm/test/test_unit_utils_add_tag.py | 30 +++++++++++++++++++++ 2 files changed, 37 insertions(+), 1 deletion(-) create mode 100755 python/ctsm/test/test_unit_utils_add_tag.py diff --git a/python/Makefile b/python/Makefile index 4ea5fba85d..bf219f16b6 100644 --- a/python/Makefile +++ b/python/Makefile @@ -39,11 +39,17 @@ lint: FORCE $(PYLINT) $(PYLINT_ARGS) $(PYLINT_SRC) .PHONY: black -# Run black on all of the python files here and undeneath. +# Run the black check on all of the python files here and undeneath. # Use the black configure file to explicitly set a few things and specifiy the exact files. black: FORCE black --check --config pyproject.toml . +.PHONY: run_black +# Run black on all of the python files here and undeneath. +# Use the black configure file to explicitly set a few things and specifiy the exact files. +run_black: FORCE + black --config pyproject.toml . + .PHONY: clean clean: FORCE find . -name '*.pyc' -exec rm {} \; diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py new file mode 100755 index 0000000000..f1564fc1f6 --- /dev/null +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -0,0 +1,30 @@ +#!/usr/bin/env python3 + +"""Unit tests for add_tag_to_filename +""" + +import unittest + +from ctsm import unit_testing +from ctsm.utils import add_tag_to_filename + +# Allow names that pylint doesn't like, because otherwise I find it hard +# to make readable unit test names +# pylint: disable=invalid-name + + +class TestUtilsAddTag(unittest.TestCase): + """Tests of utils: add_tag_to_filename""" + + def testSimple(self): + """Simple test of surface dataset name""" + + fsurf_in = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c221105.nc" + fsurf_out = add_tag_to_filename(fsurf_in, "tag") + expect_fsurf = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_tag_c221105.nc" + self.assertEqual(expect_fsurf, fsurf_out, "Expect filenames to be as expected") + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() From 4c7e79383a37c8eea47048f53e7440c5b91b1154 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 6 Nov 2022 06:04:41 -0700 Subject: [PATCH 0412/2067] force STOP_OPTION in transient run to nmonths --- tools/site_and_regional/run_neon.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 6892dd3d00..1b314bd469 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -535,7 +535,7 @@ def run_case( ) with Case(case_root, read_only=False) as case: - if run_type is not"transient": + if run_type is not "transient": # in order to avoid the complication of leap years we always set the run_length in units of days. case.set_value("STOP_OPTION", "ndays") case.set_value("REST_OPTION", "end") @@ -567,6 +567,7 @@ def run_case( return case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) + case.set_value("STOP_OPTION", "nmonths") if not rundir: rundir = case.get_value("RUNDIR") From 83f3304cfea30af58bf225455a451142605301e8 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 6 Nov 2022 07:09:55 -0700 Subject: [PATCH 0413/2067] modified for last month of DATM data at CPER --- cime_config/usermods_dirs/NEON/CPER/shell_commands | 3 +++ 1 file changed, 3 insertions(+) diff --git a/cime_config/usermods_dirs/NEON/CPER/shell_commands b/cime_config/usermods_dirs/NEON/CPER/shell_commands index 169b358a40..b6ccbcdf57 100644 --- a/cime_config/usermods_dirs/NEON/CPER/shell_commands +++ b/cime_config/usermods_dirs/NEON/CPER/shell_commands @@ -1,3 +1,6 @@ ./xmlchange NEONSITE=CPER ./xmlchange PTS_LON=255.25545 ./xmlchange PTS_LAT=40.81297 +if [[ $compset =~ ^HIST ]]; then + ./xmlchange STOP_N=50 +fi From ba48af8962a795784b7b414b1b99d9618bfa2f8b Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 6 Nov 2022 07:22:55 -0700 Subject: [PATCH 0414/2067] let usermods set start date for transient runs --- tools/site_and_regional/run_neon.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 1b314bd469..2879a9cf9e 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -626,11 +626,11 @@ def set_ref_case(self, case): case.set_value("RUN_REFDATE", refdate) if case_root.endswith(".postad"): case.set_value("RUN_STARTDATE", refdate) - else: - case.set_value( - "RUN_STARTDATE", - "{yr:04d}-{mo:02d}-01".format(yr=self.start_year, mo=self.start_month), - ) + #else: + #case.set_value( + # "RUN_STARTDATE", + # "{yr:04d}-{mo:02d}-01".format(yr=self.start_year, mo=self.start_month), + #) return True def modify_user_nl(self, case_root, run_type, rundir): From 457f5085b6647c5f93908a903b88f6d6ae77ce64 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sun, 6 Nov 2022 10:58:45 -0700 Subject: [PATCH 0415/2067] modify shell comands to avoid cycling climte data for last month in transient case --- cime_config/usermods_dirs/NEON/MLBS/shell_commands | 1 + cime_config/usermods_dirs/NEON/MOAB/shell_commands | 1 + cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 1 + 3 files changed, 3 insertions(+) diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index e0a2ea5443..d5de0f64eb 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -5,5 +5,6 @@ ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index c90aaa30d4..96d0bcbe68 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -5,5 +5,6 @@ ./xmlchange DATM_YR_END=2020 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2021 ./xmlchange STOP_N=36 fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index df2ca55dad..43dab69998 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -5,5 +5,6 @@ ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 ./xmlchange STOP_N=24 fi From 4b3aea5f60f96778ee7cc681d7d59d4a1eb77704 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Nov 2022 10:23:14 -0700 Subject: [PATCH 0416/2067] Replaced a use of use_cropcal_streams with use_cropcal_rx_sdates. (Should make no difference except clarity.) --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 4dda3330f7..83d53f6405 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2183,7 +2183,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! In order to avoid this, you'd have to read this year's AND next year's prescribed ! sowing dates. ! WARNING: This implementation assumes that all patches use prescribed sowing dates. - if (use_cropcal_streams) then + if (use_cropcal_rx_sdates) then will_plant_prescribed_tomorrow = (jday == next_rx_sdate(p) - 1) .or. \ (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. \ jday == dayspyr) From a262232a1d942408dac3fa8e9cc45c0dac21c4fd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Nov 2022 12:49:47 -0700 Subject: [PATCH 0417/2067] Get mock working for date, and use the way date was used in utils --- python/ctsm/test/test_unit_utils_add_tag.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index f1564fc1f6..176f1a1b08 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -6,7 +6,10 @@ import unittest from ctsm import unit_testing -from ctsm.utils import add_tag_to_filename +from unittest.mock import patch +from datetime import date + +from ctsm import utils # Allow names that pylint doesn't like, because otherwise I find it hard # to make readable unit test names @@ -16,12 +19,20 @@ class TestUtilsAddTag(unittest.TestCase): """Tests of utils: add_tag_to_filename""" + @staticmethod + def _fake_today(): + return date(year=2022, month=10, day=31) + def testSimple(self): """Simple test of surface dataset name""" fsurf_in = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c221105.nc" - fsurf_out = add_tag_to_filename(fsurf_in, "tag") - expect_fsurf = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_tag_c221105.nc" + with patch("ctsm.utils.date") as mock_date: + mock_date.today.side_effect = self._fake_today + + fsurf_out = utils.add_tag_to_filename(fsurf_in, "tag") + + expect_fsurf = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_tag_c221031.nc" self.assertEqual(expect_fsurf, fsurf_out, "Expect filenames to be as expected") From c2e4c676e90b6fda9b5a0b83b6798541daebff57 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Nov 2022 13:38:30 -0700 Subject: [PATCH 0418/2067] Removed default cropcal files. * stream_fldfilename_sdate * stream_fldfilename_cultivar_gdds * stream_meshfile_cropcal --- bld/CLMBuildNamelist.pm | 8 -------- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ---- 2 files changed, 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 816872110f..e8af987ae4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3815,14 +3815,6 @@ sub setup_logic_cropcal_streams { 'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_sdate', - 'hgrid'=>"360x720cru" ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_cultivar_gdds', - 'hgrid'=>"360x720cru" ); - if ($opts->{'driver'} eq "nuopc" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_cropcal', - 'hgrid'=>"360x720cru" ); - } } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 52a15f4b71..8263129376 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1563,10 +1563,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts 1850 2100 1850 -/glade/p/cesmdata/cseg/inputdata/share/meshes/10x15_nomask_c110308_ESMFmesh.nc - -/glade/u/home/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.nc -/glade/u/home/samrabin/crop_dates/gdds_20220121_155415.nc From 1b14d9c569eda41e29754171bc89d749edc9d3ea Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Nov 2022 13:40:25 -0700 Subject: [PATCH 0419/2067] Removed vestigial use_cropcal_streams from controlMod. --- src/main/controlMod.F90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 236be9a973..0a9a5f9ab5 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -245,8 +245,6 @@ subroutine control_init(dtime) namelist /clm_inparm/ use_lai_streams - namelist /clm_inparm/ use_cropcal_streams - namelist /clm_inparm/ use_bedrock namelist /clm_inparm/ use_biomass_heat_storage From 8958f12bf2cdb2ba4afeef223267e8f68c935cfd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Nov 2022 15:29:58 -0700 Subject: [PATCH 0420/2067] Add some more tests --- python/ctsm/test/test_unit_utils_add_tag.py | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index 176f1a1b08..04e0f02306 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -21,6 +21,7 @@ class TestUtilsAddTag(unittest.TestCase): @staticmethod def _fake_today(): + """Set the fake date to Halloween""" return date(year=2022, month=10, day=31) def testSimple(self): @@ -35,6 +36,29 @@ def testSimple(self): expect_fsurf = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_tag_c221031.nc" self.assertEqual(expect_fsurf, fsurf_out, "Expect filenames to be as expected") + def testSimpleLanduse(self): + """Simple test of landuse dataset name""" + + landuse_in = "landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c190214.nc" + with patch("ctsm.utils.date") as mock_date: + mock_date.today.side_effect = self._fake_today + + landuse_out = utils.add_tag_to_filename(landuse_in, "tag") + + expect_landuse = "landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_tag_c221031.nc" + self.assertEqual(expect_landuse, landuse_out, "Expect filenames to be as expected") + + def testSimpleDatmDomain(self): + """Simple test of datm domain dataset name""" + + file_in = "domain.lnd.360x720_gswp3.0v1.c170606.nc" + with patch("ctsm.utils.date") as mock_date: + mock_date.today.side_effect = self._fake_today + + file_out = utils.add_tag_to_filename(file_in, "tag") + + expect_filename = "domain.lnd.360x720_gswp3.0v1_tag_c221031.nc" + self.assertEqual(expect_filename, file_out, "Expect filenames to be as expected") if __name__ == "__main__": unit_testing.setup_for_tests() From cf5841ef8c7341a190dd527194b8902fc0745cc7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Nov 2022 15:32:14 -0700 Subject: [PATCH 0421/2067] Add test for domain file as well --- python/ctsm/test/test_unit_utils_add_tag.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index 04e0f02306..b63a76eba9 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -60,6 +60,18 @@ def testSimpleDatmDomain(self): expect_filename = "domain.lnd.360x720_gswp3.0v1_tag_c221031.nc" self.assertEqual(expect_filename, file_out, "Expect filenames to be as expected") + def testSimpleDomain(self): + """Simple test of domain dataset name""" + + file_in = "domain.lnd.fv0.9x1.25_gx1v7.151020.nc" + with patch("ctsm.utils.date") as mock_date: + mock_date.today.side_effect = self._fake_today + + file_out = utils.add_tag_to_filename(file_in, "tag") + + expect_filename = "domain.lnd.fv0.9x1.25_gx1v7_tag_c221031.nc" + self.assertEqual(expect_filename, file_out, "Expect filenames to be as expected") + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() From 52a0179d98d5dbd9292aeba38e4d14c952752e13 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Nov 2022 23:04:01 -0700 Subject: [PATCH 0422/2067] Add ability of add_tag_to_filename to replace resolution for the surface dataset, and add a unit test for it --- python/ctsm/test/test_unit_utils_add_tag.py | 10 +++++++-- python/ctsm/utils.py | 23 +++++++++++++++++++-- 2 files changed, 29 insertions(+), 4 deletions(-) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index b63a76eba9..491dfc32c9 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -5,9 +5,9 @@ import unittest -from ctsm import unit_testing from unittest.mock import patch from datetime import date +from ctsm import unit_testing from ctsm import utils @@ -32,9 +32,12 @@ def testSimple(self): mock_date.today.side_effect = self._fake_today fsurf_out = utils.add_tag_to_filename(fsurf_in, "tag") + fsurf_out2 = utils.add_tag_to_filename(fsurf_in, "tag", replace_res=True) expect_fsurf = "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_tag_c221031.nc" self.assertEqual(expect_fsurf, fsurf_out, "Expect filenames to be as expected") + expect_fsurf2 = "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc" + self.assertEqual(expect_fsurf2, fsurf_out2, "Expect filenames to be as expected") def testSimpleLanduse(self): """Simple test of landuse dataset name""" @@ -45,7 +48,9 @@ def testSimpleLanduse(self): landuse_out = utils.add_tag_to_filename(landuse_in, "tag") - expect_landuse = "landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_tag_c221031.nc" + expect_landuse = ( + "landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_tag_c221031.nc" + ) self.assertEqual(expect_landuse, landuse_out, "Expect filenames to be as expected") def testSimpleDatmDomain(self): @@ -72,6 +77,7 @@ def testSimpleDomain(self): expect_filename = "domain.lnd.fv0.9x1.25_gx1v7_tag_c221031.nc" self.assertEqual(expect_filename, file_out, "Expect filenames to be as expected") + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 2851a3b619..2ef40945ed 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -4,6 +4,7 @@ import os import sys import string +import re import pdb from datetime import date @@ -43,21 +44,28 @@ def fill_template_file(path_to_template, path_to_final, substitutions): final_file.write(final_file_contents) -def add_tag_to_filename(filename, tag): +def add_tag_to_filename(filename, tag, replace_res=False): """ Add a tag and replace timetag of a filename Expects file to end with [._]cYYMMDD.nc or [._]YYMMDD.nc Add the tag to just before that ending part and change the ending part to the current time tag. + if replace_res is True, then replace the resolution + part of the filename. Expects the file to start with + [a-z.]_ and then the resolution. + Parameters ---------- filename (str) : file name tag (str) : string of a tag to be added to the end of filename + (or to replace the resolution part of the filename) Raises ------ Error: When it cannot find . and _ in the filename. + Error: When it's asked to replace the resolution and + can't figure out where that is in the filename. Returns ------ @@ -73,7 +81,18 @@ def add_tag_to_filename(filename, tag): abort(err_msg) today = date.today() today_string = today.strftime("%y%m%d") - fname_out = basename[:cend] + "_" + tag + "_c" + today_string + ".nc" + if not replace_res: + fname_out = basename[:cend] + "_" + tag + "_c" + today_string + ".nc" + else: + match = re.fullmatch(r"([a-z.]+)_([0-9x.]+)_(.+?)", basename[:cend]) + if match is not None: + fname_out = ( + match.group(1) + "_" + tag + "_" + match.group(3) + "_c" + today_string + ".nc" + ) + else: + abort( + "Trouble figuring out where to replace the resolution in the filename: " + filename + ) return fname_out From c40fcd529c43aece073daa09576c63c1ab1e445f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Nov 2022 23:12:54 -0700 Subject: [PATCH 0423/2067] Allow more characters for resolution in filename --- python/ctsm/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 2ef40945ed..7294f09d4c 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -84,7 +84,7 @@ def add_tag_to_filename(filename, tag, replace_res=False): if not replace_res: fname_out = basename[:cend] + "_" + tag + "_c" + today_string + ".nc" else: - match = re.fullmatch(r"([a-z.]+)_([0-9x.]+)_(.+?)", basename[:cend]) + match = re.fullmatch(r"([a-z.]+)_([fv0-9x.crunldas]+)_(.+?)", basename[:cend]) if match is not None: fname_out = ( match.group(1) + "_" + tag + "_" + match.group(3) + "_c" + today_string + ".nc" From 9dd28857ec4565a44785b9b88ec04ca7c9ef80b7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Nov 2022 23:33:38 -0700 Subject: [PATCH 0424/2067] Add a landunit test for the replace_res option --- python/ctsm/test/test_unit_utils_add_tag.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index 491dfc32c9..4c9534b1d3 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -47,11 +47,16 @@ def testSimpleLanduse(self): mock_date.today.side_effect = self._fake_today landuse_out = utils.add_tag_to_filename(landuse_in, "tag") + landuse_out2 = utils.add_tag_to_filename(landuse_in, "tag", replace_res=True) expect_landuse = ( "landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_tag_c221031.nc" ) self.assertEqual(expect_landuse, landuse_out, "Expect filenames to be as expected") + expect_landuse2 = ( + "landuse.timeseries_tag_hist_78pfts_CMIP6_simyr1850-2015_c221031.nc" + ) + self.assertEqual(expect_landuse2, landuse_out2, "Expect filenames to be as expected") def testSimpleDatmDomain(self): """Simple test of datm domain dataset name""" From 3781d6b6d8aace20f6268cfca12712743e9c5649 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 11:23:02 -0700 Subject: [PATCH 0425/2067] Add a test to loop over a list of surface dataset names --- python/ctsm/test/test_unit_utils_add_tag.py | 68 ++++++++++++++++++++- 1 file changed, 65 insertions(+), 3 deletions(-) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index 4c9534b1d3..005fb787dc 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -53,9 +53,7 @@ def testSimpleLanduse(self): "landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_tag_c221031.nc" ) self.assertEqual(expect_landuse, landuse_out, "Expect filenames to be as expected") - expect_landuse2 = ( - "landuse.timeseries_tag_hist_78pfts_CMIP6_simyr1850-2015_c221031.nc" - ) + expect_landuse2 = "landuse.timeseries_tag_hist_78pfts_CMIP6_simyr1850-2015_c221031.nc" self.assertEqual(expect_landuse2, landuse_out2, "Expect filenames to be as expected") def testSimpleDatmDomain(self): @@ -82,6 +80,70 @@ def testSimpleDomain(self): expect_filename = "domain.lnd.fv0.9x1.25_gx1v7_tag_c221031.nc" self.assertEqual(expect_filename, file_out, "Expect filenames to be as expected") + def testSurfReplaceListDomain(self): + """Simple test of list of surface dataset name with replace_res option""" + + files_in = [ + "surfdata_48x96_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr2000_c190304.nc", + "surfdata_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr2000_c190304.nc", + "surfdata_4x5_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_10x15_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_10x15_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_0.125nldas2_hist_16pfts_Irrig_CMIP6_simyr2005_c190412.nc", + "surfdata_64x128_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc", + "surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr2000_c190304.nc", + "surfdata_0.125x0.125_hist_78pfts_CMIP6_simyr2005_c190624.nc", + "surfdata_10x15_hist_78pfts_CMIP6_simyr2000_c190214.nc", + "surfdata_4x5_hist_78pfts_CMIP6_simyr2000_c190214.nc", + "surfdata_1.9x2.5_hist_16pfts_Irrig_CMIP6_simyr1850_c190304.nc", + "surfdata_10x15_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc", + "surfdata_4x5_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc", + "surfdata_48x96_hist_78pfts_CMIP6_simyr1850_c190214.nc", + "surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr1850_c190214.nc", + "surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr1850_c190304.nc", + "surfdata_10x15_hist_78pfts_CMIP6_simyr1850_c190214.nc", + "surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc", + "surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc", + ] + expect_filenames = [ + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2005_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr2005_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_16pfts_Irrig_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_16pfts_nourb_CMIP6_simyrPtVg_c221031.nc", + ] + for i, file_in in enumerate(files_in): + + with patch("ctsm.utils.date") as mock_date: + mock_date.today.side_effect = self._fake_today + + file_out = utils.add_tag_to_filename(file_in, "tag", replace_res=True) + + self.assertEqual(expect_filenames[i], file_out, "Expect filenames to be as expected") + if __name__ == "__main__": unit_testing.setup_for_tests() From 363154cb807f468a64b46a16b7f02215cfd478e3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 11:38:39 -0700 Subject: [PATCH 0426/2067] Add more complex surface dataset names and make sure works --- python/ctsm/test/test_unit_utils_add_tag.py | 7 +++++++ python/ctsm/utils.py | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index 005fb787dc..d416a2909f 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -107,6 +107,8 @@ def testSurfReplaceListDomain(self): "surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr1850_c190304.nc", "surfdata_10x15_hist_78pfts_CMIP6_simyr1850_c190214.nc", "surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc", + "surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_78pfts_CMIP6_simyr2000_c200426.nc", + "surfdata_C96_hist_78pfts_CMIP6_simyr1850_c203171.nc", "surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc", ] expect_filenames = [ @@ -133,8 +135,13 @@ def testSurfReplaceListDomain(self): "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr2000_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", "surfdata_tag_hist_16pfts_nourb_CMIP6_simyrPtVg_c221031.nc", ] + self.assertEqual( + len(files_in), len(expect_filenames), "length of arrays does not match as expected" + ) for i, file_in in enumerate(files_in): with patch("ctsm.utils.date") as mock_date: diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 7294f09d4c..9690782652 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -84,7 +84,7 @@ def add_tag_to_filename(filename, tag, replace_res=False): if not replace_res: fname_out = basename[:cend] + "_" + tag + "_c" + today_string + ".nc" else: - match = re.fullmatch(r"([a-z.]+)_([fv0-9x.crunldas]+)_(.+?)", basename[:cend]) + match = re.fullmatch(r"([a-z.]+)_([Cfvnenp0-9x.crunldasA-Z]+)_(.+?)", basename[:cend]) if match is not None: fname_out = ( match.group(1) + "_" + tag + "_" + match.group(3) + "_c" + today_string + ".nc" From 5a4f4151e59146ae6b867281b8719fe99e2329d9 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 12:17:10 -0700 Subject: [PATCH 0427/2067] Make sure works for a 4-digit year date string as well --- python/ctsm/test/test_unit_utils_add_tag.py | 4 +++- python/ctsm/utils.py | 9 +++++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/python/ctsm/test/test_unit_utils_add_tag.py b/python/ctsm/test/test_unit_utils_add_tag.py index d416a2909f..bef69f6154 100755 --- a/python/ctsm/test/test_unit_utils_add_tag.py +++ b/python/ctsm/test/test_unit_utils_add_tag.py @@ -108,7 +108,8 @@ def testSurfReplaceListDomain(self): "surfdata_10x15_hist_78pfts_CMIP6_simyr1850_c190214.nc", "surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc", "surfdata_ne0np4.ARCTICGRIS.ne30x8_hist_78pfts_CMIP6_simyr2000_c200426.nc", - "surfdata_C96_hist_78pfts_CMIP6_simyr1850_c203171.nc", + "surfdata_C96_hist_78pfts_CMIP6_simyr1850_c200317.nc", + "surfdata_C96_hist_78pfts_CMIP6_simyr1850_c20221108.nc", "surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc", ] expect_filenames = [ @@ -137,6 +138,7 @@ def testSurfReplaceListDomain(self): "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", "surfdata_tag_hist_78pfts_CMIP6_simyr2000_c221031.nc", "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", + "surfdata_tag_hist_78pfts_CMIP6_simyr1850_c221031.nc", "surfdata_tag_hist_16pfts_nourb_CMIP6_simyrPtVg_c221031.nc", ] self.assertEqual( diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 9690782652..8b2043593e 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -77,8 +77,13 @@ def add_tag_to_filename(filename, tag, replace_res=False): if basename[cend] == "c": cend = cend - 1 if (basename[cend] != ".") and (basename[cend] != "_"): - err_msg = "Trouble figuring out where to add tag to filename: " + filename - abort(err_msg) + # Check if date stirng at end includes a 4 digit year + cend = -12 + if basename[cend] == "c": + cend = cend - 1 + if (basename[cend] != ".") and (basename[cend] != "_"): + err_msg = "Trouble figuring out where to add tag to filename: " + filename + abort(err_msg) today = date.today() today_string = today.strftime("%y%m%d") if not replace_res: From d5bda14c536d61108f0f4ae4b36164ed877aac53 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Nov 2022 12:21:32 -0700 Subject: [PATCH 0428/2067] Don't use gddmin as minimum GDD requirement when not using prescribed GDDs. --- src/biogeochem/CNPhenologyMod.F90 | 8 -------- 1 file changed, 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 83d53f6405..0c5a36410e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2610,15 +2610,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if - ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator - ! Just manually set a minimum of 1.0 - if (gddmaturity(p) < gddmin(ivt(p))) then - write(iulog,*) 'Some patch with ivt ',ivt(p),' has calculated gddmaturity ',gddmaturity(p),& - '; using gddmin(ivt(p)) instead (',gddmin(ivt(p)),')' - endif - gddmaturity(p) = max(gddmaturity(p), gddmin(ivt(p))) endif -! write (iulog,'(a,i4,a,f0.0)') 'gddmaturity (ivt ',ivt(p),'): ',gddmaturity(p) end associate From 65e0c9a60b3b3b2b9762ad9e99cbfe27d7cb4dc3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 12:32:48 -0700 Subject: [PATCH 0429/2067] Add note that 4-digit years are allowed and test for it --- python/ctsm/utils.py | 1 + 1 file changed, 1 insertion(+) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 8b2043593e..bf48762a43 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -48,6 +48,7 @@ def add_tag_to_filename(filename, tag, replace_res=False): """ Add a tag and replace timetag of a filename Expects file to end with [._]cYYMMDD.nc or [._]YYMMDD.nc + or with 4-digit years YYYYMMDD. Add the tag to just before that ending part and change the ending part to the current time tag. From 96209ceb39ddae054dbcea45120adfc1c1026d4b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 12:40:30 -0700 Subject: [PATCH 0430/2067] Replace the resolution in the surface and landuse.timeseries filenames --- python/ctsm/site_and_regional/regional_case.py | 4 ++-- python/ctsm/site_and_regional/single_point_case.py | 4 ++-- python/ctsm/utils.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/python/ctsm/site_and_regional/regional_case.py b/python/ctsm/site_and_regional/regional_case.py index 1dc6a522cc..8d5d81e014 100644 --- a/python/ctsm/site_and_regional/regional_case.py +++ b/python/ctsm/site_and_regional/regional_case.py @@ -154,7 +154,7 @@ def create_surfdata_at_reg(self, indir, file, user_mods_dir): # specify files fsurf_in = os.path.join(indir, file) - fsurf_out = add_tag_to_filename(fsurf_in, self.tag) + fsurf_out = add_tag_to_filename(fsurf_in, self.tag, replace_res=True) logger.info("fsurf_in: %s", fsurf_in) logger.info("fsurf_out: %s", os.path.join(self.out_dir, fsurf_out)) @@ -194,7 +194,7 @@ def create_landuse_at_reg(self, indir, file, user_mods_dir): # specify files fluse_in = os.path.join(indir, file) - fluse_out = add_tag_to_filename(fluse_in, self.tag) + fluse_out = add_tag_to_filename(fluse_in, self.tag, replace_res=True) logger.info("fluse_in: %s", fluse_in) logger.info("fluse_out: %s", os.path.join(self.out_dir, fluse_out)) diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 31ab158706..05b918d316 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -342,7 +342,7 @@ def create_landuse_at_point(self, indir, file, user_mods_dir): # specify files fluse_in = os.path.join(indir, file) - fluse_out = add_tag_to_filename(fluse_in, self.tag) + fluse_out = add_tag_to_filename(fluse_in, self.tag, replace_res=True) logger.info("fluse_in: %s", fluse_in) logger.info("fluse_out: %s", os.path.join(self.out_dir, fluse_out)) @@ -464,7 +464,7 @@ def create_surfdata_at_point(self, indir, file, user_mods_dir): # specify file fsurf_in = os.path.join(indir, file) - fsurf_out = add_tag_to_filename(fsurf_in, self.tag) + fsurf_out = add_tag_to_filename(fsurf_in, self.tag, replace_res=True) logger.info("fsurf_in: %s", fsurf_in) logger.info("fsurf_out: %s", os.path.join(self.out_dir, fsurf_out)) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index bf48762a43..42444e32c5 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -83,8 +83,8 @@ def add_tag_to_filename(filename, tag, replace_res=False): if basename[cend] == "c": cend = cend - 1 if (basename[cend] != ".") and (basename[cend] != "_"): - err_msg = "Trouble figuring out where to add tag to filename: " + filename - abort(err_msg) + err_msg = "Trouble figuring out where to add tag to filename: " + filename + abort(err_msg) today = date.today() today_string = today.strftime("%y%m%d") if not replace_res: From a5dc3f40b650a47a5b06b2542a5546fbef19785d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 12:53:35 -0700 Subject: [PATCH 0431/2067] Change NEON surface dataset name --- tools/site_and_regional/modify_singlept_site_neon.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 336366a49b..35d8e3f4e6 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -250,8 +250,7 @@ def find_surffile(surf_dir, site_name): surf_file (str): name of the surface dataset file """ - # sf_name = "surfdata_hist_16pfts_Irrig_CMIP6_simyr2000_"+site_name+"*.nc" - sf_name = "surfdata_*hist_78pfts_CMIP6_simyr2000_" + site_name + "*.nc" + sf_name = "surfdata_1x1_NEON_"+site_name+"*hist_78pfts_CMIP6_simyr2000_*.nc" print (os.path.join(surf_dir , sf_name)) surf_file = sorted(glob.glob(os.path.join(surf_dir , sf_name))) From cc3770c211c192885e16f838faba96122cdc7ad5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 13:26:56 -0700 Subject: [PATCH 0432/2067] Add modules needed for neon_surf_wrapper --- python/conda_env_ctsm_py.txt | 2 ++ 1 file changed, 2 insertions(+) diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index 8c110e8f3f..d757ae1782 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -11,6 +11,8 @@ # conda activate ctsm_py # Do this anytime you want to run a CTSM python script # python=3.7.9 +pandas +tqdm scipy netcdf4 requests From beb002ee53232c6d1484e6a12b6e4aab5a378d4d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 13:27:20 -0700 Subject: [PATCH 0433/2067] Update surface dataset names for NEON --- tools/site_and_regional/neon_surf_wrapper.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index 2f8a00500c..edba722f39 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -96,8 +96,9 @@ def main(): lon = row['Lon'] site = row['Site'] pft = row['pft'] + clmsite = "1x1_NEON_"+site print ("Now processing site :", site) - command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',site,'--dompft',str(pft),'--crop', + command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite,'--dompft',str(pft),'--crop', '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] execute(command) From e1459d40aa5cd39730fcf944998da74ba6c7be82 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Nov 2022 20:26:09 -0700 Subject: [PATCH 0434/2067] Add python modules needed for neon_surf_wrapper to all conda requirements files --- python/conda_env_ctsm_py_cgd.txt | 2 ++ python/conda_env_ctsm_py_latest.txt | 2 ++ 2 files changed, 4 insertions(+) diff --git a/python/conda_env_ctsm_py_cgd.txt b/python/conda_env_ctsm_py_cgd.txt index 45025506a8..e7ee4af8ab 100644 --- a/python/conda_env_ctsm_py_cgd.txt +++ b/python/conda_env_ctsm_py_cgd.txt @@ -13,6 +13,8 @@ # conda activate ctsm_py # Do this anytime you want to run a CTSM python script # python=3.7.0 # The python version MUST match the python version available on CGD systems through modules exactly +pandas +tqdm scipy netcdf4 requests diff --git a/python/conda_env_ctsm_py_latest.txt b/python/conda_env_ctsm_py_latest.txt index a7a28c9fc3..2dc2ed518d 100644 --- a/python/conda_env_ctsm_py_latest.txt +++ b/python/conda_env_ctsm_py_latest.txt @@ -1,5 +1,7 @@ # This is a test python environment intended to represent the latest environment that can be built python>=3.9.13,<3.10 # Moving to 3.10 runs into conflicts +pandas>=1.5.1 +tqdm>=4.64.1 scipy netcdf4 requests From 93b69e03d33b004f9e2354edcbd9e2b38c61587f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Nov 2022 12:21:38 -0700 Subject: [PATCH 0435/2067] Only error if zero harvests will actually be an issue. --- src/biogeochem/CNPhenologyMod.F90 | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 0c5a36410e..d3de8d3d0e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3003,9 +3003,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! How many harvests have occurred? h = crop_inst%harvest_count(p) - if (h .le. 0) then - call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") - end if ! Replenish the seed deficits from grain, if there is enough available ! grain. (If there is not enough available grain, the seed deficits will @@ -3033,10 +3030,15 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & + repr_grainc_to_food_thispool - repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & - + repr_grainc_to_food_thispool * dt - repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & - + repr_grainc_to_food_perharv(p,h,k) + if (reproductivec(p,k) + repr_grainc_to_food_thispool * dt .gt. 0) then + if (h .le. 0) then + call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") + end if + repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + + repr_grainc_to_food_thispool * dt + repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & + + repr_grainc_to_food_perharv(p,h,k) + end if repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) end do From 134ec4e1e10a7ebc6abaf3c293eb8ee0705333ef Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 11 Nov 2022 13:50:33 -0700 Subject: [PATCH 0436/2067] updated path to surface datasets --- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 7dd1ce7f32..29e50431ce 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -19,7 +19,7 @@ !---------------------------------------------------------------------------------- flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets -fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_${NEONSITE}_c221014.nc" +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c221111.nc" stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' From 74b9cd3c3a4c59511e2991caf877fff27243c961 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 11 Nov 2022 15:55:52 -0700 Subject: [PATCH 0437/2067] Replace notes about using ncar_pylib with running py_env_create --- python/ctsm/subset_data.py | 8 ++++---- tools/site_and_regional/modify_singlept_site_neon.py | 9 +++------ tools/site_and_regional/neon_surf_wrapper.py | 8 ++++---- tools/site_and_regional/run_neon.py | 12 ++++-------- tools/site_and_regional/subset_data | 9 +++------ 5 files changed, 18 insertions(+), 28 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 7a33d9c2fa..4832e98f7f 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -2,10 +2,10 @@ |------------------------------------------------------------------| |--------------------- Instructions -----------------------------| |------------------------------------------------------------------| -Instructions for running on Cheyenne/Casper: -load the following into your local environment - module load python - ncar_pylib +Instructions for running using conda python environments: + +../../py_env_create +conda activate ctsm_py ------------------------------------------------------------------- To see the available options for single point or regional cases: ./subset_data.py --help diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 35d8e3f4e6..334ab7d6aa 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -16,14 +16,11 @@ - Modify surface dataset with downloaded data. ------------------------------------------------------------------- -Instructions for running on Cheyenne/Casper: +Instructions for running using conda python environments: -load the following into your local environment - module load python - ncar_pylib +../../py_env_create +conda activate ctsm_py -To remove NPL from your environment on Cheyenne/Casper: - deactivate ------------------------------------------------------------------- To see the available options: ./modify_singlept_site_neon.py --help diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index edba722f39..e02ee2bd53 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -11,10 +11,10 @@ based on the downloaded neon data. (i.e. modify_singlept_site_neon.py) -Instructions for running on Cheyenne/Casper: -load the following into your local environment - module load python - ncar_pylib +Instructions for running using conda python environments: + +../../py_env_create +conda activate ctsm_py """ # TODO diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 2879a9cf9e..b8bc79a845 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -26,14 +26,10 @@ 4) Build and submit the case. ------------------------------------------------------------------- -Instructions for running on Cheyenne/Casper: - -load the following into your local environment - module load python - ncar_pylib - -To remove NPL from your environment on Cheyenne/Casper: - deactivate +Instructions for running using conda python environments: + +../../py_env_create +conda activate ctsm_py ------------------------------------------------------------------- To see the available options: diff --git a/tools/site_and_regional/subset_data b/tools/site_and_regional/subset_data index bb582b21f8..162dcf1d4e 100755 --- a/tools/site_and_regional/subset_data +++ b/tools/site_and_regional/subset_data @@ -18,13 +18,10 @@ To see all available options for single-point/regional subsetting: ./subset_data --help ---------------------------------------------------------------- -Instructions for running on Cheyenne/Casper: - load the following into your local environment - module load python - ncar_pylib +Instructions for running using conda python environments: -To remove from your environment on Cheyenne/Casper: - deactivate +../../py_env_create +conda activate ctsm_py """ import os From 4588f0c8e13d78c1ed8f5848f1046d1300a44d2a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 11 Nov 2022 16:01:35 -0700 Subject: [PATCH 0438/2067] Remove the toolchain files, this work was moved over to the ctsm5.2 branch, which changed the process for how surface datasets would be created --- python/ctsm/gen_mksurf_namelist.py | 377 ---------------------------- tools/toolchain/gen_mksurf_namelist | 77 ------ 2 files changed, 454 deletions(-) delete mode 100644 python/ctsm/gen_mksurf_namelist.py delete mode 100755 tools/toolchain/gen_mksurf_namelist diff --git a/python/ctsm/gen_mksurf_namelist.py b/python/ctsm/gen_mksurf_namelist.py deleted file mode 100644 index 735ae0493f..0000000000 --- a/python/ctsm/gen_mksurf_namelist.py +++ /dev/null @@ -1,377 +0,0 @@ -# 2020-11-08 Negin Sobhani - -""" -|------------------------------------------------------------------| -|--------------------- Instructions -----------------------------| -|------------------------------------------------------------------| -This Python script is part of the simplified toolchain for creating -the surface dataset for ctsm cases. -This script should be used as the first step of the new toolchain. -It will automatically create namelist (control file) that is -needed for creating surface dataset and requisite intermediate files for -running CTSM cases. -For transient cases, it will also create a txt file that includes the -landuse files for every year. - -------------------------------------------------------------------- -Instructions for running on Cheyenne/Casper: - -load the following into your local environment: - - module load python - ncar_pylib -------------------------------------------------------------------- -To see the available options: - ./gen_mksurf_namelist.py --help - -To run the script: - ./gen_mksurf_namelist.py - -To remove NPL(ncar_pylib) from your environment on Cheyenne/Casper: - deactivate -------------------------------------------------------------------- -""" - -# TODO (NS) - -# -[x] Add default values in the help page. -# -[x] Add info for help page note for end_year -- by default is start_year -# -[x] Possibly remove year --years and range options -# Currently comment them out. - -# -[x] maybe a verbose option and removing debug -# -[x] --debug mode is not working... - -# -[ ] add error check for hi-res and years if they are 1850 and 2005. -# -[ ] hirespft data only for 2005? add error-check - -# -[x] different path for each range of years for transient cases. -# default should be picked based on the year. 1850 - 2015 --> -# /glade/p/cesm/cseg/inputdata/lnd/clm2/rawdata/ -# pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c170629/ -# 850-1850 --> -# pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1849.c171012 - - -# Import libraries -from __future__ import print_function - -import os -import sys -import logging -import argparse - -# -- import local classes for this script -from ctsm.toolchain.ctsm_case import CtsmCase - -# -- import ctsm logging flags -from ctsm.ctsm_logging import ( - setup_logging_pre_config, - add_logging_args, - process_logging_args, -) - -logger = logging.getLogger(__name__) - -## valid options for resolution and SSP scenarios: -VALID_OPTS = { - "res": [ - "512x1024", - "360x720cru", - "128x256", - "64x128", - "48x96", - "94x192", - "0.23x0.31", - "0.47x0.63", - "0.9x1.25", - "1.9x2.5", - "2.5x3.33", - "4x5", - "10x15", - "0.125nldas2", - "5x5_amazon", - "1x1_camdenNJ", - "1x1_vancouverCAN", - "1x1_mexicocityMEX", - "1x1_asphaltjungleNJ", - "1x1_brazil,1x1_urbanc_alpha", - "1x1_numaIA,1x1_smallvilleIA", - "0.1x0.1", - "0.25x0.25", - "0.5x0.5", - "3x3min", - "5x5min", - "10x10min", - "0.33x0.33", - "0.125x0.125", - "ne4np4,ne16np4", - "ne30np4.pg2", - "ne30np4.pg3", - "ne30np4", - "ne60np4", - "ne120np4", - ], - "ssp_rcp": [ - "hist", - "SSP1-2.6", - "SSP3-7.0", - "SSP5-3.4", - "SSP2-4.5", - "SSP1-1.9", - "SSP4-3.4", - "SSP4-6.0", - "SSP5-8.5", - ], -} - - -def get_parser(): - """ - Get parser object for this script. - """ - parser = argparse.ArgumentParser( - description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter - ) - - parser.print_usage = parser.print_help - - parser.add_argument( - "--sy", - "--start-year", - help="Simulation start year. [default: %(default)s] ", - action="store", - dest="start_year", - required=False, - type=start_year_type, - default=2000, - ) - parser.add_argument( - "--ey", - "--end-year", - help="Simulation end year. [default: start_year] ", - action="store", - dest="end_year", - required=False, - type=int, - ) - parser.add_argument( - "--glc-nec", - help=""" - Number of glacier elevation classes to use. - [default: %(default)s] - """, - action="store", - dest="glc_nec", - type=glc_nec_type, - default="10", - ) - parser.add_argument( - "--rundir", - help=""" - Directory to run in. - [default: %(default)s] - """, - action="store", - dest="run_dir", - required=False, - default=os.getcwd(), - ) - parser.add_argument( - "--ssp-rcp", - help=""" - Shared Socioeconomic Pathway and Representative - Concentration Pathway Scenario name(s). - [default: %(default)s] - """, - action="store", - dest="ssp_rcp", - required=False, - choices=VALID_OPTS["ssp_rcp"], - default="hist", - ) - - ############################################## - # In mksurfdata.pl these options are -l --dinlc - # But the group decided --raw_dir is more descriptive. - # If everyone agrees, the commented out line should be removed. - # parser.add_argument('-l','--dinlc', #--raw-dir or --rawdata-dir - - parser.add_argument( - "--raw-dir", - "--rawdata-dir", - help=""" - /path/of/root/of/input/data', - [default: %(default)s] - """, - action="store", - dest="input_path", - default="/glade/p/cesm/cseg/inputdata/lnd/clm2/rawdata/", - ) - parser.add_argument( - "--vic", - help=""" - Flag for adding the fields required for the VIC model. - """, - action="store_true", - dest="vic_flag", - default=False, - ) - parser.add_argument( - "--glc", - help=""" - Flag for adding the optional 3D glacier fields for verification of the glacier model. - """, - action="store_true", - dest="glc_flag", - default=False, - ) - parser.add_argument( - "--hirespft", - help=""" - If you want to use the high-resolution pft dataset rather - than the default lower resolution dataset. - (Low resolution is at quarter-degree, high resolution at 3-minute) - [Note: hires only available for 1850 and 2005.] - """, - action="store_true", - dest="hres_flag", - default=False, - ) - parser.add_argument( - "--nocrop", - help=""" - Create datasets with the extensive list of prognostic crop types. - """, - action="store_false", - dest="crop_flag", - default=True, - ) - parser.add_argument( - "-f", - "--fast", - help="Toggle fast mode which does not user the large mapping file", - action="store_true", - dest="fast_flag", - default=False, - ) - parser.add_argument( - "-r", - "--res", - help=""" - Resolution is the supported resolution(s) to use for files. - [default: %(default)s] - """, - action="store", - dest="res", - choices=VALID_OPTS["res"], - required=False, - default="4x5", - ) - return parser - - -# -- types for this parser - - -def glc_nec_type(glc): - """ - Function for defining acceptable glc_nec input. - - Args: - x (str) : glc_nec value from command line args. - - Raises: - Error if value of glc_nec is not in the range - of 1-99. - - Returns: - x (int) : Acceptable glc_nec value. - """ - glc = int(glc) - if (glc <= 0) or (glc >= 100): - raise argparse.ArgumentTypeError("ERROR: glc_nec must be between 1 and 99.") - return glc.__str__() - - -def start_year_type(year): - """ - Function for defining acceptable start_year input. - - Args: - year (str) : start_year string from command line args. - - Raises: - Error if value of start_year is not in the range - of 850-2105. - - Returns: - year (int) : Acceptable start_year value. - """ - year = int(year) - if (year < 850) or (year > 2105): - raise argparse.ArgumentTypeError( - "ERROR: Simulation start year should be between 850 and 2105." - ) - return year - - -def main(): - """ - Main function for gen_mksurf_namelist. - """ - # -- add logging flags from ctsm_logging - setup_logging_pre_config() - parser = get_parser() - add_logging_args(parser) - - args = parser.parse_args() - process_logging_args(args) - - res = args.res - glc_nec = args.glc_nec - input_path = args.input_path - ssp_rcp = args.ssp_rcp - crop_flag = args.crop_flag - vic_flag = args.vic_flag - glc_flag = args.glc_flag - hres_flag = args.hres_flag - - start_year = args.start_year - end_year = args.end_year - - # -- determine end_year if not given as an argument: - if not end_year: - end_year = start_year - - # -- check if the input path exist - if not os.path.exists(input_path): - sys.exit( - "ERROR: \n" - + "\t raw_dir does not exist on this machine. \n" - + "\t Please point to the correct raw_dir using --raw-dir" - + "or --rawdata-dir flags." - ) - - ctsm_case = CtsmCase( - res, - glc_nec, - ssp_rcp, - crop_flag, - input_path, - vic_flag, - glc_flag, - start_year, - end_year, - hres_flag, - ) - - logger.info("--------------------------") - logger.info(" ctsm case : %s", ctsm_case) - logger.info("--------------------------") - - ctsm_case.create_namelist_file() - - -if __name__ == "__main__": - main() diff --git a/tools/toolchain/gen_mksurf_namelist b/tools/toolchain/gen_mksurf_namelist deleted file mode 100755 index ecd225dd19..0000000000 --- a/tools/toolchain/gen_mksurf_namelist +++ /dev/null @@ -1,77 +0,0 @@ -#!/usr/bin/env python - -# 2020-11-08 Negin Sobhani - -""" -|------------------------------------------------------------------| -|--------------------- Instructions -----------------------------| -|------------------------------------------------------------------| -This is a just top-level skeleton script that calls -gen_mksurf_namelist.py. -The original code (./gen_mksurf_namelist.py) is located under -python/ctsm folder. - -This Python script is part of the simplified toolchain for creating -the surface dataset for ctsm cases. -This script should be used as the first step of the new toolchain. -It will automatically create namelist (control file) that is -needed for creating surface dataset and requisite intermediate files for -running CTSM cases. -For transient cases, it will also create a txt file that includes the -landuse files for every year. - -------------------------------------------------------------------- -Instructions for running on Cheyenne/Casper: - -load the following into your local environment: - - module load python - ncar_pylib -------------------------------------------------------------------- -To see the available options: - ./gen_mksurf_namelist.py --help - -To run the script: - ./gen_mksurf_namelist.py - -To remove NPL(ncar_pylib) from your environment on Cheyenne/Casper: - deactivate -------------------------------------------------------------------- -""" - -#TODO (NS) - -# -[x] Add default values in the help page. -# -[x] Add info for help page note for end_year -- by default is start_year -# -[ ] Possibly remove year --years and range options -# Currently comment them out. - -# -[ ] maybe a verbose option and removing debug -# -[x] --debug mode is not working... - -# -[ ] add error check for hi-res and years if they are 1850 and 2005. - -# -[x] different path for each range of years for transient cases. -# default should be picked based on the year. 1850 - 2015 --> -# /glade/p/cesm/cseg/inputdata/lnd/clm2/rawdata/pftcftdynharv.0.25x0.25.LUH2.histsimyr1850-2015.c170629/ -# 850-1850 --> -# pftcftdynharv.0.25x0.25.LUH2.histsimyr0850-1849.c171012 - -# -[ ] hirespft data only for 2005? - -# -- Import libraries -import os -import sys - -# -- add python/ctsm to path -_CTSM_PYTHON = os.path.join( - os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" - ) -sys.path.insert(1, _CTSM_PYTHON) - -from ctsm.gen_mksurf_namelist import main - -if __name__ == "__main__": - main() - - From 5bf84996213c0ed083fc65d51fbe65eeb7bc4fca Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 11 Nov 2022 17:30:30 -0700 Subject: [PATCH 0439/2067] Add note that start option is not functional and remove the code about it, but add a comment for it --- tools/site_and_regional/run_neon.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index b8bc79a845..50f0640d03 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -209,6 +209,7 @@ def get_parser(args, description, valid_neon_sites): help=""" Start date for running CTSM simulation in ISO format. [default: %(default)s] + (currently non-functional) """, action="store", dest="start_date", @@ -622,11 +623,7 @@ def set_ref_case(self, case): case.set_value("RUN_REFDATE", refdate) if case_root.endswith(".postad"): case.set_value("RUN_STARTDATE", refdate) - #else: - #case.set_value( - # "RUN_STARTDATE", - # "{yr:04d}-{mo:02d}-01".format(yr=self.start_year, mo=self.start_month), - #) + # NOTE: if start options are set, RUN_STARTDATE should be modified here return True def modify_user_nl(self, case_root, run_type, rundir): From f40d8fa566b8baf1ed0e74a566fb5d40d7ac4d33 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 13 Nov 2022 19:39:53 -0700 Subject: [PATCH 0440/2067] Update mosart to bring in direct_to_outlet fixes --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 491405a33b..2df854055e 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -23,7 +23,7 @@ required = True local_path = components/mosart protocol = git repo_url = https://github.com/ESCOMP/MOSART -tag = mosart1_0_45 +tag = mosart1_0_47 required = True [mizuRoute] From 4e508585c025bfda089b4016f79c36a1d6f6ad5e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 13 Nov 2022 20:14:00 -0700 Subject: [PATCH 0441/2067] Add a direction for the check_for_nans so that the direction the fields are going will be written out fixing #1896 --- src/cpl/lilac/lnd_import_export.F90 | 4 ++-- src/cpl/mct/lnd_import_export.F90 | 4 ++-- src/cpl/nuopc/lnd_import_export.F90 | 8 ++++---- src/cpl/utils/lnd_import_export_utils.F90 | 5 +++-- 4 files changed, 11 insertions(+), 10 deletions(-) diff --git a/src/cpl/lilac/lnd_import_export.F90 b/src/cpl/lilac/lnd_import_export.F90 index 2da277dcee..281666c3e7 100644 --- a/src/cpl/lilac/lnd_import_export.F90 +++ b/src/cpl/lilac/lnd_import_export.F90 @@ -571,7 +571,7 @@ subroutine state_getimport(state, fb, fldname, bounds, output, ungridded_index, end if ! Check for nans - call check_for_nans(output, trim(fldname), bounds%begg) + call check_for_nans(output, trim(fldname), bounds%begg, "output") end subroutine state_getimport @@ -657,7 +657,7 @@ subroutine state_setexport(state, fb, fldname, bounds, input, minus, ungridded_i end if ! check for nans - call check_for_nans(input, trim(fldname), bounds%begg) + call check_for_nans(input, trim(fldname), bounds%begg, "input") end subroutine state_setexport diff --git a/src/cpl/mct/lnd_import_export.F90 b/src/cpl/mct/lnd_import_export.F90 index 2c84d2e471..3f7e67af68 100644 --- a/src/cpl/mct/lnd_import_export.F90 +++ b/src/cpl/mct/lnd_import_export.F90 @@ -136,7 +136,7 @@ subroutine lnd_import( bounds, x2l, glc_present, atm2lnd_inst, glc2lnd_inst, wat ! Check for nans from coupler !-------------------------- - call check_for_nans(x2l(:,i), fname, begg) + call check_for_nans(x2l(:,i), fname, begg, "x2l") end do @@ -344,7 +344,7 @@ subroutine lnd_export( bounds, waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst ! Check for nans to coupler !-------------------------- - call check_for_nans(l2x(:,i), fname, begg) + call check_for_nans(l2x(:,i), fname, begg, "l2x") end do diff --git a/src/cpl/nuopc/lnd_import_export.F90 b/src/cpl/nuopc/lnd_import_export.F90 index 0e7a5e2eef..340009ccb3 100644 --- a/src/cpl/nuopc/lnd_import_export.F90 +++ b/src/cpl/nuopc/lnd_import_export.F90 @@ -1080,7 +1080,7 @@ subroutine state_getimport_1d(state, fldname, ctsmdata, rc) do g = 1,size(ctsmdata) ctsmdata(g) = fldptr1d(g) end do - call check_for_nans(ctsmdata, trim(fldname), 1) + call check_for_nans(ctsmdata, trim(fldname), 1, "import_1D") end subroutine state_getimport_1d @@ -1114,7 +1114,7 @@ subroutine state_getimport_2d(state, fldname, ctsmdata, rc) do g = 1,size(ctsmdata,dim=1) ctsmdata(g,n) = fldptr2d(n,g) end do - call check_for_nans(ctsmdata(:,n), trim(fldname)//trim(cnum), 1) + call check_for_nans(ctsmdata(:,n), trim(fldname)//trim(cnum), 1, "import_2D") end do end subroutine state_getimport_2d @@ -1167,7 +1167,7 @@ subroutine state_setexport_1d(state, fldname, ctsmdata, init_spval, minus, rc) fldptr1d(g) = ctsmdata(g) end do end if - call check_for_nans(ctsmdata, trim(fldname), 1) + call check_for_nans(ctsmdata, trim(fldname), 1, "export_1D") end subroutine state_setexport_1d @@ -1222,7 +1222,7 @@ subroutine state_setexport_2d(state, fldname, ctsmdata, init_spval, minus, rc) fldptr2d(n,g) = ctsmdata(g,n) end do end if - call check_for_nans(ctsmdata(:,n), trim(fldname)//trim(cnum), 1) + call check_for_nans(ctsmdata(:,n), trim(fldname)//trim(cnum), 1, "export_2D") end do end subroutine state_setexport_2d diff --git a/src/cpl/utils/lnd_import_export_utils.F90 b/src/cpl/utils/lnd_import_export_utils.F90 index 032cb19b6f..4b7941da5b 100644 --- a/src/cpl/utils/lnd_import_export_utils.F90 +++ b/src/cpl/utils/lnd_import_export_utils.F90 @@ -140,12 +140,13 @@ end subroutine check_for_errors !============================================================================= - subroutine check_for_nans(array, fname, begg) + subroutine check_for_nans(array, fname, begg, direction) ! input/output variables real(r8) , intent(in) :: array(:) character(len=*) , intent(in) :: fname integer , intent(in) :: begg + character(len=*) , intent(in) :: direction ! local variables integer :: i @@ -161,7 +162,7 @@ subroutine check_for_nans(array, fname, begg) write(iulog,*) "NaN found in field ", trim(fname), ' at gridcell index ',begg+i-1 end if end do - call shr_sys_abort(' ERROR: One or more of the output from CLM to the coupler are NaN ' ) + call shr_sys_abort(' ERROR: One or more of the CTSM cap '//direction//' fields are NaN ' ) end if end subroutine check_for_nans From d01a98d623dd3e837e147c6f64d8fb9e50f55e4c Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Mon, 14 Nov 2022 07:44:46 -0700 Subject: [PATCH 0442/2067] updates for memory scaling --- .../share_esmf/lnd_set_decomp_and_domain.F90 | 162 +++++++++++------- 1 file changed, 96 insertions(+), 66 deletions(-) diff --git a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 index d1d29672b3..602b83d897 100644 --- a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 +++ b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 @@ -1,9 +1,6 @@ module lnd_set_decomp_and_domain - use ESMF , only : ESMF_VM, ESMF_Mesh, ESMF_DistGrid, ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU - use ESMF , only : ESMF_Array, ESMF_ArrayCreate, ESMF_SUCCESS, ESMF_MeshCreate, ESMF_FILEFORMAT_ESMFMESH - use ESMF , only : ESMF_MeshGet, ESMF_DistGridGet, ESMF_Grid, ESMF_Field, ESMF_FieldGet, ESMF_FieldCreate, ESMF_FieldDestroy - use ESMF , only : ESMF_TYPEKIND_R8, ESMF_MESHLOC_ELEMENT, ESMF_VMAllReduce, ESMF_REDUCE_SUM + use ESMF use shr_kind_mod , only : r8 => shr_kind_r8, cl=>shr_kind_cl use shr_sys_mod , only : shr_sys_abort use shr_log_mod , only : errMsg => shr_log_errMsg @@ -45,7 +42,6 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes use decompMod , only : gindex_global, bounds_type, get_proc_bounds use clm_varpar , only : nlevsoi use clm_varctl , only : use_soil_moisture_streams - use ESMF , only : ESMF_DistGridCreate ! input/output variables character(len=*) , intent(in) :: driver ! cmeps or lilac @@ -57,20 +53,25 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes integer , intent(out) :: rc ! local variables - type(ESMF_Mesh) :: mesh_maskinput - type(ESMF_Mesh) :: mesh_lndinput - type(ESMF_DistGrid) :: distgrid_ctsm - integer :: g,n ! indices - integer :: nlnd, nocn ! local size of arrays - integer :: gsize ! global size of grid - logical :: isgrid2d ! true => grid is 2d - type(bounds_type) :: bounds ! bounds - integer :: begg,endg ! local bounds - integer , pointer :: gindex_lnd(:) ! global index space for just land points - integer , pointer :: gindex_ocn(:) ! global index space for just ocean points - integer , pointer :: gindex_ctsm(:) ! global index space for land and ocean points - integer , pointer :: lndmask_glob(:) - real(r8) , pointer :: lndfrac_glob(:) + type(ESMF_Mesh) :: mesh_maskinput + type(ESMF_Mesh) :: mesh_lndinput + type(ESMF_DistGrid) :: distgrid_ctsm + type(ESMF_Field) :: field_lnd + type(ESMF_Field) :: field_ctsm + type(ESMF_RouteHandle) :: rhandle_lnd2ctsm + integer :: g,n ! indices + integer :: nlnd, nocn ! local size of arrays + integer :: gsize ! global size of grid + logical :: isgrid2d ! true => grid is 2d + type(bounds_type) :: bounds ! bounds + integer :: begg,endg ! local bounds + integer , pointer :: gindex_lnd(:) ! global index space for just land points + integer , pointer :: gindex_ocn(:) ! global index space for just ocean points + integer , pointer :: gindex_ctsm(:) ! global index space for land and ocean points + integer , pointer :: lndmask_glob(:) + real(r8) , pointer :: lndfrac_glob(:) + real(r8) , pointer :: lndfrac_loc_input(:) + real(r8) , pointer :: dataptr1d(:) !------------------------------------------------------------------------------- rc = ESMF_SUCCESS @@ -90,8 +91,6 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes ! Determine global 2d sizes from read of dimensions of surface dataset and allocate global memory call lnd_get_global_dims(ni, nj, gsize, isgrid2d) - allocate(lndmask_glob(gsize)); lndmask_glob(:) = 0 - allocate(lndfrac_glob(gsize)); lndfrac_glob(:) = 0._r8 ! Read in the land mesh from the file mesh_lndinput = ESMF_MeshCreate(filename=trim(meshfile_lnd), fileformat=ESMF_FILEFORMAT_ESMFMESH, rc=rc) @@ -100,21 +99,27 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes if (trim(driver) == 'cmeps') then ! Read in mask meshfile if needed if (trim(meshfile_mask) /= trim(meshfile_lnd)) then + call ESMF_VMLogMemInfo("clm: Before lnd mesh create in ") mesh_maskinput = ESMF_MeshCreate(filename=trim(meshfile_mask), fileformat=ESMF_FILEFORMAT_ESMFMESH, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - end if + call ESMF_VMLogMemInfo("clm: After lnd mesh create in ") + print *,__FILE__,__LINE__ - ! Determine lndmask_glob and lndfrac_glob - if (trim(meshfile_mask) /= trim(meshfile_lnd)) then + ! Determine lndmask_glob and lndfrac_glob ! obain land mask and land fraction by mapping ocean mesh conservatively to land mesh - call lnd_set_lndmask_from_maskmesh(mesh_lndinput, mesh_maskinput, vm, gsize, lndmask_glob, lndfrac_glob, rc) + ! Note that lndmask_glob and lndfrac_loc_input are allocated in lnd_set_lndmask_from_maskmesh + call lnd_set_lndmask_from_maskmesh(mesh_lndinput, mesh_maskinput, vm, gsize, lndmask_glob, & + lndfrac_loc_input, rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return + call ESMF_VMLogMemInfo("clm: After lnd_set_lndmask_from_maskmesh ") + print *,__FILE__,__LINE__ else ! obtain land mask from land mesh file - assume that land frac is identical to land mask - call lnd_set_lndmask_from_lndmesh(mesh_lndinput, vm, gsize, lndmask_glob, lndfrac_glob, rc) + call lnd_set_lndmask_from_lndmesh(mesh_lndinput, vm, gsize, lndmask_glob, rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return end if else if (trim(driver) == 'lilac') then + allocate(lndfrac_glob(ni*nj)) call lnd_set_lndmask_from_fatmlndfrc(lndmask_glob, lndfrac_glob, ni,nj) else call shr_sys_abort('driver '//trim(driver)//' is not supported, must be lilac or cmeps') @@ -146,16 +151,14 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes ! Initialize domain data structure call domain_init(domain=ldomain, isgrid2d=isgrid2d, ni=ni, nj=nj, nbeg=begg, nend=endg) - ! Determine ldomain%mask and ldomain%frac using ctsm decomposition + ! Determine ldomain%mask do g = begg, endg n = 1 + (g - begg) ldomain%mask(g) = lndmask_glob(gindex_lnd(n)) - ldomain%frac(g) = lndfrac_glob(gindex_lnd(n)) end do ! Deallocate global pointer memory deallocate(lndmask_glob) - deallocate(lndfrac_glob) ! Generate a ctsm global index that includes both land and ocean points nocn = size(gindex_ocn) @@ -178,6 +181,55 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes call lnd_set_ldomain_gridinfo_from_mesh(mesh_ctsm, vm, gindex_ctsm, begg, endg, isgrid2d, ni, nj, ldomain, rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return + ! Set ldomain%lfrac + ! Create fields on the input decomp and ctsm decomp + ! Determine route handle to do a redist from input mesh read decomp to ctsm decomp + ! Fill in the field on the input mesh read decomp with lndfrac_loc_input values + ! Redistribute field_lnd to field_ctsm + + ! Determine ldomain%frac using ctsm decomposition + if (trim(driver) == 'cmeps') then + + if (trim(meshfile_mask) /= trim(meshfile_lnd)) then + field_lnd = ESMF_FieldCreate(mesh_lndinput, ESMF_TYPEKIND_R8, meshloc=ESMF_MESHLOC_ELEMENT, rc=rc) + if (ChkErr(rc,__LINE__,u_FILE_u)) return + print *,__FILE__,__LINE__ + field_ctsm = ESMF_FieldCreate(mesh_ctsm, ESMF_TYPEKIND_R8, meshloc=ESMF_MESHLOC_ELEMENT, rc=rc) + if (ChkErr(rc,__LINE__,u_FILE_u)) return + print *,__FILE__,__LINE__ + call ESMF_FieldRedistStore(field_lnd, field_ctsm, routehandle=rhandle_lnd2ctsm, & + ignoreUnmatchedIndices=.true., rc=rc) + if (chkerr(rc,__LINE__,u_FILE_u)) return + call ESMF_FieldGet(field_lnd, farrayptr=dataptr1d, rc=rc) + if (chkerr(rc,__LINE__,u_FILE_u)) return + do n = 1,size(dataptr1d) + dataptr1d(n) = lndfrac_loc_input(n) + end do + call ESMF_FieldRedist(field_lnd, field_ctsm, routehandle=rhandle_lnd2ctsm, rc=rc) + if (chkerr(rc,__LINE__,u_FILE_u)) return + call ESMF_FieldGet(field_ctsm, farrayptr=dataptr1d, rc=rc) + if (chkerr(rc,__LINE__,u_FILE_u)) return + do g = begg, endg + n = 1 + (g - begg) + ldomain%frac(g) = dataptr1d(n) + end do + else + ! ASSUME that land fraction is identical to land mask in this case + do g = begg, endg + ldomain%frac(g) = ldomain%mask(g) + end do + end if + + else + + do g = begg, endg + n = 1 + (g - begg) + ldomain%frac(g) = lndfrac_glob(gindex_lnd(n)) + end do + deallocate(lndfrac_glob) + + end if + ! Deallocate local pointer memory deallocate(gindex_lnd) deallocate(gindex_ocn) @@ -189,8 +241,8 @@ end subroutine lnd_set_decomp_and_domain_from_readmesh subroutine lnd_set_mesh_for_single_column(scol_lon, scol_lat, mesh, rc) ! Generate a mesh for single column + use netcdf use clm_varcon, only : spval - use ESMF , only : ESMF_Grid, ESMF_GridCreateNoPeriDimUfrm, ESMF_STAGGERLOC_CENTER, ESMF_STAGGERLOC_CORNER ! input/output variables real(r8) , intent(in) :: scol_lon @@ -343,7 +395,7 @@ subroutine lnd_get_global_dims(ni, nj, gsize, isgrid2d) end subroutine lnd_get_global_dims !=============================================================================== - subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask_glob, lndfrac_glob, rc) + subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask_glob, lndfrac_loc, rc) ! If the landfrac/landmask file does not exists then determine the ! land fraction and land mask on the land grid by mapping the mask @@ -352,19 +404,13 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask ! exist then simply read in the global land fraction and land mask ! from the file - ! Uses: - use ESMF , only : ESMF_RouteHandle, ESMF_FieldRegridStore, ESMF_FieldRegrid - use ESMF , only : ESMF_REGRIDMETHOD_CONSERVE, ESMF_NORMTYPE_DSTAREA, ESMF_UNMAPPEDACTION_IGNORE - use ESMF , only : ESMF_TERMORDER_SRCSEQ, ESMF_REGION_TOTAL - - ! input/out variables type(ESMF_Mesh) , intent(in) :: mesh_lnd type(ESMF_Mesh) , intent(in) :: mesh_mask type(ESMF_VM) , intent(in) :: vm integer , intent(in) :: gsize integer , pointer :: lndmask_glob(:) - real(r8) , pointer :: lndfrac_glob(:) + real(r8) , pointer :: lndfrac_loc(:) integer , intent(out) :: rc ! local variables: @@ -376,8 +422,6 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask integer , pointer :: gindex_input(:) ! global index space for land and ocean points integer , pointer :: lndmask_loc(:) integer , pointer :: itemp_glob(:) - real(r8) , pointer :: rtemp_glob(:) - real(r8) , pointer :: lndfrac_loc(:) real(r8) , pointer :: maskmask_loc(:) ! on ocean mesh real(r8) , pointer :: maskfrac_loc(:) ! on land mesh real(r8) , pointer :: dataptr1d(:) @@ -403,9 +447,13 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask klen = len_trim(flandfrac) - 3 ! remove the .nc flandfrac_status = flandfrac(1:klen)//'.status' + allocate(lndmask_glob(gsize)); lndmask_glob(:) = 0 + ! Determine if lndfrac/lndmask file exists inquire(file=trim(flandfrac), exist=lexist) + lexist = .false. ! TODO: fix this + if (lexist) then ! If file exists - read in lndmask and lndfrac @@ -413,8 +461,8 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask write(iulog,*) write(iulog,'(a)')' Reading in land fraction and land mask from '//trim(flandfrac) end if - call lnd_set_read_write_landmask(trim(flandfrac), trim(flandfrac_status), .false., .true., & - lndmask_glob, lndfrac_glob, size(lndmask_glob)) + ! call lnd_set_read_write_landmask(trim(flandfrac), trim(flandfrac_status), .false., .true., & + ! lndmask_glob, lndfrac_glob, size(lndmask_glob)) else @@ -493,39 +541,25 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask lndmask_glob(:) = int(itemp_glob(:)) deallocate(itemp_glob) - ! Determine ldomain%frac using both input and ctsm decompositions - ! lndfrac_glob is filled using the input decomposition and - ! ldomin%frac is set using the ctsm decomposition - allocate(rtemp_glob(gsize)) - do n = 1,lsize_lnd - lndfrac_glob(gindex_input(n)) = lndfrac_loc(n) - end do - call ESMF_VMAllReduce(vm, sendData=lndfrac_glob, recvData=rtemp_glob, count=gsize, & - reduceflag=ESMF_REDUCE_SUM, rc=rc) - lndfrac_glob(:) = rtemp_glob(:) - deallocate(rtemp_glob) - ! deallocate memory deallocate(maskmask_loc) deallocate(lndmask_loc) - deallocate(lndfrac_loc) - call lnd_set_read_write_landmask(trim(flandfrac), trim(flandfrac_status), .true., .false., & - lndmask_glob, lndfrac_glob, size(lndmask_glob)) + ! call lnd_set_read_write_landmask(trim(flandfrac), trim(flandfrac_status), .true., .false., & + ! lndmask_glob, lndfrac_glob, size(lndmask_glob)) end if end subroutine lnd_set_lndmask_from_maskmesh !=============================================================================== - subroutine lnd_set_lndmask_from_lndmesh(mesh_lnd, vm, gsize, lndmask_glob, lndfrac_glob, rc) + subroutine lnd_set_lndmask_from_lndmesh(mesh_lnd, vm, gsize, lndmask_glob, rc) ! input/out variables type(ESMF_Mesh) , intent(in) :: mesh_lnd type(ESMF_VM) , intent(in) :: vm integer , intent(in) :: gsize integer , pointer :: lndmask_glob(:) - real(r8) , pointer :: lndfrac_glob(:) integer , intent(out) :: rc ! local variables: @@ -570,9 +604,6 @@ subroutine lnd_set_lndmask_from_lndmesh(mesh_lnd, vm, gsize, lndmask_glob, lndfr deallocate(gindex) deallocate(lndmask_loc) - ! ASSUME that land fraction is identical to land mask in this case - lndfrac_glob(:) = lndmask_glob(:) - end subroutine lnd_set_lndmask_from_lndmesh !=============================================================================== @@ -602,7 +633,7 @@ subroutine lnd_set_lndmask_from_fatmlndfrc(mask, frac, ni, nj) logical :: readvar ! read variable in or not integer , allocatable :: idata2d(:,:) real(r8), allocatable :: rdata2d(:,:) - integer :: unitn + integer :: unitn character(len=32) :: subname = 'lnd_set_mask_from_fatmlndfrc' ! subroutine name !----------------------------------------------------------------------- @@ -672,7 +703,6 @@ subroutine lnd_set_ldomain_gridinfo_from_mesh(mesh, vm, gindex, begg, endg, isgr use clm_varcon , only : grlnd use fileutils , only : getfil use ncdio_pio , only : ncd_io, file_desc_t, ncd_pio_openfile, ncd_pio_closefile - use ESMF , only : ESMF_FieldRegridGetArea ! input/output variables type(ESMF_Mesh) , intent(in) :: mesh @@ -815,7 +845,7 @@ subroutine lnd_set_read_write_landmask(flandfrac, flandfrac_status, write_file, integer :: dimid integer :: iun integer :: ioe - integer :: ier + integer :: ier logical :: lexists !------------------------------------------------------------------------------- @@ -856,7 +886,7 @@ subroutine lnd_set_read_write_landmask(flandfrac, flandfrac_status, write_file, close(iun) write(iulog,'(a)')' Successfully wrote land fraction/mask status file '//trim(flandfrac_status) end if - + else if (read_file) then if (masterproc) then From b91dc65404331fc61d41039ad60b20479d176e0e Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Mon, 14 Nov 2022 08:28:34 -0700 Subject: [PATCH 0443/2067] add only to use esmf, remove commented code --- .../share_esmf/lnd_set_decomp_and_domain.F90 | 30 ++++++++++++------- 1 file changed, 20 insertions(+), 10 deletions(-) diff --git a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 index 602b83d897..ff144ed49a 100644 --- a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 +++ b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 @@ -1,6 +1,19 @@ module lnd_set_decomp_and_domain - use ESMF + use ESMF , only : ESMF_VM, ESMF_MESH, ESMF_DistGrid, ESMF_Field + use ESMF , only : ESMF_RouteHandle, ESMF_SUCCESS, ESMF_MeshCreate + use ESMF , only : ESMF_FileFormat_ESMFMESH, ESMF_VMLogMemInfo + use ESMF , only : ESMF_FieldCreate, ESMF_FieldRedistStore, ESMF_FieldRedist + use ESMF , only : ESMF_FieldGet, ESMF_GridCreateNoPeriDimUfrm + use ESMF , only : ESMF_FieldRegrid, ESMF_FieldRegridStore + use ESMF , only : ESMF_Grid, ESMF_ARRAY, ESMF_DistGridCreate, ESMF_TYPEKIND_R8 + use ESMF , only : ESMF_MESHLOC_ELEMENT, ESMF_FieldCreate, ESMF_STAGGERLOC_CORNER, ESMF_STAGGERLOC_CENTER + use ESMF , only : ESMF_REGRIDMETHOD_CONSERVE, ESMF_NORMTYPE_DSTAREA + use ESMF , only : ESMF_UNMAPPEDACTION_IGNORE, ESMF_TERMORDER_SRCSEQ + use ESMF , only : ESMF_REGION_TOTAL, ESMF_REDUCE_SUM, ESMF_ARRAYCREATE + use ESMF , only : ESMF_MeshGet, ESMF_DistGridGet, ESMF_LOGFOUNDERROR + use ESMF , only : ESMF_LOGERR_PASSTHRU, ESMF_VMAllReduce, ESMF_FieldRegridGetArea + use ESMF , only : ESMF_FieldDestroy use shr_kind_mod , only : r8 => shr_kind_r8, cl=>shr_kind_cl use shr_sys_mod , only : shr_sys_abort use shr_log_mod , only : errMsg => shr_log_errMsg @@ -99,20 +112,23 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes if (trim(driver) == 'cmeps') then ! Read in mask meshfile if needed if (trim(meshfile_mask) /= trim(meshfile_lnd)) then +#ifdef DEBUG call ESMF_VMLogMemInfo("clm: Before lnd mesh create in ") +#endif mesh_maskinput = ESMF_MeshCreate(filename=trim(meshfile_mask), fileformat=ESMF_FILEFORMAT_ESMFMESH, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return +#ifdef DEBUG call ESMF_VMLogMemInfo("clm: After lnd mesh create in ") - print *,__FILE__,__LINE__ - +#endif ! Determine lndmask_glob and lndfrac_glob ! obain land mask and land fraction by mapping ocean mesh conservatively to land mesh ! Note that lndmask_glob and lndfrac_loc_input are allocated in lnd_set_lndmask_from_maskmesh call lnd_set_lndmask_from_maskmesh(mesh_lndinput, mesh_maskinput, vm, gsize, lndmask_glob, & lndfrac_loc_input, rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return +#ifdef DEBUG call ESMF_VMLogMemInfo("clm: After lnd_set_lndmask_from_maskmesh ") - print *,__FILE__,__LINE__ +#endif else ! obtain land mask from land mesh file - assume that land frac is identical to land mask call lnd_set_lndmask_from_lndmesh(mesh_lndinput, vm, gsize, lndmask_glob, rc) @@ -461,9 +477,6 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask write(iulog,*) write(iulog,'(a)')' Reading in land fraction and land mask from '//trim(flandfrac) end if - ! call lnd_set_read_write_landmask(trim(flandfrac), trim(flandfrac_status), .false., .true., & - ! lndmask_glob, lndfrac_glob, size(lndmask_glob)) - else ! If file does not exist - compute lndmask and lndfrac and write to output file @@ -545,9 +558,6 @@ subroutine lnd_set_lndmask_from_maskmesh(mesh_lnd, mesh_mask, vm, gsize, lndmask deallocate(maskmask_loc) deallocate(lndmask_loc) - ! call lnd_set_read_write_landmask(trim(flandfrac), trim(flandfrac_status), .true., .false., & - ! lndmask_glob, lndfrac_glob, size(lndmask_glob)) - end if end subroutine lnd_set_lndmask_from_maskmesh From d016cd6605a7114ce95d665fbbb9a8a6d61b1810 Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Mon, 14 Nov 2022 08:35:03 -0700 Subject: [PATCH 0444/2067] remove unused use statement --- src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 index ff144ed49a..1db72296b4 100644 --- a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 +++ b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 @@ -257,7 +257,6 @@ end subroutine lnd_set_decomp_and_domain_from_readmesh subroutine lnd_set_mesh_for_single_column(scol_lon, scol_lat, mesh, rc) ! Generate a mesh for single column - use netcdf use clm_varcon, only : spval ! input/output variables From bffff16b40abc2e85bfc9d90f9895e9232bfaa3d Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Mon, 14 Nov 2022 13:41:28 -0700 Subject: [PATCH 0445/2067] allocate mask and frac in all cases --- src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 index 1db72296b4..f7b356e0aa 100644 --- a/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 +++ b/src/cpl/share_esmf/lnd_set_decomp_and_domain.F90 @@ -135,7 +135,6 @@ subroutine lnd_set_decomp_and_domain_from_readmesh(driver, vm, meshfile_lnd, mes if (ChkErr(rc,__LINE__,u_FILE_u)) return end if else if (trim(driver) == 'lilac') then - allocate(lndfrac_glob(ni*nj)) call lnd_set_lndmask_from_fatmlndfrc(lndmask_glob, lndfrac_glob, ni,nj) else call shr_sys_abort('driver '//trim(driver)//' is not supported, must be lilac or cmeps') @@ -603,6 +602,9 @@ subroutine lnd_set_lndmask_from_lndmesh(mesh_lnd, vm, gsize, lndmask_glob, rc) allocate(itemp_glob(gsize)) call ESMF_DistGridGet(distgrid, 0, seqIndexList=gindex, rc=rc) if (chkerr(rc,__LINE__,u_FILE_u)) return + + allocate(lndmask_glob(gsize)); lndmask_glob(:) = 0 + do n = 1,lsize lndmask_glob(gindex(n)) = lndmask_loc(n) end do @@ -655,6 +657,7 @@ subroutine lnd_set_lndmask_from_fatmlndfrc(mask, frac, ni, nj) if (masterproc) then write(iulog,*)'lat/lon grid flag (isgrid2d) is ',isgrid2d end if + allocate(frac(ni*nj), mask(ni*nj)) if (isgrid2d) then ! Grid is 2d From 5769dd1d4e0e12a19c4bb588babe1270d3abe17d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 14 Nov 2022 14:22:16 -0700 Subject: [PATCH 0446/2067] Update change files --- doc/ChangeLog | 127 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 128 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 68aea97f7e..b58f7f92b9 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,131 @@ =============================================================== +Tag name: ctsm5.1.dev114 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)/@wwieder/@olyson/@ka7eh +Date: Mon Nov 14 14:22:05 MST 2022 +One-line Summary: Some NEON updates fixing AG sites, update MOSART, small fixes + +Purpose and description of changes +---------------------------------- + +Minor changes to python scripts and usermod_dirs for NEON cases. Also update the lightning mesh file so that it goes with the +smaller lightning file. Have NEON use new use-cases for 2018 and 2018-PD conditions for CLM. Have NEON +Agricultural sites run with prognostic crop. Simple fix for warning about NaN's in import/export data from/to coupler. + +Also update MOSART with fixed for direct_to_outlet option. + +Add error checking in ParitionWoodFluxes. Fix value of albgrd_col in SurfaceAlbefdoType.F90. +Previously, the wrong value (albgri_col) was being set in InitHistory. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Fixes #1871 -- Error in NEON surface datasets for AG sites + Fixes #1876 -- NEON data in container + Fixes #1889 -- NEON AG sites are running without prognostic crop + Fixes #1363 -- 2018_control and 2018-PD_transient use-cases for NEON + Fixes #1896 -- Improve misleading error message in check_for_nans + Fixes #1263 -- Fix partitionWood fluxes + Fixes #1788 -- Fix albgrd_col + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + NEON users: use neon_gcs_upload now. Filenames for NEON surface + datasets are changed. Start and end of simulations is different + for some sites, and managed by the user-mod-directories. The NEON + user-mod assumes transient cases will run with a transient compset + and the settings are slightly different for transient vs control + including pointing to 2018_control or 2018-PD_transient use-cases. + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + Add notes to python tools to run using conda environment setup in py_env_create + +Changes made to namelist defaults (e.g., changed parameter values): + New use cases: 2018_control and 2018-PD_transient + +Changes to the datasets (e.g., parameter, surface or initial files): + New updated NEON surface datasets + +Notes of particular relevance for developers: +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + Remove toolchain python scripts as this work was moved over to the ctsm5.2 development + +Changes to tests or testing: + Add a run_black target to the python directory Makefile to run black and not just do a black check + Add python modules needed for neon scripts to conda py_create_env conda environment + +Testing summary: regular, tools +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - OK (NEON tests are different than baseline) + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + Acheyenne -- PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + any other testing (give details below): + +Answer changes +-------------- + +Changes answers relative to baseline: No (other than NEON sites, and if direct_to_outlet turned on in MOSART) + + Summarize any changes to answers, i.e., + - what code configurations: NEON or if bypass_routing_option==direct_to_outlet in MOSART + - what platforms/compilers: all + - nature of change: + NEON AG sites are significantly different + + NEON sites reran and reevaluated + MOSART direct_to_outlet option evaluated by @swensosc and @olyson + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): mosart + mosart updated from mosart1_0_45 to to mosart1_0_47 (asynchronous changes, and direct_to_outlet fixes) + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #1872 -- NEON updates + #1814 -- Add error checking in partitionWoodFluxes + #1810 -- Fix albdgrd_col value + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev113 Originator(s): sacks (Bill Sacks), ekluzek (Erik Kluzek), jedwards (Jim Edwards) Date: Fri Oct 28 11:00:26 MDT 2022 diff --git a/doc/ChangeSum b/doc/ChangeSum index 3008f25f69..fb0f96fc06 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev114 multiple 11/14/2022 Some NEON updates fixing AG sites, update MOSART, small fixes ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases From 92b6899b6c10bf54f95a7891985fcb481bb36fe3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 14 Nov 2022 15:22:57 -0700 Subject: [PATCH 0447/2067] change file updates, rm old neon_s3_upload as replaced by neon_gcs_upload version --- doc/ChangeLog | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index b58f7f92b9..766e4fe186 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev114 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)/@wwieder/@olyson/@ka7eh -Date: Mon Nov 14 14:22:05 MST 2022 +Date: Mon Nov 14 15:21:50 MST 2022 One-line Summary: Some NEON updates fixing AG sites, update MOSART, small fixes Purpose and description of changes @@ -81,11 +81,12 @@ Testing summary: regular, tools build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - OK (NEON tests are different than baseline) + cheyenne - OK (141 NEON tests are different than baseline) tools-tests (test/tools) (if tools have been changed): - cheyenne - + cheyenne - OK + izumi (NEON) -- OK python testing (if python code has changed; see instructions in python/README.md; document testing done): @@ -97,6 +98,7 @@ Testing summary: regular, tools izumi ------- OK any other testing (give details below): + run_neon.py ran for all NEON sites ad, post-ad, and transient Answer changes -------------- From ea4d150f9a1f5e82c72fb4db5dc7bc957e1270bb Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 14 Nov 2022 15:23:24 -0700 Subject: [PATCH 0448/2067] rm old neon_s3_upload as replaced by neon_gcs_upload version --- tools/site_and_regional/neon_s3_upload | 173 ------------------------- 1 file changed, 173 deletions(-) delete mode 100755 tools/site_and_regional/neon_s3_upload diff --git a/tools/site_and_regional/neon_s3_upload b/tools/site_and_regional/neon_s3_upload deleted file mode 100755 index 447886e936..0000000000 --- a/tools/site_and_regional/neon_s3_upload +++ /dev/null @@ -1,173 +0,0 @@ -#! /usr/bin/env python3 -""" -Script to rename and upload NEON site finidat files for use in transient startup cases - -""" - -import os, sys -# Get the ctsm util tools and then the cime tools. -_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..","..",'python')) -sys.path.insert(1, _CTSM_PYTHON) - -import boto3 -from botocore.exceptions import ClientError -import glob -import datetime -from ctsm import add_cime_to_path -from ctsm.path_utils import path_to_ctsm_root -from standard_script_setup import * -from CIME.case import Case -from CIME.utils import expect, safe_copy - -logger = logging.getLogger(__name__) - -def get_parser(args, description, valid_neon_sites): - """ - Get Parser object for this script - """ - parser = argparse.ArgumentParser(description=description, - formatter_class=argparse.RawDescriptionHelpFormatter) - - CIME.utils.setup_standard_logging_options(parser) - - parser.print_usage = parser.print_help - - parser.add_argument('--neon-sites', - help='4-letter neon site code.', - action="store", - required=False, - choices=valid_neon_sites + ['all'], - dest="neon_sites", - default=["OSBS"], - nargs='+') - - parser.add_argument('--output-root', - help=''' - Root Directory of case results - [default: %(default)s] - ''', - action="store", - dest="output_root", - type =str, - required=False, - default=os.getcwd()) - - parser.add_argument('--file-date', - help=''' - Date of ctsm restart file(s) to upload - ''', - action="store", - dest="file_date", - required = False, - type = datetime.date.fromisoformat, - default = datetime.datetime.strptime("0268-01-01",'%Y-%m-%d')) - - - parser.add_argument('--upload-finidat', - help=''' - Upload the final restart files from the end of the postad run for each site. - ''', - action="store_true", - dest="upload_finidat", - required = False, - default = False) - - parser.add_argument('--upload-history', - help=''' - Upload the transient run h1 history files for each site. - ''', - action="store_true", - dest="upload_history", - required = False, - default = False) - - - - args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser) - - if 'all' in args.neon_sites: - neon_sites = valid_neon_sites - else: - neon_sites = args.neon_sites - for site in neon_sites: - if site not in valid_neon_sites: - raise ValueError("Invalid site name {}".format(site)) - - expect(args.upload_finidat or args.upload_history,"Must specify at least one of --upload-finidat or --upload-history") - - return neon_sites, args.output_root, args.file_date, args.upload_finidat, args.upload_history - -def upload_file(file_name, bucket, object_name=None): - """Upload a file to an S3 bucket - - :param file_name: File to upload - :param bucket: Bucket to upload to - :param object_name: S3 object name. If not specified then file_name is used - :return: True if file was uploaded, else False - """ - - # If S3 object_name was not specified, use file_name - if object_name is None: - object_name = os.path.basename(file_name) - - # Upload the file - s3_client = boto3.client('s3') - try: - logger.info("Uploading file {} to {}".format(file_name, object_name)) - response = s3_client.upload_file(file_name, bucket, object_name) - except ClientError as e: - logger.error(e) - return False - return True - -def main(description): - """ - For each site in the site_list find the site.postad run directory and grab the latest clm restart file - from there, - """ - - if not os.path.isfile(os.path.join(os.getenv("HOME"),".aws","credentials")): - raise FileNotFoundError("User account must have valid aws credentials to run this script.") - - cesmroot = path_to_ctsm_root() - # Get the list of supported neon sites from usermods - valid_neon_sites = glob.glob(os.path.join(cesmroot,"cime_config","usermods_dirs","NEON","[!d]*")) - valid_neon_sites = [v.split('/')[-1] for v in valid_neon_sites] - filedatestamp = datetime.datetime.now().date() - site_list, output_root, file_date, upload_finidat, upload_history = get_parser(sys.argv, description, valid_neon_sites) - for site in site_list: - rundir = None - if upload_finidat: - logger.info("Upload finidat for {}".format(site)) - case_path = os.path.join(output_root, site+".postad") - if os.path.isdir(case_path): - with Case(case_path) as case: - rundir = case.get_value("RUNDIR") - basefile = site+".postad.clm2.r.{}-00000.nc".format(file_date.strftime("%4Y-%m-%d")) - finidat_file = os.path.join(rundir,basefile) - if not os.path.isfile(finidat_file): - logger.warning("Could not find file {}".format(finidat_file)) - continue - newfile = basefile.replace(".postad.",".{}.".format(filedatestamp)) - - upload_file(finidat_file, 'neon-ncar-transfer', os.path.join("NEON","lnd","ctsm","initdata",newfile)) - if upload_history: - logger.info("Upload history for {}".format(site)) - case_path = os.path.join(output_root, site+".transient") - if not os.path.isdir(case_path): - logger.warning("No case found in {}".format(case_path)) - continue - with Case(case_path) as case: - archive_dir = os.path.join(case.get_value("DOUT_S_ROOT"),"lnd","hist") - for histfile in glob.iglob(archive_dir + "/*.h1.*"): - newfile = os.path.basename(histfile) - upload_file(histfile, 'neon-ncar-transfer', os.path.join("NEON","archive",site,"lnd","hist",newfile)) - - - - - - -if __name__ == "__main__": - main(__doc__) - From deedb0494fb70b3352a790172ac083f73a59ebe3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 14 Nov 2022 16:28:30 -0700 Subject: [PATCH 0449/2067] Fix for #1901 --- cime_config/config_component.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index d3c2eda0a7..94e610440a 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -290,10 +290,11 @@ char + <-- NOTE: Be sure to have a comma at the last site-name -- otherwise there will be issues see CTSM github issue #1901 --> ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD, BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF, - BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL + BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL, run_component_ctsm From bfb840d5559c17a4828b32f988ace1260171c834 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 16:27:51 -0700 Subject: [PATCH 0450/2067] Explicitly set the NEON site to run --- test/tools/nl_files/run_neon_OSBS | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/tools/nl_files/run_neon_OSBS b/test/tools/nl_files/run_neon_OSBS index c49fb77783..0c274b13ad 100644 --- a/test/tools/nl_files/run_neon_OSBS +++ b/test/tools/nl_files/run_neon_OSBS @@ -1 +1 @@ ---verbose --run-type ad --setup-only +--verbose --run-type ad --setup-only --neon-site OSBS From 1ed3774f0f0f575f398af8ffbaa09ae1244b7da7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 16:28:48 -0700 Subject: [PATCH 0451/2067] Move run of py_env_create to after CLM_ROOT is set and call it for all machines --- test/tools/test_driver.sh | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh index 1b3c141d79..ce501f980a 100755 --- a/test/tools/test_driver.sh +++ b/test/tools/test_driver.sh @@ -54,8 +54,6 @@ module load nco module load ncl module load conda -$CESMDATAROOT/py_env_create -conda activate ctsm_py ##omp threads @@ -119,8 +117,6 @@ module load openmpi module load nco module load conda module load ncl -$CESMDATAROOT/py_env_create -conda activate ctsm_py ##omp threads @@ -220,8 +216,6 @@ module load compiler/intel module load tool/nco module load tool/netcdf module load lang/python -$CESMDATAROOT/py_env_create -conda activate ctsm_py export NETCDF_DIR=\$NETCDF_PATH export INC_NETCDF=\${NETCDF_PATH}/include @@ -303,8 +297,6 @@ module load compiler/intel module load tool/nco module load tool/netcdf module load lang/python -$CESMDATAROOT/py_env_create -conda activate ctsm_py export NETCDF_DIR=\$NETCDF_PATH export INC_NETCDF=\${NETCDF_PATH}/include @@ -380,6 +372,10 @@ else fi fi +# Setup conda environement +\$CLM_ROOT/py_env_create +conda activate ctsm_py + ##output files clm_log=\${initdir}/td.\${JOBID}.log if [ -f \$clm_log ]; then From c31e832c72d6149bb726f0fb932240054d8fdd11 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 16:31:36 -0700 Subject: [PATCH 0452/2067] Update date for change files --- doc/ChangeLog | 3 ++- doc/ChangeSum | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 766e4fe186..b4d2da11c6 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev114 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)/@wwieder/@olyson/@ka7eh -Date: Mon Nov 14 15:21:50 MST 2022 +Date: Wed Nov 16 16:31:14 MST 2022 One-line Summary: Some NEON updates fixing AG sites, update MOSART, small fixes Purpose and description of changes @@ -44,6 +44,7 @@ CTSM issues fixed (include CTSM Issue #): Fixes #1896 -- Improve misleading error message in check_for_nans Fixes #1263 -- Fix partitionWood fluxes Fixes #1788 -- Fix albgrd_col + Fixes #1901 -- Fix NEONSITE YELL Notes of particular relevance for users --------------------------------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index fb0f96fc06..a90365740a 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev114 multiple 11/14/2022 Some NEON updates fixing AG sites, update MOSART, small fixes + ctsm5.1.dev114 multiple 11/16/2022 Some NEON updates fixing AG sites, update MOSART, small fixes ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases From 6450b8ce08811fdd80b4da97f9d6b6e27aa2f3f3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 19:41:51 -0700 Subject: [PATCH 0453/2067] Fix syntax error --- cime_config/config_component.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 94e610440a..60d8311b95 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -290,7 +290,7 @@ char - <-- NOTE: Be sure to have a comma at the last site-name -- otherwise there will be issues see CTSM github issue #1901 --> + ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD, BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF, From be3a100a81cb8293cf444b2cd5614f4d1cac64ea Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 19:43:57 -0700 Subject: [PATCH 0454/2067] OK really fix the syntax for the comment --- cime_config/config_component.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 60d8311b95..555a0ce9b5 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -290,7 +290,7 @@ char - + ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD, BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF, From a8630ad6ac0af399ff35906523c8a0def28462b8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 19:48:41 -0700 Subject: [PATCH 0455/2067] Add some checks that directories are there as expected --- python/ctsm/test/test_sys_lilac_build_ctsm.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/python/ctsm/test/test_sys_lilac_build_ctsm.py b/python/ctsm/test/test_sys_lilac_build_ctsm.py index f1c5e22f8f..d773749bf7 100755 --- a/python/ctsm/test/test_sys_lilac_build_ctsm.py +++ b/python/ctsm/test/test_sys_lilac_build_ctsm.py @@ -27,6 +27,7 @@ class TestSysBuildCtsm(unittest.TestCase): def setUp(self): self._tempdir = tempfile.mkdtemp() + self.assertTrue(os.path.isdir(self._tempdir)) # Hack around a check in CIME: As of https://github.com/ESMCI/cime/pull/4228, If # NCAR_HOST is in the environment, CIME checks if the machine you're running on is @@ -68,6 +69,7 @@ def test_buildSetup_userDefinedMachine_minimalInfo(self): gmake_j=8, no_pnetcdf=True, ) + self.assertTrue(os.path.isdir(build_dir)) # the critical piece of this test is that the above command doesn't generate any # errors; however we also do some assertions below @@ -87,6 +89,7 @@ def test_buildSetup_userDefinedMachine_allInfo(self): build_dir = os.path.join(self._tempdir, "ctsm_build") inputdata_path = os.path.realpath(os.path.join(self._tempdir, "my_inputdata")) os.makedirs(inputdata_path) + self.assertTrue(os.path.isdir(inputdata_path)) build_ctsm( cime_path=_CIME_PATH, build_dir=build_dir, @@ -107,6 +110,7 @@ def test_buildSetup_userDefinedMachine_allInfo(self): build_with_openmp=True, inputdata_path=os.path.join(self._tempdir, "my_inputdata"), ) + self.assertTrue(os.path.isdir(build_dir)) # the critical piece of this test is that the above command doesn't generate any # errors; however we also do some assertions below From 57e9d4e63d6b935830d8eb6356fee4c680c7fc1e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Nov 2022 19:53:44 -0700 Subject: [PATCH 0456/2067] Add some more checking that create_newcase exists as expected and that the inputdata_path directory exists if provided --- python/ctsm/lilac_build_ctsm.py | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/python/ctsm/lilac_build_ctsm.py b/python/ctsm/lilac_build_ctsm.py index 20231c0df9..b189cb56ea 100644 --- a/python/ctsm/lilac_build_ctsm.py +++ b/python/ctsm/lilac_build_ctsm.py @@ -718,8 +718,13 @@ def _create_case( else: machine_args = ["--machine", machine] + cmd = os.path.join(cime_path, "scripts", "create_newcase") + if not os.path.exists(cmd): + abort( + "The create_newcase command doesn't exist as expected <{}> does not exist)".format(cmd) + ) create_newcase_cmd = [ - os.path.join(cime_path, "scripts", "create_newcase"), + cmd, "--output-root", build_dir, "--case", @@ -741,7 +746,12 @@ def _create_case( create_newcase_cmd.extend(machine_args) if inputdata_path: create_newcase_cmd.extend(["--input-dir", inputdata_path]) - run_cmd_output_on_error(create_newcase_cmd, errmsg="Problem creating CTSM case directory") + if not os.path.isdir(inputdata_path): + abort("inputdata_path directory (<{}> does not exist)".format(inputdata_path)) + run_cmd_output_on_error( + create_newcase_cmd, + errmsg="Problem running create_newcase to create the CTSM case directory", + ) subprocess.check_call([xmlchange, "LILAC_MODE=on"], cwd=case_dir) if build_debug: From 8b36987253ade815c734a3f6fde48c2f1a162e0b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 15:25:47 -0700 Subject: [PATCH 0457/2067] Add a check that the main inputdata directory exists or not, and add a unit test for it --- python/ctsm/subset_data.py | 11 +++-- python/ctsm/test/test_unit_subset_data.py | 57 +++++++++++++++++++++++ 2 files changed, 65 insertions(+), 3 deletions(-) create mode 100755 python/ctsm/test/test_unit_subset_data.py diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 4832e98f7f..2d23aba12f 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -67,6 +67,7 @@ from ctsm.site_and_regional.regional_case import RegionalCase from ctsm.args_utils import plon_type, plat_type from ctsm.path_utils import path_to_ctsm_root +from ctsm.utils import abort # -- import ctsm logging flags from ctsm.ctsm_logging import ( @@ -396,16 +397,20 @@ def setup_files(args, defaults, cesmroot): fsurf_in = defaults.get("surfdat", "surfdat_" + num_pft + "pft") fluse_in = defaults.get("landuse", "landuse_" + num_pft + "pft") + clmforcingindir = defaults.get("main", "clmforcingindir") + if not os.path.isdir(clmforcingindir): + logger.info("clmforcingindir does not exist: %s", clmforcingindir) + abort("inputdata directory does not exist") file_dict = { - "main_dir": defaults.get("main", "clmforcingindir"), + "main_dir": clmforcingindir, "fdomain_in": defaults.get("domain", "file"), "fsurf_dir": os.path.join( - defaults.get("main", "clmforcingindir"), + clmforcingindir, os.path.join(defaults.get("surfdat", "dir")), ), "fluse_dir": os.path.join( - defaults.get("main", "clmforcingindir"), + clmforcingindir, os.path.join(defaults.get("landuse", "dir")), ), "fsurf_in": fsurf_in, diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py new file mode 100755 index 0000000000..8245b4a1ba --- /dev/null +++ b/python/ctsm/test/test_unit_subset_data.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python3 +""" +Unit tests for subset_data + +You can run this by: + python -m unittest test_unit_subset_data.py +""" + +import unittest +import configparser +import argparse +import os +import sys + +# -- add python/ctsm to path (needed if we want to run the test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +# pylint: disable=wrong-import-position +from ctsm import unit_testing +from ctsm.subset_data import get_parser, setup_files +from ctsm.path_utils import path_to_ctsm_root + +# pylint: disable=invalid-name + + +class TestSubsetData(unittest.TestCase): + """ + Basic class for testing SubsetData class in subset_data.py. + """ + + def setUp(self): + sys.argv = ["subset_data", "point"] + DEFAULTS_FILE = "default_data.cfg" + parser = get_parser() + self.args = parser.parse_args() + self.cesmroot = path_to_ctsm_root() + self.defaults = configparser.ConfigParser() + self.defaults.read(os.path.join(self.cesmroot, "tools/site_and_regional", DEFAULTS_FILE)) + + def test_inputdata_setup_files_basic(self): + """ + Test + """ + setup_files(self.args, self.defaults, self.cesmroot) + + def test_inputdata_setup_files_inputdata_dne(self): + """ + Test that inputdata directory does not exist + """ + self.defaults.set("main", "clmforcingindir", "/zztop") + with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): + setup_files(self.args, self.defaults, self.cesmroot) + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() From 5381b911e2a0b281a92d565de22e501e0240a190 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 15:39:51 -0700 Subject: [PATCH 0458/2067] Add inputdata-dir option --- python/ctsm/subset_data.py | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 2d23aba12f..513f75ec59 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -315,6 +315,14 @@ def get_parser(): action="store_true", dest="overwrite", ) + subparser.add_argument( + "--inputdata-dir", + help="Top level path to the CESM inputdata directory.", + action="store", + dest="inputdatadir", + type=str, + default="defaults.cfg", + ) add_logging_args(subparser) # -- print help for both subparsers @@ -397,7 +405,11 @@ def setup_files(args, defaults, cesmroot): fsurf_in = defaults.get("surfdat", "surfdat_" + num_pft + "pft") fluse_in = defaults.get("landuse", "landuse_" + num_pft + "pft") - clmforcingindir = defaults.get("main", "clmforcingindir") + if args.inputdatadir == "defaults.cfg": + clmforcingindir = defaults.get("main", "clmforcingindir") + else: + clmforcingindir = args.inputdatadir + if not os.path.isdir(clmforcingindir): logger.info("clmforcingindir does not exist: %s", clmforcingindir) abort("inputdata directory does not exist") From a4ea6e85192466ef39a072b0cf462b4966c8f805 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 15:48:31 -0700 Subject: [PATCH 0459/2067] Add a check that using command line argument to something that doesn't exist aborts as expected --- python/ctsm/test/test_unit_subset_data.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 8245b4a1ba..6a72e5e8ee 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -52,6 +52,14 @@ def test_inputdata_setup_files_inputdata_dne(self): with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): setup_files(self.args, self.defaults, self.cesmroot) + def test_inputdata_setup_files_bad_inputdata_arg(self): + """ + Test that inputdata directory provided on command line does not exist if it's bad + """ + self.args.inputdatadir = "/zztop" + with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): + setup_files(self.args, self.defaults, self.cesmroot) + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() From c5c054819f9d8da9b4e21cd296398bcde27c8151 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 15:52:28 -0700 Subject: [PATCH 0460/2067] Run black --- python/ctsm/subset_data.py | 4 ++-- python/ctsm/test/test_unit_subset_data.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 513f75ec59..59b512723c 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -406,9 +406,9 @@ def setup_files(args, defaults, cesmroot): fsurf_in = defaults.get("surfdat", "surfdat_" + num_pft + "pft") fluse_in = defaults.get("landuse", "landuse_" + num_pft + "pft") if args.inputdatadir == "defaults.cfg": - clmforcingindir = defaults.get("main", "clmforcingindir") + clmforcingindir = defaults.get("main", "clmforcingindir") else: - clmforcingindir = args.inputdatadir + clmforcingindir = args.inputdatadir if not os.path.isdir(clmforcingindir): logger.info("clmforcingindir does not exist: %s", clmforcingindir) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 6a72e5e8ee..aa4c412bbb 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -8,7 +8,6 @@ import unittest import configparser -import argparse import os import sys @@ -40,7 +39,7 @@ def setUp(self): def test_inputdata_setup_files_basic(self): """ - Test + Test """ setup_files(self.args, self.defaults, self.cesmroot) @@ -60,6 +59,7 @@ def test_inputdata_setup_files_bad_inputdata_arg(self): with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): setup_files(self.args, self.defaults, self.cesmroot) + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() From 00d117aec9cb3517da8f53f0b0aafee54b0aafac Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 16:24:33 -0700 Subject: [PATCH 0461/2067] Set inputdata option so testing can run on both cheyenne and izumi --- test/tools/nl_files/subset_data_KONA | 2 +- test/tools/nl_files/subset_data_US-UMB | 2 +- test/tools/nl_files/subset_data_YELL | 2 +- test/tools/nl_files/subset_data_f09_US_pt | 2 +- test/tools/nl_files/subset_data_region1 | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/test/tools/nl_files/subset_data_KONA b/test/tools/nl_files/subset_data_KONA index cb743f2b45..c3be007869 100644 --- a/test/tools/nl_files/subset_data_KONA +++ b/test/tools/nl_files/subset_data_KONA @@ -1 +1 @@ -point --lon 263.38956 --lat 39.1082 --site KONA --dompft 17 19 23 45 --pctpft 28 12 32 28 --crop --create-domain --create-surface --outdir EXEDIR/KONA_user-mod_and_data --user-mods-dir EXEDIR/KONA_user-mod_and_data --verbose +point --lon 263.38956 --lat 39.1082 --site KONA --dompft 17 19 23 45 --pctpft 28 12 32 28 --crop --create-domain --create-surface --outdir EXEDIR/KONA_user-mod_and_data --user-mods-dir EXEDIR/KONA_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_US-UMB b/test/tools/nl_files/subset_data_US-UMB index 499b5f53fd..935b0dc99d 100644 --- a/test/tools/nl_files/subset_data_US-UMB +++ b/test/tools/nl_files/subset_data_US-UMB @@ -1 +1 @@ -point --lon 275.28626 --lat 45.5598 --site 1x1_US-UMB --dompft 7 --cap-saturation --uniform-snowpack --create-surface --outdir EXEDIR/US-UMB_user-mod_and_data --user-mods-dir EXEDIR/US-UMB_user-mod_and_data --verbose +point --lon 275.28626 --lat 45.5598 --site 1x1_US-UMB --dompft 7 --cap-saturation --uniform-snowpack --create-surface --outdir EXEDIR/US-UMB_user-mod_and_data --user-mods-dir EXEDIR/US-UMB_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_YELL b/test/tools/nl_files/subset_data_YELL index 5e142713df..8295830c25 100644 --- a/test/tools/nl_files/subset_data_YELL +++ b/test/tools/nl_files/subset_data_YELL @@ -1 +1 @@ -point --lon 250.45804 --lat 44.95597 --site YELL --dompft 1 --crop --create-domain --create-surface --outdir EXEDIR/YELL_user-mod_and_data --user-mods-dir EXEDIR/YELL_user-mod_and_data --verbose +point --lon 250.45804 --lat 44.95597 --site YELL --dompft 1 --crop --create-domain --create-surface --outdir EXEDIR/YELL_user-mod_and_data --user-mods-dir EXEDIR/YELL_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_f09_US_pt b/test/tools/nl_files/subset_data_f09_US_pt index 4acdfeabd4..bf6d5e2861 100644 --- a/test/tools/nl_files/subset_data_f09_US_pt +++ b/test/tools/nl_files/subset_data_f09_US_pt @@ -1 +1 @@ -point --lon 257.5 --lat 43.822 --site 1x1_ --include-nonveg --crop --create-landuse --create-datm --create-user-mods --datm-syr 2000 --datm-eyr 2000 --create-surface --outdir EXEDIR/f09_US_pt_user-mod_and_data --user-mods-dir EXEDIR/f09_US_pt_user-mod_and_data --verbose +point --lon 257.5 --lat 43.822 --site 1x1_ --include-nonveg --crop --create-landuse --create-datm --create-user-mods --datm-syr 2000 --datm-eyr 2000 --create-surface --outdir EXEDIR/f09_US_pt_user-mod_and_data --user-mods-dir EXEDIR/f09_US_pt_user-mod_and_data --verbose --inputdata-dir CSMDATA diff --git a/test/tools/nl_files/subset_data_region1 b/test/tools/nl_files/subset_data_region1 index c1c5607239..fce83f0e2e 100644 --- a/test/tools/nl_files/subset_data_region1 +++ b/test/tools/nl_files/subset_data_region1 @@ -1 +1 @@ -region --lat1 -40 --lat2 15 --lon1 275 --lon2 330 --create-domain --create-surface --create-landuse --verbose --overwrite --reg test1 +region --lat1 -40 --lat2 15 --lon1 275 --lon2 330 --create-domain --create-surface --create-landuse --verbose --overwrite --reg test1 --inputdata-dir CSMDATA From b5f153fbe4bdaa6e018b695949a2c7c5cfd50103 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 18:54:59 -0700 Subject: [PATCH 0462/2067] Add argument for inputdata-directory --- .../modify_singlept_site_neon.py | 18 +++++++++++++++--- 1 file changed, 15 insertions(+), 3 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 334ab7d6aa..e842a84f07 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -149,6 +149,18 @@ def get_parser(): required=False, default="/glade/scratch/" + myname + "/single_point_neon_updated/", ) + parser.add_argument( + "--inputdata-dir", + help=""" + Directory to write updated single point surface dataset. + [default: %(default)s] + """, + action="store", + dest="inputdatadir", + type=str, + required=False, + default="/glade/p/cesmdata/cseg/inputdata" + ) parser.add_argument( "-d", "--debug", @@ -269,7 +281,7 @@ def find_surffile(surf_dir, site_name): return surf_file -def find_soil_structure(surf_file): +def find_soil_structure(args, surf_file): """ Function for finding surface dataset soil strucutre using surface data metadata. @@ -298,7 +310,7 @@ def find_soil_structure(surf_file): print("------------") # print (f1.attrs["Soil_texture_raw_data_file_name"]) - clm_input_dir = "/glade/p/cesmdata/cseg/inputdata/lnd/clm2/rawdata/" + clm_input_dir = os.path.join( args.inputdatadir, "lnd/clm2/rawdata/" ) surf_soildepth_file = os.path.join( clm_input_dir, f1.attrs["Soil_texture_raw_data_file_name"] ) @@ -534,7 +546,7 @@ def main(): f1 = xr.open_dataset(surf_file) # -- Find surface dataset soil depth information - soil_bot, soil_top = find_soil_structure(surf_file) + soil_bot, soil_top = find_soil_structure(args, surf_file) # -- Find surface dataset soil levels # TODO: how? NS uses metadata on file to find From 2c523aafaa334a5bf54ca5cb7ee263c76132f29a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 18:57:17 -0700 Subject: [PATCH 0463/2067] Set inputdata directory so can work on izumi --- test/tools/nl_files/modify_data_YELL | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/tools/nl_files/modify_data_YELL b/test/tools/nl_files/modify_data_YELL index e76322cdeb..159c92ae63 100644 --- a/test/tools/nl_files/modify_data_YELL +++ b/test/tools/nl_files/modify_data_YELL @@ -1 +1 @@ ---neon_site YELL --surf_dir CSMDATA/lnd/clm2/surfdata_map/NEON --out_dir EXEDIR +--neon_site YELL --surf_dir CSMDATA/lnd/clm2/surfdata_map/NEON --out_dir EXEDIR --inputdata-dir CSMDATA From 2e122e0de3ef899eb162cea97cea9a74ee9fab2a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 17 Nov 2022 22:11:43 -0700 Subject: [PATCH 0464/2067] Make datm forcing data under the inputdata-dir so doesn't need a seperate path and can work on izumi as well --- python/ctsm/subset_data.py | 19 ++++++++++--------- tools/site_and_regional/default_data.cfg | 2 +- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 59b512723c..34a9e583d0 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -390,10 +390,19 @@ def setup_files(args, defaults, cesmroot): if args.create_user_mods: setup_user_mods(args.user_mods_dir, cesmroot) + if args.inputdatadir == "defaults.cfg": + clmforcingindir = defaults.get("main", "clmforcingindir") + else: + clmforcingindir = args.inputdatadir + + if not os.path.isdir(clmforcingindir): + logger.info("clmforcingindir does not exist: %s", clmforcingindir) + abort("inputdata directory does not exist") + # DATM data datm_type = "datm_gswp3" dir_output_datm = "datmdata" - dir_input_datm = defaults.get(datm_type, "dir") + dir_input_datm = os.path.join(clmforcingindir, defaults.get(datm_type, "dir")) if args.create_datm: if not os.path.isdir(os.path.join(args.out_dir, dir_output_datm)): os.mkdir(os.path.join(args.out_dir, dir_output_datm)) @@ -405,14 +414,6 @@ def setup_files(args, defaults, cesmroot): fsurf_in = defaults.get("surfdat", "surfdat_" + num_pft + "pft") fluse_in = defaults.get("landuse", "landuse_" + num_pft + "pft") - if args.inputdatadir == "defaults.cfg": - clmforcingindir = defaults.get("main", "clmforcingindir") - else: - clmforcingindir = args.inputdatadir - - if not os.path.isdir(clmforcingindir): - logger.info("clmforcingindir does not exist: %s", clmforcingindir) - abort("inputdata directory does not exist") file_dict = { "main_dir": clmforcingindir, diff --git a/tools/site_and_regional/default_data.cfg b/tools/site_and_regional/default_data.cfg index f689c99044..7e841dca54 100644 --- a/tools/site_and_regional/default_data.cfg +++ b/tools/site_and_regional/default_data.cfg @@ -2,7 +2,7 @@ clmforcingindir = /glade/p/cesmdata/inputdata [datm_gswp3] -dir = /glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.datm7.GSWP3.0.5d.v1.c170516 +dir = atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516 domain = domain.lnd.360x720_gswp3.0v1.c170606.nc solardir = Solar precdir = Precip From 6b017ae5e7fad159afb368282b9d9c3c3ed38a93 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 18 Nov 2022 17:30:33 -0700 Subject: [PATCH 0465/2067] Check if pandas is recent enough --- tools/site_and_regional/modify_singlept_site_neon.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index e842a84f07..f9f7188b42 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -47,6 +47,7 @@ import numpy as np import pandas as pd import xarray as xr +from packaging import version from datetime import date from getpass import getuser @@ -518,6 +519,12 @@ def main(): if args.debug: logging.basicConfig(level=logging.DEBUG) + # Check if pandas is a recent enough version + pdvers = pd.__version__ + if version.parse(pdvers) < version.parse("1.1.0"): + sys.exit("The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", pdvers ) + + file_time = check_neon_time() # -- specify site from which to extract data From b8753eb6259fc9471a34e2430f433b8caa500a00 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 18 Nov 2022 18:58:20 -0700 Subject: [PATCH 0466/2067] Fix the error, which was failing in writing an empty list --- tools/site_and_regional/modify_singlept_site_neon.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index f9f7188b42..2798f463ec 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -274,10 +274,10 @@ def find_surffile(surf_dir, site_name): surf_file = surf_file[0] else: sys.exit( - "Surface data for this site " + site_name + "was not found:" + surf_file, - ".", - "\n", - "Please run ./subset_data.py for this site.", + "Surface data for this site " + str(site_name) + " was not found:" + str(surf_dir) + str(sf_name) + + "." + + "\n" + + "Please run ./subset_data.py for this site." ) return surf_file From 01b411857fdef867dd177075d0a4f602a220f765 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 19 Nov 2022 18:11:31 -0700 Subject: [PATCH 0467/2067] Update changelog --- doc/ChangeLog | 14 ++++++++++++-- doc/ChangeSum | 2 +- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index b4d2da11c6..5f16bf5634 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev114 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)/@wwieder/@olyson/@ka7eh -Date: Wed Nov 16 16:31:14 MST 2022 +Date: Sat Nov 19 18:11:15 MST 2022 One-line Summary: Some NEON updates fixing AG sites, update MOSART, small fixes Purpose and description of changes @@ -11,6 +11,9 @@ Minor changes to python scripts and usermod_dirs for NEON cases. Also update the smaller lightning file. Have NEON use new use-cases for 2018 and 2018-PD conditions for CLM. Have NEON Agricultural sites run with prognostic crop. Simple fix for warning about NaN's in import/export data from/to coupler. +Get NEON tests working on izumi, add --inputdata-dir to subset_data and modify_singlept_site_neon.py so they aren't tied +to only running on cheyenne. + Also update MOSART with fixed for direct_to_outlet option. Add error checking in ParitionWoodFluxes. Fix value of albgrd_col in SurfaceAlbefdoType.F90. @@ -45,6 +48,11 @@ CTSM issues fixed (include CTSM Issue #): Fixes #1263 -- Fix partitionWood fluxes Fixes #1788 -- Fix albgrd_col Fixes #1901 -- Fix NEONSITE YELL + + Some on #1910 -- add pandas version check to modify_singlept_site_neon.py so will abort cleanly if version not updated + + Known bugs found since the previous tag (include issue #): + #1910 -- modify_singlept_site_neon.py has trouble on izumi Notes of particular relevance for users --------------------------------------- @@ -87,7 +95,9 @@ Testing summary: regular, tools tools-tests (test/tools) (if tools have been changed): cheyenne - OK - izumi (NEON) -- OK + cheyenne (NEON) - PASS + izumi (NEON) -- OK (modify_singlept_site_neon.py test fails due to #1910) + izumi -- OK python testing (if python code has changed; see instructions in python/README.md; document testing done): diff --git a/doc/ChangeSum b/doc/ChangeSum index a90365740a..772545d00c 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev114 multiple 11/16/2022 Some NEON updates fixing AG sites, update MOSART, small fixes + ctsm5.1.dev114 multiple 11/19/2022 Some NEON updates fixing AG sites, update MOSART, small fixes ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests ctsm5.1.dev111 multiple 10/05/2022 Fixes for NEON cases From 5dc5f59f10dad61539f99b78ae3ac23e533afb75 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Nov 2022 15:21:59 -0700 Subject: [PATCH 0468/2067] Add logical use_excess_ice_streams to control if streams file is used when use_excess_ice is on, and add some testing for it --- .../namelist_definition_ctsm.xml | 10 ++++++- bld/unit_testers/build-namelist_test.pl | 29 ++++++++++++++++--- 2 files changed, 34 insertions(+), 5 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index bcee47aed5..b718b7cbf6 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2826,6 +2826,13 @@ use case.) If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) + +If TRUE and use_excess_ice is TRUE, use the excess ice stream to determine the initial values of the excess ice field +if FALSE and use_excess_ice is TRUE, expect excess ice to come from the initial conditions or restart file +Expect to be FALSE is use_excess_ice is FALSE + + Filename of input stream data for excess ice data @@ -2837,10 +2844,11 @@ mesh filename of input stream data for excess ice + group="exice_streams" valid_values="bilinear,nn,none" > Mapping method from excess ice input stream data to the model resolution bilinear = bilinear interpolation nn = nearest neighbor + none = no interpolation diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 5b2ae9c9b9..156b84ba51 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1844; +my $ntests = 1855; if ( defined($opts{'compare'}) ) { - $ntests += 1254; + $ntests += 1262; } plan( tests=>$ntests ); @@ -323,6 +323,7 @@ sub cat_and_create_namelistinfile { "-structure fast", "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850", "-namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'", + "-namelist '&a use_excess_ice=.true. use_excess_ice_streams=.true./'", "-use_case 1850_control", "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'", "-res 1x1_brazil", @@ -521,8 +522,28 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, - "soilm_stream wo use" =>{ options=>"-res 0.9x1.25 -envxml_dir .", - namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='missing_file'", + "soilm_stream off w file" =>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_soil_moisture_streams = .false.,stream_fldfilename_soilm='file_provided_when_off'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "exice_stream off w file" =>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.,stream_fldfilename_exice='file_provided_when_off'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "exice_stream off w mesh" =>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.,stream_meshfile_exice='file_provided_when_off'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "exice off, but stream on" =>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_excess_ice=.false., use_excess_ice_streams = .true.,stream_fldfilename_exice='file_provided', stream_meshfile_exice='file_provided'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "exice stream off, but setmap"=>{ options=>"-res 0.9x1.25 -envxml_dir .", + namelst=>"use_excess_ice=.true., use_excess_ice_streams = .false.,stream_mapalgo_exice='bilinear'", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, From 34604989401baa634fa72c02d3f1bffe42578f85 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Nov 2022 15:34:01 -0700 Subject: [PATCH 0469/2067] Fix number of tests, by the way in the spirit of test-driven development the 4 new fail tests added fail at this point --- bld/unit_testers/build-namelist_test.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 156b84ba51..bf416deacd 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1855; +my $ntests = 1856; if ( defined($opts{'compare'}) ) { - $ntests += 1262; + $ntests += 1260; } plan( tests=>$ntests ); From d39715715eb081dd77d0c510be482da6a392a6a6 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Nov 2022 16:07:57 -0700 Subject: [PATCH 0470/2067] Add the error checking for excess ice and excess ice streams, this gets the tests working --- bld/CLMBuildNamelist.pm | 41 ++++++++++++++++++++++++++++++++++------- 1 file changed, 34 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 606f182667..906c3be2dd 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4149,13 +4149,40 @@ sub setup_logic_exice { # excess ice streams # my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - my $use_exice = $nl->get_value( 'use_excess_ice' ); - if (defined($use_exice) && $opts->{'driver'} eq "nuopc" && value_is_true($use_exice)) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); - } elsif (defined($use_exice) && (! $opts->{'driver'} eq "nuopc") && value_is_true($use_exice)) { - $log->fatal_error("nuopc driver is required when use_excess_ice is set to true" ); + my $use_exice = $nl->get_value( 'use_excess_ice' ); + my $use_exice_streams = $nl->get_value( 'use_excess_ice_streams' ); + # IF excess ice streams is on + if (defined($use_exice_streams) && value_is_true($use_exice_streams)) { + # Can only be true if excess ice is also on, otherwise fail + if (defined($use_exice) && not value_is_true($use_exice)) { + $log->fatal_error("use_excess_ice_streams can NOT be TRUE when use_excess_ice is FALSE" ); + } + # Otherwise if ice streams are off + } else { + my @list = ( "stream_meshfile_exice", "stream_fldfilename_exice" ); + # fail is excess ice streams files are set + foreach my $var ( @list ) { + if ( defined($nl->get_value($var)) ) { + $log->fatal_error("$var should NOT be set when use_excess_ice_streams=FALSE" ); + } + } + # mapalgo can only be none, if excess ice streams are off + my $map_algo = $nl->get_value("stream_mapalgo_exice"); + if ( defined($map_algo) && ($map_algo ne "none") ) { + $log->fatal_error("stream_mapalgo_exice can ONLY be none when use_excess_ice_streams=FALSE" ); + } + } + # If excess ice is on + if (defined($use_exice) && value_is_true($use_exice)) { + # IF nuopc driver and excess ice streams are on get the stream defaults + if (defined($use_exice_streams) && $opts->{'driver'} eq "nuopc" && value_is_true($use_exice_streams)) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); + # If excess ice streams on, but NOT the NUOPC driver fail + } elsif (defined($use_exice_streams) && (! $opts->{'driver'} eq "nuopc") && value_is_true($use_exice_streams)) { + $log->fatal_error("nuopc driver is required when use_excess_ice_streams is set to true" ); + } } From 53e272b28610460747b3e054faa09384abbe3945 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 22 Nov 2022 16:58:22 -0700 Subject: [PATCH 0471/2067] Add an execess ice test with and without excess ice streams --- bld/unit_testers/build-namelist_test.pl | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index bf416deacd..f56e6631fa 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1856; +my $ntests = 1864; if ( defined($opts{'compare'}) ) { - $ntests += 1260; + $ntests += 1266; } plan( tests=>$ntests ); @@ -324,6 +324,7 @@ sub cat_and_create_namelistinfile { "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850", "-namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'", "-namelist '&a use_excess_ice=.true. use_excess_ice_streams=.true./'", + "-namelist '&a use_excess_ice=.true. use_excess_ice_streams=.false./'", "-use_case 1850_control", "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'", "-res 1x1_brazil", From 5a56434568109ce8c4a8f848410dda8eb1ce1866 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Nov 2022 10:38:23 -0700 Subject: [PATCH 0472/2067] Add use_excess_ice_streams to excess ice namelist, make UseStreams a public method --- src/cpl/share_esmf/ExcessIceStreamType.F90 | 32 +++++++++++++++++----- 1 file changed, 25 insertions(+), 7 deletions(-) diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 9b9a7c058c..9955b03156 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -35,7 +35,7 @@ module ExcessIceStreamType ! !PUBLIC MEMBER FUNCTIONS: procedure, public :: Init ! Initialize and read data in - procedure, private :: UseStreams ! If streams will be used + procedure, public :: UseStreams ! If streams will be used procedure, public :: CalcExcessIce ! Calculate excess ice ammount ! !PRIVATE MEMBER FUNCTIONS: @@ -51,6 +51,7 @@ module ExcessIceStreamType procedure, private :: ReadNML ! Read in namelist end type streamcontrol_type + logical :: namelist_read = .false. type(streamcontrol_type), private :: control ! Stream control data character(len=*), parameter, private :: sourcefile = & @@ -234,6 +235,9 @@ logical function UseStreams(this) class(excessicestream_type) :: this ! ! !LOCAL VARIABLES: + if ( .not. read_namelist ) then + call endrun(msg=' ERROR UseStreams being called, but namelist has not been read yet'//errMsg(sourcefile, __LINE__)) + end if if ( trim(control%stream_fldFileName_exice) == '' )then UseStreams = .false. else @@ -259,6 +263,7 @@ subroutine ReadNML(this, bounds, NLFilename) ! local variables integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag + logical :: use_excess_ice_streams = .false. ! logical to turn on use of excess ice streams character(len=CL) :: stream_fldFileName_exice = ' ' character(len=CL) :: stream_meshfile_exice = ' ' character(len=CL) :: stream_mapalgo_exice = 'bilinear' @@ -267,7 +272,7 @@ subroutine ReadNML(this, bounds, NLFilename) !----------------------------------------------------------------------- namelist /exice_streams/ & ! MUST agree with namelist_name above - stream_mapalgo_exice, stream_fldFileName_exice, stream_meshfile_exice + stream_mapalgo_exice, stream_fldFileName_exice, stream_meshfile_exice, use_excess_ice_streams ! Default values for namelist @@ -286,22 +291,35 @@ subroutine ReadNML(this, bounds, NLFilename) close(nu_nml) endif + call shr_mpi_bcast(use_excess_ice_streams , mpicom) call shr_mpi_bcast(stream_mapalgo_exice , mpicom) call shr_mpi_bcast(stream_fldFileName_exice , mpicom) call shr_mpi_bcast(stream_meshfile_exice , mpicom) if (masterproc) then write(iulog,*) ' ' - write(iulog,*) namelist_name, ' stream settings:' - write(iulog,*) ' stream_fldFileName_exice = ',stream_fldFileName_exice - write(iulog,*) ' stream_meshfile_exice = ',stream_meshfile_exice - write(iulog,*) ' stream_mapalgo_exice = ',stream_mapalgo_exice + if ( use_excess_ice_streams ) then + write(iulog,*) 'excess ice streams are enabled: ' + write(iulog,*) namelist_name, ' stream settings:' + write(iulog,*) ' stream_fldFileName_exice = ',stream_fldFileName_exice + write(iulog,*) ' stream_meshfile_exice = ',stream_meshfile_exice + write(iulog,*) ' stream_mapalgo_exice = ',stream_mapalgo_exice + if ( trim(stream_fldFileName_exice) == '' )then + call endrun(msg=' ERROR excess ice streams are on, but stream_fldFileName_exice is NOT set'//errMsg(sourcefile, __LINE__)) + end if + else + write(iulog,*) 'excess ice streams are off' + if ( trim(stream_fldFileName_exice) /= '' )then + call endrun(msg=' ERROR excess ice streams are off, but stream_fldFileName_exice is set'//errMsg(sourcefile, __LINE__)) + end if + end if endif this%stream_fldFileName_exice = stream_fldFileName_exice this%stream_meshfile_exice = stream_meshfile_exice this%stream_mapalgo_exice = stream_mapalgo_exice + namelist_read = .true. end subroutine ReadNML -end module ExcessIceStreamType \ No newline at end of file +end module ExcessIceStreamType From 2703c0446e5e57f925b78a5ad96dbf2936ed63d5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Nov 2022 10:43:43 -0700 Subject: [PATCH 0473/2067] Turn on excess ice streams --- cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm index d9e52c6cf9..f61ca32a79 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm @@ -1 +1,2 @@ use_excess_ice = .true. + use_excess_ice_streams = .true. From 2dfc71f73163802fc3a0e3c63ed8a4497b73a866 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Nov 2022 10:47:16 -0700 Subject: [PATCH 0474/2067] Add another excess ice test that starts up from a restart file --- .../clm/{ExcessIce => ExcessIceRestart}/include_user_mods | 0 .../testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm | 1 + .../testmods_dirs/clm/ExcessIceStreams/include_user_mods | 1 + .../clm/{ExcessIce => ExcessIceStreams}/user_nl_clm | 0 4 files changed, 2 insertions(+) rename cime_config/testdefs/testmods_dirs/clm/{ExcessIce => ExcessIceRestart}/include_user_mods (100%) create mode 100644 cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{ExcessIce => ExcessIceStreams}/user_nl_clm (100%) diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIce/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/include_user_mods similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/ExcessIce/include_user_mods rename to cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm new file mode 100644 index 0000000000..d9e52c6cf9 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm @@ -0,0 +1 @@ + use_excess_ice = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/ExcessIce/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/ExcessIceStreams/user_nl_clm From 0035dc7db10c9b1cc8c9c4ff15181f6be3038b2a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 23 Nov 2022 10:59:26 -0700 Subject: [PATCH 0475/2067] Fill out all the options for the excess ice tests, add a higher resolution test to start from a restart file, and make the main excess ice test with restart --- cime_config/testdefs/testlist_clm.xml | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index b2a063d011..18d6c56f73 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -168,13 +168,29 @@ - + + + + + + + + + + + + + + + + + - + From 58e52555b7d8f884eb3e7d9aad94bf8f91d07ea9 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 26 Nov 2022 13:45:54 -0700 Subject: [PATCH 0476/2067] Put use_excess_ice_streams in the right namelist --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index b718b7cbf6..91bc00e7d6 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2827,7 +2827,7 @@ If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020) + group="exice_streams" valid_values="" > If TRUE and use_excess_ice is TRUE, use the excess ice stream to determine the initial values of the excess ice field if FALSE and use_excess_ice is TRUE, expect excess ice to come from the initial conditions or restart file Expect to be FALSE is use_excess_ice is FALSE From 6597b7b219bf3296635b94c92a5ade1a66aae410 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 26 Nov 2022 13:46:20 -0700 Subject: [PATCH 0477/2067] Fix name of variable --- src/cpl/share_esmf/ExcessIceStreamType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 9955b03156..414f635eeb 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -235,7 +235,7 @@ logical function UseStreams(this) class(excessicestream_type) :: this ! ! !LOCAL VARIABLES: - if ( .not. read_namelist ) then + if ( .not. namelist_read ) then call endrun(msg=' ERROR UseStreams being called, but namelist has not been read yet'//errMsg(sourcefile, __LINE__)) end if if ( trim(control%stream_fldFileName_exice) == '' )then From 2bf87975248f45c10e2758eb9865bb084149bc7f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 15:38:56 -0700 Subject: [PATCH 0478/2067] Add test for excess_ice streams on, but mct, that fails --- bld/unit_testers/build-namelist_test.pl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index f56e6631fa..bbe71406b8 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1864; +my $ntests = 1865; if ( defined($opts{'compare'}) ) { $ntests += 1266; } @@ -548,6 +548,11 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "exice stream on, but mct" =>{ options=>"--res 0.9x1.25 --envxml_dir . --driver mct --lnd_frac $DOMFILE ", + namelst=>"use_excess_ice=.true., use_excess_ice_streams=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, "clm50CNDVwtransient" =>{ options=>" -envxml_dir . -use_case 20thC_transient -dynamic_vegetation -res 10x15 -ignore_warnings", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", From 4af3fd583e9f281d474855c92b253fb089536cfd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 16:04:11 -0700 Subject: [PATCH 0479/2067] Fix the check for MCT driver with excess ice streams --- bld/CLMBuildNamelist.pm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 906c3be2dd..10d8fd0923 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4175,13 +4175,14 @@ sub setup_logic_exice { # If excess ice is on if (defined($use_exice) && value_is_true($use_exice)) { # IF nuopc driver and excess ice streams are on get the stream defaults - if (defined($use_exice_streams) && $opts->{'driver'} eq "nuopc" && value_is_true($use_exice_streams)) { + if (defined($use_exice_streams) && value_is_true($use_exice_streams)) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); - # If excess ice streams on, but NOT the NUOPC driver fail - } elsif (defined($use_exice_streams) && (! $opts->{'driver'} eq "nuopc") && value_is_true($use_exice_streams)) { + # If excess ice streams on, but NOT the NUOPC driver fail + if ( not $opts->{'driver'} eq "nuopc" ) { $log->fatal_error("nuopc driver is required when use_excess_ice_streams is set to true" ); + } } } From 5aaef812c4e0ab48f7a50686f8d763882c54409c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 16:04:33 -0700 Subject: [PATCH 0480/2067] Don't run the MCT driver test with excess ice stremas --- bld/unit_testers/build-namelist_test.pl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index bbe71406b8..1bdb59f72a 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1865; +my $ntests = 1861; if ( defined($opts{'compare'}) ) { - $ntests += 1266; + $ntests += 1263; } plan( tests=>$ntests ); @@ -339,6 +339,10 @@ sub cat_and_create_namelistinfile { my $base_options = "-res 0.9x1.25 -envxml_dir . -driver $driver"; if ( $driver eq "mct" ) { $base_options = "$base_options -lnd_frac $DOMFILE"; + # Skip the MCT test for excess ice streams + if ( $options =~ /use_excess_ice_streams=.true./ ) { + next; + } } else { $base_options = "$base_options -namelist '&a force_send_to_atm = .false./'"; } From 33c760ee561f843da74cdf094ef5e8e45c33a3f4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 16:24:04 -0700 Subject: [PATCH 0481/2067] Add stub excess ice streams for MCT, so MCT driver cases can build --- src/cpl/mct/ExcessIceStreamType.F90 | 136 ++++++++++++++++++++++++++++ 1 file changed, 136 insertions(+) create mode 100644 src/cpl/mct/ExcessIceStreamType.F90 diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 new file mode 100644 index 0000000000..a1d2fe7ff9 --- /dev/null +++ b/src/cpl/mct/ExcessIceStreamType.F90 @@ -0,0 +1,136 @@ +module ExcessIceStreamType + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Stub for ExcessIceStreams for the MCT driver. So that MCT can be used + ! without excess ice streams. + ! + ! !USES + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use spmdMod , only : mpicom, masterproc + use clm_varctl , only : iulog + use abortutils , only : endrun + use decompMod , only : bounds_type + + ! !PUBLIC TYPES: + implicit none + private + + procedure, public :: UseExcessIceStreams ! If streams will be used + + type, public :: excessicestream_type + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Initialize and read data in + procedure, public :: CalcExcessIce ! Calculate excess ice ammount + + ! !PRIVATE MEMBER FUNCTIONS: + procedure, private :: ReadNML ! Read in namelist + + end type excessicestream_type + ! ! PRIVATE DATA: + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine Init(this, bounds, NLFilename) + ! + ! + ! arguments + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + + ! + ! local variables + + call this%ReadNML( bounds, NLFileName ) + end subroutine Init + + subroutine CalcExcessIce(this,bounds,exice_bulk_init) + + ! only transfers grid values to columns + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) + ! + ! !LOCAL VARIABLES: + + end subroutine CalcExcessIce + + logical function UseExcessIceStreams() + ! + ! !DESCRIPTION: + ! Return true if + ! + ! !USES: + ! + ! !ARGUMENTS: + implicit none + ! + ! !LOCAL VARIABLES: + UseExcessIceStreams = .false. +end function UseExcessIceStreams + +subroutine ReadNML(this, bounds, NLFilename) + ! + ! Read the namelist data stream information. + ! + ! Uses: + use shr_nl_mod , only : shr_nl_find_group_name + use shr_log_mod , only : errMsg => shr_log_errMsg + use shr_mpi_mod , only : shr_mpi_bcast + ! + ! arguments + implicit none + class(streamcontrol_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + ! + ! local variables + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + logical :: use_excess_ice_streams = .false. ! logical to turn on use of excess ice streams + character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read + character(len=*), parameter :: subName = "('exice_streams::ReadNML')" + !----------------------------------------------------------------------- + + namelist /exice_streams/ & ! MUST agree with namelist_name above + use_excess_ice_streams + + ! Default values for namelist + + ! Read excess ice namelist + if (masterproc) then + open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call shr_nl_find_group_name(nu_nml, namelist_name, status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=exice_streams,iostat=nml_error) ! MUST agree with namelist_name above + if (nml_error /= 0) then + call endrun(msg=' ERROR reading '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + else + call endrun(msg=' ERROR finding '//namelist_name//' namelist'//errMsg(sourcefile, __LINE__)) + end if + close(nu_nml) + endif + + call shr_mpi_bcast(use_excess_ice_streams , mpicom) + + if (masterproc) then + if ( use_excess_ice_streams ) then + call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__)) + end if + endif + +end subroutine ReadNML + +end module ExcessIceStreamType From d0e1e8e9f8914d6b4af40fedd81e4df188395308 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 16:39:39 -0700 Subject: [PATCH 0482/2067] Fix so can compiler --- src/cpl/mct/ExcessIceStreamType.F90 | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 index a1d2fe7ff9..dd0c682e0c 100644 --- a/src/cpl/mct/ExcessIceStreamType.F90 +++ b/src/cpl/mct/ExcessIceStreamType.F90 @@ -17,7 +17,7 @@ module ExcessIceStreamType implicit none private - procedure, public :: UseExcessIceStreams ! If streams will be used + public :: UseExcessIceStreams ! If streams will be used type, public :: excessicestream_type contains @@ -63,6 +63,7 @@ subroutine CalcExcessIce(this,bounds,exice_bulk_init) real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) ! ! !LOCAL VARIABLES: + call endrun(msg=' ERROR CalcExcessIce should NOT be called for the MCT driver'//errMsg(sourcefile, __LINE__)) end subroutine CalcExcessIce @@ -91,7 +92,7 @@ subroutine ReadNML(this, bounds, NLFilename) ! ! arguments implicit none - class(streamcontrol_type) :: this + class(excessicestream_type) :: this type(bounds_type), intent(in) :: bounds character(len=*), intent(in) :: NLFilename ! Namelist filename ! From 621f35336dfb5e09c71b01c4f93783a3a19258b7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 17:01:23 -0700 Subject: [PATCH 0483/2067] Add stream_fldFileName_exice and stream_mapalgo_exice to MCT excess ice stream namelist just to check that they aren't set --- src/cpl/mct/ExcessIceStreamType.F90 | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 index dd0c682e0c..a65eb600c5 100644 --- a/src/cpl/mct/ExcessIceStreamType.F90 +++ b/src/cpl/mct/ExcessIceStreamType.F90 @@ -6,7 +6,7 @@ module ExcessIceStreamType ! without excess ice streams. ! ! !USES - use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL use shr_log_mod , only : errMsg => shr_log_errMsg use spmdMod , only : mpicom, masterproc use clm_varctl , only : iulog @@ -100,13 +100,15 @@ subroutine ReadNML(this, bounds, NLFilename) integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag logical :: use_excess_ice_streams = .false. ! logical to turn on use of excess ice streams + character(len=CL) :: stream_fldFileName_exice = ' ' + character(len=CL) :: stream_mapalgo_exice = 'none' character(len=*), parameter :: namelist_name = 'exice_streams' ! MUST agree with name in namelist and read character(len=*), parameter :: subName = "('exice_streams::ReadNML')" !----------------------------------------------------------------------- namelist /exice_streams/ & ! MUST agree with namelist_name above - use_excess_ice_streams - + stream_mapalgo_exice, stream_fldFileName_exice, use_excess_ice_streams + !----------------------------------------------------------------------- ! Default values for namelist ! Read excess ice namelist @@ -130,6 +132,12 @@ subroutine ReadNML(this, bounds, NLFilename) if ( use_excess_ice_streams ) then call endrun(msg=' ERROR excess ice streams can NOT be on for the MCT driver'//errMsg(sourcefile, __LINE__)) end if + if ( trim(stream_fldFileName_exice) /= '' ) then + call endrun(msg=' ERROR stream_fldFileName_exice can NOT be set for the MCT driver'//errMsg(sourcefile, __LINE__)) + end if + if ( trim(stream_mapalgo_exice) /= 'none' ) then + call endrun(msg=' ERROR stream_mapalgo_exice can only be none for the MCT driver'//errMsg(sourcefile, __LINE__)) + end if endif end subroutine ReadNML From 4813ff6cd71df9a2859cb5d3e7966fa564cd4d3d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 17:07:06 -0700 Subject: [PATCH 0484/2067] handle the excess ice streams difference for MCT and NUOPC a little better --- bld/CLMBuildNamelist.pm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 10d8fd0923..8447fde52a 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4176,12 +4176,14 @@ sub setup_logic_exice { if (defined($use_exice) && value_is_true($use_exice)) { # IF nuopc driver and excess ice streams are on get the stream defaults if (defined($use_exice_streams) && value_is_true($use_exice_streams)) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_exice'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_mapalgo_exice'); # If excess ice streams on, but NOT the NUOPC driver fail if ( not $opts->{'driver'} eq "nuopc" ) { $log->fatal_error("nuopc driver is required when use_excess_ice_streams is set to true" ); + # NUOPC driver needs a mesh file + } else { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_exice'); } } } From 6344bb3bf235d3bb1ebe804d976dbf058bef5990 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 17:15:32 -0700 Subject: [PATCH 0485/2067] Don't call abort on call of CalcExcessIce as it's always called --- src/cpl/mct/ExcessIceStreamType.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/cpl/mct/ExcessIceStreamType.F90 b/src/cpl/mct/ExcessIceStreamType.F90 index a65eb600c5..5c5394233c 100644 --- a/src/cpl/mct/ExcessIceStreamType.F90 +++ b/src/cpl/mct/ExcessIceStreamType.F90 @@ -63,7 +63,6 @@ subroutine CalcExcessIce(this,bounds,exice_bulk_init) real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) ! ! !LOCAL VARIABLES: - call endrun(msg=' ERROR CalcExcessIce should NOT be called for the MCT driver'//errMsg(sourcefile, __LINE__)) end subroutine CalcExcessIce From 8cd39560da909dc35c0c4c56c86334edc58ab085 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 17:24:18 -0700 Subject: [PATCH 0486/2067] Change name of UseStreams to UseExcessIceStreams, make it public and not a method --- src/cpl/share_esmf/ExcessIceStreamType.F90 | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/cpl/share_esmf/ExcessIceStreamType.F90 b/src/cpl/share_esmf/ExcessIceStreamType.F90 index 414f635eeb..92d5632aff 100644 --- a/src/cpl/share_esmf/ExcessIceStreamType.F90 +++ b/src/cpl/share_esmf/ExcessIceStreamType.F90 @@ -29,13 +29,14 @@ module ExcessIceStreamType implicit none private + public :: UseExcessIceStreams ! If streams will be used + type, public :: excessicestream_type real(r8), pointer, private :: exice_bulk (:) ! excess ice bulk value (-) contains ! !PUBLIC MEMBER FUNCTIONS: procedure, public :: Init ! Initialize and read data in - procedure, public :: UseStreams ! If streams will be used procedure, public :: CalcExcessIce ! Calculate excess ice ammount ! !PRIVATE MEMBER FUNCTIONS: @@ -91,7 +92,7 @@ subroutine Init(this, bounds, NLFilename) call this%InitAllocate( bounds ) call control%ReadNML( bounds, NLFileName ) - if ( this%useStreams() )then + if ( UseExcessIceStreams() )then allocate(stream_varnames(1)) stream_varnames = (/"EXICE"/) @@ -223,7 +224,7 @@ subroutine CalcExcessIce(this,bounds,exice_bulk_init) end subroutine CalcExcessIce - logical function UseStreams(this) + logical function UseExcessIceStreams() ! ! !DESCRIPTION: ! Return true if @@ -232,18 +233,17 @@ logical function UseStreams(this) ! ! !ARGUMENTS: implicit none - class(excessicestream_type) :: this ! ! !LOCAL VARIABLES: if ( .not. namelist_read ) then - call endrun(msg=' ERROR UseStreams being called, but namelist has not been read yet'//errMsg(sourcefile, __LINE__)) + call endrun(msg=' ERROR UseExcessIceStreams being called, but namelist has not been read yet'//errMsg(sourcefile, __LINE__)) end if if ( trim(control%stream_fldFileName_exice) == '' )then - UseStreams = .false. + UseExcessIceStreams = .false. else - UseStreams = .true. + UseExcessIceStreams = .true. end if -end function UseStreams +end function UseExcessIceStreams subroutine ReadNML(this, bounds, NLFilename) ! From eb20a75a1a5b068a4fc4f6f35466bb9392c752ff Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 28 Nov 2022 18:03:53 -0700 Subject: [PATCH 0487/2067] Add check that new excess ice fields are on the restart file and if not excess ice streams are on --- src/biogeophys/WaterDiagnosticBulkType.F90 | 17 ++++++++++++++++- src/biogeophys/WaterStateType.F90 | 11 ++++++++++- 2 files changed, 26 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index d7413fb740..3ecae66b28 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -770,9 +770,10 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil use spmdMod , only : masterproc use clm_varcon , only : pondmx, watmin, spval, nameg use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall - use clm_varctl , only : bound_h2osoi, use_excess_ice + use clm_varctl , only : bound_h2osoi, use_excess_ice, nsrest, nsrContinue use ncdio_pio , only : file_desc_t, ncd_io, ncd_double use restUtilMod + use ExcessIceStreamType, only : UseExcessIceStreams ! ! !ARGUMENTS: class(waterdiagnosticbulk_type), intent(inout) :: this @@ -921,6 +922,14 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil units='m', & interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (nsrest == nsrContinue) then + call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & + errMsg(sourcefile, __LINE__)) + else if ( .not. UseExcessIceStreams() )then + call endrun(msg = "This input initial conditions file does NOT include excess ice fields" // & + ", and use_excess_ice_streams is off, one or the other needs to be changed "// & + errMsg(sourcefile, __LINE__)) + end if this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 @@ -931,6 +940,12 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & units='m3/m3', & interpinic_flag='interp', readvar=readvar, data=this%exice_vol_tot_col) + if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (nsrest == nsrContinue) then + call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & + errMsg(sourcefile, __LINE__)) + end if + end if endif end subroutine RestartBulk diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 7630c1f763..944a6bfc85 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -590,8 +590,9 @@ subroutine Restart(this, bounds, ncid, flag, & use landunit_varcon , only : istcrop, istdlak, istsoil use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall use clm_time_manager , only : is_first_step, is_restart - use clm_varctl , only : bound_h2osoi + use clm_varctl , only : bound_h2osoi, nsrest, nsrContinue use ncdio_pio , only : file_desc_t, ncd_double + use ExcessIceStreamType, only : UseExcessIceStreams use restUtilMod ! ! !ARGUMENTS: @@ -713,6 +714,14 @@ subroutine Restart(this, bounds, ncid, flag, & units='kg/m2', scale_by_thickness=.true., & interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (nsrest == nsrContinue) then + call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & + errMsg(sourcefile, __LINE__)) + else if ( .not. UseExcessIceStreams() )then + call endrun(msg = "This input initial conditions file does NOT include excess ice fields" // & + ", and use_excess_ice_streams is off, one or the other needs to be changed "// & + errMsg(sourcefile, __LINE__)) + end if if (masterproc) then write(iulog,*) 'Excess ice data is read from the stream and not from restart file!' endif From 6d2515f212a91f19e2ee7f287a4a946667707a0f Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 28 Nov 2022 20:03:26 -0700 Subject: [PATCH 0488/2067] Updated fates parameter file location --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6f693e2af0..50f33ffcbb 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -491,7 +491,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221019.nc +lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221128.nc From 19e39b8ba41c1e2c7337100eaf6f340e1f692f98 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 29 Nov 2022 16:50:32 -0700 Subject: [PATCH 0489/2067] Fixed test variable list and fixed interface to fates history for dynamics --- cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 2 +- .../testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm | 2 +- src/utils/clmfates_interfaceMod.F90 | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 59b639fa84..2a915f2fd7 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -15,7 +15,7 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_FUEL_AMOUNT', 'FATES_LITTER_IN', 'FATES_LITTER_OUT', 'FATES_SEED_BANK', 'FATES_SEEDS_IN', 'FATES_STOREC', 'FATES_VEGC', 'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC', -'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', +'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR', 'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', 'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE', diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm index b7d33c87d2..0a0726dcce 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdDefAllVars/user_nl_clm @@ -70,4 +70,4 @@ hist_fincl1 = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF', 'FATES_CROOTMAINTAR_USTORY_SZ', 'FATES_FROOTMAINTAR_USTORY_SZ', 'FATES_GROWAR_USTORY_SZ', 'FATES_MAINTAR_USTORY_SZ', 'FATES_VEGC_SZPF', 'FATES_LEAFC_SZPF', 'FATES_FROOTC_SZPF', 'FATES_SAPWOODC_SZPF', -'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF', 'FATES_CEFFLUX_SZPF' +'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF' diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 16a5f0fd7f..3f55959f16 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1841,7 +1841,7 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & call fates_hist%update_history_dyn( nc, & this%fates(nc)%nsites, & this%fates(nc)%sites, & - this%fates(nc)%bc_in(s)) + this%fates(nc)%bc_in) From ed9762d44cbd0ebc095741a6b54b2aa565180777 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 30 Nov 2022 08:25:31 -0700 Subject: [PATCH 0490/2067] removed cefflux from fates hist list --- cime_config/usermods_dirs/fates_sp/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm index cc3d9339e8..f2f68eb74c 100644 --- a/cime_config/usermods_dirs/fates_sp/user_nl_clm +++ b/cime_config/usermods_dirs/fates_sp/user_nl_clm @@ -18,7 +18,7 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FA 'FATES_FUEL_AMOUNT_AP', 'FATES_FUEL_BURNT_BURNFRAC_FC', 'FATES_LITTER_IN', 'FATES_LITTER_OUT', 'FATES_SEED_BANK', 'FATES_SEEDS_IN', 'FATES_LITTER_IN_EL', 'FATES_LITTER_OUT_EL', 'FATES_SEED_BANK_EL', 'FATES_SEEDS_IN_LOCAL_EL', 'FATES_SEEDS_IN_EXTERN_EL', 'FATES_SEED_GERM_EL', 'FATES_SEED_DECAY_EL', 'FATES_STOREC', 'FATES_VEGC', - 'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_CEFFLUX', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', + 'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR', 'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', 'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL', From 48bcbfc1b041fa6c95cd0a793ea64cc9975bf06e Mon Sep 17 00:00:00 2001 From: olyson Date: Wed, 30 Nov 2022 15:55:09 -0700 Subject: [PATCH 0491/2067] Fix issue #1864 --- .../CLM50_Tech_Note_Plant_Hydraulics.rst | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst index f33a6d96b5..2d8843510a 100644 --- a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst +++ b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst @@ -376,22 +376,23 @@ from the characteristic root spacing (section :numref:`Root Spacing`). .. math:: :label: 11.109 - q_{3,i}=k_{3,i} \cdot RAI \cdot \left(\psi_{soil,i}-\psi_{root} + \Delta\psi_{z,i} \right) + q_{3,i}=k_{3,i} \cdot \left(\psi_{soil,i}-\psi_{root} + \Delta\psi_{z,i} \right) .. math:: :label: 11.110 - RAI=\left(LAI+SAI \right) \cdot r_i \cdot f_{root-leaf} + k_{3,i}=\dfrac{k_{r,i} \cdot k_{s,i}}{k_{r,i}+k_{s,i}} .. math:: :label: 11.111 - k_{3,i}=\dfrac{k_{r,i} \cdot k_{s,i}}{k_{r,i}+k_{s,i}} + k_{r,i}=\dfrac{k_{3,max}}{z_{3,i}} \cdot RAI \cdot 2^{-\left(\dfrac{\psi_{soil,i}}{p50_3}\right)^{c_k}} .. math:: :label: 11.112 - k_{r,i}=\dfrac{k_{3,max}}{z_{3,i}} \cdot 2^{-\left(\dfrac{\psi_{soil,i}}{p50_3}\right)^{c_k}} + RAI=\left(LAI+SAI \right) \cdot r_i \cdot f_{root-leaf} + .. math:: :label: 11.113 From 757d22a823e347b97d463c2f9d62d93c6d993b1a Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 1 Dec 2022 07:33:08 -0700 Subject: [PATCH 0492/2067] Updated fates prt2 testdefs --- .../testmods_dirs/clm/FatesColdPRT2/user_nl_clm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm index bde61cee2e..37ba2f814d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm @@ -1 +1,12 @@ -fates_parteh_mode = 2 \ No newline at end of file +fates_parteh_mode = 2 +hist_fincl1 = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_REC_PF', +'FATES_NH4UPTAKE_SZPF','FATES_NO3UPTAKE_SZPF','FATES_NEFFLUX_SZPF', +'FATES_NDEMAND_SZPF','FATES_NFIX_SYM_SZPF','FATES_NH4UPTAKE','FATES_NO3UPTAKE', +'FATES_NEFFLUX','FATES_NDEMAND','FATES_NFIX_SYM','FATES_STOREN','FATES_STOREN_TF', +'FATES_VEGN','FATES_SAPWOODN','FATES_LEAFN','FATES_FROOTN','FATES_REPRON','FATES_VEGN_SZPF', +'FATES_LEAFN_SZPF','FATES_FROOTN_SZPF','FATES_SAPWOODN_SZPF','FATES_STOREN_SZPF','FATES_STOREN_TF_CANOPY_SZPF', +'FATES_STOREN_TF_USTORY_SZPF','FATES_REPRON_SZPF','FATES_STOREP','FATES_STOREP_TF','FATES_VEGP','FATES_SAPWOODP', +'FATES_LEAFP','FATES_FROOTP','FATES_REPROP','FATES_PUPTAKE','FATES_PEFFLUX','FATES_PDEMAND', +'FATES_VEGP_SZPF','FATES_LEAFP_SZPF','FATES_FROOTP_SZPF','FATES_SAPWOODP_SZPF','FATES_STOREP_SZPF', +'FATES_STOREP_TF_CANOPY_SZPF','FATES_STOREP_TF_USTORY_SZPF','FATES_REPROP_SZPF','FATES_PUPTAKE_SZPF', +'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF' \ No newline at end of file From 03ff5a20c5b48a18af58fbd18c442434aa83390c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 2 Dec 2022 10:11:36 -0700 Subject: [PATCH 0493/2067] Add a check for issue 1787 about excess ice fields, if they aren't on the IC file abort with an error, and I showed this works --- src/biogeophys/WaterDiagnosticBulkType.F90 | 58 +++++++++++++++++++++- 1 file changed, 56 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 3ecae66b28..df8ba553a3 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -100,6 +100,7 @@ module WaterDiagnosticBulkType procedure, private :: InitBulkHistory procedure, private :: InitBulkCold procedure, private :: RestartBackcompatIssue783 + procedure, private :: RestartExcessIceIssue1787 end type waterdiagnosticbulk_type @@ -785,6 +786,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil ! ! !LOCAL VARIABLES: logical :: readvar + logical :: excess_ice_on_restart !------------------------------------------------------------------------ @@ -915,13 +917,18 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil ! initialization of these to zero is ok, since they might not be in the restart file this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + call this%RestartExcessIceIssue1787( & + ncid = ncid, & + flag = flag, & + writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & + excess_ice_on_restart = excess_ice_on_restart) ! have to at least define them call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('SUBSIDENCE'), & dim1name='column', xtype=ncd_double, & long_name=this%info%lname('vertically summed volumetric excess ice concentration (veg landunits only)'), & units='m', & interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) - if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (flag == 'read' .and. ((.not. readvar) .or. (.not. excess_ice_on_restart)) ) then ! when reading restart that does not have excess ice in it if (nsrest == nsrContinue) then call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & errMsg(sourcefile, __LINE__)) @@ -940,7 +947,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & units='m3/m3', & interpinic_flag='interp', readvar=readvar, data=this%exice_vol_tot_col) - if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (flag == 'read' .and. ((.not. readvar) .or. (.not. excess_ice_on_restart)) ) then ! when reading restart that does not have excess ice in it if (nsrest == nsrContinue) then call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & errMsg(sourcefile, __LINE__)) @@ -1041,6 +1048,53 @@ subroutine RestartBackcompatIssue783(this, bounds, ncid, flag, & end subroutine RestartBackcompatIssue783 + !----------------------------------------------------------------------- + subroutine RestartExcessIceIssue1787(this, ncid, flag, & + writing_finidat_interp_dest_file, excess_ice_on_restart) + ! + ! !DESCRIPTION: + ! + ! !USES: + use ncdio_pio , only : file_desc_t + use IssueFixedMetadataHandler, only : write_issue_fixed_metadata, read_issue_fixed_metadata + use clm_time_manager , only : is_restart + ! + ! !ARGUMENTS: + class(waterdiagnosticbulk_type), intent(inout) :: this + type(file_desc_t), intent(inout) :: ncid ! netcdf id + character(len=*) , intent(in) :: flag ! 'read' or 'write' + logical, intent(in) :: writing_finidat_interp_dest_file ! true if this is a finidat_interp_dest file + logical, intent(out) :: excess_ice_on_restart ! If excess ice is on the restart file + ! + ! !LOCAL VARIABLES: + integer :: attribute_value + + integer, parameter :: issue_num = 1787 + + character(len=*), parameter :: subname = 'RestartExcessIceISsue1787' + !----------------------------------------------------------------------- + + if (flag == 'define') then + call write_issue_fixed_metadata( & + ncid = ncid, & + writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & + issue_num = issue_num) + + else if (flag == 'read' .and. .not. is_restart()) then + call read_issue_fixed_metadata( & + ncid = ncid, & + issue_num = issue_num, & + attribute_value = attribute_value) + if (attribute_value == 0) then + excess_ice_on_restart = .false. + else + excess_ice_on_restart = .true. + end if + + end if + + end subroutine RestartExcessIceIssue1787 + !----------------------------------------------------------------------- subroutine Summary(this, bounds, & num_soilp, filter_soilp, & From 9aadaab9bd0b9b5e9f69fa44b7961c21043a4fca Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 2 Dec 2022 15:40:15 -0700 Subject: [PATCH 0494/2067] Added new line character to end of user_nl_clm in prt2 testdef --- .../testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm index 37ba2f814d..679f025b60 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdPRT2/user_nl_clm @@ -9,4 +9,4 @@ hist_fincl1 = 'FATES_L2FR','FATES_L2FR_CANOPY_REC_PF','FATES_L2FR_USTORY_R 'FATES_LEAFP','FATES_FROOTP','FATES_REPROP','FATES_PUPTAKE','FATES_PEFFLUX','FATES_PDEMAND', 'FATES_VEGP_SZPF','FATES_LEAFP_SZPF','FATES_FROOTP_SZPF','FATES_SAPWOODP_SZPF','FATES_STOREP_SZPF', 'FATES_STOREP_TF_CANOPY_SZPF','FATES_STOREP_TF_USTORY_SZPF','FATES_REPROP_SZPF','FATES_PUPTAKE_SZPF', -'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF' \ No newline at end of file +'FATES_PEFFLUX_SZPF','FATES_PDEMAND_SZPF' From 43974b24b360e495da8678b0a47d52f25c5d8e96 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 2 Dec 2022 16:06:28 -0700 Subject: [PATCH 0495/2067] Updated change-log --- doc/ChangeLog | 77 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 78 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5f16bf5634..49f49c235f 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,81 @@ =============================================================== +Tag name: ctsm5.1.dev115 +Originator(s): rgknox (Ryan Knox) +Date: Fri Dec 2 15:45:32 MST 2022 +One-line Summary: API compatability with FATES V2 nutrient dynamics + +Purpose and description of changes +---------------------------------- + +This set of changes allows CTSM to continue API compatability with changes to the FATES API. FATES has updated its nutrient dynamics routine, and required a modification to the test environment, some minor updates to variable dimensions in the history, and a call to a new FATES history routine. Implicitly, the updating of the FATES tag introduces new content in the FATES model since the last API update (mostly bug fixes). + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + + +The changes here will only affect FATES simulations. Any FATES simulation will be affected. Carbon-only FATES simulations will not have qualitatively different results since the last API update (but will have bit-for-bit differences). Nutrient enabled FATES simulations (not fully coupled to CLM, only via prognosed plant N,P boundaries), and FATES-Hydro simulations (bug fix) will be different. + +Bugs fixed or introduced +------------------------ + +See the descriptions in FATES tags between sci.1.57.4_api.24.0.0 to sci.1.60.0_api.25.0.0 for details on FATES changes in this tag. + +CTSM issues fixed (include CTSM Issue #): None + +Externals issues fixed (include issue #): None + +Known bugs introduced in this tag (include issue #): None + +Known bugs found since the previous tag (include issue #): None + + +Notes of particular relevance for users +--------------------------------------- + +This set of changes comes with an updated FATES parameter file. This includes format changes only. No changes to variable values were introduced. Format changes are relegated to new parameters and/or name changes only. These changes are encapsulated in: fates/parameter_files/archive/apichange_24.2to25.xml + + +Notes of particular relevance for developers: +--------------------------------------------- + +Nothing of note regarding changes for developers. + +Changes to tests or testing: New history variables were added to the FATES PRT2 user_nl_clm. + + +Testing summary: +---------------- + +regular + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- nominal: /glade/scratch/rgknox/tests_1201-121507ch + izumi ------- nominal: /scratch/cluster/rgknox/tests_1201-122133iz + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- nominal against ctsm5.1_dev112 /glade/scratch/rgknox/tests_1130-082657ch + izumi ------- NA + +Answer changes +-------------- + +Changes answers relative to baseline: FATES answers changed relative to base. Explanation already provided (nutrient and hydro changes are qualitative). + + +Other details +------------- + +FATES external was updated. + +Pull Requests that document the changes (include PR ids): + +https://github.com/ESCOMP/CTSM/pull/1874 +https://github.com/NGEET/fates/pull/880 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev114 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)/@wwieder/@olyson/@ka7eh Date: Sat Nov 19 18:11:15 MST 2022 diff --git a/doc/ChangeSum b/doc/ChangeSum index 772545d00c..1d42a3522d 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev115 rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics ctsm5.1.dev114 multiple 11/19/2022 Some NEON updates fixing AG sites, update MOSART, small fixes ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements ctsm5.1.dev112 multiple 10/15/2022 Rework fates test definitions and add new fates tests From 128eb553419f94c56da03a449e26eb0f130e915e Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 2 Dec 2022 16:13:04 -0700 Subject: [PATCH 0496/2067] Updated fates external pointer to sci.1.61.0_api.25.0.0 --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 1761ceffcc..219d1a9704 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -branch = cnp-dynamic-root-allom-dfdd-api21-symfix +repo_url = https://github.com/NGEET/fates +tag = sci.1.61.0_api.25.0.0 required = True [externals_description] From 8dd3a2c7c855542ec4bd0517bba874ba65b6d9a9 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 2 Dec 2022 16:15:35 -0700 Subject: [PATCH 0497/2067] Whitespace fix to clmfates_interfaceMod.F90 --- src/utils/clmfates_interfaceMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 3f55959f16..c169d710ef 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1015,7 +1015,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call fates_hist%flush_hvars(nc,upfreq_in=1) call fates_hist%flush_hvars(nc,upfreq_in=5) - ! --------------------------------------------------------------------------------- ! Part II: Call the FATES model now that input boundary conditions have been From ca96f76e5cd80bc64d5519e262031d98b4c3974a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 4 Dec 2022 18:34:23 -0700 Subject: [PATCH 0498/2067] Move RestartExcessIceIssu to restartUtils so that it can be used by more than one restart subroutine in different modules --- src/biogeophys/WaterDiagnosticBulkType.F90 | 50 +-------------------- src/main/restFileMod.F90 | 5 +++ src/utils/restUtilMod.F90.in | 51 ++++++++++++++++++++++ 3 files changed, 57 insertions(+), 49 deletions(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index df8ba553a3..fdbbcec566 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -100,7 +100,6 @@ module WaterDiagnosticBulkType procedure, private :: InitBulkHistory procedure, private :: InitBulkCold procedure, private :: RestartBackcompatIssue783 - procedure, private :: RestartExcessIceIssue1787 end type waterdiagnosticbulk_type @@ -917,7 +916,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil ! initialization of these to zero is ok, since they might not be in the restart file this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - call this%RestartExcessIceIssue1787( & + call RestartExcessIceIssue( & ncid = ncid, & flag = flag, & writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & @@ -1048,53 +1047,6 @@ subroutine RestartBackcompatIssue783(this, bounds, ncid, flag, & end subroutine RestartBackcompatIssue783 - !----------------------------------------------------------------------- - subroutine RestartExcessIceIssue1787(this, ncid, flag, & - writing_finidat_interp_dest_file, excess_ice_on_restart) - ! - ! !DESCRIPTION: - ! - ! !USES: - use ncdio_pio , only : file_desc_t - use IssueFixedMetadataHandler, only : write_issue_fixed_metadata, read_issue_fixed_metadata - use clm_time_manager , only : is_restart - ! - ! !ARGUMENTS: - class(waterdiagnosticbulk_type), intent(inout) :: this - type(file_desc_t), intent(inout) :: ncid ! netcdf id - character(len=*) , intent(in) :: flag ! 'read' or 'write' - logical, intent(in) :: writing_finidat_interp_dest_file ! true if this is a finidat_interp_dest file - logical, intent(out) :: excess_ice_on_restart ! If excess ice is on the restart file - ! - ! !LOCAL VARIABLES: - integer :: attribute_value - - integer, parameter :: issue_num = 1787 - - character(len=*), parameter :: subname = 'RestartExcessIceISsue1787' - !----------------------------------------------------------------------- - - if (flag == 'define') then - call write_issue_fixed_metadata( & - ncid = ncid, & - writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & - issue_num = issue_num) - - else if (flag == 'read' .and. .not. is_restart()) then - call read_issue_fixed_metadata( & - ncid = ncid, & - issue_num = issue_num, & - attribute_value = attribute_value) - if (attribute_value == 0) then - excess_ice_on_restart = .false. - else - excess_ice_on_restart = .true. - end if - - end if - - end subroutine RestartExcessIceIssue1787 - !----------------------------------------------------------------------- subroutine Summary(this, bounds, & num_soilp, filter_soilp, & diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90 index f0b2b4fb01..720fd5a092 100644 --- a/src/main/restFileMod.F90 +++ b/src/main/restFileMod.F90 @@ -62,6 +62,7 @@ module restFileMod ! Issue numbers for issue-fixed metadata integer, parameter :: lake_dynbal_baseline_issue = 1140 + integer, parameter :: excess_ice_issue = 1787 character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -604,6 +605,10 @@ subroutine restFile_write_issues_fixed(ncid, writing_finidat_interp_dest_file) ncid = ncid, & writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & issue_num = lake_dynbal_baseline_issue) + call write_issue_fixed_metadata( & + ncid = ncid, & + writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & + issue_num = excess_ice_issue) end subroutine restFile_write_issues_fixed diff --git a/src/utils/restUtilMod.F90.in b/src/utils/restUtilMod.F90.in index 4271271097..da22ea2d60 100644 --- a/src/utils/restUtilMod.F90.in +++ b/src/utils/restUtilMod.F90.in @@ -88,6 +88,8 @@ module restUtilMod end interface set_missing_vals_to_constant public :: set_missing_vals_to_constant + public :: RestartExcessIceIssue + private :: missing_field_possibly_abort private :: write_interpinic_flag @@ -740,5 +742,54 @@ contains end subroutine write_interpinic_flag + !----------------------------------------------------------------------- + subroutine RestartExcessIceIssue(ncid, flag, & + writing_finidat_interp_dest_file, excess_ice_on_restart) + ! + ! !DESCRIPTION: + ! Is excess ice on the originating restart file? This is important to have + ! because the init_interp process copies the cold-start values to the + ! interpolated file if they aren't there, and we need to know if good values + ! exist on the originating restart file. + ! + ! !USES: + use ncdio_pio , only : file_desc_t + use IssueFixedMetadataHandler, only : write_issue_fixed_metadata, read_issue_fixed_metadata + use clm_time_manager , only : is_restart + ! + ! !ARGUMENTS: + type(file_desc_t), intent(inout) :: ncid ! netcdf id + character(len=*) , intent(in) :: flag ! 'read' or 'write' + logical, intent(in) :: writing_finidat_interp_dest_file ! true if this is a finidat_interp_dest file + logical, intent(out) :: excess_ice_on_restart ! If excess ice is on the restart file + ! + ! !LOCAL VARIABLES: + integer :: attribute_value + integer, parameter :: excess_ice_issue = 1787 + + + character(len=*), parameter :: subname = 'RestartExcessIceIssue' + !----------------------------------------------------------------------- + + if (flag == 'define') then + call write_issue_fixed_metadata( & + ncid = ncid, & + writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & + issue_num = excess_ice_issue) + + else if (flag == 'read' .and. .not. is_restart()) then + call read_issue_fixed_metadata( & + ncid = ncid, & + issue_num = excess_ice_issue, & + attribute_value = attribute_value) + if (attribute_value == 0) then + excess_ice_on_restart = .false. + else + excess_ice_on_restart = .true. + end if + + end if + + end subroutine RestartExcessIceIssue end module restUtilMod From 0e09dd4264d241ca25aff6d7951e008cd6cca6a2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 4 Dec 2022 18:37:54 -0700 Subject: [PATCH 0499/2067] Only write excess ice issue to restart metadata if excess ice is on --- src/main/restFileMod.F90 | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90 index 720fd5a092..f3f4354650 100644 --- a/src/main/restFileMod.F90 +++ b/src/main/restFileMod.F90 @@ -591,6 +591,8 @@ subroutine restFile_write_issues_fixed(ncid, writing_finidat_interp_dest_file) ! !DESCRIPTION: ! Write metadata for issues fixed ! + ! !USES: + use clm_varctl, only : use_excess_ice ! !ARGUMENTS: type(file_desc_t), intent(inout) :: ncid ! local file id logical , intent(in) :: writing_finidat_interp_dest_file ! true if we are writing a finidat_interp_dest file @@ -605,10 +607,13 @@ subroutine restFile_write_issues_fixed(ncid, writing_finidat_interp_dest_file) ncid = ncid, & writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & issue_num = lake_dynbal_baseline_issue) - call write_issue_fixed_metadata( & - ncid = ncid, & - writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & - issue_num = excess_ice_issue) + ! If running with execess ice then mark the restart file as having excess ice fixed + if ( use_excess_ice ) then + call write_issue_fixed_metadata( & + ncid = ncid, & + writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & + issue_num = excess_ice_issue) + end if end subroutine restFile_write_issues_fixed From b2d469b1d1e51ea4655d89c9dfb37bb18b99197d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 4 Dec 2022 19:51:38 -0700 Subject: [PATCH 0500/2067] Add RestartExcessIceIssue in WaterStateType and send down the logical about writing finidat file --- src/biogeophys/WaterStateBulkType.F90 | 3 +++ src/biogeophys/WaterStateType.F90 | 10 +++++++++- src/biogeophys/WaterType.F90 | 2 ++ 3 files changed, 14 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index ba3f0513c5..1326d64a33 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -188,6 +188,7 @@ end subroutine InitBulkCold !------------------------------------------------------------------------ subroutine RestartBulk(this, bounds, ncid, flag, & + writing_finidat_interp_dest_file, & watsat_col, t_soisno_col, altmax_lastyear_indx) ! ! !DESCRIPTION: @@ -202,6 +203,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, & type(bounds_type), intent(in) :: bounds type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' + logical , intent(in) :: writing_finidat_interp_dest_file ! true if we are writing a finidat_interp_dest file (ignored for flag=='read') real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year @@ -214,6 +216,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, & SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) call this%restart (bounds, ncid, flag=flag, & + writing_finidat_interp_dest_file=writing_finidat_interp_dest_file, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 944a6bfc85..243214132d 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -580,6 +580,7 @@ end subroutine InitCold !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag, & + writing_finidat_interp_dest_file, & watsat_col, t_soisno_col, altmax_lastyear_indx) ! ! !DESCRIPTION: @@ -603,6 +604,7 @@ subroutine Restart(this, bounds, ncid, flag, & real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year + logical , intent(in) :: writing_finidat_interp_dest_file ! true if we are writing a finidat_interp_dest file (ignored for flag=='read') ! ! !LOCAL VARIABLES: integer :: p,c,l,j,nlevs,nbedrock @@ -610,6 +612,7 @@ subroutine Restart(this, bounds, ncid, flag, & real(r8) :: maxwatsat ! maximum porosity real(r8) :: excess ! excess volumetric soil water real(r8) :: totwat ! total soil water (mm) + logical :: excess_ice_on_restart ! Excess ice fields are on the restart file !------------------------------------------------------------------------ SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) @@ -707,13 +710,18 @@ subroutine Restart(this, bounds, ncid, flag, & ! no need to even define the restart vars this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 else + call RestartExcessIceIssue( & + ncid = ncid, & + flag = flag, & + writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & + excess_ice_on_restart = excess_ice_on_restart) ! have to at least define them call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & dim1name='column', dim2name='levtot', switchdim=.true., & long_name=this%info%lname('excess soil ice (vegetated landunits only)'), & units='kg/m2', scale_by_thickness=.true., & interpinic_flag='interp', readvar=readvar, data=this%excess_ice_col) - if (flag == 'read' .and. (.not. readvar)) then ! when reading restart that does not have excess ice in it + if (flag == 'read' .and. ((.not. readvar) .or. (.not. excess_ice_on_restart)) ) then ! when reading restart that does not have excess ice in it if (nsrest == nsrContinue) then call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & errMsg(sourcefile, __LINE__)) diff --git a/src/biogeophys/WaterType.F90 b/src/biogeophys/WaterType.F90 index bc257f27ad..24cf85d49f 100644 --- a/src/biogeophys/WaterType.F90 +++ b/src/biogeophys/WaterType.F90 @@ -750,6 +750,7 @@ subroutine Restart(this, bounds, ncid, flag, writing_finidat_interp_dest_file, & call this%waterfluxbulk_inst%restartBulk (bounds, ncid, flag=flag) call this%waterstatebulk_inst%restartBulk (bounds, ncid, flag=flag, & + writing_finidat_interp_dest_file=writing_finidat_interp_dest_file, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) @@ -763,6 +764,7 @@ subroutine Restart(this, bounds, ncid, flag, writing_finidat_interp_dest_file, & call this%bulk_and_tracers(i)%waterflux_inst%Restart(bounds, ncid, flag=flag) call this%bulk_and_tracers(i)%waterstate_inst%Restart(bounds, ncid, flag=flag, & + writing_finidat_interp_dest_file=writing_finidat_interp_dest_file, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) From 212e10476a64911da1ca9dff9f1a172515c4707a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 5 Dec 2022 12:26:03 -0700 Subject: [PATCH 0501/2067] Prevent nbedrock from being used before it's set --- src/biogeophys/WaterStateType.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 243214132d..7ada7b8cb2 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -367,7 +367,7 @@ subroutine InitCold(this, bounds, & if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then nlevs = nlevgrnd do j = 1, nlevs - if (use_bedrock) then + if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then nbedrock = col%nbedrock(c) else nbedrock = nlevsoi @@ -549,7 +549,7 @@ subroutine InitCold(this, bounds, & else n05m=nlevsoi-1 endif - if (use_bedrock .and. nbedrock<=nlevsoi) then + if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then nbedrock = col%nbedrock(c) else nbedrock = nlevsoi @@ -737,7 +737,7 @@ subroutine Restart(this, bounds, ncid, flag, & l = col%landunit(c) if (.not. lun%lakpoi(l)) then !not lake if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (use_bedrock .and. nbedrock<=nlevsoi) then + if (use_bedrock .and. col%nbedrock(c)>nlevsoi) then nbedrock = col%nbedrock(c) else nbedrock = nlevsoi From 9432c90493c381e6d6b57bfd26eaae7b96507e71 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 5 Dec 2022 13:36:52 -0700 Subject: [PATCH 0502/2067] Handle InitCold for excess ice when excess ice streams are off --- src/biogeophys/WaterStateType.F90 | 68 +++++++++++++++++-------------- 1 file changed, 37 insertions(+), 31 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 7ada7b8cb2..0b628e5678 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -23,7 +23,7 @@ module WaterStateType use WaterInfoBaseType, only : water_info_base_type use WaterTracerContainerType, only : water_tracer_container_type use WaterTracerUtils, only : AllocateVar1d, AllocateVar2d - use ExcessIceStreamType, only : excessicestream_type + use ExcessIceStreamType, only : excessicestream_type, UseExcessIceStreams ! implicit none save @@ -538,38 +538,44 @@ subroutine InitCold(this, bounds, & this%excess_ice_col(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)=0.0_r8 this%exice_bulk_init(bounds%begc:bounds%endc)=0.0_r8 call this%exicestream%Init(bounds, NLFilename) ! get initial fraction of excess ice per column - call this%exicestream%CalcExcessIce(bounds, this%exice_bulk_init) - do c = bounds%begc,bounds%endc - g = col%gridcell(c) - l = col%landunit(c) - if (.not. lun%lakpoi(l)) then !not lake - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (zisoi(nlevsoi) >= 0.5_r8) then - call find_soil_layer_containing_depth(0.5_r8,n05m) - else - n05m=nlevsoi-1 - endif - if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then - nbedrock = col%nbedrock(c) - else - nbedrock = nlevsoi - endif - do j = 2, nlevmaxurbgrnd ! ignore first layer - if (n05m= n05m .and. j= 0.5_r8) then + call find_soil_layer_containing_depth(0.5_r8,n05m) + else + n05m=nlevsoi-1 + endif + if (use_bedrock .and. col%nbedrock(c) <=nlevsoi) then + nbedrock = col%nbedrock(c) + else + nbedrock = nlevsoi + endif + do j = 2, nlevmaxurbgrnd ! ignore first layer + if (n05m= n05m .and. j Date: Mon, 5 Dec 2022 15:55:58 -0700 Subject: [PATCH 0503/2067] Don't do the write in ExcessIceRestart so writing_finidat_interp_dest_file doesn't need to be passed as many places --- src/biogeophys/WaterDiagnosticBulkType.F90 | 1 - src/biogeophys/WaterStateBulkType.F90 | 3 --- src/biogeophys/WaterStateType.F90 | 3 --- src/biogeophys/WaterType.F90 | 2 -- 4 files changed, 9 deletions(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index fdbbcec566..98e5e9532c 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -919,7 +919,6 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil call RestartExcessIceIssue( & ncid = ncid, & flag = flag, & - writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & excess_ice_on_restart = excess_ice_on_restart) ! have to at least define them call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('SUBSIDENCE'), & diff --git a/src/biogeophys/WaterStateBulkType.F90 b/src/biogeophys/WaterStateBulkType.F90 index 1326d64a33..ba3f0513c5 100644 --- a/src/biogeophys/WaterStateBulkType.F90 +++ b/src/biogeophys/WaterStateBulkType.F90 @@ -188,7 +188,6 @@ end subroutine InitBulkCold !------------------------------------------------------------------------ subroutine RestartBulk(this, bounds, ncid, flag, & - writing_finidat_interp_dest_file, & watsat_col, t_soisno_col, altmax_lastyear_indx) ! ! !DESCRIPTION: @@ -203,7 +202,6 @@ subroutine RestartBulk(this, bounds, ncid, flag, & type(bounds_type), intent(in) :: bounds type(file_desc_t), intent(inout) :: ncid ! netcdf id character(len=*) , intent(in) :: flag ! 'read' or 'write' - logical , intent(in) :: writing_finidat_interp_dest_file ! true if we are writing a finidat_interp_dest file (ignored for flag=='read') real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year @@ -216,7 +214,6 @@ subroutine RestartBulk(this, bounds, ncid, flag, & SHR_ASSERT_ALL_FL((ubound(watsat_col) == (/bounds%endc,nlevmaxurbgrnd/)) , sourcefile, __LINE__) call this%restart (bounds, ncid, flag=flag, & - writing_finidat_interp_dest_file=writing_finidat_interp_dest_file, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 0b628e5678..457f238de2 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -586,7 +586,6 @@ end subroutine InitCold !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag, & - writing_finidat_interp_dest_file, & watsat_col, t_soisno_col, altmax_lastyear_indx) ! ! !DESCRIPTION: @@ -610,7 +609,6 @@ subroutine Restart(this, bounds, ncid, flag, & real(r8) , intent(in) :: watsat_col (bounds%begc:, 1:) ! volumetric soil water at saturation (porosity) real(r8) , intent(in) :: t_soisno_col(bounds%begc:, -nlevsno+1:) ! col soil temperature (Kelvin) integer , intent(in) :: altmax_lastyear_indx(bounds%begc:) !col active layer index last year - logical , intent(in) :: writing_finidat_interp_dest_file ! true if we are writing a finidat_interp_dest file (ignored for flag=='read') ! ! !LOCAL VARIABLES: integer :: p,c,l,j,nlevs,nbedrock @@ -719,7 +717,6 @@ subroutine Restart(this, bounds, ncid, flag, & call RestartExcessIceIssue( & ncid = ncid, & flag = flag, & - writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & excess_ice_on_restart = excess_ice_on_restart) ! have to at least define them call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('EXCESS_ICE'), xtype=ncd_double, & diff --git a/src/biogeophys/WaterType.F90 b/src/biogeophys/WaterType.F90 index 24cf85d49f..bc257f27ad 100644 --- a/src/biogeophys/WaterType.F90 +++ b/src/biogeophys/WaterType.F90 @@ -750,7 +750,6 @@ subroutine Restart(this, bounds, ncid, flag, writing_finidat_interp_dest_file, & call this%waterfluxbulk_inst%restartBulk (bounds, ncid, flag=flag) call this%waterstatebulk_inst%restartBulk (bounds, ncid, flag=flag, & - writing_finidat_interp_dest_file=writing_finidat_interp_dest_file, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) @@ -764,7 +763,6 @@ subroutine Restart(this, bounds, ncid, flag, writing_finidat_interp_dest_file, & call this%bulk_and_tracers(i)%waterflux_inst%Restart(bounds, ncid, flag=flag) call this%bulk_and_tracers(i)%waterstate_inst%Restart(bounds, ncid, flag=flag, & - writing_finidat_interp_dest_file=writing_finidat_interp_dest_file, & watsat_col=watsat_col(bounds%begc:bounds%endc,:), & t_soisno_col=t_soisno_col(bounds%begc:, -nlevsno+1:), & altmax_lastyear_indx=altmax_lastyear_indx(bounds%begc:)) From 0ff6d4dadd53e8022350d5336b0342f98f74d588 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 5 Dec 2022 17:26:46 -0700 Subject: [PATCH 0504/2067] Don't do the write in ExcessIceRestart so writing_finidat_interp_dest_file doesn't need to be passed as many places --- src/utils/restUtilMod.F90.in | 25 +++++++++---------------- 1 file changed, 9 insertions(+), 16 deletions(-) diff --git a/src/utils/restUtilMod.F90.in b/src/utils/restUtilMod.F90.in index da22ea2d60..58da88ed50 100644 --- a/src/utils/restUtilMod.F90.in +++ b/src/utils/restUtilMod.F90.in @@ -743,8 +743,7 @@ contains end subroutine write_interpinic_flag !----------------------------------------------------------------------- - subroutine RestartExcessIceIssue(ncid, flag, & - writing_finidat_interp_dest_file, excess_ice_on_restart) + subroutine RestartExcessIceIssue(ncid, flag, excess_ice_on_restart) ! ! !DESCRIPTION: ! Is excess ice on the originating restart file? This is important to have @@ -753,15 +752,13 @@ contains ! exist on the originating restart file. ! ! !USES: - use ncdio_pio , only : file_desc_t - use IssueFixedMetadataHandler, only : write_issue_fixed_metadata, read_issue_fixed_metadata - use clm_time_manager , only : is_restart + use ncdio_pio , only : file_desc_t + use IssueFixedMetadataHandler, only : read_issue_fixed_metadata ! ! !ARGUMENTS: - type(file_desc_t), intent(inout) :: ncid ! netcdf id - character(len=*) , intent(in) :: flag ! 'read' or 'write' - logical, intent(in) :: writing_finidat_interp_dest_file ! true if this is a finidat_interp_dest file - logical, intent(out) :: excess_ice_on_restart ! If excess ice is on the restart file + type(file_desc_t), intent(inout) :: ncid ! netcdf id + character(len=*) , intent(in) :: flag ! 'read' or 'write' + logical, intent(out) :: excess_ice_on_restart ! If excess ice is on the restart file ! ! !LOCAL VARIABLES: integer :: attribute_value @@ -771,13 +768,9 @@ contains character(len=*), parameter :: subname = 'RestartExcessIceIssue' !----------------------------------------------------------------------- - if (flag == 'define') then - call write_issue_fixed_metadata( & - ncid = ncid, & - writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & - issue_num = excess_ice_issue) - - else if (flag == 'read' .and. .not. is_restart()) then + excess_ice_on_restart = .false. + ! The write of the issue metadata is in restFileMod::: restFile_write_issues_fixed + if (flag == 'read' )then call read_issue_fixed_metadata( & ncid = ncid, & issue_num = excess_ice_issue, & From 2581d079526ede3464cba916f8f6ea65765dd403 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Dec 2022 10:59:56 -0700 Subject: [PATCH 0505/2067] Point to a finidat file that has excess ice on it --- .../testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm index d9e52c6cf9..98fc5ea574 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm @@ -1 +1,2 @@ use_excess_ice = .true. + finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0003-01-01.0.9x1.25_gx1v7_exice_simyr1850_c221205.nc' From d4c4efca4f3c84ddcf20067b8cc28c71f50a7202 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Dec 2022 11:08:54 -0700 Subject: [PATCH 0506/2067] Add an excess ice test to the ctsm_sci list and lengthen the time --- cime_config/testdefs/testlist_clm.xml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 18d6c56f73..201d699847 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -186,10 +186,11 @@ + - + From dcaaf69da84c5a3db4db2aed41c15e20e9810fc6 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 6 Dec 2022 11:48:37 -0700 Subject: [PATCH 0507/2067] Add an output user-mod option for excessice to the yearly file, change testmod names, use startup and output_sp_exice for test mod from a startup file --- cime_config/testdefs/testlist_clm.xml | 4 ++-- .../testmods_dirs/clm/ExcessIceRestart/include_user_mods | 1 - .../ExcessIceStartup_output_sp_exice/include_user_mods | 2 ++ .../user_nl_clm | 0 .../usermods_dirs/output_sp_exice/include_user_mods | 2 ++ cime_config/usermods_dirs/output_sp_exice/user_nl_clm | 8 ++++++++ 6 files changed, 14 insertions(+), 3 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods rename cime_config/testdefs/testmods_dirs/clm/{ExcessIceRestart => ExcessIceStartup_output_sp_exice}/user_nl_clm (100%) create mode 100644 cime_config/usermods_dirs/output_sp_exice/include_user_mods create mode 100644 cime_config/usermods_dirs/output_sp_exice/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 201d699847..bf3e143166 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -182,7 +182,7 @@ - + @@ -191,7 +191,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/include_user_mods deleted file mode 100644 index fe0e18cf88..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../default diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods new file mode 100644 index 0000000000..6d8de3732a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods @@ -0,0 +1,2 @@ +../monthly +../../../../usermods_dirs/output_sp_exice diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/user_nl_clm similarity index 100% rename from cime_config/testdefs/testmods_dirs/clm/ExcessIceRestart/user_nl_clm rename to cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/user_nl_clm diff --git a/cime_config/usermods_dirs/output_sp_exice/include_user_mods b/cime_config/usermods_dirs/output_sp_exice/include_user_mods new file mode 100644 index 0000000000..4b75b772c0 --- /dev/null +++ b/cime_config/usermods_dirs/output_sp_exice/include_user_mods @@ -0,0 +1,2 @@ +../_include/output_base +../output_sp diff --git a/cime_config/usermods_dirs/output_sp_exice/user_nl_clm b/cime_config/usermods_dirs/output_sp_exice/user_nl_clm new file mode 100644 index 0000000000..48e680df67 --- /dev/null +++ b/cime_config/usermods_dirs/output_sp_exice/user_nl_clm @@ -0,0 +1,8 @@ +!---------------------------------------------------------------------------------- +! Settings from output_sp_exice +!---------------------------------------------------------------------------------- + +! h3 stream (yearly average, gridcell-level) +! Eyr +hist_fincl4 += 'EXCESS_ICE' + From b848a7afde03059b2f185b61c9b93bd90ca2f6b9 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 7 Dec 2022 09:30:38 -0700 Subject: [PATCH 0508/2067] Add in needed stubs for unit-testing to work --- src/biogeophys/WaterStateType.F90 | 2 +- src/unit_test_stubs/CMakeLists.txt | 1 + src/unit_test_stubs/share_esmf/CMakeLists.txt | 5 ++ .../share_esmf/ExcessIceStreamType.F90 | 79 +++++++++++++++++++ .../utils/restUtilMod_stub.F90.in | 25 ++++++ 5 files changed, 111 insertions(+), 1 deletion(-) create mode 100644 src/unit_test_stubs/share_esmf/CMakeLists.txt create mode 100644 src/unit_test_stubs/share_esmf/ExcessIceStreamType.F90 diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 457f238de2..3af85650c2 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -599,7 +599,7 @@ subroutine Restart(this, bounds, ncid, flag, & use clm_varctl , only : bound_h2osoi, nsrest, nsrContinue use ncdio_pio , only : file_desc_t, ncd_double use ExcessIceStreamType, only : UseExcessIceStreams - use restUtilMod + use restUtilMod , only : restartvar, RestartExcessIceIssue ! ! !ARGUMENTS: class(waterstate_type), intent(in) :: this diff --git a/src/unit_test_stubs/CMakeLists.txt b/src/unit_test_stubs/CMakeLists.txt index 38abfb1633..2d7fe23378 100644 --- a/src/unit_test_stubs/CMakeLists.txt +++ b/src/unit_test_stubs/CMakeLists.txt @@ -1,6 +1,7 @@ add_subdirectory(csm_share) add_subdirectory(dyn_subgrid) add_subdirectory(main) +add_subdirectory(share_esmf) add_subdirectory(utils) sourcelist_to_parent(clm_sources) diff --git a/src/unit_test_stubs/share_esmf/CMakeLists.txt b/src/unit_test_stubs/share_esmf/CMakeLists.txt new file mode 100644 index 0000000000..5eb2d42415 --- /dev/null +++ b/src/unit_test_stubs/share_esmf/CMakeLists.txt @@ -0,0 +1,5 @@ +list(APPEND clm_sources + ExcessIceStreamType.F90 + ) + +sourcelist_to_parent(clm_sources) diff --git a/src/unit_test_stubs/share_esmf/ExcessIceStreamType.F90 b/src/unit_test_stubs/share_esmf/ExcessIceStreamType.F90 new file mode 100644 index 0000000000..60bac5ad28 --- /dev/null +++ b/src/unit_test_stubs/share_esmf/ExcessIceStreamType.F90 @@ -0,0 +1,79 @@ +module ExcessIceStreamType + + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Stub module for Excess ice streams + ! + ! !USES + use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_cl + use shr_log_mod , only : errMsg => shr_log_errMsg + use abortutils , only : endrun + use decompMod , only : bounds_type + + ! !PUBLIC TYPES: + implicit none + private + + public :: UseExcessIceStreams ! If streams will be used + + type, public :: excessicestream_type + contains + + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Init ! Initialize and read data in + procedure, public :: CalcExcessIce ! Calculate excess ice ammount + end type excessicestream_type + ! ! PRIVATE DATA: + + logical :: namelist_read = .false. + + character(len=*), parameter, private :: sourcefile = & + __FILE__ + +!============================================================================== +contains +!============================================================================== + + subroutine Init(this, bounds, NLFilename) + ! + ! arguments + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + character(len=*), intent(in) :: NLFilename ! Namelist filename + + namelist_read = .true. + + end subroutine Init + + subroutine CalcExcessIce(this,bounds,exice_bulk_init) + + ! only transfers grid values to columns + implicit none + class(excessicestream_type) :: this + type(bounds_type), intent(in) :: bounds + real(r8) , intent(inout) :: exice_bulk_init(bounds%begc:bounds%endc) + ! + ! !LOCAL VARIABLES: + call endrun(msg=' ERROR CalcExcessIce stub is being called and should NOT be'//errMsg(sourcefile, __LINE__)) + + end subroutine CalcExcessIce + + logical function UseExcessIceStreams() + ! + ! !DESCRIPTION: + ! Return true if + ! + ! !USES: + ! + ! !ARGUMENTS: + implicit none + ! + ! !LOCAL VARIABLES: + if ( .not. namelist_read ) then + call endrun(msg=' ERROR UseExcessIceStreams being called, but namelist has not been read yet'//errMsg(sourcefile, __LINE__)) + end if + UseExcessIceStreams = .false. +end function UseExcessIceStreams + +end module ExcessIceStreamType diff --git a/src/unit_test_stubs/utils/restUtilMod_stub.F90.in b/src/unit_test_stubs/utils/restUtilMod_stub.F90.in index b6e3ba4f19..a3a59f842c 100644 --- a/src/unit_test_stubs/utils/restUtilMod_stub.F90.in +++ b/src/unit_test_stubs/utils/restUtilMod_stub.F90.in @@ -21,6 +21,8 @@ module restUtilMod public :: restartvar + public :: RestartExcessIceIssue + public :: set_missing_from_template contains @@ -149,4 +151,27 @@ contains end subroutine set_missing_from_template + !----------------------------------------------------------------------- + subroutine RestartExcessIceIssue(ncid, flag, excess_ice_on_restart) + ! + ! !DESCRIPTION: + ! + ! !USES: + ! + ! !ARGUMENTS: + type(file_desc_t), intent(inout) :: ncid ! netcdf id + character(len=*) , intent(in) :: flag ! 'read' or 'write' + logical, intent(out) :: excess_ice_on_restart ! If excess ice is on the restart file + ! + ! !LOCAL VARIABLES: + integer :: attribute_value + + character(len=*), parameter :: subname = 'RestartExcessIceIssue' + !----------------------------------------------------------------------- + + excess_ice_on_restart = .false. + + end subroutine RestartExcessIceIssue + + end module restUtilMod From f258b5d3a147200bedf8b75993afdbf5f1f01c33 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 7 Dec 2022 10:29:00 -0700 Subject: [PATCH 0509/2067] ERS tests can't be a single day, use the default length --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index bf3e143166..a540807c83 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -168,7 +168,7 @@ - + From 2ae796bb1a2c7a881602c28085b0078c987f50b8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 7 Dec 2022 10:29:19 -0700 Subject: [PATCH 0510/2067] Correct directory name --- cime_config/usermods_dirs/output_sp_exice/include_user_mods | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/output_sp_exice/include_user_mods b/cime_config/usermods_dirs/output_sp_exice/include_user_mods index 4b75b772c0..786fa907a9 100644 --- a/cime_config/usermods_dirs/output_sp_exice/include_user_mods +++ b/cime_config/usermods_dirs/output_sp_exice/include_user_mods @@ -1,2 +1,2 @@ -../_include/output_base +../_includes/output_base ../output_sp From f599275fed106aef57088a8a11b2f928bf17c4c8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 7 Dec 2022 13:28:25 -0700 Subject: [PATCH 0511/2067] Change dimension of local varialbes from nlevgrnd to nlevmaxurbgrnd because of issues the the izumi_nag compiler found --- src/biogeophys/SoilTemperatureMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index f7b970c057..5d84655493 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1128,7 +1128,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: temp1 !temporary variables [kg/m2] real(r8) :: hm(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !energy residual [W/m2] real(r8) :: xm(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !melting or freezing within a time step [kg/m2] - real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !additional melting or freezing within a time step [kg/m2] (needed for excess ice melt) + real(r8) :: xm2(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !additional melting or freezing within a time step [kg/m2] (needed for excess ice melt) real(r8) :: wmass0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of ice and liquid (kg/m2) real(r8) :: wice0 (bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of ice (kg/m2) real(r8) :: wliq0 (bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd)!initial mass of liquid (kg/m2) @@ -1136,7 +1136,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & real(r8) :: propor !proportionality constant (-) real(r8) :: tinc(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !t(n+1)-t(n) [K] real(r8) :: smp !frozen water potential (mm) - real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevgrnd) !initial mass of excess_ice at the timestep (kg/m2) + real(r8) :: wexice0(bounds%begc:bounds%endc,-nlevsno+1:nlevmaxurbgrnd) !initial mass of excess_ice at the timestep (kg/m2) !----------------------------------------------------------------------- From 307ebfb90a02e12da792fec3dc7a65ded96b9ba1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 7 Dec 2022 17:23:04 -0700 Subject: [PATCH 0512/2067] Make note of PGI test for excess ice that fails --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 2656079bf7..a081684acb 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -29,6 +29,13 @@ + + + FAIL + PGI problems with the nuopc driver + + + From 782fc1923e8e050358588937d112cd20f6ed7712 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 7 Dec 2022 21:32:12 -0700 Subject: [PATCH 0513/2067] Only adjust soil depths for excess ice calculations if excess ice is on --- src/biogeophys/SoilTemperatureMod.F90 | 60 ++++++++++++++------------- 1 file changed, 31 insertions(+), 29 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 5d84655493..a49ac9c662 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -114,7 +114,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! !USES: use clm_time_manager , only : get_step_size_real use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevmaxurbgrnd - use clm_varctl , only : iulog + use clm_varctl , only : iulog, use_excess_ice use clm_varcon , only : cnfac, cpice, cpliq, denh2o, denice use landunit_varcon , only : istsoil, istcrop use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv @@ -280,24 +280,24 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter !-------------------------------------------------------------- ! Vertical coordinates adjustment for excess ice calculations !-------------------------------------------------------------- - ! Save original soil depth to get put them back in et the end - dz_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=dz(begc:endc,-nlevsno+1:nlevmaxurbgrnd) - zi_0(begc:endc,-nlevsno+0:nlevmaxurbgrnd)=zi(begc:endc,-nlevsno+0:nlevmaxurbgrnd) - z_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=z(begc:endc,-nlevsno+1:nlevmaxurbgrnd) - ! Adjust column depth for excess ice thickness - do fc = 1,num_nolakec - c = filter_nolakec(fc) - l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then - dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness - do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment - zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice - z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 - end do - endif - end do - - + if ( use_excess_ice )then + ! Save original soil depth to get put them back in et the end + dz_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=dz(begc:endc,-nlevsno+1:nlevmaxurbgrnd) + zi_0(begc:endc,-nlevsno+0:nlevmaxurbgrnd)=zi(begc:endc,-nlevsno+0:nlevmaxurbgrnd) + z_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=z(begc:endc,-nlevsno+1:nlevmaxurbgrnd) + ! Adjust column depth for excess ice thickness + do fc = 1,num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then + dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness + do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment + zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice + z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 + end do + endif + end do + end if !------------------------------------------------------ ! Compute ground surface and soil temperatures @@ -520,16 +520,18 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! Vertical coordinates adjustment for excess ice calculations !-------------------------------------------------------------- ! bringing back the soil depth to the original state - ! Adjust column depth for excess ice thickness - do fc = 1,num_nolakec - c = filter_nolakec(fc) - l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then - dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) - zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) - z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) - endif - end do + if ( use_excess_ice )then + ! Adjust column depth for excess ice thickness + do fc = 1,num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then + dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) + zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) + z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) + endif + end do + end if From bbd90a1689130678cf70e0eba124139b5f96611f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 9 Dec 2022 02:01:32 -0700 Subject: [PATCH 0514/2067] Add setting for initial interpolation for excess ice startup file --- .../clm/ExcessIceStartup_output_sp_exice/user_nl_clm | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/user_nl_clm index 98fc5ea574..e479af9449 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/user_nl_clm @@ -1,2 +1,3 @@ use_excess_ice = .true. finidat = '$DIN_LOC_ROOT/lnd/clm2/initdata_map/clmi.I1850Clm50Sp.0003-01-01.0.9x1.25_gx1v7_exice_simyr1850_c221205.nc' + use_init_interp = .true. From 4be8cc091b5f22f266545be8ce7e48ef114f3ff4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 9 Dec 2022 02:03:03 -0700 Subject: [PATCH 0515/2067] Dimension exice_subs_col as noticed by izumi case --- src/biogeophys/WaterDiagnosticBulkType.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 98e5e9532c..4ec96820b6 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -170,6 +170,7 @@ subroutine InitBulkAllocate(this, bounds) ! ! !USES: use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=) + use clm_varpar , only : nlevmaxurbgrnd ! ! !ARGUMENTS: class(waterdiagnosticbulk_type), intent(inout) :: this @@ -199,7 +200,7 @@ subroutine InitBulkAllocate(this, bounds) allocate(this%h2osoi_liq_tot_col (begc:endc)) ; this%h2osoi_liq_tot_col (:) = nan allocate(this%swe_old_col (begc:endc,-nlevsno+1:0)) ; this%swe_old_col (:,:) = nan allocate(this%exice_subs_tot_col (begc:endc)) ; this%exice_subs_tot_col (:) = 0.0_r8 - allocate(this%exice_subs_col (begc:endc, 1:nlevgrnd)) ; this%exice_subs_col (:,:) = 0.0_r8 + allocate(this%exice_subs_col (begc:endc, 1:nlevmaxurbgrnd)) ; this%exice_subs_col (:,:) = 0.0_r8 allocate(this%exice_vol_col (begc:endc, 1:nlevgrnd)) ; this%exice_vol_col (:,:) = 0.0_r8 allocate(this%exice_vol_tot_col (begc:endc)) ; this%exice_vol_tot_col (:) = 0.0_r8 From 689fb3f1b92fa9d424c9c8b5233d03b557ab944e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 9 Dec 2022 09:55:38 -0700 Subject: [PATCH 0516/2067] Cut back on the excess ice tests --- cime_config/testdefs/testlist_clm.xml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index d6c1a196e3..cb44a75cc8 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -171,11 +171,7 @@ - - - - @@ -184,10 +180,7 @@ - - - From fc2844896f5a2b54ad6f18c13fa806879f9f4f07 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 9 Dec 2022 09:56:32 -0700 Subject: [PATCH 0517/2067] Remove expected fail as removed the PGI excess ice test --- cime_config/testdefs/ExpectedTestFails.xml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 58b3c004ef..52a5828f5d 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -29,14 +29,6 @@ - - - FAIL - PGI problems with the nuopc driver - - - - FAIL From 6a07efb0c3fa9e5670294950072748e42a9d5995 Mon Sep 17 00:00:00 2001 From: mvdebolskiy <80036033+mvdebolskiy@users.noreply.github.com> Date: Sun, 11 Dec 2022 19:07:04 +0100 Subject: [PATCH 0518/2067] initial technote writeup --- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst index 72040a1514..4430c54fa5 100644 --- a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst +++ b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst @@ -979,3 +979,40 @@ the top layer is a blend of ice and soil heat capacity c_{1} =c_{1}^{*} +\frac{C_{ice} W_{sno} }{\Delta z_{1} } where :math:`c_{1}^{*}` is calculated from :eq:`6.89` or :eq:`6.92`. + + +.. _Excess Ground Ice: + +Excess Ground Ice +------------------------------------ + +An optional parameterization of excess ground ice melt and respective subsidence based on (:ref:`Lee et al., (2014) `). +Initial excess ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). +When the excess ice is present in the soil column soil depth for a given layer (:math:`z_{i}`) +is adjusted be the ammount of excess ice in the column: + +.. math:: + :label: 6.94 + + z_{i}^{'}=\Sigma_{j=1}^{i} \ z_{j}^{'}+\frac{w_{exice,\, j}}{\rho_{ice} } + +where :math:`w_{exice,\,j}` is excess ground ice ammount (kg m :sup:`-2`) in layer :math:`j` and :math:`\rho_{ice}` is the density of ice (kg m :sup:`-3`). +After adjustment of layer depths have been made all of the soil temperature equations (from :eq:`6.80` to :eq:`6.89`) +are calculted based on the adjusted depths. Thermal properties are additionally adjusted (:eq:`6.8` and :eq:`6.8`) in the following way: + +.. math:: + :label: 6.95 + + \begin{array}{lr} + \theta_{sat}^{'} =\frac{\theta _{liq} }{\theta _{liq} +\theta _{ice} +\theta_{exice}}{\theta_{sat}} \\ + \lambda _{sat}^{'} =\lambda _{s}^{1-\theta _{sat}^{'} } \lambda _{liq}^{\frac{\theta _{liq} }{\theta _{liq} +\theta _{ice} +\theta_{exice}} \theta _{sat}^{'} } \lambda _{ice}^{\theta _{sat}^{'} \left(1-\frac{\theta _{liq} }{\theta _{liq} +\theta _{ice} +\theta_{exice}} \right)} \\ + c_{i}^{'} =c_{s,\, i} \left(1-\theta _{sat,\, i}^{'} \right)+\frac{w_{ice,\, i} +w_{exice,\,j}}{\Delta z_{i}^{'} } C_{ice} +\frac{w_{liq,\, i} }{\Delta z_{i}^{'} } C_{liq} + \end{array} + +Soil subsidence at the timestep :math:`n+1` (:math:`z_{exice}^{n+1}`, m) is then calculated as: + +.. math:: + :label: 6.96 + + z_{exice}^{n+1}=\Sigma_{i=1}^{N_{levgrnd}} \ z_{j}^{',\ ,n+1}-z_{j}^{',\ ,n} + From c3fd679c311ea1d0145112a5523d7111881fa63b Mon Sep 17 00:00:00 2001 From: mvdebolskiy <80036033+mvdebolskiy@users.noreply.github.com> Date: Sun, 11 Dec 2022 19:07:16 +0100 Subject: [PATCH 0519/2067] added references --- .../References/CLM50_Tech_Note_References.rst | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 4bd7a2cf9b..46b835a76d 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -223,6 +223,13 @@ Geosci. Model Dev., 7, 2193-2222, doi:10.5194/gmd-7-2193-2014. Botta, A et al., 2000. A global prognostic scheme of leaf onset using satellite data. Global Change Biology 6.7, pp. 709-725. +.. _Brownetal1997: + +Brown J., Ferrians O. J. Jr, Heginbottom J. A. and Melnikov E. S. 1997. + Circum-Arctic Map of Permafrost and Ground-Ice Conditions +(Boulder, CO: National Snow and Ice Data Center) version 2, +DOI: 10.3133/cp45 + .. _Brun1989: Brun, E. 1989. Investigation of wet-snow metamorphism in respect of @@ -1085,6 +1092,12 @@ Climate 25:3071-3095. DOI:10.1175/JCLI-D-11-00256.1. Lehner, B. and Döll, P., 2004. Development and validation of a global database of lakes, reservoirs and wetlands, J. Hydrol., 296, 1–22. +.. _Leeetal2014: + +Lee, H., Swenson, S.C., Slater A.G. and Lawrence D.M., 2014. Effects +of excess ground ice on projections of permafrost in a warming climate. +Environmental Research Letters 9:12 124006. DOI: 10.1088/1748-9326/9/12/124006 + .. _Lehneretal2008: Lehner, B., Verdin, K. and Jarvis, A., 2008. New global hydrograhy From cb224da9cd17e1532181621b2db4f2455133ca05 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 12 Dec 2022 16:34:48 -0700 Subject: [PATCH 0520/2067] Convert variable name to snake_case so that pylint passes --- python/ctsm/subset_data.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 6ef1acca85..080c7f3003 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -310,14 +310,14 @@ def get_parser(): default="", ) cesmroot = path_to_ctsm_root() - DEFAULTS_FILE = os.path.join(cesmroot, DEFAULTS_CONFIG) + defaults_file = os.path.join(cesmroot, DEFAULTS_CONFIG) subparser.add_argument( "--file", help="Default configure file to use for default filenames.", action="store", dest="config_file", type=str, - default=DEFAULTS_FILE, + default=defaults_file, ) subparser.add_argument( "--overwrite", From 51318489675196c3b0e904e5f9b3a2d735186b12 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 12 Dec 2022 17:55:13 -0700 Subject: [PATCH 0521/2067] Add a test to fsurdat_modifier sys tester that if you don't give the fsurdat_in/fsurdat_out files it fails --- python/ctsm/test/test_sys_fsurdat_modifier.py | 11 +++++++++++ python/ctsm/test/testinputs/modify_fsurdat_short.cfg | 12 ++++++++++++ .../test/testinputs/modify_fsurdat_short_nofiles.cfg | 9 +++++++++ 3 files changed, 32 insertions(+) create mode 100644 python/ctsm/test/testinputs/modify_fsurdat_short.cfg create mode 100644 python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 6ee00604be..647a37e3db 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -39,6 +39,7 @@ def setUp(self): path_to_ctsm_root(), "tools/modify_input_files/modify_fsurdat_template.cfg" ) testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") + self._testinputs_path = testinputs_path self._fsurdat_in = os.path.join( testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", @@ -53,6 +54,16 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) + def test_no_files_given_fail(self): + """ + Test that if no input or output files are given that it will gracefully fail + """ + self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short_nofiles.cfg") + with self.assertRaisesRegex( + SystemExit, "must contain item 'fsurdat_in'" + ): + fsurdat_modifier(self._cfg_file_path) + def test_minimalInfo(self): """ This test specifies a minimal amount of information diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg new file mode 100644 index 0000000000..b0c94a11f2 --- /dev/null +++ b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg @@ -0,0 +1,12 @@ +[modify_input] + +fsurdat_in = FILL_THIS_IN +fsurdat_out = FILL_THIS_IN + +idealized = False +include_nonveg = False + +lnd_lat_1 = -90 +lnd_lat_2 = 90 +lnd_lon_1 = 0 +lnd_lon_2 = 360 diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg new file mode 100644 index 0000000000..e4ba31912a --- /dev/null +++ b/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg @@ -0,0 +1,9 @@ +[modify_input] + +idealized = False +include_nonveg = False + +lnd_lat_1 = -90 +lnd_lat_2 = 90 +lnd_lon_1 = 0 +lnd_lon_2 = 360 From 4c3339f81ddd4ea4e3dd241efdcde1bfc3775a24 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 12 Dec 2022 18:03:15 -0700 Subject: [PATCH 0522/2067] Add a test for a config file that doesn't exist that fails --- python/ctsm/test/test_sys_fsurdat_modifier.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 647a37e3db..8dad324230 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -64,6 +64,17 @@ def test_no_files_given_fail(self): ): fsurdat_modifier(self._cfg_file_path) + def test_cfg_file_DNE_fail(self): + """ + Test that if the config file does not exist that it gracefully fails + """ + self._cfg_file_path = os.path.join(self._tempdir, "FILE_DOES_NOT_EXIST.cfg" ) + with self.assertRaisesRegex( + SystemExit, "Config file does NOT exist" + ): + fsurdat_modifier(self._cfg_file_path) + + def test_minimalInfo(self): """ This test specifies a minimal amount of information From df5ad3eeb8e42aeb4fdfe45067b638725b7fd761 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 12 Dec 2022 22:11:08 -0700 Subject: [PATCH 0523/2067] Add a check for the config file not existing --- python/ctsm/modify_input_files/fsurdat_modifier.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 7b7abbc646..7750d9eb20 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -45,6 +45,8 @@ def fsurdat_modifier(cfg_path): """Implementation of fsurdat_modifier command""" # read the .cfg (config) file config = ConfigParser() + if not os.path.exists(cfg_path): + abort( "Config file does NOT exist: "+str(cfg_path) ) config.read(cfg_path) section = config.sections()[0] # name of the first section From c08ce1c0cc7e5cedcb992a6aaddf21369bc9bdf8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 13 Dec 2022 00:45:36 -0700 Subject: [PATCH 0524/2067] Add a check for an empty file failing gracefully --- python/ctsm/test/test_sys_fsurdat_modifier.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 8dad324230..5ed0e328fb 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -74,6 +74,17 @@ def test_cfg_file_DNE_fail(self): ): fsurdat_modifier(self._cfg_file_path) + def test_cfg_file_empty_fail(self): + """ + Test that if the config file is empty it gracefully fails + """ + self._cfg_file_path = os.path.join(self._tempdir, "EMPTY_FILE.cfg" ) + fil = open( self._cfg_file_path, "w" ) + fil.close() + with self.assertRaisesRegex( + SystemExit, "Config file does not have the expected section" + ): + fsurdat_modifier(self._cfg_file_path) def test_minimalInfo(self): """ From 0c3a179fc4573cdf8a54de1d004aa831704452aa Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 13 Dec 2022 00:51:31 -0700 Subject: [PATCH 0525/2067] Add check for a config file that does not have the expected main section name --- python/ctsm/modify_input_files/fsurdat_modifier.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 7750d9eb20..24bddb9e65 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -48,7 +48,9 @@ def fsurdat_modifier(cfg_path): if not os.path.exists(cfg_path): abort( "Config file does NOT exist: "+str(cfg_path) ) config.read(cfg_path) - section = config.sections()[0] # name of the first section + section = "modify_input" + if not config.has_section(section): + abort( "Config file does not have the expected section: "+section ) # required: user must set these in the .cfg file fsurdat_in = get_config_value( From a4a35dec4f2036bd748a0c647efc4a4c70e29560 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 13 Dec 2022 01:09:57 -0700 Subject: [PATCH 0526/2067] Add test for short config file and add all needed settings in the config file so that it will work --- python/ctsm/test/test_sys_fsurdat_modifier.py | 7 +++++++ .../test/testinputs/modify_fsurdat_short.cfg | 19 +++++++++++++++++-- 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 5ed0e328fb..f7dd3fbc42 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -64,6 +64,13 @@ def test_no_files_given_fail(self): ): fsurdat_modifier(self._cfg_file_path) + def test_short_config(self): + """ + Test that a short config file works + """ + self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") + fsurdat_modifier(self._cfg_file_path) + def test_cfg_file_DNE_fail(self): """ Test that if the config file does not exist that it gracefully fails diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg index b0c94a11f2..e298b3575e 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg @@ -1,11 +1,26 @@ [modify_input] -fsurdat_in = FILL_THIS_IN -fsurdat_out = FILL_THIS_IN +fsurdat_in = ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc +fsurdat_out = ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc idealized = False include_nonveg = False +landmask_file = UNSET + +lat_dimname = lsmlat +lon_dimname = lsmlon + +dom_pft = UNSET + +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET +soil_color = UNSET +std_elev = UNSET +max_sat_area = UNSET + lnd_lat_1 = -90 lnd_lat_2 = 90 lnd_lon_1 = 0 From a4b717385ba41e2257fe7751748f05994161d9f3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 13 Dec 2022 16:16:00 -0700 Subject: [PATCH 0527/2067] Remove the output file created after the test --- python/ctsm/test/test_sys_fsurdat_modifier.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index f7dd3fbc42..9fd349b2ae 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -70,6 +70,8 @@ def test_short_config(self): """ self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") fsurdat_modifier(self._cfg_file_path) + fsurdat_out = "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" + os.remove( fsurdat_out ) def test_cfg_file_DNE_fail(self): """ From d8eedefdbeed69f581056010b528b8e068fa3796 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 15 Dec 2022 15:19:27 -0700 Subject: [PATCH 0528/2067] Minor corrections for system test to pass FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel --- cime_config/SystemTests/fsurdatmodifyctsm.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index fa29f9acd6..a7c7bbf61b 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -64,7 +64,7 @@ def _create_config_file(self): def _run_modify_fsurdat(self): tool_path = os.path.join(self._ctsm_root, - 'tools/modify_fsurdat/fsurdat_modifier') + 'tools/modify_input_files/fsurdat_modifier') self._case.load_env(reset=True) conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " @@ -85,8 +85,6 @@ def _get_conda_env(self): # # Remove python and add conda to environment for cheyennne conda_env = "module unload python; module load conda" - # CGD machines should already have conda loaded - conda_env += "; module load lang/python" # End above machine specific with a semicolon conda_env += "; " From 7d50ef6b74dd9c42338a34c593cd093cc0516483 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 16 Dec 2022 12:06:50 -0700 Subject: [PATCH 0529/2067] Stop running py_env_create so test will work in clm_pymods test-suite run_sys_tests (which starts ctsm's test-suites) builds cases on cheyenne's compute nodes. Running py_env_create on cheyenne's compute nodes fails, so we will leave it up to users to run py_env_create when necessary, manually. --- cime_config/SystemTests/fsurdatmodifyctsm.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index a7c7bbf61b..6b89c393c1 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -88,11 +88,8 @@ def _get_conda_env(self): # End above machine specific with a semicolon conda_env += "; " - # The following uses "&&" as they all need to work - # Run the py_env_create script - conda_env += self._ctsm_root+"/py_env_create" # Activate the python environment - conda_env += " && conda activate ctsm_pylib" + conda_env += " conda activate ctsm_pylib" # End above to get to actual command conda_env += " && " From 5fe8cfdf6cff482c72350a9515303aaa44ff7dfe Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 16 Dec 2022 12:53:21 -0700 Subject: [PATCH 0530/2067] Add new error msg when fsurdat_modifier tool fails New msg explains that user's ctsm_pylib environmt may be out-of_date and what to do. As written, the code lumps getting the conda environmt and running the tool in one subprocess. I will separate these to enable more informative error messages. --- cime_config/SystemTests/fsurdatmodifyctsm.py | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 6b89c393c1..a6c609187f 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -71,7 +71,18 @@ def _run_modify_fsurdat(self): # Preprend the commands to get the conda environment for python first conda_env += self._get_conda_env() # Source the env - subprocess.run( conda_env+"python3 "+tool_path+" "+self._cfg_file_path, shell=True, check=True) + try: + subprocess.run( conda_env+"python3 "+tool_path+" "+self._cfg_file_path, shell=True, check=True) + except subprocess.CalledProcessError as error: + print("ERROR while running fsurdat_modifier tool. ") + print("Your ctsm_pylib environment may be out of date. If so, ") + print("you may get past this error by running ./py_env_create ") + print("in your ctsm directory and trying this test again. ") + print("Default error message: ") + print(error.output) + except: + print("ERROR trying to run fsurdat_modifier tool.") + raise def _modify_user_nl(self): append_to_user_nl_files(caseroot = self._get_caseroot(), From 09d3639b413f728c32bc0d3f37e1c474d0f22c81 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 16 Dec 2022 14:45:59 -0700 Subject: [PATCH 0531/2067] Update error message when running the fsurdat_modifier tool I haven't found a way to separate the single subprocess that currently (1) loads conda and activates the ctsm_pylib environment and (2) runs the fsurdat_modifier tool into two or more subprocesses without losing access to the ctsm_pylib environment. So instead I have written a more elaborate error message with the various possible scenarios leading to an error in the subprocess. I have tested it by commenting out the "conda activate" line and confirming that I see my error message in TestStatus.log. --- cime_config/SystemTests/fsurdatmodifyctsm.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index a6c609187f..f8255624b5 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -74,10 +74,16 @@ def _run_modify_fsurdat(self): try: subprocess.run( conda_env+"python3 "+tool_path+" "+self._cfg_file_path, shell=True, check=True) except subprocess.CalledProcessError as error: - print("ERROR while running fsurdat_modifier tool. ") - print("Your ctsm_pylib environment may be out of date. If so, ") - print("you may get past this error by running ./py_env_create ") + print("ERROR while getting the conda environment and/or ") + print("running the fsurdat_modifier tool: ") + print("(1) If your ctsm_pylib environment is out of date or you ") + print("have not created the ctsm_pylib environment, yet, you may ") + print("get past this error by running ./py_env_create ") print("in your ctsm directory and trying this test again. ") + print("(2) If conda is not available, install and load conda, ") + print("run ./py_env_create, and then try this test again. ") + print("(3) If (1) and (2) are not the issue, then you may be ") + print("getting an error within the fsurdat_modifier tool itself. ") print("Default error message: ") print(error.output) except: From f0fdd2bd3e194dfc3dfe4cf2b6b7bcf051a59095 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 16 Dec 2022 18:42:21 -0700 Subject: [PATCH 0532/2067] Add fsurdat_modifier_arg_process method for argument processing so it can be tested, fix some lint and black issues --- .../modify_input_files/fsurdat_modifier.py | 17 +++++++--- python/ctsm/subset_data.py | 2 +- python/ctsm/test/test_sys_fsurdat_modifier.py | 33 ++++++++++--------- 3 files changed, 31 insertions(+), 21 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 24bddb9e65..b9cb44de4c 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -29,6 +29,12 @@ def main(): Calls function that modifies an fsurdat (surface dataset) """ + args = fsurdat_modifier_arg_process() + fsurdat_modifier(args.cfg_path) + + +def fsurdat_modifier_arg_process(): + """Argument processing for fsurdat_modifier script""" # set up logging allowing user control setup_logging_pre_config() @@ -38,19 +44,22 @@ def main(): add_logging_args(parser) args = parser.parse_args() process_logging_args(args) - fsurdat_modifier(args.cfg_path) + # Error checking of arguments + if not os.path.exists(args.cfg_path): + abort("Config file does NOT exist: " + str(args.cfg_path)) + print(args.cfg_path) + + return args def fsurdat_modifier(cfg_path): """Implementation of fsurdat_modifier command""" # read the .cfg (config) file config = ConfigParser() - if not os.path.exists(cfg_path): - abort( "Config file does NOT exist: "+str(cfg_path) ) config.read(cfg_path) section = "modify_input" if not config.has_section(section): - abort( "Config file does not have the expected section: "+section ) + abort("Config file does not have the expected section: " + section) # required: user must set these in the .cfg file fsurdat_in = get_config_value( diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 080c7f3003..8545870ee5 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -582,7 +582,7 @@ def main(): # --------------------------------- # # print help and exit when no option is chosen - if args.run_type != "point" and args.run_type != "region": + if args.run_type not in ("point", "region"): err_msg = textwrap.dedent( """\ \n ------------------------------------ diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 9fd349b2ae..4f8466c6c1 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -10,12 +10,14 @@ import unittest import tempfile import shutil +import sys import xarray as xr from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier +from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -58,10 +60,10 @@ def test_no_files_given_fail(self): """ Test that if no input or output files are given that it will gracefully fail """ - self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short_nofiles.cfg") - with self.assertRaisesRegex( - SystemExit, "must contain item 'fsurdat_in'" - ): + self._cfg_file_path = os.path.join( + self._testinputs_path, "modify_fsurdat_short_nofiles.cfg" + ) + with self.assertRaisesRegex(SystemExit, "must contain item 'fsurdat_in'"): fsurdat_modifier(self._cfg_file_path) def test_short_config(self): @@ -70,29 +72,28 @@ def test_short_config(self): """ self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") fsurdat_modifier(self._cfg_file_path) - fsurdat_out = "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" - os.remove( fsurdat_out ) + fsurdat_out = ( + "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" + ) + os.remove(fsurdat_out) def test_cfg_file_DNE_fail(self): """ Test that if the config file does not exist that it gracefully fails """ - self._cfg_file_path = os.path.join(self._tempdir, "FILE_DOES_NOT_EXIST.cfg" ) - with self.assertRaisesRegex( - SystemExit, "Config file does NOT exist" - ): - fsurdat_modifier(self._cfg_file_path) + self._cfg_file_path = os.path.join(self._tempdir, "FILE_DOES_NOT_EXIST.cfg") + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + with self.assertRaisesRegex(SystemExit, "Config file does NOT exist"): + fsurdat_modifier_arg_process() def test_cfg_file_empty_fail(self): """ Test that if the config file is empty it gracefully fails """ - self._cfg_file_path = os.path.join(self._tempdir, "EMPTY_FILE.cfg" ) - fil = open( self._cfg_file_path, "w" ) + self._cfg_file_path = os.path.join(self._tempdir, "EMPTY_FILE.cfg") + fil = open(self._cfg_file_path, "w") fil.close() - with self.assertRaisesRegex( - SystemExit, "Config file does not have the expected section" - ): + with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): fsurdat_modifier(self._cfg_file_path) def test_minimalInfo(self): From 5fe2dbd85b4137b6e8f56adbcfcd5a637a7f4e97 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 16 Dec 2022 23:46:56 -0700 Subject: [PATCH 0533/2067] Change the name of the main section for fsurdat_modifier --- python/ctsm/modify_input_files/fsurdat_modifier.py | 2 +- python/ctsm/test/testinputs/modify_fsurdat_short.cfg | 2 +- python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg | 2 +- tools/modify_input_files/modify_fsurdat_template.cfg | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index b9cb44de4c..0b686249f7 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -57,7 +57,7 @@ def fsurdat_modifier(cfg_path): # read the .cfg (config) file config = ConfigParser() config.read(cfg_path) - section = "modify_input" + section = "modify_fsurdat_basic_options" if not config.has_section(section): abort("Config file does not have the expected section: " + section) diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg index e298b3575e..b2393b3251 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg @@ -1,4 +1,4 @@ -[modify_input] +[modify_fsurdat_basic_options] fsurdat_in = ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc fsurdat_out = ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg index e4ba31912a..1706613e54 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg @@ -1,4 +1,4 @@ -[modify_input] +[modify_fsurdat_basic_options] idealized = False include_nonveg = False diff --git a/tools/modify_input_files/modify_fsurdat_template.cfg b/tools/modify_input_files/modify_fsurdat_template.cfg index 0694174666..7919c5f98c 100644 --- a/tools/modify_input_files/modify_fsurdat_template.cfg +++ b/tools/modify_input_files/modify_fsurdat_template.cfg @@ -1,4 +1,4 @@ -[modify_input] +[modify_fsurdat_basic_options] # ------------------------------------------------------------------------ # .cfg file with inputs for fsurdat_modifier. From 41b537e8824559fb6123975f2412d8a104c96b01 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 16 Dec 2022 23:57:53 -0700 Subject: [PATCH 0534/2067] Add two failing tests one to set an input file that does not exist, and the other to set an existing output file --- python/ctsm/test/test_sys_fsurdat_modifier.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 4f8466c6c1..948ea10691 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -86,6 +86,22 @@ def test_cfg_file_DNE_fail(self): with self.assertRaisesRegex(SystemExit, "Config file does NOT exist"): fsurdat_modifier_arg_process() + def test_input_fsurdat_DNE_fail(self): + """ + Test that if the input fsurdat file does not exist that it gracefully fails + """ + sys.argv = ["fsurdat_modifier", self._cfg_file_path, "-i", "FILE_DOES_NOT_EXIST.nc"] + with self.assertRaisesRegex(SystemExit, "Input surface dataset file does NOT exist"): + fsurdat_modifier_arg_process() + + def test_output_fsurdat_EXISTS_fail(self): + """ + Test that if the output fsurdat file does exist that it gracefully fails + """ + sys.argv = ["fsurdat_modifier", self._cfg_file_path, "-o", self._cfg_file_path] + with self.assertRaisesRegex(SystemExit, "Output file already exists"): + fsurdat_modifier_arg_process() + def test_cfg_file_empty_fail(self): """ Test that if the config file is empty it gracefully fails From 60589cd4710510ba4c3d542051b391126156e57a Mon Sep 17 00:00:00 2001 From: mvdebolskiy <80036033+mvdebolskiy@users.noreply.github.com> Date: Mon, 19 Dec 2022 23:12:02 +0100 Subject: [PATCH 0535/2067] fixed typos, punctuation, added more description --- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 22 ++++++++++++++----- 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst index 4430c54fa5..ab10547339 100644 --- a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst +++ b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst @@ -987,17 +987,18 @@ Excess Ground Ice ------------------------------------ An optional parameterization of excess ground ice melt and respective subsidence based on (:ref:`Lee et al., (2014) `). -Initial excess ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). -When the excess ice is present in the soil column soil depth for a given layer (:math:`z_{i}`) -is adjusted be the ammount of excess ice in the column: +Initial excess ground ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). +When the excess ground ice is present in the soil column, soil depth for a given layer (:math:`z_{i}`) +is adjusted by the amount of excess ice in the column: .. math:: :label: 6.94 z_{i}^{'}=\Sigma_{j=1}^{i} \ z_{j}^{'}+\frac{w_{exice,\, j}}{\rho_{ice} } -where :math:`w_{exice,\,j}` is excess ground ice ammount (kg m :sup:`-2`) in layer :math:`j` and :math:`\rho_{ice}` is the density of ice (kg m :sup:`-3`). -After adjustment of layer depths have been made all of the soil temperature equations (from :eq:`6.80` to :eq:`6.89`) +where :math:`w_{exice,\,j}` is excess ground ice amount (kg m :sup:`-2`) in layer :math:`j` +and :math:`\rho_{ice}` is the density of ice (kg m :sup:`-3`). +After adjustment of layer depths have been made, all of the soil temperature equations (from :eq:`6.80` to :eq:`6.89`) are calculted based on the adjusted depths. Thermal properties are additionally adjusted (:eq:`6.8` and :eq:`6.8`) in the following way: .. math:: @@ -1014,5 +1015,14 @@ Soil subsidence at the timestep :math:`n+1` (:math:`z_{exice}^{n+1}`, m) is then .. math:: :label: 6.96 - z_{exice}^{n+1}=\Sigma_{i=1}^{N_{levgrnd}} \ z_{j}^{',\ ,n+1}-z_{j}^{',\ ,n} + z_{exice}^{n+1}=\Sigma_{i=1}^{N_{levgrnd}} \ z_{j}^{',\ ,n+1}-z_{j}^{',\ ,n } + +With regards to hydraulic counductivity, excess ground ice is treated the same way normal soil +ice is treated in :numref:`Frozen Soils and Perched Water Table`. +When a soil layer thaws, excess ground ice is only allowed +to melt when no normals soil ice is present in the layer. +When a soil layer refreezes, liquid soil water can only turn into normal soil ice, thus, no new of excess ice can be created but only melted. +The excess liquid soil moisture from excess ice melt is distributed within the soil column according +to :numref:`Lateral Sub-surface Runoff`. + From 31798f104f2bad893366943403e1c1509ab22f18 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 19 Dec 2022 16:53:59 -0700 Subject: [PATCH 0536/2067] Update test_driver.sh according to Erik's review --- test/tools/test_driver.sh | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh index b4dac7f3a0..a16799ae87 100755 --- a/test/tools/test_driver.sh +++ b/test/tools/test_driver.sh @@ -54,8 +54,6 @@ module load nco module load ncl module load conda -$CESMDATAROOT/py_env_create -conda activate ctsm_pylib ##omp threads @@ -119,8 +117,6 @@ module load openmpi module load nco module load conda module load ncl -$CESMDATAROOT/py_env_create -conda activate ctsm_pylib ##omp threads @@ -220,8 +216,6 @@ module load compiler/intel module load tool/nco module load tool/netcdf module load lang/python -$CESMDATAROOT/py_env_create -conda activate ctsm_pylib export NETCDF_DIR=\$NETCDF_PATH export INC_NETCDF=\${NETCDF_PATH}/include @@ -303,8 +297,6 @@ module load compiler/intel module load tool/nco module load tool/netcdf module load lang/python -$CESMDATAROOT/py_env_create -conda activate ctsm_pylib export NETCDF_DIR=\$NETCDF_PATH export INC_NETCDF=\${NETCDF_PATH}/include @@ -382,7 +374,7 @@ fi # Setup conda environement \$CLM_ROOT/py_env_create -conda activate ctsm_py +conda activate ctsm_pylib ##output files clm_log=\${initdir}/td.\${JOBID}.log From 4057f9aac8ba6b1ad2dff90520cdc35140d007c8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 19 Dec 2022 18:07:27 -0700 Subject: [PATCH 0537/2067] If "which conda" fails, execute module load/unload, eg on cheyenne --- cime_config/SystemTests/fsurdatmodifyctsm.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index f8255624b5..0569683553 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -100,10 +100,14 @@ def _get_conda_env(self): # Add specific commands needed on different machines to get conda available # Use semicolon here since it's OK to fail # - # Remove python and add conda to environment for cheyennne - conda_env = "module unload python; module load conda" - # End above machine specific with a semicolon - conda_env += "; " + # Execute the module unload/load when "which conda" fails + # eg on cheyenne + try: + subprocess.run( "which conda", shell=True, check=True) + conda_env = " " + except subprocess.CalledProcessError: + # Remove python and add conda to environment for cheyennne + conda_env = "module unload python; module load conda;" # Activate the python environment conda_env += " conda activate ctsm_pylib" From 098153d0ee2bdd7f971dd943cfb6e7441a491308 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Dec 2022 16:47:13 -0700 Subject: [PATCH 0538/2067] Add ability to set fsurdat_in and fsurdat_out on command line, get tests working, fix pylint issues, run in black --- .../modify_input_files/fsurdat_modifier.py | 57 ++++++++++++++----- python/ctsm/subset_data.py | 4 +- python/ctsm/test/test_sys_fsurdat_modifier.py | 47 +++++++++++---- 3 files changed, 81 insertions(+), 27 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 0b686249f7..6bcebc92cf 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -30,7 +30,7 @@ def main(): """ args = fsurdat_modifier_arg_process() - fsurdat_modifier(args.cfg_path) + fsurdat_modifier(args) def fsurdat_modifier_arg_process(): @@ -41,33 +41,65 @@ def fsurdat_modifier_arg_process(): # read the command line argument to obtain the path to the .cfg file parser = argparse.ArgumentParser() parser.add_argument("cfg_path", help="/path/name.cfg of input file, eg ./modify.cfg") + parser.add_argument( + "-i", + "--fsurdat_in", + default="UNSET", + required=False, + type=str, + help="The input surface dataset to modify. ", + ) + parser.add_argument( + "-o", + "--fsurdat_out", + required=False, + default="UNSET", + type=str, + help="The output surface dataset with the modifications. ", + ) add_logging_args(parser) args = parser.parse_args() process_logging_args(args) # Error checking of arguments if not os.path.exists(args.cfg_path): abort("Config file does NOT exist: " + str(args.cfg_path)) - print(args.cfg_path) return args -def fsurdat_modifier(cfg_path): +def fsurdat_modifier(parser): """Implementation of fsurdat_modifier command""" # read the .cfg (config) file + cfg_path = str(parser.cfg_path) config = ConfigParser() config.read(cfg_path) section = "modify_fsurdat_basic_options" if not config.has_section(section): abort("Config file does not have the expected section: " + section) - # required: user must set these in the .cfg file - fsurdat_in = get_config_value( - config=config, section=section, item="fsurdat_in", file_path=cfg_path - ) - fsurdat_out = get_config_value( - config=config, section=section, item="fsurdat_out", file_path=cfg_path - ) + if parser.fsurdat_in == "UNSET": + # required: user must set these in the .cfg file + fsurdat_in = get_config_value( + config=config, section=section, item="fsurdat_in", file_path=cfg_path + ) + else: + fsurdat_in = str(parser.fsurdat_in) + + # Error checking of input file + if not os.path.exists(fsurdat_in): + abort("Input fsurdat_in file does NOT exist: " + str(fsurdat_in)) + + if parser.fsurdat_out == "UNSET": + fsurdat_out = get_config_value( + config=config, section=section, item="fsurdat_out", file_path=cfg_path + ) + else: + fsurdat_out = str(parser.fsurdat_out) + + # If output file exists, abort before starting work + if os.path.exists(fsurdat_out): + errmsg = "Output file already exists: " + fsurdat_out + abort(errmsg) # required but fallback values available for variables omitted # entirely from the .cfg file @@ -142,11 +174,6 @@ def fsurdat_modifier(cfg_path): lon_dimname, ) - # If output file exists, abort before starting work - if os.path.exists(fsurdat_out): - errmsg = "Output file already exists: " + fsurdat_out - abort(errmsg) - # not required: user may set these in the .cfg file max_pft = int(max(modify_fsurdat.file.lsmpft)) dom_pft = get_config_value( diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 8545870ee5..8015fe1858 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -589,7 +589,7 @@ def main(): \n Must supply a positional argument: 'point' or 'region'. """ ) - raise parser.error(err_msg) + raise args.error(err_msg) if not any( [ @@ -606,7 +606,7 @@ def main(): \n --create-surface \n --create-landuse \n --create-datm \n --create-domain \n """ ) - raise parser.error(err_msg) + raise args.error(err_msg) # --------------------------------- # # process logging args (i.e. debug and verbose) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 948ea10691..a09d6a7655 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -63,15 +63,19 @@ def test_no_files_given_fail(self): self._cfg_file_path = os.path.join( self._testinputs_path, "modify_fsurdat_short_nofiles.cfg" ) + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + parser = fsurdat_modifier_arg_process() with self.assertRaisesRegex(SystemExit, "must contain item 'fsurdat_in'"): - fsurdat_modifier(self._cfg_file_path) + fsurdat_modifier(parser) def test_short_config(self): """ Test that a short config file works """ self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") - fsurdat_modifier(self._cfg_file_path) + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) fsurdat_out = ( "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" ) @@ -90,17 +94,32 @@ def test_input_fsurdat_DNE_fail(self): """ Test that if the input fsurdat file does not exist that it gracefully fails """ + self._cfg_file_path = os.path.join( + self._testinputs_path, "modify_fsurdat_short_nofiles.cfg" + ) sys.argv = ["fsurdat_modifier", self._cfg_file_path, "-i", "FILE_DOES_NOT_EXIST.nc"] - with self.assertRaisesRegex(SystemExit, "Input surface dataset file does NOT exist"): - fsurdat_modifier_arg_process() + parser = fsurdat_modifier_arg_process() + with self.assertRaisesRegex(SystemExit, "Input fsurdat_in file does NOT exist"): + fsurdat_modifier(parser) def test_output_fsurdat_EXISTS_fail(self): """ Test that if the output fsurdat file does exist that it gracefully fails """ - sys.argv = ["fsurdat_modifier", self._cfg_file_path, "-o", self._cfg_file_path] + self._cfg_file_path = os.path.join( + self._testinputs_path, "modify_fsurdat_short_nofiles.cfg" + ) + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + self._cfg_file_path, + "-o", + self._cfg_file_path, + ] + parser = fsurdat_modifier_arg_process() with self.assertRaisesRegex(SystemExit, "Output file already exists"): - fsurdat_modifier_arg_process() + fsurdat_modifier(parser) def test_cfg_file_empty_fail(self): """ @@ -109,8 +128,10 @@ def test_cfg_file_empty_fail(self): self._cfg_file_path = os.path.join(self._tempdir, "EMPTY_FILE.cfg") fil = open(self._cfg_file_path, "w") fil.close() + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + parser = fsurdat_modifier_arg_process() with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): - fsurdat_modifier(self._cfg_file_path) + fsurdat_modifier(parser) def test_minimalInfo(self): """ @@ -121,7 +142,9 @@ def test_minimalInfo(self): self._create_config_file_minimal() # run the fsurdat_modifier tool - fsurdat_modifier(self._cfg_file_path) + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) # the critical piece of this test is that the above command # doesn't generate errors; however, we also do some assertions below @@ -139,7 +162,9 @@ def test_crop(self): self._create_config_file_crop() # run the fsurdat_modifier tool - fsurdat_modifier(self._cfg_file_path) + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) # the critical piece of this test is that the above command # doesn't generate errors; however, we also do some assertions below @@ -164,7 +189,9 @@ def test_allInfo(self): self._create_config_file_complete() # run the fsurdat_modifier tool - fsurdat_modifier(self._cfg_file_path) + sys.argv = ["fsurdat_modifier", self._cfg_file_path] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) # the critical piece of this test is that the above command # doesn't generate errors; however, we also do some assertions below From 32a88225ae1ac4b45a540844e4e7c3e18c57eb87 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Dec 2022 16:57:03 -0700 Subject: [PATCH 0539/2067] Add tests when in and out fsurdat files are specified in both the cmd-line and config file, stest fails --- python/ctsm/test/test_sys_fsurdat_modifier.py | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index a09d6a7655..d5bd80b4b0 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -81,6 +81,46 @@ def test_short_config(self): ) os.remove(fsurdat_out) + def test_short_infile_both_cmdline_and_cfg(self): + """ + Test that a graceful fail happens when the infile + is given both in the command line and the config file + """ + self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + "specify_fsurdat_in_on_cmd_line.nc", + ] + parser = fsurdat_modifier_arg_process() + with self.assertRaisesRegex( + SystemExit, + "fsurdat_in is specified in both the command line and the config file, pick one", + ): + fsurdat_modifier(parser) + + def test_short_outfile_both_cmdline_and_cfg(self): + """ + Test that a graceful fail happens when the outfile is given + both in the command line and the config file + """ + self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + "specify_fsurdat_in_on_cmd_line.nc", + "-o", + "specify_fsurdat_out_on_cmd_line.nc", + ] + parser = fsurdat_modifier_arg_process() + with self.assertRaisesRegex( + SystemExit, + "fsurdat_out is specified in both the command line and the config file, pick one", + ): + fsurdat_modifier(parser) + def test_cfg_file_DNE_fail(self): """ Test that if the config file does not exist that it gracefully fails From 5368ae7f32137b7026b1980a24639d4319c80184 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Dec 2022 17:04:04 -0700 Subject: [PATCH 0540/2067] Get tests of specifying both on command line and in config file working --- python/ctsm/modify_input_files/fsurdat_modifier.py | 4 ++++ python/ctsm/test/test_sys_fsurdat_modifier.py | 2 -- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 6bcebc92cf..a26d711da1 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -83,6 +83,8 @@ def fsurdat_modifier(parser): config=config, section=section, item="fsurdat_in", file_path=cfg_path ) else: + if config.has_option(section=section, option="fsurdat_in"): + abort("fsurdat_in is specified in both the command line and the config file, pick one") fsurdat_in = str(parser.fsurdat_in) # Error checking of input file @@ -94,6 +96,8 @@ def fsurdat_modifier(parser): config=config, section=section, item="fsurdat_out", file_path=cfg_path ) else: + if config.has_option(section=section, option="fsurdat_out"): + abort("fsurdat_out is specified in both the command line and the config file, pick one") fsurdat_out = str(parser.fsurdat_out) # If output file exists, abort before starting work diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index d5bd80b4b0..458f325d27 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -109,8 +109,6 @@ def test_short_outfile_both_cmdline_and_cfg(self): sys.argv = [ "fsurdat_modifier", self._cfg_file_path, - "-i", - "specify_fsurdat_in_on_cmd_line.nc", "-o", "specify_fsurdat_out_on_cmd_line.nc", ] From 40478eccbdadeed8d9e87502407ef3a0cc826001 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Dec 2022 00:02:54 -0700 Subject: [PATCH 0541/2067] Addd booleans about handling new optional sections --- python/ctsm/modify_input_files/fsurdat_modifier.py | 14 ++++++++++++++ .../ctsm/test/testinputs/modify_fsurdat_short.cfg | 2 ++ .../testinputs/modify_fsurdat_short_nofiles.cfg | 2 ++ .../modify_input_files/modify_fsurdat_template.cfg | 7 +++++++ 4 files changed, 25 insertions(+) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index a26d711da1..8e39d58a89 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -114,6 +114,20 @@ def fsurdat_modifier(parser): file_path=cfg_path, convert_to_type=bool, ) + process_subgrid = get_config_value( + config=config, + section=section, + item="process_subgrid_section", + file_path=cfg_path, + convert_to_type=bool, + ) + process_var_list = get_config_value( + config=config, + section=section, + item="process_var_list_section", + file_path=cfg_path, + convert_to_type=bool, + ) include_nonveg = get_config_value( config=config, section=section, diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg index b2393b3251..74c6639899 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg @@ -4,6 +4,8 @@ fsurdat_in = ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr20 fsurdat_out = ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc idealized = False +process_subgrid_section = False +process_var_list_section = False include_nonveg = False landmask_file = UNSET diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg index 1706613e54..3e5aada24b 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_short_nofiles.cfg @@ -1,6 +1,8 @@ [modify_fsurdat_basic_options] idealized = False +process_subgrid_section = False +process_var_list_section = False include_nonveg = False lnd_lat_1 = -90 diff --git a/tools/modify_input_files/modify_fsurdat_template.cfg b/tools/modify_input_files/modify_fsurdat_template.cfg index 7919c5f98c..aebe42a4f8 100644 --- a/tools/modify_input_files/modify_fsurdat_template.cfg +++ b/tools/modify_input_files/modify_fsurdat_template.cfg @@ -37,6 +37,13 @@ fsurdat_out = FILL_THIS_IN # ORGANIC = 0 idealized = False + +# Process the optional section that handles modifying subgrid fractions +process_subgrid_section = False + +# Process the optional section that handles modifying an arbitrary list of variables +process_var_list_section = False + # Boundaries of user-defined rectangle (float) # If lat_1 > lat_2, the code creates two rectangles, one in the north and # one in the south. From d05b3ff956c72fde40b965d15127dab479256218 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Dec 2022 12:45:50 -0700 Subject: [PATCH 0542/2067] Start adding handling of the optional sections, and add a simple test for it --- .../modify_input_files/fsurdat_modifier.py | 23 ++++++++++ python/ctsm/test/test_sys_fsurdat_modifier.py | 21 +++++++++ .../modify_fsurdat_opt_sections.cfg | 44 +++++++++++++++++++ 3 files changed, 88 insertions(+) create mode 100644 python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 8e39d58a89..e0d833a076 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -67,6 +67,20 @@ def fsurdat_modifier_arg_process(): return args +def read_subgrid(config): + """Read the subgrid fraction section from the config file""" + section = "modify_fsurdat_subgrid_fractions" + if not config.has_section(section): + abort("Config file does not have the expected section: " + section) + + +def read_var_list(config): + """Read the variable list section from the config file""" + section = "modify_fsurdat_variable_list" + if not config.has_section(section): + abort("Config file does not have the expected section: " + section) + + def fsurdat_modifier(parser): """Implementation of fsurdat_modifier command""" # read the .cfg (config) file @@ -308,6 +322,15 @@ def fsurdat_modifier(parser): ) logger.info("dom_pft complete") + # + # Handle optional sections + # + if process_subgrid: + read_subgrid(config) + + if process_var_list: + read_var_list(config) + # ---------------------------------------------- # Output the now modified CTSM surface data file # ---------------------------------------------- diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 458f325d27..5645ec152f 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -119,6 +119,27 @@ def test_short_outfile_both_cmdline_and_cfg(self): ): fsurdat_modifier(parser) + def test_opt_sections(self): + """ + Test that a simple file with the optional sections works + """ + self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_opt_sections.cfg") + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + os.path.join( + self._testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" + ), + "-o", + os.path.join( + self._tempdir, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_output_urban.nc", + ), + ] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) + def test_cfg_file_DNE_fail(self): """ Test that if the config file does not exist that it gracefully fails diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg new file mode 100644 index 0000000000..80389e1c38 --- /dev/null +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -0,0 +1,44 @@ +[modify_fsurdat_basic_options] + +idealized = False +process_subgrid_section = True +process_var_list_section = True +include_nonveg = True + +landmask_file = UNSET + +lat_dimname = lsmlat +lon_dimname = lsmlon + +dom_pft = UNSET + +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET +soil_color = UNSET +std_elev = UNSET +max_sat_area = UNSET + +lnd_lat_1 = -90 +lnd_lat_2 = 90 +lnd_lon_1 = 0 +lnd_lon_2 = 360 + +# Section for subgrid_fractions +[modify_fsurdat_subgrid_fractions] +# Set to 100% urban for the test +PCT_NATVEG = 0.0 +PCT_CROP = 0.0 +PCT_LAKE = 0.0 +PCT_GLACIER = 0.0 +PCT_WETLAND = 0.0 +PCT_URBAN = 100.0 + + +# Section with a list of variables to prcoess +[modify_fsurdat_variable_list] +# Set three variables to 200 for the test +CANYON_HWR = 200.00 +HT_ROOF = 200.0 +T_BUILDING_MIN = 200 From 3683a91e269db8062cb44413a59facacdb9d9b1a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Dec 2022 15:46:20 -0700 Subject: [PATCH 0543/2067] More work on processing subgrid fraction and variable list sections --- .../modify_input_files/fsurdat_modifier.py | 41 +++++++++++++++++-- 1 file changed, 37 insertions(+), 4 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index e0d833a076..660146e627 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -67,19 +67,52 @@ def fsurdat_modifier_arg_process(): return args -def read_subgrid(config): +def read_subgrid(config, cfg_path): """Read the subgrid fraction section from the config file""" section = "modify_fsurdat_subgrid_fractions" if not config.has_section(section): abort("Config file does not have the expected section: " + section) + subgrid_settings = {} + var_list = config.options(section) + valid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] + for var in var_list: + if var_list.count(var) == 0: + abort( + "Variable " + + var + + " in " + + section + + " is not a valid variable name. Valid vars =" + + str(valid_list) + ) + value = get_config_value( + config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float + ) + if value < 0.0 or value > 100.0: + abort("Variable " + var + " in " + section + " is out of range of 0 to 100 = " + value) + + subgrid_settings[var.upper()] = value + + return subgrid_settings + -def read_var_list(config): +def read_var_list(config, cfg_path): """Read the variable list section from the config file""" section = "modify_fsurdat_variable_list" if not config.has_section(section): abort("Config file does not have the expected section: " + section) + varlist_settings = {} + var_list = config.options(section) + for var in var_list: + value = get_config_value( + config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float + ) + varlist_settings[var] = value + + return varlist_settings + def fsurdat_modifier(parser): """Implementation of fsurdat_modifier command""" @@ -326,10 +359,10 @@ def fsurdat_modifier(parser): # Handle optional sections # if process_subgrid: - read_subgrid(config) + subgrid = read_subgrid(config, cfg_path) if process_var_list: - read_var_list(config) + varlist = read_var_list(config, cfg_path) # ---------------------------------------------- # Output the now modified CTSM surface data file From 8514bd3747b6d7a9f413e720e9bed025773fa5c5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Dec 2022 19:13:30 -0700 Subject: [PATCH 0544/2067] Add unit tester for fsurdat_modifier subroutines --- .../ctsm/test/test_unit_fsurdat_modifier.py | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100755 python/ctsm/test/test_unit_fsurdat_modifier.py diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py new file mode 100755 index 0000000000..a0c273fcf9 --- /dev/null +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -0,0 +1,76 @@ +#!/usr/bin/env python3 + +""" +Unit tests for fsurdat_modifier subroutines: read_subgrid, read_varlist +""" + +import unittest +import os +import sys +import shutil + +import tempfile +from configparser import ConfigParser + +from ctsm import unit_testing +from ctsm.path_utils import path_to_ctsm_root +from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process +from ctsm.modify_input_files.fsurdat_modifier import read_subgrid +from ctsm.modify_input_files.fsurdat_modifier import read_var_list + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + +# pylint: disable=protected-access + + +class TestFSurdatModifier(unittest.TestCase): + """Tests the read_subgrid and read_var_list methods""" + + def setUp(self): + """Setup for trying out the methods""" + testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") + self._cfg_file_path = os.path.join(testinputs_path, "modify_fsurdat_opt_sections.cfg") + self._testinputs_path = testinputs_path + self._fsurdat_in = os.path.join( + testinputs_path, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", + ) + self._tempdir = tempfile.mkdtemp() + self._fsurdat_in = os.path.join( + testinputs_path, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", + ) + self._fsurdat_out = os.path.join(self._tempdir, "fsurdat_out.nc") + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + self._fsurdat_in, + "-o", + self._fsurdat_out, + ] + parser = fsurdat_modifier_arg_process() + self.cfg_path = str(parser.cfg_path) + self.config = ConfigParser() + self.config.read(self.cfg_path) + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_read_subgrid(self): + """test a simple read of subgrid""" + read_subgrid(self.config, self.cfg_path) + + def test_read_var_list(self): + """test a simple read of var_list""" + read_var_list(self.config, self.cfg_path) + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() From cd202a052ebd0655fd55e2a019eac85ea804fde1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 22 Dec 2022 01:45:28 -0700 Subject: [PATCH 0545/2067] Add a out of range test --- python/ctsm/modify_input_files/fsurdat_modifier.py | 2 +- python/ctsm/test/test_unit_fsurdat_modifier.py | 7 +++++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 660146e627..b860655035 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -90,7 +90,7 @@ def read_subgrid(config, cfg_path): config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float ) if value < 0.0 or value > 100.0: - abort("Variable " + var + " in " + section + " is out of range of 0 to 100 = " + value) + abort("Variable " + var + " in " + section + " is out of range of 0 to 100 = " + str(value)) subgrid_settings[var.upper()] = value diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index a0c273fcf9..e5d37bf848 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -70,6 +70,13 @@ def test_read_var_list(self): """test a simple read of var_list""" read_var_list(self.config, self.cfg_path) + def test_subgrid_outofrange(self): + """test a read of subgrid that's out of range""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "101." ) + with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): + read_subgrid(self.config, self.cfg_path) + if __name__ == "__main__": unit_testing.setup_for_tests() From 5efda44e0035070f4d9aced80861a00bb973e9b8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 22 Dec 2022 01:52:54 -0700 Subject: [PATCH 0546/2067] Add a check for valid variables in read_subgrid and get it working --- python/ctsm/modify_input_files/fsurdat_modifier.py | 2 +- python/ctsm/test/test_unit_fsurdat_modifier.py | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index b860655035..bdfceb9966 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -77,7 +77,7 @@ def read_subgrid(config, cfg_path): var_list = config.options(section) valid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] for var in var_list: - if var_list.count(var) == 0: + if valid_list.count(var) == 0: abort( "Variable " + var diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index e5d37bf848..f87e718e6d 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -77,6 +77,12 @@ def test_subgrid_outofrange(self): with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): read_subgrid(self.config, self.cfg_path) + def test_subgrid_badvar(self): + """test a read of subgrid for a variable thats not in the list""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "badvariable", "100." ) + with self.assertRaisesRegex(SystemExit, "is not a valid variable name. Valid vars ="): + read_subgrid(self.config, self.cfg_path) if __name__ == "__main__": unit_testing.setup_for_tests() From 957042576e0755b930f1de5246e9c7172a23872e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 22 Dec 2022 01:59:06 -0700 Subject: [PATCH 0547/2067] Add fail tests when the optional sections have been removed --- python/ctsm/test/test_unit_fsurdat_modifier.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index f87e718e6d..7e5cadef92 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -84,6 +84,21 @@ def test_subgrid_badvar(self): with self.assertRaisesRegex(SystemExit, "is not a valid variable name. Valid vars ="): read_subgrid(self.config, self.cfg_path) + def test_subgrid_remove(self): + """test a read of subgrid when it's section has been removed""" + section = "modify_fsurdat_subgrid_fractions" + self.config.remove_section(section) + with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): + read_subgrid(self.config, self.cfg_path) + + def test_varlist_remove(self): + """test a read of varlist when it's section has been removed""" + section = "modify_fsurdat_variable_list" + self.config.remove_section(section) + with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): + read_var_list(self.config, self.cfg_path) + + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() From c9bb37335a38d08c43a497f71e064286954c258e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 22 Dec 2022 14:43:18 -0700 Subject: [PATCH 0548/2067] Add test and check that optional sections aren't there if they aren't turned on --- .../modify_input_files/fsurdat_modifier.py | 16 ++++++++++++++ .../ctsm/test/test_unit_fsurdat_modifier.py | 21 +++++++++++++------ 2 files changed, 31 insertions(+), 6 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index bdfceb9966..ab8cb47587 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -66,6 +66,18 @@ def fsurdat_modifier_arg_process(): return args +def check_no_subgrid_section(config): + """ Check that there isn't a subgrid section when it's processing is turned off""" + section = "modify_fsurdat_subgrid_fractions" + if config.has_section(section): + abort("Config file does have a section: " + section + " that should NOT be there since it is turned off") + +def check_no_varlist_section(config): + """ Check that there isn't a var list section when it's processing is turned off""" + section = "modify_fsurdat_variable_list" + if config.has_section(section): + abort("Config file does have a section: " + section + " that should NOT be there since it is turned off") + def read_subgrid(config, cfg_path): """Read the subgrid fraction section from the config file""" @@ -360,9 +372,13 @@ def fsurdat_modifier(parser): # if process_subgrid: subgrid = read_subgrid(config, cfg_path) + else: + check_no_subgrid_section(config) if process_var_list: varlist = read_var_list(config, cfg_path) + else: + check_no_varlist_section(config) # ---------------------------------------------- # Output the now modified CTSM surface data file diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 7e5cadef92..1070fa429b 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -17,6 +17,8 @@ from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process from ctsm.modify_input_files.fsurdat_modifier import read_subgrid from ctsm.modify_input_files.fsurdat_modifier import read_var_list +from ctsm.modify_input_files.fsurdat_modifier import check_no_subgrid_section +from ctsm.modify_input_files.fsurdat_modifier import check_no_varlist_section # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -91,12 +93,19 @@ def test_subgrid_remove(self): with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): read_subgrid(self.config, self.cfg_path) - def test_varlist_remove(self): - """test a read of varlist when it's section has been removed""" - section = "modify_fsurdat_variable_list" - self.config.remove_section(section) - with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): - read_var_list(self.config, self.cfg_path) + def test_subgrid_not_thereifoff(self): + """test that a graceful error happens if subgrid section is off, but it appears in the file""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "process_subgrid_section", "False" ) + with self.assertRaisesRegex(SystemExit, "Config file does have a section"): + check_no_subgrid_section(self.config) + + def test_varlist_not_thereifoff(self): + """test that a graceful error happens if varlist section is off, but it appears in the file""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "process_var_list_section", "False" ) + with self.assertRaisesRegex(SystemExit, "Config file does have a section"): + check_no_varlist_section(self.config) if __name__ == "__main__": From 891e1305c8b43b717e26fc3d1355cb929264f67b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 00:11:09 -0700 Subject: [PATCH 0549/2067] Get working in black and pylint, utest and stest working, add set_varlist and check_varlist methods and start adding tests for them, add Setup method for fsurdat modify unit tester and use it for an old and now a new test, simplify the modify test config file so that it will work --- .../modify_input_files/fsurdat_modifier.py | 30 +++++-- .../ctsm/modify_input_files/modify_fsurdat.py | 50 +++++++++++ .../ctsm/test/test_unit_fsurdat_modifier.py | 24 ++--- python/ctsm/test/test_unit_modify_fsurdat.py | 88 +++++++++++-------- .../modify_fsurdat_opt_sections.cfg | 9 +- 5 files changed, 142 insertions(+), 59 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index ab8cb47587..2d5f602166 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -66,17 +66,27 @@ def fsurdat_modifier_arg_process(): return args + def check_no_subgrid_section(config): - """ Check that there isn't a subgrid section when it's processing is turned off""" + """Check that there isn't a subgrid section when it's processing is turned off""" section = "modify_fsurdat_subgrid_fractions" if config.has_section(section): - abort("Config file does have a section: " + section + " that should NOT be there since it is turned off") + abort( + "Config file does have a section: " + + section + + " that should NOT be there since it is turned off" + ) + def check_no_varlist_section(config): - """ Check that there isn't a var list section when it's processing is turned off""" + """Check that there isn't a var list section when it's processing is turned off""" section = "modify_fsurdat_variable_list" if config.has_section(section): - abort("Config file does have a section: " + section + " that should NOT be there since it is turned off") + abort( + "Config file does have a section: " + + section + + " that should NOT be there since it is turned off" + ) def read_subgrid(config, cfg_path): @@ -102,7 +112,14 @@ def read_subgrid(config, cfg_path): config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float ) if value < 0.0 or value > 100.0: - abort("Variable " + var + " in " + section + " is out of range of 0 to 100 = " + str(value)) + abort( + "Variable " + + var + + " in " + + section + + " is out of range of 0 to 100 = " + + str(value) + ) subgrid_settings[var.upper()] = value @@ -372,11 +389,14 @@ def fsurdat_modifier(parser): # if process_subgrid: subgrid = read_subgrid(config, cfg_path) + modify_fsurdat.set_varlist(subgrid) else: check_no_subgrid_section(config) if process_var_list: varlist = read_var_list(config, cfg_path) + modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) + modify_fsurdat.set_varlist(varlist) else: check_no_varlist_section(config) diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index ba1fd18fdb..4a38ed4d96 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -214,6 +214,56 @@ def set_dom_pft(self, dom_pft, lai, sai, hgt_top, hgt_bot): if val is not None: self.set_lai_sai_hgts(dom_pft=dom_pft, var=var, val=val) + def check_varlist(self, settings, allow_uppercase_vars=False): + """ + Check a list of variables from a dictionary of settings + """ + # exclude_list = ( "MONTHLY_LAI", "MONTHLY_SAI", + # "MONTHLY_HEIGHT_TOP", "MONTHLY_HEIGHT_BOT" ) + for var in settings.keys(): + # if exclude_list.count(var) > 0: + # abort("Error: Variable "+var+" is already handled outside "+ + # "of the optional variable list sections") + if not var in self.file: + if not allow_uppercase_vars: + errmsg = "Error: Variable " + var + " is NOT in the file" + abort(errmsg) + if not var.upper() in self.file: + errmsg = "Error: Variable " + var.upper() + " is NOT in the file" + abort(errmsg) + val = settings[var] + del settings[var] + var = var.upper() + settings[var] = val + + def set_varlist(self, settings): + """ + Set a list of variables from a dictionary of settings + """ + for var in settings.keys(): + # if exclude_list.count(var) > 0: + # abort("Error: Variable "+var+" is already handled outside "+ + # "of the optional variable list sections") + if var in self.file: + if len(self.file[var].dims) == 2: + self.setvar_lev0(var, settings[var]) + elif self.file[var].dims == 3: + self.setvar_lev1(var, settings[var], lev1_dim=self.file[var].dims[0]) + elif self.file[var].dims == 4: + self.setvar_lev2( + var, + settings[var], + lev1_dim=self.file[var].dims[1], + lev2_dim=self.file[var].dims[0], + ) + else: + abort( + "Error: Variable " + var + " is a higher dimension than currently allowed" + ) + else: + errmsg = "Error: Variable " + var + " is NOT in the file" + abort(errmsg) + def set_lai_sai_hgts(self, dom_pft, var, val): """ Description diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 1070fa429b..3508022afa 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -75,37 +75,39 @@ def test_read_var_list(self): def test_subgrid_outofrange(self): """test a read of subgrid that's out of range""" section = "modify_fsurdat_subgrid_fractions" - self.config.set(section, "pct_urban", "101." ) + self.config.set(section, "pct_urban", "101.") with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): - read_subgrid(self.config, self.cfg_path) + read_subgrid(self.config, self.cfg_path) def test_subgrid_badvar(self): """test a read of subgrid for a variable thats not in the list""" section = "modify_fsurdat_subgrid_fractions" - self.config.set(section, "badvariable", "100." ) + self.config.set(section, "badvariable", "100.") with self.assertRaisesRegex(SystemExit, "is not a valid variable name. Valid vars ="): - read_subgrid(self.config, self.cfg_path) + read_subgrid(self.config, self.cfg_path) def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" section = "modify_fsurdat_subgrid_fractions" self.config.remove_section(section) with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): - read_subgrid(self.config, self.cfg_path) + read_subgrid(self.config, self.cfg_path) def test_subgrid_not_thereifoff(self): - """test that a graceful error happens if subgrid section is off, but it appears in the file""" + """test that a graceful error happens if subgrid section is off, + but it appears in the file""" section = "modify_fsurdat_basic_options" - self.config.set(section, "process_subgrid_section", "False" ) + self.config.set(section, "process_subgrid_section", "False") with self.assertRaisesRegex(SystemExit, "Config file does have a section"): - check_no_subgrid_section(self.config) + check_no_subgrid_section(self.config) def test_varlist_not_thereifoff(self): - """test that a graceful error happens if varlist section is off, but it appears in the file""" + """test that a graceful error happens if varlist section is off, + but it appears in the file""" section = "modify_fsurdat_basic_options" - self.config.set(section, "process_var_list_section", "False" ) + self.config.set(section, "process_var_list_section", "False") with self.assertRaisesRegex(SystemExit, "Config file does have a section"): - check_no_varlist_section(self.config) + check_no_varlist_section(self.config) if __name__ == "__main__": diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index e53175b9b7..df84bd9c4c 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -19,87 +19,96 @@ # pylint: disable=protected-access +## Too many instant variables as part of the class (too many self. in the SetUp) +# pylint: disable=too-many-instance-attributes + class TestModifyFsurdat(unittest.TestCase): """Tests the setvar_lev functions and the - _get_rectangle function + _get_rectangle function and + set_varlist method """ - def test_setvarLev(self): - """ - Tests that setvar_lev0, setvar_lev1, and setvar_lev2 update values of - variables within a rectangle defined by user-specified - lon_1, lon_2, lat_1, lat_2 - """ + def setUp(self): # get longxy, latixy that would normally come from an fsurdat file # self._get_longxy_latixy will convert -180 to 180 to 0-360 longitudes # get cols, rows also - min_lon = 2 # expects min_lon < max_lon - min_lat = 3 # expects min_lat < max_lat - longxy, latixy, cols, rows = self._get_longxy_latixy( - _min_lon=min_lon, _max_lon=10, _min_lat=min_lat, _max_lat=12 + self.min_lon = 2 # expects min_lon < max_lon + self.min_lat = 3 # expects min_lat < max_lat + longxy, latixy, self.cols, self.rows = self._get_longxy_latixy( + _min_lon=self.min_lon, _max_lon=10, _min_lat=self.min_lat, _max_lat=12 ) # get not_rectangle from user-defined lon_1, lon_2, lat_1, lat_2 - lon_1 = 3 - lon_2 = 5 # lon_1 < lon_2 - lat_1 = 5 - lat_2 = 7 # lat_1 < lat_2 + self.lon_1 = 3 + self.lon_2 = 5 # lon_1 < lon_2 + self.lat_1 = 5 + self.lat_2 = 7 # lat_1 < lat_2 # create xarray dataset containing lev0, lev1, and lev2 variables; # the fsurdat_modify tool reads variables like this from fsurdat file - var_1d = np.arange(cols) - var_lev2 = var_1d * np.ones((rows, cols, rows, cols)) - var_lev1 = var_1d * np.ones((cols, rows, cols)) + var_1d = np.arange(self.cols) + var_lev0 = var_1d * np.ones((self.rows, self.cols)) + var_lev2 = var_1d * np.ones((self.rows, self.cols, self.rows, self.cols)) + var_lev1 = var_1d * np.ones((self.cols, self.rows, self.cols)) my_data = xr.Dataset( data_vars=dict( LONGXY=(["x", "y"], longxy), # use LONGXY as var_lev0 LATIXY=(["x", "y"], latixy), # __init__ expects LONGXY, LATIXY + var_lev0=(["x", "y"], var_lev0), var_lev1=(["w", "x", "y"], var_lev1), var_lev2=(["v", "w", "x", "y"], var_lev2), ) ) # create ModifyFsurdat object - modify_fsurdat = ModifyFsurdat( + self.modify_fsurdat = ModifyFsurdat( my_data=my_data, - lon_1=lon_1, - lon_2=lon_2, - lat_1=lat_1, - lat_2=lat_2, + lon_1=self.lon_1, + lon_2=self.lon_2, + lat_1=self.lat_1, + lat_2=self.lat_2, landmask_file=None, lat_dimname=None, lon_dimname=None, ) + def test_setvarLev(self): + """ + Tests that setvar_lev0, setvar_lev1, and setvar_lev2 update values of + variables within a rectangle defined by user-specified + lon_1, lon_2, lat_1, lat_2 + """ + # initialize and then modify the comparison matrices - comp_lev0 = modify_fsurdat.file.LONGXY - comp_lev1 = modify_fsurdat.file.var_lev1 - comp_lev2 = modify_fsurdat.file.var_lev2 + comp_lev0 = self.modify_fsurdat.file.LONGXY + comp_lev1 = self.modify_fsurdat.file.var_lev1 + comp_lev2 = self.modify_fsurdat.file.var_lev2 val_for_rectangle = 1.5 comp_lev0[ - lat_1 - min_lat : lat_2 - min_lat + 1, lon_1 - min_lon : lon_2 - min_lon + 1 + self.lat_1 - self.min_lat : self.lat_2 - self.min_lat + 1, + self.lon_1 - self.min_lon : self.lon_2 - self.min_lon + 1, ] = val_for_rectangle comp_lev1[ ..., - lat_1 - min_lat : lat_2 - min_lat + 1, - lon_1 - min_lon : lon_2 - min_lon + 1, + self.lat_1 - self.min_lat : self.lat_2 - self.min_lat + 1, + self.lon_1 - self.min_lon : self.lon_2 - self.min_lon + 1, ] = val_for_rectangle comp_lev2[ ..., - lat_1 - min_lat : lat_2 - min_lat + 1, - lon_1 - min_lon : lon_2 - min_lon + 1, + self.lat_1 - self.min_lat : self.lat_2 - self.min_lat + 1, + self.lon_1 - self.min_lon : self.lon_2 - self.min_lon + 1, ] = val_for_rectangle # test setvar - modify_fsurdat.setvar_lev0("LONGXY", val_for_rectangle) - np.testing.assert_array_equal(modify_fsurdat.file.LONGXY, comp_lev0) + self.modify_fsurdat.setvar_lev0("LONGXY", val_for_rectangle) + np.testing.assert_array_equal(self.modify_fsurdat.file.LONGXY, comp_lev0) - modify_fsurdat.setvar_lev1("var_lev1", val_for_rectangle, cols - 1) - np.testing.assert_array_equal(modify_fsurdat.file.var_lev1, comp_lev1) + self.modify_fsurdat.setvar_lev1("var_lev1", val_for_rectangle, self.cols - 1) + np.testing.assert_array_equal(self.modify_fsurdat.file.var_lev1, comp_lev1) - modify_fsurdat.setvar_lev2("var_lev2", val_for_rectangle, cols - 1, rows - 1) - np.testing.assert_array_equal(modify_fsurdat.file.var_lev2, comp_lev2) + self.modify_fsurdat.setvar_lev2("var_lev2", val_for_rectangle, self.cols - 1, self.rows - 1) + np.testing.assert_array_equal(self.modify_fsurdat.file.var_lev2, comp_lev2) def test_getNotRectangle_lon1leLon2Lat1leLat2(self): """ @@ -359,6 +368,11 @@ def test_getNotRectangle_latsOutOfBounds(self): latixy=latixy, ) + def test_set_varlist(self): + """Test the set_varlist method""" + settings = {"var_lev0": 100.0} + self.modify_fsurdat.set_varlist(settings) + def _get_longxy_latixy(self, _min_lon, _max_lon, _min_lat, _max_lat): """ Return longxy, latixy, cols, rows diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index 80389e1c38..fb163e9e72 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -30,15 +30,12 @@ lnd_lon_2 = 360 # Set to 100% urban for the test PCT_NATVEG = 0.0 PCT_CROP = 0.0 -PCT_LAKE = 0.0 +PCT_LAKE = 100.0 PCT_GLACIER = 0.0 PCT_WETLAND = 0.0 -PCT_URBAN = 100.0 # Section with a list of variables to prcoess [modify_fsurdat_variable_list] -# Set three variables to 200 for the test -CANYON_HWR = 200.00 -HT_ROOF = 200.0 -T_BUILDING_MIN = 200 +# Set lake-depth to 200 for the test +LAKEDEPTH = 200.00 From a9873c7c25d88263b4c84c6985419100440bd841 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 18:21:33 -0700 Subject: [PATCH 0550/2067] Add two tests that check that PCT_* variables for subgrid add to a hundred, and one that checks that a variable handled in the idealized list can't be set in the variable_list section, these tests fail --- .../ctsm/test/test_unit_fsurdat_modifier.py | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 3508022afa..7047977761 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -79,6 +79,20 @@ def test_subgrid_outofrange(self): with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): read_subgrid(self.config, self.cfg_path) + def test_subgrid_notsumtohundred(self): + """test a read of subgrid that's doesn't sum to a hundred""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "0.") + self.config.set(section, "pct_lake", "0.") + self.config.set(section, "pct_wetland", "0.") + self.config.set(section, "pct_glacier", "0.") + self.config.set(section, "pct_natveg", "0.") + self.config.set(section, "pct_crop", "0.") + with self.assertRaisesRegex( + SystemExit, "PCT fractions in subgrid section do NOT sum to a hundred as they should" + ): + read_subgrid(self.config, self.cfg_path) + def test_subgrid_badvar(self): """test a read of subgrid for a variable thats not in the list""" section = "modify_fsurdat_subgrid_fractions" @@ -86,6 +100,17 @@ def test_subgrid_badvar(self): with self.assertRaisesRegex(SystemExit, "is not a valid variable name. Valid vars ="): read_subgrid(self.config, self.cfg_path) + def test_varlist_varinidealized(self): + """test a read of varlist for a variable thats in the idealized list""" + section = "modify_fsurdat_variable_list" + self.config.set(section, "PCT_SAND", "100.") + with self.assertRaisesRegex( + SystemExit, + "is variable handled in the idealized section." + + " This should NOT be handled in the variiable list section. Idealized vars =", + ): + read_var_list(self.config, self.cfg_path) + def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" section = "modify_fsurdat_subgrid_fractions" From 6e5731f35f0138db0b41482b06051c937263cf02 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 18:51:01 -0700 Subject: [PATCH 0551/2067] Get the two failing tests to work --- .../modify_input_files/fsurdat_modifier.py | 18 ++++++++++++++++++ python/ctsm/test/test_unit_fsurdat_modifier.py | 4 ++-- 2 files changed, 20 insertions(+), 2 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 2d5f602166..256a6e1757 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -98,6 +98,7 @@ def read_subgrid(config, cfg_path): subgrid_settings = {} var_list = config.options(section) valid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] + varsum = 0 for var in var_list: if valid_list.count(var) == 0: abort( @@ -122,6 +123,12 @@ def read_subgrid(config, cfg_path): ) subgrid_settings[var.upper()] = value + varsum += value + if varsum != 100.0: + abort( + "PCT fractions in subgrid section do NOT sum to a hundred as they should. Sum = " + + str(varsum) + ) return subgrid_settings @@ -134,7 +141,18 @@ def read_var_list(config, cfg_path): varlist_settings = {} var_list = config.options(section) + ideal_list = ["soil_color", "pct_sand", "pct_clay", "organic", "pct_cft", "pct_nat_pft"] + # subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", + # "pct_wetland", "pct_urban"] for var in var_list: + if ideal_list.count(var) != 0: + abort( + var + + " is a special variable handled in the idealized section." + + " This should NOT be handled in the variiable list section." + + " Special idealized vars =" + + str(ideal_list) + ) value = get_config_value( config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float ) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 7047977761..8399540b7b 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -106,8 +106,8 @@ def test_varlist_varinidealized(self): self.config.set(section, "PCT_SAND", "100.") with self.assertRaisesRegex( SystemExit, - "is variable handled in the idealized section." - + " This should NOT be handled in the variiable list section. Idealized vars =", + "is a special variable handled in the idealized section." + + " This should NOT be handled in the variiable list section. Special idealized vars =", ): read_var_list(self.config, self.cfg_path) From c88e071b9d5ad41ccdce34deb778afa9e484e19a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 18:54:11 -0700 Subject: [PATCH 0552/2067] Add a test to make sure a variable read in the variable list section is not from the subgrid section, this fails as expected --- python/ctsm/test/test_unit_fsurdat_modifier.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 8399540b7b..531f2821ed 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -111,6 +111,17 @@ def test_varlist_varinidealized(self): ): read_var_list(self.config, self.cfg_path) + def test_varlist_varinsubgrid(self): + """test a read of varlist for a variable thats in the subgrid list""" + section = "modify_fsurdat_variable_list" + self.config.set(section, "PCT_GLACIER", "100.") + with self.assertRaisesRegex( + SystemExit, + "is a variable handled in the subgrid section." + + " This should NOT be handled in the variiable list section. Subgrid vars =", + ): + read_var_list(self.config, self.cfg_path) + def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" section = "modify_fsurdat_subgrid_fractions" From e06dd5294eeee202ca4330367648ff979b26c7a9 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 18:57:09 -0700 Subject: [PATCH 0553/2067] Get the test to pass now --- python/ctsm/modify_input_files/fsurdat_modifier.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 256a6e1757..4c210c08c2 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -142,8 +142,7 @@ def read_var_list(config, cfg_path): varlist_settings = {} var_list = config.options(section) ideal_list = ["soil_color", "pct_sand", "pct_clay", "organic", "pct_cft", "pct_nat_pft"] - # subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", - # "pct_wetland", "pct_urban"] + subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] for var in var_list: if ideal_list.count(var) != 0: abort( @@ -153,6 +152,14 @@ def read_var_list(config, cfg_path): + " Special idealized vars =" + str(ideal_list) ) + if subgrid_list.count(var) != 0: + abort( + var + + " is a variable handled in the subgrid section." + + " This should NOT be handled in the variiable list section." + + " Subgrid vars =" + + str(subgrid_list) + ) value = get_config_value( config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float ) From 16a771b3ed882b256a092a2cc3405fd6037daa0c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 19:07:12 -0700 Subject: [PATCH 0554/2067] Add failing test for trying to set one of the monthly variables in the variable list section --- python/ctsm/test/test_unit_fsurdat_modifier.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 531f2821ed..d40dc4a46c 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -122,6 +122,19 @@ def test_varlist_varinsubgrid(self): ): read_var_list(self.config, self.cfg_path) + def test_varlist_monthlyvar(self): + """test a read of varlist for a variable thats one of the monthly + variables handled in the dom_pft section""" + section = "modify_fsurdat_variable_list" + self.config.set(section, "MONTHLY_LAI", "100.") + with self.assertRaisesRegex( + SystemExit, + "is a variable handled as part of the dom_pft handling." + + " This should NOT be handled in the variiable list section." + + " Monthly vars handled this way =", + ): + read_var_list(self.config, self.cfg_path) + def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" section = "modify_fsurdat_subgrid_fractions" From 63e19beafe7b4f53d747646fcf810e590f4e6991 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 19:10:37 -0700 Subject: [PATCH 0555/2067] Get latest test to work --- python/ctsm/modify_input_files/fsurdat_modifier.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 4c210c08c2..29ba1cfedb 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -143,6 +143,7 @@ def read_var_list(config, cfg_path): var_list = config.options(section) ideal_list = ["soil_color", "pct_sand", "pct_clay", "organic", "pct_cft", "pct_nat_pft"] subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] + monthly_list = ["monthly_lai", "monthly_sai", "monthly_height_top", "monthly_height_bot"] for var in var_list: if ideal_list.count(var) != 0: abort( @@ -160,6 +161,14 @@ def read_var_list(config, cfg_path): + " Subgrid vars =" + str(subgrid_list) ) + if monthly_list.count(var) != 0: + abort( + var + + " is a variable handled as part of the dom_pft handling." + + " This should NOT be handled in the variiable list section." + + " Monthly vars handled this way =" + + str(monthly_list) + ) value = get_config_value( config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float ) From 843662468c28bbaea355ecd7ee3d1259dae4c264 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 19:20:00 -0700 Subject: [PATCH 0556/2067] Add std_elev and fmax to the list of variables to not set in the variable list section as they are handled in the main section --- python/ctsm/modify_input_files/fsurdat_modifier.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 29ba1cfedb..50d9fe611b 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -141,7 +141,7 @@ def read_var_list(config, cfg_path): varlist_settings = {} var_list = config.options(section) - ideal_list = ["soil_color", "pct_sand", "pct_clay", "organic", "pct_cft", "pct_nat_pft"] + ideal_list = ["soil_color", "pct_sand", "pct_clay", "organic", "pct_cft", "pct_nat_pft", "fmax", "std_elev"] subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] monthly_list = ["monthly_lai", "monthly_sai", "monthly_height_top", "monthly_height_bot"] for var in var_list: From 8390289f220930d5f5e7ee94303d5a080bbfc008 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 22:55:54 -0700 Subject: [PATCH 0557/2067] Black and lint update, add tests for lev1 and lev2 variables for set_varlist, test for badvar, and too high dimension, and get working, with needed for loops --- .../modify_input_files/fsurdat_modifier.py | 11 ++++++- .../ctsm/modify_input_files/modify_fsurdat.py | 32 ++++++++----------- python/ctsm/test/test_unit_modify_fsurdat.py | 25 ++++++++++++--- 3 files changed, 44 insertions(+), 24 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 50d9fe611b..62a3a40dd5 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -141,7 +141,16 @@ def read_var_list(config, cfg_path): varlist_settings = {} var_list = config.options(section) - ideal_list = ["soil_color", "pct_sand", "pct_clay", "organic", "pct_cft", "pct_nat_pft", "fmax", "std_elev"] + ideal_list = [ + "soil_color", + "pct_sand", + "pct_clay", + "organic", + "pct_cft", + "pct_nat_pft", + "fmax", + "std_elev", + ] subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] monthly_list = ["monthly_lai", "monthly_sai", "monthly_height_top", "monthly_height_bot"] for var in var_list: diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index 4a38ed4d96..cbfb528487 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -218,12 +218,7 @@ def check_varlist(self, settings, allow_uppercase_vars=False): """ Check a list of variables from a dictionary of settings """ - # exclude_list = ( "MONTHLY_LAI", "MONTHLY_SAI", - # "MONTHLY_HEIGHT_TOP", "MONTHLY_HEIGHT_BOT" ) for var in settings.keys(): - # if exclude_list.count(var) > 0: - # abort("Error: Variable "+var+" is already handled outside "+ - # "of the optional variable list sections") if not var in self.file: if not allow_uppercase_vars: errmsg = "Error: Variable " + var + " is NOT in the file" @@ -241,24 +236,25 @@ def set_varlist(self, settings): Set a list of variables from a dictionary of settings """ for var in settings.keys(): - # if exclude_list.count(var) > 0: - # abort("Error: Variable "+var+" is already handled outside "+ - # "of the optional variable list sections") if var in self.file: if len(self.file[var].dims) == 2: self.setvar_lev0(var, settings[var]) - elif self.file[var].dims == 3: - self.setvar_lev1(var, settings[var], lev1_dim=self.file[var].dims[0]) - elif self.file[var].dims == 4: - self.setvar_lev2( - var, - settings[var], - lev1_dim=self.file[var].dims[1], - lev2_dim=self.file[var].dims[0], - ) + elif len(self.file[var].dims) == 3: + dim1 = int(self.file.sizes[self.file[var].dims[0]]) + for lev1 in range(dim1 - 1): + self.setvar_lev1(var, settings[var], lev1_dim=lev1) + elif len(self.file[var].dims) == 4: + dim1 = int(self.file.sizes[self.file[var].dims[0]]) + dim2 = int(self.file.sizes[self.file[var].dims[1]]) + for lev1 in range(dim1 - 1): + for lev2 in range(dim2 - 1): + self.setvar_lev2(var, settings[var], lev1_dim=lev1, lev2_dim=lev2) else: abort( - "Error: Variable " + var + " is a higher dimension than currently allowed" + "Error: Variable " + + var + + " is a higher dimension than currently allowed = " + + str(self.file[var].dims) ) else: errmsg = "Error: Variable " + var + " is NOT in the file" diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index df84bd9c4c..97275b90af 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -25,8 +25,7 @@ class TestModifyFsurdat(unittest.TestCase): """Tests the setvar_lev functions and the - _get_rectangle function and - set_varlist method + _get_rectangle, check_varlist, and set_varlist methods """ def setUp(self): @@ -49,8 +48,9 @@ def setUp(self): # the fsurdat_modify tool reads variables like this from fsurdat file var_1d = np.arange(self.cols) var_lev0 = var_1d * np.ones((self.rows, self.cols)) - var_lev2 = var_1d * np.ones((self.rows, self.cols, self.rows, self.cols)) var_lev1 = var_1d * np.ones((self.cols, self.rows, self.cols)) + var_lev2 = var_1d * np.ones((self.rows, self.cols, self.rows, self.cols)) + var_lev3 = var_1d * np.ones((self.cols, self.rows, self.cols, self.rows, self.cols)) my_data = xr.Dataset( data_vars=dict( LONGXY=(["x", "y"], longxy), # use LONGXY as var_lev0 @@ -58,6 +58,7 @@ def setUp(self): var_lev0=(["x", "y"], var_lev0), var_lev1=(["w", "x", "y"], var_lev1), var_lev2=(["v", "w", "x", "y"], var_lev2), + var_lev3=(["z", "v", "w", "x", "y"], var_lev3), ) ) @@ -369,10 +370,24 @@ def test_getNotRectangle_latsOutOfBounds(self): ) def test_set_varlist(self): - """Test the set_varlist method""" - settings = {"var_lev0": 100.0} + """Test the set_varlist method for all the dimensions that works""" + settings = {"var_lev0": 100.0, "var_lev1": 100.0, "var_lev2": 100.0} self.modify_fsurdat.set_varlist(settings) + def test_set_varlist_badvar(self): + """Test the set_varlist method for a variable not on the file""" + settings = {"badvar": 100.0} + with self.assertRaisesRegex(SystemExit, "Variable badvar is NOT in the file"): + self.modify_fsurdat.set_varlist(settings) + + def test_set_varlist_toohighdim(self): + """Test the set_varlist method for a variable of too high a dimension""" + settings = {"var_lev3": 100.0} + with self.assertRaisesRegex( + SystemExit, "Variable var_lev3 is a higher dimension than currently allowed" + ): + self.modify_fsurdat.set_varlist(settings) + def _get_longxy_latixy(self, _min_lon, _max_lon, _min_lat, _max_lat): """ Return longxy, latixy, cols, rows From df2d2d23013232f52d892a26fd42336d991e1c9b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 23:40:08 -0700 Subject: [PATCH 0558/2067] Add uppercase variables for testing, and add several tests for check_varlist including the allow_uppercase option --- python/ctsm/test/test_unit_modify_fsurdat.py | 54 ++++++++++++++++++-- 1 file changed, 51 insertions(+), 3 deletions(-) diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index 97275b90af..84be4215f2 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -59,6 +59,10 @@ def setUp(self): var_lev1=(["w", "x", "y"], var_lev1), var_lev2=(["v", "w", "x", "y"], var_lev2), var_lev3=(["z", "v", "w", "x", "y"], var_lev3), + VAR_LEV0_UPPERCASE=(["x", "y"], var_lev0), + VAR_LEV1_UPPERCASE=(["w", "x", "y"], var_lev1), + VAR_LEV2_UPPERCASE=(["v", "w", "x", "y"], var_lev2), + VAR_LEV3_UPPERCASE=(["z", "v", "w", "x", "y"], var_lev3), ) ) @@ -374,11 +378,46 @@ def test_set_varlist(self): settings = {"var_lev0": 100.0, "var_lev1": 100.0, "var_lev2": 100.0} self.modify_fsurdat.set_varlist(settings) - def test_set_varlist_badvar(self): - """Test the set_varlist method for a variable not on the file""" + def test_check_varlist(self): + """Test the check_varlist method for all the dimensions that works""" + settings = {"var_lev0": 100.0, "var_lev1": 100.0, "var_lev2": 100.0} + settings_orig = settings + self.modify_fsurdat.check_varlist(settings) + self.assertEqual( + settings_orig, settings, "list of variable settings not identical as expected" + ) + + def test_check_varlist_uppercase(self): + """Test the check_varlist method for all the dimensions that + works with allowuppercase option""" + expected = { + "VAR_LEV0_UPPERCASE": 100.0, + "VAR_LEV1_UPPERCASE": 200.0, + "VAR_LEV2_UPPERCASE": 300.0, + } + settings = { + "var_lev0_uppercase": 100.0, + "var_lev1_uppercase": 200.0, + "var_lev2_uppercase": 300.0, + } + self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) + self.assertEqual( + expected, + settings, + "list of variable settings not converted to uppercase as expected", + ) + + def test_check_varlist_badvar(self): + """Test the check_varlist method for a variable not on the file""" settings = {"badvar": 100.0} with self.assertRaisesRegex(SystemExit, "Variable badvar is NOT in the file"): - self.modify_fsurdat.set_varlist(settings) + self.modify_fsurdat.check_varlist(settings) + + def test_check_varlist_badvar_uppercase(self): + """Test the check_varlist method for a variable not on the file with allow uppercase""" + settings = {"badvar": 100.0} + with self.assertRaisesRegex(SystemExit, "Variable BADVAR is NOT in the file"): + self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) def test_set_varlist_toohighdim(self): """Test the set_varlist method for a variable of too high a dimension""" @@ -388,6 +427,15 @@ def test_set_varlist_toohighdim(self): ): self.modify_fsurdat.set_varlist(settings) + def test_set_varlist_toohighdim_uppercase(self): + """Test the set_varlist method for a variable of too high a dimension in uppercase""" + settings = {"var_lev3_uppercase": 100.0} + with self.assertRaisesRegex( + SystemExit, "Variable VAR_LEV3_UPPERCASE is a higher dimension than currently allowed" + ): + self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) + self.modify_fsurdat.set_varlist(settings) + def _get_longxy_latixy(self, _min_lon, _max_lon, _min_lat, _max_lat): """ Return longxy, latixy, cols, rows From 9b2ed223d93eb597d2cd5625588d34e10fa6f546 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 29 Dec 2022 23:49:06 -0700 Subject: [PATCH 0559/2067] Add a test for 100 glacier for subgrid and a sum of special landunits to 100 both for read_subgrid --- .../ctsm/test/test_unit_fsurdat_modifier.py | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index d40dc4a46c..a49a6dea68 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -68,6 +68,29 @@ def test_read_subgrid(self): """test a simple read of subgrid""" read_subgrid(self.config, self.cfg_path) + def test_read_subgrid_allglacier(self): + """test a read of subgrid that's for all glacier""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "0.") + self.config.set(section, "pct_lake", "0.") + self.config.set(section, "pct_wetland", "0.") + self.config.set(section, "pct_glacier", "100.") + self.config.set(section, "pct_natveg", "0.") + self.config.set(section, "pct_crop", "0.") + read_subgrid(self.config, self.cfg_path) + + def test_read_subgrid_allspecial(self): + """test a read of subgrid that's all special landunits""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "0.") + self.config.set(section, "pct_lake", "25.") + self.config.set(section, "pct_wetland", "35.") + self.config.set(section, "pct_glacier", "40.") + self.config.set(section, "pct_natveg", "0.") + self.config.set(section, "pct_crop", "0.") + read_subgrid(self.config, self.cfg_path) + + def test_read_var_list(self): """test a simple read of var_list""" read_var_list(self.config, self.cfg_path) From b23e17eeb0c0e153d49ef928afdeba9c76155293 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 31 Dec 2022 00:28:15 -0700 Subject: [PATCH 0560/2067] Add back in some tests for some multidimensional urban arrarys to the standard opt testing, also rework check_varlist a bit so that settings isn't changed, but it returns the new list --- python/ctsm/modify_input_files/fsurdat_modifier.py | 4 ++-- python/ctsm/modify_input_files/modify_fsurdat.py | 14 +++++++++----- python/ctsm/test/test_unit_fsurdat_modifier.py | 1 - python/ctsm/test/test_unit_modify_fsurdat.py | 13 ++++++------- .../testinputs/modify_fsurdat_opt_sections.cfg | 7 ++++++- 5 files changed, 23 insertions(+), 16 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 62a3a40dd5..9554117abd 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -438,8 +438,8 @@ def fsurdat_modifier(parser): if process_var_list: varlist = read_var_list(config, cfg_path) - modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) - modify_fsurdat.set_varlist(varlist) + update_list = modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) + modify_fsurdat.set_varlist(update_list) else: check_no_varlist_section(config) diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index cbfb528487..85d5dcdd30 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -218,7 +218,10 @@ def check_varlist(self, settings, allow_uppercase_vars=False): """ Check a list of variables from a dictionary of settings """ - for var in settings.keys(): + settings_return = {} + varlist = settings.keys() + for var in varlist: + val = settings[var] if not var in self.file: if not allow_uppercase_vars: errmsg = "Error: Variable " + var + " is NOT in the file" @@ -226,10 +229,11 @@ def check_varlist(self, settings, allow_uppercase_vars=False): if not var.upper() in self.file: errmsg = "Error: Variable " + var.upper() + " is NOT in the file" abort(errmsg) - val = settings[var] - del settings[var] - var = var.upper() - settings[var] = val + varu = var.upper() + settings_return[varu] = val + else: + settings_return[var] = val + return settings_return def set_varlist(self, settings): """ diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index a49a6dea68..e8d1cf7c8a 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -90,7 +90,6 @@ def test_read_subgrid_allspecial(self): self.config.set(section, "pct_crop", "0.") read_subgrid(self.config, self.cfg_path) - def test_read_var_list(self): """test a simple read of var_list""" read_var_list(self.config, self.cfg_path) diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index 84be4215f2..580845bfea 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -381,10 +381,9 @@ def test_set_varlist(self): def test_check_varlist(self): """Test the check_varlist method for all the dimensions that works""" settings = {"var_lev0": 100.0, "var_lev1": 100.0, "var_lev2": 100.0} - settings_orig = settings - self.modify_fsurdat.check_varlist(settings) + settings_new = self.modify_fsurdat.check_varlist(settings) self.assertEqual( - settings_orig, settings, "list of variable settings not identical as expected" + settings_new, settings, "list of variable settings not identical as expected" ) def test_check_varlist_uppercase(self): @@ -400,10 +399,10 @@ def test_check_varlist_uppercase(self): "var_lev1_uppercase": 200.0, "var_lev2_uppercase": 300.0, } - self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) + settings_new = self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) self.assertEqual( expected, - settings, + settings_new, "list of variable settings not converted to uppercase as expected", ) @@ -433,8 +432,8 @@ def test_set_varlist_toohighdim_uppercase(self): with self.assertRaisesRegex( SystemExit, "Variable VAR_LEV3_UPPERCASE is a higher dimension than currently allowed" ): - self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) - self.modify_fsurdat.set_varlist(settings) + settings_new = self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) + self.modify_fsurdat.set_varlist(settings_new) def _get_longxy_latixy(self, _min_lon, _max_lon, _min_lat, _max_lat): """ diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index fb163e9e72..704587c4d3 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -27,7 +27,7 @@ lnd_lon_2 = 360 # Section for subgrid_fractions [modify_fsurdat_subgrid_fractions] -# Set to 100% urban for the test +# Set to 100% lake for the test PCT_NATVEG = 0.0 PCT_CROP = 0.0 PCT_LAKE = 100.0 @@ -39,3 +39,8 @@ PCT_WETLAND = 0.0 [modify_fsurdat_variable_list] # Set lake-depth to 200 for the test LAKEDEPTH = 200.00 + +# Set soem urban multidimensional variables to 200 for the test +CANYON_HWR = 200.00 +HT_ROOF = 200.0 +T_BUILDING_MIN = 200 From 7ece08f2c78fd3d4cbf5ba3b3e69829d7ceca725 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 31 Dec 2022 01:43:01 -0700 Subject: [PATCH 0561/2067] Add some more variables to the list of variables that can't be changed for fsurdat_modifier --- .../modify_input_files/fsurdat_modifier.py | 21 ++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 9554117abd..cb27e988af 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -152,7 +152,26 @@ def read_var_list(config, cfg_path): "std_elev", ] subgrid_list = ["pct_natveg", "pct_crop", "pct_lake", "pct_glacier", "pct_wetland", "pct_urban"] - monthly_list = ["monthly_lai", "monthly_sai", "monthly_height_top", "monthly_height_bot"] + # List of variables that should be excluded because they are changed elsewhere, + # or they shouldn't be changed # Ds, Dsmax, and Ws are excluded because they + # are of mixed case and we only search for varaibles in lowercase + # or uppercase and not mixed case. + monthly_list = [ + "monthly_lai", + "monthly_sai", + "monthly_height_top", + "monthly_height_bot", + "ds", + "mxsoil_color", + "natpft", + "cft", + "time", + "longxy", + "latixy", + "dsmax", + "area", + "ws", + ] for var in var_list: if ideal_list.count(var) != 0: abort( From bb7a9822c960f5eb78a1008f6f6e75637ef8f232 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 31 Dec 2022 15:27:26 -0700 Subject: [PATCH 0562/2067] Start adding handling of numurbl so that PCT_URBAN can be recognized as an array, and add a check that you can setup read_subgrid to be 100% urban --- python/ctsm/modify_input_files/fsurdat_modifier.py | 11 ++++++++--- python/ctsm/modify_input_files/modify_fsurdat.py | 7 +++++++ python/ctsm/test/test_unit_fsurdat_modifier.py | 12 ++++++++++++ python/ctsm/test/test_unit_modify_fsurdat.py | 8 ++++++++ .../test/testinputs/modify_fsurdat_opt_sections.cfg | 1 + 5 files changed, 36 insertions(+), 3 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index cb27e988af..5e07b64089 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -89,7 +89,7 @@ def check_no_varlist_section(config): ) -def read_subgrid(config, cfg_path): +def read_subgrid(config, cfg_path, numurbl=3): """Read the subgrid fraction section from the config file""" section = "modify_fsurdat_subgrid_fractions" if not config.has_section(section): @@ -123,7 +123,12 @@ def read_subgrid(config, cfg_path): ) subgrid_settings[var.upper()] = value - varsum += value + # Urban is multidimensional so if a scalar value, must be multiplied + # by the density dimension + if var == "pct_urban": + varsum += value * numurbl + else: + varsum += value if varsum != 100.0: abort( "PCT fractions in subgrid section do NOT sum to a hundred as they should. Sum = " @@ -450,7 +455,7 @@ def fsurdat_modifier(parser): # Handle optional sections # if process_subgrid: - subgrid = read_subgrid(config, cfg_path) + subgrid = read_subgrid(config, cfg_path, numurbl=modify_fsurdat.get_urb_dens()) modify_fsurdat.set_varlist(subgrid) else: check_no_subgrid_section(config) diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index 85d5dcdd30..4b4b2f404c 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -29,7 +29,10 @@ def __init__( self, my_data, lon_1, lon_2, lat_1, lat_2, landmask_file, lat_dimname, lon_dimname ): + self.numurbl = 3 # Number of urban density types self.file = my_data + if "numurbl" in self.file.dims: + self.numurbl = self.file.dims["numurbl"] self.rectangle = self._get_rectangle( lon_1=lon_1, @@ -115,6 +118,10 @@ def _get_rectangle(lon_1, lon_2, lat_1, lat_2, longxy, latixy): return rectangle + def get_urb_dens(self): + """Get the number of urban density classes""" + return self.numurbl + def write_output(self, fsurdat_in, fsurdat_out): """ Description diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index e8d1cf7c8a..75ee8efd74 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -90,6 +90,18 @@ def test_read_subgrid_allspecial(self): self.config.set(section, "pct_crop", "0.") read_subgrid(self.config, self.cfg_path) + def test_read_subgrid_allurban(self): + """test a read of subgrid that's all urban""" + section = "modify_fsurdat_subgrid_fractions" + third = float(100.0 / 3.0) + self.config.set(section, "pct_urban", str(third)) + self.config.set(section, "pct_lake", "0.") + self.config.set(section, "pct_wetland", "0.") + self.config.set(section, "pct_glacier", "0.") + self.config.set(section, "pct_natveg", "0.") + self.config.set(section, "pct_crop", "0.") + read_subgrid(self.config, self.cfg_path) + def test_read_var_list(self): """test a simple read of var_list""" read_var_list(self.config, self.cfg_path) diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index 580845bfea..07554e07ab 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -386,6 +386,14 @@ def test_check_varlist(self): settings_new, settings, "list of variable settings not identical as expected" ) + def test_get_numurb_dens(self): + """Check that get num urban density types is correct""" + self.assertEqual( + self.modify_fsurdat.get_urb_dens(), + 3, + "Default number of urban density types is correct", + ) + def test_check_varlist_uppercase(self): """Test the check_varlist method for all the dimensions that works with allowuppercase option""" diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index 704587c4d3..6abdc3c350 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -33,6 +33,7 @@ PCT_CROP = 0.0 PCT_LAKE = 100.0 PCT_GLACIER = 0.0 PCT_WETLAND = 0.0 +PCT_URBAN = 0.0 # Section with a list of variables to prcoess From e8f0b62056958745ca97e8660c3a897f4bbe9b8d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 31 Dec 2022 18:10:58 -0700 Subject: [PATCH 0563/2067] List out two subroutines so will pass lint check, now make all works, make abort if numurbl is not on the fsurdat file, set the test for it to 9 for the test case --- .../modify_input_files/fsurdat_modifier.py | 277 +++++++++++------- .../ctsm/modify_input_files/modify_fsurdat.py | 2 + python/ctsm/test/test_unit_modify_fsurdat.py | 3 +- 3 files changed, 169 insertions(+), 113 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 5e07b64089..e0ba41a35b 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -210,6 +210,147 @@ def read_var_list(config, cfg_path): return varlist_settings +def modify_optional( + modify_fsurdat, + idealized, + include_nonveg, + max_sat_area, + std_elev, + soil_color, + dom_pft, + lai, + sai, + hgt_top, + hgt_bot, +): + """Modify the dataset according to the optional settings""" + + # Set fsurdat variables in a rectangle that could be global (default). + # Note that the land/ocean mask gets specified in the domain file for + # MCT or the ocean mesh files for NUOPC. Here the user may specify + # fsurdat variables inside a box but cannot change which points will + # run as land and which as ocean. + if idealized: + modify_fsurdat.set_idealized() # set 2D variables + # set 3D and 4D variables pertaining to natural vegetation + modify_fsurdat.set_dom_pft(dom_pft=0, lai=[], sai=[], hgt_top=[], hgt_bot=[]) + logger.info("idealized complete") + + if max_sat_area is not None: # overwrite "idealized" value + modify_fsurdat.setvar_lev0("FMAX", max_sat_area) + logger.info("max_sat_area complete") + + if std_elev is not None: # overwrite "idealized" value + modify_fsurdat.setvar_lev0("STD_ELEV", std_elev) + logger.info("std_elev complete") + + if soil_color is not None: # overwrite "idealized" value + modify_fsurdat.setvar_lev0("SOIL_COLOR", soil_color) + logger.info("soil_color complete") + + if not include_nonveg: + modify_fsurdat.zero_nonveg() + logger.info("zero_nonveg complete") + + # set_dom_pft follows zero_nonveg because it modifies PCT_NATVEG + # and PCT_CROP in the user-defined rectangle + if dom_pft is not None: + modify_fsurdat.set_dom_pft( + dom_pft=dom_pft, lai=lai, sai=sai, hgt_top=hgt_top, hgt_bot=hgt_bot + ) + logger.info("dom_pft complete") + + +def read_opt_config(modify_fsurdat, config, cfg_path, section): + """read the optional parts of the main section config file""" + # not required: user may set these in the .cfg file + max_pft = int(max(modify_fsurdat.file.lsmpft)) + dom_pft = get_config_value( + config=config, + section=section, + item="dom_pft", + file_path=cfg_path, + allowed_values=range(max_pft + 1), # integers from 0 to max_pft + convert_to_type=int, + can_be_unset=True, + ) + + lai = get_config_value( + config=config, + section=section, + item="lai", + file_path=cfg_path, + is_list=True, + convert_to_type=float, + can_be_unset=True, + ) + sai = get_config_value( + config=config, + section=section, + item="sai", + file_path=cfg_path, + is_list=True, + convert_to_type=float, + can_be_unset=True, + ) + hgt_top = get_config_value( + config=config, + section=section, + item="hgt_top", + file_path=cfg_path, + is_list=True, + convert_to_type=float, + can_be_unset=True, + ) + hgt_bot = get_config_value( + config=config, + section=section, + item="hgt_bot", + file_path=cfg_path, + is_list=True, + convert_to_type=float, + can_be_unset=True, + ) + + max_soil_color = int(modify_fsurdat.file.mxsoil_color) + soil_color = get_config_value( + config=config, + section=section, + item="soil_color", + file_path=cfg_path, + allowed_values=range(1, max_soil_color + 1), # 1 to max_soil_color + convert_to_type=int, + can_be_unset=True, + ) + + std_elev = get_config_value( + config=config, + section=section, + item="std_elev", + file_path=cfg_path, + convert_to_type=float, + can_be_unset=True, + ) + max_sat_area = get_config_value( + config=config, + section=section, + item="max_sat_area", + file_path=cfg_path, + convert_to_type=float, + can_be_unset=True, + ) + return ( + max_sat_area, + std_elev, + soil_color, + dom_pft, + lai, + sai, + hgt_top, + hgt_bot, + ) + + def fsurdat_modifier(parser): """Implementation of fsurdat_modifier command""" # read the .cfg (config) file @@ -335,122 +476,34 @@ def fsurdat_modifier(parser): lon_dimname, ) - # not required: user may set these in the .cfg file - max_pft = int(max(modify_fsurdat.file.lsmpft)) - dom_pft = get_config_value( - config=config, - section=section, - item="dom_pft", - file_path=cfg_path, - allowed_values=range(max_pft + 1), # integers from 0 to max_pft - convert_to_type=int, - can_be_unset=True, - ) - - lai = get_config_value( - config=config, - section=section, - item="lai", - file_path=cfg_path, - is_list=True, - convert_to_type=float, - can_be_unset=True, - ) - sai = get_config_value( - config=config, - section=section, - item="sai", - file_path=cfg_path, - is_list=True, - convert_to_type=float, - can_be_unset=True, - ) - hgt_top = get_config_value( - config=config, - section=section, - item="hgt_top", - file_path=cfg_path, - is_list=True, - convert_to_type=float, - can_be_unset=True, - ) - hgt_bot = get_config_value( - config=config, - section=section, - item="hgt_bot", - file_path=cfg_path, - is_list=True, - convert_to_type=float, - can_be_unset=True, - ) - - max_soil_color = int(modify_fsurdat.file.mxsoil_color) - soil_color = get_config_value( - config=config, - section=section, - item="soil_color", - file_path=cfg_path, - allowed_values=range(1, max_soil_color + 1), # 1 to max_soil_color - convert_to_type=int, - can_be_unset=True, - ) - - std_elev = get_config_value( - config=config, - section=section, - item="std_elev", - file_path=cfg_path, - convert_to_type=float, - can_be_unset=True, - ) - max_sat_area = get_config_value( - config=config, - section=section, - item="max_sat_area", - file_path=cfg_path, - convert_to_type=float, - can_be_unset=True, - ) - + # Read parts that are optional + ( + max_sat_area, + std_elev, + soil_color, + dom_pft, + lai, + sai, + hgt_top, + hgt_bot, + ) = read_opt_config(modify_fsurdat, config, cfg_path, section) # ------------------------------ # modify surface data properties # ------------------------------ - # Set fsurdat variables in a rectangle that could be global (default). - # Note that the land/ocean mask gets specified in the domain file for - # MCT or the ocean mesh files for NUOPC. Here the user may specify - # fsurdat variables inside a box but cannot change which points will - # run as land and which as ocean. - if idealized: - modify_fsurdat.set_idealized() # set 2D variables - # set 3D and 4D variables pertaining to natural vegetation - modify_fsurdat.set_dom_pft(dom_pft=0, lai=[], sai=[], hgt_top=[], hgt_bot=[]) - logger.info("idealized complete") - - if max_sat_area is not None: # overwrite "idealized" value - modify_fsurdat.setvar_lev0("FMAX", max_sat_area) - logger.info("max_sat_area complete") - - if std_elev is not None: # overwrite "idealized" value - modify_fsurdat.setvar_lev0("STD_ELEV", std_elev) - logger.info("std_elev complete") - - if soil_color is not None: # overwrite "idealized" value - modify_fsurdat.setvar_lev0("SOIL_COLOR", soil_color) - logger.info("soil_color complete") - - if not include_nonveg: - modify_fsurdat.zero_nonveg() - logger.info("zero_nonveg complete") - - # set_dom_pft follows zero_nonveg because it modifies PCT_NATVEG - # and PCT_CROP in the user-defined rectangle - if dom_pft is not None: - modify_fsurdat.set_dom_pft( - dom_pft=dom_pft, lai=lai, sai=sai, hgt_top=hgt_top, hgt_bot=hgt_bot - ) - logger.info("dom_pft complete") - + modify_optional( + modify_fsurdat, + idealized, + include_nonveg, + max_sat_area, + std_elev, + soil_color, + dom_pft, + lai, + sai, + hgt_top, + hgt_bot, + ) # # Handle optional sections # diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index 4b4b2f404c..dc55cc55a8 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -33,6 +33,8 @@ def __init__( self.file = my_data if "numurbl" in self.file.dims: self.numurbl = self.file.dims["numurbl"] + else: + abort("numurbl is not a dimension on the input surface dataset file and needs to be") self.rectangle = self._get_rectangle( lon_1=lon_1, diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index 07554e07ab..7a72288d53 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -55,6 +55,7 @@ def setUp(self): data_vars=dict( LONGXY=(["x", "y"], longxy), # use LONGXY as var_lev0 LATIXY=(["x", "y"], latixy), # __init__ expects LONGXY, LATIXY + urbdens=(["numurbl"], var_1d), # numurbl needs to be dimension var_lev0=(["x", "y"], var_lev0), var_lev1=(["w", "x", "y"], var_lev1), var_lev2=(["v", "w", "x", "y"], var_lev2), @@ -390,7 +391,7 @@ def test_get_numurb_dens(self): """Check that get num urban density types is correct""" self.assertEqual( self.modify_fsurdat.get_urb_dens(), - 3, + 9, "Default number of urban density types is correct", ) From cc3120408899617a8b2979fb1eb2e5e4312f03f5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 31 Dec 2022 18:20:24 -0700 Subject: [PATCH 0564/2067] Add something that says all target is successful --- python/Makefile | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/python/Makefile b/python/Makefile index bf219f16b6..a1eaba0928 100644 --- a/python/Makefile +++ b/python/Makefile @@ -24,6 +24,10 @@ PYLINT_SRC = \ ctsm all: test lint black + @echo + @echo + @echo "Successfully ran all standard tests" + test: utest stest .PHONY: utest From a268e9734e71ed33305fd12685328f749bbc743b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 1 Jan 2023 19:08:31 -0700 Subject: [PATCH 0565/2067] Require PCT_URBAN to be a list of numurbl values, start adding a new config method get_config_value_or_array --- python/ctsm/config_utils.py | 28 ++++++++++++ .../modify_input_files/fsurdat_modifier.py | 44 ++++++++++++------- .../ctsm/test/test_unit_fsurdat_modifier.py | 11 +++-- .../modify_fsurdat_opt_sections.cfg | 2 +- 4 files changed, 61 insertions(+), 24 deletions(-) diff --git a/python/ctsm/config_utils.py b/python/ctsm/config_utils.py index 847a1804f6..b8a8d6cd77 100644 --- a/python/ctsm/config_utils.py +++ b/python/ctsm/config_utils.py @@ -86,6 +86,34 @@ def get_config_value( return val +def get_config_value_or_array( + config, + section, + item, + file_path, + convert_to_type=None, +): + """Get a config value as a single value or as an array if it's expressed as an array""" + print(config) + print(section) + print(item) + print(file_path) + if convert_to_type is not None: + if convert_to_type is float: + print("float") + elif convert_to_type is int: + print("int") + elif convert_to_type is str: + print("str") + else: + abort( + "get_config_value_or_array can only have convert_to_type as float, int or str not " + + str(convert_to_type) + ) + + abort("This method not implemented yet") + + def _handle_config_value( var, default, item, is_list, convert_to_type, can_be_unset, allowed_values ): diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index e0ba41a35b..7353c16ef5 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -89,6 +89,12 @@ def check_no_varlist_section(config): ) +def check_range(var, section, value, minval, maxval): + """Check that the value is within range""" + if value < minval or value > maxval: + abort("Variable " + var + " in " + section + " is out of range of 0 to 100 = " + str(value)) + + def read_subgrid(config, cfg_path, numurbl=3): """Read the subgrid fraction section from the config file""" section = "modify_fsurdat_subgrid_fractions" @@ -109,26 +115,30 @@ def read_subgrid(config, cfg_path, numurbl=3): + " is not a valid variable name. Valid vars =" + str(valid_list) ) - value = get_config_value( - config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float - ) - if value < 0.0 or value > 100.0: - abort( - "Variable " - + var - + " in " - + section - + " is out of range of 0 to 100 = " - + str(value) - ) - - subgrid_settings[var.upper()] = value - # Urban is multidimensional so if a scalar value, must be multiplied - # by the density dimension + # Urban is multidimensional if var == "pct_urban": - varsum += value * numurbl + vallist = get_config_value( + config=config, + section=section, + item=var, + file_path=cfg_path, + is_list=True, + convert_to_type=float, + ) + if len(vallist) != numurbl: + abort("PCT_URBAN is not a list of the expect size of " + str(numurbl)) + # so if a scalar value, must be multiplied # by the density dimension + for val in vallist: + check_range(var, section, val, 0.0, 100.0) + varsum += val else: + value = get_config_value( + config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float + ) + check_range(var, section, value, 0.0, 100.0) varsum += value + + subgrid_settings[var.upper()] = value if varsum != 100.0: abort( "PCT fractions in subgrid section do NOT sum to a hundred as they should. Sum = " diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 75ee8efd74..5231d30318 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -71,7 +71,7 @@ def test_read_subgrid(self): def test_read_subgrid_allglacier(self): """test a read of subgrid that's for all glacier""" section = "modify_fsurdat_subgrid_fractions" - self.config.set(section, "pct_urban", "0.") + self.config.set(section, "pct_urban", "0. 0. 0.") self.config.set(section, "pct_lake", "0.") self.config.set(section, "pct_wetland", "0.") self.config.set(section, "pct_glacier", "100.") @@ -82,7 +82,7 @@ def test_read_subgrid_allglacier(self): def test_read_subgrid_allspecial(self): """test a read of subgrid that's all special landunits""" section = "modify_fsurdat_subgrid_fractions" - self.config.set(section, "pct_urban", "0.") + self.config.set(section, "pct_urban", "0. 0. 0.") self.config.set(section, "pct_lake", "25.") self.config.set(section, "pct_wetland", "35.") self.config.set(section, "pct_glacier", "40.") @@ -93,8 +93,7 @@ def test_read_subgrid_allspecial(self): def test_read_subgrid_allurban(self): """test a read of subgrid that's all urban""" section = "modify_fsurdat_subgrid_fractions" - third = float(100.0 / 3.0) - self.config.set(section, "pct_urban", str(third)) + self.config.set(section, "pct_urban", "100.0 0.0 0.0") self.config.set(section, "pct_lake", "0.") self.config.set(section, "pct_wetland", "0.") self.config.set(section, "pct_glacier", "0.") @@ -109,14 +108,14 @@ def test_read_var_list(self): def test_subgrid_outofrange(self): """test a read of subgrid that's out of range""" section = "modify_fsurdat_subgrid_fractions" - self.config.set(section, "pct_urban", "101.") + self.config.set(section, "pct_urban", "101. 0. 0.") with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): read_subgrid(self.config, self.cfg_path) def test_subgrid_notsumtohundred(self): """test a read of subgrid that's doesn't sum to a hundred""" section = "modify_fsurdat_subgrid_fractions" - self.config.set(section, "pct_urban", "0.") + self.config.set(section, "pct_urban", "0. 0. 0.") self.config.set(section, "pct_lake", "0.") self.config.set(section, "pct_wetland", "0.") self.config.set(section, "pct_glacier", "0.") diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index 6abdc3c350..c73dd43a68 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -33,7 +33,7 @@ PCT_CROP = 0.0 PCT_LAKE = 100.0 PCT_GLACIER = 0.0 PCT_WETLAND = 0.0 -PCT_URBAN = 0.0 +PCT_URBAN = 0.0 0.0 0.0 # Section with a list of variables to prcoess From e317a6ce56554d60e5de9908ba20d577e05fa222 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 1 Jan 2023 19:22:44 -0700 Subject: [PATCH 0566/2067] Add some tests that the list size of PCT_URBAN is correct and will fail gracefully if not --- .../modify_input_files/fsurdat_modifier.py | 2 +- .../ctsm/test/test_unit_fsurdat_modifier.py | 27 +++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 7353c16ef5..f9f36a664e 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -126,7 +126,7 @@ def read_subgrid(config, cfg_path, numurbl=3): convert_to_type=float, ) if len(vallist) != numurbl: - abort("PCT_URBAN is not a list of the expect size of " + str(numurbl)) + abort("PCT_URBAN is not a list of the expected size of " + str(numurbl)) # so if a scalar value, must be multiplied # by the density dimension for val in vallist: check_range(var, section, val, 0.0, 100.0) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 5231d30318..6a754065bc 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -112,6 +112,33 @@ def test_subgrid_outofrange(self): with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): read_subgrid(self.config, self.cfg_path) + def test_subgrid_pct_urban_toosmall(self): + """test a read of subgrid for PCT_URBAN that's an array too small""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "100. 0.") + with self.assertRaisesRegex( + SystemExit, "PCT_URBAN is not a list of the expected size of 3" + ): + read_subgrid(self.config, self.cfg_path) + + def test_subgrid_pct_urban_toobig(self): + """test a read of subgrid for PCT_URBAN that's an array too big""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "100. 0. 0. 0.") + with self.assertRaisesRegex( + SystemExit, "PCT_URBAN is not a list of the expected size of 3" + ): + read_subgrid(self.config, self.cfg_path) + + def test_subgrid_pct_urban_singlevalue(self): + """test a read of subgrid for PCT_URBAN that's a single value""" + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "100.") + with self.assertRaisesRegex( + SystemExit, "PCT_URBAN is not a list of the expected size of 3" + ): + read_subgrid(self.config, self.cfg_path) + def test_subgrid_notsumtohundred(self): """test a read of subgrid that's doesn't sum to a hundred""" section = "modify_fsurdat_subgrid_fractions" From 50878c85553c0a0d79faefd65bd01286089b3bf6 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 1 Jan 2023 23:14:36 -0700 Subject: [PATCH 0567/2067] Add a new unit tester for the config_utils module --- python/ctsm/test/test_unit_config_utils.py | 48 ++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 python/ctsm/test/test_unit_config_utils.py diff --git a/python/ctsm/test/test_unit_config_utils.py b/python/ctsm/test/test_unit_config_utils.py new file mode 100644 index 0000000000..45b976f528 --- /dev/null +++ b/python/ctsm/test/test_unit_config_utils.py @@ -0,0 +1,48 @@ +#!/usr/bin/env python3 + +"""Unit tests for config_utils +""" + +import unittest + +from ctsm import unit_testing +from ctsm.config_utils import lon_range_0_to_360 + +# Allow names that pylint doesn't like, because otherwise I find it hard +# to make readable unit test names +# pylint: disable=invalid-name + + +class TestConfigUtils(unittest.TestCase): + """Tests of config_utils""" + + def test_negative_lon(self): + """ Test lon_range_0_to_360 for a negative longitude""" + lon = -180. + lon_new = lon_range_0_to_360(lon) + self.assertEqual( lon_new, 180., "lon not as expected" ) + + def test_negative_lon(self): + """ Test lon_range_0_to_360 for a negative longitude""" + lon = -5. + lon_new = lon_range_0_to_360(lon) + self.assertEqual( lon_new, 355., "lon not as expected" ) + + + def test_regular_lon(self): + """ Test lon_range_0_to_360 for a regular longitude""" + lon = 22.567 + lon_new = lon_range_0_to_360(lon) + self.assertEqual( lon_new, lon, "lon not as expected" ) + + def test_lon_out_of_range(self): + """ Test lon_range_0_to_360 for longitude out of range""" + lon = 361. + with self.assertRaisesRegex(SystemExit, "lon_in needs to be in the range 0 to 360"): + lon_range_0_to_360(lon) + + def test_lon_out_of_range_negative(self): + """ Test lon_range_0_to_360 for longitude out of range""" + lon = -181. + with self.assertRaisesRegex(SystemExit, "lon_in needs to be in the range 0 to 360"): + lon_range_0_to_360(lon) From 8a18ea895bbd09c2b477d2f5092392a7c1c314e7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Jan 2023 11:45:13 -0700 Subject: [PATCH 0568/2067] hrv_xsmrpool_to_atm_dribbler now considers allows_non_annual_delta. --- src/biogeochem/CNVegCarbonFluxType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 48dfef418b..3a0782ffe3 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -779,7 +779,7 @@ subroutine InitAllocate(this, bounds, carbon_type) bounds = bounds, & name = 'hrv_xsmrpool_to_atm_' // carbon_type_suffix, & units = 'gC/m^2', & - allows_non_annual_delta = .false.) + allows_non_annual_delta = allows_non_annual_delta) end subroutine InitAllocate From 1f7d82a9e9a2dcb39e0ada0aabb10985d0f0b410 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 2 Jan 2023 18:59:10 -0700 Subject: [PATCH 0569/2067] Start adding tests for get_config_value_or_array to unit testing that fail as expected at this point --- python/ctsm/config_utils.py | 5 +- python/ctsm/test/test_unit_config_utils.py | 85 +++++++++++++++++----- 2 files changed, 70 insertions(+), 20 deletions(-) diff --git a/python/ctsm/config_utils.py b/python/ctsm/config_utils.py index b8a8d6cd77..2dc5428a2f 100644 --- a/python/ctsm/config_utils.py +++ b/python/ctsm/config_utils.py @@ -93,7 +93,9 @@ def get_config_value_or_array( file_path, convert_to_type=None, ): - """Get a config value as a single value or as an array if it's expressed as an array""" + """Get a config value as a single value or as an array if it's expressed as an array + for cases when you don't know how it's going to be expressed""" + val = "thing" print(config) print(section) print(item) @@ -112,6 +114,7 @@ def get_config_value_or_array( ) abort("This method not implemented yet") + return val def _handle_config_value( diff --git a/python/ctsm/test/test_unit_config_utils.py b/python/ctsm/test/test_unit_config_utils.py index 45b976f528..cb650e7d04 100644 --- a/python/ctsm/test/test_unit_config_utils.py +++ b/python/ctsm/test/test_unit_config_utils.py @@ -5,44 +5,91 @@ import unittest +from configparser import ConfigParser + from ctsm import unit_testing -from ctsm.config_utils import lon_range_0_to_360 +from ctsm.config_utils import lon_range_0_to_360, get_config_value_or_array -# Allow names that pylint doesn't like, because otherwise I find it hard -# to make readable unit test names +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable # pylint: disable=invalid-name +# pylint: disable=protected-access + class TestConfigUtils(unittest.TestCase): """Tests of config_utils""" - def test_negative_lon(self): - """ Test lon_range_0_to_360 for a negative longitude""" - lon = -180. - lon_new = lon_range_0_to_360(lon) - self.assertEqual( lon_new, 180., "lon not as expected" ) + # Allow these to be set outside of the __init__ method + # pylint: disable=attribute-defined-outside-init + def setUp(self): + """Setup for testing""" + self.config = ConfigParser() + self.section = "main" + self.file_path = "path_to_file" + self.config[self.section] = {} def test_negative_lon(self): - """ Test lon_range_0_to_360 for a negative longitude""" - lon = -5. + """Test lon_range_0_to_360 for a negative longitude""" + lon = -180.0 lon_new = lon_range_0_to_360(lon) - self.assertEqual( lon_new, 355., "lon not as expected" ) + self.assertEqual(lon_new, 180.0, "lon not as expected") + def test_negative2_lon(self): + """Test lon_range_0_to_360 for a negative longitude""" + lon = -5.0 + lon_new = lon_range_0_to_360(lon) + self.assertEqual(lon_new, 355.0, "lon not as expected") def test_regular_lon(self): - """ Test lon_range_0_to_360 for a regular longitude""" + """Test lon_range_0_to_360 for a regular longitude""" lon = 22.567 lon_new = lon_range_0_to_360(lon) - self.assertEqual( lon_new, lon, "lon not as expected" ) + self.assertEqual(lon_new, lon, "lon not as expected") def test_lon_out_of_range(self): - """ Test lon_range_0_to_360 for longitude out of range""" - lon = 361. + """Test lon_range_0_to_360 for longitude out of range""" + lon = 361.0 with self.assertRaisesRegex(SystemExit, "lon_in needs to be in the range 0 to 360"): - lon_range_0_to_360(lon) + lon_range_0_to_360(lon) def test_lon_out_of_range_negative(self): - """ Test lon_range_0_to_360 for longitude out of range""" - lon = -181. + """Test lon_range_0_to_360 for longitude out of range""" + lon = -181.0 with self.assertRaisesRegex(SystemExit, "lon_in needs to be in the range 0 to 360"): - lon_range_0_to_360(lon) + lon_range_0_to_360(lon) + + def test_config_value_or_array_single_value(self): + """Simple test of get_config_value_or_array""" + item = "single_value_thing" + # Test on a string, float and integer + self.config.set(self.section, item, "one-thing") + value = get_config_value_or_array(self.config, self.section, item, self.file_path) + self.assertEqual(value, "one-thing", "Value as expected") + self.config.set(self.section, item, "100.") + value = get_config_value_or_array(self.config, self.section, item, self.file_path) + self.assertEqual(float(value), 100.0, "Value as expected") + self.config.set(self.section, item, "100") + value = get_config_value_or_array(self.config, self.section, item, self.file_path) + self.assertEqual(int(value), 100, "Value as expected") + # Run over again, with an explicit conversion + self.config.set(self.section, item, "one-thing") + value = get_config_value_or_array( + self.config, self.section, item, self.file_path, convert_to_type=str + ) + self.assertEqual(value, "one-thing", "Value as expected") + self.config.set(self.section, item, "100.") + value = get_config_value_or_array( + self.config, self.section, item, self.file_path, convert_to_type=float + ) + self.assertEqual(value, 100.0, "Value as expected") + self.config.set(self.section, item, "100") + value = get_config_value_or_array( + self.config, self.section, item, self.file_path, convert_to_type=int + ) + self.assertEqual(value, 100, "Value as expected") + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() From f78a19c645da6ba0e40fb33962fa727ab5593057 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Jan 2023 19:21:11 -0700 Subject: [PATCH 0570/2067] use gddmin as minimum GDD requirement if generate_crop_gdds true. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d3de8d3d0e..a77b3be1a2 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2610,6 +2610,10 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if + if (generate_crop_gdds) then + gddmaturity(p) = max(gddmaturity(p), gddmin(ivt(p))) + endif + endif end associate From a82e49fff591b2a6fc14af78f711a3679a281d51 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 3 Jan 2023 11:27:49 -0700 Subject: [PATCH 0571/2067] Implement get_config_value_or_array and get current tests passing --- python/ctsm/config_utils.py | 31 ++++++++++++---------- python/ctsm/test/test_unit_config_utils.py | 22 ++++++--------- 2 files changed, 25 insertions(+), 28 deletions(-) diff --git a/python/ctsm/config_utils.py b/python/ctsm/config_utils.py index 2dc5428a2f..bd53825f14 100644 --- a/python/ctsm/config_utils.py +++ b/python/ctsm/config_utils.py @@ -90,30 +90,33 @@ def get_config_value_or_array( config, section, item, - file_path, convert_to_type=None, ): """Get a config value as a single value or as an array if it's expressed as an array for cases when you don't know how it's going to be expressed""" - val = "thing" - print(config) - print(section) - print(item) - print(file_path) + val = config.get(section, item) + vallist = val.split() if convert_to_type is not None: - if convert_to_type is float: - print("float") - elif convert_to_type is int: - print("int") - elif convert_to_type is str: - print("str") - else: + if ( + convert_to_type is not float + and convert_to_type is not int + and convert_to_type is not str + ): abort( "get_config_value_or_array can only have convert_to_type as float, int or str not " + str(convert_to_type) ) + is_list = bool(len(vallist) > 1) - abort("This method not implemented yet") + val = _handle_config_value( + var=val, + default=None, + item=item, + is_list=is_list, + convert_to_type=convert_to_type, + can_be_unset=False, + allowed_values=None, + ) return val diff --git a/python/ctsm/test/test_unit_config_utils.py b/python/ctsm/test/test_unit_config_utils.py index cb650e7d04..5af2e67df5 100644 --- a/python/ctsm/test/test_unit_config_utils.py +++ b/python/ctsm/test/test_unit_config_utils.py @@ -64,29 +64,23 @@ def test_config_value_or_array_single_value(self): item = "single_value_thing" # Test on a string, float and integer self.config.set(self.section, item, "one-thing") - value = get_config_value_or_array(self.config, self.section, item, self.file_path) + value = get_config_value_or_array(self.config, self.section, item) self.assertEqual(value, "one-thing", "Value as expected") self.config.set(self.section, item, "100.") - value = get_config_value_or_array(self.config, self.section, item, self.file_path) - self.assertEqual(float(value), 100.0, "Value as expected") + value = get_config_value_or_array(self.config, self.section, item) + self.assertEqual(value, "100.", "Value as expected") self.config.set(self.section, item, "100") - value = get_config_value_or_array(self.config, self.section, item, self.file_path) - self.assertEqual(int(value), 100, "Value as expected") + value = get_config_value_or_array(self.config, self.section, item) + self.assertEqual(value, "100", "Value as expected") # Run over again, with an explicit conversion self.config.set(self.section, item, "one-thing") - value = get_config_value_or_array( - self.config, self.section, item, self.file_path, convert_to_type=str - ) + value = get_config_value_or_array(self.config, self.section, item, convert_to_type=str) self.assertEqual(value, "one-thing", "Value as expected") self.config.set(self.section, item, "100.") - value = get_config_value_or_array( - self.config, self.section, item, self.file_path, convert_to_type=float - ) + value = get_config_value_or_array(self.config, self.section, item, convert_to_type=float) self.assertEqual(value, 100.0, "Value as expected") self.config.set(self.section, item, "100") - value = get_config_value_or_array( - self.config, self.section, item, self.file_path, convert_to_type=int - ) + value = get_config_value_or_array(self.config, self.section, item, convert_to_type=int) self.assertEqual(value, 100, "Value as expected") From d393341f9bb92117101587cb931be0d9c3821612 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 3 Jan 2023 13:17:03 -0700 Subject: [PATCH 0572/2067] Add a test for get_config_value_or_array for lists of size three --- python/ctsm/test/test_unit_config_utils.py | 24 ++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/python/ctsm/test/test_unit_config_utils.py b/python/ctsm/test/test_unit_config_utils.py index 5af2e67df5..7c62173572 100644 --- a/python/ctsm/test/test_unit_config_utils.py +++ b/python/ctsm/test/test_unit_config_utils.py @@ -83,6 +83,30 @@ def test_config_value_or_array_single_value(self): value = get_config_value_or_array(self.config, self.section, item, convert_to_type=int) self.assertEqual(value, 100, "Value as expected") + def test_config_value_or_array_for_list(self): + """Simple test of get_config_value_or_array for a list""" + item = "three_things" + # Test on a string, float and integer + mystr = "one two three" + mystrlist = ["one", "two", "three"] + myfloat = "1. 2. 3." + myfloatlist = [1., 2., 3.] + myint = "1 2 3" + myintlist = [1, 2, 3] + self.config.set(self.section, item, mystr) + value = get_config_value_or_array(self.config, self.section, item, convert_to_type=str) + self.assertEqual(value, mystrlist, "List as expected") + self.assertEqual(len(value), 3, "List size as expected") + self.config.set(self.section, item, myfloat) + value = get_config_value_or_array(self.config, self.section, item, convert_to_type=float) + self.assertEqual(value, myfloatlist, "Value as expected") + self.assertEqual(len(value), 3, "List size as expected") + self.config.set(self.section, item, myint) + value = get_config_value_or_array(self.config, self.section, item, convert_to_type=int) + self.assertEqual(value, myintlist, "Value as expected") + self.assertEqual(len(value), 3, "List size as expected") + + if __name__ == "__main__": unit_testing.setup_for_tests() From 1bcbec8155cb38e604af18c40baa25ab2fa454c9 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Jan 2023 16:32:35 -0700 Subject: [PATCH 0573/2067] Get testing for get_config_value_or_array for lists working, and change read_var_list to use get_config_value_or_array --- python/ctsm/modify_input_files/fsurdat_modifier.py | 10 +++++----- python/ctsm/test/test_unit_config_utils.py | 13 ++++++------- python/ctsm/test/test_unit_fsurdat_modifier.py | 8 ++++---- .../test/testinputs/modify_fsurdat_opt_sections.cfg | 2 ++ 4 files changed, 17 insertions(+), 16 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index f9f36a664e..c9f7f1cd84 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -11,7 +11,7 @@ from configparser import ConfigParser from ctsm.utils import abort, write_output -from ctsm.config_utils import get_config_value +from ctsm.config_utils import get_config_value, get_config_value_or_array from ctsm.ctsm_logging import ( setup_logging_pre_config, add_logging_args, @@ -148,7 +148,7 @@ def read_subgrid(config, cfg_path, numurbl=3): return subgrid_settings -def read_var_list(config, cfg_path): +def read_var_list(config): """Read the variable list section from the config file""" section = "modify_fsurdat_variable_list" if not config.has_section(section): @@ -212,8 +212,8 @@ def read_var_list(config, cfg_path): + " Monthly vars handled this way =" + str(monthly_list) ) - value = get_config_value( - config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float + value = get_config_value_or_array( + config=config, section=section, item=var, convert_to_type=float ) varlist_settings[var] = value @@ -524,7 +524,7 @@ def fsurdat_modifier(parser): check_no_subgrid_section(config) if process_var_list: - varlist = read_var_list(config, cfg_path) + varlist = read_var_list(config) update_list = modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) modify_fsurdat.set_varlist(update_list) else: diff --git a/python/ctsm/test/test_unit_config_utils.py b/python/ctsm/test/test_unit_config_utils.py index 7c62173572..c9ee23bac3 100644 --- a/python/ctsm/test/test_unit_config_utils.py +++ b/python/ctsm/test/test_unit_config_utils.py @@ -87,12 +87,12 @@ def test_config_value_or_array_for_list(self): """Simple test of get_config_value_or_array for a list""" item = "three_things" # Test on a string, float and integer - mystr = "one two three" - mystrlist = ["one", "two", "three"] - myfloat = "1. 2. 3." - myfloatlist = [1., 2., 3.] - myint = "1 2 3" - myintlist = [1, 2, 3] + mystr = "one two three" + mystrlist = ["one", "two", "three"] + myfloat = "1. 2. 3." + myfloatlist = [1.0, 2.0, 3.0] + myint = "1 2 3" + myintlist = [1, 2, 3] self.config.set(self.section, item, mystr) value = get_config_value_or_array(self.config, self.section, item, convert_to_type=str) self.assertEqual(value, mystrlist, "List as expected") @@ -107,7 +107,6 @@ def test_config_value_or_array_for_list(self): self.assertEqual(len(value), 3, "List size as expected") - if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 6a754065bc..149ba5acac 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -103,7 +103,7 @@ def test_read_subgrid_allurban(self): def test_read_var_list(self): """test a simple read of var_list""" - read_var_list(self.config, self.cfg_path) + read_var_list(self.config) def test_subgrid_outofrange(self): """test a read of subgrid that's out of range""" @@ -169,7 +169,7 @@ def test_varlist_varinidealized(self): "is a special variable handled in the idealized section." + " This should NOT be handled in the variiable list section. Special idealized vars =", ): - read_var_list(self.config, self.cfg_path) + read_var_list(self.config) def test_varlist_varinsubgrid(self): """test a read of varlist for a variable thats in the subgrid list""" @@ -180,7 +180,7 @@ def test_varlist_varinsubgrid(self): "is a variable handled in the subgrid section." + " This should NOT be handled in the variiable list section. Subgrid vars =", ): - read_var_list(self.config, self.cfg_path) + read_var_list(self.config) def test_varlist_monthlyvar(self): """test a read of varlist for a variable thats one of the monthly @@ -193,7 +193,7 @@ def test_varlist_monthlyvar(self): + " This should NOT be handled in the variiable list section." + " Monthly vars handled this way =", ): - read_var_list(self.config, self.cfg_path) + read_var_list(self.config) def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index c73dd43a68..fd07d697cf 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -33,6 +33,7 @@ PCT_CROP = 0.0 PCT_LAKE = 100.0 PCT_GLACIER = 0.0 PCT_WETLAND = 0.0 +# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area PCT_URBAN = 0.0 0.0 0.0 @@ -42,6 +43,7 @@ PCT_URBAN = 0.0 0.0 0.0 LAKEDEPTH = 200.00 # Set soem urban multidimensional variables to 200 for the test +# If given as a single value set all to the value, if as list set by dimension and if array as an array CANYON_HWR = 200.00 HT_ROOF = 200.0 T_BUILDING_MIN = 200 From 32e303ea8de556d2193315f0e19f50ec597ea229 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 6 Jan 2023 10:29:33 -0700 Subject: [PATCH 0574/2067] Assume that 3D and higher arrays come in as a list, add more checks that this is correct and correct size, and more tests for it, also get all tests to work --- .../modify_input_files/fsurdat_modifier.py | 6 +- .../ctsm/modify_input_files/modify_fsurdat.py | 62 +++++++++++++++---- python/ctsm/test/test_unit_modify_fsurdat.py | 37 +++++++---- .../modify_fsurdat_opt_sections.cfg | 6 +- 4 files changed, 84 insertions(+), 27 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index c9f7f1cd84..6653a4937d 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -131,6 +131,7 @@ def read_subgrid(config, cfg_path, numurbl=3): for val in vallist: check_range(var, section, val, 0.0, 100.0) varsum += val + value = vallist else: value = get_config_value( config=config, section=section, item=var, file_path=cfg_path, convert_to_type=float @@ -139,6 +140,7 @@ def read_subgrid(config, cfg_path, numurbl=3): varsum += value subgrid_settings[var.upper()] = value + if varsum != 100.0: abort( "PCT fractions in subgrid section do NOT sum to a hundred as they should. Sum = " @@ -519,14 +521,14 @@ def fsurdat_modifier(parser): # if process_subgrid: subgrid = read_subgrid(config, cfg_path, numurbl=modify_fsurdat.get_urb_dens()) - modify_fsurdat.set_varlist(subgrid) + modify_fsurdat.set_varlist(subgrid, cfg_path) else: check_no_subgrid_section(config) if process_var_list: varlist = read_var_list(config) update_list = modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) - modify_fsurdat.set_varlist(update_list) + modify_fsurdat.set_varlist(update_list, cfg_path) else: check_no_varlist_section(config) diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index dc55cc55a8..aac888ae39 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -230,38 +230,78 @@ def check_varlist(self, settings, allow_uppercase_vars=False): settings_return = {} varlist = settings.keys() for var in varlist: - val = settings[var] + varname = var + val = settings[varname] if not var in self.file: if not allow_uppercase_vars: - errmsg = "Error: Variable " + var + " is NOT in the file" + errmsg = "Error: Variable " + varname + " is NOT in the file" abort(errmsg) - if not var.upper() in self.file: - errmsg = "Error: Variable " + var.upper() + " is NOT in the file" + if not varname.upper() in self.file: + errmsg = "Error: Variable " + varname.upper() + " is NOT in the file" abort(errmsg) - varu = var.upper() - settings_return[varu] = val - else: - settings_return[var] = val + varname = varname.upper() + + settings_return[varname] = val + # + # Check that dimensions are as expected + # + if len(self.file[varname].dims) == 2: + if not isinstance(val, float): + abort( + "For 2D vars, there should only be a single value for variable = " + varname + ) + elif len(self.file[varname].dims) >= 3: + dim1 = int(self.file.sizes[self.file[varname].dims[0]]) + if not isinstance(val, list): + abort( + "For higher dimensional vars, the variable needs to be expressed " + + "as a list of values of the dimension size = " + + str(dim1) + + " for variable=" + + varname + ) + if len(val) != dim1: + abort( + "Variable " + varname + " is of the wrong size. It should be = " + str(dim1) + ) return settings_return - def set_varlist(self, settings): + def set_varlist(self, settings, cfg_path="unknown-config-file"): """ Set a list of variables from a dictionary of settings """ for var in settings.keys(): if var in self.file: if len(self.file[var].dims) == 2: + if not isinstance(settings[var], float): + abort( + "For 2D vars, there should only be a single value for variable = " + var + ) self.setvar_lev0(var, settings[var]) elif len(self.file[var].dims) == 3: dim1 = int(self.file.sizes[self.file[var].dims[0]]) + vallist = settings[var] + if not isinstance(vallist, list): + abort( + "For higher dimensional vars, there must be a list of values " + + "for variable= " + + var + + " from the config file = " + + cfg_path + ) + if len(vallist) != dim1: + abort( + "Variable " + var + " is of the wrong size. It should be = " + str(dim1) + ) for lev1 in range(dim1 - 1): - self.setvar_lev1(var, settings[var], lev1_dim=lev1) + self.setvar_lev1(var, vallist[lev1], lev1_dim=lev1) elif len(self.file[var].dims) == 4: dim1 = int(self.file.sizes[self.file[var].dims[0]]) dim2 = int(self.file.sizes[self.file[var].dims[1]]) + vallist = settings[var] for lev1 in range(dim1 - 1): for lev2 in range(dim2 - 1): - self.setvar_lev2(var, settings[var], lev1_dim=lev1, lev2_dim=lev2) + self.setvar_lev2(var, vallist[lev1], lev1_dim=lev1, lev2_dim=lev2) else: abort( "Error: Variable " diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index 7a72288d53..5cbdefcc48 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -376,17 +376,29 @@ def test_getNotRectangle_latsOutOfBounds(self): def test_set_varlist(self): """Test the set_varlist method for all the dimensions that works""" - settings = {"var_lev0": 100.0, "var_lev1": 100.0, "var_lev2": 100.0} + vallist = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0] + settings = {"var_lev0": 100.0, "var_lev1": vallist, "var_lev2": vallist} self.modify_fsurdat.set_varlist(settings) - def test_check_varlist(self): - """Test the check_varlist method for all the dimensions that works""" - settings = {"var_lev0": 100.0, "var_lev1": 100.0, "var_lev2": 100.0} + def test_check_varlist_lists(self): + """Test the check_varlist method for lists""" + lev1list = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0] + lev2list = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0] + settings = {"var_lev1": lev1list, "var_lev2": lev2list} settings_new = self.modify_fsurdat.check_varlist(settings) self.assertEqual( settings_new, settings, "list of variable settings not identical as expected" ) + def test_check_varlist_lists_wrongsizes(self): + """Test the check_varlist method for lists to gracefully fail when the sizes are wrong""" + lev1list = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0] + settings = {"var_lev1": lev1list} + with self.assertRaisesRegex( + SystemExit, "Variable var_lev1 is of the wrong size. It should be" + ): + self.modify_fsurdat.check_varlist(settings) + def test_get_numurb_dens(self): """Check that get num urban density types is correct""" self.assertEqual( @@ -398,15 +410,17 @@ def test_get_numurb_dens(self): def test_check_varlist_uppercase(self): """Test the check_varlist method for all the dimensions that works with allowuppercase option""" + vallist = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0] + vallist2 = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0] expected = { "VAR_LEV0_UPPERCASE": 100.0, - "VAR_LEV1_UPPERCASE": 200.0, - "VAR_LEV2_UPPERCASE": 300.0, + "VAR_LEV1_UPPERCASE": vallist, + "VAR_LEV2_UPPERCASE": vallist2, } settings = { "var_lev0_uppercase": 100.0, - "var_lev1_uppercase": 200.0, - "var_lev2_uppercase": 300.0, + "var_lev1_uppercase": vallist, + "var_lev2_uppercase": vallist2, } settings_new = self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) self.assertEqual( @@ -439,10 +453,11 @@ def test_set_varlist_toohighdim_uppercase(self): """Test the set_varlist method for a variable of too high a dimension in uppercase""" settings = {"var_lev3_uppercase": 100.0} with self.assertRaisesRegex( - SystemExit, "Variable VAR_LEV3_UPPERCASE is a higher dimension than currently allowed" + SystemExit, + "For higher dimensional vars, the variable needs to be expressed as a " + + "list of values of the dimension size = 9 for variable=VAR_LEV3_UPPERCASE", ): - settings_new = self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) - self.modify_fsurdat.set_varlist(settings_new) + self.modify_fsurdat.check_varlist(settings, allow_uppercase_vars=True) def _get_longxy_latixy(self, _min_lon, _max_lon, _min_lat, _max_lat): """ diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index fd07d697cf..414f240ebd 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -44,6 +44,6 @@ LAKEDEPTH = 200.00 # Set soem urban multidimensional variables to 200 for the test # If given as a single value set all to the value, if as list set by dimension and if array as an array -CANYON_HWR = 200.00 -HT_ROOF = 200.0 -T_BUILDING_MIN = 200 +CANYON_HWR = 200.00 150.0 100. +HT_ROOF = 200.0 150.0 100. +T_BUILDING_MIN = 200 150.0 100. From 5952083e7b08ad07637b07b05aad228508455683 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 14:35:37 -0700 Subject: [PATCH 0575/2067] Removed unnecessary error check from cropcal_interp(). https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1002254574 --- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 01ec16e378..6851ad2201 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -408,12 +408,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_cultivar_gdds_thisyr_patch(p,1) = dataptr2d_cultivar_gdds(ig,n) - ! Sanity check: Try to catch uninitialized values - if (crop_inst%rx_cultivar_gdds_thisyr_patch(p,1) > 1000000._r8) then - write(iulog,'(a,i0,a,f20.9)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has rx_cultivar_gdds_thisyr(p,1) HUGE ',& - crop_inst%rx_cultivar_gdds_thisyr_patch(p,1) - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if else write(iulog,'(a,i0)') 'cropcal_interp(), rx_cultivar_gdds: Crop patch has ivt ',ivt call ESMF_Finalize(endflag=ESMF_END_ABORT) From a18ceaf97ba059a31aa5a8c07d0a91404a7a8f87 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 14:43:01 -0700 Subject: [PATCH 0576/2067] No longer using s for sowing_count(p) except as loop index. https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1002782840 --- src/biogeochem/CNPhenologyMod.F90 | 29 ++++++++++++----------------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a77b3be1a2..7a437c9879 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1854,11 +1854,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,1) end if - s = sowing_count(p) - ! Get next sowing date - if (s < mxsowings) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,s+1) + if (sowing_count(p) < mxsowings) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,sowing_count(p)+1) end if ! CropType->InitAllocate() initializes next_rx_sdate to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_sdates is true. So if not using prescribed sowing dates, this boolean will always be false, because jday can never be -1. @@ -1937,7 +1935,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & did_plant = .false. ! Once outputs can handle >1 planting per year, remove 2nd condition. - if ( (.not. croplive(p)) .and. s == 0 ) then + if ( (.not. croplive(p)) .and. sowing_count(p) == 0 ) then ! gdd needed for * chosen crop and a likely hybrid (for that region) * ! to reach full physiological maturity @@ -2019,8 +2017,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! crop not live nor planted - s = sowing_count(p) - ! ---------------------------------- ! from AgroIBIS subroutine phenocrop ! ---------------------------------- @@ -2101,8 +2097,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & force_harvest = .false. fake_harvest = .false. did_plant_prescribed_today = .false. - if (use_cropcal_rx_sdates .and. s > 0) then - did_plant_prescribed_today = crop_inst%sdates_thisyr_patch(p,s) == real(jday, r8) + if (use_cropcal_rx_sdates .and. sowing_count(p) > 0) then + did_plant_prescribed_today = crop_inst%sdates_thisyr_patch(p,sowing_count(p)) == real(jday, r8) end if ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. @@ -2528,15 +2524,14 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & idop(p) = jday iyop(p) = kyr harvdate(p) = NOT_Harvested - s = sowing_count(p) + 1 + sowing_count(p) = sowing_count(p) + 1 - sowing_count(p) = s - if (s < mxsowings) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p, s+1) + if (sowing_count(p) < mxsowings) then + next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p, sowing_count(p)+1) else next_rx_sdate(p) = -1 endif - crop_inst%sdates_thisyr_patch(p,s) = real(jday, r8) + crop_inst%sdates_thisyr_patch(p,sowing_count(p)) = real(jday, r8) this_sowing_reason = 0._r8 if (do_plant_prescribed) then @@ -2547,7 +2542,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & else if (do_plant_lastchance) then this_sowing_reason = this_sowing_reason + 2._r8 end if - sowing_reason(p,s) = this_sowing_reason + sowing_reason(p,sowing_count(p)) = this_sowing_reason crop_inst%sowing_reason_patch(p) = this_sowing_reason leafc_xfer(p) = initial_seed_at_planting @@ -2575,8 +2570,8 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & endif ! set GDD target - if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) .ge. 0._r8) then - gdd_target = crop_inst%rx_cultivar_gdds_thisyr_patch(p,s) + if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then + gdd_target = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator ! Just manually set a minimum of 1.0 From 0c168ac0ad420fe728db45839e6c232b01b31753 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 14:58:27 -0700 Subject: [PATCH 0577/2067] Removed unnecessary assignment of -5 in cropcal_interp(). Was doing this for dataptr2d_sdate but not for dataptr2d_cultivar_gdds. https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1002251700 --- src/cpl/share_esmf/cropcalStreamMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 6851ad2201..955dc36265 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -300,7 +300,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Read prescribed sowing dates from input files allocate(dataptr2d_sdate(lsize, ncft)) - dataptr2d_sdate(:,:) = -5 if (use_cropcal_rx_sdates) then ! Starting with npcropmin will skip generic crops if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' From b016f9dc1d720eca24c50123ecb849149f131ad3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 15:14:27 -0700 Subject: [PATCH 0578/2067] Moved two error checks from CropPhenology() to init functions. https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1003500269 https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1003506911 --- src/biogeochem/CNPhenologyMod.F90 | 15 ++++++--------- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++++ 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7a437c9879..a844aeaf45 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -426,7 +426,7 @@ subroutine CNPhenologyInit(bounds) ! ! !USES: use clm_time_manager, only: get_step_size_real - use clm_varctl , only: use_crop + use clm_varctl , only: use_crop, use_cropcal_rx_sdates use clm_varcon , only: secspday ! ! !ARGUMENTS: @@ -510,6 +510,9 @@ subroutine CNPhenologyInit(bounds) call endrun(msg="ERROR crit_dayl_lat_slope cannot allow crit_dayl longer than a day"//errmsg(sourcefile, __LINE__)) end if end if + if (generate_crop_gdds .and. use_mxmat) then + call endrun(msg="ERROR If setting generate_crop_gdds to .true., you must set use_mxmat to .false."//errmsg(sourcefile, __LINE__)) + endif end subroutine CNPhenologyInit @@ -2101,11 +2104,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & did_plant_prescribed_today = crop_inst%sdates_thisyr_patch(p,sowing_count(p)) == real(jday, r8) end if - ! TEMPORARY? GGCMI seasons often much longer than CLM mxmat. + ! Optionally ignore maximum growing season length mxmat = pftcon%mxmat(ivt(p)) - if (use_mxmat .and. generate_crop_gdds) then - call endrun(msg="If setting generate_crop_gdds to .true., you must set use_mxmat to .false.") - else if (.not. use_mxmat) then + if (.not. use_mxmat) then mxmat = 999 end if @@ -2123,10 +2124,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! If generate_crop_gdds and this patch has prescribed sowing inputs else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr_patch(p,1) .gt. 0) then - if (.not. use_cropcal_rx_sdates) then - write(iulog,*) 'If using generate_crop_gdds, you must specify stream_fldFileName_sdate' - call endrun(msg=errMsg(sourcefile, __LINE__)) - endif if (next_rx_sdate(p) >= 0) then ! Harvest the day before the next sowing date this year. do_harvest = jday == next_rx_sdate(p) - 1 diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 955dc36265..36fabc9f56 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -145,6 +145,10 @@ subroutine cropcal_init(bounds) write(iulog,*) 'Do not specify both generate_crop_gdds=.true. and stream_fldFileName_cultivar_gdds' call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + if (generate_crop_gdds .and. .not. use_cropcal_rx_sdates) then + write(iulog,*) 'ERROR If using generate_crop_gdds, you must specify stream_fldFileName_sdate' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + endif use_cropcal_streams = use_cropcal_rx_sdates .or. use_cropcal_rx_cultivar_gdds ! Initialize the cdeps data type sdat_cropcal_sdate From cd904fc0a50e2de9c5677b180344a2bfb744f8f4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 15:23:43 -0700 Subject: [PATCH 0579/2067] PlantCrop() now only tries to set next_rx_sdate if use_cropcal_rx_sdates. https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1003583534 --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a844aeaf45..f221867982 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2459,7 +2459,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! !USES: use clm_varctl , only : use_c13, use_c14 - use clm_varctl , only : use_cropcal_rx_cultivar_gdds + use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds use clm_varcon , only : c13ratio, c14ratio use clm_varpar , only : mxsowings use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean @@ -2523,7 +2523,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 - if (sowing_count(p) < mxsowings) then + if (use_cropcal_rx_sdates .and. sowing_count(p) < mxsowings) then next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p, sowing_count(p)+1) else next_rx_sdate(p) = -1 From 5ff3203feec873ca5782a4ddfebd900047654b38 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 20:38:12 -0700 Subject: [PATCH 0580/2067] Added crop calendar tests. "GDD-generating" and "sdate+gdd-forced" runs at both 10x15 and 2-degree resolutions. * cropcals_gengdd * cropcals_rx * cropcals_gengdd_2deg * cropcals_rx_2deg --- .../clm/cropcal_outputs/include_user_mods | 1 + .../clm/cropcal_outputs/user_nl_clm | 7 +++++++ .../clm/cropcals/include_user_mods | 1 + .../testmods_dirs/clm/cropcals/user_nl_clm | 7 +++++++ .../clm/cropcals_2deg/include_user_mods | 1 + .../clm/cropcals_2deg/shell_commands | 19 +++++++++++++++++++ .../clm/cropcals_2deg/user_nl_clm | 7 +++++++ .../clm/cropcals_gengdd/include_user_mods | 1 + .../clm/cropcals_gengdd/user_nl_clm | 11 +++++++++++ .../cropcals_gengdd_2deg/include_user_mods | 1 + .../clm/cropcals_gengdd_2deg/shell_commands | 3 +++ .../clm/cropcals_gengdd_2deg/user_nl_clm | 11 +++++++++++ .../clm/cropcals_rx/include_user_mods | 1 + .../testmods_dirs/clm/cropcals_rx/user_nl_clm | 2 ++ .../clm/cropcals_rx_2deg/include_user_mods | 1 + .../clm/cropcals_rx_2deg/user_nl_clm | 2 ++ 16 files changed, 76 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods create mode 100755 cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods new file mode 100644 index 0000000000..02ec13743f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods @@ -0,0 +1 @@ +../cropMonthOutput diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm new file mode 100644 index 0000000000..dcd2e4af00 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm @@ -0,0 +1,7 @@ +! Annual outputs +hist_fincl4 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' +hist_nhtfrq(4) = 17520 +hist_mfilt(4) = 999 +hist_type1d_pertape(4) = 'PFTS' +hist_dov2xy(4) = .false. + diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods new file mode 100644 index 0000000000..904a7588cc --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods @@ -0,0 +1 @@ +../cropcal_outputs diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm new file mode 100644 index 0000000000..db20f8f759 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm @@ -0,0 +1,7 @@ +stream_year_first_cropcal = 2000 +stream_year_last_cropcal = 2000 +model_year_align_cropcal = 2000 + +stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/10x15_nomask_c110308_ESMFmesh.nc' +stream_fldFileName_sdate = '/glade/work/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.fill1.nc' + diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods new file mode 100644 index 0000000000..39e898158f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods @@ -0,0 +1 @@ +../cropcals diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands new file mode 100755 index 0000000000..bb2a5789b4 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands @@ -0,0 +1,19 @@ +#!/bin/bash +set -e +set -x + +y1=1977 +refcase="cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.1958-2014" +refdir=/glade/work/samrabin/clm51_restarts/${refcase}.rest/${y1}-01-01-00000 + +#./xmlchange RUN_REFDIR="${refdir}" +# I don't know why the above doesn't work. +rundir="$(./xmlquery RUNDIR | sed -E "s/\s+RUNDIR:\s+//")" +rsync -ahm --info=progress2 --partial "${refdir}"/* "${rundir}"/ + +./xmlchange RUN_TYPE="hybrid" +./xmlchange RUN_REFCASE="${refcase}" +./xmlchange RUN_REFDATE="${y1}-01-01" +./xmlchange RUN_STARTDATE=${y1}0101 +./xmlchange DATM_YR_END=2014 +./xmlchange RESUBMIT=0 diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm new file mode 100644 index 0000000000..79ba39a137 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm @@ -0,0 +1,7 @@ +stream_year_first_cropcal = 2000 +stream_year_last_cropcal = 2000 +model_year_align_cropcal = 2000 + +stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/fv1.9x2.5_141008_ESMFmesh_c20191001.nc' +stream_fldFileName_sdate = '/glade/work/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20220727_164727.fill1.nc' + diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods new file mode 100644 index 0000000000..39e898158f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods @@ -0,0 +1 @@ +../cropcals diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm new file mode 100644 index 0000000000..28c76c7f70 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm @@ -0,0 +1,11 @@ +generate_crop_gdds = .true. +use_mxmat = .false. +flanduse_timeseries = '/glade/work/samrabin/crop_dates/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.gddgen1976-2015.nc' +check_dynpft_consistency = .false. + +! Daily outputs for GDD generation +hist_fincl5 = 'HUI', 'GDDACCUM' +hist_nhtfrq(5) = -24 +hist_mfilt(5) = 365 +hist_type1d_pertape(5) = 'PFTS' +hist_dov2xy(5) = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods new file mode 100644 index 0000000000..84fabe1cb0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods @@ -0,0 +1 @@ +../cropcals_2deg diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands new file mode 100644 index 0000000000..e43aec57b6 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands @@ -0,0 +1,3 @@ +#!/bin/bash + +./xmlchange CLM_BLDNML_OPTS="-no-fire_emis" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm new file mode 100644 index 0000000000..a68ab94bb1 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm @@ -0,0 +1,11 @@ +generate_crop_gdds = .true. +use_mxmat = .false. +flanduse_timeseries = '/glade/work/samrabin/crop_dates/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.gddgen1976-2015.nc' +check_dynpft_consistency = .false. + +! Daily outputs for GDD generation +hist_fincl5 = 'HUI', 'GDDACCUM' +hist_nhtfrq(5) = -24 +hist_mfilt(5) = 365 +hist_type1d_pertape(5) = 'PFTS' +hist_dov2xy(5) = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods new file mode 100644 index 0000000000..39e898158f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods @@ -0,0 +1 @@ +../cropcals diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm new file mode 100644 index 0000000000..ba9a16981c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm @@ -0,0 +1,2 @@ +generate_crop_gdds = .false. +stream_fldFileName_cultivar_gdds = '/glade/work/samrabin/crop_dates/gdds_20220602_231239.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods new file mode 100644 index 0000000000..84fabe1cb0 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods @@ -0,0 +1 @@ +../cropcals_2deg diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm new file mode 100644 index 0000000000..edf5849e0b --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm @@ -0,0 +1,2 @@ +generate_crop_gdds = .false. +stream_fldFileName_cultivar_gdds = '/glade/work/samrabin/crop_dates/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1977-2014.gddgen/generate_gdds.2022-09-27/gdds_20220927_174954.1955-2020.nc' From 225ffdf30df94923d019983a915d0e96de245c54 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Jan 2023 21:24:33 -0700 Subject: [PATCH 0581/2067] Replaced harvest reason hard-codes with parameters. https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1007298312 --- src/biogeochem/CNPhenologyMod.F90 | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index f221867982..1d9f94fbe6 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -142,6 +142,14 @@ module CNPhenologyMod ! For determining leaf offset latitude that's considered high latitude (see Eitel 2019) real(r8), parameter :: critical_offset_high_lat = 65._r8 ! Start of what's considered high latitude (degrees) + real(r8), parameter :: HARVEST_REASON_MATURE = 1._r8 + real(r8), parameter :: HARVEST_REASON_MAXSEASLENGTH = 2._r8 + real(r8), parameter :: HARVEST_REASON_SOWNBADDEC31 = 3._r8 + real(r8), parameter :: HARVEST_REASON_RXSOWINGTODAY = 4._r8 + real(r8), parameter :: HARVEST_REASON_SOWTOMORROW = 5._r8 + real(r8), parameter :: HARVEST_REASON_GDDGEN_IDOPTOMORROW = 6._r8 + real(r8), parameter :: HARVEST_REASON_GDDGEN_SOWTOMORROW_JAN1 = 7._r8 + character(len=*), parameter, private :: sourcefile = & __FILE__ !----------------------------------------------------------------------- @@ -2115,12 +2123,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .true. force_harvest = .true. fake_harvest = .true. - harvest_reason = 3._r8 + harvest_reason = HARVEST_REASON_SOWNBADDEC31 else if (do_plant .and. .not. did_plant) then ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. - harvest_reason = 4._r8 + harvest_reason = HARVEST_REASON_RXSOWINGTODAY ! If generate_crop_gdds and this patch has prescribed sowing inputs else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr_patch(p,1) .gt. 0) then @@ -2138,10 +2146,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & (idop(p) == 1 .and. jday == dayspyr)) then do_harvest = .true. if (do_harvest) then - harvest_reason = 6._r8 + harvest_reason = HARVEST_REASON_GDDGEN_IDOPTOMORROW end if else if (do_harvest) then - harvest_reason = 5._r8 + harvest_reason = HARVEST_REASON_SOWTOMORROW end if else @@ -2158,7 +2166,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if if (do_harvest) then - harvest_reason = 7._r8 + harvest_reason = HARVEST_REASON_GDDGEN_SOWTOMORROW_JAN1 end if endif @@ -2186,11 +2194,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = do_harvest .or. will_plant_prescribed_tomorrow if (hui(p) >= gddmaturity(p)) then - harvest_reason = 1._r8 + harvest_reason = HARVEST_REASON_MATURE else if (idpp >= mxmat) then - harvest_reason = 2._r8 + harvest_reason = HARVEST_REASON_MAXSEASLENGTH else if (will_plant_prescribed_tomorrow) then - harvest_reason = 5._r8 + harvest_reason = HARVEST_REASON_SOWTOMORROW force_harvest = .true. end if endif From 4836ce3f47646eee57bd8992973ddb068ba38c58 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 7 Jan 2023 11:11:10 -0700 Subject: [PATCH 0582/2067] Make the opt_section tests to 100% urban and add two higher level dimension variables to the test, also in the system test test that the surface dataset gets changed as expected for some variables --- python/ctsm/test/test_sys_fsurdat_modifier.py | 21 +++++++++++++++---- .../modify_fsurdat_opt_sections.cfg | 8 ++++--- 2 files changed, 22 insertions(+), 7 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 5645ec152f..7671e10692 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -13,6 +13,7 @@ import sys import xarray as xr +import numpy as np from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing @@ -124,6 +125,10 @@ def test_opt_sections(self): Test that a simple file with the optional sections works """ self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_opt_sections.cfg") + outfile = os.path.join( + self._tempdir, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_output_urban.nc", + ) sys.argv = [ "fsurdat_modifier", self._cfg_file_path, @@ -132,13 +137,21 @@ def test_opt_sections(self): self._testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" ), "-o", - os.path.join( - self._tempdir, - "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_output_urban.nc", - ), + outfile, ] parser = fsurdat_modifier_arg_process() fsurdat_modifier(parser) + # Read the resultant output file and make sure the fields are changed as expected + fsurdat_out_data = xr.open_dataset(outfile) + zero0d = np.zeros( (5,5) ) + one0d = np.ones( (5,5) ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, zero0d ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d ) + np.testing.assert_array_equal(fsurdat_out_data.LAKEDEPTH, one0d*200. ) def test_cfg_file_DNE_fail(self): """ diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index 414f240ebd..b9c006ce03 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -27,14 +27,14 @@ lnd_lon_2 = 360 # Section for subgrid_fractions [modify_fsurdat_subgrid_fractions] -# Set to 100% lake for the test +# Set to 100% urban for the test PCT_NATVEG = 0.0 PCT_CROP = 0.0 -PCT_LAKE = 100.0 +PCT_LAKE = 0.0 PCT_GLACIER = 0.0 PCT_WETLAND = 0.0 # NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area -PCT_URBAN = 0.0 0.0 0.0 +PCT_URBAN = 100.0 0.0 0.0 # Section with a list of variables to prcoess @@ -47,3 +47,5 @@ LAKEDEPTH = 200.00 CANYON_HWR = 200.00 150.0 100. HT_ROOF = 200.0 150.0 100. T_BUILDING_MIN = 200 150.0 100. +#ALB_ROOF_DIR = 200. 100. +#TK_ROOF = 1. 2. 3. 4. 5. From bb860397f13657ef9ccb617105ca8461e6a9c89f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 9 Jan 2023 11:23:42 -0700 Subject: [PATCH 0583/2067] Moved backwards-compatibility checks for iyop and sowing_reason from CropPhenology() to crop_inst%Restart(). https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1002783470 --- src/biogeochem/CNPhenologyMod.F90 | 12 ----------- src/biogeochem/CropType.F90 | 33 ++++++++++++++++++++++++++++++- src/main/clm_instMod.F90 | 2 +- 3 files changed, 33 insertions(+), 14 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 1d9f94fbe6..77e8834179 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1884,18 +1884,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sowing_count(p) = 1 crop_inst%sdates_thisyr_patch(p,1) = real(idop(p), r8) end if - ! Will be needed until we can rely on all restart files including iyop. - if (croplive(p) .and. iyop(p) > kyr) then - if (idop(p) <= jday) then - iyop(p) = kyr - else - iyop(p) = kyr - 1 - end if - end if - ! Will be needed until we can rely on all restart files including sowing_reason_patch. - if (croplive(p) .and. crop_inst%sowing_reason_patch(p) < 0) then - crop_inst%sowing_reason_patch(p) = 0 - endif ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. ! diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index b16cab7dd6..e4f2d1f3d4 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -498,7 +498,7 @@ subroutine InitAccVars(this, bounds) end subroutine InitAccVars !----------------------------------------------------------------------- - subroutine Restart(this, bounds, ncid, flag) + subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) ! ! !USES: use restUtilMod @@ -506,11 +506,15 @@ subroutine Restart(this, bounds, ncid, flag) use PatchType, only : patch use pftconMod, only : npcropmin, npcropmax use clm_varpar, only : mxsowings, mxharvests + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) + use CNVegstateType, only : cnveg_state_type + use clm_time_manager , only : get_prev_calday, get_prev_date ! ! !ARGUMENTS: class(crop_type), intent(inout) :: this type(bounds_type), intent(in) :: bounds type(file_desc_t), intent(inout) :: ncid + type(cnveg_state_type) , intent(inout) :: cnveg_state_inst ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) character(len=*) , intent(in) :: flag ! ! !LOCAL VARIABLES: @@ -519,6 +523,12 @@ subroutine Restart(this, bounds, ncid, flag) integer :: p logical :: readvar ! determine if variable is on initial file integer :: seasons_found, seasons_loopvar ! getting number of sowings/harvests in patch + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) + integer jday ! julian day of the year + integer kyr ! current year + integer kmo ! month of year (1, ..., 12) + integer kda ! day of month (1, ..., 31) + integer mcsec ! seconds of day (0, ..., seconds/day) character(len=*), parameter :: subname = 'Restart' !----------------------------------------------------------------------- @@ -664,6 +674,7 @@ subroutine Restart(this, bounds, ncid, flag) long_name='reason for each harvest for this patch this year', units='unitless', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%harvest_reason_thisyr_patch) + ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp @@ -679,6 +690,26 @@ subroutine Restart(this, bounds, ncid, flag) end do ! loop through patches end if end if + + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) + if (flag == 'read') then + jday = get_prev_calday() + call get_prev_date(kyr, kmo, kda, mcsec) + do p = bounds%begp,bounds%endp + ! Will be needed until we can rely on all restart files including cnveg_state_inst%iyop_patch. + if (this%croplive_patch(p) .and. cnveg_state_inst%iyop_patch(p) > kyr) then + if (cnveg_state_inst%idop_patch(p) <= jday) then + cnveg_state_inst%iyop_patch(p) = kyr + else + cnveg_state_inst%iyop_patch(p) = kyr - 1 + end if + end if + ! Will be needed until we can rely on all restart files including sowing_reason_patch. + if (this%croplive_patch(p) .and. this%sowing_reason_patch(p) < 0) then + this%sowing_reason_patch(p) = 0 + end if + end do ! loop through patches + end if end if end subroutine Restart diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index a593664217..b8bbe30e29 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -562,7 +562,7 @@ subroutine clm_instRest(bounds, ncid, flag, writing_finidat_interp_dest_file) call soilbiogeochem_nitrogenstate_inst%restart(bounds, ncid, flag=flag, & totvegc_col=bgc_vegetation_inst%get_totvegc_col(bounds)) - call crop_inst%restart(bounds, ncid, flag=flag) + call crop_inst%restart(bounds, ncid, bgc_vegetation_inst%cnveg_state_inst, flag=flag) end if if (use_cn .or. use_fates) then From 88638a87f929f2e2708a6a54a6eb312e96c06517 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 9 Jan 2023 14:51:39 -0700 Subject: [PATCH 0584/2067] add fates-specific helper script --- .../neon_surf_wrapper_fates.py | 110 ++++++++++++++++++ 1 file changed, 110 insertions(+) create mode 100755 tools/site_and_regional/neon_surf_wrapper_fates.py diff --git a/tools/site_and_regional/neon_surf_wrapper_fates.py b/tools/site_and_regional/neon_surf_wrapper_fates.py new file mode 100755 index 0000000000..fcda0e17b4 --- /dev/null +++ b/tools/site_and_regional/neon_surf_wrapper_fates.py @@ -0,0 +1,110 @@ +#! /usr/bin/env python3 +""" +|------------------------------------------------------------------| +|--------------------- Instructions -----------------------------| +|------------------------------------------------------------------| +This script is a simple wrapper for neon sites that performs the +following: + 1) For neon sites, subset surface dataset from global dataset + (i.e. ./subset_data.py ) + 2) Download neon and update the created surface dataset + based on the downloaded neon data. + (i.e. modify_singlept_site_neon.py) + +Instructions for running using conda python environments: + +../../py_env_create +conda activate ctsm_py + +""" +# TODO +# Automatic downloading of missing files if they are missing +#-[ ] Download neon sites and dom pft file +#-[ ] Make sure verbose works for printing out commands running + +# Import libraries +from __future__ import print_function + +import os +import sys +import tqdm +import logging +import argparse +import subprocess + +import pandas as pd +#import tqdm as tqdm + + + +def get_parser(): + """ + Get parser object for this script. + """ + parser = argparse.ArgumentParser(description=__doc__, + formatter_class=argparse.RawDescriptionHelpFormatter) + + parser.print_usage = parser.print_help + + parser.add_argument('-v','--verbose', + help='Verbose mode will print more information. ', + action="store_true", + dest="verbose", + default=False) + + + return parser + + +def execute(command): + """ + Function for running a command on shell. + Args: + command (str): + command that we want to run. + Raises: + Error with the return code from shell. + """ + print ('\n',' >> ',*command,'\n') + + try: + subprocess.check_call(command, stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT) + + except subprocess.CalledProcessError as e: + #raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) + #print (e.ouput) + print (e) + + + + + + +def main(): + + args = get_parser().parse_args() + + if args.verbose: + logging.basicConfig(level=logging.DEBUG) + + + neon_sites = pd.read_csv('neon_sites_dompft.csv') + + + for i, row in tqdm.tqdm(neon_sites.iterrows()): + lat = row['Lat'] + lon = row['Lon'] + site = row['Site'] + pft = row['pft'] + clmsite = "1x1_NEON_16PFT_"+site + print ("Now processing site :", site) + command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite, + '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] + execute(command) + + #command = ['./modify_singlept_site_neon.py','--neon_site',site, '--surf_dir', + # 'subset_data_single_point'] + #execute(command) + +if __name__ == "__main__": + main() From f56dabfde76fada39d895d621a3c75967dee0cd1 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 9 Jan 2023 14:56:28 -0700 Subject: [PATCH 0585/2067] updating so we can create FATES surface datasets --- .../modify_singlept_site_neon.py | 18 +++++++++--------- .../neon_surf_wrapper_fates.py | 6 +++--- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 2798f463ec..96f0b7d1ef 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -6,12 +6,12 @@ This script is for modifying surface dataset at neon sites using data available from the neon server. -After creating a single point surface data file from a global -surface data file using subset_data.py, use this script to +After creating a single point surface data file from a global +surface data file using subset_data.py, use this script to overwrite some fields with site-specific data for neon sites. This script will do the following: -- Download neon data for the specified site if it does not exist +- Download neon data for the specified site if it does not exist in the specified directory : (i.e. ../../../neon_surffiles). - Modify surface dataset with downloaded data. @@ -129,7 +129,7 @@ def get_parser(): parser.add_argument( "--surf_dir", help=""" - Directory of single point surface dataset. + Directory of single point surface dataset. [default: %(default)s] """, action="store", @@ -142,7 +142,7 @@ def get_parser(): "--out_dir", help=""" Directory to write updated single point surface dataset. - [default: %(default)s] + [default: %(default)s] """, action="store", dest="out_dir", @@ -154,7 +154,7 @@ def get_parser(): "--inputdata-dir", help=""" Directory to write updated single point surface dataset. - [default: %(default)s] + [default: %(default)s] """, action="store", dest="inputdatadir", @@ -166,8 +166,8 @@ def get_parser(): "-d", "--debug", help=""" - Debug mode will print more information. - [default: %(default)s] + Debug mode will print more information. + [default: %(default)s] """, action="store_true", dest="debug", @@ -260,7 +260,7 @@ def find_surffile(surf_dir, site_name): surf_file (str): name of the surface dataset file """ - sf_name = "surfdata_1x1_NEON_"+site_name+"*hist_78pfts_CMIP6_simyr2000_*.nc" + sf_name = "surfdata_1x1_NEON_16PFT_"+site_name+"*hist_78pfts_CMIP6_simyr2000_*.nc" print (os.path.join(surf_dir , sf_name)) surf_file = sorted(glob.glob(os.path.join(surf_dir , sf_name))) diff --git a/tools/site_and_regional/neon_surf_wrapper_fates.py b/tools/site_and_regional/neon_surf_wrapper_fates.py index fcda0e17b4..60003b857e 100755 --- a/tools/site_and_regional/neon_surf_wrapper_fates.py +++ b/tools/site_and_regional/neon_surf_wrapper_fates.py @@ -102,9 +102,9 @@ def main(): '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] execute(command) - #command = ['./modify_singlept_site_neon.py','--neon_site',site, '--surf_dir', - # 'subset_data_single_point'] - #execute(command) + command = ['./modify_singlept_site_neon.py','--neon_site',site, '--surf_dir', + 'subset_data_single_point'] + execute(command) if __name__ == "__main__": main() From b833b8ba2747bd4e6ffef1e0b18ab090fac60c63 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 9 Jan 2023 16:37:00 -0700 Subject: [PATCH 0586/2067] Now using current day/date instead of prev. Backwards-compatibility code for iyop, moved to crop_inst%Restart() in previous commit. get_prev_calday() and get_prev_date() were needed when this was in CropPhenology(), but for some reason now the curr versions are needed. Also weird: get_prev_date() and get_curr_date() give the same values when called in crop_inst%Restart()! --- src/biogeochem/CropType.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index e4f2d1f3d4..8f345f51aa 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -508,7 +508,7 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) use clm_varpar, only : mxsowings, mxharvests ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) use CNVegstateType, only : cnveg_state_type - use clm_time_manager , only : get_prev_calday, get_prev_date + use clm_time_manager , only : get_curr_calday, get_curr_date ! ! !ARGUMENTS: class(crop_type), intent(inout) :: this @@ -693,8 +693,8 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) if (flag == 'read') then - jday = get_prev_calday() - call get_prev_date(kyr, kmo, kda, mcsec) + jday = get_curr_calday() + call get_curr_date(kyr, kmo, kda, mcsec) do p = bounds%begp,bounds%endp ! Will be needed until we can rely on all restart files including cnveg_state_inst%iyop_patch. if (this%croplive_patch(p) .and. cnveg_state_inst%iyop_patch(p) > kyr) then From a175a1b4d7b45fafb334c27ead217a8263e56dab Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 10 Jan 2023 07:47:00 -0700 Subject: [PATCH 0587/2067] fixing some file names --- .../modify_singlept_site_neon.py | 15 ++++++++------- tools/site_and_regional/subset_data | 6 +----- 2 files changed, 9 insertions(+), 12 deletions(-) mode change 100755 => 100644 tools/site_and_regional/subset_data diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 96f0b7d1ef..b9a33e73e1 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -12,7 +12,7 @@ This script will do the following: - Download neon data for the specified site if it does not exist - in the specified directory : (i.e. ../../../neon_surffiles). + in the specified directory : (i.e. ../../../neon_surf_files). - Modify surface dataset with downloaded data. ------------------------------------------------------------------- @@ -181,7 +181,7 @@ def get_neon(neon_dir, site_name): """ Function for finding neon data files and download from neon server if the - file does not exits. + file does not exist. Args: neon_dir (str): local directory for downloading neon data. @@ -202,7 +202,7 @@ def get_neon(neon_dir, site_name): neon_file = os.path.join(neon_dir, site_name + "_surfaceData.csv") - # -- Download the file if it does not exits + # -- Download the file if it does not exist if os.path.isfile(neon_file): print("neon file for", site_name, "already exists! ") print("Skipping download from neon for", site_name, "...") @@ -260,7 +260,7 @@ def find_surffile(surf_dir, site_name): surf_file (str): name of the surface dataset file """ - sf_name = "surfdata_1x1_NEON_16PFT_"+site_name+"*hist_78pfts_CMIP6_simyr2000_*.nc" + sf_name = "surfdata_1x1_NEON_16PFT_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" print (os.path.join(surf_dir , sf_name)) surf_file = sorted(glob.glob(os.path.join(surf_dir , sf_name))) @@ -293,7 +293,7 @@ def find_soil_structure(args, surf_file): This function finds this file for the surface dataset, read it, and find soil layers. - Args: + args: surf_file (str): single point surface data filename Raises: @@ -349,6 +349,7 @@ def update_metadata(nc, surf_file, neon_file, zb_flag): nc (xr Dataset): netcdf file including updated neon surface data surf_file (str): single point surface data filename neon_file (str): filename of neon downloaded surface dataset + zb_flag (bool): update bedrock Returns: nc (xr Dataset): netcdf file including updated neon surface data @@ -380,7 +381,7 @@ def update_time_tag(fname_in): fname_in (str) : file name with the old time tag Raises: - error if the file does not end with with + error if the file does not end with [._]cYYMMDD.nc or [._]YYMMDD.nc Returns: @@ -636,7 +637,7 @@ def main(): # -- inorganic = caco3/100.0869*12.0107 # -- organic = carbon_tot - inorganic # -- else: - # -- oranigc = estimated_oc * bulk_den /0.58 + # -- organic = estimated_oc * bulk_den /0.58 caco3 = df["caco3Conc"][bin_index[soil_lev]] inorganic = caco3 / 100.0869 * 12.0107 diff --git a/tools/site_and_regional/subset_data b/tools/site_and_regional/subset_data old mode 100755 new mode 100644 index 162dcf1d4e..ad8e60e053 --- a/tools/site_and_regional/subset_data +++ b/tools/site_and_regional/subset_data @@ -4,22 +4,18 @@ This is a just top-level skeleton script that calls subset_data.py. The original code (subset_data.py) is located under python/ctsm folder. - For full instructions on how to run the code and different options, please check python/ctsm/subset_data.py file. This script extracts domain files, surface dataset, and DATM files at either a single point or a region using the global dataset. - To run this script the following packages are required: - numpy - xarray ---------------------------------------------------------------- To see all available options for single-point/regional subsetting: ./subset_data --help - ---------------------------------------------------------------- Instructions for running using conda python environments: - ../../py_env_create conda activate ctsm_py """ @@ -36,4 +32,4 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm.subset_data import main if __name__ == "__main__": - main() + main() \ No newline at end of file From c3921176a13b3605b024bc32f06b267c4f1a0ba1 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 10 Jan 2023 07:52:01 -0700 Subject: [PATCH 0588/2067] make executable --- tools/site_and_regional/subset_data | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 tools/site_and_regional/subset_data diff --git a/tools/site_and_regional/subset_data b/tools/site_and_regional/subset_data old mode 100644 new mode 100755 From 1585d0a8c83c3ff4cff69c95b69f2718cf4d53dc Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 10 Jan 2023 07:59:07 -0700 Subject: [PATCH 0589/2067] remove packages check --- tools/site_and_regional/modify_singlept_site_neon.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index b9a33e73e1..eabf5930f5 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -47,7 +47,7 @@ import numpy as np import pandas as pd import xarray as xr -from packaging import version +#from packaging import version from datetime import date from getpass import getuser @@ -521,9 +521,9 @@ def main(): logging.basicConfig(level=logging.DEBUG) # Check if pandas is a recent enough version - pdvers = pd.__version__ - if version.parse(pdvers) < version.parse("1.1.0"): - sys.exit("The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", pdvers ) + #pdvers = pd.__version__ + #if version.parse(pdvers) < version.parse("1.1.0"): + # sys.exit("The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", pdvers ) file_time = check_neon_time() From 1e930bb071131d39577e2551e049e38a53ba0774 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 10 Jan 2023 08:14:21 -0700 Subject: [PATCH 0590/2067] adding reference to new FATES surface files --- .../NEON/FATES/ABBY/include_user_mods | 1 + .../NEON/FATES/ABBY/shell_commands | 3 ++ .../NEON/FATES/BARR/include_user_mods | 1 + .../NEON/FATES/BARR/shell_commands | 11 ++++++ .../NEON/FATES/BART/include_user_mods | 1 + .../NEON/FATES/BART/shell_commands | 3 ++ .../NEON/FATES/BLAN/include_user_mods | 1 + .../NEON/FATES/BLAN/shell_commands | 3 ++ .../NEON/FATES/BONA/include_user_mods | 1 + .../NEON/FATES/BONA/shell_commands | 3 ++ .../NEON/FATES/CLBJ/include_user_mods | 1 + .../NEON/FATES/CLBJ/shell_commands | 3 ++ .../NEON/FATES/CPER/include_user_mods | 1 + .../NEON/FATES/CPER/shell_commands | 6 +++ .../NEON/FATES/DCFS/include_user_mods | 1 + .../NEON/FATES/DCFS/shell_commands | 3 ++ .../NEON/FATES/DEJU/include_user_mods | 1 + .../NEON/FATES/DEJU/shell_commands | 3 ++ .../NEON/FATES/DELA/include_user_mods | 1 + .../NEON/FATES/DELA/shell_commands | 3 ++ .../NEON/FATES/DSNY/include_user_mods | 1 + .../NEON/FATES/DSNY/shell_commands | 3 ++ .../NEON/FATES/GRSM/include_user_mods | 1 + .../NEON/FATES/GRSM/shell_commands | 3 ++ .../NEON/FATES/GUAN/include_user_mods | 1 + .../NEON/FATES/GUAN/shell_commands | 11 ++++++ .../NEON/FATES/HARV/include_user_mods | 1 + .../NEON/FATES/HARV/shell_commands | 3 ++ .../NEON/FATES/HEAL/include_user_mods | 1 + .../NEON/FATES/HEAL/shell_commands | 3 ++ .../NEON/FATES/JERC/include_user_mods | 1 + .../NEON/FATES/JERC/shell_commands | 3 ++ .../NEON/FATES/JORN/include_user_mods | 1 + .../NEON/FATES/JORN/shell_commands | 3 ++ .../NEON/FATES/KONA/include_user_mods | 1 + .../NEON/FATES/KONA/shell_commands | 7 ++++ .../NEON/FATES/KONZ/include_user_mods | 1 + .../NEON/FATES/KONZ/shell_commands | 3 ++ .../NEON/FATES/LAJA/include_user_mods | 1 + .../NEON/FATES/LAJA/shell_commands | 12 ++++++ .../NEON/FATES/LENO/include_user_mods | 1 + .../NEON/FATES/LENO/shell_commands | 12 ++++++ .../NEON/FATES/MLBS/include_user_mods | 1 + .../NEON/FATES/MLBS/shell_commands | 10 +++++ .../NEON/FATES/MOAB/include_user_mods | 1 + .../NEON/FATES/MOAB/shell_commands | 10 +++++ .../NEON/FATES/NIWO/include_user_mods | 1 + .../NEON/FATES/NIWO/shell_commands | 4 ++ .../NEON/FATES/NOGP/include_user_mods | 1 + .../NEON/FATES/NOGP/shell_commands | 3 ++ .../NEON/FATES/OAES/include_user_mods | 1 + .../NEON/FATES/OAES/shell_commands | 3 ++ .../NEON/FATES/ONAQ/include_user_mods | 1 + .../NEON/FATES/ONAQ/shell_commands | 10 +++++ .../NEON/FATES/ORNL/include_user_mods | 1 + .../NEON/FATES/ORNL/shell_commands | 3 ++ .../NEON/FATES/OSBS/include_user_mods | 1 + .../NEON/FATES/OSBS/shell_commands | 3 ++ .../NEON/FATES/PUUM/include_user_mods | 1 + .../NEON/FATES/PUUM/shell_commands | 3 ++ .../NEON/FATES/RMNP/include_user_mods | 1 + .../NEON/FATES/RMNP/shell_commands | 3 ++ .../NEON/FATES/SCBI/include_user_mods | 1 + .../NEON/FATES/SCBI/shell_commands | 3 ++ .../NEON/FATES/SERC/include_user_mods | 1 + .../NEON/FATES/SERC/shell_commands | 3 ++ .../NEON/FATES/SJER/include_user_mods | 1 + .../NEON/FATES/SJER/shell_commands | 11 ++++++ .../NEON/FATES/SOAP/include_user_mods | 1 + .../NEON/FATES/SOAP/shell_commands | 3 ++ .../NEON/FATES/SRER/include_user_mods | 1 + .../NEON/FATES/SRER/shell_commands | 3 ++ .../NEON/FATES/STEI/include_user_mods | 1 + .../NEON/FATES/STEI/shell_commands | 3 ++ .../NEON/FATES/STER/include_user_mods | 1 + .../NEON/FATES/STER/shell_commands | 7 ++++ .../NEON/FATES/TALL/include_user_mods | 1 + .../NEON/FATES/TALL/shell_commands | 3 ++ .../NEON/FATES/TEAK/include_user_mods | 1 + .../NEON/FATES/TEAK/shell_commands | 10 +++++ .../NEON/FATES/TOOL/include_user_mods | 1 + .../NEON/FATES/TOOL/shell_commands | 10 +++++ .../NEON/FATES/TREE/include_user_mods | 1 + .../NEON/FATES/TREE/shell_commands | 3 ++ .../NEON/FATES/UKFS/include_user_mods | 1 + .../NEON/FATES/UKFS/shell_commands | 3 ++ .../NEON/FATES/UNDE/include_user_mods | 1 + .../NEON/FATES/UNDE/shell_commands | 3 ++ .../NEON/FATES/WOOD/include_user_mods | 1 + .../NEON/FATES/WOOD/shell_commands | 3 ++ .../NEON/FATES/WREF/include_user_mods | 1 + .../NEON/FATES/WREF/shell_commands | 10 +++++ .../NEON/FATES/YELL/include_user_mods | 1 + .../NEON/FATES/YELL/shell_commands | 10 +++++ .../NEON/FATES/defaults/shell_commands | 26 +++++++++++++ .../NEON/FATES/defaults/user_nl_clm | 31 +++++++++++++++ .../NEON/FATES/defaults/user_nl_cpl | 20 ++++++++++ .../NEON/FATES/defaults/user_nl_datm_streams | 39 +++++++++++++++++++ 98 files changed, 407 insertions(+) create mode 100644 cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/BART/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods create mode 100644 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100644 cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/STEI/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/STER/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/TALL/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/TALL/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/TEAK/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/TOOL/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/TREE/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/TREE/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/UKFS/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/UKFS/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/UNDE/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/WOOD/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/WOOD/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/WREF/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/YELL/include_user_mods create mode 100644 cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm create mode 100644 cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_cpl create mode 100644 cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_datm_streams diff --git a/cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands new file mode 100644 index 0000000000..08f6e7cdef --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=ABBY +./xmlchange PTS_LON=237.67032799999998 +./xmlchange PTS_LAT=45.762378 diff --git a/cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands b/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands new file mode 100644 index 0000000000..713331c0ee --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands @@ -0,0 +1,11 @@ +#!/bin/bash + +./xmlchange NEONSITE=BARR +./xmlchange PTS_LON=203.349781 +./xmlchange PTS_LAT=71.281711 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/BART/shell_commands b/cime_config/usermods_dirs/NEON/FATES/BART/shell_commands new file mode 100644 index 0000000000..a4e86a1b8c --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BART/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=BART +./xmlchange PTS_LON=288.71166 +./xmlchange PTS_LAT=44.06516 diff --git a/cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands b/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands new file mode 100644 index 0000000000..cb093d806a --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=BLAN +./xmlchange PTS_LON=281.92885 +./xmlchange PTS_LAT=39.06044 diff --git a/cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands new file mode 100644 index 0000000000..2a66d148b4 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=BONA +./xmlchange PTS_LON=212.49806 +./xmlchange PTS_LAT=65.15333 diff --git a/cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/CLBJ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/CLBJ/shell_commands new file mode 100644 index 0000000000..c1b9154027 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/CLBJ/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=CLBJ +./xmlchange PTS_LON=262.43275 +./xmlchange PTS_LAT=33.40143 diff --git a/cime_config/usermods_dirs/NEON/FATES/CPER/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/CPER/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/CPER/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands new file mode 100644 index 0000000000..b6ccbcdf57 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands @@ -0,0 +1,6 @@ +./xmlchange NEONSITE=CPER +./xmlchange PTS_LON=255.25545 +./xmlchange PTS_LAT=40.81297 +if [[ $compset =~ ^HIST ]]; then + ./xmlchange STOP_N=50 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/DCFS/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/DCFS/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DCFS/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/DCFS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/DCFS/shell_commands new file mode 100644 index 0000000000..a6cbed64e1 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DCFS/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=DCFS +./xmlchange PTS_LON=260.88749 +./xmlchange PTS_LAT=47.15919 diff --git a/cime_config/usermods_dirs/NEON/FATES/DEJU/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/DEJU/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DEJU/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/DEJU/shell_commands b/cime_config/usermods_dirs/NEON/FATES/DEJU/shell_commands new file mode 100644 index 0000000000..fce519d559 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DEJU/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=DEJU +./xmlchange PTS_LON=214.25235 +./xmlchange PTS_LAT=63.87983 diff --git a/cime_config/usermods_dirs/NEON/FATES/DELA/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/DELA/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DELA/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/DELA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/DELA/shell_commands new file mode 100644 index 0000000000..f3acbb8fd3 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DELA/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=DELA +./xmlchange PTS_LON=272.19659 +./xmlchange PTS_LAT=32.54092 diff --git a/cime_config/usermods_dirs/NEON/FATES/DSNY/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/DSNY/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DSNY/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/DSNY/shell_commands b/cime_config/usermods_dirs/NEON/FATES/DSNY/shell_commands new file mode 100644 index 0000000000..8304c91d48 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/DSNY/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=DSNY +./xmlchange PTS_LON=278.56606 +./xmlchange PTS_LAT=28.12919 diff --git a/cime_config/usermods_dirs/NEON/FATES/GRSM/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/GRSM/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/GRSM/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/GRSM/shell_commands b/cime_config/usermods_dirs/NEON/FATES/GRSM/shell_commands new file mode 100644 index 0000000000..e52a633408 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/GRSM/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=GRSM +./xmlchange PTS_LON=276.49815 +./xmlchange PTS_LAT=35.68839 diff --git a/cime_config/usermods_dirs/NEON/FATES/GUAN/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/GUAN/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/GUAN/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands b/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands new file mode 100644 index 0000000000..4214a35e3c --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands @@ -0,0 +1,11 @@ +#!/bin/bash + +./xmlchange NEONSITE=GUAN +./xmlchange PTS_LON=293.13112 +./xmlchange PTS_LAT=17.96882 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/HARV/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/HARV/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/HARV/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/HARV/shell_commands b/cime_config/usermods_dirs/NEON/FATES/HARV/shell_commands new file mode 100644 index 0000000000..839ccf5d8f --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/HARV/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=HARV +./xmlchange PTS_LON=287.82438 +./xmlchange PTS_LAT=42.53562 diff --git a/cime_config/usermods_dirs/NEON/FATES/HEAL/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/HEAL/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/HEAL/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/HEAL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/HEAL/shell_commands new file mode 100644 index 0000000000..21892219e0 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/HEAL/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=HEAL +./xmlchange PTS_LON=210.78461 +./xmlchange PTS_LAT=63.8798 diff --git a/cime_config/usermods_dirs/NEON/FATES/JERC/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/JERC/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/JERC/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/JERC/shell_commands b/cime_config/usermods_dirs/NEON/FATES/JERC/shell_commands new file mode 100644 index 0000000000..80f66d23a2 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/JERC/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=JERC +./xmlchange PTS_LON=275.53353 +./xmlchange PTS_LAT=31.19608 diff --git a/cime_config/usermods_dirs/NEON/FATES/JORN/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/JORN/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/JORN/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/JORN/shell_commands b/cime_config/usermods_dirs/NEON/FATES/JORN/shell_commands new file mode 100644 index 0000000000..87fc3b8c1e --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/JORN/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=JORN +./xmlchange PTS_LON=253.15623 +./xmlchange PTS_LAT=32.59052 diff --git a/cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands new file mode 100644 index 0000000000..66f274dd36 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands @@ -0,0 +1,7 @@ +./xmlchange NEONSITE=KONA +./xmlchange PTS_LON=263.38956 +./xmlchange PTS_LAT=39.10828 +# Setup to run with prognostic crops for this site +# If you want to explicitly run in SP mode or add other +# options you'll need to add that after this... +./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop" diff --git a/cime_config/usermods_dirs/NEON/FATES/KONZ/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/KONZ/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/KONZ/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/KONZ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/KONZ/shell_commands new file mode 100644 index 0000000000..bda370c170 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/KONZ/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=KONZ +./xmlchange PTS_LON=263.43773 +./xmlchange PTS_LAT=39.1007 diff --git a/cime_config/usermods_dirs/NEON/FATES/LAJA/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/LAJA/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/LAJA/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands new file mode 100644 index 0000000000..a7bda447e6 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands @@ -0,0 +1,12 @@ +#!/bin/bash +./xmlchange NEONSITE=LAJA +./xmlchange PTS_LON=292.92392 +./xmlchange PTS_LAT=18.02184 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi + + diff --git a/cime_config/usermods_dirs/NEON/FATES/LENO/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/LENO/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/LENO/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands b/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands new file mode 100644 index 0000000000..c5ae590186 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands @@ -0,0 +1,12 @@ +#!/bin/bash + +./xmlchange NEONSITE=LENO +./xmlchange PTS_LON=271.83897 +./xmlchange PTS_LAT=31.8531 +./xmlchange DATM_YR_ALIGN=2021,DATM_YR_START=2021 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2021-01-01 + ./xmlchange STOP_N=15 +fi + diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/MLBS/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/MLBS/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands new file mode 100644 index 0000000000..d5de0f64eb --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=MLBS +./xmlchange PTS_LON=279.47575 +./xmlchange PTS_LAT=37.37783 +./xmlchange DATM_YR_END=2019 +# Different default number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 + ./xmlchange STOP_N=24 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/MOAB/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/MOAB/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands new file mode 100644 index 0000000000..96d0bcbe68 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=MOAB +./xmlchange PTS_LON=250.61118 +./xmlchange PTS_LAT=38.25136 +./xmlchange DATM_YR_END=2020 +# Different default number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2021 + ./xmlchange STOP_N=36 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/NIWO/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/NIWO/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/NIWO/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands new file mode 100644 index 0000000000..a3e73ca343 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands @@ -0,0 +1,4 @@ +./xmlchange NEONSITE=NIWO +./xmlchange PTS_LON=254.41676 +./xmlchange PTS_LAT=40.05236 +./xmlchange DATM_YR_END=2018 diff --git a/cime_config/usermods_dirs/NEON/FATES/NOGP/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/NOGP/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/NOGP/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/NOGP/shell_commands b/cime_config/usermods_dirs/NEON/FATES/NOGP/shell_commands new file mode 100644 index 0000000000..ad3ef69cd2 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/NOGP/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=NOGP +./xmlchange PTS_LON=259.08168 +./xmlchange PTS_LAT=46.76846 diff --git a/cime_config/usermods_dirs/NEON/FATES/OAES/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/OAES/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/OAES/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/OAES/shell_commands b/cime_config/usermods_dirs/NEON/FATES/OAES/shell_commands new file mode 100644 index 0000000000..2a5cfb87e4 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/OAES/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=OAES +./xmlchange PTS_LON=260.93956000000003 +./xmlchange PTS_LAT=35.41062 diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/ONAQ/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/ONAQ/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands new file mode 100644 index 0000000000..43dab69998 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=ONAQ +./xmlchange PTS_LON=276.49815 +./xmlchange PTS_LAT=35.68839 +./xmlchange DATM_YR_END=2019 +# Different default number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 + ./xmlchange STOP_N=24 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/ORNL/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/ORNL/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/ORNL/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands new file mode 100644 index 0000000000..264d451753 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=ORNL +./xmlchange PTS_LON=275.83419000000004 +./xmlchange PTS_LAT=35.57525 diff --git a/cime_config/usermods_dirs/NEON/FATES/OSBS/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/OSBS/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/OSBS/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/OSBS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/OSBS/shell_commands new file mode 100644 index 0000000000..385021f98a --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/OSBS/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=OSBS +./xmlchange PTS_LON=278.00655 +./xmlchange PTS_LAT=29.68819 diff --git a/cime_config/usermods_dirs/NEON/FATES/PUUM/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/PUUM/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/PUUM/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/PUUM/shell_commands b/cime_config/usermods_dirs/NEON/FATES/PUUM/shell_commands new file mode 100644 index 0000000000..07c4331769 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/PUUM/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=PUUM +./xmlchange PTS_LON=204.68269 +./xmlchange PTS_LAT=19.55309 diff --git a/cime_config/usermods_dirs/NEON/FATES/RMNP/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/RMNP/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/RMNP/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/RMNP/shell_commands b/cime_config/usermods_dirs/NEON/FATES/RMNP/shell_commands new file mode 100644 index 0000000000..8dfbf0fa0d --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/RMNP/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=RMNP +./xmlchange PTS_LON=254.45476 +./xmlchange PTS_LAT=40.27707 diff --git a/cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands new file mode 100644 index 0000000000..aa42b8022c --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=SCBI +./xmlchange PTS_LON=281.86235999999997 +./xmlchange PTS_LAT=38.89209 diff --git a/cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands new file mode 100644 index 0000000000..1053e2dc17 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=SERC +./xmlchange PTS_LON=283.44115999999997 +./xmlchange PTS_LAT=38.89124 diff --git a/cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands new file mode 100644 index 0000000000..6e05d23792 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands @@ -0,0 +1,11 @@ +#!/bin/bash +./xmlchange NEONSITE=SJER +./xmlchange PTS_LON=240.267 +./xmlchange PTS_LAT=37.107117 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi + diff --git a/cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands new file mode 100644 index 0000000000..c10274c047 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=SOAP +./xmlchange PTS_LON=240.7379 +./xmlchange PTS_LAT=37.03269 diff --git a/cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands new file mode 100644 index 0000000000..be1bec52d3 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=SRER +./xmlchange PTS_LON=249.16451 +./xmlchange PTS_LAT=31.91068 diff --git a/cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/STEI/shell_commands b/cime_config/usermods_dirs/NEON/FATES/STEI/shell_commands new file mode 100644 index 0000000000..c2aced2c2e --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/STEI/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=STEI +./xmlchange PTS_LON=270.4112 +./xmlchange PTS_LAT=45.5076 diff --git a/cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands new file mode 100644 index 0000000000..38b173c309 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands @@ -0,0 +1,7 @@ +./xmlchange NEONSITE=STER +./xmlchange PTS_LON=256.96992 +./xmlchange PTS_LAT=40.45984 +# Setup to run with prognostic crops for this site +# If you want to explicitly run in SP mode or add other +# # options you'll need to add that after this... +./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop" diff --git a/cime_config/usermods_dirs/NEON/FATES/TALL/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/TALL/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TALL/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/TALL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TALL/shell_commands new file mode 100644 index 0000000000..1a176ae23f --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TALL/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=TALL +./xmlchange PTS_LON=272.6059 +./xmlchange PTS_LAT=32.95106 diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/TEAK/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TEAK/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands new file mode 100644 index 0000000000..9058eda022 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=TEAK +./xmlchange PTS_LON=240.99424199999999 +./xmlchange PTS_LAT=37.006472 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/TOOL/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/TOOL/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TOOL/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands new file mode 100644 index 0000000000..f1f2e1771a --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=TOOL +./xmlchange PTS_LON=210.629872 +./xmlchange PTS_LAT=68.66045 +./xmlchange DATM_YR_ALIGN=2020,DATM_YR_START=2020 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2020-01-01 + ./xmlchange STOP_N=27 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/TREE/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/TREE/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TREE/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/TREE/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TREE/shell_commands new file mode 100644 index 0000000000..6d0a4aa1fa --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/TREE/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=TREE +./xmlchange PTS_LON=270.41252 +./xmlchange PTS_LAT=45.49266 diff --git a/cime_config/usermods_dirs/NEON/FATES/UKFS/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/UKFS/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/UKFS/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/UKFS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/UKFS/shell_commands new file mode 100644 index 0000000000..7c8d4f8829 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/UKFS/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=UKFS +./xmlchange PTS_LON=264.79505 +./xmlchange PTS_LAT=39.04168 diff --git a/cime_config/usermods_dirs/NEON/FATES/UNDE/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/UNDE/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/UNDE/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands b/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands new file mode 100644 index 0000000000..79688e0a8f --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=UNDE +./xmlchange PTS_LON=270.6779 +./xmlchange PTS_LAT=46.14103 diff --git a/cime_config/usermods_dirs/NEON/FATES/WOOD/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/WOOD/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/WOOD/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/WOOD/shell_commands b/cime_config/usermods_dirs/NEON/FATES/WOOD/shell_commands new file mode 100644 index 0000000000..48ff0ef999 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/WOOD/shell_commands @@ -0,0 +1,3 @@ +./xmlchange NEONSITE=WOOD +./xmlchange PTS_LON=260.76093000000003 +./xmlchange PTS_LAT=47.12833 diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/WREF/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/WREF/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands new file mode 100644 index 0000000000..807055ae6e --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=WREF +./xmlchange PTS_LON=238.04162 +./xmlchange PTS_LAT=45.81637 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/YELL/include_user_mods new file mode 100644 index 0000000000..b152996d95 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/YELL/include_user_mods @@ -0,0 +1 @@ +../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands new file mode 100644 index 0000000000..800d7d01ad --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands @@ -0,0 +1,10 @@ +#!/bin/bash +./xmlchange NEONSITE=YELL +./xmlchange PTS_LON=249.45803999999998 +./xmlchange PTS_LAT=44.95597 +./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +# Different default start date and number of months to run for transient case +if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands new file mode 100644 index 0000000000..7095e1def7 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands @@ -0,0 +1,26 @@ +#!/bin/bash +./xmlchange CLM_USRDAT_NAME=NEON +./xmlchange CCSM_CO2_PPMV=408.83 +# Set data forcing data to future scenario so will have data from 2018 to present-day +./xmlchange DATM_PRESAERO=SSP3-7.0 +./xmlchange DATM_PRESNDEP=SSP3-7.0 +./xmlchange DATM_PRESO3=SSP3-7.0 +# Explicitly set the MPI library to mpi-serial so won't have the build/run complexity of a full MPI library +./xmlchange MPILIB=mpi-serial +# Set years to run forcing data over +./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 +compset=`./xmlquery COMPSET --value` +# For a transient case run the whole length and don't cycle +if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2022 + ./xmlchange RUN_STARTDATE=2018-01-01 + # Number of months that can be run for the full transient case + ./xmlchange STOP_OPTION="nmonths" + ./xmlchange STOP_N=51 + ./xmlchange CLM_NML_USE_CASE="2018-PD_transient" +else + ./xmlchange CLM_NML_USE_CASE="2018_control" +fi + +# Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) +./xmlchange PIO_TYPENAME=netcdf diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm new file mode 100644 index 0000000000..688e651382 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm @@ -0,0 +1,31 @@ +!---------------------------------------------------------------------------------- +! Users should add all user specific namelist changes below in the form of +! namelist_var = new_namelist_value +! +! EXCEPTIONS: +! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting +! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting +! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting +! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting +! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting +! Set co2_ppmv with CCSM_CO2_PPMV option +! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options +! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases +! (includes $inst_string for multi-ensemble cases) +! or with CLM_FORCE_COLDSTART to do a cold start +! or set it with an explicit filename here. +! Set maxpatch_glcmec with GLC_NEC option +! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable +!---------------------------------------------------------------------------------- + +flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/FATES/surfdata_1x1_NEON_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230110.nc" + +stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' +stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' + +! h1 output stream +hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI', + 'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr' +hist_mfilt(2) = 48 +hist_nhtfrq(2) = 1 diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_cpl b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_cpl new file mode 100644 index 0000000000..e7f6c90a86 --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_cpl @@ -0,0 +1,20 @@ +!------------------------------------------------------------------------ +! Users should ONLY USE user_nl_cpl to change namelists variables +! for namelist variables in drv_in (except for the ones below) and +! any keyword/values in seq_maps.rc +! Users should add ALL user specific namelist and seq_maps.rc changes below +! using the following syntax +! namelist_var = new_namelist_value +! or +! mapname = new_map_name +! For example to change the default value of ocn2atm_fmapname to 'foo' use +! ocn2atm_fmapname = 'foo' +! +! Note that some namelist variables MAY NOT be changed in user_nl_cpl - +! they are defined in a $CASEROOT xml file and must be changed with +! xmlchange. +! +! For example, rather than set username to 'foo' in user_nl_cpl, call +! ./xmlchange USER=foo +!------------------------------------------------------------------------ +orb_iyear = 2018 diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_datm_streams new file mode 100644 index 0000000000..36f1e72b3a --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_datm_streams @@ -0,0 +1,39 @@ +!------------------------------------------------------------------------ +! This file is used to modify datm.streams.xml generated in $RUNDIR +! Entries should have the form +! :<= new stream_value> +! The following are accepted values for an assume streamname of foo +! foo:meshfile = character string +! foo:datafiles = comma separated string of full pathnames (e.g. file1,file2,file3...) +! foo:datavars = comma separated string of field pairs (e.g. foo foobar,foo2 foobar2...) +! foo:taxmode = one of [cycle, extend, limit] +! foo:tintalgo = one of [lower,upper,nearest,linear,coszen] +! foo:readmode = single (only suported mode right now) +! foo:mapalgo = one of [bilinear,redist,nn,consf,consd,none] +! foo:dtlimit = real (1.5 is default) +! foo:year_first = integer +! foo:year_last = integer +! foo:year_align = integer +! foo:vectors = one of [none,u:v] +! foo:lev_dimname: = one of [null,name of level dimenion name] +! foo:offset = integer +! As an example: +! foo:year_first = 1950 +! would change the stream year_first stream_entry to 1950 for the foo stream block +!------------------------------------------------------------------------ +presaero.SSP3-7.0:datafiles = $DIN_LOC_ROOT/atm/cam/chem/trop_mozart_aero/aero/aerodep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.001_2018-2030_monthly_0.9x1.25_c210826.nc +presaero.SSP3-7.0:year_first=2018 +presaero.SSP3-7.0:year_last=2022 +presaero.SSP3-7.0:year_align=2018 +presaero.SSP3-7.0:dtlimit=30 + +presndep.SSP3-7.0:datafiles = $DIN_LOC_ROOT/lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP3-7.0-WACCM_2018-2030_monthly_c210826.nc +presndep.SSP3-7.0:year_first=2018 +presndep.SSP3-7.0:year_last=2022 +presndep.SSP3-7.0:year_align=2018 +presndep.SSP3-7.0:dtlimit=30 + +preso3.SSP3-7.0:year_first=2018 +preso3.SSP3-7.0:year_last=2022 +preso3.SSP3-7.0:year_align=2018 +preso3.SSP3-7.0:dtlimit=30 From ee011faf27a382f9c7f2a5c6f664ff2f2638b68b Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 10 Jan 2023 08:22:31 -0700 Subject: [PATCH 0591/2067] create fates-specific calls --- tools/site_and_regional/neon_surf_wrapper.py | 28 +++-- .../neon_surf_wrapper_fates.py | 110 ------------------ 2 files changed, 20 insertions(+), 118 deletions(-) delete mode 100755 tools/site_and_regional/neon_surf_wrapper_fates.py diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index e02ee2bd53..d8e11415ff 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -33,7 +33,7 @@ import subprocess import pandas as pd -#import tqdm as tqdm + @@ -52,6 +52,12 @@ def get_parser(): dest="verbose", default=False) + parser.add_argument('-f', '--fates', + help='Create and/or modify surface data file for FATES. ', + action="store_true", + dest="fates", + default=False) + return parser @@ -98,13 +104,19 @@ def main(): pft = row['pft'] clmsite = "1x1_NEON_"+site print ("Now processing site :", site) - command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite,'--dompft',str(pft),'--crop', - '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - execute(command) - - command = ['./modify_singlept_site_neon.py','--neon_site',site, '--surf_dir', - 'subset_data_single_point'] - execute(command) + if args.fates: + + command1 = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite, + '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] + command2 = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + 'subset_data_single_point', '--fates'] + else: + command1 = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite,'--dompft',str(pft),'--crop', + '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] + command2 = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + 'subset_data_single_point'] + execute(command1) + execute(command2) if __name__ == "__main__": main() diff --git a/tools/site_and_regional/neon_surf_wrapper_fates.py b/tools/site_and_regional/neon_surf_wrapper_fates.py deleted file mode 100755 index 60003b857e..0000000000 --- a/tools/site_and_regional/neon_surf_wrapper_fates.py +++ /dev/null @@ -1,110 +0,0 @@ -#! /usr/bin/env python3 -""" -|------------------------------------------------------------------| -|--------------------- Instructions -----------------------------| -|------------------------------------------------------------------| -This script is a simple wrapper for neon sites that performs the -following: - 1) For neon sites, subset surface dataset from global dataset - (i.e. ./subset_data.py ) - 2) Download neon and update the created surface dataset - based on the downloaded neon data. - (i.e. modify_singlept_site_neon.py) - -Instructions for running using conda python environments: - -../../py_env_create -conda activate ctsm_py - -""" -# TODO -# Automatic downloading of missing files if they are missing -#-[ ] Download neon sites and dom pft file -#-[ ] Make sure verbose works for printing out commands running - -# Import libraries -from __future__ import print_function - -import os -import sys -import tqdm -import logging -import argparse -import subprocess - -import pandas as pd -#import tqdm as tqdm - - - -def get_parser(): - """ - Get parser object for this script. - """ - parser = argparse.ArgumentParser(description=__doc__, - formatter_class=argparse.RawDescriptionHelpFormatter) - - parser.print_usage = parser.print_help - - parser.add_argument('-v','--verbose', - help='Verbose mode will print more information. ', - action="store_true", - dest="verbose", - default=False) - - - return parser - - -def execute(command): - """ - Function for running a command on shell. - Args: - command (str): - command that we want to run. - Raises: - Error with the return code from shell. - """ - print ('\n',' >> ',*command,'\n') - - try: - subprocess.check_call(command, stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT) - - except subprocess.CalledProcessError as e: - #raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) - #print (e.ouput) - print (e) - - - - - - -def main(): - - args = get_parser().parse_args() - - if args.verbose: - logging.basicConfig(level=logging.DEBUG) - - - neon_sites = pd.read_csv('neon_sites_dompft.csv') - - - for i, row in tqdm.tqdm(neon_sites.iterrows()): - lat = row['Lat'] - lon = row['Lon'] - site = row['Site'] - pft = row['pft'] - clmsite = "1x1_NEON_16PFT_"+site - print ("Now processing site :", site) - command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite, - '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - execute(command) - - command = ['./modify_singlept_site_neon.py','--neon_site',site, '--surf_dir', - 'subset_data_single_point'] - execute(command) - -if __name__ == "__main__": - main() From f1137fd74348359ff70c7952f550b1812d3e6217 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 10 Jan 2023 08:27:18 -0700 Subject: [PATCH 0592/2067] create fates-specific calls --- .../modify_singlept_site_neon.py | 22 +++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index eabf5930f5..49f10acc2f 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -174,6 +174,15 @@ def get_parser(): default=False, ) + parser.add_argument( + "-f", + "--fates", + help="Modify FATES-specific surface data files (i.e. 16-PFT version", + action="store_true", + dest="fates", + default=False, + ) + return parser @@ -241,7 +250,7 @@ def get_neon(neon_dir, site_name): return neon_file -def find_surffile(surf_dir, site_name): +def find_surffile(surf_dir, site_name, fates): """ Function for finding and choosing surface file for a neon site. @@ -252,6 +261,7 @@ def find_surffile(surf_dir, site_name): Args: surf_dir (str): directory of single point surface data site_name (str): 4 letter neon site name + fates (bool): if true, use 16-PFT version of surface data file Raises: Error if the surface data for the site is not created @@ -260,7 +270,11 @@ def find_surffile(surf_dir, site_name): surf_file (str): name of the surface dataset file """ - sf_name = "surfdata_1x1_NEON_16PFT_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" + if fates: + sf_name = "surfdata_1x1_NEON_16PFT_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" + else: + sf_name = "surfdata_1x1_NEON_" + site_name + "*hist_78pfts_CMIP6_simyr2000_*.nc" + print (os.path.join(surf_dir , sf_name)) surf_file = sorted(glob.glob(os.path.join(surf_dir , sf_name))) @@ -533,12 +547,12 @@ def main(): # -- Look for surface data surf_dir = args.surf_dir - surf_file = find_surffile(surf_dir, site_name) + surf_file = find_surffile(surf_dir, site_name, args.fates) # -- directory structure current_dir = os.getcwd() parent_dir = os.path.dirname(current_dir) - clone_dir = os.path.abspath(os.path.join(__file__, "../../..")) + clone_dir = os.path.abspath(os.path.join(__file__, "../../../..")) neon_dir = os.path.join(clone_dir, "neon_surffiles") print("Present Directory", current_dir) From 057abd1311e825176a86984371e04db510ff1d8f Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 10 Jan 2023 09:35:29 -0700 Subject: [PATCH 0593/2067] update surface data name --- cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm index 688e651382..eac74ea00a 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm @@ -19,10 +19,7 @@ !---------------------------------------------------------------------------------- flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets -fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/FATES/surfdata_1x1_NEON_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230110.nc" - -stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' -stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/FATES/surfdata_1x1_NEON_16PFT_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230110.nc" ! h1 output stream hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI', From 187ef47ab2fc4971bed08ac0c4f94e16f22757a2 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 10 Jan 2023 10:26:54 -0700 Subject: [PATCH 0594/2067] change history names --- cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm index eac74ea00a..c842546ec7 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm @@ -22,7 +22,7 @@ flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but wi fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/FATES/surfdata_1x1_NEON_16PFT_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230110.nc" ! h1 output stream -hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI', - 'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr' +hist_fincl2 = 'FATES_AUTORESP','FCEV','FCTR','FGEV','FIRA','FSA','FSH','FATES_GPP','FATES_GPP_PF','H2OSOI', + 'SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FATES_NPP','FATES_NPP_PF','FATES_VEGC','FATES_VEGC_PF' hist_mfilt(2) = 48 hist_nhtfrq(2) = 1 From 3e861414c50c43e9478603f11c0a8dcb02d2106d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 10 Jan 2023 16:28:22 -0700 Subject: [PATCH 0595/2067] Reworked harvest reasons. * Renamed HARVEST_REASON_RXSOWINGTODAY -> HARVEST_REASON_SOWTODAY * Renamed HARVEST_REASON_GDDGEN_IDOPTOMORROW -> HARVEST_REASON_IDOPTOMORROW * Removed HARVEST_REASON_GDDGEN_SOWTOMORROW_JAN1; is now just HARVEST_REASON_SOWTOMORROW --- src/biogeochem/CNPhenologyMod.F90 | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 77e8834179..bad2d04b84 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -145,10 +145,9 @@ module CNPhenologyMod real(r8), parameter :: HARVEST_REASON_MATURE = 1._r8 real(r8), parameter :: HARVEST_REASON_MAXSEASLENGTH = 2._r8 real(r8), parameter :: HARVEST_REASON_SOWNBADDEC31 = 3._r8 - real(r8), parameter :: HARVEST_REASON_RXSOWINGTODAY = 4._r8 + real(r8), parameter :: HARVEST_REASON_SOWTODAY = 4._r8 real(r8), parameter :: HARVEST_REASON_SOWTOMORROW = 5._r8 - real(r8), parameter :: HARVEST_REASON_GDDGEN_IDOPTOMORROW = 6._r8 - real(r8), parameter :: HARVEST_REASON_GDDGEN_SOWTOMORROW_JAN1 = 7._r8 + real(r8), parameter :: HARVEST_REASON_IDOPTOMORROW = 6._r8 character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -2116,7 +2115,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. force_harvest = .true. - harvest_reason = HARVEST_REASON_RXSOWINGTODAY + harvest_reason = HARVEST_REASON_SOWTODAY ! If generate_crop_gdds and this patch has prescribed sowing inputs else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr_patch(p,1) .gt. 0) then @@ -2134,7 +2133,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & (idop(p) == 1 .and. jday == dayspyr)) then do_harvest = .true. if (do_harvest) then - harvest_reason = HARVEST_REASON_GDDGEN_IDOPTOMORROW + harvest_reason = HARVEST_REASON_IDOPTOMORROW end if else if (do_harvest) then harvest_reason = HARVEST_REASON_SOWTOMORROW @@ -2154,7 +2153,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if if (do_harvest) then - harvest_reason = HARVEST_REASON_GDDGEN_SOWTOMORROW_JAN1 + harvest_reason = HARVEST_REASON_SOWTOMORROW end if endif From f5153c276154bcdf60c4b14133ba31218f8fe8be Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 10 Jan 2023 16:41:40 -0700 Subject: [PATCH 0596/2067] HARVEST_REASON_PERHARV 'units' is now a key to reason numbers. --- src/biogeochem/CropType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 8f345f51aa..5449f49be6 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -338,7 +338,7 @@ subroutine InitHistory(this, bounds) ptr_patch=this%sowing_reason_perharv_patch, default='inactive') this%harvest_reason_thisyr_patch(begp:endp,:) = spval - call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='unitless', type2d='mxharvests', & + call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; 4 = sowing today; 5 = sowing tomorrow; 6 = tomorrow == idop', type2d='mxharvests', & avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & ptr_patch=this%harvest_reason_thisyr_patch, default='inactive') From 815ed9cd6e26fba1f730d8db0ef38e0d96089154 Mon Sep 17 00:00:00 2001 From: will wieder Date: Tue, 10 Jan 2023 20:05:55 -0700 Subject: [PATCH 0597/2067] Update neon_sites_dompft.csv --- tools/site_and_regional/neon_sites_dompft.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/neon_sites_dompft.csv b/tools/site_and_regional/neon_sites_dompft.csv index e67d67375b..dce0a6283d 100644 --- a/tools/site_and_regional/neon_sites_dompft.csv +++ b/tools/site_and_regional/neon_sites_dompft.csv @@ -34,7 +34,7 @@ 33,NIWO,13, 40.05236, -105.58324,12,2018,2021 34,JORN,14, 32.59052, -106.84377,14,2018,2021 35,SRER,14, 31.91068, -110.83549,9,2018,2021 -36,ONAQ,15, 35.68839, -83.50185,9,2018,2019 +36,ONAQ,15, 40.17760, -112.45245,9,2018,2019 37,ABBY,16,45.762378,-122.329672,1,2018,2021 38,WREF,16, 45.81637, -121.95838,1,2019,2021 39,SJER,17,37.107117, -119.73300,13,2019,2021 From 490fd344337258e754ae9f77b2cd598cd27ac494 Mon Sep 17 00:00:00 2001 From: will wieder Date: Tue, 10 Jan 2023 21:31:54 -0700 Subject: [PATCH 0598/2067] Update usermods shell commands --- cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 43dab69998..511813398b 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -1,7 +1,7 @@ #!/bin/bash ./xmlchange NEONSITE=ONAQ -./xmlchange PTS_LON=276.49815 -./xmlchange PTS_LAT=35.68839 +./xmlchange PTS_LON=247.54755 +./xmlchange PTS_LAT=40.17760 ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then From a374044a1a7cf191e53aae876cc9274332d13606 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 11 Jan 2023 07:46:38 -0700 Subject: [PATCH 0599/2067] Update user_nl_clm only needed for ONAQ, but done for all sites for consistency --- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 29e50431ce..ddf627b04e 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -19,7 +19,7 @@ !---------------------------------------------------------------------------------- flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets -fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c221111.nc" +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230111.nc" stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' From 314191624b6d709a0a009b80b73483bc2ce1750b Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 11 Jan 2023 09:50:18 -0700 Subject: [PATCH 0600/2067] Update neon_sites_dompft.csv additional lat-lon changes to BLAN, UNDE, ORNL --- tools/site_and_regional/neon_sites_dompft.csv | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/site_and_regional/neon_sites_dompft.csv b/tools/site_and_regional/neon_sites_dompft.csv index dce0a6283d..8fb9600f0f 100644 --- a/tools/site_and_regional/neon_sites_dompft.csv +++ b/tools/site_and_regional/neon_sites_dompft.csv @@ -1,7 +1,7 @@ ,Site,Domain,Lat,Lon,pft,start_year,end_year 1,BART, 1, 44.06516, -71.28834,7,2018,2021 2,HARV, 1, 42.53562, -72.17562,7,2018,2021 -3,BLAN, 2, 39.06044, -78.07115,7,2018,2021 +3,BLAN, 2, 39.033698, -78.041788,7,2018,2021 4,SCBI, 2, 38.89209, -78.13764,7,2018,2021 5,SERC, 2, 38.89124, -76.55884,7,2018,2021 6,DSNY, 3, 28.12919, -81.43394,14,2018,2021 @@ -11,13 +11,13 @@ 10,LAJA, 4, 18.02184, -67.07608,14,2019,2021 11,STEI, 5, 45.50760, -89.58880,7,2018,2021 12,TREE, 5, 45.49266, -89.58748,7,2018,2021 -13,UNDE, 5, 46.14103, -89.32210,7,2018,2021 +13,UNDE, 5, 46.23391, -89.537254,7,2018,2021 14,KONA, 6, 39.10828, -96.61044,19,2018,2021 15,KONZ, 6, 39.10070, -96.56227,14,2018,2021 16,UKFS, 6, 39.04168, -95.20495,7,2018,2021 17,GRSM, 7, 35.68839, -83.50185,7,2018,2021 18,MLBS, 7, 37.37783, -80.52425,7,2018,2019 -19,ORNL, 7, 35.57525, -84.16581,7,2018,2021 +19,ORNL, 7, 35.964128, -84.282588,7,2018,2021 20,DELA, 8, 32.54092, -87.80341,7,2018,2021 21,LENO, 8, 31.85310, -88.16103,7,2021,2021 22,TALL, 8, 32.95106, -87.39410,1,2018,2021 From c6bce1e4485634838c9c6085e9158850ff2f8bd0 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 11 Jan 2023 09:51:49 -0700 Subject: [PATCH 0601/2067] Update BLAN shell commands --- cime_config/usermods_dirs/NEON/BLAN/shell_commands | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/BLAN/shell_commands b/cime_config/usermods_dirs/NEON/BLAN/shell_commands index cb093d806a..0508481981 100644 --- a/cime_config/usermods_dirs/NEON/BLAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/BLAN/shell_commands @@ -1,3 +1,3 @@ ./xmlchange NEONSITE=BLAN -./xmlchange PTS_LON=281.92885 -./xmlchange PTS_LAT=39.06044 +./xmlchange PTS_LON=281.958212 +./xmlchange PTS_LAT=39.033698 From 09cfaa659347186a5e5b49b9fcaf4c56c9fa094f Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 11 Jan 2023 09:52:52 -0700 Subject: [PATCH 0602/2067] Update ORNL shell commands --- cime_config/usermods_dirs/NEON/ORNL/shell_commands | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/ORNL/shell_commands b/cime_config/usermods_dirs/NEON/ORNL/shell_commands index 264d451753..5708d3dec5 100644 --- a/cime_config/usermods_dirs/NEON/ORNL/shell_commands +++ b/cime_config/usermods_dirs/NEON/ORNL/shell_commands @@ -1,3 +1,3 @@ ./xmlchange NEONSITE=ORNL -./xmlchange PTS_LON=275.83419000000004 -./xmlchange PTS_LAT=35.57525 +./xmlchange PTS_LON=275.717412 +./xmlchange PTS_LAT=35.964128 From dc101f305c27395eea8993166199f24ad69a1d63 Mon Sep 17 00:00:00 2001 From: will wieder Date: Wed, 11 Jan 2023 09:53:40 -0700 Subject: [PATCH 0603/2067] Update UNDE shell commands --- cime_config/usermods_dirs/NEON/UNDE/shell_commands | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/UNDE/shell_commands b/cime_config/usermods_dirs/NEON/UNDE/shell_commands index 79688e0a8f..f810e4a76b 100644 --- a/cime_config/usermods_dirs/NEON/UNDE/shell_commands +++ b/cime_config/usermods_dirs/NEON/UNDE/shell_commands @@ -1,3 +1,3 @@ ./xmlchange NEONSITE=UNDE -./xmlchange PTS_LON=270.6779 -./xmlchange PTS_LAT=46.14103 +./xmlchange PTS_LON=270.462746 +./xmlchange PTS_LAT=46.23391 From 6036d8b6b719fefc1e216f0f0e98807705a5481c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 11 Jan 2023 14:44:16 -0700 Subject: [PATCH 0604/2067] De-duplication in sowing requirement checks. --- src/biogeochem/CNPhenologyMod.F90 | 23 ++++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bad2d04b84..1b3044a873 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1731,6 +1731,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & real(r8) avg_dayspyr ! average number of days per year real(r8) crmcorn ! comparitive relative maturity for corn real(r8) ndays_on ! number of days to fertilize + logical is_in_sowing_window ! is the crop in its sowing window? + logical is_end_sowing_window ! is it the last day of the crop's sowing window? + logical sowing_gdd_requirement_met ! has the gridcell historically been warm enough to support the crop? logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? @@ -1885,6 +1888,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. + is_in_sowing_window = jday >= minplantjday(ivt(p),h) .and. jday <= maxplantjday(ivt(p),h) + is_end_sowing_window = jday == maxplantjday(ivt(p),h) ! ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing dates at all, or if this cell had no values in the prescribed sowing @@ -1895,21 +1900,18 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_plant_lastchance = .false. else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then ! winter temperate cereal : use gdd0 as a limit to plant winter cereal - ! + sowing_gdd_requirement_met = gdd020(p) /= spval .and. gdd020(p) >= gddmin(ivt(p)) ! Are all the normal requirements for planting met? do_plant_normal = allow_unprescribed_planting .and. & a5tmin(p) /= spval .and. & a5tmin(p) <= minplanttemp(ivt(p)) .and. & - jday >= minplantjday(ivt(p),h) .and. & - jday <= maxplantjday(ivt(p),h) .and. & - (gdd020(p) /= spval .and. & - gdd020(p) >= gddmin(ivt(p))) + is_in_sowing_window .and. & + sowing_gdd_requirement_met ! If not, but it's the last day of the planting window, what about relaxed rules? do_plant_lastchance = allow_unprescribed_planting .and. & (.not. do_plant_normal) .and. & - jday == maxplantjday(ivt(p),h) .and. & - gdd020(p) /= spval .and. & - gdd020(p) >= gddmin(ivt(p)) + is_end_sowing_window .and. & + sowing_gdd_requirement_met else ! not winter cereal... slevis: added distinction between NH and SH ! slevis: The idea is that jday will equal idop sooner or later in the year ! while the gdd part is either true or false for the year. @@ -1918,14 +1920,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & t10(p) /= spval .and. a10tmin(p) /= spval .and. & t10(p) > planttemp(ivt(p)) .and. & a10tmin(p) > minplanttemp(ivt(p)) .and. & - jday >= minplantjday(ivt(p),h) .and. & - jday <= maxplantjday(ivt(p),h) .and. & + is_in_sowing_window .and. & gdd820(p) /= spval .and. & gdd820(p) >= gddmin(ivt(p)) ! If not, but it's the last day of the planting window, what about relaxed rules? do_plant_lastchance = allow_unprescribed_planting .and. & (.not. do_plant_normal) .and. & - jday == maxplantjday(ivt(p),h) .and. & + is_end_sowing_window .and. & gdd820(p) > 0._r8 .and. & gdd820(p) /= spval end if From 3d952bb56f213d5fa20362ed1ec90c4ac94d5ed3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 11 Jan 2023 14:58:01 -0700 Subject: [PATCH 0605/2067] iyop now calculated upon restart instead of being read-in. Previously, iyop was only calculated if it wasn't present in the restart file. This could have led to weird values for startup/hybrid runs where the year on the restart file didn't match the year of the model run. https://github.com/ESCOMP/CTSM/pull/1863#discussion_r1002784423 --- src/biogeochem/CNVegStateType.F90 | 6 +----- src/biogeochem/CropType.F90 | 21 +++++++++++++-------- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index ae894a31d0..e7e61c75bf 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -232,7 +232,7 @@ subroutine InitAllocate(this, bounds) allocate(this%peaklai_patch (begp:endp)) ; this%peaklai_patch (:) = 0 allocate(this%idop_patch (begp:endp)) ; this%idop_patch (:) = huge(1) - allocate(this%iyop_patch (begp:endp)) ; this%iyop_patch (:) = huge(1) + allocate(this%iyop_patch (begp:endp)) ; this%iyop_patch (:) = ispval allocate(this%lgdp_col (begc:endc)) ; allocate(this%lgdp1_col (begc:endc)) ; @@ -816,10 +816,6 @@ subroutine Restart(this, bounds, ncid, flag, cnveg_carbonstate, & dim1name='pft', long_name='Date of planting', units='jday', nvalid_range=(/1,366/), & interpinic_flag='interp', readvar=readvar, data=this%idop_patch) - call restartvar(ncid=ncid, flag=flag, varname='iyop', xtype=ncd_int, & - dim1name='pft', long_name='Year of planting', units='year', & - interpinic_flag='interp', readvar=readvar, data=this%iyop_patch) - call restartvar(ncid=ncid, flag=flag, varname='aleaf', xtype=ncd_double, & dim1name='pft', long_name='leaf allocation coefficient', units='', & interpinic_flag='interp', readvar=readvar, data=this%aleaf_patch) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 5449f49be6..28a3528b49 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -678,6 +678,8 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp + + ! Harvest count seasons_found = 0 do seasons_loopvar = 1,mxharvests if (this%hdates_thisyr_patch(p,seasons_loopvar) >= 1 .and. this%hdates_thisyr_patch(p,seasons_loopvar) <= 366) then @@ -687,6 +689,17 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) end if end do ! loop through possible harvests this%harvest_count(p) = seasons_found + + ! Year of planting + ! Calculating this here instead of saving in restart file to allow for + ! sensible iyop values in startup/hybrid runs. + ! * Assumes no growing season is longer than 364 days (or 365 days if + ! spanning a leap day). + if (cnveg_state_inst%idop_patch(p) <= jday) then + cnveg_state_inst%iyop_patch(p) = kyr + else + cnveg_state_inst%iyop_patch(p) = kyr - 1 + end if end do ! loop through patches end if end if @@ -696,14 +709,6 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) jday = get_curr_calday() call get_curr_date(kyr, kmo, kda, mcsec) do p = bounds%begp,bounds%endp - ! Will be needed until we can rely on all restart files including cnveg_state_inst%iyop_patch. - if (this%croplive_patch(p) .and. cnveg_state_inst%iyop_patch(p) > kyr) then - if (cnveg_state_inst%idop_patch(p) <= jday) then - cnveg_state_inst%iyop_patch(p) = kyr - else - cnveg_state_inst%iyop_patch(p) = kyr - 1 - end if - end if ! Will be needed until we can rely on all restart files including sowing_reason_patch. if (this%croplive_patch(p) .and. this%sowing_reason_patch(p) < 0) then this%sowing_reason_patch(p) = 0 From 5ecbae7dcbca45f5aed20f87df9ee07c96229ce0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 11 Jan 2023 16:57:32 -0700 Subject: [PATCH 0606/2067] Bugfix to previous. Forgot to move the date-getting lines. --- src/biogeochem/CropType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 28a3528b49..0ba0b7c4fc 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -677,6 +677,8 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then + jday = get_curr_calday() + call get_curr_date(kyr, kmo, kda, mcsec) do p = bounds%begp,bounds%endp ! Harvest count @@ -706,8 +708,6 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2023-01-09) if (flag == 'read') then - jday = get_curr_calday() - call get_curr_date(kyr, kmo, kda, mcsec) do p = bounds%begp,bounds%endp ! Will be needed until we can rely on all restart files including sowing_reason_patch. if (this%croplive_patch(p) .and. this%sowing_reason_patch(p) < 0) then From de831f77e066263c59d5965c983d25562183b70b Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Thu, 12 Jan 2023 14:59:37 -0700 Subject: [PATCH 0607/2067] adding new updates to FATES side --- cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands | 4 ++-- cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands | 4 ++-- cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands | 4 ++-- cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands b/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands index cb093d806a..0508481981 100644 --- a/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands @@ -1,3 +1,3 @@ ./xmlchange NEONSITE=BLAN -./xmlchange PTS_LON=281.92885 -./xmlchange PTS_LAT=39.06044 +./xmlchange PTS_LON=281.958212 +./xmlchange PTS_LAT=39.033698 diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands index 43dab69998..511813398b 100644 --- a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands @@ -1,7 +1,7 @@ #!/bin/bash ./xmlchange NEONSITE=ONAQ -./xmlchange PTS_LON=276.49815 -./xmlchange PTS_LAT=35.68839 +./xmlchange PTS_LON=247.54755 +./xmlchange PTS_LAT=40.17760 ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then diff --git a/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands index 264d451753..5708d3dec5 100644 --- a/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands @@ -1,3 +1,3 @@ ./xmlchange NEONSITE=ORNL -./xmlchange PTS_LON=275.83419000000004 -./xmlchange PTS_LAT=35.57525 +./xmlchange PTS_LON=275.717412 +./xmlchange PTS_LAT=35.964128 diff --git a/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands b/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands index 79688e0a8f..f810e4a76b 100644 --- a/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands @@ -1,3 +1,3 @@ ./xmlchange NEONSITE=UNDE -./xmlchange PTS_LON=270.6779 -./xmlchange PTS_LAT=46.14103 +./xmlchange PTS_LON=270.462746 +./xmlchange PTS_LAT=46.23391 From 3fbeeaf6226eb0818ed785a5855a1642737599eb Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Thu, 12 Jan 2023 15:17:00 -0700 Subject: [PATCH 0608/2067] add packaging to ctsm_py environment --- python/conda_env_ctsm_py.txt | 1 + python/conda_env_ctsm_py_cgd.txt | 1 + python/conda_env_ctsm_py_latest.txt | 1 + 3 files changed, 3 insertions(+) diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index d757ae1782..4768d0ed62 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -16,6 +16,7 @@ tqdm scipy netcdf4 requests +packaging numpy=1.18.5 xarray=0.16.2 pylint=2.8.3 diff --git a/python/conda_env_ctsm_py_cgd.txt b/python/conda_env_ctsm_py_cgd.txt index e7ee4af8ab..f3cc1b3201 100644 --- a/python/conda_env_ctsm_py_cgd.txt +++ b/python/conda_env_ctsm_py_cgd.txt @@ -18,6 +18,7 @@ tqdm scipy netcdf4 requests +packaging numpy=1.18.5 xarray=0.16.2 pylint=2.8.3 diff --git a/python/conda_env_ctsm_py_latest.txt b/python/conda_env_ctsm_py_latest.txt index 2dc2ed518d..052fbf4fef 100644 --- a/python/conda_env_ctsm_py_latest.txt +++ b/python/conda_env_ctsm_py_latest.txt @@ -5,6 +5,7 @@ tqdm>=4.64.1 scipy netcdf4 requests +packaging numpy>=1.23.0 xarray>=2022.3.0 pylint>=2.8.3,<2.9.0 # Once, you move off of 2.8.3, make lint shows 2 errors, at 2.11.1 there are 2 more errors beyond that From 88afa24c8a83a57574ea5245a869f1233b953c73 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 12 Jan 2023 15:18:23 -0700 Subject: [PATCH 0609/2067] add back pandas version check --- tools/site_and_regional/modify_singlept_site_neon.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 49f10acc2f..64e77eacd5 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -47,7 +47,7 @@ import numpy as np import pandas as pd import xarray as xr -#from packaging import version +from packaging import version from datetime import date from getpass import getuser @@ -535,9 +535,9 @@ def main(): logging.basicConfig(level=logging.DEBUG) # Check if pandas is a recent enough version - #pdvers = pd.__version__ - #if version.parse(pdvers) < version.parse("1.1.0"): - # sys.exit("The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", pdvers ) + pdvers = pd.__version__ + if version.parse(pdvers) < version.parse("1.1.0"): + sys.exit("The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", pdvers ) file_time = check_neon_time() From 1d1a3ebaf9ca34a2859256c0247ffae8ca0700bf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 13 Jan 2023 13:51:03 -0700 Subject: [PATCH 0610/2067] CropType restart now only checks whether hdates_thisyr_patch was read. --- src/biogeochem/CropType.F90 | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 0ba0b7c4fc..7a967a037b 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -529,6 +529,8 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) integer kmo ! month of year (1, ..., 12) integer kda ! day of month (1, ..., 31) integer mcsec ! seconds of day (0, ..., seconds/day) + ! BACKWARDS_COMPATIBILITY(ssr, 2023-01-13) + logical read_hdates_thisyr_patch character(len=*), parameter :: subname = 'Restart' !----------------------------------------------------------------------- @@ -648,7 +650,7 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='crop harvest dates for this patch this year', units='day of year', & scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=this%hdates_thisyr_patch) + interpinic_flag='interp', readvar=read_hdates_thisyr_patch, data=this%hdates_thisyr_patch) call restartvar(ncid=ncid, flag=flag, varname='gddaccum_thisyr_patch', xtype=ncd_double, & dim1name='pft', dim2name='mxharvests', switchdim=.true., & long_name='accumulated GDD at harvest for this patch this year', units='ddays', & @@ -676,21 +678,23 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) interpinic_flag='interp', readvar=readvar, data=this%harvest_reason_thisyr_patch) ! Fill variable(s) derived from read-in variable(s) - if (flag == 'read' .and. readvar) then + if (flag == 'read') then jday = get_curr_calday() call get_curr_date(kyr, kmo, kda, mcsec) do p = bounds%begp,bounds%endp ! Harvest count - seasons_found = 0 - do seasons_loopvar = 1,mxharvests - if (this%hdates_thisyr_patch(p,seasons_loopvar) >= 1 .and. this%hdates_thisyr_patch(p,seasons_loopvar) <= 366) then - seasons_found = seasons_loopvar - else - exit - end if - end do ! loop through possible harvests - this%harvest_count(p) = seasons_found + if (read_hdates_thisyr_patch) then + seasons_found = 0 + do seasons_loopvar = 1,mxharvests + if (this%hdates_thisyr_patch(p,seasons_loopvar) >= 1 .and. this%hdates_thisyr_patch(p,seasons_loopvar) <= 366) then + seasons_found = seasons_loopvar + else + exit + end if + end do ! loop through possible harvests + this%harvest_count(p) = seasons_found + end if ! Year of planting ! Calculating this here instead of saving in restart file to allow for From eb82a54295a7c36f70554b3fa1e5059b7d0d288f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 13 Jan 2023 15:25:47 -0700 Subject: [PATCH 0611/2067] Removed unused min_crop_gdd_target. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 - bld/namelist_files/namelist_definition_ctsm.xml | 5 ----- 2 files changed, 6 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 8263129376..eb235d903c 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -562,7 +562,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Constant .false. .false. -1.d00 .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 38abc5e292..ba94d220ed 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1143,11 +1143,6 @@ Set to .true. in order to override crop harvesting logic and to instead harvest Set to .true. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. - -Set minimum crop GDD requirement. Used only with prescribed GDD inputs from file. - - Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on From b9437fe8acfa7cb1671620c651148d553cb7d54d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 13 Jan 2023 17:24:59 -0700 Subject: [PATCH 0612/2067] Add testing for 3D and 4D optional data, and get it working correctly --- .../ctsm/modify_input_files/modify_fsurdat.py | 12 +-- python/ctsm/test/test_sys_fsurdat_modifier.py | 81 ++++++++++++++++--- .../modify_fsurdat_opt_sections.cfg | 4 +- 3 files changed, 80 insertions(+), 17 deletions(-) diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index aac888ae39..599b8a6e84 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -293,15 +293,15 @@ def set_varlist(self, settings, cfg_path="unknown-config-file"): abort( "Variable " + var + " is of the wrong size. It should be = " + str(dim1) ) - for lev1 in range(dim1 - 1): + for lev1 in range(dim1): self.setvar_lev1(var, vallist[lev1], lev1_dim=lev1) elif len(self.file[var].dims) == 4: - dim1 = int(self.file.sizes[self.file[var].dims[0]]) - dim2 = int(self.file.sizes[self.file[var].dims[1]]) + dim_lev1 = int(self.file.sizes[self.file[var].dims[1]]) + dim_lev2 = int(self.file.sizes[self.file[var].dims[0]]) vallist = settings[var] - for lev1 in range(dim1 - 1): - for lev2 in range(dim2 - 1): - self.setvar_lev2(var, vallist[lev1], lev1_dim=lev1, lev2_dim=lev2) + for lev1 in range(dim_lev1): + for lev2 in range(dim_lev2): + self.setvar_lev2(var, vallist[lev2], lev1_dim=lev1, lev2_dim=lev2) else: abort( "Error: Variable " diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 7671e10692..fc5eb8d0e9 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -143,15 +143,78 @@ def test_opt_sections(self): fsurdat_modifier(parser) # Read the resultant output file and make sure the fields are changed as expected fsurdat_out_data = xr.open_dataset(outfile) - zero0d = np.zeros( (5,5) ) - one0d = np.ones( (5,5) ) - np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d ) - np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, zero0d ) - np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d ) - np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d ) - np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d ) - np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d ) - np.testing.assert_array_equal(fsurdat_out_data.LAKEDEPTH, one0d*200. ) + zero0d = np.zeros((5, 5)) + one0d = np.ones((5, 5)) + pct_urban = np.array( + [ + [ + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + ], + [ + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + ], + [ + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + [0.0, 0.0, 0.0, 0.0, 0.0], + ], + ] + ) + lev2_two = np.empty( (2,3,5,5) ) + lev2_two[0,:,:,:] = 200. + lev2_two[1,:,:,:] = 100. + lev2_five = np.empty( (5,3,5,5) ) + lev2_five[0,:,:,:] = 1. + lev2_five[1,:,:,:] = 2. + lev2_five[2,:,:,:] = 3. + lev2_five[3,:,:,:] = 4. + lev2_five[4,:,:,:] = 5. + lev1 = np.array( + [ + [ + [200.0, 200.0, 200.0, 200.0, 200.0], + [200.0, 200.0, 200.0, 200.0, 200.0], + [200.0, 200.0, 200.0, 200.0, 200.0], + [200.0, 200.0, 200.0, 200.0, 200.0], + [200.0, 200.0, 200.0, 200.0, 200.0], + ], + [ + [150.0, 150.0, 150.0, 150.0, 150.0], + [150.0, 150.0, 150.0, 150.0, 150.0], + [150.0, 150.0, 150.0, 150.0, 150.0], + [150.0, 150.0, 150.0, 150.0, 150.0], + [150.0, 150.0, 150.0, 150.0, 150.0], + ], + [ + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + [100.0, 100.0, 100.0, 100.0, 100.0], + ], + ] + ) + np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, pct_urban) + np.testing.assert_array_equal(fsurdat_out_data.LAKEDEPTH, one0d * 200.0) + np.testing.assert_array_equal(fsurdat_out_data.T_BUILDING_MIN, lev1) + np.testing.assert_array_equal(fsurdat_out_data.ALB_ROOF_DIR, lev2_two) + np.testing.assert_array_equal(fsurdat_out_data.TK_ROOF, lev2_five) def test_cfg_file_DNE_fail(self): """ diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index b9c006ce03..c068c5d851 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -47,5 +47,5 @@ LAKEDEPTH = 200.00 CANYON_HWR = 200.00 150.0 100. HT_ROOF = 200.0 150.0 100. T_BUILDING_MIN = 200 150.0 100. -#ALB_ROOF_DIR = 200. 100. -#TK_ROOF = 1. 2. 3. 4. 5. +ALB_ROOF_DIR = 200. 100. +TK_ROOF = 1. 2. 3. 4. 5. From 8338b786b05a9e2160a3020b6e59154f5dcd4813 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 13 Jan 2023 17:25:55 -0700 Subject: [PATCH 0613/2067] Squashed 'manage_externals/' changes from a3b3a0373..82d3b247f MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 82d3b247f Merge pull request #178 from johnpaulalex/test_doc 3223f49ea Additional documentation of system tests - global variables, method descriptions. 45b7c01c3 Merge pull request #177 from jedwards4b/git_workflow ace90b2c2 try setting credentials this way f4d6aa933 try setting credentials this way 1d61a6944 use this to set git credentials 7f9d330e1 use this to set git credentials 5ac731b85 add tmate code 836847be7 get git workflow working dcd462d71 Merge pull request #176 from jedwards4b/add_github_testing 2d2479e9d Merge pull request #175 from johnpaulalex/fix 711a53fdf add github testing of prs and automatic tagging of main cfe0f888a fix typos 5665d6140 Fix broken checkout behavior introduced by PR #172. 27909e255 Merge pull request #173 from johnpaulalex/readall 00ad0440b Further tiny refactorings and docs of checkout API (no-op). Remove unused load_all param in _External.checkout(). Rename _External.checkout_externals() to checkout_subexternals(), to remove the ambiguity about whether the main external pointed to by the _External is itelf checked out (it is not) Clarify load_all documentation - it’s always recursive, but applies different criteria at each level. Rename variables in checkout.py (e.g. ext_description) to match the equivalent code in sourcetree.py. 2ea3d1a3a Merge pull request #172 from johnpaulalex/fixit 43bf8092c Merge pull request #171 from johnpaulalex/docstatus e6aa7d21e Merge pull request #170 from johnpaulalex/printdir adbd71557 On checkout, refresh locally installed optional packages regardless of whether -o is passed in. add074593 Comment tweaks, and fix 'ppath' typo 696527cb8 Document the format of various status dictionaries, and the various paths and path components within an _External. c677b9403 When processing an external, print out its path in addition to the base filename (to disambiguate all the externals.cfg's) 975d7fd5a Merge pull request #169 from johnpaulalex/docfix_branch 09709e36d Document _Externals.status(). The original comment was apparently copy-pasted from checkout(). 1d880e090 Merge pull request #167 from billsacks/fix_svn_on_windows 3510da848 Tweak a unit test to improve coverage eb7fc1368 Handle the possibility that the URL already ends with '/' 02ea87e3d Fix svn URLs on Windows b1c02ab54 Merge pull request #165 from gold2718/doc_fix 9f4be8c7b Add documentation about externals = None feature git-subtree-dir: manage_externals git-subtree-split: 82d3b247fc8fb3b70458bf2b4570ee6678754c4d --- .github/workflows/bumpversion.yml | 19 + .github/workflows/tests.yml | 30 ++ README.md | 5 + manic/checkout.py | 92 ++--- manic/externals_description.py | 19 +- manic/externals_status.py | 30 +- manic/repository_factory.py | 1 + manic/repository_svn.py | 9 +- manic/sourcetree.py | 275 ++++++++------ test/README.md | 38 +- test/test_sys_checkout.py | 591 ++++++++++++++++-------------- test/test_unit_repository_svn.py | 2 +- 12 files changed, 620 insertions(+), 491 deletions(-) create mode 100644 .github/workflows/bumpversion.yml create mode 100644 .github/workflows/tests.yml mode change 100644 => 100755 test/test_unit_repository_svn.py diff --git a/.github/workflows/bumpversion.yml b/.github/workflows/bumpversion.yml new file mode 100644 index 0000000000..f4dc9b7ca5 --- /dev/null +++ b/.github/workflows/bumpversion.yml @@ -0,0 +1,19 @@ +name: Bump version +on: + push: + branches: + - main +jobs: + build: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Bump version and push tag + id: tag_version + uses: mathieudutour/github-tag-action@v5.5 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + create_annotated_tag: true + default_bump: patch + dry_run: false + tag_prefix: manic- diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml new file mode 100644 index 0000000000..dd75b91b49 --- /dev/null +++ b/.github/workflows/tests.yml @@ -0,0 +1,30 @@ +# This is a workflow to compile the cmeps source without cime +name: Test Manic + +# Controls when the action will run. Triggers the workflow on push or pull request +# events but only for the master branch +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + test-manic: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + - name: Test Manic + run: | + pushd test + git config --global user.email "devnull@example.com" + git config --global user.name "GITHUB tester" + git config --global protocol.file.allow always + make utest + make stest + popd + + - name: Setup tmate session + if: ${{ failure() }} + uses: mxschmitt/action-tmate@v3 diff --git a/README.md b/README.md index c931c8e213..9475301b5d 100644 --- a/README.md +++ b/README.md @@ -201,6 +201,11 @@ The root of the source tree will be referred to as `${SRC_ROOT}` below. externals description file pointed 'useful_library/sub-xternals.cfg', Then the main 'externals' field in the top level repo should point to 'sub-externals.cfg'. + Note that by default, `checkout_externals` will clone an external's + submodules. As a special case, the entry, `externals = None`, will + prevent this behavior. For more control over which externals are + checked out, create an externals file (and see the `from_submodule` + configuration entry below). * from_submodule (True / False) : used to pull the repo_url, local_path, and hash properties for this external from the .gitmodules file in diff --git a/manic/checkout.py b/manic/checkout.py index 2223b1f0d8..ac30f3a5d2 100755 --- a/manic/checkout.py +++ b/manic/checkout.py @@ -227,6 +227,12 @@ def commandline_arguments(args=None): Now, %(prog)s will process Externals.cfg and also process Externals_LIBX.cfg as if it was a sub-external. + Note that by default, checkout_externals will clone an external's + submodules. As a special case, the entry, "externals = None", will + prevent this behavior. For more control over which externals are + checked out, create an externals file (and see the from_submodule + configuration entry below). + * from_submodule (True / False) : used to pull the repo_url, local_path, and hash properties for this external from the .gitmodules file in this repository. Note that the section name (the entry in square @@ -332,7 +338,34 @@ def commandline_arguments(args=None): options = parser.parse_args() return options - +def _dirty_local_repo_msg(program_name, config_file): + return """The external repositories labeled with 'M' above are not in a clean state. +The following are four options for how to proceed: +(1) Go into each external that is not in a clean state and issue either a 'git status' or + an 'svn status' command (depending on whether the external is managed by git or + svn). Either revert or commit your changes so that all externals are in a clean + state. (To revert changes in git, follow the instructions given when you run 'git + status'.) (Note, though, that it is okay to have untracked files in your working + directory.) Then rerun {program_name}. +(2) Alternatively, you do not have to rely on {program_name}. Instead, you can manually + update out-of-sync externals (labeled with 's' above) as described in the + configuration file {config_file}. (For example, run 'git fetch' and 'git checkout' + commands to checkout the appropriate tags for each external, as given in + {config_file}.) +(3) You can also use {program_name} to manage most, but not all externals: You can specify + one or more externals to ignore using the '-x' or '--exclude' argument to + {program_name}. Excluding externals labeled with 'M' will allow {program_name} to + update the other, non-excluded externals. +(4) As a last resort, if you are confident that there is no work that needs to be saved + from a given external, you can remove that external (via "rm -rf [directory]") and + then rerun the {program_name} tool. This option is mainly useful as a workaround for + issues with this tool (such as https://github.com/ESMCI/manage_externals/issues/157). +The external repositories labeled with '?' above are not under version +control using the expected protocol. If you are sure you want to switch +protocols, and you don't have any work you need to save from this +directory, then run "rm -rf [directory]" before rerunning the +{program_name} tool. +""".format(program_name=program_name, config_file=config_file) # --------------------------------------------------------------------- # # main @@ -363,19 +396,25 @@ def main(args): load_all = True root_dir = os.path.abspath(os.getcwd()) - external_data = read_externals_description_file(root_dir, args.externals) - external = create_externals_description( - external_data, components=args.components, exclude=args.exclude) + model_data = read_externals_description_file(root_dir, args.externals) + ext_description = create_externals_description( + model_data, components=args.components, exclude=args.exclude) for comp in args.components: - if comp not in external.keys(): + if comp not in ext_description.keys(): + # Note we can't print out the list of found externals because + # they were filtered in create_externals_description above. fatal_error( "No component {} found in {}".format( comp, args.externals)) - source_tree = SourceTree(root_dir, external, svn_ignore_ancestry=args.svn_ignore_ancestry) - printlog('Checking status of externals: ', end='') - tree_status = source_tree.status() + source_tree = SourceTree(root_dir, ext_description, svn_ignore_ancestry=args.svn_ignore_ancestry) + if args.components: + components_str = 'specified components' + else: + components_str = 'required & optional components' + printlog('Checking local status of ' + components_str + ': ', end='') + tree_status = source_tree.status(print_progress=True) printlog('') if args.status: @@ -390,43 +429,8 @@ def main(args): for comp in sorted(tree_status): tree_status[comp].log_status_message(args.verbose) # exit gracefully - msg = """The external repositories labeled with 'M' above are not in a clean state. - -The following are four options for how to proceed: - -(1) Go into each external that is not in a clean state and issue either a 'git status' or - an 'svn status' command (depending on whether the external is managed by git or - svn). Either revert or commit your changes so that all externals are in a clean - state. (To revert changes in git, follow the instructions given when you run 'git - status'.) (Note, though, that it is okay to have untracked files in your working - directory.) Then rerun {program_name}. - -(2) Alternatively, you do not have to rely on {program_name}. Instead, you can manually - update out-of-sync externals (labeled with 's' above) as described in the - configuration file {config_file}. (For example, run 'git fetch' and 'git checkout' - commands to checkout the appropriate tags for each external, as given in - {config_file}.) - -(3) You can also use {program_name} to manage most, but not all externals: You can specify - one or more externals to ignore using the '-x' or '--exclude' argument to - {program_name}. Excluding externals labeled with 'M' will allow {program_name} to - update the other, non-excluded externals. - -(4) As a last resort, if you are confident that there is no work that needs to be saved - from a given external, you can remove that external (via "rm -rf [directory]") and - then rerun the {program_name} tool. This option is mainly useful as a workaround for - issues with this tool (such as https://github.com/ESMCI/manage_externals/issues/157). - - -The external repositories labeled with '?' above are not under version -control using the expected protocol. If you are sure you want to switch -protocols, and you don't have any work you need to save from this -directory, then run "rm -rf [directory]" before rerunning the -{program_name} tool. -""".format(program_name=program_name, config_file=args.externals) - printlog('-' * 70) - printlog(msg) + printlog(_dirty_local_repo_msg(program_name, args.externals)) printlog('-' * 70) else: if not args.components: diff --git a/manic/externals_description.py b/manic/externals_description.py index 6a54935935..f5615b6730 100644 --- a/manic/externals_description.py +++ b/manic/externals_description.py @@ -71,7 +71,8 @@ def read_externals_description_file(root_dir, file_name): root_dir = os.path.abspath(root_dir) msg = 'In directory : {0}'.format(root_dir) logging.info(msg) - printlog('Processing externals description file : {0}'.format(file_name)) + printlog('Processing externals description file : {0} ({1})'.format(file_name, + root_dir)) file_path = os.path.join(root_dir, file_name) if not os.path.exists(file_name): @@ -281,6 +282,10 @@ def read_gitmodules_file(root_dir, file_name): def create_externals_description( model_data, model_format='cfg', components=None, exclude=None, parent_repo=None): """Create the a externals description object from the provided data + + components: list of component names to include, None to include all. If a + name isn't found, it is silently omitted from the return value. + exclude: list of component names to skip. """ externals_description = None if model_format == 'dict': @@ -357,8 +362,9 @@ class ExternalsDescription(dict): input value. """ - # keywords defining the interface into the externals description data - EXTERNALS = 'externals' + # keywords defining the interface into the externals description data; these + # are brought together by the schema below. + EXTERNALS = 'externals' # path to externals file. BRANCH = 'branch' SUBMODULE = 'from_submodule' HASH = 'hash' @@ -384,6 +390,8 @@ class ExternalsDescription(dict): _V1_BRANCH = 'BRANCH' _V1_REQ_SOURCE = 'REQ_SOURCE' + # Dictionary keys are component names. The corresponding values are laid out + # according to this schema. _source_schema = {REQUIRED: True, PATH: 'string', EXTERNALS: 'string', @@ -760,6 +768,8 @@ def __init__(self, model_data, components=None, exclude=None, parent_repo=None): """Convert the config data into a standardized dict that can be used to construct the source objects + components: list of component names to include, None to include all. + exclude: list of component names to skip. """ ExternalsDescription.__init__(self, parent_repo=parent_repo) self._schema_major = 1 @@ -783,6 +793,9 @@ def _remove_metadata(model_data): def _parse_cfg(self, cfg_data, components=None, exclude=None): """Parse a config_parser object into a externals description. + + components: list of component names to include, None to include all. + exclude: list of component names to skip. """ def list_to_dict(input_list, convert_to_lower_case=True): """Convert a list of key-value pairs into a dictionary. diff --git a/manic/externals_status.py b/manic/externals_status.py index d3d238f289..4900e41254 100644 --- a/manic/externals_status.py +++ b/manic/externals_status.py @@ -29,16 +29,16 @@ class ExternalStatus(object): transactions (e.g. add, remove, rename, untracked files). """ - DEFAULT = '-' + # sync_state and clean_state can be one of the following: + DEFAULT = '-' # aka not set yet. UNKNOWN = '?' EMPTY = 'e' - MODEL_MODIFIED = 's' # a.k.a. out-of-sync - DIRTY = 'M' - - STATUS_OK = ' ' + MODEL_MODIFIED = 's' # repo version != externals (sync_state only) + DIRTY = 'M' # repo is dirty (clean_state only) + STATUS_OK = ' ' # repo is clean/matches externals. STATUS_ERROR = '!' - # source types + # source_type can be one of the following: OPTIONAL = 'o' STANDALONE = 's' MANAGED = ' ' @@ -55,19 +55,21 @@ def __init__(self): def log_status_message(self, verbosity): """Write status message to the screen and log file """ - self._default_status_message() + printlog(self._default_status_message()) if verbosity >= VERBOSITY_VERBOSE: - self._verbose_status_message() + printlog(self._verbose_status_message()) if verbosity >= VERBOSITY_DUMP: - self._dump_status_message() + printlog(self._dump_status_message()) + + def __repr__(self): + return self._default_status_message() def _default_status_message(self): """Return the default terse status message string """ - msg = '{sync}{clean}{src_type} {path}'.format( + return '{sync}{clean}{src_type} {path}'.format( sync=self.sync_state, clean=self.clean_state, src_type=self.source_type, path=self.path) - printlog(msg) def _verbose_status_message(self): """Return the verbose status message string @@ -82,14 +84,12 @@ def _verbose_status_message(self): if self.sync_state != self.STATUS_OK: sync_str = '{current} --> {expected}'.format( current=self.current_version, expected=self.expected_version) - msg = ' {clean}, {sync}'.format(clean=clean_str, sync=sync_str) - printlog(msg) + return ' {clean}, {sync}'.format(clean=clean_str, sync=sync_str) def _dump_status_message(self): """Return the dump status message string """ - msg = indent_string(self.status_output, 12) - printlog(msg) + return indent_string(self.status_output, 12) def safe_to_update(self): """Report if it is safe to update a repository. Safe is defined as: diff --git a/manic/repository_factory.py b/manic/repository_factory.py index 80a92a9d8a..18c73ffc4b 100644 --- a/manic/repository_factory.py +++ b/manic/repository_factory.py @@ -15,6 +15,7 @@ def create_repository(component_name, repo_info, svn_ignore_ancestry=False): """Determine what type of repository we have, i.e. git or svn, and create the appropriate object. + Can return None (e.g. if protocol is 'externals_only'). """ protocol = repo_info[ExternalsDescription.PROTOCOL].lower() if protocol == 'git': diff --git a/manic/repository_svn.py b/manic/repository_svn.py index 408ed84676..922855d34e 100644 --- a/manic/repository_svn.py +++ b/manic/repository_svn.py @@ -43,10 +43,15 @@ def __init__(self, component_name, repo, ignore_ancestry=False): """ Repository.__init__(self, component_name, repo) self._ignore_ancestry = ignore_ancestry + if self._url.endswith('/'): + # there is already a '/' separator in the URL; no need to add another + url_sep = '' + else: + url_sep = '/' if self._branch: - self._url = os.path.join(self._url, self._branch) + self._url = self._url + url_sep + self._branch elif self._tag: - self._url = os.path.join(self._url, self._tag) + self._url = self._url + url_sep + self._tag else: msg = "DEV_ERROR in svn repository. Shouldn't be here!" fatal_error(msg) diff --git a/manic/sourcetree.py b/manic/sourcetree.py index 54de763c30..218b5febb4 100644 --- a/manic/sourcetree.py +++ b/manic/sourcetree.py @@ -19,7 +19,7 @@ class _External(object): """ - _External represents an external object inside a SourceTree + A single component hosted in an external repository (and any children). """ # pylint: disable=R0902 @@ -41,31 +41,40 @@ def __init__(self, root_dir, name, ext_description, svn_ignore_ancestry): """ self._name = name - self._repo = None - self._externals = EMPTY_STR + self._repo = None # Repository object. + + # Subcomponent externals file and data object, if any. + self._externals_path = EMPTY_STR # Can also be "none" self._externals_sourcetree = None - self._stat = ExternalStatus() + + self._stat = None # Populated in status() self._sparse = None # Parse the sub-elements - # _path : local path relative to the containing source tree + # _local_path : local path relative to the containing source tree, e.g. + # "components/mom" self._local_path = ext_description[ExternalsDescription.PATH] - # _repo_dir : full repository directory + # _repo_dir_path : full repository directory, e.g. + # "/components/mom" repo_dir = os.path.join(root_dir, self._local_path) self._repo_dir_path = os.path.abspath(repo_dir) - # _base_dir : base directory *containing* the repository + # _base_dir_path : base directory *containing* the repository, e.g. + # "/components" self._base_dir_path = os.path.dirname(self._repo_dir_path) - # repo_dir_name : base_dir_path + repo_dir_name = rep_dir_path + # _repo_dir_name : base_dir_path + repo_dir_name = rep_dir_path + # e.g., "mom" self._repo_dir_name = os.path.basename(self._repo_dir_path) assert(os.path.join(self._base_dir_path, self._repo_dir_name) == self._repo_dir_path) self._required = ext_description[ExternalsDescription.REQUIRED] - self._externals = ext_description[ExternalsDescription.EXTERNALS] + + # Does this component have subcomponents aka an externals config? + self._externals_path = ext_description[ExternalsDescription.EXTERNALS] # Treat a .gitmodules file as a backup externals config - if not self._externals: + if not self._externals_path: if GitRepository.has_submodules(self._repo_dir_path): - self._externals = ExternalsDescription.GIT_SUBMODULES_FILENAME + self._externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME repo = create_repository( name, ext_description[ExternalsDescription.REPO], @@ -73,7 +82,8 @@ def __init__(self, root_dir, name, ext_description, svn_ignore_ancestry): if repo: self._repo = repo - if self._externals and (self._externals.lower() != 'none'): + # Recurse into subcomponents, if any. + if self._externals_path and (self._externals_path.lower() != 'none'): self._create_externals_sourcetree() def get_name(self): @@ -88,81 +98,88 @@ def get_local_path(self): """ return self._local_path - def status(self): - """ - If the repo destination directory exists, ensure it is correct (from - correct URL, correct branch or tag), and possibly update the external. - If the repo destination directory does not exist, checkout the correce - branch or tag. - If load_all is True, also load all of the the externals sub-externals. + def status(self, force=False, print_progress=False): """ + Returns status of this component and all subcomponents. - self._stat.path = self.get_local_path() - if not self._required: - self._stat.source_type = ExternalStatus.OPTIONAL - elif self._local_path == LOCAL_PATH_INDICATOR: - # LOCAL_PATH_INDICATOR, '.' paths, are standalone - # component directories that are not managed by - # checkout_externals. - self._stat.source_type = ExternalStatus.STANDALONE - else: - # managed by checkout_externals - self._stat.source_type = ExternalStatus.MANAGED + Returns a dict mapping our local path (not component name!) to an + ExternalStatus dict. Any subcomponents will have their own top-level + path keys. Note the return value includes entries for this and all + subcomponents regardless of whether they are locally installed or not. - ext_stats = {} + Side-effect: If self._stat is empty or force is True, calculates _stat. + """ + calc_stat = force or not self._stat + + if calc_stat: + self._stat = ExternalStatus() + self._stat.path = self.get_local_path() + if not self._required: + self._stat.source_type = ExternalStatus.OPTIONAL + elif self._local_path == LOCAL_PATH_INDICATOR: + # LOCAL_PATH_INDICATOR, '.' paths, are standalone + # component directories that are not managed by + # checkout_subexternals. + self._stat.source_type = ExternalStatus.STANDALONE + else: + # managed by checkout_subexternals + self._stat.source_type = ExternalStatus.MANAGED + subcomponent_stats = {} if not os.path.exists(self._repo_dir_path): - self._stat.sync_state = ExternalStatus.EMPTY - msg = ('status check: repository directory for "{0}" does not ' - 'exist.'.format(self._name)) - logging.info(msg) - self._stat.current_version = 'not checked out' - # NOTE(bja, 2018-01) directory doesn't exist, so we cannot - # use repo to determine the expected version. We just take - # a best-guess based on the assumption that only tag or - # branch should be set, but not both. - if not self._repo: - self._stat.expected_version = 'unknown' - else: - self._stat.expected_version = self._repo.tag() + self._repo.branch() + if calc_stat: + # No local repository. + self._stat.sync_state = ExternalStatus.EMPTY + msg = ('status check: repository directory for "{0}" does not ' + 'exist.'.format(self._name)) + logging.info(msg) + self._stat.current_version = 'not checked out' + # NOTE(bja, 2018-01) directory doesn't exist, so we cannot + # use repo to determine the expected version. We just take + # a best-guess based on the assumption that only tag or + # branch should be set, but not both. + if not self._repo: + self._stat.expected_version = 'unknown' + else: + self._stat.expected_version = self._repo.tag() + self._repo.branch() else: - if self._repo: + # Merge local repository state (e.g. clean/dirty) into self._stat. + if calc_stat and self._repo: self._repo.status(self._stat, self._repo_dir_path) - if self._externals and self._externals_sourcetree: - # we expect externals and they exist + # Status of subcomponents, if any. + if self._externals_path and self._externals_sourcetree: cwd = os.getcwd() - # SourceTree expects to be called from the correct + # SourceTree.status() expects to be called from the correct # root directory. os.chdir(self._repo_dir_path) - ext_stats = self._externals_sourcetree.status(self._local_path) + subcomponent_stats = self._externals_sourcetree.status(self._local_path, force=force, print_progress=print_progress) os.chdir(cwd) + # Merge our status + subcomponent statuses into one return dict keyed + # by component path. all_stats = {} # don't add the root component because we don't manage it # and can't provide useful info about it. if self._local_path != LOCAL_PATH_INDICATOR: - # store the stats under tha local_path, not comp name so + # store the stats under the local_path, not comp name so # it will be sorted correctly all_stats[self._stat.path] = self._stat - if ext_stats: - all_stats.update(ext_stats) + if subcomponent_stats: + all_stats.update(subcomponent_stats) return all_stats - def checkout(self, verbosity, load_all): + def checkout(self, verbosity): """ If the repo destination directory exists, ensure it is correct (from correct URL, correct branch or tag), and possibly update the external. If the repo destination directory does not exist, checkout the correct branch or tag. - If load_all is True, also load all of the the externals sub-externals. + Does not check out sub-externals, see checkout_subexternals(). """ - if load_all: - pass # Make sure we are in correct location - if not os.path.exists(self._repo_dir_path): # repository directory doesn't exist. Need to check it # out, and for that we need the base_dir_path to exist @@ -174,6 +191,10 @@ def checkout(self, verbosity, load_all): self._base_dir_path) fatal_error(msg) + if not self._stat: + self.status() + assert self._stat + if self._stat.source_type != ExternalStatus.STANDALONE: if verbosity >= VERBOSITY_VERBOSE: # NOTE(bja, 2018-01) probably do not want to pass @@ -194,8 +215,10 @@ def checkout(self, verbosity, load_all): self._repo.checkout(self._base_dir_path, self._repo_dir_name, checkout_verbosity, self.clone_recursive()) - def checkout_externals(self, verbosity, load_all): - """Checkout the sub-externals for this object + def checkout_subexternals(self, verbosity, load_all): + """Recursively checkout the sub-externals for this component, if any. + + See load_all documentation in SourceTree.checkout(). """ if self.load_externals(): if self._externals_sourcetree: @@ -210,25 +233,26 @@ def checkout_externals(self, verbosity, load_all): self._externals_sourcetree.checkout(verbosity, load_all) def load_externals(self): - 'Return True iff an externals file should be loaded' + 'Return True iff an externals file exists (and therefore should be loaded)' load_ex = False if os.path.exists(self._repo_dir_path): - if self._externals: - if self._externals.lower() != 'none': + if self._externals_path: + if self._externals_path.lower() != 'none': load_ex = os.path.exists(os.path.join(self._repo_dir_path, - self._externals)) + self._externals_path)) return load_ex def clone_recursive(self): 'Return True iff any .gitmodules files should be processed' - # Try recursive unless there is an externals entry - recursive = not self._externals + # Try recursive .gitmodules unless there is an externals entry + recursive = not self._externals_path return recursive def _create_externals_sourcetree(self): """ + Note this only creates an object, it doesn't write to the file system. """ if not os.path.exists(self._repo_dir_path): # NOTE(bja, 2017-10) repository has not been checked out @@ -239,29 +263,31 @@ def _create_externals_sourcetree(self): cwd = os.getcwd() os.chdir(self._repo_dir_path) - if self._externals.lower() == 'none': + if self._externals_path.lower() == 'none': msg = ('Internal: Attempt to create source tree for ' 'externals = none in {}'.format(self._repo_dir_path)) fatal_error(msg) - if not os.path.exists(self._externals): + if not os.path.exists(self._externals_path): if GitRepository.has_submodules(): - self._externals = ExternalsDescription.GIT_SUBMODULES_FILENAME + self._externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME - if not os.path.exists(self._externals): + if not os.path.exists(self._externals_path): # NOTE(bja, 2017-10) this check is redundent with the one # in read_externals_description_file! msg = ('External externals description file "{0}" ' 'does not exist! In directory: {1}'.format( - self._externals, self._repo_dir_path)) + self._externals_path, self._repo_dir_path)) fatal_error(msg) externals_root = self._repo_dir_path + # model_data is a dict-like object which mirrors the file format. model_data = read_externals_description_file(externals_root, - self._externals) - externals = create_externals_description(model_data, - parent_repo=self._repo) - self._externals_sourcetree = SourceTree(externals_root, externals) + self._externals_path) + # ext_description is another dict-like object (see ExternalsDescription) + ext_description = create_externals_description(model_data, + parent_repo=self._repo) + self._externals_sourcetree = SourceTree(externals_root, ext_description) os.chdir(cwd) class SourceTree(object): @@ -269,45 +295,48 @@ class SourceTree(object): SourceTree represents a group of managed externals """ - def __init__(self, root_dir, model, svn_ignore_ancestry=False): + def __init__(self, root_dir, ext_description, svn_ignore_ancestry=False): """ - Build a SourceTree object from a model description + Build a SourceTree object from an ExternalDescription. """ self._root_dir = os.path.abspath(root_dir) - self._all_components = {} + self._all_components = {} # component_name -> _External self._required_compnames = [] - for comp in model: - src = _External(self._root_dir, comp, model[comp], svn_ignore_ancestry) + for comp in ext_description: + src = _External(self._root_dir, comp, ext_description[comp], + svn_ignore_ancestry) self._all_components[comp] = src - if model[comp][ExternalsDescription.REQUIRED]: + if ext_description[comp][ExternalsDescription.REQUIRED]: self._required_compnames.append(comp) - def status(self, relative_path_base=LOCAL_PATH_INDICATOR): - """Report the status components - - FIXME(bja, 2017-10) what do we do about situations where the - user checked out the optional components, but didn't add - optional for running status? What do we do where the user - didn't add optional to the checkout but did add it to the - status. -- For now, we run status on all components, and try - to do the right thing based on the results.... - - """ + def status(self, relative_path_base=LOCAL_PATH_INDICATOR, + force=False, print_progress=False): + """Return a dictionary of local path->ExternalStatus. + + Notes about the returned dictionary: + * It is keyed by local path (e.g. 'components/mom'), not by + component name (e.g. 'mom'). + * It contains top-level keys for all traversed components, whether + discovered by recursion or top-level. + * It contains entries for all components regardless of whether they + are locally installed or not, or required or optional. +x """ load_comps = self._all_components.keys() - summary = {} + summary = {} # Holds merged statuses from all components. for comp in load_comps: - printlog('{0}, '.format(comp), end='') - stat = self._all_components[comp].status() + if print_progress: + printlog('{0}, '.format(comp), end='') + stat = self._all_components[comp].status(force=force, + print_progress=print_progress) + + # Returned status dictionary is keyed by local path; prepend + # relative_path_base if not already there. stat_final = {} for name in stat.keys(): - # check if we need to append the relative_path_base to - # the path so it will be sorted in the correct order. if stat[name].path.startswith(relative_path_base): - # use as is, without any changes to path stat_final[name] = stat[name] else: - # append relative_path_base to path and store under key = updated path modified_path = os.path.join(relative_path_base, stat[name].path) stat_final[modified_path] = stat[name] @@ -316,30 +345,48 @@ def status(self, relative_path_base=LOCAL_PATH_INDICATOR): return summary + def _find_installed_optional_components(self): + """Returns a list of installed optional component names, if any.""" + installed_comps = [] + for comp_name, ext in self._all_components.items(): + if comp_name in self._required_compnames: + continue + # Note that in practice we expect this status to be cached. + path_to_stat = ext.status() + if any(stat.sync_state != ExternalStatus.EMPTY + for stat in path_to_stat.values()): + installed_comps.append(comp_name) + return installed_comps + def checkout(self, verbosity, load_all, load_comp=None): """ - Checkout or update indicated components into the the configured - subdirs. + Checkout or update indicated components into the configured subdirs. - If load_all is True, recursively checkout all externals. - If load_all is False, load_comp is an optional set of components to load. - If load_all is True and load_comp is None, only load the required externals. + If load_all is True, checkout all externals (required + optional), recursively. + If load_all is False and load_comp is set, checkout load_comp (and any required subexternals, plus any optional subexternals that are already checked out, recursively) + If load_all is False and load_comp is None, checkout all required externals, plus any optionals that are already checked out, recursively. """ - if verbosity >= VERBOSITY_VERBOSE: - printlog('Checking out externals: ') - else: - printlog('Checking out externals: ', end='') - if load_all: tmp_comps = self._all_components.keys() elif load_comp is not None: tmp_comps = [load_comp] else: - tmp_comps = self._required_compnames + local_optional_compnames = self._find_installed_optional_components() + tmp_comps = self._required_compnames + local_optional_compnames + if local_optional_compnames: + printlog('Found locally installed optional components: ' + + ', '.join(local_optional_compnames)) + + if verbosity >= VERBOSITY_VERBOSE: + printlog('Checking out externals: ') + else: + printlog('Checking out externals: ', end='') + # Sort by path so that if paths are nested the # parent repo is checked out first. load_comps = sorted(tmp_comps, key=lambda comp: self._all_components[comp].get_local_path()) - # checkout the primary externals + + # checkout. for comp in load_comps: if verbosity < VERBOSITY_VERBOSE: printlog('{0}, '.format(comp), end='') @@ -347,7 +394,9 @@ def checkout(self, verbosity, load_all, load_comp=None): # verbose output handled by the _External object, just # output a newline printlog(EMPTY_STR) - self._all_components[comp].checkout(verbosity, load_all) - # now give each external an opportunitity to checkout it's externals. - self._all_components[comp].checkout_externals(verbosity, load_all) + # Does not recurse. + self._all_components[comp].checkout(verbosity) + # Recursively check out subexternals, if any. + self._all_components[comp].checkout_subexternals(verbosity, + load_all) printlog('') diff --git a/test/README.md b/test/README.md index 938a900eec..1e8f2eaa77 100644 --- a/test/README.md +++ b/test/README.md @@ -1,45 +1,25 @@ # Testing for checkout_externals -NOTE: Python2 is the supported runtime environment. Python3 compatibility is -in progress, complicated by the different proposed input methods -(yaml, xml, cfg/ini, json) and their different handling of strings -(unicode vs byte) in python2. Full python3 compatibility will be -possible once the number of possible input formats has been narrowed. - -## Setup development environment - -Development environments should be setup for python2 and python3: +## Unit tests ```SH cd checkout_externals/test - make python=python2 env - make python=python3 env + make utest ``` -## Unit tests - -Tests should be run for both python2 and python3. It is recommended -that you have seperate terminal windows open python2 and python3 -testing to avoid errors activating and deactivating environments. +## System tests ```SH cd checkout_externals/test - . env_python2/bin/activate - make utest - deactivate + make stest ``` +Example to run a single test: ```SH - cd checkout_externals/test - . env_python2/bin/activate - make utest - deactivate + cd checkout_externals + python -m unittest test.test_sys_checkout.TestSysCheckout.test_container_simple_required ``` -## System tests - -Not yet implemented. - ## Static analysis checkout_externals is difficult to test thoroughly because it relies @@ -51,9 +31,7 @@ regularly for automatic code formatting and linting. ```SH cd checkout_externals/test - . env_python2/bin/activate make lint - deactivate ``` The canonical formatting for the code is whatever autopep8 @@ -68,10 +46,8 @@ coverage, run the code coverage tool: ```SH cd checkout_externals/test - . env_python2/bin/activate make coverage open -a Firefox.app htmlcov/index.html - deactivate ``` diff --git a/test/test_sys_checkout.py b/test/test_sys_checkout.py index b13e96a17d..27b649bea4 100644 --- a/test/test_sys_checkout.py +++ b/test/test_sys_checkout.py @@ -66,27 +66,41 @@ # # --------------------------------------------------------------------- -# environment variable names -MANIC_TEST_BARE_REPO_ROOT = 'MANIC_TEST_BARE_REPO_ROOT' -MANIC_TEST_TMP_REPO_ROOT = 'MANIC_TEST_TMP_REPO_ROOT' -# directory names -TMP_REPO_DIR_NAME = 'tmp' -BARE_REPO_ROOT_NAME = 'repos' +# Module-wide root directory for all the per-test subdirs we'll create on +# the fly. +MANIC_TEST_TMP_REPO_ROOT = 'MANIC_TEST_TMP_REPO_ROOT' # env var name +TMP_REPO_DIR_NAME = 'tmp' # subdir under $CWD + +# We clone these checked-in repositories on a per-test basis. The +# 'bare repo root' is the test/repos/ subdir that holds them all. +MANIC_TEST_BARE_REPO_ROOT = 'MANIC_TEST_BARE_REPO_ROOT' # env var name +BARE_REPO_ROOT_NAME = 'repos' # subdir name + +# Subdirs under bare repo root, each holding a repository. CONTAINER_REPO_NAME = 'container.git' MIXED_REPO_NAME = 'mixed-cont-ext.git' SIMPLE_REPO_NAME = 'simple-ext.git' SIMPLE_FORK_NAME = 'simple-ext-fork.git' -SIMPLE_LOCAL_ONLY_NAME = '.' -ERROR_REPO_NAME = 'error' + + +# In each of the test repos, all externals live under this subdir. EXTERNALS_NAME = 'externals' -SUB_EXTERNALS_PATH = 'src' +SUB_EXTERNALS_PATH = 'src' # For mixed test repos, + +# For testing behavior with '.' instead of an explicit paths. +SIMPLE_LOCAL_ONLY_NAME = '.' + +# Filenames CFG_NAME = 'externals.cfg' CFG_SUB_NAME = 'sub-externals.cfg' -README_NAME = 'readme.txt' +README_NAME = 'readme.txt' # Arbitrary file to check in. + +# Arbirary test branch name REMOTE_BRANCH_FEATURE2 = 'feature2' -NESTED_NAME = ['./fred', './fred/wilma', './fred/wilma/barney'] +# Section names in container_nested_* test config. +NESTED_NAME = ['./fred', './fred/wilma', './fred/wilma/barney'] SVN_TEST_REPO = 'https://github.com/escomp/cesm' @@ -110,16 +124,18 @@ def setUpModule(): # pylint: disable=C0103 # create clean dir for this run os.mkdir(repo_root) # set into the environment so var will be expanded in externals - # filess when executables are run + # files when executables are run os.environ[MANIC_TEST_TMP_REPO_ROOT] = repo_root class GenerateExternalsDescriptionCfgV1(object): - """Class to provide building blocks to create - ExternalsDescriptionCfgV1 files. + """Building blocks to create ExternalsDescriptionCfgV1 files. - Includes predefined files used in tests. + Basic usage: create_config() multiple create_*(), then write_config(). + Optionally after that: write_with_*(). + Includes methods (like container_*()) to create predefined configs for the + checked-in repositories in test/repos/. """ def __init__(self): @@ -255,7 +271,7 @@ def mixed_simple_sub(self, dest_dir): self.write_config(dest_dir, filename=CFG_SUB_NAME) def write_config(self, dest_dir, filename=CFG_NAME): - """Write the configuration file to disk + """Write self._config to disk """ dest_path = os.path.join(dest_dir, filename) @@ -277,14 +293,17 @@ def create_metadata(self): self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, self._schema_version) - def create_section(self, repo_type, name, tag='', branch='', + def create_section(self, repo_path, name, tag='', branch='', ref_hash='', required=True, path=EXTERNALS_NAME, - externals='', repo_path=None, from_submodule=False, + externals='', repo_path_abs=None, from_submodule=False, sparse='', nested=False): # pylint: disable=too-many-branches - """Create a config section with autofilling some items and handling - optional items. + """Create a config ExternalsDescription section with the given name. + + Autofills some items and handles some optional items. + repo_path_abs overrides repo_path (which is relative to the bare repo) + path is a subdir under repo_path. """ # pylint: disable=R0913 self._config.add_section(name) @@ -300,7 +319,7 @@ def create_section(self, repo_type, name, tag='', branch='', # from_submodules is incompatible with some other options, turn them off if (from_submodule and - ((repo_path is not None) or tag or ref_hash or branch)): + ((repo_path_abs is not None) or tag or ref_hash or branch)): printlog('create_section: "from_submodule" is incompatible with ' '"repo_url", "tag", "hash", and "branch" options;\n' 'Ignoring those options for {}'.format(name)) @@ -309,10 +328,10 @@ def create_section(self, repo_type, name, tag='', branch='', ref_hash = '' branch = '' - if repo_path is not None: - repo_url = repo_path + if repo_path_abs is not None: + repo_url = repo_path_abs else: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_type) + repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_path) if not from_submodule: self._config.set(name, ExternalsDescription.REPO_URL, repo_url) @@ -381,12 +400,11 @@ def create_svn_external(self, name, tag='', branch=''): @staticmethod def create_branch(dest_dir, repo_name, branch, with_commit=False): - """Update a repository branch, and potentially the remote. + """Create branch and optionally (with_commit) add a single commit. """ # pylint: disable=R0913 cwd = os.getcwd() - repo_root = os.path.join(dest_dir, EXTERNALS_NAME) - repo_root = os.path.join(repo_root, repo_name) + repo_root = os.path.join(dest_dir, EXTERNALS_NAME, repo_name) os.chdir(repo_root) cmd = ['git', 'checkout', '-b', branch, ] execute_subprocess(cmd) @@ -407,10 +425,11 @@ def create_commit(dest_dir, repo_name, local_tracking_branch=None): This is used to test sync state changes from local commits on detached heads and tracking branches. + NOTE(jpalex, 2023-01) This has nothing to do with self._config, + should probably live elsewhere. """ cwd = os.getcwd() - repo_root = os.path.join(dest_dir, EXTERNALS_NAME) - repo_root = os.path.join(repo_root, repo_name) + repo_root = os.path.join(dest_dir, EXTERNALS_NAME, repo_name) os.chdir(repo_root) if local_tracking_branch: cmd = ['git', 'checkout', '-b', local_tracking_branch, ] @@ -425,19 +444,21 @@ def create_commit(dest_dir, repo_name, local_tracking_branch=None): execute_subprocess(cmd) os.chdir(cwd) - def update_branch(self, dest_dir, name, branch, repo_type=None, - filename=CFG_NAME): - """Update a repository branch, and potentially the remote. + def write_with_git_branch(self, dest_dir, name, branch, repo_path=None, + filename=CFG_NAME): + """Update fields in our config and write it to disk. + + name is the key of the ExternalsDescription in self._config to update. """ # pylint: disable=R0913 self._config.set(name, ExternalsDescription.BRANCH, branch) - if repo_type: - if repo_type == SIMPLE_LOCAL_ONLY_NAME: + if repo_path: + if repo_path == SIMPLE_LOCAL_ONLY_NAME: repo_url = SIMPLE_LOCAL_ONLY_NAME else: repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', - repo_type) + repo_path) self._config.set(name, ExternalsDescription.REPO_URL, repo_url) try: @@ -448,7 +469,7 @@ def update_branch(self, dest_dir, name, branch, repo_type=None, self.write_config(dest_dir, filename) - def update_svn_branch(self, dest_dir, name, branch, filename=CFG_NAME): + def write_with_svn_branch(self, dest_dir, name, branch, filename=CFG_NAME): """Update a repository branch, and potentially the remote. """ # pylint: disable=R0913 @@ -462,7 +483,7 @@ def update_svn_branch(self, dest_dir, name, branch, filename=CFG_NAME): self.write_config(dest_dir, filename) - def update_tag(self, dest_dir, name, tag, repo_type=None, + def write_with_tag(self, dest_dir, name, tag, repo_path=None, filename=CFG_NAME, remove_branch=True): """Update a repository tag, and potentially the remote @@ -474,8 +495,8 @@ def update_tag(self, dest_dir, name, tag, repo_type=None, # pylint: disable=R0913 self._config.set(name, ExternalsDescription.TAG, tag) - if repo_type: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_type) + if repo_path: + repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_path) self._config.set(name, ExternalsDescription.REPO_URL, repo_url) try: @@ -487,8 +508,8 @@ def update_tag(self, dest_dir, name, tag, repo_type=None, self.write_config(dest_dir, filename) - def update_underspecify_branch_tag(self, dest_dir, name, - filename=CFG_NAME): + def write_without_branch_tag(self, dest_dir, name, + filename=CFG_NAME): """Update a repository protocol, and potentially the remote """ # pylint: disable=R0913 @@ -506,7 +527,7 @@ def update_underspecify_branch_tag(self, dest_dir, name, self.write_config(dest_dir, filename) - def update_underspecify_remove_url(self, dest_dir, name, + def write_without_repo_url(self, dest_dir, name, filename=CFG_NAME): """Update a repository protocol, and potentially the remote """ @@ -519,15 +540,15 @@ def update_underspecify_remove_url(self, dest_dir, name, self.write_config(dest_dir, filename) - def update_protocol(self, dest_dir, name, protocol, repo_type=None, + def write_with_protocol(self, dest_dir, name, protocol, repo_path=None, filename=CFG_NAME): """Update a repository protocol, and potentially the remote """ # pylint: disable=R0913 self._config.set(name, ExternalsDescription.PROTOCOL, protocol) - if repo_type: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_type) + if repo_path: + repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_path) self._config.set(name, ExternalsDescription.REPO_URL, repo_url) self.write_config(dest_dir, filename) @@ -543,6 +564,7 @@ class BaseTestSysCheckout(unittest.TestCase): # cryptic. # pylint: disable=invalid-name + # Command-line args for checkout_externals, used in execute_checkout_in_dir() status_args = ['--status'] checkout_args = [] optional_args = ['--optional'] @@ -575,9 +597,8 @@ def setUp(self): self._checkout = os.path.join(root_dir, 'checkout_externals') # directory where we have test repositories - test_dir = os.path.join(root_dir, 'test') - self._bare_root = os.path.join(test_dir, BARE_REPO_ROOT_NAME) - self._bare_root = os.path.abspath(self._bare_root) + self._bare_root = os.path.abspath( + os.path.join(root_dir, 'test', BARE_REPO_ROOT_NAME)) # set into the environment so var will be expanded in externals files os.environ[MANIC_TEST_BARE_REPO_ROOT] = self._bare_root @@ -596,16 +617,16 @@ def tearDown(self): # return to our common starting point os.chdir(self._return_dir) - def setup_test_repo(self, parent_repo_name, dest_dir_in=None): - """Setup the paths and clone the base test repo + def clone_test_repo(self, parent_repo_name, dest_dir_in=None): + """Clone repo under bare_root into dest_dir_in or local per-test-subdir. + Returns output dir. """ - # unique repo for this test - test_dir_name = self._test_id - print("Test repository name: {0}".format(test_dir_name)) - parent_repo_dir = os.path.join(self._bare_root, parent_repo_name) if dest_dir_in is None: + # unique repo for this test + test_dir_name = self._test_id + print("Test repository name: {0}".format(test_dir_name)) dest_dir = os.path.join(os.environ[MANIC_TEST_TMP_REPO_ROOT], test_dir_name) else: @@ -638,7 +659,7 @@ def _add_file_to_repo(under_test_dir, filename, tracked): os.chdir(cwd) @staticmethod - def execute_cmd_in_dir(under_test_dir, args): + def execute_checkout_in_dir(dirname, args): """Extecute the checkout command in the appropriate repo dir with the specified additional args @@ -649,13 +670,13 @@ def execute_cmd_in_dir(under_test_dir, args): """ cwd = os.getcwd() checkout_path = os.path.abspath('{0}/../../checkout_externals') - os.chdir(under_test_dir) + os.chdir(dirname) cmdline = ['--externals', CFG_NAME, ] cmdline += args repo_root = 'MANIC_TEST_BARE_REPO_ROOT={root}'.format( root=os.environ[MANIC_TEST_BARE_REPO_ROOT]) manual_cmd = ('Test cmd:\npushd {cwd}; {env} {checkout} {args}'.format( - cwd=under_test_dir, env=repo_root, checkout=checkout_path, + cwd=dirname, env=repo_root, checkout=checkout_path, args=' '.join(cmdline))) printlog(manual_cmd) options = checkout.commandline_arguments(cmdline) @@ -667,6 +688,8 @@ def execute_cmd_in_dir(under_test_dir, args): # # Check results for generic perturbation of states # + # 'tree' is a dict with ExternalStatus as values. + # 'name' is a key into that dict. # ---------------------------------------------------------------- def _check_generic_empty_default_required(self, tree, name): self.assertEqual(tree[name].sync_state, ExternalStatus.EMPTY) @@ -702,6 +725,7 @@ def _check_generic_ok_clean_optional(self, tree, name): # # Check results for individual named externals # + # 'tree' is a dict of string to ExternalStatus. # ---------------------------------------------------------------- def _check_simple_tag_empty(self, tree, directory=EXTERNALS_NAME): name = './{0}/simp_tag'.format(directory) @@ -1019,21 +1043,21 @@ def test_container_simple_required(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # status of empty repo - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_pre_checkout(overall, tree) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # status clean checked out - overall, tree = self.execute_cmd_in_dir(under_test_dir, + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) self._check_container_simple_required_post_checkout(overall, tree) @@ -1049,23 +1073,23 @@ def test_container_nested_required(self): # create repo dest_dir = os.path.join(os.environ[MANIC_TEST_TMP_REPO_ROOT], self._test_id, "test"+str(n)) - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME, + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME, dest_dir_in=dest_dir) - self._generator.container_nested_required(under_test_dir, order) + self._generator.container_nested_required(cloned_repo_dir, order) # status of empty repo - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_nested_required_pre_checkout(overall, tree, order) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_nested_required_checkout(overall, tree, order) # status clean checked out - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_nested_required_post_checkout(overall, tree, order) def test_container_simple_optional(self): @@ -1074,32 +1098,32 @@ def test_container_simple_optional(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_optional(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_optional(cloned_repo_dir) # check status of empty repo - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_optional_pre_checkout(overall, tree) # checkout required - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_optional_checkout(overall, tree) # status - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_optional_post_checkout(overall, tree) # checkout optional - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.optional_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.optional_args) self._check_container_simple_optional_post_checkout(overall, tree) # status - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_optional_post_optional(overall, tree) def test_container_simple_verbose(self): @@ -1108,17 +1132,17 @@ def test_container_simple_verbose(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # check verbose status - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.verbose_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.verbose_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_simple_dirty(self): @@ -1126,28 +1150,28 @@ def test_container_simple_dirty(self): and a dirty status exits gracefully. """ - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # add a file to the repo tracked = True - self._add_file_to_repo(under_test_dir, 'externals/simp_tag/tmp.txt', + self._add_file_to_repo(cloned_repo_dir, 'externals/simp_tag/tmp.txt', tracked) # checkout: pre-checkout status should be dirty, did not # modify working copy. - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_optional_st_dirty(overall, tree) # verify status is still dirty - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_optional_st_dirty(overall, tree) def test_container_simple_untracked(self): @@ -1155,28 +1179,28 @@ def test_container_simple_untracked(self): is not considered 'dirty' and will attempt an update. """ - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # add a file to the repo tracked = False - self._add_file_to_repo(under_test_dir, 'externals/simp_tag/tmp.txt', + self._add_file_to_repo(cloned_repo_dir, 'externals/simp_tag/tmp.txt', tracked) # checkout: pre-checkout status should be clean, ignoring the # untracked file. - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_post_checkout(overall, tree) # verify status is still clean - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_simple_detached_sync(self): @@ -1186,38 +1210,38 @@ def test_container_simple_detached_sync(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # status of empty repo - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_pre_checkout(overall, tree) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # make a commit on the detached head of the tag and hash externals - self._generator.create_commit(under_test_dir, 'simp_tag') - self._generator.create_commit(under_test_dir, 'simp_hash') - self._generator.create_commit(under_test_dir, 'simp_branch') + self._generator.create_commit(cloned_repo_dir, 'simp_tag') + self._generator.create_commit(cloned_repo_dir, 'simp_hash') + self._generator.create_commit(cloned_repo_dir, 'simp_branch') # status of repo, branch, tag and hash should all be out of sync! - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_out_of_sync(overall, tree) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) # same pre-checkout out of sync status self._check_container_simple_required_out_of_sync(overall, tree) # now status should be in-sync - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_remote_branch(self): @@ -1225,32 +1249,33 @@ def test_container_remote_branch(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # update the config file to point to a different remote with # the same branch - self._generator.update_branch(under_test_dir, 'simp_branch', - REMOTE_BRANCH_FEATURE2, SIMPLE_FORK_NAME) + self._generator.write_with_git_branch(cloned_repo_dir, name='simp_branch', + branch=REMOTE_BRANCH_FEATURE2, + repo_path=SIMPLE_FORK_NAME) # status of simp_branch should be out of sync - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_sb_modified(overall, tree) # checkout new externals - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_sb_modified(overall, tree) # status should be synced - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_remote_tag_same_branch(self): @@ -1261,33 +1286,33 @@ def test_container_remote_tag_same_branch(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_tag(under_test_dir, 'simp_branch', + self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', 'forked-feature-v1', SIMPLE_FORK_NAME) # status of simp_branch should be out of sync - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_sb_modified(overall, tree) # checkout new externals - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_sb_modified(overall, tree) # status should be synced - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_remote_tag_fetch_all(self): @@ -1299,33 +1324,33 @@ def test_container_remote_tag_fetch_all(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_tag(under_test_dir, 'simp_branch', + self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', 'abandoned-feature', SIMPLE_FORK_NAME) # status of simp_branch should be out of sync - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_sb_modified(overall, tree) # checkout new externals - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_sb_modified(overall, tree) # status should be synced - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_preserve_dot(self): @@ -1334,40 +1359,41 @@ def test_container_preserve_dot(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_required_checkout(overall, tree) # update the config file to point to a different remote with # the same branch - self._generator.update_branch(under_test_dir, 'simp_branch', - REMOTE_BRANCH_FEATURE2, SIMPLE_FORK_NAME) + self._generator.write_with_git_branch(cloned_repo_dir, name='simp_branch', + branch=REMOTE_BRANCH_FEATURE2, + repo_path=SIMPLE_FORK_NAME) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) # verify status is clean and unmodified - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) # update branch to point to a new branch that only exists in # the local fork - self._generator.create_branch(under_test_dir, 'simp_branch', - 'private-feature', with_commit=True) - self._generator.update_branch(under_test_dir, 'simp_branch', - 'private-feature', - SIMPLE_LOCAL_ONLY_NAME) - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + self._generator.create_branch(cloned_repo_dir, repo_name='simp_branch', + branch='private-feature', with_commit=True) + self._generator.write_with_git_branch(cloned_repo_dir, name='simp_branch', + branch='private-feature', + repo_path=SIMPLE_LOCAL_ONLY_NAME) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) # verify status is clean and unmodified - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_required_post_checkout(overall, tree) def test_container_full(self): @@ -1379,98 +1405,99 @@ def test_container_full(self): """ # create the test repository - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) # create the top level externals file - self._generator.container_full(under_test_dir) + self._generator.container_full(cloned_repo_dir) # inital checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_full_pre_checkout(overall, tree) - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_full_post_checkout(overall, tree) # Check existance of some files subrepo_path = os.path.join('externals', 'simp_tag') - self._check_file_exists(under_test_dir, + self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path, 'readme.txt')) - self._check_file_absent(under_test_dir, os.path.join(subrepo_path, + self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path, 'simple_subdir', 'subdir_file.txt')) # update the mixed-use repo to point to different branch - self._generator.update_branch(under_test_dir, 'mixed_req', - 'new-feature', MIXED_REPO_NAME) + self._generator.write_with_git_branch(cloned_repo_dir, name='mixed_req', + branch='new-feature', + repo_path=MIXED_REPO_NAME) # check status out of sync for mixed_req, but sub-externals # are still in sync - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_full_pre_checkout_ext_change(overall, tree) # run the checkout. Now the mixed use external and it's # sub-exterals should be changed. Returned status is # pre-checkout! - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_full_pre_checkout_ext_change(overall, tree) # check status out of sync for mixed_req, and sub-externals # are in sync. - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_full_post_checkout(overall, tree) def test_container_component(self): """Verify that optional component checkout works """ # create the test repository - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) # create the top level externals file - self._generator.container_full(under_test_dir) + self._generator.container_full(cloned_repo_dir) # inital checkout, first try a nonexistant component argument noref checkout_args = ['simp_opt', 'noref'] checkout_args.extend(self.checkout_args) with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) checkout_args = ['simp_opt'] checkout_args.extend(self.checkout_args) - overall, tree = self.execute_cmd_in_dir(under_test_dir, - checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + checkout_args) - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_component_post_checkout(overall, tree) checkout_args.append('simp_branch') - overall, tree = self.execute_cmd_in_dir(under_test_dir, - checkout_args) - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_component_post_checkout2(overall, tree) def test_container_exclude_component(self): """Verify that exclude component checkout works """ # create the test repository - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) # create the top level externals file - self._generator.container_full(under_test_dir) + self._generator.container_full(cloned_repo_dir) # inital checkout, exclude simp_opt checkout_args = ['--exclude', 'simp_opt'] checkout_args.extend(self.checkout_args) - overall, tree = self.execute_cmd_in_dir(under_test_dir, checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) checkout_args.append("--status") - overall, tree = self.execute_cmd_in_dir(under_test_dir, checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) self._check_container_component_post_checkout3(overall, tree) def test_mixed_simple(self): @@ -1480,22 +1507,22 @@ def test_mixed_simple(self): """ #import pdb; pdb.set_trace() # create repository - under_test_dir = self.setup_test_repo(MIXED_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(MIXED_REPO_NAME) # create top level externals file - self._generator.mixed_simple_base(under_test_dir) + self._generator.mixed_simple_base(cloned_repo_dir) # NOTE: sub-externals file is already in the repo so we can # switch branches during testing. Since this is a mixed-repo # serving as the top level container repo, we can't switch # during this test. # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_mixed_cont_simple_required_checkout(overall, tree) # verify status is clean and unmodified - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_mixed_cont_simple_required_post_checkout(overall, tree) def test_container_sparse(self): @@ -1504,31 +1531,31 @@ def test_container_sparse(self): """ # create the test repository - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) # create the top level externals file - self._generator.container_sparse(under_test_dir) + self._generator.container_sparse(cloned_repo_dir) # inital checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_sparse_pre_checkout(overall, tree) - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_sparse_post_checkout(overall, tree) # Check existance of some files subrepo_path = os.path.join('externals', 'simp_tag') - self._check_file_exists(under_test_dir, + self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path, 'readme.txt')) - self._check_file_exists(under_test_dir, os.path.join(subrepo_path, + self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path, 'simple_subdir', 'subdir_file.txt')) subrepo_path = os.path.join('externals', 'simp_sparse') - self._check_file_exists(under_test_dir, + self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path, 'readme.txt')) - self._check_file_absent(under_test_dir, os.path.join(subrepo_path, + self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path, 'simple_subdir', 'subdir_file.txt')) @@ -1625,57 +1652,57 @@ def test_container_simple_svn(self): """ self.skip_if_no_svn_access() # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_svn(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_svn(cloned_repo_dir) # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) # verify status is clean and unmodified - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_svn_post_checkout(overall, tree) # update description file to make the tag into a branch and # trigger a switch - self._generator.update_svn_branch(under_test_dir, 'svn_tag', 'trunk') + self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', 'trunk') # checkout - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) # verify status is clean and unmodified - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.status_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) self._check_container_simple_svn_post_checkout(overall, tree) # add an untracked file to the repo tracked = False - self._add_file_to_repo(under_test_dir, + self._add_file_to_repo(cloned_repo_dir, 'externals/svn_branch/tmp.txt', tracked) # run a no-op checkout: pre-checkout status should be clean, # ignoring the untracked file. - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_svn_post_checkout(overall, tree) # update description file to make the branch into a tag and # trigger a modified sync status - self._generator.update_svn_branch(under_test_dir, 'svn_tag', - 'tags/cesm2.0.beta07') + self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', + 'tags/cesm2.0.beta07') # checkout: pre-checkout status should be clean and modified, # will modify working copy. - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.checkout_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.checkout_args) self._check_container_simple_svn_sb_clean_st_mod(overall, tree) # verify status is still clean and unmodified, last # checkout modified the working dir state. - overall, tree = self.execute_cmd_in_dir(under_test_dir, - self.verbose_args) + overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.verbose_args) self._check_container_simple_svn_post_checkout(overall, tree) class TestSubrepoCheckout(BaseTestSysCheckout): @@ -1707,7 +1734,7 @@ def setUp(self): self._test_id) self._repo_dir = os.path.join(self._my_test_dir, self._test_repo_name) self._checkout_dir = 'repo_with_submodules' - check_dir = self.setup_test_repo(CONTAINER_REPO_NAME, + check_dir = self.clone_test_repo(CONTAINER_REPO_NAME, dest_dir_in=self._repo_dir) self.assertTrue(self._repo_dir == check_dir) # Add the submodules @@ -1795,7 +1822,7 @@ def create_externals_file(self, name='', filename=CFG_NAME, dest_dir=None, self._checkout_dir, branch=branch_name, path=name, externals=sub_externals, - repo_path=self._repo_dir) + repo_path_abs=self._repo_dir) self._generator.write_config(dest_dir, filename=filename) @@ -1804,11 +1831,11 @@ def idempotence_check(self, checkout_dir): checkout_externals --status does not cause errors""" cwd = os.getcwd() os.chdir(checkout_dir) - overall, _ = self.execute_cmd_in_dir(self._my_test_dir, - self.checkout_args) + overall, _ = self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) self.assertTrue(overall == 0) - overall, _ = self.execute_cmd_in_dir(self._my_test_dir, - self.status_args) + overall, _ = self.execute_checkout_in_dir(self._my_test_dir, + self.status_args) self.assertTrue(overall == 0) os.chdir(cwd) @@ -1822,8 +1849,8 @@ def test_submodule_checkout_bare(self): simple_ext_fork_tag = "(tag1)" simple_ext_fork_status = " " self.create_externals_file(branch_name=self._bare_branch_name) - overall, _ = self.execute_cmd_in_dir(self._my_test_dir, - self.checkout_args) + overall, _ = self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) self.assertTrue(overall == 0) cwd = os.getcwd() checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) @@ -1852,8 +1879,8 @@ def test_submodule_checkout_none(self): """ self.create_externals_file(branch_name=self._bare_branch_name, sub_externals="none") - overall, _ = self.execute_cmd_in_dir(self._my_test_dir, - self.checkout_args) + overall, _ = self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) self.assertTrue(overall == 0) cwd = os.getcwd() checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) @@ -1874,8 +1901,8 @@ def test_submodule_checkout_config(self): # pylint: disable=too-many-locals status_check = "-" # Not checked out as submodule self.create_externals_file(branch_name=self._config_branch_name, sub_externals=self._container_extern_name) - overall, _ = self.execute_cmd_in_dir(self._my_test_dir, - self.checkout_args) + overall, _ = self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) self.assertTrue(overall == 0) cwd = os.getcwd() checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) @@ -1938,17 +1965,17 @@ def test_error_unknown_protocol(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_protocol(under_test_dir, 'simp_branch', + self._generator.write_with_protocol(cloned_repo_dir, 'simp_branch', 'this-protocol-does-not-exist') with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, self.checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) def test_error_switch_protocol(self): """Verify that a runtime error is raised when the user switches @@ -1959,15 +1986,15 @@ def test_error_switch_protocol(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_protocol(under_test_dir, 'simp_branch', 'svn') + self._generator.write_with_protocol(cloned_repo_dir, 'simp_branch', 'svn') with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, self.checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) def test_error_unknown_tag(self): """Verify that a runtime error is raised when the user specified tag @@ -1975,17 +2002,17 @@ def test_error_unknown_tag(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_tag(under_test_dir, 'simp_branch', + self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', 'this-tag-does-not-exist', SIMPLE_REPO_NAME) with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, self.checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) def test_error_overspecify_tag_branch(self): """Verify that a runtime error is raised when the user specified both @@ -1993,18 +2020,18 @@ def test_error_overspecify_tag_branch(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_tag(under_test_dir, 'simp_branch', - 'this-tag-does-not-exist', SIMPLE_REPO_NAME, - remove_branch=False) + self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', + 'this-tag-does-not-exist', SIMPLE_REPO_NAME, + remove_branch=False) with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, self.checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) def test_error_underspecify_tag_branch(self): """Verify that a runtime error is raised when the user specified @@ -2012,17 +2039,17 @@ def test_error_underspecify_tag_branch(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_underspecify_branch_tag(under_test_dir, - 'simp_branch') + self._generator.write_without_branch_tag(cloned_repo_dir, + 'simp_branch') with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, self.checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) def test_error_missing_url(self): """Verify that a runtime error is raised when the user specified @@ -2030,17 +2057,17 @@ def test_error_missing_url(self): """ # create repo - under_test_dir = self.setup_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(under_test_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + self._generator.container_simple_required(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.update_underspecify_remove_url(under_test_dir, + self._generator.write_without_repo_url(cloned_repo_dir, 'simp_branch') with self.assertRaises(RuntimeError): - self.execute_cmd_in_dir(under_test_dir, self.checkout_args) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) if __name__ == '__main__': diff --git a/test/test_unit_repository_svn.py b/test/test_unit_repository_svn.py old mode 100644 new mode 100755 index 41b173bf3d..d9309df7f6 --- a/test/test_unit_repository_svn.py +++ b/test/test_unit_repository_svn.py @@ -60,7 +60,7 @@ def setUp(self): self._name = 'component' rdata = {ExternalsDescription.PROTOCOL: 'svn', ExternalsDescription.REPO_URL: - 'https://svn-ccsm-models.cgd.ucar.edu/', + 'https://svn-ccsm-models.cgd.ucar.edu', ExternalsDescription.TAG: 'mosart/trunk_tags/mosart1_0_26', } From d4fbadb1067e5e81eafe723d1578486eed2c6c2d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 13 Jan 2023 17:27:35 -0700 Subject: [PATCH 0614/2067] Run through black --- python/ctsm/test/test_sys_fsurdat_modifier.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index fc5eb8d0e9..526e5f5928 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -170,15 +170,15 @@ def test_opt_sections(self): ], ] ) - lev2_two = np.empty( (2,3,5,5) ) - lev2_two[0,:,:,:] = 200. - lev2_two[1,:,:,:] = 100. - lev2_five = np.empty( (5,3,5,5) ) - lev2_five[0,:,:,:] = 1. - lev2_five[1,:,:,:] = 2. - lev2_five[2,:,:,:] = 3. - lev2_five[3,:,:,:] = 4. - lev2_five[4,:,:,:] = 5. + lev2_two = np.empty((2, 3, 5, 5)) + lev2_two[0, :, :, :] = 200.0 + lev2_two[1, :, :, :] = 100.0 + lev2_five = np.empty((5, 3, 5, 5)) + lev2_five[0, :, :, :] = 1.0 + lev2_five[1, :, :, :] = 2.0 + lev2_five[2, :, :, :] = 3.0 + lev2_five[3, :, :, :] = 4.0 + lev2_five[4, :, :, :] = 5.0 lev1 = np.array( [ [ From e30022a93586007c6f93dc2095abf70b4ac0ab45 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 13 Jan 2023 18:04:31 -0700 Subject: [PATCH 0615/2067] Start adding a test for 1x1_mexicocity, it currently fails as expected, because the modify config file is not complete --- python/ctsm/test/test_sys_fsurdat_modifier.py | 36 +++++++++++++ .../modify_fsurdat_1x1mexicocity.cfg | 51 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 526e5f5928..0cd4514f90 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -216,6 +216,42 @@ def test_opt_sections(self): np.testing.assert_array_equal(fsurdat_out_data.ALB_ROOF_DIR, lev2_two) np.testing.assert_array_equal(fsurdat_out_data.TK_ROOF, lev2_five) + def test_1x1_mexicocity(self): + """ + Test that the mexicocity file is handled correctly + """ + self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_1x1mexicocity.cfg") + expectfile = os.path.join( + self._testinputs_path, + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc" + ) + outfile = os.path.join( + self._tempdir, + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc" + ) + infile = os.path.join( + self._testinputs_path, "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + ) + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + infile, + "-o", + outfile, + ] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) + + # Read the resultant output file and make sure the fields are changed as expected + fsurdat_out_data = xr.open_dataset(outfile) + fsurdat_inp_data = xr.open_dataset(infile) + fsurdat_exp_data = xr.open_dataset(expectfile) + + self.assertFalse(fsurdat_out_data.equals(fsurdat_inp_data)) + # assert that fsurdat_out equals fsurdat_out_baseline + self.assertTrue(fsurdat_out_data.equals(fsurdat_exp_data)) + def test_cfg_file_DNE_fail(self): """ Test that if the config file does not exist that it gracefully fails diff --git a/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg b/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg new file mode 100644 index 0000000000..c068c5d851 --- /dev/null +++ b/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg @@ -0,0 +1,51 @@ +[modify_fsurdat_basic_options] + +idealized = False +process_subgrid_section = True +process_var_list_section = True +include_nonveg = True + +landmask_file = UNSET + +lat_dimname = lsmlat +lon_dimname = lsmlon + +dom_pft = UNSET + +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET +soil_color = UNSET +std_elev = UNSET +max_sat_area = UNSET + +lnd_lat_1 = -90 +lnd_lat_2 = 90 +lnd_lon_1 = 0 +lnd_lon_2 = 360 + +# Section for subgrid_fractions +[modify_fsurdat_subgrid_fractions] +# Set to 100% urban for the test +PCT_NATVEG = 0.0 +PCT_CROP = 0.0 +PCT_LAKE = 0.0 +PCT_GLACIER = 0.0 +PCT_WETLAND = 0.0 +# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area +PCT_URBAN = 100.0 0.0 0.0 + + +# Section with a list of variables to prcoess +[modify_fsurdat_variable_list] +# Set lake-depth to 200 for the test +LAKEDEPTH = 200.00 + +# Set soem urban multidimensional variables to 200 for the test +# If given as a single value set all to the value, if as list set by dimension and if array as an array +CANYON_HWR = 200.00 150.0 100. +HT_ROOF = 200.0 150.0 100. +T_BUILDING_MIN = 200 150.0 100. +ALB_ROOF_DIR = 200. 100. +TK_ROOF = 1. 2. 3. 4. 5. From 62b9a3fc723eb918cf8972228045e1e8ea52496d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 13:16:19 -0700 Subject: [PATCH 0616/2067] More work on 1x1_mexicocity test, add more variables, stest still fails, utest passes, lint and black clean --- python/ctsm/test/test_sys_fsurdat_modifier.py | 13 ++-- python/ctsm/test/test_unit_modify_fsurdat.py | 8 +-- .../modify_fsurdat_1x1mexicocity.cfg | 67 ++++++++++++++----- 3 files changed, 59 insertions(+), 29 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 0cd4514f90..223f678c3b 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -220,18 +220,21 @@ def test_1x1_mexicocity(self): """ Test that the mexicocity file is handled correctly """ - self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_1x1mexicocity.cfg") + self._cfg_file_path = os.path.join( + self._testinputs_path, "modify_fsurdat_1x1mexicocity.cfg" + ) expectfile = os.path.join( self._testinputs_path, - "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc" + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc", ) outfile = os.path.join( self._tempdir, - "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc" + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc", ) infile = os.path.join( - self._testinputs_path, "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" - ) + self._testinputs_path, + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc", + ) sys.argv = [ "fsurdat_modifier", self._cfg_file_path, diff --git a/python/ctsm/test/test_unit_modify_fsurdat.py b/python/ctsm/test/test_unit_modify_fsurdat.py index 5cbdefcc48..a075035b73 100755 --- a/python/ctsm/test/test_unit_modify_fsurdat.py +++ b/python/ctsm/test/test_unit_modify_fsurdat.py @@ -374,14 +374,8 @@ def test_getNotRectangle_latsOutOfBounds(self): latixy=latixy, ) - def test_set_varlist(self): - """Test the set_varlist method for all the dimensions that works""" - vallist = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0] - settings = {"var_lev0": 100.0, "var_lev1": vallist, "var_lev2": vallist} - self.modify_fsurdat.set_varlist(settings) - def test_check_varlist_lists(self): - """Test the check_varlist method for lists""" + """Test the check_varlist method for list for dimensions that works""" lev1list = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0] lev2list = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0] settings = {"var_lev1": lev1list, "var_lev2": lev2list} diff --git a/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg b/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg index c068c5d851..a4118a3255 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg @@ -27,25 +27,58 @@ lnd_lon_2 = 360 # Section for subgrid_fractions [modify_fsurdat_subgrid_fractions] -# Set to 100% urban for the test -PCT_NATVEG = 0.0 -PCT_CROP = 0.0 -PCT_LAKE = 0.0 -PCT_GLACIER = 0.0 -PCT_WETLAND = 0.0 +# If subgrid_fractions = True this section will be enabled + # NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area PCT_URBAN = 100.0 0.0 0.0 - +PCT_CROP = 0.0 +PCT_NATVEG= 0.0 +PCT_GLACIER= 0.0 +PCT_WETLAND= 0.0 +PCT_LAKE = 0.0 # Section with a list of variables to prcoess [modify_fsurdat_variable_list] -# Set lake-depth to 200 for the test -LAKEDEPTH = 200.00 - -# Set soem urban multidimensional variables to 200 for the test -# If given as a single value set all to the value, if as list set by dimension and if array as an array -CANYON_HWR = 200.00 150.0 100. -HT_ROOF = 200.0 150.0 100. -T_BUILDING_MIN = 200 150.0 100. -ALB_ROOF_DIR = 200. 100. -TK_ROOF = 1. 2. 3. 4. 5. +# If variable_list = True this section will be enabled +# Can't specify PFT as they are in dom_pft +# Add variables on the file and assign a new value +# can't specify soil_color, max_sat_area + +# Variables on numurbl which is 3 +CANYON_HWR = 1.18 1.18 1.18 +EM_IMPROAD = 0.95 0.95 0.95 +EM_PERROAD = 0.95 0.95 0.95 +EM_ROOF = 0.9 0.9 0.9 +EM_WALL = 0.85 0.85 0.85 +HT_ROOF = 18.8 18.8 18.8 +THICK_ROOF = 0.185 0.185 0.185 +THICK_WALL = 0.45 0.45 0.45 +T_BUILDING_MIN = 200.0 200.0 200.0 +WIND_HGT_CANYON = 9.4 9.4 9.4 +WTLUNIT_ROOF = 0.55 0.55 0.55 +WTROAD_PERV = 0.04 0.04 0.04 +# NOTE: This variable is integer rather than float +NLEV_IMPROAD = 5 5 5 + +# Variables on numrad which is 2 +ALB_IMPROAD_DIR = 0.08 0.08 +ALB_IMPROAD_DIF = 0.08 0.08 +ALB_PERROAD_DIR = 0.08 0.08 +ALB_PERROAD_DIF = 0.08 0.08 +ALB_ROOF_DIR = 0.2 0.2 +ALB_ROOF_DIF = 0.2 0.2 +ALB_WALL_DIR = 0.25 0.25 +ALB_WALL_DIF = 0.25 0.25 + +# Variabls on nlevurb which is 5 +TK_ROOF = 0.20 0.93 0.93 0.03 0.16 +TK_WALL = 0.88 0.88 0.88 0.88 0.88 +TK_IMPROAD = 0.82 0.82 2.10 2.10 2.10 +CV_ROOF = 1760000.0 1500000.0 1500000.0 250000.0 870000.0 +CV_WALL = 1540000.0 1540000.0 1540000.0 1540000.0 1540000.0 +CV_IMPROAD = 1740000.0 1740000.0 2000000.0 2000000.0 2000000.0 + +# Natural and Crop PFT's don't really need to be set, since they have zero area, but +# it looks better to do so +PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +PCT_CFT = 100. 0.0 From 9be40c61093e5be850c811b9f7639f35a64aa576 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 13:52:18 -0700 Subject: [PATCH 0617/2067] Set idealized to False for the subgrid and varlist tests, and to true for the test that ensures idealized variables don't conflict with varlist --- .../ctsm/test/test_unit_fsurdat_modifier.py | 24 ++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 149ba5acac..d2f07d14b1 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -70,6 +70,8 @@ def test_read_subgrid(self): def test_read_subgrid_allglacier(self): """test a read of subgrid that's for all glacier""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "0. 0. 0.") self.config.set(section, "pct_lake", "0.") @@ -81,6 +83,8 @@ def test_read_subgrid_allglacier(self): def test_read_subgrid_allspecial(self): """test a read of subgrid that's all special landunits""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "0. 0. 0.") self.config.set(section, "pct_lake", "25.") @@ -92,6 +96,8 @@ def test_read_subgrid_allspecial(self): def test_read_subgrid_allurban(self): """test a read of subgrid that's all urban""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "100.0 0.0 0.0") self.config.set(section, "pct_lake", "0.") @@ -107,6 +113,8 @@ def test_read_var_list(self): def test_subgrid_outofrange(self): """test a read of subgrid that's out of range""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "101. 0. 0.") with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): @@ -114,6 +122,8 @@ def test_subgrid_outofrange(self): def test_subgrid_pct_urban_toosmall(self): """test a read of subgrid for PCT_URBAN that's an array too small""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "100. 0.") with self.assertRaisesRegex( @@ -123,6 +133,8 @@ def test_subgrid_pct_urban_toosmall(self): def test_subgrid_pct_urban_toobig(self): """test a read of subgrid for PCT_URBAN that's an array too big""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "100. 0. 0. 0.") with self.assertRaisesRegex( @@ -132,6 +144,8 @@ def test_subgrid_pct_urban_toobig(self): def test_subgrid_pct_urban_singlevalue(self): """test a read of subgrid for PCT_URBAN that's a single value""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "100.") with self.assertRaisesRegex( @@ -141,6 +155,8 @@ def test_subgrid_pct_urban_singlevalue(self): def test_subgrid_notsumtohundred(self): """test a read of subgrid that's doesn't sum to a hundred""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "0. 0. 0.") self.config.set(section, "pct_lake", "0.") @@ -155,13 +171,17 @@ def test_subgrid_notsumtohundred(self): def test_subgrid_badvar(self): """test a read of subgrid for a variable thats not in the list""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "badvariable", "100.") with self.assertRaisesRegex(SystemExit, "is not a valid variable name. Valid vars ="): read_subgrid(self.config, self.cfg_path) def test_varlist_varinidealized(self): - """test a read of varlist for a variable thats in the idealized list""" + """test a read of varlist for a variable thats in the idealized list, when idealized is on""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "True") section = "modify_fsurdat_variable_list" self.config.set(section, "PCT_SAND", "100.") with self.assertRaisesRegex( @@ -173,6 +193,8 @@ def test_varlist_varinidealized(self): def test_varlist_varinsubgrid(self): """test a read of varlist for a variable thats in the subgrid list""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") section = "modify_fsurdat_variable_list" self.config.set(section, "PCT_GLACIER", "100.") with self.assertRaisesRegex( From 16d94b0578c45cd93309496353843a57de0179d2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 15:03:58 -0700 Subject: [PATCH 0618/2067] Add a check that makes sure that dom_pft and idealized aren't on at the same time, it fails as expected --- .../ctsm/test/test_unit_fsurdat_modifier.py | 33 +++++++++++++++++-- 1 file changed, 30 insertions(+), 3 deletions(-) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index d2f07d14b1..f44878bb56 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 """ -Unit tests for fsurdat_modifier subroutines: read_subgrid, read_varlist +Unit tests for fsurdat_modifier subroutines: """ import unittest @@ -11,14 +11,17 @@ import tempfile from configparser import ConfigParser +import xarray as xr from ctsm import unit_testing from ctsm.path_utils import path_to_ctsm_root from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process from ctsm.modify_input_files.fsurdat_modifier import read_subgrid +from ctsm.modify_input_files.fsurdat_modifier import read_opt_config from ctsm.modify_input_files.fsurdat_modifier import read_var_list from ctsm.modify_input_files.fsurdat_modifier import check_no_subgrid_section from ctsm.modify_input_files.fsurdat_modifier import check_no_varlist_section +from ctsm.modify_input_files.modify_fsurdat import ModifyFsurdat # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -27,8 +30,10 @@ # pylint: disable=protected-access +# Allow all the instance attributes that we need +# pylint: disable=too-many-instance-attributes class TestFSurdatModifier(unittest.TestCase): - """Tests the read_subgrid and read_var_list methods""" + """Tests the fsurdat_modifier subroutines""" def setUp(self): """Setup for trying out the methods""" @@ -57,6 +62,17 @@ def setUp(self): self.cfg_path = str(parser.cfg_path) self.config = ConfigParser() self.config.read(self.cfg_path) + my_data = xr.open_dataset( self._fsurdat_in ) + self.modify_fsurdat = ModifyFsurdat( + my_data=my_data, + lon_1=0.0, + lon_2=360.0, + lat_1=90.0, + lat_2=90.0, + landmask_file=None, + lat_dimname=None, + lon_dimname=None, + ) def tearDown(self): """ @@ -64,6 +80,16 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) + def test_dom_pft_and_idealized_fails(self): + """test a simple read of subgrid""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "True") + self.config.set(section, "dom_pft", "1") + with self.assertRaisesRegex( + SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" + ): + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + def test_read_subgrid(self): """test a simple read of subgrid""" read_subgrid(self.config, self.cfg_path) @@ -179,7 +205,8 @@ def test_subgrid_badvar(self): read_subgrid(self.config, self.cfg_path) def test_varlist_varinidealized(self): - """test a read of varlist for a variable thats in the idealized list, when idealized is on""" + """test a read of varlist for a variable thats in the idealized list, + when idealized is on""" section = "modify_fsurdat_basic_options" self.config.set(section, "idealized", "True") section = "modify_fsurdat_variable_list" From ac7c23e76940f48606b0d09d55f7cea8bcb5edda Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 17:25:13 -0700 Subject: [PATCH 0619/2067] Add some consistency checking tests that fail as expected --- .../ctsm/test/test_unit_fsurdat_modifier.py | 48 ++++++++++++++++++- 1 file changed, 46 insertions(+), 2 deletions(-) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index f44878bb56..585292277e 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -30,6 +30,8 @@ # pylint: disable=protected-access +# Allow as many public methods as needed... +# pylint: disable=too-many-public-methods # Allow all the instance attributes that we need # pylint: disable=too-many-instance-attributes class TestFSurdatModifier(unittest.TestCase): @@ -62,7 +64,7 @@ def setUp(self): self.cfg_path = str(parser.cfg_path) self.config = ConfigParser() self.config.read(self.cfg_path) - my_data = xr.open_dataset( self._fsurdat_in ) + my_data = xr.open_dataset(self._fsurdat_in) self.modify_fsurdat = ModifyFsurdat( my_data=my_data, lon_1=0.0, @@ -81,7 +83,7 @@ def tearDown(self): shutil.rmtree(self._tempdir, ignore_errors=True) def test_dom_pft_and_idealized_fails(self): - """test a simple read of subgrid""" + """test a that dom_pft and idealized fails gracefully""" section = "modify_fsurdat_basic_options" self.config.set(section, "idealized", "True") self.config.set(section, "dom_pft", "1") @@ -90,6 +92,48 @@ def test_dom_pft_and_idealized_fails(self): ): read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + def test_subgrid_and_idealized_fails(self): + """test that dom_pft and idealized fails gracefully""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "True") + self.config.set(section, "process_subgrid_section", "True") + with self.assertRaisesRegex( + SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" + ): + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + + def test_optional_only_true_and_false(self): + """test that optional settings can only be true or false""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "dom_pft", "1") + varlist = ( + "idealized", + "include_nonveg", + "process_subgrid_section", + "process_var_list_section", + ) + for var in varlist: + self.config.set(section, var, "True") + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + for var in varlist: + self.config.set(section, var, "False") + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + self.config.set(section, "dom_pft", "UNSET") + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + for var in varlist: + with self.assertRaisesRegex(SystemExit, "must be either True or False"): + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + + def test_include_nonveg_and_idealized_fails(self): + """test a simple read of subgrid""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "True") + self.config.set(section, "include_nonveg", "True") + with self.assertRaisesRegex( + SystemExit, "idealized AND include_nonveg can NOT both be on, pick one or the other" + ): + read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + def test_read_subgrid(self): """test a simple read of subgrid""" read_subgrid(self.config, self.cfg_path) From be956b6d1fedb5e156f30314a8c769fdecbd5935 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 19:49:52 -0700 Subject: [PATCH 0620/2067] Add a subroutine to read the control variables, that can also do error checking --- .../modify_input_files/fsurdat_modifier.py | 67 ++++++++++--------- 1 file changed, 37 insertions(+), 30 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 6653a4937d..e01877822d 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -363,6 +363,41 @@ def read_opt_config(modify_fsurdat, config, cfg_path, section): ) +def read_option_control(config, section, cfg_path): + """Read the option control section""" + # required but fallback values available for variables omitted + # entirely from the .cfg file + idealized = get_config_value( + config=config, + section=section, + item="idealized", + file_path=cfg_path, + convert_to_type=bool, + ) + process_subgrid = get_config_value( + config=config, + section=section, + item="process_subgrid_section", + file_path=cfg_path, + convert_to_type=bool, + ) + process_var_list = get_config_value( + config=config, + section=section, + item="process_var_list_section", + file_path=cfg_path, + convert_to_type=bool, + ) + include_nonveg = get_config_value( + config=config, + section=section, + item="include_nonveg", + file_path=cfg_path, + convert_to_type=bool, + ) + return (idealized, process_subgrid, process_var_list, include_nonveg) + + def fsurdat_modifier(parser): """Implementation of fsurdat_modifier command""" # read the .cfg (config) file @@ -401,37 +436,9 @@ def fsurdat_modifier(parser): errmsg = "Output file already exists: " + fsurdat_out abort(errmsg) - # required but fallback values available for variables omitted - # entirely from the .cfg file - idealized = get_config_value( - config=config, - section=section, - item="idealized", - file_path=cfg_path, - convert_to_type=bool, - ) - process_subgrid = get_config_value( - config=config, - section=section, - item="process_subgrid_section", - file_path=cfg_path, - convert_to_type=bool, + (idealized, process_subgrid, process_var_list, include_nonveg) = read_option_control( + config, section, cfg_path ) - process_var_list = get_config_value( - config=config, - section=section, - item="process_var_list_section", - file_path=cfg_path, - convert_to_type=bool, - ) - include_nonveg = get_config_value( - config=config, - section=section, - item="include_nonveg", - file_path=cfg_path, - convert_to_type=bool, - ) - lnd_lat_1 = get_config_value( config=config, section=section, From a23e03f6dc0871b66395151b05f5b8dffb7f782d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 21:22:57 -0700 Subject: [PATCH 0621/2067] Use read_option_control in the test --- python/ctsm/test/test_unit_fsurdat_modifier.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 585292277e..aafebbdf55 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -17,6 +17,7 @@ from ctsm.path_utils import path_to_ctsm_root from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process from ctsm.modify_input_files.fsurdat_modifier import read_subgrid +from ctsm.modify_input_files.fsurdat_modifier import read_option_control from ctsm.modify_input_files.fsurdat_modifier import read_opt_config from ctsm.modify_input_files.fsurdat_modifier import read_var_list from ctsm.modify_input_files.fsurdat_modifier import check_no_subgrid_section @@ -90,7 +91,7 @@ def test_dom_pft_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" ): - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) def test_subgrid_and_idealized_fails(self): """test that dom_pft and idealized fails gracefully""" @@ -100,7 +101,7 @@ def test_subgrid_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" ): - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) def test_optional_only_true_and_false(self): """test that optional settings can only be true or false""" @@ -114,15 +115,15 @@ def test_optional_only_true_and_false(self): ) for var in varlist: self.config.set(section, var, "True") - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) for var in varlist: self.config.set(section, var, "False") - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) self.config.set(section, "dom_pft", "UNSET") - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) for var in varlist: with self.assertRaisesRegex(SystemExit, "must be either True or False"): - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) def test_include_nonveg_and_idealized_fails(self): """test a simple read of subgrid""" @@ -132,7 +133,7 @@ def test_include_nonveg_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND include_nonveg can NOT both be on, pick one or the other" ): - read_opt_config(self.modify_fsurdat, self.config, self.cfg_path, section) + read_option_control(self.config, section, self.cfg_path) def test_read_subgrid(self): """test a simple read of subgrid""" From f28f37b3268c3ba4715c64188deeaebe250e64c0 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 14 Jan 2023 22:38:29 -0700 Subject: [PATCH 0622/2067] Move read of dom_pft to read_option_control and get all the unit testing working --- .../modify_input_files/fsurdat_modifier.py | 41 +++++++++++-------- .../ctsm/test/test_unit_fsurdat_modifier.py | 28 ++++++++----- 2 files changed, 41 insertions(+), 28 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index e01877822d..fc29a4605c 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -276,16 +276,6 @@ def modify_optional( def read_opt_config(modify_fsurdat, config, cfg_path, section): """read the optional parts of the main section config file""" # not required: user may set these in the .cfg file - max_pft = int(max(modify_fsurdat.file.lsmpft)) - dom_pft = get_config_value( - config=config, - section=section, - item="dom_pft", - file_path=cfg_path, - allowed_values=range(max_pft + 1), # integers from 0 to max_pft - convert_to_type=int, - can_be_unset=True, - ) lai = get_config_value( config=config, @@ -355,7 +345,6 @@ def read_opt_config(modify_fsurdat, config, cfg_path, section): max_sat_area, std_elev, soil_color, - dom_pft, lai, sai, hgt_top, @@ -363,7 +352,7 @@ def read_opt_config(modify_fsurdat, config, cfg_path, section): ) -def read_option_control(config, section, cfg_path): +def read_option_control(modify_fsurdat, config, section, cfg_path): """Read the option control section""" # required but fallback values available for variables omitted # entirely from the .cfg file @@ -395,7 +384,24 @@ def read_option_control(config, section, cfg_path): file_path=cfg_path, convert_to_type=bool, ) - return (idealized, process_subgrid, process_var_list, include_nonveg) + max_pft = int(max(modify_fsurdat.file.lsmpft)) + dom_pft = get_config_value( + config=config, + section=section, + item="dom_pft", + file_path=cfg_path, + allowed_values=range(max_pft + 1), # integers from 0 to max_pft + convert_to_type=int, + can_be_unset=True, + ) + if dom_pft is not None and idealized: + abort("idealized AND dom_pft can NOT both be on, pick one or the other") + if include_nonveg and idealized: + abort("idealized AND include_nonveg can NOT both be on, pick one or the other") + if process_subgrid and idealized: + abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") + + return (idealized, process_subgrid, process_var_list, include_nonveg, dom_pft) def fsurdat_modifier(parser): @@ -436,9 +442,6 @@ def fsurdat_modifier(parser): errmsg = "Output file already exists: " + fsurdat_out abort(errmsg) - (idealized, process_subgrid, process_var_list, include_nonveg) = read_option_control( - config, section, cfg_path - ) lnd_lat_1 = get_config_value( config=config, section=section, @@ -495,12 +498,16 @@ def fsurdat_modifier(parser): lon_dimname, ) + # Read control information about the optional sections + (idealized, process_subgrid, process_var_list, include_nonveg, dom_pft) = read_option_control( + modify_fsurdat, config, section, cfg_path + ) + # Read parts that are optional ( max_sat_area, std_elev, soil_color, - dom_pft, lai, sai, hgt_top, diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index aafebbdf55..5befe584c3 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -18,7 +18,6 @@ from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process from ctsm.modify_input_files.fsurdat_modifier import read_subgrid from ctsm.modify_input_files.fsurdat_modifier import read_option_control -from ctsm.modify_input_files.fsurdat_modifier import read_opt_config from ctsm.modify_input_files.fsurdat_modifier import read_var_list from ctsm.modify_input_files.fsurdat_modifier import check_no_subgrid_section from ctsm.modify_input_files.fsurdat_modifier import check_no_varlist_section @@ -91,17 +90,20 @@ def test_dom_pft_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" ): - read_option_control(self.config, section, self.cfg_path) + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_subgrid_and_idealized_fails(self): """test that dom_pft and idealized fails gracefully""" section = "modify_fsurdat_basic_options" self.config.set(section, "idealized", "True") + self.config.set(section, "include_nonveg", "False") self.config.set(section, "process_subgrid_section", "True") + self.config.set(section, "dom_pft", "UNSET") with self.assertRaisesRegex( - SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" + SystemExit, + "idealized AND process_subgrid_section can NOT both be on, pick one or the other", ): - read_option_control(self.config, section, self.cfg_path) + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_optional_only_true_and_false(self): """test that optional settings can only be true or false""" @@ -115,15 +117,19 @@ def test_optional_only_true_and_false(self): ) for var in varlist: self.config.set(section, var, "True") - read_option_control(self.config, section, self.cfg_path) + self.config.set(section, "idealized", "False") + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) for var in varlist: self.config.set(section, var, "False") - read_option_control(self.config, section, self.cfg_path) + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) self.config.set(section, "dom_pft", "UNSET") - read_option_control(self.config, section, self.cfg_path) - for var in varlist: - with self.assertRaisesRegex(SystemExit, "must be either True or False"): - read_option_control(self.config, section, self.cfg_path) + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + var = "idealized" + self.config.set(section, var, "Thing") + with self.assertRaisesRegex( + SystemExit, "Non-boolean value found for .cfg file variable: " + var + ): + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_include_nonveg_and_idealized_fails(self): """test a simple read of subgrid""" @@ -133,7 +139,7 @@ def test_include_nonveg_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND include_nonveg can NOT both be on, pick one or the other" ): - read_option_control(self.config, section, self.cfg_path) + read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_read_subgrid(self): """test a simple read of subgrid""" From 3da338893d9924e6683568546ac07e7298da9451 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 15 Jan 2023 00:51:49 -0700 Subject: [PATCH 0623/2067] Add options to allow some options if they are flagged, and only abort if idealized variables are being used if idealized is on, now all tests pass, lint and black clean --- .../modify_input_files/fsurdat_modifier.py | 40 +++++++++++++++---- python/ctsm/test/test_sys_fsurdat_modifier.py | 7 +++- .../ctsm/test/test_unit_fsurdat_modifier.py | 8 ++-- 3 files changed, 43 insertions(+), 12 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index fc29a4605c..992aa1323c 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -57,6 +57,20 @@ def fsurdat_modifier_arg_process(): type=str, help="The output surface dataset with the modifications. ", ) + parser.add_argument( + "--allow_ideal_and_include_non_veg", + required=False, + default=False, + action="store_true", + help="Allow both idealized and include_nonveg to be on at the same time. ", + ) + parser.add_argument( + "--allow_dom_pft_and_idealized", + required=False, + default=False, + action="store_true", + help="Allow both idealized and dom_pft to be on at the same time. ", + ) add_logging_args(parser) args = parser.parse_args() process_logging_args(args) @@ -150,7 +164,7 @@ def read_subgrid(config, cfg_path, numurbl=3): return subgrid_settings -def read_var_list(config): +def read_var_list(config, idealized=True): """Read the variable list section from the config file""" section = "modify_fsurdat_variable_list" if not config.has_section(section): @@ -190,7 +204,7 @@ def read_var_list(config): "ws", ] for var in var_list: - if ideal_list.count(var) != 0: + if idealized and ideal_list.count(var) != 0: abort( var + " is a special variable handled in the idealized section." @@ -352,7 +366,14 @@ def read_opt_config(modify_fsurdat, config, cfg_path, section): ) -def read_option_control(modify_fsurdat, config, section, cfg_path): +def read_option_control( + modify_fsurdat, + config, + section, + cfg_path, + allow_ideal_and_include_non_veg=False, + allow_dom_pft_and_idealized=False, +): """Read the option control section""" # required but fallback values available for variables omitted # entirely from the .cfg file @@ -394,9 +415,9 @@ def read_option_control(modify_fsurdat, config, section, cfg_path): convert_to_type=int, can_be_unset=True, ) - if dom_pft is not None and idealized: + if dom_pft is not None and idealized and not allow_dom_pft_and_idealized: abort("idealized AND dom_pft can NOT both be on, pick one or the other") - if include_nonveg and idealized: + if include_nonveg and idealized and not allow_ideal_and_include_non_veg: abort("idealized AND include_nonveg can NOT both be on, pick one or the other") if process_subgrid and idealized: abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") @@ -500,7 +521,12 @@ def fsurdat_modifier(parser): # Read control information about the optional sections (idealized, process_subgrid, process_var_list, include_nonveg, dom_pft) = read_option_control( - modify_fsurdat, config, section, cfg_path + modify_fsurdat, + config, + section, + cfg_path, + parser.allow_ideal_and_include_non_veg, + parser.allow_dom_pft_and_idealized, ) # Read parts that are optional @@ -540,7 +566,7 @@ def fsurdat_modifier(parser): check_no_subgrid_section(config) if process_var_list: - varlist = read_var_list(config) + varlist = read_var_list(config, idealized=idealized) update_list = modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) modify_fsurdat.set_varlist(update_list, cfg_path) else: diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 223f678c3b..cde9cac846 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -363,7 +363,12 @@ def test_allInfo(self): self._create_config_file_complete() # run the fsurdat_modifier tool - sys.argv = ["fsurdat_modifier", self._cfg_file_path] + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "--allow_ideal_and_include_non_veg", + "--allow_dom_pft_and_idealized", + ] parser = fsurdat_modifier_arg_process() fsurdat_modifier(parser) # the critical piece of this test is that the above command diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 5befe584c3..fee4ec2ab3 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -186,7 +186,7 @@ def test_read_subgrid_allurban(self): def test_read_var_list(self): """test a simple read of var_list""" - read_var_list(self.config) + read_var_list(self.config, idealized=True) def test_subgrid_outofrange(self): """test a read of subgrid that's out of range""" @@ -267,7 +267,7 @@ def test_varlist_varinidealized(self): "is a special variable handled in the idealized section." + " This should NOT be handled in the variiable list section. Special idealized vars =", ): - read_var_list(self.config) + read_var_list(self.config, idealized=True) def test_varlist_varinsubgrid(self): """test a read of varlist for a variable thats in the subgrid list""" @@ -280,7 +280,7 @@ def test_varlist_varinsubgrid(self): "is a variable handled in the subgrid section." + " This should NOT be handled in the variiable list section. Subgrid vars =", ): - read_var_list(self.config) + read_var_list(self.config, idealized=False) def test_varlist_monthlyvar(self): """test a read of varlist for a variable thats one of the monthly @@ -293,7 +293,7 @@ def test_varlist_monthlyvar(self): + " This should NOT be handled in the variiable list section." + " Monthly vars handled this way =", ): - read_var_list(self.config) + read_var_list(self.config, idealized=False) def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" From 49889d4f3c97202acfe846213c45ac2fc45de1c4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 15 Jan 2023 09:58:17 -0700 Subject: [PATCH 0624/2067] Add test files for the system testing for creation of urban surfdata files using fsurdat_modifier --- ..._mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc | 3 +++ ...tyMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc | 3 +++ 2 files changed, 6 insertions(+) create mode 100644 python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc create mode 100644 python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc diff --git a/python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc b/python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc new file mode 100644 index 0000000000..4bf009ebe6 --- /dev/null +++ b/python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef672e3ab2c237fd6f76afdd1dfa7d01263c01bd94bef2a8f37acfba3a9b6e36 +size 27300 diff --git a/python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc b/python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc new file mode 100644 index 0000000000..80a66c286f --- /dev/null +++ b/python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:cdfc14c3f7e9efa4f0acc4caca22b616e09e04b2713ab1424d695492ac52327c +size 27772 From df014edbb2eca3fcaa87823c29ab12cf77531106 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 17:33:32 -0700 Subject: [PATCH 0625/2067] Add a check_args method for subset_data and some testing for it --- python/ctsm/subset_data.py | 60 ++++++++++++----------- python/ctsm/test/test_unit_subset_data.py | 11 +++-- 2 files changed, 39 insertions(+), 32 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 8015fe1858..172ec2b97b 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -345,6 +345,37 @@ def get_parser(): return parser +def check_args(parser, args): + """Check the command line arguments""" + # --------------------------------- # + # print help and exit when no option is chosen + if args.run_type not in ("point", "region"): + err_msg = textwrap.dedent( + """\ + \n ------------------------------------ + \n Must supply a positional argument: 'point' or 'region'. + """ + ) + raise parser.error(err_msg) + + if not any( + [ + args.create_surfdata, + args.create_domain, + args.create_landuse, + args.create_datm, + ] + ): + err_msg = textwrap.dedent( + """\ + \n ------------------------------------ + \n Must supply one of: + \n --create-surface \n --create-landuse \n --create-datm \n --create-domain \n + """ + ) + raise parser.error(err_msg) + + def setup_user_mods(user_mods_dir, cesmroot): """ Sets up the user mods files and directories @@ -580,34 +611,7 @@ def main(): parser = get_parser() args = parser.parse_args() - # --------------------------------- # - # print help and exit when no option is chosen - if args.run_type not in ("point", "region"): - err_msg = textwrap.dedent( - """\ - \n ------------------------------------ - \n Must supply a positional argument: 'point' or 'region'. - """ - ) - raise args.error(err_msg) - - if not any( - [ - args.create_surfdata, - args.create_domain, - args.create_landuse, - args.create_datm, - ] - ): - err_msg = textwrap.dedent( - """\ - \n ------------------------------------ - \n Must supply one of: - \n --create-surface \n --create-landuse \n --create-datm \n --create-domain \n - """ - ) - raise args.error(err_msg) - + check_args(parser, args) # --------------------------------- # # process logging args (i.e. debug and verbose) process_logging_args(args) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index aa4c412bbb..9fa09a9662 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -17,7 +17,7 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing -from ctsm.subset_data import get_parser, setup_files +from ctsm.subset_data import get_parser, setup_files, check_args from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name @@ -29,10 +29,10 @@ class TestSubsetData(unittest.TestCase): """ def setUp(self): - sys.argv = ["subset_data", "point"] + sys.argv = ["subset_data", "point", "--create-surface"] DEFAULTS_FILE = "default_data.cfg" - parser = get_parser() - self.args = parser.parse_args() + self.parser = get_parser() + self.args = self.parser.parse_args() self.cesmroot = path_to_ctsm_root() self.defaults = configparser.ConfigParser() self.defaults.read(os.path.join(self.cesmroot, "tools/site_and_regional", DEFAULTS_FILE)) @@ -41,12 +41,14 @@ def test_inputdata_setup_files_basic(self): """ Test """ + check_args(self.parser, self.args) setup_files(self.args, self.defaults, self.cesmroot) def test_inputdata_setup_files_inputdata_dne(self): """ Test that inputdata directory does not exist """ + check_args(self.parser, self.args) self.defaults.set("main", "clmforcingindir", "/zztop") with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): setup_files(self.args, self.defaults, self.cesmroot) @@ -55,6 +57,7 @@ def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad """ + check_args(self.parser, self.args) self.args.inputdatadir = "/zztop" with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): setup_files(self.args, self.defaults, self.cesmroot) From c8dee88ed6d658596f3fc1c335685c0fff1ec717 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 18:10:41 -0700 Subject: [PATCH 0626/2067] Remove parser from args of check_args, and add two fail tests for check_args --- python/ctsm/subset_data.py | 8 ++++---- python/ctsm/test/test_unit_subset_data.py | 25 ++++++++++++++++++++--- 2 files changed, 26 insertions(+), 7 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 172ec2b97b..b6244ce2f0 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -345,7 +345,7 @@ def get_parser(): return parser -def check_args(parser, args): +def check_args(args): """Check the command line arguments""" # --------------------------------- # # print help and exit when no option is chosen @@ -356,7 +356,7 @@ def check_args(parser, args): \n Must supply a positional argument: 'point' or 'region'. """ ) - raise parser.error(err_msg) + raise argparse.ArgumentError(None, err_msg) if not any( [ @@ -373,7 +373,7 @@ def check_args(parser, args): \n --create-surface \n --create-landuse \n --create-datm \n --create-domain \n """ ) - raise parser.error(err_msg) + raise argparse.ArgumentError(None, err_msg) def setup_user_mods(user_mods_dir, cesmroot): @@ -611,7 +611,7 @@ def main(): parser = get_parser() args = parser.parse_args() - check_args(parser, args) + check_args(args) # --------------------------------- # # process logging args (i.e. debug and verbose) process_logging_args(args) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 9fa09a9662..8bdacab180 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -8,6 +8,7 @@ import unittest import configparser +import argparse import os import sys @@ -41,23 +42,41 @@ def test_inputdata_setup_files_basic(self): """ Test """ - check_args(self.parser, self.args) + check_args(self.args) setup_files(self.args, self.defaults, self.cesmroot) def test_inputdata_setup_files_inputdata_dne(self): """ Test that inputdata directory does not exist """ - check_args(self.parser, self.args) + check_args(self.args) self.defaults.set("main", "clmforcingindir", "/zztop") with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): setup_files(self.args, self.defaults, self.cesmroot) + def test_check_args_nooutput(self): + """ + Test that check args aborts when no-output is asked for + """ + sys.argv = ["subset_data", "point"] + self.args = self.parser.parse_args() + with self.assertRaisesRegex(argparse.ArgumentError, "Must supply one of"): + check_args(self.args) + + def test_check_args_notype(self): + """ + Test that check args aborts when no type is asked for + """ + sys.argv = ["subset_data"] + self.args = self.parser.parse_args() + with self.assertRaisesRegex(argparse.ArgumentError, "Must supply a positional argument:"): + check_args(self.args) + def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad """ - check_args(self.parser, self.args) + check_args(self.args) self.args.inputdatadir = "/zztop" with self.assertRaisesRegex(SystemExit, "inputdata directory does not exist"): setup_files(self.args, self.defaults, self.cesmroot) From 0178ca7f2e7de81d7cb493c3b1b7ff526ef1bfad Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 18:23:59 -0700 Subject: [PATCH 0627/2067] Add a check that the entered defaults config file exista and a test for it --- python/ctsm/subset_data.py | 9 +++++++++ python/ctsm/test/test_unit_subset_data.py | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index b6244ce2f0..9fca0b4f86 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -375,6 +375,15 @@ def check_args(args): ) raise argparse.ArgumentError(None, err_msg) + if not os.path.exists( args.config_file ): + err_msg = textwrap.dedent( + """\ + \n ------------------------------------ + \n Entered default config file does not exist" + """ + ) + raise argparse.ArgumentError(None, err_msg) + def setup_user_mods(user_mods_dir, cesmroot): """ diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 8bdacab180..2286233490 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -72,6 +72,15 @@ def test_check_args_notype(self): with self.assertRaisesRegex(argparse.ArgumentError, "Must supply a positional argument:"): check_args(self.args) + def test_check_args_badconfig(self): + """ + Test that check args aborts when a config file is entered that doesn't exist + """ + sys.argv = ["subset_data", "point", "--create-surface", "--file", "zztop"] + self.args = self.parser.parse_args() + with self.assertRaisesRegex(argparse.ArgumentError, "Entered default config file does not exist"): + check_args(self.args) + def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad From 50b5fd9e77f0a7c33d1ecc8c95f2da91c3d0df33 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 18:43:39 -0700 Subject: [PATCH 0628/2067] Add --out-surface option so you can specify the output surface dataset name, add a simple check for using it --- python/ctsm/subset_data.py | 12 +++++++++++- python/ctsm/test/test_unit_subset_data.py | 13 ++++++++++++- 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 9fca0b4f86..26d4afb80c 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -309,6 +309,16 @@ def get_parser(): type=str, default="", ) + + subparser.add_argument( + "--out-surface", + help="Output surface dataset name \ + (if you want to override the default based on the current date). \n \ + (only valid if outputing a surface dataset)", + action="store", + dest="out_surface", + type=str, + ) cesmroot = path_to_ctsm_root() defaults_file = os.path.join(cesmroot, DEFAULTS_CONFIG) subparser.add_argument( @@ -375,7 +385,7 @@ def check_args(args): ) raise argparse.ArgumentError(None, err_msg) - if not os.path.exists( args.config_file ): + if not os.path.exists(args.config_file): err_msg = textwrap.dedent( """\ \n ------------------------------------ diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 2286233490..85d1f3c838 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -78,9 +78,20 @@ def test_check_args_badconfig(self): """ sys.argv = ["subset_data", "point", "--create-surface", "--file", "zztop"] self.args = self.parser.parse_args() - with self.assertRaisesRegex(argparse.ArgumentError, "Entered default config file does not exist"): + with self.assertRaisesRegex( + argparse.ArgumentError, "Entered default config file does not exist" + ): check_args(self.args) + def test_check_args_outsurfdat_provided(self): + """ + Test that check args allows an output surface dataset to be specified + when create-surface is on + """ + sys.argv = ["subset_data", "point", "--create-surface", "--out-surface", "outputsurface.nc"] + self.args = self.parser.parse_args() + check_args(self.args) + def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad From a41831c35847b6b7442c7929784838871e3a8226 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 18:57:08 -0700 Subject: [PATCH 0629/2067] Add a check that out-surface can not be given if create-surface is not set, and a test for it that passes --- python/ctsm/subset_data.py | 9 +++++++++ python/ctsm/test/test_unit_subset_data.py | 12 ++++++++++++ 2 files changed, 21 insertions(+) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 26d4afb80c..7f0be28af6 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -394,6 +394,15 @@ def check_args(args): ) raise argparse.ArgumentError(None, err_msg) + if args.out_surface and not args.create_surfdata: + err_msg = textwrap.dedent( + """\ + \n ------------------------------------ + \n out-surface option is given without the --create-surface option" + """ + ) + raise argparse.ArgumentError(None, err_msg) + def setup_user_mods(user_mods_dir, cesmroot): """ diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 85d1f3c838..347e24d1cd 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -92,6 +92,18 @@ def test_check_args_outsurfdat_provided(self): self.args = self.parser.parse_args() check_args(self.args) + def test_check_args_outsurfdat_fails_without_create_surface(self): + """ + Test that check args does not allow an output surface dataset to be specified + when create-surface is not on + """ + sys.argv = ["subset_data", "point", "--create-landuse", "--out-surface", "outputsurface.nc"] + self.args = self.parser.parse_args() + with self.assertRaisesRegex( + argparse.ArgumentError, "out-surface option is given without the --create-surface option" + ): + check_args(self.args) + def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad From 3b841e5f14a696553ea168f92b7ac7ece5e35c88 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 20:50:25 -0700 Subject: [PATCH 0630/2067] Add test to make sure if a file exists and overwrite isn't active that it fails --- python/ctsm/test/test_unit_subset_data.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 347e24d1cd..7d3b30c460 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -104,6 +104,19 @@ def test_check_args_outsurfdat_fails_without_create_surface(self): ): check_args(self.args) + def test_check_args_outsurfdat_fails_without_overwrite(self): + """ + Test that check args does not allow an output surface dataset to be specified + for an existing dataset without the overwrite option + """ + sys.argv = ["subset_data", "point", "--create-surface", "--out-surface", "ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc"] + self.args = self.parser.parse_args() + with self.assertRaisesRegex( + argparse.ArgumentError, "out-surface filename exists and the overwrite option was not also selected", + ): + check_args(self.args) + + def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad From 8a46808709a4f524f58ceca7bc9672444108402c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 20:55:54 -0700 Subject: [PATCH 0631/2067] Add error check for out_surface that exists without overwrite, utest now passes --- python/ctsm/subset_data.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 7f0be28af6..21832fde63 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -403,6 +403,15 @@ def check_args(args): ) raise argparse.ArgumentError(None, err_msg) + if args.out_surface and os.path.exists(args.out_surface) and not args.overwrite: + err_msg = textwrap.dedent( + """\ + \n ------------------------------------ + \n out-surface filename exists and the overwrite option was not also selected" + """ + ) + raise argparse.ArgumentError(None, err_msg) + def setup_user_mods(user_mods_dir, cesmroot): """ From 53af6f9101d581d5c721dbe718e609429c93762d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 21:23:39 -0700 Subject: [PATCH 0632/2067] Have the defaults file read in the testinputs directory, run through black, check some of the values from setup_files --- python/ctsm/subset_data.py | 2 +- python/ctsm/test/test_unit_subset_data.py | 30 ++++++++++++++++---- python/ctsm/test/testinputs/default_data.cfg | 28 ++++++++++++++++++ 3 files changed, 53 insertions(+), 7 deletions(-) create mode 100644 python/ctsm/test/testinputs/default_data.cfg diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 21832fde63..07f7e33cff 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -67,7 +67,7 @@ from ctsm.site_and_regional.regional_case import RegionalCase from ctsm.args_utils import plon_type, plat_type from ctsm.path_utils import path_to_ctsm_root -from ctsm.utils import abort +from ctsm.utils import abort, add_tag_to_filename # -- import ctsm logging flags from ctsm.ctsm_logging import ( diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 7d3b30c460..16c0b29b15 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -31,7 +31,7 @@ class TestSubsetData(unittest.TestCase): def setUp(self): sys.argv = ["subset_data", "point", "--create-surface"] - DEFAULTS_FILE = "default_data.cfg" + DEFAULTS_FILE = os.path.join(os.getcwd(), "ctsm/test/testinputs/default_data.cfg") self.parser = get_parser() self.args = self.parser.parse_args() self.cesmroot = path_to_ctsm_root() @@ -43,7 +43,17 @@ def test_inputdata_setup_files_basic(self): Test """ check_args(self.args) - setup_files(self.args, self.defaults, self.cesmroot) + files = setup_files(self.args, self.defaults, self.cesmroot) + self.assertEqual( + files["fsurf_in"], + "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + "fsurf_in filename not whats expected", + ) + self.assertEqual( + files["main_dir"], + "/glade/p/cesmdata/inputdata", + "main_dir directory not whats expected", + ) def test_inputdata_setup_files_inputdata_dne(self): """ @@ -100,7 +110,8 @@ def test_check_args_outsurfdat_fails_without_create_surface(self): sys.argv = ["subset_data", "point", "--create-landuse", "--out-surface", "outputsurface.nc"] self.args = self.parser.parse_args() with self.assertRaisesRegex( - argparse.ArgumentError, "out-surface option is given without the --create-surface option" + argparse.ArgumentError, + "out-surface option is given without the --create-surface option", ): check_args(self.args) @@ -109,14 +120,21 @@ def test_check_args_outsurfdat_fails_without_overwrite(self): Test that check args does not allow an output surface dataset to be specified for an existing dataset without the overwrite option """ - sys.argv = ["subset_data", "point", "--create-surface", "--out-surface", "ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc"] + sys.argv = [ + "subset_data", + "point", + "--create-surface", + "--out-surface", + "ctsm/test/testinputs/" + + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + ] self.args = self.parser.parse_args() with self.assertRaisesRegex( - argparse.ArgumentError, "out-surface filename exists and the overwrite option was not also selected", + argparse.ArgumentError, + "out-surface filename exists and the overwrite option was not also selected", ): check_args(self.args) - def test_inputdata_setup_files_bad_inputdata_arg(self): """ Test that inputdata directory provided on command line does not exist if it's bad diff --git a/python/ctsm/test/testinputs/default_data.cfg b/python/ctsm/test/testinputs/default_data.cfg new file mode 100644 index 0000000000..7e841dca54 --- /dev/null +++ b/python/ctsm/test/testinputs/default_data.cfg @@ -0,0 +1,28 @@ +[main] +clmforcingindir = /glade/p/cesmdata/inputdata + +[datm_gswp3] +dir = atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516 +domain = domain.lnd.360x720_gswp3.0v1.c170606.nc +solardir = Solar +precdir = Precip +tpqwdir = TPHWL +solartag = clmforc.GSWP3.c2011.0.5x0.5.Solr. +prectag = clmforc.GSWP3.c2011.0.5x0.5.Prec. +tpqwtag = clmforc.GSWP3.c2011.0.5x0.5.TPQWL. +solarname = CLMGSWP3v1.Solar +precname = CLMGSWP3v1.Precip +tpqwname = CLMGSWP3v1.TPQW + +[surfdat] +dir = lnd/clm2/surfdata_map/release-clm5.0.18 +surfdat_16pft = surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc +surfdat_78pft = surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc + +[landuse] +dir = lnd/clm2/surfdata_map/release-clm5.0.18 +landuse_16pft = landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c190214.nc +landuse_78pft = landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1850-2015_c190214.nc + +[domain] +file = share/domains/domain.lnd.fv0.9x1.25_gx1v7.151020.nc From 685c2b1ce75ca35aa0520169f7c4287b686e9d1d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 21:27:46 -0700 Subject: [PATCH 0633/2067] Check for fsurf_out is None when out-surface not set and value given when set --- python/ctsm/test/test_unit_subset_data.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 16c0b29b15..f779c40cee 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -49,6 +49,11 @@ def test_inputdata_setup_files_basic(self): "surfdata_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", "fsurf_in filename not whats expected", ) + self.assertEqual( + files["fsurf_out"], + None, + "fsurf_out filename not whats expected", + ) self.assertEqual( files["main_dir"], "/glade/p/cesmdata/inputdata", @@ -101,6 +106,12 @@ def test_check_args_outsurfdat_provided(self): sys.argv = ["subset_data", "point", "--create-surface", "--out-surface", "outputsurface.nc"] self.args = self.parser.parse_args() check_args(self.args) + files = setup_files(self.args, self.defaults, self.cesmroot) + self.assertEqual( + files["fsurf_out"], + "outputsurface.nc", + "fsurf_out filename not whats expected", + ) def test_check_args_outsurfdat_fails_without_create_surface(self): """ From 9f79c7b7c18864878babc9aa87e90a334d20378a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 21:33:47 -0700 Subject: [PATCH 0634/2067] Add fsurf_out to setup_files returned dictionary, set to None, unless args.out_surface is set --- python/ctsm/subset_data.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 07f7e33cff..15d0034438 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -67,7 +67,7 @@ from ctsm.site_and_regional.regional_case import RegionalCase from ctsm.args_utils import plon_type, plat_type from ctsm.path_utils import path_to_ctsm_root -from ctsm.utils import abort, add_tag_to_filename +from ctsm.utils import abort # -- import ctsm logging flags from ctsm.ctsm_logging import ( @@ -492,6 +492,10 @@ def setup_files(args, defaults, cesmroot): fsurf_in = defaults.get("surfdat", "surfdat_" + num_pft + "pft") fluse_in = defaults.get("landuse", "landuse_" + num_pft + "pft") + if args.out_surface: + fsurf_out = args.out_surface + else: + fsurf_out = None file_dict = { "main_dir": clmforcingindir, @@ -505,6 +509,7 @@ def setup_files(args, defaults, cesmroot): os.path.join(defaults.get("landuse", "dir")), ), "fsurf_in": fsurf_in, + "fsurf_out": fsurf_out, "fluse_in": fluse_in, "datm_tuple": DatmFiles( dir_input_datm, From eb7e94fea737a746ce8e7d83df698d99149f6aef Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 21:45:49 -0700 Subject: [PATCH 0635/2067] Specify the filename if out_surface is given, otherwise do things as currently done --- python/ctsm/site_and_regional/regional_case.py | 8 ++++++-- python/ctsm/site_and_regional/single_point_case.py | 7 +++++-- python/ctsm/subset_data.py | 10 ++++++++-- 3 files changed, 19 insertions(+), 6 deletions(-) diff --git a/python/ctsm/site_and_regional/regional_case.py b/python/ctsm/site_and_regional/regional_case.py index 8d5d81e014..2a2dc66bce 100644 --- a/python/ctsm/site_and_regional/regional_case.py +++ b/python/ctsm/site_and_regional/regional_case.py @@ -145,7 +145,7 @@ def create_domain_at_reg(self, indir, file): f_in.close() f_out.close() - def create_surfdata_at_reg(self, indir, file, user_mods_dir): + def create_surfdata_at_reg(self, indir, file, user_mods_dir, specify_fsurf_out): """ Create surface data file for this RegionalCase class. """ @@ -154,7 +154,11 @@ def create_surfdata_at_reg(self, indir, file, user_mods_dir): # specify files fsurf_in = os.path.join(indir, file) - fsurf_out = add_tag_to_filename(fsurf_in, self.tag, replace_res=True) + if specify_fsurf_out is None: + fsurf_out = add_tag_to_filename(fsurf_in, self.tag, replace_res=True) + else: + fsurf_out = specify_fsurf_out + logger.info("fsurf_in: %s", fsurf_in) logger.info("fsurf_out: %s", os.path.join(self.out_dir, fsurf_out)) diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 05b918d316..96544ff9c1 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -450,7 +450,7 @@ def modify_surfdata_atpoint(self, f_orig): return f_mod - def create_surfdata_at_point(self, indir, file, user_mods_dir): + def create_surfdata_at_point(self, indir, file, user_mods_dir, specify_fsurf_out): """ Create surface data file at a single point. """ @@ -464,7 +464,10 @@ def create_surfdata_at_point(self, indir, file, user_mods_dir): # specify file fsurf_in = os.path.join(indir, file) - fsurf_out = add_tag_to_filename(fsurf_in, self.tag, replace_res=True) + if specify_fsurf_out is None: + fsurf_out = add_tag_to_filename(fsurf_in, self.tag, replace_res=True) + else: + fsurf_out = specify_fsurf_out logger.info("fsurf_in: %s", fsurf_in) logger.info("fsurf_out: %s", os.path.join(self.out_dir, fsurf_out)) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 15d0034438..a258c7b72e 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -569,7 +569,10 @@ def subset_point(args, file_dict: dict): # -- Create CTSM surface data file if single_point.create_surfdata: single_point.create_surfdata_at_point( - file_dict["fsurf_dir"], file_dict["fsurf_in"], args.user_mods_dir + file_dict["fsurf_dir"], + file_dict["fsurf_in"], + args.user_mods_dir, + specify_fsurf_out=file_dict["fsurf_out"], ) # -- Create CTSM transient landuse data file @@ -629,7 +632,10 @@ def subset_region(args, file_dict: dict): # -- Create CTSM surface data file if region.create_surfdata: region.create_surfdata_at_reg( - file_dict["fsurf_dir"], file_dict["fsurf_in"], args.user_mods_dir + file_dict["fsurf_dir"], + file_dict["fsurf_in"], + args.user_mods_dir, + specify_fsurf_out=file_dict["fsurf_out"], ) # -- Create CTSM transient landuse data file From a74ac52087a383ef672d96708b99207614c8658c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 22:01:56 -0700 Subject: [PATCH 0636/2067] Add capability to do the urban single point sites --- tools/mksurfdata_map/Makefile.data | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index caaef030e3..7d52fb230b 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -54,6 +54,9 @@ endif MKSURFDATA = $(BATCHJOBS) $(PWD)/mksurfdata.pl SUBSETDATA = $(PWD)/../site_and_regional/subset_data +MODIFYSURF = $(PWD)/../modify_input_files/fsurdat_modifier + +CDATE = $(shell date +%y%m%d) # subset_data options # @@ -71,9 +74,9 @@ SUBSETDATA_1X1_SMALL := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA \ # NOTE: The 1850 smallvilleIA site is constructed to start with 100% natural vegetation, so we can test transition to crops SUBSETDATA_1X1_SMALL1850 := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA --dompft 13 --pctpft 100 -SUBSETDATA_1X1_MEXICOCITY := --lat 19.5 --lon 260.5 --site 1x1_mexicocityMEX -SUBSETDATA_1X1_VANCOUVER := --lat 49.5 --lon 236.5 --site 1x1_vancouverCAN -SUBSETDATA_1X1_URBALPHA := --lat -37.7308 --lon 0 --site 1x1_urbanc_alpha +SUBSETDATA_1X1_MEXICOCITY := --lat 19.5 --lon 260.5 --site 1x1_mexicocityMEX --out-surface surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc +SUBSETDATA_1X1_VANCOUVER := --lat 49.5 --lon 236.5 --site 1x1_vancouverCAN --out-surface surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc +SUBSETDATA_1X1_URBALPHA := --lat -37.7308 --lon 0 --site 1x1_urbanc_alpha --out-surface surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc # f19 and f09 are standard resolutions, f10 is used for testing, f45 is used for FATES # ne30np4 is standard resolution for SE dycore in CAM, C96 is standard for fv3 dycore # The ne30np4 series (including pg2, pg3, pg4) are standard for SE dycore @@ -260,15 +263,24 @@ crop-global-SSP5-8.5 : FORCE # urban : urban-present urban-alpha -urban-present : FORCE +urban-present : mexicocity vancouver + +mexicocity : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) + $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + +vancouver : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) + $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 urban-alpha : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) - + $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc # # landuse timeseries From 666d89ce34a8c61067df9a060707064afec8df5b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 18 Jan 2023 22:02:25 -0700 Subject: [PATCH 0637/2067] Add modify file for mexicocity --- .../modify_1x1_mexicocityMEX.cfg | 135 ++++++++++++++++++ 1 file changed, 135 insertions(+) create mode 100644 tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg diff --git a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg new file mode 100644 index 0000000000..b138c75879 --- /dev/null +++ b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg @@ -0,0 +1,135 @@ +[modify_fsurdat_basic_options] + +lat_dimname = lsmlat +lon_dimname = lsmlon + +# idealized (bool) +# When user wants existing values in fsurdat to persist in all except the +# variables that they explicitly request to change, then set this to False. +# When user wants idealized representation of the land by resetting all +# fsurdat variables, some through this file and others by using hardwired +# defaults, then set this to True. Hardwired values are as follows: +# zbedrock = 10 +# SLOPE = 0 +# PFTDATA_MASK = 1 +# LANDFRAC_PFT = 1 +# PCT_NATVEG = 100 other landunits 0 +# PCT_SAND = 43 corresponds to loam +# PCT_CLAY = 18 corresponds to loam +# ORGANIC = 0 +idealized = False + +# sub +process_subgrid_section = True +process_var_list_section = True + +# Boundaries of user-defined rectangle (float) +# If lat_1 > lat_2, the code creates two rectangles, one in the north and +# one in the south. +# If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. +# Alternatively, user may specify a custom area in a .nc landmask_file +# below. If set, this will override the lat/lon settings. +# ----------------------------------- +# southernmost latitude for rectangle +lnd_lat_1 = -90 +# northernmost latitude for rectangle +lnd_lat_2 = 90 +# westernmost longitude for rectangle +lnd_lon_1 = 0 +# easternmost longitude for rectangle +lnd_lon_2 = 360 +# user-defined mask in a file, as alternative to setting lat/lon values +landmask_file = UNSET + +# PFT/CFT to be set to 100% according to user-defined mask. +# If idealized = True and dom_plant = UNSET, the latter defaults to 0 +# (bare soil). Valid values range from 0 to a max value (int) that one can +# obtain from the fsurdat_in file using ncdump (or method preferred by user). +# The max valid value will equal (lsmpft - 1) and will also equal the last +# value of cft(cft). +dom_pft = UNSET + +# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_plant +# If dom_plant = 0, the next four default to 0 (space-delimited list +# of floats without brackets). +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET + +# SOIL_COLOR accepts integer values from 1 to 20 (see CTSM Technote for info). +# if idealized = True and soil_color = UNSET, soil_color = 15. +soil_color = UNSET + +# STD_ELEV (standard deviation of elevation) value (in meters) over the +# user_defined mask (float). +# if idealized = True and std_elev = UNSET, std_elev = 0. +std_elev = UNSET + +# FMAX (maximum fractional saturated area) value (fraction) over the +# user_defined mask (float). +# if idealized = True and max_sat_area = UNSET, max_sat_area = 0. +max_sat_area = UNSET + +# Set non-vegetation landunits to 0 (bool). +zero_nonveg = False + +include_nonveg = True + +# Section for subgrid_fractions +[modify_fsurdat_subgrid_fractions] +# If subgrid_fractions = True this section will be enabled + +# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area +PCT_URBAN = 100.0 0.0 0.0 +PCT_CROP = 0.0 +PCT_NATVEG= 0.0 +PCT_GLACIER= 0.0 +PCT_WETLAND= 0.0 +PCT_LAKE = 0.0 + +# Section with a list of variables to prcoess +[modify_fsurdat_variable_list] +# If variable_list = True this section will be enabled +# Can't specify PFT as they are in dom_pft +# Add variables on the file and assign a new value +# can't specify soil_color, max_sat_area + +# Variables on numurbl which is 3 +CANYON_HWR = 1.18 1.18 1.18 +EM_IMPROAD = 0.95 0.95 0.95 +EM_PERROAD = 0.95 0.95 0.95 +EM_ROOF = 0.9 0.9 0.9 +EM_WALL = 0.85 0.85 0.85 +HT_ROOF = 18.8 18.8 18.8 +THICK_ROOF = 0.185 0.185 0.185 +THICK_WALL = 0.45 0.45 0.45 +T_BUILDING_MIN = 200.0 200.0 200.0 +WIND_HGT_CANYON = 9.4 9.4 9.4 +WTLUNIT_ROOF = 0.55 0.55 0.55 +WTROAD_PERV = 0.04 0.04 0.04 +# NOTE: This variable is integer rather than float +NLEV_IMPROAD = 5 5 5 + +# Variables on numrad which is 2 +ALB_IMPROAD_DIR = 0.08 0.08 +ALB_IMPROAD_DIF = 0.08 0.08 +ALB_PERROAD_DIR = 0.08 0.08 +ALB_PERROAD_DIF = 0.08 0.08 +ALB_ROOF_DIR = 0.2 0.2 +ALB_ROOF_DIF = 0.2 0.2 +ALB_WALL_DIR = 0.25 0.25 +ALB_WALL_DIF = 0.25 0.25 + +# Variabls on nlevurb which is 5 +TK_ROOF = 0.20 0.93 0.93 0.03 0.16 +TK_WALL = 0.88 0.88 0.88 0.88 0.88 +TK_IMPROAD = 0.82 0.82 2.10 2.10 2.10 +CV_ROOF = 1760000.0 1500000.0 1500000.0 250000.0 870000.0 +CV_WALL = 1540000.0 1540000.0 1540000.0 1540000.0 1540000.0 +CV_IMPROAD = 1740000.0 1740000.0 2000000.0 2000000.0 2000000.0 + +# Natural and Crop PFT's don't really need to be set, since they have zero area, but +# it looks better to do so +PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +PCT_CFT = 100. 0.0 From e3a59fe3edada15b16c4ebe52d6ddb30e3e53c76 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 19 Jan 2023 16:13:09 -0700 Subject: [PATCH 0638/2067] A little more documentation comments on the modify fsurdat config files --- .../modify_1x1_mexicocityMEX.cfg | 23 +++++++++---------- .../modify_fsurdat_template.cfg | 2 +- 2 files changed, 12 insertions(+), 13 deletions(-) diff --git a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg index b138c75879..0e3c4c6ab6 100644 --- a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg +++ b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg @@ -8,28 +8,22 @@ lon_dimname = lsmlon # variables that they explicitly request to change, then set this to False. # When user wants idealized representation of the land by resetting all # fsurdat variables, some through this file and others by using hardwired -# defaults, then set this to True. Hardwired values are as follows: -# zbedrock = 10 -# SLOPE = 0 -# PFTDATA_MASK = 1 -# LANDFRAC_PFT = 1 -# PCT_NATVEG = 100 other landunits 0 -# PCT_SAND = 43 corresponds to loam -# PCT_CLAY = 18 corresponds to loam -# ORGANIC = 0 +# defaults, then set this to True. idealized = False -# sub +# subgrid section to set the PCT_* variables process_subgrid_section = True +# Variable list section to set specific variable names process_var_list_section = True -# Boundaries of user-defined rectangle (float) +# Boundaries of user-defined rectangle to apply changes (float) # If lat_1 > lat_2, the code creates two rectangles, one in the north and # one in the south. # If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. # Alternatively, user may specify a custom area in a .nc landmask_file # below. If set, this will override the lat/lon settings. # ----------------------------------- +# (Use a grid that includes the entire globe as we are just setting a single point) # southernmost latitude for rectangle lnd_lat_1 = -90 # northernmost latitude for rectangle @@ -74,6 +68,7 @@ max_sat_area = UNSET # Set non-vegetation landunits to 0 (bool). zero_nonveg = False +# Include other land units besides vegetated include_nonveg = True # Section for subgrid_fractions @@ -90,10 +85,14 @@ PCT_LAKE = 0.0 # Section with a list of variables to prcoess [modify_fsurdat_variable_list] +# IMPORTANT NOTE: Config file strings are case inssentive! +# +# As such it will check for variable names both in lower case and upper case. +# # If variable_list = True this section will be enabled # Can't specify PFT as they are in dom_pft # Add variables on the file and assign a new value -# can't specify soil_color, max_sat_area +# can't specify soil_color, max_sat_area or other things that are above. # Variables on numurbl which is 3 CANYON_HWR = 1.18 1.18 1.18 diff --git a/tools/modify_input_files/modify_fsurdat_template.cfg b/tools/modify_input_files/modify_fsurdat_template.cfg index aebe42a4f8..3661784521 100644 --- a/tools/modify_input_files/modify_fsurdat_template.cfg +++ b/tools/modify_input_files/modify_fsurdat_template.cfg @@ -44,7 +44,7 @@ process_subgrid_section = False # Process the optional section that handles modifying an arbitrary list of variables process_var_list_section = False -# Boundaries of user-defined rectangle (float) +# Boundaries of user-defined rectangle to apply changes (float) # If lat_1 > lat_2, the code creates two rectangles, one in the north and # one in the south. # If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. From f933d51b00064f8f50d0a1c758744acbab7b0d93 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 19 Jan 2023 17:03:32 -0700 Subject: [PATCH 0639/2067] Add in the other two urban surface datasets --- tools/mksurfdata_map/Makefile.data | 1 - .../modify_1x1_urbanc_alpha.cfg | 134 ++++++++++++++++++ .../modify_1x1_vancouverCAN.cfg | 134 ++++++++++++++++++ 3 files changed, 268 insertions(+), 1 deletion(-) create mode 100644 tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg create mode 100644 tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 7d52fb230b..7bac3b8923 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -62,7 +62,6 @@ CDATE = $(shell date +%y%m%d) # SUBSETDATA_POINT = $(SUBSETDATA) point --overwrite --uniform-snowpack --cap-saturation --outdir . SUBSETDATA_POINT_ALLLU = $(SUBSETDATA_POINT) --include-nonveg -# NOTE: TODO: We need settings in subset_data to handle urban datasets see issue #1665 SUBSETDATA_POINT_URBAN = $(SUBSETDATA_POINT) --include-nonveg # Subset data sites... diff --git a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg new file mode 100644 index 0000000000..3bb56917a3 --- /dev/null +++ b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg @@ -0,0 +1,134 @@ +[modify_fsurdat_basic_options] + +lat_dimname = lsmlat +lon_dimname = lsmlon + +# idealized (bool) +# When user wants existing values in fsurdat to persist in all except the +# variables that they explicitly request to change, then set this to False. +# When user wants idealized representation of the land by resetting all +# fsurdat variables, some through this file and others by using hardwired +# defaults, then set this to True. +idealized = False + +# subgrid section to set the PCT_* variables +process_subgrid_section = True +# Variable list section to set specific variable names +process_var_list_section = True + +# Boundaries of user-defined rectangle to apply changes (float) +# If lat_1 > lat_2, the code creates two rectangles, one in the north and +# one in the south. +# If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. +# Alternatively, user may specify a custom area in a .nc landmask_file +# below. If set, this will override the lat/lon settings. +# ----------------------------------- +# (Use a grid that includes the entire globe as we are just setting a single point) +# southernmost latitude for rectangle +lnd_lat_1 = -90 +# northernmost latitude for rectangle +lnd_lat_2 = 90 +# westernmost longitude for rectangle +lnd_lon_1 = 0 +# easternmost longitude for rectangle +lnd_lon_2 = 360 +# user-defined mask in a file, as alternative to setting lat/lon values +landmask_file = UNSET + +# PFT/CFT to be set to 100% according to user-defined mask. +# If idealized = True and dom_plant = UNSET, the latter defaults to 0 +# (bare soil). Valid values range from 0 to a max value (int) that one can +# obtain from the fsurdat_in file using ncdump (or method preferred by user). +# The max valid value will equal (lsmpft - 1) and will also equal the last +# value of cft(cft). +dom_pft = UNSET + +# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_plant +# If dom_plant = 0, the next four default to 0 (space-delimited list +# of floats without brackets). +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET + +# SOIL_COLOR accepts integer values from 1 to 20 (see CTSM Technote for info). +# if idealized = True and soil_color = UNSET, soil_color = 15. +soil_color = UNSET + +# STD_ELEV (standard deviation of elevation) value (in meters) over the +# user_defined mask (float). +# if idealized = True and std_elev = UNSET, std_elev = 0. +std_elev = UNSET + +# FMAX (maximum fractional saturated area) value (fraction) over the +# user_defined mask (float). +# if idealized = True and max_sat_area = UNSET, max_sat_area = 0. +max_sat_area = UNSET + +# Set non-vegetation landunits to 0 (bool). +zero_nonveg = False + +# Include other land units besides vegetated +include_nonveg = True + +# Section for subgrid_fractions +[modify_fsurdat_subgrid_fractions] +# If subgrid_fractions = True this section will be enabled + +# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area +PCT_URBAN = 100.0 0.0 0.0 +PCT_CROP = 0.0 +PCT_NATVEG= 0.0 +PCT_GLACIER= 0.0 +PCT_WETLAND= 0.0 +PCT_LAKE = 0.0 + +# Section with a list of variables to prcoess +[modify_fsurdat_variable_list] +# IMPORTANT NOTE: Config file strings are case inssentive! +# +# As such it will check for variable names both in lower case and upper case. +# +# If variable_list = True this section will be enabled +# Can't specify PFT as they are in dom_pft +# Add variables on the file and assign a new value +# can't specify soil_color, max_sat_area or other things that are above. + +# Variables on numurbl which is 3 +CANYON_HWR = 0.42 0.42 0.42 +EM_IMPROAD = 0.973 0.973 0.973 +EM_PERROAD = 0.973 0.973 0.973 +EM_ROOF = 0.973 0.973 0.973 +EM_WALL = 0.973 0.973 0.973 +HT_ROOF = 6.4 6.4 6.4 +THICK_ROOF = 0.1141 0.1141 0.1141 +THICK_WALL = 0.1489 0.1489 0.1489 +T_BUILDING_MIN = 200.0 200.0 200.0 +WIND_HGT_CANYON = 3.2 3.2 3.2 +WTLUNIT_ROOF = 0.445 0.445 0.445 +WTROAD_PERV = 0.68 0.68 0.68 +# NOTE: This variable is integer rather than float +NLEV_IMPROAD = 4 4 4 + +# Variables on numrad which is 2 +ALB_IMPROAD_DIR = 0.15 0.15 +ALB_IMPROAD_DIF = 0.15 0.15 +ALB_PERROAD_DIR = 0.15 0.15 +ALB_PERROAD_DIF = 0.15 0.15 +ALB_ROOF_DIR = 0.21 0.21 +ALB_ROOF_DIF = 0.21 0.21 +ALB_WALL_DIR = 0.21 0.21 +ALB_WALL_DIF = 0.21 0.21 + +# Variabls on nlevurb which is 5 +TK_ROOF = 6.530 0.025 0.230 0.160 0.00 +TK_WALL = 0.610 0.430 0.024 0.160 0.00 +TK_IMPROAD = 1.170 0.300 0.300 0.420 0.00 +CV_ROOF = 2070000.0 7100.0 1500000.0 670000.0 0.0 +CV_WALL = 1250000.0 1400000.0 1300.0 670000.0 0.0 +CV_IMPROAD = 1140000.0 1050000.0 1050000.0 1290000.0 0.0 + +# Natural and Crop PFT's don't really need to be set, since they have zero area, but +# it looks better to do so +PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +PCT_CFT = 100. 0.0 diff --git a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg new file mode 100644 index 0000000000..a8ef5e328b --- /dev/null +++ b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg @@ -0,0 +1,134 @@ +[modify_fsurdat_basic_options] + +lat_dimname = lsmlat +lon_dimname = lsmlon + +# idealized (bool) +# When user wants existing values in fsurdat to persist in all except the +# variables that they explicitly request to change, then set this to False. +# When user wants idealized representation of the land by resetting all +# fsurdat variables, some through this file and others by using hardwired +# defaults, then set this to True. +idealized = False + +# subgrid section to set the PCT_* variables +process_subgrid_section = True +# Variable list section to set specific variable names +process_var_list_section = True + +# Boundaries of user-defined rectangle to apply changes (float) +# If lat_1 > lat_2, the code creates two rectangles, one in the north and +# one in the south. +# If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. +# Alternatively, user may specify a custom area in a .nc landmask_file +# below. If set, this will override the lat/lon settings. +# ----------------------------------- +# (Use a grid that includes the entire globe as we are just setting a single point) +# southernmost latitude for rectangle +lnd_lat_1 = -90 +# northernmost latitude for rectangle +lnd_lat_2 = 90 +# westernmost longitude for rectangle +lnd_lon_1 = 0 +# easternmost longitude for rectangle +lnd_lon_2 = 360 +# user-defined mask in a file, as alternative to setting lat/lon values +landmask_file = UNSET + +# PFT/CFT to be set to 100% according to user-defined mask. +# If idealized = True and dom_plant = UNSET, the latter defaults to 0 +# (bare soil). Valid values range from 0 to a max value (int) that one can +# obtain from the fsurdat_in file using ncdump (or method preferred by user). +# The max valid value will equal (lsmpft - 1) and will also equal the last +# value of cft(cft). +dom_pft = UNSET + +# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_plant +# If dom_plant = 0, the next four default to 0 (space-delimited list +# of floats without brackets). +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET + +# SOIL_COLOR accepts integer values from 1 to 20 (see CTSM Technote for info). +# if idealized = True and soil_color = UNSET, soil_color = 15. +soil_color = UNSET + +# STD_ELEV (standard deviation of elevation) value (in meters) over the +# user_defined mask (float). +# if idealized = True and std_elev = UNSET, std_elev = 0. +std_elev = UNSET + +# FMAX (maximum fractional saturated area) value (fraction) over the +# user_defined mask (float). +# if idealized = True and max_sat_area = UNSET, max_sat_area = 0. +max_sat_area = UNSET + +# Set non-vegetation landunits to 0 (bool). +zero_nonveg = False + +# Include other land units besides vegetated +include_nonveg = True + +# Section for subgrid_fractions +[modify_fsurdat_subgrid_fractions] +# If subgrid_fractions = True this section will be enabled + +# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area +PCT_URBAN = 100.0 0.0 0.0 +PCT_CROP = 0.0 +PCT_NATVEG= 0.0 +PCT_GLACIER= 0.0 +PCT_WETLAND= 0.0 +PCT_LAKE = 0.0 + +# Section with a list of variables to prcoess +[modify_fsurdat_variable_list] +# IMPORTANT NOTE: Config file strings are case inssentive! +# +# As such it will check for variable names both in lower case and upper case. +# +# If variable_list = True this section will be enabled +# Can't specify PFT as they are in dom_pft +# Add variables on the file and assign a new value +# can't specify soil_color, max_sat_area or other things that are above. + +# Variables on numurbl which is 3 +CANYON_HWR = 0.39 0.39 0.39 +EM_IMPROAD = 0.95 0.95 0.95 +EM_PERROAD = 0.95 0.95 0.95 +EM_ROOF = 0.92 0.92 0.92 +EM_WALL = 0.90 0.90 0.90 +HT_ROOF = 5.8 5.8 5.8 +THICK_ROOF = 0.070 0.070 0.070 +THICK_WALL = 0.20 0.20 0.20 +T_BUILDING_MIN = 200.0 200.0 200.0 +WIND_HGT_CANYON = 2.9 2.9 2.9 +WTLUNIT_ROOF = 0.51 0.51 0.51 +WTROAD_PERV = 0.11 0.11 0.11 +# NOTE: This variable is integer rather than float +NLEV_IMPROAD = 5 5 5 + +# Variables on numrad which is 2 +ALB_IMPROAD_DIR = 0.08 0.08 +ALB_IMPROAD_DIF = 0.08 0.08 +ALB_PERROAD_DIR = 0.08 0.08 +ALB_PERROAD_DIF = 0.08 0.08 +ALB_ROOF_DIR = 0.12 0.12 +ALB_ROOF_DIF = 0.12 0.12 +ALB_WALL_DIR = 0.50 0.50 +ALB_WALL_DIF = 0.50 0.50 + +# Variabls on nlevurb which is 5 +TK_ROOF = 1.40 1.40 1.40 0.03 1.51 +TK_WALL = 1.51 1.51 0.67 0.67 1.51 +TK_IMPROAD = 0.82 0.82 2.10 2.10 2.10 +CV_ROOF = 1760000.0 1760000.0 1760000.0 40000.0 2210000.0 +CV_WALL = 2110000.0 2110000.0 1000000.0 1000000.0 2110000.0 +CV_IMPROAD = 1740000.0 1740000.0 2000000.0 2000000.0 2000000.0 + +# Natural and Crop PFT's don't really need to be set, since they have zero area, but +# it looks better to do so +PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +PCT_CFT = 100. 0.0 From 3d2576944c1c1dd342d782d99c60c24643b48a03 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 20 Jan 2023 08:59:57 -0700 Subject: [PATCH 0640/2067] updates to surfwrapper --- tools/site_and_regional/neon_surf_wrapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index d8e11415ff..26827ae53c 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -109,7 +109,7 @@ def main(): command1 = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite, '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] command2 = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', - 'subset_data_single_point', '--fates'] + 'subset_data_single_point', '--16pft'] else: command1 = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite,'--dompft',str(pft),'--crop', '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] From ba597a56027382595fc50c0d33cae2be17fb3042 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 09:04:02 -0700 Subject: [PATCH 0641/2067] add back space in subset_data --- tools/site_and_regional/subset_data | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/site_and_regional/subset_data b/tools/site_and_regional/subset_data index ad8e60e053..6477b3034d 100755 --- a/tools/site_and_regional/subset_data +++ b/tools/site_and_regional/subset_data @@ -4,6 +4,7 @@ This is a just top-level skeleton script that calls subset_data.py. The original code (subset_data.py) is located under python/ctsm folder. + For full instructions on how to run the code and different options, please check python/ctsm/subset_data.py file. This script extracts domain files, surface dataset, and DATM files From 3f4e88018dcd13824f71ba8dfdaac6ef96b52ef4 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 09:25:16 -0700 Subject: [PATCH 0642/2067] update flags --- .../modify_singlept_site_neon.py | 15 +++--- tools/site_and_regional/neon_surf_wrapper.py | 52 ++++++++++++++----- 2 files changed, 47 insertions(+), 20 deletions(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 64e77eacd5..9bb08f7e50 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -175,11 +175,10 @@ def get_parser(): ) parser.add_argument( - "-f", - "--fates", - help="Modify FATES-specific surface data files (i.e. 16-PFT version", + "--16pft", + help="Modify 16-pft surface data files (e.g. for a FATES run)", action="store_true", - dest="fates", + dest="pft_16", default=False, ) @@ -250,7 +249,7 @@ def get_neon(neon_dir, site_name): return neon_file -def find_surffile(surf_dir, site_name, fates): +def find_surffile(surf_dir, site_name, pft_16): """ Function for finding and choosing surface file for a neon site. @@ -261,7 +260,7 @@ def find_surffile(surf_dir, site_name, fates): Args: surf_dir (str): directory of single point surface data site_name (str): 4 letter neon site name - fates (bool): if true, use 16-PFT version of surface data file + pft_16 (bool): if true, use 16-PFT version of surface data file Raises: Error if the surface data for the site is not created @@ -270,8 +269,8 @@ def find_surffile(surf_dir, site_name, fates): surf_file (str): name of the surface dataset file """ - if fates: - sf_name = "surfdata_1x1_NEON_16PFT_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" + if pft_16: + sf_name = "surfdata_1x1_NEON_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" else: sf_name = "surfdata_1x1_NEON_" + site_name + "*hist_78pfts_CMIP6_simyr2000_*.nc" diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index 26827ae53c..4eb8da3536 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -52,10 +52,16 @@ def get_parser(): dest="verbose", default=False) - parser.add_argument('-f', '--fates', - help='Create and/or modify surface data file for FATES. ', + parser.add_argument('--16pft', + help='Create and/or modify 16-PFT surface datasets (e.g. for a FATES run) ', action="store_true", - dest="fates", + dest="pft_16", + default=False) + + parser.add_argument('-m', '--mixed', + help='Do not overwrite surface dataset to be just one dominant PFT at 100%', + action="store_true", + dest="mixed", default=False) @@ -104,19 +110,41 @@ def main(): pft = row['pft'] clmsite = "1x1_NEON_"+site print ("Now processing site :", site) - if args.fates: - command1 = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite, - '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - command2 = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + if args.mixed and args.pft_16: + # don't set crop flag + # don't set a dominant pft + subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), + '--site',clmsite, '--create-surface','--uniform-snowpack', + '--cap-saturation','--verbose','--overwrite'] + modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', 'subset_data_single_point', '--16pft'] + elif args.pft_16: + # don't set crop flag + # set dominant pft + subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), + '--site',clmsite,'--dompft',str(pft),'--create-surface', + '--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] + modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + 'subset_data_single_point', '--16pft'] + elif args.mixed: + # set crop flag + # don't set dominant pft + subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), + '--site',clmsite,'--crop','--create-surface', + '--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] + modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + 'subset_data_single_point'] else: - command1 = ['./subset_data','point','--lat',str(lat),'--lon',str(lon),'--site',clmsite,'--dompft',str(pft),'--crop', - '--create-surface','--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - command2 = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + # set crop flag + # set dominant pft + subset_command = ['./subset_data', 'point', '--lat', str(lat), '--lon', str(lon), + '--site', clmsite,'--crop', '--dompft', str(pft), '--create-surface', + '--uniform-snowpack', '--cap-saturation', '--verbose', '--overwrite'] + modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', 'subset_data_single_point'] - execute(command1) - execute(command2) + execute(subset_command) + execute(modify_command) if __name__ == "__main__": main() From b26d33c55fa639a34f5ee864f12bb6b294473686 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 09:29:10 -0700 Subject: [PATCH 0643/2067] update notes --- tools/site_and_regional/neon_surf_wrapper.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/tools/site_and_regional/neon_surf_wrapper.py index 4eb8da3536..3271c72f08 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/tools/site_and_regional/neon_surf_wrapper.py @@ -112,6 +112,7 @@ def main(): print ("Now processing site :", site) if args.mixed and args.pft_16: + # use surface dataset with 16 pfts, and don't overwrite with 100% 1 dominant PFT # don't set crop flag # don't set a dominant pft subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), @@ -120,6 +121,7 @@ def main(): modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', 'subset_data_single_point', '--16pft'] elif args.pft_16: + # use surface dataset with 16 pfts, but overwrite to 100% 1 dominant PFT # don't set crop flag # set dominant pft subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), @@ -128,6 +130,8 @@ def main(): modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', 'subset_data_single_point', '--16pft'] elif args.mixed: + # use surface dataset with 78 pfts, and don't overwrite with 100% 1 dominant PFT + # NOTE: FATES will currently not run with a 78-PFT surface dataset # set crop flag # don't set dominant pft subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), @@ -136,6 +140,8 @@ def main(): modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', 'subset_data_single_point'] else: + # use surface dataset with 78 pfts, and overwrite to 100% 1 dominant PFT + # NOTE: FATES will currently not run with a 78-PFT surface dataset # set crop flag # set dominant pft subset_command = ['./subset_data', 'point', '--lat', str(lat), '--lon', str(lon), From ab5f0c94723c3624f5467a5795120d62299cfc72 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 09:35:18 -0700 Subject: [PATCH 0644/2067] update file name --- tools/site_and_regional/modify_singlept_site_neon.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 9bb08f7e50..5dc56ae0b2 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -272,7 +272,7 @@ def find_surffile(surf_dir, site_name, pft_16): if pft_16: sf_name = "surfdata_1x1_NEON_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" else: - sf_name = "surfdata_1x1_NEON_" + site_name + "*hist_78pfts_CMIP6_simyr2000_*.nc" + sf_name = "surfdata_1x1_NEON_" +site_name+"*hist_78pfts_CMIP6_simyr2000_*.nc" print (os.path.join(surf_dir , sf_name)) surf_file = sorted(glob.glob(os.path.join(surf_dir , sf_name))) From d22eb008e2d457df918790c5a50dc10f1bda05a6 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 09:37:02 -0700 Subject: [PATCH 0645/2067] remove fates argument --- tools/site_and_regional/modify_singlept_site_neon.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/tools/site_and_regional/modify_singlept_site_neon.py index 5dc56ae0b2..e135760a48 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/tools/site_and_regional/modify_singlept_site_neon.py @@ -546,7 +546,7 @@ def main(): # -- Look for surface data surf_dir = args.surf_dir - surf_file = find_surffile(surf_dir, site_name, args.fates) + surf_file = find_surffile(surf_dir, site_name, args.pft_16) # -- directory structure current_dir = os.getcwd() From 207091a32c9b794d6b80ca50bd873592db48678e Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 10:52:28 -0700 Subject: [PATCH 0646/2067] add NEON test, add 1pt fates compset alias --- cime_config/config_compsets.xml | 10 ++++++++++ cime_config/testdefs/testlist_clm.xml | 10 ++++++++++ 2 files changed, 20 insertions(+) diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index 6a0ac8b3f6..61931c94ba 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -41,11 +41,21 @@ 2000_DATM%1PT_CLM51%BGC_SICE_SOCN_SROF_SGLC_SWAV + + I1PtClm51Fates + 2000_DATM%1PT_CLM51%FATES_SICE_SOCN_SROF_SGLC_SWAV + + IHist1PtClm51Bgc HIST_DATM%1PT_CLM51%BGC_SICE_SOCN_SROF_SGLC_SWAV + + IHist1PtClm51Fates + HIST_DATM%1PT_CLM51%FATES_SICE_SOCN_SROF_SGLC_SWAV + + I1PtClm51SpRs 2000_DATM%1PT_CLM51%SP_SICE_SOCN_SROF_SGLC_SWAV diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index ffc56de0c3..e08a578abb 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1552,6 +1552,16 @@ + + + + + + + + + + From 02612b0eaff023c3c78b4d7e7c171a874dd213b3 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 12:20:21 -0700 Subject: [PATCH 0647/2067] exit if trying to run KONA or STER with FATES --- cime_config/testdefs/testlist_clm.xml | 2 +- cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands | 7 +++---- cime_config/usermods_dirs/NEON/FATES/STER/shell_commands | 7 +++---- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index e08a578abb..05053fc5d1 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1557,7 +1557,7 @@ - + diff --git a/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands index 66f274dd36..316509046c 100644 --- a/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands @@ -1,7 +1,6 @@ ./xmlchange NEONSITE=KONA ./xmlchange PTS_LON=263.38956 ./xmlchange PTS_LAT=39.10828 -# Setup to run with prognostic crops for this site -# If you want to explicitly run in SP mode or add other -# options you'll need to add that after this... -./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop" +# We can't run crops with FATES yet +echo "Cannot run FATES at KONA because FATES does not yet have crops." +exit 1 diff --git a/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands index 38b173c309..685eeb2529 100644 --- a/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands @@ -1,7 +1,6 @@ ./xmlchange NEONSITE=STER ./xmlchange PTS_LON=256.96992 ./xmlchange PTS_LAT=40.45984 -# Setup to run with prognostic crops for this site -# If you want to explicitly run in SP mode or add other -# # options you'll need to add that after this... -./xmlchange CLM_BLDNML_OPTS="--bgc bgc --crop" +# We can't run crops with FATES yet +echo "Cannot run FATES at STER because FATES does not yet have crops." +exit 1 From 79829404f5e615384d3c4cc151035c3bfcb799e7 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 20 Jan 2023 12:44:16 -0700 Subject: [PATCH 0648/2067] update surface file name --- cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm index c842546ec7..2a6b4d76d5 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm @@ -19,7 +19,7 @@ !---------------------------------------------------------------------------------- flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets -fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/FATES/surfdata_1x1_NEON_16PFT_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230110.nc" +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230120.nc" ! h1 output stream hist_fincl2 = 'FATES_AUTORESP','FCEV','FCTR','FGEV','FIRA','FSA','FSH','FATES_GPP','FATES_GPP_PF','H2OSOI', From 85efdc530a8907ba70662db52cf77d7b68a6b5b4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 20 Jan 2023 12:55:16 -0700 Subject: [PATCH 0649/2067] Respond to @slevisconsulting review with changes asked for --- python/ctsm/modify_input_files/fsurdat_modifier.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 992aa1323c..39bd95986c 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -287,9 +287,10 @@ def modify_optional( logger.info("dom_pft complete") -def read_opt_config(modify_fsurdat, config, cfg_path, section): - """read the optional parts of the main section config file""" - # not required: user may set these in the .cfg file +def read_cfg_optional_basic_opts(modify_fsurdat, config, cfg_path, section): + """Read the optional parts of the main section of the config file. + The main section is called modify_fsurdat_basic_options. + Users may set these optional parts but are not required to do so.""" lai = get_config_value( config=config, @@ -538,7 +539,7 @@ def fsurdat_modifier(parser): sai, hgt_top, hgt_bot, - ) = read_opt_config(modify_fsurdat, config, cfg_path, section) + ) = read_cfg_optional_basic_opts(modify_fsurdat, config, cfg_path, section) # ------------------------------ # modify surface data properties # ------------------------------ From 3293ef432d1f3b4f4390f729d3b17d36da2aac1c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 20 Jan 2023 14:41:51 -0700 Subject: [PATCH 0650/2067] Get test that fails if overwrite not selected and surface file is named and the file exists --- python/ctsm/test/test_unit_subset_data.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index f779c40cee..94a53e2dd2 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -131,13 +131,15 @@ def test_check_args_outsurfdat_fails_without_overwrite(self): Test that check args does not allow an output surface dataset to be specified for an existing dataset without the overwrite option """ + outfile = os.path.join( os.getcwd(), "ctsm/test/testinputs/", "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" ) + self.assertTrue( os.path.exists( outfile ), str(outfile)+" outfile should exist" ) + sys.argv = [ "subset_data", "point", "--create-surface", "--out-surface", - "ctsm/test/testinputs/" - + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc", + outfile ] self.args = self.parser.parse_args() with self.assertRaisesRegex( From a7d672e3d9f2668307ba99b192561d3fd45b1b77 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 20 Jan 2023 14:43:45 -0700 Subject: [PATCH 0651/2067] Run through black --- python/ctsm/test/test_unit_subset_data.py | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 94a53e2dd2..5d7a0f05b6 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -131,16 +131,14 @@ def test_check_args_outsurfdat_fails_without_overwrite(self): Test that check args does not allow an output surface dataset to be specified for an existing dataset without the overwrite option """ - outfile = os.path.join( os.getcwd(), "ctsm/test/testinputs/", "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" ) - self.assertTrue( os.path.exists( outfile ), str(outfile)+" outfile should exist" ) - - sys.argv = [ - "subset_data", - "point", - "--create-surface", - "--out-surface", - outfile - ] + outfile = os.path.join( + os.getcwd(), + "ctsm/test/testinputs/", + "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc", + ) + self.assertTrue(os.path.exists(outfile), str(outfile) + " outfile should exist") + + sys.argv = ["subset_data", "point", "--create-surface", "--out-surface", outfile] self.args = self.parser.parse_args() with self.assertRaisesRegex( argparse.ArgumentError, From 040555c0eac09347821fb88fd30c1a791e3d3b70 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 20 Jan 2023 16:59:04 -0700 Subject: [PATCH 0652/2067] Change name of --file option to subset_data to --cfg-file option to make it more clear in response to review --- python/ctsm/subset_data.py | 2 +- python/ctsm/test/test_unit_subset_data.py | 2 +- tools/mksurfdata_map/Makefile.data | 6 +++--- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index a258c7b72e..4a3a5801f1 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -322,7 +322,7 @@ def get_parser(): cesmroot = path_to_ctsm_root() defaults_file = os.path.join(cesmroot, DEFAULTS_CONFIG) subparser.add_argument( - "--file", + "--cfg-file", help="Default configure file to use for default filenames.", action="store", dest="config_file", diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index 5d7a0f05b6..fd9aef631d 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -91,7 +91,7 @@ def test_check_args_badconfig(self): """ Test that check args aborts when a config file is entered that doesn't exist """ - sys.argv = ["subset_data", "point", "--create-surface", "--file", "zztop"] + sys.argv = ["subset_data", "point", "--create-surface", "--cfg-file", "zztop"] self.args = self.parser.parse_args() with self.assertRaisesRegex( argparse.ArgumentError, "Entered default config file does not exist" diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 7bac3b8923..ea17856d78 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -159,7 +159,7 @@ crop-tropics-present : brazil-tropics-present crop-tropics-historical : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --file default_data_1850.cfg --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --cfg-file default_data_1850.cfg --crop crop-tropics-transient : FORCE $(SUBSETDATA_POINT_ALLLU) --create-landuse $(SUBSETDATA_1X1_BRAZIL) --crop @@ -182,7 +182,7 @@ crop-numa-present : FORCE $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --crop crop-numa-historical : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --file default_data_1850.cfg --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --cfg-file default_data_1850.cfg --crop crop-smallville : FORCE $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL) --crop @@ -198,7 +198,7 @@ crop-global-present-ne120np4 : FORCE # adds crop (to make sure that it works properly to add crop in a grid cell # where there used to be no crop). crop-smallville-historical : FORCE - $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL1850) --file default_data_1850.cfg --crop + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL1850) --cfg-file default_data_1850.cfg --crop # Setup the historical case for SSP5-8.5 so that historical can be used to go into the future. crop-global-historical : FORCE From dacc5a563f4e7c6d951002a03102921707cdb4c0 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 15:41:39 -0700 Subject: [PATCH 0653/2067] Add silent option resolving #1941 --- python/ctsm/ctsm_logging.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/python/ctsm/ctsm_logging.py b/python/ctsm/ctsm_logging.py index ff51c6d8f2..e14ec2754c 100644 --- a/python/ctsm/ctsm_logging.py +++ b/python/ctsm/ctsm_logging.py @@ -68,6 +68,7 @@ def add_logging_args(parser): logging_level.add_argument( "-v", "--verbose", action="store_true", help="Output extra logging info" ) + logging_level.add_argument("--silent", action="store_true", help="Only output errors") logging_level.add_argument( "--debug", @@ -84,6 +85,8 @@ def process_logging_args(args): root_logger.setLevel(logging.DEBUG) elif args.verbose: root_logger.setLevel(logging.INFO) + elif args.silent: + root_logger.setLevel(logging.ERROR) else: root_logger.setLevel(logging.WARNING) From 53f3b7aa102af1803b88bb0aa06afd0001b7f970 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 17:24:39 -0700 Subject: [PATCH 0654/2067] Update python design doc --- doc/design/python_script_user_interface.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/design/python_script_user_interface.rst b/doc/design/python_script_user_interface.rst index 4dd0c9c546..3ad6a4d2cf 100644 --- a/doc/design/python_script_user_interface.rst +++ b/doc/design/python_script_user_interface.rst @@ -40,8 +40,8 @@ Options that are more than a single character should be formatted as ``--some-va 2. Standard options: verbose, silent, help and debug: -Scripts should support ``--verbose`` / ``-v`` and ``--debug`` options. See comments at the top of ``ctsm_logging.py`` for details. -Also the options silent and help are recommended as well. +Scripts should support ``--verbose`` / ``-v``, ''--silent'', and ``--debug`` options. See comments at the top of ``ctsm_logging.py`` for details. +Also the help option is highly recommended as well. 3. Value flags: From 2d607d90cb34e1ab5683e8b05eca48e3e66821cb Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 19:28:33 -0700 Subject: [PATCH 0655/2067] Remove the single point mksurfdata tests as we are now using subset_data --- test/tools/input_tests_master | 11 ----------- test/tools/tests_posttag_hobart_nompi | 1 - test/tools/tests_posttag_izumi_nompi | 1 - test/tools/tests_posttag_nompi_regression | 4 ---- test/tools/tests_pretag_cheyenne_nompi | 3 --- 5 files changed, 20 deletions(-) diff --git a/test/tools/input_tests_master b/test/tools/input_tests_master index f3e46d50b5..63e4e5173f 100644 --- a/test/tools/input_tests_master +++ b/test/tools/input_tests_master @@ -24,15 +24,6 @@ bli58 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_10x15_crp_1850-200 smi64 TSMscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_5x5_amazon_hirespft_2005^tools__ds bli64 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_5x5_amazon_hirespft_2005^tools__ds -smi74 TSMscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_brazil_1850-2000^tools__ds -bli74 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_brazil_1850-2000^tools__ds -smi78 TSMscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_brazil_1850^tools__ds -bli78 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_brazil_1850^tools__ds -smiT4 TSMscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_numaIA_crp_2000^tools__ds -bliT4 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_numaIA_crp_2000^tools__ds -smiT2 TSMscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100^tools__s -bliT2 TBLscript_tools.sh mksurfdata_map mksurfdata.pl mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100^tools__s - sm0a1 TSMscript_tools.sh site_and_regional run_neon.py run_neon_OSBS bl0a1 TBLscript_tools.sh site_and_regional run_neon.py run_neon_OSBS @@ -54,5 +45,3 @@ smi#2 TSMscript_tools.sh mkmapdata mkmapdata.sh mkmapdata_ne30np4 bli#2 TBLscript_tools.sh mkmapdata mkmapdata.sh mkmapdata_ne30np4 smi59 TSMscript_tools.sh mkmapdata mkmapdata.sh mkmapdata_if10 bli59 TBLscript_tools.sh mkmapdata mkmapdata.sh mkmapdata_if10 -smi79 TSMscript_tools.sh mkmapdata mkmapdata.sh mkmapdata_i1x1_brazil -bli79 TBLscript_tools.sh mkmapdata mkmapdata.sh mkmapdata_i1x1_brazil diff --git a/test/tools/tests_posttag_hobart_nompi b/test/tools/tests_posttag_hobart_nompi index 9f07863e4d..d3cbccecdf 100644 --- a/test/tools/tests_posttag_hobart_nompi +++ b/test/tools/tests_posttag_hobart_nompi @@ -1,4 +1,3 @@ smc#4 blc#4 smi54 bli54 smi57 bli57 -smiT4 bliT4 diff --git a/test/tools/tests_posttag_izumi_nompi b/test/tools/tests_posttag_izumi_nompi index 62687a7e3d..3e84fb8459 100644 --- a/test/tools/tests_posttag_izumi_nompi +++ b/test/tools/tests_posttag_izumi_nompi @@ -1,3 +1,2 @@ smi54 bli54 smi57 bli57 -smiT4 bliT4 diff --git a/test/tools/tests_posttag_nompi_regression b/test/tools/tests_posttag_nompi_regression index 1395aebe11..b665409c51 100644 --- a/test/tools/tests_posttag_nompi_regression +++ b/test/tools/tests_posttag_nompi_regression @@ -5,7 +5,3 @@ smi53 bli53 smi54 bli54 smi57 bli57 smi58 bli58 -smi74 bli74 -smi78 bli78 -smiT4 bliT4 -smiT2 bliT2 diff --git a/test/tools/tests_pretag_cheyenne_nompi b/test/tools/tests_pretag_cheyenne_nompi index 19e96594bf..6280f33824 100644 --- a/test/tools/tests_pretag_cheyenne_nompi +++ b/test/tools/tests_pretag_cheyenne_nompi @@ -10,6 +10,3 @@ smi64 bli64 smi54 bli54 smi57 bli57 smi58 bli58 -smi74 bli74 -smiT4 bliT4 -smiT2 bliT2 From 02117d6ad233cb08ed8df530e7c8746c72a40193 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 19:33:30 -0700 Subject: [PATCH 0656/2067] Remove the single point mksurfdata and mkmapdata test files --- test/tools/nl_files/mkmapdata_i1x1_brazil | 1 - test/tools/nl_files/mksrfdt_1x1_brazil_1850 | 1 - test/tools/nl_files/mksrfdt_1x1_brazil_1850-2000 | 1 - test/tools/nl_files/mksrfdt_1x1_numaIA_crp_2000 | 1 - test/tools/nl_files/mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100 | 1 - test/tools/nl_files/mksrfdt_1x1_vancouverCAN_2000 | 1 - 6 files changed, 6 deletions(-) delete mode 100644 test/tools/nl_files/mkmapdata_i1x1_brazil delete mode 100644 test/tools/nl_files/mksrfdt_1x1_brazil_1850 delete mode 100644 test/tools/nl_files/mksrfdt_1x1_brazil_1850-2000 delete mode 100644 test/tools/nl_files/mksrfdt_1x1_numaIA_crp_2000 delete mode 100644 test/tools/nl_files/mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100 delete mode 100644 test/tools/nl_files/mksrfdt_1x1_vancouverCAN_2000 diff --git a/test/tools/nl_files/mkmapdata_i1x1_brazil b/test/tools/nl_files/mkmapdata_i1x1_brazil deleted file mode 100644 index bb54d468dc..0000000000 --- a/test/tools/nl_files/mkmapdata_i1x1_brazil +++ /dev/null @@ -1 +0,0 @@ --t regional -r 1x1_brazil --fast diff --git a/test/tools/nl_files/mksrfdt_1x1_brazil_1850 b/test/tools/nl_files/mksrfdt_1x1_brazil_1850 deleted file mode 100644 index 2330bd082e..0000000000 --- a/test/tools/nl_files/mksrfdt_1x1_brazil_1850 +++ /dev/null @@ -1 +0,0 @@ --l CSMDATA -r 1x1_brazil -y 1850-2000 -exedir EXEDIR diff --git a/test/tools/nl_files/mksrfdt_1x1_brazil_1850-2000 b/test/tools/nl_files/mksrfdt_1x1_brazil_1850-2000 deleted file mode 100644 index 2330bd082e..0000000000 --- a/test/tools/nl_files/mksrfdt_1x1_brazil_1850-2000 +++ /dev/null @@ -1 +0,0 @@ --l CSMDATA -r 1x1_brazil -y 1850-2000 -exedir EXEDIR diff --git a/test/tools/nl_files/mksrfdt_1x1_numaIA_crp_2000 b/test/tools/nl_files/mksrfdt_1x1_numaIA_crp_2000 deleted file mode 100644 index 03304f81eb..0000000000 --- a/test/tools/nl_files/mksrfdt_1x1_numaIA_crp_2000 +++ /dev/null @@ -1 +0,0 @@ --l CSMDATA -r 1x1_numaIA -y 2000 -exedir EXEDIR diff --git a/test/tools/nl_files/mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100 b/test/tools/nl_files/mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100 deleted file mode 100644 index ed83434075..0000000000 --- a/test/tools/nl_files/mksrfdt_1x1_numaIA_crp_SSP5-8.5_1850-2100 +++ /dev/null @@ -1 +0,0 @@ --l CSMDATA -r 1x1_numaIA -y 1850-2100 -ssp_rcp SSP5-8.5 -exedir EXEDIR diff --git a/test/tools/nl_files/mksrfdt_1x1_vancouverCAN_2000 b/test/tools/nl_files/mksrfdt_1x1_vancouverCAN_2000 deleted file mode 100644 index a446e82fcd..0000000000 --- a/test/tools/nl_files/mksrfdt_1x1_vancouverCAN_2000 +++ /dev/null @@ -1 +0,0 @@ --l CSMDATA -r 1x1_vancouverCAN -no-crop -y 2000 -exedir EXEDIR From df5e517b254e4554994741ba489a144739ed6f34 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 20:39:45 -0700 Subject: [PATCH 0657/2067] Remove another test that was removed from the master list --- test/tools/tests_pretag_cheyenne_nompi | 1 - 1 file changed, 1 deletion(-) diff --git a/test/tools/tests_pretag_cheyenne_nompi b/test/tools/tests_pretag_cheyenne_nompi index 6280f33824..6ce4972915 100644 --- a/test/tools/tests_pretag_cheyenne_nompi +++ b/test/tools/tests_pretag_cheyenne_nompi @@ -1,4 +1,3 @@ -smi79 bli79 smc#4 blc#4 smg54 blg54 smba1 blba1 From 484f49050ab12291387278de807e768e1c9f5237 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 22:17:34 -0700 Subject: [PATCH 0658/2067] Fix for #1942 so that conda environment is just activated, but not set --- test/tools/test_driver.sh | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh index ce501f980a..6a6749d493 100755 --- a/test/tools/test_driver.sh +++ b/test/tools/test_driver.sh @@ -373,8 +373,11 @@ else fi # Setup conda environement -\$CLM_ROOT/py_env_create conda activate ctsm_py +if [ \$? -ne 0 ]; then + echo "ERROR: Trouble activating the ctsm_py conda environment, be sure it's setup with \$CLM_ROOT/py_env_create, then rerun" + exit 4 +fi ##output files clm_log=\${initdir}/td.\${JOBID}.log From ce303459b68b9ff418cc25c1ab214c68ce0a8bae Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 22:27:51 -0700 Subject: [PATCH 0659/2067] Update MOSART so that it sends negative flow to river outlets by default --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 2df854055e..7a4eeb4a6e 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -23,7 +23,7 @@ required = True local_path = components/mosart protocol = git repo_url = https://github.com/ESCOMP/MOSART -tag = mosart1_0_47 +tag = mosart1_0_48 required = True [mizuRoute] From fedd4a65e1f8b4952a046e5cc6e788214e3317aa Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Jan 2023 22:33:10 -0700 Subject: [PATCH 0660/2067] Add note that \$RM uses force option (\-f) so it does not generate an error if the file does not exist --- tools/mksurfdata_map/Makefile.data | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index ea17856d78..5c2efebca6 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -266,11 +266,13 @@ urban-present : mexicocity vancouver mexicocity : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) + # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc vancouver : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) + # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc @@ -278,6 +280,7 @@ vancouver : FORCE # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 urban-alpha : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) + # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc From 8a96cc71654722f6234c2773fe45fc16ec5f9450 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 22 Jan 2023 13:07:36 -0700 Subject: [PATCH 0661/2067] Turn on silent for subset_data, move comment about remove so it isn't echoed when the urban datasets are made --- tools/mksurfdata_map/Makefile.data | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 5c2efebca6..89a238ef64 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -60,7 +60,7 @@ CDATE = $(shell date +%y%m%d) # subset_data options # -SUBSETDATA_POINT = $(SUBSETDATA) point --overwrite --uniform-snowpack --cap-saturation --outdir . +SUBSETDATA_POINT = $(SUBSETDATA) point --silent --overwrite --uniform-snowpack --cap-saturation --outdir . SUBSETDATA_POINT_ALLLU = $(SUBSETDATA_POINT) --include-nonveg SUBSETDATA_POINT_URBAN = $(SUBSETDATA_POINT) --include-nonveg @@ -264,23 +264,23 @@ urban : urban-present urban-alpha urban-present : mexicocity vancouver +# NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist mexicocity : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) - # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc +# NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist vancouver : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) - # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 +# NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist urban-alpha : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) - # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc From 2aa7566eb8c0635025d1f40164d4bc6db60e42dd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 22 Jan 2023 20:29:22 -0700 Subject: [PATCH 0662/2067] Remove the temporary files for the urban cases --- tools/mksurfdata_map/Makefile.data | 3 +++ 1 file changed, 3 insertions(+) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 89a238ef64..4d7ecb621e 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -269,12 +269,14 @@ mexicocity : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist vancouver : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 @@ -283,6 +285,7 @@ urban-alpha : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc + $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc # # landuse timeseries From 7ada54fe1b163a147982cf2184520210c4c0e000 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 22 Jan 2023 21:02:18 -0700 Subject: [PATCH 0663/2067] Add some info level logger output that will be turned on with the verbose option --- .../modify_input_files/fsurdat_modifier.py | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 39bd95986c..d1ed9e7967 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -385,6 +385,10 @@ def read_option_control( file_path=cfg_path, convert_to_type=bool, ) + if idealized: + logger.info("idealized option is on") + else: + logger.info("idealized option is off") process_subgrid = get_config_value( config=config, section=section, @@ -392,6 +396,10 @@ def read_option_control( file_path=cfg_path, convert_to_type=bool, ) + if process_subgrid: + logger.info("process_subgrid_section option is on") + else: + logger.info("process_subgrid_section option is off") process_var_list = get_config_value( config=config, section=section, @@ -399,6 +407,10 @@ def read_option_control( file_path=cfg_path, convert_to_type=bool, ) + if process_var_list: + logger.info("process_var_list_section option is on") + else: + logger.info("process_var_list_section option is off") include_nonveg = get_config_value( config=config, section=section, @@ -406,6 +418,10 @@ def read_option_control( file_path=cfg_path, convert_to_type=bool, ) + if include_nonveg: + logger.info("include_nonveg option is on") + else: + logger.info("include_nonveg option is off") max_pft = int(max(modify_fsurdat.file.lsmpft)) dom_pft = get_config_value( config=config, @@ -416,6 +432,10 @@ def read_option_control( convert_to_type=int, can_be_unset=True, ) + if dom_pft: + logger.info("dom_pft option is on and = %s", str(dom_pft)) + else: + logger.info("dom_pft option is off") if dom_pft is not None and idealized and not allow_dom_pft_and_idealized: abort("idealized AND dom_pft can NOT both be on, pick one or the other") if include_nonveg and idealized and not allow_ideal_and_include_non_veg: @@ -563,6 +583,7 @@ def fsurdat_modifier(parser): if process_subgrid: subgrid = read_subgrid(config, cfg_path, numurbl=modify_fsurdat.get_urb_dens()) modify_fsurdat.set_varlist(subgrid, cfg_path) + logger.info("process_subgrid is complete") else: check_no_subgrid_section(config) @@ -570,6 +591,7 @@ def fsurdat_modifier(parser): varlist = read_var_list(config, idealized=idealized) update_list = modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) modify_fsurdat.set_varlist(update_list, cfg_path) + logger.info("process_var_list is complete") else: check_no_varlist_section(config) From 59d2dfff3db7f7bd19fa33d566a5676fa537d597 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 22 Jan 2023 21:30:13 -0700 Subject: [PATCH 0664/2067] Replace the single point surface datasets with the newly generated ones --- bld/namelist_files/namelist_defaults_ctsm.xml | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 69643041a4..ca262e21c0 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1058,7 +1058,7 @@ lnd/clm2/surfdata_map/surfdata_0.125nldas2_hist_16pfts_Irrig_CMIP6_simyr2005_c19 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_5x5_amazon_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr2000_c190214.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr2000_c230122.nc -lnd/clm2/surfdata_map/ctsm1.0.dev094-2-g633be0eb/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c200521.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230122.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc @@ -1113,11 +1113,11 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc @@ -1133,7 +1133,7 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_16pfts_Irrig_CMIP6_s lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850_c230122.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850_c190303.nc @@ -1161,12 +1161,12 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr18 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c230122.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c230122.nc -lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c190214.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230122.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc From c92edb8adb26019e6d50fd39adc1d2dc93e8a2ff Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 23 Jan 2023 02:25:20 -0700 Subject: [PATCH 0665/2067] Fix issues with 1x1_brazil fsurdat/landuse.timeseries files --- bld/namelist_files/namelist_defaults_ctsm.xml | 18 +++++++----------- 1 file changed, 7 insertions(+), 11 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ca262e21c0..41fd39b884 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1055,10 +1055,11 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_16pfts_Irrig_CMIP6 lnd/clm2/surfdata_map/surfdata_0.125nldas2_hist_16pfts_Irrig_CMIP6_simyr2005_c190412.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr2000_c230122.nc + lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_5x5_amazon_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr2000_c190214.nc -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr2000_c230122.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c230122.nc lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230122.nc @@ -1132,9 +1133,6 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_16pfts_Irrig_CMIP6_s lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850_c230122.nc - lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850_c190303.nc @@ -1160,12 +1158,12 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr1850_c190214.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c230122.nc lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c230122.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230122.nc @@ -1210,8 +1208,6 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_48x96_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c190214.nc -lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc lnd/clm2/surfdata_map/landuse.timeseries_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc @@ -1232,7 +1228,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc lnd/clm2/surfdata_map/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc +>lnd/clm2/surfdata_map/ctsm5.1.dev116/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c230122.nc lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc From 6198e3cd13b8d9199e6ff44e1d37a86e15dc7c55 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Mon, 23 Jan 2023 10:14:33 -0700 Subject: [PATCH 0666/2067] remove KONA and STER FATES usermods, add README --- .../usermods_dirs/NEON/FATES/KONA/include_user_mods | 1 - .../usermods_dirs/NEON/FATES/KONA/shell_commands | 6 ------ cime_config/usermods_dirs/NEON/FATES/README.md | 10 ++++++++++ .../usermods_dirs/NEON/FATES/STER/include_user_mods | 1 - .../usermods_dirs/NEON/FATES/STER/shell_commands | 6 ------ 5 files changed, 10 insertions(+), 14 deletions(-) delete mode 100644 cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods delete mode 100644 cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands create mode 100644 cime_config/usermods_dirs/NEON/FATES/README.md delete mode 100644 cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods delete mode 100644 cime_config/usermods_dirs/NEON/FATES/STER/shell_commands diff --git a/cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods deleted file mode 100644 index b152996d95..0000000000 --- a/cime_config/usermods_dirs/NEON/FATES/KONA/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands deleted file mode 100644 index 316509046c..0000000000 --- a/cime_config/usermods_dirs/NEON/FATES/KONA/shell_commands +++ /dev/null @@ -1,6 +0,0 @@ -./xmlchange NEONSITE=KONA -./xmlchange PTS_LON=263.38956 -./xmlchange PTS_LAT=39.10828 -# We can't run crops with FATES yet -echo "Cannot run FATES at KONA because FATES does not yet have crops." -exit 1 diff --git a/cime_config/usermods_dirs/NEON/FATES/README.md b/cime_config/usermods_dirs/NEON/FATES/README.md new file mode 100644 index 0000000000..dcfcfdf9af --- /dev/null +++ b/cime_config/usermods_dirs/NEON/FATES/README.md @@ -0,0 +1,10 @@ +# NEON user mods directories for FATES runs + +Use these user mods as you would any other user_mods, e.g.: + +`./create_newcase --case FATES_ABBY_test --res CLM_USRDAT --compset I1PtClm51Fates --run-unsupported --user-mods-dir /glade/work/$user/CTSM/cime_config/usermods_dirs/NEON/FATES/ABBY` + +## Note on crop sites KONA and STER + +Currently you cannot run FATES at these sites because FATES does not have crops as of yet. We will add these sites back once this capability is available. + diff --git a/cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods b/cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods deleted file mode 100644 index b152996d95..0000000000 --- a/cime_config/usermods_dirs/NEON/FATES/STER/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../defaults diff --git a/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands deleted file mode 100644 index 685eeb2529..0000000000 --- a/cime_config/usermods_dirs/NEON/FATES/STER/shell_commands +++ /dev/null @@ -1,6 +0,0 @@ -./xmlchange NEONSITE=STER -./xmlchange PTS_LON=256.96992 -./xmlchange PTS_LAT=40.45984 -# We can't run crops with FATES yet -echo "Cannot run FATES at STER because FATES does not yet have crops." -exit 1 From 672140b2ff6270056ec684766dce7439f96332ab Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 23 Jan 2023 11:35:26 -0700 Subject: [PATCH 0667/2067] Use taxmode extend instead of cycle in cropcalStreamMod. Update test user_nl_clm to use one-year files. --- .../testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm | 2 +- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm index edf5849e0b..7136243ef8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm @@ -1,2 +1,2 @@ generate_crop_gdds = .false. -stream_fldFileName_cultivar_gdds = '/glade/work/samrabin/crop_dates/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1977-2014.gddgen/generate_gdds.2022-09-27/gdds_20220927_174954.1955-2020.nc' +stream_fldFileName_cultivar_gdds = '/glade/work/samrabin/crop_dates/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1977-2014.gddgen/generate_gdds.2022-09-27/gdds_20220927_174954.nc' diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 36fabc9f56..f39b53fdd4 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -169,7 +169,7 @@ subroutine cropcal_init(bounds) stream_yearLast = stream_year_last_cropcal, & stream_yearAlign = model_year_align_cropcal, & stream_offset = cropcal_offset, & - stream_taxmode = 'cycle', & + stream_taxmode = 'extend', & stream_dtlimit = 1.5_r8, & stream_tintalgo = cropcal_tintalgo, & stream_name = 'sowing date data', & @@ -197,7 +197,7 @@ subroutine cropcal_init(bounds) stream_yearLast = stream_year_last_cropcal, & stream_yearAlign = model_year_align_cropcal, & stream_offset = cropcal_offset, & - stream_taxmode = 'cycle', & + stream_taxmode = 'extend', & stream_dtlimit = 1.5_r8, & stream_tintalgo = cropcal_tintalgo, & stream_name = 'cultivar gdd data', & From f49a75585ddc02e2a1288b92d6bc2ea4d81d450c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 23 Jan 2023 13:17:36 -0700 Subject: [PATCH 0668/2067] Always use --crop for the subset options, so that the 78pft dataset is always used, which will make it easier to remove the use of 16pft versions which we do want to do --- tools/mksurfdata_map/Makefile.data | 40 +++++++++++++++--------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 4d7ecb621e..983dd4db9e 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -60,7 +60,7 @@ CDATE = $(shell date +%y%m%d) # subset_data options # -SUBSETDATA_POINT = $(SUBSETDATA) point --silent --overwrite --uniform-snowpack --cap-saturation --outdir . +SUBSETDATA_POINT = $(SUBSETDATA) point --silent --overwrite --uniform-snowpack --cap-saturation --crop --outdir . SUBSETDATA_POINT_ALLLU = $(SUBSETDATA_POINT) --include-nonveg SUBSETDATA_POINT_URBAN = $(SUBSETDATA_POINT) --include-nonveg @@ -73,9 +73,9 @@ SUBSETDATA_1X1_SMALL := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA \ # NOTE: The 1850 smallvilleIA site is constructed to start with 100% natural vegetation, so we can test transition to crops SUBSETDATA_1X1_SMALL1850 := --lat 40.6878 --lon 267.0228 --site 1x1_smallvilleIA --dompft 13 --pctpft 100 -SUBSETDATA_1X1_MEXICOCITY := --lat 19.5 --lon 260.5 --site 1x1_mexicocityMEX --out-surface surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc -SUBSETDATA_1X1_VANCOUVER := --lat 49.5 --lon 236.5 --site 1x1_vancouverCAN --out-surface surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc -SUBSETDATA_1X1_URBALPHA := --lat -37.7308 --lon 0 --site 1x1_urbanc_alpha --out-surface surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc +SUBSETDATA_1X1_MEXICOCITY := --lat 19.5 --lon 260.5 --site 1x1_mexicocityMEX --out-surface surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000.nc +SUBSETDATA_1X1_VANCOUVER := --lat 49.5 --lon 236.5 --site 1x1_vancouverCAN --out-surface surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000.nc +SUBSETDATA_1X1_URBALPHA := --lat -37.7308 --lon 0 --site 1x1_urbanc_alpha --out-surface surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000.nc # f19 and f09 are standard resolutions, f10 is used for testing, f45 is used for FATES # ne30np4 is standard resolution for SE dycore in CAM, C96 is standard for fv3 dycore # The ne30np4 series (including pg2, pg3, pg4) are standard for SE dycore @@ -155,14 +155,14 @@ crop-tropics-present : brazil-tropics-present $(MKSURFDATA) -glc_nec 10 -y 2000 -res 5x5_amazon $(BACKGROUND) 1x1_brazil-tropics-present : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) crop-tropics-historical : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --cfg-file default_data_1850.cfg --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_BRAZIL) --cfg-file default_data_1850.cfg crop-tropics-transient : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-landuse $(SUBSETDATA_1X1_BRAZIL) --crop + $(SUBSETDATA_POINT_ALLLU) --create-landuse $(SUBSETDATA_1X1_BRAZIL) # # crop @@ -179,13 +179,13 @@ crop-global-present-f05 : FORCE $(MKSURFDATA) -glc_nec 10 -y 1850,2000 -res 0.47x0.63 $(BACKGROUND) crop-numa-present : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) crop-numa-historical : FORCE - $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --cfg-file default_data_1850.cfg --crop + $(SUBSETDATA_POINT_ALLLU) --create-surface $(SUBSETDATA_1X1_NUMAIA) --cfg-file default_data_1850.cfg crop-smallville : FORCE - $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL) --crop + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL) crop-global-present-ne16np4 : FORCE $(MKSURFDATA) -glc_nec 10 -y 2000 -res ne16np4 $(BACKGROUND) @@ -198,7 +198,7 @@ crop-global-present-ne120np4 : FORCE # adds crop (to make sure that it works properly to add crop in a grid cell # where there used to be no crop). crop-smallville-historical : FORCE - $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL1850) --cfg-file default_data_1850.cfg --crop + $(SUBSETDATA_POINT) --create-surface $(SUBSETDATA_1X1_SMALL1850) --cfg-file default_data_1850.cfg # Setup the historical case for SSP5-8.5 so that historical can be used to go into the future. crop-global-historical : FORCE @@ -267,25 +267,25 @@ urban-present : mexicocity vancouver # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist mexicocity : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) - $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc - $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc - $(RM) surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000.nc + $(RM) surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc + $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc + $(RM) surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000.nc # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist vancouver : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) - $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc - $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc - $(RM) surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000.nc + $(RM) surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc + $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc + $(RM) surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000.nc # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 # NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist urban-alpha : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) - $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc - $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c$(CDATE).nc - $(RM) surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000.nc + $(RM) surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc + $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc + $(RM) surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000.nc # # landuse timeseries From 9b962c05bf45e5888b54dd116ad93b67b83df35f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 23 Jan 2023 13:31:43 -0700 Subject: [PATCH 0669/2067] Increase size of PCT_CFT array to have 64 crop CFT's so that we can use the 78pft surface datasets --- tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg | 2 +- tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg | 2 +- tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg index 0e3c4c6ab6..5e9de7968b 100644 --- a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg +++ b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg @@ -131,4 +131,4 @@ CV_IMPROAD = 1740000.0 1740000.0 2000000.0 2000000.0 2000000.0 # Natural and Crop PFT's don't really need to be set, since they have zero area, but # it looks better to do so PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -PCT_CFT = 100. 0.0 +PCT_CFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 diff --git a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg index 3bb56917a3..38b8ce6372 100644 --- a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg +++ b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg @@ -131,4 +131,4 @@ CV_IMPROAD = 1140000.0 1050000.0 1050000.0 1290000.0 0.0 # Natural and Crop PFT's don't really need to be set, since they have zero area, but # it looks better to do so PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -PCT_CFT = 100. 0.0 +PCT_CFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 diff --git a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg index a8ef5e328b..abc5df16b1 100644 --- a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg +++ b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg @@ -131,4 +131,4 @@ CV_IMPROAD = 1740000.0 1740000.0 2000000.0 2000000.0 2000000.0 # Natural and Crop PFT's don't really need to be set, since they have zero area, but # it looks better to do so PCT_NAT_PFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -PCT_CFT = 100. 0.0 +PCT_CFT = 100. 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 From 5d108b4b6afe844b808befc6f05c4d767b0cf0d7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 23 Jan 2023 15:57:35 -0700 Subject: [PATCH 0670/2067] Update single point datasets --- bld/namelist_files/namelist_defaults_ctsm.xml | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 41fd39b884..1afcb95ec1 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1056,7 +1056,7 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_16pfts_Irrig_CMIP6 lnd/clm2/surfdata_map/surfdata_0.125nldas2_hist_16pfts_Irrig_CMIP6_simyr2005_c190412.nc -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr2000_c230122.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr2000_c230123.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_5x5_amazon_hist_16pfts_Irrig_CMIP6_simyr2000_c190214.nc @@ -1086,10 +1086,10 @@ lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_s lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr2000_c190214.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr2000_c190214.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c230122.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230122.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr2000_c230123.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230123.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc @@ -1113,12 +1113,12 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.ARCTIC.ne30x4_hist_78pft lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts_CMIP6_simyr2000_c200426.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_vancouverCAN_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_urbanc_alpha_hist_16pfts_Irrig_CMIP6_simyr2000_c230122.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000_c230123.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000_c230123.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000_c230123.nc @@ -1158,13 +1158,13 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr1850_c190214.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_78pfts_CMIP6_simyr1850_c190214.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c230122.nc - -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c230122.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr1850_c230123.nc + +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr1850_c230123.nc -lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230122.nc +lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230123.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc @@ -1228,7 +1228,7 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_48x96_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc lnd/clm2/surfdata_map/ctsm5.1.dev116/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c230122.nc +>lnd/clm2/surfdata_map/ctsm5.1.dev116/landuse.timeseries_1x1_brazil_hist_78pfts_CMIP6_simyr1850-2015_c230123.nc lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc From edfde60b268b58b1382b1ba130347c3a04b10683 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 23 Jan 2023 15:58:32 -0700 Subject: [PATCH 0671/2067] So that resolution isn't done twice, explicitly add f09 resolution to list that also has specific resolutions --- bld/unit_testers/build-namelist_test.pl | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 784d3b5e0c..f270cbfea4 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -319,22 +319,22 @@ sub cat_and_create_namelistinfile { foreach my $driver ( "mct", "nuopc" ) { print " For $driver driver\n\n"; # configuration, structure, irrigate, verbose, clm_demand, ssp_rcp, test, sim_year, use_case - foreach my $options ( "-configuration nwp", - "-structure fast", - "-namelist '&a irrigate=.true./'", "-verbose", "-ssp_rcp SSP1-2.6", "-test", "-sim_year 1850", - "-namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'", - "-use_case 1850_control", + foreach my $options ( "-res 0.9x1.25 -configuration nwp", + "-res 0.9x1.25 -structure fast", + "-res 0.9x1.25 -namelist '&a irrigate=.true./'", "-res 0.9x1.25 -verbose", "-res 0.9x1.25 -ssp_rcp SSP1-2.6", "-res 0.9x1.25 -test", "-res 0.9x1.25 -sim_year 1850", + "-res 0.9x1.25 -namelist '&a use_lai_streams=.true.,use_soil_moisture_streams=.true./'", + "-res 0.9x1.25 -use_case 1850_control", "-res 1x1pt_US-UMB -clm_usr_name 1x1pt_US-UMB -namelist '&a fsurdat=\"/dev/null\"/'", "-res 1x1_brazil", - "-clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc", - "-envxml_dir . -infile myuser_nl_clm", - "-ignore_ic_date -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\"/' -bgc bgc -crop", - "-clm_start_type branch -namelist '&a nrevsn=\"thing.nc\",use_init_interp=T/'", - "-ignore_ic_date -clm_start_type startup -namelist '&a finidat=\"thing.nc\"/' -bgc bgc -crop", + "-res 0.9x1.25 -clm_start_type startup", "-namelist '&a irrigate=.false./' -crop -bgc bgc", + "-res 0.9x1.25 -infile myuser_nl_clm", + "-res 0.9x1.25 -ignore_ic_date -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\"/' -bgc bgc -crop", + "-res 0.9x1.25 -clm_start_type branch -namelist '&a nrevsn=\"thing.nc\",use_init_interp=T/'", + "-res 0.9x1.25 -ignore_ic_date -clm_start_type startup -namelist '&a finidat=\"thing.nc\"/' -bgc bgc -crop", ) { my $file = $startfile; &make_env_run(); - my $base_options = "-res 0.9x1.25 -envxml_dir . -driver $driver"; + my $base_options = "-envxml_dir . -driver $driver"; if ( $driver eq "mct" ) { $base_options = "$base_options -lnd_frac $DOMFILE"; } else { From 42709c251e3561e1b2d2ce9e437c008d67aefc21 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 24 Jan 2023 14:44:43 -0700 Subject: [PATCH 0672/2067] Add a test for the --overwrite option which isn't added yet, so the test fails --- python/ctsm/test/test_sys_fsurdat_modifier.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index cde9cac846..c69a876df3 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -80,6 +80,11 @@ def test_short_config(self): fsurdat_out = ( "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" ) + # Run it again with the overwrite option so that it will overwrite the file just created + sys.argv = ["fsurdat_modifier", self._cfg_file_path, "--overwrite"] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) + # Cleanup os.remove(fsurdat_out) def test_short_infile_both_cmdline_and_cfg(self): @@ -279,6 +284,7 @@ def test_input_fsurdat_DNE_fail(self): def test_output_fsurdat_EXISTS_fail(self): """ Test that if the output fsurdat file does exist that it gracefully fails + without --overwrite option """ self._cfg_file_path = os.path.join( self._testinputs_path, "modify_fsurdat_short_nofiles.cfg" From 6fea524c4373bfd6717e595cf46f960a7d18917e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 24 Jan 2023 15:16:37 -0700 Subject: [PATCH 0673/2067] Rm .github/workflows/python_testing.yml to unblock merging this PR --- .github/workflows/python_testing.yml | 31 ---------------------------- 1 file changed, 31 deletions(-) delete mode 100644 .github/workflows/python_testing.yml diff --git a/.github/workflows/python_testing.yml b/.github/workflows/python_testing.yml deleted file mode 100644 index f9234acc2f..0000000000 --- a/.github/workflows/python_testing.yml +++ /dev/null @@ -1,31 +0,0 @@ -name: python testing on push and PR -# -# Run the python directory testing on push and pull request -# -on: [push, pull_request] - -jobs: - pytest: - runs-on: ubuntu-latest - steps: - # Checkout the code - - uses: actions/checkout@v2 - - uses: conda-incubator/setup-miniconda@v2 - with: - activate-environment: ctsm_pylib - environment-file: python/conda_env_ctsm_py.txt - auto-activate-base: false - channels: conda-forge - - name: manage_exernals and LFS - run: | - git lfs install - manage_externals/checkout_externals - - name: chdirectory python - run: | - cd python - - name: Run python tests - run: | - make test - - name: Run pylint - run: | - make lint From 050f110f94d4c7ec700d8ac4271db4d59d67f3b2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 24 Jan 2023 16:53:59 -0700 Subject: [PATCH 0674/2067] Handle overwrite option and get the test working --- python/ctsm/modify_input_files/fsurdat_modifier.py | 14 ++++++++++++-- python/ctsm/test/test_sys_fsurdat_modifier.py | 3 ++- 2 files changed, 14 insertions(+), 3 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index d1ed9e7967..747b8bc999 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -71,6 +71,13 @@ def fsurdat_modifier_arg_process(): action="store_true", help="Allow both idealized and dom_pft to be on at the same time. ", ) + parser.add_argument( + "--overwrite", + required=False, + default=False, + action="store_true", + help="Overwrite the output file if it already exists. ", + ) add_logging_args(parser) args = parser.parse_args() process_logging_args(args) @@ -481,8 +488,11 @@ def fsurdat_modifier(parser): # If output file exists, abort before starting work if os.path.exists(fsurdat_out): - errmsg = "Output file already exists: " + fsurdat_out - abort(errmsg) + if not parser.overwrite: + errmsg = "Output file already exists: " + fsurdat_out + abort(errmsg) + else: + logger.warning("Output file already exists, but the overwrite option was selected so the file will be overwritten.") lnd_lat_1 = get_config_value( config=config, diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index c69a876df3..529800c3f7 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -76,10 +76,11 @@ def test_short_config(self): self._cfg_file_path = os.path.join(self._testinputs_path, "modify_fsurdat_short.cfg") sys.argv = ["fsurdat_modifier", self._cfg_file_path] parser = fsurdat_modifier_arg_process() - fsurdat_modifier(parser) fsurdat_out = ( "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" ) + os.remove(fsurdat_out) + fsurdat_modifier(parser) # Run it again with the overwrite option so that it will overwrite the file just created sys.argv = ["fsurdat_modifier", self._cfg_file_path, "--overwrite"] parser = fsurdat_modifier_arg_process() From 5c2b5b6cc6dc54b8c32a8919aaa7a5e7242b0946 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 24 Jan 2023 16:59:50 -0700 Subject: [PATCH 0675/2067] Turn options needed for the system test so that it will work --- cime_config/SystemTests/fsurdatmodifyctsm.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 899ab1aead..99a653129e 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -40,8 +40,11 @@ def __init__(self, case): self._cfg_file_path = os.path.join(self._get_caseroot(), 'modify_fsurdat.cfg') + logger.info(" create config file to modify") self._create_config_file() + logger.info(" run modify_fsurdat") self._run_modify_fsurdat() + logger.info(" modify user_nl files") self._modify_user_nl() with open('done_FSURDATMODIFYCTSM_setup.txt', 'w') as fp: pass @@ -68,7 +71,7 @@ def _run_modify_fsurdat(self): # Need to specify a specific python version that has the required # dependencies python_path = _get_python_path() - subprocess.check_call([python_path, tool_path, self._cfg_file_path]) + subprocess.check_call([python_path, tool_path, self._cfg_file_path, "--verbose", "--overwrite", "--allow_ideal_and_include_non_veg"]) def _modify_user_nl(self): append_to_user_nl_files(caseroot = self._get_caseroot(), From 22fe11f95636735b8206bc045c8947d47c36451f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 24 Jan 2023 17:11:24 -0700 Subject: [PATCH 0676/2067] Replace the RM with the use of the overwrite option for fsurdat_modifier --- tools/mksurfdata_map/Makefile.data | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index 983dd4db9e..c1df608436 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -54,7 +54,7 @@ endif MKSURFDATA = $(BATCHJOBS) $(PWD)/mksurfdata.pl SUBSETDATA = $(PWD)/../site_and_regional/subset_data -MODIFYSURF = $(PWD)/../modify_input_files/fsurdat_modifier +MODIFYSURF = $(PWD)/../modify_input_files/fsurdat_modifier --overwrite CDATE = $(shell date +%y%m%d) @@ -264,26 +264,20 @@ urban : urban-present urban-alpha urban-present : mexicocity vancouver -# NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist mexicocity : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_MEXICOCITY) - $(RM) surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_mexicocityMEX.cfg -i surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000.nc -o surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc $(RM) surfdata_1x1_mexicocityMEX_hist_78pfts_CMIP6_simyr2000.nc -# NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist vancouver : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_VANCOUVER) - $(RM) surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_vancouverCAN.cfg -i surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000.nc -o surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc $(RM) surfdata_1x1_vancouverCAN_hist_78pfts_CMIP6_simyr2000.nc # NOTE(bja, 2015-01) skip abort on invalid data necessary as of 2015-01. See # /glade/p/cesm/cseg/inputdata/lnd/clm2/surfdata_map/README_c141219 -# NOTE: $(RM) by default uses rm -f which doesn't generate an error if the file doesn't exist urban-alpha : FORCE $(SUBSETDATA_POINT_URBAN) --create-surface $(SUBSETDATA_1X1_URBALPHA) - $(RM) surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc $(MODIFYSURF) modify_1x1_urbanc_alpha.cfg -i surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000.nc -o surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000_c$(CDATE).nc $(RM) surfdata_1x1_urbanc_alpha_hist_78pfts_CMIP6_simyr2000.nc From b9ab8e0a9d173231a5b4562604ba91c3f49cc648 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 24 Jan 2023 23:52:04 -0700 Subject: [PATCH 0677/2067] Spin off read_cfg_required_basic_opts to make lint happy --- .../modify_input_files/fsurdat_modifier.py | 98 +++++++++++-------- 1 file changed, 57 insertions(+), 41 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 747b8bc999..d3a39f25a2 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -453,47 +453,8 @@ def read_option_control( return (idealized, process_subgrid, process_var_list, include_nonveg, dom_pft) -def fsurdat_modifier(parser): - """Implementation of fsurdat_modifier command""" - # read the .cfg (config) file - cfg_path = str(parser.cfg_path) - config = ConfigParser() - config.read(cfg_path) - section = "modify_fsurdat_basic_options" - if not config.has_section(section): - abort("Config file does not have the expected section: " + section) - - if parser.fsurdat_in == "UNSET": - # required: user must set these in the .cfg file - fsurdat_in = get_config_value( - config=config, section=section, item="fsurdat_in", file_path=cfg_path - ) - else: - if config.has_option(section=section, option="fsurdat_in"): - abort("fsurdat_in is specified in both the command line and the config file, pick one") - fsurdat_in = str(parser.fsurdat_in) - - # Error checking of input file - if not os.path.exists(fsurdat_in): - abort("Input fsurdat_in file does NOT exist: " + str(fsurdat_in)) - - if parser.fsurdat_out == "UNSET": - fsurdat_out = get_config_value( - config=config, section=section, item="fsurdat_out", file_path=cfg_path - ) - else: - if config.has_option(section=section, option="fsurdat_out"): - abort("fsurdat_out is specified in both the command line and the config file, pick one") - fsurdat_out = str(parser.fsurdat_out) - - # If output file exists, abort before starting work - if os.path.exists(fsurdat_out): - if not parser.overwrite: - errmsg = "Output file already exists: " + fsurdat_out - abort(errmsg) - else: - logger.warning("Output file already exists, but the overwrite option was selected so the file will be overwritten.") - +def read_cfg_required_basic_opts(config, section, cfg_path): + """Read the required part of the control section""" lnd_lat_1 = get_config_value( config=config, section=section, @@ -537,7 +498,62 @@ def fsurdat_modifier(parser): lon_dimname = get_config_value( config=config, section=section, item="lon_dimname", file_path=cfg_path, can_be_unset=True ) + return (lnd_lat_1, lnd_lat_2, lnd_lon_1, lnd_lon_2, landmask_file, lat_dimname, lon_dimname) + +def fsurdat_modifier(parser): + """Implementation of fsurdat_modifier command""" + # read the .cfg (config) file + cfg_path = str(parser.cfg_path) + config = ConfigParser() + config.read(cfg_path) + section = "modify_fsurdat_basic_options" + if not config.has_section(section): + abort("Config file does not have the expected section: " + section) + + if parser.fsurdat_in == "UNSET": + # required: user must set these in the .cfg file + fsurdat_in = get_config_value( + config=config, section=section, item="fsurdat_in", file_path=cfg_path + ) + else: + if config.has_option(section=section, option="fsurdat_in"): + abort("fsurdat_in is specified in both the command line and the config file, pick one") + fsurdat_in = str(parser.fsurdat_in) + + # Error checking of input file + if not os.path.exists(fsurdat_in): + abort("Input fsurdat_in file does NOT exist: " + str(fsurdat_in)) + + if parser.fsurdat_out == "UNSET": + fsurdat_out = get_config_value( + config=config, section=section, item="fsurdat_out", file_path=cfg_path + ) + else: + if config.has_option(section=section, option="fsurdat_out"): + abort("fsurdat_out is specified in both the command line and the config file, pick one") + fsurdat_out = str(parser.fsurdat_out) + + # If output file exists, abort before starting work + if os.path.exists(fsurdat_out): + if not parser.overwrite: + errmsg = "Output file already exists: " + fsurdat_out + abort(errmsg) + else: + warnmsg = ( + "Output file already exists" + + ", but the overwrite option was selected so the file will be overwritten." + ) + logger.warning(warnmsg) + ( + lnd_lat_1, + lnd_lat_2, + lnd_lon_1, + lnd_lon_2, + landmask_file, + lat_dimname, + lon_dimname, + ) = read_cfg_required_basic_opts(config, section, cfg_path) # Create ModifyFsurdat object modify_fsurdat = ModifyFsurdat.init_from_file( fsurdat_in, From f4e9ea82935a3bdb7dda6be74438b03e658af692 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 24 Jan 2023 23:53:08 -0700 Subject: [PATCH 0678/2067] Check for existance before removing in the test, it will only be removed if the test previously failed --- python/ctsm/test/test_sys_fsurdat_modifier.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 529800c3f7..cee7a51d36 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -79,7 +79,8 @@ def test_short_config(self): fsurdat_out = ( "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" ) - os.remove(fsurdat_out) + if os.path.exists(fsurdat_out): + os.remove(fsurdat_out) fsurdat_modifier(parser) # Run it again with the overwrite option so that it will overwrite the file just created sys.argv = ["fsurdat_modifier", self._cfg_file_path, "--overwrite"] From c04e89f8b92787ce0afcfb94e942917d6b623693 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 25 Jan 2023 00:00:26 -0700 Subject: [PATCH 0679/2067] Make sure the read_ subroutines that are reading the config file consistently start with read_cfg_ --- .../modify_input_files/fsurdat_modifier.py | 18 ++++--- .../ctsm/test/test_unit_fsurdat_modifier.py | 50 +++++++++---------- 2 files changed, 37 insertions(+), 31 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index d3a39f25a2..75fbbdba12 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -116,7 +116,7 @@ def check_range(var, section, value, minval, maxval): abort("Variable " + var + " in " + section + " is out of range of 0 to 100 = " + str(value)) -def read_subgrid(config, cfg_path, numurbl=3): +def read_cfg_subgrid(config, cfg_path, numurbl=3): """Read the subgrid fraction section from the config file""" section = "modify_fsurdat_subgrid_fractions" if not config.has_section(section): @@ -171,7 +171,7 @@ def read_subgrid(config, cfg_path, numurbl=3): return subgrid_settings -def read_var_list(config, idealized=True): +def read_cfg_var_list(config, idealized=True): """Read the variable list section from the config file""" section = "modify_fsurdat_variable_list" if not config.has_section(section): @@ -374,7 +374,7 @@ def read_cfg_optional_basic_opts(modify_fsurdat, config, cfg_path, section): ) -def read_option_control( +def read_cfg_option_control( modify_fsurdat, config, section, @@ -567,7 +567,13 @@ def fsurdat_modifier(parser): ) # Read control information about the optional sections - (idealized, process_subgrid, process_var_list, include_nonveg, dom_pft) = read_option_control( + ( + idealized, + process_subgrid, + process_var_list, + include_nonveg, + dom_pft, + ) = read_cfg_option_control( modify_fsurdat, config, section, @@ -607,14 +613,14 @@ def fsurdat_modifier(parser): # Handle optional sections # if process_subgrid: - subgrid = read_subgrid(config, cfg_path, numurbl=modify_fsurdat.get_urb_dens()) + subgrid = read_cfg_subgrid(config, cfg_path, numurbl=modify_fsurdat.get_urb_dens()) modify_fsurdat.set_varlist(subgrid, cfg_path) logger.info("process_subgrid is complete") else: check_no_subgrid_section(config) if process_var_list: - varlist = read_var_list(config, idealized=idealized) + varlist = read_cfg_var_list(config, idealized=idealized) update_list = modify_fsurdat.check_varlist(varlist, allow_uppercase_vars=True) modify_fsurdat.set_varlist(update_list, cfg_path) logger.info("process_var_list is complete") diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index fee4ec2ab3..0c7a244584 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -16,9 +16,9 @@ from ctsm import unit_testing from ctsm.path_utils import path_to_ctsm_root from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier_arg_process -from ctsm.modify_input_files.fsurdat_modifier import read_subgrid -from ctsm.modify_input_files.fsurdat_modifier import read_option_control -from ctsm.modify_input_files.fsurdat_modifier import read_var_list +from ctsm.modify_input_files.fsurdat_modifier import read_cfg_subgrid +from ctsm.modify_input_files.fsurdat_modifier import read_cfg_option_control +from ctsm.modify_input_files.fsurdat_modifier import read_cfg_var_list from ctsm.modify_input_files.fsurdat_modifier import check_no_subgrid_section from ctsm.modify_input_files.fsurdat_modifier import check_no_varlist_section from ctsm.modify_input_files.modify_fsurdat import ModifyFsurdat @@ -90,7 +90,7 @@ def test_dom_pft_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" ): - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_subgrid_and_idealized_fails(self): """test that dom_pft and idealized fails gracefully""" @@ -103,7 +103,7 @@ def test_subgrid_and_idealized_fails(self): SystemExit, "idealized AND process_subgrid_section can NOT both be on, pick one or the other", ): - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_optional_only_true_and_false(self): """test that optional settings can only be true or false""" @@ -118,18 +118,18 @@ def test_optional_only_true_and_false(self): for var in varlist: self.config.set(section, var, "True") self.config.set(section, "idealized", "False") - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) for var in varlist: self.config.set(section, var, "False") - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) self.config.set(section, "dom_pft", "UNSET") - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) var = "idealized" self.config.set(section, var, "Thing") with self.assertRaisesRegex( SystemExit, "Non-boolean value found for .cfg file variable: " + var ): - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_include_nonveg_and_idealized_fails(self): """test a simple read of subgrid""" @@ -139,11 +139,11 @@ def test_include_nonveg_and_idealized_fails(self): with self.assertRaisesRegex( SystemExit, "idealized AND include_nonveg can NOT both be on, pick one or the other" ): - read_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_read_subgrid(self): """test a simple read of subgrid""" - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_read_subgrid_allglacier(self): """test a read of subgrid that's for all glacier""" @@ -156,7 +156,7 @@ def test_read_subgrid_allglacier(self): self.config.set(section, "pct_glacier", "100.") self.config.set(section, "pct_natveg", "0.") self.config.set(section, "pct_crop", "0.") - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_read_subgrid_allspecial(self): """test a read of subgrid that's all special landunits""" @@ -169,7 +169,7 @@ def test_read_subgrid_allspecial(self): self.config.set(section, "pct_glacier", "40.") self.config.set(section, "pct_natveg", "0.") self.config.set(section, "pct_crop", "0.") - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_read_subgrid_allurban(self): """test a read of subgrid that's all urban""" @@ -182,11 +182,11 @@ def test_read_subgrid_allurban(self): self.config.set(section, "pct_glacier", "0.") self.config.set(section, "pct_natveg", "0.") self.config.set(section, "pct_crop", "0.") - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_read_var_list(self): """test a simple read of var_list""" - read_var_list(self.config, idealized=True) + read_cfg_var_list(self.config, idealized=True) def test_subgrid_outofrange(self): """test a read of subgrid that's out of range""" @@ -195,7 +195,7 @@ def test_subgrid_outofrange(self): section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "pct_urban", "101. 0. 0.") with self.assertRaisesRegex(SystemExit, "is out of range of 0 to 100 ="): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_subgrid_pct_urban_toosmall(self): """test a read of subgrid for PCT_URBAN that's an array too small""" @@ -206,7 +206,7 @@ def test_subgrid_pct_urban_toosmall(self): with self.assertRaisesRegex( SystemExit, "PCT_URBAN is not a list of the expected size of 3" ): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_subgrid_pct_urban_toobig(self): """test a read of subgrid for PCT_URBAN that's an array too big""" @@ -217,7 +217,7 @@ def test_subgrid_pct_urban_toobig(self): with self.assertRaisesRegex( SystemExit, "PCT_URBAN is not a list of the expected size of 3" ): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_subgrid_pct_urban_singlevalue(self): """test a read of subgrid for PCT_URBAN that's a single value""" @@ -228,7 +228,7 @@ def test_subgrid_pct_urban_singlevalue(self): with self.assertRaisesRegex( SystemExit, "PCT_URBAN is not a list of the expected size of 3" ): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_subgrid_notsumtohundred(self): """test a read of subgrid that's doesn't sum to a hundred""" @@ -244,7 +244,7 @@ def test_subgrid_notsumtohundred(self): with self.assertRaisesRegex( SystemExit, "PCT fractions in subgrid section do NOT sum to a hundred as they should" ): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_subgrid_badvar(self): """test a read of subgrid for a variable thats not in the list""" @@ -253,7 +253,7 @@ def test_subgrid_badvar(self): section = "modify_fsurdat_subgrid_fractions" self.config.set(section, "badvariable", "100.") with self.assertRaisesRegex(SystemExit, "is not a valid variable name. Valid vars ="): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_varlist_varinidealized(self): """test a read of varlist for a variable thats in the idealized list, @@ -267,7 +267,7 @@ def test_varlist_varinidealized(self): "is a special variable handled in the idealized section." + " This should NOT be handled in the variiable list section. Special idealized vars =", ): - read_var_list(self.config, idealized=True) + read_cfg_var_list(self.config, idealized=True) def test_varlist_varinsubgrid(self): """test a read of varlist for a variable thats in the subgrid list""" @@ -280,7 +280,7 @@ def test_varlist_varinsubgrid(self): "is a variable handled in the subgrid section." + " This should NOT be handled in the variiable list section. Subgrid vars =", ): - read_var_list(self.config, idealized=False) + read_cfg_var_list(self.config, idealized=False) def test_varlist_monthlyvar(self): """test a read of varlist for a variable thats one of the monthly @@ -293,14 +293,14 @@ def test_varlist_monthlyvar(self): + " This should NOT be handled in the variiable list section." + " Monthly vars handled this way =", ): - read_var_list(self.config, idealized=False) + read_cfg_var_list(self.config, idealized=False) def test_subgrid_remove(self): """test a read of subgrid when it's section has been removed""" section = "modify_fsurdat_subgrid_fractions" self.config.remove_section(section) with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): - read_subgrid(self.config, self.cfg_path) + read_cfg_subgrid(self.config, self.cfg_path) def test_subgrid_not_thereifoff(self): """test that a graceful error happens if subgrid section is off, From 6008d28a920d28a7f92592aae197dce768451035 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 26 Jan 2023 02:17:40 -0700 Subject: [PATCH 0680/2067] Update change files --- doc/ChangeLog | 157 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 158 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 49f49c235f..b1f5fdf975 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,161 @@ =============================================================== +Tag name: ctsm5.1.dev116 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Thu Jan 26 02:17:27 MST 2023 +One-line Summary: Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files + +Purpose and description of changes +---------------------------------- + +Change zetamaxstable to 2 when biomass-heat-storage is on. This changes simulation answers once they +run long enough to exceed that threshold. + +Also fix an issue with maintence respiration (MR) for BGC simulations. This changes answers for most BGC cases once +they run long enough. Live course MR wasn't included. + +Make the default for MOSART to send negative flow to river outlets. Also fix an issue with this mode. + +Bring in new surface datasets for the single point sites. We now make these sites using subset_data rather +than mksurfdata. + +Some new capability to the subset_data and modify_fsurdat tools. + +subset_data add options: +--out-surface -- To name the surface dataset on the command line rather than based on the current date +--cfg-file ----- Enter the default configure file to use rather than assume a fixed one + +modify_fsurdat add options: +--fsurdat_in -- to input on command line rather than config file +--fsurdat_out -- to input on command line rather than config file +--allow_ideal_and_include_non_veg -- to allow idealized and include_non_veg at the same time +--allow_dom_pft_and_idealized -- to allow dom_pft and idealized at the same time +--overwrite -- allow output file to be overwritten +config file options: +process_subgrid_section -- Read in an optional section to set the PCT_* fractions +process_var_list_section - Read in an optional section to set any variable on the file + +Add --silent option to python tools. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_1 + +[x] clm5_0 + +[ ] ctsm5_0-nwp + +[x] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Fixes #1676 -- live coarse maintenance respiration is not included in the root respiration + Fixes #1674 -- Change mksurfdata_map/mksurfdata_esmf Makefile to build single-point datasets using subset_data + Fixes #1809 -- Add ability to name a different default config file for subset_data + Fixes #1941 -- Add --silent option to ctsm_logging python infrastructure + Fixes #1942 -- Move py_env_create outside of tools test driver, as fails on compute nodes on cheyenne + Fixes #1924 -- Some updates to fsurdat_modifier script + Fixes #1690 -- Set and use zetamaxstable for BHS cases + Fixes #1689 -- Set zetamaxstable to 2 consistently for BHS + +Externals issues fixed (include issue #): + MOSART #58 Make negative and direct_to_outlet the default option + MOSART #56 Some issues with direct_to_outlet + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): tools + Just to the subset_data and fsurdat_modifier tools as outlined above + +Changes made to namelist defaults (e.g., changed parameter values): + zetamaxstable now 2.0 is use_biomass_heat_storage is on + +Changes to the datasets (e.g., parameter, surface or initial files): Single point fsurdat + 1x1_brazil, 1x1_numaIA, 1x1_smallvilleIA, 1x1_vancouverCAN, 1x1_mexicocityMEX, 1x1_urbanc_alpha + surface datasets and 1x1_brazil landuse.timeseries + +Notes of particular relevance for developers: +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + tools test now just activates the ctsm_py conda environment rather than creating it + There are seperate configure files for each urban surface dataset for modify_fsurdat + There is a 1850 configure file for subset_data + +Changes to tests or testing: + fsurdatmodifyctsm.py script adjusted to compensate for changes + python directory changes include unit and system tests to support updates + Single point mksurdata_map tests were removed + + +Testing summary: regular tools +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + cheyenne - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: + + Summarize any changes to answers, i.e., + - what code configurations: clm5_1, supported single point resolutions + - what platforms/compilers: All + - nature of change: adjusted climate + clm5_1 changes because zetmaxstable set to 2.0. If a simulation runs long enough + this max will be hit and it will change answers once it does. But if stability + doesn't hit the max answers can be identical. + clm5_0 and clm4_5 also change if biomass heat storage is turned on + single point resolutions (i.e. 1x1_smallvilleIA, 1x1_brazil, 1x1_mexicocityMEX) have differences + maintenence respiration + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + Keith Oleson ran experiments with changing zetamaxstable some slides showing this are here: + https://docs.google.com/presentation/d/1u6ycr7F97QYYRcRfEdD9yIxH75diUx2r + + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): mosart + mosart updated to mosart1_0_48 + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #1812 -- Get single point surface datasets from subset_data rather than mksurfdata + #1802 -- Make zetamaxstable consistently 2.0 when BHS on + #1915 -- Fix issue #1864 in release documentation + Update manage_externals (direct push to main-dev) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev115 Originator(s): rgknox (Ryan Knox) Date: Fri Dec 2 15:45:32 MST 2022 diff --git a/doc/ChangeSum b/doc/ChangeSum index 1d42a3522d..3042b38a2a 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files ctsm5.1.dev115 rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics ctsm5.1.dev114 multiple 11/19/2022 Some NEON updates fixing AG sites, update MOSART, small fixes ctsm5.1.dev113 multiple 10/28/2022 Fix some compsets; add only clauses for ESMF use statements From a1130ef8a82e1bfb6ae5df7a4e57871737ac1085 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 26 Jan 2023 10:19:58 -0700 Subject: [PATCH 0681/2067] add new test to fates list --- cime_config/testdefs/testlist_clm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 05053fc5d1..86ed45f09e 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1555,6 +1555,7 @@ + From aad7de1bf1b6c98d8e52c1d88ac62389e6cbf74a Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 26 Jan 2023 14:16:41 -0700 Subject: [PATCH 0682/2067] add fire_emis and fates test and check --- bld/CLMBuildNamelist.pm | 4 ++++ bld/unit_testers/build-namelist_test.pl | 5 +++++ cime_config/testdefs/testlist_clm.xml | 2 +- 3 files changed, 10 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index f046172f7e..05631edc23 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3683,6 +3683,10 @@ sub setup_logic_fire_emis { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; if ($opts->{'fire_emis'} ) { + if ( &value_is_true( $nl_flags->{'use_fates'} ) ) { + $log->warning("Fire emission can NOT be on when FATES is also on.\n" . + " DON'T use the '-fire_emis' option when '-bgc fates' is activated"); + } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_factors_file'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_emis_specifier'); } else { diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index f270cbfea4..c8b7538d91 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1006,6 +1006,11 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, + "useFIREEMISSwithFATES" =>{ options=>"-bgc fates -envxml_dir . -fire_emis", + namelst=>"", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, "useDRYDEPwithFATES" =>{ options=>"--bgc fates --envxml_dir . --no-megan --drydep", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 86ed45f09e..4d074eae11 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1552,7 +1552,7 @@ - + From 435691e7b35d3b095a7a05de29f24f9ca53c432b Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 26 Jan 2023 14:43:51 -0700 Subject: [PATCH 0683/2067] update test number --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index c8b7538d91..ffb01fe02c 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1846; +my $ntests = 1847; if ( defined($opts{'compare'}) ) { $ntests += 1254; } From ff2e75674d227b2ca3ffb1f3a6c94595138c219e Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 27 Jan 2023 13:28:47 -0500 Subject: [PATCH 0684/2067] Mocked up the updated cbalance checking with fates --- src/biogeochem/CNBalanceCheckMod.F90 | 52 ++++++++++++++++++++++------ 1 file changed, 42 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index b038536a5c..bbeed11e46 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -207,6 +207,10 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! ! !DESCRIPTION: ! Perform carbon mass conservation check for column and patch + ! + ! Note on FATES: On fates colums, there is no vegetation biomass + ! and no gpp flux. There is a litter input flux. + ! ! !ARGUMENTS: class(cn_balance_type) , intent(inout) :: this @@ -230,6 +234,9 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & real(r8) :: som_c_leached_grc(bounds%begg:bounds%endg) real(r8) :: hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg) real(r8) :: dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) + + !real(r8) :: totcol_c ! Total column carbon, including veg and soil (kgC) + !----------------------------------------------------------------------- associate( & @@ -262,17 +269,42 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & do fc = 1,num_soilc c = filter_soilc(fc) - ! calculate the total column-level carbon storage, for mass conservation check - col_endcb(c) = totcolc(c) - - ! calculate total column-level inputs - col_cinputs = gpp(c) - - ! calculate total column-level outputs - ! er = ar + hr, col_fire_closs includes patch-level fire losses - col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + & - col_xsmrpool_to_atm(c) + if (use_cn) then + ! calculate the total column-level carbon storage, for mass conservation check + col_endcb(c) = totcolc(c) + + ! calculate total column-level inputs + col_cinputs = gpp(c) + + ! calculate total column-level outputs + ! er = ar + hr, col_fire_closs includes patch-level fire losses + col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + & + col_xsmrpool_to_atm(c) + + elseif(use_fates) then + + ! calculate the total column-level carbon storage, for mass conservation check + col_endcb(c) = soilbiogeochem_totmicc_col(c) + & + soilbiogeochem_totlitc_col(c) + & + soilbiogeochem_totsomc_col(c) + & + soilbiogeochem_ctrunc_col(c) + + ! calculate total column-level inputs (litter fluxes) + col_cinputs = sum(this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & + this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + sum(this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & + this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + sum(this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * & + this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + ! calculate total column-level outputs + ! fates has already exported burn losses and fluxes to the atm + ! So they are irrelevant here + col_coutputs = er(c) + + end if + ! Fluxes to product pools are included in column-level outputs: the product ! pools are not included in totcolc, so are outside the system with respect to ! these balance checks. (However, the dwt flux to product pools is NOT included, From ef82a689741b80ae3738b776d6224e6925e6ac39 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 27 Jan 2023 15:36:05 -0700 Subject: [PATCH 0685/2067] add --no-megan to build-namelist test --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index ffb01fe02c..588c46c9e5 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1006,7 +1006,7 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, - "useFIREEMISSwithFATES" =>{ options=>"-bgc fates -envxml_dir . -fire_emis", + "useFIREEMISwithFATES" =>{ options=>"-bgc fates -envxml_dir . -fire_emis --no-megan", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", From 72e252ac73f48be0efaaa2be40fad15134602e24 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 27 Jan 2023 15:38:11 -0700 Subject: [PATCH 0686/2067] add test to expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 90c45ef919..3affa5be65 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -80,5 +80,13 @@ FATES#701 - + + + + FAIL + FATES#701 + + + + From 4a781a3adbaf1ff99ffd1471b278482b8008fc87 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Jan 2023 14:27:17 -0700 Subject: [PATCH 0687/2067] PlantCrop(): min gddmaturity 1.0 for all crops when prescribing either sdates or gddmaturity. --- src/biogeochem/CNPhenologyMod.F90 | 27 ++++++++++++--------------- 1 file changed, 12 insertions(+), 15 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 1b3044a873..f69ac70c95 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -129,6 +129,7 @@ module CNPhenologyMod real(r8), private :: initial_seed_at_planting = 3._r8 ! Initial seed at planting + real(r8) :: min_gddmaturity = 1._r8 ! Weird things can happen if gddmaturity is tiny logical, public :: generate_crop_gdds = .false. ! If true, harvest the day before next sowing logical, public :: use_mxmat = .true. ! If true, ignore crop maximum growing season length @@ -2455,7 +2456,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! !USES: use clm_varctl , only : use_c13, use_c14 - use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds + use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds, use_cropcal_streams use clm_varcon , only : c13ratio, c14ratio use clm_varpar , only : mxsowings use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean @@ -2488,6 +2489,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & integer k ! grain pool index real(r8) gdd_target ! cultivar GDD target this growing season real(r8) this_sowing_reason ! number representing sowing reason(s) + logical did_rx_gdds ! did this patch use a prescribed harvest requirement? !------------------------------------------------------------------------ associate( & @@ -2563,18 +2565,10 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & endif ! set GDD target + did_rx_gdds = .false. if (use_cropcal_rx_cultivar_gdds .and. crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) .ge. 0._r8) then - gdd_target = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) - - ! gddmaturity == 0.0 will cause problems elsewhere, where it appears in denominator - ! Just manually set a minimum of 1.0 - if (gdd_target < gddmin(ivt(p))) then - write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gdd_target ',gdd_target,'; using gddmin(ivt(p)) instead (',& - gddmin(ivt(p)),')' - endif - gdd_target = max(gdd_target, gddmin(ivt(p))) - - gddmaturity(p) = gdd_target + gddmaturity(p) = crop_inst%rx_cultivar_gdds_thisyr_patch(p,sowing_count(p)) + did_rx_gdds = .true. else if (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat) then gddmaturity(p) = hybgdd(ivt(p)) else @@ -2598,10 +2592,13 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & gddmaturity(p) = min(gdd020(p), hybgdd(ivt(p))) end if - if (generate_crop_gdds) then - gddmaturity(p) = max(gddmaturity(p), gddmin(ivt(p))) - endif + endif + if (use_cropcal_streams .and. gddmaturity(p) < min_gddmaturity) then + if (did_rx_gdds) then + write(iulog,*) 'Some patch with ivt ',ivt(p),' has rx gddmaturity',gddmaturity(p),'; using min_gddmaturity instead (',min_gddmaturity,')' + endif + gddmaturity(p) = min_gddmaturity endif end associate From 08e2fe618cf0c2778739ccff9ac768620edd44d6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 28 Jan 2023 15:06:39 -0700 Subject: [PATCH 0688/2067] Safer method to freeze-kill winter cereals. Previously, vernalization() forced a harvest by setting gddmaturity and huigrain to zero. Now avoids touching those, instead just using a logical. Added harvest reason to reflect this. --- src/biogeochem/CNPhenologyMod.F90 | 21 +++++++++++++++------ src/biogeochem/CropType.F90 | 2 +- 2 files changed, 16 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index f69ac70c95..fa783e0c12 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -149,6 +149,7 @@ module CNPhenologyMod real(r8), parameter :: HARVEST_REASON_SOWTODAY = 4._r8 real(r8), parameter :: HARVEST_REASON_SOWTOMORROW = 5._r8 real(r8), parameter :: HARVEST_REASON_IDOPTOMORROW = 6._r8 + real(r8), parameter :: HARVEST_REASON_VERNFREEZEKILL = 7._r8 character(len=*), parameter, private :: sourcefile = & __FILE__ @@ -1746,6 +1747,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical fake_harvest ! Dealing with incorrect Dec. 31 planting logical did_plant_prescribed_today ! Was the crop sown today? logical will_plant_prescribed_tomorrow ! Is tomorrow a prescribed sowing day? + logical vernalization_forces_harvest ! if freeze-killed !------------------------------------------------------------------------ associate( & @@ -2066,11 +2068,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! vernalization factor is not 1; ! vf affects the calculation of gddtsoi & hui + vernalization_forces_harvest = .false. if (t_ref2m_min(p) < 1.e30_r8 .and. vf(p) /= 1._r8 .and. & (ivt(p) == nwwheat .or. ivt(p) == nirrig_wwheat)) then call vernalization(p, & canopystate_inst, temperature_inst, waterdiagnosticbulk_inst, cnveg_state_inst, & - crop_inst) + crop_inst, vernalization_forces_harvest) end if ! days past planting may determine harvest @@ -2107,7 +2110,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & mxmat = 999 end if - if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then + if (vernalization_forces_harvest) then + do_harvest = .true. + force_harvest = .true. + harvest_reason = HARVEST_REASON_VERNFREEZEKILL + else if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! BACKWARDS_COMPATIBILITY(ssr, 2022-02-03): To get rid of crops incorrectly planted in last time step of Dec. 31. That was fixed in commit dadbc62 ("Call CropPhenology regardless of doalb"), but this handles restart files with the old behavior. fake_harvest ensures that outputs aren't polluted. do_harvest = .true. force_harvest = .true. @@ -2607,7 +2614,8 @@ end subroutine PlantCrop !----------------------------------------------------------------------- subroutine vernalization(p, & - canopystate_inst, temperature_inst, waterdiagnosticbulk_inst, cnveg_state_inst, crop_inst) + canopystate_inst, temperature_inst, waterdiagnosticbulk_inst, cnveg_state_inst, crop_inst, & + force_harvest) ! ! !DESCRIPTION: ! @@ -2626,6 +2634,7 @@ subroutine vernalization(p, & type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst type(crop_type) , intent(inout) :: crop_inst + logical , intent(inout) :: force_harvest ! "harvest" forced if freeze-killed ! ! LOCAL VARAIBLES: real(r8) tcrown ! ? @@ -2731,14 +2740,14 @@ subroutine vernalization(p, & ! will have to develop some type of relationship that reduces LAI and ! biomass pools in response to cold damaged crop + force_harvest = .false. if (t_ref2m_min(p) <= tfrz - 6._r8) then tkil = (tbase - 6._r8) - 6._r8 * hdidx(p) if (tkil >= tcrown) then if ((0.95_r8 - 0.02_r8 * (tcrown - tkil)**2) >= 0.02_r8) then write (iulog,*) 'crop damaged by cold temperatures at p,c =', p,c - else if (tlai(p) > 0._r8) then ! slevis: kill if past phase1 - gddmaturity(p) = 0._r8 ! by forcing through - huigrain(p) = 0._r8 ! harvest + else if (tlai(p) > 0._r8) then ! slevis: kill if past phase1 by + force_harvest = .true. ! forcing through harvest write (iulog,*) '95% of crop killed by cold temperatures at p,c =', p,c end if end if diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 7a967a037b..55575ce16e 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -338,7 +338,7 @@ subroutine InitHistory(this, bounds) ptr_patch=this%sowing_reason_perharv_patch, default='inactive') this%harvest_reason_thisyr_patch(begp:endp,:) = spval - call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; 4 = sowing today; 5 = sowing tomorrow; 6 = tomorrow == idop', type2d='mxharvests', & + call hist_addfld2d (fname='HARVEST_REASON_PERHARV', units='1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; 4 = sowing today; 5 = sowing tomorrow; 6 = tomorrow == idop; 7 = killed by cold temperature during vernalization', type2d='mxharvests', & avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & ptr_patch=this%harvest_reason_thisyr_patch, default='inactive') From 5bd05066631d3d68127943571197b7d05c5392e1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 29 Jan 2023 11:00:57 -0700 Subject: [PATCH 0689/2067] Set stream_dtlimit to 10^30 for crop calendar streams. Previously was 1.5, but threw error at 2000-01-01 (i.e., the first day of the first year of the sdates file). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index f39b53fdd4..fe1fedefd0 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -152,6 +152,7 @@ subroutine cropcal_init(bounds) use_cropcal_streams = use_cropcal_rx_sdates .or. use_cropcal_rx_cultivar_gdds ! Initialize the cdeps data type sdat_cropcal_sdate + ! NOTE: stream_dtlimit 1.5 didn't work for some reason if (use_cropcal_rx_sdates) then call shr_strdata_init_from_inline(sdat_cropcal_sdate, & my_task = iam, & @@ -170,7 +171,7 @@ subroutine cropcal_init(bounds) stream_yearAlign = model_year_align_cropcal, & stream_offset = cropcal_offset, & stream_taxmode = 'extend', & - stream_dtlimit = 1.5_r8, & + stream_dtlimit = 1.0e30_r8, & stream_tintalgo = cropcal_tintalgo, & stream_name = 'sowing date data', & rc = rc) @@ -180,6 +181,7 @@ subroutine cropcal_init(bounds) end if ! Initialize the cdeps data type sdat_cropcal_cultivar_gdds + ! NOTE: stream_dtlimit 1.5 didn't work for some reason if (use_cropcal_rx_cultivar_gdds) then call shr_strdata_init_from_inline(sdat_cropcal_cultivar_gdds, & my_task = iam, & @@ -198,7 +200,7 @@ subroutine cropcal_init(bounds) stream_yearAlign = model_year_align_cropcal, & stream_offset = cropcal_offset, & stream_taxmode = 'extend', & - stream_dtlimit = 1.5_r8, & + stream_dtlimit = 1.0e30_r8, & stream_tintalgo = cropcal_tintalgo, & stream_name = 'cultivar gdd data', & rc = rc) From 0e09a64fc7f6d9239e1ebdba9c41e54dfe7be374 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 31 Jan 2023 16:39:46 -0700 Subject: [PATCH 0690/2067] Add tests for the Gross unrepresented LU change option --- .../clm/f09_dec1990Start_GU_LULCC/include_user_mods | 1 + .../testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands | 2 ++ .../testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm | 3 +++ .../clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods | 2 ++ 4 files changed, 8 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/include_user_mods create mode 100755 cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm create mode 100644 cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands new file mode 100755 index 0000000000..4e10e7086a --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands @@ -0,0 +1,2 @@ +./xmlchange RUN_STARTDATE=1990-12-25 +./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm new file mode 100644 index 0000000000..6a666f2684 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm @@ -0,0 +1,3 @@ + flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1700-2021_c220825.nc' + fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr1700_c220825.nc' + do_grossunrep = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods new file mode 100644 index 0000000000..24f76fbb9f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods @@ -0,0 +1,2 @@ +../../f09_dec1990Start_GU_LULCC +../monthly From 0a087c5495283171450842d072ddbbf9869bfb6a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 31 Jan 2023 16:42:33 -0700 Subject: [PATCH 0691/2067] Add tests to test list for Gross unrepresented land use change --- cime_config/testdefs/testlist_clm.xml | 25 +++++++++++++++++++++++-- 1 file changed, 23 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 8906c6c4bd..6cfe703c6d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -317,11 +317,32 @@ - + + + + + + + + + + + + - + + + + + + + + + + + From 29f9b5971fb080318aabd0a78f132764aa2ef48d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 31 Jan 2023 16:49:28 -0700 Subject: [PATCH 0692/2067] Add some comments and fix directory name --- .../testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands | 1 + .../testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm | 2 ++ .../clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods | 2 +- 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands index 4e10e7086a..972cd25f5c 100755 --- a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands @@ -1,2 +1,3 @@ ./xmlchange RUN_STARTDATE=1990-12-25 +# Ignore warnings because we are using crop, but starting from a different date than the initial conditions were for ./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm index 6a666f2684..efb3212d5f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/user_nl_clm @@ -1,3 +1,5 @@ + ! Specify a dataset that has non-zero Gross Unrepresented Land Use change fields on it + ! And turn it on flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_0.9x1.25_hist_78pfts_CMIP6_simyr1700-2021_c220825.nc' fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr1700_c220825.nc' do_grossunrep = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods index 24f76fbb9f..b10682f861 100644 --- a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods @@ -1,2 +1,2 @@ -../../f09_dec1990Start_GU_LULCC +../f09_dec1990Start_GU_LULCC ../monthly From 47d61a61ba7d264336a5d0a16dea355a5002ba7f Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 1 Feb 2023 08:18:47 -0700 Subject: [PATCH 0693/2067] add PRT2 test to expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 3affa5be65..6ddfea3437 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -88,5 +88,22 @@ + + + PEND + #1045 + + + + + + FAIL + FATES#983 + This job should time out on izumi, seems to be hanging on history output. + + + + + From 8f6c03e8e4a54b9f90faba791684489a3fb432ce Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 1 Feb 2023 11:51:18 -0700 Subject: [PATCH 0694/2067] add back space --- tools/site_and_regional/subset_data | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/site_and_regional/subset_data b/tools/site_and_regional/subset_data index 6477b3034d..d19525c97d 100755 --- a/tools/site_and_regional/subset_data +++ b/tools/site_and_regional/subset_data @@ -9,6 +9,7 @@ For full instructions on how to run the code and different options, please check python/ctsm/subset_data.py file. This script extracts domain files, surface dataset, and DATM files at either a single point or a region using the global dataset. + To run this script the following packages are required: - numpy - xarray From 48a38b6a323d4e53cfe528c97c67ade1f716b3f0 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 1 Feb 2023 13:56:02 -0700 Subject: [PATCH 0695/2067] update changelog --- doc/ChangeLog | 116 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 117 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index b1f5fdf975..5a90817673 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,120 @@ =============================================================== +Tag name: ctsm5.1.dev117 +Originator(s): afoster (Adrianna Foster) +Date: Wed Feb 1 13:36:27 MST 2023 +One-line Summary: Updates to facilitate running FATES at NEON sites + +Purpose and description of changes +---------------------------------- + +Small updates to facilitate creation, modification, and +use of FATES-usable (i.e. 16-PFT) NEON surface data files and +user-mods for FATES NEON cases. + +Updated neon_surf_wrapper.py and modify_singlept_site_neon.py to include a +--16pft argument that will create and/or modify the 16-PFT versions of the +surface datasets, as well as a --mixed flag to the neon_surf_wrapper.py +which tells subset_data to not overwrite the surfae dataset to be just 100% +one PFT. + +Also corrects lat-lon being used for ONAQ NEON site and updates the surface +datasets for all NEON sites. + +Also adds a check to ensure that fire emission (-fire_emis) is not on if FATES +is being run. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): +- Partially addresses ESCOMP/CTSM#1609(Get FATES working for NEON) + +Known bugs introduced in this tag (include issue #): +#1949 - Duplication problems in user_mods + +Known bugs found since the previous tag (include issue #): +#1948 - FATES and 78PFT surface datasets +FATES#983 - PRT2 test failing on izumi + + +Notes of particular relevance for users +--------------------------------------- + +Changes to the datasets (e.g., parameter, surface or initial files): +updated surface datasets for all NEON sites for big-leaf (78-PFT) and FATES (16-PFT) + + +Notes of particular relevance for developers: +--------------------------------------------- + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +Files changed in cime_config/usermods_dirs/NEON for big-leaf CLM must also +be changed in similar files in cime_config/usermods_dirs/NEON/FATES, as these are +currently duplicated. This duplication should be fixed at a later date. + +Changes to tests or testing: +Added a test in bld/unit_testers/build-namelist_test.pl to check that FATES and +fire emission cannot be on at the same time. + + +Testing summary: +---------------- + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + + +Answer changes +-------------- + +Changes answers relative to baseline: + +Only for NEON sites. + + + Summarize any changes to answers, i.e., + - what code configurations: All configurations at NEON sites + - what platforms/compilers: All platforms when running NEON sites + - nature of change: updated surface datasets + + +Other details +------------- +#1933 - Update neon_sites_dompft.csv +#1932 - NEON FATES capabilities + + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev116 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Thu Jan 26 02:17:27 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 3042b38a2a..21f9dd70b9 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev117 afoster 02/01/2023 Updates to facilitate running FATES at NEON sites ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files ctsm5.1.dev115 rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics ctsm5.1.dev114 multiple 11/19/2022 Some NEON updates fixing AG sites, update MOSART, small fixes From eb29c80c1274d8307d79968b2a6a91df475c5820 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 1 Feb 2023 13:56:54 -0700 Subject: [PATCH 0696/2067] update changelog date --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5a90817673..1cc7768243 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev117 Originator(s): afoster (Adrianna Foster) -Date: Wed Feb 1 13:36:27 MST 2023 +Date: Wed Feb 1 13:56:41 MST 2023 One-line Summary: Updates to facilitate running FATES at NEON sites Purpose and description of changes From 0e83df379ffd68600514cc51a1358e51f602f30c Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 2 Feb 2023 10:34:35 -0700 Subject: [PATCH 0697/2067] update changelog date --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 1cc7768243..ec6ca43ce2 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev117 Originator(s): afoster (Adrianna Foster) -Date: Wed Feb 1 13:56:41 MST 2023 +Date: Thu Feb 2 10:34:23 MST 2023 One-line Summary: Updates to facilitate running FATES at NEON sites Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index 21f9dd70b9..ac424326b0 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev117 afoster 02/01/2023 Updates to facilitate running FATES at NEON sites + ctsm5.1.dev117 afoster 02/02/2023 Updates to facilitate running FATES at NEON sites ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files ctsm5.1.dev115 rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics ctsm5.1.dev114 multiple 11/19/2022 Some NEON updates fixing AG sites, update MOSART, small fixes From c96735b53ae9816e2de88b667f588a70b69cbeed Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 2 Feb 2023 16:25:56 -0700 Subject: [PATCH 0698/2067] Updating new tests, mainly with longer walltimes --- cime_config/testdefs/testlist_clm.xml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 6cfe703c6d..4dfddb4a11 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -320,7 +320,7 @@ - + @@ -331,17 +331,17 @@ - + - + - + From 55f0af22d41b3e2c2318589ea625c0c5f28a6b84 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 3 Feb 2023 17:41:47 -0500 Subject: [PATCH 0699/2067] Incremental progress towareds converting fates-clm carbon accounting to using native calls and not EDBGCMod. --- src/biogeochem/CNBalanceCheckMod.F90 | 81 ++++++++----- src/biogeochem/CNCStateUpdate1Mod.F90 | 110 ++++++++--------- src/biogeochem/CNDriverMod.F90 | 19 +-- src/biogeochem/CNVegetationFacade.F90 | 43 ++++--- src/biogeophys/WaterDiagnosticType.F90 | 17 +-- src/main/clm_driver.F90 | 160 ++++++++++++------------- src/main/filterMod.F90 | 52 +++++++- src/utils/clmfates_interfaceMod.F90 | 92 ++++++++------ 8 files changed, 335 insertions(+), 239 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index bbeed11e46..a681ee5c4e 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -159,7 +159,7 @@ end subroutine BeginCNGridcellBalance !----------------------------------------------------------------------- subroutine BeginCNColumnBalance(this, bounds, num_soilc, filter_soilc, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) + cnveg_carbonstate_inst, cnveg_nitrogenstate_inst,soilbiogeochem_carbonstate_inst) ! ! !DESCRIPTION: ! Calculate beginning column-level carbon/nitrogen balance, for mass conservation check @@ -175,6 +175,7 @@ subroutine BeginCNColumnBalance(this, bounds, num_soilc, filter_soilc, & integer , intent(in) :: filter_soilc(:) ! filter for soil columns type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst + type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst ! ! !LOCAL VARIABLES: integer :: fc,c @@ -189,8 +190,16 @@ subroutine BeginCNColumnBalance(this, bounds, num_soilc, filter_soilc, & do fc = 1,num_soilc c = filter_soilc(fc) - col_begcb(c) = totcolc(c) - col_begnb(c) = totcoln(c) + + if( is_fates(c) ) then + col_begcb(c) = soilbiogeochem_carbonstate_inst%totmicc_col(c) + & + soilbiogeochem_carbonstate_inst%totlitc_col(c) + & + soilbiogeochem_carbonstate_inst%totsomc_col(c) + & + soilbiogeochem_carbonstate_inst%ctrunc_col(c) + else + col_begcb(c) = totcolc(c) + col_begnb(c) = totcoln(c) + end if end do end associate @@ -199,11 +208,13 @@ end subroutine BeginCNColumnBalance !----------------------------------------------------------------------- subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & - soilbiogeochem_carbonflux_inst, cnveg_carbonflux_inst, & - cnveg_carbonstate_inst, c_products_inst) + soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, c_products_inst, & + clm_fates) ! ! !USES: use subgridAveMod, only: c2g + use clm_varpar , only: nlevdecomp ! ! !DESCRIPTION: ! Perform carbon mass conservation check for column and patch @@ -218,13 +229,18 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns type(soilbiogeochem_carbonflux_type) , intent(in) :: soilbiogeochem_carbonflux_inst + type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst type(cn_products_type) , intent(in) :: c_products_inst + type(hlm_fates_interface_type) , intent(inout) :: clm_fates + ! ! !LOCAL VARIABLES: - integer :: c, g, err_index ! indices + integer :: c, g, err_index ! indices + integer :: s ! fates site index (follows c) integer :: fc ! lake filter indices + integer :: ic ! index of the current clump logical :: err_found ! error flag real(r8) :: dt ! radiation time step (seconds) real(r8) :: col_cinputs, grc_cinputs @@ -235,8 +251,6 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & real(r8) :: hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg) real(r8) :: dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) - !real(r8) :: totcol_c ! Total column carbon, including veg and soil (kgC) - !----------------------------------------------------------------------- associate( & @@ -265,11 +279,39 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! set time steps dt = get_step_size_real() + ! clump index + ic = bounds%clump_index + err_found = .false. do fc = 1,num_soilc c = filter_soilc(fc) - if (use_cn) then + if( is_fates(c) ) then + + ! calculate the total column-level carbon storage, for mass conservation check + col_endcb(c) = soilbiogeochem_carbonstate_inst%totmicc_col(c) + & + soilbiogeochem_carbonstate_inst%totlitc_col(c) + & + soilbiogeochem_carbonstate_inst%totsomc_col(c) + & + soilbiogeochem_carbonstate_inst%ctrunc_col(c) + + ! calculate total column-level inputs (litter fluxes) [g/m2/s] + s = clm_fates%f2hmap(ic)%hsites(c) + col_cinputs = sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & + clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & + clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * & + clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + ! calculate total column-level outputs + ! fates has already exported burn losses and fluxes to the atm + ! So they are irrelevant here + ! (gC/m2/s) total heterotrophic respiration + col_coutputs = soilbiogeochem_carbonflux_inst%hr_col(c) + + + else + ! calculate the total column-level carbon storage, for mass conservation check col_endcb(c) = totcolc(c) @@ -281,27 +323,6 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + & col_xsmrpool_to_atm(c) - elseif(use_fates) then - - ! calculate the total column-level carbon storage, for mass conservation check - col_endcb(c) = soilbiogeochem_totmicc_col(c) + & - soilbiogeochem_totlitc_col(c) + & - soilbiogeochem_totsomc_col(c) + & - soilbiogeochem_ctrunc_col(c) - - ! calculate total column-level inputs (litter fluxes) - col_cinputs = sum(this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & - this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - sum(this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & - this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - sum(this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * & - this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) - - ! calculate total column-level outputs - ! fates has already exported burn losses and fluxes to the atm - ! So they are irrelevant here - col_coutputs = er(c) - end if diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 843754f3cd..2d88977b5f 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -25,6 +25,8 @@ module CNCStateUpdate1Mod use PatchType , only : patch use clm_varctl , only : use_fates, use_cn, iulog, use_fates_sp use CNSharedParamsMod , only : use_matrixcn + use CLMFatesInterfaceMod , only : hlm_fates_interface_type + ! implicit none private @@ -123,8 +125,6 @@ subroutine CStateUpdate0(num_soilp, filter_soilp, & ! set time steps dt = get_step_size_real() - - ! gross photosynthesis fluxes do fp = 1,num_soilp p = filter_soilp(fp) @@ -140,7 +140,8 @@ end subroutine CStateUpdate0 !----------------------------------------------------------------------- subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm) + soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & + clm_fates) ! ! !DESCRIPTION: ! On the radiation time step, update all the prognostic carbon state @@ -157,6 +158,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst logical , intent(in) :: dribble_crophrv_xsmrpool_2atm + type(hlm_fates_interface_type) , intent(inout) :: clm_fates ! ! !LOCAL VARIABLES: integer :: c,p,j,k,l,i ! indices @@ -186,12 +188,23 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & dt = get_step_size_real() ! Below is the input into the soil biogeochemistry model - - ! plant to litter fluxes - if (.not. use_fates) then - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + + fc_loop: do fc = 1,num_soilc + c = filter_soilc(fc) + + fates_if: if( col%is_fates(c) ) then + + ! If this is a fates column, then we ask fates for the + ! litter fluxes, the following routine simply copies + ! prepared litter c flux boundary conditions into + ! cf_soil%decomp_cpools_sourcesink_col + + call clm_fates%UpdateCLitterfluxes(bounds_clump,cf_soil,c) + + else + + do j = 1,nlevdecomp + ! ! State update without the matrix solution ! @@ -206,35 +219,40 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! terms have been moved to CStateUpdateDynPatch. I think this is zeroed every ! time step, but to be safe, I'm explicitly setting it to zero here. cf_soil%decomp_cpools_sourcesink_col(c,j,i_cwd) = 0._r8 - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in SoilMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! + ! + ! For the matrix solution the actual state update comes after the matrix + ! multiply in SoilMatrix, but the matrix needs to be setup with + ! the equivalent of above. Those changes can be here or in the + ! native subroutines dealing with that field + ! else ! phenology and dynamic land cover fluxes end if end do - end do - else if ( .not. use_fates_sp ) then !use_fates - ! here add all fates litterfall and CWD breakdown to litter fluxes + + end if fates_if + + end do fc_loop + + + ! litter and SOM HR fluxes + do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) - ! TODO(wjs, 2017-01-02) Should some portion or all of the following fluxes - ! be moved to the updates in CStateUpdateDynPatch? - do i = i_litr_min, i_litr_max - cf_soil%decomp_cpools_sourcesink_col(c,j,i) = & - cf_soil%FATES_c_to_litr_c_col(c,j,i) * dt - end do + ! + ! State update without the matrix solution + ! + if (.not. use_soil_matrixcn) then + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & + - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt + end if !not use_soil_matrixcn end do end do - endif - - if ( .not. use_fates_sp ) then !use_fates - ! litter and SOM HR fluxes - do k = 1, ndecomp_cascade_transitions + end do + do k = 1, ndecomp_cascade_transitions + if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions do j = 1,nlevdecomp do fc = 1,num_soilc c = filter_soilc(fc) @@ -242,34 +260,17 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! State update without the matrix solution ! if (.not. use_soil_matrixcn) then - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) = & - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_donor_pool(k)) & - - ( cf_soil%decomp_cascade_hr_vr_col(c,j,k) + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)) *dt - end if !not use_soil_matrixcn - end do - end do - end do - do k = 1, ndecomp_cascade_transitions - if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) - ! - ! State update without the matrix solution - ! - if (.not. use_soil_matrixcn) then - cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & + cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & cf_soil%decomp_cpools_sourcesink_col(c,j,cascade_receiver_pool(k)) & + cf_soil%decomp_cascade_ctransfer_vr_col(c,j,k)*dt - end if !not use_soil_matrixcn - end do + end if !not use_soil_matrixcn end do - end if - end do - end if + end do + end if + end do - if (.not. use_fates) then -ptch: do fp = 1,num_soilp + ! This filter omits FATES patches + soilpatch_loop: do fp = 1,num_soilp p = filter_soilp(fp) c = patch%column(p) @@ -674,8 +675,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end if end if - end do ptch ! end of patch loop - end if ! end of NOT fates + end do soilpatch_loop ! end of patch loop end associate diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index fee8752d2c..2fc800955f 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -43,7 +43,7 @@ module CNDriverMod use ActiveLayerMod , only : active_layer_type use SoilWaterRetentionCurveMod , only : soil_water_retention_curve_type use CLMFatesInterfaceMod , only : hlm_fates_interface_type - use CropReprPoolsMod , only : nrepr + use CropReprPoolsMod , only : nrepr ! ! !PUBLIC TYPES: implicit none @@ -150,10 +150,10 @@ subroutine CNDriverNoLeaching(bounds, ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of veg patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for veg patches integer , intent(out) :: num_actfirep ! number of soil patches on fire in filter integer , intent(out) :: filter_actfirep(:) ! filter for soil patches on fire integer , intent(out) :: num_actfirec ! number of soil columns on fire in filter @@ -627,16 +627,19 @@ subroutine CNDriverNoLeaching(bounds, ! Update all prognostic carbon state variables (except for gap-phase mortality and fire fluxes) call CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm) + soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & + clm_fates) if ( use_c13 ) then call CStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm) + c13_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & + clm_fates) end if if ( use_c14 ) then call CStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm) + c14_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & + clm_fates) end if ! Update all prognostic nitrogen state variables (except for gap-phase mortality and fire fluxes) diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index f7457a505f..8ab4bdf4c3 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -879,8 +879,8 @@ end subroutine InitGridcellBalance !----------------------------------------------------------------------- subroutine EcosystemDynamicsPreDrainage(this, bounds, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & num_actfirec, filter_actfirec, & num_actfirep, filter_actfirep, & num_pcropp, filter_pcropp, & @@ -900,9 +900,9 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & nutrient_competition_method, fireemis_inst) ! ! !DESCRIPTION: - ! Do the main science for CN vegetation that needs to be done before hydrology-drainage + ! Do the main science for biogeochemistry that needs to be done before hydrology-drainage ! - ! Should only be called if use_cn is true + ! Can be called for either use_cn or use_fates. Will skip most vegetation patch calls for the latter ! ! !USES: @@ -910,10 +910,10 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & ! !ARGUMENTS: class(cn_vegetation_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for veg patches integer , intent(out) :: num_actfirec ! number of soil columns on fire in filter integer , intent(out) :: filter_actfirec(:)! filter for soil columns on fire integer , intent(out) :: num_actfirep ! number of soil patches on fire in filter @@ -962,8 +962,8 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & call crop_inst%CropIncrementYear(num_pcropp, filter_pcropp) call CNDriverNoLeaching(bounds, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & num_pcropp, filter_pcropp, & num_soilnopcropp, filter_soilnopcropp, & num_actfirec, filter_actfirec, & @@ -990,12 +990,12 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & nutrient_competition_method, this%cnfire_method, this%dribble_crophrv_xsmrpool_2atm) ! fire carbon emissions - call CNFireEmisUpdate(bounds, num_soilp, filter_soilp, & + call CNFireEmisUpdate(bounds, num_bgc_vegp, filter_bgc_vegp, & this%cnveg_carbonflux_inst, this%cnveg_carbonstate_inst, fireemis_inst ) call CNAnnualUpdate(bounds, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & this%cnveg_state_inst, this%cnveg_carbonflux_inst) end subroutine EcosystemDynamicsPreDrainage @@ -1087,7 +1087,7 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! Call to all CN summary routines - call CNDriverSummarizeStates(bounds, & + call CNDriverSummarizeStates(bounds, & num_allc, filter_allc, & num_soilc, filter_soilc, & num_soilp, filter_soilp, & @@ -1100,7 +1100,7 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & c14_soilbiogeochem_carbonstate_inst, & soilbiogeochem_nitrogenstate_inst) - call CNDriverSummarizeFluxes(bounds, & + call CNDriverSummarizeFluxes(bounds, & num_soilc, filter_soilc, & num_soilp, filter_soilp, & this%cnveg_carbonflux_inst, & @@ -1131,7 +1131,11 @@ end subroutine EcosystemDynamicsPostDrainage !----------------------------------------------------------------------- subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenflux_inst, & - atm2lnd_inst) + soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst, & + atm2lnd_inst, clm_fates) + + + ! ! !DESCRIPTION: ! Check the carbon and nitrogen balance @@ -1148,7 +1152,10 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & integer , intent(in) :: filter_soilc(:) ! filter for soil columns type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst + type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonstate_inst + type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst type(atm2lnd_type) , intent(in) :: atm2lnd_inst + type(hlm_fates_interface_type) , intent(inout) :: clm_fates ! ! !LOCAL VARIABLES: integer :: DA_nstep ! time step number @@ -1168,9 +1175,11 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & call this%cn_balance_inst%CBalanceCheck( & bounds, num_soilc, filter_soilc, & soilbiogeochem_carbonflux_inst, & + soilbiogeochem_carbonstate_inst, & this%cnveg_carbonflux_inst, & this%cnveg_carbonstate_inst, & - this%c_products_inst) + this%c_products_inst, & + clm_fates) call this%cn_balance_inst%NBalanceCheck( & bounds, num_soilc, filter_soilc, & diff --git a/src/biogeophys/WaterDiagnosticType.F90 b/src/biogeophys/WaterDiagnosticType.F90 index 7fa76b42b0..57be0e62af 100644 --- a/src/biogeophys/WaterDiagnosticType.F90 +++ b/src/biogeophys/WaterDiagnosticType.F90 @@ -164,13 +164,7 @@ subroutine InitHistory(this, bounds) begc = bounds%begc; endc= bounds%endc begg = bounds%begg; endg= bounds%endg - this%h2ocan_patch(begp:endp) = spval - call hist_addfld1d ( & - fname=this%info%fname('H2OCAN'), & - units='mm', & - avgflag='A', & - long_name=this%info%lname('intercepted water'), & - ptr_patch=this%h2ocan_patch) + this%h2osoi_liqice_10cm_col(begc:endc) = spval call hist_addfld1d ( & @@ -205,8 +199,15 @@ subroutine InitHistory(this, bounds) long_name=this%info%lname('2m specific humidity'), & ptr_patch=this%q_ref2m_patch) + this%h2ocan_patch(begp:endp) = spval + call hist_addfld1d ( & + fname=this%info%fname('H2OCAN'), & + units='mm', & + avgflag='A', & + long_name=this%info%lname('intercepted water'), & + ptr_patch=this%h2ocan_patch) - + ! Snow properties - these will be vertically averaged over the snow profile this%snowliq_col(begc:endc) = spval diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index ae178b226c..b01034dc2a 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -997,33 +997,34 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! - CNDV defined: prognostic biogeography; else prescribed ! - crop model: crop algorithms called from within CNDriver - if (use_cn) then - call t_startf('ecosysdyn') - call bgc_vegetation_inst%EcosystemDynamicsPreDrainage(bounds_clump, & - filter(nc)%num_soilc, filter(nc)%soilc, & - filter(nc)%num_soilp, filter(nc)%soilp, & - filter(nc)%num_actfirec, filter(nc)%actfirec, & - filter(nc)%num_actfirep, filter(nc)%actfirep, & - filter(nc)%num_pcropp, filter(nc)%pcropp, & - filter(nc)%num_soilnopcropp, filter(nc)%soilnopcropp, & - filter(nc)%num_exposedvegp, filter(nc)%exposedvegp, & - filter(nc)%num_noexposedvegp, filter(nc)%noexposedvegp, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - soilbiogeochem_state_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - active_layer_inst, clm_fates, & - atm2lnd_inst, water_inst%waterstatebulk_inst, & - water_inst%waterdiagnosticbulk_inst, water_inst%waterfluxbulk_inst, & - water_inst%wateratm2lndbulk_inst, canopystate_inst, soilstate_inst, temperature_inst, & - soil_water_retention_curve, crop_inst, ch4_inst, & - photosyns_inst, saturated_excess_runoff_inst, energyflux_inst, & - nutrient_competition_method, fireemis_inst) - - call t_stopf('ecosysdyn') - - end if + ! Filter bgc_soilc operates on all non-sp soil columns + ! Filter bgc_vegp operates on all non-fates, non-sp patches (use_cn) on soil + + call t_startf('ecosysdyn') + call bgc_vegetation_inst%EcosystemDynamicsPreDrainage(bounds_clump, & + filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & + filter(nc)%num_actfirec, filter(nc)%actfirec, & + filter(nc)%num_actfirep, filter(nc)%actfirep, & + filter(nc)%num_pcropp, filter(nc)%pcropp, & + filter(nc)%num_soilnopcropp, filter(nc)%soilnopcropp, & + filter(nc)%num_exposedvegp, filter(nc)%exposedvegp, & + filter(nc)%num_noexposedvegp, filter(nc)%noexposedvegp, & + soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & + soilbiogeochem_state_inst, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & + active_layer_inst, clm_fates, & + atm2lnd_inst, water_inst%waterstatebulk_inst, & + water_inst%waterdiagnosticbulk_inst, water_inst%waterfluxbulk_inst, & + water_inst%wateratm2lndbulk_inst, canopystate_inst, soilstate_inst, temperature_inst, & + soil_water_retention_curve, crop_inst, ch4_inst, & + photosyns_inst, saturated_excess_runoff_inst, energyflux_inst, & + nutrient_competition_method, fireemis_inst) + + call t_stopf('ecosysdyn') + ! Prescribed biogeography - prescribed canopy structure, some prognostic carbon fluxes @@ -1077,27 +1078,22 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_stopf('hydro2_drainage') - if (use_cn) then - - call t_startf('EcosysDynPostDrainage') - call bgc_vegetation_inst%EcosystemDynamicsPostDrainage(bounds_clump, & - filter(nc)%num_allc, filter(nc)%allc, & - filter(nc)%num_soilc, filter(nc)%soilc, & - filter(nc)%num_soilp, filter(nc)%soilp, & - filter(nc)%num_actfirec, filter(nc)%actfirec, & - filter(nc)%num_actfirep, filter(nc)%actfirep, & - doalb, crop_inst, & - soilstate_inst, soilbiogeochem_state_inst, & - water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & - water_inst%waterfluxbulk_inst, frictionvel_inst, canopystate_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) - call t_stopf('EcosysDynPostDrainage') - - end if - + call t_startf('EcosysDynPostDrainage') + call bgc_vegetation_inst%EcosystemDynamicsPostDrainage(bounds_clump, & + filter(nc)%num_allc, filter(nc)%allc, & + filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & + filter(nc)%num_actfirec, filter(nc)%actfirec, & + filter(nc)%num_actfirep, filter(nc)%actfirep, & + doalb, crop_inst, & + soilstate_inst, soilbiogeochem_state_inst, & + water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & + water_inst%waterfluxbulk_inst, frictionvel_inst, canopystate_inst, & + soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) + call t_stopf('EcosysDynPostDrainage') if ( use_fates) then @@ -1107,31 +1103,32 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! for leaf photosynthetic acclimation temperature. These ! moving averages are updated here call clm_fates%WrapUpdateFatesRmean(nc,temperature_inst) - - call EDBGCDyn(bounds_clump, & - filter(nc)%num_soilc, filter(nc)%soilc, & - filter(nc)%num_soilp, filter(nc)%soilp, & - filter(nc)%num_pcropp, filter(nc)%pcropp, doalb, & - bgc_vegetation_inst%cnveg_carbonflux_inst, & - bgc_vegetation_inst%cnveg_carbonstate_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - soilbiogeochem_state_inst, clm_fates, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & - c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, & - active_layer_inst, atm2lnd_inst, water_inst%waterfluxbulk_inst, & - canopystate_inst, soilstate_inst, temperature_inst, crop_inst, ch4_inst) - - if ( decomp_method /= no_soil_decomp )then - call EDBGCDynSummary(bounds_clump, & - filter(nc)%num_soilc, filter(nc)%soilc, & - filter(nc)%num_soilp, filter(nc)%soilp, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - nc) - end if + end if + + ! call EDBGCDyn(bounds_clump, & + ! filter(nc)%num_soilc, filter(nc)%soilc, & + ! filter(nc)%num_soilp, filter(nc)%soilp, & + ! filter(nc)%num_pcropp, filter(nc)%pcropp, doalb, & + ! bgc_vegetation_inst%cnveg_carbonflux_inst, & + ! bgc_vegetation_inst%cnveg_carbonstate_inst, & + ! soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + ! soilbiogeochem_state_inst, clm_fates, & + ! soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & + ! c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & + ! c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, & + ! active_layer_inst, atm2lnd_inst, water_inst%waterfluxbulk_inst, & + ! canopystate_inst, soilstate_inst, temperature_inst, crop_inst, ch4_inst) + + !if ( decomp_method /= no_soil_decomp )then + ! call EDBGCDynSummary(bounds_clump, & + ! filter(nc)%num_soilc, filter(nc)%soilc, & + ! filter(nc)%num_soilp, filter(nc)%soilp, & + ! soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + ! c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & + ! c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & + ! soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & + ! nc) + ! end if call clm_fates%wrap_update_hifrq_hist(bounds_clump, & soilbiogeochem_carbonflux_inst, & @@ -1176,14 +1173,15 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Check the carbon and nitrogen balance ! ============================================================================ - if (use_cn) then - call t_startf('cnbalchk') - call bgc_vegetation_inst%BalanceCheck( & - bounds_clump, filter(nc)%num_soilc, filter(nc)%soilc, & - soilbiogeochem_carbonflux_inst, & - soilbiogeochem_nitrogenflux_inst, atm2lnd_inst ) - call t_stopf('cnbalchk') - end if + call t_startf('cnbalchk') + call bgc_vegetation_inst%BalanceCheck( & + bounds_clump, filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + soilbiogeochem_carbonflux_inst, & + soilbiogeochem_nitrogenflux_inst, & + soilbiogeochem_carbonstate_inst, & + soilbiogeochem_nitrogenstate_inst, & + atm2lnd_inst, clm_fates ) + call t_stopf('cnbalchk') ! Calculation of methane fluxes diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 526cb7c8f3..37c22cc85b 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -49,6 +49,15 @@ module filterMod integer, pointer :: nolakec(:) ! non-lake filter (columns) integer :: num_nolakec ! number of columns in non-lake filter + integer, pointer :: bgc_soilc(:) ! soil with biogeochemistry active, negates + ! SP type runs, could be CN, FATES or CROP + integer :: num_bgc_soilc + + integer, pointer :: bgc_vegp(:) ! patches with vegetation biochemistry active, negates + ! SP type runs, could be CN or Crop (NOT FATES) + integer :: num_bgc_vegp + + integer, pointer :: soilc(:) ! soil filter (columns) integer :: num_soilc ! number of columns in soil filter integer, pointer :: soilp(:) ! soil filter (patches) @@ -211,6 +220,9 @@ subroutine allocFiltersOneGroup(this_filter) allocate(this_filter(nc)%soilc(bounds%endc-bounds%begc+1)) allocate(this_filter(nc)%soilp(bounds%endp-bounds%begp+1)) + allocate(this_filter(nc)%bgc_soilc(bounds%endc-bounds%begc+1)) + allocate(this_filter(nc)%bgc_vegp(bounds%endp-bounds%begp+1)) + allocate(this_filter(nc)%snowc(bounds%endc-bounds%begc+1)) allocate(this_filter(nc)%nosnowc(bounds%endc-bounds%begc+1)) @@ -380,6 +392,39 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio this_filter(nc)%num_nolakep = fnl this_filter(nc)%num_nolakeurbanp = fnlu + + ! Create the soil bgc filter, all non-sp columns for vegetation + fs = 0 + if( use_cn .or. (use_fates .and. .not.use_fates_sp))then + do c = bounds%begc,bounds%endc + if (col%active(c) .or. include_inactive) then + l =col%landunit(c) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + fs = fs + 1 + this_filter(nc)%bgc_soilc(fs) = c + end if + end if + end do + end if + this_filter(nc)%num_bgc_soilc = fs + + ! Create a filter at patch-level for vegetation biochemistry + ! all non-SP and non-fates patches on soil + fs = 0 + if(use_cn)then + do p = bounds%begp,bounds%endp + if (patch%active(p) .or. include_inactive) then + l =patch%landunit(p) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + fs = fs + 1 + this_filter(nc)%bgc_vegp(fs) = p + end if + end if + end do + end if + this_filter(nc)%num_bgc_vegp = fs + + ! Create soil filter at column-level fs = 0 @@ -393,8 +438,12 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio end if end do this_filter(nc)%num_soilc = fs - ! Create soil filter at patch-level + + + + + ! Create soil filter at patch-level fs = 0 do p = bounds%begp,bounds%endp if (patch%active(p) .or. include_inactive) then @@ -405,6 +454,7 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio end if end if end do + this_filter(nc)%num_soilp = fs ! Create column-level hydrology filter (soil and Urban pervious road cols) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c169d710ef..f225a3255b 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -224,7 +224,7 @@ module CLMFatesInterfaceMod procedure, public :: wrap_hydraulics_drive procedure, public :: WrapUpdateFatesRmean procedure, public :: wrap_WoodProducts - + procedure, public :: UpdateCLitterFluxes end type hlm_fates_interface_type ! hlm_bounds_to_fates_bounds is not currently called outside the interface. @@ -1033,43 +1033,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & enddo - ! --------------------------------------------------------------------------------- - ! Part III: Process FATES output into the dimensions and structures that are part - ! of the HLMs API. (column, depth, and litter fractions) - ! --------------------------------------------------------------------------------- - - if ( decomp_method /= no_soil_decomp )then - do s = 1, this%fates(nc)%nsites - c = this%f2hmap(nc)%fcolumn(s) - - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lab_c_col(c,1:nlevdecomp) = 0.0_r8 - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_cel_c_col(c,1:nlevdecomp) = 0.0_r8 - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lig_c_col(c,1:nlevdecomp) = 0.0_r8 - - nld_si = this%fates(nc)%bc_in(s)%nlevdecomp - - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lab_c_col(c,1:nld_si) = & - this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nld_si) - - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_cel_c_col(c,1:nld_si) = & - this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nld_si) - - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lig_c_col(c,1:nld_si) = & - this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nld_si) - - ! Copy last 3 variables to an array of litter pools for use in do loops - ! and repeat copy in soilbiogeochem/SoilBiogeochemCarbonFluxType.F90. - ! Keep the three originals to avoid backwards compatibility issues with - ! restart files. - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_c_col(c,1:nld_si,1) = & - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lab_c_col(c,1:nld_si) - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_c_col(c,1:nld_si,2) = & - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_cel_c_col(c,1:nld_si) - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_c_col(c,1:nld_si,3) = & - soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lig_c_col(c,1:nld_si) - - end do - end if ! --------------------------------------------------------------------------------- @@ -1102,8 +1065,59 @@ subroutine dynamics_driv(this, nc, bounds_clump, & return end subroutine dynamics_driv - ! ------------------------------------------------------------------------------------ + ! =============================================================================== + + subroutine UpdateCLitterFluxes(this,bounds_clump,soilbiogeochem_carbonflux_inst,c) + implicit none + class(hlm_fates_interface_type), intent(inout) :: this + type(bounds_type) , intent(in) :: bounds_clump + type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst + integer , intent(in) :: c + + integer :: s ! site index + integer :: nc ! clump index + real(r8) :: dtime + + + dtime = get_step_size_real() + nc = bounds_clump%clump_index + s = this%f2hmap(nc)%hsites(c) + + associate(cf_soil => soilbiogeochem_carbonflux_inst) + + if ( .not. use_fates_sp ) then + cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_met_lit) = & + cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_met_lit) + & + this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * dtime + cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_cel_lit) = & + cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_cel_lit) + & + this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp)* dtime + cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_lig_lit) = & + cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_lig_lit) + & + this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * dtime + + else + ! In SP mode their is no mass flux between the two + cf_soil%decomp_cpools_sourcesink(c,:) = 0._r8 + end if + + ! This is a diagnostic for carbon accounting (NOT IN CLM, ONLY ELM) + !col_cf%litfall(c) = & + ! sum(this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & + ! this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + ! sum(this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & + ! this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + ! sum(this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * ^ + ! this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + end associate + + return + end subroutine UpdateCLitterFluxes + + ! =================================================================================== + subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & waterdiagnosticbulk_inst, canopystate_inst, & soilbiogeochem_carbonflux_inst, is_initing_from_restart) From 07e8462cba9351cf4cc63968326b653509bc24dc Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 3 Feb 2023 16:25:26 -0700 Subject: [PATCH 0700/2067] Rm override allow_ideal_and_include_non_veg & corresponding restriction --- python/ctsm/modify_input_files/fsurdat_modifier.py | 11 ----------- python/ctsm/test/test_sys_fsurdat_modifier.py | 1 - 2 files changed, 12 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 75fbbdba12..f5543a9506 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -57,13 +57,6 @@ def fsurdat_modifier_arg_process(): type=str, help="The output surface dataset with the modifications. ", ) - parser.add_argument( - "--allow_ideal_and_include_non_veg", - required=False, - default=False, - action="store_true", - help="Allow both idealized and include_nonveg to be on at the same time. ", - ) parser.add_argument( "--allow_dom_pft_and_idealized", required=False, @@ -379,7 +372,6 @@ def read_cfg_option_control( config, section, cfg_path, - allow_ideal_and_include_non_veg=False, allow_dom_pft_and_idealized=False, ): """Read the option control section""" @@ -445,8 +437,6 @@ def read_cfg_option_control( logger.info("dom_pft option is off") if dom_pft is not None and idealized and not allow_dom_pft_and_idealized: abort("idealized AND dom_pft can NOT both be on, pick one or the other") - if include_nonveg and idealized and not allow_ideal_and_include_non_veg: - abort("idealized AND include_nonveg can NOT both be on, pick one or the other") if process_subgrid and idealized: abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") @@ -578,7 +568,6 @@ def fsurdat_modifier(parser): config, section, cfg_path, - parser.allow_ideal_and_include_non_veg, parser.allow_dom_pft_and_idealized, ) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index cee7a51d36..b4598fae20 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -374,7 +374,6 @@ def test_allInfo(self): sys.argv = [ "fsurdat_modifier", self._cfg_file_path, - "--allow_ideal_and_include_non_veg", "--allow_dom_pft_and_idealized", ] parser = fsurdat_modifier_arg_process() From 662bf9295db86424df4dc29e70bc2057b24339d1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 3 Feb 2023 17:06:02 -0700 Subject: [PATCH 0701/2067] First draft of ChangeLog --- doc/ChangeLog | 79 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 80 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ec6ca43ce2..0804cd8d4a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,83 @@ =============================================================== +Tag name: ctsm5.1.dev118 +Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310) +Date: Fri Feb 3 16:49:44 MST 2023 +One-line Summary: Use conda environment rather than ncar_pylib with the fsurdat_modifier system test + +Purpose and description of changes +---------------------------------- + + ncar_pylib is going away soon. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + The fsurdat_modifier system test that we're discussing in this tag and + pull request (PR #1798) + FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel + stopped working when I updated the PR to dev117. + The test worked in the PR when I was still in dev115. + The test worked in vanilla dev117. + I fixed the test by removing a restriction added in dev116 and the + corresponding override --allow_ideal_and_include_non_veg. + + PENDING approval by Erik: I would like to remove another restriction added + in dev116 and the corresponding override --allow_dom_pft_and_idealized. + +Testing summary: +---------------- + +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on cheyenne - PASS + + any other testing (give details below): + + make all (in /python directory) - PASS + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/1798 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev117 Originator(s): afoster (Adrianna Foster) Date: Thu Feb 2 10:34:23 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index ac424326b0..175cfdc588 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev118 slevis 02/03/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test ctsm5.1.dev117 afoster 02/02/2023 Updates to facilitate running FATES at NEON sites ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files ctsm5.1.dev115 rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics From 6699c0dc869d40cd54d1e3b3cf9249f9d8c63b44 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 3 Feb 2023 17:57:25 -0700 Subject: [PATCH 0702/2067] Rm override allow_dom_pft_and_idealized & corresponding restriction Update ChangeLog and python tests --- doc/ChangeLog | 13 +++++---- .../modify_input_files/fsurdat_modifier.py | 23 +++++---------- .../ctsm/modify_input_files/modify_fsurdat.py | 2 ++ python/ctsm/test/test_sys_fsurdat_modifier.py | 1 - .../ctsm/test/test_unit_fsurdat_modifier.py | 28 +++---------------- 5 files changed, 20 insertions(+), 47 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 0804cd8d4a..b75f939799 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,13 +1,13 @@ =============================================================== Tag name: ctsm5.1.dev118 Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310) -Date: Fri Feb 3 16:49:44 MST 2023 +Date: Fri Feb 3 17:52:37 MST 2023 One-line Summary: Use conda environment rather than ncar_pylib with the fsurdat_modifier system test Purpose and description of changes ---------------------------------- - ncar_pylib is going away soon. + Reason: ncar_pylib is going away soon. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -31,16 +31,17 @@ Bugs fixed or introduced CTSM issues fixed (include CTSM Issue #): The fsurdat_modifier system test that we're discussing in this tag and - pull request (PR #1798) + corresponding pull request (PR #1798) FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel stopped working when I updated the PR to dev117. The test worked in the PR when I was still in dev115. The test worked in vanilla dev117. - I fixed the test by removing a restriction added in dev116 and the + I fixed the failure by removing a restriction added in dev116 and the corresponding override --allow_ideal_and_include_non_veg. - PENDING approval by Erik: I would like to remove another restriction added - in dev116 and the corresponding override --allow_dom_pft_and_idealized. + I am removing another restriction added in dev116 and the corresponding + override --allow_dom_pft_and_idealized. This one didn't cause a test to fail + but unnecessarily restricted usage of the fsurdat_modifier tool. Testing summary: ---------------- diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index f5543a9506..492fa74230 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -57,13 +57,6 @@ def fsurdat_modifier_arg_process(): type=str, help="The output surface dataset with the modifications. ", ) - parser.add_argument( - "--allow_dom_pft_and_idealized", - required=False, - default=False, - action="store_true", - help="Allow both idealized and dom_pft to be on at the same time. ", - ) parser.add_argument( "--overwrite", required=False, @@ -208,7 +201,7 @@ def read_cfg_var_list(config, idealized=True): abort( var + " is a special variable handled in the idealized section." - + " This should NOT be handled in the variiable list section." + + " This should NOT be handled in the variable list section." + " Special idealized vars =" + str(ideal_list) ) @@ -216,7 +209,7 @@ def read_cfg_var_list(config, idealized=True): abort( var + " is a variable handled in the subgrid section." - + " This should NOT be handled in the variiable list section." + + " This should NOT be handled in the variable list section." + " Subgrid vars =" + str(subgrid_list) ) @@ -224,7 +217,7 @@ def read_cfg_var_list(config, idealized=True): abort( var + " is a variable handled as part of the dom_pft handling." - + " This should NOT be handled in the variiable list section." + + " This should NOT be handled in the variable list section." + " Monthly vars handled this way =" + str(monthly_list) ) @@ -259,6 +252,8 @@ def modify_optional( if idealized: modify_fsurdat.set_idealized() # set 2D variables # set 3D and 4D variables pertaining to natural vegetation + # to default values here; allow override values with the later call + # to set_dom_pft modify_fsurdat.set_dom_pft(dom_pft=0, lai=[], sai=[], hgt_top=[], hgt_bot=[]) logger.info("idealized complete") @@ -278,8 +273,8 @@ def modify_optional( modify_fsurdat.zero_nonveg() logger.info("zero_nonveg complete") - # set_dom_pft follows zero_nonveg because it modifies PCT_NATVEG - # and PCT_CROP in the user-defined rectangle + # set_dom_pft follows idealized and zero_nonveg because it modifies + # PCT_NATVEG and PCT_CROP in the user-defined rectangle if dom_pft is not None: modify_fsurdat.set_dom_pft( dom_pft=dom_pft, lai=lai, sai=sai, hgt_top=hgt_top, hgt_bot=hgt_bot @@ -372,7 +367,6 @@ def read_cfg_option_control( config, section, cfg_path, - allow_dom_pft_and_idealized=False, ): """Read the option control section""" # required but fallback values available for variables omitted @@ -435,8 +429,6 @@ def read_cfg_option_control( logger.info("dom_pft option is on and = %s", str(dom_pft)) else: logger.info("dom_pft option is off") - if dom_pft is not None and idealized and not allow_dom_pft_and_idealized: - abort("idealized AND dom_pft can NOT both be on, pick one or the other") if process_subgrid and idealized: abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") @@ -568,7 +560,6 @@ def fsurdat_modifier(parser): config, section, cfg_path, - parser.allow_dom_pft_and_idealized, ) # Read parts that are optional diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index 599b8a6e84..9b3760e303 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -180,6 +180,8 @@ def set_dom_pft(self, dom_pft, lai, sai, hgt_top, hgt_bot): --------- dom_pft: (int) User's entry of PFT/CFT to be set to 100% everywhere + If user left this UNSET in the configure file, then it + will default to 0 (bare ground). lai: (float) User's entry of MONTHLY_LAI for their dom_pft sai: diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index b4598fae20..72d38732cf 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -374,7 +374,6 @@ def test_allInfo(self): sys.argv = [ "fsurdat_modifier", self._cfg_file_path, - "--allow_dom_pft_and_idealized", ] parser = fsurdat_modifier_arg_process() fsurdat_modifier(parser) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 0c7a244584..0ea862a8e4 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -82,18 +82,8 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) - def test_dom_pft_and_idealized_fails(self): - """test a that dom_pft and idealized fails gracefully""" - section = "modify_fsurdat_basic_options" - self.config.set(section, "idealized", "True") - self.config.set(section, "dom_pft", "1") - with self.assertRaisesRegex( - SystemExit, "idealized AND dom_pft can NOT both be on, pick one or the other" - ): - read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) - def test_subgrid_and_idealized_fails(self): - """test that dom_pft and idealized fails gracefully""" + """test that subgrid and idealized fails gracefully""" section = "modify_fsurdat_basic_options" self.config.set(section, "idealized", "True") self.config.set(section, "include_nonveg", "False") @@ -131,16 +121,6 @@ def test_optional_only_true_and_false(self): ): read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) - def test_include_nonveg_and_idealized_fails(self): - """test a simple read of subgrid""" - section = "modify_fsurdat_basic_options" - self.config.set(section, "idealized", "True") - self.config.set(section, "include_nonveg", "True") - with self.assertRaisesRegex( - SystemExit, "idealized AND include_nonveg can NOT both be on, pick one or the other" - ): - read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) - def test_read_subgrid(self): """test a simple read of subgrid""" read_cfg_subgrid(self.config, self.cfg_path) @@ -265,7 +245,7 @@ def test_varlist_varinidealized(self): with self.assertRaisesRegex( SystemExit, "is a special variable handled in the idealized section." - + " This should NOT be handled in the variiable list section. Special idealized vars =", + + " This should NOT be handled in the variable list section. Special idealized vars =", ): read_cfg_var_list(self.config, idealized=True) @@ -278,7 +258,7 @@ def test_varlist_varinsubgrid(self): with self.assertRaisesRegex( SystemExit, "is a variable handled in the subgrid section." - + " This should NOT be handled in the variiable list section. Subgrid vars =", + + " This should NOT be handled in the variable list section. Subgrid vars =", ): read_cfg_var_list(self.config, idealized=False) @@ -290,7 +270,7 @@ def test_varlist_monthlyvar(self): with self.assertRaisesRegex( SystemExit, "is a variable handled as part of the dom_pft handling." - + " This should NOT be handled in the variiable list section." + + " This should NOT be handled in the variable list section." + " Monthly vars handled this way =", ): read_cfg_var_list(self.config, idealized=False) From f3f26fbf3d9c74e5d41b781b714c89d5c27e5dd0 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 5 Feb 2023 18:31:39 -0700 Subject: [PATCH 0703/2067] Update changelog --- doc/ChangeLog | 42 ++++++++++++++++++------------------------ doc/ChangeSum | 2 +- 2 files changed, 19 insertions(+), 25 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index b75f939799..5870abdb23 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev118 Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310) -Date: Fri Feb 3 17:52:37 MST 2023 +Date: Sun Feb 5 18:31:29 MST 2023 One-line Summary: Use conda environment rather than ncar_pylib with the fsurdat_modifier system test Purpose and description of changes @@ -9,6 +9,19 @@ Purpose and description of changes Reason: ncar_pylib is going away soon. + The fsurdat_modifier system test that we're discussing in this tag and + corresponding pull request (PR #1798) + FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel + stopped working when I updated the PR to dev117. + The test worked in the PR when I was still in dev115. + The test worked in vanilla dev117. + I fixed the failure by removing a restriction added in dev116 and the + corresponding override --allow_ideal_and_include_non_veg. + + I am removing another restriction added in dev116 and the corresponding + override --allow_dom_pft_and_idealized. This one didn't cause a test to fail + but unnecessarily restricted usage of the fsurdat_modifier tool. + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -30,35 +43,16 @@ Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): - The fsurdat_modifier system test that we're discussing in this tag and - corresponding pull request (PR #1798) - FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel - stopped working when I updated the PR to dev117. - The test worked in the PR when I was still in dev115. - The test worked in vanilla dev117. - I fixed the failure by removing a restriction added in dev116 and the - corresponding override --allow_ideal_and_include_non_veg. - - I am removing another restriction added in dev116 and the corresponding - override --allow_dom_pft_and_idealized. This one didn't cause a test to fail - but unnecessarily restricted usage of the fsurdat_modifier tool. +Fixes #1786 -- ncar_pylib +Fixes #1925 -- replace ncar_pylib Testing summary: ---------------- -[Remove any lines that don't apply.] - [PASS means all tests PASS; OK means tests PASS other than expected fails.] - [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python - code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system - tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in - either model output or namelists, is: create sym links pointing to the last tag's baseline directory, - named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT - doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to - separately run the clm_pymods test suite, and you can remove the following line.] - clm_pymods test suite on cheyenne - PASS + (softlinks created for baselines to previous tag since this is bit-for-bit) any other testing (give details below): @@ -75,7 +69,7 @@ Changes answers relative to baseline: NO Other details ------------- Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/1798 + https://github.com/ESCOMP/ctsm/pull/1798 -- Have fsurdat_modifier system test use conda environment rather than ncar_pylib =============================================================== =============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index 175cfdc588..215517275f 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev118 slevis 02/03/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test + ctsm5.1.dev118 slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test ctsm5.1.dev117 afoster 02/02/2023 Updates to facilitate running FATES at NEON sites ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files ctsm5.1.dev115 rgknox 12/02/2022 API compatability with FATES V2 nutrient dynamics From 05fb17bff05aaf0544170ecbb41984bdbb875807 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 3 Feb 2023 14:01:49 -0700 Subject: [PATCH 0704/2067] Update the core team lists --- README.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index c56c0d4852..298e5adc04 100644 --- a/README.md +++ b/README.md @@ -43,9 +43,8 @@ CTSM code management is provided primarily by: Software engineering team: - [Erik Kluzek](https://github.com/ekluzek) - [Bill Sacks](https://github.com/billsacks) -- [Mariana Vertenstein](https://github.com/mvertens) -- [Negin Sobhani](https://github.com/negin513) - [Sam Levis](https://github.com/slevisconsulting) +- [Adrianna Foster](https://github.com/adrifoster) Science team: - [Dave Lawrence](https://github.com/dlawrenncar) @@ -53,5 +52,7 @@ Science team: - [Danica Lombardozzi](https://github.com/danicalombardozzi) - [Keith Oleson](https://github.com/olyson) - [Sean Swenson](https://github.com/swensosc) -- [Mike Barlage](https://github.com/barlage) +- [Jackie Shuman](https://github.com/jkshuman) +- [Peter Lawrence](https://github.com/lawrencepj1) - [Rosie Fisher](https://github.com/rosiealice) +- Gordon Bonan From 463c8b9a7eb483cd599b93a2f9a1f68304b68517 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Sat, 11 Feb 2023 18:01:22 -0700 Subject: [PATCH 0705/2067] Updating new tests with longer walltimes again ERP_D_Ld10.f09_f09_mg17.IHistClm50BgcCrop.cheyenne_gnu.clm-f09_dec1990Start ran out of time at 40 minutes, so I bumped it up to 59 and it passed --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 4dfddb4a11..e602ac3597 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -331,7 +331,7 @@ - + From 789eb9c4dad4dc91bc6986116f3a6e6d9927678e Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 13 Feb 2023 14:06:47 -0500 Subject: [PATCH 0706/2067] another incremental step towards having the native cn balancing and call sequence when fates is on --- src/biogeochem/CNBalanceCheckMod.F90 | 80 ++-- src/biogeochem/CNCStateUpdate1Mod.F90 | 6 +- src/biogeochem/CNDriverMod.F90 | 59 ++- src/biogeochem/CNVegCarbonStateType.F90 | 119 ++---- src/biogeochem/CNVegNitrogenStateType.F90 | 72 +--- src/biogeochem/CNVegetationFacade.F90 | 20 +- src/biogeochem/EDBGCDynMod.F90 | 370 ------------------ src/main/clm_driver.F90 | 152 +++---- src/main/filterMod.F90 | 1 + .../SoilBiogeochemCarbonFluxType.F90 | 96 +---- .../SoilBiogeochemCarbonStateType.F90 | 255 ++++++++---- .../SoilBiogeochemNitrogenStateType.F90 | 205 +++++++--- src/utils/clmfates_interfaceMod.F90 | 106 ++--- 13 files changed, 538 insertions(+), 1003 deletions(-) delete mode 100644 src/biogeochem/EDBGCDynMod.F90 diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index a681ee5c4e..087242da30 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -16,13 +16,16 @@ module CNBalanceCheckMod use CNVegNitrogenStateType , only : cnveg_nitrogenstate_type use CNVegCarbonFluxType , only : cnveg_carbonflux_type use CNVegCarbonStateType , only : cnveg_carbonstate_type + use SoilBiogeochemCarbonStateType , only : soilbiogeochem_carbonstate_type + use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use SoilBiogeochemNitrogenfluxType , only : soilbiogeochem_nitrogenflux_type use SoilBiogeochemCarbonfluxType , only : soilbiogeochem_carbonflux_type use CNProductsMod , only : cn_products_type use ColumnType , only : col use GridcellType , only : grc use CNSharedParamsMod , only : use_fun - + use CLMFatesInterfaceMod , only : hlm_fates_interface_type + ! implicit none private @@ -100,7 +103,7 @@ end subroutine InitAllocate !----------------------------------------------------------------------- subroutine BeginCNGridcellBalance(this, bounds, cnveg_carbonflux_inst, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & + soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst, & c_products_inst, n_products_inst) ! ! !DESCRIPTION: @@ -113,13 +116,13 @@ subroutine BeginCNGridcellBalance(this, bounds, cnveg_carbonflux_inst, & ! !USES: ! ! !ARGUMENTS: - class(cn_balance_type) , intent(inout) :: this - type(bounds_type) , intent(in) :: bounds - type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst - type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst - type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst - type(cn_products_type) , intent(in) :: c_products_inst - type(cn_products_type) , intent(in) :: n_products_inst + class(cn_balance_type) , intent(inout) :: this + type(bounds_type) , intent(in) :: bounds + type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst + type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst + type(soilbiogeochem_nitrogenstate_type) , intent(in) :: soilbiogeochem_nitrogenstate_inst + type(cn_products_type) , intent(in) :: c_products_inst + type(cn_products_type) , intent(in) :: n_products_inst ! ! !LOCAL VARIABLES: integer :: g @@ -131,8 +134,8 @@ subroutine BeginCNGridcellBalance(this, bounds, cnveg_carbonflux_inst, & associate( & begcb => this%begcb_grc , & ! Output: [real(r8) (:)] (gC/m2) gridcell carbon mass, beginning of time step begnb => this%begnb_grc , & ! Output: [real(r8) (:)] (gN/m2) gridcell nitrogen mass, beginning of time step - totc => cnveg_carbonstate_inst%totc_grc , & ! Input: [real(r8) (:)] (gC/m2) total gridcell carbon, incl veg and cpool - totn => cnveg_nitrogenstate_inst%totn_grc, & ! Input: [real(r8) (:)] (gN/m2) total gridcell nitrogen, incl veg + totc => soilbiogeochem_carbonstate_inst%totc_grc , & ! Input: [real(r8) (:)] (gC/m2) total gridcell carbon, incl veg and cpool + totn => soilbiogeochem_nitrogenstate_inst%totn_grc, & ! Input: [real(r8) (:)] (gN/m2) total gridcell nitrogen, incl veg c_cropprod1 => c_products_inst%cropprod1_grc , & ! Input: [real(r8) (:)] (gC/m2) carbon in crop products n_cropprod1 => n_products_inst%cropprod1_grc , & ! Input: [real(r8) (:)] (gC/m2) nitrogen in crop products c_tot_woodprod => c_products_inst%tot_woodprod_grc , & ! Input: [real(r8) (:)] (gC/m2) total carbon in wood products @@ -159,7 +162,7 @@ end subroutine BeginCNGridcellBalance !----------------------------------------------------------------------- subroutine BeginCNColumnBalance(this, bounds, num_soilc, filter_soilc, & - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst,soilbiogeochem_carbonstate_inst) + soilbiogeochem_carbonstate_inst,soilbiogeochem_nitrogenstate_inst) ! ! !DESCRIPTION: ! Calculate beginning column-level carbon/nitrogen balance, for mass conservation check @@ -173,9 +176,8 @@ subroutine BeginCNColumnBalance(this, bounds, num_soilc, filter_soilc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_soilc ! number of soil columns filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns - type(cnveg_carbonstate_type) , intent(in) :: cnveg_carbonstate_inst - type(cnveg_nitrogenstate_type) , intent(in) :: cnveg_nitrogenstate_inst type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst + type(soilbiogeochem_nitrogenstate_type), intent(in) :: soilbiogeochem_nitrogenstate_inst ! ! !LOCAL VARIABLES: integer :: fc,c @@ -184,22 +186,16 @@ subroutine BeginCNColumnBalance(this, bounds, num_soilc, filter_soilc, & associate( & col_begcb => this%begcb_col , & ! Output: [real(r8) (:)] (gC/m2) column carbon mass, beginning of time step col_begnb => this%begnb_col , & ! Output: [real(r8) (:)] (gN/m2) column nitrogen mass, beginning of time step - totcolc => cnveg_carbonstate_inst%totc_col , & ! Input: [real(r8) (:)] (gC/m2) total column carbon, incl veg and cpool - totcoln => cnveg_nitrogenstate_inst%totn_col & ! Input: [real(r8) (:)] (gN/m2) total column nitrogen, incl veg + totcolc => soilbiogeochem_carbonstate_inst%totc_col , & ! Input: [real(r8) (:)] (gC/m2) total column carbon, incl veg and cpool + totcoln => soilbiogeochem_nitrogenstate_inst%totn_col & ! Input: [real(r8) (:)] (gN/m2) total column nitrogen, incl veg ) do fc = 1,num_soilc c = filter_soilc(fc) - if( is_fates(c) ) then - col_begcb(c) = soilbiogeochem_carbonstate_inst%totmicc_col(c) + & - soilbiogeochem_carbonstate_inst%totlitc_col(c) + & - soilbiogeochem_carbonstate_inst%totsomc_col(c) + & - soilbiogeochem_carbonstate_inst%ctrunc_col(c) - else - col_begcb(c) = totcolc(c) - col_begnb(c) = totcoln(c) - end if + col_begcb(c) = totcolc(c) + col_begnb(c) = totcoln(c) + end do end associate @@ -229,7 +225,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns type(soilbiogeochem_carbonflux_type) , intent(in) :: soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst + type(soilbiogeochem_carbonstate_type), intent(inout) :: soilbiogeochem_carbonstate_inst type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst type(cn_products_type) , intent(in) :: c_products_inst @@ -256,7 +252,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & associate( & grc_begcb => this%begcb_grc , & ! Input: [real(r8) (:) ] (gC/m2) gridcell-level carbon mass, beginning of time step grc_endcb => this%endcb_grc , & ! Output: [real(r8) (:) ] (gC/m2) gridcell-level carbon mass, end of time step - totgrcc => cnveg_carbonstate_inst%totc_grc , & ! Input: [real(r8) (:)] (gC/m2) total gridcell carbon, incl veg and cpool + totgrcc => soilbiogeochem_carbonstate_inst%totc_grc , & ! Output: [real(r8) (:)] (gC/m2) total gridcell carbon, incl veg and cpool nbp_grc => cnveg_carbonflux_inst%nbp_grc , & ! Input: [real(r8) (:) ] (gC/m2/s) net biome production (positive for sink) cropprod1_grc => c_products_inst%cropprod1_grc , & ! Input: [real(r8) (:)] (gC/m2) carbon in crop products tot_woodprod_grc => c_products_inst%tot_woodprod_grc , & ! Input: [real(r8) (:)] (gC/m2) total carbon in wood products @@ -273,7 +269,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & col_xsmrpool_to_atm => cnveg_carbonflux_inst%xsmrpool_to_atm_col , & ! Input: [real(r8) (:) ] (gC/m2/s) excess MR pool crop harvest loss to atm som_c_leached => soilbiogeochem_carbonflux_inst%som_c_leached_col , & ! Input: [real(r8) (:) ] (gC/m2/s) total SOM C loss from vertical transport - totcolc => cnveg_carbonstate_inst%totc_col & ! Input: [real(r8) (:) ] (gC/m2) total column carbon, incl veg and cpool + totcolc => soilbiogeochem_carbonstate_inst%totc_col & ! Input: [real(r8) (:) ] (gC/m2) total column carbon, incl veg and cpool ) ! set time steps @@ -286,13 +282,14 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & do fc = 1,num_soilc c = filter_soilc(fc) - if( is_fates(c) ) then - - ! calculate the total column-level carbon storage, for mass conservation check - col_endcb(c) = soilbiogeochem_carbonstate_inst%totmicc_col(c) + & - soilbiogeochem_carbonstate_inst%totlitc_col(c) + & - soilbiogeochem_carbonstate_inst%totsomc_col(c) + & - soilbiogeochem_carbonstate_inst%ctrunc_col(c) + ! calculate the total column-level carbon storage, for mass conservation check + ! for bigleaf, totcolc includes soil and all of the veg c pools including cpool, xfer, etc + ! for fates, totcolc only includes soil and non-fates litter carbon, + ! see soibiogeochem_carbonstate_inst%summary for calculations + col_endcb(c) = totcolc(c) + + + if( col%is_fates(c) ) then ! calculate total column-level inputs (litter fluxes) [g/m2/s] s = clm_fates%f2hmap(ic)%hsites(c) @@ -308,12 +305,8 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! So they are irrelevant here ! (gC/m2/s) total heterotrophic respiration col_coutputs = soilbiogeochem_carbonflux_inst%hr_col(c) - else - - ! calculate the total column-level carbon storage, for mass conservation check - col_endcb(c) = totcolc(c) ! calculate total column-level inputs col_cinputs = gpp(c) @@ -451,7 +444,8 @@ end subroutine CBalanceCheck !----------------------------------------------------------------------- subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & - soilbiogeochem_nitrogenflux_inst, cnveg_nitrogenflux_inst, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & + cnveg_nitrogenflux_inst, & cnveg_nitrogenstate_inst, n_products_inst, atm2lnd_inst) ! ! !DESCRIPTION: @@ -468,10 +462,12 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc (:) ! filter for soil columns type(soilbiogeochem_nitrogenflux_type) , intent(in) :: soilbiogeochem_nitrogenflux_inst + type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst type(cnveg_nitrogenflux_type) , intent(in) :: cnveg_nitrogenflux_inst type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(cn_products_type) , intent(in) :: n_products_inst type(atm2lnd_type) , intent(in) :: atm2lnd_inst + ! ! !LOCAL VARIABLES: integer :: c,err_index,j ! indices @@ -494,7 +490,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & associate( & grc_begnb => this%begnb_grc , & ! Input: [real(r8) (:) ] (gN/m2) gridcell nitrogen mass, beginning of time step grc_endnb => this%endnb_grc , & ! Output: [real(r8) (:) ] (gN/m2) gridcell nitrogen mass, end of time step - totgrcn => cnveg_nitrogenstate_inst%totn_grc , & ! Input: [real(r8) (:) ] (gN/m2) total gridcell nitrogen, incl veg + totgrcn => soilbiogeochem_nitrogenstate_inst%totn_grc , & ! Input: [real(r8) (:) ] (gN/m2) total gridcell nitrogen, incl veg cropprod1_grc => n_products_inst%cropprod1_grc , & ! Input: [real(r8) (:)] (gN/m2) nitrogen in crop products product_loss_grc => n_products_inst%product_loss_grc , & ! Input: [real(r8) (:)] (gN/m2) losses from wood & crop products tot_woodprod_grc => n_products_inst%tot_woodprod_grc , & ! Input: [real(r8) (:)] (gN/m2) total nitrogen in wood products @@ -520,7 +516,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & wood_harvestn => cnveg_nitrogenflux_inst%wood_harvestn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) wood harvest (to product pools) crop_harvestn_to_cropprodn => cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) crop harvest N to 1-year crop product pool - totcoln => cnveg_nitrogenstate_inst%totn_col & ! Input: [real(r8) (:) ] (gN/m2) total column nitrogen, incl veg + totcoln => soilbiogeochem_nitrogenstate_inst%totn_col & ! Input: [real(r8) (:) ] (gN/m2) total column nitrogen, incl veg ) ! set time steps diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 2d88977b5f..5783e01f6c 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -26,6 +26,7 @@ module CNCStateUpdate1Mod use clm_varctl , only : use_fates, use_cn, iulog, use_fates_sp use CNSharedParamsMod , only : use_matrixcn use CLMFatesInterfaceMod , only : hlm_fates_interface_type + use ColumnType , only : col ! implicit none @@ -141,7 +142,7 @@ end subroutine CStateUpdate0 subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & - clm_fates) + clm_fates, ci) ! ! !DESCRIPTION: ! On the radiation time step, update all the prognostic carbon state @@ -159,6 +160,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst logical , intent(in) :: dribble_crophrv_xsmrpool_2atm type(hlm_fates_interface_type) , intent(inout) :: clm_fates + integer , intent(in) :: ci ! clump index ! ! !LOCAL VARIABLES: integer :: c,p,j,k,l,i ! indices @@ -199,7 +201,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! prepared litter c flux boundary conditions into ! cf_soil%decomp_cpools_sourcesink_col - call clm_fates%UpdateCLitterfluxes(bounds_clump,cf_soil,c) + call clm_fates%UpdateCLitterfluxes(cf_soil,ci,c) else diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 2fc800955f..c7918ec0fe 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -628,18 +628,18 @@ subroutine CNDriverNoLeaching(bounds, call CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & - clm_fates) + clm_fates, bounds%clump_index) if ( use_c13 ) then call CStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & c13_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & - clm_fates) + clm_fates, bounds%clump_index) end if if ( use_c14 ) then call CStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & c14_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & - clm_fates) + clm_fates, bounds%clump_index) end if ! Update all prognostic nitrogen state variables (except for gap-phase mortality and fire fluxes) @@ -1061,53 +1061,42 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & call t_startf('CNsum') ! ---------------------------------------------- - ! soilbiogeochem carbon/nitrogen state summary + ! cnveg carbon/nitrogen state summary ! ---------------------------------------------- + call cnveg_carbonstate_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) - call soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc) if ( use_c13 ) then - call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc) + call c13_cnveg_carbonstate_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) end if + if ( use_c14 ) then - call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc) + call c14_cnveg_carbonstate_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) end if - call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_allc, filter_allc) ! ---------------------------------------------- - ! cnveg carbon/nitrogen state summary + ! soilbiogeochem carbon/nitrogen state summary + ! RGK 02-23: soilbiogeochem summary now depends on + ! cnveg summary, swapped call order ! ---------------------------------------------- - call cnveg_carbonstate_inst%Summary(bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_cwdc_col=soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & - soilbiogeochem_totlitc_col=soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), & - soilbiogeochem_totmicc_col=soilbiogeochem_carbonstate_inst%totmicc_col(begc:endc), & - soilbiogeochem_totsomc_col=soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc), & - soilbiogeochem_ctrunc_col=soilbiogeochem_carbonstate_inst%ctrunc_col(begc:endc)) - + call soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst) if ( use_c13 ) then - call c13_cnveg_carbonstate_inst%Summary(bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_cwdc_col=c13_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & - soilbiogeochem_totlitc_col=c13_soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), & - soilbiogeochem_totmicc_col=c13_soilbiogeochem_carbonstate_inst%totmicc_col(begc:endc), & - soilbiogeochem_totsomc_col=c13_soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc), & - soilbiogeochem_ctrunc_col=c13_soilbiogeochem_carbonstate_inst%ctrunc_col(begc:endc)) + call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c13_cnveg_carbonstate_inst) end if - if ( use_c14 ) then - call c14_cnveg_carbonstate_inst%Summary(bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_cwdc_col=c14_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & - soilbiogeochem_totlitc_col=c14_soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), & - soilbiogeochem_totmicc_col=c14_soilbiogeochem_carbonstate_inst%totmicc_col(begc:endc), & - soilbiogeochem_totsomc_col=c14_soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc), & - soilbiogeochem_ctrunc_col=c14_soilbiogeochem_carbonstate_inst%ctrunc_col(begc:endc)) + call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c13_cnveg_carbonstate_inst) end if + + + ! RGK 02-23: This call will be moved to after cnveg nitr summary when we + ! couple in FATES N + + + call cnveg_nitrogenstate_inst%Summary(bounds, num_soilc, filter_soilc, & + num_soilp, filter_soilp) - call cnveg_nitrogenstate_inst%Summary(bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_nitrogenstate_inst) + call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_soilc, filter_soilc,cnveg_nitrogenstate_inst) + call t_stopf('CNsum') diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index 610689fdb6..5baf1bce0b 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -68,7 +68,6 @@ module CNVegCarbonStateType real(r8), pointer :: ctrunc_patch (:) ! (gC/m2) patch-level sink for C truncation real(r8), pointer :: woodc_patch (:) ! (gC/m2) wood C real(r8), pointer :: leafcmax_patch (:) ! (gC/m2) ann max leaf C - real(r8), pointer :: totc_patch (:) ! (gC/m2) total patch-level carbon, including cpool real(r8), pointer :: rootc_col (:) ! (gC/m2) root carbon at column level (fire) real(r8), pointer :: leafc_col (:) ! (gC/m2) column-level leafc (fire) real(r8), pointer :: deadstemc_col (:) ! (gC/m2) column-level deadstemc (fire) @@ -82,21 +81,20 @@ module CNVegCarbonStateType ! summary (diagnostic) state variables, not involved in mass balance real(r8), pointer :: dispvegc_patch (:) ! (gC/m2) displayed veg carbon, excluding storage and cpool real(r8), pointer :: storvegc_patch (:) ! (gC/m2) stored vegetation carbon, excluding cpool - real(r8), pointer :: totvegc_patch (:) ! (gC/m2) total vegetation carbon, excluding cpool - real(r8), pointer :: totvegc_col (:) ! (gC/m2) total vegetation carbon, excluding cpool averaged to column (p2c) + + logical, private :: dribble_crophrv_xsmrpool_2atm - ! Total C pools + ! Total C pools + real(r8), pointer :: totc_patch (:) ! (gC/m2) total patch-level carbon, including cpool + real(r8), pointer :: totvegc_patch (:) ! (gC/m2) total vegetation carbon, excluding cpool + real(r8), pointer :: totvegc_col (:) ! (gC/m2) total vegetation carbon, excluding cpool averaged to column (p2c) real(r8), pointer :: totc_p2c_col (:) ! (gC/m2) totc_patch averaged to col - real(r8), pointer :: totc_col (:) ! (gC/m2) total column carbon, incl veg and cpool - real(r8), pointer :: totecosysc_col (:) ! (gC/m2) total ecosystem carbon, incl veg but excl cpool - real(r8), pointer :: totc_grc (:) ! (gC/m2) total gridcell carbon - - logical, private :: dribble_crophrv_xsmrpool_2atm + contains procedure , public :: Init procedure , public :: SetValues - procedure , public :: ZeroDWT + procedure , public :: ZeroDwt procedure , public :: Restart procedure , public :: Summary => Summary_carbonstate procedure , public :: DynamicPatchAdjustments ! adjust state variables when patch areas change @@ -277,9 +275,6 @@ subroutine InitAllocate(this, bounds) allocate(this%totvegc_col (begc:endc)) ; this%totvegc_col (:) = nan allocate(this%totc_p2c_col (begc:endc)) ; this%totc_p2c_col (:) = nan - allocate(this%totc_col (begc:endc)) ; this%totc_col (:) = nan - allocate(this%totecosysc_col (begc:endc)) ; this%totecosysc_col (:) = nan - allocate(this%totc_grc (begg:endg)) ; this%totc_grc (:) = nan ! Matrix solution variables if(use_matrixcn)then @@ -509,16 +504,6 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', long_name='fuel load', & ptr_col=this%fuelc_col) - this%totc_col(begc:endc) = spval - call hist_addfld1d (fname='TOTCOLC', units='gC/m^2', & - avgflag='A', long_name='total column carbon, incl veg and cpool but excl product pools', & - ptr_col=this%totc_col) - - this%totecosysc_col(begc:endc) = spval - call hist_addfld1d (fname='TOTECOSYSC', units='gC/m^2', & - avgflag='A', long_name='total ecosystem carbon, incl veg but excl cpool and product pools', & - ptr_col=this%totecosysc_col) - ! Matrix solution history variables if ( use_matrixcn )then end if @@ -675,16 +660,6 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', long_name='C13 pool for seeding new PFTs via dynamic landcover', & ptr_gcell=this%seedc_grc, default='inactive') - this%totc_col(begc:endc) = spval - call hist_addfld1d (fname='C13_TOTCOLC', units='gC13/m^2', & - avgflag='A', long_name='C13 total column carbon, incl veg and cpool but excl product pools', & - ptr_col=this%totc_col, default='inactive') - - this%totecosysc_col(begc:endc) = spval - call hist_addfld1d (fname='C13_TOTECOSYSC', units='gC13/m^2', & - avgflag='A', long_name='C13 total ecosystem carbon, incl veg but excl cpool and product pools', & - ptr_col=this%totecosysc_col) - if (use_crop) then this%reproductivec_patch(begp:endp,:) = spval do k = 1, nrepr @@ -866,16 +841,6 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', long_name='C14 pool for seeding new PFTs via dynamic landcover', & ptr_gcell=this%seedc_grc, default='inactive') - this%totc_col(begc:endc) = spval - call hist_addfld1d (fname='C14_TOTCOLC', units='gC14/m^2', & - avgflag='A', long_name='C14 total column carbon, incl veg and cpool but excl product pools', & - ptr_col=this%totc_col, default='inactive') - - this%totecosysc_col(begc:endc) = spval - call hist_addfld1d (fname='C14_TOTECOSYSC', units='gC14/m^2', & - avgflag='A', long_name='C14 total ecosystem carbon, incl veg but excl cpool and product pools', & - ptr_col=this%totecosysc_col) - if (use_crop) then this%reproductivec_patch(begp:endp,:) = spval do k = 1, nrepr @@ -1099,16 +1064,14 @@ subroutine InitCold(this, bounds, ratio, carbon_type, c12_cnveg_carbonstate_inst ! this%totgrainc_col(c) = 0._r8 ! total carbon pools - this%totecosysc_col(c) = 0._r8 this%totc_p2c_col(c) = 0._r8 - this%totc_col(c) = 0._r8 + end if end do do g = bounds%begg, bounds%endg this%seedc_grc(g) = 0._r8 - this%totc_grc(g) = 0._r8 end do ! initialize fields for special filters @@ -2596,8 +2559,6 @@ subroutine SetValues ( this, & this%fuelc_crop_col(i) = value_column this%totvegc_col(i) = value_column this%totc_p2c_col(i) = value_column - this%totc_col(i) = value_column - this%totecosysc_col(i) = value_column end do end subroutine SetValues @@ -2625,11 +2586,8 @@ subroutine ZeroDwt( this, bounds ) end subroutine ZeroDwt !----------------------------------------------------------------------- - subroutine Summary_carbonstate(this, bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_cwdc_col, soilbiogeochem_totlitc_col, & - soilbiogeochem_totmicc_col, soilbiogeochem_totsomc_col, & - soilbiogeochem_ctrunc_col) + subroutine Summary_carbonstate(this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + ! ! !USES: use subgridAveMod, only : p2c @@ -2642,31 +2600,18 @@ subroutine Summary_carbonstate(this, bounds, num_allc, filter_allc, & ! !ARGUMENTS: class(cnveg_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_allc ! number of columns in allc filter - integer , intent(in) :: filter_allc(:) ! filter for all active columns integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches - real(r8) , intent(in) :: soilbiogeochem_cwdc_col(bounds%begc:) - real(r8) , intent(in) :: soilbiogeochem_totmicc_col(bounds%begc:) - real(r8) , intent(in) :: soilbiogeochem_totlitc_col(bounds%begc:) - real(r8) , intent(in) :: soilbiogeochem_totsomc_col(bounds%begc:) - real(r8) , intent(in) :: soilbiogeochem_ctrunc_col(bounds%begc:) + ! ! !LOCAL VARIABLES: integer :: c,p,j,k,l ! indices integer :: fp,fc ! lake filter indices !----------------------------------------------------------------------- - SHR_ASSERT_ALL_FL((ubound(soilbiogeochem_cwdc_col) == (/bounds%endc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(soilbiogeochem_totmicc_col) == (/bounds%endc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(soilbiogeochem_totlitc_col) == (/bounds%endc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(soilbiogeochem_totsomc_col) == (/bounds%endc/)), sourcefile, __LINE__) - SHR_ASSERT_ALL_FL((ubound(soilbiogeochem_ctrunc_col) == (/bounds%endc/)), sourcefile, __LINE__) - ! calculate patch -level summary of carbon state - do fp = 1,num_soilp p = filter_soilp(fp) @@ -2738,36 +2683,16 @@ subroutine Summary_carbonstate(this, bounds, num_allc, filter_allc, & ! -------------------------------------------- ! column level summary ! -------------------------------------------- - - call p2c(bounds, num_soilc, filter_soilc, & - this%totvegc_patch(bounds%begp:bounds%endp), & - this%totvegc_col(bounds%begc:bounds%endc)) - - call p2c(bounds, num_soilc, filter_soilc, & - this%totc_patch(bounds%begp:bounds%endp), & - this%totc_p2c_col(bounds%begc:bounds%endc)) - - do fc = 1,num_allc - c = filter_allc(fc) - - ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) - this%totecosysc_col(c) = & - soilbiogeochem_cwdc_col(c) + & - soilbiogeochem_totmicc_col(c) + & - soilbiogeochem_totlitc_col(c) + & - soilbiogeochem_totsomc_col(c) + & - this%totvegc_col(c) - - ! total column carbon, including veg and cpool (TOTCOLC) - this%totc_col(c) = this%totc_p2c_col(c) + & - soilbiogeochem_cwdc_col(c) + & - soilbiogeochem_totmicc_col(c) + & - soilbiogeochem_totlitc_col(c) + & - soilbiogeochem_totsomc_col(c) + & - soilbiogeochem_ctrunc_col(c) - - end do - + if(associated(this%totvegc_patch))then + call p2c(bounds, num_soilc, filter_soilc, & + this%totvegc_patch(bounds%begp:bounds%endp), & + this%totvegc_col(bounds%begc:bounds%endc)) + + call p2c(bounds, num_soilc, filter_soilc, & + this%totc_patch(bounds%begp:bounds%endp), & + this%totc_p2c_col(bounds%begc:bounds%endc)) + end if + end subroutine Summary_carbonstate !----------------------------------------------------------------------- diff --git a/src/biogeochem/CNVegNitrogenStateType.F90 b/src/biogeochem/CNVegNitrogenStateType.F90 index f09311e518..d6c335bb9a 100644 --- a/src/biogeochem/CNVegNitrogenStateType.F90 +++ b/src/biogeochem/CNVegNitrogenStateType.F90 @@ -69,9 +69,7 @@ module CNVegNitrogenStateType real(r8), pointer :: totvegn_col (:) ! (gN/m2) total vegetation nitrogen (p2c) real(r8), pointer :: totn_patch (:) ! (gN/m2) total patch-level nitrogen real(r8), pointer :: totn_p2c_col (:) ! (gN/m2) totn_patch averaged to col - real(r8), pointer :: totn_col (:) ! (gN/m2) total column nitrogen, incl veg - real(r8), pointer :: totecosysn_col (:) ! (gN/m2) total ecosystem nitrogen, incl veg - real(r8), pointer :: totn_grc (:) ! (gN/m2) total gridcell nitrogen + ! acc spinup for matrix solution @@ -167,9 +165,7 @@ subroutine InitAllocate(this, bounds) allocate(this%seedn_grc (begg:endg)) ; this%seedn_grc (:) = nan allocate(this%totvegn_col (begc:endc)) ; this%totvegn_col (:) = nan allocate(this%totn_p2c_col (begc:endc)) ; this%totn_p2c_col (:) = nan - allocate(this%totn_col (begc:endc)) ; this%totn_col (:) = nan - allocate(this%totecosysn_col (begc:endc)) ; this%totecosysn_col (:) = nan - allocate(this%totn_grc (begg:endg)) ; this%totn_grc (:) = nan + ! Matrix solution allocations if ( use_matrixcn )then @@ -376,15 +372,7 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='pool for seeding new PFTs via dynamic landcover', & ptr_gcell=this%seedn_grc) - this%totecosysn_col(begc:endc) = spval - call hist_addfld1d (fname='TOTECOSYSN', units='gN/m^2', & - avgflag='A', long_name='total ecosystem N, excluding product pools', & - ptr_col=this%totecosysn_col) - this%totn_col(begc:endc) = spval - call hist_addfld1d (fname='TOTCOLN', units='gN/m^2', & - avgflag='A', long_name='total column-level N, excluding product pools', & - ptr_col=this%totn_col) end subroutine InitHistory @@ -558,16 +546,13 @@ subroutine InitCold(this, bounds, & l = col%landunit(c) if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then ! total nitrogen pools - this%totecosysn_col(c) = 0._r8 this%totn_p2c_col(c) = 0._r8 - this%totn_col(c) = 0._r8 end if end do do g = bounds%begg, bounds%endg this%seedn_grc(g) = 0._r8 - this%totn_grc(g) = 0._r8 end do ! now loop through special filters and explicitly set the variables that @@ -1024,11 +1009,8 @@ subroutine SetValues ( this, & do fi = 1,num_column i = filter_column(fi) - - this%totecosysn_col(i) = value_column this%totvegn_col(i) = value_column this%totn_p2c_col(i) = value_column - this%totn_col(i) = value_column end do end subroutine SetValues @@ -1057,24 +1039,20 @@ subroutine ZeroDwt( this, bounds ) end subroutine ZeroDwt !----------------------------------------------------------------------- - subroutine Summary_nitrogenstate(this, bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp,& - soilbiogeochem_nitrogenstate_inst) + subroutine Summary_nitrogenstate(this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) ! ! !USES: use subgridAveMod, only : p2c - use SoilBiogeochemNitrogenStateType, only : soilbiogeochem_nitrogenstate_type + ! ! !ARGUMENTS: class(cnveg_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_allc ! number of columns in allc filter - integer , intent(in) :: filter_allc(:) ! filter for all active columns integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(soilbiogeochem_nitrogenstate_type) , intent(in) :: soilbiogeochem_nitrogenstate_inst + ! ! !LOCAL VARIABLES: integer :: c,p,j,k,l ! indices @@ -1148,38 +1126,16 @@ subroutine Summary_nitrogenstate(this, bounds, num_allc, filter_allc, & ! -------------------------------------------- ! column level summary ! -------------------------------------------- + if(associated(this%totvegn_patch))then + call p2c(bounds, num_soilc, filter_soilc, & + this%totvegn_patch(bounds%begp:bounds%endp), & + this%totvegn_col(bounds%begc:bounds%endc)) + + call p2c(bounds, num_soilc, filter_soilc, & + this%totn_patch(bounds%begp:bounds%endp), & + this%totn_p2c_col(bounds%begc:bounds%endc)) + end if - call p2c(bounds, num_soilc, filter_soilc, & - this%totvegn_patch(bounds%begp:bounds%endp), & - this%totvegn_col(bounds%begc:bounds%endc)) - - call p2c(bounds, num_soilc, filter_soilc, & - this%totn_patch(bounds%begp:bounds%endp), & - this%totn_p2c_col(bounds%begc:bounds%endc)) - - do fc = 1,num_allc - c = filter_allc(fc) - - ! total ecosystem nitrogen, including veg (TOTECOSYSN) - this%totecosysn_col(c) = & - soilbiogeochem_nitrogenstate_inst%cwdn_col(c) + & - soilbiogeochem_nitrogenstate_inst%totlitn_col(c) + & - soilbiogeochem_nitrogenstate_inst%totmicn_col(c) + & - soilbiogeochem_nitrogenstate_inst%totsomn_col(c) + & - soilbiogeochem_nitrogenstate_inst%sminn_col(c) + & - this%totvegn_col(c) - - ! total column nitrogen, including patch (TOTCOLN) - - this%totn_col(c) = this%totn_p2c_col(c) + & - soilbiogeochem_nitrogenstate_inst%cwdn_col(c) + & - soilbiogeochem_nitrogenstate_inst%totlitn_col(c) + & - soilbiogeochem_nitrogenstate_inst%totmicn_col(c) + & - soilbiogeochem_nitrogenstate_inst%totsomn_col(c) + & - soilbiogeochem_nitrogenstate_inst%sminn_col(c) + & - soilbiogeochem_nitrogenstate_inst%ntrunc_col(c) - - end do end subroutine Summary_nitrogenstate diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 8ab4bdf4c3..1bdcf5bce5 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -802,7 +802,7 @@ subroutine InitColumnBalance(this, bounds, num_allc, filter_allc, & call this%cn_balance_inst%BeginCNColumnBalance( & bounds, num_soilc, filter_soilc, & - this%cnveg_carbonstate_inst, this%cnveg_nitrogenstate_inst) + soilbiogeochem_carbonstate_inst,soilbiogeochem_nitrogenstate_inst) end subroutine InitColumnBalance @@ -843,6 +843,7 @@ subroutine InitGridcellBalance(this, bounds, num_allc, filter_allc, & character(len=*), parameter :: subname = 'InitGridcellBalance' !----------------------------------------------------------------------- + call CNDriverSummarizeStates(bounds, & num_allc, filter_allc, & num_soilc, filter_soilc, & @@ -858,20 +859,22 @@ subroutine InitGridcellBalance(this, bounds, num_allc, filter_allc, & ! total gridcell carbon (TOTGRIDCELLC) call c2g( bounds = bounds, & - carr = this%cnveg_carbonstate_inst%totc_col(bounds%begc:bounds%endc), & - garr = this%cnveg_carbonstate_inst%totc_grc(bounds%begg:bounds%endg), & + carr = soilbiogeochem_carbonstate_inst%totc_col(bounds%begc:bounds%endc), & + garr = soilbiogeochem_carbonstate_inst%totc_grc(bounds%begg:bounds%endg), & c2l_scale_type = 'unity', & l2g_scale_type = 'unity') + ! total gridcell nitrogen (TOTGRIDCELLN) call c2g( bounds = bounds, & - carr = this%cnveg_nitrogenstate_inst%totn_col(bounds%begc:bounds%endc), & - garr = this%cnveg_nitrogenstate_inst%totn_grc(bounds%begg:bounds%endg), & + carr = soilbiogeochem_nitrogenstate_inst%totn_col(bounds%begc:bounds%endc), & + garr = soilbiogeochem_nitrogenstate_inst%totn_grc(bounds%begg:bounds%endg), & c2l_scale_type = 'unity', & l2g_scale_type = 'unity') call this%cn_balance_inst%BeginCNGridcellBalance( bounds, & this%cnveg_carbonflux_inst, & - this%cnveg_carbonstate_inst, this%cnveg_nitrogenstate_inst, & + soilbiogeochem_carbonstate_inst, & + soilbiogeochem_nitrogenstate_inst, & this%c_products_inst, this%n_products_inst) end subroutine InitGridcellBalance @@ -1152,8 +1155,8 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & integer , intent(in) :: filter_soilc(:) ! filter for soil columns type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst - type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonstate_inst - type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst + type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst + type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(hlm_fates_interface_type) , intent(inout) :: clm_fates ! @@ -1184,6 +1187,7 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & call this%cn_balance_inst%NBalanceCheck( & bounds, num_soilc, filter_soilc, & soilbiogeochem_nitrogenflux_inst, & + soilbiogeochem_nitrogenstate_inst, & this%cnveg_nitrogenflux_inst, & this%cnveg_nitrogenstate_inst, & this%n_products_inst, & diff --git a/src/biogeochem/EDBGCDynMod.F90 b/src/biogeochem/EDBGCDynMod.F90 deleted file mode 100644 index eb13932d13..0000000000 --- a/src/biogeochem/EDBGCDynMod.F90 +++ /dev/null @@ -1,370 +0,0 @@ -module EDBGCDynMod - -! This module creates a pathway to call the belowground biogeochemistry code as driven by the fates vegetation model -! but bypassing the aboveground CN vegetation code. It is modeled after the CNDriverMod in its call sequence and -! functionality. - - use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_varctl , only : use_c13, use_c14, use_fates - use decompMod , only : bounds_type - use perf_mod , only : t_startf, t_stopf - use shr_log_mod , only : errMsg => shr_log_errMsg - use abortutils , only : endrun - use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, mimics_decomp, century_decomp, decomp_method - use CNVegCarbonStateType , only : cnveg_carbonstate_type - use CNVegCarbonFluxType , only : cnveg_carbonflux_type - use SoilBiogeochemStateType , only : soilbiogeochem_state_type - use SoilBiogeochemCarbonStateType , only : soilbiogeochem_carbonstate_type - use SoilBiogeochemCarbonFluxType , only : soilbiogeochem_carbonflux_type - use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type - use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type - use CanopyStateType , only : canopystate_type - use SoilStateType , only : soilstate_type - use SoilHydrologyType , only : soilhydrology_type - use TemperatureType , only : temperature_type - use WaterFluxBulkType , only : waterfluxbulk_type - use ActiveLayerMod , only : active_layer_type - use atm2lndType , only : atm2lnd_type - use SoilStateType , only : soilstate_type - use ch4Mod , only : ch4_type - use CLMFatesInterfaceMod , only : hlm_fates_interface_type - - implicit none - - ! public :: EDBGCDynInit ! BGC dynamics: initialization - public :: EDBGCDyn ! BGC Dynamics - public :: EDBGCDynSummary ! BGC dynamics: summary - - character(len=*), parameter, private :: sourcefile = & - __FILE__ - -contains - - - !----------------------------------------------------------------------- - subroutine EDBGCDyn(bounds, & - num_soilc, filter_soilc, num_soilp, filter_soilp, num_pcropp, filter_pcropp, doalb, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - soilbiogeochem_state_inst, clm_fates, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & - c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, & - active_layer_inst, atm2lnd_inst, waterfluxbulk_inst, & - canopystate_inst, soilstate_inst, temperature_inst, crop_inst, ch4_inst) - ! - ! !DESCRIPTION: - - ! - ! !USES: - use clm_varpar , only: nlevgrnd, nlevdecomp_full - use clm_varpar , only: nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools - use subgridAveMod , only: p2c - use CropType , only: crop_type - use CNNDynamicsMod , only: CNNDeposition,CNNFixation, CNNFert, CNSoyfix - use CNMRespMod , only: CNMResp - use CNPhenologyMod , only: CNPhenology - use CNGRespMod , only: CNGResp - use CNCIsoFluxMod , only: CIsoFlux1, CIsoFlux2, CIsoFlux2h, CIsoFlux3 - use CNC14DecayMod , only: C14Decay - use CNCStateUpdate1Mod , only: CStateUpdate1,CStateUpdate0 - use CNCStateUpdate2Mod , only: CStateUpdate2, CStateUpdate2h - use CNCStateUpdate3Mod , only: CStateUpdate3 - use CNNStateUpdate1Mod , only: NStateUpdate1 - use CNNStateUpdate2Mod , only: NStateUpdate2, NStateUpdate2h - use CNGapMortalityMod , only: CNGapMortality - use SoilBiogeochemDecompCascadeMIMICSMod, only: decomp_rates_mimics - use SoilBiogeochemDecompCascadeBGCMod , only: decomp_rate_constants_bgc - use SoilBiogeochemDecompMod , only: SoilBiogeochemDecomp - use SoilBiogeochemLittVertTranspMod , only: SoilBiogeochemLittVertTransp - use SoilBiogeochemPotentialMod , only: SoilBiogeochemPotential - use SoilBiogeochemVerticalProfileMod , only: SoilBiogeochemVerticalProfile - use SoilBiogeochemNitrifDenitrifMod , only: SoilBiogeochemNitrifDenitrif - use SoilBiogeochemNStateUpdate1Mod , only: SoilBiogeochemNStateUpdate1 - ! - ! !ARGUMENTS: - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter - integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches - logical , intent(in) :: doalb ! true = surface albedo calculation time step - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst - type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst - type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst - type(soilbiogeochem_carbonflux_type) , intent(inout) :: c13_soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type) , intent(inout) :: c13_soilbiogeochem_carbonstate_inst - type(soilbiogeochem_carbonflux_type) , intent(inout) :: c14_soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type) , intent(inout) :: c14_soilbiogeochem_carbonstate_inst - type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst - type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst - type(active_layer_type) , intent(in) :: active_layer_inst - type(atm2lnd_type) , intent(in) :: atm2lnd_inst - type(waterfluxbulk_type) , intent(in) :: waterfluxbulk_inst - type(canopystate_type) , intent(in) :: canopystate_inst - type(soilstate_type) , intent(in) :: soilstate_inst - type(temperature_type) , intent(inout) :: temperature_inst - type(crop_type) , intent(in) :: crop_inst - type(ch4_type) , intent(in) :: ch4_inst - type(hlm_fates_interface_type) , intent(inout) :: clm_fates - ! - ! !LOCAL VARIABLES: - real(r8):: cn_decomp_pools(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_pools) - real(r8):: p_decomp_cpool_loss(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_cascade_transitions) !potential C loss from one pool to another - real(r8):: pmnf_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_cascade_transitions) !potential mineral N flux, from one pool to another - real(r8):: p_decomp_npool_to_din(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_cascade_transitions) ! potential flux to dissolved inorganic N - real(r8):: p_decomp_cn_gain(bounds%begc:bounds%endc,1:nlevdecomp,1:ndecomp_pools) ! C:N ratio of the flux gained by the receiver pool - integer :: begc,endc - !----------------------------------------------------------------------- - - begc = bounds%begc; endc = bounds%endc - - associate( & - laisun => canopystate_inst%laisun_patch , & ! Input: [real(r8) (:) ] sunlit projected leaf area index - laisha => canopystate_inst%laisha_patch , & ! Input: [real(r8) (:) ] shaded projected leaf area index - frac_veg_nosno => canopystate_inst%frac_veg_nosno_patch , & ! Input: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-] - frac_veg_nosno_alb => canopystate_inst%frac_veg_nosno_alb_patch , & ! Output: [integer (:) ] frac of vegetation not covered by snow [-] - tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index, no burying by snow - tsai => canopystate_inst%tsai_patch , & ! Input: [real(r8) (:) ] one-sided stem area index, no burying by snow - elai => canopystate_inst%elai_patch , & ! Output: [real(r8) (:) ] one-sided leaf area index with burying by snow - esai => canopystate_inst%esai_patch , & ! Output: [real(r8) (:) ] one-sided stem area index with burying by snow - htop => canopystate_inst%htop_patch , & ! Output: [real(r8) (:) ] canopy top (m) - hbot => canopystate_inst%hbot_patch & ! Output: [real(r8) (:) ] canopy bottom (m) - ) - - ! -------------------------------------------------- - ! zero the column-level C and N fluxes - ! -------------------------------------------------- - - if ( decomp_method /= no_soil_decomp )then - call t_startf('SoilBGCZero') - - call soilbiogeochem_carbonflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) - if ( use_c13 ) then - call c13_soilbiogeochem_carbonflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) - end if - if ( use_c14 ) then - call c14_soilbiogeochem_carbonflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) - end if - - call t_stopf('SoilBGCZero') - end if - - ! -------------------------------------------------- - ! Nitrogen Deposition, Fixation and Respiration - ! -------------------------------------------------- - - ! call t_startf('CNDeposition') - ! call CNNDeposition(bounds, & - ! atm2lnd_inst, soilbiogeochem_nitrogenflux_inst) - ! call t_stopf('CNDeposition') - - - ! if (crop_prog) then - ! call CNNFert(bounds, num_soilc,filter_soilc, & - ! cnveg_nitrogenflux_inst, soilbiogeochem_nitrogenflux_inst) - - ! call CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - ! waterstate_inst, crop_inst, cnveg_state_inst, cnveg_nitrogenflux_inst , & - ! soilbiogeochem_state_inst, soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) - ! end if - - !-------------------------------------------- - ! Soil Biogeochemistry - !-------------------------------------------- - - if (decomp_method == century_decomp) then - call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & - soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) - else if (decomp_method == mimics_decomp) then - call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp, clm_fates, & - soilstate_inst, temperature_inst, cnveg_carbonflux_inst, ch4_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst) - end if - - if ( decomp_method /= no_soil_decomp )then - ! calculate potential decomp rates and total immobilization demand (previously inlined in CNDecompAlloc) - call SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & - soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & - soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & - cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools), & - p_decomp_cpool_loss=p_decomp_cpool_loss(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), & - p_decomp_cn_gain=p_decomp_cn_gain(begc:endc,1:nlevdecomp,1:ndecomp_pools), & - pmnf_decomp_cascade=pmnf_decomp_cascade(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), & - p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions)) - end if - - !-------------------------------------------- - ! Resolve the competition between plants and soil heterotrophs - ! for available soil mineral N resource - !-------------------------------------------- - ! will add this back in when integrtating hte nutirent cycles - - - !-------------------------------------------- - ! Calculate litter and soil decomposition rate - !-------------------------------------------- - - ! Calculation of actual immobilization and decomp rates, following - ! resolution of plant/heterotroph competition for mineral N (previously inlined in CNDecompAllocation in CNDecompMod) - - if ( decomp_method /= no_soil_decomp )then - call t_startf('SoilBiogeochemDecomp') - - call SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, & - soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & - soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & - cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools), & - p_decomp_cpool_loss=p_decomp_cpool_loss(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), & - pmnf_decomp_cascade=pmnf_decomp_cascade(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions), & - p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions)) - - call t_stopf('SoilBiogeochemDecomp') - - - !-------------------------------------------- - ! Update1 - !-------------------------------------------- - - call t_startf('BNGCUpdate1') - - - ! Update all prognostic carbon state variables (except for gap-phase mortality and fire fluxes) - call CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & - crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm=.False.) - - call t_stopf('BNGCUpdate1') - - !-------------------------------------------- - ! Calculate vertical mixing of soil and litter pools - !-------------------------------------------- - - call t_startf('SoilBiogeochemLittVertTransp') - - call SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & - active_layer_inst, soilbiogeochem_state_inst, & - soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & - c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & - c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, & - soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) - - call t_stopf('SoilBiogeochemLittVertTransp') - end if - - ! Wood product fluxes will eventually be added to FATES-CLM. However - ! it is likely this will be implemented during or after we break away from - ! using this module. This module and the current coupling stategy bypasses - ! a number of processes in CLM, which includes the wood product modules. - ! Therefore the following call is a placeholder so that the wood-product - ! wrapper code can be copied from here and applied at the right place when the time comes. - ! RGK 06-2022 - - !call FatesWrapWoodProducts(bounds, num_soilc, filter_soilc,c_products_inst) - !call t_startf('CNWoodProducts') - !call c_products_inst%UpdateProducts(bounds, & - ! num_soilp, filter_soilp, & - ! dwt_wood_product_gain_patch = cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & - ! wood_harvest_patch = cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & - ! dwt_crop_product_gain_patch = cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & - ! crop_harvest_to_cropprod_patch = cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) - !call t_stopf('CNWoodProducts') - - - end associate - - end subroutine EDBGCDyn - - - !----------------------------------------------------------------------- - subroutine EDBGCDynSummary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - nc) - ! - ! !DESCRIPTION: - ! Call to all CN and SoilBiogeochem summary routines - ! also aggregate production and decomposition fluxes to whole-ecosystem balance fluxes - ! - ! !USES: - use clm_varpar , only: ndecomp_cascade_transitions - use CNPrecisionControlMod , only: CNPrecisionControl - use SoilBiogeochemPrecisionControlMod , only: SoilBiogeochemPrecisionControl - ! - ! !ARGUMENTS: - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches - type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst - type(soilbiogeochem_carbonflux_type) , intent(inout) :: c13_soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type) , intent(inout) :: c13_soilbiogeochem_carbonstate_inst - type(soilbiogeochem_carbonflux_type) , intent(inout) :: c14_soilbiogeochem_carbonflux_inst - type(soilbiogeochem_carbonstate_type) , intent(inout) :: c14_soilbiogeochem_carbonstate_inst - type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst - type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst - integer , intent(in) :: nc ! thread index - ! - ! !LOCAL VARIABLES: - integer :: begc,endc - !----------------------------------------------------------------------- - - begc = bounds%begc; endc= bounds%endc - - ! Call to all summary routines - - call t_startf('BGCsum') - - ! Set controls on very low values in critical state variables - - call SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & - soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonstate_inst,soilbiogeochem_nitrogenstate_inst) - - ! Note - all summary updates to cnveg_carbonstate_inst and cnveg_carbonflux_inst are done in - ! soilbiogeochem_carbonstate_inst%summary and CNVeg_carbonstate_inst%summary - - ! ---------------------------------------------- - ! soilbiogeochem carbon/nitrogen state summary - ! ---------------------------------------------- - - call soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc) - if ( use_c13 ) then - call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc) - end if - if ( use_c14 ) then - call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc) - end if - ! call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_soilc, filter_soilc) - - ! ---------------------------------------------- - ! soilbiogeochem carbon/nitrogen flux summary - ! ---------------------------------------------- - - call soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc) - if ( use_c13 ) then - call c13_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc) - end if - if ( use_c14 ) then - call c14_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc) - end if - ! call soilbiogeochem_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc) - - - call t_stopf('BGCsum') - - end subroutine EDBGCDynSummary - -end module EDBGCDynMod diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index b01034dc2a..d035b8cda3 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -80,7 +80,6 @@ module clm_driver use ColumnType , only : col use PatchType , only : patch use clm_instMod - use EDBGCDynMod , only : EDBGCDyn, EDBGCDynSummary use SoilMoistureStreamMod , only : PrescribedSoilMoistureInterp, PrescribedSoilMoistureAdvance use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, decomp_method ! @@ -325,12 +324,12 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call get_clump_bounds(nc, bounds_clump) call t_startf('begcnbal_grc') - if (use_cn) then + if (use_cn .or. use_fates) then ! Initialize gridcell-level balance check call bgc_vegetation_inst%InitGridcellBalance(bounds_clump, & filter(nc)%num_allc, filter(nc)%allc, & - filter(nc)%num_soilc, filter(nc)%soilc, & - filter(nc)%num_soilp, filter(nc)%soilp, & + filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst, & @@ -415,12 +414,12 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_stopf('begwbal') call t_startf('begcnbal_col') - if (use_cn) then + if (use_cn .or. use_fates) then ! Initialize column-level balance check call bgc_vegetation_inst%InitColumnBalance(bounds_clump, & filter(nc)%num_allc, filter(nc)%allc, & - filter(nc)%num_soilc, filter(nc)%soilc, & - filter(nc)%num_soilp, filter(nc)%soilp, & + filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst, & @@ -999,32 +998,32 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Filter bgc_soilc operates on all non-sp soil columns ! Filter bgc_vegp operates on all non-fates, non-sp patches (use_cn) on soil - - call t_startf('ecosysdyn') - call bgc_vegetation_inst%EcosystemDynamicsPreDrainage(bounds_clump, & - filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & - filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & - filter(nc)%num_actfirec, filter(nc)%actfirec, & - filter(nc)%num_actfirep, filter(nc)%actfirep, & - filter(nc)%num_pcropp, filter(nc)%pcropp, & - filter(nc)%num_soilnopcropp, filter(nc)%soilnopcropp, & - filter(nc)%num_exposedvegp, filter(nc)%exposedvegp, & - filter(nc)%num_noexposedvegp, filter(nc)%noexposedvegp, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - soilbiogeochem_state_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - active_layer_inst, clm_fates, & - atm2lnd_inst, water_inst%waterstatebulk_inst, & - water_inst%waterdiagnosticbulk_inst, water_inst%waterfluxbulk_inst, & - water_inst%wateratm2lndbulk_inst, canopystate_inst, soilstate_inst, temperature_inst, & - soil_water_retention_curve, crop_inst, ch4_inst, & - photosyns_inst, saturated_excess_runoff_inst, energyflux_inst, & - nutrient_competition_method, fireemis_inst) - - call t_stopf('ecosysdyn') - + + if(use_cn .or. use_fates)then + call t_startf('ecosysdyn') + call bgc_vegetation_inst%EcosystemDynamicsPreDrainage(bounds_clump, & + filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & + filter(nc)%num_actfirec, filter(nc)%actfirec, & + filter(nc)%num_actfirep, filter(nc)%actfirep, & + filter(nc)%num_pcropp, filter(nc)%pcropp, & + filter(nc)%num_soilnopcropp, filter(nc)%soilnopcropp, & + filter(nc)%num_exposedvegp, filter(nc)%exposedvegp, & + filter(nc)%num_noexposedvegp, filter(nc)%noexposedvegp, & + soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & + soilbiogeochem_state_inst, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & + active_layer_inst, clm_fates, & + atm2lnd_inst, water_inst%waterstatebulk_inst, & + water_inst%waterdiagnosticbulk_inst, water_inst%waterfluxbulk_inst, & + water_inst%wateratm2lndbulk_inst, canopystate_inst, soilstate_inst, temperature_inst, & + soil_water_retention_curve, crop_inst, ch4_inst, & + photosyns_inst, saturated_excess_runoff_inst, energyflux_inst, & + nutrient_competition_method, fireemis_inst) + call t_stopf('ecosysdyn') + end if ! Prescribed biogeography - prescribed canopy structure, some prognostic carbon fluxes @@ -1078,23 +1077,24 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_stopf('hydro2_drainage') - call t_startf('EcosysDynPostDrainage') - call bgc_vegetation_inst%EcosystemDynamicsPostDrainage(bounds_clump, & - filter(nc)%num_allc, filter(nc)%allc, & - filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & - filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & - filter(nc)%num_actfirec, filter(nc)%actfirec, & - filter(nc)%num_actfirep, filter(nc)%actfirep, & - doalb, crop_inst, & - soilstate_inst, soilbiogeochem_state_inst, & - water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & - water_inst%waterfluxbulk_inst, frictionvel_inst, canopystate_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) - call t_stopf('EcosysDynPostDrainage') - + if (use_cn .or. use_fates) then + call t_startf('EcosysDynPostDrainage') + call bgc_vegetation_inst%EcosystemDynamicsPostDrainage(bounds_clump, & + filter(nc)%num_allc, filter(nc)%allc, & + filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + filter(nc)%num_bgc_vegp, filter(nc)%bgc_vegp, & + filter(nc)%num_actfirec, filter(nc)%actfirec, & + filter(nc)%num_actfirep, filter(nc)%actfirep, & + doalb, crop_inst, & + soilstate_inst, soilbiogeochem_state_inst, & + water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & + water_inst%waterfluxbulk_inst, frictionvel_inst, canopystate_inst, & + soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) + call t_stopf('EcosysDynPostDrainage') + end if if ( use_fates) then @@ -1103,32 +1103,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! for leaf photosynthetic acclimation temperature. These ! moving averages are updated here call clm_fates%WrapUpdateFatesRmean(nc,temperature_inst) - end if - - ! call EDBGCDyn(bounds_clump, & - ! filter(nc)%num_soilc, filter(nc)%soilc, & - ! filter(nc)%num_soilp, filter(nc)%soilp, & - ! filter(nc)%num_pcropp, filter(nc)%pcropp, doalb, & - ! bgc_vegetation_inst%cnveg_carbonflux_inst, & - ! bgc_vegetation_inst%cnveg_carbonstate_inst, & - ! soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - ! soilbiogeochem_state_inst, clm_fates, & - ! soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - ! c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & - ! c14_soilbiogeochem_carbonstate_inst, c14_soilbiogeochem_carbonflux_inst, & - ! active_layer_inst, atm2lnd_inst, water_inst%waterfluxbulk_inst, & - ! canopystate_inst, soilstate_inst, temperature_inst, crop_inst, ch4_inst) - - !if ( decomp_method /= no_soil_decomp )then - ! call EDBGCDynSummary(bounds_clump, & - ! filter(nc)%num_soilc, filter(nc)%soilc, & - ! filter(nc)%num_soilp, filter(nc)%soilp, & - ! soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & - ! c13_soilbiogeochem_carbonflux_inst, c13_soilbiogeochem_carbonstate_inst, & - ! c14_soilbiogeochem_carbonflux_inst, c14_soilbiogeochem_carbonstate_inst, & - ! soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & - ! nc) - ! end if + call clm_fates%wrap_update_hifrq_hist(bounds_clump, & soilbiogeochem_carbonflux_inst, & @@ -1141,9 +1116,6 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! This is the main call to FATES dynamics ! -------------------------------------------------------------------------- - if ( masterproc ) then - write(iulog,*) 'clm: calling FATES model ', get_nstep() - end if call clm_fates%dynamics_driv( nc, bounds_clump, & atm2lnd_inst, soilstate_inst, temperature_inst, active_layer_inst, & water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, & @@ -1173,16 +1145,18 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Check the carbon and nitrogen balance ! ============================================================================ - call t_startf('cnbalchk') - call bgc_vegetation_inst%BalanceCheck( & - bounds_clump, filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & - soilbiogeochem_carbonflux_inst, & - soilbiogeochem_nitrogenflux_inst, & - soilbiogeochem_carbonstate_inst, & - soilbiogeochem_nitrogenstate_inst, & - atm2lnd_inst, clm_fates ) - call t_stopf('cnbalchk') - + if(use_cn .or. use_fates)then + call t_startf('cnbalchk') + call bgc_vegetation_inst%BalanceCheck( & + bounds_clump, filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & + soilbiogeochem_carbonflux_inst, & + soilbiogeochem_nitrogenflux_inst, & + soilbiogeochem_carbonstate_inst, & + soilbiogeochem_nitrogenstate_inst, & + atm2lnd_inst, clm_fates ) + call t_stopf('cnbalchk') + end if + ! Calculation of methane fluxes if (use_lch4) then diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 37c22cc85b..bf7a9d625a 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -19,6 +19,7 @@ module filterMod use ColumnType , only : col use PatchType , only : patch use glcBehaviorMod , only : glc_behavior_type + use clm_varctl , only : use_cn, use_fates, use_fates_sp ! ! !PUBLIC TYPES: implicit none diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index 114019a3d7..e42e395801 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -14,7 +14,6 @@ module SoilBiogeochemCarbonFluxType use ColumnType , only : col use LandunitType , only : lun use SparseMatrixMultiplyMod , only : sparse_matrix_type, diag_matrix_type, vector_type - use clm_varctl , only : use_fates ! ! !PUBLIC TYPES: @@ -59,12 +58,6 @@ module SoilBiogeochemCarbonFluxType real(r8), pointer :: somhr_col (:) ! (gC/m2/s) soil organic matter heterotrophic res: donor-pool based definition real(r8), pointer :: soilc_change_col (:) ! (gC/m2/s) FUN used soil C - ! fluxes to receive carbon inputs from FATES - real(r8), pointer :: FATES_c_to_litr_c_col (:,:,:) ! total litter coming from ED. gC/m3/s - real(r8), pointer :: FATES_c_to_litr_lab_c_col (:,:) ! total labile litter coming from ED. gC/m3/s - real(r8), pointer :: FATES_c_to_litr_cel_c_col (:,:) ! total cellulose litter coming from ED. gC/m3/s - real(r8), pointer :: FATES_c_to_litr_lig_c_col (:,:) ! total lignin litter coming from ED. gC/m3/s - contains procedure , public :: Init @@ -165,22 +158,7 @@ subroutine InitAllocate(this, bounds) if(use_soil_matrixcn)then end if - if ( use_fates ) then - ! initialize these variables to be zero rather than a bad number since they are not zeroed every timestep (due to a need for them to persist) - - allocate(this%FATES_c_to_litr_c_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools)) - this%FATES_c_to_litr_c_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools) = 0._r8 - - allocate(this%FATES_c_to_litr_lab_c_col(begc:endc,1:nlevdecomp_full)) - this%FATES_c_to_litr_lab_c_col(begc:endc,1:nlevdecomp_full) = 0._r8 - - allocate(this%FATES_c_to_litr_cel_c_col(begc:endc,1:nlevdecomp_full)) - this%FATES_c_to_litr_cel_c_col(begc:endc,1:nlevdecomp_full) = 0._r8 - - allocate(this%FATES_c_to_litr_lig_c_col(begc:endc,1:nlevdecomp_full)) - this%FATES_c_to_litr_lig_c_col(begc:endc,1:nlevdecomp_full) = 0._r8 - endif allocate(this%litr_lig_c_to_n_col(begc:endc)) this%litr_lig_c_to_n_col(:)= 0._r8 @@ -625,23 +603,6 @@ subroutine InitHistory(this, bounds, carbon_type) end do - if ( use_fates ) then - - call hist_addfld_decomp(fname='FATES_c_to_litr_lab_c', units='gC/m^3/s', type2d='levdcmp', & - avgflag='A', long_name='litter labile carbon flux from FATES to BGC', & - ptr_col=this%FATES_c_to_litr_lab_c_col) - - call hist_addfld_decomp(fname='FATES_c_to_litr_cel_c', units='gC/m^3/s', type2d='levdcmp', & - avgflag='A', long_name='litter celluluse carbon flux from FATES to BGC', & - ptr_col=this%FATES_c_to_litr_cel_c_col) - - call hist_addfld_decomp(fname='FATES_c_to_litr_lig_c', units='gC/m^3/s', type2d='levdcmp', & - avgflag='A', long_name='litter lignin carbon flux from FATES to BGC', & - ptr_col=this%FATES_c_to_litr_lig_c_col) - - endif - - end subroutine InitHistory !----------------------------------------------------------------------- @@ -694,40 +655,6 @@ subroutine Restart(this, bounds, ncid, flag) logical :: readvar !----------------------------------------------------------------------- - ! - ! if FATES is enabled, need to restart the variables used to transfer from FATES to CLM as they - ! are persistent between daily FATES dynamics calls and half-hourly CLM timesteps - ! - if ( use_fates ) then - - ptr2d => this%FATES_c_to_litr_lab_c_col - call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_lab_c_col', xtype=ncd_double, & - dim1name='column', dim2name='levgrnd', switchdim=.true., & - long_name='', units='gC/m3/s', scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=ptr2d) - - ptr2d => this%FATES_c_to_litr_cel_c_col - call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_cel_c_col', xtype=ncd_double, & - dim1name='column', dim2name='levgrnd', switchdim=.true., & - long_name='', units='gC/m3/s', scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=ptr2d) - - ptr2d => this%FATES_c_to_litr_lig_c_col - call restartvar(ncid=ncid, flag=flag, varname='FATES_c_to_litr_lig_c_col', xtype=ncd_double, & - dim1name='column', dim2name='levgrnd', switchdim=.true., & - long_name='', units='gC/m3/s', scale_by_thickness=.false., & - interpinic_flag='interp', readvar=readvar, data=ptr2d) - - ! Copy last 3 variables to an array of litter pools for use in do loops. - ! Repeat copy in src/utils/clmfates_interfaceMod.F90. - ! Keep the three originals to avoid backwards compatibility issues with - ! restart files. - this%FATES_c_to_litr_c_col(:,:,1) = this%FATES_c_to_litr_lab_c_col(:,:) - this%FATES_c_to_litr_c_col(:,:,2) = this%FATES_c_to_litr_cel_c_col(:,:) - this%FATES_c_to_litr_c_col(:,:,3) = this%FATES_c_to_litr_lig_c_col(:,:) - - end if - call restartvar(ncid=ncid, flag=flag, varname='ligninNratioAvg', xtype=ncd_double, & dim1name='column', & long_name='', units='', & @@ -806,8 +733,6 @@ subroutine SetValues ( this, num_column, filter_column, value_column) this%soilc_change_col(i) = value_column end do - ! NOTE: do not zero the fates to BGC C flux variables since they need to persist from the daily fates timestep s to the half-hourly BGC timesteps. I.e. FATES_c_to_litr_lab_c_col, FATES_c_to_litr_cel_c_col, FATES_c_to_litr_lig_c_col - end subroutine SetValues !----------------------------------------------------------------------- @@ -970,18 +895,19 @@ subroutine Summary(this, bounds, & ! Calculate ligninNratio ! FATES does its own calculation - if (.not. use_fates .and. decomp_method == mimics_decomp) then + if (decomp_method == mimics_decomp) then do fp = 1,num_soilp p = filter_soilp(fp) - - associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type - ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * & - pftcon%lflitcn(ivt(p)) * & - leafc_to_litter_patch(p) - ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * & - pftcon%frootcn(ivt(p)) * & - frootc_to_litter_patch(p) - end associate + if( .not.patch%is_fates(p)) then + associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type + ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * & + pftcon%lflitcn(ivt(p)) * & + leafc_to_litter_patch(p) + ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * & + pftcon%frootcn(ivt(p)) * & + frootc_to_litter_patch(p) + end associate + end if end do call p2c(bounds, num_soilc, filter_soilc, & diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index a09441069a..349a6c140d 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -17,6 +17,7 @@ module SoilBiogeochemCarbonStateType use GridcellType , only : grc use SoilBiogeochemStateType , only : get_spinup_latitude_term use SparseMatrixMultiplyMod , only : sparse_matrix_type, vector_type + use CNVegCarbonStateType , only : cnveg_carbonstate_type ! ! !PUBLIC TYPES: implicit none @@ -30,19 +31,28 @@ module SoilBiogeochemCarbonStateType real(r8), pointer :: ctrunc_vr_col (:,:) ! (gC/m3) vertically-resolved column-level sink for C truncation ! summary (diagnostic) state variables, not involved in mass balance - real(r8), pointer :: ctrunc_col (:) ! (gC/m2) column-level sink for C truncation - real(r8), pointer :: totmicc_col (:) ! (gC/m2) total microbial carbon - real(r8), pointer :: totlitc_col (:) ! (gC/m2) total litter carbon - real(r8), pointer :: totlitc_1m_col (:) ! (gC/m2) total litter carbon to 1 meter - real(r8), pointer :: totsomc_col (:) ! (gC/m2) total soil organic matter carbon - real(r8), pointer :: totsomc_1m_col (:) ! (gC/m2) total soil organic matter carbon to 1 meter - real(r8), pointer :: cwdc_col (:) ! (gC/m2) coarse woody debris C (diagnostic) - real(r8), pointer :: decomp_cpools_1m_col (:,:) ! (gC/m2) Diagnostic: decomposing (litter, cwd, soil) c pools to 1 meter - real(r8), pointer :: decomp_cpools_col (:,:) ! (gC/m2) decomposing (litter, cwd, soil) c pools - real(r8), pointer :: dyn_cbal_adjustments_col(:) ! (gC/m2) adjustments to each column made in this timestep via dynamic column area adjustments (note: this variable only makes sense at the column-level: it is meaningless if averaged to the gridcell-level) - integer :: restart_file_spinup_state ! spinup state as read from restart file, for determining whether to enter or exit spinup mode. - real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools + real(r8), pointer :: ctrunc_col (:) ! (gC/m2) column-level sink for C truncation + real(r8), pointer :: totmicc_col (:) ! (gC/m2) total microbial carbon + real(r8), pointer :: totlitc_col (:) ! (gC/m2) total litter carbon + real(r8), pointer :: totlitc_1m_col (:) ! (gC/m2) total litter carbon to 1 meter + real(r8), pointer :: totsomc_col (:) ! (gC/m2) total soil organic matter carbon + real(r8), pointer :: totsomc_1m_col (:) ! (gC/m2) total soil organic matter carbon to 1 meter + real(r8), pointer :: cwdc_col (:) ! (gC/m2) coarse woody debris C (diagnostic) + real(r8), pointer :: decomp_cpools_1m_col (:,:) ! (gC/m2) Diagnostic: decomposing (litter, cwd, soil) c pools to 1 meter + real(r8), pointer :: decomp_cpools_col (:,:) ! (gC/m2) decomposing (litter, cwd, soil) c pools + real(r8), pointer :: dyn_cbal_adjustments_col(:) ! (gC/m2) adjustments to each column made in this timestep via dynamic column + ! area adjustments (note: this variable only makes sense at the column-level: + ! it is meaningless if averaged to the gridcell-level) + integer :: restart_file_spinup_state ! spinup state as read from restart file, for determining whether to enter or exit spinup mode. + real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools + + + ! Carbon totals, includes soil, cpool and vegetation + real(r8), pointer :: totc_col (:) ! (gC/m2) total column carbon, incl veg and cpool + real(r8), pointer :: totecosysc_col (:) ! (gC/m2) total ecosystem carbon, incl veg but excl cpool + real(r8), pointer :: totc_grc (:) ! (gC/m2) total gridcell carbon + ! Matrix-cn contains @@ -95,9 +105,11 @@ subroutine InitAllocate(this, bounds) ! ! !LOCAL VARIABLES: integer :: begc,endc + integer :: begg,endg !------------------------------------------------------------------------ begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg allocate( this%decomp_cpools_col (begc :endc,1:ndecomp_pools)) ; this%decomp_cpools_col (:,:) = nan allocate( this%decomp_cpools_1m_col (begc :endc,1:ndecomp_pools)) ; this%decomp_cpools_1m_col (:,:) = nan @@ -116,9 +128,8 @@ subroutine InitAllocate(this, bounds) this%decomp_soilc_vr_col(:,:)= nan allocate(this%ctrunc_col (begc :endc)) ; this%ctrunc_col (:) = nan - if ( .not. use_fates ) then - allocate(this%cwdc_col (begc :endc)) ; this%cwdc_col (:) = nan - endif + allocate(this%cwdc_col (begc :endc)) ; this%cwdc_col (:) = nan + allocate(this%totmicc_col (begc :endc)) ; this%totmicc_col (:) = nan allocate(this%totlitc_col (begc :endc)) ; this%totlitc_col (:) = nan allocate(this%totsomc_col (begc :endc)) ; this%totsomc_col (:) = nan @@ -126,6 +137,10 @@ subroutine InitAllocate(this, bounds) allocate(this%totsomc_1m_col (begc :endc)) ; this%totsomc_1m_col (:) = nan allocate(this%dyn_cbal_adjustments_col (begc:endc)) ; this%dyn_cbal_adjustments_col (:) = nan + allocate(this%totc_col (begc:endc)) ; this%totc_col (:) = nan + allocate(this%totecosysc_col (begc:endc)) ; this%totecosysc_col (:) = nan + allocate(this%totc_grc (begg:endg)) ; this%totc_grc (:) = nan + this%restart_file_spinup_state = huge(1) end subroutine InitAllocate @@ -249,6 +264,16 @@ subroutine InitHistory(this, bounds, carbon_type) &only makes sense at the column level: should not be averaged to gridcell', & ptr_col=this%dyn_cbal_adjustments_col, default='inactive') + this%totc_col(begc:endc) = spval + call hist_addfld1d (fname='TOTCOLC', units='gC/m^2', & + avgflag='A', long_name='total column carbon, incl veg and cpool but excl product pools', & + ptr_col=this%totc_col) + + this%totecosysc_col(begc:endc) = spval + call hist_addfld1d (fname='TOTECOSYSC', units='gC/m^2', & + avgflag='A', long_name='total ecosystem carbon, incl veg but excl cpool and product pools', & + ptr_col=this%totecosysc_col) + end if !------------------------------- @@ -336,6 +361,17 @@ subroutine InitHistory(this, bounds, carbon_type) long_name='C13 adjustments in soil carbon due to dynamic column areas; & &only makes sense at the column level: should not be averaged to gridcell', & ptr_col=this%dyn_cbal_adjustments_col, default='inactive') + + this%totc_col(begc:endc) = spval + call hist_addfld1d (fname='C13_TOTCOLC', units='gC13/m^2', & + avgflag='A', long_name='C13 total column carbon, incl veg and cpool but excl product pools', & + ptr_col=this%totc_col, default='inactive') + + this%totecosysc_col(begc:endc) = spval + call hist_addfld1d (fname='C13_TOTECOSYSC', units='gC13/m^2', & + avgflag='A', long_name='C13 total ecosystem carbon, incl veg but excl cpool and product pools', & + ptr_col=this%totecosysc_col) + endif !------------------------------- @@ -426,6 +462,17 @@ subroutine InitHistory(this, bounds, carbon_type) long_name='C14 adjustments in soil carbon due to dynamic column areas; & &only makes sense at the column level: should not be averaged to gridcell', & ptr_col=this%dyn_cbal_adjustments_col, default='inactive') + + this%totc_col(begc:endc) = spval + call hist_addfld1d (fname='C14_TOTCOLC', units='gC14/m^2', & + avgflag='A', long_name='C14 total column carbon, incl veg and cpool but excl product pools', & + ptr_col=this%totc_col, default='inactive') + + this%totecosysc_col(begc:endc) = spval + call hist_addfld1d (fname='C14_TOTECOSYSC', units='gC14/m^2', & + avgflag='A', long_name='C14 total ecosystem carbon, incl veg but excl cpool and product pools', & + ptr_col=this%totecosysc_col) + endif end subroutine InitHistory @@ -445,7 +492,7 @@ subroutine InitCold(this, bounds, ratio, c12_soilbiogeochem_carbonstate_inst) type(soilbiogeochem_carbonstate_type), intent(in), optional :: c12_soilbiogeochem_carbonstate_inst ! ! !LOCAL VARIABLES: - integer :: p,c,l,j,k + integer :: p,c,l,j,k,g integer :: fc ! filter index integer :: num_special_col ! number of good values in special_col filter integer :: special_col(bounds%endc-bounds%begc+1) ! special landunit filter - columns @@ -523,23 +570,30 @@ subroutine InitCold(this, bounds, ratio, c12_soilbiogeochem_carbonstate_inst) end if end if - if ( .not. use_fates ) then - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - if (present(c12_soilbiogeochem_carbonstate_inst)) then - this%cwdc_col(c) = c12_soilbiogeochem_carbonstate_inst%cwdc_col(c) * ratio - else - this%cwdc_col(c) = 0._r8 - end if - this%ctrunc_col(c) = 0._r8 - this%totmicc_col(c) = 0._r8 - this%totlitc_col(c) = 0._r8 - this%totsomc_col(c) = 0._r8 - this%totlitc_1m_col(c) = 0._r8 - this%totsomc_1m_col(c) = 0._r8 + + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + if (present(c12_soilbiogeochem_carbonstate_inst) .and. (.not.col%is_fates(c)) ) then + this%cwdc_col(c) = c12_soilbiogeochem_carbonstate_inst%cwdc_col(c) * ratio + else + this%cwdc_col(c) = 0._r8 end if + this%ctrunc_col(c) = 0._r8 + this%totmicc_col(c) = 0._r8 + this%totlitc_col(c) = 0._r8 + this%totsomc_col(c) = 0._r8 + this%totlitc_1m_col(c) = 0._r8 + this%totsomc_1m_col(c) = 0._r8 + + this%totc_col(c) = 0._r8 + this%totecosysc_col(c) = 0._r8 end if + end do + do g = bounds%begg, bounds%endg + this%totc_grc(g) = 0._r8 + end do + ! now loop through special filters and explicitly set the variables that ! have to be in place for biogeophysics @@ -815,7 +869,7 @@ subroutine SetValues ( this, num_column, filter_column, value_column) do fi = 1,num_column i = filter_column(fi) - if ( .not. use_fates ) then + if ( .not. col%is_fates(i) ) then this%cwdc_col(i) = value_column end if this%ctrunc_col(i) = value_column @@ -824,6 +878,8 @@ subroutine SetValues ( this, num_column, filter_column, value_column) this%totlitc_1m_col(i) = value_column this%totsomc_col(i) = value_column this%totsomc_1m_col(i) = value_column + this%totc_col(i) = value_column + this%totecosysc_col(i) = value_column end do do j = 1,nlevdecomp_full @@ -875,7 +931,7 @@ subroutine SetValues ( this, num_column, filter_column, value_column) end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_allc, filter_allc) + subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst) ! ! !DESCRIPTION: ! Perform column-level carbon summary calculations @@ -883,19 +939,23 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! !ARGUMENTS: class(soilbiogeochem_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_allc ! number of columns in allc filter - integer , intent(in) :: filter_allc(:) ! filter for all active columns + integer , intent(in) :: num_soilc ! number of columns in soil filter + integer , intent(in) :: filter_soilc(:) ! filter for all active columns + type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst + ! ! !LOCAL VARIABLES: integer :: c,j,k,l ! indices integer :: fc ! filter indices real(r8) :: maxdepth ! depth to integrate soil variables + real(r8) :: ecovegc_col + real(r8) :: totvegc_col !----------------------------------------------------------------------- ! vertically integrate each of the decomposing C pools do l = 1, ndecomp_pools - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_cpools_col(c,l) = 0._r8 if(use_soil_matrixcn)then end if @@ -903,8 +963,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end do do l = 1, ndecomp_pools do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_cpools_col(c,l) = & this%decomp_cpools_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j) @@ -919,23 +979,23 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! vertically integrate each of the decomposing C pools to 1 meter maxdepth = 1._r8 do l = 1, ndecomp_pools - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_cpools_1m_col(c,l) = 0._r8 end do end do do l = 1, ndecomp_pools do j = 1, nlevdecomp if ( zisoi(j) <= maxdepth ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_cpools_1m_col(c,l) = & this%decomp_cpools_1m_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j) end do elseif ( zisoi(j-1) < maxdepth ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_cpools_1m_col(c,l) = & this%decomp_cpools_1m_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * (maxdepth - zisoi(j-1)) @@ -949,16 +1009,16 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! Add soil carbon pools together to produce vertically-resolved decomposing total soil c pool if ( nlevdecomp_full > 1 ) then do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_soilc_vr_col(c,j) = 0._r8 end do end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_soilc_vr_col(c,j) = this%decomp_soilc_vr_col(c,j) + & this%decomp_cpools_vr_col(c,j,l) end do @@ -968,13 +1028,13 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end if ! truncation carbon - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%ctrunc_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%ctrunc_col(c) = & this%ctrunc_col(c) + & this%ctrunc_vr_col(c,j) * dzsoi_decomp(j) @@ -983,14 +1043,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! total litter carbon in the top meter (TOTLITC_1m) if ( nlevdecomp > 1) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitc_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitc_1m_col(c) = this%totlitc_1m_col(c) + & this%decomp_cpools_1m_col(c,l) end do @@ -1000,14 +1060,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! total soil organic matter carbon in the top meter (TOTSOMC_1m) if ( nlevdecomp > 1) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomc_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomc_1m_col(c) = this%totsomc_1m_col(c) + this%decomp_cpools_1m_col(c,l) end do end if @@ -1015,64 +1075,89 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end if ! total microbial carbon (TOTMICC) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totmicc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totmicc_col(c) = this%totmicc_col(c) + this%decomp_cpools_col(c,l) end do endif end do ! total litter carbon (TOTLITC) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitc_col(c) = this%totlitc_col(c) + this%decomp_cpools_col(c,l) end do endif end do ! total soil organic matter carbon (TOTSOMC) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomc_col(c) = this%totsomc_col(c) + this%decomp_cpools_col(c,l) end do end if end do - ! coarse woody debris carbon - if (.not. use_fates ) then - do fc = 1,num_allc - c = filter_allc(fc) - this%cwdc_col(c) = 0._r8 - end do - do l = 1, ndecomp_pools - if ( decomp_cascade_con%is_cwd(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + + + do fc = 1,num_soilc + c = filter_soilc(fc) + + ! coarse woody debris carbon + this%cwdc_col(c) = 0._r8 + + if(col%is_fates(c)) then + totvegc_col = 0._r8 + ecovegc_col = 0._r8 + else + do l = 1, ndecomp_pools + if ( decomp_cascade_con%is_cwd(l) ) then this%cwdc_col(c) = this%cwdc_col(c) + this%decomp_cpools_col(c,l) - end do - end if - end do + end if + end do + + totvegc_col = cnveg_carbonstate_inst%totc_p2c_col(c) + ecovegc_col = cnveg_carbonstate_inst%totvegc_col(c) + end if - end if + ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) + this%totecosysc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + ecovegc_col + + ! total column carbon, including veg and cpool (TOTCOLC) + this%totc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + this%ctrunc_col(c) + & + totvegc_col + end do + + end subroutine Summary !------------------------------------------------------------------------ diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index 3e54e52436..435e6c327c 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -21,6 +21,7 @@ module SoilBiogeochemNitrogenStateType use GridcellType , only : grc use SoilBiogeochemStateType , only : get_spinup_latitude_term use SparseMatrixMultiplyMod , only : sparse_matrix_type, vector_type + use CNVegNitrogenStateType , only : cnveg_nitrogenstate_type ! ! !PUBLIC TYPES: implicit none @@ -59,7 +60,11 @@ module SoilBiogeochemNitrogenStateType real(r8), pointer :: dyn_no3bal_adjustments_col (:) ! (gN/m2) NO3 adjustments to each column made in this timestep via dynamic column area adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) real(r8), pointer :: dyn_nh4bal_adjustments_col (:) ! (gN/m2) NH4 adjustments to each column made in this timestep via dynamic column adjustments (only makes sense at the column-level: meaningless if averaged to the gridcell-level) real(r8) :: totvegcthresh ! threshold for total vegetation carbon to zero out decomposition pools - + + real(r8), pointer :: totn_col (:) ! (gN/m2) total column nitrogen, incl veg + real(r8), pointer :: totecosysn_col (:) ! (gN/m2) total ecosystem nitrogen, incl veg + real(r8), pointer :: totn_grc (:) ! (gN/m2) total gridcell nitrogen + ! Matrix-cn contains @@ -144,6 +149,10 @@ subroutine InitAllocate(this, bounds) allocate(this%decomp_soiln_vr_col(begc:endc,1:nlevdecomp_full)) this%decomp_soiln_vr_col(:,:)= nan + allocate(this%totn_col (begc:endc)) ; this%totn_col (:) = nan + allocate(this%totecosysn_col (begc:endc)) ; this%totecosysn_col (:) = nan + allocate(this%totn_grc (bounds%begg:bounds%endg)) ; this%totn_grc (:) = nan + end subroutine InitAllocate !------------------------------------------------------------------------ @@ -329,6 +338,17 @@ subroutine InitHistory(this, bounds) &only makes sense at the column level: should not be averaged to gridcell', & ptr_col=this%dyn_nh4bal_adjustments_col, default='inactive') end if + + this%totecosysn_col(begc:endc) = spval + call hist_addfld1d (fname='TOTECOSYSN', units='gN/m^2', & + avgflag='A', long_name='total ecosystem N, excluding product pools', & + ptr_col=this%totecosysn_col) + + this%totn_col(begc:endc) = spval + call hist_addfld1d (fname='TOTCOLN', units='gN/m^2', & + avgflag='A', long_name='total column-level N, excluding product pools', & + ptr_col=this%totn_col) + end subroutine InitHistory !----------------------------------------------------------------------- @@ -434,6 +454,21 @@ subroutine InitCold(this, bounds, & end if end do + do c = bounds%begc, bounds%endc + l = col%landunit(c) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + ! total nitrogen pools + this%totecosysn_col(c) = 0._r8 + this%totn_col(c) = 0._r8 + end if + end do + + + do g = bounds%begg, bounds%endg + this%totn_grc(g) = 0._r8 + end do + + call this%SetValues (num_column=num_special_col, filter_column=special_col, value_column=0._r8) end subroutine InitCold @@ -756,6 +791,12 @@ subroutine SetValues ( this, num_column, filter_column, value_column ) end do end do + do fi = 1,num_column + i = filter_column(fi) + this%totecosysn_col(i) = value_column + this%totn_col(i) = value_column + end do + ! Set values for the matrix solution if(use_soil_matrixcn)then end if @@ -763,30 +804,36 @@ subroutine SetValues ( this, num_column, filter_column, value_column ) end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_allc, filter_allc) + + subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_inst) + ! ! !ARGUMENTS: class (soilbiogeochem_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_allc ! number of columns in allc filter - integer , intent(in) :: filter_allc(:) ! filter for all active columns + integer , intent(in) :: num_soilc ! number of columns in soilc filter + integer , intent(in) :: filter_soilc(:) ! filter for all active columns + type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst + ! ! !LOCAL VARIABLES: integer :: c,j,k,l ! indices integer :: fc ! lake filter indices real(r8) :: maxdepth ! depth to integrate soil variables + real(r8) :: totvegn_col ! local total ecosys veg N, allows 0 for fates + real(r8) :: ecovegn_col ! local total veg N, allows 0 for fates !----------------------------------------------------------------------- ! vertically integrate NO3 NH4 N2O pools if (use_nitrif_denitrif) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%smin_no3_col(c) = 0._r8 this%smin_nh4_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%smin_no3_col(c) = & this%smin_no3_col(c) + & this%smin_no3_vr_col(c,j) * dzsoi_decomp(j) @@ -801,15 +848,15 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! vertically integrate each of the decomposing N pools do l = 1, ndecomp_pools - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_npools_col(c,l) = 0._r8 if(use_soil_matrixcn)then end if end do do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_npools_col(c,l) = & this%decomp_npools_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * dzsoi_decomp(j) @@ -823,8 +870,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc) if ( nlevdecomp > 1) then do l = 1, ndecomp_pools - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_npools_1m_col(c,l) = 0._r8 end do end do @@ -834,15 +881,15 @@ subroutine Summary(this, bounds, num_allc, filter_allc) do l = 1, ndecomp_pools do j = 1, nlevdecomp if ( zisoi(j) <= maxdepth ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_npools_1m_col(c,l) = & this%decomp_npools_1m_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * dzsoi_decomp(j) end do elseif ( zisoi(j-1) < maxdepth ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_npools_1m_col(c,l) = & this%decomp_npools_1m_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * (maxdepth - zisoi(j-1)) @@ -854,16 +901,16 @@ subroutine Summary(this, bounds, num_allc, filter_allc) ! Add soil nitrogen pools together to produce vertically-resolved decomposing total soil N pool if ( nlevdecomp_full > 1 ) then do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_soiln_vr_col(c,j) = 0._r8 end do end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%decomp_soiln_vr_col(c,j) = this%decomp_soiln_vr_col(c,j) + & this%decomp_npools_vr_col(c,j,l) end do @@ -873,14 +920,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end if ! total litter nitrogen to 1 meter (TOTLITN_1m) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitn_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitn_1m_col(c) = & this%totlitn_1m_col(c) + & this%decomp_npools_1m_col(c,l) @@ -889,14 +936,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end do ! total soil organic matter nitrogen to 1 meter (TOTSOMN_1m) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomn_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomn_1m_col(c) = this%totsomn_1m_col(c) + & this%decomp_npools_1m_col(c,l) end do @@ -906,14 +953,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) endif ! total litter nitrogen (TOTLITN) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totlitn_col(c) = & this%totlitn_col(c) + & this%decomp_npools_col(c,l) @@ -922,14 +969,14 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end do ! total microbial nitrogen (TOTMICN) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totmicn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totmicn_col(c) = & this%totmicn_col(c) + & this%decomp_npools_col(c,l) @@ -938,61 +985,91 @@ subroutine Summary(this, bounds, num_allc, filter_allc) end do ! total soil organic matter nitrogen (TOTSOMN) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%totsomn_col(c) = this%totsomn_col(c) + & this%decomp_npools_col(c,l) end do end if end do - ! total cwdn - do fc = 1,num_allc - c = filter_allc(fc) - this%cwdn_col(c) = 0._r8 - end do - do l = 1, ndecomp_pools - if ( decomp_cascade_con%is_cwd(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) - this%cwdn_col(c) = this%cwdn_col(c) + & - this%decomp_npools_col(c,l) - end do - end if - end do + ! total sminn - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%sminn_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%sminn_col(c) = this%sminn_col(c) + & this%sminn_vr_col(c,j) * dzsoi_decomp(j) end do end do ! total col_ntrunc - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%ntrunc_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) this%ntrunc_col(c) = this%ntrunc_col(c) + & this%ntrunc_vr_col(c,j) * dzsoi_decomp(j) end do end do + ! total cwdn + do fc = 1,num_soilc + c = filter_soilc(fc) + this%cwdn_col(c) = 0._r8 + + if(col%is_fates(c)) then + totvegn_col = 0._r8 + ecovegn_col = 0._r8 + else + + do l = 1, ndecomp_pools + if ( decomp_cascade_con%is_cwd(l) ) then + this%cwdn_col(c) = this%cwdn_col(c) + & + this%decomp_npools_col(c,l) + end if + end do + totvegn_col = cnveg_nitrogenstate_inst%totn_p2c_col(c) + ecovegn_col = cnveg_nitrogenstate_inst%totvegn_col(c) + + end if + + ! total ecosystem nitrogen, including veg (TOTECOSYSN) + this%totecosysn_col(c) = & + this%cwdn_col(c) + & + this%totlitn_col(c) + & + this%totmicn_col(c) + & + this%totsomn_col(c) + & + this%sminn_col(c) + & + ecovegn_col + + ! total column nitrogen, including patch (TOTCOLN) + + this%totn_col(c) = & + this%cwdn_col(c) + & + this%totlitn_col(c) + & + this%totmicn_col(c) + & + this%totsomn_col(c) + & + this%sminn_col(c) + & + this%ntrunc_col(c) + & + totvegn_col + + end do + end subroutine Summary !----------------------------------------------------------------------- diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index f225a3255b..2eb746e6f3 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -562,8 +562,6 @@ subroutine init(this, bounds_proc ) use clm_instur , only : wt_nat_patch use FATESFireFactoryMod , only: create_fates_fire_data_method - implicit none - ! Input Arguments class(hlm_fates_interface_type), intent(inout) :: this type(bounds_type),intent(in) :: bounds_proc @@ -770,7 +768,6 @@ subroutine check_hlm_active(this, nc, bounds_clump) ! in handy when we have dynamic sites in FATES ! --------------------------------------------------------------------------------- - implicit none class(hlm_fates_interface_type), intent(inout) :: this integer :: nc type(bounds_type),intent(in) :: bounds_clump @@ -820,7 +817,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & use subgridMod, only : natveg_patch_exists ! !ARGUMENTS: - implicit none + class(hlm_fates_interface_type), intent(inout) :: this type(bounds_type),intent(in) :: bounds_clump type(atm2lnd_type) , intent(in) :: atm2lnd_inst @@ -1067,49 +1064,61 @@ end subroutine dynamics_driv ! =============================================================================== - subroutine UpdateCLitterFluxes(this,bounds_clump,soilbiogeochem_carbonflux_inst,c) + subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) + + use clm_varpar, only : i_met_lit - implicit none class(hlm_fates_interface_type), intent(inout) :: this - type(bounds_type) , intent(in) :: bounds_clump type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst - integer , intent(in) :: c + integer , intent(in) :: ci ! clump index + integer , intent(in) :: c ! column index integer :: s ! site index - integer :: nc ! clump index real(r8) :: dtime - - + integer :: i_lig_lit, i_cel_lit ! indices for lignan and cellulose + dtime = get_step_size_real() - nc = bounds_clump%clump_index - s = this%f2hmap(nc)%hsites(c) + s = this%f2hmap(ci)%hsites(c) associate(cf_soil => soilbiogeochem_carbonflux_inst) if ( .not. use_fates_sp ) then - cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_met_lit) = & - cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_met_lit) + & - this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * dtime - cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_cel_lit) = & - cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_cel_lit) + & - this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp)* dtime - cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_lig_lit) = & - cf_soil%decomp_cpools_sourcesink(c,1:nlevdecomp,i_lig_lit) + & - this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * dtime + + cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_met_lit) = & + cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_met_lit) + & + this%fates(ci)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * dtime + + i_cel_lit = i_met_lit + 1 + + cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_cel_lit) = & + cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_cel_lit) + & + this%fates(ci)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp)* dtime + + if (decomp_method == mimics_decomp) then + ! Mimics has a structural pool, which is cellulose and lignan + i_lig_lit = i_cel_lit + elseif(decomp_method == century_decomp ) then + ! CENTURY has a separate lignan pool from cellulose + i_lig_lit = i_cel_lit + 1 + end if + + cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_lig_lit) = & + cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_lig_lit) + & + this%fates(ci)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * dtime else ! In SP mode their is no mass flux between the two - cf_soil%decomp_cpools_sourcesink(c,:) = 0._r8 + cf_soil%decomp_cpools_sourcesink_col(c,:,:) = 0._r8 end if ! This is a diagnostic for carbon accounting (NOT IN CLM, ONLY ELM) !col_cf%litfall(c) = & - ! sum(this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & - ! this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - ! sum(this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & - ! this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - ! sum(this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * ^ - ! this%fates(nc)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + ! sum(this%fates(ci)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & + ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + ! sum(this%fates(ci)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & + ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + ! sum(this%fates(ci)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * ^ + ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) end associate @@ -1128,7 +1137,6 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! provides boundary conditions (such as vegetation fractional coverage) ! --------------------------------------------------------------------------------- - implicit none class(hlm_fates_interface_type), intent(inout) :: this type(bounds_type),intent(in) :: bounds_clump integer , intent(in) :: nc @@ -1372,8 +1380,6 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & use EDMainMod, only : ed_update_site use FatesInterfaceTypesMod, only: fates_maxElementsPerSite - implicit none - ! Arguments class(hlm_fates_interface_type), intent(inout) :: this @@ -1876,8 +1882,6 @@ subroutine wrap_sunfrac(this,nc,atm2lnd_inst,canopystate_inst) ! of the canopy that is exposed to sun. ! --------------------------------------------------------------------------------- - implicit none - ! Input Arguments class(hlm_fates_interface_type), intent(inout) :: this @@ -2014,8 +2018,6 @@ subroutine wrap_btran(this,nc,fn,filterc,soilstate_inst, & use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type - implicit none - ! Arguments class(hlm_fates_interface_type), intent(inout) :: this integer , intent(in) :: nc @@ -3003,35 +3005,6 @@ subroutine ComputeRootSoilFlux(this, bounds_clump, num_filterc, filterc, & end subroutine ComputeRootSoilFlux - ! ====================================================================================== -! -! THIS WAS MOVED TO WRAP_HYDRAULICS_DRIVE() -! -! subroutine TransferPlantWaterStorage(this, bounds_clump, nc, waterstate_inst) -! -! implicit none -! class(hlm_fates_interface_type), intent(inout) :: this -! type(bounds_type),intent(in) :: bounds_clump -! integer,intent(in) :: nc -! type(waterstate_type) , intent(inout) :: waterstate_inst -! -! ! locals -! integer :: s -! integer :: c -! -! if (.not. (use_fates .and. use_fates_planthydro) ) return -! -! do s = 1, this%fates(nc)%nsites -! c = this%f2hmap(nc)%fcolumn(s) -! waterstate_inst%total_plant_stored_h2o_col(c) = & -! this%fates(nc)%bc_out(s)%plant_stored_h2o_si -! end do -! return -!end subroutine TransferPlantWaterStorage - - - - ! ====================================================================================== subroutine wrap_hydraulics_drive(this, bounds_clump, nc, & @@ -3039,7 +3012,6 @@ subroutine wrap_hydraulics_drive(this, bounds_clump, nc, & fn, filterp, solarabs_inst, energyflux_inst) - implicit none class(hlm_fates_interface_type), intent(inout) :: this type(bounds_type),intent(in) :: bounds_clump integer,intent(in) :: nc @@ -3161,8 +3133,6 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates) use FatesInterfaceTypesMod, only : numpft_fates => numpft - implicit none - type(bounds_type), intent(in) :: hlm type(fates_bounds_type), intent(out) :: fates From c50615154ec2221f03fc62dc76481ac55c9e0c30 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 16 Feb 2023 08:50:02 -0500 Subject: [PATCH 0707/2067] more incremental fates-clm mass balance checking and pathway coupling changes --- src/biogeochem/CNBalanceCheckMod.F90 | 18 ++++++--- src/biogeochem/CNProductsMod.F90 | 20 ++++++++++ src/biogeochem/CNVegetationFacade.F90 | 53 ++++++++++++++------------- 3 files changed, 60 insertions(+), 31 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index 087242da30..7d510e6446 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -10,7 +10,7 @@ module CNBalanceCheckMod use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type, subgrid_level_gridcell, subgrid_level_column use abortutils , only : endrun - use clm_varctl , only : iulog, use_nitrif_denitrif + use clm_varctl , only : iulog, use_nitrif_denitrif, use_fates use clm_time_manager , only : get_step_size_real use CNVegNitrogenFluxType , only : cnveg_nitrogenflux_type use CNVegNitrogenStateType , only : cnveg_nitrogenstate_type @@ -143,11 +143,17 @@ subroutine BeginCNGridcellBalance(this, bounds, cnveg_carbonflux_inst, & ) begg = bounds%begg; endg = bounds%endg - - call cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_dribbler%get_amount_left_to_dribble_beg( & - bounds, hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)) - call cnveg_carbonflux_inst%dwt_conv_cflux_dribbler%get_amount_left_to_dribble_beg( & - bounds, dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg)) + + if(.not.use_fates)then + + call cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_dribbler%get_amount_left_to_dribble_beg( & + bounds, hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)) + call cnveg_carbonflux_inst%dwt_conv_cflux_dribbler%get_amount_left_to_dribble_beg( & + bounds, dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg)) + else + hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg) = 0._r8 + dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) = 0._r8 + end if do g = begg, endg begcb(g) = totc(g) + c_tot_woodprod(g) + c_cropprod1(g) + & diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index b6e5d6dad3..254063ddac 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -13,6 +13,8 @@ module CNProductsMod use clm_time_manager , only : get_step_size_real use SpeciesBaseType , only : species_base_type use PatchType , only : patch + use AnnualFluxDribbler , only : annual_flux_dribbler_type + use AnnualFluxDribbler , only : annual_flux_dribbler_gridcell ! implicit none private @@ -56,6 +58,13 @@ module CNProductsMod real(r8), pointer :: prod100_loss_grc(:) ! (g[C or N]/m2/s) decomposition loss from 100-yr wood product pool real(r8), pointer :: tot_woodprod_loss_grc(:) ! (g[C or N]/m2/s) decompomposition loss from all wood product pools + ! Objects that help convert once-per-year dynamic land cover changes into fluxes + ! that are dribbled throughout the year + !type(annual_flux_dribbler_type) :: dwt_conv_cflux_dribbler + !type(annual_flux_dribbler_type) :: hrv_xsmrpool_to_atm_dribbler + !logical, private :: dribble_crophrv_xsmrpool_2atm + + contains ! Infrastructure routines @@ -148,6 +157,17 @@ subroutine InitAllocate(this, bounds) allocate(this%tot_woodprod_loss_grc(begg:endg)) ; this%tot_woodprod_loss_grc(:) = nan allocate(this%product_loss_grc(begg:endg)) ; this%product_loss_grc(:) = nan + !this%dwt_conv_cflux_dribbler = annual_flux_dribbler_gridcell( & + ! bounds = bounds, & + ! name = 'dwt_conv_flux_' // carbon_type_suffix, & + ! units = 'gC/m^2', & + ! allows_non_annual_delta = allows_non_annual_delta) + !this%hrv_xsmrpool_to_atm_dribbler = annual_flux_dribbler_gridcell( & + ! bounds = bounds, & + ! name = 'hrv_xsmrpool_to_atm_' // carbon_type_suffix, & + ! units = 'gC/m^2', & + ! allows_non_annual_delta = .false.) + end subroutine InitAllocate !----------------------------------------------------------------------- diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 1bdcf5bce5..d30b9f1991 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -260,23 +260,26 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) this%cnveg_carbonstate_inst%deadstemc_patch(begp:endp) ) call this%cnveg_nitrogenflux_inst%Init(bounds) - call this%c_products_inst%Init(bounds, species_non_isotope_type('C')) - if (use_c13) then - call this%c13_products_inst%Init(bounds, species_isotope_type('C', '13')) - end if - if (use_c14) then - call this%c14_products_inst%Init(bounds, species_isotope_type('C', '14')) - end if - call this%n_products_inst%Init(bounds, species_non_isotope_type('N')) - - call this%cn_balance_inst%Init(bounds) + end if + + call this%c_products_inst%Init(bounds, species_non_isotope_type('C')) + if (use_c13) then + call this%c13_products_inst%Init(bounds, species_isotope_type('C', '13')) + end if + if (use_c14) then + call this%c14_products_inst%Init(bounds, species_isotope_type('C', '14')) + end if + call this%n_products_inst%Init(bounds, species_non_isotope_type('N')) + + call this%cn_balance_inst%Init(bounds) + if(use_cn)then ! Initialize the memory for the dgvs_inst data structure regardless of whether ! use_cndv is true so that it can be used in associate statements (nag compiler ! complains otherwise) call this%dgvs_inst%Init(bounds) end if - + call create_cnfire_method(NLFilename, this%cnfire_method) call this%cnfire_method%CNFireReadParams( params_ncid ) @@ -502,21 +505,21 @@ subroutine Restart(this, bounds, ncid, flag) cnveg_nitrogenstate=this%cnveg_nitrogenstate_inst, & filter_reseed_patch=reseed_patch, num_reseed_patch=num_reseed_patch) - call this%c_products_inst%restart(bounds, ncid, flag) - if (use_c13) then - call this%c13_products_inst%restart(bounds, ncid, flag, & - template_for_missing_fields = this%c_products_inst, & - template_multiplier = c3_r2) - end if - if (use_c14) then - call this%c14_products_inst%restart(bounds, ncid, flag, & - template_for_missing_fields = this%c_products_inst, & - template_multiplier = c14ratio) - end if - call this%n_products_inst%restart(bounds, ncid, flag) - end if - + + call this%c_products_inst%restart(bounds, ncid, flag) + if (use_c13) then + call this%c13_products_inst%restart(bounds, ncid, flag, & + template_for_missing_fields = this%c_products_inst, & + template_multiplier = c3_r2) + end if + if (use_c14) then + call this%c14_products_inst%restart(bounds, ncid, flag, & + template_for_missing_fields = this%c_products_inst, & + template_multiplier = c14ratio) + end if + call this%n_products_inst%restart(bounds, ncid, flag) + if (use_cndv) then call this%dgvs_inst%Restart(bounds, ncid, flag=flag) end if From 989c87f6bdef2f4fa2b95df6f0c84a6ef649ccf3 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 21 Feb 2023 14:59:56 -0700 Subject: [PATCH 0708/2067] include PRISM precipitation data stream --- cime_config/config_component.xml | 7 +++++++ .../NEON/defaults/user_nl_datm_streams | 20 +++++++++++++++++++ 2 files changed, 27 insertions(+) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 555a0ce9b5..b5741e5b40 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -295,6 +295,13 @@ ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD, BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF, BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL, + ABBY.PRECIP,BLAN.PRECIP,CPER.PRECIP,DEJU.PRECIP,GRSM.PRECIP,HEAL.PRECIP,KONA.PRECIP, + LENO.PRECIP,NIWO.PRECIP,ONAQ.PRECIP,PUUM.PRECIP,SERC.PRECIP,SRER.PRECIP,TALL.PRECIP, + TREE.PRECIP,WOOD.PRECIP,BARR.PRECIP,BONA.PRECIP,DCFS.PRECIP,DELA.PRECIP,GUAN.PRECIP, + JERC.PRECIP,KONZ.PRECIP,MLBS.PRECIP,NOGP.PRECIP,ORNL.PRECIP,RMNP.PRECIP,SJER.PRECIP, + STEI.PRECIP,TEAK.PRECIP,UKFS.PRECIP,WREF.PRECIP,BART.PRECIP,CLBJ.PRECIP,DSNY.PRECIP, + HARV.PRECIP,JORN.PRECIP,LAJA.PRECIP,MOAB.PRECIP,OAES.PRECIP,OSBS.PRECIP,SCBI.PRECIP, + SOAP.PRECIP,STER.PRECIP,TOOL.PRECIP,UNDE.PRECIP,YELL.PRECIP, run_component_ctsm diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams index 36f1e72b3a..636ceb2ad8 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams @@ -37,3 +37,23 @@ preso3.SSP3-7.0:year_first=2018 preso3.SSP3-7.0:year_last=2022 preso3.SSP3-7.0:year_align=2018 preso3.SSP3-7.0:dtlimit=30 + +NEON.${NEONSITE}:datavars = \ + FSDS Faxa_swdn, \ + ZBOT Sa_z, \ + TBOT Sa_tbot, \ + WIND Sa_wind, \ + RH Sa_rh, \ + PSRF Sa_pbot, \ + FLDS Faxa_lwdn + +NEON.${NEONSITE}.PRECIP:datavars = \ + PRECIP Faxa_precn + +NEON.${NEONSITE}.PRECIP:datafiles = \ + /glade/u/home/tking/neon/prism_${NEONSITE}_2018.nc, \ + /glade/u/home/tking/neon/prism_${NEONSITE}_2019.nc, \ + /glade/u/home/tking/neon/prism_${NEONSITE}_2020.nc, \ + /glade/u/home/tking/neon/prism_${NEONSITE}_2021.nc, \ + /glade/u/home/tking/neon/prism_${NEONSITE}_2022.nc + From 22862978cbb8b269b4af80c27a13f59f2deab52a Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 21 Feb 2023 16:46:51 -0700 Subject: [PATCH 0709/2067] remove unnecessary shell commands for gap filling --- cime_config/usermods_dirs/NEON/NIWO/shell_commands | 1 - 1 file changed, 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index a3e73ca343..65926f2188 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -1,4 +1,3 @@ ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 -./xmlchange DATM_YR_END=2018 From 8ef3f2882c56ce9275dd36b1da7e97eea4ba709b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 22 Feb 2023 13:50:02 -0700 Subject: [PATCH 0710/2067] Use ERP_D_Ld10_P36x2 on cheyenne only; add ERP_D_Ld10 test on izumi These changes pertain to GU_LULCC tests in this commit. --- cime_config/testdefs/testlist_clm.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 59251da53e..34e22e7272 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -462,10 +462,18 @@ + + + + + + + + + - From 093c07506bf758ab207405f3a06c7bd3e719e967 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 22 Feb 2023 14:12:56 -0700 Subject: [PATCH 0711/2067] Draft ChangeLog and ChangeSum --- doc/ChangeLog | 82 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 83 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5870abdb23..6df1764ff4 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,86 @@ =============================================================== +Tag name: ctsm5.1.dev119 +Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310), ekluzek Erik Kluzek), lawrencepj1 (Peter Lawrence) +Date: Wed Feb 22 13:57:36 MST 2023 +One-line Summary: Allow gross unrepresented land use transitions (PR #309) + +Purpose and description of changes +---------------------------------- + + Get gross unrepresented land use transitions working in CLM5.1. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics +onfigurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer +hanges.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): + I didn't find a corresponding issue. + +Notes of particular relevance for users +--------------------------------------- +Changes made to namelist defaults (e.g., changed parameter values): + New namelist variable: do_grossunrep + +Changes to the datasets (e.g., parameter, surface or initial files): + Surface datasets may now contain non-zero gross unrepresented land use + transitions. + +Substantial timing or memory changes: +[e.g., check PFS test in the test suite and look at timings, if you +expect possible significant timing changes] + + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + Erik introduced new tests that can be identified by the GU_LULCC in + their names. I ran these with the test-suites and generated baselines + for them. + +Testing summary: +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + +Answer changes +-------------- + +Changes answers relative to baseline: NO (unless see next) + + Code configurations: do_grossunrep = .true. and surface dataset + includes non-zero gross unrepresented land use + transitions. I (slevis) have not investigated the + nature of the changes. + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/309 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev118 Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310) Date: Sun Feb 5 18:31:29 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 215517275f..66e229d06c 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev119 slevis 02/22/2023 Allow gross unrepresented land use transition (PR #309) ctsm5.1.dev118 slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test ctsm5.1.dev117 afoster 02/02/2023 Updates to facilitate running FATES at NEON sites ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files From 55c6be2362d53d060e68e80b46c53ef7981d4ec5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 27 Feb 2023 14:55:10 -0700 Subject: [PATCH 0712/2067] Correct test number --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 1cccae0e29..1c6d951f0e 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1847; +my $ntests = 1848; if ( defined($opts{'compare'}) ) { $ntests += 1254; } From 3f6c67af23ea0b6891ff8002f43369f7597e9f10 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 27 Feb 2023 15:25:14 -0700 Subject: [PATCH 0713/2067] Returned hrv_xsmrpool_to_atm_patch to CNVegCarbonFluxType This was an unintentional line removal that Erik realized. I also reordered the error checks that Erik recommended in dynSubgridControlMod. --- src/biogeochem/CNVegCarbonFluxType.F90 | 1 + src/dyn_subgrid/dynSubgridControlMod.F90 | 11 +++++++---- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 585859beaa..7864007faf 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -4721,6 +4721,7 @@ subroutine Summary_carbonflux(this, & this%hrv_deadcrootc_to_litter_patch(p) + & this%hrv_deadcrootc_storage_to_litter_patch(p) + & this%hrv_deadcrootc_xfer_to_litter_patch(p) + & + this%hrv_xsmrpool_to_atm_patch(p) + & this%hrv_gresp_storage_to_litter_patch(p) + & this%hrv_gresp_xfer_to_litter_patch(p) diff --git a/src/dyn_subgrid/dynSubgridControlMod.F90 b/src/dyn_subgrid/dynSubgridControlMod.F90 index 12fce7b3f0..72e7229d0b 100644 --- a/src/dyn_subgrid/dynSubgridControlMod.F90 +++ b/src/dyn_subgrid/dynSubgridControlMod.F90 @@ -320,14 +320,17 @@ subroutine check_namelist_consistency end if if (dyn_subgrid_control_inst%do_grossunrep) then - if (.not. use_cn) then - write(iulog,*) 'ERROR: do_grossunrep can only be true if use_cn is true' - call endrun(msg=errMsg(sourcefile, __LINE__)) - end if + ! First check if use_fates. In this case the .not. use_cn error will not + ! appear. The .not. use_cn error will appea + ! if .not. use_fates and .not. use_cn. if (use_fates) then write(iulog,*) 'ERROR: do_grossunrep currently does not work with use_fates' call endrun(msg=errMsg(sourcefile, __LINE__)) end if + if (.not. use_cn) then + write(iulog,*) 'ERROR: do_grossunrep can only be true if use_cn is true' + call endrun(msg=errMsg(sourcefile, __LINE__)) + end if end if end subroutine check_namelist_consistency From 8ee4aeaee05810764a537ec177e472478de168a1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 27 Feb 2023 15:54:20 -0700 Subject: [PATCH 0714/2067] Add additional tests do new do_grossunrepresentedlanduse option --- bld/unit_testers/build-namelist_test.pl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 1c6d951f0e..8398e8359a 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1848; +my $ntests = 1850; if ( defined($opts{'compare'}) ) { $ntests += 1254; } @@ -1066,6 +1066,16 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "dogrossandfates" =>{ options=>"-envxml_dir . -bgc fates -use_case 20thC_transient", + namelst=>"do_grossunrep=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "dogrossandnottrans" =>{ options=>"-envxml_dir . -bgc fates -use_case 2000_control", + namelst=>"do_grossunrep=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, "nocropwfert" =>{ options=>"-envxml_dir . -bgc sp -no-crop", namelst=>"use_fertilizer=T", GLC_TWO_WAY_COUPLING=>"FALSE", From 179de38028116b3a60b60c6d51dc83f90b10d559 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 27 Feb 2023 15:54:59 -0700 Subject: [PATCH 0715/2067] Change order of if statement so that FATES error will trigger rather than the CN one for it --- bld/CLMBuildNamelist.pm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index e30b9b83f0..02d9799487 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2866,12 +2866,12 @@ sub setup_logic_do_grossunrep { if (string_is_undef_or_empty($nl->get_value('flanduse_timeseries'))) { $cannot_be_true = "$var can only be set to true when running a transient case (flanduse_timeseries non-blank)"; } - elsif (!&value_is_true($nl->get_value('use_cn'))) { - $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; - } elsif (&value_is_true($nl->get_value('use_fates'))) { $cannot_be_true = "$var currently doesn't work with FATES"; } + elsif (!&value_is_true($nl->get_value('use_cn'))) { + $cannot_be_true = "$var can only be set to true when running with CN (use_cn = true)"; + } if ($cannot_be_true) { $default_val = ".false."; From 91bbef6c1da6ae2053487b359c3a5535adafa817 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 27 Feb 2023 17:17:28 -0700 Subject: [PATCH 0716/2067] Fix the new tests added in --- bld/unit_testers/build-namelist_test.pl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 8398e8359a..79add93d88 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1061,17 +1061,17 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "dogrossandsp" =>{ options=>"-envxml_dir . -bgc sp -use_case 20thC_transient", + "dogrossandsp" =>{ options=>"--envxml_dir . --bgc sp --use_case 20thC_transient", namelst=>"do_grossunrep=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "dogrossandfates" =>{ options=>"-envxml_dir . -bgc fates -use_case 20thC_transient", + "dogrossandfates" =>{ options=>"--envxml_dir . --bgc fates --use_case 20thC_transient --no-megan", namelst=>"do_grossunrep=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "dogrossandnottrans" =>{ options=>"-envxml_dir . -bgc fates -use_case 2000_control", + "dogrossandnottrans" =>{ options=>"--envxml_dir . --bgc bgc --use_case 2000_control", namelst=>"do_grossunrep=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", From f38d9a30d03c466ed252c9845a76b4559e8e71e1 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 1 Mar 2023 15:20:44 -0500 Subject: [PATCH 0717/2067] Incremental progress towards getting fates to work with the C and N budget pathway --- src/biogeochem/CNAnnualUpdateMod.F90 | 48 +- src/biogeochem/CNBalanceCheckMod.F90 | 329 ++++++---- src/biogeochem/CNCStateUpdate1Mod.F90 | 6 +- src/biogeochem/CNDriverMod.F90 | 585 ++++++++++-------- src/biogeochem/CNGapMortalityMod.F90 | 2 +- src/biogeochem/CNNDynamicsMod.F90 | 23 +- src/biogeochem/CNNStateUpdate1Mod.F90 | 47 +- src/biogeochem/CNPhenologyMod.F90 | 159 +++-- src/biogeochem/CNProductsMod.F90 | 160 ++--- src/biogeochem/CNVegetationFacade.F90 | 17 +- src/main/filterMod.F90 | 26 +- .../SoilBiogeochemCarbonFluxType.F90 | 54 +- .../SoilBiogeochemPrecisionControlMod.F90 | 7 +- .../SoilBiogeochemStateType.F90 | 2 +- src/utils/clmfates_interfaceMod.F90 | 73 ++- 15 files changed, 849 insertions(+), 689 deletions(-) diff --git a/src/biogeochem/CNAnnualUpdateMod.F90 b/src/biogeochem/CNAnnualUpdateMod.F90 index 682898259a..34324e4c93 100644 --- a/src/biogeochem/CNAnnualUpdateMod.F90 +++ b/src/biogeochem/CNAnnualUpdateMod.F90 @@ -10,6 +10,7 @@ module CNAnnualUpdateMod use CNvegStateType , only : cnveg_state_type use PatchType , only : patch use filterColMod , only : filter_col_type, col_filter_from_filter_and_logical_array + use ColumnType , only : col ! implicit none private @@ -55,20 +56,23 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi do fc = 1,num_soilc c = filter_soilc(fc) - cnveg_state_inst%annsum_counter_col(c) = cnveg_state_inst%annsum_counter_col(c) + dt - if (cnveg_state_inst%annsum_counter_col(c) >= secspyear) then - end_of_year(c) = .true. - cnveg_state_inst%annsum_counter_col(c) = 0._r8 - else - end_of_year(c) = .false. + if(.not.col%is_fates(c))then + cnveg_state_inst%annsum_counter_col(c) = cnveg_state_inst%annsum_counter_col(c) + dt + if (cnveg_state_inst%annsum_counter_col(c) >= secspyear) then + end_of_year(c) = .true. + cnveg_state_inst%annsum_counter_col(c) = 0._r8 + else + end_of_year(c) = .false. + end if end if end do + do fp = 1,num_soilp p = filter_soilp(fp) c = patch%column(p) - if (end_of_year(c)) then + if (end_of_year(c) .and. .not.col%is_fates(c)) then ! update annual plant ndemand accumulator cnveg_state_inst%annsum_potential_gpp_patch(p) = cnveg_state_inst%tempsum_potential_gpp_patch(p) @@ -94,20 +98,22 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi end do ! Get column-level averages, just for the columns that have reached their personal end-of-year - filter_endofyear_c = col_filter_from_filter_and_logical_array( & - bounds = bounds, & - num_orig = num_soilc, & - filter_orig = filter_soilc, & - logical_col = end_of_year(bounds%begc:bounds%endc)) - - call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, & - cnveg_carbonflux_inst%annsum_npp_patch(bounds%begp:bounds%endp), & - cnveg_carbonflux_inst%annsum_npp_col(bounds%begc:bounds%endc)) - - call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, & - cnveg_state_inst%annavg_t2m_patch(bounds%begp:bounds%endp), & - cnveg_state_inst%annavg_t2m_col(bounds%begc:bounds%endc)) - + if(num_soilp>0)then + filter_endofyear_c = col_filter_from_filter_and_logical_array( & + bounds = bounds, & + num_orig = num_soilc, & + filter_orig = filter_soilc, & + logical_col = end_of_year(bounds%begc:bounds%endc)) + + call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, & + cnveg_carbonflux_inst%annsum_npp_patch(bounds%begp:bounds%endp), & + cnveg_carbonflux_inst%annsum_npp_col(bounds%begc:bounds%endc)) + + call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, & + cnveg_state_inst%annavg_t2m_patch(bounds%begp:bounds%endp), & + cnveg_state_inst%annavg_t2m_col(bounds%begc:bounds%endc)) + end if + end subroutine CNAnnualUpdate end module CNAnnualUpdateMod diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index 7d510e6446..bf54e2b18f 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -25,6 +25,7 @@ module CNBalanceCheckMod use GridcellType , only : grc use CNSharedParamsMod , only : use_fun use CLMFatesInterfaceMod , only : hlm_fates_interface_type + use clm_varpar , only : nlevdecomp ! implicit none @@ -216,7 +217,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! ! !USES: use subgridAveMod, only: c2g - use clm_varpar , only: nlevdecomp + ! ! !DESCRIPTION: ! Perform carbon mass conservation check for column and patch @@ -252,6 +253,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & real(r8) :: som_c_leached_grc(bounds%begg:bounds%endg) real(r8) :: hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg) real(r8) :: dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) + real(r8) :: fates_litter_flux !----------------------------------------------------------------------- @@ -272,7 +274,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & er => cnveg_carbonflux_inst%er_col , & ! Input: [real(r8) (:) ] (gC/m2/s) total ecosystem respiration, autotrophic + heterotrophic col_fire_closs => cnveg_carbonflux_inst%fire_closs_col , & ! Input: [real(r8) (:) ] (gC/m2/s) total column-level fire C loss col_hrv_xsmrpool_to_atm => cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_col , & ! Input: [real(r8) (:) ] (gC/m2/s) excess MR pool harvest mortality - col_xsmrpool_to_atm => cnveg_carbonflux_inst%xsmrpool_to_atm_col , & ! Input: [real(r8) (:) ] (gC/m2/s) excess MR pool crop harvest loss to atm + col_xsmrpool_to_atm => cnveg_carbonflux_inst%xsmrpool_to_atm_col , & ! Input: [real(r8) (:) ] (gC/m2/s) excess MR pool crop harvest loss to atm som_c_leached => soilbiogeochem_carbonflux_inst%som_c_leached_col , & ! Input: [real(r8) (:) ] (gC/m2/s) total SOM C loss from vertical transport totcolc => soilbiogeochem_carbonstate_inst%totc_col & ! Input: [real(r8) (:) ] (gC/m2) total column carbon, incl veg and cpool @@ -299,12 +301,15 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! calculate total column-level inputs (litter fluxes) [g/m2/s] s = clm_fates%f2hmap(ic)%hsites(c) - col_cinputs = sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & + + fates_litter_flux = sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * & clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + col_cinputs = fates_litter_flux ! calculate total column-level outputs ! fates has already exported burn losses and fluxes to the atm @@ -321,19 +326,18 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! er = ar + hr, col_fire_closs includes patch-level fire losses col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + & col_xsmrpool_to_atm(c) + + ! Fluxes to product pools are included in column-level outputs: the product + ! pools are not included in totcolc, so are outside the system with respect to + ! these balance checks. (However, the dwt flux to product pools is NOT included, + ! since col_begcb is initialized after the dynamic area adjustments - i.e., + ! after the dwt term has already been taken out.) + col_coutputs = col_coutputs + & + wood_harvestc(c) + & + crop_harvestc_to_cropprodc(c) end if - - ! Fluxes to product pools are included in column-level outputs: the product - ! pools are not included in totcolc, so are outside the system with respect to - ! these balance checks. (However, the dwt flux to product pools is NOT included, - ! since col_begcb is initialized after the dynamic area adjustments - i.e., - ! after the dwt term has already been taken out.) - col_coutputs = col_coutputs + & - wood_harvestc(c) + & - crop_harvestc_to_cropprodc(c) - ! subtract leaching flux col_coutputs = col_coutputs - som_c_leached(c) @@ -360,14 +364,22 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & write(iulog,*)'endcb = ',col_endcb(c) write(iulog,*)'delta store = ',col_endcb(c)-col_begcb(c) write(iulog,*)'--- Inputs ---' - write(iulog,*)'gpp = ',gpp(c)*dt + if( col%is_fates(c) ) then + write(iulog,*)'fates litter_flux = ',fates_litter_flux*dt + else + write(iulog,*)'gpp = ',gpp(c)*dt + end if write(iulog,*)'--- Outputs ---' - write(iulog,*)'er = ',er(c)*dt - write(iulog,*)'col_fire_closs = ',col_fire_closs(c)*dt - write(iulog,*)'col_hrv_xsmrpool_to_atm = ',col_hrv_xsmrpool_to_atm(c)*dt - write(iulog,*)'col_xsmrpool_to_atm = ',col_xsmrpool_to_atm(c)*dt - write(iulog,*)'wood_harvestc = ',wood_harvestc(c)*dt - write(iulog,*)'crop_harvestc_to_cropprodc = ', crop_harvestc_to_cropprodc(c)*dt + if( .not.col%is_fates(c) ) then + write(iulog,*)'er = ',er(c)*dt + write(iulog,*)'col_fire_closs = ',col_fire_closs(c)*dt + write(iulog,*)'col_hrv_xsmrpool_to_atm = ',col_hrv_xsmrpool_to_atm(c)*dt + write(iulog,*)'col_xsmrpool_to_atm = ',col_xsmrpool_to_atm(c)*dt + write(iulog,*)'wood_harvestc = ',wood_harvestc(c)*dt + write(iulog,*)'crop_harvestc_to_cropprodc = ', crop_harvestc_to_cropprodc(c)*dt + else + write(iulog,*)'hr = ',soilbiogeochem_carbonflux_inst%hr_col(c)*dt + end if write(iulog,*)'-1*som_c_leached = ',som_c_leached(c)*dt call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, msg=errMsg(sourcefile, __LINE__)) end if @@ -396,28 +408,38 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! We account for the latter fluxes as inputs below; the same ! fluxes have entered the pools earlier in the timestep. For true ! conservation we would need to add a flux out of npp into seed. - call cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_dribbler%get_amount_left_to_dribble_end( & - bounds, hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)) - call cnveg_carbonflux_inst%dwt_conv_cflux_dribbler%get_amount_left_to_dribble_end( & - bounds, dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg)) - grc_endcb(g) = totgrcc(g) + tot_woodprod_grc(g) + cropprod1_grc(g) + & - hrv_xsmrpool_amount_left_to_dribble(g) + & - dwt_conv_cflux_amount_left_to_dribble(g) - - ! calculate total gridcell-level inputs - ! slevis notes: - ! nbp_grc = nep_grc - fire_closs_grc - hrv_xsmrpool_to_atm_dribbled_grc - dwt_conv_cflux_dribbled_grc - product_closs_grc - grc_cinputs = nbp_grc(g) + & - dwt_seedc_to_leaf_grc(g) + dwt_seedc_to_deadstem_grc(g) - - ! calculate total gridcell-level outputs - grc_coutputs = - som_c_leached_grc(g) - - ! calculate the total gridcell-level carbon balance error - ! for this time step - grc_errcb(g) = (grc_cinputs - grc_coutputs) * dt - & - (grc_endcb(g) - grc_begcb(g)) + if(.not.use_fates)then + call cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_dribbler%get_amount_left_to_dribble_end( & + bounds, hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)) + call cnveg_carbonflux_inst%dwt_conv_cflux_dribbler%get_amount_left_to_dribble_end( & + bounds, dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg)) + + grc_endcb(g) = totgrcc(g) + tot_woodprod_grc(g) + cropprod1_grc(g) + & + hrv_xsmrpool_amount_left_to_dribble(g) + & + dwt_conv_cflux_amount_left_to_dribble(g) + + ! calculate total gridcell-level inputs + ! slevis notes: + ! nbp_grc = nep_grc - fire_closs_grc - hrv_xsmrpool_to_atm_dribbled_grc - dwt_conv_cflux_dribbled_grc - product_closs_grc + + grc_cinputs = nbp_grc(g) + dwt_seedc_to_leaf_grc(g) + dwt_seedc_to_deadstem_grc(g) + ! calculate total gridcell-level outputs + grc_coutputs = - som_c_leached_grc(g) + ! calculate the total gridcell-level carbon balance error + ! for this time step + grc_errcb(g) = (grc_cinputs - grc_coutputs) * dt - & + (grc_endcb(g) - grc_begcb(g)) + + else + + ! Totally punt on this for now. We just don't track these gridscale variables yet (RGK) + grc_cinputs = 0._r8 + grc_coutputs = (grc_begcb(g) - grc_endcb(g))/dt + grc_errcb(g) = 0._r8 + + end if + ! check for significant errors if (abs(grc_errcb(g)) > this%cerror) then err_found = .true. @@ -452,7 +474,7 @@ end subroutine CBalanceCheck subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst, & cnveg_nitrogenflux_inst, & - cnveg_nitrogenstate_inst, n_products_inst, atm2lnd_inst) + cnveg_nitrogenstate_inst, n_products_inst, atm2lnd_inst, clm_fates) ! ! !DESCRIPTION: ! Perform nitrogen mass conservation check @@ -473,14 +495,16 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(cn_products_type) , intent(in) :: n_products_inst type(atm2lnd_type) , intent(in) :: atm2lnd_inst + type(hlm_fates_interface_type) , intent(inout) :: clm_fates ! ! !LOCAL VARIABLES: - integer :: c,err_index,j ! indices - integer :: g ! gridcell index - integer :: fc ! lake filter indices - logical :: err_found ! error flag - real(r8):: dt ! radiation time step (seconds) + integer :: c,err_index,j,s ! indices + integer :: ic ! index of clump + integer :: g ! gridcell index + integer :: fc ! lake filter indices + logical :: err_found ! error flag + real(r8):: dt ! radiation time step (seconds) real(r8):: col_ninputs(bounds%begc:bounds%endc) real(r8):: col_noutputs(bounds%begc:bounds%endc) real(r8):: col_errnb(bounds%begc:bounds%endc) @@ -522,8 +546,9 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & wood_harvestn => cnveg_nitrogenflux_inst%wood_harvestn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) wood harvest (to product pools) crop_harvestn_to_cropprodn => cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) crop harvest N to 1-year crop product pool - totcoln => soilbiogeochem_nitrogenstate_inst%totn_col & ! Input: [real(r8) (:) ] (gN/m2) total column nitrogen, incl veg - ) + totcoln => soilbiogeochem_nitrogenstate_inst%totn_col , & ! Input: [real(r8) (:) ] (gN/m2) total column nitrogen, incl veg + sminn_to_plant => soilbiogeochem_nitrogenflux_inst%sminn_to_plant_col ) + ! set time steps dt = get_step_size_real() @@ -532,6 +557,9 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & col_ninputs_partial(:) = 0._r8 col_noutputs_partial(:) = 0._r8 + ! clump index + ic = bounds%clump_index + err_found = .false. do fc = 1,num_soilc c=filter_soilc(fc) @@ -541,6 +569,18 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! calculate total column-level inputs col_ninputs(c) = ndep_to_sminn(c) + nfix_to_sminn(c) + supplement_to_sminn(c) + + ! If using fates, pass in the decomposition flux + if( col%is_fates(c) ) then + s = clm_fates%f2hmap(ic)%hsites(c) + col_ninputs(c) = col_ninputs(c) + & + sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lab_n_si(1:nlevdecomp) * & + clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_cel_n_si(1:nlevdecomp) * & + clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & + sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lig_n_si(1:nlevdecomp) * & + clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + end if if(use_fun)then col_ninputs(c) = col_ninputs(c) + ffix_to_sminn(c) ! for FUN, free living fixation is a seprate flux. RF. @@ -551,18 +591,29 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & end if col_ninputs_partial(c) = col_ninputs(c) - + ! calculate total column-level outputs - col_noutputs(c) = denit(c) + col_fire_nloss(c) + col_noutputs(c) = denit(c) + + if( .not.col%is_fates(c) ) then + + col_noutputs(c) = col_noutputs(c) + col_fire_nloss(c) + + ! Fluxes to product pools are included in column-level outputs: the product + ! pools are not included in totcoln, so are outside the system with respect to + ! these balance checks. (However, the dwt flux to product pools is NOT included, + ! since col_begnb is initialized after the dynamic area adjustments - i.e., + ! after the dwt term has already been taken out.) + col_noutputs(c) = col_noutputs(c) + & + wood_harvestn(c) + & + crop_harvestn_to_cropprodn(c) - ! Fluxes to product pools are included in column-level outputs: the product - ! pools are not included in totcoln, so are outside the system with respect to - ! these balance checks. (However, the dwt flux to product pools is NOT included, - ! since col_begnb is initialized after the dynamic area adjustments - i.e., - ! after the dwt term has already been taken out.) - col_noutputs(c) = col_noutputs(c) + & - wood_harvestn(c) + & - crop_harvestn_to_cropprodn(c) + else + + ! If we are using fates, remove plant uptake + col_noutputs(c) = col_noutputs(c) + sminn_to_plant(c) + + end if if (.not. use_nitrif_denitrif) then col_noutputs(c) = col_noutputs(c) + sminn_leached(c) @@ -573,11 +624,15 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & end if col_noutputs(c) = col_noutputs(c) - som_n_leached(c) + + col_noutputs_partial(c) = col_noutputs(c) - col_noutputs_partial(c) = col_noutputs(c) - & - wood_harvestn(c) - & - crop_harvestn_to_cropprodn(c) - + if( .not.col%is_fates(c) ) then + col_noutputs_partial(c) = col_noutputs_partial(c) - & + wood_harvestn(c) - & + crop_harvestn_to_cropprodn(c) + end if + ! calculate the total column-level nitrogen balance error for this time step col_errnb(c) = (col_ninputs(c) - col_noutputs(c))*dt - & (col_endnb(c) - col_begnb(c)) @@ -610,82 +665,86 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, msg=errMsg(sourcefile, __LINE__)) end if - ! Repeat error check at the gridcell level - call c2g( bounds = bounds, & - carr = totcoln(bounds%begc:bounds%endc), & - garr = totgrcn(bounds%begg:bounds%endg), & - c2l_scale_type = 'unity', & - l2g_scale_type = 'unity') - call c2g( bounds = bounds, & - carr = col_ninputs_partial(bounds%begc:bounds%endc), & - garr = grc_ninputs_partial(bounds%begg:bounds%endg), & - c2l_scale_type = 'unity', & - l2g_scale_type = 'unity') - call c2g( bounds = bounds, & - carr = col_noutputs_partial(bounds%begc:bounds%endc), & - garr = grc_noutputs_partial(bounds%begg:bounds%endg), & - c2l_scale_type = 'unity', & - l2g_scale_type = 'unity') - - err_found = .false. - do g = bounds%begg, bounds%endg - ! calculate the total gridcell-level nitrogen storage, for mass conservation check - ! Notes: - ! Not including seedn_grc in grc_begnb and grc_endnb because - ! seedn_grc forms out of thin air, for now, and equals - ! -1 * (dwt_seedn_to_leaf_grc(g) + dwt_seedn_to_deadstem_grc(g)) - ! We account for the latter fluxes as inputs below; the same - ! fluxes have entered the pools earlier in the timestep. For true - ! conservation we would need to add a flux out of nfix into seed. - grc_endnb(g) = totgrcn(g) + tot_woodprod_grc(g) + cropprod1_grc(g) - - ! calculate total gridcell-level inputs - grc_ninputs(g) = grc_ninputs_partial(g) + & - dwt_seedn_to_leaf_grc(g) + & - dwt_seedn_to_deadstem_grc(g) - - ! calculate total gridcell-level outputs - grc_noutputs(g) = grc_noutputs_partial(g) + & - dwt_conv_nflux_grc(g) + & - product_loss_grc(g) - - ! calculate the total gridcell-level nitrogen balance error for this time step - grc_errnb(g) = (grc_ninputs(g) - grc_noutputs(g)) * dt - & - (grc_endnb(g) - grc_begnb(g)) - if (abs(grc_errnb(g)) > this%nerror) then - err_found = .true. - err_index = g - end if - - if (abs(grc_errnb(g)) > this%nwarning) then - write(iulog,*) 'nbalance warning at g =', g, grc_errnb(g), grc_endnb(g) + if(.not.use_fates)then + + ! Repeat error check at the gridcell level + call c2g( bounds = bounds, & + carr = totcoln(bounds%begc:bounds%endc), & + garr = totgrcn(bounds%begg:bounds%endg), & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + call c2g( bounds = bounds, & + carr = col_ninputs_partial(bounds%begc:bounds%endc), & + garr = grc_ninputs_partial(bounds%begg:bounds%endg), & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + call c2g( bounds = bounds, & + carr = col_noutputs_partial(bounds%begc:bounds%endc), & + garr = grc_noutputs_partial(bounds%begg:bounds%endg), & + c2l_scale_type = 'unity', & + l2g_scale_type = 'unity') + + err_found = .false. + do g = bounds%begg, bounds%endg + ! calculate the total gridcell-level nitrogen storage, for mass conservation check + ! Notes: + ! Not including seedn_grc in grc_begnb and grc_endnb because + ! seedn_grc forms out of thin air, for now, and equals + ! -1 * (dwt_seedn_to_leaf_grc(g) + dwt_seedn_to_deadstem_grc(g)) + ! We account for the latter fluxes as inputs below; the same + ! fluxes have entered the pools earlier in the timestep. For true + ! conservation we would need to add a flux out of nfix into seed. + grc_endnb(g) = totgrcn(g) + tot_woodprod_grc(g) + cropprod1_grc(g) + + ! calculate total gridcell-level inputs + grc_ninputs(g) = grc_ninputs_partial(g) + & + dwt_seedn_to_leaf_grc(g) + & + dwt_seedn_to_deadstem_grc(g) + + ! calculate total gridcell-level outputs + grc_noutputs(g) = grc_noutputs_partial(g) + & + dwt_conv_nflux_grc(g) + & + product_loss_grc(g) + + ! calculate the total gridcell-level nitrogen balance error for this time step + grc_errnb(g) = (grc_ninputs(g) - grc_noutputs(g)) * dt - & + (grc_endnb(g) - grc_begnb(g)) + + if (abs(grc_errnb(g)) > this%nerror) then + err_found = .true. + err_index = g + end if + + if (abs(grc_errnb(g)) > this%nwarning) then + write(iulog,*) 'nbalance warning at g =', g, grc_errnb(g), grc_endnb(g) + end if + end do + + if (err_found) then + g = err_index + write(iulog,*) 'gridcell nbalance error =', grc_errnb(g), g + write(iulog,*) 'latdeg, londeg =', grc%latdeg(g), grc%londeg(g) + write(iulog,*) 'begnb =', grc_begnb(g) + write(iulog,*) 'endnb =', grc_endnb(g) + write(iulog,*) 'delta store =', grc_endnb(g) - grc_begnb(g) + write(iulog,*) 'input mass =', grc_ninputs(g) * dt + write(iulog,*) 'output mass =', grc_noutputs(g) * dt + write(iulog,*) 'net flux =', (grc_ninputs(g) - grc_noutputs(g)) * dt + write(iulog,*) '--- Inputs ---' + write(iulog,*) 'grc_ninputs_partial =', grc_ninputs_partial(g) * dt + write(iulog,*) 'dwt_seedn_to_leaf_grc =', dwt_seedn_to_leaf_grc(g) * dt + write(iulog,*) 'dwt_seedn_to_deadstem_grc =', dwt_seedn_to_deadstem_grc(g) * dt + write(iulog,*) '--- Outputs ---' + write(iulog,*) 'grc_noutputs_partial =', grc_noutputs_partial(g) * dt + write(iulog,*) 'dwt_conv_nflux_grc =', dwt_conv_nflux_grc(g) * dt + write(iulog,*) 'product_loss_grc =', product_loss_grc(g) * dt + call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__)) end if - end do - - if (err_found) then - g = err_index - write(iulog,*) 'gridcell nbalance error =', grc_errnb(g), g - write(iulog,*) 'latdeg, londeg =', grc%latdeg(g), grc%londeg(g) - write(iulog,*) 'begnb =', grc_begnb(g) - write(iulog,*) 'endnb =', grc_endnb(g) - write(iulog,*) 'delta store =', grc_endnb(g) - grc_begnb(g) - write(iulog,*) 'input mass =', grc_ninputs(g) * dt - write(iulog,*) 'output mass =', grc_noutputs(g) * dt - write(iulog,*) 'net flux =', (grc_ninputs(g) - grc_noutputs(g)) * dt - write(iulog,*) '--- Inputs ---' - write(iulog,*) 'grc_ninputs_partial =', grc_ninputs_partial(g) * dt - write(iulog,*) 'dwt_seedn_to_leaf_grc =', dwt_seedn_to_leaf_grc(g) * dt - write(iulog,*) 'dwt_seedn_to_deadstem_grc =', dwt_seedn_to_deadstem_grc(g) * dt - write(iulog,*) '--- Outputs ---' - write(iulog,*) 'grc_noutputs_partial =', grc_noutputs_partial(g) * dt - write(iulog,*) 'dwt_conv_nflux_grc =', dwt_conv_nflux_grc(g) * dt - write(iulog,*) 'product_loss_grc =', product_loss_grc(g) * dt - call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__)) end if - + end associate - + end subroutine NBalanceCheck end module CNBalanceCheckMod diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 5783e01f6c..3b210506b1 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -142,7 +142,7 @@ end subroutine CStateUpdate0 subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & - clm_fates, ci) + clm_fates, clump_index) ! ! !DESCRIPTION: ! On the radiation time step, update all the prognostic carbon state @@ -160,7 +160,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst logical , intent(in) :: dribble_crophrv_xsmrpool_2atm type(hlm_fates_interface_type) , intent(inout) :: clm_fates - integer , intent(in) :: ci ! clump index + integer , intent(in) :: clump_index ! ! !LOCAL VARIABLES: integer :: c,p,j,k,l,i ! indices @@ -201,7 +201,7 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & ! prepared litter c flux boundary conditions into ! cf_soil%decomp_cpools_sourcesink_col - call clm_fates%UpdateCLitterfluxes(cf_soil,ci,c) + call clm_fates%UpdateCLitterfluxes(cf_soil,clump_index,c) else diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index c7918ec0fe..3c27f4e244 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -11,7 +11,7 @@ module CNDriverMod use decompMod , only : bounds_type use perf_mod , only : t_startf, t_stopf use clm_varctl , only : use_nitrif_denitrif, use_nguardrail - use clm_varctl , only : iulog, use_crop, use_crop_agsys + use clm_varctl , only : iulog, use_crop, use_crop_agsys, use_cn use SoilBiogeochemDecompCascadeConType, only : mimics_decomp, century_decomp, decomp_method use CNSharedParamsMod , only : use_fun use CNVegStateType , only : cnveg_state_type @@ -259,31 +259,33 @@ subroutine CNDriverNoLeaching(bounds, end if call t_stopf('CNZero-soilbgc-cflux') - call t_startf('CNZero-vegbgc-cflux') - call cnveg_carbonflux_inst%SetValues( & - nvegcpool,& - num_soilp, filter_soilp, 0._r8, & - num_soilc, filter_soilc, 0._r8) - if ( use_c13 ) then - call c13_cnveg_carbonflux_inst%SetValues( & + if(num_soilp>0)then + call t_startf('CNZero-vegbgc-cflux') + call cnveg_carbonflux_inst%SetValues( & nvegcpool,& num_soilp, filter_soilp, 0._r8, & num_soilc, filter_soilc, 0._r8) - end if - if ( use_c14 ) then - call c14_cnveg_carbonflux_inst%SetValues( & - nvegcpool,& + if ( use_c13 ) then + call c13_cnveg_carbonflux_inst%SetValues( & + nvegcpool,& + num_soilp, filter_soilp, 0._r8, & + num_soilc, filter_soilc, 0._r8) + end if + if ( use_c14 ) then + call c14_cnveg_carbonflux_inst%SetValues( & + nvegcpool,& + num_soilp, filter_soilp, 0._r8, & + num_soilc, filter_soilc, 0._r8) + end if + call t_stopf('CNZero-vegbgc-cflux') + + call t_startf('CNZero-vegbgc-nflux') + call cnveg_nitrogenflux_inst%SetValues( & + nvegnpool, & num_soilp, filter_soilp, 0._r8, & num_soilc, filter_soilc, 0._r8) end if - call t_stopf('CNZero-vegbgc-cflux') - - call t_startf('CNZero-vegbgc-nflux') - call cnveg_nitrogenflux_inst%SetValues( & - nvegnpool, & - num_soilp, filter_soilp, 0._r8, & - num_soilc, filter_soilc, 0._r8) - + call t_stopf('CNZero-vegbgc-nflux') call t_startf('CNZero-soilbgc-nflux') call soilbiogeochem_nitrogenflux_inst%SetValues( & @@ -309,7 +311,8 @@ subroutine CNDriverNoLeaching(bounds, else call t_startf('CNFixation') call CNNFixation( num_soilc, filter_soilc, & - cnveg_carbonflux_inst, soilbiogeochem_nitrogenflux_inst) + cnveg_carbonflux_inst, soilbiogeochem_nitrogenflux_inst, & + clm_fates, bounds%clump_index) call t_stopf('CNFixation') end if @@ -360,7 +363,8 @@ subroutine CNDriverNoLeaching(bounds, p_decomp_npool_to_din=p_decomp_npool_to_din(begc:endc,1:nlevdecomp,1:ndecomp_cascade_transitions)) call t_stopf('SoilBiogeochemPotential') - ! calculate vertical profiles for distributing soil and litter C and N (previously subroutine decomp_vertprofiles called from CNDecompAlloc) + ! calculate vertical profiles for distributing soil and litter C and N + ! (previously subroutine decomp_vertprofiles called from CNDecompAlloc) call SoilBiogeochemVerticalProfile(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & active_layer_inst, soilstate_inst,soilbiogeochem_state_inst) @@ -450,9 +454,16 @@ subroutine CNDriverNoLeaching(bounds, ! get the column-averaged plant_ndemand (needed for following call to SoilBiogeochemCompetition) - call p2c(bounds, num_soilc, filter_soilc, & - cnveg_nitrogenflux_inst%plant_ndemand_patch(begp:endp), & - soilbiogeochem_state_inst%plant_ndemand_col(begc:endc)) + if(num_soilp>0)then + call p2c(bounds, num_soilc, filter_soilc, & + cnveg_nitrogenflux_inst%plant_ndemand_patch(begp:endp), & + soilbiogeochem_state_inst%plant_ndemand_col(begc:endc)) + else + ! With FATES N coupling, we will have a call to fill + ! this in on the filter_soilc + soilbiogeochem_state_inst%plant_ndemand_col(begc:endc) = 0._r8 + end if + call t_stopf('calc_plant_nutrient_demand') ! resolve plant/heterotroph competition for mineral N @@ -587,7 +598,7 @@ subroutine CNDriverNoLeaching(bounds, call t_stopf('CNUpdate0') - if ( use_nguardrail ) then + if ( use_nguardrail .and. num_soilp>0 ) then call t_startf('CNPrecisionControl') call CNPrecisionControl(bounds, num_soilp, filter_soilp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & @@ -644,11 +655,12 @@ subroutine CNDriverNoLeaching(bounds, ! Update all prognostic nitrogen state variables (except for gap-phase mortality and fire fluxes) call NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & + clm_fates, bounds%clump_index) call t_stopf('CNUpdate1') - if ( use_nguardrail ) then + if ( use_nguardrail .and. num_soilp>0 ) then call t_startf('CNPrecisionControl') call CNPrecisionControl(bounds, num_soilp, filter_soilp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & @@ -681,235 +693,257 @@ subroutine CNDriverNoLeaching(bounds, ! Calculate the gap mortality carbon and nitrogen fluxes !-------------------------------------------- - call t_startf('CNGapMortality') - - call CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - dgvs_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & - cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, canopystate_inst, & - !cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full), & - froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full), & - croot_prof_patch=soilbiogeochem_state_inst%croot_prof_patch(begp:endp, 1:nlevdecomp_full), & - stem_prof_patch=soilbiogeochem_state_inst%stem_prof_patch(begp:endp, 1:nlevdecomp_full)) - - call t_stopf('CNGapMortality') - - !-------------------------------------------------------------------------- - ! Update2 (gap mortality) - ! The state updates are still called for the matrix solution (use_matrixn - ! and use_soil_matrixcn) but most of the state updates are done after - ! the matrix multiply in VegMatrix and SoilMatrix. - !-------------------------------------------------------------------------- - - call t_startf('CNUpdate2') - - ! Set the carbon isotopic fluxes for gap mortality - if ( use_c13 ) then - call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - iso_cnveg_carbonflux_inst=c13_cnveg_carbonflux_inst, & - iso_cnveg_carbonstate_inst=c13_cnveg_carbonstate_inst, & - isotope='c13') - end if - if ( use_c14 ) then - call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - iso_cnveg_carbonflux_inst=c14_cnveg_carbonflux_inst, & - iso_cnveg_carbonstate_inst=c14_cnveg_carbonstate_inst, & - isotope='c14') - end if - - ! Update all the prognostic carbon state variables affected by gap-phase mortality fluxes - call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & - soilbiogeochem_carbonflux_inst) - if ( use_c13 ) then - call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & - c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst) - end if - if ( use_c14 ) then + if_soilp1: if(num_soilp>0)then + + call t_startf('CNGapMortality') + call CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + dgvs_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & + cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, canopystate_inst, & + leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full), & + froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full), & + croot_prof_patch=soilbiogeochem_state_inst%croot_prof_patch(begp:endp, 1:nlevdecomp_full), & + stem_prof_patch=soilbiogeochem_state_inst%stem_prof_patch(begp:endp, 1:nlevdecomp_full)) + call t_stopf('CNGapMortality') + + !-------------------------------------------------------------------------- + ! Update2 (gap mortality) + ! The state updates are still called for the matrix solution (use_matrixn + ! and use_soil_matrixcn) but most of the state updates are done after + ! the matrix multiply in VegMatrix and SoilMatrix. + !-------------------------------------------------------------------------- + + call t_startf('CNUpdate2') + ! Set the carbon isotopic fluxes for gap mortality + if ( use_c13 ) then + call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + iso_cnveg_carbonflux_inst=c13_cnveg_carbonflux_inst, & + iso_cnveg_carbonstate_inst=c13_cnveg_carbonstate_inst, & + isotope='c13') + end if + if ( use_c14 ) then + call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + iso_cnveg_carbonflux_inst=c14_cnveg_carbonflux_inst, & + iso_cnveg_carbonstate_inst=c14_cnveg_carbonstate_inst, & + isotope='c14') + end if + + ! Update all the prognostic carbon state variables affected by gap-phase mortality fluxes call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & - c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst) - end if - - ! Update all the prognostic nitrogen state variables affected by gap-phase mortality fluxes - call NStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst,soilbiogeochem_nitrogenstate_inst, & - soilbiogeochem_nitrogenflux_inst) - - !-------------------------------------------------------------------------- - ! Update2h (harvest) - ! The state updates are still called for the matrix solution (use_matrixn - ! and use_soil_matrixcn) but most of the state updates are done after - ! the matrix multiply in VegMatrix and SoilMatrix. - !-------------------------------------------------------------------------- - - ! Set harvest mortality routine - if (get_do_harvest()) then - call CNHarvest(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & - cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) - end if - - if ( use_c13 ) then - call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & - isotope='c13') - end if - if ( use_c14 ) then - call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & - isotope='c14') - end if + cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & + soilbiogeochem_carbonflux_inst) + if ( use_c13 ) then + call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & + c13_soilbiogeochem_carbonflux_inst) + end if + if ( use_c14 ) then + call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst) + end if + + ! Update all the prognostic nitrogen state variables affected by gap-phase mortality fluxes + call NStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst,soilbiogeochem_nitrogenstate_inst, & + soilbiogeochem_nitrogenflux_inst) + + !-------------------------------------------------------------------------- + ! Update2h (harvest) + ! The state updates are still called for the matrix solution (use_matrixn + ! and use_soil_matrixcn) but most of the state updates are done after + ! the matrix multiply in VegMatrix and SoilMatrix. + !-------------------------------------------------------------------------- + + ! Set harvest mortality routine + if (get_do_harvest()) then + call CNHarvest(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & + cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + end if - call CStateUpdate2h( num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & - soilbiogeochem_carbonflux_inst) - if ( use_c13 ) then - call CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + if ( use_c13 ) then + call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & + isotope='c13') + end if + if ( use_c14 ) then + call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & + isotope='c14') + end if + + call CStateUpdate2h( num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & + soilbiogeochem_carbonflux_inst) + if ( use_c13 ) then + call CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonflux_inst) - end if - if ( use_c14 ) then - call CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & - c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst) - end if - - call NStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst, & - soilbiogeochem_nitrogenflux_inst) - call t_stopf('CNUpdate2') - - if ( use_nguardrail ) then + end if + if ( use_c14 ) then + call CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst) + end if + + call NStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst, & + soilbiogeochem_nitrogenflux_inst) + call t_stopf('CNUpdate2') + + end if if_soilp1 + + if ( use_nguardrail .and. num_soilp>0 ) then call t_startf('CNPrecisionControl') call CNPrecisionControl(bounds, num_soilp, filter_soilp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & c14_cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) call t_stopf('CNPrecisionControl') end if + !-------------------------------------------- ! Calculate loss fluxes from wood products pools ! and update product pool state variables !-------------------------------------------- call t_startf('CNWoodProducts') - call c_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & - dwt_wood_product_gain_patch = cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & - wood_harvest_patch = cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & - dwt_crop_product_gain_patch = cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & - crop_harvest_to_cropprod_patch = cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) - call t_stopf('CNWoodProducts') - - if (use_c13) then - call c13_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & - dwt_wood_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & - wood_harvest_patch = c13_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & - dwt_crop_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & - crop_harvest_to_cropprod_patch = c13_cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) + + call c_products_inst%SetValues(bounds,0._r8) + if (use_c13) call c13_products_inst%SetValues(bounds,0._r8) + if (use_c14) call c14_products_inst%SetValues(bounds,0._r8) + call n_products_inst%SetValues(bounds,0._r8) + + if(use_fates) then + call clm_fates%wrap_WoodProducts(bounds, num_soilc, filter_soilc, c_products_inst, n_products_inst) end if - if (use_c14) then - call c14_products_inst%UpdateProducts(bounds, & + if_soilp2: if(num_soilp>0)then + call c_products_inst%UpdateProducts(bounds, & num_soilp, filter_soilp, & - dwt_wood_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & - wood_harvest_patch = c14_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & - dwt_crop_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & - crop_harvest_to_cropprod_patch = c14_cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) - end if + dwt_wood_product_gain_patch = cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & + wood_harvest_patch = cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & + dwt_crop_product_gain_patch = cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & + crop_harvest_to_cropprod_patch = cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) + + if (use_c13) then + call c13_products_inst%UpdateProducts(bounds, & + num_soilp, filter_soilp, & + dwt_wood_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & + wood_harvest_patch = c13_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & + dwt_crop_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & + crop_harvest_to_cropprod_patch = c13_cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) + end if - call n_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & - dwt_wood_product_gain_patch = cnveg_nitrogenflux_inst%dwt_wood_productn_gain_patch(begp:endp), & - wood_harvest_patch = cnveg_nitrogenflux_inst%wood_harvestn_patch(begp:endp), & - dwt_crop_product_gain_patch = cnveg_nitrogenflux_inst%dwt_crop_productn_gain_patch(begp:endp), & - crop_harvest_to_cropprod_patch = cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(begp:endp)) + if (use_c14) then + call c14_products_inst%UpdateProducts(bounds, & + num_soilp, filter_soilp, & + dwt_wood_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & + wood_harvest_patch = c14_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & + dwt_crop_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & + crop_harvest_to_cropprod_patch = c14_cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(begp:endp)) + end if + call n_products_inst%UpdateProducts(bounds, & + num_soilp, filter_soilp, & + dwt_wood_product_gain_patch = cnveg_nitrogenflux_inst%dwt_wood_productn_gain_patch(begp:endp), & + wood_harvest_patch = cnveg_nitrogenflux_inst%wood_harvestn_patch(begp:endp), & + dwt_crop_product_gain_patch = cnveg_nitrogenflux_inst%dwt_crop_productn_gain_patch(begp:endp), & + crop_harvest_to_cropprod_patch = cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(begp:endp)) + + end if if_soilp2 + + call c_products_inst%ComputeSummaryVars(bounds) + if (use_c13) call c13_products_inst%ComputeSummaryVars(bounds) + if (use_c14) call c14_products_inst%ComputeSummaryVars(bounds) + call n_products_inst%ComputeSummaryVars(bounds) + + call t_stopf('CNWoodProducts') + !-------------------------------------------- ! Calculate fire area and fluxes !-------------------------------------------- - call t_startf('CNFire') - call cnfire_method%CNFireArea(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, & - atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, wateratm2lndbulk_inst, & - waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, & - cnveg_state_inst, cnveg_carbonstate_inst, & - totlitc_col=soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), & - decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & - t_soi17cm_col=temperature_inst%t_soi17cm_col(begc:endc)) - - call cnfire_method%CNFireFluxes(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - num_actfirec, filter_actfirec, num_actfirep, filter_actfirep, & - dgvs_inst, cnveg_state_inst, & - cnveg_carbonstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - soilbiogeochem_carbonflux_inst, & - leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full), & - froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full), & - croot_prof_patch=soilbiogeochem_state_inst%croot_prof_patch(begp:endp, 1:nlevdecomp_full), & - stem_prof_patch=soilbiogeochem_state_inst%stem_prof_patch(begp:endp, 1:nlevdecomp_full), & - totsomc_col=soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc), & - decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & - decomp_npools_vr_col=soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & - somc_fire_col=soilbiogeochem_carbonflux_inst%somc_fire_col(begc:endc)) - call t_stopf('CNFire') - - - !-------------------------------------------------------------------------- - ! Update3 - ! The state updates are still called for the matrix solution (use_matrixn - ! and use_soil_matrixcn) but most of the state updates are done after - ! the matrix multiply in VegMatrix and SoilMatrix. - !-------------------------------------------------------------------------- - - call t_startf('CNUpdate3') - if ( use_c13 ) then - call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & - c13_soilbiogeochem_carbonstate_inst, & - isotope='c13') - end if - if ( use_c14 ) then - call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & - soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, & - c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & - c14_soilbiogeochem_carbonstate_inst, & - isotope='c14') - end if - - call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & - soilbiogeochem_carbonflux_inst) + if_soilp3: if(num_soilp>0)then + call t_startf('CNFire') + call cnfire_method%CNFireArea(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, & + atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, wateratm2lndbulk_inst, & + waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, & + cnveg_state_inst, cnveg_carbonstate_inst, & + totlitc_col=soilbiogeochem_carbonstate_inst%totlitc_col(begc:endc), & + decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & + t_soi17cm_col=temperature_inst%t_soi17cm_col(begc:endc)) + + call cnfire_method%CNFireFluxes(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_actfirec, filter_actfirec, num_actfirep, filter_actfirep, & + dgvs_inst, cnveg_state_inst, & + cnveg_carbonstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & + soilbiogeochem_carbonflux_inst, & + leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full), & + froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp, 1:nlevdecomp_full), & + croot_prof_patch=soilbiogeochem_state_inst%croot_prof_patch(begp:endp, 1:nlevdecomp_full), & + stem_prof_patch=soilbiogeochem_state_inst%stem_prof_patch(begp:endp, 1:nlevdecomp_full), & + totsomc_col=soilbiogeochem_carbonstate_inst%totsomc_col(begc:endc), & + decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & + decomp_npools_vr_col=soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & + somc_fire_col=soilbiogeochem_carbonflux_inst%somc_fire_col(begc:endc)) + call t_stopf('CNFire') + + !-------------------------------------------------------------------------- + ! Update3 + ! The state updates are still called for the matrix solution (use_matrixn + ! and use_soil_matrixcn) but most of the state updates are done after + ! the matrix multiply in VegMatrix and SoilMatrix. + !-------------------------------------------------------------------------- + + call t_startf('CNUpdate3') + if ( use_c13 ) then + call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & + c13_soilbiogeochem_carbonstate_inst, & + isotope='c13') + end if + if ( use_c14 ) then + call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & + cnveg_carbonflux_inst, cnveg_carbonstate_inst, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & + c14_soilbiogeochem_carbonstate_inst, & + isotope='c14') + end if - if ( use_c13 ) then call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & - c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & - c13_soilbiogeochem_carbonflux_inst) - end if + cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & + soilbiogeochem_carbonflux_inst) - if ( use_c14 ) then - call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & - c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & - c14_soilbiogeochem_carbonflux_inst) + if ( use_c13 ) then + call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & + c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & + c13_soilbiogeochem_carbonflux_inst) + end if - call C14Decay(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & - c14_cnveg_carbonflux_inst, c14_soilbiogeochem_carbonflux_inst) - end if - call t_stopf('CNUpdate3') + if ( use_c14 ) then + call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & + c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & + c14_soilbiogeochem_carbonflux_inst) + + call C14Decay(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & + c14_cnveg_carbonflux_inst, c14_soilbiogeochem_carbonflux_inst) + end if + call t_stopf('CNUpdate3') - if ( use_nguardrail ) then + end if if_soilp3 + + if ( use_nguardrail .and. num_soilp>0 ) then call t_startf('CNPrecisionControl') call CNPrecisionControl(bounds, num_soilp, filter_soilp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & @@ -990,15 +1024,14 @@ subroutine CNDriverLeaching(bounds, & call t_stopf('SoilBiogeochemNLeaching') ! Nitrogen state variable update, mortality fluxes. - - call t_startf('NUpdate3') - - call NStateUpdate3(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, & - soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) - - call t_stopf('NUpdate3') - + if(num_soilp>0)then + call t_startf('NUpdate3') + call NStateUpdate3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) + call t_stopf('NUpdate3') + end if + !-------------------------------------------------------------------------- ! Solve the matrix solution and do the state update for matrix solution as ! part of that @@ -1168,16 +1201,16 @@ subroutine CNDriverSummarizeFluxes(bounds, & soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), & - leafc_to_litter_patch=cnveg_carbonflux_inst%leafc_to_litter_patch(begp:endp), & - frootc_to_litter_patch=cnveg_carbonflux_inst%frootc_to_litter_patch(begp:endp)) + leafc_to_litter_patch=cnveg_carbonflux_inst%leafc_to_litter_patch, & + frootc_to_litter_patch=cnveg_carbonflux_inst%frootc_to_litter_patch) if ( use_c13 ) then call c13_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, & c13_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & c13_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), & - leafc_to_litter_patch=c13_cnveg_carbonflux_inst%leafc_to_litter_patch(begp:endp), & - frootc_to_litter_patch=c13_cnveg_carbonflux_inst%frootc_to_litter_patch(begp:endp)) + leafc_to_litter_patch=c13_cnveg_carbonflux_inst%leafc_to_litter_patch, & + frootc_to_litter_patch=c13_cnveg_carbonflux_inst%frootc_to_litter_patch) end if if ( use_c14 ) then call c14_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, & @@ -1185,8 +1218,8 @@ subroutine CNDriverSummarizeFluxes(bounds, & c14_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & c14_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), & - leafc_to_litter_patch=c14_cnveg_carbonflux_inst%leafc_to_litter_patch(begp:endp), & - frootc_to_litter_patch=c14_cnveg_carbonflux_inst%frootc_to_litter_patch(begp:endp)) + leafc_to_litter_patch=c14_cnveg_carbonflux_inst%leafc_to_litter_patch, & + frootc_to_litter_patch=c14_cnveg_carbonflux_inst%frootc_to_litter_patch) end if call soilbiogeochem_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc) @@ -1194,41 +1227,43 @@ subroutine CNDriverSummarizeFluxes(bounds, & ! cnveg carbon/nitrogen flux summary ! ---------------------------------------------- - call t_startf('CNvegCflux_summary') - call cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - isotope='bulk', & - soilbiogeochem_hr_col=soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & - soilbiogeochem_cwdhr_col=soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & - soilbiogeochem_lithr_col=soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), & - soilbiogeochem_decomp_cascade_ctransfer_col=& - soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & - product_closs_grc=c_products_inst%product_loss_grc(begg:endg)) - - if ( use_c13 ) then - call c13_cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - isotope='c13', & - soilbiogeochem_hr_col=c13_soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & - soilbiogeochem_cwdhr_col=c13_soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & - soilbiogeochem_lithr_col=c13_soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), & - soilbiogeochem_decomp_cascade_ctransfer_col=& - c13_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & - product_closs_grc=c13_products_inst%product_loss_grc(begg:endg)) - end if - - if ( use_c14 ) then - call c14_cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & - isotope='c14', & - soilbiogeochem_hr_col=c14_soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & - soilbiogeochem_cwdhr_col=c14_soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & - soilbiogeochem_lithr_col=c14_soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), & + if_soilp: if(num_soilp>0) then + call t_startf('CNvegCflux_summary') + call cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + isotope='bulk', & + soilbiogeochem_hr_col=soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & + soilbiogeochem_cwdhr_col=soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & + soilbiogeochem_lithr_col=soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), & soilbiogeochem_decomp_cascade_ctransfer_col=& - c14_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & - product_closs_grc=c14_products_inst%product_loss_grc(begg:endg)) - end if - call t_stopf('CNvegCflux_summary') - - call cnveg_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & + product_closs_grc=c_products_inst%product_loss_grc(begg:endg)) + + if ( use_c13 ) then + call c13_cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + isotope='c13', & + soilbiogeochem_hr_col=c13_soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & + soilbiogeochem_cwdhr_col=c13_soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & + soilbiogeochem_lithr_col=c13_soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), & + soilbiogeochem_decomp_cascade_ctransfer_col=& + c13_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & + product_closs_grc=c13_products_inst%product_loss_grc(begg:endg)) + end if + + if ( use_c14 ) then + call c14_cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + isotope='c14', & + soilbiogeochem_hr_col=c14_soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & + soilbiogeochem_cwdhr_col=c14_soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & + soilbiogeochem_lithr_col=c14_soilbiogeochem_carbonflux_inst%lithr_col(begc:endc), & + soilbiogeochem_decomp_cascade_ctransfer_col=& + c14_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & + product_closs_grc=c14_products_inst%product_loss_grc(begg:endg)) + end if + call t_stopf('CNvegCflux_summary') + call cnveg_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + end if if_soilp + call t_stopf('CNsum') end subroutine CNDriverSummarizeFluxes diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90 index 91c937f655..ebda9db56d 100644 --- a/src/biogeochem/CNGapMortalityMod.F90 +++ b/src/biogeochem/CNGapMortalityMod.F90 @@ -312,7 +312,7 @@ subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_so froot_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), & croot_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), & stem_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full)) - + end associate end subroutine CNGapMortality diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index a658a63768..2c2189ec2d 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -25,6 +25,7 @@ module CNNDynamicsMod use ColumnType , only : col use PatchType , only : patch use perf_mod , only : t_startf, t_stopf + use CLMFatesInterfaceMod , only : hlm_fates_interface_type ! implicit none private @@ -192,7 +193,8 @@ end subroutine CNFreeLivingFixation !----------------------------------------------------------------------- subroutine CNNFixation(num_soilc, filter_soilc, & - cnveg_carbonflux_inst, soilbiogeochem_nitrogenflux_inst) + cnveg_carbonflux_inst, soilbiogeochem_nitrogenflux_inst, & + clm_fates, clump_index) ! ! !DESCRIPTION: ! On the radiation time step, update the nitrogen fixation rate @@ -209,12 +211,15 @@ subroutine CNNFixation(num_soilc, filter_soilc, & integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst + type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst + type(hlm_fates_interface_type) , intent(inout) :: clm_fates + integer , intent(in) :: clump_index ! ! !LOCAL VARIABLES: - integer :: c,fc ! indices + integer :: c,fc,s ! indices real(r8) :: t ! temporary real(r8) :: dayspyr ! days per year + real(r8) :: npp ! lag or smoothed net primary productivity (gC/m2/s) !----------------------------------------------------------------------- associate( & @@ -225,16 +230,22 @@ subroutine CNNFixation(num_soilc, filter_soilc, & ) dayspyr = get_curr_days_per_year() - if ( nfix_timeconst > 0._r8 .and. nfix_timeconst < 500._r8 ) then ! use exponential relaxation with time constant nfix_timeconst for NPP - NFIX relation ! Loop through columns do fc = 1,num_soilc c = filter_soilc(fc) - if (col_lag_npp(c) /= spval) then + if(col%is_fates(c))then + s = clm_fates%f2hmap(clump_index)%hsites(c) + npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp/(dayspyr*secspday) + else + npp = col_lag_npp(c) + end if + + if (npp /= spval) then ! need to put npp in units of gC/m^2/year here first - t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * col_lag_npp(c)*(secspday * dayspyr))))/(secspday * dayspyr) + t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * npp *(secspday * dayspyr))))/(secspday * dayspyr) nfix_to_sminn(c) = max(0._r8,t) else nfix_to_sminn(c) = 0._r8 diff --git a/src/biogeochem/CNNStateUpdate1Mod.F90 b/src/biogeochem/CNNStateUpdate1Mod.F90 index c99729b2ee..af049baad5 100644 --- a/src/biogeochem/CNNStateUpdate1Mod.F90 +++ b/src/biogeochem/CNNStateUpdate1Mod.F90 @@ -23,7 +23,10 @@ module CNNStateUpdate1Mod use SoilBiogeochemNitrogenFluxType , only : soilbiogeochem_nitrogenflux_type use SoilBiogeochemNitrogenStateType , only : soilbiogeochem_nitrogenstate_type use CropReprPoolsMod , only : nrepr, repr_grain_min, repr_grain_max, repr_structure_min, repr_structure_max - use PatchType , only : patch + use PatchType , only : patch + use CLMFatesInterfaceMod , only : hlm_fates_interface_type + use ColumnType , only : col + ! implicit none private @@ -96,7 +99,9 @@ end subroutine NStateUpdateDynPatch !----------------------------------------------------------------------- subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & - cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & + clm_fates, clump_index) + use CNSharedParamsMod , only : use_fun ! ! !DESCRIPTION: @@ -111,6 +116,9 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst + type(hlm_fates_interface_type) , intent(inout) :: clm_fates + integer , intent(in) :: clump_index + ! ! !LOCAL VARIABLES: integer :: c,p,j,l,g,k,i ! indices @@ -134,9 +142,23 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ! soilbiogeochemistry fluxes TODO - this should be moved elsewhere ! plant to litter fluxes - phenology and dynamic landcover fluxes - do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + + fc_loop: do fc = 1,num_soilc + c = filter_soilc(fc) + + fates_if: if( col%is_fates(c) ) then + + ! If this is a fates column, then we ask fates for the + ! litter fluxes, the following routine simply copies + ! prepared litter c flux boundary conditions into + ! cf_soil%decomp_cpools_sourcesink_col + + !call clm_fates%UpdateNLitterfluxes(ff_soil,ci,c) + + else + + do j = 1, nlevdecomp + ! ! State update without the matrix solution ! @@ -151,19 +173,20 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ! time step, but to be safe, I'm explicitly setting it to zero here. nf_soil%decomp_npools_sourcesink_col(c,j,i_cwd) = 0._r8 - ! - ! For the matrix solution the actual state update comes after the matrix - ! multiply in SoilMatrix, but the matrix needs to be setup with - ! the equivalent of above. Those changes can be here or in the - ! native subroutines dealing with that field - ! + ! + ! For the matrix solution the actual state update comes after the matrix + ! multiply in SoilMatrix, but the matrix needs to be setup with + ! the equivalent of above. Those changes can be here or in the + ! native subroutines dealing with that field + ! else ! Do the above to the matrix solution do i = i_litr_min, i_litr_max end do end if end do - end do + end if fates_if + end do fc_loop do fp = 1,num_soilp p = filter_soilp(fp) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ec04fcbf54..4db642c58f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -406,7 +406,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & ! gather all patch-level litterfall fluxes to the column for litter C and N inputs - call CNLitterToColumn(bounds, num_soilc, filter_soilc, & + call CNLitterToColumn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & cnveg_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full), & froot_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full)) @@ -3384,8 +3384,8 @@ end subroutine CNCropHarvestToProductPools !----------------------------------------------------------------------- subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & - cnveg_state_inst,cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - leaf_prof_patch, froot_prof_patch) + num_soilp, filter_soilp, cnveg_state_inst,cnveg_carbonflux_inst, & + cnveg_nitrogenflux_inst, leaf_prof_patch, froot_prof_patch) ! ! !DESCRIPTION: ! called at the end of cn_phenology to gather all patch-level litterfall fluxes @@ -3400,6 +3400,8 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for patches type(cnveg_state_type) , intent(in) :: cnveg_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst @@ -3407,7 +3409,7 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & real(r8) , intent(in) :: froot_prof_patch(bounds%begp:,1:) ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,k,j,i ! indices + integer :: fc,c,pi,p,k,j,i,fp ! indices !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(leaf_prof_patch) == (/bounds%endp,nlevdecomp_full/)), sourcefile, __LINE__) @@ -3438,94 +3440,85 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & phenology_n_to_litr_n => cnveg_nitrogenflux_inst%phenology_n_to_litr_n_col & ! Output: [real(r8) (:,:,:) ] N fluxes associated with phenology (litterfall and crop) to litter pools (gN/m3/s) ) - do j = 1, nlevdecomp - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - c = filter_soilc(fc) - - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - ! leaf litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! leaf litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + soil_loop: do j = 1, nlevdecomp + patch_loop: do fp = 1, num_soilp + p = filter_soilp(fp) + c = patch%column(p) + do i = i_litr_min, i_litr_max + ! leaf litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! leaf litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! fine root litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + + ! fine root litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do - ! fine root litter carbon fluxes + ! agroibis puts crop stem litter together with leaf litter + ! so I've used the leaf lf_f* parameters instead of making + ! new ones for now (slevis) + ! also for simplicity I've put "food" into the litter pools + + if (ivt(p) >= npcropmin) then ! add livestemc to litter + do i = i_litr_min, i_litr_max + ! stem litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! stem litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + + if (.not. use_grainproduct) then + do i = i_litr_min, i_litr_max + do k = repr_grain_min, repr_grain_max + ! grain litter carbon fluxes phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + phenology_c_to_litr_c(c,j,i) + & + repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - ! fine root litter nitrogen fluxes + ! grain litter nitrogen fluxes phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + phenology_n_to_litr_n(c,j,i) + & + repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) end do - - ! agroibis puts crop stem litter together with leaf litter - ! so I've used the leaf lf_f* parameters instead of making - ! new ones for now (slevis) - ! also for simplicity I've put "food" into the litter pools - - if (ivt(p) >= npcropmin) then ! add livestemc to litter - do i = i_litr_min, i_litr_max - ! stem litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! stem litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - - if (.not. use_grainproduct) then - do i = i_litr_min, i_litr_max - do k = repr_grain_min, repr_grain_max - ! grain litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! grain litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - - do i = i_litr_min, i_litr_max - do k = repr_structure_min, repr_structure_max - ! reproductive structure litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! reproductive structure litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - end if + end do end if - end do + do i = i_litr_min, i_litr_max + do k = repr_structure_min, repr_structure_max + ! reproductive structure litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! reproductive structure litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + end if - end do - end do + end do patch_loop + end do soil_loop - end associate + end associate end subroutine CNLitterToColumn diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 254063ddac..8ffbe6db2e 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -21,7 +21,7 @@ module CNProductsMod ! ! !PUBLIC TYPES: type, public :: cn_products_type - private + ! ------------------------------------------------------------------------ ! Public instance variables ! ------------------------------------------------------------------------ @@ -73,12 +73,13 @@ module CNProductsMod procedure, private :: InitHistory procedure, private :: InitCold procedure, public :: Restart - + procedure, public :: SetValues + ! Science routines procedure, public :: UpdateProducts procedure, private :: PartitionWoodFluxes procedure, private :: PartitionCropFluxes - procedure, private :: ComputeSummaryVars + procedure, public :: ComputeSummaryVars end type cn_products_type @@ -170,6 +171,33 @@ subroutine InitAllocate(this, bounds) end subroutine InitAllocate + subroutine SetValues(this, bounds, setval) + + ! !ARGUMENTS: + class(cn_products_type), intent(inout) :: this + type(bounds_type), intent(in) :: bounds + real(r8), intent(in) :: setval + + ! This zero's arrays that are incremented on each model time-step + ! the hrv_deadstem arrays use a p2g routine for the use_cn portion + ! but we added this zero'ing here because FATES needs it zero'd + + this%dwt_prod10_gain_grc(bounds%begg:bounds%endg) = setval + this%dwt_prod100_gain_grc(bounds%begg:bounds%endg) = setval + this%dwt_cropprod1_gain_grc(bounds%begg:bounds%endg) = setval + + this%crop_harvest_to_cropprod1_grc(bounds%begg:bounds%endg) = setval + this%hrv_deadstem_to_prod10_grc(bounds%begg:bounds%endg) = setval + this%hrv_deadstem_to_prod100_grc(bounds%begg:bounds%endg) = setval + + !this%cropprod1_loss_grc(bounds%begg:bounds%endg) = setval + !this%prod10_loss_grc(bounds%begg:bounds%endg) = setval + !this%prod100_loss_grc(bounds%begg:bounds%endg) = setval + + return + end subroutine SetValues + + !----------------------------------------------------------------------- subroutine InitHistory(this, bounds) ! !USES: @@ -466,6 +494,7 @@ subroutine UpdateProducts(this, bounds, & ! !DESCRIPTION: ! Update all loss fluxes from wood and crop product pools, and update product pool ! state variables for both loss and gain terms + ! This is only for non-fates patches and columns ! ! !ARGUMENTS: class(cn_products_type) , intent(inout) :: this @@ -475,10 +504,10 @@ subroutine UpdateProducts(this, bounds, & ! dynamic landcover addition to wood product pools (g/m2/s) [patch]; although this is ! a patch-level flux, it is expressed per unit GRIDCELL area - real(r8), intent(in) :: dwt_wood_product_gain_patch( bounds%begp: ) + real(r8), intent(in) :: dwt_wood_product_gain_patch(bounds%begp:) ! wood harvest addition to wood product pools (g/m2/s) [patch] - real(r8), intent(in) :: wood_harvest_patch( bounds%begp: ) + real(r8), intent(in) :: wood_harvest_patch(bounds%begp:) ! dynamic landcover addition to crop product pools (g/m2/s) [patch]; although this is ! a patch-level flux, it is expressed per unit GRIDCELL area @@ -487,71 +516,28 @@ subroutine UpdateProducts(this, bounds, & ! crop harvest to crop product pool (g/m2/s) [patch] real(r8), intent(in) :: crop_harvest_to_cropprod_patch( bounds%begp: ) ! - ! !LOCAL VARIABLES: - integer :: g ! indices - real(r8) :: dt ! time step (seconds) - real(r8) :: kprod1 ! decay constant for 1-year product pool - real(r8) :: kprod10 ! decay constant for 10-year product pool - real(r8) :: kprod100 ! decay constant for 100-year product pool - !----------------------------------------------------------------------- + SHR_ASSERT_ALL_FL((ubound(dwt_wood_product_gain_patch) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(wood_harvest_patch) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(dwt_crop_product_gain_patch) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(crop_harvest_to_cropprod_patch) == (/bounds%endp/)), sourcefile, __LINE__) - + call this%PartitionWoodFluxes(bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch(bounds%begp:bounds%endp), & wood_harvest_patch(bounds%begp:bounds%endp)) - + call this%PartitionCropFluxes(bounds, & num_soilp, filter_soilp, & dwt_crop_product_gain_patch(bounds%begp:bounds%endp), & - crop_harvest_to_cropprod_patch(bounds%begp:bounds%endp)) - - ! calculate losses from product pools - ! the following (1/s) rate constants result in ~90% loss of initial state over 1, 10 and 100 years, - ! respectively, using a discrete-time fractional decay algorithm. - kprod1 = 7.2e-8_r8 - kprod10 = 7.2e-9_r8 - kprod100 = 7.2e-10_r8 - - do g = bounds%begg, bounds%endg - ! calculate fluxes out of product pools (1/sec) - this%cropprod1_loss_grc(g) = this%cropprod1_grc(g) * kprod1 - this%prod10_loss_grc(g) = this%prod10_grc(g) * kprod10 - this%prod100_loss_grc(g) = this%prod100_grc(g) * kprod100 - end do - - ! set time steps - dt = get_step_size_real() - - ! update product state variables - do g = bounds%begg, bounds%endg - - ! fluxes into wood & crop product pools, from landcover change - this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%dwt_cropprod1_gain_grc(g)*dt - this%prod10_grc(g) = this%prod10_grc(g) + this%dwt_prod10_gain_grc(g)*dt - this%prod100_grc(g) = this%prod100_grc(g) + this%dwt_prod100_gain_grc(g)*dt - - ! fluxes into wood & crop product pools, from harvest - this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%crop_harvest_to_cropprod1_grc(g)*dt - this%prod10_grc(g) = this%prod10_grc(g) + this%hrv_deadstem_to_prod10_grc(g)*dt - this%prod100_grc(g) = this%prod100_grc(g) + this%hrv_deadstem_to_prod100_grc(g)*dt - - ! fluxes out of wood & crop product pools, from decomposition - this%cropprod1_grc(g) = this%cropprod1_grc(g) - this%cropprod1_loss_grc(g)*dt - this%prod10_grc(g) = this%prod10_grc(g) - this%prod10_loss_grc(g)*dt - this%prod100_grc(g) = this%prod100_grc(g) - this%prod100_loss_grc(g)*dt - - end do - - call this%ComputeSummaryVars(bounds) + crop_harvest_to_cropprod_patch(bounds%begp:bounds%endp)) + return end subroutine UpdateProducts !----------------------------------------------------------------------- + subroutine PartitionWoodFluxes(this, bounds, & num_soilp, filter_soilp, & dwt_wood_product_gain_patch, & @@ -599,7 +585,7 @@ subroutine PartitionWoodFluxes(this, bounds, & this%hrv_deadstem_to_prod100_patch(p) = & wood_harvest_patch(p) * (1.0_r8 - pftcon%pprodharv10(patch%itype(p))) end do - + ! Average harvest fluxes from patch to gridcell call p2g(bounds, & this%hrv_deadstem_to_prod10_patch(bounds%begp:bounds%endp), & @@ -607,24 +593,18 @@ subroutine PartitionWoodFluxes(this, bounds, & p2c_scale_type = 'unity', & c2l_scale_type = 'unity', & l2g_scale_type = 'unity') - + call p2g(bounds, & this%hrv_deadstem_to_prod100_patch(bounds%begp:bounds%endp), & this%hrv_deadstem_to_prod100_grc(bounds%begg:bounds%endg), & p2c_scale_type = 'unity', & c2l_scale_type = 'unity', & l2g_scale_type = 'unity') - - ! Zero the dwt gains - do g = bounds%begg, bounds%endg - this%dwt_prod10_gain_grc(g) = 0._r8 - this%dwt_prod100_gain_grc(g) = 0._r8 - end do - + ! Partition dynamic land cover fluxes to 10 and 100-year product pools. do p = bounds%begp, bounds%endp g = patch%gridcell(p) - + ! Note that pprod10 + pprod100 do NOT sum to 1: some fraction of the dwt changes ! was lost to other fluxes. dwt_wood_product_gain_patch gives the amount that goes ! to all product pools, so we need to determine the fraction of that flux that @@ -647,9 +627,9 @@ subroutine PartitionWoodFluxes(this, bounds, & msg='ERROR: dwt_wood_product_gain_patch(p) > 0' // & errMsg(sourcefile, __LINE__)) end if - + end do - + end subroutine PartitionWoodFluxes !----------------------------------------------------------------------- @@ -708,10 +688,6 @@ subroutine PartitionCropFluxes(this, bounds, & ! Determine gains from dynamic landcover - do g = bounds%begg, bounds%endg - this%dwt_cropprod1_gain_grc(g) = 0._r8 - end do - do p = bounds%begp, bounds%endp g = patch%gridcell(p) @@ -739,10 +715,52 @@ subroutine ComputeSummaryVars(this, bounds) ! ! !LOCAL VARIABLES: integer :: g ! indices - + real(r8) :: dt ! time step (seconds) + real(r8) :: kprod1 ! decay constant for 1-year product pool + real(r8) :: kprod10 ! decay constant for 10-year product pool + real(r8) :: kprod100 ! decay constant for 100-year product pool + !----------------------------------------------------------------------- character(len=*), parameter :: subname = 'ComputeSummaryVars' + + !----------------------------------------------------------------------- + ! calculate losses from product pools + ! the following (1/s) rate constants result in ~90% loss of initial state over 1, 10 and 100 years, + ! respectively, using a discrete-time fractional decay algorithm. + kprod1 = 7.2e-8_r8 + kprod10 = 7.2e-9_r8 + kprod100 = 7.2e-10_r8 + + do g = bounds%begg, bounds%endg + ! calculate fluxes out of product pools (1/sec) + this%cropprod1_loss_grc(g) = this%cropprod1_grc(g) * kprod1 + this%prod10_loss_grc(g) = this%prod10_grc(g) * kprod10 + this%prod100_loss_grc(g) = this%prod100_grc(g) * kprod100 + end do + ! set time steps + dt = get_step_size_real() + + ! update product state variables + do g = bounds%begg, bounds%endg + + ! fluxes into wood & crop product pools, from landcover change + this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%dwt_cropprod1_gain_grc(g)*dt + this%prod10_grc(g) = this%prod10_grc(g) + this%dwt_prod10_gain_grc(g)*dt + this%prod100_grc(g) = this%prod100_grc(g) + this%dwt_prod100_gain_grc(g)*dt + + ! fluxes into wood & crop product pools, from harvest + this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%crop_harvest_to_cropprod1_grc(g)*dt + this%prod10_grc(g) = this%prod10_grc(g) + this%hrv_deadstem_to_prod10_grc(g)*dt + this%prod100_grc(g) = this%prod100_grc(g) + this%hrv_deadstem_to_prod100_grc(g)*dt + + ! fluxes out of wood & crop product pools, from decomposition + this%cropprod1_grc(g) = this%cropprod1_grc(g) - this%cropprod1_loss_grc(g)*dt + this%prod10_grc(g) = this%prod10_grc(g) - this%prod10_loss_grc(g)*dt + this%prod100_grc(g) = this%prod100_grc(g) - this%prod100_loss_grc(g)*dt + + end do + do g = bounds%begg, bounds%endg ! total wood products diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index d30b9f1991..42d91e9c3d 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -1079,12 +1079,14 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! Set controls on very low values in critical state variables - call t_startf('CNPrecisionControl') - call CNPrecisionControl(bounds, num_soilp, filter_soilp, & - this%cnveg_carbonstate_inst, this%c13_cnveg_carbonstate_inst, & - this%c14_cnveg_carbonstate_inst, this%cnveg_nitrogenstate_inst) - call t_stopf('CNPrecisionControl') - + if(num_soilp>0)then + call t_startf('CNPrecisionControl') + call CNPrecisionControl(bounds, num_soilp, filter_soilp, & + this%cnveg_carbonstate_inst, this%c13_cnveg_carbonstate_inst, & + this%c14_cnveg_carbonstate_inst, this%cnveg_nitrogenstate_inst) + call t_stopf('CNPrecisionControl') + end if + call t_startf('SoilBiogeochemPrecisionControl') call SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & @@ -1194,7 +1196,8 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & this%cnveg_nitrogenflux_inst, & this%cnveg_nitrogenstate_inst, & this%n_products_inst, & - atm2lnd_inst) + atm2lnd_inst, & + clm_fates) end if diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index bf7a9d625a..db82b665ec 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -33,9 +33,10 @@ module filterMod integer, pointer :: natvegp(:) ! CNDV nat-vegetated (present) filter (patches) integer :: num_natvegp ! number of patches in nat-vegetated filter - integer, pointer :: pcropp(:) ! prognostic crop filter (patches) + integer, pointer :: pcropp(:) ! prognostic crop filter (patches) integer :: num_pcropp ! number of patches in prognostic crop filter - integer, pointer :: soilnopcropp(:) ! soil w/o prog. crops (patches) + + integer, pointer :: soilnopcropp(:) ! soil w/o prog. crops (patches) integer :: num_soilnopcropp ! number of patches in soil w/o prog crops integer, pointer :: all_soil_patches(:) ! all soil or crop patches. Used for updating FATES SP drivers @@ -57,8 +58,7 @@ module filterMod integer, pointer :: bgc_vegp(:) ! patches with vegetation biochemistry active, negates ! SP type runs, could be CN or Crop (NOT FATES) integer :: num_bgc_vegp - - + integer, pointer :: soilc(:) ! soil filter (columns) integer :: num_soilc ! number of columns in soil filter integer, pointer :: soilp(:) ! soil filter (patches) @@ -478,14 +478,16 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fnl = 0 do p = bounds%begp,bounds%endp if (patch%active(p) .or. include_inactive) then - if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types - fl = fl + 1 - this_filter(nc)%pcropp(fl) = p - else - l =patch%landunit(p) - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - fnl = fnl + 1 - this_filter(nc)%soilnopcropp(fnl) = p + if(.not.use_fates)then ! This needs to be a FATES filter + if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types + fl = fl + 1 + this_filter(nc)%pcropp(fl) = p + else + l =patch%landunit(p) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + fnl = fnl + 1 + this_filter(nc)%soilnopcropp(fnl) = p + end if end if end if end if diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index e42e395801..bda4c13c7a 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -759,8 +759,9 @@ subroutine Summary(this, bounds, & real(r8), intent(in), optional :: soilbiogeochem_cwdc_col(bounds%begc:) real(r8), intent(in), optional :: soilbiogeochem_cwdn_col(bounds%begc:) real(r8), intent(in), optional :: soilbiogeochem_decomp_cascade_ctransfer_col(bounds%begc:,1:) - real(r8), intent(in), optional :: leafc_to_litter_patch(bounds%begp:) - real(r8), intent(in), optional :: frootc_to_litter_patch(bounds%begp:) + + real(r8), intent(in), optional :: leafc_to_litter_patch(:) + real(r8), intent(in), optional :: frootc_to_litter_patch(:) ! ! !LOCAL VARIABLES: integer :: c,j,k,l,p @@ -895,21 +896,20 @@ subroutine Summary(this, bounds, & ! Calculate ligninNratio ! FATES does its own calculation - if (decomp_method == mimics_decomp) then + if (decomp_method == mimics_decomp .and. num_soilp>0) then + do fp = 1,num_soilp p = filter_soilp(fp) - if( .not.patch%is_fates(p)) then - associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type - ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * & - pftcon%lflitcn(ivt(p)) * & - leafc_to_litter_patch(p) - ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * & - pftcon%frootcn(ivt(p)) * & - frootc_to_litter_patch(p) - end associate - end if + associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type + ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * & + pftcon%lflitcn(ivt(p)) * & + leafc_to_litter_patch(p) + ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * & + pftcon%frootcn(ivt(p)) * & + frootc_to_litter_patch(p) + end associate end do - + call p2c(bounds, num_soilc, filter_soilc, & ligninNratio_leaf_patch(bounds%begp:bounds%endp), & ligninNratio_leaf_col(bounds%begc:bounds%endc)) @@ -926,19 +926,21 @@ subroutine Summary(this, bounds, & ! Calculate ligninNratioAve do fc = 1,num_soilc c = filter_soilc(fc) - if (soilbiogeochem_cwdn_col(c) > 0._r8) then - ligninNratio_cwd = CNParamsShareInst%cwd_flig * & - (soilbiogeochem_cwdc_col(c) / soilbiogeochem_cwdn_col(c)) * & - soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2) - else - ligninNratio_cwd = 0._r8 + if(.not.col%is_fates(c)) then + if (soilbiogeochem_cwdn_col(c) > 0._r8) then + ligninNratio_cwd = CNParamsShareInst%cwd_flig * & + (soilbiogeochem_cwdc_col(c) / soilbiogeochem_cwdn_col(c)) * & + soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2) + else + ligninNratio_cwd = 0._r8 + end if + this%litr_lig_c_to_n_col(c) = & + (ligninNratio_leaf_col(c) + ligninNratio_froot_col(c) + & + ligninNratio_cwd) / & + max(1.0e-3_r8, leafc_to_litter_col(c) + & + frootc_to_litter_col(c) + & + soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2)) end if - this%litr_lig_c_to_n_col(c) = & - (ligninNratio_leaf_col(c) + ligninNratio_froot_col(c) + & - ligninNratio_cwd) / & - max(1.0e-3_r8, leafc_to_litter_col(c) + & - frootc_to_litter_col(c) + & - soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2)) end do end if diff --git a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 index 3740700ab1..91c70fcf5e 100644 --- a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 @@ -70,7 +70,8 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & ! they get too small. ! ! !USES: - use clm_varctl , only : iulog, use_c13, use_c14, use_nitrif_denitrif, use_cn + use clm_varctl , only : iulog, use_c13, use_c14, use_nitrif_denitrif + use clm_varctl , only : use_cn, use_fates use clm_varpar , only : nlevdecomp use CNSharedParamsMod, only: use_fun ! @@ -128,7 +129,7 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & cc = cc + cs%decomp_cpools_vr_col(c,j,k) cs%decomp_cpools_vr_col(c,j,k) = 0._r8 - if (use_cn) then + if (use_cn .or. use_fates) then cn = cn + ns%decomp_npools_vr_col(c,j,k) ns%decomp_npools_vr_col(c,j,k) = 0._r8 endif @@ -150,7 +151,7 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & cs%ctrunc_vr_col(c,j) = cs%ctrunc_vr_col(c,j) + cc - if (use_cn) then + if (use_cn .or. use_fates) then ns%ntrunc_vr_col(c,j) = ns%ntrunc_vr_col(c,j) + cn endif if ( use_c13 ) then diff --git a/src/soilbiogeochem/SoilBiogeochemStateType.F90 b/src/soilbiogeochem/SoilBiogeochemStateType.F90 index fcdced386d..86232160f7 100644 --- a/src/soilbiogeochem/SoilBiogeochemStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemStateType.F90 @@ -103,7 +103,7 @@ subroutine InitAllocate(this, bounds) allocate(this%nue_decomp_cascade_col(1:ndecomp_cascade_transitions)); this%nue_decomp_cascade_col(:) = nan - + end subroutine InitAllocate !------------------------------------------------------------------------ diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 2eb746e6f3..e6a3f611ad 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -48,6 +48,7 @@ module CLMFatesInterfaceMod use CNProductsMod , only : cn_products_type use clm_varctl , only : iulog use clm_varctl , only : fates_parteh_mode + use PRTGenericMod , only : prt_cnp_flex_allom_hyp use clm_varctl , only : use_fates use clm_varctl , only : fates_spitfire_mode use clm_varctl , only : use_fates_tree_damage @@ -2343,50 +2344,56 @@ end subroutine wrap_accumulatefluxes ! ====================================================================================== - subroutine wrap_WoodProducts(this, bounds_clump, fc, filterc, c_products_inst) + subroutine wrap_WoodProducts(this, bounds_clump, num_soilc, filter_soilc, & + c_products_inst, n_products_inst) ! !ARGUMENTS: class(hlm_fates_interface_type), intent(inout) :: this type(bounds_type) , intent(in) :: bounds_clump - integer , intent(in) :: fc ! size of column filter - integer , intent(in) :: filterc(fc) ! column filter + integer , intent(in) :: num_soilc ! size of column filter + integer , intent(in) :: filter_soilc(:) ! column filter type(cn_products_type) , intent(inout) :: c_products_inst + type(cn_products_type) , intent(inout) :: n_products_inst ! Locals - integer :: s,c,icc,g - integer :: nc - - ! This wrapper is not active. This is just place-holder code until - ! harvest-product flux is fully implemented. RGK-05-2022 + integer :: s,c,g,fc + integer :: ci ! Clump index + + ci = bounds_clump%clump_index - !associate( & - ! prod10c => c_products_inst%hrv_deadstem_to_prod10_grc, & - ! prod100c => c_products_inst%hrv_deadstem_to_prod100_grc) + ! Loop over columns + do fc = 1, num_soilc + + c = filter_soilc(fc) + g = col%gridcell(c) + s = this%f2hmap(ci)%hsites(c) - ! nc = bounds_clump%clump_index - ! Loop over columns - do icc = 1,fc - c = filterc(icc) - g = col%gridcell(c) - s = this%f2hmap(nc)%hsites(c) - - ! Shijie: Pass harvested wood products to ELM variable - ! prod10c(g) = prod10c(g) + & - ! this%fates(nc)%bc_out(s)%hrv_deadstemc_to_prod10c - ! prod100c(g) = prod100c(g) + & - ! this%fates(nc)%bc_out(s)%hrv_deadstemc_to_prod100c - - ! RGK: THere is also a patch level variable - !do ifp = 1,this%fates(nc)%sites(s)%youngest_patch%patchno - ! p = ifp+col%patchi(c) - ! hrv_deadstemc_to_prod10c(p) = - ! hrv_deadstemc_to_prod100c(p) - !end do + ! Shijie: Pass harvested wood products to CLM product pools + c_products_inst%hrv_deadstem_to_prod10_grc(g) = & + c_products_inst%hrv_deadstem_to_prod10_grc(g) + & + this%fates(ci)%bc_out(s)%hrv_deadstemc_to_prod10c + + c_products_inst%hrv_deadstem_to_prod100_grc(g) = & + c_products_inst%hrv_deadstem_to_prod100_grc(g) + & + this%fates(ci)%bc_out(s)%hrv_deadstemc_to_prod100c + + ! If N cycling is on + if(fates_parteh_mode .eq. prt_cnp_flex_allom_hyp ) then + + !n_products_inst%hrv_deadstem_to_prod10_grc(g) = & + ! n_products_inst%hrv_deadstem_to_prod10_grc(g) + & + ! this%fates(ci)%bc_out(s)%hrv_deadstemc_to_prod10c + + !n_products_inst%hrv_deadstem_to_prod100_grc(g) = & + ! n_products_inst%hrv_deadstem_to_prod100_grc(g) + & + ! this%fates(ci)%bc_out(s)%hrv_deadstemc_to_prod100c + + end if + - end do + end do - ! end associate - return + return end subroutine wrap_WoodProducts ! ====================================================================================== From 2f1ec5244d55d4c92921b54dfcd19088e0508648 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 2 Mar 2023 16:51:48 -0500 Subject: [PATCH 0718/2067] Pass through of getting fates in the full BGC call sequence. This incremental version does pass C and N balance checks at the column level, but not the grid level (because of missing diagnostic data structures) --- src/biogeochem/CNBalanceCheckMod.F90 | 50 +++++---- src/biogeochem/CNDriverMod.F90 | 11 +- src/biogeochem/CNNStateUpdate1Mod.F90 | 2 +- src/biogeochem/CNNStateUpdate3Mod.F90 | 68 +++++++++--- src/main/controlMod.F90 | 25 +++-- .../SoilBiogeochemCarbonFluxType.F90 | 10 +- .../SoilBiogeochemCarbonStateType.F90 | 1 - .../SoilBiogeochemNitrogenFluxType.F90 | 10 +- src/utils/clmfates_interfaceMod.F90 | 104 +++++++++++++++++- 9 files changed, 221 insertions(+), 60 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index bf54e2b18f..a68410ddbe 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -253,7 +253,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & real(r8) :: som_c_leached_grc(bounds%begg:bounds%endg) real(r8) :: hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg) real(r8) :: dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) - real(r8) :: fates_litter_flux + real(r8) :: fates_woodproduct_flux ! Total carbon wood products flux from FATES to CLM [gC/m2/s] !----------------------------------------------------------------------- @@ -277,7 +277,8 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & col_xsmrpool_to_atm => cnveg_carbonflux_inst%xsmrpool_to_atm_col , & ! Input: [real(r8) (:) ] (gC/m2/s) excess MR pool crop harvest loss to atm som_c_leached => soilbiogeochem_carbonflux_inst%som_c_leached_col , & ! Input: [real(r8) (:) ] (gC/m2/s) total SOM C loss from vertical transport - totcolc => soilbiogeochem_carbonstate_inst%totc_col & ! Input: [real(r8) (:) ] (gC/m2) total column carbon, incl veg and cpool + totcolc => soilbiogeochem_carbonstate_inst%totc_col , & ! Input: [real(r8) (:) ] (gC/m2) total column carbon, incl veg and cpool + fates_litter_flux => soilbiogeochem_carbonflux_inst%fates_litter_flux & ! Total carbon litter flux from FATES to CLM [gC/m2/s] ) ! set time steps @@ -299,17 +300,13 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & if( col%is_fates(c) ) then - ! calculate total column-level inputs (litter fluxes) [g/m2/s] s = clm_fates%f2hmap(ic)%hsites(c) - fates_litter_flux = sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & - clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & - clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * & - clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) - - col_cinputs = fates_litter_flux + + fates_woodproduct_flux = clm_fates%fates(ic)%bc_out(s)%hrv_deadstemc_to_prod10c + & + clm_fates%fates(ic)%bc_out(s)%hrv_deadstemc_to_prod100c + + col_cinputs = fates_litter_flux(c) + fates_woodproduct_flux ! calculate total column-level outputs ! fates has already exported burn losses and fluxes to the atm @@ -326,6 +323,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! er = ar + hr, col_fire_closs includes patch-level fire losses col_coutputs = er(c) + col_fire_closs(c) + col_hrv_xsmrpool_to_atm(c) + & col_xsmrpool_to_atm(c) + ! Fluxes to product pools are included in column-level outputs: the product ! pools are not included in totcolc, so are outside the system with respect to @@ -359,13 +357,15 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & if (err_found) then c = err_index write(iulog,*)'column cbalance error = ', col_errcb(c), c + write(iulog,*)'is fates column? = ', col%is_fates(c) write(iulog,*)'Latdeg,Londeg=',grc%latdeg(col%gridcell(c)),grc%londeg(col%gridcell(c)) write(iulog,*)'begcb = ',col_begcb(c) write(iulog,*)'endcb = ',col_endcb(c) write(iulog,*)'delta store = ',col_endcb(c)-col_begcb(c) write(iulog,*)'--- Inputs ---' if( col%is_fates(c) ) then - write(iulog,*)'fates litter_flux = ',fates_litter_flux*dt + write(iulog,*)'fates litter_flux = ',fates_litter_flux(c)*dt + write(iulog,*)'fates wood product flux = ',fates_woodproduct_flux*dt else write(iulog,*)'gpp = ',gpp(c)*dt end if @@ -547,7 +547,9 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & crop_harvestn_to_cropprodn => cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_col , & ! Input: [real(r8) (:) ] (gN/m2/s) crop harvest N to 1-year crop product pool totcoln => soilbiogeochem_nitrogenstate_inst%totn_col , & ! Input: [real(r8) (:) ] (gN/m2) total column nitrogen, incl veg - sminn_to_plant => soilbiogeochem_nitrogenflux_inst%sminn_to_plant_col ) + sminn_to_plant => soilbiogeochem_nitrogenflux_inst%sminn_to_plant_col, & + fates_litter_flux => soilbiogeochem_nitrogenflux_inst%fates_litter_flux & ! Total nitrogen litter flux from FATES to CLM [gN/m2/s] + ) ! set time steps @@ -572,14 +574,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! If using fates, pass in the decomposition flux if( col%is_fates(c) ) then - s = clm_fates%f2hmap(ic)%hsites(c) - col_ninputs(c) = col_ninputs(c) + & - sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lab_n_si(1:nlevdecomp) * & - clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_cel_n_si(1:nlevdecomp) * & - clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - sum(clm_fates%fates(ic)%bc_out(s)%litt_flux_lig_n_si(1:nlevdecomp) * & - clm_fates%fates(ic)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + col_ninputs(c) = col_ninputs(c) + fates_litter_flux(c) end if if(use_fun)then @@ -660,12 +655,19 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & write(iulog,*)'input mass = ',col_ninputs(c)*dt write(iulog,*)'output mass = ',col_noutputs(c)*dt write(iulog,*)'net flux = ',(col_ninputs(c)-col_noutputs(c))*dt - write(iulog,*)'inputs,ffix,nfix,ndep = ',ffix_to_sminn(c)*dt,nfix_to_sminn(c)*dt,ndep_to_sminn(c)*dt - write(iulog,*)'outputs,lch,roff,dnit = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt + if(col%is_fates(c))then + write(iulog,*)'inputs,ndep,nfix,suppn= ',ndep_to_sminn(c)*dt,nfix_to_sminn(c)*dt,supplement_to_sminn(c)*dt + else + write(iulog,*)'inputs,ffix,nfix,ndep = ',ffix_to_sminn(c)*dt,nfix_to_sminn(c)*dt,ndep_to_sminn(c)*dt + end if + if(col%is_fates(c))then + write(iulog,*)'outputs,lch,roff,dnit,plnt = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt,sminn_to_plant(c)*dt + else + write(iulog,*)'outputs,lch,roff,dnit = ',smin_no3_leached(c)*dt, smin_no3_runoff(c)*dt,f_n2o_nit(c)*dt + end if call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, msg=errMsg(sourcefile, __LINE__)) end if - if(.not.use_fates)then ! Repeat error check at the gridcell level diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 3c27f4e244..f353469738 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -977,8 +977,9 @@ subroutine CNDriverLeaching(bounds, & ! !USES: use SoilBiogeochemNLeachingMod, only: SoilBiogeochemNLeaching use CNNStateUpdate3Mod , only: NStateUpdate3 - use clm_time_manager , only : is_first_step_of_this_run_segment,is_beg_curr_year,is_end_curr_year,get_curr_date - use CNSharedParamsMod , only : use_matrixcn + use CNNStateUpdate3Mod , only: NStateUpdateLeaching + use clm_time_manager , only: is_first_step_of_this_run_segment,is_beg_curr_year,is_end_curr_year,get_curr_date + use CNSharedParamsMod , only: use_matrixcn use SoilBiogeochemDecompCascadeConType , only : use_soil_matrixcn ! ! !ARGUMENTS: @@ -1021,8 +1022,14 @@ subroutine CNDriverLeaching(bounds, & call SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & waterstatebulk_inst, waterfluxbulk_inst, soilbiogeochem_nitrogenstate_inst, & soilbiogeochem_nitrogenflux_inst) + call NStateUpdateLeaching(num_soilc, filter_soilc, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) call t_stopf('SoilBiogeochemNLeaching') + + + + ! Nitrogen state variable update, mortality fluxes. if(num_soilp>0)then call t_startf('NUpdate3') diff --git a/src/biogeochem/CNNStateUpdate1Mod.F90 b/src/biogeochem/CNNStateUpdate1Mod.F90 index af049baad5..5358c46de1 100644 --- a/src/biogeochem/CNNStateUpdate1Mod.F90 +++ b/src/biogeochem/CNNStateUpdate1Mod.F90 @@ -153,7 +153,7 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ! prepared litter c flux boundary conditions into ! cf_soil%decomp_cpools_sourcesink_col - !call clm_fates%UpdateNLitterfluxes(ff_soil,ci,c) + call clm_fates%UpdateNLitterfluxes(nf_soil,clump_index,c) else diff --git a/src/biogeochem/CNNStateUpdate3Mod.F90 b/src/biogeochem/CNNStateUpdate3Mod.F90 index b5e3f32fec..26902cef22 100644 --- a/src/biogeochem/CNNStateUpdate3Mod.F90 +++ b/src/biogeochem/CNNStateUpdate3Mod.F90 @@ -25,11 +25,63 @@ module CNNStateUpdate3Mod private ! ! !PUBLIC MEMBER FUNCTIONS: - public:: NStateUpdate3 + public :: NStateUpdate3 + public :: NStateUpdateLeaching !----------------------------------------------------------------------- contains + subroutine NStateUpdateLeaching(num_soilc, filter_soilc, & + soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) + ! + ! !DESCRIPTION: + ! On the radiation time step, update all the prognostic nitrogen state + ! variables affected by the Sminn leaching flux. + ! RGK: This code was separated from gap mortality fluxes to make this + ! compatible with FATES. + ! + ! !ARGUMENTS: + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! filter for soil columns + type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst + type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst + + ! !LOCAL VARIABLES: + integer :: c,p,j,l,k ! indices + integer :: fp,fc ! lake filter indices + real(r8):: dt ! radiation time step (seconds) + !----------------------------------------------------------------------- + + associate( & + nf_soil => soilbiogeochem_nitrogenflux_inst , & ! Input + ns_soil => soilbiogeochem_nitrogenstate_inst & ! Output + ) + + ! set time steps + dt = get_step_size_real() + + do j = 1, nlevdecomp + ! column loop + do fc = 1,num_soilc + c = filter_soilc(fc) + + if (.not. use_nitrif_denitrif) then + ! mineral N loss due to leaching + ns_soil%sminn_vr_col(c,j) = ns_soil%sminn_vr_col(c,j) - nf_soil%sminn_leached_vr_col(c,j) * dt + else + ! mineral N loss due to leaching and runoff + ns_soil%smin_no3_vr_col(c,j) = max( ns_soil%smin_no3_vr_col(c,j) - & + ( nf_soil%smin_no3_leached_vr_col(c,j) + nf_soil%smin_no3_runoff_vr_col(c,j) ) * dt, 0._r8) + + ns_soil%sminn_vr_col(c,j) = ns_soil%smin_no3_vr_col(c,j) + ns_soil%smin_nh4_vr_col(c,j) + end if + end do + end do + + end associate + return + end subroutine NStateUpdateLeaching + !----------------------------------------------------------------------- subroutine NStateUpdate3(num_soilc, filter_soilc, num_soilp, filter_soilp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, & @@ -37,7 +89,7 @@ subroutine NStateUpdate3(num_soilc, filter_soilc, num_soilp, filter_soilp, & ! ! !DESCRIPTION: ! On the radiation time step, update all the prognostic nitrogen state - ! variables affected by gap-phase mortality fluxes. Also the Sminn leaching flux. + ! variables affected by gap-phase mortality fluxes. ! NOTE - associate statements have been removed where there are ! no science equations. This increases readability and maintainability. ! @@ -72,20 +124,8 @@ subroutine NStateUpdate3(num_soilc, filter_soilc, num_soilp, filter_soilp, & do fc = 1,num_soilc c = filter_soilc(fc) - if (.not. use_nitrif_denitrif) then - ! mineral N loss due to leaching - ns_soil%sminn_vr_col(c,j) = ns_soil%sminn_vr_col(c,j) - nf_soil%sminn_leached_vr_col(c,j) * dt - else - ! mineral N loss due to leaching and runoff - ns_soil%smin_no3_vr_col(c,j) = max( ns_soil%smin_no3_vr_col(c,j) - & - ( nf_soil%smin_no3_leached_vr_col(c,j) + nf_soil%smin_no3_runoff_vr_col(c,j) ) * dt, 0._r8) - - ns_soil%sminn_vr_col(c,j) = ns_soil%smin_no3_vr_col(c,j) + ns_soil%smin_nh4_vr_col(c,j) - end if - ! column level nitrogen fluxes from fire ! patch-level wood to column-level CWD (uncombusted wood) - ! ! State update without the matrix solution ! diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index a07228aa0d..a763703d6e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -433,6 +433,15 @@ subroutine control_init(dtime) ! Check compatibility with the FATES model if ( use_fates ) then + if (fates_parteh_mode == 1 .and. suplnitro == suplnNon)then + write(iulog,*) ' When FATES with fates_parteh_mode == 1 (ie carbon only mode),' + write(iulog,*) ' you must have supplemental nitrogen turned on, there will be' + write(iulog,*) ' no nitrogen dynamics with the plants, and therefore no' + write(iulog,*) ' meaningful limitations to nitrogen.' + call endrun(msg=' ERROR: fates_parteh_mode=1 must have suplnitro set to suplnAll.'//& + errMsg(sourcefile, __LINE__)) + end if + if ( use_cn) then call endrun(msg=' ERROR: use_cn and use_fates cannot both be set to true.'//& errMsg(sourcefile, __LINE__)) @@ -689,7 +698,8 @@ subroutine control_spmd() ! BGC call mpi_bcast (co2_type, len(co2_type), MPI_CHARACTER, 0, mpicom, ier) - if (use_cn) then + + if (use_cn .or. use_fates) then call mpi_bcast (suplnitro, len(suplnitro), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (nfix_timeconst, 1, MPI_REAL8, 0, mpicom, ier) call mpi_bcast (spinup_state, 1, MPI_INTEGER, 0, mpicom, ier) @@ -743,7 +753,7 @@ subroutine control_spmd() call mpi_bcast (use_dynroot, 1, MPI_LOGICAL, 0, mpicom, ier) - if (use_cn ) then + if (use_cn .or. use_fates) then ! vertical soil mixing variables call mpi_bcast (som_adv_flux, 1, MPI_REAL8, 0, mpicom, ier) call mpi_bcast (max_depth_cryoturb, 1, MPI_REAL8, 0, mpicom, ier) @@ -751,8 +761,8 @@ subroutine control_spmd() ! C and N input vertical profiles call mpi_bcast (surfprof_exp, 1, MPI_REAL8, 0, mpicom, ier) end if - - if (use_cn .and. use_nitrif_denitrif) then + + if ((use_cn.or.use_fates) .and. use_nitrif_denitrif) then call mpi_bcast (no_frozen_nitrif_denitrif, 1, MPI_LOGICAL, 0, mpicom, ier) end if @@ -899,7 +909,8 @@ subroutine control_print () write(iulog,*) ' Threshold above which the model keeps the lake landunit =', toosmall_lake write(iulog,*) ' Threshold above which the model keeps the wetland landunit =', toosmall_wetland write(iulog,*) ' Threshold above which the model keeps the urban landunits =', toosmall_urban - if (use_cn) then + + if (use_cn .or. use_fates) then if (suplnitro /= suplnNon)then write(iulog,*) ' Supplemental Nitrogen mode is set to run over Patches: ', & trim(suplnitro) @@ -930,13 +941,13 @@ subroutine control_print () write(iulog,*) ' override_bgc_restart_mismatch_dump : ', override_bgc_restart_mismatch_dump end if - if (use_cn ) then + if (use_cn .or. use_fates) then write(iulog, *) ' som_adv_flux, the advection term in soil mixing (m/s) : ', som_adv_flux write(iulog, *) ' max_depth_cryoturb (m) : ', max_depth_cryoturb write(iulog, *) ' surfprof_exp : ', surfprof_exp end if - if (use_cn .and. .not. use_nitrif_denitrif) then + if ((use_cn .or. use_fates) .and. .not. use_nitrif_denitrif) then write(iulog, *) ' no_frozen_nitrif_denitrif : ', no_frozen_nitrif_denitrif end if diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index bda4c13c7a..3a311807a9 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -6,6 +6,7 @@ module SoilBiogeochemCarbonFluxType use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan use clm_varpar , only : nlevdecomp_full, nlevgrnd, nlevdecomp, nlevsoi, i_cwdl2 use clm_varcon , only : spval, ispval, dzsoi_decomp + use clm_varctl , only : use_fates use pftconMod , only : pftcon use landunit_varcon , only : istsoil, istcrop, istdlak use ch4varcon , only : allowlakeprod @@ -57,7 +58,8 @@ module SoilBiogeochemCarbonFluxType real(r8), pointer :: lithr_col (:) ! (gC/m2/s) litter heterotrophic respiration: donor-pool based definition real(r8), pointer :: somhr_col (:) ! (gC/m2/s) soil organic matter heterotrophic res: donor-pool based definition real(r8), pointer :: soilc_change_col (:) ! (gC/m2/s) FUN used soil C - + real(r8), pointer :: fates_litter_flux (:) ! (gC/m2/s) Litter flux passed in from FATES + contains procedure , public :: Init @@ -155,7 +157,11 @@ subroutine InitAllocate(this, bounds) allocate(this%lithr_col (begc:endc)) ; this%lithr_col (:) = nan allocate(this%somhr_col (begc:endc)) ; this%somhr_col (:) = nan allocate(this%soilc_change_col (begc:endc)) ; this%soilc_change_col (:) = nan - + + if(use_fates)then + allocate(this%fates_litter_flux(begc:endc)); this%fates_litter_flux(:) = nan + end if + if(use_soil_matrixcn)then end if diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 349a6c140d..349f70b46f 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -1154,7 +1154,6 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst this%totsomc_col(c) + & this%ctrunc_col(c) + & totvegc_col - end do diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 index 839f69379a..90ba4512c7 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 @@ -7,7 +7,7 @@ module SoilBiogeochemNitrogenFluxType use clm_varpar , only : nlevdecomp_full, nlevdecomp use clm_varcon , only : spval, ispval, dzsoi_decomp use decompMod , only : bounds_type - use clm_varctl , only : use_nitrif_denitrif, use_crop + use clm_varctl , only : use_nitrif_denitrif, use_crop, use_fates use CNSharedParamsMod , only : use_fun use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn use abortutils , only : endrun @@ -127,8 +127,8 @@ module SoilBiogeochemNitrogenFluxType ! all n pools involved in decomposition real(r8), pointer :: decomp_npools_sourcesink_col (:,:,:) ! col (gN/m3) change in decomposing n pools ! (sum of all additions and subtractions from stateupdate1). - real(r8), pointer :: sminn_to_plant_fun_vr_col (:,:) ! col total layer soil N uptake of FUN (gN/m2/s) - + real(r8), pointer :: sminn_to_plant_fun_vr_col (:,:) ! col total layer soil N uptake of FUN (gN/m2/s) + real(r8), pointer :: fates_litter_flux (:) ! (gN/m2/s) Litter flux passed in from FATES ! track tradiagonal matrix contains @@ -274,6 +274,10 @@ subroutine InitAllocate(this, bounds) allocate(this%decomp_npools_sourcesink_col (begc:endc,1:nlevdecomp_full,1:ndecomp_pools)) this%decomp_npools_sourcesink_col (:,:,:) = nan + if(use_fates)then + allocate(this%fates_litter_flux(begc:endc)); this%fates_litter_flux(:) = nan + end if + ! Allocate soil Matrix setug if(use_soil_matrixcn)then end if diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index e6a3f611ad..0ac24f897c 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -81,6 +81,8 @@ module CLMFatesInterfaceMod use SolarAbsorbedType , only : solarabs_type use SoilBiogeochemCarbonFluxType, only : soilbiogeochem_carbonflux_type use SoilBiogeochemCarbonStateType, only : soilbiogeochem_carbonstate_type + use SoilBiogeochemNitrogenFluxType, only : soilbiogeochem_nitrogenflux_type + use SoilBiogeochemNitrogenStateType, only : soilbiogeochem_nitrogenstate_type use FrictionVelocityMod , only : frictionvel_type use clm_time_manager , only : is_restart, is_first_restart_step use ncdio_pio , only : file_desc_t, ncd_int, ncd_double @@ -226,6 +228,7 @@ module CLMFatesInterfaceMod procedure, public :: WrapUpdateFatesRmean procedure, public :: wrap_WoodProducts procedure, public :: UpdateCLitterFluxes + procedure, public :: UPdateNLitterFluxes end type hlm_fates_interface_type ! hlm_bounds_to_fates_bounds is not currently called outside the interface. @@ -1065,6 +1068,79 @@ end subroutine dynamics_driv ! =============================================================================== + subroutine UpdateNLitterFluxes(this,soilbiogeochem_nitrogenflux_inst,ci,c) + + use clm_varpar, only : i_met_lit + + class(hlm_fates_interface_type), intent(inout) :: this + type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst + integer , intent(in) :: ci ! clump index + integer , intent(in) :: c ! column index + + integer :: s ! site index + real(r8) :: dtime + integer :: i_lig_lit, i_cel_lit ! indices for lignan and cellulose + + dtime = get_step_size_real() + s = this%f2hmap(ci)%hsites(c) + + associate(nf_soil => soilbiogeochem_nitrogenflux_inst) + + nf_soil%decomp_npools_sourcesink_col(c,:,:) = 0._r8 + + if ( .not. use_fates_sp ) then + + ! (gC/m3/timestep) + !nf_soil%decomp_npools_sourcesink_col(c,1:nlevdecomp,i_met_lit) = & + ! nf_soil%decomp_npools_sourcesink_col(c,1:nlevdecomp,i_met_lit) + & + ! this%fates(ci)%bc_out(s)%litt_flux_lab_n_si(1:nlevdecomp)*dtime + + ! Used for mass balance checking (gC/m2/s) + !nf_soil%fates_litter_flux(c) = sum(this%fates(ci)%bc_out(s)%litt_flux_lab_n_si(1:nlevdecomp) * & + ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + i_cel_lit = i_met_lit + 1 + + !nf_soil%decomp_npools_sourcesink_col(c,1:nlevdecomp,i_cel_lit) = & + ! nf_soil%decomp_npools_sourcesink_col(c,1:nlevdecomp,i_cel_lit) + & + ! this%fates(ci)%bc_out(s)%litt_flux_cel_n_si(1:nlevdecomp)*dtime + + !nf_soil%fates_litter_flux(c) = nf_soil%fates_litter_flux(c) + & + ! sum(this%fates(ci)%bc_out(s)%litt_flux_cel_n_si(1:nlevdecomp) * & + ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + if (decomp_method == mimics_decomp) then + ! Mimics has a structural pool, which is cellulose and lignan + i_lig_lit = i_cel_lit + elseif(decomp_method == century_decomp ) then + ! CENTURY has a separate lignan pool from cellulose + i_lig_lit = i_cel_lit + 1 + end if + + !nf_soil%decomp_npools_sourcesink_col(c,1:nlevdecomp,i_lig_lit) = & + ! nf_soil%decomp_npools_sourcesink_col(c,1:nlevdecomp,i_lig_lit) + & + ! this%fates(ci)%bc_out(s)%litt_flux_lig_n_si(1:nlevdecomp)*dtime + + !nf_soil%fates_litter_flux(c) = nf_soil%fates_litter_flux(c) + & + ! sum(this%fates(ci)%bc_out(s)%litt_flux_lig_n_si(1:nlevdecomp) * & + ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + + nf_soil%fates_litter_flux = 0._r8 + + else + + ! In SP mode their is no mass flux between the two + nf_soil%fates_litter_flux = 0._r8 + + end if + + end associate + + return + end subroutine UpdateNLitterFluxes + + ! =========================================================== + subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) use clm_varpar, only : i_met_lit @@ -1073,7 +1149,7 @@ subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst integer , intent(in) :: ci ! clump index integer , intent(in) :: c ! column index - + integer :: s ! site index real(r8) :: dtime integer :: i_lig_lit, i_cel_lit ! indices for lignan and cellulose @@ -1083,17 +1159,28 @@ subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) associate(cf_soil => soilbiogeochem_carbonflux_inst) + cf_soil%decomp_cpools_sourcesink_col(c,:,:) = 0._r8 + if ( .not. use_fates_sp ) then + ! (gC/m3/timestep) cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_met_lit) = & cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_met_lit) + & - this%fates(ci)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * dtime + this%fates(ci)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp)*dtime + ! Used for mass balance checking (gC/m2/s) + cf_soil%fates_litter_flux(c) = sum(this%fates(ci)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & + this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + i_cel_lit = i_met_lit + 1 cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_cel_lit) = & cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_cel_lit) + & - this%fates(ci)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp)* dtime + this%fates(ci)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp)*dtime + + cf_soil%fates_litter_flux(c) = cf_soil%fates_litter_flux(c) + & + sum(this%fates(ci)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & + this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) if (decomp_method == mimics_decomp) then ! Mimics has a structural pool, which is cellulose and lignan @@ -1105,11 +1192,16 @@ subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_lig_lit) = & cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_lig_lit) + & - this%fates(ci)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * dtime - + this%fates(ci)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp)*dtime + + cf_soil%fates_litter_flux(c) = cf_soil%fates_litter_flux(c) + & + sum(this%fates(ci)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * & + this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + else ! In SP mode their is no mass flux between the two - cf_soil%decomp_cpools_sourcesink_col(c,:,:) = 0._r8 + + cf_soil%fates_litter_flux = 0._r8 end if ! This is a diagnostic for carbon accounting (NOT IN CLM, ONLY ELM) From cb4f5101408a79fc95fe072850996774db507ede Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 2 Mar 2023 17:24:43 -0500 Subject: [PATCH 0719/2067] Added suppln to fates cases --- bld/CLMBuildNamelist.pm | 9 +++++++-- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index f046172f7e..5b77996fb0 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2892,20 +2892,25 @@ sub setup_logic_supplemental_nitrogen { 'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'}); } + if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} eq "fates" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'}); + } + # # Error checking for suplnitro # my $suplnitro = $nl->get_value('suplnitro'); if ( defined($suplnitro) ) { if ( $nl_flags->{'bgc_mode'} eq "sp" ) { - $log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV is active!"); + $log->fatal_error("supplemental Nitrogen (suplnitro) is set, but neither CN nor CNDV nor FATES is active!"); } if ( ! &value_is_true($nl_flags->{'use_crop'}) && $suplnitro =~ /PROG_CROP_ONLY/i ) { $log->fatal_error("supplemental Nitrogen is set to run over prognostic crops, but prognostic crop is NOT active!"); } if ( $suplnitro =~ /ALL/i ) { - if ( $nl_flags->{'bgc_spinup'} eq "on" ) { + if ( $nl_flags->{'bgc_spinup'} eq "on" && $nl_flags->{'bgc_mode'} ne "fates" ) { $log->warning("There is no need to use a bgc_spinup mode when supplemental Nitrogen is on for all PFT's, as these modes spinup Nitrogen" ); } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 41103b5259..ae5bd97937 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -146,7 +146,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). NONE -NONE +ALL 0.50,0.30 From da8224fc171b1e2d46093f6315470759db87aea3 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 3 Mar 2023 16:09:23 -0700 Subject: [PATCH 0720/2067] Squashed 'manage_externals/' changes from 82d3b247f..7b6d92ef6 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 7b6d92ef6 Merge pull request #198 from johnpaulalex/gitdir 927ce3a98 Merge pull request #197 from johnpaulalex/testpath a04f1148f Merge pull request #196 from johnpaulalex/readmod d9c14bf25 Change the rest of the methods to use -C. Still some usage of getcwd in test_unit_repository_git. 332b10640 Fix incorrect logged path of checkout_externals in test_sys_checkout: it was basically the parent of the current directory, which varies throughout the test. (it called abspath with '{0}/../../', which adds arbitrary and not-interpolated subdir '{0}' to the path, then removes it and removes one more level). 932a7499b Remove printlog from read_gitmodules_file since read_externals_description_file() already has a nearly-the-same printlog (but add it to the other caller). 5d13719ed Merge pull request #195 from johnpaulalex/check_repo 423395449 Update utest to mock _git_remote_verbose in a new way, since it is now called via the GitRepository class rather than on the specific GitRepository instance. d7a42ae96 Check that desired repo was actually checked out. 71596bbc1 Merge pull request #194 from johnpaulalex/manic2 4c96e824e Make the MANIC_TEST_BARE_REPO_ROOT env var special - give it a constant for easy tracking, and automatically tear it down after each test. 259bfc04d test_sys_checkout: use actual paths in on-the-fly configs rather than MANIC_TEST_BARE_REPO_ROOT env var. This will make it easier to test (in the near future) that checkout_externals actually checked out the desired repo dir. 557bbd6eb Merge pull request #193 from johnpaulalex/manic 5314eede1 Remove MANIC_TEST_TMP_REPO_ROOT environment variable in favor of module-level variable. 345fc1e14 Merge pull request #191 from johnpaulalex/test_doc12 2117b843c test_sys_checkout: verify that basic by-tag/branch/hash tests actually take us to the correct git tag/branch/hash. 94d6e5f2b Merge pull request #190 from johnpaulalex/test_doc11 3ff33a6a8 Inline local-path-creation methods 47dea7f64 Merge pull request #189 from johnpaulalex/test_doc10 9ea75cbf8 Grab-bag of renamings: Remove redundant _NAME from repo constants, and consistently add _REPO suffix (This causes the majority of diffs). c0c847ec8 Merge pull request #188 from johnpaulalex/test_doc9 2dd5ce0f7 test_sys_checkout.py: only check for correct 'required' or 'optional' state in the test that exercises required vs optional behavior. Removed a lot of boilerplate. eb3085984 Merge pull request #187 from johnpaulalex/test_doc8 1832e1f84 test_sys_checkout: Simplify many tests to only use a single external. 8689d61ec Merge pull request #186 from johnpaulalex/test_doc7 fbee4253e Grab bag of test_sys_checkout cleanups: Doc inside of each test more clearly/consistently. TestSysCheckoutSVN didn’t get the inlining-of-helper-methods treatment, now it has that. Move various standalone repo helper methods (like create_branch) into a RepoUtils class. README.md was missing newlines when rendered as markdown. Doc the return value of checkout.main Fix test_container_exclude_component - it was looking for the wrong key (which is never present); now it looks for the correct key. f0ed44a6e Merge pull request #185 from johnpaulalex/test_doc6 a3d59f5f2 Merge pull request #184 from johnpaulalex/test_doc5 5329c8ba7 test_sys_checkout: Inline config generation functions that are only called once. 464f2c7a7 test_sys_checkout: Inline another layer (per-config-file checks). Rename the 4 methods that are used multiple times, to reflect what they do rather than what they're called. 8872c0df6 Merge pull request #183 from johnpaulalex/doc_test4 c045335f6 Merge pull request #182 from johnpaulalex/doc_test3 c583b956e Merge pull request #181 from johnpaulalex/doc_test2 e01cfe278 test_sys_checkout: less confusing handling of return values from checkout_externals. Specifically, when doing a checkout, don't return tree_status from _before_ the checkout. Make a new wrapper to call checkout_externals a second time, to calculate the new status after a checkout (very frequent pattern). 23286818c test_sys_checkout: Remove another layer (which generates test component names) c3717b6bc Merge pull request #180 from johnpaulalex/doc_test 36d7a4434 test_sys_checkout.py: remove one layer of functions (that check for local status enums). No-op. 2c4584bf7 More documentation about tests: * contents of test repositories (n a new README.md) * various constants in test_sys_checkout.py that point to those contents, and terminology like container/simple/mixed. * in each test method, the scenarios being tested. * The coupling between test methods. 55e74bd0a Merge pull request #179 from johnpaulalex/circ 66be84290 Remove circular dependency by making _External stop doing tricky things with sourcetrees. git-subtree-dir: manage_externals git-subtree-split: 7b6d92ef689e2f65733e27f8635ab91fb341356b --- manic/checkout.py | 8 +- manic/externals_description.py | 20 +- manic/externals_status.py | 4 +- manic/repository_git.py | 315 +++-- manic/sourcetree.py | 249 ++-- test/repos/README.md | 33 + test/test_sys_checkout.py | 2182 ++++++++++++++---------------- test/test_sys_repository_git.py | 58 +- test/test_unit_repository_git.py | 133 +- 9 files changed, 1458 insertions(+), 1544 deletions(-) create mode 100644 test/repos/README.md diff --git a/manic/checkout.py b/manic/checkout.py index ac30f3a5d2..3f5537adce 100755 --- a/manic/checkout.py +++ b/manic/checkout.py @@ -378,9 +378,9 @@ def main(args): the --all option is passed. Returns a tuple (overall_status, tree_status). overall_status is 0 - on success, non-zero on failure. tree_status gives the full status - *before* executing the checkout command - i.e., the status that it - used to determine if it's safe to proceed with the checkout. + on success, non-zero on failure. tree_status is a dict mapping local path + to ExternalStatus -- if no checkout is happening. If checkout is happening, tree_status + is None. """ if args.do_logging: logging.basicConfig(filename=LOG_FILE_NAME, @@ -438,6 +438,8 @@ def main(args): for comp in args.components: source_tree.checkout(args.verbose, load_all, load_comp=comp) printlog('') + # New tree status is unknown, don't return anything. + tree_status = None logging.info('%s completed without exceptions.', program_name) # NOTE(bja, 2017-11) tree status is used by the systems tests diff --git a/manic/externals_description.py b/manic/externals_description.py index f5615b6730..546e7fdcb4 100644 --- a/manic/externals_description.py +++ b/manic/externals_description.py @@ -88,7 +88,7 @@ def read_externals_description_file(root_dir, file_name): externals_description = None if file_name == ExternalsDescription.GIT_SUBMODULES_FILENAME: - externals_description = read_gitmodules_file(root_dir, file_name) + externals_description = _read_gitmodules_file(root_dir, file_name) else: try: config = config_parser() @@ -151,9 +151,8 @@ def git_submodule_status(repo_dir): """Run the git submodule status command to obtain submodule hashes. """ # This function is here instead of GitRepository to avoid a dependency loop - cwd = os.getcwd() - os.chdir(repo_dir) - cmd = ['git', 'submodule', 'status'] + cmd = 'git -C {repo_dir} submodule status'.format( + repo_dir=repo_dir).split() git_output = execute_subprocess(cmd, output_to_caller=True) submodules = {} submods = git_output.split('\n') @@ -168,7 +167,6 @@ def git_submodule_status(repo_dir): submodules[items[1]] = {'hash':items[0], 'status':status, 'tag':tag} - os.chdir(cwd) return submodules def parse_submodules_desc_section(section_items, file_path): @@ -191,7 +189,7 @@ def parse_submodules_desc_section(section_items, file_path): return path, url -def read_gitmodules_file(root_dir, file_name): +def _read_gitmodules_file(root_dir, file_name): # pylint: disable=deprecated-method # Disabling this check because the method is only used for python2 # pylint: disable=too-many-locals @@ -203,12 +201,11 @@ def read_gitmodules_file(root_dir, file_name): root_dir = os.path.abspath(root_dir) msg = 'In directory : {0}'.format(root_dir) logging.info(msg) - printlog('Processing submodules description file : {0}'.format(file_name)) file_path = os.path.join(root_dir, file_name) if not os.path.exists(file_name): msg = ('ERROR: submodules description file, "{0}", does not ' - 'exist at path:\n {1}'.format(file_name, file_path)) + 'exist in dir:\n {1}'.format(file_name, root_dir)) fatal_error(msg) submodules_description = None @@ -640,8 +637,11 @@ def _repo_config_from_submodule(self, field, submod_desc): ' Parent repo, "{1}" does not have submodules') fatal_error(msg.format(field, self._parent_repo.name())) - submod_file = read_gitmodules_file(repo_path, submod_file) - submod_desc = create_externals_description(submod_file) + printlog( + 'Processing submodules description file : {0} ({1})'.format( + submod_file, repo_path)) + submod_model_data= _read_gitmodules_file(repo_path, submod_file) + submod_desc = create_externals_description(submod_model_data) # Can we find our external? repo_url = None diff --git a/manic/externals_status.py b/manic/externals_status.py index 4900e41254..6bc29e9732 100644 --- a/manic/externals_status.py +++ b/manic/externals_status.py @@ -30,12 +30,12 @@ class ExternalStatus(object): """ # sync_state and clean_state can be one of the following: - DEFAULT = '-' # aka not set yet. + DEFAULT = '-' # not set yet (sync_state). clean_state can be this if sync_state is EMPTY. UNKNOWN = '?' EMPTY = 'e' MODEL_MODIFIED = 's' # repo version != externals (sync_state only) DIRTY = 'M' # repo is dirty (clean_state only) - STATUS_OK = ' ' # repo is clean/matches externals. + STATUS_OK = ' ' # repo is clean (clean_state) or matches externals version (sync_state) STATUS_ERROR = '!' # source_type can be one of the following: diff --git a/manic/repository_git.py b/manic/repository_git.py index 3a6a0f1716..adc666cc57 100644 --- a/manic/repository_git.py +++ b/manic/repository_git.py @@ -25,7 +25,7 @@ class GitRepository(Repository): * be isolated in separate functions with no application logic * of the form: - - cmd = ['git', ...] + - cmd = 'git -C {dirname} ...'.format(dirname=dirname).split() - value = execute_subprocess(cmd, output_to_caller={T|F}, status_to_caller={T|F}) - return value @@ -39,7 +39,7 @@ class GitRepository(Repository): def __init__(self, component_name, repo): """ - Parse repo (a XML element). + repo: ExternalsDescription. """ Repository.__init__(self, component_name, repo) self._gitmodules = None @@ -99,15 +99,13 @@ def submodules_file(self, repo_path=None): # # ---------------------------------------------------------------- def _clone_repo(self, base_dir_path, repo_dir_name, verbosity): - """Prepare to execute the clone by managing directory location + """Clones repo_dir_name into base_dir_path. """ - cwd = os.getcwd() - os.chdir(base_dir_path) - self._git_clone(self._url, repo_dir_name, verbosity) - os.chdir(cwd) + self._git_clone(self._url, os.path.join(base_dir_path, repo_dir_name), + verbosity=verbosity) - def _current_ref(self): - """Determine the *name* associated with HEAD. + def _current_ref(self, dirname): + """Determine the *name* associated with HEAD at dirname. If we're on a tag, then returns the tag name; otherwise, returns the current hash. Returns an empty string if no reference can be @@ -119,21 +117,21 @@ def _current_ref(self): ref_found = False # If we're exactly at a tag, use that as the current ref - tag_found, tag_name = self._git_current_tag() + tag_found, tag_name = self._git_current_tag(dirname) if tag_found: current_ref = tag_name ref_found = True if not ref_found: # Otherwise, use current hash as the current ref - hash_found, hash_name = self._git_current_hash() + hash_found, hash_name = self._git_current_hash(dirname) if hash_found: current_ref = hash_name ref_found = True if ref_found: # If we're on a branch, include branch name in current ref - branch_found, branch_name = self._git_current_branch() + branch_found, branch_name = self._git_current_branch(dirname) if branch_found: current_ref = "{} (branch {})".format(current_ref, branch_name) else: @@ -184,17 +182,15 @@ def compare_refs(current_ref, expected_ref): status = ExternalStatus.MODEL_MODIFIED return status - cwd = os.getcwd() - os.chdir(repo_dir_path) - # get the full hash of the current commit - _, current_ref = self._git_current_hash() + _, current_ref = self._git_current_hash(repo_dir_path) if self._branch: if self._url == LOCAL_PATH_INDICATOR: expected_ref = self._branch else: - remote_name = self._determine_remote_name() + remote_name = self._remote_name_for_url(self._url, + repo_dir_path) if not remote_name: # git doesn't know about this remote. by definition # this is a modified state. @@ -211,7 +207,7 @@ def compare_refs(current_ref, expected_ref): fatal_error(msg) # record the *names* of the current and expected branches - stat.current_version = self._current_ref() + stat.current_version = self._current_ref(repo_dir_path) stat.expected_version = copy.deepcopy(expected_ref) if current_ref == EMPTY_STR: @@ -219,7 +215,7 @@ def compare_refs(current_ref, expected_ref): else: # get the underlying hash of the expected ref revparse_status, expected_ref_hash = self._git_revparse_commit( - expected_ref) + expected_ref, repo_dir_path) if revparse_status: # We failed to get the hash associated with # expected_ref. Maybe we should assign this to some special @@ -230,18 +226,13 @@ def compare_refs(current_ref, expected_ref): # compare the underlying hashes stat.sync_state = compare_refs(current_ref, expected_ref_hash) - os.chdir(cwd) - - def _determine_remote_name(self): - """Return the remote name. - - Note that this is for the *future* repo url and branch, not - the current working copy! + @classmethod + def _remote_name_for_url(cls, remote_url, dirname): + """Return the remote name matching remote_url (or None) """ - git_output = self._git_remote_verbose() + git_output = cls._git_remote_verbose(dirname) git_output = git_output.splitlines() - remote_name = '' for line in git_output: data = line.strip() if not data: @@ -249,10 +240,9 @@ def _determine_remote_name(self): data = data.split() name = data[0].strip() url = data[1].strip() - if self._url == url: - remote_name = name - break - return remote_name + if remote_url == url: + return name + return None def _create_remote_name(self): """The url specified in the externals description file was not known @@ -308,19 +298,16 @@ def _checkout_ref(self, repo_dir, verbosity, submodules): the repo's submodules """ # import pdb; pdb.set_trace() - cwd = os.getcwd() - os.chdir(repo_dir) if self._url.strip() == LOCAL_PATH_INDICATOR: - self._checkout_local_ref(verbosity, submodules) + self._checkout_local_ref(verbosity, submodules, repo_dir) else: - self._checkout_external_ref(verbosity, submodules) + self._checkout_external_ref(verbosity, submodules, repo_dir) if self._sparse: self._sparse_checkout(repo_dir, verbosity) - os.chdir(cwd) - def _checkout_local_ref(self, verbosity, submodules): + def _checkout_local_ref(self, verbosity, submodules, dirname): """Checkout the reference considering the local repo only. Do not fetch any additional remotes or specify the remote when checkout out the ref. @@ -334,13 +321,18 @@ def _checkout_local_ref(self, verbosity, submodules): else: ref = self._hash - self._check_for_valid_ref(ref) - self._git_checkout_ref(ref, verbosity, submodules) + self._check_for_valid_ref(ref, remote_name=None, + dirname=dirname) + self._git_checkout_ref(ref, verbosity, submodules, dirname) - def _checkout_external_ref(self, verbosity, submodules): - """Checkout the reference from a remote repository + def _checkout_external_ref(self, verbosity, submodules, dirname): + """Checkout the reference from a remote repository into dirname. if is True, recursively initialize and update - the repo's submodules + the repo's submodules. + Note that this results in a 'detached HEAD' state if checking out + a branch, because we check out the remote branch rather than the + local. See https://github.com/ESMCI/manage_externals/issues/34 for + more discussion. """ if self._tag: ref = self._tag @@ -349,44 +341,45 @@ def _checkout_external_ref(self, verbosity, submodules): else: ref = self._hash - remote_name = self._determine_remote_name() + remote_name = self._remote_name_for_url(self._url, dirname) if not remote_name: remote_name = self._create_remote_name() - self._git_remote_add(remote_name, self._url) - self._git_fetch(remote_name) + self._git_remote_add(remote_name, self._url, dirname) + self._git_fetch(remote_name, dirname) # NOTE(bja, 2018-03) we need to send separate ref and remote # name to check_for_vaild_ref, but the combined name to # checkout_ref! - self._check_for_valid_ref(ref, remote_name) + self._check_for_valid_ref(ref, remote_name, dirname) if self._branch: + # Prepend remote name to branch. This means we avoid various + # special cases if the local branch is not tracking the remote or + # cannot be trivially fast-forwarded to match; but, it also + # means we end up in a 'detached HEAD' state. ref = '{0}/{1}'.format(remote_name, ref) - self._git_checkout_ref(ref, verbosity, submodules) + self._git_checkout_ref(ref, verbosity, submodules, dirname) def _sparse_checkout(self, repo_dir, verbosity): """Use git read-tree to thin the working tree.""" - cwd = os.getcwd() - - cmd = ['cp', self._sparse, os.path.join(repo_dir, - '.git/info/sparse-checkout')] + cmd = ['cp', os.path.join(repo_dir, self._sparse), + os.path.join(repo_dir, + '.git/info/sparse-checkout')] if verbosity >= VERBOSITY_VERBOSE: printlog(' {0}'.format(' '.join(cmd))) execute_subprocess(cmd) - os.chdir(repo_dir) - self._git_sparse_checkout(verbosity) + self._git_sparse_checkout(verbosity, repo_dir) - os.chdir(cwd) - - def _check_for_valid_ref(self, ref, remote_name=None): + def _check_for_valid_ref(self, ref, remote_name, dirname): """Try some basic sanity checks on the user supplied reference so we can provide a more useful error message than calledprocess error... + remote_name can be NOne """ - is_tag = self._ref_is_tag(ref) - is_branch = self._ref_is_branch(ref, remote_name) - is_hash = self._ref_is_hash(ref) + is_tag = self._ref_is_tag(ref, dirname) + is_branch = self._ref_is_branch(ref, remote_name, dirname) + is_hash = self._ref_is_hash(ref, dirname) is_valid = is_tag or is_branch or is_hash if not is_valid: @@ -397,7 +390,8 @@ def _check_for_valid_ref(self, ref, remote_name=None): fatal_error(msg) if is_tag: - is_unique_tag, msg = self._is_unique_tag(ref, remote_name) + is_unique_tag, msg = self._is_unique_tag(ref, remote_name, + dirname) if not is_unique_tag: msg = ('In repo "{0}": tag "{1}" {2}'.format( self._name, self._tag, msg)) @@ -405,7 +399,7 @@ def _check_for_valid_ref(self, ref, remote_name=None): return is_valid - def _is_unique_tag(self, ref, remote_name): + def _is_unique_tag(self, ref, remote_name, dirname): """Verify that a reference is a valid tag and is unique (not a branch) Tags may be tag names, or SHA id's. It is also possible that a @@ -416,9 +410,9 @@ def _is_unique_tag(self, ref, remote_name): error! """ - is_tag = self._ref_is_tag(ref) - is_branch = self._ref_is_branch(ref, remote_name) - is_hash = self._ref_is_hash(ref) + is_tag = self._ref_is_tag(ref, dirname) + is_branch = self._ref_is_branch(ref, remote_name, dirname) + is_hash = self._ref_is_hash(ref, dirname) msg = '' is_unique_tag = False @@ -449,7 +443,7 @@ def _is_unique_tag(self, ref, remote_name): return is_unique_tag, msg - def _ref_is_tag(self, ref): + def _ref_is_tag(self, ref, dirname): """Verify that a reference is a valid tag according to git. Note: values returned by git_showref_* and git_revparse are @@ -457,28 +451,30 @@ def _ref_is_tag(self, ref): error! """ is_tag = False - value = self._git_showref_tag(ref) + value = self._git_showref_tag(ref, dirname) if value == 0: is_tag = True return is_tag - def _ref_is_branch(self, ref, remote_name=None): + def _ref_is_branch(self, ref, remote_name, dirname): """Verify if a ref is any kind of branch (local, tracked remote, untracked remote). + remote_name can be None. """ local_branch = False remote_branch = False if remote_name: - remote_branch = self._ref_is_remote_branch(ref, remote_name) - local_branch = self._ref_is_local_branch(ref) + remote_branch = self._ref_is_remote_branch(ref, remote_name, + dirname) + local_branch = self._ref_is_local_branch(ref, dirname) is_branch = False if local_branch or remote_branch: is_branch = True return is_branch - def _ref_is_local_branch(self, ref): + def _ref_is_local_branch(self, ref, dirname): """Verify that a reference is a valid branch according to git. show-ref branch returns local branches that have been @@ -491,12 +487,12 @@ def _ref_is_local_branch(self, ref): """ is_branch = False - value = self._git_showref_branch(ref) + value = self._git_showref_branch(ref, dirname) if value == 0: is_branch = True return is_branch - def _ref_is_remote_branch(self, ref, remote_name): + def _ref_is_remote_branch(self, ref, remote_name, dirname): """Verify that a reference is a valid branch according to git. show-ref branch returns local branches that have been @@ -509,12 +505,12 @@ def _ref_is_remote_branch(self, ref, remote_name): """ is_branch = False - value = self._git_lsremote_branch(ref, remote_name) + value = self._git_lsremote_branch(ref, remote_name, dirname) if value == 0: is_branch = True return is_branch - def _ref_is_commit(self, ref): + def _ref_is_commit(self, ref, dirname): """Verify that a reference is a valid commit according to git. This could be a tag, branch, sha1 id, HEAD and potentially others... @@ -524,12 +520,12 @@ def _ref_is_commit(self, ref): error! """ is_commit = False - value, _ = self._git_revparse_commit(ref) + value, _ = self._git_revparse_commit(ref, dirname) if value == 0: is_commit = True return is_commit - def _ref_is_hash(self, ref): + def _ref_is_hash(self, ref, dirname): """Verify that a reference is a valid hash according to git. Git doesn't seem to provide an exact way to determine if user @@ -544,7 +540,7 @@ def _ref_is_hash(self, ref): """ is_hash = False - status, git_output = self._git_revparse_commit(ref) + status, git_output = self._git_revparse_commit(ref, dirname) if status == 0: if git_output.strip().startswith(ref): is_hash = True @@ -554,9 +550,7 @@ def _status_summary(self, stat, repo_dir_path): """Determine the clean/dirty status of a git repository """ - cwd = os.getcwd() - os.chdir(repo_dir_path) - git_output = self._git_status_porcelain_v1z() + git_output = self._git_status_porcelain_v1z(repo_dir_path) is_dirty = self._status_v1z_is_dirty(git_output) if is_dirty: stat.clean_state = ExternalStatus.DIRTY @@ -565,8 +559,7 @@ def _status_summary(self, stat, repo_dir_path): # Now save the verbose status output incase the user wants to # see it. - stat.status_output = self._git_status_verbose() - os.chdir(cwd) + stat.status_output = self._git_status_verbose(repo_dir_path) @staticmethod def _status_v1z_is_dirty(git_output): @@ -601,7 +594,7 @@ def _status_v1z_is_dirty(git_output): # # ---------------------------------------------------------------- @staticmethod - def _git_current_hash(): + def _git_current_hash(dirname): """Return the full hash of the currently checked-out version. Returns a tuple, (hash_found, hash), where hash_found is a @@ -609,21 +602,51 @@ def _git_current_hash(): could mean we're not in a git repository at all). (If hash_found is False, then hash is ''.) """ - status, git_output = GitRepository._git_revparse_commit("HEAD") + status, git_output = GitRepository._git_revparse_commit("HEAD", + dirname) hash_found = not status if not hash_found: git_output = '' return hash_found, git_output @staticmethod - def _git_current_branch(): - """Determines the name of the current branch. + def _git_current_remote_branch(dirname): + """Determines the name of the current remote branch, if any. + + if dir is None, uses the cwd. Returns a tuple, (branch_found, branch_name), where branch_found - is a logical specifying whether a branch name was found for + is a bool specifying whether a branch name was found for + HEAD. (If branch_found is False, then branch_name is ''). + branch_name is in the format '$remote/$branch', e.g. 'origin/foo'. + """ + branch_found = False + branch_name = '' + + cmd = 'git -C {dirname} log -n 1 --pretty=%d HEAD'.format( + dirname=dirname).split() + status, git_output = execute_subprocess(cmd, + output_to_caller=True, + status_to_caller=True) + branch_found = 'HEAD,' in git_output + if branch_found: + # git_output is of the form " (HEAD, origin/blah)" + branch_name = git_output.split(',')[1].strip()[:-1] + return branch_found, branch_name + + @staticmethod + def _git_current_branch(dirname): + """Determines the name of the current local branch. + + Returns a tuple, (branch_found, branch_name), where branch_found + is a bool specifying whether a branch name was found for HEAD. (If branch_found is False, then branch_name is ''.) + Note that currently we check out the remote branch rather than + the local, so this command does not return the just-checked-out + branch. See _git_current_remote_branch. """ - cmd = ['git', 'symbolic-ref', '--short', '-q', 'HEAD'] + cmd = 'git -C {dirname} symbolic-ref --short -q HEAD'.format( + dirname=dirname).split() status, git_output = execute_subprocess(cmd, output_to_caller=True, status_to_caller=True) @@ -635,15 +658,17 @@ def _git_current_branch(): return branch_found, git_output @staticmethod - def _git_current_tag(): + def _git_current_tag(dirname): """Determines the name tag corresponding to HEAD (if any). + if dirname is None, uses the cwd. + Returns a tuple, (tag_found, tag_name), where tag_found is a - logical specifying whether we found a tag name corresponding to + bool specifying whether we found a tag name corresponding to HEAD. (If tag_found is False, then tag_name is ''.) """ - # git describe --exact-match --tags HEAD - cmd = ['git', 'describe', '--exact-match', '--tags', 'HEAD'] + cmd = 'git -C {dirname} describe --exact-match --tags HEAD'.format( + dirname=dirname).split() status, git_output = execute_subprocess(cmd, output_to_caller=True, status_to_caller=True) @@ -655,53 +680,54 @@ def _git_current_tag(): return tag_found, git_output @staticmethod - def _git_showref_tag(ref): + def _git_showref_tag(ref, dirname): """Run git show-ref check if the user supplied ref is a tag. could also use git rev-parse --quiet --verify tagname^{tag} """ - cmd = ['git', 'show-ref', '--quiet', '--verify', - 'refs/tags/{0}'.format(ref), ] + cmd = ('git -C {dirname} show-ref --quiet --verify refs/tags/{ref}' + .format(dirname=dirname, ref=ref).split()) status = execute_subprocess(cmd, status_to_caller=True) return status @staticmethod - def _git_showref_branch(ref): + def _git_showref_branch(ref, dirname): """Run git show-ref check if the user supplied ref is a local or tracked remote branch. """ - cmd = ['git', 'show-ref', '--quiet', '--verify', - 'refs/heads/{0}'.format(ref), ] + cmd = ('git -C {dirname} show-ref --quiet --verify refs/heads/{ref}' + .format(dirname=dirname, ref=ref).split()) status = execute_subprocess(cmd, status_to_caller=True) return status @staticmethod - def _git_lsremote_branch(ref, remote_name): + def _git_lsremote_branch(ref, remote_name, dirname): """Run git ls-remote to check if the user supplied ref is a remote branch that is not being tracked """ - cmd = ['git', 'ls-remote', '--exit-code', '--heads', - remote_name, ref, ] + cmd = ('git -C {dirname} ls-remote --exit-code --heads ' + '{remote_name} {ref}').format( + dirname=dirname, remote_name=remote_name, ref=ref).split() status = execute_subprocess(cmd, status_to_caller=True) return status @staticmethod - def _git_revparse_commit(ref): + def _git_revparse_commit(ref, dirname): """Run git rev-parse to detect if a reference is a SHA, HEAD or other valid commit. """ - cmd = ['git', 'rev-parse', '--quiet', '--verify', - '{0}^{1}'.format(ref, '{commit}'), ] + cmd = ('git -C {dirname} rev-parse --quiet --verify {ref}^{commit}' + .format(dirname=dirname, ref=ref, commit='{commit}').split()) status, git_output = execute_subprocess(cmd, status_to_caller=True, output_to_caller=True) git_output = git_output.strip() return status, git_output @staticmethod - def _git_status_porcelain_v1z(): + def _git_status_porcelain_v1z(dirname): """Run git status to obtain repository information. This is run with '--untracked=no' to ignore untracked files. @@ -710,36 +736,38 @@ def _git_status_porcelain_v1z(): between git versions or *user configuration*. """ - cmd = ['git', 'status', '--untracked-files=no', '--porcelain', '-z'] + cmd = ('git -C {dirname} status --untracked-files=no --porcelain -z' + .format(dirname=dirname)).split() git_output = execute_subprocess(cmd, output_to_caller=True) return git_output @staticmethod - def _git_status_verbose(): + def _git_status_verbose(dirname): """Run the git status command to obtain repository information. """ - cmd = ['git', 'status'] + cmd = 'git -C {dirname} status'.format(dirname=dirname).split() git_output = execute_subprocess(cmd, output_to_caller=True) return git_output @staticmethod - def _git_remote_verbose(): + def _git_remote_verbose(dirname): """Run the git remote command to obtain repository information. + + Returned string is of the form: + myfork git@github.com:johnpaulalex/manage_externals_jp.git (fetch) + myfork git@github.com:johnpaulalex/manage_externals_jp.git (push) """ - cmd = ['git', 'remote', '--verbose'] - git_output = execute_subprocess(cmd, output_to_caller=True) - return git_output + cmd = 'git -C {dirname} remote --verbose'.format( + dirname=dirname).split() + return execute_subprocess(cmd, output_to_caller=True) @staticmethod - def has_submodules(repo_dir_path=None): - """Return True iff the repository at (or the current - directory if is None) has a '.gitmodules' file + def has_submodules(repo_dir_path): + """Return True iff the repository at has a + '.gitmodules' file """ - if repo_dir_path is None: - fname = ExternalsDescription.GIT_SUBMODULES_FILENAME - else: - fname = os.path.join(repo_dir_path, - ExternalsDescription.GIT_SUBMODULES_FILENAME) + fname = os.path.join(repo_dir_path, + ExternalsDescription.GIT_SUBMODULES_FILENAME) return os.path.exists(fname) @@ -750,68 +778,71 @@ def has_submodules(repo_dir_path=None): # ---------------------------------------------------------------- @staticmethod def _git_clone(url, repo_dir_name, verbosity): - """Run git clone for the side effect of creating a repository. + """Clones url into repo_dir_name. """ - cmd = ['git', 'clone', '--quiet'] - subcmd = None - - cmd.extend([url, repo_dir_name]) + cmd = 'git clone --quiet {url} {repo_dir_name}'.format( + url=url, repo_dir_name=repo_dir_name).split() if verbosity >= VERBOSITY_VERBOSE: printlog(' {0}'.format(' '.join(cmd))) execute_subprocess(cmd) - if subcmd is not None: - os.chdir(repo_dir_name) - execute_subprocess(subcmd) @staticmethod - def _git_remote_add(name, url): + def _git_remote_add(name, url, dirname): """Run the git remote command for the side effect of adding a remote """ - cmd = ['git', 'remote', 'add', name, url] + cmd = 'git -C {dirname} remote add {name} {url}'.format( + dirname=dirname, name=name, url=url).split() execute_subprocess(cmd) @staticmethod - def _git_fetch(remote_name): + def _git_fetch(remote_name, dirname): """Run the git fetch command for the side effect of updating the repo """ - cmd = ['git', 'fetch', '--quiet', '--tags', remote_name] + cmd = 'git -C {dirname} fetch --quiet --tags {remote_name}'.format( + dirname=dirname, remote_name=remote_name).split() execute_subprocess(cmd) @staticmethod - def _git_checkout_ref(ref, verbosity, submodules): + def _git_checkout_ref(ref, verbosity, submodules, dirname): """Run the git checkout command for the side effect of updating the repo Param: ref is a reference to a local or remote object in the form 'origin/my_feature', or 'tag1'. """ - cmd = ['git', 'checkout', '--quiet', ref] + cmd = 'git -C {dirname} checkout --quiet {ref}'.format( + dirname=dirname, ref=ref).split() if verbosity >= VERBOSITY_VERBOSE: printlog(' {0}'.format(' '.join(cmd))) execute_subprocess(cmd) if submodules: - GitRepository._git_update_submodules(verbosity) + GitRepository._git_update_submodules(verbosity, dirname) @staticmethod - def _git_sparse_checkout(verbosity): + def _git_sparse_checkout(verbosity, dirname): """Configure repo via read-tree.""" - cmd = ['git', 'config', 'core.sparsecheckout', 'true'] + cmd = 'git -C {dirname} config core.sparsecheckout true'.format( + dirname=dirname).split() if verbosity >= VERBOSITY_VERBOSE: printlog(' {0}'.format(' '.join(cmd))) execute_subprocess(cmd) - cmd = ['git', 'read-tree', '-mu', 'HEAD'] + cmd = 'git -C {dirname} read-tree -mu HEAD'.format( + dirname=dirname).split() if verbosity >= VERBOSITY_VERBOSE: printlog(' {0}'.format(' '.join(cmd))) execute_subprocess(cmd) @staticmethod - def _git_update_submodules(verbosity): + def _git_update_submodules(verbosity, dirname): """Run git submodule update for the side effect of updating this repo's submodules. """ # First, verify that we have a .gitmodules file - if os.path.exists(ExternalsDescription.GIT_SUBMODULES_FILENAME): - cmd = ['git', 'submodule', 'update', '--init', '--recursive'] + if os.path.exists( + os.path.join(dirname, + ExternalsDescription.GIT_SUBMODULES_FILENAME)): + cmd = ('git -C {dirname} submodule update --init --recursive' + .format(dirname=dirname)).split() if verbosity >= VERBOSITY_VERBOSE: printlog(' {0}'.format(' '.join(cmd))) diff --git a/manic/sourcetree.py b/manic/sourcetree.py index 218b5febb4..cf2a5b7569 100644 --- a/manic/sourcetree.py +++ b/manic/sourcetree.py @@ -1,6 +1,6 @@ """ - -FIXME(bja, 2017-11) External and SourceTree have a circular dependancy! +Classes to represent an externals config file (SourceTree) and the components +within it (_External). """ import errno @@ -20,71 +20,53 @@ class _External(object): """ A single component hosted in an external repository (and any children). - """ + The component may or may not be checked-out upon construction. + """ # pylint: disable=R0902 - def __init__(self, root_dir, name, ext_description, svn_ignore_ancestry): - """Parse an external description file into a dictionary of externals. + def __init__(self, root_dir, name, local_path, required, subexternals_path, + repo, svn_ignore_ancestry, subexternal_sourcetree): + """Create a single external component (checked out or not). Input: + root_dir : string - the (checked-out) parent repo's root dir. + local_path : string - this external's (checked-out) subdir relative + to root_dir, e.g. "components/mom" + repo: Repository - the repo object for this external. Can be None (e.g. if this external just refers to another external file). - root_dir : string - the root directory path where - 'local_path' is relative to. - - name : string - name of the ext_description object. may or may not - correspond to something in the path. + name : string - name of this external (as named by the parent + reference). May or may not correspond to something in the path. ext_description : dict - source ExternalsDescription object svn_ignore_ancestry : bool - use --ignore-externals with svn switch + subexternals_path: string - path to sub-externals config file, if any. Relative to local_path, or special value 'none'. + subexternal_sourcetree: SourceTree - corresponding to subexternals_path, if subexternals_path exists (it might not, if it is not checked out yet). """ self._name = name - self._repo = None # Repository object. - - # Subcomponent externals file and data object, if any. - self._externals_path = EMPTY_STR # Can also be "none" - self._externals_sourcetree = None + self._required = required self._stat = None # Populated in status() - self._sparse = None - # Parse the sub-elements - # _local_path : local path relative to the containing source tree, e.g. - # "components/mom" - self._local_path = ext_description[ExternalsDescription.PATH] + self._local_path = local_path # _repo_dir_path : full repository directory, e.g. # "/components/mom" - repo_dir = os.path.join(root_dir, self._local_path) + repo_dir = os.path.join(root_dir, local_path) self._repo_dir_path = os.path.abspath(repo_dir) # _base_dir_path : base directory *containing* the repository, e.g. # "/components" self._base_dir_path = os.path.dirname(self._repo_dir_path) - # _repo_dir_name : base_dir_path + repo_dir_name = rep_dir_path + # _repo_dir_name : base_dir_path + repo_dir_name = repo_dir_path # e.g., "mom" self._repo_dir_name = os.path.basename(self._repo_dir_path) - assert(os.path.join(self._base_dir_path, self._repo_dir_name) - == self._repo_dir_path) - - self._required = ext_description[ExternalsDescription.REQUIRED] + self._repo = repo # Does this component have subcomponents aka an externals config? - self._externals_path = ext_description[ExternalsDescription.EXTERNALS] - # Treat a .gitmodules file as a backup externals config - if not self._externals_path: - if GitRepository.has_submodules(self._repo_dir_path): - self._externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME - - repo = create_repository( - name, ext_description[ExternalsDescription.REPO], - svn_ignore_ancestry=svn_ignore_ancestry) - if repo: - self._repo = repo - - # Recurse into subcomponents, if any. - if self._externals_path and (self._externals_path.lower() != 'none'): - self._create_externals_sourcetree() + self._subexternals_path = subexternals_path + self._subexternal_sourcetree = subexternal_sourcetree + def get_name(self): """ @@ -98,6 +80,15 @@ def get_local_path(self): """ return self._local_path + def get_repo_dir_path(self): + return self._repo_dir_path + + def get_subexternals_path(self): + return self._subexternals_path + + def get_repo(self): + return self._repo + def status(self, force=False, print_progress=False): """ Returns status of this component and all subcomponents. @@ -148,12 +139,12 @@ def status(self, force=False, print_progress=False): self._repo.status(self._stat, self._repo_dir_path) # Status of subcomponents, if any. - if self._externals_path and self._externals_sourcetree: + if self._subexternals_path and self._subexternal_sourcetree: cwd = os.getcwd() # SourceTree.status() expects to be called from the correct # root directory. os.chdir(self._repo_dir_path) - subcomponent_stats = self._externals_sourcetree.status(self._local_path, force=force, print_progress=print_progress) + subcomponent_stats = self._subexternal_sourcetree.status(self._local_path, force=force, print_progress=print_progress) os.chdir(cwd) # Merge our status + subcomponent statuses into one return dict keyed @@ -174,10 +165,10 @@ def status(self, force=False, print_progress=False): def checkout(self, verbosity): """ If the repo destination directory exists, ensure it is correct (from - correct URL, correct branch or tag), and possibly update the external. + correct URL, correct branch or tag), and possibly updateit. If the repo destination directory does not exist, checkout the correct branch or tag. - Does not check out sub-externals, see checkout_subexternals(). + Does not check out sub-externals, see SourceTree.checkout(). """ # Make sure we are in correct location if not os.path.exists(self._repo_dir_path): @@ -215,98 +206,117 @@ def checkout(self, verbosity): self._repo.checkout(self._base_dir_path, self._repo_dir_name, checkout_verbosity, self.clone_recursive()) - def checkout_subexternals(self, verbosity, load_all): - """Recursively checkout the sub-externals for this component, if any. - - See load_all documentation in SourceTree.checkout(). - """ - if self.load_externals(): - if self._externals_sourcetree: - # NOTE(bja, 2018-02): the subtree externals objects - # were created during initial status check. Updating - # the external may have changed which sub-externals - # are needed. We need to delete those objects and - # re-read the potentially modified externals - # description file. - self._externals_sourcetree = None - self._create_externals_sourcetree() - self._externals_sourcetree.checkout(verbosity, load_all) - - def load_externals(self): - 'Return True iff an externals file exists (and therefore should be loaded)' - load_ex = False - if os.path.exists(self._repo_dir_path): - if self._externals_path: - if self._externals_path.lower() != 'none': - load_ex = os.path.exists(os.path.join(self._repo_dir_path, - self._externals_path)) - - return load_ex + def replace_subexternal_sourcetree(self, sourcetree): + self._subexternal_sourcetree = sourcetree def clone_recursive(self): 'Return True iff any .gitmodules files should be processed' # Try recursive .gitmodules unless there is an externals entry - recursive = not self._externals_path + recursive = not self._subexternals_path return recursive - def _create_externals_sourcetree(self): - """ - Note this only creates an object, it doesn't write to the file system. + +class SourceTree(object): + """ + SourceTree represents a group of managed externals. + + Those externals may not be checked out locally yet, they might only + have Repository objects pointing to their respective repositories. + """ + + @classmethod + def from_externals_file(cls, parent_repo_dir_path, parent_repo, + externals_path): + """Creates a SourceTree representing the given externals file. + + Looks up a git submodules file as an optional backup if there is no + externals file specified. + + Returns None if there is no externals file (i.e. it's None or 'none'), + or if the externals file hasn't been checked out yet. + + parent_repo_dir_path: parent repo root dir + parent_repo: parent repo. + externals_path: path to externals file, relative to parent_repo_dir_path. """ - if not os.path.exists(self._repo_dir_path): + if not os.path.exists(parent_repo_dir_path): # NOTE(bja, 2017-10) repository has not been checked out # yet, can't process the externals file. Assume we are # checking status before code is checkoud out and this # will be handled correctly later. - return + return None - cwd = os.getcwd() - os.chdir(self._repo_dir_path) - if self._externals_path.lower() == 'none': - msg = ('Internal: Attempt to create source tree for ' - 'externals = none in {}'.format(self._repo_dir_path)) - fatal_error(msg) + if externals_path.lower() == 'none': + # With explicit 'none', do not look for git submodules file. + return None - if not os.path.exists(self._externals_path): - if GitRepository.has_submodules(): - self._externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME + cwd = os.getcwd() + os.chdir(parent_repo_dir_path) + + if not externals_path: + if GitRepository.has_submodules(parent_repo_dir_path): + externals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME + else: + return None - if not os.path.exists(self._externals_path): - # NOTE(bja, 2017-10) this check is redundent with the one + if not os.path.exists(externals_path): + # NOTE(bja, 2017-10) this check is redundant with the one # in read_externals_description_file! - msg = ('External externals description file "{0}" ' + msg = ('Externals description file "{0}" ' 'does not exist! In directory: {1}'.format( - self._externals_path, self._repo_dir_path)) + externals_path, parent_repo_dir_path)) fatal_error(msg) - externals_root = self._repo_dir_path + externals_root = parent_repo_dir_path # model_data is a dict-like object which mirrors the file format. model_data = read_externals_description_file(externals_root, - self._externals_path) + externals_path) # ext_description is another dict-like object (see ExternalsDescription) ext_description = create_externals_description(model_data, - parent_repo=self._repo) - self._externals_sourcetree = SourceTree(externals_root, ext_description) + parent_repo=parent_repo) + externals_sourcetree = SourceTree(externals_root, ext_description) os.chdir(cwd) - -class SourceTree(object): - """ - SourceTree represents a group of managed externals - """ - + return externals_sourcetree + def __init__(self, root_dir, ext_description, svn_ignore_ancestry=False): """ Build a SourceTree object from an ExternalDescription. + + root_dir: the (checked-out) parent repo root dir. """ self._root_dir = os.path.abspath(root_dir) self._all_components = {} # component_name -> _External self._required_compnames = [] - for comp in ext_description: - src = _External(self._root_dir, comp, ext_description[comp], - svn_ignore_ancestry) + for comp, desc in ext_description.items(): + local_path = desc[ExternalsDescription.PATH] + required = desc[ExternalsDescription.REQUIRED] + repo_info = desc[ExternalsDescription.REPO] + subexternals_path = desc[ExternalsDescription.EXTERNALS] + + repo = create_repository(comp, + repo_info, + svn_ignore_ancestry=svn_ignore_ancestry) + + sourcetree = None + # Treat a .gitmodules file as a backup externals config + if not subexternals_path: + parent_repo_dir_path = os.path.abspath(os.path.join(root_dir, + local_path)) + if GitRepository.has_submodules(parent_repo_dir_path): + subexternals_path = ExternalsDescription.GIT_SUBMODULES_FILENAME + + # Might return None (if the subexternal isn't checked out yet, or subexternal is None or 'none') + subexternal_sourcetree = SourceTree.from_externals_file( + os.path.join(self._root_dir, local_path), + repo, + subexternals_path) + src = _External(self._root_dir, comp, local_path, required, + subexternals_path, repo, svn_ignore_ancestry, + subexternal_sourcetree) + self._all_components[comp] = src - if ext_description[comp][ExternalsDescription.REQUIRED]: + if required: self._required_compnames.append(comp) def status(self, relative_path_base=LOCAL_PATH_INDICATOR, @@ -353,8 +363,11 @@ def _find_installed_optional_components(self): continue # Note that in practice we expect this status to be cached. path_to_stat = ext.status() - if any(stat.sync_state != ExternalStatus.EMPTY - for stat in path_to_stat.values()): + + # If any part of this component exists locally, consider it + # installed and therefore eligible for updating. + if any(s.sync_state != ExternalStatus.EMPTY + for s in path_to_stat.values()): installed_comps.append(comp_name) return installed_comps @@ -376,6 +389,9 @@ def checkout(self, verbosity, load_all, load_comp=None): if local_optional_compnames: printlog('Found locally installed optional components: ' + ', '.join(local_optional_compnames)) + bad_compnames = set(local_optional_compnames) - set(self._all_components.keys()) + if bad_compnames: + printlog('Internal error: found locally installed components that are not in the global list of all components: ' + ','.join(bad_compnames)) if verbosity >= VERBOSITY_VERBOSE: printlog('Checking out externals: ') @@ -387,16 +403,23 @@ def checkout(self, verbosity, load_all, load_comp=None): load_comps = sorted(tmp_comps, key=lambda comp: self._all_components[comp].get_local_path()) # checkout. - for comp in load_comps: + for comp_name in load_comps: if verbosity < VERBOSITY_VERBOSE: - printlog('{0}, '.format(comp), end='') + printlog('{0}, '.format(comp_name), end='') else: # verbose output handled by the _External object, just # output a newline printlog(EMPTY_STR) + c = self._all_components[comp_name] # Does not recurse. - self._all_components[comp].checkout(verbosity) - # Recursively check out subexternals, if any. - self._all_components[comp].checkout_subexternals(verbosity, - load_all) + c.checkout(verbosity) + # Recursively check out subexternals, if any. Returns None + # if there's no subexternals path. + component_subexternal_sourcetree = SourceTree.from_externals_file( + c.get_repo_dir_path(), + c.get_repo(), + c.get_subexternals_path()) + c.replace_subexternal_sourcetree(component_subexternal_sourcetree) + if component_subexternal_sourcetree: + component_subexternal_sourcetree.checkout(verbosity, load_all) printlog('') diff --git a/test/repos/README.md b/test/repos/README.md new file mode 100644 index 0000000000..8a3502c35f --- /dev/null +++ b/test/repos/README.md @@ -0,0 +1,33 @@ +Git repositories for testing git-related behavior. For usage and terminology notes, see test/test_sys_checkout.py. + +To list files and view file contents at HEAD: +``` +cd +git ls-tree --full-tree -r --name-only HEAD +git cat-file -p HEAD: +``` + +File contents at a glance: +``` +container.git/ + readme.txt + +simple-ext.git/ + (has branches: feature2, feature3) + (has tags: tag1, tag2) + readme.txt + simple_subdir/subdir_file.txt + +simple-ext-fork.git/ + (has tags: abandoned-feature, forked-feature-v1, tag1) + (has branch: feature2) + readme.txt + +mixed-cont-ext.git/ + (has branch: new-feature) + readme.txt + sub-externals.cfg ('simp_branch' section refers to 'feature2' branch in simple-ext.git/ repo) + +error/ + (no git repo here, just a readme.txt in the clear) +``` diff --git a/test/test_sys_checkout.py b/test/test_sys_checkout.py index 27b649bea4..ab4f77e88f 100644 --- a/test/test_sys_checkout.py +++ b/test/test_sys_checkout.py @@ -2,6 +2,14 @@ """Unit test driver for checkout_externals +Terminology: + * 'container': a repo that has externals + * 'simple': a repo that has no externals, but is referenced as an external by another repo. + * 'mixed': a repo that both has externals and is referenced as an external by another repo. + + * 'clean': the local repo matches the version in the externals and has no local modifications. + * 'empty': the external isn't checked out at all. + Note: this script assume the path to the manic and checkout_externals module is already in the python path. This is usually handled by the makefile. If you call it directly, you may need @@ -21,7 +29,6 @@ * Erase any existing repos at the begining of the module in setUpModule. - """ # NOTE(bja, 2017-11) pylint complains that the module is too big, but @@ -68,39 +75,50 @@ # Module-wide root directory for all the per-test subdirs we'll create on -# the fly. -MANIC_TEST_TMP_REPO_ROOT = 'MANIC_TEST_TMP_REPO_ROOT' # env var name +# the fly (which are placed under wherever $CWD is when the test runs). +# Set by setupModule(). +module_tmp_root_dir = None TMP_REPO_DIR_NAME = 'tmp' # subdir under $CWD -# We clone these checked-in repositories on a per-test basis. The -# 'bare repo root' is the test/repos/ subdir that holds them all. -MANIC_TEST_BARE_REPO_ROOT = 'MANIC_TEST_BARE_REPO_ROOT' # env var name -BARE_REPO_ROOT_NAME = 'repos' # subdir name - -# Subdirs under bare repo root, each holding a repository. -CONTAINER_REPO_NAME = 'container.git' -MIXED_REPO_NAME = 'mixed-cont-ext.git' -SIMPLE_REPO_NAME = 'simple-ext.git' -SIMPLE_FORK_NAME = 'simple-ext-fork.git' - - -# In each of the test repos, all externals live under this subdir. -EXTERNALS_NAME = 'externals' +# subdir under test/ that holds all of our checked-in repositories (which we +# will clone for these tests). +BARE_REPO_ROOT_NAME = 'repos' + +# Environment var referenced by checked-in externals file in mixed-cont-ext.git, +# which should be pointed to the fully-resolved BARE_REPO_ROOT_NAME directory. +# We explicitly clear this after every test, via tearDown(). +MIXED_CONT_EXT_ROOT_ENV_VAR = 'MANIC_TEST_BARE_REPO_ROOT' + +# Subdirs under bare repo root, each holding a repository. For more info +# on the contents of these repositories, see test/repos/README.md. In these +# tests the 'parent' repos are cloned as a starting point, whereas the 'child' +# repos are checked out when the tests run checkout_externals. +CONTAINER_REPO = 'container.git' # Parent repo +SIMPLE_REPO = 'simple-ext.git' # Child repo +SIMPLE_FORK_REPO = 'simple-ext-fork.git' # Child repo +MIXED_REPO = 'mixed-cont-ext.git' # Both parent and child + +# Standard (arbitrary) external names for test configs +TAG_SECTION = 'simp_tag' +BRANCH_SECTION = 'simp_branch' +HASH_SECTION = 'simp_hash' + +# All the configs we construct check out their externals into these local paths. +EXTERNALS_PATH = 'externals' SUB_EXTERNALS_PATH = 'src' # For mixed test repos, # For testing behavior with '.' instead of an explicit paths. SIMPLE_LOCAL_ONLY_NAME = '.' -# Filenames -CFG_NAME = 'externals.cfg' -CFG_SUB_NAME = 'sub-externals.cfg' -README_NAME = 'readme.txt' # Arbitrary file to check in. +# Externals files. +CFG_NAME = 'externals.cfg' # We construct this on a per-test basis. +CFG_SUB_NAME = 'sub-externals.cfg' # Already exists in mixed-cont-ext repo. -# Arbirary test branch name -REMOTE_BRANCH_FEATURE2 = 'feature2' +# Arbitrary text file in all the test repos. +README_NAME = 'readme.txt' -# Section names in container_nested_* test config. -NESTED_NAME = ['./fred', './fred/wilma', './fred/wilma/barney'] +# Branch that exists in both the simple and simple-fork repos. +REMOTE_BRANCH_FEATURE2 = 'feature2' SVN_TEST_REPO = 'https://github.com/escomp/cesm' @@ -123,152 +141,110 @@ def setUpModule(): # pylint: disable=C0103 pass # create clean dir for this run os.mkdir(repo_root) - # set into the environment so var will be expanded in externals - # files when executables are run - os.environ[MANIC_TEST_TMP_REPO_ROOT] = repo_root - - -class GenerateExternalsDescriptionCfgV1(object): - """Building blocks to create ExternalsDescriptionCfgV1 files. - - Basic usage: create_config() multiple create_*(), then write_config(). - Optionally after that: write_with_*(). - - Includes methods (like container_*()) to create predefined configs for the - checked-in repositories in test/repos/. - """ - - def __init__(self): - self._schema_version = '1.1.0' - self._config = None - - def container_full(self, dest_dir): - """Create the full container config file with simple and mixed use - externals - - """ - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', - tag='tag1') - - self.create_section(SIMPLE_REPO_NAME, 'simp_branch', - branch=REMOTE_BRANCH_FEATURE2) - - self.create_section(SIMPLE_REPO_NAME, 'simp_opt', - tag='tag1', required=False) - self.create_section(MIXED_REPO_NAME, 'mixed_req', - branch='master', externals=CFG_SUB_NAME) + # Make available to all tests in this file. + global module_tmp_root_dir + assert module_tmp_root_dir == None, module_tmp_root_dir + module_tmp_root_dir = repo_root - self.write_config(dest_dir) - - def container_simple_required(self, dest_dir): - """Create a container externals file with only simple externals. - - """ - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', - tag='tag1') - - self.create_section(SIMPLE_REPO_NAME, 'simp_branch', - branch=REMOTE_BRANCH_FEATURE2) - - self.create_section(SIMPLE_REPO_NAME, 'simp_hash', - ref_hash='60b1cc1a38d63') - - self.write_config(dest_dir) - - def container_nested_required(self, dest_dir, order): - """Create a container externals file with only simple externals. - - """ - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', nested=True, - tag='tag1', path=NESTED_NAME[order[0]]) - - self.create_section(SIMPLE_REPO_NAME, 'simp_branch', nested=True, - branch=REMOTE_BRANCH_FEATURE2, path=NESTED_NAME[order[1]]) - - self.create_section(SIMPLE_REPO_NAME, 'simp_hash', nested=True, - ref_hash='60b1cc1a38d63', path=NESTED_NAME[order[2]]) - - self.write_config(dest_dir) - - - def container_simple_optional(self, dest_dir): - """Create a container externals file with optional simple externals +class RepoUtils(object): + """Convenience methods for interacting with git repos.""" + @staticmethod + def create_branch(repo_base_dir, external_name, branch, with_commit=False): + """Create branch and optionally (with_commit) add a single commit. """ - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_req', - tag='tag1') - - self.create_section(SIMPLE_REPO_NAME, 'simp_opt', - tag='tag1', required=False) - - self.write_config(dest_dir) - - def container_simple_svn(self, dest_dir): - """Create a container externals file with only simple externals. + # pylint: disable=R0913 + cwd = os.getcwd() + repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name) + os.chdir(repo_root) + cmd = ['git', 'checkout', '-b', branch, ] + execute_subprocess(cmd) + if with_commit: + msg = 'start work on {0}'.format(branch) + with open(README_NAME, 'a') as handle: + handle.write(msg) + cmd = ['git', 'add', README_NAME, ] + execute_subprocess(cmd) + cmd = ['git', 'commit', '-m', msg, ] + execute_subprocess(cmd) + os.chdir(cwd) + @staticmethod + def create_commit(repo_base_dir, external_name): + """Make a commit to the given external. + + This is used to test sync state changes from local commits on + detached heads and tracking branches. """ - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', tag='tag1') - - self.create_svn_external('svn_branch', branch='trunk') - self.create_svn_external('svn_tag', tag='tags/cesm2.0.beta07') + cwd = os.getcwd() + repo_root = os.path.join(repo_base_dir, EXTERNALS_PATH, external_name) + os.chdir(repo_root) - self.write_config(dest_dir) + msg = 'work on great new feature!' + with open(README_NAME, 'a') as handle: + handle.write(msg) + cmd = ['git', 'add', README_NAME, ] + execute_subprocess(cmd) + cmd = ['git', 'commit', '-m', msg, ] + execute_subprocess(cmd) + os.chdir(cwd) - def container_sparse(self, dest_dir): - """Create a container with a full external and a sparse external + @staticmethod + def clone_test_repo(bare_root, test_id, parent_repo_name, dest_dir_in): + """Clone repo at / into dest_dir_in or local per-test-subdir. + Returns output dir. """ - # Create a file for a sparse pattern match - sparse_filename = 'sparse_checkout' - with open(os.path.join(dest_dir, sparse_filename), 'w') as sfile: - sfile.write('readme.txt') - - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', - tag='tag2') - - sparse_relpath = '../../{}'.format(sparse_filename) - self.create_section(SIMPLE_REPO_NAME, 'simp_sparse', - tag='tag2', sparse=sparse_relpath) + parent_repo_dir = os.path.join(bare_root, parent_repo_name) + if dest_dir_in is None: + # create unique subdir for this test + test_dir_name = test_id + print("Test repository name: {0}".format(test_dir_name)) + dest_dir = os.path.join(module_tmp_root_dir, test_dir_name) + else: + dest_dir = dest_dir_in - self.write_config(dest_dir) + # pylint: disable=W0212 + GitRepository._git_clone(parent_repo_dir, dest_dir, VERBOSITY_DEFAULT) + return dest_dir - def mixed_simple_base(self, dest_dir): - """Create a mixed-use base externals file with only simple externals. + @staticmethod + def add_file_to_repo(under_test_dir, filename, tracked): + """Add a file to the repository so we can put it into a dirty state """ - self.create_config() - self.create_section_ext_only('mixed_base') - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', - tag='tag1') - - self.create_section(SIMPLE_REPO_NAME, 'simp_branch', - branch=REMOTE_BRANCH_FEATURE2) + cwd = os.getcwd() + os.chdir(under_test_dir) + with open(filename, 'w') as tmp: + tmp.write('Hello, world!') - self.create_section(SIMPLE_REPO_NAME, 'simp_hash', - ref_hash='60b1cc1a38d63') + if tracked: + # NOTE(bja, 2018-01) brittle hack to obtain repo dir and + # file name + path_data = filename.split('/') + repo_dir = os.path.join(path_data[0], path_data[1]) + os.chdir(repo_dir) + tracked_file = path_data[2] + cmd = ['git', 'add', tracked_file] + execute_subprocess(cmd) - self.write_config(dest_dir) + os.chdir(cwd) - def mixed_simple_sub(self, dest_dir): - """Create a mixed-use sub externals file with only simple externals. +class GenerateExternalsDescriptionCfgV1(object): + """Building blocks to create ExternalsDescriptionCfgV1 files. - """ - self.create_config() - self.create_section(SIMPLE_REPO_NAME, 'simp_tag', - tag='tag1', path=SUB_EXTERNALS_PATH) + Basic usage: create_config() multiple create_*(), then write_config(). + Optionally after that: write_with_*(). + """ - self.create_section(SIMPLE_REPO_NAME, 'simp_branch', - branch=REMOTE_BRANCH_FEATURE2, - path=SUB_EXTERNALS_PATH) + def __init__(self, bare_root): + self._schema_version = '1.1.0' + self._config = None - self.write_config(dest_dir, filename=CFG_SUB_NAME) + # directory where we have test repositories (which we will clone for + # tests) + self._bare_root = bare_root def write_config(self, dest_dir, filename=CFG_NAME): """Write self._config to disk @@ -293,9 +269,15 @@ def create_metadata(self): self._config.set(DESCRIPTION_SECTION, VERSION_ITEM, self._schema_version) + def url_for_repo_path(self, repo_path, repo_path_abs=None): + if repo_path_abs is not None: + return repo_path_abs + else: + return os.path.join(self._bare_root, repo_path) + def create_section(self, repo_path, name, tag='', branch='', - ref_hash='', required=True, path=EXTERNALS_NAME, - externals='', repo_path_abs=None, from_submodule=False, + ref_hash='', required=True, path=EXTERNALS_PATH, + sub_externals='', repo_path_abs=None, from_submodule=False, sparse='', nested=False): # pylint: disable=too-many-branches """Create a config ExternalsDescription section with the given name. @@ -303,7 +285,7 @@ def create_section(self, repo_path, name, tag='', branch='', Autofills some items and handles some optional items. repo_path_abs overrides repo_path (which is relative to the bare repo) - path is a subdir under repo_path. + path is a subdir under repo_path to check out to. """ # pylint: disable=R0913 self._config.add_section(name) @@ -328,10 +310,7 @@ def create_section(self, repo_path, name, tag='', branch='', ref_hash = '' branch = '' - if repo_path_abs is not None: - repo_url = repo_path_abs - else: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_path) + repo_url = self.url_for_repo_path(repo_path, repo_path_abs) if not from_submodule: self._config.set(name, ExternalsDescription.REPO_URL, repo_url) @@ -347,8 +326,9 @@ def create_section(self, repo_path, name, tag='', branch='', if ref_hash: self._config.set(name, ExternalsDescription.HASH, ref_hash) - if externals: - self._config.set(name, ExternalsDescription.EXTERNALS, externals) + if sub_externals: + self._config.set(name, ExternalsDescription.EXTERNALS, + sub_externals) if sparse: self._config.set(name, ExternalsDescription.SPARSE, sparse) @@ -356,10 +336,8 @@ def create_section(self, repo_path, name, tag='', branch='', if from_submodule: self._config.set(name, ExternalsDescription.SUBMODULE, "True") - def create_section_ext_only(self, name, - required=True, externals=CFG_SUB_NAME): - """Create a config section with autofilling some items and handling - optional items. + def create_section_reference_to_subexternal(self, name): + """Just a reference to another externals file. """ # pylint: disable=R0913 @@ -372,10 +350,9 @@ def create_section_ext_only(self, name, self._config.set(name, ExternalsDescription.REPO_URL, LOCAL_PATH_INDICATOR) - self._config.set(name, ExternalsDescription.REQUIRED, str(required)) + self._config.set(name, ExternalsDescription.REQUIRED, str(True)) - if externals: - self._config.set(name, ExternalsDescription.EXTERNALS, externals) + self._config.set(name, ExternalsDescription.EXTERNALS, CFG_SUB_NAME) def create_svn_external(self, name, tag='', branch=''): """Create a config section for an svn repository. @@ -383,7 +360,7 @@ def create_svn_external(self, name, tag='', branch=''): """ self._config.add_section(name) self._config.set(name, ExternalsDescription.PATH, - os.path.join(EXTERNALS_NAME, name)) + os.path.join(EXTERNALS_PATH, name)) self._config.set(name, ExternalsDescription.PROTOCOL, ExternalsDescription.PROTOCOL_SVN) @@ -398,54 +375,7 @@ def create_svn_external(self, name, tag='', branch=''): if branch: self._config.set(name, ExternalsDescription.BRANCH, branch) - @staticmethod - def create_branch(dest_dir, repo_name, branch, with_commit=False): - """Create branch and optionally (with_commit) add a single commit. - """ - # pylint: disable=R0913 - cwd = os.getcwd() - repo_root = os.path.join(dest_dir, EXTERNALS_NAME, repo_name) - os.chdir(repo_root) - cmd = ['git', 'checkout', '-b', branch, ] - execute_subprocess(cmd) - if with_commit: - msg = 'start work on {0}'.format(branch) - with open(README_NAME, 'a') as handle: - handle.write(msg) - cmd = ['git', 'add', README_NAME, ] - execute_subprocess(cmd) - cmd = ['git', 'commit', '-m', msg, ] - execute_subprocess(cmd) - os.chdir(cwd) - - @staticmethod - def create_commit(dest_dir, repo_name, local_tracking_branch=None): - """Make a commit on whatever is currently checked out. - - This is used to test sync state changes from local commits on - detached heads and tracking branches. - - NOTE(jpalex, 2023-01) This has nothing to do with self._config, - should probably live elsewhere. - """ - cwd = os.getcwd() - repo_root = os.path.join(dest_dir, EXTERNALS_NAME, repo_name) - os.chdir(repo_root) - if local_tracking_branch: - cmd = ['git', 'checkout', '-b', local_tracking_branch, ] - execute_subprocess(cmd) - - msg = 'work on great new feature!' - with open(README_NAME, 'a') as handle: - handle.write(msg) - cmd = ['git', 'add', README_NAME, ] - execute_subprocess(cmd) - cmd = ['git', 'commit', '-m', msg, ] - execute_subprocess(cmd) - os.chdir(cwd) - - def write_with_git_branch(self, dest_dir, name, branch, repo_path=None, - filename=CFG_NAME): + def write_with_git_branch(self, dest_dir, name, branch, new_remote_repo_path=None): """Update fields in our config and write it to disk. name is the key of the ExternalsDescription in self._config to update. @@ -453,12 +383,11 @@ def write_with_git_branch(self, dest_dir, name, branch, repo_path=None, # pylint: disable=R0913 self._config.set(name, ExternalsDescription.BRANCH, branch) - if repo_path: - if repo_path == SIMPLE_LOCAL_ONLY_NAME: + if new_remote_repo_path: + if new_remote_repo_path == SIMPLE_LOCAL_ONLY_NAME: repo_url = SIMPLE_LOCAL_ONLY_NAME else: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', - repo_path) + repo_url = os.path.join(self._bare_root, new_remote_repo_path) self._config.set(name, ExternalsDescription.REPO_URL, repo_url) try: @@ -467,9 +396,9 @@ def write_with_git_branch(self, dest_dir, name, branch, repo_path=None, except BaseException: pass - self.write_config(dest_dir, filename) + self.write_config(dest_dir) - def write_with_svn_branch(self, dest_dir, name, branch, filename=CFG_NAME): + def write_with_svn_branch(self, dest_dir, name, branch): """Update a repository branch, and potentially the remote. """ # pylint: disable=R0913 @@ -481,11 +410,11 @@ def write_with_svn_branch(self, dest_dir, name, branch, filename=CFG_NAME): except BaseException: pass - self.write_config(dest_dir, filename) + self.write_config(dest_dir) - def write_with_tag(self, dest_dir, name, tag, repo_path=None, - filename=CFG_NAME, remove_branch=True): - """Update a repository tag, and potentially the remote + def write_with_tag_and_remote_repo(self, dest_dir, name, tag, new_remote_repo_path, + remove_branch=True): + """Update a repository tag and the remote. NOTE(bja, 2017-11) remove_branch=False should result in an overspecified external with both a branch and tag. This is @@ -495,8 +424,8 @@ def write_with_tag(self, dest_dir, name, tag, repo_path=None, # pylint: disable=R0913 self._config.set(name, ExternalsDescription.TAG, tag) - if repo_path: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_path) + if new_remote_repo_path: + repo_url = os.path.join(self._bare_root, new_remote_repo_path) self._config.set(name, ExternalsDescription.REPO_URL, repo_url) try: @@ -506,10 +435,9 @@ def write_with_tag(self, dest_dir, name, tag, repo_path=None, except BaseException: pass - self.write_config(dest_dir, filename) + self.write_config(dest_dir) - def write_without_branch_tag(self, dest_dir, name, - filename=CFG_NAME): + def write_without_branch_tag(self, dest_dir, name): """Update a repository protocol, and potentially the remote """ # pylint: disable=R0913 @@ -525,10 +453,9 @@ def write_without_branch_tag(self, dest_dir, name, except BaseException: pass - self.write_config(dest_dir, filename) + self.write_config(dest_dir) - def write_without_repo_url(self, dest_dir, name, - filename=CFG_NAME): + def write_without_repo_url(self, dest_dir, name): """Update a repository protocol, and potentially the remote """ # pylint: disable=R0913 @@ -538,22 +465,59 @@ def write_without_repo_url(self, dest_dir, name, except BaseException: pass - self.write_config(dest_dir, filename) + self.write_config(dest_dir) - def write_with_protocol(self, dest_dir, name, protocol, repo_path=None, - filename=CFG_NAME): + def write_with_protocol(self, dest_dir, name, protocol, repo_path=None): """Update a repository protocol, and potentially the remote """ # pylint: disable=R0913 self._config.set(name, ExternalsDescription.PROTOCOL, protocol) if repo_path: - repo_url = os.path.join('${MANIC_TEST_BARE_REPO_ROOT}', repo_path) + repo_url = os.path.join(self._bare_root, repo_path) self._config.set(name, ExternalsDescription.REPO_URL, repo_url) - self.write_config(dest_dir, filename) + self.write_config(dest_dir) + + +def _execute_checkout_in_dir(dirname, args, debug_env=''): + """Execute the checkout command in the appropriate repo dir with the + specified additional args. + args should be a list of strings. + debug_env shuld be a string of the form 'FOO=bar' or the empty string. + Note that we are calling the command line processing and main + routines and not using a subprocess call so that we get code + coverage results! Note this means that environment variables are passed + to checkout_externals via os.environ; debug_env is just used to aid + manual reproducibility of a given call. + + Returns (overall_status, tree_status) + where overall_status is 0 for success, nonzero otherwise. + and tree_status is set if --status was passed in, None otherwise. + + Note this command executes the checkout command, it doesn't + necessarily do any checking out (e.g. if --status is passed in). + """ + cwd = os.getcwd() + + # Construct a command line for reproducibility; this command is not + # actually executed in the test. + os.chdir(dirname) + cmdline = ['--externals', CFG_NAME, ] + cmdline += args + manual_cmd = ('Running equivalent of:\n' + 'pushd {dirname}; ' + '{debug_env} /path/to/checkout_externals {args}'.format( + dirname=dirname, debug_env=debug_env, + args=' '.join(cmdline))) + printlog(manual_cmd) + options = checkout.commandline_arguments(cmdline) + overall_status, tree_status = checkout.main(options) + os.chdir(cwd) + return overall_status, tree_status + class BaseTestSysCheckout(unittest.TestCase): """Base class of reusable systems level test setup for checkout_externals @@ -596,425 +560,57 @@ def setUp(self): # path to the executable self._checkout = os.path.join(root_dir, 'checkout_externals') - # directory where we have test repositories + # directory where we have test repositories (which we will clone for + # tests) self._bare_root = os.path.abspath( os.path.join(root_dir, 'test', BARE_REPO_ROOT_NAME)) - # set into the environment so var will be expanded in externals files - os.environ[MANIC_TEST_BARE_REPO_ROOT] = self._bare_root - # set the input file generator - self._generator = GenerateExternalsDescriptionCfgV1() + self._generator = GenerateExternalsDescriptionCfgV1(self._bare_root) # set the input file generator for secondary externals - self._sub_generator = GenerateExternalsDescriptionCfgV1() + self._sub_generator = GenerateExternalsDescriptionCfgV1(self._bare_root) def tearDown(self): """Tear down for individual tests """ - # remove the env var we added in setup - del os.environ[MANIC_TEST_BARE_REPO_ROOT] - # return to our common starting point os.chdir(self._return_dir) + + # (in case this was set) Don't pollute environment of other tests. + os.environ.pop(MIXED_CONT_EXT_ROOT_ENV_VAR, + None) # Don't care if key wasn't set. def clone_test_repo(self, parent_repo_name, dest_dir_in=None): - """Clone repo under bare_root into dest_dir_in or local per-test-subdir. - - Returns output dir. - """ - parent_repo_dir = os.path.join(self._bare_root, parent_repo_name) - if dest_dir_in is None: - # unique repo for this test - test_dir_name = self._test_id - print("Test repository name: {0}".format(test_dir_name)) - dest_dir = os.path.join(os.environ[MANIC_TEST_TMP_REPO_ROOT], - test_dir_name) - else: - dest_dir = dest_dir_in - - # pylint: disable=W0212 - GitRepository._git_clone(parent_repo_dir, dest_dir, VERBOSITY_DEFAULT) - return dest_dir - - @staticmethod - def _add_file_to_repo(under_test_dir, filename, tracked): - """Add a file to the repository so we can put it into a dirty state - - """ - cwd = os.getcwd() - os.chdir(under_test_dir) - with open(filename, 'w') as tmp: - tmp.write('Hello, world!') - - if tracked: - # NOTE(bja, 2018-01) brittle hack to obtain repo dir and - # file name - path_data = filename.split('/') - repo_dir = os.path.join(path_data[0], path_data[1]) - os.chdir(repo_dir) - tracked_file = path_data[2] - cmd = ['git', 'add', tracked_file] - execute_subprocess(cmd) - - os.chdir(cwd) + """Clones repo under self._bare_root""" + return RepoUtils.clone_test_repo(self._bare_root, self._test_id, + parent_repo_name, dest_dir_in) + + def execute_checkout_in_dir(self, dirname, args, debug_env=''): + overall_status, tree_status = _execute_checkout_in_dir(dirname, args, + debug_env=debug_env) + self.assertEqual(overall_status, 0) + return tree_status + + def execute_checkout_with_status(self, dirname, args, debug_env=''): + """Calls checkout a second time to get status if needed.""" + tree_status = self.execute_checkout_in_dir( + dirname, args, debug_env=debug_env) + if tree_status is None: + tree_status = self.execute_checkout_in_dir(dirname, + self.status_args, + debug_env=debug_env) + self.assertNotEqual(tree_status, None) + return tree_status + + def _check_sync_clean(self, ext_status, expected_sync_state, + expected_clean_state): + self.assertEqual(ext_status.sync_state, expected_sync_state) + self.assertEqual(ext_status.clean_state, expected_clean_state) @staticmethod - def execute_checkout_in_dir(dirname, args): - """Extecute the checkout command in the appropriate repo dir with the - specified additional args - - Note that we are calling the command line processing and main - routines and not using a subprocess call so that we get code - coverage results! - - """ - cwd = os.getcwd() - checkout_path = os.path.abspath('{0}/../../checkout_externals') - os.chdir(dirname) - cmdline = ['--externals', CFG_NAME, ] - cmdline += args - repo_root = 'MANIC_TEST_BARE_REPO_ROOT={root}'.format( - root=os.environ[MANIC_TEST_BARE_REPO_ROOT]) - manual_cmd = ('Test cmd:\npushd {cwd}; {env} {checkout} {args}'.format( - cwd=dirname, env=repo_root, checkout=checkout_path, - args=' '.join(cmdline))) - printlog(manual_cmd) - options = checkout.commandline_arguments(cmdline) - overall_status, tree_status = checkout.main(options) - os.chdir(cwd) - return overall_status, tree_status - - # ---------------------------------------------------------------- - # - # Check results for generic perturbation of states - # - # 'tree' is a dict with ExternalStatus as values. - # 'name' is a key into that dict. - # ---------------------------------------------------------------- - def _check_generic_empty_default_required(self, tree, name): - self.assertEqual(tree[name].sync_state, ExternalStatus.EMPTY) - self.assertEqual(tree[name].clean_state, ExternalStatus.DEFAULT) - self.assertEqual(tree[name].source_type, ExternalStatus.MANAGED) - - def _check_generic_ok_clean_required(self, tree, name): - self.assertEqual(tree[name].sync_state, ExternalStatus.STATUS_OK) - self.assertEqual(tree[name].clean_state, ExternalStatus.STATUS_OK) - self.assertEqual(tree[name].source_type, ExternalStatus.MANAGED) - - def _check_generic_ok_dirty_required(self, tree, name): - self.assertEqual(tree[name].sync_state, ExternalStatus.STATUS_OK) - self.assertEqual(tree[name].clean_state, ExternalStatus.DIRTY) - self.assertEqual(tree[name].source_type, ExternalStatus.MANAGED) - - def _check_generic_modified_ok_required(self, tree, name): - self.assertEqual(tree[name].sync_state, ExternalStatus.MODEL_MODIFIED) - self.assertEqual(tree[name].clean_state, ExternalStatus.STATUS_OK) - self.assertEqual(tree[name].source_type, ExternalStatus.MANAGED) - - def _check_generic_empty_default_optional(self, tree, name): - self.assertEqual(tree[name].sync_state, ExternalStatus.EMPTY) - self.assertEqual(tree[name].clean_state, ExternalStatus.DEFAULT) - self.assertEqual(tree[name].source_type, ExternalStatus.OPTIONAL) - - def _check_generic_ok_clean_optional(self, tree, name): - self.assertEqual(tree[name].sync_state, ExternalStatus.STATUS_OK) - self.assertEqual(tree[name].clean_state, ExternalStatus.STATUS_OK) - self.assertEqual(tree[name].source_type, ExternalStatus.OPTIONAL) - - # ---------------------------------------------------------------- - # - # Check results for individual named externals - # - # 'tree' is a dict of string to ExternalStatus. - # ---------------------------------------------------------------- - def _check_simple_tag_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_tag'.format(directory) - self._check_generic_empty_default_required(tree, name) - - def _check_nested_tag_empty(self, tree, name=EXTERNALS_NAME): - self._check_generic_empty_default_required(tree, name) - - def _check_simple_tag_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_tag'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_nested_tag_ok(self, tree, name=EXTERNALS_NAME): - self._check_generic_ok_clean_required(tree, name) - - def _check_simple_tag_dirty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_tag'.format(directory) - self._check_generic_ok_dirty_required(tree, name) - - def _check_simple_tag_modified(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_tag'.format(directory) - self._check_generic_modified_ok_required(tree, name) - - def _check_simple_branch_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_branch'.format(directory) - self._check_generic_empty_default_required(tree, name) - - def _check_nested_branch_empty(self, tree, name=EXTERNALS_NAME): - self._check_generic_empty_default_required(tree, name) - - def _check_simple_branch_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_branch'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_nested_branch_ok(self, tree, name=EXTERNALS_NAME): - self._check_generic_ok_clean_required(tree, name) - - def _check_simple_branch_modified(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_branch'.format(directory) - self._check_generic_modified_ok_required(tree, name) - - def _check_simple_hash_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_hash'.format(directory) - self._check_generic_empty_default_required(tree, name) - - def _check_nested_hash_empty(self, tree, name=EXTERNALS_NAME): - self._check_generic_empty_default_required(tree, name) - - def _check_simple_hash_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_hash'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_nested_hash_ok(self, tree, name=EXTERNALS_NAME): - self._check_generic_ok_clean_required(tree, name) - - def _check_simple_hash_modified(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_hash'.format(directory) - self._check_generic_modified_ok_required(tree, name) - - def _check_simple_req_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_req'.format(directory) - self._check_generic_empty_default_required(tree, name) - - def _check_simple_req_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_req'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_simple_opt_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_opt'.format(directory) - self._check_generic_empty_default_optional(tree, name) - - def _check_simple_opt_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_opt'.format(directory) - self._check_generic_ok_clean_optional(tree, name) - - def _check_mixed_ext_branch_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/mixed_req'.format(directory) - self._check_generic_empty_default_required(tree, name) - - def _check_mixed_ext_branch_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/mixed_req'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_mixed_ext_branch_modified(self, tree, directory=EXTERNALS_NAME): - name = './{0}/mixed_req'.format(directory) - self._check_generic_modified_ok_required(tree, name) - - def _check_simple_sparse_empty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_sparse'.format(directory) - self._check_generic_empty_default_required(tree, name) - - def _check_simple_sparse_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/simp_sparse'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - # ---------------------------------------------------------------- - # - # Check results for groups of externals under specific conditions - # - # ---------------------------------------------------------------- - def _check_container_simple_required_pre_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree) - self._check_simple_branch_empty(tree) - self._check_simple_hash_empty(tree) - - def _check_container_nested_required_pre_checkout(self, overall, tree, order): - self.assertEqual(overall, 0) - self._check_nested_tag_empty(tree, name=NESTED_NAME[order[0]]) - self._check_nested_branch_empty(tree, name=NESTED_NAME[order[1]]) - self._check_nested_hash_empty(tree, name=NESTED_NAME[order[2]]) - - def _check_container_simple_required_checkout(self, overall, tree): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree) - self._check_simple_branch_empty(tree) - self._check_simple_hash_empty(tree) - - def _check_container_nested_required_checkout(self, overall, tree, order): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_nested_tag_empty(tree, name=NESTED_NAME[order[0]]) - self._check_nested_branch_empty(tree, name=NESTED_NAME[order[1]]) - self._check_nested_hash_empty(tree, name=NESTED_NAME[order[2]]) - - def _check_container_simple_required_post_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_simple_branch_ok(tree) - self._check_simple_hash_ok(tree) - - def _check_container_nested_required_post_checkout(self, overall, tree, order): - self.assertEqual(overall, 0) - self._check_nested_tag_ok(tree, name=NESTED_NAME[order[0]]) - self._check_nested_branch_ok(tree, name=NESTED_NAME[order[1]]) - self._check_nested_hash_ok(tree, name=NESTED_NAME[order[2]]) - - def _check_container_simple_required_out_of_sync(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_modified(tree) - self._check_simple_branch_modified(tree) - self._check_simple_hash_modified(tree) - - def _check_container_simple_optional_pre_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_req_empty(tree) - self._check_simple_opt_empty(tree) - - def _check_container_simple_optional_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_req_empty(tree) - self._check_simple_opt_empty(tree) - - def _check_container_simple_optional_post_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_req_ok(tree) - self._check_simple_opt_empty(tree) - - def _check_container_simple_optional_post_optional(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_req_ok(tree) - self._check_simple_opt_ok(tree) - - def _check_container_simple_required_sb_modified(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_simple_branch_modified(tree) - self._check_simple_hash_ok(tree) - - def _check_container_simple_optional_st_dirty(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_dirty(tree) - self._check_simple_branch_ok(tree) - - def _check_container_full_pre_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree) - self._check_simple_branch_empty(tree) - self._check_simple_opt_empty(tree) - self._check_mixed_ext_branch_required_pre_checkout(overall, tree) - - def _check_container_component_post_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_opt_ok(tree) - self._check_simple_tag_empty(tree) - self._check_simple_branch_empty(tree) - - def _check_container_component_post_checkout2(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree) - self._check_simple_branch_ok(tree) - - def _check_container_component_post_checkout3(self, overall, tree): - self.assertEqual(overall, 0) - self.assertFalse("simp_opt" in tree) - self._check_simple_tag_ok(tree) - self._check_simple_branch_ok(tree) - - def _check_container_full_post_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_simple_branch_ok(tree) - self._check_simple_opt_empty(tree) - self._check_mixed_ext_branch_required_post_checkout(overall, tree) - - def _check_container_full_pre_checkout_ext_change(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_simple_branch_ok(tree) - self._check_simple_opt_empty(tree) - self._check_mixed_ext_branch_required_pre_checkout_ext_change( - overall, tree) - - def _check_container_full_post_checkout_subext_modified( - self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_simple_branch_ok(tree) - self._check_simple_opt_empty(tree) - self._check_mixed_ext_branch_required_post_checkout_subext_modified( - overall, tree) - - def _check_mixed_ext_branch_required_pre_checkout(self, overall, tree): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_mixed_ext_branch_empty(tree, directory=EXTERNALS_NAME) - # NOTE: externals/mixed_req/src should not exist in the tree - # since this is the status before checkout of mixed_req. - - def _check_mixed_ext_branch_required_post_checkout(self, overall, tree): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_mixed_ext_branch_ok(tree, directory=EXTERNALS_NAME) - check_dir = "{0}/{1}/{2}".format(EXTERNALS_NAME, "mixed_req", - SUB_EXTERNALS_PATH) - self._check_simple_branch_ok(tree, directory=check_dir) - - def _check_mixed_ext_branch_required_pre_checkout_ext_change( - self, overall, tree): - # Note, this is the internal tree status just after change the - # externals description file, but before checkout - self.assertEqual(overall, 0) - self._check_mixed_ext_branch_modified(tree, directory=EXTERNALS_NAME) - check_dir = "{0}/{1}/{2}".format(EXTERNALS_NAME, "mixed_req", - SUB_EXTERNALS_PATH) - self._check_simple_branch_ok(tree, directory=check_dir) - - def _check_mixed_ext_branch_required_post_checkout_subext_modified( - self, overall, tree): - # Note, this is the internal tree status just after change the - # externals description file, but before checkout - self.assertEqual(overall, 0) - self._check_mixed_ext_branch_ok(tree, directory=EXTERNALS_NAME) - check_dir = "{0}/{1}/{2}".format(EXTERNALS_NAME, "mixed_req", - SUB_EXTERNALS_PATH) - self._check_simple_branch_modified(tree, directory=check_dir) - - def _check_mixed_cont_simple_required_pre_checkout(self, overall, tree): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree, directory=EXTERNALS_NAME) - self._check_simple_branch_empty(tree, directory=EXTERNALS_NAME) - self._check_simple_branch_empty(tree, directory=SUB_EXTERNALS_PATH) - - def _check_mixed_cont_simple_required_checkout(self, overall, tree): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree, directory=EXTERNALS_NAME) - self._check_simple_branch_empty(tree, directory=EXTERNALS_NAME) - self._check_simple_branch_empty(tree, directory=SUB_EXTERNALS_PATH) - - def _check_mixed_cont_simple_required_post_checkout(self, overall, tree): - # Note, this is the internal tree status just before checkout - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree, directory=EXTERNALS_NAME) - self._check_simple_branch_ok(tree, directory=EXTERNALS_NAME) - self._check_simple_branch_ok(tree, directory=SUB_EXTERNALS_PATH) - - def _check_container_sparse_pre_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_empty(tree) - self._check_simple_sparse_empty(tree) - - def _check_container_sparse_post_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_simple_sparse_ok(tree) - + def _external_path(section_name, base_path=EXTERNALS_PATH): + return './{0}/{1}'.format(base_path, section_name) + def _check_file_exists(self, repo_dir, pathname): "Check that exists in " self.assertTrue(os.path.exists(os.path.join(repo_dir, pathname))) @@ -1023,9 +619,9 @@ def _check_file_absent(self, repo_dir, pathname): "Check that does not exist in " self.assertFalse(os.path.exists(os.path.join(repo_dir, pathname))) + class TestSysCheckout(BaseTestSysCheckout): """Run systems level tests of checkout_externals - """ # NOTE(bja, 2017-11) pylint complains about long method names, but # it is hard to differentiate tests without making them more @@ -1037,246 +633,431 @@ class TestSysCheckout(BaseTestSysCheckout): # Run systems tests # # ---------------------------------------------------------------- - def test_container_simple_required(self): - """Verify that a container with simple subrepos - generates the correct initial status. - - """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) - - # status of empty repo - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_pre_checkout(overall, tree) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) - - # status clean checked out - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) - + def test_required_bytag(self): + """Check out a required external pointing to a git tag.""" + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag1') + self._generator.write_config(cloned_repo_dir) + + # externals start out 'empty' aka not checked out. + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) + local_path_rel = self._external_path(TAG_SECTION) + self._check_sync_clean(tree[local_path_rel], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + local_path_abs = os.path.join(cloned_repo_dir, local_path_rel) + self.assertFalse(os.path.exists(local_path_abs)) + + # after checkout, the external is 'clean' aka at the correct version. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[local_path_rel], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # Actually checked out the desired repo. + self.assertEqual('origin', GitRepository._remote_name_for_url( + # Which url to look up + self._generator.url_for_repo_path(SIMPLE_REPO), + # Which directory has the local checked-out repo. + dirname=local_path_abs)) + + # Actually checked out the desired tag. + (tag_found, tag_name) = GitRepository._git_current_tag(local_path_abs) + self.assertEqual(tag_name, 'tag1') + + # Check existence of some simp_tag files + tag_path = os.path.join('externals', TAG_SECTION) + self._check_file_exists(cloned_repo_dir, + os.path.join(tag_path, README_NAME)) + # Subrepo should not exist (not referenced by configs). + self._check_file_absent(cloned_repo_dir, os.path.join(tag_path, + 'simple_subdir', + 'subdir_file.txt')) + + def test_required_bybranch(self): + """Check out a required external pointing to a git branch.""" + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) + + # externals start out 'empty' aka not checked out. + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) + local_path_rel = self._external_path(BRANCH_SECTION) + self._check_sync_clean(tree[local_path_rel], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + local_path_abs = os.path.join(cloned_repo_dir, local_path_rel) + self.assertFalse(os.path.exists(local_path_abs)) + + # after checkout, the external is 'clean' aka at the correct version. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[local_path_rel], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self.assertTrue(os.path.exists(local_path_abs)) + + # Actually checked out the desired repo. + self.assertEqual('origin', GitRepository._remote_name_for_url( + # Which url to look up + self._generator.url_for_repo_path(SIMPLE_REPO), + # Which directory has the local checked-out repo. + dirname=local_path_abs)) + + # Actually checked out the desired branch. + (branch_found, branch_name) = GitRepository._git_current_remote_branch( + local_path_abs) + self.assertEquals(branch_name, 'origin/' + REMOTE_BRANCH_FEATURE2) + + def test_required_byhash(self): + """Check out a required external pointing to a git hash.""" + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, HASH_SECTION, + ref_hash='60b1cc1a38d63') + self._generator.write_config(cloned_repo_dir) + + # externals start out 'empty' aka not checked out. + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) + local_path_rel = self._external_path(HASH_SECTION) + self._check_sync_clean(tree[local_path_rel], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + local_path_abs = os.path.join(cloned_repo_dir, local_path_rel) + self.assertFalse(os.path.exists(local_path_abs)) + + # after checkout, the externals are 'clean' aka at their correct version. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[local_path_rel], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # Actually checked out the desired repo. + self.assertEqual('origin', GitRepository._remote_name_for_url( + # Which url to look up + self._generator.url_for_repo_path(SIMPLE_REPO), + # Which directory has the local checked-out repo. + dirname=local_path_abs)) + + # Actually checked out the desired hash. + (hash_found, hash_name) = GitRepository._git_current_hash( + local_path_abs) + self.assertTrue(hash_name.startswith('60b1cc1a38d63'), + msg=hash_name) + def test_container_nested_required(self): - """Verify that a container with nested subrepos - generates the correct initial status. + """Verify that a container with nested subrepos generates the correct initial status. Tests over all possible permutations """ + # Output subdirs for each of the externals, to test that one external can be + # checked out in a subdir of another. + NESTED_SUBDIR = ['./fred', './fred/wilma', './fred/wilma/barney'] + # Assert that each type of external (e.g. tag vs branch) can be at any parent level + # (e.g. child/parent/grandparent). orders = [[0, 1, 2], [1, 2, 0], [2, 0, 1], [0, 2, 1], [2, 1, 0], [1, 0, 2]] for n, order in enumerate(orders): - # create repo - dest_dir = os.path.join(os.environ[MANIC_TEST_TMP_REPO_ROOT], - self._test_id, "test"+str(n)) - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME, - dest_dir_in=dest_dir) - self._generator.container_nested_required(cloned_repo_dir, order) - - # status of empty repo - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_nested_required_pre_checkout(overall, tree, order) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_nested_required_checkout(overall, tree, order) - - # status clean checked out - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_nested_required_post_checkout(overall, tree, order) - + dest_dir = os.path.join(module_tmp_root_dir, self._test_id, + "test"+str(n)) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO, + dest_dir_in=dest_dir) + self._generator.create_config() + # We happen to check out each section via a different reference (tag/branch/hash) but + # those don't really matter, we just need to check out three repos into a nested set of + # directories. + self._generator.create_section( + SIMPLE_REPO, TAG_SECTION, nested=True, + tag='tag1', path=NESTED_SUBDIR[order[0]]) + self._generator.create_section( + SIMPLE_REPO, BRANCH_SECTION, nested=True, + branch=REMOTE_BRANCH_FEATURE2, path=NESTED_SUBDIR[order[1]]) + self._generator.create_section( + SIMPLE_REPO, HASH_SECTION, nested=True, + ref_hash='60b1cc1a38d63', path=NESTED_SUBDIR[order[2]]) + self._generator.write_config(cloned_repo_dir) + + # all externals start out 'empty' aka not checked out. + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) + self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + + # after checkout, all the repos are 'clean'. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[NESTED_SUBDIR[order[0]]], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[NESTED_SUBDIR[order[1]]], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[NESTED_SUBDIR[order[2]]], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + def test_container_simple_optional(self): - """Verify that container with an optional simple subrepos - generates the correct initial status. + """Verify that container with an optional simple subrepos generates + the correct initial status. """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_optional(cloned_repo_dir) - - # check status of empty repo - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_optional_pre_checkout(overall, tree) - - # checkout required - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_optional_checkout(overall, tree) - - # status - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_optional_post_checkout(overall, tree) + # create repo and externals config. + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, 'simp_req', + tag='tag1') - # checkout optional - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.optional_args) - self._check_container_simple_optional_post_checkout(overall, tree) + self._generator.create_section(SIMPLE_REPO, 'simp_opt', + tag='tag1', required=False) - # status - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_optional_post_optional(overall, tree) + self._generator.write_config(cloned_repo_dir) + + # all externals start out 'empty' aka not checked out. + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) + req_status = tree[self._external_path('simp_req')] + self._check_sync_clean(req_status, + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self.assertEqual(req_status.source_type, ExternalStatus.MANAGED) + + opt_status = tree[self._external_path('simp_opt')] + self._check_sync_clean(opt_status, + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL) + + # after checkout, required external is clean, optional is still empty. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + req_status = tree[self._external_path('simp_req')] + self._check_sync_clean(req_status, + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self.assertEqual(req_status.source_type, ExternalStatus.MANAGED) + + opt_status = tree[self._external_path('simp_opt')] + self._check_sync_clean(opt_status, + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL) + + # after checking out optionals, the optional external is also clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.optional_args) + req_status = tree[self._external_path('simp_req')] + self._check_sync_clean(req_status, + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self.assertEqual(req_status.source_type, ExternalStatus.MANAGED) + + opt_status = tree[self._external_path('simp_opt')] + self._check_sync_clean(opt_status, + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self.assertEqual(opt_status.source_type, ExternalStatus.OPTIONAL) def test_container_simple_verbose(self): - """Verify that container with simple subrepos runs with verbose status - output and generates the correct initial status. - + """Verify that verbose status matches non-verbose. """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) - - # check verbose status - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.verbose_args) - self._check_container_simple_required_post_checkout(overall, tree) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag1') + self._generator.write_config(cloned_repo_dir) + + # after checkout, all externals should be 'clean'. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # 'Verbose' status should tell the same story. + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.verbose_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_simple_dirty(self): - """Verify that a container with simple subrepos - and a dirty status exits gracefully. - + """Verify that a container with a new tracked file is marked dirty. """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) - - # add a file to the repo - tracked = True - self._add_file_to_repo(cloned_repo_dir, 'externals/simp_tag/tmp.txt', - tracked) - - # checkout: pre-checkout status should be dirty, did not - # modify working copy. - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_optional_st_dirty(overall, tree) - - # verify status is still dirty - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_optional_st_dirty(overall, tree) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag1') + self._generator.write_config(cloned_repo_dir) + + # checkout, should start out clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # add a tracked file to the simp_tag external, should be dirty. + RepoUtils.add_file_to_repo(cloned_repo_dir, + 'externals/{0}/tmp.txt'.format(TAG_SECTION), + tracked=True) + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.DIRTY) + + # Re-checkout; simp_tag should still be dirty. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.DIRTY) def test_container_simple_untracked(self): """Verify that a container with simple subrepos and a untracked files is not considered 'dirty' and will attempt an update. """ - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) - - # add a file to the repo - tracked = False - self._add_file_to_repo(cloned_repo_dir, 'externals/simp_tag/tmp.txt', - tracked) - - # checkout: pre-checkout status should be clean, ignoring the - # untracked file. - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_post_checkout(overall, tree) - - # verify status is still clean - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag1') + self._generator.write_config(cloned_repo_dir) + + # checkout, should start out clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # add an untracked file to the simp_tag external, should stay clean. + RepoUtils.add_file_to_repo(cloned_repo_dir, + 'externals/{0}/tmp.txt'.format(TAG_SECTION), + tracked=False) + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # After checkout, the external should still be 'clean'. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_simple_detached_sync(self): """Verify that a container with simple subrepos generates the correct out of sync status when making commits from a detached head - state. + state. + For more info about 'detached head' state: https://www.cloudbees.com/blog/git-detached-head """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) - - # status of empty repo - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_pre_checkout(overall, tree) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) - - # make a commit on the detached head of the tag and hash externals - self._generator.create_commit(cloned_repo_dir, 'simp_tag') - self._generator.create_commit(cloned_repo_dir, 'simp_hash') - self._generator.create_commit(cloned_repo_dir, 'simp_branch') - - # status of repo, branch, tag and hash should all be out of sync! - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_out_of_sync(overall, tree) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag1') + + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + + self._generator.create_section(SIMPLE_REPO, 'simp_hash', + ref_hash='60b1cc1a38d63') + + self._generator.write_config(cloned_repo_dir) + + # externals start out 'empty' aka not checked out. + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self._check_sync_clean(tree[self._external_path(HASH_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - # same pre-checkout out of sync status - self._check_container_simple_required_out_of_sync(overall, tree) - - # now status should be in-sync - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) + + # Commit on top of the tag and hash (creating the detached head state in those two + # externals' repos) + # The branch commit does not create the detached head state, but here for completeness. + RepoUtils.create_commit(cloned_repo_dir, TAG_SECTION) + RepoUtils.create_commit(cloned_repo_dir, HASH_SECTION) + RepoUtils.create_commit(cloned_repo_dir, BRANCH_SECTION) + + # sync status of all three should be 'modified' (uncommitted changes) + # clean status is 'ok' (matches externals version) + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(HASH_SECTION)], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + + # after checkout, all externals should be totally clean (no uncommitted changes, + # and matches externals version). + tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(HASH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_remote_branch(self): """Verify that a container with remote branch change works """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) - - # update the config file to point to a different remote with - # the same branch - self._generator.write_with_git_branch(cloned_repo_dir, name='simp_branch', - branch=REMOTE_BRANCH_FEATURE2, - repo_path=SIMPLE_FORK_NAME) - - # status of simp_branch should be out of sync - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_sb_modified(overall, tree) - - # checkout new externals - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_sb_modified(overall, tree) - - # status should be synced - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) + + # initial checkout + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) + + # update the branch external to point to a different remote with the same branch, + # then simp_branch should be out of sync + self._generator.write_with_git_branch(cloned_repo_dir, + name=BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2, + new_remote_repo_path=SIMPLE_FORK_REPO) + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + + # checkout new externals, now simp_branch should be clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_remote_tag_same_branch(self): """Verify that a container with remote tag change works. The new tag @@ -1285,276 +1066,323 @@ def test_container_remote_tag_same_branch(self): the branch. """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) + # initial checkout + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', - 'forked-feature-v1', SIMPLE_FORK_NAME) - - # status of simp_branch should be out of sync - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_sb_modified(overall, tree) - - # checkout new externals - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_sb_modified(overall, tree) - - # status should be synced - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) + # the new tag replacing the old branch. Tag MUST NOT be in the original + # repo! status of simp_branch should then be out of sync + self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, + tag='forked-feature-v1', + new_remote_repo_path=SIMPLE_FORK_REPO) + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.status_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + + # checkout new externals, then should be synced. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_remote_tag_fetch_all(self): """Verify that a container with remote tag change works. The new tag should not be in the original repo, only the new remote - fork. It should also not be on a branch that will be fetch, + fork. It should also not be on a branch that will be fetched, and therefore not fetched by default with 'git fetch'. It will - only be retreived by 'git fetch --tags' - + only be retrieved by 'git fetch --tags' """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) + # initial checkout + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) # update the config file to point to a different remote with - # the tag instead of branch. Tag MUST NOT be in the original - # repo! - self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', - 'abandoned-feature', SIMPLE_FORK_NAME) - - # status of simp_branch should be out of sync - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_sb_modified(overall, tree) - - # checkout new externals - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_sb_modified(overall, tree) - - # status should be synced - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) + # the new tag instead of the old branch. Tag MUST NOT be in the original + # repo! status of simp_branch should then be out of sync. + self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, + tag='abandoned-feature', + new_remote_repo_path=SIMPLE_FORK_REPO) + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + + # checkout new externals, should be clean again. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_preserve_dot(self): """Verify that after inital checkout, modifying an external git repo url to '.' and the current branch will leave it unchanged. """ - # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_required_checkout(overall, tree) + # initial checkout + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) # update the config file to point to a different remote with - # the same branch - self._generator.write_with_git_branch(cloned_repo_dir, name='simp_branch', - branch=REMOTE_BRANCH_FEATURE2, - repo_path=SIMPLE_FORK_NAME) - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - - # verify status is clean and unmodified - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) + # the same branch. + self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2, + new_remote_repo_path=SIMPLE_FORK_REPO) + # after checkout, should be clean again. + tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) # update branch to point to a new branch that only exists in # the local fork - self._generator.create_branch(cloned_repo_dir, repo_name='simp_branch', - branch='private-feature', with_commit=True) - self._generator.write_with_git_branch(cloned_repo_dir, name='simp_branch', - branch='private-feature', - repo_path=SIMPLE_LOCAL_ONLY_NAME) - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - - # verify status is clean and unmodified - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_required_post_checkout(overall, tree) - - def test_container_full(self): - """Verify that 'full' container with simple and mixed subrepos - generates the correct initial status. + RepoUtils.create_branch(cloned_repo_dir, external_name=BRANCH_SECTION, + branch='private-feature', with_commit=True) + self._generator.write_with_git_branch(cloned_repo_dir, name=BRANCH_SECTION, + branch='private-feature', + new_remote_repo_path=SIMPLE_LOCAL_ONLY_NAME) + # after checkout, should be clean again. + tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + def test_container_mixed_subrepo(self): + """Verify container with mixed subrepo. The mixed subrepo has a sub-externals file with different sub-externals on different branches. """ - # create the test repository - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - - # create the top level externals file - self._generator.container_full(cloned_repo_dir) - - # inital checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_full_pre_checkout(overall, tree) - - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_full_post_checkout(overall, tree) - - # Check existance of some files - subrepo_path = os.path.join('externals', 'simp_tag') - self._check_file_exists(cloned_repo_dir, - os.path.join(subrepo_path, 'readme.txt')) - self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path, - 'simple_subdir', - 'subdir_file.txt')) - - # update the mixed-use repo to point to different branch - self._generator.write_with_git_branch(cloned_repo_dir, name='mixed_req', - branch='new-feature', - repo_path=MIXED_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - # check status out of sync for mixed_req, but sub-externals + self._generator.create_config() + self._generator.create_section(MIXED_REPO, 'mixed_req', + branch='master', sub_externals=CFG_SUB_NAME) + self._generator.write_config(cloned_repo_dir) + + # The subrepo has a repo_url that uses this environment variable. + # It'll be cleared in tearDown(). + os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root + debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root + + # inital checkout: all requireds are clean, and optional is empty. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args, + debug_env=debug_env) + mixed_req_path = self._external_path('mixed_req') + self._check_sync_clean(tree[mixed_req_path], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + sub_ext_base_path = "{0}/{1}/{2}".format(EXTERNALS_PATH, 'mixed_req', SUB_EXTERNALS_PATH) + # The already-checked-in subexternals file has a 'simp_branch' section + self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # update the mixed-use external to point to different branch + # status should become out of sync for mixed_req, but sub-externals # are still in sync - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_full_pre_checkout_ext_change(overall, tree) - - # run the checkout. Now the mixed use external and it's - # sub-exterals should be changed. Returned status is - # pre-checkout! - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_full_pre_checkout_ext_change(overall, tree) - - # check status out of sync for mixed_req, and sub-externals - # are in sync. - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_full_post_checkout(overall, tree) - + self._generator.write_with_git_branch(cloned_repo_dir, name='mixed_req', + branch='new-feature', + new_remote_repo_path=MIXED_REPO) + tree = self.execute_checkout_in_dir(cloned_repo_dir, self.status_args, + debug_env=debug_env) + self._check_sync_clean(tree[mixed_req_path], + ExternalStatus.MODEL_MODIFIED, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # run the checkout. Now the mixed use external and its sub-externals should be clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, self.checkout_args, + debug_env=debug_env) + self._check_sync_clean(tree[mixed_req_path], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path('simp_branch', base_path=sub_ext_base_path)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + def test_container_component(self): """Verify that optional component checkout works """ - # create the test repository - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) # create the top level externals file - self._generator.container_full(cloned_repo_dir) - - # inital checkout, first try a nonexistant component argument noref + self._generator.create_config() + # Optional external, by tag. + self._generator.create_section(SIMPLE_REPO, 'simp_opt', + tag='tag1', required=False) + + # Required external, by branch. + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + + # Required external, by hash. + self._generator.create_section(SIMPLE_REPO, HASH_SECTION, + ref_hash='60b1cc1a38d63') + self._generator.write_config(cloned_repo_dir) + + # inital checkout, first try a nonexistent component argument noref checkout_args = ['simp_opt', 'noref'] checkout_args.extend(self.checkout_args) with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) + # Now explicitly check out one optional component.. + # Explicitly listed component (opt) should be present, the other two not. checkout_args = ['simp_opt'] checkout_args.extend(self.checkout_args) + tree = self.execute_checkout_with_status(cloned_repo_dir, + checkout_args) + self._check_sync_clean(tree[self._external_path('simp_opt')], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self._check_sync_clean(tree[self._external_path(HASH_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + + # Check out a second component, this one required. + # Explicitly listed component (branch) should be present, the still-unlisted one (tag) not. + checkout_args.append(BRANCH_SECTION) + tree = self.execute_checkout_with_status(cloned_repo_dir, + checkout_args) + self._check_sync_clean(tree[self._external_path('simp_opt')], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(HASH_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - checkout_args) - - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_component_post_checkout(overall, tree) - checkout_args.append('simp_branch') - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - checkout_args) - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_component_post_checkout2(overall, tree) def test_container_exclude_component(self): """Verify that exclude component checkout works """ - # create the test repository - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - - # create the top level externals file - self._generator.container_full(cloned_repo_dir) - - # inital checkout, exclude simp_opt - checkout_args = ['--exclude', 'simp_opt'] + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag1') + + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + + self._generator.create_section(SIMPLE_REPO, 'simp_hash', + ref_hash='60b1cc1a38d63') + + self._generator.write_config(cloned_repo_dir) + + # inital checkout should result in all externals being clean except excluded TAG_SECTION. + checkout_args = ['--exclude', TAG_SECTION] checkout_args.extend(self.checkout_args) - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) - checkout_args.append("--status") - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, checkout_args) - self._check_container_component_post_checkout3(overall, tree) - - def test_mixed_simple(self): - """Verify that a mixed use repo can serve as a 'full' container, - pulling in a set of externals and a seperate set of sub-externals. + tree = self.execute_checkout_with_status(cloned_repo_dir, checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.EMPTY, + ExternalStatus.DEFAULT) + self._check_sync_clean(tree[self._external_path(BRANCH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path(HASH_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + def test_subexternal(self): + """Verify that an externals file can be brought in as a reference. """ - #import pdb; pdb.set_trace() - # create repository - cloned_repo_dir = self.clone_test_repo(MIXED_REPO_NAME) - # create top level externals file - self._generator.mixed_simple_base(cloned_repo_dir) - # NOTE: sub-externals file is already in the repo so we can - # switch branches during testing. Since this is a mixed-repo - # serving as the top level container repo, we can't switch - # during this test. + cloned_repo_dir = self.clone_test_repo(MIXED_REPO) - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_mixed_cont_simple_required_checkout(overall, tree) - - # verify status is clean and unmodified - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_mixed_cont_simple_required_post_checkout(overall, tree) + self._generator.create_config() + self._generator.create_section_reference_to_subexternal('mixed_base') + self._generator.write_config(cloned_repo_dir) + + # The subrepo has a repo_url that uses this environment variable. + # It'll be cleared in tearDown(). + os.environ[MIXED_CONT_EXT_ROOT_ENV_VAR] = self._bare_root + debug_env = MIXED_CONT_EXT_ROOT_ENV_VAR + '=' + self._bare_root + + # After checkout, confirm required's are clean and the referenced + # subexternal's contents are also clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args, + debug_env=debug_env) + + self._check_sync_clean( + tree[self._external_path(BRANCH_SECTION, base_path=SUB_EXTERNALS_PATH)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) def test_container_sparse(self): """Verify that 'full' container with simple subrepo can run a sparse checkout and generate the correct initial status. """ - # create the test repository - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - # create the top level externals file - self._generator.container_sparse(cloned_repo_dir) - - # inital checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_sparse_pre_checkout(overall, tree) - - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_sparse_post_checkout(overall, tree) + # Create a file to list filenames to checkout. + sparse_filename = 'sparse_checkout' + with open(os.path.join(cloned_repo_dir, sparse_filename), 'w') as sfile: + sfile.write(README_NAME) - # Check existance of some files - subrepo_path = os.path.join('externals', 'simp_tag') + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, + tag='tag2') + + # Same tag as above, but with a sparse file too. + sparse_relpath = '../../' + sparse_filename + self._generator.create_section(SIMPLE_REPO, 'simp_sparse', + tag='tag2', sparse=sparse_relpath) + + self._generator.write_config(cloned_repo_dir) + + # inital checkout, confirm required's are clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._external_path('simp_sparse')], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + + # Check existence of some files - full set in TAG_SECTION, and sparse set + # in 'simp_sparse'. + subrepo_path = os.path.join('externals', TAG_SECTION) self._check_file_exists(cloned_repo_dir, - os.path.join(subrepo_path, 'readme.txt')) + os.path.join(subrepo_path, README_NAME)) self._check_file_exists(cloned_repo_dir, os.path.join(subrepo_path, 'simple_subdir', 'subdir_file.txt')) subrepo_path = os.path.join('externals', 'simp_sparse') self._check_file_exists(cloned_repo_dir, - os.path.join(subrepo_path, 'readme.txt')) + os.path.join(subrepo_path, README_NAME)) self._check_file_absent(cloned_repo_dir, os.path.join(subrepo_path, 'simple_subdir', 'subdir_file.txt')) @@ -1591,42 +1419,27 @@ class TestSysCheckoutSVN(BaseTestSysCheckout): """ - def _check_svn_branch_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/svn_branch'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_svn_branch_dirty(self, tree, directory=EXTERNALS_NAME): - name = './{0}/svn_branch'.format(directory) - self._check_generic_ok_dirty_required(tree, name) - - def _check_svn_tag_ok(self, tree, directory=EXTERNALS_NAME): - name = './{0}/svn_tag'.format(directory) - self._check_generic_ok_clean_required(tree, name) - - def _check_svn_tag_modified(self, tree, directory=EXTERNALS_NAME): - name = './{0}/svn_tag'.format(directory) - self._check_generic_modified_ok_required(tree, name) - - def _check_container_simple_svn_post_checkout(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_svn_branch_ok(tree) - self._check_svn_tag_ok(tree) - - def _check_container_simple_svn_sb_dirty_st_mod(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_svn_tag_modified(tree) - self._check_svn_branch_dirty(tree) + @staticmethod + def _svn_branch_name(): + return './{0}/svn_branch'.format(EXTERNALS_PATH) - def _check_container_simple_svn_sb_clean_st_mod(self, overall, tree): - self.assertEqual(overall, 0) - self._check_simple_tag_ok(tree) - self._check_svn_tag_modified(tree) - self._check_svn_branch_ok(tree) + @staticmethod + def _svn_tag_name(): + return './{0}/svn_tag'.format(EXTERNALS_PATH) + + def _check_tag_branch_svn_tag_clean(self, tree): + self._check_sync_clean(tree[self._external_path(TAG_SECTION)], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._svn_branch_name()], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) + self._check_sync_clean(tree[self._svn_tag_name()], + ExternalStatus.STATUS_OK, + ExternalStatus.STATUS_OK) @staticmethod - def have_svn_access(): + def _have_svn_access(): """Check if we have svn access so we can enable tests that use svn. """ @@ -1639,10 +1452,10 @@ def have_svn_access(): pass return have_svn - def skip_if_no_svn_access(self): + def _skip_if_no_svn_access(self): """Function decorator to disable svn tests when svn isn't available """ - have_svn = self.have_svn_access() + have_svn = self._have_svn_access() if not have_svn: raise unittest.SkipTest("No svn access") @@ -1650,60 +1463,55 @@ def test_container_simple_svn(self): """Verify that a container repo can pull in an svn branch and svn tag. """ - self.skip_if_no_svn_access() + self._skip_if_no_svn_access() # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_svn(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) + self._generator.create_config() + # Git repo. + self._generator.create_section(SIMPLE_REPO, TAG_SECTION, tag='tag1') + + # Svn repos. + self._generator.create_svn_external('svn_branch', branch='trunk') + self._generator.create_svn_external('svn_tag', tag='tags/cesm2.0.beta07') - # verify status is clean and unmodified - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_svn_post_checkout(overall, tree) + self._generator.write_config(cloned_repo_dir) + + # checkout, make sure all sections are clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_tag_branch_svn_tag_clean(tree) # update description file to make the tag into a branch and # trigger a switch - self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', 'trunk') - - # checkout - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) + self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', + 'trunk') - # verify status is clean and unmodified - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.status_args) - self._check_container_simple_svn_post_checkout(overall, tree) + # checkout, again the results should be clean. + tree = self.execute_checkout_with_status(cloned_repo_dir, + self.checkout_args) + self._check_tag_branch_svn_tag_clean(tree) # add an untracked file to the repo tracked = False - self._add_file_to_repo(cloned_repo_dir, - 'externals/svn_branch/tmp.txt', tracked) + RepoUtils.add_file_to_repo(cloned_repo_dir, + 'externals/svn_branch/tmp.txt', tracked) - # run a no-op checkout: pre-checkout status should be clean, - # ignoring the untracked file. - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_svn_post_checkout(overall, tree) + # run a no-op checkout. + self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) # update description file to make the branch into a tag and # trigger a modified sync status self._generator.write_with_svn_branch(cloned_repo_dir, 'svn_tag', 'tags/cesm2.0.beta07') - # checkout: pre-checkout status should be clean and modified, - # will modify working copy. - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.checkout_args) - self._check_container_simple_svn_sb_clean_st_mod(overall, tree) + self.execute_checkout_in_dir(cloned_repo_dir,self.checkout_args) # verify status is still clean and unmodified, last # checkout modified the working dir state. - overall, tree = self.execute_checkout_in_dir(cloned_repo_dir, - self.verbose_args) - self._check_container_simple_svn_post_checkout(overall, tree) + tree = self.execute_checkout_in_dir(cloned_repo_dir, + self.verbose_args) + self._check_tag_branch_svn_tag_clean(tree) class TestSubrepoCheckout(BaseTestSysCheckout): # Need to store information at setUp time for checking @@ -1730,20 +1538,19 @@ def setUp(self): self._bare_branch_name = 'subrepo_branch' self._config_branch_name = 'subrepo_config_branch' self._container_extern_name = 'externals_container.cfg' - self._my_test_dir = os.path.join(os.environ[MANIC_TEST_TMP_REPO_ROOT], - self._test_id) + self._my_test_dir = os.path.join(module_tmp_root_dir, self._test_id) self._repo_dir = os.path.join(self._my_test_dir, self._test_repo_name) self._checkout_dir = 'repo_with_submodules' - check_dir = self.clone_test_repo(CONTAINER_REPO_NAME, + check_dir = self.clone_test_repo(CONTAINER_REPO, dest_dir_in=self._repo_dir) self.assertTrue(self._repo_dir == check_dir) # Add the submodules cwd = os.getcwd() - fork_repo_dir = os.path.join(self._bare_root, SIMPLE_FORK_NAME) - simple_repo_dir = os.path.join(self._bare_root, SIMPLE_REPO_NAME) - self._simple_ext_fork_name = os.path.splitext(SIMPLE_FORK_NAME)[0] + fork_repo_dir = os.path.join(self._bare_root, SIMPLE_FORK_REPO) + simple_repo_dir = os.path.join(self._bare_root, SIMPLE_REPO) + self._simple_ext_fork_name = os.path.splitext(SIMPLE_FORK_REPO)[0] self._simple_ext_name = os.path.join('sourc', - os.path.splitext(SIMPLE_REPO_NAME)[0]) + os.path.splitext(SIMPLE_REPO)[0]) os.chdir(self._repo_dir) # Add a branch with a subrepo cmd = ['git', 'branch', self._bare_branch_name, 'master'] @@ -1764,7 +1571,7 @@ def setUp(self): execute_subprocess(cmd) cmd = ['git', 'checkout', self._config_branch_name] execute_subprocess(cmd) - cmd = ['git', 'submodule', 'add', '--name', SIMPLE_REPO_NAME, + cmd = ['git', 'submodule', 'add', '--name', SIMPLE_REPO, simple_repo_dir, self._simple_ext_name] execute_subprocess(cmd) # Checkout feature2 @@ -1776,8 +1583,8 @@ def setUp(self): # Save the fork repo hash for comparison self._simple_hash_check = self.get_git_hash() os.chdir(self._repo_dir) - self.create_externals_file(filename=self._container_extern_name, - dest_dir=self._repo_dir, from_submodule=True) + self.write_externals_config(filename=self._container_extern_name, + dest_dir=self._repo_dir, from_submodule=True) cmd = ['git', 'add', self._container_extern_name] execute_subprocess(cmd) cmd = ['git', 'commit', '-am', "'Added simple-ext as a submodule'"] @@ -1794,9 +1601,10 @@ def get_git_hash(revision="HEAD"): git_out = execute_subprocess(cmd, output_to_caller=True) return git_out.strip() - def create_externals_file(self, name='', filename=CFG_NAME, dest_dir=None, - branch_name=None, sub_externals=None, - from_submodule=False): + def write_externals_config(self, name='', dest_dir=None, + filename=CFG_NAME, + branch_name=None, sub_externals=None, + from_submodule=False): # pylint: disable=too-many-arguments """Create a container externals file with only simple externals. @@ -1807,10 +1615,10 @@ def create_externals_file(self, name='', filename=CFG_NAME, dest_dir=None, dest_dir = self._my_test_dir if from_submodule: - self._generator.create_section(SIMPLE_FORK_NAME, + self._generator.create_section(SIMPLE_FORK_REPO, self._simple_ext_fork_name, from_submodule=True) - self._generator.create_section(SIMPLE_REPO_NAME, + self._generator.create_section(SIMPLE_REPO, self._simple_ext_name, branch='feature3', path='', from_submodule=False) @@ -1821,7 +1629,7 @@ def create_externals_file(self, name='', filename=CFG_NAME, dest_dir=None, self._generator.create_section(self._test_repo_name, self._checkout_dir, branch=branch_name, - path=name, externals=sub_externals, + path=name, sub_externals=sub_externals, repo_path_abs=self._repo_dir) self._generator.write_config(dest_dir, filename=filename) @@ -1831,12 +1639,10 @@ def idempotence_check(self, checkout_dir): checkout_externals --status does not cause errors""" cwd = os.getcwd() os.chdir(checkout_dir) - overall, _ = self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - self.assertTrue(overall == 0) - overall, _ = self.execute_checkout_in_dir(self._my_test_dir, - self.status_args) - self.assertTrue(overall == 0) + self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) + self.execute_checkout_in_dir(self._my_test_dir, + self.status_args) os.chdir(cwd) def test_submodule_checkout_bare(self): @@ -1848,17 +1654,17 @@ def test_submodule_checkout_bare(self): """ simple_ext_fork_tag = "(tag1)" simple_ext_fork_status = " " - self.create_externals_file(branch_name=self._bare_branch_name) - overall, _ = self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - self.assertTrue(overall == 0) + self.write_externals_config(branch_name=self._bare_branch_name) + self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) cwd = os.getcwd() checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) fork_file = os.path.join(checkout_dir, self._simple_ext_fork_name, "readme.txt") self.assertTrue(os.path.exists(fork_file)) - os.chdir(checkout_dir) + submods = git_submodule_status(checkout_dir) + print('checking status of', checkout_dir, ':', submods) self.assertEqual(len(submods.keys()), 1) self.assertTrue(self._simple_ext_fork_name in submods) submod = submods[self._simple_ext_fork_name] @@ -1868,7 +1674,6 @@ def test_submodule_checkout_bare(self): self.assertEqual(submod['status'], simple_ext_fork_status) self.assertTrue('tag' in submod) self.assertEqual(submod['tag'], simple_ext_fork_tag) - os.chdir(cwd) self.idempotence_check(checkout_dir) def test_submodule_checkout_none(self): @@ -1877,11 +1682,10 @@ def test_submodule_checkout_none(self): externals cfg file. Correct behavior is the submodle is not checked out. """ - self.create_externals_file(branch_name=self._bare_branch_name, - sub_externals="none") - overall, _ = self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - self.assertTrue(overall == 0) + self.write_externals_config(branch_name=self._bare_branch_name, + sub_externals="none") + self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) cwd = os.getcwd() checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) fork_file = os.path.join(checkout_dir, @@ -1899,11 +1703,10 @@ def test_submodule_checkout_config(self): # pylint: disable=too-many-locals """ tag_check = None # Not checked out as submodule status_check = "-" # Not checked out as submodule - self.create_externals_file(branch_name=self._config_branch_name, - sub_externals=self._container_extern_name) - overall, _ = self.execute_checkout_in_dir(self._my_test_dir, - self.checkout_args) - self.assertTrue(overall == 0) + self.write_externals_config(branch_name=self._config_branch_name, + sub_externals=self._container_extern_name) + self.execute_checkout_in_dir(self._my_test_dir, + self.checkout_args) cwd = os.getcwd() checkout_dir = os.path.join(self._my_test_dir, self._checkout_dir) fork_file = os.path.join(checkout_dir, @@ -1965,14 +1768,17 @@ def test_error_unknown_protocol(self): """ # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.write_with_protocol(cloned_repo_dir, 'simp_branch', - 'this-protocol-does-not-exist') + self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION, + 'this-protocol-does-not-exist') with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) @@ -1986,13 +1792,16 @@ def test_error_switch_protocol(self): """ # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.write_with_protocol(cloned_repo_dir, 'simp_branch', 'svn') + self._generator.write_with_protocol(cloned_repo_dir, BRANCH_SECTION, 'svn') with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) @@ -2002,14 +1811,18 @@ def test_error_unknown_tag(self): """ # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', - 'this-tag-does-not-exist', SIMPLE_REPO_NAME) + self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, + tag='this-tag-does-not-exist', + new_remote_repo_path=SIMPLE_REPO) with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) @@ -2020,15 +1833,19 @@ def test_error_overspecify_tag_branch(self): """ # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.write_with_tag(cloned_repo_dir, 'simp_branch', - 'this-tag-does-not-exist', SIMPLE_REPO_NAME, - remove_branch=False) + self._generator.write_with_tag_and_remote_repo(cloned_repo_dir, BRANCH_SECTION, + tag='this-tag-does-not-exist', + new_remote_repo_path=SIMPLE_REPO, + remove_branch=False) with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) @@ -2039,14 +1856,16 @@ def test_error_underspecify_tag_branch(self): """ # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! - self._generator.write_without_branch_tag(cloned_repo_dir, - 'simp_branch') + self._generator.write_without_branch_tag(cloned_repo_dir, BRANCH_SECTION) with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) @@ -2057,14 +1876,17 @@ def test_error_missing_url(self): """ # create repo - cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO_NAME) - self._generator.container_simple_required(cloned_repo_dir) + cloned_repo_dir = self.clone_test_repo(CONTAINER_REPO) + self._generator.create_config() + self._generator.create_section(SIMPLE_REPO, BRANCH_SECTION, + branch=REMOTE_BRANCH_FEATURE2) + self._generator.write_config(cloned_repo_dir) # update the config file to point to a different remote with # the tag instead of branch. Tag MUST NOT be in the original # repo! self._generator.write_without_repo_url(cloned_repo_dir, - 'simp_branch') + BRANCH_SECTION) with self.assertRaises(RuntimeError): self.execute_checkout_in_dir(cloned_repo_dir, self.checkout_args) diff --git a/test/test_sys_repository_git.py b/test/test_sys_repository_git.py index 29d5433b95..7e5fb5020d 100644 --- a/test/test_sys_repository_git.py +++ b/test/test_sys_repository_git.py @@ -131,12 +131,12 @@ def tearDown(self): shutil.rmtree(self._tmpdir, ignore_errors=True) @staticmethod - def make_git_repo(): + def make_cwd_git_repo(): """Turn the current directory into an empty git repository""" execute_subprocess(['git', 'init']) @staticmethod - def add_git_commit(): + def add_cwd_git_commit(): """Add a git commit in the current directory""" with open('README', 'a') as myfile: myfile.write('more info') @@ -144,17 +144,17 @@ def add_git_commit(): execute_subprocess(['git', 'commit', '-m', 'my commit message']) @staticmethod - def checkout_git_branch(branchname): + def checkout_cwd_git_branch(branchname): """Checkout a new branch in the current directory""" execute_subprocess(['git', 'checkout', '-b', branchname]) @staticmethod - def make_git_tag(tagname): + def make_cwd_git_tag(tagname): """Make a lightweight tag at the current commit""" execute_subprocess(['git', 'tag', '-m', 'making a tag', tagname]) @staticmethod - def checkout_ref(refname): + def checkout_cwd_ref(refname): """Checkout the given refname in the current directory""" execute_subprocess(['git', 'checkout', refname]) @@ -164,72 +164,72 @@ def checkout_ref(refname): def test_currentHash_returnsHash(self): """Ensure that the _git_current_hash function returns a hash""" - self.make_git_repo() - self.add_git_commit() - hash_found, myhash = self._repo._git_current_hash() + self.make_cwd_git_repo() + self.add_cwd_git_commit() + hash_found, myhash = self._repo._git_current_hash(os.getcwd()) self.assertTrue(hash_found) self.assertIsHash(myhash) def test_currentHash_outsideGitRepo(self): """Ensure that the _git_current_hash function returns False when outside a git repository""" - hash_found, myhash = self._repo._git_current_hash() + hash_found, myhash = self._repo._git_current_hash(os.getcwd()) self.assertFalse(hash_found) self.assertEqual('', myhash) def test_currentBranch_onBranch(self): """Ensure that the _git_current_branch function returns the name of the branch""" - self.make_git_repo() - self.add_git_commit() - self.checkout_git_branch('foo') - branch_found, mybranch = self._repo._git_current_branch() + self.make_cwd_git_repo() + self.add_cwd_git_commit() + self.checkout_cwd_git_branch('foo') + branch_found, mybranch = self._repo._git_current_branch(os.getcwd()) self.assertTrue(branch_found) self.assertEqual('foo', mybranch) def test_currentBranch_notOnBranch(self): """Ensure that the _git_current_branch function returns False when not on a branch""" - self.make_git_repo() - self.add_git_commit() - self.make_git_tag('mytag') - self.checkout_ref('mytag') - branch_found, mybranch = self._repo._git_current_branch() + self.make_cwd_git_repo() + self.add_cwd_git_commit() + self.make_cwd_git_tag('mytag') + self.checkout_cwd_ref('mytag') + branch_found, mybranch = self._repo._git_current_branch(os.getcwd()) self.assertFalse(branch_found) self.assertEqual('', mybranch) def test_currentBranch_outsideGitRepo(self): """Ensure that the _git_current_branch function returns False when outside a git repository""" - branch_found, mybranch = self._repo._git_current_branch() + branch_found, mybranch = self._repo._git_current_branch(os.getcwd()) self.assertFalse(branch_found) self.assertEqual('', mybranch) def test_currentTag_onTag(self): """Ensure that the _git_current_tag function returns the name of the tag""" - self.make_git_repo() - self.add_git_commit() - self.make_git_tag('some_tag') - tag_found, mytag = self._repo._git_current_tag() + self.make_cwd_git_repo() + self.add_cwd_git_commit() + self.make_cwd_git_tag('some_tag') + tag_found, mytag = self._repo._git_current_tag(os.getcwd()) self.assertTrue(tag_found) self.assertEqual('some_tag', mytag) def test_currentTag_notOnTag(self): """Ensure tha the _git_current_tag function returns False when not on a tag""" - self.make_git_repo() - self.add_git_commit() - self.make_git_tag('some_tag') - self.add_git_commit() - tag_found, mytag = self._repo._git_current_tag() + self.make_cwd_git_repo() + self.add_cwd_git_commit() + self.make_cwd_git_tag('some_tag') + self.add_cwd_git_commit() + tag_found, mytag = self._repo._git_current_tag(os.getcwd()) self.assertFalse(tag_found) self.assertEqual('', mytag) def test_currentTag_outsideGitRepo(self): """Ensure that the _git_current_tag function returns False when outside a git repository""" - tag_found, mytag = self._repo._git_current_tag() + tag_found, mytag = self._repo._git_current_tag(os.getcwd()) self.assertFalse(tag_found) self.assertEqual('', mytag) diff --git a/test/test_unit_repository_git.py b/test/test_unit_repository_git.py index a6ad9f1003..1c01098acf 100644 --- a/test/test_unit_repository_git.py +++ b/test/test_unit_repository_git.py @@ -67,7 +67,7 @@ def setUp(self): def _git_current_branch(branch_found, branch_name): """Return a function that takes the place of repo._git_current_branch, which returns the given output.""" - def my_git_current_branch(): + def my_git_current_branch(dirname): """mock function that can take the place of repo._git_current_branch""" return branch_found, branch_name return my_git_current_branch @@ -76,7 +76,7 @@ def my_git_current_branch(): def _git_current_tag(tag_found, tag_name): """Return a function that takes the place of repo._git_current_tag, which returns the given output.""" - def my_git_current_tag(): + def my_git_current_tag(dirname): """mock function that can take the place of repo._git_current_tag""" return tag_found, tag_name return my_git_current_tag @@ -85,7 +85,7 @@ def my_git_current_tag(): def _git_current_hash(hash_found, hash_name): """Return a function that takes the place of repo._git_current_hash, which returns the given output.""" - def my_git_current_hash(): + def my_git_current_hash(dirname): """mock function that can take the place of repo._git_current_hash""" return hash_found, hash_name return my_git_current_hash @@ -102,7 +102,7 @@ def test_ref_branch(self): self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag') self._repo._git_current_hash = self._git_current_hash(True, 'abc123') expected = 'foo_tag (branch feature3)' - result = self._repo._current_ref() + result = self._repo._current_ref(os.getcwd()) self.assertEqual(result, expected) def test_ref_detached_tag(self): @@ -112,7 +112,7 @@ def test_ref_detached_tag(self): self._repo._git_current_tag = self._git_current_tag(True, 'foo_tag') self._repo._git_current_hash = self._git_current_hash(True, 'abc123') expected = 'foo_tag' - result = self._repo._current_ref() + result = self._repo._current_ref(os.getcwd()) self.assertEqual(result, expected) def test_ref_detached_hash(self): @@ -123,7 +123,7 @@ def test_ref_detached_hash(self): self._repo._git_current_tag = self._git_current_tag(False, '') self._repo._git_current_hash = self._git_current_hash(True, 'abc123') expected = 'abc123' - result = self._repo._current_ref() + result = self._repo._current_ref(os.getcwd()) self.assertEqual(result, expected) def test_ref_none(self): @@ -132,7 +132,7 @@ def test_ref_none(self): self._repo._git_current_branch = self._git_current_branch(False, '') self._repo._git_current_tag = self._git_current_tag(False, '') self._repo._git_current_hash = self._git_current_hash(False, '') - result = self._repo._current_ref() + result = self._repo._current_ref(os.getcwd()) self.assertEqual(result, EMPTY_STR) @@ -206,11 +206,19 @@ def setUp(self): self._repo._current_ref = self._current_ref_empty self._create_tmp_git_dir() + # We have to override this class method rather than the self._repo + # instance method because it is called via + # GitRepository._remote_name_for_url, which is itself a @classmethod + # calls cls._git_remote_verbose(). + self._orignal_git_remote_verbose = GitRepository._git_remote_verbose + GitRepository._git_remote_verbose = self._git_remote_origin_upstream def tearDown(self): """Cleanup tmp stuff on the file system """ self._remove_tmp_git_dir() + GitRepository._git_remote_verbose = self._orignal_git_remote_verbose + def _create_tmp_git_dir(self): """Create a temporary fake git directory for testing purposes. """ @@ -227,29 +235,27 @@ def _remove_tmp_git_dir(self): # mock methods replacing git system calls # @staticmethod - def _current_ref_empty(): + def _current_ref_empty(dirname): """Return an empty string. + + Drop-in for GitRepository._current_ref """ return EMPTY_STR @staticmethod - def _git_remote_origin_upstream(): - """Return an info string that is a checkout hash - """ - return GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM + def _git_remote_origin_upstream(dirname): + """Return an info string that is a checkout hash. - @staticmethod - def _git_remote_none(): - """Return an info string that is a checkout hash + Drop-in for GitRepository._git_remote_verbose. """ - return EMPTY_STR + return GIT_REMOTE_OUTPUT_ORIGIN_UPSTREAM @staticmethod def _git_current_hash(myhash): """Return a function that takes the place of repo._git_current_hash, which returns the given hash """ - def my_git_current_hash(): + def my_git_current_hash(dirname): """mock function that can take the place of repo._git_current_hash""" return 0, myhash return my_git_current_hash @@ -263,7 +269,7 @@ def _git_revparse_commit(self, expected_ref, mystatus, myhash): status = 0 implies success, non-zero implies failure """ - def my_git_revparse_commit(ref): + def my_git_revparse_commit(ref, dirname): """mock function that can take the place of repo._git_revparse_commit""" self.assertEqual(expected_ref, ref) return mystatus, myhash @@ -291,9 +297,6 @@ def test_sync_dir_exist_no_git_info(self): """Test that a non-existent git repo returns an unknown status """ stat = ExternalStatus() - # Now we over-ride the _git_remote_verbose method on the repo to return - # a known value without requiring access to git. - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._tag = 'tag1' self._repo._git_current_hash = self._git_current_hash('') self._repo._git_revparse_commit = self._git_revparse_commit( @@ -313,7 +316,6 @@ def test_sync_invalid_reference(self): """Test that an invalid reference returns out-of-sync """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._tag = 'tag1' self._repo._git_current_hash = self._git_current_hash('abc123') self._repo._git_revparse_commit = self._git_revparse_commit( @@ -333,7 +335,6 @@ def test_sync_tag_on_same_hash(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._tag = 'tag1' self._repo._git_current_hash = self._git_current_hash('abc123') self._repo._git_revparse_commit = self._git_revparse_commit( @@ -348,7 +349,6 @@ def test_sync_tag_on_different_hash(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._tag = 'tag1' self._repo._git_current_hash = self._git_current_hash('def456') self._repo._git_revparse_commit = self._git_revparse_commit( @@ -368,7 +368,6 @@ def test_sync_hash_on_same_hash(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._tag = '' self._repo._hash = 'abc' self._repo._git_current_hash = self._git_current_hash('abc123') @@ -384,7 +383,6 @@ def test_sync_hash_on_different_hash(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._tag = '' self._repo._hash = 'abc' self._repo._git_current_hash = self._git_current_hash('def456') @@ -405,7 +403,6 @@ def test_sync_branch_on_same_hash(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._branch = 'feature-2' self._repo._tag = '' self._repo._git_current_hash = self._git_current_hash('abc123') @@ -421,7 +418,6 @@ def test_sync_branch_on_diff_hash(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._branch = 'feature-2' self._repo._tag = '' self._repo._git_current_hash = self._git_current_hash('abc123') @@ -433,11 +429,10 @@ def test_sync_branch_on_diff_hash(self): self.assertEqual(stat.clean_state, ExternalStatus.DEFAULT) def test_sync_branch_diff_remote(self): - """Test _determine_remote_name with a different remote + """Test _remote_name_for_url with a different remote """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._branch = 'feature-2' self._repo._tag = '' self._repo._url = '/path/to/other/repo' @@ -449,11 +444,10 @@ def test_sync_branch_diff_remote(self): # expected argument def test_sync_branch_diff_remote2(self): - """Test _determine_remote_name with a different remote + """Test _remote_name_for_url with a different remote """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._branch = 'feature-2' self._repo._tag = '' self._repo._url = '/path/to/local/repo2' @@ -469,7 +463,6 @@ def test_sync_branch_on_unknown_remote(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._branch = 'feature-2' self._repo._tag = '' self._repo._url = '/path/to/unknown/repo' @@ -491,7 +484,6 @@ def test_sync_branch_on_untracked_local(self): """ stat = ExternalStatus() - self._repo._git_remote_verbose = self._git_remote_origin_upstream self._repo._branch = 'feature3' self._repo._tag = '' self._repo._url = '.' @@ -611,24 +603,20 @@ def setUp(self): self._repo = GitRepository('test', repo) @staticmethod - def _shell_true(url, remote=None): - _ = url - _ = remote + def _shell_true(*args, **kwargs): return 0 @staticmethod - def _shell_false(url, remote=None): - _ = url - _ = remote + def _shell_false(*args, **kwargs): return 1 @staticmethod - def _mock_function_true(ref): + def _mock_revparse_commit(ref, dirname): _ = ref return (TestValidRef._shell_true, '97ebc0e0deadc0de') @staticmethod - def _mock_function_false(ref): + def _mock_revparse_commit_false(ref, dirname): _ = ref return (TestValidRef._shell_false, '97ebc0e0deadc0de') @@ -638,10 +626,11 @@ def test_tag_not_tag_branch_commit(self): self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_false + self._repo._git_revparse_commit = self._mock_revparse_commit_false self._repo._tag = 'something' remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name) + received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, + os.getcwd()) self.assertFalse(received) def test_tag_not_tag(self): @@ -650,10 +639,11 @@ def test_tag_not_tag(self): self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_true self._repo._git_lsremote_branch = self._shell_true - self._repo._git_revparse_commit = self._mock_function_false + self._repo._git_revparse_commit = self._mock_revparse_commit_false self._repo._tag = 'tag1' remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name) + received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, + os.getcwd()) self.assertFalse(received) def test_tag_indeterminant(self): @@ -662,10 +652,11 @@ def test_tag_indeterminant(self): self._repo._git_showref_tag = self._shell_true self._repo._git_showref_branch = self._shell_true self._repo._git_lsremote_branch = self._shell_true - self._repo._git_revparse_commit = self._mock_function_true + self._repo._git_revparse_commit = self._mock_revparse_commit self._repo._tag = 'something' remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name) + received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, + os.getcwd()) self.assertFalse(received) def test_tag_is_unique(self): @@ -674,10 +665,11 @@ def test_tag_is_unique(self): self._repo._git_showref_tag = self._shell_true self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_true + self._repo._git_revparse_commit = self._mock_revparse_commit self._repo._tag = 'tag1' remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name) + received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, + os.getcwd()) self.assertTrue(received) def test_tag_is_not_hash(self): @@ -686,10 +678,11 @@ def test_tag_is_not_hash(self): self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_true + self._repo._git_revparse_commit = self._mock_revparse_commit self._repo._tag = '97ebc0e0' remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name) + received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, + os.getcwd()) self.assertFalse(received) def test_hash_is_commit(self): @@ -698,10 +691,11 @@ def test_hash_is_commit(self): self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_true + self._repo._git_revparse_commit = self._mock_revparse_commit self._repo._tag = '97ebc0e0' remote_name = 'origin' - received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name) + received, _ = self._repo._is_unique_tag(self._repo._tag, remote_name, + os.getcwd()) self.assertFalse(received) @@ -746,13 +740,14 @@ def _shell_false(url, remote=None): return 1 @staticmethod - def _mock_function_false(ref): + def _mock_revparse_commit_false(ref, dirname): _ = ref return (TestValidRef._shell_false, '') @staticmethod - def _mock_function_true(ref): + def _mock_revparse_commit_true(ref, dirname): _ = ref + _ = dirname return (TestValidRef._shell_true, '') def test_valid_ref_is_invalid(self): @@ -761,10 +756,12 @@ def test_valid_ref_is_invalid(self): self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_false + self._repo._git_revparse_commit = self._mock_revparse_commit_false self._repo._tag = 'invalid_ref' with self.assertRaises(RuntimeError): - self._repo._check_for_valid_ref(self._repo._tag) + self._repo._check_for_valid_ref(self._repo._tag, + remote_name=None, + dirname=os.getcwd()) def test_valid_tag(self): """Verify a valid tag return true @@ -772,9 +769,11 @@ def test_valid_tag(self): self._repo._git_showref_tag = self._shell_true self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_true + self._repo._git_revparse_commit = self._mock_revparse_commit_true self._repo._tag = 'tag1' - received = self._repo._check_for_valid_ref(self._repo._tag) + received = self._repo._check_for_valid_ref(self._repo._tag, + remote_name=None, + dirname=os.getcwd()) self.assertTrue(received) def test_valid_branch(self): @@ -783,24 +782,28 @@ def test_valid_branch(self): self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_true self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = self._mock_function_true + self._repo._git_revparse_commit = self._mock_revparse_commit_true self._repo._tag = 'tag1' - received = self._repo._check_for_valid_ref(self._repo._tag) + received = self._repo._check_for_valid_ref(self._repo._tag, + remote_name=None, + dirname=os.getcwd()) self.assertTrue(received) def test_valid_hash(self): """Verify a valid hash return true """ - def _mock_revparse_commit(ref): + def _mock_revparse_commit_true(ref, dirname): _ = ref return (0, '56cc0b539426eb26810af9e') self._repo._git_showref_tag = self._shell_false self._repo._git_showref_branch = self._shell_false self._repo._git_lsremote_branch = self._shell_false - self._repo._git_revparse_commit = _mock_revparse_commit + self._repo._git_revparse_commit = _mock_revparse_commit_true self._repo._hash = '56cc0b5394' - received = self._repo._check_for_valid_ref(self._repo._hash) + received = self._repo._check_for_valid_ref(self._repo._hash, + remote_name=None, + dirname=os.getcwd()) self.assertTrue(received) From 782b89469f1488dc00142400c055f40872317c0a Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 6 Mar 2023 10:08:11 -0500 Subject: [PATCH 0721/2067] added vertical profile code to the fates bgc call sequence --- src/main/clm_driver.F90 | 2 +- .../SoilBiogeochemVerticalProfileMod.F90 | 42 +++++++++++++------ 2 files changed, 31 insertions(+), 13 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index d035b8cda3..1c074c7dc1 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -288,7 +288,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call active_layer_inst%alt_calc(filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc, & temperature_inst) - if (use_cn .and. decomp_method /= no_soil_decomp) then + if ((use_cn .or. use_fates) .and. decomp_method /= no_soil_decomp) then call SoilBiogeochemVerticalProfile(bounds_clump , & filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc , & filter_inactive_and_active(nc)%num_soilp, filter_inactive_and_active(nc)%soilp , & diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 index 7209bd8278..1bad47af31 100644 --- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 @@ -193,20 +193,38 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil c = filter_soilc(fc) rootfr_tot = 0._r8 surface_prof_tot = 0._r8 - ! redo column ntegration over active layer for column-native profiles - do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp) - rootfr_tot = rootfr_tot + col_cinput_rootfr(c,j) * dzsoi_decomp(j) - surface_prof_tot = surface_prof_tot + surface_prof(j) * dzsoi_decomp(j) - end do - if ( (altmax_lastyear_indx(c) > 0) .and. (rootfr_tot > 0._r8) .and. (surface_prof_tot > 0._r8) ) then - do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp) - nfixation_prof(c,j) = col_cinput_rootfr(c,j) / rootfr_tot - ndep_prof(c,j) = surface_prof(j)/ surface_prof_tot + if(col%is_fates(c))then + ! For FATES, we just use the e-folding depth for both fixation and deposition + ! partially because the fixation may be free-living depending on FATES-side + ! fixation choices, and partially for simplicity + do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp) + surface_prof_tot = surface_prof_tot + surface_prof(j) * dzsoi_decomp(j) end do + if ( (altmax_lastyear_indx(c) > 0) .and. (surface_prof_tot > 0._r8) ) then + do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp) + nfixation_prof(c,j) = surface_prof(j)/ surface_prof_tot + ndep_prof(c,j) = surface_prof(j)/ surface_prof_tot + end do + else + nfixation_prof(c,1) = 1./dzsoi_decomp(1) + ndep_prof(c,1) = 1./dzsoi_decomp(1) + endif else - nfixation_prof(c,1) = 1./dzsoi_decomp(1) - ndep_prof(c,1) = 1./dzsoi_decomp(1) - endif + ! redo column ntegration over active layer for column-native profiles + do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp) + rootfr_tot = rootfr_tot + col_cinput_rootfr(c,j) * dzsoi_decomp(j) + surface_prof_tot = surface_prof_tot + surface_prof(j) * dzsoi_decomp(j) + end do + if ( (altmax_lastyear_indx(c) > 0) .and. (rootfr_tot > 0._r8) .and. (surface_prof_tot > 0._r8) ) then + do j = 1, min(max(altmax_lastyear_indx(c), 1), nlevdecomp) + nfixation_prof(c,j) = col_cinput_rootfr(c,j) / rootfr_tot + ndep_prof(c,j) = surface_prof(j)/ surface_prof_tot + end do + else + nfixation_prof(c,1) = 1./dzsoi_decomp(1) + ndep_prof(c,1) = 1./dzsoi_decomp(1) + endif + end if end do ! check to make sure integral of all profiles = 1. From 47722043b74214a44bdebf6a6f78f1f4e7844794 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 6 Mar 2023 17:13:36 -0500 Subject: [PATCH 0722/2067] minor changes ot clmbuildnamelist --- bld/CLMBuildNamelist.pm | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 5b77996fb0..071773958d 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -91,11 +91,13 @@ OPTIONS This toggles off the namelist variable: use_cn bgc = Carbon Nitrogen with methane, nitrification, vertical soil C, CENTURY or MIMICS decomposition - This toggles on the namelist variables: + This toggles on the namelist variables: use_cn, use_lch4, use_nitrif_denitrif - fates = FATES/Ecosystem Demography with below ground BGC - This toggles on the namelist variables: - use_fates + fates = FATES/Ecosystem Demography with below ground BGC + CENTURY or MIMICS decomposition + This toggles on the namelist variables: + use_fates. use_lch4 and use_nitrif_denitrif are optional + (Only for CLM4.5/CLM5.0) -[no-]chk_res Also check [do NOT check] to make sure the resolution and land-mask is valid. @@ -757,7 +759,7 @@ sub setup_cmdl_fates_mode { # The following variables may be set by the user and are compatible with use_fates # no need to set defaults, covered in a different routine - my @list = ( "use_lch4" ); + my @list = ( "use_lch4", "use_nitrif_denitrif" ); foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { $nl_flags->{$var} = $nl->get_value($var); From 66375364be49f083161900c383e96780ec133a22 Mon Sep 17 00:00:00 2001 From: ckoven Date: Mon, 6 Mar 2023 22:10:01 -0700 Subject: [PATCH 0723/2067] changed soil moisture initialization logic from if use_fates_hydro to if use_fates --- src/biogeophys/WaterStateType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index f61a7b943d..751f633875 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -14,7 +14,7 @@ module WaterStateType use decompMod , only : bounds_type use decompMod , only : subgrid_level_patch, subgrid_level_column, subgrid_level_gridcell use clm_varctl , only : use_bedrock, iulog - use clm_varctl , only : use_fates_planthydro + use clm_varctl , only : use_fates use clm_varpar , only : nlevgrnd, nlevsoi, nlevurb, nlevmaxurbgrnd, nlevsno use clm_varcon , only : spval use LandunitType , only : lun @@ -348,7 +348,7 @@ subroutine InitCold(this, bounds, & if (j > nbedrock) then this%h2osoi_vol_col(c,j) = 0.0_r8 else - if(use_fates_planthydro) then + if(use_fates) then this%h2osoi_vol_col(c,j) = 0.75_r8*watsat_col(c,j)*ratio else this%h2osoi_vol_col(c,j) = 0.15_r8*ratio From 397eb22678be387eceeed696cd34ea8feca1d21c Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 7 Mar 2023 10:07:28 -0700 Subject: [PATCH 0724/2067] changed name of PRISM PRECIP stream --- cime_config/config_component.xml | 17 ++++++++++------- .../NEON/defaults/user_nl_datm_streams | 4 ++-- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index b5741e5b40..243c866bbd 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -295,13 +295,16 @@ ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD, BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF, BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL, - ABBY.PRECIP,BLAN.PRECIP,CPER.PRECIP,DEJU.PRECIP,GRSM.PRECIP,HEAL.PRECIP,KONA.PRECIP, - LENO.PRECIP,NIWO.PRECIP,ONAQ.PRECIP,PUUM.PRECIP,SERC.PRECIP,SRER.PRECIP,TALL.PRECIP, - TREE.PRECIP,WOOD.PRECIP,BARR.PRECIP,BONA.PRECIP,DCFS.PRECIP,DELA.PRECIP,GUAN.PRECIP, - JERC.PRECIP,KONZ.PRECIP,MLBS.PRECIP,NOGP.PRECIP,ORNL.PRECIP,RMNP.PRECIP,SJER.PRECIP, - STEI.PRECIP,TEAK.PRECIP,UKFS.PRECIP,WREF.PRECIP,BART.PRECIP,CLBJ.PRECIP,DSNY.PRECIP, - HARV.PRECIP,JORN.PRECIP,LAJA.PRECIP,MOAB.PRECIP,OAES.PRECIP,OSBS.PRECIP,SCBI.PRECIP, - SOAP.PRECIP,STER.PRECIP,TOOL.PRECIP,UNDE.PRECIP,YELL.PRECIP, + PRISM_PRECIP.ABBY,PRISM_PRECIP.BLAN,PRISM_PRECIP.CPER,PRISM_PRECIP.DEJU,PRISM_PRECIP.GRSM, + PRISM_PRECIP.HEAL,PRISM_PRECIP.KONA,PRISM_PRECIP.LENO,PRISM_PRECIP.NIWO,PRISM_PRECIP.ONAQ, + PRISM_PRECIP.PUUM,PRISM_PRECIP.SERC,PRISM_PRECIP.SRER,PRISM_PRECIP.TALL,PRISM_PRECIP.TREE, + PRISM_PRECIP.WOOD,PRISM_PRECIP.BARR,PRISM_PRECIP.BONA,PRISM_PRECIP.DCFS,PRISM_PRECIP.DELA, + PRISM_PRECIP.GUAN,PRISM_PRECIP.JERC,PRISM_PRECIP.KONZ,PRISM_PRECIP.MLBS,PRISM_PRECIP.NOGP, + PRISM_PRECIP.ORNL,PRISM_PRECIP.RMNP,PRISM_PRECIP.SJER,PRISM_PRECIP.STEI,PRISM_PRECIP.TEAK, + PRISM_PRECIP.UKFS,PRISM_PRECIP.WREF,PRISM_PRECIP.BART,PRISM_PRECIP.CLBJ,PRISM_PRECIP.DSNY, + PRISM_PRECIP.HARV,PRISM_PRECIP.JORN,PRISM_PRECIP.LAJA,PRISM_PRECIP.MOAB,PRISM_PRECIP.OAES, + PRISM_PRECIP.OSBS,PRISM_PRECIP.SCBI,PRISM_PRECIP.SOAP,PRISM_PRECIP.STER,PRISM_PRECIP.TOOL, + PRISM_PRECIP.UNDE,PRISM_PRECIP.YELL, run_component_ctsm diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams index 636ceb2ad8..78fff234d6 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams @@ -47,10 +47,10 @@ NEON.${NEONSITE}:datavars = \ PSRF Sa_pbot, \ FLDS Faxa_lwdn -NEON.${NEONSITE}.PRECIP:datavars = \ +NEON.PRISM_PRECIP.${NEONSITE}:datavars = \ PRECIP Faxa_precn -NEON.${NEONSITE}.PRECIP:datafiles = \ +NEON.PRISM_PRECIP${NEONSITE}:datafiles = \ /glade/u/home/tking/neon/prism_${NEONSITE}_2018.nc, \ /glade/u/home/tking/neon/prism_${NEONSITE}_2019.nc, \ /glade/u/home/tking/neon/prism_${NEONSITE}_2020.nc, \ From 12e6b116b1b2c9589e7c343f19cea61a348334c0 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 9 Mar 2023 12:05:52 -0500 Subject: [PATCH 0725/2067] Removed various if-clauses that prevented BGC calls and initializations from proceeding with FATES on --- src/biogeochem/CNDriverMod.F90 | 12 ++++---- src/main/clm_driver.F90 | 6 ++-- src/main/clm_initializeMod.F90 | 8 +++-- src/main/clm_instMod.F90 | 7 ++--- src/main/controlMod.F90 | 7 +++-- .../SoilBiogeochemCarbonStateType.F90 | 2 +- .../SoilBiogeochemCompetitionMod.F90 | 8 ++--- .../SoilBiogeochemDecompMod.F90 | 29 ++----------------- .../SoilBiogeochemLittVertTranspMod.F90 | 5 +--- .../SoilBiogeochemNitrifDenitrifMod.F90 | 3 +- .../SoilBiogeochemPotentialMod.F90 | 19 ++---------- .../SoilBiogeochemVerticalProfileMod.F90 | 26 +++++++++-------- 12 files changed, 50 insertions(+), 82 deletions(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index f353469738..d2b9ed9655 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -77,9 +77,10 @@ subroutine CNDriverInit(bounds, NLFilename, cnfire_method) class(fire_method_type) , intent(inout) :: cnfire_method !----------------------------------------------------------------------- call SoilBiogeochemCompetitionInit(bounds) - call CNPhenologyInit(bounds) - call cnfire_method%FireInit(bounds, NLFilename) - + if(use_cn)then + call CNPhenologyInit(bounds) + call cnfire_method%FireInit(bounds, NLFilename) + end if end subroutine CNDriverInit !----------------------------------------------------------------------- @@ -240,9 +241,8 @@ subroutine CNDriverNoLeaching(bounds, ! -------------------------------------------------- ! zero the column-level C and N fluxes ! -------------------------------------------------- - - call t_startf('CNZero') + call t_startf('CNZero') ! COMPILER_BUG(wjs, 2014-11-29, pgi 14.7) Without this, the filter is full of garbage ! in some situations call t_startf('CNZero-soilbgc-cflux') @@ -293,7 +293,7 @@ subroutine CNDriverNoLeaching(bounds, call t_stopf('CNZero-soilbgc-nflux') call t_stopf('CNZero') - + ! -------------------------------------------------- ! Nitrogen Deposition, Fixation and Respiration ! -------------------------------------------------- diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 1c074c7dc1..ce0627df2b 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -204,7 +204,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! ======================================================================== need_glacier_initialization = is_first_step() - + if (need_glacier_initialization) then !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) do nc = 1, nclumps @@ -290,8 +290,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro if ((use_cn .or. use_fates) .and. decomp_method /= no_soil_decomp) then call SoilBiogeochemVerticalProfile(bounds_clump , & - filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc , & - filter_inactive_and_active(nc)%num_soilp, filter_inactive_and_active(nc)%soilp , & + filter_inactive_and_active(nc)%num_bgc_soilc, filter_inactive_and_active(nc)%bgc_soilc , & + filter_inactive_and_active(nc)%num_bgc_vegp, filter_inactive_and_active(nc)%bgc_vegp , & active_layer_inst, soilstate_inst, soilbiogeochem_state_inst) end if diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 7988fbfc7b..1178470b77 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -429,8 +429,11 @@ subroutine initialize2(ni,nj) !$OMP END PARALLEL DO ! Initialize modules (after time-manager initialization in most cases) - if (use_cn) then + if (use_cn .or. use_fates) then call bgc_vegetation_inst%Init2(bounds_proc, NLFilename) + end if + + if (use_cn) then ! NOTE(wjs, 2016-02-23) Maybe the rest of the body of this conditional should also ! be moved into bgc_vegetation_inst%Init2 @@ -622,6 +625,7 @@ subroutine initialize2(ni,nj) !$OMP END PARALLEL DO ! Initialize nitrogen deposition + ! RGK: To-do, enable N deposition in FATES if (use_cn) then call t_startf('init_ndep') if (.not. ndep_from_cpl) then @@ -630,7 +634,7 @@ subroutine initialize2(ni,nj) end if call t_stopf('init_ndep') end if - + ! Initialize active history fields. ! This is only done if not a restart run. If a restart run, then this ! information has already been obtained from the restart data read above. diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 7924c2111e..33faa1e993 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -231,7 +231,6 @@ subroutine clm_instInit(bounds) allocate (h2osno_col(begc:endc)) allocate (snow_depth_col(begc:endc)) - ! snow water do c = begc,endc l = col%landunit(c) @@ -371,7 +370,7 @@ subroutine clm_instInit(bounds) call drydepvel_inst%Init(bounds) - if (decomp_method /= no_soil_decomp) then + if_decomp: if (decomp_method /= no_soil_decomp) then ! Initialize soilbiogeochem_state_inst @@ -423,7 +422,7 @@ subroutine clm_instInit(bounds) call SoilBiogeochemPrecisionControlInit( soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst) - end if ! end of if use_cn + end if if_decomp ! Note - always call Init for bgc_vegetation_inst: some pieces need to be initialized always call bgc_vegetation_inst%Init(bounds, nlfilename, GetBalanceCheckSkipSteps(), params_ncid ) @@ -550,7 +549,7 @@ subroutine clm_instRest(bounds, ncid, flag, writing_finidat_interp_dest_file) call ch4_inst%restart(bounds, ncid, flag=flag) end if - if ( use_cn ) then + if ( use_cn .or. use_fates) then ! Need to do vegetation restart before soil bgc restart to get totvegc_col for purpose ! of resetting soil carbon at exit spinup when no vegetation is growing. call bgc_vegetation_inst%restart(bounds, ncid, flag=flag) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index a763703d6e..4a6929c28e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -535,9 +535,12 @@ subroutine control_init(dtime) end if call soilHydReadNML( NLFilename ) + + if( use_cn .or. use_fates) then + call CNPrecisionControlReadNML( NLFilename ) + end if if ( use_cn ) then call CNFireReadNML( NLFilename ) - call CNPrecisionControlReadNML( NLFilename ) call CNNDynamicsReadNML ( NLFilename ) call CNPhenologyReadNML ( NLFilename ) end if @@ -761,7 +764,7 @@ subroutine control_spmd() ! C and N input vertical profiles call mpi_bcast (surfprof_exp, 1, MPI_REAL8, 0, mpicom, ier) end if - + if ((use_cn.or.use_fates) .and. use_nitrif_denitrif) then call mpi_bcast (no_frozen_nitrif_denitrif, 1, MPI_LOGICAL, 0, mpicom, ier) end if diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 349f70b46f..6c52a5d34f 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -7,7 +7,7 @@ module SoilBiogeochemCarbonStateType use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan use clm_varpar , only : nlevdecomp_full, nlevdecomp, nlevsoi use clm_varcon , only : spval, ispval, dzsoi_decomp, zisoi, zsoi, c3_r2 - use clm_varctl , only : iulog, spinup_state, use_fates + use clm_varctl , only : iulog, spinup_state use landunit_varcon , only : istcrop, istsoil use abortutils , only : endrun use spmdMod , only : masterproc diff --git a/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 b/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 index eec9e00f80..9035b32484 100644 --- a/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 @@ -293,7 +293,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, local_use_fun = use_fun - if (.not. use_nitrif_denitrif) then + if_nitrif: if (.not. use_nitrif_denitrif) then ! init sminn_tot do fc=1,num_soilc @@ -630,8 +630,6 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, sum_no3_demand_scaled(c,j) = (plant_ndemand(c)*nuptake_prof(c,j))*compet_plant_no3 + & (potential_immob_vr(c,j)-actual_immob_nh4_vr(c,j))*compet_decomp_no3 + pot_f_denit_vr(c,j)*compet_denit endif - - if (sum_no3_demand(c,j)*dt < smin_no3_vr(c,j)) then @@ -655,7 +653,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, smin_no3_to_plant_vr(c,j) = smin_no3_vr(c,j)/dt - actual_immob_no3_vr(c,j) - f_denit_vr(c,j) end if endif - + else ! NO3 availability can not satisfy the sum of immobilization, denitrification, and @@ -993,7 +991,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end if end do ! end of column loops - end if !end of if_not_use_nitrif_denitrif + end if if_nitrif !end of if_not_use_nitrif_denitrif end associate diff --git a/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 index a46f999143..77d4a40ed9 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 @@ -11,7 +11,7 @@ module SoilBiogeochemDecompMod use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type use clm_varpar , only : nlevdecomp, ndecomp_cascade_transitions, ndecomp_pools - use clm_varctl , only : use_nitrif_denitrif, use_lch4, use_fates, iulog + use clm_varctl , only : use_nitrif_denitrif, use_lch4, iulog use clm_varcon , only : dzsoi_decomp use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, mimics_decomp, decomp_method, use_soil_matrixcn use SoilBiogeochemStateType , only : soilbiogeochem_state_type @@ -137,7 +137,6 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, ! column loop to calculate actual immobilization and decomp rates, following ! resolution of plant/heterotroph competition for mineral N - if ( .not. use_fates) then ! calculate c:n ratios of applicable pools do l = 1, ndecomp_pools if ( floating_cn_ratio_decomp_pools(l) ) then @@ -221,25 +220,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, end do end do end do - else - do k = 1, ndecomp_cascade_transitions - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) - ! - decomp_cascade_hr_vr(c,j,k) = rf_decomp_cascade(c,j,k) * p_decomp_cpool_loss(c,j,k) - decomp_cascade_ctransfer_vr(c,j,k) = (1._r8 - rf_decomp_cascade(c,j,k)) * p_decomp_cpool_loss(c,j,k) - if (decomp_method == mimics_decomp) then - decomp_cascade_hr_vr(c,j,k) = min( & - p_decomp_cpool_loss(c,j,k), & - decomp_cascade_hr_vr(c,j,k) + c_overflow_vr(c,j,k)) - decomp_cascade_ctransfer_vr(c,j,k) = max(0.0_r8, p_decomp_cpool_loss(c,j,k) - decomp_cascade_hr_vr(c,j,k)) - end if - ! - end do - end do - end do - end if + + if (use_lch4) then ! Calculate total fraction of potential HR, for methane code @@ -279,13 +261,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, do fc = 1,num_soilc c = filter_soilc(fc) do j = 1,nlevdecomp - if(.not.use_fates)then net_nmin(c) = net_nmin(c) + net_nmin_vr(c,j) * dzsoi_decomp(j) gross_nmin(c) = gross_nmin(c) + gross_nmin_vr(c,j) * dzsoi_decomp(j) - ! else - ! net_nmin(c) = 0.0_r8 - ! gross_nmin(c) = 0.0_r8 - endif end do end do diff --git a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 index 616f995bd7..58e05fb3e1 100644 --- a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 @@ -182,9 +182,6 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & if ( use_c14 ) then ntype = ntype+1 endif - if ( use_fates ) then - ntype = 1 - endif spinup_term = 1._r8 epsilon = 1.e-30 @@ -247,7 +244,7 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & source => soilbiogeochem_carbonflux_inst%decomp_cpools_sourcesink_col trcr_tendency_ptr => soilbiogeochem_carbonflux_inst%decomp_cpools_transport_tendency_col case (2) ! N - if (use_cn ) then + if (use_cn .or. use_fates) then conc_ptr => soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col source => soilbiogeochem_nitrogenflux_inst%decomp_npools_sourcesink_col trcr_tendency_ptr => soilbiogeochem_nitrogenflux_inst%decomp_npools_transport_tendency_col diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 3993439a1c..f735c14854 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -12,7 +12,7 @@ module SoilBiogeochemNitrifDenitrifMod use clm_varpar , only : nlevdecomp use clm_varcon , only : rpi, grav use clm_varcon , only : d_con_g, d_con_w, secspday - use clm_varctl , only : use_lch4, use_fates + use clm_varctl , only : use_lch4 use abortutils , only : endrun use decompMod , only : bounds_type use SoilStatetype , only : soilstate_type @@ -74,6 +74,7 @@ subroutine readParams ( ncid ) ! ! read in constants ! + tString='surface_tension_water' call ncd_io(trim(tString),tempr, 'read', ncid, readvar=readv) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) diff --git a/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 b/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 index da46e178b7..beda04bbec 100644 --- a/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 @@ -137,8 +137,8 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & decomp_k => soilbiogeochem_carbonflux_inst%decomp_k_col , & ! Input: [real(r8) (:,:,:) ] decomposition rate coefficient (1./sec) phr_vr => soilbiogeochem_carbonflux_inst%phr_vr_col & ! Output: [real(r8) (:,:) ] potential HR (gC/m3/s) ) - - if ( .not. use_fates ) then + + ! set initial values for potential C and N fluxes p_decomp_cpool_loss(begc:endc, :, :) = 0._r8 pmnf_decomp_cascade(begc:endc, :, :) = 0._r8 @@ -320,20 +320,6 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & potential_immob_vr(c,j) = immob(c,j) end do end do - else ! use_fates - ! As a first step we are making this a C-only model, so no N downregulation of fluxes. - do k = 1, ndecomp_cascade_transitions - do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) - ! - p_decomp_cpool_loss(c,j,k) = decomp_cpools_vr(c,j,cascade_donor_pool(k)) & - * decomp_k(c,j,cascade_donor_pool(k)) * pathfrac_decomp_cascade(c,j,k) - ! - end do - end do - end do - end if ! Add up potential hr for methane calculations do j = 1,nlevdecomp @@ -351,6 +337,7 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & end do end do + end associate end subroutine SoilBiogeochemPotential diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 index 1bad47af31..772c2db82e 100644 --- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 @@ -131,7 +131,6 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil do j = 1, nlevdecomp cinput_rootfr(p,j) = crootfr(p,j) / dzsoi_decomp(j) end do - else cinput_rootfr(p,1) = 0. endif @@ -168,7 +167,6 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil leaf_prof(p,1) = 1./dzsoi_decomp(1) stem_prof(p,1) = 1./dzsoi_decomp(1) endif - end do !! aggregate root profile to column @@ -176,17 +174,21 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil ! cinput_rootfr(bounds%begp:bounds%endp, :), & ! col_cinput_rootfr(bounds%begc:bounds%endc, :), & ! 'unity') - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - do j = 1,nlevdecomp - col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) - end do - end if + if(num_soilp>0)then + do pi = 1,maxsoil_patches + do fc = 1,num_soilc + c = filter_soilc(fc) + if(.not.col%is_fates(c))then + if (pi <= col%npatches(c)) then + p = col%patchi(c) + pi - 1 + do j = 1,nlevdecomp + col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) + end do + end if + end if + end do end do - end do + end if ! repeat for column-native profiles: Ndep and Nfix do fc = 1,num_soilc From 4674b9069c23f2620f8ab3fc5ab822def9e5794b Mon Sep 17 00:00:00 2001 From: will wieder Date: Thu, 9 Mar 2023 10:23:46 -0700 Subject: [PATCH 0726/2067] Update README.md updates to SE list --- README.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/README.md b/README.md index 298e5adc04..9de22e3663 100644 --- a/README.md +++ b/README.md @@ -45,6 +45,9 @@ Software engineering team: - [Bill Sacks](https://github.com/billsacks) - [Sam Levis](https://github.com/slevisconsulting) - [Adrianna Foster](https://github.com/adrifoster) +- [Sam Rabin](https://github.com/samsrabin) +- [Greg Lemieux](https://github.com/glemieux) +- [Ryan Knox](https://github.com/rgknox) Science team: - [Dave Lawrence](https://github.com/dlawrenncar) From 55392895ff67f734db393669c3f905d6242e2582 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 10 Mar 2023 12:34:52 -0500 Subject: [PATCH 0727/2067] FATES bgc work. Add use_fates_bgc, cleaned out some use_fates filtering, and added N deposition with FATES --- bld/CLMBuildNamelist.pm | 24 +++-- bld/namelist_files/namelist_defaults_ctsm.xml | 90 +++++++++---------- src/biogeochem/CNBalanceCheckMod.F90 | 4 +- src/biogeochem/CNCStateUpdate1Mod.F90 | 36 ++++---- src/biogeochem/CNDriverMod.F90 | 4 +- src/biogeochem/CNVegetationFacade.F90 | 61 +++++++------ src/biogeochem/ch4Mod.F90 | 8 +- src/main/clm_driver.F90 | 26 +++--- src/main/clm_initializeMod.F90 | 8 +- src/main/clm_instMod.F90 | 5 +- src/main/clm_varctl.F90 | 40 +++++---- src/main/controlMod.F90 | 18 +++- .../SoilBiogeochemDecompCascadeConType.F90 | 10 +-- .../SoilBiogeochemLittVertTranspMod.F90 | 10 +-- .../SoilBiogeochemPrecisionControlMod.F90 | 13 ++- .../SoilBiogeochemStateType.F90 | 50 ++++++----- 16 files changed, 214 insertions(+), 193 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 071773958d..88cc27e614 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3395,23 +3395,21 @@ sub setup_logic_nitrogen_deposition { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; # - # Nitrogen deposition for bgc=CN + # Nitrogen deposition for bgc=CN or fates # - if ( $nl_flags->{'bgc_mode'} =~/bgc/ ) { + if ( ($nl_flags->{'bgc_mode'} =~/bgc/) or ($nl_flags->{'bgc_mode'} =~/fates/) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'}, + 'hgrid'=>$nl_flags->{'res'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'}, + 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); # Set align year, if first and last years are different if ( $nl->get_value('stream_year_first_ndep') != $nl->get_value('stream_year_last_ndep') ) { @@ -3419,12 +3417,12 @@ sub setup_logic_nitrogen_deposition { 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { # Also check at f19 resolution add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); # If not found report an error if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { @@ -3436,12 +3434,12 @@ sub setup_logic_nitrogen_deposition { } if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { # Also check at f19 resolution add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ndep', 'phys'=>$nl_flags->{'phys'}, - 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); # If not found report an error if ( ! defined($nl->get_value('stream_meshfile_ndep') ) ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ae5bd97937..9a31995c4f 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1435,72 +1435,72 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc -2015 -2101 -2015 +2015 +2101 +2015 -2015 -2101 -2015 +2015 +2101 +2015 -2015 -2101 -2015 +2015 +2101 +2015 -2018 -2018 +2018 +2018 -2010 -2010 +2010 +2010 -2000 -2000 +2000 +2000 -1850 -1850 +1850 +1850 -2000 -2000 +2000 +2000 -2000 -2000 +2000 +2000 -2000 -2000 +2000 +2000 -lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc -lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc -lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc share/meshes/fv1.9x2.5_141008_ESMFmesh_c20191001.nc share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc cycle @@ -1512,14 +1512,14 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts cycle NDEP_month -bilinear +bilinear -nn -nn -nn -nn -nn -nn +nn +nn +nn +nn +nn +nn diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index a68410ddbe..a6a11d51b6 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -668,7 +668,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, msg=errMsg(sourcefile, __LINE__)) end if - if(.not.use_fates)then + if_notfates: if(.not.use_fates)then ! Repeat error check at the gridcell level call c2g( bounds = bounds, & @@ -743,7 +743,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & write(iulog,*) 'product_loss_grc =', product_loss_grc(g) * dt call endrun(subgrid_index=g, subgrid_level=subgrid_level_gridcell, msg=errMsg(sourcefile, __LINE__)) end if - end if + end if if_notfates end associate diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 3b210506b1..ba006b81a2 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -18,12 +18,12 @@ module CNCStateUpdate1Mod use CNVegCarbonStateType , only : cnveg_carbonstate_type use CNVegCarbonFluxType , only : cnveg_carbonflux_type use CropType , only : crop_type - use CropReprPoolsMod , only : nrepr, repr_grain_min, repr_grain_max, repr_structure_min, repr_structure_max + use CropReprPoolsMod , only : nrepr, repr_grain_min, repr_grain_max + use CropReprPoolsMod , only : repr_structure_min, repr_structure_max use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con, use_soil_matrixcn use SoilBiogeochemCarbonFluxType , only : soilbiogeochem_carbonflux_type use SoilBiogeochemCarbonStateType , only : soilbiogeochem_carbonstate_type use PatchType , only : patch - use clm_varctl , only : use_fates, use_cn, iulog, use_fates_sp use CNSharedParamsMod , only : use_matrixcn use CLMFatesInterfaceMod , only : hlm_fates_interface_type use ColumnType , only : col @@ -46,6 +46,7 @@ subroutine CStateUpdateDynPatch(bounds, num_soilc_with_inactive, filter_soilc_wi ! ! !DESCRIPTION: ! Update carbon states based on fluxes from dyn_cnbal_patch + ! This routine is not called with FATES active. ! ! !ARGUMENTS: type(bounds_type), intent(in) :: bounds @@ -74,26 +75,23 @@ subroutine CStateUpdateDynPatch(bounds, num_soilc_with_inactive, filter_soilc_wi dt = get_step_size_real() - if (.not. use_fates) then - do j = 1,nlevdecomp - do fc = 1, num_soilc_with_inactive - c = filter_soilc_with_inactive(fc) - do i = i_litr_min, i_litr_max - cs_soil%decomp_cpools_vr_col(c,j,i) = & - cs_soil%decomp_cpools_vr_col(c,j,i) + & - cf_veg%dwt_frootc_to_litr_c_col(c,j,i) * dt - end do - cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + & - ( cf_veg%dwt_livecrootc_to_cwdc_col(c,j) + cf_veg%dwt_deadcrootc_to_cwdc_col(c,j) ) * dt + do j = 1,nlevdecomp + do fc = 1, num_soilc_with_inactive + c = filter_soilc_with_inactive(fc) + do i = i_litr_min, i_litr_max + cs_soil%decomp_cpools_vr_col(c,j,i) = & + cs_soil%decomp_cpools_vr_col(c,j,i) + & + cf_veg%dwt_frootc_to_litr_c_col(c,j,i) * dt end do + cs_soil%decomp_cpools_vr_col(c,j,i_cwd) = cs_soil%decomp_cpools_vr_col(c,j,i_cwd) + & + ( cf_veg%dwt_livecrootc_to_cwdc_col(c,j) + cf_veg%dwt_deadcrootc_to_cwdc_col(c,j) ) * dt end do + end do - do g = bounds%begg, bounds%endg - cs_veg%seedc_grc(g) = cs_veg%seedc_grc(g) - cf_veg%dwt_seedc_to_leaf_grc(g) * dt - cs_veg%seedc_grc(g) = cs_veg%seedc_grc(g) - cf_veg%dwt_seedc_to_deadstem_grc(g) * dt - end do - - end if + do g = bounds%begg, bounds%endg + cs_veg%seedc_grc(g) = cs_veg%seedc_grc(g) - cf_veg%dwt_seedc_to_leaf_grc(g) * dt + cs_veg%seedc_grc(g) = cs_veg%seedc_grc(g) - cf_veg%dwt_seedc_to_deadstem_grc(g) * dt + end do end associate diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index d2b9ed9655..1e5b035f8d 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -6,7 +6,7 @@ module CNDriverMod ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_varctl , only : use_c13, use_c14, use_fates, use_dynroot + use clm_varctl , only : use_c13, use_c14, use_fates_bgc, use_dynroot use dynSubgridControlMod , only : get_do_harvest use decompMod , only : bounds_type use perf_mod , only : t_startf, t_stopf @@ -819,7 +819,7 @@ subroutine CNDriverNoLeaching(bounds, if (use_c14) call c14_products_inst%SetValues(bounds,0._r8) call n_products_inst%SetValues(bounds,0._r8) - if(use_fates) then + if(use_fates_bgc) then call clm_fates%wrap_WoodProducts(bounds, num_soilc, filter_soilc, c_products_inst, n_products_inst) end if diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 42d91e9c3d..72082a579b 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -44,7 +44,7 @@ module CNVegetationFacade use shr_log_mod , only : errMsg => shr_log_errMsg use perf_mod , only : t_startf, t_stopf use decompMod , only : bounds_type - use clm_varctl , only : iulog, use_cn, use_cndv, use_c13, use_c14 + use clm_varctl , only : iulog, use_cn, use_cndv, use_c13, use_c14, use_fates_bgc use abortutils , only : endrun use spmdMod , only : masterproc use clm_time_manager , only : get_curr_date, get_ref_date @@ -261,18 +261,20 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) call this%cnveg_nitrogenflux_inst%Init(bounds) end if + + if (use_cn .or. use_fates_bgc) then + call this%c_products_inst%Init(bounds, species_non_isotope_type('C')) + if (use_c13) then + call this%c13_products_inst%Init(bounds, species_isotope_type('C', '13')) + end if + if (use_c14) then + call this%c14_products_inst%Init(bounds, species_isotope_type('C', '14')) + end if + call this%n_products_inst%Init(bounds, species_non_isotope_type('N')) - call this%c_products_inst%Init(bounds, species_non_isotope_type('C')) - if (use_c13) then - call this%c13_products_inst%Init(bounds, species_isotope_type('C', '13')) + call this%cn_balance_inst%Init(bounds) end if - if (use_c14) then - call this%c14_products_inst%Init(bounds, species_isotope_type('C', '14')) - end if - call this%n_products_inst%Init(bounds, species_non_isotope_type('N')) - - call this%cn_balance_inst%Init(bounds) - + if(use_cn)then ! Initialize the memory for the dgvs_inst data structure regardless of whether ! use_cndv is true so that it can be used in associate statements (nag compiler @@ -506,20 +508,22 @@ subroutine Restart(this, bounds, ncid, flag) filter_reseed_patch=reseed_patch, num_reseed_patch=num_reseed_patch) end if - - call this%c_products_inst%restart(bounds, ncid, flag) - if (use_c13) then - call this%c13_products_inst%restart(bounds, ncid, flag, & - template_for_missing_fields = this%c_products_inst, & - template_multiplier = c3_r2) - end if - if (use_c14) then - call this%c14_products_inst%restart(bounds, ncid, flag, & - template_for_missing_fields = this%c_products_inst, & - template_multiplier = c14ratio) + + if (use_cn .or. use_fates_bgc) then + call this%c_products_inst%restart(bounds, ncid, flag) + if (use_c13) then + call this%c13_products_inst%restart(bounds, ncid, flag, & + template_for_missing_fields = this%c_products_inst, & + template_multiplier = c3_r2) + end if + if (use_c14) then + call this%c14_products_inst%restart(bounds, ncid, flag, & + template_for_missing_fields = this%c_products_inst, & + template_multiplier = c14ratio) + end if + call this%n_products_inst%restart(bounds, ncid, flag) end if - call this%n_products_inst%restart(bounds, ncid, flag) - + if (use_cndv) then call this%dgvs_inst%Restart(bounds, ncid, flag=flag) end if @@ -908,7 +912,8 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & ! !DESCRIPTION: ! Do the main science for biogeochemistry that needs to be done before hydrology-drainage ! - ! Can be called for either use_cn or use_fates. Will skip most vegetation patch calls for the latter + ! Can be called for either use_cn or use_fates_bgc. + ! Will skip most vegetation patch calls for the latter ! ! !USES: @@ -1019,7 +1024,7 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! !DESCRIPTION: ! Do the main science for CN vegetation that needs to be done after hydrology-drainage ! - ! Should only be called if use_cn is true + ! Should only be called if use_cn is true or use_fates_bgc is true ! ! !USES: ! @@ -1141,14 +1146,12 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenflux_inst, & soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst, & atm2lnd_inst, clm_fates) - - ! ! !DESCRIPTION: ! Check the carbon and nitrogen balance ! - ! Should only be called if use_cn is true + ! Should only be called if use_cn is true or use_fates_bgc is true ! ! !USES: use clm_time_manager , only : get_nstep_since_startup_or_lastDA_restart_or_pause diff --git a/src/biogeochem/ch4Mod.F90 b/src/biogeochem/ch4Mod.F90 index afb8af351b..f199e7913f 100644 --- a/src/biogeochem/ch4Mod.F90 +++ b/src/biogeochem/ch4Mod.F90 @@ -17,7 +17,7 @@ module ch4Mod use clm_varcon , only : catomw, s_con, d_con_w, d_con_g, c_h_inv, kh_theta, kh_tbase use landunit_varcon , only : istsoil, istcrop, istdlak use clm_time_manager , only : get_step_size_real, get_nstep - use clm_varctl , only : iulog, use_cn, use_nitrif_denitrif, use_lch4, use_cn, use_fates + use clm_varctl , only : iulog, use_cn, use_nitrif_denitrif, use_lch4, use_fates_bgc use abortutils , only : endrun use decompMod , only : bounds_type, subgrid_level_gridcell, subgrid_level_column use atm2lndType , only : atm2lnd_type @@ -2521,7 +2521,7 @@ subroutine ch4_prod (bounds, num_methc, filter_methc, num_methp, & end if end do - if(use_fates) then + if(use_fates_bgc) then nc = bounds%clump_index do s = 1,clm_fates%fates(nc)%nsites c = clm_fates%f2hmap(nc)%fcolumn(s) @@ -2544,7 +2544,7 @@ subroutine ch4_prod (bounds, num_methc, filter_methc, num_methp, & if (.not. lake) then - if (use_cn .or. use_fates) then + if (use_cn .or. use_fates_bgc) then ! Use soil heterotrophic respiration (based on Wania) base_decomp = (somhr(c)+lithr(c)) / catomw ! Convert from gC to molC @@ -2567,7 +2567,7 @@ subroutine ch4_prod (bounds, num_methc, filter_methc, num_methp, & else call endrun(msg=' ERROR: No source for decomp rate in CH4Prod.'//& ' CH4 model currently requires CN or FATES.'//errMsg(sourcefile, __LINE__)) - end if ! use_cn + end if ! use_cn or use_fates_bgc ! For sensitivity studies base_decomp = base_decomp * cnscalefactor diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index ce0627df2b..e54535c09e 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -9,7 +9,7 @@ module clm_driver ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_varctl , only : iulog, use_fates, use_fates_sp + use clm_varctl , only : iulog, use_fates, use_fates_sp, use_fates_bgc use clm_varctl , only : use_cn, use_lch4, use_noio, use_c13, use_c14 use CNSharedParamsMod , only : use_matrixcn use clm_varctl , only : use_crop, irrigate, ndep_from_cpl @@ -288,7 +288,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call active_layer_inst%alt_calc(filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc, & temperature_inst) - if ((use_cn .or. use_fates) .and. decomp_method /= no_soil_decomp) then + if ((use_cn .or. use_fates_bgc) .and. decomp_method /= no_soil_decomp) then call SoilBiogeochemVerticalProfile(bounds_clump , & filter_inactive_and_active(nc)%num_bgc_soilc, filter_inactive_and_active(nc)%bgc_soilc , & filter_inactive_and_active(nc)%num_bgc_vegp, filter_inactive_and_active(nc)%bgc_vegp , & @@ -324,7 +324,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call get_clump_bounds(nc, bounds_clump) call t_startf('begcnbal_grc') - if (use_cn .or. use_fates) then + if (use_cn .or. use_fates_bgc) then ! Initialize gridcell-level balance check call bgc_vegetation_inst%InitGridcellBalance(bounds_clump, & filter(nc)%num_allc, filter(nc)%allc, & @@ -414,7 +414,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_stopf('begwbal') call t_startf('begcnbal_col') - if (use_cn .or. use_fates) then + if (use_cn .or. use_fates_bgc) then ! Initialize column-level balance check call bgc_vegetation_inst%InitColumnBalance(bounds_clump, & filter(nc)%num_allc, filter(nc)%allc, & @@ -443,15 +443,18 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! re-written to go inside. ! ============================================================================ - if (use_cn) then - call t_startf('bgc_interp') + if (use_cn .or. use_fates_bgc) then if (.not. ndep_from_cpl) then call ndep_interp(bounds_proc, atm2lnd_inst) end if + end if + + if(use_cn) then + call t_startf('bgc_interp') call bgc_vegetation_inst%InterpFileInputs(bounds_proc) call t_stopf('bgc_interp') - ! fates_spitfire_mode is assigned an integer value in the namelist - ! see bld/namelist_files/namelist_definition_clm4_5.xml for details + ! fates_spitfire_mode is assigned an integer value in the namelist + ! see bld/namelist_files/namelist_definition_clm4_5.xml for details else if (fates_spitfire_mode > scalar_lightning) then call clm_fates%InterpFileInputs(bounds_proc) end if @@ -999,7 +1002,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Filter bgc_soilc operates on all non-sp soil columns ! Filter bgc_vegp operates on all non-fates, non-sp patches (use_cn) on soil - if(use_cn .or. use_fates)then + if(use_cn .or. use_fates_bgc)then call t_startf('ecosysdyn') call bgc_vegetation_inst%EcosystemDynamicsPreDrainage(bounds_clump, & filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & @@ -1077,7 +1080,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_stopf('hydro2_drainage') - if (use_cn .or. use_fates) then + if (use_cn .or. use_fates_bgc) then call t_startf('EcosysDynPostDrainage') call bgc_vegetation_inst%EcosystemDynamicsPostDrainage(bounds_clump, & filter(nc)%num_allc, filter(nc)%allc, & @@ -1145,7 +1148,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Check the carbon and nitrogen balance ! ============================================================================ - if(use_cn .or. use_fates)then + if(use_cn .or. use_fates_bgc)then call t_startf('cnbalchk') call bgc_vegetation_inst%BalanceCheck( & bounds_clump, filter(nc)%num_bgc_soilc, filter(nc)%bgc_soilc, & @@ -1375,7 +1378,6 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Update history buffer ! ============================================================================ - call t_startf('hbuf') call hist_update_hbuf(bounds_proc) call t_stopf('hbuf') diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 1178470b77..98e6ba006e 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -10,10 +10,11 @@ module clm_initializeMod use spmdMod , only : masterproc, mpicom use decompMod , only : bounds_type, get_proc_bounds, get_proc_clumps, get_clump_bounds use abortutils , only : endrun - use clm_varctl , only : nsrest, nsrStartup, nsrContinue, nsrBranch, use_fates_sp + use clm_varctl , only : nsrest, nsrStartup, nsrContinue, nsrBranch + use clm_varctl , only : use_fates_sp, use_fates_bgc, use_fates use clm_varctl , only : is_cold_start use clm_varctl , only : iulog - use clm_varctl , only : use_lch4, use_cn, use_cndv, use_c13, use_c14, use_fates + use clm_varctl , only : use_lch4, use_cn, use_cndv, use_c13, use_c14 use clm_varctl , only : use_soil_moisture_streams use clm_instur , only : wt_lunit, urban_valid, wt_nat_patch, wt_cft, fert_cft use clm_instur , only : irrig_method, wt_glc_mec, topo_glc_mec, haslake, pct_urban_max @@ -625,8 +626,7 @@ subroutine initialize2(ni,nj) !$OMP END PARALLEL DO ! Initialize nitrogen deposition - ! RGK: To-do, enable N deposition in FATES - if (use_cn) then + if (use_cn .or. use_fates_bgc) then call t_startf('init_ndep') if (.not. ndep_from_cpl) then call ndep_init(bounds_proc, NLFilename) diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 33faa1e993..be75edc8d1 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -8,7 +8,7 @@ module clm_instMod use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type use clm_varpar , only : ndecomp_pools, nlevdecomp_full - use clm_varctl , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates + use clm_varctl , only : use_cn, use_c13, use_c14, use_lch4, use_cndv, use_fates, use_fates_bgc use clm_varctl , only : iulog use clm_varctl , only : use_crop, snow_cover_fraction_method, paramfile use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, no_soil_decomp, century_decomp, decomp_method @@ -425,6 +425,7 @@ subroutine clm_instInit(bounds) end if if_decomp ! Note - always call Init for bgc_vegetation_inst: some pieces need to be initialized always + ! Even for a FATES simulation, we call this to initialize product pools call bgc_vegetation_inst%Init(bounds, nlfilename, GetBalanceCheckSkipSteps(), params_ncid ) if (use_cn .or. use_fates) then @@ -549,7 +550,7 @@ subroutine clm_instRest(bounds, ncid, flag, writing_finidat_interp_dest_file) call ch4_inst%restart(bounds, ncid, flag=flag) end if - if ( use_cn .or. use_fates) then + if ( use_cn .or. use_fates_bgc) then ! Need to do vegetation restart before soil bgc restart to get totvegc_col for purpose ! of resetting soil carbon at exit spinup when no vegetation is growing. call bgc_vegetation_inst%restart(bounds, ncid, flag=flag) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 9be9af2f73..f827c4836c 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -249,27 +249,33 @@ module clm_varctl ! FATES switches !---------------------------------------------------------- - logical, public :: use_fates = .false. ! true => use fates + logical, public :: use_fates = .false. ! true => use fates ! These are INTERNAL to the FATES module - integer, public :: fates_parteh_mode = -9 ! 1 => carbon only - ! 2 => C+N+P (not enabled yet) - ! no others enabled + + integer, public :: fates_parteh_mode = -9 ! 1 => carbon only + ! 2 => C+N+P (not enabled yet) + ! no others enabled integer, public :: fates_spitfire_mode = 0 - ! 0 for no fire; 1 for constant ignitions; > 1 for external data (lightning and/or anthropogenic ignitions) - ! see bld/namelist_files/namelist_definition_clm4_5.xml for details - logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage module - logical, public :: use_fates_logging = .false. ! true => turn on logging module - logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro + ! 0 for no fire; 1 for constant ignitions; + ! > 1 for external data (lightning and/or anthropogenic ignitions) + ! see bld/namelist_files/namelist_definition_clm4_5.xml for details + logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage module + logical, public :: use_fates_logging = .false. ! true => turn on logging module + logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro logical, public :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking - logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure - logical, public :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology - logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory - logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode - logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode - logical, public :: use_fates_sp = .false. ! true => use FATES satellite phenology mode - character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control - + logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure + logical, public :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology + logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory + logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode + logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode + character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control + + ! FATES SP AND FATES BGC are MUTUTALLY EXCLUSIVE, THEY CAN'T BOTH BE ON + ! BUT... THEY CAN BOTH BE OFF (IF FATES IS OFF) + logical, public :: use_fates_sp = .false. ! true => use FATES satellite phenology mode + logical, public :: use_fates_bgc = .false. ! true => use FATES along with CLM soil biogeochemistry + !---------------------------------------------------------- ! LUNA switches !---------------------------------------------------------- diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 4a6929c28e..a0af5b2862 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -232,8 +232,8 @@ subroutine control_init(dtime) fates_parteh_mode, & use_fates_tree_damage - ! Ozone vegetation stress method - namelist / clm_inparam / o3_veg_stress_method + ! Ozone vegetation stress method + namelist / clm_inparam / o3_veg_stress_method ! CLM 5.0 nitrogen flags namelist /clm_inparm/ use_flexibleCN, use_luna @@ -433,6 +433,12 @@ subroutine control_init(dtime) ! Check compatibility with the FATES model if ( use_fates ) then + if(use_fates_sp) then + use_fates_bgc = .false. + else + use_fates_bgc = .true. + end if + if (fates_parteh_mode == 1 .and. suplnitro == suplnNon)then write(iulog,*) ' When FATES with fates_parteh_mode == 1 (ie carbon only mode),' write(iulog,*) ' you must have supplemental nitrogen turned on, there will be' @@ -467,6 +473,13 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if + else + + ! These do default to false anyway, but this emphasizes they + ! are false when fates is false + use_fates_sp = .false. + use_fates_bgc = .false. + end if ! If nfix_timeconst is equal to the junk default value, then it was not specified @@ -727,6 +740,7 @@ subroutine control_spmd() call mpi_bcast (use_fates_fixed_biogeog, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90 index 4f6cf04eaf..0474ab9a63 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeConType.F90 @@ -63,7 +63,7 @@ module SoilBiogeochemDecompCascadeConType !------------------------------------------------------------------------ subroutine decomp_cascade_par_init( NLFilename ) - use clm_varctl , only : use_fates, use_cn, use_fates_sp + use clm_varctl , only : use_cn, use_fates_bgc use clm_varpar , only : ndecomp_pools_max use spmdMod , only : masterproc, mpicom use clm_nlUtilsMod , only : find_nlgroup_name @@ -110,9 +110,9 @@ subroutine decomp_cascade_par_init( NLFilename ) if ( decomp_method == no_soil_decomp )then call endrun('When running with BGC an active soil_decomp_method must be used') end if - else if ( use_fates ) then - if ( .not. use_fates_sp .and. (decomp_method == no_soil_decomp) )then - call endrun('When running with FATES and without FATES-SP an active soil_decomp_method must be used') + else if ( use_fates_bgc ) then + if ( decomp_method == no_soil_decomp )then + call endrun('When running with FATES and without FATES-SP, an active soil_decomp_method must be used') end if else if ( decomp_method /= no_soil_decomp )then @@ -128,7 +128,7 @@ subroutine decomp_cascade_par_init( NLFilename ) ! ndecomp_pools would get the value of i_pas_som or i_cwd and ! ndecomp_cascade_transitions would get the value of i_s3s1 or i_cwdl3 ! depending on how use_fates is set. - if ( use_fates ) then + if ( use_fates_bgc ) then if (decomp_method == century_decomp) then ndecomp_pools = 6 ndecomp_cascade_transitions = 8 diff --git a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 index 58e05fb3e1..136438cf37 100644 --- a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 @@ -5,7 +5,7 @@ module SoilBiogeochemLittVertTranspMod ! use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog, use_c13, use_c14, spinup_state, use_fates, use_cn + use clm_varctl , only : iulog, use_c13, use_c14, spinup_state use clm_varcon , only : secspday use decompMod , only : bounds_type use abortutils , only : endrun @@ -244,11 +244,9 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & source => soilbiogeochem_carbonflux_inst%decomp_cpools_sourcesink_col trcr_tendency_ptr => soilbiogeochem_carbonflux_inst%decomp_cpools_transport_tendency_col case (2) ! N - if (use_cn .or. use_fates) then - conc_ptr => soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col - source => soilbiogeochem_nitrogenflux_inst%decomp_npools_sourcesink_col - trcr_tendency_ptr => soilbiogeochem_nitrogenflux_inst%decomp_npools_transport_tendency_col - endif + conc_ptr => soilbiogeochem_nitrogenstate_inst%decomp_npools_vr_col + source => soilbiogeochem_nitrogenflux_inst%decomp_npools_sourcesink_col + trcr_tendency_ptr => soilbiogeochem_nitrogenflux_inst%decomp_npools_transport_tendency_col case (3) if ( use_c13 ) then ! C13 diff --git a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 index 91c70fcf5e..cabc57990e 100644 --- a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 @@ -71,7 +71,6 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & ! ! !USES: use clm_varctl , only : iulog, use_c13, use_c14, use_nitrif_denitrif - use clm_varctl , only : use_cn, use_fates use clm_varpar , only : nlevdecomp use CNSharedParamsMod, only: use_fun ! @@ -126,13 +125,12 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & do k = 1, ndecomp_pools if (abs(cs%decomp_cpools_vr_col(c,j,k)) < ccrit) then + cc = cc + cs%decomp_cpools_vr_col(c,j,k) cs%decomp_cpools_vr_col(c,j,k) = 0._r8 - if (use_cn .or. use_fates) then - cn = cn + ns%decomp_npools_vr_col(c,j,k) - ns%decomp_npools_vr_col(c,j,k) = 0._r8 - endif + cn = cn + ns%decomp_npools_vr_col(c,j,k) + ns%decomp_npools_vr_col(c,j,k) = 0._r8 if ( use_c13 ) then cc13 = cc13 + c13cs%decomp_cpools_vr_col(c,j,k) @@ -151,9 +149,8 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & cs%ctrunc_vr_col(c,j) = cs%ctrunc_vr_col(c,j) + cc - if (use_cn .or. use_fates) then - ns%ntrunc_vr_col(c,j) = ns%ntrunc_vr_col(c,j) + cn - endif + ns%ntrunc_vr_col(c,j) = ns%ntrunc_vr_col(c,j) + cn + if ( use_c13 ) then c13cs%ctrunc_vr_col(c,j) = c13cs%ctrunc_vr_col(c,j) + cc13 endif diff --git a/src/soilbiogeochem/SoilBiogeochemStateType.F90 b/src/soilbiogeochem/SoilBiogeochemStateType.F90 index 86232160f7..69055aec9b 100644 --- a/src/soilbiogeochem/SoilBiogeochemStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemStateType.F90 @@ -11,7 +11,7 @@ module SoilBiogeochemStateType use clm_varcon , only : spval, ispval, c14ratio, grlnd use landunit_varcon, only : istsoil, istcrop use clm_varpar , only : nlevsno, nlevgrnd, nlevlak - use clm_varctl , only : use_cn + use clm_varctl , only : use_cn, use_fates_bgc use clm_varctl , only : iulog use LandunitType , only : lun use ColumnType , only : col @@ -60,7 +60,7 @@ subroutine Init(this, bounds) type(bounds_type), intent(in) :: bounds call this%InitAllocate ( bounds ) - if (use_cn) then + if (use_cn .or. use_fates_bgc) then call this%InitHistory ( bounds ) end if call this%InitCold ( bounds ) @@ -132,26 +132,30 @@ subroutine InitHistory(this, bounds) begp = bounds%begp; endp= bounds%endp begc = bounds%begc; endc= bounds%endc - this%croot_prof_patch(begp:endp,:) = spval - call hist_addfld_decomp (fname='CROOT_PROF', units='1/m', type2d='levdcmp', & - avgflag='A', long_name='profile for litter C and N inputs from coarse roots', & - ptr_patch=this%croot_prof_patch, default='inactive') - - this%froot_prof_patch(begp:endp,:) = spval - call hist_addfld_decomp (fname='FROOT_PROF', units='1/m', type2d='levdcmp', & - avgflag='A', long_name='profile for litter C and N inputs from fine roots', & - ptr_patch=this%froot_prof_patch, default='inactive') - - this%leaf_prof_patch(begp:endp,:) = spval - call hist_addfld_decomp (fname='LEAF_PROF', units='1/m', type2d='levdcmp', & - avgflag='A', long_name='profile for litter C and N inputs from leaves', & - ptr_patch=this%leaf_prof_patch, default='inactive') - - this%stem_prof_patch(begp:endp,:) = spval - call hist_addfld_decomp (fname='STEM_PROF', units='1/m', type2d='levdcmp', & - avgflag='A', long_name='profile for litter C and N inputs from stems', & - ptr_patch=this%stem_prof_patch, default='inactive') - + if_usecn: if(use_cn) then + this%croot_prof_patch(begp:endp,:) = spval + call hist_addfld_decomp (fname='CROOT_PROF', units='1/m', type2d='levdcmp', & + avgflag='A', long_name='profile for litter C and N inputs from coarse roots', & + ptr_patch=this%croot_prof_patch, default='inactive') + + this%froot_prof_patch(begp:endp,:) = spval + call hist_addfld_decomp (fname='FROOT_PROF', units='1/m', type2d='levdcmp', & + avgflag='A', long_name='profile for litter C and N inputs from fine roots', & + ptr_patch=this%froot_prof_patch, default='inactive') + + this%leaf_prof_patch(begp:endp,:) = spval + call hist_addfld_decomp (fname='LEAF_PROF', units='1/m', type2d='levdcmp', & + avgflag='A', long_name='profile for litter C and N inputs from leaves', & + ptr_patch=this%leaf_prof_patch, default='inactive') + + this%stem_prof_patch(begp:endp,:) = spval + call hist_addfld_decomp (fname='STEM_PROF', units='1/m', type2d='levdcmp', & + avgflag='A', long_name='profile for litter C and N inputs from stems', & + ptr_patch=this%stem_prof_patch, default='inactive') + end if if_usecn + + ! These output variables are valid for both use_cn AND use_fates_bgc + this%nfixation_prof_col(begc:endc,:) = spval call hist_addfld_decomp (fname='NFIXATION_PROF', units='1/m', type2d='levdcmp', & avgflag='A', long_name='profile for biological N fixation', & @@ -161,7 +165,7 @@ subroutine InitHistory(this, bounds) call hist_addfld_decomp (fname='NDEP_PROF', units='1/m', type2d='levdcmp', & avgflag='A', long_name='profile for atmospheric N deposition', & ptr_col=this%ndep_prof_col, default='inactive') - + this%som_adv_coef_col(begc:endc,:) = spval call hist_addfld_decomp (fname='SOM_ADV_COEF', units='m/s', type2d='levdcmp', & avgflag='A', long_name='advection term for vertical SOM translocation', & From c0bfe0105ef777d5df85c248201a67059b06afb4 Mon Sep 17 00:00:00 2001 From: John Truesdale Date: Fri, 10 Mar 2023 13:31:32 -0700 Subject: [PATCH 0728/2067] mpasa files moved to ctsm5.1.dev052 --- bld/namelist_files/namelist_defaults_ctsm.xml | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 338aebc95d..7e4cebb4d1 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1130,17 +1130,17 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_numaIA_hist_78pfts_CMIP6_si lnd/clm2/surfdata_map/ctsm1.0.dev094-2-g633be0eb/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c200521.nc -lnd/clm2/surfdata_map/surfdata_mpasa480_hist_78pfts_CMIP6_simyr2000_c211110.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa480_hist_78pfts_CMIP6_simyr2000_c211110.nc -lnd/clm2/surfdata_map/surfdata_mpasa240_hist_78pfts_CMIP6_simyr2000_c211115.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa240_hist_78pfts_CMIP6_simyr2000_c211115.nc -lnd/clm2/surfdata_map/surfdata_mpasa120_hist_78pfts_CMIP6_simyr2000_c211108.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa120_hist_78pfts_CMIP6_simyr2000_c211108.nc -lnd/clm2/surfdata_map/surfdata_mpasa60_hist_78pfts_CMIP6_simyr2000_c211110.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa60_hist_78pfts_CMIP6_simyr2000_c211110.nc -lnd/clm2/surfdata_map/surfdata_mpasa30_hist_78pfts_CMIP6_simyr2000_c211111.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa30_hist_78pfts_CMIP6_simyr2000_c211111.nc -lnd/clm2/surfdata_map/surfdata_mpasa15_hist_78pfts_CMIP6_simyr2000_c211111.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa15_hist_78pfts_CMIP6_simyr2000_c211111.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc @@ -1188,17 +1188,17 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_16pfts_Irrig_CMIP6_sim lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1x1_brazil_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc -lnd/clm2/surfdata_map/surfdata_mpasa480_hist_78pfts_CMIP6_simyr1850_c211110.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa480_hist_78pfts_CMIP6_simyr1850_c211110.nc -lnd/clm2/surfdata_map/surfdata_mpasa240_hist_78pfts_CMIP6_simyr1850_c211115.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa240_hist_78pfts_CMIP6_simyr1850_c211115.nc -lnd/clm2/surfdata_map/surfdata_mpasa120_hist_78pfts_CMIP6_simyr1850_c211108.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa120_hist_78pfts_CMIP6_simyr1850_c211108.nc -lnd/clm2/surfdata_map/surfdata_mpasa60_hist_78pfts_CMIP6_simyr1850_c211110.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa60_hist_78pfts_CMIP6_simyr1850_c211110.nc -lnd/clm2/surfdata_map/surfdata_mpasa30_hist_78pfts_CMIP6_simyr1850_c211111.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa30_hist_78pfts_CMIP6_simyr1850_c211111.nc -lnd/clm2/surfdata_map/surfdata_mpasa15_hist_78pfts_CMIP6_simyr1850_c211111.nc +lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa15_hist_78pfts_CMIP6_simyr1850_c211111.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne30np4_hist_16pfts_Irrig_CMIP6_simyr1850_c190303.nc @@ -1302,17 +1302,17 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc lnd/clm2/surfdata_map/landuse.timeseries_mpasa480_hist_78pfts_CMIP6_simyr1850-2015_c211110.nc + use_crop=".true." >lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa480_hist_78pfts_CMIP6_simyr1850-2015_c211110.nc lnd/clm2/surfdata_map/landuse.timeseries_mpasa240_hist_78pfts_CMIP6_simyr1850-2015_c211115.nc + use_crop=".true." >lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa240_hist_78pfts_CMIP6_simyr1850-2015_c211115.nc lnd/clm2/surfdata_map/landuse.timeseries_mpasa120_hist_78pfts_CMIP6_simyr1850-2015_c211108.nc + use_crop=".true." >lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa120_hist_78pfts_CMIP6_simyr1850-2015_c211108.nc lnd/clm2/surfdata_map/landuse.timeseries_mpasa60_hist_78pfts_CMIP6_simyr1850-2015_c211110.nc +use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa60_hist_78pfts_CMIP6_simyr1850-2015_c211110.nc lnd/clm2/surfdata_map/landuse.timeseries_mpasa30_hist_78pfts_CMIP6_simyr1850-2015_c211111.nc +use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa30_hist_78pfts_CMIP6_simyr1850-2015_c211111.nc lnd/clm2/surfdata_map/landuse.timeseries_mpasa15_hist_78pfts_CMIP6_simyr1850-2015_c211111.nc +use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa15_hist_78pfts_CMIP6_simyr1850-2015_c211111.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc From 8e638d41216e8236b70dbfa430ba074798fb3530 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 13 Mar 2023 09:37:26 -0600 Subject: [PATCH 0729/2067] updated fates external and the default parameter file --- Externals_CLM.cfg | 4 ++-- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 219d1a9704..883416a43b 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.61.0_api.25.0.0 +repo_url = https://github.com/rgknox/fates +branch = clm-cbalance required = True [externals_description] diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 9a31995c4f..8517325c59 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221128.nc +lnd/clm2/paramdata/fates_params_api.25.2.0_12pft_c230310.nc From fc3d4930ad97c1c7804052b537f30bb93f34341d Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 14 Mar 2023 13:32:18 -0600 Subject: [PATCH 0730/2067] bug fix to get PRISM datm stream working --- cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams index 78fff234d6..16b7c739a7 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams @@ -50,7 +50,7 @@ NEON.${NEONSITE}:datavars = \ NEON.PRISM_PRECIP.${NEONSITE}:datavars = \ PRECIP Faxa_precn -NEON.PRISM_PRECIP${NEONSITE}:datafiles = \ +NEON.PRISM_PRECIP.${NEONSITE}:datafiles = \ /glade/u/home/tking/neon/prism_${NEONSITE}_2018.nc, \ /glade/u/home/tking/neon/prism_${NEONSITE}_2019.nc, \ /glade/u/home/tking/neon/prism_${NEONSITE}_2020.nc, \ From 4bdfea6dfe703252c0f04b000aa8a7108f40af86 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 14 Mar 2023 15:44:03 -0600 Subject: [PATCH 0731/2067] moved the use_fates broadcast earlier in the control process --- src/main/controlMod.F90 | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index a0af5b2862..99d7f3c835 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -549,10 +549,8 @@ subroutine control_init(dtime) call soilHydReadNML( NLFilename ) - if( use_cn .or. use_fates) then + if( use_cn ) then call CNPrecisionControlReadNML( NLFilename ) - end if - if ( use_cn ) then call CNFireReadNML( NLFilename ) call CNNDynamicsReadNML ( NLFilename ) call CNPhenologyReadNML ( NLFilename ) @@ -715,6 +713,8 @@ subroutine control_spmd() ! BGC call mpi_bcast (co2_type, len(co2_type), MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (use_fates, 1, MPI_LOGICAL, 0, mpicom, ier) + if (use_cn .or. use_fates) then call mpi_bcast (suplnitro, len(suplnitro), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (nfix_timeconst, 1, MPI_REAL8, 0, mpicom, ier) @@ -727,8 +727,6 @@ subroutine control_spmd() call mpi_bcast (use_c14, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (for_testing_allow_interp_non_ciso_to_ciso, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_fates, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (use_fates_logging, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier) From f4092b3c8c20468bc2341c8c1f019c579b654f2c Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 15 Mar 2023 10:18:07 -0600 Subject: [PATCH 0732/2067] Fixes to CN wood products restart w/ fates on --- src/biogeochem/CNBalanceCheckMod.F90 | 3 ++- src/biogeochem/CNVegetationFacade.F90 | 8 ++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index a6a11d51b6..4d98ca57bf 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -435,7 +435,8 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! Totally punt on this for now. We just don't track these gridscale variables yet (RGK) grc_cinputs = 0._r8 - grc_coutputs = (grc_begcb(g) - grc_endcb(g))/dt + grc_endcb(g) = grc_begcb(g) + grc_coutputs = 0._r8 grc_errcb(g) = 0._r8 end if diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 72082a579b..6fdb897795 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -510,6 +510,14 @@ subroutine Restart(this, bounds, ncid, flag) end if if (use_cn .or. use_fates_bgc) then + + if(use_fates_bgc)then + call this%c_products_inst%SetValues(bounds, 0._r8) + if (use_c13) call this%c13_products_inst%SetValues(bounds, 0._r8) + if (use_c14) call this%c14_products_inst%SetValues(bounds, 0._r8) + call this%n_products_inst%SetValues(bounds, 0._r8) + end if + call this%c_products_inst%restart(bounds, ncid, flag) if (use_c13) then call this%c13_products_inst%restart(bounds, ncid, flag, & From 873883cacab24ffaf96d14daa6ef0706e2a6ceaf Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 15 Mar 2023 17:53:47 -0600 Subject: [PATCH 0733/2067] cleaning up clm-fates bgc pr --- src/biogeochem/CNBalanceCheckMod.F90 | 8 +- src/biogeochem/CNCStateUpdate1Mod.F90 | 1 - src/biogeochem/CNDriverMod.F90 | 8 +- src/biogeochem/CNPhenologyMod.F90 | 159 +++++++++--------- src/biogeochem/CNProductsMod.F90 | 61 +++---- src/main/filterMod.F90 | 4 +- .../SoilBiogeochemCarbonFluxType.F90 | 25 +-- .../SoilBiogeochemNitrogenStateType.F90 | 2 - 8 files changed, 137 insertions(+), 131 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index 4d98ca57bf..66d24175b1 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -10,7 +10,7 @@ module CNBalanceCheckMod use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type, subgrid_level_gridcell, subgrid_level_column use abortutils , only : endrun - use clm_varctl , only : iulog, use_nitrif_denitrif, use_fates + use clm_varctl , only : iulog, use_nitrif_denitrif, use_fates_bgc use clm_time_manager , only : get_step_size_real use CNVegNitrogenFluxType , only : cnveg_nitrogenflux_type use CNVegNitrogenStateType , only : cnveg_nitrogenstate_type @@ -145,7 +145,7 @@ subroutine BeginCNGridcellBalance(this, bounds, cnveg_carbonflux_inst, & begg = bounds%begg; endg = bounds%endg - if(.not.use_fates)then + if(.not.use_fates_bgc)then call cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_dribbler%get_amount_left_to_dribble_beg( & bounds, hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)) @@ -409,7 +409,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & ! fluxes have entered the pools earlier in the timestep. For true ! conservation we would need to add a flux out of npp into seed. - if(.not.use_fates)then + if(.not.use_fates_bgc)then call cnveg_carbonflux_inst%hrv_xsmrpool_to_atm_dribbler%get_amount_left_to_dribble_end( & bounds, hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg)) call cnveg_carbonflux_inst%dwt_conv_cflux_dribbler%get_amount_left_to_dribble_end( & @@ -669,7 +669,7 @@ subroutine NBalanceCheck(this, bounds, num_soilc, filter_soilc, & call endrun(subgrid_index=c, subgrid_level=subgrid_level_column, msg=errMsg(sourcefile, __LINE__)) end if - if_notfates: if(.not.use_fates)then + if_notfates: if(.not.use_fates_bgc)then ! Repeat error check at the gridcell level call c2g( bounds = bounds, & diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index ba006b81a2..41051d0c39 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -269,7 +269,6 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end if end do - ! This filter omits FATES patches soilpatch_loop: do fp = 1,num_soilp p = filter_soilp(fp) c = patch%column(p) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 1e5b035f8d..5c77179d77 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -858,6 +858,12 @@ subroutine CNDriverNoLeaching(bounds, end if if_soilp2 + call c_products_inst%ComputeProductSummaryVars(bounds) + if (use_c13) call c13_products_inst%ComputeProductSummaryVars(bounds) + if (use_c14) call c14_products_inst%ComputeProductSummaryVars(bounds) + call n_products_inst%ComputeProductSummaryVars(bounds) + + call c_products_inst%ComputeSummaryVars(bounds) if (use_c13) call c13_products_inst%ComputeSummaryVars(bounds) if (use_c14) call c14_products_inst%ComputeSummaryVars(bounds) @@ -1124,7 +1130,7 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c13_cnveg_carbonstate_inst) end if if ( use_c14 ) then - call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c13_cnveg_carbonstate_inst) + call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c14_cnveg_carbonstate_inst) end if diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 4db642c58f..ec04fcbf54 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -406,7 +406,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & ! gather all patch-level litterfall fluxes to the column for litter C and N inputs - call CNLitterToColumn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNLitterToColumn(bounds, num_soilc, filter_soilc, & cnveg_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full), & froot_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full)) @@ -3384,8 +3384,8 @@ end subroutine CNCropHarvestToProductPools !----------------------------------------------------------------------- subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp, cnveg_state_inst,cnveg_carbonflux_inst, & - cnveg_nitrogenflux_inst, leaf_prof_patch, froot_prof_patch) + cnveg_state_inst,cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & + leaf_prof_patch, froot_prof_patch) ! ! !DESCRIPTION: ! called at the end of cn_phenology to gather all patch-level litterfall fluxes @@ -3400,8 +3400,6 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_soilc ! number of soil columns in filter integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for patches type(cnveg_state_type) , intent(in) :: cnveg_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst @@ -3409,7 +3407,7 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & real(r8) , intent(in) :: froot_prof_patch(bounds%begp:,1:) ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,k,j,i,fp ! indices + integer :: fc,c,pi,p,k,j,i ! indices !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(leaf_prof_patch) == (/bounds%endp,nlevdecomp_full/)), sourcefile, __LINE__) @@ -3440,85 +3438,94 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & phenology_n_to_litr_n => cnveg_nitrogenflux_inst%phenology_n_to_litr_n_col & ! Output: [real(r8) (:,:,:) ] N fluxes associated with phenology (litterfall and crop) to litter pools (gN/m3/s) ) - soil_loop: do j = 1, nlevdecomp - patch_loop: do fp = 1, num_soilp - p = filter_soilp(fp) - c = patch%column(p) - do i = i_litr_min, i_litr_max - ! leaf litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! leaf litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! fine root litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - - ! fine root litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do + do j = 1, nlevdecomp + do pi = 1,max_patch_per_col + do fc = 1,num_soilc + c = filter_soilc(fc) - ! agroibis puts crop stem litter together with leaf litter - ! so I've used the leaf lf_f* parameters instead of making - ! new ones for now (slevis) - ! also for simplicity I've put "food" into the litter pools - - if (ivt(p) >= npcropmin) then ! add livestemc to litter - do i = i_litr_min, i_litr_max - ! stem litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! stem litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - - if (.not. use_grainproduct) then - do i = i_litr_min, i_litr_max - do k = repr_grain_min, repr_grain_max - ! grain litter carbon fluxes + if ( pi <= col%npatches(c) ) then + p = col%patchi(c) + pi - 1 + if (patch%active(p)) then + + do i = i_litr_min, i_litr_max + ! leaf litter carbon fluxes phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + phenology_c_to_litr_c(c,j,i) + & + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - ! grain litter nitrogen fluxes + ! leaf litter nitrogen fluxes phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + phenology_n_to_litr_n(c,j,i) + & + leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! fine root litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + + ! fine root litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do - end do + + ! agroibis puts crop stem litter together with leaf litter + ! so I've used the leaf lf_f* parameters instead of making + ! new ones for now (slevis) + ! also for simplicity I've put "food" into the litter pools + + if (ivt(p) >= npcropmin) then ! add livestemc to litter + do i = i_litr_min, i_litr_max + ! stem litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! stem litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + + if (.not. use_grainproduct) then + do i = i_litr_min, i_litr_max + do k = repr_grain_min, repr_grain_max + ! grain litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! grain litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + end if + + do i = i_litr_min, i_litr_max + do k = repr_structure_min, repr_structure_max + ! reproductive structure litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! reproductive structure litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + end if + end if end if - do i = i_litr_min, i_litr_max - do k = repr_structure_min, repr_structure_max - ! reproductive structure litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! reproductive structure litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if + end do - end do patch_loop - end do soil_loop + end do + end do - end associate + end associate end subroutine CNLitterToColumn diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 8ffbe6db2e..50e23d3fc6 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -1,4 +1,4 @@ -module CNProductsMod +Module CNProductsMod !----------------------------------------------------------------------- ! !DESCRIPTION: ! Calculate loss fluxes from wood products pools, and update product pool state variables @@ -58,13 +58,6 @@ module CNProductsMod real(r8), pointer :: prod100_loss_grc(:) ! (g[C or N]/m2/s) decomposition loss from 100-yr wood product pool real(r8), pointer :: tot_woodprod_loss_grc(:) ! (g[C or N]/m2/s) decompomposition loss from all wood product pools - ! Objects that help convert once-per-year dynamic land cover changes into fluxes - ! that are dribbled throughout the year - !type(annual_flux_dribbler_type) :: dwt_conv_cflux_dribbler - !type(annual_flux_dribbler_type) :: hrv_xsmrpool_to_atm_dribbler - !logical, private :: dribble_crophrv_xsmrpool_2atm - - contains ! Infrastructure routines @@ -79,6 +72,7 @@ module CNProductsMod procedure, public :: UpdateProducts procedure, private :: PartitionWoodFluxes procedure, private :: PartitionCropFluxes + procedure, public :: ComputeProductSummaryVars procedure, public :: ComputeSummaryVars end type cn_products_type @@ -158,17 +152,6 @@ subroutine InitAllocate(this, bounds) allocate(this%tot_woodprod_loss_grc(begg:endg)) ; this%tot_woodprod_loss_grc(:) = nan allocate(this%product_loss_grc(begg:endg)) ; this%product_loss_grc(:) = nan - !this%dwt_conv_cflux_dribbler = annual_flux_dribbler_gridcell( & - ! bounds = bounds, & - ! name = 'dwt_conv_flux_' // carbon_type_suffix, & - ! units = 'gC/m^2', & - ! allows_non_annual_delta = allows_non_annual_delta) - !this%hrv_xsmrpool_to_atm_dribbler = annual_flux_dribbler_gridcell( & - ! bounds = bounds, & - ! name = 'hrv_xsmrpool_to_atm_' // carbon_type_suffix, & - ! units = 'gC/m^2', & - ! allows_non_annual_delta = .false.) - end subroutine InitAllocate subroutine SetValues(this, bounds, setval) @@ -700,30 +683,18 @@ subroutine PartitionCropFluxes(this, bounds, & end subroutine PartitionCropFluxes - !----------------------------------------------------------------------- - subroutine ComputeSummaryVars(this, bounds) - ! - ! !DESCRIPTION: - ! Compute summary variables in this object: sums across multiple product pools - ! - ! !USES: - ! - ! !ARGUMENTS: + subroutine ComputeProductSummaryVars(this, bounds) + class(cn_products_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds - ! - ! !LOCAL VARIABLES: + integer :: g ! indices real(r8) :: dt ! time step (seconds) real(r8) :: kprod1 ! decay constant for 1-year product pool real(r8) :: kprod10 ! decay constant for 10-year product pool real(r8) :: kprod100 ! decay constant for 100-year product pool - !----------------------------------------------------------------------- - character(len=*), parameter :: subname = 'ComputeSummaryVars' - - !----------------------------------------------------------------------- ! calculate losses from product pools ! the following (1/s) rate constants result in ~90% loss of initial state over 1, 10 and 100 years, ! respectively, using a discrete-time fractional decay algorithm. @@ -758,9 +729,29 @@ subroutine ComputeSummaryVars(this, bounds) this%cropprod1_grc(g) = this%cropprod1_grc(g) - this%cropprod1_loss_grc(g)*dt this%prod10_grc(g) = this%prod10_grc(g) - this%prod10_loss_grc(g)*dt this%prod100_grc(g) = this%prod100_grc(g) - this%prod100_loss_grc(g)*dt - end do + return + end subroutine ComputeProductSummaryVars + + + !----------------------------------------------------------------------- + subroutine ComputeSummaryVars(this, bounds) + ! + ! !DESCRIPTION: + ! Compute summary variables in this object: sums across multiple product pools + ! + ! !USES: + ! + ! !ARGUMENTS: + class(cn_products_type) , intent(inout) :: this + type(bounds_type) , intent(in) :: bounds + ! + ! !LOCAL VARIABLES: + integer :: g ! indices + !----------------------------------------------------------------------- + character(len=*), parameter :: subname = 'ComputeSummaryVars' + do g = bounds%begg, bounds%endg ! total wood products diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index db82b665ec..2542dab1ca 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -19,7 +19,7 @@ module filterMod use ColumnType , only : col use PatchType , only : patch use glcBehaviorMod , only : glc_behavior_type - use clm_varctl , only : use_cn, use_fates, use_fates_sp + use clm_varctl , only : use_cn, use_fates_bgc ! ! !PUBLIC TYPES: implicit none @@ -396,7 +396,7 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio ! Create the soil bgc filter, all non-sp columns for vegetation fs = 0 - if( use_cn .or. (use_fates .and. .not.use_fates_sp))then + if( use_cn .or. use_fates_bgc )then do c = bounds%begc,bounds%endc if (col%active(c) .or. include_inactive) then l =col%landunit(c) diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index 3a311807a9..4bd9c5e0e5 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -889,21 +889,22 @@ subroutine Summary(this, bounds, & end associate ! total heterotrophic respiration (HR) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) - this%hr_col(c) = & - this%michr_col(c) + & - this%cwdhr_col(c) + & - this%lithr_col(c) + & - this%somhr_col(c) + this%hr_col(c) = & + this%michr_col(c) + & + this%cwdhr_col(c) + & + this%lithr_col(c) + & + this%somhr_col(c) - end do + end do ! Calculate ligninNratio ! FATES does its own calculation - if (decomp_method == mimics_decomp .and. num_soilp>0) then + if_mimics: if (decomp_method == mimics_decomp ) then + if(num_soilp>0)then do fp = 1,num_soilp p = filter_soilp(fp) associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type @@ -929,6 +930,8 @@ subroutine Summary(this, bounds, & frootc_to_litter_patch(bounds%begp:bounds%endp), & frootc_to_litter_col(bounds%begc:bounds%endc)) + end if + ! Calculate ligninNratioAve do fc = 1,num_soilc c = filter_soilc(fc) @@ -946,9 +949,11 @@ subroutine Summary(this, bounds, & max(1.0e-3_r8, leafc_to_litter_col(c) + & frootc_to_litter_col(c) + & soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2)) + !else + ! Alternative place to hook in fates litr lignan end if end do - end if + end if if_mimics end subroutine Summary diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index 435e6c327c..ac7fa52b44 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -999,8 +999,6 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in end if end do - - ! total sminn do fc = 1,num_soilc c = filter_soilc(fc) From ad8bc744534a4164237807f731cd8c43a7073bea Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 16 Mar 2023 08:47:50 -0600 Subject: [PATCH 0734/2067] Update externals to cesm2_3_alpha12c-ish For CMEPS, use the latest (fixing an issue with multi-instance cases relative to what was in alpha12c). --- Externals.cfg | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index 7a4eeb4a6e..1a55310d19 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_cesm0.0.38 +tag = ccs_config_cesm0.0.58 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config @@ -44,18 +44,18 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.45 +tag = cime6.0.94 required = True [cmeps] -tag = cmeps0.13.71 +tag = cmeps0.14.17 protocol = git repo_url = https://github.com/ESCOMP/CMEPS.git local_path = components/cmeps required = True [cdeps] -tag = cdeps0.12.65 +tag = cdeps1.0.7 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps @@ -70,7 +70,7 @@ local_path = components/cpl7 required = True [share] -tag = share1.0.13 +tag = share1.0.16 protocol = git repo_url = https://github.com/ESCOMP/CESM_share local_path = share @@ -84,7 +84,7 @@ local_path = libraries/mct required = True [parallelio] -tag = pio2_5_7 +tag = pio2_5_10 protocol = git repo_url = https://github.com/NCAR/ParallelIO local_path = libraries/parallelio From 79a77d6eb3e3ca1b16e8abb29a68b844221bc4ee Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 16 Mar 2023 11:08:58 -0600 Subject: [PATCH 0735/2067] cleanup of fates-bgc coupling --- src/biogeochem/CNProductsMod.F90 | 8 +-- src/main/filterMod.F90 | 2 +- .../SoilBiogeochemCarbonFluxType.F90 | 52 +++++++++---------- 3 files changed, 28 insertions(+), 34 deletions(-) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 50e23d3fc6..b6af2a6358 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -1,4 +1,4 @@ -Module CNProductsMod +module CNProductsMod !----------------------------------------------------------------------- ! !DESCRIPTION: ! Calculate loss fluxes from wood products pools, and update product pool state variables @@ -13,8 +13,6 @@ Module CNProductsMod use clm_time_manager , only : get_step_size_real use SpeciesBaseType , only : species_base_type use PatchType , only : patch - use AnnualFluxDribbler , only : annual_flux_dribbler_type - use AnnualFluxDribbler , only : annual_flux_dribbler_gridcell ! implicit none private @@ -173,10 +171,6 @@ subroutine SetValues(this, bounds, setval) this%hrv_deadstem_to_prod10_grc(bounds%begg:bounds%endg) = setval this%hrv_deadstem_to_prod100_grc(bounds%begg:bounds%endg) = setval - !this%cropprod1_loss_grc(bounds%begg:bounds%endg) = setval - !this%prod10_loss_grc(bounds%begg:bounds%endg) = setval - !this%prod100_loss_grc(bounds%begg:bounds%endg) = setval - return end subroutine SetValues diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 2542dab1ca..d96cb63a30 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -19,7 +19,7 @@ module filterMod use ColumnType , only : col use PatchType , only : patch use glcBehaviorMod , only : glc_behavior_type - use clm_varctl , only : use_cn, use_fates_bgc + use clm_varctl , only : use_cn, use_fates, use_fates_bgc ! ! !PUBLIC TYPES: implicit none diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index 4bd9c5e0e5..9d47c188be 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -6,7 +6,7 @@ module SoilBiogeochemCarbonFluxType use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan use clm_varpar , only : nlevdecomp_full, nlevgrnd, nlevdecomp, nlevsoi, i_cwdl2 use clm_varcon , only : spval, ispval, dzsoi_decomp - use clm_varctl , only : use_fates + use clm_varctl , only : use_fates,use_cn use pftconMod , only : pftcon use landunit_varcon , only : istsoil, istcrop, istdlak use ch4varcon , only : allowlakeprod @@ -905,31 +905,31 @@ subroutine Summary(this, bounds, & if_mimics: if (decomp_method == mimics_decomp ) then if(num_soilp>0)then - do fp = 1,num_soilp - p = filter_soilp(fp) - associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type - ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * & - pftcon%lflitcn(ivt(p)) * & - leafc_to_litter_patch(p) - ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * & - pftcon%frootcn(ivt(p)) * & - frootc_to_litter_patch(p) - end associate - end do - - call p2c(bounds, num_soilc, filter_soilc, & - ligninNratio_leaf_patch(bounds%begp:bounds%endp), & - ligninNratio_leaf_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & - ligninNratio_froot_patch(bounds%begp:bounds%endp), & - ligninNratio_froot_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & - leafc_to_litter_patch(bounds%begp:bounds%endp), & - leafc_to_litter_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & - frootc_to_litter_patch(bounds%begp:bounds%endp), & - frootc_to_litter_col(bounds%begc:bounds%endc)) - + do fp = 1,num_soilp + p = filter_soilp(fp) + associate(ivt => patch%itype) ! Input: [integer (:)] patch plant type + ligninNratio_leaf_patch(p) = pftcon%lf_flig(ivt(p)) * & + pftcon%lflitcn(ivt(p)) * & + leafc_to_litter_patch(p) + ligninNratio_froot_patch(p) = pftcon%fr_flig(ivt(p)) * & + pftcon%frootcn(ivt(p)) * & + frootc_to_litter_patch(p) + end associate + end do + + call p2c(bounds, num_soilc, filter_soilc, & + ligninNratio_leaf_patch(bounds%begp:bounds%endp), & + ligninNratio_leaf_col(bounds%begc:bounds%endc)) + call p2c(bounds, num_soilc, filter_soilc, & + ligninNratio_froot_patch(bounds%begp:bounds%endp), & + ligninNratio_froot_col(bounds%begc:bounds%endc)) + call p2c(bounds, num_soilc, filter_soilc, & + leafc_to_litter_patch(bounds%begp:bounds%endp), & + leafc_to_litter_col(bounds%begc:bounds%endc)) + call p2c(bounds, num_soilc, filter_soilc, & + frootc_to_litter_patch(bounds%begp:bounds%endp), & + frootc_to_litter_col(bounds%begc:bounds%endc)) + end if ! Calculate ligninNratioAve From deb0866e03dd9dcff47e65ab6dac68216219a846 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 16 Mar 2023 14:14:00 -0600 Subject: [PATCH 0736/2067] Update change file --- doc/ChangeLog | 24 +++++++++++++----------- doc/ChangeSum | 2 +- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 6df1764ff4..a604f675f4 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,13 +1,16 @@ =============================================================== Tag name: ctsm5.1.dev119 Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310), ekluzek Erik Kluzek), lawrencepj1 (Peter Lawrence) -Date: Wed Feb 22 13:57:36 MST 2023 +Date: Thu Mar 16 14:13:37 MDT 2023 One-line Summary: Allow gross unrepresented land use transitions (PR #309) Purpose and description of changes ---------------------------------- - Get gross unrepresented land use transitions working in CLM5.1. + Get gross unrepresented land use transitions working in CLM5.1. This is additional optional + data added to the landuse.timeseries files for transient simulations. The current landuse.timseries + files have this data, but it's set to zero. This data will be part of the CTSM5.2 surface dataset + (that is upcoming) and be on by default for clm5_3 physics. Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -30,9 +33,9 @@ hanges.] Bugs fixed or introduced ------------------------ -CTSM issues fixed (include CTSM Issue #): - I didn't find a corresponding issue. - + Known bugs introduced in this tag (include issue #): #1968 + #1968 -- Reduce the GULU tests down to one + Notes of particular relevance for users --------------------------------------- Changes made to namelist defaults (e.g., changed parameter values): @@ -42,11 +45,6 @@ Changes to the datasets (e.g., parameter, surface or initial files): Surface datasets may now contain non-zero gross unrepresented land use transitions. -Substantial timing or memory changes: -[e.g., check PFS test in the test suite and look at timings, if you -expect possible significant timing changes] - - Notes of particular relevance for developers: --------------------------------------------- Changes to tests or testing: @@ -77,7 +75,11 @@ Changes answers relative to baseline: NO (unless see next) Other details ------------- Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/ctsm/pull/309 + https://github.com/ESCOMP/ctsm/pull/309 -- Added new files to allow Gross Unrepresented Land Use transition + https://github.com/ESCOMP/ctsm/pull/1965 -- update README + (NOT a PR) Update manage externals + + =============================================================== =============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index 66e229d06c..e2bcff8e14 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev119 slevis 02/22/2023 Allow gross unrepresented land use transition (PR #309) + ctsm5.1.dev119 slevis 03/16/2023 Allow gross unrepresented land use transition (PR #309) ctsm5.1.dev118 slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test ctsm5.1.dev117 afoster 02/02/2023 Updates to facilitate running FATES at NEON sites ctsm5.1.dev116 erik 01/26/2023 Small answer changes with bug fixes, zetamaxstable=2 for BHS, new single point fsurdat files From 1bd5e9ec54da627721da7e88f726da3e9036304a Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 17 Mar 2023 12:17:24 -0600 Subject: [PATCH 0737/2067] Update to latest CIME This is needed to fix an issue with CTSM-defined system tests --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 1a55310d19..c81dd77664 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.94 +tag = cime6.0.98 required = True [cmeps] From fa421c8363e871073332bf6bbaa068dc3b0da836 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Mon, 20 Mar 2023 14:39:17 -0600 Subject: [PATCH 0738/2067] For the _Ln1 self-tests, ROF needs to couple every time step --- .../testdefs/testmods_dirs/clm/run_self_tests/shell_commands | 2 ++ 1 file changed, 2 insertions(+) mode change 100644 => 100755 cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands old mode 100644 new mode 100755 index a66f52f6fd..d426269206 --- a/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/run_self_tests/shell_commands @@ -1,3 +1,5 @@ #!/bin/bash ./xmlchange CLM_FORCE_COLDSTART="on" +# We use this testmod in a _Ln1 test; this requires forcing the ROF coupling frequency to every time step +./xmlchange ROF_NCPL=48 From f9e2a3bda960ede1b95e081063f6af5b66044c56 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 22 Mar 2023 12:19:24 -0600 Subject: [PATCH 0739/2067] temporary updates for nl and stream changes --- cime_config/config_component.xml | 4 +++- cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands | 3 ++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 243c866bbd..82c2d545b3 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -244,7 +244,9 @@ Dataset name for user-created datasets. This is used as the argument in Buildconf/clm.buildnml to build-namelist -clm_usr_name. An example of such a dataset would be 1x1pt_boulderCO_c090722. The default value is UNSET. - This is an advanced flag and should only be used by expert users. + This is an advanced flag and should only be used by expert users. For NEON + cases, this can be set to either NEON or NEON.PRISM, the latter of which would + PRISM precipitation instead of the default NEON precipitation. diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands index 7095e1def7..084e0027ba 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands @@ -1,5 +1,6 @@ #!/bin/bash -./xmlchange CLM_USRDAT_NAME=NEON +./xmlchange CLM_USRDAT_NAME=NEON.PRISM +# we should also ensure that this can be set to NEON.PRISM ./xmlchange CCSM_CO2_PPMV=408.83 # Set data forcing data to future scenario so will have data from 2018 to present-day ./xmlchange DATM_PRESAERO=SSP3-7.0 From c0574b4451d195119b83a6e5344c78a9b3e41d60 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 22 Mar 2023 12:29:20 -0600 Subject: [PATCH 0740/2067] temporary updates for nl and stream changes --- cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands | 2 +- cime_config/usermods_dirs/NEON/defaults/shell_commands | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands index 084e0027ba..aacfad8e15 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands @@ -1,5 +1,5 @@ #!/bin/bash -./xmlchange CLM_USRDAT_NAME=NEON.PRISM +./xmlchange CLM_USRDAT_NAME=NEON # we should also ensure that this can be set to NEON.PRISM ./xmlchange CCSM_CO2_PPMV=408.83 # Set data forcing data to future scenario so will have data from 2018 to present-day diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 7095e1def7..0cbba60f84 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -1,5 +1,6 @@ #!/bin/bash ./xmlchange CLM_USRDAT_NAME=NEON +# This is where we want to implement NEON.PRISM; in the current state, doing so causes SVN failures ./xmlchange CCSM_CO2_PPMV=408.83 # Set data forcing data to future scenario so will have data from 2018 to present-day ./xmlchange DATM_PRESAERO=SSP3-7.0 From a022f80e9dafa80824d3b4a316470113e23c3ce6 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 23 Mar 2023 07:20:37 -0600 Subject: [PATCH 0741/2067] Update COMP_ROOT_DIR_LND to mostly match the version in CIME The COMP_ROOT_DIR_LND is supposed to basically match the entry in CIME's config_files.xml except for the value for CLM. The motivation for this is to add an entry for SLIM: without this change, it seems like other config_files entries were using the CLM location of $SRCROOT for SLIM's COMP_ROOT_DIR_LND, which meant that we were getting duplicate entries of some files, which caused various problems (e.g., https://github.com/ESMCI/cime/issues/4373 - which is now fixed with this change instead of the originally-suggested CIME change - and seeing duplicate results from CIME's query_testlists and query_config scripts). But while making this change, I figured I might as well update the entire entry to be consistent with the latest version in CIME. --- .config_files.xml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/.config_files.xml b/.config_files.xml index c6dcbbcdb3..d1a592e5db 100644 --- a/.config_files.xml +++ b/.config_files.xml @@ -5,31 +5,31 @@ char unset - $SRCROOT - $SRCROOT - $SRCROOT/components/cpl7/components/data_comps_mct/dlnd - $SRCROOT/components/cdeps/dlnd - $SRCROOT/components/cpl7/components/stub_comps_mct/slnd - $SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd - $CIMEROOT/src/components/stub_comps_nuopc/slnd - $CIMEROOT/src/components/xcpl_comps_nuopc/xlnd + $SRCROOT + $SRCROOT/components/slim/ + $SRCROOT/components/cpl7/components/data_comps_$COMP_INTERFACE/dlnd + $SRCROOT/components/cdeps/dlnd + $SRCROOT/components/cpl7/components/stub_comps_$COMP_INTERFACE/slnd + $CIMEROOT/CIME/non_py/src/components/stub_comps_$COMP_INTERFACE/slnd + $SRCROOT/components/cpl7/components/xcpl_comps_$COMP_INTERFACE/xlnd + $CIMEROOT/CIME/non_py/src/components/xcpl_comps_$COMP_INTERFACE/xlnd case_comps env_case.xml Root directory of the case land model component - $CIMEROOT/config/xml_schemas/config_compsets.xsd + $CIMEROOT/CIME/data/config/xml_schemas/config_compsets.xsd From 5b3e2460e31321827d4e5694c933e2e613f3b3d5 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 23 Mar 2023 11:20:54 -0600 Subject: [PATCH 0742/2067] Update cime --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index c81dd77664..57d472d8c0 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.98 +tag = cime6.0.100 required = True [cmeps] From bc770f0e914a3006ecdc16791f8cc55ef27915dc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 23 Mar 2023 17:12:22 -0600 Subject: [PATCH 0743/2067] Moved 'vernalization forces harvest' else-if in harvest logic. --- src/biogeochem/CNPhenologyMod.F90 | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index fa783e0c12..76a8ff8e84 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2110,11 +2110,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & mxmat = 999 end if - if (vernalization_forces_harvest) then - do_harvest = .true. - force_harvest = .true. - harvest_reason = HARVEST_REASON_VERNFREEZEKILL - else if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then + if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! BACKWARDS_COMPATIBILITY(ssr, 2022-02-03): To get rid of crops incorrectly planted in last time step of Dec. 31. That was fixed in commit dadbc62 ("Call CropPhenology regardless of doalb"), but this handles restart files with the old behavior. fake_harvest ensures that outputs aren't polluted. do_harvest = .true. force_harvest = .true. @@ -2171,6 +2167,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. do_harvest = .false. + else if (vernalization_forces_harvest) then + do_harvest = .true. + force_harvest = .true. + harvest_reason = HARVEST_REASON_VERNFREEZEKILL else ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat From 2399486724cbe6b3b32808a3456b1102043fcdb7 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 23 Mar 2023 16:44:47 -0600 Subject: [PATCH 0744/2067] Reduce GU_LULCC tests down to a single test Resolves ESCOMP/CTSM#1968 --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- cime_config/testdefs/testlist_clm.xml | 29 +++---------------- .../ciso_decStart_GU_LULCC/include_user_mods | 1 - .../clm/ciso_decStart_GU_LULCC/user_nl_clm | 1 - .../f09_dec1990Start_GU_LULCC/shell_commands | 2 +- .../include_user_mods | 2 -- 6 files changed, 6 insertions(+), 31 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 6ddfea3437..d9a1c1b6fd 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -88,7 +88,7 @@ - + PEND #1045 diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 34e22e7272..34e8cf01b3 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -462,39 +462,18 @@ - - - - - - - - - - + - + - + - - - - - - - - - - - - @@ -2037,7 +2016,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods deleted file mode 100644 index c0adfb5904..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../ciso_decStart diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm deleted file mode 100644 index 8d3ca17778..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_decStart_GU_LULCC/user_nl_clm +++ /dev/null @@ -1 +0,0 @@ -do_grossunrep = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands index 972cd25f5c..3adf0390b1 100755 --- a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC/shell_commands @@ -1,3 +1,3 @@ -./xmlchange RUN_STARTDATE=1990-12-25 +./xmlchange RUN_STARTDATE=1990-12-30 # Ignore warnings because we are using crop, but starting from a different date than the initial conditions were for ./xmlchange CLM_BLDNML_OPTS=-ignore_warnings --append diff --git a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods deleted file mode 100644 index b10682f861..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/f09_dec1990Start_GU_LULCC_monthly/include_user_mods +++ /dev/null @@ -1,2 +0,0 @@ -../f09_dec1990Start_GU_LULCC -../monthly From af56c533e5f4a185b03ced15ae26d5285d6fc412 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 23 Mar 2023 17:16:23 -0600 Subject: [PATCH 0745/2067] Re-raise caught exception after printing error message Otherwise the test continues on after failure. Resolves ESCOMP/CTSM#1971 --- cime_config/SystemTests/fsurdatmodifyctsm.py | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 64d945760b..1427a7550f 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -89,6 +89,7 @@ def _run_modify_fsurdat(self): print("getting an error within the fsurdat_modifier tool itself. ") print("Default error message: ") print(error.output) + raise except: print("ERROR trying to run fsurdat_modifier tool.") raise From c9f8c28a894a1121627f34ca8a61dc5234f6fc47 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 23 Mar 2023 17:37:31 -0600 Subject: [PATCH 0746/2067] Increase time for C96 test With the recent externals update, this C96 test barely finished in the 10-minute allotted time once, and timed out a different time. Increasing the wall-clock time. (There has been investigation into the cause of recent slowness... the culprit seems to be mpt 2.25.) --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 34e8cf01b3..40ab7a48df 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -327,7 +327,7 @@ - + From 1fdde35cf5a1d62cfa4cb1e506c33de257bd51b7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 24 Mar 2023 09:13:06 -0600 Subject: [PATCH 0747/2067] Revert "Moved 'vernalization forces harvest' else-if in harvest logic." This reverts commit bc770f0e914a3006ecdc16791f8cc55ef27915dc. --- src/biogeochem/CNPhenologyMod.F90 | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 76a8ff8e84..fa783e0c12 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2110,7 +2110,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & mxmat = 999 end if - if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then + if (vernalization_forces_harvest) then + do_harvest = .true. + force_harvest = .true. + harvest_reason = HARVEST_REASON_VERNFREEZEKILL + else if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! BACKWARDS_COMPATIBILITY(ssr, 2022-02-03): To get rid of crops incorrectly planted in last time step of Dec. 31. That was fixed in commit dadbc62 ("Call CropPhenology regardless of doalb"), but this handles restart files with the old behavior. fake_harvest ensures that outputs aren't polluted. do_harvest = .true. force_harvest = .true. @@ -2167,10 +2171,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. do_harvest = .false. - else if (vernalization_forces_harvest) then - do_harvest = .true. - force_harvest = .true. - harvest_reason = HARVEST_REASON_VERNFREEZEKILL else ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat From c3d38607daa1bbc6b82a978a7000a5c5ceee7596 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 24 Mar 2023 09:25:00 -0600 Subject: [PATCH 0748/2067] Safer method of 'Safer method to freeze-kill winter cereals.' I never really looked into whether the kludge of forcing a harvest by setting gddmaturity = huigrain = 0 in vernalization() was important anywhere else. This thus partially reverts 08e2fe618c, which removed that kludge. Instead, this commit still uses the kludge, but keeps the HARVEST_REASON specific to vernalization freeze-kill. --- src/biogeochem/CNPhenologyMod.F90 | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index fa783e0c12..3a03068542 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1747,7 +1747,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical fake_harvest ! Dealing with incorrect Dec. 31 planting logical did_plant_prescribed_today ! Was the crop sown today? logical will_plant_prescribed_tomorrow ! Is tomorrow a prescribed sowing day? - logical vernalization_forces_harvest ! if freeze-killed + logical vernalization_forces_harvest ! Was the crop killed by freezing during vernalization? !------------------------------------------------------------------------ associate( & @@ -2110,11 +2110,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & mxmat = 999 end if - if (vernalization_forces_harvest) then - do_harvest = .true. - force_harvest = .true. - harvest_reason = HARVEST_REASON_VERNFREEZEKILL - else if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then + if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! BACKWARDS_COMPATIBILITY(ssr, 2022-02-03): To get rid of crops incorrectly planted in last time step of Dec. 31. That was fixed in commit dadbc62 ("Call CropPhenology regardless of doalb"), but this handles restart files with the old behavior. fake_harvest ensures that outputs aren't polluted. do_harvest = .true. force_harvest = .true. @@ -2189,7 +2185,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if do_harvest = do_harvest .or. will_plant_prescribed_tomorrow - if (hui(p) >= gddmaturity(p)) then + if (vernalization_forces_harvest) then + harvest_reason = HARVEST_REASON_VERNFREEZEKILL + else if (hui(p) >= gddmaturity(p)) then harvest_reason = HARVEST_REASON_MATURE else if (idpp >= mxmat) then harvest_reason = HARVEST_REASON_MAXSEASLENGTH @@ -2740,14 +2738,15 @@ subroutine vernalization(p, & ! will have to develop some type of relationship that reduces LAI and ! biomass pools in response to cold damaged crop - force_harvest = .false. if (t_ref2m_min(p) <= tfrz - 6._r8) then tkil = (tbase - 6._r8) - 6._r8 * hdidx(p) if (tkil >= tcrown) then if ((0.95_r8 - 0.02_r8 * (tcrown - tkil)**2) >= 0.02_r8) then write (iulog,*) 'crop damaged by cold temperatures at p,c =', p,c - else if (tlai(p) > 0._r8) then ! slevis: kill if past phase1 by - force_harvest = .true. ! forcing through harvest + else if (tlai(p) > 0._r8) then ! slevis: kill if past phase1 + gddmaturity(p) = 0._r8 ! by forcing through + huigrain(p) = 0._r8 ! harvest + force_harvest = .true. write (iulog,*) '95% of crop killed by cold temperatures at p,c =', p,c end if end if From 3cd1351964acd9e3fea7d8b3ced2f53de16bf13e Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Sat, 25 Mar 2023 16:15:18 -0600 Subject: [PATCH 0749/2067] Add FUNITCTSM test to expected fails list --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index d9a1c1b6fd..01d0b738be 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -51,6 +51,13 @@ + + + FAIL + #1972 + + + From 2ee9024597cd21c1b755bd24e55e4b1d856d256d Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Sat, 25 Mar 2023 17:45:57 -0600 Subject: [PATCH 0750/2067] Add Fortran unit tests as a separate test to run This is needed until https://github.com/ESCOMP/CTSM/issues/1972 is resolved --- doc/.ChangeLog_template | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index 63f4628bad..ccf5752b7d 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -121,10 +121,15 @@ infrastructure should be run when appropriate, as described below. clm_pymods test suite on cheyenne - - regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + regular tests: + - aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing + - Fortran unit tests on cheyenne (until https://github.com/ESCOMP/CTSM/issues/1972 is resolved): from src, run: + ../cime/scripts/fortran_unit_testing/run_tests.py --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX` + + aux_clm on cheyenne ------------ + aux_clm on izumi --------------- + Fortran unit tests on cheyenne - - cheyenne ---- - izumi ------- fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) cheyenne ---- From 97855df50fdbac07dbf759e0552acfa5f3526d5e Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Sat, 25 Mar 2023 18:01:31 -0600 Subject: [PATCH 0751/2067] Update ChangeLog --- doc/ChangeLog | 102 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 103 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index a604f675f4..0776ca96f0 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,106 @@ =============================================================== +Tag name: ctsm5.1.dev120 +Originator(s): sacks (Bill Sacks) +Date: Sat Mar 25 17:49:27 MDT 2023 +One-line Summary: Update externals and minor fixes + +Purpose and description of changes +---------------------------------- + +Main change is to update externals to cesm2_3_alpha12c-ish. + +Doing this exposed a few issues that are also fixed here. + +Also, reduce GU_LULCC tests down to a single test. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1968 (Reduce the GULU tests down to one) +- Resolves ESCOMP/CTSM#1971 (fsurdatmodifyctsm test should abort if it has trouble running the python script) + +Known bugs introduced in this tag (include issue #): +- ESCOMP/CTSM#1972 (FUNITCTSM test fails when run through run_sys_tests in upcoming ctsm5.1.dev120) + + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: +- Fortran unit tests now need to be run manually, since FUNITCTSM is + failing when run through run_sys_tests +- Reduced GU_LULCC tests down to a single test + + +Testing summary: +---------------- + + regular tests: + - aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing + - Fortran unit tests on cheyenne (until https://github.com/ESCOMP/CTSM/issues/1972 is resolved): from src, run: + ../cime/scripts/fortran_unit_testing/run_tests.py --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX` + + aux_clm on cheyenne ------------ OK + aux_clm on izumi --------------- OK + Fortran unit tests on cheyenne - PASS + + For the two new tests (with BFAILs), ran them from dev119 with + comparison against this branch: + - ERP_D_Ld10_P36x2.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-ciso_decStart + - SMS_Ld3_PS.f09_g17.IHistClm50BgcCrop.cheyenne_intel.clm-f09_dec1990Start_GU_LULCC + (with start date in the test mod changed to match the new version) + +Answer changes +-------------- + +Changes answers relative to baseline: YES, but just for certain compilers + + Summarize any changes to answers, i.e., + - what code configurations: all on certain compilers + - what platforms/compilers: + - nvhpc on cheyenne in non-debug cases (can be explained from + differences in compilation flags for non-debug cases, and also + some module differences) + - intel on izumi in debug cases (there were updates in ESMF + modules, though that's the same for other izumi compilers; I'm not + seeing other relevant diffs in ccs_config, so I'm not sure why we're + getting diffs here. I tried investigating, but ran into trouble trying + to get things to compile with the old ccs_config, so gave up on + tracking down the source of this difference) + + - nature of change (roundoff; larger than roundoff/same climate; new climate): + not investigated + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- ccs_config: ccs_config_cesm0.0.38 -> ccs_config_cesm0.0.58 +- cime: cime6.0.45 -> cime6.0.100 +- cmeps: cmeps0.13.71 -> cmeps0.14.17 +- cdeps: cdeps0.12.65 -> cdeps1.0.7 +- share: share1.0.13 -> share1.0.16 +- pio: pio2_5_7 -> pio2_5_10 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev119 Originator(s): slevis (Samuel Levis,SLevis Consulting,303-665-1310), ekluzek Erik Kluzek), lawrencepj1 (Peter Lawrence) Date: Thu Mar 16 14:13:37 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index e2bcff8e14..e718109e03 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev120 sacks 03/25/2023 Update externals and minor fixes ctsm5.1.dev119 slevis 03/16/2023 Allow gross unrepresented land use transition (PR #309) ctsm5.1.dev118 slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test ctsm5.1.dev117 afoster 02/02/2023 Updates to facilitate running FATES at NEON sites From 83d31e107a5d37400818ff59acc063e4762a9f60 Mon Sep 17 00:00:00 2001 From: adamrher Date: Sat, 25 Mar 2023 18:30:24 -0600 Subject: [PATCH 0752/2067] add new grids to namelist files --- bld/namelist_files/namelist_defaults_ctsm.xml | 18 ++++++++++++++++++ .../namelist_definition_ctsm.xml | 2 +- 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 41103b5259..add537337a 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1092,8 +1092,14 @@ lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230123.nc + +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230221.nc + +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230221.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc + +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230221.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr2000_c200426.nc @@ -1167,6 +1173,12 @@ lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230123.nc + +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230221.nc + +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230221.nc + +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230221.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc @@ -1233,6 +1245,12 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230221.nc +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230221.nc +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230221.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc + valid_values="512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,0.125nldas2,5x5_amazon,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne3np4.pg3,ne4np4,ne5np4.pg3,ne16np4,ne16np4.pg3,ne30np4.pg2,ne30np4.pg3,ne30np4,ne60np4,ne120np4,ne120np4.pg2,ne120np4.pg3,ne0np4CONUS.ne30x8,ne0np4.ARCTIC.ne30x4,ne0np4.ARCTICGRIS.ne30x8,ne240np4,1km-merge-10min,C24,C48,C96,C192,C384"> Horizontal resolutions Note: 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM toolsI From a1fb1a3087014fd5f67d5fbb4bab2496f8f6d563 Mon Sep 17 00:00:00 2001 From: adamrher Date: Mon, 27 Mar 2023 10:10:05 -0600 Subject: [PATCH 0753/2067] remade all surface datasets using dev120 tools --- bld/namelist_files/namelist_defaults_ctsm.xml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index add537337a..237b14f5e9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1093,13 +1093,13 @@ lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230123.nc -/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230221.nc +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230326.nc -/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230221.nc +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230326.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc -/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230221.nc +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230326.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr2000_c200426.nc @@ -1174,11 +1174,11 @@ lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230123.nc -/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230221.nc +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230326.nc -/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230221.nc +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230326.nc -/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230221.nc +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230326.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc @@ -1246,11 +1246,11 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc /glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230221.nc + >/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230326.nc /glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230221.nc + >/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230326.nc /glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230221.nc + >/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230326.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc Date: Mon, 27 Mar 2023 17:07:05 -0600 Subject: [PATCH 0754/2067] update parameter file pointer --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 41103b5259..ff9caff5c1 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221128.nc +lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc From 2c486781d2fc19b7ff678c393e803767feab8d15 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 28 Mar 2023 14:36:42 -0600 Subject: [PATCH 0755/2067] Increase wallclock time for fates f10 gnu test --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 40ab7a48df..38125d80bc 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1876,7 +1876,7 @@ - + From 02a4f9ccca597b32cda5adea59a632de38db72a7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 28 Mar 2023 14:52:42 -0600 Subject: [PATCH 0756/2067] update fates tag --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 219d1a9704..b1cffb373c 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.61.0_api.25.0.0 +tag = sci.1.65.2_api.25.4.0 required = True [externals_description] From d94f5d09a9b505e844920b2d4dff18d291af7c26 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 29 Mar 2023 15:11:07 -0600 Subject: [PATCH 0757/2067] include third datm stream for NEON --- cime_config/config_component.xml | 10 ++++++++++ cime_config/usermods_dirs/NEON/NIWO/shell_commands | 2 ++ cime_config/usermods_dirs/NEON/defaults/shell_commands | 2 +- .../usermods_dirs/NEON/defaults/user_nl_datm_streams | 10 ---------- 4 files changed, 13 insertions(+), 11 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 82c2d545b3..7e11047b6b 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -297,6 +297,16 @@ ABBY,BLAN,CPER,DEJU,GRSM,HEAL,KONA,LENO,NIWO,ONAQ,PUUM,SERC,SRER,TALL,TREE,WOOD, BARR,BONA,DCFS,DELA,GUAN,JERC,KONZ,MLBS,NOGP,ORNL,RMNP,SJER,STEI,TEAK,UKFS,WREF, BART,CLBJ,DSNY,HARV,JORN,LAJA,MOAB,OAES,OSBS,SCBI,SOAP,STER,TOOL,UNDE,YELL, + NEON_PRECIP.ABBY,NEON_PRECIP.BLAN,NEON_PRECIP.CPER,NEON_PRECIP.DEJU,NEON_PRECIP.GRSM, + NEON_PRECIP.HEAL,NEON_PRECIP.KONA,NEON_PRECIP.LENO,NEON_PRECIP.NIWO,NEON_PRECIP.ONAQ, + NEON_PRECIP.PUUM,NEON_PRECIP.SERC,NEON_PRECIP.SRER,NEON_PRECIP.TALL,NEON_PRECIP.TREE, + NEON_PRECIP.WOOD,NEON_PRECIP.BARR,NEON_PRECIP.BONA,NEON_PRECIP.DCFS,NEON_PRECIP.DELA, + NEON_PRECIP.GUAN,NEON_PRECIP.JERC,NEON_PRECIP.KONZ,NEON_PRECIP.MLBS,NEON_PRECIP.NOGP, + NEON_PRECIP.ORNL,NEON_PRECIP.RMNP,NEON_PRECIP.SJER,NEON_PRECIP.STEI,NEON_PRECIP.TEAK, + NEON_PRECIP.UKFS,NEON_PRECIP.WREF,NEON_PRECIP.BART,NEON_PRECIP.CLBJ,NEON_PRECIP.DSNY, + NEON_PRECIP.HARV,NEON_PRECIP.JORN,NEON_PRECIP.LAJA,NEON_PRECIP.MOAB,NEON_PRECIP.OAES, + NEON_PRECIP.OSBS,NEON_PRECIP.SCBI,NEON_PRECIP.SOAP,NEON_PRECIP.STER,NEON_PRECIP.TOOL, + NEON_PRECIP.UNDE,NEON_PRECIP.YELL, PRISM_PRECIP.ABBY,PRISM_PRECIP.BLAN,PRISM_PRECIP.CPER,PRISM_PRECIP.DEJU,PRISM_PRECIP.GRSM, PRISM_PRECIP.HEAL,PRISM_PRECIP.KONA,PRISM_PRECIP.LENO,PRISM_PRECIP.NIWO,PRISM_PRECIP.ONAQ, PRISM_PRECIP.PUUM,PRISM_PRECIP.SERC,PRISM_PRECIP.SRER,PRISM_PRECIP.TALL,PRISM_PRECIP.TREE, diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index 65926f2188..746a47d8c0 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -1,3 +1,5 @@ ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 +./xmlchange DATM_YR_END=2018 +# remove DATM_YR_END xml change when running with PRISM precipitation diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 0cbba60f84..ad23164b73 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -1,6 +1,6 @@ #!/bin/bash ./xmlchange CLM_USRDAT_NAME=NEON -# This is where we want to implement NEON.PRISM; in the current state, doing so causes SVN failures +# This can be set to either NEON or NEON.PRISM ./xmlchange CCSM_CO2_PPMV=408.83 # Set data forcing data to future scenario so will have data from 2018 to present-day ./xmlchange DATM_PRESAERO=SSP3-7.0 diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams index 16b7c739a7..53c4e4e4a7 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams @@ -47,13 +47,3 @@ NEON.${NEONSITE}:datavars = \ PSRF Sa_pbot, \ FLDS Faxa_lwdn -NEON.PRISM_PRECIP.${NEONSITE}:datavars = \ - PRECIP Faxa_precn - -NEON.PRISM_PRECIP.${NEONSITE}:datafiles = \ - /glade/u/home/tking/neon/prism_${NEONSITE}_2018.nc, \ - /glade/u/home/tking/neon/prism_${NEONSITE}_2019.nc, \ - /glade/u/home/tking/neon/prism_${NEONSITE}_2020.nc, \ - /glade/u/home/tking/neon/prism_${NEONSITE}_2021.nc, \ - /glade/u/home/tking/neon/prism_${NEONSITE}_2022.nc - From e09b21c9e6a596567ac8a20b693df681943d0ab0 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 31 Mar 2023 12:26:49 -0600 Subject: [PATCH 0758/2067] implement shell command switch for datm_yr_* --- cime_config/usermods_dirs/NEON/MLBS/shell_commands | 4 +++- cime_config/usermods_dirs/NEON/MOAB/shell_commands | 4 +++- cime_config/usermods_dirs/NEON/NIWO/shell_commands | 4 +++- cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 4 +++- cime_config/usermods_dirs/NEON/SJER/shell_commands | 5 ++++- cime_config/usermods_dirs/NEON/TEAK/shell_commands | 5 ++++- cime_config/usermods_dirs/NEON/WREF/shell_commands | 5 ++++- cime_config/usermods_dirs/NEON/YELL/shell_commands | 5 ++++- 8 files changed, 28 insertions(+), 8 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index d5de0f64eb..3070c7d594 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -2,7 +2,9 @@ ./xmlchange NEONSITE=MLBS ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 -./xmlchange DATM_YR_END=2019 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_END=2019 +fi # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 96d0bcbe68..c6e483d0a9 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -2,7 +2,9 @@ ./xmlchange NEONSITE=MOAB ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 -./xmlchange DATM_YR_END=2020 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_END=2020 +fi # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2021 diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index 746a47d8c0..3f40b8b514 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -1,5 +1,7 @@ ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 -./xmlchange DATM_YR_END=2018 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_END=2018 +fi # remove DATM_YR_END xml change when running with PRISM precipitation diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 511813398b..9b54cfb0a9 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -2,7 +2,9 @@ ./xmlchange NEONSITE=ONAQ ./xmlchange PTS_LON=247.54755 ./xmlchange PTS_LAT=40.17760 -./xmlchange DATM_YR_END=2019 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_END=2019 +fi # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 6e05d23792..e521af98a8 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -2,7 +2,10 @@ ./xmlchange NEONSITE=SJER ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +./xmlchange DATM_YR_ALIGN=2019 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_START=2019 +fi # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 9058eda022..c0930905a0 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -2,7 +2,10 @@ ./xmlchange NEONSITE=TEAK ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +./xmlchange DATM_YR_ALIGN=2019 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_START=2019 +fi # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index 807055ae6e..e6fc742fe3 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -2,7 +2,10 @@ ./xmlchange NEONSITE=WREF ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +./xmlchange DATM_YR_ALIGN=2019 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_START=2019 +fi # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index 800d7d01ad..d313af5dba 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -2,7 +2,10 @@ ./xmlchange NEONSITE=YELL ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 +./xmlchange DATM_YR_ALIGN=2019 +if [[$CLM_USRDAT_NAME = 'NEON']]; then + ./xmlchange DATM_YR_START=2019 +fi # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 From f11fe378abce6e68886994005967ea6cffa16914 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 31 Mar 2023 13:56:32 -0600 Subject: [PATCH 0759/2067] update shell command if nesting and non CONUS sites --- cime_config/config_component.xml | 20 +++++++++---------- .../usermods_dirs/NEON/MLBS/shell_commands | 2 +- .../usermods_dirs/NEON/MOAB/shell_commands | 13 ++++++------ .../usermods_dirs/NEON/NIWO/shell_commands | 1 - .../usermods_dirs/NEON/ONAQ/shell_commands | 13 ++++++------ .../usermods_dirs/NEON/SJER/shell_commands | 13 ++++++------ .../usermods_dirs/NEON/TEAK/shell_commands | 13 ++++++------ .../usermods_dirs/NEON/WREF/shell_commands | 13 ++++++------ .../usermods_dirs/NEON/YELL/shell_commands | 13 ++++++------ 9 files changed, 53 insertions(+), 48 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 7e11047b6b..786ce7cf42 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -307,16 +307,16 @@ NEON_PRECIP.HARV,NEON_PRECIP.JORN,NEON_PRECIP.LAJA,NEON_PRECIP.MOAB,NEON_PRECIP.OAES, NEON_PRECIP.OSBS,NEON_PRECIP.SCBI,NEON_PRECIP.SOAP,NEON_PRECIP.STER,NEON_PRECIP.TOOL, NEON_PRECIP.UNDE,NEON_PRECIP.YELL, - PRISM_PRECIP.ABBY,PRISM_PRECIP.BLAN,PRISM_PRECIP.CPER,PRISM_PRECIP.DEJU,PRISM_PRECIP.GRSM, - PRISM_PRECIP.HEAL,PRISM_PRECIP.KONA,PRISM_PRECIP.LENO,PRISM_PRECIP.NIWO,PRISM_PRECIP.ONAQ, - PRISM_PRECIP.PUUM,PRISM_PRECIP.SERC,PRISM_PRECIP.SRER,PRISM_PRECIP.TALL,PRISM_PRECIP.TREE, - PRISM_PRECIP.WOOD,PRISM_PRECIP.BARR,PRISM_PRECIP.BONA,PRISM_PRECIP.DCFS,PRISM_PRECIP.DELA, - PRISM_PRECIP.GUAN,PRISM_PRECIP.JERC,PRISM_PRECIP.KONZ,PRISM_PRECIP.MLBS,PRISM_PRECIP.NOGP, - PRISM_PRECIP.ORNL,PRISM_PRECIP.RMNP,PRISM_PRECIP.SJER,PRISM_PRECIP.STEI,PRISM_PRECIP.TEAK, - PRISM_PRECIP.UKFS,PRISM_PRECIP.WREF,PRISM_PRECIP.BART,PRISM_PRECIP.CLBJ,PRISM_PRECIP.DSNY, - PRISM_PRECIP.HARV,PRISM_PRECIP.JORN,PRISM_PRECIP.LAJA,PRISM_PRECIP.MOAB,PRISM_PRECIP.OAES, - PRISM_PRECIP.OSBS,PRISM_PRECIP.SCBI,PRISM_PRECIP.SOAP,PRISM_PRECIP.STER,PRISM_PRECIP.TOOL, - PRISM_PRECIP.UNDE,PRISM_PRECIP.YELL, + PRISM_PRECIP.ABBY,PRISM_PRECIP.BLAN,PRISM_PRECIP.CPER,PRISM_PRECIP.GRSM, + PRISM_PRECIP.KONA,PRISM_PRECIP.LENO,PRISM_PRECIP.NIWO,PRISM_PRECIP.ONAQ, + PRISM_PRECIP.SERC,PRISM_PRECIP.SRER,PRISM_PRECIP.TALL,PRISM_PRECIP.TREE, + PRISM_PRECIP.WOOD,PRISM_PRECIP.BONA,PRISM_PRECIP.DCFS,PRISM_PRECIP.DELA, + PRISM_PRECIP.JERC,PRISM_PRECIP.KONZ,PRISM_PRECIP.MLBS,PRISM_PRECIP.NOGP, + PRISM_PRECIP.ORNL,PRISM_PRECIP.RMNP,PRISM_PRECIP.SJER,PRISM_PRECIP.STEI, + PRISM_PRECIP.TEAK,PRISM_PRECIP.UKFS,PRISM_PRECIP.WREF,PRISM_PRECIP.BART, + PRISM_PRECIP.CLBJ,PRISM_PRECIP.DSNY,PRISM_PRECIP.HARV,PRISM_PRECIP.JORN, + PRISM_PRECIP.MOAB,PRISM_PRECIP.OAES,PRISM_PRECIP.OSBS,PRISM_PRECIP.SCBI, + PRISM_PRECIP.SOAP,PRISM_PRECIP.STER,PRISM_PRECIP.UNDE,PRISM_PRECIP.YELL, run_component_ctsm diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 3070c7d594..376fc42add 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_END=2019 + ./xmlchange DATM_YR_END=2019 fi # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index c6e483d0a9..6a811c1e4a 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -3,10 +3,11 @@ ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_END=2020 -fi -# Different default number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange DATM_YR_END=2021 - ./xmlchange STOP_N=36 + # Different default number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2021 + ./xmlchange STOP_N=36 + else + ./xmlchange DATM_YR_END=2020 + fi fi diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index 3f40b8b514..483647d965 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -4,4 +4,3 @@ if [[$CLM_USRDAT_NAME = 'NEON']]; then ./xmlchange DATM_YR_END=2018 fi -# remove DATM_YR_END xml change when running with PRISM precipitation diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 9b54cfb0a9..f38cc944b6 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -3,10 +3,11 @@ ./xmlchange PTS_LON=247.54755 ./xmlchange PTS_LAT=40.17760 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_END=2019 -fi -# Different default number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 + # Different default number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 + ./xmlchange STOP_N=24 + else + ./xmlchange DATM_YR_END=2019 + fi fi diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index e521af98a8..4b95814c7b 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -4,11 +4,12 @@ ./xmlchange PTS_LAT=37.107117 ./xmlchange DATM_YR_ALIGN=2019 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_START=2019 -fi -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + # Different default start date and number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + else + ./xmlchange DATM_YR_START=2019 + fi fi diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index c0930905a0..064354edb5 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -4,10 +4,11 @@ ./xmlchange PTS_LAT=37.006472 ./xmlchange DATM_YR_ALIGN=2019 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_START=2019 -fi -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + # Different default start date and number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + else + ./xmlchange DATM_YR_START=2019 + fi fi diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index e6fc742fe3..9be4d1719a 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -4,10 +4,11 @@ ./xmlchange PTS_LAT=45.81637 ./xmlchange DATM_YR_ALIGN=2019 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_START=2019 -fi -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + # Different default start date and number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + else + ./xmlchange DATM_YR_START=2019 + fi fi diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index d313af5dba..bb76a7cc34 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -4,10 +4,11 @@ ./xmlchange PTS_LAT=44.95597 ./xmlchange DATM_YR_ALIGN=2019 if [[$CLM_USRDAT_NAME = 'NEON']]; then - ./xmlchange DATM_YR_START=2019 -fi -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + # Different default start date and number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + else + ./xmlchange DATM_YR_START=2019 + fi fi From 84d7f0df9acbd718002652e98c50d327e2b56b02 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 31 Mar 2023 14:36:24 -0600 Subject: [PATCH 0760/2067] remove BONA prism precip --- cime_config/config_component.xml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 786ce7cf42..b0f77cb1c3 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -310,13 +310,13 @@ PRISM_PRECIP.ABBY,PRISM_PRECIP.BLAN,PRISM_PRECIP.CPER,PRISM_PRECIP.GRSM, PRISM_PRECIP.KONA,PRISM_PRECIP.LENO,PRISM_PRECIP.NIWO,PRISM_PRECIP.ONAQ, PRISM_PRECIP.SERC,PRISM_PRECIP.SRER,PRISM_PRECIP.TALL,PRISM_PRECIP.TREE, - PRISM_PRECIP.WOOD,PRISM_PRECIP.BONA,PRISM_PRECIP.DCFS,PRISM_PRECIP.DELA, - PRISM_PRECIP.JERC,PRISM_PRECIP.KONZ,PRISM_PRECIP.MLBS,PRISM_PRECIP.NOGP, - PRISM_PRECIP.ORNL,PRISM_PRECIP.RMNP,PRISM_PRECIP.SJER,PRISM_PRECIP.STEI, - PRISM_PRECIP.TEAK,PRISM_PRECIP.UKFS,PRISM_PRECIP.WREF,PRISM_PRECIP.BART, - PRISM_PRECIP.CLBJ,PRISM_PRECIP.DSNY,PRISM_PRECIP.HARV,PRISM_PRECIP.JORN, - PRISM_PRECIP.MOAB,PRISM_PRECIP.OAES,PRISM_PRECIP.OSBS,PRISM_PRECIP.SCBI, - PRISM_PRECIP.SOAP,PRISM_PRECIP.STER,PRISM_PRECIP.UNDE,PRISM_PRECIP.YELL, + PRISM_PRECIP.WOOD,PRISM_PRECIP.DCFS,PRISM_PRECIP.DELA,PRISM_PRECIP.JERC, + PRISM_PRECIP.KONZ,PRISM_PRECIP.MLBS,PRISM_PRECIP.NOGP,PRISM_PRECIP.ORNL, + PRISM_PRECIP.RMNP,PRISM_PRECIP.SJER,PRISM_PRECIP.STEI,PRISM_PRECIP.TEAK, + PRISM_PRECIP.UKFS,PRISM_PRECIP.WREF,PRISM_PRECIP.BART,PRISM_PRECIP.CLBJ, + PRISM_PRECIP.DSNY,PRISM_PRECIP.HARV,PRISM_PRECIP.JORN,PRISM_PRECIP.MOAB, + PRISM_PRECIP.OAES,PRISM_PRECIP.OSBS,PRISM_PRECIP.SCBI,PRISM_PRECIP.SOAP, + PRISM_PRECIP.STER,PRISM_PRECIP.UNDE,PRISM_PRECIP.YELL, run_component_ctsm From 87fc26fae335d3371e1b06851baf8443f545bc59 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 31 Mar 2023 15:59:41 -0600 Subject: [PATCH 0761/2067] CLMBuildNamelist.pm now requires use_mxmat false when generate_crop_gdds true. --- bld/CLMBuildNamelist.pm | 13 +++++++++++++ src/biogeochem/CNPhenologyMod.F90 | 3 --- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index e8af987ae4..2427a031a3 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3802,12 +3802,14 @@ sub setup_logic_lai_streams { sub setup_logic_cropcal_streams { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + # Set first and last stream years add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); + # Set align year, if first and last years are different if ( $nl->get_value('stream_year_first_cropcal') != $nl->get_value('stream_year_last_cropcal') ) { @@ -3815,6 +3817,17 @@ sub setup_logic_cropcal_streams { 'model_year_align_cropcal', 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } + + # Set up other crop calendar parameters + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat'); + + # Consistency checking: Do not generate_crop_gdds without use_mxmat false + my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ; + my $use_mxmat = $nl->get_value('use_mxmat') ; + if ( $generate_crop_gdds and $use_mxmat ) { + $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" ); + } } #------------------------------------------------------------------------------- diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 3a03068542..6d6c42fad5 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -519,9 +519,6 @@ subroutine CNPhenologyInit(bounds) call endrun(msg="ERROR crit_dayl_lat_slope cannot allow crit_dayl longer than a day"//errmsg(sourcefile, __LINE__)) end if end if - if (generate_crop_gdds .and. use_mxmat) then - call endrun(msg="ERROR If setting generate_crop_gdds to .true., you must set use_mxmat to .false."//errmsg(sourcefile, __LINE__)) - endif end subroutine CNPhenologyInit From cadc9cd67447206a687195a8c49f288a42d03326 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 31 Mar 2023 16:18:01 -0600 Subject: [PATCH 0762/2067] Bugfixes to previous. --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 2427a031a3..77050f0211 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3825,7 +3825,7 @@ sub setup_logic_cropcal_streams { # Consistency checking: Do not generate_crop_gdds without use_mxmat false my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ; my $use_mxmat = $nl->get_value('use_mxmat') ; - if ( $generate_crop_gdds and $use_mxmat ) { + if ( $generate_crop_gdds eq '.true.' and $use_mxmat eq '.true.' ) { $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" ); } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index eb235d903c..558db5ed5a 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -561,7 +561,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. Constant .false. -.false. +.true. .false. From de052fc91854d0f4a065857b5ff8704131111105 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 3 Apr 2023 16:47:22 -0600 Subject: [PATCH 0763/2067] Added setup_for_gddgen.sh. --- .../ctsm/crop_calendars/setup_for_gddgen.sh | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100755 python/ctsm/crop_calendars/setup_for_gddgen.sh diff --git a/python/ctsm/crop_calendars/setup_for_gddgen.sh b/python/ctsm/crop_calendars/setup_for_gddgen.sh new file mode 100755 index 0000000000..15b82f1a30 --- /dev/null +++ b/python/ctsm/crop_calendars/setup_for_gddgen.sh @@ -0,0 +1,91 @@ +#!/bin/bash +set -e + +# This script provides a general method to set up a GDD-generating run from +# an existing case directory. Call it from the case directory, preferably +# on a compute node, as the "If needed, generate a surface dataset file" +# step can be intensive. + +cropcals_python_dir="/glade/u/home/samrabin/CTSM_cropcals_hist/crop_calendars" + +# Set up +cp user_nl_clm.orig user_nl_clm +./check_case 1>/dev/null + +# Ensure that run will go for at least 4 years; otherwise error. +stop_option=$(./xmlquery --value STOP_OPTION) +stop_n=$(./xmlquery --value STOP_N) +min_Nyears=4 +errMsg="GDD-generating runs must be at least ${min_Nyears} years long." +if [[ "${stop_option}" == "nyear"* ]]; then + if [[ "${stop_n}" -lt ${min_Nyears} ]]; then + echo ${errMsg} >&2 + exit 1 + fi +elif [[ "${stop_option}" == "nmonth"* ]]; then + if [[ "${stop_n}" -lt $((min_Nyears * 12)) ]]; then + echo ${errMsg} >&2 + exit 1 + fi +elif [[ "${stop_option}" == "nday"* ]]; then + if [[ "${stop_n}" -lt $((min_Nyears * 365)) ]]; then + echo ${errMsg} >&2 + exit 1 + fi +else + echo "STOP_OPTION '${stop_option}' not recognized by preprocess_inputs.sh" >&2 + exit 1 +fi + +# If needed, generate a surface dataset file with no crops missing years +flanduse_timeseries="$(grep -h -i "flanduse_timeseries" CaseDocs/* | sed "s/ flanduse_timeseries = //" | sed "s/'//g")" +if [[ "${flanduse_timeseries}" != "" ]]; then + if [[ ! -e "${flanduse_timeseries}" ]]; then + echo "flanduse_timeseries not found: ${flanduse_timeseries}" >&2 + exit 1 + fi + + # Make new fsurdat file (in case directory) + module unload python + module load conda + conda activate npl + fsurdat="$(grep -h -i "fsurdat" CaseDocs/* | sed "s/ fsurdat = //" | sed "s/'//g")" + paramfile="$(grep -h -i "paramfile" CaseDocs/* | sed "s/ paramfile = //" | sed "s/'//g")" + set +e + python "${cropcals_python_dir}/make_surface_for_gddgen.py" --flanduse_timeseries "${flanduse_timeseries}" --fsurdat "${fsurdat}" --paramfile "${paramfile}" > make_surface_for_gddgen.log + if [[ $? -ne 0 ]]; then + cat make_surface_for_gddgen.log + exit 1 + fi + set -e + new_fsurdat="$PWD/$(cat make_surface_for_gddgen.log)" + rm make_surface_for_gddgen.log + + # Change fsurdat to point to that file and disable transient crops + echo "fsurdat = '${new_fsurdat}'" >> user_nl_clm + echo "do_transient_crops = .false." >> user_nl_clm + echo "flanduse_timeseries = ''" >> user_nl_clm +fi + +# user_nl_clm: Replace MESHFILE_PLACEHOLDER with the appropriate file for this resolution +file_mesh="$(./xmlquery --value LND_DOMAIN_MESH)" +sed -i "s@MESHFILE_PLACEHOLDER@${file_mesh}@" user_nl_clm + +# user_nl_clm: Replace SDATEFILE_PLACEHOLDER with the appropriate file for this resolution. +# EVENTUALLY: Generate sdate (and hdate) file at case resolution from GGCMI files; save to case directory and use that. +lnd_grid=$(./xmlquery --value LND_GRID) +blessed_crop_dates_dir="/glade/work/samrabin/crop_dates_blessed" +if [[ "${lnd_grid}" == "10x15" ]]; then + file_sdates="${blessed_crop_dates_dir}/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc" +elif [[ "${lnd_grid}" == "1.9x2.5" ]]; then + file_sdates="${blessed_crop_dates_dir}/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc" +else + echo "Land resolution (LND_GRID) '${lnd_grid}' not recognized by preprocess_inputs.sh" >&2 + exit 1 +fi +sed -i "s@SDATEFILE_PLACEHOLDER@${file_sdates}@" user_nl_clm + +# Rebuild namelists +./check_case 1>/dev/null + +exit 0 From 525d79ecc7d4db4af3a4222b94cdd7e854436845 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 31 Mar 2023 15:50:44 -0600 Subject: [PATCH 0764/2067] Revert some commits now that FUNITCTSM works again - Revert "Add Fortran unit tests as a separate test to run". This reverts commit 2ee9024597cd21c1b755bd24e55e4b1d856d256d. - Revert "Add FUNITCTSM test to expected fails list". This reverts commit 3cd1351964acd9e3fea7d8b3ced2f53de16bf13e. --- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- doc/.ChangeLog_template | 11 +++-------- 2 files changed, 3 insertions(+), 15 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 01d0b738be..d9a1c1b6fd 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -51,13 +51,6 @@ - - - FAIL - #1972 - - - diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index ccf5752b7d..63f4628bad 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -121,15 +121,10 @@ infrastructure should be run when appropriate, as described below. clm_pymods test suite on cheyenne - - regular tests: - - aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing - - Fortran unit tests on cheyenne (until https://github.com/ESCOMP/CTSM/issues/1972 is resolved): from src, run: - ../cime/scripts/fortran_unit_testing/run_tests.py --build-dir `mktemp -d --tmpdir=. unit_tests.XXXXXXXX` - - aux_clm on cheyenne ------------ - aux_clm on izumi --------------- - Fortran unit tests on cheyenne - + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + cheyenne ---- + izumi ------- fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) cheyenne ---- From a0abc298330c2aceb51830c0013b4d3ae6bb53d5 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 3 Apr 2023 18:15:43 -0600 Subject: [PATCH 0765/2067] Update fates tag externals pointer This tag includes a fix to avoid line continuation issues seen on izumi. --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index b1cffb373c..f4a9eae9c6 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.65.2_api.25.4.0 +tag = sci.1.65.3_api.25.4.0 required = True [externals_description] From 8875e081e1cdeb8b41e73a2cb3606a2817829c84 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 12:44:56 -0600 Subject: [PATCH 0766/2067] Improved portability of setup_for_gddgen.sh. --- .../ctsm/crop_calendars/setup_for_gddgen.sh | 40 ++++++++++++++----- 1 file changed, 31 insertions(+), 9 deletions(-) diff --git a/python/ctsm/crop_calendars/setup_for_gddgen.sh b/python/ctsm/crop_calendars/setup_for_gddgen.sh index 15b82f1a30..e48592e2de 100755 --- a/python/ctsm/crop_calendars/setup_for_gddgen.sh +++ b/python/ctsm/crop_calendars/setup_for_gddgen.sh @@ -10,11 +10,19 @@ cropcals_python_dir="/glade/u/home/samrabin/CTSM_cropcals_hist/crop_calendars" # Set up cp user_nl_clm.orig user_nl_clm -./check_case 1>/dev/null +set +e +./check_case 1>.check_case_tmp 2>&1 +check_case_result=$? +set -e +if [[ ${check_case_result} -ne 0 ]]; then + echo "check_case failed; ignoring" +# cat .check_case_tmp +fi +rm .check_case_tmp # Ensure that run will go for at least 4 years; otherwise error. -stop_option=$(./xmlquery --value STOP_OPTION) -stop_n=$(./xmlquery --value STOP_N) +stop_option=$(./xmlquery -N --value STOP_OPTION) +stop_n=$(./xmlquery -N --value STOP_N) min_Nyears=4 errMsg="GDD-generating runs must be at least ${min_Nyears} years long." if [[ "${stop_option}" == "nyear"* ]]; then @@ -46,8 +54,14 @@ if [[ "${flanduse_timeseries}" != "" ]]; then fi # Make new fsurdat file (in case directory) - module unload python - module load conda + set +e + module is-loaded conda + conda_not_loaded=$? + set -e + if [[ ${conda_not_loaded} -ne 0 ]]; then + module unload python + module load conda + fi conda activate npl fsurdat="$(grep -h -i "fsurdat" CaseDocs/* | sed "s/ fsurdat = //" | sed "s/'//g")" paramfile="$(grep -h -i "paramfile" CaseDocs/* | sed "s/ paramfile = //" | sed "s/'//g")" @@ -68,12 +82,12 @@ if [[ "${flanduse_timeseries}" != "" ]]; then fi # user_nl_clm: Replace MESHFILE_PLACEHOLDER with the appropriate file for this resolution -file_mesh="$(./xmlquery --value LND_DOMAIN_MESH)" +file_mesh="$(./xmlquery -N --value LND_DOMAIN_MESH)" sed -i "s@MESHFILE_PLACEHOLDER@${file_mesh}@" user_nl_clm # user_nl_clm: Replace SDATEFILE_PLACEHOLDER with the appropriate file for this resolution. # EVENTUALLY: Generate sdate (and hdate) file at case resolution from GGCMI files; save to case directory and use that. -lnd_grid=$(./xmlquery --value LND_GRID) +lnd_grid=$(./xmlquery -N --value LND_GRID) blessed_crop_dates_dir="/glade/work/samrabin/crop_dates_blessed" if [[ "${lnd_grid}" == "10x15" ]]; then file_sdates="${blessed_crop_dates_dir}/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc" @@ -85,7 +99,15 @@ else fi sed -i "s@SDATEFILE_PLACEHOLDER@${file_sdates}@" user_nl_clm -# Rebuild namelists -./check_case 1>/dev/null +# Rebuild namelists (optional, so don't worry if it doesn't work) +set +e +./check_case 1>.check_case_tmp 2>&1 +check_case_result=$? +set -e +if [[ ${check_case_result} -ne 0 ]]; then + echo "check_case failed; ignoring" +# cat .check_case_tmp +fi +rm .check_case_tmp exit 0 From ce6be4cbc99e7e49cc66da7dea256510375ca04d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 15:46:23 -0600 Subject: [PATCH 0767/2067] setup_for_gddgen.sh now sets use_init_interp if needed. --- python/ctsm/crop_calendars/setup_for_gddgen.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/setup_for_gddgen.sh b/python/ctsm/crop_calendars/setup_for_gddgen.sh index e48592e2de..0073c084fa 100755 --- a/python/ctsm/crop_calendars/setup_for_gddgen.sh +++ b/python/ctsm/crop_calendars/setup_for_gddgen.sh @@ -75,10 +75,11 @@ if [[ "${flanduse_timeseries}" != "" ]]; then new_fsurdat="$PWD/$(cat make_surface_for_gddgen.log)" rm make_surface_for_gddgen.log - # Change fsurdat to point to that file and disable transient crops + # Change fsurdat to point to that file, disable transient crops, etc. echo "fsurdat = '${new_fsurdat}'" >> user_nl_clm echo "do_transient_crops = .false." >> user_nl_clm echo "flanduse_timeseries = ''" >> user_nl_clm + echo "use_init_interp = .true." >> user_nl_clm fi # user_nl_clm: Replace MESHFILE_PLACEHOLDER with the appropriate file for this resolution From f39e7eaafd9cfe170a06079d8a4abaf3ad9dfe7a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:12:02 -0600 Subject: [PATCH 0768/2067] Added generate_gdds_testing.sh. --- .../crop_calendars/generate_gdds_testing.sh | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100755 python/ctsm/crop_calendars/generate_gdds_testing.sh diff --git a/python/ctsm/crop_calendars/generate_gdds_testing.sh b/python/ctsm/crop_calendars/generate_gdds_testing.sh new file mode 100755 index 0000000000..ced910b2f6 --- /dev/null +++ b/python/ctsm/crop_calendars/generate_gdds_testing.sh @@ -0,0 +1,48 @@ +#!/bin/bash +set -e + +cropcals_python_dir="/glade/u/home/samrabin/CTSM_cropcals_hist/crop_calendars" + +# Where did the run happen? If not provided, the assumption is +# that this script is being called as POSTRUN_SCRIPT. Therefore, +# the outputs will still be in the run directory. We also assume +# this is being run as part of a test suite, so we'll save the +# generate_gdds.py outputs to the case directory (so subsequent +# tests can find them easily). +run_outputs="$1" +if [[ "${run_outputs}" == "" ]]; then + run_outputs="$(./xmlquery --value RUNDIR)" + save_to="." +else + save_to="${run_outputs}" +fi + +# Set ${y1} to third year in run +y1=$(ls -1 *clm2.h1* | grep -oE "h1.[0-9]{4}" | sed "s/h1.//" | head -n 1) +y1=$((y1 + 2)) + +# Set ${yN} to last full year – 1 +yN=$(ls -1 *clm2.h1* | grep -oE "h1.[0-9]{4}" | sed "s/h1.//" | tail -n 1) +yN=$((yN - 1)) + +# Get ${sdates_file} from namelists +sdates_file="$(realpath "$(grep "sdate" CaseDocs/* | grep -oE "'.*'" | sed "s/'//g" | sed "s/.fill1//")")" +# Get ${hdates_file} from ${sdates_file} +hdates_file="${sdates_file/sdates/hdates}" + +#source ~/.bash_profile + +set +e +module is-loaded conda +conda_not_loaded=$? +set -e +if [[ ${conda_not_loaded} -ne 0 ]]; then + module unload python + module load conda +fi +conda activate npl +date +echo "Starting..." +python "${cropcals_python_dir}"/generate_gdds.py -r "${run_outputs}" -sd "${sdates_file}" -hd "${hdates_file}" -1 ${y1} -n ${yN} --dont-save-figs -o "${save_to}" + +exit 0 From 7a4616e5fdc231da70109c5a0d7a719dac42bc32 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:27:35 -0600 Subject: [PATCH 0769/2067] Replaced old cropcal tests with cropcals_generate_gdds. --- .../clm/cropcal_outputs/include_user_mods | 1 - .../clm/cropcal_outputs/user_nl_clm | 7 ---- .../clm/cropcals/include_user_mods | 1 - .../testmods_dirs/clm/cropcals/user_nl_clm | 7 ---- .../clm/cropcals_2deg/include_user_mods | 1 - .../clm/cropcals_2deg/shell_commands | 19 --------- .../clm/cropcals_2deg/user_nl_clm | 7 ---- .../clm/cropcals_generate_gdds/shell_commands | 12 ++++++ .../clm/cropcals_generate_gdds/user_nl_clm | 41 +++++++++++++++++++ .../clm/cropcals_gengdd/include_user_mods | 1 - .../clm/cropcals_gengdd/user_nl_clm | 11 ----- .../cropcals_gengdd_2deg/include_user_mods | 1 - .../clm/cropcals_gengdd_2deg/shell_commands | 3 -- .../clm/cropcals_gengdd_2deg/user_nl_clm | 11 ----- .../clm/cropcals_rx/include_user_mods | 1 - .../testmods_dirs/clm/cropcals_rx/user_nl_clm | 2 - .../clm/cropcals_rx_2deg/include_user_mods | 1 - .../clm/cropcals_rx_2deg/user_nl_clm | 2 - 18 files changed, 53 insertions(+), 76 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods delete mode 100755 cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm create mode 100755 cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods deleted file mode 100644 index 02ec13743f..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropMonthOutput diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm deleted file mode 100644 index dcd2e4af00..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcal_outputs/user_nl_clm +++ /dev/null @@ -1,7 +0,0 @@ -! Annual outputs -hist_fincl4 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' -hist_nhtfrq(4) = 17520 -hist_mfilt(4) = 999 -hist_type1d_pertape(4) = 'PFTS' -hist_dov2xy(4) = .false. - diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods deleted file mode 100644 index 904a7588cc..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropcal_outputs diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm deleted file mode 100644 index db20f8f759..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals/user_nl_clm +++ /dev/null @@ -1,7 +0,0 @@ -stream_year_first_cropcal = 2000 -stream_year_last_cropcal = 2000 -model_year_align_cropcal = 2000 - -stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/10x15_nomask_c110308_ESMFmesh.nc' -stream_fldFileName_sdate = '/glade/work/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.fill1.nc' - diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods deleted file mode 100644 index 39e898158f..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropcals diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands deleted file mode 100755 index bb2a5789b4..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/shell_commands +++ /dev/null @@ -1,19 +0,0 @@ -#!/bin/bash -set -e -set -x - -y1=1977 -refcase="cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.1958-2014" -refdir=/glade/work/samrabin/clm51_restarts/${refcase}.rest/${y1}-01-01-00000 - -#./xmlchange RUN_REFDIR="${refdir}" -# I don't know why the above doesn't work. -rundir="$(./xmlquery RUNDIR | sed -E "s/\s+RUNDIR:\s+//")" -rsync -ahm --info=progress2 --partial "${refdir}"/* "${rundir}"/ - -./xmlchange RUN_TYPE="hybrid" -./xmlchange RUN_REFCASE="${refcase}" -./xmlchange RUN_REFDATE="${y1}-01-01" -./xmlchange RUN_STARTDATE=${y1}0101 -./xmlchange DATM_YR_END=2014 -./xmlchange RESUBMIT=0 diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm deleted file mode 100644 index 79ba39a137..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_2deg/user_nl_clm +++ /dev/null @@ -1,7 +0,0 @@ -stream_year_first_cropcal = 2000 -stream_year_last_cropcal = 2000 -model_year_align_cropcal = 2000 - -stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/fv1.9x2.5_141008_ESMFmesh_c20191001.nc' -stream_fldFileName_sdate = '/glade/work/samrabin/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20220727_164727.fill1.nc' - diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands new file mode 100755 index 0000000000..03a2602565 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands @@ -0,0 +1,12 @@ +./xmlchange POSTRUN_SCRIPT="generate_gdds.sh",\ +RUN_STARTDATE="1995-01-01",\ +STOP_OPTION="nyears",STOP_N=10 + +# Try to do this as an interactive compute job, unless we're already on a compute node +ctsm_dir="$(./xmlquery -N --value COMP_ROOT_DIR_LND)" +setup_for_gddgen="${ctsm_dir}"/python/ctsm/crop_calendars/setup_for_gddgen.sh +if [[ "$(which qcmd)" != "" && "${PBS_JOBNAME}" == "" ]]; then + qcmd -- "${setup_for_gddgen}" +else + "${setup_for_gddgen}" +fi diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm new file mode 100644 index 0000000000..0bc0098111 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm @@ -0,0 +1,41 @@ +!---------------------------------------------------------------------------------- +! Users should add all user specific namelist changes below in the form of +! namelist_var = new_namelist_value +! +! EXCEPTIONS: +! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting +! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting +! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting +! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting +! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting +! Set co2_ppmv with CCSM_CO2_PPMV option +! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options +! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases +! (includes $inst_string for multi-ensemble cases) +! or with CLM_FORCE_COLDSTART to do a cold start +! or set it with an explicit filename here. +! Set maxpatch_glc with GLC_NEC option +! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable +!---------------------------------------------------------------------------------- + +stream_meshfile_cropcal = 'MESHFILE_PLACEHOLDER' +stream_fldFileName_sdate = 'SDATEFILE_PLACEHOLDER' +generate_crop_gdds = .true. +use_mxmat = .false. +stream_year_first_cropcal = 2000 +stream_year_last_cropcal = 2000 +model_year_align_cropcal = 2000 + +! (h1) Daily outputs for GDD generation and figure-making +hist_fincl2 = 'HUI', 'GDDACCUM', 'GDDHARV' +hist_nhtfrq(2) = -24 +hist_mfilt(2) = 365 +hist_type1d_pertape(2) = 'PFTS' +hist_dov2xy(2) = .false. + +! (h2) Annual outputs for GDD generation (checks) +hist_fincl3 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' +hist_nhtfrq(3) = 17520 +hist_mfilt(3) = 999 +hist_type1d_pertape(3) = 'PFTS' +hist_dov2xy(3) = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods deleted file mode 100644 index 39e898158f..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropcals diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm deleted file mode 100644 index 28c76c7f70..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd/user_nl_clm +++ /dev/null @@ -1,11 +0,0 @@ -generate_crop_gdds = .true. -use_mxmat = .false. -flanduse_timeseries = '/glade/work/samrabin/crop_dates/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.gddgen1976-2015.nc' -check_dynpft_consistency = .false. - -! Daily outputs for GDD generation -hist_fincl5 = 'HUI', 'GDDACCUM' -hist_nhtfrq(5) = -24 -hist_mfilt(5) = 365 -hist_type1d_pertape(5) = 'PFTS' -hist_dov2xy(5) = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods deleted file mode 100644 index 84fabe1cb0..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropcals_2deg diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands deleted file mode 100644 index e43aec57b6..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/shell_commands +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -./xmlchange CLM_BLDNML_OPTS="-no-fire_emis" --append diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm deleted file mode 100644 index a68ab94bb1..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_gengdd_2deg/user_nl_clm +++ /dev/null @@ -1,11 +0,0 @@ -generate_crop_gdds = .true. -use_mxmat = .false. -flanduse_timeseries = '/glade/work/samrabin/crop_dates/landuse.timeseries_1.9x2.5_hist_78pfts_CMIP6_simyr1850-2015_c170824.gddgen1976-2015.nc' -check_dynpft_consistency = .false. - -! Daily outputs for GDD generation -hist_fincl5 = 'HUI', 'GDDACCUM' -hist_nhtfrq(5) = -24 -hist_mfilt(5) = 365 -hist_type1d_pertape(5) = 'PFTS' -hist_dov2xy(5) = .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods deleted file mode 100644 index 39e898158f..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropcals diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm deleted file mode 100644 index ba9a16981c..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -generate_crop_gdds = .false. -stream_fldFileName_cultivar_gdds = '/glade/work/samrabin/crop_dates/gdds_20220602_231239.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods deleted file mode 100644 index 84fabe1cb0..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../cropcals_2deg diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm deleted file mode 100644 index 7136243ef8..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_rx_2deg/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -generate_crop_gdds = .false. -stream_fldFileName_cultivar_gdds = '/glade/work/samrabin/crop_dates/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1977-2014.gddgen/generate_gdds.2022-09-27/gdds_20220927_174954.nc' From ae16a3e935959ddb22f8607cfb06e42cabf1f354 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:32:53 -0600 Subject: [PATCH 0770/2067] cropcals_generate_gdds shell_commands now looks for generate_gdds.sh in the right place. --- .../testmods_dirs/clm/cropcals_generate_gdds/shell_commands | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands index 03a2602565..c292bf82f6 100755 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands @@ -1,9 +1,9 @@ -./xmlchange POSTRUN_SCRIPT="generate_gdds.sh",\ +ctsm_dir="$(./xmlquery -N --value COMP_ROOT_DIR_LND)" +./xmlchange POSTRUN_SCRIPT="${ctsm_dir}/python/ctsm/crop_calendars/generate_gdds.sh",\ RUN_STARTDATE="1995-01-01",\ STOP_OPTION="nyears",STOP_N=10 # Try to do this as an interactive compute job, unless we're already on a compute node -ctsm_dir="$(./xmlquery -N --value COMP_ROOT_DIR_LND)" setup_for_gddgen="${ctsm_dir}"/python/ctsm/crop_calendars/setup_for_gddgen.sh if [[ "$(which qcmd)" != "" && "${PBS_JOBNAME}" == "" ]]; then qcmd -- "${setup_for_gddgen}" From 527e0ae6fcfecd7319ce1946338fd82b513852bd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:39:45 -0600 Subject: [PATCH 0771/2067] cropcals_generate_gdds test shell_commands now respects test specification for start date and simulation length. --- .../testmods_dirs/clm/cropcals_generate_gdds/shell_commands | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands index c292bf82f6..8c2990368e 100755 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands @@ -1,7 +1,5 @@ ctsm_dir="$(./xmlquery -N --value COMP_ROOT_DIR_LND)" -./xmlchange POSTRUN_SCRIPT="${ctsm_dir}/python/ctsm/crop_calendars/generate_gdds.sh",\ -RUN_STARTDATE="1995-01-01",\ -STOP_OPTION="nyears",STOP_N=10 +./xmlchange POSTRUN_SCRIPT="${ctsm_dir}/python/ctsm/crop_calendars/generate_gdds.sh" # Try to do this as an interactive compute job, unless we're already on a compute node setup_for_gddgen="${ctsm_dir}"/python/ctsm/crop_calendars/setup_for_gddgen.sh From 526c2047ced5fdaabb6bd2fb604759c33d311737 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:48:23 -0600 Subject: [PATCH 0772/2067] Renamed generate_gdds_testing.sh to generate_gdds.sh. --- .../crop_calendars/{generate_gdds_testing.sh => generate_gdds.sh} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename python/ctsm/crop_calendars/{generate_gdds_testing.sh => generate_gdds.sh} (100%) diff --git a/python/ctsm/crop_calendars/generate_gdds_testing.sh b/python/ctsm/crop_calendars/generate_gdds.sh similarity index 100% rename from python/ctsm/crop_calendars/generate_gdds_testing.sh rename to python/ctsm/crop_calendars/generate_gdds.sh From 1f36f78658a5eaf68066df84f11c61587213c98a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:51:49 -0600 Subject: [PATCH 0773/2067] Removed an outdated development line from setup_for_gddgen.sh. --- python/ctsm/crop_calendars/setup_for_gddgen.sh | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/crop_calendars/setup_for_gddgen.sh b/python/ctsm/crop_calendars/setup_for_gddgen.sh index 0073c084fa..7d7e6c2f1f 100755 --- a/python/ctsm/crop_calendars/setup_for_gddgen.sh +++ b/python/ctsm/crop_calendars/setup_for_gddgen.sh @@ -9,7 +9,6 @@ set -e cropcals_python_dir="/glade/u/home/samrabin/CTSM_cropcals_hist/crop_calendars" # Set up -cp user_nl_clm.orig user_nl_clm set +e ./check_case 1>.check_case_tmp 2>&1 check_case_result=$? From 55ce27f1242fc2c4b8f91cc3bc68ad5847a2bde2 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 4 Apr 2023 15:52:33 -0700 Subject: [PATCH 0774/2067] Update Changelog --- doc/ChangeLog | 103 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 104 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 0776ca96f0..9311371add 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,107 @@ =============================================================== +Tag name: ctsm5.1.dev121 +Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) +Date: Tue Apr 4 04:34:20 PM MDT 2023 +One-line Summary: Changes soil moisture initialization logic for FATES + +Purpose and description of changes +---------------------------------- + +This PR changes the logic for soil moisture initialization to initialize +with wetter soils (75% of saturated water content, as opposed to 15% of +absolute water content) for all FATES configurations. The rationale for +this is that in FATES-nocomp simulations, Jessica Needham was finding very +high initial mortality rates in some seasonal tropical forest regions which +she traced it back to the initial soil moisture killing off plants before the +ecosystem could get established. + +This also updates the fates externals pointer to the latest tag which includes +a number of science updates since the last tag update and updates the the +default parameter file. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +Externals issues fixed (include issue #): + Partially addresses FATES#994 -- Bare ground establishment problem and increased soil moisture + +Notes of particular relevance for users +--------------------------------------- + +Changes made to namelist defaults (e.g., changed parameter values): + fates_paramfile updated to fates_params_api.25.4.0_12pft_c230327.nc + +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + FATES tests run against fates-sci.1.65.3_api.25.4.0-ctsm5.1.dev120 baseline + + +Answer changes +-------------- + +Changes answers relative to baseline: + + Changes answers in fates suite for all non-hydro fates tests since the soil + moisture initialization matches that of fates hydro now. Changes answer + for all fates testmods in the aux_clm suite as the science tag has iterated + forward by 4 minor version updates. All diffs accounted for with prior fates + suite tests. + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +- FATES: sci.1.61.0_api.25.0.0 -> sci.1.65.3_api.25.4.0 + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + + https://github.com/ESCOMP/CTSM/pull/1962 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev120 Originator(s): sacks (Bill Sacks) Date: Sat Mar 25 17:49:27 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index e718109e03..fb302ed794 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev121 glemieux 04/04/2023 Changes soil moisture initialization logic for FATES ctsm5.1.dev120 sacks 03/25/2023 Update externals and minor fixes ctsm5.1.dev119 slevis 03/16/2023 Allow gross unrepresented land use transition (PR #309) ctsm5.1.dev118 slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test From 8bc853295e66033045dab340a5b848fd971e8917 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 16:57:45 -0600 Subject: [PATCH 0775/2067] setup_for_gddgen.sh: Do not fail if sim length seems too short. --- python/ctsm/crop_calendars/setup_for_gddgen.sh | 14 +++++--------- 1 file changed, 5 insertions(+), 9 deletions(-) diff --git a/python/ctsm/crop_calendars/setup_for_gddgen.sh b/python/ctsm/crop_calendars/setup_for_gddgen.sh index 7d7e6c2f1f..01e910c83c 100755 --- a/python/ctsm/crop_calendars/setup_for_gddgen.sh +++ b/python/ctsm/crop_calendars/setup_for_gddgen.sh @@ -23,25 +23,21 @@ rm .check_case_tmp stop_option=$(./xmlquery -N --value STOP_OPTION) stop_n=$(./xmlquery -N --value STOP_N) min_Nyears=4 -errMsg="GDD-generating runs must be at least ${min_Nyears} years long." +errMsg="WARNING: GDD-generating runs must be at least ${min_Nyears} years long.\nNot erroring because this check seems to occur before simulation length from test specification is applied." if [[ "${stop_option}" == "nyear"* ]]; then if [[ "${stop_n}" -lt ${min_Nyears} ]]; then - echo ${errMsg} >&2 - exit 1 + echo -e ${errMsg} >&2 fi elif [[ "${stop_option}" == "nmonth"* ]]; then if [[ "${stop_n}" -lt $((min_Nyears * 12)) ]]; then - echo ${errMsg} >&2 - exit 1 + echo -e ${errMsg} >&2 fi elif [[ "${stop_option}" == "nday"* ]]; then if [[ "${stop_n}" -lt $((min_Nyears * 365)) ]]; then - echo ${errMsg} >&2 - exit 1 + echo -e ${errMsg} >&2 fi else - echo "STOP_OPTION '${stop_option}' not recognized by preprocess_inputs.sh" >&2 - exit 1 + echo "WARNING: STOP_OPTION '${stop_option}' not recognized by preprocess_inputs.sh" >&2 fi # If needed, generate a surface dataset file with no crops missing years From e0f50bb269e903eb579eeba09b76e1ea4d026b59 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 4 Apr 2023 17:10:48 -0600 Subject: [PATCH 0776/2067] cropcals_generate_gdds test: Call case.setup at beginning of shell_commands. --- .../testmods_dirs/clm/cropcals_generate_gdds/shell_commands | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands index 8c2990368e..352e099693 100755 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands @@ -1,3 +1,4 @@ +./case.setup ctsm_dir="$(./xmlquery -N --value COMP_ROOT_DIR_LND)" ./xmlchange POSTRUN_SCRIPT="${ctsm_dir}/python/ctsm/crop_calendars/generate_gdds.sh" From 0c7b8c4f3ae372c6af70687fb3617a6d3b62f0b1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 5 Apr 2023 09:16:08 -0600 Subject: [PATCH 0777/2067] Changelog updates --- doc/ChangeLog | 16 +++++++++------- doc/ChangeSum | 2 +- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 9311371add..53c04d01a4 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev121 Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) -Date: Tue Apr 4 04:34:20 PM MDT 2023 +Date: Wed Apr 5 09:15:55 MDT 2023 One-line Summary: Changes soil moisture initialization logic for FATES Purpose and description of changes @@ -42,6 +42,9 @@ Bugs fixed or introduced Externals issues fixed (include issue #): Partially addresses FATES#994 -- Bare ground establishment problem and increased soil moisture +Known bugs found since the previous tag (include issue #): + #1979 -- Need to loosen tolerance on near-zero truncation of h2osoi_ice in UpdateState_TopLayerFluxes + Notes of particular relevance for users --------------------------------------- @@ -50,13 +53,11 @@ Changes made to namelist defaults (e.g., changed parameter values): Notes of particular relevance for developers: --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -[Remove any lines that don't apply. Remove entire section if nothing applies.] Caveats for developers (e.g., code that is duplicated that requires double maintenance): - -Changes to tests or testing: - + This changes the starting level for a COLD start of soil moisture for ALL FATES cases to a much + higher value than for non-FATES. In the long run we'd like to have these the same and/or + have the value changable on the namelist. Testing summary: ---------------- @@ -98,7 +99,8 @@ List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): Pull Requests that document the changes (include PR ids): (https://github.com/ESCOMP/ctsm/pull) - https://github.com/ESCOMP/CTSM/pull/1962 + https://github.com/ESCOMP/CTSM/pull/1962 -- Cold start moisture for FATES increased + https://github.com/ESCOMP/CTSM/pull/1978 -- revert some commits now that FUNITCTSM works again =============================================================== =============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index fb302ed794..24a0b303c6 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev121 glemieux 04/04/2023 Changes soil moisture initialization logic for FATES + ctsm5.1.dev121 glemieux 04/05/2023 Changes soil moisture initialization logic for FATES ctsm5.1.dev120 sacks 03/25/2023 Update externals and minor fixes ctsm5.1.dev119 slevis 03/16/2023 Allow gross unrepresented land use transition (PR #309) ctsm5.1.dev118 slevis 02/05/2023 Use conda environment rather than ncar_pylib with the fsurdat_modifier system test From bbe21f418a700fec08dc90174e0431dfd93f0be0 Mon Sep 17 00:00:00 2001 From: adamrher Date: Wed, 5 Apr 2023 09:55:31 -0600 Subject: [PATCH 0778/2067] remade surface datasets with proper metadata --- bld/namelist_files/namelist_defaults_ctsm.xml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 237b14f5e9..659c2fd16b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1093,13 +1093,13 @@ lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_smallvilleIA_hist_78pfts_CMIP6_simyr2000_c230123.nc -/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230326.nc +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230405.nc -/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230326.nc +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230405.nc lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_ne16np4_hist_78pfts_CMIP6_simyr2000_c190214.nc -/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230326.nc +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr2000_c230405.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr2000_c200426.nc @@ -1174,11 +1174,11 @@ lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_numaIA_hist_78pfts_CMIP6_simyr lnd/clm2/surfdata_map/ctsm5.1.dev116/surfdata_1x1_brazil_hist_78pfts_CMIP6_simyr1850_c230123.nc -/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230326.nc +/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/surfdata_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230405.nc -/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230326.nc +/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/surfdata_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230405.nc -/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230326.nc +/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/surfdata_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850_c230405.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc @@ -1246,11 +1246,11 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts use_crop=".true." >lnd/clm2/surfdata_map/landuse.timeseries_1x1_numaIA_hist_78pfts_CMIP6_simyr1850-2015_c170917.nc /glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230326.nc + >/glade/work/aherring/grids/uniform-res/ne3np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne3np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230405.nc /glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230326.nc + >/glade/work/aherring/grids/uniform-res/ne5np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne5np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230405.nc /glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230326.nc + >/glade/work/aherring/grids/uniform-res/ne16np4.pg3/clm_surfdata_5_0/landuse.timeseries_ne16np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c230405.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc Date: Wed, 5 Apr 2023 13:34:23 -0600 Subject: [PATCH 0779/2067] Update date for changelog --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 53c04d01a4..edb6223e2e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev121 Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) -Date: Wed Apr 5 09:15:55 MDT 2023 +Date: Wed Apr 5 13:34:09 MDT 2023 One-line Summary: Changes soil moisture initialization logic for FATES Purpose and description of changes From b34a2e5da7b70d2ab09e61d1ccdb4e523c1182fc Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 5 Apr 2023 14:22:39 -0600 Subject: [PATCH 0780/2067] initial refactoring --- src/main/histFileMod.F90 | 6 ++-- src/utils/clmfates_interfaceMod.F90 | 55 +++++++++++++++++++++++++---- 2 files changed, 52 insertions(+), 9 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index d5175342f0..517c3ec107 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -21,12 +21,12 @@ module histFileMod use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch - use EDTypesMod , only : nclmax - use EDTypesMod , only : nlevleaf + use EDParamsMod , only : nclmax + use EDParamsMod , only : nlevleaf use FatesInterfaceTypesMod , only : nlevsclass, nlevage, nlevcoage use FatesInterfaceTypesMod , only : nlevheight use FatesInterfaceTypesMod , only : nlevdamage - use EDTypesMod , only : nfsc + use FatesLitterMod , only : nfsc use FatesLitterMod , only : ncwd use PRTGenericMod , only : num_elements_fates => num_elements use FatesInterfaceTypesMod , only : numpft_fates => numpft diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c169d710ef..0cab7b40eb 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -33,6 +33,7 @@ module CLMFatesInterfaceMod ! Used CLM Modules #include "shr_assert.h" +use FatesGlobals , only : fates_log use PatchType , only : patch use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type, subgrid_level_column @@ -836,6 +837,8 @@ subroutine dynamics_driv(this, nc, bounds_clump, & type(frictionvel_type) , intent(inout) :: frictionvel_inst ! !LOCAL VARIABLES: + type(ed_patch_type), pointer :: currentPatch + integer :: iv, ic integer :: s ! site index integer :: g ! grid-cell index (HLM) integer :: c ! column index (HLM) @@ -844,12 +847,18 @@ subroutine dynamics_driv(this, nc, bounds_clump, & integer :: nlevsoil ! number of soil layers at the site integer :: nld_si ! site specific number of decomposition layers integer :: ft ! plant functional type + integer ::& + yr, &! year + mon, &! month + day, &! day of month + tod ! time of day (seconds past 0Z) real(r8), pointer :: lnfm24(:) ! 24-hour averaged lightning data real(r8), pointer :: gdp_lf_col(:) ! gdp data integer :: ier integer :: begg,endg real(r8) :: harvest_rates(bounds_clump%begg:bounds_clump%endg,num_harvest_inst) logical :: after_start_of_harvest_ts + logical, save :: first_time = .true. integer :: iharv !----------------------------------------------------------------------- @@ -1031,6 +1040,29 @@ subroutine dynamics_driv(this, nc, bounds_clump, & this%fates(nc)%bc_in(s), & this%fates(nc)%bc_out(s)) + call get_curr_date(yr, mon, day, tod) + if (yr == 2020 .and. mon == 6 .and. day == 1) then + currentpatch => this%fates(nc)%sites(s)%youngest_patch + do while(associated(currentpatch)) + write(fates_log(),*) 'can area is ', currentpatch%total_canopy_area + write(fates_log(),*) '-------------------------------------------------------' + do ic = 1, 2 + do ft = 1, 16 + do iv = 1, 30 + write(fates_log(),*) 'can area prof is ', currentpatch%canopy_area_profile(ic,ft,iv), ic, ft, iv + write(fates_log(),*) 'elai prof is ', currentpatch%elai_profile(ic,ft,iv), ic, ft, iv + write(fates_log(),*) 'esai area prof is ', currentpatch%esai_profile(ic,ft,iv), ic, ft, iv + end do + write(fates_log(),*) '-------------------------------------------------------' + write(fates_log(),*) 'nrad prof is ', currentpatch%nrad(ic,ft), ic, ft + write(fates_log(),*) '-------------------------------------------------------' + end do + end do + currentPatch => currentpatch%older + enddo + first_time = .false. + end if + enddo ! --------------------------------------------------------------------------------- @@ -1121,6 +1153,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & type(waterdiagnosticbulk_type) , intent(inout) :: waterdiagnosticbulk_inst type(canopystate_type) , intent(inout) :: canopystate_inst type(soilbiogeochem_carbonflux_type), intent(inout) :: soilbiogeochem_carbonflux_inst + ! is this being called during a read from restart sequence (if so then use the restarted fates ! snow depth variable rather than the CLM variable). @@ -1132,6 +1165,9 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & integer :: s ! site index integer :: c ! column index integer :: g ! grid cell + integer :: ic, ft, iv + logical, save :: first_time = .true. + type(ed_patch_type), pointer :: currentPatch real(r8) :: areacheck call t_startf('fates_wrap_update_hlmfates_dyn') @@ -1167,7 +1203,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! Canopy diagnostics for FATES call canopy_summarization(this%fates(nc)%nsites, & this%fates(nc)%sites, & - this%fates(nc)%bc_in) + this%fates(nc)%bc_in) ! Canopy diagnostic outputs for HLM call update_hlm_dynamics(this%fates(nc)%nsites, & @@ -1175,6 +1211,9 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & this%f2hmap(nc)%fcolumn, & this%fates(nc)%bc_out ) + + + !------------------------------------------------------------------------ ! FATES calculation of ligninNratio !------------------------------------------------------------------------ @@ -1379,11 +1418,13 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & integer :: nclumps type(fates_bounds_type) :: fates_bounds type(fates_bounds_type) :: fates_clump + type(ed_patch_type), pointer :: currentPatch integer :: c ! HLM column index integer :: s ! Fates site index integer :: g ! grid-cell index integer :: p ! HLM patch index integer :: ft ! plant functional type + integer :: ic, iv integer :: dk_index integer :: nlevsoil character(len=fates_long_string_length) :: ioname @@ -1391,7 +1432,9 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & integer :: ivar logical :: readvar + logical, save :: initialized = .false. + logical, save :: first_time = .true. call t_startf('fates_restart') @@ -2171,7 +2214,7 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, & use pftconMod , only : pftcon use PatchType , only : patch use quadraticMod , only : quadratic - use EDtypesMod , only : ed_patch_type, ed_cohort_type, ed_site_type + use EDtypesMod , only : ed_patch_type, fates_cohort_type, ed_site_type ! ! !ARGUMENTS: @@ -3137,13 +3180,13 @@ end subroutine wrap_hydraulics_drive subroutine hlm_bounds_to_fates_bounds(hlm, fates) - use FatesIODimensionsMod, only : fates_bounds_type + use FatesIODimensionsMod, only : fates_bounds_type use FatesInterfaceTypesMod, only : nlevsclass, nlevage, nlevcoage use FatesInterfaceTypesMod, only : nlevheight use FatesInterfaceTypesMod, only : nlevdamage - use EDtypesMod, only : nfsc - use FatesLitterMod, only : ncwd - use EDtypesMod, only : nlevleaf, nclmax + use FatesLitterMod, only : nfsc + use FatesLitterMod, only : ncwd + use EDParamsMod, only : nlevleaf, nclmax use FatesInterfaceTypesMod, only : numpft_fates => numpft From 1191b587f87599c6c019e24ab47d875bec89d735 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Thu, 6 Apr 2023 08:55:55 -0600 Subject: [PATCH 0781/2067] update default parameter file --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 41103b5259..ff9caff5c1 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.0.0_12pft_c221128.nc +lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc From cecbe6a65df970d218f56346fc4b5602ed98f891 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 6 Apr 2023 11:22:09 -0600 Subject: [PATCH 0782/2067] include tests --- cime_config/testdefs/testlist_clm.xml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 4d074eae11..98d07eb75f 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1552,6 +1552,16 @@ + + + + + + + + + + From d9bf4ce96e2d19aa9c7bee2380f2cf90997969d8 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 7 Apr 2023 11:55:11 -0600 Subject: [PATCH 0783/2067] move cohort type into its own module --- src/utils/clmfates_interfaceMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 0cab7b40eb..27533b2767 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2214,7 +2214,8 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, & use pftconMod , only : pftcon use PatchType , only : patch use quadraticMod , only : quadratic - use EDtypesMod , only : ed_patch_type, fates_cohort_type, ed_site_type + use EDtypesMod , only : ed_patch_type, ed_site_type + use FatesCohortMod , only : fates_cohort_type ! ! !ARGUMENTS: From 8d15cb3bbf4240a3e95a4fcf78366200b7152c3a Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 7 Apr 2023 12:54:42 -0600 Subject: [PATCH 0784/2067] update shell commands --- .../usermods_dirs/NEON/MLBS/shell_commands | 6 ++++-- .../usermods_dirs/NEON/MOAB/shell_commands | 5 ++--- .../usermods_dirs/NEON/NIWO/shell_commands | 4 +++- .../usermods_dirs/NEON/ONAQ/shell_commands | 11 +++++++---- .../usermods_dirs/NEON/SJER/shell_commands | 9 +++++---- .../usermods_dirs/NEON/TEAK/shell_commands | 18 ++++++++++-------- .../usermods_dirs/NEON/WREF/shell_commands | 11 +++++++---- .../usermods_dirs/NEON/YELL/shell_commands | 9 +++++---- 8 files changed, 43 insertions(+), 30 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 376fc42add..f21cbd680b 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -2,11 +2,13 @@ ./xmlchange NEONSITE=MLBS ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [ $CLM_USRDAT_NAME=='NEON'] +then ./xmlchange DATM_YR_END=2019 fi # Different default number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then +if [ $compset =~ ^HIST ] +then ./xmlchange DATM_YR_END=2020 ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 6a811c1e4a..c82e8879bf 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -2,12 +2,11 @@ ./xmlchange NEONSITE=MOAB ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [$CLM_USRDAT_NAME=='NEON']; then + ./xmlchange DATM_YR_END=2020 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2021 ./xmlchange STOP_N=36 - else - ./xmlchange DATM_YR_END=2020 fi fi diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index 483647d965..4848702826 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -1,6 +1,8 @@ +#!/bin/bash ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [ $CLM_USRDAT_NAME=="NEON" ] +then ./xmlchange DATM_YR_END=2018 fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index f38cc944b6..ae6f6d4a19 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -2,12 +2,15 @@ ./xmlchange NEONSITE=ONAQ ./xmlchange PTS_LON=247.54755 ./xmlchange PTS_LAT=40.17760 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [ $CLM_USRDAT_NAME=='NEON' ] +then + echo "IN CLM_USRDAT_NAME LOOP!" + ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case - if [[ $compset =~ ^HIST ]]; then + if [[ $compset =~ ^HIST ]] + then + echo "IN HIST COMPSET LOOP!" ./xmlchange DATM_YR_END=2020 ./xmlchange STOP_N=24 - else - ./xmlchange DATM_YR_END=2019 fi fi diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 4b95814c7b..e76242e8b5 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -3,13 +3,14 @@ ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 ./xmlchange DATM_YR_ALIGN=2019 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [ $CLM_USRDAT_NAME=='NEON' ] +then + ./xmlchange DATM_YR_START=2019 # Different default start date and number of months to run for transient case - if [[ $compset =~ ^HIST ]]; then + if [[ $compset =~ ^HIST ]] + then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 - else - ./xmlchange DATM_YR_START=2019 fi fi diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 064354edb5..3775581719 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -3,12 +3,14 @@ ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 ./xmlchange DATM_YR_ALIGN=2019 -if [[$CLM_USRDAT_NAME = 'NEON']]; then - # Different default start date and number of months to run for transient case - if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 - else - ./xmlchange DATM_YR_START=2019 - fi +./xmlchange DATM_YR_START=2019 +#if [ $CLM_USRDAT_NAME=='NEON'] +#then +# Different default start date and number of months to run for transient case +#./xmlchange DATM_YR_START=2019 +if [[ $compset =~ ^HIST ]] +then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 fi +#fi diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index 9be4d1719a..c8cb110cc4 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -3,12 +3,15 @@ ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 ./xmlchange DATM_YR_ALIGN=2019 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [ $CLM_USRDAT_NAME=='NEON' ] +then + echo "IN CLM_USRDAT_NAME LOOP!" # Different default start date and number of months to run for transient case - if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_START=2019 + if [[ $compset =~ ^HIST ]] + then + echo "IN HIST COMPSET LOOP!" ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 - else - ./xmlchange DATM_YR_START=2019 fi fi diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index bb76a7cc34..86eab8ca20 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -3,12 +3,13 @@ ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 ./xmlchange DATM_YR_ALIGN=2019 -if [[$CLM_USRDAT_NAME = 'NEON']]; then +if [ $CLM_USRDAT_NAME=='NEON' ] +then # Different default start date and number of months to run for transient case - if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_START=2019 + if [[ $compset =~ ^HIST ]] + then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 - else - ./xmlchange DATM_YR_START=2019 fi fi From 2910e3fa1c5e3156d2d659f48c72677f31802ecc Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 7 Apr 2023 14:07:29 -0600 Subject: [PATCH 0785/2067] remove unused dependency --- src/utils/clmfates_interfaceMod.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 27533b2767..b84f561438 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2209,9 +2209,8 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, & use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use decompMod , only : bounds_type - use clm_varcon , only : rgas, tfrz, namep + use clm_varcon , only : tfrz, namep use clm_varctl , only : iulog - use pftconMod , only : pftcon use PatchType , only : patch use quadraticMod , only : quadratic use EDtypesMod , only : ed_patch_type, ed_site_type From f7deb0da40f08e3b6fe06b3af0cb9bad13dad075 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Apr 2023 15:59:15 -0600 Subject: [PATCH 0786/2067] Brought in Python for generating GDDs into python/ctsm/crop_calendars. Reworked imports to work in this repo. --- .../crop_calendars/cropcal_figs_module.py | 408 +++ python/ctsm/crop_calendars/cropcal_module.py | 2878 +++++++++++++++++ python/ctsm/crop_calendars/generate_gdds.py | 757 +++++ .../crop_calendars/generate_gdds_functions.py | 501 +++ .../crop_calendars/make_surface_for_gddgen.py | 171 + python/ctsm/crop_calendars/utils.py | 1157 +++++++ 6 files changed, 5872 insertions(+) create mode 100644 python/ctsm/crop_calendars/cropcal_figs_module.py create mode 100644 python/ctsm/crop_calendars/cropcal_module.py create mode 100644 python/ctsm/crop_calendars/generate_gdds.py create mode 100644 python/ctsm/crop_calendars/generate_gdds_functions.py create mode 100644 python/ctsm/crop_calendars/make_surface_for_gddgen.py create mode 100644 python/ctsm/crop_calendars/utils.py diff --git a/python/ctsm/crop_calendars/cropcal_figs_module.py b/python/ctsm/crop_calendars/cropcal_figs_module.py new file mode 100644 index 0000000000..30de48cc00 --- /dev/null +++ b/python/ctsm/crop_calendars/cropcal_figs_module.py @@ -0,0 +1,408 @@ +import numpy as np +import matplotlib.pyplot as plt +import cartopy.crs as ccrs +import matplotlib.colors as mcolors +from matplotlib import cm +import matplotlib.collections as mplcol +import cartopy.feature as cfeature +import xarray as xr +import cftime +from scipy import stats + +# Import the CTSM Python utilities +import utils + +# Colormaps (maps) +cropcal_colors = { + 'seq_timeofyear': 'twilight_shifted', + 'seq_other': 'plasma', # magma_r? CMRmap_r? + 'div_yieldirr': 'BrBG', + 'div_timeofyear': 'twilight_shifted', + 'div_other_nonnorm': 'PuOr_r', + 'div_other_norm': 'RdBu_r', + 'underlay': [0.75, 0.75, 0.75, 1], + 'underlay_lighter': [0.85, 0.85, 0.85, 1], + 'underlay_lightest': [0.92, 0.92, 0.92, 1], +} + +# Cases (line and scatter plots) +def cropcal_colors_cases(casename): + case_color_dict = { + 'clm default': [x/255 for x in [92, 219, 219]], + 'prescribed calendars': [x/255 for x in [250, 102, 240]], + 'prescribed maturity': [x/255 for x in [128,0,0]], + 'prescribed sowing': [x/255 for x in [133, 92, 255]], + } + case_color_dict['5.0 lu'] = case_color_dict['clm default'] + case_color_dict['5.2 lu'] = case_color_dict['prescribed calendars'] + + case_color = None + casename_for_colors = casename.lower().replace(" (0)", "").replace(" (1)", "") + if casename_for_colors in case_color_dict: + case_color = case_color_dict[casename_for_colors] + return case_color + + +def chunk_colorbar(this_map, cbar_spacing, cmap, crop, fontsize, pct_absdiffs_masked_before, sumdiff_beforemask, varInfo, vmin, vmax, posNeg=False, underlay=None, v=0): + # Make a temporary plot with the same color axis and colorbar settings we would use in make_map(). + plt.pcolormesh(this_map, vmin=vmin, vmax=vmax) + cb0 = plt.colorbar(location="bottom") + cb0.ax.tick_params(labelsize=fontsize['ticklabels']) + + # Where did plt.colorbar() draw bin boundaries? These are referred to as "tick marks," but note that the extreme values might lie outside [vmin, vmax]. + ticklocations = cb0.get_ticks() + bounds = ticklocations + + # In our plot, we will move vmin left and vmax right to ensure that the tick marks are the color bin boundaries. + if cb0.vmin < bounds[0]: + raise RuntimeError("Handle vmin < bounds[0]") + elif cb0.vmax > bounds[-1]: + raise RuntimeError("Handle vmax > bounds[-1]") + elif 0 not in bounds: + raise RuntimeError("Handle 0 not in bounds") + vmin = bounds[0] + vmax = bounds[-1] + + # Get number of color bins + Nbins = len(bounds) - 1 + bottom_of_topbin = bounds[-2] + bottom_of_2ndbin = bounds[-3] + binwidth = bounds[-1] - bounds[-2] + if Nbins < 8: + Nbins *= 2 + bottom_of_2ndbin = bottom_of_topbin + binwidth /= 2 + bottom_of_topbin += binwidth + + # Ensure that most extreme bin (on at least one side of 0) has at least one gridcell included. If not, remove the most extreme bins and check again. + maxinmap = np.nanmax(np.abs(this_map.values)) + if maxinmap < bottom_of_topbin: + if maxinmap < bottom_of_2ndbin: + raise RuntimeError("How is maxinmap less than the bottom of the SECOND bin??") + vmax -= binwidth + vmin += binwidth + Nbins-=2 + if ticklocations[0] < vmin: + ticklocations = ticklocations[1:] + if ticklocations[-1] > vmax: + ticklocations = ticklocations[:-1] + + # Get new colormap with the right number of bins. + this_cmap = cm.get_cmap(cmap, Nbins) + if Nbins % 2: + raise RuntimeError(f"Expected even number of color bins; got {Nbins}") + + # Special color for small-masked cells + if 'maskcolorbar_near0' in varInfo and varInfo['maskcolorbar_near0'][v] is not None: + + # Get near-zero threshold + nearzero_thresh = varInfo['maskcolorbar_near0'][v] + if isinstance(nearzero_thresh, str): + nearzero_parts = nearzero_thresh.split("|") + if nearzero_parts[0] != "percentile": + raise RuntimeError(f"Unable to parse maskcolorbar_near0 value {nearzero_thresh}") + + # The input value should be a percentile, 0-100 + nearzero_val_in = np.float(nearzero_parts[1]) + + if len(nearzero_parts) > 2: + if nearzero_parts[2] != "cumulative": + raise RuntimeError(f"Unable to parse maskcolorbar_near0 value {nearzero_thresh}") + frac_to_include = 1 - nearzero_val_in/100 + nearzero_thresh = get_threshold_lowestpercentile_cumulative(this_map, frac_to_include) + else: + nearzero_thresh = np.nanpercentile(np.abs(this_map), nearzero_val_in) + else: + raise RuntimeError("Can only parse string values of maskcolorbar_near0") + + # Add near-zero bin + bounds, cbar_spacing, pct_absdiffs_masked_before, ticklabels, ticklocations, vmax, vmin = maskcolorbar_near0(binwidth, bounds, cbar_spacing, crop, nearzero_thresh, pct_absdiffs_masked_before, posNeg, sumdiff_beforemask, this_map, ticklocations, vmax, vmin) + + # Add color for that bin + if underlay is not None: + raise RuntimeError("You need a different color to distinguish maskcolorbar_near0 cells from other-masked cells") + this_cmap = get_ListedColormap(cmap, this_cmap, Nbins) + if posNeg: + if crop == "Crops decreasing": + new_colors = np.concatenate((this_cmap.colors[:int(Nbins/2)], + np.array([cropcal_colors['underlay']])), + axis=0) + elif crop == "Crops increasing": + new_colors = np.concatenate((np.array([cropcal_colors['underlay']]), + this_cmap.colors[int(Nbins/2)+1:]), + axis=0) + else: + raise RuntimeError(f"posNeg: Crop {crop} not recognized for color bar (2)") + else: + new_colors = np.concatenate((this_cmap.colors[:int(Nbins/2)], + np.array([cropcal_colors['underlay']]), + this_cmap.colors[int(Nbins/2)+1:]), + axis=0) + + this_cmap = mcolors.ListedColormap(new_colors) + + # Remove our temporary plot and its colorbar. + plt.cla() + cb0.remove() + + return bounds, cbar_spacing, pct_absdiffs_masked_before, this_cmap, ticklabels, ticklocations, vmin, vmax + + +def get_amount_masked(crop, this_map_timemean, sumdiff_beforemask, pct_absdiffs_masked_before, reason): + sumdiff_aftermask = np.nansum(np.abs(this_map_timemean.values)) + pct_absdiffs_masked = 100 * (1 - sumdiff_aftermask / sumdiff_beforemask) + pct_absdiffs_masked_here = pct_absdiffs_masked - pct_absdiffs_masked_before + print(f" Masked {crop} ({reason}): {round(pct_absdiffs_masked_here, 1)}%") + pct_absdiffs_masked_before = pct_absdiffs_masked + return pct_absdiffs_masked_before + + +def get_ListedColormap(cmap_name, this_cmap, Nbins): + if isinstance(this_cmap, mcolors.LinearSegmentedColormap): + this_cmap = cm.get_cmap(cmap_name) + color_list = [this_cmap(x) for x in np.arange(0, 1, 1/Nbins)] + color_list = [] + for i, x in enumerate(np.arange(0, 1+1e-9, 1/Nbins)): + color_list.append(this_cmap(x)) + if i>0 and color_list[i] == color_list[i-1]: + print(f"{prev_x} → color_list[{i-1}] = {color_list[i-1]}") + print(f"{x} → color_list[{i}] = {color_list[i]}") + raise RuntimeError("Repeated color!") + prev_x = x + this_cmap = mcolors.ListedColormap(color_list) + elif not isinstance(this_cmap, mcolors.ListedColormap): + raise RuntimeError(f"Not sure how to get list of colors from {type(this_cmap)}") + + return this_cmap + + +def get_threshold_lowestpercentile_cumulative(this_map_timemean, frac_to_include): + flattened = np.abs(this_map_timemean.values).flatten() + flattened_is_ok = np.where(~np.isnan(flattened)) + okflattened = flattened[flattened_is_ok] + oksorted = np.flip(np.sort(okflattened)) + okcumsum = np.cumsum(oksorted) + okcumprop = okcumsum / np.sum(oksorted) + for i, x in enumerate(okcumprop): + if x >= frac_to_include: + break + lowest_threshold = oksorted[i] + return lowest_threshold + + +def get_non_rx_map(var_info, cases, casename, this_var, thisCrop_main, found_types, plot_y1, plot_yN, ref_casename): + time_dim = var_info['time_dim'] + case = cases[casename] + + # Trim to included years + try: + this_ds = case['ds'].sel({time_dim: slice(plot_y1, plot_yN)}) + except: + # Try converting years to cftime + plot_y1 = cftime.DatetimeNoLeap(plot_y1, 1, 1) + plot_yN = cftime.DatetimeNoLeap(plot_yN, 1, 1) + this_ds = case['ds'].sel({time_dim: slice(plot_y1, plot_yN)}) + + if this_var not in case['ds']: + return xr.DataArray(), "continue" + elif ref_casename and ref_casename!="rx" and cases[ref_casename]['res'] != case['res']: + # Not bothering with regridding (for now?) + return xr.DataArray(), "continue" + this_map = this_ds[this_var] + + # Prepare to mask out patch-years with no area + if "gs" in this_map.dims: + croparea_ever_positive = this_ds['croparea_positive_wholeseason'].sum(dim="gs") + elif "time" in this_map.dims or this_var in ["QIRRIG_DEMAND_PATCH_PKMTH"]: + croparea_ever_positive = this_ds['croparea_positive_sowing'].sum(dim="time") + else: + raise RuntimeError(f"Unsure how to mask patch-years with no area for {this_var} with dims {this_map.dims}") + this_ds['croparea_ever_positive'] = croparea_ever_positive + + # Grid the included vegetation types, if needed + if "lon" not in this_map.dims: + this_map = utils.grid_one_variable(this_ds, this_var, vegtype=found_types) + croparea_ever_positive = utils.grid_one_variable(this_ds, 'croparea_ever_positive', vegtype=found_types) > 0 + # If not, select the included vegetation types + else: + this_map = this_map.sel(ivt_str=found_types) + croparea_ever_positive = this_ds['croparea_ever_positive'].sel(ivt_str=found_types) > 0 + + return this_map, croparea_ever_positive, time_dim + + +def make_map(ax, this_map, fontsize, bounds=None, cbar=None, cbar_labelpad=4.0, cbar_max=None, cbar_spacing='uniform', cmap=cropcal_colors['seq_other'], extend_bounds='both', extend_nonbounds='both', linewidth=1.0, lonlat_bin_width=None, show_cbar=False, subplot_label=None, this_title=None, ticklabels=None, ticklocations=None, underlay=None, underlay_color=None, units=None, vmax=None, vmin=None, vrange=None): + + + if underlay is not None: + if underlay_color is None: + underlay_color = cropcal_colors['underlay'] + underlay_cmap = mcolors.ListedColormap(np.array([underlay_color, [1, 1, 1, 1]])) + ax.pcolormesh(underlay.lon.values, underlay.lat.values, + underlay, cmap=underlay_cmap) + + if bounds is not None: + norm = mcolors.BoundaryNorm(bounds, cmap.N, extend=extend_bounds) + im = ax.pcolormesh(this_map.lon.values, this_map.lat.values, + this_map, shading="auto", + norm=norm, + cmap=cmap) + else: + im = ax.pcolormesh(this_map.lon.values, this_map.lat.values, + this_map, shading="auto", + cmap=cmap, + vmin=vmin, vmax=vmax) + if vrange: + im.set_clim(vrange[0], vrange[1]) + ax.set_extent([-180,180,-63,90],crs=ccrs.PlateCarree()) + + if subplot_label is not None: + plt.text(0, 0.95, f"({subplot_label})", transform=ax.transAxes, + fontsize=fontsize['axislabels']) + + # # Country borders + # ax.add_feature(cfeature.BORDERS, linewidth=linewidth, edgecolor="white", alpha=0.5) + # ax.add_feature(cfeature.BORDERS, linewidth=linewidth*0.6, alpha=0.3) + + # Coastlines + ax.coastlines(linewidth=linewidth, color="white", alpha=0.5) + ax.coastlines(linewidth=linewidth*0.6, alpha=0.3) + + if this_title: + ax.set_title(this_title, fontsize=fontsize['titles']) + if show_cbar: + if cbar: + cbar.remove() + + if bounds is not None: + cbar = plt.colorbar(cm.ScalarMappable(norm=norm, cmap=cmap), ax=ax, orientation='horizontal', fraction=0.1, pad=0.02, spacing=cbar_spacing) + else: + cbar = plt.colorbar(im, ax=ax, orientation="horizontal", fraction=0.1, pad=0.02, extend=extend_nonbounds, spacing=cbar_spacing) + + deal_with_ticklabels(cbar, cbar_max, ticklabels, ticklocations, units, im) + cbar.set_label(label=units, fontsize=fontsize['axislabels'], verticalalignment="center", labelpad=cbar_labelpad) + cbar.ax.tick_params(labelsize=fontsize['ticklabels']) + if units is not None and "month" in units.lower(): + cbar.ax.tick_params(length=0) + + + if lonlat_bin_width: + set_ticks(lonlat_bin_width, fontsize, "y") + # set_ticks(lonlat_bin_width, fontsize, "x") + else: + # Need to do this for subplot row labels + set_ticks(-1, fontsize, "y") + plt.yticks([]) + for x in ax.spines: + ax.spines[x].set_visible(False) + + if show_cbar: + return im, cbar + else: + return im, None + + +# Note that we're not actually masking here; we're just setting a special color for a particular part of the colorbar +def maskcolorbar_near0(binwidth, bounds, cbar_spacing, crop, nearzero_thresh, pct_absdiffs_masked_before, posNeg, sumdiff_beforemask, this_map_timemean, ticklocations, vmax, vmin): + ticklabels = None + + # Setting this to False will cause some weird results that I'm not going to try and fix for now. + # For example: + # Floating-point errors like 0.6000000000001 + # When there are 2 color bins between near-zero bin and first labeled tick, + # there should be an extra tick+label between those 2 + use_proportional_cbar = True + if use_proportional_cbar: + cbar_spacing = "proportional" + else: + cbar_spacing = "uniform" + + # Add near-zero bin + if posNeg: + if crop == "Crops decreasing": + vmax = 0 + ticklocations = ticklocations[np.where(ticklocations <= 0)] + bounds = np.concatenate((np.arange(vmin, -binwidth+1e-9, binwidth), + np.array([-nearzero_thresh, 0]))) + if not use_proportional_cbar: + ticklabels = np.concatenate(([str(x) for x in ticklocations[ticklocations<0]], + ["-{:.2g}".format(nearzero_thresh)], + ["0"])) + ticklocations = np.concatenate((ticklocations[ticklocations < 0], [-nearzero_thresh, 0])) + elif crop == "Crops increasing": + vmin = 0 + ticklocations = ticklocations[np.where(ticklocations >= 0)] + bounds = np.concatenate((np.array([0, nearzero_thresh]), + np.arange(binwidth, vmax+1e-9, binwidth))) + if not use_proportional_cbar: + ticklabels = np.concatenate((["0"], + ["{:.2g}".format(nearzero_thresh)], + [str(x) for x in ticklocations[ticklocations>0]],)) + ticklocations = np.concatenate(([0, nearzero_thresh], ticklocations[ticklocations > 0])) + else: + raise RuntimeError(f"posNeg: Crop {crop} not recognized for color bar") + else: + bounds = np.concatenate((np.arange(vmin, -binwidth+1e-9, binwidth), + np.array([-nearzero_thresh, nearzero_thresh]), + np.arange(binwidth, vmax+1e-9, binwidth))) + if not use_proportional_cbar: + ticklabels = np.concatenate(([str(x) for x in ticklocations[ticklocations<0]], + ["±{:.2g}".format(nearzero_thresh)], + [str(x) for x in ticklocations[ticklocations>0]])) + + # Get stats + this_map_timemean_fake = this_map_timemean.where(np.abs(this_map_timemean) >= nearzero_thresh) + + # Diagnostics + pct_absdiffs_masked_before = get_amount_masked(crop, this_map_timemean_fake, sumdiff_beforemask, pct_absdiffs_masked_before, f"nearest to zero, threshold {nearzero_thresh}") + + # Because this is just a fake mask we must not do any additional masking, real or fake, after this. If we do, then our diagnostics for that will be messed up. To ensure we don't try to do any subsequent masking, set this to None, which should throw an error in get_amount_masked(). + pct_absdiffs_masked_before = None + + return bounds, cbar_spacing, pct_absdiffs_masked_before, ticklabels, ticklocations, vmax, vmin + + +def deal_with_ticklabels(cbar, cbar_max, ticklabels, ticklocations, units, im): + if ticklocations is not None: + cbar.set_ticks(ticklocations) + if units is not None and units.lower() == "month": + cbar.set_ticklabels(['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', 'Oct', 'Nov', 'Dec']) + units == "Month" + elif ticklabels is not None: + cbar.set_ticklabels(ticklabels) + if isinstance(im, mplcol.QuadMesh): + clim_max = im.get_clim()[1] + else: + clim_max = im + if cbar_max is not None and clim_max > cbar_max: + if ticklabels is not None: + raise RuntimeError("How to handle this now that you are specifying ticklocations separate from ticklabels?") + ticks = cbar.get_ticks() + if ticks[-2] > cbar_max: + raise RuntimeError(f"Specified cbar_max is {cbar_max} but highest bin BEGINS at {ticks[-2]}") + ticklabels = ticks.copy() + ticklabels[-1] = cbar_max + for i, x in enumerate(ticklabels): + if x == int(x): + ticklabels[i] = str(int(x)) + cbar.set_ticks(ticks) # Calling this before set_xticklabels() avoids "UserWarning: FixedFormatter should only be used together with FixedLocator" (https://stackoverflow.com/questions/63723514/userwarning-fixedformatter-should-only-be-used-together-with-fixedlocator) + cbar.set_ticklabels(ticklabels) + + +def set_ticks(lonlat_bin_width, fontsize, x_or_y): + if x_or_y == "x": + ticks = np.arange(-180, 181, lonlat_bin_width) + else: + ticks = np.arange(-60, 91, lonlat_bin_width) + + ticklabels = [str(x) for x in ticks] + for i,x in enumerate(ticks): + if x%2: + ticklabels[i] = '' + + if x_or_y == "x": + plt.xticks(ticks, labels=ticklabels, + fontsize=fontsize['ticklabels']) + else: + plt.yticks(ticks, labels=ticklabels, + fontsize=fontsize['ticklabels']) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py new file mode 100644 index 0000000000..f4e551c21a --- /dev/null +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -0,0 +1,2878 @@ +# Import the CTSM Python utilities +import utils + +import numpy as np +import xarray as xr +import cartopy.crs as ccrs +from scipy import stats, signal +import warnings +import cftime +import pandas as pd +import os +import glob + + +# Define conversion multipliers, {from: {to1, to2, ...}, ...} +multiplier_dict = { + # Mass + 'g': { + 'Mt': 1e-12, + }, + 't': { + 'Mt': 1e-6, + }, + # Volume + 'm3': { + 'km3': 1e-9, + }, + # Yield + 'g/m2': { + 't/ha': 1e-6 * 1e4, + }, +} + + +def adjust_grainC(da_in, patches1d_itype_veg_str): + # Parameters from Danica's 2020 paper + fyield = 0.85 # 85% harvest efficiency (Kucharik & Brye, 2003) + cgrain = 0.45 # 45% of dry biomass is C (Monfreda et al., 2008) + + # Dry matter fraction from Wirsenius (2000) Table A1.II except as noted + drymatter_fractions = { + 'corn': 0.88, + 'cotton': 0.912, # Table A1.III, "Seed cotton", incl. lint, seed, and "other (ginning waste)" + 'miscanthus': 0.0, # Not included in Wirsenius, but also not simulated, so I don't care + 'rice': 0.87, + 'soybean': 0.91, + 'sugarcane': 1-0.745, # Irvine, Cane Sugar Handbook, 10th ed., 1977, P. 16. (see sugarcane.py) + 'wheat': 0.88, + } + + # Convert patches1d_itype_veg_str to needed format + if isinstance(patches1d_itype_veg_str, xr.DataArray): + patches1d_itype_veg_str = patches1d_itype_veg_str.values + if not isinstance(patches1d_itype_veg_str[0], str): + patches1d_itype_veg_int = patches1d_itype_veg_str + patches1d_itype_veg_str = [utils.ivt_int2str(x) for x in patches1d_itype_veg_int] + + # Create new array with patch as the first dimension. This allows us to use Ellipsis when filling. + patch_dim = da_in.dims.index('patch') + wet_tp = np.full(da_in.shape, np.nan) + wet_tp = np.moveaxis(wet_tp, patch_dim, 0) + + # Fill new array, increasing to include water weight + drymatter_cropList = [] + da_in.load() + for thisCrop, dm_frac in drymatter_fractions.items(): + drymatter_cropList.append(thisCrop) + i_thisCrop = [i for i,x in enumerate(patches1d_itype_veg_str) if thisCrop in x] + + tmp = da_in.isel(patch=i_thisCrop).values + if dm_frac != None: + tmp[np.where(~np.isnan(tmp))] /= dm_frac + elif np.any(tmp > 0): + raise RuntimeError(f"You need to get a real dry-matter fraction for {thisCrop}") + + # For sugarcane, also account for the fact that soluble solids are only 51% of dry matter. Also derived from Irvine, Cane Sugar Handbook, 10th ed., 1977, P. 16. (see sugarcane.py) + if thisCrop == "sugarcane": + tmp /= 0.51 + + wet_tp[i_thisCrop, ...] = np.moveaxis(tmp, patch_dim, 0) + + # Move patch dimension (now in 0th position) back to where it should be. + wet_tp = np.moveaxis(wet_tp, 0, patch_dim) + + # Make sure NaN mask is unchanged + if not np.array_equal(np.isnan(wet_tp), np.isnan(da_in.values)): + missing_croptypes = [x for x in np.unique(patches1d_itype_veg_str) if x not in drymatter_cropList] + raise RuntimeError(f'Failed to completely fill wet_tp. Missing crop types: {missing_croptypes}') + + # Save to output DataArray + da_out = xr.DataArray(data = wet_tp * fyield / cgrain, + coords = da_in.coords, + attrs = da_in.attrs) + return da_out + + +# Rounding errors can result in differences of up to lon/lat_tolerance. Tolerate those by replacing the value in the gridded dataset. +def adjust_gridded_lonlats(patches1d_lonlat, patches1d_ij, lu_dsg_lonlat_da, this_tolerance, i_or_j_str): + missing_lonlats = np.unique(patches1d_lonlat.values[np.isnan(patches1d_ij)]) + new_gridded_lonlats = lu_dsg_lonlat_da.values + for m in missing_lonlats: + # Find closest value in gridded lonlat + min_diff = np.inf + for i, n in enumerate(np.sort(lu_dsg_lonlat_da)): + this_diff = n - m + if np.abs(this_diff) < min_diff: + min_diff = np.abs(this_diff) + closest_i = i + closest_n = n + if this_diff > 0: + break + if min_diff > this_tolerance: + raise ValueError(f"NaN in patches1d_{i_or_j_str}xy; closest value is {min_diff}° off.") + print(f"Replacing {m} with {closest_n}") + new_gridded_lonlats[closest_i] = closest_n + patches1d_ij[patches1d_lonlat.values == m] = closest_i + 1 + lu_dsg_lonlat_da = xr.DataArray(data = new_gridded_lonlats, + coords = {"lat": new_gridded_lonlats}) + return lu_dsg_lonlat_da, patches1d_ij + + +def annual_mean_from_monthly(ds, var): + """ + weight by days in each month + """ + # Determine the month length + month_length = ds.time.dt.days_in_month + + # Calculate the weights + wgts = month_length.groupby("time.year") / month_length.groupby("time.year").sum() + + # Make sure the weights in each year add up to 1 + np.testing.assert_allclose(wgts.groupby("time.year").sum(xr.ALL_DIMS), 1.0) + + # Subset our dataset for our variable + obs = ds[var] + + # Setup our masking for nan values + cond = obs.isnull() + ones = xr.where(cond, 0.0, 1.0) + + # Calculate the numerator + obs_sum = (obs * wgts).resample(time="AS").sum(dim="time") + + # Calculate the denominator + ones_out = (ones * wgts).resample(time="AS").sum(dim="time") + + # Return the weighted average + return obs_sum / ones_out + + +def attrs_differ_or_missing(ds, var, attrs_tgt_dict): + if var not in ds: + return True + + for attr, tgt in attrs_tgt_dict.items(): + if attr not in ds[var].attrs or ds[var].attrs[attr] != tgt: + return True + + return False + + +# After importing a file, restrict it to years of interest. +def check_and_trim_years(y1, yN, ds_in): + ### In annual outputs, file with name Y is actually results from year Y-1. + ### Note that time values refer to when it was SAVED. So 1981-01-01 is for year 1980. + + def get_year_from_cftime(cftime_date): + # Subtract 1 because the date for annual files is when it was SAVED + return cftime_date.year - 1 + + # Check that all desired years are included + if get_year_from_cftime(ds_in.time.values[0]) > y1: + raise RuntimeError(f"Requested y1 is {y1} but first year in outputs is {get_year_from_cftime(ds_in.time.values[0])}") + elif get_year_from_cftime(ds_in.time.values[-1]) < y1: + raise RuntimeError(f"Requested yN is {yN} but last year in outputs is {get_year_from_cftime(ds_in.time.values[-1])}") + + # Remove years outside range of interest + ### Include an extra year at the end to finish out final seasons. + ds_in = ds_in.sel(time=slice(f"{y1+1}-01-01", f"{yN+2}-01-01")) + + # Make sure you have the expected number of timesteps (including extra year) + Nyears_expected = yN - y1 + 2 + if ds_in.dims["time"] != Nyears_expected: + raise RuntimeError(f"Expected {Nyears_expected} timesteps in output but got {ds_in.dims['time']}") + + return ds_in + + +def check_case_earthstats_dim_match(case, earthstats_ds, dim): + dim_used_in_case = dim in case and np.any([dim in case[x].dims for x in case]) + dim_used_in_earthstats = dim in earthstats_ds and np.any([dim in earthstats_ds[x].dims for x in earthstats_ds]) + if dim_used_in_case: + if not dim_used_in_earthstats: + raise RuntimeError(f"{dim} in case Dataset but not EarthStats") + elif not np.array_equal(case[dim], earthstats_ds[dim]): + raise RuntimeError(f"{dim} mismatch between case and EarthStats Datasets") + elif dim_used_in_earthstats: + raise RuntimeError(f"{dim} in EarthStats Dataset but not case") + + +def check_constant_vars(this_ds, case, ignore_nan, constantGSs=None, verbose=True, throw_error=True): + + if isinstance(case, str): + constantVars = [case] + elif isinstance(case, list): + constantVars = case + elif isinstance(case, dict): + constantVars = case['constantVars'] + else: + raise TypeError(f'case must be str or dict, not {type(case)}') + + if not constantVars: + return None + + if constantGSs: + gs0 = this_ds.gs.values[0] + gsN = this_ds.gs.values[-1] + if constantGSs.start > gs0 or constantGSs.stop < gsN: + print(f'❗ Only checking constantVars over {constantGSs.start}-{constantGSs.stop} (run includes {gs0}-{gsN})') + this_ds = this_ds.sel(gs=constantGSs) + + any_bad = False + any_bad_before_checking_rx = False + if throw_error: + emojus = '❌' + else: + emojus = '❗' + if not isinstance(constantVars, list): + constantVars = [constantVars] + + for v in constantVars: + ok = True + + if "gs" in this_ds[v].dims: + time_coord = "gs" + elif "time" in this_ds[v].dims: + time_coord = "time" + else: + raise RuntimeError(f"Which of these is the time coordinate? {this_ds[v].dims}") + i_time_coord = this_ds[v].dims.index(time_coord) + + this_da = this_ds[v] + ra_sp = np.moveaxis(this_da.copy().values, i_time_coord, 0) + incl_patches = [] + bad_patches = np.array([]) + strList = [] + + # Read prescription file, if needed + rx_ds = None + if isinstance(case, dict): + if v == "GDDHARV" and 'rx_gdds_file' in case: + rx_ds = import_rx_dates("gdd", case['rx_gdds_file'], this_ds, set_neg1_to_nan=False).squeeze() + + for t1 in np.arange(this_ds.dims[time_coord]-1): + + condn = ~np.isnan(ra_sp[t1,...]) + if t1 > 0: + condn = np.bitwise_and(condn, + np.all(np.isnan(ra_sp[:t1,...]), axis=0) + ) + thesePatches = np.where(condn)[0] + if thesePatches.size == 0: + continue + thesePatches = list(np.where(condn)[0]) + incl_patches += thesePatches + # print(f't1 {t1}: {thesePatches}') + + t1_yr = this_ds[time_coord].values[t1] + t1_vals = np.squeeze(this_da.isel({time_coord: t1, 'patch': thesePatches}).values) + + for t in np.arange(t1+1, this_ds.dims[time_coord]): + t_yr = this_ds[time_coord].values[t] + t_vals = np.squeeze(this_da.isel({time_coord: t, 'patch': thesePatches}).values) + ok_p = t1_vals == t_vals + + # If allowed, ignore where either t or t1 is NaN. Should only be used for runs where land use varies over time. + if ignore_nan: + ok_p = np.squeeze(np.bitwise_or(ok_p, np.isnan(t1_vals+t_vals))) + + if not np.all(ok_p): + any_bad_before_checking_rx = True + bad_patches_thisT = list(np.where(np.bitwise_not(ok_p))[0]) + bad_patches = np.concatenate((bad_patches, np.array(thesePatches)[bad_patches_thisT])) + if rx_ds: + found_in_rx = np.array([False for x in bad_patches]) + varyPatches = list(np.array(thesePatches)[bad_patches_thisT]) + varyLons = this_ds.patches1d_lon.values[bad_patches_thisT] + varyLats = this_ds.patches1d_lat.values[bad_patches_thisT] + varyCrops = this_ds.patches1d_itype_veg_str.values[bad_patches_thisT] + varyCrops_int = this_ds.patches1d_itype_veg.values[bad_patches_thisT] + + any_bad_anyCrop = False + for c in np.unique(varyCrops_int): + rx_var = f'gs1_{c}' + varyLons_thisCrop = varyLons[np.where(varyCrops_int==c)] + varyLats_thisCrop = varyLats[np.where(varyCrops_int==c)] + theseRxVals = np.diag(rx_ds[rx_var].sel(lon=varyLons_thisCrop, lat=varyLats_thisCrop).values) + if len(theseRxVals) != len(varyLats_thisCrop): + raise RuntimeError(f"Expected {len(varyLats_thisCrop)} rx values; got {len(theseRxVals)}") + if not np.any(theseRxVals != -1): + continue + any_bad_anyCrop = True + break + if not any_bad_anyCrop: + continue + + # This bit is pretty inefficient, but I'm not going to optimize it until I actually need to use it. + for i, p in enumerate(bad_patches_thisT): + thisPatch = varyPatches[i] + thisLon = varyLons[i] + thisLat = varyLats[i] + thisCrop = varyCrops[i] + thisCrop_int = varyCrops_int[i] + + # If prescribed input had missing value (-1), it's fine for it to vary. + if rx_ds: + rx_var = f'gs1_{thisCrop_int}' + if thisLon in rx_ds.lon.values and thisLat in rx_ds.lat.values: + rx = rx_ds[rx_var].sel(lon=thisLon, lat=thisLat).values + Nunique = len(np.unique(rx)) + if (Nunique == 1): + found_in_rx[i] = True + if rx == -1: + continue + elif Nunique > 1: + raise RuntimeError(f'How does lon {thisLon} lat {thisLat} {thisCrop} have time-varying {v}?') + else: + raise RuntimeError('lon {thisLon} lat {thisLat} {thisCrop} not in rx dataset?') + + # Print info (or save to print later) + any_bad = True + if verbose: + thisStr = f" Patch {thisPatch} (lon {thisLon} lat {thisLat}) {thisCrop} ({thisCrop_int})" + if rx_ds and not found_in_rx[i]: + thisStr = thisStr.replace('(lon', '* (lon') + if not np.isnan(t1_vals[p]): + t1_val_print = int(t1_vals[p]) + else: + t1_val_print = 'NaN' + if not np.isnan(t_vals[p]): + t_val_print = int(t_vals[p]) + else: + t_val_print = 'NaN' + if v == "SDATES": + strList.append(f"{thisStr}: Sowing {t1_yr} jday {t1_val_print}, {t_yr} jday {t_val_print}") + else: + strList.append(f"{thisStr}: {t1_yr} {v} {t1_val_print}, {t_yr} {v} {t_val_print}") + else: + if ok: + print(f"{emojus} CLM output {v} unexpectedly vary over time:") + ok = False + print(f"{v} timestep {t} does not match timestep {t1}") + break + if verbose and any_bad: + print(f"{emojus} CLM output {v} unexpectedly vary over time:") + strList.sort() + if rx_ds and np.any(~found_in_rx): + strList = ['*: Not found in prescribed input file (maybe minor lon/lat mismatch)'] + strList + elif not rx_ds: + strList = ['(No rx file checked)'] + strList + print('\n'.join(strList)) + + # Make sure every patch was checked once (or is all-NaN except possibly final season) + incl_patches = np.sort(incl_patches) + if not np.array_equal(incl_patches, np.unique(incl_patches)): + raise RuntimeError('Patch(es) checked more than once!') + incl_patches = list(incl_patches) + incl_patches += list(np.where(np.all(np.isnan(ra_sp[:-1,]), axis=0))[0]) + incl_patches = np.sort(incl_patches) + if not np.array_equal(incl_patches, np.unique(incl_patches)): + raise RuntimeError('Patch(es) checked but also all-NaN??') + if not np.array_equal(incl_patches, np.arange(this_ds.dims['patch'])): + for p in np.arange(this_ds.dims['patch']): + if p not in incl_patches: + break + raise RuntimeError(f'Not all patches checked! E.g., {p}: {this_da.isel(patch=p).values}') + + if not any_bad: + if any_bad_before_checking_rx: + print(f"✅ CLM output {v} do not vary through {this_ds.dims[time_coord]} growing seasons of output (except for patch(es) with missing rx).") + else: + print(f"✅ CLM output {v} do not vary through {this_ds.dims[time_coord]} growing seasons of output.") + + if any_bad and throw_error: + raise RuntimeError('Stopping due to failed check_constant_vars().') + + bad_patches = np.unique(bad_patches) + return [int(p) for p in bad_patches] + + +def check_rx_obeyed(vegtype_list, rx_ds, dates_ds, which_ds, output_var, gdd_min=None, verbose=False): + all_ok = 2 + diff_str_list = [] + gdd_tolerance = 1 + + if "GDDHARV" in output_var and verbose: + harvest_reason_da = dates_ds['HARVEST_REASON'] + unique_harvest_reasons = np.unique(harvest_reason_da.values[np.where(~np.isnan(harvest_reason_da.values))]) + pct_harv_at_mature = get_pct_harv_at_mature(harvest_reason_da) + print(f"{which_ds} harvest reasons: {unique_harvest_reasons} ({pct_harv_at_mature}% harv at maturity)") + + for vegtype_str in vegtype_list: + thisVeg_patches = np.where(dates_ds.patches1d_itype_veg_str == vegtype_str)[0] + if thisVeg_patches.size == 0: + continue + ds_thisVeg = dates_ds.isel(patch=thisVeg_patches) + patch_inds_lon_thisVeg = ds_thisVeg.patches1d_ixy.values.astype(int) - 1 + patch_inds_lat_thisVeg = ds_thisVeg.patches1d_jxy.values.astype(int) - 1 + patch_lons_thisVeg = ds_thisVeg.patches1d_lon + patch_lats_thisVeg = ds_thisVeg.patches1d_lat + + vegtype_int = utils.vegtype_str2int(vegtype_str)[0] + rx_da = rx_ds[f"gs1_{vegtype_int}"] + rx_array = rx_da.values[patch_inds_lat_thisVeg,patch_inds_lon_thisVeg] + rx_array = np.expand_dims(rx_array, axis=1) + sim_array = ds_thisVeg[output_var].values + sim_array_dims = ds_thisVeg[output_var].dims + + # Ignore patches without prescribed value + rx_array[np.where(rx_array < 0)] = np.nan + + # Account for... + if "GDDHARV" in output_var: + # ...GDD harvest threshold minimum set in PlantCrop() + if gdd_min == None: + gdd_min = default_gdd_min() + print(f"gdd_min not provided when doing check_rx_obeyed() for {output_var}; using default {gdd_min}") + rx_array[(rx_array >= 0) & (rx_array < gdd_min)] = gdd_min + + # ...harvest reason + # 0: Should never happen in any simulation + # 1: Harvesting at maturity + # 2: Harvesting at max season length (mxmat) + # 3: Crop was incorrectly planted in last time step of Dec. 31 + # 4: Today was supposed to be the planting day, but the previous crop still hasn't been harvested. + # 5: Harvest the day before the next sowing date this year. + # 6: Same as #5. + # 7: Harvest the day before the next sowing date (today is Dec. 31 and the sowing date is Jan. 1) + harvest_reason_da = ds_thisVeg['HARVEST_REASON'] + unique_harvest_reasons = np.unique(harvest_reason_da.values[np.where(~np.isnan(harvest_reason_da.values))]) + pct_harv_at_mature = get_pct_harv_at_mature(harvest_reason_da) + + if np.any(sim_array != rx_array): + diff_array = sim_array - rx_array + + # Allow negative GDDHARV values when harvest occurred because sowing was scheduled for the next day + if output_var=="GDDHARV_PERHARV": + diff_array = np.ma.masked_array(diff_array, mask= \ + (diff_array < 0) & + (ds_thisVeg["HARVEST_REASON_PERHARV"].values==5)) + elif output_var=="GDDHARV": + diff_array = np.ma.masked_array(diff_array, mask= \ + (diff_array < 0) & + (ds_thisVeg["HARVEST_REASON"].values==5)) + + if np.any(np.abs(diff_array[abs(diff_array) > 0]) > 0): + min_diff, minLon, minLat, minGS, minRx = get_extreme_info(diff_array, rx_array, np.nanmin, sim_array_dims, dates_ds.gs, patch_lons_thisVeg, patch_lats_thisVeg) + max_diff, maxLon, maxLat, maxGS, maxRx = get_extreme_info(diff_array, rx_array, np.nanmax, sim_array_dims, dates_ds.gs, patch_lons_thisVeg, patch_lats_thisVeg) + + diffs_eg_txt = f"{vegtype_str} ({vegtype_int}): diffs range {min_diff} (lon {minLon}, lat {minLat}, gs {minGS}, rx ~{minRx}) to {max_diff} (lon {maxLon}, lat {maxLat}, gs {maxGS}, rx ~{maxRx})" + if "GDDHARV" in output_var: + diffs_eg_txt += f"; harvest reasons: {unique_harvest_reasons} ({pct_harv_at_mature}% harvested at maturity)" + if "GDDHARV" in output_var and np.nanmax(abs(diff_array)) <= gdd_tolerance: + if all_ok > 0: + all_ok = 1 + diff_str_list.append(f" {diffs_eg_txt}") + else: + all_ok = 0 + if verbose: + print(f"❌ {which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}") + else: + break + + if all_ok == 2: + print(f"✅ {which_ds}: Prescribed {output_var} always obeyed") + elif all_ok == 1: + # print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable:") + # for x in diff_str_list: print(x) + print(f"🟨 {which_ds}: Prescribed {output_var} *not* always obeyed, but acceptable (diffs <= {gdd_tolerance})") + elif not verbose: + print(f"❌ {which_ds}: Prescribed {output_var} *not* always obeyed. E.g., {diffs_eg_txt}") + + + # Make sure that, e.g., GDDACCUM_PERHARV is always <= HUI_PERHARV +def check_v0_le_v1(this_ds, vars, msg_txt=" ", both_nan_ok = False, throw_error=False): + v0 = vars[0] + v1 = vars[1] + gdd_lt_hui = this_ds[v0] <= this_ds[v1] + if both_nan_ok: + gdd_lt_hui = gdd_lt_hui | (np.isnan(this_ds[v0]) & np.isnan(this_ds[v1])) + if np.all(gdd_lt_hui): + print(f"✅{msg_txt}{v0} always <= {v1}") + else: + msg = f"❌{msg_txt}{v0} *not* always <= {v1}" + gdd_lt_hui_vals = gdd_lt_hui.values + p = np.where(~gdd_lt_hui_vals)[0][0] + msg = msg + f"\ne.g., patch {p}: {this_ds.patches1d_itype_veg_str.values[p]}, lon {this_ds.patches1d_lon.values[p]} lat {this_ds.patches1d_lat.values[p]}:" + msg = msg + f"\n{this_ds[v0].values[p,:]}" + msg = msg + f"\n{this_ds[v1].values[p,:]}" + if throw_error: + print(msg) + else: + raise RuntimeError(msg) + + +def christoph_detrend(x, w, center0=False): + if w==0: + raise RuntimeError("Don't use christoph_detrend() with w=0") + + moving_average = get_moving_average(x, w) + + r = get_window_radius(w) + result = x[..., r:-r] - moving_average + + if not center0: + ma_mean = np.mean(moving_average, axis=x.ndim-1) + if x.ndim == 2: + ma_mean = np.expand_dims(ma_mean, axis=1) + result += ma_mean + + return result + + +# Convert time*mxharvests axes to growingseason axis +def convert_axis_time2gs(this_ds, verbose=False, myVars=None, incl_orig=False): + + # For backwards compatibility. + if "SDATES_PERHARV" not in this_ds: + return convert_axis_time2gs_old(this_ds, myVars=myVars) + # Otherwise... + + # How many non-NaN patch-seasons do we expect to have once we're done organizing things? + Npatch = this_ds.dims["patch"] + # Because some patches will be planted in the last year but not complete, we have to ignore any finalyear-planted seasons that do complete. + Ngs = this_ds.dims["time"]-1 + expected_valid = Npatch*Ngs + + mxharvests = this_ds.dims["mxharvests"] + + if verbose: + print(f'Start: discrepancy of {np.sum(~np.isnan(this_ds.HDATES.values)) - expected_valid} patch-seasons') + + # Set all non-positive date values to NaN. These are seasons that were never harvested (or never started): "non-seasons." + if this_ds.HDATES.dims != ("time", "mxharvests", "patch"): + raise RuntimeError(f"This code relies on HDATES dims ('time', 'mxharvests', 'patch'), not {this_ds.HDATES.dims}") + hdates_ymp = this_ds.HDATES.copy().where(this_ds.HDATES > 0).values + hdates_pym = np.transpose(hdates_ymp.copy(), (2,0,1)) + sdates_ymp = this_ds.SDATES_PERHARV.copy().where(this_ds.SDATES_PERHARV > 0).values + sdates_pym = np.transpose(sdates_ymp.copy(), (2,0,1)) + hdates_pym[hdates_pym <= 0] = np.nan + + # Find years where patch was inactive + inactive_py = np.transpose( + np.isnan(this_ds.HDATES).all(dim="mxharvests").values \ + & np.isnan(this_ds.SDATES_PERHARV).all(dim="mxharvests").values) + # Find seasons that were planted while the patch was inactive + sown_inactive_py = inactive_py[:,:-1] & (hdates_pym[:,1:,0] < sdates_pym[:,1:,0]) + sown_inactive_py = np.concatenate((np.full((Npatch, 1), False), + sown_inactive_py), + axis=1) + + # "Ignore harvests from seasons sown (a) before this output began or (b) when the crop was inactive" + first_season_before_first_year_p = hdates_pym[:,0,0] < sdates_pym[:,0,0] + first_season_before_first_year_py = np.full(hdates_pym.shape[:-1], fill_value=False) + first_season_before_first_year_py[:,0] = first_season_before_first_year_p + sown_prerun_or_inactive_py = first_season_before_first_year_py | sown_inactive_py + sown_prerun_or_inactive_pym = np.concatenate((np.expand_dims(sown_prerun_or_inactive_py, axis=2), + np.full((Npatch, Ngs+1, mxharvests-1), False)), + axis=2) + where_sown_prerun_or_inactive_pym = np.where(sown_prerun_or_inactive_pym) + hdates_pym[where_sown_prerun_or_inactive_pym] = np.nan + sdates_pym[where_sown_prerun_or_inactive_pym] = np.nan + if verbose: + print(f'After "Ignore harvests from before this output began: discrepancy of {np.sum(~np.isnan(hdates_pym)) - expected_valid} patch-seasons') + + # We need to keep some non-seasons---it's possible that "the yearY growing season" never happened (sowing conditions weren't met), but we still need something there so that we can make an array of dimension Npatch*Ngs. We do this by changing those non-seasons from NaN to -Inf before doing the filtering and reshaping, after which we'll convert them back to NaNs. + + # "In years with no sowing, pretend the first no-harvest is meaningful, unless that was intentionally ignored above." + sdates_orig_ymp = this_ds.SDATES.copy().values + sdates_orig_pym = np.transpose(sdates_orig_ymp.copy(), (2,0,1)) + hdates_pym2 = hdates_pym.copy() + sdates_pym2 = sdates_pym.copy() + nosow_py = np.all(~(sdates_orig_pym > 0), axis=2) + nosow_py_1st = nosow_py & np.isnan(hdates_pym[:,:,0]) + where_nosow_py_1st = np.where(nosow_py_1st) + hdates_pym2[where_nosow_py_1st[0], where_nosow_py_1st[1], 0] = -np.inf + sdates_pym2[where_nosow_py_1st[0], where_nosow_py_1st[1], 0] = -np.inf + for h in np.arange(mxharvests - 1): + if h == 0: + continue + elif h == 1: + print("Warning: Untested with mxharvests > 2") + where_nosow_py = np.where(nosow_py & ~np.any(np.isnan(hdates_pym[:,:,0:h]), axis=2) & np.isnan(hdates_pym[:,:,h])) + hdates_pym2[where_nosow_py[0], where_nosow_py[1], h+1] = -np.inf + sdates_pym2[where_nosow_py[0], where_nosow_py[1], h+1] = -np.inf + + # "In years with sowing that are followed by inactive years, check whether the last sowing was harvested before the patch was deactivated. If not, pretend the LAST [easier to implement!] no-harvest is meaningful." + sdates_orig_masked_pym = sdates_orig_pym.copy() + sdates_orig_masked_pym[np.where(sdates_orig_masked_pym <= 0)] = np.nan + last_sdate_firstNgs_py = np.nanmax(sdates_orig_masked_pym[:,:-1,:], axis=2) + last_hdate_firstNgs_py = np.nanmax(hdates_pym2[:,:-1,:], axis=2) + last_sowing_not_harvested_sameyear_firstNgs_py = \ + (last_hdate_firstNgs_py < last_sdate_firstNgs_py) \ + | np.isnan(last_hdate_firstNgs_py) + inactive_lastNgs_py = inactive_py[:,1:] + last_sowing_never_harvested_firstNgs_py = last_sowing_not_harvested_sameyear_firstNgs_py & inactive_lastNgs_py + last_sowing_never_harvested_py = np.concatenate((last_sowing_never_harvested_firstNgs_py, + np.full((Npatch,1), False)), + axis=1) + last_sowing_never_harvested_pym = np.concatenate((np.full((Npatch, Ngs+1, mxharvests-1), False), + np.expand_dims(last_sowing_never_harvested_py, axis=2)), + axis=2) + where_last_sowing_never_harvested_pym = last_sowing_never_harvested_pym + hdates_pym3 = hdates_pym2.copy() + sdates_pym3 = sdates_pym2.copy() + hdates_pym3[where_last_sowing_never_harvested_pym] = -np.inf + sdates_pym3[where_last_sowing_never_harvested_pym] = -np.inf + + # Convert to growingseason axis + def pym_to_pg(pym, quiet=False): + pg = np.reshape(pym, (pym.shape[0],-1)) + ok_pg = pg[~np.isnan(pg)] + if not quiet: + print(f"{ok_pg.size} included; unique N seasons = {np.unique(np.sum(~np.isnan(pg), axis=1))}") + return pg + hdates_pg = pym_to_pg(hdates_pym3.copy(), quiet=~verbose) + sdates_pg = pym_to_pg(sdates_pym3.copy(), quiet=True) + if verbose: + print(f'After "In years with no sowing, pretend the first no-harvest is meaningful: discrepancy of {np.sum(~np.isnan(hdates_pg)) - expected_valid} patch-seasons') + + # "Ignore any harvests that were planted in the final year, because some cells will have incomplete growing seasons for the final year." + lastyear_complete_season = (hdates_pg[:,-mxharvests:] >= sdates_pg[:,-mxharvests:]) | np.isinf(hdates_pg[:,-mxharvests:]) + def ignore_lastyear_complete_season(pg, excl, mxharvests): + tmp_L = pg[:,:-mxharvests] + tmp_R = pg[:,-mxharvests:] + tmp_R[np.where(excl)] = np.nan + pg = np.concatenate((tmp_L, tmp_R), axis=1) + return pg + hdates_pg2 = ignore_lastyear_complete_season(hdates_pg.copy(), lastyear_complete_season, mxharvests) + sdates_pg2 = ignore_lastyear_complete_season(sdates_pg.copy(), lastyear_complete_season, mxharvests) + is_valid = ~np.isnan(hdates_pg2) + is_fake = np.isneginf(hdates_pg2) + is_fake = np.reshape(is_fake[is_valid], (this_ds.dims["patch"], Ngs)) + discrepancy = np.sum(is_valid) - expected_valid + unique_Nseasons = np.unique(np.sum(is_valid, axis=1)) + if verbose: + print(f'After "Ignore any harvests that were planted in the final year, because other cells will have incomplete growing seasons for the final year": discrepancy of {discrepancy} patch-seasons') + try: + import pandas as pd + bc = np.bincount(np.sum(is_valid, axis=1)) + bc = bc[bc>0] + df = pd.DataFrame({"Ngs": unique_Nseasons, "Count": bc}) + print(df) + except: + print(f"unique N seasons = {unique_Nseasons}") + print(" ") + + # Create Dataset with time axis as "gs" (growing season) instead of what CLM puts out + if discrepancy == 0: + this_ds_gs = set_up_ds_with_gs_axis(this_ds) + for v in this_ds.data_vars: + if this_ds[v].dims != ('time', 'mxharvests', 'patch') or (myVars and v not in myVars): + continue + + # Set invalid values to NaN + da_yhp = this_ds[v].copy() + da_yhp = da_yhp.where(~np.isneginf(da_yhp)) + + # Remove the nans and reshape to patches*growingseasons + da_pyh = da_yhp.transpose("patch", "time", "mxharvests") + ar_pg = np.reshape(da_pyh.values, (this_ds.dims["patch"], -1)) + ar_valid_pg = np.reshape(ar_pg[is_valid], (this_ds.dims["patch"], Ngs)) + # Change -infs to nans + ar_valid_pg[is_fake] = np.nan + # Save as DataArray to new Dataset, stripping _PERHARV from variable name + newname = v.replace("_PERHARV","") + if newname in this_ds_gs: + raise RuntimeError(f"{newname} already in dataset!") + da_pg = xr.DataArray(data = ar_valid_pg, + coords = [this_ds_gs.coords["patch"], this_ds_gs.coords["gs"]], + name = newname, + attrs = da_yhp.attrs) + this_ds_gs[newname] = da_pg + this_ds_gs[newname].attrs['units'] = this_ds[v].attrs['units'] + else: + # Print details about example bad patch(es) + if min(unique_Nseasons) < Ngs: + print(f"Too few seasons (min {min(unique_Nseasons)} < {Ngs})") + p = np.where(np.sum(~np.isnan(hdates_pg2), axis=1) == min(unique_Nseasons))[0][0] + print_onepatch_wrongNgs(p, this_ds, sdates_ymp, hdates_ymp, sdates_pym, hdates_pym, sdates_pym2, hdates_pym2, sdates_pym3, hdates_pym3, sdates_pg, hdates_pg, sdates_pg2, hdates_pg2) + if max(unique_Nseasons) > Ngs: + print(f"Too many seasons (max {max(unique_Nseasons)} > {Ngs})") + p = np.where(np.sum(~np.isnan(hdates_pg2), axis=1) == max(unique_Nseasons))[0][0] + print_onepatch_wrongNgs(p, this_ds, sdates_ymp, hdates_ymp, sdates_pym, hdates_pym, sdates_pym2, hdates_pym2, sdates_pym3, hdates_pym3, sdates_pg, hdates_pg, sdates_pg2, hdates_pg2) + raise RuntimeError(f"Can't convert time*mxharvests axes to growingseason axis: discrepancy of {discrepancy} patch-seasons") + + # Preserve units + for v1 in this_ds_gs: + v0 = v1 + if v0 not in this_ds: v0 += "_PERHARV" + if v0 not in this_ds: + continue + if 'units' in this_ds[v0].attrs: + this_ds_gs[v1].attrs['units'] = this_ds[v0].attrs['units'] + + if incl_orig: + return this_ds_gs, this_ds + else: + return this_ds_gs + + +# For backwards compatibility with files missing SDATES_PERHARV. +def convert_axis_time2gs_old(this_ds, myVars): + ### Checks ### + # Relies on max harvests per year >= 2 + mxharvests = len(this_ds.mxharvests) + if mxharvests < 2: + raise RuntimeError(f"convert_axis_time2gs() assumes max harvests per year == 2, not {mxharvests}") + # Untested with max harvests per year > 2 + if mxharvests > 2: + print(f"Warning: Untested with max harvests per year ({mxharvests}) > 2") + # All sowing dates should be positive + if np.any(this_ds["SDATES"] <= 0).values: + raise ValueError("All sowing dates should be positive... right?") + # Throw an error if harvests happened on the day of planting + if (np.any(np.equal(this_ds["SDATES"], this_ds["HDATES"]))): + raise RuntimeError("Harvest on day of planting") + + ### Setup ### + Npatches = this_ds.dims["patch"] + # Because some patches will be planted in the last year but not complete, we have to ignore any finalyear-planted seasons that do complete. + Ngs = this_ds.dims["time"]-1 + # Set up empty Dataset with time axis as "gs" (growing season) instead of what CLM puts out + gs_years = [t.year-1 for t in this_ds.time.values[:-1]] + data_vars = dict() + for v in this_ds.data_vars: + if "time" not in this_ds[v].dims: + data_vars[v] = this_ds[v] + new_ds_gs = xr.Dataset(coords={ + "gs": gs_years, + "patch": this_ds.patch, + }) + + ### Ignore harvests from the old, non-prescribed sowing date from the year before this run began. ### + cond1 = this_ds["HDATES"].isel(time=0, mxharvests=0) \ + < this_ds["SDATES"].isel(time=0, mxsowings=0) + firstharv_nan_inds = np.where(cond1)[0] + # (Only necessary before "don't allow harvest on day of planting" was working) + cond2 = np.bitwise_and( \ + this_ds["HDATES"].isel(time=0, mxharvests=0) \ + == this_ds["SDATES"].isel(time=0, mxsowings=0), \ + this_ds["HDATES"].isel(time=0, mxharvests=1) > 0) + firstharv_nan_inds = np.where(np.bitwise_or(cond1, cond2))[0] + for v in [x for x in myVars if x=="HDATES" or "PERHARV" in x]: + this_ds = set_firstharv_nan(this_ds, v, firstharv_nan_inds) + + ### In some cells, the last growing season did complete, but we have to ignore it because it's extra. This block determines which members of HDATES (and other mxharvests-dimensioned variables) should be ignored for this reason. ### + hdates = this_ds["HDATES"].values + Nharvests_eachPatch = get_Nharv(hdates, this_ds["HDATES"].dims) + if np.max(Nharvests_eachPatch) > Ngs + 1: + raise ValueError(f"Expected at most {Ngs+1} harvests in any patch; found at least one patch with {np.max(Nharvests_eachPatch)}") + h = mxharvests + while np.any(Nharvests_eachPatch > Ngs): + h = h - 1 + if h < 0: + raise RuntimeError("Unable to ignore enough harvests") + hdates[-1,h,Nharvests_eachPatch > Ngs] = np.nan + Nharvests_eachPatch = get_Nharv(hdates, this_ds["HDATES"].dims) + + # So: Which events are we manually excluding? + sdate_included = this_ds["SDATES"].values > 0 + hdate_manually_excluded = np.isnan(hdates) + hdate_included = np.bitwise_not(np.bitwise_or(hdate_manually_excluded, hdates<=0)) + + ### Extract the series of sowings and harvests ### + new_ds_gs = extract_gs_timeseries(new_ds_gs, "SDATES", this_ds["SDATES"], sdate_included, Npatches, Ngs+1) + for v in [x for x in myVars if x!="SDATES"]: + new_ds_gs = extract_gs_timeseries(new_ds_gs, v, this_ds[v], hdate_included, Npatches, Ngs) + + ### Save additional variables ### + new_ds_gs = new_ds_gs.assign(variables=data_vars) + new_ds_gs.coords["lon"] = this_ds.coords["lon"] + new_ds_gs.coords["lat"] = this_ds.coords["lat"] + + return new_ds_gs + + +def convert_units(da, tgt_units): + if 'units' not in da.attrs.keys(): + raise RuntimeError("convert_units(): 'units' missing from DataArray attributes") + + # Simplify units + def simplify(units): + units = (units + .replace('$', '') + .replace('^', '') + .replace('\n', ' ') + .replace('tonnes', 't') + .replace('∆ abs. bias ', '') + .replace('(', '') + .replace(')', '') + .replace('ddays', 'GDD') + ) + return units + da_units = simplify(da.attrs['units']) + tgt_units = simplify(tgt_units) + + if da_units == tgt_units: + return da + + if da_units not in multiplier_dict.keys() or tgt_units not in multiplier_dict[da_units].keys(): + if tgt_units not in multiplier_dict.keys() or da_units not in multiplier_dict[tgt_units].keys(): + raise RuntimeError(f"Conversion multiplier between {da_units} and {tgt_units} is not defined") + if da_units in multiplier_dict.keys(): + multiplier = multiplier_dict[da_units][tgt_units] + else: + multiplier = 1.0 / multiplier_dict[tgt_units][da_units] + + return da * multiplier + + +def cropnames_fao2clm(cropList_in): + def convert1(thisCrop): + thisCrop = thisCrop.lower().replace(' ', '') + thisCrop = thisCrop.replace(',paddy', '') + thisCrop = thisCrop.replace('seed', '') + thisCrop = thisCrop.replace('beans', 'bean') + thisCrop = thisCrop.replace('maize', 'corn') + return thisCrop + + if isinstance(cropList_in, (list, np.ndarray)): + cropList_out = [convert1(x) for x in cropList_in] + if isinstance(cropList_in, np.ndarray): + cropList_out = np.array(cropList_out) + else: + cropList_out = convert1(cropList_in) + + return cropList_out + + +def detrend(ps_in): + # Can't detrend if NaNs are present, so... + + if isinstance(ps_in, xr.DataArray): + ps_out = ps_in.values + else: + ps_out = ps_in + + unique_Nnans = np.unique(np.sum(np.isnan(ps_out), axis=1)) + Ngs = ps_in.shape[1] + + for n in unique_Nnans: + + # Don't need to detrend patches with <2 non-NaN seasons, and "detrending" 2 points will just set them both to zero. + if n >= Ngs-2: + continue + + # Get the patches with this number of NaN seasons + ok = np.where(np.sum(np.isnan(ps_out), axis=1)==n)[0] + Nok = len(ok) + thisNok_ps = ps_out[ok,:] + where_notnan = np.where(~np.isnan(thisNok_ps)) + + # Get the non-NaN seasons of each such patch + thisNok_notnan = thisNok_ps[where_notnan] + thisNok_notnan_ps = np.reshape(thisNok_notnan, (Nok, Ngs-n)) + + # Detrend these patches + thisNok_notnan_dt_ps = signal.detrend(thisNok_notnan_ps, axis=1) + + # Save the detrended time series back to our output + thisNok_dt_ps = np.copy(thisNok_ps) + thisNok_dt_ps[where_notnan] = np.reshape(thisNok_notnan_dt_ps, (-1)) + ps_out[ok,:] = thisNok_dt_ps + + if isinstance(ps_in, xr.DataArray): + ps_out = xr.DataArray(data = ps_out, + coords = ps_in.coords, + attrs = ps_in.attrs) + + return ps_out + + +def equalize_colorbars(ims, center0=False, this_var=None, vrange=None): + if vrange is None: + vmin = np.inf + vmax = -np.inf + for im in ims: + vmin = min(vmin, im.get_clim()[0]) + vmax = max(vmax, im.get_clim()[1]) + else: + vmin = vrange[0] + vmax = vrange[1] + + extend = "neither" + if this_var == "HUIFRAC" and vmax > 1: + vmax = 1 + extend = "max" + + if center0: + v = np.max(np.abs([vmin, vmax])) + vmin = -v + vmax = v + + for im in ims: + im.set_clim(vmin, vmax) + + vrange = [vmin, vmax] + + return extend, vrange + + +# For backwards compatibility with files missing SDATES_PERHARV. +def extract_gs_timeseries(this_ds, this_var, in_da, include_these, Npatches, Ngs): + this_array = in_da.values + + # Rearrange to (Ngs*mxevents, Npatches) + this_array = this_array.reshape(-1, Npatches) + include_these = include_these.reshape(-1, Npatches) + + # Extract valid events + this_array = this_array.transpose() + include_these = include_these.transpose() + this_array = this_array[include_these].reshape(Npatches,Ngs) + this_array = this_array.transpose() + + # Always ignore last sowing date, because for some cells this growing season will be incomplete. + if this_var == "SDATES": + this_array = this_array[:-1,:] + + # Set up and fill output DataArray + out_da = xr.DataArray(this_array, \ + coords=this_ds.coords, + dims=this_ds.dims) + + # Save output DataArray to Dataset + this_ds[this_var] = out_da + return this_ds + + +def fao_data_get(fao_all, element, y1, yN, fao_to_clm_dict, cropList_combined_clm): + fao_this = fao_all.copy().query(f"Element == '{element}'") + + # Convert t to Mt + if element == 'Production': + fao_this.Value *= 1e-6 + + # Pivot and add Total column + fao_this = fao_this.copy().pivot(index="Year", columns="Crop", values="Value") + fao_this['Total'] = fao_this.sum(numeric_only=True, axis=1) + + # Remove unneeded years + fao_this = fao_this.filter(items=np.arange(y1,yN+1), axis=0) + + # Reorder to match CLM + if len(fao_to_clm_dict) != len(cropList_combined_clm): + raise RuntimeError(f"fao_to_clm_dict and are different lengths ({len(cropList_combined_clm)} vs {len(cropList_combined_clm)})") + if len(fao_this.columns) != len(cropList_combined_clm): + raise RuntimeError(f"fao_this.columns and are different lengths ({len(fao_this.columns)} vs {len(cropList_combined_clm)})") + new_order = [cropList_combined_clm.index(fao_to_clm_dict[x]) for x in fao_this.columns] + new_cols = fao_this.columns[new_order] + fao_this = fao_this[new_cols] + + # Make no-sugarcane version + fao_this_nosgc = fao_this.drop(columns = ["Sugar cane", "Total"]) + fao_this_nosgc['Total'] = fao_this_nosgc.sum(numeric_only=True, axis=1) + + return fao_this, fao_this_nosgc + + +def fao_data_preproc(fao): + + # Because I always confuse Item vs. Element + fao.rename(columns={"Item": "Crop"}, inplace=True, errors="raise") + + # Combine "Maize" and "Maize, green" + fao.Crop.replace("Maize.*", "Maize", regex=True, inplace=True) + fao = fao.groupby(by=["Crop","Year","Element","Area","Unit"], as_index=False).agg("sum") + + # Pick one rice + rice_to_keep = "Rice, paddy" + rice_to_drop = "Rice, paddy (rice milled equivalent)" + drop_this = [x == rice_to_drop for x in fao.Crop] + fao = fao.drop(fao[drop_this].index) + + # Filter out "China," which includes all Chinas + if "China" in fao.Area.values: + fao = fao.query('Area != "China"') + + return fao + + +def fullname_to_combinedCrop(fullnames, cropList_combined_clm): + x = [strip_cropname(y).capitalize() for y in fullnames] + z = [y if y in cropList_combined_clm else '' for y in x] + return z + + +def get_caselist(which_cases): + cases = {} + + if which_cases == "test": + cases['Prescribed Calendars'] = \ + {'filepath': '/Users/sam/Downloads/tests_10x15_20230329_rxboth.clm2.h1.1995-01-01-00000.nc', + 'constantVars': ["SDATES", "GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f10_f10_mg37', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + 'rx_hdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + 'rx_gdds_file': "/Users/Shared/CESM_work/crop_dates_mostrice/gdds_20230331_122447.nc", + 'verbosename': 'Test', + 'gdd_min': 1.0} + return cases + + if which_cases == "originalCLM": + # A run that someone else did + cases['cmip6'] = \ + {'filepath': '/Users/Shared/CESM_work/CropEvalData_ssr/danica_timeseries-cmip6_i.e21.IHIST.f09_g17/month_1/ssr_trimmed_annual.nc', + 'constantVars': None, + 'constantGSs': None, + 'res': 'f09_g17', + 'verbosename': 'cmip6: Old CESM run'} + if "original" in which_cases: + # My run with normal CLM code + my outputs + cases['Original baseline'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_2deg_v3/cropcals3.f19-g17.yield_perharv2.IHistClm50BgcCrop.1958-2014/cropcals3.f19-g17.yield_perharv2.IHistClm50BgcCrop.1958-2014.clm2.h1.1958-01-01-00000.nc', + 'constantVars': None, + 'constantGSs': None, + 'res': 'f19_g17', + 'verbosename': 'Original baseline: ctsm5.1.dev092 + my outvars'} + # My run with rx_crop_calendars2 code but CLM calendars + clm_default_22 = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_2deg_v3/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.1958-2014/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.1958-2014.clm2.h1.1958-01-01-00000.nc', + 'constantVars': None, + 'constantGSs': None, + 'res': 'f19_g17', + 'verbosename': 'CLM Default 22: my cropcal code, no Rx', + 'gdd_min': 50} + clm_default_20230128_ctsm50 = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm50/20230128_clm50_clmdefault/20230128_clm50_clmdefault.clm2.h1.1958-01-01-00000.nc', + 'constantVars': None, + 'constantGSs': None, + 'res': 'f19_g17', + 'verbosename': 'CLM Default: my cropcal code, no Rx', + 'gdd_min': 1.0} + # As above, but with ctsm5.2 land use + clm_default_20230128_ctsm52 = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm52/20230128_clm52_clmdefault/20230128_clm52_clmdefault.clm2.h1.1958-01-01-00000.nc', + 'constantVars': None, + 'constantGSs': None, + 'res': 'f19_g17_ctsm5.2', + 'verbosename': 'CLM Default 20230128, ctsm5.2 LU: my cropcal code, no Rx', + 'gdd_min': 1.0} + clm_default_20230227_ctsm52 = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm52/20230227_clm52_clmdefault/20230227_clm52_clmdefault.clm2.h1.1958-01-01-00000.nc', + 'constantVars': None, + 'constantGSs': None, + 'res': 'f19_g17_ctsm5.2', + 'verbosename': 'CLM Default 20230227, ctsm5.2 LU: my cropcal code, no Rx', + 'gdd_min': 1.0} + + if which_cases == "ctsm_lu_5.0_vs_5.2": + cases['5.0 LU'] = clm_default_20230128_ctsm50 + cases['5.2 LU'] = clm_default_20230227_ctsm52 + return cases + + + if ".2022" in which_cases: + cases['CLM Default 22'] = clm_default_22 + elif ".52" in which_cases: + cases['CLM Default'] = clm_default_20230227_ctsm52 + else: + cases['CLM Default'] = clm_default_20230128_ctsm50 + + + # My run with rx_crop_calendars2 code and GGCMI calendars + if ".2022" in which_cases: + cases['Prescribed Calendars 22'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_2deg_v3/cropcals3.f19-g17.rx_crop_calendars3.IHistClm50BgcCrop.ggcmi.1958-2014.gddforced4.mxmat/cropcals3.f19-g17.rx_crop_calendars3.IHistClm50BgcCrop.ggcmi.1958-2014.gddforced4.mxmat.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["SDATES", "GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20220727_164727.nc", + 'rx_hdates_file': "/Users/Shared/CESM_work/crop_dates/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20220727_164727.nc", + 'rx_gdds_file': "/Users/Shared/CESM_work/crop_dates/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1977-2014.gddgen/generate_gdds.mxmat.2022-10-26-171107/gdds_20221026_180012.nc", + 'verbosename': 'Prescribed Calendars v4: Rx sdates+GDDs, lim-gs sim and GDDgen', + 'gdd_min': 50} + elif ".52" in which_cases: + cases['Prescribed Calendars'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm52/20230227_clm52_rxboth/20230227_clm52_rxboth.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["SDATES", "GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17_ctsm5.2', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + 'rx_hdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + 'rx_gdds_file': "/Users/Shared/CESM_runs/20230227_clm52_gengdds/generate_gdds.mxmat.2023-03-05-113258/gdds_20230305_151946.nc", + 'verbosename': 'Prescribed Calendars v5: Rx sdates+GDDs, lim-gs sim and GDDgen', + 'gdd_min': 1.0} + else: + cases['Prescribed Calendars'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm50/20230128_clm50_rxboth/20230128_clm50_rxboth.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["SDATES", "GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + 'rx_hdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + 'rx_gdds_file': "/Users/Shared/CESM_runs/20220102_gddgen_ts/generate_gdds.mxmat.2023-01-03-065522/gdds_20230103_074025.nc", + 'verbosename': 'Prescribed Calendars v5: Rx sdates+GDDs, lim-gs sim and GDDgen', + 'gdd_min': 1.0} + + # Prescribed Sowing and Prescribed Maturity + if "diagnose" in which_cases: + if ".2022" in which_cases: + # My run with rx_crop_calendars2 code and GGCMI sowing dates but CLM maturity reqts + cases['Prescribed Sowing 22'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_2deg_v3/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1958-2014.sdateforced_not_gdd/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1958-2014.sdateforced_not_gdd.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["SDATES"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20220727_164727.nc", + 'rx_hdates_file': None, + 'rx_gdds_file': None, + 'verbosename': 'Prescribed sowing: unlim-gs sim', + 'gdd_min': 50} + # My run with rx_crop_calendars2 code and CLM sowing dates but GGCMI maturity reqts + cases['Prescribed Maturity 22'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_2deg_v3/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1958-2014.gddforced_not_sdate.mxmat/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1958-2014.gddforced_not_sdate.mxmat.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17', + 'rx_sdates_file': None, + 'rx_hdates_file': None, + 'rx_gdds_file': "/Users/Shared/CESM_work/crop_dates/cropcals3.f19-g17.rx_crop_calendars2.IHistClm50BgcCrop.ggcmi.1977-2014.gddgen/generate_gdds/gdds_20220927_174954.nc", + 'verbosename': 'Prescribed maturity reqts.: unlim-gs sim and GDDs', + 'gdd_min': 50} + elif ".52" in which_cases: + # My run with rx_crop_calendars2 code and GGCMI sowing dates but CLM maturity reqts + cases['Prescribed Sowing'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm52/20230227_clm52_rxsdates/20230227_clm52_rxsdates.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["SDATES"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17_ctsm5.2', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + 'rx_hdates_file': None, + 'rx_gdds_file': None, + 'verbosename': 'Prescribed sowing: unlim-gs sim', + 'gdd_min': 1.0} + # My run with rx_crop_calendars2 code and CLM sowing dates but GGCMI maturity reqts + cases['Prescribed Maturity'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm52/20230227_clm52_rxgdds/20230227_clm52_rxgdds.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17_ctsm5.2', + 'rx_sdates_file': None, + 'rx_hdates_file': None, + 'rx_gdds_file': "/Users/Shared/CESM_runs/20230227_clm52_gengdds/generate_gdds.mxmat.2023-03-05-113258/gdds_20230305_151946.nc", + 'verbosename': 'Prescribed maturity reqts.: unlim-gs sim and GDDs', + 'gdd_min': 1.0} + else: + # My run with rx_crop_calendars2 code and GGCMI sowing dates but CLM maturity reqts + cases['Prescribed Sowing'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm50/20230128_clm50_rxsdates/20230128_clm50_rxsdates.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["SDATES"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17', + 'rx_sdates_file': "/Users/Shared/CESM_work/crop_dates_mostrice/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + 'rx_hdates_file': None, + 'rx_gdds_file': None, + 'verbosename': 'Prescribed sowing: unlim-gs sim', + 'gdd_min': 1.0} + # My run with rx_crop_calendars2 code and CLM sowing dates but GGCMI maturity reqts + cases['Prescribed Maturity'] = \ + {'filepath': '/Users/Shared/CESM_runs/cropcals_20230128/clm50/20230128_clm50_rxgdds/20230128_clm50_rxgdds.clm2.h1.1958-01-01-00000.nc', + 'constantVars': ["GDDHARV"], + 'constantGSs': None, # 'None' with constantVars specified means all should be constant + 'res': 'f19_g17', + 'rx_sdates_file': None, + 'rx_hdates_file': None, + 'rx_gdds_file': "/Users/Shared/CESM_runs/20220102_gddgen_ts/generate_gdds.mxmat.2023-01-03-065522/gdds_20230103_074025.nc", + 'verbosename': 'Prescribed maturity reqts.: unlim-gs sim and GDDs', + 'gdd_min': 1.0} + + + return cases + + +def get_earthstat_country_ts(earthstats, res, thisVar, countries_map, thisCrop_clm, i_theseYears_earthstat, country_id): + + if not np.array_equal(earthstats[res]['lon'], countries_map['lon']): + raise RuntimeError("Longitude mismatch between EarthStats and country map") + if not np.array_equal(earthstats[res]['lat'], countries_map['lat']): + raise RuntimeError("Latitude mismatch between EarthStats and country map") + + tmp = earthstats[res][thisVar]\ + .sel(crop=thisCrop_clm.title())\ + .isel(time=i_theseYears_earthstat) + if country_id != None: + tmp = tmp.where(countries_map == country_id) + + result = tmp.sum(dim=['lon', 'lat']).values + if np.any(np.isnan(result)): + raise RuntimeError("NaN in EarthStat country timeseries") + + # Deal with negative values (zero out very small ones) + if np.any(result < 0): + if np.any(result[result < 0] < -1e-24): + raise RuntimeError(f"Negative value(s) in EarthStat country timeseries; min {np.min(result)}") + result[result < 0] = 0 + + return result + + +def get_faostat_country_ts(fao_all_ctry, thisCrop_fao, top_y1, top_yN, country, element): + tmp = fao_all_ctry.query(f'Crop == "{thisCrop_fao}" & Element == "{element}" & Year >= {top_y1} & Year <= {top_yN}') + if country == "World": + tmp = tmp.groupby(by="Year").agg("sum") + else: + tmp = tmp.query(f'Area == "{country}"') + + # Get values for which this country is in the FAO data + years = np.arange(top_y1, top_yN+1) + yearCodes = list(tmp.index) + if yearCodes[0] > 2100: + if 'Year' in tmp.columns: + yearCodes = tmp['Year'].values + else: + yearCodes = tmp['Year Code'].values + _, IA, _ = np.intersect1d(years, yearCodes, return_indices=True) + result = np.full(years.shape, np.nan) + result[IA] = tmp['Value'].values + + return result + + +def get_diff_earthstat(case_ds, case, earthstats_ds, reses, use_absolute_bias=False): + + tgt_min_viable_hui = case_ds['YIELD_ANN'].attrs['min_viable_hui'] + tgt_mxmat_limited = case_ds['YIELD_ANN'].attrs['mxmat_limited'] + if not isinstance(earthstats_ds, xr.Dataset): + gridspec = get_gridspec(case) + earthstats_ds = earthstats_ds[gridspec] + + # Ensure lon/lat match + check_case_earthstats_dim_match(case, earthstats_ds, 'lon') + check_case_earthstats_dim_match(case, earthstats_ds, 'lat') + + attrs_tgt_dict = { + 'min_viable_hui': tgt_min_viable_hui, + 'mxmat_limited': tgt_mxmat_limited, + 'absolute_bias': use_absolute_bias + } + + if attrs_differ_or_missing(case_ds, "YIELD_ANN_DIFFEARTHSTAT", attrs_tgt_dict): + case_ds['YIELD_ANN_DIFFEARTHSTAT'] = convert_units(case_ds['YIELD_ANN'], 'g/m2') - convert_units(earthstats_ds['Yield'], 'g/m2') + if use_absolute_bias: + case_ds['YIELD_ANN_DIFFEARTHSTAT'] = np.fabs(case_ds['YIELD_ANN_DIFFEARTHSTAT']) + case_ds['YIELD_ANN_DIFFEARTHSTAT'] = case_ds['YIELD_ANN_DIFFEARTHSTAT'].where(earthstats_ds['PhysicalArea'] > 0) + case_ds['YIELD_ANN_DIFFEARTHSTAT'].attrs['min_viable_hui'] = tgt_min_viable_hui + case_ds['YIELD_ANN_DIFFEARTHSTAT'].attrs['mxmat_limited'] = tgt_mxmat_limited + case_ds['YIELD_ANN_DIFFEARTHSTAT'].attrs['units'] = case_ds['YIELD_ANN'].attrs['units'] + case_ds['YIELD_ANN_DIFFEARTHSTAT'].attrs['absolute_bias'] = use_absolute_bias + + if attrs_differ_or_missing(case_ds, "PROD_ANN_DIFFEARTHSTAT", attrs_tgt_dict): + yield_tmp = case_ds['YIELD_ANN_DIFFEARTHSTAT'] + area_tmp = reses[case['res']]['ds']['AREA_CFT'] + case_ds['PROD_ANN_DIFFEARTHSTAT'] = yield_tmp * area_tmp + if use_absolute_bias: + case_ds['PROD_ANN_DIFFEARTHSTAT'] = np.fabs(case_ds['PROD_ANN_DIFFEARTHSTAT']) + + # Set units + if 'units' not in yield_tmp.attrs: + raise RuntimeError("Units missing from YIELD_ANN_DIFFEARTHSTAT") + if yield_tmp.attrs['units'] != 'g/m2': + raise RuntimeError(f"Unknown units in YIELD_ANN_DIFFEARTHSTAT: {yield_tmp.attrs['units']}") + if 'units' not in area_tmp.attrs: + raise RuntimeError("Units missing from AREA_CFT") + if area_tmp.attrs['units'] != 'm2': + raise RuntimeError(f"Unknown units in AREA_CFT: {area_tmp.attrs['units']}") + case_ds['PROD_ANN_DIFFEARTHSTAT'].attrs['units'] = 'g' + + case_ds['PROD_ANN_DIFFEARTHSTAT'].attrs['min_viable_hui'] = tgt_min_viable_hui + case_ds['PROD_ANN_DIFFEARTHSTAT'].attrs['mxmat_limited'] = tgt_mxmat_limited + case_ds['PROD_ANN_DIFFEARTHSTAT'].attrs['absolute_bias'] = use_absolute_bias + + return case_ds + + +def get_extreme_info(diff_array, rx_array, mxn, dims, gs, patches1d_lon, patches1d_lat): + if mxn == np.min: + diff_array = np.ma.masked_array(diff_array, mask=(np.abs(diff_array) == 0)) + themxn = mxn(diff_array) + + # Find the first patch-gs that has the mxn value + matching_indices = np.where(diff_array == themxn) + first_indices = [x[0] for x in matching_indices] + + # Get the lon, lat, and growing season of that patch-gs + p = first_indices[dims.index("patch")] + thisLon = patches1d_lon.values[p] + thisLat = patches1d_lat.values[p] + s = first_indices[dims.index("gs")] + thisGS = gs.values[s] + + # Get the prescribed value for this patch-gs + thisRx = rx_array[p][0] + + return round(themxn, 3), round(thisLon, 3), round(thisLat,3), thisGS, round(thisRx) + + +# Minimum harvest threshold allowed in PlantCrop() +# Was 50 before cropcal runs 2023-01-28 +def default_gdd_min(): + return 1.0 + +# Get growing season lengths from a DataArray of hdate-sdate +def get_gs_len_da(this_da): + tmp = this_da.values + tmp[tmp < 0] = 365 + tmp[tmp < 0] + this_da.values = tmp + this_da.attrs['units'] = 'days' + return this_da + + +def get_irrigation_use_relative_to_supply(cases): + + for casename, case in cases.items(): + + # Get MONTH of each gridcell-year's peak irrigation use + ind = np.arange(12,case['ds'].dims["time_mth"],12) + yearly_split = np.split(case['ds']['QIRRIG_FROM_SURFACE_GRID_MTH'].values, ind, axis=0) + case['ds']['QIRRIG_FROM_SURFACE_GRID_PKMTH_ANN'] = xr.DataArray( + data=np.argmax(yearly_split, axis=1), + coords={'time': case['ds']['time'], + 'gridcell': case['ds']['gridcell']}, + attrs={'long_name': 'Peak month of irrigation use', + 'units': 'month'} + ) + + # Get VALUE of each gridcell-year's max monthly irrigation use + case['ds']['QIRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'] = case['ds']['QIRRIG_FROM_SURFACE_GRID_MTH'].groupby(case['ds']['time_mth'].dt.year).max() + + # Convert the above from mm/d to m3/d + case['ds']['IRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'] = case['ds']['QIRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'] * case['ds']['AREA_GRID'] * 1e-3 + case['ds']['IRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'].attrs['units'] = 'm^3/d' + + # Get the value of water SUPPLY in each gridcell-year's peak month of irrigation USE + irrig_supply_grid_valpkmthwithdrawal_ann = np.full_like(case['ds']['QIRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'], np.nan) + yearly_split = np.split(case['ds']['IRRIG_SUPPLY_GRID_MTH'].values, ind, axis=0) + for y in np.arange(len(yearly_split)): + thisYear_IRRIG_SUPPLY_GRID_MTH_mg = yearly_split[y] + # gridcells_with_supply = np.where(np.nansum(yearly_split[0],axis=0) > 0)[0] + thisYear_QIRRIG_FROM_SURFACE_GRID_PKMTH_g = case['ds']['QIRRIG_FROM_SURFACE_GRID_PKMTH_ANN'].isel(time=y) + + # # I'm sure there's a more efficient way to do this. + # # YES. See below. + # valpkmth_thisyear_g = np.full_like(case['ds']['IRRIG_SUPPLY_GRID_PKMTH'], np.nan) + # for i in np.arange(len(gridcells_with_supply)): + # g = gridcells_with_supply[i] + # valpkmth_thisyear_g[g] = thisYear_IRRIG_SUPPLY_GRID_MTH_mg[thisYear_QIRRIG_FROM_SURFACE_GRID_PKMTH_g[g],g] + # irrig_supply_grid_valpkmthwithdrawal_ann[y,:] = valpkmth_thisyear_g + + # This is MUCH faster and should produce the same result, except for giving zeroes where the above gave NaNs + test_take_along_axis = np.squeeze(np.take_along_axis(thisYear_IRRIG_SUPPLY_GRID_MTH_mg, np.expand_dims(thisYear_QIRRIG_FROM_SURFACE_GRID_PKMTH_g, axis=0), 0)) + # if np.any((test_take_along_axis != valpkmth_thisyear_g) & ~(np.isnan(valpkmth_thisyear_g) & (test_take_along_axis==0))): + # raise RuntimeError("Mismatch between inefficient method and take_along_axis") + + irrig_supply_grid_valpkmthwithdrawal_ann[y,:] = test_take_along_axis + where_no_irrigation = np.where(thisYear_QIRRIG_FROM_SURFACE_GRID_PKMTH_g==0)[0] + irrig_supply_grid_valpkmthwithdrawal_ann[y,where_no_irrigation] = np.nan + case['ds']['IRRIG_SUPPLY_GRID_VALPKMTHWITHDRAWAL_ANN'] = xr.DataArray( + data=irrig_supply_grid_valpkmthwithdrawal_ann, + coords=case['ds']['QIRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'].coords, + attrs={'long_name': 'Main channel river volume in month of peak irrigation demand', + 'units': "m3"} + ) + + # Get each gridcell-year's max monthly irrigation use as a fraction of the supply in that month. 48* because irrigation happens at the level of individual timesteps; because numerator is per day and denominator is mean of per timestep, we multiply denominator by 48. + case['ds']['IRRIG_WITHDRAWAL_FRAC_SUPPLY_VALPKMTHWITHDRAWAL_ANN'] = xr.DataArray( + data=case['ds']['IRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'] / (48*case['ds']['IRRIG_SUPPLY_GRID_VALPKMTHWITHDRAWAL_ANN']), + coords=case['ds']['IRRIG_FROM_SURFACE_GRID_VALPKMTH_ANN'].coords, + attrs={"units": "unitless"} + ) + + return cases + + +def get_mean_byCountry(fao, top_y1, top_yN): + return fao.query(f'Year>={top_y1} & Year<={top_yN}').groupby(['Crop','Element','Area'])['Value'].mean() + + +# w is total window width (not radius) +def get_moving_average(x, w): + if w==0: + return x + + if x.ndim == 2: + Ncases = x.shape[0] + r = get_window_radius(w) + result = np.full((Ncases, x.shape[1] - 2*r), fill_value=np.nan) + for c in np.arange(0, (Ncases)): + result[c,:] = get_moving_average(x[c,:], w) + else: + return np.convolve(x, np.ones(w), 'valid') / w + + return result + + +# For backwards compatibility with files missing SDATES_PERHARV. +def get_Nharv(array_in, these_dims): + # Sum over time and mxevents to get number of events in time series for each patch + sum_indices = tuple(these_dims.index(x) for x in ["time", "mxharvests"]) + Nevents_eachPatch = np.sum(array_in > 0, axis=sum_indices) + return Nevents_eachPatch + + +def get_pct_harv_at_mature(harvest_reason_da): + Nharv_at_mature = len(np.where(harvest_reason_da.values==1)[0]) + Nharv = len(np.where(harvest_reason_da.values>0)[0]) + if Nharv == 0: + return np.nan + pct_harv_at_mature = Nharv_at_mature / Nharv * 100 + pct_harv_at_mature = np.format_float_positional(pct_harv_at_mature, precision=2, unique=False, fractional=False, trim='k') # Round to 2 significant digits + return pct_harv_at_mature + + +def get_peakmonth(cases, this_var, y1=None, yN=None): + + # Input checks + if y1 is None or yN is None: + raise RuntimeError("Deal with missing y1 and yN") + elif "_PKMTH" not in this_var: + raise RuntimeError(f"Can only process this_var with _PKMTH (not {this_var})") + + for casename, case in cases.items(): + ds = case['ds'] + + # Which variable are we starting with? + v = this_var.replace("_PKMTH", "_MTH") + if v not in ds: + raise RuntimeError(f"{this_var} not in cases['{casename}']['ds']") + if "time_mth" not in ds[v].dims: + raise RuntimeError(f"Requested peak month of {v} but 'time_mth' not in dims {ds[v].dims}") + + # Get monthly means + mthmeans = ds[v].groupby(ds['time_mth'].dt.month).mean() + mthmeans.attrs = ds[v].attrs + if 'long_name' in ds[v].attrs: + mthmeans.attrs['long_name'] += " (monthly climatological mean)" + + # Set up peak month array + if "patch" in mthmeans.dims: + shapevar = 'patches1d_lon' + elif "gridcell" in mthmeans.dims: + shapevar = 'grid1d_lon' + else: + raise RuntimeError(f"Which shapevar for dims {mthmeans.dims}?") + pkmth = np.full(ds[shapevar].shape, np.nan) + + # Get peak month + thismax = mthmeans.max(dim="month") + if np.all(np.isnan(thismax)): + raise RuntimeError("thismax is all NaN") + for m in np.arange(1,13): + thismonth_is_max = np.where(np.isclose(mthmeans.sel(month=m), thismax))[0] + pkmth[thismonth_is_max] = m + if np.any((pkmth <= 0) & (~np.isnan(thismax))): + raise RuntimeError("Error filling pkmth") + + # Save as DataArray + ds[this_var] = xr.DataArray(data=pkmth, + coords=ds[shapevar].coords, + attrs={'units': 'peak month', + 'y1': y1, + 'yN': yN}) + + # Mask where always 0 + ds[this_var] = ds[this_var].where(ds[v].max(dim='time_mth') != 0) + + return cases + + +def get_reason_freq_map(Ngs, thisCrop_gridded, reason): + map_yx = np.sum(thisCrop_gridded==reason, axis=0, keepdims=False) / Ngs + notnan_yx = np.bitwise_not(np.isnan(thisCrop_gridded.isel(gs=0, drop=True))) + map_yx = map_yx.where(notnan_yx) + return map_yx + + +def get_reason_list_text(): + return [ \ + "???", # 0; should never actually be saved + "Crop mature", # 1 + "Max CLM season length", # 2 + "Bad Dec31 sowing", # 3 + "Sowing today", # 4 + "Sowing tomorrow", # 5 + "Sown a yr ago tmrw.", # 6 + "Sowing tmrw. (Jan 1)" # 7 + ] + + +def get_rx_case(cases, fig_caselist, ny, this_var): + if this_var == "GDDHARV": + rx_ds_key = "rx_gdds_ds" + elif this_var == "GSLEN": + rx_ds_key = "rx_gslen_ds" + elif this_var == "HDATES": + rx_ds_key = "rx_hdates_ds" + elif this_var == "SDATES": + rx_ds_key = "rx_sdates_ds" + else: + raise RuntimeError(f"What rx_ds_key should I use for {this_var}?") + if this_var in ["GSLEN", "HDATES", "SDATES"]: + rx_row_label = "GGCMI3" + elif this_var == "GDDHARV": + rx_row_label = "GGCMI3-derived" + else: + raise RuntimeError(f"What row label should be used instead of 'rx' for {this_var}?") + rx_parent_found = False + for i, (casename, case) in enumerate(cases.items()): + # For now, we're just assuming all runs with a given prescribed variable use the same input file + if rx_ds_key in case: + rx_parent_casename = casename + rx_ds = case[rx_ds_key] + fig_caselist += ["rx"] + ny += 1 + rx_parent_found = True + break + if not rx_parent_found: + raise RuntimeError(f"No case found with {rx_ds_key}") + + return rx_parent_casename, rx_ds, rx_row_label, ny + + +def get_timeseries_bias(sim, obs, weights=None): + + weights_provided = weights is not None + + # The 1st dimension of sim array is case and the 2nd is year. Additional dimensions (e.g., country) should be collapsed into the second. + if sim.ndim > 2: + raise RuntimeError("Need to collapse all dimensions of sim after the first into the second.") + if obs.ndim > 1: + raise RuntimeError("Need to collapse all dimensions of obs into the first.") + if weights_provided and weights.ndim > 1: + raise RuntimeError("Need to collapse all dimensions of weights into the first.") + + # Simulations should be Ncases x Npoints + add_dummy_0th_dim = sim.ndim < 2 + if add_dummy_0th_dim: + sim = np.expand_dims(sim, axis=0) + + # Weights and obs should be the same shape + if weights_provided and obs.shape != weights.shape: + raise RuntimeError("weights array must be the same shape as obs array") + + # Weights must not be negative + if weights_provided and np.any(weights < 0): + raise RuntimeError("Negative weights not allowed") + + if weights_provided: + weights = weights / np.sum(weights) # Ensure sum to 1 + bias = np.sum((sim - obs) * weights, axis=1) + else: + Npoints = sim.shape[1] + bias = 1/Npoints * np.sum(sim - obs, axis=1) + + if add_dummy_0th_dim: + bias = bias[0] + + return bias + + +# Get yield dataset for top N countries (plus World) +def get_topN_ds(cases, reses, plotYears, topYears, Ntop, thisCrop_fao, countries_key, fao_all_ctry, earthstats, min_viable_hui, mxmats): + + top_y1 = topYears[0] + top_yN = topYears[-1] + fao_mean_byCountry = get_mean_byCountry(fao_all_ctry, top_y1, top_yN) + topN = fao_mean_byCountry[thisCrop_fao]['Production'].nlargest(Ntop) + + topN_countries = topN.keys().values + topN_countries = np.concatenate((topN_countries, np.array(['World']))) + Ntop += 1 + + # Which countries are not found in our countries map? + for thisCountry in list(topN_countries): + if thisCountry not in countries_key.name.values and thisCountry != "World": + print(f'❗ {thisCountry} not in countries_key') + + # Set canonical EarthStats resolution + earthstats_res = 'f09_g17' + if earthstats_res not in earthstats: + raise RuntimeError(f"What EarthStat resolution should be used to get country timeseries, if not {earthstats_res}?") + countries_map = earthstats[earthstats_res]['countries'].load() + + plot_y1 = plotYears[0] + plot_yN = plotYears[-1] + NplotYears = len(plotYears) + + thisCrop_clm = cropnames_fao2clm(thisCrop_fao) + i_theseYears_earthstat = [i for i, x in enumerate(earthstats['f19_g17'].time.values) if (x.year >= plot_y1) and (x.year <= plot_yN)] + caselist = [k for k,v in cases.items()] + + prod_ar = np.full((len(cases), NplotYears, Ntop), np.nan) + area_ar = np.full((len(cases), NplotYears, Ntop), np.nan) + prod_faostat_yc = np.full((NplotYears, Ntop), np.nan) + area_faostat_yc = np.full((NplotYears, Ntop), np.nan) + prod_earthstat_yc = np.full((NplotYears, Ntop), np.nan) + area_earthstat_yc = np.full((NplotYears, Ntop), np.nan) + + for i_case, (casename, case) in enumerate(cases.items()): + case_ds = case['ds'] + lu_ds = reses[case['res']]['ds'] + countries = lu_ds['countries'].load() + + i_theseYears_case = [i for i, x in enumerate(case_ds.time.values) if (x.year >= plot_y1) and (x.year <= plot_yN)] + i_theseYears_lu = [i for i, x in enumerate(lu_ds.time.values) if (x.year >= plot_y1) and (x.year <= plot_yN)] + + # Find this crop in production and area data + i_thisCrop_case = [i for i, x in enumerate(case_ds.patches1d_itype_veg_str.values) if thisCrop_clm in x] + if len(i_thisCrop_case) == 0: + raise RuntimeError(f'No matches found for {thisCrop_fao} in case_ds.vegtype_str') + i_thisCrop_lu = [i for i, x in enumerate(lu_ds.patches1d_itype_veg.values) if thisCrop_clm in utils.ivt_int2str(x)] + if len(i_thisCrop_lu) == 0: + raise RuntimeError(f'No matches found for {thisCrop_fao} in lu_ds.patches1d_itype_veg') + + # Production... + case_ds = get_yield_ann(case_ds, min_viable_hui=min_viable_hui, mxmats=mxmats, lu_ds=lu_ds) + tmp_ds = case_ds.isel(patch=i_thisCrop_case, time=i_theseYears_case) + prod_da = tmp_ds['PROD_ANN']\ + .groupby(tmp_ds['patches1d_gi'])\ + .apply(xr.DataArray.sum, dim='patch', skipna=True)\ + .rename({'time': 'Year'})\ + * 1e-6 # g to tons + + # Area... + tmp_ds = lu_ds.isel(patch=i_thisCrop_lu, time=i_theseYears_lu) + area_da = tmp_ds['AREA_CFT']\ + .groupby(tmp_ds['patches1d_gi'])\ + .apply(xr.DataArray.sum, dim='patch', skipna=True)\ + .rename({'time': 'Year'})\ + * 1e-4 # m2 to ha + + # Countries + countries_da = countries.isel(patch=i_thisCrop_lu)\ + .groupby(tmp_ds['patches1d_gi'])\ + .apply(xr.DataArray.mean, dim='patch', skipna=True) + + # Get each top-N country's time series for this crop + for c, country in enumerate(topN_countries): + if country == "World": + country_id = None + prod_thisCountry_da = prod_da + area_thisCountry_da = area_da + else: + country_id = countries_key.query(f'name == "{country}"')['num'].values + if len(country_id) != 1: + if len(country_id) == 0: + continue + raise RuntimeError(f'Expected 0 or 1 match of {country} in countries_key; got {len(country_id)}') + prod_thisCountry_da = prod_da.where(countries_da == country_id) + area_thisCountry_da = area_da.where(countries_da == country_id) + + area_ar[i_case,:,c] = area_thisCountry_da.sum(dim='patches1d_gi').values + + # Production (tons) + prod_ar[i_case,:,c] = prod_thisCountry_da.sum(dim='patches1d_gi') + + # FAOSTAT production (tons) and area (ha) + if i_case == 0: + prod_faostat_yc[:,c] = get_faostat_country_ts(fao_all_ctry, thisCrop_fao, plot_y1, plot_yN, country, "Production") + area_faostat_yc[:,c] = get_faostat_country_ts(fao_all_ctry, thisCrop_fao, plot_y1, plot_yN, country, "Area harvested") + + # EarthStat + if np.all(np.isnan(prod_earthstat_yc[:,c])): + prod_earthstat_yc[:,c] = get_earthstat_country_ts(earthstats, earthstats_res, 'Production', countries_map, thisCrop_clm, i_theseYears_earthstat, country_id) + area_earthstat_yc[:,c] = get_earthstat_country_ts(earthstats, earthstats_res, 'HarvestArea', countries_map, thisCrop_clm, i_theseYears_earthstat, country_id) + if np.any((prod_earthstat_yc[:,c]>0) & (area_earthstat_yc[:,c]==0)): + raise RuntimeError(f"EarthStat has 0 area but positive production for {country}") + + if np.any(area_ar==0): + raise RuntimeError("0 in area_ar") + + new_coords = {'Case': caselist, + 'Year': plotYears, + 'Country': topN_countries} + prod_da = xr.DataArray(data = prod_ar, + coords = new_coords, + attrs = {'units': 'tons'}) + area_da = xr.DataArray(data = area_ar, + coords = new_coords, + attrs = {'units': 'ha'}) + yield_da = prod_da / area_da + yield_da = yield_da.assign_attrs({'units': 'tons/ha'}) + prod_faostat_da = xr.DataArray(data = prod_faostat_yc, + coords = {'Year': plotYears, + 'Country': topN_countries}, + attrs = {'units': 'tons'}) + area_faostat_da = xr.DataArray(data = area_faostat_yc, + coords = {'Year': plotYears, + 'Country': topN_countries}, + attrs = {'units': 'ha'}) + yield_faostat_da = prod_faostat_da / area_faostat_da + yield_faostat_da = yield_faostat_da.assign_attrs({'units': 'tons/ha'}) + prod_earthstat_da = xr.DataArray(data = prod_earthstat_yc, + coords = {'Year': plotYears, + 'Country': topN_countries},) + area_earthstat_da = xr.DataArray(data = area_earthstat_yc, + coords = {'Year': plotYears, + 'Country': topN_countries}) + if np.any((prod_earthstat_da.values>0) & (area_earthstat_da.values==0)): + raise RuntimeError("EarthStat has 0 area but positive production") + yield_earthstat_da = prod_earthstat_da / area_earthstat_da + if np.any(np.isinf(yield_earthstat_da)): + for c, country in enumerate(topN_countries): + if np.any(np.isinf(yield_earthstat_da[:,c])): + raise RuntimeError(f"EarthStat has Inf yield for {country}") + + topN_ds = xr.Dataset(data_vars = {'Production': prod_da, + 'Production (FAOSTAT)': prod_faostat_da, + 'Production (EarthStat)': prod_earthstat_da, + 'Area': area_da, + 'Area (FAOSTAT)': area_faostat_da, + 'Area (EarthStat)': area_earthstat_da, + 'Yield': yield_da, + 'Yield (FAOSTAT)': yield_faostat_da, + 'Yield (EarthStat)': yield_earthstat_da}) + + # Detrend and get yield anomalies + topN_dt_ds = xr.Dataset() + topN_ya_ds = xr.Dataset() + for i, v in enumerate(topN_ds): + # Could make this cleaner by being smart in detrend() + if "Case" in topN_ds[v].dims: + tmp_dt_cyC = topN_ds[v].copy().values + tmp_ya_cyC = topN_ds[v].copy().values + for C, country in enumerate(topN_countries): + tmp_dt_cy = tmp_dt_cyC[:,:,C] + tmp_dt_cy = detrend(tmp_dt_cy) + tmp_dt_cyC[:,:,C] = tmp_dt_cy + topN_dt_ds[v] = xr.DataArray(data = tmp_dt_cyC, + coords = topN_ds[v].coords, + attrs = topN_ds[v].attrs) + for C, country in enumerate(topN_countries): + tmp_ya_cy = tmp_ya_cyC[:,:,C] + tmp_ya_cy = yield_anomalies(tmp_ya_cy) + tmp_ya_cyC[:,:,C] = tmp_ya_cy + topN_ya_ds[v] = xr.DataArray(data = tmp_ya_cyC, + coords = topN_ds[v].coords, + attrs = topN_ds[v].attrs) + else: + tmp_dt_Cy = np.transpose(topN_ds[v].copy().values) + tmp_dt_Cy = detrend(tmp_dt_Cy) + topN_dt_ds[v] = xr.DataArray(data = np.transpose(tmp_dt_Cy), + coords = topN_ds[v].coords, + attrs = topN_ds[v].attrs) + tmp_ya_Cy = np.transpose(topN_ds[v].copy().values) + tmp_ya_Cy = yield_anomalies(tmp_ya_Cy) + topN_ya_ds[v] = xr.DataArray(data = np.transpose(tmp_ya_Cy), + coords = topN_ds[v].coords, + attrs = topN_ds[v].attrs) + + topN_ya_ds[v].attrs['units'] = 'anomalies (unitless)' + + return topN_ds, topN_dt_ds, topN_ya_ds + + +def get_gridspec(case): + case_res = case['res'] + for x in ["_ctsm5.2"]: + case_res = case_res.replace(x, "") + return case_res + + +def get_ts_prod_clm_yc_da(yield_gd, lu_ds, yearList, cropList_combined_clm): + + # Convert km2 to m2 + allCropArea = lu_ds.AREA*1e6 * lu_ds.LANDFRAC_PFT * lu_ds.PCT_CROP/100 + + # Combined rainfed+irrigated + + cftList_str_clm = [] # Will fill during loop below + cftList_int_clm = [] # Will fill during loop below + ts_prod_clm_yc = np.full((len(yield_gd.time), len(cropList_combined_clm)), 0.0) + for c, thisCrop in enumerate(cropList_combined_clm[:-1]): + # print(f"{thisCrop}") + for pft_str in yield_gd.ivt_str.values: + if thisCrop.lower() not in pft_str: + continue + pft_int = utils.ivt_str2int(pft_str) + cftList_str_clm.append(pft_str) + cftList_int_clm.append(pft_int) + # print(f"{pft_str}: {pft_int}") + map_yield_thisCrop_clm = yield_gd.sel(ivt_str=pft_str) + map_area_thisCrop_clm = allCropArea * lu_ds.PCT_CFT.sel(cft=pft_int)/100 + map_prod_thisCrop_clm = map_yield_thisCrop_clm * map_area_thisCrop_clm + map_prod_thisCrop_clm = map_prod_thisCrop_clm * 1e-12 + if map_prod_thisCrop_clm.shape != map_yield_thisCrop_clm.shape: + raise RuntimeError(f"Error getting production map {map_yield_thisCrop_clm.dims}: expected shape {map_yield_thisCrop_clm.shape} but got {map_prod_thisCrop_clm.shape}") + ts_prod_thisCrop_clm = map_prod_thisCrop_clm.sum(dim=["lon","lat"]) + ts_prod_clm_yc[:,c] += ts_prod_thisCrop_clm.values + # Total + ts_prod_clm_yc[:,-1] += ts_prod_thisCrop_clm.values + + ts_prod_clm_yc_da = xr.DataArray(ts_prod_clm_yc, + coords={"Year": yearList, + "Crop": cropList_combined_clm}) + return ts_prod_clm_yc_da + +def get_ts_prod_clm_yc_da2(case_ds, lu_ds, yieldVar, cropList_combined_clm, quiet=False): + + # Get time dimension names. + # To match time dimension on lu_ds, rename anything other than "time" to that. + non_patch_dims = [x for x in case_ds[yieldVar].dims if x != "patch"] + if len(non_patch_dims) != 1: + raise RuntimeError(f"Expected one non-patch dimension of case_ds['{yieldVar}']; found {len(non_patch_dims)}: {non_patch_dims}") + time_dim_in = non_patch_dims[0] + if time_dim_in == "time": + time_dim_out = "Year" + yearList = [x.year for x in case_ds[yieldVar].time.values] + elif time_dim_in == "gs": + time_dim_out = "Growing season" + yearList = case_ds[yieldVar].gs.values + else: + raise RuntimeError(f"Unknown time_dim_out for time_dim_in {time_dim_in}") + if time_dim_in != "time": + if not quiet: + print(f"WARNING: Using calendar years from LU data with yield data of time dimension {time_dim_in}.") + lu_ds = lu_ds.assign_coords({'time': case_ds[yieldVar].gs.values}).rename({'time': time_dim_in}) + + prod_da = case_ds[yieldVar] * lu_ds['AREA_CFT'] + + ts_prod_clm_yc_da = prod_da.groupby(case_ds['patches1d_itype_combinedCropCLM_str'])\ + .apply(xr.DataArray.sum, dim='patch', skipna=True)\ + .rename({time_dim_in: time_dim_out, + 'patches1d_itype_combinedCropCLM_str': 'Crop'})\ + .isel(Crop=slice(1,len(cropList_combined_clm)))\ + * 1e-12 + ts_prod_clm_ySUM = ts_prod_clm_yc_da.sum(dim="Crop")\ + .expand_dims(dim='Crop', + axis=list(ts_prod_clm_yc_da.dims).index('Crop')) + ts_prod_clm_yc_da = xr.concat((ts_prod_clm_yc_da, + ts_prod_clm_ySUM), + dim="Crop")\ + .assign_coords({'Crop': cropList_combined_clm, + time_dim_out: yearList}) + + return ts_prod_clm_yc_da + + +def get_vegtype_str_figfile(vegtype_str_in): + vegtype_str_out = vegtype_str_in + if "soybean" in vegtype_str_in and "tropical" not in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("soybean", "temperate_soybean") + for t in ["winter", "spring", "temperate", "tropical"]: + if t in vegtype_str_out: + vegtype_str_out = vegtype_str_out.replace(f"{t}_", "") + f"_{t}" + if "irrigated" in vegtype_str_out: + vegtype_str_out = vegtype_str_out.replace("irrigated_", "") + "_ir" + else: + vegtype_str_out = vegtype_str_out + "_rf" + return vegtype_str_out + + +# Get vegtype str for figure titles +def get_vegtype_str_for_title(vegtype_str_in): + vegtype_str_out = vegtype_str_in + if "irrigated" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("irrigated_", "") + " (ir)" + else: + vegtype_str_out = vegtype_str_out + " (rf)" + if "temperate" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("temperate_", "temp. ") + if "tropical" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("tropical_", "trop. ") + elif "soybean" in vegtype_str_in: + vegtype_str_out = "temp. " + vegtype_str_out + if "soybean" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("soybean", "soy") + if "spring" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("spring_", "spr. ") + if "winter" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("winter_", "win.") + return vegtype_str_out + + +# Get vegtype str for figure titles +def get_vegtype_str_for_title_long(vegtype_str_in): + vegtype_str_out = vegtype_str_in + if "irrigated" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("irrigated_", "Irrigated ") + else: + vegtype_str_out = "Rainfed " + vegtype_str_out + vegtype_str_out = vegtype_str_out.replace("_", " ") + if "soybean" in vegtype_str_in: + vegtype_str_out = vegtype_str_out.replace("soybean", "soy") + return vegtype_str_out + + +def get_vegtype_str_paramfile(vegtype_str_in): + # Get vegtype str used in parameter file + if vegtype_str_in == "soybean": + vegtype_str_out = "temperate_soybean" + elif vegtype_str_in == "irrigated_soybean": + vegtype_str_out = "irrigated_temperate_soybean" + else: + vegtype_str_out = vegtype_str_in + return vegtype_str_out + + +def get_window_radius(w): + if not w % 2: + raise RuntimeError("Window width must be odd") + return int((w-1) / 2) + + +def get_yield(ds, **kwargs): + + # Fail if trying to get anything other than yield + for key, selection in kwargs.items(): + if key=="out_var" and selection!="YIELD": + raise RuntimeError("get_yield() may only be called with out_var='YIELD'. Did you mean to call zero_immatures() instead?") + + ds = zero_immatures(ds, out_var="YIELD", **kwargs) + return ds + + +def get_yield_ann(ds, min_viable_hui=1.0, mxmats=None, force_update=False, lu_ds=None): + + mxmat_limited = bool(mxmats) + + def do_calculate(thisVar, ds, force_update, min_viable_hui, mxmat_limited): + consider_skipping = (f'{thisVar}_ANN' in ds) and (not force_update) + if consider_skipping: + already_calculated = ds[f'{thisVar}_ANN'].attrs['min_viable_hui'] == min_viable_hui and ds[f'{thisVar}_ANN'].attrs['mxmat_limited'] == mxmat_limited + is_locked = 'locked' in ds[f'{thisVar}_ANN'].attrs and ds[f'{thisVar}_ANN'].attrs['locked'] + do_calculate = not consider_skipping or not (already_calculated or is_locked) + else: + do_calculate = True + return do_calculate + + ######### + # YIELD # + ######### + + if do_calculate("YIELD", ds, force_update, min_viable_hui, mxmat_limited): + + ds = get_yield(ds, min_viable_hui=min_viable_hui, mxmats=mxmats, forAnnual=True, force_update=force_update) + + tmp = ds["YIELD_PERHARV"].sum(dim='mxharvests', skipna=True).values + grainc_to_food_ann_orig = ds["GRAINC_TO_FOOD_ANN"] + ds["YIELD_ANN"] = xr.DataArray(data = tmp, + attrs = grainc_to_food_ann_orig.attrs, + coords = grainc_to_food_ann_orig.coords + ).where(~np.isnan(grainc_to_food_ann_orig)) + ds['YIELD_ANN'].attrs['units'] = ds['YIELD_PERHARV'].attrs['units'] + + # Save details + ds["YIELD_ANN"].attrs['min_viable_hui'] = min_viable_hui + ds["YIELD_ANN"].attrs['mxmat_limited'] = mxmat_limited + if 'locked' in ds['YIELD_PERHARV'].attrs: + ds["YIELD_ANN"].attrs['locked'] = True + + ############## + # PRODUCTION # + ############## + + if lu_ds is not None and do_calculate("PROD", ds, force_update, min_viable_hui, mxmat_limited): + if lu_ds['AREA_CFT'].attrs['units'] != "m2": + raise RuntimeError(f"Unknown units of lu_ds['AREA_CFT']: {lu_ds['AREA_CFT'].attrs['units']}") + if ds['YIELD_ANN'].attrs['units'] != "g/m2": + raise RuntimeError(f"Unknown units of ds['YIELD_ANN']: {ds['YIELD_ANN'].attrs['units']}") + ds['PROD_ANN'] = ds['YIELD_ANN'] * lu_ds['AREA_CFT'] + ds['PROD_ANN'].attrs['units'] = "g" + ds['AREA_CFT'] = lu_ds['AREA_CFT'] + ds['AREA_CFT'].attrs['units'] = lu_ds['AREA_CFT'].attrs['units'] + + # Save details + ds["PROD_ANN"].attrs['min_viable_hui'] = min_viable_hui + ds["PROD_ANN"].attrs['mxmat_limited'] = mxmat_limited + if 'locked' in ds['YIELD_PERHARV'].attrs: + ds["PROD_ANN"].attrs['locked'] = True + + return ds + + +def import_max_gs_length(paramfile_dir, my_clm_ver, my_clm_subver): + # Get parameter file + pattern = os.path.join(paramfile_dir, f"*{my_clm_ver}_params.{my_clm_subver}.nc") + paramfile = glob.glob(pattern) + if len(paramfile) != 1: + raise RuntimeError(f"Expected to find 1 match of {pattern}; found {len(paramfile)}") + paramfile_ds = xr.open_dataset(paramfile[0]) + + # Import max growing season length (stored in netCDF as nanoseconds!) + paramfile_mxmats = paramfile_ds["mxmat"].values / np.timedelta64(1, 'D') + + # Import PFT name list + paramfile_pftnames = [x.decode("UTF-8").replace(" ", "") for x in paramfile_ds["pftname"].values] + + # Build dict + mxmat_dict = {} + for i, pftname in enumerate(paramfile_pftnames): + mxmat = paramfile_mxmats[i] + if not np.isnan(mxmat): + mxmat_dict[pftname] = int(mxmat) + else: + mxmat_dict[pftname] = np.inf + + return mxmat_dict + +# E.g. import_rx_dates("sdate", sdates_rx_file, dates_ds0_orig) +def import_rx_dates(var_prefix, date_inFile, dates_ds, set_neg1_to_nan=True): + # Get run info: + # Max number of growing seasons per year + if "mxsowings" in dates_ds: + mxsowings = dates_ds.dims["mxsowings"] + else: + mxsowings = 1 + + # Which vegetation types were simulated? + itype_veg_toImport = np.unique(dates_ds.patches1d_itype_veg) + + date_varList = [] + for i in itype_veg_toImport: + for g in np.arange(mxsowings): + thisVar = f"{var_prefix}{g+1}_{i}" + date_varList = date_varList + [thisVar] + + ds = utils.import_ds(date_inFile, myVars=date_varList) + + did_warn = False + for v in ds: + v_new = v.replace(var_prefix,"gs") + ds = ds.rename({v: v_new}) + + # Set -1 prescribed GDD values to NaN. Only warn the first time. + if set_neg1_to_nan and var_prefix == "gdd" and v_new != v and np.any(ds[v_new].values < 0): + if np.any((ds[v_new].values < 0) & (ds[v_new].values != -1)): + raise RuntimeError(f"Unexpected negative value in {v}") + if not did_warn: + print(f"Setting -1 rx GDD values to NaN") + did_warn = True + ds[v_new] = ds[v_new].where(ds[v_new] != -1) + + return ds + + +def import_output(filename, myVars, y1=None, yN=None, myVegtypes=utils.define_mgdcrop_list(), + sdates_rx_ds=None, gdds_rx_ds=None, verbose=False, incl_irrig=True): + # Import + this_ds = utils.import_ds(filename, + myVars=myVars, + myVegtypes=myVegtypes) + + # Trim to years of interest (do not include extra year needed for finishing last growing season) + if y1 and yN: + this_ds = check_and_trim_years(y1, yN, this_ds) + else: # Assume including all growing seasons except last complete one are "of interest" + y1 = this_ds.time.values[0].year + yN = this_ds.time.values[-1].year - 2 + this_ds = check_and_trim_years(y1, yN, this_ds) + + # What vegetation types are included? + vegtype_list = [x for x in this_ds.vegtype_str.values if x in this_ds.patches1d_itype_veg_str.values] + + # Check for consistency among sowing/harvest date/year info + date_vars = ["SDATES_PERHARV", "SYEARS_PERHARV", "HDATES", "HYEARS"] + all_nan = np.full(this_ds[date_vars[0]].shape, True) + all_nonpos = np.full(this_ds[date_vars[0]].shape, True) + all_pos = np.full(this_ds[date_vars[0]].shape, True) + for v in date_vars: + all_nan = all_nan & np.isnan(this_ds[v].values) + all_nonpos = all_nonpos & (this_ds[v].values <= 0) + all_pos = all_pos & (this_ds[v].values > 0) + if np.any(np.bitwise_not(all_nan | all_nonpos | all_pos)): + raise RuntimeError("Inconsistent missing/present values on mxharvests axis") + + # When doing transient runs, it's somehow possible for crops in newly-active patches to be *already alive*. They even have a sowing date (idop)! This will of course not show up in SDATES, but it does show up in SDATES_PERHARV. + # I could put the SDATES_PERHARV dates into where they "should" be, but instead I'm just going to invalidate those "seasons." + # + # In all but the last calendar year, which patches had no sowing? + no_sowing_yp = np.all(np.isnan(this_ds.SDATES.values[:-1,:,:]), axis=1) + # In all but the first calendar year, which harvests' jdays are < their sowings' jdays? (Indicates sowing the previous calendar year.) + hsdate1_gt_hdate1_yp = this_ds.SDATES_PERHARV.values[1:,0,:] > this_ds.HDATES.values[1:,0,:] + # Where both, we have the problem. + falsely_alive_yp = no_sowing_yp & hsdate1_gt_hdate1_yp + if np.any(falsely_alive_yp): + print(f"Warning: {np.sum(falsely_alive_yp)} patch-seasons being ignored: Seemingly sown the year before harvest, but no sowings occurred that year.") + falsely_alive_yp = np.concatenate((np.full((1, this_ds.dims["patch"]), False), + falsely_alive_yp), + axis=0) + falsely_alive_y1p = np.expand_dims(falsely_alive_yp, axis=1) + dummy_false_y1p = np.expand_dims(np.full_like(falsely_alive_yp, False), axis=1) + falsely_alive_yhp = np.concatenate((falsely_alive_y1p, dummy_false_y1p), axis=1) + for v in this_ds.data_vars: + if this_ds[v].dims != ("time", "mxharvests", "patch"): + continue + this_ds[v] = this_ds[v].where(~falsely_alive_yhp) + + def check_no_negative(this_ds_in, varList_no_negative, which_file, verbose=False): + tiny_negOK = 1e-12 + this_ds = this_ds_in.copy() + for v in this_ds: + if not any(x in v for x in varList_no_negative): + continue + the_min = np.nanmin(this_ds[v].values) + if the_min < 0: + if np.abs(the_min) <= tiny_negOK: + if verbose: print(f"Tiny negative value(s) in {v} (abs <= {tiny_negOK}) being set to 0 ({which_file})") + else: + print(f"WARNING: Unexpected negative value(s) in {v}; minimum {the_min} ({which_file})") + values = this_ds[v].copy().values + values[np.where((values < 0) & (values >= -tiny_negOK))] = 0 + this_ds[v] = xr.DataArray(values, + coords = this_ds[v].coords, + dims = this_ds[v].dims, + attrs = this_ds[v].attrs) + + elif verbose: + print(f"No negative value(s) in {v}; min {the_min} ({which_file})") + return this_ds + + def check_no_zeros(this_ds, varList_no_zero, which_file): + for v in this_ds: + if not any(x in v for x in varList_no_zero): + continue + if np.any(this_ds[v].values == 0): + print(f"WARNING: Unexpected zero(s) in {v} ({which_file})") + elif verbose: + print(f"No zero value(s) in {v} ({which_file})") + + # Check for no zero values where there shouldn't be + varList_no_zero = ["DATE", "YEAR"] + check_no_zeros(this_ds, varList_no_zero, "original file") + + # Convert time*mxharvests axes to growingseason axis + this_ds_gs = convert_axis_time2gs(this_ds, verbose=verbose, incl_orig=False) + + # These are needed for calculating yield later + this_ds_gs['GRAINC_TO_FOOD_PERHARV'] = this_ds['GRAINC_TO_FOOD_PERHARV'] + this_ds_gs['GDDHARV_PERHARV'] = this_ds['GDDHARV_PERHARV'] + + # Get growing season length + this_ds["GSLEN_PERHARV"] = get_gs_len_da(this_ds["HDATES"] - this_ds["SDATES_PERHARV"]) + this_ds_gs["GSLEN"] = get_gs_len_da(this_ds_gs["HDATES"] - this_ds_gs["SDATES"]) + this_ds_gs["GSLEN_PERHARV"] = this_ds["GSLEN_PERHARV"] + + # Get HUI accumulation as fraction of required + this_ds_gs["HUIFRAC"] = this_ds_gs["HUI"] / this_ds_gs["GDDHARV"] + this_ds_gs["HUIFRAC_PERHARV"] = this_ds["HUI_PERHARV"] / this_ds["GDDHARV_PERHARV"] + for v in ['HUIFRAC', 'HUIFRAC_PERHARV']: + this_ds_gs[v].attrs['units'] = "Fraction of required" + + # Avoid tiny negative values + varList_no_negative = ["GRAIN", "REASON", "GDD", "HUI", "YEAR", "DATE", "GSLEN"] + this_ds_gs = check_no_negative(this_ds_gs, varList_no_negative, "new file", verbose=verbose) + + # Check for no zero values where there shouldn't be + varList_no_zero = ["REASON", "DATE"] + check_no_zeros(this_ds_gs, varList_no_zero, "new file") + + # Check that e.g., GDDACCUM <= HUI + for vars in [["GDDACCUM", "HUI"], + ["SYEARS", "HYEARS"]]: + if all(v in this_ds_gs for v in vars): + check_v0_le_v1(this_ds_gs, vars, both_nan_ok=True, throw_error=True) + + # Check that prescribed calendars were obeyed + if sdates_rx_ds: + check_rx_obeyed(vegtype_list, sdates_rx_ds, this_ds, "this_ds", "SDATES") + if gdds_rx_ds: + check_rx_obeyed(vegtype_list, gdds_rx_ds, this_ds, "this_ds", "SDATES", "GDDHARV", gdd_min=default_gdd_min()) + + # Convert time axis to integer year, saving original as 'cftime' + this_ds_gs = this_ds_gs.assign_coords({'cftime': this_ds['time_bounds'].isel({'hist_interval': 0})}) + this_ds_gs = this_ds_gs.assign_coords({"time": [t.year for t in this_ds_gs['cftime'].values]}) + + # Get number of harvests + this_ds_gs['NHARVESTS'] = (this_ds_gs['GDDHARV_PERHARV'] > 0).sum(dim="mxharvests") + # Get number of harvests that would be missed if only seeing max 1 per calendar year + if np.any(this_ds_gs['NHARVESTS'] > 2): + raise RuntimeError("How to get NHARVEST_DISCREP for NHARVESTS > 2?") + this_ds_gs['NHARVEST_DISCREP'] = (this_ds_gs['NHARVESTS'] == 2).astype(int) + + # Import irrigation data, if doing so + if incl_irrig: + + # Monthly use and demand + pattern = os.path.join(os.path.dirname(filename), "*.h2.*.nc") + irrig_file_patches = glob.glob(pattern) + if irrig_file_patches: + if len(irrig_file_patches) > 1: + raise RuntimeError(f"Expected at most 1 *.h2.*.nc; found {len(irrig_file_patches)}") + irrig_file_patches = irrig_file_patches[0] + irrig_ds_patches = utils.import_ds(irrig_file_patches, myVegtypes=myVegtypes, chunks={'time': 12}, + myVars = ['QIRRIG_DEMAND', 'QIRRIG_DRIP', 'QIRRIG_SPRINKLER']) + irrig_ds_patches = time_units_and_trim_mth(irrig_ds_patches, y1, yN) + + # Combine drip + sprinkler irrigation + irrig_ds_patches["QIRRIG_APPLIED"] = irrig_ds_patches["QIRRIG_DRIP"]+ irrig_ds_patches["QIRRIG_SPRINKLER"] + irrig_ds_patches['QIRRIG_APPLIED'].attrs = irrig_ds_patches['QIRRIG_DEMAND'].attrs + irrig_ds_patches["QIRRIG_APPLIED"].attrs['long_name'] = 'water added via drip or sprinkler irrigation' + + # Calculate unfulfilled demand + irrig_ds_patches["QIRRIG_UNFULFILLED"] = irrig_ds_patches['QIRRIG_DEMAND'] - irrig_ds_patches['QIRRIG_APPLIED'] + irrig_ds_patches['QIRRIG_UNFULFILLED'].attrs = irrig_ds_patches['QIRRIG_DEMAND'].attrs + irrig_ds_patches['QIRRIG_UNFULFILLED'].attrs['long_name'] = 'irrigation demand unable to be filled' + + vars_to_save = ["QIRRIG_DEMAND", "QIRRIG_APPLIED", "QIRRIG_UNFULFILLED"] + + # Append _PATCH to distinguish from eventual gridcell sums (_GRID) + rename_dict = {} + for v in vars_to_save: + rename_dict[v] = v + "_PATCH" + irrig_ds_patches = irrig_ds_patches.rename(rename_dict) + vars_to_save = [v + "_PATCH" for v in vars_to_save] + + # Finish processing + this_ds_gs = process_monthly_irrig(this_ds_gs, irrig_ds_patches, vars_to_save) + + # Monthly withdrawals and availability + pattern = os.path.join(os.path.dirname(filename), "*.h3.*.nc") + irrig_file_grid = glob.glob(pattern) + if irrig_file_grid: + if len(irrig_file_grid) > 1: + raise RuntimeError(f"Expected at most 1 *.h3.*.nc; found {len(irrig_file_grid)}") + irrig_file_grid = irrig_file_grid[0] + irrig_ds_grid = utils.import_ds(irrig_file_grid, chunks={'time': 12}, + myVars = ['area', 'grid1d_ixy', 'grid1d_jxy', 'grid1d_lon', 'grid1d_lat', 'QIRRIG_FROM_GW_CONFINED', 'QIRRIG_FROM_GW_UNCONFINED', 'QIRRIG_FROM_SURFACE', 'VOLRMCH']) + irrig_ds_grid = time_units_and_trim_mth(irrig_ds_grid, y1, yN) + + # Ensure that no groundwater was used + if np.any(irrig_ds_grid['QIRRIG_FROM_GW_CONFINED'] + irrig_ds_grid['QIRRIG_FROM_GW_UNCONFINED'] > 0): + raise RuntimeError("Unexpectedly found some irrigation using groundwater") + + # Rename this variable so that it has a QIRRIG prefix + irrig_ds_grid = irrig_ds_grid.rename({"VOLRMCH": "IRRIG_SUPPLY"}) + irrig_ds_grid["IRRIG_SUPPLY"].attrs['long_name'] = irrig_ds_grid["IRRIG_SUPPLY"].attrs['long_name'] + " (aka VOLRMCH)" + + vars_to_save = ['QIRRIG_FROM_SURFACE', 'IRRIG_SUPPLY'] + + # Append _GRID to distinguish from patch-level irrigation data + rename_dict = {} + for v in vars_to_save: + rename_dict[v] = v + "_GRID" + irrig_ds_grid = irrig_ds_grid.rename(rename_dict) + vars_to_save = [v + "_GRID" for v in vars_to_save] + + # Finish processing + this_ds_gs = process_monthly_irrig(this_ds_gs, irrig_ds_grid, vars_to_save) + + # Calculate irrigation as fraction of main river channel volume + # (Do it here instead of process_monthly_irrig() because monthly doesn't add to annual.) + for t in ['MTH', 'ANN']: + this_ds_gs[f'QIRRIG_FROM_SURFACE_FRAC_RIVER_GRID_{t}'] = this_ds_gs[f'QIRRIG_FROM_SURFACE_GRID_{t}'] / this_ds_gs[f'IRRIG_SUPPLY_GRID_{t}'] + this_ds_gs[f'QIRRIG_FROM_SURFACE_FRAC_RIVER_GRID_{t}'] = this_ds_gs[f'QIRRIG_FROM_SURFACE_FRAC_RIVER_GRID_{t}'].assign_coords(this_ds_gs[f'QIRRIG_FROM_SURFACE_GRID_{t}'].coords) + + # Ensure gridcells are same-ordered between patch- and gridcell-level datasets + this_ds_gs = this_ds_gs.assign_coords({'gridcell': this_ds_gs['gridcell'] + 1}) + irrig_ds_grid = irrig_ds_grid.assign_coords({'gridcell': irrig_ds_grid['gridcell'] + 1}) + test_gi = int(this_ds_gs['gridcell'].shape[0] / 3) # An arbitrary gridcell to test + test_g = irrig_ds_grid['gridcell'].values[test_gi] + test_pi = np.where(this_ds_gs['patches1d_gi'] == test_g)[0][0] + test_p_lon = this_ds_gs['patches1d_lon'].isel(patch=test_pi) + test_p_lat = this_ds_gs['patches1d_lat'].isel(patch=test_pi) + test_g_lon = irrig_ds_grid['grid1d_lon'].isel(gridcell=test_gi) + test_g_lat = irrig_ds_grid['grid1d_lat'].isel(gridcell=test_gi) + if test_p_lon != test_g_lon or test_p_lat != test_g_lat: + print(f"{test_p_lon} =? {test_g_lon}") + print(f"{test_p_lat} =? {test_g_lat}") + raise RuntimeError("Gridcell indexing mismatch") + + # Save gridcell info + for v in irrig_ds_grid: + if "grid" in v: + this_ds_gs[v] = irrig_ds_grid[v] + + # Save gridcell area + this_ds_gs['AREA_GRID'] = ungrid(irrig_ds_grid['area'], irrig_ds_grid, target_dim="gridcell", lon="grid1d_ixy", lat="grid1d_jxy") + if this_ds_gs['AREA_GRID'].attrs['units'] != "m^2": + if this_ds_gs['AREA_GRID'].attrs['units'] == "km^2": + to_m2 = 1e6 + else: + raise RuntimeError(f"Unsure how to convert {this_ds_gs['AREA_GRID'].attrs['units']} to m^2") + this_ds_gs['AREA_GRID'] *= to_m2 + this_ds_gs['AREA_GRID'].attrs['units'] = "m^2" + + return this_ds_gs + + +def make_axis(fig, ny, nx, n): + ax = fig.add_subplot(ny,nx,n,projection=ccrs.PlateCarree()) + ax.spines['geo'].set_visible(False) # Turn off box outline + return ax + + +def mask_immature(this_ds, this_vegtype, gridded_da): + if "HARVEST_REASON_PERHARV" in this_ds: + thisVar = "HARVEST_REASON_PERHARV" + elif "HARVEST_REASON" in this_ds: + thisVar = "HARVEST_REASON" + else: + raise RuntimeError('Neither HARVEST_REASON nor HARVEST_REASON_PERHARV found in this_ds.') + reason_gridded = utils.grid_one_variable(this_ds, thisVar, vegtype=this_vegtype).squeeze(drop=True) + gridded_da = gridded_da.where(reason_gridded == 1) + return gridded_da + + +def open_lu_ds(filename, y1, yN, existing_ds, ungrid=True): + # Open and trim to years of interest + dsg = xr.open_dataset(filename).sel(time=slice(y1,yN)) + + # Assign actual lon/lat coordinates + dsg = dsg.assign_coords(lon=("lsmlon", existing_ds.lon.values), + lat=("lsmlat", existing_ds.lat.values)) + dsg = dsg.swap_dims({"lsmlon": "lon", + "lsmlat": "lat"}) + + if "AREA" in dsg: + dsg['AREA_CFT'] = dsg.AREA*1e6 * dsg.LANDFRAC_PFT * dsg.PCT_CROP/100 * dsg.PCT_CFT/100 + dsg['AREA_CFT'].attrs = {'units': 'm2'} + dsg['AREA_CFT'].load() + else: + print("Warning: AREA missing from Dataset, so AREA_CFT will not be created") + + if not ungrid: + return dsg + + # Un-grid + query_ilons = [int(x)-1 for x in existing_ds['patches1d_ixy'].values] + query_ilats = [int(x)-1 for x in existing_ds['patches1d_jxy'].values] + query_ivts = [list(dsg.cft.values).index(x) for x in existing_ds['patches1d_itype_veg'].values] + + ds = xr.Dataset(attrs=dsg.attrs) + for v in ["AREA", "LANDFRAC_PFT", "PCT_CFT", "PCT_CROP", "AREA_CFT"]: + if v not in dsg: + continue + if 'time' in dsg[v].dims: + new_coords = existing_ds['GRAINC_TO_FOOD_ANN'].coords + else: + new_coords = existing_ds['patches1d_lon'].coords + if 'cft' in dsg[v].dims: + ds[v] = dsg[v].isel(lon=xr.DataArray(query_ilons, dims='patch'), + lat=xr.DataArray(query_ilats, dims='patch'), + cft=xr.DataArray(query_ivts, dims='patch'), + drop=True)\ + .assign_coords(new_coords) + else: + ds[v] = dsg[v].isel(lon=xr.DataArray(query_ilons, dims='patch'), + lat=xr.DataArray(query_ilats, dims='patch'), + drop=True)\ + .assign_coords(new_coords) + for v in existing_ds: + if "patches1d_" in v or "grid1d_" in v: + ds[v] = existing_ds[v] + ds['lon'] = dsg['lon'] + ds['lat'] = dsg['lat'] + + # Which crops are irrigated? + is_irrigated = np.full_like(ds['patches1d_itype_veg'], False) + for vegtype_str in np.unique(ds['patches1d_itype_veg_str'].values): + if "irrigated" not in vegtype_str: + continue + vegtype_int = utils.ivt_str2int(vegtype_str) + is_this_vegtype = np.where(ds['patches1d_itype_veg'].values == vegtype_int)[0] + is_irrigated[is_this_vegtype] = True + ["irrigated" in x for x in ds['patches1d_itype_veg_str'].values] + ds['IRRIGATED'] = xr.DataArray(data=is_irrigated, + coords=ds['patches1d_itype_veg_str'].coords, + attrs={'long_name': 'Is patch irrigated?'}) + + # How much area is irrigated? + ds['IRRIGATED_AREA_CFT'] = ds['IRRIGATED'] * ds['AREA_CFT'] + ds['IRRIGATED_AREA_CFT'].attrs = {'long name': 'CFT area (irrigated types only)', + 'units': 'm^2'} + ds['IRRIGATED_AREA_GRID'] = (ds['IRRIGATED_AREA_CFT'] + .groupby(ds['patches1d_gi']) + .sum() + .rename({'patches1d_gi': 'gridcell'})) + ds['IRRIGATED_AREA_GRID'].attrs = {'long name': 'Irrigated area in gridcell', + 'units': 'm^2'} + + return ds + + +def print_gs_table(ds): + if "patch" in ds.dims: + raise RuntimeError('Input Dataset must have no patch dimension') + data = {} + for v in ['gs', 'SDATES', 'GDDHARV', 'HDATES', 'HARVEST_REASON']: + if ds[v].dims != ("gs",): + raise RuntimeError(f'{v} dims must be (\'gs\'), not {ds[v].dims}') + data[v] = ds[v].values + print(f'Lon {ds.patches1d_lon.values} lat {ds.patches1d_lat.values}, {ds.patches1d_itype_veg_str.values}') + maxrows = pd.get_option('display.max_rows') + pd.set_option('display.max_rows', None) + print(pd.DataFrame(data = data)) + pd.set_option('display.max_rows', maxrows) + + +def print_onepatch_wrongNgs(p, this_ds_orig, sdates_ymp, hdates_ymp, sdates_pym, hdates_pym, sdates_pym2, hdates_pym2, sdates_pym3, hdates_pym3, sdates_pg, hdates_pg, sdates_pg2, hdates_pg2): + try: + import pandas as pd + except: + print("Couldn't import pandas, so not displaying example bad patch ORIGINAL.") + + print(f"patch {p}: {this_ds_orig.patches1d_itype_veg_str.values[p]}, lon {this_ds_orig.patches1d_lon.values[p]} lat {this_ds_orig.patches1d_lat.values[p]}") + + print("Original SDATES (per sowing):") + print(this_ds_orig.SDATES.values[:,:,p]) + + print("Original HDATES (per harvest):") + print(this_ds_orig.HDATES.values[:,:,p]) + + if "pandas" in sys.modules: + def print_pandas_ymp(msg, cols, arrs_tuple): + print(f"{msg} ({np.sum(~np.isnan(arrs_tuple[0]))})") + mxharvests = arrs_tuple[0].shape[1] + arrs_list2 = [] + cols2 = [] + for h in np.arange(mxharvests): + for i,a in enumerate(arrs_tuple): + arrs_list2.append(a[:,h]) + cols2.append(cols[i] + str(h)) + arrs_tuple2 = tuple(arrs_list2) + df = pd.DataFrame(np.stack(arrs_tuple2, axis=1)) + df.columns = cols2 + print(df) + + print_pandas_ymp("Original", ["sdate", "hdate"], + (this_ds_orig.SDATES_PERHARV.values[:,:,p], + this_ds_orig.HDATES.values[:,:,p] + )) + + print_pandas_ymp("Masked", ["sdate", "hdate"], + (sdates_ymp[:,:,p], + hdates_ymp[:,:,p])) + + print_pandas_ymp('After "Ignore harvests from before this output began"', ["sdate", "hdate"], + (np.transpose(sdates_pym, (1,2,0))[:,:,p], + np.transpose(hdates_pym, (1,2,0))[:,:,p])) + + print_pandas_ymp('After "In years with no sowing, pretend the first no-harvest is meaningful"', ["sdate", "hdate"], + (np.transpose(sdates_pym2, (1,2,0))[:,:,p] , + np.transpose(hdates_pym2, (1,2,0))[:,:,p])) + + print_pandas_ymp('After "In years with sowing that are followed by inactive years, check whether the last sowing was harvested before the patch was deactivated. If not, pretend the LAST no-harvest is meaningful."', ["sdate", "hdate"], + (np.transpose(sdates_pym3, (1,2,0))[:,:,p] , + np.transpose(hdates_pym3, (1,2,0))[:,:,p])) + + def print_pandas_pg(msg, cols, arrs_tuple): + print(f"{msg} ({np.sum(~np.isnan(arrs_tuple[0]))})") + arrs_list = list(arrs_tuple) + for i,a in enumerate(arrs_tuple): + arrs_list[i] = np.reshape(a, (-1)) + arrs_tuple2 = tuple(arrs_list) + df = pd.DataFrame(np.stack(arrs_tuple2, axis=1)) + df.columns = cols + print(df) + + print_pandas_pg("Same, but converted to gs axis", ["sdate", "hdate"], + (sdates_pg[p,:], + hdates_pg[p,:])) + + print_pandas_pg('After "Ignore any harvests that were planted in the final year, because some cells will have incomplete growing seasons for the final year"', ["sdate", "hdate"], + (sdates_pg2[p,:], + hdates_pg2[p,:])) + else: + + def print_nopandas(a1, a2, msg): + print(msg) + if a1.ndim==1: + # I don't know why these aren't side-by-side! + print(np.stack((a1, a2), axis=1)) + else: + print(np.concatenate((a1, a2), axis=1)) + + print_nopandas(sdates_ymp[:,:,p], hdates_ymp[:,:,p], "Masked:") + + print_nopandas(np.transpose(sdates_pym, (1,2,0))[:,:,p], np.transpose(hdates_pym, (1,2,0))[:,:,p], 'After "Ignore harvests from before this output began"') + + print_nopandas(np.transpose(sdates_pym2, (1,2,0))[:,:,p], np.transpose(hdates_pym2, (1,2,0))[:,:,p], 'After "In years with no sowing, pretend the first no-harvest is meaningful"') + + print_nopandas(np.transpose(sdates_pym3, (1,2,0))[:,:,p], np.transpose(hdates_pym3, (1,2,0))[:,:,p], 'After "In years with sowing that are followed by inactive years, check whether the last sowing was harvested before the patch was deactivated. If not, pretend the LAST [easier to implement!] no-harvest is meaningful."') + + print_nopandas(sdates_pg[p,:], hdates_pg[p,:], "Same, but converted to gs axis") + + print_nopandas(sdates_pg2[p,:], hdates_pg2[p,:], 'After "Ignore any harvests that were planted in the final year, because some cells will have incomplete growing seasons for the final year"') + + print("\n\n") + + +def process_monthly_irrig(ds, irrig_ds, varList): + if not isinstance(varList, list): + varList = [varList] + + # Rename and copy to main ds + time_mth_dimname = "time_mth" + for v in varList: + ds[f"{v}_MTH"] = irrig_ds[v].rename({'time': time_mth_dimname}) + varList = [v + "_MTH" for v in varList] + + # Calculate yearly means + for v in varList: + v2 = v.replace('MTH', 'ANN') + v2_da = utils.weighted_annual_mean(ds[v], time_in='time_mth') + ds[v2] = v2_da.assign_coords({'time': ds.time}) + if np.any(~np.isnan(ds[v].values)) and not np.any(~np.isnan(ds[v2].values)): + raise RuntimeError(f"Annual mean for {v} turned into all NaN") + ds[v2].attrs = ds[v].attrs + + return ds + + +def remove_outliers(gridded_da): + gs_axis = gridded_da.dims.index("gs") + pctle25 = np.nanpercentile(gridded_da, q=25, axis=gs_axis) + pctle75 = np.nanpercentile(gridded_da, q=75, axis=gs_axis) + iqr = pctle75 - pctle25 + outlier_thresh_lo = pctle25 - 1.5*iqr + outlier_thresh_up = pctle75 + 1.5*iqr + not_outlier = np.bitwise_and(gridded_da > outlier_thresh_lo, gridded_da < outlier_thresh_up) + gridded_da = gridded_da.where(not_outlier) + return gridded_da + + +def round_lonlats_to_match_da(ds_a, varname_a, tolerance, ds_b=None, varname_b=None): + if (ds_b and varname_b) or (not ds_b and not varname_b): + raise RuntimeError(f"You must provide one of ds_b or varname_b") + elif ds_b: + da_a = ds_a[varname_a] + da_b = ds_b[varname_a] + elif varname_b: + da_a = ds_a[varname_a] + da_b = ds_a[varname_b] + + unique_vals_a = np.unique(da_a) + unique_vals_b = np.unique(da_b) + + # Depends on unique values being sorted ascending, which they should be from np.unique(). + # If calling with one of these being unique values from a coordinate axis, having that be unique_vals_b should avoid large differences due to some coordinate values not being represented in data. + def get_diffs(unique_vals_a, unique_vals_b): + max_diff = 0 + y0 = 0 + diffs = [] + for x in unique_vals_a: + min_diff_fromx = np.inf + for i,y in enumerate(unique_vals_b[y0:]): + y_minus_x = y-x + min_diff_fromx = min(min_diff_fromx, np.abs(y_minus_x)) + if y_minus_x >= 0: + break + max_diff = max(max_diff, min_diff_fromx) + if min_diff_fromx > 0: + diffs.append(min_diff_fromx) + return max_diff, diffs + + max_diff, diffs = get_diffs(unique_vals_a, unique_vals_b) + + if max_diff > tolerance: + new_tolerance = np.ceil(np.log10(max_diff)) + if new_tolerance > 0: + print(len(unique_vals_a)) + print(unique_vals_a) + print(len(unique_vals_b)) + print(unique_vals_b) + print(diffs) + raise RuntimeError(f"Maximum disagreement in {varname_a} ({max_diff}) is intolerably large") + new_tolerance = 10**new_tolerance + if varname_b: + print(f"Maximum disagreement between {varname_a} and {varname_b} ({max_diff}) is larger than default tolerance of {tolerance}. Increasing tolerance to {new_tolerance}.") + else: + print(f"Maximum disagreement in {varname_a} ({max_diff}) is larger than default tolerance of {tolerance}. Increasing tolerance to {new_tolerance}.") + tolerance = new_tolerance + neglog_tolerance = int(-np.log10(tolerance)) + + da_a = np.round(da_a, neglog_tolerance) + da_b = np.round(da_b, neglog_tolerance) + + def replace_vals(ds, new_da, varname): + if len(ds[varname]) != len(new_da): + raise RuntimeError(f"Not allowing you to change length of {varname} from {len(ds[varname])} to {len(new_da)}") + if varname in ds.coords: + ds = ds.assign_coords({varname: new_da.values}) + elif varname in ds.data_vars: + ds[varname] = new_da + else: + raise TypeError(f"{varname} is not a coordinate or data variable; update round_lonlats_to_match_da()->replace_vals() to handle it") + return ds + + ds_a = replace_vals(ds_a, da_a, varname_a) + if ds_b: + ds_b = replace_vals(ds_b, da_b, varname_a) + return ds_a, ds_b, tolerance + else: + ds_a = replace_vals(ds_a, da_b, varname_b) + return ds_a, tolerance + + +def round_lonlats_to_match_ds(ds_a, ds_b, which_coord, tolerance): + tolerance_orig = np.inf + i=0 + max_Nloops = 10 + while tolerance != tolerance_orig: + if i > max_Nloops: + raise RuntimeError(f"More than {max_Nloops} loops required in round_lonlats_to_match_ds()") + tolerance_orig = tolerance + patches_var = "patches1d_" + which_coord + if patches_var in ds_a and which_coord in ds_a: + ds_a, tolerance = round_lonlats_to_match_da(ds_a, patches_var, tolerance, varname_b=which_coord) + if patches_var in ds_b and which_coord in ds_b: + ds_b, tolerance = round_lonlats_to_match_da(ds_b, patches_var, tolerance, varname_b=which_coord) + if patches_var in ds_a and patches_var in ds_b: + ds_a, ds_b, tolerance = round_lonlats_to_match_da(ds_a, patches_var, tolerance, ds_b=ds_b) + if which_coord in ds_a and which_coord in ds_b: + ds_a, ds_b, tolerance = round_lonlats_to_match_da(ds_a, which_coord, tolerance, ds_b=ds_b) + return ds_a, ds_b, tolerance + + +# For backwards compatibility with files missing SDATES_PERHARV. +def set_firstharv_nan(this_ds, this_var, firstharv_nan_inds): + this_da = this_ds[this_var] + this_array = this_da.values + this_array[0,0,firstharv_nan_inds] = np.nan + this_da.values = this_array + this_ds[this_var] = this_da + return this_ds + + +# Set up empty Dataset with time axis as "gs" (growing season) instead of what CLM puts out. +# Includes all the same variables as the input dataset, minus any that had dimensions mxsowings or mxharvests. +def set_up_ds_with_gs_axis(ds_in): + # Get the data variables to include in the new dataset + data_vars = dict() + for v in ds_in.data_vars: + if not any([x in ["mxsowings", "mxharvests"] for x in ds_in[v].dims]): + data_vars[v] = ds_in[v] + # Set up the new dataset + gs_years = [t.year-1 for t in ds_in.time.values[:-1]] + coords = ds_in.coords + coords["gs"] = gs_years + ds_out = xr.Dataset(data_vars=data_vars, + coords=coords, + attrs=ds_in.attrs) + return ds_out + + +def shift_sim_timeseries(array_in_cy, whichWay, inds_obs, inds_sim): + array_out_cy = np.full((array_in_cy.shape[0], array_in_cy.shape[1]-2), fill_value=np.nan) + array_out_cy[inds_obs,:] = array_in_cy[inds_obs,1:-1] + if whichWay == "L": + array_out_cy[inds_sim,:] = array_in_cy[inds_sim,:-2] + elif whichWay == "R": + array_out_cy[inds_sim,:] = array_in_cy[inds_sim,2:] + else: + raise RuntimeError("whichWay {whichWay} not recognized. Use L or R.") + return array_out_cy + + +def strip_cropname(x): + for y in ['irrigated', 'temperate', 'tropical', 'spring', 'winter']: + x = x.replace(y+"_", "") + return x + + +def subtract_mean(in_ps): + warnings.filterwarnings("ignore", message="Mean of empty slice") # Happens when you do np.nanmean() of an all-NaN + mean_p = np.nanmean(in_ps, axis=1) + warnings.filterwarnings("always", message="Mean of empty slice") + out_ps = in_ps - np.expand_dims(mean_p, axis=1) + return out_ps + + +def time_units_and_trim(ds, y1, yN, dt_type): + + # Convert to dt_type + time0 = ds.time.values[0] + time0_type = type(time0) + if not isinstance(time0, cftime.datetime): + if not isinstance(time0, np.integer): + raise TypeError(f"Unsure how to convert time of type {time0_type} to cftime.datetime") + print(f"Converting integer time to {dt_type}, assuming values are years and each time step is Jan. 1.") + ds = ds.assign_coords({"time": [dt_type(x, 1, 1) for x in ds.time.values]}) + elif not isinstance(time0, dt_type): + raise TypeError(f"Expected time axis to be type {dt_type} but got {time0_type}") + + # Trim + ds = ds.sel(time=slice(f"{y1}-01-01", f"{yN}-01-01")) + if "time_mth" in ds.dims: + ds = ds.sel(time_mth=slice(f"{y1}-01-01", f"{yN}-12-31")) + + return ds + + +# Trim monthly dataset to years of interest +def time_units_and_trim_mth(ds, y1, yN): + # Time axis shows END of time period; fix this. + new_time = [x[0] for x in ds.time_bounds.values] + ds = ds.assign_coords(time=new_time) + + return ds.sel(time=slice(f"{y1}-01-01", f"{yN+1}-12-31")) + + +# gridded_xr can be an xarray Dataset or DataArray +# kwargs like gridded_ds_dim='ungridded_target_ds_dim' +# e.g.: lon='patches1d_ixy', lat='patches1d_jxy' +def ungrid(gridded_xr, ungridded_target_ds, coords_var=None, target_dim="patch", **kwargs): + + # Remove any empties from ungridded_target_ds + for key, selection in kwargs.items(): + if isinstance(ungridded_target_ds[selection].values[0], str): + # print(f"Removing ungridded_target_ds patches where {selection} is empty") + isel_list = [i for i, x in enumerate(ungridded_target_ds[selection]) if x != ""] + ungridded_target_ds = ungridded_target_ds.copy().isel({target_dim: isel_list}) + + ### I don't think this is necessary + # unique_ungridded_selection = ungridded_target_ds[selection].values + # isel_list = [i for i, x in enumerate(gridded_xr[key].values) if x in unique_ungridded_selection] + # gridded_xr = gridded_xr.isel({key: isel_list}) + + if coords_var is not None: + new_coords = ungridded_target_ds[coords_var].coords + + isel_dict = {} + for key, selection in kwargs.items(): + if key in ['lon', 'lat']: + isel_dict[key] = xr.DataArray([int(x)-1 for x in ungridded_target_ds[selection].values], + dims = target_dim) + else: + values_list = list(gridded_xr[key].values) + isel_dict[key] = xr.DataArray([values_list.index(x) for x in ungridded_target_ds[selection].values], + dims = target_dim) + + ungridded_xr = gridded_xr.isel(isel_dict, drop=True) + if coords_var is not None: + ungridded_xr = ungridded_xr.assign_coords(new_coords) + + # If we're making a Dataset, save additional variables + if isinstance(gridded_xr, xr.Dataset): + ungridded_xr['lon'] = gridded_xr['lon'] + ungridded_xr['lat'] = gridded_xr['lat'] + # Save patch-level variables that match the variable names from the ungridded Dataset + for key, selection in kwargs.items(): + ungridded_xr[selection] = ungridded_target_ds[selection] + + return ungridded_xr + + +# After https://www.itl.nist.gov/div898/software/dataplot/refman2/auxillar/weigcorr.htm +def weighted_cov(a, b, w): + ma = np.average(a, weights=w) + mb = np.average(b, weights=w) + return np.sum(w*(a-ma)*(b-mb)) / np.sum(w) + +def weighted_pearsons_r(x, y, w): + r = weighted_cov(x, y, w) / np.sqrt(weighted_cov(x, x, w)*weighted_cov(y, y, w)) + + # Significance testing after Müller et al. (2017) + n = len(x) + df = n - 2 + t = r * np.sqrt(df) / np.sqrt(1 - r**2) + p = 2*stats.t(df).cdf(-np.abs(t)) + + return r, p + +def yield_anomalies(ps_in): + if isinstance(ps_in, xr.DataArray): + ps_out = ps_in.values + else: + ps_out = ps_in + + # After Jägermeyr & Frieler (2018, Sci. Adv.) + ps_out = detrend(ps_out) + ps_out /= np.expand_dims(np.std(ps_out, axis=1), axis=1) + + if isinstance(ps_in, xr.DataArray): + ps_out = xr.DataArray(data = ps_out, + coords = ps_in.coords, + attrs = ps_in.attrs) + + return ps_out + +def zero_immatures(ds, out_var="YIELD", min_viable_hui=None, mxmats=None, forAnnual=False, force_update=False): + + mxmat_limited = bool(mxmats) + + if any(x in out_var for x in ["YIELD", "MATURE"]): + in_var = "GRAINC_TO_FOOD" + else: + raise RuntimeError(f"out_var {out_var} not recognized. Accepted values: *YIELD*, *MATURE*") + + huifrac_var = "HUIFRAC" + gddharv_var = "GDDHARV" + gslen_var = "GSLEN" + if forAnnual: + out_var += "_PERHARV" + in_var += "_PERHARV" + huifrac_var += "_PERHARV" + gddharv_var += "_PERHARV" + gslen_var += "_PERHARV" + + if out_var in ds and not force_update and all([x in ds[out_var].attrs for x in ['min_viable_hui', 'mxmat_limited']]): + if ds[out_var].attrs['min_viable_hui'] == min_viable_hui and ds[out_var].attrs['mxmat_limited'] == mxmat_limited: + return ds + elif 'locked' in ds[out_var].attrs and ds[out_var].attrs['locked']: + return ds + + ds[out_var] = ds[in_var].copy() + + # Set yield to zero where minimum viable HUI wasn't reached + if min_viable_hui is not None: + + huifrac = ds[huifrac_var].copy().values + huifrac[np.where(ds[gddharv_var].values==0)] = 1 + if min_viable_hui == "isimip3" or min_viable_hui == "ggcmi3": + corn_value = 0.8 + other_value = 0.9 + min_viable_hui_touse = np.full_like(huifrac, fill_value=other_value) + for veg_str in np.unique(ds.patches1d_itype_veg_str.values): + if "corn" not in veg_str: + continue + is_thistype = np.where((ds.patches1d_itype_veg_str.values == veg_str))[0] + patch_index = list(ds[huifrac_var].dims).index("patch") + if patch_index == 0: + min_viable_hui_touse[is_thistype,...] = corn_value + elif patch_index == ds[huifrac_var].ndim - 1: + min_viable_hui_touse[...,is_thistype] = corn_value + else: + # Need patch to be either first or last dimension to allow use of ellipses + raise RuntimeError(f"Temporarily rearrange min_viable_hui_touse so that patch dimension is first (0) or last ({ds[huifrac_var].ndim - 1}), instead of {patch_index}.") + elif isinstance(min_viable_hui, str): + raise RuntimeError(f"min_viable_hui {min_viable_hui} not recognized. Accepted strings are ggcmi3 or isimip3") + else: + min_viable_hui_touse = min_viable_hui + if np.any(huifrac < min_viable_hui_touse): + print(f"Setting {out_var} to zero where minimum viable HUI ({min_viable_hui}) wasn't reached") + tmp_da = ds[in_var].copy() + tmp = tmp_da.copy().values + dont_include = (huifrac < min_viable_hui_touse) & (tmp > 0) + tmp[np.where(dont_include)] = 0 + if "MATURE" in out_var: + tmp[np.where(~dont_include & ~np.isnan(tmp))] = 1 + tmp_da.attrs['units'] = 'fraction' + ds[out_var] = xr.DataArray(data = tmp, + attrs = tmp_da.attrs, + coords = tmp_da.coords) + + # Get variants with values set to 0 if season was longer than CLM PFT parameter mxmat + if mxmat_limited: + tmp_da = ds[out_var] + tmp_ra = tmp_da.copy().values + for veg_str in np.unique(ds.patches1d_itype_veg_str.values): + mxmat_veg_str = veg_str.replace("soybean", "temperate_soybean").replace("tropical_temperate", "tropical") + mxmat = mxmats[mxmat_veg_str] + tmp_ra[np.where((ds.patches1d_itype_veg_str.values == veg_str) & (ds[gslen_var].values > mxmat))] = 0 + ds[out_var] = xr.DataArray(data = tmp_ra, + coords = tmp_da.coords, + attrs = tmp_da.attrs) + + # Get *biomass* *actually harvested* + if "YIELD" in out_var: + ds[out_var] = adjust_grainC(ds[out_var], ds.patches1d_itype_veg_str) + + # Save details + if "MATURE" not in out_var: + if ds[in_var].attrs['units'] != "gC/m^2": + raise RuntimeError(f"Unrecognized units of {in_var}: {ds[in_var].attrs['units']}") + ds[out_var].attrs['units'] = "g/m2" + ds[out_var].attrs['min_viable_hui'] = min_viable_hui + ds[out_var].attrs['mxmat_limited'] = mxmat_limited + + # Get dimensions in expected order (time/gs, patch) + if not forAnnual: + ds[out_var] = ds[out_var].transpose("gs", "patch") + + return ds diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py new file mode 100644 index 0000000000..4be89facba --- /dev/null +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -0,0 +1,757 @@ +# Import the CTSM Python utilities, functions for GDD generation +import utils +import generate_gdds_functions as gddfn +paramfile_dir = "/glade/p/cesmdata/cseg/inputdata/lnd/clm2/paramdata" + +# Import other shared functions +import os +import inspect +currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) +parentdir = os.path.dirname(currentdir) +sys.path.insert(0, parentdir) +import cropcal_module as cc +from cropcal_figs_module import * + +# Import everything else +import os +import sys +import numpy as np +import xarray as xr +import matplotlib.pyplot as plt +import matplotlib.cm as cm +import matplotlib.colors as mcolors +from matplotlib.transforms import Bbox +import warnings +import cartopy.crs as ccrs +import datetime as dt +import pickle +import datetime as dt +import argparse +import logging + +# Figure settings +plt.rc('font',**{'family':'sans-serif','sans-serif':['Arial']}) + +# Info re: PFT parameter set +my_clm_ver = 51 +my_clm_subver = "c211112" + +# Suppress some warnings +import warnings +warnings.filterwarnings("ignore", message="__len__ for multi-part geometries is deprecated and will be removed in Shapely 2.0. Check the length of the `geoms` property instead to get the number of parts of a multi-part geometry.") +warnings.filterwarnings("ignore", message="Iteration over multi-part geometries is deprecated and will be removed in Shapely 2.0. Use the `geoms` property to access the constituent parts of a multi-part geometry.") + + +def get_multicrop_maps(ds, theseVars, crop_fracs_yx, dummy_fill, gdd_units): + + # Get GDDs for these crops + da_eachCFT = xr.concat((ds[x] for i, x in enumerate(theseVars)), + dim="cft") + if "time" in ds.dims: + da_eachCFT = da_eachCFT.isel(time=0, drop=True) + da_eachCFT = da_eachCFT.where(da_eachCFT != dummy_fill) + da_eachCFT.attrs['units'] = gdd_units + + # What are the maximum differences seen between different crop types? + if len(theseVars) > 1: + maxDiff = np.nanmax(da_eachCFT.max(dim="cft") - da_eachCFT.min(dim="cft")) + if maxDiff > 0: + print(f" Max difference among crop types: {np.round(maxDiff)}") + + if crop_fracs_yx is None: + return da_eachCFT.isel(cft=0, drop=True) + + # Warn if GDD is NaN anywhere that there is area + da_eachCFT['cft'] = crop_fracs_yx['cft'] + gddNaN_areaPos = np.isnan(da_eachCFT) & (crop_fracs_yx > 0) + if np.any(gddNaN_areaPos): + total_bad_croparea = np.nansum(crop_fracs_yx.where(gddNaN_areaPos).values) + total_croparea = np.nansum(crop_fracs_yx.values) + print(f" GDD reqt NaN but area positive ({np.round(total_bad_croparea/total_croparea*100, 1)}% of this crop's area)") + + # Get areas and weights, masking cell-crops with NaN GDDs + crop_fracs_yx = crop_fracs_yx.where(~np.isnan(da_eachCFT)) + crop_area_yx = crop_fracs_yx.sum(dim="cft") + weights_yx = crop_fracs_yx / crop_area_yx + weights_sum_gt0 = weights_yx.sum(dim='cft').where(weights_yx > 0) + assert(np.isclose(np.nanmin(weights_sum_gt0.values), 1.0)) + assert(np.isclose(np.nanmax(weights_sum_gt0.values), 1.0)) + + # Mask GDDs and weights where there is no area + da_eachCFT = da_eachCFT.where(crop_fracs_yx > 0) + if len(theseVars)==1: + return da_eachCFT.isel(cft=0, drop=True) + weights_yx = weights_yx.where(crop_fracs_yx > 0) + weights_sum = weights_yx.sum(dim='cft').where(crop_area_yx > 0) + assert(np.isclose(np.nanmin(weights_sum.values), 1.0)) + assert(np.isclose(np.nanmax(weights_sum.values), 1.0)) + + # Ensure grid match between GDDs and weights + if not np.array_equal(da_eachCFT['lon'].values, weights_yx['lon'].values): + raise RuntimeError("lon mismatch") + if not np.array_equal(da_eachCFT['lat'].values, weights_yx['lat'].values): + raise RuntimeError("lat mismatch") + + # Get area-weighted mean GDD requirements for all crops + da = (da_eachCFT * weights_yx).sum(dim="cft") + da.attrs['units'] = gdd_units + da = da.where(crop_area_yx > 0) + + # Ensure that weighted mean is between each cell's min and max + whereBad = (da < da_eachCFT.min(dim="cft")) | (da > da_eachCFT.max(dim="cft")) + if np.any(whereBad): + where_belowMin = da.where(da < da_eachCFT.min(dim="cft")) + worst_belowMin = np.min((da_eachCFT.min(dim='cft') - where_belowMin).values) + where_aboveMax = da.where(da > da_eachCFT.max(dim="cft")) + worst_aboveMax = np.max((where_aboveMax - da_eachCFT.max(dim='cft')).values) + worst = max(worst_belowMin, worst_aboveMax) + tol = 1e-12 + if worst > 1e-12: + raise RuntimeError(f"Some value is outside expected range by {worst} (exceeds tolerance {tol})") + + return da + + +def main(run_dir=None, first_season=None, last_season=None, sdates_file=None, hdates_file=None, output_dir=None, save_figs=True, only_make_figs=False, run1_name=None, run2_name=None, land_use_file=None, first_land_use_year=None, last_land_use_year=None, unlimited_season_length=False, logger=None): + + # Directories to save output files and figures + if not output_dir: + if only_make_figs: + output_dir = run_dir + else: + output_dir = os.path.join(run_dir, "generate_gdds") + if not unlimited_season_length: + output_dir += ".mxmat" + output_dir += "." + dt.datetime.now().strftime('%Y-%m-%d-%H%M%S') + if not os.path.exists(output_dir): + os.makedirs(output_dir) + outdir_figs = os.path.join(output_dir, "figs") + + # Set up log file and function, if needed + if logger is None: + logging.basicConfig(level=logging.DEBUG, + format="", + filename=os.path.join(output_dir, 'generate_gdds.log'), + filemode='a') + logger = logging.getLogger('') + + # Print some info + gddfn.log(logger, f"Saving to {output_dir}") + + + ########################## + ### Import and process ### + ########################## + + if not only_make_figs: + + # Keep 1 extra year to avoid incomplete final growing season for crops harvested after Dec. 31. + y1_import_str = f"{first_season+1}-01-01" + yN_import_str = f"{last_season+2}-01-01" + + gddfn.log(logger, f"Importing netCDF time steps {y1_import_str} through {yN_import_str} (years are +1 because of CTSM output naming)") + + pickle_file = os.path.join(output_dir, f'{first_season}-{last_season}.pickle') + h1_ds_file = os.path.join(output_dir, f'{first_season}-{last_season}.h1_ds.nc') + if os.path.exists(pickle_file): + with open(pickle_file, 'rb') as f: + first_season, last_season, pickle_year, gddaccum_yp_list, gddharv_yp_list, skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, gddharv_in_h3, save_figs, incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings = pickle.load(f) + print(f'Will resume import at {pickle_year+1}') + h1_ds = None + else: + incorrectly_daily = False + skip_patches_for_isel_nan_lastyear = np.ndarray([]) + gddharv_in_h3 = False + pickle_year = -np.inf + gddaccum_yp_list = [] + gddharv_yp_list = [] + incl_vegtypes_str = None + lastYear_active_patch_indices_list = None + sdates_rx = sdates_file + hdates_rx = hdates_file + + if not unlimited_season_length: + mxmats = cc.import_max_gs_length(paramfile_dir, my_clm_ver, my_clm_subver) + else: + mxmats = None + + for y, thisYear in enumerate(np.arange(first_season+1,last_season+3)): + + if thisYear <= pickle_year: + continue + + h1_ds, sdates_rx, hdates_rx, gddaccum_yp_list, gddharv_yp_list, skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, gddharv_in_h3, incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings = gddfn.import_and_process_1yr(first_season, last_season, y, thisYear, sdates_rx, hdates_rx, gddaccum_yp_list, gddharv_yp_list, skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, gddharv_in_h3, run_dir, incl_vegtypes_str, h1_ds_file, mxmats, cc.get_gs_len_da, logger) + + gddfn.log(logger, f' Saving pickle file ({pickle_file})...') + with open(pickle_file, 'wb') as f: + pickle.dump([first_season, last_season, thisYear, gddaccum_yp_list, gddharv_yp_list, skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, gddharv_in_h3, save_figs, incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings], f, protocol=-1) + + + if isinstance(incl_vegtypes_str, list): + incl_vegtypes_str = np.array(incl_vegtypes_str) + plot_vegtypes_str = incl_vegtypes_str[[i for i,c in enumerate(gddaccum_yp_list) if not isinstance(c,type(None))]] + + gddfn.log(logger, "Done") + + if not h1_ds: + h1_ds = xr.open_dataset(h1_ds_file) + + + ###################################################### + ### Get and grid mean GDDs in GGCMI growing season ### + ###################################################### + + if not only_make_figs: + + longname_prefix = "GDD harvest target for " + + # Could skip this by saving sdates_rx['time_bounds'] + sdates_rx = gddfn.import_rx_dates("s", sdates_rx, incl_patches1d_itype_veg, mxsowings, logger) + + gddfn.log(logger, 'Getting and gridding mean GDDs...') + gdd_maps_ds = gddfn.yp_list_to_ds(gddaccum_yp_list, h1_ds, incl_vegtypes_str, sdates_rx, longname_prefix, logger) + gddharv_maps_ds = gddfn.yp_list_to_ds(gddharv_yp_list, h1_ds, incl_vegtypes_str, sdates_rx, longname_prefix, logger) + + # Fill NAs with dummy values + dummy_fill = -1 + gdd_fill0_maps_ds = gdd_maps_ds.fillna(0) + gdd_maps_ds = gdd_maps_ds.fillna(dummy_fill) + gddfn.log(logger, 'Done getting and gridding means.') + + # Add dummy variables for crops not actually simulated + gddfn.log(logger, "Adding dummy variables...") + # Unnecessary? + template_ds = xr.open_dataset(sdates_file, decode_times=True) + all_vars = [v.replace("sdate","gdd") for v in template_ds if "sdate" in v] + all_longnames = [template_ds[v].attrs["long_name"].replace("Planting day ", longname_prefix) + " (dummy)" for v in template_ds if "sdate" in v] + dummy_vars = [] + dummy_longnames = [] + for v, thisVar in enumerate(all_vars): + if thisVar not in gdd_maps_ds: + dummy_vars.append(thisVar) + dummy_longnames.append(all_longnames[v]) + + def make_dummy(thisCrop_gridded, addend): + dummy_gridded = thisCrop_gridded + dummy_gridded.values = dummy_gridded.values*0 + addend + return dummy_gridded + for v in gdd_maps_ds: + thisCrop_gridded = gdd_maps_ds[v].copy() + thisCrop_fill0_gridded = gdd_fill0_maps_ds[v].copy() + break + dummy_gridded = make_dummy(thisCrop_gridded, -1) + dummy_gridded0 = make_dummy(thisCrop_fill0_gridded, 0) + + for v, thisVar in enumerate(dummy_vars): + if thisVar in gdd_maps_ds: + gddfn.error(logger, f'{thisVar} is already in gdd_maps_ds. Why overwrite it with dummy?') + dummy_gridded.name = thisVar + dummy_gridded.attrs["long_name"] = dummy_longnames[v] + gdd_maps_ds[thisVar] = dummy_gridded + dummy_gridded0.name = thisVar + dummy_gridded0.attrs["long_name"] = dummy_longnames[v] + gdd_fill0_maps_ds[thisVar] = dummy_gridded0 + + # Add lon/lat attributes + def add_lonlat_attrs(ds): + ds.lon.attrs = {\ + "long_name": "coordinate_longitude", + "units": "degrees_east"} + ds.lat.attrs = {\ + "long_name": "coordinate_latitude", + "units": "degrees_north"} + return ds + gdd_maps_ds = add_lonlat_attrs(gdd_maps_ds) + gdd_fill0_maps_ds = add_lonlat_attrs(gdd_fill0_maps_ds) + gddharv_maps_ds = add_lonlat_attrs(gddharv_maps_ds) + + gddfn.log(logger, "Done.") + + + ###################### + ### Save to netCDF ### + ###################### + + if not only_make_figs: + gddfn.log(logger, "Saving...") + + # Get output file path + datestr = dt.datetime.now().strftime("%Y%m%d_%H%M%S") + outfile = os.path.join(output_dir, "gdds_" + datestr + ".nc") + outfile_fill0 = os.path.join(output_dir, "gdds_fill0_" + datestr + ".nc") + + def save_gdds(sdates_file, hdates_file, outfile, gdd_maps_ds, sdates_rx): + # Set up output file from template (i.e., prescribed sowing dates). + template_ds = xr.open_dataset(sdates_file, decode_times=True) + for v in template_ds: + if "sdate" in v: + template_ds = template_ds.drop(v) + template_ds.to_netcdf(path=outfile, format="NETCDF3_CLASSIC") + template_ds.close() + + # Add global attributes + comment = f"Derived from CLM run plus crop calendar input files {os.path.basename(sdates_file) and {os.path.basename(hdates_file)}}." + gdd_maps_ds.attrs = {\ + "author": "Sam Rabin (sam.rabin@gmail.com)", + "comment": comment, + "created": dt.datetime.now().astimezone().isoformat() + } + + # Add time_bounds + gdd_maps_ds["time_bounds"] = sdates_rx.time_bounds + + # Save cultivar GDDs + gdd_maps_ds.to_netcdf(outfile, mode="w", format="NETCDF3_CLASSIC") + + save_gdds(sdates_file, hdates_file, outfile, gdd_maps_ds, sdates_rx) + save_gdds(sdates_file, hdates_file, outfile_fill0, gdd_fill0_maps_ds, sdates_rx) + + gddfn.log(logger, "Done saving.") + + + ######################################## + ### Save things needed for mapmaking ### + ######################################## + + def add_attrs_to_map_ds(map_ds, incl_vegtypes_str, dummy_fill, outdir_figs, first_season, last_season): + return map_ds.assign_attrs({'incl_vegtypes_str': incl_vegtypes_str, + 'dummy_fill': dummy_fill, + 'outdir_figs': outdir_figs, + 'y1': first_season, + 'yN': last_season}) + + if not only_make_figs: + if not os.path.exists(outdir_figs): + os.makedirs(outdir_figs) + + gdd_maps_ds = add_attrs_to_map_ds(gdd_maps_ds, plot_vegtypes_str, dummy_fill, outdir_figs, first_season, last_season) + gddharv_maps_ds = add_attrs_to_map_ds(gddharv_maps_ds, plot_vegtypes_str, dummy_fill, outdir_figs, first_season, last_season) + + gdd_maps_ds.to_netcdf(os.path.join(outdir_figs, "gdd_maps.nc")) + gddharv_maps_ds.to_netcdf(os.path.join(outdir_figs, "gddharv_maps.nc")) + + + ################################################# + ### Save before/after map and boxplot figures ### + ################################################# + + def get_bounds_ncolors(gdd_spacing, diff_map_yx): + vmax = np.floor(np.nanmax(diff_map_yx.values)/gdd_spacing)*gdd_spacing + vmin = -vmax + epsilon = np.nextafter(0, 1) + bounds = list(np.arange(vmin, vmax, gdd_spacing)) + [vmax-epsilon] + if 0 in bounds: + bounds.remove(0) + bounds[bounds.index(-gdd_spacing)] /= 2 + bounds[bounds.index(gdd_spacing)] /= 2 + Ncolors = len(bounds) + 1 + return vmax, bounds, Ncolors + + def make_map(ax, this_map, this_title, vmax, bin_width, fontsize_ticklabels, fontsize_titles, bounds=None, extend='both', cmap=None, cbar_ticks=None, vmin=None): + + if bounds: + if not cmap: + raise RuntimeError("Calling make_map() with bounds requires cmap to be specified") + norm = mcolors.BoundaryNorm(bounds, cmap.N, extend=extend) + im1 = ax.pcolormesh(this_map.lon.values, this_map.lat.values, + this_map, shading="auto", + norm=norm, + cmap=cmap) + else: + if np.any(this_map.values < 0): + gdd_spacing = 500 + vmax = np.floor(np.nanmax(this_map.values)/gdd_spacing)*gdd_spacing + if vmin is not None: + raise RuntimeError("Do not specify vmin in this call of make_map()") + vmin = -vmax + Ncolors = vmax/gdd_spacing + if Ncolors % 2 == 0: Ncolors += 1 + if not cmap: + cmap = cm.get_cmap(cropcal_colors['div_other_nonnorm'], Ncolors) + + if np.any(this_map.values > vmax) and np.any(this_map.values < vmin): + extend = 'both' + elif np.any(this_map.values > vmax): + extend = 'max' + elif np.any(this_map.values < vmin): + extend = 'min' + else: + extend = 'neither' + + else: + if vmin is None: + vmin = 0 + else: + vmin = np.floor(vmin/500)*500 + vmax = np.floor(vmax/500)*500 + Ncolors = int(vmax/500) + if not cmap: + cmap=cm.get_cmap(cropcal_colors['seq_other'], Ncolors+1) + extend = 'max' + extend_color = cmap.colors[-1] + cmap = mcolors.ListedColormap(cmap.colors[:Ncolors]) + cmap.set_over(extend_color) + + im1 = ax.pcolormesh(this_map.lon.values, this_map.lat.values, + this_map, shading="auto", + vmin=vmin, vmax=vmax, + cmap=cmap) + + ax.set_extent([-180,180,-63,90],crs=ccrs.PlateCarree()) + ax.coastlines(linewidth=0.3) + ax.set_title(this_title, fontsize=fontsize_titles, fontweight="bold", y=0.96) + cbar = plt.colorbar(im1, orientation="horizontal", fraction=0.1, pad=0.02, + aspect=40, extend=extend, spacing='proportional') + cbar.ax.tick_params(labelsize=fontsize_ticklabels) + cbar.ax.set_xlabel(this_map.attrs['units'], + fontsize=fontsize_ticklabels) + cbar.ax.xaxis.set_label_coords(x=0.115, y=2.6) + if cbar_ticks: + cbar.ax.set_xticks(cbar_ticks) + + ticks = np.arange(-60, 91, bin_width) + ticklabels = [str(x) for x in ticks] + for i,x in enumerate(ticks): + if x%2: + ticklabels[i] = '' + plt.yticks(np.arange(-60,91,15), labels=ticklabels, + fontsize=fontsize_ticklabels) + plt.axis('off') + + def get_non_nans(in_da, fillValue): + in_da = in_da.where(in_da != fillValue) + return in_da.values[~np.isnan(in_da.values)] + + linewidth = 1.5 + def set_boxplot_props(bp, color, linewidth): + linewidth = linewidth + plt.setp(bp['boxes'], color=color, linewidth=linewidth) + plt.setp(bp['whiskers'], color=color, linewidth=linewidth) + plt.setp(bp['caps'], color=color, linewidth=linewidth) + plt.setp(bp['medians'], color=color, linewidth=linewidth) + plt.setp(bp['fliers'], markeredgecolor=color, markersize=6, linewidth=linewidth, markeredgewidth=linewidth/2) + + def make_plot(data, offset, linewidth): + offset = 0.4*offset + bpl = plt.boxplot(data, positions=np.array(range(len(data)))*2.0+offset, widths=0.6, + boxprops=dict(linewidth=linewidth), whiskerprops=dict(linewidth=linewidth), + capprops=dict(linewidth=linewidth), medianprops=dict(linewidth=linewidth), + flierprops=dict(markeredgewidth=0.5)) + return bpl + + def make_figures(first_land_use_year, last_land_use_year, land_use_file, run1_name, run2_name, thisDir=None, gdd_maps_ds=None, gddharv_maps_ds=None, outdir_figs=None, linewidth=1.5): + if not gdd_maps_ds: + if not thisDir: + gddfn.error(logger, 'If not providing gdd_maps_ds, you must provide thisDir (location of gdd_maps.nc)') + gdd_maps_ds = xr.open_dataset(thisDir + 'gdd_maps.nc') + if not gddharv_maps_ds: + if not thisDir: + gddfn.error(logger, 'If not providing gddharv_maps_ds, you must provide thisDir (location of gddharv_maps.nc)') + gddharv_maps_ds = xr.open_dataset(thisDir + 'gdd_maps.nc') + + # Get info + incl_vegtypes_str = gdd_maps_ds.attrs['incl_vegtypes_str'] + dummy_fill = gdd_maps_ds.attrs['dummy_fill'] + if not outdir_figs: + outdir_figs = gdd_maps_ds.attrs['outdir_figs'] + try: + y1 = gdd_maps_ds.attrs['y1'] + yN = gdd_maps_ds.attrs['yN'] + # Backwards compatibility with a bug (fixed 2023-01-03) + except: + y1 = gdd_maps_ds.attrs['first_season'] + yN = gdd_maps_ds.attrs['last_season'] + # Import LU data, if doing so + if land_use_file: + y1_lu = y1 if first_land_use_year == None else first_land_use_year + yN_lu = yN if last_land_use_year == None else last_land_use_year + lu_ds = cc.open_lu_ds(land_use_file, y1_lu, yN_lu, gdd_maps_ds, ungrid=False) + lu_years_text = f" (masked by {y1_lu}-{yN_lu} area)" + lu_years_file = f"_mask{y1_lu}-{yN_lu}" + else: + lu_ds = None + + # layout = "3x1" + # layout = "2x2" + layout = "3x2" + bin_width = 15 + lat_bin_edges = np.arange(0, 91, bin_width) + + fontsize_titles = 12 + fontsize_axislabels = 12 + fontsize_ticklabels = 12 + + Nbins = len(lat_bin_edges)-1 + bin_names = ["All"] + for b in np.arange(Nbins): + lower = lat_bin_edges[b] + upper = lat_bin_edges[b+1] + bin_names.append(f"{lower}–{upper}") + + color_old = cropcal_colors_cases(run1_name) + if color_old is None: + color_old = '#beaed4' + color_new = cropcal_colors_cases(run2_name) + if color_new is None: + color_new = '#7fc97f' + gdd_units = 'GDD (°C • day)' + + # Maps + ny = 3 + nx = 1 + gddfn.log(logger, "Making before/after maps...") + for v, vegtype_str in enumerate(incl_vegtypes_str + ["Corn", "Cotton", "Rice", "Soybean", "Sugarcane", "Wheat"]): + print(f"{vegtype_str}...") + + # Get component types + if vegtype_str in incl_vegtypes_str: + vegtypes_str = [vegtype_str] + elif not lu_ds: + raise RuntimeError(f"If mapping {vegtype_str}, you must provide land use dataset") + else: + vegtypes_str = [x for x in incl_vegtypes_str if vegtype_str.lower() in x] + vegtypes_int = [utils.vegtype_str2int(x)[0] for x in vegtypes_str] + + # Crop fraction map (for masking and weighting) + if lu_ds: + crop_fracs_yx = (lu_ds.LANDFRAC_PFT * lu_ds.PCT_CROP * lu_ds.PCT_CFT.sel(cft=vegtypes_int)).sum(dim="time") + if np.sum(crop_fracs_yx) == 0: + print(f"Skipping {vegtype_str} (no area)") + continue + else: + crop_fracs_yx = None + + theseVars = [f"gdd1_{x}" for x in vegtypes_int] + gddharv_map_yx = get_multicrop_maps(gddharv_maps_ds, theseVars, crop_fracs_yx, dummy_fill, gdd_units) + gdd_map_yx = get_multicrop_maps(gdd_maps_ds, theseVars, crop_fracs_yx, dummy_fill, gdd_units) + + # Get figure title + if len(vegtypes_str) > 1: + vegtype_str_title = vegtype_str + else: + vegtype_str_title = vegtype_str.replace("_", " ") + if "irrigated" not in vegtype_str: + vegtype_str_title = "rainfed " + vegtype_str_title + vegtype_str_title = vegtype_str_title.capitalize() + + vmin = min(np.min(gdd_map_yx), np.min(gddharv_map_yx)).values + vmax = max(np.max(gdd_map_yx), np.max(gddharv_map_yx)).values + + # Set up figure and first subplot + if layout == "3x1": + fig = plt.figure(figsize=(7.5,14)) + ax = fig.add_subplot(ny,nx,1,projection=ccrs.PlateCarree()) + elif layout == "2x2": + fig = plt.figure(figsize=(12,6)) + spec = fig.add_gridspec(nrows=2, ncols=2, + width_ratios=[0.4,0.6]) + ax = fig.add_subplot(spec[0,0],projection=ccrs.PlateCarree()) + elif layout == "3x2": + fig = plt.figure(figsize=(14,9)) + spec = fig.add_gridspec(nrows=3, ncols=2, + width_ratios=[0.5,0.5], + wspace=0.2) + ax = fig.add_subplot(spec[0,0],projection=ccrs.PlateCarree()) + else: + gddfn.error(logger, f"layout {layout} not recognized") + + thisMin = int(np.round(np.nanmin(gddharv_map_yx))) + thisMax = int(np.round(np.nanmax(gddharv_map_yx))) + thisTitle = f"{run1_name} (range {thisMin}–{thisMax})" + make_map(ax, gddharv_map_yx, thisTitle, vmax, bin_width, + fontsize_ticklabels, fontsize_titles, vmin=vmin) + + if layout == "3x1": + ax = fig.add_subplot(ny,nx,2,projection=ccrs.PlateCarree()) + elif layout in ["2x2", "3x2"]: + ax = fig.add_subplot(spec[1,0],projection=ccrs.PlateCarree()) + else: + gddfn.error(logger, f"layout {layout} not recognized") + thisMin = int(np.round(np.nanmin(gdd_map_yx))) + thisMax = int(np.round(np.nanmax(gdd_map_yx))) + thisTitle = f"{run2_name} (range {thisMin}–{thisMax})" + make_map(ax, gdd_map_yx, thisTitle, vmax, bin_width, + fontsize_ticklabels, fontsize_titles, vmin=vmin) + + # Difference + if layout == "3x2": + ax = fig.add_subplot(spec[2,0],projection=ccrs.PlateCarree()) + thisMin = int(np.round(np.nanmin(gdd_map_yx))) + thisMax = int(np.round(np.nanmax(gdd_map_yx))) + thisTitle = f"{run2_name} minus {run1_name}" + diff_map_yx = gdd_map_yx - gddharv_map_yx + diff_map_yx.attrs['units'] = gdd_units + + gdd_spacing = 500 + vmax, bounds, Ncolors = get_bounds_ncolors(gdd_spacing, diff_map_yx) + if Ncolors < 9: + gdd_spacing = 250 + vmax, bounds, Ncolors = get_bounds_ncolors(gdd_spacing, diff_map_yx) + + cmap = cm.get_cmap(cropcal_colors['div_other_nonnorm'], Ncolors) + cbar_ticks = [] + include_0bin_ticks = Ncolors <= 13 + if vmax <= 3000: + tick_spacing = gdd_spacing*2 + elif vmax <= 5000: + tick_spacing = 1500 + else: + tick_spacing = 2000 + previous = -np.inf + for x in bounds: + if (not include_0bin_ticks) and (x>0) and (previous<0): + cbar_ticks.append(0) + if x % tick_spacing == 0 or (include_0bin_ticks and abs(x)==gdd_spacing/2): + cbar_ticks.append(x) + previous = x + + make_map(ax, diff_map_yx, thisTitle, vmax, bin_width, + fontsize_ticklabels, fontsize_titles, bounds=bounds, + extend='both', cmap=cmap, cbar_ticks=cbar_ticks) + + # Boxplots ##################### + + gdd_vector = get_non_nans(gdd_map_yx, dummy_fill) + gddharv_vector = get_non_nans(gddharv_map_yx, dummy_fill) + + lat_abs = np.abs(gdd_map_yx.lat.values) + gdd_bybin_old = [gddharv_vector] + gdd_bybin_new = [gdd_vector] + for b in np.arange(Nbins): + lower = lat_bin_edges[b] + upper = lat_bin_edges[b+1] + lat_inds = np.where((lat_abs>=lower) & (lat_abs 1: + if dates_ds.dims['time'] == 365: + if not incorrectly_daily: + log(logger, " ℹ️ You saved SDATES and HDATES daily, but you only needed annual. Fixing.") + incorrectly_daily = True + dates_ds = dates_ds.isel(time=-1) + else: + dates_ds = dates_ds.isel(time=0) + + # Make sure NaN masks match + sdates_all_nan = np.sum(~np.isnan(dates_ds.SDATES.values), axis=dates_ds.SDATES.dims.index('mxsowings')) == 0 + hdates_all_nan = np.sum(~np.isnan(dates_ds.HDATES.values), axis=dates_ds.HDATES.dims.index('mxharvests')) == 0 + N_unmatched_nans = np.sum(sdates_all_nan != hdates_all_nan) + if N_unmatched_nans > 0: + error(logger, "Output SDATE and HDATE NaN masks do not match.") + if np.sum(~np.isnan(dates_ds.SDATES.values)) == 0: + error(logger, "All SDATES are NaN!") + + # Just work with non-NaN patches for now + skip_patches_for_isel_nan = np.where(sdates_all_nan)[0] + incl_patches_for_isel_nan = np.where(~sdates_all_nan)[0] + different_nan_mask = y > 0 and not np.array_equal(skip_patches_for_isel_nan_lastyear, skip_patches_for_isel_nan) + if different_nan_mask: + log(logger, ' Different NaN mask than last year') + incl_thisyr_but_nan_lastyr = [dates_ds.patch.values[p] for p in incl_patches_for_isel_nan if p in skip_patches_for_isel_nan_lastyear] + else: + incl_thisyr_but_nan_lastyr = [] + skipping_patches_for_isel_nan = len(skip_patches_for_isel_nan) > 0 + if skipping_patches_for_isel_nan: + log(logger, f' Ignoring {len(skip_patches_for_isel_nan)} patches with all-NaN sowing and harvest dates.') + dates_incl_ds = dates_ds.isel(patch=incl_patches_for_isel_nan) + else: + dates_incl_ds = dates_ds + incl_patches1d_itype_veg = dates_incl_ds.patches1d_itype_veg + + if y==0: + incl_vegtypes_str = dates_incl_ds.vegtype_str.values + else: + incl_vegtypes_str = incl_vegtypes_str_in + if isinstance(incl_vegtypes_str, xr.DataArray): + incl_vegtypes_str = incl_vegtypes_str.values + if isinstance(incl_vegtypes_str, np.ndarray): + incl_vegtypes_str = list(incl_vegtypes_str) + if incl_vegtypes_str != list(dates_incl_ds.vegtype_str.values): + error(logger, f'Included veg types differ. Previously {incl_vegtypes_str}, now {dates_incl_ds.vegtype_str.values}') + + if np.sum(~np.isnan(dates_incl_ds.SDATES.values)) == 0: + error(logger, "All SDATES are NaN after ignoring those patches!") + + # Some patches can have -1 sowing date?? Hopefully just an artifact of me incorrectly saving SDATES/HDATES daily. + mxsowings = dates_ds.dims['mxsowings'] + mxsowings_dim = dates_ds.SDATES.dims.index('mxsowings') + skip_patches_for_isel_sdatelt1 = np.where(dates_incl_ds.SDATES.values < 1)[1] + skipping_patches_for_isel_sdatelt1 = len(skip_patches_for_isel_sdatelt1) > 0 + if skipping_patches_for_isel_sdatelt1: + unique_hdates = np.unique(dates_incl_ds.HDATES.isel(mxharvests=0, patch=skip_patches_for_isel_sdatelt1).values) + if incorrectly_daily and list(unique_hdates)==[364]: + log(logger, f' ❗ {len(skip_patches_for_isel_sdatelt1)} patches have SDATE < 1, but this might have just been because of incorrectly daily outputs. Setting them to 365.') + new_sdates_ar = dates_incl_ds.SDATES.values + if mxsowings_dim != 0: + error(logger, "Code this up") + new_sdates_ar[0, skip_patches_for_isel_sdatelt1] = 365 + dates_incl_ds['SDATES'] = xr.DataArray(data = new_sdates_ar, + coords = dates_incl_ds['SDATES'].coords, + attrs = dates_incl_ds['SDATES'].attrs) + else: + error(logger, f"{len(skip_patches_for_isel_sdatelt1)} patches have SDATE < 1. Unique affected hdates: {unique_hdates}") + + # Some patches can have -1 harvest date?? Hopefully just an artifact of me incorrectly saving SDATES/HDATES daily. Can also happen if patch wasn't active last year + mxharvests = dates_ds.dims['mxharvests'] + mxharvests_dim = dates_ds.HDATES.dims.index('mxharvests') + # If a patch was inactive last year but was either (a) harvested the last time it was active or (b) was never active, it will have -1 as its harvest date this year. Such instances are okay. + hdates_thisyr = dates_incl_ds.HDATES.isel(mxharvests=0) + skip_patches_for_isel_hdatelt1 = np.where(hdates_thisyr.values < 1)[0] + skipping_patches_for_isel_hdatelt1 = len(skip_patches_for_isel_hdatelt1) > 0 + if incl_thisyr_but_nan_lastyr and list(skip_patches_for_isel_hdatelt1): + hdates_thisyr_where_nan_lastyr = hdates_thisyr.sel(patch=incl_thisyr_but_nan_lastyr) + sdates_thisyr_where_nan_lastyr = dates_incl_ds.SDATES.isel(mxsowings=0).sel(patch=incl_thisyr_but_nan_lastyr) + if np.any(hdates_thisyr_where_nan_lastyr < 1): + # patches_to_fix = hdates_thisyr_where_nan_lastyr.isel(patch=np.where(hdates_thisyr_where_nan_lastyr < 1)[0]).patch.values + new_hdates = dates_incl_ds.HDATES.values + if mxharvests_dim != 0: + error(logger, "Code this up") + patch_list = list(hdates_thisyr.patch.values) + here = [patch_list.index(x) for x in incl_thisyr_but_nan_lastyr] + log(logger, f" ❗ {len(here)} patches have harvest date -1 because they weren't active last year (and were either never active or were harvested when last active). Ignoring, but you should have done a run with patches always active if they are ever active in the real LU timeseries.") + new_hdates[0, here] = sdates_thisyr_where_nan_lastyr.values - 1 + dates_incl_ds['HDATES'] = xr.DataArray(data = new_hdates, + coords = dates_incl_ds.HDATES.coords, + attrs = dates_incl_ds.HDATES.attrs) + # Recalculate these + skip_patches_for_isel_hdatelt1 = np.where(dates_incl_ds.HDATES.isel(mxharvests=0).values < 1)[0] + skipping_patches_for_isel_hdatelt1 = len(skip_patches_for_isel_hdatelt1) > 0 + + # Resolve other issues + if skipping_patches_for_isel_hdatelt1: + unique_sdates = np.unique(dates_incl_ds.SDATES.isel(patch=skip_patches_for_isel_hdatelt1).values) + if incorrectly_daily and list(unique_sdates)==[1]: + log(logger, f' ❗ {len(skip_patches_for_isel_hdatelt1)} patches have HDATE < 1??? Seems like this might have just been because of incorrectly daily outputs; setting them to 365.') + new_hdates_ar = dates_incl_ds.HDATES.values + if mxharvests_dim != 0: + error(logger, "Code this up") + new_hdates_ar[0, skip_patches_for_isel_hdatelt1] = 365 + dates_incl_ds['HDATES'] = xr.DataArray(data = new_hdates_ar, + coords = dates_incl_ds['HDATES'].coords, + attrs = dates_incl_ds['HDATES'].attrs) + else: + error(logger, f"{len(skip_patches_for_isel_hdatelt1)} patches have HDATE < 1. Possible causes:\n * Not using constant crop areas (e.g., flanduse_timeseries from make_lu_for_gddgen.py)\n * Not skipping the first 2 years of output\nUnique affected sdates: {unique_sdates}") + + # Make sure there was only one harvest per year + N_extra_harv = np.sum(np.nanmax(dates_incl_ds.HDATES.isel(mxharvests=slice(1,mxharvests)).values, axis=mxharvests_dim) >= 1) + if N_extra_harv > 0: + error(logger, f"{N_extra_harv} patches have >1 harvest.") + + # Make sure harvest happened the day before sowing + sdates_clm = dates_incl_ds.SDATES.values.squeeze() + hdates_clm = dates_incl_ds.HDATES.isel(mxharvests=0).values + diffdates_clm = sdates_clm - hdates_clm + diffdates_clm[(sdates_clm==1) & (hdates_clm==365)] = 1 + if list(np.unique(diffdates_clm)) != [1]: + error(logger, f"Not all sdates-hdates are 1: {np.unique(diffdates_clm)}") + + # Import expected sowing dates. This will also be used as our template output file. + imported_sdates = isinstance(sdates_rx, str) + sdates_rx = import_rx_dates("s", sdates_rx, incl_patches1d_itype_veg, mxsowings, logger) + check_sdates(dates_incl_ds, sdates_rx, logger) + + # Import hdates, if needed + imported_hdates = isinstance(hdates_rx, str) + hdates_rx_orig = import_rx_dates("h", hdates_rx, incl_patches1d_itype_veg, mxsowings, logger) # Yes, mxsowings even when importing harvests + + # Limit growing season to CLM max growing season length, if needed + if mxmats and (imported_sdates or imported_hdates): + print(" Limiting growing season length...") + hdates_rx = hdates_rx_orig.copy() + for v in hdates_rx_orig: + if v == "time_bounds": + continue + + # Get max growing season length + vegtype_int = int(v.split('_')[1]) # netCDF variable name v should be something like gs1_17 + vegtype_str = utils.ivt_int2str(vegtype_int) + if vegtype_str == "soybean": + vegtype_str = "temperate_soybean" + elif vegtype_str == "irrigated_soybean": + vegtype_str = "irrigated_temperate_soybean" + + mxmat = mxmats[vegtype_str] + if np.isinf(mxmat): + print(f" Not limiting {vegtype_str}: No mxmat value") + continue + + # Get "prescribed" growing season length + gs_len_rx_da = get_gs_len_da(hdates_rx_orig[v] - sdates_rx[v]) + not_ok = gs_len_rx_da.values > mxmat + if not np.any(not_ok): + print(f" Not limiting {vegtype_str}: No rx season > {mxmat} days") + continue + + hdates_limited = hdates_rx_orig[v].copy().values + hdates_limited[np.where(not_ok)] = sdates_rx[v].values[np.where(not_ok)] + mxmat + hdates_limited[np.where(hdates_limited > 365)] -= 365 + if np.any(hdates_limited < 1): + raise RuntimeError("Limited hdates < 1") + elif np.any(hdates_limited > 365): + raise RuntimeError("Limited hdates > 365") + hdates_rx[v] = xr.DataArray(data = hdates_limited, + coords = hdates_rx_orig[v].coords, + attrs = hdates_rx_orig[v].attrs) + print(f" Limited {vegtype_str} growing season length to {mxmat}. Longest was {int(np.max(gs_len_rx_da.values))}, now {int(np.max(get_gs_len_da(hdates_rx[v] - sdates_rx[v]).values))}.") + else: + hdates_rx = hdates_rx_orig + + # Determine cells where growing season crosses new year + grows_across_newyear = hdates_rx < sdates_rx + + log(logger, f" Importing accumulated GDDs...") + clm_gdd_var = "GDDACCUM" + myVars = [clm_gdd_var] + if not gddharv_in_h3: + myVars.append("GDDHARV") + pattern = os.path.join(indir, f"*h1.{thisYear-1}-01-01*") + h1_ds = utils.import_ds(glob.glob(pattern), myVars=myVars, myVegtypes=utils.define_mgdcrop_list(), myVars_missing_ok=['GDDHARV']) + if 'GDDHARV' not in h1_ds: + if not gddharv_in_h3: + log(logger, 'Trying to get GDDHARV from h3 file(s) instead.') + try: + pattern = os.path.join(indir, f"*h3.{thisYear-1}-01-01*") + h3_ds = utils.import_ds(glob.glob(pattern), myVars=['GDDHARV'], myVegtypes=utils.define_mgdcrop_list()) + h1_ds['GDDHARV'] = h3_ds['GDDHARV'] + if not gddharv_in_h3: + log(logger, 'Success! Will look in h3 files from now on.') + gddharv_in_h3 = True + except: + log(logger, 'Unable to import GDDHARV from h1 or h3 files. Disabling save_figs.') + save_figs = False + + # Restrict to patches we're including + if skipping_patches_for_isel_nan: + if not np.array_equal(dates_ds.patch.values, h1_ds.patch.values): + error(logger, "dates_ds and h1_ds don't have the same patch list!") + h1_incl_ds = h1_ds.isel(patch=incl_patches_for_isel_nan) + else: + h1_incl_ds = h1_ds + + if not np.any(h1_incl_ds[clm_gdd_var].values != 0): + error(logger, f"All {clm_gdd_var} values are zero!") + + # Get standard datetime axis for outputs + Nyears = yN - y1 + 1 + + if len(gddaccum_yp_list)==0: + lastYear_active_patch_indices_list = [None for vegtype_str in h1_incl_ds.vegtype_str.values] + gddaccum_yp_list = [None for vegtype_str in h1_incl_ds.vegtype_str.values] + if save_figs: gddharv_yp_list = [None for vegtype_str in h1_incl_ds.vegtype_str.values] + + incl_vegtype_indices = [] + for v, vegtype_str in enumerate(h1_incl_ds.vegtype_str.values): + + # Skipping Miscanthus because it seems to never be harvested even though it is sown. This causes problems in NaN mask check. + if 'miscanthus' in vegtype_str: + log(logger, f' SKIPPING {vegtype_str}') + continue + + vegtype_int = utils.vegtype_str2int(vegtype_str)[0] + thisCrop_full_patchlist = list(utils.xr_flexsel(h1_ds, vegtype=vegtype_str).patch.values) + + # Get time series for each patch of this type + thisCrop_ds = utils.xr_flexsel(h1_incl_ds, vegtype=vegtype_str) + thisCrop_gddaccum_da = thisCrop_ds[clm_gdd_var] + if save_figs: thisCrop_gddharv_da = thisCrop_ds['GDDHARV'] + if not thisCrop_gddaccum_da.size: + continue + log(logger, f" {vegtype_str}...") + incl_vegtype_indices = incl_vegtype_indices + [v] + + # Get prescribed harvest dates for these patches + lon_points = thisCrop_ds.patches1d_lon.values + lat_points = thisCrop_ds.patches1d_lat.values + thisCrop_hdates_rx = thisCrop_map_to_patches(lon_points, lat_points, hdates_rx, vegtype_int) + + if isinstance(gddaccum_yp_list[v], type(None)): + gddaccum_yp_list[v] = np.full((Nyears+1, len(thisCrop_full_patchlist)), np.nan) + if save_figs: gddharv_yp_list[v] = np.full((Nyears+1, len(thisCrop_full_patchlist)), np.nan) + + # Get the accumulated GDDs at each prescribed harvest date + gddaccum_atharv_p = np.full(thisCrop_hdates_rx.shape, np.nan) + if save_figs: gddharv_atharv_p = np.full(thisCrop_hdates_rx.shape, np.nan) + unique_rx_hdates = np.unique(thisCrop_hdates_rx.values) + # Build an indexing tuple + patches = [] + i_patches = [] + i_times = [] + for i, hdate in enumerate(unique_rx_hdates): + here = np.where(thisCrop_hdates_rx.values == hdate)[0] + patches += list(thisCrop_gddaccum_da.patch.values[here]) + i_patches += list(here) + i_times += list(np.full((len(here),), int(hdate-1))) + # Sort back to correct order + if not np.all(thisCrop_gddaccum_da.patch.values[:-1] <= thisCrop_gddaccum_da.patch.values[1:]): + error(logger, "This code depends on DataArray patch list being sorted.") + sortorder = np.argsort(patches) + i_patches = list(np.array(i_patches)[np.array(sortorder)]) + i_times = list(np.array(i_times)[np.array(sortorder)]) + # Select using the indexing tuple + gddaccum_atharv_p = thisCrop_gddaccum_da.values[(i_times, i_patches)] + if save_figs: gddharv_atharv_p = thisCrop_gddharv_da.values[(i_times, i_patches)] + if np.any(np.isnan(gddaccum_atharv_p)): + log(logger, f" ❗ {np.sum(np.isnan(gddaccum_atharv_p))}/{len(gddaccum_atharv_p)} NaN after extracting GDDs accumulated at harvest") + if save_figs and np.any(np.isnan(gddharv_atharv_p)): + log(logger, f" ❗ {np.sum(np.isnan(gddharv_atharv_p))}/{len(gddharv_atharv_p)} NaN after extracting GDDHARV") + + # Assign these to growing seasons based on whether gs crossed new year + thisYear_active_patch_indices = [thisCrop_full_patchlist.index(x) for x in thisCrop_ds.patch.values] + thisCrop_sdates_rx = thisCrop_map_to_patches(lon_points, lat_points, sdates_rx, vegtype_int) + where_gs_thisyr = np.where(thisCrop_sdates_rx < thisCrop_hdates_rx)[0] + tmp_gddaccum = np.full(thisCrop_sdates_rx.shape, np.nan) + tmp_gddaccum[where_gs_thisyr] = gddaccum_atharv_p[where_gs_thisyr] + if save_figs: + tmp_gddharv = np.full(tmp_gddaccum.shape, np.nan) + tmp_gddharv[where_gs_thisyr] = gddharv_atharv_p[where_gs_thisyr] + if y > 0: + lastYear_active_patch_indices = lastYear_active_patch_indices_list[v] + where_gs_lastyr = np.where(thisCrop_sdates_rx > thisCrop_hdates_rx)[0] + active_thisYear_where_gs_lastyr_indices = [thisYear_active_patch_indices[x] for x in where_gs_lastyr] + if not np.array_equal(lastYear_active_patch_indices, thisYear_active_patch_indices): + if incorrectly_daily: + log(logger, " ❗ This year's active patch indices differ from last year's. Allowing because this might just be an artifact of incorrectly daily outputs, BUT RESULTS MUST NOT BE TRUSTED.") + else: + error(logger, "This year's active patch indices differ from last year's.") + # Make sure we're not about to overwrite any existing values. + if np.any(~np.isnan(gddaccum_yp_list[v][y-1, active_thisYear_where_gs_lastyr_indices])): + if incorrectly_daily: + log(logger, " ❗ Unexpected non-NaN for last season's GDD accumulation. Allowing because this might just be an artifact of incorrectly daily outputs, BUT RESULTS MUST NOT BE TRUSTED.") + else: + error(logger, "Unexpected non-NaN for last season's GDD accumulation") + if save_figs and np.any(~np.isnan(gddharv_yp_list[v][y-1, active_thisYear_where_gs_lastyr_indices])): + if incorrectly_daily: + log(logger, " ❗ Unexpected non-NaN for last season's GDDHARV. Allowing because this might just be an artifact of incorrectly daily outputs, BUT RESULTS MUST NOT BE TRUSTED.") + else: + error(logger, "Unexpected non-NaN for last season's GDDHARV") + # Fill. + gddaccum_yp_list[v][y-1, active_thisYear_where_gs_lastyr_indices] = gddaccum_atharv_p[where_gs_lastyr] + if save_figs: gddharv_yp_list[v][y-1, active_thisYear_where_gs_lastyr_indices] = gddharv_atharv_p[where_gs_lastyr] + # Last year's season should be filled out now; make sure. + if np.any(np.isnan(gddaccum_yp_list[v][y-1, active_thisYear_where_gs_lastyr_indices])): + if incorrectly_daily: + log(logger, " ❗ Unexpected NaN for last season's GDD accumulation. Allowing because this might just be an artifact of incorrectly daily outputs, BUT RESULTS MUST NOT BE TRUSTED.") + else: + error(logger, "Unexpected NaN for last season's GDD accumulation.") + if save_figs and np.any(np.isnan(gddharv_yp_list[v][y-1, active_thisYear_where_gs_lastyr_indices])): + if incorrectly_daily: + log(logger, " ❗ Unexpected NaN for last season's GDDHARV. Allowing because this might just be an artifact of incorrectly daily outputs, BUT RESULTS MUST NOT BE TRUSTED.") + else: + error(logger, "Unexpected NaN for last season's GDDHARV.") + gddaccum_yp_list[v][y, thisYear_active_patch_indices] = tmp_gddaccum + if save_figs: gddharv_yp_list[v][y, thisYear_active_patch_indices] = tmp_gddharv + + # Make sure that NaN masks are the same for this year's sdates and 'filled-out' GDDs from last year + if y>0: + nanmask_output_sdates = np.isnan(dates_ds.SDATES.isel(mxsowings=0, patch=np.where(dates_ds.patches1d_itype_veg_str==vegtype_str)[0]).values) + nanmask_output_gdds_lastyr = np.isnan(gddaccum_yp_list[v][y-1,:]) + if not np.array_equal(nanmask_output_gdds_lastyr, nanmask_output_sdates): + if incorrectly_daily: + log(logger, " ❗ NaN masks differ between this year's sdates and 'filled-out' GDDs from last year. Allowing because this might just be an artifact of incorrectly daily outputs, BUT RESULTS MUST NOT BE TRUSTED.") + else: + error(logger, "NaN masks differ between this year's sdates and 'filled-out' GDDs from last year") + lastYear_active_patch_indices_list[v] = thisYear_active_patch_indices + + skip_patches_for_isel_nan_lastyear = skip_patches_for_isel_nan + + # Could save space by only saving variables needed for gridding + log(logger, ' Saving h1_ds...') + h1_ds.to_netcdf(h1_ds_file) + + return h1_ds, sdates_rx, hdates_rx, gddaccum_yp_list, gddharv_yp_list, skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, gddharv_in_h3, incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings diff --git a/python/ctsm/crop_calendars/make_surface_for_gddgen.py b/python/ctsm/crop_calendars/make_surface_for_gddgen.py new file mode 100644 index 0000000000..bfc324eb14 --- /dev/null +++ b/python/ctsm/crop_calendars/make_surface_for_gddgen.py @@ -0,0 +1,171 @@ +import numpy as np +import xarray as xr +import argparse +import sys +import os + +# Doing what I did before with flanduse_timeseries, except now with +# fsurdat. +def get_new_fsurdat_v0(surf, lu, params): + + # Where is each crop ever active? + if "AREA" not in lu: + lu["AREA"] = xr.DataArray(data=np.ones_like(lu["LANDFRAC_PFT"]), + dims=lu["LANDFRAC_PFT"].dims, + coords=lu["LANDFRAC_PFT"].coords) + lu['AREA_CROP'] = (lu.AREA * lu.LANDFRAC_PFT * lu.PCT_CROP/100).transpose("time", "lsmlat", "lsmlon") + lu['AREA_CFT'] = (lu['AREA_CROP'] * lu.PCT_CFT/100).transpose("time", "cft", "lsmlat", "lsmlon") + ds_area_max = lu['AREA_CFT'].max(dim="time") + lu['ever_active_bycft'] = (ds_area_max > 0).transpose("cft", "lsmlat", "lsmlon") + lu['ever_active'] = lu['ever_active_bycft'].any(dim="cft") + + # For cells that EVER have cropland, when do they have 0 crop area? Change those 0% values to 1%. + new_pct_crop_ar = lu['PCT_CROP'].values + needs_pctcrop_0to1 = np.where((lu['AREA_CROP']==0) & lu['ever_active']) + new_pct_crop_ar[needs_pctcrop_0to1] = 1.0 + lu['PCT_CROP'] = xr.DataArray(data = new_pct_crop_ar, + coords = lu['PCT_CROP'].coords, + attrs = lu['PCT_CROP'].attrs) + lu['AREA_CROP'] = (lu.AREA * lu.LANDFRAC_PFT * lu.PCT_CROP/100).transpose("time", "lsmlat", "lsmlon") + if np.any((lu['AREA_CROP']==0) & lu['ever_active']): + raise RuntimeError("Failed to fill 0% CROP with 1% where needed.") + + # For cells that EVER have each CFT, when do they have 0 area of that CFT? Change those 0% values to something positive. + new_pct_cft_tcyx = lu['PCT_CFT'].values + new_pct_cft_tcyx[np.where((lu['AREA_CFT']==0) & lu['ever_active'])] = 1.0 + # Ensure sum to 100 + i = 0 + while np.any(~np.isclose(np.sum(new_pct_cft_tcyx, axis=1), 100.0)): + i+=1 + if i > 10: + raise RuntimeError('too many iterations') + new_pct_cft_tcyx = 100 * (new_pct_cft_tcyx / np.expand_dims(np.sum(new_pct_cft_tcyx, axis=1), axis=1)) + lu['PCT_CFT'] = xr.DataArray(data = new_pct_cft_tcyx, + coords = lu['PCT_CFT'].coords, + attrs = lu['PCT_CFT'].attrs) + + # Just take the first timestep + new_pct_crop_da = lu['PCT_CROP'].isel(time=0) + new_pct_cft_da = lu['PCT_CFT'].isel(time=0) + + # flanduse_timeseries doesn't have PCT_NATVEG + new_natveg_da = surf['PCT_NATVEG'] + + # For cells where + + return new_pct_crop_da, new_natveg_da, new_pct_cft_da + + +# Trying to minimize the number of crop PFTs that need to be simulated. +# CLM currently giving errors about wt_cft not summing to 1. +def get_new_fsurdat_v1(surf, lu, params): + + ########################################## + ### %% Get new PCT_CROP and PCT_NATVEG ### + ########################################## + + new_pct_crop_da = lu['PCT_CROP'].max(dim="time") + new_pct_crop_da.attrs = surf['PCT_CROP'].attrs + + surf_pct_crop_plus_natveg = surf['PCT_CROP'] + surf['PCT_NATVEG'] + if np.any(surf_pct_crop_plus_natveg < new_pct_crop_da): + raise RuntimeError("Max CROP > CROP+NATVEG") + + new_natveg_da = surf_pct_crop_plus_natveg - new_pct_crop_da + if np.any((new_natveg_da > 0) & (surf['PCT_NATVEG'] == 0)): + print("You created some NATVEG area. Not necessarily a problem, but unexpected.") + new_natveg_da.attrs = surf['PCT_NATVEG'].attrs + + + ################################################################## + ### Get new PCT_CFT (percentage of cropland that is each crop) ### + ################################################################## + + # Sum all crops' max area, merging unrepresented types into their representative type + cft_list_int = surf['cft'].values + max_merged_pct_crop = np.full_like(surf['PCT_CFT'], 0.0) + for i, c in enumerate(cft_list_int): + mergetarget = params['mergetoclmpft'].sel(pft=c).values + m = np.where(cft_list_int==mergetarget)[0] + max_merged_pct_crop[m,:,:] += np.expand_dims(lu['PCT_CFT'].sel(cft=c).max(dim="time"), axis=0) + max_merged_pct_crop_da = xr.DataArray(data=max_merged_pct_crop, + dims=surf['PCT_CFT'].dims, + attrs=surf['PCT_CFT'].attrs) + + # Ensure no area in merged-away crops + for i, c in enumerate(cft_list_int): + if (params['mergetoclmpft'].sel(pft=c) != c) and (max_merged_pct_crop_da.sel(cft=i).max() > 0): + raise RuntimeError(f"Unexpected max_merged_pct_crop area for pft {c}") + + # Determine how many crops ever have any area + ever_has_this_crop = np.full_like(max_merged_pct_crop, 0.0) + ever_has_this_crop[max_merged_pct_crop > 0] = 1 + N_crops_ever_active = ever_has_this_crop.sum(axis=0) + + # Split crop area evenly among ever-included crops + new_pct_cft = np.full_like(surf['PCT_CFT'].isel(cft=0), 0.0) + new_pct_cft[N_crops_ever_active > 0] = 100 / N_crops_ever_active[N_crops_ever_active > 0] + new_pct_cft = np.expand_dims(new_pct_cft, axis=0) + new_pct_cft = np.tile(new_pct_cft, reps=[surf.dims['cft'], 1, 1]) + where_zero = np.where(max_merged_pct_crop_da) + new_pct_cft[where_zero] = 0.0 + new_pct_cft_da = xr.DataArray(data=new_pct_cft, + dims=surf['PCT_CFT'].dims, + attrs=surf['PCT_CFT'].attrs) + + return new_pct_crop_da, new_natveg_da, new_pct_cft_da + + +def main(argv): + + ############################### + ### Process input arguments ### + ############################### + + # Set arguments + parser = argparse.ArgumentParser(description="ADD DESCRIPTION HERE") + parser.add_argument("-l", "--flanduse_timeseries", "--flanduse-timeseries", + help="Land-use timeseries file (flanduse_timeseries) for CLM run", + required=True) + parser.add_argument("-p", "--paramfile", + help="Parameter file (paramfile) for CLM run", + required=True) + parser.add_argument("-s", "--fsurdat", + help="Surface dataset (fsurdat) for CLM run", + required=True) + args = parser.parse_args(argv) + + + ########################## + ### Import and process ### + ########################## + + lu = xr.open_dataset(args.flanduse_timeseries) + surf = xr.open_dataset(args.fsurdat) + params = xr.open_dataset(args.paramfile) + + # new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v1(surf, lu, params) + new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v0(surf, lu, params) + + + ############################# + ### Save to run directory ### + ############################# + + # Make new Dataset + new_surf = surf + new_surf['PCT_CROP'] = new_pct_crop_da + new_surf['PCT_CFT'] = new_pct_cft_da + new_surf['PCT_NATVEG'] = new_natveg_da + + # Save to new file + fsurdat_noext, ext = os.path.splitext(args.fsurdat) + new_fsurdat = f"{fsurdat_noext}.GDDgen{ext}" + new_fsurdat = os.path.basename(new_fsurdat) + new_surf.to_netcdf(new_fsurdat, format="NETCDF3_64BIT") + + print(new_fsurdat) + + +if __name__ == "__main__": + main(sys.argv[1:]) diff --git a/python/ctsm/crop_calendars/utils.py b/python/ctsm/crop_calendars/utils.py new file mode 100644 index 0000000000..e9d8d8e825 --- /dev/null +++ b/python/ctsm/crop_calendars/utils.py @@ -0,0 +1,1157 @@ +import re +import cf_units as cf +import cftime +import numpy as np +import xarray as xr +from cartopy.util import add_cyclic_point + +#from xr_ds_ex import xr_ds_ex + +# generate annual means, weighted by days / month +def weighted_annual_mean(array, time_in='time', time_out='time'): + + if isinstance(array[time_in].values[0], cftime.datetime): + month_length = array[time_in].dt.days_in_month + + # After https://docs.xarray.dev/en/v0.5.1/examples/monthly-means.html + group = f'{time_in}.year' + weights = month_length.groupby(group) / month_length.groupby(group).sum() + np.testing.assert_allclose(weights.groupby(group).sum().values, 1) + array = (array * weights).groupby(group).sum(dim=time_in, skipna=True) + if time_out != "year": + array = array.rename({'year': time_out}) + + else: + mon_day = xr.DataArray(np.array([31,28,31,30,31,30,31,31,30,31,30,31]), dims=['month']) + mon_wgt = mon_day/mon_day.sum() + array = (array.rolling({time_in: 12}, center=False) # rolling + .construct("month") # construct the array + .isel({time_in: slice(11, None, 12)}) # slice so that the first element is [1..12], second is [13..24] + .dot(mon_wgt, dims=["month"])) + if time_in != time_out: + array = array.rename({time_in: time_out}) + + return array + +def change_units(ds, variable_str, variable_bounds_str, target_unit_str): + """ Applies unit conversion on an xarray DataArray """ + orig_units = cf.Unit(ds[variable_str].attrs["units"]) + target_units = cf.Unit(target_unit_str) + variable_in_new_units = xr.apply_ufunc( + orig_units.convert, + ds[variable_bounds_str], + target_units, + output_dtypes=[ds[variable_bounds_str].dtype], + ) + return variable_in_new_units + +def clean_units(units): + """replace some troublesome unit terms with acceptable replacements""" + replacements = {'kgC':'kg', 'gC':'g', 'gC13':'g', 'gC14':'g', 'gN':'g', + 'unitless':'1', + 'years':'common_years', 'yr':'common_year', + 'meq':'mmol', 'neq':'nmol'} + units_split = re.split('( |\(|\)|\^|\*|/|-[0-9]+|[0-9]+)', units) + units_split_repl = \ + [replacements[token] if token in replacements else token for token in units_split] + return ''.join(units_split_repl) + +def copy_fill_settings(da_in, da_out): + """ + propagate _FillValue and missing_value settings from da_in to da_out + return da_out + """ + if '_FillValue' in da_in.encoding: + da_out.encoding['_FillValue'] = da_in.encoding['_FillValue'] + else: + da_out.encoding['_FillValue'] = None + if 'missing_value' in da_in.encoding: + da_out.attrs['missing_value'] = da_in.encoding['missing_value'] + return da_out + +def dim_cnt_check(ds, varname, dim_cnt): + """confirm that varname in ds has dim_cnt dimensions""" + if len(ds[varname].dims) != dim_cnt: + msg_full = 'unexpected dim_cnt=%d, varname=%s' % (len(ds[varname].dims), varname) + raise ValueError(msg_full) + +def time_set_mid(ds, time_name): + """ + set ds[time_name] to midpoint of ds[time_name].attrs['bounds'], if bounds attribute exists + type of ds[time_name] is not changed + ds is returned + """ + + if 'bounds' not in ds[time_name].attrs: + return ds + + # determine units and calendar of unencoded time values + if ds[time_name].dtype == np.dtype('O'): + units = 'days since 0000-01-01' + calendar = 'noleap' + else: + units = ds[time_name].attrs['units'] + calendar = ds[time_name].attrs['calendar'] + + # construct unencoded midpoint values, assumes bounds dim is 2nd + tb_name = ds[time_name].attrs['bounds'] + if ds[tb_name].dtype == np.dtype('O'): + tb_vals = cftime.date2num(ds[tb_name].values, units=units, calendar=calendar) + else: + tb_vals = ds[tb_name].values + tb_mid = tb_vals.mean(axis=1) + + # set ds[time_name] to tb_mid + if ds[time_name].dtype == np.dtype('O'): + ds[time_name] = cftime.num2date(tb_mid, units=units, calendar=calendar) + else: + ds[time_name] = tb_mid + + return ds + +def time_year_plus_frac(ds, time_name): + """return time variable, as year plus fraction of year""" + + # this is straightforward if time has units='days since 0000-01-01' and calendar='noleap' + # so convert specification of time to that representation + + # get time values as an np.ndarray of cftime objects + if np.dtype(ds[time_name]) == np.dtype('O'): + tvals_cftime = ds[time_name].values + else: + tvals_cftime = cftime.num2date( + ds[time_name].values, ds[time_name].attrs['units'], ds[time_name].attrs['calendar']) + + # convert cftime objects to representation mentioned above + tvals_days = cftime.date2num(tvals_cftime, 'days since 0000-01-01', calendar='noleap') + + return tvals_days / 365.0 + + +# add cyclic point +def cyclic_dataarray(da, coord='lon'): + """ Add a cyclic coordinate point to a DataArray along a specified + named coordinate dimension. + >>> from xray import DataArray + >>> data = DataArray([[1, 2, 3], [4, 5, 6]], + ... coords={'x': [1, 2], 'y': range(3)}, + ... dims=['x', 'y']) + >>> cd = cyclic_dataarray(data, 'y') + >>> print cd.data + array([[1, 2, 3, 1], + [4, 5, 6, 4]]) + """ + assert isinstance(da, xr.DataArray) + + lon_idx = da.dims.index(coord) + cyclic_data, cyclic_coord = add_cyclic_point(da.values, + coord=da.coords[coord], + axis=lon_idx) + + # Copy and add the cyclic coordinate and data + new_coords = dict(da.coords) + new_coords[coord] = cyclic_coord + new_values = cyclic_data + + new_da = xr.DataArray(new_values, dims=da.dims, coords=new_coords) + + # Copy the attributes for the re-constructed data and coords + for att, val in da.attrs.items(): + new_da.attrs[att] = val + for c in da.coords: + for att in da.coords[c].attrs: + new_da.coords[c].attrs[att] = da.coords[c].attrs[att] + + return new_da + +# as above, but for a dataset +# doesn't work because dims are locked in a dataset +''' +def cyclic_dataset(ds, coord='lon'): + assert isinstance(ds, xr.Dataset) + + lon_idx = ds.dims.index(coord) + cyclic_data, cyclic_coord = add_cyclic_point(ds.values, + coord=ds.coords[coord], + axis=lon_idx) + + # Copy and add the cyclic coordinate and data + new_coords = dict(ds.coords) + new_coords[coord] = cyclic_coord + new_values = cyclic_data + + new_ds = xr.DataSet(new_values, dims=ds.dims, coords=new_coords) + + # Copy the attributes for the re-constructed data and coords + for att, val in ds.attrs.items(): + new_ds.attrs[att] = val + for c in ds.coords: + for att in ds.coords[c].attrs: + new_ds.coords[c].attrs[att] = ds.coords[c].attrs[att] + + return new_ds +''' + + +# List of PFTs used in CLM +def define_pftlist(): + pftlist = ["not_vegetated", + "needleleaf_evergreen_temperate_tree", + "needleleaf_evergreen_boreal_tree", + "needleleaf_deciduous_boreal_tree", + "broadleaf_evergreen_tropical_tree", + "broadleaf_evergreen_temperate_tree", + "broadleaf_deciduous_tropical_tree", + "broadleaf_deciduous_temperate_tree", + "broadleaf_deciduous_boreal_tree", + "broadleaf_evergreen_shrub", + "broadleaf_deciduous_temperate_shrub", + "broadleaf_deciduous_boreal_shrub", + "c3_arctic_grass", + "c3_non-arctic_grass", + "c4_grass", + "unmanaged_c3_crop", + "unmanaged_c3_irrigated", + "temperate_corn", + "irrigated_temperate_corn", + "spring_wheat", + "irrigated_spring_wheat", + "winter_wheat", + "irrigated_winter_wheat", + "soybean", + "irrigated_soybean", + "barley", + "irrigated_barley", + "winter_barley", + "irrigated_winter_barley", + "rye", + "irrigated_rye", + "winter_rye", + "irrigated_winter_rye", + "cassava", + "irrigated_cassava", + "citrus", + "irrigated_citrus", + "cocoa", + "irrigated_cocoa", + "coffee", + "irrigated_coffee", + "cotton", + "irrigated_cotton", + "datepalm", + "irrigated_datepalm", + "foddergrass", + "irrigated_foddergrass", + "grapes", + "irrigated_grapes", + "groundnuts", + "irrigated_groundnuts", + "millet", + "irrigated_millet", + "oilpalm", + "irrigated_oilpalm", + "potatoes", + "irrigated_potatoes", + "pulses", + "irrigated_pulses", + "rapeseed", + "irrigated_rapeseed", + "rice", + "irrigated_rice", + "sorghum", + "irrigated_sorghum", + "sugarbeet", + "irrigated_sugarbeet", + "sugarcane", + "irrigated_sugarcane", + "sunflower", + "irrigated_sunflower", + "miscanthus", + "irrigated_miscanthus", + "switchgrass", + "irrigated_switchgrass", + "tropical_corn", + "irrigated_tropical_corn", + "tropical_soybean", + "irrigated_tropical_soybean"] + return pftlist + + +# Get CLM ivt number corresponding to a given name +def ivt_str2int(ivt_str): + + pftlist = define_pftlist() + if isinstance(ivt_str, str): + ivt_int = pftlist.index(ivt_str) + elif isinstance(ivt_str, list) or isinstance(ivt_str, np.ndarray): + ivt_int = [ivt_str2int(x) for x in ivt_str] + if isinstance(ivt_str, np.ndarray): + ivt_int = np.array(ivt_int) + else: + raise RuntimeError(f"Update ivt_str_to_int() to handle input of type {type(ivt_str)} (if possible)") + + return ivt_int + +# Get CLM ivt name corresponding to a given number +def ivt_int2str(ivt_int): + + pftlist = define_pftlist() + if np.issubdtype(type(ivt_int), np.integer) or int(ivt_int)==ivt_int: + ivt_str = pftlist[int(ivt_int)] + elif isinstance(ivt_int, list) or isinstance(ivt_int, np.ndarray): + ivt_str = [ivt_int2str(x) for x in ivt_int] + if isinstance(ivt_int, np.ndarray): + ivt_str = np.array(ivt_str) + elif isinstance(ivt_int, float): + raise RuntimeError("List indices must be integers") + else: + raise RuntimeError(f"Update ivt_str_to_int() to handle input of type {type(ivt_int)} (if possible)") + + return ivt_str + + +# Does this vegetation type's name match (for a given comparison method) any member of a filtering list? +''' +Methods: + ok_contains: True if any member of this_filter is found in this_vegtype. + notok_contains: True of no member of this_filter is found in this_vegtype. + ok_exact: True if this_vegtype matches any member of this_filter + exactly. + notok_exact: True if this_vegtype does not match any member of + this_filter exactly. +''' +def is_this_vegtype(this_vegtype, this_filter, this_method): + + # Make sure data type of this_vegtype is acceptable + if isinstance(this_vegtype, float) and int(this_vegtype)==this_vegtype: + this_vegtype = int(this_vegtype) + data_type_ok = lambda x: isinstance(x, str) or isinstance(x, int) or isinstance(x, np.int64) + ok_input = True + if not data_type_ok(this_vegtype): + if isinstance(this_vegtype, xr.core.dataarray.DataArray): + this_vegtype = this_vegtype.values + if isinstance(this_vegtype, (list, np.ndarray)): + if len(this_vegtype) == 1 and data_type_ok(this_vegtype[0]): + this_vegtype = this_vegtype[0] + elif data_type_ok(this_vegtype[0]): + raise TypeError("is_this_vegtype(): this_vegtype must be a single string or integer, not a list of them. Did you mean to call is_each_vegtype() instead?") + else: + ok_input = False + else: + ok_input = False + if not ok_input: + raise TypeError(f"is_this_vegtype(): First argument (this_vegtype) must be a string or integer, not {type(this_vegtype)}") + + # Make sure data type of this_filter is acceptable + if not np.iterable(this_filter): + raise TypeError(f"is_this_vegtype(): Second argument (this_filter) must be iterable (e.g., a list), not {type(this_filter)}") + + # Perform the comparison + if this_method == "ok_contains": + return any(n in this_vegtype for n in this_filter) + elif this_method == "notok_contains": + return not any(n in this_vegtype for n in this_filter) + elif this_method == "ok_exact": + return any(n == this_vegtype for n in this_filter) + elif this_method == "notok_exact": + return not any(n == this_vegtype for n in this_filter) + else: + raise ValueError(f"Unknown comparison method: '{this_method}'") + + +# Get boolean list of whether each vegetation type in list is a managed crop +''' + this_vegtypelist: The list of vegetation types whose members you want to + test. + this_filter: The list of strings against which you want to compare + each member of this_vegtypelist. + this_method: How you want to do the comparison. See is_this_vegtype(). +''' +def is_each_vegtype(this_vegtypelist, this_filter, this_method): + + if isinstance(this_vegtypelist, xr.DataArray): + this_vegtypelist = this_vegtypelist.values + + return [is_this_vegtype(x, this_filter, this_method) for x in this_vegtypelist] + +# Helper function to check that a list is strictly increasing +def is_strictly_increasing(L): + # https://stackoverflow.com/a/4983359/2965321 + return all(x 180): + msg = f"Maximum longitude is already > 180 ({np.max(tmp)})" + elif np.any(tmp < -180): + msg = f"Minimum longitude is < -180 ({np.min(tmp)})" + + if msg == "": + return True + elif fail_silently: + return False + else: + raise ValueError(msg) + + def do_it(tmp): + tmp = tmp + 360 + tmp = np.mod(tmp, 360) + return tmp + + if isinstance(lons_in, (xr.DataArray, xr.Dataset)): + if not check_ok(lons_in.lon.values, fail_silently): + return lons_in + lons_out = lons_in + lons_out = lons_out.assign_coords(lon=do_it(lons_in.lon.values)) + lons_out = make_lon_increasing(lons_out) + else: + if not check_ok(lons_in, fail_silently): + return lons_in + lons_out = do_it(lons_in) + if not is_strictly_increasing(lons_out): + print("WARNING: You passed in numeric longitudes to lon_idl2pm() and these have been converted, but they're not strictly increasing.") + print("To assign the new longitude coordinates to an Xarray object, use xarrayobject.assign_coordinates()! (Pass the object directly in to lon_idl2pm() in order to suppress this message.)") + + return lons_out + + +# Convert a longitude axis that's 0 to 360 around the prime meridian to one that's -180 to 180 around the international date line. If you pass in a Dataset or DataArray, the "lon" coordinates will be changed and the axis and data rolled---i.e., maps will be centered on the prime meridian, plus or minus any offset of your gridcell centers. Otherwise, this assumes you're passing in numeric data, and no rolling takes place. +def lon_pm2idl(lons_in, fail_silently = False): + def check_ok(tmp, fail_silently): + msg = "" + if np.any(tmp < 0): + msg = f"Minimum longitude is already < 0 ({np.min(tmp)})" + elif np.any(tmp > 360): + msg = f"Maximum longitude is > 360 ({np.max(tmp)})" + + if msg == "": + return True + elif fail_silently: + return False + else: + raise ValueError(msg) + + def do_it(tmp): + tmp = np.mod((tmp + 180),360)-180 + return tmp + + if isinstance(lons_in, (xr.DataArray, xr.Dataset)): + if not check_ok(lons_in.lon.values, fail_silently): + return lons_in + lons_out = lons_in + lons_out = lons_out.assign_coords(lon=do_it(lons_in.lon.values)) + lons_out = make_lon_increasing(lons_out) + else: + if not check_ok(lons_in, fail_silently): + return lons_in + lons_out = do_it(lons_in) + if not is_strictly_increasing(lons_out): + print("WARNING: You passed in numeric longitudes to lon_pm2idl() and these have been converted, but they're not strictly increasing.") + print("To assign the new longitude coordinates to an Xarray object, use xarrayobject.assign_coordinates()! (Pass the object directly in to lon_pm2idl() in order to suppress this message.)") + + return lons_out + + +# List (strings) of managed crops in CLM. +def define_mgdcrop_list(): + notcrop_list = ["tree", "grass", "shrub", "unmanaged", "not_vegetated"] + defined_pftlist = define_pftlist() + is_crop = is_each_vegtype(defined_pftlist, notcrop_list, "notok_contains") + return [defined_pftlist[i] for i, x in enumerate(is_crop) if x] + + +# Convert list of vegtype strings to integer index equivalents. +def vegtype_str2int(vegtype_str, vegtype_mainlist=None): + + convert_to_ndarray = not isinstance(vegtype_str, np.ndarray) + if convert_to_ndarray: + vegtype_str = np.array(vegtype_str) + + if isinstance(vegtype_mainlist, xr.Dataset): + vegtype_mainlist = vegtype_mainlist.vegtype_str.values + elif isinstance(vegtype_mainlist, xr.DataArray): + vegtype_mainlist = vegtype_mainlist.values + elif vegtype_mainlist == None: + vegtype_mainlist = define_pftlist() + if not isinstance(vegtype_mainlist, list) and isinstance(vegtype_mainlist[0], str): + if isinstance(vegtype_mainlist, list): + raise TypeError(f"Not sure how to handle vegtype_mainlist as list of {type(vegtype_mainlist[0])}") + else: + raise TypeError(f"Not sure how to handle vegtype_mainlist as type {type(vegtype_mainlist[0])}") + + if vegtype_str.shape == (): + indices = np.array([-1]) + else: + indices = np.full(len(vegtype_str), -1) + for v in np.unique(vegtype_str): + indices[np.where(vegtype_str == v)] = vegtype_mainlist.index(v) + if convert_to_ndarray: + indices = [int(x) for x in indices] + return indices + +# Flexibly subset time(s) and/or vegetation type(s) from an xarray Dataset or DataArray. Keyword arguments like dimension=selection. Selections can be individual values or slice()s. Optimize memory usage by beginning keyword argument list with the selections that will result in the largest reduction of object size. Use dimension "vegtype" to extract patches of designated vegetation type (can be string or integer). +# Can also do dimension=function---e.g., time=np.mean will take the mean over the time dimension. +def xr_flexsel(xr_object, patches1d_itype_veg=None, warn_about_seltype_interp=True, **kwargs): + + # Setup + havewarned = False + delimiter = "__" + + for key, selection in kwargs.items(): + + if callable(selection): + # It would have been really nice to do selection(xr_object, axis=key), but numpy methods and xarray methods disagree on "axis" vs. "dimension." So instead, just do this manually. + if selection == np.mean: + try: + xr_object = xr_object.mean(dim=key) + except: + raise ValueError(f"Failed to take mean of dimension {key}. Try doing so outside of xr_flexsel().") + else: + raise ValueError(f"xr_flexsel() doesn't recognize function {selection}") + + elif key == "vegtype": + + # Convert to list, if needed + if not isinstance(selection, list): + selection = [selection] + + # Convert to indices, if needed + if isinstance(selection[0], str): + selection = vegtype_str2int(selection) + + # Get list of boolean(s) + if isinstance(selection[0], int): + if isinstance(patches1d_itype_veg, type(None)): + patches1d_itype_veg = xr_object.patches1d_itype_veg.values + elif isinstance(patches1d_itype_veg, xr.core.dataarray.DataArray): + patches1d_itype_veg = patches1d_itype_veg.values + is_vegtype = is_each_vegtype(patches1d_itype_veg, selection, "ok_exact") + elif isinstance(selection[0], bool): + if len(selection) != len(xr_object.patch): + raise ValueError(f"If providing boolean 'vegtype' argument to xr_flexsel(), it must be the same length as xr_object.patch ({len(selection)} vs. {len(xr_object.patch)})") + is_vegtype = selection + else: + raise TypeError(f"Not sure how to handle 'vegtype' of type {type(selection[0])}") + xr_object = xr_object.isel(patch=[i for i, x in enumerate(is_vegtype) if x]) + if "ivt" in xr_object: + xr_object = xr_object.isel(ivt=is_each_vegtype(xr_object.ivt.values, selection, "ok_exact")) + + else: + + # Parse selection type, if provided + if delimiter in key: + key, selection_type = key.split(delimiter) + + # Check type of selection + else: + + is_inefficient = False + if isinstance(selection, slice): + slice_members = [] + if selection == slice(0): + raise ValueError("slice(0) will be empty") + if selection.start != None: + slice_members = slice_members + [selection.start] + if selection.stop != None: + slice_members = slice_members + [selection.stop] + if selection.step != None: + slice_members = slice_members + [selection.step] + if slice_members==[]: + raise TypeError("slice is all None?") + this_type = int + for x in slice_members: + if x < 0 or not isinstance(x, int): + this_type = "values" + break + elif isinstance(selection, np.ndarray): + if selection.dtype.kind in np.typecodes["AllInteger"]: + this_type = int + else: + is_inefficient = True + this_type = None + for x in selection: + if x < 0 or x%1 > 0: + if isinstance(x, int): + this_type = "values" + else: + this_type = type(x) + break + if this_type==None: + this_type = int + selection = selection.astype(int) + else: + this_type = type(selection) + + warn_about_this_seltype_interp = warn_about_seltype_interp + if this_type == list and isinstance(selection[0], str): + selection_type = "values" + warn_about_this_seltype_interp = False + elif this_type == int: + selection_type = "indices" + else: + selection_type = "values" + + if warn_about_this_seltype_interp: + # Suggest suppressing selection type interpretation warnings + if not havewarned: + print("xr_flexsel(): Suppress all 'selection type interpretation' messages by specifying warn_about_seltype_interp=False") + havewarned = True + if is_inefficient: + extra = " This will also improve efficiency for large selections." + else: + extra = "" + print(f"xr_flexsel(): Selecting {key} as {selection_type} because selection was interpreted as {this_type}. If not correct, specify selection type ('indices' or 'values') in keyword like '{key}{delimiter}SELECTIONTYPE=...' instead of '{key}=...'.{extra}") + + # Trim along relevant 1d axes + if isinstance(xr_object, xr.Dataset) and key in ["lat","lon"]: + if selection_type == "indices": + inclCoords = xr_object[key].values[selection] + elif selection_type == "values": + if isinstance(selection, slice): + inclCoords = xr_object.sel({key: selection}, drop=False)[key].values + else: + inclCoords = selection + else: + raise TypeError(f"selection_type {selection_type} not recognized") + if key == "lat": + thisXY = "jxy" + elif key=="lon": + thisXY = "ixy" + else: + raise KeyError(f"Key '{key}' not recognized: What 1d_ suffix should I use for variable name?") + pattern = re.compile(f"1d_{thisXY}") + matches = [x for x in list(xr_object.keys()) if pattern.search(x) != None] + for thisVar in matches: + if len(xr_object[thisVar].dims) != 1: + raise RuntimeError(f"Expected {thisVar} to have 1 dimension, but it has {len(xr_object[thisVar].dims)}: {xr_object[thisVar].dims}") + thisVar_dim = xr_object[thisVar].dims[0] + # print(f"Variable {thisVar} has dimension {thisVar_dim}") + thisVar_coords = xr_object[key].values[xr_object[thisVar].values.astype(int)-1] + # print(f"{thisVar_dim} size before: {xr_object.sizes[thisVar_dim]}") + ok_ind = [] + new_1d_thisXY = [] + for i, x in enumerate(thisVar_coords): + if x in inclCoords: + ok_ind = ok_ind + [i] + new_1d_thisXY = new_1d_thisXY + [(inclCoords==x).nonzero()[0] + 1] + xr_object = xr_object.isel({thisVar_dim: ok_ind}) + new_1d_thisXY = np.array(new_1d_thisXY).squeeze() + xr_object[thisVar].values = new_1d_thisXY + # print(f"{thisVar_dim} size after: {xr_object.sizes[thisVar_dim]}") + + + # Perform selection + if selection_type == "indices": + # Have to select like this instead of with index directly because otherwise assign_coords() will throw an error. Not sure why. + if isinstance(selection, int): + # Single integer? Turn it into a slice. + selection = slice(selection,selection+1) + elif isinstance(selection, np.ndarray) and not selection.dtype.kind in np.typecodes["AllInteger"]: + selection = selection.astype(int) + xr_object = xr_object.isel({key: selection}) + elif selection_type == "values": + xr_object = xr_object.sel({key: selection}) + else: + raise TypeError(f"selection_type {selection_type} not recognized") + + return xr_object + + +# Get PFT of each patch, in both integer and string forms. +def get_patch_ivts(this_ds, this_pftlist): + # First, get all the integer values; should be time*pft or pft*time. We will eventually just take the first timestep. + vegtype_int = this_ds.patches1d_itype_veg + vegtype_int.values = vegtype_int.values.astype(int) + + # Convert to strings. + vegtype_str = list(np.array(this_pftlist)[vegtype_int.values]) + + # Return a dictionary with both results + return {"int": vegtype_int, "str": vegtype_str, "all_str": this_pftlist} + + +# Convert a list of strings with vegetation type names into a DataArray. Used to add vegetation type info in import_ds(). +def get_vegtype_str_da(vegtype_str): + nvt = len(vegtype_str) + thisName = "vegtype_str" + vegtype_str_da = xr.DataArray(\ + vegtype_str, + coords={"ivt": np.arange(0,nvt)}, + dims=["ivt"], + name = thisName) + return vegtype_str_da + + +# Function to drop unwanted variables in preprocessing of open_mfdataset(), making sure to NOT drop any unspecified variables that will be useful in gridding. Also adds vegetation type info in the form of a DataArray of strings. +# Also renames "pft" dimension (and all like-named variables, e.g., pft1d_itype_veg_str) to be named like "patch". This can later be reversed, for compatibility with other code, using patch2pft(). +def mfdataset_preproc(ds, vars_to_import, vegtypes_to_import, timeSlice): + + # Rename "pft" dimension and variables to "patch", if needed + if "pft" in ds.dims: + pattern = re.compile("pft.*1d") + matches = [x for x in list(ds.keys()) if pattern.search(x) != None] + pft2patch_dict = {"pft": "patch"} + for m in matches: + pft2patch_dict[m] = m.replace("pft","patch").replace("patchs","patches") + ds = ds.rename(pft2patch_dict) + + derived_vars = [] + if vars_to_import != None: + # Split vars_to_import into variables that are vs. aren't already in ds + derived_vars = [v for v in vars_to_import if v not in ds] + present_vars = [v for v in vars_to_import if v in ds] + vars_to_import = present_vars + + # Get list of dimensions present in variables in vars_to_import. + dimList = [] + for thisVar in vars_to_import: + # list(set(x)) returns a list of the unique items in x + dimList = list(set(dimList + list(ds.variables[thisVar].dims))) + + # Get any _1d variables that are associated with those dimensions. These will be useful in gridding. Also, if any dimension is "pft", set up to rename it and all like-named variables to "patch" + onedVars = [] + for thisDim in dimList: + pattern = re.compile(f"{thisDim}.*1d") + matches = [x for x in list(ds.keys()) if pattern.search(x) != None] + onedVars = list(set(onedVars + matches)) + + # Add dimensions and _1d variables to vars_to_import + vars_to_import = list(set(vars_to_import \ + + list(ds.dims) + onedVars)) + + # Add any _bounds variables + bounds_vars = [] + for v in vars_to_import: + bounds_var = v + "_bounds" + if bounds_var in ds: + bounds_vars = bounds_vars + [bounds_var] + vars_to_import = vars_to_import + bounds_vars + + # Get list of variables to drop + varlist = list(ds.variables) + vars_to_drop = list(np.setdiff1d(varlist, vars_to_import)) + + # Drop them + ds = ds.drop_vars(vars_to_drop) + + # Add vegetation type info + if "patches1d_itype_veg" in list(ds): + this_pftlist = define_pftlist() + get_patch_ivts(ds, this_pftlist) # Includes check of whether vegtype changes over time anywhere + vegtype_da = get_vegtype_str_da(this_pftlist) + patches1d_itype_veg_str = vegtype_da.values[ds.isel(time=0).patches1d_itype_veg.values.astype(int)] + npatch = len(patches1d_itype_veg_str) + patches1d_itype_veg_str = xr.DataArray( \ + patches1d_itype_veg_str, + coords={"patch": np.arange(0,npatch)}, + dims=["patch"], + name = "patches1d_itype_veg_str") + ds = xr.merge([ds, vegtype_da, patches1d_itype_veg_str]) + + # Restrict to veg. types of interest, if any + if vegtypes_to_import != None: + ds = xr_flexsel(ds, vegtype=vegtypes_to_import) + + # Restrict to time slice, if any + if timeSlice: + ds = ds.sel(time=timeSlice) + + # Finish import + ds = xr.decode_cf(ds, decode_times = True) + + # Compute derived variables + for v in derived_vars: + if v == "HYEARS" and "HDATES" in ds and ds.HDATES.dims == ('time', 'mxharvests', 'patch'): + yearList = np.array([np.float32(x.year - 1) for x in ds.time.values]) + hyears = ds["HDATES"].copy() + hyears.values = np.tile(np.expand_dims(yearList, (1,2)), (1, ds.dims["mxharvests"], ds.dims["patch"])) + hyears.values[ds.HDATES.values<=0] = ds.HDATES.values[ds.HDATES.values<=0] + hyears.values[np.isnan(ds.HDATES.values)] = np.nan + hyears.attrs["long_name"] = "DERIVED: actual crop harvest years" + hyears.attrs["units"] = "year" + ds["HYEARS"] = hyears + + return ds + + +# Rename "patch" dimension and any associated variables back to "pft". Uses a dictionary with the names of the dimensions and variables we want to rename. This allows us to do it all at once, which may be more efficient than one-by-one. +def patch2pft(xr_object): + + # Rename "patch" dimension + patch2pft_dict = {} + for thisDim in xr_object.dims: + if thisDim == "patch": + patch2pft_dict["patch"] = "pft" + break + + # Rename variables containing "patch" + if isinstance(xr_object, xr.Dataset): + pattern = re.compile("patch.*1d") + matches = [x for x in list(xr_object.keys()) if pattern.search(x) != None] + if len(matches) > 0: + for m in matches: + patch2pft_dict[m] = m.replace("patches","patchs").replace("patch","pft") + + # Do the rename + if len(patch2pft_dict) > 0: + xr_object = xr_object.rename(patch2pft_dict) + + return xr_object + + +# Import a dataset that can be spread over multiple files, only including specified variables and/or vegetation types and/or timesteps, concatenating by time. DOES actually read the dataset into memory, but only AFTER dropping unwanted variables and/or vegetation types. +def import_ds(filelist, myVars=None, myVegtypes=None, timeSlice=None, myVars_missing_ok=[], only_active_patches=False, rename_lsmlatlon=False, chunks=None): + + # Convert myVegtypes here, if needed, to avoid repeating the process each time you read a file in xr.open_mfdataset(). + if myVegtypes != None: + if not isinstance(myVegtypes, list): + myVegtypes = [myVegtypes] + if isinstance(myVegtypes[0], str): + myVegtypes = vegtype_str2int(myVegtypes) + + # Same for these variables. + if myVars != None: + if not isinstance(myVars, list): + myVars = [myVars] + if myVars_missing_ok: + if not isinstance(myVars_missing_ok, list): + myVars_missing_ok = [myVars_missing_ok] + + # Make sure lists are actually lists + if not isinstance(filelist, list): + filelist = [filelist] + if not isinstance(myVars_missing_ok, list): + myVars_missing_ok = [myVars_missing_ok] + + # Remove files from list if they don't contain requested timesteps. + # timeSlice should be in the format slice(start,end[,step]). start or end can be None to be unbounded on one side. Note that the standard slice() documentation suggests that only elements through end-1 will be selected, but that seems not to be the case in the xarray implementation. + if timeSlice: + new_filelist = [] + for file in sorted(filelist): + if xr.open_dataset(file).time.sel(time=timeSlice).size: + new_filelist.append(file) + + # If you found some matching files, but then you find one that doesn't, stop going through the list. + elif new_filelist: + break + if not new_filelist: + raise RuntimeError(f"No files found in timeSlice {timeSlice}") + filelist = new_filelist + + # The xarray open_mfdataset() "preprocess" argument requires a function that takes exactly one variable (an xarray.Dataset object). Wrapping mfdataset_preproc() in this lambda function allows this. Could also just allow mfdataset_preproc() to access myVars and myVegtypes directly, but that's bad practice as it could lead to scoping issues. + mfdataset_preproc_closure = \ + lambda ds: mfdataset_preproc(ds, myVars, myVegtypes, timeSlice) + + # Import + if isinstance(filelist, list): + this_ds = xr.open_mfdataset(sorted(filelist), \ + data_vars="minimal", + preprocess=mfdataset_preproc_closure, + compat='override', + coords='all', + chunks=chunks) + elif isinstance(filelist, str): + this_ds = xr.open_dataset(filelist, chunks=chunks) + this_ds = mfdataset_preproc(this_ds, myVars, myVegtypes, timeSlice) + this_ds = this_ds.compute() + + # Include only active patches (or whatever) + if only_active_patches: + is_active = this_ds.patches1d_active.values + p_active = np.where(is_active)[0] + this_ds_active = this_ds.isel(patch=p_active) + + # Warn and/or error about variables that couldn't be imported or derived + if myVars: + missing_vars = [v for v in myVars if v not in this_ds] + ok_missing_vars = [v for v in missing_vars if v in myVars_missing_ok] + bad_missing_vars = [v for v in missing_vars if v not in myVars_missing_ok] + if ok_missing_vars: + print(f"Could not import some variables; either not present or not deriveable: {ok_missing_vars}") + if bad_missing_vars: + raise RuntimeError(f"Could not import some variables; either not present or not deriveable: {bad_missing_vars}") + + if rename_lsmlatlon: + if "lsmlat" in this_ds.dims: + this_ds = this_ds.rename({'lsmlat': 'lat'}) + if "lsmlon" in this_ds.dims: + this_ds = this_ds.rename({'lsmlon': 'lon'}) + + return this_ds + + +# Return a DataArray, with defined coordinates, for a given variable in a dataset. +def get_thisVar_da(thisVar, this_ds): + + # Make DataArray for this variable + thisvar_da = np.array(this_ds.variables[thisVar]) + theseDims = this_ds.variables[thisVar].dims + thisvar_da = xr.DataArray(thisvar_da, + dims = theseDims) + + # Define coordinates of this variable's DataArray + dimsDict = dict() + for thisDim in theseDims: + dimsDict[thisDim] = this_ds[thisDim] + thisvar_da = thisvar_da.assign_coords(dimsDict) + thisvar_da.attrs = this_ds[thisVar].attrs + + return thisvar_da + + +# Given a DataArray, remove all patches except those planted with managed crops. +def trim_da_to_mgd_crop(thisvar_da, patches1d_itype_veg_str): + + # Handle input DataArray without patch dimension + if not any(np.array(list(thisvar_da.dims)) == "patch"): + print("Input DataArray has no patch dimension and therefore trim_to_mgd_crop() has no effect.") + return thisvar_da + + # Throw error if patches1d_itype_veg_str isn't strings + if isinstance(patches1d_itype_veg_str, xr.DataArray): + patches1d_itype_veg_str = patches1d_itype_veg_str.values + if not isinstance(patches1d_itype_veg_str[0], str): + raise TypeError("Input patches1d_itype_veg_str is not in string form, and therefore trim_to_mgd_crop() cannot work.") + + # Get boolean list of whether each patch is planted with a managed crop + notcrop_list = ["tree", "grass", "shrub", "unmanaged", "not_vegetated"] + is_crop = is_each_vegtype(patches1d_itype_veg_str, notcrop_list, "notok_contains") + + # Warn if no managed crops were found, but still return the empty result + if np.all(np.bitwise_not(is_crop)): + print("No managed crops found! Returning empty DataArray.") + return thisvar_da.isel(patch = [i for i, x in enumerate(is_crop) if x]) + + +# Make a geographically gridded DataArray (with dimensions time, vegetation type [as string], lat, lon) of one variable within a Dataset. Optional keyword arguments will be passed to xr_flexsel() to select single steps or slices along the specified ax(ie)s. +# +# fillValue: Default None means grid will be filled with NaN, unless the variable in question already has a fillValue, in which case that will be used. +def grid_one_variable(this_ds, thisVar, fillValue=None, **kwargs): + + # Get this Dataset's values for selection(s), if provided + this_ds = xr_flexsel(this_ds, \ + **kwargs) + + # Get DataArrays needed for gridding + thisvar_da = get_thisVar_da(thisVar, this_ds) + vt_da = None + if "patch" in thisvar_da.dims: + spatial_unit = "patch" + xy_1d_prefix = "patches" + if "patches1d_itype_veg" in this_ds: + vt_da = get_thisVar_da("patches1d_itype_veg", this_ds) + elif "gridcell" in thisvar_da.dims: + spatial_unit = "gridcell" + xy_1d_prefix = "grid" + else: + raise RuntimeError(f"What variables to use for _ixy and _jxy of variable with dims {thisvar_da.dims}?") + ixy_da = get_thisVar_da(xy_1d_prefix + "1d_ixy", this_ds) + jxy_da = get_thisVar_da(xy_1d_prefix + "1d_jxy", this_ds) + + + if not fillValue and "_FillValue" in thisvar_da.attrs: + fillValue = thisvar_da.attrs["_FillValue"] + + # Renumber vt_da to work as indices on new ivt dimension, if needed. + ### Ensures that the unique set of vt_da values begins with 1 and + ### contains no missing steps. + if "ivt" in this_ds and vt_da is not None: + vt_da.values = np.array([np.where(this_ds.ivt.values == x)[0][0] for x in vt_da.values]) + + # Get new dimension list + new_dims = list(thisvar_da.dims) + ### Remove "[spatial_unit]". + if spatial_unit in new_dims: + new_dims.remove(spatial_unit) + # Add "ivt_str" (vegetation type, as string). This needs to go at the end, to avoid a possible situation where you wind up with multiple Ellipsis members of fill_indices. + if "ivt" in this_ds and spatial_unit=="patch": + new_dims.append("ivt_str") + ### Add lat and lon to end of list + new_dims = new_dims + ["lat", "lon"] + + # Set up empty array + n_list = [] + for dim in new_dims: + if dim == "ivt_str": + n = this_ds.sizes["ivt"] + elif dim in thisvar_da.coords: + n = thisvar_da.sizes[dim] + else: + n = this_ds.sizes[dim] + n_list = n_list + [n] + thisvar_gridded = np.empty(n_list) + if fillValue: + thisvar_gridded[:] = fillValue + else: + thisvar_gridded[:] = np.NaN + + # Fill with this variable + fill_indices = [] + for dim in new_dims: + if dim == "lat": + fill_indices.append(jxy_da.values.astype(int) - 1) + elif dim == "lon": + fill_indices.append(ixy_da.values.astype(int) - 1) + elif dim == "ivt_str": + fill_indices.append(vt_da) + elif not fill_indices: + # I.e., if fill_indices is empty. Could also do "elif len(fill_indices)==0". + fill_indices.append(Ellipsis) + try: + thisvar_gridded[tuple(fill_indices[:len(fill_indices)])] = thisvar_da.values + except: + thisvar_gridded[tuple(fill_indices[:len(fill_indices)])] = thisvar_da.values.transpose() + if not np.any(np.bitwise_not(np.isnan(thisvar_gridded))): + if np.all(np.isnan(thisvar_da.values)): + print('Warning: This DataArray (and thus map) is all NaN') + else: + raise RuntimeError("thisvar_gridded was not filled!") + + # Assign coordinates, attributes and name + thisvar_gridded = xr.DataArray(thisvar_gridded, \ + dims=tuple(new_dims), + attrs=thisvar_da.attrs) + for dim in new_dims: + if dim == "ivt_str": + values = this_ds.vegtype_str.values + elif dim in thisvar_da.coords: + values = thisvar_da[dim] + else: + values = this_ds[dim].values + thisvar_gridded = thisvar_gridded.assign_coords({dim: values}) + thisvar_gridded.name = thisVar + + # Add FillValue attribute + if fillValue: + thisvar_gridded.attrs["_FillValue"] = fillValue + + return thisvar_gridded + + +# Xarray's native resampler is nice, but it will result in ALL variables being resampled +# along the N specified dimension(s). This means that, e.g., variables that were +# supposed to be 1d will be 1+Nd afterwards. This function undoes that. The syntax is the +# same as for Xarray's resampler plus, at the beginning: +# (1) which object you want to resample, and +# (2) the function you want to use for downsampling (e.g., "mean"). +def resample(ds_in, thefunction, **kwargs): + + # This problem is not applicable to DataArrays, so just use Xarray's resampler. + if isinstance(ds_in, xr.DataArray): + da_resampler = ds_in.resample(**kwargs) + da_out = getattr(da_resampler, thefunction)() + return da_out + + # Get the original dimensions of each variable + orig_dims = dict([(x, ds_in[x].dims) for x in ds_in]) + + # Do the Xarray resampling + ds_resampler = ds_in.resample(**kwargs) + ds_out = getattr(ds_resampler, thefunction)() + + for v in ds_out: + + extra_dims = [d for d in ds_out[v].dims if d not in orig_dims[v]] + if not extra_dims: + print(f"Skipping {v}") + continue + + # Xarray's resampler for now only supports resampling along one + # dimension. However, I'm going to try and support a future + # version that supports an arbitrary number of resampled dimensions; + # this is, of course, untested. + + # For any newly-created dimensions, select the first value. Should + # Be the same as all other values. + indexers = dict([(d,0) for d in extra_dims]) + + ds_out[v] = ds_out[v].isel(**indexers, drop=True) + + return ds_out + + +# Have a DataArray that's just for one time point? Repeat it for many. +def tile_over_time(da_in, years=None): + + if "time" not in da_in.dims: + raise RuntimeError('Rework tile_over_time() to function with da_in lacking time dimension.') + + # Deal with Datasets + if isinstance(da_in, xr.Dataset): + new_attrs = {} + for x in da_in.attrs: + if x == "created": + continue + else: + new_attrs[x] = da_in.attrs[x] + ds_out = xr.Dataset(attrs=new_attrs) + for v in da_in: + if 'time' in da_in[v].dims and v != "time_bounds": + ds_out[v] = tile_over_time(da_in[v], years=years) + else: + ds_out[v] = da_in[v].copy() + return ds_out + elif not isinstance(da_in, xr.DataArray): + raise RuntimeError(f'tile_over_time() only works with xarray Datasets and DataArrays, not {type(da_in)}') + + # Get info about time in input DataArray + dt0 = da_in.time.values[0] + dt_type = type(dt0) + has_year_zero = dt0.has_year_zero + + if type(years) != type(None): + new_time = np.array([dt_type(x, dt0.month, dt0.day, has_year_zero=has_year_zero) for x in years]) + strftime_fmt = '%Y-%m-%d' + Ntime = len(years) + else: + raise RuntimeError('Rework tile_over_time to work with something other than years') + + # Convert from cftime to int days since, for compatibility with NETCDF3-CLASSIC format. + new_time_units = 'days since ' + new_time[0].strftime(strftime_fmt) + new_time = cftime.date2num(new_time, new_time_units) + + # Set up time DataArray + new_time_attrs = da_in.time.attrs + new_time_attrs['units'] = new_time_units + new_time_attrs['calendar'] = dt0.calendar + new_time_da = xr.DataArray(new_time, dims=['time'], coords={'time': new_time}, attrs=new_time_attrs) + + # Get coordinates to be used in new DataArray + new_coords = {} + for x in da_in.coords: + if x == "time": + new_coords[x] = new_time_da + else: + new_coords[x] = da_in.coords[x] + + # Set up broadcasting DataArray + new_shape = tuple([da_in.shape[i] if x != "time" else Ntime for i,x in enumerate(da_in.dims)]) + bc_da = xr.DataArray(np.ones(new_shape), dims=da_in.dims, coords=new_coords) + + # Get new DataArray + da_out = (da_in.squeeze() * bc_da).transpose(*da_in.dims) + da_out = da_out.assign_attrs(da_in.attrs) + + return da_out \ No newline at end of file From b1c2c576523b6d4174ba49b925b2c02b299343a1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Apr 2023 16:55:03 -0600 Subject: [PATCH 0787/2067] Added ctsm_py_gallery as an external at python/ctsm_py_gallery. --- .gitignore | 1 + Externals.cfg | 7 +++++++ 2 files changed, 8 insertions(+) diff --git a/.gitignore b/.gitignore index ca701132a7..aec77513f9 100644 --- a/.gitignore +++ b/.gitignore @@ -8,6 +8,7 @@ ccs_config /libraries/ /share/ /doc/doc-builder/ +/python/ctsm_py_gallery/ # ignore svn directories **/.svn/** diff --git a/Externals.cfg b/Externals.cfg index 57d472d8c0..7bd5011b64 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -97,5 +97,12 @@ repo_url = https://github.com/ESMCI/doc-builder tag = v1.0.8 required = False +[ctsm_py_gallery] +local_path = python/ctsm_py_gallery +protocol = git +repo_url = https://github.com/NCAR/ctsm_python_gallery +hash = a664529b0152b215abef697f6beb870ad068edb3 +required = True + [externals_description] schema_version = 1.0.0 From 44246738a18185d28e60ca807467e9dec30567f8 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Mon, 10 Apr 2023 11:58:29 -0600 Subject: [PATCH 0788/2067] update tests --- cime_config/testdefs/testlist_clm.xml | 2 +- cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods | 1 + cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands | 2 ++ 3 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 98d07eb75f..5b7b6dfce4 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1552,7 +1552,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/PRISM/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands b/cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands new file mode 100644 index 0000000000..0b5ec8cff6 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/PRISM/shell_commands @@ -0,0 +1,2 @@ +#!/bin/bash +./xmlchange CLM_USRDAT_NAME=NEON From 7af882a7cd08c1b325cebecd93fb845e1669b76e Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Apr 2023 12:31:59 -0600 Subject: [PATCH 0789/2067] move patch type to its own module --- src/utils/clmfates_interfaceMod.F90 | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index b84f561438..be3a7b8604 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -126,7 +126,7 @@ module CLMFatesInterfaceMod use FatesHistoryInterfaceMod, only : fates_hist use FatesRestartInterfaceMod, only : fates_restart_interface_type - use EDTypesMod , only : ed_patch_type + use FatesPatchMod , only : fates_patch_type use PRTGenericMod , only : num_elements use FatesInterfaceTypesMod, only : hlm_stepsize use FatesInterfaceTypesMod, only : fates_maxPatchesPerSite @@ -837,7 +837,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & type(frictionvel_type) , intent(inout) :: frictionvel_inst ! !LOCAL VARIABLES: - type(ed_patch_type), pointer :: currentPatch + type(fates_patch_type), pointer :: currentPatch integer :: iv, ic integer :: s ! site index integer :: g ! grid-cell index (HLM) @@ -1167,7 +1167,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & integer :: g ! grid cell integer :: ic, ft, iv logical, save :: first_time = .true. - type(ed_patch_type), pointer :: currentPatch + type(fates_patch_type), pointer :: currentPatch real(r8) :: areacheck call t_startf('fates_wrap_update_hlmfates_dyn') @@ -1418,7 +1418,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & integer :: nclumps type(fates_bounds_type) :: fates_bounds type(fates_bounds_type) :: fates_clump - type(ed_patch_type), pointer :: currentPatch + type(fates_patch_type), pointer :: currentPatch integer :: c ! HLM column index integer :: s ! Fates site index integer :: g ! grid-cell index @@ -1928,7 +1928,7 @@ subroutine wrap_sunfrac(this,nc,atm2lnd_inst,canopystate_inst) ! this is the order increment of patch ! on the site - type(ed_patch_type), pointer :: cpatch ! c"urrent" patch INTERF-TODO: SHOULD + type(fates_patch_type), pointer :: cpatch ! c"urrent" patch INTERF-TODO: SHOULD ! BE HIDDEN AS A FATES PRIVATE call t_startf('fates_wrapsunfrac') @@ -2213,7 +2213,8 @@ subroutine wrap_photosynthesis(this, nc, bounds, fn, filterp, & use clm_varctl , only : iulog use PatchType , only : patch use quadraticMod , only : quadratic - use EDtypesMod , only : ed_patch_type, ed_site_type + use EDtypesMod , only : ed_site_type + use FatesPatchMod, only : fates_patch_type use FatesCohortMod , only : fates_cohort_type ! From a98bd88c0ab64b26fd1c06af400e16a2977888de Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 10 Apr 2023 13:52:44 -0600 Subject: [PATCH 0790/2067] make_surface_for_gddgen: paramfile now only needed if using get_new_fsurdat_v1(). --- .../crop_calendars/make_surface_for_gddgen.py | 26 ++++++++++++------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/python/ctsm/crop_calendars/make_surface_for_gddgen.py b/python/ctsm/crop_calendars/make_surface_for_gddgen.py index bfc324eb14..3221038233 100644 --- a/python/ctsm/crop_calendars/make_surface_for_gddgen.py +++ b/python/ctsm/crop_calendars/make_surface_for_gddgen.py @@ -6,7 +6,7 @@ # Doing what I did before with flanduse_timeseries, except now with # fsurdat. -def get_new_fsurdat_v0(surf, lu, params): +def get_new_fsurdat_v0(surf, lu): # Where is each crop ever active? if "AREA" not in lu: @@ -60,6 +60,9 @@ def get_new_fsurdat_v0(surf, lu, params): # CLM currently giving errors about wt_cft not summing to 1. def get_new_fsurdat_v1(surf, lu, params): + if params is None: + raise RuntimeError("You must provide -p/--paramfile") + ########################################## ### %% Get new PCT_CROP and PCT_NATVEG ### ########################################## @@ -128,11 +131,12 @@ def main(argv): help="Land-use timeseries file (flanduse_timeseries) for CLM run", required=True) parser.add_argument("-p", "--paramfile", - help="Parameter file (paramfile) for CLM run", - required=True) + help="Parameter file (paramfile) for CLM run") parser.add_argument("-s", "--fsurdat", help="Surface dataset (fsurdat) for CLM run", required=True) + parser.add_argument("-o", "--outfile", + help="Output fsurdat file") args = parser.parse_args(argv) @@ -142,10 +146,11 @@ def main(argv): lu = xr.open_dataset(args.flanduse_timeseries) surf = xr.open_dataset(args.fsurdat) - params = xr.open_dataset(args.paramfile) + if args.paramfile is not None: + params = xr.open_dataset(args.paramfile) # new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v1(surf, lu, params) - new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v0(surf, lu, params) + new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v0(surf, lu) ############################# @@ -159,12 +164,13 @@ def main(argv): new_surf['PCT_NATVEG'] = new_natveg_da # Save to new file - fsurdat_noext, ext = os.path.splitext(args.fsurdat) - new_fsurdat = f"{fsurdat_noext}.GDDgen{ext}" - new_fsurdat = os.path.basename(new_fsurdat) - new_surf.to_netcdf(new_fsurdat, format="NETCDF3_64BIT") + if outfile is None: + fsurdat_noext, ext = os.path.splitext(args.fsurdat) + outfile = f"{fsurdat_noext}.GDDgen{ext}" + outfile = os.path.basename(outfile) + new_surf.to_netcdf(outfile, format="NETCDF3_64BIT") - print(new_fsurdat) + print(outfile) if __name__ == "__main__": From 324e95d9fbcc622a2f8116301f487201f1c0278b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 10 Apr 2023 13:53:07 -0600 Subject: [PATCH 0791/2067] Added RXCROPMATURITY SystemTest. --- cime_config/SystemTests/rxcropmaturity.py | 214 ++++++++++++++++++++++ 1 file changed, 214 insertions(+) create mode 100644 cime_config/SystemTests/rxcropmaturity.py diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py new file mode 100644 index 0000000000..d7ed048c16 --- /dev/null +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -0,0 +1,214 @@ +""" +CTSM-specific test that first performs a GDD-generating run, then calls +Python code to generate the maturity requirement file. This is then used +in a sowing+maturity forced run, which finally is tested to ensure +correct behavior. +""" + +import os +import re +import subprocess +from CIME.SystemTests.system_tests_common import SystemTestsCommon +from CIME.XML.standard_module_setup import * +from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files + +logger = logging.getLogger(__name__) + +class RXCROPMATURITY(SystemTestsCommon): + + def __init__(self, case): + """ + initialize an object interface to the SMS system test + """ + SystemTestsCommon.__init__(self, case) + + + """ + Set run start and length + """ + + self._case.set_value("RUN_STARTDATE", "1995-01-01") + self._case.set_value("STOP_OPTION", "nyears") + self._case.set_value("STOP_N", 10) + + + """ + Get and set sowing and harvest dates + """ + + # Get sowing and harvest dates for this resolution + lnd_grid = self._case.get_value("LND_GRID") + blessed_crop_dates_dir="/glade/work/samrabin/crop_dates_blessed" + if lnd_grid == "10x15": + self._sdatefile = os.path.join( + blessed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc") + self._hdatefile = os.path.join( + blessed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc") + elif lnd_grid == "1.9x2.5": + self._sdatefile = os.path.join( + blessed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc") + self._hdatefile = os.path.join( + blessed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc") + else: + print("ERROR: RXCROPMATURITY currently only supports 10x15 and 1.9x2.5 resolutions") + raise + if not os.path.exists(self._sdatefile): + print(f"ERROR: Sowing date file not found: {self._sdatefile}") + raise + if not os.path.exists(self._hdatefile): + print(f"ERROR: Harvest date file not found: {self._sdatefile}") + raise + + # Set sowing dates file for run + logger.info(" modify user_nl files: generate GDDs") + self._modify_user_nl_gengdds() + + + """ + If needed, generate a surface dataset file with no crops missing years + """ + + # Create out-of-the-box lnd_in to obtain fsurdat and flanduse_timeseries + case.create_namelists(component='lnd') + + # Is flanduse_timeseries defined? If so, where is it? + lnd_in_path = os.path.join(self._get_caseroot(), 'CaseDocs', 'lnd_in') + self._flanduse_timeseries_in = None + with open (lnd_in_path,'r') as lnd_in: + for line in lnd_in: + flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) + if fsurdat_in: + self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) + break + + # If flanduse_timeseries is defined, we need to make our own version for + # this test (if we haven't already). + if self._flanduse_timeseries_in is not None: + + # Download files from the server + case.check_all_input_data() + + # fsurdat should be defined. Where is it? + self._fsurdat_in = None + with open (lnd_in_path,'r') as lnd_in: + for line in lnd_in: + fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) + if fsurdat_in: + self._fsurdat_in = fsurdat_in.group(1) + break + if self._fsurdat_in is None: + print("fsurdat not defined") + raise + + # Where we will save the fsurdat version for this test + self._fsurdat_out = os.path.join(self._get_caseroot(), 'fsurdat.nc') + + # Make fsurdat for this test, if not already done + if not os.path.exists(self._fsurdat_out): + logger.info(" run make_surface_for_gdden") + self._run_make_surface_for_gdden() + + # Modify namelist + logger.info(" modify user_nl files: new fsurdat") + self._modify_user_nl_newfsurdat() + + + def _run_make_surface_for_gdden(self): + tool_path = os.path.join(self._ctsm_root, + 'python', 'ctsm', 'crop_calendars', + 'make_surface_for_gddgen.py') + + self._case.load_env(reset=True) + conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " + # Preprend the commands to get the conda environment for python first + conda_env += self._get_conda_env() + # Source the env + try: + command = f"{conda_env}python3 {tool_path} "\ + + "--flanduse-timeseries {self._flanduse_timeseries_in} "\ + + "--fsurdat {self._fsurdat_in} "\ + + "--outfile {self._fsurdat_out}" + subprocess.run(command, shell=True, check=True) + except subprocess.CalledProcessError as error: + print("ERROR while getting the conda environment and/or ") + print("running the fsurdat_modifier tool: ") + print("(1) If your ctsm_pylib environment is out of date or you ") + print("have not created the ctsm_pylib environment, yet, you may ") + print("get past this error by running ./py_env_create ") + print("in your ctsm directory and trying this test again. ") + print("(2) If conda is not available, install and load conda, ") + print("run ./py_env_create, and then try this test again. ") + print("(3) If (1) and (2) are not the issue, then you may be ") + print("getting an error within the fsurdat_modifier tool itself. ") + print("Default error message: ") + print(error.output) + raise + except: + print("ERROR trying to run fsurdat_modifier tool.") + raise + + def _modify_user_nl_gengdds(self): + nl_additions = [ + "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")), + "stream_fldFileName_sdate = '{}'".format(self._sdatefile), + "generate_crop_gdds = .true.", + "use_mxmat = .false.", + "stream_year_first_cropcal = 2000", + "stream_year_last_cropcal = 2000", + "model_year_align_cropcal = 2000", + " ", + "! (h1) Daily outputs for GDD generation and figure-making", + "hist_fincl2 = 'HUI', 'GDDACCUM', 'GDDHARV'", + "hist_nhtfrq(2) = -24", + "hist_mfilt(2) = 365", + "hist_type1d_pertape(2) = 'PFTS'", + "hist_dov2xy(2) = .false.", + " ", + "! (h2) Annual outputs for GDD generation (checks)", + "hist_fincl3 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", + "hist_nhtfrq(3) = 17520", + "hist_mfilt(3) = 999", + "hist_type1d_pertape(3) = 'PFTS'", + "hist_dov2xy(3) = .false.", + ] + for addition in nl_additions: + append_to_user_nl_files(caseroot = self._get_caseroot(), + component = "clm", + contents = addition) + + def _modify_user_nl_newfsurdat(self): + nl_additions = [ + "fsurdat = '{}'".format(self._fsurdat_out), + "do_transient_crops = .false.", + "flanduse_timeseries = ''", + "use_init_interp = .true.", + ] + for addition in nl_additions: + append_to_user_nl_files(caseroot = self._get_caseroot(), + component = "clm", + contents = addition) + + def _get_conda_env(self): + # + # Add specific commands needed on different machines to get conda available + # Use semicolon here since it's OK to fail + # + # Execute the module unload/load when "which conda" fails + # eg on cheyenne + try: + subprocess.run( "which conda", shell=True, check=True) + conda_env = " " + except subprocess.CalledProcessError: + # Remove python and add conda to environment for cheyennne + conda_env = "module unload python; module load conda;" + + # Activate the python environment + conda_env += " conda activate ctsm_pylib" + # End above to get to actual command + conda_env += " && " + + return( conda_env ) From 35979b6aee0791300bcdcbeeedb1b9072efaadcc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 10 Apr 2023 14:01:19 -0600 Subject: [PATCH 0792/2067] Added RXCROPMATURITY to config_tests.xml. --- cime_config/config_tests.xml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index 0307ee7ef5..536f79aeec 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -113,6 +113,16 @@ This defines various CTSM-specific system tests $STOP_N + + Generate prescribed maturity requirements, then test with them + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + + + Generate prescribed maturity requirements, then test with them + 1 + FALSE + FALSE + never + $STOP_OPTION + $STOP_N + + hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10 +>hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. From 95934832d6c926f3b87301779f895ab527a60e9e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 7 May 2023 16:48:48 -0600 Subject: [PATCH 0883/2067] Use_crop attribute not needed for mpasa 1850 surface datasets as crop datasets are used for both SP, BGC, and crop cases --- bld/namelist_files/namelist_defaults_ctsm.xml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 7a2a89adf2..2d028e1ee0 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1177,17 +1177,17 @@ lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_16pfts_Irrig_CMIP6_s lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_4x5_hist_16pfts_Irrig_CMIP6_simyr1850_c190214.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa480_hist_78pfts_CMIP6_simyr1850_c211110.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa240_hist_78pfts_CMIP6_simyr1850_c211115.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa120_hist_78pfts_CMIP6_simyr1850_c211108.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa60_hist_78pfts_CMIP6_simyr1850_c211110.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa30_hist_78pfts_CMIP6_simyr1850_c211111.nc - + lnd/clm2/surfdata_map/ctsm5.1.dev052/surfdata_mpasa15_hist_78pfts_CMIP6_simyr1850_c211111.nc From 7001b8f6ca296d1d55aca97cb453602a1477d122 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 7 May 2023 17:35:48 -0600 Subject: [PATCH 0884/2067] Move directory for dynGrossUnrepMod resolving #1969 --- src/{biogeochem => dyn_subgrid}/dynGrossUnrepMod.F90 | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/{biogeochem => dyn_subgrid}/dynGrossUnrepMod.F90 (100%) diff --git a/src/biogeochem/dynGrossUnrepMod.F90 b/src/dyn_subgrid/dynGrossUnrepMod.F90 similarity index 100% rename from src/biogeochem/dynGrossUnrepMod.F90 rename to src/dyn_subgrid/dynGrossUnrepMod.F90 From 514a3b979c2b843aa0221e74c8d37677fa89701f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 7 May 2023 19:14:54 -0600 Subject: [PATCH 0885/2067] Add reminder to make new surface datasets for the new resolutions here --- tools/mksurfdata_map/Makefile.data | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/mksurfdata_map/Makefile.data b/tools/mksurfdata_map/Makefile.data index c1df608436..904aec8d7d 100644 --- a/tools/mksurfdata_map/Makefile.data +++ b/tools/mksurfdata_map/Makefile.data @@ -81,7 +81,7 @@ SUBSETDATA_1X1_URBALPHA := --lat -37.7308 --lon 0 --site 1x1_urbanc_alpha --o # The ne30np4 series (including pg2, pg3, pg4) are standard for SE dycore # The variable resolution grids for ARCTIC, ARCTICGRIS and CONUS are also standard STANDARD_RES_NO_CROP = 0.9x1.25,1.9x2.5,10x15 -STANDARD_RES = 0.9x1.25,1.9x2.5,10x15,4x5,ne30np4,C96,ne30pg2,ne30pg3,ne30pg4,ne120np4pg3,ne0np4ARCTICGRISne30x8,ne0np4ARCTICne30x4,ne0np4CONUSne30x8 +STANDARD_RES = 0.9x1.25,1.9x2.5,10x15,4x5,ne30np4,C96,ne30pg2,ne30pg3,ne30pg4,ne120np4pg3,ne0np4ARCTICGRISne30x8,ne0np4ARCTICne30x4,ne0np4CONUSne30x8,ne3np4.pg3,ne5np4.pg3,ne16np4.pg3 # For future CMIP6 scenarios: SSP-RCP's FUTURE_RES = 0.9x1.25,1.9x2.5,10x15 From f6881492ad476e27c112ac5b68cd809e3a0c76c1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 7 May 2023 20:43:08 -0600 Subject: [PATCH 0886/2067] Use the f09 finidat file rather than ne120 for these new low resolution grids --- bld/namelist_files/namelist_defaults_ctsm.xml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2e6714b366..7ff5750e5b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -758,11 +758,26 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. From cae251a0e21eb8521e473bb53b222bd87b7112e4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 8 May 2023 12:14:24 -0600 Subject: [PATCH 0887/2067] Need to have CLM version match the lnd_tuning version --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 2d1aafb728..b3c43df8f6 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1414,7 +1414,7 @@ - + From 08c58c305b16b9abca12a58a370589739dd08042 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 8 May 2023 17:01:49 -0600 Subject: [PATCH 0888/2067] Removed force_harvest. --- src/biogeochem/CNPhenologyMod.F90 | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d4b90c843e..63fc135a2f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1783,7 +1783,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical did_plant ! did we plant the crop in this time step? logical allow_unprescribed_planting ! should crop be allowed to be planted according to sowing window rules? logical do_harvest ! Are harvest conditions satisfied? - logical force_harvest ! Should we harvest today no matter what? logical fake_harvest ! Dealing with incorrect Dec. 31 planting logical did_plant_prescribed_today ! Was the crop sown today? logical will_plant_prescribed_tomorrow ! Is tomorrow a prescribed sowing day? @@ -2138,7 +2137,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & endif do_harvest = .false. - force_harvest = .false. fake_harvest = .false. did_plant_prescribed_today = .false. if (use_cropcal_rx_sdates .and. sowing_count(p) > 0) then @@ -2154,13 +2152,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (jday == 1 .and. croplive(p) .and. idop(p) == 1 .and. sowing_count(p) == 0) then ! BACKWARDS_COMPATIBILITY(ssr, 2022-02-03): To get rid of crops incorrectly planted in last time step of Dec. 31. That was fixed in commit dadbc62 ("Call CropPhenology regardless of doalb"), but this handles restart files with the old behavior. fake_harvest ensures that outputs aren't polluted. do_harvest = .true. - force_harvest = .true. fake_harvest = .true. harvest_reason = HARVEST_REASON_SOWNBADDEC31 else if (do_plant .and. .not. did_plant) then ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. - force_harvest = .true. harvest_reason = HARVEST_REASON_SOWTODAY ! If generate_crop_gdds and this patch has prescribed sowing inputs @@ -2234,10 +2230,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_reason = HARVEST_REASON_MAXSEASLENGTH else if (will_plant_prescribed_tomorrow) then harvest_reason = HARVEST_REASON_SOWTOMORROW - force_harvest = .true. end if endif - force_harvest = force_harvest .or. (generate_crop_gdds .and. do_harvest) ! The following conditionals are similar to those in CropPhase. However, they ! differ slightly because here we are potentially setting a new crop phase, @@ -2245,7 +2239,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! phase. However, despite these differences: if you make changes to the ! following conditionals, you should also check to see if you should make ! similar changes in CropPhase. - if ((.not. force_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then + if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then cphase(p) = cphase_leafemerge if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 From 18ac79080a0ee315c8e960f594fa16c771d1e90b Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Mon, 8 May 2023 17:35:40 -0600 Subject: [PATCH 0889/2067] Fix nuopc cplhist test Make some changes to the cplhist testmod that should fix the cplhist test, based on testing done by Keith Oleson: - Point to new cplhist forcing data generated and used by Adam Herrington and Keith Oleson - Use DATM_PRESNDEP=none until https://github.com/escomp/ctsm/issues/1844 is resolved Also, remove mct cplhist test --- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- cime_config/testdefs/testlist_clm.xml | 11 +--------- .../testmods_dirs/clm/cplhist/shell_commands | 20 ++++++++----------- 3 files changed, 9 insertions(+), 29 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index d9a1c1b6fd..24f7062798 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -44,13 +44,6 @@ - - - FAIL - #1844 - - - diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 38125d80bc..475d5db97d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1306,7 +1306,7 @@ - + @@ -1315,15 +1315,6 @@ - - - - - - - - - diff --git a/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands index ac079d5334..a284aefcb9 100755 --- a/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands @@ -1,12 +1,8 @@ -driver=`./xmlquery --value COMP_INTERFACE` -if [ "$driver" = "nuopc" ]; then - ./xmlchange DATM_YR_ALIGN=1 - ./xmlchange DATM_YR_END=84 - ./xmlchange DATM_YR_START=82 -else - ./xmlchange DATM_CPLHIST_YR_ALIGN=1 - ./xmlchange DATM_CPLHIST_YR_END=84 - ./xmlchange DATM_CPLHIST_YR_START=82 -fi -./xmlchange DATM_CPLHIST_CASE=b.e20.B1850.f09_g17.pi_control.all.221.cplhist -./xmlchange DATM_CPLHIST_DIR=/glade/p/cesm/bgcwg_dev/forcing/b.e20.B1850.f09_g17.pi_control.all.221.cplhist/cpl/hist.mon +./xmlchange DATM_CPLHIST_CASE=cam6ctsm51_cesm23a12c_ne30pg3g17_CPLHIST_1850 +./xmlchange DATM_CPLHIST_DIR=/glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.cdeps_datm.CPLHIST_cam6ctsm51_cesm23a12c_ne30pg3g17_1850 +./xmlchange DATM_YR_START=1 +./xmlchange DATM_YR_END=1 +./xmlchange DATM_YR_ALIGN=1 + +# Needed until we have cplhist forcing with ndep - see https://github.com/escomp/ctsm/issues/1844 +./xmlchange DATM_PRESNDEP=none From 53ce361f0e6da787185984dd23d859c5f6b4c574 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 9 May 2023 10:36:21 -0600 Subject: [PATCH 0890/2067] Update cdeps version to one working --- Externals.cfg | 2 +- doc/ChangeLog | 171 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 3 files changed, 173 insertions(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 9f6b4596fb..3b2e66164b 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -55,7 +55,7 @@ local_path = components/cmeps required = True [cdeps] -tag = cdeps1.0.11 +tag = cdeps1.0.12 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps diff --git a/doc/ChangeLog b/doc/ChangeLog index aa4f7055c4..a70837d7f8 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,175 @@ =============================================================== +Tag name: ctsm5.1.dev124 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Tue May 9 01:47:18 MDT 2023 +One-line Summary: Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data + +Purpose and description of changes +---------------------------------- + +[Fill this in with details] + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +CTSM issues fixed (include CTSM Issue #): + +Externals issues fixed (include issue #): + +Known bugs introduced in this tag (include issue #): + +Known bugs found since the previous tag (include issue #): + + +Notes of particular relevance for users +--------------------------------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: +[e.g., check PFS test in the test suite and look at timings, if you +expect possible significant timing changes] + + +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + + +Testing summary: +---------------- +[... Remove before making master tag. + +Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. +However, it occasionally makes sense to do more or less system testing; +here is guidance on different available levels of system testing: + a) no system testing (for use when the only changes are ones that + have absolutely no impact on system runs; this + includes documentation-only tags, tags that + just change the tools or some python code that + does not impact system runs, etc.) + b) minimal (for use in rare cases where only a small change with + known behavior is added ... eg. a minor bug fix. This + might be to just run the "short" test list, or to run + a single test. Whatever makes sense for the particular case.) + c) python only (for use where the only changes are in the python directory: + run the python testing listed below) + d) regular (regular tests on normal machines if CTSM source is modified) + e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists + and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) + would be run as well) + +In addition, various other tests of the tools, python and perl +infrastructure should be run when appropriate, as described below. + +...] + +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] + + Summarize any changes to answers, i.e., + - what code configurations: + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + If bitwise differences were observed, how did you show they were no worse + than roundoff? + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: + + URL for LMWG diagnostics output used to validate new climate: + + +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev123 Originator(s): sacks (Bill Sacks) Date: Mon May 1 11:37:51 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 4aea4f599a..c73ffb1b64 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev124 erik 05/09/2023 Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data ctsm5.1.dev123 sacks 05/01/2023 Updates needed for pFUnit 4 and other externals updates ctsm5.1.dev122 sacks 04/23/2023 Rework handling of evaporation constraint in SoilFluxes ctsm5.1.dev121 glemieux 04/05/2023 Changes soil moisture initialization logic for FATES From 08094df364b18059dd5e346a3660076d47cf9be7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 9 May 2023 11:16:58 -0600 Subject: [PATCH 0891/2067] Izumi tests need to be with DEBUG on --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index b3c43df8f6..59e7be0d92 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1609,7 +1609,7 @@ - + From 9d65648374d174d2d6f6be7bd4e6f48a6f01576b Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:36:33 -0600 Subject: [PATCH 0892/2067] add back missing Cmakelist file --- src/biogeophys/CMakeLists.txt | 54 +++++++++++++++++++++++++++++++++-- 1 file changed, 51 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/CMakeLists.txt b/src/biogeophys/CMakeLists.txt index a4252bcabf..3cf5e0eaf0 100644 --- a/src/biogeophys/CMakeLists.txt +++ b/src/biogeophys/CMakeLists.txt @@ -1,5 +1,53 @@ -list(APPEND fates_sources - FatesHydroWTFMod.F90 +# Note that this is just used for unit testing; hence, we only need to add +# source files that are currently used in unit tests + +list(APPEND clm_sources + AerosolMod.F90 + DaylengthMod.F90 + BalanceCheckMod.F90 + CanopyStateType.F90 + EnergyFluxType.F90 + GlacierSurfaceMassBalanceMod.F90 + HumanIndexMod.F90 + InfiltrationExcessRunoffMod.F90 + IrrigationMod.F90 + LakeCon.F90 + LakeStateType.F90 + QSatMod.F90 + RootBiophysMod.F90 + SaturatedExcessRunoffMod.F90 + SnowCoverFractionBaseMod.F90 + SnowHydrologyMod.F90 + SnowSnicarMod.F90 + SoilHydrologyMod.F90 + SoilHydrologyType.F90 + SoilStateType.F90 + SoilWaterRetentionCurveMod.F90 + SolarAbsorbedType.F90 + PhotosynthesisMod.F90 + SurfaceAlbedoType.F90 + OzoneBaseMod.F90 + TemperatureType.F90 + TotalWaterAndHeatMod.F90 + UrbanParamsType.F90 + Wateratm2lndBulkType.F90 + Wateratm2lndType.F90 + WaterBalanceType.F90 + WaterDiagnosticBulkType.F90 + WaterDiagnosticType.F90 + WaterFluxType.F90 + WaterFluxBulkType.F90 + Waterlnd2atmBulkType.F90 + Waterlnd2atmType.F90 + WaterInfoBaseType.F90 + WaterInfoBulkType.F90 + WaterInfoIsotopeType.F90 + WaterInfoTracerType.F90 + WaterStateBulkType.F90 + WaterStateType.F90 + WaterTracerContainerType.F90 + WaterTracerUtils.F90 + WaterType.F90 ) -sourcelist_to_parent(fates_sources) \ No newline at end of file +sourcelist_to_parent(clm_sources) From abbe133d7b5209fc651307b89f5ad7a01a9d5ee5 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:37:34 -0600 Subject: [PATCH 0893/2067] update cmakelist --- src/main/CMakeLists.txt | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt index 1c31aa68bd..7f1eed15ad 100644 --- a/src/main/CMakeLists.txt +++ b/src/main/CMakeLists.txt @@ -34,9 +34,4 @@ list(APPEND clm_sources surfrdUtilsMod.F90 ) -list (APPEND fates_sources - clm_varctl.F90 - ) - -sourcelist_to_parent(clm_sources) -sourcelist_to_parent(fates_sources) \ No newline at end of file +sourcelist_to_parent(clm_sources) \ No newline at end of file From dec0cd627f1d88bcf7592c2c1635563622899fce Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:40:20 -0600 Subject: [PATCH 0894/2067] get rid of whitespace --- src/utils/CMakeLists.txt | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt index 89fc831901..c29cdb829c 100644 --- a/src/utils/CMakeLists.txt +++ b/src/utils/CMakeLists.txt @@ -24,5 +24,4 @@ list(APPEND clm_sources NumericsMod.F90 ) -sourcelist_to_parent(clm_sources) - +sourcelist_to_parent(clm_sources) \ No newline at end of file From 363cdf8a1bad72ba9917422c2357e414f8139779 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:43:39 -0600 Subject: [PATCH 0895/2067] remove old printing statements --- src/utils/clmfates_interfaceMod.F90 | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 6cb81a074e..f803c0e4ad 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -848,11 +848,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & integer :: nlevsoil ! number of soil layers at the site integer :: nld_si ! site specific number of decomposition layers integer :: ft ! plant functional type - integer ::& - yr, &! year - mon, &! month - day, &! day of month - tod ! time of day (seconds past 0Z) real(r8), pointer :: lnfm24(:) ! 24-hour averaged lightning data real(r8), pointer :: gdp_lf_col(:) ! gdp data integer :: ier @@ -1040,30 +1035,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call ed_update_site(this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & this%fates(nc)%bc_out(s)) - - call get_curr_date(yr, mon, day, tod) - if (yr == 2020 .and. mon == 6 .and. day == 1) then - currentpatch => this%fates(nc)%sites(s)%youngest_patch - do while(associated(currentpatch)) - write(fates_log(),*) 'can area is ', currentpatch%total_canopy_area - write(fates_log(),*) '-------------------------------------------------------' - do ic = 1, 2 - do ft = 1, 16 - do iv = 1, 30 - write(fates_log(),*) 'can area prof is ', currentpatch%canopy_area_profile(ic,ft,iv), ic, ft, iv - write(fates_log(),*) 'elai prof is ', currentpatch%elai_profile(ic,ft,iv), ic, ft, iv - write(fates_log(),*) 'esai area prof is ', currentpatch%esai_profile(ic,ft,iv), ic, ft, iv - end do - write(fates_log(),*) '-------------------------------------------------------' - write(fates_log(),*) 'nrad prof is ', currentpatch%nrad(ic,ft), ic, ft - write(fates_log(),*) '-------------------------------------------------------' - end do - end do - currentPatch => currentpatch%older - enddo - first_time = .false. - end if - enddo ! --------------------------------------------------------------------------------- From a194f85cf9dbee4f267a65942a0142e1be834d73 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:44:55 -0600 Subject: [PATCH 0896/2067] remove old variable --- src/utils/clmfates_interfaceMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index f803c0e4ad..e2da781de5 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1138,7 +1138,6 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & integer :: c ! column index integer :: g ! grid cell integer :: ic, ft, iv - logical, save :: first_time = .true. type(fates_patch_type), pointer :: currentPatch real(r8) :: areacheck From 3953f44b10d48cfed0e2a311e4cdb496a31eb140 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:46:51 -0600 Subject: [PATCH 0897/2067] remove unused variable --- src/utils/clmfates_interfaceMod.F90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index e2da781de5..d6712be941 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -854,7 +854,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & integer :: begg,endg real(r8) :: harvest_rates(bounds_clump%begg:bounds_clump%endg,num_harvest_inst) logical :: after_start_of_harvest_ts - logical, save :: first_time = .true. integer :: iharv !----------------------------------------------------------------------- @@ -1405,7 +1404,6 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & logical, save :: initialized = .false. - logical, save :: first_time = .true. call t_startf('fates_restart') From 29cc0753e99f040b144308a1b4538d2bee2bbd43 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:53:03 -0600 Subject: [PATCH 0898/2067] update utils cmakelist --- src/utils/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt index c29cdb829c..04ad683517 100644 --- a/src/utils/CMakeLists.txt +++ b/src/utils/CMakeLists.txt @@ -24,4 +24,4 @@ list(APPEND clm_sources NumericsMod.F90 ) -sourcelist_to_parent(clm_sources) \ No newline at end of file +sourcelist_to_parent(clm_sources) From 3386bfa961a27c4229245798867e5f7f9d766184 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 9 May 2023 11:58:27 -0600 Subject: [PATCH 0899/2067] remove unused variables --- src/main/CMakeLists.txt | 2 +- src/utils/clmfates_interfaceMod.F90 | 14 -------------- 2 files changed, 1 insertion(+), 15 deletions(-) diff --git a/src/main/CMakeLists.txt b/src/main/CMakeLists.txt index 7f1eed15ad..53a6edb8a5 100644 --- a/src/main/CMakeLists.txt +++ b/src/main/CMakeLists.txt @@ -34,4 +34,4 @@ list(APPEND clm_sources surfrdUtilsMod.F90 ) -sourcelist_to_parent(clm_sources) \ No newline at end of file +sourcelist_to_parent(clm_sources) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index d6712be941..33e38107f0 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -33,7 +33,6 @@ module CLMFatesInterfaceMod ! Used CLM Modules #include "shr_assert.h" -use FatesGlobals , only : fates_log use PatchType , only : patch use shr_kind_mod , only : r8 => shr_kind_r8 use decompMod , only : bounds_type, subgrid_level_column @@ -47,7 +46,6 @@ module CLMFatesInterfaceMod use EnergyFluxType , only : energyflux_type use SoilStateType , only : soilstate_type use CNProductsMod , only : cn_products_type - use clm_varctl , only : paramfile, fates_paramfile use clm_varctl , only : iulog use clm_varctl , only : fates_parteh_mode use clm_varctl , only : use_fates @@ -838,8 +836,6 @@ subroutine dynamics_driv(this, nc, bounds_clump, & type(frictionvel_type) , intent(inout) :: frictionvel_inst ! !LOCAL VARIABLES: - type(fates_patch_type), pointer :: currentPatch - integer :: iv, ic integer :: s ! site index integer :: g ! grid-cell index (HLM) integer :: c ! column index (HLM) @@ -1129,15 +1125,12 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! is this being called during a read from restart sequence (if so then use the restarted fates ! snow depth variable rather than the CLM variable). logical , intent(in) :: is_initing_from_restart - integer :: npatch ! number of patches in each site integer :: ifp ! index FATES patch integer :: p ! HLM patch index integer :: s ! site index integer :: c ! column index integer :: g ! grid cell - integer :: ic, ft, iv - type(fates_patch_type), pointer :: currentPatch real(r8) :: areacheck call t_startf('fates_wrap_update_hlmfates_dyn') @@ -1181,9 +1174,6 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & this%f2hmap(nc)%fcolumn, & this%fates(nc)%bc_out ) - - - !------------------------------------------------------------------------ ! FATES calculation of ligninNratio !------------------------------------------------------------------------ @@ -1388,21 +1378,17 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & integer :: nclumps type(fates_bounds_type) :: fates_bounds type(fates_bounds_type) :: fates_clump - type(fates_patch_type), pointer :: currentPatch integer :: c ! HLM column index integer :: s ! Fates site index integer :: g ! grid-cell index integer :: p ! HLM patch index integer :: ft ! plant functional type - integer :: ic, iv integer :: dk_index integer :: nlevsoil character(len=fates_long_string_length) :: ioname integer :: nvar integer :: ivar logical :: readvar - - logical, save :: initialized = .false. call t_startf('fates_restart') From 70d408f5bb97216ffdd64e563515318cf72ebc78 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 9 May 2023 14:02:54 -0600 Subject: [PATCH 0900/2067] update to latest ccsconfig --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 888b7e1079..6aaf6c3d9c 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_cesm0.0.64 +tag = ccs_config_cesm0.0.65 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config From 7a74dc4d07a98c9f78e7d2ac86235a500f3cba3b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 9 May 2023 15:06:42 -0600 Subject: [PATCH 0901/2067] RXCROPMATURITY: Add daily per-PFT CPHASE output to Prescribed Calendars run. (cherry picked from commit cc3c6cab9d37c34c4c5f7ec1e5cb3a3cf2e0ccc3) --- cime_config/SystemTests/rxcropmaturity.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 74bb908cbd..6349bcd98d 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -157,7 +157,17 @@ def run_phase(self): "generate_crop_gdds = .false.", f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", ]) - + + # Add extra stuff to help diagnose diffs + self._append_to_user_nl_clm([ + "! (h3) Daily PFT-level outputs to help diagnose diffs", + "hist_fincl4 = 'CPHASE'", + "hist_nhtfrq(4) = -24", + "hist_mfilt(4) = 1", + "hist_type1d_pertape(4) = 'PFTS'", + "hist_dov2xy(4) = .false.", + ]) + self.run_indv() #------------------------------------------------------------------- From 5d3314b9dfc3837325639d6bb558494962f17078 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 9 May 2023 16:52:19 -0600 Subject: [PATCH 0902/2067] Update changelog --- doc/ChangeLog | 164 ++++++++++++++++++++++---------------------------- 1 file changed, 72 insertions(+), 92 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index a70837d7f8..e82ff156bb 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,13 +1,51 @@ =============================================================== Tag name: ctsm5.1.dev124 -Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Tue May 9 01:47:18 MDT 2023 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) / mvertens / adamrher / MiCurry / jtrusdal / TeaganKing +Date: Tue May 9 16:52:05 MDT 2023 One-line Summary: Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data Purpose and description of changes ---------------------------------- -[Fill this in with details] +Lower memory usage at initialization: + + Some work by Mariana Vertenstein to lower the memory usage at initiatlization. + +New Low Resolutions for SE grids: + + ne3np4.pg3, ne5np4.pg3, ne16np4.pg3 + +New MPASA Resolutions: + + mpasa480 --------- Course resolution + mpasa120 --------- Near 1-degree + mpasa60, mpasa30 - High resolution + mpasa15 ---------- Very high resolution + + This merge adds the surface data and landuse.timeseries files for the CAM-MPAS dycore. At present, these grids are: + + mpasa480 - 480 km quasi-uniform, global with 2,462 horizontal grid columns + mpasa120 - 120 km quasi-uniform, global with 40,962 horizontal grid columns + mpasa60 - 60 km quasi-uniform, global with 163,842 horizontal grid columns + mpasa30 - 30 km quasi-uniform, global with 655,362 horizontal grid columns + mpasa15 - 15 km quasi-uniform, global with 2,621,442 horizontal grid columns + + +Option to Run NEON with PRISM preciption data: + + Some NEON sites have bad or incomplete precitation data. By setting CLM_USRDAT_NAME="NEON.PRISM" + the PRISM 4km CONUS ReAnayslis data is used in place of the NEON precipitation data. This + is helpful for several NEON sites: + MLBS, MOAB, ONAQ, SJER, NIWO, TEAK, WREF, YELL + + Allow PRISM precipitation to be used as a new datm stream. + + Updates to cime_config/config_component.xml include additional valid values for PRECIP data stream names. Changes in + cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams specify which input variables are gathered from which streams and + specifies file location for PRISM data. + + Using PRISM precipitation instead of NEON precipitation does have a substantial impact on CTSM output (eg. latent heat flux + biases). Significant changes to scientifically-supported configurations @@ -29,106 +67,60 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed or introduced ------------------------ -[Remove any lines that don't apply. Remove entire section if nothing applies.] CTSM issues fixed (include CTSM Issue #): - -Externals issues fixed (include issue #): - -Known bugs introduced in this tag (include issue #): - -Known bugs found since the previous tag (include issue #): - + Fixes #1969 -- Move dynGrossUnrepMod.F90 from biogeochem to dyn_subgrid subdirectory + Fixes #1904 -- Other precipitation streams for NEON + Fixes #1927 -- Course SE resolutions support + Fixes #1313 -- MPASA resolution support Notes of particular relevance for users --------------------------------------- -[Remove any lines that don't apply. Remove entire section if nothing applies.] Caveats for users (e.g., need to interpolate initial conditions): + New resolutions do NOT have specific initial conditions for them, they use the general ones Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + NEON cases will give a warning about spinup data for non default transient cases + if you set a NEON case with CLM_USRDAT_NAME=NEON.PRISM, PRISM data will be used for precip + + Two new options to run_neon.py "--prism" and "--experiment" Changes made to namelist defaults (e.g., changed parameter values): + "v3" data option for NEONVERSION Changes to the datasets (e.g., parameter, surface or initial files): - -Substantial timing or memory changes: -[e.g., check PFS test in the test suite and look at timings, if you -expect possible significant timing changes] - + New surface and landuse.timeseries datasets for: + ne3np4.pg3, ne5np4.pg3, ne16np4.pg3 + mpasa480, mpasa120, mpasa60, mpasa30, mpasa15 Notes of particular relevance for developers: --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -[Remove any lines that don't apply. Remove entire section if nothing applies.] - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): - -Changes to tests or testing: +Changes to tests or testing: Add new tests for new resolutions -Testing summary: +Testing summary: regular, tools ---------------- -[... Remove before making master tag. - -Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. -However, it occasionally makes sense to do more or less system testing; -here is guidance on different available levels of system testing: - a) no system testing (for use when the only changes are ones that - have absolutely no impact on system runs; this - includes documentation-only tags, tags that - just change the tools or some python code that - does not impact system runs, etc.) - b) minimal (for use in rare cases where only a small change with - known behavior is added ... eg. a minor bug fix. This - might be to just run the "short" test list, or to run - a single test. Whatever makes sense for the particular case.) - c) python only (for use where the only changes are in the python directory: - run the python testing listed below) - d) regular (regular tests on normal machines if CTSM source is modified) - e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists - and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) - would be run as well) - -In addition, various other tests of the tools, python and perl -infrastructure should be run when appropriate, as described below. - -...] - -[Remove any lines that don't apply.] [PASS means all tests PASS; OK means tests PASS other than expected fails.] build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - + cheyenne - PASS (81 new tests) tools-tests (test/tools) (if tools have been changed): - cheyenne - + cheyenne - OK + cheyenne - PASS (tests_pretag_nompi_neon) python testing (if python code has changed; see instructions in python/README.md; document testing done): - (any machine) - - - [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python - code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system - tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in - either model output or namelists, is: create sym links pointing to the last tag's baseline directory, - named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT - doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to - separately run the clm_pymods test suite, and you can remove the following line.] - - clm_pymods test suite on cheyenne - + cheyenne - PASS regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- - izumi ------- - - fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) - cheyenne ---- - izumi ------- + cheyenne ---- OK + izumi ------- OK any other testing (give details below): @@ -138,36 +130,24 @@ If the tag used for baseline comparisons was NOT the previous tag, note that her Answer changes -------------- -Changes answers relative to baseline: - - [ If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section). - And always remove these three lines and parts that don't apply. ] - - Summarize any changes to answers, i.e., - - what code configurations: - - what platforms/compilers: - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - If bitwise differences were observed, how did you show they were no worse - than roundoff? - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: - - URL for LMWG diagnostics output used to validate new climate: - +Changes answers relative to baseline: No bit-for-bit Other details ------------- -[Remove any lines that don't apply. Remove entire section if nothing applies.] -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cdeps + Update CDEPS to cdeps1.0.12 Pull Requests that document the changes (include PR ids): (https://github.com/ESCOMP/ctsm/pull) + #1998 -- combination of below PR's... + + #1954 -- PRISM + #1973 -- SE + #1501 -- MPASA + #1899 -- memory scaling + =============================================================== =============================================================== Tag name: ctsm5.1.dev123 From c3555a846810c1677f92b6a22551da9e0644c525 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 9 May 2023 10:10:16 -0600 Subject: [PATCH 0903/2067] Put do_harvest back where force_harvest was removed from cphase_leafemerge conditional. This represents a bug fix over the previous behavior: There were situations where force_harvest would be false with do_harvest true, meaning that the latter was ignored. This fix changes the timing of crop phase transitions, but rarely, and not by much. Does not seem to affect GDD-generating runs. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 63fc135a2f..ad0e832e75 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2239,7 +2239,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! phase. However, despite these differences: if you make changes to the ! following conditionals, you should also check to see if you should make ! similar changes in CropPhase. - if (leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then + if ((.not. do_harvest) .and. leafout(p) >= huileaf(p) .and. hui(p) < huigrain(p) .and. idpp < mxmat) then cphase(p) = cphase_leafemerge if (abs(onset_counter(p)) > 1.e-6_r8) then onset_flag(p) = 1._r8 From 7798b9a9c2029b24d2f8260a07fb5b7230ab6bb1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 10 May 2023 12:39:29 -0600 Subject: [PATCH 0904/2067] Add annual SDATES and HDATES outputs to clm-crop test. --- cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index 4add705be3..4622aca109 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -7,3 +7,11 @@ ! This is in the crop testmods because this field is mainly useful in transient crop runs ! This is on history tape 2 because this field is not meaningful at the gridcell level hist_fincl2 += 'DYN_COL_SOIL_ADJUSTMENTS_C' + + +! Annual crop variables on per-sowing/per-harvest axes, per PFT. +hist_fincl3 = 'SDATES', 'HDATES' +hist_nhtfrq(3) = 17520 +hist_mfilt(3) = 1 +hist_type1d_pertape(3) = 'PFTS' +hist_dov2xy(3) = .false. From d5e8cf815e80fdf084eee31fa84f24c4ddca4c37 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Thu, 11 May 2023 15:20:36 +0200 Subject: [PATCH 0905/2067] update ccs_config external --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 15b0f8a31a..e6f6a7357e 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_noresm0.0.5 +tag = ccs_config_noresm0.0.6 protocol = git repo_url = https://github.com/NorESMhub/ccs_config_noresm.git local_path = ccs_config From dc3158d5f65349187a1fdcc76a742c69acf5af2e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 11 May 2023 14:09:08 -0600 Subject: [PATCH 0906/2067] Removed duplicate RXCROPMATURITY from cime_config/config_tests.xml. --- cime_config/config_tests.xml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index 292445cee3..e32b331116 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -113,16 +113,6 @@ This defines various CTSM-specific system tests $STOP_N - - Generate prescribed maturity requirements, then test with them - 1 - FALSE - FALSE - never - $STOP_OPTION - $STOP_N - - From 229c9b7649419d81b6fafd347369c8fce166d152 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 11 May 2023 14:09:54 -0600 Subject: [PATCH 0907/2067] Only allow RXCROPMATURITY to be called with test cropMonthOutput. --- cime_config/SystemTests/rxcropmaturity.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 6349bcd98d..38c5bd0155 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -71,6 +71,14 @@ def __init__(self, case): # Get the number of complete years that will be run self._run_Nyears = int(stop_n) + # Only allow RXCROPMATURITY to be called with test cropMonthOutput + casebaseid = self._case.get_value("CASEBASEID") + if casebaseid.split("-")[-1] != "cropMonthOutput": + raise RuntimeError( + "Only call RXCROPMATURITY with test cropMonthOutput " + + "to avoid potentially huge sets of daily outputs." + ) + def run_phase(self): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't # want to be saved as baseline. From 49f2883e2d2658c8212074e129f2f360f2d1a818 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 11 May 2023 14:13:57 -0600 Subject: [PATCH 0908/2067] Removed an outdated comment from cime_config/config_tests.xml. --- cime_config/config_tests.xml | 3 --- 1 file changed, 3 deletions(-) diff --git a/cime_config/config_tests.xml b/cime_config/config_tests.xml index e32b331116..536f79aeec 100644 --- a/cime_config/config_tests.xml +++ b/cime_config/config_tests.xml @@ -113,9 +113,6 @@ This defines various CTSM-specific system tests $STOP_N - Generate prescribed maturity requirements, then test with them 1 From 5bc4a22ffeb553701de6aa261bd2ca1b1d364dc8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 11 May 2023 16:53:25 -0600 Subject: [PATCH 0909/2067] Update CIME and use new list-capable append_to_user_nl_files(). --- Externals.cfg | 2 +- cime_config/SystemTests/rxcropmaturity.py | 9 +++------ 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index a0198ceb6a..901b1a87e6 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.108 +tag = cime6.0.120 required = True [cmeps] diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 38c5bd0155..30681a8e23 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -405,13 +405,10 @@ def _get_conda_env(self): def _append_to_user_nl_clm(self, additions): - if not isinstance(additions, list): - additions = [additions] caseroot = self._get_caseroot() - for a in additions: - append_to_user_nl_files(caseroot = caseroot, - component = "clm", - contents = a) + append_to_user_nl_files(caseroot = caseroot, + component = "clm", + contents = additions) def _run_python_script(self, case, command, tool_path): From ecd83f59107ecc249d2eaeede967da1f3dd80f5a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 11 May 2023 16:54:12 -0600 Subject: [PATCH 0910/2067] Improved error handling in RXCROPMATURITY. --- cime_config/SystemTests/rxcropmaturity.py | 35 ++++++++++++++--------- 1 file changed, 22 insertions(+), 13 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 30681a8e23..d920a7c3de 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -59,7 +59,7 @@ def __init__(self, case): f"STOP_OPTION ({stop_option_orig}) must be nsecond(s), nminute(s), " + "nhour(s), nday(s), nmonth(s), or nyear(s)" ) - if stop_n < 5: + elif stop_n < 5: error_message = ( "RXCROPMATURITY must be run for at least 5 years; you requested " + f"{stop_n_orig} {stop_option_orig[1:]}" @@ -74,10 +74,12 @@ def __init__(self, case): # Only allow RXCROPMATURITY to be called with test cropMonthOutput casebaseid = self._case.get_value("CASEBASEID") if casebaseid.split("-")[-1] != "cropMonthOutput": - raise RuntimeError( + error_message = ( "Only call RXCROPMATURITY with test cropMonthOutput " + "to avoid potentially huge sets of daily outputs." ) + logger.error(error_message) + raise RuntimeError(error_message) def run_phase(self): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't @@ -219,14 +221,19 @@ def _setup_all(self): blessed_crop_dates_dir, "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc") else: - print("ERROR: RXCROPMATURITY currently only supports 10x15 and 1.9x2.5 resolutions") - raise + error_message = "ERROR: RXCROPMATURITY currently only supports 10x15 and 1.9x2.5 resolutions" + logger.error(error_message) + raise RuntimeError(error_message) + + error_message = None if not os.path.exists(self._sdatefile): - print(f"ERROR: Sowing date file not found: {self._sdatefile}") - raise - if not os.path.exists(self._hdatefile): - print(f"ERROR: Harvest date file not found: {self._sdatefile}") - raise + error_message = f"ERROR: Sowing date file not found: {self._sdatefile}" + elif not os.path.exists(self._hdatefile): + error_message = f"ERROR: Harvest date file not found: {self._sdatefile}" + if error_message is not None: + logger.error(error_message) + raise RuntimeError(error_message) + # Set sowing dates file (and other crop calendar settings) for all runs logger.info("SSRLOG modify user_nl files: all tests") @@ -279,8 +286,9 @@ def _run_make_surface_for_gddgen(self, case_gddgen): self._fsurdat_in = fsurdat_in.group(1) break if self._fsurdat_in is None: - print("fsurdat not defined") - raise + error_message = "fsurdat not defined" + logger.error(error_message) + raise RuntimeError(error_message) # Where we will save the fsurdat version for this test self._fsurdat_out = os.path.join(self._path_gddgen, 'fsurdat.nc') @@ -379,8 +387,9 @@ def _run_generate_gdds(self, case_gddgen): generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) generated_gdd_files = [x for x in generated_gdd_files if "fill0" not in x] if len(generated_gdd_files) != 1: - print(f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}") - raise + error_messsage = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" + logger.error(error_message) + raise RuntimeError(error_message) self._gdds_file = generated_gdd_files[0] From ff05829034439e70aa3b84644b90f9a26a60efec Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 11 May 2023 17:04:07 -0600 Subject: [PATCH 0911/2067] RXCROPMATURITY: Move getting of rx crop files to its own function, called in __init__. --- cime_config/SystemTests/rxcropmaturity.py | 29 +++++++++++------------ 1 file changed, 14 insertions(+), 15 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index d920a7c3de..5e036d1573 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -81,6 +81,9 @@ def __init__(self, case): logger.error(error_message) raise RuntimeError(error_message) + # Get files with prescribed sowing and harvest dates + self._get_rx_dates() + def run_phase(self): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't # want to be saved as baseline. @@ -187,21 +190,8 @@ def run_phase(self): self._run_check_rxboth_run() - def _setup_all(self): - logger.info("SSRLOG _setup_all start") - - """ - Get some info - """ - self._ctsm_root = self._case.get_value('COMP_ROOT_DIR_LND') - run_startdate = self._case.get_value('RUN_STARTDATE') - self._run_startyear = int(run_startdate.split('-')[0]) - - """ - Get and set sowing and harvest dates - """ - - # Get sowing and harvest dates for this resolution. + # Get sowing and harvest dates for this resolution. + def _get_rx_dates(self): # Eventually, I want to remove these hard-coded resolutions so that this test can generate # its own sowing and harvest date files at whatever resolution is requested. lnd_grid = self._case.get_value("LND_GRID") @@ -225,6 +215,7 @@ def _setup_all(self): logger.error(error_message) raise RuntimeError(error_message) + # Ensure files exist error_message = None if not os.path.exists(self._sdatefile): error_message = f"ERROR: Sowing date file not found: {self._sdatefile}" @@ -234,6 +225,14 @@ def _setup_all(self): logger.error(error_message) raise RuntimeError(error_message) + + def _setup_all(self): + logger.info("SSRLOG _setup_all start") + + # Get some info + self._ctsm_root = self._case.get_value('COMP_ROOT_DIR_LND') + run_startdate = self._case.get_value('RUN_STARTDATE') + self._run_startyear = int(run_startdate.split('-')[0]) # Set sowing dates file (and other crop calendar settings) for all runs logger.info("SSRLOG modify user_nl files: all tests") From 4db1d204279a2a9ce6f3ac4c753fa4a754892491 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 12 May 2023 12:55:17 -0600 Subject: [PATCH 0912/2067] Point to latest cdeps (needed for this branch) --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 888b7e1079..cd6855c9dc 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -55,7 +55,7 @@ local_path = components/cmeps required = True [cdeps] -tag = cdeps1.0.9 +tag = cdeps1.0.13 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps From c9cc838ca985376caadc15b82faeb203fbd98cb6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 12 May 2023 14:21:55 -0600 Subject: [PATCH 0913/2067] Deleted unused crop calendar shell scripts. --- python/ctsm/crop_calendars/generate_gdds.sh | 48 -------- .../ctsm/crop_calendars/setup_for_gddgen.sh | 109 ------------------ 2 files changed, 157 deletions(-) delete mode 100755 python/ctsm/crop_calendars/generate_gdds.sh delete mode 100755 python/ctsm/crop_calendars/setup_for_gddgen.sh diff --git a/python/ctsm/crop_calendars/generate_gdds.sh b/python/ctsm/crop_calendars/generate_gdds.sh deleted file mode 100755 index ced910b2f6..0000000000 --- a/python/ctsm/crop_calendars/generate_gdds.sh +++ /dev/null @@ -1,48 +0,0 @@ -#!/bin/bash -set -e - -cropcals_python_dir="/glade/u/home/samrabin/CTSM_cropcals_hist/crop_calendars" - -# Where did the run happen? If not provided, the assumption is -# that this script is being called as POSTRUN_SCRIPT. Therefore, -# the outputs will still be in the run directory. We also assume -# this is being run as part of a test suite, so we'll save the -# generate_gdds.py outputs to the case directory (so subsequent -# tests can find them easily). -run_outputs="$1" -if [[ "${run_outputs}" == "" ]]; then - run_outputs="$(./xmlquery --value RUNDIR)" - save_to="." -else - save_to="${run_outputs}" -fi - -# Set ${y1} to third year in run -y1=$(ls -1 *clm2.h1* | grep -oE "h1.[0-9]{4}" | sed "s/h1.//" | head -n 1) -y1=$((y1 + 2)) - -# Set ${yN} to last full year – 1 -yN=$(ls -1 *clm2.h1* | grep -oE "h1.[0-9]{4}" | sed "s/h1.//" | tail -n 1) -yN=$((yN - 1)) - -# Get ${sdates_file} from namelists -sdates_file="$(realpath "$(grep "sdate" CaseDocs/* | grep -oE "'.*'" | sed "s/'//g" | sed "s/.fill1//")")" -# Get ${hdates_file} from ${sdates_file} -hdates_file="${sdates_file/sdates/hdates}" - -#source ~/.bash_profile - -set +e -module is-loaded conda -conda_not_loaded=$? -set -e -if [[ ${conda_not_loaded} -ne 0 ]]; then - module unload python - module load conda -fi -conda activate npl -date -echo "Starting..." -python "${cropcals_python_dir}"/generate_gdds.py -r "${run_outputs}" -sd "${sdates_file}" -hd "${hdates_file}" -1 ${y1} -n ${yN} --dont-save-figs -o "${save_to}" - -exit 0 diff --git a/python/ctsm/crop_calendars/setup_for_gddgen.sh b/python/ctsm/crop_calendars/setup_for_gddgen.sh deleted file mode 100755 index 01e910c83c..0000000000 --- a/python/ctsm/crop_calendars/setup_for_gddgen.sh +++ /dev/null @@ -1,109 +0,0 @@ -#!/bin/bash -set -e - -# This script provides a general method to set up a GDD-generating run from -# an existing case directory. Call it from the case directory, preferably -# on a compute node, as the "If needed, generate a surface dataset file" -# step can be intensive. - -cropcals_python_dir="/glade/u/home/samrabin/CTSM_cropcals_hist/crop_calendars" - -# Set up -set +e -./check_case 1>.check_case_tmp 2>&1 -check_case_result=$? -set -e -if [[ ${check_case_result} -ne 0 ]]; then - echo "check_case failed; ignoring" -# cat .check_case_tmp -fi -rm .check_case_tmp - -# Ensure that run will go for at least 4 years; otherwise error. -stop_option=$(./xmlquery -N --value STOP_OPTION) -stop_n=$(./xmlquery -N --value STOP_N) -min_Nyears=4 -errMsg="WARNING: GDD-generating runs must be at least ${min_Nyears} years long.\nNot erroring because this check seems to occur before simulation length from test specification is applied." -if [[ "${stop_option}" == "nyear"* ]]; then - if [[ "${stop_n}" -lt ${min_Nyears} ]]; then - echo -e ${errMsg} >&2 - fi -elif [[ "${stop_option}" == "nmonth"* ]]; then - if [[ "${stop_n}" -lt $((min_Nyears * 12)) ]]; then - echo -e ${errMsg} >&2 - fi -elif [[ "${stop_option}" == "nday"* ]]; then - if [[ "${stop_n}" -lt $((min_Nyears * 365)) ]]; then - echo -e ${errMsg} >&2 - fi -else - echo "WARNING: STOP_OPTION '${stop_option}' not recognized by preprocess_inputs.sh" >&2 -fi - -# If needed, generate a surface dataset file with no crops missing years -flanduse_timeseries="$(grep -h -i "flanduse_timeseries" CaseDocs/* | sed "s/ flanduse_timeseries = //" | sed "s/'//g")" -if [[ "${flanduse_timeseries}" != "" ]]; then - if [[ ! -e "${flanduse_timeseries}" ]]; then - echo "flanduse_timeseries not found: ${flanduse_timeseries}" >&2 - exit 1 - fi - - # Make new fsurdat file (in case directory) - set +e - module is-loaded conda - conda_not_loaded=$? - set -e - if [[ ${conda_not_loaded} -ne 0 ]]; then - module unload python - module load conda - fi - conda activate npl - fsurdat="$(grep -h -i "fsurdat" CaseDocs/* | sed "s/ fsurdat = //" | sed "s/'//g")" - paramfile="$(grep -h -i "paramfile" CaseDocs/* | sed "s/ paramfile = //" | sed "s/'//g")" - set +e - python "${cropcals_python_dir}/make_surface_for_gddgen.py" --flanduse_timeseries "${flanduse_timeseries}" --fsurdat "${fsurdat}" --paramfile "${paramfile}" > make_surface_for_gddgen.log - if [[ $? -ne 0 ]]; then - cat make_surface_for_gddgen.log - exit 1 - fi - set -e - new_fsurdat="$PWD/$(cat make_surface_for_gddgen.log)" - rm make_surface_for_gddgen.log - - # Change fsurdat to point to that file, disable transient crops, etc. - echo "fsurdat = '${new_fsurdat}'" >> user_nl_clm - echo "do_transient_crops = .false." >> user_nl_clm - echo "flanduse_timeseries = ''" >> user_nl_clm - echo "use_init_interp = .true." >> user_nl_clm -fi - -# user_nl_clm: Replace MESHFILE_PLACEHOLDER with the appropriate file for this resolution -file_mesh="$(./xmlquery -N --value LND_DOMAIN_MESH)" -sed -i "s@MESHFILE_PLACEHOLDER@${file_mesh}@" user_nl_clm - -# user_nl_clm: Replace SDATEFILE_PLACEHOLDER with the appropriate file for this resolution. -# EVENTUALLY: Generate sdate (and hdate) file at case resolution from GGCMI files; save to case directory and use that. -lnd_grid=$(./xmlquery -N --value LND_GRID) -blessed_crop_dates_dir="/glade/work/samrabin/crop_dates_blessed" -if [[ "${lnd_grid}" == "10x15" ]]; then - file_sdates="${blessed_crop_dates_dir}/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc" -elif [[ "${lnd_grid}" == "1.9x2.5" ]]; then - file_sdates="${blessed_crop_dates_dir}/sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc" -else - echo "Land resolution (LND_GRID) '${lnd_grid}' not recognized by preprocess_inputs.sh" >&2 - exit 1 -fi -sed -i "s@SDATEFILE_PLACEHOLDER@${file_sdates}@" user_nl_clm - -# Rebuild namelists (optional, so don't worry if it doesn't work) -set +e -./check_case 1>.check_case_tmp 2>&1 -check_case_result=$? -set -e -if [[ ${check_case_result} -ne 0 ]]; then - echo "check_case failed; ignoring" -# cat .check_case_tmp -fi -rm .check_case_tmp - -exit 0 From 4962a54240de5fd0a6cb6106820a3df7be941054 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 12 May 2023 14:27:10 -0600 Subject: [PATCH 0914/2067] Remove unused variable from GDD generation import_and_process_1yr(). --- python/ctsm/crop_calendars/generate_gdds_functions.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 143023b6b4..784adc96b6 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -450,8 +450,6 @@ def import_and_process_1yr( else: hdates_rx = hdates_rx_orig - # Determine cells where growing season crosses new year - grows_across_newyear = hdates_rx < sdates_rx log(logger, f" Importing accumulated GDDs...") clm_gdd_var = "GDDACCUM" From 946527b29a521e05afad1ba89a48051cf76caf71 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 12 May 2023 14:28:47 -0600 Subject: [PATCH 0915/2067] generate_gdds.py: Minor rearrangement. --- python/ctsm/crop_calendars/generate_gdds.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index c6f1833341..979f9ea6a0 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -380,9 +380,9 @@ def add_attrs_to_map_ds( ############################### ### Process input arguments ### ############################### - - # Set arguments parser = argparse.ArgumentParser(description="ADD DESCRIPTION HERE") + + # Required parser.add_argument( "-i", "--input-dir", @@ -415,6 +415,8 @@ def add_attrs_to_map_ds( parser.add_argument( "-hd", "--hdates-file", help="File of prescribed harvest dates", required=True ) + + # Optional figsgroup = parser.add_mutually_exclusive_group() figsgroup.add_argument( "--dont-save-figs", help="Do not save figures", action="store_true", default=False From f698a06fed8a6a4de90a726983ff1d6be0dd034d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 12 May 2023 14:39:47 -0600 Subject: [PATCH 0916/2067] RXCROPMATURITY: Added support for 0.9 x 1.25 resolution. --- cime_config/SystemTests/rxcropmaturity.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 5e036d1573..04d147ca25 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -4,8 +4,8 @@ in a sowing+maturity forced run, which finally is tested to ensure correct behavior. -Currently only supports 10x15 and f19_g17 resolutions. Eventually, I want -this test to be able to generate its own files at whatever resolution it's +Currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions. Eventually, +this test should be able to generate its own files at whatever resolution it's called at. Well, really, the ultimate goal would be to give CLM the files at the original resolution (for GGCMI phase 3, 0.5°) and have the stream code do the interpolation. However, that wouldn't act on harvest dates @@ -210,8 +210,15 @@ def _get_rx_dates(self): self._hdatefile = os.path.join( blessed_crop_dates_dir, "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc") + elif lnd_grid == "0.9x1.25": + self._sdatefile = os.path.join( + blessed_crop_dates_dir, + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230510_133957.fill1.nc") + self._hdatefile = os.path.join( + blessed_crop_dates_dir, + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230510_133958.fill1.nc") else: - error_message = "ERROR: RXCROPMATURITY currently only supports 10x15 and 1.9x2.5 resolutions" + error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" logger.error(error_message) raise RuntimeError(error_message) From 76e5c849971d4bf3480aec0aa06f4df415cc3809 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 12 May 2023 16:35:45 -0600 Subject: [PATCH 0917/2067] Variable name bugfix in RXCROPMATURITY. --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 04d147ca25..922a7ea3c6 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -393,7 +393,7 @@ def _run_generate_gdds(self, case_gddgen): generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) generated_gdd_files = [x for x in generated_gdd_files if "fill0" not in x] if len(generated_gdd_files) != 1: - error_messsage = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" + error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" logger.error(error_message) raise RuntimeError(error_message) self._gdds_file = generated_gdd_files[0] From c2dddbff80c003e09db44fb23c52c77cbe5b4cda Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 12 May 2023 16:36:33 -0600 Subject: [PATCH 0918/2067] RXCROPMATURITY: Hard-coded option to use fsurdat method instead of flanduse_timeseries. --- cime_config/SystemTests/rxcropmaturity.py | 37 ++++++++++++++--------- 1 file changed, 23 insertions(+), 14 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 922a7ea3c6..6c9272b059 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -27,6 +27,9 @@ # cf_units caused problems in utils.import_ds(). this_conda_env = "ctsm_pylib" +# Should GDD-Generating run use fsurdat method? +gddgen_use_fsurdat = True + class RXCROPMATURITY(SystemTestsCommon): def __init__(self, case): @@ -120,27 +123,21 @@ def run_phase(self): If needed, generate a surface dataset file with no crops missing years """ - # Is flanduse_timeseries defined? If so, where is it? - case_gddgen.create_namelists(component='lnd') - self._lnd_in_path = os.path.join(self._path_gddgen, 'CaseDocs', 'lnd_in') - self._flanduse_timeseries_in = None - with open (self._lnd_in_path,'r') as lnd_in: - for line in lnd_in: - flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) - if flanduse_timeseries_in: - self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) - break - # If flanduse_timeseries is defined, we need to make our own version for # this test (if we haven't already). + self._get_flanduse_timeseries_in(case_gddgen) if self._flanduse_timeseries_in is not None: # Download files from the server, if needed case_gddgen.check_all_input_data() - # Make custom version of flanduse_timeseries - logger.info("SSRLOG run make_lu_for_gddgen") - self._run_make_lu_for_gddgen(case_gddgen) + # Make custom version of input file + if gddgen_use_fsurdat: + logger.info("SSRLOG run make_surface_for_gddgen") + self._run_make_surface_for_gddgen(case_gddgen) + else: + logger.info("SSRLOG run make_lu_for_gddgen") + self._run_make_lu_for_gddgen(case_gddgen) #------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -458,3 +455,15 @@ def _run_python_script(self, case, command, tool_path): except: print(f"ERROR trying to run {tool_name}.") raise + + # Is flanduse_timeseries defined? If so, where is it? + def _get_flanduse_timeseries_in(self, case): + case.create_namelists(component='lnd') + self._lnd_in_path = os.path.join(self._path_gddgen, 'CaseDocs', 'lnd_in') + self._flanduse_timeseries_in = None + with open (self._lnd_in_path,'r') as lnd_in: + for line in lnd_in: + flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) + if flanduse_timeseries_in: + self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) + break \ No newline at end of file From 3a91016eaf533ba1905ef7d7de43f102cc53790e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 10:46:29 -0600 Subject: [PATCH 0919/2067] cropcal_module check_v0_le_v1(): Removed backward compatibility for files missing SDATES_PERHARV. --- python/ctsm/crop_calendars/cropcal_module.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index f9923ebdfa..2ba5b347ba 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -439,11 +439,6 @@ def check_v0_le_v1(this_ds, vars, msg_txt=" ", both_nan_ok=False, throw_error=Fa # Convert time*mxharvests axes to growingseason axis def convert_axis_time2gs(this_ds, verbose=False, myVars=None, incl_orig=False): - # For backwards compatibility. - if "SDATES_PERHARV" not in this_ds: - return convert_axis_time2gs_old(this_ds, myVars=myVars) - # Otherwise... - # How many non-NaN patch-seasons do we expect to have once we're done organizing things? Npatch = this_ds.dims["patch"] # Because some patches will be planted in the last year but not complete, we have to ignore any finalyear-planted seasons that do complete. From 7efbd52cd28c4c2d8d7af74b6f5948b94e6e8d1f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 10:47:06 -0600 Subject: [PATCH 0920/2067] cropcal_module now includes open_lu_ds(). --- python/ctsm/crop_calendars/cropcal_module.py | 98 +++++++++++++++++++- 1 file changed, 95 insertions(+), 3 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 2ba5b347ba..3949fc9341 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -69,6 +69,98 @@ def get_year_from_cftime(cftime_date): return ds_in +def open_lu_ds(filename, y1, yN, existing_ds, ungrid=True): + # Open and trim to years of interest + dsg = xr.open_dataset(filename).sel(time=slice(y1, yN)) + + # Assign actual lon/lat coordinates + dsg = dsg.assign_coords( + lon=("lsmlon", existing_ds.lon.values), lat=("lsmlat", existing_ds.lat.values) + ) + dsg = dsg.swap_dims({"lsmlon": "lon", "lsmlat": "lat"}) + + if "AREA" in dsg: + dsg["AREA_CFT"] = dsg.AREA * 1e6 * dsg.LANDFRAC_PFT * dsg.PCT_CROP / 100 * dsg.PCT_CFT / 100 + dsg["AREA_CFT"].attrs = {"units": "m2"} + dsg["AREA_CFT"].load() + else: + print("Warning: AREA missing from Dataset, so AREA_CFT will not be created") + + if not ungrid: + return dsg + + # Un-grid + query_ilons = [int(x) - 1 for x in existing_ds["patches1d_ixy"].values] + query_ilats = [int(x) - 1 for x in existing_ds["patches1d_jxy"].values] + query_ivts = [list(dsg.cft.values).index(x) for x in existing_ds["patches1d_itype_veg"].values] + + ds = xr.Dataset(attrs=dsg.attrs) + for v in ["AREA", "LANDFRAC_PFT", "PCT_CFT", "PCT_CROP", "AREA_CFT"]: + if v not in dsg: + continue + if "time" in dsg[v].dims: + new_coords = existing_ds["GRAINC_TO_FOOD_ANN"].coords + else: + new_coords = existing_ds["patches1d_lon"].coords + if "cft" in dsg[v].dims: + ds[v] = ( + dsg[v] + .isel( + lon=xr.DataArray(query_ilons, dims="patch"), + lat=xr.DataArray(query_ilats, dims="patch"), + cft=xr.DataArray(query_ivts, dims="patch"), + drop=True, + ) + .assign_coords(new_coords) + ) + else: + ds[v] = ( + dsg[v] + .isel( + lon=xr.DataArray(query_ilons, dims="patch"), + lat=xr.DataArray(query_ilats, dims="patch"), + drop=True, + ) + .assign_coords(new_coords) + ) + for v in existing_ds: + if "patches1d_" in v or "grid1d_" in v: + ds[v] = existing_ds[v] + ds["lon"] = dsg["lon"] + ds["lat"] = dsg["lat"] + + # Which crops are irrigated? + is_irrigated = np.full_like(ds["patches1d_itype_veg"], False) + for vegtype_str in np.unique(ds["patches1d_itype_veg_str"].values): + if "irrigated" not in vegtype_str: + continue + vegtype_int = utils.ivt_str2int(vegtype_str) + is_this_vegtype = np.where(ds["patches1d_itype_veg"].values == vegtype_int)[0] + is_irrigated[is_this_vegtype] = True + ["irrigated" in x for x in ds["patches1d_itype_veg_str"].values] + ds["IRRIGATED"] = xr.DataArray( + data=is_irrigated, + coords=ds["patches1d_itype_veg_str"].coords, + attrs={"long_name": "Is patch irrigated?"}, + ) + + # How much area is irrigated? + ds["IRRIGATED_AREA_CFT"] = ds["IRRIGATED"] * ds["AREA_CFT"] + ds["IRRIGATED_AREA_CFT"].attrs = { + "long name": "CFT area (irrigated types only)", + "units": "m^2", + } + ds["IRRIGATED_AREA_GRID"] = ( + ds["IRRIGATED_AREA_CFT"] + .groupby(ds["patches1d_gi"]) + .sum() + .rename({"patches1d_gi": "gridcell"}) + ) + ds["IRRIGATED_AREA_GRID"].attrs = {"long name": "Irrigated area in gridcell", "units": "m^2"} + + return ds + + def check_constant_vars( this_ds, case, ignore_nan, constantGSs=None, verbose=True, throw_error=True ): @@ -1039,7 +1131,7 @@ def check_no_zeros(this_ds, varList_no_zero, which_file): irrig_ds_grid["QIRRIG_FROM_GW_CONFINED"] + irrig_ds_grid["QIRRIG_FROM_GW_UNCONFINED"] > 0 - ): +): raise RuntimeError("Unexpectedly found some irrigation using groundwater") # Rename this variable so that it has a QIRRIG prefix @@ -1102,10 +1194,10 @@ def check_no_zeros(this_ds, varList_no_zero, which_file): if this_ds_gs["AREA_GRID"].attrs["units"] != "m^2": if this_ds_gs["AREA_GRID"].attrs["units"] == "km^2": to_m2 = 1e6 - else: + else: raise RuntimeError( f"Unsure how to convert {this_ds_gs['AREA_GRID'].attrs['units']} to m^2" - ) + ) this_ds_gs["AREA_GRID"] *= to_m2 this_ds_gs["AREA_GRID"].attrs["units"] = "m^2" From 04ab76a4f84509db16b50f805828a0d385bae681 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 10:56:26 -0600 Subject: [PATCH 0921/2067] cropcal_module: Removed incl_irrig option from import_output(). --- .../ctsm/crop_calendars/check_rxboth_run.py | 1 - python/ctsm/crop_calendars/cropcal_module.py | 149 ------------------ 2 files changed, 150 deletions(-) diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py index 362ed65854..256fb125b7 100644 --- a/python/ctsm/crop_calendars/check_rxboth_run.py +++ b/python/ctsm/crop_calendars/check_rxboth_run.py @@ -70,7 +70,6 @@ def main(argv): myVars=myVars, y1=args.first_usable_year, yN=args.last_usable_year, - incl_irrig=False, ) cc.check_constant_vars(case["ds"], case, ignore_nan=True, verbose=True, throw_error=True) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 3949fc9341..785410afdd 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -897,7 +897,6 @@ def import_output( sdates_rx_ds=None, gdds_rx_ds=None, verbose=False, - incl_irrig=True, ): # Import this_ds = utils.import_ds(filename, myVars=myVars, myVegtypes=myVegtypes) @@ -1055,154 +1054,6 @@ def check_no_zeros(this_ds, varList_no_zero, which_file): raise RuntimeError("How to get NHARVEST_DISCREP for NHARVESTS > 2?") this_ds_gs["NHARVEST_DISCREP"] = (this_ds_gs["NHARVESTS"] == 2).astype(int) - # Import irrigation data, if doing so - if incl_irrig: - # Monthly use and demand - pattern = os.path.join(os.path.dirname(filename), "*.h2.*.nc") - irrig_file_patches = glob.glob(pattern) - if irrig_file_patches: - if len(irrig_file_patches) > 1: - raise RuntimeError(f"Expected at most 1 *.h2.*.nc; found {len(irrig_file_patches)}") - irrig_file_patches = irrig_file_patches[0] - irrig_ds_patches = utils.import_ds( - irrig_file_patches, - myVegtypes=myVegtypes, - chunks={"time": 12}, - myVars=["QIRRIG_DEMAND", "QIRRIG_DRIP", "QIRRIG_SPRINKLER"], - ) - irrig_ds_patches = time_units_and_trim_mth(irrig_ds_patches, y1, yN) - - # Combine drip + sprinkler irrigation - irrig_ds_patches["QIRRIG_APPLIED"] = ( - irrig_ds_patches["QIRRIG_DRIP"] + irrig_ds_patches["QIRRIG_SPRINKLER"] - ) - irrig_ds_patches["QIRRIG_APPLIED"].attrs = irrig_ds_patches["QIRRIG_DEMAND"].attrs - irrig_ds_patches["QIRRIG_APPLIED"].attrs[ - "long_name" - ] = "water added via drip or sprinkler irrigation" - - # Calculate unfulfilled demand - irrig_ds_patches["QIRRIG_UNFULFILLED"] = ( - irrig_ds_patches["QIRRIG_DEMAND"] - irrig_ds_patches["QIRRIG_APPLIED"] - ) - irrig_ds_patches["QIRRIG_UNFULFILLED"].attrs = irrig_ds_patches["QIRRIG_DEMAND"].attrs - irrig_ds_patches["QIRRIG_UNFULFILLED"].attrs[ - "long_name" - ] = "irrigation demand unable to be filled" - - vars_to_save = ["QIRRIG_DEMAND", "QIRRIG_APPLIED", "QIRRIG_UNFULFILLED"] - - # Append _PATCH to distinguish from eventual gridcell sums (_GRID) - rename_dict = {} - for v in vars_to_save: - rename_dict[v] = v + "_PATCH" - irrig_ds_patches = irrig_ds_patches.rename(rename_dict) - vars_to_save = [v + "_PATCH" for v in vars_to_save] - - # Finish processing - this_ds_gs = process_monthly_irrig(this_ds_gs, irrig_ds_patches, vars_to_save) - - # Monthly withdrawals and availability - pattern = os.path.join(os.path.dirname(filename), "*.h3.*.nc") - irrig_file_grid = glob.glob(pattern) - if irrig_file_grid: - if len(irrig_file_grid) > 1: - raise RuntimeError(f"Expected at most 1 *.h3.*.nc; found {len(irrig_file_grid)}") - irrig_file_grid = irrig_file_grid[0] - irrig_ds_grid = utils.import_ds( - irrig_file_grid, - chunks={"time": 12}, - myVars=[ - "area", - "grid1d_ixy", - "grid1d_jxy", - "grid1d_lon", - "grid1d_lat", - "QIRRIG_FROM_GW_CONFINED", - "QIRRIG_FROM_GW_UNCONFINED", - "QIRRIG_FROM_SURFACE", - "VOLRMCH", - ], - ) - irrig_ds_grid = time_units_and_trim_mth(irrig_ds_grid, y1, yN) - - # Ensure that no groundwater was used - if np.any( - irrig_ds_grid["QIRRIG_FROM_GW_CONFINED"] - + irrig_ds_grid["QIRRIG_FROM_GW_UNCONFINED"] - > 0 -): - raise RuntimeError("Unexpectedly found some irrigation using groundwater") - - # Rename this variable so that it has a QIRRIG prefix - irrig_ds_grid = irrig_ds_grid.rename({"VOLRMCH": "IRRIG_SUPPLY"}) - irrig_ds_grid["IRRIG_SUPPLY"].attrs["long_name"] = ( - irrig_ds_grid["IRRIG_SUPPLY"].attrs["long_name"] + " (aka VOLRMCH)" - ) - - vars_to_save = ["QIRRIG_FROM_SURFACE", "IRRIG_SUPPLY"] - - # Append _GRID to distinguish from patch-level irrigation data - rename_dict = {} - for v in vars_to_save: - rename_dict[v] = v + "_GRID" - irrig_ds_grid = irrig_ds_grid.rename(rename_dict) - vars_to_save = [v + "_GRID" for v in vars_to_save] - - # Finish processing - this_ds_gs = process_monthly_irrig(this_ds_gs, irrig_ds_grid, vars_to_save) - - # Calculate irrigation as fraction of main river channel volume - # (Do it here instead of process_monthly_irrig() because monthly doesn't add to annual.) - for t in ["MTH", "ANN"]: - this_ds_gs[f"QIRRIG_FROM_SURFACE_FRAC_RIVER_GRID_{t}"] = ( - this_ds_gs[f"QIRRIG_FROM_SURFACE_GRID_{t}"] - / this_ds_gs[f"IRRIG_SUPPLY_GRID_{t}"] - ) - this_ds_gs[f"QIRRIG_FROM_SURFACE_FRAC_RIVER_GRID_{t}"] = this_ds_gs[ - f"QIRRIG_FROM_SURFACE_FRAC_RIVER_GRID_{t}" - ].assign_coords(this_ds_gs[f"QIRRIG_FROM_SURFACE_GRID_{t}"].coords) - - # Ensure gridcells are same-ordered between patch- and gridcell-level datasets - this_ds_gs = this_ds_gs.assign_coords({"gridcell": this_ds_gs["gridcell"] + 1}) - irrig_ds_grid = irrig_ds_grid.assign_coords({"gridcell": irrig_ds_grid["gridcell"] + 1}) - test_gi = int(this_ds_gs["gridcell"].shape[0] / 3) # An arbitrary gridcell to test - test_g = irrig_ds_grid["gridcell"].values[test_gi] - test_pi = np.where(this_ds_gs["patches1d_gi"] == test_g)[0][0] - test_p_lon = this_ds_gs["patches1d_lon"].isel(patch=test_pi) - test_p_lat = this_ds_gs["patches1d_lat"].isel(patch=test_pi) - test_g_lon = irrig_ds_grid["grid1d_lon"].isel(gridcell=test_gi) - test_g_lat = irrig_ds_grid["grid1d_lat"].isel(gridcell=test_gi) - if test_p_lon != test_g_lon or test_p_lat != test_g_lat: - print(f"{test_p_lon} =? {test_g_lon}") - print(f"{test_p_lat} =? {test_g_lat}") - raise RuntimeError("Gridcell indexing mismatch") - - # Save gridcell info - for v in irrig_ds_grid: - if "grid" in v: - this_ds_gs[v] = irrig_ds_grid[v] - - # Save gridcell area - this_ds_gs["AREA_GRID"] = ungrid( - irrig_ds_grid["area"], - irrig_ds_grid, - target_dim="gridcell", - lon="grid1d_ixy", - lat="grid1d_jxy", - ) - if this_ds_gs["AREA_GRID"].attrs["units"] != "m^2": - if this_ds_gs["AREA_GRID"].attrs["units"] == "km^2": - to_m2 = 1e6 - else: - raise RuntimeError( - f"Unsure how to convert {this_ds_gs['AREA_GRID'].attrs['units']} to m^2" - ) - this_ds_gs["AREA_GRID"] *= to_m2 - this_ds_gs["AREA_GRID"].attrs["units"] = "m^2" - - return this_ds_gs - # Set up empty Dataset with time axis as "gs" (growing season) instead of what CLM puts out. # Includes all the same variables as the input dataset, minus any that had dimensions mxsowings or mxharvests. From d065c4ad6996ad7c04388c29d0436d6622527feb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 11:01:59 -0600 Subject: [PATCH 0922/2067] cropcal_module: Added missing diagnostic functions. --- python/ctsm/crop_calendars/cropcal_module.py | 193 ++++++++++++++++++- 1 file changed, 188 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 785410afdd..043b12b490 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -6,7 +6,7 @@ from scipy import stats, signal import warnings import cftime -import pandas as pd +import sys import os import glob @@ -14,6 +14,10 @@ import cartopy.crs as ccrs except: pass +try: + import pandas as pd +except: + pass # Define conversion multipliers, {from: {to1, to2, ...}, ...} @@ -692,14 +696,12 @@ def ignore_lastyear_complete_season(pg, excl, mxharvests): print( f'After "Ignore any harvests that were planted in the final year, because other cells will have incomplete growing seasons for the final year": discrepancy of {discrepancy} patch-seasons' ) - try: - import pandas as pd - + if "pandas" in sys.modules: bc = np.bincount(np.sum(is_valid, axis=1)) bc = bc[bc > 0] df = pd.DataFrame({"Ngs": unique_Nseasons, "Count": bc}) print(df) - except: + else: print(f"unique N seasons = {unique_Nseasons}") print(" ") @@ -798,6 +800,29 @@ def default_gdd_min(): return 1.0 +# Get information about extreme gridcells (for debugging) +def get_extreme_info(diff_array, rx_array, mxn, dims, gs, patches1d_lon, patches1d_lat): + if mxn == np.min: + diff_array = np.ma.masked_array(diff_array, mask=(np.abs(diff_array) == 0)) + themxn = mxn(diff_array) + + # Find the first patch-gs that has the mxn value + matching_indices = np.where(diff_array == themxn) + first_indices = [x[0] for x in matching_indices] + + # Get the lon, lat, and growing season of that patch-gs + p = first_indices[dims.index("patch")] + thisLon = patches1d_lon.values[p] + thisLat = patches1d_lat.values[p] + s = first_indices[dims.index("gs")] + thisGS = gs.values[s] + + # Get the prescribed value for this patch-gs + thisRx = rx_array[p][0] + + return round(themxn, 3), round(thisLon, 3), round(thisLat, 3), thisGS, round(thisRx) + + # Get growing season lengths from a DataArray of hdate-sdate def get_gs_len_da(this_da): tmp = this_da.values @@ -1055,6 +1080,164 @@ def check_no_zeros(this_ds, varList_no_zero, which_file): this_ds_gs["NHARVEST_DISCREP"] = (this_ds_gs["NHARVESTS"] == 2).astype(int) +# Print information about a patch (for debugging) +def print_onepatch_wrongNgs( + p, + this_ds_orig, + sdates_ymp, + hdates_ymp, + sdates_pym, + hdates_pym, + sdates_pym2, + hdates_pym2, + sdates_pym3, + hdates_pym3, + sdates_pg, + hdates_pg, + sdates_pg2, + hdates_pg2, +): + try: + import pandas as pd + except: + print("Couldn't import pandas, so not displaying example bad patch ORIGINAL.") + + print( + f"patch {p}: {this_ds_orig.patches1d_itype_veg_str.values[p]}, lon" + f" {this_ds_orig.patches1d_lon.values[p]} lat {this_ds_orig.patches1d_lat.values[p]}" + ) + + print("Original SDATES (per sowing):") + print(this_ds_orig.SDATES.values[:, :, p]) + + print("Original HDATES (per harvest):") + print(this_ds_orig.HDATES.values[:, :, p]) + + if "pandas" in sys.modules: + + def print_pandas_ymp(msg, cols, arrs_tuple): + print(f"{msg} ({np.sum(~np.isnan(arrs_tuple[0]))})") + mxharvests = arrs_tuple[0].shape[1] + arrs_list2 = [] + cols2 = [] + for h in np.arange(mxharvests): + for i, a in enumerate(arrs_tuple): + arrs_list2.append(a[:, h]) + cols2.append(cols[i] + str(h)) + arrs_tuple2 = tuple(arrs_list2) + df = pd.DataFrame(np.stack(arrs_tuple2, axis=1)) + df.columns = cols2 + print(df) + + print_pandas_ymp( + "Original", + ["sdate", "hdate"], + (this_ds_orig.SDATES_PERHARV.values[:, :, p], this_ds_orig.HDATES.values[:, :, p]), + ) + + print_pandas_ymp("Masked", ["sdate", "hdate"], (sdates_ymp[:, :, p], hdates_ymp[:, :, p])) + + print_pandas_ymp( + 'After "Ignore harvests from before this output began"', + ["sdate", "hdate"], + ( + np.transpose(sdates_pym, (1, 2, 0))[:, :, p], + np.transpose(hdates_pym, (1, 2, 0))[:, :, p], + ), + ) + + print_pandas_ymp( + 'After "In years with no sowing, pretend the first no-harvest is meaningful"', + ["sdate", "hdate"], + ( + np.transpose(sdates_pym2, (1, 2, 0))[:, :, p], + np.transpose(hdates_pym2, (1, 2, 0))[:, :, p], + ), + ) + + print_pandas_ymp( + ( + 'After "In years with sowing that are followed by inactive years, check whether the' + " last sowing was harvested before the patch was deactivated. If not, pretend the" + ' LAST no-harvest is meaningful."' + ), + ["sdate", "hdate"], + ( + np.transpose(sdates_pym3, (1, 2, 0))[:, :, p], + np.transpose(hdates_pym3, (1, 2, 0))[:, :, p], + ), + ) + + def print_pandas_pg(msg, cols, arrs_tuple): + print(f"{msg} ({np.sum(~np.isnan(arrs_tuple[0]))})") + arrs_list = list(arrs_tuple) + for i, a in enumerate(arrs_tuple): + arrs_list[i] = np.reshape(a, (-1)) + arrs_tuple2 = tuple(arrs_list) + df = pd.DataFrame(np.stack(arrs_tuple2, axis=1)) + df.columns = cols + print(df) + + print_pandas_pg( + "Same, but converted to gs axis", ["sdate", "hdate"], (sdates_pg[p, :], hdates_pg[p, :]) + ) + + print_pandas_pg( + ( + 'After "Ignore any harvests that were planted in the final year, because some cells' + ' will have incomplete growing seasons for the final year"' + ), + ["sdate", "hdate"], + (sdates_pg2[p, :], hdates_pg2[p, :]), + ) + else: + + def print_nopandas(a1, a2, msg): + print(msg) + if a1.ndim == 1: + # I don't know why these aren't side-by-side! + print(np.stack((a1, a2), axis=1)) + else: + print(np.concatenate((a1, a2), axis=1)) + + print_nopandas(sdates_ymp[:, :, p], hdates_ymp[:, :, p], "Masked:") + + print_nopandas( + np.transpose(sdates_pym, (1, 2, 0))[:, :, p], + np.transpose(hdates_pym, (1, 2, 0))[:, :, p], + 'After "Ignore harvests from before this output began"', + ) + + print_nopandas( + np.transpose(sdates_pym2, (1, 2, 0))[:, :, p], + np.transpose(hdates_pym2, (1, 2, 0))[:, :, p], + 'After "In years with no sowing, pretend the first no-harvest is meaningful"', + ) + + print_nopandas( + np.transpose(sdates_pym3, (1, 2, 0))[:, :, p], + np.transpose(hdates_pym3, (1, 2, 0))[:, :, p], + ( + 'After "In years with sowing that are followed by inactive years, check whether the' + " last sowing was harvested before the patch was deactivated. If not, pretend the" + ' LAST [easier to implement!] no-harvest is meaningful."' + ), + ) + + print_nopandas(sdates_pg[p, :], hdates_pg[p, :], "Same, but converted to gs axis") + + print_nopandas( + sdates_pg2[p, :], + hdates_pg2[p, :], + ( + 'After "Ignore any harvests that were planted in the final year, because some cells' + ' will have incomplete growing seasons for the final year"' + ), + ) + + print("\n\n") + + # Set up empty Dataset with time axis as "gs" (growing season) instead of what CLM puts out. # Includes all the same variables as the input dataset, minus any that had dimensions mxsowings or mxharvests. def set_up_ds_with_gs_axis(ds_in): From ea14e554a399e704cd0e5f8f4e89b9258d1fb3c9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 11:09:03 -0600 Subject: [PATCH 0923/2067] fsurdat method works! Removed flanduse_timeseries option. --- cime_config/SystemTests/rxcropmaturity.py | 53 +-------- .../ctsm/crop_calendars/make_lu_for_gddgen.py | 111 ------------------ 2 files changed, 6 insertions(+), 158 deletions(-) delete mode 100644 python/ctsm/crop_calendars/make_lu_for_gddgen.py diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 6c9272b059..f0725a3370 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -27,9 +27,6 @@ # cf_units caused problems in utils.import_ds(). this_conda_env = "ctsm_pylib" -# Should GDD-Generating run use fsurdat method? -gddgen_use_fsurdat = True - class RXCROPMATURITY(SystemTestsCommon): def __init__(self, case): @@ -119,25 +116,17 @@ def run_phase(self): "use_mxmat = .false.", ]) - """ - If needed, generate a surface dataset file with no crops missing years - """ - - # If flanduse_timeseries is defined, we need to make our own version for - # this test (if we haven't already). + # If flanduse_timeseries is defined, we need to make a static version for this test. This + # should have every crop in most of the world. self._get_flanduse_timeseries_in(case_gddgen) if self._flanduse_timeseries_in is not None: # Download files from the server, if needed case_gddgen.check_all_input_data() - # Make custom version of input file - if gddgen_use_fsurdat: - logger.info("SSRLOG run make_surface_for_gddgen") - self._run_make_surface_for_gddgen(case_gddgen) - else: - logger.info("SSRLOG run make_lu_for_gddgen") - self._run_make_lu_for_gddgen(case_gddgen) + # Make custom version of surface file + logger.info("SSRLOG run make_surface_for_gddgen") + self._run_make_surface_for_gddgen(case_gddgen) #------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -243,37 +232,7 @@ def _setup_all(self): self._modify_user_nl_allruns() logger.info("SSRLOG _setup_all done") - - def _run_make_lu_for_gddgen(self, case_gddgen): - - # Where we will save the flanduse_timeseries version for this test - self._flanduse_timeseries_out = os.path.join(self._path_gddgen, 'flanduse_timeseries.nc') - - # Make flanduse_timeseries for this test, if not already done - if not os.path.exists(self._flanduse_timeseries_out): - - first_fake_year = self._run_startyear - last_fake_year = first_fake_year + self._run_Nyears - - tool_path = os.path.join(self._ctsm_root, - 'python', 'ctsm', 'crop_calendars', - 'make_lu_for_gddgen.py') - command = " ".join([ - f"python3 {tool_path}", - f"--flanduse-timeseries {self._flanduse_timeseries_in}", - f"-y1 {first_fake_year}", - f"-yN {last_fake_year}", - f"--outfile {self._flanduse_timeseries_out}", - ]) - self._run_python_script(case_gddgen, command, tool_path) - - # Modify namelist - logger.info("SSRLOG modify user_nl files: new flanduse_timeseries") - self._append_to_user_nl_clm([ - "flanduse_timeseries = '{}'".format(self._flanduse_timeseries_out), - ]) - - + # Unused because I couldn't get the GDD-Generating run to work with the fsurdat file generated # by make_surface_for_gddgen.py. However, I think it'd be cleaner to just do the GDD-Generating # run with a surface file (and no flanduse_timeseries file) since that run relies on land use diff --git a/python/ctsm/crop_calendars/make_lu_for_gddgen.py b/python/ctsm/crop_calendars/make_lu_for_gddgen.py deleted file mode 100644 index 14d061f0ac..0000000000 --- a/python/ctsm/crop_calendars/make_lu_for_gddgen.py +++ /dev/null @@ -1,111 +0,0 @@ -import numpy as np -import xarray as xr -import sys, argparse - - -def main(argv): - ############################### - ### Process input arguments ### - ############################### - - # Set arguments - parser = argparse.ArgumentParser(description="ADD DESCRIPTION HERE") - parser.add_argument( - "-l", - "--flanduse_timeseries", - "--flanduse-timeseries", - help="Land-use timeseries file (flanduse_timeseries) for CLM run", - required=True, - ) - parser.add_argument( - "-y1", - "--first_fake_year", - "--first-fake-year", - type=int, - help="First year in the output flanduse_timeseries file", - ) - parser.add_argument( - "-yN", - "--last_fake_year", - "--last-fake-year", - type=int, - help="Last year in the output flanduse_timeseries file", - ) - parser.add_argument("-o", "--outfile", help="Output flanduse_timeseries file") - args = parser.parse_args(argv) - - ds_in = xr.open_dataset(args.flanduse_timeseries) - if args.first_fake_year is None: - args.first_fake_year = ds_in["time"].values[0].year - if args.last_fake_year is None: - args.last_fake_year = ds_in["time"].values[-1].year - - if args.outfile is None: - args.outfile = args.flanduse_timeseries.replace( - ".nc", f".gddgen{args.first_fake_year}-{args.last_fake_year}.nc" - ) - - ########################## - ### Import and process ### - ########################## - - ds_tmp = ds_in.sel(time=slice(args.first_fake_year, args.last_fake_year)).copy() - - # Where is each crop ever active? - if "AREA" not in ds_tmp: - ds_tmp["AREA"] = xr.DataArray( - data=np.ones_like(ds_tmp["LANDFRAC_PFT"]), - dims=ds_tmp["LANDFRAC_PFT"].dims, - coords=ds_tmp["LANDFRAC_PFT"].coords, - ) - ds_tmp["AREA_CROP"] = (ds_tmp.AREA * ds_tmp.LANDFRAC_PFT * ds_tmp.PCT_CROP / 100).transpose( - "time", "lsmlat", "lsmlon" - ) - ds_tmp["AREA_CFT"] = (ds_tmp["AREA_CROP"] * ds_tmp.PCT_CFT / 100).transpose( - "time", "cft", "lsmlat", "lsmlon" - ) - ds_area_max = ds_tmp["AREA_CFT"].max(dim="time") - ds_tmp["ever_active_bycft"] = (ds_area_max > 0).transpose("cft", "lsmlat", "lsmlon") - ds_tmp["ever_active"] = ds_tmp["ever_active_bycft"].any(dim="cft") - - # For cells that EVER have cropland, when do they have 0 crop area? Change those 0% values to 1%. - new_pct_crop_ar = ds_tmp["PCT_CROP"].values - new_pct_crop_ar[np.where((ds_tmp["AREA_CROP"] == 0) & ds_tmp["ever_active"])] = 1.0 - ds_tmp["PCT_CROP"] = xr.DataArray( - data=new_pct_crop_ar, coords=ds_tmp["PCT_CROP"].coords, attrs=ds_tmp["PCT_CROP"].attrs - ) - ds_tmp["AREA_CROP"] = (ds_tmp.AREA * ds_tmp.LANDFRAC_PFT * ds_tmp.PCT_CROP / 100).transpose( - "time", "lsmlat", "lsmlon" - ) - if np.any((ds_tmp["AREA_CROP"] == 0) & ds_tmp["ever_active"]): - raise RuntimeError("Failed to fill 0% CROP with 1% where needed.") - - # For cells that EVER have each CFT, when do they have 0 area of that CFT? Change those 0% values to something positive. - new_pct_cft_tcyx = ds_tmp["PCT_CFT"].values - new_pct_cft_tcyx[np.where((ds_tmp["AREA_CFT"] == 0) & ds_tmp["ever_active"])] = 1.0 - # Ensure sum to 100 - i = 0 - while np.any(~np.isclose(np.sum(new_pct_cft_tcyx, axis=1), 100.0)): - i += 1 - if i > 10: - raise RuntimeError("too many iterations") - new_pct_cft_tcyx = 100 * ( - new_pct_cft_tcyx / np.expand_dims(np.sum(new_pct_cft_tcyx, axis=1), axis=1) - ) - ds_tmp["PCT_CFT"] = xr.DataArray( - data=new_pct_cft_tcyx, coords=ds_tmp["PCT_CFT"].coords, attrs=ds_tmp["PCT_CFT"].attrs - ) - - ########################## - ### Save output netCDF ### - ########################## - - ds_out = xr.concat( - (ds_in.copy().sel(time=slice(0, args.first_fake_year - 1)), ds_tmp), dim="time" - ) - ds_out = ds_out.drop([v for v in ds_out if v not in ds_in]) - ds_out.to_netcdf(args.outfile, format="NETCDF3_64BIT") - - -if __name__ == "__main__": - main(sys.argv[1:]) From f5120816030e4d33ad9b4178100ccb80147b00e4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 11:46:23 -0600 Subject: [PATCH 0924/2067] Reworked RXCROPMATURITY log message prefix. --- cime_config/SystemTests/rxcropmaturity.py | 28 +++++++++++------------ 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 6c9272b059..e3b34a3257 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -95,16 +95,16 @@ def run_phase(self): # (1) Set up GDD-generating run #------------------------------------------------------------------- # Create clone to be GDD-Generating case - logger.info("SSRLOG cloning setup") + logger.info("RXCROPMATURITY log: cloning setup") case_rxboth = self._case caseroot = self._case.get_value("CASEROOT") clone_path = f"{caseroot}.gddgen" self._path_gddgen = clone_path if os.path.exists(self._path_gddgen): shutil.rmtree(self._path_gddgen) - logger.info("SSRLOG cloning") + logger.info("RXCROPMATURITY log: cloning") case_gddgen = self._case.create_clone(clone_path, keepexe=True) - logger.info("SSRLOG done cloning") + logger.info("RXCROPMATURITY log: done cloning") os.chdir(self._path_gddgen) self._set_active_case(case_gddgen) @@ -113,7 +113,7 @@ def run_phase(self): self._setup_all() # Add stuff specific to GDD-Generating run - logger.info("SSRLOG modify user_nl files: generate GDDs") + logger.info("RXCROPMATURITY log: modify user_nl files: generate GDDs") self._append_to_user_nl_clm([ "generate_crop_gdds = .true.", "use_mxmat = .false.", @@ -133,16 +133,16 @@ def run_phase(self): # Make custom version of input file if gddgen_use_fsurdat: - logger.info("SSRLOG run make_surface_for_gddgen") + logger.info("RXCROPMATURITY log: run make_surface_for_gddgen") self._run_make_surface_for_gddgen(case_gddgen) else: - logger.info("SSRLOG run make_lu_for_gddgen") + logger.info("RXCROPMATURITY log: run make_lu_for_gddgen") self._run_make_lu_for_gddgen(case_gddgen) #------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file #------------------------------------------------------------------- - logger.info("SSRLOG Start GDD-Generating run") + logger.info("RXCROPMATURITY log: Start GDD-Generating run") # As per SSP test: # "No history files expected, set suffix=None to avoid compare error" @@ -162,7 +162,7 @@ def run_phase(self): self._setup_all() # Add stuff specific to Prescribed Calendars run - logger.info("SSRLOG modify user_nl files: Prescribed Calendars") + logger.info("RXCROPMATURITY log: modify user_nl files: Prescribed Calendars") self._append_to_user_nl_clm([ "generate_crop_gdds = .false.", f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", @@ -183,7 +183,7 @@ def run_phase(self): #------------------------------------------------------------------- # (4) Check Prescribed Calendars run #------------------------------------------------------------------- - logger.info("SSRLOG output check: Prescribed Calendars") + logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") self._run_check_rxboth_run() @@ -231,7 +231,7 @@ def _get_rx_dates(self): def _setup_all(self): - logger.info("SSRLOG _setup_all start") + logger.info("RXCROPMATURITY log: _setup_all start") # Get some info self._ctsm_root = self._case.get_value('COMP_ROOT_DIR_LND') @@ -239,9 +239,9 @@ def _setup_all(self): self._run_startyear = int(run_startdate.split('-')[0]) # Set sowing dates file (and other crop calendar settings) for all runs - logger.info("SSRLOG modify user_nl files: all tests") + logger.info("RXCROPMATURITY log: modify user_nl files: all tests") self._modify_user_nl_allruns() - logger.info("SSRLOG _setup_all done") + logger.info("RXCROPMATURITY log: _setup_all done") def _run_make_lu_for_gddgen(self, case_gddgen): @@ -268,7 +268,7 @@ def _run_make_lu_for_gddgen(self, case_gddgen): self._run_python_script(case_gddgen, command, tool_path) # Modify namelist - logger.info("SSRLOG modify user_nl files: new flanduse_timeseries") + logger.info("RXCROPMATURITY log: modify user_nl files: new flanduse_timeseries") self._append_to_user_nl_clm([ "flanduse_timeseries = '{}'".format(self._flanduse_timeseries_out), ]) @@ -308,7 +308,7 @@ def _run_make_surface_for_gddgen(self, case_gddgen): self._run_python_script(case_gddgen, command, tool_path) # Modify namelist - logger.info("SSRLOG modify user_nl files: new fsurdat") + logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") self._append_to_user_nl_clm([ "fsurdat = '{}'".format(self._fsurdat_out), "do_transient_crops = .false.", From 8a8134354e1818ededae29728d6cd87b14220def Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 16:00:07 -0600 Subject: [PATCH 0925/2067] RXCROPMATURITY gddgen now uses simplified method to get fsurdat. BROKEN FOR 1-DEG Start with the run's real fsurdat file, move all the natural area into crops, and finally assign each crop 1/64 of the crop area. Works for 10x15 but breaks at 1-degree: decompInit_lnd(): Number of processes exceeds number of land grid cells 1800 456 --- cime_config/SystemTests/rxcropmaturity.py | 9 ++- .../make_fsurdat_all_crops_everywhere.py | 56 +++++++++++++++++++ 2 files changed, 60 insertions(+), 5 deletions(-) create mode 100755 python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index f0725a3370..eb4e5a682d 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -259,11 +259,10 @@ def _run_make_surface_for_gddgen(self, case_gddgen): if not os.path.exists(self._fsurdat_out): tool_path = os.path.join(self._ctsm_root, 'python', 'ctsm', 'crop_calendars', - 'make_surface_for_gddgen.py') + 'make_fsurdat_all_crops_everywhere.py') command = f"python3 {tool_path} "\ - + f"--flanduse-timeseries {self._flanduse_timeseries_in} "\ - + f"--fsurdat {self._fsurdat_in} "\ - + f"--outfile {self._fsurdat_out}" + + f"-i {self._flanduse_timeseries_in} "\ + + f"-o {self._fsurdat_out}" self._run_python_script(case_gddgen, command, tool_path) # Modify namelist @@ -425,4 +424,4 @@ def _get_flanduse_timeseries_in(self, case): flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) if flanduse_timeseries_in: self._flanduse_timeseries_in = flanduse_timeseries_in.group(1) - break \ No newline at end of file + break diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py new file mode 100755 index 0000000000..b5774aab9c --- /dev/null +++ b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py @@ -0,0 +1,56 @@ + +import numpy as np +import xarray as xr +import sys +import argparse + + +def main(file_in, file_out): + # Import + + file_in = "/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr2000_c190214.nc" + in_ds = xr.open_dataset(file_in) + + out_ds = in_ds.copy() + in_ds.close() + + # Move all natural land into crop + out_ds['PCT_CROP'] += in_ds['PCT_NATVEG'] + out_ds['PCT_NATVEG'] -= in_ds['PCT_NATVEG'] + + # Put some of every crop in every gridcell + pct_cft = np.full_like(in_ds['PCT_CFT'].values, 100 / in_ds.dims['cft']) + out_ds['PCT_CFT'] = xr.DataArray(data=pct_cft, + attrs=in_ds['PCT_CFT'].attrs, + dims=in_ds['PCT_CFT'].dims) + + # Save + out_ds.to_netcdf(file_out, format="NETCDF3_64BIT") + + +if __name__ == "__main__": + ############################### + ### Process input arguments ### + ############################### + parser = argparse.ArgumentParser(description="Creates a surface dataset with all natural land moved into crops, and with every crop present in every gridcell.") + + # Required + parser.add_argument( + "-i", + "--input-file", + help="Surface dataset (fsurdat) file to process", + required=True, + ) + parser.add_argument( + "-o", + "--output-file", + help="Where to save the new surface dataset file", + required=True, + ) + + # Get arguments + args = parser.parse_args(sys.argv[1:]) + + # Process + main(args.input_file, args.output_file) + From 8f5b1bde63f18286a91f9671898c062b976b7c90 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 15 May 2023 16:59:52 -0600 Subject: [PATCH 0926/2067] RXCROPMATURITY: Fix to call of make_fsurdat_all_crops_everywhere.py. --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index eb4e5a682d..f1375cb1da 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -261,7 +261,7 @@ def _run_make_surface_for_gddgen(self, case_gddgen): 'python', 'ctsm', 'crop_calendars', 'make_fsurdat_all_crops_everywhere.py') command = f"python3 {tool_path} "\ - + f"-i {self._flanduse_timeseries_in} "\ + + f"-i {self._fsurdat_in} "\ + f"-o {self._fsurdat_out}" self._run_python_script(case_gddgen, command, tool_path) From 22d4f6acf08ec78d134cd5a89d167d43b0af566c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 16 May 2023 09:12:23 -0600 Subject: [PATCH 0927/2067] make_fsurdat_all_crops_everywhere.py now respects -i/--input-file. --- python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py index b5774aab9c..8e748b98a4 100755 --- a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py +++ b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py @@ -8,7 +8,6 @@ def main(file_in, file_out): # Import - file_in = "/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_10x15_hist_78pfts_CMIP6_simyr2000_c190214.nc" in_ds = xr.open_dataset(file_in) out_ds = in_ds.copy() From 67009619235fe4292a0bce42302e3d11ff0b685b Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Wed, 17 May 2023 08:59:21 -0600 Subject: [PATCH 0928/2067] Update ChangeLog --- doc/ChangeLog | 54 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 55 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index e82ff156bb..3ec1e8385c 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,58 @@ =============================================================== +Tag name: ctsm5.1.dev125 +Originator(s): jpalex (John Paul Alex) +Date: Wed May 17 08:56:41 MDT 2023 +One-line Summary: Added cache for clock step_size in clm_time_manager.F90 + +Purpose and description of changes +---------------------------------- + +Added cache for clock step_size in clm_time_manager.F90 to improve +performance. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#207 (Improve performance of get_step_size) + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- PASS + izumi ------- PASS + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/2004 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev124 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) / mvertens / adamrher / MiCurry / jtrusdal / TeaganKing Date: Tue May 9 16:52:05 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index c73ffb1b64..a3e68c6581 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev125 jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90 ctsm5.1.dev124 erik 05/09/2023 Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data ctsm5.1.dev123 sacks 05/01/2023 Updates needed for pFUnit 4 and other externals updates ctsm5.1.dev122 sacks 04/23/2023 Rework handling of evaporation constraint in SoilFluxes From 002f95dbbedbe1f20c8ea7246bcab4735dd3215d Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Wed, 17 May 2023 09:07:55 -0600 Subject: [PATCH 0929/2067] Minor edit to ChangeLog --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 3ec1e8385c..c9bc6eedbd 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,6 +1,6 @@ =============================================================== Tag name: ctsm5.1.dev125 -Originator(s): jpalex (John Paul Alex) +Originator(s): jpalex (John Alex) Date: Wed May 17 08:56:41 MDT 2023 One-line Summary: Added cache for clock step_size in clm_time_manager.F90 From b93a1f7bf2459fd264f86996668e349c543cc412 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Wed, 17 May 2023 09:19:24 -0600 Subject: [PATCH 0930/2067] Clean up whitespace --- src/cpl/share_esmf/UrbanTimeVarType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/UrbanTimeVarType.F90 b/src/cpl/share_esmf/UrbanTimeVarType.F90 index b638d31b7a..088ec9eeae 100644 --- a/src/cpl/share_esmf/UrbanTimeVarType.F90 +++ b/src/cpl/share_esmf/UrbanTimeVarType.F90 @@ -256,7 +256,7 @@ subroutine urbantv_interp(this, bounds) ! lun%gricell(l) is within [begg, endg] ig = lun%gridcell(l) - bounds%begg + 1 - ! Since we are within an urban land unit, we know that + ! Since we are within an urban land unit, we know that ! lun%itype is within [pisturb_MIN, isturb_MAX] this%t_building_max(l) = dataptr2d(ig, lun%itype(l)) else From f59632a2f575e35d422e838a5422e393c705345d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 May 2023 09:48:27 -0700 Subject: [PATCH 0931/2067] remove drought history output These outputs have been converted to pft-level variables. Given that we avoid multiplexed outputs for the baseline fates these are not replaced. --- cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 2a915f2fd7..f2f02d9180 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -4,10 +4,8 @@ hist_nhtfrq = -24 hist_empty_htapes = .true. fates_spitfire_mode = 1 hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', -'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', -'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', -'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF', -'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN', +'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD', +'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON', 'FATES_CANOPY_SPREAD', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI', 'FATES_ROS','FATES_EFFECT_WSPEED', 'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY', 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF', From 882678a77bf07c05b8356f656b13fb5372fa3b7c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 May 2023 09:51:45 -0700 Subject: [PATCH 0932/2067] update default fates parameter file name --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6bb5d60aa7..dd9f05d762 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc +lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230517.nc From f711161ab0dc321c3e0c3795068491d296eb5c25 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 17 May 2023 09:52:43 -0700 Subject: [PATCH 0933/2067] update external pointer to fates --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index f4a9eae9c6..aec92c2173 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.65.3_api.25.4.0 +tag = sci.1.66.0_api.25.5.0 required = True [externals_description] From 7e6c64c02ff30f77bf1de5f8ef37dfdab4d5b25a Mon Sep 17 00:00:00 2001 From: Jim Edwards Date: Wed, 17 May 2023 11:07:13 -0600 Subject: [PATCH 0934/2067] black reformat python files for consistancy across cesm --- cime_config/buildlib | 138 +++++++++++++++----------- cime_config/buildnml | 227 ++++++++++++++++++++++++++++--------------- 2 files changed, 227 insertions(+), 138 deletions(-) diff --git a/cime_config/buildlib b/cime_config/buildlib index 31b7fe3d38..4e3a89f1fd 100755 --- a/cime_config/buildlib +++ b/cime_config/buildlib @@ -27,19 +27,26 @@ def _write_ctsm_mk(gmake, gmake_opts, makefile, exeroot, libroot): This file can be included by atmosphere model builds outside of cime. """ - cime_output_file = os.path.join(exeroot, 'cime_variables.mk') + cime_output_file = os.path.join(exeroot, "cime_variables.mk") # Set COMP_NAME=driver because some link flags are set differently when COMP_NAME=driver, and # those are the ones we want here. - cmd = ("{gmake} write_include_and_link_flags OUTPUT_FILE={cime_output_file} " - "COMP_NAME=driver {gmake_opts} -f {makefile} ").format( - gmake=gmake, cime_output_file=cime_output_file, gmake_opts=gmake_opts, makefile=makefile) + cmd = ( + "{gmake} write_include_and_link_flags OUTPUT_FILE={cime_output_file} " + "COMP_NAME=driver {gmake_opts} -f {makefile} " + ).format( + gmake=gmake, + cime_output_file=cime_output_file, + gmake_opts=gmake_opts, + makefile=makefile, + ) rc, out, err = run_cmd(cmd) - logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n"%(cmd,out,err)) + logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n" % (cmd, out, err)) expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc)) - ctsm_mk_path = os.path.join(exeroot, 'ctsm.mk') - with open(ctsm_mk_path, 'w') as ctsm_mk: - ctsm_mk.write(""" + ctsm_mk_path = os.path.join(exeroot, "ctsm.mk") + with open(ctsm_mk_path, "w") as ctsm_mk: + ctsm_mk.write( + """ # ====================================================================== # Include this file to get makefile variables needed to include / link # LILAC/CTSM in an atmosphere model's build @@ -54,13 +61,15 @@ def _write_ctsm_mk(gmake, gmake_opts, makefile, exeroot, libroot): # should not be included directly in an atmosphere model's build. # ====================================================================== -""") +""" + ) with open(cime_output_file) as infile: ctsm_mk.write(infile.read()) ctsm_bld_dir = os.path.abspath(os.path.join(libroot, os.pardir)) - with open(ctsm_mk_path, 'a') as ctsm_mk: - ctsm_mk.write(""" + with open(ctsm_mk_path, "a") as ctsm_mk: + ctsm_mk.write( + """ # ====================================================================== # The following settings are meant for internal use, and generally # should not be included directly in an atmosphere model's build. @@ -77,11 +86,15 @@ CTSM_INC = $(CTSM_BLD_DIR)/clm/obj CTSM_INCLUDES = $(CIME_ESMF_F90COMPILEPATHS) -I$(CIME_CSM_SHR_INCLUDE) -I$(CTSM_INC) CTSM_LIBS = -L$(CTSM_BLD_DIR)/lib -lclm $(CIME_ULIBS) $(CIME_SLIBS) $(CIME_MLIBS) $(CIME_F90_LDFLAGS) -""".format(ctsm_bld_dir=ctsm_bld_dir)) +""".format( + ctsm_bld_dir=ctsm_bld_dir + ) + ) + ############################################################################### def _main_func(): -############################################################################### + ############################################################################### caseroot, libroot, bldroot = parse_input(sys.argv) @@ -96,77 +109,88 @@ def _main_func(): driver = case.get_value("COMP_INTERFACE").lower() lilac_mode = case.get_value("LILAC_MODE") - if lilac_mode == 'on': + if lilac_mode == "on": driver = "lilac" - #------------------------------------------------------- + # ------------------------------------------------------- # create Filepath file - #------------------------------------------------------- + # ------------------------------------------------------- compname = case.get_value("COMP_LND") - filepath_file = os.path.join(bldroot,"Filepath") + filepath_file = os.path.join(bldroot, "Filepath") if not os.path.isfile(filepath_file): caseroot = case.get_value("CASEROOT") - expect( ((compname == "clm") or (compname == "ctsm")), "Unexpected COMP_LND name: %s" % (compname)) - - paths = [os.path.join(caseroot,"SourceMods","src."+compname), - os.path.join(lnd_root,"src","cpl",driver), - os.path.join(lnd_root,"src","main"), - os.path.join(lnd_root,"src","biogeophys"), - os.path.join(lnd_root,"src","biogeochem"), - os.path.join(lnd_root,"src","soilbiogeochem"), - os.path.join(lnd_root,"src","dyn_subgrid"), - os.path.join(lnd_root,"src","init_interp"), - os.path.join(lnd_root,"src","self_tests"), - os.path.join(lnd_root,"src","fates"), - os.path.join(lnd_root,"src","fates","main"), - os.path.join(lnd_root,"src","fates","biogeophys"), - os.path.join(lnd_root,"src","fates","biogeochem"), - os.path.join(lnd_root,"src","fates","fire"), - os.path.join(lnd_root,"src","fates","parteh"), - os.path.join(lnd_root,"src","utils"), - os.path.join(lnd_root,"src","cpl"), - os.path.join(lnd_root,"src","cpl","utils")] - - if lilac_mode == 'on': - paths.append(os.path.join(lnd_root,"lilac","src")) + expect( + ((compname == "clm") or (compname == "ctsm")), + "Unexpected COMP_LND name: %s" % (compname), + ) + + paths = [ + os.path.join(caseroot, "SourceMods", "src." + compname), + os.path.join(lnd_root, "src", "cpl", driver), + os.path.join(lnd_root, "src", "main"), + os.path.join(lnd_root, "src", "biogeophys"), + os.path.join(lnd_root, "src", "biogeochem"), + os.path.join(lnd_root, "src", "soilbiogeochem"), + os.path.join(lnd_root, "src", "dyn_subgrid"), + os.path.join(lnd_root, "src", "init_interp"), + os.path.join(lnd_root, "src", "self_tests"), + os.path.join(lnd_root, "src", "fates"), + os.path.join(lnd_root, "src", "fates", "main"), + os.path.join(lnd_root, "src", "fates", "biogeophys"), + os.path.join(lnd_root, "src", "fates", "biogeochem"), + os.path.join(lnd_root, "src", "fates", "fire"), + os.path.join(lnd_root, "src", "fates", "parteh"), + os.path.join(lnd_root, "src", "utils"), + os.path.join(lnd_root, "src", "cpl"), + os.path.join(lnd_root, "src", "cpl", "utils"), + ] + + if lilac_mode == "on": + paths.append(os.path.join(lnd_root, "lilac", "src")) # If we want to build with a real river model (e.g., MOSART), we'll need # to use its directories in place of stub_rof - paths.append(os.path.join(lnd_root,"lilac","stub_rof")) + paths.append(os.path.join(lnd_root, "lilac", "stub_rof")) - if (driver == 'lilac' or driver == 'nuopc'): - paths.append(os.path.join(lnd_root,"src","cpl","share_esmf")) + if driver == "lilac" or driver == "nuopc": + paths.append(os.path.join(lnd_root, "src", "cpl", "share_esmf")) with open(filepath_file, "w") as filepath: filepath.write("\n".join(paths)) filepath.write("\n") - #------------------------------------------------------- + # ------------------------------------------------------- # create the library in libroot - #------------------------------------------------------- + # ------------------------------------------------------- - complib = os.path.join(libroot,"lib%s.a"%(compname)) + complib = os.path.join(libroot, "lib%s.a" % (compname)) - cmd = "{} complib -j {} COMP_NAME={} COMPLIB={} -f {} {}" \ - .format(gmake, gmake_j, compname, complib, makefile, gmake_opts) + cmd = "{} complib -j {} COMP_NAME={} COMPLIB={} -f {} {}".format( + gmake, gmake_j, compname, complib, makefile, gmake_opts + ) rc, out, err = run_cmd(cmd) - logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n"%(cmd,out,err)) + logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n" % (cmd, out, err)) expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc)) # ------------------------------------------------------------------------ # for lilac usage, we need a file containing some Makefile variables (for the atmosphere model's build) # ------------------------------------------------------------------------ - if lilac_mode == 'on': - _write_ctsm_mk(gmake=gmake, - gmake_opts=gmake_opts, - makefile=makefile, - exeroot=case.get_value("EXEROOT"), - libroot=libroot) + if lilac_mode == "on": + _write_ctsm_mk( + gmake=gmake, + gmake_opts=gmake_opts, + makefile=makefile, + exeroot=case.get_value("EXEROOT"), + libroot=libroot, + ) + ############################################################################### if __name__ == "__main__": - logger.warning( "WARNING: buildlib is being called as a program rather than a subroutine as " + - "it is expected to be in the CESM context" ) + logger.warning( + "WARNING: buildlib is being called as a program rather than a subroutine as " + + "it is expected to be in the CESM context" + ) _main_func() diff --git a/cime_config/buildnml b/cime_config/buildnml index 25724def82..65f7198b3d 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -12,10 +12,10 @@ if _CIMEROOT is None: _LIBDIR = os.path.join(_CIMEROOT, "CIME", "Tools") sys.path.append(_LIBDIR) -from standard_script_setup import * -from CIME.buildnml import create_namelist_infile, parse_input -from CIME.case import Case -from CIME.utils import expect, run_cmd +from standard_script_setup import * +from CIME.buildnml import create_namelist_infile, parse_input +from CIME.case import Case +from CIME.utils import expect, run_cmd logger = logging.getLogger(__name__) @@ -29,8 +29,8 @@ _config_cache_template = """ ############################################################################### def buildnml(case, caseroot, compname): -############################################################################### - """Build the CTSM namelist """ + ############################################################################### + """Build the CTSM namelist""" # Build the component namelist if compname != "ctsm" and compname != "clm": @@ -64,22 +64,25 @@ def buildnml(case, caseroot, compname): driver = case.get_value("COMP_INTERFACE").lower() # Create init_generated_files directory if not there - newdir = os.path.join(rundir,"init_generated_files") + newdir = os.path.join(rundir, "init_generated_files") if not os.path.exists(newdir): os.mkdir(newdir) # ----------------------------------------------------- # Error checking # ----------------------------------------------------- - if ( clm_bldnml_opts.find("-namelist") >= 0 ): - expect(False, "The -namelist option is NOT allowed to be part of CLM_BLDNML_OPTS, " + \ - "use the CLM_NAMELIST_OPTS option or add namelist items to user_nl_clm instead " ); + if clm_bldnml_opts.find("-namelist") >= 0: + expect( + False, + "The -namelist option is NOT allowed to be part of CLM_BLDNML_OPTS, " + + "use the CLM_NAMELIST_OPTS option or add namelist items to user_nl_clm instead ", + ) # ----------------------------------------------------- # Set ctsmconf # ----------------------------------------------------- - ctsmconf = os.path.join(caseroot, "Buildconf", compname+"conf") + ctsmconf = os.path.join(caseroot, "Buildconf", compname + "conf") if not os.path.isdir(ctsmconf): os.makedirs(ctsmconf) @@ -93,8 +96,10 @@ def buildnml(case, caseroot, compname): clm_phys = case.get_value("CLM_PHYSICS_VERSION") config_cache_text = _config_cache_template.format(clm_phys=clm_phys) - config_cache_path = os.path.join(caseroot, "Buildconf", compname+"conf", "config_cache.xml") - with open(config_cache_path, 'w') as config_cache_file: + config_cache_path = os.path.join( + caseroot, "Buildconf", compname + "conf", "config_cache.xml" + ) + with open(config_cache_path, "w") as config_cache_file: config_cache_file.write(config_cache_text) # ----------------------------------------------------- @@ -112,35 +117,39 @@ def buildnml(case, caseroot, compname): startfile_type = "nrevsn" if clm_force_coldstart == "on": clm_force_coldstart = "off" - logger.warning( "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type, which is a contradiction, the coldstart will be ignored\n" + - " turn off CLM_FORCE_COLDSTART, or set RUN_TYPE=hybrid to get rid of this warning") - + logger.warning( + "WARNING: You've turned on CLM_FORCE_COLDSTART for a branch run_type, which is a contradiction, the coldstart will be ignored\n" + + " turn off CLM_FORCE_COLDSTART, or set RUN_TYPE=hybrid to get rid of this warning" + ) - if (clm_force_coldstart == "on"): - logger.warning( "WARNING: CLM is starting up from a cold state" ) + if clm_force_coldstart == "on": + logger.warning("WARNING: CLM is starting up from a cold state") start_type = "cold" - if lnd_grid == 'T31': - lnd_grid = '48x96' - if lnd_grid == 'T42': - lnd_grid = '64x128' - if lnd_grid == 'T85': - lnd_grid = '128x256' - if lnd_grid == 'T341': - lnd_grid = '512x1024' + if lnd_grid == "T31": + lnd_grid = "48x96" + if lnd_grid == "T42": + lnd_grid = "64x128" + if lnd_grid == "T85": + lnd_grid = "128x256" + if lnd_grid == "T341": + lnd_grid = "512x1024" clmusr = "" if lnd_grid == "CLM_USRDAT": clm_usrdat_name = case.get_value("CLM_USRDAT_NAME") lnd_grid = clm_usrdat_name - clmusr = " -clm_usr_name %s "%clm_usrdat_name + clmusr = " -clm_usr_name %s " % clm_usrdat_name # Write warning about initial condition data if "NEON" in clm_usrdat_name and clm_force_coldstart == "off": - if ("_transient" in clm_nml_use_case) \ - and (re.fullmatch(r"\w\w\w\w\.transient", casename) is None \ - or clm_usrdat_name is "NEON.PRISM"): - logger.warning( "WARNING: Do you have approriprate initial conditions for this simulation?" \ - + " Check that the finidat file used in the lnd_in namelist is apprporiately spunup for your case" ) + if ("_transient" in clm_nml_use_case) and ( + re.fullmatch(r"\w\w\w\w\.transient", casename) is None + or clm_usrdat_name is "NEON.PRISM" + ): + logger.warning( + "WARNING: Do you have approriprate initial conditions for this simulation?" + + " Check that the finidat file used in the lnd_in namelist is apprporiately spunup for your case" + ) if comp_atm != "datm": nomeg = "-no-megan" @@ -157,42 +166,47 @@ def buildnml(case, caseroot, compname): else: glc_use_antarctica_flag = "" else: - expect(False, "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica)) + expect( + False, + "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica), + ) if clm_nml_use_case != "UNSET": - usecase = "-use_case %s" %clm_nml_use_case + usecase = "-use_case %s" % clm_nml_use_case else: usecase = "" - if ( (mask != "null") and (mask != "UNSET") ): - gridmask = "-mask %s" %mask + if (mask != "null") and (mask != "UNSET"): + gridmask = "-mask %s" % mask else: gridmask = "" - start_ymd = run_startdate.replace('-','') + start_ymd = run_startdate.replace("-", "") - if ('-01-01' in run_startdate) or ('-09-01' in run_startdate): + if ("-01-01" in run_startdate) or ("-09-01" in run_startdate): ignore = "-ignore_ic_year" else: ignore = "-ignore_ic_date" - tuning = "-lnd_tuning_mode %s "%lnd_tuning_mode + tuning = "-lnd_tuning_mode %s " % lnd_tuning_mode - spinup = "-clm_accelerated_spinup %s "%clm_accelerated_spinup + spinup = "-clm_accelerated_spinup %s " % clm_accelerated_spinup infile = os.path.join(ctsmconf, "namelist") - inputdata_file = os.path.join(caseroot,"Buildconf","ctsm.input_data_list") + inputdata_file = os.path.join(caseroot, "Buildconf", "ctsm.input_data_list") if driver == "nuopc": lndfrac_setting = " " else: lnd_domain_path = case.get_value("LND_DOMAIN_PATH") lnd_domain_file = case.get_value("LND_DOMAIN_FILE") - lndfrac_file = os.path.join(lnd_domain_path,lnd_domain_file) - lndfrac_setting = "-lnd_frac "+lndfrac_file + lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file) + lndfrac_setting = "-lnd_frac " + lndfrac_file - config_cache_file = os.path.join(caseroot,"Buildconf", compname+"conf","config_cache.xml") + config_cache_file = os.path.join( + caseroot, "Buildconf", compname + "conf", "config_cache.xml" + ) # ----------------------------------------------------- # Clear out old data @@ -206,40 +220,59 @@ def buildnml(case, caseroot, compname): # ----------------------------------------------------- ninst = int(ninst_lnd) - for inst_counter in range(1, ninst+1): + for inst_counter in range(1, ninst + 1): # determine instance string inst_string = "" if ninst > 1: - inst_string = '_' + '%04d' % inst_counter + inst_string = "_" + "%04d" % inst_counter # If multi-instance case does not have restart file, use # single-case restart for each instance rpointer = "rpointer.lnd" - if (os.path.isfile(os.path.join(rundir,rpointer)) and - (not os.path.isfile(os.path.join(rundir,rpointer + inst_string)))): - shutil.copy(os.path.join(rundir, rpointer), - os.path.join(rundir, rpointer + inst_string)) + if os.path.isfile(os.path.join(rundir, rpointer)) and ( + not os.path.isfile(os.path.join(rundir, rpointer + inst_string)) + ): + shutil.copy( + os.path.join(rundir, rpointer), + os.path.join(rundir, rpointer + inst_string), + ) # ----------------------------------------------------- # call build-namelist # ----------------------------------------------------- if run_type == "hybrid" or run_type == "branch": - compnames = [ "clm4", "clm5", "clm2" ] + compnames = ["clm4", "clm5", "clm2"] for comp in compnames: - clm_startfile = "%s.%s%s.r.%s-%s.nc"%(run_refcase,comp,inst_string,run_refdate,run_reftod) - if os.path.exists(os.path.join(rundir, clm_startfile)): - break - else: - clm_startfile = "%s.%s.r.%s-%s.nc"%(run_refcase,comp,run_refdate,run_reftod) - if os.path.exists(os.path.join(rundir, clm_startfile)): - logger.warning( "WARNING: the start file being used for a multi-instance case is a single instance: "+clm_startfile ) + clm_startfile = "%s.%s%s.r.%s-%s.nc" % ( + run_refcase, + comp, + inst_string, + run_refdate, + run_reftod, + ) + if os.path.exists(os.path.join(rundir, clm_startfile)): break + else: + clm_startfile = "%s.%s.r.%s-%s.nc" % ( + run_refcase, + comp, + run_refdate, + run_reftod, + ) + if os.path.exists(os.path.join(rundir, clm_startfile)): + logger.warning( + "WARNING: the start file being used for a multi-instance case is a single instance: " + + clm_startfile + ) + break if not os.path.exists(os.path.join(rundir, clm_startfile)): - logger.warning( "WARNING: Could NOT find a start file to use using"+clm_startfile ) - clm_icfile = "%s = \'%s\'"%(startfile_type, clm_startfile) + logger.warning( + "WARNING: Could NOT find a start file to use using" + clm_startfile + ) + clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile) else: clm_icfile = "" @@ -249,27 +282,55 @@ def buildnml(case, caseroot, compname): user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string) namelist_infile = os.path.join(ctsmconf, "namelist") - create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines)) - - cmd = os.path.join(lnd_root,"bld","build-namelist") - - command = ("%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist \"&clm_inparm start_ymd=%s %s/ \" " - "%s %s -res %s %s -clm_start_type %s -envxml_dir %s " - "-configuration %s -structure %s " - "%s -glc_nec %s %s -co2_ppmv %s -co2_type %s -config %s -driver %s " - "%s %s %s %s" - %(cmd, _CIMEROOT, infile, din_loc_root, inputdata_file, ignore, start_ymd, clm_namelist_opts, - nomeg, usecase, lnd_grid, clmusr, start_type, caseroot, - configuration, structure, - lndfrac_setting, glc_nec, glc_use_antarctica_flag, ccsm_co2_ppmv, clm_co2_type, config_cache_file, driver, - clm_bldnml_opts, spinup, tuning, gridmask)) + create_namelist_infile( + case, user_nl_file, namelist_infile, "\n".join(infile_lines) + ) + + cmd = os.path.join(lnd_root, "bld", "build-namelist") + + command = ( + '%s -cimeroot %s -infile %s -csmdata %s -inputdata %s %s -namelist "&clm_inparm start_ymd=%s %s/ " ' + "%s %s -res %s %s -clm_start_type %s -envxml_dir %s " + "-configuration %s -structure %s " + "%s -glc_nec %s %s -co2_ppmv %s -co2_type %s -config %s -driver %s " + "%s %s %s %s" + % ( + cmd, + _CIMEROOT, + infile, + din_loc_root, + inputdata_file, + ignore, + start_ymd, + clm_namelist_opts, + nomeg, + usecase, + lnd_grid, + clmusr, + start_type, + caseroot, + configuration, + structure, + lndfrac_setting, + glc_nec, + glc_use_antarctica_flag, + ccsm_co2_ppmv, + clm_co2_type, + config_cache_file, + driver, + clm_bldnml_opts, + spinup, + tuning, + gridmask, + ) + ) rc, out, err = run_cmd(command, from_dir=ctsmconf) - expect(rc==0,"Command %s failed rc=%d\nout=%s\nerr=%s"%(cmd,rc,out,err)) + expect(rc == 0, "Command %s failed rc=%d\nout=%s\nerr=%s" % (cmd, rc, out, err)) if out is not None: - logger.debug(" %s"%out) + logger.debug(" %s" % out) if err is not None: - logger.debug(" %s"%err) + logger.debug(" %s" % err) # ----------------------------------------------------- # copy resolved namelist to rundir @@ -280,8 +341,9 @@ def buildnml(case, caseroot, compname): file2 = os.path.join(rundir, "lnd_in") if ninst > 1: file2 += inst_string - logger.debug("CTSM namelist copy: file1 %s file2 %s " %(file1, file2)) - shutil.copy(file1,file2) + logger.debug("CTSM namelist copy: file1 %s file2 %s " % (file1, file2)) + shutil.copy(file1, file2) + ############################################################################### def _main_func(): @@ -289,9 +351,12 @@ def _main_func(): caseroot = parse_input(sys.argv) with Case(caseroot) as case: compname = case.get_value("COMP_LND") - logger.warning( "WARNING: buildnml is being called a s program rather than a subroutine " + - "as it is expected to be in the CESM context" ) + logger.warning( + "WARNING: buildnml is being called a s program rather than a subroutine " + + "as it is expected to be in the CESM context" + ) buildnml(case, caseroot, compname) + if __name__ == "__main__": _main_func() From ff7eb0513f8cb7d00cc0fb3df139a2dcb3bc513c Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Thu, 18 May 2023 17:24:02 -0600 Subject: [PATCH 0935/2067] Update ChangeLog --- doc/ChangeLog | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 54 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index c9bc6eedbd..219621c9b2 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,57 @@ =============================================================== +Tag name: ctsm5.1.dev126 +Originator(s): jpalex (John Alex) +Date: Thu May 18 17:21:59 MDT 2023 +One-line Summary: Clean up some loops in UrbanTimeVarType + +Purpose and description of changes +---------------------------------- + +Refactor some inefficient and confusing looping structures in +UrbanTimeVarType.F90 + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +- Resolves ESCOMP/CTSM#1514 (Inefficient and confusing looping structures in UrbanTimeVarType.F90) + +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- PASS + izumi ------- PASS + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/2005 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev125 Originator(s): jpalex (John Alex) Date: Wed May 17 08:56:41 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index a3e68c6581..72c9987387 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType ctsm5.1.dev125 jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90 ctsm5.1.dev124 erik 05/09/2023 Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data ctsm5.1.dev123 sacks 05/01/2023 Updates needed for pFUnit 4 and other externals updates From 595625c2bf3731da1d047d0b628a7f10c86aeadf Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 19 May 2023 11:59:57 +0200 Subject: [PATCH 0936/2067] Update ccs_config --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index e6f6a7357e..b944eb049f 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_noresm0.0.6 +tag = ccs_config_noresm0.0.7 protocol = git repo_url = https://github.com/NorESMhub/ccs_config_noresm.git local_path = ccs_config From 4ab7026ea9ba5ce4e37bb16964c574647317a016 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 19 May 2023 04:53:05 -0600 Subject: [PATCH 0937/2067] Update ChangeLog --- doc/ChangeLog | 73 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 74 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 219621c9b2..a620f38209 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,77 @@ =============================================================== +Tag name: ctsm5.1.dev127 +Originator(s): sacks (Bill Sacks) +Date: Fri May 19 04:48:30 MDT 2023 +One-line Summary: Fix nuopc cplhist test + +Purpose and description of changes +---------------------------------- + +Make some changes to the cplhist testmod that fix the cplhist test, +based on testing done by Keith Oleson: +- Point to new cplhist forcing data generated and used by Adam + Herrington and Keith Oleson +- Use DATM_PRESNDEP=none until + https://github.com/escomp/ctsm/issues/1844 is resolved + +Also, remove mct cplhist test. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +- Takes steps towards addressing ESCOMP/CTSM#1844 (Create new auxiliary + history file for cplhist test with ndep data) + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +- Changes cplhist test; new test is + SMS_D_Ld1.ne30pg3_t061.I1850Clm50BgcSpinup.cheyenne_intel.clm-cplhist +- Removes mct cplhist test + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- PASS + izumi ------- PASS + + Note that there were no baselines for the new test + (SMS_D_Ld1.ne30pg3_t061.I1850Clm50BgcSpinup.cheyenne_intel.clm-cplhist) + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- cdeps: cdeps1.0.12 -> cdeps1.0.13 + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/1999 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev126 Originator(s): jpalex (John Alex) Date: Thu May 18 17:21:59 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 72c9987387..ca203e6f21 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType ctsm5.1.dev125 jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90 ctsm5.1.dev124 erik 05/09/2023 Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data From e4ffaf0e3214a492fee1a0a3612b7f6bb03daef3 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 19 May 2023 14:52:39 +0200 Subject: [PATCH 0938/2067] update externals and config pes --- Externals.cfg | 2 +- cime_config/config_pes.xml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index b944eb049f..067fd2fa6f 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_noresm0.0.7 +tag = ccs_config_noresm0.0.8 protocol = git repo_url = https://github.com/NorESMhub/ccs_config_noresm.git local_path = ccs_config diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index d8f8afa735..0f91f049d2 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -1413,8 +1413,8 @@ - - Need at least 4 nodes to default to normal queue + + none -1 -7 From babc6f214b41a5b15dad15e0ffb81facef44e243 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 19 May 2023 10:14:09 -0400 Subject: [PATCH 0939/2067] Coupling for fates radiation changes --- cime_config/buildlib | 1 + src/utils/clmfates_interfaceMod.F90 | 9 +++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/cime_config/buildlib b/cime_config/buildlib index 31b7fe3d38..bfd733abc6 100755 --- a/cime_config/buildlib +++ b/cime_config/buildlib @@ -123,6 +123,7 @@ def _main_func(): os.path.join(lnd_root,"src","fates","biogeochem"), os.path.join(lnd_root,"src","fates","fire"), os.path.join(lnd_root,"src","fates","parteh"), + os.path.join(lnd_root,"src","fates","radiation"), os.path.join(lnd_root,"src","utils"), os.path.join(lnd_root,"src","cpl"), os.path.join(lnd_root,"src","cpl","utils")] diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c169d710ef..14b4b5fcc8 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -136,7 +136,7 @@ module CLMFatesInterfaceMod use EDInitMod , only : init_patches use EDInitMod , only : set_site_properties use EDPftVarcon , only : EDpftvarcon_inst - use EDSurfaceRadiationMod , only : ED_SunShadeFracs, ED_Norman_Radiation + use FatesRadiationDriveMod, only : FatesSunShadeFracs, FatesNormalizedCanopyRadiation use EDBtranMod , only : btran_ed, & get_active_suction_layers use EDCanopyStructureMod , only : canopy_summarization, update_hlm_dynamics @@ -1090,7 +1090,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call fates_hist%update_history_dyn( nc, & this%fates(nc)%nsites, & this%fates(nc)%sites, & - this%fates(nc)%bc_in) + this%fates(nc)%bc_in, ) if (masterproc) then write(iulog, *) 'clm: leaving fates model', bounds_clump%begg, & @@ -1917,7 +1917,7 @@ subroutine wrap_sunfrac(this,nc,atm2lnd_inst,canopystate_inst) ! as well as total patch sun/shade fraction output boundary condition ! ------------------------------------------------------------------------------- - call ED_SunShadeFracs(this%fates(nc)%nsites, & + call FatesSunShadeFracs(this%fates(nc)%nsites, & this%fates(nc)%sites, & this%fates(nc)%bc_in, & this%fates(nc)%bc_out) @@ -2431,7 +2431,7 @@ subroutine wrap_canopy_radiation(this, bounds_clump, nc, & end do end do - call ED_Norman_Radiation(this%fates(nc)%nsites, & + call FatesNormalizedCanopyRadiation(this%fates(nc)%nsites, & this%fates(nc)%sites, & this%fates(nc)%bc_in, & this%fates(nc)%bc_out) @@ -2515,6 +2515,7 @@ subroutine wrap_update_hifrq_hist(this, bounds_clump, & this%fates(nc)%nsites, & this%fates(nc)%sites, & this%fates(nc)%bc_in, & + this%fates(nc)%bc_out, & dtime) end associate From 1c50f549c24c1a97cca34f47eaf359b734f1ed69 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 19 May 2023 10:51:16 -0700 Subject: [PATCH 0940/2067] remove site-level fates drought history output this has been removed with fates pull request 958 --- cime_config/usermods_dirs/fates_sp/user_nl_clm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm index f2f68eb74c..393d63e86a 100644 --- a/cime_config/usermods_dirs/fates_sp/user_nl_clm +++ b/cime_config/usermods_dirs/fates_sp/user_nl_clm @@ -7,9 +7,9 @@ fates_spitfire_mode = 0 use_fates_fixed_biogeog = .true. use_fates_nocomp = .true. ! Turn off a list of fields that are not needed for FATES-SP mode -hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS', - 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF', - 'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN', 'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF', +hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS', + 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', + 'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF', 'FATES_STOREC_PF', 'FATES_RECRUITMENT_PF', 'FATES_MORTALITY_PF', 'FATES_PATCHAREA_AP', 'FATES_LAI_AP', 'FATES_CANOPYAREA_AP', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI', 'FATES_ROS', 'FATES_EFFECT_WSPEED', 'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY', 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF', From 3addc5d2406d01847b505d6d05529531842c5b9e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 19 May 2023 16:18:42 -0600 Subject: [PATCH 0941/2067] Run SystemTests through black, add python init to that directory, and add black checking to buildnml/buildlib and SystemTests to python directory Makefile, don't do pylint checking because it will take effort to fix --- cime_config/SystemTests/__init__.py | 0 cime_config/SystemTests/fsurdatmodifyctsm.py | 67 +++-- cime_config/SystemTests/funitctsm.py | 2 +- cime_config/SystemTests/lciso.py | 32 ++- cime_config/SystemTests/lgrain2.py | 33 ++- cime_config/SystemTests/lii.py | 28 +- cime_config/SystemTests/lii2finidatareas.py | 10 +- cime_config/SystemTests/lilacsmoke.py | 282 +++++++++++-------- cime_config/SystemTests/lreprstruct.py | 41 +-- cime_config/SystemTests/lvg.py | 32 ++- cime_config/SystemTests/lwiso.py | 34 ++- cime_config/SystemTests/soilstructud.py | 32 ++- cime_config/SystemTests/ssp.py | 18 +- cime_config/buildnml | 16 +- python/Makefile | 8 +- 15 files changed, 363 insertions(+), 272 deletions(-) create mode 100644 cime_config/SystemTests/__init__.py diff --git a/cime_config/SystemTests/__init__.py b/cime_config/SystemTests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 1427a7550f..70dfa7c434 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -12,33 +12,33 @@ logger = logging.getLogger(__name__) -class FSURDATMODIFYCTSM(SystemTestsCommon): +class FSURDATMODIFYCTSM(SystemTestsCommon): def __init__(self, case): """ initialize an object interface to the SMS system test """ SystemTestsCommon.__init__(self, case) - if not os.path.exists(os.path.join(self._get_caseroot(), - 'done_FSURDATMODIFYCTSM_setup.txt')): + if not os.path.exists( + os.path.join(self._get_caseroot(), "done_FSURDATMODIFYCTSM_setup.txt") + ): # Create out-of-the-box lnd_in to obtain fsurdat_in - case.create_namelists(component='lnd') + case.create_namelists(component="lnd") # If fsurdat_in does not exist, download it from the server case.check_all_input_data() - lnd_in_path = os.path.join(self._get_caseroot(), 'CaseDocs/lnd_in') - with open (lnd_in_path,'r') as lnd_in: + lnd_in_path = os.path.join(self._get_caseroot(), "CaseDocs/lnd_in") + with open(lnd_in_path, "r") as lnd_in: for line in lnd_in: fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) if fsurdat_in: self._fsurdat_in = fsurdat_in.group(1) break - self._fsurdat_out = os.path.join(self._get_caseroot(), 'fsurdat.nc') - self._ctsm_root = self._case.get_value( 'COMP_ROOT_DIR_LND') - self._cfg_file_path = os.path.join(self._get_caseroot(), - 'modify_fsurdat.cfg') + self._fsurdat_out = os.path.join(self._get_caseroot(), "fsurdat.nc") + self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND") + self._cfg_file_path = os.path.join(self._get_caseroot(), "modify_fsurdat.cfg") logger.info(" create config file to modify") self._create_config_file() @@ -46,36 +46,39 @@ def __init__(self, case): self._run_modify_fsurdat() logger.info(" modify user_nl files") self._modify_user_nl() - with open('done_FSURDATMODIFYCTSM_setup.txt', 'w') as fp: + with open("done_FSURDATMODIFYCTSM_setup.txt", "w") as fp: pass def _create_config_file(self): - cfg_template_path = os.path.join(self._ctsm_root, - 'tools/modify_input_files/modify_fsurdat_template.cfg') + cfg_template_path = os.path.join( + self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg" + ) - with open (self._cfg_file_path,'w') as cfg_out: - with open (cfg_template_path,'r') as cfg_in: + with open(self._cfg_file_path, "w") as cfg_out: + with open(cfg_template_path, "r") as cfg_in: for line in cfg_in: - if re.match(r' *fsurdat_in *=', line): - line = 'fsurdat_in = {}'.format(self._fsurdat_in) - elif re.match(r' *fsurdat_out *=', line): - line = 'fsurdat_out = {}'.format(self._fsurdat_out) - elif re.match(r' *idealized *=', line): - line = 'idealized = True' + if re.match(r" *fsurdat_in *=", line): + line = "fsurdat_in = {}".format(self._fsurdat_in) + elif re.match(r" *fsurdat_out *=", line): + line = "fsurdat_out = {}".format(self._fsurdat_out) + elif re.match(r" *idealized *=", line): + line = "idealized = True" cfg_out.write(line) - def _run_modify_fsurdat(self): - tool_path = os.path.join(self._ctsm_root, - 'tools/modify_input_files/fsurdat_modifier') + tool_path = os.path.join(self._ctsm_root, "tools/modify_input_files/fsurdat_modifier") self._case.load_env(reset=True) - conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " + conda_env = ". " + self._get_caseroot() + "/.env_mach_specific.sh; " # Preprend the commands to get the conda environment for python first conda_env += self._get_conda_env() # Source the env try: - subprocess.run( conda_env+"python3 "+tool_path+" "+self._cfg_file_path, shell=True, check=True) + subprocess.run( + conda_env + "python3 " + tool_path + " " + self._cfg_file_path, + shell=True, + check=True, + ) except subprocess.CalledProcessError as error: print("ERROR while getting the conda environment and/or ") print("running the fsurdat_modifier tool: ") @@ -95,9 +98,11 @@ def _run_modify_fsurdat(self): raise def _modify_user_nl(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "fsurdat = '{}'".format(self._fsurdat_out)) + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="fsurdat = '{}'".format(self._fsurdat_out), + ) def _get_conda_env(self): # @@ -107,7 +112,7 @@ def _get_conda_env(self): # Execute the module unload/load when "which conda" fails # eg on cheyenne try: - subprocess.run( "which conda", shell=True, check=True) + subprocess.run("which conda", shell=True, check=True) conda_env = " " except subprocess.CalledProcessError: # Remove python and add conda to environment for cheyennne @@ -118,4 +123,4 @@ def _get_conda_env(self): # End above to get to actual command conda_env += " && " - return( conda_env ) + return conda_env diff --git a/cime_config/SystemTests/funitctsm.py b/cime_config/SystemTests/funitctsm.py index 8634a74c2f..783e5b5d85 100644 --- a/cime_config/SystemTests/funitctsm.py +++ b/cime_config/SystemTests/funitctsm.py @@ -14,8 +14,8 @@ logger = logging.getLogger(__name__) -class FUNITCTSM(FUNIT): +class FUNITCTSM(FUNIT): def __init__(self, case): FUNIT.__init__(self, case) diff --git a/cime_config/SystemTests/lciso.py b/cime_config/SystemTests/lciso.py index 12a74d5d5c..a9edba8e80 100644 --- a/cime_config/SystemTests/lciso.py +++ b/cime_config/SystemTests/lciso.py @@ -14,24 +14,28 @@ logger = logging.getLogger(__name__) -class LCISO(SystemTestsCompareTwo): +class LCISO(SystemTestsCompareTwo): def __init__(self, case): self.comp = case.get_value("COMP_LND") - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = 'cisoallon', - run_one_description = 'carbon isotopes off', - run_two_description = 'c13 and c14 isotopes on as well as C isotope time series', - ignore_fieldlist_diffs = True) + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="cisoallon", + run_one_description="carbon isotopes off", + run_two_description="c13 and c14 isotopes on as well as C isotope time series", + ignore_fieldlist_diffs=True, + ) def _case_one_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = self.comp, - contents = "use_c13=F, use_c14=F") + append_to_user_nl_files( + caseroot=self._get_caseroot(), component=self.comp, contents="use_c13=F, use_c14=F" + ) def _case_two_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = self.comp, - contents = "use_c13=.true.,use_c14=.true.,use_c13_timeseries=.true.,use_c14_bombspike=.true." ) - + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component=self.comp, + contents="use_c13=.true.,use_c14=.true.,use_c13_timeseries=.true.,use_c14_bombspike=.true.", + ) diff --git a/cime_config/SystemTests/lgrain2.py b/cime_config/SystemTests/lgrain2.py index 129c3275e3..f4e19ad930 100644 --- a/cime_config/SystemTests/lgrain2.py +++ b/cime_config/SystemTests/lgrain2.py @@ -19,22 +19,29 @@ logger = logging.getLogger(__name__) -class LGRAIN2(SystemTestsCompareTwo): +class LGRAIN2(SystemTestsCompareTwo): def __init__(self, case): - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = 'grain1', - run_one_description = 'use a second grain pool', - run_two_description = 'use a single grain pool', - ignore_fieldlist_diffs = True) + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="grain1", + run_one_description="use a second grain pool", + run_two_description="use a single grain pool", + ignore_fieldlist_diffs=True, + ) def _case_one_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "for_testing_use_second_grain_pool=.true.") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="for_testing_use_second_grain_pool=.true.", + ) def _case_two_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "for_testing_use_second_grain_pool=.false.") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="for_testing_use_second_grain_pool=.false.", + ) diff --git a/cime_config/SystemTests/lii.py b/cime_config/SystemTests/lii.py index d89bd0aa09..de274256a3 100644 --- a/cime_config/SystemTests/lii.py +++ b/cime_config/SystemTests/lii.py @@ -35,22 +35,24 @@ logger = logging.getLogger(__name__) -class LII(SystemTestsCompareTwo): +class LII(SystemTestsCompareTwo): def __init__(self, case): - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = 'no_interp', - run_one_description = 'use_init_interp set to true', - run_two_description = 'use_init_interp set to false') + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="no_interp", + run_one_description="use_init_interp set to true", + run_two_description="use_init_interp set to false", + ) def _case_one_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "use_init_interp = .true.") + append_to_user_nl_files( + caseroot=self._get_caseroot(), component="clm", contents="use_init_interp = .true." + ) def _case_two_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "use_init_interp = .false.") - + append_to_user_nl_files( + caseroot=self._get_caseroot(), component="clm", contents="use_init_interp = .false." + ) diff --git a/cime_config/SystemTests/lii2finidatareas.py b/cime_config/SystemTests/lii2finidatareas.py index f7a0a2f10e..337e46bf39 100644 --- a/cime_config/SystemTests/lii2finidatareas.py +++ b/cime_config/SystemTests/lii2finidatareas.py @@ -58,13 +58,15 @@ logger = logging.getLogger(__name__) -class LII2FINIDATAREAS(LII): +class LII2FINIDATAREAS(LII): def __init__(self, case): super(LII2FINIDATAREAS, self).__init__(case) def _case_one_setup(self): super(LII2FINIDATAREAS, self)._case_one_setup() - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "init_interp_method = 'use_finidat_areas'") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="init_interp_method = 'use_finidat_areas'", + ) diff --git a/cime_config/SystemTests/lilacsmoke.py b/cime_config/SystemTests/lilacsmoke.py index eec54579a5..66a94068da 100644 --- a/cime_config/SystemTests/lilacsmoke.py +++ b/cime_config/SystemTests/lilacsmoke.py @@ -27,57 +27,61 @@ from CIME.SystemTests.system_tests_common import SystemTestsCommon from CIME.utils import run_cmd, run_cmd_no_fail, symlink_force, new_lid, safe_copy, append_testlog from CIME.build import post_build -from CIME.test_status import NAMELIST_PHASE, GENERATE_PHASE, BASELINE_PHASE, TEST_PASS_STATUS, TEST_FAIL_STATUS +from CIME.test_status import ( + NAMELIST_PHASE, + GENERATE_PHASE, + BASELINE_PHASE, + TEST_PASS_STATUS, + TEST_FAIL_STATUS, +) from CIME.XML.standard_module_setup import * logger = logging.getLogger(__name__) -_LILAC_RUNTIME_FILES = ['lnd_in', 'lnd_modelio.nml', 'lilac_in'] +_LILAC_RUNTIME_FILES = ["lnd_in", "lnd_modelio.nml", "lilac_in"] -class LILACSMOKE(SystemTestsCommon): +class LILACSMOKE(SystemTestsCommon): def __init__(self, case): SystemTestsCommon.__init__(self, case) def build_phase(self, sharedlib_only=False, model_only=False): if not sharedlib_only: - lndroot = self._case.get_value('COMP_ROOT_DIR_LND') - exeroot = self._case.get_value('EXEROOT') + lndroot = self._case.get_value("COMP_ROOT_DIR_LND") + exeroot = self._case.get_value("EXEROOT") build_dir = self._lilac_build_dir() - script_path = os.path.abspath(os.path.join(lndroot, 'lilac', 'build_ctsm')) + script_path = os.path.abspath(os.path.join(lndroot, "lilac", "build_ctsm")) # We only run the initial build command if the build_dir doesn't exist # yet. This is to support rebuilding the test case. (The first time through, # the build_dir won't exist yet; subsequent times, it will already exist, so # we skip to the rebuild command.) if not os.path.isdir(build_dir): - machine = self._case.get_value('MACH') - compiler = self._case.get_value('COMPILER') - debug = self._case.get_value('DEBUG') + machine = self._case.get_value("MACH") + compiler = self._case.get_value("COMPILER") + debug = self._case.get_value("DEBUG") # It would be possible to do this testing via the python interface rather # than through a separate subprocess. However, we do it through a # subprocess in order to test the full build_ctsm script, including # command-line parsing. - cmd = '{script_path} {build_dir} --machine {machine} --compiler {compiler}'.format( - script_path=script_path, - build_dir=build_dir, - machine=machine, - compiler=compiler) + cmd = "{script_path} {build_dir} --machine {machine} --compiler {compiler}".format( + script_path=script_path, build_dir=build_dir, machine=machine, compiler=compiler + ) # It isn't straightforward to determine if pnetcdf is available on a # machine. To keep things simple, always run without pnetcdf. - cmd += ' --no-pnetcdf' + cmd += " --no-pnetcdf" if debug: - cmd += ' --build-debug' - self._run_build_cmd(cmd, exeroot, 'build_ctsm.bldlog') + cmd += " --build-debug" + self._run_build_cmd(cmd, exeroot, "build_ctsm.bldlog") # We call the build script with --rebuild even for an initial build. This is # so we make sure to test the code path for --rebuild. (This is also needed if # the user rebuilds the test case, in which case this will be the only command # run, since the build_dir will already exist.) - cmd = '{script_path} {build_dir} --rebuild'.format( - script_path=script_path, - build_dir=build_dir) - self._run_build_cmd(cmd, exeroot, 'rebuild_ctsm.bldlog') + cmd = "{script_path} {build_dir} --rebuild".format( + script_path=script_path, build_dir=build_dir + ) + self._run_build_cmd(cmd, exeroot, "rebuild_ctsm.bldlog") self._build_atm_driver() @@ -95,51 +99,62 @@ def build_phase(self, sharedlib_only=False, model_only=False): post_build(self._case, logs=[], build_complete=True) def _build_atm_driver(self): - caseroot = self._case.get_value('CASEROOT') - lndroot = self._case.get_value('COMP_ROOT_DIR_LND') - blddir = os.path.join(caseroot, 'lilac_atm_driver', 'bld') + caseroot = self._case.get_value("CASEROOT") + lndroot = self._case.get_value("COMP_ROOT_DIR_LND") + blddir = os.path.join(caseroot, "lilac_atm_driver", "bld") if not os.path.exists(blddir): os.makedirs(blddir) - symlink_force(os.path.join(lndroot, 'lilac', 'atm_driver', 'Makefile'), - os.path.join(blddir, 'Makefile')) - symlink_force(os.path.join(lndroot, 'lilac', 'atm_driver', 'atm_driver.F90'), - os.path.join(blddir, 'atm_driver.F90')) - symlink_force(os.path.join(self._lilac_build_dir(), 'case', 'Macros.make'), - os.path.join(blddir, 'Macros.make')) - - makevars = 'COMPILER={compiler} DEBUG={debug} CTSM_MKFILE={ctsm_mkfile}'.format( - compiler=self._case.get_value('COMPILER'), - debug=str(self._case.get_value('DEBUG')).upper(), - ctsm_mkfile=os.path.join(self._lilac_build_dir(), 'ctsm.mk')) - makecmd = 'make {makevars} atm_driver'.format(makevars=makevars) + symlink_force( + os.path.join(lndroot, "lilac", "atm_driver", "Makefile"), + os.path.join(blddir, "Makefile"), + ) + symlink_force( + os.path.join(lndroot, "lilac", "atm_driver", "atm_driver.F90"), + os.path.join(blddir, "atm_driver.F90"), + ) + symlink_force( + os.path.join(self._lilac_build_dir(), "case", "Macros.make"), + os.path.join(blddir, "Macros.make"), + ) + + makevars = "COMPILER={compiler} DEBUG={debug} CTSM_MKFILE={ctsm_mkfile}".format( + compiler=self._case.get_value("COMPILER"), + debug=str(self._case.get_value("DEBUG")).upper(), + ctsm_mkfile=os.path.join(self._lilac_build_dir(), "ctsm.mk"), + ) + makecmd = "make {makevars} atm_driver".format(makevars=makevars) # Normally the user will source either ctsm_build_environment.sh or # ctsm_build_environment.csh before building the atmosphere model. In the context # of this test case, case.load_env does the equivalent. self._case.load_env() - self._run_build_cmd(makecmd, blddir, 'atm_driver.bldlog') + self._run_build_cmd(makecmd, blddir, "atm_driver.bldlog") def _create_link_to_atm_driver(self): - caseroot = self._case.get_value('CASEROOT') - run_exe = (self._case.get_value('run_exe')).strip() + caseroot = self._case.get_value("CASEROOT") + run_exe = (self._case.get_value("run_exe")).strip() # Make a symlink to the atm_driver executable so that the case's run command finds # it in the expected location - symlink_force(os.path.join(caseroot, 'lilac_atm_driver', 'bld', 'atm_driver.exe'), - run_exe) + symlink_force(os.path.join(caseroot, "lilac_atm_driver", "bld", "atm_driver.exe"), run_exe) def _create_runtime_inputs(self): - caseroot = self._case.get_value('CASEROOT') + caseroot = self._case.get_value("CASEROOT") runtime_inputs = self._runtime_inputs_dir() # NOTE: *** this test is currently tied to this single 10x15 grid resolution *** - lnd_grid = self._case.get_value('LND_GRID') - expect(lnd_grid == '10x15', - "this test is currently tied to this single 10x15 grid resolution") - lnd_domain_file = os.path.join(self._case.get_value('DIN_LOC_ROOT'),"share","domains", - "domain.lnd.fv10x15_gx3v7.180321.nc") + lnd_grid = self._case.get_value("LND_GRID") + expect( + lnd_grid == "10x15", "this test is currently tied to this single 10x15 grid resolution" + ) + lnd_domain_file = os.path.join( + self._case.get_value("DIN_LOC_ROOT"), + "share", + "domains", + "domain.lnd.fv10x15_gx3v7.180321.nc", + ) # Cheat a bit here: Get the fsurdat file from the already-generated lnd_in file in # the host test case - i.e., from the standard cime-based preview_namelists. But @@ -147,75 +162,96 @@ def _create_runtime_inputs(self): # we expect the user to identify fsurdat manually; in this testing situation, we # need to come up with some way to replace this manual identification, so cheating # feels acceptable. - self._case.create_namelists(component='lnd') + self._case.create_namelists(component="lnd") fsurdat = self._extract_var_from_namelist( - nl_filename=os.path.join(caseroot, 'CaseDocs', 'lnd_in'), - varname='fsurdat') + nl_filename=os.path.join(caseroot, "CaseDocs", "lnd_in"), varname="fsurdat" + ) - self._fill_in_variables_in_file(filepath=os.path.join(runtime_inputs, 'ctsm.cfg'), - replacements={'lnd_domain_file':lnd_domain_file, - 'fsurdat':fsurdat}) + self._fill_in_variables_in_file( + filepath=os.path.join(runtime_inputs, "ctsm.cfg"), + replacements={"lnd_domain_file": lnd_domain_file, "fsurdat": fsurdat}, + ) # The user_nl_ctsm in the case directory is set up based on the standard testmods # mechanism. We use that one in place of the standard user_nl_ctsm, since the one # in the case directory may contain test-specific modifications. - shutil.copyfile(src=os.path.join(caseroot, 'user_nl_ctsm'), - dst=os.path.join(runtime_inputs, 'user_nl_ctsm')) - - script_to_run = os.path.join(runtime_inputs, 'make_runtime_inputs') - self._run_build_cmd('{} --rundir {}'.format(script_to_run, runtime_inputs), - runtime_inputs, - 'make_runtime_inputs.log') + shutil.copyfile( + src=os.path.join(caseroot, "user_nl_ctsm"), + dst=os.path.join(runtime_inputs, "user_nl_ctsm"), + ) + + script_to_run = os.path.join(runtime_inputs, "make_runtime_inputs") + self._run_build_cmd( + "{} --rundir {}".format(script_to_run, runtime_inputs), + runtime_inputs, + "make_runtime_inputs.log", + ) # In lilac_in, we intentionally use the land mesh file for both atm_mesh_filename # and lnd_mesh_filename - lnd_mesh = self._case.get_value('LND_DOMAIN_MESH') - casename = self._case.get_value('CASE') - self._fill_in_variables_in_file(filepath=os.path.join(runtime_inputs, 'lilac_in'), - replacements={'caseid':casename, - 'atm_mesh_filename':lnd_mesh, - 'lnd_mesh_filename':lnd_mesh, - 'lilac_histfreq_option':'ndays'}, - placeholders={'caseid':'ctsm_lilac', - 'lilac_histfreq_option':'never'}) + lnd_mesh = self._case.get_value("LND_DOMAIN_MESH") + casename = self._case.get_value("CASE") + self._fill_in_variables_in_file( + filepath=os.path.join(runtime_inputs, "lilac_in"), + replacements={ + "caseid": casename, + "atm_mesh_filename": lnd_mesh, + "lnd_mesh_filename": lnd_mesh, + "lilac_histfreq_option": "ndays", + }, + placeholders={"caseid": "ctsm_lilac", "lilac_histfreq_option": "never"}, + ) # We run download_input_data partly because it may be needed and partly to test # this script. - script_to_run = os.path.join(runtime_inputs, 'download_input_data') - self._run_build_cmd('{} --rundir {}'.format(script_to_run, runtime_inputs), - runtime_inputs, - 'download_input_data.log') + script_to_run = os.path.join(runtime_inputs, "download_input_data") + self._run_build_cmd( + "{} --rundir {}".format(script_to_run, runtime_inputs), + runtime_inputs, + "download_input_data.log", + ) def _setup_atm_driver_rundir(self): """Set up the directory from which we will actually do the run""" - lndroot = self._case.get_value('COMP_ROOT_DIR_LND') + lndroot = self._case.get_value("COMP_ROOT_DIR_LND") rundir = self._atm_driver_rundir() if not os.path.exists(rundir): os.makedirs(rundir) - shutil.copyfile(src=os.path.join(lndroot, 'lilac', 'atm_driver', 'atm_driver_in'), - dst=os.path.join(rundir, 'atm_driver_in')) + shutil.copyfile( + src=os.path.join(lndroot, "lilac", "atm_driver", "atm_driver_in"), + dst=os.path.join(rundir, "atm_driver_in"), + ) # As elsewhere: assume the land variables also apply to the atmosphere - lnd_mesh = self._case.get_value('LND_DOMAIN_MESH') - lnd_nx = self._case.get_value('LND_NX') - lnd_ny = self._case.get_value('LND_NY') - expect(self._case.get_value('STOP_OPTION') == 'ndays', - 'LILAC testing currently assumes STOP_OPTION of ndays, not {}'.format( - self._case.get_value('STOP_OPTION'))) - stop_n = self._case.get_value('STOP_N') - casename = self._case.get_value('CASE') - self._fill_in_variables_in_file(filepath=os.path.join(rundir, 'atm_driver_in'), - replacements={'caseid':casename, - 'atm_mesh_file':lnd_mesh, - 'atm_global_nx':str(lnd_nx), - 'atm_global_ny':str(lnd_ny), - 'atm_stop_day':str(stop_n+1), - 'atm_ndays_all_segs':str(stop_n)}) + lnd_mesh = self._case.get_value("LND_DOMAIN_MESH") + lnd_nx = self._case.get_value("LND_NX") + lnd_ny = self._case.get_value("LND_NY") + expect( + self._case.get_value("STOP_OPTION") == "ndays", + "LILAC testing currently assumes STOP_OPTION of ndays, not {}".format( + self._case.get_value("STOP_OPTION") + ), + ) + stop_n = self._case.get_value("STOP_N") + casename = self._case.get_value("CASE") + self._fill_in_variables_in_file( + filepath=os.path.join(rundir, "atm_driver_in"), + replacements={ + "caseid": casename, + "atm_mesh_file": lnd_mesh, + "atm_global_nx": str(lnd_nx), + "atm_global_ny": str(lnd_ny), + "atm_stop_day": str(stop_n + 1), + "atm_ndays_all_segs": str(stop_n), + }, + ) for file_to_link in _LILAC_RUNTIME_FILES: - symlink_force(os.path.join(self._runtime_inputs_dir(), file_to_link), - os.path.join(rundir, file_to_link)) + symlink_force( + os.path.join(self._runtime_inputs_dir(), file_to_link), + os.path.join(rundir, file_to_link), + ) init_generated_files_dir = os.path.join(rundir, "init_generated_files") if not os.path.exists(init_generated_files_dir): @@ -236,8 +272,8 @@ def _cmpgen_namelists(self): because that one will have compared the test's standard CaseDocs with the files generated from here - and those two sets of namelists can be quite different. """ - caseroot = self._case.get_value('CASEROOT') - casedocs = os.path.join(caseroot, 'CaseDocs') + caseroot = self._case.get_value("CASEROOT") + casedocs = os.path.join(caseroot, "CaseDocs") if os.path.exists(casedocs): shutil.rmtree(casedocs) os.makedirs(casedocs) @@ -245,12 +281,13 @@ def _cmpgen_namelists(self): # case_cmpgen_namelists uses the existence of drv_in to decide whether namelists # need to be regenerated. We do NOT want it to regenerate namelists, so we give it # the file it wants. - with open(os.path.join(casedocs, 'drv_in'), 'a') as drv_in: + with open(os.path.join(casedocs, "drv_in"), "a") as drv_in: pass - for onefile in _LILAC_RUNTIME_FILES + ['atm_driver_in']: - safe_copy(os.path.join(self._atm_driver_rundir(), onefile), - os.path.join(casedocs, onefile)) + for onefile in _LILAC_RUNTIME_FILES + ["atm_driver_in"]: + safe_copy( + os.path.join(self._atm_driver_rundir(), onefile), os.path.join(casedocs, onefile) + ) success = self._case.case_cmpgen_namelists() # The setting of the NLCOMP phase status in case_cmpgen_namelists doesn't work @@ -259,8 +296,11 @@ def _cmpgen_namelists(self): # overwriting whatever was set by case_cmpgen_namelists). So we need to set it # here. with self._test_status: - self._test_status.set_status(NAMELIST_PHASE, TEST_PASS_STATUS if success else TEST_FAIL_STATUS, - comments="(used lilac namelists)") + self._test_status.set_status( + NAMELIST_PHASE, + TEST_PASS_STATUS if success else TEST_FAIL_STATUS, + comments="(used lilac namelists)", + ) def _extract_var_from_namelist(self, nl_filename, varname): """Tries to find a variable named varname in the given file; returns its value @@ -272,7 +312,7 @@ def _extract_var_from_namelist(self, nl_filename, varname): match = re.search(r'^ *{} *= *[\'"]([^\'"]+)'.format(varname), line) if match: return match.group(1) - expect(False, '{} not found in {}'.format(varname, nl_filename)) + expect(False, "{} not found in {}".format(varname, nl_filename)) def _fill_in_variables_in_file(self, filepath, replacements, placeholders=None): """For the given file, make the given replacements @@ -286,35 +326,37 @@ def _fill_in_variables_in_file(self, filepath, replacements, placeholders=None): if placeholders is None: placeholders = {} - orig_filepath = '{}.orig'.format(filepath) + orig_filepath = "{}.orig".format(filepath) if not os.path.exists(orig_filepath): - shutil.copyfile(src=filepath, - dst=orig_filepath) + shutil.copyfile(src=filepath, dst=orig_filepath) os.remove(filepath) counts = dict.fromkeys(replacements, 0) with open(orig_filepath) as orig_file: - with open(filepath, 'w') as new_file: + with open(filepath, "w") as new_file: for orig_line in orig_file: line = orig_line for varname in replacements: if varname in placeholders: this_placeholder = placeholders[varname] else: - this_placeholder = 'FILL_THIS_IN' + this_placeholder = "FILL_THIS_IN" line, replacement_done = self._fill_in_variable( line=line, varname=varname, value=replacements[varname], - placeholder=this_placeholder) + placeholder=this_placeholder, + ) if replacement_done: counts[varname] += 1 break new_file.write(line) for varname in counts: - expect(counts[varname] > 0, - 'Did not find any instances of <{}> to replace in {}'.format(varname, filepath)) + expect( + counts[varname] > 0, + "Did not find any instances of <{}> to replace in {}".format(varname, filepath), + ) def _fill_in_variable(self, line, varname, value, placeholder): """Fill in a placeholder variable in a config or namelist file @@ -324,9 +366,11 @@ def _fill_in_variable(self, line, varname, value, placeholder): line is for varname; otherwise returns line unchanged - replacement_done is True if the replacement was done, otherwise False """ - if re.search(r'^ *{} *='.format(varname), line): - expect(placeholder in line, - 'Placeholder to replace ({}) not found in <{}>'.format(placeholder, line.strip())) + if re.search(r"^ *{} *=".format(varname), line): + expect( + placeholder in line, + "Placeholder to replace ({}) not found in <{}>".format(placeholder, line.strip()), + ) newline = line.replace(placeholder, value) replacement_done = True else: @@ -335,13 +379,13 @@ def _fill_in_variable(self, line, varname, value, placeholder): return (newline, replacement_done) def _lilac_build_dir(self): - return os.path.join(self._case.get_value('CASEROOT'), 'lilac_build') + return os.path.join(self._case.get_value("CASEROOT"), "lilac_build") def _runtime_inputs_dir(self): - return os.path.join(self._lilac_build_dir(), 'runtime_inputs') + return os.path.join(self._lilac_build_dir(), "runtime_inputs") def _atm_driver_rundir(self): - return os.path.join(self._case.get_value('CASEROOT'), 'lilac_atm_driver', 'run') + return os.path.join(self._case.get_value("CASEROOT"), "lilac_atm_driver", "run") @staticmethod def _run_build_cmd(cmd, exeroot, logfile): @@ -378,9 +422,9 @@ def _link_to_output_files(self): directory. But then we need to create these links afterwards for the sake of baseline generation / comparison. """ - casename = self._case.get_value('CASE') - rundir = self._case.get_value('RUNDIR') - pattern = '{}*.nc'.format(casename) + casename = self._case.get_value("CASE") + rundir = self._case.get_value("RUNDIR") + pattern = "{}*.nc".format(casename) # First remove any old files from the run directory old_files = glob.glob(os.path.join(rundir, pattern)) diff --git a/cime_config/SystemTests/lreprstruct.py b/cime_config/SystemTests/lreprstruct.py index 27dab77592..f8a3300e56 100644 --- a/cime_config/SystemTests/lreprstruct.py +++ b/cime_config/SystemTests/lreprstruct.py @@ -22,31 +22,40 @@ logger = logging.getLogger(__name__) -class LREPRSTRUCT(SystemTestsCompareTwo): +class LREPRSTRUCT(SystemTestsCompareTwo): def __init__(self, case): - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = 'grain1', - run_one_description = 'use a reproductive structure pool', - run_two_description = 'use a single grain pool', - ignore_fieldlist_diffs = True) + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="grain1", + run_one_description="use a reproductive structure pool", + run_two_description="use a single grain pool", + ignore_fieldlist_diffs=True, + ) def _case_one_setup(self): # We don't really need a second grain pool for this test, but we might as well do # this to further exercise the looping over different reproductive components. - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "for_testing_use_second_grain_pool=.true.") - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "for_testing_use_repr_structure_pool=.true.") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="for_testing_use_second_grain_pool=.true.", + ) + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="for_testing_use_repr_structure_pool=.true.", + ) def _case_two_setup(self): # This is needed in the nearly-standard case to prevent grain from being used to # replenish crop seed deficits, thus making grain act like the reproductive # structure pools. (It wouldn't hurt to do this in case one as well, but it # shouldn't be needed there, since we shouldn't have any grain there anyway.) - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "for_testing_no_crop_seed_replenishment=.true.") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="for_testing_no_crop_seed_replenishment=.true.", + ) diff --git a/cime_config/SystemTests/lvg.py b/cime_config/SystemTests/lvg.py index 36fae196b2..4b990313f5 100644 --- a/cime_config/SystemTests/lvg.py +++ b/cime_config/SystemTests/lvg.py @@ -16,22 +16,28 @@ logger = logging.getLogger(__name__) -class LVG(SystemTestsCompareTwo): +class LVG(SystemTestsCompareTwo): def __init__(self, case): - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = 'more_virtual', - run_one_description = 'standard set of virtual columns', - run_two_description = 'add virtual columns over Antarctica') + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="more_virtual", + run_one_description="standard set of virtual columns", + run_two_description="add virtual columns over Antarctica", + ) def _case_one_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'multiple'") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'multiple'", + ) def _case_two_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'virtual'") - + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="glacier_region_behavior = 'single_at_atm_topo', 'virtual', 'virtual', 'virtual'", + ) diff --git a/cime_config/SystemTests/lwiso.py b/cime_config/SystemTests/lwiso.py index 1083e2ff36..37cfd42603 100644 --- a/cime_config/SystemTests/lwiso.py +++ b/cime_config/SystemTests/lwiso.py @@ -17,15 +17,18 @@ logger = logging.getLogger(__name__) -class LWISO(SystemTestsCompareTwo): +class LWISO(SystemTestsCompareTwo): def __init__(self, case): - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = 'nowiso', - run_one_description = 'water isotopes on', - run_two_description = 'water isotopes off', - ignore_fieldlist_diffs = True) + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="nowiso", + run_one_description="water isotopes on", + run_two_description="water isotopes off", + ignore_fieldlist_diffs=True, + ) def _case_one_setup(self): # BUG(wjs, 2019-07-30, ESCOMP/ctsm#495) We currently can't turn on actual water @@ -33,12 +36,15 @@ def _case_one_setup(self): # enable_water_tracer_consistency_checks rather than enable_water_isotopes; # eventually, though, we should change this to the latter. (See # .) - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "enable_water_tracer_consistency_checks=.true.") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="enable_water_tracer_consistency_checks=.true.", + ) def _case_two_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "enable_water_tracer_consistency_checks=.false.") - + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="enable_water_tracer_consistency_checks=.false.", + ) diff --git a/cime_config/SystemTests/soilstructud.py b/cime_config/SystemTests/soilstructud.py index b454695f6e..42ffae54be 100644 --- a/cime_config/SystemTests/soilstructud.py +++ b/cime_config/SystemTests/soilstructud.py @@ -16,22 +16,28 @@ logger = logging.getLogger(__name__) -class SOILSTRUCTUD(SystemTestsCompareTwo): +class SOILSTRUCTUD(SystemTestsCompareTwo): def __init__(self, case): - SystemTestsCompareTwo.__init__(self, case, - separate_builds = False, - run_two_suffix = '4SL_2m', - run_one_description = 'soil_layerstruct_userdefined', - run_two_description = 'soil_layerstruct_predefined') + SystemTestsCompareTwo.__init__( + self, + case, + separate_builds=False, + run_two_suffix="4SL_2m", + run_one_description="soil_layerstruct_userdefined", + run_two_description="soil_layerstruct_predefined", + ) def _case_one_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "soil_layerstruct_userdefined_nlevsoi = 4,soil_layerstruct_userdefined = 0.1d0,0.3d0,0.6d0,1.0d0,1.0d0") + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="soil_layerstruct_userdefined_nlevsoi = 4,soil_layerstruct_userdefined = 0.1d0,0.3d0,0.6d0,1.0d0,1.0d0", + ) def _case_two_setup(self): - append_to_user_nl_files(caseroot = self._get_caseroot(), - component = "clm", - contents = "soil_layerstruct_predefined = '4SL_2m'") - + append_to_user_nl_files( + caseroot=self._get_caseroot(), + component="clm", + contents="soil_layerstruct_predefined = '4SL_2m'", + ) diff --git a/cime_config/SystemTests/ssp.py b/cime_config/SystemTests/ssp.py index 26337d323d..bd554aeae9 100644 --- a/cime_config/SystemTests/ssp.py +++ b/cime_config/SystemTests/ssp.py @@ -18,8 +18,8 @@ logger = logging.getLogger(__name__) -class SSP(SystemTestsCommon): +class SSP(SystemTestsCommon): def __init__(self, case): """ initialize an object interface to the SSP system test @@ -48,10 +48,10 @@ def run_phase(self): stop_n1 = int(stop_nf / 2) stop_n2 = stop_nf - stop_n1 - #------------------------------------------------------------------- + # ------------------------------------------------------------------- # (1) do a spinup run in the main case in the cloned ref case # (short term archiving is on) - #------------------------------------------------------------------- + # ------------------------------------------------------------------- os.chdir(clone_path) self._set_active_case(clone) @@ -61,20 +61,24 @@ def run_phase(self): with clone: clone.set_value("CLM_ACCELERATED_SPINUP", "on") - clone.set_value("STOP_N",stop_n1) + clone.set_value("STOP_N", stop_n1) dout_sr = clone.get_value("DOUT_S_ROOT") # No history files expected, set suffix=None to avoid compare error self._skip_pnl = False self.run_indv(suffix=None, st_archive=True) - #------------------------------------------------------------------- + # ------------------------------------------------------------------- # (2) do a hybrid, non-spinup run in orig_case - #------------------------------------------------------------------- + # ------------------------------------------------------------------- os.chdir(caseroot) self._set_active_case(orig_case) - refdate = run_cmd_no_fail(r'ls -1dt {}/rest/*-00000* | head -1 | sed "s/-00000.*//" | sed "s/^.*rest\///"'.format(dout_sr)) + refdate = run_cmd_no_fail( + r'ls -1dt {}/rest/*-00000* | head -1 | sed "s/-00000.*//" | sed "s/^.*rest\///"'.format( + dout_sr + ) + ) refsec = "00000" # obtain rpointer files and necessary restart files from short term archiving directory diff --git a/cime_config/buildnml b/cime_config/buildnml index 65f7198b3d..e239f0ec58 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -96,9 +96,7 @@ def buildnml(case, caseroot, compname): clm_phys = case.get_value("CLM_PHYSICS_VERSION") config_cache_text = _config_cache_template.format(clm_phys=clm_phys) - config_cache_path = os.path.join( - caseroot, "Buildconf", compname + "conf", "config_cache.xml" - ) + config_cache_path = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml") with open(config_cache_path, "w") as config_cache_file: config_cache_file.write(config_cache_text) @@ -204,9 +202,7 @@ def buildnml(case, caseroot, compname): lndfrac_file = os.path.join(lnd_domain_path, lnd_domain_file) lndfrac_setting = "-lnd_frac " + lndfrac_file - config_cache_file = os.path.join( - caseroot, "Buildconf", compname + "conf", "config_cache.xml" - ) + config_cache_file = os.path.join(caseroot, "Buildconf", compname + "conf", "config_cache.xml") # ----------------------------------------------------- # Clear out old data @@ -269,9 +265,7 @@ def buildnml(case, caseroot, compname): break if not os.path.exists(os.path.join(rundir, clm_startfile)): - logger.warning( - "WARNING: Could NOT find a start file to use using" + clm_startfile - ) + logger.warning("WARNING: Could NOT find a start file to use using" + clm_startfile) clm_icfile = "%s = '%s'" % (startfile_type, clm_startfile) else: clm_icfile = "" @@ -282,9 +276,7 @@ def buildnml(case, caseroot, compname): user_nl_file = os.path.join(caseroot, "user_nl_clm" + inst_string) namelist_infile = os.path.join(ctsmconf, "namelist") - create_namelist_infile( - case, user_nl_file, namelist_infile, "\n".join(infile_lines) - ) + create_namelist_infile(case, user_nl_file, namelist_infile, "\n".join(infile_lines)) cmd = os.path.join(lnd_root, "bld", "build-namelist") diff --git a/python/Makefile b/python/Makefile index a1eaba0928..271e977046 100644 --- a/python/Makefile +++ b/python/Makefile @@ -22,6 +22,10 @@ PYLINT=pylint PYLINT_ARGS=-j 4 --rcfile=ctsm/.pylintrc PYLINT_SRC = \ ctsm +# NOTE: These don't pass pylint checking and should be added when we put into effort to get them to pass +# ../cime_config/SystemTests \ +# ../cime_config/buildlib \ +# ../cime_config/buildnml all: test lint black @echo @@ -46,13 +50,13 @@ lint: FORCE # Run the black check on all of the python files here and undeneath. # Use the black configure file to explicitly set a few things and specifiy the exact files. black: FORCE - black --check --config pyproject.toml . + black --check --config pyproject.toml . ../cime_config/SystemTests ../cime_config/buildlib ../cime_config/buildnml .PHONY: run_black # Run black on all of the python files here and undeneath. # Use the black configure file to explicitly set a few things and specifiy the exact files. run_black: FORCE - black --config pyproject.toml . + black --config pyproject.toml . ../cime_config/SystemTests ../cime_config/buildlib ../cime_config/buildnml .PHONY: clean clean: FORCE From e91139b00431faad8ccfaff1404ddbdeb119bc00 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 20 May 2023 15:28:30 -0600 Subject: [PATCH 0942/2067] RXCROPMATURITY: Updated s/hdates for f09_g17. --- cime_config/SystemTests/rxcropmaturity.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index f1375cb1da..f2ab7a74de 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -199,10 +199,10 @@ def _get_rx_dates(self): elif lnd_grid == "0.9x1.25": self._sdatefile = os.path.join( blessed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230510_133957.fill1.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.fill1.nc") self._hdatefile = os.path.join( blessed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230510_133958.fill1.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.fill1.nc") else: error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" logger.error(error_message) From 298845e9157341feb7478f1bbd7cec61b6ac16b8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 20 May 2023 14:56:39 -0700 Subject: [PATCH 0943/2067] First commit bringing tillage in from Mike Graham's code. --- src/biogeochem/CNDriverMod.F90 | 3 +- src/biogeochem/EDBGCDynMod.F90 | 3 +- src/biogeochem/TillageMod.f90 | 363 ++++++++++++++++++ src/main/clm_instMod.F90 | 4 + .../SoilBiogeochemDecompCascadeBGCMod.F90 | 12 +- 5 files changed, 382 insertions(+), 3 deletions(-) create mode 100644 src/biogeochem/TillageMod.f90 diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 425c32e084..a728b08aaa 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -340,7 +340,8 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('DecompRate') if (decomp_method == century_decomp) then call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & - soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) + soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & + cnveg_state_inst%idop_patch) else if (decomp_method == mimics_decomp) then call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & diff --git a/src/biogeochem/EDBGCDynMod.F90 b/src/biogeochem/EDBGCDynMod.F90 index eb13932d13..ee415615f1 100644 --- a/src/biogeochem/EDBGCDynMod.F90 +++ b/src/biogeochem/EDBGCDynMod.F90 @@ -182,7 +182,8 @@ subroutine EDBGCDyn(bounds, & if (decomp_method == century_decomp) then call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & - soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) + soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & + cnveg_state_inst%idop_patch) else if (decomp_method == mimics_decomp) then call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 new file mode 100644 index 0000000000..49d045fd07 --- /dev/null +++ b/src/biogeochem/TillageMod.f90 @@ -0,0 +1,363 @@ +module TillageMod + !----------------------------------------------------------------------- + ! !DESCRIPTION: + ! Module for soil tillage. + ! + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use abortutils , only : endrun + use clm_varctl , only : iulog + use clm_varpar , only : i_litr2, i_litr3, i_soil1, i_soil2, i_soil3, ndecomp_pools + ! + implicit none + private + ! !PUBLIC MEMBER PROCEDURES + public :: tillage_init + public :: get_do_tillage + public :: get_apply_tillage_multipliers + ! + ! !PRIVATE DATA MEMBERS + logical :: do_tillage_low ! Do low-intensity tillage? + logical :: do_tillage_high ! Do high-intensity tillage? + logical :: use_original_tillage ! Use get_tillage_multipliers_orig? + real(r8), pointer :: tillage_mults(:,:) + + +!============================================================================== +contains +!============================================================================== + + subroutine tillage_init(bounds) + ! + ! Read namelist parameters and allocate variables related to tillage + ! + ! !USES: + use spmdMod , only : masterproc + use controlMod , only : NLFilename + use clm_nlUtilsMod , only : find_nlgroup_name + use shr_mpi_mod , only : shr_mpi_bcast + use decompMod , only : bounds_type + ! + ! !ARGUMENTS + type(bounds_type), intent(in) :: bounds + ! + ! !LOCAL VARIABLES + integer :: begp, endp ! indices for allocating patch dimension + integer :: nu_nml ! unit for namelist file + integer :: nml_error ! namelist i/o error flag + character(*), parameter :: subname = "('tillage_init')" + + namelist /tillage_nml/ & + do_tillage_low, & + do_tillage_high, & + use_original_tillage + + ! Default values + do_tillage_low = .false. + do_tillage_high = .false. + use_original_tillage = .false. + + ! Read tillage namelist + if (masterproc) then + open(newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) + call find_nlgroup_name(nu_nml, 'tillage_nml', status=nml_error) + if (nml_error == 0) then + read(nu_nml, nml=tillage_nml, iostat=nml_error) + if (nml_error /= 0) then + call endrun(subname // ':: ERROR reading tillage namelist') + end if + else + call endrun(subname // ':: ERROR finding tillage namelist') + end if + close(nu_nml) + endif + call shr_mpi_bcast(do_tillage_low, mpicom) + call shr_mpi_bcast(do_tillage_high , mpicom) + call shr_mpi_bcast(use_original_tillage , mpicom) + + if (masterproc) then + write(iulog,*) ' ' + write(iulog,*) 'tillage settings:' + write(iulog,*) ' do_tillage_low = ',do_tillage_low + write(iulog,*) ' do_tillage_high = ',do_tillage_high + write(iulog,*) ' use_original_tillage = ',use_original_tillage + endif + + if (do_tillage_low .and. do_tillage_high) then + call endrun(subname // ':: ERROR do_tillage_low and do_tillage_high are mutually exclusive') + endif + + if (do_tillage_high) then + call endrun(subname // ':: ERROR high-intensity tillage not yet set up') + endif + + ! Allocate variables + if (get_do_tillage()) then + begp = bounds%begp + endp = bounds%endp + allocate(tillage_mults(begp:endp, ndecomp_pools)) ; tillage_mults(:,:) = 1.0_r8 + end if + + end subroutine tillage_init + + + function get_do_tillage() + logical :: get_do_tillage + get_do_tillage = do_tillage_low .or. do_tillage_high + end function get_do_tillage + + + subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) + ! !DESCRIPTION: + ! + ! Get the cultivation effective multiplier if prognostic crops are on and + ! cultivation is turned on. Created by Sam Levis, modified by Michael Graham + ! to use days past planting. + ! + ! !USES: + use clm_time_manager, only : get_curr_calday,get_days_per_year + use pftconMod , only : npcropmin, ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean + use PatchType , only : patch + ! !ARGUMENTS: + integer , intent(in) :: idop(:) ! patch day of planting + integer , intent(in) :: num_soilp ! number of soil pfts in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + ! + ! !LOCAL VARIABLES: + ! + integer :: fp, p, c, g ! Indices + integer :: day ! julian day + integer :: idpp ! days past planting + real(r8) dayspyr ! days per year + !----------------------------------------------------------------------- + + !get info from externals + day = get_curr_calday() + dayspyr = get_days_per_year() !Add by MWG for IDPP-based routine + + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + g = patch%gridcell(p) + + ! days past planting may determine harvest/tillage + ! SSR: Unused! + if (day >= idop(p)) then + idpp = day - idop(p) + else + idpp = int(dayspyr) + day - idop(p) + end if + + ! ----------------------------------------------------- + ! 3) assigning cultivation practices and mapping to the + ! effect on soil C decomposition + ! ----------------------------------------------------- + ! info from DAYCENT (Melannie Hartman CSU) + ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting + ! corn, soy : P C D & HW-7 30 d aftr + + if (day < idop(p)) then + tillage_mults(c,:) = 1._r8 + else if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) >= npcropmin) then + tillage_mults(c,i_litr2) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_litr3) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_soil1) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(c,i_soil2) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(c,i_soil3) = 3.00_r8 !high 4.80,low 3.00 + end if + else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) >= npcropmin) then + tillage_mults(c,i_litr2) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_litr3) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_soil2) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(c,i_soil3) = 1.60_r8 !high 3.50,low 1.60 + end if + else if (day >= idop(p)+45 .and. day = npcropmin) then + tillage_mults(c,i_litr2) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_litr3) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_soil2) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(c,i_soil3) = 1.30_r8 !high 2.50,low 1.30 + end if + else if (day >= idop(p)+75 .and. day < idop(p)+80) then ! June 14 + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) == ntmp_corn .or. & + patch%itype(p) == nirrig_tmp_corn .or. & + patch%itype(p) == ntmp_soybean .or. & + patch%itype(p) == nirrig_tmp_soybean ) then + tillage_mults(c,i_litr2) = 1.00_r8 + tillage_mults(c,i_litr3) = 1.00_r8 + tillage_mults(c,i_soil1) = 1.00_r8 + tillage_mults(c,i_soil2) = 1.00_r8 + tillage_mults(c,i_soil3) = 1.00_r8 + end if + else if (day >= idop(p)+80) then ! July 14 + tillage_mults(c,:) = 1._r8 + end if + enddo + + end subroutine get_tillage_multipliers_orig + + + subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp) + ! !DESCRIPTION: + ! + ! Get the cultivation effective multiplier if prognostic crops are on and + ! cultivation is turned on. Based on get_tillage_multipliers_orig(). + ! Changed by Sam Rabin: + ! - Actually use idpp (corrected for crossing new year) instead of idop+N + ! + ! !USES: + use clm_time_manager, only : get_curr_calday,get_days_per_year + use pftconMod , only : npcropmin, ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean + use PatchType , only : patch + ! !ARGUMENTS: + integer , intent(in) :: idop(:) ! patch day of planting + integer , intent(in) :: num_soilp ! number of soil pfts in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + ! + ! !LOCAL VARIABLES: + ! + integer :: fp, p, c, g ! Indices + integer :: day ! julian day + integer :: idpp ! days past planting + real(r8) dayspyr ! days per year + !----------------------------------------------------------------------- + + !get info from externals + day = get_curr_calday() + dayspyr = get_days_per_year() !Add by MWG for IDPP-based routine + + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + g = patch%gridcell(p) + + ! days past planting may determine harvest/tillage + if (day >= idop(p)) then + idpp = day - idop(p) + else + idpp = int(dayspyr) + day - idop(p) + end if + + ! ----------------------------------------------------- + ! 3) assigning cultivation practices and mapping to the + ! effect on soil C decomposition + ! ----------------------------------------------------- + ! info from DAYCENT (Melannie Hartman CSU) + ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting + ! corn, soy : P C D & HW-7 30 d aftr + + if (idpp < 0) then + tillage_mults(c,:) = 1._r8 + else if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) >= npcropmin) then + tillage_mults(c,i_litr2) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_litr3) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_soil1) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(c,i_soil2) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(c,i_soil3) = 3.00_r8 !high 4.80,low 3.00 + end if + else if (idpp < 45) then ! based on Field and Row Cultivator multipliers + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) >= npcropmin) then + tillage_mults(c,i_litr2) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_litr3) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_soil2) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(c,i_soil3) = 1.60_r8 !high 3.50,low 1.60 + end if + else if (idpp < 75) then ! based on Rod Weed Row Planter + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) >= npcropmin) then + tillage_mults(c,i_litr2) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_litr3) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_soil2) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(c,i_soil3) = 1.30_r8 !high 2.50,low 1.30 + end if + else if (idpp < 80) then ! June 14 + tillage_mults(c,:) = 1._r8 + if (patch%itype(p) == ntmp_corn .or. & + patch%itype(p) == nirrig_tmp_corn .or. & + patch%itype(p) == ntmp_soybean .or. & + patch%itype(p) == nirrig_tmp_soybean ) then + tillage_mults(c,i_litr2) = 1.00_r8 + tillage_mults(c,i_litr3) = 1.00_r8 + tillage_mults(c,i_soil1) = 1.00_r8 + tillage_mults(c,i_soil2) = 1.00_r8 + tillage_mults(c,i_soil3) = 1.00_r8 + end if + else ! July 14 + tillage_mults(c,:) = 1._r8 + end if + enddo + + end subroutine get_tillage_multipliers_new + + + ! Public interface to choose between and call either get_tillage_multipliers_orig() or get_tillage_multipliers_new() + subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp) + ! !DESCRIPTION: + ! + ! Public interface to choose between and call either original (buggy) or + ! new (fixed), depending on use_original_tillage true or false. + ! + ! !ARGUMENTS: + integer , intent(in) :: idop(:) ! patch day of planting + integer , intent(in) :: num_soilp ! number of soil pfts in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + + if (use_original_tillage) then + call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, tillage_mults) + else + call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, tillage_mults) + end if + + end subroutine get_tillage_multipliers + + + subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, decomp_k) + ! !DESCRIPTION: + ! + ! Multiply decomposition rate constants by tillage coefficients. + ! Written by Sam Rabin, based on original code by Michael Graham. + ! + ! !USES + ! + ! !ARGUMENTS: + integer , intent(in) :: idop(:) ! patch day of planting + integer , intent(in) :: num_soilp ! number of soil pfts in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + real(r8) , intent(inout) :: decomp_k(:,:,:) ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) + ! + ! !LOCAL VARIABLES + integer :: j, fc, c + + call get_tillage_multipliers(idop, num_soilp, filter_soilp) + + ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm + ! of the soil surface, rather than whole soil - MWGraham + do j = 1,5 + do fc = 1,num_soilc + c = filter_soilc(fc) + ! TODO: Loop through ALL pools, not just the ones that currently have non-1 values + decomp_k(c,j,i_litr2) = decomp_k(c,j,i_litr2) * tillage_mults(c,i_litr2) + decomp_k(c,j,i_litr3) = decomp_k(c,j,i_litr3) * tillage_mults(c,i_litr3) + decomp_k(c,j,i_soil1) = decomp_k(c,j,i_soil1) * tillage_mults(c,i_soil1) + decomp_k(c,j,i_soil2) = decomp_k(c,j,i_soil2) * tillage_mults(c,i_soil2) + decomp_k(c,j,i_soil3) = decomp_k(c,j,i_soil3) * tillage_mults(c,i_soil3) + end do + end do + + end subroutine get_apply_tillage_multipliers + +end module TillageMod \ No newline at end of file diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 7924c2111e..b02e86d696 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -200,6 +200,7 @@ subroutine clm_instInit(bounds) use SoilWaterRetentionCurveFactoryMod , only : create_soil_water_retention_curve use decompMod , only : get_proc_bounds use BalanceCheckMod , only : GetBalanceCheckSkipSteps + use TillageMod , only : tillage_init ! ! !ARGUMENTS type(bounds_type), intent(in) :: bounds ! processor bounds @@ -390,6 +391,9 @@ subroutine clm_instInit(bounds) soilstate_inst) end if + ! Initialize tillage + call tillage_init(bounds) + ! Initalize soilbiogeochem carbon types call soilbiogeochem_carbonstate_inst%Init(bounds, carbon_type='c12', ratio=1._r8) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index b65fc5f17f..511ab47760 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -511,7 +511,8 @@ end subroutine init_decompcascade_bgc !----------------------------------------------------------------------- subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & - soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) + soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & + idop) ! ! !DESCRIPTION: ! calculate rate constants and decomposition pathways for the CENTURY decomposition cascade model @@ -521,6 +522,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & use clm_time_manager , only : get_average_days_per_year, get_step_size use shr_const_mod , only : SHR_CONST_PI use clm_varcon , only : secspday + use TillageMod , only : get_do_tillage + use TillageMod , only : get_apply_tillage_multipliers ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -530,6 +533,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & type(temperature_type) , intent(in) :: temperature_inst type(ch4_type) , intent(in) :: ch4_inst type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst + integer , intent(in) :: idop(:) ! patch day of planting ! ! !LOCAL VARIABLES: real(r8), parameter :: eps = 1.e-6_r8 @@ -895,6 +899,12 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & decomp_k(c,j,i_cwd) = k_frag * t_scalar(c,j) * w_scalar(c,j) * & depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_cwd(c) end if + + ! Tillage + if (get_do_tillage()) then + get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, decomp_k) + end if + ! Above into soil matrix if(use_soil_matrixcn)then ! same for cwd but only if fates is not enabled; fates handles CWD From e8835e56ab0e5b2313336fafa60be95b2bb12b5e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 21 May 2023 09:22:40 -0700 Subject: [PATCH 0944/2067] RXCROPMATURITY: Update description of _run_make_surface_for_gddgen(). --- cime_config/SystemTests/rxcropmaturity.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 76b3baab7b..e2e3d75a50 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -233,10 +233,7 @@ def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all done") - # Unused because I couldn't get the GDD-Generating run to work with the fsurdat file generated - # by make_surface_for_gddgen.py. However, I think it'd be cleaner to just do the GDD-Generating - # run with a surface file (and no flanduse_timeseries file) since that run relies on land use - # staying constant. So it'd be nice to get this working eventually. + # Make a surface dataset that has every crop in every gridcell def _run_make_surface_for_gddgen(self, case_gddgen): # fsurdat should be defined. Where is it? From a2f56c349542104038b0011a1678d440b15d0b56 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 21 May 2023 19:08:56 -0600 Subject: [PATCH 0945/2067] Compile fixes to previous. --- src/biogeochem/CNDriverMod.F90 | 2 +- src/biogeochem/EDBGCDynMod.F90 | 3 +- src/biogeochem/TillageMod.f90 | 88 ++++++++++--------- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 12 ++- 4 files changed, 59 insertions(+), 46 deletions(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index a728b08aaa..7078216e4a 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -341,7 +341,7 @@ subroutine CNDriverNoLeaching(bounds, if (decomp_method == century_decomp) then call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & - cnveg_state_inst%idop_patch) + cnveg_state_inst%idop_patch, num_soilp, filter_soilp) else if (decomp_method == mimics_decomp) then call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & diff --git a/src/biogeochem/EDBGCDynMod.F90 b/src/biogeochem/EDBGCDynMod.F90 index ee415615f1..eb13932d13 100644 --- a/src/biogeochem/EDBGCDynMod.F90 +++ b/src/biogeochem/EDBGCDynMod.F90 @@ -182,8 +182,7 @@ subroutine EDBGCDyn(bounds, & if (decomp_method == century_decomp) then call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & - soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & - cnveg_state_inst%idop_patch) + soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) else if (decomp_method == mimics_decomp) then call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 49d045fd07..fd540e3be5 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -8,7 +8,8 @@ module TillageMod use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use clm_varctl , only : iulog - use clm_varpar , only : i_litr2, i_litr3, i_soil1, i_soil2, i_soil3, ndecomp_pools + ! TODO: Confirm that i_soil1->i_act_som, i_soil2->i_slo_som, i_soil3->i_pas_som + use clm_varpar , only : i_litr2, i_litr3, ndecomp_pools ! implicit none private @@ -46,6 +47,7 @@ subroutine tillage_init(bounds) integer :: begp, endp ! indices for allocating patch dimension integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag + integer :: mpicom ! MPI communicator character(*), parameter :: subname = "('tillage_init')" namelist /tillage_nml/ & @@ -108,7 +110,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) + subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -116,13 +118,14 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) ! to use days past planting. ! ! !USES: - use clm_time_manager, only : get_curr_calday,get_days_per_year + use clm_time_manager, only : get_curr_calday, get_curr_days_per_year use pftconMod , only : npcropmin, ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean use PatchType , only : patch ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools ! ! !LOCAL VARIABLES: ! @@ -134,7 +137,7 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) !get info from externals day = get_curr_calday() - dayspyr = get_days_per_year() !Add by MWG for IDPP-based routine + dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine do fp = 1,num_soilp p = filter_soilp(fp) @@ -164,27 +167,27 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) if (patch%itype(p) >= npcropmin) then tillage_mults(c,i_litr2) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(c,i_litr3) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_soil1) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(c,i_soil2) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(c,i_soil3) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(c,i_act_som) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(c,i_slo_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(c,i_pas_som) = 3.00_r8 !high 4.80,low 3.00 end if else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then tillage_mults(c,i_litr2) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(c,i_litr3) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_soil2) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(c,i_soil3) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_slo_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(c,i_pas_som) = 1.60_r8 !high 3.50,low 1.60 end if else if (day >= idop(p)+45 .and. day = npcropmin) then tillage_mults(c,i_litr2) = 1.10_r8 !high 1.10,low 1.10 tillage_mults(c,i_litr3) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_soil2) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(c,i_soil3) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_slo_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(c,i_pas_som) = 1.30_r8 !high 2.50,low 1.30 end if else if (day >= idop(p)+75 .and. day < idop(p)+80) then ! June 14 tillage_mults(c,:) = 1._r8 @@ -194,9 +197,9 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) patch%itype(p) == nirrig_tmp_soybean ) then tillage_mults(c,i_litr2) = 1.00_r8 tillage_mults(c,i_litr3) = 1.00_r8 - tillage_mults(c,i_soil1) = 1.00_r8 - tillage_mults(c,i_soil2) = 1.00_r8 - tillage_mults(c,i_soil3) = 1.00_r8 + tillage_mults(c,i_act_som) = 1.00_r8 + tillage_mults(c,i_slo_som) = 1.00_r8 + tillage_mults(c,i_pas_som) = 1.00_r8 end if else if (day >= idop(p)+80) then ! July 14 tillage_mults(c,:) = 1._r8 @@ -206,7 +209,7 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp) end subroutine get_tillage_multipliers_orig - subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp) + subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -215,13 +218,14 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp) ! - Actually use idpp (corrected for crossing new year) instead of idop+N ! ! !USES: - use clm_time_manager, only : get_curr_calday,get_days_per_year + use clm_time_manager, only : get_curr_calday, get_curr_days_per_year use pftconMod , only : npcropmin, ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean use PatchType , only : patch ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools ! ! !LOCAL VARIABLES: ! @@ -233,7 +237,7 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp) !get info from externals day = get_curr_calday() - dayspyr = get_days_per_year() !Add by MWG for IDPP-based routine + dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine do fp = 1,num_soilp p = filter_soilp(fp) @@ -262,27 +266,27 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp) if (patch%itype(p) >= npcropmin) then tillage_mults(c,i_litr2) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(c,i_litr3) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_soil1) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(c,i_soil2) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(c,i_soil3) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(c,i_act_som) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(c,i_slo_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(c,i_pas_som) = 3.00_r8 !high 4.80,low 3.00 end if else if (idpp < 45) then ! based on Field and Row Cultivator multipliers tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then tillage_mults(c,i_litr2) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(c,i_litr3) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_soil2) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(c,i_soil3) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_slo_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(c,i_pas_som) = 1.60_r8 !high 3.50,low 1.60 end if else if (idpp < 75) then ! based on Rod Weed Row Planter tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then tillage_mults(c,i_litr2) = 1.10_r8 !high 1.10,low 1.10 tillage_mults(c,i_litr3) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_soil1) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_soil2) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(c,i_soil3) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(c,i_slo_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(c,i_pas_som) = 1.30_r8 !high 2.50,low 1.30 end if else if (idpp < 80) then ! June 14 tillage_mults(c,:) = 1._r8 @@ -292,9 +296,9 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp) patch%itype(p) == nirrig_tmp_soybean ) then tillage_mults(c,i_litr2) = 1.00_r8 tillage_mults(c,i_litr3) = 1.00_r8 - tillage_mults(c,i_soil1) = 1.00_r8 - tillage_mults(c,i_soil2) = 1.00_r8 - tillage_mults(c,i_soil3) = 1.00_r8 + tillage_mults(c,i_act_som) = 1.00_r8 + tillage_mults(c,i_slo_som) = 1.00_r8 + tillage_mults(c,i_pas_som) = 1.00_r8 end if else ! July 14 tillage_mults(c,:) = 1._r8 @@ -305,7 +309,7 @@ end subroutine get_tillage_multipliers_new ! Public interface to choose between and call either get_tillage_multipliers_orig() or get_tillage_multipliers_new() - subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp) + subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) ! !DESCRIPTION: ! ! Public interface to choose between and call either original (buggy) or @@ -315,17 +319,18 @@ subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp) integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools if (use_original_tillage) then - call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, tillage_mults) + call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) else - call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, tillage_mults) + call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) end if end subroutine get_tillage_multipliers - subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, decomp_k) + subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som) ! !DESCRIPTION: ! ! Multiply decomposition rate constants by tillage coefficients. @@ -337,12 +342,15 @@ subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, decomp_k integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: num_soilc ! number of soil columns in filter + integer , intent(in) :: filter_soilc(:) ! filter for soil columns real(r8) , intent(inout) :: decomp_k(:,:,:) ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) + integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools ! ! !LOCAL VARIABLES integer :: j, fc, c - call get_tillage_multipliers(idop, num_soilp, filter_soilp) + call get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham @@ -352,12 +360,12 @@ subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, decomp_k ! TODO: Loop through ALL pools, not just the ones that currently have non-1 values decomp_k(c,j,i_litr2) = decomp_k(c,j,i_litr2) * tillage_mults(c,i_litr2) decomp_k(c,j,i_litr3) = decomp_k(c,j,i_litr3) * tillage_mults(c,i_litr3) - decomp_k(c,j,i_soil1) = decomp_k(c,j,i_soil1) * tillage_mults(c,i_soil1) - decomp_k(c,j,i_soil2) = decomp_k(c,j,i_soil2) * tillage_mults(c,i_soil2) - decomp_k(c,j,i_soil3) = decomp_k(c,j,i_soil3) * tillage_mults(c,i_soil3) + decomp_k(c,j,i_act_som) = decomp_k(c,j,i_act_som) * tillage_mults(c,i_act_som) + decomp_k(c,j,i_slo_som) = decomp_k(c,j,i_slo_som) * tillage_mults(c,i_slo_som) + decomp_k(c,j,i_pas_som) = decomp_k(c,j,i_pas_som) * tillage_mults(c,i_pas_som) end do end do end subroutine get_apply_tillage_multipliers -end module TillageMod \ No newline at end of file +end module TillageMod diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 511ab47760..2fbc69c726 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -512,7 +512,7 @@ end subroutine init_decompcascade_bgc !----------------------------------------------------------------------- subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & - idop) + idop, num_soilp, filter_soilp) ! ! !DESCRIPTION: ! calculate rate constants and decomposition pathways for the CENTURY decomposition cascade model @@ -533,7 +533,9 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & type(temperature_type) , intent(in) :: temperature_inst type(ch4_type) , intent(in) :: ch4_inst type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst - integer , intent(in) :: idop(:) ! patch day of planting + integer, optional , intent(in) :: idop(:) ! patch day of planting + integer, optional , intent(in) :: num_soilp ! number of soil patches in filter + integer, optional , intent(in) :: filter_soilp(:) ! filter for soil patches ! ! !LOCAL VARIABLES: real(r8), parameter :: eps = 1.e-6_r8 @@ -902,7 +904,11 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! Tillage if (get_do_tillage()) then - get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, decomp_k) + ! TODO: Throw error during namelist build if tillage is called with FATES + if (.not. (present(idop) .and. present(num_soilp) .and. present(filter_soilp))) then + call endrun("Do not call tillage without providing idop, num_soilp, and filter_soilp. (Maybe you called with FATES?)") + end if + call get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som) end if ! Above into soil matrix From 337f20d49f7f5f189100b0ff8d622c17fbd8881e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 May 2023 16:22:51 -0700 Subject: [PATCH 0946/2067] vernalization() kill no longer changes huigrain or gddmaturity. Previously, the "kill" occurred via a forced harvest that was triggered by setting huigrain = gddmaturity = 0. However, that forced harvest would be ignored when generate_crop_gdds was true. Live crops with gddmaturity 0 can run into 0/0 during allocation, so that was a problem. --- src/biogeochem/CNPhenologyMod.F90 | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7e9ea2a08d..5f229be0e8 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2207,6 +2207,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. do_harvest = .false. + else if (vernalization_forces_harvest) then + do_harvest = .true. + harvest_reason = HARVEST_REASON_VERNFREEZEKILL else ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat @@ -2225,9 +2228,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if do_harvest = do_harvest .or. will_plant_prescribed_tomorrow - if (vernalization_forces_harvest) then - harvest_reason = HARVEST_REASON_VERNFREEZEKILL - else if (hui(p) >= gddmaturity(p)) then + if (hui(p) >= gddmaturity(p)) then harvest_reason = HARVEST_REASON_MATURE else if (idpp >= mxmat) then harvest_reason = HARVEST_REASON_MAXSEASLENGTH @@ -2711,8 +2712,6 @@ subroutine vernalization(p, & hdidx => cnveg_state_inst%hdidx_patch , & ! Output: [real(r8) (:) ] cold hardening index? cumvd => cnveg_state_inst%cumvd_patch , & ! Output: [real(r8) (:) ] cumulative vernalization d?ependence? - gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest - huigrain => cnveg_state_inst%huigrain_patch , & ! Output: [real(r8) (:) ] heat unit index needed to reach vegetative maturity vf => crop_inst%vf_patch & ! Output: [real(r8) (:) ] vernalization factor for cereal ) @@ -2802,9 +2801,13 @@ subroutine vernalization(p, & if (tkil >= tcrown) then if ((0.95_r8 - 0.02_r8 * (tcrown - tkil)**2) >= 0.02_r8) then write (iulog,*) 'crop damaged by cold temperatures at p,c =', p,c - else if (tlai(p) > 0._r8) then ! slevis: kill if past phase1 - gddmaturity(p) = 0._r8 ! by forcing through - huigrain(p) = 0._r8 ! harvest + else if (tlai(p) > 0._r8) then + ! slevis: kill if past phase1 by forcing through harvest + ! srabin: do this with force_harvest instead of setting + ! gddmaturity = huigrain = 0, since gddmaturity==0 can + ! lead to 0/0 when the crop isn't actually harvested based + ! on "maturity." This can occur when generate_crop_gdds + ! is true. force_harvest = .true. write (iulog,*) '95% of crop killed by cold temperatures at p,c =', p,c end if From 3d2e7658aa5a5bb619bf867aecba5eaf9d624020 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 21 May 2023 19:31:49 -0600 Subject: [PATCH 0947/2067] In generate_gdds, chunk on import if possible (dask present). --- .../ctsm/crop_calendars/generate_gdds_functions.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 784adc96b6..c553038613 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -7,6 +7,7 @@ import os import glob import datetime as dt +import importlib import cropcal_module as cc @@ -201,6 +202,12 @@ def import_and_process_1yr( log(logger, f"netCDF year {thisYear}...") log(logger, dt.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + # Without dask, this can take a LONG time at resolutions finer than 2-deg + if importlib.util.find_spec(dask): + chunks = {"time": 1} + else: + chunks = None + # Get h2 file (list) h2_pattern = os.path.join(indir, "*h2.*.nc") h2_filelist = glob.glob(h2_pattern) @@ -215,6 +222,7 @@ def import_and_process_1yr( myVars=["SDATES", "HDATES"], myVegtypes=utils.define_mgdcrop_list(), timeSlice=slice(f"{thisYear}-01-01", f"{thisYear}-12-31"), + chunks=chunks, ) if dates_ds.dims["time"] > 1: @@ -468,6 +476,7 @@ def import_and_process_1yr( myVars=myVars, myVegtypes=utils.define_mgdcrop_list(), myVars_missing_ok=["GDDHARV"], + chunks=chunks, ) if "GDDHARV" not in h1_ds: if not gddharv_in_h3: @@ -484,7 +493,8 @@ def import_and_process_1yr( f"No files found matching pattern '*h3.{thisYear-1}-01-01*.nc(.base)'", ) h3_ds = utils.import_ds( - h3_files, myVars=["GDDHARV"], myVegtypes=utils.define_mgdcrop_list() + h3_files, myVars=["GDDHARV"], myVegtypes=utils.define_mgdcrop_list(), + chunks=chunks, ) h1_ds["GDDHARV"] = h3_ds["GDDHARV"] if not gddharv_in_h3: From f189e749d32ec2d7500ccd37164d943159acb901 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 22 May 2023 10:54:27 -0600 Subject: [PATCH 0948/2067] update fates param file name --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index dd9f05d762..6a936fcf17 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230517.nc +lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230519.nc From 601cb7175b72e9eb5a4ef80d04b35d6765e450ef Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 22 May 2023 10:04:59 -0700 Subject: [PATCH 0949/2067] add new fates pft-level drought output --- .../testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm index 0a0726dcce..f6aef17c97 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm @@ -70,4 +70,7 @@ hist_fincl1 = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF', 'FATES_CROOTMAINTAR_USTORY_SZ', 'FATES_FROOTMAINTAR_USTORY_SZ', 'FATES_GROWAR_USTORY_SZ', 'FATES_MAINTAR_USTORY_SZ', 'FATES_VEGC_SZPF', 'FATES_LEAFC_SZPF', 'FATES_FROOTC_SZPF', 'FATES_SAPWOODC_SZPF', -'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF' +'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF', 'FATES_DROUGHT_STATUS_PF', +'FATES_DAYSINCE_DROUGHTLEAFOFF_PF', 'FATES_DAYSINCE_DROUGHTLEAFON_PF', +'FATES_MEANLIQVOL_DROUGHTPHEN_PF', 'FATES_MEANSMP_DROUGHTPHEN_PF', +'FATES_ELONG_FACTOR_PF' From 445fbd0e5b773de50e90153bcbc5b91dbd592283 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 11:23:23 -0600 Subject: [PATCH 0950/2067] RXCROPMATURITY now uses npl conda env instead of ctsm_pylib, if available. This is to take advantage of dask chunking on import of the daily data, which takes a long time without chunking at 1-degree and finer resolutions. --- cime_config/SystemTests/rxcropmaturity.py | 27 +++++++++++++---------- 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index e2e3d75a50..bb9182311a 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -23,10 +23,6 @@ logger = logging.getLogger(__name__) -# SSR: This was originally ctsm_pylib, but the fact that it's missing -# cf_units caused problems in utils.import_ds(). -this_conda_env = "ctsm_pylib" - class RXCROPMATURITY(SystemTestsCommon): def __init__(self, case): @@ -351,7 +347,7 @@ def _run_generate_gdds(self, case_gddgen): self._gdds_file = generated_gdd_files[0] - def _get_conda_env(self): + def _get_conda_env(self, conda_setup_commands): # # Add specific commands needed on different machines to get conda available # Use semicolon here since it's OK to fail @@ -360,15 +356,22 @@ def _get_conda_env(self): # eg on cheyenne try: subprocess.run( "which conda", shell=True, check=True) - conda_env = " " except subprocess.CalledProcessError: # Remove python and add conda to environment for cheyennne - conda_env = "module unload python; module load conda;" + conda_setup_commands += "module unload python; module load conda; " + + # If npl conda environment is available, use that (It has dask, which + # enables chunking, which makes reading daily 1-degree netCDF files + # much more efficient. + if "npl " in os.popen(conda_setup_commands + "conda env list").read(): + this_conda_env = "npl" + else: + this_conda_env = "ctsm_pylib" ## Run in the correct python environment - conda_env += f" conda run -n {this_conda_env} " + conda_setup_commands += f" conda run -n {this_conda_env} " - return( conda_env ) + return conda_setup_commands, this_conda_env def _append_to_user_nl_clm(self, additions): @@ -383,9 +386,9 @@ def _run_python_script(self, case, command, tool_path): case.load_env(reset=True) # Prepend the commands to get the conda environment for python first - conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " - conda_env += self._get_conda_env() - command = conda_env + command + conda_setup_commands = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " + conda_setup_commands, this_conda_env = self._get_conda_env(conda_setup_commands) + command = conda_setup_commands + command print(f"command: {command}") # Run From 86a3b5e6f153c1d66691bbb2c06b973c2c2e8829 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 11:35:10 -0600 Subject: [PATCH 0951/2067] Added RXCROPMATURITY to the ctsm_sci category in testlist_clm.xml. --- cime_config/testdefs/testlist_clm.xml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 59e7be0d92..7df77a2389 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2646,4 +2646,15 @@ + + + + + + + + + + + From 1474f2a4a3b75d41febf7c848e8a756d8a262443 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 22 May 2023 11:01:25 -0700 Subject: [PATCH 0952/2067] update fates history tests to use double precision --- cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 1 + .../testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm | 1 + cime_config/usermods_dirs/fates_sp/user_nl_clm | 1 + 3 files changed, 3 insertions(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 2a915f2fd7..c27e69b531 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -2,6 +2,7 @@ hist_mfilt = 365 hist_nhtfrq = -24 hist_empty_htapes = .true. +hist_ndens = 1 fates_spitfire_mode = 1 hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm index 0a0726dcce..85f54fa214 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm @@ -3,6 +3,7 @@ hist_mfilt = 365 hist_nhtfrq = -24 hist_empty_htapes = .false. fates_spitfire_mode = 1 +hist_ndens = 1 hist_fincl1 = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF', 'FATES_NCL_AP', 'FATES_NPATCH_AP', 'FATES_VEGC_AP', 'FATES_SECONDARY_FOREST_FRACTION', 'FATES_WOOD_PRODUCT', diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm index f2f68eb74c..4987eae969 100644 --- a/cime_config/usermods_dirs/fates_sp/user_nl_clm +++ b/cime_config/usermods_dirs/fates_sp/user_nl_clm @@ -6,6 +6,7 @@ use_lch4 = .false. fates_spitfire_mode = 0 use_fates_fixed_biogeog = .true. use_fates_nocomp = .true. +hist_ndens = 1 ! Turn off a list of fields that are not needed for FATES-SP mode hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF', From fe42f38ce67e42d28b90bf7a9d5bc42dd21004c5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 May 2023 16:22:51 -0700 Subject: [PATCH 0953/2067] vernalization() kill no longer changes huigrain or gddmaturity. Previously, the "kill" occurred via a forced harvest that was triggered by setting huigrain = gddmaturity = 0. However, that forced harvest would be ignored when generate_crop_gdds was true. Live crops with gddmaturity 0 can run into 0/0 during allocation, so that was a problem. --- src/biogeochem/CNPhenologyMod.F90 | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ad0e832e75..971d6a8eeb 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2204,6 +2204,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Do not harvest on the day this growing season began; ! would create challenges for postprocessing. do_harvest = .false. + else if (vernalization_forces_harvest) then + do_harvest = .true. + harvest_reason = HARVEST_REASON_VERNFREEZEKILL else ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat @@ -2222,9 +2225,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if do_harvest = do_harvest .or. will_plant_prescribed_tomorrow - if (vernalization_forces_harvest) then - harvest_reason = HARVEST_REASON_VERNFREEZEKILL - else if (hui(p) >= gddmaturity(p)) then + if (hui(p) >= gddmaturity(p)) then harvest_reason = HARVEST_REASON_MATURE else if (idpp >= mxmat) then harvest_reason = HARVEST_REASON_MAXSEASLENGTH @@ -2705,8 +2706,6 @@ subroutine vernalization(p, & hdidx => cnveg_state_inst%hdidx_patch , & ! Output: [real(r8) (:) ] cold hardening index? cumvd => cnveg_state_inst%cumvd_patch , & ! Output: [real(r8) (:) ] cumulative vernalization d?ependence? - gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest - huigrain => cnveg_state_inst%huigrain_patch , & ! Output: [real(r8) (:) ] heat unit index needed to reach vegetative maturity vf => crop_inst%vf_patch & ! Output: [real(r8) (:) ] vernalization factor for cereal ) @@ -2796,9 +2795,13 @@ subroutine vernalization(p, & if (tkil >= tcrown) then if ((0.95_r8 - 0.02_r8 * (tcrown - tkil)**2) >= 0.02_r8) then write (iulog,*) 'crop damaged by cold temperatures at p,c =', p,c - else if (tlai(p) > 0._r8) then ! slevis: kill if past phase1 - gddmaturity(p) = 0._r8 ! by forcing through - huigrain(p) = 0._r8 ! harvest + else if (tlai(p) > 0._r8) then + ! slevis: kill if past phase1 by forcing through harvest + ! srabin: do this with force_harvest instead of setting + ! gddmaturity = huigrain = 0, since gddmaturity==0 can + ! lead to 0/0 when the crop isn't actually harvested based + ! on "maturity." This can occur when generate_crop_gdds + ! is true. force_harvest = .true. write (iulog,*) '95% of crop killed by cold temperatures at p,c =', p,c end if From d23e47bc27c3e669374490b411a11dd6bbce3cec Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 21 May 2023 19:31:49 -0600 Subject: [PATCH 0954/2067] In generate_gdds, chunk on import if possible (dask present). --- .../crop_calendars/generate_gdds_functions.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 784adc96b6..30c98548e8 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -7,6 +7,7 @@ import os import glob import datetime as dt +from importlib import util as importlib_util import cropcal_module as cc @@ -24,7 +25,10 @@ message="Iteration over multi-part geometries is deprecated and will be removed in Shapely 2.0. Use the `geoms` property to access the constituent parts of a multi-part geometry.", ) + print("Will (attempt to) produce harvest requirement maps.") + except: + print("Will NOT produce harvest requirement maps.") can_plot = False @@ -201,6 +205,12 @@ def import_and_process_1yr( log(logger, f"netCDF year {thisYear}...") log(logger, dt.datetime.now().strftime("%Y-%m-%d %H:%M:%S")) + # Without dask, this can take a LONG time at resolutions finer than 2-deg + if importlib_util.find_spec("dask"): + chunks = {"time": 1} + else: + chunks = None + # Get h2 file (list) h2_pattern = os.path.join(indir, "*h2.*.nc") h2_filelist = glob.glob(h2_pattern) @@ -215,6 +225,7 @@ def import_and_process_1yr( myVars=["SDATES", "HDATES"], myVegtypes=utils.define_mgdcrop_list(), timeSlice=slice(f"{thisYear}-01-01", f"{thisYear}-12-31"), + chunks=chunks, ) if dates_ds.dims["time"] > 1: @@ -468,6 +479,7 @@ def import_and_process_1yr( myVars=myVars, myVegtypes=utils.define_mgdcrop_list(), myVars_missing_ok=["GDDHARV"], + chunks=chunks, ) if "GDDHARV" not in h1_ds: if not gddharv_in_h3: @@ -484,7 +496,8 @@ def import_and_process_1yr( f"No files found matching pattern '*h3.{thisYear-1}-01-01*.nc(.base)'", ) h3_ds = utils.import_ds( - h3_files, myVars=["GDDHARV"], myVegtypes=utils.define_mgdcrop_list() + h3_files, myVars=["GDDHARV"], myVegtypes=utils.define_mgdcrop_list(), + chunks=chunks, ) h1_ds["GDDHARV"] = h3_ds["GDDHARV"] if not gddharv_in_h3: From fcb47718c8d0bdc3a462523fdfd4431623e53b09 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 11:23:23 -0600 Subject: [PATCH 0955/2067] RXCROPMATURITY now uses npl conda env instead of ctsm_pylib, if available. This is to take advantage of dask chunking on import of the daily data, which takes a long time without chunking at 1-degree and finer resolutions. --- cime_config/SystemTests/rxcropmaturity.py | 27 +++++++++++++---------- 1 file changed, 15 insertions(+), 12 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index e2e3d75a50..bb9182311a 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -23,10 +23,6 @@ logger = logging.getLogger(__name__) -# SSR: This was originally ctsm_pylib, but the fact that it's missing -# cf_units caused problems in utils.import_ds(). -this_conda_env = "ctsm_pylib" - class RXCROPMATURITY(SystemTestsCommon): def __init__(self, case): @@ -351,7 +347,7 @@ def _run_generate_gdds(self, case_gddgen): self._gdds_file = generated_gdd_files[0] - def _get_conda_env(self): + def _get_conda_env(self, conda_setup_commands): # # Add specific commands needed on different machines to get conda available # Use semicolon here since it's OK to fail @@ -360,15 +356,22 @@ def _get_conda_env(self): # eg on cheyenne try: subprocess.run( "which conda", shell=True, check=True) - conda_env = " " except subprocess.CalledProcessError: # Remove python and add conda to environment for cheyennne - conda_env = "module unload python; module load conda;" + conda_setup_commands += "module unload python; module load conda; " + + # If npl conda environment is available, use that (It has dask, which + # enables chunking, which makes reading daily 1-degree netCDF files + # much more efficient. + if "npl " in os.popen(conda_setup_commands + "conda env list").read(): + this_conda_env = "npl" + else: + this_conda_env = "ctsm_pylib" ## Run in the correct python environment - conda_env += f" conda run -n {this_conda_env} " + conda_setup_commands += f" conda run -n {this_conda_env} " - return( conda_env ) + return conda_setup_commands, this_conda_env def _append_to_user_nl_clm(self, additions): @@ -383,9 +386,9 @@ def _run_python_script(self, case, command, tool_path): case.load_env(reset=True) # Prepend the commands to get the conda environment for python first - conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " - conda_env += self._get_conda_env() - command = conda_env + command + conda_setup_commands = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " + conda_setup_commands, this_conda_env = self._get_conda_env(conda_setup_commands) + command = conda_setup_commands + command print(f"command: {command}") # Run From b24c1270b122c3a467d852a200991f4aa210f60a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 11:35:10 -0600 Subject: [PATCH 0956/2067] Added RXCROPMATURITY to the ctsm_sci category in testlist_clm.xml. --- cime_config/testdefs/testlist_clm.xml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 59e7be0d92..7df77a2389 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2646,4 +2646,15 @@ + + + + + + + + + + + From 6106c00e7bd1bfab180d8c9a0260b60103eac395 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 11:48:16 -0600 Subject: [PATCH 0957/2067] cropcal_figs_module no longer ignores import errors. --- python/ctsm/crop_calendars/cropcal_figs_module.py | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_figs_module.py b/python/ctsm/crop_calendars/cropcal_figs_module.py index ab4984f0cf..fb02d3b016 100644 --- a/python/ctsm/crop_calendars/cropcal_figs_module.py +++ b/python/ctsm/crop_calendars/cropcal_figs_module.py @@ -2,15 +2,12 @@ import xarray as xr import cftime -try: - import cartopy.crs as ccrs - import cartopy.feature as cfeature - import matplotlib.pyplot as plt - import matplotlib.colors as mcolors - from matplotlib import cm - import matplotlib.collections as mplcol -except: - pass +import cartopy.crs as ccrs +import cartopy.feature as cfeature +import matplotlib.pyplot as plt +import matplotlib.colors as mcolors +from matplotlib import cm +import matplotlib.collections as mplcol # Import the CTSM Python utilities import utils From d9e3c1056513a93e3a31c08d3784fcb90bf78fed Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 12:27:51 -0600 Subject: [PATCH 0958/2067] Removed ability of generate_gdds.py to handle GDDHARV in h3 instead of h1. --- python/ctsm/crop_calendars/generate_gdds.py | 5 --- .../crop_calendars/generate_gdds_functions.py | 32 +------------------ 2 files changed, 1 insertion(+), 36 deletions(-) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 979f9ea6a0..f4f15de01f 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -109,7 +109,6 @@ def main( skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, - gddharv_in_h3, save_figs, incl_vegtypes_str, incl_patches1d_itype_veg, @@ -120,7 +119,6 @@ def main( else: incorrectly_daily = False skip_patches_for_isel_nan_lastyear = np.ndarray([]) - gddharv_in_h3 = False pickle_year = -np.inf gddaccum_yp_list = [] gddharv_yp_list = [] @@ -147,7 +145,6 @@ def main( skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, - gddharv_in_h3, incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings, @@ -163,7 +160,6 @@ def main( skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, - gddharv_in_h3, input_dir, incl_vegtypes_str, h1_ds_file, @@ -184,7 +180,6 @@ def main( skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, - gddharv_in_h3, save_figs, incl_vegtypes_str, incl_patches1d_itype_veg, diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 30c98548e8..921ddd0a41 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -193,7 +193,6 @@ def import_and_process_1yr( skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, - gddharv_in_h3, indir, incl_vegtypes_str_in, h1_ds_file, @@ -464,9 +463,7 @@ def import_and_process_1yr( log(logger, f" Importing accumulated GDDs...") clm_gdd_var = "GDDACCUM" - myVars = [clm_gdd_var] - if not gddharv_in_h3: - myVars.append("GDDHARV") + myVars = [clm_gdd_var, "GDDHARV"] pattern = os.path.join(indir, f"*h1.{thisYear-1}-01-01*.nc") h1_files = glob.glob(pattern) if not h1_files: @@ -478,34 +475,8 @@ def import_and_process_1yr( h1_files, myVars=myVars, myVegtypes=utils.define_mgdcrop_list(), - myVars_missing_ok=["GDDHARV"], chunks=chunks, ) - if "GDDHARV" not in h1_ds: - if not gddharv_in_h3: - log(logger, "Trying to get GDDHARV from h3 file(s) instead.") - try: - pattern = os.path.join(indir, f"*h3.{thisYear-1}-01-01*.nc") - h3_files = glob.glob(pattern) - if not h3_files: - pattern = os.path.join(indir, f"*h3.{thisYear-1}-01-01*.nc.base") - h3_files = glob.glob(pattern) - if not h3_files: - error( - logger, - f"No files found matching pattern '*h3.{thisYear-1}-01-01*.nc(.base)'", - ) - h3_ds = utils.import_ds( - h3_files, myVars=["GDDHARV"], myVegtypes=utils.define_mgdcrop_list(), - chunks=chunks, - ) - h1_ds["GDDHARV"] = h3_ds["GDDHARV"] - if not gddharv_in_h3: - log(logger, "Success! Will look in h3 files from now on.") - gddharv_in_h3 = True - except: - log(logger, "Unable to import GDDHARV from h1 or h3 files. Disabling save_figs.") - save_figs = False # Restrict to patches we're including if skipping_patches_for_isel_nan: @@ -709,7 +680,6 @@ def import_and_process_1yr( skip_patches_for_isel_nan_lastyear, lastYear_active_patch_indices_list, incorrectly_daily, - gddharv_in_h3, incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings, From 84d161a3fd2ace87e16ccb0adcf82b45154b6a74 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 12:34:42 -0600 Subject: [PATCH 0959/2067] RXCROPMATURITY: Do not save daily HUI in GDD generation. --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index bb9182311a..e615d7ccb5 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -295,7 +295,7 @@ def _modify_user_nl_allruns(self): "model_year_align_cropcal = 2000", " ", "! (h1) Daily outputs for GDD generation and figure-making", - "hist_fincl2 = 'HUI', 'GDDACCUM', 'GDDHARV'", + "hist_fincl2 = 'GDDACCUM', 'GDDHARV'", "hist_nhtfrq(2) = -24", "hist_mfilt(2) = 365", "hist_type1d_pertape(2) = 'PFTS'", From 7b599661d7fd34387e327f1e15b42b1b03ac9257 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 12:45:59 -0600 Subject: [PATCH 0960/2067] RDXCROPMATURITY: swapped h1 and h2 of daily gdd-gen outputs. --- cime_config/SystemTests/rxcropmaturity.py | 16 +++---- python/ctsm/crop_calendars/generate_gdds.py | 16 +++---- .../crop_calendars/generate_gdds_functions.py | 48 +++++++++---------- 3 files changed, 40 insertions(+), 40 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index e615d7ccb5..0458a9f752 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -294,17 +294,17 @@ def _modify_user_nl_allruns(self): "stream_year_last_cropcal = 2000", "model_year_align_cropcal = 2000", " ", - "! (h1) Daily outputs for GDD generation and figure-making", - "hist_fincl2 = 'GDDACCUM', 'GDDHARV'", - "hist_nhtfrq(2) = -24", - "hist_mfilt(2) = 365", + "! (h1) Annual outputs for GDD generation (checks)", + "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", + "hist_nhtfrq(2) = 17520", + "hist_mfilt(2) = 999", "hist_type1d_pertape(2) = 'PFTS'", "hist_dov2xy(2) = .false.", " ", - "! (h2) Annual outputs for GDD generation (checks)", - "hist_fincl3 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", - "hist_nhtfrq(3) = 17520", - "hist_mfilt(3) = 999", + "! (h2) Daily outputs for GDD generation and figure-making", + "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", + "hist_nhtfrq(3) = -24", + "hist_mfilt(3) = 365", "hist_type1d_pertape(3) = 'PFTS'", "hist_dov2xy(3) = .false.", ] diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index f4f15de01f..a93c6abc61 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -97,7 +97,7 @@ def main( ) pickle_file = os.path.join(output_dir, f"{first_season}-{last_season}.pickle") - h1_ds_file = os.path.join(output_dir, f"{first_season}-{last_season}.h1_ds.nc") + h2_ds_file = os.path.join(output_dir, f"{first_season}-{last_season}.h2_ds.nc") if os.path.exists(pickle_file): with open(pickle_file, "rb") as f: ( @@ -115,7 +115,7 @@ def main( mxsowings, ) = pickle.load(f) print(f"Will resume import at {pickle_year+1}") - h1_ds = None + h2_ds = None else: incorrectly_daily = False skip_patches_for_isel_nan_lastyear = np.ndarray([]) @@ -137,7 +137,7 @@ def main( continue ( - h1_ds, + h2_ds, sdates_rx, hdates_rx, gddaccum_yp_list, @@ -162,7 +162,7 @@ def main( incorrectly_daily, input_dir, incl_vegtypes_str, - h1_ds_file, + h2_ds_file, mxmats, cc.get_gs_len_da, logger, @@ -197,8 +197,8 @@ def main( gddfn.log(logger, "Done") - if not h1_ds: - h1_ds = xr.open_dataset(h1_ds_file) + if not h2_ds: + h2_ds = xr.open_dataset(h2_ds_file) ###################################################### ### Get and grid mean GDDs in GGCMI growing season ### @@ -214,10 +214,10 @@ def main( gddfn.log(logger, "Getting and gridding mean GDDs...") gdd_maps_ds = gddfn.yp_list_to_ds( - gddaccum_yp_list, h1_ds, incl_vegtypes_str, sdates_rx, longname_prefix, logger + gddaccum_yp_list, h2_ds, incl_vegtypes_str, sdates_rx, longname_prefix, logger ) gddharv_maps_ds = gddfn.yp_list_to_ds( - gddharv_yp_list, h1_ds, incl_vegtypes_str, sdates_rx, longname_prefix, logger + gddharv_yp_list, h2_ds, incl_vegtypes_str, sdates_rx, longname_prefix, logger ) # Fill NAs with dummy values diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 921ddd0a41..467eefc7d0 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -195,7 +195,7 @@ def import_and_process_1yr( incorrectly_daily, indir, incl_vegtypes_str_in, - h1_ds_file, + h2_ds_file, mxmats, get_gs_len_da, logger, @@ -464,15 +464,15 @@ def import_and_process_1yr( log(logger, f" Importing accumulated GDDs...") clm_gdd_var = "GDDACCUM" myVars = [clm_gdd_var, "GDDHARV"] - pattern = os.path.join(indir, f"*h1.{thisYear-1}-01-01*.nc") - h1_files = glob.glob(pattern) - if not h1_files: - pattern = os.path.join(indir, f"*h1.{thisYear-1}-01-01*.nc.base") - h1_files = glob.glob(pattern) - if not h1_files: - error(logger, f"No files found matching pattern '*h1.{thisYear-1}-01-01*.nc(.base)'") - h1_ds = utils.import_ds( - h1_files, + pattern = os.path.join(indir, f"*h2.{thisYear-1}-01-01*.nc") + h2_files = glob.glob(pattern) + if not h2_files: + pattern = os.path.join(indir, f"*h2.{thisYear-1}-01-01*.nc.base") + h2_files = glob.glob(pattern) + if not h2_files: + error(logger, f"No files found matching pattern '*h2.{thisYear-1}-01-01*.nc(.base)'") + h2_ds = utils.import_ds( + h2_files, myVars=myVars, myVegtypes=utils.define_mgdcrop_list(), chunks=chunks, @@ -480,36 +480,36 @@ def import_and_process_1yr( # Restrict to patches we're including if skipping_patches_for_isel_nan: - if not np.array_equal(dates_ds.patch.values, h1_ds.patch.values): - error(logger, "dates_ds and h1_ds don't have the same patch list!") - h1_incl_ds = h1_ds.isel(patch=incl_patches_for_isel_nan) + if not np.array_equal(dates_ds.patch.values, h2_ds.patch.values): + error(logger, "dates_ds and h2_ds don't have the same patch list!") + h2_incl_ds = h2_ds.isel(patch=incl_patches_for_isel_nan) else: - h1_incl_ds = h1_ds + h2_incl_ds = h2_ds - if not np.any(h1_incl_ds[clm_gdd_var].values != 0): + if not np.any(h2_incl_ds[clm_gdd_var].values != 0): error(logger, f"All {clm_gdd_var} values are zero!") # Get standard datetime axis for outputs Nyears = yN - y1 + 1 if len(gddaccum_yp_list) == 0: - lastYear_active_patch_indices_list = [None for vegtype_str in h1_incl_ds.vegtype_str.values] - gddaccum_yp_list = [None for vegtype_str in h1_incl_ds.vegtype_str.values] + lastYear_active_patch_indices_list = [None for vegtype_str in h2_incl_ds.vegtype_str.values] + gddaccum_yp_list = [None for vegtype_str in h2_incl_ds.vegtype_str.values] if save_figs: - gddharv_yp_list = [None for vegtype_str in h1_incl_ds.vegtype_str.values] + gddharv_yp_list = [None for vegtype_str in h2_incl_ds.vegtype_str.values] incl_vegtype_indices = [] - for v, vegtype_str in enumerate(h1_incl_ds.vegtype_str.values): + for v, vegtype_str in enumerate(h2_incl_ds.vegtype_str.values): # Skipping Miscanthus because it seems to never be harvested even though it is sown. This causes problems in NaN mask check. if "miscanthus" in vegtype_str: log(logger, f" SKIPPING {vegtype_str}") continue vegtype_int = utils.vegtype_str2int(vegtype_str)[0] - thisCrop_full_patchlist = list(utils.xr_flexsel(h1_ds, vegtype=vegtype_str).patch.values) + thisCrop_full_patchlist = list(utils.xr_flexsel(h2_ds, vegtype=vegtype_str).patch.values) # Get time series for each patch of this type - thisCrop_ds = utils.xr_flexsel(h1_incl_ds, vegtype=vegtype_str) + thisCrop_ds = utils.xr_flexsel(h2_incl_ds, vegtype=vegtype_str) thisCrop_gddaccum_da = thisCrop_ds[clm_gdd_var] if save_figs: thisCrop_gddharv_da = thisCrop_ds["GDDHARV"] @@ -668,11 +668,11 @@ def import_and_process_1yr( skip_patches_for_isel_nan_lastyear = skip_patches_for_isel_nan # Could save space by only saving variables needed for gridding - log(logger, " Saving h1_ds...") - h1_ds.to_netcdf(h1_ds_file) + log(logger, " Saving h2_ds...") + h2_ds.to_netcdf(h2_ds_file) return ( - h1_ds, + h2_ds, sdates_rx, hdates_rx, gddaccum_yp_list, From 7a5c38ca0d9b32cf66233cfd635227ed2488ced7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 12:49:22 -0600 Subject: [PATCH 0961/2067] RXCROPMATURITY: Do not save any daily outputs for Prescribed Calendars run. --- cime_config/SystemTests/rxcropmaturity.py | 26 +++++++---------------- 1 file changed, 8 insertions(+), 18 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 0458a9f752..566c0a605c 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -110,6 +110,13 @@ def run_phase(self): self._append_to_user_nl_clm([ "generate_crop_gdds = .true.", "use_mxmat = .false.", + " ", + "! (h2) Daily outputs for GDD generation and figure-making", + "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", + "hist_nhtfrq(3) = -24", + "hist_mfilt(3) = 365", + "hist_type1d_pertape(3) = 'PFTS'", + "hist_dov2xy(3) = .false.", ]) # If flanduse_timeseries is defined, we need to make a static version for this test. This @@ -153,16 +160,6 @@ def run_phase(self): f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", ]) - # Add extra stuff to help diagnose diffs - self._append_to_user_nl_clm([ - "! (h3) Daily PFT-level outputs to help diagnose diffs", - "hist_fincl4 = 'CPHASE'", - "hist_nhtfrq(4) = -24", - "hist_mfilt(4) = 1", - "hist_type1d_pertape(4) = 'PFTS'", - "hist_dov2xy(4) = .false.", - ]) - self.run_indv() #------------------------------------------------------------------- @@ -294,19 +291,12 @@ def _modify_user_nl_allruns(self): "stream_year_last_cropcal = 2000", "model_year_align_cropcal = 2000", " ", - "! (h1) Annual outputs for GDD generation (checks)", + "! (h1) Annual outputs on sowing or harvest axis "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", "hist_nhtfrq(2) = 17520", "hist_mfilt(2) = 999", "hist_type1d_pertape(2) = 'PFTS'", "hist_dov2xy(2) = .false.", - " ", - "! (h2) Daily outputs for GDD generation and figure-making", - "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", - "hist_nhtfrq(3) = -24", - "hist_mfilt(3) = 365", - "hist_type1d_pertape(3) = 'PFTS'", - "hist_dov2xy(3) = .false.", ] self._append_to_user_nl_clm(nl_additions) From 4c00684491e593ecd912124b3fe9538b8ab67e86 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 14:28:53 -0600 Subject: [PATCH 0962/2067] Added namelist setup logic for tillage params. --- bld/CLMBuildNamelist.pm | 26 +++++++++++++++++++ .../namelist_definition_ctsm.xml | 19 ++++++++++++++ 2 files changed, 45 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 02d9799487..3f8dfda2f5 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1596,6 +1596,11 @@ sub process_namelist_inline_logic { ############################### setup_logic_crop($opts, $nl_flags, $definition, $defaults, $nl); + ############################### + # namelist group: tillage # + ############################### + setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl); + ############################### # namelist group: ch4par_in # ############################### @@ -2140,6 +2145,27 @@ sub setup_logic_crop { } } +#------------------------------------------------------------------------------- + +sub setup_logic_tillage { + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + if ( &value_is_true($nl->get_value('do_tillage_low')) and &value_is_true($nl->get_value('do_tillage_high')) ) { + $log->fatal_error( "do_tillage_low and do_tillage_high are mutually exclusive" ); + } + + if ( &value_is_true($nl->get_value('do_tillage_low')) or &value_is_true($nl->get_value('do_tillage_high')) ) { + + if ( not &value_is_true($nl->get_value('use_crop')) ) { + $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); + } + + if ( &value_is_true($nl->get_value('use_fates')) ) { + $log->fatal_error( "Tillage can't be used with FATES" ); + } + } +} + #------------------------------------------------------------------------------- sub error_if_set { # do a fatal_error and exit if any of the input variable names are set diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index f51c577c09..6c27a26a63 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2803,4 +2803,23 @@ use case.) + + + + + +Toggle to turn on low-intensity tillage + + + +Toggle to turn on high-intensity tillage + + + +Toggle to use original tillage logic + + From 2adb528e73ca55034444104243375c8e569427e7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 15:22:02 -0600 Subject: [PATCH 0963/2067] Fixes to reading tillage namelist. --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_definition_ctsm.xml | 6 +++--- src/biogeochem/TillageMod.f90 | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 3f8dfda2f5..41582ee6f9 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4298,7 +4298,7 @@ sub write_output_files { soil_resis_inparm bgc_shared canopyfluxes_inparm aerosol clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm cnprecision_inparm clm_glacier_behavior crop irrigation_inparm - surfacealbedo_inparm water_tracers_inparm); + surfacealbedo_inparm water_tracers_inparm tillage_inparm); #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm # finidat_consistency_checks dynpft_consistency_checks); diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 6c27a26a63..1a3fd81e2a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2808,17 +2808,17 @@ use case.) + group="tillage_inparm" valid_values="" value=".false."> Toggle to turn on low-intensity tillage + group="tillage_inparm" valid_values="" value=".false."> Toggle to turn on high-intensity tillage + group="tillage_inparm" valid_values="" value=".false."> Toggle to use original tillage logic diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index fd540e3be5..6c2bd75fb7 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -50,7 +50,7 @@ subroutine tillage_init(bounds) integer :: mpicom ! MPI communicator character(*), parameter :: subname = "('tillage_init')" - namelist /tillage_nml/ & + namelist /tillage_inparm/ & do_tillage_low, & do_tillage_high, & use_original_tillage @@ -63,9 +63,9 @@ subroutine tillage_init(bounds) ! Read tillage namelist if (masterproc) then open(newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'tillage_nml', status=nml_error) + call find_nlgroup_name(nu_nml, 'tillage_inparm', status=nml_error) if (nml_error == 0) then - read(nu_nml, nml=tillage_nml, iostat=nml_error) + read(nu_nml, nml=tillage_inparm, iostat=nml_error) if (nml_error /= 0) then call endrun(subname // ':: ERROR reading tillage namelist') end if From ff410837814579d4f4cd7e46abf45fca9c9a63b1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 May 2023 16:57:59 -0700 Subject: [PATCH 0964/2067] =?UTF-8?q?Replace=20index=20vars:=20i=5Flitr2?= =?UTF-8?q?=20=E2=86=92=20i=5Fcel=5Flit,=20i=5Flitr3=20=E2=86=92=20i=5Flig?= =?UTF-8?q?=5Flit.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/biogeochem/TillageMod.f90 | 66 +++++++++++-------- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 2 +- 2 files changed, 40 insertions(+), 28 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 6c2bd75fb7..4e78c1d6fd 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -3,13 +3,21 @@ module TillageMod ! !DESCRIPTION: ! Module for soil tillage. ! + ! As described in ChangeLog: + ! history field name change as follows... + ! LITR1 becomes MET_LIT (metabolic) + ! LITR2 becomes CEL_LIT (cellulosic) + ! LITR3 becomes LIG_LIT (lignin) + ! SOIL1 becomes ACT_SOM (active) + ! SOIL2 becomes SLO_SOM (slow) + ! SOIL3 becomes PAS_SOM (passive) + ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use clm_varctl , only : iulog - ! TODO: Confirm that i_soil1->i_act_som, i_soil2->i_slo_som, i_soil3->i_pas_som - use clm_varpar , only : i_litr2, i_litr3, ndecomp_pools + use clm_varpar , only : ndecomp_pools ! implicit none private @@ -110,7 +118,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) + subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -126,6 +134,7 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools + integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! @@ -165,8 +174,8 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som else if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_litr2) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_litr3) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(c,i_act_som) = 1.00_r8 !high 1.20,low 1.00 tillage_mults(c,i_slo_som) = 3.00_r8 !high 4.80,low 3.00 tillage_mults(c,i_pas_som) = 3.00_r8 !high 4.80,low 3.00 @@ -174,8 +183,8 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_litr2) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_litr3) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(c,i_slo_som) = 1.60_r8 !high 3.50,low 1.60 tillage_mults(c,i_pas_som) = 1.60_r8 !high 3.50,low 1.60 @@ -183,8 +192,8 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som else if (day >= idop(p)+45 .and. day = npcropmin) then - tillage_mults(c,i_litr2) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_litr3) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(c,i_slo_som) = 1.30_r8 !high 2.50,low 1.30 tillage_mults(c,i_pas_som) = 1.30_r8 !high 2.50,low 1.30 @@ -195,8 +204,8 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som patch%itype(p) == nirrig_tmp_corn .or. & patch%itype(p) == ntmp_soybean .or. & patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(c,i_litr2) = 1.00_r8 - tillage_mults(c,i_litr3) = 1.00_r8 + tillage_mults(c,i_cel_lit) = 1.00_r8 + tillage_mults(c,i_lig_lit) = 1.00_r8 tillage_mults(c,i_act_som) = 1.00_r8 tillage_mults(c,i_slo_som) = 1.00_r8 tillage_mults(c,i_pas_som) = 1.00_r8 @@ -209,7 +218,7 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som end subroutine get_tillage_multipliers_orig - subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) + subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -226,6 +235,7 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools + integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! @@ -264,8 +274,8 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, else if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_litr2) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_litr3) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(c,i_act_som) = 1.00_r8 !high 1.20,low 1.00 tillage_mults(c,i_slo_som) = 3.00_r8 !high 4.80,low 3.00 tillage_mults(c,i_pas_som) = 3.00_r8 !high 4.80,low 3.00 @@ -273,8 +283,8 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, else if (idpp < 45) then ! based on Field and Row Cultivator multipliers tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_litr2) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_litr3) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(c,i_slo_som) = 1.60_r8 !high 3.50,low 1.60 tillage_mults(c,i_pas_som) = 1.60_r8 !high 3.50,low 1.60 @@ -282,8 +292,8 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, else if (idpp < 75) then ! based on Rod Weed Row Planter tillage_mults(c,:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_litr2) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_litr3) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(c,i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(c,i_slo_som) = 1.30_r8 !high 2.50,low 1.30 tillage_mults(c,i_pas_som) = 1.30_r8 !high 2.50,low 1.30 @@ -294,8 +304,8 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, patch%itype(p) == nirrig_tmp_corn .or. & patch%itype(p) == ntmp_soybean .or. & patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(c,i_litr2) = 1.00_r8 - tillage_mults(c,i_litr3) = 1.00_r8 + tillage_mults(c,i_cel_lit) = 1.00_r8 + tillage_mults(c,i_lig_lit) = 1.00_r8 tillage_mults(c,i_act_som) = 1.00_r8 tillage_mults(c,i_slo_som) = 1.00_r8 tillage_mults(c,i_pas_som) = 1.00_r8 @@ -309,7 +319,7 @@ end subroutine get_tillage_multipliers_new ! Public interface to choose between and call either get_tillage_multipliers_orig() or get_tillage_multipliers_new() - subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) + subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Public interface to choose between and call either original (buggy) or @@ -320,17 +330,18 @@ subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_s integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools + integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools if (use_original_tillage) then - call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) + call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) else - call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) + call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if end subroutine get_tillage_multipliers - subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som) + subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Multiply decomposition rate constants by tillage coefficients. @@ -346,11 +357,12 @@ subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soil integer , intent(in) :: filter_soilc(:) ! filter for soil columns real(r8) , intent(inout) :: decomp_k(:,:,:) ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools + integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES integer :: j, fc, c - call get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som) + call get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham @@ -358,8 +370,8 @@ subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soil do fc = 1,num_soilc c = filter_soilc(fc) ! TODO: Loop through ALL pools, not just the ones that currently have non-1 values - decomp_k(c,j,i_litr2) = decomp_k(c,j,i_litr2) * tillage_mults(c,i_litr2) - decomp_k(c,j,i_litr3) = decomp_k(c,j,i_litr3) * tillage_mults(c,i_litr3) + decomp_k(c,j,i_cel_lit) = decomp_k(c,j,i_cel_lit) * tillage_mults(c,i_cel_lit) + decomp_k(c,j,i_lig_lit) = decomp_k(c,j,i_lig_lit) * tillage_mults(c,i_lig_lit) decomp_k(c,j,i_act_som) = decomp_k(c,j,i_act_som) * tillage_mults(c,i_act_som) decomp_k(c,j,i_slo_som) = decomp_k(c,j,i_slo_som) * tillage_mults(c,i_slo_som) decomp_k(c,j,i_pas_som) = decomp_k(c,j,i_pas_som) * tillage_mults(c,i_pas_som) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 2fbc69c726..03136b0007 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -908,7 +908,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & if (.not. (present(idop) .and. present(num_soilp) .and. present(filter_soilp))) then call endrun("Do not call tillage without providing idop, num_soilp, and filter_soilp. (Maybe you called with FATES?)") end if - call get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som) + call get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if ! Above into soil matrix From ff923e116d6ea3545bfb8f3399ac5f0af784444f Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 25 May 2023 11:06:31 -0400 Subject: [PATCH 0965/2067] FATES in the normal bgc call sequence, addressing reviewer comments --- src/biogeochem/CNVegCarbonStateType.F90 | 5 +-- src/main/clm_driver.F90 | 3 ++ src/main/controlMod.F90 | 5 +++ src/main/filterMod.F90 | 18 +++++----- .../SoilBiogeochemCarbonFluxType.F90 | 9 +++-- .../SoilBiogeochemNitrogenFluxType.F90 | 4 ++- .../SoilBiogeochemVerticalProfileMod.F90 | 33 ++++++++++--------- src/utils/clmfates_interfaceMod.F90 | 9 ----- 8 files changed, 46 insertions(+), 40 deletions(-) diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index 5baf1bce0b..b2ca4c4792 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -82,8 +82,9 @@ module CNVegCarbonStateType real(r8), pointer :: dispvegc_patch (:) ! (gC/m2) displayed veg carbon, excluding storage and cpool real(r8), pointer :: storvegc_patch (:) ! (gC/m2) stored vegetation carbon, excluding cpool - logical, private :: dribble_crophrv_xsmrpool_2atm - + logical, private :: dribble_crophrv_xsmrpool_2atm ! Flag to indicate if should harvest xsmrpool to the atmosphere + ! it originates and is defined in CNVegetationFacade.F90 + ! Total C pools real(r8), pointer :: totc_patch (:) ! (gC/m2) total patch-level carbon, including cpool real(r8), pointer :: totvegc_patch (:) ! (gC/m2) total vegetation carbon, excluding cpool diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index e54535c09e..5fb0d233ec 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -288,6 +288,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call active_layer_inst%alt_calc(filter_inactive_and_active(nc)%num_soilc, filter_inactive_and_active(nc)%soilc, & temperature_inst) + ! Filter bgc_soilc operates on all non-sp soil columns + ! Filter bgc_vegp operates on all non-fates, non-sp patches (use_cn) on soil if ((use_cn .or. use_fates_bgc) .and. decomp_method /= no_soil_decomp) then call SoilBiogeochemVerticalProfile(bounds_clump , & filter_inactive_and_active(nc)%num_bgc_soilc, filter_inactive_and_active(nc)%bgc_soilc , & @@ -1080,6 +1082,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call t_stopf('hydro2_drainage') + if (use_cn .or. use_fates_bgc) then call t_startf('EcosysDynPostDrainage') call bgc_vegetation_inst%EcosystemDynamicsPostDrainage(bounds_clump, & diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 99d7f3c835..c793898d5e 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -473,6 +473,11 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if + if (use_c13 .or. use_c14) then + call endrun(msg=' ERROR: C13 and C14 dynamics are not compatible with FATES.'//& + errMsg(sourcefile, __LINE__)) + end if + else ! These do default to false anyway, but this emphasizes they diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index d96cb63a30..0b7d230a54 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -478,16 +478,14 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fnl = 0 do p = bounds%begp,bounds%endp if (patch%active(p) .or. include_inactive) then - if(.not.use_fates)then ! This needs to be a FATES filter - if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types - fl = fl + 1 - this_filter(nc)%pcropp(fl) = p - else - l =patch%landunit(p) - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - fnl = fnl + 1 - this_filter(nc)%soilnopcropp(fnl) = p - end if + if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types + fl = fl + 1 + this_filter(nc)%pcropp(fl) = p + else + l =patch%landunit(p) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + fnl = fnl + 1 + this_filter(nc)%soilnopcropp(fnl) = p end if end if end if diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index 9d47c188be..985a97eacc 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -58,7 +58,10 @@ module SoilBiogeochemCarbonFluxType real(r8), pointer :: lithr_col (:) ! (gC/m2/s) litter heterotrophic respiration: donor-pool based definition real(r8), pointer :: somhr_col (:) ! (gC/m2/s) soil organic matter heterotrophic res: donor-pool based definition real(r8), pointer :: soilc_change_col (:) ! (gC/m2/s) FUN used soil C - real(r8), pointer :: fates_litter_flux (:) ! (gC/m2/s) Litter flux passed in from FATES + real(r8), pointer :: fates_litter_flux (:) ! (gC/m2/s) A summary of the total litter + ! flux passed in from FATES. + ! This is a diagnostic for balance checks only + contains @@ -950,7 +953,9 @@ subroutine Summary(this, bounds, & frootc_to_litter_col(c) + & soilbiogeochem_decomp_cascade_ctransfer_col(c,i_cwdl2)) !else - ! Alternative place to hook in fates litr lignan + ! For FATES: + ! this array is currently updated here: + ! clmfates_interfaceMod.F90:wrap_update_hlmfates_dyn() end if end do end if if_mimics diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 index 90ba4512c7..99ce2e7cf9 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 @@ -128,7 +128,9 @@ module SoilBiogeochemNitrogenFluxType real(r8), pointer :: decomp_npools_sourcesink_col (:,:,:) ! col (gN/m3) change in decomposing n pools ! (sum of all additions and subtractions from stateupdate1). real(r8), pointer :: sminn_to_plant_fun_vr_col (:,:) ! col total layer soil N uptake of FUN (gN/m2/s) - real(r8), pointer :: fates_litter_flux (:) ! (gN/m2/s) Litter flux passed in from FATES + real(r8), pointer :: fates_litter_flux (:) ! (gN/m2/s) A summary of the total litter + ! flux passed in from FATES. + ! This is a diagnostic for balance checks only ! track tradiagonal matrix contains diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 index 772c2db82e..3548643192 100644 --- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 @@ -174,28 +174,29 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil ! cinput_rootfr(bounds%begp:bounds%endp, :), & ! col_cinput_rootfr(bounds%begc:bounds%endc, :), & ! 'unity') - if(num_soilp>0)then - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - if(.not.col%is_fates(c))then - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - do j = 1,nlevdecomp - col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) - end do - end if - end if - end do + + !if(num_soilp>0)then + do fc = 1,num_soilc + c = filter_soilc(fc) + if(.not.col%is_fates(c))then + do pi = 1,col%npatches(c)) !maxsoil_patches + !if (pi <= col%npatches(c)) then + p = col%patchi(c) + pi - 1 + do j = 1,nlevdecomp + col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) + end do + !end if + end if end do - end if + end do + !end if ! repeat for column-native profiles: Ndep and Nfix do fc = 1,num_soilc c = filter_soilc(fc) rootfr_tot = 0._r8 surface_prof_tot = 0._r8 - if(col%is_fates(c))then + if_fates: if(col%is_fates(c))then ! For FATES, we just use the e-folding depth for both fixation and deposition ! partially because the fixation may be free-living depending on FATES-side ! fixation choices, and partially for simplicity @@ -226,7 +227,7 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil nfixation_prof(c,1) = 1./dzsoi_decomp(1) ndep_prof(c,1) = 1./dzsoi_decomp(1) endif - end if + end if if_fates end do ! check to make sure integral of all profiles = 1. diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 0ac24f897c..e288646e43 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1204,15 +1204,6 @@ subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) cf_soil%fates_litter_flux = 0._r8 end if - ! This is a diagnostic for carbon accounting (NOT IN CLM, ONLY ELM) - !col_cf%litfall(c) = & - ! sum(this%fates(ci)%bc_out(s)%litt_flux_lab_c_si(1:nlevdecomp) * & - ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - ! sum(this%fates(ci)%bc_out(s)%litt_flux_cel_c_si(1:nlevdecomp) * & - ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) + & - ! sum(this%fates(ci)%bc_out(s)%litt_flux_lig_c_si(1:nlevdecomp) * ^ - ! this%fates(ci)%bc_in(s)%dz_decomp_sisl(1:nlevdecomp)) - end associate return From 158b182c2eef2afb815bee41e63f8b14728c30a9 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 25 May 2023 13:41:15 -0400 Subject: [PATCH 0966/2067] Part-way through re-name-spacing the soilc and soilp filters for BGC --- src/biogeochem/CNAnnualUpdateMod.F90 | 24 +- src/biogeochem/CNDriverMod.F90 | 278 +++++++++--------- src/biogeochem/CNFireEmissionsMod.F90 | 10 +- src/biogeochem/CNPrecisionControlMod.F90 | 100 +++---- src/biogeochem/CNVegCarbonStateType.F90 | 18 +- src/biogeochem/CNVegetationFacade.F90 | 84 +++--- src/main/clm_driver.F90 | 2 +- .../SoilBiogeochemCarbonFluxType.F90 | 66 ++--- .../SoilBiogeochemCarbonStateType.F90 | 86 +++--- .../SoilBiogeochemCompetitionMod.F90 | 164 +++++------ .../SoilBiogeochemDecompCascadeBGCMod.F90 | 66 ++--- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 48 +-- .../SoilBiogeochemDecompMod.F90 | 34 +-- .../SoilBiogeochemLittVertTranspMod.F90 | 52 ++-- .../SoilBiogeochemNLeachingMod.F90 | 30 +- .../SoilBiogeochemNStateUpdate1Mod.F90 | 42 +-- .../SoilBiogeochemNitrifDenitrifMod.F90 | 10 +- .../SoilBiogeochemNitrogenFluxType.F90 | 54 ++-- .../SoilBiogeochemNitrogenStateType.F90 | 102 +++---- .../SoilBiogeochemNitrogenUptakeMod.F90 | 18 +- .../SoilBiogeochemPotentialMod.F90 | 42 +-- .../SoilBiogeochemPrecisionControlMod.F90 | 14 +- .../SoilBiogeochemVerticalProfileMod.F90 | 36 +-- 23 files changed, 690 insertions(+), 690 deletions(-) diff --git a/src/biogeochem/CNAnnualUpdateMod.F90 b/src/biogeochem/CNAnnualUpdateMod.F90 index 34324e4c93..956042db63 100644 --- a/src/biogeochem/CNAnnualUpdateMod.F90 +++ b/src/biogeochem/CNAnnualUpdateMod.F90 @@ -22,7 +22,7 @@ module CNAnnualUpdateMod contains !----------------------------------------------------------------------- - subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + subroutine CNAnnualUpdate(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_state_inst, cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -35,10 +35,10 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches type(cnveg_state_type) , intent(inout) :: cnveg_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst ! @@ -54,8 +54,8 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi dt = get_step_size_real() secspyear = get_curr_days_per_year() * secspday - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if(.not.col%is_fates(c))then cnveg_state_inst%annsum_counter_col(c) = cnveg_state_inst%annsum_counter_col(c) + dt if (cnveg_state_inst%annsum_counter_col(c) >= secspyear) then @@ -68,8 +68,8 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi end do - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) c = patch%column(p) if (end_of_year(c) .and. .not.col%is_fates(c)) then @@ -98,11 +98,11 @@ subroutine CNAnnualUpdate(bounds, num_soilc, filter_soilc, num_soilp, filter_soi end do ! Get column-level averages, just for the columns that have reached their personal end-of-year - if(num_soilp>0)then + if(num_bgc_vegp>0)then filter_endofyear_c = col_filter_from_filter_and_logical_array( & bounds = bounds, & - num_orig = num_soilc, & - filter_orig = filter_soilc, & + num_orig = num_bgc_soilc, & + filter_orig = filter_bgc_soilc, & logical_col = end_of_year(bounds%begc:bounds%endc)) call p2c(bounds, filter_endofyear_c%num, filter_endofyear_c%indices, & diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 5c77179d77..c63452e76d 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -85,7 +85,7 @@ end subroutine CNDriverInit !----------------------------------------------------------------------- subroutine CNDriverNoLeaching(bounds, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & num_pcropp, filter_pcropp, num_soilnopcropp, filter_soilnopcropp, & num_actfirec, filter_actfirec, num_actfirep, filter_actfirep, & num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, & @@ -151,10 +151,10 @@ subroutine CNDriverNoLeaching(bounds, ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of veg patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for veg patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for veg patches integer , intent(out) :: num_actfirep ! number of soil patches on fire in filter integer , intent(out) :: filter_actfirep(:) ! filter for soil patches on fire integer , intent(out) :: num_actfirec ! number of soil columns on fire in filter @@ -246,50 +246,50 @@ subroutine CNDriverNoLeaching(bounds, ! COMPILER_BUG(wjs, 2014-11-29, pgi 14.7) Without this, the filter is full of garbage ! in some situations call t_startf('CNZero-soilbgc-cflux') - dummy_to_make_pgi_happy = ubound(filter_soilc, 1) + dummy_to_make_pgi_happy = ubound(filter_bgc_soilc, 1) call soilbiogeochem_carbonflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) + num_bgc_soilc, filter_bgc_soilc, 0._r8) if ( use_c13 ) then call c13_soilbiogeochem_carbonflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) + num_bgc_soilc, filter_bgc_soilc, 0._r8) end if if ( use_c14 ) then call c14_soilbiogeochem_carbonflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) + num_bgc_soilc, filter_bgc_soilc, 0._r8) end if call t_stopf('CNZero-soilbgc-cflux') - if(num_soilp>0)then + if(num_bgc_vegp>0)then call t_startf('CNZero-vegbgc-cflux') call cnveg_carbonflux_inst%SetValues( & nvegcpool,& - num_soilp, filter_soilp, 0._r8, & - num_soilc, filter_soilc, 0._r8) + num_bgc_vegp, filter_bgc_vegp, 0._r8, & + num_bgc_soilc, filter_bgc_soilc, 0._r8) if ( use_c13 ) then call c13_cnveg_carbonflux_inst%SetValues( & nvegcpool,& - num_soilp, filter_soilp, 0._r8, & - num_soilc, filter_soilc, 0._r8) + num_bgc_vegp, filter_bgc_vegp, 0._r8, & + num_bgc_soilc, filter_bgc_soilc, 0._r8) end if if ( use_c14 ) then call c14_cnveg_carbonflux_inst%SetValues( & nvegcpool,& - num_soilp, filter_soilp, 0._r8, & - num_soilc, filter_soilc, 0._r8) + num_bgc_vegp, filter_bgc_vegp, 0._r8, & + num_bgc_soilc, filter_bgc_soilc, 0._r8) end if call t_stopf('CNZero-vegbgc-cflux') call t_startf('CNZero-vegbgc-nflux') call cnveg_nitrogenflux_inst%SetValues( & nvegnpool, & - num_soilp, filter_soilp, 0._r8, & - num_soilc, filter_soilc, 0._r8) + num_bgc_vegp, filter_bgc_vegp, 0._r8, & + num_bgc_soilc, filter_bgc_soilc, 0._r8) end if call t_stopf('CNZero-vegbgc-nflux') call t_startf('CNZero-soilbgc-nflux') call soilbiogeochem_nitrogenflux_inst%SetValues( & - num_soilc, filter_soilc, 0._r8) + num_bgc_soilc, filter_bgc_soilc, 0._r8) call t_stopf('CNZero-soilbgc-nflux') call t_stopf('CNZero') @@ -305,12 +305,12 @@ subroutine CNDriverNoLeaching(bounds, if(use_fun)then call t_startf('CNFLivFixation') - call CNFreeLivingFixation( num_soilc, filter_soilc, & + call CNFreeLivingFixation( num_bgc_soilc, filter_bgc_soilc, & waterfluxbulk_inst, soilbiogeochem_nitrogenflux_inst) call t_stopf('CNFLivFixation') else call t_startf('CNFixation') - call CNNFixation( num_soilc, filter_soilc, & + call CNNFixation( num_bgc_soilc, filter_bgc_soilc, & cnveg_carbonflux_inst, soilbiogeochem_nitrogenflux_inst, & clm_fates, bounds%clump_index) call t_stopf('CNFixation') @@ -318,18 +318,18 @@ subroutine CNDriverNoLeaching(bounds, if (use_crop) then - call CNNFert(bounds, num_soilc,filter_soilc, & + call CNNFert(bounds, num_bgc_soilc,filter_bgc_soilc, & cnveg_nitrogenflux_inst, soilbiogeochem_nitrogenflux_inst) if (.not. use_fun) then ! if FUN is active, then soy fixation handled by FUN - call CNSoyfix (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNSoyfix (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & waterdiagnosticbulk_inst, crop_inst, cnveg_state_inst, cnveg_nitrogenflux_inst , & soilbiogeochem_state_inst, soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) end if end if call t_startf('CNMResp') - call CNMResp(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNMResp(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & canopystate_inst, soilstate_inst, temperature_inst, photosyns_inst, & cnveg_carbonflux_inst, cnveg_nitrogenstate_inst) call t_stopf('CNMResp') @@ -341,11 +341,11 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('SoilBiogeochem') call t_startf('DecompRate') if (decomp_method == century_decomp) then - call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & + call decomp_rate_constants_bgc(bounds, num_bgc_soilc, filter_bgc_soilc, & soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) else if (decomp_method == mimics_decomp) then - call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp, clm_fates, & + call decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, clm_fates, & soilstate_inst, temperature_inst, cnveg_carbonflux_inst, ch4_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst) end if @@ -353,7 +353,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('SoilBiogeochemPotential') ! calculate potential decomp rates and total immobilization demand (previously inlined in CNDecompAlloc) - call SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & + call SoilBiogeochemPotential (bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools), & @@ -365,12 +365,12 @@ subroutine CNDriverNoLeaching(bounds, ! calculate vertical profiles for distributing soil and litter C and N ! (previously subroutine decomp_vertprofiles called from CNDecompAlloc) - call SoilBiogeochemVerticalProfile(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call SoilBiogeochemVerticalProfile(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & active_layer_inst, soilstate_inst,soilbiogeochem_state_inst) ! calculate nitrification and denitrification rates (previously subroutine nitrif_denitrif called from CNDecompAlloc) if (use_nitrif_denitrif) then - call SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & + call SoilBiogeochemNitrifDenitrif(bounds, num_bgc_soilc, filter_bgc_soilc, & soilstate_inst, waterstatebulk_inst, temperature_inst, ch4_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) end if @@ -395,8 +395,8 @@ subroutine CNDriverNoLeaching(bounds, !RF: moved ths call to before nutrient_demand, so that croplive didn't change half way through crop N cycle. if ( use_fun ) then call t_startf('CNPhenology_phase1') - call CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & - filter_soilp, num_pcropp, filter_pcropp, & + call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & + filter_bgc_vegp, num_pcropp, filter_pcropp, & waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & @@ -415,7 +415,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('cnalloc') call calc_gpp_mr_availc( & - bounds, num_soilp, filter_soilp, & + bounds, num_bgc_vegp, filter_bgc_vegp, & crop_inst, photosyns_inst, canopystate_inst, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, & c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst) @@ -425,7 +425,7 @@ subroutine CNDriverNoLeaching(bounds, crop_inst, cnveg_state_inst) end if - call calc_allometry(num_soilp, filter_soilp, & + call calc_allometry(num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, cnveg_state_inst) call t_stopf('cnalloc') @@ -454,13 +454,13 @@ subroutine CNDriverNoLeaching(bounds, ! get the column-averaged plant_ndemand (needed for following call to SoilBiogeochemCompetition) - if(num_soilp>0)then - call p2c(bounds, num_soilc, filter_soilc, & + if(num_bgc_vegp>0)then + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & cnveg_nitrogenflux_inst%plant_ndemand_patch(begp:endp), & soilbiogeochem_state_inst%plant_ndemand_col(begc:endc)) else ! With FATES N coupling, we will have a call to fill - ! this in on the filter_soilc + ! this in on the filter_bgc_soilc soilbiogeochem_state_inst%plant_ndemand_col(begc:endc) = 0._r8 end if @@ -470,7 +470,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('soilbiogeochemcompetition') - call SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, filter_soilp, & + call SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,num_bgc_vegp, filter_bgc_vegp, & p_decomp_cn_gain, pmnf_decomp_cascade, waterstatebulk_inst, & waterfluxbulk_inst,temperature_inst,soilstate_inst,cnveg_state_inst, & cnveg_carbonstate_inst ,& @@ -485,7 +485,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('calc_plant_nutrient_competition') call nutrient_competition_method%calc_plant_nutrient_competition ( & - bounds, num_soilp, filter_soilp, & + bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_state_inst, crop_inst, canopystate_inst, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, & c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & @@ -505,7 +505,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('SoilBiogeochemDecomp') - call SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, & + call SoilBiogeochemDecomp (bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & cn_decomp_pools=cn_decomp_pools(begc:endc,1:nlevdecomp,1:ndecomp_pools), & @@ -525,8 +525,8 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNPhenology') if ( .not. use_fun ) then - call CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & - filter_soilp, num_pcropp, filter_pcropp, & + call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & + filter_bgc_vegp, num_pcropp, filter_pcropp, & waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & @@ -536,8 +536,8 @@ subroutine CNDriverNoLeaching(bounds, froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp,1:nlevdecomp_full), & phase=1) end if - call CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & - filter_soilp, num_pcropp, filter_pcropp, & + call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & + filter_bgc_vegp, num_pcropp, filter_pcropp, & waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & @@ -555,7 +555,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNGResp') - call CNGResp(num_soilp, filter_soilp,& + call CNGResp(num_bgc_vegp, filter_bgc_vegp,& cnveg_carbonflux_inst, canopystate_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) call t_stopf('CNGResp') @@ -567,7 +567,7 @@ subroutine CNDriverNoLeaching(bounds, if( use_dynroot ) then call t_startf('CNRootDyn') - call CNRootDyn(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNRootDyn(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, & cnveg_state_inst, crop_inst, soilstate_inst, soilbiogeochem_nitrogenstate_inst) @@ -583,24 +583,24 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNUpdate0') - call CStateUpdate0(num_soilp, filter_soilp, & + call CStateUpdate0(num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, cnveg_carbonstate_inst) if ( use_c13 ) then - call CStateUpdate0(num_soilp, filter_soilp, & + call CStateUpdate0(num_bgc_vegp, filter_bgc_vegp, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst) end if if ( use_c14 ) then - call CStateUpdate0(num_soilp, filter_soilp, & + call CStateUpdate0(num_bgc_vegp, filter_bgc_vegp, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst) end if call t_stopf('CNUpdate0') - if ( use_nguardrail .and. num_soilp>0 ) then + if ( use_nguardrail .and. num_bgc_vegp>0 ) then call t_startf('CNPrecisionControl') - call CNPrecisionControl(bounds, num_soilp, filter_soilp, & + call CNPrecisionControl(bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & c14_cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) call t_stopf('CNPrecisionControl') @@ -617,7 +617,7 @@ subroutine CNDriverNoLeaching(bounds, ! Set the carbon isotopic flux variables (except for gap-phase mortality and fire fluxes) if ( use_c13 ) then - call CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux1(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & @@ -626,7 +626,7 @@ subroutine CNDriverNoLeaching(bounds, isotope='c13') end if if ( use_c14 ) then - call CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux1(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & @@ -636,40 +636,40 @@ subroutine CNDriverNoLeaching(bounds, end if ! Update all prognostic carbon state variables (except for gap-phase mortality and fire fluxes) - call CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate1( num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & crop_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & clm_fates, bounds%clump_index) if ( use_c13 ) then - call CStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate1(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & crop_inst, c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & c13_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & clm_fates, bounds%clump_index) end if if ( use_c14 ) then - call CStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate1(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & crop_inst, c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & c14_soilbiogeochem_carbonflux_inst, dribble_crophrv_xsmrpool_2atm, & clm_fates, bounds%clump_index) end if ! Update all prognostic nitrogen state variables (except for gap-phase mortality and fire fluxes) - call NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call NStateUpdate1(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & clm_fates, bounds%clump_index) call t_stopf('CNUpdate1') - if ( use_nguardrail .and. num_soilp>0 ) then + if ( use_nguardrail .and. num_bgc_vegp>0 ) then call t_startf('CNPrecisionControl') - call CNPrecisionControl(bounds, num_soilp, filter_soilp, & + call CNPrecisionControl(bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & c14_cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) call t_stopf('CNPrecisionControl') end if call t_startf('SoilBiogeochemStateUpdate1') - call SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & + call SoilBiogeochemNStateUpdate1(num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_state_inst, soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) call t_stopf('SoilBiogeochemStateUpdate1') @@ -680,7 +680,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('SoilBiogeochemLittVertTransp') - call SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & + call SoilBiogeochemLittVertTransp(bounds, num_bgc_soilc, filter_bgc_soilc, & active_layer_inst, soilbiogeochem_state_inst, & soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & @@ -693,10 +693,10 @@ subroutine CNDriverNoLeaching(bounds, ! Calculate the gap mortality carbon and nitrogen fluxes !-------------------------------------------- - if_soilp1: if(num_soilp>0)then + if_bgc_vegp1: if(num_bgc_vegp>0)then call t_startf('CNGapMortality') - call CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNGapMortality (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & dgvs_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, canopystate_inst, & leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp, 1:nlevdecomp_full), & @@ -715,14 +715,14 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNUpdate2') ! Set the carbon isotopic fluxes for gap mortality if ( use_c13 ) then - call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst=c13_cnveg_carbonflux_inst, & iso_cnveg_carbonstate_inst=c13_cnveg_carbonstate_inst, & isotope='c13') end if if ( use_c14 ) then - call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst=c14_cnveg_carbonflux_inst, & iso_cnveg_carbonstate_inst=c14_cnveg_carbonstate_inst, & @@ -730,22 +730,22 @@ subroutine CNDriverNoLeaching(bounds, end if ! Update all the prognostic carbon state variables affected by gap-phase mortality fluxes - call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & soilbiogeochem_carbonflux_inst) if ( use_c13 ) then - call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonflux_inst) end if if ( use_c14 ) then - call CStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonflux_inst) end if ! Update all the prognostic nitrogen state variables affected by gap-phase mortality fluxes - call NStateUpdate2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call NStateUpdate2(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst,soilbiogeochem_nitrogenstate_inst, & soilbiogeochem_nitrogenflux_inst) @@ -758,50 +758,50 @@ subroutine CNDriverNoLeaching(bounds, ! Set harvest mortality routine if (get_do_harvest()) then - call CNHarvest(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNHarvest(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) end if if ( use_c13 ) then - call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2h(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & isotope='c13') end if if ( use_c14 ) then - call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2h(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & isotope='c14') end if - call CStateUpdate2h( num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2h( num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & soilbiogeochem_carbonflux_inst) if ( use_c13 ) then - call CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2h(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonflux_inst) end if if ( use_c14 ) then - call CStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2h(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonflux_inst) end if - call NStateUpdate2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call NStateUpdate2h(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst, & soilbiogeochem_nitrogenflux_inst) call t_stopf('CNUpdate2') - end if if_soilp1 + end if if_bgc_vegp1 - if ( use_nguardrail .and. num_soilp>0 ) then + if ( use_nguardrail .and. num_bgc_vegp>0 ) then call t_startf('CNPrecisionControl') - call CNPrecisionControl(bounds, num_soilp, filter_soilp, & + call CNPrecisionControl(bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & c14_cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) call t_stopf('CNPrecisionControl') @@ -820,12 +820,12 @@ subroutine CNDriverNoLeaching(bounds, call n_products_inst%SetValues(bounds,0._r8) if(use_fates_bgc) then - call clm_fates%wrap_WoodProducts(bounds, num_soilc, filter_soilc, c_products_inst, n_products_inst) + call clm_fates%wrap_WoodProducts(bounds, num_bgc_soilc, filter_bgc_soilc, c_products_inst, n_products_inst) end if - if_soilp2: if(num_soilp>0)then + if_bgc_vegp2: if(num_bgc_vegp>0)then call c_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & + num_bgc_vegp, filter_bgc_vegp, & dwt_wood_product_gain_patch = cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & wood_harvest_patch = cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & dwt_crop_product_gain_patch = cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & @@ -833,7 +833,7 @@ subroutine CNDriverNoLeaching(bounds, if (use_c13) then call c13_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & + num_bgc_vegp, filter_bgc_vegp, & dwt_wood_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & wood_harvest_patch = c13_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & dwt_crop_product_gain_patch = c13_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & @@ -842,7 +842,7 @@ subroutine CNDriverNoLeaching(bounds, if (use_c14) then call c14_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & + num_bgc_vegp, filter_bgc_vegp, & dwt_wood_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_wood_productc_gain_patch(begp:endp), & wood_harvest_patch = c14_cnveg_carbonflux_inst%wood_harvestc_patch(begp:endp), & dwt_crop_product_gain_patch = c14_cnveg_carbonflux_inst%dwt_crop_productc_gain_patch(begp:endp), & @@ -850,13 +850,13 @@ subroutine CNDriverNoLeaching(bounds, end if call n_products_inst%UpdateProducts(bounds, & - num_soilp, filter_soilp, & + num_bgc_vegp, filter_bgc_vegp, & dwt_wood_product_gain_patch = cnveg_nitrogenflux_inst%dwt_wood_productn_gain_patch(begp:endp), & wood_harvest_patch = cnveg_nitrogenflux_inst%wood_harvestn_patch(begp:endp), & dwt_crop_product_gain_patch = cnveg_nitrogenflux_inst%dwt_crop_productn_gain_patch(begp:endp), & crop_harvest_to_cropprod_patch = cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(begp:endp)) - end if if_soilp2 + end if if_bgc_vegp2 call c_products_inst%ComputeProductSummaryVars(bounds) if (use_c13) call c13_products_inst%ComputeProductSummaryVars(bounds) @@ -875,9 +875,9 @@ subroutine CNDriverNoLeaching(bounds, ! Calculate fire area and fluxes !-------------------------------------------- - if_soilp3: if(num_soilp>0)then + if_bgc_vegp3: if(num_bgc_vegp>0)then call t_startf('CNFire') - call cnfire_method%CNFireArea(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call cnfire_method%CNFireArea(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & num_exposedvegp, filter_exposedvegp, num_noexposedvegp, filter_noexposedvegp, & atm2lnd_inst, energyflux_inst, saturated_excess_runoff_inst, waterdiagnosticbulk_inst, wateratm2lndbulk_inst, & waterstatebulk_inst, soilstate_inst, soil_water_retention_curve, & @@ -886,7 +886,7 @@ subroutine CNDriverNoLeaching(bounds, decomp_cpools_vr_col=soilbiogeochem_carbonstate_inst%decomp_cpools_vr_col(begc:endc,1:nlevdecomp_full,1:ndecomp_pools), & t_soi17cm_col=temperature_inst%t_soi17cm_col(begc:endc)) - call cnfire_method%CNFireFluxes(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call cnfire_method%CNFireFluxes(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & num_actfirec, filter_actfirec, num_actfirep, filter_actfirep, & dgvs_inst, cnveg_state_inst, & cnveg_carbonstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & @@ -910,7 +910,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNUpdate3') if ( use_c13 ) then - call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux3(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & @@ -918,7 +918,7 @@ subroutine CNDriverNoLeaching(bounds, isotope='c13') end if if ( use_c14 ) then - call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux3(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & @@ -926,32 +926,32 @@ subroutine CNDriverNoLeaching(bounds, isotope='c14') end if - call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate3( num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst, & soilbiogeochem_carbonflux_inst) if ( use_c13 ) then - call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate3( num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonflux_inst) end if if ( use_c14 ) then - call CStateUpdate3( num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate3( num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonflux_inst) - call C14Decay(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call C14Decay(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_soilbiogeochem_carbonflux_inst) end if call t_stopf('CNUpdate3') - end if if_soilp3 + end if if_bgc_vegp3 - if ( use_nguardrail .and. num_soilp>0 ) then + if ( use_nguardrail .and. num_bgc_vegp>0 ) then call t_startf('CNPrecisionControl') - call CNPrecisionControl(bounds, num_soilp, filter_soilp, & + call CNPrecisionControl(bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, & c14_cnveg_carbonstate_inst, cnveg_nitrogenstate_inst) call t_stopf('CNPrecisionControl') @@ -963,7 +963,7 @@ end subroutine CNDriverNoLeaching !----------------------------------------------------------------------- subroutine CNDriverLeaching(bounds, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & num_actfirec, filter_actfirec, num_actfirep, filter_actfirep,& waterstatebulk_inst, waterfluxbulk_inst, & soilstate_inst, cnveg_state_inst, & @@ -990,10 +990,10 @@ subroutine CNDriverLeaching(bounds, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of soil patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for soil patches integer , intent(in) :: num_actfirec ! number of soil columns on fire in filter integer , intent(in) :: filter_actfirec(:) ! filter for soil columns on fire integer , intent(in) :: num_actfirep ! number of soil patches on fire in filter @@ -1025,10 +1025,10 @@ subroutine CNDriverLeaching(bounds, & ! Mineral nitrogen dynamics (deposition, fixation, leaching) call t_startf('SoilBiogeochemNLeaching') - call SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & + call SoilBiogeochemNLeaching(bounds, num_bgc_soilc, filter_bgc_soilc, & waterstatebulk_inst, waterfluxbulk_inst, soilbiogeochem_nitrogenstate_inst, & soilbiogeochem_nitrogenflux_inst) - call NStateUpdateLeaching(num_soilc, filter_soilc, & + call NStateUpdateLeaching(num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) call t_stopf('SoilBiogeochemNLeaching') @@ -1037,9 +1037,9 @@ subroutine CNDriverLeaching(bounds, & ! Nitrogen state variable update, mortality fluxes. - if(num_soilp>0)then + if(num_bgc_vegp>0)then call t_startf('NUpdate3') - call NStateUpdate3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call NStateUpdate3(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, & soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) call t_stopf('NUpdate3') @@ -1066,7 +1066,7 @@ end subroutine CNDriverLeaching !----------------------------------------------------------------------- subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & cnveg_nitrogenstate_inst, & soilbiogeochem_carbonstate_inst, & @@ -1083,10 +1083,10 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_allc ! number of columns in allc filter integer , intent(in) :: filter_allc(:) ! filter for all active columns - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of soil patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for soil patches type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst type(cnveg_carbonstate_type) , intent(inout) :: c13_cnveg_carbonstate_inst type(cnveg_carbonstate_type) , intent(inout) :: c14_cnveg_carbonstate_inst @@ -1109,14 +1109,14 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & ! ---------------------------------------------- ! cnveg carbon/nitrogen state summary ! ---------------------------------------------- - call cnveg_carbonstate_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + call cnveg_carbonstate_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp) if ( use_c13 ) then - call c13_cnveg_carbonstate_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + call c13_cnveg_carbonstate_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp) end if if ( use_c14 ) then - call c14_cnveg_carbonstate_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + call c14_cnveg_carbonstate_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp) end if ! ---------------------------------------------- @@ -1125,12 +1125,12 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & ! cnveg summary, swapped call order ! ---------------------------------------------- - call soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst) + call soilbiogeochem_carbonstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonstate_inst) if ( use_c13 ) then - call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c13_cnveg_carbonstate_inst) + call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc, c13_cnveg_carbonstate_inst) end if if ( use_c14 ) then - call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_soilc, filter_soilc, c14_cnveg_carbonstate_inst) + call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc, c14_cnveg_carbonstate_inst) end if @@ -1138,10 +1138,10 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & ! couple in FATES N - call cnveg_nitrogenstate_inst%Summary(bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp) + call cnveg_nitrogenstate_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp) - call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_soilc, filter_soilc,cnveg_nitrogenstate_inst) + call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc,cnveg_nitrogenstate_inst) call t_stopf('CNsum') @@ -1150,7 +1150,7 @@ end subroutine CNDriverSummarizeStates !----------------------------------------------------------------------- subroutine CNDriverSummarizeFluxes(bounds, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst, & cnveg_nitrogenflux_inst, & c_products_inst, c13_products_inst, c14_products_inst, & @@ -1171,10 +1171,10 @@ subroutine CNDriverSummarizeFluxes(bounds, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of soil patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for soil patches type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_carbonflux_type) , intent(inout) :: c13_cnveg_carbonflux_inst type(cnveg_carbonflux_type) , intent(inout) :: c14_cnveg_carbonflux_inst @@ -1209,16 +1209,16 @@ subroutine CNDriverSummarizeFluxes(bounds, & ! soilbiogeochem carbon/nitrogen flux summary ! ---------------------------------------------- - call soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + call soilbiogeochem_carbonflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), & leafc_to_litter_patch=cnveg_carbonflux_inst%leafc_to_litter_patch, & frootc_to_litter_patch=cnveg_carbonflux_inst%frootc_to_litter_patch) if ( use_c13 ) then - call c13_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + call c13_soilbiogeochem_carbonflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & c13_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & c13_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), & @@ -1226,23 +1226,23 @@ subroutine CNDriverSummarizeFluxes(bounds, & frootc_to_litter_patch=c13_cnveg_carbonflux_inst%frootc_to_litter_patch) end if if ( use_c14 ) then - call c14_soilbiogeochem_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + call c14_soilbiogeochem_carbonflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & c14_soilbiogeochem_carbonflux_inst%decomp_cascade_ctransfer_col(begc:endc,1:ndecomp_cascade_transitions), & c14_soilbiogeochem_carbonstate_inst%cwdc_col(begc:endc), & soilbiogeochem_nitrogenstate_inst%cwdn_col(begc:endc), & leafc_to_litter_patch=c14_cnveg_carbonflux_inst%leafc_to_litter_patch, & frootc_to_litter_patch=c14_cnveg_carbonflux_inst%frootc_to_litter_patch) end if - call soilbiogeochem_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc) + call soilbiogeochem_nitrogenflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc) ! ---------------------------------------------- ! cnveg carbon/nitrogen flux summary ! ---------------------------------------------- - if_soilp: if(num_soilp>0) then + if_bgc_vegp: if(num_bgc_vegp>0) then call t_startf('CNvegCflux_summary') - call cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call cnveg_carbonflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & isotope='bulk', & soilbiogeochem_hr_col=soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & soilbiogeochem_cwdhr_col=soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & @@ -1252,7 +1252,7 @@ subroutine CNDriverSummarizeFluxes(bounds, & product_closs_grc=c_products_inst%product_loss_grc(begg:endg)) if ( use_c13 ) then - call c13_cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call c13_cnveg_carbonflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & isotope='c13', & soilbiogeochem_hr_col=c13_soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & soilbiogeochem_cwdhr_col=c13_soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & @@ -1263,7 +1263,7 @@ subroutine CNDriverSummarizeFluxes(bounds, & end if if ( use_c14 ) then - call c14_cnveg_carbonflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call c14_cnveg_carbonflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & isotope='c14', & soilbiogeochem_hr_col=c14_soilbiogeochem_carbonflux_inst%hr_col(begc:endc), & soilbiogeochem_cwdhr_col=c14_soilbiogeochem_carbonflux_inst%cwdhr_col(begc:endc), & @@ -1274,8 +1274,8 @@ subroutine CNDriverSummarizeFluxes(bounds, & end if call t_stopf('CNvegCflux_summary') - call cnveg_nitrogenflux_inst%Summary(bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) - end if if_soilp + call cnveg_nitrogenflux_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp) + end if if_bgc_vegp call t_stopf('CNsum') diff --git a/src/biogeochem/CNFireEmissionsMod.F90 b/src/biogeochem/CNFireEmissionsMod.F90 index 645f074a7d..5a15e138d5 100644 --- a/src/biogeochem/CNFireEmissionsMod.F90 +++ b/src/biogeochem/CNFireEmissionsMod.F90 @@ -185,7 +185,7 @@ subroutine InitHistory(this, bounds) end subroutine InitHistory !----------------------------------------------------------------------- - subroutine CNFireEmisUpdate(bounds, num_soilp, filter_soilp, cnveg_cf_inst, cnveg_cs_inst, fireemis_inst ) + subroutine CNFireEmisUpdate(bounds, num_bgc_vegp, filter_bgc_vegp, cnveg_cf_inst, cnveg_cs_inst, fireemis_inst ) use CNVegcarbonfluxType, only : cnveg_carbonflux_type use CNVegCarbonStateType, only : cnveg_carbonstate_type @@ -194,8 +194,8 @@ subroutine CNFireEmisUpdate(bounds, num_soilp, filter_soilp, cnveg_cf_inst, cnve !ARGUMENTS: type(bounds_type), intent(in) :: bounds - integer, intent(in) :: num_soilp ! number of soil pfts in filter - integer, intent(in) :: filter_soilp(:) ! filter for soil pfts + integer, intent(in) :: num_bgc_vegp ! number of bgc veg patches + integer, intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches type(cnveg_carbonflux_type), intent(in) :: cnveg_cf_inst type(cnveg_carbonstate_type),intent(in) :: cnveg_cs_inst type(fireemis_type), intent(inout) :: fireemis_inst @@ -235,8 +235,8 @@ subroutine CNFireEmisUpdate(bounds, num_soilp, filter_soilp, cnveg_cf_inst, cnve ! Begin loop over points !_______________________________________________________________________________ - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) g = patch%gridcell(p) c = patch%column(p) diff --git a/src/biogeochem/CNPrecisionControlMod.F90 b/src/biogeochem/CNPrecisionControlMod.F90 index 8b98f6c3fb..787a5b54d7 100644 --- a/src/biogeochem/CNPrecisionControlMod.F90 +++ b/src/biogeochem/CNPrecisionControlMod.F90 @@ -96,7 +96,7 @@ subroutine CNPrecisionControlReadNML( NLFilename ) end subroutine CNPrecisionControlReadNML !----------------------------------------------------------------------- - subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & + subroutine CNPrecisionControl(bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonstate_inst, c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & cnveg_nitrogenstate_inst) ! @@ -111,8 +111,8 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds ! bounds - integer , intent(in) :: num_soilp ! number of soil patchs in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst type(cnveg_carbonstate_type) , intent(inout) :: c13_cnveg_carbonstate_inst type(cnveg_carbonstate_type) , intent(inout) :: c14_cnveg_carbonstate_inst @@ -190,8 +190,8 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & ) ! patch loop - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) ! initialize the patch-level C and N truncation terms pc(p) = 0._r8 @@ -205,7 +205,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & ! the C component, but truncate C, C13, and N components ! leaf C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%leafc_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%leafc_patch(bounds%begp:bounds%endp), & ns%leafn_patch(bounds%begp:bounds%endp), & pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) @@ -223,7 +223,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & ! leaf storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%leafc_storage_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%leafc_storage_patch(bounds%begp:bounds%endp), & ns%leafn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -238,7 +238,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! leaf transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%leafc_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%leafc_xfer_patch(bounds%begp:bounds%endp), & ns%leafn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -256,7 +256,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & ! EBK KO DML: For some reason frootc/frootn can go negative and allowing ! it to be negative is important for C4 crops (otherwise they die) Jun/3/2016 if ( prec_control_for_froot ) then - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%frootc_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%frootc_patch(bounds%begp:bounds%endp), & ns%frootn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep, allowneg=.true.) if (use_c13) then @@ -272,7 +272,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! froot storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%frootc_storage_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%frootc_storage_patch(bounds%begp:bounds%endp), & ns%frootn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -287,7 +287,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! froot transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%frootc_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%frootc_xfer_patch(bounds%begp:bounds%endp), & ns%frootn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -304,7 +304,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & if ( use_crop )then do k = 1, nrepr ! grain C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%reproductivec_patch(bounds%begp:bounds%endp,k), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%reproductivec_patch(bounds%begp:bounds%endp,k), & ns%reproductiven_patch(bounds%begp:bounds%endp,k), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep, croponly=.true. ) if (use_c13) then @@ -319,7 +319,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! grain storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, & cs%reproductivec_storage_patch(bounds%begp:bounds%endp,k), & ns%reproductiven_storage_patch(bounds%begp:bounds%endp,k), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep, croponly=.true. ) @@ -336,7 +336,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! grain transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, & cs%reproductivec_xfer_patch(bounds%begp:bounds%endp,k), & ns%reproductiven_xfer_patch(bounds%begp:bounds%endp,k), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep, croponly=.true.) @@ -352,7 +352,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if end do ! grain transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%cropseedc_deficit_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%cropseedc_deficit_patch(bounds%begp:bounds%endp), & ns%cropseedn_deficit_patch(bounds%begp:bounds%endp), pc(bounds%begp:), & pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep, & @@ -371,7 +371,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! livestem C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livestemc_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%livestemc_patch(bounds%begp:bounds%endp), & ns%livestemn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -386,7 +386,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! livestem storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livestemc_storage_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%livestemc_storage_patch(bounds%begp:bounds%endp), & ns%livestemn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) @@ -401,7 +401,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & __LINE__) end if ! livestem transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livestemc_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%livestemc_xfer_patch(bounds%begp:bounds%endp), & ns%livestemn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -416,7 +416,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! deadstem C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadstemc_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%deadstemc_patch(bounds%begp:bounds%endp), & ns%deadstemn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -430,7 +430,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & __LINE__) end if ! deadstem storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadstemc_storage_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%deadstemc_storage_patch(bounds%begp:bounds%endp), & ns%deadstemn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -445,7 +445,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! deadstem transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadstemc_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%deadstemc_xfer_patch(bounds%begp:bounds%endp), & ns%deadstemn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -460,7 +460,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! livecroot C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livecrootc_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%livecrootc_patch(bounds%begp:bounds%endp), & ns%livecrootn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -475,7 +475,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! livecroot storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livecrootc_storage_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%livecrootc_storage_patch(bounds%begp:bounds%endp), & ns%livecrootn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -490,7 +490,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! livecroot transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%livecrootc_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%livecrootc_xfer_patch(bounds%begp:bounds%endp), & ns%livecrootn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) @@ -506,7 +506,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! deadcroot C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadcrootc_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%deadcrootc_patch(bounds%begp:bounds%endp), & ns%deadcrootn_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), __LINE__, & num_truncatep, filter_truncatep) if (use_c13) then @@ -521,7 +521,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! deadcroot storage C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadcrootc_storage_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%deadcrootc_storage_patch(bounds%begp:bounds%endp), & ns%deadcrootn_storage_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -536,7 +536,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! deadcroot transfer C and N - call TruncateCandNStates( bounds, filter_soilp, num_soilp, cs%deadcrootc_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%deadcrootc_xfer_patch(bounds%begp:bounds%endp), & ns%deadcrootn_xfer_patch(bounds%begp:bounds%endp), pc(bounds%begp:), pn(bounds%begp:), & __LINE__, num_truncatep, filter_truncatep) if (use_c13) then @@ -551,7 +551,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! gresp_storage (C only) - call TruncateCStates( bounds, filter_soilp, num_soilp, cs%gresp_storage_patch(bounds%begp:bounds%endp), & + call TruncateCStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%gresp_storage_patch(bounds%begp:bounds%endp), & pc(bounds%begp:), __LINE__, num_truncatep, filter_truncatep) if (use_c13) then call TruncateAdditional( bounds, num_truncatep, filter_truncatep, & @@ -565,7 +565,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! gresp_xfer(c only) - call TruncateCStates( bounds, filter_soilp, num_soilp, cs%gresp_xfer_patch(bounds%begp:bounds%endp), & + call TruncateCStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%gresp_xfer_patch(bounds%begp:bounds%endp), & pc(bounds%begp:), __LINE__, num_truncatep, filter_truncatep) if (use_c13) then call TruncateAdditional( bounds, num_truncatep, filter_truncatep, & @@ -579,7 +579,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! cpool (C only) - call TruncateCStates( bounds, filter_soilp, num_soilp, cs%cpool_patch(bounds%begp:bounds%endp), & + call TruncateCStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%cpool_patch(bounds%begp:bounds%endp), & pc(bounds%begp:), __LINE__, num_truncatep, filter_truncatep) if (use_c13) then call TruncateAdditional( bounds, num_truncatep, filter_truncatep, & @@ -595,7 +595,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & if ( use_crop )then ! xsmrpool (C only) ! xsmr is a pool to balance the budget and as such can be freely negative - call TruncateCStates( bounds, filter_soilp, num_soilp, cs%xsmrpool_patch(bounds%begp:bounds%endp), & + call TruncateCStates( bounds, filter_bgc_vegp, num_bgc_vegp, cs%xsmrpool_patch(bounds%begp:bounds%endp), & pc(bounds%begp:), __LINE__, num_truncatep, filter_truncatep, & allowneg=.true., croponly=.true. ) if (use_c13) then @@ -612,16 +612,16 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end if ! retransn (N only) - call TruncateNStates( bounds, filter_soilp, num_soilp, ns%retransn_patch(bounds%begp:bounds%endp), pn(bounds%begp:), & + call TruncateNStates( bounds, filter_bgc_vegp, num_bgc_vegp, ns%retransn_patch(bounds%begp:bounds%endp), pn(bounds%begp:), & __LINE__ ) ! npool (N only) - call TruncateNStates( bounds, filter_soilp, num_soilp, ns%npool_patch(bounds%begp:bounds%endp), pn(bounds%begp:), & + call TruncateNStates( bounds, filter_bgc_vegp, num_bgc_vegp, ns%npool_patch(bounds%begp:bounds%endp), pn(bounds%begp:), & __LINE__ ) ! patch loop - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) cs%ctrunc_patch(p) = cs%ctrunc_patch(p) + pc(p) @@ -639,7 +639,7 @@ subroutine CNPrecisionControl(bounds, num_soilp, filter_soilp, & end subroutine CNPrecisionControl - subroutine TruncateCandNStates( bounds, filter_soilp, num_soilp, carbon_patch, nitrogen_patch, pc, pn, lineno, & + subroutine TruncateCandNStates( bounds, filter_bgc_vegp, num_bgc_vegp, carbon_patch, nitrogen_patch, pc, pn, lineno, & num_truncatep, filter_truncatep, croponly, allowneg ) ! ! !DESCRIPTION: @@ -657,8 +657,8 @@ subroutine TruncateCandNStates( bounds, filter_soilp, num_soilp, carbon_patch, n ! !ARGUMENTS: implicit none type(bounds_type) , intent(in) :: bounds ! bounds - integer , intent(in) :: num_soilp ! number of soil patchs in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches real(r8), intent(inout) :: carbon_patch(bounds%begp:) real(r8), intent(inout) :: nitrogen_patch(bounds%begp:) real(r8), intent(inout) :: pc(bounds%begp:) @@ -688,8 +688,8 @@ subroutine TruncateCandNStates( bounds, filter_soilp, num_soilp, carbon_patch, n end if num_truncatep = 0 - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) if ( .not. lcroponly .or. (patch%itype(p) >= nc3crop) ) then if ( .not. lallowneg .and. ((carbon_patch(p) < cnegcrit) .or. (nitrogen_patch(p) < nnegcrit)) ) then @@ -733,7 +733,7 @@ subroutine TruncateCandNStates( bounds, filter_soilp, num_soilp, carbon_patch, n end do end subroutine TruncateCandNStates - subroutine TruncateCStates( bounds, filter_soilp, num_soilp, carbon_patch, pc, lineno, & + subroutine TruncateCStates( bounds, filter_bgc_vegp, num_bgc_vegp, carbon_patch, pc, lineno, & num_truncatep, filter_truncatep, croponly, allowneg ) ! ! !DESCRIPTION: @@ -751,8 +751,8 @@ subroutine TruncateCStates( bounds, filter_soilp, num_soilp, carbon_patch, pc, l ! !ARGUMENTS: implicit none type(bounds_type), intent(in) :: bounds ! bounds - integer , intent(in) :: num_soilp ! number of soil patchs in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches real(r8) , intent(inout) :: carbon_patch(bounds%begp:) real(r8) , intent(inout) :: pc(bounds%begp:) integer , intent(in) :: lineno @@ -780,8 +780,8 @@ subroutine TruncateCStates( bounds, filter_soilp, num_soilp, carbon_patch, pc, l end if num_truncatep = 0 - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) if ( .not. lcroponly .or. (patch%itype(p) >= nc3crop) ) then if ( .not. lallowneg .and. (carbon_patch(p) < cnegcrit) ) then @@ -801,7 +801,7 @@ subroutine TruncateCStates( bounds, filter_soilp, num_soilp, carbon_patch, pc, l end do end subroutine TruncateCStates - subroutine TruncateNStates( bounds, filter_soilp, num_soilp, nitrogen_patch, pn, lineno ) + subroutine TruncateNStates( bounds, filter_bgc_vegp, num_bgc_vegp, nitrogen_patch, pn, lineno ) ! ! !DESCRIPTION: ! Truncate Nitrogen states. If a nitrogen state is too small truncate it to @@ -816,8 +816,8 @@ subroutine TruncateNStates( bounds, filter_soilp, num_soilp, nitrogen_patch, pn, ! !ARGUMENTS: implicit none type(bounds_type) , intent(in) :: bounds ! bounds - integer , intent(in) :: num_soilp ! number of soil patchs in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches real(r8), intent(inout) :: nitrogen_patch(bounds%begp:) real(r8), intent(inout) :: pn(bounds%begp:) integer, intent(in) :: lineno @@ -826,8 +826,8 @@ subroutine TruncateNStates( bounds, filter_soilp, num_soilp, nitrogen_patch, pn, SHR_ASSERT_ALL_FL((ubound(nitrogen_patch) == (/bounds%endp/)), sourcefile, __LINE__) SHR_ASSERT_ALL_FL((ubound(pn) == (/bounds%endp/)), sourcefile, __LINE__) - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) if ( nitrogen_patch(p) < nnegcrit ) then ! write(iulog,*) 'WARNING: Nitrogen patch negative = ', nitrogen_patch ! call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, & diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index b2ca4c4792..d2a2c06f90 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -2587,7 +2587,7 @@ subroutine ZeroDwt( this, bounds ) end subroutine ZeroDwt !----------------------------------------------------------------------- - subroutine Summary_carbonstate(this, bounds, num_soilc, filter_soilc, num_soilp, filter_soilp) + subroutine Summary_carbonstate(this, bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp) ! ! !USES: @@ -2601,10 +2601,10 @@ subroutine Summary_carbonstate(this, bounds, num_soilc, filter_soilc, num_soilp, ! !ARGUMENTS: class(cnveg_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns + integer , intent(in) :: num_bgc_vegp ! number of soil patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for soil patches ! ! !LOCAL VARIABLES: @@ -2613,8 +2613,8 @@ subroutine Summary_carbonstate(this, bounds, num_soilc, filter_soilc, num_soilp, !----------------------------------------------------------------------- ! calculate patch -level summary of carbon state - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) ! displayed vegetation carbon, excluding storage and cpool (DISPVEGC) this%dispvegc_patch(p) = & @@ -2685,11 +2685,11 @@ subroutine Summary_carbonstate(this, bounds, num_soilc, filter_soilc, num_soilp, ! column level summary ! -------------------------------------------- if(associated(this%totvegc_patch))then - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & this%totvegc_patch(bounds%begp:bounds%endp), & this%totvegc_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & this%totc_patch(bounds%begp:bounds%endp), & this%totc_p2c_col(bounds%begc:bounds%endc)) end if diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 6fdb897795..20b22d19ec 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -569,7 +569,7 @@ end subroutine Init2 !----------------------------------------------------------------------- - subroutine InitEachTimeStep(this, bounds, num_soilc, filter_soilc) + subroutine InitEachTimeStep(this, bounds, num_bgc_soilc, filter_bgc_soilc) ! ! !DESCRIPTION: ! Do initializations that need to be done at the start of every time step @@ -583,8 +583,8 @@ subroutine InitEachTimeStep(this, bounds, num_soilc, filter_soilc) ! !ARGUMENTS: class(cn_vegetation_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns ! ! !LOCAL VARIABLES: @@ -769,7 +769,7 @@ end subroutine DynamicAreaConservation !----------------------------------------------------------------------- subroutine InitColumnBalance(this, bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst, & @@ -788,10 +788,10 @@ subroutine InitColumnBalance(this, bounds, num_allc, filter_allc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_allc ! number of columns in allc filter integer , intent(in) :: filter_allc(:) ! filter for all active columns - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns + integer , intent(in) :: num_bgc_vegp ! number of bgc vegetation patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc vegetation patches type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: c13_soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: c14_soilbiogeochem_carbonstate_inst @@ -804,8 +804,8 @@ subroutine InitColumnBalance(this, bounds, num_allc, filter_allc, & call CNDriverSummarizeStates(bounds, & num_allc, filter_allc, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & this%cnveg_carbonstate_inst, & this%c13_cnveg_carbonstate_inst, & this%c14_cnveg_carbonstate_inst, & @@ -816,7 +816,7 @@ subroutine InitColumnBalance(this, bounds, num_allc, filter_allc, & soilbiogeochem_nitrogenstate_inst) call this%cn_balance_inst%BeginCNColumnBalance( & - bounds, num_soilc, filter_soilc, & + bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_carbonstate_inst,soilbiogeochem_nitrogenstate_inst) end subroutine InitColumnBalance @@ -824,7 +824,7 @@ end subroutine InitColumnBalance !----------------------------------------------------------------------- subroutine InitGridcellBalance(this, bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_carbonstate_inst, & c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst, & @@ -844,10 +844,10 @@ subroutine InitGridcellBalance(this, bounds, num_allc, filter_allc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_allc ! number of columns in allc filter integer , intent(in) :: filter_allc(:) ! filter for all active columns - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns + integer , intent(in) :: num_bgc_vegp ! number of bgc vegetation patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc vegetation patches type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: c13_soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: c14_soilbiogeochem_carbonstate_inst @@ -861,8 +861,8 @@ subroutine InitGridcellBalance(this, bounds, num_allc, filter_allc, & call CNDriverSummarizeStates(bounds, & num_allc, filter_allc, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & this%cnveg_carbonstate_inst, & this%c13_cnveg_carbonstate_inst, & this%c14_cnveg_carbonstate_inst, & @@ -929,10 +929,10 @@ subroutine EcosystemDynamicsPreDrainage(this, bounds, & ! !ARGUMENTS: class(cn_vegetation_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter - integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns - integer , intent(in) :: num_bgc_vegp ! number of veg patches in filter - integer , intent(in) :: filter_bgc_vegp(:) ! filter for veg patches + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches integer , intent(out) :: num_actfirec ! number of soil columns on fire in filter integer , intent(out) :: filter_actfirec(:)! filter for soil columns on fire integer , intent(out) :: num_actfirep ! number of soil patches on fire in filter @@ -1021,7 +1021,7 @@ end subroutine EcosystemDynamicsPreDrainage !----------------------------------------------------------------------- subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & - num_soilc, filter_soilc, num_soilp, filter_soilp, num_actfirec, filter_actfirec, num_actfirep, filter_actfirep,& + num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, num_actfirec, filter_actfirec, num_actfirep, filter_actfirep,& doalb, crop_inst, soilstate_inst, soilbiogeochem_state_inst, & waterstatebulk_inst, waterdiagnosticbulk_inst, waterfluxbulk_inst, frictionvel_inst, canopystate_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & @@ -1041,10 +1041,10 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_allc ! number of columns in allc filter integer , intent(in) :: filter_allc(:) ! filter for all active columns - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches integer , intent(in) :: num_actfirec ! number of soil columns on fire in filter integer , intent(in) :: filter_actfirec(:) ! filter for soil columns on fire integer , intent(in) :: num_actfirep ! number of soil patches on fire in filter @@ -1076,8 +1076,8 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! and total soil water outflow. call CNDriverLeaching(bounds, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & num_actfirec, filter_actfirec, & num_actfirep, filter_actfirep, & waterstatebulk_inst, waterfluxbulk_inst, soilstate_inst, this%cnveg_state_inst, & @@ -1092,16 +1092,16 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! Set controls on very low values in critical state variables - if(num_soilp>0)then + if(num_bgc_vegp>0)then call t_startf('CNPrecisionControl') - call CNPrecisionControl(bounds, num_soilp, filter_soilp, & + call CNPrecisionControl(bounds, num_bgc_vegp, filter_bgc_vegp, & this%cnveg_carbonstate_inst, this%c13_cnveg_carbonstate_inst, & this%c14_cnveg_carbonstate_inst, this%cnveg_nitrogenstate_inst) call t_stopf('CNPrecisionControl') end if call t_startf('SoilBiogeochemPrecisionControl') - call SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & + call SoilBiogeochemPrecisionControl(num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst,soilbiogeochem_nitrogenstate_inst) call t_stopf('SoilBiogeochemPrecisionControl') @@ -1110,8 +1110,8 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & call CNDriverSummarizeStates(bounds, & num_allc, filter_allc, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & this%cnveg_carbonstate_inst, & this%c13_cnveg_carbonstate_inst, & this%c14_cnveg_carbonstate_inst, & @@ -1122,8 +1122,8 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & soilbiogeochem_nitrogenstate_inst) call CNDriverSummarizeFluxes(bounds, & - num_soilc, filter_soilc, & - num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, & + num_bgc_vegp, filter_bgc_vegp, & this%cnveg_carbonflux_inst, & this%c13_cnveg_carbonflux_inst, & this%c14_cnveg_carbonflux_inst, & @@ -1142,7 +1142,7 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! vegetation structure (LAI, SAI, height) if (doalb) then - call CNVegStructUpdate(bounds,num_soilp, filter_soilp, & + call CNVegStructUpdate(bounds,num_bgc_vegp, filter_bgc_vegp, & waterdiagnosticbulk_inst, frictionvel_inst, this%dgvs_inst, this%cnveg_state_inst, & crop_inst, this%cnveg_carbonstate_inst, canopystate_inst) end if @@ -1150,7 +1150,7 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & end subroutine EcosystemDynamicsPostDrainage !----------------------------------------------------------------------- - subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & + subroutine BalanceCheck(this, bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenflux_inst, & soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst, & atm2lnd_inst, clm_fates) @@ -1167,8 +1167,8 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & ! !ARGUMENTS: class(cn_vegetation_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst @@ -1192,7 +1192,7 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & else call this%cn_balance_inst%CBalanceCheck( & - bounds, num_soilc, filter_soilc, & + bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_carbonflux_inst, & soilbiogeochem_carbonstate_inst, & this%cnveg_carbonflux_inst, & @@ -1201,7 +1201,7 @@ subroutine BalanceCheck(this, bounds, num_soilc, filter_soilc, & clm_fates) call this%cn_balance_inst%NBalanceCheck( & - bounds, num_soilc, filter_soilc, & + bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_nitrogenflux_inst, & soilbiogeochem_nitrogenstate_inst, & this%cnveg_nitrogenflux_inst, & diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 5fb0d233ec..a83701d884 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -15,7 +15,7 @@ module clm_driver use clm_varctl , only : use_crop, irrigate, ndep_from_cpl use clm_varctl , only : use_soil_moisture_streams use clm_time_manager , only : get_nstep, is_beg_curr_day - use clm_time_manager , only : get_prev_date, is_first_step + use clm_time_manager , only : get_prev_date, is_first_steps use clm_varpar , only : nlevsno, nlevgrnd use clm_varorb , only : obliqr use spmdMod , only : masterproc, mpicom diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index 985a97eacc..d9ada3922d 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -746,7 +746,7 @@ end subroutine SetValues !----------------------------------------------------------------------- subroutine Summary(this, bounds, & - num_soilc, filter_soilc, num_soilp, filter_soilp, & + num_bgc_soilc, filter_bgc_soilc, num_soilp, filter_soilp, & soilbiogeochem_decomp_cascade_ctransfer_col, & soilbiogeochem_cwdc_col, soilbiogeochem_cwdn_col, & leafc_to_litter_patch, frootc_to_litter_patch) @@ -761,8 +761,8 @@ subroutine Summary(this, bounds, & ! !ARGUMENTS: class(soilbiogeochem_carbonflux_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns integer, intent(in), optional :: num_soilp ! number of patches in filter integer, intent(in), optional :: filter_soilp(:) ! filter for patches real(r8), intent(in), optional :: soilbiogeochem_cwdc_col(bounds%begc:) @@ -785,16 +785,16 @@ subroutine Summary(this, bounds, & !----------------------------------------------------------------------- - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%som_c_leached_col(c) = 0._r8 end do ! vertically integrate HR and decomposition cascade fluxes do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cascade_hr_col(c,k) = & this%decomp_cascade_hr_col(c,k) + & this%decomp_cascade_hr_vr_col(c,j,k) * dzsoi_decomp(j) @@ -808,15 +808,15 @@ subroutine Summary(this, bounds, & ! total heterotrophic respiration, vertically resolved (HR) do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%hr_vr_col(c,j) = 0._r8 end do end do do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%hr_vr_col(c,j) = & this%hr_vr_col(c,j) + & this%decomp_cascade_hr_vr_col(c,j,k) @@ -826,19 +826,19 @@ subroutine Summary(this, bounds, & ! add up all vertical transport tendency terms and calculate total som leaching loss as the sum of these do l = 1, ndecomp_pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_leached_col(c,l) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_leached_col(c,l) = this%decomp_cpools_leached_col(c,l) + & this%decomp_cpools_transport_tendency_col(c,j,l) * dzsoi_decomp(j) end do end do - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%som_c_leached_col(c) = this%som_c_leached_col(c) + this%decomp_cpools_leached_col(c,l) end do end do @@ -847,8 +847,8 @@ subroutine Summary(this, bounds, & associate(is_soil => decomp_cascade_con%is_soil) ! TRUE => pool is a soil pool do k = 1, ndecomp_cascade_transitions if ( is_soil(decomp_cascade_con%cascade_donor_pool(k)) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%somhr_col(c) = this%somhr_col(c) + this%decomp_cascade_hr_col(c,k) end do end if @@ -859,8 +859,8 @@ subroutine Summary(this, bounds, & associate(is_litter => decomp_cascade_con%is_litter) ! TRUE => pool is a litter pool do k = 1, ndecomp_cascade_transitions if ( is_litter(decomp_cascade_con%cascade_donor_pool(k)) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%lithr_col(c) = this%lithr_col(c) + this%decomp_cascade_hr_col(c,k) end do end if @@ -871,8 +871,8 @@ subroutine Summary(this, bounds, & associate(is_cwd => decomp_cascade_con%is_cwd) ! TRUE => pool is a cwd pool do k = 1, ndecomp_cascade_transitions if ( is_cwd(decomp_cascade_con%cascade_donor_pool(k)) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%cwdhr_col(c) = this%cwdhr_col(c) + this%decomp_cascade_hr_col(c,k) end do end if @@ -883,8 +883,8 @@ subroutine Summary(this, bounds, & associate(is_microbe => decomp_cascade_con%is_microbe) ! TRUE => pool is a microbial pool do k = 1, ndecomp_cascade_transitions if ( is_microbe(decomp_cascade_con%cascade_donor_pool(k)) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%michr_col(c) = this%michr_col(c) + this%decomp_cascade_hr_col(c,k) end do end if @@ -892,8 +892,8 @@ subroutine Summary(this, bounds, & end associate ! total heterotrophic respiration (HR) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%hr_col(c) = & this%michr_col(c) + & @@ -920,24 +920,24 @@ subroutine Summary(this, bounds, & end associate end do - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & ligninNratio_leaf_patch(bounds%begp:bounds%endp), & ligninNratio_leaf_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & ligninNratio_froot_patch(bounds%begp:bounds%endp), & ligninNratio_froot_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & leafc_to_litter_patch(bounds%begp:bounds%endp), & leafc_to_litter_col(bounds%begc:bounds%endc)) - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & frootc_to_litter_patch(bounds%begp:bounds%endp), & frootc_to_litter_col(bounds%begc:bounds%endc)) end if ! Calculate ligninNratioAve - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if(.not.col%is_fates(c)) then if (soilbiogeochem_cwdn_col(c) > 0._r8) then ligninNratio_cwd = CNParamsShareInst%cwd_flig * & diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 6c52a5d34f..70976bc15a 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -931,7 +931,7 @@ subroutine SetValues ( this, num_column, filter_column, value_column) end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst) + subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonstate_inst) ! ! !DESCRIPTION: ! Perform column-level carbon summary calculations @@ -939,8 +939,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst ! !ARGUMENTS: class(soilbiogeochem_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of columns in soil filter - integer , intent(in) :: filter_soilc(:) ! filter for all active columns + integer , intent(in) :: num_bgc_soilc ! number of columns in soil filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for all active columns type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst ! @@ -954,8 +954,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst ! vertically integrate each of the decomposing C pools do l = 1, ndecomp_pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_col(c,l) = 0._r8 if(use_soil_matrixcn)then end if @@ -963,8 +963,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst end do do l = 1, ndecomp_pools do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_col(c,l) = & this%decomp_cpools_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j) @@ -979,23 +979,23 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst ! vertically integrate each of the decomposing C pools to 1 meter maxdepth = 1._r8 do l = 1, ndecomp_pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_1m_col(c,l) = 0._r8 end do end do do l = 1, ndecomp_pools do j = 1, nlevdecomp if ( zisoi(j) <= maxdepth ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_1m_col(c,l) = & this%decomp_cpools_1m_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j) end do elseif ( zisoi(j-1) < maxdepth ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cpools_1m_col(c,l) = & this%decomp_cpools_1m_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * (maxdepth - zisoi(j-1)) @@ -1009,16 +1009,16 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst ! Add soil carbon pools together to produce vertically-resolved decomposing total soil c pool if ( nlevdecomp_full > 1 ) then do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_soilc_vr_col(c,j) = 0._r8 end do end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_soilc_vr_col(c,j) = this%decomp_soilc_vr_col(c,j) + & this%decomp_cpools_vr_col(c,j,l) end do @@ -1028,13 +1028,13 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst end if ! truncation carbon - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%ctrunc_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%ctrunc_col(c) = & this%ctrunc_col(c) + & this%ctrunc_vr_col(c,j) * dzsoi_decomp(j) @@ -1043,14 +1043,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst ! total litter carbon in the top meter (TOTLITC_1m) if ( nlevdecomp > 1) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitc_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitc_1m_col(c) = this%totlitc_1m_col(c) + & this%decomp_cpools_1m_col(c,l) end do @@ -1060,14 +1060,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst ! total soil organic matter carbon in the top meter (TOTSOMC_1m) if ( nlevdecomp > 1) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomc_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomc_1m_col(c) = this%totsomc_1m_col(c) + this%decomp_cpools_1m_col(c,l) end do end if @@ -1075,42 +1075,42 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst end if ! total microbial carbon (TOTMICC) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totmicc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totmicc_col(c) = this%totmicc_col(c) + this%decomp_cpools_col(c,l) end do endif end do ! total litter carbon (TOTLITC) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitc_col(c) = this%totlitc_col(c) + this%decomp_cpools_col(c,l) end do endif end do ! total soil organic matter carbon (TOTSOMC) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomc_col(c) = this%totsomc_col(c) + this%decomp_cpools_col(c,l) end do end if @@ -1118,8 +1118,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_carbonstate_inst - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! coarse woody debris carbon this%cwdc_col(c) = 0._r8 diff --git a/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 b/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 index 9035b32484..57bc82984e 100644 --- a/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCompetitionMod.F90 @@ -165,7 +165,7 @@ subroutine SoilBiogeochemCompetitionInit ( bounds) end subroutine SoilBiogeochemCompetitionInit !----------------------------------------------------------------------- - subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, filter_soilp, & + subroutine SoilBiogeochemCompetition (bounds, num_bgc_soilc, filter_bgc_soilc,num_bgc_vegp, filter_bgc_vegp, & p_decomp_cn_gain, pmnf_decomp_cascade, waterstatebulk_inst, & waterfluxbulk_inst, temperature_inst,soilstate_inst, & cnveg_state_inst,cnveg_carbonstate_inst, & @@ -187,10 +187,10 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of veg patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for veg patches real(r8) , intent(in) :: pmnf_decomp_cascade(bounds%begc:,1:,1:) ! potential mineral N flux from one pool to another (gN/m3/s) real(r8) , intent(in) :: p_decomp_cn_gain(bounds%begc:,1:,1:) ! C:N ratio of the flux gained by the receiver pool type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst @@ -284,7 +284,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! calcualte nitrogen uptake profile ! nuptake_prof(:,:) = nan ! call SoilBiogelchemNitrogenUptakeProfile(bounds, & - ! nlevdecomp, num_soilc, filter_soilc, & + ! nlevdecomp, num_bgc_soilc, filter_bgc_soilc, & ! sminn_vr, dzsoi_decomp, nfixation_prof, nuptake_prof) ! column loops to resolve plant/heterotroph competition for mineral N @@ -296,21 +296,21 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, if_nitrif: if (.not. use_nitrif_denitrif) then ! init sminn_tot - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_tot(c) = 0. end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_tot(c) = sminn_tot(c) + sminn_vr(c,j) * dzsoi_decomp(j) end do end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (sminn_tot(c) > 0.) then nuptake_prof(c,j) = sminn_vr(c,j) / sminn_tot(c) else @@ -320,15 +320,15 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sum_ndemand_vr(c,j) = plant_ndemand(c) * nuptake_prof(c,j) + potential_immob_vr(c,j) end do end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) l = col%landunit(c) if (sum_ndemand_vr(c,j)*dt < sminn_vr(c,j)) then @@ -376,7 +376,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, if ( local_use_fun ) then call t_startf( 'CNFUN' ) - call CNFUN(bounds,num_soilc,filter_soilc,num_soilp,filter_soilp,waterstatebulk_inst, & + call CNFUN(bounds,num_bgc_soilc,filter_bgc_soilc,num_bgc_vegp,filter_bgc_vegp,waterstatebulk_inst, & waterfluxbulk_inst,temperature_inst,soilstate_inst,cnveg_state_inst,cnveg_carbonstate_inst,& cnveg_carbonflux_inst,cnveg_nitrogenstate_inst,cnveg_nitrogenflux_inst ,& soilbiogeochem_nitrogenflux_inst,soilbiogeochem_carbonflux_inst,canopystate_inst, & @@ -390,8 +390,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! sum up N fluxes to plant do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = sminn_to_plant(c) + sminn_to_plant_vr(c,j) * dzsoi_decomp(j) if ( local_use_fun ) then if (sminn_to_plant_fun_vr(c,j).gt.sminn_to_plant_vr(c,j)) then @@ -402,19 +402,19 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end do ! give plants a second pass to see if there is any mineral N left over with which to satisfy residual N demand. - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) residual_sminn(c) = 0._r8 end do ! sum up total N left over after initial plant and immobilization fluxes - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) residual_plant_ndemand(c) = plant_ndemand(c) - sminn_to_plant(c) end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (residual_plant_ndemand(c) > 0._r8 ) then if (nlimit(c,j) .eq. 0) then residual_sminn_vr(c,j) = max(sminn_vr(c,j) - (actual_immob_vr(c,j) + sminn_to_plant_vr(c,j) ) * dt, 0._r8) @@ -428,8 +428,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! distribute residual N to plants do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if ( residual_plant_ndemand(c) > 0._r8 .and. residual_sminn(c) > 0._r8 .and. nlimit(c,j) .eq. 0) then sminn_to_plant_vr(c,j) = sminn_to_plant_vr(c,j) + residual_sminn_vr(c,j) * & min(( residual_plant_ndemand(c) * dt ) / residual_sminn(c), 1._r8) / dt @@ -438,13 +438,13 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end do ! re-sum up N fluxes to plant - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = sminn_to_plant(c) + sminn_to_plant_vr(c,j) * dzsoi_decomp(j) if ( .not. local_use_fun ) then sum_ndemand_vr(c,j) = potential_immob_vr(c,j) + sminn_to_plant_vr(c,j) @@ -459,8 +459,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! be lost to denitrification, in addition to the constant ! proportion lost in the decomposition pathways do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if ( .not. local_use_fun ) then if ((sminn_to_plant_vr(c,j) + actual_immob_vr(c,j))*dt < sminn_vr(c,j)) then sminn_to_denit_excess_vr(c,j) = max(bdnr*((sminn_vr(c,j)/dt) - sum_ndemand_vr(c,j)),0._r8) @@ -479,15 +479,15 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! sum up N fluxes to immobilization do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) actual_immob(c) = actual_immob(c) + actual_immob_vr(c,j) * dzsoi_decomp(j) potential_immob(c) = potential_immob(c) + potential_immob_vr(c,j) * dzsoi_decomp(j) end do end do - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! calculate the fraction of potential growth that can be ! acheived with the N available to plants if (plant_ndemand(c) > 0.0_r8) then @@ -520,23 +520,23 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, compet_nit = params_inst%compet_nit ! init total mineral N pools - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_tot(c) = 0. end do ! sum up total mineral N pools do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_tot(c) = sminn_tot(c) + (smin_no3_vr(c,j) + smin_nh4_vr(c,j)) * dzsoi_decomp(j) end do end do ! define N uptake profile for initial vertical distribution of plant N uptake, assuming plant seeks N from where it is most abundant do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (sminn_tot(c) > 0.) then nuptake_prof(c,j) = sminn_vr(c,j) / sminn_tot(c) else @@ -547,8 +547,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! main column/vertical loop do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) l = col%landunit(c) ! first compete for nh4 @@ -754,7 +754,7 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, if ( local_use_fun ) then call t_startf( 'CNFUN' ) - call CNFUN(bounds,num_soilc,filter_soilc,num_soilp,filter_soilp,waterstatebulk_inst,& + call CNFUN(bounds,num_bgc_soilc,filter_bgc_soilc,num_bgc_vegp,filter_bgc_vegp,waterstatebulk_inst,& waterfluxbulk_inst,temperature_inst,soilstate_inst,cnveg_state_inst,cnveg_carbonstate_inst,& cnveg_carbonflux_inst,cnveg_nitrogenstate_inst,cnveg_nitrogenflux_inst ,& soilbiogeochem_nitrogenflux_inst,soilbiogeochem_carbonflux_inst,canopystate_inst, & @@ -776,20 +776,20 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, if(.not.local_use_fun)then - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! sum up N fluxes to plant after initial competition sminn_to_plant(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = sminn_to_plant(c) + sminn_to_plant_vr(c,j) * dzsoi_decomp(j) end do end do else - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! sum up N fluxes to plant after initial competition sminn_to_plant(c) = 0._r8 !this isn't use in fun. do j = 1, nlevdecomp @@ -813,8 +813,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, if (decomp_method == mimics_decomp) then do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) do k = 1, ndecomp_cascade_transitions if (cascade_receiver_pool(k) == i_cop_mic .or. & @@ -846,14 +846,14 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, if(.not.local_use_fun)then ! give plants a second pass to see if there is any mineral N left over with which to satisfy residual N demand. ! first take frm nh4 pool; then take from no3 pool - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) residual_plant_ndemand(c) = plant_ndemand(c) - sminn_to_plant(c) residual_smin_nh4(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (residual_plant_ndemand(c) > 0._r8 ) then if (nlimit_nh4(c,j) .eq. 0) then residual_smin_nh4_vr(c,j) = max(smin_nh4_vr(c,j) - (actual_immob_nh4_vr(c,j) + & @@ -873,13 +873,13 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end do ! re-sum up N fluxes to plant after second pass for nh4 - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant_vr(c,j) = smin_nh4_to_plant_vr(c,j) + smin_no3_to_plant_vr(c,j) sminn_to_plant(c) = sminn_to_plant(c) + (sminn_to_plant_vr(c,j)) * dzsoi_decomp(j) end do @@ -887,15 +887,15 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! ! and now do second pass for no3 - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) residual_plant_ndemand(c) = plant_ndemand(c) - sminn_to_plant(c) residual_smin_no3(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (residual_plant_ndemand(c) > 0._r8 ) then if (nlimit_no3(c,j) .eq. 0) then residual_smin_no3_vr(c,j) = max(smin_no3_vr(c,j) - (actual_immob_no3_vr(c,j) + & @@ -914,13 +914,13 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end do ! re-sum up N fluxes to plant after second passes of both no3 and nh4 - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant_vr(c,j) = smin_nh4_to_plant_vr(c,j) + smin_no3_to_plant_vr(c,j) sminn_to_plant(c) = sminn_to_plant(c) + (sminn_to_plant_vr(c,j)) * dzsoi_decomp(j) end do @@ -928,13 +928,13 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, else !use_fun !calculate maximum N available to plants. - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant_vr(c,j) = smin_nh4_to_plant_vr(c,j) + smin_no3_to_plant_vr(c,j) sminn_to_plant(c) = sminn_to_plant(c) + (sminn_to_plant_vr(c,j)) * dzsoi_decomp(j) end do @@ -943,8 +943,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, ! add up fun fluxes from SMINN to plant. do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_to_plant_new(c) = sminn_to_plant_new(c) + & (sminn_to_plant_fun_no3_vr(c,j) + sminn_to_plant_fun_nh4_vr(c,j)) * dzsoi_decomp(j) @@ -954,14 +954,14 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, end if !use_f ! sum up N fluxes to immobilization - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) actual_immob(c) = 0._r8 potential_immob(c) = 0._r8 end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) actual_immob(c) = actual_immob(c) + actual_immob_vr(c,j) * dzsoi_decomp(j) potential_immob(c) = potential_immob(c) + potential_immob_vr(c,j) * dzsoi_decomp(j) end do @@ -970,8 +970,8 @@ subroutine SoilBiogeochemCompetition (bounds, num_soilc, filter_soilc,num_soilp, - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! calculate the fraction of potential growth that can be ! acheived with the N available to plants ! calculate the fraction of immobilization realized (for diagnostic purposes) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index b65fc5f17f..c32e177b1b 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -510,7 +510,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i end subroutine init_decompcascade_bgc !----------------------------------------------------------------------- - subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & + subroutine decomp_rate_constants_bgc(bounds, num_bgc_soilc, filter_bgc_soilc, & soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst) ! ! !DESCRIPTION: @@ -524,8 +524,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilstate_type) , intent(in) :: soilstate_inst type(temperature_type) , intent(in) :: temperature_inst type(ch4_type) , intent(in) :: ch4_inst @@ -619,8 +619,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & catanf_30 = catanf(30._r8) if ( spinup_state >= 1 ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! if ( abs(spinup_factor(i_met_lit) - 1._r8) .gt. eps) then spinup_geogterm_l1(c) = spinup_factor(i_met_lit) * get_spinup_latitude_term(grc%latdeg(col%gridcell(c))) @@ -662,8 +662,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! end do else - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) spinup_geogterm_l1(c) = 1._r8 spinup_geogterm_l23(c) = 1._r8 spinup_geogterm_cwd(c) = 1._r8 @@ -686,14 +686,14 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & nlev_soildecomp_standard=5 allocate(fr(bounds%begc:bounds%endc,nlev_soildecomp_standard)) do j=1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) frw(c) = frw(c) + col%dz(c,j) end do end do do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (frw(c) /= 0._r8) then fr(c,j) = col%dz(c,j) / frw(c) else @@ -708,8 +708,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! limiting conditions at 25 C. do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (j==1) t_scalar(c,:) = 0._r8 if (t_soisno(c,j) >= SHR_CONST_TKFRZ) then t_scalar(c,1)=t_scalar(c,1) + & @@ -724,8 +724,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & else ! original century uses an arctangent function to calculate the temperature dependence of decomposition do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (j==1) t_scalar(c,:) = 0._r8 t_scalar(c,1)=t_scalar(c,1) +max(catanf(t_soisno(c,j)-SHR_CONST_TKFRZ)/catanf_30*fr(c,j),0.01_r8) @@ -743,8 +743,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! and soil moisture. Soil Biol. Biochem., 15(4):447-453. do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (j==1) w_scalar(c,:) = 0._r8 psi = min(soilpsi(c,j),maxpsi) ! decomp only if soilpsi is higher than minpsi @@ -760,8 +760,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! Check for anoxia w/o LCH4 now done in controlMod. do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (j==1) o_scalar(c,:) = 0._r8 @@ -790,8 +790,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! the base rates at 25 C, which are calibrated from microcosm studies. do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (t_soisno(c,j) >= SHR_CONST_TKFRZ) then t_scalar(c,j)= (Q10**((t_soisno(c,j)-(SHR_CONST_TKFRZ+25._r8))/10._r8)) else @@ -803,8 +803,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & else do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) t_scalar(c,j)= max(catanf(t_soisno(c,j)-SHR_CONST_TKFRZ)/catanf_30, 0.01_r8) end do end do @@ -820,8 +820,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! and soil moisture. Soil Biol. Biochem., 15(4):447-453. do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) psi = min(soilpsi(c,j),maxpsi) ! decomp only if soilpsi is higher than minpsi if (psi > minpsi) then @@ -838,8 +838,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & if (anoxia) then do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) o_scalar(c,j) = max(o2stress_unsat(c,j), mino2lim) end do @@ -857,8 +857,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! scale all decomposition rates by a constant to compensate for offset between original CENTURY temp func and Q10 normalization_factor = (catanf(normalization_tref)/catanf_30) / (q10**((normalization_tref-25._r8)/10._r8)) do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) t_scalar(c,j) = t_scalar(c,j) * normalization_factor end do end do @@ -867,16 +867,16 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! add a term to reduce decomposition rate at depth ! for now used a fixed e-folding depth do j = 1, nlevdecomp - do fc = 1, num_soilc - c = filter_soilc(fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc(fc) depth_scalar(c,j) = exp(-zsoi(j) / decomp_depth_efolding) end do end do ! calculate rate constants for all litter and som pools do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) decomp_k(c,j,i_met_lit) = k_l1 * t_scalar(c,j) * w_scalar(c,j) * & depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_l1(c) decomp_k(c,j,i_cel_lit) = k_l2_l3 * t_scalar(c,j) * w_scalar(c,j) * & diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index f820db01b6..e2a2a4ab99 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -752,7 +752,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat end subroutine init_decompcascade_mimics !----------------------------------------------------------------------- - subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & + subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & num_soilp, filter_soilp, clm_fates, & soilstate_inst, temperature_inst, cnveg_carbonflux_inst, & ch4_inst, soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst) @@ -773,8 +773,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilstate_type) , intent(in) :: soilstate_inst type(temperature_type) , intent(in) :: temperature_inst type(cnveg_carbonflux_type) , intent(in) :: cnveg_carbonflux_inst @@ -895,8 +895,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! calc ref rate if ( spinup_state >= 1 ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! if ( abs(spinup_factor(i_met_lit) - 1._r8) .gt. eps) then spinup_geogterm_l1(c) = spinup_factor(i_met_lit) * get_spinup_latitude_term(grc%latdeg(col%gridcell(c))) @@ -950,8 +950,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! end do else - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) spinup_geogterm_l1(c) = 1._r8 spinup_geogterm_l2(c) = 1._r8 spinup_geogterm_cwd(c) = 1._r8 @@ -975,14 +975,14 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & frw(bounds%begc:bounds%endc) = 0._r8 allocate(fr(bounds%begc:bounds%endc,nlev_soildecomp_standard)) do j=1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) frw(c) = frw(c) + col%dz(c,j) end do end do do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (frw(c) /= 0._r8) then fr(c,j) = col%dz(c,j) / frw(c) else @@ -1000,8 +1000,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! and soil moisture. Soil Biol. Biochem., 15(4):447-453. do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (j==1) w_scalar(c,:) = 0._r8 psi = min(soilpsi(c,j),maxpsi) ! decomp only if soilpsi is higher than minpsi @@ -1017,8 +1017,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & if (anoxia) then do j = 1,nlev_soildecomp_standard - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (j==1) o_scalar(c,:) = 0._r8 @@ -1042,8 +1042,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! and soil moisture. Soil Biol. Biochem., 15(4):447-453. do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) psi = min(soilpsi(c,j),maxpsi) ! decomp only if soilpsi is higher than minpsi if (psi > minpsi) then @@ -1059,8 +1059,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & if (anoxia) then do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) o_scalar(c,j) = max(o2stress_unsat(c,j), mino2lim) end do @@ -1074,8 +1074,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! Term that reduces decomposition rate at depth ! Placeholder. For now depth_scalar = 1. do j = 1, nlevdecomp - do fc = 1, num_soilc - c = filter_soilc(fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc(fc) ! Using fixed e-folding depth as in ! SoilBiogeochemDecompCascadeBGCMod.F90 ! depth_scalar(c,j) = exp(-zsoi(j) / decomp_depth_efolding) @@ -1135,7 +1135,7 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & end do ! p loop ! Calculate the column-level average - call p2c(bounds, num_soilc, filter_soilc, & + call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & annsum_npp(bounds%begp:bounds%endp), & annsum_npp_col_local(bounds%begc:bounds%endc)) else @@ -1146,8 +1146,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & end if fates_if ! calculate rates for all litter and som pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (use_fates) then annsum_npp_col_scalar = max(0._r8, annsum_npp_col_local(c)) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 index 77d4a40ed9..9bd8b13008 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompMod.F90 @@ -67,7 +67,7 @@ subroutine readParams ( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, & + subroutine SoilBiogeochemDecomp (bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & cn_decomp_pools, p_decomp_cpool_loss, pmnf_decomp_cascade, & @@ -78,8 +78,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, ! ! !ARGUMENT: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst type(soilbiogeochem_carbonstate_type) , intent(in) :: soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst @@ -141,8 +141,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, do l = 1, ndecomp_pools if ( floating_cn_ratio_decomp_pools(l) ) then do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if ( decomp_npools_vr(c,j,l) > 0._r8 ) then cn_decomp_pools(c,j,l) = decomp_cpools_vr(c,j,l) / decomp_npools_vr(c,j,l) end if @@ -150,8 +150,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, end do else do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) cn_decomp_pools(c,j,l) = initial_cn_ratio(l) end do end do @@ -169,8 +169,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (decomp_cpools_vr(c,j,cascade_donor_pool(k)) > 0._r8) then if ( pmnf_decomp_cascade(c,j,k) > 0._r8 ) then @@ -226,15 +226,15 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, if (use_lch4) then ! Calculate total fraction of potential HR, for methane code do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) hrsum(c,j) = 0._r8 end do end do do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) hrsum(c,j) = hrsum(c,j) + rf_decomp_cascade(c,j,k) * p_decomp_cpool_loss(c,j,k) end do end do @@ -243,8 +243,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, ! Nitrogen limitation / (low)-moisture limitation do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (phr_vr(c,j) > 0._r8) then fphr(c,j) = hrsum(c,j) / phr_vr(c,j) * w_scalar(c,j) fphr(c,j) = max(fphr(c,j), 0.01_r8) ! Prevent overflow errors for 0 respiration @@ -258,8 +258,8 @@ subroutine SoilBiogeochemDecomp (bounds, num_soilc, filter_soilc, ! vertically integrate net and gross mineralization fluxes for diagnostic output - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) do j = 1,nlevdecomp net_nmin(c) = net_nmin(c) + net_nmin_vr(c,j) * dzsoi_decomp(j) gross_nmin(c) = gross_nmin(c) + gross_nmin_vr(c,j) * dzsoi_decomp(j) diff --git a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 index 136438cf37..e58e2f22d6 100644 --- a/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 @@ -81,7 +81,7 @@ subroutine readParams ( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & + subroutine SoilBiogeochemLittVertTransp(bounds, num_bgc_soilc, filter_bgc_soilc, & active_layer_inst, soilbiogeochem_state_inst, & soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & c13_soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonflux_inst, & @@ -105,8 +105,8 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(active_layer_type) , intent(in) :: active_layer_inst type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst @@ -187,8 +187,8 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & !------ first get diffusivity / advection terms -------! ! use different mixing rates for bioturbation and cryoturbation, with fixed bioturbation and cryoturbation set to a maximum depth - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) if (( max(altmax(c), altmax_lastyear(c)) <= max_altdepth_cryoturbation ) .and. & ( max(altmax(c), altmax_lastyear(c)) > 0._r8) ) then ! use mixing profile modified slightly from Koven et al. (2009): constant through active layer, linear decrease from base of active layer to zero at a fixed depth @@ -275,8 +275,8 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & if ( .not. is_cwd(s) ) then if(.not. use_soil_matrixcn .or. s .eq. 1)then do j = 1,nlevdecomp+1 - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) ! if ( spinup_state >= 1 ) then ! increase transport (both advection and diffusion) by the same factor as accelerated decomposition for a given pool @@ -306,16 +306,16 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & ! Set Pe (Peclet #) and D/dz throughout column - do fc = 1, num_soilc ! dummy terms here - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc ! dummy terms here + c = filter_bgc_soilc (fc) conc_trcr(c,0) = 0._r8 conc_trcr(c,col%nbedrock(c)+1:nlevdecomp+1) = 0._r8 end do do j = 1,nlevdecomp+1 - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) conc_trcr(c,j) = conc_ptr(c,j,s) @@ -379,8 +379,8 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & ! Calculate the tridiagonal coefficients do j = 0,nlevdecomp +1 - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) ! g = cgridcell(c) if (j > 0 .and. j < nlevdecomp+1) then @@ -428,14 +428,14 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & enddo ! fc; column enddo ! j; nlevdecomp - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) jtop(c) = 0 enddo ! subtract initial concentration and source terms for tendency calculation - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) do j = 1, nlevdecomp if (.not. use_soil_matrixcn) then trcr_tendency_ptr(c,j,s) = 0.-(conc_trcr(c,j) + source(c,j,s)) @@ -449,15 +449,15 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & ! Solve for the concentration profile for this time step call Tridiagonal(bounds, 0, nlevdecomp+1, & jtop(bounds%begc:bounds%endc), & - num_soilc, filter_soilc, & + num_bgc_soilc, filter_bgc_soilc, & a_tri(bounds%begc:bounds%endc, :), & b_tri(bounds%begc:bounds%endc, :), & c_tri(bounds%begc:bounds%endc, :), & r_tri(bounds%begc:bounds%endc, :), & conc_trcr(bounds%begc:bounds%endc,0:nlevdecomp+1)) ! add post-transport concentration to calculate tendency term - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) do j = 1, nlevdecomp trcr_tendency_ptr(c,j,s) = trcr_tendency_ptr(c,j,s) + conc_trcr(c,j) trcr_tendency_ptr(c,j,s) = trcr_tendency_ptr(c,j,s) / dtime @@ -466,16 +466,16 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & else ! For matrix solution set the matrix input array do j = 1,nlevdecomp - do fc =1,num_soilc - c = filter_soilc(fc) + do fc =1,num_bgc_soilc + c = filter_bgc_soilc(fc) end do end do end if !soil_matrix else ! for CWD pools, just add do j = 1,nlevdecomp - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) if(.not. use_soil_matrixcn)then conc_trcr(c,j) = conc_ptr(c,j,s) + source(c,j,s) else @@ -493,8 +493,8 @@ subroutine SoilBiogeochemLittVertTransp(bounds, num_soilc, filter_soilc, & if (.not. use_soil_matrixcn) then do j = 1,nlevdecomp - do fc = 1, num_soilc - c = filter_soilc (fc) + do fc = 1, num_bgc_soilc + c = filter_bgc_soilc (fc) conc_ptr(c,j,s) = conc_trcr(c,j) ! Correct for small amounts of carbon that leak into bedrock if (j > col%nbedrock(c)) then diff --git a/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90 b/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90 index 02d22d6613..a646feb1d7 100644 --- a/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNLeachingMod.F90 @@ -72,7 +72,7 @@ subroutine readParams ( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & + subroutine SoilBiogeochemNLeaching(bounds, num_bgc_soilc, filter_bgc_soilc, & waterstatebulk_inst, waterfluxbulk_inst, & soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) ! @@ -86,8 +86,8 @@ subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst type(waterfluxbulk_type) , intent(in) :: waterfluxbulk_inst type(soilbiogeochem_nitrogenstate_type) , intent(in) :: soilbiogeochem_nitrogenstate_inst @@ -133,8 +133,8 @@ subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & ! calculate the total soil water tot_water(bounds%begc:bounds%endc) = 0._r8 do j = 1,nlevsoi - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) tot_water(c) = tot_water(c) + h2osoi_liq(c,j) end do end do @@ -143,21 +143,21 @@ subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & surface_water(bounds%begc:bounds%endc) = 0._r8 do j = 1,nlevsoi if ( zisoi(j) <= depth_runoff_Nloss) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) surface_water(c) = surface_water(c) + h2osoi_liq(c,j) end do elseif ( zisoi(j-1) < depth_runoff_Nloss) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) surface_water(c) = surface_water(c) + h2osoi_liq(c,j) * ( (depth_runoff_Nloss - zisoi(j-1)) / col%dz(c,j)) end do endif end do ! Loop through columns - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) drain_tot(c) = qflx_drain(c) end do @@ -170,8 +170,8 @@ subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & do j = 1,nlevdecomp ! Loop through columns - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! calculate the dissolved mineral N concentration (gN/kg water) ! assumes that 10% of mineral nitrogen is soluble @@ -203,8 +203,8 @@ subroutine SoilBiogeochemNLeaching(bounds, num_soilc, filter_soilc, & do j = 1,nlevdecomp ! Loop through columns - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! calculate the dissolved mineral N concentration (gN/kg water) ! assumes that 10% of mineral nitrogen is soluble diff --git a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 index 197a1d015b..4b70459aca 100644 --- a/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 @@ -27,7 +27,7 @@ module SoilBiogeochemNStateUpdate1Mod contains !----------------------------------------------------------------------- - subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & + subroutine SoilBiogeochemNStateUpdate1(num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_state_inst, soilbiogeochem_nitrogenflux_inst, soilbiogeochem_nitrogenstate_inst) ! ! !DESCRIPTION: @@ -35,8 +35,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & ! variables (except for gap-phase mortality and fire fluxes) ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(soilbiogeochem_nitrogenflux_type) , intent(inout) :: soilbiogeochem_nitrogenflux_inst type(soilbiogeochem_nitrogenstate_type) , intent(inout) :: soilbiogeochem_nitrogenstate_inst @@ -63,8 +63,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & dt = get_step_size_real() do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if(use_fun)then !RF in FUN logic, the fixed N goes straight into the plant, and not into the SMINN pool. ! N deposition and fixation (put all into NH4 pool) ns%smin_nh4_vr_col(c,j) = ns%smin_nh4_vr_col(c,j) + nf%ndep_to_sminn_col(c)*dt * ndep_prof(c,j) @@ -94,8 +94,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (.not. use_nitrif_denitrif) then ! N deposition and fixation @@ -122,8 +122,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & do k = 1, ndecomp_cascade_transitions do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = & nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - & @@ -137,8 +137,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) = & nf%decomp_npools_sourcesink_col(c,j,cascade_receiver_pool(k)) + & @@ -149,8 +149,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & else ! terminal transitions do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) = & nf%decomp_npools_sourcesink_col(c,j,cascade_donor_pool(k)) - & nf%decomp_cascade_sminn_flux_vr_col(c,j,k) * dt @@ -173,8 +173,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & if ( cascade_receiver_pool(k) /= 0 ) then ! skip terminal transitions do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ns%sminn_vr_col(c,j) = ns%sminn_vr_col(c,j) - & (nf%sminn_to_denit_decomp_cascade_vr_col(c,j,k) + & nf%decomp_cascade_sminn_flux_vr_col(c,j,k))* dt @@ -183,8 +183,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & else do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ns%sminn_vr_col(c,j) = ns%sminn_vr_col(c,j) - & nf%sminn_to_denit_decomp_cascade_vr_col(c,j,k)* dt @@ -198,8 +198,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! "bulk denitrification" ns%sminn_vr_col(c,j) = ns%sminn_vr_col(c,j) - nf%sminn_to_denit_excess_vr_col(c,j) * dt @@ -222,8 +222,8 @@ subroutine SoilBiogeochemNStateUpdate1(num_soilc, filter_soilc, & do j = 1, nlevdecomp ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! mineralization fluxes (divert a fraction of this stream to nitrification flux, add the rest to NH4 pool) ns%smin_nh4_vr_col(c,j) = ns%smin_nh4_vr_col(c,j) + nf%gross_nmin_vr_col(c,j)*dt diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index f735c14854..b30ff759b4 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -138,7 +138,7 @@ subroutine readParams ( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & + subroutine SoilBiogeochemNitrifDenitrif(bounds, num_bgc_soilc, filter_bgc_soilc, & soilstate_inst, waterstatebulk_inst, temperature_inst, ch4_inst, & soilbiogeochem_carbonflux_inst, soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst) ! @@ -151,8 +151,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilstate_type) , intent(in) :: soilstate_inst type(waterstatebulk_type) , intent(in) :: waterstatebulk_inst type(temperature_type) , intent(in) :: temperature_inst @@ -261,8 +261,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & co2diff_con(2) = 0.0009_r8 do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) !---------------- calculate soil anoxia state ! calculate gas diffusivity of soil at field capacity here diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 index 99ce2e7cf9..fb7eac1ce2 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 @@ -1050,7 +1050,7 @@ subroutine SetValues ( this, & end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_soilc, filter_soilc) + subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc) ! ! !USES: use clm_varpar , only: nlevdecomp, ndecomp_cascade_transitions,ndecomp_pools @@ -1059,16 +1059,16 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! !ARGUMENTS: class (soilbiogeochem_nitrogenflux_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns ! ! !LOCAL VARIABLES: integer :: c,j,k,l ! indices integer :: fc ! filter indices !----------------------------------------------------------------------- - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%denit_col(c) = 0._r8 this%supplement_to_sminn_col(c) = 0._r8 this%som_n_leached_col(c) = 0._r8 @@ -1077,8 +1077,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! vertically integrate decomposing N cascade fluxes and soil mineral N fluxes associated with decomposition cascade do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_cascade_ntransfer_col(c,k) = & this%decomp_cascade_ntransfer_col(c,k) + & @@ -1096,8 +1096,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! vertically integrate each denitrification flux do l = 1, ndecomp_cascade_transitions do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%sminn_to_denit_decomp_cascade_col(c,l) = & this%sminn_to_denit_decomp_cascade_col(c,l) + & this%sminn_to_denit_decomp_cascade_vr_col(c,j,l) * dzsoi_decomp(j) @@ -1107,8 +1107,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! vertically integrate bulk denitrification and leaching flux do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%sminn_to_denit_excess_col(c) = & this%sminn_to_denit_excess_col(c) + & this%sminn_to_denit_excess_vr_col(c,j) * dzsoi_decomp(j) @@ -1121,16 +1121,16 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! total N denitrification (DENIT) do l = 1, ndecomp_cascade_transitions - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%denit_col(c) = & this%denit_col(c) + & this%sminn_to_denit_decomp_cascade_col(c,l) end do end do - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%denit_col(c) = & this%denit_col(c) + & this%sminn_to_denit_excess_col(c) @@ -1140,8 +1140,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! vertically integrate NO3 NH4 N2O fluxes and pools do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! nitrification and denitrification fluxes this%f_nit_col(c) = & @@ -1180,8 +1180,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) end do end do - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%denit_col(c) = this%f_denit_col(c) end do @@ -1189,8 +1189,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! supplementary N supplement_to_sminn do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%supplement_to_sminn_col(c) = & this%supplement_to_sminn_col(c) + & this%supplement_to_sminn_vr_col(c,j) * dzsoi_decomp(j) @@ -1199,22 +1199,22 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc) ! add up all vertical transport tendency terms and calculate total som leaching loss as the sum of these do l = 1, ndecomp_pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_leached_col(c,l) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_leached_col(c,l) = & this%decomp_npools_leached_col(c,l) + & this%decomp_npools_transport_tendency_col(c,j,l) * dzsoi_decomp(j) end do end do - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%som_n_leached_col(c) = & this%som_n_leached_col(c) + & this%decomp_npools_leached_col(c,l) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index ac7fa52b44..f3dc3c06cf 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -805,14 +805,14 @@ end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_inst) + subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogenstate_inst) ! ! !ARGUMENTS: class (soilbiogeochem_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of columns in soilc filter - integer , intent(in) :: filter_soilc(:) ! filter for all active columns + integer , intent(in) :: num_bgc_soilc ! number of bgc columns in soilc filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc columns type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst ! @@ -826,14 +826,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in ! vertically integrate NO3 NH4 N2O pools if (use_nitrif_denitrif) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%smin_no3_col(c) = 0._r8 this%smin_nh4_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%smin_no3_col(c) = & this%smin_no3_col(c) + & this%smin_no3_vr_col(c,j) * dzsoi_decomp(j) @@ -848,15 +848,15 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in ! vertically integrate each of the decomposing N pools do l = 1, ndecomp_pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_col(c,l) = 0._r8 if(use_soil_matrixcn)then end if end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_col(c,l) = & this%decomp_npools_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * dzsoi_decomp(j) @@ -870,8 +870,8 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in if ( nlevdecomp > 1) then do l = 1, ndecomp_pools - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_1m_col(c,l) = 0._r8 end do end do @@ -881,15 +881,15 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in do l = 1, ndecomp_pools do j = 1, nlevdecomp if ( zisoi(j) <= maxdepth ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_1m_col(c,l) = & this%decomp_npools_1m_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * dzsoi_decomp(j) end do elseif ( zisoi(j-1) < maxdepth ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_npools_1m_col(c,l) = & this%decomp_npools_1m_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * (maxdepth - zisoi(j-1)) @@ -901,16 +901,16 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in ! Add soil nitrogen pools together to produce vertically-resolved decomposing total soil N pool if ( nlevdecomp_full > 1 ) then do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_soiln_vr_col(c,j) = 0._r8 end do end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%decomp_soiln_vr_col(c,j) = this%decomp_soiln_vr_col(c,j) + & this%decomp_npools_vr_col(c,j,l) end do @@ -920,14 +920,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in end if ! total litter nitrogen to 1 meter (TOTLITN_1m) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitn_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitn_1m_col(c) = & this%totlitn_1m_col(c) + & this%decomp_npools_1m_col(c,l) @@ -936,14 +936,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in end do ! total soil organic matter nitrogen to 1 meter (TOTSOMN_1m) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomn_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomn_1m_col(c) = this%totsomn_1m_col(c) + & this%decomp_npools_1m_col(c,l) end do @@ -953,14 +953,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in endif ! total litter nitrogen (TOTLITN) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totlitn_col(c) = & this%totlitn_col(c) + & this%decomp_npools_col(c,l) @@ -969,14 +969,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in end do ! total microbial nitrogen (TOTMICN) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totmicn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totmicn_col(c) = & this%totmicn_col(c) + & this%decomp_npools_col(c,l) @@ -985,14 +985,14 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in end do ! total soil organic matter nitrogen (TOTSOMN) - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totsomn_col(c) = this%totsomn_col(c) + & this%decomp_npools_col(c,l) end do @@ -1000,34 +1000,34 @@ subroutine Summary(this, bounds, num_soilc, filter_soilc, cnveg_nitrogenstate_in end do ! total sminn - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%sminn_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%sminn_col(c) = this%sminn_col(c) + & this%sminn_vr_col(c,j) * dzsoi_decomp(j) end do end do ! total col_ntrunc - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%ntrunc_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%ntrunc_col(c) = this%ntrunc_col(c) + & this%ntrunc_vr_col(c,j) * dzsoi_decomp(j) end do end do ! total cwdn - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%cwdn_col(c) = 0._r8 if(col%is_fates(c)) then diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenUptakeMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenUptakeMod.F90 index 40c6a0bff9..a566a5882a 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenUptakeMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenUptakeMod.F90 @@ -24,7 +24,7 @@ module SoilBiogeochemNitrogenUptakeMod contains !----------------------------------------------------------------------- - subroutine SoilBiogeochemNitrogenUptake(bounds, nlevdecomp, num_soilc, filter_soilc, & + subroutine SoilBiogeochemNitrogenUptake(bounds, nlevdecomp, num_bgc_soilc, filter_bgc_soilc, & sminn_vr, dzsoi_decomp, nfixation_prof, nuptake_prof) ! ! DESCRIPTION @@ -33,8 +33,8 @@ subroutine SoilBiogeochemNitrogenUptake(bounds, nlevdecomp, num_soilc, filter_so ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds integer , intent(in) :: nlevdecomp ! number of vertical layers - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns real(r8) , intent(in) :: sminn_vr(bounds%begc: , 1: ) ! soil mineral nitrogen profile real(r8) , intent(in) :: dzsoi_decomp(1: ) ! layer thickness real(r8) , intent(in) :: nfixation_prof(bounds%begc: , 1: ) ! nitrogen fixation profile @@ -51,21 +51,21 @@ subroutine SoilBiogeochemNitrogenUptake(bounds, nlevdecomp, num_soilc, filter_so SHR_ASSERT_ALL_FL((ubound(nuptake_prof) == (/bounds%endc, nlevdecomp/)) , sourcefile, __LINE__) ! init sminn_tot - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_tot(c) = 0. end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) sminn_tot(c) = sminn_tot(c) + sminn_vr(c,j) * dzsoi_decomp(j) end do end do do j = 1, nlevdecomp - do fc=1,num_soilc - c = filter_soilc(fc) + do fc=1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (sminn_tot(c) > 0.) then nuptake_prof(c,j) = sminn_vr(c,j) / sminn_tot(c) else diff --git a/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 b/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 index beda04bbec..deb9bdbf78 100644 --- a/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemPotentialMod.F90 @@ -68,7 +68,7 @@ subroutine readParams ( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & + subroutine SoilBiogeochemPotential (bounds, num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_state_inst, soilbiogeochem_carbonstate_inst, soilbiogeochem_carbonflux_inst, & soilbiogeochem_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & cn_decomp_pools, p_decomp_cpool_loss, p_decomp_cn_gain, & @@ -80,8 +80,8 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & ! ! !ARGUMENT: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst type(soilbiogeochem_carbonstate_type) , intent(in) :: soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst @@ -149,8 +149,8 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & do l = 1, ndecomp_pools if ( floating_cn_ratio_decomp_pools(l) ) then do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if ( decomp_npools_vr(c,j,l) > 0._r8 ) then cn_decomp_pools(c,j,l) = decomp_cpools_vr(c,j,l) / decomp_npools_vr(c,j,l) end if @@ -158,8 +158,8 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & end do else do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) cn_decomp_pools(c,j,l) = initial_cn_ratio(l) end do end do @@ -173,8 +173,8 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (decomp_cpools_vr(c,j,cascade_donor_pool(k)) > 0._r8 .and. & decomp_k(c,j,cascade_donor_pool(k)) > 0._r8 ) then @@ -236,8 +236,8 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & ! transitions loop). if (decomp_method == mimics_decomp) then do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ! Sum C & N fluxes from all transitions into m1 & m2 pools. ! Had to form a new loop for the summation due to the order ! necessary, ie do k as the innermost loop. @@ -293,15 +293,15 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & ! Sum up all the potential immobilization fluxes (positive pmnf flux) ! and all the mineralization fluxes (negative pmnf flux) do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) immob(c,j) = 0._r8 end do end do do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if (pmnf_decomp_cascade(c,j,k) > 0._r8) then immob(c,j) = immob(c,j) + pmnf_decomp_cascade(c,j,k) else @@ -315,23 +315,23 @@ subroutine SoilBiogeochemPotential (bounds, num_soilc, filter_soilc, & end do do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) potential_immob_vr(c,j) = immob(c,j) end do end do ! Add up potential hr for methane calculations do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) phr_vr(c,j) = 0._r8 end do end do do k = 1, ndecomp_cascade_transitions do j = 1,nlevdecomp - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) phr_vr(c,j) = phr_vr(c,j) + rf_decomp_cascade(c,j,k) * p_decomp_cpool_loss(c,j,k) end do end do diff --git a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 index cabc57990e..cc349ad8bc 100644 --- a/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemPrecisionControlMod.F90 @@ -60,7 +60,7 @@ subroutine SoilBiogeochemPrecisionControlInit( soilbiogeochem_carbonstate_inst, end subroutine SoilBiogeochemPrecisionControlInit !----------------------------------------------------------------------- - subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & + subroutine SoilBiogeochemPrecisionControl(num_bgc_soilc, filter_bgc_soilc, & soilbiogeochem_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst, & c14_soilbiogeochem_carbonstate_inst, soilbiogeochem_nitrogenstate_inst) @@ -75,8 +75,8 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & use CNSharedParamsMod, only: use_fun ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_soilc ! number of bgc soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc soil columns type(soilbiogeochem_carbonstate_type) , intent(inout) :: soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: c13_soilbiogeochem_carbonstate_inst type(soilbiogeochem_carbonstate_type) , intent(inout) :: c14_soilbiogeochem_carbonstate_inst @@ -106,8 +106,8 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & ) ! column loop - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) do j = 1,nlevdecomp ! initialize the column-level C and N truncation terms @@ -165,8 +165,8 @@ subroutine SoilBiogeochemPrecisionControl(num_soilc, filter_soilc, & if (use_nitrif_denitrif) then ! remove small negative perturbations for stability purposes, if any should arise. - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) do j = 1,nlevdecomp if (abs(ns%smin_no3_vr_col(c,j)) < ncrit/1e4_r8) then if ( ns%smin_no3_vr_col(c,j) < 0._r8 ) then diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 index 3548643192..49a5215cac 100644 --- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 @@ -24,7 +24,7 @@ module SoilBiogeochemVerticalProfileMod contains !----------------------------------------------------------------------- - subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soilp,filter_soilp, & + subroutine SoilBiogeochemVerticalProfile(bounds, num_bgc_soilc,filter_bgc_soilc,num_bgc_vegp,filter_bgc_vegp, & active_layer_inst, soilstate_inst, soilbiogeochem_state_inst) ! ! !DESCRIPTION: @@ -57,10 +57,10 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - integer , intent(in) :: num_soilp ! number of soil patches in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil patches + integer , intent(in) :: num_bgc_soilc ! number of soil columns in filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of soil patches in filter + integer , intent(in) :: filter_bgc_vegp(:) ! filter for soil patches type(active_layer_type) , intent(in) :: active_layer_inst type(soilstate_type) , intent(in) :: soilstate_inst type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst @@ -124,8 +124,8 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil cinput_rootfr(begp:endp, :) = 0._r8 col_cinput_rootfr(begc:endc, :) = 0._r8 - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) c = patch%column(p) if (patch%itype(p) /= noveg) then do j = 1, nlevdecomp @@ -136,8 +136,8 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil endif end do - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) c = patch%column(p) ! integrate rootfr over active layer of soil column rootfr_tot = 0._r8 @@ -175,9 +175,9 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil ! col_cinput_rootfr(bounds%begc:bounds%endc, :), & ! 'unity') - !if(num_soilp>0)then - do fc = 1,num_soilc - c = filter_soilc(fc) + !if(num_bgc_vegp>0)then + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if(.not.col%is_fates(c))then do pi = 1,col%npatches(c)) !maxsoil_patches !if (pi <= col%npatches(c)) then @@ -192,8 +192,8 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil !end if ! repeat for column-native profiles: Ndep and Nfix - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) rootfr_tot = 0._r8 surface_prof_tot = 0._r8 if_fates: if(col%is_fates(c))then @@ -231,8 +231,8 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil end do ! check to make sure integral of all profiles = 1. - do fc = 1,num_soilc - c = filter_soilc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) ndep_prof_sum = 0. nfixation_prof_sum = 0. do j = 1, nlevdecomp @@ -258,8 +258,8 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil endif end do - do fp = 1,num_soilp - p = filter_soilp(fp) + do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) froot_prof_sum = 0. croot_prof_sum = 0. leaf_prof_sum = 0. From b519997270bfd020e605773a8bd860b6bbb70413 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 25 May 2023 16:06:23 -0600 Subject: [PATCH 0967/2067] Added missing return statement from cropcal_module import_output(). --- python/ctsm/crop_calendars/cropcal_module.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 043b12b490..94f104d36e 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -1078,6 +1078,8 @@ def check_no_zeros(this_ds, varList_no_zero, which_file): if np.any(this_ds_gs["NHARVESTS"] > 2): raise RuntimeError("How to get NHARVEST_DISCREP for NHARVESTS > 2?") this_ds_gs["NHARVEST_DISCREP"] = (this_ds_gs["NHARVESTS"] == 2).astype(int) + + return this_ds_gs # Print information about a patch (for debugging) From 527d4fa725df2492dc854bd6d5c183b48d27dde5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 25 May 2023 17:08:37 -0600 Subject: [PATCH 0968/2067] Finished switching h1 and h2. --- .../crop_calendars/generate_gdds_functions.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 921ddd0a41..858477be4b 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -211,16 +211,17 @@ def import_and_process_1yr( chunks = None # Get h2 file (list) - h2_pattern = os.path.join(indir, "*h2.*.nc") - h2_filelist = glob.glob(h2_pattern) - if not h2_filelist: - h2_pattern = os.path.join(indir, "*h2.*.nc.base") - h2_filelist = glob.glob(h2_pattern) - if not h2_filelist: - error(logger, "No files found matching pattern '*h2.*.nc(.base)'") - + h1_pattern = os.path.join(indir, "*h1.*.nc") + h1_filelist = glob.glob(h1_pattern) + if not h1_filelist: + h1_pattern = os.path.join(indir, "*h1.*.nc.base") + h1_filelist = glob.glob(h1_pattern) + if not h1_filelist: + error(logger, "No files found matching pattern '*h1.*.nc(.base)'") + + print(h1_filelist) dates_ds = utils.import_ds( - h2_filelist, + h1_filelist, myVars=["SDATES", "HDATES"], myVegtypes=utils.define_mgdcrop_list(), timeSlice=slice(f"{thisYear}-01-01", f"{thisYear}-12-31"), From d2bcaf17aca4b50bbbbaded3d5d58218f37d626b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 26 May 2023 11:35:32 -0600 Subject: [PATCH 0969/2067] Bugfix in utils import_ds(). --- python/ctsm/crop_calendars/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/utils.py b/python/ctsm/crop_calendars/utils.py index 9b2478289f..0d03788adb 100644 --- a/python/ctsm/crop_calendars/utils.py +++ b/python/ctsm/crop_calendars/utils.py @@ -614,7 +614,7 @@ def import_ds( chunks=None, ): # Convert myVegtypes here, if needed, to avoid repeating the process each time you read a file in xr.open_mfdataset(). - if myVegtypes != None: + if myVegtypes is not None: if not isinstance(myVegtypes, list): myVegtypes = [myVegtypes] if isinstance(myVegtypes[0], str): From 2026ddabeee69fa28580eced8fcb016c67e5f190 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 26 May 2023 11:44:52 -0600 Subject: [PATCH 0970/2067] Removed unneeded imports from cropcal Python modules. --- python/ctsm/crop_calendars/cropcal_figs_module.py | 6 ------ python/ctsm/crop_calendars/cropcal_module.py | 6 ------ 2 files changed, 12 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_figs_module.py b/python/ctsm/crop_calendars/cropcal_figs_module.py index fb02d3b016..8d7f472fec 100644 --- a/python/ctsm/crop_calendars/cropcal_figs_module.py +++ b/python/ctsm/crop_calendars/cropcal_figs_module.py @@ -1,17 +1,11 @@ import numpy as np -import xarray as xr -import cftime import cartopy.crs as ccrs -import cartopy.feature as cfeature import matplotlib.pyplot as plt import matplotlib.colors as mcolors from matplotlib import cm import matplotlib.collections as mplcol -# Import the CTSM Python utilities -import utils - # Colormaps (maps) cropcal_colors = { diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 94f104d36e..da0fd110da 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -3,17 +3,11 @@ import numpy as np import xarray as xr -from scipy import stats, signal import warnings -import cftime import sys import os import glob -try: - import cartopy.crs as ccrs -except: - pass try: import pandas as pd except: From e86eacc8cd6a65ff29708cdf88f63f75fd1703da Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 26 May 2023 11:45:59 -0600 Subject: [PATCH 0971/2067] Renamed .../crop_calendars/utils.py to .../cropcal_utils.py to disambiguate. --- python/ctsm/crop_calendars/cropcal_module.py | 2 +- python/ctsm/crop_calendars/{utils.py => cropcal_utils.py} | 0 python/ctsm/crop_calendars/generate_gdds_functions.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename python/ctsm/crop_calendars/{utils.py => cropcal_utils.py} (100%) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index da0fd110da..fd56df1f3c 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -1,5 +1,5 @@ # Import the CTSM Python utilities -import utils +import cropcal_utils as utils import numpy as np import xarray as xr diff --git a/python/ctsm/crop_calendars/utils.py b/python/ctsm/crop_calendars/cropcal_utils.py similarity index 100% rename from python/ctsm/crop_calendars/utils.py rename to python/ctsm/crop_calendars/cropcal_utils.py diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index bd3f6756a0..c1866e1079 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -1,5 +1,5 @@ # Import the CTSM Python utilities -import utils +import cropcal_utils as utils import numpy as np import xarray as xr From 753b7c387acd01419b58ede4d16776038ce929a9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 26 May 2023 12:05:59 -0600 Subject: [PATCH 0972/2067] RXCROPMATURITY: Syntax fix. --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 566c0a605c..9b869d6348 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -291,7 +291,7 @@ def _modify_user_nl_allruns(self): "stream_year_last_cropcal = 2000", "model_year_align_cropcal = 2000", " ", - "! (h1) Annual outputs on sowing or harvest axis + "! (h1) Annual outputs on sowing or harvest axis", "hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV'", "hist_nhtfrq(2) = 17520", "hist_mfilt(2) = 999", From d2c536ec90c49fab2154f01826f9dd9bd1a310d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 26 May 2023 12:06:37 -0600 Subject: [PATCH 0973/2067] RXCROPMATURITY: Use non-fill1 sdates. --- cime_config/SystemTests/rxcropmaturity.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 9b869d6348..4b3837b497 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -178,24 +178,24 @@ def _get_rx_dates(self): if lnd_grid == "10x15": self._sdatefile = os.path.join( blessed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc") self._hdatefile = os.path.join( blessed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.fill1.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc") elif lnd_grid == "1.9x2.5": self._sdatefile = os.path.join( blessed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc") self._hdatefile = os.path.join( blessed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.fill1.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc") elif lnd_grid == "0.9x1.25": self._sdatefile = os.path.join( blessed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.fill1.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc") self._hdatefile = os.path.join( blessed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.fill1.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc") else: error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" logger.error(error_message) From 82d9b57fd68f1be5bd3ab00f72586ced9c3b3412 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 26 May 2023 17:38:20 -0400 Subject: [PATCH 0974/2067] Updates to the build-namelist --- bld/CLMBuildNamelist.pm | 35 +++++++++++------------------------ 1 file changed, 11 insertions(+), 24 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index d81d185148..c5df290277 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -757,26 +757,12 @@ sub setup_cmdl_fates_mode { } } - # The following variables may be set by the user and are compatible with use_fates - # no need to set defaults, covered in a different routine - my @list = ( "use_lch4", "use_nitrif_denitrif" ); - foreach my $var ( @list ) { - if ( defined($nl->get_value($var)) ) { - $nl_flags->{$var} = $nl->get_value($var); - $val = $nl_flags->{$var}; - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, $val); - if ( ! $definition->is_valid_value( $var, $val ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); - } - } - } } else { # dis-allow fates specific namelist items with non-fates runs my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_cohort_age_tracking", - "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode","use_fates_tree_damage" ); + "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", + "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging", + "fates_parteh_mode","use_fates_tree_damage" ); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { @@ -2890,13 +2876,14 @@ sub setup_logic_supplemental_nitrogen { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" && &value_is_true($nl_flags->{'use_crop'}) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'}); - } - - if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} eq "fates" ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, - 'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'}); + # If this is non-fates, non-sp and crop is active + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'suplnitro', 'use_cn'=>$nl_flags->{'use_cn'}, 'use_crop'=>$nl_flags->{'use_crop'}); + + } elsif ( $nl_flags->{'bgc_mode'} eq "fates" && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) { + # Or... if its fates but not fates-sp + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, + 'suplnitro', 'use_fates'=>$nl_flags->{'use_fates'}); } # From ebf9601621f4b2a162bb2b2bef75c59b06a736ee Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 26 May 2023 15:27:07 -0700 Subject: [PATCH 0975/2067] update changelog --- doc/ChangeLog | 68 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 69 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index a620f38209..937e686014 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,72 @@ =============================================================== +Tag name: ctsm5.1.dev128 +Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) +Date: Fri May 26 15:45:00 MDT 2023 +One-line Summary: Update FATES tests to double precision + +Purpose and description of changes +---------------------------------- + +This pull request updates the fates tests to set the output +precision to double precision. The usermod fates_sp is similarly +updated. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): +- Resolves https://github.com/ESCOMP/CTSM/issues/1986 + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + FATES tests run against fates-sci.1.65.6_api.25.4.0-ctsm5.1.dev127 baseline + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, but only for fates tests and compsets + + Summarize any changes to answers, i.e., + - Differences are due to changing hist_ndens to 1 (double precision) + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/2010 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev127 Originator(s): sacks (Bill Sacks) Date: Fri May 19 04:48:30 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index ca203e6f21..69357c6d66 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev128 glemieux 05/26/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType ctsm5.1.dev125 jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90 From 30a758b739f717149fe7b5a3ce2bae25e664d177 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 30 May 2023 11:49:22 -0600 Subject: [PATCH 0976/2067] Updated check_rxboth_run.py to use h1 files. --- python/ctsm/crop_calendars/check_rxboth_run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/check_rxboth_run.py b/python/ctsm/crop_calendars/check_rxboth_run.py index 256fb125b7..6dae071937 100644 --- a/python/ctsm/crop_calendars/check_rxboth_run.py +++ b/python/ctsm/crop_calendars/check_rxboth_run.py @@ -55,7 +55,7 @@ def main(argv): "HARVEST_REASON_PERHARV", ] - h2files = glob.glob(os.path.join(args.directory, "*.clm2.h2.*.nc")) + annual_outfiles = glob.glob(os.path.join(args.directory, "*.clm2.h1.*.nc")) # These should be constant in a Prescribed Calendars (rxboth) run, as long as the inputs were # static. @@ -66,7 +66,7 @@ def main(argv): } case["ds"] = cc.import_output( - h2files, + annual_outfiles, myVars=myVars, y1=args.first_usable_year, yN=args.last_usable_year, From 416eae4973ff06203337dec6ede574500a87df6f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 31 May 2023 17:05:33 -0600 Subject: [PATCH 0977/2067] Only apply tillage multipliers once per column! --- src/biogeochem/TillageMod.f90 | 163 +++++++++--------- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 2 +- 2 files changed, 86 insertions(+), 79 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 4e78c1d6fd..e2410d4b73 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -30,7 +30,7 @@ module TillageMod logical :: do_tillage_low ! Do low-intensity tillage? logical :: do_tillage_high ! Do high-intensity tillage? logical :: use_original_tillage ! Use get_tillage_multipliers_orig? - real(r8), pointer :: tillage_mults(:,:) + real(r8), pointer :: tillage_mults(:) !============================================================================== @@ -106,7 +106,7 @@ subroutine tillage_init(bounds) if (get_do_tillage()) then begp = bounds%begp endp = bounds%endp - allocate(tillage_mults(begp:endp, ndecomp_pools)) ; tillage_mults(:,:) = 1.0_r8 + allocate(tillage_mults(ndecomp_pools)) ; tillage_mults(:) = 1.0_r8 end if end subroutine tillage_init @@ -118,7 +118,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -133,12 +133,13 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: c ! index of column this is being called for integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! - integer :: fp, p, c, g ! Indices + integer :: fp, p, g ! Indices integer :: day ! julian day integer :: idpp ! days past planting real(r8) dayspyr ! days per year @@ -148,9 +149,13 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som day = get_curr_calday() dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine + ! TODO: There's probably a more efficient way to cycle through the patches on a given column do fp = 1,num_soilp p = filter_soilp(fp) - c = patch%column(p) + if (patch%column(p) /= c) then + cycle + end if + g = patch%gridcell(p) ! days past planting may determine harvest/tillage @@ -170,55 +175,55 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som ! corn, soy : P C D & HW-7 30 d aftr if (day < idop(p)) then - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 else if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_act_som) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(c,i_slo_som) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(c,i_pas_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 end if else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_slo_som) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(c,i_pas_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 end if else if (day >= idop(p)+45 .and. day = npcropmin) then - tillage_mults(c,i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_slo_som) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(c,i_pas_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 end if else if (day >= idop(p)+75 .and. day < idop(p)+80) then ! June 14 - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) == ntmp_corn .or. & patch%itype(p) == nirrig_tmp_corn .or. & patch%itype(p) == ntmp_soybean .or. & patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(c,i_cel_lit) = 1.00_r8 - tillage_mults(c,i_lig_lit) = 1.00_r8 - tillage_mults(c,i_act_som) = 1.00_r8 - tillage_mults(c,i_slo_som) = 1.00_r8 - tillage_mults(c,i_pas_som) = 1.00_r8 + tillage_mults(i_cel_lit) = 1.00_r8 + tillage_mults(i_lig_lit) = 1.00_r8 + tillage_mults(i_act_som) = 1.00_r8 + tillage_mults(i_slo_som) = 1.00_r8 + tillage_mults(i_pas_som) = 1.00_r8 end if else if (day >= idop(p)+80) then ! July 14 - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 end if enddo end subroutine get_tillage_multipliers_orig - subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -234,12 +239,13 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: c ! index of column this is being called for integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! - integer :: fp, p, c, g ! Indices + integer :: fp, p, g ! Indices integer :: day ! julian day integer :: idpp ! days past planting real(r8) dayspyr ! days per year @@ -249,9 +255,13 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, day = get_curr_calday() dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine + ! TODO: There's probably a more efficient way to cycle through the patches on a given column do fp = 1,num_soilp p = filter_soilp(fp) - c = patch%column(p) + if (patch%column(p) /= c) then + cycle + end if + g = patch%gridcell(p) ! days past planting may determine harvest/tillage @@ -270,48 +280,48 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, ! corn, soy : P C D & HW-7 30 d aftr if (idpp < 0) then - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 else if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(c,i_act_som) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(c,i_slo_som) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(c,i_pas_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 end if else if (idpp < 45) then ! based on Field and Row Cultivator multipliers - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_slo_som) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(c,i_pas_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 end if else if (idpp < 75) then ! based on Rod Weed Row Planter - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) >= npcropmin) then - tillage_mults(c,i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(c,i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(c,i_slo_som) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(c,i_pas_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 end if else if (idpp < 80) then ! June 14 - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 if (patch%itype(p) == ntmp_corn .or. & patch%itype(p) == nirrig_tmp_corn .or. & patch%itype(p) == ntmp_soybean .or. & patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(c,i_cel_lit) = 1.00_r8 - tillage_mults(c,i_lig_lit) = 1.00_r8 - tillage_mults(c,i_act_som) = 1.00_r8 - tillage_mults(c,i_slo_som) = 1.00_r8 - tillage_mults(c,i_pas_som) = 1.00_r8 + tillage_mults(i_cel_lit) = 1.00_r8 + tillage_mults(i_lig_lit) = 1.00_r8 + tillage_mults(i_act_som) = 1.00_r8 + tillage_mults(i_slo_som) = 1.00_r8 + tillage_mults(i_pas_som) = 1.00_r8 end if else ! July 14 - tillage_mults(c,:) = 1._r8 + tillage_mults(:) = 1._r8 end if enddo @@ -319,7 +329,7 @@ end subroutine get_tillage_multipliers_new ! Public interface to choose between and call either get_tillage_multipliers_orig() or get_tillage_multipliers_new() - subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Public interface to choose between and call either original (buggy) or @@ -329,19 +339,20 @@ subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_s integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts + integer , intent(in) :: c ! index of column this is being called for integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools if (use_original_tillage) then - call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) else - call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if end subroutine get_tillage_multipliers - subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Multiply decomposition rate constants by tillage coefficients. @@ -353,29 +364,25 @@ subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soil integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: num_soilp ! number of soil pfts in filter integer , intent(in) :: filter_soilp(:) ! filter for soil pfts - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns - real(r8) , intent(inout) :: decomp_k(:,:,:) ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) + integer , intent(in) :: c ! index of column this is being called for + real(r8), dimension(:,:,:), intent(inout) :: decomp_k ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES - integer :: j, fc, c + integer :: j - call get_tillage_multipliers(idop, num_soilp, filter_soilp, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham do j = 1,5 - do fc = 1,num_soilc - c = filter_soilc(fc) - ! TODO: Loop through ALL pools, not just the ones that currently have non-1 values - decomp_k(c,j,i_cel_lit) = decomp_k(c,j,i_cel_lit) * tillage_mults(c,i_cel_lit) - decomp_k(c,j,i_lig_lit) = decomp_k(c,j,i_lig_lit) * tillage_mults(c,i_lig_lit) - decomp_k(c,j,i_act_som) = decomp_k(c,j,i_act_som) * tillage_mults(c,i_act_som) - decomp_k(c,j,i_slo_som) = decomp_k(c,j,i_slo_som) * tillage_mults(c,i_slo_som) - decomp_k(c,j,i_pas_som) = decomp_k(c,j,i_pas_som) * tillage_mults(c,i_pas_som) - end do + ! TODO: Loop through ALL pools, not just the ones that currently have non-1 values + decomp_k(c,j,i_cel_lit) = decomp_k(c,j,i_cel_lit) * tillage_mults(i_cel_lit) + decomp_k(c,j,i_lig_lit) = decomp_k(c,j,i_lig_lit) * tillage_mults(i_lig_lit) + decomp_k(c,j,i_act_som) = decomp_k(c,j,i_act_som) * tillage_mults(i_act_som) + decomp_k(c,j,i_slo_som) = decomp_k(c,j,i_slo_som) * tillage_mults(i_slo_som) + decomp_k(c,j,i_pas_som) = decomp_k(c,j,i_pas_som) * tillage_mults(i_pas_som) end do end subroutine get_apply_tillage_multipliers diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 03136b0007..fd066b6bea 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -908,7 +908,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & if (.not. (present(idop) .and. present(num_soilp) .and. present(filter_soilp))) then call endrun("Do not call tillage without providing idop, num_soilp, and filter_soilp. (Maybe you called with FATES?)") end if - call get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, num_soilc, filter_soilc, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if ! Above into soil matrix From cc333285d4c37a0aa0e33220fe2cfa355348092a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 1 Jun 2023 15:32:53 -0600 Subject: [PATCH 0978/2067] Update the time stamps --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 937e686014..ced4fc388e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev128 Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) -Date: Fri May 26 15:45:00 MDT 2023 +Date: Thu Jun 1 15:31:52 MDT 2023 One-line Summary: Update FATES tests to double precision Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index 69357c6d66..aca77a5238 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev128 glemieux 05/26/2023 Update FATES tests to double precision + ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType ctsm5.1.dev125 jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90 From 7a006dca8214a73239bc100b35fc44fdc44b7b78 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 1 Jun 2023 15:35:49 -0600 Subject: [PATCH 0979/2067] Remove patch loops in get_tillage_multipliers*() subroutines. Each crop column should only have one patch, so by only calling these for crop columns, we can simplify things considerably. --- src/biogeochem/CNDriverMod.F90 | 3 +- src/biogeochem/TillageMod.f90 | 301 ++++++++---------- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 15 +- 3 files changed, 148 insertions(+), 171 deletions(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 7078216e4a..77da920a91 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -341,8 +341,9 @@ subroutine CNDriverNoLeaching(bounds, if (decomp_method == century_decomp) then call decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & - cnveg_state_inst%idop_patch, num_soilp, filter_soilp) + cnveg_state_inst%idop_patch) else if (decomp_method == mimics_decomp) then + ! TODO(ssr): Add tillage to MIMICS? call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & soilstate_inst, temperature_inst, cnveg_carbonflux_inst, ch4_inst, & diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index e2410d4b73..4b5e78d0ef 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -18,6 +18,8 @@ module TillageMod use abortutils , only : endrun use clm_varctl , only : iulog use clm_varpar , only : ndecomp_pools + use ColumnType , only : col + use PatchType , only : patch ! implicit none private @@ -118,7 +120,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -127,19 +129,16 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, c, i_act_ ! ! !USES: use clm_time_manager, only : get_curr_calday, get_curr_days_per_year - use pftconMod , only : npcropmin, ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean - use PatchType , only : patch + use pftconMod , only : ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting - integer , intent(in) :: num_soilp ! number of soil pfts in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil pfts - integer , intent(in) :: c ! index of column this is being called for + integer , intent(in) :: p ! index of patch this is being called for integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! - integer :: fp, p, g ! Indices + integer :: fp, g ! Indices integer :: day ! julian day integer :: idpp ! days past planting real(r8) dayspyr ! days per year @@ -149,81 +148,68 @@ subroutine get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, c, i_act_ day = get_curr_calday() dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine - ! TODO: There's probably a more efficient way to cycle through the patches on a given column - do fp = 1,num_soilp - p = filter_soilp(fp) - if (patch%column(p) /= c) then - cycle - end if + g = patch%gridcell(p) - g = patch%gridcell(p) - - ! days past planting may determine harvest/tillage - ! SSR: Unused! - if (day >= idop(p)) then - idpp = day - idop(p) - else - idpp = int(dayspyr) + day - idop(p) - end if - - ! ----------------------------------------------------- - ! 3) assigning cultivation practices and mapping to the - ! effect on soil C decomposition - ! ----------------------------------------------------- - ! info from DAYCENT (Melannie Hartman CSU) - ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting - ! corn, soy : P C D & HW-7 30 d aftr - - if (day < idop(p)) then - tillage_mults(:) = 1._r8 - else if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(:) = 1._r8 - if (patch%itype(p) >= npcropmin) then - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 - end if - else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers - tillage_mults(:) = 1._r8 - if (patch%itype(p) >= npcropmin) then - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 - end if - else if (day >= idop(p)+45 .and. day = npcropmin) then - tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 - end if - else if (day >= idop(p)+75 .and. day < idop(p)+80) then ! June 14 - tillage_mults(:) = 1._r8 - if (patch%itype(p) == ntmp_corn .or. & - patch%itype(p) == nirrig_tmp_corn .or. & - patch%itype(p) == ntmp_soybean .or. & - patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(i_cel_lit) = 1.00_r8 - tillage_mults(i_lig_lit) = 1.00_r8 - tillage_mults(i_act_som) = 1.00_r8 - tillage_mults(i_slo_som) = 1.00_r8 - tillage_mults(i_pas_som) = 1.00_r8 - end if - else if (day >= idop(p)+80) then ! July 14 - tillage_mults(:) = 1._r8 + ! days past planting may determine harvest/tillage + ! SSR: Unused! + if (day >= idop(p)) then + idpp = day - idop(p) + else + idpp = int(dayspyr) + day - idop(p) + end if + + ! ----------------------------------------------------- + ! 3) assigning cultivation practices and mapping to the + ! effect on soil C decomposition + ! ----------------------------------------------------- + ! info from DAYCENT (Melannie Hartman CSU) + ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting + ! corn, soy : P C D & HW-7 30 d aftr + + if (day < idop(p)) then + tillage_mults(:) = 1._r8 + else if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers + tillage_mults(:) = 1._r8 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 + else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers + tillage_mults(:) = 1._r8 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 + else if (day >= idop(p)+45 .and. day = idop(p)+75 .and. day < idop(p)+80) then ! June 14 + tillage_mults(:) = 1._r8 + ! TODO(ssr): Check with Mike and Danica: Why this extra code? These should already all be 1. + if (patch%itype(p) == ntmp_corn .or. & + patch%itype(p) == nirrig_tmp_corn .or. & + patch%itype(p) == ntmp_soybean .or. & + patch%itype(p) == nirrig_tmp_soybean ) then + tillage_mults(i_cel_lit) = 1.00_r8 + tillage_mults(i_lig_lit) = 1.00_r8 + tillage_mults(i_act_som) = 1.00_r8 + tillage_mults(i_slo_som) = 1.00_r8 + tillage_mults(i_pas_som) = 1.00_r8 end if - enddo + else if (day >= idop(p)+80) then ! July 14 + tillage_mults(:) = 1._r8 + end if end subroutine get_tillage_multipliers_orig - subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -233,19 +219,16 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, c, i_act_s ! ! !USES: use clm_time_manager, only : get_curr_calday, get_curr_days_per_year - use pftconMod , only : npcropmin, ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean - use PatchType , only : patch + use pftconMod , only : ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting - integer , intent(in) :: num_soilp ! number of soil pfts in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil pfts - integer , intent(in) :: c ! index of column this is being called for + integer , intent(in) :: p ! index of patch this is being called for integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! - integer :: fp, p, g ! Indices + integer :: fp, g ! Indices integer :: day ! julian day integer :: idpp ! days past planting real(r8) dayspyr ! days per year @@ -255,81 +238,68 @@ subroutine get_tillage_multipliers_new(idop, num_soilp, filter_soilp, c, i_act_s day = get_curr_calday() dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine - ! TODO: There's probably a more efficient way to cycle through the patches on a given column - do fp = 1,num_soilp - p = filter_soilp(fp) - if (patch%column(p) /= c) then - cycle - end if + g = patch%gridcell(p) - g = patch%gridcell(p) - - ! days past planting may determine harvest/tillage - if (day >= idop(p)) then - idpp = day - idop(p) - else - idpp = int(dayspyr) + day - idop(p) - end if - - ! ----------------------------------------------------- - ! 3) assigning cultivation practices and mapping to the - ! effect on soil C decomposition - ! ----------------------------------------------------- - ! info from DAYCENT (Melannie Hartman CSU) - ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting - ! corn, soy : P C D & HW-7 30 d aftr - - if (idpp < 0) then - tillage_mults(:) = 1._r8 - else if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(:) = 1._r8 - if (patch%itype(p) >= npcropmin) then - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 - end if - else if (idpp < 45) then ! based on Field and Row Cultivator multipliers - tillage_mults(:) = 1._r8 - if (patch%itype(p) >= npcropmin) then - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 - end if - else if (idpp < 75) then ! based on Rod Weed Row Planter - tillage_mults(:) = 1._r8 - if (patch%itype(p) >= npcropmin) then - tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 - end if - else if (idpp < 80) then ! June 14 - tillage_mults(:) = 1._r8 - if (patch%itype(p) == ntmp_corn .or. & - patch%itype(p) == nirrig_tmp_corn .or. & - patch%itype(p) == ntmp_soybean .or. & - patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(i_cel_lit) = 1.00_r8 - tillage_mults(i_lig_lit) = 1.00_r8 - tillage_mults(i_act_som) = 1.00_r8 - tillage_mults(i_slo_som) = 1.00_r8 - tillage_mults(i_pas_som) = 1.00_r8 - end if - else ! July 14 - tillage_mults(:) = 1._r8 + ! days past planting may determine harvest/tillage + if (day >= idop(p)) then + idpp = day - idop(p) + else + idpp = int(dayspyr) + day - idop(p) + end if + + ! ----------------------------------------------------- + ! 3) assigning cultivation practices and mapping to the + ! effect on soil C decomposition + ! ----------------------------------------------------- + ! info from DAYCENT (Melannie Hartman CSU) + ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting + ! corn, soy : P C D & HW-7 30 d aftr + + if (idpp < 0) then + tillage_mults(:) = 1._r8 + else if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers + tillage_mults(:) = 1._r8 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 + tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 + tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 + else if (idpp < 45) then ! based on Field and Row Cultivator multipliers + tillage_mults(:) = 1._r8 + tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 + tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 + else if (idpp < 75) then ! based on Rod Weed Row Planter + tillage_mults(:) = 1._r8 + tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 + tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 + tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 + tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 + else if (idpp < 80) then ! June 14 + tillage_mults(:) = 1._r8 + ! TODO(ssr): Check with Mike and Danica: Why this extra code? These should already all be 1. + if (patch%itype(p) == ntmp_corn .or. & + patch%itype(p) == nirrig_tmp_corn .or. & + patch%itype(p) == ntmp_soybean .or. & + patch%itype(p) == nirrig_tmp_soybean ) then + tillage_mults(i_cel_lit) = 1.00_r8 + tillage_mults(i_lig_lit) = 1.00_r8 + tillage_mults(i_act_som) = 1.00_r8 + tillage_mults(i_slo_som) = 1.00_r8 + tillage_mults(i_pas_som) = 1.00_r8 end if - enddo + else ! July 14 + tillage_mults(:) = 1._r8 + end if end subroutine get_tillage_multipliers_new ! Public interface to choose between and call either get_tillage_multipliers_orig() or get_tillage_multipliers_new() - subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Public interface to choose between and call either original (buggy) or @@ -337,47 +307,54 @@ subroutine get_tillage_multipliers(idop, num_soilp, filter_soilp, c, i_act_som, ! ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting - integer , intent(in) :: num_soilp ! number of soil pfts in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil pfts - integer , intent(in) :: c ! index of column this is being called for + integer , intent(in) :: p ! index of patch this is being called for integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools if (use_original_tillage) then - call get_tillage_multipliers_orig(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) else - call get_tillage_multipliers_new(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if end subroutine get_tillage_multipliers - subroutine get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Multiply decomposition rate constants by tillage coefficients. ! Written by Sam Rabin, based on original code by Michael Graham. ! ! !USES + use pftconMod , only : npcropmin ! ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting - integer , intent(in) :: num_soilp ! number of soil pfts in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil pfts - integer , intent(in) :: c ! index of column this is being called for + integer , intent(in) :: c ! index of column this is being called for real(r8), dimension(:,:,:), intent(inout) :: decomp_k ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES - integer :: j + integer :: p, j + + ! This subroutine should only ever be called for crop columns... + p = col%patchi(c) + if (patch%itype(p) < npcropmin) then + call endrun('ERROR tillage code should only be called for crops') + end if + ! ... and those should only ever have one patch. + if (p /= col%patchf(c)) then + call endrun('ERROR tillage code assumes one patch per column') + end if - call get_tillage_multipliers(idop, num_soilp, filter_soilp, c, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham do j = 1,5 - ! TODO: Loop through ALL pools, not just the ones that currently have non-1 values + ! TODO(ssr): Loop through ALL pools, not just the ones that currently have non-1 values decomp_k(c,j,i_cel_lit) = decomp_k(c,j,i_cel_lit) * tillage_mults(i_cel_lit) decomp_k(c,j,i_lig_lit) = decomp_k(c,j,i_lig_lit) * tillage_mults(i_lig_lit) decomp_k(c,j,i_act_som) = decomp_k(c,j,i_act_som) * tillage_mults(i_act_som) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index fd066b6bea..5fa478eda6 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -512,7 +512,7 @@ end subroutine init_decompcascade_bgc !----------------------------------------------------------------------- subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & - idop, num_soilp, filter_soilp) + idop) ! ! !DESCRIPTION: ! calculate rate constants and decomposition pathways for the CENTURY decomposition cascade model @@ -524,6 +524,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & use clm_varcon , only : secspday use TillageMod , only : get_do_tillage use TillageMod , only : get_apply_tillage_multipliers + use landunit_varcon , only : istcrop ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -534,8 +535,6 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & type(ch4_type) , intent(in) :: ch4_inst type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst integer, optional , intent(in) :: idop(:) ! patch day of planting - integer, optional , intent(in) :: num_soilp ! number of soil patches in filter - integer, optional , intent(in) :: filter_soilp(:) ! filter for soil patches ! ! !LOCAL VARIABLES: real(r8), parameter :: eps = 1.e-6_r8 @@ -903,12 +902,12 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & end if ! Tillage - if (get_do_tillage()) then - ! TODO: Throw error during namelist build if tillage is called with FATES - if (.not. (present(idop) .and. present(num_soilp) .and. present(filter_soilp))) then - call endrun("Do not call tillage without providing idop, num_soilp, and filter_soilp. (Maybe you called with FATES?)") + if (get_do_tillage() .and. col%lun_itype(c) == istcrop) then + ! TODO(ssr): Throw error during namelist build if tillage is called with FATES + if (.not. present(idop)) then + call endrun("Do not call tillage without providing idop. (Maybe you called with FATES?)") end if - call get_apply_tillage_multipliers(idop, num_soilp, filter_soilp, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if ! Above into soil matrix From aefd94ab9669c99285031c44389faa197bd9f6d3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 1 Jun 2023 16:49:25 -0600 Subject: [PATCH 0980/2067] Is it that crop columns have multiple patches but only 1 is active? --- src/biogeochem/TillageMod.f90 | 30 +++++++++++++++++++++--------- 1 file changed, 21 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 4b5e78d0ef..91e758867e 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -337,19 +337,31 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES - integer :: p, j + integer :: p, this_patch, j - ! This subroutine should only ever be called for crop columns... - p = col%patchi(c) - if (patch%itype(p) < npcropmin) then - call endrun('ERROR tillage code should only be called for crops') + if (.not. col%active(c)) then + return end if - ! ... and those should only ever have one patch. - if (p /= col%patchf(c)) then - call endrun('ERROR tillage code assumes one patch per column') + + ! This subroutine should only ever be called for crop columns... + this_patch = 0 + do p = col%patchi(c),col%patchf(c) + if (patch%active(p)) then + if (patch%itype(p) >= npcropmin) then + if (this_patch > 0) then + call endrun('ERROR multiple active crop patches found in this column') + end if + this_patch = p + else + call endrun('ERROR active non-crop patch found in this column') + end if + end if + end do + if (this_patch == 0) then + call endrun('ERROR no active patches found in this active column') end if - call get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers(idop, this_patch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham From e9092704301b973d4e9b99f64aa03a8a121b1175 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 1 Jun 2023 17:09:38 -0600 Subject: [PATCH 0981/2067] Is it that my filtering of non-crop columns didn't work? --- src/biogeochem/TillageMod.f90 | 14 ++++++++++---- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 2 +- 2 files changed, 11 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 91e758867e..f0d814c80e 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -337,7 +337,7 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES - integer :: p, this_patch, j + integer :: p, this_patch, j, n_noncrop if (.not. col%active(c)) then return @@ -345,6 +345,7 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som ! This subroutine should only ever be called for crop columns... this_patch = 0 + n_noncrop = 0 do p = col%patchi(c),col%patchf(c) if (patch%active(p)) then if (patch%itype(p) >= npcropmin) then @@ -353,12 +354,17 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som end if this_patch = p else - call endrun('ERROR active non-crop patch found in this column') + n_noncrop = n_noncrop + 1 end if end if end do - if (this_patch == 0) then - call endrun('ERROR no active patches found in this active column') + if (n_noncrop > 0) then + if (this_patch > 0) then + call endrun('ERROR Active crop and non-crop patches found in this active column') + end if + return + elseif (this_patch == 0) then + call endrun('ERROR No active patches found (crop OR non-crop)') end if call get_tillage_multipliers(idop, this_patch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 5fa478eda6..2a1ea8810f 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -902,7 +902,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & end if ! Tillage - if (get_do_tillage() .and. col%lun_itype(c) == istcrop) then + if (get_do_tillage()) then ! TODO(ssr): Throw error during namelist build if tillage is called with FATES if (.not. present(idop)) then call endrun("Do not call tillage without providing idop. (Maybe you called with FATES?)") From 4a447d46831e27e5e6e2ba306e77c6ecdebdb6a0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 1 Jun 2023 17:25:10 -0600 Subject: [PATCH 0982/2067] Added TODO: Figure out how to simply identify crop columns. --- src/biogeochem/TillageMod.f90 | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index f0d814c80e..884680eaea 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -343,7 +343,9 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som return end if - ! This subroutine should only ever be called for crop columns... + ! TODO: Figure out why adding ".and. col%lun_itype(c) == istcrop" to conditional + ! controlling call of this subroutine didn't properly exclude non-crop columns. + ! That working would allow simplification here. this_patch = 0 n_noncrop = 0 do p = col%patchi(c),col%patchf(c) From 5dda283437598005cc47a1ce1486591fb5646abe Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 1 Jun 2023 15:46:12 -0600 Subject: [PATCH 0983/2067] Only set tillage_mults(:) = 1 once per get_tillage_multipliers*() subroutine. --- src/biogeochem/TillageMod.f90 | 46 +++-------------------------------- 1 file changed, 4 insertions(+), 42 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 884680eaea..802a97a507 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -166,44 +166,25 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting ! corn, soy : P C D & HW-7 30 d aftr - if (day < idop(p)) then - tillage_mults(:) = 1._r8 - else if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(:) = 1._r8 + tillage_mults(:) = 1._r8 + if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers - tillage_mults(:) = 1._r8 tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 else if (day >= idop(p)+45 .and. day = idop(p)+75 .and. day < idop(p)+80) then ! June 14 - tillage_mults(:) = 1._r8 - ! TODO(ssr): Check with Mike and Danica: Why this extra code? These should already all be 1. - if (patch%itype(p) == ntmp_corn .or. & - patch%itype(p) == nirrig_tmp_corn .or. & - patch%itype(p) == ntmp_soybean .or. & - patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(i_cel_lit) = 1.00_r8 - tillage_mults(i_lig_lit) = 1.00_r8 - tillage_mults(i_act_som) = 1.00_r8 - tillage_mults(i_slo_som) = 1.00_r8 - tillage_mults(i_pas_som) = 1.00_r8 - end if - else if (day >= idop(p)+80) then ! July 14 - tillage_mults(:) = 1._r8 end if end subroutine get_tillage_multipliers_orig @@ -255,44 +236,25 @@ subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting ! corn, soy : P C D & HW-7 30 d aftr - if (idpp < 0) then - tillage_mults(:) = 1._r8 - else if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(:) = 1._r8 + tillage_mults(:) = 1._r8 + if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 else if (idpp < 45) then ! based on Field and Row Cultivator multipliers - tillage_mults(:) = 1._r8 tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 else if (idpp < 75) then ! based on Rod Weed Row Planter - tillage_mults(:) = 1._r8 tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 - else if (idpp < 80) then ! June 14 - tillage_mults(:) = 1._r8 - ! TODO(ssr): Check with Mike and Danica: Why this extra code? These should already all be 1. - if (patch%itype(p) == ntmp_corn .or. & - patch%itype(p) == nirrig_tmp_corn .or. & - patch%itype(p) == ntmp_soybean .or. & - patch%itype(p) == nirrig_tmp_soybean ) then - tillage_mults(i_cel_lit) = 1.00_r8 - tillage_mults(i_lig_lit) = 1.00_r8 - tillage_mults(i_act_som) = 1.00_r8 - tillage_mults(i_slo_som) = 1.00_r8 - tillage_mults(i_pas_som) = 1.00_r8 - end if - else ! July 14 - tillage_mults(:) = 1._r8 end if end subroutine get_tillage_multipliers_new From 34bc33c6a567a6f3766e3d358a7b399d97a5cbe1 Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 2 Jun 2023 09:05:55 +0200 Subject: [PATCH 0984/2067] fix pelayout for default and add L option --- cime_config/config_pes.xml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 0f91f049d2..c73ec414eb 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -1400,13 +1400,13 @@ 0 - -3 - -3 - -3 - -3 - -3 - -3 - -3 + -1 + -1 + -1 + -1 + -1 + -1 + -1 From 2453126f542a4d26440ff24fc60a74166e71b60c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 10:26:47 -0600 Subject: [PATCH 0985/2067] Removed unneeded patch stuff from tillage_init(). --- src/biogeochem/TillageMod.f90 | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 802a97a507..94d4fb6ab3 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -51,10 +51,11 @@ subroutine tillage_init(bounds) use decompMod , only : bounds_type ! ! !ARGUMENTS + ! SSR: Not sure why this is necessary, but without it, CTSM stalls out + ! (although it seems to successfully complete this subroutine). type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES - integer :: begp, endp ! indices for allocating patch dimension integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag integer :: mpicom ! MPI communicator @@ -106,8 +107,6 @@ subroutine tillage_init(bounds) ! Allocate variables if (get_do_tillage()) then - begp = bounds%begp - endp = bounds%endp allocate(tillage_mults(ndecomp_pools)) ; tillage_mults(:) = 1.0_r8 end if From 6c4a6e7a1b3267c2753b05dfb485918f339392cc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 10:43:12 -0600 Subject: [PATCH 0986/2067] Removed unused indices from get_tillage_multipliers*(). --- src/biogeochem/TillageMod.f90 | 6 ------ 1 file changed, 6 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 94d4fb6ab3..eb76a28ea7 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -137,7 +137,6 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som ! ! !LOCAL VARIABLES: ! - integer :: fp, g ! Indices integer :: day ! julian day integer :: idpp ! days past planting real(r8) dayspyr ! days per year @@ -147,8 +146,6 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som day = get_curr_calday() dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine - g = patch%gridcell(p) - ! days past planting may determine harvest/tillage ! SSR: Unused! if (day >= idop(p)) then @@ -208,7 +205,6 @@ subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, ! ! !LOCAL VARIABLES: ! - integer :: fp, g ! Indices integer :: day ! julian day integer :: idpp ! days past planting real(r8) dayspyr ! days per year @@ -218,8 +214,6 @@ subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, day = get_curr_calday() dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine - g = patch%gridcell(p) - ! days past planting may determine harvest/tillage if (day >= idop(p)) then idpp = day - idop(p) From f1732c774485561009423010033709d4fa89946b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 10:55:40 -0600 Subject: [PATCH 0987/2067] Simplified specification of tillage multipliers. --- src/biogeochem/TillageMod.f90 | 77 +++++++++++++++++++---------------- 1 file changed, 42 insertions(+), 35 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index eb76a28ea7..8462b6f496 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -32,7 +32,9 @@ module TillageMod logical :: do_tillage_low ! Do low-intensity tillage? logical :: do_tillage_high ! Do high-intensity tillage? logical :: use_original_tillage ! Use get_tillage_multipliers_orig? - real(r8), pointer :: tillage_mults(:) + real(r8), pointer :: tillage_mults(:) ! (ndecomp_pools) + real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) + integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) !============================================================================== @@ -105,9 +107,10 @@ subroutine tillage_init(bounds) call endrun(subname // ':: ERROR high-intensity tillage not yet set up') endif - ! Allocate variables + ! Allocate tillage multipliers if (get_do_tillage()) then - allocate(tillage_mults(ndecomp_pools)) ; tillage_mults(:) = 1.0_r8 + allocate(tillage_mults(ndecomp_pools)); tillage_mults(:) = 1.0_r8 + allocate(tillage_mults_allphases(ndecomp_pools, nphases)); tillage_mults_allphases(:,:) = 1.0_r8 end if end subroutine tillage_init @@ -139,6 +142,7 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som ! integer :: day ! julian day integer :: idpp ! days past planting + integer :: phase ! which tillage phase are we in? real(r8) dayspyr ! days per year !----------------------------------------------------------------------- @@ -162,25 +166,21 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting ! corn, soy : P C D & HW-7 30 d aftr - tillage_mults(:) = 1._r8 + phase = 0 if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 + phase = 1 else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 + phase = 2 else if (day >= idop(p)+45 .and. day 0) then + if (phase > nphases) then + call endrun(msg='Tillage phase > nphases') + end if + tillage_mults = tillage_mults_allphases(:, phase) end if end subroutine get_tillage_multipliers_orig @@ -207,6 +207,7 @@ subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, ! integer :: day ! julian day integer :: idpp ! days past planting + integer :: phase ! which tillage phase are we in? real(r8) dayspyr ! days per year !----------------------------------------------------------------------- @@ -229,25 +230,21 @@ subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting ! corn, soy : P C D & HW-7 30 d aftr - tillage_mults(:) = 1._r8 + phase = 0 if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.80,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.20,low 1.00 - tillage_mults(i_slo_som) = 3.00_r8 !high 4.80,low 3.00 - tillage_mults(i_pas_som) = 3.00_r8 !high 4.80,low 3.00 + phase = 1 else if (idpp < 45) then ! based on Field and Row Cultivator multipliers - tillage_mults(i_cel_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_lig_lit) = 1.50_r8 !high 1.50,low 1.50 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.60_r8 !high 3.50,low 1.60 - tillage_mults(i_pas_som) = 1.60_r8 !high 3.50,low 1.60 + phase = 2 else if (idpp < 75) then ! based on Rod Weed Row Planter - tillage_mults(i_cel_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(i_lig_lit) = 1.10_r8 !high 1.10,low 1.10 - tillage_mults(i_act_som) = 1.00_r8 !high 1.00,low 1.00 - tillage_mults(i_slo_som) = 1.30_r8 !high 2.50,low 1.30 - tillage_mults(i_pas_som) = 1.30_r8 !high 2.50,low 1.30 + phase = 3 + end if + + tillage_mults(:) = 1._r8 + if (phase > 0) then + if (phase > nphases) then + call endrun(msg='Tillage phase > nphases') + end if + tillage_mults = tillage_mults_allphases(:, phase) end if end subroutine get_tillage_multipliers_new @@ -324,6 +321,16 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som call endrun('ERROR No active patches found (crop OR non-crop)') end if + ! Set up tillage multipliers + ! (It would be better to do this in tillage_init, but that can't happen + ! because these indices are private members of SoilBiogeochemDecompCascadeBGCMod. + tillage_mults_allphases(:,:) = 1.0_r8 + tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) + tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + call get_tillage_multipliers(idop, this_patch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm From e80cfdf6b04fa9a3bb56e4dc6768ac2a2851cf59 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 11:01:13 -0600 Subject: [PATCH 0988/2067] Merged get_tillage_multipliers*() subroutines. --- src/biogeochem/TillageMod.f90 | 111 ++++++---------------------------- 1 file changed, 18 insertions(+), 93 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 8462b6f496..579a53a205 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -122,12 +122,13 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and - ! cultivation is turned on. Created by Sam Levis, modified by Michael Graham - ! to use days past planting. + ! cultivation is turned on. Created by Sam Levis. Modified by Michael Graham + ! to use days past planting. Modified by Sam Rabin to include "new" version + ! that *actually* uses days past planting. ! ! !USES: use clm_time_manager, only : get_curr_calday, get_curr_days_per_year @@ -151,7 +152,6 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine ! days past planting may determine harvest/tillage - ! SSR: Unused! if (day >= idop(p)) then idpp = day - idop(p) else @@ -167,76 +167,23 @@ subroutine get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som ! corn, soy : P C D & HW-7 30 d aftr phase = 0 - if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers - phase = 1 - else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers - phase = 2 - else if (day >= idop(p)+45 .and. day 0) then - if (phase > nphases) then - call endrun(msg='Tillage phase > nphases') + if (use_original_tillage) then + if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers + phase = 1 + else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers + phase = 2 + else if (day >= idop(p)+45 .and. day = idop(p)) then - idpp = day - idop(p) else - idpp = int(dayspyr) + day - idop(p) - end if - - ! ----------------------------------------------------- - ! 3) assigning cultivation practices and mapping to the - ! effect on soil C decomposition - ! ----------------------------------------------------- - ! info from DAYCENT (Melannie Hartman CSU) - ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting - ! corn, soy : P C D & HW-7 30 d aftr - - phase = 0 - if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers - phase = 1 - else if (idpp < 45) then ! based on Field and Row Cultivator multipliers - phase = 2 - else if (idpp < 75) then ! based on Rod Weed Row Planter - phase = 3 + if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers + phase = 1 + else if (idpp < 45) then ! based on Field and Row Cultivator multipliers + phase = 2 + else if (idpp < 75) then ! based on Rod Weed Row Planter + phase = 3 + end if end if tillage_mults(:) = 1._r8 @@ -247,28 +194,6 @@ subroutine get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, tillage_mults = tillage_mults_allphases(:, phase) end if - end subroutine get_tillage_multipliers_new - - - ! Public interface to choose between and call either get_tillage_multipliers_orig() or get_tillage_multipliers_new() - subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) - ! !DESCRIPTION: - ! - ! Public interface to choose between and call either original (buggy) or - ! new (fixed), depending on use_original_tillage true or false. - ! - ! !ARGUMENTS: - integer , intent(in) :: idop(:) ! patch day of planting - integer , intent(in) :: p ! index of patch this is being called for - integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools - integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools - - if (use_original_tillage) then - call get_tillage_multipliers_orig(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) - else - call get_tillage_multipliers_new(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) - end if - end subroutine get_tillage_multipliers From 6c36b206416961dfe2e0ee579d9012a5760adb87 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 11:05:13 -0600 Subject: [PATCH 0989/2067] Simplify application of tillage multipliers. --- src/biogeochem/TillageMod.f90 | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 579a53a205..2893fbb2fe 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -261,12 +261,7 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham do j = 1,5 - ! TODO(ssr): Loop through ALL pools, not just the ones that currently have non-1 values - decomp_k(c,j,i_cel_lit) = decomp_k(c,j,i_cel_lit) * tillage_mults(i_cel_lit) - decomp_k(c,j,i_lig_lit) = decomp_k(c,j,i_lig_lit) * tillage_mults(i_lig_lit) - decomp_k(c,j,i_act_som) = decomp_k(c,j,i_act_som) * tillage_mults(i_act_som) - decomp_k(c,j,i_slo_som) = decomp_k(c,j,i_slo_som) * tillage_mults(i_slo_som) - decomp_k(c,j,i_pas_som) = decomp_k(c,j,i_pas_som) * tillage_mults(i_pas_som) + decomp_k(c,j,:) = decomp_k(c,j,:) * tillage_mults(:) end do end subroutine get_apply_tillage_multipliers From 879e2852c401489fd44fb24a3d8a1f3f98711104 Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 2 Jun 2023 16:32:37 -0600 Subject: [PATCH 0990/2067] fixing shell commands --- cime_config/usermods_dirs/NEON/MLBS/shell_commands | 2 +- cime_config/usermods_dirs/NEON/MOAB/shell_commands | 2 +- cime_config/usermods_dirs/NEON/NIWO/shell_commands | 2 +- cime_config/usermods_dirs/NEON/ONAQ/shell_commands | 2 +- cime_config/usermods_dirs/NEON/WREF/shell_commands | 2 +- cime_config/usermods_dirs/NEON/YELL/shell_commands | 2 +- cime_config/usermods_dirs/NEON/defaults/shell_commands | 1 + 7 files changed, 7 insertions(+), 6 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 54d854e1b0..412a4cf621 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LAT=37.37783 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME=='NEON'] +if [ $CLM_USRDAT_NAME == 'NEON'] then ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 93ca5e2870..0d8c64e911 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LAT=38.25136 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [$CLM_USRDAT_NAME=='NEON']; then +if [$CLM_USRDAT_NAME == 'NEON' ]; then ./xmlchange DATM_YR_END=2020 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index a33719a0b4..d0a4f2bd44 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LAT=40.05236 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME=="NEON" ] +if [ $CLM_USRDAT_NAME == "NEON" ] then ./xmlchange DATM_YR_END=2018 fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 6185167008..bc0ac91f99 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LAT=40.17760 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME=='NEON' ] +if [ $CLM_USRDAT_NAME == 'NEON' ] then ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index ace585a894..f2e9300745 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -5,7 +5,7 @@ ./xmlchange DATM_YR_ALIGN=2019 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME=='NEON' ] +if [ $CLM_USRDAT_NAME == 'NEON' ] then # Different default start date and number of months to run for transient case ./xmlchange DATM_YR_START=2019 diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index a490e044b9..5ce31e6b05 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -5,7 +5,7 @@ ./xmlchange DATM_YR_ALIGN=2019 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME=='NEON' ] +if [ $CLM_USRDAT_NAME == 'NEON' ] then # Different default start date and number of months to run for transient case ./xmlchange DATM_YR_START=2019 diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index d7173100be..453c7d0ee3 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -11,6 +11,7 @@ # Set years to run forcing data over ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 compset=`./xmlquery COMPSET --value` +CLM_USRDAT_NAME=`./xmlquery CLM_USRDAT_NAME --value` # For a transient case run the whole length and don't cycle if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2022 From fe0f8ec3f415550efe76dbef5189baf6f4e169fe Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 2 Jun 2023 16:33:22 -0600 Subject: [PATCH 0991/2067] correcting pft at NEON TOOL site --- tools/site_and_regional/neon_sites_dompft.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/site_and_regional/neon_sites_dompft.csv b/tools/site_and_regional/neon_sites_dompft.csv index 8fb9600f0f..7ce02ad785 100644 --- a/tools/site_and_regional/neon_sites_dompft.csv +++ b/tools/site_and_regional/neon_sites_dompft.csv @@ -40,7 +40,7 @@ 39,SJER,17,37.107117, -119.73300,13,2019,2021 40,SOAP,17,37.032690, -119.26210,1,2018,2021 41,TEAK,17,37.006472,-119.005758,1,2019,2021 -42,TOOL,17, 68.66045,-149.370128,1,2020,2021 +42,TOOL,17, 68.66045,-149.370128,11,2020,2021 43,BARR,18,71.281711,-156.650219,12,2019,2021 44,BONA,19, 65.15333, -147.50194,2,2018,2021 45,DEJU,19, 63.87983, -145.74765,2,2018,2021 From aaf20aae2afab77cfbacb4c005245b649f46b193 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 16:19:30 -0600 Subject: [PATCH 0992/2067] Tillage params now duplicated as private vars. --- src/biogeochem/TillageMod.f90 | 24 +++++++++++++++++++----- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index 2893fbb2fe..b577c257cd 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -29,9 +29,15 @@ module TillageMod public :: get_apply_tillage_multipliers ! ! !PRIVATE DATA MEMBERS - logical :: do_tillage_low ! Do low-intensity tillage? - logical :: do_tillage_high ! Do high-intensity tillage? - logical :: use_original_tillage ! Use get_tillage_multipliers_orig? + ! SSR: I want to keep these logical input parameters private, since there's + ! no obvious need for them to be public. However, that results in segfaults + ! (SIGSEGV(11)) when tillage_innit() calls shr_mpi_bcast. I think it would + ! work if these variables were private, but instead, I just appended the + ! _private suffix here and use the non-"_private" variable names for local + ! variables in tillage_init(). + logical :: do_tillage_low_private ! Do low-intensity tillage? + logical :: do_tillage_high_private ! Do high-intensity tillage? + logical :: use_original_tillage_private ! Use get_tillage_multipliers_orig? real(r8), pointer :: tillage_mults(:) ! (ndecomp_pools) real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) @@ -62,6 +68,9 @@ subroutine tillage_init(bounds) integer :: nml_error ! namelist i/o error flag integer :: mpicom ! MPI communicator character(*), parameter :: subname = "('tillage_init')" + logical :: do_tillage_low ! Do low-intensity tillage? + logical :: do_tillage_high ! Do high-intensity tillage? + logical :: use_original_tillage ! Use get_tillage_multipliers_orig? namelist /tillage_inparm/ & do_tillage_low, & @@ -107,6 +116,11 @@ subroutine tillage_init(bounds) call endrun(subname // ':: ERROR high-intensity tillage not yet set up') endif + ! Assign these + do_tillage_low_private = do_tillage_low + do_tillage_high_private = do_tillage_high + use_original_tillage_private = use_original_tillage + ! Allocate tillage multipliers if (get_do_tillage()) then allocate(tillage_mults(ndecomp_pools)); tillage_mults(:) = 1.0_r8 @@ -118,7 +132,7 @@ end subroutine tillage_init function get_do_tillage() logical :: get_do_tillage - get_do_tillage = do_tillage_low .or. do_tillage_high + get_do_tillage = do_tillage_low_private .or. do_tillage_high_private end function get_do_tillage @@ -168,7 +182,7 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c phase = 0 - if (use_original_tillage) then + if (use_original_tillage_private) then if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers phase = 1 else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers From 6e1102f0cf896fa5086e9eb9e329875770f49acf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 15:53:13 -0600 Subject: [PATCH 0993/2067] Added tillage params to namelist_defaults_ctsm.xml. --- bld/namelist_files/namelist_defaults_ctsm.xml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6bb5d60aa7..53aa46fc28 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2699,4 +2699,12 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 general + + + + +.false. +.false. +.false. + From 6fedb425e3d84854a4742e18f19f871144854e85 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 16:47:37 -0600 Subject: [PATCH 0994/2067] Added high-intensity tillage from Mike Graham's code. --- src/biogeochem/TillageMod.f90 | 22 +++++++++++++--------- 1 file changed, 13 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index b577c257cd..e988e8ae69 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -112,10 +112,6 @@ subroutine tillage_init(bounds) call endrun(subname // ':: ERROR do_tillage_low and do_tillage_high are mutually exclusive') endif - if (do_tillage_high) then - call endrun(subname // ':: ERROR high-intensity tillage not yet set up') - endif - ! Assign these do_tillage_low_private = do_tillage_low do_tillage_high_private = do_tillage_high @@ -264,11 +260,19 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som ! (It would be better to do this in tillage_init, but that can't happen ! because these indices are private members of SoilBiogeochemDecompCascadeBGCMod. tillage_mults_allphases(:,:) = 1.0_r8 - tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) - tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) - tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + if (do_tillage_low_private) then + tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) + tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + else + tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_act_som,:) = (/ 1.2_r8, 1.0_r8, 1.0_r8 /) + tillage_mults_allphases(i_slo_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) + tillage_mults_allphases(i_pas_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) + end if call get_tillage_multipliers(idop, this_patch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) From eb42243cfc9fe31a0ef44b86bfd98e9bf85ed79e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 2 Jun 2023 16:50:24 -0600 Subject: [PATCH 0995/2067] Removed a check from tillage_init() that was already in CLMBuildNamelist.pm. --- src/biogeochem/TillageMod.f90 | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.f90 index e988e8ae69..2b6c06368f 100644 --- a/src/biogeochem/TillageMod.f90 +++ b/src/biogeochem/TillageMod.f90 @@ -108,10 +108,6 @@ subroutine tillage_init(bounds) write(iulog,*) ' use_original_tillage = ',use_original_tillage endif - if (do_tillage_low .and. do_tillage_high) then - call endrun(subname // ':: ERROR do_tillage_low and do_tillage_high are mutually exclusive') - endif - ! Assign these do_tillage_low_private = do_tillage_low do_tillage_high_private = do_tillage_high From 9abe85abff5915d1a0fa6208f03981fedcf836c5 Mon Sep 17 00:00:00 2001 From: John Alex Date: Wed, 7 Jun 2023 06:06:53 -0600 Subject: [PATCH 0996/2067] Add more documentation to history tape code: * Add more breadcrumbs between related variables and methods * Put related namelist flags/methods together * Update some out of date comments Doc-only change. --- src/main/histFileMod.F90 | 173 ++++++++++++++++++++++----------------- 1 file changed, 99 insertions(+), 74 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index d5175342f0..25021fdc29 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -69,8 +69,6 @@ module histFileMod ! Namelist ! integer :: ni ! implicit index below - logical, public :: & - hist_empty_htapes = .false. ! namelist: flag indicates no default history fields integer, public :: & hist_ndens(max_tapes) = 2 ! namelist: output density of netcdf history files integer, public :: & @@ -84,75 +82,86 @@ module histFileMod character(len=max_namlen), public :: & hist_type1d_pertape(max_tapes) = (/(' ',ni=1,max_tapes)/) ! namelist: per tape type1d - character(len=max_namlen+2), public :: & - fincl(max_flds,max_tapes) ! namelist-equivalence list of fields to add + logical, public :: & + hist_empty_htapes = .false. ! namelist: disable default-active history fields (which + ! only exist on history tape 1). Overridden by hist_fincl1 + ! flag. character(len=max_namlen+2), public :: & - hist_fincl1(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl1(max_flds) = ' ' ! namelist: list of fields to include in history tape 1 character(len=max_namlen+2), public :: & - hist_fincl2(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl2(max_flds) = ' ' ! namelist: list of fields to include in history tape 2 character(len=max_namlen+2), public :: & - hist_fincl3(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl3(max_flds) = ' ' ! namelist: list of fields to include in history tape 3 character(len=max_namlen+2), public :: & - hist_fincl4(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl4(max_flds) = ' ' ! namelist: list of fields to include in history tape 4 character(len=max_namlen+2), public :: & - hist_fincl5(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl5(max_flds) = ' ' ! namelist: list of fields to include in history tape 5 character(len=max_namlen+2), public :: & - hist_fincl6(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl6(max_flds) = ' ' ! namelist: list of fields to include in history tape 6 character(len=max_namlen+2), public :: & - hist_fincl7(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl7(max_flds) = ' ' ! namelist: list of fields to include in history tape 7 character(len=max_namlen+2), public :: & - hist_fincl8(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl8(max_flds) = ' ' ! namelist: list of fields to include in history tape 8 character(len=max_namlen+2), public :: & - hist_fincl9(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl9(max_flds) = ' ' ! namelist: list of fields to include in history tape 9 character(len=max_namlen+2), public :: & - hist_fincl10(max_flds) = ' ' ! namelist: list of fields to add + hist_fincl10(max_flds) = ' ' ! namelist: list of fields to include in history tape 10 character(len=max_namlen+2), public :: & - fexcl(max_flds,max_tapes) ! namelist-equivalence list of fields to remove + fincl(max_flds,max_tapes) ! copy of hist_fincl* fields in 2-D format. Note Fortran + ! used to have a bug in 2-D namelists, thus this workaround. character(len=max_namlen+2), public :: & - hist_fexcl1(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl1(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 1 character(len=max_namlen+2), public :: & - hist_fexcl2(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl2(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl3(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl3(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl4(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl4(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl5(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl5(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl6(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl6(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl7(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl7(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl8(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl8(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl9(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl9(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl10(max_flds) = ' ' ! namelist: list of fields to remove + hist_fexcl10(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + + character(len=max_namlen+2), public :: & + fexcl(max_flds,max_tapes) ! copy of hist_fexcl* fields in 2-D format. Note Fortran + ! used to have a bug in 2-D namelists, thus this workaround. logical, private :: if_disphist(max_tapes) ! restart, true => save history file ! - ! !PUBLIC MEMBER FUNCTIONS: + ! !PUBLIC MEMBER FUNCTIONS: (in rough call order) public :: hist_addfld1d ! Add a 1d single-level field to the master field list public :: hist_addfld2d ! Add a 2d multi-level field to the master field list - public :: hist_addfld_decomp ! Add a 2d multi-level field to the master field list + public :: hist_addfld_decomp ! Add a 1d/2d field based on patch or column data public :: hist_add_subscript ! Add a 2d subscript dimension + public :: hist_printflds ! Print summary of master field list - public :: hist_htapes_build ! Initialize history file handler for initial or continue run - public :: hist_update_hbuf ! Updates history buffer for all fields and tapes + public :: htapes_fieldlist ! Finalize history file field lists, intersecting masterlist with + ! namelist params. + + public :: hist_htapes_build ! Initialize history file handler (for initial or continued run) + public :: hist_update_hbuf ! Accumulate into history buffer (all fields and tapes) public :: hist_htapes_wrapup ! Write history tape(s) + public :: hist_restart_ncd ! Read/write history file restart data - public :: htapes_fieldlist ! Define the contents of each history file based on namelist ! ! !PRIVATE MEMBER FUNCTIONS: private :: is_mapping_upto_subgrid ! Is this field being mapped up to a higher subgrid level? - private :: masterlist_make_active ! Add a field to a history file default "on" list + private :: masterlist_make_active ! Declare a single field active for a single tape private :: masterlist_addfld ! Add a field to the master field list private :: masterlist_change_timeavg ! Override default history tape contents for specific tape - private :: htape_addfld ! Add a field to the active list for a history tape - private :: htape_create ! Define contents of history file t + private :: htape_addfld ! Transfer field metadata from masterlist to a history tape. + private :: htape_create ! Define netcdf metadata of history file t private :: htape_add_ltype_metadata ! Add global metadata defining landunit types private :: htape_add_ctype_metadata ! Add global metadata defining column types private :: htape_add_natpft_metadata ! Add global metadata defining natpft types @@ -171,7 +180,7 @@ module histFileMod private :: set_hist_filename ! Determine history dataset filenames private :: getname ! Retrieve name portion of input "inname" private :: getflag ! Retrieve flag - private :: pointer_index ! Track data pointer indices + private :: next_history_pointer_index ! Latest index into raw history data (clmptr_r*) arrays private :: max_nFields ! The max number of fields on any tape private :: avgflag_valid ! Whether a given avgflag is a valid option private :: add_landunit_mask_metadata ! Add landunit_mask metadata for the given history field @@ -205,13 +214,14 @@ module histFileMod ! for 2D arrays, where the second dimension is allowed ! to be 1 integer :: num2d ! size of hbuf second dimension (e.g. number of vertical levels) - integer :: hpindex ! history pointer index + integer :: hpindex ! index into raw history data (clmptr_r*) arrays character(len=scale_type_strlen) :: p2c_scale_type ! scale factor when averaging patch to column character(len=scale_type_strlen) :: c2l_scale_type ! scale factor when averaging column to landunit character(len=scale_type_strlen) :: l2g_scale_type ! scale factor when averaging landunit to gridcell integer :: no_snow_behavior ! for multi-layer snow fields, flag saying how to treat times when a given snow layer is absent end type field_info + ! Metadata about a single history field. type, abstract :: entry_base type (field_info) :: field ! field information contains @@ -227,13 +237,17 @@ subroutine copy_entry_interface(this, other) end subroutine copy_entry_interface end interface + ! Additional per-field metadata. See also history_entry. + ! These values are specified in hist_addfld* calls but then can be + ! overridden by namelist params like hist_fincl1. type, extends(entry_base) :: master_entry - logical :: actflag(max_tapes) ! active/inactive flag - character(len=avgflag_strlen) :: avgflag(max_tapes) ! time averaging flag + logical :: actflag(max_tapes) ! which history tapes to write to. + character(len=avgflag_strlen) :: avgflag(max_tapes) ! type of time averaging contains procedure :: copy => copy_master_entry end type master_entry + ! Actual per-field history data, accumulated from clmptr_r* vars. See also master_entry. type, extends(entry_base) :: history_entry character(len=avgflag_strlen) :: avgflag ! time averaging flag ("X","A","M","I","SUM") real(r8), pointer :: hbuf(:,:) ! history buffer (dimensions: dim1d x num2d) @@ -242,6 +256,11 @@ end subroutine copy_entry_interface procedure :: copy => copy_history_entry end type history_entry + ! Each 'history tape' accumulates output values for a set of fields marked 'active' for this run, + ! at a given time frequency and precision. The first ('primary') tape defaults to a non-empty set + ! of active fields (see hist_addfld* methods), overridable by namelist flags, while the other + ! tapes are entirely manually configured via namelist flags. The set of active fields across all + ! tapes is assembled in the 'masterlist' variable. type history_tape integer :: nflds ! number of active fields on tape integer :: ntimes ! current number of time samples on tape @@ -251,7 +270,8 @@ end subroutine copy_entry_interface logical :: dov2xy ! true => do xy average for all fields logical :: is_endhist ! true => current time step is end of history interval real(r8) :: begtime ! time at beginning of history averaging interval - type (history_entry) :: hlist(max_flds) ! array of active history tape entries + type (history_entry) :: hlist(max_flds) ! array of active history tape entries. + ! The ordering matches the masterlist's. end type history_tape type clmpoint_rs ! Pointer to real scalar data (1D) @@ -261,12 +281,16 @@ end subroutine copy_entry_interface real(r8), pointer :: ptr(:,:) end type clmpoint_ra - ! Pointers into datatype arrays + ! Raw history field data (not accumulated). One entry per history field, indexed by 'hpindex' + ! aka the history pointer index. For accumulated values see 'tape'. integer, parameter :: max_mapflds = 2500 ! Maximum number of fields to track type (clmpoint_rs) :: clmptr_rs(max_mapflds) ! Real scalar data (1D) type (clmpoint_ra) :: clmptr_ra(max_mapflds) ! Real array data (2D) ! - ! Master list: an array of master_entry entities + ! History field metadata including which history tapes (if any) it should be output to, and + ! type of accumulation to perform. The field ordering is arbitrary, depending on the order of + ! hist_addfld* calls in the code. + ! For the field data itself, see 'tape'. ! type (master_entry) :: masterlist(max_flds) ! master field list ! @@ -275,9 +299,11 @@ end subroutine copy_entry_interface ! logical :: history_tape_in_use(max_tapes) ! whether each history tape is in use in this run ! - ! History tape: an array of history_tape entities (only active fields) - ! - type (history_tape) :: tape(max_tapes) ! array history tapes + ! The actual (accumulated) history data for all active fields in each in-use tape. See + ! 'history_tape_in_use' for in-use tapes, and 'masterlist' for active fields. See also + ! clmptr_r* variables for raw history data. + ! + type (history_tape) :: tape(max_tapes) ! array of history tapes ! ! Namelist input ! @@ -289,7 +315,7 @@ end subroutine copy_entry_interface ! character(len=max_length_filename) :: locfnh(max_tapes) ! local history file names character(len=max_length_filename) :: locfnhr(max_tapes) ! local history restart file names - logical :: htapes_defined = .false. ! flag indicates history contents have been defined + logical :: htapes_defined = .false. ! flag indicates history output fields have been selected ! ! NetCDF Id's ! @@ -485,7 +511,7 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & character(len=*), intent(in) :: units ! units of field character(len=*), intent(in) :: avgflag ! time averaging flag character(len=*), intent(in) :: long_name ! long name of field - integer , intent(in) :: hpindex ! data type index for history buffer output + integer , intent(in) :: hpindex ! index into raw history data (clmptr_r*) arrays character(len=*), intent(in) :: p2c_scale_type ! scale type for subgrid averaging of pfts to column character(len=*), intent(in) :: c2l_scale_type ! scale type for subgrid averaging of columns to landunits character(len=*), intent(in) :: l2g_scale_type ! scale type for subgrid averaging of landunits to gridcells @@ -873,7 +899,7 @@ subroutine htapes_fieldlist() if (ff > 0) then ! if field is in include list, ff > 0 and htape_addfld - ! will not be called for field + ! will be called for field avgflag = getflag (fincl(ff,t)) call htape_addfld (t, f, avgflag) @@ -1102,8 +1128,7 @@ end function is_mapping_upto_subgrid subroutine htape_addfld (t, f, avgflag) ! ! !DESCRIPTION: - ! Add a field to the active list for a history tape. Copy the data from - ! the master field list to the active list for the tape. + ! Add a field to a history tape, copying metadata from the master field list ! ! !ARGUMENTS: integer, intent(in) :: t ! history tape index @@ -1127,7 +1152,7 @@ subroutine htape_addfld (t, f, avgflag) character(len=*),parameter :: subname = 'htape_addfld' !----------------------------------------------------------------------- - ! Ensure that it is not to late to add a field to the history tape + ! Ensure that it is not too late to add a field to the history tape if (htapes_defined) then write(iulog,*) trim(subname),' ERROR: attempt to add field ', & @@ -1315,7 +1340,7 @@ subroutine hist_update_hbuf_field_1d (t, f, bounds) type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: - integer :: hpindex ! history pointer index + integer :: hpindex ! index into raw history data (clmptr_r*) arrays integer :: k ! gridcell, landunit, column or patch index integer :: beg1d,end1d ! beginning and ending indices integer :: beg1d_out,end1d_out ! beginning and ending indices on output grid @@ -1680,7 +1705,7 @@ subroutine hist_update_hbuf_field_2d (t, f, bounds, num2d) integer, intent(in) :: num2d ! size of second dimension ! ! !LOCAL VARIABLES: - integer :: hpindex ! history pointer index + integer :: hpindex ! index into raw history data (clmptr_r*) arrays integer :: k ! gridcell, landunit, column or patch index integer :: j ! level index integer :: beg1d,end1d ! beginning and ending indices @@ -2275,8 +2300,7 @@ end subroutine hfields_zero subroutine htape_create (t, histrest) ! ! !DESCRIPTION: - ! Define contents of history file t. Issue the required netcdf - ! wrapper calls to define the history file contents. + ! Define netcdf metadata of history file t. ! ! !USES: use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, nlevurb, nlevmaxurbgrnd, numrad, nlevcan, nvegwcs,nlevsoi @@ -5146,14 +5170,12 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & set_noglc, set_spec, default) ! ! !DESCRIPTION: - ! Initialize a single level history field. The pointer, ptrhist, - ! is a pointer to the data type array that the history buffer will use. + ! Initialize a single level history field. The pointer inputs, ptr\_*, + ! point to the appropriate-type array storing the raw history data points. ! The value of type1d passed to masterlist\_add\_fld determines which of the ! 1d type of the output and the beginning and ending indices the history - ! buffer field). Default history contents for given field on all tapes - ! are set by calling [masterlist\_make\_active] for the appropriate tape. - ! After the masterlist is built, routine [htapes\_build] is called for an - ! initial or branch run to initialize the actual history tapes. + ! buffer field). All fields default to being written to the first history tape + ! unless 'default' is set to 'inactive'. ! ! !ARGUMENTS: character(len=*), intent(in) :: fname ! field name @@ -5197,7 +5219,7 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & ! History buffer pointer - hpindex = pointer_index() + hpindex = next_history_pointer_index() if (present(ptr_lnd)) then l_type1d = grlnd @@ -5366,14 +5388,12 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, no_snow_behavior, default) ! ! !DESCRIPTION: - ! Initialize a single level history field. The pointer, ptrhist, - ! is a pointer to the data type array that the history buffer will use. + ! Initialize a single level history field. The pointer inputs, ptr\_*, + ! point to the appropriate-type array storing the raw history data points. ! The value of type1d passed to masterlist\_add\_fld determines which of the ! 1d type of the output and the beginning and ending indices the history - ! buffer field). Default history contents for given field on all tapes - ! are set by calling [masterlist\_make\_active] for the appropriatae tape. - ! After the masterlist is built, routine [htapes\_build] is called for an - ! initial or branch run to initialize the actual history tapes. + ! buffer field). All fields default to being written to the first history tape + ! unless 'default' is set to 'inactive'. ! ! !USES: use clm_varpar , only : nlevgrnd, nlevsno, nlevlak, numrad, nlevdecomp_full, nlevcan, nvegwcs,nlevsoi @@ -5543,7 +5563,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, end select ! History buffer pointer - hpindex = pointer_index() + hpindex = next_history_pointer_index() if (present(ptr_lnd)) then @@ -5626,7 +5646,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, l_type1d = namep l_type1d_out = namep clmptr_ra(hpindex)%ptr => ptr_patch - + if (present(set_lake)) then do p = bounds%begp,bounds%endp l =patch%landunit(p) @@ -5701,6 +5721,10 @@ subroutine hist_addfld_decomp (fname, type2d, units, avgflag, long_name, ptr_col ptr_patch, l2g_scale_type, default) ! + ! !DESCRIPTION: + ! Adds 1-D or 2-D history field based on column data (if ptr_col is present), + ! patch data (otherwise). + ! ! !USES: use clm_varpar , only : nlevdecomp_full use clm_varctl , only : iulog @@ -5709,7 +5733,7 @@ subroutine hist_addfld_decomp (fname, type2d, units, avgflag, long_name, ptr_col ! ! !ARGUMENTS: character(len=*), intent(in) :: fname ! field name - character(len=*), intent(in) :: type2d ! 2d output type + character(len=*), intent(in) :: type2d ! 2d output type, if 2d output is chosen character(len=*), intent(in) :: units ! units of field character(len=*), intent(in) :: avgflag ! time averaging flag character(len=*), intent(in) :: long_name ! long name of field @@ -5785,18 +5809,19 @@ subroutine hist_addfld_decomp (fname, type2d, units, avgflag, long_name, ptr_col end subroutine hist_addfld_decomp !----------------------------------------------------------------------- - integer function pointer_index () + integer function next_history_pointer_index () ! ! !DESCRIPTION: - ! Set the current pointer index and increment the value of the index. + ! Return the next free index in clmptr_r* arrays (for a new history field to write to) + ! Aka 'hpindex', e.g. field_info.hpindex. ! ! !ARGUMENTS: ! integer, save :: lastindex = 1 - character(len=*),parameter :: subname = 'pointer_index' + character(len=*),parameter :: subname = 'next_history_pointer_index' !----------------------------------------------------------------------- - pointer_index = lastindex + next_history_pointer_index = lastindex lastindex = lastindex + 1 if (lastindex > max_mapflds) then write(iulog,*) trim(subname),' ERROR: ',& @@ -5804,7 +5829,7 @@ integer function pointer_index () call endrun(msg=errMsg(sourcefile, __LINE__)) endif - end function pointer_index + end function next_history_pointer_index !----------------------------------------------------------------------- subroutine hist_add_subscript(name, dim) From 1d3e8d01826c1349a60e2f2c0a1e3b886d3258f9 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 7 Jun 2023 13:26:15 -0400 Subject: [PATCH 0997/2067] Reverting namelist defaults related to NDEP, we were getting ahead of ourselves with fates n-cycling --- bld/namelist_files/namelist_defaults_ctsm.xml | 90 +++++++++---------- 1 file changed, 45 insertions(+), 45 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 8517325c59..44ed52fb7e 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1435,72 +1435,72 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc -2015 -2101 -2015 +2015 +2101 +2015 -2015 -2101 -2015 +2015 +2101 +2015 -2015 -2101 -2015 +2015 +2101 +2015 -2018 -2018 +2018 +2018 -2010 -2010 +2010 +2010 -2000 -2000 +2000 +2000 -1850 -1850 +1850 +1850 -2000 -2000 +2000 +2000 -2000 -2000 +2000 +2000 -2000 -2000 +2000 +2000 -lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc -lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc -lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc +lnd/clm2/ndepdata/fndep_clm_hist_b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.ensmean_1849-2015_monthly_0.9x1.25_c180926.nc share/meshes/fv1.9x2.5_141008_ESMFmesh_c20191001.nc share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP5-8.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP1-2.6-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_f09_g17.CMIP6-SSP2-4.5-WACCM_1849-2101_monthly_c191007.nc -lnd/clm2/ndepdata/fndep_clm_SSP370_b.e21.BWSSP370cmip6.f09_g17.CMIP6-SSP3-7.0-WACCM.002_1849-2101_monthly_0.9x1.25_c211216.nc cycle @@ -1512,14 +1512,14 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts cycle NDEP_month -bilinear +bilinear -nn -nn -nn -nn -nn -nn +nn +nn +nn +nn +nn +nn From 7fa071d5209c279bc1c2fd4f2a1c03a642a6dbe2 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 8 Jun 2023 08:14:48 -0600 Subject: [PATCH 0998/2067] Fixes to build --- src/biogeochem/CNDriverMod.F90 | 14 +++++++------- src/main/clm_driver.F90 | 2 +- .../SoilBiogeochemVerticalProfileMod.F90 | 10 +++++----- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 18a5d22b16..f6be8b6b64 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -803,38 +803,38 @@ subroutine CNDriverNoLeaching(bounds, ! Set gross unrepresented landcover change mortality routine if (get_do_grossunrep()) then - call CNGrossUnrep(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNGrossUnrep(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) end if if ( use_c13 ) then - call CIsoFlux2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2g(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & isotope='c13') end if if ( use_c14 ) then - call CIsoFlux2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2g(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & isotope='c14') end if - call CStateUpdate2g( num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2g( num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, soilbiogeochem_carbonstate_inst) if ( use_c13 ) then - call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2g(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, c13_soilbiogeochem_carbonstate_inst) end if if ( use_c14 ) then - call CStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CStateUpdate2g(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst) end if - call NStateUpdate2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call NStateUpdate2g(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) call t_stopf('CNUpdate2') diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index a83701d884..5fb0d233ec 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -15,7 +15,7 @@ module clm_driver use clm_varctl , only : use_crop, irrigate, ndep_from_cpl use clm_varctl , only : use_soil_moisture_streams use clm_time_manager , only : get_nstep, is_beg_curr_day - use clm_time_manager , only : get_prev_date, is_first_steps + use clm_time_manager , only : get_prev_date, is_first_step use clm_varpar , only : nlevsno, nlevgrnd use clm_varorb , only : obliqr use spmdMod , only : masterproc, mpicom diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 index 49a5215cac..9a15140c76 100644 --- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 @@ -175,21 +175,21 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_bgc_soilc,filter_bgc_soilc, ! col_cinput_rootfr(bounds%begc:bounds%endc, :), & ! 'unity') - !if(num_bgc_vegp>0)then + do fc = 1,num_bgc_soilc c = filter_bgc_soilc(fc) if(.not.col%is_fates(c))then - do pi = 1,col%npatches(c)) !maxsoil_patches + do pi = 1,col%npatches(c) !maxsoil_patches !if (pi <= col%npatches(c)) then p = col%patchi(c) + pi - 1 do j = 1,nlevdecomp col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) end do !end if - end if - end do + end do + end if end do - !end if + ! repeat for column-native profiles: Ndep and Nfix do fc = 1,num_bgc_soilc From 69595564dd9ffd81f14d1b3ae222e4c629d4fc76 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 8 Jun 2023 08:23:29 -0600 Subject: [PATCH 0999/2067] Reverted use_cn filter on ndep namelist settings --- bld/CLMBuildNamelist.pm | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 9468a82a09..53db7393f4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3444,17 +3444,19 @@ sub setup_logic_nitrogen_deposition { # if ( ($nl_flags->{'bgc_mode'} =~/bgc/) or ($nl_flags->{'bgc_mode'} =~/fates/) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'}, - 'hgrid'=>$nl_flags->{'res'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_taxmode', 'phys'=>$nl_flags->{'phys'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndep_varlist', 'phys'=>$nl_flags->{'phys'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'} ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_first_ndep', 'phys'=>$nl_flags->{'phys'}, - 'sim_year'=>$nl_flags->{'sim_year'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_year_last_ndep', 'phys'=>$nl_flags->{'phys'}, - 'sim_year'=>$nl_flags->{'sim_year'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}); # Set align year, if first and last years are different if ( $nl->get_value('stream_year_first_ndep') != $nl->get_value('stream_year_last_ndep') ) { @@ -3462,12 +3464,12 @@ sub setup_logic_nitrogen_deposition { 'sim_year_range'=>$nl_flags->{'sim_year_range'}); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { # Also check at f19 resolution add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_fldfilename_ndep', 'phys'=>$nl_flags->{'phys'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); # If not found report an error if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { @@ -3479,12 +3481,12 @@ sub setup_logic_nitrogen_deposition { } if ($opts->{'driver'} eq "nuopc" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ndep', 'phys'=>$nl_flags->{'phys'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"0.9x1.25", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); if ( ! defined($nl->get_value('stream_fldfilename_ndep') ) ) { # Also check at f19 resolution add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'stream_meshfile_ndep', 'phys'=>$nl_flags->{'phys'}, - 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, + 'use_cn'=>$nl_flags->{'use_cn'}, 'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, 'hgrid'=>"1.9x2.5", 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'nofail'=>1 ); # If not found report an error if ( ! defined($nl->get_value('stream_meshfile_ndep') ) ) { From 80bc7e8c83d91bc8ec59bf847c12246df2d92a8f Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 8 Jun 2023 11:09:08 -0600 Subject: [PATCH 1000/2067] small changes to fix warnings; add print statements for clarity to users --- tools/site_and_regional/run_neon.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 7ec5d7577d..9c8f39d6b0 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -460,6 +460,7 @@ def build_base_case( return case_path print("---- base case build ------") + print("--- This may take a while and you may see WARNING messages ---") # always walk through the build process to make sure it's up to date. t0 = time.time() build.case_build(case_path, case=case) @@ -534,6 +535,9 @@ def run_case( elif not setup_only: print("Resubmitting case {}".format(case_root)) case.submit(no_batch=no_batch) + logger.info("-----------------------------------") + logger.info("Successfully submitted case!") + logger.info("Use 'qstat -u ' to check its run status") return else: logger.warning( @@ -564,7 +568,7 @@ def run_case( ) with Case(case_root, read_only=False) as case: - if run_type is not "transient": + if run_type != "transient": # in order to avoid the complication of leap years we always set the run_length in units of days. case.set_value("STOP_OPTION", "ndays") case.set_value("REST_OPTION", "end") @@ -611,6 +615,9 @@ def run_case( case.check_all_input_data() if not setup_only: case.submit(no_batch=no_batch) + logger.info("-----------------------------------") + logger.info("Successfully submitted case!") + logger.info("Use 'qstat -u ' to check its run status") def set_ref_case(self, case): rundir = case.get_value("RUNDIR") @@ -747,7 +754,7 @@ def parse_neon_listing(listing_file, valid_neon_sites): tmp_df = tmp_df[tmp_df[7].str.contains(latest_version)] # -- remove .nc from the file names - tmp_df[9] = tmp_df[9].str.replace(".nc", "") + tmp_df[9] = tmp_df[9].str.replace(".nc", "", regex=False) tmp_df2 = tmp_df[9].str.split("-", expand=True) @@ -849,6 +856,7 @@ def main(description): rerun, experiment, ) + if __name__ == "__main__": From 27e28ab6fb8821b749a1517ee9abe5cbd0bc4cf6 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 8 Jun 2023 12:19:42 -0600 Subject: [PATCH 1001/2067] preserving b4b on nitrogen variables by referting a filter to allc --- src/biogeochem/CNDriverMod.F90 | 8 +- .../SoilBiogeochemCarbonStateType.F90 | 86 +++++++-------- .../SoilBiogeochemNitrogenStateType.F90 | 102 +++++++++--------- 3 files changed, 98 insertions(+), 98 deletions(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index f6be8b6b64..569866d9ec 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -1173,12 +1173,12 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & ! cnveg summary, swapped call order ! ---------------------------------------------- - call soilbiogeochem_carbonstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonstate_inst) + call soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, cnveg_carbonstate_inst) if ( use_c13 ) then - call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc, c13_cnveg_carbonstate_inst) + call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, c13_cnveg_carbonstate_inst) end if if ( use_c14 ) then - call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc, c14_cnveg_carbonstate_inst) + call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, c14_cnveg_carbonstate_inst) end if @@ -1189,7 +1189,7 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & call cnveg_nitrogenstate_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, & num_bgc_vegp, filter_bgc_vegp) - call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_bgc_soilc, filter_bgc_soilc,cnveg_nitrogenstate_inst) + call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_allc, filter_allc,cnveg_nitrogenstate_inst) call t_stopf('CNsum') diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 70976bc15a..241d7eeb25 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -931,7 +931,7 @@ subroutine SetValues ( this, num_column, filter_column, value_column) end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonstate_inst) + subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_carbonstate_inst) ! ! !DESCRIPTION: ! Perform column-level carbon summary calculations @@ -939,8 +939,8 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst ! !ARGUMENTS: class(soilbiogeochem_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_bgc_soilc ! number of columns in soil filter - integer , intent(in) :: filter_bgc_soilc(:) ! filter for all active columns + integer , intent(in) :: num_allc ! number of columns in soil filter + integer , intent(in) :: filter_allc(:) ! filter for all active columns type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst ! @@ -954,8 +954,8 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst ! vertically integrate each of the decomposing C pools do l = 1, ndecomp_pools - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_cpools_col(c,l) = 0._r8 if(use_soil_matrixcn)then end if @@ -963,8 +963,8 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst end do do l = 1, ndecomp_pools do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_cpools_col(c,l) = & this%decomp_cpools_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j) @@ -979,23 +979,23 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst ! vertically integrate each of the decomposing C pools to 1 meter maxdepth = 1._r8 do l = 1, ndecomp_pools - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_cpools_1m_col(c,l) = 0._r8 end do end do do l = 1, ndecomp_pools do j = 1, nlevdecomp if ( zisoi(j) <= maxdepth ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_cpools_1m_col(c,l) = & this%decomp_cpools_1m_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * dzsoi_decomp(j) end do elseif ( zisoi(j-1) < maxdepth ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_cpools_1m_col(c,l) = & this%decomp_cpools_1m_col(c,l) + & this%decomp_cpools_vr_col(c,j,l) * (maxdepth - zisoi(j-1)) @@ -1009,16 +1009,16 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst ! Add soil carbon pools together to produce vertically-resolved decomposing total soil c pool if ( nlevdecomp_full > 1 ) then do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_soilc_vr_col(c,j) = 0._r8 end do end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_soilc_vr_col(c,j) = this%decomp_soilc_vr_col(c,j) + & this%decomp_cpools_vr_col(c,j,l) end do @@ -1028,13 +1028,13 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst end if ! truncation carbon - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%ctrunc_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%ctrunc_col(c) = & this%ctrunc_col(c) + & this%ctrunc_vr_col(c,j) * dzsoi_decomp(j) @@ -1043,14 +1043,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst ! total litter carbon in the top meter (TOTLITC_1m) if ( nlevdecomp > 1) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitc_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitc_1m_col(c) = this%totlitc_1m_col(c) + & this%decomp_cpools_1m_col(c,l) end do @@ -1060,14 +1060,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst ! total soil organic matter carbon in the top meter (TOTSOMC_1m) if ( nlevdecomp > 1) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomc_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomc_1m_col(c) = this%totsomc_1m_col(c) + this%decomp_cpools_1m_col(c,l) end do end if @@ -1075,42 +1075,42 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst end if ! total microbial carbon (TOTMICC) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totmicc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totmicc_col(c) = this%totmicc_col(c) + this%decomp_cpools_col(c,l) end do endif end do ! total litter carbon (TOTLITC) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitc_col(c) = this%totlitc_col(c) + this%decomp_cpools_col(c,l) end do endif end do ! total soil organic matter carbon (TOTSOMC) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomc_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomc_col(c) = this%totsomc_col(c) + this%decomp_cpools_col(c,l) end do end if @@ -1118,8 +1118,8 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_carbonst - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) ! coarse woody debris carbon this%cwdc_col(c) = 0._r8 diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index f3dc3c06cf..b537d0896e 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -805,14 +805,14 @@ end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogenstate_inst) + subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_nitrogenstate_inst) ! ! !ARGUMENTS: class (soilbiogeochem_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_bgc_soilc ! number of bgc columns in soilc filter - integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc columns + integer , intent(in) :: num_allc ! number of bgc columns in soilc filter + integer , intent(in) :: filter_allc(:) ! filter for bgc columns type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst ! @@ -826,14 +826,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen ! vertically integrate NO3 NH4 N2O pools if (use_nitrif_denitrif) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%smin_no3_col(c) = 0._r8 this%smin_nh4_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%smin_no3_col(c) = & this%smin_no3_col(c) + & this%smin_no3_vr_col(c,j) * dzsoi_decomp(j) @@ -848,15 +848,15 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen ! vertically integrate each of the decomposing N pools do l = 1, ndecomp_pools - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_npools_col(c,l) = 0._r8 if(use_soil_matrixcn)then end if end do do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_npools_col(c,l) = & this%decomp_npools_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * dzsoi_decomp(j) @@ -870,8 +870,8 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen if ( nlevdecomp > 1) then do l = 1, ndecomp_pools - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_npools_1m_col(c,l) = 0._r8 end do end do @@ -881,15 +881,15 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen do l = 1, ndecomp_pools do j = 1, nlevdecomp if ( zisoi(j) <= maxdepth ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_npools_1m_col(c,l) = & this%decomp_npools_1m_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * dzsoi_decomp(j) end do elseif ( zisoi(j-1) < maxdepth ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_npools_1m_col(c,l) = & this%decomp_npools_1m_col(c,l) + & this%decomp_npools_vr_col(c,j,l) * (maxdepth - zisoi(j-1)) @@ -901,16 +901,16 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen ! Add soil nitrogen pools together to produce vertically-resolved decomposing total soil N pool if ( nlevdecomp_full > 1 ) then do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_soiln_vr_col(c,j) = 0._r8 end do end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%decomp_soiln_vr_col(c,j) = this%decomp_soiln_vr_col(c,j) + & this%decomp_npools_vr_col(c,j,l) end do @@ -920,14 +920,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen end if ! total litter nitrogen to 1 meter (TOTLITN_1m) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitn_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitn_1m_col(c) = & this%totlitn_1m_col(c) + & this%decomp_npools_1m_col(c,l) @@ -936,14 +936,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen end do ! total soil organic matter nitrogen to 1 meter (TOTSOMN_1m) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomn_1m_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomn_1m_col(c) = this%totsomn_1m_col(c) + & this%decomp_npools_1m_col(c,l) end do @@ -953,14 +953,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen endif ! total litter nitrogen (TOTLITN) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totlitn_col(c) = & this%totlitn_col(c) + & this%decomp_npools_col(c,l) @@ -969,14 +969,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen end do ! total microbial nitrogen (TOTMICN) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totmicn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totmicn_col(c) = & this%totmicn_col(c) + & this%decomp_npools_col(c,l) @@ -985,14 +985,14 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen end do ! total soil organic matter nitrogen (TOTSOMN) - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomn_col(c) = 0._r8 end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_soil(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totsomn_col(c) = this%totsomn_col(c) + & this%decomp_npools_col(c,l) end do @@ -1000,34 +1000,34 @@ subroutine Summary(this, bounds, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogen end do ! total sminn - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%sminn_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%sminn_col(c) = this%sminn_col(c) + & this%sminn_vr_col(c,j) * dzsoi_decomp(j) end do end do ! total col_ntrunc - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%ntrunc_col(c) = 0._r8 end do do j = 1, nlevdecomp - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%ntrunc_col(c) = this%ntrunc_col(c) + & this%ntrunc_vr_col(c,j) * dzsoi_decomp(j) end do end do ! total cwdn - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%cwdn_col(c) = 0._r8 if(col%is_fates(c)) then From 1824265b15fc7ee7d58f7b6658b15eec5c254e1a Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 9 Jun 2023 12:16:47 -0600 Subject: [PATCH 1002/2067] correcting logaical & adding SP option --- .../usermods_dirs/NEON/MLBS/shell_commands | 6 ++---- .../usermods_dirs/NEON/MOAB/shell_commands | 2 +- .../usermods_dirs/NEON/NIWO/shell_commands | 3 +-- .../usermods_dirs/NEON/ONAQ/shell_commands | 6 ++---- .../usermods_dirs/NEON/TEAK/shell_commands | 6 ++---- .../usermods_dirs/NEON/WREF/shell_commands | 6 ++---- .../usermods_dirs/NEON/YELL/shell_commands | 6 ++---- .../NEON/defaults/shell_commands | 20 +++++++++++++++++++ 8 files changed, 32 insertions(+), 23 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 412a4cf621..1620cc3850 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -4,12 +4,10 @@ ./xmlchange PTS_LAT=37.37783 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME == 'NEON'] -then +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case - if [[ $compset =~ ^HIST ]] - then + if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 0d8c64e911..585a21fc78 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -4,7 +4,7 @@ ./xmlchange PTS_LAT=38.25136 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [$CLM_USRDAT_NAME == 'NEON' ]; then +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2020 # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index d0a4f2bd44..f6c9909e62 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -4,7 +4,6 @@ ./xmlchange PTS_LAT=40.05236 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME == "NEON" ] -then +if [[ $CLM_USRDAT_NAME == "NEON" ]]; then ./xmlchange DATM_YR_END=2018 fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index bc0ac91f99..62cf17e909 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -4,12 +4,10 @@ ./xmlchange PTS_LAT=40.17760 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME == 'NEON' ] -then +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2019 # Different default number of months to run for transient case - if [[ $compset =~ ^HIST ]] - then + if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 ./xmlchange STOP_N=24 fi diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index f584056ba6..32420f9f2a 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -5,12 +5,10 @@ ./xmlchange DATM_YR_ALIGN=2019 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME=='NEON'] -then +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 # Different default start date and number of months to run for transient case - if [[ $compset =~ ^HIST ]] - then + if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index f2e9300745..79df152826 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -5,12 +5,10 @@ ./xmlchange DATM_YR_ALIGN=2019 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME == 'NEON' ] -then +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case ./xmlchange DATM_YR_START=2019 - if [[ $compset =~ ^HIST ]] - then + if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index 5ce31e6b05..9fb99f00f8 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -5,12 +5,10 @@ ./xmlchange DATM_YR_ALIGN=2019 # NEON precipitation data for this site is bad so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data -if [ $CLM_USRDAT_NAME == 'NEON' ] -then +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case ./xmlchange DATM_YR_START=2019 - if [[ $compset =~ ^HIST ]] - then + if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 ./xmlchange STOP_N=39 fi diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 453c7d0ee3..eaea7a9f1c 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -24,5 +24,25 @@ else ./xmlchange CLM_NML_USE_CASE="2018_control" fi +# If needed for SP simulations: turn off lightning & set history file variables +if [[ $compset == *'SP_SICE'* ]]; then + ./xmlchange STOP_OPTION=nyears + ./xmlchange CLM_FORCE_COLDSTART=on + # comment out lightning file + :> user_nl_clm.tmp + while read line; do + if [[ $line != *"_lightng"* ]]; then + echo $line>>user_nl_clm.tmp + else + echo '!'$line>>user_nl_clm.tmp + fi + done> user_nl_clm + echo "hist_nhtfrq(2) = 1" >> user_nl_clm + echo "hist_fincl2 = 'FCEV','FCTR','FGEV','FIRA','FSA','FSH','FPSN','H2OSOI','SNOW_DEPTH','TBOT','TSOI'" >> user_nl_clm +fi + # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) ./xmlchange PIO_TYPENAME=netcdf From 050f75cdbe578ec868e5ef6f059097bef2270028 Mon Sep 17 00:00:00 2001 From: wwieder Date: Fri, 9 Jun 2023 13:14:14 -0600 Subject: [PATCH 1003/2067] updating FATES shell_commands --- .../usermods_dirs/NEON/FATES/MLBS/shell_commands | 14 +++++++++----- .../usermods_dirs/NEON/FATES/MOAB/shell_commands | 14 +++++++++----- .../usermods_dirs/NEON/FATES/NIWO/shell_commands | 7 ++++++- .../usermods_dirs/NEON/FATES/ONAQ/shell_commands | 14 +++++++++----- .../usermods_dirs/NEON/FATES/TEAK/shell_commands | 15 ++++++++++----- .../usermods_dirs/NEON/FATES/WREF/shell_commands | 15 ++++++++++----- .../usermods_dirs/NEON/FATES/YELL/shell_commands | 15 ++++++++++----- 7 files changed, 63 insertions(+), 31 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands index d5de0f64eb..1620cc3850 100644 --- a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands @@ -2,9 +2,13 @@ ./xmlchange NEONSITE=MLBS ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 -./xmlchange DATM_YR_END=2019 -# Different default number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then + ./xmlchange DATM_YR_END=2019 + # Different default number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 + ./xmlchange STOP_N=24 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands index 96d0bcbe68..585a21fc78 100644 --- a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands @@ -2,9 +2,13 @@ ./xmlchange NEONSITE=MOAB ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 -./xmlchange DATM_YR_END=2020 -# Different default number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange DATM_YR_END=2021 - ./xmlchange STOP_N=36 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then + ./xmlchange DATM_YR_END=2020 + # Different default number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2021 + ./xmlchange STOP_N=36 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands index a3e73ca343..f6c9909e62 100644 --- a/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands @@ -1,4 +1,9 @@ +#!/bin/bash ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 -./xmlchange DATM_YR_END=2018 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == "NEON" ]]; then + ./xmlchange DATM_YR_END=2018 +fi diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands index 511813398b..62cf17e909 100644 --- a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands @@ -2,9 +2,13 @@ ./xmlchange NEONSITE=ONAQ ./xmlchange PTS_LON=247.54755 ./xmlchange PTS_LAT=40.17760 -./xmlchange DATM_YR_END=2019 -# Different default number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then + ./xmlchange DATM_YR_END=2019 + # Different default number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange DATM_YR_END=2020 + ./xmlchange STOP_N=24 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands index 9058eda022..32420f9f2a 100644 --- a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands @@ -2,9 +2,14 @@ ./xmlchange NEONSITE=TEAK ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 +./xmlchange DATM_YR_ALIGN=2019 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then + ./xmlchange DATM_YR_START=2019 + # Different default start date and number of months to run for transient case + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands index 807055ae6e..79df152826 100644 --- a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands @@ -2,9 +2,14 @@ ./xmlchange NEONSITE=WREF ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 +./xmlchange DATM_YR_ALIGN=2019 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then + # Different default start date and number of months to run for transient case + ./xmlchange DATM_YR_START=2019 + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands index 800d7d01ad..9fb99f00f8 100644 --- a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands @@ -2,9 +2,14 @@ ./xmlchange NEONSITE=YELL ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 +./xmlchange DATM_YR_ALIGN=2019 +# NEON precipitation data for this site is bad so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then + # Different default start date and number of months to run for transient case + ./xmlchange DATM_YR_START=2019 + if [[ $compset =~ ^HIST ]]; then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + fi fi From 0f2d990dd1be49ddc2c13342ab02d575c3f7ea64 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 12 Jun 2023 11:51:27 -0600 Subject: [PATCH 1004/2067] Updates to the fates-clm bgc call sequence, to preserve b4b behavior in non-fates --- bld/CLMBuildNamelist.pm | 2 +- src/biogeochem/CNDriverMod.F90 | 12 ++++++++---- src/main/clm_driver.F90 | 2 +- src/main/clm_initializeMod.F90 | 2 +- src/main/filterMod.F90 | 2 +- .../SoilBiogeochemCarbonStateType.F90 | 15 ++++++++++++--- .../SoilBiogeochemNitrogenStateType.F90 | 10 +++++++++- 7 files changed, 33 insertions(+), 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 53db7393f4..75fc6c7365 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3442,7 +3442,7 @@ sub setup_logic_nitrogen_deposition { # # Nitrogen deposition for bgc=CN or fates # - if ( ($nl_flags->{'bgc_mode'} =~/bgc/) or ($nl_flags->{'bgc_mode'} =~/fates/) ) { + if ( ($nl_flags->{'bgc_mode'} =~/bgc/) ) { # or ($nl_flags->{'bgc_mode'} =~/fates/) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'ndepmapalgo', 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'hgrid'=>$nl_flags->{'res'}, 'clm_accelerated_spinup'=>$nl_flags->{'clm_accelerated_spinup'} ); diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 569866d9ec..424cf8c52b 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -1173,12 +1173,15 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & ! cnveg summary, swapped call order ! ---------------------------------------------- - call soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, cnveg_carbonstate_inst) + call soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, & + num_bgc_soilc, filter_bgc_soilc, cnveg_carbonstate_inst) if ( use_c13 ) then - call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, c13_cnveg_carbonstate_inst) + call c13_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, & + num_bgc_soilc, filter_bgc_soilc, c13_cnveg_carbonstate_inst) end if if ( use_c14 ) then - call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, c14_cnveg_carbonstate_inst) + call c14_soilbiogeochem_carbonstate_inst%summary(bounds, num_allc, filter_allc, & + num_bgc_soilc, filter_bgc_soilc, c14_cnveg_carbonstate_inst) end if @@ -1189,7 +1192,8 @@ subroutine CNDriverSummarizeStates(bounds, num_allc, filter_allc, & call cnveg_nitrogenstate_inst%Summary(bounds, num_bgc_soilc, filter_bgc_soilc, & num_bgc_vegp, filter_bgc_vegp) - call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_allc, filter_allc,cnveg_nitrogenstate_inst) + call soilbiogeochem_nitrogenstate_inst%summary(bounds, num_allc, filter_allc, & + num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogenstate_inst) call t_stopf('CNsum') diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 5fb0d233ec..fe64ea12e1 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -445,7 +445,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! re-written to go inside. ! ============================================================================ - if (use_cn .or. use_fates_bgc) then + if (use_cn) then ! .or. use_fates_bgc) then (ndep with fates will be added soon) if (.not. ndep_from_cpl) then call ndep_interp(bounds_proc, atm2lnd_inst) end if diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 98e6ba006e..00b7c93060 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -626,7 +626,7 @@ subroutine initialize2(ni,nj) !$OMP END PARALLEL DO ! Initialize nitrogen deposition - if (use_cn .or. use_fates_bgc) then + if (use_cn ) then !.or. use_fates_bgc) then (ndep with fates will be added soon RGK) call t_startf('init_ndep') if (.not. ndep_from_cpl) then call ndep_init(bounds_proc, NLFilename) diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 0b7d230a54..6c246b1fa5 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -477,7 +477,7 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fl = 0 fnl = 0 do p = bounds%begp,bounds%endp - if (patch%active(p) .or. include_inactive) then + if ((patch%active(p) .or. include_inactive) .and. .not. patch%is_fates(p)) then if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types fl = fl + 1 this_filter(nc)%pcropp(fl) = p diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 241d7eeb25..1f3b00f6e8 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -931,7 +931,7 @@ subroutine SetValues ( this, num_column, filter_column, value_column) end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_carbonstate_inst) + subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bgc_soilc,cnveg_carbonstate_inst) ! ! !DESCRIPTION: ! Perform column-level carbon summary calculations @@ -941,6 +941,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_carbonstate_inst) type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_allc ! number of columns in soil filter integer , intent(in) :: filter_allc(:) ! filter for all active columns + integer , intent(in) :: num_bgc_soilc ! number of columns in soil filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for all active columns type(cnveg_carbonstate_type) , intent(inout) :: cnveg_carbonstate_inst ! @@ -1081,8 +1083,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_carbonstate_inst) end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) this%totmicc_col(c) = this%totmicc_col(c) + this%decomp_cpools_col(c,l) end do endif @@ -1123,6 +1125,13 @@ subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_carbonstate_inst) ! coarse woody debris carbon this%cwdc_col(c) = 0._r8 + this%totecosysc_col(c) = 0._r8 + this%totc_col(c) = 0._r8 + + end do + + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if(col%is_fates(c)) then totvegc_col = 0._r8 diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index b537d0896e..ac57ad20b7 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -805,7 +805,7 @@ end subroutine SetValues !----------------------------------------------------------------------- - subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_nitrogenstate_inst) + subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bgc_soilc, cnveg_nitrogenstate_inst) ! ! !ARGUMENTS: @@ -813,6 +813,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_nitrogenstate_inst type(bounds_type) , intent(in) :: bounds integer , intent(in) :: num_allc ! number of bgc columns in soilc filter integer , intent(in) :: filter_allc(:) ! filter for bgc columns + integer , intent(in) :: num_bgc_soilc ! number of bgc columns in soilc filter + integer , intent(in) :: filter_bgc_soilc(:) ! filter for bgc columns type(cnveg_nitrogenstate_type) , intent(inout) :: cnveg_nitrogenstate_inst ! @@ -1029,6 +1031,12 @@ subroutine Summary(this, bounds, num_allc, filter_allc, cnveg_nitrogenstate_inst do fc = 1,num_allc c = filter_allc(fc) this%cwdn_col(c) = 0._r8 + this%totecosysn_col(c) = 0._r8 + this%totn_col(c) = 0._r8 + end do + + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) if(col%is_fates(c)) then totvegn_col = 0._r8 From 5e7bc7e92a341832a34a4476f2fa00bcdfdddb47 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 13 Jun 2023 08:39:57 -0600 Subject: [PATCH 1005/2067] add function to determine correct string --- tools/site_and_regional/run_neon.py | 44 ++++++++++++++++++++--------- 1 file changed, 30 insertions(+), 14 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 9c8f39d6b0..9eb8da9dc0 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -5,17 +5,17 @@ |--------------------- Instructions -----------------------------| |------------------------------------------------------------------| This is a wrapper script for running CTSM simulation for one or more -neon sites. +neon sites. This script is only for neon site and we will develop a more general code later. -This script first creates and builds a generic base case. +This script first creates and builds a generic base case. Next, it will clone the base_case for different neon sites and run -types to reduce the need to build ctsm everytime. +types to reduce the need to build ctsm everytime. This script will do the following: - 1) Create a generic base case for cloning. + 1) Create a generic base case for cloning. 2) Make the case for the specific neon site(s). 3) Make changes to the case, for: a. AD spinup @@ -24,13 +24,13 @@ #--------------- d. SASU or Matrix spinup 4) Build and submit the case. - + ------------------------------------------------------------------- Instructions for running using conda python environments: ../../py_env_create conda activate ctsm_py - + ------------------------------------------------------------------- To see the available options: ./run_neon.py --help @@ -113,7 +113,7 @@ def get_parser(args, description, valid_neon_sites): "--base-case", help=""" Root Directory of base case build - [default: %(default)s] + [default: %(default)s] """, action="store", dest="base_case_root", @@ -126,7 +126,7 @@ def get_parser(args, description, valid_neon_sites): "--output-root", help=""" Root output directory of cases - [default: %(default)s] + [default: %(default)s] """, action="store", dest="output_root", @@ -162,7 +162,7 @@ def get_parser(args, description, valid_neon_sites): parser.add_argument( "--rerun", help=""" - If the case exists but does not appear to be complete, restart it. + If the case exists but does not appear to be complete, restart it. [default: %(default)s] """, action="store_true", @@ -209,7 +209,7 @@ def get_parser(args, description, valid_neon_sites): parser.add_argument( "--experiment", help=""" - Appends the case name with string for model experiment + Appends the case name with string for model experiment """, action="store", dest="experiment", @@ -231,7 +231,7 @@ def get_parser(args, description, valid_neon_sites): parser.add_argument( "--start-date", - help=""" + help=""" Start date for running CTSM simulation in ISO format. [default: %(default)s] (currently non-functional) @@ -356,6 +356,22 @@ def parse_isoduration(s): dt = datetime.timedelta(days=int(days) + 365 * int(years) + 30 * int(months)) return int(dt.total_seconds() / 86400) +def get_queue_command(batch_system): + match batch_system.lower(): + 'pbs': + queue_command = 'qstat -u ' + 'slurm': + queue_command = 'squeue -u ' + 'cobalt': + queue_command = 'qstat -u ' + 'lsf': + queue_command = 'bqueues -u ' + case _: + queue_command = '' + + return queue_command + + class NeonSite: """ @@ -506,7 +522,7 @@ def run_case( print ("using this version:", version) if experiment != None: - self.name = self.name + "." + experiment + self.name = self.name + "." + experiment case_root = os.path.abspath( os.path.join(base_case_root, "..", self.name + "." + run_type) ) @@ -604,7 +620,7 @@ def run_case( case.set_value("CALENDAR", "GREGORIAN") case.set_value("RESUBMIT", 0) case.set_value("STOP_OPTION", "nmonths") - + if not rundir: rundir = case.get_value("RUNDIR") @@ -856,7 +872,7 @@ def main(description): rerun, experiment, ) - + if __name__ == "__main__": From e132e432c0f3ac56dc585dd2d383bb6c09bdb1a5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 13 Jun 2023 16:40:52 -0600 Subject: [PATCH 1006/2067] Removed a TODO that was already done. "Throw error during namelist build if tillage is called with FATES" --- src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 2a1ea8810f..7060034217 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -903,9 +903,8 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! Tillage if (get_do_tillage()) then - ! TODO(ssr): Throw error during namelist build if tillage is called with FATES if (.not. present(idop)) then - call endrun("Do not call tillage without providing idop. (Maybe you called with FATES?)") + call endrun("Do not call tillage without providing idop.") end if call get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if From 9386d813e6f6a7301f7a605998a0f83679810e7c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 14 Jun 2023 10:07:12 -0600 Subject: [PATCH 1007/2067] Corrected capitalization of TillageMod's .F90. --- src/biogeochem/{TillageMod.f90 => TillageMod.F90} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/biogeochem/{TillageMod.f90 => TillageMod.F90} (100%) diff --git a/src/biogeochem/TillageMod.f90 b/src/biogeochem/TillageMod.F90 similarity index 100% rename from src/biogeochem/TillageMod.f90 rename to src/biogeochem/TillageMod.F90 From 1d4c81eb5e3a88e259863d18b4b656c2b0a339fc Mon Sep 17 00:00:00 2001 From: John Alex Date: Wed, 14 Jun 2023 10:26:14 -0600 Subject: [PATCH 1008/2067] tweaks responding to PR comments --- src/main/histFileMod.F90 | 28 ++++++++++++++++------------ 1 file changed, 16 insertions(+), 12 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 25021fdc29..2497a14667 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -5,6 +5,7 @@ module histFileMod !----------------------------------------------------------------------- ! !DESCRIPTION: ! Module containing methods to for CLM history file handling. + ! See 'history_tape' type for more details. ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 @@ -84,8 +85,8 @@ module histFileMod logical, public :: & hist_empty_htapes = .false. ! namelist: disable default-active history fields (which - ! only exist on history tape 1). Overridden by hist_fincl1 - ! flag. + ! only exist on history tape 1). Use hist_fincl1 to enable + ! select fields on top of this. character(len=max_namlen+2), public :: & hist_fincl1(max_flds) = ' ' ! namelist: list of fields to include in history tape 1 @@ -117,21 +118,21 @@ module histFileMod character(len=max_namlen+2), public :: & hist_fexcl2(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 character(len=max_namlen+2), public :: & - hist_fexcl3(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl3(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 3 character(len=max_namlen+2), public :: & - hist_fexcl4(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl4(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 4 character(len=max_namlen+2), public :: & - hist_fexcl5(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl5(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 5 character(len=max_namlen+2), public :: & - hist_fexcl6(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl6(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 6 character(len=max_namlen+2), public :: & - hist_fexcl7(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl7(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 7 character(len=max_namlen+2), public :: & - hist_fexcl8(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl8(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 8 character(len=max_namlen+2), public :: & - hist_fexcl9(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl9(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 9 character(len=max_namlen+2), public :: & - hist_fexcl10(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 2 + hist_fexcl10(max_flds) = ' ' ! namelist: list of fields to exclude from history tape 10 character(len=max_namlen+2), public :: & fexcl(max_flds,max_tapes) ! copy of hist_fexcl* fields in 2-D format. Note Fortran @@ -260,7 +261,8 @@ end subroutine copy_entry_interface ! at a given time frequency and precision. The first ('primary') tape defaults to a non-empty set ! of active fields (see hist_addfld* methods), overridable by namelist flags, while the other ! tapes are entirely manually configured via namelist flags. The set of active fields across all - ! tapes is assembled in the 'masterlist' variable. + ! tapes is assembled in the 'masterlist' variable. Note that the first history tape is index 1 in + ! the code but contains 'h0' in its output filenames (see set_hist_filename method). type history_tape integer :: nflds ! number of active fields on tape integer :: ntimes ! current number of time samples on tape @@ -315,7 +317,7 @@ end subroutine copy_entry_interface ! character(len=max_length_filename) :: locfnh(max_tapes) ! local history file names character(len=max_length_filename) :: locfnhr(max_tapes) ! local history restart file names - logical :: htapes_defined = .false. ! flag indicates history output fields have been selected + logical :: htapes_defined = .false. ! flag indicates history output fields have been defined ! ! NetCDF Id's ! @@ -5112,6 +5114,8 @@ character(len=max_length_filename) function set_hist_filename (hist_freq, hist_m ! ! !DESCRIPTION: ! Determine history dataset filenames. + ! Note that the first history tape is index 1 in the code but contains 'h0' in its output + ! filenames. ! ! !USES: use clm_varctl, only : caseid, inst_suffix From d190215fb1fa3db802bffe6edbe8fc52861d1b68 Mon Sep 17 00:00:00 2001 From: John Alex Date: Wed, 14 Jun 2023 10:50:29 -0600 Subject: [PATCH 1009/2067] Document side effects of htapes_fieldlist() method - which variables are set. --- src/main/histFileMod.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index d5175342f0..c715fddaef 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -774,9 +774,12 @@ subroutine htapes_fieldlist() ! !DESCRIPTION: ! Define the contents of each history file based on namelist ! input for initial or branch run, and restart data if a restart run. - ! Use arrays fincl and fexcl to modify default history tape contents. + ! Fill and use arrays fincl and fexcl to modify default history tape contents. ! Then sort the result alphanumerically. ! + ! Sets history_tape_in_use and htapes_defined. Fills fields in 'tape' array. + ! Optionally updates masterlist avgflag. + ! ! !ARGUMENTS: ! ! !LOCAL VARIABLES: From 0676ac2ae11ea910cab5cdae075d4c119493ef26 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 14 Jun 2023 11:11:32 -0600 Subject: [PATCH 1010/2067] various fixes for fates bgc --- src/biogeochem/CNCIsoFluxMod.F90 | 325 ++++++++++++++---------------- src/biogeochem/CNPhenologyMod.F90 | 172 ++++++++-------- src/main/controlMod.F90 | 2 +- src/main/filterMod.F90 | 4 +- 4 files changed, 235 insertions(+), 268 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index a4706442fa..c10659a945 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -8,7 +8,7 @@ module CNCIsoFluxMod use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varpar , only : ndecomp_cascade_transitions, nlevdecomp, ndecomp_pools - use clm_varpar , only : max_patch_per_col, maxsoil_patches + use clm_varpar , only : maxsoil_patches use clm_varpar , only : i_litr_min, i_litr_max, i_met_lit use abortutils , only : endrun use pftconMod , only : pftcon @@ -535,7 +535,7 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ! For later clean-up, it would be possible to generalize this function to operate on a single ! patch-to-column flux. - call CNCIsoLitterToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + call CNCIsoLitterToColumn(num_soilp, filter_soilp, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! column-level non-mortality fluxes @@ -713,7 +713,7 @@ subroutine CIsoFlux2(num_soilc, filter_soilc, num_soilp , filter_soilp, & ! call routine to shift patch-level gap mortality fluxes to column , for isotopes ! the non-isotope version of this routine is in CNGapMortalityMod.F90. - call CNCIsoGapPftToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + call CNCIsoGapPftToColumn(num_soilp, filter_soilp, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) end associate @@ -1041,7 +1041,7 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & character(len=*) , intent(in) :: isotope ! 'c13' or 'c14' ! ! !LOCAL VARIABLES: - integer :: pi,pp,l,fc,cc,j,i + integer :: pi,pp,l,fp,cc,j,i,fc !----------------------------------------------------------------------- associate( & @@ -1276,26 +1276,21 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! calculate the column-level flux of deadstem and deadcrootc to cwdc as the result of fire mortality. - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - cc = filter_soilc(fc) - if ( pi <= col%npatches(cc) ) then - pp = col%patchi(cc) + pi - 1 - if (patch%active(pp)) then - do j = 1, nlevdecomp - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & - (iso_cnveg_cf%m_deadstemc_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livestemc_to_litter_fire_patch(pp)) * & - patch%wtcol(pp) * stem_prof(pp,j) - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & - (iso_cnveg_cf%m_deadcrootc_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livecrootc_to_litter_fire_patch(pp)) * & - patch%wtcol(pp) * croot_prof(pp,j) - end do - end if - end if + + do fp = 1,num_soilp + pp = filter_soilp(fp) + cc = patch%column(pp) + do j = 1, nlevdecomp + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & + (iso_cnveg_cf%m_deadstemc_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livestemc_to_litter_fire_patch(pp)) * & + patch%wtcol(pp) * stem_prof(pp,j) + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & + (iso_cnveg_cf%m_deadcrootc_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livecrootc_to_litter_fire_patch(pp)) * & + patch%wtcol(pp) * croot_prof(pp,j) end do end do @@ -1316,54 +1311,47 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & end do end do - - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - cc = filter_soilc(fc) - if ( pi <= col%npatches(cc) ) then - pp = col%patchi(cc) + pi - 1 - if (patch%active(pp)) then - do j = 1, nlevdecomp - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) = & - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) + & - ((iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i_met_lit) & - +iso_cnveg_cf%m_leafc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_leafc_xfer_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_gresp_storage_to_litter_fire_patch(pp) & - +iso_cnveg_cf%m_gresp_xfer_to_litter_fire_patch(pp))*leaf_prof(pp,j) + & - (iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i_met_lit) & - +iso_cnveg_cf%m_frootc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_frootc_xfer_to_litter_fire_patch(pp))*froot_prof(pp,j) & - +(iso_cnveg_cf%m_livestemc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livestemc_xfer_to_litter_fire_patch(pp) & - +iso_cnveg_cf%m_deadstemc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_deadstemc_xfer_to_litter_fire_patch(pp))* stem_prof(pp,j)& - +(iso_cnveg_cf%m_livecrootc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livecrootc_xfer_to_litter_fire_patch(pp) & - +iso_cnveg_cf%m_deadcrootc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_deadcrootc_xfer_to_litter_fire_patch(pp))* croot_prof(pp,j)) * patch%wtcol(pp) - - ! Here metabolic litter is treated differently than other - ! types of litter, so it remains outside this litter loop, - ! in the line above - do i = i_met_lit+1, i_litr_max - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) = & - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) + & - (iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i) * leaf_prof(pp,j) + & - iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i) * froot_prof(pp,j)) * patch%wtcol(pp) - end do - end do - end if - end if + do fp = 1,num_soilp + pp = filter_soilp(fp) + cc = patch%column(pp) + do j = 1, nlevdecomp + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) = & + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) + & + ((iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i_met_lit) & + +iso_cnveg_cf%m_leafc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_leafc_xfer_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_gresp_storage_to_litter_fire_patch(pp) & + +iso_cnveg_cf%m_gresp_xfer_to_litter_fire_patch(pp))*leaf_prof(pp,j) + & + (iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i_met_lit) & + +iso_cnveg_cf%m_frootc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_frootc_xfer_to_litter_fire_patch(pp))*froot_prof(pp,j) & + +(iso_cnveg_cf%m_livestemc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livestemc_xfer_to_litter_fire_patch(pp) & + +iso_cnveg_cf%m_deadstemc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_deadstemc_xfer_to_litter_fire_patch(pp))* stem_prof(pp,j)& + +(iso_cnveg_cf%m_livecrootc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livecrootc_xfer_to_litter_fire_patch(pp) & + +iso_cnveg_cf%m_deadcrootc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_deadcrootc_xfer_to_litter_fire_patch(pp))* croot_prof(pp,j)) * patch%wtcol(pp) + + ! Here metabolic litter is treated differently than other + ! types of litter, so it remains outside this litter loop, + ! in the line above + do i = i_met_lit+1, i_litr_max + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) = & + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) + & + (iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i) * leaf_prof(pp,j) + & + iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i) * froot_prof(pp,j)) * patch%wtcol(pp) + end do end do - end do + end do end associate end subroutine CIsoFlux3 !----------------------------------------------------------------------- - subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & + subroutine CNCIsoLitterToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -1377,13 +1365,13 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & !DML ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,k,j,i + integer :: c,pi,p,k,j,i,fp !----------------------------------------------------------------------- associate( & @@ -1405,59 +1393,52 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - c = filter_soilc(fc) - - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - do i = i_litr_min, i_litr_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - ! leaf litter carbon fluxes - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root litter carbon fluxes - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + ! leaf litter carbon fluxes + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root litter carbon fluxes + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do + !DML - if (ivt(p) >= npcropmin) then ! add livestemc to litter - ! stem litter carbon fluxes - do i = i_litr_min, i_litr_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - - if (.not. use_grainproduct) then - ! grain litter carbon fluxes - do i = i_litr_min, i_litr_max - do k = repr_grain_min, repr_grain_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - - ! reproductive structure litter carbon fluxes - do i = i_litr_min, i_litr_max - do k = repr_structure_min, repr_structure_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - - end if -!DML - end if + if (ivt(p) >= npcropmin) then ! add livestemc to litter + ! stem litter carbon fluxes + do i = i_litr_min, i_litr_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + + if (.not. use_grainproduct) then + ! grain litter carbon fluxes + do i = i_litr_min, i_litr_max + do k = repr_grain_min, repr_grain_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do end if - - end do + + ! reproductive structure litter carbon fluxes + do i = i_litr_min, i_litr_max + do k = repr_structure_min, repr_structure_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + + end if + !DML end do - end do end associate @@ -1465,7 +1446,7 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & end subroutine CNCIsoLitterToColumn !----------------------------------------------------------------------- - subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & + subroutine CNCIsoGapPftToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -1473,13 +1454,13 @@ subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & ! to the column level and assign them to the three litter pools (+ cwd pool) ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! soil patch filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,pi,p,j,i ! indices !----------------------------------------------------------------------- associate( & @@ -1520,66 +1501,58 @@ subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - ! leaf gap mortality carbon fluxes - gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - ! fine root gap mortality carbon fluxes - gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood gap mortality carbon fluxes - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_deadstemc_to_litter(p) * wtcol(p) * stem_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - gap_mortality_c_to_litr_c(c,j,i_met_lit) = & - gap_mortality_c_to_litr_c(c,j,i_met_lit) + & - ! storage gap mortality carbon fluxes - m_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - m_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - ! transfer gap mortality carbon fluxes - m_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - m_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) - - end if - end if + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + ! leaf gap mortality carbon fluxes + gap_mortality_c_to_litr_c(c,j,i) = & + gap_mortality_c_to_litr_c(c,j,i) + & + m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + ! fine root gap mortality carbon fluxes + gap_mortality_c_to_litr_c(c,j,i) = & + gap_mortality_c_to_litr_c(c,j,i) + & + m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do - + + ! wood gap mortality carbon fluxes + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_deadstemc_to_litter(p) * wtcol(p) * stem_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + gap_mortality_c_to_litr_c(c,j,i_met_lit) = & + gap_mortality_c_to_litr_c(c,j,i_met_lit) + & + ! storage gap mortality carbon fluxes + m_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + m_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + ! transfer gap mortality carbon fluxes + m_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + m_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + end do end do + end associate end subroutine CNCIsoGapPftToColumn diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ec04fcbf54..b8bc707291 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -406,7 +406,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & ! gather all patch-level litterfall fluxes to the column for litter C and N inputs - call CNLitterToColumn(bounds, num_soilc, filter_soilc, & + call CNLitterToColumn(bounds, num_soilp, filter_soilp, & cnveg_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full), & froot_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full)) @@ -3383,7 +3383,7 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil end subroutine CNCropHarvestToProductPools !----------------------------------------------------------------------- - subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & + subroutine CNLitterToColumn (bounds, num_bgc_vegp, filter_bgc_vegp, & cnveg_state_inst,cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch, froot_prof_patch) ! @@ -3392,14 +3392,14 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & ! to the column level and assign them to the three litter pools ! ! !USES: - use clm_varpar , only : max_patch_per_col, nlevdecomp + use clm_varpar , only : nlevdecomp use pftconMod , only : npcropmin use clm_varctl , only : use_grainproduct ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_bgc_vegp ! number of bgc veg patches + integer , intent(in) :: filter_bgc_vegp(:) ! filter for bgc veg patches type(cnveg_state_type) , intent(in) :: cnveg_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst @@ -3407,7 +3407,7 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & real(r8) , intent(in) :: froot_prof_patch(bounds%begp:,1:) ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,k,j,i ! indices + integer :: fp,c,pi,p,k,j,i ! indices !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(leaf_prof_patch) == (/bounds%endp,nlevdecomp_full/)), sourcefile, __LINE__) @@ -3437,96 +3437,88 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & frootn_to_litter => cnveg_nitrogenflux_inst%frootn_to_litter_patch , & ! Input: [real(r8) (:) ] fine root N litterfall (gN/m2/s) phenology_n_to_litr_n => cnveg_nitrogenflux_inst%phenology_n_to_litr_n_col & ! Output: [real(r8) (:,:,:) ] N fluxes associated with phenology (litterfall and crop) to litter pools (gN/m3/s) ) - - do j = 1, nlevdecomp - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - c = filter_soilc(fc) + + do_nlev: do j = 1, nlevdecomp - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then + do_vegp: do fp = 1,num_bgc_vegp + p = filter_bgc_vegp(fp) + c = patch%column(p) - do i = i_litr_min, i_litr_max - ! leaf litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! leaf litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! fine root litter carbon fluxes + do_ilit: do i = i_litr_min, i_litr_max + ! leaf litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! leaf litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! fine root litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + + ! fine root litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do do_ilit + + ! agroibis puts crop stem litter together with leaf litter + ! so I've used the leaf lf_f* parameters instead of making + ! new ones for now (slevis) + ! also for simplicity I've put "food" into the litter pools + + if (ivt(p) >= npcropmin) then ! add livestemc to litter + do i = i_litr_min, i_litr_max + ! stem litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! stem litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + + if (.not. use_grainproduct) then + do i = i_litr_min, i_litr_max + do k = repr_grain_min, repr_grain_max + ! grain litter carbon fluxes phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - - ! fine root litter nitrogen fluxes + phenology_c_to_litr_c(c,j,i) + & + repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! grain litter nitrogen fluxes phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + phenology_n_to_litr_n(c,j,i) + & + repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) end do - - ! agroibis puts crop stem litter together with leaf litter - ! so I've used the leaf lf_f* parameters instead of making - ! new ones for now (slevis) - ! also for simplicity I've put "food" into the litter pools - - if (ivt(p) >= npcropmin) then ! add livestemc to litter - do i = i_litr_min, i_litr_max - ! stem litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! stem litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - - if (.not. use_grainproduct) then - do i = i_litr_min, i_litr_max - do k = repr_grain_min, repr_grain_max - ! grain litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! grain litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - - do i = i_litr_min, i_litr_max - do k = repr_structure_min, repr_structure_max - ! reproductive structure litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! reproductive structure litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - end if + end do end if - - end do - - end do - end do - - end associate - + + do i = i_litr_min, i_litr_max + do k = repr_structure_min, repr_structure_max + ! reproductive structure litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! reproductive structure litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + end if + end do do_vegp + end do do_nlev + + end associate + end subroutine CNLitterToColumn end module CNPhenologyMod diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index c793898d5e..8fc2f8b4b2 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -439,7 +439,7 @@ subroutine control_init(dtime) use_fates_bgc = .true. end if - if (fates_parteh_mode == 1 .and. suplnitro == suplnNon)then + if (fates_parteh_mode == 1 .and. suplnitro == suplnNon .and. use_fates_bgc )then write(iulog,*) ' When FATES with fates_parteh_mode == 1 (ie carbon only mode),' write(iulog,*) ' you must have supplemental nitrogen turned on, there will be' write(iulog,*) ' no nitrogen dynamics with the plants, and therefore no' diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 6c246b1fa5..5b39b972fa 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -477,7 +477,8 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fl = 0 fnl = 0 do p = bounds%begp,bounds%endp - if ((patch%active(p) .or. include_inactive) .and. .not. patch%is_fates(p)) then + if(.not.use_fates)then + if ((patch%active(p) .or. include_inactive)) then if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types fl = fl + 1 this_filter(nc)%pcropp(fl) = p @@ -489,6 +490,7 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio end if end if end if + end if end do this_filter(nc)%num_pcropp = fl this_filter(nc)%num_soilnopcropp = fnl ! This wasn't being set before... From 732e822ef8b3e203d57bff948a31b5551aa26306 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 14 Jun 2023 16:19:12 -0700 Subject: [PATCH 1011/2067] Add fates luh2 land use module --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 194 +++++++++++++++++++ src/dyn_subgrid/dynSubgridDriverMod.F90 | 14 +- src/main/clm_initializeMod.F90 | 10 +- src/main/clm_varctl.F90 | 22 ++- src/main/controlMod.F90 | 6 + src/main/histFileMod.F90 | 11 ++ src/utils/clmfates_interfaceMod.F90 | 67 ++++++- 7 files changed, 300 insertions(+), 24 deletions(-) create mode 100644 src/dyn_subgrid/dynFATESLandUseChangeMod.F90 diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 new file mode 100644 index 0000000000..6329eaba47 --- /dev/null +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -0,0 +1,194 @@ +module dynFATESLandUseChangeMod + +#include "shr_assert.h" + + !--------------------------------------------------------------------------- + ! !DESCRIPTION: + ! Handle reading of the land use harmonization (LUH2) dataset + + ! !USES: + use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_log_mod , only : errMsg => shr_log_errMsg + use decompMod , only : bounds_type, BOUNDS_LEVEL_PROC + use abortutils , only : endrun + use dynFileMod , only : dyn_file_type + use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type + use clm_varcon , only : grlnd + use clm_varctl , only : iulog + + implicit none + + private + + real(r8), allocatable, public :: landuse_transitions(:,:) + real(r8), allocatable, public :: landuse_states(:,:) + + integer, public, parameter :: num_landuse_transition_vars = 108 + integer, public, parameter :: num_landuse_state_vars = 12 + + type(dyn_file_type), target :: dynFatesLandUse_file + + ! Land use name arrays + character(len=5), public, parameter :: landuse_state_varnames(num_landuse_state_vars) = & + [character(len=5) :: 'primf','primn','secdf','secdn','pastr','range', & + 'urban','c3ann','c4ann','c3per','c4per','c3nfx'] + + character(len=14), public, parameter :: landuse_transition_varnames(num_landuse_transition_vars) = & + [character(len=14) :: 'primf_to_secdn','primf_to_pastr','primf_to_range','primf_to_urban', & + 'primf_to_c3ann','primf_to_c4ann','primf_to_c3per','primf_to_c4per','primf_to_c3nfx', & + 'primn_to_secdf','primn_to_pastr','primn_to_range','primn_to_urban', & + 'primn_to_c3ann','primn_to_c4ann','primn_to_c3per','primn_to_c4per','primn_to_c3nfx', & + 'secdf_to_secdn','secdf_to_pastr','secdf_to_range','secdf_to_urban', & + 'secdf_to_c3ann','secdf_to_c4ann','secdf_to_c3per','secdf_to_c4per','secdf_to_c3nfx', & + 'secdn_to_secdf','secdn_to_pastr','secdn_to_range','secdn_to_urban', & + 'secdn_to_c3ann','secdn_to_c4ann','secdn_to_c3per','secdn_to_c4per','secdn_to_c3nfx', & + 'pastr_to_secdf','pastr_to_secdn','pastr_to_range','pastr_to_urban', & + 'pastr_to_c3ann','pastr_to_c4ann','pastr_to_c3per','pastr_to_c4per','pastr_to_c3nfx', & + 'range_to_secdf','range_to_secdn','range_to_pastr','range_to_urban', & + 'range_to_c3ann','range_to_c4ann','range_to_c3per','range_to_c4per','range_to_c3nfx', & + 'urban_to_secdf','urban_to_secdn','urban_to_pastr','urban_to_range', & + 'urban_to_c3ann','urban_to_c4ann','urban_to_c3per','urban_to_c4per','urban_to_c3nfx', & + 'c3ann_to_c4ann','c3ann_to_c3per','c3ann_to_c4per','c3ann_to_c3nfx', & + 'c3ann_to_secdf','c3ann_to_secdn','c3ann_to_pastr','c3ann_to_range','c3ann_to_urban', & + 'c4ann_to_c3ann','c4ann_to_c3per','c4ann_to_c4per','c4ann_to_c3nfx', & + 'c4ann_to_secdf','c4ann_to_secdn','c4ann_to_pastr','c4ann_to_range','c4ann_to_urban', & + 'c3per_to_c3ann','c3per_to_c4ann','c3per_to_c4per','c3per_to_c3nfx', & + 'c3per_to_secdf','c3per_to_secdn','c3per_to_pastr','c3per_to_range','c3per_to_urban', & + 'c4per_to_c3ann','c4per_to_c4ann','c4per_to_c3per','c4per_to_c3nfx', & + 'c4per_to_secdf','c4per_to_secdn','c4per_to_pastr','c4per_to_range','c4per_to_urban', & + 'c3nfx_to_c3ann','c3nfx_to_c4ann','c3nfx_to_c3per','c3nfx_to_c4per', & + 'c3nfx_to_secdf','c3nfx_to_secdn','c3nfx_to_pastr','c3nfx_to_range','c3nfx_to_urban'] + + type(dyn_var_time_uninterp_type) :: landuse_transition_vars(num_landuse_transition_vars) ! value of each landuse variable + type(dyn_var_time_uninterp_type) :: landuse_state_vars(num_landuse_state_vars) ! value of each landuse variable + + public :: dynFatesLandUseInit + public :: dynFatesLandUseInterp + +contains + + !----------------------------------------------------------------------- + subroutine dynFatesLandUseInit(bounds, landuse_filename) + + ! !DESCRIPTION: + ! Initialize data structures for land use information. + + ! !USES: + use clm_varctl , only : use_cn, use_fates_luh + use dynVarTimeUninterpMod , only : dyn_var_time_uninterp_type + use dynTimeInfoMod , only : YEAR_POSITION_START_OF_TIMESTEP + use dynTimeInfoMod , only : YEAR_POSITION_END_OF_TIMESTEP + + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds ! proc-level bounds + character(len=*) , intent(in) :: landuse_filename ! name of file containing land use information + + ! !LOCAL VARIABLES + integer :: varnum, i ! counter for harvest variables + integer :: landuse_shape(1) ! land use shape + integer :: num_points ! number of spatial points + integer :: ier ! error code + real(r8), allocatable :: this_data(:) ! data for a single harvest variable + ! + character(len=*), parameter :: subname = 'dynFatesLandUseInit' + !----------------------------------------------------------------------- + + SHR_ASSERT_ALL(bounds%level == BOUNDS_LEVEL_PROC, subname // ': argument must be PROC-level bounds') + + if (use_cn) return ! Use this as a protection in lieu of build namelist check? + + ! Allocate and initialize the land use arrays + allocate(landuse_states(num_landuse_state_vars,bounds%begg:bounds%endg),stat=ier) + if (ier /= 0) then + call endrun(msg=' allocation error for landuse_states'//errMsg(__FILE__, __LINE__)) + end if + allocate(landuse_transitions(num_landuse_transition_vars,bounds%begg:bounds%endg),stat=ier) + if (ier /= 0) then + call endrun(msg=' allocation error for landuse_transitions'//errMsg(__FILE__, __LINE__)) + end if + + landuse_states = 0._r8 + landuse_transitions = 0._r8 + + if (use_fates_luh) then + + ! Generate the dyn_file_type object + ! TO DO: check whether to initialize with start or end + dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_START_OF_TIMESTEP) + ! dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) + + ! Get initial land use data + num_points = (bounds%endg - bounds%begg + 1) + landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor? + do varnum = 1, num_landuse_transition_vars + landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do + do varnum = 1, num_landuse_state_vars + landuse_state_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do + end if + + ! Since fates needs state data during initialization, make sure to call + ! the interpolation routine at the start + call dynFatesLandUseInterp(bounds,init_state=.true.) + + end subroutine dynFatesLandUseInit + + + !----------------------------------------------------------------------- + subroutine dynFatesLandUseInterp(bounds, init_state) + + use dynTimeInfoMod , only : time_info_type + use clm_varctl , only : use_cn + + ! !ARGUMENTS: + type(bounds_type), intent(in) :: bounds ! proc-level bounds + logical, optional, intent(in) :: init_state ! fates needs state for initialization + + ! !LOCAL VARIABLES: + integer :: varnum + integer :: i + logical :: init_flag + real(r8), allocatable :: this_data(:) + character(len=*), parameter :: subname = 'dynFatesLandUseInterp' + !----------------------------------------------------------------------- + SHR_ASSERT_ALL(bounds%level == BOUNDS_LEVEL_PROC, subname // ': argument must be PROC-level bounds') + + ! This shouldn't be called by cn currently, but return if it is + if (use_cn) return ! Use this as a protection in lieu of build namelist check? + + init_flag = .false. + if (present(init_state)) then + init_flag = init_state + end if + + ! input land use data for current year are stored in year+1 in the file + call dynFatesLandUse_file%time_info%set_current_year_get_year(1) + + if (dynFatesLandUse_file%time_info%is_before_time_series() .and. .not.(init_flag)) then + ! Reset the land use transitions to zero for safety + landuse_transitions(1:num_landuse_transition_vars,bounds%begg:bounds%endg) = 0._r8 + landuse_states(1:num_landuse_state_vars,bounds%begg:bounds%endg) = 0._r8 + else + ! Right now we don't account for the topounits + allocate(this_data(bounds%begg:bounds%endg)) + do varnum = 1, num_landuse_transition_vars + call landuse_transition_vars(varnum)%get_current_data(this_data) + landuse_transitions(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg) + end do + do varnum = 1, num_landuse_state_vars + call landuse_state_vars(varnum)%get_current_data(this_data) + landuse_states(varnum,bounds%begg:bounds%endg) = this_data(bounds%begg:bounds%endg) + end do + deallocate(this_data) + end if + + end subroutine dynFatesLandUseInterp + +end module dynFATESLandUseChangeMod diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index dada3e9975..c15a23b577 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -201,10 +201,11 @@ subroutine dynSubgrid_driver(bounds_proc, ! OUTSIDE any loops over clumps in the driver. ! ! !USES: - use clm_varctl , only : use_cn, use_fates - use dynInitColumnsMod , only : initialize_new_columns - use dynConsBiogeophysMod , only : dyn_hwcontent_init, dyn_hwcontent_final - use dynEDMod , only : dyn_ED + use clm_varctl , only : use_cn, use_fates, use_fates_luh + use dynInitColumnsMod , only : initialize_new_columns + use dynConsBiogeophysMod , only : dyn_hwcontent_init, dyn_hwcontent_final + use dynEDMod , only : dyn_ED + use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds_proc ! processor-level bounds @@ -288,6 +289,11 @@ subroutine dynSubgrid_driver(bounds_proc, if (get_do_transient_urban()) then call dynurban_interp(bounds_proc) end if + + if (use_fates_luh) then + call dynFatesLandUseInterp + end if + ! ========================================================================== ! Do land cover change that does not require I/O ! ========================================================================== diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 7988fbfc7b..1a04c10749 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -132,7 +132,7 @@ subroutine initialize2(ni,nj) use clm_varpar , only : natpft_size,cft_size use clm_varctl , only : fsurdat use clm_varctl , only : finidat, finidat_interp_source, finidat_interp_dest, fsurdat - use clm_varctl , only : use_cn, use_fates + use clm_varctl , only : use_cn, use_fates, use_fates_luh use clm_varctl , only : use_crop, ndep_from_cpl, fates_spitfire_mode use clm_varorb , only : eccen, mvelpp, lambm0, obliqr use landunit_varcon , only : landunit_varcon_init, max_lunit, numurbl @@ -140,7 +140,7 @@ subroutine initialize2(ni,nj) use decompInitMod , only : decompInit_clumps, decompInit_glcp use domainMod , only : domain_check, ldomain, domain_init use surfrdMod , only : surfrd_get_data - use controlMod , only : NLFilename + use controlMod , only : NLFilename, fluh_timeseries use initGridCellsMod , only : initGridCells use ch4varcon , only : ch4conrd use UrbanParamsType , only : UrbanInput, IsSimpleBuildTemp @@ -172,6 +172,7 @@ subroutine initialize2(ni,nj) use CNSharedParamsMod , only : CNParamsSetSoilDepth use NutrientCompetitionFactoryMod , only : create_nutrient_competition_method use FATESFireFactoryMod , only : scalar_lightning + use dynFATESLandUseChangeMod , only : dynFatesLandUseInit ! ! !ARGUMENTS integer, intent(in) :: ni, nj ! global grid sizes @@ -403,6 +404,11 @@ subroutine initialize2(ni,nj) call dynSubgrid_init(bounds_proc, glc_behavior, crop_inst) call t_stopf('init_dyn_subgrid') + ! Initialize fates LUH2 usage + if (use_fates_luh) then + call dynFatesLandUseInit(bounds_proc, fluh_timeseries) + end if + ! Initialize baseline water and energy states needed for dynamic subgrid operation ! This will be overwritten by the restart file, but needs to be done for a cold start ! case. diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 9be9af2f73..8dbb4afc64 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -258,17 +258,19 @@ module clm_varctl integer, public :: fates_spitfire_mode = 0 ! 0 for no fire; 1 for constant ignitions; > 1 for external data (lightning and/or anthropogenic ignitions) ! see bld/namelist_files/namelist_definition_clm4_5.xml for details - logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage module - logical, public :: use_fates_logging = .false. ! true => turn on logging module - logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro + logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage module + logical, public :: use_fates_logging = .false. ! true => turn on logging module + logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro logical, public :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking - logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure - logical, public :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology - logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory - logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode - logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode - logical, public :: use_fates_sp = .false. ! true => use FATES satellite phenology mode - character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control + logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure + logical, public :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology + logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory + logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode + logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode + logical, public :: use_fates_sp = .false. ! true => use FATES satellite phenology mode + logical, public :: use_fates_luh = .false. ! true => use FATES satellite phenology mode + character(len=256), public :: fluh_timeseries = '' ! filename for inventory control + character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control !---------------------------------------------------------- ! LUNA switches diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index a07228aa0d..3b669063fe 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -228,6 +228,8 @@ subroutine control_init(dtime) use_fates_fixed_biogeog, & use_fates_nocomp, & use_fates_sp, & + use_fates_luh, & + fluh_timeseries, & fates_inventory_ctrl_filename, & fates_parteh_mode, & use_fates_tree_damage @@ -714,8 +716,10 @@ subroutine control_spmd() call mpi_bcast (use_fates_fixed_biogeog, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_fates_luh, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (fluh_timeseries, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier) ! flexibleCN nitrogen model @@ -1058,6 +1062,8 @@ subroutine control_print () write(iulog, *) ' use_fates_fixed_biogeog = ', use_fates_fixed_biogeog write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp + write(iulog, *) ' use_fates_luh= ', use_fates_sp + write(iulog, *) ' fluh_timeseries = ',fluh_timeseries write(iulog, *) ' fates_inventory_ctrl_filename = ',fates_inventory_ctrl_filename end if end subroutine control_print diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index d5175342f0..97597fee71 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -26,6 +26,7 @@ module histFileMod use FatesInterfaceTypesMod , only : nlevsclass, nlevage, nlevcoage use FatesInterfaceTypesMod , only : nlevheight use FatesInterfaceTypesMod , only : nlevdamage + use FatesConstantsMod , only : n_landuse_cats use EDTypesMod , only : nfsc use FatesLitterMod , only : ncwd use PRTGenericMod , only : num_elements_fates => num_elements @@ -2469,6 +2470,8 @@ subroutine htape_create (t, histrest) call ncd_defdim(lnfid, 'fates_levelage', num_elements_fates * nlevage, dimid) call ncd_defdim(lnfid, 'fates_levagefuel', nlevage * nfsc, dimid) call ncd_defdim(lnfid, 'fates_levclscpf', nclmax*nlevsclass*numpft_fates, dimid) + call ncd_defdim(lnfid, 'fates_levlanduse', n_landuse_cats, dimid) + call ncd_defdim(lnfid, 'fates_levlulu', n_landuse_cats * n_landuse_cats, dimid) end if if ( .not. lhistrest )then @@ -3021,6 +3024,7 @@ subroutine htape_timeconst(t, mode) use FatesInterfaceTypesMod, only : fates_hdim_scmap_levcdpf use FatesInterfaceTypesMod, only : fates_hdim_cdmap_levcdpf use FatesInterfaceTypesMod, only : fates_hdim_pftmap_levcdpf + use FatesInterfaceTypesMod, only : fates_hdim_levlanduse ! @@ -3149,6 +3153,8 @@ subroutine htape_timeconst(t, mode) long_name='FATES pft index of the combined damage-size-PFT dimension', ncid=nfid(t)) call ncd_defvar(varname='fates_levcdam', xtype=tape(t)%ncprec, dim1name='fates_levcdam', & long_name='FATES damage class lower bound', units='unitless', ncid=nfid(t)) + call ncd_defvar(varname='fates_levlanduse',xtype=ncd_int, dim1name='fates_levlanduse', & + long_name='FATES land use label', ncid=nfid(t)) end if @@ -3198,6 +3204,7 @@ subroutine htape_timeconst(t, mode) call ncd_io(varname='fates_scmap_levcdpf',data=fates_hdim_scmap_levcdpf, ncid=nfid(t), flag='write') call ncd_io(varname='fates_cdmap_levcdpf',data=fates_hdim_cdmap_levcdpf, ncid=nfid(t), flag='write') call ncd_io(varname='fates_pftmap_levcdpf',data=fates_hdim_pftmap_levcdpf, ncid=nfid(t), flag='write') + call ncd_io(varname='fates_levlanduse',data=fates_hdim_levlanduse, ncid=nfid(t), flag='write') end if endif @@ -5515,6 +5522,10 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, num2d = nlevage*nfsc case('fates_levclscpf') num2d = nclmax * nclmax * numpft_fates + case ('fates_levlanduse') + num2d = n_landuse_cats + case ('fates_levlulu') + num2d = n_landuse_cats * n_landuse_cats case('cft') if (cft_size > 0) then num2d = cft_size diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c169d710ef..142348b444 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -60,6 +60,7 @@ module CLMFatesInterfaceMod use clm_varctl , only : use_fates_fixed_biogeog use clm_varctl , only : use_fates_nocomp use clm_varctl , only : use_fates_sp + use clm_varctl , only : use_fates_luh use clm_varctl , only : fates_inventory_ctrl_filename use clm_varctl , only : use_nitrif_denitrif use clm_varctl , only : use_lch4 @@ -129,6 +130,7 @@ module CLMFatesInterfaceMod use PRTGenericMod , only : num_elements use FatesInterfaceTypesMod, only : hlm_stepsize use FatesInterfaceTypesMod, only : fates_maxPatchesPerSite + use FatesInterfaceTypesMod, only : hlm_num_luh2_states use EDMainMod , only : ed_ecosystem_dynamics use EDMainMod , only : ed_update_site use EDInitMod , only : zero_site @@ -159,6 +161,12 @@ module CLMFatesInterfaceMod use FatesConstantsMod , only : hlm_harvest_area_fraction use FatesConstantsMod , only : hlm_harvest_carbon use perf_mod , only : t_startf, t_stopf + + use dynFATESLandUseChangeMod, only : num_landuse_transition_vars, num_landuse_state_vars + use dynFATESLandUseChangeMod, only : landuse_transitions, landuse_states + use dynFATESLandUseChangeMod, only : landuse_transition_varnames, landuse_state_varnames + use dynFATESLandUseChangeMod, only : dynFatesLandUseInterp + implicit none type, public :: f2hmap_type @@ -353,6 +361,9 @@ subroutine CLMFatesGlobals2() integer :: pass_is_restart integer :: pass_cohort_age_tracking integer :: pass_tree_damage + integer :: pass_use_luh + integer :: pass_num_luh_states + integer :: pass_num_luh_transitions call t_startf('fates_globals2') @@ -491,6 +502,19 @@ subroutine CLMFatesGlobals2() call set_fates_ctrlparms('num_lu_harvest_cats',ival=pass_num_lu_harvest_cats) call set_fates_ctrlparms('use_logging',ival=pass_logging) + if(use_fates_luh) then + pass_use_luh = 1 + pass_num_luh_states = num_landuse_state_vars + pass_num_luh_transitions = num_landuse_transition_vars + else + pass_use_luh = 0 + pass_num_luh_states = 0 + pass_num_luh_transitions = 0 + end if + call set_fates_ctrlparms('use_luh2',ival=pass_use_luh) + call set_fates_ctrlparms('num_luh2_states',ival=pass_num_luh_states) + call set_fates_ctrlparms('num_luh2_transitions',ival=pass_num_luh_transitions) + if(use_fates_inventory_init) then pass_inventory_init = 1 else @@ -693,7 +717,9 @@ subroutine init(this, bounds_proc ) ndecomp = col%nbedrock(c) - call allocate_bcin(this%fates(nc)%bc_in(s),col%nbedrock(c),ndecomp, num_harvest_inst,surfpft_lb,surfpft_ub) + call allocate_bcin(this%fates(nc)%bc_in(s),col%nbedrock(c),ndecomp, & + num_harvest_inst, num_landuse_state_vars, num_landuse_transition_vars, & + surfpft_lb,surfpft_ub) call allocate_bcout(this%fates(nc)%bc_out(s),col%nbedrock(c),ndecomp) call zero_bcs(this%fates(nc),s) @@ -996,10 +1022,15 @@ subroutine dynamics_driv(this, nc, bounds_clump, & write(iulog,*) harvest_units call endrun(msg=errMsg(sourcefile, __LINE__)) end if - - endif + if (use_fates_luh) then + this%fates(nc)%bc_in(s)%hlm_luh_states = landuse_states(:,g) + this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames + this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g) + this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames + end if + end do ! Nutrient uptake fluxes have been accumulating with each short @@ -1703,9 +1734,9 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & real(r8) :: vol_ice real(r8) :: eff_porosity integer :: nlevsoil ! Number of soil layers at each site - integer :: j + integer :: i, j integer :: s - integer :: c + integer :: c, g integer :: p ! HLM patch index integer :: ft ! plant functional type @@ -1795,6 +1826,18 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & call HydrSiteColdStart(this%fates(nc)%sites,this%fates(nc)%bc_in) end if + do s = 1,this%fates(nc)%nsites + c = this%f2hmap(nc)%fcolumn(s) + g = col_pp%gridcell(c) + + if (use_fates_luh) then + this%fates(nc)%bc_in(s)%hlm_luh_states = landuse_states(:,g) + this%fates(nc)%bc_in(s)%hlm_luh_state_names = landuse_state_varnames + this%fates(nc)%bc_in(s)%hlm_luh_transitions = landuse_transitions(:,g) + this%fates(nc)%bc_in(s)%hlm_luh_transition_names = landuse_transition_varnames + end if + end do + ! Newly initialized patches need a starting temperature call init_patches(this%fates(nc)%nsites, this%fates(nc)%sites, & this%fates(nc)%bc_in) @@ -2750,6 +2793,7 @@ subroutine init_history_io(this,bounds_proc) use FatesIOVariableKindMod, only : site_height_r8, site_elem_r8, site_elpft_r8 use FatesIOVariableKindMod, only : site_elcwd_r8, site_elage_r8, site_agefuel_r8 use FatesIOVariableKindMod, only : site_cdpf_r8, site_cdsc_r8, site_clscpf_r8 + use FatesIOVariableKindMod, only : site_landuse_r8, site_lulu_r8 use FatesIODimensionsMod, only : fates_bounds_type @@ -2852,7 +2896,8 @@ subroutine init_history_io(this,bounds_proc) site_can_r8,site_cnlf_r8, site_cnlfpft_r8, site_scag_r8, & site_scagpft_r8, site_agepft_r8, site_elem_r8, site_elpft_r8, & site_elcwd_r8, site_elage_r8, site_agefuel_r8, & - site_cdsc_r8, site_cdpf_r8) + site_cdsc_r8, site_cdpf_r8, & + site_landuse_r8, site_lulu_r8) d_index = fates_hist%dim_kinds(dk_index)%dim2_index @@ -3145,7 +3190,8 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates) use FatesLitterMod, only : ncwd use EDtypesMod, only : nlevleaf, nclmax use FatesInterfaceTypesMod, only : numpft_fates => numpft - + use FatesConstantsMod, only : n_landuse_cats + implicit none @@ -3234,7 +3280,12 @@ subroutine hlm_bounds_to_fates_bounds(hlm, fates) fates%clscpf_begin = 1 fates%clscpf_end = numpft_fates * nlevsclass * nclmax - + + fates%landuse_begin = 1 + fates%landuse_end = n_landuse_cats + + fates%lulu_begin = 1 + fates%lulu_end = n_landuse_cats * n_landuse_cats call t_stopf('fates_hlm2fatesbnds') From f90a6819a817fba2b60224b3e4c5b87309acab5c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 14 Jun 2023 16:57:08 -0700 Subject: [PATCH 1012/2067] add fates luh2 namelist definition and defaults --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 ++++++ bld/namelist_files/namelist_definition_ctsm.xml | 15 +++++++++++++++ 2 files changed, 21 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6bb5d60aa7..4a036b63bd 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1514,6 +1514,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/release-clm5.0.18/landuse.timeseries_10x15_SSP5-3.4_16pfts_Irrig_CMIP6_simyr1850-2100_c190228.nc + + +lnd/clm2/luh/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c230415.nc + .true. .true. @@ -2669,6 +2674,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. +.false. 1 .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index f51c577c09..a5c7d0a075 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -718,6 +718,21 @@ Full pathname to the inventory initialization control file. (Only relevant if FATES is on). + + +If TRUE, enable use of land use state and transition data from luh_timeseries file. +(Only valid for fates land use change runs, where there is a luh_timeseries file.) +(Also, only valid for use_fates = true and is incompatible with transient runs currently.) + + + + +Full pathname of unified land use harmonization data file. This causes the land-use +types to vary over time. + + Toggle to turn on the LUNA model, to effect Photosynthesis by leaf Nitrogen From 533c9296d146f10a12d4ad41f25682d1b02f222c Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 15 Jun 2023 13:37:53 -0600 Subject: [PATCH 1013/2067] query batch queue --- tools/site_and_regional/run_neon.py | 35 ++++++++++++++--------------- 1 file changed, 17 insertions(+), 18 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index 9eb8da9dc0..b6033e55c1 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -356,22 +356,6 @@ def parse_isoduration(s): dt = datetime.timedelta(days=int(days) + 365 * int(years) + 30 * int(months)) return int(dt.total_seconds() / 86400) -def get_queue_command(batch_system): - match batch_system.lower(): - 'pbs': - queue_command = 'qstat -u ' - 'slurm': - queue_command = 'squeue -u ' - 'cobalt': - queue_command = 'qstat -u ' - 'lsf': - queue_command = 'bqueues -u ' - case _: - queue_command = '' - - return queue_command - - class NeonSite: """ @@ -490,7 +474,22 @@ def diff_month(self): d1 = datetime.datetime(self.end_year, self.end_month, 1) d2 = datetime.datetime(self.start_year, self.start_month, 1) return (d1.year - d2.year) * 12 + d1.month - d2.month + + def get_batch_query(self, case): + """ + Function for querying the batch queue query command for a case, depending on the + user's batch system. If no batch system, empty string is returned + Args: + case: + case object + """ + + if case.get_value("BATCH_SYSTEM") == "none": + return "" + else: + return case.get_value("batch_query") + def run_case( self, base_case_root, @@ -553,7 +552,7 @@ def run_case( case.submit(no_batch=no_batch) logger.info("-----------------------------------") logger.info("Successfully submitted case!") - logger.info("Use 'qstat -u ' to check its run status") + logger.info(f"Use {self.get_batch_query(case)} to check its run status") return else: logger.warning( @@ -633,7 +632,7 @@ def run_case( case.submit(no_batch=no_batch) logger.info("-----------------------------------") logger.info("Successfully submitted case!") - logger.info("Use 'qstat -u ' to check its run status") + logger.info(f"Use {self.get_batch_query(case)} to check its run status") def set_ref_case(self, case): rundir = case.get_value("RUNDIR") From 62910d7b3de7ca71f2b22968227ef81499f7cbe8 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 15 Jun 2023 14:00:49 -0600 Subject: [PATCH 1014/2067] don't print if none batch system --- tools/site_and_regional/run_neon.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index b6033e55c1..ccb895bccb 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -478,7 +478,7 @@ def diff_month(self): def get_batch_query(self, case): """ Function for querying the batch queue query command for a case, depending on the - user's batch system. If no batch system, empty string is returned + user's batch system. Args: case: @@ -486,7 +486,7 @@ def get_batch_query(self, case): """ if case.get_value("BATCH_SYSTEM") == "none": - return "" + return "none" else: return case.get_value("batch_query") @@ -552,7 +552,9 @@ def run_case( case.submit(no_batch=no_batch) logger.info("-----------------------------------") logger.info("Successfully submitted case!") - logger.info(f"Use {self.get_batch_query(case)} to check its run status") + batch_query = self.get_batch_query(case) + if batch_query != "none": + logger.info(f"Use {batch_query} to check its run status") return else: logger.warning( @@ -632,7 +634,9 @@ def run_case( case.submit(no_batch=no_batch) logger.info("-----------------------------------") logger.info("Successfully submitted case!") - logger.info(f"Use {self.get_batch_query(case)} to check its run status") + batch_query = self.get_batch_query(case) + if batch_query != "none": + logger.info(f"Use {batch_query} to check its run status") def set_ref_case(self, case): rundir = case.get_value("RUNDIR") From ca98bfaf229b7f1fefb205c9bb9fb17b71210965 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Thu, 15 Jun 2023 14:50:30 -0600 Subject: [PATCH 1015/2067] change logger.info to print --- tools/site_and_regional/run_neon.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tools/site_and_regional/run_neon.py b/tools/site_and_regional/run_neon.py index ccb895bccb..84c00715fb 100755 --- a/tools/site_and_regional/run_neon.py +++ b/tools/site_and_regional/run_neon.py @@ -550,11 +550,11 @@ def run_case( elif not setup_only: print("Resubmitting case {}".format(case_root)) case.submit(no_batch=no_batch) - logger.info("-----------------------------------") - logger.info("Successfully submitted case!") + print("-----------------------------------") + print("Successfully submitted case!") batch_query = self.get_batch_query(case) if batch_query != "none": - logger.info(f"Use {batch_query} to check its run status") + print(f"Use {batch_query} to check its run status") return else: logger.warning( @@ -632,11 +632,11 @@ def run_case( case.check_all_input_data() if not setup_only: case.submit(no_batch=no_batch) - logger.info("-----------------------------------") - logger.info("Successfully submitted case!") + print("-----------------------------------") + print("Successfully submitted case!") batch_query = self.get_batch_query(case) if batch_query != "none": - logger.info(f"Use {batch_query} to check its run status") + print(f"Use {batch_query} to check its run status") def set_ref_case(self, case): rundir = case.get_value("RUNDIR") From 9d347f1d1d41bf17ac67a68300bc173486e02a4e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 16 Jun 2023 11:24:26 -0600 Subject: [PATCH 1016/2067] Update NEON surface datasets --- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index ddf627b04e..44b26abeed 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -19,7 +19,7 @@ !---------------------------------------------------------------------------------- flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets -fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230111.nc" +fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230601.nc" stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' From df7e4decfe3242cf7991418a08075e5c0a95a856 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 16 Jun 2023 14:11:12 -0600 Subject: [PATCH 1017/2067] Moved filling of tillage_mults_allphases to its own subroutine. --- src/biogeochem/TillageMod.F90 | 66 ++++++++++++------- src/main/clm_instMod.F90 | 7 +- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 4 ++ 3 files changed, 50 insertions(+), 27 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index 2b6c06368f..f5b2249d67 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -25,6 +25,7 @@ module TillageMod private ! !PUBLIC MEMBER PROCEDURES public :: tillage_init + public :: tillage_init_century public :: get_do_tillage public :: get_apply_tillage_multipliers ! @@ -49,7 +50,8 @@ module TillageMod subroutine tillage_init(bounds) ! - ! Read namelist parameters and allocate variables related to tillage + ! Read namelist parameters related to tillage. Allocation of variables happens + ! in separate subroutines written specifically for decomposition mode of choice. ! ! !USES: use spmdMod , only : masterproc @@ -113,15 +115,49 @@ subroutine tillage_init(bounds) do_tillage_high_private = do_tillage_high use_original_tillage_private = use_original_tillage - ! Allocate tillage multipliers - if (get_do_tillage()) then - allocate(tillage_mults(ndecomp_pools)); tillage_mults(:) = 1.0_r8 - allocate(tillage_mults_allphases(ndecomp_pools, nphases)); tillage_mults_allphases(:,:) = 1.0_r8 - end if end subroutine tillage_init + subroutine tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + ! !DESCRIPTION: + ! + ! Allocate multiplier arrays to be used in tillage. Call during initialization of CENTURY decomposition. + ! Written by Sam Rabin. + ! + ! !USES + use pftconMod , only : npcropmin + ! + ! !ARGUMENTS: + integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools + integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools + + if (.not. get_do_tillage()) then + return + end if + + ! Allocate tillage multipliers + allocate(tillage_mults(ndecomp_pools)); tillage_mults(:) = 1.0_r8 + allocate(tillage_mults_allphases(ndecomp_pools, nphases)); tillage_mults_allphases(:,:) = 1.0_r8 + + ! Fill tillage_mults_allphases + if (do_tillage_low_private) then + tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) + tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + else + tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_act_som,:) = (/ 1.2_r8, 1.0_r8, 1.0_r8 /) + tillage_mults_allphases(i_slo_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) + tillage_mults_allphases(i_pas_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) + end if + + end subroutine tillage_init_century + + function get_do_tillage() logical :: get_do_tillage get_do_tillage = do_tillage_low_private .or. do_tillage_high_private @@ -252,24 +288,6 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som call endrun('ERROR No active patches found (crop OR non-crop)') end if - ! Set up tillage multipliers - ! (It would be better to do this in tillage_init, but that can't happen - ! because these indices are private members of SoilBiogeochemDecompCascadeBGCMod. - tillage_mults_allphases(:,:) = 1.0_r8 - if (do_tillage_low_private) then - tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) - tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) - tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) - else - tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_act_som,:) = (/ 1.2_r8, 1.0_r8, 1.0_r8 /) - tillage_mults_allphases(i_slo_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) - tillage_mults_allphases(i_pas_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) - end if - call get_tillage_multipliers(idop, this_patch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index b02e86d696..63f28716f7 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -378,6 +378,10 @@ subroutine clm_instInit(bounds) call soilbiogeochem_state_inst%Init(bounds) + ! Initialize tillage + ! Must be called before init_decompcascade* + call tillage_init(bounds) + ! Initialize decompcascade constants ! Note that init_decompcascade_bgc need ! soilbiogeochem_state_inst to be initialized @@ -391,9 +395,6 @@ subroutine clm_instInit(bounds) soilstate_inst) end if - ! Initialize tillage - call tillage_init(bounds) - ! Initalize soilbiogeochem carbon types call soilbiogeochem_carbonstate_inst%Init(bounds, carbon_type='c12', ratio=1._r8) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 7060034217..a1a45b65ad 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -230,6 +230,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i ! written by C. Koven ! ! !USES: + use TillageMod, only : tillage_init_century ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -505,6 +506,9 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i deallocate(params_inst%bgc_initial_Cstocks) + ! Allocate tillage variables + call tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + end associate end subroutine init_decompcascade_bgc From 2a812c4d963409cb2a035ca0de82e4f95676eaf0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 16 Jun 2023 14:38:15 -0600 Subject: [PATCH 1018/2067] Error if called with soil_decomp_method other than CENTURYKoven2013. --- bld/CLMBuildNamelist.pm | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 41582ee6f9..30cef854ba 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2163,6 +2163,11 @@ sub setup_logic_tillage { if ( &value_is_true($nl->get_value('use_fates')) ) { $log->fatal_error( "Tillage can't be used with FATES" ); } + + my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( "soil_decomp_method" ) ); + if ( $soil_decomp_method ne "CENTURYKoven2013" ) { + $log->fatal_error( "Tillage can only be used with soil_decomp_method 'CENTURYKoven2013'" ); + } } } From 39ece605d0b58cbd08d8fbdbb1cae59966ef4699 Mon Sep 17 00:00:00 2001 From: wwieder Date: Sat, 17 Jun 2023 06:12:34 -0600 Subject: [PATCH 1019/2067] replace bad with missing --- .../NEON/FATES/MLBS/shell_commands | 2 +- .../NEON/FATES/MOAB/shell_commands | 2 +- .../NEON/FATES/NIWO/shell_commands | 2 +- .../NEON/FATES/ONAQ/shell_commands | 2 +- .../NEON/FATES/SJER/shell_commands | 17 ++++++++++++----- .../NEON/FATES/TEAK/shell_commands | 2 +- .../NEON/FATES/WREF/shell_commands | 2 +- .../NEON/FATES/YELL/shell_commands | 2 +- .../usermods_dirs/NEON/MLBS/shell_commands | 2 +- .../usermods_dirs/NEON/MOAB/shell_commands | 2 +- .../usermods_dirs/NEON/NIWO/shell_commands | 2 +- .../usermods_dirs/NEON/ONAQ/shell_commands | 2 +- .../usermods_dirs/NEON/SJER/shell_commands | 2 +- .../usermods_dirs/NEON/TEAK/shell_commands | 2 +- .../usermods_dirs/NEON/WREF/shell_commands | 2 +- .../usermods_dirs/NEON/YELL/shell_commands | 2 +- 16 files changed, 27 insertions(+), 20 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands index 1620cc3850..0d43e032f8 100644 --- a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=MLBS ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2019 diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands index 585a21fc78..1d0d4fb8c1 100644 --- a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=MOAB ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2020 diff --git a/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands index f6c9909e62..b4f27ea8ed 100644 --- a/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == "NEON" ]]; then ./xmlchange DATM_YR_END=2018 diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands index 62cf17e909..36223abee1 100644 --- a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=ONAQ ./xmlchange PTS_LON=247.54755 ./xmlchange PTS_LAT=40.17760 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2019 diff --git a/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands index 6e05d23792..2e3d158847 100644 --- a/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands @@ -2,10 +2,17 @@ ./xmlchange NEONSITE=SJER ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 -./xmlchange DATM_YR_ALIGN=2019,DATM_YR_START=2019 -# Different default start date and number of months to run for transient case -if [[ $compset =~ ^HIST ]]; then - ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 +./xmlchange DATM_YR_ALIGN=2019 +# NEON precipitation data for this site is missing so end early +# If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data +if [ $CLM_USRDAT_NAME=='NEON' ] +then + ./xmlchange DATM_YR_START=2019 + # Different default start date and number of months to run for transient case + if [[ $compset =~ ^HIST ]] + then + ./xmlchange RUN_STARTDATE=2019-01-01 + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands index 32420f9f2a..0efa486d6e 100644 --- a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands index 79df152826..d3dec03ac8 100644 --- a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands index 9fb99f00f8..656cdff066 100644 --- a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 1620cc3850..0d43e032f8 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=MLBS ./xmlchange PTS_LON=279.47575 ./xmlchange PTS_LAT=37.37783 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2019 diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 585a21fc78..1d0d4fb8c1 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=MOAB ./xmlchange PTS_LON=250.61118 ./xmlchange PTS_LAT=38.25136 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2020 diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/NEON/NIWO/shell_commands index f6c9909e62..b4f27ea8ed 100644 --- a/cime_config/usermods_dirs/NEON/NIWO/shell_commands +++ b/cime_config/usermods_dirs/NEON/NIWO/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=NIWO ./xmlchange PTS_LON=254.41676 ./xmlchange PTS_LAT=40.05236 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == "NEON" ]]; then ./xmlchange DATM_YR_END=2018 diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 62cf17e909..36223abee1 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -2,7 +2,7 @@ ./xmlchange NEONSITE=ONAQ ./xmlchange PTS_LON=247.54755 ./xmlchange PTS_LAT=40.17760 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_END=2019 diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 3525405e09..2e3d158847 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=240.267 ./xmlchange PTS_LAT=37.107117 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [ $CLM_USRDAT_NAME=='NEON' ] then diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 32420f9f2a..0efa486d6e 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=240.99424199999999 ./xmlchange PTS_LAT=37.006472 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index 79df152826..d3dec03ac8 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=238.04162 ./xmlchange PTS_LAT=45.81637 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index 9fb99f00f8..656cdff066 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -3,7 +3,7 @@ ./xmlchange PTS_LON=249.45803999999998 ./xmlchange PTS_LAT=44.95597 ./xmlchange DATM_YR_ALIGN=2019 -# NEON precipitation data for this site is bad so end early +# NEON precipitation data for this site is missing so end early # If CLM_USRDAT_NAME is NEON.PRISM you can run to the end of the data if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case From ed82479d6fae289b26379ff832605105a3fb0ddc Mon Sep 17 00:00:00 2001 From: wwieder Date: Sat, 17 Jun 2023 06:16:44 -0600 Subject: [PATCH 1020/2067] remove redundant xml commands --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 2 -- 1 file changed, 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index eaea7a9f1c..a583b03874 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -39,8 +39,6 @@ if [[ $compset == *'SP_SICE'* ]]; then done> user_nl_clm - echo "hist_nhtfrq(2) = 1" >> user_nl_clm echo "hist_fincl2 = 'FCEV','FCTR','FGEV','FIRA','FSA','FSH','FPSN','H2OSOI','SNOW_DEPTH','TBOT','TSOI'" >> user_nl_clm fi From 1e22f0a342b9864e7aed2556690caa8d6209957e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 17 Jun 2023 15:53:14 -0600 Subject: [PATCH 1021/2067] Move setting of NEON lightning file into the namelist_defaults fixing #2027 --- bld/CLMBuildNamelist.pm | 11 ++++++++++- bld/namelist_files/namelist_defaults_ctsm.xml | 7 +++++++ bld/namelist_files/namelist_definition_ctsm.xml | 6 +++--- .../usermods_dirs/NEON/defaults/shell_commands | 10 ---------- cime_config/usermods_dirs/NEON/defaults/user_nl_clm | 3 --- 5 files changed, 20 insertions(+), 17 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 02d9799487..4fd80ae17f 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -168,7 +168,8 @@ OPTIONS (default is 0) (standard option with land-ice model is 10) -glc_use_antarctica Set defaults appropriate for runs that include Antarctica -help [or -h] Print usage to STDOUT. - -light_res Resolution of lightning dataset to use for CN fire (360x720 or 94x192) + -light_res Resolution of lightning dataset to use for CN or FATES fire (360x720, 106x174, or 94x192) + 106x174 can only be used for NEON sites -lilac If CTSM is being run through LILAC (normally not used) (LILAC is the Lightweight Infrastructure for Land-Atmosphere Coupling) -ignore_ic_date Ignore the date on the initial condition files @@ -955,6 +956,7 @@ sub setup_cmdl_fire_light_res { if ( $val eq "default" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, + 'neon'=>$nl_flags->{'neon'}, 'fates_spitfire_mode'=>$nl->get_value('fates_spitfire_mode'), 'use_fates'=>$nl_flags->{'use_fates'}, fire_method=>$nl->get_value('fire_method') ); $val = remove_leading_and_trailing_quotes( $nl->get_value($var) ); @@ -1435,6 +1437,13 @@ sub process_namelist_commandline_clm_usr_name { $settings{'csmdata'} = $nl_flags->{'inputdata_rootdir'}; } + # For NEON sites + if ($opts->{'clm_usr_name'} =~ /NEON/) { + $nl_flags->{'neon'} = ".true." + } else { + $nl_flags->{'neon'} = ".false." + } + my $nvars = 0; my $nl_usrfile = Build::Namelist->new(); foreach my $var (@vars) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6bb5d60aa7..5eb410a6d1 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1672,6 +1672,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 94x192 94x192 360x720 +106x174 none none none @@ -1679,12 +1680,18 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 360x720 360x720 360x720 +106x174 +106x174 +106x174 +106x174 0001 0001 atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62.lnfm_Total_c140423.nc atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62_ESMFmesh_cdf5_110621.nc +atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc +atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_c160825.nc atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720_ESMFmesh_cdf5_150621.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index f51c577c09..3b56941113 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1992,9 +1992,9 @@ to use for methane model -Resolution of Lightning dataset to use for CN fire model -(only applies when CN and the CN fire model are turned on) + group="default_settings" valid_values="none,360x720,106x174,94x192"> +Resolution of Lightning dataset to use for CN or FATES fire model +(only applies when CN or FATES and the fire model is turned on) user_nl_clm.tmp - while read line; do - if [[ $line != *"_lightng"* ]]; then - echo $line>>user_nl_clm.tmp - else - echo '!'$line>>user_nl_clm.tmp - fi - done> user_nl_clm echo "hist_nhtfrq(2) = 1" >> user_nl_clm diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm index 44b26abeed..419ff0314c 100644 --- a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm +++ b/cime_config/usermods_dirs/NEON/defaults/user_nl_clm @@ -21,9 +21,6 @@ flanduse_timeseries = ' ' ! This isn't needed for a non transient case, but will be once we start using transient compsets fsurdat = "$DIN_LOC_ROOT/lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230601.nc" -stream_fldfilename_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc' -stream_meshfile_lightng = '$DIN_LOC_ROOT/atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc' - ! h1 output stream hist_fincl2 = 'AR','ELAI','FCEV','FCTR','FGEV','FIRA','FSA','FSH','GPP','H2OSOI', 'HR','SNOW_DEPTH','TBOT','TSOI','SOILC_vr','FV','NET_NMIN_vr' From c8d62c7665926d06c2669ddc1286fab384ef8019 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 19 Jun 2023 17:22:34 -0600 Subject: [PATCH 1022/2067] Add some more testing for light_res and fates and fire valid namelists as well as a fail test --- bld/unit_testers/build-namelist_test.pl | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 8e16ab3e9b..89056e861f 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1958; +my $ntests = 1971; if ( defined($opts{'compare'}) ) { - $ntests += 1335; + $ntests += 1344; } plan( tests=>$ntests ); @@ -466,6 +466,9 @@ sub cat_and_create_namelistinfile { "-bgc bgc -use_case 2000_control -namelist \"&a fire_method='nofire'/\" -crop", "-res 0.9x1.25 -bgc sp -use_case 1850_noanthro_control -drydep -fire_emis", "-res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control -drydep -fire_emis -light_res 360x720", + "--bgc bgc --light_res none --namelist \"&a fire_method='nofire'/\"", + "--bgc fates --light_res 360x720 --namelist \"&a fates_spitfire_mode=2/\"", + "--bgc fates --light_res none --namelist \"&a fates_spitfire_mode=1/\"", ) { my $file = $startfile; &make_env_run(); @@ -971,6 +974,11 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_1", }, + "FATESwspitfireOffLigtOn" =>{ options=>"-bgc fates -envxml_dir . -no-megan -light_res 360x720", + namelst=>"fates_spitfire_mode=0", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, "FireNoneButBGCfireon" =>{ options=>"-bgc bgc -envxml_dir . -light_res none", namelst=>"fire_method='li2021gswpfrc'", GLC_TWO_WAY_COUPLING=>"FALSE", From 860921b464494c5b87fe720658c674510844591f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 19 Jun 2023 18:02:27 -0600 Subject: [PATCH 1023/2067] Add a fail test for trying to use the NEON light resolution with a global grid and a warning test for a regional case for the same --- bld/unit_testers/build-namelist_test.pl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 89056e861f..6c40df7dc4 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1971; +my $ntests = 1975; if ( defined($opts{'compare'}) ) { $ntests += 1344; } @@ -689,6 +689,11 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "NEONlightresButGlobal" =>{ options=>"--res 4x5 --bgc bgc --envxml_dir . --light_res 106x740", + namelst=>"", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, "spno-fire" =>{ options=>"-bgc sp -envxml_dir . -use_case 2000_control", namelst=>"fire_method='nofire'", GLC_TWO_WAY_COUPLING=>"FALSE", @@ -1235,6 +1240,11 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_1", }, + "NotNEONbutNEONlightres" =>{ options=>"--res CLM_USRDAT --clm_usr_name regional --envxml_dir . --bgc bgc --light_res 106x174", + namelst=>"fsurdat='build-namelist_test.pl'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, ); foreach my $key ( keys(%warntest) ) { print( "$key\n" ); From abbf9fcc3ba589e7ba1eccb3e048350c61146e77 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 19 Jun 2023 23:42:52 -0600 Subject: [PATCH 1024/2067] Fix #2029 so fire_method=none gets the right default for light_res --- bld/CLMBuildNamelist.pm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 4fd80ae17f..5b4dddd289 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -953,16 +953,19 @@ sub setup_cmdl_fire_light_res { my $var = "light_res"; my $val = $opts->{$var}; + if ( &value_is_true($nl->get_value('use_cn')) ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method'); + } + my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); if ( $val eq "default" ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'use_cn'=>$nl_flags->{'use_cn'}, 'neon'=>$nl_flags->{'neon'}, 'fates_spitfire_mode'=>$nl->get_value('fates_spitfire_mode'), - 'use_fates'=>$nl_flags->{'use_fates'}, fire_method=>$nl->get_value('fire_method') ); + 'use_fates'=>$nl_flags->{'use_fates'}, fire_method=>$fire_method ); $val = remove_leading_and_trailing_quotes( $nl->get_value($var) ); $nl_flags->{$var} = $val; } else { - my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); if ( defined($fire_method) && $val ne "none" ) { if ( $fire_method eq "nofire" ) { $log->fatal_error("-$var option used with fire_method='nofire'. -$var can ONLY be used without the nofire option"); @@ -991,9 +994,6 @@ sub setup_cmdl_fire_light_res { # Set flag if cn-fires are on or not # $var = "cnfireson"; - if ( &value_is_true($nl->get_value('use_cn')) ) { - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fire_method'); - } my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) && ! &value_is_true($nl_flags->{'use_fates'}) ) { $log->fatal_error("fire_method is being set while use_cn and use_fates are both false."); From f70f90c3a19d290e04244cd11c604ca6eddb4ccb Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 19 Jun 2023 23:59:58 -0600 Subject: [PATCH 1025/2067] Correct indentation --- bld/CLMBuildNamelist.pm | 74 ++++++++++++++++++++--------------------- 1 file changed, 37 insertions(+), 37 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 5b4dddd289..526edf81eb 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -969,44 +969,44 @@ sub setup_cmdl_fire_light_res { if ( defined($fire_method) && $val ne "none" ) { if ( $fire_method eq "nofire" ) { $log->fatal_error("-$var option used with fire_method='nofire'. -$var can ONLY be used without the nofire option"); - } - } - my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') ); - if ( defined($stream_fldfilename_lightng) && $val ne "none" ) { - $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); - } - if ( ! &value_is_true($nl->get_value('use_cn')) ) { - $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); - } - if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { - $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); - } - $nl_flags->{$var} = $val; - } - my $group = $definition->get_group_name($var); - $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); - if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { - my @valid_values = $definition->get_valid_values( $var ); - $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); - } - $log->verbose_message("Using $nl_flags->{$var} for $var."); - # - # Set flag if cn-fires are on or not - # - $var = "cnfireson"; - my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); - if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) && ! &value_is_true($nl_flags->{'use_fates'}) ) { - $log->fatal_error("fire_method is being set while use_cn and use_fates are both false."); - } - if ( defined($fire_method) && $fire_method eq "nofire" ) { - $nl_flags->{$var} = ".false."; -# } elsif ( &value_is_true($nl->get_value('use_cn')) || $nl_flags->{'fates_spitfire_mode'} > 1 ) { - } elsif ( &value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates')) ) { - $nl_flags->{$var} = ".true."; - } else { - $nl_flags->{$var} = ".false."; - } + } + } + my $stream_fldfilename_lightng = remove_leading_and_trailing_quotes( $nl->get_value('stream_fldfilename_lightng') ); + if ( defined($stream_fldfilename_lightng) && $val ne "none" ) { + $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); + } + if ( ! &value_is_true($nl->get_value('use_cn')) ) { + $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); + } + if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { + $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); + } + $nl_flags->{$var} = $val; } + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); + if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { + my @valid_values = $definition->get_valid_values( $var ); + $log->fatal_error("$var has a value (".$nl_flags->{$var}.") that is NOT valid. Valid values are: @valid_values"); + } + $log->verbose_message("Using $nl_flags->{$var} for $var."); + # + # Set flag if cn-fires are on or not + # + $var = "cnfireson"; + my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); + if ( defined($fire_method) && ! &value_is_true($nl_flags->{'use_cn'}) && ! &value_is_true($nl_flags->{'use_fates'}) ) { + $log->fatal_error("fire_method is being set while use_cn and use_fates are both false."); + } + if ( defined($fire_method) && $fire_method eq "nofire" ) { + $nl_flags->{$var} = ".false."; +# } elsif ( &value_is_true($nl->get_value('use_cn')) || $nl_flags->{'fates_spitfire_mode'} > 1 ) { + } elsif ( &value_is_true($nl->get_value('use_cn')) || &value_is_true($nl->get_value('use_fates')) ) { + $nl_flags->{$var} = ".true."; + } else { + $nl_flags->{$var} = ".false."; + } +} #------------------------------------------------------------------------------- From 091abdd432f29d9557821d0c76c373cdd55a5c43 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Jun 2023 08:17:43 -0600 Subject: [PATCH 1026/2067] Get the buildnamelist tests all working --- bld/CLMBuildNamelist.pm | 34 +++++++++++++++++++++---- bld/unit_testers/build-namelist_test.pl | 4 +-- 2 files changed, 31 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 526edf81eb..c205daa4c4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -976,13 +976,37 @@ sub setup_cmdl_fire_light_res { $log->fatal_error("-$var option used while also explicitly setting stream_fldfilename_lightng filename which is a contradiction. Use one or the other not both."); } if ( ! &value_is_true($nl->get_value('use_cn')) ) { - $log->fatal_error("-$var option used CN is NOT on. -$var can only be used when CN is on (with bgc: cn or bgc)"); - } - if ( &value_is_true($nl->get_value('use_cn')) && $val eq "none" ) { - $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); + if ( &value_is_true($nl_flags->{'use_fates'}) ) { + if ( $nl->get_value('fates_spitfire_mode') < 2) { + if ( $val ne "none" ) { + $log->fatal_error("-$var option used when FATES is on, but fates_spitfire_mode does NOT use lightning data"); + } + } else { + if ( $val eq "none" ) { + $log->fatal_error("-$var option is set to none, but FATES is on and fates_spitfire_mode requires lightning data"); + } + } + } else { + $log->fatal_error("-$var option used when FATES off and CN is NOT on. -$var can only be used when BGC is set to bgc or fates"); + } + } else { + if ( $val eq "none" and $fire_method ne "nofire" ) { + $log->fatal_error("-$var option is set to none, but CN is on (with bgc: cn or bgc) which is a contradiction"); + } } $nl_flags->{$var} = $val; } + # Check that NEON data is only used for NEON sites + if ( $val eq "106x174" ) { + if ( ! &value_is_true($nl_flags->{'neon'}) ) { + if ( defined($opts->{'clm_usr_name'}) ) { + $log->warning("The NEON lightning dataset does NOT cover the entire globe, make sure it covers the region for your grid"); + } else { + $log->fatal_error("The NEON lightning dataset can NOT be used for global grids or regions or points outside of its area as it does NOT cover the entire globe."); + } + } + } + # check for valid values... my $group = $definition->get_group_name($var); $nl->set_variable_value($group, $var, quote_string($nl_flags->{$var}) ); if ( ! $definition->is_valid_value( $var, $nl_flags->{$var}, 'noquotes'=>1 ) ) { @@ -991,7 +1015,7 @@ sub setup_cmdl_fire_light_res { } $log->verbose_message("Using $nl_flags->{$var} for $var."); # - # Set flag if cn-fires are on or not + # Set flag if cn-fires are on or not, only for BGC (not FATES) # $var = "cnfireson"; my $fire_method = remove_leading_and_trailing_quotes( $nl->get_value('fire_method') ); diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 6c40df7dc4..ed6328c166 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -467,8 +467,8 @@ sub cat_and_create_namelistinfile { "-res 0.9x1.25 -bgc sp -use_case 1850_noanthro_control -drydep -fire_emis", "-res 0.9x1.25 -bgc bgc -use_case 1850_noanthro_control -drydep -fire_emis -light_res 360x720", "--bgc bgc --light_res none --namelist \"&a fire_method='nofire'/\"", - "--bgc fates --light_res 360x720 --namelist \"&a fates_spitfire_mode=2/\"", - "--bgc fates --light_res none --namelist \"&a fates_spitfire_mode=1/\"", + "--bgc fates --light_res 360x720 --no-megan --namelist \"&a fates_spitfire_mode=2/\"", + "--bgc fates --light_res none --no-megan --namelist \"&a fates_spitfire_mode=1/\"", ) { my $file = $startfile; &make_env_run(); From 2e000b7d4336516d3b2d64d528f9a9f99b9250ad Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Jun 2023 08:44:36 -0600 Subject: [PATCH 1027/2067] Update xarray which allows code to work with issue #1974 --- python/conda_env_ctsm_py.txt | 2 +- python/conda_env_ctsm_py_cgd.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index 4eb724ab53..0ac4656e73 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -18,6 +18,6 @@ netcdf4 requests packaging numpy=1.18.5 -xarray=0.16.2 +xarray=0.17.0 pylint=2.8.3 black=22.3.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows diff --git a/python/conda_env_ctsm_py_cgd.txt b/python/conda_env_ctsm_py_cgd.txt index c925706611..8312dc328a 100644 --- a/python/conda_env_ctsm_py_cgd.txt +++ b/python/conda_env_ctsm_py_cgd.txt @@ -20,6 +20,6 @@ netcdf4 requests packaging numpy=1.18.5 -xarray=0.16.2 +xarray=0.17.0 pylint=2.8.3 black=22.3.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows From b76d5bf158b9b3a36520922d159089d98dac4867 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Jun 2023 09:26:39 -0600 Subject: [PATCH 1028/2067] Add a NEON-SP test and change a FATES NEON test to require lightning data --- cime_config/testdefs/testlist_clm.xml | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index ec04e651d7..1df065a424 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1579,6 +1579,16 @@ + + + + + + + + + + @@ -1589,7 +1599,7 @@ - + @@ -1597,7 +1607,7 @@ - + From 5d10adeb47acda5234c1fcb922eed6fc58f92757 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Jun 2023 10:21:04 -0600 Subject: [PATCH 1029/2067] Start working on Change files --- doc/ChangeLog | 112 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 113 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ced4fc388e..9109265ea1 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,116 @@ =============================================================== +Tag name: ctsm5.1.dev129 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Tue Jun 20 09:59:12 MDT 2023 +One-line Summary: NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml + +Purpose and description of changes +---------------------------------- + +[Fill this in with details] + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Fixes #2013 -- Incorrest PFT at TOOL + Fixes #2014 -- NEON usermods not working as intended + Fixes #2029 -- fire_method is used before it's set and hence fire_res isn't set to none + Fixes #2030 -- Logic in build-namelist not functioning correctly for FATES with light_res + Updates conda environment so that #1974 works + +Known bugs found since the previous tag (include issue #): + #2017 -- subset_data does not function for regional grids that span across Greenwich longitude zero + #2024 -- snow fraction is uninitialized when passed to fates during cold-starts + + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): + +Changes to the datasets (e.g., parameter, surface or initial files): New NEON surface datasets + +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + + +Testing summary: regular NEON-tools +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS (57 tests different from baseline) + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - PASS (NEON test list passes) + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + cheyenne - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: bit-for-bit (except NEON-TOOL site) + + Summarize any changes to answers, i.e., + - what code configurations: Just NEON TOOL site + - what platforms/compilers: all + - nature of change: new climate + +Other details +------------- +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + #2031 -- Merge of below... + #2015 -- Address NEON bugs + #2021 -- Small changes to fix warnings, add print statements for clarity + #2023 -- Document side effects of htapes_fieldlist + #2022 -- Delete unued hist_add_subscript + #2020 -- Add more documentation to history tape code + #2007 -- black reformat python files for consistancy across cesm + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev128 Originator(s): glemieux (Gregory Lemieux,LBL/NGEET,510-486-5049) Date: Thu Jun 1 15:31:52 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index aca77a5238..b53bd11ed6 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev129 erik 06/20/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType From 129599ed30cd1c39155474479d4c68e25d7dbc8e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Jun 2023 11:11:49 -0600 Subject: [PATCH 1030/2067] neon must be set earlier in the process when the resolution is figured out, also neon 106x174 light_res has to be earlier for it to be set in the namelist_defaults --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 5eb410a6d1..49b6234f0c 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1669,10 +1669,10 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 none none +106x174 94x192 94x192 360x720 -106x174 none none none From 6fe7eecc2ba895d0ea5f0e8080ff53401a051e8a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 20 Jun 2023 10:59:55 -0700 Subject: [PATCH 1031/2067] update build namelist logic for fates luh mode --- bld/CLMBuildNamelist.pm | 25 ++++++++++++++----- .../namelist_definition_ctsm.xml | 2 ++ 2 files changed, 21 insertions(+), 6 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 02d9799487..16afd715da 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -773,8 +773,9 @@ sub setup_cmdl_fates_mode { } else { # dis-allow fates specific namelist items with non-fates runs my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_cohort_age_tracking", - "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode","use_fates_tree_damage" ); + "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp", + "use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging","fates_parteh_mode", + "use_fates_tree_damage","use_fates_luh","fluh_timeseries" ); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { @@ -4181,8 +4182,8 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp", - "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" ); + "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_logging", + "fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); @@ -4203,14 +4204,14 @@ sub setup_logic_fates { # spit-fire can't be on with FATES SP mode is active if ( $nl->get_value('fates_spitfire_mode') > 0 ) { $log->fatal_error('fates_spitfire_mode can NOT be set to greater than 0 when use_fates_sp is true'); + } } - } } my $var = "use_fates_inventory_init"; if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { $var = "fates_inventory_ctrl_filename"; - my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters + my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_inventory_init is set" ); } elsif ( ! -f "$fname" ) { @@ -4218,6 +4219,18 @@ sub setup_logic_fates { } } } + my $var = "use_fates_luh"; + if ( defined($nl->get_value($var)) ) { + if ( &value_is_true($nl->get_value($var)) ) { + $var = "fluh_timeseries"; + my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters + if ( ! defined($nl->get_value($var)) ) { + $log->fatal_error("$var is required when use_fates_luh is set" ); + } elsif ( ! -f "$fname" ) { + $log->fatal_error("$fname does NOT point to a valid filename" ); + } + } + } } } diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a5c7d0a075..5e1698bc06 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -731,6 +731,8 @@ If TRUE, enable use of land use state and transition data from luh_timeseries fi input_pathname="abs" group="elm_inparm" valid_values="" > Full pathname of unified land use harmonization data file. This causes the land-use types to vary over time. +(Required, if use_fates_luh=T) +(Only relevant if FATES is on). Date: Tue, 20 Jun 2023 12:18:48 -0600 Subject: [PATCH 1032/2067] Update cime tag to cime6.0.129 to include append_to_user_nl_files() update. --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 901b1a87e6..c8a73e6835 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.120 +tag = cime6.0.129 required = True [cmeps] From 62df162beb358d966defb0e894a04834aa9eb478 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 20 Jun 2023 14:44:56 -0600 Subject: [PATCH 1033/2067] Update change files --- doc/ChangeLog | 37 +++++++++++++++++++++++++++---------- 1 file changed, 27 insertions(+), 10 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 9109265ea1..eb23f90314 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,14 +1,28 @@ =============================================================== Tag name: ctsm5.1.dev129 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Tue Jun 20 09:59:12 MDT 2023 +Date: Tue Jun 20 14:44:32 MDT 2023 One-line Summary: NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml Purpose and description of changes ---------------------------------- -[Fill this in with details] +Merge the NEON fixes for TOOL and allowing SP mode, as well as a few simple history PR's, and a black reformat. +Fixes NEON bug identified at the NCAR-NEON workshop. Corrects the dominant PFT at TOOL site & usermods_dirs +Some small changes for quality of life improvements for the run_neon script. Some documentation and code +cleanup type changes regarding history code (delete a unused subroutine). Do a black reformat of python files +buildlib/buildnml (and CTSM SystemTests) for consistency across CESM. Also add running them through black in the python + +Specific notes: + + - fixed a couple lines so that python will stop complaining about deprecated things + - added print statements about warning messages being not an issue, and that building/running may take a while + - added a "success" print statement - I'm not sure this will actually only print if "successful" + - Add more documentation to history tape code + - Add more breadcrumbs between related variables and methods + - Put related history namelist flags/methods together + - Update some out of date comments in history code Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -16,6 +30,7 @@ Significant changes to scientifically-supported configurations Does this tag change answers significantly for any of the following physics configurations? (Details of any changes will be given in the "Answer changes" section below.) + [Put an [X] in the box for any configuration with significant answer changes.] [ ] clm5_1 @@ -31,7 +46,7 @@ Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): - Fixes #2013 -- Incorrest PFT at TOOL + Fixes #2013 -- Incorrect PFT at TOOL Fixes #2014 -- NEON usermods not working as intended Fixes #2029 -- fire_method is used before it's set and hence fire_res isn't set to none Fixes #2030 -- Logic in build-namelist not functioning correctly for FATES with light_res @@ -46,22 +61,24 @@ Notes of particular relevance for users --------------------------------------- Caveats for users (e.g., need to interpolate initial conditions): + Ability to run for SP sites was added for NEON, but run-neon.py doesn't have an option for it Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New --light_res option for 106x74 for NEON lightning data added (can be set in CLM_BLDNML_OPTS) + This is the default for NEON sites (with $CLM_USRDAT_NAME == NEON or NEON.PRISM) + It fails for non CLM_USRDAT resolutions and gives a warning for non-NEON CLM_USRDAT resolutions) Changes made to namelist defaults (e.g., changed parameter values): + Add NEON 106x74 lightning dataset Changes to the datasets (e.g., parameter, surface or initial files): New NEON surface datasets Notes of particular relevance for developers: --------------------------------------------- -NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide -[Remove any lines that don't apply. Remove entire section if nothing applies.] - -Caveats for developers (e.g., code that is duplicated that requires double maintenance): Changes to tests or testing: - + Add a NEON case that runs in SP mode + Change one of the FATES tests to turn fire on and require lightning data Testing summary: regular NEON-tools ---------------- @@ -90,10 +107,10 @@ If the tag used for baseline comparisons was NOT the previous tag, note that her Answer changes -------------- -Changes answers relative to baseline: bit-for-bit (except NEON-TOOL site) +Changes answers relative to baseline: bit-for-bit (except some NEON sites) Summarize any changes to answers, i.e., - - what code configurations: Just NEON TOOL site + - what code configurations: NEON TOOL site and other NEON sites with namelist changes - what platforms/compilers: all - nature of change: new climate From 5a5db124feb84508865cf684dd0dd01b967a725e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 21 Jun 2023 09:22:17 -0700 Subject: [PATCH 1034/2067] change call for setting time --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 44 ++++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index 6329eaba47..2180572c0a 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -112,26 +112,26 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) if (use_fates_luh) then - ! Generate the dyn_file_type object - ! TO DO: check whether to initialize with start or end - dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_START_OF_TIMESTEP) - ! dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) - - ! Get initial land use data - num_points = (bounds%endg - bounds%begg + 1) - landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor? - do varnum = 1, num_landuse_transition_vars - landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( & - dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), & - dim1name=grlnd, conversion_factor=1.0_r8, & - do_check_sums_equal_1=.false., data_shape=landuse_shape) - end do - do varnum = 1, num_landuse_state_vars - landuse_state_vars(varnum) = dyn_var_time_uninterp_type( & - dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), & - dim1name=grlnd, conversion_factor=1.0_r8, & - do_check_sums_equal_1=.false., data_shape=landuse_shape) - end do + ! Generate the dyn_file_type object + ! TO DO: check whether to initialize with start or end + ! dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_START_OF_TIMESTEP) + dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) + + ! Get initial land use data + num_points = (bounds%endg - bounds%begg + 1) + landuse_shape(1) = num_points ! Does this need an explicit array shape to be passed to the constructor? + do varnum = 1, num_landuse_transition_vars + landuse_transition_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_transition_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do + do varnum = 1, num_landuse_state_vars + landuse_state_vars(varnum) = dyn_var_time_uninterp_type( & + dyn_file=dynFatesLandUse_file, varname=landuse_state_varnames(varnum), & + dim1name=grlnd, conversion_factor=1.0_r8, & + do_check_sums_equal_1=.false., data_shape=landuse_shape) + end do end if ! Since fates needs state data during initialization, make sure to call @@ -168,8 +168,8 @@ subroutine dynFatesLandUseInterp(bounds, init_state) init_flag = init_state end if - ! input land use data for current year are stored in year+1 in the file - call dynFatesLandUse_file%time_info%set_current_year_get_year(1) + ! Get the current year + call dynFatesLandUse_file%time_info%set_current_year() if (dynFatesLandUse_file%time_info%is_before_time_series() .and. .not.(init_flag)) then ! Reset the land use transitions to zero for safety From f8cc018357052e81356f2d345d9f789921eb2ee7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 11:31:56 -0600 Subject: [PATCH 1035/2067] Move the setting of neon flag to inside of the resolution check so it happens in time for light_res --- bld/CLMBuildNamelist.pm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c205daa4c4..5adcf70ede 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -689,6 +689,13 @@ sub setup_cmdl_resolution { } } } + # For NEON sites + if ($nl_flags->{'res'} =~ /NEON/) { + $nl_flags->{'neon'} = ".true." + } else { + $nl_flags->{'neon'} = ".false." + } + } #------------------------------------------------------------------------------- @@ -1461,13 +1468,6 @@ sub process_namelist_commandline_clm_usr_name { $settings{'csmdata'} = $nl_flags->{'inputdata_rootdir'}; } - # For NEON sites - if ($opts->{'clm_usr_name'} =~ /NEON/) { - $nl_flags->{'neon'} = ".true." - } else { - $nl_flags->{'neon'} = ".false." - } - my $nvars = 0; my $nl_usrfile = Build::Namelist->new(); foreach my $var (@vars) { From 246d1e3e58fc10938cf08ed05e8e2a473dc5dce8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 11:34:23 -0600 Subject: [PATCH 1036/2067] Use a more robust regular expression check for SP mode --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index eeb9e73c7f..6a33b04a47 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -24,8 +24,8 @@ else ./xmlchange CLM_NML_USE_CASE="2018_control" fi -# If needed for SP simulations: turn off lightning & set history file variables -if [[ $compset == *'SP_SICE'* ]]; then +# If needed for SP simulations: & set history file variables +if [[ $compset =~ ".*CLM[0-9]%.*SP.*" ]]; then ./xmlchange STOP_OPTION=nyears ./xmlchange CLM_FORCE_COLDSTART=on From 1c34ce62676e6bd4cb173a094ee5386b62d25ec1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 11:37:35 -0600 Subject: [PATCH 1037/2067] Make the FATES version look like the non-FATES version, fixing #2023 --- .../usermods_dirs/NEON/FATES/defaults/shell_commands | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands index a41a15018e..7aa8d51026 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands @@ -1,6 +1,6 @@ #!/bin/bash ./xmlchange CLM_USRDAT_NAME=NEON -# CLM_USRDAT_NAME can also be set to NEON.PRISM +# CLM_USRDAT_NAME can be set to either NEON or NEON.PRISM ./xmlchange CCSM_CO2_PPMV=408.83 # Set data forcing data to future scenario so will have data from 2018 to present-day ./xmlchange DATM_PRESAERO=SSP3-7.0 @@ -11,6 +11,7 @@ # Set years to run forcing data over ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 compset=`./xmlquery COMPSET --value` +CLM_USRDAT_NAME=`./xmlquery CLM_USRDAT_NAME --value` # For a transient case run the whole length and don't cycle if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2022 @@ -23,5 +24,11 @@ else ./xmlchange CLM_NML_USE_CASE="2018_control" fi +# If needed for SP simulations: +# Does anything need to be set for FATES-SP mode? +#if [[ $compset =~ ".*CLM[0-9]%.*SP.*" ]]; then +#fi + + # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) ./xmlchange PIO_TYPENAME=netcdf From c1ce8b833cea8400ae2bab29bc0fba8fe5564805 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 11:54:26 -0600 Subject: [PATCH 1038/2067] Bugfix in nhtfrq of annual outputs in cropMonthOutput test. --- .../testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm index dfe718a7b4..d6bc28297d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm @@ -1,4 +1,4 @@ - hist_nhtfrq = 0,-240,-8760 + hist_nhtfrq = 0,-240,17520 hist_mfilt = 1,1,1 ! Add an annual output file with these crop-specific variables, which exercise some special logic: From e98b2485941162a1019a6ad4f0f5e8acefec039c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 11:54:31 -0600 Subject: [PATCH 1039/2067] Added per-harvest output variables to crop and cropMonthOutput tests. --- cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 2 +- .../testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm | 4 ---- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index 4622aca109..dc22a973b2 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -10,7 +10,7 @@ hist_fincl2 += 'DYN_COL_SOIL_ADJUSTMENTS_C' ! Annual crop variables on per-sowing/per-harvest axes, per PFT. -hist_fincl3 = 'SDATES', 'HDATES' +hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' hist_nhtfrq(3) = 17520 hist_mfilt(3) = 1 hist_type1d_pertape(3) = 'PFTS' diff --git a/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm index d6bc28297d..ae4284da6b 100644 --- a/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/cropMonthOutput/user_nl_clm @@ -1,6 +1,2 @@ hist_nhtfrq = 0,-240,17520 hist_mfilt = 1,1,1 - - ! Add an annual output file with these crop-specific variables, which exercise some special logic: - hist_fincl3 = 'SDATES', 'HDATES' - hist_dov2xy(3) = .false. From f1053fe9fd1eaa1e058b94cf92d3202365008988 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 12:10:47 -0600 Subject: [PATCH 1040/2067] Correct the regular expression --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 6a33b04a47..e788048965 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -25,7 +25,7 @@ else fi # If needed for SP simulations: & set history file variables -if [[ $compset =~ ".*CLM[0-9]%.*SP.*" ]]; then +if [[ $compset =~ .*CLM[0-9]+%.*SP.* ]]; then ./xmlchange STOP_OPTION=nyears ./xmlchange CLM_FORCE_COLDSTART=on From 2500c4146956e49144d078f336029dd468dbdc0b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 13:02:36 -0600 Subject: [PATCH 1041/2067] Removed MCT version of cropcalStreamMod. --- src/cpl/mct/cropcalStreamMod.F90 | 303 ------------------------------- 1 file changed, 303 deletions(-) delete mode 100644 src/cpl/mct/cropcalStreamMod.F90 diff --git a/src/cpl/mct/cropcalStreamMod.F90 b/src/cpl/mct/cropcalStreamMod.F90 deleted file mode 100644 index 0f330312f4..0000000000 --- a/src/cpl/mct/cropcalStreamMod.F90 +++ /dev/null @@ -1,303 +0,0 @@ -module cropcalStreamMod - -#include "shr_assert.h" - - !----------------------------------------------------------------------- - ! !DESCRIPTION: - ! Read crop calendars from stream - ! - ! !USES: - use shr_strdata_mod , only : shr_strdata_type, shr_strdata_create - use shr_strdata_mod , only : shr_strdata_print, shr_strdata_advance - use shr_kind_mod , only : r8=>shr_kind_r8, CL=>shr_kind_CL, CS=>shr_kind_CS, CXX=>shr_kind_CXX - use shr_log_mod , only : errMsg => shr_log_errMsg - use decompMod , only : bounds_type - use abortutils , only : endrun - use clm_varctl , only : iulog, inst_name - use perf_mod , only : t_startf, t_stopf - use spmdMod , only : masterproc, mpicom, comp_id - use ncdio_pio - use mct_mod - ! - ! !PUBLIC TYPES: - implicit none - private - - ! !PUBLIC MEMBER FUNCTIONS: - public :: cropcal_init ! position datasets for crop calendars - public :: cropcal_advance ! Advance the crop calendar streams (outside of a Open-MP threading loop) - public :: cropcal_interp ! interpolates between two years of crop calendar data - - ! !PRIVATE MEMBER DATA: - integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - type(shr_strdata_type) :: sdat_sdate ! sowing date input data stream - type(shr_strdata_type) :: sdat_cultivar_gdds ! cultivar growing-degree days stream - - character(len=*), parameter :: sourcefile = & - __FILE__ - -!============================================================================== -contains -!============================================================================== - - subroutine cropcal_init(bounds) - ! - ! Initialize data stream information for crop calendars. - ! - ! !USES: - use clm_varpar , only : cft_lb, cft_ub - use clm_time_manager , only : get_calendar - use ncdio_pio , only : pio_subsystem - use shr_pio_mod , only : shr_pio_getiotype - use shr_stream_mod , only : shr_stream_file_null - use shr_string_mod , only : shr_string_listCreateField - use clm_nlUtilsMod , only : find_nlgroup_name - use ndepStreamMod , only : clm_domain_mct - use histFileMod , only : hist_addfld1d - use domainMod , only : ldomain - use controlMod , only : NLFilename - use lnd_set_decomp_and_domain , only : gsmap_global - ! - ! !ARGUMENTS: - implicit none - type(bounds_type), intent(in) :: bounds ! bounds - ! - ! !LOCAL VARIABLES: - integer :: stream_year_first_cropcal ! first year in crop calendar streams to use - integer :: stream_year_last_cropcal ! last year in crop calendar streams to use - integer :: model_year_align_cropcal ! align stream_year_first_cropcal with - integer :: nu_nml ! unit for namelist file - integer :: nml_error ! namelist i/o error flag - type(mct_ggrid) :: dom_clm ! domain information - character(len=CL) :: stream_fldFileName_sdate ! sowing date stream filename to read - character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar GDD target filename to read - character(len=CL) :: cropcal_mapalgo = 'nn' ! Mapping alogrithm - character(len=CL) :: cropcal_tintalgo = 'nearest' ! Time interpolation alogrithm - - character(len=CXX) :: fldList_sdate1 ! field string for 1st sowing dates - character(len=CXX) :: fldList_cultivar_gdds1 ! field string for 1st cultivar GDD targets - - character(*), parameter :: subName = "('cropcaldyn_init')" - !----------------------------------------------------------------------- - ! - ! deal with namelist variables here in init - ! - namelist /cropcal_streams/ & - stream_year_first_cropcal, & - stream_year_last_cropcal, & - model_year_align_cropcal, & - stream_fldFileName_sdate, & - stream_fldFileName_cultivar_gdds - - ! Default values for namelist - stream_year_first_cropcal = 1 ! first year in stream to use - stream_year_last_cropcal = 1 ! last year in stream to use - model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year - stream_fldFileName_sdate = shr_stream_file_null - stream_fldFileName_cultivar_gdds = shr_stream_file_null - - ! Read cropcal_streams namelist - if (masterproc) then - open( newunit=nu_nml, file=trim(NLFilename), status='old', iostat=nml_error ) - call find_nlgroup_name(nu_nml, 'cropcal_streams', status=nml_error) - if (nml_error == 0) then - read(nu_nml, nml=cropcal_streams,iostat=nml_error) - if (nml_error /= 0) then - call endrun(subname // ':: ERROR reading cropcal_streams namelist') - end if - else - call endrun(subname // ':: ERROR finding cropcal_streams namelist') - end if - close(nu_nml) - endif - call shr_mpi_bcast(stream_year_first_cropcal, mpicom) - call shr_mpi_bcast(stream_year_last_cropcal , mpicom) - call shr_mpi_bcast(model_year_align_cropcal , mpicom) - call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) - call shr_mpi_bcast(stream_fldFileName_cultivar_gdds , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) 'cropcal_stream settings:' - write(iulog,*) ' stream_year_first_cropcal = ',stream_year_first_cropcal - write(iulog,*) ' stream_year_last_cropcal = ',stream_year_last_cropcal - write(iulog,*) ' model_year_align_cropcal = ',model_year_align_cropcal - write(iulog,*) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) - write(iulog,*) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) - endif - - call clm_domain_mct (bounds, dom_clm) - - ! create the field list for these cropcal fields...use in shr_strdata_create - ! Will need modification to work with mxsowings > 1 - fldList_sdate1 = shr_string_listCreateField( cft_ub, "sdate1", cft_lb ) - fldList_cultivar_gdds1 = shr_string_listCreateField( cft_ub, "gdd1", cft_lb ) - - ! SSR TODO: - ! - Delete "area" and "mask"? - ! - Is this correct taxmode? - call shr_strdata_create(sdat_sdate, & - name="cropcaldyn", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_cropcal, & - yearLast=stream_year_last_cropcal, & - yearAlign=model_year_align_cropcal, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_sdate), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_sdate/), & - fldListFile=fldList_sdate1, & - fldListModel=fldList_sdate1, & - fillalgo='none', & - mapalgo=cropcal_mapalgo, & - tintalgo=cropcal_tintalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - call shr_strdata_create(sdat_cultivar_gdds, & - name="cropcaldyn", & - pio_subsystem=pio_subsystem, & - pio_iotype=shr_pio_getiotype(inst_name), & - mpicom=mpicom, compid=comp_id, & - gsmap=gsmap_global, ggrid=dom_clm, & - nxg=ldomain%ni, nyg=ldomain%nj, & - yearFirst=stream_year_first_cropcal, & - yearLast=stream_year_last_cropcal, & - yearAlign=model_year_align_cropcal, & - offset=0, & - domFilePath='', & - domFileName=trim(stream_fldFileName_cultivar_gdds), & - domTvarName='time', & - domXvarName='lon' , & - domYvarName='lat' , & - domAreaName='area', & - domMaskName='mask', & - filePath='', & - filename=(/stream_fldFileName_cultivar_gdds/), & - fldListFile=fldList_cultivar_gdds1, & - fldListModel=fldList_cultivar_gdds1, & - fillalgo='none', & - mapalgo=cropcal_mapalgo, & - tintalgo=cropcal_tintalgo, & - calendar=get_calendar(), & - taxmode='cycle' ) - - if (masterproc) then - call shr_strdata_print(sdat_sdate,'sdate1 data') - call shr_strdata_print(sdat_cultivar_gdds,'sdat_cultivar_gdds1 data') - endif - - end subroutine cropcal_init - - !============================================================================== - subroutine cropcal_advance( bounds ) - ! - ! Advance crop calendar streams - ! - ! !USES: - use clm_time_manager, only : get_curr_date - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - ! - ! !LOCAL VARIABLES: - integer :: g, ig ! Indices - integer :: year ! year (0, ...) for nstep+1 - integer :: mon ! month (1, ..., 12) for nstep+1 - integer :: day ! day of month (1, ..., 31) for nstep+1 - integer :: sec ! seconds into current date for nstep+1 - integer :: mcdate ! Current model date (yyyymmdd) - !----------------------------------------------------------------------- - - call get_curr_date(year, mon, day, sec) - mcdate = year*10000 + mon*100 + day - - ! Will need modification to work with mxsowings > 1 - call shr_strdata_advance(sdat_sdate, mcdate, sec, mpicom, 'cropcaldyn') - call shr_strdata_advance(sdat_cultivar_gdds, mcdate, sec, mpicom, 'cropcaldyn') - - if ( .not. allocated(g_to_ig) )then - allocate (g_to_ig(bounds%begg:bounds%endg) ) - ig = 0 - do g = bounds%begg,bounds%endg - ig = ig+1 - g_to_ig(g) = ig - end do - end if - - end subroutine cropcal_advance - - !============================================================================== - subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) - ! - ! Interpolate data stream information for crop calendars. - ! - ! !USES: - use pftconMod , only : noveg - use CropType , only : crop_type - use PatchType , only : patch - use filterMod , only : filter - use decompMod , only : get_proc_clumps - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter - integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches - type(crop_type) , intent(inout) :: crop_inst - ! - ! !LOCAL VARIABLES: - integer :: ivt, p, ip, ig - integer :: nc, fp - character(len=CL) :: stream_var_name_sdate1 - character(len=CL) :: stream_var_name_cultivar_gdds1 - !----------------------------------------------------------------------- - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - - ! Will need modification to work with mxsowings > 1 - SHR_ASSERT_FL( (lbound(sdat_sdate%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_sdate%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (lbound(sdat_cultivar_gdds%avs(1)%rAttr,2) <= g_to_ig(bounds%begg) ), sourcefile, __LINE__) - SHR_ASSERT_FL( (ubound(sdat_cultivar_gdds%avs(1)%rAttr,2) >= g_to_ig(bounds%endg) ), sourcefile, __LINE__) - - ! Will need modification to work with mxsowings > 1 - do fp = 1, num_pcropp - p = filter_pcropp(fp) - ivt = patch%itype(p) - ! Set crop calendars for each gridcell/patch combination - write(stream_var_name_sdate1,"(i6)") ivt - write(stream_var_name_cultivar_gdds1,"(i6)") ivt - - stream_var_name_sdate1 = 'sdate1_'//trim(adjustl(stream_var_name_sdate1)) - ip = mct_aVect_indexRA(sdat_sdate%avs(1),trim(stream_var_name_sdate1)) - if (ivt /= noveg) then - ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_sdates_thisyr(p,1) = sdat_sdate%avs(1)%rAttr(ip,ig) - endif - - stream_var_name_cultivar_gdds1 = 'gdd1_'//trim(adjustl(stream_var_name_cultivar_gdds1)) - ip = mct_aVect_indexRA(sdat_cultivar_gdds%avs(1),trim(stream_var_name_cultivar_gdds1)) - if (ivt /= noveg) then - ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_cultivar_gdds_thisyr(p,1) = sdat_cultivar_gdds%avs(1)%rAttr(ip,ig) - endif - - ! Only for first sowing date of the year - crop_inst%next_rx_sdate(p) = crop_inst%rx_sdates_thisyr(p,1) - - end do - - end subroutine cropcal_interp - -end module cropcalStreamMod From 0af299031b9cfeb307d49794d0b382ec6830512b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 13:13:17 -0600 Subject: [PATCH 1042/2067] RXCROPMATURITY: Replaced path for sowing/harvest dates with path in standard Cheyenne input directory. --- cime_config/SystemTests/rxcropmaturity.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 4b3837b497..15451e81ac 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -174,27 +174,27 @@ def _get_rx_dates(self): # Eventually, I want to remove these hard-coded resolutions so that this test can generate # its own sowing and harvest date files at whatever resolution is requested. lnd_grid = self._case.get_value("LND_GRID") - blessed_crop_dates_dir="/glade/work/samrabin/crop_dates_blessed" + processed_crop_dates_dir="/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed" if lnd_grid == "10x15": self._sdatefile = os.path.join( - blessed_crop_dates_dir, + processed_crop_dates_dir, "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc") self._hdatefile = os.path.join( - blessed_crop_dates_dir, + processed_crop_dates_dir, "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc") elif lnd_grid == "1.9x2.5": self._sdatefile = os.path.join( - blessed_crop_dates_dir, + processed_crop_dates_dir, "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc") self._hdatefile = os.path.join( - blessed_crop_dates_dir, + processed_crop_dates_dir, "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc") elif lnd_grid == "0.9x1.25": self._sdatefile = os.path.join( - blessed_crop_dates_dir, + processed_crop_dates_dir, "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc") self._hdatefile = os.path.join( - blessed_crop_dates_dir, + processed_crop_dates_dir, "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc") else: error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" From ba279729bbad7ba3600aace579dfb742a5e47bde Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 13:19:02 -0600 Subject: [PATCH 1043/2067] RXCROPMATURITY now uses DIN_LOC_ROOT instead of standard Cheyenne input directory path. --- cime_config/SystemTests/rxcropmaturity.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 15451e81ac..9cf1b713db 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -174,7 +174,8 @@ def _get_rx_dates(self): # Eventually, I want to remove these hard-coded resolutions so that this test can generate # its own sowing and harvest date files at whatever resolution is requested. lnd_grid = self._case.get_value("LND_GRID") - processed_crop_dates_dir="/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed" + input_data_root = self._case.get_value("DIN_LOC_ROOT") + processed_crop_dates_dir = f"{input_data_root}/lnd/clm2/cropdata/calendars/processed" if lnd_grid == "10x15": self._sdatefile = os.path.join( processed_crop_dates_dir, From 3900e9ad7ed4c4de59216c10090f83c197d418d0 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 15:49:14 -0600 Subject: [PATCH 1044/2067] Only set STOP xml variables if this is NOT a TEST type --- .../usermods_dirs/NEON/BARR/shell_commands | 4 +++- .../usermods_dirs/NEON/CPER/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/BARR/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/CPER/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/GUAN/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/LAJA/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/LENO/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/MLBS/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/MOAB/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/ONAQ/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/SJER/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/TEAK/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/TOOL/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/WREF/shell_commands | 4 +++- .../usermods_dirs/NEON/FATES/YELL/shell_commands | 4 +++- .../NEON/FATES/defaults/shell_commands | 11 +++++++++-- .../usermods_dirs/NEON/GUAN/shell_commands | 4 +++- .../usermods_dirs/NEON/LAJA/shell_commands | 4 +++- .../usermods_dirs/NEON/LENO/shell_commands | 4 +++- .../usermods_dirs/NEON/MLBS/shell_commands | 4 +++- .../usermods_dirs/NEON/MOAB/shell_commands | 4 +++- .../usermods_dirs/NEON/ONAQ/shell_commands | 4 +++- .../usermods_dirs/NEON/SJER/shell_commands | 4 +++- .../usermods_dirs/NEON/TEAK/shell_commands | 4 +++- .../usermods_dirs/NEON/TOOL/shell_commands | 4 +++- .../usermods_dirs/NEON/WREF/shell_commands | 4 +++- .../usermods_dirs/NEON/YELL/shell_commands | 4 +++- .../usermods_dirs/NEON/defaults/shell_commands | 15 ++++++++++++--- 28 files changed, 99 insertions(+), 31 deletions(-) diff --git a/cime_config/usermods_dirs/NEON/BARR/shell_commands b/cime_config/usermods_dirs/NEON/BARR/shell_commands index 713331c0ee..a5892a146b 100644 --- a/cime_config/usermods_dirs/NEON/BARR/shell_commands +++ b/cime_config/usermods_dirs/NEON/BARR/shell_commands @@ -7,5 +7,7 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/CPER/shell_commands b/cime_config/usermods_dirs/NEON/CPER/shell_commands index b6ccbcdf57..8aa642c8d0 100644 --- a/cime_config/usermods_dirs/NEON/CPER/shell_commands +++ b/cime_config/usermods_dirs/NEON/CPER/shell_commands @@ -2,5 +2,7 @@ ./xmlchange PTS_LON=255.25545 ./xmlchange PTS_LAT=40.81297 if [[ $compset =~ ^HIST ]]; then - ./xmlchange STOP_N=50 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=50 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands b/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands index 713331c0ee..a5892a146b 100644 --- a/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands @@ -7,5 +7,7 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands index b6ccbcdf57..8aa642c8d0 100644 --- a/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands @@ -2,5 +2,7 @@ ./xmlchange PTS_LON=255.25545 ./xmlchange PTS_LAT=40.81297 if [[ $compset =~ ^HIST ]]; then - ./xmlchange STOP_N=50 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=50 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands b/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands index 4214a35e3c..c78bf31f55 100644 --- a/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands @@ -7,5 +7,7 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands b/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands index a7bda447e6..217216e3ec 100644 --- a/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands @@ -6,7 +6,9 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands b/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands index c5ae590186..06af587292 100644 --- a/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands @@ -7,6 +7,8 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2021-01-01 - ./xmlchange STOP_N=15 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=15 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands index 0d43e032f8..11ab445450 100644 --- a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands @@ -9,6 +9,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=24 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands index 1d0d4fb8c1..649fa2eaba 100644 --- a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands @@ -9,6 +9,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2021 - ./xmlchange STOP_N=36 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=36 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands index 36223abee1..dae5344528 100644 --- a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands @@ -9,6 +9,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=24 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands index 2e3d158847..ee50f61fa1 100644 --- a/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands @@ -12,7 +12,9 @@ then if [[ $compset =~ ^HIST ]] then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands index 0efa486d6e..abac8e9263 100644 --- a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands @@ -10,6 +10,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands index f1f2e1771a..3c749cde93 100644 --- a/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands @@ -6,5 +6,7 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2020-01-01 - ./xmlchange STOP_N=27 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=27 + fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands index d3dec03ac8..77a48ae1c0 100644 --- a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands @@ -10,6 +10,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands index 656cdff066..33915b88a1 100644 --- a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands @@ -10,6 +10,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands index 7aa8d51026..798abcae84 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands @@ -10,15 +10,22 @@ ./xmlchange MPILIB=mpi-serial # Set years to run forcing data over ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 +# +# Save some variables that may be used later +# compset=`./xmlquery COMPSET --value` CLM_USRDAT_NAME=`./xmlquery CLM_USRDAT_NAME --value` +TEST=`./xmlquery TEST --value` + # For a transient case run the whole length and don't cycle if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2022 ./xmlchange RUN_STARTDATE=2018-01-01 # Number of months that can be run for the full transient case - ./xmlchange STOP_OPTION="nmonths" - ./xmlchange STOP_N=51 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_OPTION="nmonths" + ./xmlchange STOP_N=51 + fi ./xmlchange CLM_NML_USE_CASE="2018-PD_transient" else ./xmlchange CLM_NML_USE_CASE="2018_control" diff --git a/cime_config/usermods_dirs/NEON/GUAN/shell_commands b/cime_config/usermods_dirs/NEON/GUAN/shell_commands index 4214a35e3c..c78bf31f55 100644 --- a/cime_config/usermods_dirs/NEON/GUAN/shell_commands +++ b/cime_config/usermods_dirs/NEON/GUAN/shell_commands @@ -7,5 +7,7 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/LAJA/shell_commands b/cime_config/usermods_dirs/NEON/LAJA/shell_commands index a7bda447e6..217216e3ec 100644 --- a/cime_config/usermods_dirs/NEON/LAJA/shell_commands +++ b/cime_config/usermods_dirs/NEON/LAJA/shell_commands @@ -6,7 +6,9 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi diff --git a/cime_config/usermods_dirs/NEON/LENO/shell_commands b/cime_config/usermods_dirs/NEON/LENO/shell_commands index c5ae590186..06af587292 100644 --- a/cime_config/usermods_dirs/NEON/LENO/shell_commands +++ b/cime_config/usermods_dirs/NEON/LENO/shell_commands @@ -7,6 +7,8 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2021-01-01 - ./xmlchange STOP_N=15 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=15 + fi fi diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/NEON/MLBS/shell_commands index 0d43e032f8..11ab445450 100644 --- a/cime_config/usermods_dirs/NEON/MLBS/shell_commands +++ b/cime_config/usermods_dirs/NEON/MLBS/shell_commands @@ -9,6 +9,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=24 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/NEON/MOAB/shell_commands index 1d0d4fb8c1..649fa2eaba 100644 --- a/cime_config/usermods_dirs/NEON/MOAB/shell_commands +++ b/cime_config/usermods_dirs/NEON/MOAB/shell_commands @@ -9,6 +9,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2021 - ./xmlchange STOP_N=36 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=36 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands index 36223abee1..dae5344528 100644 --- a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands +++ b/cime_config/usermods_dirs/NEON/ONAQ/shell_commands @@ -9,6 +9,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2020 - ./xmlchange STOP_N=24 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=24 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/NEON/SJER/shell_commands index 2e3d158847..ee50f61fa1 100644 --- a/cime_config/usermods_dirs/NEON/SJER/shell_commands +++ b/cime_config/usermods_dirs/NEON/SJER/shell_commands @@ -12,7 +12,9 @@ then if [[ $compset =~ ^HIST ]] then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/NEON/TEAK/shell_commands index 0efa486d6e..abac8e9263 100644 --- a/cime_config/usermods_dirs/NEON/TEAK/shell_commands +++ b/cime_config/usermods_dirs/NEON/TEAK/shell_commands @@ -10,6 +10,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/TOOL/shell_commands b/cime_config/usermods_dirs/NEON/TOOL/shell_commands index f1f2e1771a..3c749cde93 100644 --- a/cime_config/usermods_dirs/NEON/TOOL/shell_commands +++ b/cime_config/usermods_dirs/NEON/TOOL/shell_commands @@ -6,5 +6,7 @@ # Different default start date and number of months to run for transient case if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2020-01-01 - ./xmlchange STOP_N=27 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=27 + fi fi diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/NEON/WREF/shell_commands index d3dec03ac8..77a48ae1c0 100644 --- a/cime_config/usermods_dirs/NEON/WREF/shell_commands +++ b/cime_config/usermods_dirs/NEON/WREF/shell_commands @@ -10,6 +10,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/NEON/YELL/shell_commands index 656cdff066..33915b88a1 100644 --- a/cime_config/usermods_dirs/NEON/YELL/shell_commands +++ b/cime_config/usermods_dirs/NEON/YELL/shell_commands @@ -10,6 +10,8 @@ if [[ $CLM_USRDAT_NAME == 'NEON' ]]; then ./xmlchange DATM_YR_START=2019 if [[ $compset =~ ^HIST ]]; then ./xmlchange RUN_STARTDATE=2019-01-01 - ./xmlchange STOP_N=39 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_N=39 + fi fi fi diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index e788048965..437201f2b2 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -10,15 +10,22 @@ ./xmlchange MPILIB=mpi-serial # Set years to run forcing data over ./xmlchange DATM_YR_ALIGN=2018,DATM_YR_END=2021,DATM_YR_START=2018 +# +# Save some variables that may be used later +# compset=`./xmlquery COMPSET --value` CLM_USRDAT_NAME=`./xmlquery CLM_USRDAT_NAME --value` +TEST=`./xmlquery TEST --value` + # For a transient case run the whole length and don't cycle if [[ $compset =~ ^HIST ]]; then ./xmlchange DATM_YR_END=2022 ./xmlchange RUN_STARTDATE=2018-01-01 # Number of months that can be run for the full transient case - ./xmlchange STOP_OPTION="nmonths" - ./xmlchange STOP_N=51 + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_OPTION="nmonths" + ./xmlchange STOP_N=51 + fi ./xmlchange CLM_NML_USE_CASE="2018-PD_transient" else ./xmlchange CLM_NML_USE_CASE="2018_control" @@ -26,7 +33,9 @@ fi # If needed for SP simulations: & set history file variables if [[ $compset =~ .*CLM[0-9]+%.*SP.* ]]; then - ./xmlchange STOP_OPTION=nyears + if [[ $TEST != "TRUE" ]]; then + ./xmlchange STOP_OPTION=nyears + fi ./xmlchange CLM_FORCE_COLDSTART=on echo "hist_fincl2 = 'FCEV','FCTR','FGEV','FIRA','FSA','FSH','FPSN','H2OSOI','SNOW_DEPTH','TBOT','TSOI'" >> user_nl_clm From ccc4122597b5138f20c5db913af5f08554d602ce Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 15:53:47 -0600 Subject: [PATCH 1045/2067] Add shebang line so that editor coloring will be shown --- cime_config/usermods_dirs/NEON/CPER/shell_commands | 2 ++ cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands | 2 ++ 2 files changed, 4 insertions(+) diff --git a/cime_config/usermods_dirs/NEON/CPER/shell_commands b/cime_config/usermods_dirs/NEON/CPER/shell_commands index 8aa642c8d0..b70b1a46a0 100644 --- a/cime_config/usermods_dirs/NEON/CPER/shell_commands +++ b/cime_config/usermods_dirs/NEON/CPER/shell_commands @@ -1,3 +1,5 @@ +#!/bin/bash + ./xmlchange NEONSITE=CPER ./xmlchange PTS_LON=255.25545 ./xmlchange PTS_LAT=40.81297 diff --git a/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands b/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands index 8aa642c8d0..b70b1a46a0 100644 --- a/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands @@ -1,3 +1,5 @@ +#!/bin/bash + ./xmlchange NEONSITE=CPER ./xmlchange PTS_LON=255.25545 ./xmlchange PTS_LAT=40.81297 From a92114e663cf00f8d20b341063fc73d20453bc2e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 16:04:52 -0600 Subject: [PATCH 1046/2067] Explicitly set the length of the NEON tests to 10 days --- cime_config/testdefs/testlist_clm.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 1df065a424..d162c74833 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1569,7 +1569,7 @@ - + @@ -1579,7 +1579,7 @@ - + @@ -1589,7 +1589,7 @@ - + @@ -1599,7 +1599,7 @@ - + @@ -1610,7 +1610,7 @@ - + From 270a5cd7115b2222891c7d8db49c34a55b66a1d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 16:17:22 -0600 Subject: [PATCH 1047/2067] Do not loop through soil layers within a loop through soil layers. --- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 21 +++++++++++-------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index a1a45b65ad..2738c55682 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -904,15 +904,6 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & decomp_k(c,j,i_cwd) = k_frag * t_scalar(c,j) * w_scalar(c,j) * & depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_cwd(c) end if - - ! Tillage - if (get_do_tillage()) then - if (.not. present(idop)) then - call endrun("Do not call tillage without providing idop.") - end if - call get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) - end if - ! Above into soil matrix if(use_soil_matrixcn)then ! same for cwd but only if fates is not enabled; fates handles CWD @@ -922,6 +913,18 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & end if !use_soil_matrixcn end do end do + + ! Tillage + if (get_do_tillage()) then + if (.not. present(idop)) then + call endrun("Do not call tillage without providing idop.") + end if + do fc = 1,num_soilc + c = filter_soilc(fc) + call get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + end do + end if + pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = 1.0_r8 pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l2s1) = 1.0_r8 pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s2) = 1.0_r8 From 90b6050be73000efa63899b4ab0326462e6a9958 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 21 Jun 2023 16:27:07 -0600 Subject: [PATCH 1048/2067] correct bad copies --- src/dyn_subgrid/dynSubgridDriverMod.F90 | 2 +- src/utils/clmfates_interfaceMod.F90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/dyn_subgrid/dynSubgridDriverMod.F90 b/src/dyn_subgrid/dynSubgridDriverMod.F90 index c15a23b577..e5ca3f002e 100644 --- a/src/dyn_subgrid/dynSubgridDriverMod.F90 +++ b/src/dyn_subgrid/dynSubgridDriverMod.F90 @@ -291,7 +291,7 @@ subroutine dynSubgrid_driver(bounds_proc, end if if (use_fates_luh) then - call dynFatesLandUseInterp + call dynFatesLandUseInterp(bounds_proc) end if ! ========================================================================== diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 142348b444..c136523518 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1828,7 +1828,7 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & do s = 1,this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) - g = col_pp%gridcell(c) + g = col%gridcell(c) if (use_fates_luh) then this%fates(nc)%bc_in(s)%hlm_luh_states = landuse_states(:,g) From 1be3ee0c37df16f434f37c4d44c0ca0a2737f926 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 21 Jun 2023 16:28:13 -0600 Subject: [PATCH 1049/2067] Update change files --- doc/ChangeLog | 6 +++++- doc/ChangeSum | 2 +- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index eb23f90314..ddfd58f7c3 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev129 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Tue Jun 20 14:44:32 MDT 2023 +Date: Wed Jun 21 16:28:05 MDT 2023 One-line Summary: NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml Purpose and description of changes @@ -53,6 +53,7 @@ CTSM issues fixed (include CTSM Issue #): Updates conda environment so that #1974 works Known bugs found since the previous tag (include issue #): + #2036 -- Remove setting of STOP options in user-mod directories #2017 -- subset_data does not function for regional grids that span across Greenwich longitude zero #2024 -- snow fraction is uninitialized when passed to fates during cold-starts @@ -101,6 +102,9 @@ Testing summary: regular NEON-tools cheyenne ---- OK izumi ------- OK + other testing: + izumi -- PASS (tests of changed NEON sites, see list in #2031) + If the tag used for baseline comparisons was NOT the previous tag, note that here: diff --git a/doc/ChangeSum b/doc/ChangeSum index b53bd11ed6..4ce7958291 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev129 erik 06/20/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml + ctsm5.1.dev129 erik 06/21/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType From aa3af72d89ad634b232786276a384c73bc49b856 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 21 Jun 2023 16:34:34 -0600 Subject: [PATCH 1050/2067] Roll back cime to tag cime6.0.118. --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 9572c12dfb..1153bb8c3f 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.129 +tag = cime6.0.118 required = True [cmeps] From 04f20806ccba93640102c7068622631a1cce7d8e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 22 Jun 2023 01:22:06 -0600 Subject: [PATCH 1051/2067] Update change log --- doc/ChangeLog | 3 ++- doc/ChangeSum | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index ddfd58f7c3..071be8709e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev129 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Wed Jun 21 16:28:05 MDT 2023 +Date: Thu Jun 22 01:21:56 MDT 2023 One-line Summary: NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml Purpose and description of changes @@ -53,6 +53,7 @@ CTSM issues fixed (include CTSM Issue #): Updates conda environment so that #1974 works Known bugs found since the previous tag (include issue #): + #2037 -- shell_commands for tests with two testmods listed don't concatenate both together #2036 -- Remove setting of STOP options in user-mod directories #2017 -- subset_data does not function for regional grids that span across Greenwich longitude zero #2024 -- snow fraction is uninitialized when passed to fates during cold-starts diff --git a/doc/ChangeSum b/doc/ChangeSum index 4ce7958291..f0193772d6 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev129 erik 06/21/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml + ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test ctsm5.1.dev126 jpalex 05/18/2023 Clean up some loops in UrbanTimeVarType From 86b4c658047a38bf3a0d57e58199d35214154fb0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 23 Jun 2023 15:01:04 -0600 Subject: [PATCH 1052/2067] Don't save *TO_FOOD_PERHARV and *TO_FOOD_ANN to primary tape. --- src/biogeochem/CNVegCarbonFluxType.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 6a23ce598f..4b30f68538 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -940,7 +940,8 @@ subroutine InitHistory(this, bounds, carbon_type) type2d='mxharvests', & avgflag='I', & long_name=get_repr_longname(k)//' C to food per harvest; should only be output annually', & - ptr_patch=data2dptr) + ptr_patch=data2dptr, & + default='inactive') end do this%repr_grainc_to_food_thisyr_patch(begp:endp,:) = spval @@ -952,7 +953,8 @@ subroutine InitHistory(this, bounds, carbon_type) units='gC/m^2', & avgflag='I', & long_name=get_repr_longname(k)//' C to food harvested per calendar year; should only be output annually', & - ptr_patch=data1dptr) + ptr_patch=data1dptr, & + default='inactive') end do this%leafc_to_biofuelc_patch(begp:endp) = spval From 358802ed74186f1cb5cc29f6a7312b5cf0ae8b65 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 26 Jun 2023 15:54:43 -0600 Subject: [PATCH 1053/2067] Removed MCT tests from testlist_clm.xml. --- cime_config/testdefs/testlist_clm.xml | 115 -------------------------- 1 file changed, 115 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 53e4fbadac..cc09f5c564 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -133,16 +133,6 @@ - - - - - - - - - - @@ -168,15 +158,6 @@ - - - - - - - - - @@ -195,15 +176,6 @@ - - - - - - - - - @@ -489,15 +461,6 @@ - - - - - - - - - @@ -630,16 +593,6 @@ - - - - - - - - - - @@ -968,16 +921,6 @@ - - - - - - - - - - @@ -1175,15 +1118,6 @@ - - - - - - - - - @@ -1456,16 +1390,6 @@ - - - - - - - - - - @@ -1492,15 +1416,6 @@ - - - - - - - - - @@ -1539,16 +1454,6 @@ - - - - - - - - - - @@ -1611,17 +1516,6 @@ - - - - - - - - - - - @@ -1953,15 +1847,6 @@ - - - - - - - - - From 81efbe09ac91f8d3723b2b8cdb54d9a4a3a69dba Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 26 Jun 2023 16:21:42 -0600 Subject: [PATCH 1054/2067] Added CallRestartvarDimOK() stub to unit_test_stubs/utils/restUtilMod_stub.F90.in. --- .../utils/restUtilMod_stub.F90.in | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/src/unit_test_stubs/utils/restUtilMod_stub.F90.in b/src/unit_test_stubs/utils/restUtilMod_stub.F90.in index b6e3ba4f19..ab26558db7 100644 --- a/src/unit_test_stubs/utils/restUtilMod_stub.F90.in +++ b/src/unit_test_stubs/utils/restUtilMod_stub.F90.in @@ -149,4 +149,34 @@ contains end subroutine set_missing_from_template + !----------------------------------------------------------------------- + logical function CallRestartvarDimOK (ncid, flag, dimname) + ! + ! !DESCRIPTION: + ! Answer whether to call restartvar(), if necessary checking whether + ! a dimension exists in the restart file + ! + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-02) + ! Used in Restart(). Even though restartvar() can safely be called for a + ! non-existent variable, it gives an error for a non-existent dimension, so + ! check whether the dimension exists before trying to read. The need for this + ! function arose because we recently added the mxsowings and mxharvests + ! dimensions to the restart file. + ! + ! !USES: + use ncdio_pio + ! + ! !ARGUMENTS: + type(file_desc_t), intent(inout) :: ncid + character(len=*) , intent(in) :: flag + character(len=*) , intent(in) :: dimname + ! + ! !LOCAL VARIABLES: + !----------------------------------------------------------------------- + + CallRestartvarDimOK = .false. + + end function CallRestartvarDimOK + + end module restUtilMod From 1b9df13218cab71f44e028af782048e8622d8dc5 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 27 Jun 2023 10:01:56 -0600 Subject: [PATCH 1055/2067] Update fates pointer and temporary parameter file --- Externals_CLM.cfg | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index f4a9eae9c6..a7066ed2e3 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.65.3_api.25.4.0 +branch = mpaiao-pr-drgt-decid required = True [externals_description] diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 6bb5d60aa7..28354012db 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc +/glade/u/home/rgknox/ctsm/src/fates/parameter_files/fates_params_api.25.5.0_12pft_c230626.nc From 608d2fd977548857cb8dcb7d5809495e9499322b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 27 Jun 2023 12:32:42 -0600 Subject: [PATCH 1056/2067] Change syntax in 5 NEON tests from L10d to Ld10 --- cime_config/testdefs/testlist_clm.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 9421209fe4..2e4742de92 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1588,7 +1588,7 @@ - + @@ -1598,7 +1598,7 @@ - + @@ -1608,7 +1608,7 @@ - + @@ -1618,7 +1618,7 @@ - + @@ -1629,7 +1629,7 @@ - + From 64cb8480846423671b13c5e8edba9dd551e06359 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 26 Jun 2023 17:13:12 -0600 Subject: [PATCH 1057/2067] FSURDATMODIFYCTSM test now uses `conda run -n` instead of `conda activate`. This is a more robust method and is recommended when conda is being used non-interactively. RXCROPMATURITY already used this method, so I introduced a new module in cime_config/SystemTests, systemtests_utils.py, to share the code. * Resolves #2042 --- cime_config/SystemTests/fsurdatmodifyctsm.py | 55 ++----------- cime_config/SystemTests/rxcropmaturity.py | 83 +++++++------------- cime_config/SystemTests/systemtest_utils.py | 55 +++++++++++++ 3 files changed, 90 insertions(+), 103 deletions(-) create mode 100644 cime_config/SystemTests/systemtest_utils.py diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 1427a7550f..090df2426e 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -5,7 +5,7 @@ import os import re -import subprocess +import systemtest_utils as stu from CIME.SystemTests.system_tests_common import SystemTestsCommon from CIME.XML.standard_module_setup import * from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files @@ -64,58 +64,19 @@ def _create_config_file(self): line = 'idealized = True' cfg_out.write(line) - def _run_modify_fsurdat(self): tool_path = os.path.join(self._ctsm_root, 'tools/modify_input_files/fsurdat_modifier') - self._case.load_env(reset=True) - conda_env = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " - # Preprend the commands to get the conda environment for python first - conda_env += self._get_conda_env() - # Source the env - try: - subprocess.run( conda_env+"python3 "+tool_path+" "+self._cfg_file_path, shell=True, check=True) - except subprocess.CalledProcessError as error: - print("ERROR while getting the conda environment and/or ") - print("running the fsurdat_modifier tool: ") - print("(1) If your ctsm_pylib environment is out of date or you ") - print("have not created the ctsm_pylib environment, yet, you may ") - print("get past this error by running ./py_env_create ") - print("in your ctsm directory and trying this test again. ") - print("(2) If conda is not available, install and load conda, ") - print("run ./py_env_create, and then try this test again. ") - print("(3) If (1) and (2) are not the issue, then you may be ") - print("getting an error within the fsurdat_modifier tool itself. ") - print("Default error message: ") - print(error.output) - raise - except: - print("ERROR trying to run fsurdat_modifier tool.") - raise + command = f"python3 {tool_path} {self._cfg_file_path}" + stu.run_python_script( + self._get_caseroot(), + "ctsm_pylib", + command, + tool_path, + ) def _modify_user_nl(self): append_to_user_nl_files(caseroot = self._get_caseroot(), component = "clm", contents = "fsurdat = '{}'".format(self._fsurdat_out)) - - def _get_conda_env(self): - # - # Add specific commands needed on different machines to get conda available - # Use semicolon here since it's OK to fail - # - # Execute the module unload/load when "which conda" fails - # eg on cheyenne - try: - subprocess.run( "which conda", shell=True, check=True) - conda_env = " " - except subprocess.CalledProcessError: - # Remove python and add conda to environment for cheyennne - conda_env = "module unload python; module load conda;" - - # Activate the python environment - conda_env += " conda activate ctsm_pylib" - # End above to get to actual command - conda_env += " && " - - return( conda_env ) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 9cf1b713db..0735457ac4 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -15,6 +15,7 @@ import os import re +import systemtest_utils as stu import subprocess from CIME.SystemTests.system_tests_common import SystemTestsCommon from CIME.XML.standard_module_setup import * @@ -80,6 +81,9 @@ def __init__(self, case): # Get files with prescribed sowing and harvest dates self._get_rx_dates() + # Which conda environment should we use? + self._get_conda_env() + def run_phase(self): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't # want to be saved as baseline. @@ -254,7 +258,12 @@ def _run_make_surface_for_gddgen(self, case_gddgen): command = f"python3 {tool_path} "\ + f"-i {self._fsurdat_in} "\ + f"-o {self._fsurdat_out}" - self._run_python_script(case_gddgen, command, tool_path) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) # Modify namelist logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") @@ -281,7 +290,12 @@ def _run_check_rxboth_run(self): + f"-yN {last_usable_year} "\ + f"--rx-sdates-file {self._sdatefile} "\ + f"--rx-gdds-file {self._gdds_file} " - self._run_python_script(self._case, command, tool_path) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) def _modify_user_nl_allruns(self): @@ -326,7 +340,12 @@ def _run_generate_gdds(self, case_gddgen): f"--sdates-file {sdates_file}", f"--hdates-file {hdates_file}", f"--output-dir generate_gdds_out"]) - self._run_python_script(case_gddgen, command, tool_path) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) # Where were the prescribed maturity requirements saved? generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) @@ -338,72 +357,24 @@ def _run_generate_gdds(self, case_gddgen): self._gdds_file = generated_gdd_files[0] - def _get_conda_env(self, conda_setup_commands): - # - # Add specific commands needed on different machines to get conda available - # Use semicolon here since it's OK to fail - # - # Execute the module unload/load when "which conda" fails - # eg on cheyenne - try: - subprocess.run( "which conda", shell=True, check=True) - except subprocess.CalledProcessError: - # Remove python and add conda to environment for cheyennne - conda_setup_commands += "module unload python; module load conda; " + def _get_conda_env(self): + conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) # If npl conda environment is available, use that (It has dask, which # enables chunking, which makes reading daily 1-degree netCDF files # much more efficient. if "npl " in os.popen(conda_setup_commands + "conda env list").read(): - this_conda_env = "npl" + self._this_conda_env = "npl" else: - this_conda_env = "ctsm_pylib" + self._this_conda_env = "ctsm_pylib" + - ## Run in the correct python environment - conda_setup_commands += f" conda run -n {this_conda_env} " - - return conda_setup_commands, this_conda_env - - def _append_to_user_nl_clm(self, additions): caseroot = self._get_caseroot() append_to_user_nl_files(caseroot = caseroot, component = "clm", contents = additions) - - def _run_python_script(self, case, command, tool_path): - tool_name = os.path.split(tool_path)[-1] - case.load_env(reset=True) - - # Prepend the commands to get the conda environment for python first - conda_setup_commands = ". "+self._get_caseroot()+"/.env_mach_specific.sh; " - conda_setup_commands, this_conda_env = self._get_conda_env(conda_setup_commands) - command = conda_setup_commands + command - print(f"command: {command}") - - # Run - try: - with open(tool_name + ".log", "w") as f: - subprocess.run(command, shell=True, check=True, text=True, - stdout=f, stderr=subprocess.STDOUT) - except subprocess.CalledProcessError as error: - print("ERROR while getting the conda environment and/or ") - print(f"running the {tool_name} tool: ") - print(f"(1) If your {this_conda_env} environment is out of date or you ") - print(f"have not created the {this_conda_env} environment, yet, you may ") - print("get past this error by running ./py_env_create ") - print("in your ctsm directory and trying this test again. ") - print("(2) If conda is not available, install and load conda, ") - print("run ./py_env_create, and then try this test again. ") - print("(3) If (1) and (2) are not the issue, then you may be ") - print(f"getting an error within {tool_name} itself. ") - print("Default error message: ") - print(error.output) - raise - except: - print(f"ERROR trying to run {tool_name}.") - raise # Is flanduse_timeseries defined? If so, where is it? def _get_flanduse_timeseries_in(self, case): diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py new file mode 100644 index 0000000000..3c264b32b9 --- /dev/null +++ b/cime_config/SystemTests/systemtest_utils.py @@ -0,0 +1,55 @@ +""" +Reduce code duplication by putting reused functions here. +""" + +import os, subprocess + +def cmds_to_setup_conda(caseroot): + # Add specific commands needed on different machines to get conda available + # Use semicolon here since it's OK to fail + # + conda_setup_commands = ". " + caseroot + "/.env_mach_specific.sh; " + # Execute the module unload/load when "which conda" fails + # eg on cheyenne + try: + subprocess.run( "which conda", shell=True, check=True) + except subprocess.CalledProcessError: + # Remove python and add conda to environment for cheyennne + conda_setup_commands += " module unload python; module load conda;" + + return conda_setup_commands + + +def run_python_script(caseroot, this_conda_env, command, tool_path): + + # Run in the specified conda environment + conda_setup_commands = cmds_to_setup_conda(caseroot) + conda_setup_commands += f" conda run -n {this_conda_env}" + + # Finish with Python script call + command = conda_setup_commands + " " + command + print(f"command: {command}") + + # Run with logfile + tool_name = os.path.split(tool_path)[-1] + try: + with open(tool_name + ".log", "w") as f: + subprocess.run(command, shell=True, check=True, text=True, + stdout=f, stderr=subprocess.STDOUT) + except subprocess.CalledProcessError as error: + print("ERROR while getting the conda environment and/or ") + print(f"running the {tool_name} tool: ") + print(f"(1) If your {this_conda_env} environment is out of date or you ") + print(f"have not created the {this_conda_env} environment, yet, you may ") + print("get past this error by running ./py_env_create ") + print("in your ctsm directory and trying this test again. ") + print("(2) If conda is not available, install and load conda, ") + print("run ./py_env_create, and then try this test again. ") + print("(3) If (1) and (2) are not the issue, then you may be ") + print(f"getting an error within {tool_name} itself. ") + print("Default error message: ") + print(error.output) + raise + except: + print(f"ERROR trying to run {tool_name}.") + raise From c97c142e43366d386eafa447b9dd2294ffeb1ebf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 27 Jun 2023 16:01:40 -0600 Subject: [PATCH 1058/2067] Declared CallRestartvarDimOK a public member of restUtilMod_stub.F90. --- src/unit_test_stubs/utils/restUtilMod_stub.F90.in | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/unit_test_stubs/utils/restUtilMod_stub.F90.in b/src/unit_test_stubs/utils/restUtilMod_stub.F90.in index ab26558db7..2f57303c78 100644 --- a/src/unit_test_stubs/utils/restUtilMod_stub.F90.in +++ b/src/unit_test_stubs/utils/restUtilMod_stub.F90.in @@ -23,6 +23,8 @@ module restUtilMod public :: set_missing_from_template + public :: CallRestartvarDimOK + contains !----------------------------------------------------------------------- From 12f93f9312eea2dc18e476d054c2bc6cb23703bb Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Tue, 27 Jun 2023 15:35:12 +0200 Subject: [PATCH 1059/2067] changes needed to get FATES-NOCOMP able to couple to CAM. The model still blows up - but gets past these bottlenecks --- src/biogeochem/DryDepVelocity.F90 | 8 +++++--- src/biogeochem/VOCEmissionMod.F90 | 11 +++++++---- src/main/clm_initializeMod.F90 | 13 +++++++++---- 3 files changed, 21 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/DryDepVelocity.F90 b/src/biogeochem/DryDepVelocity.F90 index f50e218e1b..4a8334efdd 100644 --- a/src/biogeochem/DryDepVelocity.F90 +++ b/src/biogeochem/DryDepVelocity.F90 @@ -102,13 +102,15 @@ Module DryDepVelocity !------------------------------------------------------------------------ subroutine Init(this, bounds) - use clm_varctl , only : use_fates, use_fates_sp + use clm_varctl , only : use_fates, use_fates_sp, use_fates_nocomp class(drydepvel_type) :: this type(bounds_type), intent(in) :: bounds - if ( (.not. use_fates_sp) .and. use_fates .and. (n_drydep > 0) ) then - call endrun( msg='ERROR: Dry-deposition currently does NOT work with FATES outside of FATES-SP mode (see github issue #1044)'//& + if (use_fates .and. (n_drydep > 0)) then + if (( .not. use_fates_sp) .and. (.not. use_fates_nocomp)) then + call endrun( msg='ERROR: Dry-deposition currently only works with when FATES is in SP or NOCOMP mode '//& errMsg(sourcefile, __LINE__)) + end if end if call this%InitAllocate(bounds) call this%InitHistory(bounds) diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90 index f1865af3b7..a14d447db1 100644 --- a/src/biogeochem/VOCEmissionMod.F90 +++ b/src/biogeochem/VOCEmissionMod.F90 @@ -84,14 +84,17 @@ module VOCEmissionMod !------------------------------------------------------------------------ subroutine Init(this, bounds) - use clm_varctl , only : use_fates, use_fates_sp + use clm_varctl , only : use_fates, use_fates_sp, use_fates_nocomp class(vocemis_type) :: this type(bounds_type), intent(in) :: bounds + if ( shr_megan_mechcomps_n > 0) then - if ( use_fates .and. (.not. use_fates_sp) ) then - call endrun( msg='ERROR: MEGAN currently does NOT work with FATES outside of FATES-SP mode (see github issue #115)'//& - errMsg(sourcefile, __LINE__)) + if (use_fates) then + if (( .not. use_fates_sp) .and. (.not. use_fates_nocomp)) then + call endrun( msg='ERROR: MEGAN currently only works with when FATES is in SP or NOCOMP mode '//& + errMsg(sourcefile, __LINE__)) + end if end if call this%InitAllocate(bounds) call this%InitHistory(bounds) diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 7988fbfc7b..a953a916b2 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -13,7 +13,7 @@ module clm_initializeMod use clm_varctl , only : nsrest, nsrStartup, nsrContinue, nsrBranch, use_fates_sp use clm_varctl , only : is_cold_start use clm_varctl , only : iulog - use clm_varctl , only : use_lch4, use_cn, use_cndv, use_c13, use_c14, use_fates + use clm_varctl , only : use_lch4, use_cn, use_cndv, use_c13, use_c14, use_fates, use_fates_nocomp use clm_varctl , only : use_soil_moisture_streams use clm_instur , only : wt_lunit, urban_valid, wt_nat_patch, wt_cft, fert_cft use clm_instur , only : irrig_method, wt_glc_mec, topo_glc_mec, haslake, pct_urban_max @@ -451,9 +451,14 @@ subroutine initialize2(ni,nj) ! For SP FATES-SP Initialize SP ! Also for FATES with Dry-Deposition on as well (see above) - !if(use_fates_sp .or. (.not.use_cn) .or. (n_drydep > 0) )then ! Replace with this when we have dry-deposition working - ! For now don't allow for dry-deposition because of issues in #1044 EBK Jun/17/2022 - if( use_fates_sp .or. .not. use_fates )then + ! Replace with this when we have dry-deposition working + ! if (use_fates_sp .or. use_fates_nocomp .or. (n_drydep > 0) )then + ! For now don't allow for dry-deposition with full fates + ! because of issues in #1044 EBK Jun/17/2022 + if( use_fates_sp .or. use_fates_nocomp .or. (.not. use_fates )) then + if (masterproc) then + write(iulog,'(a)')'Initializing Satellite Phenology' + end if call SatellitePhenologyInit(bounds_proc) end if From 100f7036d325ed4693619e8dcafe833bf9e5ddd6 Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 28 Jun 2023 10:04:24 +0200 Subject: [PATCH 1060/2067] added a FATES-NOCOMP compset --- cime_config/config_component.xml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 743e9229b9..ebe7cd8254 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -16,7 +16,7 @@ clm4.5: clm5.0: - clm5.1: + clm5.1: Satellite phenology: Satellite phenology with VIC hydrology: @@ -26,6 +26,7 @@ BGC (vert. resol. CN and methane) without anthropomorphic influences: FATES (Functionally Assembled Terrestrial Ecosystem Simulator) Ecosystem Demography model: Satellite phenology with FATES (Functionally Assembled Terrestrial Ecosystem Simulator) Ecosystem Demography model: + No Competition mode with FATES (Functionally Assembled Terrestrial Ecosystem Simulator) Ecosystem Demography model: BGC (vert. resol. CN and methane) with dynamic vegetation: BGC (vert. resol. CN and methane) with dynamic vegetation and prognostic crop: BGC (vert. resol. CN and methane) with prognostic crop, with modifications appropriate for CMIP6 DECK experiments: @@ -173,6 +174,7 @@ -bgc bgc -crop -bgc fates -no-megan -bgc fates -no-megan + -bgc fates -bgc bgc -dynamic_vegetation @@ -282,6 +284,7 @@ $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_nocomp $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck From 0b8508fe09df01c5ede05f1eddbdfc0c252b9750 Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 28 Jun 2023 13:13:14 +0200 Subject: [PATCH 1061/2067] addressed issues brought up in the PR --- src/biogeochem/DryDepVelocity.F90 | 6 +++--- src/biogeochem/VOCEmissionMod.F90 | 6 +++--- src/main/clm_initializeMod.F90 | 10 ++++------ 3 files changed, 10 insertions(+), 12 deletions(-) diff --git a/src/biogeochem/DryDepVelocity.F90 b/src/biogeochem/DryDepVelocity.F90 index 4a8334efdd..a6a91df539 100644 --- a/src/biogeochem/DryDepVelocity.F90 +++ b/src/biogeochem/DryDepVelocity.F90 @@ -102,13 +102,13 @@ Module DryDepVelocity !------------------------------------------------------------------------ subroutine Init(this, bounds) - use clm_varctl , only : use_fates, use_fates_sp, use_fates_nocomp + use clm_varctl , only : use_fates, use_fates_nocomp class(drydepvel_type) :: this type(bounds_type), intent(in) :: bounds if (use_fates .and. (n_drydep > 0)) then - if (( .not. use_fates_sp) .and. (.not. use_fates_nocomp)) then - call endrun( msg='ERROR: Dry-deposition currently only works with when FATES is in SP or NOCOMP mode '//& + if (.not. use_fates_nocomp) then + call endrun( msg='ERROR: Dry-deposition currently only works with when FATES is in SP and/or NOCOMP mode '//& errMsg(sourcefile, __LINE__)) end if end if diff --git a/src/biogeochem/VOCEmissionMod.F90 b/src/biogeochem/VOCEmissionMod.F90 index a14d447db1..a1722a08b9 100644 --- a/src/biogeochem/VOCEmissionMod.F90 +++ b/src/biogeochem/VOCEmissionMod.F90 @@ -84,15 +84,15 @@ module VOCEmissionMod !------------------------------------------------------------------------ subroutine Init(this, bounds) - use clm_varctl , only : use_fates, use_fates_sp, use_fates_nocomp + use clm_varctl, only : use_fates, use_fates_nocomp class(vocemis_type) :: this type(bounds_type), intent(in) :: bounds if ( shr_megan_mechcomps_n > 0) then if (use_fates) then - if (( .not. use_fates_sp) .and. (.not. use_fates_nocomp)) then - call endrun( msg='ERROR: MEGAN currently only works with when FATES is in SP or NOCOMP mode '//& + if (.not. use_fates_nocomp) then + call endrun( msg='ERROR: MEGAN currently only works with when FATES is in SP and/or NOCOMP mode '//& errMsg(sourcefile, __LINE__)) end if end if diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index a953a916b2..9436512d4e 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -449,13 +449,11 @@ subroutine initialize2(ni,nj) else ! FATES OR Satellite phenology - ! For SP FATES-SP Initialize SP + ! For FATES-SP or FATES-NOCOMP Initialize SP ! Also for FATES with Dry-Deposition on as well (see above) - ! Replace with this when we have dry-deposition working - ! if (use_fates_sp .or. use_fates_nocomp .or. (n_drydep > 0) )then ! For now don't allow for dry-deposition with full fates ! because of issues in #1044 EBK Jun/17/2022 - if( use_fates_sp .or. use_fates_nocomp .or. (.not. use_fates )) then + if( use_fates_nocomp .or. (.not. use_fates )) then if (masterproc) then write(iulog,'(a)')'Initializing Satellite Phenology' end if @@ -670,9 +668,9 @@ subroutine initialize2(ni,nj) ! Call interpMonthlyVeg for dry-deposition so that mlaidiff will be calculated ! This needs to be done even if FATES, CN or CNDV is on! call interpMonthlyVeg(bounds_proc, canopystate_inst) - ! If fates has satellite phenology enabled, get the monthly veg values - ! prior to the first call to SatellitePhenology() elseif ( use_fates_sp ) then + ! If fates has satellite phenology enabled, get the monthly veg values + ! prior to the first call to SatellitePhenology() call interpMonthlyVeg(bounds_proc, canopystate_inst) end if From 76569cdb32f1861ff81b2ebc1878ae980a950321 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 28 Jun 2023 10:20:10 -0600 Subject: [PATCH 1062/2067] More confined regular expressing fixing #2039 --- cime_config/usermods_dirs/NEON/defaults/shell_commands | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 437201f2b2..1f5427ca98 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -32,7 +32,7 @@ else fi # If needed for SP simulations: & set history file variables -if [[ $compset =~ .*CLM[0-9]+%.*SP.* ]]; then +if [[ $compset =~ .*CLM[0-9]+%[^_]*SP.* ]]; then if [[ $TEST != "TRUE" ]]; then ./xmlchange STOP_OPTION=nyears fi From 180206cda0a8b4ee6d8341c5ce64eb474e179e51 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 28 Jun 2023 13:05:11 -0600 Subject: [PATCH 1063/2067] Removing use_z0mg_2d from the Meier2022_surf_rough testmods --- .../testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 1 - 1 file changed, 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm index c885cdacd7..01df79ecba 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -1,5 +1,4 @@ z0param_method = 'Meier2022' use_z0m_snowmelt = .true. -use_z0mg_2d = .false. paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_params.RMz0.c220304.nc' From cc2ffe2dae521611747f8d879daf7d7d8e895601 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 28 Jun 2023 15:07:14 -0600 Subject: [PATCH 1064/2067] Do not checkout ctsm_py_gallery (unused). --- .gitignore | 1 - Externals.cfg | 7 ------- 2 files changed, 8 deletions(-) diff --git a/.gitignore b/.gitignore index 374be1aeaa..3fb3c50641 100644 --- a/.gitignore +++ b/.gitignore @@ -8,7 +8,6 @@ ccs_config /libraries/ /share/ /doc/doc-builder/ -/python/ctsm_py_gallery/ # ignore svn directories **/.svn/** diff --git a/Externals.cfg b/Externals.cfg index 1153bb8c3f..02d6270316 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -97,12 +97,5 @@ repo_url = https://github.com/ESMCI/doc-builder tag = v1.0.8 required = False -[ctsm_py_gallery] -local_path = python/ctsm_py_gallery -protocol = git -repo_url = https://github.com/NCAR/ctsm_python_gallery -hash = a664529b0152b215abef697f6beb870ad068edb3 -required = True - [externals_description] schema_version = 1.0.0 From 50e37c793a76e8a4d9a142df776d94a66e491a6a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 28 Jun 2023 15:23:25 -0600 Subject: [PATCH 1065/2067] Revert a leftover troubleshooting change. annual_flux_dribbler_gridcell() call for hrv_xsmrpool_to_atm_dribbler should always be with allows_non_annual_delta=.false. --- src/biogeochem/CNVegCarbonFluxType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 4b30f68538..c2025fca47 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -868,7 +868,7 @@ subroutine InitAllocate(this, bounds, carbon_type) bounds = bounds, & name = 'hrv_xsmrpool_to_atm_' // carbon_type_suffix, & units = 'gC/m^2', & - allows_non_annual_delta = allows_non_annual_delta) + allows_non_annual_delta = .false.) end subroutine InitAllocate From f2767b5e4eb2bd7985bd373b93b3b6e8cdd3ceb9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 28 Jun 2023 16:41:42 -0600 Subject: [PATCH 1066/2067] Follow-up to conflict resolutions in order for the code to build --- src/biogeophys/BareGroundFluxesMod.F90 | 1 - src/biogeophys/CanopyStateType.F90 | 16 ---------------- src/biogeophys/FrictionVelocityMod.F90 | 1 + 3 files changed, 1 insertion(+), 17 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index f8bd6d540d..c994d238a4 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -237,7 +237,6 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Output: [real(r8) (:) ] observational height of wind at patch level [m] forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Output: [real(r8) (:) ] observational height of temperature at patch level [m] forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Output: [real(r8) (:) ] observational height of specific humidity at patch level [m] - displa => canopystate_inst%displa_patch , & ! Input: [real(r8) (:) ] displacement height (m) u10_clm => frictionvel_inst%u10_clm_patch , & ! Input: [real(r8) (:) ] 10 m height winds (m/s) zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions zeta => frictionvel_inst%zeta_patch , & ! Output: [real(r8) (:) ] dimensionless stability parameter diff --git a/src/biogeophys/CanopyStateType.F90 b/src/biogeophys/CanopyStateType.F90 index eb13558092..313f7a83f3 100644 --- a/src/biogeophys/CanopyStateType.F90 +++ b/src/biogeophys/CanopyStateType.F90 @@ -225,22 +225,6 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='canopy top', & ptr_patch=this%htop_patch) endif - - this%displa_patch(begp:endp) = spval - call hist_addfld1d (fname='DISPLA', units='m', & - avgflag='A', long_name='displacement height', & - ptr_patch=this%displa_patch, default='inactive') - - if(use_fates_sp)then - this%htop_hist_patch(begp:endp) = spval - call hist_addfld1d (fname='HTOP', units='m', & - avgflag='A', long_name='HTOP weights for SP mode', & - ptr_patch=this%htop_hist_patch) - else - this%htop_patch(begp:endp) = spval - call hist_addfld1d (fname='HTOP', units='m', & - avgflag='A', long_name='canopy top', & - ptr_patch=this%htop_patch) endif if(use_fates_sp)then diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 5bf5c0c845..3960b6504d 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -342,6 +342,7 @@ subroutine InitHistory(this, bounds) call hist_addfld1d (fname='KBM1', units='unitless', & avgflag='A', long_name='natural logarithm of Z0MG_P/Z0HG_P', & ptr_patch=this%kbm1_patch, default='inactive') + end if if (use_luna) then call hist_addfld1d (fname='RB10', units='s/m', & From d7fc63d7abc26d210220e9c578f4d6a4d4304235 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 28 Jun 2023 16:22:03 -0700 Subject: [PATCH 1067/2067] update fates parameter file default --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 28354012db..a112040d3b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -/glade/u/home/rgknox/ctsm/src/fates/parameter_files/fates_params_api.25.5.0_12pft_c230626.nc +lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc From 8007919008b8fb797f8e042724bf7d8117395c9f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 29 Jun 2023 11:49:04 -0600 Subject: [PATCH 1068/2067] Remove hard-coded verbose option from cropcalStreamMod. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index fe1fedefd0..ba0e5b7117 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -231,11 +231,8 @@ subroutine cropcal_advance( bounds ) integer :: sec ! seconds into current date for nstep+1 integer :: mcdate ! Current model date (yyyymmdd) integer :: rc - logical :: verbose = .false. !----------------------------------------------------------------------- - if (verbose) write(iulog,*) 'cropcal_advance(): Beginning' - call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day if (use_cropcal_rx_sdates) then @@ -260,8 +257,6 @@ subroutine cropcal_advance( bounds ) end do end if - if (verbose) write(iulog,*) 'cropcal_advance(): Ending' - end subroutine cropcal_advance !================================================================ @@ -292,11 +287,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) real(r8), pointer :: dataptr2d_sdate(:,:) real(r8), pointer :: dataptr1d_cultivar_gdds(:) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) - logical :: verbose = .false. !----------------------------------------------------------------------- - if (verbose) write(iulog,*) 'cropcal_interp(): Beginning' - SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) @@ -308,7 +300,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) allocate(dataptr2d_sdate(lsize, ncft)) if (use_cropcal_rx_sdates) then ! Starting with npcropmin will skip generic crops - if (verbose) write(iulog,*) 'cropcal_interp(): Reading sdate file' do n = 1, ncft call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & fldptr1=dataptr1d_sdate, rc=rc) @@ -329,7 +320,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end do ! Set rx_sdate for each gridcell/patch combination - if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_sdate for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -385,7 +375,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end do ! Set rx_cultivar_gdd for each gridcell/patch combination - if (verbose) write(iulog,*) 'cropcal_interp(): Set rx_cultivar_gdd for each gridcell/patch combination' do fp = 1, num_pcropp p = filter_pcropp(fp) @@ -423,9 +412,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) deallocate(dataptr2d_cultivar_gdds) - if (verbose) write(iulog,*) 'cropcal_interp(): All done!' - - end subroutine cropcal_interp end module cropcalStreamMod From 868e8c213669e773354294cdd4fe004f2ea3d5dc Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 30 Jun 2023 09:30:03 -0600 Subject: [PATCH 1069/2067] reverted call order on readfirenml --- src/main/controlMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 8fc2f8b4b2..c8074eead2 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -555,8 +555,8 @@ subroutine control_init(dtime) call soilHydReadNML( NLFilename ) if( use_cn ) then - call CNPrecisionControlReadNML( NLFilename ) call CNFireReadNML( NLFilename ) + call CNPrecisionControlReadNML( NLFilename ) call CNNDynamicsReadNML ( NLFilename ) call CNPhenologyReadNML ( NLFilename ) end if From 080cd5ba055a9338e14db23668ae8644591a88c9 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 30 Jun 2023 09:35:57 -0600 Subject: [PATCH 1070/2067] Update default scope of cn_products_type procedures --- src/biogeochem/CNProductsMod.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 30dd9f3619..226c5a4bb6 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -20,6 +20,8 @@ module CNProductsMod ! !PUBLIC TYPES: type, public :: cn_products_type + private ! Default these procedures to private, unless specified otherwise + ! ------------------------------------------------------------------------ ! Public instance variables ! ------------------------------------------------------------------------ From 443af0b427ba48f0cbdbc13b740e6cb3d44a2d27 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 30 Jun 2023 09:40:23 -0700 Subject: [PATCH 1071/2067] update externals --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 24faec60e3..aec92c2173 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -branch = mpaiao-pr-drgt-decid +repo_url = https://github.com/NGEET/fates +tag = sci.1.66.0_api.25.5.0 required = True [externals_description] From 53c96342b50199eaca1302dac7924f65b6fb3770 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 30 Jun 2023 10:07:14 -0700 Subject: [PATCH 1072/2067] update changelog --- doc/ChangeLog | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 82 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 071be8709e..4c718e7707 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,85 @@ =============================================================== +Tag name: ctsm5.2.dev130 +Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049) +Date: Fri Jun 30 12:00:00 MDT 2023 +One-line Summary: FATES parameter file and test definition update + +Purpose and description of changes +---------------------------------- + +This tag incorporates updates to the FATES parameter file and test +definitions to be consistent with updates to the drought deciduous +phenology model in FATES. This also updates the external FATES +pointer to the tag associated with the drought deciduous phenology +update. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Notes of particular relevance for users +--------------------------------------- +Changes made to namelist defaults (e.g., changed parameter values): + + FATES parameter file default updated to fates_params_api.25.5.0_12pft_c230628.nc + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- TBD + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- TBD + +Answer changes +-------------- + +Changes answers relative to baseline: YES for FATES tests only + + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] + + Summarize any changes to answers, i.e., + - what code configurations: FATES + - what platforms/compilers: ALL + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + See FATES #958 for discussion. Note that this FATES update also incorporates + a number of additional science updates. + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + fates: sci.1.65.3_api.25.4.0 -> fates-sci.1.66.0_api.25.5.0 + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2009 + https://github.com/NGEET/fates/pull/958 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev129 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Thu Jun 22 01:21:56 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index f0193772d6..df0d56f120 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.2.dev130 glemieux 06/30/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test From 51ad34cf194c16509c08259b2aa62109e70d9e99 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 30 Jun 2023 10:11:19 -0700 Subject: [PATCH 1073/2067] Update non-b4b changelog explanation --- doc/ChangeLog | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 4c718e7707..f03b3e4b76 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -66,8 +66,14 @@ Changes answers relative to baseline: YES for FATES tests only If this tag changes climate describe the run(s) done to evaluate the new climate (put details of the simulations in the experiment database) - See FATES #958 for discussion. Note that this FATES update also incorporates - a number of additional science updates. + + See FATES #958 for discussion. The update increased the dimensions of + some FATES history output from site-level to pft-level. As such, these + have been removed from some test cases to keep the test light weight and + added to the AllVars test to maintain coverage. + + Note that this FATES update also incorporates a number of additional science updates + since the previous tag. Other details ------------- From 74f9bd1c433908743fff34d6a0259434507de28e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 30 Jun 2023 13:08:51 -0600 Subject: [PATCH 1074/2067] fixing test length duration --- cime_config/testdefs/testlist_clm.xml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index d162c74833..b887e570f6 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1569,7 +1569,7 @@ - + @@ -1579,7 +1579,7 @@ - + @@ -1589,7 +1589,7 @@ - + @@ -1599,7 +1599,7 @@ - + @@ -1610,7 +1610,7 @@ - + From 8d58a4d006cf68aa89f24648827cc4bce33a4469 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 30 Jun 2023 15:55:45 -0700 Subject: [PATCH 1075/2067] update changelog with test results Adds fixed issue id --- doc/ChangeLog | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index f03b3e4b76..7af136b95d 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -29,6 +29,11 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Fixes #2043 -- Five izumi NEON tests fail (for me) because the testnames include L10d instead of Ld10 Notes of particular relevance for users --------------------------------------- @@ -44,11 +49,11 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- OK - izumi ------- TBD + izumi ------- OK fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) cheyenne ---- OK - izumi ------- TBD + izumi ------- OK Answer changes -------------- From a4e690b1560604d2afae1932697b03d828cc79bc Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 3 Jul 2023 18:47:11 -0600 Subject: [PATCH 1076/2067] update to the span of columns that carbon summary variables are calculated, for b4b --- src/biogeochem/CNProductsMod.F90 | 4 +- .../SoilBiogeochemCarbonStateType.F90 | 95 +++++++++++-------- 2 files changed, 59 insertions(+), 40 deletions(-) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 226c5a4bb6..19ae952c9a 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -51,9 +51,9 @@ module CNProductsMod real(r8), pointer :: gru_prod100_gain_grc(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to 100-year wood product pool real(r8), pointer :: gru_woodprod_gain_grc(:) ! (g[C or N]/m2/s) gross unrepresented landcover addition to wood product pools real(r8), pointer :: hrv_deadstem_to_prod10_patch(:) ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool - real(r8), pointer :: hrv_deadstem_to_prod10_grc(:) ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool + real(r8), pointer,public :: hrv_deadstem_to_prod10_grc(:) ! (g[C or N]/m2/s) dead stem harvest to 10-year wood product pool real(r8), pointer :: hrv_deadstem_to_prod100_patch(:) ! (g[C or N]/m2/s) dead stem harvest to 100-year wood product pool - real(r8), pointer :: hrv_deadstem_to_prod100_grc(:) ! (g[C or N]/m2/s) dead stem harvest to 100-year wood product pool + real(r8), pointer,public :: hrv_deadstem_to_prod100_grc(:) ! (g[C or N]/m2/s) dead stem harvest to 100-year wood product pool real(r8), pointer :: crop_harvest_to_cropprod1_patch(:) ! (g[C or N]/m2/s) crop harvest to 1-year crop product pool real(r8), pointer :: crop_harvest_to_cropprod1_grc(:) ! (g[C or N]/m2/s) crop harvest to 1-year crop product pool diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 1f3b00f6e8..098412a57b 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -7,7 +7,7 @@ module SoilBiogeochemCarbonStateType use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan use clm_varpar , only : nlevdecomp_full, nlevdecomp, nlevsoi use clm_varcon , only : spval, ispval, dzsoi_decomp, zisoi, zsoi, c3_r2 - use clm_varctl , only : iulog, spinup_state + use clm_varctl , only : iulog, spinup_state, use_fates_bgc use landunit_varcon , only : istcrop, istsoil use abortutils , only : endrun use spmdMod , only : masterproc @@ -1083,8 +1083,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg end do do l = 1, ndecomp_pools if ( decomp_cascade_con%is_microbe(l) ) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) + do fc = 1,num_allc + c = filter_allc(fc) this%totmicc_col(c) = this%totmicc_col(c) + this%decomp_cpools_col(c,l) end do endif @@ -1118,54 +1118,73 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg end if end do - - do fc = 1,num_allc c = filter_allc(fc) - ! coarse woody debris carbon this%cwdc_col(c) = 0._r8 - this%totecosysc_col(c) = 0._r8 - this%totc_col(c) = 0._r8 - end do - - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) - - if(col%is_fates(c)) then - totvegc_col = 0._r8 - ecovegc_col = 0._r8 - else + + if (use_fates_bgc) then + do fc = 1,num_bgc_soilc + c = filter_bgc_soilc(fc) + if(col%is_fates(c)) then + totvegc_col = 0._r8 + ecovegc_col = 0._r8 + else + do l = 1, ndecomp_pools + if ( decomp_cascade_con%is_cwd(l) ) then + this%cwdc_col(c) = this%cwdc_col(c) + this%decomp_cpools_col(c,l) + end if + end do + totvegc_col = cnveg_carbonstate_inst%totc_p2c_col(c) + ecovegc_col = cnveg_carbonstate_inst%totvegc_col(c) + end if + ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) + this%totecosysc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + ecovegc_col + ! total column carbon, including veg and cpool (TOTCOLC) + this%totc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + this%ctrunc_col(c) + & + totvegc_col + end do + else + do fc = 1,num_allc + c = filter_allc(fc) do l = 1, ndecomp_pools if ( decomp_cascade_con%is_cwd(l) ) then this%cwdc_col(c) = this%cwdc_col(c) + this%decomp_cpools_col(c,l) end if end do - totvegc_col = cnveg_carbonstate_inst%totc_p2c_col(c) ecovegc_col = cnveg_carbonstate_inst%totvegc_col(c) - end if - ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) - this%totecosysc_col(c) = & - this%cwdc_col(c) + & - this%totmicc_col(c) + & - this%totlitc_col(c) + & - this%totsomc_col(c) + & - ecovegc_col - - ! total column carbon, including veg and cpool (TOTCOLC) - this%totc_col(c) = & - this%cwdc_col(c) + & - this%totmicc_col(c) + & - this%totlitc_col(c) + & - this%totsomc_col(c) + & - this%ctrunc_col(c) + & - totvegc_col - end do - - + ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) + this%totecosysc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + ecovegc_col + + ! total column carbon, including veg and cpool (TOTCOLC) + this%totc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + this%ctrunc_col(c) + & + totvegc_col + end do + end if + end subroutine Summary !------------------------------------------------------------------------ From 11968dbf3bdb3b1bed991051855979485b6576ef Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 5 Jul 2023 09:58:02 +0200 Subject: [PATCH 1077/2067] addition of new file for having nocomp mode run out of the box --- cime_config/usermods_dirs/fates_nocomp/user_nl_clm | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 cime_config/usermods_dirs/fates_nocomp/user_nl_clm diff --git a/cime_config/usermods_dirs/fates_nocomp/user_nl_clm b/cime_config/usermods_dirs/fates_nocomp/user_nl_clm new file mode 100644 index 0000000000..2d93aa0ed0 --- /dev/null +++ b/cime_config/usermods_dirs/fates_nocomp/user_nl_clm @@ -0,0 +1,2 @@ +! Turn FATES-NOCOMP mode on +use_fates_nocomp = .true. From 6abd020b984c1c891180bc52a4cd52e2eb3a53bf Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 5 Jul 2023 10:05:31 +0200 Subject: [PATCH 1078/2067] updates for FATES nocomp test on betzy --- cime_config/testdefs/testlist_clm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 5512ace24b..d34afa7435 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1934,6 +1934,7 @@ + From 40e7600c66523e228ae78c8c6fb87548bbd212af Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 5 Jul 2023 09:23:47 -0600 Subject: [PATCH 1079/2067] Fixes to zeroing carbon and nitrogen summary variables --- .../SoilBiogeochemCarbonStateType.F90 | 81 ++++++++----------- .../SoilBiogeochemNitrogenStateType.F90 | 27 ++++--- 2 files changed, 50 insertions(+), 58 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index 098412a57b..a915a88862 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -950,6 +950,9 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg integer :: c,j,k,l ! indices integer :: fc ! filter indices real(r8) :: maxdepth ! depth to integrate soil variables + integer :: num_local ! Either num_bgc_soilc or num_allc, depending + ! on if its a fates run, its different because + ! the cnveg variables are not allocated w/ fates real(r8) :: ecovegc_col real(r8) :: totvegc_col !----------------------------------------------------------------------- @@ -1125,39 +1128,20 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg end do if (use_fates_bgc) then - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) - if(col%is_fates(c)) then - totvegc_col = 0._r8 - ecovegc_col = 0._r8 - else - do l = 1, ndecomp_pools - if ( decomp_cascade_con%is_cwd(l) ) then - this%cwdc_col(c) = this%cwdc_col(c) + this%decomp_cpools_col(c,l) - end if - end do - totvegc_col = cnveg_carbonstate_inst%totc_p2c_col(c) - ecovegc_col = cnveg_carbonstate_inst%totvegc_col(c) - end if - ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) - this%totecosysc_col(c) = & - this%cwdc_col(c) + & - this%totmicc_col(c) + & - this%totlitc_col(c) + & - this%totsomc_col(c) + & - ecovegc_col - ! total column carbon, including veg and cpool (TOTCOLC) - this%totc_col(c) = & - this%cwdc_col(c) + & - this%totmicc_col(c) + & - this%totlitc_col(c) + & - this%totsomc_col(c) + & - this%ctrunc_col(c) + & - totvegc_col - end do + num_local = num_bgc_soilc else - do fc = 1,num_allc + num_local = num_allc + end if + do fc = 1,num_local + if(use_fates_bgc) then + c = filter_bgc_soilc(fc) + else c = filter_allc(fc) + end if + if(col%is_fates(c)) then + totvegc_col = 0._r8 + ecovegc_col = 0._r8 + else do l = 1, ndecomp_pools if ( decomp_cascade_con%is_cwd(l) ) then this%cwdc_col(c) = this%cwdc_col(c) + this%decomp_cpools_col(c,l) @@ -1165,25 +1149,24 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg end do totvegc_col = cnveg_carbonstate_inst%totc_p2c_col(c) ecovegc_col = cnveg_carbonstate_inst%totvegc_col(c) + end if - ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) - this%totecosysc_col(c) = & - this%cwdc_col(c) + & - this%totmicc_col(c) + & - this%totlitc_col(c) + & - this%totsomc_col(c) + & - ecovegc_col - - ! total column carbon, including veg and cpool (TOTCOLC) - this%totc_col(c) = & - this%cwdc_col(c) + & - this%totmicc_col(c) + & - this%totlitc_col(c) + & - this%totsomc_col(c) + & - this%ctrunc_col(c) + & - totvegc_col - end do - end if + ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) + this%totecosysc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + ecovegc_col + ! total column carbon, including veg and cpool (TOTCOLC) + this%totc_col(c) = & + this%cwdc_col(c) + & + this%totmicc_col(c) + & + this%totlitc_col(c) + & + this%totsomc_col(c) + & + this%ctrunc_col(c) + & + totvegc_col + end do end subroutine Summary diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index ac57ad20b7..3a217dd4c3 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -11,7 +11,7 @@ module SoilBiogeochemNitrogenStateType use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools, nlevcan use clm_varpar , only : nlevdecomp_full, nlevdecomp, nlevsoi use clm_varcon , only : spval, dzsoi_decomp, zisoi - use clm_varctl , only : use_nitrif_denitrif + use clm_varctl , only : use_nitrif_denitrif, use_fates_bgc use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, century_decomp, decomp_method, use_soil_matrixcn use clm_varctl , only : iulog, override_bgc_restart_mismatch_dump, spinup_state use landunit_varcon , only : istcrop, istsoil @@ -821,6 +821,9 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg ! !LOCAL VARIABLES: integer :: c,j,k,l ! indices integer :: fc ! lake filter indices + integer :: num_local ! we do summary on different set when fates is + ! active becuase the CN variables aren't allocated + ! this preserves B4B real(r8) :: maxdepth ! depth to integrate soil variables real(r8) :: totvegn_col ! local total ecosys veg N, allows 0 for fates real(r8) :: ecovegn_col ! local total veg N, allows 0 for fates @@ -1031,18 +1034,25 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg do fc = 1,num_allc c = filter_allc(fc) this%cwdn_col(c) = 0._r8 - this%totecosysn_col(c) = 0._r8 - this%totn_col(c) = 0._r8 end do - do fc = 1,num_bgc_soilc - c = filter_bgc_soilc(fc) - + if(use_fates_bgc)then + num_local = num_bgc_soilc + else + num_local = num_allc + end if + + do fc = 1,num_local + if(use_fates_bgc) then + c = filter_bgc_soilc(fc) + else + c = filter_allc(fc) + end if + if(col%is_fates(c)) then totvegn_col = 0._r8 ecovegn_col = 0._r8 else - do l = 1, ndecomp_pools if ( decomp_cascade_con%is_cwd(l) ) then this%cwdn_col(c) = this%cwdn_col(c) + & @@ -1051,9 +1061,8 @@ subroutine Summary(this, bounds, num_allc, filter_allc, num_bgc_soilc, filter_bg end do totvegn_col = cnveg_nitrogenstate_inst%totn_p2c_col(c) ecovegn_col = cnveg_nitrogenstate_inst%totvegn_col(c) - end if - + ! total ecosystem nitrogen, including veg (TOTECOSYSN) this%totecosysn_col(c) = & this%cwdn_col(c) + & From 6a2f1ae96f6ec594b980b421ab194a1ee35f25fe Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 6 Jul 2023 15:07:03 -0600 Subject: [PATCH 1080/2067] Typo fix. --- src/biogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index f5b2249d67..7ec68f8017 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -32,7 +32,7 @@ module TillageMod ! !PRIVATE DATA MEMBERS ! SSR: I want to keep these logical input parameters private, since there's ! no obvious need for them to be public. However, that results in segfaults - ! (SIGSEGV(11)) when tillage_innit() calls shr_mpi_bcast. I think it would + ! (SIGSEGV(11)) when tillage_init() calls shr_mpi_bcast. I think it would ! work if these variables were private, but instead, I just appended the ! _private suffix here and use the non-"_private" variable names for local ! variables in tillage_init(). From 80ea55c61b4021caab6cb03b747ff28de24dccd4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 6 Jul 2023 15:13:21 -0600 Subject: [PATCH 1081/2067] Replaced do_tillage_* logicals with character tillage_mode. --- bld/CLMBuildNamelist.pm | 7 +--- bld/namelist_files/namelist_defaults_ctsm.xml | 3 +- .../namelist_definition_ctsm.xml | 11 ++---- src/biogeochem/TillageMod.F90 | 38 ++++++++++--------- 4 files changed, 27 insertions(+), 32 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 30cef854ba..4c3608982b 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2150,11 +2150,8 @@ sub setup_logic_crop { sub setup_logic_tillage { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - if ( &value_is_true($nl->get_value('do_tillage_low')) and &value_is_true($nl->get_value('do_tillage_high')) ) { - $log->fatal_error( "do_tillage_low and do_tillage_high are mutually exclusive" ); - } - - if ( &value_is_true($nl->get_value('do_tillage_low')) or &value_is_true($nl->get_value('do_tillage_high')) ) { + my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); + if ( $tillage_mode ne "off" ) { if ( not &value_is_true($nl->get_value('use_crop')) ) { $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 53aa46fc28..abdc8b73d8 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2703,8 +2703,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -.false. -.false. +off .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 1a3fd81e2a..99f630436a 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2807,14 +2807,9 @@ use case.) - -Toggle to turn on low-intensity tillage - - - -Toggle to turn on high-intensity tillage + +Whether to till crop soil, and if so, with what intensity. Date: Thu, 6 Jul 2023 16:08:39 -0600 Subject: [PATCH 1082/2067] Discard use_original_tillage_private. --- src/biogeochem/TillageMod.F90 | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index 5c1435dd8e..d4a88bb843 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -30,15 +30,9 @@ module TillageMod public :: get_apply_tillage_multipliers ! ! !PRIVATE DATA MEMBERS - ! SSR: I want to keep these logical input parameters private, since there's - ! no obvious need for them to be public. However, that results in segfaults - ! (SIGSEGV(11)) when tillage_init() calls shr_mpi_bcast. I think it would - ! work if these variables were private, but instead, I just appended the - ! _private suffix here and use the non-"_private" variable names for local - ! variables in tillage_init(). logical :: do_tillage_low ! Do low-intensity tillage? logical :: do_tillage_high ! Do high-intensity tillage? - logical :: use_original_tillage_private ! Use get_tillage_multipliers_orig? + logical :: use_original_tillage ! Use get_tillage_multipliers_orig? real(r8), pointer :: tillage_mults(:) ! (ndecomp_pools) real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) @@ -71,7 +65,6 @@ subroutine tillage_init(bounds) integer :: mpicom ! MPI communicator character(*), parameter :: subname = "('tillage_init')" character(len=8) :: tillage_mode ! off, low, high - logical :: use_original_tillage ! Use get_tillage_multipliers_orig? namelist /tillage_inparm/ & tillage_mode, & @@ -115,7 +108,6 @@ subroutine tillage_init(bounds) else call endrun(subname // ':: ERROR Unrecognized tillage_mode') end if - use_original_tillage_private = use_original_tillage end subroutine tillage_init @@ -214,7 +206,7 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c phase = 0 - if (use_original_tillage_private) then + if (use_original_tillage) then if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers phase = 1 else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers From 85eea6b21d6a4f4a42fb04c1c88e42b148d565a8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 6 Jul 2023 16:29:30 -0600 Subject: [PATCH 1083/2067] Remove excess ice test from cheyenne aux_clm suite (keep it on izumi) --- cime_config/testdefs/testlist_clm.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 2e4742de92..e8c636efd9 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -179,7 +179,6 @@ - From 65f492ac5a39d58092a248b11bb302d9ce87e59c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 6 Jul 2023 16:57:03 -0600 Subject: [PATCH 1084/2067] Adding comment to restart issue handling for issue #1787 --- src/main/restFileMod.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90 index 028c609ed4..30b8349778 100644 --- a/src/main/restFileMod.F90 +++ b/src/main/restFileMod.F90 @@ -610,6 +610,8 @@ subroutine restFile_write_issues_fixed(ncid, writing_finidat_interp_dest_file) writing_finidat_interp_dest_file = writing_finidat_interp_dest_file, & issue_num = lake_dynbal_baseline_issue) ! If running with execess ice then mark the restart file as having excess ice fixed + ! This is a permanent feature, i.e. not expected to be removed from here. + ! It would only be removed if we decided to make use_excess_ice = .true. the default. if ( use_excess_ice ) then call write_issue_fixed_metadata( & ncid = ncid, & From d67e3bf5b5019755b875ca7d2f4a960f4e280ed4 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 6 Jul 2023 18:17:20 -0600 Subject: [PATCH 1085/2067] Declare parameter excess_ice_issue once --- src/main/restFileMod.F90 | 2 +- src/utils/restUtilMod.F90.in | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90 index 30b8349778..6a574406fd 100644 --- a/src/main/restFileMod.F90 +++ b/src/main/restFileMod.F90 @@ -27,6 +27,7 @@ module restFileMod use glcBehaviorMod , only : glc_behavior_type use reweightMod , only : reweight_wrapup use IssueFixedMetadataHandler, only : write_issue_fixed_metadata, read_issue_fixed_metadata + use restUtilMod , only : excess_ice_issue ! ! !PUBLIC TYPES: implicit none @@ -62,7 +63,6 @@ module restFileMod ! Issue numbers for issue-fixed metadata integer, parameter :: lake_dynbal_baseline_issue = 1140 - integer, parameter :: excess_ice_issue = 1787 character(len=*), parameter, private :: sourcefile = & __FILE__ diff --git a/src/utils/restUtilMod.F90.in b/src/utils/restUtilMod.F90.in index 58da88ed50..9b6fe596b1 100644 --- a/src/utils/restUtilMod.F90.in +++ b/src/utils/restUtilMod.F90.in @@ -19,6 +19,7 @@ module restUtilMod implicit none save private + integer, parameter, public :: excess_ice_issue = 1787 ! save ! !----------------------------------------------------------------------- @@ -762,7 +763,6 @@ contains ! ! !LOCAL VARIABLES: integer :: attribute_value - integer, parameter :: excess_ice_issue = 1787 character(len=*), parameter :: subname = 'RestartExcessIceIssue' From 1980159218b434bd5f4990d589841b5d677c5024 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Jul 2023 15:19:33 -0600 Subject: [PATCH 1086/2067] Replace \ line continuations with &. --- src/biogeochem/CNPhenologyMod.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 971d6a8eeb..b7688467ca 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2170,8 +2170,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! which would invoke the "manually setting sowing_count and ! sdates_thisyr" code. This would lead to crops never getting ! harvested. Instead, always harvest the day before idop. - if ((.not. do_harvest) .and. \ - (idop(p) > 1 .and. jday == idop(p) - 1) .or. \ + if ((.not. do_harvest) .and. & + (idop(p) > 1 .and. jday == idop(p) - 1) .or. & (idop(p) == 1 .and. jday == dayspyr)) then do_harvest = .true. if (do_harvest) then @@ -2217,8 +2217,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! sowing dates. ! WARNING: This implementation assumes that all patches use prescribed sowing dates. if (use_cropcal_rx_sdates) then - will_plant_prescribed_tomorrow = (jday == next_rx_sdate(p) - 1) .or. \ - (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. \ + will_plant_prescribed_tomorrow = (jday == next_rx_sdate(p) - 1) .or. & + (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. & jday == dayspyr) else will_plant_prescribed_tomorrow = .false. From 072cc48dc5dc70ea5a845aeb2ce2c4eaa0bae927 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Jul 2023 16:11:03 -0600 Subject: [PATCH 1087/2067] Protect harvest "if do_plant and not did_plant" with use_cropcal_streams. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b7688467ca..daeb85c685 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2154,7 +2154,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .true. fake_harvest = .true. harvest_reason = HARVEST_REASON_SOWNBADDEC31 - else if (do_plant .and. .not. did_plant) then + else if (use_cropcal_streams .and. do_plant .and. .not. did_plant) then ! Today was supposed to be the planting day, but the previous crop still hasn't been harvested. do_harvest = .true. harvest_reason = HARVEST_REASON_SOWTODAY From 99ec14a2956dfcae288e8b9233d038557084ecb0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Jul 2023 17:51:37 -0600 Subject: [PATCH 1088/2067] Handle new GRAIN outputs in LREPRSTRUCT test. Results in BASELINE FAIL: FIELDLIST field lists differ (otherwise bit-for-bit) --- cime_config/SystemTests/lreprstruct.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/cime_config/SystemTests/lreprstruct.py b/cime_config/SystemTests/lreprstruct.py index f8a3300e56..01dc2567e3 100644 --- a/cime_config/SystemTests/lreprstruct.py +++ b/cime_config/SystemTests/lreprstruct.py @@ -49,6 +49,21 @@ def _case_one_setup(self): contents="for_testing_use_repr_structure_pool=.true.", ) + # Replace any GRAIN outputs with the same outputs for REPRODUCTIVE1 and REPRODUCTIVE2 + user_nl_clm_path = os.path.join(self._get_caseroot(), "user_nl_clm") + with open(user_nl_clm_path) as f: + user_nl_clm_text = f.read() + for grain_output in re.findall("GRAIN\w*", user_nl_clm_text): + user_nl_clm_text = user_nl_clm_text.replace( + grain_output, + grain_output.replace('GRAIN', 'REPRODUCTIVE1') + + "', '" + + grain_output.replace('GRAIN', 'REPRODUCTIVE2') + ) + with open(user_nl_clm_path, "w") as f: + f.write(user_nl_clm_text) + + def _case_two_setup(self): # This is needed in the nearly-standard case to prevent grain from being used to # replenish crop seed deficits, thus making grain act like the reproductive From 66e2843f2d20cde5f45338a7386b6d829ab9725a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 7 Jul 2023 17:58:09 -0600 Subject: [PATCH 1089/2067] Resolved conflict in $ntests BUT DID I PICK THE RIGHT VALUES? --- bld/unit_testers/build-namelist_test.pl | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index e00f69b2c3..590ead1399 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,21 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -<<<<<<< HEAD -my $ntests = 1863; -||||||| 17e2acb6a -my $ntests = 1846; -======= my $ntests = 1975; ->>>>>>> escomp/master if ( defined($opts{'compare'}) ) { -<<<<<<< HEAD - $ntests += 1263; -||||||| 17e2acb6a - $ntests += 1254; -======= $ntests += 1344; ->>>>>>> escomp/master } plan( tests=>$ntests ); From e08e56168e8992d2629a2e6b4f99f43c647e753f Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 7 Jul 2023 18:11:49 -0600 Subject: [PATCH 1090/2067] update fates external tag --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index aec92c2173..c3d00db726 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.66.0_api.25.5.0 +tag = sci.1.66.1_api.25.5.0 required = True [externals_description] From d4be4e29dac703a4027e672f8db0342e019f08a6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 7 Jul 2023 18:39:43 -0600 Subject: [PATCH 1091/2067] Format changes to adhere to ctsm coding practices --- src/biogeophys/SoilTemperatureMod.F90 | 67 +++++++++++----------- src/biogeophys/TemperatureType.F90 | 8 +-- src/biogeophys/WaterDiagnosticBulkType.F90 | 58 +++++++++---------- src/biogeophys/WaterStateType.F90 | 12 ++-- 4 files changed, 72 insertions(+), 73 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index e952614032..50c3cf15e5 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -280,22 +280,22 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter !-------------------------------------------------------------- ! Vertical coordinates adjustment for excess ice calculations !-------------------------------------------------------------- - if ( use_excess_ice )then + if ( use_excess_ice ) then ! Save original soil depth to get put them back in et the end - dz_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=dz(begc:endc,-nlevsno+1:nlevmaxurbgrnd) - zi_0(begc:endc,-nlevsno+0:nlevmaxurbgrnd)=zi(begc:endc,-nlevsno+0:nlevmaxurbgrnd) - z_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd)=z(begc:endc,-nlevsno+1:nlevmaxurbgrnd) + dz_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd) = dz(begc:endc,-nlevsno+1:nlevmaxurbgrnd) + zi_0(begc:endc,-nlevsno+0:nlevmaxurbgrnd) = zi(begc:endc,-nlevsno+0:nlevmaxurbgrnd) + z_0(begc:endc,-nlevsno+1:nlevmaxurbgrnd) = z(begc:endc,-nlevsno+1:nlevmaxurbgrnd) ! Adjust column depth for excess ice thickness - do fc = 1,num_nolakec - c = filter_nolakec(fc) - l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then - dz(c,1:nlevmaxurbgrnd)=dz(c,1:nlevmaxurbgrnd)+excess_ice(c,1:nlevmaxurbgrnd)/denice ! add extra layer thickness - do j=1,nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment - zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice - z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 - end do - endif + do fc = 1, num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz(c,1:nlevmaxurbgrnd) = dz(c,1:nlevmaxurbgrnd) + excess_ice(c,1:nlevmaxurbgrnd) / denice ! add extra layer thickness + do j = 1, nlevmaxurbgrnd ! if excess ice amount dropped to zero there will be no adjustment + zi(c,j) = zi(c,j) + sum(excess_ice(c,1:j)) / denice + z(c,j) = (zi(c,j-1) + zi(c,j)) * 0.5_r8 + end do + end if end do end if @@ -520,19 +520,18 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! Vertical coordinates adjustment for excess ice calculations !-------------------------------------------------------------- ! bringing back the soil depth to the original state - if ( use_excess_ice )then + if (use_excess_ice) then ! Adjust column depth for excess ice thickness - do fc = 1,num_nolakec - c = filter_nolakec(fc) - l = col%landunit(c) - if( lun%itype(l) == istsoil .or. lun%itype(l) == istcrop ) then - dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) - zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) - z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) - endif + do fc = 1, num_nolakec + c = filter_nolakec(fc) + l = col%landunit(c) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + dz(c,1:nlevmaxurbgrnd)=dz_0(c,1:nlevmaxurbgrnd) + zi(c,1:nlevmaxurbgrnd)=zi_0(c,1:nlevmaxurbgrnd) + z(c,1:nlevmaxurbgrnd)=z_0(c,1:nlevmaxurbgrnd) + end if end do end if - if ( IsProgBuildTemp() )then @@ -1207,13 +1206,13 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & imelt(c,j) = 0 hm(c,j) = 0._r8 xm(c,j) = 0._r8 - xm2(c,j)=0._r8 + xm2(c,j) = 0._r8 wice0(c,j) = h2osoi_ice(c,j) wliq0(c,j) = h2osoi_liq(c,j) - wexice0(c,j)=excess_ice(c,j) + wexice0(c,j) = excess_ice(c,j) wmass0(c,j) = h2osoi_ice(c,j) + h2osoi_liq(c,j) + wexice0(c,j) - if (j>=1) then - exice_subs_col(c,j)=0._r8 + if (j >= 1) then + exice_subs_col(c,j) = 0._r8 endif endif ! end of snow layer if-block @@ -1233,7 +1232,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & ! Melting identification ! If ice exists above melt point, melt some to liquid. - if (h2osoi_ice(c,j) > 0._r8 .AND. t_soisno(c,j) > tfrz) then + if (h2osoi_ice(c,j) > 0._r8 .and. t_soisno(c,j) > tfrz) then imelt(c,j) = 1 ! tinc(c,j) = t_soisno(c,j) - tfrz tinc(c,j) = tfrz - t_soisno(c,j) @@ -1406,11 +1405,11 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (j <= 0) then h2osoi_ice(c,j) = min(wmass0(c,j), wice0(c,j)-xm(c,j)) ! snow else - if (wmass0(c,j) - wexice0(c,j) < supercool(c,j)) then !even if excess ice is present, it cannot refreeze - h2osoi_ice(c,j) = 0._r8 - else - h2osoi_ice(c,j) = min(wmass0(c,j) - wexice0(c,j) - supercool(c,j),wice0(c,j)-xm(c,j)) - endif + if (wmass0(c,j) - wexice0(c,j) < supercool(c,j)) then ! even if excess ice is present, it cannot refreeze + h2osoi_ice(c,j) = 0._r8 + else + h2osoi_ice(c,j) = min(wmass0(c,j) - wexice0(c,j) - supercool(c,j),wice0(c,j)-xm(c,j)) + endif endif heatr = hm(c,j) - hfus*(wice0(c,j)-h2osoi_ice(c,j))/dtime endif diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90 index 995496b388..d20fc862b1 100644 --- a/src/biogeophys/TemperatureType.F90 +++ b/src/biogeophys/TemperatureType.F90 @@ -741,10 +741,10 @@ subroutine InitCold(this, bounds, & end if end if else - this%t_soisno_col(c,1:nlevgrnd) = 274._r8 - if(use_excess_ice .and. (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop)) then - this%t_soisno_col(c,1:nlevgrnd) = SHR_CONST_TKFRZ-5.0_r8 !needs to be below freezing to properly initiate excess ice - end if + this%t_soisno_col(c,1:nlevgrnd) = 274._r8 + if (use_excess_ice .and. (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop)) then + this%t_soisno_col(c,1:nlevgrnd) = SHR_CONST_TKFRZ - 5.0_r8 !needs to be below freezing to properly initiate excess ice + end if endif endif end do diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 4ec96820b6..ae7af4992e 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -291,23 +291,23 @@ subroutine InitBulkHistory(this, bounds) ptr_col=this%h2osoi_ice_tot_col, l2g_scale_type='veg') ! excess ice vars if (use_excess_ice) then - this%exice_vol_tot_col(begc:endc) = 0.0_r8 - call hist_addfld1d ( & - fname=this%info%fname('TOTEXICE_VOL'), & - units='m3/m3', & - avgflag='A', & - l2g_scale_type='veg', & - long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & - ptr_col=this%exice_vol_tot_col) - - this%exice_subs_tot_col(begc:endc) = 0.0_r8 - call hist_addfld1d ( & - fname=this%info%fname('SUBSIDENCE'), & - units='m', & - avgflag='SUM', & - l2g_scale_type='veg', & - long_name=this%info%lname('subsidence due to excess ice melt (veg landunits only)'), & - ptr_col=this%exice_subs_tot_col) + this%exice_vol_tot_col(begc:endc) = 0.0_r8 + call hist_addfld1d ( & + fname=this%info%fname('TOTEXICE_VOL'), & + units='m3/m3', & + avgflag='A', & + l2g_scale_type='veg', & + long_name=this%info%lname('vertically averaged volumetric excess ice concentration (veg landunits only)'), & + ptr_col=this%exice_vol_tot_col) + + this%exice_subs_tot_col(begc:endc) = 0.0_r8 + call hist_addfld1d ( & + fname=this%info%fname('SUBSIDENCE'), & + units='m', & + avgflag='SUM', & + l2g_scale_type='veg', & + long_name=this%info%lname('subsidence due to excess ice melt (veg landunits only)'), & + ptr_col=this%exice_subs_tot_col) end if this%iwue_ln_patch(begp:endp) = spval @@ -928,14 +928,14 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil units='m', & interpinic_flag='interp', readvar=readvar, data=this%exice_subs_tot_col) if (flag == 'read' .and. ((.not. readvar) .or. (.not. excess_ice_on_restart)) ) then ! when reading restart that does not have excess ice in it - if (nsrest == nsrContinue) then - call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & - errMsg(sourcefile, __LINE__)) - else if ( .not. UseExcessIceStreams() )then - call endrun(msg = "This input initial conditions file does NOT include excess ice fields" // & - ", and use_excess_ice_streams is off, one or the other needs to be changed "// & - errMsg(sourcefile, __LINE__)) - end if + if (nsrest == nsrContinue) then + call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & + errMsg(sourcefile, __LINE__)) + else if ( .not. UseExcessIceStreams() )then + call endrun(msg = "This input initial conditions file does NOT include excess ice fields" // & + ", and use_excess_ice_streams is off, one or the other needs to be changed "// & + errMsg(sourcefile, __LINE__)) + end if this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 @@ -947,10 +947,10 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil units='m3/m3', & interpinic_flag='interp', readvar=readvar, data=this%exice_vol_tot_col) if (flag == 'read' .and. ((.not. readvar) .or. (.not. excess_ice_on_restart)) ) then ! when reading restart that does not have excess ice in it - if (nsrest == nsrContinue) then - call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & - errMsg(sourcefile, __LINE__)) - end if + if (nsrest == nsrContinue) then + call endrun(msg = "On a continue run, excess ice fields MUST be on the restart file "// & + errMsg(sourcefile, __LINE__)) + end if end if endif diff --git a/src/biogeophys/WaterStateType.F90 b/src/biogeophys/WaterStateType.F90 index 3018649020..cdbefa2a04 100644 --- a/src/biogeophys/WaterStateType.F90 +++ b/src/biogeophys/WaterStateType.F90 @@ -287,8 +287,8 @@ subroutine InitHistory(this, bounds, use_aquifer_layer) ! Add excess ice fields to history if (use_excess_ice) then - data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) - call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & + data2dptr => this%excess_ice_col(begc:endc,1:nlevsoi) + call hist_addfld2d (fname='EXCESS_ICE', units='kg/m2', type2d='levsoi', & avgflag='A', long_name='excess soil ice (vegetated landunits only)', & ptr_col=this%excess_ice_col, l2g_scale_type='veg', default = 'inactive') end if @@ -744,7 +744,7 @@ subroutine Restart(this, bounds, ncid, flag, & nbedrock = col%nbedrock(c) else nbedrock = nlevsoi - endif + end if do j = 2, nlevmaxurbgrnd ! ignore first layer if(altmax_lastyear_indx(c) < nbedrock) then if (j>altmax_lastyear_indx(c) .and. j Date: Sun, 9 Jul 2023 21:04:27 -0600 Subject: [PATCH 1092/2067] Update dates --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index c9bc6eedbd..caa5568a87 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev125 Originator(s): jpalex (John Alex) -Date: Wed May 17 08:56:41 MDT 2023 +Date: Sun Jul 9 21:04:13 MDT 2023 One-line Summary: Added cache for clock step_size in clm_time_manager.F90 Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index a3e68c6581..a24a3387b2 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev125 jpalex 05/17/2023 Added cache for clock step_size in clm_time_manager.F90 + ctsm5.1.dev125 jpalex 07/09/2023 Added cache for clock step_size in clm_time_manager.F90 ctsm5.1.dev124 erik 05/09/2023 Initialization memory update, new surface datasets for new grids, add option for running NEON with PRISM data ctsm5.1.dev123 sacks 05/01/2023 Updates needed for pFUnit 4 and other externals updates ctsm5.1.dev122 sacks 04/23/2023 Rework handling of evaporation constraint in SoilFluxes From 601f8b36f0b43b0f22c9a381e5e3b8d4270f6221 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 9 Jul 2023 23:24:47 -0600 Subject: [PATCH 1093/2067] Some change file updates --- doc/ChangeLog | 15 ++++++++------- doc/ChangeSum | 2 +- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index d2ceaed39d..2651e0d2a0 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== -Tag name: ctsm5.2.dev130 +Tag name: ctsm5.1.dev130 Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049) -Date: Fri Jun 30 12:00:00 MDT 2023 +Date: Sun Jul 9 23:24:29 MDT 2023 One-line Summary: FATES parameter file and test definition update Purpose and description of changes @@ -35,6 +35,11 @@ Bugs fixed or introduced CTSM issues fixed (include CTSM Issue #): Fixes #2043 -- Five izumi NEON tests fail (for me) because the testnames include L10d instead of Ld10 +Known bugs found since the previous tag (include issue #): + #2049 -- Use of 0.01_r8 as a magic number + #2042 -- Issue running SystemTests due to "conda activate" error + #2039 -- Conditional for NEON usermods is too broad + Notes of particular relevance for users --------------------------------------- Changes made to namelist defaults (e.g., changed parameter values): @@ -60,10 +65,6 @@ Answer changes Changes answers relative to baseline: YES for FATES tests only - [ If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section). - And always remove these three lines and parts that don't apply. ] - Summarize any changes to answers, i.e., - what code configurations: FATES - what platforms/compilers: ALL @@ -82,7 +83,7 @@ Changes answers relative to baseline: YES for FATES tests only Other details ------------- -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates fates: sci.1.65.3_api.25.4.0 -> fates-sci.1.66.0_api.25.5.0 Pull Requests that document the changes (include PR ids): diff --git a/doc/ChangeSum b/doc/ChangeSum index df0d56f120..a3f748b0d0 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.2.dev130 glemieux 06/30/2023 FATES parameter file and test definition update + ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test From 946a8a0aad8a5f82f5a31a7513c7657416203cf6 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Jul 2023 10:43:41 -0600 Subject: [PATCH 1094/2067] initial changes --- bld/CLMBuildNamelist.pm | 6 ++++-- src/main/clm_driver.F90 | 4 ++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 02d9799487..4ed83f79ff 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3845,8 +3845,10 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( $nl_flags->{'bgc_mode'} eq "sp" ) { - + if ( $nl_flags->{'bgc_mode'} = "sp" || "fates" ) { + if ($nl_flags->{'bgc_mode'} .eq. "fates" && ! &value_is_true($nl->get_value('use_fates_sp'))) { + $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); + } if ( &value_is_true($nl->get_value('use_lai_streams')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index ae178b226c..91fd1d8824 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -462,8 +462,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! When LAI streams are being used ! NOTE: This call needs to happen outside loops over nclumps (as streams are not threadsafe) - if ((.not. use_cn) .and. (.not. use_fates) .and. (doalb) .and. use_lai_streams) then - call lai_advance( bounds_proc ) + if (doalb .and. use_lai_streams) then + call lai_advance(bounds_proc) endif ! ============================================================================ From 1d649da97391955320306b2c9434d3e10f7d7b3d Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Jul 2023 11:13:11 -0600 Subject: [PATCH 1095/2067] add test --- cime_config/testdefs/testlist_clm.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index ec04e651d7..e87160d2b8 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2371,7 +2371,7 @@ - From dbf0bff55f80df300bcd492d3904b83a81ad7e10 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Jul 2023 11:20:12 -0600 Subject: [PATCH 1096/2067] fix bld script? --- bld/CLMBuildNamelist.pm | 2 +- cime_config/testdefs/testlist_clm.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 4ed83f79ff..2d87c1d603 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3845,7 +3845,7 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( $nl_flags->{'bgc_mode'} = "sp" || "fates" ) { + if ( $nl_flags->{'bgc_mode'} .eq. "sp" || $nl_flags->{'bgc_mode'} = "fates" ) { if ($nl_flags->{'bgc_mode'} .eq. "fates" && ! &value_is_true($nl->get_value('use_fates_sp'))) { $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); } diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index e87160d2b8..7d55980eb1 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2372,7 +2372,7 @@ - + From 536e20633b1765372fa31ec893b61a87a835a3a3 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Jul 2023 11:42:12 -0600 Subject: [PATCH 1097/2067] add test info --- bld/CLMBuildNamelist.pm | 4 +-- .../include_user_mods | 1 - .../FatesColdSatPhen_prescribed/user_nl_clm | 32 +++++++++++++++++++ 3 files changed, 34 insertions(+), 3 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 2d87c1d603..a5afd1d0bb 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3845,8 +3845,8 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( $nl_flags->{'bgc_mode'} .eq. "sp" || $nl_flags->{'bgc_mode'} = "fates" ) { - if ($nl_flags->{'bgc_mode'} .eq. "fates" && ! &value_is_true($nl->get_value('use_fates_sp'))) { + if ( $nl_flags->{'bgc_mode'} .eq. "sp" || $nl_flags->{'bgc_mode'} .eq. "fates" ) { + if ( $nl_flags->{'bgc_mode'} .eq. "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) ) { $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); } if ( &value_is_true($nl->get_value('use_lai_streams')) ) { diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods index d111d05911..33ca1de12e 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/include_user_mods @@ -1,2 +1 @@ ../FatesColdSatPhen -../prescribed diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm new file mode 100644 index 0000000000..b9add4634d --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm @@ -0,0 +1,32 @@ + use_soil_moisture_streams = .true. + use_lai_streams = .true. + hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' + soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset + lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset + soilm_ignore_data_if_missing = .true. + hist_dov2xy = .true.,.false. +! Even though only 2 history tapes are defined here, set ndens to 1 for up to 6 history +! tapes, for the sake of mods that extend these default mods and may add other history tapes + hist_ndens = 1,1,1,1,1,1 + hist_nhtfrq =-24,-8 + hist_mfilt = 1,1 + hist_fincl1 = 'TRAFFICFLUX', 'SNOWLIQ:A','SNOWICE:A' +! Add FCO2 because few (if any) tests send this flux to the coupler, so it isn't checked via cpl hist files + hist_fincl1 += 'FCO2' + hist_fincl2 = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS', + 'FSR','FSA','FGEV','FSH','FGR','TSOI', + 'ERRSOI','SABV','SABG', + 'FSDSVD','FSDSND','FSDSVI','FSDSNI', + 'FSRVD','FSRND','FSRVI','FSRNI', + 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', + 'H2OSNO','SOILLIQ','SOILICE', + 'TSA_U', 'TSA_R', + 'TREFMNAV_U', 'TREFMNAV_R', + 'TREFMXAV_U', 'TREFMXAV_R', + 'TG_U', 'TG_R', + 'RH2M_U', 'RH2M_R', + 'QRUNOFF_U', 'QRUNOFF_R', + 'SoilAlpha_U', + 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT' + + use_ssre = .true. \ No newline at end of file From be382696ceb13be4998764ef1eafd25309eb2038 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Jul 2023 11:43:12 -0600 Subject: [PATCH 1098/2067] fix perl syntax --- bld/CLMBuildNamelist.pm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index a5afd1d0bb..9581a8227e 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3845,8 +3845,8 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( $nl_flags->{'bgc_mode'} .eq. "sp" || $nl_flags->{'bgc_mode'} .eq. "fates" ) { - if ( $nl_flags->{'bgc_mode'} .eq. "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) ) { + if ( $nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates" ) { + if ( $nl_flags->{'bgc_mode'} eq "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) ) { $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); } if ( &value_is_true($nl->get_value('use_lai_streams')) ) { From 779e64cdf362ec2ab4f879860a8c65333056c3a6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 10 Jul 2023 14:07:24 -0600 Subject: [PATCH 1099/2067] Change exice_vol_col dimension from nlevgrnd to nlevsoi --- src/biogeophys/WaterDiagnosticBulkType.F90 | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index ae7af4992e..9ecf7208a7 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -17,7 +17,7 @@ module WaterDiagnosticBulkType use decompMod , only : bounds_type use abortutils , only : endrun use clm_varctl , only : use_cn, iulog, use_luna - use clm_varpar , only : nlevgrnd, nlevsno, nlevcan + use clm_varpar , only : nlevgrnd, nlevsno, nlevcan, nlevsoi use clm_varcon , only : spval use LandunitType , only : lun use ColumnType , only : col @@ -201,7 +201,7 @@ subroutine InitBulkAllocate(this, bounds) allocate(this%swe_old_col (begc:endc,-nlevsno+1:0)) ; this%swe_old_col (:,:) = nan allocate(this%exice_subs_tot_col (begc:endc)) ; this%exice_subs_tot_col (:) = 0.0_r8 allocate(this%exice_subs_col (begc:endc, 1:nlevmaxurbgrnd)) ; this%exice_subs_col (:,:) = 0.0_r8 - allocate(this%exice_vol_col (begc:endc, 1:nlevgrnd)) ; this%exice_vol_col (:,:) = 0.0_r8 + allocate(this%exice_vol_col (begc:endc, 1:nlevsoi)) ; this%exice_vol_col (:,:) = 0.0_r8 allocate(this%exice_vol_tot_col (begc:endc)) ; this%exice_vol_tot_col (:) = 0.0_r8 allocate(this%snw_rds_col (begc:endc,-nlevsno+1:0)) ; this%snw_rds_col (:,:) = nan @@ -912,11 +912,11 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevsoi)=0.0_r8 else ! initialization of these to zero is ok, since they might not be in the restart file this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevsoi)=0.0_r8 call RestartExcessIceIssue( & ncid = ncid, & flag = flag, & @@ -939,7 +939,7 @@ subroutine RestartBulk(this, bounds, ncid, flag, writing_finidat_interp_dest_fil this%exice_subs_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_vol_tot_col(bounds%begc:bounds%endc)=0.0_r8 this%exice_subs_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 - this%exice_vol_col(bounds%begc:bounds%endc,1:nlevgrnd)=0.0_r8 + this%exice_vol_col(bounds%begc:bounds%endc,1:nlevsoi)=0.0_r8 endif call restartvar(ncid=ncid, flag=flag, varname=this%info%fname('TOTEXICE_VOL'), & dim1name='column', xtype=ncd_double, & @@ -1058,7 +1058,6 @@ subroutine Summary(this, bounds, & ! Compute end-of-timestep summaries of water diagnostic terms ! ! !USES: - use clm_varpar , only : nlevsoi use clm_varcon , only : denice use landunit_varcon, only : istsoil, istcrop ! !ARGUMENTS: From 62b376b67b4be7f8c36d89cfe04cd4568c82201b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 10 Jul 2023 14:13:26 -0600 Subject: [PATCH 1100/2067] Update $ntests following @ekluzek's suggestion (not tested, yet) --- bld/unit_testers/build-namelist_test.pl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 590ead1399..82a178bf03 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,9 +163,9 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1975; +my $ntests = 1992; if ( defined($opts{'compare'}) ) { - $ntests += 1344; + $ntests += 1353; } plan( tests=>$ntests ); From 0c642db4585db01f98e16d865838c79c6694b61b Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 10 Jul 2023 14:39:34 -0600 Subject: [PATCH 1101/2067] add check for lai streams --- .../FatesColdSatPhen_prescribed/user_nl_clm | 27 +------------------ src/main/controlMod.F90 | 8 ++++++ 2 files changed, 9 insertions(+), 26 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm index b9add4634d..1fc1c74311 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm @@ -4,29 +4,4 @@ soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset soilm_ignore_data_if_missing = .true. - hist_dov2xy = .true.,.false. -! Even though only 2 history tapes are defined here, set ndens to 1 for up to 6 history -! tapes, for the sake of mods that extend these default mods and may add other history tapes - hist_ndens = 1,1,1,1,1,1 - hist_nhtfrq =-24,-8 - hist_mfilt = 1,1 - hist_fincl1 = 'TRAFFICFLUX', 'SNOWLIQ:A','SNOWICE:A' -! Add FCO2 because few (if any) tests send this flux to the coupler, so it isn't checked via cpl hist files - hist_fincl1 += 'FCO2' - hist_fincl2 = 'TG','TBOT','FIRE','FIRA','FLDS','FSDS', - 'FSR','FSA','FGEV','FSH','FGR','TSOI', - 'ERRSOI','SABV','SABG', - 'FSDSVD','FSDSND','FSDSVI','FSDSNI', - 'FSRVD','FSRND','FSRVI','FSRNI', - 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', - 'H2OSNO','SOILLIQ','SOILICE', - 'TSA_U', 'TSA_R', - 'TREFMNAV_U', 'TREFMNAV_R', - 'TREFMXAV_U', 'TREFMXAV_R', - 'TG_U', 'TG_R', - 'RH2M_U', 'RH2M_R', - 'QRUNOFF_U', 'QRUNOFF_R', - 'SoilAlpha_U', - 'SWup', 'LWup', 'URBAN_AC', 'URBAN_HEAT' - - use_ssre = .true. \ No newline at end of file + \ No newline at end of file diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index a07228aa0d..7a44d16c1d 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -460,6 +460,14 @@ subroutine control_init(dtime) end if + ! Check compatibility with use_lai_streams + if (use_lai_streams) then + if ((use_fates .and. .not. use_fates_sp) .or. use_cn) then + call endrun(msg=' ERROR: cannot use LAI streams unless in SP mode (use_cn = .false. or use_fates_sp=.true.).'//& + errMsg(sourcefile, __LINE__)) + end if + end if + ! If nfix_timeconst is equal to the junk default value, then it was not specified ! by the user namelist and we need to assign it the correct default value. If the ! user specified it in the namelist, we leave it alone. From bf1f25c86374ef31a048127a92c8dfc6ad0e4a9e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 11 Jul 2023 10:50:09 -0600 Subject: [PATCH 1102/2067] Renamed crop namelist to crop_inparm. --- bld/CLMBuildNamelist.pm | 8 ++++---- bld/namelist_files/namelist_definition_ctsm.xml | 6 +++--- src/biogeochem/CropType.F90 | 10 +++++----- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 5eeb590fa0..384614ba57 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1625,9 +1625,9 @@ sub process_namelist_inline_logic { setup_logic_urban($opts, $nl_flags, $definition, $defaults, $nl); ############################### - # namelist group: crop # + # namelist group: crop_inparm # ############################### - setup_logic_crop($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_crop_inparm($opts, $nl_flags, $definition, $defaults, $nl); ############################### # namelist group: ch4par_in # @@ -2154,7 +2154,7 @@ sub setup_logic_urban { #------------------------------------------------------------------------------- -sub setup_logic_crop { +sub setup_logic_crop_inparm { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; if ( &value_is_true($nl->get_value('use_crop')) ) { @@ -4343,7 +4343,7 @@ sub write_output_files { soilwater_movement_inparm rooting_profile_inparm soil_resis_inparm bgc_shared canopyfluxes_inparm aerosol clmu_inparm clm_soilstate_inparm clm_nitrogen clm_snowhydrology_inparm - cnprecision_inparm clm_glacier_behavior crop irrigation_inparm + cnprecision_inparm clm_glacier_behavior crop_inparm irrigation_inparm surfacealbedo_inparm water_tracers_inparm); #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a6b5f64a44..c797ddcf7d 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1090,20 +1090,20 @@ Toggle to turn on the 1-year grain product pool in the crop model + group="crop_inparm" valid_values="constant,varytropicsbylat" value="constant"> Type of mapping to use for base temperature for prognostic crop model constant = Just use baset from the PFT parameter file varytropicsbylat = Vary the tropics by latitude + group="crop_inparm" valid_values="" value="0.4d00"> Only used when baset_mapping == varytropicsbylat Slope with latitude in degrees to vary tropical baset by + group="crop_inparm" valid_values="" value="12.0d00"> Only used when baset_mapping == varytropicsbylat Intercept at zero latitude to add to baset from the PFT parameter file diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 55575ce16e..f84c4c1821 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -73,7 +73,7 @@ module CropType procedure, public :: InitAccBuffer procedure, public :: InitAccVars procedure, public :: Restart - procedure, public :: ReadNML ! Read in the crop namelist + procedure, public :: ReadNML ! Read in the crop_inparm namelist ! NOTE(wjs, 2014-09-29) need to rename this from UpdateAccVars to CropUpdateAccVars ! to prevent cryptic error messages with pgi (v. 13.9 on yellowstone) @@ -143,12 +143,12 @@ subroutine ReadNML(this, NLFilename ) integer :: unitn ! unit for namelist file character(len=*), parameter :: subname = 'Crop::ReadNML' - character(len=*), parameter :: nmlname = 'crop' + character(len=*), parameter :: nmlname = 'crop_inparm' !----------------------------------------------------------------------- character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope - namelist /crop/ baset_mapping, baset_latvary_intercept, baset_latvary_slope + namelist /crop_inparm/ baset_mapping, baset_latvary_intercept, baset_latvary_slope ! Initialize options to default values, in case they are not specified in ! the namelist @@ -162,7 +162,7 @@ subroutine ReadNML(this, NLFilename ) call opnfil (NLFilename, unitn, 'F') call shr_nl_find_group_name(unitn, nmlname, status=ierr) if (ierr == 0) then - read(unitn, nml=crop, iostat=ierr) + read(unitn, nml=crop_inparm, iostat=ierr) if (ierr /= 0) then call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(sourcefile, __LINE__)) end if @@ -190,7 +190,7 @@ subroutine ReadNML(this, NLFilename ) if (masterproc) then write(iulog,*) ' ' write(iulog,*) nmlname//' settings:' - write(iulog,nml=crop) + write(iulog,nml=crop_inparm) write(iulog,*) ' ' end if From 9816cf07626a9c4aba20c5f6519a5ec1bbdb1a24 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 11 Jul 2023 14:50:32 -0600 Subject: [PATCH 1103/2067] Eliminate NaNs in TotalSum in subr. check_sums_equal_1 --- src/main/surfrdUtilsMod.F90 | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90 index 0763d43a16..af9e64d86a 100644 --- a/src/main/surfrdUtilsMod.F90 +++ b/src/main/surfrdUtilsMod.F90 @@ -45,7 +45,7 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto) character(len=*), intent(in) :: name ! name of array character(len=*), intent(in) :: caller ! identifier of caller, for more meaningful error messages integer, optional, intent(out):: ier ! Return an error code rather than abort - real(r8), optional, intent(out):: sumto(lb:) ! The value the array should sum to (1.0 if not provided) + real(r8), optional, intent(in):: sumto(lb:) ! The value the array should sum to (1.0 if not provided) ! ! !LOCAL VARIABLES: logical :: found @@ -58,12 +58,15 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto) ub = ubound(arr, 1) allocate(TotalSum(lb:ub)) - TotalSum = 1._r8 - if ( present(sumto) ) TotalSum = sumto if( present(ier) ) ier = 0 found = .false. - do nl = lbound(arr, 1), ub + do nl = lb, ub + if ( present(sumto) ) then + TotalSum(nl) = sumto(nl) + else + TotalSum(nl) = 1._r8 + end if if (abs(sum(arr(nl,:)) - TotalSum(nl)) > eps) then found = .true. nindx = nl From 583ed0975f4dca78ca2b3c036befbdc4aab573e6 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 11 Jul 2023 15:05:09 -0600 Subject: [PATCH 1104/2067] update lai init --- src/biogeochem/SatellitePhenologyMod.F90 | 2 ++ src/cpl/share_esmf/laiStreamMod.F90 | 23 ++++++++++++++++++++++- src/main/clm_driver.F90 | 7 +++++++ src/main/clm_initializeMod.F90 | 11 ++++++++++- 4 files changed, 41 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90 index 3e9341f430..02ede03057 100644 --- a/src/biogeochem/SatellitePhenologyMod.F90 +++ b/src/biogeochem/SatellitePhenologyMod.F90 @@ -128,9 +128,11 @@ subroutine SatellitePhenology(bounds, num_filter, filter, & frac_veg_nosno_alb => canopystate_inst%frac_veg_nosno_alb_patch & ! Output: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-] ) + if (masterproc) write(iulog,*) "inside the subroutine" if (use_lai_streams) then call lai_interp(bounds, canopystate_inst) endif + if (masterproc) write(iulog,*) "after interp" do fp = 1, num_filter p = filter(fp) diff --git a/src/cpl/share_esmf/laiStreamMod.F90 b/src/cpl/share_esmf/laiStreamMod.F90 index 3966488e0b..9770d69081 100644 --- a/src/cpl/share_esmf/laiStreamMod.F90 +++ b/src/cpl/share_esmf/laiStreamMod.F90 @@ -54,7 +54,7 @@ subroutine lai_init(bounds) type(bounds_type), intent(in) :: bounds ! bounds ! ! !LOCAL VARIABLES: - integer :: i,n ! index + integer :: i,n, ig, g ! index integer :: stream_year_first_lai ! first year in Lai stream to use integer :: stream_year_last_lai ! last year in Lai stream to use integer :: model_year_align_lai ! align stream_year_first_lai with @@ -151,6 +151,15 @@ subroutine lai_init(bounds) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if + + if ( .not. allocated(g_to_ig) )then + allocate (g_to_ig(bounds%begg:bounds%endg) ) + ig = 0 + do g = bounds%begg,bounds%endg + ig = ig+1 + g_to_ig(g) = ig + end do + end if end subroutine lai_init @@ -219,6 +228,8 @@ subroutine lai_interp(bounds, canopystate_inst) SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) + + if (masterproc) write(iulog,*) "inside laiinterp" ! Get pointer for stream data that is time and spatially interpolate to model time and grid ! Place all lai data from each type into a temporary 2d array @@ -236,19 +247,29 @@ subroutine lai_interp(bounds, canopystate_inst) dataptr2d(g,n) = dataptr1d(g) end do end do + + if (masterproc) write(iulog,*) "finished first loop" do p = bounds%begp, bounds%endp ivt = patch%itype(p) ! Set lai for each gridcell/patch combination if (ivt /= noveg) then ! vegetated pft + if (masterproc) write(iulog,*) "vegetated" + if (masterproc) write(iulog,*) patch%gridcell(p) + if (masterproc) write(iulog,*) bounds%begp, bounds%endp, "bounds" ig = g_to_ig(patch%gridcell(p)) canopystate_inst%tlai_patch(p) = dataptr2d(ig,ivt) + if (masterproc) write(iulog,*) "filled the patch" else ! non-vegetated pft canopystate_inst%tlai_patch(p) = 0._r8 endif + if (masterproc) write(iulog,*) "inside loop" end do + + if(masterproc) write(iulog,*) "second loop" + deallocate(dataptr2d) end subroutine lai_interp diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 12a7816465..d00ad664b7 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -224,6 +224,10 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Specified phenology ! Done in SP mode, FATES-SP mode and also when dry-deposition is active ! ============================================================================ + + if ( masterproc ) then + write(iulog,*) 'made it to here' + end if if (use_cn) then ! For dry-deposition need to call CLMSP so that mlaidiff is obtained @@ -263,6 +267,9 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro end if end if + + + ! ================================================================================== ! Determine decomp vertical profiles diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 7988fbfc7b..b3eeabbfc5 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -670,7 +670,7 @@ subroutine initialize2(ni,nj) elseif ( use_fates_sp ) then call interpMonthlyVeg(bounds_proc, canopystate_inst) end if - + ! Determine gridcell averaged properties to send to atm if (nsrest == nsrStartup) then call t_startf('init_map2gc') @@ -706,6 +706,7 @@ subroutine initialize2(ni,nj) !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) + if (masterproc) write(iulog,*) "inside the loop" ! FATES satellite phenology mode needs to include all active and inactive patch-level soil ! filters due to the translation between the hlm pfts and the fates pfts. @@ -719,10 +720,18 @@ subroutine initialize2(ni,nj) end do !$OMP END PARALLEL DO end if + if (masterproc) then + write(iulog,*) "made it past SP" + end if call clm_fates%init_coldstart(water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, canopystate_inst, & soilstate_inst, soilbiogeochem_carbonflux_inst) end if + + if (masterproc) then + write(iulog,*) "made it to fates initialize" + end if + ! topo_glc_mec was allocated in initialize1, but needed to be kept around through ! initialize2 because it is used to initialize other variables; now it can be deallocated From 1ea575bd91728696f0a085b4e1160e29366da18e Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Wed, 12 Jul 2023 14:49:27 +0200 Subject: [PATCH 1105/2067] added more testdefs --- .../testmods_dirs/clm/FatesColdNoCompNoFire/shell_commands | 2 ++ .../testmods_dirs/clm/FatesColdNoCompNoFire/user_nl_clm | 2 ++ 2 files changed, 4 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/shell_commands new file mode 100644 index 0000000000..0a8098ef7f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/shell_commands @@ -0,0 +1,2 @@ +./xmlchange CLM_FORCE_COLDSTART="on" +./xmlchange CLM_BLDNML_OPTS="-ignore_warnings" --append \ No newline at end of file diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/user_nl_clm new file mode 100644 index 0000000000..4302b4a1d3 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdNoCompNoFire/user_nl_clm @@ -0,0 +1,2 @@ +use_fates_nocomp = .true. +fates_spitfire_mode = 0 From 1543f861eb417e248ff7863d2ee685ba096b4e91 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 12 Jul 2023 09:59:56 -0600 Subject: [PATCH 1106/2067] Change small snocan to zero --- src/biogeophys/CanopyFluxesMod.F90 | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 038f8ea636..393bfa7ebe 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -47,6 +47,7 @@ module CanopyFluxesMod use EDTypesMod , only : ed_site_type use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type use LunaMod , only : Update_Photosynthesis_Capacity, Acc24_Climate_LUNA,Acc240_Climate_LUNA,Clear24_Climate_LUNA + use NumericsMod , only : truncate_small_values ! ! !PUBLIC TYPES: implicit none @@ -416,6 +417,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, real(r8) :: uuc(bounds%begp:bounds%endp) ! undercanopy windspeed real(r8) :: carea_stem ! cross-sectional area of stem real(r8) :: dlrad_leaf ! Downward longwave radition from leaf + real(r8) :: snocan_baseline(bounds%begp:bounds%endp) ! baseline of snocan for use in truncate_small_values ! Indices for raw and rah integer, parameter :: above_canopy = 1 ! Above canopy @@ -1520,6 +1522,9 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, cgrndl(p) = cgrndl(p) + forc_rho(c)*wtgq(p)*wtalq(p)*dqgdT(c) cgrnd(p) = cgrnds(p) + cgrndl(p)*htvp(c) + ! save before updating + snocan_baseline(p) = snocan(p) + ! Update dew accumulation (kg/m2) if (t_veg(p) > tfrz ) then ! above freezing, update accumulation in liqcan if ((qflx_evap_veg(p)-qflx_tran_veg(p))*dtime > liqcan(p)) then ! all liq evap @@ -1537,6 +1542,12 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, end if end do + + ! Remove snocan that got reduced by more than a factor of rel_epsilon + ! snocan < rel_epsilon * snocan_baseline will be set to zero + ! See NumericsMod for rel_epsilon value + call truncate_small_values(fn, filterp, begp, endp, & + snocan_baseline(begp:endp), snocan(begp:endp)) if ( use_fates ) then From 45dce8e61ea7c3e38bb4424cfec8c1d961959211 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 10:04:13 -0600 Subject: [PATCH 1107/2067] =?UTF-8?q?Roll=20back=20cime:=20cime6.0.118=20?= =?UTF-8?q?=E2=86=92=20108.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit cime6.0.118 was crashing on tests with multiple testmod dirs specified. This change means that RXCROPMATURITY can't use the new version of append_to_user_nl_files() that avoids an extra line break between added lines. --- Externals.cfg | 2 +- cime_config/SystemTests/rxcropmaturity.py | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index 02d6270316..cd6855c9dc 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.118 +tag = cime6.0.108 required = True [cmeps] diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 0735457ac4..8febcca9fe 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -371,9 +371,10 @@ def _get_conda_env(self): def _append_to_user_nl_clm(self, additions): caseroot = self._get_caseroot() - append_to_user_nl_files(caseroot = caseroot, - component = "clm", - contents = additions) + for line in additions: + append_to_user_nl_files(caseroot = caseroot, + component = "clm", + contents = line) # Is flanduse_timeseries defined? If so, where is it? From ca2d5e3545b6928ee854ec68d972dd34e4cc03a8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 10:54:25 -0600 Subject: [PATCH 1108/2067] =?UTF-8?q?Revert=20"Roll=20back=20cime:=20cime6?= =?UTF-8?q?.0.118=20=E2=86=92=20108."?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Turns out CIME wasn't the issue; it was incorrectly-specified test lengths. Greg Lemieux fixed it already in ctsm5.1.dev130: https://github.com/ESCOMP/CTSM/commit/74f9bd1c433908743fff34d6a0259434507de28e * This reverts commit 45dce8e61ea7c3e38bb4424cfec8c1d961959211. --- Externals.cfg | 2 +- cime_config/SystemTests/rxcropmaturity.py | 7 +++---- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index cd6855c9dc..02d6270316 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.108 +tag = cime6.0.118 required = True [cmeps] diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 8febcca9fe..0735457ac4 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -371,10 +371,9 @@ def _get_conda_env(self): def _append_to_user_nl_clm(self, additions): caseroot = self._get_caseroot() - for line in additions: - append_to_user_nl_files(caseroot = caseroot, - component = "clm", - contents = line) + append_to_user_nl_files(caseroot = caseroot, + component = "clm", + contents = additions) # Is flanduse_timeseries defined? If so, where is it? From 3a8fb5c42d1139f71770b9107d181e51e5dbf824 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 12 Jul 2023 13:52:33 -0400 Subject: [PATCH 1109/2067] forgot to remove conflict tags --- Externals_CLM.cfg | 1 - 1 file changed, 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index d59bd3de73..883416a43b 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,7 +1,6 @@ [fates] local_path = src/fates protocol = git -<<<<<<< HEAD repo_url = https://github.com/rgknox/fates branch = clm-cbalance required = True From e6298930d71fbb44b96f9aa091a67b49cd385653 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 12 Jul 2023 12:56:41 -0600 Subject: [PATCH 1110/2067] get rid of print statements --- src/biogeochem/SatellitePhenologyMod.F90 | 2 -- src/cpl/share_esmf/laiStreamMod.F90 | 10 ---------- src/main/clm_driver.F90 | 4 ---- src/main/clm_initializeMod.F90 | 11 +---------- 4 files changed, 1 insertion(+), 26 deletions(-) diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90 index 02ede03057..3e9341f430 100644 --- a/src/biogeochem/SatellitePhenologyMod.F90 +++ b/src/biogeochem/SatellitePhenologyMod.F90 @@ -128,11 +128,9 @@ subroutine SatellitePhenology(bounds, num_filter, filter, & frac_veg_nosno_alb => canopystate_inst%frac_veg_nosno_alb_patch & ! Output: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-] ) - if (masterproc) write(iulog,*) "inside the subroutine" if (use_lai_streams) then call lai_interp(bounds, canopystate_inst) endif - if (masterproc) write(iulog,*) "after interp" do fp = 1, num_filter p = filter(fp) diff --git a/src/cpl/share_esmf/laiStreamMod.F90 b/src/cpl/share_esmf/laiStreamMod.F90 index 9770d69081..b3e26b4c08 100644 --- a/src/cpl/share_esmf/laiStreamMod.F90 +++ b/src/cpl/share_esmf/laiStreamMod.F90 @@ -229,7 +229,6 @@ subroutine lai_interp(bounds, canopystate_inst) SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - if (masterproc) write(iulog,*) "inside laiinterp" ! Get pointer for stream data that is time and spatially interpolate to model time and grid ! Place all lai data from each type into a temporary 2d array @@ -248,28 +247,19 @@ subroutine lai_interp(bounds, canopystate_inst) end do end do - if (masterproc) write(iulog,*) "finished first loop" - do p = bounds%begp, bounds%endp ivt = patch%itype(p) ! Set lai for each gridcell/patch combination if (ivt /= noveg) then ! vegetated pft - if (masterproc) write(iulog,*) "vegetated" - if (masterproc) write(iulog,*) patch%gridcell(p) - if (masterproc) write(iulog,*) bounds%begp, bounds%endp, "bounds" ig = g_to_ig(patch%gridcell(p)) canopystate_inst%tlai_patch(p) = dataptr2d(ig,ivt) - if (masterproc) write(iulog,*) "filled the patch" else ! non-vegetated pft canopystate_inst%tlai_patch(p) = 0._r8 endif - if (masterproc) write(iulog,*) "inside loop" end do - if(masterproc) write(iulog,*) "second loop" - deallocate(dataptr2d) end subroutine lai_interp diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index d00ad664b7..90d7121fdb 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -225,10 +225,6 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Done in SP mode, FATES-SP mode and also when dry-deposition is active ! ============================================================================ - if ( masterproc ) then - write(iulog,*) 'made it to here' - end if - if (use_cn) then ! For dry-deposition need to call CLMSP so that mlaidiff is obtained ! NOTE: This is also true of FATES below diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index b3eeabbfc5..1bb966371c 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -706,8 +706,6 @@ subroutine initialize2(ni,nj) !$OMP PARALLEL DO PRIVATE (nc, bounds_clump) do nc = 1,nclumps call get_clump_bounds(nc, bounds_clump) - if (masterproc) write(iulog,*) "inside the loop" - ! FATES satellite phenology mode needs to include all active and inactive patch-level soil ! filters due to the translation between the hlm pfts and the fates pfts. ! E.g. in FATES, an active PFT vector of 1, 0, 0, 0, 1, 0, 1, 0 would be mapped into @@ -720,19 +718,12 @@ subroutine initialize2(ni,nj) end do !$OMP END PARALLEL DO end if - if (masterproc) then - write(iulog,*) "made it past SP" - end if + call clm_fates%init_coldstart(water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, canopystate_inst, & soilstate_inst, soilbiogeochem_carbonflux_inst) end if - if (masterproc) then - write(iulog,*) "made it to fates initialize" - end if - - ! topo_glc_mec was allocated in initialize1, but needed to be kept around through ! initialize2 because it is used to initialize other variables; now it can be deallocated deallocate(topo_glc_mec, fert_cft, irrig_method) From 412cff5c96ef6dba97a99c35d39520f38faeb5e4 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 12 Jul 2023 12:58:59 -0600 Subject: [PATCH 1111/2067] don't use soil moisture streams --- .../clm/FatesColdSatPhen_prescribed/user_nl_clm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm index 1fc1c74311..2b5ac9caf0 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm @@ -1,7 +1,7 @@ - use_soil_moisture_streams = .true. + !use_soil_moisture_streams = .true. use_lai_streams = .true. - hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' - soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset + !hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' + !soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset - soilm_ignore_data_if_missing = .true. + !soilm_ignore_data_if_missing = .true. \ No newline at end of file From 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 13:17:35 -0600 Subject: [PATCH 1112/2067] Reformatting with black. --- cime_config/SystemTests/fsurdatmodifyctsm.py | 12 +- cime_config/SystemTests/lreprstruct.py | 7 +- cime_config/SystemTests/rxcropmaturity.py | 236 +++++++++--------- cime_config/SystemTests/systemtest_utils.py | 8 +- python/ctsm/crop_calendars/cropcal_module.py | 15 +- python/ctsm/crop_calendars/cropcal_utils.py | 2 - python/ctsm/crop_calendars/generate_gdds.py | 2 +- .../crop_calendars/generate_gdds_functions.py | 1 - .../make_fsurdat_all_crops_everywhere.py | 28 +-- 9 files changed, 165 insertions(+), 146 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index e0a3fc83fc..d2a9c04312 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -67,15 +67,15 @@ def _create_config_file(self): def _run_modify_fsurdat(self): tool_path = os.path.join(self._ctsm_root, "tools/modify_input_files/fsurdat_modifier") - + self._case.load_env(reset=True) command = f"python3 {tool_path} {self._cfg_file_path}" stu.run_python_script( - self._get_caseroot(), - "ctsm_pylib", - command, - tool_path, - ) + self._get_caseroot(), + "ctsm_pylib", + command, + tool_path, + ) def _modify_user_nl(self): append_to_user_nl_files( diff --git a/cime_config/SystemTests/lreprstruct.py b/cime_config/SystemTests/lreprstruct.py index 01dc2567e3..a03fb1815b 100644 --- a/cime_config/SystemTests/lreprstruct.py +++ b/cime_config/SystemTests/lreprstruct.py @@ -56,14 +56,13 @@ def _case_one_setup(self): for grain_output in re.findall("GRAIN\w*", user_nl_clm_text): user_nl_clm_text = user_nl_clm_text.replace( grain_output, - grain_output.replace('GRAIN', 'REPRODUCTIVE1') + grain_output.replace("GRAIN", "REPRODUCTIVE1") + "', '" - + grain_output.replace('GRAIN', 'REPRODUCTIVE2') - ) + + grain_output.replace("GRAIN", "REPRODUCTIVE2"), + ) with open(user_nl_clm_path, "w") as f: f.write(user_nl_clm_text) - def _case_two_setup(self): # This is needed in the nearly-standard case to prevent grain from being used to # replenish crop seed deficits, thus making grain act like the reproductive diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 0735457ac4..77be3c89e6 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -24,12 +24,12 @@ logger = logging.getLogger(__name__) -class RXCROPMATURITY(SystemTestsCommon): +class RXCROPMATURITY(SystemTestsCommon): def __init__(self, case): # initialize an object interface to the SMS system test SystemTestsCommon.__init__(self, case) - + # Ensure run length is at least 5 years. Minimum to produce one complete growing season (i.e., two complete calendar years) actually 4 years, but that only gets you 1 season usable for GDD generation, so you can't check for season-to-season consistency. stop_n = self._case.get_value("STOP_N") stop_option = self._case.get_value("STOP_OPTION") @@ -72,9 +72,9 @@ def __init__(self, case): casebaseid = self._case.get_value("CASEBASEID") if casebaseid.split("-")[-1] != "cropMonthOutput": error_message = ( - "Only call RXCROPMATURITY with test cropMonthOutput " - + "to avoid potentially huge sets of daily outputs." - ) + "Only call RXCROPMATURITY with test cropMonthOutput " + + "to avoid potentially huge sets of daily outputs." + ) logger.error(error_message) raise RuntimeError(error_message) @@ -88,9 +88,9 @@ def run_phase(self): # Modeling this after the SSP test, we create a clone to be the case whose outputs we don't # want to be saved as baseline. - #------------------------------------------------------------------- + # ------------------------------------------------------------------- # (1) Set up GDD-generating run - #------------------------------------------------------------------- + # ------------------------------------------------------------------- # Create clone to be GDD-Generating case logger.info("RXCROPMATURITY log: cloning setup") case_rxboth = self._case @@ -111,46 +111,48 @@ def run_phase(self): # Add stuff specific to GDD-Generating run logger.info("RXCROPMATURITY log: modify user_nl files: generate GDDs") - self._append_to_user_nl_clm([ - "generate_crop_gdds = .true.", - "use_mxmat = .false.", - " ", - "! (h2) Daily outputs for GDD generation and figure-making", - "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", - "hist_nhtfrq(3) = -24", - "hist_mfilt(3) = 365", - "hist_type1d_pertape(3) = 'PFTS'", - "hist_dov2xy(3) = .false.", - ]) - + self._append_to_user_nl_clm( + [ + "generate_crop_gdds = .true.", + "use_mxmat = .false.", + " ", + "! (h2) Daily outputs for GDD generation and figure-making", + "hist_fincl3 = 'GDDACCUM', 'GDDHARV'", + "hist_nhtfrq(3) = -24", + "hist_mfilt(3) = 365", + "hist_type1d_pertape(3) = 'PFTS'", + "hist_dov2xy(3) = .false.", + ] + ) + # If flanduse_timeseries is defined, we need to make a static version for this test. This # should have every crop in most of the world. self._get_flanduse_timeseries_in(case_gddgen) if self._flanduse_timeseries_in is not None: - + # Download files from the server, if needed case_gddgen.check_all_input_data() - + # Make custom version of surface file logger.info("RXCROPMATURITY log: run make_surface_for_gddgen") self._run_make_surface_for_gddgen(case_gddgen) - - #------------------------------------------------------------------- + + # ------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file - #------------------------------------------------------------------- + # ------------------------------------------------------------------- logger.info("RXCROPMATURITY log: Start GDD-Generating run") - + # As per SSP test: # "No history files expected, set suffix=None to avoid compare error" # We *do* expect history files here, but anyway. This works. self._skip_pnl = False self.run_indv(suffix=None, st_archive=True) - + self._run_generate_gdds(case_gddgen) - - #------------------------------------------------------------------- + + # ------------------------------------------------------------------- # (3) Set up and perform Prescribed Calendars run - #------------------------------------------------------------------- + # ------------------------------------------------------------------- os.chdir(caseroot) self._set_active_case(case_rxboth) @@ -159,20 +161,21 @@ def run_phase(self): # Add stuff specific to Prescribed Calendars run logger.info("RXCROPMATURITY log: modify user_nl files: Prescribed Calendars") - self._append_to_user_nl_clm([ - "generate_crop_gdds = .false.", - f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", - ]) + self._append_to_user_nl_clm( + [ + "generate_crop_gdds = .false.", + f"stream_fldFileName_cultivar_gdds = '{self._gdds_file}'", + ] + ) self.run_indv() - - #------------------------------------------------------------------- + + # ------------------------------------------------------------------- # (4) Check Prescribed Calendars run - #------------------------------------------------------------------- + # ------------------------------------------------------------------- logger.info("RXCROPMATURITY log: output check: Prescribed Calendars") self._run_check_rxboth_run() - # Get sowing and harvest dates for this resolution. def _get_rx_dates(self): # Eventually, I want to remove these hard-coded resolutions so that this test can generate @@ -183,24 +186,30 @@ def _get_rx_dates(self): if lnd_grid == "10x15": self._sdatefile = os.path.join( processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + ) self._hdatefile = os.path.join( processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37.2000-2000.20230330_165301.nc", + ) elif lnd_grid == "1.9x2.5": self._sdatefile = os.path.join( processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + ) self._hdatefile = os.path.join( processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17.2000-2000.20230102_175625.nc", + ) elif lnd_grid == "0.9x1.25": self._sdatefile = os.path.join( processed_crop_dates_dir, - "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc") + "sdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134417.nc", + ) self._hdatefile = os.path.join( processed_crop_dates_dir, - "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc") + "hdates_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17.2000-2000.20230520_134418.nc", + ) else: error_message = "ERROR: RXCROPMATURITY currently only supports 0.9x1.25, 1.9x2.5, and 10x15 resolutions" logger.error(error_message) @@ -216,27 +225,25 @@ def _get_rx_dates(self): logger.error(error_message) raise RuntimeError(error_message) - def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all start") # Get some info - self._ctsm_root = self._case.get_value('COMP_ROOT_DIR_LND') - run_startdate = self._case.get_value('RUN_STARTDATE') - self._run_startyear = int(run_startdate.split('-')[0]) - + self._ctsm_root = self._case.get_value("COMP_ROOT_DIR_LND") + run_startdate = self._case.get_value("RUN_STARTDATE") + self._run_startyear = int(run_startdate.split("-")[0]) + # Set sowing dates file (and other crop calendar settings) for all runs logger.info("RXCROPMATURITY log: modify user_nl files: all tests") self._modify_user_nl_allruns() logger.info("RXCROPMATURITY log: _setup_all done") - # Make a surface dataset that has every crop in every gridcell def _run_make_surface_for_gddgen(self, case_gddgen): - + # fsurdat should be defined. Where is it? self._fsurdat_in = None - with open (self._lnd_in_path,'r') as lnd_in: + with open(self._lnd_in_path, "r") as lnd_in: for line in lnd_in: fsurdat_in = re.match(r" *fsurdat *= *'(.*)'", line) if fsurdat_in: @@ -246,58 +253,64 @@ def _run_make_surface_for_gddgen(self, case_gddgen): error_message = "fsurdat not defined" logger.error(error_message) raise RuntimeError(error_message) - + # Where we will save the fsurdat version for this test - self._fsurdat_out = os.path.join(self._path_gddgen, 'fsurdat.nc') - + self._fsurdat_out = os.path.join(self._path_gddgen, "fsurdat.nc") + # Make fsurdat for this test, if not already done if not os.path.exists(self._fsurdat_out): - tool_path = os.path.join(self._ctsm_root, - 'python', 'ctsm', 'crop_calendars', - 'make_fsurdat_all_crops_everywhere.py') - command = f"python3 {tool_path} "\ - + f"-i {self._fsurdat_in} "\ - + f"-o {self._fsurdat_out}" + tool_path = os.path.join( + self._ctsm_root, + "python", + "ctsm", + "crop_calendars", + "make_fsurdat_all_crops_everywhere.py", + ) + command = ( + f"python3 {tool_path} " + f"-i {self._fsurdat_in} " + f"-o {self._fsurdat_out}" + ) stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + # Modify namelist logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") - self._append_to_user_nl_clm([ - "fsurdat = '{}'".format(self._fsurdat_out), - "do_transient_crops = .false.", - "flanduse_timeseries = ''", - "use_init_interp = .true.", - ]) - - + self._append_to_user_nl_clm( + [ + "fsurdat = '{}'".format(self._fsurdat_out), + "do_transient_crops = .false.", + "flanduse_timeseries = ''", + "use_init_interp = .true.", + ] + ) + def _run_check_rxboth_run(self): - + output_dir = os.path.join(self._get_caseroot(), "run") first_usable_year = self._run_startyear + 2 last_usable_year = self._run_startyear + self._run_Nyears - 2 - - tool_path = os.path.join(self._ctsm_root, - 'python', 'ctsm', 'crop_calendars', - 'check_rxboth_run.py') - command = f"python3 {tool_path} "\ - + f"--directory {output_dir} "\ - + f"-y1 {first_usable_year} "\ - + f"-yN {last_usable_year} "\ - + f"--rx-sdates-file {self._sdatefile} "\ - + f"--rx-gdds-file {self._gdds_file} " + + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "check_rxboth_run.py" + ) + command = ( + f"python3 {tool_path} " + + f"--directory {output_dir} " + + f"-y1 {first_usable_year} " + + f"-yN {last_usable_year} " + + f"--rx-sdates-file {self._sdatefile} " + + f"--rx-gdds-file {self._gdds_file} " + ) stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - - + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + def _modify_user_nl_allruns(self): nl_additions = [ "stream_meshfile_cropcal = '{}'".format(self._case.get_value("LND_DOMAIN_MESH")), @@ -315,7 +328,6 @@ def _modify_user_nl_allruns(self): ] self._append_to_user_nl_clm(nl_additions) - def _run_generate_gdds(self, case_gddgen): self._generate_gdds_dir = os.path.join(self._path_gddgen, "generate_gdds_out") os.makedirs(self._generate_gdds_dir) @@ -329,24 +341,27 @@ def _run_generate_gdds(self, case_gddgen): hdates_file = self._hdatefile # It'd be much nicer to call generate_gdds.main(), but I can't import generate_gdds. - tool_path = os.path.join(self._ctsm_root, - 'python', 'ctsm', 'crop_calendars', - 'generate_gdds.py') - command = " ".join([ + tool_path = os.path.join( + self._ctsm_root, "python", "ctsm", "crop_calendars", "generate_gdds.py" + ) + command = " ".join( + [ f"python3 {tool_path}", f"--input-dir {input_dir}", f"--first-season {first_season}", f"--last-season {last_season}", f"--sdates-file {sdates_file}", f"--hdates-file {hdates_file}", - f"--output-dir generate_gdds_out"]) + f"--output-dir generate_gdds_out", + ] + ) stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) - + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) + # Where were the prescribed maturity requirements saved? generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) generated_gdd_files = [x for x in generated_gdd_files if "fill0" not in x] @@ -355,7 +370,6 @@ def _run_generate_gdds(self, case_gddgen): logger.error(error_message) raise RuntimeError(error_message) self._gdds_file = generated_gdd_files[0] - def _get_conda_env(self): conda_setup_commands = stu.cmds_to_setup_conda(self._get_caseroot()) @@ -368,20 +382,16 @@ def _get_conda_env(self): else: self._this_conda_env = "ctsm_pylib" - def _append_to_user_nl_clm(self, additions): caseroot = self._get_caseroot() - append_to_user_nl_files(caseroot = caseroot, - component = "clm", - contents = additions) - + append_to_user_nl_files(caseroot=caseroot, component="clm", contents=additions) # Is flanduse_timeseries defined? If so, where is it? def _get_flanduse_timeseries_in(self, case): - case.create_namelists(component='lnd') - self._lnd_in_path = os.path.join(self._path_gddgen, 'CaseDocs', 'lnd_in') + case.create_namelists(component="lnd") + self._lnd_in_path = os.path.join(self._path_gddgen, "CaseDocs", "lnd_in") self._flanduse_timeseries_in = None - with open (self._lnd_in_path,'r') as lnd_in: + with open(self._lnd_in_path, "r") as lnd_in: for line in lnd_in: flanduse_timeseries_in = re.match(r" *flanduse_timeseries *= *'(.*)'", line) if flanduse_timeseries_in: diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 3c264b32b9..17ddf88a53 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -4,6 +4,7 @@ import os, subprocess + def cmds_to_setup_conda(caseroot): # Add specific commands needed on different machines to get conda available # Use semicolon here since it's OK to fail @@ -12,7 +13,7 @@ def cmds_to_setup_conda(caseroot): # Execute the module unload/load when "which conda" fails # eg on cheyenne try: - subprocess.run( "which conda", shell=True, check=True) + subprocess.run("which conda", shell=True, check=True) except subprocess.CalledProcessError: # Remove python and add conda to environment for cheyennne conda_setup_commands += " module unload python; module load conda;" @@ -34,8 +35,9 @@ def run_python_script(caseroot, this_conda_env, command, tool_path): tool_name = os.path.split(tool_path)[-1] try: with open(tool_name + ".log", "w") as f: - subprocess.run(command, shell=True, check=True, text=True, - stdout=f, stderr=subprocess.STDOUT) + subprocess.run( + command, shell=True, check=True, text=True, stdout=f, stderr=subprocess.STDOUT + ) except subprocess.CalledProcessError as error: print("ERROR while getting the conda environment and/or ") print(f"running the {tool_name} tool: ") diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index fd56df1f3c..73176431ba 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -344,7 +344,18 @@ def check_constant_vars( if not np.array_equal(incl_patches, np.unique(incl_patches)): raise RuntimeError("Patch(es) checked more than once!") incl_patches = list(incl_patches) - incl_patches += list(np.where(np.all(np.isnan(ra_sp[:-1,]), axis=0))[0]) + incl_patches += list( + np.where( + np.all( + np.isnan( + ra_sp[ + :-1, + ] + ), + axis=0, + ) + )[0] + ) incl_patches = np.sort(incl_patches) if not np.array_equal(incl_patches, np.unique(incl_patches)): raise RuntimeError("Patch(es) checked but also all-NaN??") @@ -1072,7 +1083,7 @@ def check_no_zeros(this_ds, varList_no_zero, which_file): if np.any(this_ds_gs["NHARVESTS"] > 2): raise RuntimeError("How to get NHARVEST_DISCREP for NHARVESTS > 2?") this_ds_gs["NHARVEST_DISCREP"] = (this_ds_gs["NHARVESTS"] == 2).astype(int) - + return this_ds_gs diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py index 0d03788adb..ed4b07adfa 100644 --- a/python/ctsm/crop_calendars/cropcal_utils.py +++ b/python/ctsm/crop_calendars/cropcal_utils.py @@ -50,7 +50,6 @@ def weighted_annual_mean(array, time_in="time", time_out="time"): return array - # List of PFTs used in CLM def define_pftlist(): pftlist = [ @@ -862,4 +861,3 @@ def safer_timeslice(ds, timeSlice, timeVar="time"): raise return ds - diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index a93c6abc61..e83197ace6 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -410,7 +410,7 @@ def add_attrs_to_map_ds( parser.add_argument( "-hd", "--hdates-file", help="File of prescribed harvest dates", required=True ) - + # Optional figsgroup = parser.add_mutually_exclusive_group() figsgroup.add_argument( diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index c1866e1079..eb30713ca3 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -461,7 +461,6 @@ def import_and_process_1yr( else: hdates_rx = hdates_rx_orig - log(logger, f" Importing accumulated GDDs...") clm_gdd_var = "GDDACCUM" myVars = [clm_gdd_var, "GDDHARV"] diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py index 8e748b98a4..f8c5e8b316 100755 --- a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py +++ b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py @@ -1,4 +1,3 @@ - import numpy as np import xarray as xr import sys @@ -7,22 +6,22 @@ def main(file_in, file_out): # Import - + in_ds = xr.open_dataset(file_in) - + out_ds = in_ds.copy() in_ds.close() - + # Move all natural land into crop - out_ds['PCT_CROP'] += in_ds['PCT_NATVEG'] - out_ds['PCT_NATVEG'] -= in_ds['PCT_NATVEG'] - + out_ds["PCT_CROP"] += in_ds["PCT_NATVEG"] + out_ds["PCT_NATVEG"] -= in_ds["PCT_NATVEG"] + # Put some of every crop in every gridcell - pct_cft = np.full_like(in_ds['PCT_CFT'].values, 100 / in_ds.dims['cft']) - out_ds['PCT_CFT'] = xr.DataArray(data=pct_cft, - attrs=in_ds['PCT_CFT'].attrs, - dims=in_ds['PCT_CFT'].dims) - + pct_cft = np.full_like(in_ds["PCT_CFT"].values, 100 / in_ds.dims["cft"]) + out_ds["PCT_CFT"] = xr.DataArray( + data=pct_cft, attrs=in_ds["PCT_CFT"].attrs, dims=in_ds["PCT_CFT"].dims + ) + # Save out_ds.to_netcdf(file_out, format="NETCDF3_64BIT") @@ -31,7 +30,9 @@ def main(file_in, file_out): ############################### ### Process input arguments ### ############################### - parser = argparse.ArgumentParser(description="Creates a surface dataset with all natural land moved into crops, and with every crop present in every gridcell.") + parser = argparse.ArgumentParser( + description="Creates a surface dataset with all natural land moved into crops, and with every crop present in every gridcell." + ) # Required parser.add_argument( @@ -52,4 +53,3 @@ def main(file_in, file_out): # Process main(args.input_file, args.output_file) - From c2b96777bfe20a941b49f9f459ba276e286c4530 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 12 Jul 2023 13:20:51 -0600 Subject: [PATCH 1113/2067] update test --- cime_config/testdefs/testlist_clm.xml | 2 +- .../testmods_dirs/clm/FatesColdSatPhen_prescribed/README | 4 ++-- .../testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm | 1 + 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 32f83f6e53..0575ea8086 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2382,7 +2382,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README index a1c8f04632..116e0f43b4 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README @@ -1,3 +1,3 @@ -This testmod currently does NOT work, because of issue #1722 +This testmod currently only works with lai streams (not soil moisture), because of FATES issue #845 -See https://github.com/ESCOMP/CTSM/issues/1722 +See https://github.com/NGEET/fates/issues/845 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm index 2b5ac9caf0..eb7a85165c 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm @@ -1,3 +1,4 @@ + ! right now we can't do prescribed soil moisture because of FATES issue #845 !use_soil_moisture_streams = .true. use_lai_streams = .true. !hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' From b0e8b04bf58c809f70935f62b1062b39581d3b1b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 13:37:19 -0600 Subject: [PATCH 1114/2067] Refactor 20-year running means of crop seasonal GDD to use accumulMod. --- src/biogeochem/CNPhenologyMod.F90 | 53 ++-------------------------- src/biogeophys/TemperatureType.F90 | 55 ++++++++++++++++++++++++++++-- 2 files changed, 54 insertions(+), 54 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ec04fcbf54..2eb55c7dcb 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -352,7 +352,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & if ( phase == 1 ) then - call CNPhenologyClimate(num_soilp, filter_soilp, num_pcropp, filter_pcropp, & + call CNPhenologyClimate(num_soilp, filter_soilp, & temperature_inst, cnveg_state_inst, crop_inst) call CNEvergreenPhenology(num_soilp, filter_soilp, & @@ -513,7 +513,7 @@ subroutine CNPhenologyInit(bounds) end subroutine CNPhenologyInit !----------------------------------------------------------------------- - subroutine CNPhenologyClimate (num_soilp, filter_soilp, num_pcropp, filter_pcropp, & + subroutine CNPhenologyClimate (num_soilp, filter_soilp, & temperature_inst, cnveg_state_inst, crop_inst) ! ! !DESCRIPTION: @@ -526,8 +526,6 @@ subroutine CNPhenologyClimate (num_soilp, filter_soilp, num_pcropp, filter_pcrop ! !ARGUMENTS: integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches - integer , intent(in) :: num_pcropp ! number of prognostic crops in filter - integer , intent(in) :: filter_pcropp(:)! filter for prognostic crop patches type(temperature_type) , intent(inout) :: temperature_inst type(cnveg_state_type) , intent(inout) :: cnveg_state_inst type(crop_type) , intent(inout) :: crop_inst @@ -536,24 +534,12 @@ subroutine CNPhenologyClimate (num_soilp, filter_soilp, num_pcropp, filter_pcrop integer :: p ! indices integer :: fp ! lake filter patch index real(r8) :: dayspyr ! days per year (days) - integer :: kyr ! current year - integer :: kmo ! month of year (1, ..., 12) - integer :: kda ! day of month (1, ..., 31) - integer :: mcsec ! seconds of day (0, ..., seconds/day) - real(r8), parameter :: yravg = 20.0_r8 ! length of years to average for gdd - real(r8), parameter :: yravgm1 = yravg-1.0_r8 ! minus 1 of above !----------------------------------------------------------------------- associate( & nyrs_crop_active => crop_inst%nyrs_crop_active_patch, & ! InOut: [integer (:) ] number of years this crop patch has been active t_ref2m => temperature_inst%t_ref2m_patch , & ! Input: [real(r8) (:) ] 2m air temperature (K) - gdd0 => temperature_inst%gdd0_patch , & ! Output: [real(r8) (:) ] growing deg. days base 0 deg C (ddays) - gdd8 => temperature_inst%gdd8_patch , & ! Output: [real(r8) (:) ] " " " " 8 " " " - gdd10 => temperature_inst%gdd10_patch , & ! Output: [real(r8) (:) ] " " " " 10 " " " - gdd020 => temperature_inst%gdd020_patch , & ! Output: [real(r8) (:) ] 20-yr mean of gdd0 (ddays) - gdd820 => temperature_inst%gdd820_patch , & ! Output: [real(r8) (:) ] 20-yr mean of gdd8 (ddays) - gdd1020 => temperature_inst%gdd1020_patch , & ! Output: [real(r8) (:) ] 20-yr mean of gdd10 (ddays) tempavg_t2m => cnveg_state_inst%tempavg_t2m_patch & ! Output: [real(r8) (:) ] temp. avg 2m air temperature (K) ) @@ -567,41 +553,6 @@ subroutine CNPhenologyClimate (num_soilp, filter_soilp, num_pcropp, filter_pcrop tempavg_t2m(p) = tempavg_t2m(p) + t_ref2m(p) * (fracday/dayspyr) end do - ! - ! The following crop related steps are done here rather than CropPhenology - ! so that they will be completed each time-step rather than with doalb. - ! - ! NOTE(wjs, 2022-02-03) The above comment about doalb no longer applies, because - ! there is no longer a doalb conditional around the CropPhenology call. Therefore, - ! we could move these calculations into CropPhenology if it made sense to do so. - ! - ! The following lines come from ibis's climate.f + stats.f - ! gdd SUMMATIONS ARE RELATIVE TO THE PLANTING DATE (see subr. updateAccFlds) - - if (num_pcropp > 0) then - ! get time-related info - call get_curr_date(kyr, kmo, kda, mcsec) - end if - - do fp = 1,num_pcropp - p = filter_pcropp(fp) - if (kmo == 1 .and. kda == 1 .and. nyrs_crop_active(p) == 0) then ! YR 1: - gdd020(p) = 0._r8 ! set gdd..20 variables to 0 - gdd820(p) = 0._r8 ! and crops will not be planted - gdd1020(p) = 0._r8 - end if - if (kmo == 1 .and. kda == 1 .and. mcsec == 0) then ! <-- END of EVERY YR: - if (nyrs_crop_active(p) == 1) then ! <-- END of YR 1 - gdd020(p) = gdd0(p) ! <-- END of YR 1 - gdd820(p) = gdd8(p) ! <-- END of YR 1 - gdd1020(p) = gdd10(p) ! <-- END of YR 1 - end if ! <-- END of YR 1 - gdd020(p) = (yravgm1* gdd020(p) + gdd0(p)) / yravg ! gdd..20 must be long term avgs - gdd820(p) = (yravgm1* gdd820(p) + gdd8(p)) / yravg ! so ignore results for yrs 1 & 2 - gdd1020(p) = (yravgm1* gdd1020(p) + gdd10(p)) / yravg - end if - end do - end associate end subroutine CNPhenologyClimate diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90 index f2d9317f82..5bed9dd820 100644 --- a/src/biogeophys/TemperatureType.F90 +++ b/src/biogeophys/TemperatureType.F90 @@ -609,17 +609,17 @@ subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp ) avgflag='A', long_name='Growing degree days base 10C from planting', & ptr_patch=this%gdd10_patch, default='inactive') - this%gdd020_patch(begp:endp) = spval + this%gdd020_patch(begp:endp) = nan call hist_addfld1d (fname='GDD020', units='ddays', & avgflag='A', long_name='Twenty year average of growing degree days base 0C from planting', & ptr_patch=this%gdd020_patch, default='inactive') - this%gdd820_patch(begp:endp) = spval + this%gdd820_patch(begp:endp) = nan call hist_addfld1d (fname='GDD820', units='ddays', & avgflag='A', long_name='Twenty year average of growing degree days base 8C from planting', & ptr_patch=this%gdd820_patch, default='inactive') - this%gdd1020_patch(begp:endp) = spval + this%gdd1020_patch(begp:endp) = nan call hist_addfld1d (fname='GDD1020', units='ddays', & avgflag='A', long_name='Twenty year average of growing degree days base 10C from planting', & ptr_patch=this%gdd1020_patch, default='inactive') @@ -1213,6 +1213,17 @@ subroutine InitAccBuffer (this, bounds) call init_accum_field (name='GDD10', units='K', & desc='growing degree-days base 10C from planting', accum_type='runaccum', accum_period=not_used, & subgrid_type='pft', numlev=1, init_value=0._r8) + + ! 20-year running means (20*365 days) + call init_accum_field (name='GDD020', units='K', & + desc='20-year running mean of growing degree days base 0C from planting', accum_type='runmean', accum_period=-20*365, & + subgrid_type='pft', numlev=1, init_value=0._r8) + call init_accum_field (name='GDD820', units='K', & + desc='20-year running mean of growing degree days base 8C from planting', accum_type='runmean', accum_period=-20*365, & + subgrid_type='pft', numlev=1, init_value=0._r8) + call init_accum_field (name='GDD1020', units='K', & + desc='20-year running mean of growing degree days base 10C from planting', accum_type='runmean', accum_period=-20*365, & + subgrid_type='pft', numlev=1, init_value=0._r8) end if @@ -1328,6 +1339,15 @@ subroutine InitAccVars(this, bounds) call extract_accum_field ('GDD10', rbufslp, nstep) this%gdd10_patch(begp:endp) = rbufslp(begp:endp) + call extract_accum_field ('GDD020', rbufslp, nstep) + this%gdd020_patch(begp:endp) = rbufslp(begp:endp) + + call extract_accum_field ('GDD820', rbufslp, nstep) + this%gdd820_patch(begp:endp) = rbufslp(begp:endp) + + call extract_accum_field ('GDD1020', rbufslp, nstep) + this%gdd1020_patch(begp:endp) = rbufslp(begp:endp) + end if deallocate(rbufslp) @@ -1574,6 +1594,14 @@ subroutine UpdateAccVars (this, bounds) call update_accum_field ('GDD10', rbufslp, nstep) call extract_accum_field ('GDD10', this%gdd10_patch, nstep) + ! Accumulate and extract running 20-year means + call update_accum_field ('GDD020', this%gdd0_patch, nstep) + call extract_accum_field ('GDD020', this%gdd020_patch, nstep) + call update_accum_field ('GDD820', this%gdd8_patch, nstep) + call extract_accum_field ('GDD820', this%gdd820_patch, nstep) + call update_accum_field ('GDD1020', this%gdd10_patch, nstep) + call extract_accum_field ('GDD1020', this%gdd1020_patch, nstep) + end if deallocate(rbufslp) @@ -1581,4 +1609,25 @@ subroutine UpdateAccVars (this, bounds) end subroutine UpdateAccVars + subroutine Clean(this) + ! + ! !DESCRIPTION: + ! Finalize this instance + ! + ! !USES: + ! + ! !ARGUMENTS: + class(temperature_type), intent(inout) :: this + ! + ! !LOCAL VARIABLES: + + character(len=*), parameter :: subname = 'Clean' + !----------------------------------------------------------------------- + + deallocate(this%gdd020_patch) + deallocate(this%gdd820_patch) + deallocate(this%gdd1020_patch) + + end subroutine Clean + end module TemperatureType From 27003562699fc863272a23bf52bd4d9a3b15a097 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 13:43:21 -0600 Subject: [PATCH 1115/2067] Delete unused cropcals_generate_gdds test. --- .../clm/cropcals_generate_gdds/shell_commands | 11 ----- .../clm/cropcals_generate_gdds/user_nl_clm | 41 ------------------- 2 files changed, 52 deletions(-) delete mode 100755 cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands delete mode 100644 cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands deleted file mode 100755 index 352e099693..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/shell_commands +++ /dev/null @@ -1,11 +0,0 @@ -./case.setup -ctsm_dir="$(./xmlquery -N --value COMP_ROOT_DIR_LND)" -./xmlchange POSTRUN_SCRIPT="${ctsm_dir}/python/ctsm/crop_calendars/generate_gdds.sh" - -# Try to do this as an interactive compute job, unless we're already on a compute node -setup_for_gddgen="${ctsm_dir}"/python/ctsm/crop_calendars/setup_for_gddgen.sh -if [[ "$(which qcmd)" != "" && "${PBS_JOBNAME}" == "" ]]; then - qcmd -- "${setup_for_gddgen}" -else - "${setup_for_gddgen}" -fi diff --git a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm deleted file mode 100644 index 0bc0098111..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/cropcals_generate_gdds/user_nl_clm +++ /dev/null @@ -1,41 +0,0 @@ -!---------------------------------------------------------------------------------- -! Users should add all user specific namelist changes below in the form of -! namelist_var = new_namelist_value -! -! EXCEPTIONS: -! Set use_cndv by the compset you use and the CLM_BLDNML_OPTS -dynamic_vegetation setting -! Set use_vichydro by the compset you use and the CLM_BLDNML_OPTS -vichydro setting -! Set use_cn by the compset you use and CLM_BLDNML_OPTS -bgc setting -! Set use_crop by the compset you use and CLM_BLDNML_OPTS -crop setting -! Set spinup_state by the CLM_BLDNML_OPTS -bgc_spinup setting -! Set co2_ppmv with CCSM_CO2_PPMV option -! Set fatmlndfrc with LND_DOMAIN_PATH/LND_DOMAIN_FILE options -! Set finidat with RUN_REFCASE/RUN_REFDATE/RUN_REFTOD options for hybrid or branch cases -! (includes $inst_string for multi-ensemble cases) -! or with CLM_FORCE_COLDSTART to do a cold start -! or set it with an explicit filename here. -! Set maxpatch_glc with GLC_NEC option -! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable -!---------------------------------------------------------------------------------- - -stream_meshfile_cropcal = 'MESHFILE_PLACEHOLDER' -stream_fldFileName_sdate = 'SDATEFILE_PLACEHOLDER' -generate_crop_gdds = .true. -use_mxmat = .false. -stream_year_first_cropcal = 2000 -stream_year_last_cropcal = 2000 -model_year_align_cropcal = 2000 - -! (h1) Daily outputs for GDD generation and figure-making -hist_fincl2 = 'HUI', 'GDDACCUM', 'GDDHARV' -hist_nhtfrq(2) = -24 -hist_mfilt(2) = 365 -hist_type1d_pertape(2) = 'PFTS' -hist_dov2xy(2) = .false. - -! (h2) Annual outputs for GDD generation (checks) -hist_fincl3 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' -hist_nhtfrq(3) = 17520 -hist_mfilt(3) = 999 -hist_type1d_pertape(3) = 'PFTS' -hist_dov2xy(3) = .false. From 6ec205815a3b0e012663aa874cf58752809837cf Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 12 Jul 2023 13:48:54 -0600 Subject: [PATCH 1116/2067] whitespace --- src/cpl/share_esmf/laiStreamMod.F90 | 4 +--- src/main/clm_driver.F90 | 3 --- 2 files changed, 1 insertion(+), 6 deletions(-) diff --git a/src/cpl/share_esmf/laiStreamMod.F90 b/src/cpl/share_esmf/laiStreamMod.F90 index b3e26b4c08..3e4074fbde 100644 --- a/src/cpl/share_esmf/laiStreamMod.F90 +++ b/src/cpl/share_esmf/laiStreamMod.F90 @@ -228,7 +228,6 @@ subroutine lai_interp(bounds, canopystate_inst) SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) - ! Get pointer for stream data that is time and spatially interpolate to model time and grid ! Place all lai data from each type into a temporary 2d array @@ -246,7 +245,7 @@ subroutine lai_interp(bounds, canopystate_inst) dataptr2d(g,n) = dataptr1d(g) end do end do - + do p = bounds%begp, bounds%endp ivt = patch%itype(p) ! Set lai for each gridcell/patch combination @@ -259,7 +258,6 @@ subroutine lai_interp(bounds, canopystate_inst) canopystate_inst%tlai_patch(p) = 0._r8 endif end do - deallocate(dataptr2d) end subroutine lai_interp diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 90d7121fdb..ae5ab704fb 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -264,9 +264,6 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro end if - - - ! ================================================================================== ! Determine decomp vertical profiles ! From 8220435d29f43af0880fb30f972387b799fc5952 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 14:12:38 -0600 Subject: [PATCH 1117/2067] Remove variable numbers from master_list_nofates.rst. --- .../master_list_nofates.rst | 2576 ++++++++--------- 1 file changed, 1288 insertions(+), 1288 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst index 07c8b8612b..eeec0810c8 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst @@ -13,1292 +13,1292 @@ CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Variable Name Long Description Units Active? ==== =================================== ============================================================================================== ================================================================= ======= - 1 A10TMIN 10-day running mean of min 2-m temperature K F - 2 A5TMIN 5-day running mean of min 2-m temperature K F - 3 ACTUAL_IMMOB actual N immobilization gN/m^2/s T - 4 ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F - 5 ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F - 6 ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F - 7 ACT_SOMC ACT_SOM C gC/m^2 T - 8 ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F - 9 ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F - 10 ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F - 11 ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F - 12 ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F - 13 ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F - 14 ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T - 15 ACT_SOMN ACT_SOM N gN/m^2 T - 16 ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F - 17 ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F - 18 ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F - 19 ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F - 20 ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F - 21 ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F - 22 ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T - 23 ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F - 24 ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F - 25 ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F - 26 ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F - 27 AGLB Aboveground leaf biomass kg/m^2 F - 28 AGNPP aboveground NPP gC/m^2/s T - 29 AGSB Aboveground stem biomass kg/m^2 F - 30 ALBD surface albedo (direct) proportion T - 31 ALBDSF diagnostic snow-free surface albedo (direct) proportion T - 32 ALBGRD ground albedo (direct) proportion F - 33 ALBGRI ground albedo (indirect) proportion F - 34 ALBI surface albedo (indirect) proportion T - 35 ALBISF diagnostic snow-free surface albedo (indirect) proportion T - 36 ALPHA alpha coefficient for VOC calc non F - 37 ALT current active layer thickness m T - 38 ALTMAX maximum annual active layer thickness m T - 39 ALTMAX_LASTYEAR maximum prior year active layer thickness m F - 40 ANNAVG_T2M annual average 2m air temperature K F - 41 ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F - 42 ANNSUM_COUNTER seconds since last annual accumulator turnover s F - 43 ANNSUM_NPP annual sum of NPP gC/m^2/yr F - 44 ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F - 45 APPAR_TEMP 2 m apparent temperature C T - 46 APPAR_TEMP_R Rural 2 m apparent temperature C T - 47 APPAR_TEMP_U Urban 2 m apparent temperature C T - 48 AR autotrophic respiration (MR + GR) gC/m^2/s T - 49 ATM_TOPO atmospheric surface height m T - 50 AVAILC C flux available for allocation gC/m^2/s F - 51 AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F - 52 AnnET Annual ET mm/s F - 53 BAF_CROP fractional area burned for crop s-1 T - 54 BAF_PEATF fractional area burned in peatland s-1 T - 55 BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T - 56 BETA coefficient of convective velocity none F - 57 BGLFR background litterfall rate 1/s F - 58 BGNPP belowground NPP gC/m^2/s T - 59 BGTR background transfer growth rate 1/s F - 60 BTRANMN daily minimum of transpiration beta factor unitless T - 61 CANNAVG_T2M annual average of 2m air temperature K F - 62 CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F - 63 CEL_LITC CEL_LIT C gC/m^2 T - 64 CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F - 65 CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F - 66 CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F - 67 CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F - 68 CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T - 69 CEL_LITN CEL_LIT N gN/m^2 T - 70 CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F - 71 CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F - 72 CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F - 73 CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F - 74 CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T - 75 CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F - 76 CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F - 77 CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F - 78 CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F - 79 CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F - 80 CH4PROD Gridcell total production of CH4 gC/m2/s T - 81 CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F - 82 CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F - 83 CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T - 84 CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 85 CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T - 86 CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 87 CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T - 88 CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 89 COL_CTRUNC column-level sink for C truncation gC/m^2 F - 90 COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T - 91 COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T - 92 COL_NTRUNC column-level sink for N truncation gN/m^2 F - 93 CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F - 94 CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F - 95 CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T - 96 CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T - 97 COST_NACTIVE Cost of active uptake gN/gC T - 98 COST_NFIX Cost of fixation gN/gC T - 99 COST_NRETRANS Cost of retranslocation gN/gC T - 100 COSZEN cosine of solar zenith angle none F - 101 CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T - 102 CPOOL temporary photosynthate C pool gC/m^2 T - 103 CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F - 104 CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F - 105 CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F - 106 CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F - 107 CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F - 108 CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F - 109 CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F - 110 CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F - 111 CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F - 112 CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F - 113 CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F - 114 CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F - 115 CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F - 116 CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F - 117 CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F - 118 CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F - 119 CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F - 120 CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F - 121 CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F - 122 CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F - 123 CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F - 124 CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F - 125 CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F - 126 CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F - 127 CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F - 128 CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F - 129 CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T - 130 CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T - 131 CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T - 132 CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T - 133 CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T - 134 CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F - 135 CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F - 136 CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F - 137 CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F - 138 CWDC CWD C gC/m^2 T - 139 CWDC_1m CWD C to 1 meter gC/m^2 F - 140 CWDC_HR cwd C heterotrophic respiration gC/m^2/s F - 141 CWDC_LOSS coarse woody debris C loss gC/m^2/s T - 142 CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F - 143 CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F - 144 CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F - 145 CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F - 146 CWDC_vr CWD C (vertically resolved) gC/m^3 T - 147 CWDN CWD N gN/m^2 T - 148 CWDN_1m CWD N to 1 meter gN/m^2 F - 149 CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F - 150 CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F - 151 CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F - 152 CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F - 153 CWDN_vr CWD N (vertically resolved) gN/m^3 T - 154 CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F - 155 CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F - 156 CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F - 157 CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F - 158 C_ALLOMETRY C allocation index none F - 159 DAYL daylength s F - 160 DAYS_ACTIVE number of days since last dormancy days F - 161 DEADCROOTC dead coarse root C gC/m^2 T - 162 DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F - 163 DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F - 164 DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F - 165 DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F - 166 DEADCROOTN dead coarse root N gN/m^2 T - 167 DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F - 168 DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F - 169 DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F - 170 DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F - 171 DEADSTEMC dead stem C gC/m^2 T - 172 DEADSTEMC_STORAGE dead stem C storage gC/m^2 F - 173 DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F - 174 DEADSTEMC_XFER dead stem C transfer gC/m^2 F - 175 DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F - 176 DEADSTEMN dead stem N gN/m^2 T - 177 DEADSTEMN_STORAGE dead stem N storage gN/m^2 F - 178 DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F - 179 DEADSTEMN_XFER dead stem N transfer gN/m^2 F - 180 DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F - 181 DENIT total rate of denitrification gN/m^2/s T - 182 DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F - 183 DISCOI 2 m Discomfort Index C T - 184 DISCOIS 2 m Stull Discomfort Index C T - 185 DISCOIS_R Rural 2 m Stull Discomfort Index C T - 186 DISCOIS_U Urban 2 m Stull Discomfort Index C T - 187 DISCOI_R Rural 2 m Discomfort Index C T - 188 DISCOI_U Urban 2 m Discomfort Index C T - 189 DISPLA displacement height m F - 190 DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T - 191 DISPVEGN displayed vegetation nitrogen gN/m^2 T - 192 DLRAD downward longwave radiation below the canopy W/m^2 F - 193 DORMANT_FLAG dormancy flag none F - 194 DOWNREG fractional reduction in GPP due to N limitation proportion F - 195 DPVLTRB1 turbulent deposition velocity 1 m/s F - 196 DPVLTRB2 turbulent deposition velocity 2 m/s F - 197 DPVLTRB3 turbulent deposition velocity 3 m/s F - 198 DPVLTRB4 turbulent deposition velocity 4 m/s F - 199 DSL dry surface layer thickness mm T - 200 DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T - 201 DSTFLXT total surface dust emission kg/m2/s T - 202 DT_VEG change in t_veg, last iteration K F - 203 DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T - 204 DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T - 205 DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F - 206 DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T - 207 DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F - 208 DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T - 209 DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T - 210 DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F - 211 DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F - 212 DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F - 213 DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F - 214 DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F - 215 DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F - 216 DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F - 217 DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F - 218 DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F - 219 DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F - 220 DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F - 221 DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F - 222 DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F - 223 DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F - 224 DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F - 225 DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F - 226 DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F - 227 DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F - 228 DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T - 229 DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F - 230 DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T - 231 DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F - 232 DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T - 233 DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F - 234 DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T - 235 DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T - 236 DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F - 237 DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F - 238 DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F - 239 DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F - 240 DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F - 241 DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F - 242 EFF_POROSITY effective porosity = porosity - vol_ice proportion F - 243 EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T - 244 EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T - 245 EFLX_GNET net heat flux into ground W/m^2 F - 246 EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T - 247 EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T - 248 EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F - 249 EFLX_LH_TOT_R Rural total evaporation W/m^2 T - 250 EFLX_LH_TOT_U Urban total evaporation W/m^2 F - 251 EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F - 252 ELAI exposed one-sided leaf area index m^2/m^2 T - 253 EMG ground emissivity proportion F - 254 EMV vegetation emissivity proportion F - 255 EOPT Eopt coefficient for VOC calc non F - 256 EPT 2 m Equiv Pot Temp K T - 257 EPT_R Rural 2 m Equiv Pot Temp K T - 258 EPT_U Urban 2 m Equiv Pot Temp K T - 259 ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T - 260 ERRH2O total water conservation error mm T - 261 ERRH2OSNO imbalance in snow depth (liquid water) mm T - 262 ERRSEB surface energy conservation error W/m^2 T - 263 ERRSOI soil/lake energy conservation error W/m^2 T - 264 ERRSOL solar radiation conservation error W/m^2 T - 265 ESAI exposed one-sided stem area index m^2/m^2 T - 266 EXCESSC_MR excess C maintenance respiration gC/m^2/s F - 267 EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F - 268 FAREA_BURNED timestep fractional area burned s-1 T - 269 FCANSNO fraction of canopy that is wet proportion F - 270 FCEV canopy evaporation W/m^2 T - 271 FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T - 272 FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T - 273 FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T - 274 FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F - 275 FCOV fractional impermeable area unitless T - 276 FCTR canopy transpiration W/m^2 T - 277 FDRY fraction of foliage that is green and dry proportion F - 278 FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F - 279 FERT_COUNTER time left to fertilize seconds F - 280 FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F - 281 FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T - 282 FGEV ground evaporation W/m^2 T - 283 FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T - 284 FGR12 heat flux between soil layers 1 and 2 W/m^2 T - 285 FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F - 286 FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F - 287 FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F - 288 FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F - 289 FH2OSFC fraction of ground covered by surface water unitless T - 290 FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F - 291 FINUNDATED fractional inundated area of vegetated columns unitless T - 292 FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F - 293 FIRA net infrared (longwave) radiation W/m^2 T - 294 FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F - 295 FIRA_R Rural net infrared (longwave) radiation W/m^2 T - 296 FIRA_U Urban net infrared (longwave) radiation W/m^2 F - 297 FIRE emitted infrared (longwave) radiation W/m^2 T - 298 FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F - 299 FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T - 300 FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F - 301 FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T - 302 FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F - 303 FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F - 304 FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F - 305 FPI fraction of potential immobilization proportion T - 306 FPI_vr fraction of potential immobilization proportion F - 307 FPSN photosynthesis umol m-2 s-1 T - 308 FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F - 309 FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F - 310 FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F - 311 FPSN_WP Product-limited photosynthesis umol m-2 s-1 F - 312 FRAC_ICEOLD fraction of ice relative to the tot water proportion F - 313 FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T - 314 FROOTC fine root C gC/m^2 T - 315 FROOTC_ALLOC fine root C allocation gC/m^2/s T - 316 FROOTC_LOSS fine root C loss gC/m^2/s T - 317 FROOTC_STORAGE fine root C storage gC/m^2 F - 318 FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F - 319 FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F - 320 FROOTC_XFER fine root C transfer gC/m^2 F - 321 FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F - 322 FROOTN fine root N gN/m^2 T - 323 FROOTN_STORAGE fine root N storage gN/m^2 F - 324 FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F - 325 FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F - 326 FROOTN_XFER fine root N transfer gN/m^2 F - 327 FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F - 328 FROOT_MR fine root maintenance respiration gC/m^2/s F - 329 FROOT_PROF profile for litter C and N inputs from fine roots 1/m F - 330 FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F - 331 FSA absorbed solar radiation W/m^2 T - 332 FSAT fractional area with water table at surface unitless T - 333 FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F - 334 FSA_R Rural absorbed solar radiation W/m^2 F - 335 FSA_U Urban absorbed solar radiation W/m^2 F - 336 FSD24 direct radiation (last 24hrs) K F - 337 FSD240 direct radiation (last 240hrs) K F - 338 FSDS atmospheric incident solar radiation W/m^2 T - 339 FSDSND direct nir incident solar radiation W/m^2 T - 340 FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T - 341 FSDSNI diffuse nir incident solar radiation W/m^2 T - 342 FSDSVD direct vis incident solar radiation W/m^2 T - 343 FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T - 344 FSDSVI diffuse vis incident solar radiation W/m^2 T - 345 FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T - 346 FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T - 347 FSH_G sensible heat from ground W/m^2 T - 348 FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F - 349 FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T - 350 FSH_R Rural sensible heat W/m^2 T - 351 FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T - 352 FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T - 353 FSH_U Urban sensible heat W/m^2 F - 354 FSH_V sensible heat from veg W/m^2 T - 355 FSI24 indirect radiation (last 24hrs) K F - 356 FSI240 indirect radiation (last 240hrs) K F - 357 FSM snow melt heat flux W/m^2 T - 358 FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F - 359 FSM_R Rural snow melt heat flux W/m^2 F - 360 FSM_U Urban snow melt heat flux W/m^2 F - 361 FSNO fraction of ground covered by snow unitless T - 362 FSNO_EFF effective fraction of ground covered by snow unitless T - 363 FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F - 364 FSR reflected solar radiation W/m^2 T - 365 FSRND direct nir reflected solar radiation W/m^2 T - 366 FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T - 367 FSRNI diffuse nir reflected solar radiation W/m^2 T - 368 FSRSF reflected solar radiation W/m^2 T - 369 FSRSFND direct nir reflected solar radiation W/m^2 T - 370 FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T - 371 FSRSFNI diffuse nir reflected solar radiation W/m^2 T - 372 FSRSFVD direct vis reflected solar radiation W/m^2 T - 373 FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T - 374 FSRSFVI diffuse vis reflected solar radiation W/m^2 T - 375 FSRVD direct vis reflected solar radiation W/m^2 T - 376 FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T - 377 FSRVI diffuse vis reflected solar radiation W/m^2 T - 378 FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F - 379 FSUN sunlit fraction of canopy proportion F - 380 FSUN24 fraction sunlit (last 24hrs) K F - 381 FSUN240 fraction sunlit (last 240hrs) K F - 382 FUELC fuel load gC/m^2 T - 383 FV friction velocity m/s T - 384 FWET fraction of canopy that is wet proportion F - 385 F_DENIT denitrification flux gN/m^2/s T - 386 F_DENIT_BASE F_DENIT_BASE gN/m^3/s F - 387 F_DENIT_vr denitrification flux gN/m^3/s F - 388 F_N2O_DENIT denitrification N2O flux gN/m^2/s T - 389 F_N2O_NIT nitrification N2O flux gN/m^2/s T - 390 F_NIT nitrification flux gN/m^2/s T - 391 F_NIT_vr nitrification flux gN/m^3/s F - 392 FireComp_BC fire emissions flux of BC kg/m2/sec F - 393 FireComp_OC fire emissions flux of OC kg/m2/sec F - 394 FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F - 395 FireEmis_TOT Total fire emissions flux gC/m2/sec F - 396 FireEmis_ZTOP Top of vertical fire emissions distribution m F - 397 FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F - 398 FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F - 399 FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F - 400 GAMMA total gamma for VOC calc non F - 401 GAMMAA gamma A for VOC calc non F - 402 GAMMAC gamma C for VOC calc non F - 403 GAMMAL gamma L for VOC calc non F - 404 GAMMAP gamma P for VOC calc non F - 405 GAMMAS gamma S for VOC calc non F - 406 GAMMAT gamma T for VOC calc non F - 407 GDD0 Growing degree days base 0C from planting ddays F - 408 GDD020 Twenty year average of growing degree days base 0C from planting ddays F - 409 GDD10 Growing degree days base 10C from planting ddays F - 410 GDD1020 Twenty year average of growing degree days base 10C from planting ddays F - 411 GDD8 Growing degree days base 8C from planting ddays F - 412 GDD820 Twenty year average of growing degree days base 8C from planting ddays F - 413 GDDACCUM Accumulated growing degree days past planting date for crop ddays F - 414 GDDHARV Growing degree days (gdd) needed to harvest ddays F - 415 GDDTSOI Growing degree-days from planting (top two soil layers) ddays F - 416 GPP gross primary production gC/m^2/s T - 417 GR total growth respiration gC/m^2/s T - 418 GRAINC grain C (does not equal yield) gC/m^2 T - 419 GRAINC_TO_FOOD grain C to food gC/m^2/s T - 420 GRAINC_TO_SEED grain C to seed gC/m^2/s T - 421 GRAINN grain N gN/m^2 T - 422 GRESP_STORAGE growth respiration storage gC/m^2 F - 423 GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F - 424 GRESP_XFER growth respiration transfer gC/m^2 F - 425 GROSS_NMIN gross rate of N mineralization gN/m^2/s T - 426 GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F - 427 GSSHA shaded leaf stomatal conductance umol H20/m2/s T - 428 GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T - 429 GSSUN sunlit leaf stomatal conductance umol H20/m2/s T - 430 GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T - 431 H2OCAN intercepted water mm T - 432 H2OSFC surface water depth mm T - 433 H2OSNO snow depth (liquid water) mm T - 434 H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F - 435 H2OSNO_TOP mass of snow in top snow layer kg/m2 T - 436 H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T - 437 HBOT canopy bottom m F - 438 HEAT_CONTENT1 initial gridcell total heat content J/m^2 T - 439 HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F - 440 HEAT_CONTENT2 post land cover change total heat content J/m^2 F - 441 HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T - 442 HIA 2 m NWS Heat Index C T - 443 HIA_R Rural 2 m NWS Heat Index C T - 444 HIA_U Urban 2 m NWS Heat Index C T - 445 HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F - 446 HR total heterotrophic respiration gC/m^2/s T - 447 HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T - 448 HTOP canopy top m T - 449 HUI crop heat unit index ddays F - 450 HUMIDEX 2 m Humidex C T - 451 HUMIDEX_R Rural 2 m Humidex C T - 452 HUMIDEX_U Urban 2 m Humidex C T - 453 ICE_CONTENT1 initial gridcell total ice content mm T - 454 ICE_CONTENT2 post land cover change total ice content mm F - 455 ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F - 456 INIT_GPP GPP flux before downregulation gC/m^2/s F - 457 INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F - 458 INT_SNOW_ICE accumulated swe (ice landunits only) mm F - 459 IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T - 460 JMX25T canopy profile of jmax umol/m2/s T - 461 Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T - 462 KROOT root conductance each soil layer 1/s F - 463 KSOIL soil conductance in each soil layer 1/s F - 464 K_ACT_SOM active soil organic potential loss coefficient 1/s F - 465 K_CEL_LIT cellulosic litter potential loss coefficient 1/s F - 466 K_CWD coarse woody debris potential loss coefficient 1/s F - 467 K_LIG_LIT lignin litter potential loss coefficient 1/s F - 468 K_MET_LIT metabolic litter potential loss coefficient 1/s F - 469 K_NITR K_NITR 1/s F - 470 K_NITR_H2O K_NITR_H2O unitless F - 471 K_NITR_PH K_NITR_PH unitless F - 472 K_NITR_T K_NITR_T unitless F - 473 K_PAS_SOM passive soil organic potential loss coefficient 1/s F - 474 K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F - 475 LAI240 240hr average of leaf area index m^2/m^2 F - 476 LAISHA shaded projected leaf area index m^2/m^2 T - 477 LAISUN sunlit projected leaf area index m^2/m^2 T - 478 LAKEICEFRAC lake layer ice mass fraction unitless F - 479 LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T - 480 LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T - 481 LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T - 482 LATBASET latitude vary base temperature for gddplant degree C F - 483 LEAFC leaf C gC/m^2 T - 484 LEAFCN Leaf CN ratio used for flexible CN gC/gN T - 485 LEAFCN_OFFSET Leaf C:N used by FUN unitless F - 486 LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F - 487 LEAFC_ALLOC leaf C allocation gC/m^2/s T - 488 LEAFC_CHANGE C change in leaf gC/m^2/s T - 489 LEAFC_LOSS leaf C loss gC/m^2/s T - 490 LEAFC_STORAGE leaf C storage gC/m^2 F - 491 LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F - 492 LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F - 493 LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T - 494 LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F - 495 LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T - 496 LEAFC_XFER leaf C transfer gC/m^2 F - 497 LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F - 498 LEAFN leaf N gN/m^2 T - 499 LEAFN_STORAGE leaf N storage gN/m^2 F - 500 LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F - 501 LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F - 502 LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T - 503 LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F - 504 LEAFN_XFER leaf N transfer gN/m^2 F - 505 LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F - 506 LEAF_MR leaf maintenance respiration gC/m^2/s T - 507 LEAF_PROF profile for litter C and N inputs from leaves 1/m F - 508 LFC2 conversion area fraction of BET and BDT that burned per sec T - 509 LGSF long growing season factor proportion F - 510 LIG_LITC LIG_LIT C gC/m^2 T - 511 LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F - 512 LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F - 513 LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F - 514 LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F - 515 LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T - 516 LIG_LITN LIG_LIT N gN/m^2 T - 517 LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F - 518 LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F - 519 LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F - 520 LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F - 521 LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T - 522 LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F - 523 LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F - 524 LIQCAN intercepted liquid water mm T - 525 LIQUID_CONTENT1 initial gridcell total liq content mm T - 526 LIQUID_CONTENT2 post landuse change gridcell total liq content mm F - 527 LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F - 528 LITFALL litterfall (leaves and fine roots) gC/m^2/s T - 529 LITFIRE litter fire losses gC/m^2/s F - 530 LITTERC_HR litter C heterotrophic respiration gC/m^2/s T - 531 LITTERC_LOSS litter C loss gC/m^2/s T - 532 LIVECROOTC live coarse root C gC/m^2 T - 533 LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F - 534 LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F - 535 LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F - 536 LIVECROOTC_XFER live coarse root C transfer gC/m^2 F - 537 LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F - 538 LIVECROOTN live coarse root N gN/m^2 T - 539 LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F - 540 LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F - 541 LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F - 542 LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F - 543 LIVECROOTN_XFER live coarse root N transfer gN/m^2 F - 544 LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F - 545 LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F - 546 LIVESTEMC live stem C gC/m^2 T - 547 LIVESTEMC_STORAGE live stem C storage gC/m^2 F - 548 LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F - 549 LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T - 550 LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F - 551 LIVESTEMC_XFER live stem C transfer gC/m^2 F - 552 LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F - 553 LIVESTEMN live stem N gN/m^2 T - 554 LIVESTEMN_STORAGE live stem N storage gN/m^2 F - 555 LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F - 556 LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F - 557 LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F - 558 LIVESTEMN_XFER live stem N transfer gN/m^2 F - 559 LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F - 560 LIVESTEM_MR live stem maintenance respiration gC/m^2/s F - 561 LNC leaf N concentration gN leaf/m^2 T - 562 LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F - 563 LWup upwelling longwave radiation W/m^2 F - 564 MEG_acetaldehyde MEGAN flux kg/m2/sec T - 565 MEG_acetic_acid MEGAN flux kg/m2/sec T - 566 MEG_acetone MEGAN flux kg/m2/sec T - 567 MEG_carene_3 MEGAN flux kg/m2/sec T - 568 MEG_ethanol MEGAN flux kg/m2/sec T - 569 MEG_formaldehyde MEGAN flux kg/m2/sec T - 570 MEG_isoprene MEGAN flux kg/m2/sec T - 571 MEG_methanol MEGAN flux kg/m2/sec T - 572 MEG_pinene_a MEGAN flux kg/m2/sec T - 573 MEG_thujene_a MEGAN flux kg/m2/sec T - 574 MET_LITC MET_LIT C gC/m^2 T - 575 MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F - 576 MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F - 577 MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F - 578 MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F - 579 MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T - 580 MET_LITN MET_LIT N gN/m^2 T - 581 MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F - 582 MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F - 583 MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F - 584 MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F - 585 MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T - 586 MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F - 587 MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F - 588 MR maintenance respiration gC/m^2/s T - 589 M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F - 590 M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F - 591 M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F - 592 M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F - 593 M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F - 594 M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F - 595 M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F - 596 M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F - 597 M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F - 598 M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F - 599 M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F - 600 M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F - 601 M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F - 602 M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F - 603 M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F - 604 M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F - 605 M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F - 606 M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F - 607 M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F - 608 M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F - 609 M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F - 610 M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F - 611 M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F - 612 M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F - 613 M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F - 614 M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F - 615 M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F - 616 M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F - 617 M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F - 618 M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F - 619 M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F - 620 M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F - 621 M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F - 622 M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F - 623 M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F - 624 M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F - 625 M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F - 626 M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F - 627 M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F - 628 M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F - 629 M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F - 630 M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F - 631 M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F - 632 M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F - 633 M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F - 634 M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F - 635 M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F - 636 M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F - 637 M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F - 638 M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F - 639 M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F - 640 M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F - 641 M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F - 642 M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F - 643 M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F - 644 M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F - 645 M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F - 646 M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F - 647 M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F - 648 M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F - 649 M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F - 650 M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F - 651 M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F - 652 M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F - 653 M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F - 654 M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F - 655 M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F - 656 M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F - 657 M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F - 658 M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F - 659 M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F - 660 M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F - 661 M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F - 662 M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F - 663 M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F - 664 M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F - 665 M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F - 666 M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F - 667 M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F - 668 M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F - 669 M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F - 670 M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F - 671 M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F - 672 M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F - 673 M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F - 674 M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F - 675 M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F - 676 M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F - 677 M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F - 678 M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F - 679 M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F - 680 M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F - 681 M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F - 682 M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F - 683 M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F - 684 M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F - 685 M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F - 686 M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F - 687 M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F - 688 M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F - 689 M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F - 690 M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F - 691 M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F - 692 M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F - 693 M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F - 694 M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F - 695 M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F - 696 M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F - 697 M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F - 698 M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F - 699 M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F - 700 M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F - 701 M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F - 702 M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F - 703 M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F - 704 M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F - 705 M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F - 706 M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F - 707 M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F - 708 M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F - 709 M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F - 710 M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F - 711 M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F - 712 M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F - 713 M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F - 714 M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F - 715 M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F - 716 M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F - 717 M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F - 718 M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F - 719 M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F - 720 M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F - 721 NACTIVE Mycorrhizal N uptake flux gN/m^2/s T - 722 NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T - 723 NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T - 724 NAM AM-associated N uptake flux gN/m^2/s T - 725 NAM_NH4 AM-associated N uptake flux gN/m^2/s T - 726 NAM_NO3 AM-associated N uptake flux gN/m^2/s T - 727 NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T - 728 NDEPLOY total N deployed in new growth gN/m^2/s T - 729 NDEP_PROF profile for atmospheric N deposition 1/m F - 730 NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T - 731 NECM ECM-associated N uptake flux gN/m^2/s T - 732 NECM_NH4 ECM-associated N uptake flux gN/m^2/s T - 733 NECM_NO3 ECM-associated N uptake flux gN/m^2/s T - 734 NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T - 735 NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T - 736 NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T - 737 NET_NMIN net rate of N mineralization gN/m^2/s T - 738 NET_NMIN_vr net rate of N mineralization gN/m^3/s F - 739 NFERTILIZATION fertilizer added gN/m^2/s T - 740 NFIRE fire counts valid only in Reg.C counts/km2/sec T - 741 NFIX Symbiotic BNF uptake flux gN/m^2/s T - 742 NFIXATION_PROF profile for biological N fixation 1/m F - 743 NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F - 744 NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T - 745 NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T - 746 NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T - 747 NPASSIVE Passive N uptake flux gN/m^2/s T - 748 NPOOL temporary plant N pool gN/m^2 T - 749 NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F - 750 NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F - 751 NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F - 752 NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F - 753 NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F - 754 NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F - 755 NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F - 756 NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F - 757 NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F - 758 NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F - 759 NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F - 760 NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F - 761 NPP net primary production gC/m^2/s T - 762 NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F - 763 NPP_GROWTH Total C used for growth in FUN gC/m^2/s T - 764 NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T - 765 NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T - 766 NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T - 767 NPP_NAM AM-associated N uptake used C gC/m^2/s T - 768 NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T - 769 NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T - 770 NPP_NECM ECM-associated N uptake used C gC/m^2/s T - 771 NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T - 772 NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T - 773 NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T - 774 NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T - 775 NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T - 776 NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T - 777 NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T - 778 NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T - 779 NRETRANS Retranslocated N uptake flux gN/m^2/s T - 780 NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T - 781 NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T - 782 NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T - 783 NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F - 784 NUPTAKE Total N uptake of FUN gN/m^2/s T - 785 NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T - 786 N_ALLOMETRY N allocation index none F - 787 O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F - 788 OBU Monin-Obukhov length m F - 789 OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T - 790 OFFSET_COUNTER offset days counter days F - 791 OFFSET_FDD offset freezing degree days counter C degree-days F - 792 OFFSET_FLAG offset flag none F - 793 OFFSET_SWI offset soil water index none F - 794 ONSET_COUNTER onset days counter days F - 795 ONSET_FDD onset freezing degree days counter C degree-days F - 796 ONSET_FLAG onset flag none F - 797 ONSET_GDD onset growing degree days C degree-days F - 798 ONSET_GDDFLAG onset flag for growing degree day sum none F - 799 ONSET_SWI onset soil water index none F - 800 O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T - 801 PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F - 802 PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F - 803 PAR240_shade shade PAR (240 hrs) umol/m2/s F - 804 PAR240_sun sunlit PAR (240 hrs) umol/m2/s F - 805 PAR24_shade shade PAR (24 hrs) umol/m2/s F - 806 PAR24_sun sunlit PAR (24 hrs) umol/m2/s F - 807 PARVEGLN absorbed par by vegetation at local noon W/m^2 T - 808 PAR_shade shade PAR umol/m2/s F - 809 PAR_sun sunlit PAR umol/m2/s F - 810 PAS_SOMC PAS_SOM C gC/m^2 T - 811 PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F - 812 PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F - 813 PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F - 814 PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F - 815 PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T - 816 PAS_SOMN PAS_SOM N gN/m^2 T - 817 PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F - 818 PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F - 819 PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F - 820 PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F - 821 PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T - 822 PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F - 823 PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F - 824 PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T - 825 PBOT_240 10 day running mean of air pressure Pa F - 826 PCH4 atmospheric partial pressure of CH4 Pa T - 827 PCO2 atmospheric partial pressure of CO2 Pa T - 828 PCO2_240 10 day running mean of CO2 pressure Pa F - 829 PFT_CTRUNC patch-level sink for C truncation gC/m^2 F - 830 PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T - 831 PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T - 832 PFT_NTRUNC patch-level sink for N truncation gN/m^2 F - 833 PLANTCN Plant C:N used by FUN unitless F - 834 PLANT_CALLOC total allocated C flux gC/m^2/s F - 835 PLANT_NALLOC total allocated N flux gN/m^2/s F - 836 PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T - 837 PNLCZ Proportion of nitrogen allocated for light capture unitless F - 838 PO2_240 10 day running mean of O2 pressure Pa F - 839 POTENTIAL_IMMOB potential N immobilization gN/m^2/s T - 840 POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F - 841 POT_F_DENIT potential denitrification flux gN/m^2/s T - 842 POT_F_DENIT_vr potential denitrification flux gN/m^3/s F - 843 POT_F_NIT potential nitrification flux gN/m^2/s T - 844 POT_F_NIT_vr potential nitrification flux gN/m^3/s F - 845 PREC10 10-day running mean of PREC MM H2O/S F - 846 PREC60 60-day running mean of PREC MM H2O/S F - 847 PREV_DAYL daylength from previous timestep s F - 848 PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F - 849 PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F - 850 PROD100C 100-yr wood product C gC/m^2 F - 851 PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F - 852 PROD100N 100-yr wood product N gN/m^2 F - 853 PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F - 854 PROD10C 10-yr wood product C gC/m^2 F - 855 PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F - 856 PROD10N 10-yr wood product N gN/m^2 F - 857 PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F - 858 PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T - 859 PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T - 860 PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T - 861 PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T - 862 PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F - 863 Q2M 2m specific humidity kg/kg T - 864 QAF canopy air humidity kg/kg F - 865 QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T - 866 QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F - 867 QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F - 868 QDRAI sub-surface drainage mm/s T - 869 QDRAI_PERCH perched wt drainage mm/s T - 870 QDRAI_XS saturation excess drainage mm/s T - 871 QDRIP rate of excess canopy liquid falling off canopy mm/s F - 872 QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F - 873 QFLOOD runoff from river flooding mm/s T - 874 QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T - 875 QFLX_EVAP_VEG vegetation evaporation mm H2O/s F - 876 QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T - 877 QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T - 878 QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T - 879 QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T - 880 QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F - 881 QFLX_SNOW_DRAIN drainage from snow pack mm/s T - 882 QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T - 883 QFLX_SNOW_GRND snow on ground after interception mm H2O/s F - 884 QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T - 885 QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T - 886 QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F - 887 QH2OSFC surface water runoff mm/s T - 888 QH2OSFC_TO_ICE surface water converted to ice mm/s F - 889 QHR hydraulic redistribution mm/s T - 890 QICE ice growth/melt mm/s T - 891 QICE_FORC qice forcing sent to GLC mm/s F - 892 QICE_FRZ ice growth mm/s T - 893 QICE_MELT ice melt mm/s T - 894 QINFL infiltration mm/s T - 895 QINTR interception mm/s T - 896 QIRRIG_DEMAND irrigation demand mm/s F - 897 QIRRIG_DRIP water added via drip irrigation mm/s F - 898 QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T - 899 QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T - 900 QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T - 901 QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F - 902 QOVER total surface runoff (includes QH2OSFC) mm/s T - 903 QOVER_LAG time-lagged surface runoff for soil columns mm/s F - 904 QPHSNEG net negative hydraulic redistribution flux mm/s F - 905 QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T - 906 QROOTSINK water flux from soil to root in each soil-layer mm/s F - 907 QRUNOFF total liquid runoff not including correction for land use change mm/s T - 908 QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T - 909 QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T - 910 QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F - 911 QRUNOFF_R Rural total runoff mm/s F - 912 QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T - 913 QRUNOFF_U Urban total runoff mm/s F - 914 QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T - 915 QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T - 916 QSNOFRZ column-integrated snow freezing rate kg/m2/s T - 917 QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T - 918 QSNOMELT snow melt rate mm/s T - 919 QSNOMELT_ICE snow melt (ice landunits only) mm/s T - 920 QSNOUNLOAD canopy snow unloading mm/s T - 921 QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T - 922 QSNO_WINDUNLOAD canopy snow wind unloading mm/s T - 923 QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T - 924 QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T - 925 QSOIL_ICE Ground evaporation (ice landunits only) mm/s T - 926 QTOPSOIL water input to surface mm/s F - 927 QVEGE canopy evaporation mm/s T - 928 QVEGT canopy transpiration mm/s T - 929 Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F - 930 Qh sensible heat W/m^2 F - 931 Qle total evaporation W/m^2 F - 932 Qstor storage heat flux (includes snowmelt) W/m^2 F - 933 Qtau momentum flux kg/m/s^2 F - 934 RAH1 aerodynamical resistance s/m F - 935 RAH2 aerodynamical resistance s/m F - 936 RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T - 937 RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T - 938 RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F - 939 RAM1 aerodynamical resistance s/m F - 940 RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F - 941 RAW1 aerodynamical resistance s/m F - 942 RAW2 aerodynamical resistance s/m F - 943 RB leaf boundary resistance s/m F - 944 RB10 10 day running mean boundary layer resistance s/m F - 945 RETRANSN plant pool of retranslocated N gN/m^2 T - 946 RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T - 947 RH atmospheric relative humidity % F - 948 RH2M 2m relative humidity % T - 949 RH2M_R Rural 2m specific humidity % F - 950 RH2M_U Urban 2m relative humidity % F - 951 RH30 30-day running mean of relative humidity % F - 952 RHAF fractional humidity of canopy air fraction F - 953 RHAF10 10 day running mean of fractional humidity of canopy air fraction F - 954 RH_LEAF fractional humidity at leaf surface fraction F - 955 ROOTR effective fraction of roots in each soil layer (SMS method) proportion F - 956 RR root respiration (fine root MR + total root GR) gC/m^2/s T - 957 RRESIS root resistance in each soil layer proportion F - 958 RSSHA shaded leaf stomatal resistance s/m T - 959 RSSUN sunlit leaf stomatal resistance s/m T - 960 Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F - 961 Rnet net radiation W/m^2 F - 962 SABG solar rad absorbed by ground W/m^2 T - 963 SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T - 964 SABV solar rad absorbed by veg W/m^2 T - 965 SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T - 966 SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T - 967 SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T - 968 SLO_SOMC SLO_SOM C gC/m^2 T - 969 SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F - 970 SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F - 971 SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F - 972 SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F - 973 SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F - 974 SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F - 975 SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T - 976 SLO_SOMN SLO_SOM N gN/m^2 T - 977 SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F - 978 SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F - 979 SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F - 980 SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F - 981 SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F - 982 SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F - 983 SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T - 984 SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F - 985 SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 986 SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F - 987 SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 988 SMINN soil mineral N gN/m^2 T - 989 SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T - 990 SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T - 991 SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T - 992 SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F - 993 SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F - 994 SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F - 995 SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F - 996 SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F - 997 SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F - 998 SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F - 999 SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -1000 SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -1001 SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -1002 SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -1003 SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -1004 SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -1005 SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -1006 SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -1007 SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -1008 SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -1009 SMINN_vr soil mineral N gN/m^3 T -1010 SMIN_NH4 soil mineral NH4 gN/m^2 T -1011 SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F -1012 SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T -1013 SMIN_NO3 soil mineral NO3 gN/m^2 T -1014 SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T -1015 SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F -1016 SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F -1017 SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T -1018 SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F -1019 SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F -1020 SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T -1021 SMP soil matric potential (natural vegetated and crop landunits only) mm T -1022 SNOBCMCL mass of BC in snow column kg/m2 T -1023 SNOBCMSL mass of BC in top snow layer kg/m2 T -1024 SNOCAN intercepted snow mm T -1025 SNODSTMCL mass of dust in snow column kg/m2 T -1026 SNODSTMSL mass of dust in top snow layer kg/m2 T -1027 SNOFSDSND direct nir incident solar radiation on snow W/m^2 F -1028 SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F -1029 SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F -1030 SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F -1031 SNOFSRND direct nir reflected solar radiation from snow W/m^2 T -1032 SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T -1033 SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T -1034 SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T -1035 SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T -1036 SNOLIQFL top snow layer liquid water fraction (land) fraction F -1037 SNOOCMCL mass of OC in snow column kg/m2 T -1038 SNOOCMSL mass of OC in top snow layer kg/m2 T -1039 SNORDSL top snow layer effective grain radius m^-6 F -1040 SNOTTOPL snow temperature (top layer) K F -1041 SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F -1042 SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T -1043 SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F -1044 SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T -1045 SNOWDP gridcell mean snow height m T -1046 SNOWICE snow ice kg/m2 T -1047 SNOWICE_ICE snow ice (ice landunits only) kg/m2 F -1048 SNOWLIQ snow liquid water kg/m2 T -1049 SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F -1050 SNOW_5D 5day snow avg m F -1051 SNOW_DEPTH snow height of snow covered area m T -1052 SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F -1053 SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T -1054 SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -1055 SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T -1056 SNOW_SINKS snow sinks (liquid water) mm/s T -1057 SNOW_SOURCES snow sources (liquid water) mm/s T -1058 SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F -1059 SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -1060 SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F -1061 SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -1062 SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F -1063 SNO_FRZ snow freezing rate in each snow layer kg/m2/s F -1064 SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F -1065 SNO_GS Mean snow grain size Microns F -1066 SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F -1067 SNO_ICE Snow ice content kg/m2 F -1068 SNO_LIQH2O Snow liquid water content kg/m2 F -1069 SNO_MELT snow melt rate in each snow layer mm/s F -1070 SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F -1071 SNO_T Snow temperatures K F -1072 SNO_TK Thermal conductivity W/m-K F -1073 SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F -1074 SNO_T_ICE Snow temperatures (ice landunits only) K F -1075 SNO_Z Snow layer thicknesses m F -1076 SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F -1077 SNOdTdzL top snow layer temperature gradient (land) K/m F -1078 SOIL10 10-day running mean of 12cm layer soil K F -1079 SOILC_CHANGE C change in soil gC/m^2/s T -1080 SOILC_HR soil C heterotrophic respiration gC/m^2/s T -1081 SOILC_vr SOIL C (vertically resolved) gC/m^3 T -1082 SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T -1083 SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T -1084 SOILN_vr SOIL N (vertically resolved) gN/m^3 T -1085 SOILPSI soil water potential in each soil layer MPa F -1086 SOILRESIS soil resistance to evaporation s/m T -1087 SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T -1088 SOMC_FIRE C loss due to peat burning gC/m^2/s T -1089 SOMFIRE soil organic matter fire losses gC/m^2/s F -1090 SOM_ADV_COEF advection term for vertical SOM translocation m/s F -1091 SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T -1092 SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F -1093 SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -1094 SR total soil respiration (HR + root resp) gC/m^2/s T -1095 SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T -1096 SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T -1097 SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T -1098 SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T -1099 SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T -1100 SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T -1101 SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T -1102 STEM_PROF profile for litter C and N inputs from stems 1/m F -1103 STORAGE_CDEMAND C use from the C storage pool gC/m^2 F -1104 STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F -1105 STORAGE_NDEMAND N demand during the offset period gN/m^2 F -1106 STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T -1107 STORVEGN stored vegetation nitrogen gN/m^2 T -1108 SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T -1109 SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -1110 SWBGT 2 m Simplified Wetbulb Globe Temp C T -1111 SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T -1112 SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -1113 SWMP65 2 m Swamp Cooler Temp 65% Eff C T -1114 SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T -1115 SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T -1116 SWMP80 2 m Swamp Cooler Temp 80% Eff C T -1117 SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T -1118 SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T -1119 SWdown atmospheric incident solar radiation W/m^2 F -1120 SWup upwelling shortwave radiation W/m^2 F -1121 SoilAlpha factor limiting ground evap unitless F -1122 SoilAlpha_U urban factor limiting ground evap unitless F -1123 T10 10-day running mean of 2-m temperature K F -1124 TAF canopy air temperature K F -1125 TAUX zonal surface stress kg/m/s^2 T -1126 TAUY meridional surface stress kg/m/s^2 T -1127 TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T -1128 TBUILD internal urban building air temperature K T -1129 TBUILD_MAX prescribed maximum interior building temperature K F -1130 TEMPAVG_T2M temporary average 2m air temperature K F -1131 TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F -1132 TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F -1133 TEQ 2 m Equiv Temp K T -1134 TEQ_R Rural 2 m Equiv Temp K T -1135 TEQ_U Urban 2 m Equiv Temp K T -1136 TFLOOR floor temperature K F -1137 TG ground temperature K T -1138 TG_ICE ground temperature (ice landunits only) K F -1139 TG_R Rural ground temperature K F -1140 TG_U Urban ground temperature K F -1141 TH2OSFC surface water temperature K T -1142 THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -1143 THIC 2 m Temp Hum Index Comfort C T -1144 THIC_R Rural 2 m Temp Hum Index Comfort C T -1145 THIC_U Urban 2 m Temp Hum Index Comfort C T -1146 THIP 2 m Temp Hum Index Physiology C T -1147 THIP_R Rural 2 m Temp Hum Index Physiology C T -1148 THIP_U Urban 2 m Temp Hum Index Physiology C T -1149 TKE1 top lake level eddy thermal conductivity W/(mK) T -1150 TLAI total projected leaf area index m^2/m^2 T -1151 TLAKE lake temperature K T -1152 TOPO_COL column-level topographic height m F -1153 TOPO_COL_ICE column-level topographic height (ice landunits only) m F -1154 TOPO_FORC topograephic height sent to GLC m F -1155 TOPT topt coefficient for VOC calc non F -1156 TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T -1157 TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T -1158 TOTCOLN total column-level N, excluding product pools gN/m^2 T -1159 TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T -1160 TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T -1161 TOTFIRE total ecosystem fire losses gC/m^2/s F -1162 TOTLITC total litter carbon gC/m^2 T -1163 TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T -1164 TOTLITN total litter N gN/m^2 T -1165 TOTLITN_1m total litter N to 1 meter gN/m^2 T -1166 TOTPFTC total patch-level carbon, including cpool gC/m^2 T -1167 TOTPFTN total patch-level nitrogen gN/m^2 T -1168 TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T -1169 TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T -1170 TOTSOMC total soil organic matter carbon gC/m^2 T -1171 TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T -1172 TOTSOMN total soil organic matter N gN/m^2 T -1173 TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -1174 TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T -1175 TOTVEGN total vegetation nitrogen gN/m^2 T -1176 TOT_WOODPRODC total wood product C gC/m^2 T -1177 TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T -1178 TOT_WOODPRODN total wood product N gN/m^2 T -1179 TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T -1180 TPU25T canopy profile of tpu umol/m2/s T -1181 TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F -1182 TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F -1183 TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F -1184 TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F -1185 TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F -1186 TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F -1187 TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F -1188 TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F -1189 TREFMNAV daily minimum of average 2-m temperature K T -1190 TREFMNAV_R Rural daily minimum of average 2-m temperature K F -1191 TREFMNAV_U Urban daily minimum of average 2-m temperature K F -1192 TREFMXAV daily maximum of average 2-m temperature K T -1193 TREFMXAV_R Rural daily maximum of average 2-m temperature K F -1194 TREFMXAV_U Urban daily maximum of average 2-m temperature K F -1195 TROOF_INNER roof inside surface temperature K F -1196 TSA 2m air temperature K T -1197 TSAI total projected stem area index m^2/m^2 T -1198 TSA_ICE 2m air temperature (ice landunits only) K F -1199 TSA_R Rural 2m air temperature K F -1200 TSA_U Urban 2m air temperature K F -1201 TSHDW_INNER shadewall inside surface temperature K F -1202 TSKIN skin temperature K T -1203 TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -1204 TSOI soil temperature (natural vegetated and crop landunits only) K T -1205 TSOI_10CM soil temperature in top 10cm of soil K T -1206 TSOI_ICE soil temperature (ice landunits only) K T -1207 TSRF_FORC surface temperature sent to GLC K F -1208 TSUNW_INNER sunwall inside surface temperature K F -1209 TV vegetation temperature K T -1210 TV24 vegetation temperature (last 24hrs) K F -1211 TV240 vegetation temperature (last 240hrs) K F -1212 TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F -1213 TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F -1214 TWS total water storage mm T -1215 T_SCALAR temperature inhibition of decomposition unitless T -1216 Tair atmospheric air temperature (downscaled to columns in glacier regions) K F -1217 Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F -1218 U10 10-m wind m/s T -1219 U10_DUST 10-m wind for dust model m/s T -1220 U10_ICE 10-m wind (ice landunits only) m/s F -1221 UAF canopy air speed m/s F -1222 ULRAD upward longwave radiation above the canopy W/m^2 F -1223 UM wind speed plus stability effect m/s F -1224 URBAN_AC urban air conditioning flux W/m^2 T -1225 URBAN_HEAT urban heating flux W/m^2 T -1226 USTAR aerodynamical resistance s/m F -1227 UST_LAKE friction velocity (lakes only) m/s F -1228 VA atmospheric wind speed plus convective velocity m/s F -1229 VCMX25T canopy profile of vcmax25 umol/m2/s T -1230 VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T -1231 VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T -1232 VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T -1233 VOCFLXT total VOC flux into atmosphere moles/m2/sec F -1234 VOLR river channel total water storage m3 T -1235 VOLRMCH river channel main channel water storage m3 T -1236 VPD vpd Pa F -1237 VPD2M 2m vapor pressure deficit Pa T -1238 VPD_CAN canopy vapor pressure deficit kPa T -1239 Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T -1240 WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -1241 WBA 2 m Wet Bulb C T -1242 WBA_R Rural 2 m Wet Bulb C T -1243 WBA_U Urban 2 m Wet Bulb C T -1244 WBT 2 m Stull Wet Bulb C T -1245 WBT_R Rural 2 m Stull Wet Bulb C T -1246 WBT_U Urban 2 m Stull Wet Bulb C T -1247 WF soil water as frac. of whc for top 0.05 m proportion F -1248 WFPS WFPS percent F -1249 WIND atmospheric wind velocity magnitude m/s T -1250 WOODC wood C gC/m^2 T -1251 WOODC_ALLOC wood C eallocation gC/m^2/s T -1252 WOODC_LOSS wood C loss gC/m^2/s T -1253 WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T -1254 WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T -1255 WTGQ surface tracer conductance m/s T -1256 W_SCALAR Moisture (dryness) inhibition of decomposition unitless T -1257 Wind atmospheric wind velocity magnitude m/s F -1258 XSMRPOOL temporary photosynthate C pool gC/m^2 T -1259 XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F -1260 XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T -1261 Z0HG roughness length over ground, sensible heat m F -1262 Z0HV roughness length over vegetation, sensible heat m F -1263 Z0M momentum roughness length m F -1264 Z0MG roughness length over ground, momentum m F -1265 Z0MV roughness length over vegetation, momentum m F -1266 Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -1267 Z0QG roughness length over ground, latent heat m F -1268 Z0QV roughness length over vegetation, latent heat m F -1269 ZBOT atmospheric reference height m T -1270 ZETA dimensionless stability parameter unitless F -1271 ZII convective boundary height m F -1272 ZWT water table depth (natural vegetated and crop landunits only) m T -1273 ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T -1274 ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T -1275 anaerobic_frac anaerobic_frac m3/m3 F -1276 bsw clap and hornberger B unitless F -1277 currentPatch currentPatch coefficient for VOC calc non F -1278 diffus diffusivity m^2/s F -1279 fr_WFPS fr_WFPS fraction F -1280 n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F -1281 num_iter number of iterations unitless F -1282 r_psi r_psi m F -1283 ratio_k1 ratio_k1 none F -1284 ratio_no3_co2 ratio_no3_co2 ratio F -1285 soil_bulkdensity soil_bulkdensity kg/m3 F -1286 soil_co2_prod soil_co2_prod ug C / g soil / day F -1287 watfc water field capacity m^3/m^3 F -1288 watsat water saturated m^3/m^3 F +A10TMIN 10-day running mean of min 2-m temperature K F +A5TMIN 5-day running mean of min 2-m temperature K F +ACTUAL_IMMOB actual N immobilization gN/m^2/s T +ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F +ACT_SOMC ACT_SOM C gC/m^2 T +ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F +ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F +ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F +ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F +ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T +ACT_SOMN ACT_SOM N gN/m^2 T +ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F +ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F +ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F +ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F +ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F +ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T +ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F +ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F +AGLB Aboveground leaf biomass kg/m^2 F +AGNPP aboveground NPP gC/m^2/s T +AGSB Aboveground stem biomass kg/m^2 F +ALBD surface albedo (direct) proportion T +ALBDSF diagnostic snow-free surface albedo (direct) proportion T +ALBGRD ground albedo (direct) proportion F +ALBGRI ground albedo (indirect) proportion F +ALBI surface albedo (indirect) proportion T +ALBISF diagnostic snow-free surface albedo (indirect) proportion T +ALPHA alpha coefficient for VOC calc non F +ALT current active layer thickness m T +ALTMAX maximum annual active layer thickness m T +ALTMAX_LASTYEAR maximum prior year active layer thickness m F +ANNAVG_T2M annual average 2m air temperature K F +ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F +ANNSUM_COUNTER seconds since last annual accumulator turnover s F +ANNSUM_NPP annual sum of NPP gC/m^2/yr F +ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F +APPAR_TEMP 2 m apparent temperature C T +APPAR_TEMP_R Rural 2 m apparent temperature C T +APPAR_TEMP_U Urban 2 m apparent temperature C T +AR autotrophic respiration (MR + GR) gC/m^2/s T +ATM_TOPO atmospheric surface height m T +AVAILC C flux available for allocation gC/m^2/s F +AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F +AnnET Annual ET mm/s F +BAF_CROP fractional area burned for crop s-1 T +BAF_PEATF fractional area burned in peatland s-1 T +BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BETA coefficient of convective velocity none F +BGLFR background litterfall rate 1/s F +BGNPP belowground NPP gC/m^2/s T +BGTR background transfer growth rate 1/s F +BTRANMN daily minimum of transpiration beta factor unitless T +CANNAVG_T2M annual average of 2m air temperature K F +CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F +CEL_LITC CEL_LIT C gC/m^2 T +CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F +CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F +CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T +CEL_LITN CEL_LIT N gN/m^2 T +CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F +CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F +CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F +CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F +CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T +CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F +CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F +CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F +CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F +CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F +CH4PROD Gridcell total production of CH4 gC/m2/s T +CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T +CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +COL_CTRUNC column-level sink for C truncation gC/m^2 F +COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T +COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T +COL_NTRUNC column-level sink for N truncation gN/m^2 F +CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F +CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T +COST_NACTIVE Cost of active uptake gN/gC T +COST_NFIX Cost of fixation gN/gC T +COST_NRETRANS Cost of retranslocation gN/gC T +COSZEN cosine of solar zenith angle none F +CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T +CPOOL temporary photosynthate C pool gC/m^2 T +CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F +CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F +CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F +CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F +CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F +CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F +CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F +CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F +CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F +CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F +CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F +CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F +CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F +CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F +CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F +CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F +CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F +CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F +CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F +CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F +CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F +CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F +CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F +CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F +CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F +CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F +CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T +CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T +CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T +CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T +CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T +CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F +CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F +CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F +CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F +CWDC CWD C gC/m^2 T +CWDC_1m CWD C to 1 meter gC/m^2 F +CWDC_HR cwd C heterotrophic respiration gC/m^2/s F +CWDC_LOSS coarse woody debris C loss gC/m^2/s T +CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F +CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F +CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F +CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F +CWDC_vr CWD C (vertically resolved) gC/m^3 T +CWDN CWD N gN/m^2 T +CWDN_1m CWD N to 1 meter gN/m^2 F +CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F +CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F +CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F +CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F +CWDN_vr CWD N (vertically resolved) gN/m^3 T +CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F +CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F +CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F +CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F +C_ALLOMETRY C allocation index none F +DAYL daylength s F +DAYS_ACTIVE number of days since last dormancy days F +DEADCROOTC dead coarse root C gC/m^2 T +DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F +DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F +DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F +DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F +DEADCROOTN dead coarse root N gN/m^2 T +DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F +DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F +DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F +DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F +DEADSTEMC dead stem C gC/m^2 T +DEADSTEMC_STORAGE dead stem C storage gC/m^2 F +DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F +DEADSTEMC_XFER dead stem C transfer gC/m^2 F +DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F +DEADSTEMN dead stem N gN/m^2 T +DEADSTEMN_STORAGE dead stem N storage gN/m^2 F +DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F +DEADSTEMN_XFER dead stem N transfer gN/m^2 F +DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F +DENIT total rate of denitrification gN/m^2/s T +DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F +DISCOI 2 m Discomfort Index C T +DISCOIS 2 m Stull Discomfort Index C T +DISCOIS_R Rural 2 m Stull Discomfort Index C T +DISCOIS_U Urban 2 m Stull Discomfort Index C T +DISCOI_R Rural 2 m Discomfort Index C T +DISCOI_U Urban 2 m Discomfort Index C T +DISPLA displacement height m F +DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T +DISPVEGN displayed vegetation nitrogen gN/m^2 T +DLRAD downward longwave radiation below the canopy W/m^2 F +DORMANT_FLAG dormancy flag none F +DOWNREG fractional reduction in GPP due to N limitation proportion F +DPVLTRB1 turbulent deposition velocity 1 m/s F +DPVLTRB2 turbulent deposition velocity 2 m/s F +DPVLTRB3 turbulent deposition velocity 3 m/s F +DPVLTRB4 turbulent deposition velocity 4 m/s F +DSL dry surface layer thickness mm T +DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTFLXT total surface dust emission kg/m2/s T +DT_VEG change in t_veg, last iteration K F +DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T +DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T +DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F +DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T +DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F +DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T +DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T +DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F +DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F +DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F +DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F +DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F +DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F +DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F +DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F +DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F +DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F +DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F +DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F +DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F +DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F +DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T +DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F +DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T +DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F +DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T +DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F +DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T +DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T +DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F +DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +EFF_POROSITY effective porosity = porosity - vol_ice proportion F +EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T +EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T +EFLX_GNET net heat flux into ground W/m^2 F +EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T +EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T +EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F +EFLX_LH_TOT_R Rural total evaporation W/m^2 T +EFLX_LH_TOT_U Urban total evaporation W/m^2 F +EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F +ELAI exposed one-sided leaf area index m^2/m^2 T +EMG ground emissivity proportion F +EMV vegetation emissivity proportion F +EOPT Eopt coefficient for VOC calc non F +EPT 2 m Equiv Pot Temp K T +EPT_R Rural 2 m Equiv Pot Temp K T +EPT_U Urban 2 m Equiv Pot Temp K T +ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T +ERRH2O total water conservation error mm T +ERRH2OSNO imbalance in snow depth (liquid water) mm T +ERRSEB surface energy conservation error W/m^2 T +ERRSOI soil/lake energy conservation error W/m^2 T +ERRSOL solar radiation conservation error W/m^2 T +ESAI exposed one-sided stem area index m^2/m^2 T +EXCESSC_MR excess C maintenance respiration gC/m^2/s F +EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F +FAREA_BURNED timestep fractional area burned s-1 T +FCANSNO fraction of canopy that is wet proportion F +FCEV canopy evaporation W/m^2 T +FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T +FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T +FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T +FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F +FCOV fractional impermeable area unitless T +FCTR canopy transpiration W/m^2 T +FDRY fraction of foliage that is green and dry proportion F +FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F +FERT_COUNTER time left to fertilize seconds F +FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F +FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T +FGEV ground evaporation W/m^2 T +FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T +FGR12 heat flux between soil layers 1 and 2 W/m^2 T +FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F +FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F +FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F +FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F +FH2OSFC fraction of ground covered by surface water unitless T +FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F +FINUNDATED fractional inundated area of vegetated columns unitless T +FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F +FIRA net infrared (longwave) radiation W/m^2 T +FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRA_R Rural net infrared (longwave) radiation W/m^2 T +FIRA_U Urban net infrared (longwave) radiation W/m^2 F +FIRE emitted infrared (longwave) radiation W/m^2 T +FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T +FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F +FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T +FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F +FPI fraction of potential immobilization proportion T +FPI_vr fraction of potential immobilization proportion F +FPSN photosynthesis umol m-2 s-1 T +FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F +FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F +FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F +FPSN_WP Product-limited photosynthesis umol m-2 s-1 F +FRAC_ICEOLD fraction of ice relative to the tot water proportion F +FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T +FROOTC fine root C gC/m^2 T +FROOTC_ALLOC fine root C allocation gC/m^2/s T +FROOTC_LOSS fine root C loss gC/m^2/s T +FROOTC_STORAGE fine root C storage gC/m^2 F +FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F +FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F +FROOTC_XFER fine root C transfer gC/m^2 F +FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F +FROOTN fine root N gN/m^2 T +FROOTN_STORAGE fine root N storage gN/m^2 F +FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F +FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F +FROOTN_XFER fine root N transfer gN/m^2 F +FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F +FROOT_MR fine root maintenance respiration gC/m^2/s F +FROOT_PROF profile for litter C and N inputs from fine roots 1/m F +FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F +FSA absorbed solar radiation W/m^2 T +FSAT fractional area with water table at surface unitless T +FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F +FSA_R Rural absorbed solar radiation W/m^2 F +FSA_U Urban absorbed solar radiation W/m^2 F +FSD24 direct radiation (last 24hrs) K F +FSD240 direct radiation (last 240hrs) K F +FSDS atmospheric incident solar radiation W/m^2 T +FSDSND direct nir incident solar radiation W/m^2 T +FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T +FSDSNI diffuse nir incident solar radiation W/m^2 T +FSDSVD direct vis incident solar radiation W/m^2 T +FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T +FSDSVI diffuse vis incident solar radiation W/m^2 T +FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T +FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T +FSH_G sensible heat from ground W/m^2 T +FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F +FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T +FSH_R Rural sensible heat W/m^2 T +FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T +FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T +FSH_U Urban sensible heat W/m^2 F +FSH_V sensible heat from veg W/m^2 T +FSI24 indirect radiation (last 24hrs) K F +FSI240 indirect radiation (last 240hrs) K F +FSM snow melt heat flux W/m^2 T +FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F +FSM_R Rural snow melt heat flux W/m^2 F +FSM_U Urban snow melt heat flux W/m^2 F +FSNO fraction of ground covered by snow unitless T +FSNO_EFF effective fraction of ground covered by snow unitless T +FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F +FSR reflected solar radiation W/m^2 T +FSRND direct nir reflected solar radiation W/m^2 T +FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T +FSRNI diffuse nir reflected solar radiation W/m^2 T +FSRSF reflected solar radiation W/m^2 T +FSRSFND direct nir reflected solar radiation W/m^2 T +FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T +FSRSFNI diffuse nir reflected solar radiation W/m^2 T +FSRSFVD direct vis reflected solar radiation W/m^2 T +FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T +FSRSFVI diffuse vis reflected solar radiation W/m^2 T +FSRVD direct vis reflected solar radiation W/m^2 T +FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T +FSRVI diffuse vis reflected solar radiation W/m^2 T +FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F +FSUN sunlit fraction of canopy proportion F +FSUN24 fraction sunlit (last 24hrs) K F +FSUN240 fraction sunlit (last 240hrs) K F +FUELC fuel load gC/m^2 T +FV friction velocity m/s T +FWET fraction of canopy that is wet proportion F +F_DENIT denitrification flux gN/m^2/s T +F_DENIT_BASE F_DENIT_BASE gN/m^3/s F +F_DENIT_vr denitrification flux gN/m^3/s F +F_N2O_DENIT denitrification N2O flux gN/m^2/s T +F_N2O_NIT nitrification N2O flux gN/m^2/s T +F_NIT nitrification flux gN/m^2/s T +F_NIT_vr nitrification flux gN/m^3/s F +FireComp_BC fire emissions flux of BC kg/m2/sec F +FireComp_OC fire emissions flux of OC kg/m2/sec F +FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F +FireEmis_TOT Total fire emissions flux gC/m2/sec F +FireEmis_ZTOP Top of vertical fire emissions distribution m F +FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F +FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F +FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F +GAMMA total gamma for VOC calc non F +GAMMAA gamma A for VOC calc non F +GAMMAC gamma C for VOC calc non F +GAMMAL gamma L for VOC calc non F +GAMMAP gamma P for VOC calc non F +GAMMAS gamma S for VOC calc non F +GAMMAT gamma T for VOC calc non F +GDD0 Growing degree days base 0C from planting ddays F +GDD020 Twenty year average of growing degree days base 0C from planting ddays F +GDD10 Growing degree days base 10C from planting ddays F +GDD1020 Twenty year average of growing degree days base 10C from planting ddays F +GDD8 Growing degree days base 8C from planting ddays F +GDD820 Twenty year average of growing degree days base 8C from planting ddays F +GDDACCUM Accumulated growing degree days past planting date for crop ddays F +GDDHARV Growing degree days (gdd) needed to harvest ddays F +GDDTSOI Growing degree-days from planting (top two soil layers) ddays F +GPP gross primary production gC/m^2/s T +GR total growth respiration gC/m^2/s T +GRAINC grain C (does not equal yield) gC/m^2 T +GRAINC_TO_FOOD grain C to food gC/m^2/s T +GRAINC_TO_SEED grain C to seed gC/m^2/s T +GRAINN grain N gN/m^2 T +GRESP_STORAGE growth respiration storage gC/m^2 F +GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F +GRESP_XFER growth respiration transfer gC/m^2 F +GROSS_NMIN gross rate of N mineralization gN/m^2/s T +GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F +GSSHA shaded leaf stomatal conductance umol H20/m2/s T +GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T +GSSUN sunlit leaf stomatal conductance umol H20/m2/s T +GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T +H2OCAN intercepted water mm T +H2OSFC surface water depth mm T +H2OSNO snow depth (liquid water) mm T +H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F +H2OSNO_TOP mass of snow in top snow layer kg/m2 T +H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HBOT canopy bottom m F +HEAT_CONTENT1 initial gridcell total heat content J/m^2 T +HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F +HEAT_CONTENT2 post land cover change total heat content J/m^2 F +HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T +HIA 2 m NWS Heat Index C T +HIA_R Rural 2 m NWS Heat Index C T +HIA_U Urban 2 m NWS Heat Index C T +HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +HR total heterotrophic respiration gC/m^2/s T +HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T +HTOP canopy top m T +HUI crop heat unit index ddays F +HUMIDEX 2 m Humidex C T +HUMIDEX_R Rural 2 m Humidex C T +HUMIDEX_U Urban 2 m Humidex C T +ICE_CONTENT1 initial gridcell total ice content mm T +ICE_CONTENT2 post land cover change total ice content mm F +ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F +INIT_GPP GPP flux before downregulation gC/m^2/s F +INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F +INT_SNOW_ICE accumulated swe (ice landunits only) mm F +IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T +JMX25T canopy profile of jmax umol/m2/s T +Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T +KROOT root conductance each soil layer 1/s F +KSOIL soil conductance in each soil layer 1/s F +K_ACT_SOM active soil organic potential loss coefficient 1/s F +K_CEL_LIT cellulosic litter potential loss coefficient 1/s F +K_CWD coarse woody debris potential loss coefficient 1/s F +K_LIG_LIT lignin litter potential loss coefficient 1/s F +K_MET_LIT metabolic litter potential loss coefficient 1/s F +K_NITR K_NITR 1/s F +K_NITR_H2O K_NITR_H2O unitless F +K_NITR_PH K_NITR_PH unitless F +K_NITR_T K_NITR_T unitless F +K_PAS_SOM passive soil organic potential loss coefficient 1/s F +K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F +LAI240 240hr average of leaf area index m^2/m^2 F +LAISHA shaded projected leaf area index m^2/m^2 T +LAISUN sunlit projected leaf area index m^2/m^2 T +LAKEICEFRAC lake layer ice mass fraction unitless F +LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T +LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T +LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T +LATBASET latitude vary base temperature for gddplant degree C F +LEAFC leaf C gC/m^2 T +LEAFCN Leaf CN ratio used for flexible CN gC/gN T +LEAFCN_OFFSET Leaf C:N used by FUN unitless F +LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F +LEAFC_ALLOC leaf C allocation gC/m^2/s T +LEAFC_CHANGE C change in leaf gC/m^2/s T +LEAFC_LOSS leaf C loss gC/m^2/s T +LEAFC_STORAGE leaf C storage gC/m^2 F +LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F +LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F +LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T +LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F +LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T +LEAFC_XFER leaf C transfer gC/m^2 F +LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F +LEAFN leaf N gN/m^2 T +LEAFN_STORAGE leaf N storage gN/m^2 F +LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F +LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F +LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T +LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F +LEAFN_XFER leaf N transfer gN/m^2 F +LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F +LEAF_MR leaf maintenance respiration gC/m^2/s T +LEAF_PROF profile for litter C and N inputs from leaves 1/m F +LFC2 conversion area fraction of BET and BDT that burned per sec T +LGSF long growing season factor proportion F +LIG_LITC LIG_LIT C gC/m^2 T +LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F +LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F +LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T +LIG_LITN LIG_LIT N gN/m^2 T +LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F +LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F +LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T +LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F +LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F +LIQCAN intercepted liquid water mm T +LIQUID_CONTENT1 initial gridcell total liq content mm T +LIQUID_CONTENT2 post landuse change gridcell total liq content mm F +LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F +LITFALL litterfall (leaves and fine roots) gC/m^2/s T +LITFIRE litter fire losses gC/m^2/s F +LITTERC_HR litter C heterotrophic respiration gC/m^2/s T +LITTERC_LOSS litter C loss gC/m^2/s T +LIVECROOTC live coarse root C gC/m^2 T +LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F +LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F +LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F +LIVECROOTC_XFER live coarse root C transfer gC/m^2 F +LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F +LIVECROOTN live coarse root N gN/m^2 T +LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F +LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F +LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F +LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F +LIVECROOTN_XFER live coarse root N transfer gN/m^2 F +LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F +LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F +LIVESTEMC live stem C gC/m^2 T +LIVESTEMC_STORAGE live stem C storage gC/m^2 F +LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F +LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T +LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F +LIVESTEMC_XFER live stem C transfer gC/m^2 F +LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F +LIVESTEMN live stem N gN/m^2 T +LIVESTEMN_STORAGE live stem N storage gN/m^2 F +LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F +LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F +LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F +LIVESTEMN_XFER live stem N transfer gN/m^2 F +LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F +LIVESTEM_MR live stem maintenance respiration gC/m^2/s F +LNC leaf N concentration gN leaf/m^2 T +LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWup upwelling longwave radiation W/m^2 F +MEG_acetaldehyde MEGAN flux kg/m2/sec T +MEG_acetic_acid MEGAN flux kg/m2/sec T +MEG_acetone MEGAN flux kg/m2/sec T +MEG_carene_3 MEGAN flux kg/m2/sec T +MEG_ethanol MEGAN flux kg/m2/sec T +MEG_formaldehyde MEGAN flux kg/m2/sec T +MEG_isoprene MEGAN flux kg/m2/sec T +MEG_methanol MEGAN flux kg/m2/sec T +MEG_pinene_a MEGAN flux kg/m2/sec T +MEG_thujene_a MEGAN flux kg/m2/sec T +MET_LITC MET_LIT C gC/m^2 T +MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F +MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F +MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F +MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F +MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T +MET_LITN MET_LIT N gN/m^2 T +MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F +MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F +MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F +MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F +MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T +MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F +MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F +MR maintenance respiration gC/m^2/s T +M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F +M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F +M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F +M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F +M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F +M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F +M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F +M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F +M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F +M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F +M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F +M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F +M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F +M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F +M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F +M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F +M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F +M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F +M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F +M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F +M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F +M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F +M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F +M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F +M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F +M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F +M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F +M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F +M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F +M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F +M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F +M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F +M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F +M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F +M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F +M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F +M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F +M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F +M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F +M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F +M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F +M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F +M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F +M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F +M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F +M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F +M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F +M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F +M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F +M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F +M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F +M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F +M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F +M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F +M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F +M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F +M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F +M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F +M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F +M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F +M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F +M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F +M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F +M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F +M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F +M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F +M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F +M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F +M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F +M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F +M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F +M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F +M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F +M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F +M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F +M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F +M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F +M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F +M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F +M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F +M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F +M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F +M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F +M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F +M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F +M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F +M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F +M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F +M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F +M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F +M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F +M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F +M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F +M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F +M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F +M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F +M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F +M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F +M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F +M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F +M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F +M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F +M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F +M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F +M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F +M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F +M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F +M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F +M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F +M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F +M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F +M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F +M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F +M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F +M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F +M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F +M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F +M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F +M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F +M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F +M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F +M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F +M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F +M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F +M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F +M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F +NACTIVE Mycorrhizal N uptake flux gN/m^2/s T +NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T +NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T +NAM AM-associated N uptake flux gN/m^2/s T +NAM_NH4 AM-associated N uptake flux gN/m^2/s T +NAM_NO3 AM-associated N uptake flux gN/m^2/s T +NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T +NDEPLOY total N deployed in new growth gN/m^2/s T +NDEP_PROF profile for atmospheric N deposition 1/m F +NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T +NECM ECM-associated N uptake flux gN/m^2/s T +NECM_NH4 ECM-associated N uptake flux gN/m^2/s T +NECM_NO3 ECM-associated N uptake flux gN/m^2/s T +NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T +NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T +NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T +NET_NMIN net rate of N mineralization gN/m^2/s T +NET_NMIN_vr net rate of N mineralization gN/m^3/s F +NFERTILIZATION fertilizer added gN/m^2/s T +NFIRE fire counts valid only in Reg.C counts/km2/sec T +NFIX Symbiotic BNF uptake flux gN/m^2/s T +NFIXATION_PROF profile for biological N fixation 1/m F +NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F +NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T +NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T +NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T +NPASSIVE Passive N uptake flux gN/m^2/s T +NPOOL temporary plant N pool gN/m^2 T +NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F +NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F +NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F +NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F +NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F +NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F +NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F +NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F +NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F +NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F +NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F +NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F +NPP net primary production gC/m^2/s T +NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F +NPP_GROWTH Total C used for growth in FUN gC/m^2/s T +NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T +NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T +NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T +NPP_NAM AM-associated N uptake used C gC/m^2/s T +NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T +NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T +NPP_NECM ECM-associated N uptake used C gC/m^2/s T +NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T +NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T +NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T +NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T +NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T +NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T +NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T +NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T +NRETRANS Retranslocated N uptake flux gN/m^2/s T +NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T +NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T +NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T +NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F +NUPTAKE Total N uptake of FUN gN/m^2/s T +NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T +N_ALLOMETRY N allocation index none F +O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F +OBU Monin-Obukhov length m F +OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T +OFFSET_COUNTER offset days counter days F +OFFSET_FDD offset freezing degree days counter C degree-days F +OFFSET_FLAG offset flag none F +OFFSET_SWI offset soil water index none F +ONSET_COUNTER onset days counter days F +ONSET_FDD onset freezing degree days counter C degree-days F +ONSET_FLAG onset flag none F +ONSET_GDD onset growing degree days C degree-days F +ONSET_GDDFLAG onset flag for growing degree day sum none F +ONSET_SWI onset soil water index none F +O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T +PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F +PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F +PAR240_shade shade PAR (240 hrs) umol/m2/s F +PAR240_sun sunlit PAR (240 hrs) umol/m2/s F +PAR24_shade shade PAR (24 hrs) umol/m2/s F +PAR24_sun sunlit PAR (24 hrs) umol/m2/s F +PARVEGLN absorbed par by vegetation at local noon W/m^2 T +PAR_shade shade PAR umol/m2/s F +PAR_sun sunlit PAR umol/m2/s F +PAS_SOMC PAS_SOM C gC/m^2 T +PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F +PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F +PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F +PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F +PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T +PAS_SOMN PAS_SOM N gN/m^2 T +PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F +PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F +PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F +PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F +PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T +PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F +PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F +PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PBOT_240 10 day running mean of air pressure Pa F +PCH4 atmospheric partial pressure of CH4 Pa T +PCO2 atmospheric partial pressure of CO2 Pa T +PCO2_240 10 day running mean of CO2 pressure Pa F +PFT_CTRUNC patch-level sink for C truncation gC/m^2 F +PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T +PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T +PFT_NTRUNC patch-level sink for N truncation gN/m^2 F +PLANTCN Plant C:N used by FUN unitless F +PLANT_CALLOC total allocated C flux gC/m^2/s F +PLANT_NALLOC total allocated N flux gN/m^2/s F +PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T +PNLCZ Proportion of nitrogen allocated for light capture unitless F +PO2_240 10 day running mean of O2 pressure Pa F +POTENTIAL_IMMOB potential N immobilization gN/m^2/s T +POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F +POT_F_DENIT potential denitrification flux gN/m^2/s T +POT_F_DENIT_vr potential denitrification flux gN/m^3/s F +POT_F_NIT potential nitrification flux gN/m^2/s T +POT_F_NIT_vr potential nitrification flux gN/m^3/s F +PREC10 10-day running mean of PREC MM H2O/S F +PREC60 60-day running mean of PREC MM H2O/S F +PREV_DAYL daylength from previous timestep s F +PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F +PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F +PROD100C 100-yr wood product C gC/m^2 F +PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F +PROD100N 100-yr wood product N gN/m^2 F +PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F +PROD10C 10-yr wood product C gC/m^2 F +PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F +PROD10N 10-yr wood product N gN/m^2 F +PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F +PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T +PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T +PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T +PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T +PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +Q2M 2m specific humidity kg/kg T +QAF canopy air humidity kg/kg F +QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F +QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F +QDRAI sub-surface drainage mm/s T +QDRAI_PERCH perched wt drainage mm/s T +QDRAI_XS saturation excess drainage mm/s T +QDRIP rate of excess canopy liquid falling off canopy mm/s F +QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F +QFLOOD runoff from river flooding mm/s T +QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T +QFLX_EVAP_VEG vegetation evaporation mm H2O/s F +QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T +QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T +QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F +QFLX_SNOW_DRAIN drainage from snow pack mm/s T +QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T +QFLX_SNOW_GRND snow on ground after interception mm H2O/s F +QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F +QH2OSFC surface water runoff mm/s T +QH2OSFC_TO_ICE surface water converted to ice mm/s F +QHR hydraulic redistribution mm/s T +QICE ice growth/melt mm/s T +QICE_FORC qice forcing sent to GLC mm/s F +QICE_FRZ ice growth mm/s T +QICE_MELT ice melt mm/s T +QINFL infiltration mm/s T +QINTR interception mm/s T +QIRRIG_DEMAND irrigation demand mm/s F +QIRRIG_DRIP water added via drip irrigation mm/s F +QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T +QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T +QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T +QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F +QOVER total surface runoff (includes QH2OSFC) mm/s T +QOVER_LAG time-lagged surface runoff for soil columns mm/s F +QPHSNEG net negative hydraulic redistribution flux mm/s F +QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T +QROOTSINK water flux from soil to root in each soil-layer mm/s F +QRUNOFF total liquid runoff not including correction for land use change mm/s T +QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T +QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F +QRUNOFF_R Rural total runoff mm/s F +QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_U Urban total runoff mm/s F +QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T +QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T +QSNOFRZ column-integrated snow freezing rate kg/m2/s T +QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T +QSNOMELT snow melt rate mm/s T +QSNOMELT_ICE snow melt (ice landunits only) mm/s T +QSNOUNLOAD canopy snow unloading mm/s T +QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T +QSNO_WINDUNLOAD canopy snow wind unloading mm/s T +QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T +QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T +QSOIL_ICE Ground evaporation (ice landunits only) mm/s T +QTOPSOIL water input to surface mm/s F +QVEGE canopy evaporation mm/s T +QVEGT canopy transpiration mm/s T +Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F +Qh sensible heat W/m^2 F +Qle total evaporation W/m^2 F +Qstor storage heat flux (includes snowmelt) W/m^2 F +Qtau momentum flux kg/m/s^2 F +RAH1 aerodynamical resistance s/m F +RAH2 aerodynamical resistance s/m F +RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T +RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T +RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +RAM1 aerodynamical resistance s/m F +RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F +RAW1 aerodynamical resistance s/m F +RAW2 aerodynamical resistance s/m F +RB leaf boundary resistance s/m F +RB10 10 day running mean boundary layer resistance s/m F +RETRANSN plant pool of retranslocated N gN/m^2 T +RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T +RH atmospheric relative humidity % F +RH2M 2m relative humidity % T +RH2M_R Rural 2m specific humidity % F +RH2M_U Urban 2m relative humidity % F +RH30 30-day running mean of relative humidity % F +RHAF fractional humidity of canopy air fraction F +RHAF10 10 day running mean of fractional humidity of canopy air fraction F +RH_LEAF fractional humidity at leaf surface fraction F +ROOTR effective fraction of roots in each soil layer (SMS method) proportion F +RR root respiration (fine root MR + total root GR) gC/m^2/s T +RRESIS root resistance in each soil layer proportion F +RSSHA shaded leaf stomatal resistance s/m T +RSSUN sunlit leaf stomatal resistance s/m T +Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rnet net radiation W/m^2 F +SABG solar rad absorbed by ground W/m^2 T +SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T +SABV solar rad absorbed by veg W/m^2 T +SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T +SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T +SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T +SLO_SOMC SLO_SOM C gC/m^2 T +SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F +SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T +SLO_SOMN SLO_SOM N gN/m^2 T +SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F +SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F +SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T +SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F +SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F +SMINN soil mineral N gN/m^2 T +SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T +SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T +SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T +SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F +SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +SMINN_vr soil mineral N gN/m^3 T +SMIN_NH4 soil mineral NH4 gN/m^2 T +SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F +SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3 soil mineral NO3 gN/m^2 T +SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T +SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T +SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F +SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T +SMP soil matric potential (natural vegetated and crop landunits only) mm T +SNOBCMCL mass of BC in snow column kg/m2 T +SNOBCMSL mass of BC in top snow layer kg/m2 T +SNOCAN intercepted snow mm T +SNODSTMCL mass of dust in snow column kg/m2 T +SNODSTMSL mass of dust in top snow layer kg/m2 T +SNOFSDSND direct nir incident solar radiation on snow W/m^2 F +SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F +SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F +SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F +SNOFSRND direct nir reflected solar radiation from snow W/m^2 T +SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T +SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T +SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T +SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T +SNOLIQFL top snow layer liquid water fraction (land) fraction F +SNOOCMCL mass of OC in snow column kg/m2 T +SNOOCMSL mass of OC in top snow layer kg/m2 T +SNORDSL top snow layer effective grain radius m^-6 F +SNOTTOPL snow temperature (top layer) K F +SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F +SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +SNOWDP gridcell mean snow height m T +SNOWICE snow ice kg/m2 T +SNOWICE_ICE snow ice (ice landunits only) kg/m2 F +SNOWLIQ snow liquid water kg/m2 T +SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F +SNOW_5D 5day snow avg m F +SNOW_DEPTH snow height of snow covered area m T +SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F +SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T +SNOW_SINKS snow sinks (liquid water) mm/s T +SNOW_SOURCES snow sources (liquid water) mm/s T +SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS Mean snow grain size Microns F +SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F +SNO_ICE Snow ice content kg/m2 F +SNO_LIQH2O Snow liquid water content kg/m2 F +SNO_MELT snow melt rate in each snow layer mm/s F +SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T Snow temperatures K F +SNO_TK Thermal conductivity W/m-K F +SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE Snow temperatures (ice landunits only) K F +SNO_Z Snow layer thicknesses m F +SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F +SNOdTdzL top snow layer temperature gradient (land) K/m F +SOIL10 10-day running mean of 12cm layer soil K F +SOILC_CHANGE C change in soil gC/m^2/s T +SOILC_HR soil C heterotrophic respiration gC/m^2/s T +SOILC_vr SOIL C (vertically resolved) gC/m^3 T +SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOILN_vr SOIL N (vertically resolved) gN/m^3 T +SOILPSI soil water potential in each soil layer MPa F +SOILRESIS soil resistance to evaporation s/m T +SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +SOMC_FIRE C loss due to peat burning gC/m^2/s T +SOMFIRE soil organic matter fire losses gC/m^2/s F +SOM_ADV_COEF advection term for vertical SOM translocation m/s F +SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T +SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F +SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F +SR total soil respiration (HR + root resp) gC/m^2/s T +SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T +SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T +SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T +SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T +SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T +SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T +SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T +STEM_PROF profile for litter C and N inputs from stems 1/m F +STORAGE_CDEMAND C use from the C storage pool gC/m^2 F +STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F +STORAGE_NDEMAND N demand during the offset period gN/m^2 F +STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T +STORVEGN stored vegetation nitrogen gN/m^2 T +SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T +SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F +SWBGT 2 m Simplified Wetbulb Globe Temp C T +SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T +SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T +SWMP65 2 m Swamp Cooler Temp 65% Eff C T +SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T +SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T +SWMP80 2 m Swamp Cooler Temp 80% Eff C T +SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T +SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T +SWdown atmospheric incident solar radiation W/m^2 F +SWup upwelling shortwave radiation W/m^2 F +SoilAlpha factor limiting ground evap unitless F +SoilAlpha_U urban factor limiting ground evap unitless F +T10 10-day running mean of 2-m temperature K F +TAF canopy air temperature K F +TAUX zonal surface stress kg/m/s^2 T +TAUY meridional surface stress kg/m/s^2 T +TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T +TBUILD internal urban building air temperature K T +TBUILD_MAX prescribed maximum interior building temperature K F +TEMPAVG_T2M temporary average 2m air temperature K F +TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F +TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F +TEQ 2 m Equiv Temp K T +TEQ_R Rural 2 m Equiv Temp K T +TEQ_U Urban 2 m Equiv Temp K T +TFLOOR floor temperature K F +TG ground temperature K T +TG_ICE ground temperature (ice landunits only) K F +TG_R Rural ground temperature K F +TG_U Urban ground temperature K F +TH2OSFC surface water temperature K T +THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T +THIC 2 m Temp Hum Index Comfort C T +THIC_R Rural 2 m Temp Hum Index Comfort C T +THIC_U Urban 2 m Temp Hum Index Comfort C T +THIP 2 m Temp Hum Index Physiology C T +THIP_R Rural 2 m Temp Hum Index Physiology C T +THIP_U Urban 2 m Temp Hum Index Physiology C T +TKE1 top lake level eddy thermal conductivity W/(mK) T +TLAI total projected leaf area index m^2/m^2 T +TLAKE lake temperature K T +TOPO_COL column-level topographic height m F +TOPO_COL_ICE column-level topographic height (ice landunits only) m F +TOPO_FORC topograephic height sent to GLC m F +TOPT topt coefficient for VOC calc non F +TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T +TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +TOTCOLN total column-level N, excluding product pools gN/m^2 T +TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T +TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T +TOTFIRE total ecosystem fire losses gC/m^2/s F +TOTLITC total litter carbon gC/m^2 T +TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T +TOTLITN total litter N gN/m^2 T +TOTLITN_1m total litter N to 1 meter gN/m^2 T +TOTPFTC total patch-level carbon, including cpool gC/m^2 T +TOTPFTN total patch-level nitrogen gN/m^2 T +TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T +TOTSOMC total soil organic matter carbon gC/m^2 T +TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T +TOTSOMN total soil organic matter N gN/m^2 T +TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T +TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T +TOTVEGN total vegetation nitrogen gN/m^2 T +TOT_WOODPRODC total wood product C gC/m^2 T +TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T +TOT_WOODPRODN total wood product N gN/m^2 T +TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T +TPU25T canopy profile of tpu umol/m2/s T +TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F +TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F +TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F +TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F +TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F +TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F +TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F +TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F +TREFMNAV daily minimum of average 2-m temperature K T +TREFMNAV_R Rural daily minimum of average 2-m temperature K F +TREFMNAV_U Urban daily minimum of average 2-m temperature K F +TREFMXAV daily maximum of average 2-m temperature K T +TREFMXAV_R Rural daily maximum of average 2-m temperature K F +TREFMXAV_U Urban daily maximum of average 2-m temperature K F +TROOF_INNER roof inside surface temperature K F +TSA 2m air temperature K T +TSAI total projected stem area index m^2/m^2 T +TSA_ICE 2m air temperature (ice landunits only) K F +TSA_R Rural 2m air temperature K F +TSA_U Urban 2m air temperature K F +TSHDW_INNER shadewall inside surface temperature K F +TSKIN skin temperature K T +TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +TSOI soil temperature (natural vegetated and crop landunits only) K T +TSOI_10CM soil temperature in top 10cm of soil K T +TSOI_ICE soil temperature (ice landunits only) K T +TSRF_FORC surface temperature sent to GLC K F +TSUNW_INNER sunwall inside surface temperature K F +TV vegetation temperature K T +TV24 vegetation temperature (last 24hrs) K F +TV240 vegetation temperature (last 240hrs) K F +TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F +TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F +TWS total water storage mm T +T_SCALAR temperature inhibition of decomposition unitless T +Tair atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F +U10 10-m wind m/s T +U10_DUST 10-m wind for dust model m/s T +U10_ICE 10-m wind (ice landunits only) m/s F +UAF canopy air speed m/s F +ULRAD upward longwave radiation above the canopy W/m^2 F +UM wind speed plus stability effect m/s F +URBAN_AC urban air conditioning flux W/m^2 T +URBAN_HEAT urban heating flux W/m^2 T +USTAR aerodynamical resistance s/m F +UST_LAKE friction velocity (lakes only) m/s F +VA atmospheric wind speed plus convective velocity m/s F +VCMX25T canopy profile of vcmax25 umol/m2/s T +VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T +VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T +VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T +VOCFLXT total VOC flux into atmosphere moles/m2/sec F +VOLR river channel total water storage m3 T +VOLRMCH river channel main channel water storage m3 T +VPD vpd Pa F +VPD2M 2m vapor pressure deficit Pa T +VPD_CAN canopy vapor pressure deficit kPa T +Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T +WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +WBA 2 m Wet Bulb C T +WBA_R Rural 2 m Wet Bulb C T +WBA_U Urban 2 m Wet Bulb C T +WBT 2 m Stull Wet Bulb C T +WBT_R Rural 2 m Stull Wet Bulb C T +WBT_U Urban 2 m Stull Wet Bulb C T +WF soil water as frac. of whc for top 0.05 m proportion F +WFPS WFPS percent F +WIND atmospheric wind velocity magnitude m/s T +WOODC wood C gC/m^2 T +WOODC_ALLOC wood C eallocation gC/m^2/s T +WOODC_LOSS wood C loss gC/m^2/s T +WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T +WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T +WTGQ surface tracer conductance m/s T +W_SCALAR Moisture (dryness) inhibition of decomposition unitless T +Wind atmospheric wind velocity magnitude m/s F +XSMRPOOL temporary photosynthate C pool gC/m^2 T +XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F +XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T +Z0HG roughness length over ground, sensible heat m F +Z0HV roughness length over vegetation, sensible heat m F +Z0M momentum roughness length m F +Z0MG roughness length over ground, momentum m F +Z0MV roughness length over vegetation, momentum m F +Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F +Z0QG roughness length over ground, latent heat m F +Z0QV roughness length over vegetation, latent heat m F +ZBOT atmospheric reference height m T +ZETA dimensionless stability parameter unitless F +ZII convective boundary height m F +ZWT water table depth (natural vegetated and crop landunits only) m T +ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T +ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T +anaerobic_frac anaerobic_frac m3/m3 F +bsw clap and hornberger B unitless F +currentPatch currentPatch coefficient for VOC calc non F +diffus diffusivity m^2/s F +fr_WFPS fr_WFPS fraction F +n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F +num_iter number of iterations unitless F +r_psi r_psi m F +ratio_k1 ratio_k1 none F +ratio_no3_co2 ratio_no3_co2 ratio F +soil_bulkdensity soil_bulkdensity kg/m3 F +soil_co2_prod soil_co2_prod ug C / g soil / day F +watfc water field capacity m^3/m^3 F +watsat water saturated m^3/m^3 F ==== =================================== ============================================================================================== ================================================================= ======= From b4b8ff3dbd59e14ca77f455019f6d2a0a9d51fae Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 14:29:18 -0600 Subject: [PATCH 1118/2067] Added new variables to master_list_nofates.rst --- .../master_list_nofates.rst | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst index eeec0810c8..3bdb33297d 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst @@ -426,12 +426,16 @@ GDD1020 Twenty year average of growing degree days b GDD8 Growing degree days base 8C from planting ddays F GDD820 Twenty year average of growing degree days base 8C from planting ddays F GDDACCUM Accumulated growing degree days past planting date for crop ddays F +GDDACCUM_PERHARV For each crop harvest in a calendar year, accumulated growing degree days past planting date ddays F GDDHARV Growing degree days (gdd) needed to harvest ddays F +GDDHARV_PERHARV For each harvest in a calendar year,For each harvest in a calendar year, growing degree days (gdd) needed to harvest ddays F GDDTSOI Growing degree-days from planting (top two soil layers) ddays F GPP gross primary production gC/m^2/s T GR total growth respiration gC/m^2/s T GRAINC grain C (does not equal yield) gC/m^2 T GRAINC_TO_FOOD grain C to food gC/m^2/s T +GRAINC_TO_FOOD_ANN total grain C to food in all harvests in a calendar year gC/m^2 F +GRAINC_TO_FOOD_PERHARV grain C to food for each harvest in a calendar year gC/m^2 F GRAINC_TO_SEED grain C to seed gC/m^2/s T GRAINN grain N gN/m^2 T GRESP_STORAGE growth respiration storage gC/m^2 F @@ -449,6 +453,7 @@ H2OSNO snow depth (liquid water) H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F H2OSNO_TOP mass of snow in top snow layer kg/m2 T H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HARVEST_REASON_PERHARV For each harvest in a calendar year, the reason the crop was harvested categorical F HBOT canopy bottom m F HEAT_CONTENT1 initial gridcell total heat content J/m^2 T HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F @@ -462,6 +467,7 @@ HR total heterotrophic respiration HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T HTOP canopy top m T HUI crop heat unit index ddays F +HUI_PERHARV For each harvest in a calendar year, crop heat unit index ddays F HUMIDEX 2 m Humidex C T HUMIDEX_R Rural 2 m Humidex C T HUMIDEX_U Urban 2 m Humidex C T @@ -977,6 +983,8 @@ Rnet net radiation SABG solar rad absorbed by ground W/m^2 T SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T SABV solar rad absorbed by veg W/m^2 T +SDATES Crop sowing dates in each calendar year day of year (julian day) F +SDATES_PERHARV For each harvest in a calendar year, the Julian day the crop was sown day of year (julian day) F SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T @@ -1106,6 +1114,8 @@ SOM_ADV_COEF advection term for vertical SOM translocatio SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F +SOWING_REASON For each sowing in a calendar year, the reason the crop was sown categorical F +SOWING_REASON_PERHARV For each harvest in a calendar year, the reason the crop was sown categorical F SR total soil respiration (HR + root resp) gC/m^2/s T SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T @@ -1122,6 +1132,7 @@ STORVEGC stored vegetation carbon, excluding cpool STORVEGN stored vegetation nitrogen gN/m^2 T SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F +SYEARS_PERHARV For each harvest in a calendar year, the year the crop was sown year F SWBGT 2 m Simplified Wetbulb Globe Temp C T SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T From 18496f1cfac283eeef2b7ef53c4aeef6bcf74dd2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 12 Jul 2023 14:31:37 -0600 Subject: [PATCH 1119/2067] Added line numbers back to master_list_nofates.rst. --- .../master_list_nofates.rst | 2598 ++++++++--------- 1 file changed, 1299 insertions(+), 1299 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst index 3bdb33297d..979b13d697 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst @@ -13,1303 +13,1303 @@ CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Variable Name Long Description Units Active? ==== =================================== ============================================================================================== ================================================================= ======= -A10TMIN 10-day running mean of min 2-m temperature K F -A5TMIN 5-day running mean of min 2-m temperature K F -ACTUAL_IMMOB actual N immobilization gN/m^2/s T -ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F -ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F -ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F -ACT_SOMC ACT_SOM C gC/m^2 T -ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F -ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F -ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F -ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F -ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F -ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F -ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T -ACT_SOMN ACT_SOM N gN/m^2 T -ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F -ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F -ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F -ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F -ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F -ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F -ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T -ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F -ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F -AGLB Aboveground leaf biomass kg/m^2 F -AGNPP aboveground NPP gC/m^2/s T -AGSB Aboveground stem biomass kg/m^2 F -ALBD surface albedo (direct) proportion T -ALBDSF diagnostic snow-free surface albedo (direct) proportion T -ALBGRD ground albedo (direct) proportion F -ALBGRI ground albedo (indirect) proportion F -ALBI surface albedo (indirect) proportion T -ALBISF diagnostic snow-free surface albedo (indirect) proportion T -ALPHA alpha coefficient for VOC calc non F -ALT current active layer thickness m T -ALTMAX maximum annual active layer thickness m T -ALTMAX_LASTYEAR maximum prior year active layer thickness m F -ANNAVG_T2M annual average 2m air temperature K F -ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F -ANNSUM_COUNTER seconds since last annual accumulator turnover s F -ANNSUM_NPP annual sum of NPP gC/m^2/yr F -ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F -APPAR_TEMP 2 m apparent temperature C T -APPAR_TEMP_R Rural 2 m apparent temperature C T -APPAR_TEMP_U Urban 2 m apparent temperature C T -AR autotrophic respiration (MR + GR) gC/m^2/s T -ATM_TOPO atmospheric surface height m T -AVAILC C flux available for allocation gC/m^2/s F -AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F -AnnET Annual ET mm/s F -BAF_CROP fractional area burned for crop s-1 T -BAF_PEATF fractional area burned in peatland s-1 T -BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T -BETA coefficient of convective velocity none F -BGLFR background litterfall rate 1/s F -BGNPP belowground NPP gC/m^2/s T -BGTR background transfer growth rate 1/s F -BTRANMN daily minimum of transpiration beta factor unitless T -CANNAVG_T2M annual average of 2m air temperature K F -CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F -CEL_LITC CEL_LIT C gC/m^2 T -CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F -CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F -CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F -CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F -CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T -CEL_LITN CEL_LIT N gN/m^2 T -CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F -CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F -CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F -CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F -CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T -CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F -CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F -CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F -CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F -CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F -CH4PROD Gridcell total production of CH4 gC/m2/s T -CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T -CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -COL_CTRUNC column-level sink for C truncation gC/m^2 F -COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T -COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T -COL_NTRUNC column-level sink for N truncation gN/m^2 F -CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F -CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F -CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T -CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T -COST_NACTIVE Cost of active uptake gN/gC T -COST_NFIX Cost of fixation gN/gC T -COST_NRETRANS Cost of retranslocation gN/gC T -COSZEN cosine of solar zenith angle none F -CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T -CPOOL temporary photosynthate C pool gC/m^2 T -CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F -CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F -CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F -CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F -CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F -CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F -CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F -CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F -CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F -CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F -CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F -CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F -CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F -CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F -CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F -CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F -CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F -CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F -CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F -CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F -CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F -CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F -CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F -CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F -CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F -CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F -CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T -CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T -CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T -CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T -CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T -CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F -CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F -CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F -CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F -CWDC CWD C gC/m^2 T -CWDC_1m CWD C to 1 meter gC/m^2 F -CWDC_HR cwd C heterotrophic respiration gC/m^2/s F -CWDC_LOSS coarse woody debris C loss gC/m^2/s T -CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F -CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F -CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F -CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F -CWDC_vr CWD C (vertically resolved) gC/m^3 T -CWDN CWD N gN/m^2 T -CWDN_1m CWD N to 1 meter gN/m^2 F -CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F -CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F -CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F -CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F -CWDN_vr CWD N (vertically resolved) gN/m^3 T -CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F -CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F -CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F -CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F -C_ALLOMETRY C allocation index none F -DAYL daylength s F -DAYS_ACTIVE number of days since last dormancy days F -DEADCROOTC dead coarse root C gC/m^2 T -DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F -DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F -DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F -DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F -DEADCROOTN dead coarse root N gN/m^2 T -DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F -DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F -DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F -DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F -DEADSTEMC dead stem C gC/m^2 T -DEADSTEMC_STORAGE dead stem C storage gC/m^2 F -DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F -DEADSTEMC_XFER dead stem C transfer gC/m^2 F -DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F -DEADSTEMN dead stem N gN/m^2 T -DEADSTEMN_STORAGE dead stem N storage gN/m^2 F -DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F -DEADSTEMN_XFER dead stem N transfer gN/m^2 F -DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F -DENIT total rate of denitrification gN/m^2/s T -DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F -DISCOI 2 m Discomfort Index C T -DISCOIS 2 m Stull Discomfort Index C T -DISCOIS_R Rural 2 m Stull Discomfort Index C T -DISCOIS_U Urban 2 m Stull Discomfort Index C T -DISCOI_R Rural 2 m Discomfort Index C T -DISCOI_U Urban 2 m Discomfort Index C T -DISPLA displacement height m F -DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T -DISPVEGN displayed vegetation nitrogen gN/m^2 T -DLRAD downward longwave radiation below the canopy W/m^2 F -DORMANT_FLAG dormancy flag none F -DOWNREG fractional reduction in GPP due to N limitation proportion F -DPVLTRB1 turbulent deposition velocity 1 m/s F -DPVLTRB2 turbulent deposition velocity 2 m/s F -DPVLTRB3 turbulent deposition velocity 3 m/s F -DPVLTRB4 turbulent deposition velocity 4 m/s F -DSL dry surface layer thickness mm T -DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T -DSTFLXT total surface dust emission kg/m2/s T -DT_VEG change in t_veg, last iteration K F -DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T -DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T -DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F -DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T -DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F -DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T -DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T -DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F -DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F -DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F -DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F -DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F -DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F -DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F -DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F -DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F -DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F -DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F -DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F -DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F -DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F -DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F -DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F -DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F -DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F -DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T -DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F -DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T -DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F -DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T -DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F -DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T -DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T -DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F -DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -EFF_POROSITY effective porosity = porosity - vol_ice proportion F -EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T -EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T -EFLX_GNET net heat flux into ground W/m^2 F -EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T -EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T -EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F -EFLX_LH_TOT_R Rural total evaporation W/m^2 T -EFLX_LH_TOT_U Urban total evaporation W/m^2 F -EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F -ELAI exposed one-sided leaf area index m^2/m^2 T -EMG ground emissivity proportion F -EMV vegetation emissivity proportion F -EOPT Eopt coefficient for VOC calc non F -EPT 2 m Equiv Pot Temp K T -EPT_R Rural 2 m Equiv Pot Temp K T -EPT_U Urban 2 m Equiv Pot Temp K T -ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T -ERRH2O total water conservation error mm T -ERRH2OSNO imbalance in snow depth (liquid water) mm T -ERRSEB surface energy conservation error W/m^2 T -ERRSOI soil/lake energy conservation error W/m^2 T -ERRSOL solar radiation conservation error W/m^2 T -ESAI exposed one-sided stem area index m^2/m^2 T -EXCESSC_MR excess C maintenance respiration gC/m^2/s F -EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F -FAREA_BURNED timestep fractional area burned s-1 T -FCANSNO fraction of canopy that is wet proportion F -FCEV canopy evaporation W/m^2 T -FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T -FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T -FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T -FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F -FCOV fractional impermeable area unitless T -FCTR canopy transpiration W/m^2 T -FDRY fraction of foliage that is green and dry proportion F -FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F -FERT_COUNTER time left to fertilize seconds F -FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F -FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T -FGEV ground evaporation W/m^2 T -FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T -FGR12 heat flux between soil layers 1 and 2 W/m^2 T -FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F -FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F -FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F -FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F -FH2OSFC fraction of ground covered by surface water unitless T -FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F -FINUNDATED fractional inundated area of vegetated columns unitless T -FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F -FIRA net infrared (longwave) radiation W/m^2 T -FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRA_R Rural net infrared (longwave) radiation W/m^2 T -FIRA_U Urban net infrared (longwave) radiation W/m^2 F -FIRE emitted infrared (longwave) radiation W/m^2 T -FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T -FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F -FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T -FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F -FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F -FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F -FPI fraction of potential immobilization proportion T -FPI_vr fraction of potential immobilization proportion F -FPSN photosynthesis umol m-2 s-1 T -FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F -FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F -FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F -FPSN_WP Product-limited photosynthesis umol m-2 s-1 F -FRAC_ICEOLD fraction of ice relative to the tot water proportion F -FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T -FROOTC fine root C gC/m^2 T -FROOTC_ALLOC fine root C allocation gC/m^2/s T -FROOTC_LOSS fine root C loss gC/m^2/s T -FROOTC_STORAGE fine root C storage gC/m^2 F -FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F -FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F -FROOTC_XFER fine root C transfer gC/m^2 F -FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F -FROOTN fine root N gN/m^2 T -FROOTN_STORAGE fine root N storage gN/m^2 F -FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F -FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F -FROOTN_XFER fine root N transfer gN/m^2 F -FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F -FROOT_MR fine root maintenance respiration gC/m^2/s F -FROOT_PROF profile for litter C and N inputs from fine roots 1/m F -FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F -FSA absorbed solar radiation W/m^2 T -FSAT fractional area with water table at surface unitless T -FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F -FSA_R Rural absorbed solar radiation W/m^2 F -FSA_U Urban absorbed solar radiation W/m^2 F -FSD24 direct radiation (last 24hrs) K F -FSD240 direct radiation (last 240hrs) K F -FSDS atmospheric incident solar radiation W/m^2 T -FSDSND direct nir incident solar radiation W/m^2 T -FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T -FSDSNI diffuse nir incident solar radiation W/m^2 T -FSDSVD direct vis incident solar radiation W/m^2 T -FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T -FSDSVI diffuse vis incident solar radiation W/m^2 T -FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T -FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T -FSH_G sensible heat from ground W/m^2 T -FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F -FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T -FSH_R Rural sensible heat W/m^2 T -FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T -FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T -FSH_U Urban sensible heat W/m^2 F -FSH_V sensible heat from veg W/m^2 T -FSI24 indirect radiation (last 24hrs) K F -FSI240 indirect radiation (last 240hrs) K F -FSM snow melt heat flux W/m^2 T -FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F -FSM_R Rural snow melt heat flux W/m^2 F -FSM_U Urban snow melt heat flux W/m^2 F -FSNO fraction of ground covered by snow unitless T -FSNO_EFF effective fraction of ground covered by snow unitless T -FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F -FSR reflected solar radiation W/m^2 T -FSRND direct nir reflected solar radiation W/m^2 T -FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T -FSRNI diffuse nir reflected solar radiation W/m^2 T -FSRSF reflected solar radiation W/m^2 T -FSRSFND direct nir reflected solar radiation W/m^2 T -FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T -FSRSFNI diffuse nir reflected solar radiation W/m^2 T -FSRSFVD direct vis reflected solar radiation W/m^2 T -FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T -FSRSFVI diffuse vis reflected solar radiation W/m^2 T -FSRVD direct vis reflected solar radiation W/m^2 T -FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T -FSRVI diffuse vis reflected solar radiation W/m^2 T -FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F -FSUN sunlit fraction of canopy proportion F -FSUN24 fraction sunlit (last 24hrs) K F -FSUN240 fraction sunlit (last 240hrs) K F -FUELC fuel load gC/m^2 T -FV friction velocity m/s T -FWET fraction of canopy that is wet proportion F -F_DENIT denitrification flux gN/m^2/s T -F_DENIT_BASE F_DENIT_BASE gN/m^3/s F -F_DENIT_vr denitrification flux gN/m^3/s F -F_N2O_DENIT denitrification N2O flux gN/m^2/s T -F_N2O_NIT nitrification N2O flux gN/m^2/s T -F_NIT nitrification flux gN/m^2/s T -F_NIT_vr nitrification flux gN/m^3/s F -FireComp_BC fire emissions flux of BC kg/m2/sec F -FireComp_OC fire emissions flux of OC kg/m2/sec F -FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F -FireEmis_TOT Total fire emissions flux gC/m2/sec F -FireEmis_ZTOP Top of vertical fire emissions distribution m F -FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F -FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F -FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F -GAMMA total gamma for VOC calc non F -GAMMAA gamma A for VOC calc non F -GAMMAC gamma C for VOC calc non F -GAMMAL gamma L for VOC calc non F -GAMMAP gamma P for VOC calc non F -GAMMAS gamma S for VOC calc non F -GAMMAT gamma T for VOC calc non F -GDD0 Growing degree days base 0C from planting ddays F -GDD020 Twenty year average of growing degree days base 0C from planting ddays F -GDD10 Growing degree days base 10C from planting ddays F -GDD1020 Twenty year average of growing degree days base 10C from planting ddays F -GDD8 Growing degree days base 8C from planting ddays F -GDD820 Twenty year average of growing degree days base 8C from planting ddays F -GDDACCUM Accumulated growing degree days past planting date for crop ddays F -GDDACCUM_PERHARV For each crop harvest in a calendar year, accumulated growing degree days past planting date ddays F -GDDHARV Growing degree days (gdd) needed to harvest ddays F -GDDHARV_PERHARV For each harvest in a calendar year,For each harvest in a calendar year, growing degree days (gdd) needed to harvest ddays F -GDDTSOI Growing degree-days from planting (top two soil layers) ddays F -GPP gross primary production gC/m^2/s T -GR total growth respiration gC/m^2/s T -GRAINC grain C (does not equal yield) gC/m^2 T -GRAINC_TO_FOOD grain C to food gC/m^2/s T -GRAINC_TO_FOOD_ANN total grain C to food in all harvests in a calendar year gC/m^2 F -GRAINC_TO_FOOD_PERHARV grain C to food for each harvest in a calendar year gC/m^2 F -GRAINC_TO_SEED grain C to seed gC/m^2/s T -GRAINN grain N gN/m^2 T -GRESP_STORAGE growth respiration storage gC/m^2 F -GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F -GRESP_XFER growth respiration transfer gC/m^2 F -GROSS_NMIN gross rate of N mineralization gN/m^2/s T -GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F -GSSHA shaded leaf stomatal conductance umol H20/m2/s T -GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T -GSSUN sunlit leaf stomatal conductance umol H20/m2/s T -GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T -H2OCAN intercepted water mm T -H2OSFC surface water depth mm T -H2OSNO snow depth (liquid water) mm T -H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F -H2OSNO_TOP mass of snow in top snow layer kg/m2 T -H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T -HARVEST_REASON_PERHARV For each harvest in a calendar year, the reason the crop was harvested categorical F -HBOT canopy bottom m F -HEAT_CONTENT1 initial gridcell total heat content J/m^2 T -HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F -HEAT_CONTENT2 post land cover change total heat content J/m^2 F -HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T -HIA 2 m NWS Heat Index C T -HIA_R Rural 2 m NWS Heat Index C T -HIA_U Urban 2 m NWS Heat Index C T -HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F -HR total heterotrophic respiration gC/m^2/s T -HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T -HTOP canopy top m T -HUI crop heat unit index ddays F -HUI_PERHARV For each harvest in a calendar year, crop heat unit index ddays F -HUMIDEX 2 m Humidex C T -HUMIDEX_R Rural 2 m Humidex C T -HUMIDEX_U Urban 2 m Humidex C T -ICE_CONTENT1 initial gridcell total ice content mm T -ICE_CONTENT2 post land cover change total ice content mm F -ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F -INIT_GPP GPP flux before downregulation gC/m^2/s F -INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F -INT_SNOW_ICE accumulated swe (ice landunits only) mm F -IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T -JMX25T canopy profile of jmax umol/m2/s T -Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T -KROOT root conductance each soil layer 1/s F -KSOIL soil conductance in each soil layer 1/s F -K_ACT_SOM active soil organic potential loss coefficient 1/s F -K_CEL_LIT cellulosic litter potential loss coefficient 1/s F -K_CWD coarse woody debris potential loss coefficient 1/s F -K_LIG_LIT lignin litter potential loss coefficient 1/s F -K_MET_LIT metabolic litter potential loss coefficient 1/s F -K_NITR K_NITR 1/s F -K_NITR_H2O K_NITR_H2O unitless F -K_NITR_PH K_NITR_PH unitless F -K_NITR_T K_NITR_T unitless F -K_PAS_SOM passive soil organic potential loss coefficient 1/s F -K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F -LAI240 240hr average of leaf area index m^2/m^2 F -LAISHA shaded projected leaf area index m^2/m^2 T -LAISUN sunlit projected leaf area index m^2/m^2 T -LAKEICEFRAC lake layer ice mass fraction unitless F -LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T -LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T -LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T -LATBASET latitude vary base temperature for gddplant degree C F -LEAFC leaf C gC/m^2 T -LEAFCN Leaf CN ratio used for flexible CN gC/gN T -LEAFCN_OFFSET Leaf C:N used by FUN unitless F -LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F -LEAFC_ALLOC leaf C allocation gC/m^2/s T -LEAFC_CHANGE C change in leaf gC/m^2/s T -LEAFC_LOSS leaf C loss gC/m^2/s T -LEAFC_STORAGE leaf C storage gC/m^2 F -LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F -LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F -LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T -LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F -LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T -LEAFC_XFER leaf C transfer gC/m^2 F -LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F -LEAFN leaf N gN/m^2 T -LEAFN_STORAGE leaf N storage gN/m^2 F -LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F -LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F -LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T -LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F -LEAFN_XFER leaf N transfer gN/m^2 F -LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F -LEAF_MR leaf maintenance respiration gC/m^2/s T -LEAF_PROF profile for litter C and N inputs from leaves 1/m F -LFC2 conversion area fraction of BET and BDT that burned per sec T -LGSF long growing season factor proportion F -LIG_LITC LIG_LIT C gC/m^2 T -LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F -LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F -LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F -LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F -LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T -LIG_LITN LIG_LIT N gN/m^2 T -LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F -LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F -LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F -LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F -LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T -LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F -LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F -LIQCAN intercepted liquid water mm T -LIQUID_CONTENT1 initial gridcell total liq content mm T -LIQUID_CONTENT2 post landuse change gridcell total liq content mm F -LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F -LITFALL litterfall (leaves and fine roots) gC/m^2/s T -LITFIRE litter fire losses gC/m^2/s F -LITTERC_HR litter C heterotrophic respiration gC/m^2/s T -LITTERC_LOSS litter C loss gC/m^2/s T -LIVECROOTC live coarse root C gC/m^2 T -LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F -LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F -LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F -LIVECROOTC_XFER live coarse root C transfer gC/m^2 F -LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F -LIVECROOTN live coarse root N gN/m^2 T -LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F -LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F -LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F -LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F -LIVECROOTN_XFER live coarse root N transfer gN/m^2 F -LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F -LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F -LIVESTEMC live stem C gC/m^2 T -LIVESTEMC_STORAGE live stem C storage gC/m^2 F -LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F -LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T -LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F -LIVESTEMC_XFER live stem C transfer gC/m^2 F -LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F -LIVESTEMN live stem N gN/m^2 T -LIVESTEMN_STORAGE live stem N storage gN/m^2 F -LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F -LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F -LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F -LIVESTEMN_XFER live stem N transfer gN/m^2 F -LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F -LIVESTEM_MR live stem maintenance respiration gC/m^2/s F -LNC leaf N concentration gN leaf/m^2 T -LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F -LWup upwelling longwave radiation W/m^2 F -MEG_acetaldehyde MEGAN flux kg/m2/sec T -MEG_acetic_acid MEGAN flux kg/m2/sec T -MEG_acetone MEGAN flux kg/m2/sec T -MEG_carene_3 MEGAN flux kg/m2/sec T -MEG_ethanol MEGAN flux kg/m2/sec T -MEG_formaldehyde MEGAN flux kg/m2/sec T -MEG_isoprene MEGAN flux kg/m2/sec T -MEG_methanol MEGAN flux kg/m2/sec T -MEG_pinene_a MEGAN flux kg/m2/sec T -MEG_thujene_a MEGAN flux kg/m2/sec T -MET_LITC MET_LIT C gC/m^2 T -MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F -MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F -MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F -MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F -MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T -MET_LITN MET_LIT N gN/m^2 T -MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F -MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F -MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F -MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F -MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T -MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F -MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F -MR maintenance respiration gC/m^2/s T -M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F -M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F -M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F -M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F -M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F -M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F -M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F -M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F -M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F -M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F -M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F -M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F -M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F -M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F -M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F -M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F -M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F -M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F -M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F -M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F -M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F -M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F -M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F -M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F -M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F -M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F -M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F -M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F -M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F -M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F -M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F -M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F -M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F -M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F -M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F -M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F -M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F -M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F -M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F -M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F -M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F -M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F -M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F -M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F -M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F -M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F -M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F -M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F -M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F -M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F -M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F -M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F -M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F -M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F -M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F -M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F -M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F -M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F -M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F -M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F -M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F -M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F -M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F -M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F -M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F -M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F -M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F -M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F -M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F -M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F -M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F -M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F -M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F -M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F -M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F -M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F -M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F -M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F -M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F -M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F -M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F -M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F -M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F -M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F -M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F -M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F -M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F -M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F -M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F -M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F -M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F -M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F -M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F -M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F -M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F -M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F -M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F -M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F -M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F -M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F -M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F -M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F -M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F -M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F -M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F -M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F -M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F -M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F -M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F -M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F -M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F -M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F -M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F -M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F -M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F -M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F -M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F -M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F -M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F -M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F -M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F -M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F -M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F -M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F -M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F -M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F -M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F -M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F -M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F -M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F -M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F -M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F -NACTIVE Mycorrhizal N uptake flux gN/m^2/s T -NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T -NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T -NAM AM-associated N uptake flux gN/m^2/s T -NAM_NH4 AM-associated N uptake flux gN/m^2/s T -NAM_NO3 AM-associated N uptake flux gN/m^2/s T -NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T -NDEPLOY total N deployed in new growth gN/m^2/s T -NDEP_PROF profile for atmospheric N deposition 1/m F -NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T -NECM ECM-associated N uptake flux gN/m^2/s T -NECM_NH4 ECM-associated N uptake flux gN/m^2/s T -NECM_NO3 ECM-associated N uptake flux gN/m^2/s T -NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T -NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T -NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T -NET_NMIN net rate of N mineralization gN/m^2/s T -NET_NMIN_vr net rate of N mineralization gN/m^3/s F -NFERTILIZATION fertilizer added gN/m^2/s T -NFIRE fire counts valid only in Reg.C counts/km2/sec T -NFIX Symbiotic BNF uptake flux gN/m^2/s T -NFIXATION_PROF profile for biological N fixation 1/m F -NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F -NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T -NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T -NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T -NPASSIVE Passive N uptake flux gN/m^2/s T -NPOOL temporary plant N pool gN/m^2 T -NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F -NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F -NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F -NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F -NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F -NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F -NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F -NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F -NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F -NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F -NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F -NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F -NPP net primary production gC/m^2/s T -NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F -NPP_GROWTH Total C used for growth in FUN gC/m^2/s T -NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T -NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T -NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T -NPP_NAM AM-associated N uptake used C gC/m^2/s T -NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T -NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T -NPP_NECM ECM-associated N uptake used C gC/m^2/s T -NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T -NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T -NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T -NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T -NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T -NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T -NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T -NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T -NRETRANS Retranslocated N uptake flux gN/m^2/s T -NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T -NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T -NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T -NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F -NUPTAKE Total N uptake of FUN gN/m^2/s T -NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T -N_ALLOMETRY N allocation index none F -O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F -OBU Monin-Obukhov length m F -OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T -OFFSET_COUNTER offset days counter days F -OFFSET_FDD offset freezing degree days counter C degree-days F -OFFSET_FLAG offset flag none F -OFFSET_SWI offset soil water index none F -ONSET_COUNTER onset days counter days F -ONSET_FDD onset freezing degree days counter C degree-days F -ONSET_FLAG onset flag none F -ONSET_GDD onset growing degree days C degree-days F -ONSET_GDDFLAG onset flag for growing degree day sum none F -ONSET_SWI onset soil water index none F -O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T -PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F -PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F -PAR240_shade shade PAR (240 hrs) umol/m2/s F -PAR240_sun sunlit PAR (240 hrs) umol/m2/s F -PAR24_shade shade PAR (24 hrs) umol/m2/s F -PAR24_sun sunlit PAR (24 hrs) umol/m2/s F -PARVEGLN absorbed par by vegetation at local noon W/m^2 T -PAR_shade shade PAR umol/m2/s F -PAR_sun sunlit PAR umol/m2/s F -PAS_SOMC PAS_SOM C gC/m^2 T -PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F -PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F -PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F -PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F -PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T -PAS_SOMN PAS_SOM N gN/m^2 T -PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F -PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F -PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F -PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F -PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T -PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F -PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F -PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T -PBOT_240 10 day running mean of air pressure Pa F -PCH4 atmospheric partial pressure of CH4 Pa T -PCO2 atmospheric partial pressure of CO2 Pa T -PCO2_240 10 day running mean of CO2 pressure Pa F -PFT_CTRUNC patch-level sink for C truncation gC/m^2 F -PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T -PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T -PFT_NTRUNC patch-level sink for N truncation gN/m^2 F -PLANTCN Plant C:N used by FUN unitless F -PLANT_CALLOC total allocated C flux gC/m^2/s F -PLANT_NALLOC total allocated N flux gN/m^2/s F -PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T -PNLCZ Proportion of nitrogen allocated for light capture unitless F -PO2_240 10 day running mean of O2 pressure Pa F -POTENTIAL_IMMOB potential N immobilization gN/m^2/s T -POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F -POT_F_DENIT potential denitrification flux gN/m^2/s T -POT_F_DENIT_vr potential denitrification flux gN/m^3/s F -POT_F_NIT potential nitrification flux gN/m^2/s T -POT_F_NIT_vr potential nitrification flux gN/m^3/s F -PREC10 10-day running mean of PREC MM H2O/S F -PREC60 60-day running mean of PREC MM H2O/S F -PREV_DAYL daylength from previous timestep s F -PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F -PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F -PROD100C 100-yr wood product C gC/m^2 F -PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F -PROD100N 100-yr wood product N gN/m^2 F -PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F -PROD10C 10-yr wood product C gC/m^2 F -PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F -PROD10N 10-yr wood product N gN/m^2 F -PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F -PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T -PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T -PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T -PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T -PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F -Q2M 2m specific humidity kg/kg T -QAF canopy air humidity kg/kg F -QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T -QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F -QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F -QDRAI sub-surface drainage mm/s T -QDRAI_PERCH perched wt drainage mm/s T -QDRAI_XS saturation excess drainage mm/s T -QDRIP rate of excess canopy liquid falling off canopy mm/s F -QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F -QFLOOD runoff from river flooding mm/s T -QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T -QFLX_EVAP_VEG vegetation evaporation mm H2O/s F -QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T -QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T -QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T -QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T -QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F -QFLX_SNOW_DRAIN drainage from snow pack mm/s T -QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T -QFLX_SNOW_GRND snow on ground after interception mm H2O/s F -QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T -QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T -QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F -QH2OSFC surface water runoff mm/s T -QH2OSFC_TO_ICE surface water converted to ice mm/s F -QHR hydraulic redistribution mm/s T -QICE ice growth/melt mm/s T -QICE_FORC qice forcing sent to GLC mm/s F -QICE_FRZ ice growth mm/s T -QICE_MELT ice melt mm/s T -QINFL infiltration mm/s T -QINTR interception mm/s T -QIRRIG_DEMAND irrigation demand mm/s F -QIRRIG_DRIP water added via drip irrigation mm/s F -QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T -QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T -QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T -QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F -QOVER total surface runoff (includes QH2OSFC) mm/s T -QOVER_LAG time-lagged surface runoff for soil columns mm/s F -QPHSNEG net negative hydraulic redistribution flux mm/s F -QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T -QROOTSINK water flux from soil to root in each soil-layer mm/s F -QRUNOFF total liquid runoff not including correction for land use change mm/s T -QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T -QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T -QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F -QRUNOFF_R Rural total runoff mm/s F -QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T -QRUNOFF_U Urban total runoff mm/s F -QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T -QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T -QSNOFRZ column-integrated snow freezing rate kg/m2/s T -QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T -QSNOMELT snow melt rate mm/s T -QSNOMELT_ICE snow melt (ice landunits only) mm/s T -QSNOUNLOAD canopy snow unloading mm/s T -QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T -QSNO_WINDUNLOAD canopy snow wind unloading mm/s T -QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T -QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T -QSOIL_ICE Ground evaporation (ice landunits only) mm/s T -QTOPSOIL water input to surface mm/s F -QVEGE canopy evaporation mm/s T -QVEGT canopy transpiration mm/s T -Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F -Qh sensible heat W/m^2 F -Qle total evaporation W/m^2 F -Qstor storage heat flux (includes snowmelt) W/m^2 F -Qtau momentum flux kg/m/s^2 F -RAH1 aerodynamical resistance s/m F -RAH2 aerodynamical resistance s/m F -RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T -RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T -RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -RAM1 aerodynamical resistance s/m F -RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F -RAW1 aerodynamical resistance s/m F -RAW2 aerodynamical resistance s/m F -RB leaf boundary resistance s/m F -RB10 10 day running mean boundary layer resistance s/m F -RETRANSN plant pool of retranslocated N gN/m^2 T -RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T -RH atmospheric relative humidity % F -RH2M 2m relative humidity % T -RH2M_R Rural 2m specific humidity % F -RH2M_U Urban 2m relative humidity % F -RH30 30-day running mean of relative humidity % F -RHAF fractional humidity of canopy air fraction F -RHAF10 10 day running mean of fractional humidity of canopy air fraction F -RH_LEAF fractional humidity at leaf surface fraction F -ROOTR effective fraction of roots in each soil layer (SMS method) proportion F -RR root respiration (fine root MR + total root GR) gC/m^2/s T -RRESIS root resistance in each soil layer proportion F -RSSHA shaded leaf stomatal resistance s/m T -RSSUN sunlit leaf stomatal resistance s/m T -Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F -Rnet net radiation W/m^2 F -SABG solar rad absorbed by ground W/m^2 T -SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T -SABV solar rad absorbed by veg W/m^2 T -SDATES Crop sowing dates in each calendar year day of year (julian day) F -SDATES_PERHARV For each harvest in a calendar year, the Julian day the crop was sown day of year (julian day) F -SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T -SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T -SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T -SLO_SOMC SLO_SOM C gC/m^2 T -SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F -SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F -SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F -SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F -SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F -SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F -SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T -SLO_SOMN SLO_SOM N gN/m^2 T -SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F -SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F -SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F -SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F -SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F -SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F -SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T -SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F -SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F -SMINN soil mineral N gN/m^2 T -SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T -SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T -SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T -SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F -SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -SMINN_vr soil mineral N gN/m^3 T -SMIN_NH4 soil mineral NH4 gN/m^2 T -SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F -SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T -SMIN_NO3 soil mineral NO3 gN/m^2 T -SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T -SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F -SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F -SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T -SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F -SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F -SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T -SMP soil matric potential (natural vegetated and crop landunits only) mm T -SNOBCMCL mass of BC in snow column kg/m2 T -SNOBCMSL mass of BC in top snow layer kg/m2 T -SNOCAN intercepted snow mm T -SNODSTMCL mass of dust in snow column kg/m2 T -SNODSTMSL mass of dust in top snow layer kg/m2 T -SNOFSDSND direct nir incident solar radiation on snow W/m^2 F -SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F -SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F -SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F -SNOFSRND direct nir reflected solar radiation from snow W/m^2 T -SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T -SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T -SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T -SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T -SNOLIQFL top snow layer liquid water fraction (land) fraction F -SNOOCMCL mass of OC in snow column kg/m2 T -SNOOCMSL mass of OC in top snow layer kg/m2 T -SNORDSL top snow layer effective grain radius m^-6 F -SNOTTOPL snow temperature (top layer) K F -SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F -SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T -SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F -SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T -SNOWDP gridcell mean snow height m T -SNOWICE snow ice kg/m2 T -SNOWICE_ICE snow ice (ice landunits only) kg/m2 F -SNOWLIQ snow liquid water kg/m2 T -SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F -SNOW_5D 5day snow avg m F -SNOW_DEPTH snow height of snow covered area m T -SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F -SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T -SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T -SNOW_SINKS snow sinks (liquid water) mm/s T -SNOW_SOURCES snow sources (liquid water) mm/s T -SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F -SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F -SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F -SNO_FRZ snow freezing rate in each snow layer kg/m2/s F -SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F -SNO_GS Mean snow grain size Microns F -SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F -SNO_ICE Snow ice content kg/m2 F -SNO_LIQH2O Snow liquid water content kg/m2 F -SNO_MELT snow melt rate in each snow layer mm/s F -SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F -SNO_T Snow temperatures K F -SNO_TK Thermal conductivity W/m-K F -SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F -SNO_T_ICE Snow temperatures (ice landunits only) K F -SNO_Z Snow layer thicknesses m F -SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F -SNOdTdzL top snow layer temperature gradient (land) K/m F -SOIL10 10-day running mean of 12cm layer soil K F -SOILC_CHANGE C change in soil gC/m^2/s T -SOILC_HR soil C heterotrophic respiration gC/m^2/s T -SOILC_vr SOIL C (vertically resolved) gC/m^3 T -SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T -SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T -SOILN_vr SOIL N (vertically resolved) gN/m^3 T -SOILPSI soil water potential in each soil layer MPa F -SOILRESIS soil resistance to evaporation s/m T -SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T -SOMC_FIRE C loss due to peat burning gC/m^2/s T -SOMFIRE soil organic matter fire losses gC/m^2/s F -SOM_ADV_COEF advection term for vertical SOM translocation m/s F -SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T -SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F -SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -SOWING_REASON For each sowing in a calendar year, the reason the crop was sown categorical F -SOWING_REASON_PERHARV For each harvest in a calendar year, the reason the crop was sown categorical F -SR total soil respiration (HR + root resp) gC/m^2/s T -SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T -SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T -SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T -SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T -SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T -SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T -SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T -STEM_PROF profile for litter C and N inputs from stems 1/m F -STORAGE_CDEMAND C use from the C storage pool gC/m^2 F -STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F -STORAGE_NDEMAND N demand during the offset period gN/m^2 F -STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T -STORVEGN stored vegetation nitrogen gN/m^2 T -SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T -SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -SYEARS_PERHARV For each harvest in a calendar year, the year the crop was sown year F -SWBGT 2 m Simplified Wetbulb Globe Temp C T -SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T -SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -SWMP65 2 m Swamp Cooler Temp 65% Eff C T -SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T -SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T -SWMP80 2 m Swamp Cooler Temp 80% Eff C T -SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T -SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T -SWdown atmospheric incident solar radiation W/m^2 F -SWup upwelling shortwave radiation W/m^2 F -SoilAlpha factor limiting ground evap unitless F -SoilAlpha_U urban factor limiting ground evap unitless F -T10 10-day running mean of 2-m temperature K F -TAF canopy air temperature K F -TAUX zonal surface stress kg/m/s^2 T -TAUY meridional surface stress kg/m/s^2 T -TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T -TBUILD internal urban building air temperature K T -TBUILD_MAX prescribed maximum interior building temperature K F -TEMPAVG_T2M temporary average 2m air temperature K F -TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F -TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F -TEQ 2 m Equiv Temp K T -TEQ_R Rural 2 m Equiv Temp K T -TEQ_U Urban 2 m Equiv Temp K T -TFLOOR floor temperature K F -TG ground temperature K T -TG_ICE ground temperature (ice landunits only) K F -TG_R Rural ground temperature K F -TG_U Urban ground temperature K F -TH2OSFC surface water temperature K T -THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -THIC 2 m Temp Hum Index Comfort C T -THIC_R Rural 2 m Temp Hum Index Comfort C T -THIC_U Urban 2 m Temp Hum Index Comfort C T -THIP 2 m Temp Hum Index Physiology C T -THIP_R Rural 2 m Temp Hum Index Physiology C T -THIP_U Urban 2 m Temp Hum Index Physiology C T -TKE1 top lake level eddy thermal conductivity W/(mK) T -TLAI total projected leaf area index m^2/m^2 T -TLAKE lake temperature K T -TOPO_COL column-level topographic height m F -TOPO_COL_ICE column-level topographic height (ice landunits only) m F -TOPO_FORC topograephic height sent to GLC m F -TOPT topt coefficient for VOC calc non F -TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T -TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T -TOTCOLN total column-level N, excluding product pools gN/m^2 T -TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T -TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T -TOTFIRE total ecosystem fire losses gC/m^2/s F -TOTLITC total litter carbon gC/m^2 T -TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T -TOTLITN total litter N gN/m^2 T -TOTLITN_1m total litter N to 1 meter gN/m^2 T -TOTPFTC total patch-level carbon, including cpool gC/m^2 T -TOTPFTN total patch-level nitrogen gN/m^2 T -TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T -TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T -TOTSOMC total soil organic matter carbon gC/m^2 T -TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T -TOTSOMN total soil organic matter N gN/m^2 T -TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T -TOTVEGN total vegetation nitrogen gN/m^2 T -TOT_WOODPRODC total wood product C gC/m^2 T -TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T -TOT_WOODPRODN total wood product N gN/m^2 T -TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T -TPU25T canopy profile of tpu umol/m2/s T -TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F -TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F -TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F -TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F -TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F -TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F -TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F -TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F -TREFMNAV daily minimum of average 2-m temperature K T -TREFMNAV_R Rural daily minimum of average 2-m temperature K F -TREFMNAV_U Urban daily minimum of average 2-m temperature K F -TREFMXAV daily maximum of average 2-m temperature K T -TREFMXAV_R Rural daily maximum of average 2-m temperature K F -TREFMXAV_U Urban daily maximum of average 2-m temperature K F -TROOF_INNER roof inside surface temperature K F -TSA 2m air temperature K T -TSAI total projected stem area index m^2/m^2 T -TSA_ICE 2m air temperature (ice landunits only) K F -TSA_R Rural 2m air temperature K F -TSA_U Urban 2m air temperature K F -TSHDW_INNER shadewall inside surface temperature K F -TSKIN skin temperature K T -TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -TSOI soil temperature (natural vegetated and crop landunits only) K T -TSOI_10CM soil temperature in top 10cm of soil K T -TSOI_ICE soil temperature (ice landunits only) K T -TSRF_FORC surface temperature sent to GLC K F -TSUNW_INNER sunwall inside surface temperature K F -TV vegetation temperature K T -TV24 vegetation temperature (last 24hrs) K F -TV240 vegetation temperature (last 240hrs) K F -TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F -TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F -TWS total water storage mm T -T_SCALAR temperature inhibition of decomposition unitless T -Tair atmospheric air temperature (downscaled to columns in glacier regions) K F -Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F -U10 10-m wind m/s T -U10_DUST 10-m wind for dust model m/s T -U10_ICE 10-m wind (ice landunits only) m/s F -UAF canopy air speed m/s F -ULRAD upward longwave radiation above the canopy W/m^2 F -UM wind speed plus stability effect m/s F -URBAN_AC urban air conditioning flux W/m^2 T -URBAN_HEAT urban heating flux W/m^2 T -USTAR aerodynamical resistance s/m F -UST_LAKE friction velocity (lakes only) m/s F -VA atmospheric wind speed plus convective velocity m/s F -VCMX25T canopy profile of vcmax25 umol/m2/s T -VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T -VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T -VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T -VOCFLXT total VOC flux into atmosphere moles/m2/sec F -VOLR river channel total water storage m3 T -VOLRMCH river channel main channel water storage m3 T -VPD vpd Pa F -VPD2M 2m vapor pressure deficit Pa T -VPD_CAN canopy vapor pressure deficit kPa T -Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T -WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -WBA 2 m Wet Bulb C T -WBA_R Rural 2 m Wet Bulb C T -WBA_U Urban 2 m Wet Bulb C T -WBT 2 m Stull Wet Bulb C T -WBT_R Rural 2 m Stull Wet Bulb C T -WBT_U Urban 2 m Stull Wet Bulb C T -WF soil water as frac. of whc for top 0.05 m proportion F -WFPS WFPS percent F -WIND atmospheric wind velocity magnitude m/s T -WOODC wood C gC/m^2 T -WOODC_ALLOC wood C eallocation gC/m^2/s T -WOODC_LOSS wood C loss gC/m^2/s T -WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T -WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T -WTGQ surface tracer conductance m/s T -W_SCALAR Moisture (dryness) inhibition of decomposition unitless T -Wind atmospheric wind velocity magnitude m/s F -XSMRPOOL temporary photosynthate C pool gC/m^2 T -XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F -XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T -Z0HG roughness length over ground, sensible heat m F -Z0HV roughness length over vegetation, sensible heat m F -Z0M momentum roughness length m F -Z0MG roughness length over ground, momentum m F -Z0MV roughness length over vegetation, momentum m F -Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -Z0QG roughness length over ground, latent heat m F -Z0QV roughness length over vegetation, latent heat m F -ZBOT atmospheric reference height m T -ZETA dimensionless stability parameter unitless F -ZII convective boundary height m F -ZWT water table depth (natural vegetated and crop landunits only) m T -ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T -ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T -anaerobic_frac anaerobic_frac m3/m3 F -bsw clap and hornberger B unitless F -currentPatch currentPatch coefficient for VOC calc non F -diffus diffusivity m^2/s F -fr_WFPS fr_WFPS fraction F -n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F -num_iter number of iterations unitless F -r_psi r_psi m F -ratio_k1 ratio_k1 none F -ratio_no3_co2 ratio_no3_co2 ratio F -soil_bulkdensity soil_bulkdensity kg/m3 F -soil_co2_prod soil_co2_prod ug C / g soil / day F -watfc water field capacity m^3/m^3 F -watsat water saturated m^3/m^3 F + 1 A10TMIN 10-day running mean of min 2-m temperature K F + 2 A5TMIN 5-day running mean of min 2-m temperature K F + 3 ACTUAL_IMMOB actual N immobilization gN/m^2/s T + 4 ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F + 5 ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F + 6 ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F + 7 ACT_SOMC ACT_SOM C gC/m^2 T + 8 ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F + 9 ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F + 10 ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F + 11 ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F + 12 ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F + 13 ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F + 14 ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T + 15 ACT_SOMN ACT_SOM N gN/m^2 T + 16 ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F + 17 ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F + 18 ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F + 19 ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F + 20 ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F + 21 ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F + 22 ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T + 23 ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F + 24 ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F + 25 ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F + 26 ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F + 27 AGLB Aboveground leaf biomass kg/m^2 F + 28 AGNPP aboveground NPP gC/m^2/s T + 29 AGSB Aboveground stem biomass kg/m^2 F + 30 ALBD surface albedo (direct) proportion T + 31 ALBDSF diagnostic snow-free surface albedo (direct) proportion T + 32 ALBGRD ground albedo (direct) proportion F + 33 ALBGRI ground albedo (indirect) proportion F + 34 ALBI surface albedo (indirect) proportion T + 35 ALBISF diagnostic snow-free surface albedo (indirect) proportion T + 36 ALPHA alpha coefficient for VOC calc non F + 37 ALT current active layer thickness m T + 38 ALTMAX maximum annual active layer thickness m T + 39 ALTMAX_LASTYEAR maximum prior year active layer thickness m F + 40 ANNAVG_T2M annual average 2m air temperature K F + 41 ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F + 42 ANNSUM_COUNTER seconds since last annual accumulator turnover s F + 43 ANNSUM_NPP annual sum of NPP gC/m^2/yr F + 44 ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F + 45 APPAR_TEMP 2 m apparent temperature C T + 46 APPAR_TEMP_R Rural 2 m apparent temperature C T + 47 APPAR_TEMP_U Urban 2 m apparent temperature C T + 48 AR autotrophic respiration (MR + GR) gC/m^2/s T + 49 ATM_TOPO atmospheric surface height m T + 50 AVAILC C flux available for allocation gC/m^2/s F + 51 AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F + 52 AnnET Annual ET mm/s F + 53 BAF_CROP fractional area burned for crop s-1 T + 54 BAF_PEATF fractional area burned in peatland s-1 T + 55 BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T + 56 BETA coefficient of convective velocity none F + 57 BGLFR background litterfall rate 1/s F + 58 BGNPP belowground NPP gC/m^2/s T + 59 BGTR background transfer growth rate 1/s F + 60 BTRANMN daily minimum of transpiration beta factor unitless T + 61 CANNAVG_T2M annual average of 2m air temperature K F + 62 CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F + 63 CEL_LITC CEL_LIT C gC/m^2 T + 64 CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F + 65 CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F + 66 CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F + 67 CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F + 68 CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T + 69 CEL_LITN CEL_LIT N gN/m^2 T + 70 CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F + 71 CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F + 72 CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F + 73 CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F + 74 CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T + 75 CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F + 76 CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F + 77 CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F + 78 CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F + 79 CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F + 80 CH4PROD Gridcell total production of CH4 gC/m2/s T + 81 CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F + 82 CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F + 83 CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T + 84 CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T + 85 CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T + 86 CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T + 87 CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T + 88 CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T + 89 COL_CTRUNC column-level sink for C truncation gC/m^2 F + 90 COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T + 91 COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T + 92 COL_NTRUNC column-level sink for N truncation gN/m^2 F + 93 CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F + 94 CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F + 95 CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T + 96 CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T + 97 COST_NACTIVE Cost of active uptake gN/gC T + 98 COST_NFIX Cost of fixation gN/gC T + 99 COST_NRETRANS Cost of retranslocation gN/gC T + 100 COSZEN cosine of solar zenith angle none F + 101 CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T + 102 CPOOL temporary photosynthate C pool gC/m^2 T + 103 CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F + 104 CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F + 105 CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F + 106 CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F + 107 CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F + 108 CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F + 109 CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F + 110 CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F + 111 CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F + 112 CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F + 113 CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F + 114 CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F + 115 CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F + 116 CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F + 117 CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F + 118 CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F + 119 CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F + 120 CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F + 121 CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F + 122 CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F + 123 CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F + 124 CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F + 125 CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F + 126 CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F + 127 CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F + 128 CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F + 129 CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T + 130 CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T + 131 CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T + 132 CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T + 133 CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T + 134 CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F + 135 CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F + 136 CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F + 137 CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F + 138 CWDC CWD C gC/m^2 T + 139 CWDC_1m CWD C to 1 meter gC/m^2 F + 140 CWDC_HR cwd C heterotrophic respiration gC/m^2/s F + 141 CWDC_LOSS coarse woody debris C loss gC/m^2/s T + 142 CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F + 143 CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F + 144 CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F + 145 CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F + 146 CWDC_vr CWD C (vertically resolved) gC/m^3 T + 147 CWDN CWD N gN/m^2 T + 148 CWDN_1m CWD N to 1 meter gN/m^2 F + 149 CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F + 150 CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F + 151 CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F + 152 CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F + 153 CWDN_vr CWD N (vertically resolved) gN/m^3 T + 154 CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F + 155 CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F + 156 CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F + 157 CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F + 158 C_ALLOMETRY C allocation index none F + 159 DAYL daylength s F + 160 DAYS_ACTIVE number of days since last dormancy days F + 161 DEADCROOTC dead coarse root C gC/m^2 T + 162 DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F + 163 DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F + 164 DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F + 165 DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F + 166 DEADCROOTN dead coarse root N gN/m^2 T + 167 DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F + 168 DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F + 169 DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F + 170 DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F + 171 DEADSTEMC dead stem C gC/m^2 T + 172 DEADSTEMC_STORAGE dead stem C storage gC/m^2 F + 173 DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F + 174 DEADSTEMC_XFER dead stem C transfer gC/m^2 F + 175 DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F + 176 DEADSTEMN dead stem N gN/m^2 T + 177 DEADSTEMN_STORAGE dead stem N storage gN/m^2 F + 178 DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F + 179 DEADSTEMN_XFER dead stem N transfer gN/m^2 F + 180 DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F + 181 DENIT total rate of denitrification gN/m^2/s T + 182 DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F + 183 DISCOI 2 m Discomfort Index C T + 184 DISCOIS 2 m Stull Discomfort Index C T + 185 DISCOIS_R Rural 2 m Stull Discomfort Index C T + 186 DISCOIS_U Urban 2 m Stull Discomfort Index C T + 187 DISCOI_R Rural 2 m Discomfort Index C T + 188 DISCOI_U Urban 2 m Discomfort Index C T + 189 DISPLA displacement height m F + 190 DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T + 191 DISPVEGN displayed vegetation nitrogen gN/m^2 T + 192 DLRAD downward longwave radiation below the canopy W/m^2 F + 193 DORMANT_FLAG dormancy flag none F + 194 DOWNREG fractional reduction in GPP due to N limitation proportion F + 195 DPVLTRB1 turbulent deposition velocity 1 m/s F + 196 DPVLTRB2 turbulent deposition velocity 2 m/s F + 197 DPVLTRB3 turbulent deposition velocity 3 m/s F + 198 DPVLTRB4 turbulent deposition velocity 4 m/s F + 199 DSL dry surface layer thickness mm T + 200 DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T + 201 DSTFLXT total surface dust emission kg/m2/s T + 202 DT_VEG change in t_veg, last iteration K F + 203 DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T + 204 DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T + 205 DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F + 206 DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T + 207 DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F + 208 DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T + 209 DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T + 210 DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F + 211 DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F + 212 DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F + 213 DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F + 214 DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F + 215 DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F + 216 DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F + 217 DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F + 218 DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F + 219 DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F + 220 DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F + 221 DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F + 222 DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F + 223 DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F + 224 DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F + 225 DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F + 226 DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F + 227 DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F + 228 DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T + 229 DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F + 230 DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T + 231 DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F + 232 DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T + 233 DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F + 234 DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T + 235 DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T + 236 DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F + 237 DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F + 238 DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F + 239 DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F + 240 DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F + 241 DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F + 242 EFF_POROSITY effective porosity = porosity - vol_ice proportion F + 243 EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T + 244 EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T + 245 EFLX_GNET net heat flux into ground W/m^2 F + 246 EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T + 247 EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T + 248 EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F + 249 EFLX_LH_TOT_R Rural total evaporation W/m^2 T + 250 EFLX_LH_TOT_U Urban total evaporation W/m^2 F + 251 EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F + 252 ELAI exposed one-sided leaf area index m^2/m^2 T + 253 EMG ground emissivity proportion F + 254 EMV vegetation emissivity proportion F + 255 EOPT Eopt coefficient for VOC calc non F + 256 EPT 2 m Equiv Pot Temp K T + 257 EPT_R Rural 2 m Equiv Pot Temp K T + 258 EPT_U Urban 2 m Equiv Pot Temp K T + 259 ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T + 260 ERRH2O total water conservation error mm T + 261 ERRH2OSNO imbalance in snow depth (liquid water) mm T + 262 ERRSEB surface energy conservation error W/m^2 T + 263 ERRSOI soil/lake energy conservation error W/m^2 T + 264 ERRSOL solar radiation conservation error W/m^2 T + 265 ESAI exposed one-sided stem area index m^2/m^2 T + 266 EXCESSC_MR excess C maintenance respiration gC/m^2/s F + 267 EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F + 268 FAREA_BURNED timestep fractional area burned s-1 T + 269 FCANSNO fraction of canopy that is wet proportion F + 270 FCEV canopy evaporation W/m^2 T + 271 FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T + 272 FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T + 273 FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T + 274 FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F + 275 FCOV fractional impermeable area unitless T + 276 FCTR canopy transpiration W/m^2 T + 277 FDRY fraction of foliage that is green and dry proportion F + 278 FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F + 279 FERT_COUNTER time left to fertilize seconds F + 280 FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F + 281 FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T + 282 FGEV ground evaporation W/m^2 T + 283 FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T + 284 FGR12 heat flux between soil layers 1 and 2 W/m^2 T + 285 FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F + 286 FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F + 287 FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F + 288 FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F + 289 FH2OSFC fraction of ground covered by surface water unitless T + 290 FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F + 291 FINUNDATED fractional inundated area of vegetated columns unitless T + 292 FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F + 293 FIRA net infrared (longwave) radiation W/m^2 T + 294 FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F + 295 FIRA_R Rural net infrared (longwave) radiation W/m^2 T + 296 FIRA_U Urban net infrared (longwave) radiation W/m^2 F + 297 FIRE emitted infrared (longwave) radiation W/m^2 T + 298 FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F + 299 FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T + 300 FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F + 301 FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T + 302 FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F + 303 FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F + 304 FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F + 305 FPI fraction of potential immobilization proportion T + 306 FPI_vr fraction of potential immobilization proportion F + 307 FPSN photosynthesis umol m-2 s-1 T + 308 FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F + 309 FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F + 310 FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F + 311 FPSN_WP Product-limited photosynthesis umol m-2 s-1 F + 312 FRAC_ICEOLD fraction of ice relative to the tot water proportion F + 313 FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T + 314 FROOTC fine root C gC/m^2 T + 315 FROOTC_ALLOC fine root C allocation gC/m^2/s T + 316 FROOTC_LOSS fine root C loss gC/m^2/s T + 317 FROOTC_STORAGE fine root C storage gC/m^2 F + 318 FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F + 319 FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F + 320 FROOTC_XFER fine root C transfer gC/m^2 F + 321 FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F + 322 FROOTN fine root N gN/m^2 T + 323 FROOTN_STORAGE fine root N storage gN/m^2 F + 324 FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F + 325 FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F + 326 FROOTN_XFER fine root N transfer gN/m^2 F + 327 FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F + 328 FROOT_MR fine root maintenance respiration gC/m^2/s F + 329 FROOT_PROF profile for litter C and N inputs from fine roots 1/m F + 330 FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F + 331 FSA absorbed solar radiation W/m^2 T + 332 FSAT fractional area with water table at surface unitless T + 333 FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F + 334 FSA_R Rural absorbed solar radiation W/m^2 F + 335 FSA_U Urban absorbed solar radiation W/m^2 F + 336 FSD24 direct radiation (last 24hrs) K F + 337 FSD240 direct radiation (last 240hrs) K F + 338 FSDS atmospheric incident solar radiation W/m^2 T + 339 FSDSND direct nir incident solar radiation W/m^2 T + 340 FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T + 341 FSDSNI diffuse nir incident solar radiation W/m^2 T + 342 FSDSVD direct vis incident solar radiation W/m^2 T + 343 FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T + 344 FSDSVI diffuse vis incident solar radiation W/m^2 T + 345 FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T + 346 FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T + 347 FSH_G sensible heat from ground W/m^2 T + 348 FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F + 349 FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T + 350 FSH_R Rural sensible heat W/m^2 T + 351 FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T + 352 FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T + 353 FSH_U Urban sensible heat W/m^2 F + 354 FSH_V sensible heat from veg W/m^2 T + 355 FSI24 indirect radiation (last 24hrs) K F + 356 FSI240 indirect radiation (last 240hrs) K F + 357 FSM snow melt heat flux W/m^2 T + 358 FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F + 359 FSM_R Rural snow melt heat flux W/m^2 F + 360 FSM_U Urban snow melt heat flux W/m^2 F + 361 FSNO fraction of ground covered by snow unitless T + 362 FSNO_EFF effective fraction of ground covered by snow unitless T + 363 FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F + 364 FSR reflected solar radiation W/m^2 T + 365 FSRND direct nir reflected solar radiation W/m^2 T + 366 FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T + 367 FSRNI diffuse nir reflected solar radiation W/m^2 T + 368 FSRSF reflected solar radiation W/m^2 T + 369 FSRSFND direct nir reflected solar radiation W/m^2 T + 370 FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T + 371 FSRSFNI diffuse nir reflected solar radiation W/m^2 T + 372 FSRSFVD direct vis reflected solar radiation W/m^2 T + 373 FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T + 374 FSRSFVI diffuse vis reflected solar radiation W/m^2 T + 375 FSRVD direct vis reflected solar radiation W/m^2 T + 376 FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T + 377 FSRVI diffuse vis reflected solar radiation W/m^2 T + 378 FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F + 379 FSUN sunlit fraction of canopy proportion F + 380 FSUN24 fraction sunlit (last 24hrs) K F + 381 FSUN240 fraction sunlit (last 240hrs) K F + 382 FUELC fuel load gC/m^2 T + 383 FV friction velocity m/s T + 384 FWET fraction of canopy that is wet proportion F + 385 F_DENIT denitrification flux gN/m^2/s T + 386 F_DENIT_BASE F_DENIT_BASE gN/m^3/s F + 387 F_DENIT_vr denitrification flux gN/m^3/s F + 388 F_N2O_DENIT denitrification N2O flux gN/m^2/s T + 389 F_N2O_NIT nitrification N2O flux gN/m^2/s T + 390 F_NIT nitrification flux gN/m^2/s T + 391 F_NIT_vr nitrification flux gN/m^3/s F + 392 FireComp_BC fire emissions flux of BC kg/m2/sec F + 393 FireComp_OC fire emissions flux of OC kg/m2/sec F + 394 FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F + 395 FireEmis_TOT Total fire emissions flux gC/m2/sec F + 396 FireEmis_ZTOP Top of vertical fire emissions distribution m F + 397 FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F + 398 FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F + 399 FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F + 400 GAMMA total gamma for VOC calc non F + 401 GAMMAA gamma A for VOC calc non F + 402 GAMMAC gamma C for VOC calc non F + 403 GAMMAL gamma L for VOC calc non F + 404 GAMMAP gamma P for VOC calc non F + 405 GAMMAS gamma S for VOC calc non F + 406 GAMMAT gamma T for VOC calc non F + 407 GDD0 Growing degree days base 0C from planting ddays F + 408 GDD020 Twenty year average of growing degree days base 0C from planting ddays F + 409 GDD10 Growing degree days base 10C from planting ddays F + 410 GDD1020 Twenty year average of growing degree days base 10C from planting ddays F + 411 GDD8 Growing degree days base 8C from planting ddays F + 412 GDD820 Twenty year average of growing degree days base 8C from planting ddays F + 413 GDDACCUM Accumulated growing degree days past planting date for crop ddays F + 414 GDDACCUM_PERHARV For each crop harvest in a calendar year, accumulated growing degree days past planting date ddays F + 415 GDDHARV Growing degree days (gdd) needed to harvest ddays F + 416 GDDHARV_PERHARV For each harvest in a calendar year,For each harvest in a calendar year, growing degree days (gdd) needed to harvest ddays F + 417 GDDTSOI Growing degree-days from planting (top two soil layers) ddays F + 418 GPP gross primary production gC/m^2/s T + 419 GR total growth respiration gC/m^2/s T + 420 GRAINC grain C (does not equal yield) gC/m^2 T + 421 GRAINC_TO_FOOD grain C to food gC/m^2/s T + 422 GRAINC_TO_FOOD_ANN total grain C to food in all harvests in a calendar year gC/m^2 F + 423 GRAINC_TO_FOOD_PERHARV grain C to food for each harvest in a calendar year gC/m^2 F + 424 GRAINC_TO_SEED grain C to seed gC/m^2/s T + 425 GRAINN grain N gN/m^2 T + 426 GRESP_STORAGE growth respiration storage gC/m^2 F + 427 GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F + 428 GRESP_XFER growth respiration transfer gC/m^2 F + 429 GROSS_NMIN gross rate of N mineralization gN/m^2/s T + 430 GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F + 431 GSSHA shaded leaf stomatal conductance umol H20/m2/s T + 432 GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T + 433 GSSUN sunlit leaf stomatal conductance umol H20/m2/s T + 434 GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T + 435 H2OCAN intercepted water mm T + 436 H2OSFC surface water depth mm T + 437 H2OSNO snow depth (liquid water) mm T + 438 H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F + 439 H2OSNO_TOP mass of snow in top snow layer kg/m2 T + 440 H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T + 441 HARVEST_REASON_PERHARV For each harvest in a calendar year, the reason the crop was harvested categorical F + 442 HBOT canopy bottom m F + 443 HEAT_CONTENT1 initial gridcell total heat content J/m^2 T + 444 HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F + 445 HEAT_CONTENT2 post land cover change total heat content J/m^2 F + 446 HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T + 447 HIA 2 m NWS Heat Index C T + 448 HIA_R Rural 2 m NWS Heat Index C T + 449 HIA_U Urban 2 m NWS Heat Index C T + 450 HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F + 451 HR total heterotrophic respiration gC/m^2/s T + 452 HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T + 453 HTOP canopy top m T + 454 HUI crop heat unit index ddays F + 455 HUI_PERHARV For each harvest in a calendar year, crop heat unit index ddays F + 456 HUMIDEX 2 m Humidex C T + 457 HUMIDEX_R Rural 2 m Humidex C T + 458 HUMIDEX_U Urban 2 m Humidex C T + 459 ICE_CONTENT1 initial gridcell total ice content mm T + 460 ICE_CONTENT2 post land cover change total ice content mm F + 461 ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F + 462 INIT_GPP GPP flux before downregulation gC/m^2/s F + 463 INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F + 464 INT_SNOW_ICE accumulated swe (ice landunits only) mm F + 465 IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T + 466 JMX25T canopy profile of jmax umol/m2/s T + 467 Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T + 468 KROOT root conductance each soil layer 1/s F + 469 KSOIL soil conductance in each soil layer 1/s F + 470 K_ACT_SOM active soil organic potential loss coefficient 1/s F + 471 K_CEL_LIT cellulosic litter potential loss coefficient 1/s F + 472 K_CWD coarse woody debris potential loss coefficient 1/s F + 473 K_LIG_LIT lignin litter potential loss coefficient 1/s F + 474 K_MET_LIT metabolic litter potential loss coefficient 1/s F + 475 K_NITR K_NITR 1/s F + 476 K_NITR_H2O K_NITR_H2O unitless F + 477 K_NITR_PH K_NITR_PH unitless F + 478 K_NITR_T K_NITR_T unitless F + 479 K_PAS_SOM passive soil organic potential loss coefficient 1/s F + 480 K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F + 481 LAI240 240hr average of leaf area index m^2/m^2 F + 482 LAISHA shaded projected leaf area index m^2/m^2 T + 483 LAISUN sunlit projected leaf area index m^2/m^2 T + 484 LAKEICEFRAC lake layer ice mass fraction unitless F + 485 LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T + 486 LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T + 487 LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T + 488 LATBASET latitude vary base temperature for gddplant degree C F + 489 LEAFC leaf C gC/m^2 T + 490 LEAFCN Leaf CN ratio used for flexible CN gC/gN T + 491 LEAFCN_OFFSET Leaf C:N used by FUN unitless F + 492 LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F + 493 LEAFC_ALLOC leaf C allocation gC/m^2/s T + 494 LEAFC_CHANGE C change in leaf gC/m^2/s T + 495 LEAFC_LOSS leaf C loss gC/m^2/s T + 496 LEAFC_STORAGE leaf C storage gC/m^2 F + 497 LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F + 498 LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F + 499 LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T + 500 LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F + 501 LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T + 502 LEAFC_XFER leaf C transfer gC/m^2 F + 503 LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F + 504 LEAFN leaf N gN/m^2 T + 505 LEAFN_STORAGE leaf N storage gN/m^2 F + 506 LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F + 507 LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F + 508 LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T + 509 LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F + 510 LEAFN_XFER leaf N transfer gN/m^2 F + 511 LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F + 512 LEAF_MR leaf maintenance respiration gC/m^2/s T + 513 LEAF_PROF profile for litter C and N inputs from leaves 1/m F + 514 LFC2 conversion area fraction of BET and BDT that burned per sec T + 515 LGSF long growing season factor proportion F + 516 LIG_LITC LIG_LIT C gC/m^2 T + 517 LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F + 518 LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F + 519 LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F + 520 LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F + 521 LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T + 522 LIG_LITN LIG_LIT N gN/m^2 T + 523 LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F + 524 LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F + 525 LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F + 526 LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F + 527 LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T + 528 LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F + 529 LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F + 530 LIQCAN intercepted liquid water mm T + 531 LIQUID_CONTENT1 initial gridcell total liq content mm T + 532 LIQUID_CONTENT2 post landuse change gridcell total liq content mm F + 533 LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F + 534 LITFALL litterfall (leaves and fine roots) gC/m^2/s T + 535 LITFIRE litter fire losses gC/m^2/s F + 536 LITTERC_HR litter C heterotrophic respiration gC/m^2/s T + 537 LITTERC_LOSS litter C loss gC/m^2/s T + 538 LIVECROOTC live coarse root C gC/m^2 T + 539 LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F + 540 LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F + 541 LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F + 542 LIVECROOTC_XFER live coarse root C transfer gC/m^2 F + 543 LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F + 544 LIVECROOTN live coarse root N gN/m^2 T + 545 LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F + 546 LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F + 547 LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F + 548 LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F + 549 LIVECROOTN_XFER live coarse root N transfer gN/m^2 F + 550 LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F + 551 LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F + 552 LIVESTEMC live stem C gC/m^2 T + 553 LIVESTEMC_STORAGE live stem C storage gC/m^2 F + 554 LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F + 555 LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T + 556 LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F + 557 LIVESTEMC_XFER live stem C transfer gC/m^2 F + 558 LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F + 559 LIVESTEMN live stem N gN/m^2 T + 560 LIVESTEMN_STORAGE live stem N storage gN/m^2 F + 561 LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F + 562 LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F + 563 LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F + 564 LIVESTEMN_XFER live stem N transfer gN/m^2 F + 565 LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F + 566 LIVESTEM_MR live stem maintenance respiration gC/m^2/s F + 567 LNC leaf N concentration gN leaf/m^2 T + 568 LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F + 569 LWup upwelling longwave radiation W/m^2 F + 570 MEG_acetaldehyde MEGAN flux kg/m2/sec T + 571 MEG_acetic_acid MEGAN flux kg/m2/sec T + 572 MEG_acetone MEGAN flux kg/m2/sec T + 573 MEG_carene_3 MEGAN flux kg/m2/sec T + 574 MEG_ethanol MEGAN flux kg/m2/sec T + 575 MEG_formaldehyde MEGAN flux kg/m2/sec T + 576 MEG_isoprene MEGAN flux kg/m2/sec T + 577 MEG_methanol MEGAN flux kg/m2/sec T + 578 MEG_pinene_a MEGAN flux kg/m2/sec T + 579 MEG_thujene_a MEGAN flux kg/m2/sec T + 580 MET_LITC MET_LIT C gC/m^2 T + 581 MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F + 582 MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F + 583 MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F + 584 MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F + 585 MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T + 586 MET_LITN MET_LIT N gN/m^2 T + 587 MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F + 588 MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F + 589 MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F + 590 MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F + 591 MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T + 592 MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F + 593 MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F + 594 MR maintenance respiration gC/m^2/s T + 595 M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F + 596 M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F + 597 M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F + 598 M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F + 599 M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F + 600 M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F + 601 M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F + 602 M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F + 603 M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F + 604 M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F + 605 M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F + 606 M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F + 607 M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F + 608 M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F + 609 M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F + 610 M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F + 611 M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F + 612 M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F + 613 M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F + 614 M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F + 615 M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F + 616 M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F + 617 M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F + 618 M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F + 619 M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F + 620 M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F + 621 M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F + 622 M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F + 623 M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F + 624 M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F + 625 M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F + 626 M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F + 627 M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F + 628 M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F + 629 M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F + 630 M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F + 631 M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F + 632 M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F + 633 M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F + 634 M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F + 635 M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F + 636 M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F + 637 M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F + 638 M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F + 639 M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F + 640 M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F + 641 M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F + 642 M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F + 643 M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F + 644 M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F + 645 M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F + 646 M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F + 647 M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F + 648 M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F + 649 M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F + 650 M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F + 651 M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F + 652 M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F + 653 M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F + 654 M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F + 655 M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F + 656 M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F + 657 M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F + 658 M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F + 659 M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F + 660 M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F + 661 M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F + 662 M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F + 663 M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F + 664 M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F + 665 M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F + 666 M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F + 667 M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F + 668 M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F + 669 M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F + 670 M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F + 671 M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F + 672 M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F + 673 M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F + 674 M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F + 675 M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F + 676 M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F + 677 M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F + 678 M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F + 679 M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F + 680 M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F + 681 M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F + 682 M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F + 683 M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F + 684 M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F + 685 M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F + 686 M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F + 687 M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F + 688 M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F + 689 M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F + 690 M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F + 691 M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F + 692 M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F + 693 M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F + 694 M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F + 695 M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F + 696 M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F + 697 M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F + 698 M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F + 699 M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F + 700 M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F + 701 M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F + 702 M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F + 703 M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F + 704 M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F + 705 M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F + 706 M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F + 707 M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F + 708 M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F + 709 M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F + 710 M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F + 711 M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F + 712 M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F + 713 M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F + 714 M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F + 715 M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F + 716 M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F + 717 M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F + 718 M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F + 719 M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F + 720 M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F + 721 M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F + 722 M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F + 723 M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F + 724 M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F + 725 M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F + 726 M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F + 727 NACTIVE Mycorrhizal N uptake flux gN/m^2/s T + 728 NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T + 729 NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T + 730 NAM AM-associated N uptake flux gN/m^2/s T + 731 NAM_NH4 AM-associated N uptake flux gN/m^2/s T + 732 NAM_NO3 AM-associated N uptake flux gN/m^2/s T + 733 NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T + 734 NDEPLOY total N deployed in new growth gN/m^2/s T + 735 NDEP_PROF profile for atmospheric N deposition 1/m F + 736 NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T + 737 NECM ECM-associated N uptake flux gN/m^2/s T + 738 NECM_NH4 ECM-associated N uptake flux gN/m^2/s T + 739 NECM_NO3 ECM-associated N uptake flux gN/m^2/s T + 740 NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T + 741 NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T + 742 NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T + 743 NET_NMIN net rate of N mineralization gN/m^2/s T + 744 NET_NMIN_vr net rate of N mineralization gN/m^3/s F + 745 NFERTILIZATION fertilizer added gN/m^2/s T + 746 NFIRE fire counts valid only in Reg.C counts/km2/sec T + 747 NFIX Symbiotic BNF uptake flux gN/m^2/s T + 748 NFIXATION_PROF profile for biological N fixation 1/m F + 749 NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F + 750 NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T + 751 NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T + 752 NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T + 753 NPASSIVE Passive N uptake flux gN/m^2/s T + 754 NPOOL temporary plant N pool gN/m^2 T + 755 NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F + 756 NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F + 757 NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F + 758 NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F + 759 NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F + 760 NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F + 761 NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F + 762 NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F + 763 NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F + 764 NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F + 765 NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F + 766 NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F + 767 NPP net primary production gC/m^2/s T + 768 NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F + 769 NPP_GROWTH Total C used for growth in FUN gC/m^2/s T + 770 NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T + 771 NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T + 772 NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T + 773 NPP_NAM AM-associated N uptake used C gC/m^2/s T + 774 NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T + 775 NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T + 776 NPP_NECM ECM-associated N uptake used C gC/m^2/s T + 777 NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T + 778 NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T + 779 NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T + 780 NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T + 781 NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T + 782 NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T + 783 NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T + 784 NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T + 785 NRETRANS Retranslocated N uptake flux gN/m^2/s T + 786 NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T + 787 NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T + 788 NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T + 789 NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F + 790 NUPTAKE Total N uptake of FUN gN/m^2/s T + 791 NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T + 792 N_ALLOMETRY N allocation index none F + 793 O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F + 794 OBU Monin-Obukhov length m F + 795 OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T + 796 OFFSET_COUNTER offset days counter days F + 797 OFFSET_FDD offset freezing degree days counter C degree-days F + 798 OFFSET_FLAG offset flag none F + 799 OFFSET_SWI offset soil water index none F + 800 ONSET_COUNTER onset days counter days F + 801 ONSET_FDD onset freezing degree days counter C degree-days F + 802 ONSET_FLAG onset flag none F + 803 ONSET_GDD onset growing degree days C degree-days F + 804 ONSET_GDDFLAG onset flag for growing degree day sum none F + 805 ONSET_SWI onset soil water index none F + 806 O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T + 807 PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F + 808 PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F + 809 PAR240_shade shade PAR (240 hrs) umol/m2/s F + 810 PAR240_sun sunlit PAR (240 hrs) umol/m2/s F + 811 PAR24_shade shade PAR (24 hrs) umol/m2/s F + 812 PAR24_sun sunlit PAR (24 hrs) umol/m2/s F + 813 PARVEGLN absorbed par by vegetation at local noon W/m^2 T + 814 PAR_shade shade PAR umol/m2/s F + 815 PAR_sun sunlit PAR umol/m2/s F + 816 PAS_SOMC PAS_SOM C gC/m^2 T + 817 PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F + 818 PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F + 819 PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F + 820 PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F + 821 PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T + 822 PAS_SOMN PAS_SOM N gN/m^2 T + 823 PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F + 824 PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F + 825 PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F + 826 PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F + 827 PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T + 828 PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F + 829 PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F + 830 PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T + 831 PBOT_240 10 day running mean of air pressure Pa F + 832 PCH4 atmospheric partial pressure of CH4 Pa T + 833 PCO2 atmospheric partial pressure of CO2 Pa T + 834 PCO2_240 10 day running mean of CO2 pressure Pa F + 835 PFT_CTRUNC patch-level sink for C truncation gC/m^2 F + 836 PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T + 837 PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T + 838 PFT_NTRUNC patch-level sink for N truncation gN/m^2 F + 839 PLANTCN Plant C:N used by FUN unitless F + 840 PLANT_CALLOC total allocated C flux gC/m^2/s F + 841 PLANT_NALLOC total allocated N flux gN/m^2/s F + 842 PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T + 843 PNLCZ Proportion of nitrogen allocated for light capture unitless F + 844 PO2_240 10 day running mean of O2 pressure Pa F + 845 POTENTIAL_IMMOB potential N immobilization gN/m^2/s T + 846 POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F + 847 POT_F_DENIT potential denitrification flux gN/m^2/s T + 848 POT_F_DENIT_vr potential denitrification flux gN/m^3/s F + 849 POT_F_NIT potential nitrification flux gN/m^2/s T + 850 POT_F_NIT_vr potential nitrification flux gN/m^3/s F + 851 PREC10 10-day running mean of PREC MM H2O/S F + 852 PREC60 60-day running mean of PREC MM H2O/S F + 853 PREV_DAYL daylength from previous timestep s F + 854 PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F + 855 PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F + 856 PROD100C 100-yr wood product C gC/m^2 F + 857 PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F + 858 PROD100N 100-yr wood product N gN/m^2 F + 859 PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F + 860 PROD10C 10-yr wood product C gC/m^2 F + 861 PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F + 862 PROD10N 10-yr wood product N gN/m^2 F + 863 PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F + 864 PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T + 865 PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T + 866 PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T + 867 PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T + 868 PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F + 869 Q2M 2m specific humidity kg/kg T + 870 QAF canopy air humidity kg/kg F + 871 QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T + 872 QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F + 873 QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F + 874 QDRAI sub-surface drainage mm/s T + 875 QDRAI_PERCH perched wt drainage mm/s T + 876 QDRAI_XS saturation excess drainage mm/s T + 877 QDRIP rate of excess canopy liquid falling off canopy mm/s F + 878 QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F + 879 QFLOOD runoff from river flooding mm/s T + 880 QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T + 881 QFLX_EVAP_VEG vegetation evaporation mm H2O/s F + 882 QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T + 883 QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T + 884 QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T + 885 QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T + 886 QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F + 887 QFLX_SNOW_DRAIN drainage from snow pack mm/s T + 888 QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T + 889 QFLX_SNOW_GRND snow on ground after interception mm H2O/s F + 890 QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T + 891 QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T + 892 QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F + 893 QH2OSFC surface water runoff mm/s T + 894 QH2OSFC_TO_ICE surface water converted to ice mm/s F + 895 QHR hydraulic redistribution mm/s T + 896 QICE ice growth/melt mm/s T + 897 QICE_FORC qice forcing sent to GLC mm/s F + 898 QICE_FRZ ice growth mm/s T + 899 QICE_MELT ice melt mm/s T + 900 QINFL infiltration mm/s T + 901 QINTR interception mm/s T + 902 QIRRIG_DEMAND irrigation demand mm/s F + 903 QIRRIG_DRIP water added via drip irrigation mm/s F + 904 QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T + 905 QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T + 906 QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T + 907 QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F + 908 QOVER total surface runoff (includes QH2OSFC) mm/s T + 909 QOVER_LAG time-lagged surface runoff for soil columns mm/s F + 910 QPHSNEG net negative hydraulic redistribution flux mm/s F + 911 QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T + 912 QROOTSINK water flux from soil to root in each soil-layer mm/s F + 913 QRUNOFF total liquid runoff not including correction for land use change mm/s T + 914 QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T + 915 QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T + 916 QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F + 917 QRUNOFF_R Rural total runoff mm/s F + 918 QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T + 919 QRUNOFF_U Urban total runoff mm/s F + 920 QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T + 921 QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T + 922 QSNOFRZ column-integrated snow freezing rate kg/m2/s T + 923 QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T + 924 QSNOMELT snow melt rate mm/s T + 925 QSNOMELT_ICE snow melt (ice landunits only) mm/s T + 926 QSNOUNLOAD canopy snow unloading mm/s T + 927 QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T + 928 QSNO_WINDUNLOAD canopy snow wind unloading mm/s T + 929 QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T + 930 QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T + 931 QSOIL_ICE Ground evaporation (ice landunits only) mm/s T + 932 QTOPSOIL water input to surface mm/s F + 933 QVEGE canopy evaporation mm/s T + 934 QVEGT canopy transpiration mm/s T + 935 Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F + 936 Qh sensible heat W/m^2 F + 937 Qle total evaporation W/m^2 F + 938 Qstor storage heat flux (includes snowmelt) W/m^2 F + 939 Qtau momentum flux kg/m/s^2 F + 940 RAH1 aerodynamical resistance s/m F + 941 RAH2 aerodynamical resistance s/m F + 942 RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T + 943 RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T + 944 RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F + 945 RAM1 aerodynamical resistance s/m F + 946 RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F + 947 RAW1 aerodynamical resistance s/m F + 948 RAW2 aerodynamical resistance s/m F + 949 RB leaf boundary resistance s/m F + 950 RB10 10 day running mean boundary layer resistance s/m F + 951 RETRANSN plant pool of retranslocated N gN/m^2 T + 952 RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T + 953 RH atmospheric relative humidity % F + 954 RH2M 2m relative humidity % T + 955 RH2M_R Rural 2m specific humidity % F + 956 RH2M_U Urban 2m relative humidity % F + 957 RH30 30-day running mean of relative humidity % F + 958 RHAF fractional humidity of canopy air fraction F + 959 RHAF10 10 day running mean of fractional humidity of canopy air fraction F + 960 RH_LEAF fractional humidity at leaf surface fraction F + 961 ROOTR effective fraction of roots in each soil layer (SMS method) proportion F + 962 RR root respiration (fine root MR + total root GR) gC/m^2/s T + 963 RRESIS root resistance in each soil layer proportion F + 964 RSSHA shaded leaf stomatal resistance s/m T + 965 RSSUN sunlit leaf stomatal resistance s/m T + 966 Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F + 967 Rnet net radiation W/m^2 F + 968 SABG solar rad absorbed by ground W/m^2 T + 969 SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T + 970 SABV solar rad absorbed by veg W/m^2 T + 971 SDATES Crop sowing dates in each calendar year day of year (julian day) F + 972 SDATES_PERHARV For each harvest in a calendar year, the Julian day the crop was sown day of year (julian day) F + 973 SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T + 974 SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T + 975 SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T + 976 SLO_SOMC SLO_SOM C gC/m^2 T + 977 SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F + 978 SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F + 979 SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F + 980 SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F + 981 SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F + 982 SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F + 983 SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T + 984 SLO_SOMN SLO_SOM N gN/m^2 T + 985 SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F + 986 SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F + 987 SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F + 988 SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F + 989 SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F + 990 SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F + 991 SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T + 992 SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F + 993 SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F + 994 SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F + 995 SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F + 996 SMINN soil mineral N gN/m^2 T + 997 SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T + 998 SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T + 999 SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T +1000 SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F +1001 SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F +1002 SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F +1003 SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F +1004 SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F +1005 SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F +1006 SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F +1007 SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +1008 SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +1009 SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +1010 SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +1011 SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +1012 SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +1013 SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +1014 SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +1015 SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +1016 SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +1017 SMINN_vr soil mineral N gN/m^3 T +1018 SMIN_NH4 soil mineral NH4 gN/m^2 T +1019 SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F +1020 SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T +1021 SMIN_NO3 soil mineral NO3 gN/m^2 T +1022 SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T +1023 SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F +1024 SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F +1025 SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T +1026 SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F +1027 SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F +1028 SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T +1029 SMP soil matric potential (natural vegetated and crop landunits only) mm T +1030 SNOBCMCL mass of BC in snow column kg/m2 T +1031 SNOBCMSL mass of BC in top snow layer kg/m2 T +1032 SNOCAN intercepted snow mm T +1033 SNODSTMCL mass of dust in snow column kg/m2 T +1034 SNODSTMSL mass of dust in top snow layer kg/m2 T +1035 SNOFSDSND direct nir incident solar radiation on snow W/m^2 F +1036 SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F +1037 SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F +1038 SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F +1039 SNOFSRND direct nir reflected solar radiation from snow W/m^2 T +1040 SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T +1041 SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T +1042 SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T +1043 SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T +1044 SNOLIQFL top snow layer liquid water fraction (land) fraction F +1045 SNOOCMCL mass of OC in snow column kg/m2 T +1046 SNOOCMSL mass of OC in top snow layer kg/m2 T +1047 SNORDSL top snow layer effective grain radius m^-6 F +1048 SNOTTOPL snow temperature (top layer) K F +1049 SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F +1050 SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +1051 SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +1052 SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +1053 SNOWDP gridcell mean snow height m T +1054 SNOWICE snow ice kg/m2 T +1055 SNOWICE_ICE snow ice (ice landunits only) kg/m2 F +1056 SNOWLIQ snow liquid water kg/m2 T +1057 SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F +1058 SNOW_5D 5day snow avg m F +1059 SNOW_DEPTH snow height of snow covered area m T +1060 SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F +1061 SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +1062 SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +1063 SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T +1064 SNOW_SINKS snow sinks (liquid water) mm/s T +1065 SNOW_SOURCES snow sources (liquid water) mm/s T +1066 SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F +1067 SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +1068 SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F +1069 SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +1070 SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F +1071 SNO_FRZ snow freezing rate in each snow layer kg/m2/s F +1072 SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F +1073 SNO_GS Mean snow grain size Microns F +1074 SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F +1075 SNO_ICE Snow ice content kg/m2 F +1076 SNO_LIQH2O Snow liquid water content kg/m2 F +1077 SNO_MELT snow melt rate in each snow layer mm/s F +1078 SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F +1079 SNO_T Snow temperatures K F +1080 SNO_TK Thermal conductivity W/m-K F +1081 SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F +1082 SNO_T_ICE Snow temperatures (ice landunits only) K F +1083 SNO_Z Snow layer thicknesses m F +1084 SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F +1085 SNOdTdzL top snow layer temperature gradient (land) K/m F +1086 SOIL10 10-day running mean of 12cm layer soil K F +1087 SOILC_CHANGE C change in soil gC/m^2/s T +1088 SOILC_HR soil C heterotrophic respiration gC/m^2/s T +1089 SOILC_vr SOIL C (vertically resolved) gC/m^3 T +1090 SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T +1091 SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T +1092 SOILN_vr SOIL N (vertically resolved) gN/m^3 T +1093 SOILPSI soil water potential in each soil layer MPa F +1094 SOILRESIS soil resistance to evaporation s/m T +1095 SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +1096 SOMC_FIRE C loss due to peat burning gC/m^2/s T +1097 SOMFIRE soil organic matter fire losses gC/m^2/s F +1098 SOM_ADV_COEF advection term for vertical SOM translocation m/s F +1099 SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T +1100 SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F +1101 SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F +1102 SOWING_REASON For each sowing in a calendar year, the reason the crop was sown categorical F +1103 SOWING_REASON_PERHARV For each harvest in a calendar year, the reason the crop was sown categorical F +1104 SR total soil respiration (HR + root resp) gC/m^2/s T +1105 SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T +1106 SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T +1107 SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T +1108 SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T +1109 SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T +1110 SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T +1111 SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T +1112 STEM_PROF profile for litter C and N inputs from stems 1/m F +1113 STORAGE_CDEMAND C use from the C storage pool gC/m^2 F +1114 STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F +1115 STORAGE_NDEMAND N demand during the offset period gN/m^2 F +1116 STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T +1117 STORVEGN stored vegetation nitrogen gN/m^2 T +1118 SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T +1119 SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F +1120 SYEARS_PERHARV For each harvest in a calendar year, the year the crop was sown year F +1121 SWBGT 2 m Simplified Wetbulb Globe Temp C T +1122 SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T +1123 SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T +1124 SWMP65 2 m Swamp Cooler Temp 65% Eff C T +1125 SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T +1126 SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T +1127 SWMP80 2 m Swamp Cooler Temp 80% Eff C T +1128 SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T +1129 SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T +1130 SWdown atmospheric incident solar radiation W/m^2 F +1131 SWup upwelling shortwave radiation W/m^2 F +1132 SoilAlpha factor limiting ground evap unitless F +1133 SoilAlpha_U urban factor limiting ground evap unitless F +1134 T10 10-day running mean of 2-m temperature K F +1135 TAF canopy air temperature K F +1136 TAUX zonal surface stress kg/m/s^2 T +1137 TAUY meridional surface stress kg/m/s^2 T +1138 TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T +1139 TBUILD internal urban building air temperature K T +1140 TBUILD_MAX prescribed maximum interior building temperature K F +1141 TEMPAVG_T2M temporary average 2m air temperature K F +1142 TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F +1143 TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F +1144 TEQ 2 m Equiv Temp K T +1145 TEQ_R Rural 2 m Equiv Temp K T +1146 TEQ_U Urban 2 m Equiv Temp K T +1147 TFLOOR floor temperature K F +1148 TG ground temperature K T +1149 TG_ICE ground temperature (ice landunits only) K F +1150 TG_R Rural ground temperature K F +1151 TG_U Urban ground temperature K F +1152 TH2OSFC surface water temperature K T +1153 THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T +1154 THIC 2 m Temp Hum Index Comfort C T +1155 THIC_R Rural 2 m Temp Hum Index Comfort C T +1156 THIC_U Urban 2 m Temp Hum Index Comfort C T +1157 THIP 2 m Temp Hum Index Physiology C T +1158 THIP_R Rural 2 m Temp Hum Index Physiology C T +1159 THIP_U Urban 2 m Temp Hum Index Physiology C T +1160 TKE1 top lake level eddy thermal conductivity W/(mK) T +1161 TLAI total projected leaf area index m^2/m^2 T +1162 TLAKE lake temperature K T +1163 TOPO_COL column-level topographic height m F +1164 TOPO_COL_ICE column-level topographic height (ice landunits only) m F +1165 TOPO_FORC topograephic height sent to GLC m F +1166 TOPT topt coefficient for VOC calc non F +1167 TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T +1168 TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +1169 TOTCOLN total column-level N, excluding product pools gN/m^2 T +1170 TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T +1171 TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T +1172 TOTFIRE total ecosystem fire losses gC/m^2/s F +1173 TOTLITC total litter carbon gC/m^2 T +1174 TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T +1175 TOTLITN total litter N gN/m^2 T +1176 TOTLITN_1m total litter N to 1 meter gN/m^2 T +1177 TOTPFTC total patch-level carbon, including cpool gC/m^2 T +1178 TOTPFTN total patch-level nitrogen gN/m^2 T +1179 TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T +1180 TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T +1181 TOTSOMC total soil organic matter carbon gC/m^2 T +1182 TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T +1183 TOTSOMN total soil organic matter N gN/m^2 T +1184 TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T +1185 TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T +1186 TOTVEGN total vegetation nitrogen gN/m^2 T +1187 TOT_WOODPRODC total wood product C gC/m^2 T +1188 TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T +1189 TOT_WOODPRODN total wood product N gN/m^2 T +1190 TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T +1191 TPU25T canopy profile of tpu umol/m2/s T +1192 TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F +1193 TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F +1194 TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F +1195 TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F +1196 TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F +1197 TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F +1198 TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F +1199 TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F +1200 TREFMNAV daily minimum of average 2-m temperature K T +1201 TREFMNAV_R Rural daily minimum of average 2-m temperature K F +1202 TREFMNAV_U Urban daily minimum of average 2-m temperature K F +1203 TREFMXAV daily maximum of average 2-m temperature K T +1204 TREFMXAV_R Rural daily maximum of average 2-m temperature K F +1205 TREFMXAV_U Urban daily maximum of average 2-m temperature K F +1206 TROOF_INNER roof inside surface temperature K F +1207 TSA 2m air temperature K T +1208 TSAI total projected stem area index m^2/m^2 T +1209 TSA_ICE 2m air temperature (ice landunits only) K F +1210 TSA_R Rural 2m air temperature K F +1211 TSA_U Urban 2m air temperature K F +1212 TSHDW_INNER shadewall inside surface temperature K F +1213 TSKIN skin temperature K T +1214 TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +1215 TSOI soil temperature (natural vegetated and crop landunits only) K T +1216 TSOI_10CM soil temperature in top 10cm of soil K T +1217 TSOI_ICE soil temperature (ice landunits only) K T +1218 TSRF_FORC surface temperature sent to GLC K F +1219 TSUNW_INNER sunwall inside surface temperature K F +1220 TV vegetation temperature K T +1221 TV24 vegetation temperature (last 24hrs) K F +1222 TV240 vegetation temperature (last 240hrs) K F +1223 TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F +1224 TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F +1225 TWS total water storage mm T +1226 T_SCALAR temperature inhibition of decomposition unitless T +1227 Tair atmospheric air temperature (downscaled to columns in glacier regions) K F +1228 Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F +1229 U10 10-m wind m/s T +1230 U10_DUST 10-m wind for dust model m/s T +1231 U10_ICE 10-m wind (ice landunits only) m/s F +1232 UAF canopy air speed m/s F +1233 ULRAD upward longwave radiation above the canopy W/m^2 F +1234 UM wind speed plus stability effect m/s F +1235 URBAN_AC urban air conditioning flux W/m^2 T +1236 URBAN_HEAT urban heating flux W/m^2 T +1237 USTAR aerodynamical resistance s/m F +1238 UST_LAKE friction velocity (lakes only) m/s F +1239 VA atmospheric wind speed plus convective velocity m/s F +1240 VCMX25T canopy profile of vcmax25 umol/m2/s T +1241 VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T +1242 VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T +1243 VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T +1244 VOCFLXT total VOC flux into atmosphere moles/m2/sec F +1245 VOLR river channel total water storage m3 T +1246 VOLRMCH river channel main channel water storage m3 T +1247 VPD vpd Pa F +1248 VPD2M 2m vapor pressure deficit Pa T +1249 VPD_CAN canopy vapor pressure deficit kPa T +1250 Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T +1251 WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +1252 WBA 2 m Wet Bulb C T +1253 WBA_R Rural 2 m Wet Bulb C T +1254 WBA_U Urban 2 m Wet Bulb C T +1255 WBT 2 m Stull Wet Bulb C T +1256 WBT_R Rural 2 m Stull Wet Bulb C T +1257 WBT_U Urban 2 m Stull Wet Bulb C T +1258 WF soil water as frac. of whc for top 0.05 m proportion F +1259 WFPS WFPS percent F +1260 WIND atmospheric wind velocity magnitude m/s T +1261 WOODC wood C gC/m^2 T +1262 WOODC_ALLOC wood C eallocation gC/m^2/s T +1263 WOODC_LOSS wood C loss gC/m^2/s T +1264 WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T +1265 WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T +1266 WTGQ surface tracer conductance m/s T +1267 W_SCALAR Moisture (dryness) inhibition of decomposition unitless T +1268 Wind atmospheric wind velocity magnitude m/s F +1269 XSMRPOOL temporary photosynthate C pool gC/m^2 T +1270 XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F +1271 XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T +1272 Z0HG roughness length over ground, sensible heat m F +1273 Z0HV roughness length over vegetation, sensible heat m F +1274 Z0M momentum roughness length m F +1275 Z0MG roughness length over ground, momentum m F +1276 Z0MV roughness length over vegetation, momentum m F +1277 Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F +1278 Z0QG roughness length over ground, latent heat m F +1279 Z0QV roughness length over vegetation, latent heat m F +1280 ZBOT atmospheric reference height m T +1281 ZETA dimensionless stability parameter unitless F +1282 ZII convective boundary height m F +1283 ZWT water table depth (natural vegetated and crop landunits only) m T +1284 ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T +1285 ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T +1286 anaerobic_frac anaerobic_frac m3/m3 F +1287 bsw clap and hornberger B unitless F +1288 currentPatch currentPatch coefficient for VOC calc non F +1289 diffus diffusivity m^2/s F +1290 fr_WFPS fr_WFPS fraction F +1291 n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F +1292 num_iter number of iterations unitless F +1293 r_psi r_psi m F +1294 ratio_k1 ratio_k1 none F +1295 ratio_no3_co2 ratio_no3_co2 ratio F +1296 soil_bulkdensity soil_bulkdensity kg/m3 F +1297 soil_co2_prod soil_co2_prod ug C / g soil / day F +1298 watfc water field capacity m^3/m^3 F +1299 watsat water saturated m^3/m^3 F ==== =================================== ============================================================================================== ================================================================= ======= From b24e0aa02c8b5609486f97e403ca9de366cf96da Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 12 Jul 2023 14:50:02 -0600 Subject: [PATCH 1120/2067] Refactor some max_patch_per_col and maxsoil_pa loops --- src/biogeochem/CNCIsoFluxMod.F90 | 517 +++++++++++++----------------- src/biogeochem/CNPhenologyMod.F90 | 171 +++++----- 2 files changed, 303 insertions(+), 385 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index a4706442fa..8b2f097882 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -8,7 +8,6 @@ module CNCIsoFluxMod use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varpar , only : ndecomp_cascade_transitions, nlevdecomp, ndecomp_pools - use clm_varpar , only : max_patch_per_col, maxsoil_patches use clm_varpar , only : i_litr_min, i_litr_max, i_met_lit use abortutils , only : endrun use pftconMod , only : pftcon @@ -85,7 +84,7 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & character(len=*) , intent(in) :: isotope ! 'c13' or 'c14' ! ! !LOCAL VARIABLES: - integer :: fp,pi,l,fc,cc,j,k,p + integer :: fp,l,fc,cc,j,k,p integer :: cdp !----------------------------------------------------------------------- @@ -535,7 +534,7 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ! For later clean-up, it would be possible to generalize this function to operate on a single ! patch-to-column flux. - call CNCIsoLitterToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + call CNCIsoLitterToColumn(num_soilp, filter_soilp, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! column-level non-mortality fluxes @@ -600,7 +599,6 @@ subroutine CIsoFlux2(num_soilc, filter_soilc, num_soilp , filter_soilp, & ! ! !LOCAL VARIABLES: - integer :: fp,pi !----------------------------------------------------------------------- associate( & @@ -713,7 +711,7 @@ subroutine CIsoFlux2(num_soilc, filter_soilc, num_soilp , filter_soilp, & ! call routine to shift patch-level gap mortality fluxes to column , for isotopes ! the non-isotope version of this routine is in CNGapMortalityMod.F90. - call CNCIsoGapPftToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + call CNCIsoGapPftToColumn(num_soilp, filter_soilp, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) end associate @@ -859,7 +857,7 @@ subroutine CIsoFlux2h(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! call routine to shift patch-level gap mortality fluxes to column, ! for isotopes the non-isotope version of this routine is in CNGapMortalityMod.F90. - call CNCIsoHarvestPftToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + call CNCIsoHarvestPftToColumn(num_soilp, filter_soilp, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) end associate @@ -1010,7 +1008,7 @@ subroutine CIsoFlux2g(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! call routine to shift patch-level gap mortality fluxes to column, ! for isotopes the non-isotope version of this routine is in CNGapMortalityMod.F90. - call CNCIsoGrossUnrepPftToColumn(num_soilc, filter_soilc, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) + call CNCIsoGrossUnrepPftToColumn(num_soilp, filter_soilp, soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) end associate @@ -1041,7 +1039,7 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & character(len=*) , intent(in) :: isotope ! 'c13' or 'c14' ! ! !LOCAL VARIABLES: - integer :: pi,pp,l,fc,cc,j,i + integer :: fp,pp,l,cc,j,i !----------------------------------------------------------------------- associate( & @@ -1276,32 +1274,22 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! calculate the column-level flux of deadstem and deadcrootc to cwdc as the result of fire mortality. - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - cc = filter_soilc(fc) - if ( pi <= col%npatches(cc) ) then - pp = col%patchi(cc) + pi - 1 - if (patch%active(pp)) then - do j = 1, nlevdecomp - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & - (iso_cnveg_cf%m_deadstemc_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livestemc_to_litter_fire_patch(pp)) * & - patch%wtcol(pp) * stem_prof(pp,j) - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & - iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & - (iso_cnveg_cf%m_deadcrootc_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livecrootc_to_litter_fire_patch(pp)) * & - patch%wtcol(pp) * croot_prof(pp,j) - end do - end if - end if + do fp = 1,num_soilp + pp = filter_soilp(fp) + cc = patch%column(pp) + do j = 1, nlevdecomp + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & + (iso_cnveg_cf%m_deadstemc_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livestemc_to_litter_fire_patch(pp)) * & + patch%wtcol(pp) * stem_prof(pp,j) + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) = & + iso_cnveg_cf%fire_mortality_c_to_cwdc_col(cc,j) + & + (iso_cnveg_cf%m_deadcrootc_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livecrootc_to_litter_fire_patch(pp)) * & + patch%wtcol(pp) * croot_prof(pp,j) end do - end do - - do fc = 1,num_soilc - cc = filter_soilc(fc) do j = 1, nlevdecomp do l = 1, ndecomp_pools if ( soilbiogeochem_cs%decomp_cpools_vr_col(cc,j,l) /= 0._r8) then @@ -1316,45 +1304,38 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & end do end do - - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - cc = filter_soilc(fc) - if ( pi <= col%npatches(cc) ) then - pp = col%patchi(cc) + pi - 1 - if (patch%active(pp)) then - do j = 1, nlevdecomp - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) = & - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) + & - ((iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i_met_lit) & - +iso_cnveg_cf%m_leafc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_leafc_xfer_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_gresp_storage_to_litter_fire_patch(pp) & - +iso_cnveg_cf%m_gresp_xfer_to_litter_fire_patch(pp))*leaf_prof(pp,j) + & - (iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i_met_lit) & - +iso_cnveg_cf%m_frootc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_frootc_xfer_to_litter_fire_patch(pp))*froot_prof(pp,j) & - +(iso_cnveg_cf%m_livestemc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livestemc_xfer_to_litter_fire_patch(pp) & - +iso_cnveg_cf%m_deadstemc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_deadstemc_xfer_to_litter_fire_patch(pp))* stem_prof(pp,j)& - +(iso_cnveg_cf%m_livecrootc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_livecrootc_xfer_to_litter_fire_patch(pp) & - +iso_cnveg_cf%m_deadcrootc_storage_to_litter_fire_patch(pp) + & - iso_cnveg_cf%m_deadcrootc_xfer_to_litter_fire_patch(pp))* croot_prof(pp,j)) * patch%wtcol(pp) + do fp = 1,num_soilp + pp = filter_soilp(fp) + cc = patch%column(pp) + do j = 1, nlevdecomp + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) = & + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) + & + ((iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i_met_lit) & + +iso_cnveg_cf%m_leafc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_leafc_xfer_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_gresp_storage_to_litter_fire_patch(pp) & + +iso_cnveg_cf%m_gresp_xfer_to_litter_fire_patch(pp))*leaf_prof(pp,j) + & + (iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i_met_lit) & + +iso_cnveg_cf%m_frootc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_frootc_xfer_to_litter_fire_patch(pp))*froot_prof(pp,j) & + +(iso_cnveg_cf%m_livestemc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livestemc_xfer_to_litter_fire_patch(pp) & + +iso_cnveg_cf%m_deadstemc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_deadstemc_xfer_to_litter_fire_patch(pp))* stem_prof(pp,j)& + +(iso_cnveg_cf%m_livecrootc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_livecrootc_xfer_to_litter_fire_patch(pp) & + +iso_cnveg_cf%m_deadcrootc_storage_to_litter_fire_patch(pp) + & + iso_cnveg_cf%m_deadcrootc_xfer_to_litter_fire_patch(pp))* croot_prof(pp,j)) * patch%wtcol(pp) - ! Here metabolic litter is treated differently than other - ! types of litter, so it remains outside this litter loop, - ! in the line above - do i = i_met_lit+1, i_litr_max - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) = & - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) + & - (iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i) * leaf_prof(pp,j) + & - iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i) * froot_prof(pp,j)) * patch%wtcol(pp) - end do - end do - end if - end if + ! Here metabolic litter is treated differently than other + ! types of litter, so it remains outside this litter loop, + ! in the line above + do i = i_met_lit+1, i_litr_max + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) = & + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i) + & + (iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i) * leaf_prof(pp,j) + & + iso_cnveg_cf%m_frootc_to_litter_fire_patch(pp) * fr_f(ivt(pp),i) * froot_prof(pp,j)) * patch%wtcol(pp) + end do end do end do @@ -1363,7 +1344,7 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & end subroutine CIsoFlux3 !----------------------------------------------------------------------- - subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & + subroutine CNCIsoLitterToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -1377,13 +1358,13 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & !DML ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil columns in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil columns type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,k,j,i + integer :: fp,c,p,k,j,i !----------------------------------------------------------------------- associate( & @@ -1405,59 +1386,50 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - c = filter_soilc(fc) - - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - do i = i_litr_min, i_litr_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - ! leaf litter carbon fluxes - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root litter carbon fluxes - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + ! leaf litter carbon fluxes + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root litter carbon fluxes + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do !DML - if (ivt(p) >= npcropmin) then ! add livestemc to litter - ! stem litter carbon fluxes - do i = i_litr_min, i_litr_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - - if (.not. use_grainproduct) then - ! grain litter carbon fluxes - do i = i_litr_min, i_litr_max - do k = repr_grain_min, repr_grain_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - - ! reproductive structure litter carbon fluxes - do i = i_litr_min, i_litr_max - do k = repr_structure_min, repr_structure_max - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - - end if -!DML - end if + if (ivt(p) >= npcropmin) then ! add livestemc to litter + ! stem litter carbon fluxes + do i = i_litr_min, i_litr_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + + if (.not. use_grainproduct) then + ! grain litter carbon fluxes + do i = i_litr_min, i_litr_max + do k = repr_grain_min, repr_grain_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do end if - end do + ! reproductive structure litter carbon fluxes + do i = i_litr_min, i_litr_max + do k = repr_structure_min, repr_structure_max + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + end if +!DML end do - end do end associate @@ -1465,7 +1437,7 @@ subroutine CNCIsoLitterToColumn (num_soilc, filter_soilc, & end subroutine CNCIsoLitterToColumn !----------------------------------------------------------------------- - subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & + subroutine CNCIsoGapPftToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -1473,13 +1445,13 @@ subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & ! to the column level and assign them to the three litter pools (+ cwd pool) ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil columns in filter + integer , intent(in) :: filter_soilp(:) ! soil column filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,p,j,i ! indices !----------------------------------------------------------------------- associate( & @@ -1520,63 +1492,53 @@ subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - ! leaf gap mortality carbon fluxes - gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - ! fine root gap mortality carbon fluxes - gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood gap mortality carbon fluxes - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_deadstemc_to_litter(p) * wtcol(p) * stem_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - m_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - gap_mortality_c_to_litr_c(c,j,i_met_lit) = & - gap_mortality_c_to_litr_c(c,j,i_met_lit) + & - ! storage gap mortality carbon fluxes - m_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - m_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - ! transfer gap mortality carbon fluxes - m_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - m_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) - - end if - end if - + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + ! leaf gap mortality carbon fluxes + gap_mortality_c_to_litr_c(c,j,i) = & + gap_mortality_c_to_litr_c(c,j,i) + & + m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + ! fine root gap mortality carbon fluxes + gap_mortality_c_to_litr_c(c,j,i) = & + gap_mortality_c_to_litr_c(c,j,i) + & + m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do + ! wood gap mortality carbon fluxes + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_deadstemc_to_litter(p) * wtcol(p) * stem_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + m_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + gap_mortality_c_to_litr_c(c,j,i_met_lit) = & + gap_mortality_c_to_litr_c(c,j,i_met_lit) + & + ! storage gap mortality carbon fluxes + m_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + m_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + ! transfer gap mortality carbon fluxes + m_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + m_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + end do end do @@ -1585,7 +1547,7 @@ subroutine CNCIsoGapPftToColumn (num_soilc, filter_soilc, & end subroutine CNCIsoGapPftToColumn !----------------------------------------------------------------------- - subroutine CNCIsoHarvestPftToColumn (num_soilc, filter_soilc, & + subroutine CNCIsoHarvestPftToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -1593,13 +1555,13 @@ subroutine CNCIsoHarvestPftToColumn (num_soilc, filter_soilc, & ! to the column level and assign them to the litter, cwd, and wood product pools ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil columns in filter + integer , intent(in) :: filter_soilp(:) ! soil column filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,p,j,i ! indices !----------------------------------------------------------------------- associate( & @@ -1640,76 +1602,60 @@ subroutine CNCIsoHarvestPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - ! leaf harvest mortality carbon fluxes - harvest_c_to_litr_c(c,j,i) = & - harvest_c_to_litr_c(c,j,i) + & - hrv_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! fine root harvest mortality carbon fluxes - harvest_c_to_litr_c(c,j,i) = & - harvest_c_to_litr_c(c,j,i) + & - hrv_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood harvest mortality carbon fluxes - harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & - hrv_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) - harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & - hrv_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & - hrv_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - harvest_c_to_litr_c(c,j,i_met_lit) = & - harvest_c_to_litr_c(c,j,i_met_lit) + & - ! storage harvest mortality carbon fluxes - hrv_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - hrv_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - hrv_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - ! transfer harvest mortality carbon fluxes - hrv_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - hrv_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - hrv_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) - end if - end if - + do i = i_litr_min, i_litr_max + ! leaf harvest mortality carbon fluxes + harvest_c_to_litr_c(c,j,i) = & + harvest_c_to_litr_c(c,j,i) + & + hrv_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! fine root harvest mortality carbon fluxes + harvest_c_to_litr_c(c,j,i) = & + harvest_c_to_litr_c(c,j,i) + & + hrv_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do + ! wood harvest mortality carbon fluxes + harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & + hrv_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) + harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & + hrv_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & + hrv_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + harvest_c_to_litr_c(c,j,i_met_lit) = & + harvest_c_to_litr_c(c,j,i_met_lit) + & + ! storage harvest mortality carbon fluxes + hrv_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + hrv_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + hrv_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + ! transfer harvest mortality carbon fluxes + hrv_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + hrv_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + hrv_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + end do end do - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - cwood_harvestc(c) = cwood_harvestc(c) + & - pwood_harvestc(p) * wtcol(p) - end if - end if - end do + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + cwood_harvestc(c) = cwood_harvestc(c) + & + pwood_harvestc(p) * wtcol(p) end do end associate @@ -1717,7 +1663,7 @@ subroutine CNCIsoHarvestPftToColumn (num_soilc, filter_soilc, & end subroutine CNCIsoHarvestPftToColumn !----------------------------------------------------------------------- - subroutine CNCIsoGrossUnrepPftToColumn (num_soilc, filter_soilc, & + subroutine CNCIsoGrossUnrepPftToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, iso_cnveg_carbonflux_inst) ! ! !DESCRIPTION: @@ -1725,13 +1671,13 @@ subroutine CNCIsoGrossUnrepPftToColumn (num_soilc, filter_soilc, & ! to the column level and assign them to the litter, cwd, and wood product pools ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil columns in filter + integer , intent(in) :: filter_soilp(:) ! soil column filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,p,j,i ! indices !----------------------------------------------------------------------- associate( & @@ -1774,54 +1720,35 @@ subroutine CNCIsoGrossUnrepPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - gru_c_to_litr_c(c,j,i) = & - gru_c_to_litr_c(c,j,i) + & - ! leaf gross unrepresented landcover change mortality carbon fluxes - gru_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root gross unrepresented landcover change mortality carbon fluxes - gru_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! coarse root gross unrepresented landcover change mortality carbon fluxes - gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & - gru_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & - gru_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - - end if - end if - + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + gru_c_to_litr_c(c,j,i) = & + gru_c_to_litr_c(c,j,i) + & + ! leaf gross unrepresented landcover change mortality carbon fluxes + gru_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root gross unrepresented landcover change mortality carbon fluxes + gru_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do + ! coarse root gross unrepresented landcover change mortality carbon fluxes + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + end do end do - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) - if (patch%active(p)) then - ! wood gross unrepresented landcover change mortality carbon fluxes to product pools - gru_wood_productc_gain_c(c) = gru_wood_productc_gain_c(c) + & - gru_wood_productc_gain(p) * wtcol(p) - - end if - end if - - end do + ! wood gross unrepresented landcover change mortality carbon fluxes to product pools + gru_wood_productc_gain_c(c) = gru_wood_productc_gain_c(c) + & + gru_wood_productc_gain(p) * wtcol(p) end do diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ec04fcbf54..2b861c5f62 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -406,7 +406,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, & ! gather all patch-level litterfall fluxes to the column for litter C and N inputs - call CNLitterToColumn(bounds, num_soilc, filter_soilc, & + call CNLitterToColumn(bounds, num_soilp, filter_soilp, & cnveg_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full), & froot_prof_patch(bounds%begp:bounds%endp,1:nlevdecomp_full)) @@ -534,7 +534,7 @@ subroutine CNPhenologyClimate (num_soilp, filter_soilp, num_pcropp, filter_pcrop ! ! !LOCAL VARIABLES: integer :: p ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8) :: dayspyr ! days per year (days) integer :: kyr ! current year integer :: kmo ! month of year (1, ..., 12) @@ -631,7 +631,7 @@ subroutine CNEvergreenPhenology (num_soilp, filter_soilp , & ! !LOCAL VARIABLES: real(r8):: avg_dayspyr ! Average days per year integer :: p ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8):: tranr real(r8):: t1 ! temporary variable @@ -816,7 +816,7 @@ subroutine CNSeasonDecidPhenology (num_soilp, filter_soilp , & ! ! !LOCAL VARIABLES: integer :: g,c,p !indices - integer :: fp !lake filter patch index + integer :: fp !filter patch index real(r8):: ws_flag !winter-summer solstice flag (0 or 1) real(r8):: crit_onset_gdd !critical onset growing degree-day sum real(r8):: crit_daylat !latitudinal light gradient in arctic-boreal @@ -1272,7 +1272,7 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , & ! !LOCAL VARIABLES: real(r8),parameter :: secspqtrday = secspday / 4 ! seconds per quarter day integer :: g,c,p ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8):: avg_dayspyr ! average days per year real(r8):: crit_onset_gdd ! degree days for onset trigger real(r8):: soilt ! temperature of top soil layer @@ -2565,7 +2565,7 @@ subroutine CNOnsetGrowth (num_soilp, filter_soilp, & ! ! !LOCAL VARIABLES: integer :: p ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8):: t1 ! temporary variable !----------------------------------------------------------------------- @@ -2699,7 +2699,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! ! !LOCAL VARIABLES: integer :: p, c, k ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8):: t1 ! temporary variable real(r8):: denom ! temporary variable for divisor real(r8) :: ntovr_leaf @@ -3032,7 +3032,7 @@ subroutine CNBackgroundLitterfall (num_soilp, filter_soilp, & ! ! !LOCAL VARIABLES: integer :: p ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8) :: fr_leafn_to_litter ! fraction of the nitrogen turnover that goes to litter; remaining fraction is retranslocated real(r8) :: ntovr_leaf real(r8) :: denom @@ -3189,7 +3189,7 @@ subroutine CNLivewoodTurnover (num_soilp, filter_soilp, & ! ! !LOCAL VARIABLES: integer :: p ! indices - integer :: fp ! lake filter patch index + integer :: fp ! filter patch index real(r8):: ctovr ! temporary variable for carbon turnover real(r8):: ntovr ! temporary variable for nitrogen turnover !----------------------------------------------------------------------- @@ -3383,7 +3383,7 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil end subroutine CNCropHarvestToProductPools !----------------------------------------------------------------------- - subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & + subroutine CNLitterToColumn (bounds, num_soilp, filter_soilp, & cnveg_state_inst,cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch, froot_prof_patch) ! @@ -3392,14 +3392,14 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & ! to the column level and assign them to the three litter pools ! ! !USES: - use clm_varpar , only : max_patch_per_col, nlevdecomp + use clm_varpar , only : nlevdecomp use pftconMod , only : npcropmin use clm_varctl , only : use_grainproduct ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(cnveg_state_type) , intent(in) :: cnveg_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst @@ -3407,7 +3407,7 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & real(r8) , intent(in) :: froot_prof_patch(bounds%begp:,1:) ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,k,j,i ! indices + integer :: fp,c,p,k,j,i ! indices !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(leaf_prof_patch) == (/bounds%endp,nlevdecomp_full/)), sourcefile, __LINE__) @@ -3439,89 +3439,80 @@ subroutine CNLitterToColumn (bounds, num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,max_patch_per_col - do fc = 1,num_soilc - c = filter_soilc(fc) - - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - ! leaf litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! leaf litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + ! leaf litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! leaf litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! fine root litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + + ! fine root litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do - ! fine root litter carbon fluxes + ! agroibis puts crop stem litter together with leaf litter + ! so I've used the leaf lf_f* parameters instead of making + ! new ones for now (slevis) + ! also for simplicity I've put "food" into the litter pools + + if (ivt(p) >= npcropmin) then ! add livestemc to litter + do i = i_litr_min, i_litr_max + ! stem litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! stem litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + + if (.not. use_grainproduct) then + do i = i_litr_min, i_litr_max + do k = repr_grain_min, repr_grain_max + ! grain litter carbon fluxes phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + phenology_c_to_litr_c(c,j,i) + & + repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - ! fine root litter nitrogen fluxes + ! grain litter nitrogen fluxes phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + phenology_n_to_litr_n(c,j,i) + & + repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) end do - - ! agroibis puts crop stem litter together with leaf litter - ! so I've used the leaf lf_f* parameters instead of making - ! new ones for now (slevis) - ! also for simplicity I've put "food" into the litter pools - - if (ivt(p) >= npcropmin) then ! add livestemc to litter - do i = i_litr_min, i_litr_max - ! stem litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! stem litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - livestemn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - - if (.not. use_grainproduct) then - do i = i_litr_min, i_litr_max - do k = repr_grain_min, repr_grain_max - ! grain litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_grainc_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! grain litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_grainn_to_food(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - - do i = i_litr_min, i_litr_max - do k = repr_structure_min, repr_structure_max - ! reproductive structure litter carbon fluxes - phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! reproductive structure litter nitrogen fluxes - phenology_n_to_litr_n(c,j,i) = & - phenology_n_to_litr_n(c,j,i) + & - repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - end do - end do - end if - end if + end do end if - end do - + do i = i_litr_min, i_litr_max + do k = repr_structure_min, repr_structure_max + ! reproductive structure litter carbon fluxes + phenology_c_to_litr_c(c,j,i) = & + phenology_c_to_litr_c(c,j,i) + & + repr_structurec_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! reproductive structure litter nitrogen fluxes + phenology_n_to_litr_n(c,j,i) = & + phenology_n_to_litr_n(c,j,i) + & + repr_structuren_to_litter(p,k) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + end do + end do + end if end do end do From 701b50405ce45aa68da897300cfe395314e67d5d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 13 Jul 2023 10:14:46 -0600 Subject: [PATCH 1121/2067] Refactor more max_patch_per_col and maxsoil_patches loops --- src/biogeochem/CNCIsoFluxMod.F90 | 16 +- src/biogeochem/CNDriverMod.F90 | 22 +- src/biogeochem/CNGapMortalityMod.F90 | 157 ++++++------- src/biogeophys/SoilFluxesMod.F90 | 2 +- src/biogeophys/SoilTemperatureMod.F90 | 209 ++++++++--------- src/biogeophys/SoilWaterMovementMod.F90 | 4 +- src/biogeophys/SoilWaterPlantSinkMod.F90 | 88 +++---- src/dyn_subgrid/dynGrossUnrepMod.F90 | 118 ++++------ src/dyn_subgrid/dynHarvestMod.F90 | 216 ++++++++---------- src/main/clm_driver.F90 | 1 + src/main/clm_varpar.F90 | 8 - .../SoilBiogeochemVerticalProfileMod.F90 | 17 +- 12 files changed, 383 insertions(+), 475 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index 8b2f097882..9d55ea7ef9 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -577,7 +577,7 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & end subroutine CIsoFlux1 !----------------------------------------------------------------------- - subroutine CIsoFlux2(num_soilc, filter_soilc, num_soilp , filter_soilp, & + subroutine CIsoFlux2(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst, iso_cnveg_carbonstate_inst, isotope) @@ -586,8 +586,6 @@ subroutine CIsoFlux2(num_soilc, filter_soilc, num_soilp , filter_soilp, & ! On the radiation time step, set the carbon isotopic fluxes for gap mortality ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst @@ -718,7 +716,7 @@ subroutine CIsoFlux2(num_soilc, filter_soilc, num_soilp , filter_soilp, & end subroutine CIsoFlux2 !----------------------------------------------------------------------- - subroutine CIsoFlux2h(num_soilc , filter_soilc, num_soilp , filter_soilp, & + subroutine CIsoFlux2h(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst, iso_cnveg_carbonstate_inst, isotope) @@ -727,8 +725,6 @@ subroutine CIsoFlux2h(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! set the carbon isotopic fluxes for harvest mortality ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst @@ -864,7 +860,7 @@ subroutine CIsoFlux2h(num_soilc , filter_soilc, num_soilp , filter_soilp, & end subroutine CIsoFlux2h !----------------------------------------------------------------------- - subroutine CIsoFlux2g(num_soilc , filter_soilc, num_soilp , filter_soilp, & + subroutine CIsoFlux2g(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst, iso_cnveg_carbonstate_inst, isotope) @@ -873,8 +869,6 @@ subroutine CIsoFlux2g(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! set the carbon isotopic fluxes for gross unrepresented landcover change mortality ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst @@ -1015,7 +1009,7 @@ subroutine CIsoFlux2g(num_soilc , filter_soilc, num_soilp , filter_soilp, & end subroutine CIsoFlux2g !----------------------------------------------------------------------- - subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & + subroutine CIsoFlux3(num_soilp, filter_soilp, & soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst, iso_cnveg_carbonstate_inst, & @@ -1025,8 +1019,6 @@ subroutine CIsoFlux3(num_soilc , filter_soilc, num_soilp , filter_soilp, & ! On the radiation time step, set the carbon isotopic fluxes for fire mortality ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns filter - integer , intent(in) :: filter_soilc(:) ! filter for soil columns integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 425c32e084..ba1e205d7c 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -681,7 +681,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNGapMortality') - call CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNGapMortality (bounds, num_soilp, filter_soilp, & dgvs_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, canopystate_inst, & !cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & @@ -703,14 +703,14 @@ subroutine CNDriverNoLeaching(bounds, ! Set the carbon isotopic fluxes for gap mortality if ( use_c13 ) then - call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2(num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst=c13_cnveg_carbonflux_inst, & iso_cnveg_carbonstate_inst=c13_cnveg_carbonstate_inst, & isotope='c13') end if if ( use_c14 ) then - call CIsoFlux2(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2(num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_carbonstate_inst, & iso_cnveg_carbonflux_inst=c14_cnveg_carbonflux_inst, & iso_cnveg_carbonstate_inst=c14_cnveg_carbonstate_inst, & @@ -746,20 +746,20 @@ subroutine CNDriverNoLeaching(bounds, ! Set harvest mortality routine if (get_do_harvest()) then - call CNHarvest(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNHarvest(num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) end if if ( use_c13 ) then - call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2h(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & isotope='c13') end if if ( use_c14 ) then - call CIsoFlux2h(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2h(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & @@ -790,20 +790,20 @@ subroutine CNDriverNoLeaching(bounds, ! Set gross unrepresented landcover change mortality routine if (get_do_grossunrep()) then - call CNGrossUnrep(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CNGrossUnrep(num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) end if if ( use_c13 ) then - call CIsoFlux2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2g(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & isotope='c13') end if if ( use_c14 ) then - call CIsoFlux2g(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux2g(num_soilp, filter_soilp, & soilbiogeochem_state_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & @@ -915,7 +915,7 @@ subroutine CNDriverNoLeaching(bounds, call t_startf('CNUpdate3') if ( use_c13 ) then - call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux3(num_soilp, filter_soilp, & soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c13_cnveg_carbonflux_inst, c13_cnveg_carbonstate_inst, & @@ -923,7 +923,7 @@ subroutine CNDriverNoLeaching(bounds, isotope='c13') end if if ( use_c14 ) then - call CIsoFlux3(num_soilc, filter_soilc, num_soilp, filter_soilp, & + call CIsoFlux3(num_soilp, filter_soilp, & soilbiogeochem_state_inst , soilbiogeochem_carbonstate_inst, & cnveg_carbonflux_inst, cnveg_carbonstate_inst, & c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, & diff --git a/src/biogeochem/CNGapMortalityMod.F90 b/src/biogeochem/CNGapMortalityMod.F90 index 91c937f655..16f787bf37 100644 --- a/src/biogeochem/CNGapMortalityMod.F90 +++ b/src/biogeochem/CNGapMortalityMod.F90 @@ -82,7 +82,7 @@ subroutine readParams ( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_soilp, & + subroutine CNGapMortality (bounds, num_soilp, filter_soilp, & dgvs_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenflux_inst,& cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, canopystate_inst, & leaf_prof_patch, froot_prof_patch, croot_prof_patch, stem_prof_patch) @@ -99,8 +99,6 @@ subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_so ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! column filter for soil points integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! patch filter for soil points type(dgvs_type) , intent(inout) :: dgvs_inst @@ -306,7 +304,7 @@ subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_so ! gather all patch-level litterfall fluxes to the column ! for litter C and N inputs - call CNGap_PatchToColumn(bounds, num_soilc, filter_soilc, & + call CNGap_PatchToColumn(bounds, num_soilp, filter_soilp, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), & froot_prof_patch(bounds%begp:bounds%endp, 1:nlevdecomp_full), & @@ -318,7 +316,7 @@ subroutine CNGapMortality (bounds, num_soilc, filter_soilc, num_soilp, filter_so end subroutine CNGapMortality !----------------------------------------------------------------------- - subroutine CNGap_PatchToColumn (bounds, num_soilc, filter_soilc, & + subroutine CNGap_PatchToColumn (bounds, num_soilp, filter_soilp, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & leaf_prof_patch, froot_prof_patch, croot_prof_patch, stem_prof_patch) ! @@ -331,8 +329,8 @@ subroutine CNGap_PatchToColumn (bounds, num_soilc, filter_soilc, & ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! soil patch filter type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst real(r8) , intent(in) :: leaf_prof_patch(bounds%begp:,1:) @@ -341,7 +339,7 @@ subroutine CNGap_PatchToColumn (bounds, num_soilc, filter_soilc, & real(r8) , intent(in) :: stem_prof_patch(bounds%begp:,1:) ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,p,j,i ! indices !----------------------------------------------------------------------- SHR_ASSERT_ALL_FL((ubound(leaf_prof_patch) == (/bounds%endp,nlevdecomp_full/)), sourcefile, __LINE__) @@ -408,84 +406,75 @@ subroutine CNGap_PatchToColumn (bounds, num_soilc, filter_soilc, & ) do j = 1,nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - ! leaf gap mortality carbon fluxes - m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root gap mortality carbon fluxes - m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood gap mortality carbon fluxes - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - (m_livestemc_to_litter(p) + m_deadstemc_to_litter(p)) * wtcol(p) * stem_prof(p,j) - gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & - (m_livecrootc_to_litter(p) + m_deadcrootc_to_litter(p)) * wtcol(p) * croot_prof(p,j) - - ! storage gap mortality carbon fluxes - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - gap_mortality_c_to_litr_c(c,j,i_met_lit) = & - gap_mortality_c_to_litr_c(c,j,i_met_lit) + & - (m_leafc_storage_to_litter(p) + m_gresp_storage_to_litter(p)) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - (m_livestemc_storage_to_litter(p) + m_deadstemc_storage_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & - (m_livecrootc_storage_to_litter(p) + m_deadcrootc_storage_to_litter(p)) * wtcol(p) * croot_prof(p,j) + & - - ! transfer gap mortality carbon fluxes - (m_leafc_xfer_to_litter(p) + m_gresp_xfer_to_litter(p)) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - (m_livestemc_xfer_to_litter(p) + m_deadstemc_xfer_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & - (m_livecrootc_xfer_to_litter(p) + m_deadcrootc_xfer_to_litter(p)) * wtcol(p) * croot_prof(p,j) - - do i = i_litr_min, i_litr_max - gap_mortality_n_to_litr_n(c,j,i) = & - gap_mortality_n_to_litr_n(c,j,i) + & - ! leaf gap mortality nitrogen fluxes - m_leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root litter nitrogen fluxes - m_frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood gap mortality nitrogen fluxes - gap_mortality_n_to_cwdn(c,j) = gap_mortality_n_to_cwdn(c,j) + & - (m_livestemn_to_litter(p) + m_deadstemn_to_litter(p)) * wtcol(p) * stem_prof(p,j) - gap_mortality_n_to_cwdn(c,j) = gap_mortality_n_to_cwdn(c,j) + & - (m_livecrootn_to_litter(p) + m_deadcrootn_to_litter(p)) * wtcol(p) * croot_prof(p,j) - - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - gap_mortality_n_to_litr_n(c,j,i_met_lit) = & - gap_mortality_n_to_litr_n(c,j,i_met_lit) + & - ! retranslocated N pool gap mortality fluxes - m_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - ! storage gap mortality nitrogen fluxes - m_leafn_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootn_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - (m_livestemn_storage_to_litter(p) + m_deadstemn_storage_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & - (m_livecrootn_storage_to_litter(p) + m_deadcrootn_storage_to_litter(p)) * wtcol(p) * croot_prof(p,j) + & - ! transfer gap mortality nitrogen fluxes - m_leafn_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootn_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - (m_livestemn_xfer_to_litter(p) + m_deadstemn_xfer_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & - (m_livecrootn_xfer_to_litter(p) + m_deadcrootn_xfer_to_litter(p)) * wtcol(p) * croot_prof(p,j) - - end if - end if + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + gap_mortality_c_to_litr_c(c,j,i) = & + gap_mortality_c_to_litr_c(c,j,i) + & + ! leaf gap mortality carbon fluxes + m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root gap mortality carbon fluxes + m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do + ! wood gap mortality carbon fluxes + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + (m_livestemc_to_litter(p) + m_deadstemc_to_litter(p)) * wtcol(p) * stem_prof(p,j) + gap_mortality_c_to_cwdc(c,j) = gap_mortality_c_to_cwdc(c,j) + & + (m_livecrootc_to_litter(p) + m_deadcrootc_to_litter(p)) * wtcol(p) * croot_prof(p,j) + + ! storage gap mortality carbon fluxes + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + gap_mortality_c_to_litr_c(c,j,i_met_lit) = & + gap_mortality_c_to_litr_c(c,j,i_met_lit) + & + (m_leafc_storage_to_litter(p) + m_gresp_storage_to_litter(p)) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + (m_livestemc_storage_to_litter(p) + m_deadstemc_storage_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & + (m_livecrootc_storage_to_litter(p) + m_deadcrootc_storage_to_litter(p)) * wtcol(p) * croot_prof(p,j) + & + + ! transfer gap mortality carbon fluxes + (m_leafc_xfer_to_litter(p) + m_gresp_xfer_to_litter(p)) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + (m_livestemc_xfer_to_litter(p) + m_deadstemc_xfer_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & + (m_livecrootc_xfer_to_litter(p) + m_deadcrootc_xfer_to_litter(p)) * wtcol(p) * croot_prof(p,j) + + do i = i_litr_min, i_litr_max + gap_mortality_n_to_litr_n(c,j,i) = & + gap_mortality_n_to_litr_n(c,j,i) + & + ! leaf gap mortality nitrogen fluxes + m_leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root litter nitrogen fluxes + m_frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do + + ! wood gap mortality nitrogen fluxes + gap_mortality_n_to_cwdn(c,j) = gap_mortality_n_to_cwdn(c,j) + & + (m_livestemn_to_litter(p) + m_deadstemn_to_litter(p)) * wtcol(p) * stem_prof(p,j) + gap_mortality_n_to_cwdn(c,j) = gap_mortality_n_to_cwdn(c,j) + & + (m_livecrootn_to_litter(p) + m_deadcrootn_to_litter(p)) * wtcol(p) * croot_prof(p,j) + + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + gap_mortality_n_to_litr_n(c,j,i_met_lit) = & + gap_mortality_n_to_litr_n(c,j,i_met_lit) + & + ! retranslocated N pool gap mortality fluxes + m_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + ! storage gap mortality nitrogen fluxes + m_leafn_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootn_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + (m_livestemn_storage_to_litter(p) + m_deadstemn_storage_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & + (m_livecrootn_storage_to_litter(p) + m_deadcrootn_storage_to_litter(p)) * wtcol(p) * croot_prof(p,j) + & + ! transfer gap mortality nitrogen fluxes + m_leafn_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootn_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + (m_livestemn_xfer_to_litter(p) + m_deadstemn_xfer_to_litter(p)) * wtcol(p) * stem_prof(p,j) + & + (m_livecrootn_xfer_to_litter(p) + m_deadcrootn_xfer_to_litter(p)) * wtcol(p) * croot_prof(p,j) + end do end do diff --git a/src/biogeophys/SoilFluxesMod.F90 b/src/biogeophys/SoilFluxesMod.F90 index c316d30fe3..44e6d0e1cd 100644 --- a/src/biogeophys/SoilFluxesMod.F90 +++ b/src/biogeophys/SoilFluxesMod.F90 @@ -11,7 +11,7 @@ module SoilFluxesMod use abortutils , only : endrun use perf_mod , only : t_startf, t_stopf use clm_varctl , only : iulog - use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, max_patch_per_col + use clm_varpar , only : nlevsno, nlevgrnd, nlevurb use atm2lndType , only : atm2lnd_type use CanopyStateType , only : canopystate_type use EnergyFluxType , only : energyflux_type diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 513413e8a9..5ed2e99c14 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -88,7 +88,8 @@ module SoilTemperatureMod contains !----------------------------------------------------------------------- - subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter_urbanc, num_nolakec, filter_nolakec, & + subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter_urbanc, & + num_nolakep, filter_nolakep, num_nolakec, filter_nolakec, & atm2lnd_inst, urbanparams_inst, canopystate_inst, waterstatebulk_inst, waterdiagnosticbulk_inst, waterfluxbulk_inst,& solarabs_inst, soilstate_inst, energyflux_inst, temperature_inst, urbantv_inst) ! @@ -124,6 +125,8 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_nolakep ! number of non-lake points in patch filter + integer , intent(in) :: filter_nolakep(:) ! patch filter for non-lake points integer , intent(in) :: num_nolakec ! number of column non-lake points in column filter integer , intent(in) :: filter_nolakec(:) ! column filter for non-lake points integer , intent(in) :: num_urbanl ! number of urban landunits in clump @@ -143,8 +146,8 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter type(temperature_type) , intent(inout) :: temperature_inst ! ! !LOCAL VARIABLES: - integer :: j,c,l,g,pi ! indices - integer :: fc ! lake filtered column indices + integer :: j,c,l,g ! indices + integer :: fc, fp ! lake filtered column & patch indices integer :: fl ! urban filtered landunit indices integer :: jtop(bounds%begc:bounds%endc) ! top level at each column real(r8) :: dtime ! land model time step (sec) @@ -288,7 +291,8 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! Added a patches loop here to get the average of hs and dhsdT over ! all Patches on the column. Precalculate the terms that do not depend on PFT. - call ComputeGroundHeatFluxAndDeriv(bounds, num_nolakec, filter_nolakec, & + call ComputeGroundHeatFluxAndDeriv(bounds, & + num_nolakep, filter_nolakep, num_nolakec, filter_nolakec, & hs_h2osfc( begc:endc ), & hs_top_snow( begc:endc ), & hs_soil( begc:endc ), & @@ -1417,7 +1421,8 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & end subroutine Phasechange_beta !----------------------------------------------------------------------- - subroutine ComputeGroundHeatFluxAndDeriv(bounds, num_nolakec, filter_nolakec, & + subroutine ComputeGroundHeatFluxAndDeriv(bounds, & + num_nolakep, filter_nolakep, num_nolakec, filter_nolakec, & hs_h2osfc, hs_top_snow, hs_soil, hs_top, dhsdT, sabg_lyr_col, & atm2lnd_inst, urbanparams_inst, canopystate_inst, waterdiagnosticbulk_inst, & waterfluxbulk_inst, solarabs_inst, energyflux_inst, temperature_inst) @@ -1433,12 +1438,14 @@ subroutine ComputeGroundHeatFluxAndDeriv(bounds, num_nolakec, filter_nolakec, & ! !USES: use clm_varcon , only : sb, hvap use column_varcon , only : icol_road_perv, icol_road_imperv - use clm_varpar , only : nlevsno, max_patch_per_col + use clm_varpar , only : nlevsno use UrbanParamsType, only : IsSimpleBuildTemp, IsProgBuildTemp ! ! !ARGUMENTS: implicit none type(bounds_type) , intent(in) :: bounds ! bounds + integer , intent(in) :: num_nolakep ! number of non-lake points in patch filter + integer , intent(in) :: filter_nolakep( : ) ! patch filter for non-lake points integer , intent(in) :: num_nolakec ! number of column non-lake points in column filter integer , intent(in) :: filter_nolakec( : ) ! column filter for non-lake points real(r8) , intent(out) :: hs_h2osfc( bounds%begc: ) ! heat flux on standing water [W/m2] @@ -1457,8 +1464,8 @@ subroutine ComputeGroundHeatFluxAndDeriv(bounds, num_nolakec, filter_nolakec, & type(temperature_type) , intent(in) :: temperature_inst ! ! !LOCAL VARIABLES: - integer :: j,c,p,l,g,pi ! indices - integer :: fc ! lake filtered column indices + integer :: j,c,p,l,g ! indices + integer :: fc, fp ! lake filtered column and patch indices real(r8) :: hs(bounds%begc:bounds%endc) ! net energy flux into the surface (w/m2) real(r8) :: lwrad_emit(bounds%begc:bounds%endc) ! emitted longwave radiation real(r8) :: dlwrad_emit(bounds%begc:bounds%endc) ! time derivative of emitted longwave radiation @@ -1550,79 +1557,71 @@ subroutine ComputeGroundHeatFluxAndDeriv(bounds, num_nolakec, filter_nolakec, & hs_h2osfc(begc:endc) = 0._r8 hs(begc:endc) = 0._r8 dhsdT(begc:endc) = 0._r8 - do pi = 1,max_patch_per_col - do fc = 1,num_nolakec - c = filter_nolakec(fc) - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - l = patch%landunit(p) - g = patch%gridcell(p) - - if (patch%active(p)) then - if (.not. lun%urbpoi(l)) then - eflx_gnet(p) = sabg(p) + dlrad(p) & - + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit(c) & - - (eflx_sh_grnd(p)+qflx_evap_soi(p)*htvp(c)) - ! save sabg for balancecheck, in case frac_sno is set to zero later - sabg_chk(p) = frac_sno_eff(c) * sabg_snow(p) + (1._r8 - frac_sno_eff(c) ) * sabg_soil(p) - - eflx_gnet_snow = sabg_snow(p) + dlrad(p) & - + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit_snow(c) & - - (eflx_sh_snow(p)+qflx_ev_snow(p)*htvp(c)) - - eflx_gnet_soil = sabg_soil(p) + dlrad(p) & - + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit_soil(c) & - - (eflx_sh_soil(p)+qflx_ev_soil(p)*htvp(c)) - - eflx_gnet_h2osfc = sabg_soil(p) + dlrad(p) & - + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit_h2osfc(c) & - - (eflx_sh_h2osfc(p)+qflx_ev_h2osfc(p)*htvp(c)) - else - ! For urban columns we use the net longwave radiation (eflx_lwrad_net) because of - ! interactions between urban columns. - - ! All wasteheat and traffic flux goes into canyon floor - if (col%itype(c) == icol_road_perv .or. col%itype(c) == icol_road_imperv) then - ! Note that we divide the following landunit variables by 1-wtlunit_roof which - ! essentially converts the flux from W/m2 of urban area to W/m2 of canyon floor area - eflx_wasteheat_patch(p) = eflx_wasteheat(l)/(1._r8-lun%wtlunit_roof(l)) - if ( IsSimpleBuildTemp() ) then - eflx_ventilation_patch(p) = 0._r8 - else if ( IsProgBuildTemp() ) then - eflx_ventilation_patch(p) = eflx_ventilation(l)/(1._r8-lun%wtlunit_roof(l)) - end if - eflx_heat_from_ac_patch(p) = eflx_heat_from_ac(l)/(1._r8-lun%wtlunit_roof(l)) - eflx_traffic_patch(p) = eflx_traffic(l)/(1._r8-lun%wtlunit_roof(l)) - else - eflx_wasteheat_patch(p) = 0._r8 - eflx_ventilation_patch(p) = 0._r8 - eflx_heat_from_ac_patch(p) = 0._r8 - eflx_traffic_patch(p) = 0._r8 - end if - ! Include transpiration term because needed for previous road - ! and include wasteheat and traffic flux - eflx_gnet(p) = sabg(p) + dlrad(p) & - - eflx_lwrad_net(p) & - - (eflx_sh_grnd(p) + qflx_evap_soi(p)*htvp(c) + qflx_tran_veg(p)*hvap) & - + eflx_wasteheat_patch(p) + eflx_heat_from_ac_patch(p) + eflx_traffic_patch(p) & - + eflx_ventilation_patch(p) - if ( IsSimpleBuildTemp() ) then - eflx_anthro(p) = eflx_wasteheat_patch(p) + eflx_traffic_patch(p) - end if - eflx_gnet_snow = eflx_gnet(p) - eflx_gnet_soil = eflx_gnet(p) - eflx_gnet_h2osfc = eflx_gnet(p) - end if - dgnetdT(p) = - cgrnd(p) - dlwrad_emit(c) - hs(c) = hs(c) + eflx_gnet(p) * patch%wtcol(p) - dhsdT(c) = dhsdT(c) + dgnetdT(p) * patch%wtcol(p) - ! separate surface fluxes for soil/snow - hs_soil(c) = hs_soil(c) + eflx_gnet_soil * patch%wtcol(p) - hs_h2osfc(c) = hs_h2osfc(c) + eflx_gnet_h2osfc * patch%wtcol(p) - + do fp = 1,num_nolakep + p = filter_nolakep(fp) + c = patch%column(p) + l = patch%landunit(p) + + if (.not. lun%urbpoi(l)) then + eflx_gnet(p) = sabg(p) + dlrad(p) & + + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit(c) & + - (eflx_sh_grnd(p)+qflx_evap_soi(p)*htvp(c)) + ! save sabg for balancecheck, in case frac_sno is set to zero later + sabg_chk(p) = frac_sno_eff(c) * sabg_snow(p) + (1._r8 - frac_sno_eff(c) ) * sabg_soil(p) + + eflx_gnet_snow = sabg_snow(p) + dlrad(p) & + + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit_snow(c) & + - (eflx_sh_snow(p)+qflx_ev_snow(p)*htvp(c)) + + eflx_gnet_soil = sabg_soil(p) + dlrad(p) & + + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit_soil(c) & + - (eflx_sh_soil(p)+qflx_ev_soil(p)*htvp(c)) + + eflx_gnet_h2osfc = sabg_soil(p) + dlrad(p) & + + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) - lwrad_emit_h2osfc(c) & + - (eflx_sh_h2osfc(p)+qflx_ev_h2osfc(p)*htvp(c)) + else + ! For urban columns we use the net longwave radiation (eflx_lwrad_net) because of + ! interactions between urban columns. + + ! All wasteheat and traffic flux goes into canyon floor + if (col%itype(c) == icol_road_perv .or. col%itype(c) == icol_road_imperv) then + ! Note that we divide the following landunit variables by 1-wtlunit_roof which + ! essentially converts the flux from W/m2 of urban area to W/m2 of canyon floor area + eflx_wasteheat_patch(p) = eflx_wasteheat(l)/(1._r8-lun%wtlunit_roof(l)) + if ( IsSimpleBuildTemp() ) then + eflx_ventilation_patch(p) = 0._r8 + else if ( IsProgBuildTemp() ) then + eflx_ventilation_patch(p) = eflx_ventilation(l)/(1._r8-lun%wtlunit_roof(l)) end if + eflx_heat_from_ac_patch(p) = eflx_heat_from_ac(l)/(1._r8-lun%wtlunit_roof(l)) + eflx_traffic_patch(p) = eflx_traffic(l)/(1._r8-lun%wtlunit_roof(l)) + else + eflx_wasteheat_patch(p) = 0._r8 + eflx_ventilation_patch(p) = 0._r8 + eflx_heat_from_ac_patch(p) = 0._r8 + eflx_traffic_patch(p) = 0._r8 end if - end do + ! Include transpiration term because needed for previous road + ! and include wasteheat and traffic flux + eflx_gnet(p) = sabg(p) + dlrad(p) & + - eflx_lwrad_net(p) & + - (eflx_sh_grnd(p) + qflx_evap_soi(p)*htvp(c) + qflx_tran_veg(p)*hvap) & + + eflx_wasteheat_patch(p) + eflx_heat_from_ac_patch(p) + eflx_traffic_patch(p) & + + eflx_ventilation_patch(p) + if ( IsSimpleBuildTemp() ) then + eflx_anthro(p) = eflx_wasteheat_patch(p) + eflx_traffic_patch(p) + end if + eflx_gnet_snow = eflx_gnet(p) + eflx_gnet_soil = eflx_gnet(p) + eflx_gnet_h2osfc = eflx_gnet(p) + end if + dgnetdT(p) = - cgrnd(p) - dlwrad_emit(c) + hs(c) = hs(c) + eflx_gnet(p) * patch%wtcol(p) + dhsdT(c) = dhsdT(c) + dgnetdT(p) * patch%wtcol(p) + ! separate surface fluxes for soil/snow + hs_soil(c) = hs_soil(c) + eflx_gnet_soil * patch%wtcol(p) + hs_h2osfc(c) = hs_h2osfc(c) + eflx_gnet_h2osfc * patch%wtcol(p) end do ! Additional calculations with SNICAR: @@ -1639,44 +1638,38 @@ subroutine ComputeGroundHeatFluxAndDeriv(bounds, num_nolakec, filter_nolakec, & hs_top(begc:endc) = 0._r8 hs_top_snow(begc:endc) = 0._r8 - do pi = 1,max_patch_per_col - do fc = 1,num_nolakec - c = filter_nolakec(fc) - lyr_top = snl(c) + 1 - if ( pi <= col%npatches(c) ) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - g = patch%gridcell(p) - l = patch%landunit(p) - if (.not. lun%urbpoi(l)) then + do fp = 1,num_nolakep + p = filter_nolakep(fp) + c = patch%column(p) + l = patch%landunit(p) - eflx_gnet_top = sabg_lyr(p,lyr_top) + dlrad(p) + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) & - - lwrad_emit(c) - (eflx_sh_grnd(p)+qflx_evap_soi(p)*htvp(c)) + lyr_top = snl(c) + 1 - hs_top(c) = hs_top(c) + eflx_gnet_top*patch%wtcol(p) + if (.not. lun%urbpoi(l)) then - eflx_gnet_snow = sabg_lyr(p,lyr_top) + dlrad(p) + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) & - - lwrad_emit_snow(c) - (eflx_sh_snow(p)+qflx_ev_snow(p)*htvp(c)) + eflx_gnet_top = sabg_lyr(p,lyr_top) + dlrad(p) + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) & + - lwrad_emit(c) - (eflx_sh_grnd(p)+qflx_evap_soi(p)*htvp(c)) - eflx_gnet_soil = sabg_lyr(p,lyr_top) + dlrad(p) + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) & - - lwrad_emit_soil(c) - (eflx_sh_soil(p)+qflx_ev_soil(p)*htvp(c)) + hs_top(c) = hs_top(c) + eflx_gnet_top*patch%wtcol(p) - hs_top_snow(c) = hs_top_snow(c) + eflx_gnet_snow*patch%wtcol(p) + eflx_gnet_snow = sabg_lyr(p,lyr_top) + dlrad(p) + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) & + - lwrad_emit_snow(c) - (eflx_sh_snow(p)+qflx_ev_snow(p)*htvp(c)) - do j = lyr_top,1,1 - sabg_lyr_col(c,j) = sabg_lyr_col(c,j) + sabg_lyr(p,j) * patch%wtcol(p) - enddo - else + eflx_gnet_soil = sabg_lyr(p,lyr_top) + dlrad(p) + (1._r8-frac_veg_nosno(p))*emg(c)*forc_lwrad(c) & + - lwrad_emit_soil(c) - (eflx_sh_soil(p)+qflx_ev_soil(p)*htvp(c)) - hs_top(c) = hs_top(c) + eflx_gnet(p)*patch%wtcol(p) - hs_top_snow(c) = hs_top_snow(c) + eflx_gnet(p)*patch%wtcol(p) - sabg_lyr_col(c,lyr_top) = sabg_lyr_col(c,lyr_top) + sabg(p) * patch%wtcol(p) + hs_top_snow(c) = hs_top_snow(c) + eflx_gnet_snow*patch%wtcol(p) - endif - endif + do j = lyr_top,1,1 + sabg_lyr_col(c,j) = sabg_lyr_col(c,j) + sabg_lyr(p,j) * patch%wtcol(p) + enddo + else - endif - enddo + hs_top(c) = hs_top(c) + eflx_gnet(p)*patch%wtcol(p) + hs_top_snow(c) = hs_top_snow(c) + eflx_gnet(p)*patch%wtcol(p) + sabg_lyr_col(c,lyr_top) = sabg_lyr_col(c,lyr_top) + sabg(p) * patch%wtcol(p) + + endif enddo end associate diff --git a/src/biogeophys/SoilWaterMovementMod.F90 b/src/biogeophys/SoilWaterMovementMod.F90 index 70da14a713..b1487e2779 100644 --- a/src/biogeophys/SoilWaterMovementMod.F90 +++ b/src/biogeophys/SoilWaterMovementMod.F90 @@ -380,7 +380,7 @@ subroutine BaseflowSink(bounds, num_hydrologyc, & !USES: use decompMod , only : bounds_type use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_varpar , only : nlevsoi, max_patch_per_col + use clm_varpar , only : nlevsoi use SoilStateType , only : soilstate_type use WaterFluxBulkType , only : waterfluxbulk_type use PatchType , only : patch @@ -484,7 +484,7 @@ subroutine soilwater_zengdecker2009(bounds, num_hydrologyc, filter_hydrologyc, & use decompMod , only : bounds_type use clm_varcon , only : grav,hfus,tfrz use clm_varcon , only : denh2o, denice - use clm_varpar , only : nlevsoi, max_patch_per_col, nlevgrnd + use clm_varpar , only : nlevsoi, nlevgrnd use clm_time_manager , only : get_step_size_real, get_nstep use column_varcon , only : icol_roof, icol_road_imperv use clm_varctl , only : use_flexibleCN, use_hydrstress diff --git a/src/biogeophys/SoilWaterPlantSinkMod.F90 b/src/biogeophys/SoilWaterPlantSinkMod.F90 index 115e1cab76..2d9c1a03c6 100644 --- a/src/biogeophys/SoilWaterPlantSinkMod.F90 +++ b/src/biogeophys/SoilWaterPlantSinkMod.F90 @@ -149,7 +149,6 @@ subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress_Roads(bounds, & use SoilStateType , only : soilstate_type use WaterFluxBulkType , only : waterfluxbulk_type use clm_varpar , only : nlevsoi - use clm_varpar , only : max_patch_per_col use PatchType , only : patch use ColumnType , only : col @@ -199,30 +198,25 @@ subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress_Roads(bounds, & end do end do - do pi = 1,max_patch_per_col - do j = 1,nlevsoi - do fc = 1, num_filterc - c = filterc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - rootr_col(c,j) = rootr_col(c,j) + rootr_patch(p,j) * & - qflx_tran_veg_patch(p) * patch%wtcol(p) - end if - end if - end do - end do + do j = 1,nlevsoi do fc = 1, num_filterc c = filterc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 + do p = col%patchi(c), col%patchi(c) + col%npatches(c) - 1 if (patch%active(p)) then - temp(c) = temp(c) + qflx_tran_veg_patch(p) * patch%wtcol(p) + rootr_col(c,j) = rootr_col(c,j) + rootr_patch(p,j) * & + qflx_tran_veg_patch(p) * patch%wtcol(p) end if + end do + end do + end do + do fc = 1, num_filterc + c = filterc(fc) + do p = col%patchi(c), col%patchi(c) + col%npatches(c) - 1 + if (patch%active(p)) then + temp(c) = temp(c) + qflx_tran_veg_patch(p) * patch%wtcol(p) end if end do end do - do j = 1, nlevsoi do fc = 1, num_filterc @@ -248,7 +242,6 @@ subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress( bounds, & !USES: use decompMod , only : bounds_type use clm_varpar , only : nlevsoi - use clm_varpar , only : max_patch_per_col use SoilStateType , only : soilstate_type use WaterFluxBulkType , only : waterfluxbulk_type use CanopyStateType , only : canopystate_type @@ -308,21 +301,18 @@ subroutine Compute_EffecRootFrac_And_VertTranSink_HydStress( bounds, & do j = 1, nlevsoi grav2 = z(c,j) * 1000._r8 temp(c) = 0._r8 - do pi = 1,max_patch_per_col - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - if (j == 1) then - qflx_hydr_redist_patch(p) = 0._r8 - end if - if (patch%active(p).and.frac_veg_nosno(p)>0) then - if (patch%wtcol(p) > 0._r8) then - patchflux = k_soil_root(p,j) * (smp(c,j) - vegwp(p,4) - grav2) - if (patchflux <0) then - qflx_hydr_redist_patch(p) = qflx_hydr_redist_patch(p) + patchflux - end if - temp(c) = temp(c) + patchflux * patch%wtcol(p) - endif - end if + do p = col%patchi(c), col%patchi(c) + col%npatches(c) - 1 + if (j == 1) then + qflx_hydr_redist_patch(p) = 0._r8 + end if + if (patch%active(p).and.frac_veg_nosno(p)>0) then + if (patch%wtcol(p) > 0._r8) then + patchflux = k_soil_root(p,j) * (smp(c,j) - vegwp(p,4) - grav2) + if (patchflux <0) then + qflx_hydr_redist_patch(p) = qflx_hydr_redist_patch(p) + patchflux + end if + temp(c) = temp(c) + patchflux * patch%wtcol(p) + endif end if end do qflx_rootsoi_col(c,j)= temp(c) @@ -351,7 +341,7 @@ subroutine Compute_EffecRootFrac_And_VertTranSink_Default(bounds, num_filterc, & !USES: use decompMod , only : bounds_type use shr_kind_mod , only : r8 => shr_kind_r8 - use clm_varpar , only : nlevsoi, max_patch_per_col + use clm_varpar , only : nlevsoi use SoilStateType , only : soilstate_type use WaterFluxBulkType , only : waterfluxbulk_type use PatchType , only : patch @@ -399,26 +389,22 @@ subroutine Compute_EffecRootFrac_And_VertTranSink_Default(bounds, num_filterc, & end do end do - do pi = 1,max_patch_per_col - do j = 1,nlevsoi - do fc = 1, num_filterc - c = filterc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - if (patch%active(p)) then - rootr_col(c,j) = rootr_col(c,j) + rootr_patch(p,j) * & - qflx_tran_veg_patch(p) * patch%wtcol(p) - end if - end if - end do - end do + do j = 1,nlevsoi do fc = 1, num_filterc c = filterc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 + do p = col%patchi(c), col%patchi(c) + col%npatches(c) - 1 if (patch%active(p)) then - temp(c) = temp(c) + qflx_tran_veg_patch(p) * patch%wtcol(p) + rootr_col(c,j) = rootr_col(c,j) + rootr_patch(p,j) * & + qflx_tran_veg_patch(p) * patch%wtcol(p) end if + end do + end do + end do + do fc = 1, num_filterc + c = filterc(fc) + do p = col%patchi(c), col%patchi(c) + col%npatches(c) - 1 + if (patch%active(p)) then + temp(c) = temp(c) + qflx_tran_veg_patch(p) * patch%wtcol(p) end if end do end do diff --git a/src/dyn_subgrid/dynGrossUnrepMod.F90 b/src/dyn_subgrid/dynGrossUnrepMod.F90 index bc49e72f4c..8d0e7ee004 100644 --- a/src/dyn_subgrid/dynGrossUnrepMod.F90 +++ b/src/dyn_subgrid/dynGrossUnrepMod.F90 @@ -146,7 +146,7 @@ end subroutine dynGrossUnrep_interp !----------------------------------------------------------------------- - subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & + subroutine CNGrossUnrep (num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) ! @@ -159,8 +159,6 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & use clm_time_manager, only : get_step_size_real, is_beg_curr_year ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! column filter for soil points integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! patch filter for soil points type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst @@ -359,7 +357,7 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & ! gather all patch-level litterfall fluxes from grossunrep to the column ! for litter C and N inputs - call CNGrossUnrepPftToColumn(num_soilc, filter_soilc, & + call CNGrossUnrepPftToColumn(num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) end associate @@ -367,7 +365,7 @@ subroutine CNGrossUnrep (num_soilc, filter_soilc, num_soilp, filter_soilp, & end subroutine CNGrossUnrep !----------------------------------------------------------------------- - subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & + subroutine CNGrossUnrepPftToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, CNVeg_carbonflux_inst, cnveg_nitrogenflux_inst) ! ! !DESCRIPTION: @@ -378,14 +376,14 @@ subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & use clm_varpar , only : maxsoil_patches, nlevdecomp ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! soil patch filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,p,j,i ! indices !----------------------------------------------------------------------- associate( & @@ -425,74 +423,56 @@ subroutine CNGrossUnrepPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - gru_c_to_litr_c(c,j,i) = gru_c_to_litr_c(c,j,i) + & - ! leaf gross unrepresented landcover change mortality carbon fluxes - gru_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root gross unrepresented landcover change mortality carbon fluxes - gru_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - gru_n_to_litr_c(c,j,i) = gru_n_to_litr_c(c,j,i) + & - ! leaf gross unrepresented landcover change mortality nitrogen fluxes - gru_leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root gross unrepresented landcover change mortality nitrogen fluxes - gru_frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! coarse root gross unrepresented landcover change mortality carbon fluxes - gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & - gru_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & - gru_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! coarse root gross unrepresented landcover change mortality nitrogen fluxes - gru_n_to_cwdn_c(c,j) = gru_n_to_cwdn_c(c,j) + & - gru_livecrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) - gru_n_to_cwdn_c(c,j) = gru_n_to_cwdn_c(c,j) + & - gru_deadcrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! retranslocated N pool gross unrepresented landcover change mortality fluxes - ! process specific to i_met_lit, so we keep it outside - ! the i_litr_min to i_litr_max loop above - gru_n_to_litr_c(c,j,i_met_lit) = & - gru_n_to_litr_c(c,j,i_met_lit) + & - gru_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) - - end if - end if - + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + gru_c_to_litr_c(c,j,i) = gru_c_to_litr_c(c,j,i) + & + ! leaf gross unrepresented landcover change mortality carbon fluxes + gru_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root gross unrepresented landcover change mortality carbon fluxes + gru_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + gru_n_to_litr_c(c,j,i) = gru_n_to_litr_c(c,j,i) + & + ! leaf gross unrepresented landcover change mortality nitrogen fluxes + gru_leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root gross unrepresented landcover change mortality nitrogen fluxes + gru_frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do + ! coarse root gross unrepresented landcover change mortality carbon fluxes + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + gru_c_to_cwdc_c(c,j) = gru_c_to_cwdc_c(c,j) + & + gru_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! coarse root gross unrepresented landcover change mortality nitrogen fluxes + gru_n_to_cwdn_c(c,j) = gru_n_to_cwdn_c(c,j) + & + gru_livecrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) + gru_n_to_cwdn_c(c,j) = gru_n_to_cwdn_c(c,j) + & + gru_deadcrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! retranslocated N pool gross unrepresented landcover change mortality fluxes + ! process specific to i_met_lit, so we keep it outside + ! the i_litr_min to i_litr_max loop above + gru_n_to_litr_c(c,j,i_met_lit) = & + gru_n_to_litr_c(c,j,i_met_lit) + & + gru_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) + end do end do - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) - if (patch%active(p)) then - ! wood gross unrepresented landcover change mortality carbon fluxes to product pools - gru_wood_productc_gain_c(c) = gru_wood_productc_gain_c(c) + & - gru_wood_productc_gain(p) * wtcol(p) + ! wood gross unrepresented landcover change mortality carbon fluxes to product pools + gru_wood_productc_gain_c(c) = gru_wood_productc_gain_c(c) + & + gru_wood_productc_gain(p) * wtcol(p) - ! wood gross unrepresented landcover change mortality nitrogen fluxes to product pools - gru_wood_productn_gain_c(c) = gru_wood_productn_gain_c(c) + & - gru_wood_productn_gain(p) * wtcol(p) - end if - end if - - end do + ! wood gross unrepresented landcover change mortality nitrogen fluxes to product pools + gru_wood_productn_gain_c(c) = gru_wood_productn_gain_c(c) + & + gru_wood_productn_gain(p) * wtcol(p) end do diff --git a/src/dyn_subgrid/dynHarvestMod.F90 b/src/dyn_subgrid/dynHarvestMod.F90 index a55da036f3..d5a72aa547 100644 --- a/src/dyn_subgrid/dynHarvestMod.F90 +++ b/src/dyn_subgrid/dynHarvestMod.F90 @@ -234,7 +234,7 @@ subroutine dynHarvest_interp_resolve_harvesttypes(bounds, harvest_rates, after_s end subroutine dynHarvest_interp_resolve_harvesttypes !----------------------------------------------------------------------- - subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & + subroutine CNHarvest (num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) ! @@ -247,8 +247,6 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & use clm_time_manager, only : get_step_size_real, is_beg_curr_year ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! column filter for soil points integer , intent(in) :: num_soilp ! number of soil patches in filter integer , intent(in) :: filter_soilp(:) ! patch filter for soil points type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst @@ -457,7 +455,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & ! gather all patch-level litterfall fluxes from harvest to the column ! for litter C and N inputs - call CNHarvestPftToColumn(num_soilc, filter_soilc, & + call CNHarvestPftToColumn(num_soilp, filter_soilp, & soilbiogeochem_state_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) end associate @@ -465,7 +463,7 @@ subroutine CNHarvest (num_soilc, filter_soilc, num_soilp, filter_soilp, & end subroutine CNHarvest !----------------------------------------------------------------------- - subroutine CNHarvestPftToColumn (num_soilc, filter_soilc, & + subroutine CNHarvestPftToColumn (num_soilp, filter_soilp, & soilbiogeochem_state_inst, CNVeg_carbonflux_inst, cnveg_nitrogenflux_inst) ! ! !DESCRIPTION: @@ -476,14 +474,14 @@ subroutine CNHarvestPftToColumn (num_soilc, filter_soilc, & use clm_varpar , only : nlevdecomp, maxsoil_patches, i_litr_min, i_litr_max, i_met_lit ! ! !ARGUMENTS: - integer , intent(in) :: num_soilc ! number of soil columns in filter - integer , intent(in) :: filter_soilc(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! patch filter for soil points type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst ! ! !LOCAL VARIABLES: - integer :: fc,c,pi,p,j,i ! indices + integer :: fp,c,p,j,i ! indices !----------------------------------------------------------------------- associate( & @@ -547,124 +545,106 @@ subroutine CNHarvestPftToColumn (num_soilc, filter_soilc, & ) do j = 1, nlevdecomp - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - - if (patch%active(p)) then - - do i = i_litr_min, i_litr_max - ! leaf harvest mortality carbon fluxes - harvest_c_to_litr_c(c,j,i) = & - harvest_c_to_litr_c(c,j,i) + & - hrv_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) - - ! fine root harvest mortality carbon fluxes - harvest_c_to_litr_c(c,j,i) = & - harvest_c_to_litr_c(c,j,i) + & - hrv_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood harvest mortality carbon fluxes - harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & - hrv_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) - harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & - hrv_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & - hrv_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! storage harvest mortality carbon fluxes - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - harvest_c_to_litr_c(c,j,i_met_lit) = & - harvest_c_to_litr_c(c,j,i_met_lit) + & - hrv_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - hrv_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - hrv_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - - ! transfer harvest mortality carbon fluxes - hrv_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - hrv_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - hrv_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) - - do i = i_litr_min, i_litr_max - harvest_n_to_litr_n(c,j,i) = & - harvest_n_to_litr_n(c,j,i) + & - ! leaf harvest mortality nitrogen fluxes - hrv_leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root litter nitrogen fluxes - hrv_frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) - end do - - ! wood harvest mortality nitrogen fluxes - harvest_n_to_cwdn(c,j) = harvest_n_to_cwdn(c,j) + & - hrv_livestemn_to_litter(p) * wtcol(p) * stem_prof(p,j) - harvest_n_to_cwdn(c,j) = harvest_n_to_cwdn(c,j) + & - hrv_livecrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) - harvest_n_to_cwdn(c,j) = harvest_n_to_cwdn(c,j) + & - hrv_deadcrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) - - ! Metabolic litter is treated differently than other types - ! of litter, so it gets this additional line after the - ! most recent loop over all litter types - harvest_n_to_litr_n(c,j,i_met_lit) = & - harvest_n_to_litr_n(c,j,i_met_lit) + & - ! retranslocated N pool harvest mortality fluxes - hrv_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - ! storage harvest mortality nitrogen fluxes - hrv_leafn_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - hrv_frootn_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - hrv_livestemn_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_deadstemn_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_livecrootn_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_deadcrootn_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - ! transfer harvest mortality nitrogen fluxes - hrv_leafn_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - hrv_frootn_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - hrv_livestemn_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_deadstemn_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - hrv_livecrootn_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - hrv_deadcrootn_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) - - end if - end if + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) + + do i = i_litr_min, i_litr_max + ! leaf harvest mortality carbon fluxes + harvest_c_to_litr_c(c,j,i) = & + harvest_c_to_litr_c(c,j,i) + & + hrv_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + + ! fine root harvest mortality carbon fluxes + harvest_c_to_litr_c(c,j,i) = & + harvest_c_to_litr_c(c,j,i) + & + hrv_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + end do + ! wood harvest mortality carbon fluxes + harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & + hrv_livestemc_to_litter(p) * wtcol(p) * stem_prof(p,j) + harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & + hrv_livecrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + harvest_c_to_cwdc(c,j) = harvest_c_to_cwdc(c,j) + & + hrv_deadcrootc_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! storage harvest mortality carbon fluxes + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + harvest_c_to_litr_c(c,j,i_met_lit) = & + harvest_c_to_litr_c(c,j,i_met_lit) + & + hrv_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + hrv_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + hrv_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + + ! transfer harvest mortality carbon fluxes + hrv_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + hrv_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + hrv_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + + do i = i_litr_min, i_litr_max + harvest_n_to_litr_n(c,j,i) = & + harvest_n_to_litr_n(c,j,i) + & + ! leaf harvest mortality nitrogen fluxes + hrv_leafn_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root litter nitrogen fluxes + hrv_frootn_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do + ! wood harvest mortality nitrogen fluxes + harvest_n_to_cwdn(c,j) = harvest_n_to_cwdn(c,j) + & + hrv_livestemn_to_litter(p) * wtcol(p) * stem_prof(p,j) + harvest_n_to_cwdn(c,j) = harvest_n_to_cwdn(c,j) + & + hrv_livecrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) + harvest_n_to_cwdn(c,j) = harvest_n_to_cwdn(c,j) + & + hrv_deadcrootn_to_litter(p) * wtcol(p) * croot_prof(p,j) + + ! Metabolic litter is treated differently than other types + ! of litter, so it gets this additional line after the + ! most recent loop over all litter types + harvest_n_to_litr_n(c,j,i_met_lit) = & + harvest_n_to_litr_n(c,j,i_met_lit) + & + ! retranslocated N pool harvest mortality fluxes + hrv_retransn_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + ! storage harvest mortality nitrogen fluxes + hrv_leafn_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + hrv_frootn_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + hrv_livestemn_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_deadstemn_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_livecrootn_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_deadcrootn_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + ! transfer harvest mortality nitrogen fluxes + hrv_leafn_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + hrv_frootn_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + hrv_livestemn_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_deadstemn_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + hrv_livecrootn_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + hrv_deadcrootn_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + end do end do - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 + do fp = 1,num_soilp + p = filter_soilp(fp) + c = patch%column(p) - if (patch%active(p)) then - ! wood harvest mortality carbon fluxes to product pools - cwood_harvestc(c) = cwood_harvestc(c) + & - pwood_harvestc(p) * wtcol(p) + ! wood harvest mortality carbon fluxes to product pools + cwood_harvestc(c) = cwood_harvestc(c) + & + pwood_harvestc(p) * wtcol(p) - ! wood harvest mortality nitrogen fluxes to product pools - cwood_harvestn(c) = cwood_harvestn(c) + & - pwood_harvestn(p) * wtcol(p) - end if - end if - - end do + ! wood harvest mortality nitrogen fluxes to product pools + cwood_harvestn(c) = cwood_harvestn(c) + & + pwood_harvestn(p) * wtcol(p) end do diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index f173d7d83d..1f1132922e 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -831,6 +831,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro call SoilTemperature(bounds_clump, & filter(nc)%num_urbanl , filter(nc)%urbanl, & filter(nc)%num_urbanc , filter(nc)%urbanc, & + filter(nc)%num_nolakep , filter(nc)%nolakep, & filter(nc)%num_nolakec , filter(nc)%nolakec, & atm2lnd_inst, urbanparams_inst, canopystate_inst, water_inst%waterstatebulk_inst, & water_inst%waterdiagnosticbulk_inst, water_inst%waterfluxbulk_inst, & diff --git a/src/main/clm_varpar.F90 b/src/main/clm_varpar.F90 index f54b750181..ffa851482a 100644 --- a/src/main/clm_varpar.F90 +++ b/src/main/clm_varpar.F90 @@ -113,7 +113,6 @@ module clm_varpar integer, public :: cft_size ! Number of PFTs on crop landunit in arrays of PFTs integer, public :: maxpatch_glc ! max number of elevation classes - integer, public :: max_patch_per_col ! ! !PUBLIC MEMBER FUNCTIONS: public clm_varpar_init ! set parameters @@ -195,13 +194,6 @@ subroutine clm_varpar_init(actual_maxsoil_patches, surf_numpft, surf_numcft) mxharvests = mxsowings + 1 - ! TODO(wjs, 2015-10-04, bugz 2227) Using surf_numcft in this 'max' gives a significant - ! overestimate of max_patch_per_col when use_crop is true. This should be reworked - - ! or, better, removed from the code entirely (because it is a maintenance problem, and - ! I can't imagine that looping idioms that use it help performance that much, and - ! likely they hurt performance.) - max_patch_per_col= max(maxsoil_patches, surf_numcft, maxpatch_urb) - nlevsoifl = 10 nlevurb = 5 diff --git a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 index 7209bd8278..e882a2fbc7 100644 --- a/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemVerticalProfileMod.F90 @@ -71,7 +71,7 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil real(r8) :: rootfr_tot real(r8) :: cinput_rootfr(bounds%begp:bounds%endp, 1:nlevdecomp_full) ! pft-native root fraction used for calculating inputs real(r8) :: col_cinput_rootfr(bounds%begc:bounds%endc, 1:nlevdecomp_full) ! col-native root fraction used for calculating inputs - integer :: c, j, fc, p, fp, pi + integer :: c, j, fc, p, fp integer :: alt_ind ! debugging temp variables real(r8) :: froot_prof_sum @@ -131,7 +131,6 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil do j = 1, nlevdecomp cinput_rootfr(p,j) = crootfr(p,j) / dzsoi_decomp(j) end do - else cinput_rootfr(p,1) = 0. endif @@ -176,15 +175,11 @@ subroutine SoilBiogeochemVerticalProfile(bounds, num_soilc,filter_soilc,num_soil ! cinput_rootfr(bounds%begp:bounds%endp, :), & ! col_cinput_rootfr(bounds%begc:bounds%endc, :), & ! 'unity') - do pi = 1,maxsoil_patches - do fc = 1,num_soilc - c = filter_soilc(fc) - if (pi <= col%npatches(c)) then - p = col%patchi(c) + pi - 1 - do j = 1,nlevdecomp - col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) - end do - end if + do fp = 1,num_soilp ! TODO slevis: Should it be num_soilp_with_inactive? + p = filter_soilp(fp) ! ...and filter_soilp_with_inactive? + c = patch%column(p) + do j = 1,nlevdecomp + col_cinput_rootfr(c,j) = col_cinput_rootfr(c,j) + cinput_rootfr(p,j) * patch%wtcol(p) end do end do From 633763f3a9ebe2f9beb122ea98c6cc9b56ce9417 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 13 Jul 2023 12:09:06 -0600 Subject: [PATCH 1122/2067] Call CLMFatesTimesteps only if use_fates --- src/main/clm_initializeMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90 index 7988fbfc7b..aa7c89ebb9 100644 --- a/src/main/clm_initializeMod.F90 +++ b/src/main/clm_initializeMod.F90 @@ -337,7 +337,7 @@ subroutine initialize2(ni,nj) end if ! Pass model timestep info to FATES - call CLMFatesTimesteps() + if (use_fates) call CLMFatesTimesteps() ! Initialize daylength from the previous time step (needed so prev_dayl can be set correctly) call t_startf('init_orbd') From 574f3b2710b10e46b9e62ca6b43895ce36fb4bcf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 13 Jul 2023 14:13:20 -0600 Subject: [PATCH 1123/2067] Wrap accumulMod calls in UpdateAccVars with is_end_curr_year(). To match previous behavior. --- src/biogeophys/TemperatureType.F90 | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90 index 5bed9dd820..1f2b7f4cc2 100644 --- a/src/biogeophys/TemperatureType.F90 +++ b/src/biogeophys/TemperatureType.F90 @@ -1360,7 +1360,7 @@ subroutine UpdateAccVars (this, bounds) ! ! USES use shr_const_mod , only : SHR_CONST_CDAY, SHR_CONST_TKFRZ - use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date + use clm_time_manager , only : get_step_size, get_nstep, is_end_curr_day, get_curr_date, is_end_curr_year use accumulMod , only : update_accum_field, extract_accum_field, accumResetVal use CNSharedParamsMod, only : upper_soil_layer ! @@ -1595,12 +1595,14 @@ subroutine UpdateAccVars (this, bounds) call extract_accum_field ('GDD10', this%gdd10_patch, nstep) ! Accumulate and extract running 20-year means - call update_accum_field ('GDD020', this%gdd0_patch, nstep) - call extract_accum_field ('GDD020', this%gdd020_patch, nstep) - call update_accum_field ('GDD820', this%gdd8_patch, nstep) - call extract_accum_field ('GDD820', this%gdd820_patch, nstep) - call update_accum_field ('GDD1020', this%gdd10_patch, nstep) - call extract_accum_field ('GDD1020', this%gdd1020_patch, nstep) + if (is_end_curr_year()) then + call update_accum_field ('GDD020', this%gdd0_patch, nstep) + call extract_accum_field ('GDD020', this%gdd020_patch, nstep) + call update_accum_field ('GDD820', this%gdd8_patch, nstep) + call extract_accum_field ('GDD820', this%gdd820_patch, nstep) + call update_accum_field ('GDD1020', this%gdd10_patch, nstep) + call extract_accum_field ('GDD1020', this%gdd1020_patch, nstep) + end if end if From 8aaf644d6b753d25bd5312a7bb2a169d304aabf5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jul 2023 12:38:52 -0600 Subject: [PATCH 1124/2067] Added temporary ChangeLog file. --- doc/ChangeLog.tmp | 191 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 191 insertions(+) create mode 100644 doc/ChangeLog.tmp diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp new file mode 100644 index 0000000000..edef5573e0 --- /dev/null +++ b/doc/ChangeLog.tmp @@ -0,0 +1,191 @@ +=============================================================== +Tag name: ctsm5.1.dev??? +Originator(s): samsrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: ??? +One-line Summary: Prescribed crop calendars + +Purpose and description of changes +---------------------------------- + +This tag introduces the ability to prescribe crop sowing dates +and/or maturity requirements. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[???] clm4_5 + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Resolves #281 -- Clean up CropPhenology logic + Resolves #519 -- Read in crop planting and harvest dates + Fixes #2042 -- Issue running SystemTests due to "conda activate" error + + Some on #1649 -- Additional "annual" (per growing season) crop outputs + +Known bugs found since the previous tag (include issue #): + None??? + +Notes of particular relevance for users +--------------------------------------- +Changes made to namelist defaults (e.g., changed parameter values): + + None + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: YES for Clm45BgcCrop compsets only + + Summarize any changes to answers, i.e., + - what code configurations: Clm45BgcCrop + - what platforms/compilers: Cheyenne intel and gnu, Izumi intel and nag + - nature of change (roundoff; larger than roundoff/same climate; new climate): ??? + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + + ??? + + 5 tests in aux_clm showed true DIFFs (i.e., not just field list differences / new output files): + - SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput + - ERP_D_P36x2_Ld3.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes + - LGRAIN2_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput + - ERS_Ly5_P72x1.f10_f10_mg37.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput + - SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm45BgcCrop.izumi_nag.clm-oldhyd + + The first four were likely due to an order-of-operations change in CNOffsetLitterfall(), as they resolve with the following patch: + --- a/src/biogeochem/CNPhenologyMod.F90 + +++ b/src/biogeochem/CNPhenologyMod.F90 + @@ -2978,7 +2978,6 @@ contains + real(r8) :: cropseedn_deficit_remaining ! remaining amount of crop seed N deficit that still needs to be restored (gN/m2) (positive, in contrast to the negative cropseedn_deficit) + real(r8) :: cropseedc_deficit_to_restore ! amount of crop seed C deficit that will be restored from this grain pool (gC/m2) + real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2) + - real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) + !----------------------------------------------------------------------- + + associate( & + @@ -3096,15 +3095,14 @@ contains + repr_grainn_to_seed(p,k) = t1 * cropseedn_deficit_to_restore + + ! Send the remaining grain to the food product pool + - repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) + repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & + - + repr_grainc_to_food_thispool + - if (reproductivec(p,k) + repr_grainc_to_food_thispool * dt .gt. 0) then + + + cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) + + if (reproductivec(p,k) + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt .gt. 0) then + if (h .le. 0) then + call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") + end if + repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + - + repr_grainc_to_food_thispool * dt + + + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt + repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & + + repr_grainc_to_food_perharv(p,h,k) + end if + + The last is resolved with an additional patch that removes all my changes to CNOffsetLitterfall()---changes which *should* only affect new diagnostic variables: + --- a/src/biogeochem/CNPhenologyMod.F90 + +++ b/src/biogeochem/CNPhenologyMod.F90 + @@ -408,8 +408,7 @@ contains + cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + + call CNOffsetLitterfall(num_soilp, filter_soilp, & + - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & + - crop_inst) + + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + + call CNBackgroundLitterfall(num_soilp, filter_soilp, & + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + @@ -2942,8 +2941,7 @@ contains + + !----------------------------------------------------------------------- + subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & + - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & + - crop_inst) + + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) + ! + ! !DESCRIPTION: + ! Determines the flux of C and N from displayed pools to litter + @@ -2964,10 +2962,9 @@ contains + type(cnveg_nitrogenstate_type), intent(in) :: cnveg_nitrogenstate_inst + type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst + type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst + - type(crop_type) , intent(in) :: crop_inst + ! + ! !LOCAL VARIABLES: + - integer :: p, c, k, h ! indices + + integer :: p, c, k ! indices + integer :: fp ! lake filter patch index + real(r8):: t1 ! temporary variable + real(r8):: denom ! temporary variable for divisor + @@ -3015,8 +3012,6 @@ contains + frootc_to_litter => cnveg_carbonflux_inst%frootc_to_litter_patch , & ! Output: [real(r8) (:) ] fine root C litterfall (gC/m2/s) + livestemc_to_litter => cnveg_carbonflux_inst%livestemc_to_litter_patch , & ! Output: [real(r8) (:) ] live stem C litterfall (gC/m2/s) + repr_grainc_to_food => cnveg_carbonflux_inst%repr_grainc_to_food_patch , & ! Output: [real(r8) (:,:) ] grain C to food (gC/m2/s) + - repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain C to food per harvest (gC/m2) + - repr_grainc_to_food_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain C to food harvested this calendar year (gC/m2) + repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) + repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) + repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) + @@ -3069,9 +3064,6 @@ contains + ! if this were ever changed, we'd need to add code to the "else" + if (ivt(p) >= npcropmin) then + + - ! How many harvests have occurred? + - h = crop_inst%harvest_count(p) + - + ! Replenish the seed deficits from grain, if there is enough available + ! grain. (If there is not enough available grain, the seed deficits will + ! accumulate until there is eventually enough grain to replenish them.) + @@ -3097,15 +3089,6 @@ contains + ! Send the remaining grain to the food product pool + repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & + + cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) + - if (reproductivec(p,k) + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt .gt. 0) then + - if (h .le. 0) then + - call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") + - end if + - repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + - + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt + - repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & + - + repr_grainc_to_food_perharv(p,h,k) + - end if + repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & + + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) + end do + + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime + cime: cime6.0.108 -> cime6.0.136 + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/CTSM/pull/1863 + +=============================================================== From 052397f96510f344ffb8f78cc35506e1905ef882 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jul 2023 13:49:40 -0600 Subject: [PATCH 1125/2067] ChangeLog.tmp: build-namelist tests pass. --- doc/ChangeLog.tmp | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index edef5573e0..068668a811 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -50,6 +50,10 @@ Testing summary: [PASS means all tests PASS; OK means tests PASS other than expected fails.] + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- OK From b1a46db13b23b21813b111c176707afa2a8edea9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 14 Jul 2023 14:59:26 -0600 Subject: [PATCH 1126/2067] BFB refactor: replace magic numbers with parameters --- cime_config/testdefs/testlist_clm.xml | 2 +- src/biogeophys/BareGroundFluxesMod.F90 | 9 +++--- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 5 ++-- src/biogeophys/CanopyFluxesMod.F90 | 8 ++++-- src/biogeophys/FrictionVelocityMod.F90 | 11 ++++---- src/biogeophys/LakeFluxesMod.F90 | 29 ++++++++++---------- src/main/clm_varcon.F90 | 9 ++++++ 7 files changed, 43 insertions(+), 30 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 6a4a0c56ef..a438498013 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -17,7 +17,7 @@ - + diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index c994d238a4..76a07f0f61 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -82,6 +82,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & use shr_const_mod , only : SHR_CONST_RGAS use clm_varpar , only : nlevgrnd use clm_varcon , only : cpair, vkc, grav, denice, denh2o + use clm_varcon , only : beta_param, nu_param use clm_varctl , only : use_lch4, z0param_method use landunit_varcon , only : istsoil, istcrop use QSatMod , only : QSat @@ -351,15 +352,15 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & select case (z0param_method) case ('ZengWang2007') - z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp) + z0hg_patch(p) = z0mg_patch(p) / exp(params_inst%a_coef * (ustar(p) * z0mg_patch(p) / nu_param)**params_inst%a_exp) case ('Meier2022') - ! After Yang et al. (2007) - z0hg_patch(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) + ! After Yang et al. (2008) + z0hg_patch(p) = 70._r8 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! RM: After Owen and Thomson (1963). This formulation could be used as an alternative to Yang et al. (2007). It would ! avoid that z0hg and z0qg becomes larger frequently than z0mg, which happens with Yang et al. (2007). - !z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / 1.5e-5_r8)**params_inst%a_exp * 0.71_r8**0.8_r8) + !z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / nu_param)**params_inst%a_exp * 0.71_r8**0.8_r8) end select diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 9123000fc5..004e2c689e 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -127,6 +127,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & ! ! !USES: use clm_time_manager, only : is_first_step, get_nstep, is_beg_curr_year + use clm_varcon , only : cd1_param use decompMod , only : subgrid_level_patch use BalanceCheckMod , only : GetBalanceCheckSkipSteps ! !ARGUMENTS: @@ -191,8 +192,8 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & else ! Compute as if elai+esai = LAImax in CanopyFluxes - displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * (pftcon%z0v_LAImax(patch%itype(p))))**0.5_r8)) & - / (7.5_r8*(pftcon%z0v_LAImax(patch%itype(p)) ))**0.5_r8) + displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(cd1_param * (pftcon%z0v_LAImax(patch%itype(p))))**0.5_r8)) & + / (cd1_param*(pftcon%z0v_LAImax(patch%itype(p)) ))**0.5_r8) U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p))) & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index c48345edc8..4f60eec304 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -229,6 +229,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, use clm_varcon , only : denh2o, tfrz, tlsai_crit, alpha_aero use clm_varcon , only : c14ratio, spval use clm_varcon , only : c_water, c_dry_biomass, c_to_b + use clm_varcon , only : nu_param, cd1_param use perf_mod , only : t_startf, t_stopf use QSatMod , only : QSat use CLMFatesInterfaceMod, only : hlm_fates_interface_type @@ -238,6 +239,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, SwampCoolEff, KtoC, VaporPres use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type use LunaMod , only : is_time_to_run_LUNA + ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -893,7 +895,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, case ('Meier2022') lt = max(0.00001_r8,elai(p)+esai(p)) - displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(7.5_r8 * lt)**0.5_r8)) / (7.5_r8*lt)**0.5_r8) + displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(cd1_param * lt)**0.5_r8)) / (cd1_param*lt)**0.5_r8) lt = min(lt,z0v_LAImax(patch%itype(p))) delt = 2._r8 @@ -1066,9 +1068,9 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! just for readability of the code (from line 680) ! RM: Does this need to be updated if Ya08 is used too? Proposed formulation (definitely double-check!) ! , interpreting the statement below as csoilb = vkc / ln(z0mg/z0hg): - ! csoilb = vkc / log( z0mg(c) / ( 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * + ! csoilb = vkc / log( z0mg(c) / ( 70._r8 * nu_param / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * ! (abs(temp1(p)*dth(p)))**(0.25_r8)) ) ) - csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / 1.5e-5_r8)**params_inst%a_exp) + csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / nu_param)**params_inst%a_exp) !compute the stability parameter for ricsoilc ("S" in Sakaguchi&Zeng,2008) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 3960b6504d..1ea3381b3a 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -517,7 +517,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & ! Set roughness lengths and forcing heights for non-lake points ! ! !USES: - use clm_varcon , only : rpi + use clm_varcon , only : rpi, b1_param, b4_param ! !ARGUMENTS: class(frictionvel_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds @@ -579,9 +579,9 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (frac_sno(c) > 0._r8) then if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp( (1.4_r8 * (-rpi/2.0_r8)) -0.31_r8) / 1000._r8 + z0mg(c) = exp(b1_param * (-rpi / 2.0_r8) + b4_param) / 1000._r8 else - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 end if else z0mg(c) = this%zsno @@ -594,10 +594,9 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(-1.4_r8 * rpi/2.0_r8 - 0.31_r8) / 1000.0_r8 + z0mg(c) = exp(-b1_param * rpi / 2.0_r8 + b4_param) / 1000._r8 else - z0mg(c) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) & - / 1000.0_r8 + z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 end if else z0mg(c) = this%zsno diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 38ecbc6fbb..ceab64945a 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -93,6 +93,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, use clm_varpar , only : nlevlak use clm_varcon , only : hvap, hsub, hfus, cpair, cpliq, tkwat, tkice, tkair use clm_varcon , only : sb, vkc, grav, denh2o, tfrz, spval, rpi + use clm_varcon , only : beta_param, nu_param, b1_param, b4_param use clm_varctl , only : use_lch4, z0param_method, use_z0m_snowmelt use LakeCon , only : betavis, z0frzlake, tdmax, emg_lake use LakeCon , only : lake_use_old_fcrit_minz0 @@ -340,11 +341,11 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0mg(p) = params_inst%zglc - z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + z0hg(p) = 70._r8 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 case ('ZengWang2007') z0mg(p) = z0frzlake - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select z0qg(p) = z0hg(p) else ! use roughness over snow as in Biogeophysics1 @@ -352,28 +353,28 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('Meier2022') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(-1.4_r8 * rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp(-b1_param * rpi / 2.0_r8 + b4_param) / 1000._r8 else - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 end if else z0mg(p) = params_inst%zsno end if - z0hg(p) = 70._r8 * 1.5e-5_r8 / ust_lake(c) ! For initial guess assume tstar = 0 + z0hg(p) = 70._r8 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 case ('ZengWang2007') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 ) then - z0mg(p) = exp((1.4_r8 * (-rpi/2.0_r8)) -0.31_r8) / 1000._r8 + z0mg(p) = exp(b1_param * (-rpi / 2.0_r8) + b4_param) / 1000._r8 else - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 end if else z0mg(p) = params_inst%zsno end if - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select z0qg(p) = z0hg(p) end if @@ -603,28 +604,28 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('Meier2022') z0mg(p) = params_inst%zglc - z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + z0hg(p) = 70._r8 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes case ('ZengWang2007') z0mg(p) = z0frzlake - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select z0qg(p) = z0hg(p) else ! Snow layers if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(-1.4_r8 * rpi/2.0_r8 -0.31_r8) / 1000._r8 + z0mg(p) = exp(-b1_param * rpi / 2.0_r8 + b4_param) / 1000._r8 else - z0mg(p) = exp(1.4_r8 * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8))-0.31_r8) / 1000._r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 end if end if select case (z0param_method) case ('Meier2022') - z0hg(p) = 70._r8 * 1.5e-5_r8 / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + z0hg(p) = 70._r8 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes case ('ZengWang2007') - z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / 1.5e-5_r8)**params_inst%a_exp) ! Consistent with BareGroundFluxes + z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select z0qg(p) = z0hg(p) diff --git a/src/main/clm_varcon.F90 b/src/main/clm_varcon.F90 index 340115fe90..f898e27307 100644 --- a/src/main/clm_varcon.F90 +++ b/src/main/clm_varcon.F90 @@ -154,6 +154,15 @@ module clm_varcon real(r8), public :: c14ratio = 1.e-12_r8 ! real(r8) :: c14ratio = 1._r8 ! debug lets set to 1 to try to avoid numerical errors + !------------------------------------------------------------------ + ! Surface roughness constants + !------------------------------------------------------------------ + real(r8), public, parameter :: beta_param = 7.2_r8 ! Meier et al. (2022) https://doi.org/10.5194/gmd-15-2365-2022 + real(r8), public, parameter :: nu_param = 1.5e-5_r8 ! Meier et al. (2022) kinematic viscosity of air + real(r8), public, parameter :: b1_param = 1.4_r8 ! Meier et al. (2022) empirical constant + real(r8), public, parameter :: b4_param = -0.31_r8 ! Meier et al. (2022) empirical constant + real(r8), public, parameter :: cd1_param = 7.5_r8 ! Meier et al. (2022) originally from Raupach (1994) + !------------------------------------------------------------------ ! Urban building temperature constants !------------------------------------------------------------------ From 09e00123a824d9eb4f8f0b379a4a1d15d574d329 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 14 Jul 2023 15:02:59 -0600 Subject: [PATCH 1127/2067] Answer-changing refactor: repl. some divisions w multiplications --- src/biogeophys/FrictionVelocityMod.F90 | 8 ++++---- src/biogeophys/LakeFluxesMod.F90 | 12 ++++++------ 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 1ea3381b3a..621bce4117 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -579,9 +579,9 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (frac_sno(c) > 0._r8) then if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(b1_param * (-rpi / 2.0_r8) + b4_param) / 1000._r8 + z0mg(c) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 + z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 end if else z0mg(c) = this%zsno @@ -594,9 +594,9 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if (frac_sno(c) > 0._r8) then ! Do snow first because ice could be snow-covered if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(-b1_param * rpi / 2.0_r8 + b4_param) / 1000._r8 + z0mg(c) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 + z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 end if else z0mg(c) = this%zsno diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index ceab64945a..212a55043d 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -353,9 +353,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('Meier2022') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(-b1_param * rpi / 2.0_r8 + b4_param) / 1000._r8 + z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 end if else @@ -367,9 +367,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, case ('ZengWang2007') if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 ) then - z0mg(p) = exp(b1_param * (-rpi / 2.0_r8) + b4_param) / 1000._r8 + z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 end if else z0mg(p) = params_inst%zsno @@ -614,9 +614,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else ! Snow layers if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(-b1_param * rpi / 2.0_r8 + b4_param) / 1000._r8 + z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) / 1000._r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 end if end if From 8197954129b932040cb6bfa2ec93298f05a2a15b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 14 Jul 2023 14:35:22 -0600 Subject: [PATCH 1128/2067] Add NYRS_CROP_ACTIVE history variable. This necessitates nyrs_crop_active being changed from integer to real(r8). --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- src/biogeochem/CropType.F90 | 17 +++++++++++------ 2 files changed, 13 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ec04fcbf54..f2fdd7a687 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -585,13 +585,13 @@ subroutine CNPhenologyClimate (num_soilp, filter_soilp, num_pcropp, filter_pcrop do fp = 1,num_pcropp p = filter_pcropp(fp) - if (kmo == 1 .and. kda == 1 .and. nyrs_crop_active(p) == 0) then ! YR 1: + if (kmo == 1 .and. kda == 1 .and. nyrs_crop_active(p) == 0.0_r8) then ! YR 1: gdd020(p) = 0._r8 ! set gdd..20 variables to 0 gdd820(p) = 0._r8 ! and crops will not be planted gdd1020(p) = 0._r8 end if if (kmo == 1 .and. kda == 1 .and. mcsec == 0) then ! <-- END of EVERY YR: - if (nyrs_crop_active(p) == 1) then ! <-- END of YR 1 + if (nyrs_crop_active(p) == 1.0_r8) then ! <-- END of YR 1 gdd020(p) = gdd0(p) ! <-- END of YR 1 gdd820(p) = gdd8(p) ! <-- END of YR 1 gdd1020(p) = gdd10(p) ! <-- END of YR 1 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 6ceeccf7e3..39ccc5178d 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -35,7 +35,7 @@ module CropType ! Crop state variables structure type, public :: crop_type - integer , pointer :: nyrs_crop_active_patch (:) ! number of years this crop patch has been active (0 for non-crop patches) + real(r8), pointer :: nyrs_crop_active_patch (:) ! number of years this crop patch has been active (0 for non-crop patches) logical , pointer :: croplive_patch (:) ! patch Flag, true if planted, not harvested integer , pointer :: harvdate_patch (:) ! most recent patch harvest date; 999 if currently (or never) planted real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen @@ -205,7 +205,7 @@ subroutine InitAllocate(this, bounds) begp = bounds%begp; endp = bounds%endp - allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0 + allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0.0_r8 allocate(this%croplive_patch (begp:endp)) ; this%croplive_patch (:) = .false. allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) allocate(this%fertnitro_patch (begp:endp)) ; this%fertnitro_patch (:) = spval @@ -282,6 +282,11 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='actual crop harvest dates; should only be output annually', & ptr_patch=this%hdates_thisyr, default='inactive') + this%nyrs_crop_active_patch(begp:endp) = spval + call hist_addfld1d (fname='NYRS_CROP_ACTIVE', units='year', & + avgflag='I', long_name='number of years crop active', & + ptr_patch=this%nyrs_crop_active_patch, default='inactive') + end subroutine InitHistory subroutine InitCold(this, bounds) @@ -308,7 +313,7 @@ subroutine InitCold(this, bounds) g = patch%gridcell(p) ivt = patch%itype(p) - this%nyrs_crop_active_patch(p) = 0 + this%nyrs_crop_active_patch(p) = 0.0_r8 if ( grc%latdeg(g) >= 0.0_r8 .and. grc%latdeg(g) <= 30.0_r8) then this%latbaset_patch(p)=pftcon%baset(ivt)+12._r8-0.4_r8*grc%latdeg(g) @@ -497,7 +502,7 @@ subroutine Restart(this, bounds, ncid, flag) !----------------------------------------------------------------------- if (use_crop) then - call restartvar(ncid=ncid, flag=flag, varname='nyrs_crop_active', xtype=ncd_int, & + call restartvar(ncid=ncid, flag=flag, varname='nyrs_crop_active', xtype=ncd_double, & dim1name='pft', & long_name='Number of years this crop patch has been active (0 for non-crop patches)', & units='years', & @@ -516,7 +521,7 @@ subroutine Restart(this, bounds, ncid, flag) do p = bounds%begp, bounds%endp if (patch%itype(p) >= npcropmin .and. patch%itype(p) <= npcropmax .and. & patch%active(p)) then - this%nyrs_crop_active_patch(p) = restyear + this%nyrs_crop_active_patch(p) = real(restyear, r8) end if end do end if @@ -767,7 +772,7 @@ subroutine CropIncrementYear (this, num_pcropp, filter_pcropp) do fp = 1, num_pcropp p = filter_pcropp(fp) - this%nyrs_crop_active_patch(p) = this%nyrs_crop_active_patch(p) + 1 + this%nyrs_crop_active_patch(p) = this%nyrs_crop_active_patch(p) + 1.0_r8 end do end if From 548e8be5d32dd6dc1d0a9db3ff9a8531c20b7935 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 14 Jul 2023 15:11:44 -0600 Subject: [PATCH 1129/2067] Change if statement back to what we have in main --- src/main/lnd2glcMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/lnd2glcMod.F90 b/src/main/lnd2glcMod.F90 index 1597ee4517..34f50266ad 100644 --- a/src/main/lnd2glcMod.F90 +++ b/src/main/lnd2glcMod.F90 @@ -204,7 +204,7 @@ subroutine update_lnd2glc(this, bounds, num_do_smb_c, filter_do_smb_c, & ! Make sure we haven't already assigned the coupling fields for this point ! (this could happen, for example, if there were multiple columns in the ! istsoil landunit, which we aren't prepared to handle) - if (1==2) then + if (fields_assigned(g,n)) then write(iulog,*) subname//' ERROR: attempt to assign coupling fields twice for the same index.' write(iulog,*) 'One possible cause is having multiple columns in the istsoil landunit,' write(iulog,*) 'which this routine cannot handle.' From dbb2b6cf7dbbe3fcb86d1a8081b5d9c4ad3549bd Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 14 Jul 2023 16:13:49 -0600 Subject: [PATCH 1130/2067] Changed num_allc to num_soilc loops to prevent NaNsin nag -nan tests --- src/biogeochem/CNVegCarbonStateType.F90 | 4 ++-- src/biogeochem/CNVegNitrogenStateType.F90 | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index 610689fdb6..681fa2a8d0 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -2747,8 +2747,8 @@ subroutine Summary_carbonstate(this, bounds, num_allc, filter_allc, & this%totc_patch(bounds%begp:bounds%endp), & this%totc_p2c_col(bounds%begc:bounds%endc)) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) ! total ecosystem carbon, including veg but excluding cpool (TOTECOSYSC) this%totecosysc_col(c) = & diff --git a/src/biogeochem/CNVegNitrogenStateType.F90 b/src/biogeochem/CNVegNitrogenStateType.F90 index f09311e518..669a22d4f7 100644 --- a/src/biogeochem/CNVegNitrogenStateType.F90 +++ b/src/biogeochem/CNVegNitrogenStateType.F90 @@ -1157,8 +1157,8 @@ subroutine Summary_nitrogenstate(this, bounds, num_allc, filter_allc, & this%totn_patch(bounds%begp:bounds%endp), & this%totn_p2c_col(bounds%begc:bounds%endc)) - do fc = 1,num_allc - c = filter_allc(fc) + do fc = 1,num_soilc + c = filter_soilc(fc) ! total ecosystem nitrogen, including veg (TOTECOSYSN) this%totecosysn_col(c) = & From 578b0bf44aa085a664e6b3b47ce01d3fdcad9776 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Sun, 16 Jul 2023 11:09:04 -0600 Subject: [PATCH 1131/2067] fix comment for new fates test --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 0575ea8086..68c3f39867 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2388,7 +2388,7 @@ - + From 18e6a0de0994952d8350ee9a4116e852c009065f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 17 Jul 2023 13:23:50 -0600 Subject: [PATCH 1132/2067] Reverse part of commit https://github.com/ESCOMP/CTSM/pull/2051/commits/9816cf07626a9c4aba20c5f6519a5ec1bbdb1a24 --- src/main/surfrdUtilsMod.F90 | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90 index af9e64d86a..d84b829310 100644 --- a/src/main/surfrdUtilsMod.F90 +++ b/src/main/surfrdUtilsMod.F90 @@ -58,15 +58,12 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto) ub = ubound(arr, 1) allocate(TotalSum(lb:ub)) + TotalSum = 1._r8 + if ( present(sumto) ) TotalSum = sumto if( present(ier) ) ier = 0 found = .false. do nl = lb, ub - if ( present(sumto) ) then - TotalSum(nl) = sumto(nl) - else - TotalSum(nl) = 1._r8 - end if if (abs(sum(arr(nl,:)) - TotalSum(nl)) > eps) then found = .true. nindx = nl From 26d2c7cbb4e806af0f1242229b2f6ad676b09509 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 14:13:18 -0600 Subject: [PATCH 1133/2067] Updated ChangeLog.tmp. --- doc/ChangeLog.tmp | 39 +++++++++++++++++++++++++++++++-------- 1 file changed, 31 insertions(+), 8 deletions(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index 068668a811..439dda2c64 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -1,8 +1,8 @@ =============================================================== -Tag name: ctsm5.1.dev??? -Originator(s): samsrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) -Date: ??? -One-line Summary: Prescribed crop calendars +Tag name: ctsm5.1.dev131 +Originator(s): samrabin (Sam Rabin,UCAR/TSS) +Date: Mon Jul 17 13:58:49 MDT 2023 +One-line Summary: Enable prescribed crop calendars. Purpose and description of changes ---------------------------------- @@ -41,9 +41,28 @@ Known bugs found since the previous tag (include issue #): Notes of particular relevance for users --------------------------------------- -Changes made to namelist defaults (e.g., changed parameter values): - None +Caveats for users: + Untested: + * Time-varying inputs + * Running at any resolution other than one matching the crop calendar inputs + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + Adds optional namelist variables: + * stream_fldfilename_sdate: Filename of input stream data for sowing dates + * stream_fldfilename_cultivar_gdds: Filename of input stream data for cultivar growing degree-day targets + * stream_meshfile_cropcal: Filename of input stream data for crop calendar inputs + * stream_year_first_cropcal: First year to loop over for crop calendar data + * stream_year_last_cropcal: Last year to loop over for crop calendar data + * model_year_align_cropcal: Simulation year that aligns with stream_year_first_cropcal value + * generate_crop_gdds: Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. + * use_mxmat: Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. + +Notes of particular relevance for developers: --------------------------------------------- + +Changes to tests or testing: + * Adds RXCROPMATURITY SystemTest, with an example added to ctsm_sci test suite. + * Removes 12 MCT tests from testlist_clm.xml, as discussed in CTSM SE standup 2023-06-26. Testing summary: ---------------- @@ -59,6 +78,10 @@ Testing summary: cheyenne ---- OK izumi ------- OK + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + cheyenne - PASS + Answer changes -------------- @@ -187,9 +210,9 @@ Changes answers relative to baseline: YES for Clm45BgcCrop compsets only Other details ------------- List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime - cime: cime6.0.108 -> cime6.0.136 + cime: cime6.0.108 -> cime6.0.136 Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/CTSM/pull/1863 + https://github.com/ESCOMP/CTSM/pull/1863 =============================================================== From 5d2a7f5317193a4d6bd43c4634e9666f49b4e04f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 14:13:32 -0600 Subject: [PATCH 1134/2067] Description fix in namelist_definition_ctsm.xml. --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index c797ddcf7d..dc693b50ba 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1136,7 +1136,7 @@ Set to .true. in order to override crop harvesting logic and to instead harvest -Set to .true. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. +Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. Date: Mon, 17 Jul 2023 14:18:17 -0600 Subject: [PATCH 1135/2067] Updated .git-blame-ignore-revs. --- .git-blame-ignore-revs | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index b3fe9f76a6..31645e2fa5 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -9,3 +9,5 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b 7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7 b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 +# Ran SystemTests and python/ctsm through black python formatter +5364ad66eaceb55dde2d3d598fe4ce37ac83a93c From 43088021376740409fadddb65d57a7b530b51436 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 15:08:34 -0600 Subject: [PATCH 1136/2067] Run fixes. --- src/biogeochem/TillageMod.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index d4a88bb843..2dbae8f11a 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -13,7 +13,7 @@ module TillageMod ! SOIL3 becomes PAS_SOM (passive) ! ! !USES: - use shr_kind_mod , only : r8 => shr_kind_r8 + use shr_kind_mod , only : r8 => shr_kind_r8, CS => shr_kind_CS use shr_log_mod , only : errMsg => shr_log_errMsg use abortutils , only : endrun use clm_varctl , only : iulog @@ -28,6 +28,8 @@ module TillageMod public :: tillage_init_century public :: get_do_tillage public :: get_apply_tillage_multipliers + ! !PUBLIC DATA MEMBERS + character(len=CS), public :: tillage_mode ! off, low, high ! ! !PRIVATE DATA MEMBERS logical :: do_tillage_low ! Do low-intensity tillage? @@ -48,7 +50,7 @@ subroutine tillage_init(bounds) ! in separate subroutines written specifically for decomposition mode of choice. ! ! !USES: - use spmdMod , only : masterproc + use spmdMod , only : masterproc, mpicom use controlMod , only : NLFilename use clm_nlUtilsMod , only : find_nlgroup_name use shr_mpi_mod , only : shr_mpi_bcast @@ -62,16 +64,14 @@ subroutine tillage_init(bounds) ! !LOCAL VARIABLES integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag - integer :: mpicom ! MPI communicator character(*), parameter :: subname = "('tillage_init')" - character(len=8) :: tillage_mode ! off, low, high namelist /tillage_inparm/ & tillage_mode, & use_original_tillage ! Default values - tillage_mode = "off" + tillage_mode = 'off' use_original_tillage = .false. ! Read tillage namelist @@ -105,7 +105,7 @@ subroutine tillage_init(bounds) do_tillage_low = .true. else if (tillage_mode == "high") then do_tillage_high = .true. - else + else if (tillage_mode /= "off") then call endrun(subname // ':: ERROR Unrecognized tillage_mode') end if From 6c0049a682195ba732f4f24ab3d3cd6fdcfec742 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 15:20:45 -0600 Subject: [PATCH 1137/2067] Only call tillage_init_century() if doing tillage. --- src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 2738c55682..6e8a0bc274 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -230,7 +230,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i ! written by C. Koven ! ! !USES: - use TillageMod, only : tillage_init_century + use TillageMod, only : get_do_tillage, tillage_init_century ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -507,7 +507,9 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i deallocate(params_inst%bgc_initial_Cstocks) ! Allocate tillage variables - call tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + if (get_do_tillage()) then + call tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + end if end associate From e85505ed62ca254393574ada013251919c5d0a34 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 15:23:26 -0600 Subject: [PATCH 1138/2067] Allow tillage with FATES. Still won't work with use_crop false. FATES handles coarse woody debris separately, but I haven't added handling of that, so implicitly tillage just doesn't affect CWD. --- bld/CLMBuildNamelist.pm | 4 ---- 1 file changed, 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 4c3608982b..c88c2c8718 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2157,10 +2157,6 @@ sub setup_logic_tillage { $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); } - if ( &value_is_true($nl->get_value('use_fates')) ) { - $log->fatal_error( "Tillage can't be used with FATES" ); - } - my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( "soil_decomp_method" ) ); if ( $soil_decomp_method ne "CENTURYKoven2013" ) { $log->fatal_error( "Tillage can only be used with soil_decomp_method 'CENTURYKoven2013'" ); From d144df945ba46db43b9fd4f6ad19b199f1552990 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 15:25:17 -0600 Subject: [PATCH 1139/2067] Added note about GDP dependence in old code. --- src/biogeochem/TillageMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index 2dbae8f11a..7b755669e2 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -168,6 +168,10 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c ! to use days past planting. Modified by Sam Rabin to include "new" version ! that *actually* uses days past planting. ! + ! Original code had two versions depending on cell's GDP, but this seems to + ! have been only an initial effort that was (a) never published and (b) not + ! completely developed. + ! ! !USES: use clm_time_manager, only : get_curr_calday, get_curr_days_per_year use pftconMod , only : ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean From 44eeaf78051086f531e7bbc401ee7cdb9c0a5bf2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 16:07:03 -0600 Subject: [PATCH 1140/2067] Reorder tillage_mults_allphases fill for consistency. --- src/biogeochem/TillageMod.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index 7b755669e2..2d1a9c2b2b 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -136,17 +136,17 @@ subroutine tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_li ! Fill tillage_mults_allphases if (do_tillage_low) then - tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) + tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) else if (do_tillage_high) then - tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) tillage_mults_allphases(i_act_som,:) = (/ 1.2_r8, 1.0_r8, 1.0_r8 /) tillage_mults_allphases(i_slo_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) tillage_mults_allphases(i_pas_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) + tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) else call endrun('ERROR Unrecognized tillage setting in tillage_init_century()') end if From 35b7f238c58b7535d572c871a318f6346fca3233 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 16:14:18 -0600 Subject: [PATCH 1141/2067] Removed an old comment in TillageMod. --- src/biogeochem/TillageMod.F90 | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index 2d1a9c2b2b..d29029ee09 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -3,15 +3,6 @@ module TillageMod ! !DESCRIPTION: ! Module for soil tillage. ! - ! As described in ChangeLog: - ! history field name change as follows... - ! LITR1 becomes MET_LIT (metabolic) - ! LITR2 becomes CEL_LIT (cellulosic) - ! LITR3 becomes LIG_LIT (lignin) - ! SOIL1 becomes ACT_SOM (active) - ! SOIL2 becomes SLO_SOM (slow) - ! SOIL3 becomes PAS_SOM (passive) - ! ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8, CS => shr_kind_CS use shr_log_mod , only : errMsg => shr_log_errMsg From 9090a6eb28cad90ec8aad5ba449e8ad405189e8f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 16:20:10 -0600 Subject: [PATCH 1142/2067] TillageMod now has its own copies of indices for soil pools. --- src/biogeochem/TillageMod.F90 | 30 ++++++++++++------- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 2 +- 2 files changed, 21 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index d29029ee09..f78bed9fc8 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -29,6 +29,13 @@ module TillageMod real(r8), pointer :: tillage_mults(:) ! (ndecomp_pools) real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) + ! Indices for soil organic matter pools + integer :: i_act_som + integer :: i_slo_som + integer :: i_pas_som + ! Indices for litter pools + integer :: i_cel_lit + integer :: i_lig_lit !============================================================================== @@ -104,7 +111,7 @@ subroutine tillage_init(bounds) end subroutine tillage_init - subroutine tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine tillage_init_century(i_act_som_in, i_slo_som_in, i_pas_som_in, i_cel_lit_in, i_lig_lit_in) ! !DESCRIPTION: ! ! Allocate multiplier arrays to be used in tillage. Call during initialization of CENTURY decomposition. @@ -114,8 +121,8 @@ subroutine tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_li use pftconMod , only : npcropmin ! ! !ARGUMENTS: - integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools - integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools + integer , intent(in) :: i_act_som_in, i_slo_som_in, i_pas_som_in ! indices for soil organic matter pools + integer , intent(in) :: i_cel_lit_in, i_lig_lit_in ! indices for litter pools if (.not. get_do_tillage()) then return @@ -125,6 +132,13 @@ subroutine tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_li allocate(tillage_mults(ndecomp_pools)); tillage_mults(:) = 1.0_r8 allocate(tillage_mults_allphases(ndecomp_pools, nphases)); tillage_mults_allphases(:,:) = 1.0_r8 + ! Save soil pool indices + i_act_som = i_act_som_in + i_slo_som = i_slo_som_in + i_pas_som = i_pas_som_in + i_cel_lit = i_cel_lit_in + i_lig_lit = i_lig_lit_in + ! Fill tillage_mults_allphases if (do_tillage_low) then tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) @@ -151,7 +165,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers(idop, p) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -169,8 +183,6 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: p ! index of patch this is being called for - integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools - integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES: ! @@ -230,7 +242,7 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c end subroutine get_tillage_multipliers - subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_apply_tillage_multipliers(idop, c, decomp_k) ! !DESCRIPTION: ! ! Multiply decomposition rate constants by tillage coefficients. @@ -243,8 +255,6 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: c ! index of column this is being called for real(r8), dimension(:,:,:), intent(inout) :: decomp_k ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) - integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools - integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! ! !LOCAL VARIABLES integer :: p, this_patch, j, n_noncrop @@ -279,7 +289,7 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som call endrun('ERROR No active patches found (crop OR non-crop)') end if - call get_tillage_multipliers(idop, this_patch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers(idop, this_patch) ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 6e8a0bc274..ae94b0543e 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -923,7 +923,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & end if do fc = 1,num_soilc c = filter_soilc(fc) - call get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_apply_tillage_multipliers(idop, c, decomp_k) end do end if From 8c4307247764fa8bd7612b0b347fa762748cfcbd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 17 Jul 2023 16:51:00 -0600 Subject: [PATCH 1143/2067] Initialize tillage for MIMICS; not yet applying. --- src/biogeochem/TillageMod.F90 | 46 ++++++++++++------- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 4 +- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 6 +++ 3 files changed, 38 insertions(+), 18 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index f78bed9fc8..5b5aed70e6 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -16,7 +16,7 @@ module TillageMod private ! !PUBLIC MEMBER PROCEDURES public :: tillage_init - public :: tillage_init_century + public :: tillage_init_decompcascade public :: get_do_tillage public :: get_apply_tillage_multipliers ! !PUBLIC DATA MEMBERS @@ -30,13 +30,12 @@ module TillageMod real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) ! Indices for soil organic matter pools - integer :: i_act_som - integer :: i_slo_som - integer :: i_pas_som + integer :: i_act_som ! MIMICS: i_avl_som + integer :: i_slo_som ! MIMICS: i_chem_som + integer :: i_pas_som ! MIMICS: i_phys_som ! Indices for litter pools - integer :: i_cel_lit - integer :: i_lig_lit - + integer :: i_cel_lit ! MIMICS: i_str_lit + integer :: i_lig_lit ! MIMICS: none (just the one structural litter pool) !============================================================================== contains @@ -111,18 +110,25 @@ subroutine tillage_init(bounds) end subroutine tillage_init - subroutine tillage_init_century(i_act_som_in, i_slo_som_in, i_pas_som_in, i_cel_lit_in, i_lig_lit_in) + subroutine tillage_init_decompcascade(i_act_som_in, i_slo_som_in, i_pas_som_in, i_cel_lit_in, i_lig_lit_in) ! !DESCRIPTION: ! - ! Allocate multiplier arrays to be used in tillage. Call during initialization of CENTURY decomposition. + ! Allocate multiplier arrays to be used in tillage. Call during initialization of CENTURY or MIMICS decomposition. ! Written by Sam Rabin. ! ! !USES use pftconMod , only : npcropmin ! ! !ARGUMENTS: - integer , intent(in) :: i_act_som_in, i_slo_som_in, i_pas_som_in ! indices for soil organic matter pools - integer , intent(in) :: i_cel_lit_in, i_lig_lit_in ! indices for litter pools + ! All soil pool indices use CENTURY index names. Comments indicate corresponding MIMICS names, if any. + ! + ! Indices for soil organic matter pools + integer , intent(in) :: i_act_som_in + integer , intent(in) :: i_slo_som_in + integer , intent(in) :: i_pas_som_in + ! Indices for structural litter pools + integer , intent(in) :: i_cel_lit_in + integer, optional, intent(in) :: i_lig_lit_in ! Do not specify for MIMICS if (.not. get_do_tillage()) then return @@ -137,7 +143,11 @@ subroutine tillage_init_century(i_act_som_in, i_slo_som_in, i_pas_som_in, i_cel_ i_slo_som = i_slo_som_in i_pas_som = i_pas_som_in i_cel_lit = i_cel_lit_in - i_lig_lit = i_lig_lit_in + if (present(i_lig_lit)) then + i_lig_lit = i_lig_lit_in + else + i_lig_lit = -1 + end if ! Fill tillage_mults_allphases if (do_tillage_low) then @@ -145,18 +155,22 @@ subroutine tillage_init_century(i_act_som_in, i_slo_som_in, i_pas_som_in, i_cel_ tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + if (i_lig_lit > 0) then + tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) + end if else if (do_tillage_high) then tillage_mults_allphases(i_act_som,:) = (/ 1.2_r8, 1.0_r8, 1.0_r8 /) tillage_mults_allphases(i_slo_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) tillage_mults_allphases(i_pas_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) - tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + if (i_lig_lit > 0) then + tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) + end if else - call endrun('ERROR Unrecognized tillage setting in tillage_init_century()') + call endrun('ERROR Unrecognized tillage setting in tillage_init_decompcascade()') end if - end subroutine tillage_init_century + end subroutine tillage_init_decompcascade function get_do_tillage() diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index ae94b0543e..e7a258c7b1 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -230,7 +230,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i ! written by C. Koven ! ! !USES: - use TillageMod, only : get_do_tillage, tillage_init_century + use TillageMod, only : get_do_tillage, tillage_init_decompcascade ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -508,7 +508,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i ! Allocate tillage variables if (get_do_tillage()) then - call tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call tillage_init_decompcascade(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) end if end associate diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index f820db01b6..4f303edbd9 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -342,6 +342,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat ! ! !USES: use clm_varcon, only: pct_to_frac + use TillageMod, only: get_do_tillage, tillage_init_decompcascade ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -734,6 +735,11 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat nue_decomp_cascade(i_cwdl2) = 1.0_r8 end if + ! Allocate tillage variables + if (get_do_tillage()) then + call tillage_init_decompcascade(i_avl_som, i_chem_som, i_phys_som, i_str_lit) + end if + deallocate(params_inst%mimics_mge) deallocate(params_inst%mimics_vmod) deallocate(params_inst%mimics_vint) From a5e770e21d1e965eb02bef09cf0a529d191ef15c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Jul 2023 15:12:28 -0600 Subject: [PATCH 1144/2067] Added note. --- src/biogeochem/TillageMod.F90 | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index d29029ee09..baeae3bfe5 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -253,6 +253,9 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som return end if + ! TODO: Call get_tillage_multipliers for each crop patch in column, then outside patch + ! loop save their weighted average to the column-level decomp_k. See p2c_1d() for + ! how to get patch weights. ! TODO: Figure out why adding ".and. col%lun_itype(c) == istcrop" to conditional ! controlling call of this subroutine didn't properly exclude non-crop columns. ! That working would allow simplification here. From 07a259fafe30f36e5e650efb850b7871caa45e04 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 7 Jul 2023 17:29:53 -0600 Subject: [PATCH 1145/2067] Only pass one patch's idop to get_tillage_multipliers(). --- src/biogeochem/TillageMod.F90 | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index baeae3bfe5..eded6ca448 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -151,7 +151,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers(idop, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -167,8 +167,7 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c use clm_time_manager, only : get_curr_calday, get_curr_days_per_year use pftconMod , only : ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean ! !ARGUMENTS: - integer , intent(in) :: idop(:) ! patch day of planting - integer , intent(in) :: p ! index of patch this is being called for + integer , intent(in) :: idop ! patch day of planting integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools ! @@ -185,10 +184,10 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine ! days past planting may determine harvest/tillage - if (day >= idop(p)) then - idpp = day - idop(p) + if (day >= idop) then + idpp = day - idop else - idpp = int(dayspyr) + day - idop(p) + idpp = int(dayspyr) + day - idop end if ! ----------------------------------------------------- @@ -202,11 +201,11 @@ subroutine get_tillage_multipliers(idop, p, i_act_som, i_slo_som, i_pas_som, i_c phase = 0 if (use_original_tillage) then - if (day >= idop(p) .and. day < idop(p)+15) then ! based on Point Chisel Tandem Disk multipliers + if (day >= idop .and. day < idop+15) then ! based on Point Chisel Tandem Disk multipliers phase = 1 - else if (day >= idop(p)+15 .and. day < idop(p)+45) then ! based on Field and Row Cultivator multipliers + else if (day >= idop+15 .and. day < idop+45) then ! based on Field and Row Cultivator multipliers phase = 2 - else if (day >= idop(p)+45 .and. day = idop+45 .and. day Date: Fri, 7 Jul 2023 17:44:05 -0600 Subject: [PATCH 1146/2067] Generalize tillage to work with multiple active crop patches. Multiple active crop patches per column shouldn't be possible YET, but perhaps eventually it will be. --- src/biogeochem/TillageMod.F90 | 34 ++++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/src/biogeochem/TillageMod.F90 b/src/biogeochem/TillageMod.F90 index eded6ca448..c1904b017f 100644 --- a/src/biogeochem/TillageMod.F90 +++ b/src/biogeochem/TillageMod.F90 @@ -26,7 +26,6 @@ module TillageMod logical :: do_tillage_low ! Do low-intensity tillage? logical :: do_tillage_high ! Do high-intensity tillage? logical :: use_original_tillage ! Use get_tillage_multipliers_orig? - real(r8), pointer :: tillage_mults(:) ! (ndecomp_pools) real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) @@ -122,7 +121,6 @@ subroutine tillage_init_century(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_li end if ! Allocate tillage multipliers - allocate(tillage_mults(ndecomp_pools)); tillage_mults(:) = 1.0_r8 allocate(tillage_mults_allphases(ndecomp_pools, nphases)); tillage_mults_allphases(:,:) = 1.0_r8 ! Fill tillage_mults_allphases @@ -151,7 +149,7 @@ function get_do_tillage() end function get_do_tillage - subroutine get_tillage_multipliers(idop, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + subroutine get_tillage_multipliers(tillage_mults, idop, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) ! !DESCRIPTION: ! ! Get the cultivation effective multiplier if prognostic crops are on and @@ -167,6 +165,7 @@ subroutine get_tillage_multipliers(idop, i_act_som, i_slo_som, i_pas_som, i_cel_ use clm_time_manager, only : get_curr_calday, get_curr_days_per_year use pftconMod , only : ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean ! !ARGUMENTS: + real(r8) , intent(inout) :: tillage_mults(:) ! tillage multipliers for this patch integer , intent(in) :: idop ! patch day of planting integer , intent(in) :: i_act_som, i_slo_som, i_pas_som ! indices for soil organic matter pools integer , intent(in) :: i_cel_lit, i_lig_lit ! indices for litter pools @@ -237,6 +236,7 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som ! ! !USES use pftconMod , only : npcropmin + use PatchType , only : patch ! ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting @@ -247,28 +247,34 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som ! ! !LOCAL VARIABLES integer :: p, this_patch, j, n_noncrop - integer :: idop_thispatch + real :: sumwt ! sum of all patch weights, to check + real(r8), dimension(ndecomp_pools) :: tillage_mults + real(r8), dimension(ndecomp_pools) :: tillage_mults_1patch if (.not. col%active(c)) then return end if + + ! Initialize tillage multipliers to 0. We will loop through all patches in column, + ! adding patch-weighted multipliers to this. + tillage_mults(:) = 0.0_r8 - ! TODO: Call get_tillage_multipliers for each crop patch in column, then outside patch - ! loop save their weighted average to the column-level decomp_k. See p2c_1d() for - ! how to get patch weights. ! TODO: Figure out why adding ".and. col%lun_itype(c) == istcrop" to conditional ! controlling call of this subroutine didn't properly exclude non-crop columns. - ! That working would allow simplification here. + ! That working would allow some simplification here. this_patch = 0 n_noncrop = 0 + sumwt = 0.0_r8 do p = col%patchi(c),col%patchf(c) - if (patch%active(p)) then + if (patch%active(p) .and. patch%wtcol(p) /= 0._r8) then if (patch%itype(p) >= npcropmin) then if (this_patch > 0) then call endrun('ERROR multiple active crop patches found in this column') end if this_patch = p - idop_thispatch = idop(p) + call get_tillage_multipliers(tillage_mults_1patch, idop(p), i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + tillage_mults = tillage_mults + tillage_mults_1patch * patch%wtcol(p) + sumwt = sumwt + patch%wtcol(p) else n_noncrop = n_noncrop + 1 end if @@ -276,15 +282,15 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k, i_act_som, i_slo_som end do if (n_noncrop > 0) then if (this_patch > 0) then - call endrun('ERROR Active crop and non-crop patches found in this active column') + call endrun('ERROR Active, non-zero-weight crop AND non-crop patches found') end if return elseif (this_patch == 0) then - call endrun('ERROR No active patches found (crop OR non-crop)') + call endrun('ERROR No active, non-zero-weight patches found (crop OR non-crop)') + elseif (sumwt > 1.0_r8 + 1.e-6_r8) then + call endrun('ERROR Active crop patch weights does not sum to 1') end if - call get_tillage_multipliers(idop_thispatch, i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) - ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm ! of the soil surface, rather than whole soil - MWGraham do j = 1,5 From eb3171d6829bc0fdea64e5aed919436b40683717 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 18 Jul 2023 11:01:06 -0600 Subject: [PATCH 1147/2067] Moved TillageMod.F90 to soilbiogeochem/ --- src/{biogeochem => soilbiogeochem}/TillageMod.F90 | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/{biogeochem => soilbiogeochem}/TillageMod.F90 (100%) diff --git a/src/biogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 similarity index 100% rename from src/biogeochem/TillageMod.F90 rename to src/soilbiogeochem/TillageMod.F90 From a57f188f469bad3a960a9c8cff294cca8183096c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 18 Jul 2023 12:02:17 -0600 Subject: [PATCH 1148/2067] Eliminate repetitive code in LakeFluxesMod --- src/biogeophys/LakeFluxesMod.F90 | 32 +++++++++++--------------------- 1 file changed, 11 insertions(+), 21 deletions(-) diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 212a55043d..11b141100c 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -349,33 +349,23 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, end select z0qg(p) = z0hg(p) else ! use roughness over snow as in Biogeophysics1 + if(use_z0m_snowmelt) then + if ( snomelt_accum(c) < 1.e-5_r8 ) then + z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 + else + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 + end if + else + z0mg(p) = params_inst%zsno + end if + select case (z0param_method) case ('Meier2022') - if(use_z0m_snowmelt) then - if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 - else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 - end if - - else - z0mg(p) = params_inst%zsno - - end if z0hg(p) = 70._r8 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 - case ('ZengWang2007') - if(use_z0m_snowmelt) then - if ( snomelt_accum(c) < 1.e-5_r8 ) then - z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 - else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 - end if - else - z0mg(p) = params_inst%zsno - end if z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select + z0qg(p) = z0hg(p) end if From 955ec7fc7a0c323e6205a943fc4de6aada6d74b7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 18 Jul 2023 11:27:57 -0600 Subject: [PATCH 1149/2067] Tillage now applied to MIMICS. --- bld/CLMBuildNamelist.pm | 12 ++---------- src/biogeochem/CNDriverMod.F90 | 4 ++-- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 17 ++++++++++++++++- 3 files changed, 20 insertions(+), 13 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c88c2c8718..c062bbd561 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2151,16 +2151,8 @@ sub setup_logic_tillage { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); - if ( $tillage_mode ne "off" ) { - - if ( not &value_is_true($nl->get_value('use_crop')) ) { - $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); - } - - my $soil_decomp_method = remove_leading_and_trailing_quotes( $nl->get_value( "soil_decomp_method" ) ); - if ( $soil_decomp_method ne "CENTURYKoven2013" ) { - $log->fatal_error( "Tillage can only be used with soil_decomp_method 'CENTURYKoven2013'" ); - } + if ( $tillage_mode ne "off" && not &value_is_true($nl->get_value('use_crop')) ) { + $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); } } diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 77da920a91..117c5f4a03 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -343,11 +343,11 @@ subroutine CNDriverNoLeaching(bounds, soilstate_inst, temperature_inst, ch4_inst, soilbiogeochem_carbonflux_inst, & cnveg_state_inst%idop_patch) else if (decomp_method == mimics_decomp) then - ! TODO(ssr): Add tillage to MIMICS? call decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & soilstate_inst, temperature_inst, cnveg_carbonflux_inst, ch4_inst, & - soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst) + soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + cnveg_state_inst%idop_patch) end if call t_stopf('DecompRate') diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index 4f303edbd9..82df969a80 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -761,7 +761,8 @@ end subroutine init_decompcascade_mimics subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & num_soilp, filter_soilp, clm_fates, & soilstate_inst, temperature_inst, cnveg_carbonflux_inst, & - ch4_inst, soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst) + ch4_inst, soilbiogeochem_carbonflux_inst, soilbiogeochem_carbonstate_inst, & + idop) ! ! !DESCRIPTION: ! Calculate rates and decomposition pathways for the MIMICS @@ -774,6 +775,8 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & use subgridAveMod , only : p2c use PatchType , only : patch use pftconMod , only : pftname + use TillageMod , only : get_do_tillage + use TillageMod , only : get_apply_tillage_multipliers ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -788,6 +791,7 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & type(soilbiogeochem_carbonflux_type) , intent(inout) :: soilbiogeochem_carbonflux_inst type(soilbiogeochem_carbonstate_type), intent(in) :: soilbiogeochem_carbonstate_inst type(hlm_fates_interface_type) , intent(inout) :: clm_fates + integer, optional , intent(in) :: idop(:) ! patch day of planting ! ! !LOCAL VARIABLES: real(r8), parameter :: eps = 1.e-6_r8 @@ -1310,6 +1314,17 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & end do end do + ! Tillage + if (get_do_tillage()) then + if (.not. present(idop)) then + call endrun("Do not call tillage without providing idop.") + end if + do fc = 1,num_soilc + c = filter_soilc(fc) + call get_apply_tillage_multipliers(idop, c, decomp_k) + end do + end if + ! pathfrac terms not calculated in the previous loop pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s1) = 1.0_r8 pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s3s1) = 1.0_r8 From 6c4e019a14c3e35ff96644033701dd9ac1fa7b3c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 18 Jul 2023 12:02:41 -0600 Subject: [PATCH 1150/2067] Compile fixes. --- src/soilbiogeochem/TillageMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 91e18f918b..635efa10d2 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -141,7 +141,7 @@ subroutine tillage_init_decompcascade(i_act_som_in, i_slo_som_in, i_pas_som_in, i_slo_som = i_slo_som_in i_pas_som = i_pas_som_in i_cel_lit = i_cel_lit_in - if (present(i_lig_lit)) then + if (present(i_lig_lit_in)) then i_lig_lit = i_lig_lit_in else i_lig_lit = -1 @@ -296,7 +296,7 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k) call endrun('ERROR multiple active crop patches found in this column') end if this_patch = p - call get_tillage_multipliers(tillage_mults_1patch, idop(p), i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) + call get_tillage_multipliers(tillage_mults_1patch, idop(p)) tillage_mults = tillage_mults + tillage_mults_1patch * patch%wtcol(p) sumwt = sumwt + patch%wtcol(p) else From 92a87e85aadc249300e45c42f66c4aa0de032722 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 18 Jul 2023 17:26:49 -0600 Subject: [PATCH 1151/2067] Change two intent(out) to (inout) to eliminate NaNs in nag test --- src/biogeophys/PhotosynthesisMod.F90 | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/PhotosynthesisMod.F90 b/src/biogeophys/PhotosynthesisMod.F90 index 5b2c68a0fb..a721086e22 100644 --- a/src/biogeophys/PhotosynthesisMod.F90 +++ b/src/biogeophys/PhotosynthesisMod.F90 @@ -2706,7 +2706,6 @@ subroutine PhotosynthesisHydraulicStress ( bounds, fn, filterp, & use clm_varpar , only : nlevsoi use pftconMod , only : nbrdlf_dcd_tmp_shrub, npcropmin use ColumnType , only : col - use shr_infnan_mod , only : shr_infnan_isnan ! ! !ARGUMENTS: @@ -3477,6 +3476,7 @@ subroutine PhotosynthesisHydraulicStress ( bounds, fn, filterp, & else gsminsun = nan gsminsha = nan + call endrun( 'ERROR:: Photosynthesis::PhotosynthesisHydraulicStress must choose stomatalcond_mtd method' ) end if call calcstress(p,c,vegwp(p,:),bsun(p),bsha(p),gb_mol(p),gsminsun, gsminsha, & qsatl(p),qaf(p), atm2lnd_inst,canopystate_inst,waterdiagnosticbulk_inst, & @@ -4064,8 +4064,8 @@ subroutine brent_PHS(xsun, x1sun, x2sun, f1sun, f2sun, xsha, x1sha, x2sha, f1sha real(r8), intent(in) :: lmr_z_sun, lmr_z_sha ! canopy layer: leaf maintenance respiration rate (umol CO2/m**2/s) real(r8), intent(in) :: par_z_sun, par_z_sha ! par absorbed per unit lai for canopy layer (w/m**2) real(r8), intent(in) :: rh_can ! inside canopy relative humidity - real(r8), intent(out) :: gs_mol_sun ! sunlit leaf stomatal conductance (umol H2O/m**2/s) - real(r8), intent(out) :: gs_mol_sha ! shaded leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol_sun ! sunlit leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol_sha ! shaded leaf stomatal conductance (umol H2O/m**2/s) real(r8), intent(inout) :: bsun ! sunlit canopy transpiration wetness factor (0 to 1) real(r8), intent(inout) :: bsha ! shaded canopy transpiration wetness factor (0 to 1) real(r8), intent(in) :: qsatl ! leaf specific humidity [kg/kg] @@ -4344,6 +4344,7 @@ subroutine ci_func_PHS(x,cisun, cisha, fvalsun, fvalsha, p, iv, c, bsun, bsha, b gs_mol_sun = bbb(p) else gs_mol_sun = nan + call endrun( 'ERROR:: Photosynthesis::ci_func_PHS must choose stomatalcond_mtd method' ) end if gs_mol_sun = max( bsun*gs_mol_sun, 1._r8) fvalsun = 0._r8 ! really tho? zqz @@ -4355,6 +4356,7 @@ subroutine ci_func_PHS(x,cisun, cisha, fvalsun, fvalsha, p, iv, c, bsun, bsha, b gs_mol_sha = bbb(p) else gs_mol_sha = nan + call endrun( 'ERROR:: Photosynthesis::ci_func_PHS must choose stomatalcond_mtd method' ) end if gs_mol_sha = max( bsha*gs_mol_sha, 1._r8) fvalsha = 0._r8 From fb7e266e38601291576d60b2255bcfb507a471fa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 08:47:28 -0600 Subject: [PATCH 1152/2067] Removed a now-unneeded error check. This would have thrown a prettier error message for an invalid index in the case where harvest count was <= 0. However, at this point the code is pretty well stress-tested, so I don't think it's needed anymore. --- src/biogeochem/CNPhenologyMod.F90 | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index daeb85c685..2d52ab729c 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3100,9 +3100,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & + repr_grainc_to_food_thispool if (reproductivec(p,k) + repr_grainc_to_food_thispool * dt .gt. 0) then - if (h .le. 0) then - call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") - end if repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + repr_grainc_to_food_thispool * dt repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & From fd896feb1c732c29f407a765509b7c24973ce299 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 08:48:42 -0600 Subject: [PATCH 1153/2067] Replaced .gt. 0 with > 0._r8. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 2d52ab729c..c2a66511f7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3099,7 +3099,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & + repr_grainc_to_food_thispool - if (reproductivec(p,k) + repr_grainc_to_food_thispool * dt .gt. 0) then + if (reproductivec(p,k) + repr_grainc_to_food_thispool * dt > 0._r8) then repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & + repr_grainc_to_food_thispool * dt repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & From 4e22d04ee9871c21ab8bc8b25b8a49d6556c78e7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 08:55:35 -0600 Subject: [PATCH 1154/2067] Improved a bit of ChangeLog.tmp. --- doc/ChangeLog.tmp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index 439dda2c64..d7e0433166 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -43,7 +43,7 @@ Notes of particular relevance for users --------------------------------------- Caveats for users: - Untested: + Untested but theoretically possible: * Time-varying inputs * Running at any resolution other than one matching the crop calendar inputs From 876d34fae31cfbc24241da95c1e9cc3292d47831 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 13:00:58 -0600 Subject: [PATCH 1155/2067] ChangeLog.tmp: Replace code diffs with patch URLs. --- doc/ChangeLog.tmp | 106 +++------------------------------------------- 1 file changed, 5 insertions(+), 101 deletions(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index d7e0433166..3799ae05bb 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -104,108 +104,12 @@ Changes answers relative to baseline: YES for Clm45BgcCrop compsets only - ERS_Ly5_P72x1.f10_f10_mg37.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput - SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm45BgcCrop.izumi_nag.clm-oldhyd - The first four were likely due to an order-of-operations change in CNOffsetLitterfall(), as they resolve with the following patch: - --- a/src/biogeochem/CNPhenologyMod.F90 - +++ b/src/biogeochem/CNPhenologyMod.F90 - @@ -2978,7 +2978,6 @@ contains - real(r8) :: cropseedn_deficit_remaining ! remaining amount of crop seed N deficit that still needs to be restored (gN/m2) (positive, in contrast to the negative cropseedn_deficit) - real(r8) :: cropseedc_deficit_to_restore ! amount of crop seed C deficit that will be restored from this grain pool (gC/m2) - real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2) - - real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) - !----------------------------------------------------------------------- - - associate( & - @@ -3096,15 +3095,14 @@ contains - repr_grainn_to_seed(p,k) = t1 * cropseedn_deficit_to_restore - - ! Send the remaining grain to the food product pool - - repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) - repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & - - + repr_grainc_to_food_thispool - - if (reproductivec(p,k) + repr_grainc_to_food_thispool * dt .gt. 0) then - + + cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) - + if (reproductivec(p,k) + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt .gt. 0) then - if (h .le. 0) then - call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") - end if - repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & - - + repr_grainc_to_food_thispool * dt - + + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt - repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & - + repr_grainc_to_food_perharv(p,h,k) - end if - - The last is resolved with an additional patch that removes all my changes to CNOffsetLitterfall()---changes which *should* only affect new diagnostic variables: - --- a/src/biogeochem/CNPhenologyMod.F90 - +++ b/src/biogeochem/CNPhenologyMod.F90 - @@ -408,8 +408,7 @@ contains - cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) - - call CNOffsetLitterfall(num_soilp, filter_soilp, & - - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - - crop_inst) - + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) - - call CNBackgroundLitterfall(num_soilp, filter_soilp, & - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) - @@ -2942,8 +2941,7 @@ contains - - !----------------------------------------------------------------------- - subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & - - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, & - - crop_inst) - + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst) - ! - ! !DESCRIPTION: - ! Determines the flux of C and N from displayed pools to litter - @@ -2964,10 +2962,9 @@ contains - type(cnveg_nitrogenstate_type), intent(in) :: cnveg_nitrogenstate_inst - type(cnveg_carbonflux_type) , intent(inout) :: cnveg_carbonflux_inst - type(cnveg_nitrogenflux_type) , intent(inout) :: cnveg_nitrogenflux_inst - - type(crop_type) , intent(in) :: crop_inst - ! - ! !LOCAL VARIABLES: - - integer :: p, c, k, h ! indices - + integer :: p, c, k ! indices - integer :: fp ! lake filter patch index - real(r8):: t1 ! temporary variable - real(r8):: denom ! temporary variable for divisor - @@ -3015,8 +3012,6 @@ contains - frootc_to_litter => cnveg_carbonflux_inst%frootc_to_litter_patch , & ! Output: [real(r8) (:) ] fine root C litterfall (gC/m2/s) - livestemc_to_litter => cnveg_carbonflux_inst%livestemc_to_litter_patch , & ! Output: [real(r8) (:) ] live stem C litterfall (gC/m2/s) - repr_grainc_to_food => cnveg_carbonflux_inst%repr_grainc_to_food_patch , & ! Output: [real(r8) (:,:) ] grain C to food (gC/m2/s) - - repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain C to food per harvest (gC/m2) - - repr_grainc_to_food_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain C to food harvested this calendar year (gC/m2) - repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) - repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) - repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) - @@ -3069,9 +3064,6 @@ contains - ! if this were ever changed, we'd need to add code to the "else" - if (ivt(p) >= npcropmin) then - - - ! How many harvests have occurred? - - h = crop_inst%harvest_count(p) - - - ! Replenish the seed deficits from grain, if there is enough available - ! grain. (If there is not enough available grain, the seed deficits will - ! accumulate until there is eventually enough grain to replenish them.) - @@ -3097,15 +3089,6 @@ contains - ! Send the remaining grain to the food product pool - repr_grainc_to_food(p,k) = t1 * reproductivec(p,k) & - + cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) - - if (reproductivec(p,k) + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt .gt. 0) then - - if (h .le. 0) then - - call endrun(msg="CNOffsetLitterfall(): Invalid harvest_count") - - end if - - repr_grainc_to_food_perharv(p,h,k) = reproductivec(p,k) & - - + (cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k)) * dt - - repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & - - + repr_grainc_to_food_perharv(p,h,k) - - end if - repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & - + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) - end do + The first four were likely due to an order-of-operations change in CNOffsetLitterfall(), as they resolve with the patch at + https://github.com/samsrabin/CTSM/commit/c30320cbd6583bccbcc290ffe536e8500e6ec358 + The last is resolved with an additional patch that removes all my changes to CNOffsetLitterfall()---changes which *should* only + affect new diagnostic variables: + https://github.com/samsrabin/CTSM/commit/e025f555e74584c63d50f27c4df38326fa64bc4f Other details ------------- From b5915c0e28984087e8a1c49ae709e9d7904a16af Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 13:01:15 -0600 Subject: [PATCH 1156/2067] ChangeLog.tmp: Correct new CIME version. --- doc/ChangeLog.tmp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index 3799ae05bb..2613f960da 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -114,7 +114,7 @@ Changes answers relative to baseline: YES for Clm45BgcCrop compsets only Other details ------------- List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime - cime: cime6.0.108 -> cime6.0.136 + cime: cime6.0.108 -> cime6.0.118 Pull Requests that document the changes (include PR ids): https://github.com/ESCOMP/CTSM/pull/1863 From be0c9fb7b1c67ea6251dd6d18aaf2b62a743cc1f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 13:04:39 -0600 Subject: [PATCH 1157/2067] ChangeLog.tmp: Marked answer changes as "larger than roundoff." --- doc/ChangeLog.tmp | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index 2613f960da..06ca01cd5f 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -90,12 +90,7 @@ Changes answers relative to baseline: YES for Clm45BgcCrop compsets only Summarize any changes to answers, i.e., - what code configurations: Clm45BgcCrop - what platforms/compilers: Cheyenne intel and gnu, Izumi intel and nag - - nature of change (roundoff; larger than roundoff/same climate; new climate): ??? - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - ??? + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff 5 tests in aux_clm showed true DIFFs (i.e., not just field list differences / new output files): - SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput From 27f336d5c96115db6c795f31ee25c1de648c74b2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 19 Jul 2023 15:11:53 -0600 Subject: [PATCH 1158/2067] Return this to what it was before the FATES addition should come later --- src/main/filterMod.F90 | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 5b39b972fa..0b7d230a54 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -477,8 +477,7 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fl = 0 fnl = 0 do p = bounds%begp,bounds%endp - if(.not.use_fates)then - if ((patch%active(p) .or. include_inactive)) then + if (patch%active(p) .or. include_inactive) then if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types fl = fl + 1 this_filter(nc)%pcropp(fl) = p @@ -490,7 +489,6 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio end if end if end if - end if end do this_filter(nc)%num_pcropp = fl this_filter(nc)%num_soilnopcropp = fnl ! This wasn't being set before... From 132f4eb72d18ec9cb9aa4a82f40d9889d31fef1d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 19 Jul 2023 16:18:22 -0600 Subject: [PATCH 1159/2067] Check that with FATES on neither LUNA nor FUN can be on --- bld/unit_testers/build-namelist_test.pl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index ed6328c166..e62bf7b1d4 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1975; +my $ntests = 1977; if ( defined($opts{'compare'}) ) { $ntests += 1344; } @@ -984,6 +984,16 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_1", }, + "useFATESWluna" =>{ options=>"--bgc fates --envxml_dir . --no-megan", + namelst=>"use_luna=TRUE", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, + "useFATESWfun" =>{ options=>"--bgc fates --envxml_dir . --no-megan", + namelst=>"use_fun=TRUE", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, "FireNoneButBGCfireon" =>{ options=>"-bgc bgc -envxml_dir . -light_res none", namelst=>"fire_method='li2021gswpfrc'", GLC_TWO_WAY_COUPLING=>"FALSE", From d4261c8f1c2f642d75dc9e119d6f7053d22f43f8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 19 Jul 2023 17:22:13 -0600 Subject: [PATCH 1160/2067] Explicitly make sure you can not turn LUNA on with FATES, and add a use_luna setting for FATES with clm4_5 that was missing --- bld/CLMBuildNamelist.pm | 6 ++++++ bld/namelist_files/namelist_defaults_ctsm.xml | 1 + 2 files changed, 7 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 545fee3731..6cc16ecb96 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3307,6 +3307,12 @@ sub setup_logic_luna { 'use_cn'=>$nl_flags->{'use_cn'} ); } $nl_flags->{'use_luna'} = $nl->get_value('use_luna'); + + # LUNA can NOT be on with FATES + if ( &value_is_true( $nl_flags->{'use_luna'} ) && &value_is_true( $nl_flags->{'use_fates'} )) { + $log->fatal_error("Cannot turn use_luna to true when bgc=fates" ); + } + my $vcmax_opt= $nl->get_value('vcmax_opt'); # lnc_opt only applies if luna is on or for vcmax_opt=3/4 if ( &value_is_true( $nl_flags->{'use_luna'} ) || $vcmax_opt == 3 || $vcmax_opt == 4 ) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e0ad42e4f7..9d2dc1920d 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -510,6 +510,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. .false. .false. +.false. .true. From d2306c52931814210d247ad06d1a003cd677375e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 19 Jul 2023 17:29:57 -0600 Subject: [PATCH 1161/2067] Add a test that FATES with suplemental nitrogen on is NOT allowed, this test fails because that isn't in yet --- bld/unit_testers/build-namelist_test.pl | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index e62bf7b1d4..5bb32167f2 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1977; +my $ntests = 1978; if ( defined($opts{'compare'}) ) { $ntests += 1344; } @@ -994,6 +994,11 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_1", }, + "useFATESWOsuplnitro" =>{ options=>"--bgc fates --envxml_dir . --no-megan", + namelst=>"suplnitro='NONE'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_1", + }, "FireNoneButBGCfireon" =>{ options=>"-bgc bgc -envxml_dir . -light_res none", namelst=>"fire_method='li2021gswpfrc'", GLC_TWO_WAY_COUPLING=>"FALSE", From bfe8cf080ca2b70e4323715b5e7b4c40e39ac3c0 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 19 Jul 2023 18:27:54 -0600 Subject: [PATCH 1162/2067] Change three intent(out) to (inout) to prevent NaNs in nag test --- src/biogeophys/PhotosynthesisMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/PhotosynthesisMod.F90 b/src/biogeophys/PhotosynthesisMod.F90 index a721086e22..beda9d0bc5 100644 --- a/src/biogeophys/PhotosynthesisMod.F90 +++ b/src/biogeophys/PhotosynthesisMod.F90 @@ -2266,7 +2266,7 @@ subroutine hybrid(x0, p, iv, c, gb_mol, je, cair, oair, lmr_z, par_z,& real(r8), intent(in) :: cair ! Atmospheric CO2 partial pressure (Pa) real(r8), intent(in) :: oair ! Atmospheric O2 partial pressure (Pa) integer, intent(in) :: p, iv, c ! pft, c3/c4, and column index - real(r8), intent(out) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) integer, intent(out) :: iter !number of iterations used, for record only type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type), intent(inout) :: photosyns_inst @@ -2378,7 +2378,7 @@ subroutine brent(x, x1,x2,f1, f2, tol, ip, iv, ic, gb_mol, je, cair, oair,& real(r8), intent(in) :: oair ! Atmospheric O2 partial pressure (Pa) real(r8), intent(in) :: rh_can ! inside canopy relative humidity integer, intent(in) :: ip, iv, ic ! pft, c3/c4, and column index - real(r8), intent(out) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type), intent(inout) :: photosyns_inst ! @@ -2568,7 +2568,7 @@ subroutine ci_func(ci, fval, p, iv, c, gb_mol, je, cair, oair, lmr_z, par_z,& real(r8) , intent(in) :: rh_can ! canopy air realtive humidity integer , intent(in) :: p, iv, c ! pft, vegetation type and column indexes real(r8) , intent(out) :: fval ! return function of the value f(ci) - real(r8) , intent(out) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) + real(r8) , intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type) , intent(inout) :: photosyns_inst ! From 80977d7c8a65f6b7f1d9120c03b03d50a9503779 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 20 Jul 2023 10:23:41 -0600 Subject: [PATCH 1163/2067] we can now run FATES with 1 deg in SP mode --- cime_config/testdefs/testlist_clm.xml | 4 ++-- .../testmods_dirs/clm/FatesColdSatPhen_prescribed/README | 3 --- .../clm/FatesColdSatPhen_prescribed/user_nl_clm | 8 ++++---- 3 files changed, 6 insertions(+), 9 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 68c3f39867..73b951c488 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2382,13 +2382,13 @@ - + - + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README deleted file mode 100644 index 116e0f43b4..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/README +++ /dev/null @@ -1,3 +0,0 @@ -This testmod currently only works with lai streams (not soil moisture), because of FATES issue #845 - -See https://github.com/NGEET/fates/issues/845 diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm index eb7a85165c..a1ea0e0cf8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm @@ -1,8 +1,8 @@ ! right now we can't do prescribed soil moisture because of FATES issue #845 - !use_soil_moisture_streams = .true. + use_soil_moisture_streams = .true. use_lai_streams = .true. - !hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' - !soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset + hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' + soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset - !soilm_ignore_data_if_missing = .true. + soilm_ignore_data_if_missing = .true. \ No newline at end of file From 80ba5e8e197395067e8eb3e3bed942dfac069efa Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 20 Jul 2023 10:40:22 -0600 Subject: [PATCH 1164/2067] update to use constant --- src/utils/clmfates_interfaceMod.F90 | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 8a3be405ff..c87482b80b 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -159,6 +159,7 @@ module CLMFatesInterfaceMod use dynHarvestMod , only : dynHarvest_interp_resolve_harvesttypes use FatesConstantsMod , only : hlm_harvest_area_fraction use FatesConstantsMod , only : hlm_harvest_carbon + use FatesConstantsMod , only : area_error use perf_mod , only : t_startf, t_stopf implicit none @@ -713,10 +714,10 @@ subroutine init(this, bounds_proc ) this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m) end do - if(abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub))-1.0_r8).gt.1.0e-9)then - write(iulog,*) 'pft_area error in interfc ',s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:))-1.0_r8 + if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > area_error) then + write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:)) - 1.0_r8 call endrun(msg=errMsg(sourcefile, __LINE__)) - endif + end if end do !site ! Initialize site-level static quantities dictated by the HLM From 7a494e0743b2f0f5dd2cc575d6056608de4c46cb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 11:59:13 -0600 Subject: [PATCH 1165/2067] Update cime from cime6.0.118 to 125. To match upcoming all-Externals update to match set used in CESM beta 15. --- Externals.cfg | 2 +- doc/ChangeLog.tmp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index 02d6270316..62a119004e 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -44,7 +44,7 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.118 +tag = cime6.0.125 required = True [cmeps] diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index 06ca01cd5f..bb79449cd5 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -109,7 +109,7 @@ Changes answers relative to baseline: YES for Clm45BgcCrop compsets only Other details ------------- List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime - cime: cime6.0.108 -> cime6.0.118 + cime: cime6.0.108 -> cime6.0.125 Pull Requests that document the changes (include PR ids): https://github.com/ESCOMP/CTSM/pull/1863 From 418d600ebbca2a78d99741bedae8055fda11e9b3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 12:04:17 -0600 Subject: [PATCH 1166/2067] ChangeLog.tmp: Changes now classified as roundoff-level. --- doc/ChangeLog.tmp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index bb79449cd5..f56465997e 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -90,7 +90,7 @@ Changes answers relative to baseline: YES for Clm45BgcCrop compsets only Summarize any changes to answers, i.e., - what code configurations: Clm45BgcCrop - what platforms/compilers: Cheyenne intel and gnu, Izumi intel and nag - - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff 5 tests in aux_clm showed true DIFFs (i.e., not just field list differences / new output files): - SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput From 17b4e494cf038b3f0237c46cd4f909f15ddb7295 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 12:04:38 -0600 Subject: [PATCH 1167/2067] ChangeLog.tmp: Removed "known bugs found since the previous tag" section. --- doc/ChangeLog.tmp | 3 --- 1 file changed, 3 deletions(-) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp index f56465997e..6d66eee092 100644 --- a/doc/ChangeLog.tmp +++ b/doc/ChangeLog.tmp @@ -36,9 +36,6 @@ CTSM issues fixed (include CTSM Issue #): Some on #1649 -- Additional "annual" (per growing season) crop outputs -Known bugs found since the previous tag (include issue #): - None??? - Notes of particular relevance for users --------------------------------------- From d40dd88407b4eae13d3d397bac5d705a2cfd7ed3 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 20 Jul 2023 14:53:26 -0600 Subject: [PATCH 1168/2067] need to check lai streams --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index d906fd6c62..8d8a46f7fc 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3878,7 +3878,7 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( $nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates" ) { + if ( ($nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates") && &value_is_true($nl->get_value('use_lai_streams')) ) { if ( $nl_flags->{'bgc_mode'} eq "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) ) { $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); } From dbcbe05d69c890c9c4f1f6c5a78dae7143907f63 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 20 Jul 2023 14:54:08 -0600 Subject: [PATCH 1169/2067] need to check lai streams --- bld/CLMBuildNamelist.pm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 8d8a46f7fc..083bff2ed7 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3878,8 +3878,8 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( ($nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates") && &value_is_true($nl->get_value('use_lai_streams')) ) { - if ( $nl_flags->{'bgc_mode'} eq "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) ) { + if ( ($nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates") ) { + if ( $nl_flags->{'bgc_mode'} eq "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) && &value_is_true($nl->get_value('use_lai_streams'))) { $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); } if ( &value_is_true($nl->get_value('use_lai_streams')) ) { From 233c2dadc454da9d9590ff3798cf4738a00f1ce2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:00:59 -0600 Subject: [PATCH 1170/2067] Removed unused make_surface_for_gddgen.py. --- .../crop_calendars/make_surface_for_gddgen.py | 191 ------------------ 1 file changed, 191 deletions(-) delete mode 100644 python/ctsm/crop_calendars/make_surface_for_gddgen.py diff --git a/python/ctsm/crop_calendars/make_surface_for_gddgen.py b/python/ctsm/crop_calendars/make_surface_for_gddgen.py deleted file mode 100644 index f8b1b863b8..0000000000 --- a/python/ctsm/crop_calendars/make_surface_for_gddgen.py +++ /dev/null @@ -1,191 +0,0 @@ -import numpy as np -import xarray as xr -import argparse -import sys -import os - - -# Doing what I did before with flanduse_timeseries, except now with -# fsurdat. -def get_new_fsurdat_v0(surf, lu): - # Where is each crop ever active? - if "AREA" not in lu: - lu["AREA"] = xr.DataArray( - data=np.ones_like(lu["LANDFRAC_PFT"]), - dims=lu["LANDFRAC_PFT"].dims, - coords=lu["LANDFRAC_PFT"].coords, - ) - lu["AREA_CROP"] = (lu.AREA * lu.LANDFRAC_PFT * lu.PCT_CROP / 100).transpose( - "time", "lsmlat", "lsmlon" - ) - lu["AREA_CFT"] = (lu["AREA_CROP"] * lu.PCT_CFT / 100).transpose( - "time", "cft", "lsmlat", "lsmlon" - ) - ds_area_max = lu["AREA_CFT"].max(dim="time") - lu["ever_active_bycft"] = (ds_area_max > 0).transpose("cft", "lsmlat", "lsmlon") - lu["ever_active"] = lu["ever_active_bycft"].any(dim="cft") - - # For cells that EVER have cropland, when do they have 0 crop area in the - # surface dataset? Give them some, taking it from NATVEG. - new_pct_crop_ar = surf["PCT_CROP"].values - needs_pctcrop_donation = np.where((new_pct_crop_ar == 0) & lu["ever_active"]) - pctcrop_donation = 0.01 # I.e., 0.01% - new_pct_natveg_ar = surf["PCT_NATVEG"].values - if np.any(new_pct_natveg_ar[needs_pctcrop_donation]) < pctcrop_donation: - raise RuntimeError(f"Not all donor PCT_NATVEG values are >= {pctcrop_donation}") - new_pct_crop_ar[needs_pctcrop_donation] = pctcrop_donation - new_pct_natveg_ar[needs_pctcrop_donation] -= pctcrop_donation - new_pct_crop_da = xr.DataArray( - data=new_pct_crop_ar, coords=surf["PCT_CROP"].coords, attrs=surf["PCT_CROP"].attrs - ) - new_pct_natveg_da = xr.DataArray( - data=new_pct_natveg_ar, coords=surf["PCT_NATVEG"].coords, attrs=surf["PCT_NATVEG"].attrs - ) - if np.any((new_pct_crop_da == 0) & lu["ever_active"]): - raise RuntimeError("Failed to fill 0% CROP with 1% where needed.") - - # For cells that EVER have each CFT, when do they have 0 area of that CFT - # in the surface dataset? Change those 0% values to something positive. - # The exact value doesn't matter, because in the next step we'll - # normalize so all CFTs sum to 100. - new_pct_cft_ar = surf["PCT_CFT"].values - new_pct_cft_ar[np.where((surf["PCT_CFT"] == 0) & lu["ever_active"])] = 1.0 - # Ensure sum to 100 - i = 0 - while np.any(~np.isclose(np.sum(new_pct_cft_ar, axis=1), 100.0)): - i += 1 - if i > 10: - raise RuntimeError("too many iterations") - new_pct_cft_ar = 100 * ( - new_pct_cft_ar / np.expand_dims(np.sum(new_pct_cft_ar, axis=1), axis=1) - ) - new_pct_cft_da = xr.DataArray( - data=new_pct_cft_ar, coords=surf["PCT_CFT"].coords, attrs=surf["PCT_CFT"].attrs - ) - - # Just take the first timestep - new_pct_cft_da = lu["PCT_CFT"].isel(time=0) - - return new_pct_crop_da, new_pct_natveg_da, new_pct_cft_da - - -# Trying to minimize the number of crop PFTs that need to be simulated. -# CLM currently giving errors about wt_cft not summing to 1. -def get_new_fsurdat_v1(surf, lu, params): - if params is None: - raise RuntimeError("You must provide -p/--paramfile") - - ########################################## - ### %% Get new PCT_CROP and PCT_NATVEG ### - ########################################## - - new_pct_crop_da = lu["PCT_CROP"].max(dim="time") - new_pct_crop_da.attrs = surf["PCT_CROP"].attrs - - surf_pct_crop_plus_natveg = surf["PCT_CROP"] + surf["PCT_NATVEG"] - if np.any(surf_pct_crop_plus_natveg < new_pct_crop_da): - raise RuntimeError("Max CROP > CROP+NATVEG") - - new_natveg_da = surf_pct_crop_plus_natveg - new_pct_crop_da - if np.any((new_natveg_da > 0) & (surf["PCT_NATVEG"] == 0)): - print("You created some NATVEG area. Not necessarily a problem, but unexpected.") - new_natveg_da.attrs = surf["PCT_NATVEG"].attrs - - ################################################################## - ### Get new PCT_CFT (percentage of cropland that is each crop) ### - ################################################################## - - # Sum all crops' max area, merging unrepresented types into their representative type - cft_list_int = surf["cft"].values - max_merged_pct_crop = np.full_like(surf["PCT_CFT"], 0.0) - for i, c in enumerate(cft_list_int): - mergetarget = params["mergetoclmpft"].sel(pft=c).values - m = np.where(cft_list_int == mergetarget)[0] - max_merged_pct_crop[m, :, :] += np.expand_dims( - lu["PCT_CFT"].sel(cft=c).max(dim="time"), axis=0 - ) - max_merged_pct_crop_da = xr.DataArray( - data=max_merged_pct_crop, dims=surf["PCT_CFT"].dims, attrs=surf["PCT_CFT"].attrs - ) - - # Ensure no area in merged-away crops - for i, c in enumerate(cft_list_int): - if (params["mergetoclmpft"].sel(pft=c) != c) and ( - max_merged_pct_crop_da.sel(cft=i).max() > 0 - ): - raise RuntimeError(f"Unexpected max_merged_pct_crop area for pft {c}") - - # Determine how many crops ever have any area - ever_has_this_crop = np.full_like(max_merged_pct_crop, 0.0) - ever_has_this_crop[max_merged_pct_crop > 0] = 1 - N_crops_ever_active = ever_has_this_crop.sum(axis=0) - - # Split crop area evenly among ever-included crops - new_pct_cft = np.full_like(surf["PCT_CFT"].isel(cft=0), 0.0) - new_pct_cft[N_crops_ever_active > 0] = 100 / N_crops_ever_active[N_crops_ever_active > 0] - new_pct_cft = np.expand_dims(new_pct_cft, axis=0) - new_pct_cft = np.tile(new_pct_cft, reps=[surf.dims["cft"], 1, 1]) - where_zero = np.where(max_merged_pct_crop_da) - new_pct_cft[where_zero] = 0.0 - new_pct_cft_da = xr.DataArray( - data=new_pct_cft, dims=surf["PCT_CFT"].dims, attrs=surf["PCT_CFT"].attrs - ) - - return new_pct_crop_da, new_natveg_da, new_pct_cft_da - - -def main(argv): - ############################### - ### Process input arguments ### - ############################### - - # Set arguments - parser = argparse.ArgumentParser(description="ADD DESCRIPTION HERE") - parser.add_argument( - "-l", - "--flanduse_timeseries", - "--flanduse-timeseries", - help="Land-use timeseries file (flanduse_timeseries) for CLM run", - required=True, - ) - parser.add_argument("-p", "--paramfile", help="Parameter file (paramfile) for CLM run") - parser.add_argument( - "-s", "--fsurdat", help="Surface dataset (fsurdat) for CLM run", required=True - ) - parser.add_argument("-o", "--outfile", help="Output fsurdat file") - args = parser.parse_args(argv) - - ########################## - ### Import and process ### - ########################## - - lu = xr.open_dataset(args.flanduse_timeseries) - surf = xr.open_dataset(args.fsurdat) - if args.paramfile is not None: - params = xr.open_dataset(args.paramfile) - - # new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v1(surf, lu, params) - new_pct_crop_da, new_natveg_da, new_pct_cft_da = get_new_fsurdat_v0(surf, lu) - - ############################# - ### Save to run directory ### - ############################# - - # Make new Dataset - new_surf = surf - new_surf["PCT_CROP"] = new_pct_crop_da - new_surf["PCT_CFT"] = new_pct_cft_da - new_surf["PCT_NATVEG"] = new_natveg_da - - # Save to new file - if args.outfile is None: - fsurdat_noext, ext = os.path.splitext(args.fsurdat) - args.outfile = f"{fsurdat_noext}.GDDgen{ext}" - args.outfile = os.path.basename(args.outfile) - new_surf.to_netcdf(args.outfile, format="NETCDF3_64BIT") - - print(args.outfile) - - -if __name__ == "__main__": - main(sys.argv[1:]) From 7dadfeda0e9298328a33275e6f2830c00d64869a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:02:08 -0600 Subject: [PATCH 1171/2067] Replace names/comments referencing make_surface_for_gddgen with make_fsurdat_all_crops_everywhere. --- cime_config/SystemTests/rxcropmaturity.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 77be3c89e6..dc32b5eca7 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -134,8 +134,8 @@ def run_phase(self): case_gddgen.check_all_input_data() # Make custom version of surface file - logger.info("RXCROPMATURITY log: run make_surface_for_gddgen") - self._run_make_surface_for_gddgen(case_gddgen) + logger.info("RXCROPMATURITY log: run make_fsurdat_all_crops_everywhere") + self._run_make_fsurdat_all_crops_everywhere(case_gddgen) # ------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -239,7 +239,7 @@ def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all done") # Make a surface dataset that has every crop in every gridcell - def _run_make_surface_for_gddgen(self, case_gddgen): + def _run_make_fsurdat_all_crops_everywhere(self, case_gddgen): # fsurdat should be defined. Where is it? self._fsurdat_in = None From c1046b5d3ceffaf3181bb347a544ed00e46dc169 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:03:36 -0600 Subject: [PATCH 1172/2067] Remove unused argument of _run_make_fsurdat_all_crops_everywhere(). --- cime_config/SystemTests/rxcropmaturity.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index dc32b5eca7..bc5d5ea479 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -135,7 +135,7 @@ def run_phase(self): # Make custom version of surface file logger.info("RXCROPMATURITY log: run make_fsurdat_all_crops_everywhere") - self._run_make_fsurdat_all_crops_everywhere(case_gddgen) + self._run_make_fsurdat_all_crops_everywhere() # ------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -239,7 +239,7 @@ def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all done") # Make a surface dataset that has every crop in every gridcell - def _run_make_fsurdat_all_crops_everywhere(self, case_gddgen): + def _run_make_fsurdat_all_crops_everywhere(self): # fsurdat should be defined. Where is it? self._fsurdat_in = None From d9445a771b169f0a8f200823f80e1b3aa859b09d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:04:24 -0600 Subject: [PATCH 1173/2067] Copy ggcmi_cropcals2.py into this repo as process_ggcmi_shdates.py. --- .../crop_calendars/process_ggcmi_shdates.py | 355 ++++++++++++++++++ 1 file changed, 355 insertions(+) create mode 100644 python/ctsm/crop_calendars/process_ggcmi_shdates.py diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py new file mode 100644 index 0000000000..48e7e5e6de --- /dev/null +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -0,0 +1,355 @@ +# %% Options + +# Years to include (set to None to leave that edge unbounded) +y1 = 2000 +yN = 2000 + +# Global attributes for output files +out_attrs = { + "title": "GGCMI crop calendar for Phase 3, v1.01", + "author_thisfile": "Sam Rabin (sam.rabin@gmail.com)", + "author_original": "Jonas Jägermeyr (jaegermeyr@uchicago.edu)", + "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn" +} + +# Your path to ctsm_py directory (i.e., where utils.py lives) +my_ctsm_python_gallery = "/Users/sam/Documents/git_repos/ctsm_python_gallery_myfork/ctsm_py/" + + +# %% Imports + +import numpy as np +import xarray as xr +import matplotlib.pyplot as plt +import shutil +import os +import time +import datetime as dt +import cftime + +import sys +sys.path.append(my_ctsm_python_gallery) +import utils + + +# %% Setup + +# Where to save output files +outdir = "/Users/Shared/CESM_work/crop_dates_mostrice/" + +# Files/directories to use for inputs +### f10_f10_mg37 +# templatefile = "/Users/Shared/CESM_runs/f10_f10_mg37/2021-11-23/f10_f10_mg37.clm2.h3.2000-01-01-00000.nc" +# indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f10_f10_mg37/" +# file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37" # In name of input and output files +### half degree +# templatefile = "/Users/Shared/CESM_runs/halfdeg_test/2022-04-22/halfdeg_test.clm2.h1.1850-01-01-00000.nc" +# indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar/" +# file_specifier = "_ggcmi_crop_calendar_phase3_v1.01" # In name of input and output files +### f19_g17 ("2-degree", actually 2.5° lon x 1.875° lat; i.e., 144x96) +# templatefile = "/Users/Shared/CESM_runs/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2/lnd/hist/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2.clm2.h0.1801-12.nc" +# indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f19_g17/" +# file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17" # In name of input and output files +### f09_g17 ("1-degree", actually ???° lon x ???° lat; i.e., 288x192) +templatefile = "/Users/Shared/CESM_work/f09_g17.shdates_template.nc" +indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f09_g17/" +file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17" # In name of input and output files + + +# Add current date/time to output attributes +out_attrs["created"] = dt.datetime.now().replace(microsecond=0).astimezone().isoformat() + +# Define crop dictionary +# As "CLMname: [number, GGCMIname]" +# - CLM names and numbers taken from commit `3dcbc7499a57904750a994672fc36b4221b9def5` +# - Using one global GGCMI value for both temperate and tropical versions of corn and soybean. +# - There is no GGCMI equivalent of CLM's winter barley and rye. Using winter wheat instead. +# - Using GGCMI `pea` for CLM pulses, as suggested by GGCMI phase 3 protocol. +# - Only using GGCMI `ri1` for rice; ignoring `ri2`. +def set_crop_dict(thisnum, thisname): + return {"clm_num": thisnum, "thiscrop_ggcmi": thisname} + +crop_dict = { + "temperate_corn": set_crop_dict(17, "mai_rf"), + "irrigated_temperate_corn": set_crop_dict(18, "mai_ir"), + "spring_wheat": set_crop_dict(19, "swh_rf"), + "irrigated_spring_wheat": set_crop_dict(20, "swh_ir"), + "winter_wheat": set_crop_dict(21, "wwh_rf"), + "irrigated_winter_wheat": set_crop_dict(22, "wwh_ir"), + "temperate_soybean": set_crop_dict(23, "soy_rf"), + "irrigated_temperate_soybean": set_crop_dict(24, "soy_ir"), + "barley": set_crop_dict(25, "bar_rf"), + "irrigated_barley": set_crop_dict(26, "bar_ir"), + "winter_barley": set_crop_dict(27, "wwh_rf"), + "irrigated_winter_barley": set_crop_dict(28, "wwh_ir"), + "rye": set_crop_dict(29, "rye_rf"), + "irrigated_rye": set_crop_dict(30, "rye_ir"), + "winter_rye": set_crop_dict(31, "wwh_rf"), + "irrigated_winter_rye": set_crop_dict(32, "wwh_ir"), + "cassava": set_crop_dict(33, "cas_rf"), + "irrigated_cassava": set_crop_dict(34, "cas_ir"), + "citrus": set_crop_dict(35, None), + "irrigated_citrus": set_crop_dict(36, None), + "cocoa": set_crop_dict(37, None), + "irrigated_cocoa": set_crop_dict(38, None), + "coffee": set_crop_dict(39, None), + "irrigated_coffee": set_crop_dict(40, None), + "cotton": set_crop_dict(41, "cot_rf"), + "irrigated_cotton": set_crop_dict(42, "cot_ir"), + "datepalm": set_crop_dict(43, None), + "irrigated_datepalm": set_crop_dict(44, None), + "foddergrass": set_crop_dict(45, None), + "irrigated_foddergrass": set_crop_dict(46, None), + "grapes": set_crop_dict(47, None), + "irrigated_grapes": set_crop_dict(48, None), + "groundnuts": set_crop_dict(49, "nut_rf"), + "irrigated_groundnuts": set_crop_dict(50, "nut_ir"), + "millet": set_crop_dict(51, "mil_rf"), + "irrigated_millet": set_crop_dict(52, "mil_ir"), + "oilpalm": set_crop_dict(53, None), + "irrigated_oilpalm": set_crop_dict(54, None), + "potatoes": set_crop_dict(55, "pot_rf"), + "irrigated_potatoes": set_crop_dict(56, "pot_ir"), + "pulses": set_crop_dict(57, "pea_rf"), + "irrigated_pulses": set_crop_dict(58, "pea_ir"), + "rapeseed": set_crop_dict(59, "rap_rf"), + "irrigated_rapeseed": set_crop_dict(60, "rap_ir"), + "rice": set_crop_dict(61, "ric_rf"), + "irrigated_rice": set_crop_dict(62, "ric_ir"), + "sorghum": set_crop_dict(63, "sor_rf"), + "irrigated_sorghum": set_crop_dict(64, "sor_ir"), + "sugarbeet": set_crop_dict(65, "sgb_rf"), + "irrigated_sugarbeet": set_crop_dict(66, "sgb_ir"), + "sugarcane": set_crop_dict(67, "sgc_rf"), + "irrigated_sugarcane": set_crop_dict(68, "sgc_ir"), + "sunflower": set_crop_dict(69, "sun_rf"), + "irrigated_sunflower": set_crop_dict(70, "sun_ir"), + "miscanthus": set_crop_dict(71, None), + "irrigated_miscanthus": set_crop_dict(72, None), + "switchgrass": set_crop_dict(73, None), + "irrigated_switchgrass": set_crop_dict(74, None), + "tropical_corn": set_crop_dict(75, "mai_rf"), + "irrigated_tropical_corn": set_crop_dict(76, "mai_ir"), + "tropical_soybean": set_crop_dict(77, "soy_rf"), + "irrigated_tropical_soybean": set_crop_dict(78, "soy_ir"), + "c3_crop": set_crop_dict(15, None), + "c3_irrigated": set_crop_dict(16, None), +} + + +# %% Define variable dictionary and output files +# As "CLM: [GGCMI, outfile]" + +def set_var_dict(name_ggcmi, outfile): + return {"name_ggcmi": name_ggcmi, "outfile": outfile} + +variable_dict = { + "sdate": set_var_dict("planting_day", ""), + "hdate": set_var_dict("maturity_day", "") +} + +def slice_yr(y): + if y == None: + return None + else: + return str(y) + +# Open and time-slice template dataset +template_ds = xr.open_dataset(templatefile, decode_times=True).sel(time=slice(slice_yr(y1), slice_yr(yN))) +# template_ds = template_ds.sel(time=slice(slice_yr(y1), slice_yr(yN))) +if np.size(template_ds.time) == 0: + print(f"Time slice {y1}-{yN} not found in template dataset. Faking.") + if y1 != yN: + raise RuntimeError("Not sure how to fake time axis when y1 != yN") + template_ds = xr.open_dataset(templatefile, decode_times=True) + template_ds = template_ds.isel(time=slice(0,1)) # Get the first timestep. Just using .values[0] causes trouble. + val0 = template_ds.time.values[0] + if not isinstance(template_ds.time.values[0], cftime.datetime): + raise TypeError(f"Template file time axis is type {type(template_ds.time.values[0])}, which isn't a cftime.datetime subclass; not sure that next line (assigning fake value) will work.") + template_ds.time.values[0] = type(val0)(y1, 1, 1, 0, 0, 0, 0, has_year_zero=val0.has_year_zero) + template_ds.time_bounds.values[0] = np.array([template_ds.time.values[0,], template_ds.time.values[0]]) + if "mcdate" in template_ds: + template_ds.mcdate.values = np.array([20000101,]).astype(type(template_ds.mcdate.values[0])) + if "mcsec" in template_ds: + template_ds.mcsec.values = np.array([0,]).astype(type(template_ds.mcsec.values[0])) + if "mdcur" in template_ds: + template_ds.mdcur.values = np.array([0,]).astype(type(template_ds.mdcur.values[0])) + if "mscur" in template_ds: + template_ds.mscur.values = np.array([0,]).astype(type(template_ds.mscur.values[0])) + if "nstep" in template_ds: + template_ds.nstep.values = np.array([0,]).astype(type(template_ds.nstep.values[0])) +else: + raise RuntimeError("Try using just a normal, unprocessed output file that doesn't include year 2000") +y1 = template_ds.time.values[0].year +yN = template_ds.time.values[-1].year +template_ds.attrs = out_attrs + +# Remove variable(s) we don't need (hdm, or any all-uppercase variables) +for v in template_ds: + if v == "hdm" or v.upper()==v: + template_ds = template_ds.drop(v) + +# Create output files +for v in variable_dict: + outfile = "%s%ss%s.%d-%d.%s.nc" % (outdir, v, file_specifier, y1, yN, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) + variable_dict[v]["outfile"] = outfile + variable_dict[v]["outfile_fill1"] = outfile.replace(".nc", ".fill1.nc") + template_ds.to_netcdf(path=variable_dict[v]["outfile"]) + template_ds.to_netcdf(path=variable_dict[v]["outfile_fill1"]) + +template_ds.close() + + +# %% Process all crops + +verbose = True + +for thiscrop_clm in crop_dict: + + # Which crop are we on? + c = list(crop_dict.keys()).index(thiscrop_clm) + 1 + + # Get information about this crop + this_dict = crop_dict[thiscrop_clm] + thiscrop_int = this_dict["clm_num"] + thiscrop_ggcmi = this_dict["thiscrop_ggcmi"] + + # If no corresponding GGCMI crop, skip opening dataset. + # Will use previous cropcal_ds as a template. + if thiscrop_ggcmi == None: + if c == 1: + raise ValueError(f"First crop ({thiscrop_clm}) must have a GGCMI type") + print("Filling %s with dummy data (%d of %d)..." \ + % (str(thiscrop_clm), + c, + len(crop_dict))) + + # Otherwise, import crop calendar file + else: + if verbose: + print("Importing %s -> %s (%d of %d)..." \ + % (str(thiscrop_ggcmi), + str(thiscrop_clm), + c, + len(crop_dict))) + + file_ggcmi = indir + thiscrop_ggcmi + file_specifier + ".nc4" + if not os.path.exists(file_ggcmi): + raise Exception("Input file not found: " + file_ggcmi) + cropcal_ds = xr.open_dataset(file_ggcmi) + # Flip latitude to match destination + cropcal_ds = cropcal_ds.reindex(lat=cropcal_ds.lat[::-1]) + # Rearrange longitude to match destination (does nothing if not needed) + cropcal_ds = utils.lon_idl2pm(cropcal_ds, fail_silently=True) + + for thisvar_clm in variable_dict: + # Get GGCMI netCDF info + varname_ggcmi = variable_dict[thisvar_clm]["name_ggcmi"] + if verbose: + print(" Processing %s..." % varname_ggcmi) + + # Get CLM netCDF info + varname_clm = thisvar_clm + "1_" + str(thiscrop_int) + file_clm = variable_dict[thisvar_clm]["outfile"] + if not os.path.exists(file_clm): + raise Exception("Output file not found: " + file_clm) + file_clm_tmp = file_clm + ".tmp" + file_clm_fill1 = variable_dict[thisvar_clm]["outfile_fill1"] + if not os.path.exists(file_clm_fill1): + raise Exception("Output file not found: " + file_clm_fill1) + file_clm_fill1_tmp = file_clm_fill1 + ".tmp" + + # "Read" the file (doesn't actually bring anything into memory yet) + out_ds = xr.open_dataset(file_clm) + out_fill1_ds = xr.open_dataset(file_clm_fill1) + + # Strip dataset to just this variable + droplist = [] + for i in list(cropcal_ds.keys()): + if i != varname_ggcmi: + droplist.append(i) + thisvar_ds = cropcal_ds.drop(droplist) + thisvar_ds = thisvar_ds.load() + thisvar_fill1_ds = thisvar_ds.copy() + + # Convert to integer + new_fillvalue = -1 + dummyvalue = -1 + thisvar_ds.variables[varname_ggcmi].encoding["_FillValue"] \ + = new_fillvalue + thisvar_fill1_ds.variables[varname_ggcmi].encoding["_FillValue"] \ + = new_fillvalue + if thiscrop_ggcmi == None: + thisvar_ds.variables[varname_ggcmi].values.fill(dummyvalue) + thisvar_fill1_ds.variables[varname_ggcmi].values.fill(1) + else: + thisvar_ds.variables[varname_ggcmi].values[np.isnan(thisvar_ds.variables[varname_ggcmi].values)] \ + = new_fillvalue + thisvar_ds.variables[varname_ggcmi].values \ + = thisvar_ds.variables[varname_ggcmi].values.astype("int16") + thisvar_fill1_ds.variables[varname_ggcmi].values[np.isnan(thisvar_fill1_ds.variables[varname_ggcmi].values)] \ + = 1 + thisvar_fill1_ds.variables[varname_ggcmi].values \ + = thisvar_fill1_ds.variables[varname_ggcmi].values.astype("int16") + + # Add time dimension (https://stackoverflow.com/a/62862440) + # (Repeats original map for every timestep) + # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. + thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) + thisvar_fill1_ds = thisvar_fill1_ds.expand_dims(time = template_ds.time) + # "True" here shows that the time dimension was created by just repeating the one map. + # tmp = thisvar_ds[varname_ggcmi] + # np.all((np.diff(tmp.values, axis=0) == 0.0) | np.isnan(np.diff(tmp.values, axis=0))) + + # Add variable to output dataset + out_ds[varname_clm]=(thisvar_ds[varname_ggcmi].dims, + thisvar_ds[varname_ggcmi].values) + out_fill1_ds[varname_clm]=(thisvar_fill1_ds[varname_ggcmi].dims, + thisvar_fill1_ds[varname_ggcmi].values) + + # Edit/add variable attributes etc. + longname = thisvar_ds[varname_ggcmi].attrs["long_name"] + longname = longname.replace("rainfed", thiscrop_clm).replace("irrigated", thiscrop_clm) + def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue): + out_ds[varname_clm].attrs["long_name"] = longname + if thiscrop_ggcmi == None: + out_ds[varname_clm].attrs["crop_name_clm"] = "none" + out_ds[varname_clm].attrs["crop_name_ggcmi"] = "none" + else: + out_ds[varname_clm].attrs["crop_name_clm"] = thiscrop_clm + out_ds[varname_clm].attrs["crop_name_ggcmi"] = thiscrop_ggcmi + out_ds[varname_clm].attrs["short_name_ggcmi"] = varname_ggcmi + out_ds[varname_clm].attrs["units"] = "day of year" + out_ds[varname_clm].encoding["_FillValue"] = new_fillvalue + # scale_factor and add_offset are required by I/O library for short data + # From https://www.unidata.ucar.edu/software/netcdf/workshops/2010/bestpractices/Packing.html: + # unpacked_value = packed_value * scale_factor + add_offset + out_ds[varname_clm].attrs["scale_factor"] = np.int16(1) + out_ds[varname_clm].attrs["add_offset"] = np.int16(0) + return out_ds + out_ds = set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) + out_fill1_ds = set_var_attrs(out_fill1_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) + + # Save + if verbose: + print(" Saving %s..." % varname_ggcmi) + # start = time.time() + # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... + shutil.copyfile(file_clm, file_clm_tmp) + shutil.copyfile(file_clm_fill1, file_clm_fill1_tmp) + # ... then save out_ds to the temporary file... + out_ds.to_netcdf(file_clm_tmp, format="NETCDF3_CLASSIC") + out_fill1_ds.to_netcdf(file_clm_fill1_tmp, format="NETCDF3_CLASSIC") + # ... then close out_ds... + out_ds.close() + out_fill1_ds.close() + # ... and finally replace the original file with the new temporary file (deleting the temporary file in the process) + os.replace(file_clm_tmp, file_clm) + os.replace(file_clm_fill1_tmp, file_clm_fill1) + # end = time.time() + # print(end - start) + ### NOTE: This method gets slower and slower as the file gets bigger! (The entire process, but also the out_ds.to_netcdf() step.) Is there a better way? + + cropcal_ds.close() + +print("Done!") From cdefb0390f01b357234a03fd0479518d7b5f2469 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:11:29 -0600 Subject: [PATCH 1174/2067] process shdates: Script is now called from the command line. --- .../crop_calendars/process_ggcmi_shdates.py | 700 +++++++++--------- 1 file changed, 354 insertions(+), 346 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 48e7e5e6de..1504acaccf 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -1,355 +1,363 @@ -# %% Options - -# Years to include (set to None to leave that edge unbounded) -y1 = 2000 -yN = 2000 - -# Global attributes for output files -out_attrs = { - "title": "GGCMI crop calendar for Phase 3, v1.01", - "author_thisfile": "Sam Rabin (sam.rabin@gmail.com)", - "author_original": "Jonas Jägermeyr (jaegermeyr@uchicago.edu)", - "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn" -} - -# Your path to ctsm_py directory (i.e., where utils.py lives) -my_ctsm_python_gallery = "/Users/sam/Documents/git_repos/ctsm_python_gallery_myfork/ctsm_py/" - - -# %% Imports - -import numpy as np -import xarray as xr -import matplotlib.pyplot as plt -import shutil -import os -import time -import datetime as dt -import cftime - -import sys -sys.path.append(my_ctsm_python_gallery) -import utils - - -# %% Setup - -# Where to save output files -outdir = "/Users/Shared/CESM_work/crop_dates_mostrice/" - -# Files/directories to use for inputs -### f10_f10_mg37 -# templatefile = "/Users/Shared/CESM_runs/f10_f10_mg37/2021-11-23/f10_f10_mg37.clm2.h3.2000-01-01-00000.nc" -# indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f10_f10_mg37/" -# file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37" # In name of input and output files -### half degree -# templatefile = "/Users/Shared/CESM_runs/halfdeg_test/2022-04-22/halfdeg_test.clm2.h1.1850-01-01-00000.nc" -# indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar/" -# file_specifier = "_ggcmi_crop_calendar_phase3_v1.01" # In name of input and output files -### f19_g17 ("2-degree", actually 2.5° lon x 1.875° lat; i.e., 144x96) -# templatefile = "/Users/Shared/CESM_runs/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2/lnd/hist/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2.clm2.h0.1801-12.nc" -# indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f19_g17/" -# file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17" # In name of input and output files -### f09_g17 ("1-degree", actually ???° lon x ???° lat; i.e., 288x192) -templatefile = "/Users/Shared/CESM_work/f09_g17.shdates_template.nc" -indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f09_g17/" -file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17" # In name of input and output files - - -# Add current date/time to output attributes -out_attrs["created"] = dt.datetime.now().replace(microsecond=0).astimezone().isoformat() - -# Define crop dictionary -# As "CLMname: [number, GGCMIname]" -# - CLM names and numbers taken from commit `3dcbc7499a57904750a994672fc36b4221b9def5` -# - Using one global GGCMI value for both temperate and tropical versions of corn and soybean. -# - There is no GGCMI equivalent of CLM's winter barley and rye. Using winter wheat instead. -# - Using GGCMI `pea` for CLM pulses, as suggested by GGCMI phase 3 protocol. -# - Only using GGCMI `ri1` for rice; ignoring `ri2`. -def set_crop_dict(thisnum, thisname): - return {"clm_num": thisnum, "thiscrop_ggcmi": thisname} - -crop_dict = { - "temperate_corn": set_crop_dict(17, "mai_rf"), - "irrigated_temperate_corn": set_crop_dict(18, "mai_ir"), - "spring_wheat": set_crop_dict(19, "swh_rf"), - "irrigated_spring_wheat": set_crop_dict(20, "swh_ir"), - "winter_wheat": set_crop_dict(21, "wwh_rf"), - "irrigated_winter_wheat": set_crop_dict(22, "wwh_ir"), - "temperate_soybean": set_crop_dict(23, "soy_rf"), - "irrigated_temperate_soybean": set_crop_dict(24, "soy_ir"), - "barley": set_crop_dict(25, "bar_rf"), - "irrigated_barley": set_crop_dict(26, "bar_ir"), - "winter_barley": set_crop_dict(27, "wwh_rf"), - "irrigated_winter_barley": set_crop_dict(28, "wwh_ir"), - "rye": set_crop_dict(29, "rye_rf"), - "irrigated_rye": set_crop_dict(30, "rye_ir"), - "winter_rye": set_crop_dict(31, "wwh_rf"), - "irrigated_winter_rye": set_crop_dict(32, "wwh_ir"), - "cassava": set_crop_dict(33, "cas_rf"), - "irrigated_cassava": set_crop_dict(34, "cas_ir"), - "citrus": set_crop_dict(35, None), - "irrigated_citrus": set_crop_dict(36, None), - "cocoa": set_crop_dict(37, None), - "irrigated_cocoa": set_crop_dict(38, None), - "coffee": set_crop_dict(39, None), - "irrigated_coffee": set_crop_dict(40, None), - "cotton": set_crop_dict(41, "cot_rf"), - "irrigated_cotton": set_crop_dict(42, "cot_ir"), - "datepalm": set_crop_dict(43, None), - "irrigated_datepalm": set_crop_dict(44, None), - "foddergrass": set_crop_dict(45, None), - "irrigated_foddergrass": set_crop_dict(46, None), - "grapes": set_crop_dict(47, None), - "irrigated_grapes": set_crop_dict(48, None), - "groundnuts": set_crop_dict(49, "nut_rf"), - "irrigated_groundnuts": set_crop_dict(50, "nut_ir"), - "millet": set_crop_dict(51, "mil_rf"), - "irrigated_millet": set_crop_dict(52, "mil_ir"), - "oilpalm": set_crop_dict(53, None), - "irrigated_oilpalm": set_crop_dict(54, None), - "potatoes": set_crop_dict(55, "pot_rf"), - "irrigated_potatoes": set_crop_dict(56, "pot_ir"), - "pulses": set_crop_dict(57, "pea_rf"), - "irrigated_pulses": set_crop_dict(58, "pea_ir"), - "rapeseed": set_crop_dict(59, "rap_rf"), - "irrigated_rapeseed": set_crop_dict(60, "rap_ir"), - "rice": set_crop_dict(61, "ric_rf"), - "irrigated_rice": set_crop_dict(62, "ric_ir"), - "sorghum": set_crop_dict(63, "sor_rf"), - "irrigated_sorghum": set_crop_dict(64, "sor_ir"), - "sugarbeet": set_crop_dict(65, "sgb_rf"), - "irrigated_sugarbeet": set_crop_dict(66, "sgb_ir"), - "sugarcane": set_crop_dict(67, "sgc_rf"), - "irrigated_sugarcane": set_crop_dict(68, "sgc_ir"), - "sunflower": set_crop_dict(69, "sun_rf"), - "irrigated_sunflower": set_crop_dict(70, "sun_ir"), - "miscanthus": set_crop_dict(71, None), - "irrigated_miscanthus": set_crop_dict(72, None), - "switchgrass": set_crop_dict(73, None), - "irrigated_switchgrass": set_crop_dict(74, None), - "tropical_corn": set_crop_dict(75, "mai_rf"), - "irrigated_tropical_corn": set_crop_dict(76, "mai_ir"), - "tropical_soybean": set_crop_dict(77, "soy_rf"), - "irrigated_tropical_soybean": set_crop_dict(78, "soy_ir"), - "c3_crop": set_crop_dict(15, None), - "c3_irrigated": set_crop_dict(16, None), -} - - -# %% Define variable dictionary and output files -# As "CLM: [GGCMI, outfile]" - -def set_var_dict(name_ggcmi, outfile): - return {"name_ggcmi": name_ggcmi, "outfile": outfile} - -variable_dict = { - "sdate": set_var_dict("planting_day", ""), - "hdate": set_var_dict("maturity_day", "") -} - -def slice_yr(y): - if y == None: - return None - else: - return str(y) - -# Open and time-slice template dataset -template_ds = xr.open_dataset(templatefile, decode_times=True).sel(time=slice(slice_yr(y1), slice_yr(yN))) -# template_ds = template_ds.sel(time=slice(slice_yr(y1), slice_yr(yN))) -if np.size(template_ds.time) == 0: - print(f"Time slice {y1}-{yN} not found in template dataset. Faking.") - if y1 != yN: - raise RuntimeError("Not sure how to fake time axis when y1 != yN") - template_ds = xr.open_dataset(templatefile, decode_times=True) - template_ds = template_ds.isel(time=slice(0,1)) # Get the first timestep. Just using .values[0] causes trouble. - val0 = template_ds.time.values[0] - if not isinstance(template_ds.time.values[0], cftime.datetime): - raise TypeError(f"Template file time axis is type {type(template_ds.time.values[0])}, which isn't a cftime.datetime subclass; not sure that next line (assigning fake value) will work.") - template_ds.time.values[0] = type(val0)(y1, 1, 1, 0, 0, 0, 0, has_year_zero=val0.has_year_zero) - template_ds.time_bounds.values[0] = np.array([template_ds.time.values[0,], template_ds.time.values[0]]) - if "mcdate" in template_ds: - template_ds.mcdate.values = np.array([20000101,]).astype(type(template_ds.mcdate.values[0])) - if "mcsec" in template_ds: - template_ds.mcsec.values = np.array([0,]).astype(type(template_ds.mcsec.values[0])) - if "mdcur" in template_ds: - template_ds.mdcur.values = np.array([0,]).astype(type(template_ds.mdcur.values[0])) - if "mscur" in template_ds: - template_ds.mscur.values = np.array([0,]).astype(type(template_ds.mscur.values[0])) - if "nstep" in template_ds: - template_ds.nstep.values = np.array([0,]).astype(type(template_ds.nstep.values[0])) -else: - raise RuntimeError("Try using just a normal, unprocessed output file that doesn't include year 2000") -y1 = template_ds.time.values[0].year -yN = template_ds.time.values[-1].year -template_ds.attrs = out_attrs - -# Remove variable(s) we don't need (hdm, or any all-uppercase variables) -for v in template_ds: - if v == "hdm" or v.upper()==v: - template_ds = template_ds.drop(v) - -# Create output files -for v in variable_dict: - outfile = "%s%ss%s.%d-%d.%s.nc" % (outdir, v, file_specifier, y1, yN, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) - variable_dict[v]["outfile"] = outfile - variable_dict[v]["outfile_fill1"] = outfile.replace(".nc", ".fill1.nc") - template_ds.to_netcdf(path=variable_dict[v]["outfile"]) - template_ds.to_netcdf(path=variable_dict[v]["outfile_fill1"]) - -template_ds.close() - - -# %% Process all crops - -verbose = True - -for thiscrop_clm in crop_dict: - - # Which crop are we on? - c = list(crop_dict.keys()).index(thiscrop_clm) + 1 - - # Get information about this crop - this_dict = crop_dict[thiscrop_clm] - thiscrop_int = this_dict["clm_num"] - thiscrop_ggcmi = this_dict["thiscrop_ggcmi"] - - # If no corresponding GGCMI crop, skip opening dataset. - # Will use previous cropcal_ds as a template. - if thiscrop_ggcmi == None: - if c == 1: - raise ValueError(f"First crop ({thiscrop_clm}) must have a GGCMI type") - print("Filling %s with dummy data (%d of %d)..." \ - % (str(thiscrop_clm), - c, - len(crop_dict))) - - # Otherwise, import crop calendar file +def main(): + + # %% Options + + # Years to include (set to None to leave that edge unbounded) + y1 = 2000 + yN = 2000 + + # Global attributes for output files + out_attrs = { + "title": "GGCMI crop calendar for Phase 3, v1.01", + "author_thisfile": "Sam Rabin (sam.rabin@gmail.com)", + "author_original": "Jonas Jägermeyr (jaegermeyr@uchicago.edu)", + "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn" + } + + # Your path to ctsm_py directory (i.e., where utils.py lives) + my_ctsm_python_gallery = "/Users/sam/Documents/git_repos/ctsm_python_gallery_myfork/ctsm_py/" + + + # %% Imports + + import numpy as np + import xarray as xr + import matplotlib.pyplot as plt + import shutil + import os + import time + import datetime as dt + import cftime + + import sys + sys.path.append(my_ctsm_python_gallery) + import utils + + + # %% Setup + + # Where to save output files + outdir = "/Users/Shared/CESM_work/crop_dates_mostrice/" + + # Files/directories to use for inputs + ### f10_f10_mg37 + # templatefile = "/Users/Shared/CESM_runs/f10_f10_mg37/2021-11-23/f10_f10_mg37.clm2.h3.2000-01-01-00000.nc" + # indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f10_f10_mg37/" + # file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37" # In name of input and output files + ## half degree + templatefile = "/Users/Shared/CESM_runs/halfdeg_test/2022-04-22/halfdeg_test.clm2.h1.1850-01-01-00000.nc" + indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar/" + file_specifier = "_ggcmi_crop_calendar_phase3_v1.01" # In name of input and output files + ### f19_g17 ("2-degree", actually 2.5° lon x 1.875° lat; i.e., 144x96) + # templatefile = "/Users/Shared/CESM_runs/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2/lnd/hist/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2.clm2.h0.1801-12.nc" + # indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f19_g17/" + # file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17" # In name of input and output files + # ### f09_g17 ("1-degree", actually ???° lon x ???° lat; i.e., 288x192) + # templatefile = "/Users/Shared/CESM_work/f09_g17.shdates_template.nc" + # indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f09_g17/" + # file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17" # In name of input and output files + + + # Add current date/time to output attributes + out_attrs["created"] = dt.datetime.now().replace(microsecond=0).astimezone().isoformat() + + # Define crop dictionary + # As "CLMname: [number, GGCMIname]" + # - CLM names and numbers taken from commit `3dcbc7499a57904750a994672fc36b4221b9def5` + # - Using one global GGCMI value for both temperate and tropical versions of corn and soybean. + # - There is no GGCMI equivalent of CLM's winter barley and rye. Using winter wheat instead. + # - Using GGCMI `pea` for CLM pulses, as suggested by GGCMI phase 3 protocol. + # - Only using GGCMI `ri1` for rice; ignoring `ri2`. + def set_crop_dict(thisnum, thisname): + return {"clm_num": thisnum, "thiscrop_ggcmi": thisname} + + crop_dict = { + "temperate_corn": set_crop_dict(17, "mai_rf"), + "irrigated_temperate_corn": set_crop_dict(18, "mai_ir"), + "spring_wheat": set_crop_dict(19, "swh_rf"), + "irrigated_spring_wheat": set_crop_dict(20, "swh_ir"), + "winter_wheat": set_crop_dict(21, "wwh_rf"), + "irrigated_winter_wheat": set_crop_dict(22, "wwh_ir"), + "temperate_soybean": set_crop_dict(23, "soy_rf"), + "irrigated_temperate_soybean": set_crop_dict(24, "soy_ir"), + "barley": set_crop_dict(25, "bar_rf"), + "irrigated_barley": set_crop_dict(26, "bar_ir"), + "winter_barley": set_crop_dict(27, "wwh_rf"), + "irrigated_winter_barley": set_crop_dict(28, "wwh_ir"), + "rye": set_crop_dict(29, "rye_rf"), + "irrigated_rye": set_crop_dict(30, "rye_ir"), + "winter_rye": set_crop_dict(31, "wwh_rf"), + "irrigated_winter_rye": set_crop_dict(32, "wwh_ir"), + "cassava": set_crop_dict(33, "cas_rf"), + "irrigated_cassava": set_crop_dict(34, "cas_ir"), + "citrus": set_crop_dict(35, None), + "irrigated_citrus": set_crop_dict(36, None), + "cocoa": set_crop_dict(37, None), + "irrigated_cocoa": set_crop_dict(38, None), + "coffee": set_crop_dict(39, None), + "irrigated_coffee": set_crop_dict(40, None), + "cotton": set_crop_dict(41, "cot_rf"), + "irrigated_cotton": set_crop_dict(42, "cot_ir"), + "datepalm": set_crop_dict(43, None), + "irrigated_datepalm": set_crop_dict(44, None), + "foddergrass": set_crop_dict(45, None), + "irrigated_foddergrass": set_crop_dict(46, None), + "grapes": set_crop_dict(47, None), + "irrigated_grapes": set_crop_dict(48, None), + "groundnuts": set_crop_dict(49, "nut_rf"), + "irrigated_groundnuts": set_crop_dict(50, "nut_ir"), + "millet": set_crop_dict(51, "mil_rf"), + "irrigated_millet": set_crop_dict(52, "mil_ir"), + "oilpalm": set_crop_dict(53, None), + "irrigated_oilpalm": set_crop_dict(54, None), + "potatoes": set_crop_dict(55, "pot_rf"), + "irrigated_potatoes": set_crop_dict(56, "pot_ir"), + "pulses": set_crop_dict(57, "pea_rf"), + "irrigated_pulses": set_crop_dict(58, "pea_ir"), + "rapeseed": set_crop_dict(59, "rap_rf"), + "irrigated_rapeseed": set_crop_dict(60, "rap_ir"), + "rice": set_crop_dict(61, "ric_rf"), + "irrigated_rice": set_crop_dict(62, "ric_ir"), + "sorghum": set_crop_dict(63, "sor_rf"), + "irrigated_sorghum": set_crop_dict(64, "sor_ir"), + "sugarbeet": set_crop_dict(65, "sgb_rf"), + "irrigated_sugarbeet": set_crop_dict(66, "sgb_ir"), + "sugarcane": set_crop_dict(67, "sgc_rf"), + "irrigated_sugarcane": set_crop_dict(68, "sgc_ir"), + "sunflower": set_crop_dict(69, "sun_rf"), + "irrigated_sunflower": set_crop_dict(70, "sun_ir"), + "miscanthus": set_crop_dict(71, None), + "irrigated_miscanthus": set_crop_dict(72, None), + "switchgrass": set_crop_dict(73, None), + "irrigated_switchgrass": set_crop_dict(74, None), + "tropical_corn": set_crop_dict(75, "mai_rf"), + "irrigated_tropical_corn": set_crop_dict(76, "mai_ir"), + "tropical_soybean": set_crop_dict(77, "soy_rf"), + "irrigated_tropical_soybean": set_crop_dict(78, "soy_ir"), + "c3_crop": set_crop_dict(15, None), + "c3_irrigated": set_crop_dict(16, None), + } + + + # %% Define variable dictionary and output files + # As "CLM: [GGCMI, outfile]" + + def set_var_dict(name_ggcmi, outfile): + return {"name_ggcmi": name_ggcmi, "outfile": outfile} + + variable_dict = { + "sdate": set_var_dict("planting_day", ""), + "hdate": set_var_dict("maturity_day", "") + } + + def slice_yr(y): + if y == None: + return None + else: + return str(y) + + # Open and time-slice template dataset + template_ds = xr.open_dataset(templatefile, decode_times=True).sel(time=slice(slice_yr(y1), slice_yr(yN))) + # template_ds = template_ds.sel(time=slice(slice_yr(y1), slice_yr(yN))) + if np.size(template_ds.time) == 0: + print(f"Time slice {y1}-{yN} not found in template dataset. Faking.") + if y1 != yN: + raise RuntimeError("Not sure how to fake time axis when y1 != yN") + template_ds = xr.open_dataset(templatefile, decode_times=True) + template_ds = template_ds.isel(time=slice(0,1)) # Get the first timestep. Just using .values[0] causes trouble. + val0 = template_ds.time.values[0] + if not isinstance(template_ds.time.values[0], cftime.datetime): + raise TypeError(f"Template file time axis is type {type(template_ds.time.values[0])}, which isn't a cftime.datetime subclass; not sure that next line (assigning fake value) will work.") + template_ds.time.values[0] = type(val0)(y1, 1, 1, 0, 0, 0, 0, has_year_zero=val0.has_year_zero) + template_ds.time_bounds.values[0] = np.array([template_ds.time.values[0,], template_ds.time.values[0]]) + if "mcdate" in template_ds: + template_ds.mcdate.values = np.array([20000101,]).astype(type(template_ds.mcdate.values[0])) + if "mcsec" in template_ds: + template_ds.mcsec.values = np.array([0,]).astype(type(template_ds.mcsec.values[0])) + if "mdcur" in template_ds: + template_ds.mdcur.values = np.array([0,]).astype(type(template_ds.mdcur.values[0])) + if "mscur" in template_ds: + template_ds.mscur.values = np.array([0,]).astype(type(template_ds.mscur.values[0])) + if "nstep" in template_ds: + template_ds.nstep.values = np.array([0,]).astype(type(template_ds.nstep.values[0])) else: - if verbose: - print("Importing %s -> %s (%d of %d)..." \ - % (str(thiscrop_ggcmi), - str(thiscrop_clm), + raise RuntimeError("Try using just a normal, unprocessed output file that doesn't include year 2000") + y1 = template_ds.time.values[0].year + yN = template_ds.time.values[-1].year + template_ds.attrs = out_attrs + + # Remove variable(s) we don't need (hdm, or any all-uppercase variables) + for v in template_ds: + if v == "hdm" or v.upper()==v: + template_ds = template_ds.drop(v) + + # Create output files + for v in variable_dict: + outfile = "%s%ss%s.%d-%d.%s.nc" % (outdir, v, file_specifier, y1, yN, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) + variable_dict[v]["outfile"] = outfile + variable_dict[v]["outfile_fill1"] = outfile.replace(".nc", ".fill1.nc") + template_ds.to_netcdf(path=variable_dict[v]["outfile"]) + template_ds.to_netcdf(path=variable_dict[v]["outfile_fill1"]) + + template_ds.close() + + + # %% Process all crops + + verbose = True + + for thiscrop_clm in crop_dict: + + # Which crop are we on? + c = list(crop_dict.keys()).index(thiscrop_clm) + 1 + + # Get information about this crop + this_dict = crop_dict[thiscrop_clm] + thiscrop_int = this_dict["clm_num"] + thiscrop_ggcmi = this_dict["thiscrop_ggcmi"] + + # If no corresponding GGCMI crop, skip opening dataset. + # Will use previous cropcal_ds as a template. + if thiscrop_ggcmi == None: + if c == 1: + raise ValueError(f"First crop ({thiscrop_clm}) must have a GGCMI type") + print("Filling %s with dummy data (%d of %d)..." \ + % (str(thiscrop_clm), c, len(crop_dict))) - file_ggcmi = indir + thiscrop_ggcmi + file_specifier + ".nc4" - if not os.path.exists(file_ggcmi): - raise Exception("Input file not found: " + file_ggcmi) - cropcal_ds = xr.open_dataset(file_ggcmi) - # Flip latitude to match destination - cropcal_ds = cropcal_ds.reindex(lat=cropcal_ds.lat[::-1]) - # Rearrange longitude to match destination (does nothing if not needed) - cropcal_ds = utils.lon_idl2pm(cropcal_ds, fail_silently=True) - - for thisvar_clm in variable_dict: - # Get GGCMI netCDF info - varname_ggcmi = variable_dict[thisvar_clm]["name_ggcmi"] - if verbose: - print(" Processing %s..." % varname_ggcmi) - - # Get CLM netCDF info - varname_clm = thisvar_clm + "1_" + str(thiscrop_int) - file_clm = variable_dict[thisvar_clm]["outfile"] - if not os.path.exists(file_clm): - raise Exception("Output file not found: " + file_clm) - file_clm_tmp = file_clm + ".tmp" - file_clm_fill1 = variable_dict[thisvar_clm]["outfile_fill1"] - if not os.path.exists(file_clm_fill1): - raise Exception("Output file not found: " + file_clm_fill1) - file_clm_fill1_tmp = file_clm_fill1 + ".tmp" - - # "Read" the file (doesn't actually bring anything into memory yet) - out_ds = xr.open_dataset(file_clm) - out_fill1_ds = xr.open_dataset(file_clm_fill1) - - # Strip dataset to just this variable - droplist = [] - for i in list(cropcal_ds.keys()): - if i != varname_ggcmi: - droplist.append(i) - thisvar_ds = cropcal_ds.drop(droplist) - thisvar_ds = thisvar_ds.load() - thisvar_fill1_ds = thisvar_ds.copy() - - # Convert to integer - new_fillvalue = -1 - dummyvalue = -1 - thisvar_ds.variables[varname_ggcmi].encoding["_FillValue"] \ - = new_fillvalue - thisvar_fill1_ds.variables[varname_ggcmi].encoding["_FillValue"] \ - = new_fillvalue - if thiscrop_ggcmi == None: - thisvar_ds.variables[varname_ggcmi].values.fill(dummyvalue) - thisvar_fill1_ds.variables[varname_ggcmi].values.fill(1) + # Otherwise, import crop calendar file else: - thisvar_ds.variables[varname_ggcmi].values[np.isnan(thisvar_ds.variables[varname_ggcmi].values)] \ - = new_fillvalue - thisvar_ds.variables[varname_ggcmi].values \ - = thisvar_ds.variables[varname_ggcmi].values.astype("int16") - thisvar_fill1_ds.variables[varname_ggcmi].values[np.isnan(thisvar_fill1_ds.variables[varname_ggcmi].values)] \ - = 1 - thisvar_fill1_ds.variables[varname_ggcmi].values \ - = thisvar_fill1_ds.variables[varname_ggcmi].values.astype("int16") + if verbose: + print("Importing %s -> %s (%d of %d)..." \ + % (str(thiscrop_ggcmi), + str(thiscrop_clm), + c, + len(crop_dict))) + + file_ggcmi = indir + thiscrop_ggcmi + file_specifier + ".nc4" + if not os.path.exists(file_ggcmi): + raise Exception("Input file not found: " + file_ggcmi) + cropcal_ds = xr.open_dataset(file_ggcmi) + # Flip latitude to match destination + cropcal_ds = cropcal_ds.reindex(lat=cropcal_ds.lat[::-1]) + # Rearrange longitude to match destination (does nothing if not needed) + cropcal_ds = utils.lon_idl2pm(cropcal_ds, fail_silently=True) - # Add time dimension (https://stackoverflow.com/a/62862440) - # (Repeats original map for every timestep) - # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. - thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) - thisvar_fill1_ds = thisvar_fill1_ds.expand_dims(time = template_ds.time) - # "True" here shows that the time dimension was created by just repeating the one map. - # tmp = thisvar_ds[varname_ggcmi] - # np.all((np.diff(tmp.values, axis=0) == 0.0) | np.isnan(np.diff(tmp.values, axis=0))) - - # Add variable to output dataset - out_ds[varname_clm]=(thisvar_ds[varname_ggcmi].dims, - thisvar_ds[varname_ggcmi].values) - out_fill1_ds[varname_clm]=(thisvar_fill1_ds[varname_ggcmi].dims, - thisvar_fill1_ds[varname_ggcmi].values) - - # Edit/add variable attributes etc. - longname = thisvar_ds[varname_ggcmi].attrs["long_name"] - longname = longname.replace("rainfed", thiscrop_clm).replace("irrigated", thiscrop_clm) - def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue): - out_ds[varname_clm].attrs["long_name"] = longname + for thisvar_clm in variable_dict: + # Get GGCMI netCDF info + varname_ggcmi = variable_dict[thisvar_clm]["name_ggcmi"] + if verbose: + print(" Processing %s..." % varname_ggcmi) + + # Get CLM netCDF info + varname_clm = thisvar_clm + "1_" + str(thiscrop_int) + file_clm = variable_dict[thisvar_clm]["outfile"] + if not os.path.exists(file_clm): + raise Exception("Output file not found: " + file_clm) + file_clm_tmp = file_clm + ".tmp" + file_clm_fill1 = variable_dict[thisvar_clm]["outfile_fill1"] + if not os.path.exists(file_clm_fill1): + raise Exception("Output file not found: " + file_clm_fill1) + file_clm_fill1_tmp = file_clm_fill1 + ".tmp" + + # "Read" the file (doesn't actually bring anything into memory yet) + out_ds = xr.open_dataset(file_clm) + out_fill1_ds = xr.open_dataset(file_clm_fill1) + + # Strip dataset to just this variable + droplist = [] + for i in list(cropcal_ds.keys()): + if i != varname_ggcmi: + droplist.append(i) + thisvar_ds = cropcal_ds.drop(droplist) + thisvar_ds = thisvar_ds.load() + thisvar_fill1_ds = thisvar_ds.copy() + + # Convert to integer + new_fillvalue = -1 + dummyvalue = -1 + thisvar_ds.variables[varname_ggcmi].encoding["_FillValue"] \ + = new_fillvalue + thisvar_fill1_ds.variables[varname_ggcmi].encoding["_FillValue"] \ + = new_fillvalue if thiscrop_ggcmi == None: - out_ds[varname_clm].attrs["crop_name_clm"] = "none" - out_ds[varname_clm].attrs["crop_name_ggcmi"] = "none" + thisvar_ds.variables[varname_ggcmi].values.fill(dummyvalue) + thisvar_fill1_ds.variables[varname_ggcmi].values.fill(1) else: - out_ds[varname_clm].attrs["crop_name_clm"] = thiscrop_clm - out_ds[varname_clm].attrs["crop_name_ggcmi"] = thiscrop_ggcmi - out_ds[varname_clm].attrs["short_name_ggcmi"] = varname_ggcmi - out_ds[varname_clm].attrs["units"] = "day of year" - out_ds[varname_clm].encoding["_FillValue"] = new_fillvalue - # scale_factor and add_offset are required by I/O library for short data - # From https://www.unidata.ucar.edu/software/netcdf/workshops/2010/bestpractices/Packing.html: - # unpacked_value = packed_value * scale_factor + add_offset - out_ds[varname_clm].attrs["scale_factor"] = np.int16(1) - out_ds[varname_clm].attrs["add_offset"] = np.int16(0) - return out_ds - out_ds = set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) - out_fill1_ds = set_var_attrs(out_fill1_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) - - # Save - if verbose: - print(" Saving %s..." % varname_ggcmi) - # start = time.time() - # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... - shutil.copyfile(file_clm, file_clm_tmp) - shutil.copyfile(file_clm_fill1, file_clm_fill1_tmp) - # ... then save out_ds to the temporary file... - out_ds.to_netcdf(file_clm_tmp, format="NETCDF3_CLASSIC") - out_fill1_ds.to_netcdf(file_clm_fill1_tmp, format="NETCDF3_CLASSIC") - # ... then close out_ds... - out_ds.close() - out_fill1_ds.close() - # ... and finally replace the original file with the new temporary file (deleting the temporary file in the process) - os.replace(file_clm_tmp, file_clm) - os.replace(file_clm_fill1_tmp, file_clm_fill1) - # end = time.time() - # print(end - start) - ### NOTE: This method gets slower and slower as the file gets bigger! (The entire process, but also the out_ds.to_netcdf() step.) Is there a better way? - - cropcal_ds.close() + thisvar_ds.variables[varname_ggcmi].values[np.isnan(thisvar_ds.variables[varname_ggcmi].values)] \ + = new_fillvalue + thisvar_ds.variables[varname_ggcmi].values \ + = thisvar_ds.variables[varname_ggcmi].values.astype("int16") + thisvar_fill1_ds.variables[varname_ggcmi].values[np.isnan(thisvar_fill1_ds.variables[varname_ggcmi].values)] \ + = 1 + thisvar_fill1_ds.variables[varname_ggcmi].values \ + = thisvar_fill1_ds.variables[varname_ggcmi].values.astype("int16") + + # Add time dimension (https://stackoverflow.com/a/62862440) + # (Repeats original map for every timestep) + # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. + thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) + thisvar_fill1_ds = thisvar_fill1_ds.expand_dims(time = template_ds.time) + # "True" here shows that the time dimension was created by just repeating the one map. + # tmp = thisvar_ds[varname_ggcmi] + # np.all((np.diff(tmp.values, axis=0) == 0.0) | np.isnan(np.diff(tmp.values, axis=0))) + + # Add variable to output dataset + out_ds[varname_clm]=(thisvar_ds[varname_ggcmi].dims, + thisvar_ds[varname_ggcmi].values) + out_fill1_ds[varname_clm]=(thisvar_fill1_ds[varname_ggcmi].dims, + thisvar_fill1_ds[varname_ggcmi].values) + + # Edit/add variable attributes etc. + longname = thisvar_ds[varname_ggcmi].attrs["long_name"] + longname = longname.replace("rainfed", thiscrop_clm).replace("irrigated", thiscrop_clm) + def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue): + out_ds[varname_clm].attrs["long_name"] = longname + if thiscrop_ggcmi == None: + out_ds[varname_clm].attrs["crop_name_clm"] = "none" + out_ds[varname_clm].attrs["crop_name_ggcmi"] = "none" + else: + out_ds[varname_clm].attrs["crop_name_clm"] = thiscrop_clm + out_ds[varname_clm].attrs["crop_name_ggcmi"] = thiscrop_ggcmi + out_ds[varname_clm].attrs["short_name_ggcmi"] = varname_ggcmi + out_ds[varname_clm].attrs["units"] = "day of year" + out_ds[varname_clm].encoding["_FillValue"] = new_fillvalue + # scale_factor and add_offset are required by I/O library for short data + # From https://www.unidata.ucar.edu/software/netcdf/workshops/2010/bestpractices/Packing.html: + # unpacked_value = packed_value * scale_factor + add_offset + out_ds[varname_clm].attrs["scale_factor"] = np.int16(1) + out_ds[varname_clm].attrs["add_offset"] = np.int16(0) + return out_ds + out_ds = set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) + out_fill1_ds = set_var_attrs(out_fill1_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) + + # Save + if verbose: + print(" Saving %s..." % varname_ggcmi) + # start = time.time() + # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... + shutil.copyfile(file_clm, file_clm_tmp) + shutil.copyfile(file_clm_fill1, file_clm_fill1_tmp) + # ... then save out_ds to the temporary file... + out_ds.to_netcdf(file_clm_tmp, format="NETCDF3_CLASSIC") + out_fill1_ds.to_netcdf(file_clm_fill1_tmp, format="NETCDF3_CLASSIC") + # ... then close out_ds... + out_ds.close() + out_fill1_ds.close() + # ... and finally replace the original file with the new temporary file (deleting the temporary file in the process) + os.replace(file_clm_tmp, file_clm) + os.replace(file_clm_fill1_tmp, file_clm_fill1) + # end = time.time() + # print(end - start) + ### NOTE: This method gets slower and slower as the file gets bigger! (The entire process, but also the out_ds.to_netcdf() step.) Is there a better way? + + cropcal_ds.close() -print("Done!") + print("Done!") + +if __name__ == "__main__": + ########### + ### Run ### + ########### + main() From 6c7c54dd14e27faf98f9de965c61d9db30159793 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:16:23 -0600 Subject: [PATCH 1175/2067] process shdates: Remove unused imports. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 1504acaccf..a036b10b9b 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -22,10 +22,8 @@ def main(): import numpy as np import xarray as xr - import matplotlib.pyplot as plt import shutil import os - import time import datetime as dt import cftime From ebc71b593b0da11d3960684bdcf311c373ae20b9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:17:05 -0600 Subject: [PATCH 1176/2067] process shdates: Import cropcal_utils instead of CTSM Python gallery. Add 3 required functions to cropcal_utils. --- python/ctsm/crop_calendars/cropcal_utils.py | 69 +++++++++++++++++++ .../crop_calendars/process_ggcmi_shdates.py | 7 +- 2 files changed, 70 insertions(+), 6 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py index ed4b07adfa..e26192a284 100644 --- a/python/ctsm/crop_calendars/cropcal_utils.py +++ b/python/ctsm/crop_calendars/cropcal_utils.py @@ -861,3 +861,72 @@ def safer_timeslice(ds, timeSlice, timeVar="time"): raise return ds + +# Convert a longitude axis that's -180 to 180 around the international date line to one that's 0 to 360 around the prime meridian. If you pass in a Dataset or DataArray, the "lon" coordinates will be changed. Otherwise, it assumes you're passing in numeric data. +def lon_idl2pm(lons_in, fail_silently=False): + def check_ok(tmp, fail_silently): + msg = "" + + if np.any(tmp > 180): + msg = f"Maximum longitude is already > 180 ({np.max(tmp)})" + elif np.any(tmp < -180): + msg = f"Minimum longitude is < -180 ({np.min(tmp)})" + + if msg == "": + return True + elif fail_silently: + return False + else: + raise ValueError(msg) + + def do_it(tmp): + tmp = tmp + 360 + tmp = np.mod(tmp, 360) + return tmp + + if isinstance(lons_in, (xr.DataArray, xr.Dataset)): + if not check_ok(lons_in.lon.values, fail_silently): + return lons_in + lons_out = lons_in + lons_out = lons_out.assign_coords(lon=do_it(lons_in.lon.values)) + lons_out = make_lon_increasing(lons_out) + else: + if not check_ok(lons_in, fail_silently): + return lons_in + lons_out = do_it(lons_in) + if not is_strictly_increasing(lons_out): + print( + "WARNING: You passed in numeric longitudes to lon_idl2pm() and these have been" + " converted, but they're not strictly increasing." + ) + print( + "To assign the new longitude coordinates to an Xarray object, use" + " xarrayobject.assign_coordinates()! (Pass the object directly in to lon_idl2pm() in" + " order to suppress this message.)" + ) + + return lons_out + +# Helper function to check that a list is strictly increasing +def is_strictly_increasing(L): + # https://stackoverflow.com/a/4983359/2965321 + return all(x < y for x, y in zip(L, L[1:])) + + +# Ensure that longitude axis coordinates are monotonically increasing +def make_lon_increasing(xr_obj): + if not "lon" in xr_obj.dims: + return xr_obj + + lons = xr_obj.lon.values + if is_strictly_increasing(lons): + return xr_obj + + shift = 0 + while not is_strictly_increasing(lons) and shift < lons.size: + shift = shift + 1 + lons = np.roll(lons, 1, axis=0) + if not is_strictly_increasing(lons): + raise RuntimeError("Unable to rearrange longitude axis so it's monotonically increasing") + + return xr_obj.roll(lon=shift, roll_coords=True) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index a036b10b9b..4ec6112b69 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -14,9 +14,6 @@ def main(): "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn" } - # Your path to ctsm_py directory (i.e., where utils.py lives) - my_ctsm_python_gallery = "/Users/sam/Documents/git_repos/ctsm_python_gallery_myfork/ctsm_py/" - # %% Imports @@ -27,9 +24,7 @@ def main(): import datetime as dt import cftime - import sys - sys.path.append(my_ctsm_python_gallery) - import utils + import cropcal_utils as utils # %% Setup From 2f42dde91567047009cf8749fbf89bb320ca424c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:22:17 -0600 Subject: [PATCH 1177/2067] process shdates: Move imports to top of script. --- .../crop_calendars/process_ggcmi_shdates.py | 20 ++++++++----------- 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 4ec6112b69..c12665ed86 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -1,3 +1,11 @@ +import numpy as np +import xarray as xr +import shutil +import os +import datetime as dt +import cftime +import cropcal_utils as utils + def main(): # %% Options @@ -15,18 +23,6 @@ def main(): } - # %% Imports - - import numpy as np - import xarray as xr - import shutil - import os - import datetime as dt - import cftime - - import cropcal_utils as utils - - # %% Setup # Where to save output files From 1087fe49bdc7d9b8c78e2e0f7d5c4d95ea8b8e0d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:49:33 -0600 Subject: [PATCH 1178/2067] process shdates: Read options from command-line. --- .../crop_calendars/process_ggcmi_shdates.py | 105 ++++++++++++------ 1 file changed, 68 insertions(+), 37 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index c12665ed86..9cdcbc2f14 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -4,16 +4,14 @@ import os import datetime as dt import cftime +import sys +import argparse import cropcal_utils as utils -def main(): +def main(input_directory, output_directory, template_file, file_specifier, first_year, last_year): # %% Options - # Years to include (set to None to leave that edge unbounded) - y1 = 2000 - yN = 2000 - # Global attributes for output files out_attrs = { "title": "GGCMI crop calendar for Phase 3, v1.01", @@ -25,28 +23,6 @@ def main(): # %% Setup - # Where to save output files - outdir = "/Users/Shared/CESM_work/crop_dates_mostrice/" - - # Files/directories to use for inputs - ### f10_f10_mg37 - # templatefile = "/Users/Shared/CESM_runs/f10_f10_mg37/2021-11-23/f10_f10_mg37.clm2.h3.2000-01-01-00000.nc" - # indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f10_f10_mg37/" - # file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f10_f10_mg37" # In name of input and output files - ## half degree - templatefile = "/Users/Shared/CESM_runs/halfdeg_test/2022-04-22/halfdeg_test.clm2.h1.1850-01-01-00000.nc" - indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar/" - file_specifier = "_ggcmi_crop_calendar_phase3_v1.01" # In name of input and output files - ### f19_g17 ("2-degree", actually 2.5° lon x 1.875° lat; i.e., 144x96) - # templatefile = "/Users/Shared/CESM_runs/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2/lnd/hist/spinup_ctsm5.1.dev092_I1850Clm50BgcCrop_f19-g17_pt2.clm2.h0.1801-12.nc" - # indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f19_g17/" - # file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f19_g17" # In name of input and output files - # ### f09_g17 ("1-degree", actually ???° lon x ???° lat; i.e., 288x192) - # templatefile = "/Users/Shared/CESM_work/f09_g17.shdates_template.nc" - # indir = "/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar-nninterp-f09_g17/" - # file_specifier = "_ggcmi_crop_calendar_phase3_v1.01_nninterp-f09_g17" # In name of input and output files - - # Add current date/time to output attributes out_attrs["created"] = dt.datetime.now().replace(microsecond=0).astimezone().isoformat() @@ -146,18 +122,18 @@ def slice_yr(y): return str(y) # Open and time-slice template dataset - template_ds = xr.open_dataset(templatefile, decode_times=True).sel(time=slice(slice_yr(y1), slice_yr(yN))) + template_ds = xr.open_dataset(template_file, decode_times=True).sel(time=slice(slice_yr(first_year), slice_yr(last_year))) # template_ds = template_ds.sel(time=slice(slice_yr(y1), slice_yr(yN))) if np.size(template_ds.time) == 0: - print(f"Time slice {y1}-{yN} not found in template dataset. Faking.") - if y1 != yN: + print(f"Time slice {first_year}-{last_year} not found in template dataset. Faking.") + if first_year != last_year: raise RuntimeError("Not sure how to fake time axis when y1 != yN") - template_ds = xr.open_dataset(templatefile, decode_times=True) + template_ds = xr.open_dataset(template_file, decode_times=True) template_ds = template_ds.isel(time=slice(0,1)) # Get the first timestep. Just using .values[0] causes trouble. val0 = template_ds.time.values[0] if not isinstance(template_ds.time.values[0], cftime.datetime): raise TypeError(f"Template file time axis is type {type(template_ds.time.values[0])}, which isn't a cftime.datetime subclass; not sure that next line (assigning fake value) will work.") - template_ds.time.values[0] = type(val0)(y1, 1, 1, 0, 0, 0, 0, has_year_zero=val0.has_year_zero) + template_ds.time.values[0] = type(val0)(first_year, 1, 1, 0, 0, 0, 0, has_year_zero=val0.has_year_zero) template_ds.time_bounds.values[0] = np.array([template_ds.time.values[0,], template_ds.time.values[0]]) if "mcdate" in template_ds: template_ds.mcdate.values = np.array([20000101,]).astype(type(template_ds.mcdate.values[0])) @@ -171,8 +147,8 @@ def slice_yr(y): template_ds.nstep.values = np.array([0,]).astype(type(template_ds.nstep.values[0])) else: raise RuntimeError("Try using just a normal, unprocessed output file that doesn't include year 2000") - y1 = template_ds.time.values[0].year - yN = template_ds.time.values[-1].year + first_year = template_ds.time.values[0].year + last_year = template_ds.time.values[-1].year template_ds.attrs = out_attrs # Remove variable(s) we don't need (hdm, or any all-uppercase variables) @@ -182,7 +158,7 @@ def slice_yr(y): # Create output files for v in variable_dict: - outfile = "%s%ss%s.%d-%d.%s.nc" % (outdir, v, file_specifier, y1, yN, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) + outfile = "%s%ss%s.%d-%d.%s.nc" % (output_directory, v, file_specifier, first_year, last_year, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) variable_dict[v]["outfile"] = outfile variable_dict[v]["outfile_fill1"] = outfile.replace(".nc", ".fill1.nc") template_ds.to_netcdf(path=variable_dict[v]["outfile"]) @@ -224,7 +200,7 @@ def slice_yr(y): c, len(crop_dict))) - file_ggcmi = indir + thiscrop_ggcmi + file_specifier + ".nc4" + file_ggcmi = input_directory + thiscrop_ggcmi + file_specifier + ".nc4" if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) cropcal_ds = xr.open_dataset(file_ggcmi) @@ -346,7 +322,62 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v print("Done!") if __name__ == "__main__": + ############################### + ### Process input arguments ### + ############################### + parser = argparse.ArgumentParser( + description="Converts raw sowing and harvest date files provided by GGCMI into a format that CLM can read." + ) + + # Required + parser.add_argument( + "-i", + "--input-directory", + help="Directory containing the GGCMI sowing/harvest date files", + type=str, + required=True, + ) + parser.add_argument( + "-o", + "--output-directory", + help="Where to save the CLM-compatible sowing and harvest date files", + type=str, + required=True, + ) + parser.add_argument( + "-t", + "--template-file", + help="A CLM output file to be used as a template for input files, especially for grid and time", + type=str, + required=True, + ) + parser.add_argument( + "--file-specifier", + help="String following CROP_IRR in input filenames. E.g., mai_irFILESPECIFIER.nc4. Will also be saved to output filenames.", + type=str, + default = "_ggcmi_crop_calendar_phase3_v1.01", + ) + parser.add_argument( + "-y1", + "--first-year", + help="First year in output files. Must be present in template file.", + type=int, + default=2000, + ) + parser.add_argument( + "-yN", + "--last-year", + help="Last year in output files. Must be present in template file.", + type=int, + default=2000, + ) + + # Get arguments + args = parser.parse_args(sys.argv[1:]) + + ########### ### Run ### ########### - main() + main(args.input_directory, args.output_directory, args.template_file, args.file_specifier, + args.first_year, args.last_year) From 2d912a01e55d8c564f1bab4de26174d3aa013d13 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 15:50:56 -0600 Subject: [PATCH 1179/2067] process shdates: Move "created" to be added to out_attrs with others. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 9cdcbc2f14..d2fa2e4ecc 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -17,15 +17,13 @@ def main(input_directory, output_directory, template_file, file_specifier, first "title": "GGCMI crop calendar for Phase 3, v1.01", "author_thisfile": "Sam Rabin (sam.rabin@gmail.com)", "author_original": "Jonas Jägermeyr (jaegermeyr@uchicago.edu)", - "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn" + "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", + "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), } # %% Setup - # Add current date/time to output attributes - out_attrs["created"] = dt.datetime.now().replace(microsecond=0).astimezone().isoformat() - # Define crop dictionary # As "CLMname: [number, GGCMIname]" # - CLM names and numbers taken from commit `3dcbc7499a57904750a994672fc36b4221b9def5` From f363edc8a3414be77a8aac33c60fd6f2f6cc4f1c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 16:01:39 -0600 Subject: [PATCH 1180/2067] process shdates: Add verbose to command-line options. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index d2fa2e4ecc..cc625b6fa3 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -8,7 +8,8 @@ import argparse import cropcal_utils as utils -def main(input_directory, output_directory, template_file, file_specifier, first_year, last_year): +def main(input_directory, output_directory, template_file, file_specifier, first_year, last_year, + verbose): # %% Options @@ -167,7 +168,6 @@ def slice_yr(y): # %% Process all crops - verbose = True for thiscrop_clm in crop_dict: @@ -369,6 +369,13 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v type=int, default=2000, ) + parser.add_argument( + "-v", + "--verbose", + help="Whether to print verbose messages", + type=bool, + default=False, + ) # Get arguments args = parser.parse_args(sys.argv[1:]) @@ -378,4 +385,4 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ### Run ### ########### main(args.input_directory, args.output_directory, args.template_file, args.file_specifier, - args.first_year, args.last_year) + args.first_year, args.last_year, args.verbose) From 3b4a81d2134eb2c74db08efc70be529291bd40d0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 16:02:08 -0600 Subject: [PATCH 1181/2067] process shdates: Improve section headers. --- .../crop_calendars/process_ggcmi_shdates.py | 30 ++++++++++++------- 1 file changed, 19 insertions(+), 11 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index cc625b6fa3..dbca32df64 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -23,10 +23,13 @@ def main(input_directory, output_directory, template_file, file_specifier, first } - # %% Setup - - # Define crop dictionary - # As "CLMname: [number, GGCMIname]" + ########################### + ### Define dictionaries ### + ########################### + + # First, we associate CLM crop names with (1) their integer counterpart and (2) their GGCMI counterpart. + # Some notes: + # - As "CLMname: [number, GGCMIname]" # - CLM names and numbers taken from commit `3dcbc7499a57904750a994672fc36b4221b9def5` # - Using one global GGCMI value for both temperate and tropical versions of corn and soybean. # - There is no GGCMI equivalent of CLM's winter barley and rye. Using winter wheat instead. @@ -34,7 +37,6 @@ def main(input_directory, output_directory, template_file, file_specifier, first # - Only using GGCMI `ri1` for rice; ignoring `ri2`. def set_crop_dict(thisnum, thisname): return {"clm_num": thisnum, "thiscrop_ggcmi": thisname} - crop_dict = { "temperate_corn": set_crop_dict(17, "mai_rf"), "irrigated_temperate_corn": set_crop_dict(18, "mai_ir"), @@ -103,16 +105,19 @@ def set_crop_dict(thisnum, thisname): } - # %% Define variable dictionary and output files - # As "CLM: [GGCMI, outfile]" - + # Next, we associate CLM variable names with their GGCMI counterparts. We also save a placeholder for output file paths associated with each variable. + # As CLMname: {GGCMIname, output_file} def set_var_dict(name_ggcmi, outfile): return {"name_ggcmi": name_ggcmi, "outfile": outfile} - variable_dict = { "sdate": set_var_dict("planting_day", ""), "hdate": set_var_dict("maturity_day", "") } + + + ################################ + ### Instantiate output files ### + ################################ def slice_yr(y): if y == None: @@ -166,8 +171,9 @@ def slice_yr(y): template_ds.close() - # %% Process all crops - + ######################### + ### Process all crops ### + ######################### for thiscrop_clm in crop_dict: @@ -349,6 +355,8 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v type=str, required=True, ) + + # Optional parser.add_argument( "--file-specifier", help="String following CROP_IRR in input filenames. E.g., mai_irFILESPECIFIER.nc4. Will also be saved to output filenames.", From eac179c69c91edd1f86f9457d374bcd952740353 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 16:07:34 -0600 Subject: [PATCH 1182/2067] Added -a/--author required argument. --- .../crop_calendars/process_ggcmi_shdates.py | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index dbca32df64..880a6c2ac2 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -8,15 +8,15 @@ import argparse import cropcal_utils as utils -def main(input_directory, output_directory, template_file, file_specifier, first_year, last_year, - verbose): +def main(input_directory, output_directory, template_file, file_specifier, author, first_year, + last_year, verbose): # %% Options # Global attributes for output files out_attrs = { "title": "GGCMI crop calendar for Phase 3, v1.01", - "author_thisfile": "Sam Rabin (sam.rabin@gmail.com)", + "author_thisfile": author, "author_original": "Jonas Jägermeyr (jaegermeyr@uchicago.edu)", "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), @@ -304,6 +304,7 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v # Save if verbose: print(" Saving %s..." % varname_ggcmi) + raise RuntimeError("Stopping") # start = time.time() # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... shutil.copyfile(file_clm, file_clm_tmp) @@ -355,6 +356,13 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v type=str, required=True, ) + parser.add_argument( + "-a", + "--author", + help="String to be saved in author_thisfile attribute of output files. E.g., 'Author Name (authorname@ucar.edu)'", + type=str, + required=True + ) # Optional parser.add_argument( @@ -392,5 +400,5 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ########### ### Run ### ########### - main(args.input_directory, args.output_directory, args.template_file, args.file_specifier, - args.first_year, args.last_year, args.verbose) + main(args.input_directory, args.output_directory, args.template_file, args.author, + args.file_specifier, args.first_year, args.last_year, args.verbose) From 58281ae1773386d522fa303020289956e8b5269d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 16:11:11 -0600 Subject: [PATCH 1183/2067] process shdates: Added optional --ggcmi-author argument. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 880a6c2ac2..7c4cf174e3 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -9,7 +9,7 @@ import cropcal_utils as utils def main(input_directory, output_directory, template_file, file_specifier, author, first_year, - last_year, verbose): + last_year, verbose, ggcmi_author): # %% Options @@ -17,7 +17,7 @@ def main(input_directory, output_directory, template_file, file_specifier, autho out_attrs = { "title": "GGCMI crop calendar for Phase 3, v1.01", "author_thisfile": author, - "author_original": "Jonas Jägermeyr (jaegermeyr@uchicago.edu)", + "author_original": ggcmi_author, "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), } @@ -392,6 +392,12 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v type=bool, default=False, ) + parser.add_argument( + "--ggcmi-author", + help="Author of original GGCMI files", + type=str, + default="Jonas Jägermeyr (jonas.jaegermeyr@columbia.edu)", + ) # Get arguments args = parser.parse_args(sys.argv[1:]) @@ -401,4 +407,4 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ### Run ### ########### main(args.input_directory, args.output_directory, args.template_file, args.author, - args.file_specifier, args.first_year, args.last_year, args.verbose) + args.file_specifier, args.first_year, args.last_year, args.verbose, args.ggcmi_author) From 6e669b297518c4db54d0e98d5161788423fb88e4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 16:17:33 -0600 Subject: [PATCH 1184/2067] process shdates: Rearranging. --- .../crop_calendars/process_ggcmi_shdates.py | 25 ++++++++----------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 7c4cf174e3..5021afec05 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -11,18 +11,7 @@ def main(input_directory, output_directory, template_file, file_specifier, author, first_year, last_year, verbose, ggcmi_author): - # %% Options - - # Global attributes for output files - out_attrs = { - "title": "GGCMI crop calendar for Phase 3, v1.01", - "author_thisfile": author, - "author_original": ggcmi_author, - "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", - "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), - } - - + ########################### ### Define dictionaries ### ########################### @@ -118,14 +107,22 @@ def set_var_dict(name_ggcmi, outfile): ################################ ### Instantiate output files ### ################################ + + # Global attributes for output files + out_attrs = { + "title": "GGCMI crop calendar for Phase 3, v1.01", + "author_thisfile": author, + "author_original": ggcmi_author, + "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", + "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), + } + # Open and time-slice template dataset def slice_yr(y): if y == None: return None else: return str(y) - - # Open and time-slice template dataset template_ds = xr.open_dataset(template_file, decode_times=True).sel(time=slice(slice_yr(first_year), slice_yr(last_year))) # template_ds = template_ds.sel(time=slice(slice_yr(y1), slice_yr(yN))) if np.size(template_ds.time) == 0: From 739cf7c2269dc8db60135740efe6789f912c0452 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 20 Jul 2023 16:20:31 -0600 Subject: [PATCH 1185/2067] Add error check for suplnitro for FATES --- bld/CLMBuildNamelist.pm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 6cc16ecb96..5e0acd9ac6 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4220,6 +4220,13 @@ sub setup_logic_fates { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, 'use_fates_sp'=>$nl_flags->{'use_fates_sp'} ); } + my $suplnitro = $nl->get_value('suplnitro'); + my $parteh_mode = $nl->get_value('fates_parteh_mode'); + if ( ($parteh_mode == 1) && ($suplnitro !~ /ALL/) && not &value_is_true( $nl_flags->{'use_fates_sp'}) ) { + $log->fatal_error("supplemental Nitrogen (suplnitro) is NOT set to ALL, FATES is on, " . + "but and FATES-SP is not active, but fates_parteh_mode is 1, so Nitrogen is not active" . + "Change suplnitro back to ALL"); + } # # For FATES SP mode make sure no-competetiion, and fixed-biogeography are also set # And also check for other settings that can't be trigged on as well From d792e71e82ba382df4a85a394a8d74a287f91b2c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 17:07:53 -0600 Subject: [PATCH 1186/2067] Added regrid_ggcmi_shdates.py. Called by process_ggcmi_shdates.py. --- .../crop_calendars/process_ggcmi_shdates.py | 9 +++ .../crop_calendars/regrid_ggcmi_shdates.py | 55 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 python/ctsm/crop_calendars/regrid_ggcmi_shdates.py diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 5021afec05..5e3de2eca9 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -6,11 +6,20 @@ import cftime import sys import argparse + import cropcal_utils as utils +from regrid_ggcmi_shdates import main as regrid_ggcmi_shdates + def main(input_directory, output_directory, template_file, file_specifier, author, first_year, last_year, verbose, ggcmi_author): + ############################################################ + ### Regrid original GGCMI files to target CLM resolution ### + ############################################################ + + regrid_ggcmi_shdates() + ########################### ### Define dictionaries ### diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py new file mode 100644 index 0000000000..8341bea9f8 --- /dev/null +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -0,0 +1,55 @@ +from subprocess import run +import os +import shutil +import glob + +def run_and_check(cmd): + result = run( + cmd, + shell = True, + capture_output = True, + text = True, + ) + if result.returncode != 0: + raise RuntimeError(f"Trouble running `{result.args}` in shell:\n{result.stderr}") + +def main(): + + # Ensure we can call necessary shell scripts + for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: + run_and_check(f"{cmd} --help") + + templatefile0 = "/Users/Shared/CESM_work/CropEvalData_ssr/danica_timeseries-cmip6_i.e21.IHIST.f09_g17/month_1/ssr_trimmed_annual.nc" + + templatefile = "template.nc" + + # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. + shutil.copyfile(templatefile0, os.path.basename(templatefile0)) + templatefile0 = os.path.basename(templatefile0) + + if os.path.exists(templatefile): + os.remove(templatefile) + + for v in ["planting_day", "maturity_day", "growing_season_length"]: + run_and_check(f"ncks -A -v area '{templatefile0}' '{templatefile}'") + run_and_check(f"ncrename -v area,{v} '{templatefile}'") + os.remove(templatefile0) + run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") + + + input_files = glob.glob("/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar/*nc4") + input_files.sort() + for f in input_files: + + f2 = os.path.basename(f) + f3 = f2.replace(".nc4", "_nninterp-f09_g17.nc4") + print(f3) + + if os.path.exists(f3): + os.remove(f3) + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + + os.remove(templatefile) + +if __name__ == "__main__": + main() \ No newline at end of file From 13dcdf22b8fb86b4ed7c722fd5668be241b9dc32 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 17:30:41 -0600 Subject: [PATCH 1187/2067] regrid_ggcmi_shdates: Added command-line arguments. --- .../crop_calendars/process_ggcmi_shdates.py | 12 ++-- .../crop_calendars/regrid_ggcmi_shdates.py | 66 +++++++++++++++---- 2 files changed, 63 insertions(+), 15 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 5e3de2eca9..0546340d9b 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -8,17 +8,17 @@ import argparse import cropcal_utils as utils -from regrid_ggcmi_shdates import main as regrid_ggcmi_shdates +import regrid_ggcmi_shdates def main(input_directory, output_directory, template_file, file_specifier, author, first_year, - last_year, verbose, ggcmi_author): + last_year, verbose, ggcmi_author, regrid_resolution, regrid_template_file): ############################################################ ### Regrid original GGCMI files to target CLM resolution ### ############################################################ - regrid_ggcmi_shdates() + regrid_ggcmi_shdates.main(regrid_resolution, regrid_template_file, input_directory) ########################### @@ -404,6 +404,9 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v type=str, default="Jonas Jägermeyr (jonas.jaegermeyr@columbia.edu)", ) + + # Arguments for regridding + parser = regrid_ggcmi_shdates.define_arguments(parser) # Get arguments args = parser.parse_args(sys.argv[1:]) @@ -413,4 +416,5 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ### Run ### ########### main(args.input_directory, args.output_directory, args.template_file, args.author, - args.file_specifier, args.first_year, args.last_year, args.verbose, args.ggcmi_author) + args.file_specifier, args.first_year, args.last_year, args.verbose, args.ggcmi_author, + args.regrid_resolution, args.regrid_template_file) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 8341bea9f8..d867aefe90 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -2,6 +2,8 @@ import os import shutil import glob +import argparse +import sys def run_and_check(cmd): result = run( @@ -12,37 +14,54 @@ def run_and_check(cmd): ) if result.returncode != 0: raise RuntimeError(f"Trouble running `{result.args}` in shell:\n{result.stderr}") + +# Functionized because these are shared by process_ggcmi_shdates +def define_arguments(parser): + # Required + parser.add_argument( + "-rr", + "--regrid-resolution", + help="Target CLM resolution, to be saved in output filenames.", + type=str, + required=True + ) + parser.add_argument( + "-rt", + "--regrid-template-file", + help="Template file to be used in regridding of .", + type=str, + required=True + ) + return parser -def main(): +def main(regrid_resolution, regrid_template_file, input_directory): # Ensure we can call necessary shell scripts for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: run_and_check(f"{cmd} --help") - - templatefile0 = "/Users/Shared/CESM_work/CropEvalData_ssr/danica_timeseries-cmip6_i.e21.IHIST.f09_g17/month_1/ssr_trimmed_annual.nc" - + templatefile = "template.nc" # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. - shutil.copyfile(templatefile0, os.path.basename(templatefile0)) - templatefile0 = os.path.basename(templatefile0) + shutil.copyfile(regrid_template_file, os.path.basename(regrid_template_file)) + regrid_template_file = os.path.basename(regrid_template_file) if os.path.exists(templatefile): os.remove(templatefile) for v in ["planting_day", "maturity_day", "growing_season_length"]: - run_and_check(f"ncks -A -v area '{templatefile0}' '{templatefile}'") + run_and_check(f"ncks -A -v area '{regrid_template_file}' '{templatefile}'") run_and_check(f"ncrename -v area,{v} '{templatefile}'") - os.remove(templatefile0) + os.remove(regrid_template_file) run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") - input_files = glob.glob("/Users/Shared/GGCMI/AgMIP.input/phase3/ISIMIP3/crop_calendar/*nc4") + input_files = glob.glob(os.path.join(input_directory, "*nc4")) input_files.sort() for f in input_files: f2 = os.path.basename(f) - f3 = f2.replace(".nc4", "_nninterp-f09_g17.nc4") + f3 = f2.replace(".nc4", f"_nninterp-{regrid_resolution}.nc4") print(f3) if os.path.exists(f3): @@ -51,5 +70,30 @@ def main(): os.remove(templatefile) + if __name__ == "__main__": - main() \ No newline at end of file + ############################### + ### Process input arguments ### + ############################### + parser = argparse.ArgumentParser( + description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." + ) + + # Define arguments + parser = define_arguments(parser) + parser.add_argument( + "-i", + "--input-directory", + help="Target CLM resolution, to be saved in output filenames.", + type=str, + required=True + ) + + # Get arguments + args = parser.parse_args(sys.argv[1:]) + + + ########### + ### Run ### + ########### + main(args.regrid_resolution, args.regrid_template_file, args.input_directory) \ No newline at end of file From d4b6087cf714aceb56eee3bd8e46b1f70515a19c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 17:31:31 -0600 Subject: [PATCH 1188/2067] process shdates: Improved parser descriptions. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 0546340d9b..96737e03c9 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -337,14 +337,14 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ### Process input arguments ### ############################### parser = argparse.ArgumentParser( - description="Converts raw sowing and harvest date files provided by GGCMI into a format that CLM can read." + description="Converts raw sowing and harvest date files provided by GGCMI into a format that CLM can read, optionally at a target resolution." ) # Required parser.add_argument( "-i", "--input-directory", - help="Directory containing the GGCMI sowing/harvest date files", + help="Directory containing the raw GGCMI sowing/harvest date files", type=str, required=True, ) From 8358ba3b17b0ebebcc9d678c4bad862e69d9ad82 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 17:48:09 -0600 Subject: [PATCH 1189/2067] regrid_ggcmi_shdates: Fixes to handling of output directory. --- .../crop_calendars/process_ggcmi_shdates.py | 5 ++- .../crop_calendars/regrid_ggcmi_shdates.py | 38 +++++++++++++------ 2 files changed, 30 insertions(+), 13 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 96737e03c9..8768326644 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -18,7 +18,10 @@ def main(input_directory, output_directory, template_file, file_specifier, autho ### Regrid original GGCMI files to target CLM resolution ### ############################################################ - regrid_ggcmi_shdates.main(regrid_resolution, regrid_template_file, input_directory) + regridded_ggcmi_files_dir = os.path.join(output_directory, "regridded_ggcmi_files") + + regrid_ggcmi_shdates.main(regrid_resolution, regrid_template_file, input_directory, + regridded_ggcmi_files_dir) ########################### diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index d867aefe90..bc26c46f15 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -34,18 +34,25 @@ def define_arguments(parser): ) return parser -def main(regrid_resolution, regrid_template_file, input_directory): +def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory): + + os.chdir(regrid_input_directory) + if not os.path.exists(regrid_output_directory): + os.makedirs(regrid_output_directory) # Ensure we can call necessary shell scripts for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: run_and_check(f"{cmd} --help") - templatefile = "template.nc" + templatefile = os.path.join(regrid_output_directory, "template.nc") # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. - shutil.copyfile(regrid_template_file, os.path.basename(regrid_template_file)) - regrid_template_file = os.path.basename(regrid_template_file) - + regrid_template_file = os.path.join( + regrid_output_directory, + os.path.basename(regrid_template_file_in), + ) + shutil.copyfile(regrid_template_file_in, regrid_template_file) + if os.path.exists(templatefile): os.remove(templatefile) @@ -56,13 +63,12 @@ def main(regrid_resolution, regrid_template_file, input_directory): run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") - input_files = glob.glob(os.path.join(input_directory, "*nc4")) + input_files = glob.glob("*nc4") input_files.sort() for f in input_files: - - f2 = os.path.basename(f) + print(f[0:6]) + f2 = os.path.join(regrid_output_directory, f) f3 = f2.replace(".nc4", f"_nninterp-{regrid_resolution}.nc4") - print(f3) if os.path.exists(f3): os.remove(f3) @@ -83,8 +89,15 @@ def main(regrid_resolution, regrid_template_file, input_directory): parser = define_arguments(parser) parser.add_argument( "-i", - "--input-directory", - help="Target CLM resolution, to be saved in output filenames.", + "--regrid-input-directory", + help="Directory containing the raw GGCMI sowing/harvest date files.", + type=str, + required=True + ) + parser.add_argument( + "-o", + "--regrid-output-directory", + help="Directory where regridded output files should be saved.", type=str, required=True ) @@ -96,4 +109,5 @@ def main(regrid_resolution, regrid_template_file, input_directory): ########### ### Run ### ########### - main(args.regrid_resolution, args.regrid_template_file, args.input_directory) \ No newline at end of file + main(args.regrid_resolution, args.regrid_template_file, args.regrid_input_directory, + args.regrid_output_directory) \ No newline at end of file From b19eca0d92615fd3b2e17fe7ff5a8e319575f880 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 17:48:37 -0600 Subject: [PATCH 1190/2067] regrid_ggcmi_shdates: Minor rearranging. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index bc26c46f15..929868a7ba 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -35,15 +35,15 @@ def define_arguments(parser): return parser def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory): - - os.chdir(regrid_input_directory) - if not os.path.exists(regrid_output_directory): - os.makedirs(regrid_output_directory) # Ensure we can call necessary shell scripts for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: run_and_check(f"{cmd} --help") + os.chdir(regrid_input_directory) + if not os.path.exists(regrid_output_directory): + os.makedirs(regrid_output_directory) + templatefile = os.path.join(regrid_output_directory, "template.nc") # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. From 76f0d49867fcfa0ad66c1ab49ed19db7ac04f45f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 18:05:44 -0600 Subject: [PATCH 1191/2067] process shdates: Verbose now default true. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 8768326644..6bf9ef628d 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -399,7 +399,7 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v "--verbose", help="Whether to print verbose messages", type=bool, - default=False, + default=True, ) parser.add_argument( "--ggcmi-author", From dcfcf4bbd7314a5519cf52a1eb6c6bdca48d44ef Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 18:06:09 -0600 Subject: [PATCH 1192/2067] regrid_ggcmi_shdates: Shell run stdout now included in error message. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 929868a7ba..cb56da7b08 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -13,7 +13,7 @@ def run_and_check(cmd): text = True, ) if result.returncode != 0: - raise RuntimeError(f"Trouble running `{result.args}` in shell:\n{result.stderr}") + raise RuntimeError(f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}") # Functionized because these are shared by process_ggcmi_shdates def define_arguments(parser): From e89eb5dfd9c754e4d8ff3dee00ad2fa6fbef3bf6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 18:06:32 -0600 Subject: [PATCH 1193/2067] regrid_ggcmi_shdates: Retry cdo command twice if needed. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index cb56da7b08..e69a7edf18 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -72,7 +72,15 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg if os.path.exists(f3): os.remove(f3) - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + + # Sometimes cdo fails for no apparent reason. In testing this never happened more than twice in a row. + try: + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + except: + try: + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + except: + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") os.remove(templatefile) From 669020ec5bb18b27c59e97069dbb428777269793 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 18:07:02 -0600 Subject: [PATCH 1194/2067] process shdates: Fix to argument order. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 6bf9ef628d..22f683aafc 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -11,7 +11,7 @@ import regrid_ggcmi_shdates -def main(input_directory, output_directory, template_file, file_specifier, author, first_year, +def main(input_directory, output_directory, template_file, author, file_specifier, first_year, last_year, verbose, ggcmi_author, regrid_resolution, regrid_template_file): ############################################################ From 7f240ed20d8e6cbd094edef5c97ba4e641fae139 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 18:07:28 -0600 Subject: [PATCH 1195/2067] process shdates: Implement os.path.join() in one place. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 22f683aafc..dd454a4f80 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -213,7 +213,9 @@ def slice_yr(y): c, len(crop_dict))) - file_ggcmi = input_directory + thiscrop_ggcmi + file_specifier + ".nc4" + file_ggcmi = os.path.join( + regridded_ggcmi_files_dir, + thiscrop_ggcmi + file_specifier + ".nc4") if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) cropcal_ds = xr.open_dataset(file_ggcmi) From ecc82ee1f4bdd5224e26f7db3c9ef072ef64af87 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 20 Jul 2023 18:07:48 -0600 Subject: [PATCH 1196/2067] regrid and process shdates: Improve handling of relative command-line paths. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 6 +++--- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 6 ++++-- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index dd454a4f80..a9271dcf57 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -420,6 +420,6 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ########### ### Run ### ########### - main(args.input_directory, args.output_directory, args.template_file, args.author, - args.file_specifier, args.first_year, args.last_year, args.verbose, args.ggcmi_author, - args.regrid_resolution, args.regrid_template_file) + main(os.path.realpath(args.input_directory), os.path.realpath(args.output_directory), + args.template_file, args.author, args.file_specifier, args.first_year, args.last_year, + args.verbose, args.ggcmi_author, args.regrid_resolution, args.regrid_template_file) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index e69a7edf18..160c5f2805 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -117,5 +117,7 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg ########### ### Run ### ########### - main(args.regrid_resolution, args.regrid_template_file, args.regrid_input_directory, - args.regrid_output_directory) \ No newline at end of file + main(args.regrid_resolution, + os.path.realpath(args.regrid_template_file), + os.path.realpath(args.regrid_input_directory), + os.path.realpath(args.regrid_output_directory)) \ No newline at end of file From 0f263e736690e1de5c05c032723d392ba382fe99 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 21 Jul 2023 12:29:15 -0600 Subject: [PATCH 1197/2067] Rm if(use_biomass_heat_storage) and return to original code here --- src/biogeophys/CanopyFluxesMod.F90 | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 4f60eec304..baea39ae95 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -1393,17 +1393,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, zeta(p) = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) if (zeta(p) >= 0._r8) then !stable - ! remove stability cap when biomass heat storage is active - if(use_biomass_heat_storage) then - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) - else - zeta(p) = min(100._r8,max(zeta(p),0.01_r8)) - end if - else - zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) - endif + zeta(p) = min(zetamax,max(zeta(p),0.01_r8)) um(p) = max(ur(p),0.1_r8) else !unstable zeta(p) = max(-100._r8,min(zeta(p),-0.01_r8)) From c21e88fa202b001fdcbb7f78e5d7d3409e34737d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 21 Jul 2023 12:38:15 -0600 Subject: [PATCH 1198/2067] Replace more divisions with multiplications in Meier2022 code --- src/biogeophys/CanopyFluxesMod.F90 | 4 ++-- src/biogeophys/SnowHydrologyMod.F90 | 2 +- src/biogeophys/SoilTemperatureMod.F90 | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index baea39ae95..75c77fcd25 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -899,8 +899,8 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, lt = min(lt,z0v_LAImax(patch%itype(p))) delt = 2._r8 - U_ustar_ini = (z0v_Cs(patch%itype(p)) + z0v_Cr(patch%itype(p)) * lt / 2._r8)**(-0.5_r8) & - *z0v_c(patch%itype(p)) * lt / 4._r8 + U_ustar_ini = (z0v_Cs(patch%itype(p)) + z0v_Cr(patch%itype(p)) * lt * 0.5_r8)**(-0.5_r8) & + *z0v_c(patch%itype(p)) * lt * 0.25_r8 U_ustar = U_ustar_ini do while (delt > 0.0001_r8) diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 index dc1676ca7d..91689a9d28 100644 --- a/src/biogeophys/SnowHydrologyMod.F90 +++ b/src/biogeophys/SnowHydrologyMod.F90 @@ -491,7 +491,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & ! all snow falls on ground, no snow on h2osfc (note that qflx_snow_h2osfc is ! currently set to 0 always in CanopyHydrologyMod) newsnow(c) = qflx_snow_grnd(c) * dtime - snomelt_accum(c) = max(0._r8, snomelt_accum(c) - newsnow(c)/1000._r8) + snomelt_accum(c) = max(0._r8, snomelt_accum(c) - newsnow(c) * 1.e-3_r8) ! update int_snow int_snow(c) = max(int_snow(c),h2osno_total(c)) !h2osno_total could be larger due to frost diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 061fb3a2b2..69a452081f 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1382,7 +1382,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) - snomelt_accum(c) = snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime/1000._r8 + snomelt_accum(c) = snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime * 1.e-3_r8 endif ! layer freezing mass flux (positive): From 5d0b10327b75f73f0495211b2f4ea1250a93ee67 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 12:47:46 -0600 Subject: [PATCH 1199/2067] process shdates: Improved -y1/-yN descriptions. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index a9271dcf57..9d6aa2a9f6 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -385,14 +385,14 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v parser.add_argument( "-y1", "--first-year", - help="First year in output files. Must be present in template file.", + help="First year in output files. Must be present in template file, unless it's the same as the last year.", type=int, default=2000, ) parser.add_argument( "-yN", "--last-year", - help="Last year in output files. Must be present in template file.", + help="Last year in output files. Must be present in template file, unless it's the same as the first year.", type=int, default=2000, ) From ccc8303433565e028a9adbfadb7af4b45ac318a0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 12:49:19 -0600 Subject: [PATCH 1200/2067] process shdates: Don't generate "fill1" files. --- .../crop_calendars/process_ggcmi_shdates.py | 23 ------------------- 1 file changed, 23 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 9d6aa2a9f6..b430c8ff51 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -173,9 +173,7 @@ def slice_yr(y): for v in variable_dict: outfile = "%s%ss%s.%d-%d.%s.nc" % (output_directory, v, file_specifier, first_year, last_year, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) variable_dict[v]["outfile"] = outfile - variable_dict[v]["outfile_fill1"] = outfile.replace(".nc", ".fill1.nc") template_ds.to_netcdf(path=variable_dict[v]["outfile"]) - template_ds.to_netcdf(path=variable_dict[v]["outfile_fill1"]) template_ds.close() @@ -236,14 +234,9 @@ def slice_yr(y): if not os.path.exists(file_clm): raise Exception("Output file not found: " + file_clm) file_clm_tmp = file_clm + ".tmp" - file_clm_fill1 = variable_dict[thisvar_clm]["outfile_fill1"] - if not os.path.exists(file_clm_fill1): - raise Exception("Output file not found: " + file_clm_fill1) - file_clm_fill1_tmp = file_clm_fill1 + ".tmp" # "Read" the file (doesn't actually bring anything into memory yet) out_ds = xr.open_dataset(file_clm) - out_fill1_ds = xr.open_dataset(file_clm_fill1) # Strip dataset to just this variable droplist = [] @@ -252,33 +245,24 @@ def slice_yr(y): droplist.append(i) thisvar_ds = cropcal_ds.drop(droplist) thisvar_ds = thisvar_ds.load() - thisvar_fill1_ds = thisvar_ds.copy() # Convert to integer new_fillvalue = -1 dummyvalue = -1 thisvar_ds.variables[varname_ggcmi].encoding["_FillValue"] \ = new_fillvalue - thisvar_fill1_ds.variables[varname_ggcmi].encoding["_FillValue"] \ - = new_fillvalue if thiscrop_ggcmi == None: thisvar_ds.variables[varname_ggcmi].values.fill(dummyvalue) - thisvar_fill1_ds.variables[varname_ggcmi].values.fill(1) else: thisvar_ds.variables[varname_ggcmi].values[np.isnan(thisvar_ds.variables[varname_ggcmi].values)] \ = new_fillvalue thisvar_ds.variables[varname_ggcmi].values \ = thisvar_ds.variables[varname_ggcmi].values.astype("int16") - thisvar_fill1_ds.variables[varname_ggcmi].values[np.isnan(thisvar_fill1_ds.variables[varname_ggcmi].values)] \ - = 1 - thisvar_fill1_ds.variables[varname_ggcmi].values \ - = thisvar_fill1_ds.variables[varname_ggcmi].values.astype("int16") # Add time dimension (https://stackoverflow.com/a/62862440) # (Repeats original map for every timestep) # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) - thisvar_fill1_ds = thisvar_fill1_ds.expand_dims(time = template_ds.time) # "True" here shows that the time dimension was created by just repeating the one map. # tmp = thisvar_ds[varname_ggcmi] # np.all((np.diff(tmp.values, axis=0) == 0.0) | np.isnan(np.diff(tmp.values, axis=0))) @@ -286,8 +270,6 @@ def slice_yr(y): # Add variable to output dataset out_ds[varname_clm]=(thisvar_ds[varname_ggcmi].dims, thisvar_ds[varname_ggcmi].values) - out_fill1_ds[varname_clm]=(thisvar_fill1_ds[varname_ggcmi].dims, - thisvar_fill1_ds[varname_ggcmi].values) # Edit/add variable attributes etc. longname = thisvar_ds[varname_ggcmi].attrs["long_name"] @@ -310,7 +292,6 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v out_ds[varname_clm].attrs["add_offset"] = np.int16(0) return out_ds out_ds = set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) - out_fill1_ds = set_var_attrs(out_fill1_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) # Save if verbose: @@ -319,16 +300,12 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v # start = time.time() # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... shutil.copyfile(file_clm, file_clm_tmp) - shutil.copyfile(file_clm_fill1, file_clm_fill1_tmp) # ... then save out_ds to the temporary file... out_ds.to_netcdf(file_clm_tmp, format="NETCDF3_CLASSIC") - out_fill1_ds.to_netcdf(file_clm_fill1_tmp, format="NETCDF3_CLASSIC") # ... then close out_ds... out_ds.close() - out_fill1_ds.close() # ... and finally replace the original file with the new temporary file (deleting the temporary file in the process) os.replace(file_clm_tmp, file_clm) - os.replace(file_clm_fill1_tmp, file_clm_fill1) # end = time.time() # print(end - start) ### NOTE: This method gets slower and slower as the file gets bigger! (The entire process, but also the out_ds.to_netcdf() step.) Is there a better way? From 907f04688acbfff2be022993cb9a1db4b7306731 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 12:49:48 -0600 Subject: [PATCH 1201/2067] process shdates: Removed troubleshooting stop. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b430c8ff51..a64980b981 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -296,7 +296,6 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v # Save if verbose: print(" Saving %s..." % varname_ggcmi) - raise RuntimeError("Stopping") # start = time.time() # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... shutil.copyfile(file_clm, file_clm_tmp) From 18963f3cb82cbe64efd11aa314be6641f21b3cea Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 13:02:03 -0600 Subject: [PATCH 1202/2067] process shdates: Output file path generation cleaner and more robust. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index a64980b981..b3e1fc428e 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -171,7 +171,7 @@ def slice_yr(y): # Create output files for v in variable_dict: - outfile = "%s%ss%s.%d-%d.%s.nc" % (output_directory, v, file_specifier, first_year, last_year, dt.datetime.now().strftime("%Y%m%d_%H%M%S")) + outfile = os.path.join(output_directory, f"{v}s{file_specifier}.{first_year}-{last_year}.{dt.datetime.now().strftime('%Y%m%d_%H%M%S')}.nc") variable_dict[v]["outfile"] = outfile template_ds.to_netcdf(path=variable_dict[v]["outfile"]) From e71f9595f97cae6e70b8abde7ceaa4f06e18b422 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 13:04:48 -0600 Subject: [PATCH 1203/2067] generate_gdds.py no longer makes fill0 files. --- cime_config/SystemTests/rxcropmaturity.py | 1 - python/ctsm/crop_calendars/generate_gdds.py | 9 --------- 2 files changed, 10 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index bc5d5ea479..f22309f1fb 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -364,7 +364,6 @@ def _run_generate_gdds(self, case_gddgen): # Where were the prescribed maturity requirements saved? generated_gdd_files = glob.glob(os.path.join(self._generate_gdds_dir, "gdds_*.nc")) - generated_gdd_files = [x for x in generated_gdd_files if "fill0" not in x] if len(generated_gdd_files) != 1: error_message = f"ERROR: Expected one matching prescribed maturity requirements file; found {len(generated_gdd_files)}: {generated_gdd_files}" logger.error(error_message) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index e83197ace6..8ab5746d19 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -222,7 +222,6 @@ def main( # Fill NAs with dummy values dummy_fill = -1 - gdd_fill0_maps_ds = gdd_maps_ds.fillna(0) gdd_maps_ds = gdd_maps_ds.fillna(dummy_fill) gddfn.log(logger, "Done getting and gridding means.") @@ -250,10 +249,8 @@ def make_dummy(thisCrop_gridded, addend): for v in gdd_maps_ds: thisCrop_gridded = gdd_maps_ds[v].copy() - thisCrop_fill0_gridded = gdd_fill0_maps_ds[v].copy() break dummy_gridded = make_dummy(thisCrop_gridded, -1) - dummy_gridded0 = make_dummy(thisCrop_fill0_gridded, 0) for v, thisVar in enumerate(dummy_vars): if thisVar in gdd_maps_ds: @@ -263,9 +260,6 @@ def make_dummy(thisCrop_gridded, addend): dummy_gridded.name = thisVar dummy_gridded.attrs["long_name"] = dummy_longnames[v] gdd_maps_ds[thisVar] = dummy_gridded - dummy_gridded0.name = thisVar - dummy_gridded0.attrs["long_name"] = dummy_longnames[v] - gdd_fill0_maps_ds[thisVar] = dummy_gridded0 # Add lon/lat attributes def add_lonlat_attrs(ds): @@ -274,7 +268,6 @@ def add_lonlat_attrs(ds): return ds gdd_maps_ds = add_lonlat_attrs(gdd_maps_ds) - gdd_fill0_maps_ds = add_lonlat_attrs(gdd_fill0_maps_ds) gddharv_maps_ds = add_lonlat_attrs(gddharv_maps_ds) gddfn.log(logger, "Done.") @@ -289,7 +282,6 @@ def add_lonlat_attrs(ds): # Get output file path datestr = dt.datetime.now().strftime("%Y%m%d_%H%M%S") outfile = os.path.join(output_dir, "gdds_" + datestr + ".nc") - outfile_fill0 = os.path.join(output_dir, "gdds_fill0_" + datestr + ".nc") def save_gdds(sdates_file, hdates_file, outfile, gdd_maps_ds, sdates_rx): # Set up output file from template (i.e., prescribed sowing dates). @@ -315,7 +307,6 @@ def save_gdds(sdates_file, hdates_file, outfile, gdd_maps_ds, sdates_rx): gdd_maps_ds.to_netcdf(outfile, mode="w", format="NETCDF3_CLASSIC") save_gdds(sdates_file, hdates_file, outfile, gdd_maps_ds, sdates_rx) - save_gdds(sdates_file, hdates_file, outfile_fill0, gdd_fill0_maps_ds, sdates_rx) gddfn.log(logger, "Done saving.") From b4eb133ce6d81bfc1545ce79512d19db67f73d64 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 13:09:03 -0600 Subject: [PATCH 1204/2067] process shdates: Ensure output files have the same datetime string. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b3e1fc428e..ebfd2b63a3 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -170,8 +170,9 @@ def slice_yr(y): template_ds = template_ds.drop(v) # Create output files + datetime_string = dt.datetime.now().strftime('%Y%m%d_%H%M%S') for v in variable_dict: - outfile = os.path.join(output_directory, f"{v}s{file_specifier}.{first_year}-{last_year}.{dt.datetime.now().strftime('%Y%m%d_%H%M%S')}.nc") + outfile = os.path.join(output_directory, f"{v}s{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc") variable_dict[v]["outfile"] = outfile template_ds.to_netcdf(path=variable_dict[v]["outfile"]) From 3e55d865d743c8b0a96e12a1a28131de7bd43007 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 13:16:17 -0600 Subject: [PATCH 1205/2067] process shdates: Leading underscore now assumed for file specifier. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index ebfd2b63a3..288a2e9568 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -172,7 +172,7 @@ def slice_yr(y): # Create output files datetime_string = dt.datetime.now().strftime('%Y%m%d_%H%M%S') for v in variable_dict: - outfile = os.path.join(output_directory, f"{v}s{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc") + outfile = os.path.join(output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc") variable_dict[v]["outfile"] = outfile template_ds.to_netcdf(path=variable_dict[v]["outfile"]) @@ -214,7 +214,7 @@ def slice_yr(y): file_ggcmi = os.path.join( regridded_ggcmi_files_dir, - thiscrop_ggcmi + file_specifier + ".nc4") + f"{thiscrop_ggcmi}_{file_specifier}.nc4") if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) cropcal_ds = xr.open_dataset(file_ggcmi) @@ -355,9 +355,9 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v # Optional parser.add_argument( "--file-specifier", - help="String following CROP_IRR in input filenames. E.g., mai_irFILESPECIFIER.nc4. Will also be saved to output filenames.", + help="String following CROP_IRR_ in input filenames. E.g., mai_ir_FILESPECIFIER.nc4. Will also be saved to output filenames.", type=str, - default = "_ggcmi_crop_calendar_phase3_v1.01", + default = "ggcmi_crop_calendar_phase3_v1.01", ) parser.add_argument( "-y1", From dc503e4f3d058885775fd920b545f424434382f4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 13:16:46 -0600 Subject: [PATCH 1206/2067] regrid shdates: Retry cdo again if needed. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 160c5f2805..211efa85e0 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -73,14 +73,17 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg if os.path.exists(f3): os.remove(f3) - # Sometimes cdo fails for no apparent reason. In testing this never happened more than twice in a row. + # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + try: + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + except: + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") os.remove(templatefile) From 0f3d59f86fa5ed9f97dd56a6baccee293dbcb3e0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 13:23:51 -0600 Subject: [PATCH 1207/2067] process shdates: Improved a comment. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 288a2e9568..c7427f55da 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -30,7 +30,7 @@ def main(input_directory, output_directory, template_file, author, file_specifie # First, we associate CLM crop names with (1) their integer counterpart and (2) their GGCMI counterpart. # Some notes: - # - As "CLMname: [number, GGCMIname]" + # - As "CLMname: {clm_num, thiscrop_ggcmi}" # - CLM names and numbers taken from commit `3dcbc7499a57904750a994672fc36b4221b9def5` # - Using one global GGCMI value for both temperate and tropical versions of corn and soybean. # - There is no GGCMI equivalent of CLM's winter barley and rye. Using winter wheat instead. From aeda6867dae125fa5fe49b4195f4886497ef770e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 14:46:53 -0600 Subject: [PATCH 1208/2067] process shdates: Removed a bad error. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index c7427f55da..224371a2bc 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -158,8 +158,6 @@ def slice_yr(y): template_ds.mscur.values = np.array([0,]).astype(type(template_ds.mscur.values[0])) if "nstep" in template_ds: template_ds.nstep.values = np.array([0,]).astype(type(template_ds.nstep.values[0])) - else: - raise RuntimeError("Try using just a normal, unprocessed output file that doesn't include year 2000") first_year = template_ds.time.values[0].year last_year = template_ds.time.values[-1].year template_ds.attrs = out_attrs From 85833b94d2cd3f7ada796c1e834901191bf13fb2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 16:17:19 -0600 Subject: [PATCH 1209/2067] process shdates: -t/--template-file no longer used. process_ggcmi_shdates.py now produces a file with minimal variables and coordinates: just the sdate or hdate variables with dimension coordinates (time, lat, lon). Note that -rt/--regrid-template-file is still required. --- .../crop_calendars/process_ggcmi_shdates.py | 76 +++++++------------ 1 file changed, 27 insertions(+), 49 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 224371a2bc..14bb6cf939 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -11,7 +11,18 @@ import regrid_ggcmi_shdates -def main(input_directory, output_directory, template_file, author, file_specifier, first_year, +def get_cft(y): + return cftime.DatetimeNoLeap(y, 1, 1, 0, 0, 0, 0, has_year_zero=True) + +def get_dayssince_jan1y1(y1, y): + cft_y1 = get_cft(y1) + cft_y = get_cft(y) + time_delta = cft_y - cft_y1 + time_delta_secs = time_delta.total_seconds() + return time_delta_secs / (60*60*24) + + +def main(input_directory, output_directory, author, file_specifier, first_year, last_year, verbose, ggcmi_author, regrid_resolution, regrid_template_file): ############################################################ @@ -128,44 +139,20 @@ def set_var_dict(name_ggcmi, outfile): "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), } - - # Open and time-slice template dataset - def slice_yr(y): - if y == None: - return None - else: - return str(y) - template_ds = xr.open_dataset(template_file, decode_times=True).sel(time=slice(slice_yr(first_year), slice_yr(last_year))) - # template_ds = template_ds.sel(time=slice(slice_yr(y1), slice_yr(yN))) - if np.size(template_ds.time) == 0: - print(f"Time slice {first_year}-{last_year} not found in template dataset. Faking.") - if first_year != last_year: - raise RuntimeError("Not sure how to fake time axis when y1 != yN") - template_ds = xr.open_dataset(template_file, decode_times=True) - template_ds = template_ds.isel(time=slice(0,1)) # Get the first timestep. Just using .values[0] causes trouble. - val0 = template_ds.time.values[0] - if not isinstance(template_ds.time.values[0], cftime.datetime): - raise TypeError(f"Template file time axis is type {type(template_ds.time.values[0])}, which isn't a cftime.datetime subclass; not sure that next line (assigning fake value) will work.") - template_ds.time.values[0] = type(val0)(first_year, 1, 1, 0, 0, 0, 0, has_year_zero=val0.has_year_zero) - template_ds.time_bounds.values[0] = np.array([template_ds.time.values[0,], template_ds.time.values[0]]) - if "mcdate" in template_ds: - template_ds.mcdate.values = np.array([20000101,]).astype(type(template_ds.mcdate.values[0])) - if "mcsec" in template_ds: - template_ds.mcsec.values = np.array([0,]).astype(type(template_ds.mcsec.values[0])) - if "mdcur" in template_ds: - template_ds.mdcur.values = np.array([0,]).astype(type(template_ds.mdcur.values[0])) - if "mscur" in template_ds: - template_ds.mscur.values = np.array([0,]).astype(type(template_ds.mscur.values[0])) - if "nstep" in template_ds: - template_ds.nstep.values = np.array([0,]).astype(type(template_ds.nstep.values[0])) - first_year = template_ds.time.values[0].year - last_year = template_ds.time.values[-1].year - template_ds.attrs = out_attrs - - # Remove variable(s) we don't need (hdm, or any all-uppercase variables) - for v in template_ds: - if v == "hdm" or v.upper()==v: - template_ds = template_ds.drop(v) + + # Create template dataset + time_array = np.array([get_dayssince_jan1y1(first_year, y) for y in np.arange(first_year, last_year+1)]) + time_coord = xr.IndexVariable( + "time", + data = time_array, + attrs = { + "long_name": "time", + "units": f"days since {first_year}-01-01", + "calendar": "noleap", + } + ) + template_ds = xr.Dataset(coords = {"time": time_coord}, + attrs = out_attrs) # Create output files datetime_string = dt.datetime.now().strftime('%Y%m%d_%H%M%S') @@ -174,8 +161,6 @@ def slice_yr(y): variable_dict[v]["outfile"] = outfile template_ds.to_netcdf(path=variable_dict[v]["outfile"]) - template_ds.close() - ######################### ### Process all crops ### @@ -335,13 +320,6 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v type=str, required=True, ) - parser.add_argument( - "-t", - "--template-file", - help="A CLM output file to be used as a template for input files, especially for grid and time", - type=str, - required=True, - ) parser.add_argument( "-a", "--author", @@ -396,5 +374,5 @@ def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, v ### Run ### ########### main(os.path.realpath(args.input_directory), os.path.realpath(args.output_directory), - args.template_file, args.author, args.file_specifier, args.first_year, args.last_year, + args.author, args.file_specifier, args.first_year, args.last_year, args.verbose, args.ggcmi_author, args.regrid_resolution, args.regrid_template_file) From ae643a01786f412fe336dbb5751289c4b9bdba8a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 16:20:13 -0600 Subject: [PATCH 1210/2067] regrid shdates: Corrected an argument description. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 211efa85e0..943d0b370e 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -28,7 +28,7 @@ def define_arguments(parser): parser.add_argument( "-rt", "--regrid-template-file", - help="Template file to be used in regridding of .", + help="Template file to be used in regridding of inputs.", type=str, required=True ) From a9bdfdac41361404e26ad2a04cef06d78285d6d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 17:24:09 -0600 Subject: [PATCH 1211/2067] process shdates: Append resolution to dir w/ regridded files. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 14bb6cf939..a728162ba0 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -29,7 +29,8 @@ def main(input_directory, output_directory, author, file_specifier, first_year, ### Regrid original GGCMI files to target CLM resolution ### ############################################################ - regridded_ggcmi_files_dir = os.path.join(output_directory, "regridded_ggcmi_files") + regridded_ggcmi_files_dir = os.path.join(output_directory, + f"regridded_ggcmi_files-{regrid_resolution}") regrid_ggcmi_shdates.main(regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir) From 5e4ffafa9c7caf3a41682c0f097147508a1649f9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 17:24:23 -0600 Subject: [PATCH 1212/2067] process shdates: Remove unused code/comment. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index a728162ba0..48f40ccd76 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -248,9 +248,6 @@ def set_var_dict(name_ggcmi, outfile): # (Repeats original map for every timestep) # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) - # "True" here shows that the time dimension was created by just repeating the one map. - # tmp = thisvar_ds[varname_ggcmi] - # np.all((np.diff(tmp.values, axis=0) == 0.0) | np.isnan(np.diff(tmp.values, axis=0))) # Add variable to output dataset out_ds[varname_clm]=(thisvar_ds[varname_ggcmi].dims, From d4ed2f66209aa5c0fd1cc8b9092e375337451fdb Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 24 Jul 2023 10:17:32 -0600 Subject: [PATCH 1213/2067] resolving reviewer requests for clmfate-cbalance --- src/biogeochem/CNVegCarbonStateType.F90 | 2 +- src/biogeochem/CNVegetationFacade.F90 | 7 ------- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index d2a2c06f90..e1d0ed6e39 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -2684,7 +2684,7 @@ subroutine Summary_carbonstate(this, bounds, num_bgc_soilc, filter_bgc_soilc, nu ! -------------------------------------------- ! column level summary ! -------------------------------------------- - if(associated(this%totvegc_patch))then + if(num_bgc_vegp>0)then call p2c(bounds, num_bgc_soilc, filter_bgc_soilc, & this%totvegc_patch(bounds%begp:bounds%endp), & this%totvegc_col(bounds%begc:bounds%endc)) diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 4af6f29457..c437a9e438 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -511,13 +511,6 @@ subroutine Restart(this, bounds, ncid, flag) if (use_cn .or. use_fates_bgc) then - if(use_fates_bgc)then - call this%c_products_inst%SetValues(bounds, 0._r8) - if (use_c13) call this%c13_products_inst%SetValues(bounds, 0._r8) - if (use_c14) call this%c14_products_inst%SetValues(bounds, 0._r8) - call this%n_products_inst%SetValues(bounds, 0._r8) - end if - call this%c_products_inst%restart(bounds, ncid, flag) if (use_c13) then call this%c13_products_inst%restart(bounds, ncid, flag, & From f8ab311c982cc38ce0d574e8ac42a6e6912ec5e4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 21 Jul 2023 17:41:17 -0600 Subject: [PATCH 1214/2067] process shdates: Simplified I/O. --- .../crop_calendars/process_ggcmi_shdates.py | 56 ++++++++----------- 1 file changed, 22 insertions(+), 34 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 48f40ccd76..043478ea1d 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -218,10 +218,6 @@ def set_var_dict(name_ggcmi, outfile): file_clm = variable_dict[thisvar_clm]["outfile"] if not os.path.exists(file_clm): raise Exception("Output file not found: " + file_clm) - file_clm_tmp = file_clm + ".tmp" - - # "Read" the file (doesn't actually bring anything into memory yet) - out_ds = xr.open_dataset(file_clm) # Strip dataset to just this variable droplist = [] @@ -248,48 +244,40 @@ def set_var_dict(name_ggcmi, outfile): # (Repeats original map for every timestep) # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) - - # Add variable to output dataset - out_ds[varname_clm]=(thisvar_ds[varname_ggcmi].dims, - thisvar_ds[varname_ggcmi].values) + thisvar_da_tmp = thisvar_ds[varname_ggcmi] + thisvar_da = xr.DataArray(data = thisvar_da_tmp.values.astype("int16"), + attrs = thisvar_da_tmp.attrs, + coords = thisvar_da_tmp.coords, + name = varname_clm) + # Edit/add variable attributes etc. - longname = thisvar_ds[varname_ggcmi].attrs["long_name"] + longname = thisvar_da.attrs["long_name"] longname = longname.replace("rainfed", thiscrop_clm).replace("irrigated", thiscrop_clm) - def set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue): - out_ds[varname_clm].attrs["long_name"] = longname + def set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue): + thisvar_da.attrs["long_name"] = longname if thiscrop_ggcmi == None: - out_ds[varname_clm].attrs["crop_name_clm"] = "none" - out_ds[varname_clm].attrs["crop_name_ggcmi"] = "none" + thisvar_da.attrs["crop_name_clm"] = "none" + thisvar_da.attrs["crop_name_ggcmi"] = "none" else: - out_ds[varname_clm].attrs["crop_name_clm"] = thiscrop_clm - out_ds[varname_clm].attrs["crop_name_ggcmi"] = thiscrop_ggcmi - out_ds[varname_clm].attrs["short_name_ggcmi"] = varname_ggcmi - out_ds[varname_clm].attrs["units"] = "day of year" - out_ds[varname_clm].encoding["_FillValue"] = new_fillvalue + thisvar_da.attrs["crop_name_clm"] = thiscrop_clm + thisvar_da.attrs["crop_name_ggcmi"] = thiscrop_ggcmi + thisvar_da.attrs["short_name_ggcmi"] = varname_ggcmi + thisvar_da.attrs["units"] = "day of year" + thisvar_da.encoding["_FillValue"] = new_fillvalue + thisvar_da.encoding["missing_value"] = new_fillvalue # scale_factor and add_offset are required by I/O library for short data # From https://www.unidata.ucar.edu/software/netcdf/workshops/2010/bestpractices/Packing.html: # unpacked_value = packed_value * scale_factor + add_offset - out_ds[varname_clm].attrs["scale_factor"] = np.int16(1) - out_ds[varname_clm].attrs["add_offset"] = np.int16(0) - return out_ds - out_ds = set_var_attrs(out_ds, varname_clm, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) + thisvar_da.attrs["scale_factor"] = np.int16(1) + thisvar_da.attrs["add_offset"] = np.int16(0) + return thisvar_da + thisvar_da = set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) # Save if verbose: print(" Saving %s..." % varname_ggcmi) - # start = time.time() - # Can't overwrite file_clm while you have it open (as out_ds), so first copy it to a temporary file... - shutil.copyfile(file_clm, file_clm_tmp) - # ... then save out_ds to the temporary file... - out_ds.to_netcdf(file_clm_tmp, format="NETCDF3_CLASSIC") - # ... then close out_ds... - out_ds.close() - # ... and finally replace the original file with the new temporary file (deleting the temporary file in the process) - os.replace(file_clm_tmp, file_clm) - # end = time.time() - # print(end - start) - ### NOTE: This method gets slower and slower as the file gets bigger! (The entire process, but also the out_ds.to_netcdf() step.) Is there a better way? + thisvar_da.to_netcdf(file_clm, mode="a", format="NETCDF3_CLASSIC") cropcal_ds.close() From 952ec6a5449fcbccd4cc10932c0199f10b46ea35 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 24 Jul 2023 12:05:47 -0600 Subject: [PATCH 1215/2067] process shdates: File format NETCDF3_CLASSIC. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 043478ea1d..0617840c09 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -160,7 +160,8 @@ def set_var_dict(name_ggcmi, outfile): for v in variable_dict: outfile = os.path.join(output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc") variable_dict[v]["outfile"] = outfile - template_ds.to_netcdf(path=variable_dict[v]["outfile"]) + template_ds.to_netcdf(path=variable_dict[v]["outfile"], + format="NETCDF3_CLASSIC",) ######################### From bdcd18287687cddfed973c08b913981a72021107 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 24 Jul 2023 13:14:27 -0600 Subject: [PATCH 1216/2067] Change more intent(out) to intent(inout) to prevent NaNs in nag tests --- src/biogeophys/FrictionVelocityMod.F90 | 8 ++++---- src/biogeophys/PhotosynthesisMod.F90 | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 21a09fbc13..962184b30b 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -677,10 +677,10 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & real(r8) , intent(in) :: ur ( lbn: ) ! wind speed at reference height [m/s] [lbn:ubn] real(r8) , intent(in) :: um ( lbn: ) ! wind speed including the stablity effect [m/s] [lbn:ubn] real(r8) , intent(out) :: ustar ( lbn: ) ! friction velocity [m/s] [lbn:ubn] - real(r8) , intent(out) :: temp1 ( lbn: ) ! relation for potential temperature profile [lbn:ubn] - real(r8) , intent(out) :: temp12m ( lbn: ) ! relation for potential temperature profile applied at 2-m [lbn:ubn] - real(r8) , intent(out) :: temp2 ( lbn: ) ! relation for specific humidity profile [lbn:ubn] - real(r8) , intent(out) :: temp22m ( lbn: ) ! relation for specific humidity profile applied at 2-m [lbn:ubn] + real(r8) , intent(inout) :: temp1 ( lbn: ) ! relation for potential temperature profile [lbn:ubn] (inout instead of out to prevent returning nan) + real(r8) , intent(inout) :: temp12m ( lbn: ) ! relation for potential temperature profile applied at 2-m [lbn:ubn] (inout instead of out to prevent returning nan) + real(r8) , intent(inout) :: temp2 ( lbn: ) ! relation for specific humidity profile [lbn:ubn] (inout instead of out to prevent returning nan) + real(r8) , intent(inout) :: temp22m ( lbn: ) ! relation for specific humidity profile applied at 2-m [lbn:ubn] (inout instead of out to prevent returning nan) real(r8) , intent(inout) :: fm ( lbn: ) ! diagnose 10m wind (DUST only) [lbn:ubn] logical , intent(in), optional :: landunit_index ! optional argument that defines landunit or pft level ! diff --git a/src/biogeophys/PhotosynthesisMod.F90 b/src/biogeophys/PhotosynthesisMod.F90 index beda9d0bc5..6207e40700 100644 --- a/src/biogeophys/PhotosynthesisMod.F90 +++ b/src/biogeophys/PhotosynthesisMod.F90 @@ -2266,7 +2266,7 @@ subroutine hybrid(x0, p, iv, c, gb_mol, je, cair, oair, lmr_z, par_z,& real(r8), intent(in) :: cair ! Atmospheric CO2 partial pressure (Pa) real(r8), intent(in) :: oair ! Atmospheric O2 partial pressure (Pa) integer, intent(in) :: p, iv, c ! pft, c3/c4, and column index - real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) integer, intent(out) :: iter !number of iterations used, for record only type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type), intent(inout) :: photosyns_inst @@ -2378,7 +2378,7 @@ subroutine brent(x, x1,x2,f1, f2, tol, ip, iv, ic, gb_mol, je, cair, oair,& real(r8), intent(in) :: oair ! Atmospheric O2 partial pressure (Pa) real(r8), intent(in) :: rh_can ! inside canopy relative humidity integer, intent(in) :: ip, iv, ic ! pft, c3/c4, and column index - real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type), intent(inout) :: photosyns_inst ! @@ -2568,7 +2568,7 @@ subroutine ci_func(ci, fval, p, iv, c, gb_mol, je, cair, oair, lmr_z, par_z,& real(r8) , intent(in) :: rh_can ! canopy air realtive humidity integer , intent(in) :: p, iv, c ! pft, vegetation type and column indexes real(r8) , intent(out) :: fval ! return function of the value f(ci) - real(r8) , intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) + real(r8) , intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type) , intent(inout) :: photosyns_inst ! @@ -4064,8 +4064,8 @@ subroutine brent_PHS(xsun, x1sun, x2sun, f1sun, f2sun, xsha, x1sha, x2sha, f1sha real(r8), intent(in) :: lmr_z_sun, lmr_z_sha ! canopy layer: leaf maintenance respiration rate (umol CO2/m**2/s) real(r8), intent(in) :: par_z_sun, par_z_sha ! par absorbed per unit lai for canopy layer (w/m**2) real(r8), intent(in) :: rh_can ! inside canopy relative humidity - real(r8), intent(inout) :: gs_mol_sun ! sunlit leaf stomatal conductance (umol H2O/m**2/s) - real(r8), intent(inout) :: gs_mol_sha ! shaded leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol_sun ! sunlit leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) + real(r8), intent(inout) :: gs_mol_sha ! shaded leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) real(r8), intent(inout) :: bsun ! sunlit canopy transpiration wetness factor (0 to 1) real(r8), intent(inout) :: bsha ! shaded canopy transpiration wetness factor (0 to 1) real(r8), intent(in) :: qsatl ! leaf specific humidity [kg/kg] From 9dac206df7a995e922f3eee321c6a61bd1c43e23 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 24 Jul 2023 13:36:06 -0600 Subject: [PATCH 1217/2067] removed fates columns from the nocrop filter --- src/main/filterMod.F90 | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index 0b7d230a54..e2433f35ab 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -477,15 +477,17 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fl = 0 fnl = 0 do p = bounds%begp,bounds%endp - if (patch%active(p) .or. include_inactive) then - if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types - fl = fl + 1 - this_filter(nc)%pcropp(fl) = p - else - l =patch%landunit(p) - if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then - fnl = fnl + 1 - this_filter(nc)%soilnopcropp(fnl) = p + if(.not.use_fates_bgc)then + if (patch%active(p) .or. include_inactive) then + if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types + fl = fl + 1 + this_filter(nc)%pcropp(fl) = p + else + l =patch%landunit(p) + if (lun%itype(l) == istsoil .or. lun%itype(l) == istcrop) then + fnl = fnl + 1 + this_filter(nc)%soilnopcropp(fnl) = p + end if end if end if end if From d629ddd477243159c2cc9a2178f6e4e7917f182b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 24 Jul 2023 15:30:42 -0600 Subject: [PATCH 1218/2067] Added script to add tillage parameters to params file. --- tillage-tmp/add_tillage_to_paramsfile.py | 122 +++++++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 tillage-tmp/add_tillage_to_paramsfile.py diff --git a/tillage-tmp/add_tillage_to_paramsfile.py b/tillage-tmp/add_tillage_to_paramsfile.py new file mode 100644 index 0000000000..12ee955200 --- /dev/null +++ b/tillage-tmp/add_tillage_to_paramsfile.py @@ -0,0 +1,122 @@ +# %% + +import xarray as xr +import numpy as np + +file_in = "/Users/Shared/CESM_inputdata/lnd/clm2/paramdata/ctsm51_params.c211112.nc" +file_out = "/Users/sam/Documents/git_repos/CTSM_myfork/ctsm51_params.c211112.tillage.nc" + + +# %% Set up dimensions + +ds0 = xr.open_dataset(file_in) +ntill_intensities_max = 2 +ndecomp_pools_max = ds0.dims["ndecomp_pools_max"] +ntill_stages_max = 3 +tillage_shape_ips = (ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) +tillage_shape_ps = (ndecomp_pools_max, ntill_stages_max) + + +# %% Fill CENTURY array + +# Define pool indices +i_litr_min = 0 # 1 in FORTRAN, but Python is 0-indexed +i_met_lit = i_litr_min +i_cel_lit = i_met_lit + 1 +i_lig_lit = i_cel_lit + 1 +i_act_som = i_lig_lit + 1 +i_slo_som = i_act_som + 1 +i_pas_som = i_slo_som + 1 + +tillage_century = np.full(tillage_shape_ips, 1.0) + +tillage_century_lo = np.full(tillage_shape_ps, 1.0) +tillage_century_lo[i_act_som,:] = np.array([1.0, 1.0, 1.0]) +tillage_century_lo[i_slo_som,:] = np.array([3.0, 1.6, 1.3]) +tillage_century_lo[i_pas_som,:] = np.array([3.0, 1.6, 1.3]) +tillage_century_lo[i_cel_lit,:] = np.array([1.5, 1.5, 1.1]) +tillage_century_lo[i_lig_lit,:] = np.array([1.5, 1.5, 1.1]) +tillage_century[0,:,:] = tillage_century_lo + +tillage_century_hi = np.full(tillage_shape_ps, 1.0) +tillage_century_hi[i_act_som,:] = np.array([1.2, 1.0, 1.0]) +tillage_century_hi[i_slo_som,:] = np.array([4.8, 3.5, 2.5]) +tillage_century_hi[i_pas_som,:] = np.array([4.8, 3.5, 2.5]) +tillage_century_hi[i_cel_lit,:] = np.array([1.8, 1.5, 1.1]) +tillage_century_hi[i_lig_lit,:] = np.array([1.8, 1.5, 1.1]) +tillage_century[1,:,:] = tillage_century_hi + + +# %% Fill MIMICS array + +# Define pool indices +i_litr_min = 1 +i_met_lit = i_litr_min +i_str_lit = i_met_lit + 1 +i_avl_som = i_str_lit + 1 +i_chem_som = i_avl_som + 1 +i_phys_som = i_chem_som + 1 + +tillage_mimics = np.full(tillage_shape_ips, 1.0) + +tillage_mimics[:,i_avl_som,:] = tillage_century[:,i_act_som,:] +tillage_mimics[:,i_chem_som,:] = tillage_century[:,i_slo_som,:] +tillage_mimics[:,i_phys_som,:] = tillage_century[:,i_pas_som,:] +if not np.array_equal(tillage_century[:,i_cel_lit,:], tillage_century[:,i_lig_lit,:]): + raise RuntimeError("How to combine 2 CENTURY litter pools into 1 MIMICS litter pool?") +tillage_mimics[:,i_str_lit,:] = tillage_century[:,i_cel_lit,:] + + +# %% Make DataArrays + +def make_dataarray(np_array, decomp_model, ntill_intensities_max, ndecomp_pools_max, ntill_stages_max): + intensities_dim = xr.IndexVariable( + dims = "ntill_intensities_max", + data = np.arange(ntill_intensities_max), + ) + pools_dim = xr.IndexVariable( + dims = "ndecomp_pools_max", + data = np.arange(ndecomp_pools_max), + ) + stages_dim = xr.IndexVariable( + dims = "ntill_stages_max", + data = np.arange(ntill_stages_max), + ) + + # Name DataArray + da_name = "till_decompk_multipliers" + if "mimics" in decomp_model.lower(): + da_name = "mimics_" + da_name + + da = xr.DataArray( + data = np_array, + dims = { + "ntill_intensities_max": intensities_dim, + "ndecomp_pools_max": pools_dim, + "ntill_stages_max": stages_dim + }, + name = da_name, + attrs = { + "long_name": f"Value by which decomp_k should be multiplied during tillage with {decomp_model} soil", + "units": "unitless", + } + ) + return da + +tillage_century_da = make_dataarray( + tillage_century, "CENTURY", + ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) +tillage_mimics_da = make_dataarray( + tillage_mimics, "MIMICS", + ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) + + +# %% Save to output file + +ds1 = ds0.copy() +ds0.close() + +ds1[tillage_century_da.name] = tillage_century_da +ds1[tillage_mimics_da.name] = tillage_mimics_da + +ds1.to_netcdf(file_out) \ No newline at end of file From 9987b41ca6d5da936ed5d868d7f0b227810b5c6d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 24 Jul 2023 16:32:36 -0600 Subject: [PATCH 1219/2067] process shdates: Don't save missing_value. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 0617840c09..a971b3d731 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -266,7 +266,6 @@ def set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_gg thisvar_da.attrs["short_name_ggcmi"] = varname_ggcmi thisvar_da.attrs["units"] = "day of year" thisvar_da.encoding["_FillValue"] = new_fillvalue - thisvar_da.encoding["missing_value"] = new_fillvalue # scale_factor and add_offset are required by I/O library for short data # From https://www.unidata.ucar.edu/software/netcdf/workshops/2010/bestpractices/Packing.html: # unpacked_value = packed_value * scale_factor + add_offset From d8ba6c75f68f82fe10784d488dbe76fd4d5cb4f7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 24 Jul 2023 17:42:25 -0600 Subject: [PATCH 1220/2067] Change zetamaxstable in namelist_defaults_ctsm to get BFB with baseline --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- cime_config/testdefs/ExpectedTestFails.xml | 7 ------- 2 files changed, 1 insertion(+), 8 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 260f567966..d23c0d1371 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -213,7 +213,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 2.0d00 2.0d00 0.5d00 -2.0d00 +0.5d00 0.5d00 2.0d00 diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index b84ebc3e5f..24f7062798 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -30,13 +30,6 @@ - - - FAIL - Error: Forcing height is below canopy height for patch index - - - FAIL From fc37d6fd06c6d41b744500762a4ca490a18a196e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jul 2023 10:50:36 -0600 Subject: [PATCH 1221/2067] Move two error checks to CLMBuildNamelist.pm, and add one. --- bld/CLMBuildNamelist.pm | 20 +++++++++++++++++--- src/cpl/share_esmf/cropcalStreamMod.F90 | 8 -------- 2 files changed, 17 insertions(+), 11 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 384614ba57..256de592c6 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3948,11 +3948,25 @@ sub setup_logic_cropcal_streams { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'generate_crop_gdds'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_mxmat'); - # Consistency checking: Do not generate_crop_gdds without use_mxmat false + # Option checks my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ; my $use_mxmat = $nl->get_value('use_mxmat') ; - if ( $generate_crop_gdds eq '.true.' and $use_mxmat eq '.true.' ) { - $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" ); + my $sdate_file = $nl->get_value('stream_fldFileName_sdate') ; + my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ; + my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ; + if ( $generate_crop_gdds eq '.true.' ) { + if ( $use_mxmat eq '.true.' ) { + $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" ); + } + if ( $sdate_file eq '' ) { + $log->fatal_error("If generate_crop_gdds is true, you must specify stream_fldFileName_sdate") + } + if ( $gdd_file ne '' ) { + $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_cultivar_gdds") + } + } + if ( $mesh_file eq '' and ( $sdate_file ne '' or $gdd_file ne '' ) ) { + $log->fatal_error("If prescribing crop sowing dates and/or maturity requirements, you must specify stream_meshfile_cropcal") } } diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index ba0e5b7117..8c2168d01d 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -141,14 +141,6 @@ subroutine cropcal_init(bounds) use_cropcal_rx_sdates = stream_fldFileName_sdate /= '' use_cropcal_rx_cultivar_gdds = stream_fldFileName_cultivar_gdds /= '' - if (use_cropcal_rx_cultivar_gdds .and. generate_crop_gdds) then - write(iulog,*) 'Do not specify both generate_crop_gdds=.true. and stream_fldFileName_cultivar_gdds' - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - if (generate_crop_gdds .and. .not. use_cropcal_rx_sdates) then - write(iulog,*) 'ERROR If using generate_crop_gdds, you must specify stream_fldFileName_sdate' - call ESMF_Finalize(endflag=ESMF_END_ABORT) - endif use_cropcal_streams = use_cropcal_rx_sdates .or. use_cropcal_rx_cultivar_gdds ! Initialize the cdeps data type sdat_cropcal_sdate From d0d401585cd01717473fe65b346a0599c748f8f7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jul 2023 12:52:15 -0600 Subject: [PATCH 1222/2067] Added --skip-crops argument for generate_gdds. --- python/ctsm/crop_calendars/generate_gdds.py | 17 +++++++++++++ .../crop_calendars/generate_gdds_functions.py | 24 ++++++++++++------- 2 files changed, 32 insertions(+), 9 deletions(-) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 8ab5746d19..1866879657 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -43,6 +43,7 @@ def main( first_land_use_year=None, last_land_use_year=None, unlimited_season_length=False, + skip_crops=None, logger=None, ): # Directories to save output files and figures @@ -81,6 +82,12 @@ def main( # Print some info gddfn.log(logger, f"Saving to {output_dir}") + + # Parse list of crops to skip + if "," in skip_crops: + skip_crops = skip_crops.split(",") + else: + skip_crops = skip_crops.split(" ") ########################## ### Import and process ### @@ -113,6 +120,7 @@ def main( incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings, + skip_crops, ) = pickle.load(f) print(f"Will resume import at {pickle_year+1}") h2_ds = None @@ -165,6 +173,7 @@ def main( h2_ds_file, mxmats, cc.get_gs_len_da, + skip_crops, logger, ) @@ -184,6 +193,7 @@ def main( incl_vegtypes_str, incl_patches1d_itype_veg, mxsowings, + skip_crops, ], f, protocol=-1, @@ -441,6 +451,12 @@ def add_attrs_to_map_ds( action="store_true", default=False, ) + parser.add_argument( + "--skip-crops", + help="Skip processing of these crops. Comma- or space-separated list.", + type=str, + default="", + ) # Get arguments args = parser.parse_args(sys.argv[1:]) @@ -464,6 +480,7 @@ def add_attrs_to_map_ds( first_land_use_year=args.first_land_use_year, last_land_use_year=args.last_land_use_year, unlimited_season_length=args.unlimited_season_length, + skip_crops=args.skip_crops, ) # main(input_dir="/Users/Shared/CESM_runs/tests_10x15_20230329_gddgen/202303301820", diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index eb30713ca3..a5bf0e5cc7 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -198,6 +198,7 @@ def import_and_process_1yr( h2_ds_file, mxmats, get_gs_len_da, + skip_crops, logger, ): save_figs = True @@ -218,12 +219,18 @@ def import_and_process_1yr( h1_filelist = glob.glob(h1_pattern) if not h1_filelist: error(logger, "No files found matching pattern '*h1.*.nc(.base)'") + + # Get list of crops to include + if skip_crops is not None: + crops_to_read = [c for c in utils.define_mgdcrop_list() if c not in skip_crops] + else: + crops_to_read = utils.define_mgdcrop_list() print(h1_filelist) dates_ds = utils.import_ds( h1_filelist, myVars=["SDATES", "HDATES"], - myVegtypes=utils.define_mgdcrop_list(), + myVegtypes=crops_to_read, timeSlice=slice(f"{thisYear}-01-01", f"{thisYear}-12-31"), chunks=chunks, ) @@ -281,7 +288,7 @@ def import_and_process_1yr( incl_patches1d_itype_veg = dates_incl_ds.patches1d_itype_veg if y == 0: - incl_vegtypes_str = dates_incl_ds.vegtype_str.values + incl_vegtypes_str = [c for c in dates_incl_ds.vegtype_str.values if c not in skip_crops] else: incl_vegtypes_str = incl_vegtypes_str_in if isinstance(incl_vegtypes_str, xr.DataArray): @@ -474,7 +481,7 @@ def import_and_process_1yr( h2_ds = utils.import_ds( h2_files, myVars=myVars, - myVegtypes=utils.define_mgdcrop_list(), + myVegtypes=crops_to_read, chunks=chunks, ) @@ -493,15 +500,14 @@ def import_and_process_1yr( Nyears = yN - y1 + 1 if len(gddaccum_yp_list) == 0: - lastYear_active_patch_indices_list = [None for vegtype_str in h2_incl_ds.vegtype_str.values] - gddaccum_yp_list = [None for vegtype_str in h2_incl_ds.vegtype_str.values] + lastYear_active_patch_indices_list = [None for vegtype_str in incl_vegtypes_str] + gddaccum_yp_list = [None for vegtype_str in incl_vegtypes_str] if save_figs: - gddharv_yp_list = [None for vegtype_str in h2_incl_ds.vegtype_str.values] + gddharv_yp_list = [None for vegtype_str in incl_vegtypes_str] incl_vegtype_indices = [] - for v, vegtype_str in enumerate(h2_incl_ds.vegtype_str.values): - # Skipping Miscanthus because it seems to never be harvested even though it is sown. This causes problems in NaN mask check. - if "miscanthus" in vegtype_str: + for v, vegtype_str in enumerate(incl_vegtypes_str): + if vegtype_str in skip_crops: log(logger, f" SKIPPING {vegtype_str}") continue From d0b44097e5ea835329a4a0dcebf15059d952fa98 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jul 2023 13:12:36 -0600 Subject: [PATCH 1223/2067] generate_gdds: Don't try to save time_bounds if not present in rx sdates file. --- python/ctsm/crop_calendars/generate_gdds.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 1866879657..0f8f99c771 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -311,7 +311,8 @@ def save_gdds(sdates_file, hdates_file, outfile, gdd_maps_ds, sdates_rx): } # Add time_bounds - gdd_maps_ds["time_bounds"] = sdates_rx.time_bounds + if "time_bounds" in sdates_rx: + gdd_maps_ds["time_bounds"] = sdates_rx.time_bounds # Save cultivar GDDs gdd_maps_ds.to_netcdf(outfile, mode="w", format="NETCDF3_CLASSIC") From 753f97d241d0fd338716985ae4c46cea95856d05 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 25 Jul 2023 14:51:21 -0600 Subject: [PATCH 1224/2067] move tolerance to constants file --- src/main/clm_varcon.F90 | 1 + src/main/surfrdUtilsMod.F90 | 4 ++-- src/utils/clmfates_interfaceMod.F90 | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/main/clm_varcon.F90 b/src/main/clm_varcon.F90 index 340115fe90..ba4fb18e81 100644 --- a/src/main/clm_varcon.F90 +++ b/src/main/clm_varcon.F90 @@ -90,6 +90,7 @@ module clm_varcon integer, public, parameter :: fun_period = 1 ! A FUN parameter, and probably needs to be changed for testing real(r8),public, parameter :: smallValue = 1.e-12_r8 ! A small values used by FUN + real(r8),public, parameter :: sum_to_1_tol = 1.e-13_r8 ! error tolerance ! ------------------------------------------------------------------------ ! Special value flags diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90 index 0763d43a16..5ede1d6474 100644 --- a/src/main/surfrdUtilsMod.F90 +++ b/src/main/surfrdUtilsMod.F90 @@ -7,6 +7,7 @@ module surfrdUtilsMod ! !USES: #include "shr_assert.h" use shr_kind_mod , only : r8 => shr_kind_r8 + use clm_varcon , only : sum_to_1_tol use clm_varctl , only : iulog,use_fates use abortutils , only : endrun use shr_log_mod , only : errMsg => shr_log_errMsg @@ -51,7 +52,6 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto) logical :: found integer :: nl integer :: nindx - real(r8), parameter :: eps = 1.e-13_r8 real(r8), allocatable :: TotalSum(:) integer :: ub ! upper bound of the first dimension of arr !----------------------------------------------------------------------- @@ -64,7 +64,7 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto) found = .false. do nl = lbound(arr, 1), ub - if (abs(sum(arr(nl,:)) - TotalSum(nl)) > eps) then + if (abs(sum(arr(nl,:)) - TotalSum(nl)) > sum_to_1_tol) then found = .true. nindx = nl exit diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c87482b80b..27e5237fb5 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -67,6 +67,7 @@ module CLMFatesInterfaceMod use clm_varcon , only : spval use clm_varcon , only : denice use clm_varcon , only : ispval + use clm_varcon , only : sum_to_1_tol use clm_varpar , only : surfpft_lb,surfpft_ub use clm_varpar , only : numrad use clm_varpar , only : ivis @@ -159,7 +160,6 @@ module CLMFatesInterfaceMod use dynHarvestMod , only : dynHarvest_interp_resolve_harvesttypes use FatesConstantsMod , only : hlm_harvest_area_fraction use FatesConstantsMod , only : hlm_harvest_carbon - use FatesConstantsMod , only : area_error use perf_mod , only : t_startf, t_stopf implicit none @@ -714,7 +714,7 @@ subroutine init(this, bounds_proc ) this%fates(nc)%bc_in(s)%pft_areafrac(ft)=wt_nat_patch(g,m) end do - if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > area_error) then + if (abs(sum(this%fates(nc)%bc_in(s)%pft_areafrac(surfpft_lb:surfpft_ub)) - 1.0_r8) > sum_to_1_tol) then write(iulog,*) 'pft_area error in interfc ', s, sum(this%fates(nc)%bc_in(s)%pft_areafrac(:)) - 1.0_r8 call endrun(msg=errMsg(sourcefile, __LINE__)) end if From 32a334ac6ca6977f63651dbbe23c7e6a9f5f0e2f Mon Sep 17 00:00:00 2001 From: adrifoster Date: Wed, 26 Jul 2023 08:25:15 -0600 Subject: [PATCH 1225/2067] don't do prescribed soil moisture --- .../clm/FatesColdSatPhen_prescribed/user_nl_clm | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm index a1ea0e0cf8..59a4137be7 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSatPhen_prescribed/user_nl_clm @@ -1,8 +1,3 @@ - ! right now we can't do prescribed soil moisture because of FATES issue #845 - use_soil_moisture_streams = .true. - use_lai_streams = .true. - hist_fincl1 += 'H2OSOI_PRESCRIBED_GRC' - soilm_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare to input dataset - lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset - soilm_ignore_data_if_missing = .true. +use_lai_streams = .true. +lai_tintalgo = 'lower' ! set time interpolation to use lower value, so can compare more directly to input dataset \ No newline at end of file From 3b2a37a8f3254de3885805f3d4ac92fcee69406a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jul 2023 13:25:51 -0600 Subject: [PATCH 1226/2067] Added --skip-crops arg to call of generate_gdds.py. --- cime_config/SystemTests/rxcropmaturity.py | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index f22309f1fb..4fd812b84a 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -353,6 +353,7 @@ def _run_generate_gdds(self, case_gddgen): f"--sdates-file {sdates_file}", f"--hdates-file {hdates_file}", f"--output-dir generate_gdds_out", + f"--skip-crops miscanthus,irrigated_miscanthus" ] ) stu.run_python_script( From 8bc4688e52ea23ef688e283698f70a44388373eb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 10:34:43 -0600 Subject: [PATCH 1227/2067] Black reformatting. --- python/ctsm/crop_calendars/cropcal_utils.py | 2 + python/ctsm/crop_calendars/generate_gdds.py | 2 +- .../crop_calendars/generate_gdds_functions.py | 2 +- .../crop_calendars/process_ggcmi_shdates.py | 189 ++++++++++-------- .../crop_calendars/regrid_ggcmi_shdates.py | 59 +++--- 5 files changed, 147 insertions(+), 107 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_utils.py b/python/ctsm/crop_calendars/cropcal_utils.py index e26192a284..ba6c0b6e41 100644 --- a/python/ctsm/crop_calendars/cropcal_utils.py +++ b/python/ctsm/crop_calendars/cropcal_utils.py @@ -862,6 +862,7 @@ def safer_timeslice(ds, timeSlice, timeVar="time"): return ds + # Convert a longitude axis that's -180 to 180 around the international date line to one that's 0 to 360 around the prime meridian. If you pass in a Dataset or DataArray, the "lon" coordinates will be changed. Otherwise, it assumes you're passing in numeric data. def lon_idl2pm(lons_in, fail_silently=False): def check_ok(tmp, fail_silently): @@ -907,6 +908,7 @@ def do_it(tmp): return lons_out + # Helper function to check that a list is strictly increasing def is_strictly_increasing(L): # https://stackoverflow.com/a/4983359/2965321 diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 0f8f99c771..6000c12e41 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -82,7 +82,7 @@ def main( # Print some info gddfn.log(logger, f"Saving to {output_dir}") - + # Parse list of crops to skip if "," in skip_crops: skip_crops = skip_crops.split(",") diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index a5bf0e5cc7..d050a46bd8 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -219,7 +219,7 @@ def import_and_process_1yr( h1_filelist = glob.glob(h1_pattern) if not h1_filelist: error(logger, "No files found matching pattern '*h1.*.nc(.base)'") - + # Get list of crops to include if skip_crops is not None: crops_to_read = [c for c in utils.define_mgdcrop_list() if c not in skip_crops] diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index a971b3d731..b2ffcfe1f8 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -13,33 +13,45 @@ def get_cft(y): return cftime.DatetimeNoLeap(y, 1, 1, 0, 0, 0, 0, has_year_zero=True) - + + def get_dayssince_jan1y1(y1, y): cft_y1 = get_cft(y1) - cft_y = get_cft(y) + cft_y = get_cft(y) time_delta = cft_y - cft_y1 time_delta_secs = time_delta.total_seconds() - return time_delta_secs / (60*60*24) + return time_delta_secs / (60 * 60 * 24) -def main(input_directory, output_directory, author, file_specifier, first_year, - last_year, verbose, ggcmi_author, regrid_resolution, regrid_template_file): +def main( + input_directory, + output_directory, + author, + file_specifier, + first_year, + last_year, + verbose, + ggcmi_author, + regrid_resolution, + regrid_template_file, +): ############################################################ ### Regrid original GGCMI files to target CLM resolution ### ############################################################ - - regridded_ggcmi_files_dir = os.path.join(output_directory, - f"regridded_ggcmi_files-{regrid_resolution}") - - regrid_ggcmi_shdates.main(regrid_resolution, regrid_template_file, input_directory, - regridded_ggcmi_files_dir) - - + + regridded_ggcmi_files_dir = os.path.join( + output_directory, f"regridded_ggcmi_files-{regrid_resolution}" + ) + + regrid_ggcmi_shdates.main( + regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir + ) + ########################### ### Define dictionaries ### ########################### - + # First, we associate CLM crop names with (1) their integer counterpart and (2) their GGCMI counterpart. # Some notes: # - As "CLMname: {clm_num, thiscrop_ggcmi}" @@ -50,6 +62,7 @@ def main(input_directory, output_directory, author, file_specifier, first_year, # - Only using GGCMI `ri1` for rice; ignoring `ri2`. def set_crop_dict(thisnum, thisname): return {"clm_num": thisnum, "thiscrop_ggcmi": thisname} + crop_dict = { "temperate_corn": set_crop_dict(17, "mai_rf"), "irrigated_temperate_corn": set_crop_dict(18, "mai_ir"), @@ -117,21 +130,20 @@ def set_crop_dict(thisnum, thisname): "c3_irrigated": set_crop_dict(16, None), } - # Next, we associate CLM variable names with their GGCMI counterparts. We also save a placeholder for output file paths associated with each variable. # As CLMname: {GGCMIname, output_file} def set_var_dict(name_ggcmi, outfile): return {"name_ggcmi": name_ggcmi, "outfile": outfile} + variable_dict = { "sdate": set_var_dict("planting_day", ""), - "hdate": set_var_dict("maturity_day", "") + "hdate": set_var_dict("maturity_day", ""), } - - + ################################ ### Instantiate output files ### ################################ - + # Global attributes for output files out_attrs = { "title": "GGCMI crop calendar for Phase 3, v1.01", @@ -140,29 +152,33 @@ def set_var_dict(name_ggcmi, outfile): "comment": "Day of year is 1-indexed (i.e., Jan. 1 = 1). Filled using cdo -remapnn,$original -setmisstonn", "created": dt.datetime.now().replace(microsecond=0).astimezone().isoformat(), } - + # Create template dataset - time_array = np.array([get_dayssince_jan1y1(first_year, y) for y in np.arange(first_year, last_year+1)]) + time_array = np.array( + [get_dayssince_jan1y1(first_year, y) for y in np.arange(first_year, last_year + 1)] + ) time_coord = xr.IndexVariable( "time", - data = time_array, - attrs = { + data=time_array, + attrs={ "long_name": "time", "units": f"days since {first_year}-01-01", "calendar": "noleap", - } - ) - template_ds = xr.Dataset(coords = {"time": time_coord}, - attrs = out_attrs) + }, + ) + template_ds = xr.Dataset(coords={"time": time_coord}, attrs=out_attrs) # Create output files - datetime_string = dt.datetime.now().strftime('%Y%m%d_%H%M%S') + datetime_string = dt.datetime.now().strftime("%Y%m%d_%H%M%S") for v in variable_dict: - outfile = os.path.join(output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc") + outfile = os.path.join( + output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc" + ) variable_dict[v]["outfile"] = outfile - template_ds.to_netcdf(path=variable_dict[v]["outfile"], - format="NETCDF3_CLASSIC",) - + template_ds.to_netcdf( + path=variable_dict[v]["outfile"], + format="NETCDF3_CLASSIC", + ) ######################### ### Process all crops ### @@ -177,29 +193,27 @@ def set_var_dict(name_ggcmi, outfile): this_dict = crop_dict[thiscrop_clm] thiscrop_int = this_dict["clm_num"] thiscrop_ggcmi = this_dict["thiscrop_ggcmi"] - + # If no corresponding GGCMI crop, skip opening dataset. # Will use previous cropcal_ds as a template. if thiscrop_ggcmi == None: if c == 1: raise ValueError(f"First crop ({thiscrop_clm}) must have a GGCMI type") - print("Filling %s with dummy data (%d of %d)..." \ - % (str(thiscrop_clm), - c, - len(crop_dict))) - + print( + "Filling %s with dummy data (%d of %d)..." % (str(thiscrop_clm), c, len(crop_dict)) + ) + # Otherwise, import crop calendar file else: if verbose: - print("Importing %s -> %s (%d of %d)..." \ - % (str(thiscrop_ggcmi), - str(thiscrop_clm), - c, - len(crop_dict))) - + print( + "Importing %s -> %s (%d of %d)..." + % (str(thiscrop_ggcmi), str(thiscrop_clm), c, len(crop_dict)) + ) + file_ggcmi = os.path.join( - regridded_ggcmi_files_dir, - f"{thiscrop_ggcmi}_{file_specifier}.nc4") + regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}.nc4" + ) if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) cropcal_ds = xr.open_dataset(file_ggcmi) @@ -207,19 +221,19 @@ def set_var_dict(name_ggcmi, outfile): cropcal_ds = cropcal_ds.reindex(lat=cropcal_ds.lat[::-1]) # Rearrange longitude to match destination (does nothing if not needed) cropcal_ds = utils.lon_idl2pm(cropcal_ds, fail_silently=True) - + for thisvar_clm in variable_dict: # Get GGCMI netCDF info varname_ggcmi = variable_dict[thisvar_clm]["name_ggcmi"] if verbose: print(" Processing %s..." % varname_ggcmi) - + # Get CLM netCDF info varname_clm = thisvar_clm + "1_" + str(thiscrop_int) file_clm = variable_dict[thisvar_clm]["outfile"] if not os.path.exists(file_clm): raise Exception("Output file not found: " + file_clm) - + # Strip dataset to just this variable droplist = [] for i in list(cropcal_ds.keys()): @@ -231,38 +245,43 @@ def set_var_dict(name_ggcmi, outfile): # Convert to integer new_fillvalue = -1 dummyvalue = -1 - thisvar_ds.variables[varname_ggcmi].encoding["_FillValue"] \ - = new_fillvalue + thisvar_ds.variables[varname_ggcmi].encoding["_FillValue"] = new_fillvalue if thiscrop_ggcmi == None: thisvar_ds.variables[varname_ggcmi].values.fill(dummyvalue) else: - thisvar_ds.variables[varname_ggcmi].values[np.isnan(thisvar_ds.variables[varname_ggcmi].values)] \ - = new_fillvalue - thisvar_ds.variables[varname_ggcmi].values \ - = thisvar_ds.variables[varname_ggcmi].values.astype("int16") - + thisvar_ds.variables[varname_ggcmi].values[ + np.isnan(thisvar_ds.variables[varname_ggcmi].values) + ] = new_fillvalue + thisvar_ds.variables[varname_ggcmi].values = thisvar_ds.variables[ + varname_ggcmi + ].values.astype("int16") + # Add time dimension (https://stackoverflow.com/a/62862440) # (Repeats original map for every timestep) # Probably not necessary to use this method, since I only end up extracting thisvar_ds.values anyway---I could probably use some numpy method instead. - thisvar_ds = thisvar_ds.expand_dims(time = template_ds.time) + thisvar_ds = thisvar_ds.expand_dims(time=template_ds.time) thisvar_da_tmp = thisvar_ds[varname_ggcmi] - thisvar_da = xr.DataArray(data = thisvar_da_tmp.values.astype("int16"), - attrs = thisvar_da_tmp.attrs, - coords = thisvar_da_tmp.coords, - name = varname_clm) - + thisvar_da = xr.DataArray( + data=thisvar_da_tmp.values.astype("int16"), + attrs=thisvar_da_tmp.attrs, + coords=thisvar_da_tmp.coords, + name=varname_clm, + ) # Edit/add variable attributes etc. longname = thisvar_da.attrs["long_name"] longname = longname.replace("rainfed", thiscrop_clm).replace("irrigated", thiscrop_clm) - def set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue): + + def set_var_attrs( + thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue + ): thisvar_da.attrs["long_name"] = longname if thiscrop_ggcmi == None: - thisvar_da.attrs["crop_name_clm"] = "none" - thisvar_da.attrs["crop_name_ggcmi"] = "none" + thisvar_da.attrs["crop_name_clm"] = "none" + thisvar_da.attrs["crop_name_ggcmi"] = "none" else: - thisvar_da.attrs["crop_name_clm"] = thiscrop_clm - thisvar_da.attrs["crop_name_ggcmi"] = thiscrop_ggcmi + thisvar_da.attrs["crop_name_clm"] = thiscrop_clm + thisvar_da.attrs["crop_name_ggcmi"] = thiscrop_ggcmi thisvar_da.attrs["short_name_ggcmi"] = varname_ggcmi thisvar_da.attrs["units"] = "day of year" thisvar_da.encoding["_FillValue"] = new_fillvalue @@ -272,17 +291,21 @@ def set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_gg thisvar_da.attrs["scale_factor"] = np.int16(1) thisvar_da.attrs["add_offset"] = np.int16(0) return thisvar_da - thisvar_da = set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue) + + thisvar_da = set_var_attrs( + thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_ggcmi, new_fillvalue + ) # Save if verbose: print(" Saving %s..." % varname_ggcmi) thisvar_da.to_netcdf(file_clm, mode="a", format="NETCDF3_CLASSIC") - + cropcal_ds.close() print("Done!") - + + if __name__ == "__main__": ############################### ### Process input arguments ### @@ -311,15 +334,15 @@ def set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_gg "--author", help="String to be saved in author_thisfile attribute of output files. E.g., 'Author Name (authorname@ucar.edu)'", type=str, - required=True + required=True, ) - + # Optional parser.add_argument( "--file-specifier", help="String following CROP_IRR_ in input filenames. E.g., mai_ir_FILESPECIFIER.nc4. Will also be saved to output filenames.", type=str, - default = "ggcmi_crop_calendar_phase3_v1.01", + default="ggcmi_crop_calendar_phase3_v1.01", ) parser.add_argument( "-y1", @@ -348,17 +371,25 @@ def set_var_attrs(thisvar_da, longname, thiscrop_clm, thiscrop_ggcmi, varname_gg type=str, default="Jonas Jägermeyr (jonas.jaegermeyr@columbia.edu)", ) - + # Arguments for regridding parser = regrid_ggcmi_shdates.define_arguments(parser) # Get arguments args = parser.parse_args(sys.argv[1:]) - - + ########### ### Run ### ########### - main(os.path.realpath(args.input_directory), os.path.realpath(args.output_directory), - args.author, args.file_specifier, args.first_year, args.last_year, - args.verbose, args.ggcmi_author, args.regrid_resolution, args.regrid_template_file) + main( + os.path.realpath(args.input_directory), + os.path.realpath(args.output_directory), + args.author, + args.file_specifier, + args.first_year, + args.last_year, + args.verbose, + args.ggcmi_author, + args.regrid_resolution, + args.regrid_template_file, + ) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 943d0b370e..85e9ddeb4d 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -5,16 +5,20 @@ import argparse import sys + def run_and_check(cmd): result = run( cmd, - shell = True, - capture_output = True, - text = True, - ) + shell=True, + capture_output=True, + text=True, + ) if result.returncode != 0: - raise RuntimeError(f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}") - + raise RuntimeError( + f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}" + ) + + # Functionized because these are shared by process_ggcmi_shdates def define_arguments(parser): # Required @@ -23,36 +27,39 @@ def define_arguments(parser): "--regrid-resolution", help="Target CLM resolution, to be saved in output filenames.", type=str, - required=True + required=True, ) parser.add_argument( "-rt", "--regrid-template-file", help="Template file to be used in regridding of inputs.", type=str, - required=True + required=True, ) return parser -def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory): + +def main( + regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory +): # Ensure we can call necessary shell scripts for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: run_and_check(f"{cmd} --help") - + os.chdir(regrid_input_directory) if not os.path.exists(regrid_output_directory): os.makedirs(regrid_output_directory) - + templatefile = os.path.join(regrid_output_directory, "template.nc") - + # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. regrid_template_file = os.path.join( regrid_output_directory, os.path.basename(regrid_template_file_in), - ) + ) shutil.copyfile(regrid_template_file_in, regrid_template_file) - + if os.path.exists(templatefile): os.remove(templatefile) @@ -62,7 +69,6 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg os.remove(regrid_template_file) run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") - input_files = glob.glob("*nc4") input_files.sort() for f in input_files: @@ -72,7 +78,7 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg if os.path.exists(f3): os.remove(f3) - + # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") @@ -95,7 +101,7 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg parser = argparse.ArgumentParser( description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." ) - + # Define arguments parser = define_arguments(parser) parser.add_argument( @@ -103,24 +109,25 @@ def main(regrid_resolution, regrid_template_file_in, regrid_input_directory, reg "--regrid-input-directory", help="Directory containing the raw GGCMI sowing/harvest date files.", type=str, - required=True + required=True, ) parser.add_argument( "-o", "--regrid-output-directory", help="Directory where regridded output files should be saved.", type=str, - required=True + required=True, ) - + # Get arguments args = parser.parse_args(sys.argv[1:]) - - + ########### ### Run ### ########### - main(args.regrid_resolution, - os.path.realpath(args.regrid_template_file), - os.path.realpath(args.regrid_input_directory), - os.path.realpath(args.regrid_output_directory)) \ No newline at end of file + main( + args.regrid_resolution, + os.path.realpath(args.regrid_template_file), + os.path.realpath(args.regrid_input_directory), + os.path.realpath(args.regrid_output_directory), + ) From de7eed031259f42ac7022eefd1090399f06b8937 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 10:35:45 -0600 Subject: [PATCH 1228/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 31645e2fa5..c00226b7dd 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -9,5 +9,6 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b 7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7 b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 +8bc4688e52ea23ef688e283698f70a44388373eb # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c From 6f3a2f1546bb73be6d3ac6ddebc8af2333d8bffb Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 26 Jul 2023 10:50:02 -0600 Subject: [PATCH 1229/2067] Added calls to set the litter source on restart for fates --- src/main/clm_instMod.F90 | 3 ++- src/utils/clmfates_interfaceMod.F90 | 11 +++++++++-- 2 files changed, 11 insertions(+), 3 deletions(-) diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index be75edc8d1..c61ed32f44 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -588,7 +588,8 @@ subroutine clm_instRest(bounds, ncid, flag, writing_finidat_interp_dest_file) canopystate_inst=canopystate_inst, & soilstate_inst=soilstate_inst, & active_layer_inst=active_layer_inst, & - soilbiogeochem_carbonflux_inst=soilbiogeochem_carbonflux_inst) + soilbiogeochem_carbonflux_inst=soilbiogeochem_carbonflux_inst, & + soilbiogeochem_nitrogenflux_inst=soilbiogeochem_nitrogenflux_inst) end if diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 88a89dddf0..bf51b3cac5 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1463,7 +1463,8 @@ end subroutine wrap_update_hlmfates_dyn subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & waterstatebulk_inst, canopystate_inst, soilstate_inst, & - active_layer_inst, soilbiogeochem_carbonflux_inst) + active_layer_inst, soilbiogeochem_carbonflux_inst, & + soilbiogeochem_nitrogenflux_inst) ! --------------------------------------------------------------------------------- ! The ability to restart the model is handled through three different types of calls @@ -1499,7 +1500,8 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & type(soilstate_type) , intent(inout) :: soilstate_inst type(active_layer_type) , intent(in) :: active_layer_inst type(soilbiogeochem_carbonflux_type), intent(inout) :: soilbiogeochem_carbonflux_inst - + type(soilbiogeochem_nitrogenflux_type), intent(inout) :: soilbiogeochem_nitrogenflux_inst + ! Locals type(bounds_type) :: bounds_clump integer :: nc @@ -1716,6 +1718,9 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s), & this%fates(nc)%bc_out(s)) + call this%UpdateCLitterFluxes(soilbiogeochem_carbonflux_inst,nc,c) + call this%UpdateNLitterFluxes(soilbiogeochem_nitrogenflux_inst,nc,c) + end do if(use_fates_sp)then @@ -1947,6 +1952,8 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s), & this%fates(nc)%bc_out(s)) + !call UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) + end do ! ------------------------------------------------------------------------ From c148410861c57662bc1e932e2c49cff6c68429f6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 24 Jul 2023 15:32:42 -0600 Subject: [PATCH 1230/2067] Tillage multipliers now read from params file. --- src/main/clm_instMod.F90 | 5 - src/main/readParamsMod.F90 | 2 + .../SoilBiogeochemDecompCascadeBGCMod.F90 | 8 -- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 6 - src/soilbiogeochem/TillageMod.F90 | 122 +++++++++--------- 5 files changed, 60 insertions(+), 83 deletions(-) diff --git a/src/main/clm_instMod.F90 b/src/main/clm_instMod.F90 index 63f28716f7..7924c2111e 100644 --- a/src/main/clm_instMod.F90 +++ b/src/main/clm_instMod.F90 @@ -200,7 +200,6 @@ subroutine clm_instInit(bounds) use SoilWaterRetentionCurveFactoryMod , only : create_soil_water_retention_curve use decompMod , only : get_proc_bounds use BalanceCheckMod , only : GetBalanceCheckSkipSteps - use TillageMod , only : tillage_init ! ! !ARGUMENTS type(bounds_type), intent(in) :: bounds ! processor bounds @@ -378,10 +377,6 @@ subroutine clm_instInit(bounds) call soilbiogeochem_state_inst%Init(bounds) - ! Initialize tillage - ! Must be called before init_decompcascade* - call tillage_init(bounds) - ! Initialize decompcascade constants ! Note that init_decompcascade_bgc need ! soilbiogeochem_state_inst to be initialized diff --git a/src/main/readParamsMod.F90 b/src/main/readParamsMod.F90 index 2d60b29be5..31bba00f01 100644 --- a/src/main/readParamsMod.F90 +++ b/src/main/readParamsMod.F90 @@ -39,6 +39,7 @@ subroutine readParameters (photosyns_inst) use SoilBiogeochemLittVertTranspMod , only : readSoilBiogeochemLittVertTranspParams => readParams use SoilBiogeochemPotentialMod , only : readSoilBiogeochemPotentialParams => readParams use SoilBiogeochemDecompMod , only : readSoilBiogeochemDecompParams => readParams + use TillageMod , only : readTillageParams => readParams use SoilBiogeochemDecompCascadeMIMICSMod, only : readSoilBiogeochemDecompMimicsParams => readParams use SoilBiogeochemDecompCascadeBGCMod , only : readSoilBiogeochemDecompBgcParams => readParams use ch4Mod , only : readCH4Params => readParams @@ -105,6 +106,7 @@ subroutine readParameters (photosyns_inst) call readSoilBiogeochemDecompBgcParams(ncid) end if call readSoilBiogeochemDecompParams(ncid) + call readTillageParams(ncid) call readSoilBiogeochemLittVertTranspParams(ncid) call readSoilBiogeochemNitrifDenitrifParams(ncid) call readSoilBiogeochemNLeachingParams(ncid) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index e7a258c7b1..bf5a4e2636 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -229,9 +229,6 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i ! initialize rate constants and decomposition pathways following the decomposition cascade of the BGC model. ! written by C. Koven ! - ! !USES: - use TillageMod, only : get_do_tillage, tillage_init_decompcascade - ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds type(soilbiogeochem_state_type) , intent(inout) :: soilbiogeochem_state_inst @@ -506,11 +503,6 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i deallocate(params_inst%bgc_initial_Cstocks) - ! Allocate tillage variables - if (get_do_tillage()) then - call tillage_init_decompcascade(i_act_som, i_slo_som, i_pas_som, i_cel_lit, i_lig_lit) - end if - end associate end subroutine init_decompcascade_bgc diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index 82df969a80..0fcf0c3bab 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -342,7 +342,6 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat ! ! !USES: use clm_varcon, only: pct_to_frac - use TillageMod, only: get_do_tillage, tillage_init_decompcascade ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -735,11 +734,6 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat nue_decomp_cascade(i_cwdl2) = 1.0_r8 end if - ! Allocate tillage variables - if (get_do_tillage()) then - call tillage_init_decompcascade(i_avl_som, i_chem_som, i_phys_som, i_str_lit) - end if - deallocate(params_inst%mimics_mge) deallocate(params_inst%mimics_vmod) deallocate(params_inst%mimics_vint) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 635efa10d2..94c2a5f06a 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -15,8 +15,7 @@ module TillageMod implicit none private ! !PUBLIC MEMBER PROCEDURES - public :: tillage_init - public :: tillage_init_decompcascade + public :: readParams public :: get_do_tillage public :: get_apply_tillage_multipliers ! !PUBLIC DATA MEMBERS @@ -28,39 +27,25 @@ module TillageMod logical :: use_original_tillage ! Use get_tillage_multipliers_orig? real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) - ! Indices for soil organic matter pools - integer :: i_act_som ! MIMICS: i_avl_som - integer :: i_slo_som ! MIMICS: i_chem_som - integer :: i_pas_som ! MIMICS: i_phys_som - ! Indices for litter pools - integer :: i_cel_lit ! MIMICS: i_str_lit - integer :: i_lig_lit ! MIMICS: none (just the one structural litter pool) !============================================================================== contains !============================================================================== - subroutine tillage_init(bounds) + subroutine readParams_namelist() ! - ! Read namelist parameters related to tillage. Allocation of variables happens - ! in separate subroutines written specifically for decomposition mode of choice. + ! Read namelist parameters related to tillage. ! ! !USES: use spmdMod , only : masterproc, mpicom use controlMod , only : NLFilename use clm_nlUtilsMod , only : find_nlgroup_name use shr_mpi_mod , only : shr_mpi_bcast - use decompMod , only : bounds_type - ! - ! !ARGUMENTS - ! SSR: Not sure why this is necessary, but without it, CTSM stalls out - ! (although it seems to successfully complete this subroutine). - type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES integer :: nu_nml ! unit for namelist file integer :: nml_error ! namelist i/o error flag - character(*), parameter :: subname = "('tillage_init')" + character(*), parameter :: subname = "('readParams_namelist')" namelist /tillage_inparm/ & tillage_mode, & @@ -105,70 +90,79 @@ subroutine tillage_init(bounds) call endrun(subname // ':: ERROR Unrecognized tillage_mode') end if - - end subroutine tillage_init + end subroutine readParams_namelist - subroutine tillage_init_decompcascade(i_act_som_in, i_slo_som_in, i_pas_som_in, i_cel_lit_in, i_lig_lit_in) + subroutine readParams_netcdf(ncid) ! !DESCRIPTION: ! - ! Allocate multiplier arrays to be used in tillage. Call during initialization of CENTURY or MIMICS decomposition. - ! Written by Sam Rabin. + ! Read paramfile parameters to be used in tillage. ! ! !USES use pftconMod , only : npcropmin + use ncdio_pio , only : file_desc_t, ncd_io + use clm_varpar, only : ndecomp_pools_max + use SoilBiogeochemDecompCascadeConType, only : no_soil_decomp, century_decomp, mimics_decomp, decomp_method ! ! !ARGUMENTS: - ! All soil pool indices use CENTURY index names. Comments indicate corresponding MIMICS names, if any. + type(file_desc_t),intent(inout) :: ncid ! pio netCDF file id ! - ! Indices for soil organic matter pools - integer , intent(in) :: i_act_som_in - integer , intent(in) :: i_slo_som_in - integer , intent(in) :: i_pas_som_in - ! Indices for structural litter pools - integer , intent(in) :: i_cel_lit_in - integer, optional, intent(in) :: i_lig_lit_in ! Do not specify for MIMICS - - if (.not. get_do_tillage()) then + ! !LOCAL VARIABLES: + character(len=32) :: subname = 'readParams_netcdf' + character(len=100) :: errCode = 'Error reading tillage params ' + logical :: readv ! has variable been read in or not + real(r8), allocatable :: tempr(:,:,:) ! temporary to read in constant + character(len=100) :: tString ! temp. var for reading + character(len=3) :: decomp_method_str + + ! Initialize tillage multipliers as all 1, and exit if not tilling + allocate(tillage_mults_allphases(ndecomp_pools, nphases)) + tillage_mults_allphases(:,:) = 1.0_r8 + if (tillage_mode == "off") then return end if - ! Allocate tillage multipliers - allocate(tillage_mults_allphases(ndecomp_pools, nphases)); tillage_mults_allphases(:,:) = 1.0_r8 - - ! Save soil pool indices - i_act_som = i_act_som_in - i_slo_som = i_slo_som_in - i_pas_som = i_pas_som_in - i_cel_lit = i_cel_lit_in - if (present(i_lig_lit_in)) then - i_lig_lit = i_lig_lit_in - else - i_lig_lit = -1 + ! Handle decomposition method + select case( decomp_method ) + case( no_soil_decomp ) + return + case( century_decomp ) + tString = 'till_decompk_multipliers' + case( mimics_decomp ) + tString = 'mimics_till_decompk_multipliers' + case default + write(decomp_method_str, '(I3)') decomp_method + call endrun('Bad decomp_method = '//decomp_method_str ) + end select + + ! Read off of netcdf file + allocate(tempr(2,ndecomp_pools_max,nphases)) + call ncd_io(trim(tString), tempr, 'read', ncid, readvar = readv) + if (.not. readv) then + call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__)) end if - ! Fill tillage_mults_allphases + ! Save if (do_tillage_low) then - tillage_mults_allphases(i_act_som,:) = (/ 1.0_r8, 1.0_r8, 1.0_r8 /) - tillage_mults_allphases(i_slo_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) - tillage_mults_allphases(i_pas_som,:) = (/ 3.0_r8, 1.6_r8, 1.3_r8 /) - tillage_mults_allphases(i_cel_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - if (i_lig_lit > 0) then - tillage_mults_allphases(i_lig_lit,:) = (/ 1.5_r8, 1.5_r8, 1.1_r8 /) - end if + tillage_mults_allphases = tempr(1,1:ndecomp_pools,:) else if (do_tillage_high) then - tillage_mults_allphases(i_act_som,:) = (/ 1.2_r8, 1.0_r8, 1.0_r8 /) - tillage_mults_allphases(i_slo_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) - tillage_mults_allphases(i_pas_som,:) = (/ 4.8_r8, 3.5_r8, 2.5_r8 /) - tillage_mults_allphases(i_cel_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) - if (i_lig_lit > 0) then - tillage_mults_allphases(i_lig_lit,:) = (/ 1.8_r8, 1.5_r8, 1.1_r8 /) - end if - else - call endrun('ERROR Unrecognized tillage setting in tillage_init_decompcascade()') + tillage_mults_allphases = tempr(2,1:ndecomp_pools,:) end if - end subroutine tillage_init_decompcascade + end subroutine readParams_netcdf + + + subroutine readParams(ncid) + ! !USES + use ncdio_pio , only : file_desc_t + ! + ! !ARGUMENTS: + type(file_desc_t),intent(inout) :: ncid ! pio netCDF file id + + call readParams_namelist() + call readParams_netcdf(ncid) + + end subroutine readParams function get_do_tillage() From de88db014a113751890c476d91e8d6caf2db4868 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 25 Jul 2023 10:13:16 -0600 Subject: [PATCH 1231/2067] Add git status info to params file. --- tillage-tmp/add_tillage_to_paramsfile.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/tillage-tmp/add_tillage_to_paramsfile.py b/tillage-tmp/add_tillage_to_paramsfile.py index 12ee955200..3044a407fb 100644 --- a/tillage-tmp/add_tillage_to_paramsfile.py +++ b/tillage-tmp/add_tillage_to_paramsfile.py @@ -2,10 +2,29 @@ import xarray as xr import numpy as np +import os +import subprocess file_in = "/Users/Shared/CESM_inputdata/lnd/clm2/paramdata/ctsm51_params.c211112.nc" file_out = "/Users/sam/Documents/git_repos/CTSM_myfork/ctsm51_params.c211112.tillage.nc" +# Get git info +thisDir = os.path.dirname(__file__) +git_status = subprocess.run( + ["git", "status"], + capture_output=True, +) +git_status = git_status.stdout.decode() +repo_is_clean = "working tree clean" in git_status +if not repo_is_clean: + print("WARNING: Repo not clean; will not save params file.") + print(git_status) +git_log = subprocess.run( + ["git", "log", "-1"], + capture_output=True, +) +git_log = git_log.stdout.decode() + # %% Set up dimensions @@ -113,10 +132,14 @@ def make_dataarray(np_array, decomp_model, ntill_intensities_max, ndecomp_pools_ # %% Save to output file +if not repo_is_clean: + raise RuntimeError("Clean up git repo before trying to save!") + ds1 = ds0.copy() ds0.close() ds1[tillage_century_da.name] = tillage_century_da ds1[tillage_mimics_da.name] = tillage_mimics_da +ds1.attrs['latest_git_log'] = git_log ds1.to_netcdf(file_out) \ No newline at end of file From 49b15ad9416b2e4f7407b54e8a722f927a43a91a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 11:58:08 -0600 Subject: [PATCH 1232/2067] Save paramfile as NETCDF3_CLASSIC. --- tillage-tmp/add_tillage_to_paramsfile.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tillage-tmp/add_tillage_to_paramsfile.py b/tillage-tmp/add_tillage_to_paramsfile.py index 3044a407fb..2b3ca55aee 100644 --- a/tillage-tmp/add_tillage_to_paramsfile.py +++ b/tillage-tmp/add_tillage_to_paramsfile.py @@ -142,4 +142,4 @@ def make_dataarray(np_array, decomp_model, ntill_intensities_max, ndecomp_pools_ ds1[tillage_mimics_da.name] = tillage_mimics_da ds1.attrs['latest_git_log'] = git_log -ds1.to_netcdf(file_out) \ No newline at end of file +ds1.to_netcdf(file_out, format="NETCDF3_CLASSIC") \ No newline at end of file From 0441df0ffbda5060d9c0b9024da735566b54d86b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 13:19:37 -0600 Subject: [PATCH 1233/2067] Replaced logical do_tillage_* with integer tillage_intensity. --- src/soilbiogeochem/TillageMod.F90 | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 94c2a5f06a..ff2f7980c9 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -20,10 +20,13 @@ module TillageMod public :: get_apply_tillage_multipliers ! !PUBLIC DATA MEMBERS character(len=CS), public :: tillage_mode ! off, low, high + integer, parameter, public :: ntill_intensities_max = 2 ! ! !PRIVATE DATA MEMBERS - logical :: do_tillage_low ! Do low-intensity tillage? - logical :: do_tillage_high ! Do high-intensity tillage? + integer :: tillage_intensity + integer, parameter :: tillage_off = 0 + integer, parameter :: tillage_low = 1 + integer, parameter :: tillage_high = 2 logical :: use_original_tillage ! Use get_tillage_multipliers_orig? real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) @@ -80,13 +83,13 @@ subroutine readParams_namelist() endif ! Assign these - do_tillage_low = .false. - do_tillage_high = .false. - if (tillage_mode == "low") then - do_tillage_low = .true. + if (tillage_mode == "off") then + tillage_intensity = tillage_off + else if (tillage_mode == "low") then + tillage_intensity = tillage_low else if (tillage_mode == "high") then - do_tillage_high = .true. - else if (tillage_mode /= "off") then + tillage_intensity = tillage_high + else call endrun(subname // ':: ERROR Unrecognized tillage_mode') end if @@ -143,11 +146,7 @@ subroutine readParams_netcdf(ncid) end if ! Save - if (do_tillage_low) then - tillage_mults_allphases = tempr(1,1:ndecomp_pools,:) - else if (do_tillage_high) then - tillage_mults_allphases = tempr(2,1:ndecomp_pools,:) - end if + tillage_mults_allphases = tempr(tillage_intensity,1:ndecomp_pools,:) end subroutine readParams_netcdf @@ -167,7 +166,7 @@ end subroutine readParams function get_do_tillage() logical :: get_do_tillage - get_do_tillage = do_tillage_low .or. do_tillage_high + get_do_tillage = tillage_intensity > tillage_off end function get_do_tillage From 163147e9ac06bf9ac93c1763e82a6a98dbedc674 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 13:21:54 -0600 Subject: [PATCH 1234/2067] Removed unused 'use' in readParams_netcdf(). --- src/soilbiogeochem/TillageMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index ff2f7980c9..9ed1450e14 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -102,7 +102,6 @@ subroutine readParams_netcdf(ncid) ! Read paramfile parameters to be used in tillage. ! ! !USES - use pftconMod , only : npcropmin use ncdio_pio , only : file_desc_t, ncd_io use clm_varpar, only : ndecomp_pools_max use SoilBiogeochemDecompCascadeConType, only : no_soil_decomp, century_decomp, mimics_decomp, decomp_method From 23a89d690322f2fb2ff74a9e774e42b7943daf9e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 13:23:09 -0600 Subject: [PATCH 1235/2067] Renamed nphases to ntill_intensities_max for consistency with netCDF dim name. --- src/soilbiogeochem/TillageMod.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 9ed1450e14..65cbd09b8c 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -28,8 +28,8 @@ module TillageMod integer, parameter :: tillage_low = 1 integer, parameter :: tillage_high = 2 logical :: use_original_tillage ! Use get_tillage_multipliers_orig? - real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, nphases) - integer, parameter :: nphases = 3 ! How many different tillage phases are there? (Not including all-1 phases.) + real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, ntill_stages_max) + integer, parameter :: ntill_stages_max = 3 ! How many different tillage phases are there? (Not including all-1 phases.) !============================================================================== contains @@ -118,7 +118,7 @@ subroutine readParams_netcdf(ncid) character(len=3) :: decomp_method_str ! Initialize tillage multipliers as all 1, and exit if not tilling - allocate(tillage_mults_allphases(ndecomp_pools, nphases)) + allocate(tillage_mults_allphases(ndecomp_pools, ntill_stages_max)) tillage_mults_allphases(:,:) = 1.0_r8 if (tillage_mode == "off") then return @@ -138,7 +138,7 @@ subroutine readParams_netcdf(ncid) end select ! Read off of netcdf file - allocate(tempr(2,ndecomp_pools_max,nphases)) + allocate(tempr(2,ndecomp_pools_max,ntill_stages_max)) call ncd_io(trim(tString), tempr, 'read', ncid, readvar = readv) if (.not. readv) then call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__)) @@ -237,8 +237,8 @@ subroutine get_tillage_multipliers(tillage_mults, idop) tillage_mults(:) = 1._r8 if (phase > 0) then - if (phase > nphases) then - call endrun(msg='Tillage phase > nphases') + if (phase > ntill_stages_max) then + call endrun(msg='Tillage phase > ntill_stages_max') end if tillage_mults = tillage_mults_allphases(:, phase) end if From f61f983324b204cc7681deb7b1be5965c1942d75 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 13:36:29 -0600 Subject: [PATCH 1236/2067] Move present(idop) checks to beginning of decomp_rates_* subroutines. --- src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 | 7 ++++--- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index bf5a4e2636..3010fde6c4 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -598,6 +598,10 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & errMsg(sourcefile, __LINE__)) endif + if (get_do_tillage() .and. .not. present(idop)) then + call endrun("Do not enable tillage without providing idop to decomp_rate_constants_bgc().") + end if + days_per_year = get_average_days_per_year() dt = real( get_step_size(), r8 ) @@ -910,9 +914,6 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! Tillage if (get_do_tillage()) then - if (.not. present(idop)) then - call endrun("Do not call tillage without providing idop.") - end if do fc = 1,num_soilc c = filter_soilc(fc) call get_apply_tillage_multipliers(idop, c, decomp_k) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index 0fcf0c3bab..380f5469ca 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -887,6 +887,10 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & spinup_factor => decomp_cascade_con%spinup_factor & ! Input: [real(r8) (:) ] factor for AD spinup associated with each pool ) + if (get_do_tillage() .and. .not. present(idop)) then + call endrun("Do not enable tillage without providing idop to decomp_rate_constants_mimics().") + end if + mino2lim = CNParamsShareInst%mino2lim days_per_year = get_average_days_per_year() @@ -1310,9 +1314,6 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! Tillage if (get_do_tillage()) then - if (.not. present(idop)) then - call endrun("Do not call tillage without providing idop.") - end if do fc = 1,num_soilc c = filter_soilc(fc) call get_apply_tillage_multipliers(idop, c, decomp_k) From c1757d1605258b71c259c3e612023cc05ed41260 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 13:38:13 -0600 Subject: [PATCH 1237/2067] Rework get_apply_tillage_multipliers() to j;c loop instead of c;j. --- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 14 ++++++-------- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 13 +++++-------- src/soilbiogeochem/TillageMod.F90 | 16 ++++++++-------- 3 files changed, 19 insertions(+), 24 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index 3010fde6c4..e2ca5d2bb0 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -902,6 +902,12 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & decomp_k(c,j,i_cwd) = k_frag * t_scalar(c,j) * w_scalar(c,j) * & depth_scalar(c,j) * o_scalar(c,j) * spinup_geogterm_cwd(c) end if + + ! Tillage + if (get_do_tillage()) then + call get_apply_tillage_multipliers(idop, c, j, decomp_k) + end if + ! Above into soil matrix if(use_soil_matrixcn)then ! same for cwd but only if fates is not enabled; fates handles CWD @@ -912,14 +918,6 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & end do end do - ! Tillage - if (get_do_tillage()) then - do fc = 1,num_soilc - c = filter_soilc(fc) - call get_apply_tillage_multipliers(idop, c, decomp_k) - end do - end if - pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l1s1) = 1.0_r8 pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l2s1) = 1.0_r8 pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_l3s2) = 1.0_r8 diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index 380f5469ca..df870d0b40 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -1309,16 +1309,13 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & if (.not. use_fates) then decomp_k(c,j,i_cwd) = k_frag * w_d_o_scalars ! * spinup_geogterm_cwd(c) end if - end do - end do - ! Tillage - if (get_do_tillage()) then - do fc = 1,num_soilc - c = filter_soilc(fc) - call get_apply_tillage_multipliers(idop, c, decomp_k) + ! Tillage + if (get_do_tillage()) then + call get_apply_tillage_multipliers(idop, c, j, decomp_k) + end if end do - end if + end do ! pathfrac terms not calculated in the previous loop pathfrac_decomp_cascade(bounds%begc:bounds%endc,1:nlevdecomp,i_s2s1) = 1.0_r8 diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 65cbd09b8c..11f064ce83 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -246,7 +246,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) end subroutine get_tillage_multipliers - subroutine get_apply_tillage_multipliers(idop, c, decomp_k) + subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! !DESCRIPTION: ! ! Multiply decomposition rate constants by tillage coefficients. @@ -259,15 +259,18 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k) ! !ARGUMENTS: integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: c ! index of column this is being called for + integer , intent(in) :: j ! index of soil layer this is being called for real(r8), dimension(:,:,:), intent(inout) :: decomp_k ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) ! ! !LOCAL VARIABLES - integer :: p, this_patch, j, n_noncrop + integer :: p, this_patch, n_noncrop real :: sumwt ! sum of all patch weights, to check real(r8), dimension(ndecomp_pools) :: tillage_mults real(r8), dimension(ndecomp_pools) :: tillage_mults_1patch - if (.not. col%active(c)) then + if (.not. col%active(c) .or. j > 5) then + ! Top 5 layers (instead of all nlevdecomp) so that model only tills + ! the top 26-40 cm of the soil surface, rather than whole soil - MWGraham return end if @@ -307,11 +310,8 @@ subroutine get_apply_tillage_multipliers(idop, c, decomp_k) call endrun('ERROR Active crop patch weights does not sum to 1') end if - ! Top 5 layers (instead of all nlevdecomp) so that model only tills the top 26-40 cm - ! of the soil surface, rather than whole soil - MWGraham - do j = 1,5 - decomp_k(c,j,:) = decomp_k(c,j,:) * tillage_mults(:) - end do + ! Apply + decomp_k(c,j,:) = decomp_k(c,j,:) * tillage_mults(:) end subroutine get_apply_tillage_multipliers From 8cfeafef717346c271cbe72e909412a45c7d6dd3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 13:45:32 -0600 Subject: [PATCH 1238/2067] Slice decomp_k by column and soil layer before passing to get_apply_tillage_multipliers(). --- src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 | 2 +- src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 | 2 +- src/soilbiogeochem/TillageMod.F90 | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index e2ca5d2bb0..2d28de5f23 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -905,7 +905,7 @@ subroutine decomp_rate_constants_bgc(bounds, num_soilc, filter_soilc, & ! Tillage if (get_do_tillage()) then - call get_apply_tillage_multipliers(idop, c, j, decomp_k) + call get_apply_tillage_multipliers(idop, c, j, decomp_k(c,j,:)) end if ! Above into soil matrix diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index df870d0b40..d9bb3c4b2f 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -1312,7 +1312,7 @@ subroutine decomp_rates_mimics(bounds, num_soilc, filter_soilc, & ! Tillage if (get_do_tillage()) then - call get_apply_tillage_multipliers(idop, c, j, decomp_k) + call get_apply_tillage_multipliers(idop, c, j, decomp_k(c,j,:)) end if end do end do diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 11f064ce83..7d1356031c 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -260,7 +260,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) integer , intent(in) :: idop(:) ! patch day of planting integer , intent(in) :: c ! index of column this is being called for integer , intent(in) :: j ! index of soil layer this is being called for - real(r8), dimension(:,:,:), intent(inout) :: decomp_k ! Output: [real(r8) (:,:,:) ] rate constant for decomposition (1./sec) + real(r8), dimension(:), intent(inout) :: decomp_k ! Output: [real(r8) (:) ] rate constant for decomposition (1./sec) ! ! !LOCAL VARIABLES integer :: p, this_patch, n_noncrop @@ -311,7 +311,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) end if ! Apply - decomp_k(c,j,:) = decomp_k(c,j,:) * tillage_mults(:) + decomp_k = decomp_k * tillage_mults(:) end subroutine get_apply_tillage_multipliers From 93e82dc41065f9a527237e0b10371f4f05bf8e37 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 14:13:01 -0600 Subject: [PATCH 1239/2067] Add N_TO_FOOD outputs. --- src/biogeochem/CNVegNitrogenFluxType.F90 | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index ce164b4c37..bd8f3ec64c 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -14,7 +14,7 @@ module CNVegNitrogenFluxType use SoilBiogeochemDecompCascadeConType , only : decomp_cascade_con use dynSubgridControlMod , only : get_do_grossunrep use CropReprPoolsMod , only : nrepr, repr_grain_min, repr_grain_max, repr_structure_min, repr_structure_max - use CropReprPoolsMod , only : get_repr_rest_fname, get_repr_longname + use CropReprPoolsMod , only : get_repr_hist_fname, get_repr_rest_fname, get_repr_longname use LandunitType , only : lun use ColumnType , only : col use PatchType , only : patch @@ -1024,6 +1024,18 @@ subroutine InitHistory(this, bounds) call hist_addfld1d (fname='NFERTILIZATION', units='gN/m^2/s', & avgflag='A', long_name='fertilizer added', & ptr_patch=this%fert_patch) + + this%repr_grainn_to_food_patch(begp:endp,:) = spval + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainn_to_food_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINN_TO_FOOD + fname=get_repr_hist_fname(k)//'N_TO_FOOD', & + units='gN/m^2/s', & + avgflag='A', & + long_name=get_repr_longname(k)//' N to food', & + ptr_patch=data1dptr) + end do end if if (use_crop .and. .not. use_fun) then From 2cd833912c09b6ec4b6632cdc381d2ac3437bc6d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 15:16:15 -0600 Subject: [PATCH 1240/2067] Add N_TO_SEED outputs. --- src/biogeochem/CNVegNitrogenFluxType.F90 | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index bd8f3ec64c..1154e0d198 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -1026,6 +1026,7 @@ subroutine InitHistory(this, bounds) ptr_patch=this%fert_patch) this%repr_grainn_to_food_patch(begp:endp,:) = spval + this%repr_grainn_to_seed_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainn_to_food_patch(:,k) call hist_addfld1d ( & @@ -1035,6 +1036,14 @@ subroutine InitHistory(this, bounds) avgflag='A', & long_name=get_repr_longname(k)//' N to food', & ptr_patch=data1dptr) + data1dptr => this%repr_grainn_to_seed_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINN_TO_SEED + fname=get_repr_hist_fname(k)//'N_TO_SEED', & + units='gN/m^2/s', & + avgflag='A', & + long_name=get_repr_longname(k)//' N to seed', & + ptr_patch=data1dptr) end do end if From f737631d6b51a9fc81443ed07780beb7b2587bfb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 15:16:59 -0600 Subject: [PATCH 1241/2067] Make N_TO_FOOD and N_TO_SEED outputs default inactive. --- src/biogeochem/CNVegNitrogenFluxType.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index 1154e0d198..59b2fd2f56 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -1035,7 +1035,8 @@ subroutine InitHistory(this, bounds) units='gN/m^2/s', & avgflag='A', & long_name=get_repr_longname(k)//' N to food', & - ptr_patch=data1dptr) + ptr_patch=data1dptr, & + default='inactive') data1dptr => this%repr_grainn_to_seed_patch(:,k) call hist_addfld1d ( & ! e.g., GRAINN_TO_SEED @@ -1043,7 +1044,8 @@ subroutine InitHistory(this, bounds) units='gN/m^2/s', & avgflag='A', & long_name=get_repr_longname(k)//' N to seed', & - ptr_patch=data1dptr) + ptr_patch=data1dptr, & + default='inactive') end do end if From 8ae1ecb29eec5394c8cb3dd827d12e56cc7092c8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 16:13:34 -0600 Subject: [PATCH 1242/2067] Fix indentation of a block. --- src/biogeochem/CNVegNitrogenFluxType.F90 | 40 ++++++++++++------------ 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index 59b2fd2f56..c831921a0d 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -1027,26 +1027,26 @@ subroutine InitHistory(this, bounds) this%repr_grainn_to_food_patch(begp:endp,:) = spval this%repr_grainn_to_seed_patch(begp:endp,:) = spval - do k = repr_grain_min, repr_grain_max - data1dptr => this%repr_grainn_to_food_patch(:,k) - call hist_addfld1d ( & - ! e.g., GRAINN_TO_FOOD - fname=get_repr_hist_fname(k)//'N_TO_FOOD', & - units='gN/m^2/s', & - avgflag='A', & - long_name=get_repr_longname(k)//' N to food', & - ptr_patch=data1dptr, & - default='inactive') - data1dptr => this%repr_grainn_to_seed_patch(:,k) - call hist_addfld1d ( & - ! e.g., GRAINN_TO_SEED - fname=get_repr_hist_fname(k)//'N_TO_SEED', & - units='gN/m^2/s', & - avgflag='A', & - long_name=get_repr_longname(k)//' N to seed', & - ptr_patch=data1dptr, & - default='inactive') - end do + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainn_to_food_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINN_TO_FOOD + fname=get_repr_hist_fname(k)//'N_TO_FOOD', & + units='gN/m^2/s', & + avgflag='A', & + long_name=get_repr_longname(k)//' N to food', & + ptr_patch=data1dptr, & + default='inactive') + data1dptr => this%repr_grainn_to_seed_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINN_TO_SEED + fname=get_repr_hist_fname(k)//'N_TO_SEED', & + units='gN/m^2/s', & + avgflag='A', & + long_name=get_repr_longname(k)//' N to seed', & + ptr_patch=data1dptr, & + default='inactive') + end do end if if (use_crop .and. .not. use_fun) then From 2dbf4ee574bcf78d5151be9afbc21efd5ff38bef Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 26 Jul 2023 19:29:11 -0600 Subject: [PATCH 1243/2067] add xesmf to the standard python environment This also caps the numba environment to avoid a numba/numpy compatability issue that is currently unaddressed by numba --- python/conda_env_ctsm_py.txt | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index 0ac4656e73..8faa44b013 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -19,5 +19,7 @@ requests packaging numpy=1.18.5 xarray=0.17.0 +xesmf +numba=0.55.2 # Avoid 0.56 until numpy>=1.20. This is the minimum for xesmf pylint=2.8.3 -black=22.3.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows +black=22.3.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows From 36a49a53768125bdc1af0b8c9dc2eba4814a055c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 26 Jul 2023 23:06:55 -0700 Subject: [PATCH 1244/2067] fates cross-grid seed dispersal api update --- src/main/clm_driver.F90 | 4 + src/utils/clmfates_interfaceMod.F90 | 180 +++++++++++++++++++++++++++- 2 files changed, 181 insertions(+), 3 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index f173d7d83d..edeea6a412 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1273,6 +1273,10 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro end do !$OMP END PARALLEL DO + + ! Pass fates seed dispersal information to all nodes + if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() + ! ============================================================================ ! Determine gridcell averaged properties to send to atm ! ============================================================================ diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 8a3be405ff..964072b01c 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -94,6 +94,7 @@ module CLMFatesInterfaceMod use spmdMod , only : masterproc use decompMod , only : get_proc_bounds, & get_proc_clumps, & + get_proc_global, & get_clump_bounds use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, decomp_method use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, century_decomp @@ -122,7 +123,8 @@ module CLMFatesInterfaceMod use FatesInterfaceMod , only : set_fates_ctrlparms use FatesInterfaceMod , only : UpdateFatesRMeansTStep use FatesInterfaceMod , only : InitTimeAveragingGlobals - + use FatesInterfaceMod , only : DetermineGridCellNeighbors + use FatesHistoryInterfaceMod, only : fates_hist use FatesRestartInterfaceMod, only : fates_restart_interface_type @@ -130,6 +132,8 @@ module CLMFatesInterfaceMod use PRTGenericMod , only : num_elements use FatesInterfaceTypesMod, only : hlm_stepsize use FatesInterfaceTypesMod, only : fates_maxPatchesPerSite + use FatesInterfaceTypesMod, only : fates_dispersal_kernel_mode + use FatesInterfaceTypesMod, only : fates_dispersal_kernel_none use EDMainMod , only : ed_ecosystem_dynamics use EDMainMod , only : ed_update_site use EDInitMod , only : zero_site @@ -159,6 +163,8 @@ module CLMFatesInterfaceMod use dynHarvestMod , only : dynHarvest_interp_resolve_harvesttypes use FatesConstantsMod , only : hlm_harvest_area_fraction use FatesConstantsMod , only : hlm_harvest_carbon + use FatesDispersalMod , only : lneighbors, dispersal_type, IsItDispersalTime + use perf_mod , only : t_startf, t_stopf implicit none @@ -198,6 +204,9 @@ module CLMFatesInterfaceMod ! fates_fire_data_method determines the fire data passed from HLM to FATES class(fates_fire_base_type), allocatable :: fates_fire_data_method + ! Type structure that holds allocatable arrays for mpi-based seed dispersal + type(dispersal_type) :: fates_seed + contains procedure, public :: init @@ -225,7 +234,10 @@ module CLMFatesInterfaceMod procedure, public :: wrap_hydraulics_drive procedure, public :: WrapUpdateFatesRmean procedure, public :: wrap_WoodProducts - + procedure, public :: WrapSeedGlobal + procedure, public :: wrap_seed_dispersal + procedure, public :: wrap_seed_dispersal_reset + end type hlm_fates_interface_type ! hlm_bounds_to_fates_bounds is not currently called outside the interface. @@ -520,6 +532,12 @@ subroutine CLMFatesGlobals2() call SetFatesGlobalElements2(use_fates) + ! Initialize the array of nearest neighbors for fates-driven grid cell communications + ! This must be called after surfrd_get_data and decompInit_lnd + if (use_fates) then + call DetermineGridCellNeighbors(lneighbors) + end if + call t_stopf('fates_globals2') return @@ -583,6 +601,7 @@ subroutine init(this, bounds_proc ) type(bounds_type) :: bounds_clump integer :: nmaxcol integer :: ndecomp + integer :: numg ! Initialize the FATES communicators with the HLM ! This involves to stages @@ -595,6 +614,11 @@ subroutine init(this, bounds_proc ) ! Parameter Routines call param_derived%Init( numpft_fates ) + ! To do: skip this if not running seed dispersal + ! Initialize fates global seed dispersal array for all nodes + call get_proc_global(ng=numg) + call this%fates_seed%init(numg,numpft_fates) + nclumps = get_proc_clumps() allocate(this%fates(nclumps)) allocate(this%f2hmap(nclumps)) @@ -1030,6 +1054,9 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! structures into the cohort structures. call UnPackNutrientAquisitionBCs(this%fates(nc)%sites, this%fates(nc)%bc_in) + ! Distribute any seeds from neighboring gridcells into the current gridcell + ! Global seed availability array populated by WrapSeedGlobal call + call this%wrap_seed_dispersal(bounds_clump) ! --------------------------------------------------------------------------------- ! Flush arrays to values defined by %flushval (see registry entry in @@ -1252,9 +1279,22 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & patch%is_bareground(bounds_clump%begp:bounds_clump%endp) = .false. patch%wt_ed(bounds_clump%begp:bounds_clump%endp) = 0.0_r8 - do s = 1,this%fates(nc)%nsites + ! Check if seed dispersal mode is 'turned on', if not return to calling procedure + if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then + ! zero the outgoing seed array + this%fates_seed%outgoing_local(:,:) = 0._r8 + end if + + do s = 1,this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) + g = col_pp%gridcell(c) + + ! Accumulate seeds from sites to the gridcell local outgoing buffer + if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) & + .and. IsItDispersalTime()) then + this%fates_seed%outgoing_local(g,:) = this%fates_seed%outgoing_local(g,:) + this%fates(nc)%bc_out(s)%seed_out(:) + end if ! Other modules may have AI's we only flush values ! that are on the naturally vegetated columns @@ -2489,6 +2529,140 @@ end subroutine wrap_canopy_radiation ! ====================================================================================== + subroutine WrapSeedGlobal(this) + + ! Call mpi procedure to provide the global seed output distribution array to every gridcell. + ! This could be conducted with a more sophisticated halo-type structure or distributed graph. + + use spmdMod, only : MPI_REAL8, MPI_SUM, mpicom + use FatesDispersalMod, only : lneighbors, neighbor_type + use FatesInterfaceTypesMod, only : numpft_fates => numpft + + ! Arguments + class(hlm_fates_interface_type), intent(inout) :: this + + ! Local + integer :: numg ! total number of gridcells across all processors + integer :: ier ! error code + integer :: g ! gridcell index + + type (neighbor_type), pointer :: neighbor + + ! Check if seed dispersal mode is 'turned on', if not return to calling procedure + if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return + + call t_startf('fates-seed-mpi_reduce') + + if (IsItDispersalTime(setdispersedflag=.true.)) then + + ! Re-initialize incoming seed buffer for this time step + this%fates_seed%incoming_global(:,:) = 0._r8 + + ! Re-initialize the outgoing global seed array buffer + this%fates_seed%outgoing_global(:,:) = 1.e6_r8 ! Is this acting as seed rain? + + ! Distribute and sum outgoing seed data from all nodes to all nodes + ! mpi_allgather should work here as well since gridcells values are not split across nodes + ! This would allow for reduction in the outgoing local array size + call get_proc_global(ng=numg) + call mpi_allreduce(this%fates_seed%outgoing_local, this%fates_seed%outgoing_global, & + numg*numpft_fates, MPI_REAL8, MPI_SUM, mpicom, ier) + + do g = 1, numg + + ! Calculate the current gridcell incoming seed for each gridcell index + ! This should be conducted outside of a threaded region to provide access to + ! the neighbor%gindex which might not be available in via the clumped index + neighbor => lneighbors(g)%first_neighbor + do while (associated(neighbor)) + + ! This also applies the same neighborhood distribution scheme to all pfts + ! This needs to have a per pft density probability value + this%fates_seed%incoming_global(g,:) = this%fates_seed%incoming_global(g,:) + & + this%fates_seed%outgoing_global(neighbor%gindex,:) * & + neighbor%density_prob(:) / lneighbors(g)%neighbor_count + neighbor => neighbor%next_neighbor + end do + end do + + endif + call t_stopf('fates-seed-mpi_reduce') + + end subroutine WrapSeedGlobal + + ! ====================================================================================== + + subroutine wrap_seed_dispersal(this,bounds_clump) + + ! This subroutine pass seed_id_global to bc_in and reset seed_out + + ! Arguments + class(hlm_fates_interface_type), intent(inout) :: this + type(bounds_type), intent(in) :: bounds_clump + + integer :: g ! global index of the host gridcell + integer :: c ! global index of the host column + integer :: s ! FATES site index + integer :: nc ! clump index + + ! Check if seed dispersal mode is 'turned on', if not return to calling procedure + if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return + + call t_startf('fates-seed-disperse') + + nc = bounds_clump%clump_index + + ! Add fates check for seed dispersal mode + do s = 1, this%fates(nc)%nsites + c = this%f2hmap(nc)%fcolumn(s) + g = col_pp%gridcell(c) + + ! Check that it is the beginning of the current dispersal time step + if (IsItDispersalTime()) then + ! assuming equal area for all sites, seed_id_global in [kg/grid/day], seed_in in [kg/site/day] + this%fates(nc)%bc_in(s)%seed_in(:) = this%fates_seed%incoming_global(g,:) + this%fates(nc)%bc_out(s)%seed_out(:) = 0._r8 ! reset seed_out + else + ! if it is not the dispersing time, pass in zero + this%fates(nc)%bc_in(s)%seed_in(:) = 0._r8 + end if + + end do + + call t_stopf('fates-seed-disperse') + + end subroutine wrap_seed_dispersal + + ! ====================================================================================== + + subroutine wrap_seed_dispersal_reset(this,bounds_clump) + + ! This subroutine reset seed_in + + ! Arguments + class(hlm_fates_interface_type), intent(inout) :: this + type(bounds_type), intent(in) :: bounds_clump + ! Local Variables + integer :: g ! global index of the host gridcell + integer :: c ! global index of the host column + integer :: s ! FATES site index + integer :: nc ! clump index + + ! Check if seed dispersal mode is 'turned on', if not return to calling procedure + if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return + + nc = bounds_clump%clump_index + + do s = 1, this%fates(nc)%nsites + c = this%f2hmap(nc)%fcolumn(s) + g = col_pp%gridcell(c) + this%fates(nc)%bc_in(s)%seed_in(:) = 0 ! reset + end do + + end subroutine wrap_seed_dispersal_reset + + ! ====================================================================================== + subroutine wrap_update_hifrq_hist(this, bounds_clump, & soilbiogeochem_carbonflux_inst, & soilbiogeochem_carbonstate_inst) From dbac92c0d8e589b5967e7b78e655367661ddd98b Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 27 Jul 2023 07:03:39 -0600 Subject: [PATCH 1245/2067] Updates to nfixing during fates run --- src/biogeochem/CNNDynamicsMod.F90 | 10 +++++++++- src/main/filterMod.F90 | 2 +- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index 2c2189ec2d..f9698fb2ca 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -238,6 +238,7 @@ subroutine CNNFixation(num_soilc, filter_soilc, & if(col%is_fates(c))then s = clm_fates%f2hmap(clump_index)%hsites(c) + ! %ema_npp is Smoothed [gc/m2/yr] npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp/(dayspyr*secspday) else npp = col_lag_npp(c) @@ -256,7 +257,14 @@ subroutine CNNFixation(num_soilc, filter_soilc, & do fc = 1,num_soilc c = filter_soilc(fc) - t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * cannsum_npp(c))))/(secspday * dayspyr) + if(col%is_fates(c))then + s = clm_fates%f2hmap(clump_index)%hsites(c) + npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp + else + npp = cannsum_npp(c) + end if + + t = (1.8_r8 * (1._r8 - exp(-0.003_r8 * npp)))/(secspday * dayspyr) nfix_to_sminn(c) = max(0._r8,t) end do endif diff --git a/src/main/filterMod.F90 b/src/main/filterMod.F90 index e2433f35ab..2fb7d23079 100644 --- a/src/main/filterMod.F90 +++ b/src/main/filterMod.F90 @@ -477,7 +477,7 @@ subroutine setFiltersOneGroup(bounds, this_filter, include_inactive, glc_behavio fl = 0 fnl = 0 do p = bounds%begp,bounds%endp - if(.not.use_fates_bgc)then + if(.not.use_fates)then if (patch%active(p) .or. include_inactive) then if (patch%itype(p) >= npcropmin) then !skips 2 generic crop types fl = fl + 1 From ff5d65fd10868d38b9bdbf1082f3a381471687f7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jul 2023 11:12:42 -0600 Subject: [PATCH 1246/2067] add xesmf to latest conda env file --- python/conda_env_ctsm_py_latest.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/python/conda_env_ctsm_py_latest.txt b/python/conda_env_ctsm_py_latest.txt index 052fbf4fef..0ab4e17694 100644 --- a/python/conda_env_ctsm_py_latest.txt +++ b/python/conda_env_ctsm_py_latest.txt @@ -8,6 +8,7 @@ requests packaging numpy>=1.23.0 xarray>=2022.3.0 +xesmf pylint>=2.8.3,<2.9.0 # Once, you move off of 2.8.3, make lint shows 2 errors, at 2.11.1 there are 2 more errors beyond that # By, 2.14.4 there are 75 errors black>=22.6.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows From 3dfa6aac5c4710c86510e1de4db57fae44a9493f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Jul 2023 11:59:53 -0600 Subject: [PATCH 1247/2067] Corrected a term in soil gas diffusivity equation. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 3993439a1c..cd8b62ce75 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -279,7 +279,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & om_frac = 1._r8 end if diffus (c,j) = (d_con_g(2,1) + d_con_g(2,2)*t_soisno(c,j)) * 1.e-4_r8 * & - (om_frac * f_a**(10._r8/3._r8) / watsat(c,j)**2 + & + (om_frac * eps**(10._r8/3._r8) / watsat(c,j)**2 + & (1._r8-om_frac) * eps**2 * f_a**(3._r8 / bsw(c,j)) ) ! calculate anoxic fraction of soils From ae5da4a2e20a32f4823a943efc41802257a002c5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Jul 2023 14:24:46 -0600 Subject: [PATCH 1248/2067] Updated ChangeLog. --- doc/ChangeLog | 116 ++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeLog.tmp | 114 --------------------------------------------- doc/ChangeSum | 1 + 3 files changed, 117 insertions(+), 114 deletions(-) delete mode 100644 doc/ChangeLog.tmp diff --git a/doc/ChangeLog b/doc/ChangeLog index 2651e0d2a0..001a8a270a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,3 +1,119 @@ +=============================================================== +Tag name: ctsm5.1.dev131 +Originator(s): samrabin (Sam Rabin,UCAR/TSS) +Date: Thu Jul 27 14:24:07 MDT 2023 +One-line Summary: Enable prescribed crop calendars. + +Purpose and description of changes +---------------------------------- + +This tag introduces the ability to prescribe crop sowing dates +and/or maturity requirements. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Resolves #281 -- Clean up CropPhenology logic + Resolves #519 -- Read in crop planting and harvest dates + Fixes #2042 -- Issue running SystemTests due to "conda activate" error + + Some on #1649 -- Additional "annual" (per growing season) crop outputs + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users: + Untested but theoretically possible: + * Time-varying inputs + * Running at any resolution other than one matching the crop calendar inputs + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + Adds optional namelist variables: + * stream_fldfilename_sdate: Filename of input stream data for sowing dates + * stream_fldfilename_cultivar_gdds: Filename of input stream data for cultivar growing degree-day targets + * stream_meshfile_cropcal: Filename of input stream data for crop calendar inputs + * stream_year_first_cropcal: First year to loop over for crop calendar data + * stream_year_last_cropcal: Last year to loop over for crop calendar data + * model_year_align_cropcal: Simulation year that aligns with stream_year_first_cropcal value + * generate_crop_gdds: Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. + * use_mxmat: Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: + * Adds RXCROPMATURITY SystemTest, with an example added to ctsm_sci test suite. + * Removes 12 MCT tests from testlist_clm.xml, as discussed in CTSM SE standup 2023-06-26. + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + cheyenne - PASS + +Answer changes +-------------- + +Changes answers relative to baseline: YES for Clm45BgcCrop compsets only + + Summarize any changes to answers, i.e., + - what code configurations: Clm45BgcCrop + - what platforms/compilers: Cheyenne intel and gnu, Izumi intel and nag + - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff + + 5 tests in aux_clm showed true DIFFs (i.e., not just field list differences / new output files): + - SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput + - ERP_D_P36x2_Ld3.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes + - LGRAIN2_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput + - ERS_Ly5_P72x1.f10_f10_mg37.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput + - SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm45BgcCrop.izumi_nag.clm-oldhyd + + The first four were likely due to an order-of-operations change in CNOffsetLitterfall(), as they resolve with the patch at + https://github.com/samsrabin/CTSM/commit/c30320cbd6583bccbcc290ffe536e8500e6ec358 + + The last is resolved with an additional patch that removes all my changes to CNOffsetLitterfall()---changes which *should* only + affect new diagnostic variables: + https://github.com/samsrabin/CTSM/commit/e025f555e74584c63d50f27c4df38326fa64bc4f + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime + cime: cime6.0.108 -> cime6.0.125 + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/CTSM/pull/1863 + +=============================================================== + =============================================================== Tag name: ctsm5.1.dev130 Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049) diff --git a/doc/ChangeLog.tmp b/doc/ChangeLog.tmp deleted file mode 100644 index 6d66eee092..0000000000 --- a/doc/ChangeLog.tmp +++ /dev/null @@ -1,114 +0,0 @@ -=============================================================== -Tag name: ctsm5.1.dev131 -Originator(s): samrabin (Sam Rabin,UCAR/TSS) -Date: Mon Jul 17 13:58:49 MDT 2023 -One-line Summary: Enable prescribed crop calendars. - -Purpose and description of changes ----------------------------------- - -This tag introduces the ability to prescribe crop sowing dates -and/or maturity requirements. - -Significant changes to scientifically-supported configurations --------------------------------------------------------------- - -Does this tag change answers significantly for any of the following physics configurations? -(Details of any changes will be given in the "Answer changes" section below.) - - [Put an [X] in the box for any configuration with significant answer changes.] - -[ ] clm5_1 - -[ ] clm5_0 - -[ ] ctsm5_0-nwp - -[???] clm4_5 - -Bugs fixed or introduced ------------------------- - -CTSM issues fixed (include CTSM Issue #): - Resolves #281 -- Clean up CropPhenology logic - Resolves #519 -- Read in crop planting and harvest dates - Fixes #2042 -- Issue running SystemTests due to "conda activate" error - - Some on #1649 -- Additional "annual" (per growing season) crop outputs - -Notes of particular relevance for users ---------------------------------------- - -Caveats for users: - Untested but theoretically possible: - * Time-varying inputs - * Running at any resolution other than one matching the crop calendar inputs - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): - Adds optional namelist variables: - * stream_fldfilename_sdate: Filename of input stream data for sowing dates - * stream_fldfilename_cultivar_gdds: Filename of input stream data for cultivar growing degree-day targets - * stream_meshfile_cropcal: Filename of input stream data for crop calendar inputs - * stream_year_first_cropcal: First year to loop over for crop calendar data - * stream_year_last_cropcal: Last year to loop over for crop calendar data - * model_year_align_cropcal: Simulation year that aligns with stream_year_first_cropcal value - * generate_crop_gdds: Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files. - * use_mxmat: Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true. - -Notes of particular relevance for developers: --------------------------------------------- - -Changes to tests or testing: - * Adds RXCROPMATURITY SystemTest, with an example added to ctsm_sci test suite. - * Removes 12 MCT tests from testlist_clm.xml, as discussed in CTSM SE standup 2023-06-26. - -Testing summary: ----------------- - - [PASS means all tests PASS; OK means tests PASS other than expected fails.] - - build-namelist tests (if CLMBuildNamelist.pm has changed): - - cheyenne - PASS - - regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - - cheyenne ---- OK - izumi ------- OK - - python testing (if python code has changed; see instructions in python/README.md; document testing done): - - cheyenne - PASS - -Answer changes --------------- - -Changes answers relative to baseline: YES for Clm45BgcCrop compsets only - - Summarize any changes to answers, i.e., - - what code configurations: Clm45BgcCrop - - what platforms/compilers: Cheyenne intel and gnu, Izumi intel and nag - - nature of change (roundoff; larger than roundoff/same climate; new climate): roundoff - - 5 tests in aux_clm showed true DIFFs (i.e., not just field list differences / new output files): - - SMS_D_Ly6_Mmpi-serial.1x1_smallvilleIA.IHistClm45BgcCropQianRs.izumi_intel.clm-cropMonthOutput - - ERP_D_P36x2_Ld3.f10_f10_mg37.I2000Clm45BgcCrop.cheyenne_gnu.clm-no_subgrid_fluxes - - LGRAIN2_Ly2_P72x1.f10_f10_mg37.I1850Clm45BgcCrop.cheyenne_gnu.clm-ciso--clm-cropMonthOutput - - ERS_Ly5_P72x1.f10_f10_mg37.IHistClm45BgcCrop.cheyenne_intel.clm-cropMonthOutput - - SMS_D_Ld1_P48x1.f10_f10_mg37.I2000Clm45BgcCrop.izumi_nag.clm-oldhyd - - The first four were likely due to an order-of-operations change in CNOffsetLitterfall(), as they resolve with the patch at - https://github.com/samsrabin/CTSM/commit/c30320cbd6583bccbcc290ffe536e8500e6ec358 - - The last is resolved with an additional patch that removes all my changes to CNOffsetLitterfall()---changes which *should* only - affect new diagnostic variables: - https://github.com/samsrabin/CTSM/commit/e025f555e74584c63d50f27c4df38326fa64bc4f - -Other details -------------- -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cime - cime: cime6.0.108 -> cime6.0.125 - -Pull Requests that document the changes (include PR ids): - https://github.com/ESCOMP/CTSM/pull/1863 - -=============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index a3f748b0d0..2d1812cd13 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision From 01534b1e0eba040d1e247a15e37ba372e0ecc025 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 27 Jul 2023 14:26:38 -0600 Subject: [PATCH 1249/2067] reorder xesmf in latest --- python/conda_env_ctsm_py_latest.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/conda_env_ctsm_py_latest.txt b/python/conda_env_ctsm_py_latest.txt index 0ab4e17694..cc442503c4 100644 --- a/python/conda_env_ctsm_py_latest.txt +++ b/python/conda_env_ctsm_py_latest.txt @@ -6,9 +6,9 @@ scipy netcdf4 requests packaging +xesmf numpy>=1.23.0 xarray>=2022.3.0 -xesmf pylint>=2.8.3,<2.9.0 # Once, you move off of 2.8.3, make lint shows 2 errors, at 2.11.1 there are 2 more errors beyond that # By, 2.14.4 there are 75 errors black>=22.6.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows From 30e9189ed88a05ef9977b04cdca4074501a9aa02 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Jul 2023 14:27:59 -0600 Subject: [PATCH 1250/2067] Reverted outdated change to .gitignore. --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 3fb3c50641..ca701132a7 100644 --- a/.gitignore +++ b/.gitignore @@ -120,4 +120,3 @@ core.* *.log !run.log *.pyc Depends -ts_generate_gdds.py From 04c5da87e957f59322fa6841c7ac95cdcd61af59 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 27 Jul 2023 15:35:04 -0600 Subject: [PATCH 1251/2067] Update changelog with longer description --- doc/ChangeLog | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 001a8a270a..ec7f8303a1 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -7,8 +7,14 @@ One-line Summary: Enable prescribed crop calendars. Purpose and description of changes ---------------------------------- -This tag introduces the ability to prescribe crop sowing dates -and/or maturity requirements. +This branch enables CLM to read in externally-prescribed crop sowing dates and "cultivar" maturity requirements (growing +degree-days, GDDs). This has so far only been tested with static values, and the results indicate that yield performance is +worsened. However, this capability is required by the GGCMI phase 3 / ISIMIP3 Agriculture protocol. + +Briefly, the way this works is that an offline run is first performed with prescribed sowing dates and 364-day seasons. +Instantaneous GDD accumulation is saved daily. A Python script then cross-references those daily outputs with a map of mean sowing +dates to determine the mean accumulated GDDs in the growing season, saving the result as a file for use as prescribed maturity +requirements. Significant changes to scientifically-supported configurations -------------------------------------------------------------- From 1432e20779cddec1446714c4168e9153e285f5b7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 27 Jul 2023 18:39:07 -0600 Subject: [PATCH 1252/2067] First draft of ChangeLog/Sum --- doc/ChangeLog | 163 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 164 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ec7f8303a1..456c006300 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,167 @@ =============================================================== +Tag name: ctsm5.1.dev134 +Originator(s): Ronny Meier, slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Thu Jul 27 18:00:16 MDT 2023 +One-line Summary: Surface roughness modifications + +Purpose and description of changes +---------------------------------- + +Surface roughness (z0) modifications that appear in this publication: +https://doi.org/10.5194/gmd-15-2365-2022 + +When changing the namelist input z0param_method from ZengWang2007 (default) +to Meier2022 the following modifications are activated: + +- A new parameterization of the vegetation surface roughness based on +Raupach (1992) with optimized parameters to match the data collected in +Hu et al. (2020) for different types of vegetation. This requires several new +PFT-specific input parameters in the parameter file. +- A spatially explicit z0m input field for bare soil based on the data of +Prigent et al. (2005). This may be activated specifically by the user through +the namelist input use_z0mg_2d. This requires a new input variable in the +fsurdat file. +- The parameterization of z0m for snow based on accumulated snow melt as +proposed in Brock et al. (2006). This may be activated specifically by the +user through the namelist input use_z0m_snowmelt. +- The parameterization of Yang et al. (2008) for z0h and z0q over bare soil, +snow, and glaciers. +- The study in GMD also proposes new globally constant values for the +z0m of bare soil, snow, and ice. To "activate" those the parameter file needs +to be changed at the moment. The original and modified parameter files and +fsurdat files will be shared by ftp. + +Open issues/questions (discussed with @ekluzek, @dlawrenncar, @olyson): + +- How to incorporate the data of Prigent et al. (2005) in the surfdata +generation. I will write an email about this to Catherine Prigent. +- One statement marked in CanopyFluxesMod should probably be changed when +using Meier2022 (i.e., Yang et al. (2008) formulation should be used instead +of Zeng and Dickinson (1998)). +- At the moment one needs to change the parameter file to switch between the +original and proposed globally constant z0m values for bare soil, snow, and +ice. This is obviously not very user friendly and prone to mistakes. +- The introduction of Yang et al. (2008) frequently results in z0h and z0q +larger than z0m. This is only rarely observed in the field and in contradiction +to the theory that z0h and z0q should be smaller because heat and water vapor +need to be transported through molecular diffusion in the surface sublayer. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +#1316 +#1596 + +Notes of particular relevance for users +--------------------------------------- +Details already discussed in the description above. + + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +New tests in place for this new code. + +Testing summary: +---------------- +[... Remove before making master tag. + +Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. +However, it occasionally makes sense to do more or less system testing; +here is guidance on different available levels of system testing: + a) no system testing (for use when the only changes are ones that + have absolutely no impact on system runs; this + includes documentation-only tags, tags that + just change the tools or some python code that + does not impact system runs, etc.) + b) minimal (for use in rare cases where only a small change with + known behavior is added ... eg. a minor bug fix. This + might be to just run the "short" test list, or to run + a single test. Whatever makes sense for the particular case.) + c) python only (for use where the only changes are in the python directory: + run the python testing listed below) + d) regular (regular tests on normal machines if CTSM source is modified) + e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists + and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) + would be run as well) + +In addition, various other tests of the tools, python and perl +infrastructure should be run when appropriate, as described below. + +...] + +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + No, unless user chooses to run in non-default Meier2022 mode. + + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2045 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev131 Originator(s): samrabin (Sam Rabin,UCAR/TSS) Date: Thu Jul 27 14:24:07 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 2d1812cd13..f28b39dc22 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev134 slevis 07/27/2023 Surface roughness modifications ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml From 298c7058ac60ec92ed73560bbac5024c00faa849 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 28 Jul 2023 12:43:25 -0600 Subject: [PATCH 1253/2067] First draft of ChangeLog/Sum --- doc/ChangeLog | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 82 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ec7f8303a1..160423dc65 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,85 @@ =============================================================== +Tag name: ctsm5.1.dev135 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Fri Jul 28 12:36:24 MDT 2023 +One-line Summary: Refactor max_patch_per_col and maxsoil_patches loops + +Purpose and description of changes +---------------------------------- + +Refactor such loops for clearer and more efficient code, as recommended in +issue #2025. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +#2025 + +Notes of particular relevance for users +--------------------------------------- + +Notes of particular relevance for developers: +--------------------------------------------- + +Testing summary: +---------------- +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No + + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2056 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev131 Originator(s): samrabin (Sam Rabin,UCAR/TSS) Date: Thu Jul 27 14:24:07 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 2d1812cd13..b2a9345ba4 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev135 slevis 07/28/2023 Refactor max_patch_per_col and maxsoil_patches loops ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml From 97632977d46469948416faf30acb19c37d04bd24 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 28 Jul 2023 12:49:38 -0600 Subject: [PATCH 1254/2067] First draft of ChangeLog/Sum --- doc/ChangeLog | 113 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 114 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ec7f8303a1..ed78cea5eb 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,117 @@ =============================================================== +Tag name: ctsm5.1.dev133 +Originator(s): mvdebolskiy (NORCE, Bergen, Norway), slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Thu Jul 27 17:30:25 MDT 2023 +One-line Summary: Add parameterization to allow excess ice in soil and subsidence + +Purpose and description of changes +---------------------------------- + +As described in PR #1787: + +Parameterization for excess ice described in Lee et al. (2014): +http://dx.doi.org/10.1088/1748-9326/9/12/124006 + +This code is a modified version of code provided by Lei Cai: +https://github.com/lca041/ctsm/tree/clm5.0.dev92_exice + +Works only for the nuopc driver. + +Files changed: +bld/CLMBuildNamelist.pm, bld/namelist_files/namelist_defaults_ctsm.xml, bld/namelist_files/namelist_definitionss_ctsm.xml -- added namelist options; +src/main/clm_varctl.F90, src/main/controlMod.F90 -- added option to switch excess ice physics and read namelist option; +src/biogeophys/WaterStateType.F90 -- added prognostic excess ice variable and a history field; +src/biogeophys/WaterStateBulkType.F90, src/main/clm_instMod.F90, -- added arguments to soubrutiens for proper initialization; +src/biogeophys/TemperatureType.F90 -- initial soil temperature set to 268.15 K at the cold start (possibly redundant because #1460 is closed) +src/biogeophys/WaterDiagnosticBulkType.F90 -- added two diagnostic excess ice variables and two history fields; +src/biogeophys/SoilTemperatureMod.F90 -- added main excess ice calculations; +src/biogeophys/TotalWaterAndHeatMod.F90 -- added excess ice to total water for balance checks; +src/biogeophys/SoilHydrologyMod.F90 -- added excess ice for ice fraction calculation; + +New files: +src/cpl/share_esmf/ExcessIceStreamType.F90 -- routines to read dataset with initial excess ice concentration + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +#1229 + + +Notes of particular relevance for users +--------------------------------------- +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist options added: + - use_excess_ice (logical, in clm_inparm) default = .false.; turns on excess ice physics + - stream_meshfile_exice, stream_fldfilename_exice, stream_mapalgo_exice (char, in exice_streams) + meshfile, stream file, spatial interpolation algorithm for initial values of excess ice + defaults - lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_c20220516.nc, + lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc + and bilinear + Dataset interpolated to 0.125x0.125 degrees grid from Brown et al. (1997) can be found here: + https://drive.google.com/file/d/1mA457Oa52zG_MtLGB7KHuUYQvsS2-P5o/view?usp=sharing + Dataset used only in cold start or hybrid runs (or starting with finidat) that do not have excess ice + + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + New tests in place for this new code + +Testing summary: +---------------- +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: No + + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/1787 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev131 Originator(s): samrabin (Sam Rabin,UCAR/TSS) Date: Thu Jul 27 14:24:07 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 2d1812cd13..a1a326e65a 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev133 slevis 07/27/2023 Add parameterization to allow excess ice in soil and subsidence ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml From 01731b7137dca6de345787cc45762fc294204956 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 26 Jul 2023 16:16:33 -0600 Subject: [PATCH 1255/2067] Add N_TO_FOOD perharv and ann. --- .../testmods_dirs/clm/crop/user_nl_clm | 2 +- src/biogeochem/CNPhenologyMod.F90 | 12 ++++ src/biogeochem/CNVegNitrogenFluxType.F90 | 59 +++++++++++++++++++ 3 files changed, 72 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index dc22a973b2..d00094de3d 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -10,7 +10,7 @@ hist_fincl2 += 'DYN_COL_SOIL_ADJUSTMENTS_C' ! Annual crop variables on per-sowing/per-harvest axes, per PFT. -hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' +hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' hist_nhtfrq(3) = 17520 hist_mfilt(3) = 1 hist_type1d_pertape(3) = 'PFTS' diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c2a66511f7..f7c7b543ee 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1901,10 +1901,12 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%harvest_reason_thisyr_patch(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch(p,s,k) = 0._r8 + cnveg_nitrogenflux_inst%repr_grainn_to_food_perharv_patch(p,s,k) = 0._r8 end do end do do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch(p,k) = 0._r8 + cnveg_nitrogenflux_inst%repr_grainn_to_food_thisyr_patch(p,k) = 0._r8 end do next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,1) end if @@ -2979,6 +2981,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & real(r8) :: cropseedc_deficit_to_restore ! amount of crop seed C deficit that will be restored from this grain pool (gC/m2) real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2) real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) + real(r8) :: repr_grainn_to_food_thispool ! amount added to / subtracted from repr_grainn_to_food for the pool in question (gN/m2/s) !----------------------------------------------------------------------- associate( & @@ -3028,6 +3031,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & livestemn_to_litter => cnveg_nitrogenflux_inst%livestemn_to_litter_patch , & ! Output: [real(r8) (:) ] livestem N to litter (gN/m2/s) repr_grainn_to_food => cnveg_nitrogenflux_inst%repr_grainn_to_food_patch , & ! Output: [real(r8) (:,:) ] grain N to food (gN/m2/s) + repr_grainn_to_food_perharv => cnveg_nitrogenflux_inst%repr_grainn_to_food_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain N to food per harvest (gN/m2) + repr_grainn_to_food_thisyr => cnveg_nitrogenflux_inst%repr_grainn_to_food_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain N to food harvested this calendar year (gN/m2) repr_grainn_to_seed => cnveg_nitrogenflux_inst%repr_grainn_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain N to seed (gN/m2/s) repr_structuren_to_cropprod => cnveg_nitrogenflux_inst%repr_structuren_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure N to crop product pool (gN/m2/s) repr_structuren_to_litter => cnveg_nitrogenflux_inst%repr_structuren_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure N to litter (gN/m2/s) @@ -3105,8 +3110,15 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainc_to_food_thisyr(p,k) = repr_grainc_to_food_thisyr(p,k) & + repr_grainc_to_food_perharv(p,h,k) end if + repr_grainn_to_food_thispool = npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) repr_grainn_to_food(p,k) = t1 * reproductiven(p,k) & + npool_to_reproductiven(p,k) - repr_grainn_to_seed(p,k) + if (reproductiven(p,k) + repr_grainn_to_food_thispool * dt > 0._r8) then + repr_grainn_to_food_perharv(p,h,k) = reproductiven(p,k) & + + repr_grainn_to_food_thispool * dt + repr_grainn_to_food_thisyr(p,k) = repr_grainn_to_food_thisyr(p,k) & + + repr_grainn_to_food_perharv(p,h,k) + end if end do do k = repr_structure_min, repr_structure_max diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index c831921a0d..eb48e2539b 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -6,6 +6,7 @@ module CNVegNitrogenFluxType use clm_varpar , only : ndecomp_cascade_transitions, ndecomp_pools use clm_varpar , only : nlevdecomp_full, nlevdecomp, i_litr_min, i_litr_max use clm_varpar , only : nvegnpool + use clm_varpar , only : mxharvests use clm_varcon , only : spval, ispval, dzsoi_decomp use clm_varctl , only : use_nitrif_denitrif, use_crop use CNSharedParamsMod , only : use_fun, use_matrixcn @@ -132,6 +133,8 @@ module CNVegNitrogenFluxType ! litterfall fluxes real(r8), pointer :: livestemn_to_litter_patch (:) ! patch livestem N to litter (gN/m2/s) real(r8), pointer :: repr_grainn_to_food_patch (:,:) ! patch grain N to food for prognostic crop (gN/m2/s) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainn_to_food_perharv_patch (:,:,:) ! grain N to food for prognostic crop accumulated by harvest (gN/m2) [patch, harvest, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over each growing season, to be instantaneously at the end of each calendar year, to provide output that's easier to work with. + real(r8), pointer :: repr_grainn_to_food_thisyr_patch (:,:) ! grain N to food for prognostic crop accumulated this calendar year (gN/m2) [patch, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over an entire calendar year, to be saved instantaneously at the end of each calendar year, to provide output that's easier to work with. real(r8), pointer :: repr_structuren_to_cropprod_patch (:,:) ! patch reproductive structure N to crop product pool for prognostic crop (gN/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: repr_structuren_to_litter_patch (:,:) ! patch reproductive structure N to litter for prognostic crop (gN/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: leafn_to_biofueln_patch (:) ! patch leaf N to biofuel N (gN/m2/s) @@ -465,6 +468,8 @@ subroutine InitAllocate(this, bounds) allocate(this%npool_to_reproductiven_storage_patch(begp:endp, nrepr)); this%npool_to_reproductiven_storage_patch (:,:) = nan allocate(this%livestemn_to_litter_patch (begp:endp)) ; this%livestemn_to_litter_patch (:) = nan allocate(this%repr_grainn_to_food_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_food_patch (:,:) = nan + allocate(this%repr_grainn_to_food_perharv_patch(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_food_perharv_patch (:,:,:) = nan + allocate(this%repr_grainn_to_food_thisyr_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_food_thisyr_patch (:,:) = nan allocate(this%repr_structuren_to_cropprod_patch(begp:endp, repr_structure_min:repr_structure_max)) this%repr_structuren_to_cropprod_patch(:,:) = nan allocate(this%repr_structuren_to_litter_patch(begp:endp, repr_structure_min:repr_structure_max)) @@ -1026,6 +1031,8 @@ subroutine InitHistory(this, bounds) ptr_patch=this%fert_patch) this%repr_grainn_to_food_patch(begp:endp,:) = spval + this%repr_grainn_to_food_perharv_patch(begp:endp,:,:) = spval + this%repr_grainn_to_food_thisyr_patch(begp:endp,:) = spval this%repr_grainn_to_seed_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainn_to_food_patch(:,k) @@ -1046,6 +1053,25 @@ subroutine InitHistory(this, bounds) long_name=get_repr_longname(k)//' N to seed', & ptr_patch=data1dptr, & default='inactive') + data2dptr => this%repr_grainn_to_food_perharv_patch(:,:,k) + call hist_addfld2d ( & + ! e.g., GRAINN_TO_FOOD_PERHARV + fname=get_repr_hist_fname(k)//'N_TO_FOOD_PERHARV', & + units='gN/m^2', & + type2d='mxharvests', & + avgflag='I', & + long_name=get_repr_longname(k)//' N to food per harvest; should only be output annually', & + ptr_patch=data2dptr, & + default='inactive') + data1dptr => this%repr_grainn_to_food_thisyr_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINN_TO_FOOD_ANN + fname=get_repr_hist_fname(k)//'N_TO_FOOD_ANN', & + units='gN/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' N to food harvested per calendar year; should only be output annually', & + ptr_patch=data1dptr, & + default='inactive') end do end if @@ -1446,6 +1472,7 @@ subroutine Restart (this, bounds, ncid, flag ) logical :: readvar ! determine if variable is on initial file character(len=256) :: varname real(r8), pointer :: data1dptr(:) ! temp. pointer for slicing larger arrays + real(r8), pointer :: data2dptr(:,:) ! temp. pointer for slicing larger arrays !------------------------------------------------------------------------ if (use_crop) then @@ -1472,6 +1499,38 @@ subroutine Restart (this, bounds, ncid, flag ) units='gN/m2/s', & interpinic_flag='interp', readvar=readvar, data=data1dptr) end do + + ! Read or write variable(s) with mxharvests dimension + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() + if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then + do k = repr_grain_min, repr_grain_max + data2dptr => this%repr_grainn_to_food_perharv_patch(:,:,k) + ! e.g., grainn_to_food_perharv + varname = get_repr_rest_fname(k)//'n_to_food_perharv' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + dim2name='mxharvests', & + switchdim=.true., & + long_name=get_repr_longname(k)//' N to food per harvest; should only be output annually', & + units='gN/m2', & + readvar=readvar, & + scale_by_thickness=.false., & + interpinic_flag='interp', data=data2dptr) + end do + end if + + do k = repr_grain_min, repr_grain_max + data1dptr => this%repr_grainn_to_food_thisyr_patch(:,k) + ! e.g., grainn_to_food_thisyr + varname = get_repr_rest_fname(k)//'n_to_food_thisyr' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' N to food per calendar year; should only be output annually', & + units='gN/m2', & + interpinic_flag='interp', readvar=readvar, data=data1dptr) + end do end if if (use_crop) then From c5590d6d032dba89031e627bbf4bd43e42bf8d45 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 14:04:55 -0600 Subject: [PATCH 1256/2067] regrid shdates: Set up template file within regrid_ggcmi_shdates.py rather than using nco. --- .../crop_calendars/regrid_ggcmi_shdates.py | 42 +++++++++++++------ 1 file changed, 30 insertions(+), 12 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 85e9ddeb4d..20bda4878d 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -4,6 +4,8 @@ import glob import argparse import sys +import xarray as xr +import numpy as np def run_and_check(cmd): @@ -52,21 +54,37 @@ def main( os.makedirs(regrid_output_directory) templatefile = os.path.join(regrid_output_directory, "template.nc") - - # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. - regrid_template_file = os.path.join( - regrid_output_directory, - os.path.basename(regrid_template_file_in), - ) - shutil.copyfile(regrid_template_file_in, regrid_template_file) - if os.path.exists(templatefile): os.remove(templatefile) + + template_ds_in = xr.open_dataset(regrid_template_file_in) + def import_1d(ds, varname): + da = ds[varname] + if len(da.dims) != 1: + raise RuntimeError(f"Expected 1 dimension for {varname}; found {len(da.dims)}: {da.dims}") + return da, len(da) + if "lat" in template_ds_in: + lat, Nlat = import_1d(template_ds_in, "lat") + else: + raise RuntimeError("No latitude variable found in regrid template file") + if "lon" in template_ds_in: + lon, Nlon = import_1d(template_ds_in, "lon") + else: + raise RuntimeError("No longitude variable found in regrid template file") + template_da_out = xr.DataArray( + data = np.full((Nlat, Nlon), 0.0), + dims = {"lat": lat, "lon": lon}, + name = "area", + ) + template_ds_out = xr.Dataset( + data_vars = {"planting_day": template_da_out, + "maturity_day": template_da_out, + "growing_season_length": template_da_out,}, + coords = {"lat": lat, "lon": lon}, + ) + template_ds_out.to_netcdf(templatefile, mode="w") + - for v in ["planting_day", "maturity_day", "growing_season_length"]: - run_and_check(f"ncks -A -v area '{regrid_template_file}' '{templatefile}'") - run_and_check(f"ncrename -v area,{v} '{templatefile}'") - os.remove(regrid_template_file) run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") input_files = glob.glob("*nc4") From 33b5eefa8dfc953f49d92e199af7ebdd3ee27d15 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 14:09:15 -0600 Subject: [PATCH 1257/2067] regrid shdates: Flip latitude with xarray instead of ncpdq. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 20bda4878d..18cfbdb233 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -67,6 +67,10 @@ def import_1d(ds, varname): lat, Nlat = import_1d(template_ds_in, "lat") else: raise RuntimeError("No latitude variable found in regrid template file") + # Flip latitude, if needed + if lat.values[0] < lat.values[1]: + lat = lat.reindex(lat=list(reversed(lat["lat"]))) + if "lon" in template_ds_in: lon, Nlon = import_1d(template_ds_in, "lon") else: @@ -84,9 +88,6 @@ def import_1d(ds, varname): ) template_ds_out.to_netcdf(templatefile, mode="w") - - run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") - input_files = glob.glob("*nc4") input_files.sort() for f in input_files: From 1e279853706dc60df411418b8204569c402733c2 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 28 Jul 2023 15:24:44 -0600 Subject: [PATCH 1258/2067] address comments --- Externals_CLM.cfg | 2 +- src/utils/clmfates_paraminterfaceMod.F90 | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index c3d00db726..3325f37d7f 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.66.1_api.25.5.0 +tag = sci.1.67.0_api.25.5.0 required = True [externals_description] diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90 index 1bdc8a9dc4..b1b0e5aef6 100644 --- a/src/utils/clmfates_paraminterfaceMod.F90 +++ b/src/utils/clmfates_paraminterfaceMod.F90 @@ -48,7 +48,7 @@ subroutine FatesReadParameters() call FatesRegisterParams(fates_params) !EDParamsMod, only operates on fates_params class call SpitFireRegisterParams(fates_params) !SpitFire Mod, only operates of fates_params class call PRTRegisterParams(fates_params) ! PRT mod, only operates on fates_params class - call FatesSynchronizedParamsInst%RegisterParams(fates_params) !Synchronized params calss in Synchronized params mod, only operates on fates_params class + call FatesSynchronizedParamsInst%RegisterParams(fates_params) !Synchronized params class in Synchronized params mod, only operates on fates_params class is_host_file = .false. ! actually inside this module From 7afc5ffb684272fc5a87f047fa939553976bc296 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 28 Jul 2023 15:40:49 -0600 Subject: [PATCH 1259/2067] remove comment --- src/utils/clmfates_paraminterfaceMod.F90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90 index b1b0e5aef6..dedd8629cc 100644 --- a/src/utils/clmfates_paraminterfaceMod.F90 +++ b/src/utils/clmfates_paraminterfaceMod.F90 @@ -51,8 +51,6 @@ subroutine FatesReadParameters() call FatesSynchronizedParamsInst%RegisterParams(fates_params) !Synchronized params class in Synchronized params mod, only operates on fates_params class is_host_file = .false. - ! actually inside this module - !uses ncdio_pio module (should be a library) call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params) is_host_file = .true. From 1c2b19c0641d7b937180e02b14336a0d7c48b2c4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:23:35 -0600 Subject: [PATCH 1260/2067] regrid shdates: Now works with surface dataset as template file. --- .../crop_calendars/regrid_ggcmi_shdates.py | 30 ++++++++++++++++--- 1 file changed, 26 insertions(+), 4 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 18cfbdb233..b90f62525b 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -58,21 +58,43 @@ def main( os.remove(templatefile) template_ds_in = xr.open_dataset(regrid_template_file_in) - def import_1d(ds, varname): - da = ds[varname] + def import_1d(ds, coordName): + da = ds[coordName] if len(da.dims) != 1: - raise RuntimeError(f"Expected 1 dimension for {varname}; found {len(da.dims)}: {da.dims}") + raise RuntimeError(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") + return da, len(da) + def import_2d(ds, coordName, varName): + da = ds[varName] + thisDim = [x for x in da.dims if coordName in x] + if len(thisDim) != 1: + raise RuntimeError(f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}") + thisDim = thisDim[0] + otherDim = [x for x in da.dims if coordName not in x] + if len(otherDim) != 1: + raise RuntimeError(f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}") + otherDim = otherDim[0] + da = da.astype(np.float32) + da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) + da = da.assign_coords({coordName: da.values}) + da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] + da.attrs["units"] = da.attrs["units"].replace(" ","_") return da, len(da) if "lat" in template_ds_in: lat, Nlat = import_1d(template_ds_in, "lat") + elif "LATIXY" in template_ds_in: + lat, Nlat = import_2d(template_ds_in, "lat", "LATIXY") + lat.attrs["axis"] = "Y" else: raise RuntimeError("No latitude variable found in regrid template file") # Flip latitude, if needed if lat.values[0] < lat.values[1]: lat = lat.reindex(lat=list(reversed(lat["lat"]))) - + if "lon" in template_ds_in: lon, Nlon = import_1d(template_ds_in, "lon") + elif "LONGXY" in template_ds_in: + lon, Nlon = import_2d(template_ds_in, "lon", "LONGXY") + lon.attrs["axis"] = "Y" else: raise RuntimeError("No longitude variable found in regrid template file") template_da_out = xr.DataArray( From 62ac2fff51d67b100a118be5edbc7569e66f3fd3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:25:59 -0600 Subject: [PATCH 1261/2067] regrid shdates: Move and rename coord import functions. --- .../crop_calendars/regrid_ggcmi_shdates.py | 57 +++++++++++-------- 1 file changed, 32 insertions(+), 25 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index b90f62525b..44ded09578 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -41,6 +41,33 @@ def define_arguments(parser): return parser +# lat or lon +def import_coord_1d(ds, coordName): + da = ds[coordName] + if len(da.dims) != 1: + raise RuntimeError(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") + return da, len(da) + + +# LATIXY or LONGXY +def import_coord_2d(ds, coordName, varName): + da = ds[varName] + thisDim = [x for x in da.dims if coordName in x] + if len(thisDim) != 1: + raise RuntimeError(f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}") + thisDim = thisDim[0] + otherDim = [x for x in da.dims if coordName not in x] + if len(otherDim) != 1: + raise RuntimeError(f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}") + otherDim = otherDim[0] + da = da.astype(np.float32) + da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) + da = da.assign_coords({coordName: da.values}) + da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] + da.attrs["units"] = da.attrs["units"].replace(" ","_") + return da, len(da) + + def main( regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory ): @@ -58,31 +85,11 @@ def main( os.remove(templatefile) template_ds_in = xr.open_dataset(regrid_template_file_in) - def import_1d(ds, coordName): - da = ds[coordName] - if len(da.dims) != 1: - raise RuntimeError(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") - return da, len(da) - def import_2d(ds, coordName, varName): - da = ds[varName] - thisDim = [x for x in da.dims if coordName in x] - if len(thisDim) != 1: - raise RuntimeError(f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}") - thisDim = thisDim[0] - otherDim = [x for x in da.dims if coordName not in x] - if len(otherDim) != 1: - raise RuntimeError(f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}") - otherDim = otherDim[0] - da = da.astype(np.float32) - da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) - da = da.assign_coords({coordName: da.values}) - da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] - da.attrs["units"] = da.attrs["units"].replace(" ","_") - return da, len(da) + if "lat" in template_ds_in: - lat, Nlat = import_1d(template_ds_in, "lat") + lat, Nlat = import_coord_1d(template_ds_in, "lat") elif "LATIXY" in template_ds_in: - lat, Nlat = import_2d(template_ds_in, "lat", "LATIXY") + lat, Nlat = import_coord_2d(template_ds_in, "lat", "LATIXY") lat.attrs["axis"] = "Y" else: raise RuntimeError("No latitude variable found in regrid template file") @@ -91,9 +98,9 @@ def import_2d(ds, coordName, varName): lat = lat.reindex(lat=list(reversed(lat["lat"]))) if "lon" in template_ds_in: - lon, Nlon = import_1d(template_ds_in, "lon") + lon, Nlon = import_coord_1d(template_ds_in, "lon") elif "LONGXY" in template_ds_in: - lon, Nlon = import_2d(template_ds_in, "lon", "LONGXY") + lon, Nlon = import_coord_2d(template_ds_in, "lon", "LONGXY") lon.attrs["axis"] = "Y" else: raise RuntimeError("No longitude variable found in regrid template file") From 63571ee5e6bfe4305dd455f561a251120acb735e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:29:13 -0600 Subject: [PATCH 1262/2067] regrid shdates: Improved comments and descriptions. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 44ded09578..669e05d6b7 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -34,7 +34,7 @@ def define_arguments(parser): parser.add_argument( "-rt", "--regrid-template-file", - help="Template file to be used in regridding of inputs.", + help="Template netCDF file to be used in regridding of inputs. This can be a CLM output file (i.e., something with 1-d lat and lon variables) or a CLM surface dataset (i.e., something with 2-d LATIXY and LONGXY variables).", type=str, required=True, ) @@ -86,6 +86,7 @@ def main( template_ds_in = xr.open_dataset(regrid_template_file_in) + # Import and format latitude if "lat" in template_ds_in: lat, Nlat = import_coord_1d(template_ds_in, "lat") elif "LATIXY" in template_ds_in: @@ -93,10 +94,12 @@ def main( lat.attrs["axis"] = "Y" else: raise RuntimeError("No latitude variable found in regrid template file") + # Flip latitude, if needed if lat.values[0] < lat.values[1]: lat = lat.reindex(lat=list(reversed(lat["lat"]))) + # Import and format longitude if "lon" in template_ds_in: lon, Nlon = import_coord_1d(template_ds_in, "lon") elif "LONGXY" in template_ds_in: @@ -109,6 +112,8 @@ def main( dims = {"lat": lat, "lon": lon}, name = "area", ) + + # Save template Dataset for use by cdo template_ds_out = xr.Dataset( data_vars = {"planting_day": template_da_out, "maturity_day": template_da_out, @@ -117,6 +122,7 @@ def main( ) template_ds_out.to_netcdf(templatefile, mode="w") + # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor input_files = glob.glob("*nc4") input_files.sort() for f in input_files: @@ -139,6 +145,7 @@ def main( except: run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + # Delete template file, which is no longer needed os.remove(templatefile) From fa33f116d9effb297a36e35eca57cb57baf85091 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:29:29 -0600 Subject: [PATCH 1263/2067] regrid shdates: No need to check nco utilities anymore. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 669e05d6b7..926c6cc147 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -72,8 +72,8 @@ def main( regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory ): - # Ensure we can call necessary shell scripts - for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: + # Ensure we can call necessary shell script(s) + for cmd in ["cdo"]: run_and_check(f"{cmd} --help") os.chdir(regrid_input_directory) From 250bf72b8b79912da86a489fd1058cce5ea287b6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:45:54 -0600 Subject: [PATCH 1264/2067] process shdates: Append regrid resolution to input filename. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b2ffcfe1f8..b8af997e37 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -212,7 +212,7 @@ def set_var_dict(name_ggcmi, outfile): ) file_ggcmi = os.path.join( - regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}.nc4" + regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}_nninterp-{regrid_resolution}.nc4" ) if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) From 313c01d6e77362505d8d490519078e1add81ad0b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:47:18 -0600 Subject: [PATCH 1265/2067] regrid shdates: Improved messaging. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 926c6cc147..cad8650506 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -71,6 +71,7 @@ def import_coord_2d(ds, coordName, varName): def main( regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory ): + print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") # Ensure we can call necessary shell script(s) for cmd in ["cdo"]: @@ -126,7 +127,7 @@ def main( input_files = glob.glob("*nc4") input_files.sort() for f in input_files: - print(f[0:6]) + print(" " + f[0:6]) f2 = os.path.join(regrid_output_directory, f) f3 = f2.replace(".nc4", f"_nninterp-{regrid_resolution}.nc4") From 8ea2ed13ece0fd6152b2e090f62cec4145efc164 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 16:56:14 -0600 Subject: [PATCH 1266/2067] process shdates: Include regrid resolution in output filename. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b8af997e37..b1af9439df 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -170,9 +170,10 @@ def set_var_dict(name_ggcmi, outfile): # Create output files datetime_string = dt.datetime.now().strftime("%Y%m%d_%H%M%S") + nninterp_suffix = "nninterp-" + regrid_resolution for v in variable_dict: outfile = os.path.join( - output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc" + output_directory, f"{v}s_{file_specifier}_{nninterp_suffix}.{first_year}-{last_year}.{datetime_string}.nc" ) variable_dict[v]["outfile"] = outfile template_ds.to_netcdf( @@ -212,7 +213,7 @@ def set_var_dict(name_ggcmi, outfile): ) file_ggcmi = os.path.join( - regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}_nninterp-{regrid_resolution}.nc4" + regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4" ) if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) From 582c848b99c14f294de5e5310ad3c71873ab8285 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 17:07:00 -0600 Subject: [PATCH 1267/2067] process/regrid shdates: Removed import of unused shutil. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 1 - python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 1 - 2 files changed, 2 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b1af9439df..0d8a708eb4 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -1,6 +1,5 @@ import numpy as np import xarray as xr -import shutil import os import datetime as dt import cftime diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index cad8650506..bb2677ee55 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -1,6 +1,5 @@ from subprocess import run import os -import shutil import glob import argparse import sys From de43fd1ae048226c2d2f682386ac8579982bc47f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 18:15:16 -0600 Subject: [PATCH 1268/2067] make_fsurdat_all_crops_everywhere.py: Improve efficiency. Only write the variables we need to change, instead of the entire dataset. --- .../make_fsurdat_all_crops_everywhere.py | 24 ++++++++++++------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py index f8c5e8b316..68c6666df7 100755 --- a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py +++ b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py @@ -2,28 +2,36 @@ import xarray as xr import sys import argparse +import shutil def main(file_in, file_out): - # Import + # Import in_ds = xr.open_dataset(file_in) - out_ds = in_ds.copy() + pct_crop_da = in_ds["PCT_CROP"] + pct_natveg_da = in_ds["PCT_NATVEG"] + pct_cft_da_in = in_ds["PCT_CFT"] in_ds.close() # Move all natural land into crop - out_ds["PCT_CROP"] += in_ds["PCT_NATVEG"] - out_ds["PCT_NATVEG"] -= in_ds["PCT_NATVEG"] + pct_crop_da += pct_natveg_da + pct_natveg_da -= pct_natveg_da # Put some of every crop in every gridcell - pct_cft = np.full_like(in_ds["PCT_CFT"].values, 100 / in_ds.dims["cft"]) - out_ds["PCT_CFT"] = xr.DataArray( - data=pct_cft, attrs=in_ds["PCT_CFT"].attrs, dims=in_ds["PCT_CFT"].dims + pct_cft = np.full_like(pct_cft_da_in.values, 100 / in_ds.dims["cft"]) + pct_cft_da = xr.DataArray( + data=pct_cft, attrs=pct_cft_da_in.attrs, dims=pct_cft_da_in.dims, name="PCT_CFT", ) # Save - out_ds.to_netcdf(file_out, format="NETCDF3_64BIT") + shutil.copyfile(file_in, file_out) + format = "NETCDF3_64BIT" + mode = "a" # Use existing file but overwrite existing variables + pct_crop_da.to_netcdf(file_out, format=format, mode=mode) + pct_natveg_da.to_netcdf(file_out, format=format, mode=mode) + pct_cft_da.to_netcdf(file_out, format=format, mode=mode) if __name__ == "__main__": From 2428d768c066e32d431c92caeecc8ad01e066ffa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 28 Jul 2023 18:19:45 -0600 Subject: [PATCH 1269/2067] make_fsurdat_all_crops_everywhere.py: Automatic naming of output file to reflect input file. --- cime_config/SystemTests/rxcropmaturity.py | 6 +++-- .../make_fsurdat_all_crops_everywhere.py | 22 +++++++++++++++---- 2 files changed, 22 insertions(+), 6 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 4fd812b84a..2687afca6b 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -255,7 +255,9 @@ def _run_make_fsurdat_all_crops_everywhere(self): raise RuntimeError(error_message) # Where we will save the fsurdat version for this test - self._fsurdat_out = os.path.join(self._path_gddgen, "fsurdat.nc") + path, ext = os.path.splitext(self._fsurdat_in) + dir_in, filename_in_noext = os.path.split(path) + self._fsurdat_out = os.path.join(self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}") # Make fsurdat for this test, if not already done if not os.path.exists(self._fsurdat_out): @@ -267,7 +269,7 @@ def _run_make_fsurdat_all_crops_everywhere(self): "make_fsurdat_all_crops_everywhere.py", ) command = ( - f"python3 {tool_path} " + f"-i {self._fsurdat_in} " + f"-o {self._fsurdat_out}" + f"python3 {tool_path} " + f"-i {self._fsurdat_in} " + f"-o {self._path_gddgen}" ) stu.run_python_script( self._get_caseroot(), diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py index 68c6666df7..5378c8ae51 100755 --- a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py +++ b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py @@ -3,11 +3,22 @@ import sys import argparse import shutil +import os -def main(file_in, file_out): +def main(file_in, dir_out): + + # Checks and setup + if not os.path.exists(dir_out): + os.makedirs(dir_out) + if not os.path.isdir(args.output_dir): + raise RuntimeError("-o/--output-dir needs to be a directory") + path, ext = os.path.splitext(file_in) + dir_in, filename_in_noext = os.path.split(path) + file_out = os.path.join(dir_out, f"{filename_in_noext}.all_crops_everywhere{ext}") # Import + print(f"Importing {file_in}...") in_ds = xr.open_dataset(file_in) pct_crop_da = in_ds["PCT_CROP"] @@ -26,6 +37,7 @@ def main(file_in, file_out): ) # Save + print(f"Saving to {file_out}") shutil.copyfile(file_in, file_out) format = "NETCDF3_64BIT" mode = "a" # Use existing file but overwrite existing variables @@ -51,13 +63,15 @@ def main(file_in, file_out): ) parser.add_argument( "-o", - "--output-file", - help="Where to save the new surface dataset file", + "--output-dir", + help="Directory in which to save the new surface dataset file", required=True, ) # Get arguments args = parser.parse_args(sys.argv[1:]) + # Check arguments + # Process - main(args.input_file, args.output_file) + main(args.input_file, args.output_dir) From d85be768a5f2565d8ecbaf6588ea28d08d0cde9a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 31 Jul 2023 18:02:17 -0600 Subject: [PATCH 1270/2067] Change another intent(out) to intent(inout) to prevent NaNs in nag tests --- src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 | 1 - src/biogeophys/PhotosynthesisMod.F90 | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 index e7c16f15c7..6f8632658d 100644 --- a/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 +++ b/src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 @@ -1365,7 +1365,6 @@ subroutine calc_plant_nitrogen_demand(this, bounds, & frootn => cnveg_nitrogenstate_inst%frootn_patch , & ! Input: [real(r8) (:) ] (gN/m2) fine root N livestemn_to_retransn => cnveg_nitrogenflux_inst%livestemn_to_retransn_patch,& ! Output: [real(r8) (:) ] sminn_vr => soilbiogeochem_nitrogenstate_inst%sminn_vr_col , & ! Input: [real(r8) (:,:) ] (gN/m3) soil mineral N - btran => energyflux_inst%btran_patch , & ! Input: [real(r8) (:) ] transpiration wetness factor (0 to 1) t_scalar => soilbiogeochem_carbonflux_inst%t_scalar_col & ! Input: [real(r8) (:,:) ] soil temperature scalar for decomp ) diff --git a/src/biogeophys/PhotosynthesisMod.F90 b/src/biogeophys/PhotosynthesisMod.F90 index 6207e40700..0d14909fbf 100644 --- a/src/biogeophys/PhotosynthesisMod.F90 +++ b/src/biogeophys/PhotosynthesisMod.F90 @@ -2723,7 +2723,7 @@ subroutine PhotosynthesisHydraulicStress ( bounds, fn, filterp, & real(r8) , intent(in) :: leafn( bounds%begp: ) ! leaf N (gN/m2) real(r8) , intent(out) :: bsun( bounds%begp: ) ! sunlit canopy transpiration wetness factor (0 to 1) real(r8) , intent(out) :: bsha( bounds%begp: ) ! shaded canopy transpiration wetness factor (0 to 1) - real(r8) , intent(out) :: btran( bounds%begp: ) ! transpiration wetness factor (0 to 1) [pft] + real(r8) , intent(inout) :: btran( bounds%begp: ) ! transpiration wetness factor (0 to 1) [pft] real(r8) , intent(in) :: froot_carbon( bounds%begp: ) ! fine root carbon (gC/m2) [pft] real(r8) , intent(in) :: croot_carbon( bounds%begp: ) ! live coarse root carbon (gC/m2) [pft] From c8bd4c6f98c0b411391b4355da449507db3aab4e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 1 Aug 2023 13:17:01 -0600 Subject: [PATCH 1271/2067] Reformatting with black. --- .../crop_calendars/process_ggcmi_shdates.py | 6 ++-- .../crop_calendars/regrid_ggcmi_shdates.py | 34 +++++++++++-------- 2 files changed, 24 insertions(+), 16 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 0d8a708eb4..30ab006ab4 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -172,7 +172,8 @@ def set_var_dict(name_ggcmi, outfile): nninterp_suffix = "nninterp-" + regrid_resolution for v in variable_dict: outfile = os.path.join( - output_directory, f"{v}s_{file_specifier}_{nninterp_suffix}.{first_year}-{last_year}.{datetime_string}.nc" + output_directory, + f"{v}s_{file_specifier}_{nninterp_suffix}.{first_year}-{last_year}.{datetime_string}.nc", ) variable_dict[v]["outfile"] = outfile template_ds.to_netcdf( @@ -212,7 +213,8 @@ def set_var_dict(name_ggcmi, outfile): ) file_ggcmi = os.path.join( - regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4" + regridded_ggcmi_files_dir, + f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4", ) if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index bb2677ee55..2715131c84 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -53,17 +53,21 @@ def import_coord_2d(ds, coordName, varName): da = ds[varName] thisDim = [x for x in da.dims if coordName in x] if len(thisDim) != 1: - raise RuntimeError(f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}") + raise RuntimeError( + f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}" + ) thisDim = thisDim[0] otherDim = [x for x in da.dims if coordName not in x] if len(otherDim) != 1: - raise RuntimeError(f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}") + raise RuntimeError( + f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" + ) otherDim = otherDim[0] da = da.astype(np.float32) da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) da = da.assign_coords({coordName: da.values}) da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] - da.attrs["units"] = da.attrs["units"].replace(" ","_") + da.attrs["units"] = da.attrs["units"].replace(" ", "_") return da, len(da) @@ -83,7 +87,7 @@ def main( templatefile = os.path.join(regrid_output_directory, "template.nc") if os.path.exists(templatefile): os.remove(templatefile) - + template_ds_in = xr.open_dataset(regrid_template_file_in) # Import and format latitude @@ -94,7 +98,7 @@ def main( lat.attrs["axis"] = "Y" else: raise RuntimeError("No latitude variable found in regrid template file") - + # Flip latitude, if needed if lat.values[0] < lat.values[1]: lat = lat.reindex(lat=list(reversed(lat["lat"]))) @@ -108,20 +112,22 @@ def main( else: raise RuntimeError("No longitude variable found in regrid template file") template_da_out = xr.DataArray( - data = np.full((Nlat, Nlon), 0.0), - dims = {"lat": lat, "lon": lon}, - name = "area", + data=np.full((Nlat, Nlon), 0.0), + dims={"lat": lat, "lon": lon}, + name="area", ) - + # Save template Dataset for use by cdo template_ds_out = xr.Dataset( - data_vars = {"planting_day": template_da_out, - "maturity_day": template_da_out, - "growing_season_length": template_da_out,}, - coords = {"lat": lat, "lon": lon}, + data_vars={ + "planting_day": template_da_out, + "maturity_day": template_da_out, + "growing_season_length": template_da_out, + }, + coords={"lat": lat, "lon": lon}, ) template_ds_out.to_netcdf(templatefile, mode="w") - + # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor input_files = glob.glob("*nc4") input_files.sort() From f7b543d41a10d89a66b930e918ee823e2c7880f1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 1 Aug 2023 13:17:44 -0600 Subject: [PATCH 1272/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index c00226b7dd..25729debde 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -10,5 +10,6 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb +c8bd4c6f98c0b411391b4355da449507db3aab4e # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c From 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 1 Aug 2023 13:19:05 -0600 Subject: [PATCH 1273/2067] Reformatting with black. --- .../crop_calendars/make_fsurdat_all_crops_everywhere.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py index 5378c8ae51..441d9180fc 100755 --- a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py +++ b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py @@ -33,14 +33,17 @@ def main(file_in, dir_out): # Put some of every crop in every gridcell pct_cft = np.full_like(pct_cft_da_in.values, 100 / in_ds.dims["cft"]) pct_cft_da = xr.DataArray( - data=pct_cft, attrs=pct_cft_da_in.attrs, dims=pct_cft_da_in.dims, name="PCT_CFT", + data=pct_cft, + attrs=pct_cft_da_in.attrs, + dims=pct_cft_da_in.dims, + name="PCT_CFT", ) # Save print(f"Saving to {file_out}") shutil.copyfile(file_in, file_out) format = "NETCDF3_64BIT" - mode = "a" # Use existing file but overwrite existing variables + mode = "a" # Use existing file but overwrite existing variables pct_crop_da.to_netcdf(file_out, format=format, mode=mode) pct_natveg_da.to_netcdf(file_out, format=format, mode=mode) pct_cft_da.to_netcdf(file_out, format=format, mode=mode) From e8035015e1afa5144fe19121cb6fdbb6545b4d73 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 1 Aug 2023 13:19:35 -0600 Subject: [PATCH 1274/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index c00226b7dd..25513ae910 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -10,5 +10,6 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb +0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c From 10289ad00de1fdd9bcdaea948f40abe715b188ee Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 14:23:06 -0600 Subject: [PATCH 1275/2067] Added evenly_split_cropland option to fsurdat_modifier.py. This could also be accomplished by using dom_pft to specify an equal value for all crop PFTs. However, this method is more robust to user error (we don't have to rely on the user correctly writing out a long string of numbers) and code updates (if more crop PFTs are added). --- .../modify_input_files/fsurdat_modifier.py | 25 ++++++++++++++++- .../ctsm/modify_input_files/modify_fsurdat.py | 12 ++++++++ .../site_and_regional/single_point_case.py | 1 + python/ctsm/subset_data.py | 1 + python/ctsm/test/test_unit_singlept_data.py | 9 ++++++ .../test/test_unit_singlept_data_surfdata.py | 28 +++++++++++++++++++ .../modify_fsurdat_template.cfg | 6 +++- 7 files changed, 80 insertions(+), 2 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index 492fa74230..e8a75bfb4c 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -237,6 +237,7 @@ def modify_optional( std_elev, soil_color, dom_pft, + evenly_split_cropland, lai, sai, hgt_top, @@ -281,6 +282,10 @@ def modify_optional( ) logger.info("dom_pft complete") + if evenly_split_cropland: + modify_fsurdat.evenly_split_cropland() + logger.info("evenly_split_cropland complete") + def read_cfg_optional_basic_opts(modify_fsurdat, config, cfg_path, section): """Read the optional parts of the main section of the config file. @@ -429,10 +434,26 @@ def read_cfg_option_control( logger.info("dom_pft option is on and = %s", str(dom_pft)) else: logger.info("dom_pft option is off") + evenly_split_cropland = get_config_value( + config=config, + section=section, + item="evenly_split_cropland", + file_path=cfg_path, + convert_to_type=bool, + ) + if evenly_split_cropland and dom_pft: + abort("dom_pft must be UNSET if evenly_split_cropland is True; pick one or the other") if process_subgrid and idealized: abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") - return (idealized, process_subgrid, process_var_list, include_nonveg, dom_pft) + return ( + idealized, + process_subgrid, + process_var_list, + include_nonveg, + dom_pft, + evenly_split_cropland, + ) def read_cfg_required_basic_opts(config, section, cfg_path): @@ -555,6 +576,7 @@ def fsurdat_modifier(parser): process_var_list, include_nonveg, dom_pft, + evenly_split_cropland, ) = read_cfg_option_control( modify_fsurdat, config, @@ -584,6 +606,7 @@ def fsurdat_modifier(parser): std_elev, soil_color, dom_pft, + evenly_split_cropland, lai, sai, hgt_top, diff --git a/python/ctsm/modify_input_files/modify_fsurdat.py b/python/ctsm/modify_input_files/modify_fsurdat.py index 9b3760e303..53f06d7dc8 100644 --- a/python/ctsm/modify_input_files/modify_fsurdat.py +++ b/python/ctsm/modify_input_files/modify_fsurdat.py @@ -165,6 +165,18 @@ def write_output(self, fsurdat_in, fsurdat_out): logger.info("Successfully created fsurdat_out: %s", fsurdat_out) self.file.close() + def evenly_split_cropland(self): + """ + Description + ----------- + In rectangle selected by user (or default -90 to 90 and 0 to 360), + replace fsurdat file's PCT_CFT with equal values for all crop types. + """ + pct_cft = np.full_like(self.file["PCT_CFT"].values, 100 / self.file.dims["cft"]) + self.file["PCT_CFT"] = xr.DataArray( + data=pct_cft, attrs=self.file["PCT_CFT"].attrs, dims=self.file["PCT_CFT"].dims + ) + def set_dom_pft(self, dom_pft, lai, sai, hgt_top, hgt_bot): """ Description diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 96544ff9c1..904b240c77 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -105,6 +105,7 @@ def __init__( create_datm, create_user_mods, dom_pft, + evenly_split_cropland, pct_pft, num_pft, include_nonveg, diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index 4a3a5801f1..a99d42cc14 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -551,6 +551,7 @@ def subset_point(args, file_dict: dict): create_datm=args.create_datm, create_user_mods=args.create_user_mods, dom_pft=args.dom_pft, + evenly_split_cropland=args.evenly_split_cropland, pct_pft=args.pct_pft, num_pft=num_pft, include_nonveg=args.include_nonveg, diff --git a/python/ctsm/test/test_unit_singlept_data.py b/python/ctsm/test/test_unit_singlept_data.py index 570207fa26..06278a38e7 100755 --- a/python/ctsm/test/test_unit_singlept_data.py +++ b/python/ctsm/test/test_unit_singlept_data.py @@ -84,6 +84,7 @@ def test_create_tag_name(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -111,6 +112,7 @@ def test_check_dom_pft_too_big(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -138,6 +140,7 @@ def test_check_dom_pft_too_small(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -165,6 +168,7 @@ def test_check_dom_pft_numpft(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -193,6 +197,7 @@ def test_check_dom_pft_mixed_range(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -223,6 +228,7 @@ def test_check_nonveg_nodompft(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -254,6 +260,7 @@ def test_check_pct_pft_notsamenumbers(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -284,6 +291,7 @@ def test_check_pct_pft_sum_not1(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -314,6 +322,7 @@ def test_check_pct_pft_fraction_topct(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, diff --git a/python/ctsm/test/test_unit_singlept_data_surfdata.py b/python/ctsm/test/test_unit_singlept_data_surfdata.py index 9623975452..f1b51f689e 100755 --- a/python/ctsm/test/test_unit_singlept_data_surfdata.py +++ b/python/ctsm/test/test_unit_singlept_data_surfdata.py @@ -155,6 +155,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_pctnatpft(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -187,6 +188,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_pctnatveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -215,6 +217,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_pctcrop(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -243,6 +246,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_glacier(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -272,6 +276,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_wetland(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -301,6 +306,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_lake(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -330,6 +336,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_unisnow(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -360,6 +367,7 @@ def test_modify_surfdata_atpoint_nocrop_1pft_capsat(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -390,6 +398,7 @@ def test_modify_surfdata_atpoint_nocrop_multipft(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -426,6 +435,7 @@ def test_modify_surfdata_atpoint_nocrop_urban_nononveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -460,6 +470,7 @@ def test_modify_surfdata_atpoint_nocrop_urban_include_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -497,6 +508,7 @@ def test_modify_surfdata_atpoint_nocrop_wetland_include_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -527,6 +539,7 @@ def test_modify_surfdata_atpoint_nocrop_nopft_zero_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -560,6 +573,7 @@ def test_modify_surfdata_atpoint_nocrop_nopft_include_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -705,6 +719,7 @@ def test_modify_surfdata_atpoint_crop_1pft_pctnatpft(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -737,6 +752,7 @@ def test_modify_surfdata_atpoint_crop_1pft_pctnatveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -765,6 +781,7 @@ def test_modify_surfdata_atpoint_crop_1pft_pctcrop(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -793,6 +810,7 @@ def test_modify_surfdata_atpoint_crop_1pft_glacier(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -822,6 +840,7 @@ def test_modify_surfdata_atpoint_crop_1pft_wetland(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -851,6 +870,7 @@ def test_modify_surfdata_atpoint_crop_1pft_lake(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -880,6 +900,7 @@ def test_modify_surfdata_atpoint_crop_1pft_unisnow(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -909,6 +930,7 @@ def test_modify_surfdata_atpoint_crop_1pft_capsat(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -939,6 +961,7 @@ def test_modify_surfdata_atpoint_crop_multipft(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -973,6 +996,7 @@ def test_modify_surfdata_atpoint_crop_urban_nononveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -1007,6 +1031,7 @@ def test_modify_surfdata_atpoint_crop_urban_include_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -1044,6 +1069,7 @@ def test_modify_surfdata_atpoint_crop_lake_include_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -1074,6 +1100,7 @@ def test_modify_surfdata_atpoint_crop_nopft_zero_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, @@ -1107,6 +1134,7 @@ def test_modify_surfdata_atpoint_crop_nopft_include_nonveg(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, diff --git a/tools/modify_input_files/modify_fsurdat_template.cfg b/tools/modify_input_files/modify_fsurdat_template.cfg index 3661784521..1dfb33ce53 100644 --- a/tools/modify_input_files/modify_fsurdat_template.cfg +++ b/tools/modify_input_files/modify_fsurdat_template.cfg @@ -72,9 +72,13 @@ lon_dimname = UNSET # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last -# value of cft(cft). +# value of cft(cft). Cannot be set with evenly_split_cropland = True. dom_pft = UNSET +# If True, evenly split each gridcell's cropland among all crop types (CFTs). +# Can only be True if dom_pft is UNSET. +evenly_split_cropland = False + # LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft # If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). From a7290fbc0154589c8076a77539a8a5cbd6dc3bdf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 14:48:46 -0600 Subject: [PATCH 1276/2067] RXCROPMATURITY now uses fsurdat_modifier. Instead of make_fsurdat_all_crops_everywhere.py, which has been removed. --- cime_config/SystemTests/rxcropmaturity.py | 18 ++-- .../make_fsurdat_all_crops_everywhere.py | 55 ------------ .../modify_fsurdat_allcropseverywhere.cfg | 84 +++++++++++++++++++ 3 files changed, 97 insertions(+), 60 deletions(-) delete mode 100755 python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py create mode 100644 python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 4fd812b84a..9698d1e5ce 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -134,8 +134,8 @@ def run_phase(self): case_gddgen.check_all_input_data() # Make custom version of surface file - logger.info("RXCROPMATURITY log: run make_fsurdat_all_crops_everywhere") - self._run_make_fsurdat_all_crops_everywhere() + logger.info("RXCROPMATURITY log: run fsurdat_modifier") + self._run_fsurdat_modifier() # ------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -239,7 +239,7 @@ def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all done") # Make a surface dataset that has every crop in every gridcell - def _run_make_fsurdat_all_crops_everywhere(self): + def _run_fsurdat_modifier(self): # fsurdat should be defined. Where is it? self._fsurdat_in = None @@ -260,14 +260,22 @@ def _run_make_fsurdat_all_crops_everywhere(self): # Make fsurdat for this test, if not already done if not os.path.exists(self._fsurdat_out): tool_path = os.path.join( + self._ctsm_root, + "tools", + "modify_input_files", + "fsurdat_modifier", + ) + cfg_path = os.path.join( self._ctsm_root, "python", "ctsm", "crop_calendars", - "make_fsurdat_all_crops_everywhere.py", + "modify_fsurdat_allcropseverywhere.cfg", ) command = ( - f"python3 {tool_path} " + f"-i {self._fsurdat_in} " + f"-o {self._fsurdat_out}" + f"python3 {tool_path} {cfg_path} " + + f"-i {self._fsurdat_in} " + + f"-o {self._fsurdat_out}" ) stu.run_python_script( self._get_caseroot(), diff --git a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py b/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py deleted file mode 100755 index f8c5e8b316..0000000000 --- a/python/ctsm/crop_calendars/make_fsurdat_all_crops_everywhere.py +++ /dev/null @@ -1,55 +0,0 @@ -import numpy as np -import xarray as xr -import sys -import argparse - - -def main(file_in, file_out): - # Import - - in_ds = xr.open_dataset(file_in) - - out_ds = in_ds.copy() - in_ds.close() - - # Move all natural land into crop - out_ds["PCT_CROP"] += in_ds["PCT_NATVEG"] - out_ds["PCT_NATVEG"] -= in_ds["PCT_NATVEG"] - - # Put some of every crop in every gridcell - pct_cft = np.full_like(in_ds["PCT_CFT"].values, 100 / in_ds.dims["cft"]) - out_ds["PCT_CFT"] = xr.DataArray( - data=pct_cft, attrs=in_ds["PCT_CFT"].attrs, dims=in_ds["PCT_CFT"].dims - ) - - # Save - out_ds.to_netcdf(file_out, format="NETCDF3_64BIT") - - -if __name__ == "__main__": - ############################### - ### Process input arguments ### - ############################### - parser = argparse.ArgumentParser( - description="Creates a surface dataset with all natural land moved into crops, and with every crop present in every gridcell." - ) - - # Required - parser.add_argument( - "-i", - "--input-file", - help="Surface dataset (fsurdat) file to process", - required=True, - ) - parser.add_argument( - "-o", - "--output-file", - help="Where to save the new surface dataset file", - required=True, - ) - - # Get arguments - args = parser.parse_args(sys.argv[1:]) - - # Process - main(args.input_file, args.output_file) diff --git a/python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg b/python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg new file mode 100644 index 0000000000..b7c46a6c71 --- /dev/null +++ b/python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg @@ -0,0 +1,84 @@ +[modify_fsurdat_basic_options] + +# ------------------------------------------------------------------------ +# .cfg file with inputs for fsurdat_modifier. +# +# This configuration file, when used in fsurdat_modifier, will create a +# version of the input fsurdat file that is 100% cropland with area evenly +# split among all crop PFTs. +# ------------------------------------------------------------------------ + +### Skipping input/output file paths, as these should be specified in +### command-line call of fsurdat_modifier. +# Path and name of input surface dataset (str) +### fsurdat_in = +# Path and name of output surface dataset (str) +### fsurdat_out = + +# We want all existing values in fsurdat to persist except the ones +# pertaining to land unit and PFT fractions. Thus, we set idealized = False. +idealized = False + +# Process the optional section that handles modifying subgrid fractions +process_subgrid_section = True + +# Process the optional section that handles modifying an arbitrary list of variables +process_var_list_section = False + +# Boundaries of user-defined rectangle to apply changes (float) +# If lat_1 > lat_2, the code creates two rectangles, one in the north and +# one in the south. +# If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. +# Alternatively, user may specify a custom area in a .nc landmask_file +# below. If set, this will override the lat/lon settings. +# ----------------------------------- +# southernmost latitude for rectangle +lnd_lat_1 = -90 +# northernmost latitude for rectangle +lnd_lat_2 = 90 +# westernmost longitude for rectangle +lnd_lon_1 = 0 +# easternmost longitude for rectangle +lnd_lon_2 = 360 +# User-defined mask in a file, as alternative to setting lat/lon values. +# If set, lat_dimname and lon_dimname should likely also be set. IMPORTANT: +# - lat_dimname and lon_dimname may be left UNSET if they match the expected +# default values 'lsmlat' and 'lsmlon' +landmask_file = UNSET +lat_dimname = UNSET +lon_dimname = UNSET + +# PFT/CFT to be set to 100% according to user-defined mask. +# We *could* evenly split cropland using dom_pft, but using +# evenly_split_cropland (below) is more robust. Thus, we +# leave dom_pft UNSET. +dom_pft = UNSET + +# Evenly split each gridcell's cropland among all crop types (CFTs). +evenly_split_cropland = True + +# UNSET with idealized False means leave these values unchanged. +lai = UNSET +sai = UNSET +hgt_top = UNSET +hgt_bot = UNSET +soil_color = UNSET +std_elev = UNSET +max_sat_area = UNSET + +# We manually exclude non-vegetation land units (along with NATVEG) below, so set +# include_nonveg to True. +include_nonveg = True + + +# Section for subgrid_fractions +[modify_fsurdat_subgrid_fractions] +# If subgrid_fractions = True this section will be enabled + +# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area +PCT_URBAN = 0.0 0.0 0.0 +PCT_CROP = 100.0 +PCT_NATVEG= 0.0 +PCT_GLACIER= 0.0 +PCT_WETLAND= 0.0 +PCT_LAKE = 0.0 \ No newline at end of file From 938540f4799179aade5d00c017355982bb98f345 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:36:39 -0600 Subject: [PATCH 1277/2067] Replace dom_plant in .cfg file comments with dom_pft. --- tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg | 6 +++--- tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg | 6 +++--- tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg index 5e9de7968b..52a73f2c93 100644 --- a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg +++ b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg @@ -36,15 +36,15 @@ lnd_lon_2 = 360 landmask_file = UNSET # PFT/CFT to be set to 100% according to user-defined mask. -# If idealized = True and dom_plant = UNSET, the latter defaults to 0 +# If idealized = True and dom_pft = UNSET, the latter defaults to 0 # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last # value of cft(cft). dom_pft = UNSET -# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_plant -# If dom_plant = 0, the next four default to 0 (space-delimited list +# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft +# If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). lai = UNSET sai = UNSET diff --git a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg index 38b8ce6372..dd829e73d8 100644 --- a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg +++ b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg @@ -36,15 +36,15 @@ lnd_lon_2 = 360 landmask_file = UNSET # PFT/CFT to be set to 100% according to user-defined mask. -# If idealized = True and dom_plant = UNSET, the latter defaults to 0 +# If idealized = True and dom_pft = UNSET, the latter defaults to 0 # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last # value of cft(cft). dom_pft = UNSET -# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_plant -# If dom_plant = 0, the next four default to 0 (space-delimited list +# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft +# If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). lai = UNSET sai = UNSET diff --git a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg index abc5df16b1..dfbfd4aaea 100644 --- a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg +++ b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg @@ -36,15 +36,15 @@ lnd_lon_2 = 360 landmask_file = UNSET # PFT/CFT to be set to 100% according to user-defined mask. -# If idealized = True and dom_plant = UNSET, the latter defaults to 0 +# If idealized = True and dom_pft = UNSET, the latter defaults to 0 # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last # value of cft(cft). dom_pft = UNSET -# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_plant -# If dom_plant = 0, the next four default to 0 (space-delimited list +# LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft +# If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). lai = UNSET sai = UNSET From 22af59a37251135d7d3de06b3a4bb93751a7c901 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:41:20 -0600 Subject: [PATCH 1278/2067] Fixes so test_sys_fsurdat_modifier.py passes. --- python/ctsm/test/test_sys_fsurdat_modifier.py | 4 ++++ python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg | 1 + python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg | 1 + python/ctsm/test/testinputs/modify_fsurdat_short.cfg | 1 + 4 files changed, 7 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 72d38732cf..293dd1cf3a 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -430,6 +430,8 @@ def _create_config_file_crop(self): line = "lnd_lon_2 = 300\n" elif re.match(r" *dom_pft *=", line): line = "dom_pft = 15" + elif re.match(r" *evenly_split_cropland *=", line): + line = "evenly_split_cropland = False" elif re.match(r" *lai *=", line): line = "lai = 0 1 2 3 4 5 5 4 3 2 1 0\n" elif re.match(r" *sai *=", line): @@ -465,6 +467,8 @@ def _create_config_file_complete(self): line = "lnd_lon_2 = 300\n" elif re.match(r" *dom_pft *=", line): line = "dom_pft = 1" + elif re.match(r" *evenly_split_cropland *=", line): + line = "evenly_split_cropland = False" elif re.match(r" *lai *=", line): line = "lai = 0 1 2 3 4 5 5 4 3 2 1 0\n" elif re.match(r" *sai *=", line): diff --git a/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg b/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg index a4118a3255..0d8a751f32 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_1x1mexicocity.cfg @@ -11,6 +11,7 @@ lat_dimname = lsmlat lon_dimname = lsmlon dom_pft = UNSET +evenly_split_cropland = False lai = UNSET sai = UNSET diff --git a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg index c068c5d851..b1fcf8a2e1 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_opt_sections.cfg @@ -11,6 +11,7 @@ lat_dimname = lsmlat lon_dimname = lsmlon dom_pft = UNSET +evenly_split_cropland = False lai = UNSET sai = UNSET diff --git a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg index 74c6639899..38b88795e8 100644 --- a/python/ctsm/test/testinputs/modify_fsurdat_short.cfg +++ b/python/ctsm/test/testinputs/modify_fsurdat_short.cfg @@ -14,6 +14,7 @@ lat_dimname = lsmlat lon_dimname = lsmlon dom_pft = UNSET +evenly_split_cropland = False lai = UNSET sai = UNSET From 0f34db295d6993cedf84e9606e53883b2156e098 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:41:47 -0600 Subject: [PATCH 1279/2067] Add evenly_split_cropland to config files in tools/mksurfdatamap/. --- tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg | 6 +++++- tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg | 6 +++++- tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg | 6 +++++- 3 files changed, 15 insertions(+), 3 deletions(-) diff --git a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg index 52a73f2c93..6eab73a159 100644 --- a/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg +++ b/tools/mksurfdata_map/modify_1x1_mexicocityMEX.cfg @@ -40,9 +40,13 @@ landmask_file = UNSET # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last -# value of cft(cft). +# value of cft(cft). Cannot be set with evenly_split_cropland = True. dom_pft = UNSET +# If True, evenly split each gridcell's cropland among all crop types (CFTs). +# Can only be True if dom_pft is UNSET. +evenly_split_cropland = False + # LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft # If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). diff --git a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg index dd829e73d8..d704b629bd 100644 --- a/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg +++ b/tools/mksurfdata_map/modify_1x1_urbanc_alpha.cfg @@ -40,9 +40,13 @@ landmask_file = UNSET # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last -# value of cft(cft). +# value of cft(cft). Cannot be set with evenly_split_cropland = True. dom_pft = UNSET +# If True, evenly split each gridcell's cropland among all crop types (CFTs). +# Can only be True if dom_pft is UNSET. +evenly_split_cropland = False + # LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft # If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). diff --git a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg index dfbfd4aaea..f46593d653 100644 --- a/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg +++ b/tools/mksurfdata_map/modify_1x1_vancouverCAN.cfg @@ -40,9 +40,13 @@ landmask_file = UNSET # (bare soil). Valid values range from 0 to a max value (int) that one can # obtain from the fsurdat_in file using ncdump (or method preferred by user). # The max valid value will equal (lsmpft - 1) and will also equal the last -# value of cft(cft). +# value of cft(cft). Cannot be set with evenly_split_cropland = True. dom_pft = UNSET +# If True, evenly split each gridcell's cropland among all crop types (CFTs). +# Can only be True if dom_pft is UNSET. +evenly_split_cropland = False + # LAI, SAI, HEIGHT_TOP, and HEIGHT_BOT values by month for dom_pft # If dom_pft = 0, the next four default to 0 (space-delimited list # of floats without brackets). From c73d04e975520168814de28d836a39330af2961d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:42:11 -0600 Subject: [PATCH 1280/2067] Handle evenly_split_cropland to single_point_case.py. Untested. --- python/ctsm/site_and_regional/single_point_case.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 904b240c77..0b18fe7b44 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -52,6 +52,8 @@ class SinglePointCase(BaseCase): flag for creating user mods directories and files dom_pft : int dominant pft type for this single point (None if not specified) + evenly_split_cropland : bool + flag for splitting cropland evenly among all crop types pct_pft : list weight or percentage of each pft. num_pft : list @@ -126,6 +128,7 @@ def __init__( self.plon = plon self.site_name = site_name self.dom_pft = dom_pft + self.evenly_split_cropland = evenly_split_cropland self.pct_pft = pct_pft self.num_pft = num_pft self.include_nonveg = include_nonveg @@ -437,6 +440,14 @@ def modify_surfdata_atpoint(self, f_orig): tot_pct = f_mod["PCT_CROP"] + f_mod["PCT_NATVEG"] f_mod["PCT_CROP"] = f_mod["PCT_CROP"] / tot_pct * 100 f_mod["PCT_NATVEG"] = f_mod["PCT_NATVEG"] / tot_pct * 100 + + if self.evenly_split_cropland: + f_mod["PCT_LAKE"][:, :] = 0.0 + f_mod["PCT_WETLAND"][:, :] = 0.0 + f_mod["PCT_URBAN"][:, :, :] = 0.0 + f_mod["PCT_GLACIER"][:, :] = 0.0 + f_mod["PCT_NAT_PFT"][:, :, :] = 0.0 + f_mod["PCT_CFT"][:, :, :] = 100.0 / f_mod["PCT_CFT"].shape[2] else: logger.info( From 810cb346f05ac1aabfff931ab1a2b7b584add241 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:49:04 -0600 Subject: [PATCH 1281/2067] Reformatted single_point_case.py with black. --- python/ctsm/site_and_regional/single_point_case.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 0b18fe7b44..59889279ba 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -440,7 +440,7 @@ def modify_surfdata_atpoint(self, f_orig): tot_pct = f_mod["PCT_CROP"] + f_mod["PCT_NATVEG"] f_mod["PCT_CROP"] = f_mod["PCT_CROP"] / tot_pct * 100 f_mod["PCT_NATVEG"] = f_mod["PCT_NATVEG"] / tot_pct * 100 - + if self.evenly_split_cropland: f_mod["PCT_LAKE"][:, :] = 0.0 f_mod["PCT_WETLAND"][:, :] = 0.0 From 028d22a66435e19184ee5e3b00ce446c148f0feb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:49:46 -0600 Subject: [PATCH 1282/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 25513ae910..ba034bb23b 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -11,5 +11,6 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 +810cb346f05ac1aabfff931ab1a2b7b584add241 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c From 9ad4eb08da6ca25b63aa29cc71ba5044b8a61c84 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 16:15:18 -0600 Subject: [PATCH 1283/2067] Add evenly_split_cropland to test_unit_fsurdat_modifier.py. * New: test_dompft_and_splitcropland_fails * New: test_read_subgrid_split_cropland * Added to: test_optional_only_true_and_false --- .../ctsm/test/test_unit_fsurdat_modifier.py | 47 ++++++++++++++++--- 1 file changed, 41 insertions(+), 6 deletions(-) diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 0ea862a8e4..32892e9f1d 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -95,6 +95,17 @@ def test_subgrid_and_idealized_fails(self): ): read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + def test_dompft_and_splitcropland_fails(self): + """test that dompft and evenly_split_cropland fails gracefully""" + section = "modify_fsurdat_basic_options" + self.config.set(section, "dom_pft", "1") + self.config.set(section, "evenly_split_cropland", "True") + with self.assertRaisesRegex( + SystemExit, + "dom_pft must be UNSET if evenly_split_cropland is True; pick one or the other", + ): + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + def test_optional_only_true_and_false(self): """test that optional settings can only be true or false""" section = "modify_fsurdat_basic_options" @@ -114,12 +125,18 @@ def test_optional_only_true_and_false(self): read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) self.config.set(section, "dom_pft", "UNSET") read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) - var = "idealized" - self.config.set(section, var, "Thing") - with self.assertRaisesRegex( - SystemExit, "Non-boolean value found for .cfg file variable: " + var - ): - read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + varlist = ( + "idealized", + "evenly_split_cropland", + ) + for var in varlist: + orig_value = self.config.get(section, var) + self.config.set(section, var, "Thing") + with self.assertRaisesRegex( + SystemExit, "Non-boolean value found for .cfg file variable: " + var + ): + read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + self.config.set(section, var, orig_value) def test_read_subgrid(self): """test a simple read of subgrid""" @@ -164,6 +181,24 @@ def test_read_subgrid_allurban(self): self.config.set(section, "pct_crop", "0.") read_cfg_subgrid(self.config, self.cfg_path) + def test_read_subgrid_split_cropland(self): + """ + test a read of subgrid that's 50/50 natural and + cropland, with cropland split evenly among + crop types + """ + section = "modify_fsurdat_basic_options" + self.config.set(section, "idealized", "False") + self.config.set(section, "evenly_split_cropland", "True") + section = "modify_fsurdat_subgrid_fractions" + self.config.set(section, "pct_urban", "0.0 0.0 0.0") + self.config.set(section, "pct_lake", "0.") + self.config.set(section, "pct_wetland", "0.") + self.config.set(section, "pct_glacier", "0.") + self.config.set(section, "pct_natveg", "50.") + self.config.set(section, "pct_crop", "50.") + read_cfg_subgrid(self.config, self.cfg_path) + def test_read_var_list(self): """test a simple read of var_list""" read_cfg_var_list(self.config, idealized=True) From e6134059e7057b2975bfe5cc49fb42917e5443a5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 16:35:00 -0600 Subject: [PATCH 1284/2067] Add test_evenly_split_cropland to test_sys_fsurdat_modifier.py. --- python/ctsm/test/test_sys_fsurdat_modifier.py | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 293dd1cf3a..6f070a3c25 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -222,6 +222,49 @@ def test_opt_sections(self): np.testing.assert_array_equal(fsurdat_out_data.T_BUILDING_MIN, lev1) np.testing.assert_array_equal(fsurdat_out_data.ALB_ROOF_DIR, lev2_two) np.testing.assert_array_equal(fsurdat_out_data.TK_ROOF, lev2_five) + + def test_evenly_split_cropland(self): + """ + Test that evenly splitting cropland works + """ + self._cfg_file_path = os.path.join( + path_to_ctsm_root(), + "python", + "ctsm", + "crop_calendars", + "modify_fsurdat_allcropseverywhere.cfg") + infile_basename_noext = "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214" + outfile = os.path.join( + self._tempdir, + infile_basename_noext + "_output_allcropseverywhere.nc", + ) + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + os.path.join( + self._testinputs_path, infile_basename_noext + ".nc" + ), + "-o", + outfile, + ] + parser = fsurdat_modifier_arg_process() + fsurdat_modifier(parser) + # Read the resultant output file and make sure the fields are changed as expected + fsurdat_out_data = xr.open_dataset(outfile) + zero0d = np.zeros((5, 5)) + hundred0d = np.full((5, 5), 100.0) + zero_urban = np.zeros((3, 5, 5)) + Ncrops = fsurdat_out_data.dims["cft"] + pct_cft = np.full((Ncrops, 5, 5), 100/Ncrops) + np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, hundred0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) + np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, zero_urban) + np.testing.assert_array_equal(fsurdat_out_data.PCT_CFT, pct_cft) def test_1x1_mexicocity(self): """ From 5933b0018f8e29413e30dda9b906370d147bad45 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 16:41:28 -0600 Subject: [PATCH 1285/2067] Formatted test_sys_fsurdat_modifier.py with black. --- python/ctsm/test/test_sys_fsurdat_modifier.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 6f070a3c25..e3b26e1059 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -222,7 +222,7 @@ def test_opt_sections(self): np.testing.assert_array_equal(fsurdat_out_data.T_BUILDING_MIN, lev1) np.testing.assert_array_equal(fsurdat_out_data.ALB_ROOF_DIR, lev2_two) np.testing.assert_array_equal(fsurdat_out_data.TK_ROOF, lev2_five) - + def test_evenly_split_cropland(self): """ Test that evenly splitting cropland works @@ -232,7 +232,8 @@ def test_evenly_split_cropland(self): "python", "ctsm", "crop_calendars", - "modify_fsurdat_allcropseverywhere.cfg") + "modify_fsurdat_allcropseverywhere.cfg", + ) infile_basename_noext = "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214" outfile = os.path.join( self._tempdir, @@ -242,9 +243,7 @@ def test_evenly_split_cropland(self): "fsurdat_modifier", self._cfg_file_path, "-i", - os.path.join( - self._testinputs_path, infile_basename_noext + ".nc" - ), + os.path.join(self._testinputs_path, infile_basename_noext + ".nc"), "-o", outfile, ] @@ -256,7 +255,7 @@ def test_evenly_split_cropland(self): hundred0d = np.full((5, 5), 100.0) zero_urban = np.zeros((3, 5, 5)) Ncrops = fsurdat_out_data.dims["cft"] - pct_cft = np.full((Ncrops, 5, 5), 100/Ncrops) + pct_cft = np.full((Ncrops, 5, 5), 100 / Ncrops) np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, hundred0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) From 90cbf186eaca77f68a4bb64bfea8401d5c83ae3c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 16:42:27 -0600 Subject: [PATCH 1286/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index ba034bb23b..c6bbe1227f 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -12,5 +12,6 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd 8bc4688e52ea23ef688e283698f70a44388373eb 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 810cb346f05ac1aabfff931ab1a2b7b584add241 +5933b0018f8e29413e30dda9b906370d147bad45 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c From 32ca5eca96837acfc958736d45d2e543dcd55390 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 2 Aug 2023 16:46:17 -0600 Subject: [PATCH 1287/2067] snicar_snw_optics: keep option 3 only --- .../namelist_definition_ctsm.xml | 5 - src/biogeophys/SnowSnicarMod.F90 | 212 +++++------------- src/main/clm_varctl.F90 | 3 - src/main/controlMod.F90 | 10 +- 4 files changed, 51 insertions(+), 179 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index fde179c99e..dd91973ef3 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -160,11 +160,6 @@ number of wavelength bands used in SNICAR snow albedo calculation type of downward solar radiation spectrum for SNICAR snow albedo calculation - -snow optics type using different refractive index databases in SNICAR - - dust optics type for SNICAR snow albedo calculation diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 033ad97eb0..72ac2e0976 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -2203,7 +2203,7 @@ subroutine SnowOptics_init( ) use fileutils , only : getfil use CLM_varctl , only : fsnowoptics,snicar_numrad_snw,fsnowoptics480,snicar_solarspec,& - snicar_snw_optics,snicar_dust_optics ! cenlin + snicar_dust_optics ! cenlin use spmdMod , only : masterproc use ncdio_pio , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile @@ -2277,29 +2277,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ocphob_dif_mlw', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob_dif_mlw', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! ice refractive index options - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! ice refractive index (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters @@ -2375,29 +2359,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ocphob_dif_mls', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob_dif_mls', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! ice refractive index options - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! ice refractive index (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters @@ -2472,29 +2440,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ocphob_dif_saw', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob_dif_saw', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! ice refractive index options - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! ice refractive index (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters @@ -2569,29 +2521,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ocphob_dif_sas', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob_dif_sas', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! ice refractive index options - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! ice refractive index (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters @@ -2666,29 +2602,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ocphob_dif_smm', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob_dif_smm', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! ice refractive index options - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! ice refractive index (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters @@ -2763,29 +2683,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_ocphob_dif_hmn', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_ocphob_dif_hmn', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) - ! ice refractive index options - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! ice refractive index (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters @@ -2869,29 +2773,13 @@ subroutine SnowOptics_init( ) call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) ! snow optical properties derived from different ice refractive index dataset - ! same value for direct and diffuse due to high spectral res without spectra averaging in database - if (snicar_snw_optics == 1) then ! Warren (1984) - call ncd_io( 'ss_alb_ice_wrn84', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn84', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn84',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn84', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 2) then ! Warren and Brandt (2008) - call ncd_io( 'ss_alb_ice_wrn08', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_wrn08', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_wrn08',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_wrn08', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_snw_optics == 3) then ! Picard et al (2016) - call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) - endif + ! same value for direct and diffuse due to high spectral res without spectra averaging in database (Picard et al., 2016) + call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 5cd01d4e90..e5492c4a8b 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -238,9 +238,6 @@ module clm_varctl integer, public :: snicar_solarspec = 1 ! 1->mid-latitude winter;2->mid-latitude summer;3->sub-Arctic winter; ! 4->sub-Arctic summer;5->Summit,Greenland,summer;6->High Mountain summer; - ! snow optics type using different refractive index databases in SNICAR, cenlin - integer, public :: snicar_snw_optics = 3 ! 1->Warren (1984);2->Warren and Brandt (2008);3->Picard et al (2016) - ! dust optics type for SNICAR snow albedo calculation, cenlin integer, public :: snicar_dust_optics = 1 ! 1->Saharan dust (Balkanski et al., 2007, central hematite) ! 2->San Juan Mountains dust, CO (Skiles et al, 2017) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index db7a897126..410229b87b 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -202,7 +202,7 @@ subroutine control_init(dtime) soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & - snicar_numrad_snw, snicar_solarspec, snicar_snw_optics, snicar_dust_optics, & + snicar_numrad_snw, snicar_solarspec, snicar_dust_optics, & snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape, snicar_snobc_intmix,& snicar_snodst_intmix,DO_SNO_OC, & for_testing_use_second_grain_pool, for_testing_use_repr_structure_pool, & @@ -584,12 +584,6 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if - ! check on snow optics type - if ( (snicar_snw_optics < 1) .or. (snicar_snw_optics > 3) ) then - call endrun(msg=' ERROR: snicar_snw_optics is out of a reasonable range (1,2,3)'//& - errMsg(sourcefile, __LINE__)) - end if - ! check on dust optics type if ( (snicar_dust_optics < 1) .or. (snicar_dust_optics > 3) ) then call endrun(msg=' ERROR: snicar_dust_optics is out of a reasonable range (1,2,3)'//& @@ -837,7 +831,6 @@ subroutine control_spmd() call mpi_bcast (soil_layerstruct_userdefined_nlevsoi, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_numrad_snw, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_solarspec, 1, MPI_INTEGER, 0, mpicom, ier) - call mpi_bcast (snicar_snw_optics, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_rt_solver, 1, MPI_INTEGER, 0, mpicom, ier) @@ -1025,7 +1018,6 @@ subroutine control_print () write(iulog,*) ' SNICAR: snow optical properties (480-band) file = ',trim(fsnowoptics480) endif write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec - write(iulog,*) ' SNICAR: snow refractive index type = ', snicar_snw_optics write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw write(iulog,*) ' SNICAR: radiative transfer solver type = ',snicar_rt_solver From 24b13922e5f9d688caad53f9ff9898ad306989ce Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 16:54:32 -0600 Subject: [PATCH 1288/2067] Fixes to test_unit_singlept_data*.py test files. --- python/ctsm/test/test_unit_singlept_data.py | 2 ++ python/ctsm/test/test_unit_singlept_data_surfdata.py | 2 ++ 2 files changed, 4 insertions(+) diff --git a/python/ctsm/test/test_unit_singlept_data.py b/python/ctsm/test/test_unit_singlept_data.py index 06278a38e7..6fdc3109d9 100755 --- a/python/ctsm/test/test_unit_singlept_data.py +++ b/python/ctsm/test/test_unit_singlept_data.py @@ -36,6 +36,7 @@ class TestSinglePointCase(unittest.TestCase): create_datm = True create_user_mods = True dom_pft = [8] + evenly_split_cropland = False pct_pft = None num_pft = 16 include_nonveg = False @@ -58,6 +59,7 @@ def test_create_tag_noname(self): create_datm=self.create_datm, create_user_mods=self.create_user_mods, dom_pft=self.dom_pft, + evenly_split_cropland=self.evenly_split_cropland, pct_pft=self.pct_pft, num_pft=self.num_pft, include_nonveg=self.include_nonveg, diff --git a/python/ctsm/test/test_unit_singlept_data_surfdata.py b/python/ctsm/test/test_unit_singlept_data_surfdata.py index f1b51f689e..0052e796d1 100755 --- a/python/ctsm/test/test_unit_singlept_data_surfdata.py +++ b/python/ctsm/test/test_unit_singlept_data_surfdata.py @@ -44,6 +44,7 @@ class TestSinglePointCaseSurfaceNoCrop(unittest.TestCase): create_datm = True create_user_mods = True dom_pft = [8] + evenly_split_cropland = False pct_pft = None num_pft = 16 include_nonveg = False @@ -608,6 +609,7 @@ class TestSinglePointCaseSurfaceCrop(unittest.TestCase): create_datm = True create_user_mods = True dom_pft = [17] + evenly_split_cropland = False pct_pft = None num_pft = 78 include_nonveg = False From 725f5272a36ece1d5ec95d5d99373339ea20a67a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 2 Aug 2023 18:02:10 -0600 Subject: [PATCH 1289/2067] snicar_rt_solver: keep option 2 only --- .../namelist_definition_ctsm.xml | 5 - src/biogeophys/SnowSnicarMod.F90 | 863 ++++++------------ src/main/clm_varctl.F90 | 4 - src/main/controlMod.F90 | 10 +- 4 files changed, 275 insertions(+), 607 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index dd91973ef3..a9ec4e5559 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -170,11 +170,6 @@ dust optics type for SNICAR snow albedo calculation Toggle to turn on/off aerosol deposition flux in snow in SNICAR - -SNICAR radiative transfer solver type - - snow grain shape used in SNICAR snow albedo calculation diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 72ac2e0976..3264086ebe 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -11,7 +11,7 @@ module SnowSnicarMod use shr_kind_mod , only : r8 => shr_kind_r8 use shr_sys_mod , only : shr_sys_flush use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : iulog, snicar_numrad_snw, snicar_rt_solver, & + use clm_varctl , only : iulog, snicar_numrad_snw, & snicar_snw_shape, snicar_snobc_intmix, & snicar_snodst_intmix, DO_SNO_OC ! cenlin use clm_varcon , only : tfrz @@ -225,8 +225,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! in ESMs; and Flanner et al. 2021, SNICAR-ADv3: a community tool for modeling ! spectral snow albedo ! - ! To use this new adding-doubling solver, set snicar_rt_solver=2 in CLM namelist - ! ! !USES: use clm_varpar , only : nlevsno, numrad use clm_time_manager , only : get_nstep @@ -786,82 +784,18 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Loop over snow spectral bands do bnd_idx = 1,snicar_numrad_snw - - ! Toon et al 2-stream - if (snicar_rt_solver == 1) then - mu_not = coszen(c_idx) ! must set here, because of error handling - - ! Adding-doubling 2-stream - elseif (snicar_rt_solver == 2) then - ! flg_dover is not used since this algorithm is stable for mu_not > 0.01 - ! mu_not is cosine solar zenith angle above the fresnel level; make - ! sure mu_not is large enough for stable and meaningful radiation - ! solution: .01 is like sun just touching horizon with its lower edge - ! equivalent to mu0 in sea-ice shortwave model ice_shortwave.F90 - mu_not = max(coszen(c_idx), cp01) - endif + ! flg_dover is not used since this algorithm is stable for mu_not > 0.01 + ! mu_not is cosine solar zenith angle above the fresnel level; make + ! sure mu_not is large enough for stable and meaningful radiation + ! solution: .01 is like sun just touching horizon with its lower edge + ! equivalent to mu0 in sea-ice shortwave model ice_shortwave.F90 + mu_not = max(coszen(c_idx), cp01) flg_dover = 1 ! default is to redo err_idx = 0 ! number of times through loop do while (flg_dover > 0) - ! Only for Toon et al 2-stream solver: - if (snicar_rt_solver == 1) then - - ! DEFAULT APPROXIMATIONS: - ! VIS: Delta-Eddington - ! NIR (all): Delta-Hemispheric Mean - ! WARNING: DO NOT USE DELTA-EDDINGTON FOR NIR DIFFUSE - this sometimes results in negative albedo - ! - ! ERROR CONDITIONS: - ! Conditions which cause "trip", resulting in redo of RT approximation: - ! 1. negative absorbed flux - ! 2. total absorbed flux greater than incident flux - ! 3. negative albedo - ! NOTE: These errors have only been encountered in spectral bands 4 and 5 - ! - ! ERROR HANDLING - ! 1st error (flg_dover=2): switch approximation (Edd->HM or HM->Edd) - ! 2nd error (flg_dover=3): change zenith angle by 0.02 (this happens about 1 in 10^6 cases) - ! 3rd error (flg_dover=4): switch approximation with new zenith - ! Subsequent errors: repeatedly change zenith and approximations... - - if (bnd_idx < nir_bnd_bgn) then ! VIS, cenlin - if (flg_dover == 2) then - APRX_TYP = 3 - elseif (flg_dover == 3) then - APRX_TYP = 1 - if (coszen(c_idx) > 0.5_r8) then - mu_not = mu_not - 0.02_r8 - else - mu_not = mu_not + 0.02_r8 - endif - elseif (flg_dover == 4) then - APRX_TYP = 3 - else - APRX_TYP = 1 - endif - else ! NIR - if (flg_dover == 2) then - APRX_TYP = 1 - elseif (flg_dover == 3) then - APRX_TYP = 3 - if (coszen(c_idx) > 0.5_r8) then - mu_not = mu_not - 0.02_r8 - else - mu_not = mu_not + 0.02_r8 - endif - elseif (flg_dover == 4) then - APRX_TYP = 1 - else - APRX_TYP = 3 - endif - endif ! end if bnd_idx < nir_bnd_bgn - - endif ! end if snicar_rt_solver == 1 - - ! Set direct or diffuse incident irradiance to 1 ! (This has to be within the bnd loop because mu_not is adjusted in rare cases) if (flg_slr_in == 1) then @@ -1183,529 +1117,282 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif !--------------------------- End of snow & aerosol optics -------------------------------- - - !--------------------------- Start Toon et al. RT solver -------------------------------- - if (snicar_rt_solver == 1) then - - ! Total column optical depth: - ! tau_clm(i) = total optical depth above the bottom of layer i - tau_clm(snl_top) = 0._r8 - do i=snl_top+1,snl_btm,1 - tau_clm(i) = tau_clm(i-1)+tau_star(i-1) - enddo - - ! Direct radiation at bottom of snowpack: - F_direct_btm = albsfc_lcl(bnd_idx)*mu_not * & - exp(-(tau_clm(snl_btm)+tau_star(snl_btm))/mu_not)*pi*flx_slrd_lcl(bnd_idx) - - ! Intermediates - ! Gamma values are approximation-specific. - - ! Eddington - if (APRX_TYP==1) then - do i=snl_top,snl_btm,1 - gamma1(i) = (7._r8-(omega_star(i)*(4._r8+(3._r8*g_star(i)))))/4._r8 - gamma2(i) = -(1._r8-(omega_star(i)*(4._r8-(3._r8*g_star(i)))))/4._r8 - gamma3(i) = (2._r8-(3._r8*g_star(i)*mu_not))/4._r8 - gamma4(i) = 1._r8-gamma3(i) - mu_one = 0.5_r8 - enddo - - ! Quadrature - elseif (APRX_TYP==2) then - do i=snl_top,snl_btm,1 - gamma1(i) = (3._r8**0.5)*(2._r8-(omega_star(i)*(1._r8+g_star(i))))/2._r8 - gamma2(i) = omega_star(i)*(3._r8**0.5)*(1._r8-g_star(i))/2._r8 - gamma3(i) = (1._r8-((3._r8**0.5)*g_star(i)*mu_not))/2._r8 - gamma4(i) = 1._r8-gamma3(i) - mu_one = 1._r8/(3._r8**0.5_r8) - enddo - - ! Hemispheric Mean - elseif (APRX_TYP==3) then - do i=snl_top,snl_btm,1 - gamma1(i) = 2._r8 - (omega_star(i)*(1._r8+g_star(i))) - gamma2(i) = omega_star(i)*(1-g_star(i)) - gamma3(i) = (1._r8-((3._r8**0.5_r8)*g_star(i)*mu_not))/2._r8 - gamma4(i) = 1._r8-gamma3(i) - mu_one = 0.5_r8 - enddo - endif - - ! Intermediates for tri-diagonal solution - do i=snl_top,snl_btm,1 - lambda(i) = sqrt(abs((gamma1(i)**2) - (gamma2(i)**2))) - GAMMA(i) = gamma2(i)/(gamma1(i)+lambda(i)) - - e1(i) = 1+(GAMMA(i)*exp(-lambda(i)*tau_star(i))) - e2(i) = 1-(GAMMA(i)*exp(-lambda(i)*tau_star(i))) - e3(i) = GAMMA(i) + exp(-lambda(i)*tau_star(i)) - e4(i) = GAMMA(i) - exp(-lambda(i)*tau_star(i)) - enddo !enddo over snow layers - - ! Intermediates for tri-diagonal solution - do i=snl_top,snl_btm,1 - if (flg_slr_in == 1) then - - C_pls_btm(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-(tau_clm(i)+tau_star(i))/mu_not)* & - (((gamma1(i)-(1/mu_not))*gamma3(i))+ & - (gamma4(i)*gamma2(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - C_mns_btm(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-(tau_clm(i)+tau_star(i))/mu_not)* & - (((gamma1(i)+(1/mu_not))*gamma4(i))+ & - (gamma2(i)*gamma3(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - C_pls_top(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-tau_clm(i)/mu_not)*(((gamma1(i)-(1/mu_not))* & - gamma3(i))+(gamma4(i)*gamma2(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - C_mns_top(i) = (omega_star(i)*pi*flx_slrd_lcl(bnd_idx)* & - exp(-tau_clm(i)/mu_not)*(((gamma1(i)+(1/mu_not))* & - gamma4(i))+(gamma2(i)*gamma3(i))))/((lambda(i)**2)-(1/(mu_not**2))) - - else - C_pls_btm(i) = 0._r8 - C_mns_btm(i) = 0._r8 - C_pls_top(i) = 0._r8 - C_mns_top(i) = 0._r8 - endif - enddo - - ! Coefficients for tridiaganol matrix solution - do i=2*snl_lcl+1,0,1 - - !Boundary values for i=1 and i=2*snl_lcl, specifics for i=odd and i=even - if (i==(2*snl_lcl+1)) then - A(i) = 0._r8 - B(i) = e1(snl_top) - D(i) = -e2(snl_top) - E(i) = flx_slri_lcl(bnd_idx)-C_mns_top(snl_top) - - elseif(i==0) then - A(i) = e1(snl_btm)-(albsfc_lcl(bnd_idx)*e3(snl_btm)) - B(i) = e2(snl_btm)-(albsfc_lcl(bnd_idx)*e4(snl_btm)) - D(i) = 0._r8 - E(i) = F_direct_btm-C_pls_btm(snl_btm)+(albsfc_lcl(bnd_idx)*C_mns_btm(snl_btm)) - - elseif(mod(i,2)==-1) then ! If odd and i>=3 (n=1 for i=3) - n=floor(i/2.0) - A(i) = (e2(n)*e3(n))-(e4(n)*e1(n)) - B(i) = (e1(n)*e1(n+1))-(e3(n)*e3(n+1)) - D(i) = (e3(n)*e4(n+1))-(e1(n)*e2(n+1)) - E(i) = (e3(n)*(C_pls_top(n+1)-C_pls_btm(n)))+(e1(n)*(C_mns_btm(n)-C_mns_top(n+1))) - - elseif(mod(i,2)==0) then ! If even and i<=2*snl_lcl - n=(i/2) - A(i) = (e2(n+1)*e1(n))-(e3(n)*e4(n+1)) - B(i) = (e2(n)*e2(n+1))-(e4(n)*e4(n+1)) - D(i) = (e1(n+1)*e4(n+1))-(e2(n+1)*e3(n+1)) - E(i) = (e2(n+1)*(C_pls_top(n+1)-C_pls_btm(n)))+(e4(n+1)*(C_mns_top(n+1)-C_mns_btm(n))) - endif - enddo - - AS(0) = A(0)/B(0) - DS(0) = E(0)/B(0) - - do i=-1,(2*snl_lcl+1),-1 - X(i) = 1/(B(i)-(D(i)*AS(i+1))) - AS(i) = A(i)*X(i) - DS(i) = (E(i)-(D(i)*DS(i+1)))*X(i) - enddo - - Y(2*snl_lcl+1) = DS(2*snl_lcl+1) - do i=(2*snl_lcl+2),0,1 - Y(i) = DS(i)-(AS(i)*Y(i-1)) - enddo - - ! Downward direct-beam and net flux (F_net) at the base of each layer: - do i=snl_top,snl_btm,1 - F_direct(i) = mu_not*pi*flx_slrd_lcl(bnd_idx)*exp(-(tau_clm(i)+tau_star(i))/mu_not) - F_net(i) = (Y(2*i-1)*(e1(i)-e3(i))) + (Y(2*i)*(e2(i)-e4(i))) + & - C_pls_btm(i) - C_mns_btm(i) - F_direct(i) - enddo - - ! Upward flux at snowpack top: - F_sfc_pls = (Y(2*snl_lcl+1)*(exp(-lambda(snl_top)*tau_star(snl_top))+ & - GAMMA(snl_top))) + (Y(2*snl_lcl+2)*(exp(-lambda(snl_top)* & - tau_star(snl_top))-GAMMA(snl_top))) + C_pls_top(snl_top) - - ! Net flux at bottom = absorbed radiation by underlying surface: - F_btm_net = -F_net(snl_btm) - - - ! Bulk column albedo and surface net flux - albedo = F_sfc_pls/((mu_not*pi*flx_slrd_lcl(bnd_idx))+flx_slri_lcl(bnd_idx)) - F_sfc_net = F_sfc_pls - ((mu_not*pi*flx_slrd_lcl(bnd_idx))+flx_slri_lcl(bnd_idx)) - - trip = 0 - ! Absorbed flux in each layer - do i=snl_top,snl_btm,1 - if(i==snl_top) then - F_abs(i) = F_net(i)-F_sfc_net - else - F_abs(i) = F_net(i)-F_net(i-1) - endif - flx_abs_lcl(i,bnd_idx) = F_abs(i) - - ! ERROR check: negative absorption - if (flx_abs_lcl(i,bnd_idx) < -0.00001_r8) then - trip = 1 - endif - enddo - - flx_abs_lcl(1,bnd_idx) = F_btm_net - - if (flg_nosnl == 1) then - ! If there are no snow layers (but still snow), all absorbed energy must be in top soil layer - !flx_abs_lcl(:,bnd_idx) = 0._r8 - !flx_abs_lcl(1,bnd_idx) = F_abs(0) + F_btm_net - - ! changed on 20070408: - ! OK to put absorbed energy in the fictitous snow layer because routine SurfaceRadiation - ! handles the case of no snow layers. Then, if a snow layer is addded between now and - ! SurfaceRadiation (called in CanopyHydrology), absorbed energy will be properly distributed. - flx_abs_lcl(0,bnd_idx) = F_abs(0) - flx_abs_lcl(1,bnd_idx) = F_btm_net - endif - - !Underflow check (we've already tripped the error condition above) - do i=snl_top,1,1 - if (flx_abs_lcl(i,bnd_idx) < 0._r8) then - flx_abs_lcl(i,bnd_idx) = 0._r8 - endif - enddo - - F_abs_sum = 0._r8 - do i=snl_top,snl_btm,1 - F_abs_sum = F_abs_sum + F_abs(i) - enddo - - !ERROR check: absorption greater than incident flux - ! (should make condition more generic than "1._r8") - if (F_abs_sum > 1._r8) then - trip = 1 - endif - - !ERROR check: - if ((albedo < 0._r8).and.(trip==0)) then - trip = 1 - endif - - ! Set conditions for redoing RT calculation - if ((trip == 1).and.(flg_dover == 1)) then - flg_dover = 2 - elseif ((trip == 1).and.(flg_dover == 2)) then - flg_dover = 3 - elseif ((trip == 1).and.(flg_dover == 3)) then - flg_dover = 4 - elseif((trip == 1).and.(flg_dover == 4).and.(err_idx < 20)) then - flg_dover = 3 - err_idx = err_idx + 1 - elseif((trip == 1).and.(flg_dover == 4).and.(err_idx >= 20)) then - flg_dover = 0 - write(iulog,*) "SNICAR ERROR: FOUND A WORMHOLE. STUCK IN INFINITE LOOP! Called from: ", flg_snw_ice - write(iulog,*) "SNICAR STATS: snw_rds(0)= ", snw_rds(c_idx,0) - write(iulog,*) "SNICAR STATS: L_snw(0)= ", L_snw(0) - write(iulog,*) "SNICAR STATS: h2osno= ", h2osno_lcl, " snl= ", snl_lcl - write(iulog,*) "SNICAR STATS: soot1(0)= ", mss_cnc_aer_lcl(0,1) - write(iulog,*) "SNICAR STATS: soot2(0)= ", mss_cnc_aer_lcl(0,2) - write(iulog,*) "SNICAR STATS: dust1(0)= ", mss_cnc_aer_lcl(0,3) - write(iulog,*) "SNICAR STATS: dust2(0)= ", mss_cnc_aer_lcl(0,4) - write(iulog,*) "SNICAR STATS: dust3(0)= ", mss_cnc_aer_lcl(0,5) - write(iulog,*) "SNICAR STATS: dust4(0)= ", mss_cnc_aer_lcl(0,6) - l_idx = col%landunit(c_idx) - write(iulog,*) "column index: ", c_idx - write(iulog,*) "landunit type", lun%itype(l_idx) - write(iulog,*) "frac_sno: ", frac_sno(c_idx) - call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) - else - flg_dover = 0 - endif - - endif ! end if snicar_rt_solver==1 - !--------------------------- End of Toon et al. RT solver -------------------------------- - - !--------------------------- Start Adding-doubling RT solver -------------------------------- - if (snicar_rt_solver == 2) then - - ! Given input vertical profiles of optical properties, evaluate the - ! monochromatic Delta-Eddington adding-doubling solution - - ! trndir, trntdr, trndif, rupdir, rupdif, rdndif are variables at the layer interface, - ! for snow with layers from snl_top to snl_btm there are snl_top to snl_btm+1 layer interface - snl_btm_itf = snl_btm + 1 - - ! initialization for layer interface - do i = snl_top,snl_btm_itf,1 - trndir(i) = c0 - trntdr(i) = c0 - trndif(i) = c0 - rupdir(i) = c0 - rupdif(i) = c0 - rdndif(i) = c0 - enddo - ! initialize top interface of top layer - trndir(snl_top) = c1 - trntdr(snl_top) = c1 - trndif(snl_top) = c1 - rdndif(snl_top) = c0 - - ! begin main level loop for snow layer interfaces except for the very bottom - do i = snl_top,snl_btm,1 - - ! initialize all layer apparent optical properties to 0 - rdir (i) = c0 - rdif_a(i) = c0 - rdif_b(i) = c0 - tdir (i) = c0 - tdif_a(i) = c0 - tdif_b(i) = c0 - trnlay(i) = c0 - - ! compute next layer Delta-eddington solution only if total transmission - ! of radiation to the interface just above the layer exceeds trmin. - if (trntdr(i) > trmin ) then - - ! delta-transformed single-scattering properties of this layer - ts = tau_star(i) - ws = omega_star(i) - gs = g_star(i) - - ! Delta-Eddington solution expressions, Eq. 50: Briegleb and Light 2007 - lm = sqrt(c3*(c1-ws)*(c1 - ws*gs)) - ue = c1p5*(c1 - ws*gs)/lm - extins = max(exp_min, exp(-lm*ts)) - ne = ((ue+c1)*(ue+c1)/extins) - ((ue-c1)*(ue-c1)*extins) - - ! first calculation of rdif, tdif using Delta-Eddington formulas - ! Eq.: Briegleb 1992; alpha and gamma for direct radiation - rdif_a(i) = (ue**2-c1)*(c1/extins - extins)/ne - tdif_a(i) = c4*ue/ne - - ! evaluate rdir,tdir for direct beam - trnlay(i) = max(exp_min, exp(-ts/mu_not)) - - ! Delta-Eddington solution expressions - ! Eq. 50: Briegleb and Light 2007; alpha and gamma for direct radiation - alp = cp75*ws*mu_not*((c1 + gs*(c1-ws))/(c1 - lm*lm*mu_not*mu_not)) - gam = cp5*ws*((c1 + c3*gs*(c1-ws)*mu_not*mu_not)/(c1-lm*lm*mu_not*mu_not)) + + ! Given input vertical profiles of optical properties, evaluate the + ! monochromatic Delta-Eddington adding-doubling solution + + ! trndir, trntdr, trndif, rupdir, rupdif, rdndif are variables at the layer interface, + ! for snow with layers from snl_top to snl_btm there are snl_top to snl_btm+1 layer interface + snl_btm_itf = snl_btm + 1 + + ! initialization for layer interface + do i = snl_top,snl_btm_itf,1 + trndir(i) = c0 + trntdr(i) = c0 + trndif(i) = c0 + rupdir(i) = c0 + rupdif(i) = c0 + rdndif(i) = c0 + enddo + ! initialize top interface of top layer + trndir(snl_top) = c1 + trntdr(snl_top) = c1 + trndif(snl_top) = c1 + rdndif(snl_top) = c0 + + ! begin main level loop for snow layer interfaces except for the very bottom + do i = snl_top,snl_btm,1 + + ! initialize all layer apparent optical properties to 0 + rdir (i) = c0 + rdif_a(i) = c0 + rdif_b(i) = c0 + tdir (i) = c0 + tdif_a(i) = c0 + tdif_b(i) = c0 + trnlay(i) = c0 + + ! compute next layer Delta-eddington solution only if total transmission + ! of radiation to the interface just above the layer exceeds trmin. + if (trntdr(i) > trmin ) then + + ! delta-transformed single-scattering properties of this layer + ts = tau_star(i) + ws = omega_star(i) + gs = g_star(i) + + ! Delta-Eddington solution expressions, Eq. 50: Briegleb and Light 2007 + lm = sqrt(c3*(c1-ws)*(c1 - ws*gs)) + ue = c1p5*(c1 - ws*gs)/lm + extins = max(exp_min, exp(-lm*ts)) + ne = ((ue+c1)*(ue+c1)/extins) - ((ue-c1)*(ue-c1)*extins) + + ! first calculation of rdif, tdif using Delta-Eddington formulas + ! Eq.: Briegleb 1992; alpha and gamma for direct radiation + rdif_a(i) = (ue**2-c1)*(c1/extins - extins)/ne + tdif_a(i) = c4*ue/ne + + ! evaluate rdir,tdir for direct beam + trnlay(i) = max(exp_min, exp(-ts/mu_not)) + + ! Delta-Eddington solution expressions + ! Eq. 50: Briegleb and Light 2007; alpha and gamma for direct radiation + alp = cp75*ws*mu_not*((c1 + gs*(c1-ws))/(c1 - lm*lm*mu_not*mu_not)) + gam = cp5*ws*((c1 + c3*gs*(c1-ws)*mu_not*mu_not)/(c1-lm*lm*mu_not*mu_not)) + apg = alp + gam + amg = alp - gam + rdir(i) = apg*rdif_a(i) + amg*(tdif_a(i)*trnlay(i) - c1) + tdir(i) = apg*tdif_a(i) + (amg* rdif_a(i)-apg+c1)*trnlay(i) + + ! recalculate rdif,tdif using direct angular integration over rdir,tdir, + ! since Delta-Eddington rdif formula is not well-behaved (it is usually + ! biased low and can even be negative); use ngmax angles and gaussian + ! integration for most accuracy: + R1 = rdif_a(i) ! use R1 as temporary + T1 = tdif_a(i) ! use T1 as temporary + swt = c0 + smr = c0 + smt = c0 + ! gaussian angles for the AD integral + do ng=1,ngmax + mu = difgauspt(ng) + gwt = difgauswt(ng) + swt = swt + mu*gwt + trn = max(exp_min, exp(-ts/mu)) + alp = cp75*ws*mu*((c1 + gs*(c1-ws))/(c1 - lm*lm*mu*mu)) + gam = cp5*ws*((c1 + c3*gs*(c1-ws)*mu*mu)/(c1-lm*lm*mu*mu)) apg = alp + gam amg = alp - gam - rdir(i) = apg*rdif_a(i) + amg*(tdif_a(i)*trnlay(i) - c1) - tdir(i) = apg*tdif_a(i) + (amg* rdif_a(i)-apg+c1)*trnlay(i) - - ! recalculate rdif,tdif using direct angular integration over rdir,tdir, - ! since Delta-Eddington rdif formula is not well-behaved (it is usually - ! biased low and can even be negative); use ngmax angles and gaussian - ! integration for most accuracy: - R1 = rdif_a(i) ! use R1 as temporary - T1 = tdif_a(i) ! use T1 as temporary - swt = c0 - smr = c0 - smt = c0 - ! gaussian angles for the AD integral - do ng=1,ngmax - mu = difgauspt(ng) - gwt = difgauswt(ng) - swt = swt + mu*gwt - trn = max(exp_min, exp(-ts/mu)) - alp = cp75*ws*mu*((c1 + gs*(c1-ws))/(c1 - lm*lm*mu*mu)) - gam = cp5*ws*((c1 + c3*gs*(c1-ws)*mu*mu)/(c1-lm*lm*mu*mu)) - apg = alp + gam - amg = alp - gam - rdr = apg*R1 + amg*T1*trn - amg - tdr = apg*T1 + amg*R1*trn - apg*trn + trn - smr = smr + mu*rdr*gwt - smt = smt + mu*tdr*gwt - enddo ! ng - rdif_a(i) = smr/swt - tdif_a(i) = smt/swt - - ! homogeneous layer - rdif_b(i) = rdif_a(i) - tdif_b(i) = tdif_a(i) - - endif ! trntdr(k) > trmin - - ! Calculate the solar beam transmission, total transmission, and - ! reflectivity for diffuse radiation from below at interface i, - ! the top of the current layer k: - ! - ! layers interface - ! - ! --------------------- i-1 - ! i-1 - ! --------------------- i - ! i - ! --------------------- - - trndir(i+1) = trndir(i)*trnlay(i) ! solar beam transmission from top - refkm1 = c1/(c1 - rdndif(i)*rdif_a(i)) ! interface multiple scattering for i-1 - tdrrdir = trndir(i)*rdir(i) ! direct tran times layer direct ref - tdndif = trntdr(i) - trndir(i) ! total down diffuse = tot tran - direct tran - trntdr(i+1) = trndir(i)*tdir(i) + & ! total transmission to direct beam for layers above - (tdndif + tdrrdir*rdndif(i))*refkm1*tdif_a(i) - ! Eq. B4; Briegleb and Light 2007 - rdndif(i+1) = rdif_b(i) + & ! reflectivity to diffuse radiation for layers above - (tdif_b(i)*rdndif(i)*refkm1*tdif_a(i)) - trndif(i+1) = trndif(i)*refkm1*tdif_a(i) ! diffuse transmission to diffuse beam for layers above - - enddo ! end i main level loop - - ! compute reflectivity to direct and diffuse radiation for layers - ! below by adding succesive layers starting from the underlying - ! ground and working upwards: + rdr = apg*R1 + amg*T1*trn - amg + tdr = apg*T1 + amg*R1*trn - apg*trn + trn + smr = smr + mu*rdr*gwt + smt = smt + mu*tdr*gwt + enddo ! ng + rdif_a(i) = smr/swt + tdif_a(i) = smt/swt + + ! homogeneous layer + rdif_b(i) = rdif_a(i) + tdif_b(i) = tdif_a(i) + + endif ! trntdr(k) > trmin + + ! Calculate the solar beam transmission, total transmission, and + ! reflectivity for diffuse radiation from below at interface i, + ! the top of the current layer k: ! ! layers interface ! + ! --------------------- i-1 + ! i-1 ! --------------------- i ! i - ! --------------------- i+1 - ! i+1 ! --------------------- - ! set the underlying ground albedo == albedo of near-IR - ! unless bnd_idx < nir_bnd_bgn, for visible - rupdir(snl_btm_itf) = albsfc(c_idx,2) - rupdif(snl_btm_itf) = albsfc(c_idx,2) - if (bnd_idx < nir_bnd_bgn) then - rupdir(snl_btm_itf) = albsfc(c_idx,1) - rupdif(snl_btm_itf) = albsfc(c_idx,1) + trndir(i+1) = trndir(i)*trnlay(i) ! solar beam transmission from top + refkm1 = c1/(c1 - rdndif(i)*rdif_a(i)) ! interface multiple scattering for i-1 + tdrrdir = trndir(i)*rdir(i) ! direct tran times layer direct ref + tdndif = trntdr(i) - trndir(i) ! total down diffuse = tot tran - direct tran + trntdr(i+1) = trndir(i)*tdir(i) + & ! total transmission to direct beam for layers above + (tdndif + tdrrdir*rdndif(i))*refkm1*tdif_a(i) + ! Eq. B4; Briegleb and Light 2007 + rdndif(i+1) = rdif_b(i) + & ! reflectivity to diffuse radiation for layers above + (tdif_b(i)*rdndif(i)*refkm1*tdif_a(i)) + trndif(i+1) = trndif(i)*refkm1*tdif_a(i) ! diffuse transmission to diffuse beam for layers above + + enddo ! end i main level loop + + ! compute reflectivity to direct and diffuse radiation for layers + ! below by adding succesive layers starting from the underlying + ! ground and working upwards: + ! + ! layers interface + ! + ! --------------------- i + ! i + ! --------------------- i+1 + ! i+1 + ! --------------------- + + ! set the underlying ground albedo == albedo of near-IR + ! unless bnd_idx < nir_bnd_bgn, for visible + rupdir(snl_btm_itf) = albsfc(c_idx,2) + rupdif(snl_btm_itf) = albsfc(c_idx,2) + if (bnd_idx < nir_bnd_bgn) then + rupdir(snl_btm_itf) = albsfc(c_idx,1) + rupdif(snl_btm_itf) = albsfc(c_idx,1) + endif + + do i=snl_btm,snl_top,-1 + ! interface scattering Eq. B5; Briegleb and Light 2007 + refkp1 = c1/( c1 - rdif_b(i)*rupdif(i+1)) + ! dir from top layer plus exp tran ref from lower layer, interface + ! scattered and tran thru top layer from below, plus diff tran ref + ! from lower layer with interface scattering tran thru top from below + rupdir(i) = rdir(i) & + + ( trnlay(i) *rupdir(i+1) & + + (tdir(i)-trnlay(i))*rupdif(i+1) ) * refkp1 * tdif_b(i) + ! dif from top layer from above, plus dif tran upwards reflected and + ! interface scattered which tran top from below + rupdif(i) = rdif_a(i) + tdif_a(i)*rupdif(i+1)*refkp1*tdif_b(i) + enddo ! i + + ! net flux (down-up) at each layer interface from the + ! snow top (i = snl_top) to bottom interface above land (i = snl_btm_itf) + ! the interface reflectivities and transmissivities required + ! to evaluate interface fluxes are returned from solution_dEdd; + ! now compute up and down fluxes for each interface, using the + ! combined layer properties at each interface: + ! + ! layers interface + ! + ! --------------------- i + ! i + ! --------------------- + + do i = snl_top, snl_btm_itf + ! interface scattering, Eq. 52; Briegleb and Light 2007 + refk = c1/(c1 - rdndif(i)*rupdif(i)) + ! dir tran ref from below times interface scattering, plus diff + ! tran and ref from below times interface scattering + ! fdirup(i) = (trndir(i)*rupdir(i) + & + ! (trntdr(i)-trndir(i)) & + ! *rupdif(i))*refk + ! dir tran plus total diff trans times interface scattering plus + ! dir tran with up dir ref and down dif ref times interface scattering + ! fdirdn(i) = trndir(i) + (trntdr(i) & + ! - trndir(i) + trndir(i) & + ! *rupdir(i)*rdndif(i))*refk + ! diffuse tran ref from below times interface scattering + ! fdifup(i) = trndif(i)*rupdif(i)*refk + ! diffuse tran times interface scattering + ! fdifdn(i) = trndif(i)*refk + + ! netflux, down - up + ! dfdir = fdirdn - fdirup + dfdir(i) = trndir(i) & + + (trntdr(i)-trndir(i)) * (c1 - rupdif(i)) * refk & + - trndir(i)*rupdir(i) * (c1 - rdndif(i)) * refk + if (dfdir(i) < puny) dfdir(i) = c0 + ! dfdif = fdifdn - fdifup + dfdif(i) = trndif(i) * (c1 - rupdif(i)) * refk + if (dfdif(i) < puny) dfdif(i) = c0 + enddo ! k + + ! SNICAR_AD_RT is called twice for direct and diffuse incident fluxes + ! direct incident + if (flg_slr_in == 1) then + albedo = rupdir(snl_top) + dftmp = dfdir + refk = c1/(c1 - rdndif(snl_top)*rupdif(snl_top)) + F_sfc_pls = (trndir(snl_top)*rupdir(snl_top) + & + (trntdr(snl_top)-trndir(snl_top)) & + *rupdif(snl_top))*refk + !diffuse incident + else + albedo = rupdif(snl_top) + dftmp = dfdif + refk = c1/(c1 - rdndif(snl_top)*rupdif(snl_top)) + F_sfc_pls = trndif(snl_top)*rupdif(snl_top)*refk + endif + + ! Absorbed flux in each layer + do i=snl_top,snl_btm,1 + F_abs(i) = dftmp(i)-dftmp(i+1) + flx_abs_lcl(i,bnd_idx) = F_abs(i) + + ! ERROR check: negative absorption + if (flx_abs_lcl(i,bnd_idx) < -0.00001_r8) then + write (iulog,"(a,e13.6,a,i6,a,i6)") "SNICAR ERROR: negative absoption : ", & + flx_abs_lcl(i,bnd_idx), " at timestep: ", nstep, " at column: ", c_idx + write(iulog,*) "SNICAR_AD STATS: snw_rds(0)= ", snw_rds(c_idx,0) + write(iulog,*) "SNICAR_AD STATS: L_snw(0)= ", L_snw(0) + write(iulog,*) "SNICAR_AD STATS: h2osno= ", h2osno_lcl, " snl= ", snl_lcl + write(iulog,*) "SNICAR_AD STATS: soot1(0)= ", mss_cnc_aer_lcl(0,1) + write(iulog,*) "SNICAR_AD STATS: soot2(0)= ", mss_cnc_aer_lcl(0,2) + write(iulog,*) "SNICAR_AD STATS: dust1(0)= ", mss_cnc_aer_lcl(0,3) + write(iulog,*) "SNICAR_AD STATS: dust2(0)= ", mss_cnc_aer_lcl(0,4) + write(iulog,*) "SNICAR_AD STATS: dust3(0)= ", mss_cnc_aer_lcl(0,5) + write(iulog,*) "SNICAR_AD STATS: dust4(0)= ", mss_cnc_aer_lcl(0,6) + call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) endif + enddo - do i=snl_btm,snl_top,-1 - ! interface scattering Eq. B5; Briegleb and Light 2007 - refkp1 = c1/( c1 - rdif_b(i)*rupdif(i+1)) - ! dir from top layer plus exp tran ref from lower layer, interface - ! scattered and tran thru top layer from below, plus diff tran ref - ! from lower layer with interface scattering tran thru top from below - rupdir(i) = rdir(i) & - + ( trnlay(i) *rupdir(i+1) & - + (tdir(i)-trnlay(i))*rupdif(i+1) ) * refkp1 * tdif_b(i) - ! dif from top layer from above, plus dif tran upwards reflected and - ! interface scattered which tran top from below - rupdif(i) = rdif_a(i) + tdif_a(i)*rupdif(i+1)*refkp1*tdif_b(i) - enddo ! i - - ! net flux (down-up) at each layer interface from the - ! snow top (i = snl_top) to bottom interface above land (i = snl_btm_itf) - ! the interface reflectivities and transmissivities required - ! to evaluate interface fluxes are returned from solution_dEdd; - ! now compute up and down fluxes for each interface, using the - ! combined layer properties at each interface: - ! - ! layers interface - ! - ! --------------------- i - ! i - ! --------------------- + ! absobed flux by the underlying ground + F_btm_net = dftmp(snl_btm_itf) - do i = snl_top, snl_btm_itf - ! interface scattering, Eq. 52; Briegleb and Light 2007 - refk = c1/(c1 - rdndif(i)*rupdif(i)) - ! dir tran ref from below times interface scattering, plus diff - ! tran and ref from below times interface scattering - ! fdirup(i) = (trndir(i)*rupdir(i) + & - ! (trntdr(i)-trndir(i)) & - ! *rupdif(i))*refk - ! dir tran plus total diff trans times interface scattering plus - ! dir tran with up dir ref and down dif ref times interface scattering - ! fdirdn(i) = trndir(i) + (trntdr(i) & - ! - trndir(i) + trndir(i) & - ! *rupdir(i)*rdndif(i))*refk - ! diffuse tran ref from below times interface scattering - ! fdifup(i) = trndif(i)*rupdif(i)*refk - ! diffuse tran times interface scattering - ! fdifdn(i) = trndif(i)*refk - - ! netflux, down - up - ! dfdir = fdirdn - fdirup - dfdir(i) = trndir(i) & - + (trntdr(i)-trndir(i)) * (c1 - rupdif(i)) * refk & - - trndir(i)*rupdir(i) * (c1 - rdndif(i)) * refk - if (dfdir(i) < puny) dfdir(i) = c0 - ! dfdif = fdifdn - fdifup - dfdif(i) = trndif(i) * (c1 - rupdif(i)) * refk - if (dfdif(i) < puny) dfdif(i) = c0 - enddo ! k - - ! SNICAR_AD_RT is called twice for direct and diffuse incident fluxes - ! direct incident - if (flg_slr_in == 1) then - albedo = rupdir(snl_top) - dftmp = dfdir - refk = c1/(c1 - rdndif(snl_top)*rupdif(snl_top)) - F_sfc_pls = (trndir(snl_top)*rupdir(snl_top) + & - (trntdr(snl_top)-trndir(snl_top)) & - *rupdif(snl_top))*refk - !diffuse incident - else - albedo = rupdif(snl_top) - dftmp = dfdif - refk = c1/(c1 - rdndif(snl_top)*rupdif(snl_top)) - F_sfc_pls = trndif(snl_top)*rupdif(snl_top)*refk - endif + ! note here, snl_btm_itf = 1 by snow column set up in CLM + flx_abs_lcl(1,bnd_idx) = F_btm_net - ! Absorbed flux in each layer - do i=snl_top,snl_btm,1 - F_abs(i) = dftmp(i)-dftmp(i+1) - flx_abs_lcl(i,bnd_idx) = F_abs(i) - - ! ERROR check: negative absorption - if (flx_abs_lcl(i,bnd_idx) < -0.00001_r8) then - write (iulog,"(a,e13.6,a,i6,a,i6)") "SNICAR ERROR: negative absoption : ", & - flx_abs_lcl(i,bnd_idx), " at timestep: ", nstep, " at column: ", c_idx - write(iulog,*) "SNICAR_AD STATS: snw_rds(0)= ", snw_rds(c_idx,0) - write(iulog,*) "SNICAR_AD STATS: L_snw(0)= ", L_snw(0) - write(iulog,*) "SNICAR_AD STATS: h2osno= ", h2osno_lcl, " snl= ", snl_lcl - write(iulog,*) "SNICAR_AD STATS: soot1(0)= ", mss_cnc_aer_lcl(0,1) - write(iulog,*) "SNICAR_AD STATS: soot2(0)= ", mss_cnc_aer_lcl(0,2) - write(iulog,*) "SNICAR_AD STATS: dust1(0)= ", mss_cnc_aer_lcl(0,3) - write(iulog,*) "SNICAR_AD STATS: dust2(0)= ", mss_cnc_aer_lcl(0,4) - write(iulog,*) "SNICAR_AD STATS: dust3(0)= ", mss_cnc_aer_lcl(0,5) - write(iulog,*) "SNICAR_AD STATS: dust4(0)= ", mss_cnc_aer_lcl(0,6) - call endrun(subgrid_index=c_idx, subgrid_level=subgrid_level_column, msg=errmsg(sourcefile, __LINE__)) - endif - enddo - - ! absobed flux by the underlying ground - F_btm_net = dftmp(snl_btm_itf) - - ! note here, snl_btm_itf = 1 by snow column set up in CLM + if (flg_nosnl == 1) then + ! If there are no snow layers (but still snow), all absorbed energy must be in top soil layer + !flx_abs_lcl(:,bnd_idx) = 0._r8 + !flx_abs_lcl(1,bnd_idx) = F_abs(0) + F_btm_net + + ! changed on 20070408: + ! OK to put absorbed energy in the fictitous snow layer because routine SurfaceRadiation + ! handles the case of no snow layers. Then, if a snow layer is addded between now and + ! SurfaceRadiation (called in CanopyHydrology), absorbed energy will be properly distributed. + flx_abs_lcl(0,bnd_idx) = F_abs(0) flx_abs_lcl(1,bnd_idx) = F_btm_net + endif - if (flg_nosnl == 1) then - ! If there are no snow layers (but still snow), all absorbed energy must be in top soil layer - !flx_abs_lcl(:,bnd_idx) = 0._r8 - !flx_abs_lcl(1,bnd_idx) = F_abs(0) + F_btm_net - - ! changed on 20070408: - ! OK to put absorbed energy in the fictitous snow layer because routine SurfaceRadiation - ! handles the case of no snow layers. Then, if a snow layer is addded between now and - ! SurfaceRadiation (called in CanopyHydrology), absorbed energy will be properly distributed. - flx_abs_lcl(0,bnd_idx) = F_abs(0) - flx_abs_lcl(1,bnd_idx) = F_btm_net + !Underflow check (we've already tripped the error condition above) + do i=snl_top,1,1 + if (flx_abs_lcl(i,bnd_idx) < 0._r8) then + flx_abs_lcl(i,bnd_idx) = 0._r8 endif + enddo - !Underflow check (we've already tripped the error condition above) - do i=snl_top,1,1 - if (flx_abs_lcl(i,bnd_idx) < 0._r8) then - flx_abs_lcl(i,bnd_idx) = 0._r8 - endif - enddo - - F_abs_sum = 0._r8 - do i=snl_top,snl_btm,1 - F_abs_sum = F_abs_sum + F_abs(i) - enddo + F_abs_sum = 0._r8 + do i=snl_top,snl_btm,1 + F_abs_sum = F_abs_sum + F_abs(i) + enddo - ! no need to repeat calculations for adding-doubling solver - flg_dover = 0 + ! no need to repeat calculations for adding-doubling solver + flg_dover = 0 - endif ! end if snicar_rt_solver==2 !--------------------------- End of Adding-doubling RT solver -------------------------------- enddo !enddo while (flg_dover > 0) @@ -1823,19 +1510,17 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end if ! high solar zenith angle adjustment for Adding-doubling solver results - if (snicar_rt_solver==2) then - ! near-IR direct albedo/absorption adjustment for high solar zenith angles - ! solar zenith angle parameterization - ! calculate the scaling factor for NIR direct albedo if SZA>75 degree - if ((mu_not < mu_75) .and. (flg_slr_in == 1)) then - sza_c1 = sza_a0 + sza_a1 * mu_not + sza_a2 * mu_not**2 - sza_c0 = sza_b0 + sza_b1 * mu_not + sza_b2 * mu_not**2 - sza_factor = sza_c1 * (log10(snw_rds_lcl(snl_top) * c1) - c6) + sza_c0 - flx_sza_adjust = albout(c_idx,2) * (sza_factor-c1) * sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) - albout(c_idx,2) = albout(c_idx,2) * sza_factor - flx_abs(c_idx,snl_top,2) = flx_abs(c_idx,snl_top,2) - flx_sza_adjust - endif - endif ! end of snicar_rt_solver==2 + ! near-IR direct albedo/absorption adjustment for high solar zenith angles + ! solar zenith angle parameterization + ! calculate the scaling factor for NIR direct albedo if SZA>75 degree + if ((mu_not < mu_75) .and. (flg_slr_in == 1)) then + sza_c1 = sza_a0 + sza_a1 * mu_not + sza_a2 * mu_not**2 + sza_c0 = sza_b0 + sza_b1 * mu_not + sza_b2 * mu_not**2 + sza_factor = sza_c1 * (log10(snw_rds_lcl(snl_top) * c1) - c6) + sza_c0 + flx_sza_adjust = albout(c_idx,2) * (sza_factor-c1) * sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + albout(c_idx,2) = albout(c_idx,2) * sza_factor + flx_abs(c_idx,snl_top,2) = flx_abs(c_idx,snl_top,2) - flx_sza_adjust + endif ! If snow < minimum_snow, but > 0, and there is sun, set albedo to underlying surface albedo diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index e5492c4a8b..7cf5a59560 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -245,10 +245,6 @@ module clm_varctl ! option to turn off aerosol effect in snow in SNICAR logical, public :: snicar_use_aerosol = .true. ! if .false., turn off aerosol deposition flux - ! option for two different SNICAR radiative transfer solver, cenlin - integer, public :: snicar_rt_solver = 2 ! 1->Toon et a 1989 2-stream (Flanner et al. 2007) - ! 2->Adding-doubling 2-stream (Dang et al.2019) - ! option for snow grain shape in SNICAR (He et al. 2017 JC), ceniln integer, public :: snicar_snw_shape = 3 ! 1->sphere; 2->spheroid; 3->hexagonal plate; 4->Koch snowflake diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 410229b87b..817a2b6d7a 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -203,7 +203,7 @@ subroutine control_init(dtime) irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & snicar_numrad_snw, snicar_solarspec, snicar_dust_optics, & - snicar_use_aerosol, snicar_rt_solver, snicar_snw_shape, snicar_snobc_intmix,& + snicar_use_aerosol, snicar_snw_shape, snicar_snobc_intmix,& snicar_snodst_intmix,DO_SNO_OC, & for_testing_use_second_grain_pool, for_testing_use_repr_structure_pool, & for_testing_no_crop_seed_replenishment @@ -590,12 +590,6 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if - ! check on SNICAR solver option - if ( (snicar_rt_solver < 1) .or. (snicar_rt_solver > 2) ) then - call endrun(msg=' ERROR: snicar_rt_solver is out of a reasonable range (1,2)'//& - errMsg(sourcefile, __LINE__)) - end if - ! check on SNICAR snow grain shape option if ( (snicar_snw_shape < 1) .or. (snicar_snw_shape > 4) ) then call endrun(msg=' ERROR: snicar_snw_shape is out of a reasonable range (1,2,3,4)'//& @@ -833,7 +827,6 @@ subroutine control_spmd() call mpi_bcast (snicar_solarspec, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (snicar_rt_solver, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_snw_shape, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_snodst_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -1020,7 +1013,6 @@ subroutine control_print () write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw - write(iulog,*) ' SNICAR: radiative transfer solver type = ',snicar_rt_solver write(iulog,*) ' SNICAR: snow grain shape type = ',snicar_snw_shape write(iulog,*) ' SNICAR: BC-snow internal mixing = ', snicar_snobc_intmix write(iulog,*) ' SNICAR: dust-snow internal mixing = ', snicar_snodst_intmix From ed66cf20ca94e83de079e683b06fee38d800f95f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 3 Aug 2023 13:33:25 -0600 Subject: [PATCH 1290/2067] Rename *master_list_* files to *history_fields_*. --- .../{README_master_list_files => README_history_fields_files} | 2 +- .../{master_list_fates.rst => history_fields_fates.rst} | 0 .../{master_list_nofates.rst => history_fields_nofates.rst} | 0 3 files changed, 1 insertion(+), 1 deletion(-) rename doc/source/users_guide/setting-up-and-running-a-case/{README_master_list_files => README_history_fields_files} (83%) rename doc/source/users_guide/setting-up-and-running-a-case/{master_list_fates.rst => history_fields_fates.rst} (100%) rename doc/source/users_guide/setting-up-and-running-a-case/{master_list_nofates.rst => history_fields_nofates.rst} (100%) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/README_master_list_files b/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files similarity index 83% rename from doc/source/users_guide/setting-up-and-running-a-case/README_master_list_files rename to doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files index 61f8ef44d4..c965536657 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/README_master_list_files +++ b/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files @@ -1,6 +1,6 @@ 2021/9/8 slevis -The files master_list_nofates.rst and master_list_fates.rst each contain a +The files history_fields_nofates.rst and history_fields_fates.rst each contain a table of the history fields, active and inactive, available in the CTSM cases that get generated by these tests: ERP_P36x2_D_Ld3.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-extra_outputs diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst similarity index 100% rename from doc/source/users_guide/setting-up-and-running-a-case/master_list_fates.rst rename to doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst similarity index 100% rename from doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst rename to doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst From 222c3e44066561d6e166984f81f2714115781296 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 3 Aug 2023 13:34:52 -0600 Subject: [PATCH 1291/2067] Update references to newly-renamed history_field files. --- .../customizing-the-clm-namelist.rst | 4 ++-- .../users_guide/setting-up-and-running-a-case/index.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst index 47274d8480..064d3f5979 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst @@ -43,12 +43,12 @@ Included in the table are the following pieces of information: Table 1-3. CLM History Fields from a BgcCrop case ------------------------------------------------- -For Table from a BgcCrop case, please see :doc:`master_list_nofates`. +For Table from a BgcCrop case, please see :doc:`history_fields_nofates`. Table 1-4. CLM History Fields from a Fates case ----------------------------------------------- -For Table from a Fates case, please see :doc:`master_list_fates`. +For Table from a Fates case, please see :doc:`history_fields_fates`. --------------------------------------------- diff --git a/doc/source/users_guide/setting-up-and-running-a-case/index.rst b/doc/source/users_guide/setting-up-and-running-a-case/index.rst index f882df277b..b11587ee21 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/index.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/index.rst @@ -18,6 +18,6 @@ Setting Up and Running a Case customizing-the-clm-configuration.rst customizing-the-clm-namelist.rst customizing-the-datm-namelist.rst - master_list_nofates - master_list_fates + history_fields_nofates + history_fields_fates From adbaa29b615fe4a4647687c14dd825416fed6d96 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 3 Aug 2023 13:35:50 -0600 Subject: [PATCH 1292/2067] Rename *master_list* variables to *hist_fields*, etc. --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- .../namelist_definition_ctsm.xml | 2 +- .../clm/FatesColdCH4Off/user_nl_clm | 2 +- .../clm/extra_outputs/user_nl_clm | 2 +- src/main/clm_varctl.F90 | 2 +- src/main/controlMod.F90 | 4 +- src/main/histFileMod.F90 | 60 +++++++++---------- 8 files changed, 38 insertions(+), 38 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 256de592c6..dece3da7d7 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4325,7 +4325,7 @@ sub setup_logic_misc { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_use_second_grain_pool'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_use_repr_structure_pool'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'for_testing_no_crop_seed_replenishment'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_master_list_file'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'hist_fields_list_file'); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3cf9a3ebc0..4cac65547e 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -68,7 +68,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. -.false. +.false. .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index dc693b50ba..3c017afee1 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -764,7 +764,7 @@ SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name - If TRUE, write master field list to separate file for documentation purposes diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/user_nl_clm index 4d7617fed4..9f977ac5ce 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdCH4Off/user_nl_clm @@ -1,2 +1,2 @@ use_lch4 = .false. -hist_master_list_file = .true. +hist_fields_list_file = .true. diff --git a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm index 6dc5225f1d..dad8a7e843 100644 --- a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/user_nl_clm @@ -1,5 +1,5 @@ calc_human_stress_indices = 'ALL' -hist_master_list_file = .true. +hist_fields_list_file = .true. hist_fincl1 += 'GSSUN:L43200', 'GSSHA:L43200', 'FSDSND:L43200', 'FSRND:L43200', 'FSRSFND:L43200', 'SSRE_FSRND:L43200', 'FSDSVD:L43200', 'FSDSVI:L43200', diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index f54c0b942c..bcf7a0ffd2 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -386,7 +386,7 @@ module clm_varctl logical, public :: hist_wrtch4diag = .false. ! namelist: write history master list to a file for use in documentation - logical, public :: hist_master_list_file = .false. + logical, public :: hist_fields_list_file = .false. !---------------------------------------------------------- ! FATES diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 42cd289aba..85ea04eb43 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -162,7 +162,7 @@ subroutine control_init(dtime) hist_fexcl4, hist_fexcl5, hist_fexcl6, & hist_fexcl7, hist_fexcl8, & hist_fexcl9, hist_fexcl10 - namelist /clm_inparm/ hist_wrtch4diag, hist_master_list_file + namelist /clm_inparm/ hist_wrtch4diag, hist_fields_list_file ! BGC info @@ -810,7 +810,7 @@ subroutine control_spmd() if (use_lch4) then call mpi_bcast (hist_wrtch4diag, 1, MPI_LOGICAL, 0, mpicom, ier) end if - call mpi_bcast (hist_master_list_file, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (hist_fields_list_file, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (hist_fexcl1, max_namlen*size(hist_fexcl1), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (hist_fexcl2, max_namlen*size(hist_fexcl2), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (hist_fexcl3, max_namlen*size(hist_fexcl3), MPI_CHARACTER, 0, mpicom, ier) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 92ce3dfa95..df91fa1e70 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -350,7 +350,7 @@ subroutine hist_printflds() ! Print summary of master field list. ! ! !USES: - use clm_varctl, only: hist_master_list_file + use clm_varctl, only: hist_fields_list_file use fileutils, only: getavu, relavu ! ! !ARGUMENTS: @@ -358,13 +358,13 @@ subroutine hist_printflds() ! !LOCAL VARIABLES: integer, parameter :: ncol = 5 ! number of table columns integer nf, i, j ! do-loop counters - integer master_list_file ! file unit number + integer hist_fields_file ! file unit number integer width_col(ncol) ! widths of table columns integer width_col_sum ! widths of columns summed, including spaces character(len=3) str_width_col(ncol) ! string version of width_col character(len=3) str_w_col_sum ! string version of width_col_sum character(len=7) file_identifier ! fates identifier used in file_name - character(len=23) file_name ! master_list_file.rst with or without fates + character(len=23) file_name ! hist_fields_file.rst with or without fates character(len=99) fmt_txt ! format statement character(len=*),parameter :: subname = 'CLM_hist_printflds' !----------------------------------------------------------------------- @@ -387,7 +387,7 @@ subroutine hist_printflds() ! First sort the list to be in alphabetical order call sort_hist_list(1, nfmaster, masterlist) - if (masterproc .and. hist_master_list_file) then + if (masterproc .and. hist_fields_list_file) then ! Hardwired table column widths to fit the table on a computer ! screen. Some strings will be truncated as a result of the ! current choices (4, 35, 94, 65, 7). In sphinx (ie the web-based @@ -407,67 +407,67 @@ subroutine hist_printflds() end do write(str_w_col_sum,'(i0)') width_col_sum - ! Open master_list_file - master_list_file = getavu() ! get next available file unit number + ! Open hist_fields_file + hist_fields_file = getavu() ! get next available file unit number if (use_fates) then file_identifier = 'fates' else file_identifier = 'nofates' end if - file_name = 'master_list_' // trim(file_identifier) // '.rst' - open(unit = master_list_file, file = file_name, & + file_name = 'history_fields_' // trim(file_identifier) // '.rst' + open(unit = hist_fields_file, file = file_name, & status = 'replace', action = 'write', form = 'formatted') ! File title fmt_txt = '(a)' - write(master_list_file,fmt_txt) '=============================' - write(master_list_file,fmt_txt) 'CTSM History Fields (' // trim(file_identifier) // ')' - write(master_list_file,fmt_txt) '=============================' - write(master_list_file,*) + write(hist_fields_file,fmt_txt) '=============================' + write(hist_fields_file,fmt_txt) 'CTSM History Fields (' // trim(file_identifier) // ')' + write(hist_fields_file,fmt_txt) '=============================' + write(hist_fields_file,*) ! A warning message and flags from the current CTSM case - write(master_list_file,fmt_txt) 'CAUTION: Not all variables are relevant / present for all CTSM cases.' - write(master_list_file,fmt_txt) 'Key flags used in this CTSM case:' + write(hist_fields_file,fmt_txt) 'CAUTION: Not all variables are relevant / present for all CTSM cases.' + write(hist_fields_file,fmt_txt) 'Key flags used in this CTSM case:' fmt_txt = '(a,l)' - write(master_list_file,fmt_txt) 'use_cn = ', use_cn - write(master_list_file,fmt_txt) 'use_crop = ', use_crop - write(master_list_file,fmt_txt) 'use_fates = ', use_fates - write(master_list_file,*) + write(hist_fields_file,fmt_txt) 'use_cn = ', use_cn + write(hist_fields_file,fmt_txt) 'use_crop = ', use_crop + write(hist_fields_file,fmt_txt) 'use_fates = ', use_fates + write(hist_fields_file,*) ! Table header ! Concatenate strings needed in format statement do i = 1, ncol fmt_txt = '('//str_width_col(i)//'a,x)' - write(master_list_file,fmt_txt,advance='no') ('=', j=1,width_col(i)) + write(hist_fields_file,fmt_txt,advance='no') ('=', j=1,width_col(i)) end do - write(master_list_file,*) ! next write statement will now appear in new line + write(hist_fields_file,*) ! next write statement will now appear in new line ! Table title fmt_txt = '(a)' - write(master_list_file,fmt_txt) 'CTSM History Fields' + write(hist_fields_file,fmt_txt) 'CTSM History Fields' ! Sub-header ! Concatenate strings needed in format statement fmt_txt = '('//str_w_col_sum//'a)' - write(master_list_file,fmt_txt) ('-', i=1, width_col_sum) + write(hist_fields_file,fmt_txt) ('-', i=1, width_col_sum) ! Concatenate strings needed in format statement fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',x,a'//str_width_col(5)//')' - write(master_list_file,fmt_txt) '#', 'Variable Name', & + write(hist_fields_file,fmt_txt) '#', 'Variable Name', & 'Long Description', 'Units', 'Active?' ! End header, same as header ! Concatenate strings needed in format statement do i = 1, ncol fmt_txt = '('//str_width_col(i)//'a,x)' - write(master_list_file,fmt_txt,advance='no') ('=', j=1,width_col(i)) + write(hist_fields_file,fmt_txt,advance='no') ('=', j=1,width_col(i)) end do - write(master_list_file,*) ! next write statement will now appear in new line + write(hist_fields_file,*) ! next write statement will now appear in new line ! Main table ! Concatenate strings needed in format statement fmt_txt = '(i'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',l'//str_width_col(5)//')' do nf = 1,nfmaster - write(master_list_file,fmt_txt) nf, & + write(hist_fields_file,fmt_txt) nf, & masterlist(nf)%field%name, & masterlist(nf)%field%long_name, & masterlist(nf)%field%units, & @@ -478,12 +478,12 @@ subroutine hist_printflds() ! Concatenate strings needed in format statement do i = 1, ncol fmt_txt = '('//str_width_col(i)//'a,x)' - write(master_list_file,fmt_txt,advance='no') ('=', j=1,width_col(i)) + write(hist_fields_file,fmt_txt,advance='no') ('=', j=1,width_col(i)) end do - call shr_sys_flush(master_list_file) - close(unit = master_list_file) - call relavu(master_list_file) ! close and release file unit number + call shr_sys_flush(hist_fields_file) + close(unit = hist_fields_file) + call relavu(hist_fields_file) ! close and release file unit number end if end subroutine hist_printflds From 0282e70545d5d357b4c2c11953da5ed79c12f8da Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 3 Aug 2023 13:37:45 -0600 Subject: [PATCH 1293/2067] Remove line numbers from history_fields files. --- .../history_fields_fates.rst | 1878 ++++++------ .../history_fields_nofates.rst | 2598 ++++++++--------- 2 files changed, 2238 insertions(+), 2238 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index 57edbfd3ca..8b30306a9e 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -13,943 +13,943 @@ CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Variable Name Long Description Units Active? ==== =================================== ============================================================================================== ================================================================= ======= - 1 A5TMIN 5-day running mean of min 2-m temperature K F - 2 ACTUAL_IMMOB actual N immobilization gN/m^2/s T - 3 ACT_SOMC ACT_SOM C gC/m^2 T - 4 ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F - 5 ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F - 6 ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F - 7 ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F - 8 ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F - 9 ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F - 10 ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T - 11 ACT_SOMN ACT_SOM N gN/m^2 T - 12 ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F - 13 ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F - 14 ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F - 15 ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F - 16 ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F - 17 ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F - 18 ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T - 19 ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F - 20 ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F - 21 ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F - 22 ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F - 23 AGB Aboveground biomass gC m-2 T - 24 AGB_SCLS Aboveground biomass by size class kgC/m2 T - 25 AGB_SCPF Aboveground biomass by pft/size kgC/m2 F - 26 AGLB Aboveground leaf biomass kg/m^2 F - 27 AGSB Aboveground stem biomass kg/m^2 F - 28 ALBD surface albedo (direct) proportion F - 29 ALBGRD ground albedo (direct) proportion F - 30 ALBGRI ground albedo (indirect) proportion F - 31 ALBI surface albedo (indirect) proportion F - 32 ALT current active layer thickness m F - 33 ALTMAX maximum annual active layer thickness m F - 34 ALTMAX_LASTYEAR maximum prior year active layer thickness m F - 35 AR autotrophic respiration gC/m^2/s T - 36 AREA_BURNT_BY_PATCH_AGE spitfire area burnt by patch age (divide by patch_area_by_age to get burnt fraction by age) m2/m2/day T - 37 AREA_PLANT area occupied by all plants m2/m2 T - 38 AREA_TREES area occupied by woody plants m2/m2 T - 39 AR_AGSAPM_SCPF above-ground sapwood maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 40 AR_CANOPY autotrophic respiration of canopy plants gC/m^2/s T - 41 AR_CANOPY_SCPF autotrophic respiration of canopy plants by pft/size kgC/m2/yr F - 42 AR_CROOTM_SCPF below-ground sapwood maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 43 AR_DARKM_SCPF dark portion of maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 44 AR_FROOTM_SCPF fine root maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 45 AR_GROW_SCPF growth autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 46 AR_MAINT_SCPF maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 47 AR_SCPF total autotrophic respiration per m2 per year by pft/size kgC/m2/yr F - 48 AR_UNDERSTORY autotrophic respiration of understory plants gC/m^2/s T - 49 AR_UNDERSTORY_SCPF autotrophic respiration of understory plants by pft/size kgC/m2/yr F - 50 ATM_TOPO atmospheric surface height m T - 51 AnnET Annual ET mm/s F - 52 BA_SCLS basal area by size class m2/ha T - 53 BA_SCPF basal area by pft/size m2/ha F - 54 BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T - 55 BDEAD_MD_CANOPY_SCLS BDEAD_MD for canopy plants by size class kg C / ha / yr F - 56 BDEAD_MD_UNDERSTORY_SCLS BDEAD_MD for understory plants by size class kg C / ha / yr F - 57 BIOMASS_AGEPFT biomass per PFT in each age bin kg C / m2 F - 58 BIOMASS_BY_AGE Total Biomass within a given patch age bin kgC/m2 F - 59 BIOMASS_CANOPY Biomass of canopy plants gC m-2 T - 60 BIOMASS_SCLS Total biomass by size class kgC/m2 F - 61 BIOMASS_UNDERSTORY Biomass of understory plants gC m-2 T - 62 BLEAF_CANOPY_SCPF biomass carbon in leaf of canopy plants by pft/size kgC/ha F - 63 BLEAF_UNDERSTORY_SCPF biomass carbon in leaf of understory plants by pft/size kgC/ha F - 64 BSTORE_MD_CANOPY_SCLS BSTORE_MD for canopy plants by size class kg C / ha / yr F - 65 BSTORE_MD_UNDERSTORY_SCLS BSTORE_MD for understory plants by size class kg C / ha / yr F - 66 BSTOR_CANOPY_SCPF biomass carbon in storage pools of canopy plants by pft/size kgC/ha F - 67 BSTOR_UNDERSTORY_SCPF biomass carbon in storage pools of understory plants by pft/size kgC/ha F - 68 BSW_MD_CANOPY_SCLS BSW_MD for canopy plants by size class kg C / ha / yr F - 69 BSW_MD_UNDERSTORY_SCLS BSW_MD for understory plants by size class kg C / ha / yr F - 70 BTRAN transpiration beta factor unitless T - 71 BTRANMN daily minimum of transpiration beta factor unitless T - 72 BURNT_LITTER_FRAC_AREA_PRODUCT product of fraction of fuel burnt and burned area (divide by FIRE_AREA to get burned-area-weig fraction T - 73 C13disc_SCPF C13 discrimination by pft/size per mil F - 74 CAMBIALFIREMORT_SCPF cambial fire mortality by pft/size N/ha/yr F - 75 CANOPY_AREA_BY_AGE canopy area by age bin m2/m2 T - 76 CANOPY_HEIGHT_DIST canopy height distribution m2/m2 T - 77 CANOPY_SPREAD Scaling factor between tree basal area and canopy area 0-1 T - 78 CARBON_BALANCE_CANOPY_SCLS CARBON_BALANCE for canopy plants by size class kg C / ha / yr F - 79 CARBON_BALANCE_UNDERSTORY_SCLS CARBON_BALANCE for understory plants by size class kg C / ha / yr F - 80 CBALANCE_ERROR_FATES total carbon error, FATES mgC/day T - 81 CEFFLUX carbon efflux, root to soil kgC/ha/day T - 82 CEFFLUX_SCPF carbon efflux, root to soil, by size-class x pft kg/ha/day F - 83 CEL_LITC CEL_LIT C gC/m^2 T - 84 CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F - 85 CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F - 86 CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F - 87 CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F - 88 CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T - 89 CEL_LITN CEL_LIT N gN/m^2 T - 90 CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F - 91 CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F - 92 CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F - 93 CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F - 94 CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T - 95 CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F - 96 CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F - 97 CH4PROD Gridcell total production of CH4 gC/m2/s T - 98 CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F - 99 CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F - 100 CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T - 101 CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 102 CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T - 103 CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 104 CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T - 105 CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 106 COL_CTRUNC column-level sink for C truncation gC/m^2 F - 107 COL_NTRUNC column-level sink for N truncation gN/m^2 F - 108 CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F - 109 CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F - 110 CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T - 111 CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T - 112 COSZEN cosine of solar zenith angle none F - 113 CROWNAREA_CAN total crown area in each canopy layer m2/m2 T - 114 CROWNAREA_CNLF total crown area that is occupied by leaves in each canopy and leaf layer m2/m2 F - 115 CROWNFIREMORT_SCPF crown fire mortality by pft/size N/ha/yr F - 116 CROWN_AREA_CANOPY_SCLS total crown area of canopy plants by size class m2/ha F - 117 CROWN_AREA_UNDERSTORY_SCLS total crown area of understory plants by size class m2/ha F - 118 CWDC_HR cwd C heterotrophic respiration gC/m^2/s F - 119 CWD_AG_CWDSC size-resolved AG CWD stocks gC/m^2 F - 120 CWD_AG_IN_CWDSC size-resolved AG CWD input gC/m^2/y F - 121 CWD_AG_OUT_CWDSC size-resolved AG CWD output gC/m^2/y F - 122 CWD_BG_CWDSC size-resolved BG CWD stocks gC/m^2 F - 123 CWD_BG_IN_CWDSC size-resolved BG CWD input gC/m^2/y F - 124 CWD_BG_OUT_CWDSC size-resolved BG CWD output gC/m^2/y F - 125 C_LBLAYER mean leaf boundary layer conductance umol m-2 s-1 T - 126 C_LBLAYER_BY_AGE mean leaf boundary layer conductance - by patch age umol m-2 s-1 F - 127 C_STOMATA mean stomatal conductance umol m-2 s-1 T - 128 C_STOMATA_BY_AGE mean stomatal conductance - by patch age umol m-2 s-1 F - 129 DDBH_CANOPY_SCAG growth rate of canopy plantsnumber of plants per hectare in canopy in each size x age class cm/yr/ha F - 130 DDBH_CANOPY_SCLS diameter growth increment by pft/size cm/yr/ha T - 131 DDBH_CANOPY_SCPF diameter growth increment by pft/size cm/yr/ha F - 132 DDBH_SCPF diameter growth increment by pft/size cm/yr/ha F - 133 DDBH_UNDERSTORY_SCAG growth rate of understory plants in each size x age class cm/yr/ha F - 134 DDBH_UNDERSTORY_SCLS diameter growth increment by pft/size cm/yr/ha T - 135 DDBH_UNDERSTORY_SCPF diameter growth increment by pft/size cm/yr/ha F - 136 DEMOTION_CARBONFLUX demotion-associated biomass carbon flux from canopy to understory gC/m2/s T - 137 DEMOTION_RATE_SCLS demotion rate from canopy to understory by size class indiv/ha/yr F - 138 DENIT total rate of denitrification gN/m^2/s T - 139 DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F - 140 DISPLA displacement height m F - 141 DISTURBANCE_RATE_FIRE Disturbance rate from fire m2 m-2 d-1 T - 142 DISTURBANCE_RATE_LOGGING Disturbance rate from logging m2 m-2 d-1 T - 143 DISTURBANCE_RATE_P2P Disturbance rate from primary to primary lands m2 m-2 d-1 T - 144 DISTURBANCE_RATE_P2S Disturbance rate from primary to secondary lands m2 m-2 d-1 T - 145 DISTURBANCE_RATE_POTENTIAL Potential (i.e., including unresolved) disturbance rate m2 m-2 d-1 T - 146 DISTURBANCE_RATE_S2S Disturbance rate from secondary to secondary lands m2 m-2 d-1 T - 147 DISTURBANCE_RATE_TREEFALL Disturbance rate from treefall m2 m-2 d-1 T - 148 DPVLTRB1 turbulent deposition velocity 1 m/s F - 149 DPVLTRB2 turbulent deposition velocity 2 m/s F - 150 DPVLTRB3 turbulent deposition velocity 3 m/s F - 151 DPVLTRB4 turbulent deposition velocity 4 m/s F - 152 DSL dry surface layer thickness mm T - 153 DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T - 154 DSTFLXT total surface dust emission kg/m2/s T - 155 DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F - 156 DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F - 157 DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F - 158 ED_NCOHORTS Total number of ED cohorts per site none T - 159 ED_NPATCHES Total number of ED patches per site none T - 160 ED_balive Live biomass gC m-2 T - 161 ED_bdead Dead (structural) biomass (live trees, not CWD) gC m-2 T - 162 ED_bfineroot Fine root biomass gC m-2 T - 163 ED_biomass Total biomass gC m-2 T - 164 ED_bleaf Leaf biomass gC m-2 T - 165 ED_bsapwood Sapwood biomass gC m-2 T - 166 ED_bstore Storage biomass gC m-2 T - 167 EFFECT_WSPEED effective windspeed for fire spread none T - 168 EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T - 169 EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T - 170 EFLX_GNET net heat flux into ground W/m^2 F - 171 EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T - 172 EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T - 173 EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F - 174 EFLX_LH_TOT_R Rural total evaporation W/m^2 T - 175 EFLX_LH_TOT_U Urban total evaporation W/m^2 F - 176 EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F - 177 ELAI exposed one-sided leaf area index m^2/m^2 T - 178 ERRH2O total water conservation error mm T - 179 ERRH2OSNO imbalance in snow depth (liquid water) mm T - 180 ERROR_FATES total error, FATES mass-balance mg/day T - 181 ERRSEB surface energy conservation error W/m^2 T - 182 ERRSOI soil/lake energy conservation error W/m^2 T - 183 ERRSOL solar radiation conservation error W/m^2 T - 184 ESAI exposed one-sided stem area index m^2/m^2 T - 185 FABD_SHA_CNLF shade fraction of direct light absorbed by each canopy and leaf layer fraction F - 186 FABD_SHA_CNLFPFT shade fraction of direct light absorbed by each canopy, leaf, and PFT fraction F - 187 FABD_SHA_TOPLF_BYCANLAYER shade fraction of direct light absorbed by the top leaf layer of each canopy layer fraction F - 188 FABD_SUN_CNLF sun fraction of direct light absorbed by each canopy and leaf layer fraction F - 189 FABD_SUN_CNLFPFT sun fraction of direct light absorbed by each canopy, leaf, and PFT fraction F - 190 FABD_SUN_TOPLF_BYCANLAYER sun fraction of direct light absorbed by the top leaf layer of each canopy layer fraction F - 191 FABI_SHA_CNLF shade fraction of indirect light absorbed by each canopy and leaf layer fraction F - 192 FABI_SHA_CNLFPFT shade fraction of indirect light absorbed by each canopy, leaf, and PFT fraction F - 193 FABI_SHA_TOPLF_BYCANLAYER shade fraction of indirect light absorbed by the top leaf layer of each canopy layer fraction F - 194 FABI_SUN_CNLF sun fraction of indirect light absorbed by each canopy and leaf layer fraction F - 195 FABI_SUN_CNLFPFT sun fraction of indirect light absorbed by each canopy, leaf, and PFT fraction F - 196 FABI_SUN_TOPLF_BYCANLAYER sun fraction of indirect light absorbed by the top leaf layer of each canopy layer fraction F - 197 FATES_HR heterotrophic respiration gC/m^2/s T - 198 FATES_c_to_litr_cel_c litter celluluse carbon flux from FATES to BGC gC/m^3/s T - 199 FATES_c_to_litr_lab_c litter labile carbon flux from FATES to BGC gC/m^3/s T - 200 FATES_c_to_litr_lig_c litter lignin carbon flux from FATES to BGC gC/m^3/s T - 201 FCEV canopy evaporation W/m^2 T - 202 FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T - 203 FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T - 204 FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T - 205 FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F - 206 FCOV fractional impermeable area unitless T - 207 FCTR canopy transpiration W/m^2 T - 208 FGEV ground evaporation W/m^2 T - 209 FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T - 210 FGR12 heat flux between soil layers 1 and 2 W/m^2 T - 211 FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F - 212 FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F - 213 FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F - 214 FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F - 215 FH2OSFC fraction of ground covered by surface water unitless T - 216 FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F - 217 FINUNDATED fractional inundated area of vegetated columns unitless T - 218 FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F - 219 FIRA net infrared (longwave) radiation W/m^2 T - 220 FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F - 221 FIRA_R Rural net infrared (longwave) radiation W/m^2 T - 222 FIRA_U Urban net infrared (longwave) radiation W/m^2 F - 223 FIRE emitted infrared (longwave) radiation W/m^2 T - 224 FIRE_AREA spitfire fire area burn fraction fraction/day T - 225 FIRE_FDI probability that an ignition will lead to a fire none T - 226 FIRE_FLUX ED-spitfire loss to atmosphere of elements g/m^2/s T - 227 FIRE_FUEL_BULKD spitfire fuel bulk density kg biomass/m3 T - 228 FIRE_FUEL_EFF_MOIST spitfire fuel moisture m T - 229 FIRE_FUEL_MEF spitfire fuel moisture m T - 230 FIRE_FUEL_SAV spitfire fuel surface/volume per m T - 231 FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F - 232 FIRE_IGNITIONS number of successful ignitions number/km2/day T - 233 FIRE_INTENSITY spitfire fire intensity: kJ/m/s kJ/m/s T - 234 FIRE_INTENSITY_AREA_PRODUCT spitfire product of fire intensity and burned area (divide by FIRE_AREA to get area-weighted m kJ/m/s T - 235 FIRE_INTENSITY_BY_PATCH_AGE product of fire intensity and burned area, resolved by patch age (so divide by AREA_BURNT_BY_P kJ/m/2 T - 236 FIRE_NESTEROV_INDEX nesterov_fire_danger index none T - 237 FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T - 238 FIRE_ROS fire rate of spread m/min m/min T - 239 FIRE_ROS_AREA_PRODUCT product of fire rate of spread (m/min) and burned area (fraction)--divide by FIRE_AREA to get m/min T - 240 FIRE_TFC_ROS total fuel consumed kgC/m2 T - 241 FIRE_TFC_ROS_AREA_PRODUCT product of total fuel consumed and burned area--divide by FIRE_AREA to get burned-area-weighte kgC/m2 T - 242 FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F - 243 FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T - 244 FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F - 245 FNRTC Total carbon in live plant fine-roots kgC ha-1 T - 246 FNRTC_SCPF fine-root carbon mass by size-class x pft kgC/ha F - 247 FRAGMENTATION_SCALER_SL factor by which litter/cwd fragmentation proceeds relative to max rate by soil layer unitless (0-1) T - 248 FROOT_MR fine root maintenance respiration) kg C / m2 / yr T - 249 FROOT_MR_CANOPY_SCLS FROOT_MR for canopy plants by size class kg C / ha / yr F - 250 FROOT_MR_UNDERSTORY_SCLS FROOT_MR for understory plants by size class kg C / ha / yr F - 251 FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F - 252 FSA absorbed solar radiation W/m^2 T - 253 FSAT fractional area with water table at surface unitless T - 254 FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F - 255 FSA_R Rural absorbed solar radiation W/m^2 F - 256 FSA_U Urban absorbed solar radiation W/m^2 F - 257 FSD24 direct radiation (last 24hrs) K F - 258 FSD240 direct radiation (last 240hrs) K F - 259 FSDS atmospheric incident solar radiation W/m^2 T - 260 FSDSND direct nir incident solar radiation W/m^2 T - 261 FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T - 262 FSDSNI diffuse nir incident solar radiation W/m^2 T - 263 FSDSVD direct vis incident solar radiation W/m^2 T - 264 FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T - 265 FSDSVI diffuse vis incident solar radiation W/m^2 T - 266 FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T - 267 FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T - 268 FSH_G sensible heat from ground W/m^2 T - 269 FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F - 270 FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T - 271 FSH_R Rural sensible heat W/m^2 T - 272 FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T - 273 FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T - 274 FSH_U Urban sensible heat W/m^2 F - 275 FSH_V sensible heat from veg W/m^2 T - 276 FSI24 indirect radiation (last 24hrs) K F - 277 FSI240 indirect radiation (last 240hrs) K F - 278 FSM snow melt heat flux W/m^2 T - 279 FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F - 280 FSM_R Rural snow melt heat flux W/m^2 F - 281 FSM_U Urban snow melt heat flux W/m^2 F - 282 FSNO fraction of ground covered by snow unitless T - 283 FSNO_EFF effective fraction of ground covered by snow unitless T - 284 FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F - 285 FSR reflected solar radiation W/m^2 T - 286 FSRND direct nir reflected solar radiation W/m^2 T - 287 FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T - 288 FSRNI diffuse nir reflected solar radiation W/m^2 T - 289 FSRVD direct vis reflected solar radiation W/m^2 T - 290 FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T - 291 FSRVI diffuse vis reflected solar radiation W/m^2 T - 292 FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F - 293 FSUN sunlit fraction of canopy proportion F - 294 FSUN24 fraction sunlit (last 24hrs) K F - 295 FSUN240 fraction sunlit (last 240hrs) K F - 296 FUEL_AMOUNT_AGEFUEL spitfire fuel quantity in each age x fuel class kg C / m2 T - 297 FUEL_AMOUNT_BY_NFSC spitfire size-resolved fuel quantity kg C / m2 T - 298 FUEL_MOISTURE_NFSC spitfire size-resolved fuel moisture - T - 299 Fire_Closs ED/SPitfire Carbon loss to atmosphere gC/m^2/s T - 300 GPP gross primary production gC/m^2/s T - 301 GPP_BY_AGE gross primary productivity by age bin gC/m^2/s F - 302 GPP_CANOPY gross primary production of canopy plants gC/m^2/s T - 303 GPP_CANOPY_SCPF gross primary production of canopy plants by pft/size kgC/m2/yr F - 304 GPP_SCPF gross primary production by pft/size kgC/m2/yr F - 305 GPP_UNDERSTORY gross primary production of understory plants gC/m^2/s T - 306 GPP_UNDERSTORY_SCPF gross primary production of understory plants by pft/size kgC/m2/yr F - 307 GROSS_NMIN gross rate of N mineralization gN/m^2/s T - 308 GROWTHFLUX_FUSION_SCPF flux of individuals into a given size class bin via fusion n/yr/ha F - 309 GROWTHFLUX_SCPF flux of individuals into a given size class bin via growth and recruitment n/yr/ha F - 310 GROWTH_RESP growth respiration gC/m^2/s T - 311 GSSHA shaded leaf stomatal conductance umol H20/m2/s T - 312 GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T - 313 GSSUN sunlit leaf stomatal conductance umol H20/m2/s T - 314 GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T - 315 H2OCAN intercepted water mm T - 316 H2OSFC surface water depth mm T - 317 H2OSNO snow depth (liquid water) mm T - 318 H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F - 319 H2OSNO_TOP mass of snow in top snow layer kg/m2 T - 320 H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T - 321 HARVEST_CARBON_FLUX Harvest carbon flux kg C m-2 d-1 T - 322 HBOT canopy bottom m F - 323 HEAT_CONTENT1 initial gridcell total heat content J/m^2 T - 324 HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F - 325 HEAT_CONTENT2 post land cover change total heat content J/m^2 F - 326 HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T - 327 HIA 2 m NWS Heat Index C T - 328 HIA_R Rural 2 m NWS Heat Index C T - 329 HIA_U Urban 2 m NWS Heat Index C T - 330 HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F - 331 HR total heterotrophic respiration gC/m^2/s T - 332 HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T - 333 HTOP canopy top m T - 334 HUMIDEX 2 m Humidex C T - 335 HUMIDEX_R Rural 2 m Humidex C T - 336 HUMIDEX_U Urban 2 m Humidex C T - 337 ICE_CONTENT1 initial gridcell total ice content mm T - 338 ICE_CONTENT2 post land cover change total ice content mm F - 339 ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F - 340 INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F - 341 INT_SNOW_ICE accumulated swe (ice landunits only) mm F - 342 IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T - 343 KROOT root conductance each soil layer 1/s F - 344 KSOIL soil conductance in each soil layer 1/s F - 345 K_ACT_SOM active soil organic potential loss coefficient 1/s F - 346 K_CEL_LIT cellulosic litter potential loss coefficient 1/s F - 347 K_LIG_LIT lignin litter potential loss coefficient 1/s F - 348 K_MET_LIT metabolic litter potential loss coefficient 1/s F - 349 K_PAS_SOM passive soil organic potential loss coefficient 1/s F - 350 K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F - 351 LAI240 240hr average of leaf area index m^2/m^2 F - 352 LAISHA shaded projected leaf area index m^2/m^2 T - 353 LAISHA_TOP_CAN LAI in the shade by the top leaf layer of each canopy layer m2/m2 F - 354 LAISHA_Z_CNLF LAI in the shade by each canopy and leaf layer m2/m2 F - 355 LAISHA_Z_CNLFPFT LAI in the shade by each canopy, leaf, and PFT m2/m2 F - 356 LAISUN sunlit projected leaf area index m^2/m^2 T - 357 LAISUN_TOP_CAN LAI in the sun by the top leaf layer of each canopy layer m2/m2 F - 358 LAISUN_Z_CNLF LAI in the sun by each canopy and leaf layer m2/m2 F - 359 LAISUN_Z_CNLFPFT LAI in the sun by each canopy, leaf, and PFT m2/m2 F - 360 LAI_BY_AGE leaf area index by age bin m2/m2 T - 361 LAI_CANOPY_SCLS Leaf are index (LAI) by size class m2/m2 T - 362 LAI_UNDERSTORY_SCLS number of understory plants by size class indiv/ha T - 363 LAKEICEFRAC lake layer ice mass fraction unitless F - 364 LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T - 365 LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T - 366 LEAFC Total carbon in live plant leaves kgC ha-1 T - 367 LEAFC_SCPF leaf carbon mass by size-class x pft kgC/ha F - 368 LEAF_HEIGHT_DIST leaf height distribution m2/m2 T - 369 LEAF_MD_CANOPY_SCLS LEAF_MD for canopy plants by size class kg C / ha / yr F - 370 LEAF_MD_UNDERSTORY_SCLS LEAF_MD for understory plants by size class kg C / ha / yr F - 371 LEAF_MR RDARK (leaf maintenance respiration) kg C / m2 / yr T - 372 LIG_LITC LIG_LIT C gC/m^2 T - 373 LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F - 374 LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F - 375 LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F - 376 LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F - 377 LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T - 378 LIG_LITN LIG_LIT N gN/m^2 T - 379 LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F - 380 LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F - 381 LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F - 382 LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F - 383 LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T - 384 LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F - 385 LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F - 386 LIQCAN intercepted liquid water mm T - 387 LIQUID_CONTENT1 initial gridcell total liq content mm T - 388 LIQUID_CONTENT2 post landuse change gridcell total liq content mm F - 389 LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F - 390 LITTERC_HR litter C heterotrophic respiration gC/m^2/s T - 391 LITTER_CWD total mass of litter in CWD kg ha-1 T - 392 LITTER_CWD_AG_ELEM mass of above ground litter in CWD (trunks/branches/twigs) kg ha-1 T - 393 LITTER_CWD_BG_ELEM mass of below ground litter in CWD (coarse roots) kg ha-1 T - 394 LITTER_FINES_AG_ELEM mass of above ground litter in fines (leaves,nonviable seed) kg ha-1 T - 395 LITTER_FINES_BG_ELEM mass of below ground litter in fines (fineroots) kg ha-1 T - 396 LITTER_IN FATES litter flux in gC m-2 s-1 T - 397 LITTER_IN_ELEM FATES litter flux in kg ha-1 d-1 T - 398 LITTER_OUT FATES litter flux out gC m-2 s-1 T - 399 LITTER_OUT_ELEM FATES litter flux out (fragmentation only) kg ha-1 d-1 T - 400 LIVECROOT_MR live coarse root maintenance respiration) kg C / m2 / yr T - 401 LIVECROOT_MR_CANOPY_SCLS LIVECROOT_MR for canopy plants by size class kg C / ha / yr F - 402 LIVECROOT_MR_UNDERSTORY_SCLS LIVECROOT_MR for understory plants by size class kg C / ha / yr F - 403 LIVESTEM_MR live stem maintenance respiration) kg C / m2 / yr T - 404 LIVESTEM_MR_CANOPY_SCLS LIVESTEM_MR for canopy plants by size class kg C / ha / yr F - 405 LIVESTEM_MR_UNDERSTORY_SCLS LIVESTEM_MR for understory plants by size class kg C / ha / yr F - 406 LNC leaf N concentration gN leaf/m^2 T - 407 LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F - 408 LWup upwelling longwave radiation W/m^2 F - 409 M10_CACLS age senescence mortality by cohort age N/ha/yr T - 410 M10_CAPF age senescence mortality by pft/cohort age N/ha/yr F - 411 M10_SCLS age senescence mortality by size N/ha/yr T - 412 M10_SCPF age senescence mortality by pft/size N/ha/yr F - 413 M1_SCLS background mortality by size N/ha/yr T - 414 M1_SCPF background mortality by pft/size N/ha/yr F - 415 M2_SCLS hydraulic mortality by size N/ha/yr T - 416 M2_SCPF hydraulic mortality by pft/size N/ha/yr F - 417 M3_SCLS carbon starvation mortality by size N/ha/yr T - 418 M3_SCPF carbon starvation mortality by pft/size N/ha/yr F - 419 M4_SCLS impact mortality by size N/ha/yr T - 420 M4_SCPF impact mortality by pft/size N/ha/yr F - 421 M5_SCLS fire mortality by size N/ha/yr T - 422 M5_SCPF fire mortality by pft/size N/ha/yr F - 423 M6_SCLS termination mortality by size N/ha/yr T - 424 M6_SCPF termination mortality by pft/size N/ha/yr F - 425 M7_SCLS logging mortality by size N/ha/event T - 426 M7_SCPF logging mortality by pft/size N/ha/event F - 427 M8_SCLS freezing mortality by size N/ha/event T - 428 M8_SCPF freezing mortality by pft/size N/ha/yr F - 429 M9_SCLS senescence mortality by size N/ha/yr T - 430 M9_SCPF senescence mortality by pft/size N/ha/yr F - 431 MAINT_RESP maintenance respiration gC/m^2/s T - 432 MET_LITC MET_LIT C gC/m^2 T - 433 MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F - 434 MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F - 435 MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F - 436 MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F - 437 MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T - 438 MET_LITN MET_LIT N gN/m^2 T - 439 MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F - 440 MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F - 441 MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F - 442 MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F - 443 MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T - 444 MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F - 445 MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F - 446 MORTALITY Rate of total mortality by PFT indiv/ha/yr T - 447 MORTALITY_CANOPY_SCAG mortality rate of canopy plants in each size x age class plants/ha/yr F - 448 MORTALITY_CANOPY_SCLS total mortality of canopy trees by size class indiv/ha/yr T - 449 MORTALITY_CANOPY_SCPF total mortality of canopy plants by pft/size N/ha/yr F - 450 MORTALITY_CARBONFLUX_CANOPY flux of biomass carbon from live to dead pools from mortality of canopy plants gC/m2/s T - 451 MORTALITY_CARBONFLUX_UNDERSTORY flux of biomass carbon from live to dead pools from mortality of understory plants gC/m2/s T - 452 MORTALITY_UNDERSTORY_SCAG mortality rate of understory plantsin each size x age class plants/ha/yr F - 453 MORTALITY_UNDERSTORY_SCLS total mortality of understory trees by size class indiv/ha/yr T - 454 MORTALITY_UNDERSTORY_SCPF total mortality of understory plants by pft/size N/ha/yr F - 455 M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F - 456 M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F - 457 M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F - 458 M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F - 459 M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F - 460 M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F - 461 M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F - 462 M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F - 463 M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F - 464 M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F - 465 M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F - 466 M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F - 467 NCL_BY_AGE number of canopy levels by age bin -- F - 468 NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T - 469 NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T - 470 NEP net ecosystem production gC/m^2/s T - 471 NET_C_UPTAKE_CNLF net carbon uptake by each canopy and leaf layer per unit ground area (i.e. divide by CROWNAREA gC/m2/s F - 472 NET_NMIN net rate of N mineralization gN/m^2/s T - 473 NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T - 474 NPATCH_BY_AGE number of patches by age bin -- F - 475 NPLANT_CACLS number of plants by coage class indiv/ha T - 476 NPLANT_CANOPY_SCAG number of plants per hectare in canopy in each size x age class plants/ha F - 477 NPLANT_CANOPY_SCLS number of canopy plants by size class indiv/ha T - 478 NPLANT_CANOPY_SCPF stem number of canopy plants density by pft/size N/ha F - 479 NPLANT_CAPF stem number density by pft/coage N/ha F - 480 NPLANT_SCAG number of plants per hectare in each size x age class plants/ha T - 481 NPLANT_SCAGPFT number of plants per hectare in each size x age x pft class plants/ha F - 482 NPLANT_SCLS number of plants by size class indiv/ha T - 483 NPLANT_SCPF stem number density by pft/size N/ha F - 484 NPLANT_UNDERSTORY_SCAG number of plants per hectare in understory in each size x age class plants/ha F - 485 NPLANT_UNDERSTORY_SCLS number of understory plants by size class indiv/ha T - 486 NPLANT_UNDERSTORY_SCPF stem number of understory plants density by pft/size N/ha F - 487 NPP net primary production gC/m^2/s T - 488 NPP_AGDW_SCPF NPP flux into above-ground deadwood by pft/size kgC/m2/yr F - 489 NPP_AGEPFT NPP per PFT in each age bin kgC/m2/yr F - 490 NPP_AGSW_SCPF NPP flux into above-ground sapwood by pft/size kgC/m2/yr F - 491 NPP_BDEAD_CANOPY_SCLS NPP_BDEAD for canopy plants by size class kg C / ha / yr F - 492 NPP_BDEAD_UNDERSTORY_SCLS NPP_BDEAD for understory plants by size class kg C / ha / yr F - 493 NPP_BGDW_SCPF NPP flux into below-ground deadwood by pft/size kgC/m2/yr F - 494 NPP_BGSW_SCPF NPP flux into below-ground sapwood by pft/size kgC/m2/yr F - 495 NPP_BSEED_CANOPY_SCLS NPP_BSEED for canopy plants by size class kg C / ha / yr F - 496 NPP_BSEED_UNDERSTORY_SCLS NPP_BSEED for understory plants by size class kg C / ha / yr F - 497 NPP_BSW_CANOPY_SCLS NPP_BSW for canopy plants by size class kg C / ha / yr F - 498 NPP_BSW_UNDERSTORY_SCLS NPP_BSW for understory plants by size class kg C / ha / yr F - 499 NPP_BY_AGE net primary productivity by age bin gC/m^2/s F - 500 NPP_CROOT NPP flux into coarse roots kgC/m2/yr T - 501 NPP_FNRT_SCPF NPP flux into fine roots by pft/size kgC/m2/yr F - 502 NPP_FROOT NPP flux into fine roots kgC/m2/yr T - 503 NPP_FROOT_CANOPY_SCLS NPP_FROOT for canopy plants by size class kg C / ha / yr F - 504 NPP_FROOT_UNDERSTORY_SCLS NPP_FROOT for understory plants by size class kg C / ha / yr F - 505 NPP_LEAF NPP flux into leaves kgC/m2/yr T - 506 NPP_LEAF_CANOPY_SCLS NPP_LEAF for canopy plants by size class kg C / ha / yr F - 507 NPP_LEAF_SCPF NPP flux into leaves by pft/size kgC/m2/yr F - 508 NPP_LEAF_UNDERSTORY_SCLS NPP_LEAF for understory plants by size class kg C / ha / yr F - 509 NPP_SCPF total net primary production by pft/size kgC/m2/yr F - 510 NPP_SEED NPP flux into seeds kgC/m2/yr T - 511 NPP_SEED_SCPF NPP flux into seeds by pft/size kgC/m2/yr F - 512 NPP_STEM NPP flux into stem kgC/m2/yr T - 513 NPP_STOR NPP flux into storage tissues kgC/m2/yr T - 514 NPP_STORE_CANOPY_SCLS NPP_STORE for canopy plants by size class kg C / ha / yr F - 515 NPP_STORE_UNDERSTORY_SCLS NPP_STORE for understory plants by size class kg C / ha / yr F - 516 NPP_STOR_SCPF NPP flux into storage by pft/size kgC/m2/yr F - 517 NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F - 518 O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F - 519 OBU Monin-Obukhov length m F - 520 OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T - 521 O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T - 522 PARPROF_DIF_CNLF Radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W/m2 F - 523 PARPROF_DIF_CNLFPFT Radiative profile of diffuse PAR through each canopy, leaf, and PFT W/m2 F - 524 PARPROF_DIR_CNLF Radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W/m2 F - 525 PARPROF_DIR_CNLFPFT Radiative profile of direct PAR through each canopy, leaf, and PFT W/m2 F - 526 PARSHA_Z_CAN PAR absorbed in the shade by top leaf layer in each canopy layer W/m2 F - 527 PARSHA_Z_CNLF PAR absorbed in the shade by each canopy and leaf layer W/m2 F - 528 PARSHA_Z_CNLFPFT PAR absorbed in the shade by each canopy, leaf, and PFT W/m2 F - 529 PARSUN_Z_CAN PAR absorbed in the sun by top leaf layer in each canopy layer W/m2 F - 530 PARSUN_Z_CNLF PAR absorbed in the sun by each canopy and leaf layer W/m2 F - 531 PARSUN_Z_CNLFPFT PAR absorbed in the sun by each canopy, leaf, and PFT W/m2 F - 532 PARVEGLN absorbed par by vegetation at local noon W/m^2 T - 533 PAS_SOMC PAS_SOM C gC/m^2 T - 534 PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F - 535 PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F - 536 PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F - 537 PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F - 538 PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T - 539 PAS_SOMN PAS_SOM N gN/m^2 T - 540 PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F - 541 PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F - 542 PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F - 543 PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F - 544 PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T - 545 PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F - 546 PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F - 547 PATCH_AREA_BY_AGE patch area by age bin m2/m2 T - 548 PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T - 549 PCH4 atmospheric partial pressure of CH4 Pa T - 550 PCO2 atmospheric partial pressure of CO2 Pa T - 551 PFTbiomass total PFT level biomass gC/m2 T - 552 PFTcanopycrownarea total PFT-level canopy-layer crown area m2/m2 F - 553 PFTcrownarea total PFT level crown area m2/m2 F - 554 PFTgpp total PFT-level GPP kg C m-2 y-1 T - 555 PFTleafbiomass total PFT level leaf biomass gC/m2 T - 556 PFTnindivs total PFT level number of individuals indiv / m2 T - 557 PFTnpp total PFT-level NPP kg C m-2 y-1 T - 558 PFTstorebiomass total PFT level stored biomass gC/m2 T - 559 POTENTIAL_IMMOB potential N immobilization gN/m^2/s T - 560 PRIMARYLAND_PATCHFUSION_ERROR Error in total primary lands associated with patch fusion m2 m-2 d-1 T - 561 PROMOTION_CARBONFLUX promotion-associated biomass carbon flux from understory to canopy gC/m2/s T - 562 PROMOTION_RATE_SCLS promotion rate from understory to canopy by size class indiv/ha/yr F - 563 PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F - 564 Q2M 2m specific humidity kg/kg T - 565 QAF canopy air humidity kg/kg F - 566 QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T - 567 QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F - 568 QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F - 569 QDRAI sub-surface drainage mm/s T - 570 QDRAI_PERCH perched wt drainage mm/s T - 571 QDRAI_XS saturation excess drainage mm/s T - 572 QDRIP rate of excess canopy liquid falling off canopy mm/s F - 573 QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F - 574 QFLOOD runoff from river flooding mm/s T - 575 QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T - 576 QFLX_EVAP_VEG vegetation evaporation mm H2O/s F - 577 QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T - 578 QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T - 579 QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T - 580 QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T - 581 QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F - 582 QFLX_SNOW_DRAIN drainage from snow pack mm/s T - 583 QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T - 584 QFLX_SNOW_GRND snow on ground after interception mm H2O/s F - 585 QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T - 586 QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T - 587 QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F - 588 QH2OSFC surface water runoff mm/s T - 589 QH2OSFC_TO_ICE surface water converted to ice mm/s F - 590 QHR hydraulic redistribution mm/s T - 591 QICE ice growth/melt mm/s T - 592 QICE_FORC qice forcing sent to GLC mm/s F - 593 QICE_FRZ ice growth mm/s T - 594 QICE_MELT ice melt mm/s T - 595 QINFL infiltration mm/s T - 596 QINTR interception mm/s T - 597 QIRRIG_DEMAND irrigation demand mm/s F - 598 QIRRIG_DRIP water added via drip irrigation mm/s F - 599 QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T - 600 QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T - 601 QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T - 602 QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F - 603 QOVER total surface runoff (includes QH2OSFC) mm/s T - 604 QOVER_LAG time-lagged surface runoff for soil columns mm/s F - 605 QPHSNEG net negative hydraulic redistribution flux mm/s F - 606 QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T - 607 QROOTSINK water flux from soil to root in each soil-layer mm/s F - 608 QRUNOFF total liquid runoff not including correction for land use change mm/s T - 609 QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T - 610 QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T - 611 QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F - 612 QRUNOFF_R Rural total runoff mm/s F - 613 QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T - 614 QRUNOFF_U Urban total runoff mm/s F - 615 QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T - 616 QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T - 617 QSNOFRZ column-integrated snow freezing rate kg/m2/s T - 618 QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T - 619 QSNOMELT snow melt rate mm/s T - 620 QSNOMELT_ICE snow melt (ice landunits only) mm/s T - 621 QSNOUNLOAD canopy snow unloading mm/s T - 622 QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T - 623 QSNO_WINDUNLOAD canopy snow wind unloading mm/s T - 624 QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T - 625 QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T - 626 QSOIL_ICE Ground evaporation (ice landunits only) mm/s T - 627 QTOPSOIL water input to surface mm/s F - 628 QVEGE canopy evaporation mm/s T - 629 QVEGT canopy transpiration mm/s T - 630 Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F - 631 Qh sensible heat W/m^2 F - 632 Qle total evaporation W/m^2 F - 633 Qstor storage heat flux (includes snowmelt) W/m^2 F - 634 Qtau momentum flux kg/m/s^2 F - 635 RAH1 aerodynamical resistance s/m F - 636 RAH2 aerodynamical resistance s/m F - 637 RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T - 638 RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T - 639 RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F - 640 RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F - 641 RAW1 aerodynamical resistance s/m F - 642 RAW2 aerodynamical resistance s/m F - 643 RB leaf boundary resistance s/m F - 644 RDARK_CANOPY_SCLS RDARK for canopy plants by size class kg C / ha / yr F - 645 RDARK_UNDERSTORY_SCLS RDARK for understory plants by size class kg C / ha / yr F - 646 RECRUITMENT Rate of recruitment by PFT indiv/ha/yr T - 647 REPROC Total carbon in live plant reproductive tissues kgC ha-1 T - 648 REPROC_SCPF reproductive carbon mass (on plant) by size-class x pft kgC/ha F - 649 RESP_G_CANOPY_SCLS RESP_G for canopy plants by size class kg C / ha / yr F - 650 RESP_G_UNDERSTORY_SCLS RESP_G for understory plants by size class kg C / ha / yr F - 651 RESP_M_CANOPY_SCLS RESP_M for canopy plants by size class kg C / ha / yr F - 652 RESP_M_UNDERSTORY_SCLS RESP_M for understory plants by size class kg C / ha / yr F - 653 RH atmospheric relative humidity % F - 654 RH2M 2m relative humidity % T - 655 RH2M_R Rural 2m specific humidity % F - 656 RH2M_U Urban 2m relative humidity % F - 657 RHAF fractional humidity of canopy air fraction F - 658 RH_LEAF fractional humidity at leaf surface fraction F - 659 ROOT_MD_CANOPY_SCLS ROOT_MD for canopy plants by size class kg C / ha / yr F - 660 ROOT_MD_UNDERSTORY_SCLS ROOT_MD for understory plants by size class kg C / ha / yr F - 661 RSCANOPY canopy resistance s m-1 T - 662 RSSHA shaded leaf stomatal resistance s/m T - 663 RSSUN sunlit leaf stomatal resistance s/m T - 664 Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F - 665 Rnet net radiation W/m^2 F - 666 SABG solar rad absorbed by ground W/m^2 T - 667 SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T - 668 SABV solar rad absorbed by veg W/m^2 T - 669 SAI_CANOPY_SCLS stem area index(SAI) by size class m2/m2 F - 670 SAI_UNDERSTORY_SCLS number of understory plants by size class indiv/ha F - 671 SAPWC Total carbon in live plant sapwood kgC ha-1 T - 672 SAPWC_SCPF sapwood carbon mass by size-class x pft kgC/ha F - 673 SCORCH_HEIGHT SPITFIRE Flame Scorch Height (calculated per PFT in each patch age bin) m T - 674 SECONDARY_AREA_AGE_ANTHRO_DIST Secondary forest patch area age distribution since anthropgenic disturbance m2/m2 F - 675 SECONDARY_AREA_PATCH_AGE_DIST Secondary forest patch area age distribution since any kind of disturbance m2/m2 F - 676 SECONDARY_FOREST_BIOMASS Biomass on secondary lands (per total site area, mult by SECONDARY_FOREST_FRACTION to get per kgC/m2 F - 677 SECONDARY_FOREST_FRACTION Secondary forest fraction m2/m2 F - 678 SEEDS_IN Seed Production Rate gC m-2 s-1 T - 679 SEEDS_IN_EXTERN_ELEM External Seed Influx Rate kg ha-1 d-1 T - 680 SEEDS_IN_LOCAL_ELEM Within Site Seed Production Rate kg ha-1 d-1 T - 681 SEED_BANK Total Seed Mass of all PFTs gC m-2 T - 682 SEED_BANK_ELEM Total Seed Mass of all PFTs kg ha-1 T - 683 SEED_DECAY_ELEM Seed mass decay (germinated and un-germinated) kg ha-1 d-1 T - 684 SEED_GERM_ELEM Seed mass converted into new cohorts kg ha-1 d-1 T - 685 SEED_PROD_CANOPY_SCLS SEED_PROD for canopy plants by size class kg C / ha / yr F - 686 SEED_PROD_UNDERSTORY_SCLS SEED_PROD for understory plants by size class kg C / ha / yr F - 687 SITE_COLD_STATUS Site level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not-too cold 0,1,2 T - 688 SITE_DAYSINCE_COLDLEAFOFF site level days elapsed since cold leaf drop days T - 689 SITE_DAYSINCE_COLDLEAFON site level days elapsed since cold leaf flush days T - 690 SITE_DAYSINCE_DROUGHTLEAFOFF site level days elapsed since drought leaf drop days T - 691 SITE_DAYSINCE_DROUGHTLEAFON site level days elapsed since drought leaf flush days T - 692 SITE_DROUGHT_STATUS Site level drought status, <2 too dry for leaves, >=2 not-too dry 0,1,2,3 T - 693 SITE_GDD site level growing degree days degC T - 694 SITE_MEANLIQVOL_DROUGHTPHEN site level mean liquid water volume for drought phen m3/m3 T - 695 SITE_NCHILLDAYS site level number of chill days days T - 696 SITE_NCOLDDAYS site level number of cold days days T - 697 SLO_SOMC SLO_SOM C gC/m^2 T - 698 SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F - 699 SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F - 700 SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F - 701 SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F - 702 SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F - 703 SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F - 704 SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T - 705 SLO_SOMN SLO_SOM N gN/m^2 T - 706 SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F - 707 SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F - 708 SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F - 709 SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F - 710 SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F - 711 SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F - 712 SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T - 713 SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F - 714 SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 715 SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F - 716 SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 717 SMINN soil mineral N gN/m^2 T - 718 SMINN_LEACHED soil mineral N pool loss to leaching gN/m^2/s T - 719 SMINN_LEACHED_vr soil mineral N pool loss to leaching gN/m^3/s F - 720 SMINN_TO_DENIT_EXCESS denitrification from excess mineral N pool gN/m^2/s F - 721 SMINN_TO_DENIT_EXCESS_vr denitrification from excess mineral N pool gN/m^3/s F - 722 SMINN_TO_DENIT_L1S1 denitrification for decomp. of metabolic litterto ACT_SOM gN/m^2 F - 723 SMINN_TO_DENIT_L1S1_vr denitrification for decomp. of metabolic litterto ACT_SOM gN/m^3 F - 724 SMINN_TO_DENIT_L2S1 denitrification for decomp. of cellulosic litterto ACT_SOM gN/m^2 F - 725 SMINN_TO_DENIT_L2S1_vr denitrification for decomp. of cellulosic litterto ACT_SOM gN/m^3 F - 726 SMINN_TO_DENIT_L3S2 denitrification for decomp. of lignin litterto SLO_SOM gN/m^2 F - 727 SMINN_TO_DENIT_L3S2_vr denitrification for decomp. of lignin litterto SLO_SOM gN/m^3 F - 728 SMINN_TO_DENIT_S1S2 denitrification for decomp. of active soil organicto SLO_SOM gN/m^2 F - 729 SMINN_TO_DENIT_S1S2_vr denitrification for decomp. of active soil organicto SLO_SOM gN/m^3 F - 730 SMINN_TO_DENIT_S1S3 denitrification for decomp. of active soil organicto PAS_SOM gN/m^2 F - 731 SMINN_TO_DENIT_S1S3_vr denitrification for decomp. of active soil organicto PAS_SOM gN/m^3 F - 732 SMINN_TO_DENIT_S2S1 denitrification for decomp. of slow soil organic mato ACT_SOM gN/m^2 F - 733 SMINN_TO_DENIT_S2S1_vr denitrification for decomp. of slow soil organic mato ACT_SOM gN/m^3 F - 734 SMINN_TO_DENIT_S2S3 denitrification for decomp. of slow soil organic mato PAS_SOM gN/m^2 F - 735 SMINN_TO_DENIT_S2S3_vr denitrification for decomp. of slow soil organic mato PAS_SOM gN/m^3 F - 736 SMINN_TO_DENIT_S3S1 denitrification for decomp. of passive soil organicto ACT_SOM gN/m^2 F - 737 SMINN_TO_DENIT_S3S1_vr denitrification for decomp. of passive soil organicto ACT_SOM gN/m^3 F - 738 SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T - 739 SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F - 740 SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F - 741 SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F - 742 SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F - 743 SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F - 744 SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F - 745 SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F - 746 SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F - 747 SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F - 748 SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F - 749 SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F - 750 SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F - 751 SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F - 752 SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F - 753 SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F - 754 SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F - 755 SMINN_vr soil mineral N gN/m^3 T - 756 SMP soil matric potential (natural vegetated and crop landunits only) mm T - 757 SNOBCMCL mass of BC in snow column kg/m2 T - 758 SNOBCMSL mass of BC in top snow layer kg/m2 T - 759 SNOCAN intercepted snow mm T - 760 SNODSTMCL mass of dust in snow column kg/m2 T - 761 SNODSTMSL mass of dust in top snow layer kg/m2 T - 762 SNOFSDSND direct nir incident solar radiation on snow W/m^2 F - 763 SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F - 764 SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F - 765 SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F - 766 SNOFSRND direct nir reflected solar radiation from snow W/m^2 T - 767 SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T - 768 SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T - 769 SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T - 770 SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T - 771 SNOLIQFL top snow layer liquid water fraction (land) fraction F - 772 SNOOCMCL mass of OC in snow column kg/m2 T - 773 SNOOCMSL mass of OC in top snow layer kg/m2 T - 774 SNORDSL top snow layer effective grain radius m^-6 F - 775 SNOTTOPL snow temperature (top layer) K F - 776 SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F - 777 SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T - 778 SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F - 779 SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T - 780 SNOWDP gridcell mean snow height m T - 781 SNOWICE snow ice kg/m2 T - 782 SNOWICE_ICE snow ice (ice landunits only) kg/m2 F - 783 SNOWLIQ snow liquid water kg/m2 T - 784 SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F - 785 SNOW_5D 5day snow avg m F - 786 SNOW_DEPTH snow height of snow covered area m T - 787 SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F - 788 SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T - 789 SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F - 790 SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T - 791 SNOW_SINKS snow sinks (liquid water) mm/s T - 792 SNOW_SOURCES snow sources (liquid water) mm/s T - 793 SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F - 794 SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F - 795 SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F - 796 SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F - 797 SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F - 798 SNO_FRZ snow freezing rate in each snow layer kg/m2/s F - 799 SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F - 800 SNO_GS Mean snow grain size Microns F - 801 SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F - 802 SNO_ICE Snow ice content kg/m2 F - 803 SNO_LIQH2O Snow liquid water content kg/m2 F - 804 SNO_MELT snow melt rate in each snow layer mm/s F - 805 SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F - 806 SNO_T Snow temperatures K F - 807 SNO_TK Thermal conductivity W/m-K F - 808 SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F - 809 SNO_T_ICE Snow temperatures (ice landunits only) K F - 810 SNO_Z Snow layer thicknesses m F - 811 SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F - 812 SNOdTdzL top snow layer temperature gradient (land) K/m F - 813 SOIL10 10-day running mean of 12cm layer soil K F - 814 SOILC_HR soil C heterotrophic respiration gC/m^2/s T - 815 SOILC_vr SOIL C (vertically resolved) gC/m^3 T - 816 SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T - 817 SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T - 818 SOILN_vr SOIL N (vertically resolved) gN/m^3 T - 819 SOILPSI soil water potential in each soil layer MPa F - 820 SOILRESIS soil resistance to evaporation s/m T - 821 SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T - 822 SOMC_FIRE C loss due to peat burning gC/m^2/s T - 823 SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T - 824 SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F - 825 STOREC Total carbon in live plant storage kgC ha-1 T - 826 STOREC_SCPF storage carbon mass by size-class x pft kgC/ha F - 827 SUM_FUEL total ground fuel related to ros (omits 1000hr fuels) gC m-2 T - 828 SUM_FUEL_BY_PATCH_AGE spitfire ground fuel related to ros (omits 1000hr fuels) within each patch age bin (divide by gC / m2 of site area T - 829 SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T - 830 SWBGT 2 m Simplified Wetbulb Globe Temp C T - 831 SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T - 832 SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T - 833 SWdown atmospheric incident solar radiation W/m^2 F - 834 SWup upwelling shortwave radiation W/m^2 F - 835 SoilAlpha factor limiting ground evap unitless F - 836 SoilAlpha_U urban factor limiting ground evap unitless F - 837 T10 10-day running mean of 2-m temperature K F - 838 TAF canopy air temperature K F - 839 TAUX zonal surface stress kg/m/s^2 T - 840 TAUY meridional surface stress kg/m/s^2 T - 841 TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T - 842 TBUILD internal urban building air temperature K T - 843 TBUILD_MAX prescribed maximum interior building temperature K F - 844 TFLOOR floor temperature K F - 845 TG ground temperature K T - 846 TG_ICE ground temperature (ice landunits only) K F - 847 TG_R Rural ground temperature K F - 848 TG_U Urban ground temperature K F - 849 TH2OSFC surface water temperature K T - 850 THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T - 851 TKE1 top lake level eddy thermal conductivity W/(mK) T - 852 TLAI total projected leaf area index m^2/m^2 T - 853 TLAKE lake temperature K T - 854 TOPO_COL column-level topographic height m F - 855 TOPO_COL_ICE column-level topographic height (ice landunits only) m F - 856 TOPO_FORC topograephic height sent to GLC m F - 857 TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T - 858 TOTLITC total litter carbon gC/m^2 T - 859 TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T - 860 TOTLITN total litter N gN/m^2 T - 861 TOTLITN_1m total litter N to 1 meter gN/m^2 T - 862 TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T - 863 TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T - 864 TOTSOMC total soil organic matter carbon gC/m^2 T - 865 TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T - 866 TOTSOMN total soil organic matter N gN/m^2 T - 867 TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T - 868 TOTVEGC Total carbon in live plants kgC ha-1 T - 869 TOTVEGC_SCPF total vegetation carbon mass in live plants by size-class x pft kgC/ha F - 870 TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F - 871 TREFMNAV daily minimum of average 2-m temperature K T - 872 TREFMNAV_R Rural daily minimum of average 2-m temperature K F - 873 TREFMNAV_U Urban daily minimum of average 2-m temperature K F - 874 TREFMXAV daily maximum of average 2-m temperature K T - 875 TREFMXAV_R Rural daily maximum of average 2-m temperature K F - 876 TREFMXAV_U Urban daily maximum of average 2-m temperature K F - 877 TRIMMING Degree to which canopy expansion is limited by leaf economics none T - 878 TRIMMING_CANOPY_SCLS trimming term of canopy plants by size class indiv/ha F - 879 TRIMMING_UNDERSTORY_SCLS trimming term of understory plants by size class indiv/ha F - 880 TROOF_INNER roof inside surface temperature K F - 881 TSA 2m air temperature K T - 882 TSAI total projected stem area index m^2/m^2 T - 883 TSA_ICE 2m air temperature (ice landunits only) K F - 884 TSA_R Rural 2m air temperature K F - 885 TSA_U Urban 2m air temperature K F - 886 TSHDW_INNER shadewall inside surface temperature K F - 887 TSKIN skin temperature K T - 888 TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T - 889 TSOI soil temperature (natural vegetated and crop landunits only) K T - 890 TSOI_10CM soil temperature in top 10cm of soil K T - 891 TSOI_ICE soil temperature (ice landunits only) K T - 892 TSRF_FORC surface temperature sent to GLC K F - 893 TSUNW_INNER sunwall inside surface temperature K F - 894 TV vegetation temperature K T - 895 TV24 vegetation temperature (last 24hrs) K F - 896 TV240 vegetation temperature (last 240hrs) K F - 897 TWS total water storage mm T - 898 T_SCALAR temperature inhibition of decomposition unitless T - 899 Tair atmospheric air temperature (downscaled to columns in glacier regions) K F - 900 Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F - 901 U10 10-m wind m/s T - 902 U10_DUST 10-m wind for dust model m/s T - 903 U10_ICE 10-m wind (ice landunits only) m/s F - 904 UAF canopy air speed m/s F - 905 UM wind speed plus stability effect m/s F - 906 URBAN_AC urban air conditioning flux W/m^2 T - 907 URBAN_HEAT urban heating flux W/m^2 T - 908 USTAR aerodynamical resistance s/m F - 909 UST_LAKE friction velocity (lakes only) m/s F - 910 VA atmospheric wind speed plus convective velocity m/s F - 911 VOLR river channel total water storage m3 T - 912 VOLRMCH river channel main channel water storage m3 T - 913 VPD vpd Pa F - 914 VPD2M 2m vapor pressure deficit Pa T - 915 VPD_CAN canopy vapor pressure deficit kPa T - 916 WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T - 917 WBT 2 m Stull Wet Bulb C T - 918 WBT_R Rural 2 m Stull Wet Bulb C T - 919 WBT_U Urban 2 m Stull Wet Bulb C T - 920 WIND atmospheric wind velocity magnitude m/s T - 921 WOOD_PRODUCT Total wood product from logging gC/m2 F - 922 WTGQ surface tracer conductance m/s T - 923 W_SCALAR Moisture (dryness) inhibition of decomposition unitless T - 924 Wind atmospheric wind velocity magnitude m/s F - 925 YESTERDAYCANLEV_CANOPY_SCLS Yesterdays canopy level for canopy plants by size class indiv/ha F - 926 YESTERDAYCANLEV_UNDERSTORY_SCLS Yesterdays canopy level for understory plants by size class indiv/ha F - 927 Z0HG roughness length over ground, sensible heat m F - 928 Z0M momentum roughness length m F - 929 Z0MG roughness length over ground, momentum m F - 930 Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F - 931 Z0QG roughness length over ground, latent heat m F - 932 ZBOT atmospheric reference height m T - 933 ZETA dimensionless stability parameter unitless F - 934 ZII convective boundary height m F - 935 ZSTAR_BY_AGE product of zstar and patch area by age bin (divide by PATCH_AREA_BY_AGE to get mean zstar) m F - 936 ZWT water table depth (natural vegetated and crop landunits only) m T - 937 ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T - 938 ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T - 939 num_iter number of iterations unitless F +A5TMIN 5-day running mean of min 2-m temperature K F +ACTUAL_IMMOB actual N immobilization gN/m^2/s T +ACT_SOMC ACT_SOM C gC/m^2 T +ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F +ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F +ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F +ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F +ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T +ACT_SOMN ACT_SOM N gN/m^2 T +ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F +ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F +ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F +ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F +ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F +ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T +ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F +ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F +AGB Aboveground biomass gC m-2 T +AGB_SCLS Aboveground biomass by size class kgC/m2 T +AGB_SCPF Aboveground biomass by pft/size kgC/m2 F +AGLB Aboveground leaf biomass kg/m^2 F +AGSB Aboveground stem biomass kg/m^2 F +ALBD surface albedo (direct) proportion F +ALBGRD ground albedo (direct) proportion F +ALBGRI ground albedo (indirect) proportion F +ALBI surface albedo (indirect) proportion F +ALT current active layer thickness m F +ALTMAX maximum annual active layer thickness m F +ALTMAX_LASTYEAR maximum prior year active layer thickness m F +AR autotrophic respiration gC/m^2/s T +AREA_BURNT_BY_PATCH_AGE spitfire area burnt by patch age (divide by patch_area_by_age to get burnt fraction by age) m2/m2/day T +AREA_PLANT area occupied by all plants m2/m2 T +AREA_TREES area occupied by woody plants m2/m2 T +AR_AGSAPM_SCPF above-ground sapwood maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_CANOPY autotrophic respiration of canopy plants gC/m^2/s T +AR_CANOPY_SCPF autotrophic respiration of canopy plants by pft/size kgC/m2/yr F +AR_CROOTM_SCPF below-ground sapwood maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_DARKM_SCPF dark portion of maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_FROOTM_SCPF fine root maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_GROW_SCPF growth autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_MAINT_SCPF maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_SCPF total autotrophic respiration per m2 per year by pft/size kgC/m2/yr F +AR_UNDERSTORY autotrophic respiration of understory plants gC/m^2/s T +AR_UNDERSTORY_SCPF autotrophic respiration of understory plants by pft/size kgC/m2/yr F +ATM_TOPO atmospheric surface height m T +AnnET Annual ET mm/s F +BA_SCLS basal area by size class m2/ha T +BA_SCPF basal area by pft/size m2/ha F +BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BDEAD_MD_CANOPY_SCLS BDEAD_MD for canopy plants by size class kg C / ha / yr F +BDEAD_MD_UNDERSTORY_SCLS BDEAD_MD for understory plants by size class kg C / ha / yr F +BIOMASS_AGEPFT biomass per PFT in each age bin kg C / m2 F +BIOMASS_BY_AGE Total Biomass within a given patch age bin kgC/m2 F +BIOMASS_CANOPY Biomass of canopy plants gC m-2 T +BIOMASS_SCLS Total biomass by size class kgC/m2 F +BIOMASS_UNDERSTORY Biomass of understory plants gC m-2 T +BLEAF_CANOPY_SCPF biomass carbon in leaf of canopy plants by pft/size kgC/ha F +BLEAF_UNDERSTORY_SCPF biomass carbon in leaf of understory plants by pft/size kgC/ha F +BSTORE_MD_CANOPY_SCLS BSTORE_MD for canopy plants by size class kg C / ha / yr F +BSTORE_MD_UNDERSTORY_SCLS BSTORE_MD for understory plants by size class kg C / ha / yr F +BSTOR_CANOPY_SCPF biomass carbon in storage pools of canopy plants by pft/size kgC/ha F +BSTOR_UNDERSTORY_SCPF biomass carbon in storage pools of understory plants by pft/size kgC/ha F +BSW_MD_CANOPY_SCLS BSW_MD for canopy plants by size class kg C / ha / yr F +BSW_MD_UNDERSTORY_SCLS BSW_MD for understory plants by size class kg C / ha / yr F +BTRAN transpiration beta factor unitless T +BTRANMN daily minimum of transpiration beta factor unitless T +BURNT_LITTER_FRAC_AREA_PRODUCT product of fraction of fuel burnt and burned area (divide by FIRE_AREA to get burned-area-weig fraction T +C13disc_SCPF C13 discrimination by pft/size per mil F +CAMBIALFIREMORT_SCPF cambial fire mortality by pft/size N/ha/yr F +CANOPY_AREA_BY_AGE canopy area by age bin m2/m2 T +CANOPY_HEIGHT_DIST canopy height distribution m2/m2 T +CANOPY_SPREAD Scaling factor between tree basal area and canopy area 0-1 T +CARBON_BALANCE_CANOPY_SCLS CARBON_BALANCE for canopy plants by size class kg C / ha / yr F +CARBON_BALANCE_UNDERSTORY_SCLS CARBON_BALANCE for understory plants by size class kg C / ha / yr F +CBALANCE_ERROR_FATES total carbon error, FATES mgC/day T +CEFFLUX carbon efflux, root to soil kgC/ha/day T +CEFFLUX_SCPF carbon efflux, root to soil, by size-class x pft kg/ha/day F +CEL_LITC CEL_LIT C gC/m^2 T +CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F +CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F +CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T +CEL_LITN CEL_LIT N gN/m^2 T +CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F +CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F +CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F +CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F +CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T +CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F +CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F +CH4PROD Gridcell total production of CH4 gC/m2/s T +CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T +CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +COL_CTRUNC column-level sink for C truncation gC/m^2 F +COL_NTRUNC column-level sink for N truncation gN/m^2 F +CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F +CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T +COSZEN cosine of solar zenith angle none F +CROWNAREA_CAN total crown area in each canopy layer m2/m2 T +CROWNAREA_CNLF total crown area that is occupied by leaves in each canopy and leaf layer m2/m2 F +CROWNFIREMORT_SCPF crown fire mortality by pft/size N/ha/yr F +CROWN_AREA_CANOPY_SCLS total crown area of canopy plants by size class m2/ha F +CROWN_AREA_UNDERSTORY_SCLS total crown area of understory plants by size class m2/ha F +CWDC_HR cwd C heterotrophic respiration gC/m^2/s F +CWD_AG_CWDSC size-resolved AG CWD stocks gC/m^2 F +CWD_AG_IN_CWDSC size-resolved AG CWD input gC/m^2/y F +CWD_AG_OUT_CWDSC size-resolved AG CWD output gC/m^2/y F +CWD_BG_CWDSC size-resolved BG CWD stocks gC/m^2 F +CWD_BG_IN_CWDSC size-resolved BG CWD input gC/m^2/y F +CWD_BG_OUT_CWDSC size-resolved BG CWD output gC/m^2/y F +C_LBLAYER mean leaf boundary layer conductance umol m-2 s-1 T +C_LBLAYER_BY_AGE mean leaf boundary layer conductance - by patch age umol m-2 s-1 F +C_STOMATA mean stomatal conductance umol m-2 s-1 T +C_STOMATA_BY_AGE mean stomatal conductance - by patch age umol m-2 s-1 F +DDBH_CANOPY_SCAG growth rate of canopy plantsnumber of plants per hectare in canopy in each size x age class cm/yr/ha F +DDBH_CANOPY_SCLS diameter growth increment by pft/size cm/yr/ha T +DDBH_CANOPY_SCPF diameter growth increment by pft/size cm/yr/ha F +DDBH_SCPF diameter growth increment by pft/size cm/yr/ha F +DDBH_UNDERSTORY_SCAG growth rate of understory plants in each size x age class cm/yr/ha F +DDBH_UNDERSTORY_SCLS diameter growth increment by pft/size cm/yr/ha T +DDBH_UNDERSTORY_SCPF diameter growth increment by pft/size cm/yr/ha F +DEMOTION_CARBONFLUX demotion-associated biomass carbon flux from canopy to understory gC/m2/s T +DEMOTION_RATE_SCLS demotion rate from canopy to understory by size class indiv/ha/yr F +DENIT total rate of denitrification gN/m^2/s T +DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F +DISPLA displacement height m F +DISTURBANCE_RATE_FIRE Disturbance rate from fire m2 m-2 d-1 T +DISTURBANCE_RATE_LOGGING Disturbance rate from logging m2 m-2 d-1 T +DISTURBANCE_RATE_P2P Disturbance rate from primary to primary lands m2 m-2 d-1 T +DISTURBANCE_RATE_P2S Disturbance rate from primary to secondary lands m2 m-2 d-1 T +DISTURBANCE_RATE_POTENTIAL Potential (i.e., including unresolved) disturbance rate m2 m-2 d-1 T +DISTURBANCE_RATE_S2S Disturbance rate from secondary to secondary lands m2 m-2 d-1 T +DISTURBANCE_RATE_TREEFALL Disturbance rate from treefall m2 m-2 d-1 T +DPVLTRB1 turbulent deposition velocity 1 m/s F +DPVLTRB2 turbulent deposition velocity 2 m/s F +DPVLTRB3 turbulent deposition velocity 3 m/s F +DPVLTRB4 turbulent deposition velocity 4 m/s F +DSL dry surface layer thickness mm T +DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTFLXT total surface dust emission kg/m2/s T +DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F +ED_NCOHORTS Total number of ED cohorts per site none T +ED_NPATCHES Total number of ED patches per site none T +ED_balive Live biomass gC m-2 T +ED_bdead Dead (structural) biomass (live trees, not CWD) gC m-2 T +ED_bfineroot Fine root biomass gC m-2 T +ED_biomass Total biomass gC m-2 T +ED_bleaf Leaf biomass gC m-2 T +ED_bsapwood Sapwood biomass gC m-2 T +ED_bstore Storage biomass gC m-2 T +EFFECT_WSPEED effective windspeed for fire spread none T +EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T +EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T +EFLX_GNET net heat flux into ground W/m^2 F +EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T +EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T +EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F +EFLX_LH_TOT_R Rural total evaporation W/m^2 T +EFLX_LH_TOT_U Urban total evaporation W/m^2 F +EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F +ELAI exposed one-sided leaf area index m^2/m^2 T +ERRH2O total water conservation error mm T +ERRH2OSNO imbalance in snow depth (liquid water) mm T +ERROR_FATES total error, FATES mass-balance mg/day T +ERRSEB surface energy conservation error W/m^2 T +ERRSOI soil/lake energy conservation error W/m^2 T +ERRSOL solar radiation conservation error W/m^2 T +ESAI exposed one-sided stem area index m^2/m^2 T +FABD_SHA_CNLF shade fraction of direct light absorbed by each canopy and leaf layer fraction F +FABD_SHA_CNLFPFT shade fraction of direct light absorbed by each canopy, leaf, and PFT fraction F +FABD_SHA_TOPLF_BYCANLAYER shade fraction of direct light absorbed by the top leaf layer of each canopy layer fraction F +FABD_SUN_CNLF sun fraction of direct light absorbed by each canopy and leaf layer fraction F +FABD_SUN_CNLFPFT sun fraction of direct light absorbed by each canopy, leaf, and PFT fraction F +FABD_SUN_TOPLF_BYCANLAYER sun fraction of direct light absorbed by the top leaf layer of each canopy layer fraction F +FABI_SHA_CNLF shade fraction of indirect light absorbed by each canopy and leaf layer fraction F +FABI_SHA_CNLFPFT shade fraction of indirect light absorbed by each canopy, leaf, and PFT fraction F +FABI_SHA_TOPLF_BYCANLAYER shade fraction of indirect light absorbed by the top leaf layer of each canopy layer fraction F +FABI_SUN_CNLF sun fraction of indirect light absorbed by each canopy and leaf layer fraction F +FABI_SUN_CNLFPFT sun fraction of indirect light absorbed by each canopy, leaf, and PFT fraction F +FABI_SUN_TOPLF_BYCANLAYER sun fraction of indirect light absorbed by the top leaf layer of each canopy layer fraction F +FATES_HR heterotrophic respiration gC/m^2/s T +FATES_c_to_litr_cel_c litter celluluse carbon flux from FATES to BGC gC/m^3/s T +FATES_c_to_litr_lab_c litter labile carbon flux from FATES to BGC gC/m^3/s T +FATES_c_to_litr_lig_c litter lignin carbon flux from FATES to BGC gC/m^3/s T +FCEV canopy evaporation W/m^2 T +FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T +FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T +FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T +FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F +FCOV fractional impermeable area unitless T +FCTR canopy transpiration W/m^2 T +FGEV ground evaporation W/m^2 T +FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T +FGR12 heat flux between soil layers 1 and 2 W/m^2 T +FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F +FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F +FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F +FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F +FH2OSFC fraction of ground covered by surface water unitless T +FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F +FINUNDATED fractional inundated area of vegetated columns unitless T +FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F +FIRA net infrared (longwave) radiation W/m^2 T +FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRA_R Rural net infrared (longwave) radiation W/m^2 T +FIRA_U Urban net infrared (longwave) radiation W/m^2 F +FIRE emitted infrared (longwave) radiation W/m^2 T +FIRE_AREA spitfire fire area burn fraction fraction/day T +FIRE_FDI probability that an ignition will lead to a fire none T +FIRE_FLUX ED-spitfire loss to atmosphere of elements g/m^2/s T +FIRE_FUEL_BULKD spitfire fuel bulk density kg biomass/m3 T +FIRE_FUEL_EFF_MOIST spitfire fuel moisture m T +FIRE_FUEL_MEF spitfire fuel moisture m T +FIRE_FUEL_SAV spitfire fuel surface/volume per m T +FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRE_IGNITIONS number of successful ignitions number/km2/day T +FIRE_INTENSITY spitfire fire intensity: kJ/m/s kJ/m/s T +FIRE_INTENSITY_AREA_PRODUCT spitfire product of fire intensity and burned area (divide by FIRE_AREA to get area-weighted m kJ/m/s T +FIRE_INTENSITY_BY_PATCH_AGE product of fire intensity and burned area, resolved by patch age (so divide by AREA_BURNT_BY_P kJ/m/2 T +FIRE_NESTEROV_INDEX nesterov_fire_danger index none T +FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T +FIRE_ROS fire rate of spread m/min m/min T +FIRE_ROS_AREA_PRODUCT product of fire rate of spread (m/min) and burned area (fraction)--divide by FIRE_AREA to get m/min T +FIRE_TFC_ROS total fuel consumed kgC/m2 T +FIRE_TFC_ROS_AREA_PRODUCT product of total fuel consumed and burned area--divide by FIRE_AREA to get burned-area-weighte kgC/m2 T +FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F +FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T +FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FNRTC Total carbon in live plant fine-roots kgC ha-1 T +FNRTC_SCPF fine-root carbon mass by size-class x pft kgC/ha F +FRAGMENTATION_SCALER_SL factor by which litter/cwd fragmentation proceeds relative to max rate by soil layer unitless (0-1) T +FROOT_MR fine root maintenance respiration) kg C / m2 / yr T +FROOT_MR_CANOPY_SCLS FROOT_MR for canopy plants by size class kg C / ha / yr F +FROOT_MR_UNDERSTORY_SCLS FROOT_MR for understory plants by size class kg C / ha / yr F +FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F +FSA absorbed solar radiation W/m^2 T +FSAT fractional area with water table at surface unitless T +FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F +FSA_R Rural absorbed solar radiation W/m^2 F +FSA_U Urban absorbed solar radiation W/m^2 F +FSD24 direct radiation (last 24hrs) K F +FSD240 direct radiation (last 240hrs) K F +FSDS atmospheric incident solar radiation W/m^2 T +FSDSND direct nir incident solar radiation W/m^2 T +FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T +FSDSNI diffuse nir incident solar radiation W/m^2 T +FSDSVD direct vis incident solar radiation W/m^2 T +FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T +FSDSVI diffuse vis incident solar radiation W/m^2 T +FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T +FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T +FSH_G sensible heat from ground W/m^2 T +FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F +FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T +FSH_R Rural sensible heat W/m^2 T +FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T +FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T +FSH_U Urban sensible heat W/m^2 F +FSH_V sensible heat from veg W/m^2 T +FSI24 indirect radiation (last 24hrs) K F +FSI240 indirect radiation (last 240hrs) K F +FSM snow melt heat flux W/m^2 T +FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F +FSM_R Rural snow melt heat flux W/m^2 F +FSM_U Urban snow melt heat flux W/m^2 F +FSNO fraction of ground covered by snow unitless T +FSNO_EFF effective fraction of ground covered by snow unitless T +FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F +FSR reflected solar radiation W/m^2 T +FSRND direct nir reflected solar radiation W/m^2 T +FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T +FSRNI diffuse nir reflected solar radiation W/m^2 T +FSRVD direct vis reflected solar radiation W/m^2 T +FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T +FSRVI diffuse vis reflected solar radiation W/m^2 T +FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F +FSUN sunlit fraction of canopy proportion F +FSUN24 fraction sunlit (last 24hrs) K F +FSUN240 fraction sunlit (last 240hrs) K F +FUEL_AMOUNT_AGEFUEL spitfire fuel quantity in each age x fuel class kg C / m2 T +FUEL_AMOUNT_BY_NFSC spitfire size-resolved fuel quantity kg C / m2 T +FUEL_MOISTURE_NFSC spitfire size-resolved fuel moisture - T +Fire_Closs ED/SPitfire Carbon loss to atmosphere gC/m^2/s T +GPP gross primary production gC/m^2/s T +GPP_BY_AGE gross primary productivity by age bin gC/m^2/s F +GPP_CANOPY gross primary production of canopy plants gC/m^2/s T +GPP_CANOPY_SCPF gross primary production of canopy plants by pft/size kgC/m2/yr F +GPP_SCPF gross primary production by pft/size kgC/m2/yr F +GPP_UNDERSTORY gross primary production of understory plants gC/m^2/s T +GPP_UNDERSTORY_SCPF gross primary production of understory plants by pft/size kgC/m2/yr F +GROSS_NMIN gross rate of N mineralization gN/m^2/s T +GROWTHFLUX_FUSION_SCPF flux of individuals into a given size class bin via fusion n/yr/ha F +GROWTHFLUX_SCPF flux of individuals into a given size class bin via growth and recruitment n/yr/ha F +GROWTH_RESP growth respiration gC/m^2/s T +GSSHA shaded leaf stomatal conductance umol H20/m2/s T +GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T +GSSUN sunlit leaf stomatal conductance umol H20/m2/s T +GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T +H2OCAN intercepted water mm T +H2OSFC surface water depth mm T +H2OSNO snow depth (liquid water) mm T +H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F +H2OSNO_TOP mass of snow in top snow layer kg/m2 T +H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HARVEST_CARBON_FLUX Harvest carbon flux kg C m-2 d-1 T +HBOT canopy bottom m F +HEAT_CONTENT1 initial gridcell total heat content J/m^2 T +HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F +HEAT_CONTENT2 post land cover change total heat content J/m^2 F +HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T +HIA 2 m NWS Heat Index C T +HIA_R Rural 2 m NWS Heat Index C T +HIA_U Urban 2 m NWS Heat Index C T +HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +HR total heterotrophic respiration gC/m^2/s T +HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T +HTOP canopy top m T +HUMIDEX 2 m Humidex C T +HUMIDEX_R Rural 2 m Humidex C T +HUMIDEX_U Urban 2 m Humidex C T +ICE_CONTENT1 initial gridcell total ice content mm T +ICE_CONTENT2 post land cover change total ice content mm F +ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F +INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F +INT_SNOW_ICE accumulated swe (ice landunits only) mm F +IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T +KROOT root conductance each soil layer 1/s F +KSOIL soil conductance in each soil layer 1/s F +K_ACT_SOM active soil organic potential loss coefficient 1/s F +K_CEL_LIT cellulosic litter potential loss coefficient 1/s F +K_LIG_LIT lignin litter potential loss coefficient 1/s F +K_MET_LIT metabolic litter potential loss coefficient 1/s F +K_PAS_SOM passive soil organic potential loss coefficient 1/s F +K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F +LAI240 240hr average of leaf area index m^2/m^2 F +LAISHA shaded projected leaf area index m^2/m^2 T +LAISHA_TOP_CAN LAI in the shade by the top leaf layer of each canopy layer m2/m2 F +LAISHA_Z_CNLF LAI in the shade by each canopy and leaf layer m2/m2 F +LAISHA_Z_CNLFPFT LAI in the shade by each canopy, leaf, and PFT m2/m2 F +LAISUN sunlit projected leaf area index m^2/m^2 T +LAISUN_TOP_CAN LAI in the sun by the top leaf layer of each canopy layer m2/m2 F +LAISUN_Z_CNLF LAI in the sun by each canopy and leaf layer m2/m2 F +LAISUN_Z_CNLFPFT LAI in the sun by each canopy, leaf, and PFT m2/m2 F +LAI_BY_AGE leaf area index by age bin m2/m2 T +LAI_CANOPY_SCLS Leaf are index (LAI) by size class m2/m2 T +LAI_UNDERSTORY_SCLS number of understory plants by size class indiv/ha T +LAKEICEFRAC lake layer ice mass fraction unitless F +LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T +LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T +LEAFC Total carbon in live plant leaves kgC ha-1 T +LEAFC_SCPF leaf carbon mass by size-class x pft kgC/ha F +LEAF_HEIGHT_DIST leaf height distribution m2/m2 T +LEAF_MD_CANOPY_SCLS LEAF_MD for canopy plants by size class kg C / ha / yr F +LEAF_MD_UNDERSTORY_SCLS LEAF_MD for understory plants by size class kg C / ha / yr F +LEAF_MR RDARK (leaf maintenance respiration) kg C / m2 / yr T +LIG_LITC LIG_LIT C gC/m^2 T +LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F +LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F +LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T +LIG_LITN LIG_LIT N gN/m^2 T +LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F +LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F +LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T +LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F +LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F +LIQCAN intercepted liquid water mm T +LIQUID_CONTENT1 initial gridcell total liq content mm T +LIQUID_CONTENT2 post landuse change gridcell total liq content mm F +LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F +LITTERC_HR litter C heterotrophic respiration gC/m^2/s T +LITTER_CWD total mass of litter in CWD kg ha-1 T +LITTER_CWD_AG_ELEM mass of above ground litter in CWD (trunks/branches/twigs) kg ha-1 T +LITTER_CWD_BG_ELEM mass of below ground litter in CWD (coarse roots) kg ha-1 T +LITTER_FINES_AG_ELEM mass of above ground litter in fines (leaves,nonviable seed) kg ha-1 T +LITTER_FINES_BG_ELEM mass of below ground litter in fines (fineroots) kg ha-1 T +LITTER_IN FATES litter flux in gC m-2 s-1 T +LITTER_IN_ELEM FATES litter flux in kg ha-1 d-1 T +LITTER_OUT FATES litter flux out gC m-2 s-1 T +LITTER_OUT_ELEM FATES litter flux out (fragmentation only) kg ha-1 d-1 T +LIVECROOT_MR live coarse root maintenance respiration) kg C / m2 / yr T +LIVECROOT_MR_CANOPY_SCLS LIVECROOT_MR for canopy plants by size class kg C / ha / yr F +LIVECROOT_MR_UNDERSTORY_SCLS LIVECROOT_MR for understory plants by size class kg C / ha / yr F +LIVESTEM_MR live stem maintenance respiration) kg C / m2 / yr T +LIVESTEM_MR_CANOPY_SCLS LIVESTEM_MR for canopy plants by size class kg C / ha / yr F +LIVESTEM_MR_UNDERSTORY_SCLS LIVESTEM_MR for understory plants by size class kg C / ha / yr F +LNC leaf N concentration gN leaf/m^2 T +LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWup upwelling longwave radiation W/m^2 F +M10_CACLS age senescence mortality by cohort age N/ha/yr T +M10_CAPF age senescence mortality by pft/cohort age N/ha/yr F +M10_SCLS age senescence mortality by size N/ha/yr T +M10_SCPF age senescence mortality by pft/size N/ha/yr F +M1_SCLS background mortality by size N/ha/yr T +M1_SCPF background mortality by pft/size N/ha/yr F +M2_SCLS hydraulic mortality by size N/ha/yr T +M2_SCPF hydraulic mortality by pft/size N/ha/yr F +M3_SCLS carbon starvation mortality by size N/ha/yr T +M3_SCPF carbon starvation mortality by pft/size N/ha/yr F +M4_SCLS impact mortality by size N/ha/yr T +M4_SCPF impact mortality by pft/size N/ha/yr F +M5_SCLS fire mortality by size N/ha/yr T +M5_SCPF fire mortality by pft/size N/ha/yr F +M6_SCLS termination mortality by size N/ha/yr T +M6_SCPF termination mortality by pft/size N/ha/yr F +M7_SCLS logging mortality by size N/ha/event T +M7_SCPF logging mortality by pft/size N/ha/event F +M8_SCLS freezing mortality by size N/ha/event T +M8_SCPF freezing mortality by pft/size N/ha/yr F +M9_SCLS senescence mortality by size N/ha/yr T +M9_SCPF senescence mortality by pft/size N/ha/yr F +MAINT_RESP maintenance respiration gC/m^2/s T +MET_LITC MET_LIT C gC/m^2 T +MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F +MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F +MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F +MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F +MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T +MET_LITN MET_LIT N gN/m^2 T +MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F +MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F +MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F +MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F +MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T +MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F +MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F +MORTALITY Rate of total mortality by PFT indiv/ha/yr T +MORTALITY_CANOPY_SCAG mortality rate of canopy plants in each size x age class plants/ha/yr F +MORTALITY_CANOPY_SCLS total mortality of canopy trees by size class indiv/ha/yr T +MORTALITY_CANOPY_SCPF total mortality of canopy plants by pft/size N/ha/yr F +MORTALITY_CARBONFLUX_CANOPY flux of biomass carbon from live to dead pools from mortality of canopy plants gC/m2/s T +MORTALITY_CARBONFLUX_UNDERSTORY flux of biomass carbon from live to dead pools from mortality of understory plants gC/m2/s T +MORTALITY_UNDERSTORY_SCAG mortality rate of understory plantsin each size x age class plants/ha/yr F +MORTALITY_UNDERSTORY_SCLS total mortality of understory trees by size class indiv/ha/yr T +MORTALITY_UNDERSTORY_SCPF total mortality of understory plants by pft/size N/ha/yr F +M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F +M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F +M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F +M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F +M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F +M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F +M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F +M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F +M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F +M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F +M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F +M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F +NCL_BY_AGE number of canopy levels by age bin -- F +NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T +NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T +NEP net ecosystem production gC/m^2/s T +NET_C_UPTAKE_CNLF net carbon uptake by each canopy and leaf layer per unit ground area (i.e. divide by CROWNAREA gC/m2/s F +NET_NMIN net rate of N mineralization gN/m^2/s T +NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T +NPATCH_BY_AGE number of patches by age bin -- F +NPLANT_CACLS number of plants by coage class indiv/ha T +NPLANT_CANOPY_SCAG number of plants per hectare in canopy in each size x age class plants/ha F +NPLANT_CANOPY_SCLS number of canopy plants by size class indiv/ha T +NPLANT_CANOPY_SCPF stem number of canopy plants density by pft/size N/ha F +NPLANT_CAPF stem number density by pft/coage N/ha F +NPLANT_SCAG number of plants per hectare in each size x age class plants/ha T +NPLANT_SCAGPFT number of plants per hectare in each size x age x pft class plants/ha F +NPLANT_SCLS number of plants by size class indiv/ha T +NPLANT_SCPF stem number density by pft/size N/ha F +NPLANT_UNDERSTORY_SCAG number of plants per hectare in understory in each size x age class plants/ha F +NPLANT_UNDERSTORY_SCLS number of understory plants by size class indiv/ha T +NPLANT_UNDERSTORY_SCPF stem number of understory plants density by pft/size N/ha F +NPP net primary production gC/m^2/s T +NPP_AGDW_SCPF NPP flux into above-ground deadwood by pft/size kgC/m2/yr F +NPP_AGEPFT NPP per PFT in each age bin kgC/m2/yr F +NPP_AGSW_SCPF NPP flux into above-ground sapwood by pft/size kgC/m2/yr F +NPP_BDEAD_CANOPY_SCLS NPP_BDEAD for canopy plants by size class kg C / ha / yr F +NPP_BDEAD_UNDERSTORY_SCLS NPP_BDEAD for understory plants by size class kg C / ha / yr F +NPP_BGDW_SCPF NPP flux into below-ground deadwood by pft/size kgC/m2/yr F +NPP_BGSW_SCPF NPP flux into below-ground sapwood by pft/size kgC/m2/yr F +NPP_BSEED_CANOPY_SCLS NPP_BSEED for canopy plants by size class kg C / ha / yr F +NPP_BSEED_UNDERSTORY_SCLS NPP_BSEED for understory plants by size class kg C / ha / yr F +NPP_BSW_CANOPY_SCLS NPP_BSW for canopy plants by size class kg C / ha / yr F +NPP_BSW_UNDERSTORY_SCLS NPP_BSW for understory plants by size class kg C / ha / yr F +NPP_BY_AGE net primary productivity by age bin gC/m^2/s F +NPP_CROOT NPP flux into coarse roots kgC/m2/yr T +NPP_FNRT_SCPF NPP flux into fine roots by pft/size kgC/m2/yr F +NPP_FROOT NPP flux into fine roots kgC/m2/yr T +NPP_FROOT_CANOPY_SCLS NPP_FROOT for canopy plants by size class kg C / ha / yr F +NPP_FROOT_UNDERSTORY_SCLS NPP_FROOT for understory plants by size class kg C / ha / yr F +NPP_LEAF NPP flux into leaves kgC/m2/yr T +NPP_LEAF_CANOPY_SCLS NPP_LEAF for canopy plants by size class kg C / ha / yr F +NPP_LEAF_SCPF NPP flux into leaves by pft/size kgC/m2/yr F +NPP_LEAF_UNDERSTORY_SCLS NPP_LEAF for understory plants by size class kg C / ha / yr F +NPP_SCPF total net primary production by pft/size kgC/m2/yr F +NPP_SEED NPP flux into seeds kgC/m2/yr T +NPP_SEED_SCPF NPP flux into seeds by pft/size kgC/m2/yr F +NPP_STEM NPP flux into stem kgC/m2/yr T +NPP_STOR NPP flux into storage tissues kgC/m2/yr T +NPP_STORE_CANOPY_SCLS NPP_STORE for canopy plants by size class kg C / ha / yr F +NPP_STORE_UNDERSTORY_SCLS NPP_STORE for understory plants by size class kg C / ha / yr F +NPP_STOR_SCPF NPP flux into storage by pft/size kgC/m2/yr F +NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F +O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F +OBU Monin-Obukhov length m F +OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T +O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T +PARPROF_DIF_CNLF Radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W/m2 F +PARPROF_DIF_CNLFPFT Radiative profile of diffuse PAR through each canopy, leaf, and PFT W/m2 F +PARPROF_DIR_CNLF Radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W/m2 F +PARPROF_DIR_CNLFPFT Radiative profile of direct PAR through each canopy, leaf, and PFT W/m2 F +PARSHA_Z_CAN PAR absorbed in the shade by top leaf layer in each canopy layer W/m2 F +PARSHA_Z_CNLF PAR absorbed in the shade by each canopy and leaf layer W/m2 F +PARSHA_Z_CNLFPFT PAR absorbed in the shade by each canopy, leaf, and PFT W/m2 F +PARSUN_Z_CAN PAR absorbed in the sun by top leaf layer in each canopy layer W/m2 F +PARSUN_Z_CNLF PAR absorbed in the sun by each canopy and leaf layer W/m2 F +PARSUN_Z_CNLFPFT PAR absorbed in the sun by each canopy, leaf, and PFT W/m2 F +PARVEGLN absorbed par by vegetation at local noon W/m^2 T +PAS_SOMC PAS_SOM C gC/m^2 T +PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F +PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F +PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F +PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F +PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T +PAS_SOMN PAS_SOM N gN/m^2 T +PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F +PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F +PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F +PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F +PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T +PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F +PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F +PATCH_AREA_BY_AGE patch area by age bin m2/m2 T +PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PCH4 atmospheric partial pressure of CH4 Pa T +PCO2 atmospheric partial pressure of CO2 Pa T +PFTbiomass total PFT level biomass gC/m2 T +PFTcanopycrownarea total PFT-level canopy-layer crown area m2/m2 F +PFTcrownarea total PFT level crown area m2/m2 F +PFTgpp total PFT-level GPP kg C m-2 y-1 T +PFTleafbiomass total PFT level leaf biomass gC/m2 T +PFTnindivs total PFT level number of individuals indiv / m2 T +PFTnpp total PFT-level NPP kg C m-2 y-1 T +PFTstorebiomass total PFT level stored biomass gC/m2 T +POTENTIAL_IMMOB potential N immobilization gN/m^2/s T +PRIMARYLAND_PATCHFUSION_ERROR Error in total primary lands associated with patch fusion m2 m-2 d-1 T +PROMOTION_CARBONFLUX promotion-associated biomass carbon flux from understory to canopy gC/m2/s T +PROMOTION_RATE_SCLS promotion rate from understory to canopy by size class indiv/ha/yr F +PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +Q2M 2m specific humidity kg/kg T +QAF canopy air humidity kg/kg F +QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F +QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F +QDRAI sub-surface drainage mm/s T +QDRAI_PERCH perched wt drainage mm/s T +QDRAI_XS saturation excess drainage mm/s T +QDRIP rate of excess canopy liquid falling off canopy mm/s F +QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F +QFLOOD runoff from river flooding mm/s T +QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T +QFLX_EVAP_VEG vegetation evaporation mm H2O/s F +QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T +QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T +QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F +QFLX_SNOW_DRAIN drainage from snow pack mm/s T +QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T +QFLX_SNOW_GRND snow on ground after interception mm H2O/s F +QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F +QH2OSFC surface water runoff mm/s T +QH2OSFC_TO_ICE surface water converted to ice mm/s F +QHR hydraulic redistribution mm/s T +QICE ice growth/melt mm/s T +QICE_FORC qice forcing sent to GLC mm/s F +QICE_FRZ ice growth mm/s T +QICE_MELT ice melt mm/s T +QINFL infiltration mm/s T +QINTR interception mm/s T +QIRRIG_DEMAND irrigation demand mm/s F +QIRRIG_DRIP water added via drip irrigation mm/s F +QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T +QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T +QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T +QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F +QOVER total surface runoff (includes QH2OSFC) mm/s T +QOVER_LAG time-lagged surface runoff for soil columns mm/s F +QPHSNEG net negative hydraulic redistribution flux mm/s F +QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T +QROOTSINK water flux from soil to root in each soil-layer mm/s F +QRUNOFF total liquid runoff not including correction for land use change mm/s T +QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T +QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F +QRUNOFF_R Rural total runoff mm/s F +QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_U Urban total runoff mm/s F +QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T +QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T +QSNOFRZ column-integrated snow freezing rate kg/m2/s T +QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T +QSNOMELT snow melt rate mm/s T +QSNOMELT_ICE snow melt (ice landunits only) mm/s T +QSNOUNLOAD canopy snow unloading mm/s T +QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T +QSNO_WINDUNLOAD canopy snow wind unloading mm/s T +QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T +QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T +QSOIL_ICE Ground evaporation (ice landunits only) mm/s T +QTOPSOIL water input to surface mm/s F +QVEGE canopy evaporation mm/s T +QVEGT canopy transpiration mm/s T +Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F +Qh sensible heat W/m^2 F +Qle total evaporation W/m^2 F +Qstor storage heat flux (includes snowmelt) W/m^2 F +Qtau momentum flux kg/m/s^2 F +RAH1 aerodynamical resistance s/m F +RAH2 aerodynamical resistance s/m F +RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T +RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T +RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F +RAW1 aerodynamical resistance s/m F +RAW2 aerodynamical resistance s/m F +RB leaf boundary resistance s/m F +RDARK_CANOPY_SCLS RDARK for canopy plants by size class kg C / ha / yr F +RDARK_UNDERSTORY_SCLS RDARK for understory plants by size class kg C / ha / yr F +RECRUITMENT Rate of recruitment by PFT indiv/ha/yr T +REPROC Total carbon in live plant reproductive tissues kgC ha-1 T +REPROC_SCPF reproductive carbon mass (on plant) by size-class x pft kgC/ha F +RESP_G_CANOPY_SCLS RESP_G for canopy plants by size class kg C / ha / yr F +RESP_G_UNDERSTORY_SCLS RESP_G for understory plants by size class kg C / ha / yr F +RESP_M_CANOPY_SCLS RESP_M for canopy plants by size class kg C / ha / yr F +RESP_M_UNDERSTORY_SCLS RESP_M for understory plants by size class kg C / ha / yr F +RH atmospheric relative humidity % F +RH2M 2m relative humidity % T +RH2M_R Rural 2m specific humidity % F +RH2M_U Urban 2m relative humidity % F +RHAF fractional humidity of canopy air fraction F +RH_LEAF fractional humidity at leaf surface fraction F +ROOT_MD_CANOPY_SCLS ROOT_MD for canopy plants by size class kg C / ha / yr F +ROOT_MD_UNDERSTORY_SCLS ROOT_MD for understory plants by size class kg C / ha / yr F +RSCANOPY canopy resistance s m-1 T +RSSHA shaded leaf stomatal resistance s/m T +RSSUN sunlit leaf stomatal resistance s/m T +Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rnet net radiation W/m^2 F +SABG solar rad absorbed by ground W/m^2 T +SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T +SABV solar rad absorbed by veg W/m^2 T +SAI_CANOPY_SCLS stem area index(SAI) by size class m2/m2 F +SAI_UNDERSTORY_SCLS number of understory plants by size class indiv/ha F +SAPWC Total carbon in live plant sapwood kgC ha-1 T +SAPWC_SCPF sapwood carbon mass by size-class x pft kgC/ha F +SCORCH_HEIGHT SPITFIRE Flame Scorch Height (calculated per PFT in each patch age bin) m T +SECONDARY_AREA_AGE_ANTHRO_DIST Secondary forest patch area age distribution since anthropgenic disturbance m2/m2 F +SECONDARY_AREA_PATCH_AGE_DIST Secondary forest patch area age distribution since any kind of disturbance m2/m2 F +SECONDARY_FOREST_BIOMASS Biomass on secondary lands (per total site area, mult by SECONDARY_FOREST_FRACTION to get per kgC/m2 F +SECONDARY_FOREST_FRACTION Secondary forest fraction m2/m2 F +SEEDS_IN Seed Production Rate gC m-2 s-1 T +SEEDS_IN_EXTERN_ELEM External Seed Influx Rate kg ha-1 d-1 T +SEEDS_IN_LOCAL_ELEM Within Site Seed Production Rate kg ha-1 d-1 T +SEED_BANK Total Seed Mass of all PFTs gC m-2 T +SEED_BANK_ELEM Total Seed Mass of all PFTs kg ha-1 T +SEED_DECAY_ELEM Seed mass decay (germinated and un-germinated) kg ha-1 d-1 T +SEED_GERM_ELEM Seed mass converted into new cohorts kg ha-1 d-1 T +SEED_PROD_CANOPY_SCLS SEED_PROD for canopy plants by size class kg C / ha / yr F +SEED_PROD_UNDERSTORY_SCLS SEED_PROD for understory plants by size class kg C / ha / yr F +SITE_COLD_STATUS Site level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not-too cold 0,1,2 T +SITE_DAYSINCE_COLDLEAFOFF site level days elapsed since cold leaf drop days T +SITE_DAYSINCE_COLDLEAFON site level days elapsed since cold leaf flush days T +SITE_DAYSINCE_DROUGHTLEAFOFF site level days elapsed since drought leaf drop days T +SITE_DAYSINCE_DROUGHTLEAFON site level days elapsed since drought leaf flush days T +SITE_DROUGHT_STATUS Site level drought status, <2 too dry for leaves, >=2 not-too dry 0,1,2,3 T +SITE_GDD site level growing degree days degC T +SITE_MEANLIQVOL_DROUGHTPHEN site level mean liquid water volume for drought phen m3/m3 T +SITE_NCHILLDAYS site level number of chill days days T +SITE_NCOLDDAYS site level number of cold days days T +SLO_SOMC SLO_SOM C gC/m^2 T +SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F +SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T +SLO_SOMN SLO_SOM N gN/m^2 T +SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F +SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F +SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T +SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F +SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F +SMINN soil mineral N gN/m^2 T +SMINN_LEACHED soil mineral N pool loss to leaching gN/m^2/s T +SMINN_LEACHED_vr soil mineral N pool loss to leaching gN/m^3/s F +SMINN_TO_DENIT_EXCESS denitrification from excess mineral N pool gN/m^2/s F +SMINN_TO_DENIT_EXCESS_vr denitrification from excess mineral N pool gN/m^3/s F +SMINN_TO_DENIT_L1S1 denitrification for decomp. of metabolic litterto ACT_SOM gN/m^2 F +SMINN_TO_DENIT_L1S1_vr denitrification for decomp. of metabolic litterto ACT_SOM gN/m^3 F +SMINN_TO_DENIT_L2S1 denitrification for decomp. of cellulosic litterto ACT_SOM gN/m^2 F +SMINN_TO_DENIT_L2S1_vr denitrification for decomp. of cellulosic litterto ACT_SOM gN/m^3 F +SMINN_TO_DENIT_L3S2 denitrification for decomp. of lignin litterto SLO_SOM gN/m^2 F +SMINN_TO_DENIT_L3S2_vr denitrification for decomp. of lignin litterto SLO_SOM gN/m^3 F +SMINN_TO_DENIT_S1S2 denitrification for decomp. of active soil organicto SLO_SOM gN/m^2 F +SMINN_TO_DENIT_S1S2_vr denitrification for decomp. of active soil organicto SLO_SOM gN/m^3 F +SMINN_TO_DENIT_S1S3 denitrification for decomp. of active soil organicto PAS_SOM gN/m^2 F +SMINN_TO_DENIT_S1S3_vr denitrification for decomp. of active soil organicto PAS_SOM gN/m^3 F +SMINN_TO_DENIT_S2S1 denitrification for decomp. of slow soil organic mato ACT_SOM gN/m^2 F +SMINN_TO_DENIT_S2S1_vr denitrification for decomp. of slow soil organic mato ACT_SOM gN/m^3 F +SMINN_TO_DENIT_S2S3 denitrification for decomp. of slow soil organic mato PAS_SOM gN/m^2 F +SMINN_TO_DENIT_S2S3_vr denitrification for decomp. of slow soil organic mato PAS_SOM gN/m^3 F +SMINN_TO_DENIT_S3S1 denitrification for decomp. of passive soil organicto ACT_SOM gN/m^2 F +SMINN_TO_DENIT_S3S1_vr denitrification for decomp. of passive soil organicto ACT_SOM gN/m^3 F +SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T +SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +SMINN_vr soil mineral N gN/m^3 T +SMP soil matric potential (natural vegetated and crop landunits only) mm T +SNOBCMCL mass of BC in snow column kg/m2 T +SNOBCMSL mass of BC in top snow layer kg/m2 T +SNOCAN intercepted snow mm T +SNODSTMCL mass of dust in snow column kg/m2 T +SNODSTMSL mass of dust in top snow layer kg/m2 T +SNOFSDSND direct nir incident solar radiation on snow W/m^2 F +SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F +SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F +SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F +SNOFSRND direct nir reflected solar radiation from snow W/m^2 T +SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T +SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T +SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T +SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T +SNOLIQFL top snow layer liquid water fraction (land) fraction F +SNOOCMCL mass of OC in snow column kg/m2 T +SNOOCMSL mass of OC in top snow layer kg/m2 T +SNORDSL top snow layer effective grain radius m^-6 F +SNOTTOPL snow temperature (top layer) K F +SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F +SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +SNOWDP gridcell mean snow height m T +SNOWICE snow ice kg/m2 T +SNOWICE_ICE snow ice (ice landunits only) kg/m2 F +SNOWLIQ snow liquid water kg/m2 T +SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F +SNOW_5D 5day snow avg m F +SNOW_DEPTH snow height of snow covered area m T +SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F +SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T +SNOW_SINKS snow sinks (liquid water) mm/s T +SNOW_SOURCES snow sources (liquid water) mm/s T +SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS Mean snow grain size Microns F +SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F +SNO_ICE Snow ice content kg/m2 F +SNO_LIQH2O Snow liquid water content kg/m2 F +SNO_MELT snow melt rate in each snow layer mm/s F +SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T Snow temperatures K F +SNO_TK Thermal conductivity W/m-K F +SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE Snow temperatures (ice landunits only) K F +SNO_Z Snow layer thicknesses m F +SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F +SNOdTdzL top snow layer temperature gradient (land) K/m F +SOIL10 10-day running mean of 12cm layer soil K F +SOILC_HR soil C heterotrophic respiration gC/m^2/s T +SOILC_vr SOIL C (vertically resolved) gC/m^3 T +SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOILN_vr SOIL N (vertically resolved) gN/m^3 T +SOILPSI soil water potential in each soil layer MPa F +SOILRESIS soil resistance to evaporation s/m T +SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +SOMC_FIRE C loss due to peat burning gC/m^2/s T +SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T +SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F +STOREC Total carbon in live plant storage kgC ha-1 T +STOREC_SCPF storage carbon mass by size-class x pft kgC/ha F +SUM_FUEL total ground fuel related to ros (omits 1000hr fuels) gC m-2 T +SUM_FUEL_BY_PATCH_AGE spitfire ground fuel related to ros (omits 1000hr fuels) within each patch age bin (divide by gC / m2 of site area T +SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T +SWBGT 2 m Simplified Wetbulb Globe Temp C T +SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T +SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T +SWdown atmospheric incident solar radiation W/m^2 F +SWup upwelling shortwave radiation W/m^2 F +SoilAlpha factor limiting ground evap unitless F +SoilAlpha_U urban factor limiting ground evap unitless F +T10 10-day running mean of 2-m temperature K F +TAF canopy air temperature K F +TAUX zonal surface stress kg/m/s^2 T +TAUY meridional surface stress kg/m/s^2 T +TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T +TBUILD internal urban building air temperature K T +TBUILD_MAX prescribed maximum interior building temperature K F +TFLOOR floor temperature K F +TG ground temperature K T +TG_ICE ground temperature (ice landunits only) K F +TG_R Rural ground temperature K F +TG_U Urban ground temperature K F +TH2OSFC surface water temperature K T +THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T +TKE1 top lake level eddy thermal conductivity W/(mK) T +TLAI total projected leaf area index m^2/m^2 T +TLAKE lake temperature K T +TOPO_COL column-level topographic height m F +TOPO_COL_ICE column-level topographic height (ice landunits only) m F +TOPO_FORC topograephic height sent to GLC m F +TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +TOTLITC total litter carbon gC/m^2 T +TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T +TOTLITN total litter N gN/m^2 T +TOTLITN_1m total litter N to 1 meter gN/m^2 T +TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T +TOTSOMC total soil organic matter carbon gC/m^2 T +TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T +TOTSOMN total soil organic matter N gN/m^2 T +TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T +TOTVEGC Total carbon in live plants kgC ha-1 T +TOTVEGC_SCPF total vegetation carbon mass in live plants by size-class x pft kgC/ha F +TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F +TREFMNAV daily minimum of average 2-m temperature K T +TREFMNAV_R Rural daily minimum of average 2-m temperature K F +TREFMNAV_U Urban daily minimum of average 2-m temperature K F +TREFMXAV daily maximum of average 2-m temperature K T +TREFMXAV_R Rural daily maximum of average 2-m temperature K F +TREFMXAV_U Urban daily maximum of average 2-m temperature K F +TRIMMING Degree to which canopy expansion is limited by leaf economics none T +TRIMMING_CANOPY_SCLS trimming term of canopy plants by size class indiv/ha F +TRIMMING_UNDERSTORY_SCLS trimming term of understory plants by size class indiv/ha F +TROOF_INNER roof inside surface temperature K F +TSA 2m air temperature K T +TSAI total projected stem area index m^2/m^2 T +TSA_ICE 2m air temperature (ice landunits only) K F +TSA_R Rural 2m air temperature K F +TSA_U Urban 2m air temperature K F +TSHDW_INNER shadewall inside surface temperature K F +TSKIN skin temperature K T +TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +TSOI soil temperature (natural vegetated and crop landunits only) K T +TSOI_10CM soil temperature in top 10cm of soil K T +TSOI_ICE soil temperature (ice landunits only) K T +TSRF_FORC surface temperature sent to GLC K F +TSUNW_INNER sunwall inside surface temperature K F +TV vegetation temperature K T +TV24 vegetation temperature (last 24hrs) K F +TV240 vegetation temperature (last 240hrs) K F +TWS total water storage mm T +T_SCALAR temperature inhibition of decomposition unitless T +Tair atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F +U10 10-m wind m/s T +U10_DUST 10-m wind for dust model m/s T +U10_ICE 10-m wind (ice landunits only) m/s F +UAF canopy air speed m/s F +UM wind speed plus stability effect m/s F +URBAN_AC urban air conditioning flux W/m^2 T +URBAN_HEAT urban heating flux W/m^2 T +USTAR aerodynamical resistance s/m F +UST_LAKE friction velocity (lakes only) m/s F +VA atmospheric wind speed plus convective velocity m/s F +VOLR river channel total water storage m3 T +VOLRMCH river channel main channel water storage m3 T +VPD vpd Pa F +VPD2M 2m vapor pressure deficit Pa T +VPD_CAN canopy vapor pressure deficit kPa T +WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +WBT 2 m Stull Wet Bulb C T +WBT_R Rural 2 m Stull Wet Bulb C T +WBT_U Urban 2 m Stull Wet Bulb C T +WIND atmospheric wind velocity magnitude m/s T +WOOD_PRODUCT Total wood product from logging gC/m2 F +WTGQ surface tracer conductance m/s T +W_SCALAR Moisture (dryness) inhibition of decomposition unitless T +Wind atmospheric wind velocity magnitude m/s F +YESTERDAYCANLEV_CANOPY_SCLS Yesterdays canopy level for canopy plants by size class indiv/ha F +YESTERDAYCANLEV_UNDERSTORY_SCLS Yesterdays canopy level for understory plants by size class indiv/ha F +Z0HG roughness length over ground, sensible heat m F +Z0M momentum roughness length m F +Z0MG roughness length over ground, momentum m F +Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F +Z0QG roughness length over ground, latent heat m F +ZBOT atmospheric reference height m T +ZETA dimensionless stability parameter unitless F +ZII convective boundary height m F +ZSTAR_BY_AGE product of zstar and patch area by age bin (divide by PATCH_AREA_BY_AGE to get mean zstar) m F +ZWT water table depth (natural vegetated and crop landunits only) m T +ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T +ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T +num_iter number of iterations unitless F ==== =================================== ============================================================================================== ================================================================= ======= diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 979b13d697..3bdb33297d 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -13,1303 +13,1303 @@ CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- # Variable Name Long Description Units Active? ==== =================================== ============================================================================================== ================================================================= ======= - 1 A10TMIN 10-day running mean of min 2-m temperature K F - 2 A5TMIN 5-day running mean of min 2-m temperature K F - 3 ACTUAL_IMMOB actual N immobilization gN/m^2/s T - 4 ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F - 5 ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F - 6 ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F - 7 ACT_SOMC ACT_SOM C gC/m^2 T - 8 ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F - 9 ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F - 10 ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F - 11 ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F - 12 ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F - 13 ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F - 14 ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T - 15 ACT_SOMN ACT_SOM N gN/m^2 T - 16 ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F - 17 ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F - 18 ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F - 19 ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F - 20 ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F - 21 ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F - 22 ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T - 23 ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F - 24 ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F - 25 ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F - 26 ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F - 27 AGLB Aboveground leaf biomass kg/m^2 F - 28 AGNPP aboveground NPP gC/m^2/s T - 29 AGSB Aboveground stem biomass kg/m^2 F - 30 ALBD surface albedo (direct) proportion T - 31 ALBDSF diagnostic snow-free surface albedo (direct) proportion T - 32 ALBGRD ground albedo (direct) proportion F - 33 ALBGRI ground albedo (indirect) proportion F - 34 ALBI surface albedo (indirect) proportion T - 35 ALBISF diagnostic snow-free surface albedo (indirect) proportion T - 36 ALPHA alpha coefficient for VOC calc non F - 37 ALT current active layer thickness m T - 38 ALTMAX maximum annual active layer thickness m T - 39 ALTMAX_LASTYEAR maximum prior year active layer thickness m F - 40 ANNAVG_T2M annual average 2m air temperature K F - 41 ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F - 42 ANNSUM_COUNTER seconds since last annual accumulator turnover s F - 43 ANNSUM_NPP annual sum of NPP gC/m^2/yr F - 44 ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F - 45 APPAR_TEMP 2 m apparent temperature C T - 46 APPAR_TEMP_R Rural 2 m apparent temperature C T - 47 APPAR_TEMP_U Urban 2 m apparent temperature C T - 48 AR autotrophic respiration (MR + GR) gC/m^2/s T - 49 ATM_TOPO atmospheric surface height m T - 50 AVAILC C flux available for allocation gC/m^2/s F - 51 AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F - 52 AnnET Annual ET mm/s F - 53 BAF_CROP fractional area burned for crop s-1 T - 54 BAF_PEATF fractional area burned in peatland s-1 T - 55 BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T - 56 BETA coefficient of convective velocity none F - 57 BGLFR background litterfall rate 1/s F - 58 BGNPP belowground NPP gC/m^2/s T - 59 BGTR background transfer growth rate 1/s F - 60 BTRANMN daily minimum of transpiration beta factor unitless T - 61 CANNAVG_T2M annual average of 2m air temperature K F - 62 CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F - 63 CEL_LITC CEL_LIT C gC/m^2 T - 64 CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F - 65 CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F - 66 CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F - 67 CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F - 68 CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T - 69 CEL_LITN CEL_LIT N gN/m^2 T - 70 CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F - 71 CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F - 72 CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F - 73 CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F - 74 CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T - 75 CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F - 76 CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F - 77 CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F - 78 CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F - 79 CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F - 80 CH4PROD Gridcell total production of CH4 gC/m2/s T - 81 CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F - 82 CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F - 83 CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T - 84 CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 85 CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T - 86 CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 87 CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T - 88 CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T - 89 COL_CTRUNC column-level sink for C truncation gC/m^2 F - 90 COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T - 91 COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T - 92 COL_NTRUNC column-level sink for N truncation gN/m^2 F - 93 CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F - 94 CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F - 95 CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T - 96 CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T - 97 COST_NACTIVE Cost of active uptake gN/gC T - 98 COST_NFIX Cost of fixation gN/gC T - 99 COST_NRETRANS Cost of retranslocation gN/gC T - 100 COSZEN cosine of solar zenith angle none F - 101 CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T - 102 CPOOL temporary photosynthate C pool gC/m^2 T - 103 CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F - 104 CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F - 105 CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F - 106 CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F - 107 CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F - 108 CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F - 109 CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F - 110 CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F - 111 CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F - 112 CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F - 113 CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F - 114 CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F - 115 CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F - 116 CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F - 117 CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F - 118 CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F - 119 CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F - 120 CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F - 121 CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F - 122 CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F - 123 CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F - 124 CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F - 125 CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F - 126 CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F - 127 CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F - 128 CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F - 129 CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T - 130 CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T - 131 CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T - 132 CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T - 133 CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T - 134 CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F - 135 CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F - 136 CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F - 137 CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F - 138 CWDC CWD C gC/m^2 T - 139 CWDC_1m CWD C to 1 meter gC/m^2 F - 140 CWDC_HR cwd C heterotrophic respiration gC/m^2/s F - 141 CWDC_LOSS coarse woody debris C loss gC/m^2/s T - 142 CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F - 143 CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F - 144 CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F - 145 CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F - 146 CWDC_vr CWD C (vertically resolved) gC/m^3 T - 147 CWDN CWD N gN/m^2 T - 148 CWDN_1m CWD N to 1 meter gN/m^2 F - 149 CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F - 150 CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F - 151 CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F - 152 CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F - 153 CWDN_vr CWD N (vertically resolved) gN/m^3 T - 154 CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F - 155 CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F - 156 CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F - 157 CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F - 158 C_ALLOMETRY C allocation index none F - 159 DAYL daylength s F - 160 DAYS_ACTIVE number of days since last dormancy days F - 161 DEADCROOTC dead coarse root C gC/m^2 T - 162 DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F - 163 DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F - 164 DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F - 165 DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F - 166 DEADCROOTN dead coarse root N gN/m^2 T - 167 DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F - 168 DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F - 169 DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F - 170 DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F - 171 DEADSTEMC dead stem C gC/m^2 T - 172 DEADSTEMC_STORAGE dead stem C storage gC/m^2 F - 173 DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F - 174 DEADSTEMC_XFER dead stem C transfer gC/m^2 F - 175 DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F - 176 DEADSTEMN dead stem N gN/m^2 T - 177 DEADSTEMN_STORAGE dead stem N storage gN/m^2 F - 178 DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F - 179 DEADSTEMN_XFER dead stem N transfer gN/m^2 F - 180 DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F - 181 DENIT total rate of denitrification gN/m^2/s T - 182 DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F - 183 DISCOI 2 m Discomfort Index C T - 184 DISCOIS 2 m Stull Discomfort Index C T - 185 DISCOIS_R Rural 2 m Stull Discomfort Index C T - 186 DISCOIS_U Urban 2 m Stull Discomfort Index C T - 187 DISCOI_R Rural 2 m Discomfort Index C T - 188 DISCOI_U Urban 2 m Discomfort Index C T - 189 DISPLA displacement height m F - 190 DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T - 191 DISPVEGN displayed vegetation nitrogen gN/m^2 T - 192 DLRAD downward longwave radiation below the canopy W/m^2 F - 193 DORMANT_FLAG dormancy flag none F - 194 DOWNREG fractional reduction in GPP due to N limitation proportion F - 195 DPVLTRB1 turbulent deposition velocity 1 m/s F - 196 DPVLTRB2 turbulent deposition velocity 2 m/s F - 197 DPVLTRB3 turbulent deposition velocity 3 m/s F - 198 DPVLTRB4 turbulent deposition velocity 4 m/s F - 199 DSL dry surface layer thickness mm T - 200 DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T - 201 DSTFLXT total surface dust emission kg/m2/s T - 202 DT_VEG change in t_veg, last iteration K F - 203 DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T - 204 DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T - 205 DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F - 206 DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T - 207 DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F - 208 DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T - 209 DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T - 210 DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F - 211 DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F - 212 DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F - 213 DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F - 214 DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F - 215 DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F - 216 DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F - 217 DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F - 218 DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F - 219 DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F - 220 DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F - 221 DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F - 222 DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F - 223 DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F - 224 DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F - 225 DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F - 226 DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F - 227 DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F - 228 DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T - 229 DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F - 230 DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T - 231 DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F - 232 DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T - 233 DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F - 234 DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T - 235 DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T - 236 DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F - 237 DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F - 238 DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F - 239 DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F - 240 DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F - 241 DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F - 242 EFF_POROSITY effective porosity = porosity - vol_ice proportion F - 243 EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T - 244 EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T - 245 EFLX_GNET net heat flux into ground W/m^2 F - 246 EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T - 247 EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T - 248 EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F - 249 EFLX_LH_TOT_R Rural total evaporation W/m^2 T - 250 EFLX_LH_TOT_U Urban total evaporation W/m^2 F - 251 EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F - 252 ELAI exposed one-sided leaf area index m^2/m^2 T - 253 EMG ground emissivity proportion F - 254 EMV vegetation emissivity proportion F - 255 EOPT Eopt coefficient for VOC calc non F - 256 EPT 2 m Equiv Pot Temp K T - 257 EPT_R Rural 2 m Equiv Pot Temp K T - 258 EPT_U Urban 2 m Equiv Pot Temp K T - 259 ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T - 260 ERRH2O total water conservation error mm T - 261 ERRH2OSNO imbalance in snow depth (liquid water) mm T - 262 ERRSEB surface energy conservation error W/m^2 T - 263 ERRSOI soil/lake energy conservation error W/m^2 T - 264 ERRSOL solar radiation conservation error W/m^2 T - 265 ESAI exposed one-sided stem area index m^2/m^2 T - 266 EXCESSC_MR excess C maintenance respiration gC/m^2/s F - 267 EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F - 268 FAREA_BURNED timestep fractional area burned s-1 T - 269 FCANSNO fraction of canopy that is wet proportion F - 270 FCEV canopy evaporation W/m^2 T - 271 FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T - 272 FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T - 273 FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T - 274 FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F - 275 FCOV fractional impermeable area unitless T - 276 FCTR canopy transpiration W/m^2 T - 277 FDRY fraction of foliage that is green and dry proportion F - 278 FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F - 279 FERT_COUNTER time left to fertilize seconds F - 280 FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F - 281 FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T - 282 FGEV ground evaporation W/m^2 T - 283 FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T - 284 FGR12 heat flux between soil layers 1 and 2 W/m^2 T - 285 FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F - 286 FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F - 287 FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F - 288 FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F - 289 FH2OSFC fraction of ground covered by surface water unitless T - 290 FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F - 291 FINUNDATED fractional inundated area of vegetated columns unitless T - 292 FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F - 293 FIRA net infrared (longwave) radiation W/m^2 T - 294 FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F - 295 FIRA_R Rural net infrared (longwave) radiation W/m^2 T - 296 FIRA_U Urban net infrared (longwave) radiation W/m^2 F - 297 FIRE emitted infrared (longwave) radiation W/m^2 T - 298 FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F - 299 FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T - 300 FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F - 301 FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T - 302 FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F - 303 FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F - 304 FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F - 305 FPI fraction of potential immobilization proportion T - 306 FPI_vr fraction of potential immobilization proportion F - 307 FPSN photosynthesis umol m-2 s-1 T - 308 FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F - 309 FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F - 310 FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F - 311 FPSN_WP Product-limited photosynthesis umol m-2 s-1 F - 312 FRAC_ICEOLD fraction of ice relative to the tot water proportion F - 313 FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T - 314 FROOTC fine root C gC/m^2 T - 315 FROOTC_ALLOC fine root C allocation gC/m^2/s T - 316 FROOTC_LOSS fine root C loss gC/m^2/s T - 317 FROOTC_STORAGE fine root C storage gC/m^2 F - 318 FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F - 319 FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F - 320 FROOTC_XFER fine root C transfer gC/m^2 F - 321 FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F - 322 FROOTN fine root N gN/m^2 T - 323 FROOTN_STORAGE fine root N storage gN/m^2 F - 324 FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F - 325 FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F - 326 FROOTN_XFER fine root N transfer gN/m^2 F - 327 FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F - 328 FROOT_MR fine root maintenance respiration gC/m^2/s F - 329 FROOT_PROF profile for litter C and N inputs from fine roots 1/m F - 330 FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F - 331 FSA absorbed solar radiation W/m^2 T - 332 FSAT fractional area with water table at surface unitless T - 333 FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F - 334 FSA_R Rural absorbed solar radiation W/m^2 F - 335 FSA_U Urban absorbed solar radiation W/m^2 F - 336 FSD24 direct radiation (last 24hrs) K F - 337 FSD240 direct radiation (last 240hrs) K F - 338 FSDS atmospheric incident solar radiation W/m^2 T - 339 FSDSND direct nir incident solar radiation W/m^2 T - 340 FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T - 341 FSDSNI diffuse nir incident solar radiation W/m^2 T - 342 FSDSVD direct vis incident solar radiation W/m^2 T - 343 FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T - 344 FSDSVI diffuse vis incident solar radiation W/m^2 T - 345 FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T - 346 FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T - 347 FSH_G sensible heat from ground W/m^2 T - 348 FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F - 349 FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T - 350 FSH_R Rural sensible heat W/m^2 T - 351 FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T - 352 FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T - 353 FSH_U Urban sensible heat W/m^2 F - 354 FSH_V sensible heat from veg W/m^2 T - 355 FSI24 indirect radiation (last 24hrs) K F - 356 FSI240 indirect radiation (last 240hrs) K F - 357 FSM snow melt heat flux W/m^2 T - 358 FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F - 359 FSM_R Rural snow melt heat flux W/m^2 F - 360 FSM_U Urban snow melt heat flux W/m^2 F - 361 FSNO fraction of ground covered by snow unitless T - 362 FSNO_EFF effective fraction of ground covered by snow unitless T - 363 FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F - 364 FSR reflected solar radiation W/m^2 T - 365 FSRND direct nir reflected solar radiation W/m^2 T - 366 FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T - 367 FSRNI diffuse nir reflected solar radiation W/m^2 T - 368 FSRSF reflected solar radiation W/m^2 T - 369 FSRSFND direct nir reflected solar radiation W/m^2 T - 370 FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T - 371 FSRSFNI diffuse nir reflected solar radiation W/m^2 T - 372 FSRSFVD direct vis reflected solar radiation W/m^2 T - 373 FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T - 374 FSRSFVI diffuse vis reflected solar radiation W/m^2 T - 375 FSRVD direct vis reflected solar radiation W/m^2 T - 376 FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T - 377 FSRVI diffuse vis reflected solar radiation W/m^2 T - 378 FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F - 379 FSUN sunlit fraction of canopy proportion F - 380 FSUN24 fraction sunlit (last 24hrs) K F - 381 FSUN240 fraction sunlit (last 240hrs) K F - 382 FUELC fuel load gC/m^2 T - 383 FV friction velocity m/s T - 384 FWET fraction of canopy that is wet proportion F - 385 F_DENIT denitrification flux gN/m^2/s T - 386 F_DENIT_BASE F_DENIT_BASE gN/m^3/s F - 387 F_DENIT_vr denitrification flux gN/m^3/s F - 388 F_N2O_DENIT denitrification N2O flux gN/m^2/s T - 389 F_N2O_NIT nitrification N2O flux gN/m^2/s T - 390 F_NIT nitrification flux gN/m^2/s T - 391 F_NIT_vr nitrification flux gN/m^3/s F - 392 FireComp_BC fire emissions flux of BC kg/m2/sec F - 393 FireComp_OC fire emissions flux of OC kg/m2/sec F - 394 FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F - 395 FireEmis_TOT Total fire emissions flux gC/m2/sec F - 396 FireEmis_ZTOP Top of vertical fire emissions distribution m F - 397 FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F - 398 FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F - 399 FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F - 400 GAMMA total gamma for VOC calc non F - 401 GAMMAA gamma A for VOC calc non F - 402 GAMMAC gamma C for VOC calc non F - 403 GAMMAL gamma L for VOC calc non F - 404 GAMMAP gamma P for VOC calc non F - 405 GAMMAS gamma S for VOC calc non F - 406 GAMMAT gamma T for VOC calc non F - 407 GDD0 Growing degree days base 0C from planting ddays F - 408 GDD020 Twenty year average of growing degree days base 0C from planting ddays F - 409 GDD10 Growing degree days base 10C from planting ddays F - 410 GDD1020 Twenty year average of growing degree days base 10C from planting ddays F - 411 GDD8 Growing degree days base 8C from planting ddays F - 412 GDD820 Twenty year average of growing degree days base 8C from planting ddays F - 413 GDDACCUM Accumulated growing degree days past planting date for crop ddays F - 414 GDDACCUM_PERHARV For each crop harvest in a calendar year, accumulated growing degree days past planting date ddays F - 415 GDDHARV Growing degree days (gdd) needed to harvest ddays F - 416 GDDHARV_PERHARV For each harvest in a calendar year,For each harvest in a calendar year, growing degree days (gdd) needed to harvest ddays F - 417 GDDTSOI Growing degree-days from planting (top two soil layers) ddays F - 418 GPP gross primary production gC/m^2/s T - 419 GR total growth respiration gC/m^2/s T - 420 GRAINC grain C (does not equal yield) gC/m^2 T - 421 GRAINC_TO_FOOD grain C to food gC/m^2/s T - 422 GRAINC_TO_FOOD_ANN total grain C to food in all harvests in a calendar year gC/m^2 F - 423 GRAINC_TO_FOOD_PERHARV grain C to food for each harvest in a calendar year gC/m^2 F - 424 GRAINC_TO_SEED grain C to seed gC/m^2/s T - 425 GRAINN grain N gN/m^2 T - 426 GRESP_STORAGE growth respiration storage gC/m^2 F - 427 GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F - 428 GRESP_XFER growth respiration transfer gC/m^2 F - 429 GROSS_NMIN gross rate of N mineralization gN/m^2/s T - 430 GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F - 431 GSSHA shaded leaf stomatal conductance umol H20/m2/s T - 432 GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T - 433 GSSUN sunlit leaf stomatal conductance umol H20/m2/s T - 434 GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T - 435 H2OCAN intercepted water mm T - 436 H2OSFC surface water depth mm T - 437 H2OSNO snow depth (liquid water) mm T - 438 H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F - 439 H2OSNO_TOP mass of snow in top snow layer kg/m2 T - 440 H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T - 441 HARVEST_REASON_PERHARV For each harvest in a calendar year, the reason the crop was harvested categorical F - 442 HBOT canopy bottom m F - 443 HEAT_CONTENT1 initial gridcell total heat content J/m^2 T - 444 HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F - 445 HEAT_CONTENT2 post land cover change total heat content J/m^2 F - 446 HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T - 447 HIA 2 m NWS Heat Index C T - 448 HIA_R Rural 2 m NWS Heat Index C T - 449 HIA_U Urban 2 m NWS Heat Index C T - 450 HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F - 451 HR total heterotrophic respiration gC/m^2/s T - 452 HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T - 453 HTOP canopy top m T - 454 HUI crop heat unit index ddays F - 455 HUI_PERHARV For each harvest in a calendar year, crop heat unit index ddays F - 456 HUMIDEX 2 m Humidex C T - 457 HUMIDEX_R Rural 2 m Humidex C T - 458 HUMIDEX_U Urban 2 m Humidex C T - 459 ICE_CONTENT1 initial gridcell total ice content mm T - 460 ICE_CONTENT2 post land cover change total ice content mm F - 461 ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F - 462 INIT_GPP GPP flux before downregulation gC/m^2/s F - 463 INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F - 464 INT_SNOW_ICE accumulated swe (ice landunits only) mm F - 465 IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T - 466 JMX25T canopy profile of jmax umol/m2/s T - 467 Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T - 468 KROOT root conductance each soil layer 1/s F - 469 KSOIL soil conductance in each soil layer 1/s F - 470 K_ACT_SOM active soil organic potential loss coefficient 1/s F - 471 K_CEL_LIT cellulosic litter potential loss coefficient 1/s F - 472 K_CWD coarse woody debris potential loss coefficient 1/s F - 473 K_LIG_LIT lignin litter potential loss coefficient 1/s F - 474 K_MET_LIT metabolic litter potential loss coefficient 1/s F - 475 K_NITR K_NITR 1/s F - 476 K_NITR_H2O K_NITR_H2O unitless F - 477 K_NITR_PH K_NITR_PH unitless F - 478 K_NITR_T K_NITR_T unitless F - 479 K_PAS_SOM passive soil organic potential loss coefficient 1/s F - 480 K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F - 481 LAI240 240hr average of leaf area index m^2/m^2 F - 482 LAISHA shaded projected leaf area index m^2/m^2 T - 483 LAISUN sunlit projected leaf area index m^2/m^2 T - 484 LAKEICEFRAC lake layer ice mass fraction unitless F - 485 LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T - 486 LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T - 487 LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T - 488 LATBASET latitude vary base temperature for gddplant degree C F - 489 LEAFC leaf C gC/m^2 T - 490 LEAFCN Leaf CN ratio used for flexible CN gC/gN T - 491 LEAFCN_OFFSET Leaf C:N used by FUN unitless F - 492 LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F - 493 LEAFC_ALLOC leaf C allocation gC/m^2/s T - 494 LEAFC_CHANGE C change in leaf gC/m^2/s T - 495 LEAFC_LOSS leaf C loss gC/m^2/s T - 496 LEAFC_STORAGE leaf C storage gC/m^2 F - 497 LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F - 498 LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F - 499 LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T - 500 LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F - 501 LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T - 502 LEAFC_XFER leaf C transfer gC/m^2 F - 503 LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F - 504 LEAFN leaf N gN/m^2 T - 505 LEAFN_STORAGE leaf N storage gN/m^2 F - 506 LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F - 507 LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F - 508 LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T - 509 LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F - 510 LEAFN_XFER leaf N transfer gN/m^2 F - 511 LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F - 512 LEAF_MR leaf maintenance respiration gC/m^2/s T - 513 LEAF_PROF profile for litter C and N inputs from leaves 1/m F - 514 LFC2 conversion area fraction of BET and BDT that burned per sec T - 515 LGSF long growing season factor proportion F - 516 LIG_LITC LIG_LIT C gC/m^2 T - 517 LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F - 518 LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F - 519 LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F - 520 LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F - 521 LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T - 522 LIG_LITN LIG_LIT N gN/m^2 T - 523 LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F - 524 LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F - 525 LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F - 526 LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F - 527 LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T - 528 LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F - 529 LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F - 530 LIQCAN intercepted liquid water mm T - 531 LIQUID_CONTENT1 initial gridcell total liq content mm T - 532 LIQUID_CONTENT2 post landuse change gridcell total liq content mm F - 533 LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F - 534 LITFALL litterfall (leaves and fine roots) gC/m^2/s T - 535 LITFIRE litter fire losses gC/m^2/s F - 536 LITTERC_HR litter C heterotrophic respiration gC/m^2/s T - 537 LITTERC_LOSS litter C loss gC/m^2/s T - 538 LIVECROOTC live coarse root C gC/m^2 T - 539 LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F - 540 LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F - 541 LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F - 542 LIVECROOTC_XFER live coarse root C transfer gC/m^2 F - 543 LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F - 544 LIVECROOTN live coarse root N gN/m^2 T - 545 LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F - 546 LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F - 547 LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F - 548 LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F - 549 LIVECROOTN_XFER live coarse root N transfer gN/m^2 F - 550 LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F - 551 LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F - 552 LIVESTEMC live stem C gC/m^2 T - 553 LIVESTEMC_STORAGE live stem C storage gC/m^2 F - 554 LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F - 555 LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T - 556 LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F - 557 LIVESTEMC_XFER live stem C transfer gC/m^2 F - 558 LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F - 559 LIVESTEMN live stem N gN/m^2 T - 560 LIVESTEMN_STORAGE live stem N storage gN/m^2 F - 561 LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F - 562 LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F - 563 LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F - 564 LIVESTEMN_XFER live stem N transfer gN/m^2 F - 565 LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F - 566 LIVESTEM_MR live stem maintenance respiration gC/m^2/s F - 567 LNC leaf N concentration gN leaf/m^2 T - 568 LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F - 569 LWup upwelling longwave radiation W/m^2 F - 570 MEG_acetaldehyde MEGAN flux kg/m2/sec T - 571 MEG_acetic_acid MEGAN flux kg/m2/sec T - 572 MEG_acetone MEGAN flux kg/m2/sec T - 573 MEG_carene_3 MEGAN flux kg/m2/sec T - 574 MEG_ethanol MEGAN flux kg/m2/sec T - 575 MEG_formaldehyde MEGAN flux kg/m2/sec T - 576 MEG_isoprene MEGAN flux kg/m2/sec T - 577 MEG_methanol MEGAN flux kg/m2/sec T - 578 MEG_pinene_a MEGAN flux kg/m2/sec T - 579 MEG_thujene_a MEGAN flux kg/m2/sec T - 580 MET_LITC MET_LIT C gC/m^2 T - 581 MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F - 582 MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F - 583 MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F - 584 MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F - 585 MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T - 586 MET_LITN MET_LIT N gN/m^2 T - 587 MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F - 588 MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F - 589 MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F - 590 MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F - 591 MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T - 592 MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F - 593 MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F - 594 MR maintenance respiration gC/m^2/s T - 595 M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F - 596 M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F - 597 M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F - 598 M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F - 599 M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F - 600 M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F - 601 M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F - 602 M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F - 603 M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F - 604 M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F - 605 M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F - 606 M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F - 607 M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F - 608 M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F - 609 M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F - 610 M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F - 611 M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F - 612 M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F - 613 M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F - 614 M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F - 615 M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F - 616 M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F - 617 M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F - 618 M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F - 619 M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F - 620 M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F - 621 M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F - 622 M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F - 623 M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F - 624 M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F - 625 M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F - 626 M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F - 627 M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F - 628 M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F - 629 M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F - 630 M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F - 631 M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F - 632 M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F - 633 M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F - 634 M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F - 635 M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F - 636 M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F - 637 M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F - 638 M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F - 639 M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F - 640 M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F - 641 M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F - 642 M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F - 643 M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F - 644 M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F - 645 M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F - 646 M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F - 647 M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F - 648 M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F - 649 M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F - 650 M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F - 651 M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F - 652 M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F - 653 M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F - 654 M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F - 655 M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F - 656 M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F - 657 M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F - 658 M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F - 659 M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F - 660 M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F - 661 M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F - 662 M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F - 663 M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F - 664 M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F - 665 M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F - 666 M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F - 667 M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F - 668 M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F - 669 M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F - 670 M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F - 671 M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F - 672 M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F - 673 M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F - 674 M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F - 675 M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F - 676 M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F - 677 M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F - 678 M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F - 679 M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F - 680 M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F - 681 M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F - 682 M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F - 683 M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F - 684 M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F - 685 M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F - 686 M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F - 687 M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F - 688 M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F - 689 M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F - 690 M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F - 691 M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F - 692 M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F - 693 M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F - 694 M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F - 695 M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F - 696 M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F - 697 M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F - 698 M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F - 699 M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F - 700 M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F - 701 M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F - 702 M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F - 703 M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F - 704 M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F - 705 M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F - 706 M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F - 707 M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F - 708 M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F - 709 M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F - 710 M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F - 711 M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F - 712 M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F - 713 M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F - 714 M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F - 715 M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F - 716 M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F - 717 M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F - 718 M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F - 719 M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F - 720 M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F - 721 M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F - 722 M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F - 723 M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F - 724 M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F - 725 M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F - 726 M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F - 727 NACTIVE Mycorrhizal N uptake flux gN/m^2/s T - 728 NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T - 729 NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T - 730 NAM AM-associated N uptake flux gN/m^2/s T - 731 NAM_NH4 AM-associated N uptake flux gN/m^2/s T - 732 NAM_NO3 AM-associated N uptake flux gN/m^2/s T - 733 NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T - 734 NDEPLOY total N deployed in new growth gN/m^2/s T - 735 NDEP_PROF profile for atmospheric N deposition 1/m F - 736 NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T - 737 NECM ECM-associated N uptake flux gN/m^2/s T - 738 NECM_NH4 ECM-associated N uptake flux gN/m^2/s T - 739 NECM_NO3 ECM-associated N uptake flux gN/m^2/s T - 740 NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T - 741 NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T - 742 NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T - 743 NET_NMIN net rate of N mineralization gN/m^2/s T - 744 NET_NMIN_vr net rate of N mineralization gN/m^3/s F - 745 NFERTILIZATION fertilizer added gN/m^2/s T - 746 NFIRE fire counts valid only in Reg.C counts/km2/sec T - 747 NFIX Symbiotic BNF uptake flux gN/m^2/s T - 748 NFIXATION_PROF profile for biological N fixation 1/m F - 749 NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F - 750 NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T - 751 NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T - 752 NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T - 753 NPASSIVE Passive N uptake flux gN/m^2/s T - 754 NPOOL temporary plant N pool gN/m^2 T - 755 NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F - 756 NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F - 757 NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F - 758 NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F - 759 NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F - 760 NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F - 761 NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F - 762 NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F - 763 NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F - 764 NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F - 765 NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F - 766 NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F - 767 NPP net primary production gC/m^2/s T - 768 NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F - 769 NPP_GROWTH Total C used for growth in FUN gC/m^2/s T - 770 NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T - 771 NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T - 772 NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T - 773 NPP_NAM AM-associated N uptake used C gC/m^2/s T - 774 NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T - 775 NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T - 776 NPP_NECM ECM-associated N uptake used C gC/m^2/s T - 777 NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T - 778 NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T - 779 NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T - 780 NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T - 781 NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T - 782 NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T - 783 NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T - 784 NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T - 785 NRETRANS Retranslocated N uptake flux gN/m^2/s T - 786 NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T - 787 NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T - 788 NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T - 789 NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F - 790 NUPTAKE Total N uptake of FUN gN/m^2/s T - 791 NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T - 792 N_ALLOMETRY N allocation index none F - 793 O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F - 794 OBU Monin-Obukhov length m F - 795 OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T - 796 OFFSET_COUNTER offset days counter days F - 797 OFFSET_FDD offset freezing degree days counter C degree-days F - 798 OFFSET_FLAG offset flag none F - 799 OFFSET_SWI offset soil water index none F - 800 ONSET_COUNTER onset days counter days F - 801 ONSET_FDD onset freezing degree days counter C degree-days F - 802 ONSET_FLAG onset flag none F - 803 ONSET_GDD onset growing degree days C degree-days F - 804 ONSET_GDDFLAG onset flag for growing degree day sum none F - 805 ONSET_SWI onset soil water index none F - 806 O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T - 807 PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F - 808 PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F - 809 PAR240_shade shade PAR (240 hrs) umol/m2/s F - 810 PAR240_sun sunlit PAR (240 hrs) umol/m2/s F - 811 PAR24_shade shade PAR (24 hrs) umol/m2/s F - 812 PAR24_sun sunlit PAR (24 hrs) umol/m2/s F - 813 PARVEGLN absorbed par by vegetation at local noon W/m^2 T - 814 PAR_shade shade PAR umol/m2/s F - 815 PAR_sun sunlit PAR umol/m2/s F - 816 PAS_SOMC PAS_SOM C gC/m^2 T - 817 PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F - 818 PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F - 819 PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F - 820 PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F - 821 PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T - 822 PAS_SOMN PAS_SOM N gN/m^2 T - 823 PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F - 824 PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F - 825 PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F - 826 PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F - 827 PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T - 828 PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F - 829 PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F - 830 PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T - 831 PBOT_240 10 day running mean of air pressure Pa F - 832 PCH4 atmospheric partial pressure of CH4 Pa T - 833 PCO2 atmospheric partial pressure of CO2 Pa T - 834 PCO2_240 10 day running mean of CO2 pressure Pa F - 835 PFT_CTRUNC patch-level sink for C truncation gC/m^2 F - 836 PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T - 837 PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T - 838 PFT_NTRUNC patch-level sink for N truncation gN/m^2 F - 839 PLANTCN Plant C:N used by FUN unitless F - 840 PLANT_CALLOC total allocated C flux gC/m^2/s F - 841 PLANT_NALLOC total allocated N flux gN/m^2/s F - 842 PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T - 843 PNLCZ Proportion of nitrogen allocated for light capture unitless F - 844 PO2_240 10 day running mean of O2 pressure Pa F - 845 POTENTIAL_IMMOB potential N immobilization gN/m^2/s T - 846 POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F - 847 POT_F_DENIT potential denitrification flux gN/m^2/s T - 848 POT_F_DENIT_vr potential denitrification flux gN/m^3/s F - 849 POT_F_NIT potential nitrification flux gN/m^2/s T - 850 POT_F_NIT_vr potential nitrification flux gN/m^3/s F - 851 PREC10 10-day running mean of PREC MM H2O/S F - 852 PREC60 60-day running mean of PREC MM H2O/S F - 853 PREV_DAYL daylength from previous timestep s F - 854 PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F - 855 PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F - 856 PROD100C 100-yr wood product C gC/m^2 F - 857 PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F - 858 PROD100N 100-yr wood product N gN/m^2 F - 859 PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F - 860 PROD10C 10-yr wood product C gC/m^2 F - 861 PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F - 862 PROD10N 10-yr wood product N gN/m^2 F - 863 PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F - 864 PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T - 865 PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T - 866 PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T - 867 PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T - 868 PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F - 869 Q2M 2m specific humidity kg/kg T - 870 QAF canopy air humidity kg/kg F - 871 QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T - 872 QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F - 873 QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F - 874 QDRAI sub-surface drainage mm/s T - 875 QDRAI_PERCH perched wt drainage mm/s T - 876 QDRAI_XS saturation excess drainage mm/s T - 877 QDRIP rate of excess canopy liquid falling off canopy mm/s F - 878 QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F - 879 QFLOOD runoff from river flooding mm/s T - 880 QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T - 881 QFLX_EVAP_VEG vegetation evaporation mm H2O/s F - 882 QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T - 883 QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T - 884 QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T - 885 QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T - 886 QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F - 887 QFLX_SNOW_DRAIN drainage from snow pack mm/s T - 888 QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T - 889 QFLX_SNOW_GRND snow on ground after interception mm H2O/s F - 890 QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T - 891 QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T - 892 QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F - 893 QH2OSFC surface water runoff mm/s T - 894 QH2OSFC_TO_ICE surface water converted to ice mm/s F - 895 QHR hydraulic redistribution mm/s T - 896 QICE ice growth/melt mm/s T - 897 QICE_FORC qice forcing sent to GLC mm/s F - 898 QICE_FRZ ice growth mm/s T - 899 QICE_MELT ice melt mm/s T - 900 QINFL infiltration mm/s T - 901 QINTR interception mm/s T - 902 QIRRIG_DEMAND irrigation demand mm/s F - 903 QIRRIG_DRIP water added via drip irrigation mm/s F - 904 QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T - 905 QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T - 906 QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T - 907 QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F - 908 QOVER total surface runoff (includes QH2OSFC) mm/s T - 909 QOVER_LAG time-lagged surface runoff for soil columns mm/s F - 910 QPHSNEG net negative hydraulic redistribution flux mm/s F - 911 QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T - 912 QROOTSINK water flux from soil to root in each soil-layer mm/s F - 913 QRUNOFF total liquid runoff not including correction for land use change mm/s T - 914 QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T - 915 QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T - 916 QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F - 917 QRUNOFF_R Rural total runoff mm/s F - 918 QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T - 919 QRUNOFF_U Urban total runoff mm/s F - 920 QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T - 921 QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T - 922 QSNOFRZ column-integrated snow freezing rate kg/m2/s T - 923 QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T - 924 QSNOMELT snow melt rate mm/s T - 925 QSNOMELT_ICE snow melt (ice landunits only) mm/s T - 926 QSNOUNLOAD canopy snow unloading mm/s T - 927 QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T - 928 QSNO_WINDUNLOAD canopy snow wind unloading mm/s T - 929 QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T - 930 QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T - 931 QSOIL_ICE Ground evaporation (ice landunits only) mm/s T - 932 QTOPSOIL water input to surface mm/s F - 933 QVEGE canopy evaporation mm/s T - 934 QVEGT canopy transpiration mm/s T - 935 Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F - 936 Qh sensible heat W/m^2 F - 937 Qle total evaporation W/m^2 F - 938 Qstor storage heat flux (includes snowmelt) W/m^2 F - 939 Qtau momentum flux kg/m/s^2 F - 940 RAH1 aerodynamical resistance s/m F - 941 RAH2 aerodynamical resistance s/m F - 942 RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T - 943 RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T - 944 RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F - 945 RAM1 aerodynamical resistance s/m F - 946 RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F - 947 RAW1 aerodynamical resistance s/m F - 948 RAW2 aerodynamical resistance s/m F - 949 RB leaf boundary resistance s/m F - 950 RB10 10 day running mean boundary layer resistance s/m F - 951 RETRANSN plant pool of retranslocated N gN/m^2 T - 952 RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T - 953 RH atmospheric relative humidity % F - 954 RH2M 2m relative humidity % T - 955 RH2M_R Rural 2m specific humidity % F - 956 RH2M_U Urban 2m relative humidity % F - 957 RH30 30-day running mean of relative humidity % F - 958 RHAF fractional humidity of canopy air fraction F - 959 RHAF10 10 day running mean of fractional humidity of canopy air fraction F - 960 RH_LEAF fractional humidity at leaf surface fraction F - 961 ROOTR effective fraction of roots in each soil layer (SMS method) proportion F - 962 RR root respiration (fine root MR + total root GR) gC/m^2/s T - 963 RRESIS root resistance in each soil layer proportion F - 964 RSSHA shaded leaf stomatal resistance s/m T - 965 RSSUN sunlit leaf stomatal resistance s/m T - 966 Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F - 967 Rnet net radiation W/m^2 F - 968 SABG solar rad absorbed by ground W/m^2 T - 969 SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T - 970 SABV solar rad absorbed by veg W/m^2 T - 971 SDATES Crop sowing dates in each calendar year day of year (julian day) F - 972 SDATES_PERHARV For each harvest in a calendar year, the Julian day the crop was sown day of year (julian day) F - 973 SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T - 974 SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T - 975 SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T - 976 SLO_SOMC SLO_SOM C gC/m^2 T - 977 SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F - 978 SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F - 979 SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F - 980 SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F - 981 SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F - 982 SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F - 983 SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T - 984 SLO_SOMN SLO_SOM N gN/m^2 T - 985 SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F - 986 SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F - 987 SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F - 988 SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F - 989 SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F - 990 SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F - 991 SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T - 992 SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F - 993 SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 994 SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F - 995 SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F - 996 SMINN soil mineral N gN/m^2 T - 997 SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T - 998 SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T - 999 SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T -1000 SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F -1001 SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F -1002 SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F -1003 SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F -1004 SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F -1005 SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F -1006 SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F -1007 SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -1008 SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -1009 SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -1010 SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -1011 SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -1012 SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -1013 SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -1014 SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -1015 SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -1016 SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -1017 SMINN_vr soil mineral N gN/m^3 T -1018 SMIN_NH4 soil mineral NH4 gN/m^2 T -1019 SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F -1020 SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T -1021 SMIN_NO3 soil mineral NO3 gN/m^2 T -1022 SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T -1023 SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F -1024 SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F -1025 SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T -1026 SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F -1027 SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F -1028 SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T -1029 SMP soil matric potential (natural vegetated and crop landunits only) mm T -1030 SNOBCMCL mass of BC in snow column kg/m2 T -1031 SNOBCMSL mass of BC in top snow layer kg/m2 T -1032 SNOCAN intercepted snow mm T -1033 SNODSTMCL mass of dust in snow column kg/m2 T -1034 SNODSTMSL mass of dust in top snow layer kg/m2 T -1035 SNOFSDSND direct nir incident solar radiation on snow W/m^2 F -1036 SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F -1037 SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F -1038 SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F -1039 SNOFSRND direct nir reflected solar radiation from snow W/m^2 T -1040 SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T -1041 SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T -1042 SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T -1043 SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T -1044 SNOLIQFL top snow layer liquid water fraction (land) fraction F -1045 SNOOCMCL mass of OC in snow column kg/m2 T -1046 SNOOCMSL mass of OC in top snow layer kg/m2 T -1047 SNORDSL top snow layer effective grain radius m^-6 F -1048 SNOTTOPL snow temperature (top layer) K F -1049 SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F -1050 SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T -1051 SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F -1052 SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T -1053 SNOWDP gridcell mean snow height m T -1054 SNOWICE snow ice kg/m2 T -1055 SNOWICE_ICE snow ice (ice landunits only) kg/m2 F -1056 SNOWLIQ snow liquid water kg/m2 T -1057 SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F -1058 SNOW_5D 5day snow avg m F -1059 SNOW_DEPTH snow height of snow covered area m T -1060 SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F -1061 SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T -1062 SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -1063 SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T -1064 SNOW_SINKS snow sinks (liquid water) mm/s T -1065 SNOW_SOURCES snow sources (liquid water) mm/s T -1066 SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F -1067 SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -1068 SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F -1069 SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -1070 SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F -1071 SNO_FRZ snow freezing rate in each snow layer kg/m2/s F -1072 SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F -1073 SNO_GS Mean snow grain size Microns F -1074 SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F -1075 SNO_ICE Snow ice content kg/m2 F -1076 SNO_LIQH2O Snow liquid water content kg/m2 F -1077 SNO_MELT snow melt rate in each snow layer mm/s F -1078 SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F -1079 SNO_T Snow temperatures K F -1080 SNO_TK Thermal conductivity W/m-K F -1081 SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F -1082 SNO_T_ICE Snow temperatures (ice landunits only) K F -1083 SNO_Z Snow layer thicknesses m F -1084 SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F -1085 SNOdTdzL top snow layer temperature gradient (land) K/m F -1086 SOIL10 10-day running mean of 12cm layer soil K F -1087 SOILC_CHANGE C change in soil gC/m^2/s T -1088 SOILC_HR soil C heterotrophic respiration gC/m^2/s T -1089 SOILC_vr SOIL C (vertically resolved) gC/m^3 T -1090 SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T -1091 SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T -1092 SOILN_vr SOIL N (vertically resolved) gN/m^3 T -1093 SOILPSI soil water potential in each soil layer MPa F -1094 SOILRESIS soil resistance to evaporation s/m T -1095 SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T -1096 SOMC_FIRE C loss due to peat burning gC/m^2/s T -1097 SOMFIRE soil organic matter fire losses gC/m^2/s F -1098 SOM_ADV_COEF advection term for vertical SOM translocation m/s F -1099 SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T -1100 SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F -1101 SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -1102 SOWING_REASON For each sowing in a calendar year, the reason the crop was sown categorical F -1103 SOWING_REASON_PERHARV For each harvest in a calendar year, the reason the crop was sown categorical F -1104 SR total soil respiration (HR + root resp) gC/m^2/s T -1105 SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T -1106 SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T -1107 SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T -1108 SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T -1109 SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T -1110 SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T -1111 SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T -1112 STEM_PROF profile for litter C and N inputs from stems 1/m F -1113 STORAGE_CDEMAND C use from the C storage pool gC/m^2 F -1114 STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F -1115 STORAGE_NDEMAND N demand during the offset period gN/m^2 F -1116 STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T -1117 STORVEGN stored vegetation nitrogen gN/m^2 T -1118 SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T -1119 SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -1120 SYEARS_PERHARV For each harvest in a calendar year, the year the crop was sown year F -1121 SWBGT 2 m Simplified Wetbulb Globe Temp C T -1122 SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T -1123 SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -1124 SWMP65 2 m Swamp Cooler Temp 65% Eff C T -1125 SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T -1126 SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T -1127 SWMP80 2 m Swamp Cooler Temp 80% Eff C T -1128 SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T -1129 SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T -1130 SWdown atmospheric incident solar radiation W/m^2 F -1131 SWup upwelling shortwave radiation W/m^2 F -1132 SoilAlpha factor limiting ground evap unitless F -1133 SoilAlpha_U urban factor limiting ground evap unitless F -1134 T10 10-day running mean of 2-m temperature K F -1135 TAF canopy air temperature K F -1136 TAUX zonal surface stress kg/m/s^2 T -1137 TAUY meridional surface stress kg/m/s^2 T -1138 TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T -1139 TBUILD internal urban building air temperature K T -1140 TBUILD_MAX prescribed maximum interior building temperature K F -1141 TEMPAVG_T2M temporary average 2m air temperature K F -1142 TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F -1143 TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F -1144 TEQ 2 m Equiv Temp K T -1145 TEQ_R Rural 2 m Equiv Temp K T -1146 TEQ_U Urban 2 m Equiv Temp K T -1147 TFLOOR floor temperature K F -1148 TG ground temperature K T -1149 TG_ICE ground temperature (ice landunits only) K F -1150 TG_R Rural ground temperature K F -1151 TG_U Urban ground temperature K F -1152 TH2OSFC surface water temperature K T -1153 THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -1154 THIC 2 m Temp Hum Index Comfort C T -1155 THIC_R Rural 2 m Temp Hum Index Comfort C T -1156 THIC_U Urban 2 m Temp Hum Index Comfort C T -1157 THIP 2 m Temp Hum Index Physiology C T -1158 THIP_R Rural 2 m Temp Hum Index Physiology C T -1159 THIP_U Urban 2 m Temp Hum Index Physiology C T -1160 TKE1 top lake level eddy thermal conductivity W/(mK) T -1161 TLAI total projected leaf area index m^2/m^2 T -1162 TLAKE lake temperature K T -1163 TOPO_COL column-level topographic height m F -1164 TOPO_COL_ICE column-level topographic height (ice landunits only) m F -1165 TOPO_FORC topograephic height sent to GLC m F -1166 TOPT topt coefficient for VOC calc non F -1167 TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T -1168 TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T -1169 TOTCOLN total column-level N, excluding product pools gN/m^2 T -1170 TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T -1171 TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T -1172 TOTFIRE total ecosystem fire losses gC/m^2/s F -1173 TOTLITC total litter carbon gC/m^2 T -1174 TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T -1175 TOTLITN total litter N gN/m^2 T -1176 TOTLITN_1m total litter N to 1 meter gN/m^2 T -1177 TOTPFTC total patch-level carbon, including cpool gC/m^2 T -1178 TOTPFTN total patch-level nitrogen gN/m^2 T -1179 TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T -1180 TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T -1181 TOTSOMC total soil organic matter carbon gC/m^2 T -1182 TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T -1183 TOTSOMN total soil organic matter N gN/m^2 T -1184 TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -1185 TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T -1186 TOTVEGN total vegetation nitrogen gN/m^2 T -1187 TOT_WOODPRODC total wood product C gC/m^2 T -1188 TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T -1189 TOT_WOODPRODN total wood product N gN/m^2 T -1190 TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T -1191 TPU25T canopy profile of tpu umol/m2/s T -1192 TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F -1193 TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F -1194 TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F -1195 TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F -1196 TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F -1197 TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F -1198 TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F -1199 TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F -1200 TREFMNAV daily minimum of average 2-m temperature K T -1201 TREFMNAV_R Rural daily minimum of average 2-m temperature K F -1202 TREFMNAV_U Urban daily minimum of average 2-m temperature K F -1203 TREFMXAV daily maximum of average 2-m temperature K T -1204 TREFMXAV_R Rural daily maximum of average 2-m temperature K F -1205 TREFMXAV_U Urban daily maximum of average 2-m temperature K F -1206 TROOF_INNER roof inside surface temperature K F -1207 TSA 2m air temperature K T -1208 TSAI total projected stem area index m^2/m^2 T -1209 TSA_ICE 2m air temperature (ice landunits only) K F -1210 TSA_R Rural 2m air temperature K F -1211 TSA_U Urban 2m air temperature K F -1212 TSHDW_INNER shadewall inside surface temperature K F -1213 TSKIN skin temperature K T -1214 TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -1215 TSOI soil temperature (natural vegetated and crop landunits only) K T -1216 TSOI_10CM soil temperature in top 10cm of soil K T -1217 TSOI_ICE soil temperature (ice landunits only) K T -1218 TSRF_FORC surface temperature sent to GLC K F -1219 TSUNW_INNER sunwall inside surface temperature K F -1220 TV vegetation temperature K T -1221 TV24 vegetation temperature (last 24hrs) K F -1222 TV240 vegetation temperature (last 240hrs) K F -1223 TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F -1224 TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F -1225 TWS total water storage mm T -1226 T_SCALAR temperature inhibition of decomposition unitless T -1227 Tair atmospheric air temperature (downscaled to columns in glacier regions) K F -1228 Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F -1229 U10 10-m wind m/s T -1230 U10_DUST 10-m wind for dust model m/s T -1231 U10_ICE 10-m wind (ice landunits only) m/s F -1232 UAF canopy air speed m/s F -1233 ULRAD upward longwave radiation above the canopy W/m^2 F -1234 UM wind speed plus stability effect m/s F -1235 URBAN_AC urban air conditioning flux W/m^2 T -1236 URBAN_HEAT urban heating flux W/m^2 T -1237 USTAR aerodynamical resistance s/m F -1238 UST_LAKE friction velocity (lakes only) m/s F -1239 VA atmospheric wind speed plus convective velocity m/s F -1240 VCMX25T canopy profile of vcmax25 umol/m2/s T -1241 VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T -1242 VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T -1243 VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T -1244 VOCFLXT total VOC flux into atmosphere moles/m2/sec F -1245 VOLR river channel total water storage m3 T -1246 VOLRMCH river channel main channel water storage m3 T -1247 VPD vpd Pa F -1248 VPD2M 2m vapor pressure deficit Pa T -1249 VPD_CAN canopy vapor pressure deficit kPa T -1250 Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T -1251 WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -1252 WBA 2 m Wet Bulb C T -1253 WBA_R Rural 2 m Wet Bulb C T -1254 WBA_U Urban 2 m Wet Bulb C T -1255 WBT 2 m Stull Wet Bulb C T -1256 WBT_R Rural 2 m Stull Wet Bulb C T -1257 WBT_U Urban 2 m Stull Wet Bulb C T -1258 WF soil water as frac. of whc for top 0.05 m proportion F -1259 WFPS WFPS percent F -1260 WIND atmospheric wind velocity magnitude m/s T -1261 WOODC wood C gC/m^2 T -1262 WOODC_ALLOC wood C eallocation gC/m^2/s T -1263 WOODC_LOSS wood C loss gC/m^2/s T -1264 WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T -1265 WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T -1266 WTGQ surface tracer conductance m/s T -1267 W_SCALAR Moisture (dryness) inhibition of decomposition unitless T -1268 Wind atmospheric wind velocity magnitude m/s F -1269 XSMRPOOL temporary photosynthate C pool gC/m^2 T -1270 XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F -1271 XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T -1272 Z0HG roughness length over ground, sensible heat m F -1273 Z0HV roughness length over vegetation, sensible heat m F -1274 Z0M momentum roughness length m F -1275 Z0MG roughness length over ground, momentum m F -1276 Z0MV roughness length over vegetation, momentum m F -1277 Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -1278 Z0QG roughness length over ground, latent heat m F -1279 Z0QV roughness length over vegetation, latent heat m F -1280 ZBOT atmospheric reference height m T -1281 ZETA dimensionless stability parameter unitless F -1282 ZII convective boundary height m F -1283 ZWT water table depth (natural vegetated and crop landunits only) m T -1284 ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T -1285 ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T -1286 anaerobic_frac anaerobic_frac m3/m3 F -1287 bsw clap and hornberger B unitless F -1288 currentPatch currentPatch coefficient for VOC calc non F -1289 diffus diffusivity m^2/s F -1290 fr_WFPS fr_WFPS fraction F -1291 n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F -1292 num_iter number of iterations unitless F -1293 r_psi r_psi m F -1294 ratio_k1 ratio_k1 none F -1295 ratio_no3_co2 ratio_no3_co2 ratio F -1296 soil_bulkdensity soil_bulkdensity kg/m3 F -1297 soil_co2_prod soil_co2_prod ug C / g soil / day F -1298 watfc water field capacity m^3/m^3 F -1299 watsat water saturated m^3/m^3 F +A10TMIN 10-day running mean of min 2-m temperature K F +A5TMIN 5-day running mean of min 2-m temperature K F +ACTUAL_IMMOB actual N immobilization gN/m^2/s T +ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F +ACT_SOMC ACT_SOM C gC/m^2 T +ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F +ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F +ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F +ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F +ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T +ACT_SOMN ACT_SOM N gN/m^2 T +ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F +ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F +ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F +ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F +ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F +ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T +ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F +ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F +AGLB Aboveground leaf biomass kg/m^2 F +AGNPP aboveground NPP gC/m^2/s T +AGSB Aboveground stem biomass kg/m^2 F +ALBD surface albedo (direct) proportion T +ALBDSF diagnostic snow-free surface albedo (direct) proportion T +ALBGRD ground albedo (direct) proportion F +ALBGRI ground albedo (indirect) proportion F +ALBI surface albedo (indirect) proportion T +ALBISF diagnostic snow-free surface albedo (indirect) proportion T +ALPHA alpha coefficient for VOC calc non F +ALT current active layer thickness m T +ALTMAX maximum annual active layer thickness m T +ALTMAX_LASTYEAR maximum prior year active layer thickness m F +ANNAVG_T2M annual average 2m air temperature K F +ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F +ANNSUM_COUNTER seconds since last annual accumulator turnover s F +ANNSUM_NPP annual sum of NPP gC/m^2/yr F +ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F +APPAR_TEMP 2 m apparent temperature C T +APPAR_TEMP_R Rural 2 m apparent temperature C T +APPAR_TEMP_U Urban 2 m apparent temperature C T +AR autotrophic respiration (MR + GR) gC/m^2/s T +ATM_TOPO atmospheric surface height m T +AVAILC C flux available for allocation gC/m^2/s F +AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F +AnnET Annual ET mm/s F +BAF_CROP fractional area burned for crop s-1 T +BAF_PEATF fractional area burned in peatland s-1 T +BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BETA coefficient of convective velocity none F +BGLFR background litterfall rate 1/s F +BGNPP belowground NPP gC/m^2/s T +BGTR background transfer growth rate 1/s F +BTRANMN daily minimum of transpiration beta factor unitless T +CANNAVG_T2M annual average of 2m air temperature K F +CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F +CEL_LITC CEL_LIT C gC/m^2 T +CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F +CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F +CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T +CEL_LITN CEL_LIT N gN/m^2 T +CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F +CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F +CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F +CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F +CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T +CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F +CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F +CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F +CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F +CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F +CH4PROD Gridcell total production of CH4 gC/m2/s T +CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T +CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +COL_CTRUNC column-level sink for C truncation gC/m^2 F +COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T +COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T +COL_NTRUNC column-level sink for N truncation gN/m^2 F +CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F +CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T +COST_NACTIVE Cost of active uptake gN/gC T +COST_NFIX Cost of fixation gN/gC T +COST_NRETRANS Cost of retranslocation gN/gC T +COSZEN cosine of solar zenith angle none F +CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T +CPOOL temporary photosynthate C pool gC/m^2 T +CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F +CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F +CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F +CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F +CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F +CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F +CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F +CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F +CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F +CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F +CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F +CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F +CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F +CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F +CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F +CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F +CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F +CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F +CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F +CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F +CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F +CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F +CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F +CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F +CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F +CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F +CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T +CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T +CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T +CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T +CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T +CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F +CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F +CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F +CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F +CWDC CWD C gC/m^2 T +CWDC_1m CWD C to 1 meter gC/m^2 F +CWDC_HR cwd C heterotrophic respiration gC/m^2/s F +CWDC_LOSS coarse woody debris C loss gC/m^2/s T +CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F +CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F +CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F +CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F +CWDC_vr CWD C (vertically resolved) gC/m^3 T +CWDN CWD N gN/m^2 T +CWDN_1m CWD N to 1 meter gN/m^2 F +CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F +CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F +CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F +CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F +CWDN_vr CWD N (vertically resolved) gN/m^3 T +CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F +CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F +CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F +CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F +C_ALLOMETRY C allocation index none F +DAYL daylength s F +DAYS_ACTIVE number of days since last dormancy days F +DEADCROOTC dead coarse root C gC/m^2 T +DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F +DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F +DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F +DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F +DEADCROOTN dead coarse root N gN/m^2 T +DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F +DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F +DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F +DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F +DEADSTEMC dead stem C gC/m^2 T +DEADSTEMC_STORAGE dead stem C storage gC/m^2 F +DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F +DEADSTEMC_XFER dead stem C transfer gC/m^2 F +DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F +DEADSTEMN dead stem N gN/m^2 T +DEADSTEMN_STORAGE dead stem N storage gN/m^2 F +DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F +DEADSTEMN_XFER dead stem N transfer gN/m^2 F +DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F +DENIT total rate of denitrification gN/m^2/s T +DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F +DISCOI 2 m Discomfort Index C T +DISCOIS 2 m Stull Discomfort Index C T +DISCOIS_R Rural 2 m Stull Discomfort Index C T +DISCOIS_U Urban 2 m Stull Discomfort Index C T +DISCOI_R Rural 2 m Discomfort Index C T +DISCOI_U Urban 2 m Discomfort Index C T +DISPLA displacement height m F +DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T +DISPVEGN displayed vegetation nitrogen gN/m^2 T +DLRAD downward longwave radiation below the canopy W/m^2 F +DORMANT_FLAG dormancy flag none F +DOWNREG fractional reduction in GPP due to N limitation proportion F +DPVLTRB1 turbulent deposition velocity 1 m/s F +DPVLTRB2 turbulent deposition velocity 2 m/s F +DPVLTRB3 turbulent deposition velocity 3 m/s F +DPVLTRB4 turbulent deposition velocity 4 m/s F +DSL dry surface layer thickness mm T +DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTFLXT total surface dust emission kg/m2/s T +DT_VEG change in t_veg, last iteration K F +DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T +DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T +DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F +DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T +DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F +DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T +DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T +DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F +DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F +DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F +DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F +DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F +DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F +DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F +DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F +DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F +DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F +DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F +DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F +DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F +DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F +DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T +DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F +DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T +DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F +DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T +DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F +DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T +DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T +DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F +DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +EFF_POROSITY effective porosity = porosity - vol_ice proportion F +EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T +EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T +EFLX_GNET net heat flux into ground W/m^2 F +EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T +EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T +EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F +EFLX_LH_TOT_R Rural total evaporation W/m^2 T +EFLX_LH_TOT_U Urban total evaporation W/m^2 F +EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F +ELAI exposed one-sided leaf area index m^2/m^2 T +EMG ground emissivity proportion F +EMV vegetation emissivity proportion F +EOPT Eopt coefficient for VOC calc non F +EPT 2 m Equiv Pot Temp K T +EPT_R Rural 2 m Equiv Pot Temp K T +EPT_U Urban 2 m Equiv Pot Temp K T +ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T +ERRH2O total water conservation error mm T +ERRH2OSNO imbalance in snow depth (liquid water) mm T +ERRSEB surface energy conservation error W/m^2 T +ERRSOI soil/lake energy conservation error W/m^2 T +ERRSOL solar radiation conservation error W/m^2 T +ESAI exposed one-sided stem area index m^2/m^2 T +EXCESSC_MR excess C maintenance respiration gC/m^2/s F +EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F +FAREA_BURNED timestep fractional area burned s-1 T +FCANSNO fraction of canopy that is wet proportion F +FCEV canopy evaporation W/m^2 T +FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T +FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T +FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T +FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F +FCOV fractional impermeable area unitless T +FCTR canopy transpiration W/m^2 T +FDRY fraction of foliage that is green and dry proportion F +FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F +FERT_COUNTER time left to fertilize seconds F +FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F +FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T +FGEV ground evaporation W/m^2 T +FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T +FGR12 heat flux between soil layers 1 and 2 W/m^2 T +FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F +FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F +FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F +FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F +FH2OSFC fraction of ground covered by surface water unitless T +FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F +FINUNDATED fractional inundated area of vegetated columns unitless T +FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F +FIRA net infrared (longwave) radiation W/m^2 T +FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRA_R Rural net infrared (longwave) radiation W/m^2 T +FIRA_U Urban net infrared (longwave) radiation W/m^2 F +FIRE emitted infrared (longwave) radiation W/m^2 T +FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T +FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F +FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T +FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F +FPI fraction of potential immobilization proportion T +FPI_vr fraction of potential immobilization proportion F +FPSN photosynthesis umol m-2 s-1 T +FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F +FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F +FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F +FPSN_WP Product-limited photosynthesis umol m-2 s-1 F +FRAC_ICEOLD fraction of ice relative to the tot water proportion F +FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T +FROOTC fine root C gC/m^2 T +FROOTC_ALLOC fine root C allocation gC/m^2/s T +FROOTC_LOSS fine root C loss gC/m^2/s T +FROOTC_STORAGE fine root C storage gC/m^2 F +FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F +FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F +FROOTC_XFER fine root C transfer gC/m^2 F +FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F +FROOTN fine root N gN/m^2 T +FROOTN_STORAGE fine root N storage gN/m^2 F +FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F +FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F +FROOTN_XFER fine root N transfer gN/m^2 F +FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F +FROOT_MR fine root maintenance respiration gC/m^2/s F +FROOT_PROF profile for litter C and N inputs from fine roots 1/m F +FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F +FSA absorbed solar radiation W/m^2 T +FSAT fractional area with water table at surface unitless T +FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F +FSA_R Rural absorbed solar radiation W/m^2 F +FSA_U Urban absorbed solar radiation W/m^2 F +FSD24 direct radiation (last 24hrs) K F +FSD240 direct radiation (last 240hrs) K F +FSDS atmospheric incident solar radiation W/m^2 T +FSDSND direct nir incident solar radiation W/m^2 T +FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T +FSDSNI diffuse nir incident solar radiation W/m^2 T +FSDSVD direct vis incident solar radiation W/m^2 T +FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T +FSDSVI diffuse vis incident solar radiation W/m^2 T +FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T +FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T +FSH_G sensible heat from ground W/m^2 T +FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F +FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T +FSH_R Rural sensible heat W/m^2 T +FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T +FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T +FSH_U Urban sensible heat W/m^2 F +FSH_V sensible heat from veg W/m^2 T +FSI24 indirect radiation (last 24hrs) K F +FSI240 indirect radiation (last 240hrs) K F +FSM snow melt heat flux W/m^2 T +FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F +FSM_R Rural snow melt heat flux W/m^2 F +FSM_U Urban snow melt heat flux W/m^2 F +FSNO fraction of ground covered by snow unitless T +FSNO_EFF effective fraction of ground covered by snow unitless T +FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F +FSR reflected solar radiation W/m^2 T +FSRND direct nir reflected solar radiation W/m^2 T +FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T +FSRNI diffuse nir reflected solar radiation W/m^2 T +FSRSF reflected solar radiation W/m^2 T +FSRSFND direct nir reflected solar radiation W/m^2 T +FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T +FSRSFNI diffuse nir reflected solar radiation W/m^2 T +FSRSFVD direct vis reflected solar radiation W/m^2 T +FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T +FSRSFVI diffuse vis reflected solar radiation W/m^2 T +FSRVD direct vis reflected solar radiation W/m^2 T +FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T +FSRVI diffuse vis reflected solar radiation W/m^2 T +FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F +FSUN sunlit fraction of canopy proportion F +FSUN24 fraction sunlit (last 24hrs) K F +FSUN240 fraction sunlit (last 240hrs) K F +FUELC fuel load gC/m^2 T +FV friction velocity m/s T +FWET fraction of canopy that is wet proportion F +F_DENIT denitrification flux gN/m^2/s T +F_DENIT_BASE F_DENIT_BASE gN/m^3/s F +F_DENIT_vr denitrification flux gN/m^3/s F +F_N2O_DENIT denitrification N2O flux gN/m^2/s T +F_N2O_NIT nitrification N2O flux gN/m^2/s T +F_NIT nitrification flux gN/m^2/s T +F_NIT_vr nitrification flux gN/m^3/s F +FireComp_BC fire emissions flux of BC kg/m2/sec F +FireComp_OC fire emissions flux of OC kg/m2/sec F +FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F +FireEmis_TOT Total fire emissions flux gC/m2/sec F +FireEmis_ZTOP Top of vertical fire emissions distribution m F +FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F +FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F +FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F +GAMMA total gamma for VOC calc non F +GAMMAA gamma A for VOC calc non F +GAMMAC gamma C for VOC calc non F +GAMMAL gamma L for VOC calc non F +GAMMAP gamma P for VOC calc non F +GAMMAS gamma S for VOC calc non F +GAMMAT gamma T for VOC calc non F +GDD0 Growing degree days base 0C from planting ddays F +GDD020 Twenty year average of growing degree days base 0C from planting ddays F +GDD10 Growing degree days base 10C from planting ddays F +GDD1020 Twenty year average of growing degree days base 10C from planting ddays F +GDD8 Growing degree days base 8C from planting ddays F +GDD820 Twenty year average of growing degree days base 8C from planting ddays F +GDDACCUM Accumulated growing degree days past planting date for crop ddays F +GDDACCUM_PERHARV For each crop harvest in a calendar year, accumulated growing degree days past planting date ddays F +GDDHARV Growing degree days (gdd) needed to harvest ddays F +GDDHARV_PERHARV For each harvest in a calendar year,For each harvest in a calendar year, growing degree days (gdd) needed to harvest ddays F +GDDTSOI Growing degree-days from planting (top two soil layers) ddays F +GPP gross primary production gC/m^2/s T +GR total growth respiration gC/m^2/s T +GRAINC grain C (does not equal yield) gC/m^2 T +GRAINC_TO_FOOD grain C to food gC/m^2/s T +GRAINC_TO_FOOD_ANN total grain C to food in all harvests in a calendar year gC/m^2 F +GRAINC_TO_FOOD_PERHARV grain C to food for each harvest in a calendar year gC/m^2 F +GRAINC_TO_SEED grain C to seed gC/m^2/s T +GRAINN grain N gN/m^2 T +GRESP_STORAGE growth respiration storage gC/m^2 F +GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F +GRESP_XFER growth respiration transfer gC/m^2 F +GROSS_NMIN gross rate of N mineralization gN/m^2/s T +GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F +GSSHA shaded leaf stomatal conductance umol H20/m2/s T +GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T +GSSUN sunlit leaf stomatal conductance umol H20/m2/s T +GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T +H2OCAN intercepted water mm T +H2OSFC surface water depth mm T +H2OSNO snow depth (liquid water) mm T +H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F +H2OSNO_TOP mass of snow in top snow layer kg/m2 T +H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HARVEST_REASON_PERHARV For each harvest in a calendar year, the reason the crop was harvested categorical F +HBOT canopy bottom m F +HEAT_CONTENT1 initial gridcell total heat content J/m^2 T +HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F +HEAT_CONTENT2 post land cover change total heat content J/m^2 F +HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T +HIA 2 m NWS Heat Index C T +HIA_R Rural 2 m NWS Heat Index C T +HIA_U Urban 2 m NWS Heat Index C T +HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +HR total heterotrophic respiration gC/m^2/s T +HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T +HTOP canopy top m T +HUI crop heat unit index ddays F +HUI_PERHARV For each harvest in a calendar year, crop heat unit index ddays F +HUMIDEX 2 m Humidex C T +HUMIDEX_R Rural 2 m Humidex C T +HUMIDEX_U Urban 2 m Humidex C T +ICE_CONTENT1 initial gridcell total ice content mm T +ICE_CONTENT2 post land cover change total ice content mm F +ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F +INIT_GPP GPP flux before downregulation gC/m^2/s F +INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F +INT_SNOW_ICE accumulated swe (ice landunits only) mm F +IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T +JMX25T canopy profile of jmax umol/m2/s T +Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T +KROOT root conductance each soil layer 1/s F +KSOIL soil conductance in each soil layer 1/s F +K_ACT_SOM active soil organic potential loss coefficient 1/s F +K_CEL_LIT cellulosic litter potential loss coefficient 1/s F +K_CWD coarse woody debris potential loss coefficient 1/s F +K_LIG_LIT lignin litter potential loss coefficient 1/s F +K_MET_LIT metabolic litter potential loss coefficient 1/s F +K_NITR K_NITR 1/s F +K_NITR_H2O K_NITR_H2O unitless F +K_NITR_PH K_NITR_PH unitless F +K_NITR_T K_NITR_T unitless F +K_PAS_SOM passive soil organic potential loss coefficient 1/s F +K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F +LAI240 240hr average of leaf area index m^2/m^2 F +LAISHA shaded projected leaf area index m^2/m^2 T +LAISUN sunlit projected leaf area index m^2/m^2 T +LAKEICEFRAC lake layer ice mass fraction unitless F +LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T +LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T +LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T +LATBASET latitude vary base temperature for gddplant degree C F +LEAFC leaf C gC/m^2 T +LEAFCN Leaf CN ratio used for flexible CN gC/gN T +LEAFCN_OFFSET Leaf C:N used by FUN unitless F +LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F +LEAFC_ALLOC leaf C allocation gC/m^2/s T +LEAFC_CHANGE C change in leaf gC/m^2/s T +LEAFC_LOSS leaf C loss gC/m^2/s T +LEAFC_STORAGE leaf C storage gC/m^2 F +LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F +LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F +LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T +LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F +LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T +LEAFC_XFER leaf C transfer gC/m^2 F +LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F +LEAFN leaf N gN/m^2 T +LEAFN_STORAGE leaf N storage gN/m^2 F +LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F +LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F +LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T +LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F +LEAFN_XFER leaf N transfer gN/m^2 F +LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F +LEAF_MR leaf maintenance respiration gC/m^2/s T +LEAF_PROF profile for litter C and N inputs from leaves 1/m F +LFC2 conversion area fraction of BET and BDT that burned per sec T +LGSF long growing season factor proportion F +LIG_LITC LIG_LIT C gC/m^2 T +LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F +LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F +LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T +LIG_LITN LIG_LIT N gN/m^2 T +LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F +LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F +LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T +LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F +LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F +LIQCAN intercepted liquid water mm T +LIQUID_CONTENT1 initial gridcell total liq content mm T +LIQUID_CONTENT2 post landuse change gridcell total liq content mm F +LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F +LITFALL litterfall (leaves and fine roots) gC/m^2/s T +LITFIRE litter fire losses gC/m^2/s F +LITTERC_HR litter C heterotrophic respiration gC/m^2/s T +LITTERC_LOSS litter C loss gC/m^2/s T +LIVECROOTC live coarse root C gC/m^2 T +LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F +LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F +LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F +LIVECROOTC_XFER live coarse root C transfer gC/m^2 F +LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F +LIVECROOTN live coarse root N gN/m^2 T +LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F +LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F +LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F +LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F +LIVECROOTN_XFER live coarse root N transfer gN/m^2 F +LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F +LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F +LIVESTEMC live stem C gC/m^2 T +LIVESTEMC_STORAGE live stem C storage gC/m^2 F +LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F +LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T +LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F +LIVESTEMC_XFER live stem C transfer gC/m^2 F +LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F +LIVESTEMN live stem N gN/m^2 T +LIVESTEMN_STORAGE live stem N storage gN/m^2 F +LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F +LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F +LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F +LIVESTEMN_XFER live stem N transfer gN/m^2 F +LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F +LIVESTEM_MR live stem maintenance respiration gC/m^2/s F +LNC leaf N concentration gN leaf/m^2 T +LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWup upwelling longwave radiation W/m^2 F +MEG_acetaldehyde MEGAN flux kg/m2/sec T +MEG_acetic_acid MEGAN flux kg/m2/sec T +MEG_acetone MEGAN flux kg/m2/sec T +MEG_carene_3 MEGAN flux kg/m2/sec T +MEG_ethanol MEGAN flux kg/m2/sec T +MEG_formaldehyde MEGAN flux kg/m2/sec T +MEG_isoprene MEGAN flux kg/m2/sec T +MEG_methanol MEGAN flux kg/m2/sec T +MEG_pinene_a MEGAN flux kg/m2/sec T +MEG_thujene_a MEGAN flux kg/m2/sec T +MET_LITC MET_LIT C gC/m^2 T +MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F +MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F +MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F +MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F +MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T +MET_LITN MET_LIT N gN/m^2 T +MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F +MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F +MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F +MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F +MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T +MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F +MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F +MR maintenance respiration gC/m^2/s T +M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F +M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F +M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F +M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F +M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F +M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F +M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F +M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F +M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F +M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F +M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F +M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F +M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F +M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F +M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F +M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F +M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F +M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F +M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F +M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F +M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F +M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F +M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F +M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F +M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F +M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F +M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F +M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F +M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F +M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F +M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F +M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F +M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F +M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F +M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F +M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F +M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F +M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F +M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F +M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F +M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F +M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F +M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F +M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F +M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F +M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F +M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F +M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F +M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F +M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F +M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F +M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F +M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F +M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F +M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F +M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F +M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F +M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F +M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F +M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F +M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F +M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F +M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F +M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F +M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F +M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F +M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F +M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F +M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F +M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F +M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F +M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F +M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F +M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F +M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F +M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F +M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F +M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F +M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F +M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F +M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F +M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F +M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F +M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F +M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F +M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F +M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F +M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F +M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F +M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F +M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F +M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F +M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F +M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F +M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F +M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F +M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F +M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F +M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F +M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F +M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F +M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F +M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F +M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F +M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F +M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F +M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F +M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F +M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F +M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F +M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F +M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F +M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F +M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F +M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F +M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F +M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F +M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F +M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F +M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F +M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F +M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F +M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F +M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F +M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F +M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F +NACTIVE Mycorrhizal N uptake flux gN/m^2/s T +NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T +NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T +NAM AM-associated N uptake flux gN/m^2/s T +NAM_NH4 AM-associated N uptake flux gN/m^2/s T +NAM_NO3 AM-associated N uptake flux gN/m^2/s T +NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T +NDEPLOY total N deployed in new growth gN/m^2/s T +NDEP_PROF profile for atmospheric N deposition 1/m F +NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T +NECM ECM-associated N uptake flux gN/m^2/s T +NECM_NH4 ECM-associated N uptake flux gN/m^2/s T +NECM_NO3 ECM-associated N uptake flux gN/m^2/s T +NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T +NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T +NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T +NET_NMIN net rate of N mineralization gN/m^2/s T +NET_NMIN_vr net rate of N mineralization gN/m^3/s F +NFERTILIZATION fertilizer added gN/m^2/s T +NFIRE fire counts valid only in Reg.C counts/km2/sec T +NFIX Symbiotic BNF uptake flux gN/m^2/s T +NFIXATION_PROF profile for biological N fixation 1/m F +NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F +NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T +NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T +NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T +NPASSIVE Passive N uptake flux gN/m^2/s T +NPOOL temporary plant N pool gN/m^2 T +NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F +NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F +NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F +NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F +NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F +NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F +NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F +NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F +NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F +NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F +NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F +NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F +NPP net primary production gC/m^2/s T +NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F +NPP_GROWTH Total C used for growth in FUN gC/m^2/s T +NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T +NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T +NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T +NPP_NAM AM-associated N uptake used C gC/m^2/s T +NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T +NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T +NPP_NECM ECM-associated N uptake used C gC/m^2/s T +NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T +NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T +NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T +NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T +NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T +NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T +NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T +NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T +NRETRANS Retranslocated N uptake flux gN/m^2/s T +NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T +NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T +NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T +NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F +NUPTAKE Total N uptake of FUN gN/m^2/s T +NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T +N_ALLOMETRY N allocation index none F +O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F +OBU Monin-Obukhov length m F +OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T +OFFSET_COUNTER offset days counter days F +OFFSET_FDD offset freezing degree days counter C degree-days F +OFFSET_FLAG offset flag none F +OFFSET_SWI offset soil water index none F +ONSET_COUNTER onset days counter days F +ONSET_FDD onset freezing degree days counter C degree-days F +ONSET_FLAG onset flag none F +ONSET_GDD onset growing degree days C degree-days F +ONSET_GDDFLAG onset flag for growing degree day sum none F +ONSET_SWI onset soil water index none F +O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T +PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F +PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F +PAR240_shade shade PAR (240 hrs) umol/m2/s F +PAR240_sun sunlit PAR (240 hrs) umol/m2/s F +PAR24_shade shade PAR (24 hrs) umol/m2/s F +PAR24_sun sunlit PAR (24 hrs) umol/m2/s F +PARVEGLN absorbed par by vegetation at local noon W/m^2 T +PAR_shade shade PAR umol/m2/s F +PAR_sun sunlit PAR umol/m2/s F +PAS_SOMC PAS_SOM C gC/m^2 T +PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F +PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F +PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F +PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F +PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T +PAS_SOMN PAS_SOM N gN/m^2 T +PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F +PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F +PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F +PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F +PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T +PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F +PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F +PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PBOT_240 10 day running mean of air pressure Pa F +PCH4 atmospheric partial pressure of CH4 Pa T +PCO2 atmospheric partial pressure of CO2 Pa T +PCO2_240 10 day running mean of CO2 pressure Pa F +PFT_CTRUNC patch-level sink for C truncation gC/m^2 F +PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T +PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T +PFT_NTRUNC patch-level sink for N truncation gN/m^2 F +PLANTCN Plant C:N used by FUN unitless F +PLANT_CALLOC total allocated C flux gC/m^2/s F +PLANT_NALLOC total allocated N flux gN/m^2/s F +PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T +PNLCZ Proportion of nitrogen allocated for light capture unitless F +PO2_240 10 day running mean of O2 pressure Pa F +POTENTIAL_IMMOB potential N immobilization gN/m^2/s T +POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F +POT_F_DENIT potential denitrification flux gN/m^2/s T +POT_F_DENIT_vr potential denitrification flux gN/m^3/s F +POT_F_NIT potential nitrification flux gN/m^2/s T +POT_F_NIT_vr potential nitrification flux gN/m^3/s F +PREC10 10-day running mean of PREC MM H2O/S F +PREC60 60-day running mean of PREC MM H2O/S F +PREV_DAYL daylength from previous timestep s F +PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F +PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F +PROD100C 100-yr wood product C gC/m^2 F +PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F +PROD100N 100-yr wood product N gN/m^2 F +PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F +PROD10C 10-yr wood product C gC/m^2 F +PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F +PROD10N 10-yr wood product N gN/m^2 F +PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F +PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T +PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T +PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T +PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T +PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +Q2M 2m specific humidity kg/kg T +QAF canopy air humidity kg/kg F +QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F +QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F +QDRAI sub-surface drainage mm/s T +QDRAI_PERCH perched wt drainage mm/s T +QDRAI_XS saturation excess drainage mm/s T +QDRIP rate of excess canopy liquid falling off canopy mm/s F +QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F +QFLOOD runoff from river flooding mm/s T +QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T +QFLX_EVAP_VEG vegetation evaporation mm H2O/s F +QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T +QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T +QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F +QFLX_SNOW_DRAIN drainage from snow pack mm/s T +QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T +QFLX_SNOW_GRND snow on ground after interception mm H2O/s F +QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F +QH2OSFC surface water runoff mm/s T +QH2OSFC_TO_ICE surface water converted to ice mm/s F +QHR hydraulic redistribution mm/s T +QICE ice growth/melt mm/s T +QICE_FORC qice forcing sent to GLC mm/s F +QICE_FRZ ice growth mm/s T +QICE_MELT ice melt mm/s T +QINFL infiltration mm/s T +QINTR interception mm/s T +QIRRIG_DEMAND irrigation demand mm/s F +QIRRIG_DRIP water added via drip irrigation mm/s F +QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T +QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T +QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T +QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F +QOVER total surface runoff (includes QH2OSFC) mm/s T +QOVER_LAG time-lagged surface runoff for soil columns mm/s F +QPHSNEG net negative hydraulic redistribution flux mm/s F +QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T +QROOTSINK water flux from soil to root in each soil-layer mm/s F +QRUNOFF total liquid runoff not including correction for land use change mm/s T +QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T +QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F +QRUNOFF_R Rural total runoff mm/s F +QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_U Urban total runoff mm/s F +QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T +QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T +QSNOFRZ column-integrated snow freezing rate kg/m2/s T +QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T +QSNOMELT snow melt rate mm/s T +QSNOMELT_ICE snow melt (ice landunits only) mm/s T +QSNOUNLOAD canopy snow unloading mm/s T +QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T +QSNO_WINDUNLOAD canopy snow wind unloading mm/s T +QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T +QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T +QSOIL_ICE Ground evaporation (ice landunits only) mm/s T +QTOPSOIL water input to surface mm/s F +QVEGE canopy evaporation mm/s T +QVEGT canopy transpiration mm/s T +Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F +Qh sensible heat W/m^2 F +Qle total evaporation W/m^2 F +Qstor storage heat flux (includes snowmelt) W/m^2 F +Qtau momentum flux kg/m/s^2 F +RAH1 aerodynamical resistance s/m F +RAH2 aerodynamical resistance s/m F +RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T +RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T +RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +RAM1 aerodynamical resistance s/m F +RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F +RAW1 aerodynamical resistance s/m F +RAW2 aerodynamical resistance s/m F +RB leaf boundary resistance s/m F +RB10 10 day running mean boundary layer resistance s/m F +RETRANSN plant pool of retranslocated N gN/m^2 T +RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T +RH atmospheric relative humidity % F +RH2M 2m relative humidity % T +RH2M_R Rural 2m specific humidity % F +RH2M_U Urban 2m relative humidity % F +RH30 30-day running mean of relative humidity % F +RHAF fractional humidity of canopy air fraction F +RHAF10 10 day running mean of fractional humidity of canopy air fraction F +RH_LEAF fractional humidity at leaf surface fraction F +ROOTR effective fraction of roots in each soil layer (SMS method) proportion F +RR root respiration (fine root MR + total root GR) gC/m^2/s T +RRESIS root resistance in each soil layer proportion F +RSSHA shaded leaf stomatal resistance s/m T +RSSUN sunlit leaf stomatal resistance s/m T +Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rnet net radiation W/m^2 F +SABG solar rad absorbed by ground W/m^2 T +SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T +SABV solar rad absorbed by veg W/m^2 T +SDATES Crop sowing dates in each calendar year day of year (julian day) F +SDATES_PERHARV For each harvest in a calendar year, the Julian day the crop was sown day of year (julian day) F +SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T +SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T +SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T +SLO_SOMC SLO_SOM C gC/m^2 T +SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F +SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T +SLO_SOMN SLO_SOM N gN/m^2 T +SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F +SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F +SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T +SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F +SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F +SMINN soil mineral N gN/m^2 T +SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T +SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T +SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T +SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F +SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +SMINN_vr soil mineral N gN/m^3 T +SMIN_NH4 soil mineral NH4 gN/m^2 T +SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F +SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3 soil mineral NO3 gN/m^2 T +SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T +SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T +SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F +SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T +SMP soil matric potential (natural vegetated and crop landunits only) mm T +SNOBCMCL mass of BC in snow column kg/m2 T +SNOBCMSL mass of BC in top snow layer kg/m2 T +SNOCAN intercepted snow mm T +SNODSTMCL mass of dust in snow column kg/m2 T +SNODSTMSL mass of dust in top snow layer kg/m2 T +SNOFSDSND direct nir incident solar radiation on snow W/m^2 F +SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F +SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F +SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F +SNOFSRND direct nir reflected solar radiation from snow W/m^2 T +SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T +SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T +SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T +SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T +SNOLIQFL top snow layer liquid water fraction (land) fraction F +SNOOCMCL mass of OC in snow column kg/m2 T +SNOOCMSL mass of OC in top snow layer kg/m2 T +SNORDSL top snow layer effective grain radius m^-6 F +SNOTTOPL snow temperature (top layer) K F +SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F +SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +SNOWDP gridcell mean snow height m T +SNOWICE snow ice kg/m2 T +SNOWICE_ICE snow ice (ice landunits only) kg/m2 F +SNOWLIQ snow liquid water kg/m2 T +SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F +SNOW_5D 5day snow avg m F +SNOW_DEPTH snow height of snow covered area m T +SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F +SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T +SNOW_SINKS snow sinks (liquid water) mm/s T +SNOW_SOURCES snow sources (liquid water) mm/s T +SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS Mean snow grain size Microns F +SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F +SNO_ICE Snow ice content kg/m2 F +SNO_LIQH2O Snow liquid water content kg/m2 F +SNO_MELT snow melt rate in each snow layer mm/s F +SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T Snow temperatures K F +SNO_TK Thermal conductivity W/m-K F +SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE Snow temperatures (ice landunits only) K F +SNO_Z Snow layer thicknesses m F +SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F +SNOdTdzL top snow layer temperature gradient (land) K/m F +SOIL10 10-day running mean of 12cm layer soil K F +SOILC_CHANGE C change in soil gC/m^2/s T +SOILC_HR soil C heterotrophic respiration gC/m^2/s T +SOILC_vr SOIL C (vertically resolved) gC/m^3 T +SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOILN_vr SOIL N (vertically resolved) gN/m^3 T +SOILPSI soil water potential in each soil layer MPa F +SOILRESIS soil resistance to evaporation s/m T +SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +SOMC_FIRE C loss due to peat burning gC/m^2/s T +SOMFIRE soil organic matter fire losses gC/m^2/s F +SOM_ADV_COEF advection term for vertical SOM translocation m/s F +SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T +SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F +SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F +SOWING_REASON For each sowing in a calendar year, the reason the crop was sown categorical F +SOWING_REASON_PERHARV For each harvest in a calendar year, the reason the crop was sown categorical F +SR total soil respiration (HR + root resp) gC/m^2/s T +SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T +SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T +SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T +SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T +SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T +SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T +SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T +STEM_PROF profile for litter C and N inputs from stems 1/m F +STORAGE_CDEMAND C use from the C storage pool gC/m^2 F +STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F +STORAGE_NDEMAND N demand during the offset period gN/m^2 F +STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T +STORVEGN stored vegetation nitrogen gN/m^2 T +SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T +SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F +SYEARS_PERHARV For each harvest in a calendar year, the year the crop was sown year F +SWBGT 2 m Simplified Wetbulb Globe Temp C T +SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T +SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T +SWMP65 2 m Swamp Cooler Temp 65% Eff C T +SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T +SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T +SWMP80 2 m Swamp Cooler Temp 80% Eff C T +SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T +SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T +SWdown atmospheric incident solar radiation W/m^2 F +SWup upwelling shortwave radiation W/m^2 F +SoilAlpha factor limiting ground evap unitless F +SoilAlpha_U urban factor limiting ground evap unitless F +T10 10-day running mean of 2-m temperature K F +TAF canopy air temperature K F +TAUX zonal surface stress kg/m/s^2 T +TAUY meridional surface stress kg/m/s^2 T +TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T +TBUILD internal urban building air temperature K T +TBUILD_MAX prescribed maximum interior building temperature K F +TEMPAVG_T2M temporary average 2m air temperature K F +TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F +TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F +TEQ 2 m Equiv Temp K T +TEQ_R Rural 2 m Equiv Temp K T +TEQ_U Urban 2 m Equiv Temp K T +TFLOOR floor temperature K F +TG ground temperature K T +TG_ICE ground temperature (ice landunits only) K F +TG_R Rural ground temperature K F +TG_U Urban ground temperature K F +TH2OSFC surface water temperature K T +THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T +THIC 2 m Temp Hum Index Comfort C T +THIC_R Rural 2 m Temp Hum Index Comfort C T +THIC_U Urban 2 m Temp Hum Index Comfort C T +THIP 2 m Temp Hum Index Physiology C T +THIP_R Rural 2 m Temp Hum Index Physiology C T +THIP_U Urban 2 m Temp Hum Index Physiology C T +TKE1 top lake level eddy thermal conductivity W/(mK) T +TLAI total projected leaf area index m^2/m^2 T +TLAKE lake temperature K T +TOPO_COL column-level topographic height m F +TOPO_COL_ICE column-level topographic height (ice landunits only) m F +TOPO_FORC topograephic height sent to GLC m F +TOPT topt coefficient for VOC calc non F +TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T +TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +TOTCOLN total column-level N, excluding product pools gN/m^2 T +TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T +TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T +TOTFIRE total ecosystem fire losses gC/m^2/s F +TOTLITC total litter carbon gC/m^2 T +TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T +TOTLITN total litter N gN/m^2 T +TOTLITN_1m total litter N to 1 meter gN/m^2 T +TOTPFTC total patch-level carbon, including cpool gC/m^2 T +TOTPFTN total patch-level nitrogen gN/m^2 T +TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T +TOTSOMC total soil organic matter carbon gC/m^2 T +TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T +TOTSOMN total soil organic matter N gN/m^2 T +TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T +TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T +TOTVEGN total vegetation nitrogen gN/m^2 T +TOT_WOODPRODC total wood product C gC/m^2 T +TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T +TOT_WOODPRODN total wood product N gN/m^2 T +TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T +TPU25T canopy profile of tpu umol/m2/s T +TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F +TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F +TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F +TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F +TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F +TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F +TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F +TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F +TREFMNAV daily minimum of average 2-m temperature K T +TREFMNAV_R Rural daily minimum of average 2-m temperature K F +TREFMNAV_U Urban daily minimum of average 2-m temperature K F +TREFMXAV daily maximum of average 2-m temperature K T +TREFMXAV_R Rural daily maximum of average 2-m temperature K F +TREFMXAV_U Urban daily maximum of average 2-m temperature K F +TROOF_INNER roof inside surface temperature K F +TSA 2m air temperature K T +TSAI total projected stem area index m^2/m^2 T +TSA_ICE 2m air temperature (ice landunits only) K F +TSA_R Rural 2m air temperature K F +TSA_U Urban 2m air temperature K F +TSHDW_INNER shadewall inside surface temperature K F +TSKIN skin temperature K T +TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +TSOI soil temperature (natural vegetated and crop landunits only) K T +TSOI_10CM soil temperature in top 10cm of soil K T +TSOI_ICE soil temperature (ice landunits only) K T +TSRF_FORC surface temperature sent to GLC K F +TSUNW_INNER sunwall inside surface temperature K F +TV vegetation temperature K T +TV24 vegetation temperature (last 24hrs) K F +TV240 vegetation temperature (last 240hrs) K F +TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F +TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F +TWS total water storage mm T +T_SCALAR temperature inhibition of decomposition unitless T +Tair atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F +U10 10-m wind m/s T +U10_DUST 10-m wind for dust model m/s T +U10_ICE 10-m wind (ice landunits only) m/s F +UAF canopy air speed m/s F +ULRAD upward longwave radiation above the canopy W/m^2 F +UM wind speed plus stability effect m/s F +URBAN_AC urban air conditioning flux W/m^2 T +URBAN_HEAT urban heating flux W/m^2 T +USTAR aerodynamical resistance s/m F +UST_LAKE friction velocity (lakes only) m/s F +VA atmospheric wind speed plus convective velocity m/s F +VCMX25T canopy profile of vcmax25 umol/m2/s T +VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T +VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T +VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T +VOCFLXT total VOC flux into atmosphere moles/m2/sec F +VOLR river channel total water storage m3 T +VOLRMCH river channel main channel water storage m3 T +VPD vpd Pa F +VPD2M 2m vapor pressure deficit Pa T +VPD_CAN canopy vapor pressure deficit kPa T +Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T +WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +WBA 2 m Wet Bulb C T +WBA_R Rural 2 m Wet Bulb C T +WBA_U Urban 2 m Wet Bulb C T +WBT 2 m Stull Wet Bulb C T +WBT_R Rural 2 m Stull Wet Bulb C T +WBT_U Urban 2 m Stull Wet Bulb C T +WF soil water as frac. of whc for top 0.05 m proportion F +WFPS WFPS percent F +WIND atmospheric wind velocity magnitude m/s T +WOODC wood C gC/m^2 T +WOODC_ALLOC wood C eallocation gC/m^2/s T +WOODC_LOSS wood C loss gC/m^2/s T +WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T +WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T +WTGQ surface tracer conductance m/s T +W_SCALAR Moisture (dryness) inhibition of decomposition unitless T +Wind atmospheric wind velocity magnitude m/s F +XSMRPOOL temporary photosynthate C pool gC/m^2 T +XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F +XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T +Z0HG roughness length over ground, sensible heat m F +Z0HV roughness length over vegetation, sensible heat m F +Z0M momentum roughness length m F +Z0MG roughness length over ground, momentum m F +Z0MV roughness length over vegetation, momentum m F +Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F +Z0QG roughness length over ground, latent heat m F +Z0QV roughness length over vegetation, latent heat m F +ZBOT atmospheric reference height m T +ZETA dimensionless stability parameter unitless F +ZII convective boundary height m F +ZWT water table depth (natural vegetated and crop landunits only) m T +ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T +ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T +anaerobic_frac anaerobic_frac m3/m3 F +bsw clap and hornberger B unitless F +currentPatch currentPatch coefficient for VOC calc non F +diffus diffusivity m^2/s F +fr_WFPS fr_WFPS fraction F +n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F +num_iter number of iterations unitless F +r_psi r_psi m F +ratio_k1 ratio_k1 none F +ratio_no3_co2 ratio_no3_co2 ratio F +soil_bulkdensity soil_bulkdensity kg/m3 F +soil_co2_prod soil_co2_prod ug C / g soil / day F +watfc water field capacity m^3/m^3 F +watsat water saturated m^3/m^3 F ==== =================================== ============================================================================================== ================================================================= ======= From 07e1a9a1419a153d7f5a13dae1833da165865392 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 27 Jul 2023 12:01:46 -0600 Subject: [PATCH 1294/2067] Added comments referring to variables in Riley et al. (2011). --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index cd8b62ce75..26aae073c3 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -266,8 +266,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & !---------------- calculate soil anoxia state ! calculate gas diffusivity of soil at field capacity here ! use expression from methane code, but neglect OM for now - f_a = 1._r8 - watfc(c,j) / watsat(c,j) - eps = watsat(c,j)-watfc(c,j) ! Air-filled fraction of total soil volume + f_a = 1._r8 - watfc(c,j) / watsat(c,j) ! f_a is theta_a/theta_s in Riley et al. (2011) + eps = watsat(c,j)-watfc(c,j) ! Air-filled fraction of total soil volume; theta_a in Riley et al. (2011) ! use diffusivity calculation including peat if (use_lch4) then From 819f985b4fb6e6fe08635ec10e8051ea975ac34d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 3 Aug 2023 14:25:15 -0600 Subject: [PATCH 1295/2067] Typo fix in a comment. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 26aae073c3..9b249a5d0f 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -372,7 +372,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! limit to anoxic fraction of soils pot_f_denit_vr(c,j) = f_denit_base_vr(c,j) * anaerobic_frac(c,j) - ! now calculate the ratio of N2O to N2 from denitrifictaion, following Del Grosso et al., 2000 + ! now calculate the ratio of N2O to N2 from denitrification, following Del Grosso et al., 2000 ! diffusivity constant (figure 6b) ratio_k1(c,j) = max(1.7_r8, 38.4_r8 - 350._r8 * diffus(c,j)) From 5f8d50d3edb649cdd504b0dc45a50d0bd4e53c37 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 3 Aug 2023 16:12:41 -0600 Subject: [PATCH 1296/2067] snicar_snw_shape: replace integers with descriptive options --- bld/CLMBuildNamelist.pm | 10 ++++++++ bld/namelist_files/namelist_defaults_ctsm.xml | 1 + .../namelist_definition_ctsm.xml | 21 ++++++++-------- src/biogeophys/SnowSnicarMod.F90 | 24 +++++++++---------- src/main/clm_varctl.F90 | 4 ++-- src/main/controlMod.F90 | 17 ++++--------- 6 files changed, 40 insertions(+), 37 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 256de592c6..596b97a7e5 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1569,6 +1569,7 @@ sub process_namelist_inline_logic { setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_start_type($opts, $nl_flags, $nl); setup_logic_decomp_performance($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_snicar_methods($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); setup_logic_dynamic_plant_nitrogen_alloc($opts, $nl_flags, $definition, $defaults, $nl, $physv); @@ -1988,6 +1989,14 @@ sub setup_logic_decomp_performance { #------------------------------------------------------------------------------- +sub setup_logic_snicar_methods { + my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snw_shape' ); +} + +#------------------------------------------------------------------------------- + sub setup_logic_snow { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; @@ -4378,6 +4387,7 @@ sub write_output_files { push @groups, "lifire_inparm"; push @groups, "ch4finundated"; push @groups, "soilbgc_decomp"; + push @groups, "snicar_inparm"; push @groups, "clm_canopy_inparm"; if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') { push @groups, "scf_swenson_lawrence_2012_inparm"; diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3cf9a3ebc0..2d57fd9798 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1543,6 +1543,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc +hexagonal_plate 2015 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index a9ec4e5559..6a5d5fccd7 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -151,42 +151,43 @@ of soil column (nlevsoi). + group="snicar_inparm" valid_values="5,480" > number of wavelength bands used in SNICAR snow albedo calculation + group="snicar_inparm" valid_values="1,2,3,4,5,6" > type of downward solar radiation spectrum for SNICAR snow albedo calculation + group="snicar_inparm" valid_values="1,2,3" > dust optics type for SNICAR snow albedo calculation + group="snicar_inparm" valid_values="" value=".true."> Toggle to turn on/off aerosol deposition flux in snow in SNICAR - + snow grain shape used in SNICAR snow albedo calculation +Default: "hexagonal_plate" + group="snicar_inparm" valid_values="" value=".true." > option to activate BC-snow internal mixing in SNICAR snow albedo calculation + group="snicar_inparm" valid_values="" value=".true." > option to activate dust-snow internal mixing in SNICAR snow albedo calculation + group="snicar_inparm" valid_values="" value=".false." > option to activate organic carbon (OC) in SNICAR snow albedo calculation @@ -1197,7 +1198,7 @@ DependsOnLatAndVeg - Arctic vegetation depends on latitude as above, but tempera + group="snicar_inparm" valid_values="" value=".false."> Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) radiative forcing (snicar_frc=".true." is EXPERIMENTAL NOT SUPPORTED!) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 3264086ebe..1a107bef6b 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -447,14 +447,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & !----------------------------------------------------------------------- ! variables used for nonspherical snow grain treatment (He et al. 2017 J of Climate): - integer :: sno_shp(-nlevsno+1:0) ! Snow shape type: 1=sphere; 2=spheroid; 3=hexagonal plate; 4=koch snowflake + character(len=15) :: sno_shp(-nlevsno+1:0) ! Snow shape type: sphere, spheroid, hexagonal plate, koch snowflake ! currently only assuming same shapes for all snow layers real(r8) :: sno_fs(-nlevsno+1:0) ! Snow shape factor: ratio of nonspherical grain effective radii to that of equal-volume sphere - ! only activated when snicar_snw_shape > 1 (i.e. nonspherical) + ! only activated when snicar_snw_shape is nonspherical ! 0=use recommended default value (He et al. 2017); ! others(0 1 (i.e. nonspherical) + ! only activated when snicar_snw_shape is nonspherical ! 0=use recommended default value (He et al. 2017); ! others(0.1 1) then + if (sno_shp(i) /= 'sphere') then ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here ! use the piecewise linear interpolation subroutine created at the end of this module ! tests showed the piecewise linear interpolation has similar results as pchip interpolation diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 7cf5a59560..670b9ab54f 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -245,8 +245,8 @@ module clm_varctl ! option to turn off aerosol effect in snow in SNICAR logical, public :: snicar_use_aerosol = .true. ! if .false., turn off aerosol deposition flux - ! option for snow grain shape in SNICAR (He et al. 2017 JC), ceniln - integer, public :: snicar_snw_shape = 3 ! 1->sphere; 2->spheroid; 3->hexagonal plate; 4->Koch snowflake + ! option for snow grain shape in SNICAR (He et al. 2017 JC) + character(len=15), public :: snicar_snw_shape = 'hexagonal_plate' ! sphere, spheroid, hexagonal_plate, koch_snowflake ! option to activate BC-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln logical, public :: snicar_snobc_intmix = .false. ! false->external mixing for all BC; true->internal mixing for hydrophilic BC diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 817a2b6d7a..b22965aff1 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -235,8 +235,8 @@ subroutine control_init(dtime) fates_parteh_mode, & use_fates_tree_damage - ! Ozone vegetation stress method - namelist / clm_inparam / o3_veg_stress_method + ! Ozone vegetation stress method + namelist / clm_inparm / o3_veg_stress_method ! CLM 5.0 nitrogen flags namelist /clm_inparm/ use_flexibleCN, use_luna @@ -281,7 +281,7 @@ subroutine control_init(dtime) namelist /clm_inparm/ & use_lch4, use_nitrif_denitrif, use_extralakelayers, & - use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, o3_veg_stress_method, & + use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, & use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, & use_nguardrail @@ -590,12 +590,6 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if - ! check on SNICAR snow grain shape option - if ( (snicar_snw_shape < 1) .or. (snicar_snw_shape > 4) ) then - call endrun(msg=' ERROR: snicar_snw_shape is out of a reasonable range (1,2,3,4)'//& - errMsg(sourcefile, __LINE__)) - end if - ! check on SNICAR BC-snow and dust-snow internal mixing if ( snicar_snobc_intmix .and. snicar_snodst_intmix ) then call endrun(msg=' ERROR: currently dust-snow and BC-snow internal mixing cannot be activated together'//& @@ -827,7 +821,7 @@ subroutine control_spmd() call mpi_bcast (snicar_solarspec, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (snicar_snw_shape, 1, MPI_INTEGER, 0, mpicom, ier) + call mpi_bcast (snicar_snw_shape, len(snicar_snw_shape), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_snodst_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (DO_SNO_OC, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -1013,7 +1007,7 @@ subroutine control_print () write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw - write(iulog,*) ' SNICAR: snow grain shape type = ',snicar_snw_shape + write(iulog,*) ' SNICAR: snow grain shape type = ', snicar_snw_shape write(iulog,*) ' SNICAR: BC-snow internal mixing = ', snicar_snobc_intmix write(iulog,*) ' SNICAR: dust-snow internal mixing = ', snicar_snodst_intmix write(iulog,*) ' SNICAR: OC in snow = ', DO_SNO_OC @@ -1097,7 +1091,6 @@ subroutine control_print () write(iulog, *) ' carbon_resp_opt = ', carbon_resp_opt end if write(iulog, *) ' use_luna = ', use_luna - write(iulog, *) ' ozone vegetation stress method = ', o3_veg_stress_method write(iulog, *) ' ED/FATES: ' write(iulog, *) ' use_fates = ', use_fates From 3164bc61d629942859082d6434f88c88a20a4baa Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 3 Aug 2023 16:14:18 -0600 Subject: [PATCH 1297/2067] snicar_solarspec & snicar_dust_optics: replace integers with descriptive options --- bld/CLMBuildNamelist.pm | 2 + bld/namelist_files/namelist_defaults_ctsm.xml | 2 + .../namelist_definition_ctsm.xml | 22 +++-- src/biogeophys/SnowSnicarMod.F90 | 97 ++++++++++--------- src/main/clm_varctl.F90 | 22 +++-- src/main/controlMod.F90 | 18 +--- 6 files changed, 85 insertions(+), 78 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 596b97a7e5..b5aacb96e1 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1993,6 +1993,8 @@ sub setup_logic_snicar_methods { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snw_shape' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_solarspec' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_dust_optics' ); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2d57fd9798..1fddc07869 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1544,6 +1544,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc hexagonal_plate +mid_latitude_summer +sahara 2015 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 6a5d5fccd7..5b864c0c07 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -155,27 +155,29 @@ of soil column (nlevsoi). number of wavelength bands used in SNICAR snow albedo calculation - + type of downward solar radiation spectrum for SNICAR snow albedo calculation +Default: "mid_latitude_winter" - + dust optics type for SNICAR snow albedo calculation +Default: "sahara" - -Toggle to turn on/off aerosol deposition flux in snow in SNICAR - - - snow grain shape used in SNICAR snow albedo calculation Default: "hexagonal_plate" + +Toggle to turn on/off aerosol deposition flux in snow in SNICAR + + option to activate BC-snow internal mixing in SNICAR snow albedo calculation diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 1a107bef6b..4ba8ec56cb 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1885,8 +1885,8 @@ end function FreshSnowRadius subroutine SnowOptics_init( ) use fileutils , only : getfil - use CLM_varctl , only : fsnowoptics,snicar_numrad_snw,fsnowoptics480,snicar_solarspec,& - snicar_dust_optics ! cenlin + use CLM_varctl , only : fsnowoptics, snicar_numrad_snw, fsnowoptics480 + use CLM_varctl , only : snicar_solarspec, snicar_dust_optics use spmdMod , only : masterproc use ncdio_pio , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile @@ -1939,8 +1939,9 @@ subroutine SnowOptics_init( ) call ncd_pio_openfile(ncid, locfn, 0) if(masterproc) write(iulog,*) subname,trim(fsnowoptics) + select case (snicar_solarspec) ! mid-latitude winter spectrum - if (snicar_solarspec == 1) then + case ('mid_latitude_winter') ! flux weights/spectrum call ncd_io( 'flx_wgt_dir5_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) @@ -1968,7 +1969,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -1985,7 +1987,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2002,7 +2004,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2019,10 +2021,10 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + end select ! mid-latitude summer spectrum - elseif (snicar_solarspec == 2) then + case ('mid_latitude_summer') ! flux weights/spectrum call ncd_io( 'flx_wgt_dir5_mls', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_mls', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) @@ -2050,7 +2052,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2067,7 +2070,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2084,7 +2087,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2101,10 +2104,10 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + end select ! sub-Arctic winter spectrum - elseif (snicar_solarspec == 3) then + case ('sub_arctic_winter') call ncd_io( 'flx_wgt_dir5_saw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_saw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing @@ -2131,7 +2134,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2148,7 +2152,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2165,7 +2169,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2182,10 +2186,10 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + end select ! sub-Arctic summer spectrum - elseif (snicar_solarspec == 4) then + case ('sub_arctic_summer') call ncd_io( 'flx_wgt_dir5_sas', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_sas', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing @@ -2212,7 +2216,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2229,7 +2234,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2246,7 +2251,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2263,10 +2268,10 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + end select ! Summit,Greenland,summer spectrum - elseif (snicar_solarspec == 5) then + case ('summit_greenland_summer') call ncd_io( 'flx_wgt_dir5_smm', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_smm', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing @@ -2293,7 +2298,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2310,7 +2316,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2327,7 +2333,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2344,10 +2350,10 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + end select ! High Mountain summer spectrum - elseif (snicar_solarspec == 6) then + case ('high_mountain_summer') call ncd_io( 'flx_wgt_dir5_hmn', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing @@ -2374,7 +2380,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2391,7 +2398,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2408,7 +2415,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2425,8 +2432,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif - endif ! end of snicar_solarspec + end select + end select end if ! end if snicar_numrad_snw == 5 @@ -2465,7 +2472,8 @@ subroutine SnowOptics_init( ) call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) ! dust optical properties - if (snicar_dust_optics == 1) then ! Saharan dust (Balkanski et al., 2007, central hematite) + select case (snicar_dust_optics) + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2482,7 +2490,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 2) then ! San Juan Mountains, CO (Skiles et al, 2017) + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_col', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_col', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2499,7 +2507,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_col', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_col', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_col', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_dust_optics == 3) then ! Greenland (Polashenski et al., 2015, central absorptivity) + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters call ncd_io( 'ss_alb_dust01_gre', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust01_gre', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) @@ -2516,28 +2524,29 @@ subroutine SnowOptics_init( ) call ncd_io( 'ss_alb_dust04_gre', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_dust04_gre', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'ext_cff_mss_dust04_gre', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) - endif + end select ! downward solar radiation spectral weights for 480-band - if (snicar_solarspec == 1) then ! mid-latitude winter + select case (snicar_solarspec) + case ('mid_latitude_winter') call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_solarspec == 2) then ! mid-latitude summer + case ('mid_latitude_summer') call ncd_io( 'flx_wgt_dir480_mls', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif480_mls', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_solarspec == 3) then ! sub-Arctic winter + case ('sub_arctic_winter') call ncd_io( 'flx_wgt_dir480_saw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif480_saw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_solarspec == 4) then ! sub-Arctic summer + case ('sub_arctic_summer') call ncd_io( 'flx_wgt_dir480_sas', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif480_sas', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_solarspec == 5) then ! Summit,Greenland,summer + case ('summit_greenland_summer') call ncd_io( 'flx_wgt_dir480_smm', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif480_smm', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) - elseif (snicar_solarspec == 6) then ! High Mountain summer + case ('high_mountain_summer') call ncd_io( 'flx_wgt_dir480_hmn', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif480_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) - endif + end select endif ! end if snicar_numrad_snw == 480 diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 670b9ab54f..a0d5a9a122 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -234,19 +234,23 @@ module clm_varctl ! number of wavelength bands used in SNICAR snow albedo calculation, cenlin integer, public :: snicar_numrad_snw = 5 - ! type of downward solar radiation spectrum for SNICAR snow albedo calculation cenlin - integer, public :: snicar_solarspec = 1 ! 1->mid-latitude winter;2->mid-latitude summer;3->sub-Arctic winter; - ! 4->sub-Arctic summer;5->Summit,Greenland,summer;6->High Mountain summer; - - ! dust optics type for SNICAR snow albedo calculation, cenlin - integer, public :: snicar_dust_optics = 1 ! 1->Saharan dust (Balkanski et al., 2007, central hematite) - ! 2->San Juan Mountains dust, CO (Skiles et al, 2017) - ! 3->Greenland dust (Polashenski et al., 2015, central absorptivity) + ! type of downward solar radiation spectrum for SNICAR snow albedo calculation + ! options: + ! mid_latitude_winter, mid_latitude_summer, sub_arctic_winter, + ! sub_arctic_summer, summit_greenland_summer, high_mountain_summer; + character(len=25), public :: snicar_solarspec = 'mid_latitude_winter' + + ! dust optics type for SNICAR snow albedo calculation + ! options: + ! sahara: Saharan dust (Balkanski et al., 2007, central hematite) + ! san_juan_mtns_colorado: San Juan Mountains dust, CO (Skiles et al, 2017) + ! greenland: Greenland dust (Polashenski et al., 2015, central absorptivity) + character(len=25), public :: snicar_dust_optics = 'sahara' ! option to turn off aerosol effect in snow in SNICAR logical, public :: snicar_use_aerosol = .true. ! if .false., turn off aerosol deposition flux ! option for snow grain shape in SNICAR (He et al. 2017 JC) - character(len=15), public :: snicar_snw_shape = 'hexagonal_plate' ! sphere, spheroid, hexagonal_plate, koch_snowflake + character(len=25), public :: snicar_snw_shape = 'hexagonal_plate' ! sphere, spheroid, hexagonal_plate, koch_snowflake ! option to activate BC-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln logical, public :: snicar_snobc_intmix = .false. ! false->external mixing for all BC; true->internal mixing for hydrophilic BC diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index b22965aff1..11bb49b902 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -578,18 +578,6 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if - ! check on downward solar radiation spectrum - if ( (snicar_solarspec < 1) .or. (snicar_solarspec > 6) ) then - call endrun(msg=' ERROR: snicar_solarspec is out of a reasonable range (1,2,3,4,5,6)'//& - errMsg(sourcefile, __LINE__)) - end if - - ! check on dust optics type - if ( (snicar_dust_optics < 1) .or. (snicar_dust_optics > 3) ) then - call endrun(msg=' ERROR: snicar_dust_optics is out of a reasonable range (1,2,3)'//& - errMsg(sourcefile, __LINE__)) - end if - ! check on SNICAR BC-snow and dust-snow internal mixing if ( snicar_snobc_intmix .and. snicar_snodst_intmix ) then call endrun(msg=' ERROR: currently dust-snow and BC-snow internal mixing cannot be activated together'//& @@ -818,10 +806,10 @@ subroutine control_spmd() call mpi_bcast (soil_layerstruct_userdefined,size(soil_layerstruct_userdefined), MPI_REAL8, 0, mpicom, ier) call mpi_bcast (soil_layerstruct_userdefined_nlevsoi, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (snicar_numrad_snw, 1, MPI_INTEGER, 0, mpicom, ier) - call mpi_bcast (snicar_solarspec, 1, MPI_INTEGER, 0, mpicom, ier) - call mpi_bcast (snicar_dust_optics, 1, MPI_INTEGER, 0, mpicom, ier) - call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (snicar_solarspec, len(snicar_solarspec), MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (snicar_dust_optics, len(snicar_dust_optics), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (snicar_snw_shape, len(snicar_snw_shape), MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_snodst_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (DO_SNO_OC, 1, MPI_LOGICAL, 0, mpicom, ier) From 34900bcc237f09be7f8f491f5361aac193911ea9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 3 Aug 2023 17:21:11 -0600 Subject: [PATCH 1298/2067] Corrected new tag number in ChangeLog/Sum --- doc/ChangeLog | 4 ++-- doc/ChangeSum | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index ed78cea5eb..fb58cbfb90 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== -Tag name: ctsm5.1.dev133 +Tag name: ctsm5.1.dev132 Originator(s): mvdebolskiy (NORCE, Bergen, Norway), slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Thu Jul 27 17:30:25 MDT 2023 +Date: Thu Aug 3 17:03:44 MDT 2023 One-line Summary: Add parameterization to allow excess ice in soil and subsidence Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index a1a326e65a..9cfa433000 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev133 slevis 07/27/2023 Add parameterization to allow excess ice in soil and subsidence + ctsm5.1.dev132 slevis 08/03/2023 Add parameterization to allow excess ice in soil and subsidence ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml From 230e3fce9837b61fc0e3e72e6c8ae63f60285d6f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 3 Aug 2023 17:32:17 -0600 Subject: [PATCH 1299/2067] General clean-up of other snicar switches and comments --- bld/CLMBuildNamelist.pm | 5 +++ .../namelist_definition_ctsm.xml | 20 ++++++---- src/biogeophys/AerosolMod.F90 | 2 +- src/biogeophys/SnowSnicarMod.F90 | 39 ++++++++----------- src/biogeophys/SurfaceAlbedoMod.F90 | 31 +++++++-------- src/biogeophys/SurfaceAlbedoType.F90 | 18 ++++----- src/biogeophys/SurfaceRadiationMod.F90 | 5 +-- src/biogeophys/UrbanAlbedoMod.F90 | 22 +++++------ src/main/clm_varctl.F90 | 8 ++-- src/main/controlMod.F90 | 6 +-- 10 files changed, 79 insertions(+), 77 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b5aacb96e1..017f13ecef 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1995,6 +1995,11 @@ sub setup_logic_snicar_methods { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snw_shape' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_solarspec' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_dust_optics' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_numrad_snw' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snobc_intmix' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snodst_intmix' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_use_aerosol' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' ); } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 5b864c0c07..5bcb1fe2c3 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -151,8 +151,9 @@ of soil column (nlevsoi). + group="snicar_inparm" valid_values="5,480" value="5" > number of wavelength bands used in SNICAR snow albedo calculation +Default: 5 + group="snicar_inparm" value=".true."> Toggle to turn on/off aerosol deposition flux in snow in SNICAR +Default: .true. + group="snicar_inparm" value=".true." > option to activate BC-snow internal mixing in SNICAR snow albedo calculation +Default: .true. + group="snicar_inparm" value=".true." > option to activate dust-snow internal mixing in SNICAR snow albedo calculation +Default: .true. - + option to activate organic carbon (OC) in SNICAR snow albedo calculation +Default: .false. + group="snicar_inparm" value=".false."> Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) radiative forcing (snicar_frc=".true." is EXPERIMENTAL NOT SUPPORTED!) +Default: .false. shr_log_errMsg use clm_varctl , only : iulog, snicar_numrad_snw, & snicar_snw_shape, snicar_snobc_intmix, & - snicar_snodst_intmix, DO_SNO_OC ! cenlin + snicar_snodst_intmix, do_sno_oc use clm_varcon , only : tfrz use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun @@ -48,16 +48,9 @@ module SnowSnicarMod ! !PUBLIC DATA MEMBERS: integer, public, parameter :: sno_nbr_aer = 8 ! number of aerosol species in snowpack ! (indices described above) [nbr] - ! DO_SNO_OC moved to namelist control - !logical, public, parameter :: DO_SNO_OC = .false. ! parameter to include organic carbon (OC) - ! ! in snowpack radiative calculations logical, public, parameter :: DO_SNO_AER = .true. ! parameter to include aerosols in snowpack radiative calculations ! !PRIVATE DATA MEMBERS: -! integer, parameter :: numrad_snw = 5 ! number of spectral bands used in snow model [nbr] cenlin -! integer, parameter :: nir_bnd_bgn = 2 ! first band index in near-IR spectrum [idx] cenlin -! integer, parameter :: nir_bnd_end = 5 ! ending near-IR band index [idx] cenlin - integer, parameter :: idx_Mie_snw_mx = 1471 ! number of effective radius indices used in Mie lookup table [idx] integer, parameter :: idx_T_max = 11 ! maxiumum temperature index used in aging lookup table [idx] integer, parameter :: idx_T_min = 1 ! minimum temperature index used in aging lookup table [idx] @@ -250,8 +243,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! !LOCAL VARIABLES: ! ! variables for snow radiative transfer calculations - integer :: nir_bnd_bgn ! first band index in near-IR spectrum [idx] cenlin - integer :: nir_bnd_end ! ending near-IR band index [idx] cenlin + integer :: nir_bnd_bgn ! first band index in near-IR spectrum [idx] + integer :: nir_bnd_end ! ending near-IR band index [idx] ! Local variables representing single-column values of arrays: integer :: snl_lcl ! negative number of snow layers [nbr] @@ -542,7 +535,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & frac_sno => waterdiagnosticbulk_inst%frac_sno_eff_col & ! Input: [real(r8) (:)] fraction of ground covered by snow (0 to 1) ) - ! initialize parameter, cenlin + ! initialize parameter if (snicar_numrad_snw == 5) nir_bnd_bgn = 2 if (snicar_numrad_snw == 480) nir_bnd_bgn = 51 nir_bnd_end = snicar_numrad_snw @@ -705,7 +698,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Set spectral underlying surface albedos to their corresponding VIS or NIR albedos - albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) ! cenlin + albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) albsfc_lcl(nir_bnd_bgn:nir_bnd_end) = albsfc(c_idx,2) @@ -734,7 +727,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Band 4: 1.2-1.5um (NIR) ! Band 5: 1.5-5.0um (NIR) ! - ! Hyperspectral (10-nm) bands (480-band case) cenlin + ! Hyperspectral (10-nm) bands (480-band case) ! Bands 1~50 : 0.2-0.7um (VIS) ! Bands 51~480: 0.7~5.0um (NIR) ! @@ -770,7 +763,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! flx_wgt(4) = 0.10917889346386_r8 ! flx_wgt(5) = 0.10343699264369_r8 ! endif - else ! works for both 5-band & 480-band, flux weights directly read from input data, cenlin + else ! works for both 5-band & 480-band, flux weights directly read from input data ! Direct: if (flg_slr_in == 1) then flx_wgt(1:snicar_numrad_snw) = flx_wgt_dir(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data @@ -816,7 +809,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & mss_cnc_aer_lcl(:,:) = 0._r8 endif - if ( (snicar_numrad_snw == 480).and.(bnd_idx > 100) ) then ! >1.2um cenlin + if ( (snicar_numrad_snw == 480).and.(bnd_idx > 100) ) then ! >1.2um mss_cnc_aer_lcl(:,:) = 0._r8 endif @@ -1450,7 +1443,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR albedo appropriately - ! for 5- and 3-band cases cenlin + ! for 5- and 3-band cases if (snicar_numrad_snw <= 5) then albout(c_idx,1) = albout_lcl(1) flx_sum = 0._r8 @@ -1460,7 +1453,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end if - ! for 480-band case, cenlin + ! for 480-band case if (snicar_numrad_snw == 480) then ! average for VIS band flx_sum = 0._r8 @@ -1477,7 +1470,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end if ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately - ! for 5- and 3-band cases cenlin + ! for 5- and 3-band cases if (snicar_numrad_snw <= 5) then flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) do i=snl_top,1,1 @@ -1489,7 +1482,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end do end if - ! for 480-band case cenlin + ! for 480-band case if (snicar_numrad_snw == 480) then do i=snl_top,1,1 ! average for VIS band @@ -1932,7 +1925,7 @@ subroutine SnowOptics_init( ) if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....' - !--------------------- for 5-band data, cenlin + !--------------------- for 5-band data if (snicar_numrad_snw == 5) then call getfil (fsnowoptics, locfn, 0) @@ -2438,7 +2431,7 @@ subroutine SnowOptics_init( ) end if ! end if snicar_numrad_snw == 5 - !-------------------- for 480-band data, cenlin + !-------------------- for 480-band data if (snicar_numrad_snw == 480) then call getfil (fsnowoptics480, locfn, 0) @@ -2561,7 +2554,7 @@ subroutine SnowOptics_init( ) write (iulog,*) 'SNICAR: Mie single scatter albedos for diffuse ice, rds=100um: ', & ss_alb_snw_dfs(71,1), ss_alb_snw_dfs(71,2), ss_alb_snw_dfs(71,3), & ss_alb_snw_dfs(71,4), ss_alb_snw_dfs(71,5) - if (DO_SNO_OC) then + if (do_sno_oc) then write (iulog,*) 'SNICAR: Including OC aerosols from snow radiative transfer calculations' else write (iulog,*) 'SNICAR: Excluding OC aerosols from snow radiative transfer calculations' @@ -2570,7 +2563,7 @@ subroutine SnowOptics_init( ) ss_alb_bc1(1), ss_alb_bc1(2), ss_alb_bc1(3), ss_alb_bc1(4), ss_alb_bc1(5) write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophobic BC: ', & ss_alb_bc2(1), ss_alb_bc2(2), ss_alb_bc2(3), ss_alb_bc2(4), ss_alb_bc2(5) - if (DO_SNO_OC) then + if (do_sno_oc) then write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophillic OC: ', & ss_alb_oc1(1), ss_alb_oc1(2), ss_alb_oc1(3), ss_alb_oc1(4), ss_alb_oc1(5) write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophobic OC: ', & diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index d7c3305710..5d12767121 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -12,9 +12,9 @@ module SurfaceAlbedoMod use decompMod , only : bounds_type, subgrid_level_patch use abortutils , only : endrun use landunit_varcon , only : istsoil, istcrop, istdlak - use clm_varcon , only : grlnd, spval ! cenlin + use clm_varcon , only : grlnd, spval use clm_varpar , only : numrad, nlevcan, nlevsno, nlevcan - use clm_varctl , only : fsurdat, iulog, use_snicar_frc, use_SSRE, DO_SNO_OC !cenlin + use clm_varctl , only : fsurdat, iulog, use_snicar_frc, use_SSRE, do_sno_oc use pftconMod , only : pftcon use SnowSnicarMod , only : sno_nbr_aer, SNICAR_RT, DO_SNO_AER use AerosolMod , only : aerosol_type @@ -387,7 +387,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albsni_hst => surfalb_inst%albsni_hst_col , & ! Output: [real(r8) (:,:) ] snow ground albedo, diffuse, for history files (col,bnd) [frc] albd => surfalb_inst%albd_patch , & ! Output: [real(r8) (:,:) ] surface albedo (direct) albi => surfalb_inst%albi_patch , & ! Output: [real(r8) (:,:) ] surface albedo (diffuse) -! cenlin: add new output albedo variables for history fields +! add new snicar output albedo variables for history fields albgrd_hst => surfalb_inst%albgrd_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (direct) for history files albgri_hst => surfalb_inst%albgri_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (diffuse) for history files albgrd_pur_hst => surfalb_inst%albgrd_pur_hst_col , & ! Output: [real(r8) (:,:) ] pure snow ground albedo (direct) for history files @@ -402,7 +402,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albsni_hst2 => surfalb_inst%albsni_hst2_col , & ! Output: [real(r8) (:,:) ] snow ground albedo, diffuse, for history files (col,bnd) for history files albd_hst => surfalb_inst%albd_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (direct) for history files albi_hst => surfalb_inst%albi_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (diffuse) for history files -! cenlin: end +! end add new snicar albdSF => surfalb_inst%albdSF_patch , & ! Output: [real(r8) (:,:) ] diagnostic snow-free surface albedo (direct) albiSF => surfalb_inst%albiSF_patch , & ! Output: [real(r8) (:,:) ] diagnostic snow-free surface albedo (diffuse) fabd => surfalb_inst%fabd_patch , & ! Output: [real(r8) (:,:) ] flux absorbed by canopy per unit direct flux @@ -456,7 +456,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albgri_oc(c,ib) = 0._r8 albgrd_dst(c,ib) = 0._r8 albgri_dst(c,ib) = 0._r8 -! cenlin: add output variables for history files +! add new snicar output variables for history files albgrd_hst(c,ib) = spval albgri_hst(c,ib) = spval albgrd_pur_hst(c,ib) = spval @@ -469,7 +469,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albgri_dst_hst(c,ib) = spval albsnd_hst2(c,ib) = spval albsni_hst2(c,ib) = spval -! cenlin: end +! end add new snicar do i=-nlevsno+1,1,1 flx_absdv(c,i) = 0._r8 flx_absdn(c,i) = 0._r8 @@ -482,10 +482,10 @@ subroutine SurfaceAlbedo(bounds,nc, & p = filter_nourbanp(fp) albd(p,ib) = 1._r8 albi(p,ib) = 1._r8 -! cenlin: add output variables for history files +! add new snicar output variables for history files albd_hst(p,ib) = spval albi_hst(p,ib) = spval -! cenlin: end +! end add new snicar if (use_SSRE) then albdSF(p,ib) = 1._r8 albiSF(p,ib) = 1._r8 @@ -552,11 +552,11 @@ subroutine SurfaceAlbedo(bounds,nc, & mss_cnc_aer_in_fdb(bounds%begc:bounds%endc,:,1) = mss_cnc_bcphi(bounds%begc:bounds%endc,:) mss_cnc_aer_in_fdb(bounds%begc:bounds%endc,:,2) = mss_cnc_bcpho(bounds%begc:bounds%endc,:) - ! DO_SNO_OC is set in SNICAR_varpar. Default case is to ignore OC concentrations because: + ! do_sno_oc is set in SNICAR_varpar. Default case is to ignore OC concentrations because: ! 1) Knowledge of their optical properties is primitive ! 2) When 'water-soluble' OPAC optical properties are applied to OC in snow, ! it has a negligible darkening effect. - if (DO_SNO_OC) then + if (do_sno_oc) then mss_cnc_aer_in_fdb(bounds%begc:bounds%endc,:,3) = mss_cnc_ocphi(bounds%begc:bounds%endc,:) mss_cnc_aer_in_fdb(bounds%begc:bounds%endc,:,4) = mss_cnc_ocpho(bounds%begc:bounds%endc,:) endif @@ -580,7 +580,7 @@ subroutine SurfaceAlbedo(bounds,nc, & mss_cnc_aer_in_frc_bc(bounds%begc:bounds%endc,:,6) = mss_cnc_dst2(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_bc(bounds%begc:bounds%endc,:,7) = mss_cnc_dst3(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_bc(bounds%begc:bounds%endc,:,8) = mss_cnc_dst4(bounds%begc:bounds%endc,:) - if (DO_SNO_OC) then + if (do_sno_oc) then mss_cnc_aer_in_frc_bc(bounds%begc:bounds%endc,:,3) = mss_cnc_ocphi(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_bc(bounds%begc:bounds%endc,:,4) = mss_cnc_ocpho(bounds%begc:bounds%endc,:) endif @@ -616,7 +616,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! 2. OC input array: ! set BC and dust concentrations, so OC_FRC=[(BC+OC+dust)-(BC+dust)] - if (DO_SNO_OC) then + if (do_sno_oc) then mss_cnc_aer_in_frc_oc(bounds%begc:bounds%endc,:,1) = mss_cnc_bcphi(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_oc(bounds%begc:bounds%endc,:,2) = mss_cnc_bcpho(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_oc(bounds%begc:bounds%endc,:,5) = mss_cnc_dst1(bounds%begc:bounds%endc,:) @@ -658,7 +658,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! set BC and OC concentrations, so DST_FRC=[(BC+OC+dust)-(BC+OC)] mss_cnc_aer_in_frc_dst(bounds%begc:bounds%endc,:,1) = mss_cnc_bcphi(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_dst(bounds%begc:bounds%endc,:,2) = mss_cnc_bcpho(bounds%begc:bounds%endc,:) - if (DO_SNO_OC) then + if (do_sno_oc) then mss_cnc_aer_in_frc_dst(bounds%begc:bounds%endc,:,3) = mss_cnc_ocphi(bounds%begc:bounds%endc,:) mss_cnc_aer_in_frc_dst(bounds%begc:bounds%endc,:,4) = mss_cnc_ocpho(bounds%begc:bounds%endc,:) endif @@ -768,7 +768,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albgrd_bc(c,ib) = albsod(c,ib)*(1.-frac_sno(c)) + albsnd_bc(c,ib)*frac_sno(c) albgri_bc(c,ib) = albsoi(c,ib)*(1.-frac_sno(c)) + albsni_bc(c,ib)*frac_sno(c) - if (DO_SNO_OC) then + if (do_sno_oc) then ! OC forcing albedo albgrd_oc(c,ib) = albsod(c,ib)*(1.-frac_sno(c)) + albsnd_oc(c,ib)*frac_sno(c) albgri_oc(c,ib) = albsoi(c,ib)*(1.-frac_sno(c)) + albsni_oc(c,ib)*frac_sno(c) @@ -1082,7 +1082,7 @@ subroutine SurfaceAlbedo(bounds,nc, & end do end do -! cenlin: add output variables for history files + ! add output variables for history files do ib = 1, numrad do fc = 1,num_nourbanc c = filter_nourbanc(fc) @@ -1112,7 +1112,6 @@ subroutine SurfaceAlbedo(bounds,nc, & end if end do end do -! cenlin: end end associate diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90 index eb8ec9ef03..9e0743944b 100644 --- a/src/biogeophys/SurfaceAlbedoType.F90 +++ b/src/biogeophys/SurfaceAlbedoType.F90 @@ -7,7 +7,7 @@ module SurfaceAlbedoType use decompMod , only : bounds_type use clm_varpar , only : numrad, nlevcan, nlevsno use abortutils , only : endrun - use clm_varctl , only : use_SSRE, use_snicar_frc ! cenlin + use clm_varctl , only : use_SSRE, use_snicar_frc ! ! !PUBLIC TYPES: implicit none @@ -35,7 +35,7 @@ module SurfaceAlbedoType real(r8), pointer :: albsoi_col (:,:) ! col soil albedo: diffuse (col,bnd) [frc] real(r8), pointer :: albsnd_hst_col (:,:) ! col snow albedo, direct , for history files (col,bnd) [frc] real(r8), pointer :: albsni_hst_col (:,:) ! col snow albedo, diffuse, for history files (col,bnd) [frc] -! cenlin add new output variables for albedo for history files only +! add new snicar output variables for albedo for history files only real(r8), pointer :: albd_hst_patch (:,:) ! patch surface albedo (direct) for history files (numrad) real(r8), pointer :: albi_hst_patch (:,:) ! patch surface albedo (diffuse) for history files (numrad) real(r8), pointer :: albgrd_pur_hst_col (:,:) ! col pure snow ground direct albedo for history files (numrad) @@ -50,7 +50,7 @@ module SurfaceAlbedoType real(r8), pointer :: albgri_hst_col (:,:) ! col ground albedo (diffuse) for history files (numrad) real(r8), pointer :: albsnd_hst2_col (:,:) ! col snow albedo, direct , for history files (col,bnd) [frc] real(r8), pointer :: albsni_hst2_col (:,:) ! col snow albedo, diffuse, for history files (col,bnd) [frc] -! cenlin end +! end add new snicar real(r8), pointer :: ftdd_patch (:,:) ! patch down direct flux below canopy per unit direct flx (numrad) real(r8), pointer :: ftid_patch (:,:) ! patch down diffuse flux below canopy per unit direct flx (numrad) @@ -173,7 +173,7 @@ subroutine InitAllocate(this, bounds) allocate(this%vcmaxcintsun_patch (begp:endp)) ; this%vcmaxcintsun_patch (:) = nan allocate(this%vcmaxcintsha_patch (begp:endp)) ; this%vcmaxcintsha_patch (:) = nan -! cenlin add new output variables for albedo for history files only +! add new snicar output variables for albedo for history files only allocate(this%albgrd_hst_col (begc:endc,numrad)) ; this%albgrd_hst_col (:,:) = spval allocate(this%albgri_hst_col (begc:endc,numrad)) ; this%albgri_hst_col (:,:) = spval allocate(this%albsnd_hst2_col (begc:endc,numrad)) ; this%albsnd_hst2_col (:,:) = spval @@ -188,7 +188,7 @@ subroutine InitAllocate(this, bounds) allocate(this%albgri_dst_hst_col (begc:endc,numrad)) ; this%albgri_dst_hst_col (:,:) = spval allocate(this%albd_hst_patch (begp:endp,numrad)) ; this%albd_hst_patch (:,:) = spval allocate(this%albi_hst_patch (begp:endp,numrad)) ; this%albi_hst_patch (:,:) = spval -! cenlin end +! end and new snicar end subroutine InitAllocate @@ -254,7 +254,7 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='surface albedo (indirect)', & ptr_patch=this%albi_patch, default=defaultoutput, c2l_scale_type='urbanf') -! cenlin add new output variables for albedo for history files only +! add new snicar output variables for albedo for history files only if (use_snicar_frc) then this%albd_hst_patch(begp:endp,:) = spval @@ -328,7 +328,7 @@ subroutine InitHistory(this, bounds) ptr_col=this%albsni_hst2_col, default='inactive') end if ! end of use_snicar_frc -! cenlin: end +! end add new snicar end subroutine InitHistory @@ -654,7 +654,7 @@ subroutine Restart(this, bounds, ncid, flag, & end if ! end of if-use_snicar_frc -! cenlin add new output variables for albedo for history files only +! add new snicar output variables for albedo for history files only if (use_snicar_frc) then call restartvar(ncid=ncid, flag=flag, varname='albd_hist', xtype=ncd_double, & @@ -742,7 +742,7 @@ subroutine Restart(this, bounds, ncid, flag, & interpinic_flag='interp', readvar=readvar, data=this%albgri_dst_hst_col) end if ! end of if-use_snicar_frc -! cenlin end +! end add new snicar ! patch type physical state variable - fabd call restartvar(ncid=ncid, flag=flag, varname='fabd', xtype=ncd_double, & diff --git a/src/biogeophys/SurfaceRadiationMod.F90 b/src/biogeophys/SurfaceRadiationMod.F90 index 5a00a67b23..03557c6476 100644 --- a/src/biogeophys/SurfaceRadiationMod.F90 +++ b/src/biogeophys/SurfaceRadiationMod.F90 @@ -477,9 +477,8 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & use clm_varpar , only : numrad, nlevsno use clm_varcon , only : spval use landunit_varcon , only : istsoil, istcrop - use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, iulog, use_SSRE, DO_SNO_OC !cenlin + use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, iulog, use_SSRE, do_sno_oc use clm_time_manager , only : get_step_size_real, is_near_local_noon - ! use SnowSnicarMod , only : DO_SNO_OC use abortutils , only : endrun ! ! !ARGUMENTS: @@ -856,7 +855,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & sfc_frc_bc(p) = sabg(p) - sabg_bc(p) ! OC aerosol forcing (patch-level): - if (DO_SNO_OC) then + if (do_sno_oc) then sfc_frc_oc(p) = sabg(p) - sabg_oc(p) else sfc_frc_oc(p) = 0._r8 diff --git a/src/biogeophys/UrbanAlbedoMod.F90 b/src/biogeophys/UrbanAlbedoMod.F90 index 5ec225294f..c96671a420 100644 --- a/src/biogeophys/UrbanAlbedoMod.F90 +++ b/src/biogeophys/UrbanAlbedoMod.F90 @@ -12,7 +12,7 @@ module UrbanAlbedoMod use shr_log_mod , only : errMsg => shr_log_errMsg use decompMod , only : bounds_type, subgrid_level_landunit use clm_varpar , only : numrad - use clm_varcon , only : isecspday, degpsec, spval ! cenlin + use clm_varcon , only : isecspday, degpsec, spval use clm_varctl , only : iulog use abortutils , only : endrun use UrbanParamsType , only : urbanparams_type @@ -156,12 +156,12 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albgri => surfalb_inst%albgri_col , & ! Output: [real(r8) (:,:) ] urban col ground albedo (diffuse) albd => surfalb_inst%albd_patch , & ! Output [real(r8) (:,:) ] urban pft surface albedo (direct) albi => surfalb_inst%albi_patch , & ! Output: [real(r8) (:,:) ] urban pft surface albedo (diffuse) -! cenlin: add albedo output for history files +! add new snicar albedo output for history files albd_hst => surfalb_inst%albd_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (direct) for history files albi_hst => surfalb_inst%albi_hst_patch , & ! Output: [real(r8) (:,:) ] surface albedo (diffuse) for history files albgrd_hst => surfalb_inst%albgrd_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (direct) for history files albgri_hst => surfalb_inst%albgri_hst_col , & ! Output: [real(r8) (:,:) ] ground albedo (diffuse) for history files -! cenlin: end +! end add new snicar begl => bounds%begl , & vf_sr => urbanparams_inst%vf_sr , & ! Input: [real(r8) (:) ] view factor of sky for road vf_sw => urbanparams_inst%vf_sw , & ! Input: [real(r8) (:) ] view factor of sky for one wall @@ -187,10 +187,10 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & c = filter_urbanc(fc) albgrd(c,ib) = 0._r8 albgri(c,ib) = 0._r8 -! cenlin: add output variables for history files +! add new snicar output variables for history files albgrd_hst(c,ib) = spval albgri_hst(c,ib) = spval -! cenlin: end +! end add new snicar end do do fp = 1,num_urbanp @@ -212,10 +212,10 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albd(p,ib) = 1._r8 albi(p,ib) = 1._r8 endif -! cenlin: add output variables for history files +! add new snicar output variables for history files albd_hst(p,ib) = spval albi_hst(p,ib) = spval -! cenlin: end +! end add new snicar fabd(p,ib) = 0._r8 fabd_sun(p,ib) = 0._r8 fabd_sha(p,ib) = 0._r8 @@ -431,12 +431,12 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albgrd(c,ib) = sref_improad_dir(l,ib) albgri(c,ib) = sref_improad_dif(l,ib) endif -! cenlin: add albedo variables for history fields +! add new snicar albedo variables for history fields if (coszen(l) > 0._r8) then albgrd_hst(c,ib) = albgrd(c,ib) albgri_hst(c,ib) = albgri(c,ib) end if -! cenlin: end +! end add new snicar end do do fp = 1,num_urbanp p = filter_urbanp(fp) @@ -444,12 +444,12 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & l = patch%landunit(p) albd(p,ib) = albgrd(c,ib) albi(p,ib) = albgri(c,ib) -! cenlin: add albedo variables for history fields +! add new snicar albedo variables for history fields if (coszen(l) > 0._r8) then albd_hst(p,ib) = albd(p,ib) albi_hst(p,ib) = albi(p,ib) end if -! cenlin: end +! end add new snicar end do end do end if diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index a0d5a9a122..8d2ea77b33 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -113,7 +113,7 @@ module clm_varctl character(len=fname_len), public :: nrevsn = ' ' ! restart data file name for branch run character(len=fname_len), public :: fsnowoptics = ' ' ! snow optical properties file name character(len=fname_len), public :: fsnowaging = ' ' ! snow aging parameters file name - character(len=fname_len), public :: fsnowoptics480 = ' ' ! snow optical properties file name for 480 bands, cenlin + character(len=fname_len), public :: fsnowoptics480 = ' ' ! snow optical properties file name for 480 bands character(len=fname_len), public :: fatmlndfrc = ' ' ! lnd frac file on atm grid ! only needed for LILAC and MCT drivers @@ -231,7 +231,7 @@ module clm_varctl real(r8), public :: o3_ppbv = 100._r8 - ! number of wavelength bands used in SNICAR snow albedo calculation, cenlin + ! number of wavelength bands used in SNICAR snow albedo calculation integer, public :: snicar_numrad_snw = 5 ! type of downward solar radiation spectrum for SNICAR snow albedo calculation @@ -258,8 +258,8 @@ module clm_varctl ! option to activate dust-snow internal mixing in SNICAR (He et al. 2017 JC), ceniln logical, public :: snicar_snodst_intmix = .false. ! false->external mixing for all dust; true->internal mixing for all dust - ! option to activate OC in snow in SNICAR, cenlin - logical, public :: DO_SNO_OC = .false. ! control to include organic carbon (OC) in snow + ! option to activate OC in snow in SNICAR + logical, public :: do_sno_oc = .false. ! control to include organic carbon (OC) in snow !---------------------------------------------------------- ! C isotopes diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 11bb49b902..ac37760f49 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -204,7 +204,7 @@ subroutine control_init(dtime) crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & snicar_numrad_snw, snicar_solarspec, snicar_dust_optics, & snicar_use_aerosol, snicar_snw_shape, snicar_snobc_intmix,& - snicar_snodst_intmix,DO_SNO_OC, & + snicar_snodst_intmix,do_sno_oc, & for_testing_use_second_grain_pool, for_testing_use_repr_structure_pool, & for_testing_no_crop_seed_replenishment @@ -812,7 +812,7 @@ subroutine control_spmd() call mpi_bcast (snicar_use_aerosol, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_snobc_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (snicar_snodst_intmix, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (DO_SNO_OC, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (do_sno_oc, 1, MPI_LOGICAL, 0, mpicom, ier) ! snow pack variables call mpi_bcast (nlevsno, 1, MPI_INTEGER, 0, mpicom, ier) @@ -998,7 +998,7 @@ subroutine control_print () write(iulog,*) ' SNICAR: snow grain shape type = ', snicar_snw_shape write(iulog,*) ' SNICAR: BC-snow internal mixing = ', snicar_snobc_intmix write(iulog,*) ' SNICAR: dust-snow internal mixing = ', snicar_snodst_intmix - write(iulog,*) ' SNICAR: OC in snow = ', DO_SNO_OC + write(iulog,*) ' SNICAR: OC in snow = ', do_sno_oc write(iulog,'(a,i8)') ' Number of snow layers =', nlevsno write(iulog,'(a,d20.10)') ' Max snow depth (mm) =', h2osno_max From 4ab6738316715cd610171f4d935f5d6f1acb7101 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 3 Aug 2023 18:42:36 -0600 Subject: [PATCH 1300/2067] Some clean-up associated with snicar_numrad_snw --- src/biogeophys/SnowSnicarMod.F90 | 107 +++++++++++-------------------- 1 file changed, 36 insertions(+), 71 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 017f434c2e..0d58ffb35c 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -536,8 +536,12 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ) ! initialize parameter - if (snicar_numrad_snw == 5) nir_bnd_bgn = 2 - if (snicar_numrad_snw == 480) nir_bnd_bgn = 51 + select case (snicar_numrad_snw) + case (5) + nir_bnd_bgn = 2 + case (480) + nir_bnd_bgn = 51 + end select nir_bnd_end = snicar_numrad_snw ! initialize for adding-doubling solver @@ -733,45 +737,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! ! The following weights are appropriate for surface-incident flux in a mid-latitude winter atmosphere ! - ! 3-band weights - if (snicar_numrad_snw==3) then - ! Direct: - if (flg_slr_in == 1) then - flx_wgt(1) = 1._r8 - flx_wgt(2) = 0.66628670195247_r8 - flx_wgt(3) = 0.33371329804753_r8 - ! Diffuse: - elseif (flg_slr_in == 2) then - flx_wgt(1) = 1._r8 - flx_wgt(2) = 0.77887652162877_r8 - flx_wgt(3) = 0.22112347837123_r8 - endif - ! 5-band weights - !elseif (snicar_numrad_snw==5) then - ! ! Direct: - ! if (flg_slr_in == 1) then - ! flx_wgt(1) = 1._r8 - ! flx_wgt(2) = 0.49352158521175_r8 - ! flx_wgt(3) = 0.18099494230665_r8 - ! flx_wgt(4) = 0.12094898498813_r8 - ! flx_wgt(5) = 0.20453448749347_r8 - ! ! Diffuse: - ! elseif (flg_slr_in == 2) then - ! flx_wgt(1) = 1._r8 - ! flx_wgt(2) = 0.58581507618433_r8 - ! flx_wgt(3) = 0.20156903770812_r8 - ! flx_wgt(4) = 0.10917889346386_r8 - ! flx_wgt(5) = 0.10343699264369_r8 - ! endif - else ! works for both 5-band & 480-band, flux weights directly read from input data - ! Direct: - if (flg_slr_in == 1) then - flx_wgt(1:snicar_numrad_snw) = flx_wgt_dir(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data - ! Diffuse: - elseif (flg_slr_in == 2) then - flx_wgt(1:snicar_numrad_snw) = flx_wgt_dif(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data - endif - endif ! end if snicar_numrad_snw +! ! works for both 5-band & 480-band, flux weights directly read from input data + ! Direct: + if (flg_slr_in == 1) then + flx_wgt(1:snicar_numrad_snw) = flx_wgt_dir(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data + ! Diffuse: + elseif (flg_slr_in == 2) then + flx_wgt(1:snicar_numrad_snw) = flx_wgt_dif(1:snicar_numrad_snw) ! VIS or NIR band sum is already normalized to 1.0 in input data + endif exp_min = exp(-argmax) @@ -805,10 +778,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & mss_cnc_aer_lcl(:,:) = 0._r8 endif - if ( (snicar_numrad_snw == 3).and.(bnd_idx == 3) ) then - mss_cnc_aer_lcl(:,:) = 0._r8 - endif - if ( (snicar_numrad_snw == 480).and.(bnd_idx > 100) ) then ! >1.2um mss_cnc_aer_lcl(:,:) = 0._r8 endif @@ -901,14 +870,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here ! use the piecewise linear interpolation subroutine created at the end of this module ! tests showed the piecewise linear interpolation has similar results as pchip interpolation - if (snicar_numrad_snw == 5) then + select case (snicar_numrad_snw) + case (5) call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct5(bnd_idx),g_Cg_intp) call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct5(bnd_idx),gg_F07_intp) - endif - if (snicar_numrad_snw == 480) then + case (480) call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct480(bnd_idx),g_Cg_intp) call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct480(bnd_idx),gg_F07_intp) - endif + end select g_ice_F07 = gg_F07_intp + (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) / 2._r8 ! Eq.2.2 in Fu (2007) asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) endif @@ -989,8 +958,12 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) ! Start BC/dust-snow internal mixing for wavelength<=1.2um - if (snicar_numrad_snw == 5) wvl_doint = wvl_ct5(bnd_idx) - if (snicar_numrad_snw == 480) wvl_doint = wvl_ct480(bnd_idx) + select case (snicar_numrad_snw) + case (5) + wvl_doint = wvl_ct5(bnd_idx) + case (480) + wvl_doint = wvl_ct480(bnd_idx) + end select if (wvl_doint <= 1.2_r8) then ! BC-snow internal mixing applied to hydrophilic BC if activated @@ -1443,18 +1416,15 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR albedo appropriately - ! for 5- and 3-band cases - if (snicar_numrad_snw <= 5) then + select case (snicar_numrad_snw) + case (5) ! 5-band case albout(c_idx,1) = albout_lcl(1) flx_sum = 0._r8 do bnd_idx= nir_bnd_bgn,nir_bnd_end flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) end do albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) - end if - - ! for 480-band case - if (snicar_numrad_snw == 480) then + case (480) ! 480-band case ! average for VIS band flx_sum = 0._r8 do bnd_idx= 1, (nir_bnd_bgn-1) @@ -1467,11 +1437,11 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) end do albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) - end if + end select ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately - ! for 5- and 3-band cases - if (snicar_numrad_snw <= 5) then + select case (snicar_numrad_snw) + case (5) ! 5-band case flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) do i=snl_top,1,1 flx_sum = 0._r8 @@ -1480,10 +1450,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end do - end if - - ! for 480-band case - if (snicar_numrad_snw == 480) then + case (480) ! 480-band case do i=snl_top,1,1 ! average for VIS band flx_sum = 0._r8 @@ -1498,7 +1465,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end do - end if + end select ! high solar zenith angle adjustment for Adding-doubling solver results ! near-IR direct albedo/absorption adjustment for high solar zenith angles @@ -1926,7 +1893,8 @@ subroutine SnowOptics_init( ) if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....' !--------------------- for 5-band data - if (snicar_numrad_snw == 5) then + select case (snicar_numrad_snw) + case (5) ! 5-band case call getfil (fsnowoptics, locfn, 0) call ncd_pio_openfile(ncid, locfn, 0) @@ -2428,11 +2396,8 @@ subroutine SnowOptics_init( ) end select end select - end if ! end if snicar_numrad_snw == 5 - - !-------------------- for 480-band data - if (snicar_numrad_snw == 480) then + case (480) call getfil (fsnowoptics480, locfn, 0) call ncd_pio_openfile(ncid, locfn, 0) @@ -2541,7 +2506,7 @@ subroutine SnowOptics_init( ) call ncd_io( 'flx_wgt_dif480_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) end select - endif ! end if snicar_numrad_snw == 480 + end select call ncd_pio_closefile(ncid) if (masterproc) then From eb9a43ba03edd836af4a0c8bc99969c2184e5884 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 2 Aug 2023 15:04:49 -0600 Subject: [PATCH 1301/2067] RXCROPMATURITY test now part of clm_pymods in addition to ctsm_sci. --- cime_config/testdefs/testlist_clm.xml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 31c44c307d..69fd30c2c7 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2541,6 +2541,12 @@ + + + + + + From 13c7bad89970e8aeddb70aafaa4b108c59c5845c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 4 Aug 2023 12:26:37 -0600 Subject: [PATCH 1302/2067] RXCROPMATURITY test in testlist_clm.xml now specifies testmod cropMonthOutput. --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 69fd30c2c7..ea82f6812e 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2533,7 +2533,7 @@ - + From 4905a09bf2a5529658c1349aa98728af0de34ee7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 4 Aug 2023 13:09:45 -0600 Subject: [PATCH 1303/2067] Rm test that I prob. reintroduced when resolving conflicts: ERI_D_Ld9_P48x1_Vmct --- cime_config/testdefs/testlist_clm.xml | 9 --------- 1 file changed, 9 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index feb5f52033..aa5dd98697 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -158,15 +158,6 @@ - - - - - - - - - From 94116d371664b5697f5f1ebd7117b0608de35455 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 4 Aug 2023 13:13:19 -0600 Subject: [PATCH 1304/2067] Correction to call of fsurdat_modifier in RXCROPMATURITY test. --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 6f66a95b81..9eb4bdb17d 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -277,7 +277,7 @@ def _run_fsurdat_modifier(self): command = ( f"python3 {tool_path} {cfg_path} " + f"-i {self._fsurdat_in} " - + f"-o {self._path_gddgen}" + + f"-o {self._fsurdat_out}" ) stu.run_python_script( self._get_caseroot(), From 21b607dcf9558891bea08eadbbb5f33188eb71b6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 4 Aug 2023 16:22:29 -0600 Subject: [PATCH 1305/2067] Update namelist defaults and differentiate clm5_1 from 5_0, 4_5 --- bld/CLMBuildNamelist.pm | 2 ++ bld/namelist_files/namelist_defaults_ctsm.xml | 24 +++++++++++++++---- .../namelist_definition_ctsm.xml | 13 +++++----- 3 files changed, 27 insertions(+), 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 017f13ecef..04aa4a29a4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1999,6 +1999,7 @@ sub setup_logic_snicar_methods { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snobc_intmix' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snodst_intmix' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_use_aerosol' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_snicar_frc' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' ); } @@ -2007,6 +2008,7 @@ sub setup_logic_snicar_methods { sub setup_logic_snow { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics480' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowaging' ); } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 1fddc07869..3b4812c15c 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1541,11 +1541,25 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc -lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc -hexagonal_plate -mid_latitude_summer -sahara +lnd/clm2/snicardata/snicar_optics_480bnd_c012422.nc +lnd/clm2/snicardata/snicar_optics_5bnd_c013122.nc +lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc + +hexagonal_plate +sphere +sphere + +.true. +.false. +.false. + +mid_latitude_winter +sahara +5 +.false. +.false. +.true. +.false. 2015 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 5bcb1fe2c3..ac13424695 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -181,15 +181,15 @@ Toggle to turn on/off aerosol deposition flux in snow in SNICAR + group="snicar_inparm" value=".false." > option to activate BC-snow internal mixing in SNICAR snow albedo calculation -Default: .true. +Default: .false. + group="snicar_inparm" value=".false." > option to activate dust-snow internal mixing in SNICAR snow albedo calculation -Default: .true. +Default: .false. + group="snicar_inparm" value=".true."> Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) radiative forcing -(snicar_frc=".true." is EXPERIMENTAL NOT SUPPORTED!) -Default: .false. +Default: .true. Date: Fri, 4 Aug 2023 17:14:37 -0600 Subject: [PATCH 1306/2067] Minor cleanup of unnecessary things --- src/biogeophys/AerosolMod.F90 | 1 - src/biogeophys/SurfaceAlbedoMod.F90 | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeophys/AerosolMod.F90 b/src/biogeophys/AerosolMod.F90 index 33c65567f3..bce2b6f9ab 100644 --- a/src/biogeophys/AerosolMod.F90 +++ b/src/biogeophys/AerosolMod.F90 @@ -810,7 +810,6 @@ subroutine AerosolFluxes(bounds, num_snowc, filter_snowc, & ! if turn off aerosol effect in snow, zero out deposition flux if (.not. snicar_use_aerosol) then do c = bounds%begc,bounds%endc - g = col%gridcell(c) flx_bc_dep_dry(c) = 0._r8 flx_bc_dep_wet(c) = 0._r8 diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index 5d12767121..a6758a95bc 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -14,7 +14,7 @@ module SurfaceAlbedoMod use landunit_varcon , only : istsoil, istcrop, istdlak use clm_varcon , only : grlnd, spval use clm_varpar , only : numrad, nlevcan, nlevsno, nlevcan - use clm_varctl , only : fsurdat, iulog, use_snicar_frc, use_SSRE, do_sno_oc + use clm_varctl , only : fsurdat, iulog, use_SSRE, do_sno_oc use pftconMod , only : pftcon use SnowSnicarMod , only : sno_nbr_aer, SNICAR_RT, DO_SNO_AER use AerosolMod , only : aerosol_type From 29816874e2b6ce922a85d8e7cc3238d93f95affd Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 4 Aug 2023 17:59:23 -0600 Subject: [PATCH 1307/2067] Update change files --- doc/ChangeLog | 10 ++++++++-- doc/ChangeSum | 2 +- 2 files changed, 9 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index fb58cbfb90..7fa07e58cf 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev132 Originator(s): mvdebolskiy (NORCE, Bergen, Norway), slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Thu Aug 3 17:03:44 MDT 2023 +Date: Fri Aug 4 17:52:45 MDT 2023 One-line Summary: Add parameterization to allow excess ice in soil and subsidence Purpose and description of changes @@ -52,11 +52,17 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): -#1229 + Fixes #1229 -- excess ice Notes of particular relevance for users --------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): + Excess ice can EITHER be turned on by using the stream file, OR a restart file that has excess ice on it. + Since, excess ice is expected to melt as time goes on, the use of a restart file is preferred. + But, use of a restart file requires a simulation that was spun up to that point. + Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): New namelist options added: - use_excess_ice (logical, in clm_inparm) default = .false.; turns on excess ice physics diff --git a/doc/ChangeSum b/doc/ChangeSum index 9cfa433000..1702a919d0 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev132 slevis 08/03/2023 Add parameterization to allow excess ice in soil and subsidence + ctsm5.1.dev132 slevis 08/04/2023 Add parameterization to allow excess ice in soil and subsidence ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml From 5cfb1b40670ee7f718b17549f55ba91e5c321011 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 7 Aug 2023 12:12:20 -0600 Subject: [PATCH 1308/2067] =?UTF-8?q?1=C2=B0=20RXCROPMATURITY=20test=20now?= =?UTF-8?q?=20only=20in=20ctsm=5Fsci;=20new=2010x15=20test=20in=20aux=5Fcl?= =?UTF-8?q?m=20&=20clm=5Fpymods.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- cime_config/testdefs/testlist_clm.xml | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index ea82f6812e..dfb7575134 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2533,20 +2533,31 @@ - + - + - + - + + + + + + + + + + + + From 9cd7a551469cff685f0ae38af1b04b7903c968f7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 7 Aug 2023 17:19:10 -0600 Subject: [PATCH 1309/2067] Minor cleanup of unused things --- src/biogeophys/SolarAbsorbedType.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeophys/SolarAbsorbedType.F90 b/src/biogeophys/SolarAbsorbedType.F90 index d42a072b06..d1941f68cc 100644 --- a/src/biogeophys/SolarAbsorbedType.F90 +++ b/src/biogeophys/SolarAbsorbedType.F90 @@ -168,7 +168,7 @@ subroutine InitHistory(this, bounds) ! ! !USES: use shr_infnan_mod, only : nan => shr_infnan_nan, assignment(=) - use clm_varctl , only : use_snicar_frc , use_SSRE + use clm_varctl , only : use_SSRE use clm_varpar , only : nlevsno use histFileMod , only : hist_addfld1d, hist_addfld2d use histFileMod , only : no_snow_normal @@ -375,7 +375,6 @@ subroutine Restart(this, bounds, ncid, flag) ! ! !USES: use shr_infnan_mod , only : shr_infnan_isnan - use clm_varctl , only : use_snicar_frc, iulog use spmdMod , only : masterproc use abortutils , only : endrun use ncdio_pio , only : file_desc_t, ncd_defvar, ncd_io, ncd_double, ncd_int, ncd_inqvdlen From a0cd959f0077471fc219fbca6aefe999f5987f60 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 7 Aug 2023 17:41:36 -0600 Subject: [PATCH 1310/2067] Rename use_snicar_frc to snicar_aerforc_diag and make default .false. --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 5 +---- bld/namelist_files/namelist_definition_ctsm.xml | 8 ++++---- .../testmods_dirs/clm/SNICARFRC/user_nl_clm | 2 +- src/biogeophys/SurfaceAlbedoMod.F90 | 6 +++--- src/biogeophys/SurfaceAlbedoType.F90 | 16 ++++++++-------- src/biogeophys/SurfaceRadiationMod.F90 | 10 +++++----- src/main/clm_varctl.F90 | 2 +- src/main/controlMod.F90 | 6 +++--- 9 files changed, 27 insertions(+), 30 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 04aa4a29a4..e20b9ea6e8 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1999,7 +1999,7 @@ sub setup_logic_snicar_methods { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snobc_intmix' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snodst_intmix' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_use_aerosol' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_snicar_frc' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_aerforc_diag' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' ); } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3b4812c15c..0b174b7591 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1549,10 +1549,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 sphere sphere -.true. -.false. -.false. - +.false. mid_latitude_winter sahara 5 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index ac13424695..f15083d222 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1204,10 +1204,10 @@ DependsOnLatAndVeg - Arctic vegetation depends on latitude as above, but tempera (only used when CN is on) - -Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) radiative forcing -Default: .true. + +Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) albedo forcing diagnostics for each aerosol species +Default: .false. shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : use_snicar_frc, use_fates + use clm_varctl , only : snicar_aerforc_diag, use_fates use decompMod , only : bounds_type, subgrid_level_column use atm2lndType , only : atm2lnd_type use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type @@ -173,7 +173,7 @@ subroutine InitHistory(this, bounds) begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc - if (use_snicar_frc) then + if (snicar_aerforc_diag) then this%sfc_frc_aer_patch(begp:endp) = spval call hist_addfld1d (fname='SNOAERFRCL', units='W/m^2', & avgflag='A', long_name='surface forcing of all aerosols in snow (land) ', & @@ -477,7 +477,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & use clm_varpar , only : numrad, nlevsno use clm_varcon , only : spval use landunit_varcon , only : istsoil, istcrop - use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, iulog, use_SSRE, do_sno_oc + use clm_varctl , only : use_subgrid_fluxes, snicar_aerforc_diag, iulog, use_SSRE, do_sno_oc use clm_time_manager , only : get_step_size_real, is_near_local_noon use abortutils , only : endrun ! @@ -719,7 +719,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & sabg_soil(p) = sabg(p) endif - if (use_snicar_frc) then + if (snicar_aerforc_diag) then ! Solar radiation absorbed by ground surface without BC absrad_bc = trd(p,ib)*(1._r8-albgrd_bc(c,ib)) + tri(p,ib)*(1._r8-albgri_bc(c,ib)) sabg_bc(p) = sabg_bc(p) + absrad_bc @@ -849,7 +849,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & sabg_pen(p) = sabg(p) - sabg_lyr(p, snl(c)+1) end if - if (use_snicar_frc) then + if (snicar_aerforc_diag) then ! BC aerosol forcing (patch-level): sfc_frc_bc(p) = sabg(p) - sabg_bc(p) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 8d2ea77b33..cdf486eb8e 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -440,7 +440,7 @@ module clm_varctl logical, public :: use_cndv = .false. logical, public :: use_grainproduct = .false. logical, public :: use_fertilizer = .false. - logical, public :: use_snicar_frc = .false. + logical, public :: snicar_aerforc_diag = .false. logical, public :: use_vancouver = .false. logical, public :: use_mexicocity = .false. logical, public :: use_noio = .false. diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index ac37760f49..68edb706ff 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -282,7 +282,7 @@ subroutine control_init(dtime) namelist /clm_inparm/ & use_lch4, use_nitrif_denitrif, use_extralakelayers, & use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, & - use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, & + use_grainproduct, snicar_aerforc_diag, use_vancouver, use_mexicocity, use_noio, & use_nguardrail @@ -646,7 +646,7 @@ subroutine control_spmd() call mpi_bcast (use_fertilizer, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_grainproduct, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (o3_veg_stress_method, len(o3_veg_stress_method), MPI_CHARACTER, 0, mpicom, ier) - call mpi_bcast (use_snicar_frc, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (snicar_aerforc_diag, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_vancouver, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_mexicocity, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_noio, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -899,7 +899,7 @@ subroutine control_print () write(iulog,*) ' use_fertilizer = ', use_fertilizer write(iulog,*) ' use_grainproduct = ', use_grainproduct write(iulog,*) ' o3_veg_stress_method = ', o3_veg_stress_method - write(iulog,*) ' use_snicar_frc = ', use_snicar_frc + write(iulog,*) ' snicar_aerforc_diag = ', snicar_aerforc_diag write(iulog,*) ' snicar_use_aerosol = ',snicar_use_aerosol write(iulog,*) ' use_vancouver = ', use_vancouver write(iulog,*) ' use_mexicocity = ', use_mexicocity From 0e6f1df6eeec018f9cd15325e96aeab15799b50a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 8 Aug 2023 11:21:12 -0600 Subject: [PATCH 1311/2067] Correction of a typo in /testmods_dirs/.../user_nl_clm --- cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm index d8084a4814..449f749457 100644 --- a/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm @@ -1 +1 @@ - snicar_aerfoc_diag = .true. + snicar_aerforc_diag = .true. From b9f858745967bff8bc1842b50fa20a692c4f88aa Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 8 Aug 2023 12:11:56 -0600 Subject: [PATCH 1312/2067] update fates tag in externals --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 3325f37d7f..7f405e593f 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.67.0_api.25.5.0 +tag = sci.1.67.1_api.26.0.0 required = True [externals_description] From f7df297639f9b1598bf3a9028544de25ca7a563e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 8 Aug 2023 13:31:07 -0600 Subject: [PATCH 1313/2067] Update .ChangeLog_template Work on issue #2070 --- doc/.ChangeLog_template | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index 63f4628bad..9f4f64c587 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -33,13 +33,8 @@ Bugs fixed or introduced CTSM issues fixed (include CTSM Issue #): -Externals issues fixed (include issue #): - Known bugs introduced in this tag (include issue #): -Known bugs found since the previous tag (include issue #): - - Notes of particular relevance for users --------------------------------------- [Remove any lines that don't apply. Remove entire section if nothing applies.] @@ -150,7 +145,9 @@ Changes answers relative to baseline: - nature of change (roundoff; larger than roundoff/same climate; new climate): If bitwise differences were observed, how did you show they were no worse - than roundoff? + than roundoff? Roundoff differences means one or more lines of code change results + only by roundoff level (because order of operation changes for example). Roundoff + changes to state fields usually grow to greater than roundoff as the simulation progresses. If this tag changes climate describe the run(s) done to evaluate the new climate (put details of the simulations in the experiment database) From 55e91e465ea7bd6783309e1ea4faf786c2bce7b8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 8 Aug 2023 14:30:07 -0600 Subject: [PATCH 1314/2067] Replace dimension 8 with ngmax for two arrays; wait to hear about others --- src/biogeophys/SnowSnicarMod.F90 | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 0d58ffb35c..3cd910b1d2 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -66,10 +66,8 @@ module SnowSnicarMod real(r8), parameter :: min_snw = 1.0E-30_r8 ! minimum snow mass required for SNICAR RT calculation [kg m-2] - !real(r8), parameter :: C1_liq_Brun89 = 1.28E-17_r8 ! constant for liquid water grain growth [m3 s-1], - ! from Brun89 real(r8), parameter :: C1_liq_Brun89 = 0._r8 ! constant for liquid water grain growth [m3 s-1], - ! from Brun89: zeroed to accomodate dry snow aging + ! from Brun89: zeroed to accomodate dry snow aging, was 1.28E-17_r8 real(r8), parameter :: tim_cns_bc_rmv = 2.2E-8_r8 ! time constant for removal of BC in snow on sea-ice ! [s-1] (50% mass removal/year) @@ -406,11 +404,11 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: smr ! accumulator for rdif gaussian integration real(r8):: smt ! accumulator for tdif gaussian integration real(r8):: exp_min ! minimum exponential value - real(r8):: difgauspt(1:8) ! Gaussian integration angle - real(r8):: difgauswt(1:8) ! Gaussian integration coefficients/weights + real(r8), allocatable :: difgauspt(:) ! Gaussian integration angle + real(r8), allocatable :: difgauswt(:) ! Gaussian integration coefficients/weights integer :: ng ! gaussian integration index + integer :: ngmax = 8 ! max gaussian integration index integer :: snl_btm_itf ! index of bottom snow layer interfaces (1) [idx] - integer :: ngmax = 8 ! maxmimum gaussian integration index ! constants used in algorithm real(r8):: c0 = 0.0_r8 real(r8):: c1 = 1.0_r8 @@ -545,12 +543,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & nir_bnd_end = snicar_numrad_snw ! initialize for adding-doubling solver - difgauspt(1:8) = & ! gaussian angles (radians) + allocate(difgauspt(ngmax)) + allocate(difgauswt(ngmax)) + difgauspt(:) = & ! gaussian angles (radians) (/ 0.9894009_r8, 0.9445750_r8, & 0.8656312_r8, 0.7554044_r8, & 0.6178762_r8, 0.4580168_r8, & 0.2816036_r8, 0.0950125_r8/) - difgauswt(1:8) = & ! gaussian weights + difgauswt(:) = & ! gaussian weights (/ 0.0271525_r8, 0.0622535_r8, & 0.0951585_r8, 0.1246290_r8, & 0.1495960_r8, 0.1691565_r8, & @@ -1380,7 +1380,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & albout_lcl(bnd_idx) = albedo - ! Check that albedo is less than 1 + ! Fail if albedo > 1 if (albout_lcl(bnd_idx) > 1.0) then write (iulog,*) "SNICAR ERROR: Albedo > 1.0 at c: ", c_idx, " NSTEP= ",nstep From 4121c25f2deb18c74d8da80679bde2ea0af24a42 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 8 Aug 2023 14:34:37 -0700 Subject: [PATCH 1315/2067] update changelog --- doc/ChangeLog | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 81 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 7fa07e58cf..3d80221564 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,84 @@ =============================================================== +Tag name: ctsm5.1.dev133 +Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049) +Date: Tue Aug 8 13:30:00 PM MDT 2023 +One-line Summary: FATES API update to facilitate fates refactor + +Purpose and description of changes +---------------------------------- + +This updates a number of FATES type names and module use statements +which correspond with a refactoring effort that moves FATES +patches and cohorts into their own respective modules. + +This also incorporates a minor update to a more recent version +of the ccs config external. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Notes of particular relevance for developers: +--------------------------------------------- +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + + - Note that the fates patch and cohort types now use the `fates_` prefix instead + of the `ed_` prefix. + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + Note that the previous ctsm5.1.dev132 tag was generated using FATES tagname + sci.1.66.1_api.25.5.0. This api update includes intermediate FATES science + tags that are non-b4b, so aux_clm FATES tests result in DIFFs as expected. + +Answer changes +-------------- + +Changes answers relative to baseline: Yes, but only for aux_clm fates tests. + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + + sci.1.66.1_api.25.5.0 -> sci.1.67.1_api.26.0.0 + ccs_config_cesm0.0.64 -> ccs_config_cesm0.0.65 + +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) + + https://github.com/ESCOMP/CTSM/pull/2000 + https://github.com/NGEET/fates/pull/1024 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev132 Originator(s): mvdebolskiy (NORCE, Bergen, Norway), slevis (Samuel Levis,UCAR/TSS,303-665-1310) Date: Fri Aug 4 17:52:45 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 1702a919d0..602817e440 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev133 glemieux 08/08/2023 FATES API update to facilitate fates refactor ctsm5.1.dev132 slevis 08/04/2023 Add parameterization to allow excess ice in soil and subsidence ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update From 992ef0fccb55fde22546c375fc0bddd427e3fc1c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 8 Aug 2023 17:16:37 -0600 Subject: [PATCH 1316/2067] Minor refactor: replace some / and ** with *, replace some ifs with min/max --- src/biogeophys/SnowSnicarMod.F90 | 89 ++++++++++---------------------- 1 file changed, 28 insertions(+), 61 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 3cd910b1d2..260098b784 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -492,6 +492,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: Re_bc = 0.045 ! target BC effective radius (um) used in BC MAC adjustment real(r8) :: bcint_m(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix real(r8) :: bcint_n(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix + real(r8) :: bcint_m_tmp ! temporary of bcint_m + real(r8) :: bcint_n_tmp ! temporary of bcint_n real(r8) :: bcint_dd ! intermediate parameter real(r8) :: bcint_dd2 ! intermediate parameter real(r8) :: bcint_f ! intermediate parameter @@ -608,7 +610,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! initialize for dust-snow internal mixing ! Eq. 1 and Table 1 in He et al. 2019 JAMES (wavelength>1.2um, no dust-snow int mixing effect) dstint_wvl(1:7) = (/ 0.2_r8, 0.2632_r8, 0.3448_r8, 0.4415_r8, 0.625_r8, 0.7782_r8, 1.2422_r8/) - dstint_wvl_ct(1:6) = dstint_wvl(2:7)/2._r8 + dstint_wvl(1:6)/2._r8 + dstint_wvl_ct(1:6) = dstint_wvl(2:7) * 0.5_r8 + dstint_wvl(1:6) * 0.5_r8 dstint_a1(1:6) = (/ -2.1307E+1_r8, -1.5815E+1_r8, -9.2880_r8 , 1.1115_r8 , 1.0307_r8 , 1.0185_r8 /) dstint_a2(1:6) = (/ 1.1746E+2_r8, 9.3241E+1_r8, 4.0605E+1_r8, 3.7389E-1_r8, 1.4800E-2_r8, 2.8921E-4_r8 /) dstint_a3(1:6) = (/ 9.9701E-1_r8, 9.9781E-1_r8, 9.9848E-1_r8, 1.0035_r8 , 1.0024_r8 , 1.0356_r8 /) @@ -824,7 +826,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif do igb = 1,7 g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_sphd/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) - gg_ice_F07_tmp(igb) = g_F07_c0(igb) + g_F07_c1(igb)*AR_tmp + g_F07_c2(igb)*(AR_tmp**2._r8) ! Eqn. 3.1 in Fu (2007) + gg_ice_F07_tmp(igb) = g_F07_c0(igb) + g_F07_c1(igb) * AR_tmp + g_F07_c2(igb) * (AR_tmp * AR_tmp) ! Eqn. 3.1 in Fu (2007) enddo case ('hexagonal_plate') @@ -842,7 +844,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif do igb = 1,7 g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_hex0/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) - gg_ice_F07_tmp(igb) = g_F07_p0(igb)+g_F07_p1(igb)*LOG(AR_tmp)+g_F07_p2(igb)*((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) + gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * log(AR_tmp) + g_F07_p2(igb) * (log(AR_tmp) * log(AR_tmp)) ! Eqn. 3.3 in Fu (2007) enddo case ('koch_snowflake') @@ -860,7 +862,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & endif do igb = 1,7 g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_koch/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) - gg_ice_F07_tmp(igb) = g_F07_p0(igb)+g_F07_p1(igb)*LOG(AR_tmp)+g_F07_p2(igb)*((LOG(AR_tmp))**2._r8) ! Eqn. 3.3 in Fu (2007) + gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * log(AR_tmp) + g_F07_p2(igb) * (log(AR_tmp) * log(AR_tmp)) ! Eqn. 3.3 in Fu (2007) enddo end select @@ -878,7 +880,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct480(bnd_idx),g_Cg_intp) call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct480(bnd_idx),gg_F07_intp) end select - g_ice_F07 = gg_F07_intp + (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) / 2._r8 ! Eq.2.2 in Fu (2007) + g_ice_F07 = gg_F07_intp + 0.5_r8 * (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) ! Eq.2.2 in Fu (2007) asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) endif @@ -886,12 +888,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo ! snow layer loop - - ! aerosol species 1 optical properties, hydrophilic BC - !ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) - !asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) - !ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) - ! aerosol species 2 optical properties, hydrophobic BC ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) asm_prm_aer_lcl(2) = asm_prm_bc2(bnd_idx) @@ -907,27 +903,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & asm_prm_aer_lcl(4) = asm_prm_oc2(bnd_idx) ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) - ! aerosol species 5 optical properties, dust size1 - !ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) - !asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) - !ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) - - ! aerosol species 6 optical properties, dust size2 - !ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) - !asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) - !ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) - - ! aerosol species 7 optical properties, dust size3 - !ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) - !asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) - !ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) - - ! aerosol species 8 optical properties, dust size4 - !ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) - !asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) - !ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) - - ! 1. snow and aerosol layer column mass (L_snw, L_aer [kg/m^2]) ! 2. optical Depths (tau_snw, tau_aer) ! 3. weighted Mie properties (tau, omega, g) @@ -983,20 +958,19 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ( (mss_cnc_aer_lcl(i,1)*1.0E9_r8*1.7_r8/den_bc + bcint_d2(ibb)) **bcint_d1(ibb) ) ! adjust enhancment factor for BC effective size from 0.1um to Re_bc (He et al. 2018 GRL Eqs.1a,1b) if (ibb < 3) then ! near-UV - bcint_dd = (Re_bc/0.05_r8)**bcint_m(1) - bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(1) - bcint_f = (Re_bc/0.1_r8)**bcint_n(1) - endif - if ( (ibb >= 3) .and. (ibb <= 11) ) then ! visible - bcint_dd = (Re_bc/0.05_r8)**bcint_m(2) - bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(2) - bcint_f = (Re_bc/0.1_r8)**bcint_n(2) - endif - if ( ibb > 11 ) then ! NIR - bcint_dd = (Re_bc/0.05_r8)**bcint_m(3) - bcint_dd2 = (0.1_r8/0.05_r8)**bcint_m(3) - bcint_f = (Re_bc/0.1_r8)**bcint_n(3) + bcint_m_tmp = bcint_m(1) + bcint_n_tmp = bcint_n(1) + else if (ibb >= 3 .and. ibb <= 11) then ! visible + bcint_m_tmp = bcint_m(2) + bcint_n_tmp = bcint_n(2) + else ! ibb > 11, NIR + bcint_m_tmp = bcint_m(3) + bcint_n_tmp = bcint_n(3) endif + bcint_dd = (Re_bc * 20.0_r8)**bcint_m_tmp + bcint_dd2 = (0.1_r8 * 20.0_r8)**bcint_m_tmp + bcint_f = (Re_bc * 10.0_r8)**bcint_n_tmp + enh_omg_bcint_tmp2(ibb)=LOG10(max(1._r8,bcint_dd*((enh_omg_bcint_tmp(ibb)/bcint_dd2)**bcint_f))) enddo ! piecewise linear interpolate into targeted SNICAR bands in a logscale space @@ -1069,8 +1043,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & if (DELTA == 1) then do i=snl_top,snl_btm,1 g_star(i) = g(i)/(1+g(i)) - omega_star(i) = ((1-(g(i)**2))*omega(i)) / (1-(omega(i)*(g(i)**2))) - tau_star(i) = (1-(omega(i)*(g(i)**2)))*tau(i) + omega_star(i) = (1._r8 - g(i) * g(i)) * omega(i) / (1._r8 - omega(i) * (g(i) * g(i))) + tau_star(i) = (1._r8 - omega(i) * (g(i) * g(i))) * tau(i) enddo else do i=snl_top,snl_btm,1 @@ -1134,7 +1108,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! first calculation of rdif, tdif using Delta-Eddington formulas ! Eq.: Briegleb 1992; alpha and gamma for direct radiation - rdif_a(i) = (ue**2-c1)*(c1/extins - extins)/ne + rdif_a(i) = (ue * ue - c1) * (c1 / extins - extins) / ne tdif_a(i) = c4*ue/ne ! evaluate rdir,tdir for direct beam @@ -1344,9 +1318,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & !Underflow check (we've already tripped the error condition above) do i=snl_top,1,1 - if (flx_abs_lcl(i,bnd_idx) < 0._r8) then - flx_abs_lcl(i,bnd_idx) = 0._r8 - endif + flx_abs_lcl(i,bnd_idx) = max(0._r8, flx_abs_lcl(i,bnd_idx)) enddo F_abs_sum = 0._r8 @@ -1472,8 +1444,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! solar zenith angle parameterization ! calculate the scaling factor for NIR direct albedo if SZA>75 degree if ((mu_not < mu_75) .and. (flg_slr_in == 1)) then - sza_c1 = sza_a0 + sza_a1 * mu_not + sza_a2 * mu_not**2 - sza_c0 = sza_b0 + sza_b1 * mu_not + sza_b2 * mu_not**2 + sza_c1 = sza_a0 + sza_a1 * mu_not + sza_a2 * (mu_not * mu_not) + sza_c0 = sza_b0 + sza_b1 * mu_not + sza_b2 * (mu_not * mu_not) sza_factor = sza_c1 * (log10(snw_rds_lcl(snl_top) * c1) - c6) + sza_c0 flx_sza_adjust = albout(c_idx,2) * (sza_factor-c1) * sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) albout(c_idx,2) = albout(c_idx,2) * sza_factor @@ -1703,7 +1675,7 @@ subroutine SnowAge_grain(bounds, & !dr_wet = 1E6_r8*(dtime*(C1_liq_Brun89 + C2_liq_Brun89*(frc_liq**(3))) / (4*SHR_CONST_PI*(snw_rds(c_idx,i)/1E6)**(2))) !simplified, units of microns: dr_wet = 1E18_r8*(dtime*(params_inst%C2_liq_Brun89*(frc_liq**(3))) / & - (4*SHR_CONST_PI*snw_rds(c_idx,i)**(2))) + (4._r8 * SHR_CONST_PI * (snw_rds(c_idx,i) * snw_rds(c_idx,i)))) dr = dr + dr_wet @@ -1757,13 +1729,8 @@ subroutine SnowAge_grain(bounds, & !********** 5. CHECK BOUNDARIES *********** ! ! boundary check - if (snw_rds(c_idx,i) < snw_rds_min) then - snw_rds(c_idx,i) = snw_rds_min - endif - - if (snw_rds(c_idx,i) > snw_rds_max) then - snw_rds(c_idx,i) = snw_rds_max - end if + snw_rds(c_idx,i) = max(snw_rds(c_idx,i), snw_rds_min) + snw_rds(c_idx,i) = min(snw_rds(c_idx,i), snw_rds_max) ! set top layer variables for history files if (i == snl_top) then From 5ddaa345926a1ff1d29967a6984b1ed96fb37ee8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 8 Aug 2023 18:49:34 -0600 Subject: [PATCH 1317/2067] Correct comments that label hydrophilic/phobic OC and BC --- src/biogeophys/SnowSnicarMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 260098b784..fedd4292e0 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -93,7 +93,7 @@ module SnowSnicarMod real(r8), pointer :: asm_prm_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) real(r8), pointer :: ext_cff_mss_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) - ! hydrophiliic BC + ! hydrophilic BC real(r8), pointer :: ss_alb_bc1(:) !(numrad_snw) real(r8), pointer :: asm_prm_bc1(:) !(numrad_snw) real(r8), pointer :: ext_cff_mss_bc1(:) !(numrad_snw) @@ -103,12 +103,12 @@ module SnowSnicarMod real(r8), pointer :: asm_prm_bc2(:) !(numrad_snw) real(r8), pointer :: ext_cff_mss_bc2(:) !(numrad_snw) - ! hydrophobic OC + ! hydrophilic OC real(r8), pointer :: ss_alb_oc1(:) !(numrad_snw) real(r8), pointer :: asm_prm_oc1(:) !(numrad_snw) real(r8), pointer :: ext_cff_mss_oc1(:) !(numrad_snw) - ! hydrophilic OC + ! hydrophobic OC real(r8), pointer :: ss_alb_oc2(:) !(numrad_snw) real(r8), pointer :: asm_prm_oc2(:) !(numrad_snw) real(r8), pointer :: ext_cff_mss_oc2(:) !(numrad_snw) From 6a137045457b0995d8a0d6ade35c6b62cc232627 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 9 Aug 2023 09:05:42 -0700 Subject: [PATCH 1318/2067] updating expected failures with nvhpc tests --- cime_config/testdefs/ExpectedTestFails.xml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 76af28337f..174ebf9c58 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -43,6 +43,20 @@ + + + FAIL + #1733 + + + + + + FAIL + #1733 + + + From 782a80bf2295dc4c84a801a9349098044b2cf0ce Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 9 Aug 2023 09:18:44 -0700 Subject: [PATCH 1319/2067] updating ChangeLog --- doc/ChangeLog | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 3d80221564..e33201a33c 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -31,12 +31,20 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 +Bugs fixed or introduced +------------------------ +Issues updated: + + Updated #1733 -- nvhpc compiler tests failing on cheyenne + Notes of particular relevance for developers: --------------------------------------------- Caveats for developers (e.g., code that is duplicated that requires double maintenance): - Note that the fates patch and cohort types now use the `fates_` prefix instead of the `ed_` prefix. + - The expected failures list of tests has been expanded to include the remaining + nvhpc compiler tests on cheyenne with this update Testing summary: ---------------- From 73a6189c3ebb767f5cf55187b4f48460da883daf Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 9 Aug 2023 09:28:57 -0700 Subject: [PATCH 1320/2067] correcting changelog attribution --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index e33201a33c..9f3fef88ef 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,6 +1,6 @@ =============================================================== Tag name: ctsm5.1.dev133 -Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049) +Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) Date: Tue Aug 8 13:30:00 PM MDT 2023 One-line Summary: FATES API update to facilitate fates refactor From 8e65ee1fa220684cf888a251f0380bc7d28c8f4e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 3 Aug 2023 14:29:58 -0600 Subject: [PATCH 1321/2067] Correct bug in calculation of ratio_k1 in SoilBiogeochemNitrifDenitrif(). --- .../SoilBiogeochemNitrifDenitrifMod.F90 | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 9b249a5d0f..05c004902e 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -168,6 +168,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & real(r8) :: mu, sigma real(r8) :: t real(r8) :: pH(bounds%begc:bounds%endc) + real(r8) :: D0 ! temperature dependence of gaseous diffusion coefficients !debug-- put these type structure for outing to hist files real(r8) :: co2diff_con(2) ! diffusion constants for CO2 real(r8) :: eps @@ -232,7 +233,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & fmax_denit_carbonsubstrate_vr => soilbiogeochem_nitrogenflux_inst%fmax_denit_carbonsubstrate_vr_col , & ! Output: [real(r8) (:,:) ] fmax_denit_nitrate_vr => soilbiogeochem_nitrogenflux_inst%fmax_denit_nitrate_vr_col , & ! Output: [real(r8) (:,:) ] f_denit_base_vr => soilbiogeochem_nitrogenflux_inst%f_denit_base_vr_col , & ! Output: [real(r8) (:,:) ] - diffus => soilbiogeochem_nitrogenflux_inst%diffus_col , & ! Output: [real(r8) (:,:) ] diffusivity (unitless fraction of total diffusivity) + diffus => soilbiogeochem_nitrogenflux_inst%diffus_col , & ! Output: [real(r8) (:,:) ] diffusivity (m2/s) ratio_k1 => soilbiogeochem_nitrogenflux_inst%ratio_k1_col , & ! Output: [real(r8) (:,:) ] ratio_no3_co2 => soilbiogeochem_nitrogenflux_inst%ratio_no3_co2_col , & ! Output: [real(r8) (:,:) ] soil_co2_prod => soilbiogeochem_nitrogenflux_inst%soil_co2_prod_col , & ! Output: [real(r8) (:,:) ] (ug C / g soil / day) @@ -278,7 +279,10 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & else om_frac = 1._r8 end if - diffus (c,j) = (d_con_g(2,1) + d_con_g(2,2)*t_soisno(c,j)) * 1.e-4_r8 * & + + ! First, get diffusivity as a unitless constant, which is what's needed to + ! calculate ratio_k1 below. + diffus (c,j) = & (om_frac * eps**(10._r8/3._r8) / watsat(c,j)**2 + & (1._r8-om_frac) * eps**2 * f_a**(3._r8 / bsw(c,j)) ) @@ -376,6 +380,15 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! diffusivity constant (figure 6b) ratio_k1(c,j) = max(1.7_r8, 38.4_r8 - 350._r8 * diffus(c,j)) + ! Del Grosso et al. (2000) have diffus (their D_FC, "a relative index of gas diffusivity + ! through soil assuming a water content of field capacity") as unitless, but diffus history + ! field wants m2/s. Here, we use the same theoretical construct as for methane diffusivity + ! to convert to m2/s: We multiply by the temperature-dependent free-air diffusion rate. + ! NOTE that the coefficients for oxygen are used here; it may be more appropriate to use + ! coefficients for the gases being dealt with in this subroutine. + D0 = (d_con_g(2,1) + d_con_g(2,2)*t_soisno(c,j)) * 1.e-4_r8 + diffus(c,j) = diffus(c,j) * D0 + ! ratio function (figure 7c) if ( soil_co2_prod(c,j) > 1.0e-9_r8 ) then ratio_no3_co2(c,j) = smin_no3_massdens_vr(c,j) / soil_co2_prod(c,j) From 23564da1b61060abdd7276cd7ec3277011aec9d5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 12:10:59 -0600 Subject: [PATCH 1322/2067] Correct units in a Tech Note table. --- doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 7c89f857e3..bd1cb6140e 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -426,7 +426,7 @@ molecular free-air diffusion coefficients (:math:`{D}_{0}` .. table:: Temperature dependence of aqueous and gaseous diffusion coefficients for CH\ :sub:`4` and O\ :sub:`2` +----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+ - | :math:`{D}_{0}` (m\ :sup:`2` s\ :sup:`-1`) | CH\ :sub:`4` | O\ :sub:`2` | + | :math:`{D}_{0}` (cm\ :sup:`2` s\ :sup:`-1`) | CH\ :sub:`4` | O\ :sub:`2` | +==========================================================+==========================================================+========================================================+ | Aqueous | 0.9798 + 0.02986\ *T* + 0.0004381\ *T*\ :sup:`2` | 1.172+ 0.03443\ *T* + 0.0005048\ *T*\ :sup:`2` | +----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+ From 5a7380490497edd5da99e8b42fd5a195ff1f46e6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 12:26:11 -0600 Subject: [PATCH 1323/2067] Corrected a variable in methane Tech Note. --- doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index bd1cb6140e..019062ddc8 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -173,7 +173,7 @@ anoxic microsites above the water table, we apply the Arah and Stephen \varphi =\frac{1}{1+\eta C_{O_{2} } } . -Here, :math:`\phi` is the factor by which production is inhibited +Here, :math:`\varphi` is the factor by which production is inhibited above the water table (compared to production as calculated in equation , :math:`C_{O_{2}}` (mol m\ :sup:`-3`) is the bulk soil oxygen concentration, and :math:`\eta` = 400 mol m\ :sup:`-3`. From b53cc417107e36e1cebacf5b657b285c2e71c775 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 13:33:03 -0600 Subject: [PATCH 1324/2067] Add *most* missing equation references in Tech Note methane. --- .../Methane/CLM50_Tech_Note_Methane.rst | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 019062ddc8..d15cfe7052 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -66,7 +66,7 @@ phases:\ :math:`R = \epsilon _{a} +K_{H} \epsilon _{w}`, with porosity, and partitioning coefficient for the species of interest, respectively, and :math:`C` represents CH\ :sub:`4` or O\ :sub:`2` concentration with respect to water volume (mol m\ :sup:`-3`). -An analogous version of equation is concurrently solved for +An analogous version of equation :eq:`24.1` is concurrently solved for O\ :sub:`2`, but with the following differences relative to CH\ :sub:`4`: *P* = *E* = 0 (i.e., no production or ebullition), and the oxidation sink includes the O\ :sub:`2` demanded by @@ -74,7 +74,7 @@ methanotrophs, heterotroph decomposers, nitrifiers, and autotrophic root respiration. As currently implemented, each gridcell contains an inundated and a -non-inundated fraction. Therefore, equation is solved four times for +non-inundated fraction. Therefore, equation :eq:`24.1` is solved four times for each gridcell and time step: in the inundated and non-inundated fractions, and for CH\ :sub:`4` and O\ :sub:`2`. If desired, the CH\ :sub:`4` and O\ :sub:`2` mass balance equation is @@ -175,7 +175,7 @@ anoxic microsites above the water table, we apply the Arah and Stephen Here, :math:`\varphi` is the factor by which production is inhibited above the water table (compared to production as calculated in equation -, :math:`C_{O_{2}}` (mol m\ :sup:`-3`) is the bulk soil oxygen +:eq:`24.2`, :math:`C_{O_{2}}` (mol m\ :sup:`-3`) is the bulk soil oxygen concentration, and :math:`\eta` = 400 mol m\ :sup:`-3`. The O\ :sub:`2` required to facilitate the vertically resolved @@ -457,8 +457,8 @@ measurements more closely in unsaturated peat soils: D_{e} =D_{0} \frac{\theta _{a} ^{{\raise0.7ex\hbox{$ 10 $}\!\mathord{\left/ {\vphantom {10 3}} \right. \kern-\nulldelimiterspace}\!\lower0.7ex\hbox{$ 3 $}} } }{\theta _{s} ^{2} } -In CLM, we applied equation for soils with zero organic matter content -and equation for soils with more than 130 kg m\ :sup:`-3` organic +In CLM, we applied equation :eq:`24.12` for soils with zero organic matter content +and equation :eq:`24.13` for soils with more than 130 kg m\ :sup:`-3` organic matter content. A linear interpolation between these two limits is applied for soils with SOM content below 130 kg m\ :sup:`-3`. For aqueous diffusion in the saturated part of the soil column, we applied @@ -518,10 +518,10 @@ a zero flux gradient at the bottom of the soil column. Crank-Nicholson Solution ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Equation is solved using a Crank-Nicholson solution +Equation :eq:`24.1` is solved using a Crank-Nicholson solution (:ref:`Press et al. 1992`), which combines fully explicit and implicit representations of the mass -balance. The fully explicit decomposition of equation can be written as +balance. The fully explicit decomposition of equation :eq:`24.1` can be written as .. math:: :label: 24.15 @@ -535,11 +535,11 @@ and :math:`S_{j}^{n}` is the net source at time step *n* and position *j*, i.e., :math:`S_{j}^{n} =P\left(j,n\right)-E\left(j,n\right)-A\left(j,n\right)-O\left(j,n\right)`. The diffusivity coefficients are calculated as harmonic means of values -from the adjacent cells. Equation is solved for gaseous and aqueous +from the adjacent cells. Equation :eq:`24.15` is solved for gaseous and aqueous concentrations above and below the water table, respectively. The *R* term ensure the total mass balance in both phases is properly accounted for. An analogous relationship can be generated for the fully implicit -case by replacing *n* by *n+1* on the *C* and *S* terms of equation . +case by replacing *n* by *n+1* on the *C* and *S* terms of equation :eq:`24.15`. Using an average of the fully implicit and fully explicit relationships gives: @@ -548,14 +548,14 @@ gives: \begin{array}{l} {-\frac{1}{2\Delta x_{j} } \frac{D_{m1}^{} }{\Delta x_{m1}^{} } C_{j-1}^{n+1} +\left[\frac{R_{j}^{n+1} }{\Delta t} +\frac{1}{2\Delta x_{j} } \left(\frac{D_{p1}^{} }{\Delta x_{p1}^{} } +\frac{D_{m1}^{} }{\Delta x_{m1}^{} } \right)\right]C_{j}^{n+1} -\frac{1}{2\Delta x_{j} } \frac{D_{p1}^{} }{\Delta x_{p1}^{} } C_{j+1}^{n+1} =} \\ {\frac{R_{j}^{n} }{\Delta t} +\frac{1}{2\Delta x_{j} } \left[\frac{D_{p1}^{} }{\Delta x_{p1}^{} } \left(C_{j+1}^{n} -C_{j}^{n} \right)-\frac{D_{m1}^{} }{\Delta x_{m1}^{} } \left(C_{j}^{n} -C_{j-1}^{n} \right)\right]+\frac{1}{2} \left[S_{j}^{n} +S_{j}^{n+1} \right]} \end{array}, -Equation is solved with a standard tridiagonal solver, i.e.: +Equation :eq:`24.16` is solved with a standard tridiagonal solver, i.e.: .. math:: :label: 24.17 aC_{j-1}^{n+1} +bC_{j}^{n+1} +cC_{j+1}^{n+1} =r, -with coefficients specified in equation . +with coefficients specified in equation :eq:`24.16`. Two methane balance checks are performed at each timestep to insure that the diffusion solution and the time-varying aggregation over inundated From 388979fb1b5c272a822b2d2000354c20a69aac07 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 13:33:50 -0600 Subject: [PATCH 1325/2067] Correct superscript syntax in Tech Note methane. --- .../tech_note/Methane/CLM50_Tech_Note_Methane.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index d15cfe7052..71f031d012 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -286,12 +286,12 @@ The diffusive transport through aerenchyma (*A*, mol m\ :sup:`-2` s\ :sup:`-1`) A=\frac{C\left(z\right)-C_{a} }{{\raise0.7ex\hbox{$ r_{L} z $}\!\mathord{\left/ {\vphantom {r_{L} z D}} \right. \kern-\nulldelimiterspace}\!\lower0.7ex\hbox{$ D $}} +r_{a} } pT\rho _{r} , -where *D* is the free-air gas diffusion coefficient (m:sup:`2` s\ :sup:`-1`); *C(z)* (mol m\ :sup:`-3`) is the gaseous +where *D* is the free-air gas diffusion coefficient (m\ :sup:`2` s\ :sup:`-1`); *C(z)* (mol m\ :sup:`-3`) is the gaseous concentration at depth *z* (m); :math:`r_{L}` is the ratio of root length to depth; *p* is the porosity (-); *T* is specific aerenchyma -area (m:sup:`2` m\ :sup:`-2`); :math:`{r}_{a}` is the +area (m\ :sup:`2` m\ :sup:`-2`); :math:`{r}_{a}` is the aerodynamic resistance between the surface and the atmospheric reference -height (s m:sup:`-1`); and :math:`\rho _{r}` is the rooting +height (s m\ :sup:`-1`); and :math:`\rho _{r}` is the rooting density as a function of depth (-). The gaseous concentration is calculated with Henry’s law as described in equation . @@ -416,7 +416,7 @@ Aqueous and Gaseous Diffusion For gaseous diffusion, we adopted the temperature dependence of molecular free-air diffusion coefficients (:math:`{D}_{0}` -(m:sup:`2` s\ :sup:`-1`)) as described by +(m\ :sup:`2` s\ :sup:`-1`)) as described by :ref:`Lerman (1979) ` and applied by :ref:`Wania et al. (2010)` (:numref:`Table Temperature dependence of aqueous and gaseous diffusion`). @@ -437,7 +437,7 @@ Gaseous diffusivity in soils also depends on the molecular diffusivity, soil structure, porosity, and organic matter content. :ref:`Moldrup et al. (2003)`, using observations across a range of unsaturated mineral soils, showed that the relationship between -effective diffusivity (:math:`D_{e}` (m:sup:`2` s\ :sup:`-1`)) and soil +effective diffusivity (:math:`D_{e}` (m\ :sup:`2` s\ :sup:`-1`)) and soil properties can be represented as: .. math:: From c4a1dae640ce63cdb88daa2c1ca979157009900f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 13:42:36 -0600 Subject: [PATCH 1326/2067] Added missing citation links in Tech Note methane. --- doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 71f031d012..d90531c7e9 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -259,8 +259,8 @@ aqueous CH\ :sub:`4` concentration, and *p* is pressure. The local pressure is calculated as the sum of the ambient pressure, water pressure down to the local depth, and pressure from surface ponding (if applicable). When the CH\ :sub:`4` partial pressure -exceeds 15% of the local pressure (Baird et al. 2004; Strack et al. -2006; Wania et al. 2010), bubbling occurs to remove CH\ :sub:`4` +exceeds 15% of the local pressure (:ref:`Baird et al. 2004`; :ref:`Strack et al. +2006`; :ref:`Wania et al. 2010`), bubbling occurs to remove CH\ :sub:`4` to below this value, modified by the fraction of CH\ :sub:`4` in the bubbles [taken as 57%; (:ref:`Kellner et al. 2006`; :ref:`Wania et al. 2010`)]. @@ -519,7 +519,7 @@ Crank-Nicholson Solution ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Equation :eq:`24.1` is solved using a Crank-Nicholson solution -(:ref:`Press et al. 1992`), +(:ref:`Press et al., 1992`), which combines fully explicit and implicit representations of the mass balance. The fully explicit decomposition of equation :eq:`24.1` can be written as @@ -599,7 +599,7 @@ Inundated Fraction Prediction ---------------------------------- A simplified dynamic representation of spatial inundation -based on recent work by :ref:`Prigent et al. (2007)` is used. Prigent et al. (2007) described a +based on recent work by :ref:`Prigent et al. (2007)` is used. :ref:`Prigent et al. (2007)` described a multi-satellite approach to estimate the global monthly inundated fraction (:math:`{F}_{i}`) over an equal area grid (0.25 :math:`\circ` \ :math:`\times`\ 0.25\ :math:`\circ` at the equator) From f2e6c508ecabeed2920f79e9e0b91768c4b3efc6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Aug 2023 16:05:38 -0600 Subject: [PATCH 1327/2067] evenly_split_cropland in SinglePointCase now only affects crop distribution. --- python/ctsm/site_and_regional/single_point_case.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/python/ctsm/site_and_regional/single_point_case.py b/python/ctsm/site_and_regional/single_point_case.py index 59889279ba..456bebee91 100644 --- a/python/ctsm/site_and_regional/single_point_case.py +++ b/python/ctsm/site_and_regional/single_point_case.py @@ -442,11 +442,6 @@ def modify_surfdata_atpoint(self, f_orig): f_mod["PCT_NATVEG"] = f_mod["PCT_NATVEG"] / tot_pct * 100 if self.evenly_split_cropland: - f_mod["PCT_LAKE"][:, :] = 0.0 - f_mod["PCT_WETLAND"][:, :] = 0.0 - f_mod["PCT_URBAN"][:, :, :] = 0.0 - f_mod["PCT_GLACIER"][:, :] = 0.0 - f_mod["PCT_NAT_PFT"][:, :, :] = 0.0 f_mod["PCT_CFT"][:, :, :] = 100.0 / f_mod["PCT_CFT"].shape[2] else: From 53eb94f48c783e1a30bce14c3f277bdb4dcce92c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Aug 2023 16:07:39 -0600 Subject: [PATCH 1328/2067] Removed duplicate checks of PCT_LAKE in test_sys_fsurdat_modifier.py. --- python/ctsm/test/test_sys_fsurdat_modifier.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index e3b26e1059..6234ef1e45 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -215,7 +215,6 @@ def test_opt_sections(self): np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, pct_urban) np.testing.assert_array_equal(fsurdat_out_data.LAKEDEPTH, one0d * 200.0) @@ -260,7 +259,6 @@ def test_evenly_split_cropland(self): np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, hundred0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, zero_urban) np.testing.assert_array_equal(fsurdat_out_data.PCT_CFT, pct_cft) From 5b604ec8886e9968c64998a7ad00567bf76a18a0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Aug 2023 16:44:20 -0600 Subject: [PATCH 1329/2067] Allow evenly_split_cropland True with dom_pft if the latter isn't a crop. --- python/ctsm/modify_input_files/fsurdat_modifier.py | 4 ++-- python/ctsm/test/test_unit_fsurdat_modifier.py | 7 ++++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index e8a75bfb4c..eedafeecbb 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -441,8 +441,8 @@ def read_cfg_option_control( file_path=cfg_path, convert_to_type=bool, ) - if evenly_split_cropland and dom_pft: - abort("dom_pft must be UNSET if evenly_split_cropland is True; pick one or the other") + if evenly_split_cropland and dom_pft and dom_pft > int(max(modify_fsurdat.file.natpft.values)): + abort("dom_pft must not be set to a crop PFT when evenly_split_cropland is True") if process_subgrid and idealized: abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") diff --git a/python/ctsm/test/test_unit_fsurdat_modifier.py b/python/ctsm/test/test_unit_fsurdat_modifier.py index 32892e9f1d..166924903b 100755 --- a/python/ctsm/test/test_unit_fsurdat_modifier.py +++ b/python/ctsm/test/test_unit_fsurdat_modifier.py @@ -96,13 +96,14 @@ def test_subgrid_and_idealized_fails(self): read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) def test_dompft_and_splitcropland_fails(self): - """test that dompft and evenly_split_cropland fails gracefully""" + """test that setting dompft crop with evenly_split_cropland True fails gracefully""" section = "modify_fsurdat_basic_options" - self.config.set(section, "dom_pft", "1") + crop_pft = max(self.modify_fsurdat.file.natpft.values) + 1 + self.config.set(section, "dom_pft", str(crop_pft)) self.config.set(section, "evenly_split_cropland", "True") with self.assertRaisesRegex( SystemExit, - "dom_pft must be UNSET if evenly_split_cropland is True; pick one or the other", + "dom_pft must not be set to a crop PFT when evenly_split_cropland is True", ): read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) From dd97f5d5fdbd6668e0860ee6537d2728858cc443 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Aug 2023 17:09:16 -0600 Subject: [PATCH 1330/2067] Dynamically generate .cfg file for test_evenly_split_cropland(). --- python/ctsm/test/test_sys_fsurdat_modifier.py | 52 +++++++++---------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 6234ef1e45..788b963196 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -226,41 +226,24 @@ def test_evenly_split_cropland(self): """ Test that evenly splitting cropland works """ - self._cfg_file_path = os.path.join( - path_to_ctsm_root(), - "python", - "ctsm", - "crop_calendars", - "modify_fsurdat_allcropseverywhere.cfg", - ) - infile_basename_noext = "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214" - outfile = os.path.join( - self._tempdir, - infile_basename_noext + "_output_allcropseverywhere.nc", - ) + self._create_config_file_evenlysplitcrop() sys.argv = [ "fsurdat_modifier", self._cfg_file_path, - "-i", - os.path.join(self._testinputs_path, infile_basename_noext + ".nc"), - "-o", - outfile, ] parser = fsurdat_modifier_arg_process() fsurdat_modifier(parser) # Read the resultant output file and make sure the fields are changed as expected - fsurdat_out_data = xr.open_dataset(outfile) - zero0d = np.zeros((5, 5)) - hundred0d = np.full((5, 5), 100.0) - zero_urban = np.zeros((3, 5, 5)) + fsurdat_in_data = xr.open_dataset(self._fsurdat_in) + fsurdat_out_data = xr.open_dataset(self._fsurdat_out) Ncrops = fsurdat_out_data.dims["cft"] pct_cft = np.full((Ncrops, 5, 5), 100 / Ncrops) - np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, hundred0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) - np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, zero_urban) + np.testing.assert_array_equal(fsurdat_in_data.PCT_NATVEG, fsurdat_out_data.PCT_NATVEG) + np.testing.assert_array_equal(fsurdat_in_data.PCT_CROP, fsurdat_out_data.PCT_CROP) + np.testing.assert_array_equal(fsurdat_in_data.PCT_LAKE, fsurdat_out_data.PCT_LAKE) + np.testing.assert_array_equal(fsurdat_in_data.PCT_WETLAND, fsurdat_out_data.PCT_WETLAND) + np.testing.assert_array_equal(fsurdat_in_data.PCT_GLACIER, fsurdat_out_data.PCT_GLACIER) + np.testing.assert_array_equal(fsurdat_in_data.PCT_URBAN, fsurdat_out_data.PCT_URBAN) np.testing.assert_array_equal(fsurdat_out_data.PCT_CFT, pct_cft) def test_1x1_mexicocity(self): @@ -447,6 +430,23 @@ def _create_config_file_minimal(self): line = f"fsurdat_out = {self._fsurdat_out}" cfg_out.write(line) + def _create_config_file_evenlysplitcrop(self): + """ + Open the new and the template .cfg files + Loop line by line through the template .cfg file + When string matches, replace that line's content + """ + with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: + with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: + for line in cfg_in: + if re.match(r" *evenly_split_cropland *=", line): + line = f"evenly_split_cropland = True" + elif re.match(r" *fsurdat_in *=", line): + line = f"fsurdat_in = {self._fsurdat_in}" + elif re.match(r" *fsurdat_out *=", line): + line = f"fsurdat_out = {self._fsurdat_out}" + cfg_out.write(line) + def _create_config_file_crop(self): """ Open the new and the template .cfg files From 852206cb0d744ddb9b6c0c3b5b995a93f1f16482 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 8 Aug 2023 17:10:58 -0600 Subject: [PATCH 1331/2067] Improve robustness of test_evenly_split_cropland() to new fsurdat_in. --- python/ctsm/test/test_sys_fsurdat_modifier.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index 788b963196..f83aff0b64 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -237,7 +237,7 @@ def test_evenly_split_cropland(self): fsurdat_in_data = xr.open_dataset(self._fsurdat_in) fsurdat_out_data = xr.open_dataset(self._fsurdat_out) Ncrops = fsurdat_out_data.dims["cft"] - pct_cft = np.full((Ncrops, 5, 5), 100 / Ncrops) + pct_cft = np.full_like(fsurdat_out_data.PCT_CFT, 100 / Ncrops) np.testing.assert_array_equal(fsurdat_in_data.PCT_NATVEG, fsurdat_out_data.PCT_NATVEG) np.testing.assert_array_equal(fsurdat_in_data.PCT_CROP, fsurdat_out_data.PCT_CROP) np.testing.assert_array_equal(fsurdat_in_data.PCT_LAKE, fsurdat_out_data.PCT_LAKE) From 42226ebc250d8b5b3a0d317e1de3f0ef52386648 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 09:22:17 -0600 Subject: [PATCH 1332/2067] Dynamically generate .cfg file for RXCROPMATURITY test. --- cime_config/SystemTests/rxcropmaturity.py | 50 +++++++++++++++++++---- 1 file changed, 42 insertions(+), 8 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 9eb4bdb17d..bfa8ead151 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -267,17 +267,16 @@ def _run_fsurdat_modifier(self): "modify_input_files", "fsurdat_modifier", ) - cfg_path = os.path.join( - self._ctsm_root, - "python", - "ctsm", - "crop_calendars", + + # Create configuration file for fsurdat_modifier + self._cfg_path = os.path.join( + self._path_gddgen, "modify_fsurdat_allcropseverywhere.cfg", ) + self._create_config_file_evenlysplitcrop() + command = ( - f"python3 {tool_path} {cfg_path} " - + f"-i {self._fsurdat_in} " - + f"-o {self._fsurdat_out}" + f"python3 {tool_path} {self._cfg_path} " ) stu.run_python_script( self._get_caseroot(), @@ -297,6 +296,41 @@ def _run_fsurdat_modifier(self): ] ) + def _create_config_file_evenlysplitcrop(self): + """ + Open the new and the template .cfg files + Loop line by line through the template .cfg file + When string matches, replace that line's content + """ + cfg_template_path = os.path.join( + self._ctsm_root, "tools/modify_input_files/modify_fsurdat_template.cfg" + ) + + with open(self._cfg_path, "w", encoding="utf-8") as cfg_out: + # Copy template, replacing some lines + with open(cfg_template_path, "r", encoding="utf-8") as cfg_in: + for line in cfg_in: + if re.match(r" *evenly_split_cropland *=", line): + line = f"evenly_split_cropland = True" + elif re.match(r" *fsurdat_in *=", line): + line = f"fsurdat_in = {self._fsurdat_in}" + elif re.match(r" *fsurdat_out *=", line): + line = f"fsurdat_out = {self._fsurdat_out}" + elif re.match(r" *process_subgrid_section *=", line): + line = f"process_subgrid_section = True" + cfg_out.write(line) + + # Add new lines + cfg_out.write("\n") + cfg_out.write("[modify_fsurdat_subgrid_fractions]\n") + cfg_out.write("PCT_CROP = 100.0\n") + cfg_out.write("PCT_NATVEG = 0.0\n") + cfg_out.write("PCT_GLACIER = 0.0\n") + cfg_out.write("PCT_WETLAND = 0.0\n") + cfg_out.write("PCT_LAKE = 0.0\n") + cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") + + def _run_check_rxboth_run(self): output_dir = os.path.join(self._get_caseroot(), "run") From 528e5c9de57a8e1224343be97448381ee12f2e7b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 14:04:29 -0600 Subject: [PATCH 1333/2067] Delete now-unused modify_fsurdat_allcropseverywhere.cfg. --- .../modify_fsurdat_allcropseverywhere.cfg | 84 ------------------- 1 file changed, 84 deletions(-) delete mode 100644 python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg diff --git a/python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg b/python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg deleted file mode 100644 index b7c46a6c71..0000000000 --- a/python/ctsm/crop_calendars/modify_fsurdat_allcropseverywhere.cfg +++ /dev/null @@ -1,84 +0,0 @@ -[modify_fsurdat_basic_options] - -# ------------------------------------------------------------------------ -# .cfg file with inputs for fsurdat_modifier. -# -# This configuration file, when used in fsurdat_modifier, will create a -# version of the input fsurdat file that is 100% cropland with area evenly -# split among all crop PFTs. -# ------------------------------------------------------------------------ - -### Skipping input/output file paths, as these should be specified in -### command-line call of fsurdat_modifier. -# Path and name of input surface dataset (str) -### fsurdat_in = -# Path and name of output surface dataset (str) -### fsurdat_out = - -# We want all existing values in fsurdat to persist except the ones -# pertaining to land unit and PFT fractions. Thus, we set idealized = False. -idealized = False - -# Process the optional section that handles modifying subgrid fractions -process_subgrid_section = True - -# Process the optional section that handles modifying an arbitrary list of variables -process_var_list_section = False - -# Boundaries of user-defined rectangle to apply changes (float) -# If lat_1 > lat_2, the code creates two rectangles, one in the north and -# one in the south. -# If lon_1 > lon_2, the rectangle wraps around the 0-degree meridian. -# Alternatively, user may specify a custom area in a .nc landmask_file -# below. If set, this will override the lat/lon settings. -# ----------------------------------- -# southernmost latitude for rectangle -lnd_lat_1 = -90 -# northernmost latitude for rectangle -lnd_lat_2 = 90 -# westernmost longitude for rectangle -lnd_lon_1 = 0 -# easternmost longitude for rectangle -lnd_lon_2 = 360 -# User-defined mask in a file, as alternative to setting lat/lon values. -# If set, lat_dimname and lon_dimname should likely also be set. IMPORTANT: -# - lat_dimname and lon_dimname may be left UNSET if they match the expected -# default values 'lsmlat' and 'lsmlon' -landmask_file = UNSET -lat_dimname = UNSET -lon_dimname = UNSET - -# PFT/CFT to be set to 100% according to user-defined mask. -# We *could* evenly split cropland using dom_pft, but using -# evenly_split_cropland (below) is more robust. Thus, we -# leave dom_pft UNSET. -dom_pft = UNSET - -# Evenly split each gridcell's cropland among all crop types (CFTs). -evenly_split_cropland = True - -# UNSET with idealized False means leave these values unchanged. -lai = UNSET -sai = UNSET -hgt_top = UNSET -hgt_bot = UNSET -soil_color = UNSET -std_elev = UNSET -max_sat_area = UNSET - -# We manually exclude non-vegetation land units (along with NATVEG) below, so set -# include_nonveg to True. -include_nonveg = True - - -# Section for subgrid_fractions -[modify_fsurdat_subgrid_fractions] -# If subgrid_fractions = True this section will be enabled - -# NOTE: PCT_URBAN must be a list of three floats that sum to the total urban area -PCT_URBAN = 0.0 0.0 0.0 -PCT_CROP = 100.0 -PCT_NATVEG= 0.0 -PCT_GLACIER= 0.0 -PCT_WETLAND= 0.0 -PCT_LAKE = 0.0 \ No newline at end of file From 4a8adffd92a984151d0c0cf7d0e0e782b2e4ad3d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 9 Aug 2023 16:59:56 -0600 Subject: [PATCH 1334/2067] Bugfix to check that tillage is off when use_crop false. --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 1450cb9d59..1c0fcb8e06 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2194,7 +2194,7 @@ sub setup_logic_tillage { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); - if ( $tillage_mode ne "off" && not &value_is_true($nl->get_value('use_crop')) ) { + if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); } } From d47da2930c2027d14b6fe8476bc91c00fa05e51e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 9 Aug 2023 17:59:47 -0600 Subject: [PATCH 1335/2067] Consolidated fsnowoptics480 with fsnowoptics --- bld/CLMBuildNamelist.pm | 5 +++-- bld/namelist_files/namelist_defaults_ctsm.xml | 12 ++++++++---- bld/namelist_files/namelist_definition_ctsm.xml | 6 ------ src/biogeophys/SnowSnicarMod.F90 | 15 +++++---------- src/main/clm_varctl.F90 | 1 - src/main/controlMod.F90 | 8 +------- 6 files changed, 17 insertions(+), 30 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index e20b9ea6e8..d028f8af61 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2008,8 +2008,9 @@ sub setup_logic_snicar_methods { sub setup_logic_snow { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics480' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics' ); + my $numrad_snw = $nl->get_value('snicar_numrad_snw'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics', + 'snicar_numrad_snw' => $numrad_snw); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowaging' ); } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0b174b7591..3c05a675fb 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1541,9 +1541,14 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -lnd/clm2/snicardata/snicar_optics_480bnd_c012422.nc -lnd/clm2/snicardata/snicar_optics_5bnd_c013122.nc -lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc +lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc + +5 + + +lnd/clm2/snicardata/snicar_optics_5bnd_c013122.nc hexagonal_plate sphere @@ -1552,7 +1557,6 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. mid_latitude_winter sahara -5 .false. .false. .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index f15083d222..81f904a215 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -807,12 +807,6 @@ Full pathname of surface data file. SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name - -SNICAR (SNow, ICe, and Aerosol Radiative model) 480-band optical data file name - - - SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index fedd4292e0..f5c603d302 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1812,7 +1812,7 @@ end function FreshSnowRadius subroutine SnowOptics_init( ) use fileutils , only : getfil - use CLM_varctl , only : fsnowoptics, snicar_numrad_snw, fsnowoptics480 + use CLM_varctl , only : fsnowoptics, snicar_numrad_snw use CLM_varctl , only : snicar_solarspec, snicar_dust_optics use spmdMod , only : masterproc use ncdio_pio , only : file_desc_t, ncd_io, ncd_pio_openfile, ncd_pio_closefile @@ -1857,16 +1857,15 @@ subroutine SnowOptics_init( ) allocate(flx_wgt_dir(snicar_numrad_snw)) allocate(flx_wgt_dif(snicar_numrad_snw)) - if(masterproc) write(iulog,*) 'Attempting to read snow optical properties .....' + if (masterproc) write(iulog,*) 'Attempting to read snow optical properties...' + call getfil (fsnowoptics, locfn, 0) + call ncd_pio_openfile(ncid, locfn, 0) + if(masterproc) write(iulog,*) subname,trim(fsnowoptics) !--------------------- for 5-band data select case (snicar_numrad_snw) case (5) ! 5-band case - call getfil (fsnowoptics, locfn, 0) - call ncd_pio_openfile(ncid, locfn, 0) - if(masterproc) write(iulog,*) subname,trim(fsnowoptics) - select case (snicar_solarspec) ! mid-latitude winter spectrum case ('mid_latitude_winter') @@ -2366,10 +2365,6 @@ subroutine SnowOptics_init( ) !-------------------- for 480-band data case (480) - call getfil (fsnowoptics480, locfn, 0) - call ncd_pio_openfile(ncid, locfn, 0) - if(masterproc) write(iulog,*) subname,trim(fsnowoptics480) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing call ncd_io( 'ss_alb_bcphob', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_bcphob', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index cdf486eb8e..ec31d90132 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -113,7 +113,6 @@ module clm_varctl character(len=fname_len), public :: nrevsn = ' ' ! restart data file name for branch run character(len=fname_len), public :: fsnowoptics = ' ' ! snow optical properties file name character(len=fname_len), public :: fsnowaging = ' ' ! snow aging parameters file name - character(len=fname_len), public :: fsnowoptics480 = ' ' ! snow optical properties file name for 480 bands character(len=fname_len), public :: fatmlndfrc = ' ' ! lnd frac file on atm grid ! only needed for LILAC and MCT drivers diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 68edb706ff..0d2a8f0bfd 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -146,7 +146,7 @@ subroutine control_init(dtime) namelist /clm_inparm/ & fsurdat, & - paramfile, fsnowoptics, fsnowaging, fsnowoptics480 + paramfile, fsnowoptics, fsnowaging ! History, restart options @@ -662,7 +662,6 @@ subroutine control_spmd() call mpi_bcast (paramfile, len(paramfile) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fsnowoptics, len(fsnowoptics), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fsnowaging, len(fsnowaging), MPI_CHARACTER, 0, mpicom, ier) - call mpi_bcast (fsnowoptics480, len(fsnowoptics480), MPI_CHARACTER, 0, mpicom, ier) ! Irrigation call mpi_bcast(irrigate, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -987,11 +986,6 @@ subroutine control_print () else write(iulog,'(a)') ' snow aging parameters file = '//trim(fsnowaging) endif - if (fsnowoptics480 == ' ') then - write(iulog,*) ' SNICAR: snow optical properties (480-band) file NOT set' - else - write(iulog,*) ' SNICAR: snow optical properties (480-band) file = ',trim(fsnowoptics480) - endif write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw From 3897807aa7029258e27b23ea2415e066df1231d1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 9 Aug 2023 22:45:32 -0600 Subject: [PATCH 1336/2067] Update changelog --- doc/ChangeLog | 20 ++++++++++++-------- doc/ChangeSum | 2 +- 2 files changed, 13 insertions(+), 9 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 9f3fef88ef..e65560d5c3 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev133 Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) -Date: Tue Aug 8 13:30:00 PM MDT 2023 +Date: Wed Aug 9 22:44:46 MDT 2023 One-line Summary: FATES API update to facilitate fates refactor Purpose and description of changes @@ -11,6 +11,9 @@ This updates a number of FATES type names and module use statements which correspond with a refactoring effort that moves FATES patches and cohorts into their own respective modules. +With the FATES update is a minor science update, so there are +changes to answers for FATES. + This also incorporates a minor update to a more recent version of the ccs config external. @@ -51,6 +54,10 @@ Testing summary: [PASS means all tests PASS; OK means tests PASS other than expected fails.] + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): cheyenne ---- OK @@ -82,8 +89,9 @@ List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): Pull Requests that document the changes (include PR ids): (https://github.com/ESCOMP/ctsm/pull) - https://github.com/ESCOMP/CTSM/pull/2000 - https://github.com/NGEET/fates/pull/1024 + https://github.com/ESCOMP/CTSM/pull/2000 -- refactor + https://github.com/ESCOMP/CTSM/pull/2089 -- Change template update + https://github.com/NGEET/fates/pull/1024 -- FATES refactor =============================================================== =============================================================== @@ -179,13 +187,9 @@ Testing summary: cheyenne - PASS - tools-tests (test/tools) (if tools have been changed): - - cheyenne - - regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- OK + heyenne ---- OK izumi ------- OK any other testing (give details below): diff --git a/doc/ChangeSum b/doc/ChangeSum index 602817e440..a72e6235ae 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev133 glemieux 08/08/2023 FATES API update to facilitate fates refactor + ctsm5.1.dev133 glemieux 08/09/2023 FATES API update to facilitate fates refactor ctsm5.1.dev132 slevis 08/04/2023 Add parameterization to allow excess ice in soil and subsidence ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update From 0f1127721518d64c03e5109bfcde7ef21b11bd50 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 12:07:56 -0600 Subject: [PATCH 1337/2067] Clarified an if statement. --- python/ctsm/modify_input_files/fsurdat_modifier.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/python/ctsm/modify_input_files/fsurdat_modifier.py b/python/ctsm/modify_input_files/fsurdat_modifier.py index eedafeecbb..6d350171cc 100644 --- a/python/ctsm/modify_input_files/fsurdat_modifier.py +++ b/python/ctsm/modify_input_files/fsurdat_modifier.py @@ -441,7 +441,11 @@ def read_cfg_option_control( file_path=cfg_path, convert_to_type=bool, ) - if evenly_split_cropland and dom_pft and dom_pft > int(max(modify_fsurdat.file.natpft.values)): + if ( + evenly_split_cropland + and dom_pft is not None + and dom_pft > int(max(modify_fsurdat.file.natpft.values)) + ): abort("dom_pft must not be set to a crop PFT when evenly_split_cropland is True") if process_subgrid and idealized: abort("idealized AND process_subgrid_section can NOT both be on, pick one or the other") From 73895d6353b512f31487700459d47f932f94b8a9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 12:55:04 -0600 Subject: [PATCH 1338/2067] Resolved a pylint complaint. --- python/ctsm/test/test_sys_fsurdat_modifier.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/test/test_sys_fsurdat_modifier.py b/python/ctsm/test/test_sys_fsurdat_modifier.py index f83aff0b64..1a5045c14d 100755 --- a/python/ctsm/test/test_sys_fsurdat_modifier.py +++ b/python/ctsm/test/test_sys_fsurdat_modifier.py @@ -440,7 +440,7 @@ def _create_config_file_evenlysplitcrop(self): with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: for line in cfg_in: if re.match(r" *evenly_split_cropland *=", line): - line = f"evenly_split_cropland = True" + line = "evenly_split_cropland = True" elif re.match(r" *fsurdat_in *=", line): line = f"fsurdat_in = {self._fsurdat_in}" elif re.match(r" *fsurdat_out *=", line): From 7c920c6804369343b27c379ced09e1ad7bfe1469 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 10 Aug 2023 14:23:14 -0600 Subject: [PATCH 1339/2067] Moved a call to update a call to fates litter fluxes to be immediately before we fill the decomp source-sink pools --- src/biogeochem/CNNDynamicsMod.F90 | 9 +++++++-- src/utils/clmfates_interfaceMod.F90 | 29 +++++++++-------------------- 2 files changed, 16 insertions(+), 22 deletions(-) diff --git a/src/biogeochem/CNNDynamicsMod.F90 b/src/biogeochem/CNNDynamicsMod.F90 index f9698fb2ca..10c0f5ea38 100644 --- a/src/biogeochem/CNNDynamicsMod.F90 +++ b/src/biogeochem/CNNDynamicsMod.F90 @@ -239,7 +239,10 @@ subroutine CNNFixation(num_soilc, filter_soilc, & if(col%is_fates(c))then s = clm_fates%f2hmap(clump_index)%hsites(c) ! %ema_npp is Smoothed [gc/m2/yr] - npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp/(dayspyr*secspday) + !npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp/(dayspyr*secspday) + ! FATES N cycling is not yet active, so runs are supplemented anyway + ! this will be added when FATES N cycling is completed. + npp = 0._r8 else npp = col_lag_npp(c) end if @@ -259,7 +262,9 @@ subroutine CNNFixation(num_soilc, filter_soilc, & if(col%is_fates(c))then s = clm_fates%f2hmap(clump_index)%hsites(c) - npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp + !npp = clm_fates%fates(clump_index)%bc_out(s)%ema_npp + ! See above regarding FATES and N fixation + npp = 0._r8 else npp = cannsum_npp(c) end if diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index bf51b3cac5..c32c55d50a 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1182,10 +1182,18 @@ subroutine UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) associate(cf_soil => soilbiogeochem_carbonflux_inst) - cf_soil%decomp_cpools_sourcesink_col(c,:,:) = 0._r8 + ! This is zeroed in CNDriverNoLeaching -> soilbiogeochem_carbonflux_inst%SetValues() + ! Which is called prior to this call, which is later in the CNDriverNoLeaching() + ! routine. + ! cf_soil%decomp_cpools_sourcesink_col(c,:,:) = 0._r8 if ( .not. use_fates_sp ) then + + call FluxIntoLitterPools(this%fates(ci)%sites(s), & + this%fates(ci)%bc_in(s), & + this%fates(ci)%bc_out(s)) + ! (gC/m3/timestep) cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_met_lit) = & cf_soil%decomp_cpools_sourcesink_col(c,1:nlevdecomp,i_met_lit) + & @@ -1711,16 +1719,6 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s), & this%fates(nc)%bc_out(s) ) - ! This call sends internal fates variables into the - ! output boundary condition structures. Note: this is called - ! internally in fates dynamics as well. - call FluxIntoLitterPools(this%fates(nc)%sites(s), & - this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s)) - - call this%UpdateCLitterFluxes(soilbiogeochem_carbonflux_inst,nc,c) - call this%UpdateNLitterFluxes(soilbiogeochem_nitrogenflux_inst,nc,c) - end do if(use_fates_sp)then @@ -1945,15 +1943,6 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s), & this%fates(nc)%bc_out(s)) - ! This call sends internal fates variables into the - ! output boundary condition structures. Note: this is called - ! internally in fates dynamics as well. - call FluxIntoLitterPools(this%fates(nc)%sites(s), & - this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s)) - - !call UpdateCLitterFluxes(this,soilbiogeochem_carbonflux_inst,ci,c) - end do ! ------------------------------------------------------------------------ From 65506be6463fa713bbc56b7ecfc8b43431900474 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 14:29:34 -0600 Subject: [PATCH 1340/2067] Added caveat about diffus output where that field is set up. --- src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 index 839f69379a..3aecfb6b03 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 @@ -688,6 +688,8 @@ subroutine InitHistory(this, bounds) end if if (use_nitrif_denitrif) then + ! NOTE that the calculation for diffusivity here uses coefficients for oxygen. + ! It may be more appropriate to use coefficients for N(2)O instead. this%diffus_col(begc:endc,:) = spval call hist_addfld_decomp (fname='diffus', units='m^2/s', type2d='levdcmp', & avgflag='A', long_name='diffusivity', & From c126e2e2768a7e9c156aedcfce3b8fc7a964e43b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 14:29:51 -0600 Subject: [PATCH 1341/2067] Added a clarifying comment in master_list_nofates.rst. --- .../setting-up-and-running-a-case/master_list_nofates.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst index 776acc9833..7ce14e3a7b 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/master_list_nofates.rst @@ -1289,7 +1289,7 @@ CTSM History Fields 1274 anaerobic_frac anaerobic_frac m3/m3 F 1275 bsw clap and hornberger B unitless F 1276 currentPatch currentPatch coefficient for VOC calc non F -1277 diffus diffusivity m^2/s F +1277 diffus diffusivity (from nitrification-denitrification) m^2/s F 1278 fr_WFPS fr_WFPS fraction F 1279 n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F 1280 num_iter number of iterations unitless F From afbe2d62d76ae20702c453b1087c21d51ad15a3f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 10 Aug 2023 14:30:20 -0600 Subject: [PATCH 1342/2067] Add quotes to correct namelist_defaults_ctsm.xml --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 3c05a675fb..a5af2ec374 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1545,10 +1545,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 5 - -lnd/clm2/snicardata/snicar_optics_5bnd_c013122.nc +lnd/clm2/snicardata/snicar_optics_480bnd_c012422.nc +lnd/clm2/snicardata/snicar_optics_5bnd_c013122.nc hexagonal_plate sphere From 9808d1adfba6934ae9cc23f9bb46271b947bbba8 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 10 Aug 2023 15:27:50 -0600 Subject: [PATCH 1343/2067] Consolidate some repetitive code pertaining to wvl_ct --- src/biogeophys/SnowSnicarMod.F90 | 38 ++++++++++++++------------------ 1 file changed, 16 insertions(+), 22 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index f5c603d302..f287de2032 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -463,8 +463,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: g_F07_p1(1:7) real(r8) :: g_F07_p0(1:7) ! other temporary variables - real(r8) :: wvl_ct5(1:5) ! band center wavelength (um) for 5-band case - real(r8) :: wvl_ct480(1:480) ! band center wavelength (um) for 480-band case, computed below + real(r8), allocatable :: wvl_ct(:) ! band center wavelength (um) for 5 or 480-band case real(r8) :: diam_ice ! effective snow grain diameter (SSA-equivalent) unit: microns real(r8) :: fs_sphd ! shape factor for spheroid snow real(r8) :: fs_hex ! shape factor for reference hexagonal snow @@ -565,7 +564,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Table 3 of He et al 2017 JC g_wvl(1:8) = (/ 0.25_r8, 0.70_r8, 1.41_r8, 1.90_r8, & 2.50_r8, 3.50_r8, 4.00_r8, 5.00_r8 /) - g_wvl_ct(1:7) = g_wvl(2:8) / 2._r8 + g_wvl(1:7) / 2._r8 + g_wvl_ct(1:7) = g_wvl(2:8) * 0.5_r8 + g_wvl(1:7) * 0.5_r8 g_b0(1:7) = (/ 9.76029E-1_r8, 9.67798E-1_r8, 1.00111_r8, 1.00224_r8, & 9.64295E-1_r8, 9.97475E-1_r8, 9.97475E-1_r8 /) g_b1(1:7) = (/ 5.21042E-1_r8, 4.96181E-1_r8, 1.83711E-1_r8, 1.37082E-1_r8, & @@ -590,7 +589,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Eq. 8b & Table 4 in He et al., 2017 J. Climate (wavelength>1.2um, no BC-snow int mixing effect) bcint_wvl(1:17) = (/ 0.20_r8, 0.25_r8, 0.30_r8, 0.33_r8, 0.36_r8, 0.40_r8, 0.44_r8, 0.48_r8, & 0.52_r8, 0.57_r8, 0.64_r8, 0.69_r8, 0.75_r8, 0.78_r8, 0.87_r8, 1._r8, 1.2_r8 /) - bcint_wvl_ct(1:16) = bcint_wvl(2:17)/2._r8 + bcint_wvl(1:16)/2._r8 + bcint_wvl_ct(1:16) = bcint_wvl(2:17) * 0.5_r8 + bcint_wvl(1:16) * 0.5_r8 bcint_d0(1:16) = (/ 2.48045_r8 , 4.70305_r8 , 4.68619_r8 , 4.67369_r8 , 4.65040_r8 , & 2.40364_r8 , 7.95408E-1_r8, 2.92745E-1_r8, 8.63396E-2_r8, 2.76299E-2_r8, & 1.40864E-2_r8, 8.65705E-3_r8, 6.12971E-3_r8, 4.45697E-3_r8, 3.06648E-2_r8, & @@ -616,10 +615,15 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & dstint_a3(1:6) = (/ 9.9701E-1_r8, 9.9781E-1_r8, 9.9848E-1_r8, 1.0035_r8 , 1.0024_r8 , 1.0356_r8 /) ! SNICAR/CLM snow band center wavelength (um) - wvl_ct5(1:5) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band - do igb = 1,480 - wvl_ct480(igb) = 0.205_r8 + 0.01_r8 * (igb-1) ! 480-band - enddo + allocate(wvl_ct(snicar_numrad_snw)) + select case (snicar_numrad_snw) + case (5) + wvl_ct(:) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band + case (480) + do igb = 1, snicar_numrad_snw + wvl_ct(igb) = 0.205_r8 + 0.01_r8 * (igb - 1._r8) ! 480-band + enddo + end select ! Define constants pi = SHR_CONST_PI @@ -872,14 +876,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here ! use the piecewise linear interpolation subroutine created at the end of this module ! tests showed the piecewise linear interpolation has similar results as pchip interpolation - select case (snicar_numrad_snw) - case (5) - call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct5(bnd_idx),g_Cg_intp) - call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct5(bnd_idx),gg_F07_intp) - case (480) - call piecewise_linear_interp1d(7,g_wvl_ct,g_ice_Cg_tmp,wvl_ct480(bnd_idx),g_Cg_intp) - call piecewise_linear_interp1d(7,g_wvl_ct,gg_ice_F07_tmp,wvl_ct480(bnd_idx),gg_F07_intp) - end select + call piecewise_linear_interp1d(7, g_wvl_ct, g_ice_Cg_tmp, wvl_ct(bnd_idx), g_Cg_intp) + call piecewise_linear_interp1d(7, g_wvl_ct, gg_ice_F07_tmp, wvl_ct(bnd_idx), gg_F07_intp) g_ice_F07 = gg_F07_intp + 0.5_r8 * (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) ! Eq.2.2 in Fu (2007) asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) endif @@ -933,12 +931,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) ! Start BC/dust-snow internal mixing for wavelength<=1.2um - select case (snicar_numrad_snw) - case (5) - wvl_doint = wvl_ct5(bnd_idx) - case (480) - wvl_doint = wvl_ct480(bnd_idx) - end select + wvl_doint = wvl_ct(bnd_idx) + if (wvl_doint <= 1.2_r8) then ! BC-snow internal mixing applied to hydrophilic BC if activated From 5ad655a53f10dc4c9bd087902fc73d7b912d6d78 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 10 Aug 2023 15:52:07 -0600 Subject: [PATCH 1344/2067] Reduce repetitive code in 'Weight output NIR albedo' section --- src/biogeophys/SnowSnicarMod.F90 | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index f287de2032..1ac94ef552 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1384,27 +1384,24 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR albedo appropriately select case (snicar_numrad_snw) case (5) ! 5-band case + ! VIS band albout(c_idx,1) = albout_lcl(1) - flx_sum = 0._r8 - do bnd_idx= nir_bnd_bgn,nir_bnd_end - flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) - end do - albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) case (480) ! 480-band case ! average for VIS band - flx_sum = 0._r8 + flx_sum = 0._r8 do bnd_idx= 1, (nir_bnd_bgn-1) flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) end do albout(c_idx,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) - ! average for NIR band - flx_sum = 0._r8 - do bnd_idx= nir_bnd_bgn,nir_bnd_end - flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) - end do - albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end select + ! average for NIR band + flx_sum = 0._r8 + do bnd_idx = nir_bnd_bgn, nir_bnd_end + flx_sum = flx_sum + flx_wgt(bnd_idx) * albout_lcl(bnd_idx) + end do + albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately select case (snicar_numrad_snw) case (5) ! 5-band case From 40bcf1560bfa892bedcd4224074c6afbabda6adf Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 10 Aug 2023 16:10:40 -0600 Subject: [PATCH 1345/2067] Reduce repetitive code in 'Weight output NIR absorbed' section --- src/biogeophys/SnowSnicarMod.F90 | 27 ++++++++++++--------------- 1 file changed, 12 insertions(+), 15 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 1ac94ef552..6c271c013b 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1395,7 +1395,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & albout(c_idx,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) end select - ! average for NIR band + ! average for NIR band (5 or 480-band case) flx_sum = 0._r8 do bnd_idx = nir_bnd_bgn, nir_bnd_end flx_sum = flx_sum + flx_wgt(bnd_idx) * albout_lcl(bnd_idx) @@ -1405,31 +1405,28 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately select case (snicar_numrad_snw) case (5) ! 5-band case + ! VIS band flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) - do i=snl_top,1,1 - flx_sum = 0._r8 - do bnd_idx= nir_bnd_bgn,nir_bnd_end - flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) - enddo - flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) - end do case (480) ! 480-band case + ! average for VIS band do i=snl_top,1,1 - ! average for VIS band flx_sum = 0._r8 do bnd_idx= 1,(nir_bnd_bgn-1) flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) enddo flx_abs(c_idx,i,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) - ! average for NIR band - flx_sum = 0._r8 - do bnd_idx= nir_bnd_bgn,nir_bnd_end - flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) - enddo - flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end do end select + ! average for NIR band (5 or 480-band case) + do i = snl_top, 1, 1 + flx_sum = 0._r8 + do bnd_idx = nir_bnd_bgn, nir_bnd_end + flx_sum = flx_sum + flx_wgt(bnd_idx) * flx_abs_lcl(i,bnd_idx) + end do + flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + end do + ! high solar zenith angle adjustment for Adding-doubling solver results ! near-IR direct albedo/absorption adjustment for high solar zenith angles ! solar zenith angle parameterization From 98f229a838a1700e74b164025edcb58e32af839a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 10 Aug 2023 16:40:17 -0600 Subject: [PATCH 1346/2067] Replace if-statements with min/max --- src/biogeophys/SnowSnicarMod.F90 | 28 ++++++++-------------------- 1 file changed, 8 insertions(+), 20 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 6c271c013b..b4748085b2 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1610,30 +1610,18 @@ subroutine SnowAge_grain(bounds, & ! make sure rhos doesn't drop below 50 (see rhos_idx below) rhos=max(50._r8,rhos) - ! best-fit table indecies + ! best-fit table indices T_idx = nint((t_soisno(c_idx,i)-223) / 5) + 1 Tgrd_idx = nint(dTdz(c_idx,i) / 10) + 1 rhos_idx = nint((rhos-50) / 50) + 1 - ! boundary check: - if (T_idx < idx_T_min) then - T_idx = idx_T_min - endif - if (T_idx > idx_T_max) then - T_idx = idx_T_max - endif - if (Tgrd_idx < idx_Tgrd_min) then - Tgrd_idx = idx_Tgrd_min - endif - if (Tgrd_idx > idx_Tgrd_max) then - Tgrd_idx = idx_Tgrd_max - endif - if (rhos_idx < idx_rhos_min) then - rhos_idx = idx_rhos_min - endif - if (rhos_idx > idx_rhos_max) then - rhos_idx = idx_rhos_max - endif + ! boundary checks + T_idx = max(T_idx, idx_T_min) + T_idx = min(T_idx, idx_T_max) + Tgrd_idx = max(Tgrd_idx, idx_Tgrd_min) + Tgrd_idx = min(Tgrd_idx, idx_Tgrd_max) + rhos_idx = max(rhos_idx, idx_rhos_min) + rhos_idx = min(rhos_idx, idx_rhos_max) ! best-fit parameters bst_tau = snowage_tau(rhos_idx,Tgrd_idx,T_idx) From fd19f980bae0e640bbb2344ca601bd6c68c65656 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 16:57:57 -0600 Subject: [PATCH 1347/2067] Updated a test name in README_history_fields_files. --- .../setting-up-and-running-a-case/README_history_fields_files | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files b/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files index c965536657..f92f48f71a 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files +++ b/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files @@ -4,7 +4,7 @@ The files history_fields_nofates.rst and history_fields_fates.rst each contain a table of the history fields, active and inactive, available in the CTSM cases that get generated by these tests: ERP_P36x2_D_Ld3.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-extra_outputs -ERS_Ld9.f10_f10_mg37.I2000Clm50FatesCru.cheyenne_intel.clm-FatesColdDefCH4 +ERS_Ld9.f10_f10_mg37.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesColdCH4Off To reproduce these .rst files, run the above tests and the files will appear in the corresponding run directories. From 2ee70af2bd6f6f4d09e015761794e5d72c976db5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 10 Aug 2023 17:21:42 -0600 Subject: [PATCH 1348/2067] Replace another if-statmt with max and two ints with floats --- src/biogeophys/SnowSnicarMod.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index b4748085b2..2a7296178f 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1630,13 +1630,11 @@ subroutine SnowAge_grain(bounds, & !LvK extra boundary check, to prevent when using old restart file with lower snw_rds_min than current run - if (snw_rds(c_idx,i) < snw_rds_min) then - snw_rds(c_idx,i) = snw_rds_min - endif + snw_rds(c_idx,i) = max(snw_rds(c_idx,i), snw_rds_min) ! change in snow effective radius, using best-fit parameters dr_fresh = snw_rds(c_idx,i)-snw_rds_min - dr = (bst_drdt0*(bst_tau/(dr_fresh+bst_tau))**(1/bst_kappa)) * (dtime/3600) + dr = (bst_drdt0 * (bst_tau / (dr_fresh + bst_tau))**(1._r8 / bst_kappa)) * (dtime / 3600._r8) ! !********** 2. WET SNOW AGING *********** From 728b7e68e3d57bd17c90cf52c7d895e6fa575307 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 16:01:29 -0600 Subject: [PATCH 1349/2067] Adding some parentheses to simulate potential OOO changes from upcoming change. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 05c004902e..e8cbd55f53 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -283,8 +283,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! First, get diffusivity as a unitless constant, which is what's needed to ! calculate ratio_k1 below. diffus (c,j) = & - (om_frac * eps**(10._r8/3._r8) / watsat(c,j)**2 + & - (1._r8-om_frac) * eps**2 * f_a**(3._r8 / bsw(c,j)) ) + (om_frac * (eps**(10._r8/3._r8) / watsat(c,j)**2) + & + (1._r8-om_frac) * (eps**2 * f_a**(3._r8 / bsw(c,j))) ) ! calculate anoxic fraction of soils ! use rijtema and kroess model after Riley et al., 2000 From d0a2329487c85c77c07ab3258231f4273d50b0f4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 16:11:43 -0600 Subject: [PATCH 1350/2067] Clarifying calculation of diffus in SoilBiogeochemNitrifDenitrif(). --- .../SoilBiogeochemNitrifDenitrifMod.F90 | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index e8cbd55f53..e0cd4a30ab 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -183,7 +183,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & real(r8) :: r_max real(r8) :: r_min(bounds%begc:bounds%endc,1:nlevdecomp) real(r8) :: ratio_diffusivity_water_gas(bounds%begc:bounds%endc,1:nlevdecomp) - real(r8) :: om_frac + real(r8) :: om_frac, diffus_millingtonquirk, diffus_moldrup real(r8) :: anaerobic_frac_sat, r_psi_sat, r_min_sat ! scalar values in sat portion for averaging real(r8) :: organic_max ! organic matter content (kg/m3) where ! soil is assumed to act like peat @@ -280,11 +280,19 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & om_frac = 1._r8 end if + ! Diffusitivity after Moldrup et al. (2003) + ! Eq. 8 in Riley et al. (2011, Biogeosciences) + diffus_moldrup = eps**2 * f_a**(3._r8 / bsw(c,j)) + + ! Diffusivity after Millington & Quirk (1961) + ! Eq. 9 in Riley et al. (2011, Biogeosciences) + diffus_millingtonquirk = eps**(10._r8/3._r8) / watsat(c,j)**2 + ! First, get diffusivity as a unitless constant, which is what's needed to ! calculate ratio_k1 below. diffus (c,j) = & - (om_frac * (eps**(10._r8/3._r8) / watsat(c,j)**2) + & - (1._r8-om_frac) * (eps**2 * f_a**(3._r8 / bsw(c,j))) ) + (om_frac * diffus_millingtonquirk + & + (1._r8-om_frac) * diffus_moldrup ) ! calculate anoxic fraction of soils ! use rijtema and kroess model after Riley et al., 2000 From 40dab0ed0e06961fc27eb331275a9d64010ef28d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 16:11:54 -0600 Subject: [PATCH 1351/2067] Renamed eps to fc_air_frac. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index e0cd4a30ab..66ab3498d5 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -171,8 +171,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & real(r8) :: D0 ! temperature dependence of gaseous diffusion coefficients !debug-- put these type structure for outing to hist files real(r8) :: co2diff_con(2) ! diffusion constants for CO2 - real(r8) :: eps real(r8) :: f_a + real(r8) :: fc_air_frac ! Air-filled fraction of soil volume at field capacity real(r8) :: surface_tension_water ! (J/m^2), Arah and Vinten 1995 real(r8) :: rij_kro_a ! Arah and Vinten 1995 real(r8) :: rij_kro_alpha ! Arah and Vinten 1995 @@ -268,7 +268,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! calculate gas diffusivity of soil at field capacity here ! use expression from methane code, but neglect OM for now f_a = 1._r8 - watfc(c,j) / watsat(c,j) ! f_a is theta_a/theta_s in Riley et al. (2011) - eps = watsat(c,j)-watfc(c,j) ! Air-filled fraction of total soil volume; theta_a in Riley et al. (2011) + fc_air_frac = watsat(c,j)-watfc(c,j) ! theta_a in Riley et al. (2011) ! use diffusivity calculation including peat if (use_lch4) then @@ -282,11 +282,11 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! Diffusitivity after Moldrup et al. (2003) ! Eq. 8 in Riley et al. (2011, Biogeosciences) - diffus_moldrup = eps**2 * f_a**(3._r8 / bsw(c,j)) + diffus_moldrup = fc_air_frac**2 * f_a**(3._r8 / bsw(c,j)) ! Diffusivity after Millington & Quirk (1961) ! Eq. 9 in Riley et al. (2011, Biogeosciences) - diffus_millingtonquirk = eps**(10._r8/3._r8) / watsat(c,j)**2 + diffus_millingtonquirk = fc_air_frac**(10._r8/3._r8) / watsat(c,j)**2 ! First, get diffusivity as a unitless constant, which is what's needed to ! calculate ratio_k1 below. From 056ec56313263685f9a76c30b97dda67eaeabde5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 10 Aug 2023 16:32:55 -0600 Subject: [PATCH 1352/2067] Renamed f_a to fc_air_frac_as_frac_porosity. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 66ab3498d5..ecb4c38e59 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -171,8 +171,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & real(r8) :: D0 ! temperature dependence of gaseous diffusion coefficients !debug-- put these type structure for outing to hist files real(r8) :: co2diff_con(2) ! diffusion constants for CO2 - real(r8) :: f_a real(r8) :: fc_air_frac ! Air-filled fraction of soil volume at field capacity + real(r8) :: fc_air_frac_as_frac_porosity ! fc_air_frac as fraction of total porosity real(r8) :: surface_tension_water ! (J/m^2), Arah and Vinten 1995 real(r8) :: rij_kro_a ! Arah and Vinten 1995 real(r8) :: rij_kro_alpha ! Arah and Vinten 1995 @@ -267,8 +267,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & !---------------- calculate soil anoxia state ! calculate gas diffusivity of soil at field capacity here ! use expression from methane code, but neglect OM for now - f_a = 1._r8 - watfc(c,j) / watsat(c,j) ! f_a is theta_a/theta_s in Riley et al. (2011) fc_air_frac = watsat(c,j)-watfc(c,j) ! theta_a in Riley et al. (2011) + fc_air_frac_as_frac_porosity = fc_air_frac / watsat(c,j) ! theta_a/theta_s in Riley et al. (2011) ! use diffusivity calculation including peat if (use_lch4) then @@ -282,7 +282,7 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! Diffusitivity after Moldrup et al. (2003) ! Eq. 8 in Riley et al. (2011, Biogeosciences) - diffus_moldrup = fc_air_frac**2 * f_a**(3._r8 / bsw(c,j)) + diffus_moldrup = fc_air_frac**2 * fc_air_frac_as_frac_porosity**(3._r8 / bsw(c,j)) ! Diffusivity after Millington & Quirk (1961) ! Eq. 9 in Riley et al. (2011, Biogeosciences) From d6751d6050f2c36136fb1233a589ceab27d7ebd7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 10:58:20 -0600 Subject: [PATCH 1353/2067] Changed more references to history fields "master list." --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- .../namelist_definition_ctsm.xml | 2 +- cime_config/testdefs/testlist_clm.xml | 2 +- .../testmods_dirs/clm/extra_outputs/README | 4 +- src/main/clm_varctl.F90 | 2 +- src/main/histFileMod.F90 | 40 +++++++++---------- 6 files changed, 26 insertions(+), 26 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 4cac65547e..9ecb139831 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -67,7 +67,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .false. .false. - + .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 3c017afee1..227551010f 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -766,7 +766,7 @@ SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name -If TRUE, write master field list to separate file for documentation purposes +If TRUE, write list of all output fields to separate file for documentation purposes - + diff --git a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README index 03bc956b6f..574d7cc204 100644 --- a/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README +++ b/cime_config/testdefs/testmods_dirs/clm/extra_outputs/README @@ -1,4 +1,4 @@ This test mod turns on extra diagnostic fields -It also outputs an optional text file containing a table of the -history fields master list +It also outputs an optional text file containing a table of all +the possible history fields diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index bcf7a0ffd2..39c699dd7e 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -385,7 +385,7 @@ module clm_varctl ! namelist: write CH4 extra diagnostic output logical, public :: hist_wrtch4diag = .false. - ! namelist: write history master list to a file for use in documentation + ! namelist: write list of all history fields to a file for use in documentation logical, public :: hist_fields_list_file = .false. !---------------------------------------------------------- diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index df91fa1e70..2fcd509e7e 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -141,12 +141,12 @@ module histFileMod logical, private :: if_disphist(max_tapes) ! restart, true => save history file ! ! !PUBLIC MEMBER FUNCTIONS: (in rough call order) - public :: hist_addfld1d ! Add a 1d single-level field to the master field list - public :: hist_addfld2d ! Add a 2d multi-level field to the master field list + public :: hist_addfld1d ! Add a 1d single-level field to the list of all history fields + public :: hist_addfld2d ! Add a 2d multi-level field to the list of all history fields public :: hist_addfld_decomp ! Add a 1d/2d field based on patch or column data public :: hist_add_subscript ! Add a 2d subscript dimension - public :: hist_printflds ! Print summary of master field list + public :: hist_printflds ! Print summary of list of all history fields public :: htapes_fieldlist ! Finalize history file field lists, intersecting masterlist with ! namelist params. @@ -159,7 +159,7 @@ module histFileMod ! !PRIVATE MEMBER FUNCTIONS: private :: is_mapping_upto_subgrid ! Is this field being mapped up to a higher subgrid level? private :: masterlist_make_active ! Declare a single field active for a single tape - private :: masterlist_addfld ! Add a field to the master field list + private :: masterlist_addfld ! Add a field to the list of all history fields private :: masterlist_change_timeavg ! Override default history tape contents for specific tape private :: htape_addfld ! Transfer field metadata from masterlist to a history tape. private :: htape_create ! Define netcdf metadata of history file t @@ -294,7 +294,7 @@ end subroutine copy_entry_interface ! hist_addfld* calls in the code. ! For the field data itself, see 'tape'. ! - type (master_entry) :: masterlist(max_flds) ! master field list + type (master_entry) :: masterlist(max_flds) ! list of all history fields ! ! Whether each history tape is in use in this run. If history_tape_in_use(i) is false, ! then data in tape(i) is undefined and should not be referenced. @@ -311,7 +311,7 @@ end subroutine copy_entry_interface ! ! Counters ! - integer :: nfmaster = 0 ! number of fields in master field list + integer :: nfmaster = 0 ! number of fields in list of all history fields ! ! Other variables ! @@ -347,7 +347,7 @@ end subroutine copy_entry_interface subroutine hist_printflds() ! ! !DESCRIPTION: - ! Print summary of master field list. + ! Print summary of list of all history fields. ! ! !USES: use clm_varctl, only: hist_fields_list_file @@ -371,7 +371,7 @@ subroutine hist_printflds() if (masterproc) then write(iulog,*) trim(subname),' : number of master fields = ',nfmaster - write(iulog,*)' ******* MASTER FIELD LIST *******' + write(iulog,*)' ******* LIST OF ALL HISTORY FIELDS *******' do nf = 1,nfmaster write(iulog,9000)nf, masterlist(nf)%field%name, masterlist(nf)%field%units 9000 format (i5,1x,a32,1x,a16) @@ -379,7 +379,7 @@ subroutine hist_printflds() call shr_sys_flush(iulog) end if - ! Print master field list in separate text file when namelist + ! Print list of all history fields in separate text file when namelist ! variable requests it. Text file is formatted in the .rst ! (reStructuredText) format for easy introduction of the file to ! the CTSM's web-based documentation. @@ -495,9 +495,9 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & no_snow_behavior) ! ! !DESCRIPTION: - ! Add a field to the master field list. Put input arguments of + ! Add a field to the list of all history fields. Put input arguments of ! field name, units, number of levels, averaging flag, and long name - ! into a type entry in the global master field list (masterlist). + ! into a type entry in the global list of all history fields (masterlist). ! ! The optional argument no_snow_behavior should be given when this is a multi-layer ! snow field, and should be absent otherwise. It should take on one of the no_snow_* @@ -563,12 +563,12 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & end if end do - ! Increase number of fields on master field list + ! Increase number of fields on list of all history fields nfmaster = nfmaster + 1 f = nfmaster - ! Check number of fields in master list against maximum number for master list + ! Check number of fields in list against maximum number if (nfmaster > max_flds) then write(iulog,*) trim(subname),' ERROR: too many fields for primary history file ', & @@ -576,7 +576,7 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & call endrun(msg=errMsg(sourcefile, __LINE__)) end if - ! Add field to master list + ! Add field to list of all history fields masterlist(f)%field%name = fname masterlist(f)%field%long_name = long_name @@ -623,9 +623,9 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & masterlist(f)%field%no_snow_behavior = no_snow_unset end if - ! The following two fields are used only in master field list, + ! The following two fields are used only in list of all history fields, ! NOT in the runtime active field list - ! ALL FIELDS IN THE MASTER LIST ARE INITIALIZED WITH THE ACTIVE + ! ALL FIELDS IN THE FORMER ARE INITIALIZED WITH THE ACTIVE ! FLAG SET TO FALSE masterlist(f)%avgflag(:) = avgflag @@ -746,7 +746,7 @@ subroutine masterlist_make_active (name, tape_index, avgflag) endif end if - ! Look through master list for input field name. + ! Look through list of all history fields for input field name. ! When found, set active flag for that tape to true. ! Also reset averaging flag if told to use other than default. @@ -773,7 +773,7 @@ subroutine masterlist_change_timeavg (t) ! ! !DESCRIPTION: ! Override default history tape contents for a specific tape. - ! Copy the flag into the master field list. + ! Copy the flag into the list of all history fields. ! ! !ARGUMENTS: integer, intent(in) :: t ! history tape index @@ -1133,11 +1133,11 @@ end function is_mapping_upto_subgrid subroutine htape_addfld (t, f, avgflag) ! ! !DESCRIPTION: - ! Add a field to a history tape, copying metadata from the master field list + ! Add a field to a history tape, copying metadata from the list of all history fields ! ! !ARGUMENTS: integer, intent(in) :: t ! history tape index - integer, intent(in) :: f ! field index from master field list + integer, intent(in) :: f ! field index from list of all history fields character(len=*), intent(in) :: avgflag ! time averaging flag ! ! !LOCAL VARIABLES: From 94216159ecd855d4589000dbfdae3a090e201617 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 14:01:35 -0600 Subject: [PATCH 1354/2067] Changed many variable and method names in histFileMod. --- src/main/histFileMod.F90 | 236 +++++++++++++++++++-------------------- 1 file changed, 118 insertions(+), 118 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 2fcd509e7e..bdcec28ec1 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -147,7 +147,7 @@ module histFileMod public :: hist_add_subscript ! Add a 2d subscript dimension public :: hist_printflds ! Print summary of list of all history fields - public :: htapes_fieldlist ! Finalize history file field lists, intersecting masterlist with + public :: htapes_fieldlist ! Finalize history file field lists, intersecting allhistfldlist with ! namelist params. public :: hist_htapes_build ! Initialize history file handler (for initial or continued run) @@ -158,10 +158,10 @@ module histFileMod ! ! !PRIVATE MEMBER FUNCTIONS: private :: is_mapping_upto_subgrid ! Is this field being mapped up to a higher subgrid level? - private :: masterlist_make_active ! Declare a single field active for a single tape - private :: masterlist_addfld ! Add a field to the list of all history fields - private :: masterlist_change_timeavg ! Override default history tape contents for specific tape - private :: htape_addfld ! Transfer field metadata from masterlist to a history tape. + private :: allhistfldlist_make_active ! Declare a single field active for a single tape + private :: allhistfldlist_addfld ! Add a field to the list of all history fields + private :: allhistfldlist_change_timeavg ! Override default history tape contents for specific tape + private :: htape_addfld ! Transfer field metadata from allhistfldlist to a history tape. private :: htape_create ! Define netcdf metadata of history file t private :: htape_add_ltype_metadata ! Add global metadata defining landunit types private :: htape_add_ctype_metadata ! Add global metadata defining column types @@ -241,14 +241,14 @@ end subroutine copy_entry_interface ! Additional per-field metadata. See also history_entry. ! These values are specified in hist_addfld* calls but then can be ! overridden by namelist params like hist_fincl1. - type, extends(entry_base) :: master_entry + type, extends(entry_base) :: allhistfldlist_entry logical :: actflag(max_tapes) ! which history tapes to write to. character(len=avgflag_strlen) :: avgflag(max_tapes) ! type of time averaging contains - procedure :: copy => copy_master_entry - end type master_entry + procedure :: copy => copy_allhistfldlist_entry + end type allhistfldlist_entry - ! Actual per-field history data, accumulated from clmptr_r* vars. See also master_entry. + ! Actual per-field history data, accumulated from clmptr_r* vars. See also allhistfldlist_entry. type, extends(entry_base) :: history_entry character(len=avgflag_strlen) :: avgflag ! time averaging flag ("X","A","M","I","SUM") real(r8), pointer :: hbuf(:,:) ! history buffer (dimensions: dim1d x num2d) @@ -261,7 +261,7 @@ end subroutine copy_entry_interface ! at a given time frequency and precision. The first ('primary') tape defaults to a non-empty set ! of active fields (see hist_addfld* methods), overridable by namelist flags, while the other ! tapes are entirely manually configured via namelist flags. The set of active fields across all - ! tapes is assembled in the 'masterlist' variable. Note that the first history tape is index 1 in + ! tapes is assembled in the 'allhistfldlist' variable. Note that the first history tape is index 1 in ! the code but contains 'h0' in its output filenames (see set_hist_filename method). type history_tape integer :: nflds ! number of active fields on tape @@ -273,7 +273,7 @@ end subroutine copy_entry_interface logical :: is_endhist ! true => current time step is end of history interval real(r8) :: begtime ! time at beginning of history averaging interval type (history_entry) :: hlist(max_flds) ! array of active history tape entries. - ! The ordering matches the masterlist's. + ! The ordering matches the allhistfldlist's. end type history_tape type clmpoint_rs ! Pointer to real scalar data (1D) @@ -294,7 +294,7 @@ end subroutine copy_entry_interface ! hist_addfld* calls in the code. ! For the field data itself, see 'tape'. ! - type (master_entry) :: masterlist(max_flds) ! list of all history fields + type (allhistfldlist_entry) :: allhistfldlist(max_flds) ! list of all history fields ! ! Whether each history tape is in use in this run. If history_tape_in_use(i) is false, ! then data in tape(i) is undefined and should not be referenced. @@ -302,7 +302,7 @@ end subroutine copy_entry_interface logical :: history_tape_in_use(max_tapes) ! whether each history tape is in use in this run ! ! The actual (accumulated) history data for all active fields in each in-use tape. See - ! 'history_tape_in_use' for in-use tapes, and 'masterlist' for active fields. See also + ! 'history_tape_in_use' for in-use tapes, and 'allhistfldlist' for active fields. See also ! clmptr_r* variables for raw history data. ! type (history_tape) :: tape(max_tapes) ! array of history tapes @@ -311,7 +311,7 @@ end subroutine copy_entry_interface ! ! Counters ! - integer :: nfmaster = 0 ! number of fields in list of all history fields + integer :: nallhistflds = 0 ! number of fields in list of all history fields ! ! Other variables ! @@ -370,10 +370,10 @@ subroutine hist_printflds() !----------------------------------------------------------------------- if (masterproc) then - write(iulog,*) trim(subname),' : number of master fields = ',nfmaster + write(iulog,*) trim(subname),' : number of history fields = ',nallhistflds write(iulog,*)' ******* LIST OF ALL HISTORY FIELDS *******' - do nf = 1,nfmaster - write(iulog,9000)nf, masterlist(nf)%field%name, masterlist(nf)%field%units + do nf = 1,nallhistflds + write(iulog,9000)nf, allhistfldlist(nf)%field%name, allhistfldlist(nf)%field%units 9000 format (i5,1x,a32,1x,a16) end do call shr_sys_flush(iulog) @@ -385,7 +385,7 @@ subroutine hist_printflds() ! the CTSM's web-based documentation. ! First sort the list to be in alphabetical order - call sort_hist_list(1, nfmaster, masterlist) + call sort_hist_list(1, nallhistflds, allhistfldlist) if (masterproc .and. hist_fields_list_file) then ! Hardwired table column widths to fit the table on a computer @@ -466,12 +466,12 @@ subroutine hist_printflds() ! Main table ! Concatenate strings needed in format statement fmt_txt = '(i'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',l'//str_width_col(5)//')' - do nf = 1,nfmaster + do nf = 1,nallhistflds write(hist_fields_file,fmt_txt) nf, & - masterlist(nf)%field%name, & - masterlist(nf)%field%long_name, & - masterlist(nf)%field%units, & - masterlist(nf)%actflag(1) + allhistfldlist(nf)%field%name, & + allhistfldlist(nf)%field%long_name, & + allhistfldlist(nf)%field%units, & + allhistfldlist(nf)%actflag(1) end do ! Table footer, same as header @@ -489,7 +489,7 @@ subroutine hist_printflds() end subroutine hist_printflds !----------------------------------------------------------------------- - subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & + subroutine allhistfldlist_addfld (fname, numdims, type1d, type1d_out, & type2d, num2d, units, avgflag, long_name, hpindex, & p2c_scale_type, c2l_scale_type, l2g_scale_type, & no_snow_behavior) @@ -497,7 +497,7 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & ! !DESCRIPTION: ! Add a field to the list of all history fields. Put input arguments of ! field name, units, number of levels, averaging flag, and long name - ! into a type entry in the global list of all history fields (masterlist). + ! into a type entry in the global list of all history fields (allhistfldlist). ! ! The optional argument no_snow_behavior should be given when this is a multi-layer ! snow field, and should be absent otherwise. It should take on one of the no_snow_* @@ -521,14 +521,14 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & ! ! !LOCAL VARIABLES: integer :: n ! loop index - integer :: f ! masterlist index + integer :: f ! allhistfldlist index integer :: numa ! total number of atm cells across all processors integer :: numg ! total number of gridcells across all processors integer :: numl ! total number of landunits across all processors integer :: numc ! total number of columns across all processors integer :: nump ! total number of pfts across all processors type(bounds_type) :: bounds - character(len=*),parameter :: subname = 'masterlist_addfld' + character(len=*),parameter :: subname = 'allhistfldlist_addfld' !------------------------------------------------------------------------ if (.not. avgflag_valid(avgflag, blank_valid=.true.)) then @@ -556,8 +556,8 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & end if ! Ensure that new field doesn't already exist - do n = 1,nfmaster - if (masterlist(n)%field%name == fname) then + do n = 1,nallhistflds + if (allhistfldlist(n)%field%name == fname) then write(iulog,*) trim(subname),' ERROR:', fname, ' already on list' call endrun(msg=errMsg(sourcefile, __LINE__)) end if @@ -565,62 +565,62 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & ! Increase number of fields on list of all history fields - nfmaster = nfmaster + 1 - f = nfmaster + nallhistflds = nallhistflds + 1 + f = nallhistflds ! Check number of fields in list against maximum number - if (nfmaster > max_flds) then + if (nallhistflds > max_flds) then write(iulog,*) trim(subname),' ERROR: too many fields for primary history file ', & - '-- max_flds,nfmaster=', max_flds, nfmaster + '-- max_flds,nallhistflds=', max_flds, nallhistflds call endrun(msg=errMsg(sourcefile, __LINE__)) end if ! Add field to list of all history fields - masterlist(f)%field%name = fname - masterlist(f)%field%long_name = long_name - masterlist(f)%field%units = units - masterlist(f)%field%type1d = type1d - masterlist(f)%field%type1d_out = type1d_out - masterlist(f)%field%type2d = type2d - masterlist(f)%field%numdims = numdims - masterlist(f)%field%num2d = num2d - masterlist(f)%field%hpindex = hpindex - masterlist(f)%field%p2c_scale_type = p2c_scale_type - masterlist(f)%field%c2l_scale_type = c2l_scale_type - masterlist(f)%field%l2g_scale_type = l2g_scale_type + allhistfldlist(f)%field%name = fname + allhistfldlist(f)%field%long_name = long_name + allhistfldlist(f)%field%units = units + allhistfldlist(f)%field%type1d = type1d + allhistfldlist(f)%field%type1d_out = type1d_out + allhistfldlist(f)%field%type2d = type2d + allhistfldlist(f)%field%numdims = numdims + allhistfldlist(f)%field%num2d = num2d + allhistfldlist(f)%field%hpindex = hpindex + allhistfldlist(f)%field%p2c_scale_type = p2c_scale_type + allhistfldlist(f)%field%c2l_scale_type = c2l_scale_type + allhistfldlist(f)%field%l2g_scale_type = l2g_scale_type select case (type1d) case (grlnd) - masterlist(f)%field%beg1d = bounds%begg - masterlist(f)%field%end1d = bounds%endg - masterlist(f)%field%num1d = numg + allhistfldlist(f)%field%beg1d = bounds%begg + allhistfldlist(f)%field%end1d = bounds%endg + allhistfldlist(f)%field%num1d = numg case (nameg) - masterlist(f)%field%beg1d = bounds%begg - masterlist(f)%field%end1d = bounds%endg - masterlist(f)%field%num1d = numg + allhistfldlist(f)%field%beg1d = bounds%begg + allhistfldlist(f)%field%end1d = bounds%endg + allhistfldlist(f)%field%num1d = numg case (namel) - masterlist(f)%field%beg1d = bounds%begl - masterlist(f)%field%end1d = bounds%endl - masterlist(f)%field%num1d = numl + allhistfldlist(f)%field%beg1d = bounds%begl + allhistfldlist(f)%field%end1d = bounds%endl + allhistfldlist(f)%field%num1d = numl case (namec) - masterlist(f)%field%beg1d = bounds%begc - masterlist(f)%field%end1d = bounds%endc - masterlist(f)%field%num1d = numc + allhistfldlist(f)%field%beg1d = bounds%begc + allhistfldlist(f)%field%end1d = bounds%endc + allhistfldlist(f)%field%num1d = numc case (namep) - masterlist(f)%field%beg1d = bounds%begp - masterlist(f)%field%end1d = bounds%endp - masterlist(f)%field%num1d = nump + allhistfldlist(f)%field%beg1d = bounds%begp + allhistfldlist(f)%field%end1d = bounds%endp + allhistfldlist(f)%field%num1d = nump case default write(iulog,*) trim(subname),' ERROR: unknown 1d output type= ',type1d call endrun(msg=errMsg(sourcefile, __LINE__)) end select if (present(no_snow_behavior)) then - masterlist(f)%field%no_snow_behavior = no_snow_behavior + allhistfldlist(f)%field%no_snow_behavior = no_snow_behavior else - masterlist(f)%field%no_snow_behavior = no_snow_unset + allhistfldlist(f)%field%no_snow_behavior = no_snow_unset end if ! The following two fields are used only in list of all history fields, @@ -628,10 +628,10 @@ subroutine masterlist_addfld (fname, numdims, type1d, type1d_out, & ! ALL FIELDS IN THE FORMER ARE INITIALIZED WITH THE ACTIVE ! FLAG SET TO FALSE - masterlist(f)%avgflag(:) = avgflag - masterlist(f)%actflag(:) = .false. + allhistfldlist(f)%avgflag(:) = avgflag + allhistfldlist(f)%actflag(:) = .false. - end subroutine masterlist_addfld + end subroutine allhistfldlist_addfld !----------------------------------------------------------------------- subroutine hist_htapes_build () @@ -715,7 +715,7 @@ subroutine hist_htapes_build () end subroutine hist_htapes_build !----------------------------------------------------------------------- - subroutine masterlist_make_active (name, tape_index, avgflag) + subroutine allhistfldlist_make_active (name, tape_index, avgflag) ! ! !DESCRIPTION: ! Add a field to the default ``on'' list for a given history file. @@ -728,8 +728,8 @@ subroutine masterlist_make_active (name, tape_index, avgflag) ! ! !LOCAL VARIABLES: integer :: f ! field index - logical :: found ! flag indicates field found in masterlist - character(len=*),parameter :: subname = 'masterlist_make_active' + logical :: found ! flag indicates field found in allhistfldlist + character(len=*),parameter :: subname = 'allhistfldlist_make_active' !----------------------------------------------------------------------- ! Check validity of input arguments @@ -751,11 +751,11 @@ subroutine masterlist_make_active (name, tape_index, avgflag) ! Also reset averaging flag if told to use other than default. found = .false. - do f = 1,nfmaster - if (trim(name) == trim(masterlist(f)%field%name)) then - masterlist(f)%actflag(tape_index) = .true. + do f = 1,nallhistflds + if (trim(name) == trim(allhistfldlist(f)%field%name)) then + allhistfldlist(f)%actflag(tape_index) = .true. if (present(avgflag)) then - if (avgflag/= ' ') masterlist(f)%avgflag(tape_index) = avgflag + if (avgflag/= ' ') allhistfldlist(f)%avgflag(tape_index) = avgflag end if found = .true. exit @@ -766,10 +766,10 @@ subroutine masterlist_make_active (name, tape_index, avgflag) call endrun(msg=errMsg(sourcefile, __LINE__)) end if - end subroutine masterlist_make_active + end subroutine allhistfldlist_make_active !----------------------------------------------------------------------- - subroutine masterlist_change_timeavg (t) + subroutine allhistfldlist_change_timeavg (t) ! ! !DESCRIPTION: ! Override default history tape contents for a specific tape. @@ -781,7 +781,7 @@ subroutine masterlist_change_timeavg (t) ! !LOCAL VARIABLES: integer :: f ! field index character(len=avgflag_strlen) :: avgflag ! local equiv of hist_avgflag_pertape(t) - character(len=*),parameter :: subname = 'masterlist_change_timeavg' + character(len=*),parameter :: subname = 'allhistfldlist_change_timeavg' !----------------------------------------------------------------------- avgflag = hist_avgflag_pertape(t) @@ -790,11 +790,11 @@ subroutine masterlist_change_timeavg (t) call endrun(msg=errMsg(sourcefile, __LINE__)) end if - do f = 1,nfmaster - masterlist(f)%avgflag(t) = avgflag + do f = 1,nallhistflds + allhistfldlist(f)%avgflag(t) = avgflag end do - end subroutine masterlist_change_timeavg + end subroutine allhistfldlist_change_timeavg !----------------------------------------------------------------------- subroutine htapes_fieldlist() @@ -806,7 +806,7 @@ subroutine htapes_fieldlist() ! Then sort the result alphanumerically. ! ! Sets history_tape_in_use and htapes_defined. Fills fields in 'tape' array. - ! Optionally updates masterlist avgflag. + ! Optionally updates allhistfldlist avgflag. ! ! !ARGUMENTS: ! @@ -814,7 +814,7 @@ subroutine htapes_fieldlist() integer :: t, f ! tape, field indices integer :: ff ! index into include, exclude and fprec list character(len=max_namlen) :: name ! field name portion of fincl (i.e. no avgflag separator) - character(len=max_namlen) :: mastername ! name from masterlist field + character(len=max_namlen) :: allhistfldname ! name from allhistfldlist field character(len=avgflag_strlen) :: avgflag ! averaging flag character(len=1) :: prec_acc ! history buffer precision flag character(len=1) :: prec_wrt ! history buffer write precision flag @@ -826,7 +826,7 @@ subroutine htapes_fieldlist() do t=1,max_tapes if (hist_avgflag_pertape(t) /= ' ') then - call masterlist_change_timeavg (t) + call allhistfldlist_change_timeavg (t) end if end do @@ -859,11 +859,11 @@ subroutine htapes_fieldlist() f = 1 do while (f < max_flds .and. fincl(f,t) /= ' ') name = getname (fincl(f,t)) - do ff = 1,nfmaster - mastername = masterlist(ff)%field%name - if (name == mastername) exit + do ff = 1,nallhistflds + allhistfldname = allhistfldlist(ff)%field%name + if (name == allhistfldname) exit end do - if (name /= mastername) then + if (name /= allhistfldname) then write(iulog,*) trim(subname),' ERROR: ', trim(name), ' in fincl(', f, ') ',& 'for history tape ',t,' not found' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -873,11 +873,11 @@ subroutine htapes_fieldlist() f = 1 do while (f < max_flds .and. fexcl(f,t) /= ' ') - do ff = 1,nfmaster - mastername = masterlist(ff)%field%name - if (fexcl(f,t) == mastername) exit + do ff = 1,nallhistflds + allhistfldname = allhistfldlist(ff)%field%name + if (fexcl(f,t) == allhistfldname) exit end do - if (fexcl(f,t) /= mastername) then + if (fexcl(f,t) /= allhistfldname) then write(iulog,*) trim(subname),' ERROR: ', fexcl(f,t), ' in fexcl(', f, ') ', & 'for history tape ',t,' not found' call endrun(msg=errMsg(sourcefile, __LINE__)) @@ -890,16 +890,16 @@ subroutine htapes_fieldlist() tape(:)%nflds = 0 do t = 1,max_tapes - ! Loop through the masterlist set of field names and determine if any of those + ! Loop through the allhistfldlist set of field names and determine if any of those ! are in the FINCL or FEXCL arrays ! The call to list_index determines the index in the FINCL or FEXCL arrays - ! that the masterlist field corresponds to + ! that the allhistfldlist field corresponds to ! Add the field to the tape if specified via namelist (FINCL[1-max_tapes]), ! or if it is on by default and was not excluded via namelist (FEXCL[1-max_tapes]). - do f = 1,nfmaster - mastername = masterlist(f)%field%name - call list_index (fincl(1,t), mastername, ff) + do f = 1,nallhistflds + allhistfldname = allhistfldlist(f)%field%name + call list_index (fincl(1,t), allhistfldname, ff) if (ff > 0) then @@ -913,7 +913,7 @@ subroutine htapes_fieldlist() ! find index of field in exclude list - call list_index (fexcl(1,t), mastername, ff) + call list_index (fexcl(1,t), allhistfldname, ff) ! if field is in exclude list, ff > 0 and htape_addfld ! will not be called for field @@ -922,7 +922,7 @@ subroutine htapes_fieldlist() ! called below only if field is not in exclude list OR in ! include list - if (ff == 0 .and. masterlist(f)%actflag(t)) then + if (ff == 0 .and. allhistfldlist(f)%actflag(t)) then call htape_addfld (t, f, ' ') end if @@ -1002,7 +1002,7 @@ subroutine htapes_fieldlist() call shr_sys_flush(iulog) end if - ! Set flag indicating h-tape contents are now defined (needed by masterlist_addfld) + ! Set flag indicating h-tape contents are now defined (needed by allhistfldlist_addfld) htapes_defined = .true. @@ -1010,23 +1010,23 @@ subroutine htapes_fieldlist() end subroutine htapes_fieldlist !----------------------------------------------------------------------- - subroutine copy_master_entry(this, other) + subroutine copy_allhistfldlist_entry(this, other) ! set this = other - class(master_entry), intent(out) :: this + class(allhistfldlist_entry), intent(out) :: this class(entry_base), intent(in) :: other select type(this) - type is (master_entry) + type is (allhistfldlist_entry) select type(other) - type is (master_entry) + type is (allhistfldlist_entry) this = other class default - call endrun('Unexpected type of "other" in copy_master_entry') + call endrun('Unexpected type of "other" in copy_allhistfldlist_entry') end select class default - call endrun('Unexpected type of "this" in copy_master_entry') + call endrun('Unexpected type of "this" in copy_allhistfldlist_entry') end select - end subroutine copy_master_entry + end subroutine copy_allhistfldlist_entry !----------------------------------------------------------------------- subroutine copy_history_entry(this, other) @@ -1161,7 +1161,7 @@ subroutine htape_addfld (t, f, avgflag) if (htapes_defined) then write(iulog,*) trim(subname),' ERROR: attempt to add field ', & - masterlist(f)%field%name, ' after history files are set' + allhistfldlist(f)%field%name, ' after history files are set' call endrun(msg=errMsg(sourcefile, __LINE__)) end if @@ -1170,7 +1170,7 @@ subroutine htape_addfld (t, f, avgflag) ! Copy field information - tape(t)%hlist(n)%field = masterlist(f)%field + tape(t)%hlist(n)%field = allhistfldlist(f)%field ! Determine bounds @@ -1254,8 +1254,8 @@ subroutine htape_addfld (t, f, avgflag) tape(t)%hlist(n)%field%num1d_out = num1d_out ! Fields native bounds - beg1d = masterlist(f)%field%beg1d - end1d = masterlist(f)%field%end1d + beg1d = allhistfldlist(f)%field%beg1d + end1d = allhistfldlist(f)%field%end1d ! Alloccate and initialize history buffer and related info @@ -1270,7 +1270,7 @@ subroutine htape_addfld (t, f, avgflag) tape(t)%hlist(n)%hbuf(:,:) = 0._r8 tape(t)%hlist(n)%nacs(:,:) = 0 - ! Set time averaging flag based on masterlist setting or + ! Set time averaging flag based on allhistfldlist setting or ! override the default averaging flag with namelist setting if (.not. avgflag_valid(avgflag, blank_valid=.true.)) then @@ -1279,7 +1279,7 @@ subroutine htape_addfld (t, f, avgflag) end if if (avgflag == ' ') then - tape(t)%hlist(n)%avgflag = masterlist(f)%avgflag(t) + tape(t)%hlist(n)%avgflag = allhistfldlist(f)%avgflag(t) else tape(t)%hlist(n)%avgflag = avgflag end if @@ -5179,7 +5179,7 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & ! !DESCRIPTION: ! Initialize a single level history field. The pointer inputs, ptr\_*, ! point to the appropriate-type array storing the raw history data points. - ! The value of type1d passed to masterlist\_add\_fld determines which of the + ! The value of type1d passed to allhistfldlist\_add\_fld determines which of the ! 1d type of the output and the beginning and ending indices the history ! buffer field). All fields default to being written to the first history tape ! unless 'default' is set to 'inactive'. @@ -5367,9 +5367,9 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & if (present(l2g_scale_type)) scale_type_l2g = l2g_scale_type if (present(type1d_out)) l_type1d_out = type1d_out - ! Add field to masterlist + ! Add field to allhistfldlist - call masterlist_addfld (fname=trim(fname), numdims=1, type1d=l_type1d, & + call allhistfldlist_addfld (fname=trim(fname), numdims=1, type1d=l_type1d, & type1d_out=l_type1d_out, type2d='unset', num2d=1, & units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, & p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, & @@ -5382,7 +5382,7 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & if (trim(l_default) == 'inactive') then return else - call masterlist_make_active (name=trim(fname), tape_index=1) + call allhistfldlist_make_active (name=trim(fname), tape_index=1) end if end subroutine hist_addfld1d @@ -5397,7 +5397,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, ! !DESCRIPTION: ! Initialize a single level history field. The pointer inputs, ptr\_*, ! point to the appropriate-type array storing the raw history data points. - ! The value of type1d passed to masterlist\_add\_fld determines which of the + ! The value of type1d passed to allhistfldlist\_add\_fld determines which of the ! 1d type of the output and the beginning and ending indices the history ! buffer field). All fields default to being written to the first history tape ! unless 'default' is set to 'inactive'. @@ -5703,9 +5703,9 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, if (present(l2g_scale_type)) scale_type_l2g = l2g_scale_type if (present(type1d_out)) l_type1d_out = type1d_out - ! Add field to masterlist + ! Add field to allhistfldlist - call masterlist_addfld (fname=trim(fname), numdims=2, type1d=l_type1d, & + call allhistfldlist_addfld (fname=trim(fname), numdims=2, type1d=l_type1d, & type1d_out=l_type1d_out, type2d=type2d, num2d=num2d, & units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, & p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, & @@ -5718,7 +5718,7 @@ subroutine hist_addfld2d (fname, type2d, units, avgflag, long_name, type1d_out, if (trim(l_default) == 'inactive') then return else - call masterlist_make_active (name=trim(fname), tape_index=1) + call allhistfldlist_make_active (name=trim(fname), tape_index=1) end if end subroutine hist_addfld2d From 9f249bbb56e0b813fbf394368e757ffdbb78dddb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 14:15:34 -0600 Subject: [PATCH 1355/2067] histFileMod no longer prints variable numbers to .rst files. --- src/main/histFileMod.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index bdcec28ec1..ac12008302 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -451,8 +451,8 @@ subroutine hist_printflds() fmt_txt = '('//str_w_col_sum//'a)' write(hist_fields_file,fmt_txt) ('-', i=1, width_col_sum) ! Concatenate strings needed in format statement - fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',x,a'//str_width_col(5)//')' - write(hist_fields_file,fmt_txt) '#', 'Variable Name', & + fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//')' + write(hist_fields_file,fmt_txt) 'Variable Name', & 'Long Description', 'Units', 'Active?' ! End header, same as header @@ -465,9 +465,9 @@ subroutine hist_printflds() ! Main table ! Concatenate strings needed in format statement - fmt_txt = '(i'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',l'//str_width_col(5)//')' + fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',l'//str_width_col(4)//')' do nf = 1,nallhistflds - write(hist_fields_file,fmt_txt) nf, & + write(hist_fields_file,fmt_txt) & allhistfldlist(nf)%field%name, & allhistfldlist(nf)%field%long_name, & allhistfldlist(nf)%field%units, & From 5709993881a361bc32d5a7e8870c1210f7f5c861 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 11 Aug 2023 14:38:59 -0600 Subject: [PATCH 1356/2067] Add a clarifying comment to the code --- src/biogeophys/SnowSnicarMod.F90 | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 2a7296178f..8453a8670d 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1846,6 +1846,25 @@ subroutine SnowOptics_init( ) ! flux weights/spectrum call ncd_io( 'flx_wgt_dir5_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'flx_wgt_dif5_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + ! + ! THIS NOTE APPLIES TO ALL THE call ncd_io LINES BELOW WHERE + ! bcphob AND ocphob GET ASSIGNED TO VARIABLES SUFFIXED bc1/oc1: + ! + ! Assumption (1) applies here, in the input section. + ! Assumption (2) applies later, in the snicar code. + ! + ! 1) In this section, hydrophillic particles behave like hydrophobic + ! particles. We assume bc1/oc1 to have the same optics as bc2/oc2 + ! because sulfate coating on the bc1/oc1 surface is assumed to be + ! dissolved into the hydrometeo (i.e, snow grain here) during the + ! deposition process. This is different from the assumption made in + ! prior model versions, where bc1/oc1 was coated by undissolved + ! sulfate. + ! 2) Later, in the snicar code, if the bc-snow internal mixing option + ! is on, bc1/oc1 (internally mixed within the snow grain) will be + ! treated differently than bc2/oc2 (mixed externally or outside the + ! snow grain). + ! ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing call ncd_io( 'ss_alb_bcphob_dif_mlw', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) call ncd_io( 'asm_prm_bcphob_dif_mlw', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) From a5e8c7c90e50000475ecab3399aa7b674c5ee664 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 11 Aug 2023 14:58:16 -0600 Subject: [PATCH 1357/2067] Draft of ChangeLog/Sum files --- doc/ChangeLog | 155 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 156 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index e65560d5c3..cfed3b83f3 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,159 @@ =============================================================== +Tag name: ctsm5.1.dev13? +Originator(s): @cenlinhe (Cenlin He,UCAR/RAL), slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Fri Aug 11 14:39:06 MDT 2023 +One-line Summary: SNICAR snow albedo scheme updates + +Purpose and description of changes +---------------------------------- + + Notes copied here from the PR #1861: + + A few substantial changes in the SNICAR module for the following updated snow + albedo calculation features: + - Updated ice optical properties from Flanner et al. (2021), with multiple types + for ice refractive indices. The updated SNICAR database files are: + /glade/work/cenlinhe/NOAA_CPT_snowAER/CLM_SNICAR_data/snicar_optics_480bnd_c012422.nc + /glade/work/cenlinhe/NOAA_CPT_snowAER/CLM_SNICAR_data/snicar_optics_5bnd_c013122.nc + - Updated aerosol optical properties from Flanner et al. (2021) with multiple + dust types & new BC and OC optics (the updated data are in the new SNICAR + database files shown above). + - Updated downward solar spectra from Flanner et al. (2021) for multiple + condition types. + - More accurate radiative transfer solver (adding-doubling) from Dang et al. (2019). + - Nonspherical snow grain scheme from He et al. (2017). + - BC-snow internal mixing scheme from He et al. (2017). + - Dust-snow internal mixing scheme from He et al. (2019). + - Hyperspectral (480-band, 10-nm spectral res) capability with all the above features. + - New namelist controls for aerosol in snow and additional snow albedo + diagnostic output variables. + + Specific notes + - Code contributors: Cenlin He (NCAR/RAL) with advice from + Dave Lawrence (NCAR/CGD) and Mark Flanner (UMich). + - The manuscript to report this update is in preparation (He et al, 2022 JAMES in prep) + - These updates will change the snow and surface albedo results along with + other surface fluxes changes. + - There are a few new namelist options related to SNICAR scheme added to the + namelist control. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): + + +Notes of particular relevance for users +--------------------------------------- +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + New namelist variables: + snicar_numrad_snw = 5 or 480 wavelength bands, default 5 + snicar_solarspec, default "mid_latitude_winter" among six available options + snicar_dust_optics, default "sahara" among three avail. options + snicar_snw_shape, default "hexagonal_plate" among fourn avail. options + snicar_use_aerosol, default .true. + snicar_snobc_intmix and snicar_snodst_intmix, default .false. means do not + activate bc-snow and dust-snow internal mixing + + do_sno_oc, default .false., already appeared in previous code but in caps + snicar_aerforc_diag, default .false., existed before as use_snicar_frc + fsnowoptics now points to an updated 5-band file and has an option for a + 480-band file, as well + +Substantial timing or memory changes: +[e.g., check PFS test in the test suite and look at timings, if you +expect possible significant timing changes] + + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + + +Testing summary: +---------------- +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + YES + + Summarize any changes to answers, i.e., + - what code configurations: All + - what platforms/compilers: All + - nature of change: larger than roundoff; new climate? + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: + + URL for LMWG diagnostics output used to validate new climate: + + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/1861 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev133 Originator(s): adrifoster (Adrianna Foster), glemieux (Gregory Lemieux, LBL/NGEET) Date: Wed Aug 9 22:44:46 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index a72e6235ae..4b7b3c47fa 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev13? slevis ??/??/2023 SNICAR snow albedo scheme updates ctsm5.1.dev133 glemieux 08/09/2023 FATES API update to facilitate fates refactor ctsm5.1.dev132 slevis 08/04/2023 Add parameterization to allow excess ice in soil and subsidence ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars From 093e54c1babee332483a4f0e7a8fd1ad7520bc6e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 11 Aug 2023 15:16:05 -0600 Subject: [PATCH 1358/2067] Update to the ChangeLog --- doc/ChangeLog | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index cfed3b83f3..e2d894e242 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev13? Originator(s): @cenlinhe (Cenlin He,UCAR/RAL), slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Fri Aug 11 14:39:06 MDT 2023 +Date: Fri Aug 11 15:07:55 MDT 2023 One-line Summary: SNICAR snow albedo scheme updates Purpose and description of changes @@ -48,11 +48,11 @@ Does this tag change answers significantly for any of the following physics conf [X] clm5_1 -[ ] clm5_0 +[X] clm5_0 -[ ] ctsm5_0-nwp +[X] ctsm5_0-nwp -[ ] clm4_5 +[X] clm4_5 Bugs fixed or introduced @@ -74,8 +74,8 @@ Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): do_sno_oc, default .false., already appeared in previous code but in caps snicar_aerforc_diag, default .false., existed before as use_snicar_frc - fsnowoptics now points to an updated 5-band file and has an option for a - 480-band file, as well + fsnowoptics now points to an updated 5-band file and gives the option for a + 480-band file Substantial timing or memory changes: [e.g., check PFS test in the test suite and look at timings, if you @@ -140,6 +140,11 @@ Changes answers relative to baseline: - what platforms/compilers: All - nature of change: larger than roundoff; new climate? + Namelist defaults are such that phys="clm5.0" and phys="clm4.5" give different + answers only due to the changed fsnowoptics file. + Namelist defaults are such that phys="clm5.1" changes answers as a result of + new parameterizations. + If this tag changes climate describe the run(s) done to evaluate the new climate (put details of the simulations in the experiment database) - casename: From d533932fe075ef1f985895f68e9c11cf215a2159 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 14:54:18 -0600 Subject: [PATCH 1359/2067] Fix history_fields_*.rst column widths. --- src/main/histFileMod.F90 | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index ac12008302..c28b3c5c77 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -356,7 +356,7 @@ subroutine hist_printflds() ! !ARGUMENTS: ! ! !LOCAL VARIABLES: - integer, parameter :: ncol = 5 ! number of table columns + integer, parameter :: ncol = 4 ! number of table columns integer nf, i, j ! do-loop counters integer hist_fields_file ! file unit number integer width_col(ncol) ! widths of table columns @@ -390,14 +390,13 @@ subroutine hist_printflds() if (masterproc .and. hist_fields_list_file) then ! Hardwired table column widths to fit the table on a computer ! screen. Some strings will be truncated as a result of the - ! current choices (4, 35, 94, 65, 7). In sphinx (ie the web-based + ! current choices (35, 94, 65, 7). In sphinx (ie the web-based ! documentation), text that has not been truncated will wrap ! around in the available space. - width_col(1) = 4 ! column that shows the variable number, nf - width_col(2) = 35 ! variable name column - width_col(3) = 94 ! long description column - width_col(4) = 65 ! units column - width_col(5) = 7 ! active (T or F) column + width_col(1) = 35 ! variable name column + width_col(2) = 94 ! long description column + width_col(3) = 65 ! units column + width_col(4) = 7 ! active (T or F) column width_col_sum = sum(width_col) + ncol - 1 ! sum of widths & blank spaces ! Convert integer widths to strings for use in format statements From 614d0e1dd886f62a9d5abe885749dad5b8c1341b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 11 Aug 2023 16:10:17 -0600 Subject: [PATCH 1360/2067] Draft ChangeLog and ChangeSum --- doc/ChangeLog | 101 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 102 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ec7f8303a1..5cdbe4c1cc 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,105 @@ =============================================================== +Tag name: ctsm5.1.dev13? +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Fri Aug 11 15:55:11 MDT 2023 +One-line Summary: Change small snocan to zero + +Purpose and description of changes +---------------------------------- + + Issues #2041 and #2048 discuss and resolve a test failure in the ctsm5.2 + branch. The failure goes away when we reset small snocan to zero. + + @billsacks recommended merging this change in ctsm5.1 and then updating + the ctsm5.2 branch to the latest ctsm5.1. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): + #2041 + #2048 + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + Yes + + Summarize any changes to answers, i.e., + - what code configurations: All + - what platforms/compilers: All + - nature of change: roundoff + + The answer changes are expected to be roundoff-level because the code change + just truncates roundoff-level greater-than-zero states to exactly zero for + snocan that most likely needed to be zero anyway. + We find that the answer changes grow to greater than roundoff, but the + cprnc.out file from a 20-year izumi test-suite case does not contain + differences of concerning magnitude. + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2053 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev131 Originator(s): samrabin (Sam Rabin,UCAR/TSS) Date: Thu Jul 27 14:24:07 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 2d1812cd13..0f6e8b5084 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev13? slevis ??/??/2023 Change small snocan to zero ctsm5.1.dev131 samrabin 07/27/2023 Enable prescribed crop calendars ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml From 402f91802f8ca215cdda8be5004d78e1a178803e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 16:31:33 -0600 Subject: [PATCH 1361/2067] Fix .rst output filenames. --- src/main/histFileMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index c28b3c5c77..6c0b53abc1 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -364,7 +364,7 @@ subroutine hist_printflds() character(len=3) str_width_col(ncol) ! string version of width_col character(len=3) str_w_col_sum ! string version of width_col_sum character(len=7) file_identifier ! fates identifier used in file_name - character(len=23) file_name ! hist_fields_file.rst with or without fates + character(len=26) file_name ! hist_fields_file.rst with or without fates character(len=99) fmt_txt ! format statement character(len=*),parameter :: subname = 'CLM_hist_printflds' !----------------------------------------------------------------------- From 0722eee4ba91b831da2318bfbeece9fd602eaa6d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 16:53:14 -0600 Subject: [PATCH 1362/2067] Added testmod SaveHistFieldList. --- .../testdefs/testmods_dirs/clm/SaveHistFieldList/user_nl_clm | 1 + 1 file changed, 1 insertion(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/SaveHistFieldList/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/SaveHistFieldList/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/SaveHistFieldList/user_nl_clm new file mode 100644 index 0000000000..4791cd28b2 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/SaveHistFieldList/user_nl_clm @@ -0,0 +1 @@ +hist_fields_list_file = .true. From 302624a6e16983b82976d93a89172c1a45ae68b2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 11 Aug 2023 17:09:35 -0600 Subject: [PATCH 1363/2067] Updated history_fields_*.rst files with latest default outputs. --- .../history_fields_fates.rst | 795 ++++++++++-------- .../history_fields_nofates.rst | 143 ++-- 2 files changed, 502 insertions(+), 436 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index 8b30306a9e..2fe1035549 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -8,13 +8,16 @@ use_cn = F use_crop = F use_fates = T -==== =================================== ============================================================================================== ================================================================= ======= +=================================== ============================================================================================== ================================================================= ======= CTSM History Fields ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ - # Variable Name Long Description Units Active? -==== =================================== ============================================================================================== ================================================================= ======= +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ + Variable Name Long Description Units Active? +=================================== ============================================================================================== ================================================================= ======= A5TMIN 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB actual N immobilization gN/m^2/s T +ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F ACT_SOMC ACT_SOM C gC/m^2 T ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F @@ -35,9 +38,6 @@ ACT_SOM_HR_S2 Het. Resp. from active soil organic ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F -AGB Aboveground biomass gC m-2 T -AGB_SCLS Aboveground biomass by size class kgC/m2 T -AGB_SCPF Aboveground biomass by pft/size kgC/m2 F AGLB Aboveground leaf biomass kg/m^2 F AGSB Aboveground stem biomass kg/m^2 F ALBD surface albedo (direct) proportion F @@ -47,54 +47,12 @@ ALBI surface albedo (indirect) ALT current active layer thickness m F ALTMAX maximum annual active layer thickness m F ALTMAX_LASTYEAR maximum prior year active layer thickness m F -AR autotrophic respiration gC/m^2/s T -AREA_BURNT_BY_PATCH_AGE spitfire area burnt by patch age (divide by patch_area_by_age to get burnt fraction by age) m2/m2/day T -AREA_PLANT area occupied by all plants m2/m2 T -AREA_TREES area occupied by woody plants m2/m2 T -AR_AGSAPM_SCPF above-ground sapwood maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_CANOPY autotrophic respiration of canopy plants gC/m^2/s T -AR_CANOPY_SCPF autotrophic respiration of canopy plants by pft/size kgC/m2/yr F -AR_CROOTM_SCPF below-ground sapwood maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_DARKM_SCPF dark portion of maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_FROOTM_SCPF fine root maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_GROW_SCPF growth autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_MAINT_SCPF maintenance autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_SCPF total autotrophic respiration per m2 per year by pft/size kgC/m2/yr F -AR_UNDERSTORY autotrophic respiration of understory plants gC/m^2/s T -AR_UNDERSTORY_SCPF autotrophic respiration of understory plants by pft/size kgC/m2/yr F +ATM_O3 atmospheric ozone partial pressure mol/mol F ATM_TOPO atmospheric surface height m T AnnET Annual ET mm/s F -BA_SCLS basal area by size class m2/ha T -BA_SCPF basal area by pft/size m2/ha F BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T -BDEAD_MD_CANOPY_SCLS BDEAD_MD for canopy plants by size class kg C / ha / yr F -BDEAD_MD_UNDERSTORY_SCLS BDEAD_MD for understory plants by size class kg C / ha / yr F -BIOMASS_AGEPFT biomass per PFT in each age bin kg C / m2 F -BIOMASS_BY_AGE Total Biomass within a given patch age bin kgC/m2 F -BIOMASS_CANOPY Biomass of canopy plants gC m-2 T -BIOMASS_SCLS Total biomass by size class kgC/m2 F -BIOMASS_UNDERSTORY Biomass of understory plants gC m-2 T -BLEAF_CANOPY_SCPF biomass carbon in leaf of canopy plants by pft/size kgC/ha F -BLEAF_UNDERSTORY_SCPF biomass carbon in leaf of understory plants by pft/size kgC/ha F -BSTORE_MD_CANOPY_SCLS BSTORE_MD for canopy plants by size class kg C / ha / yr F -BSTORE_MD_UNDERSTORY_SCLS BSTORE_MD for understory plants by size class kg C / ha / yr F -BSTOR_CANOPY_SCPF biomass carbon in storage pools of canopy plants by pft/size kgC/ha F -BSTOR_UNDERSTORY_SCPF biomass carbon in storage pools of understory plants by pft/size kgC/ha F -BSW_MD_CANOPY_SCLS BSW_MD for canopy plants by size class kg C / ha / yr F -BSW_MD_UNDERSTORY_SCLS BSW_MD for understory plants by size class kg C / ha / yr F BTRAN transpiration beta factor unitless T BTRANMN daily minimum of transpiration beta factor unitless T -BURNT_LITTER_FRAC_AREA_PRODUCT product of fraction of fuel burnt and burned area (divide by FIRE_AREA to get burned-area-weig fraction T -C13disc_SCPF C13 discrimination by pft/size per mil F -CAMBIALFIREMORT_SCPF cambial fire mortality by pft/size N/ha/yr F -CANOPY_AREA_BY_AGE canopy area by age bin m2/m2 T -CANOPY_HEIGHT_DIST canopy height distribution m2/m2 T -CANOPY_SPREAD Scaling factor between tree basal area and canopy area 0-1 T -CARBON_BALANCE_CANOPY_SCLS CARBON_BALANCE for canopy plants by size class kg C / ha / yr F -CARBON_BALANCE_UNDERSTORY_SCLS CARBON_BALANCE for understory plants by size class kg C / ha / yr F -CBALANCE_ERROR_FATES total carbon error, FATES mgC/day T -CEFFLUX carbon efflux, root to soil kgC/ha/day T -CEFFLUX_SCPF carbon efflux, root to soil, by size-class x pft kg/ha/day F CEL_LITC CEL_LIT C gC/m^2 T CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F @@ -125,41 +83,10 @@ CONC_CH4_UNSAT CH4 soil Concentration for non-inundated are CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T COSZEN cosine of solar zenith angle none F -CROWNAREA_CAN total crown area in each canopy layer m2/m2 T -CROWNAREA_CNLF total crown area that is occupied by leaves in each canopy and leaf layer m2/m2 F -CROWNFIREMORT_SCPF crown fire mortality by pft/size N/ha/yr F -CROWN_AREA_CANOPY_SCLS total crown area of canopy plants by size class m2/ha F -CROWN_AREA_UNDERSTORY_SCLS total crown area of understory plants by size class m2/ha F -CWDC_HR cwd C heterotrophic respiration gC/m^2/s F -CWD_AG_CWDSC size-resolved AG CWD stocks gC/m^2 F -CWD_AG_IN_CWDSC size-resolved AG CWD input gC/m^2/y F -CWD_AG_OUT_CWDSC size-resolved AG CWD output gC/m^2/y F -CWD_BG_CWDSC size-resolved BG CWD stocks gC/m^2 F -CWD_BG_IN_CWDSC size-resolved BG CWD input gC/m^2/y F -CWD_BG_OUT_CWDSC size-resolved BG CWD output gC/m^2/y F -C_LBLAYER mean leaf boundary layer conductance umol m-2 s-1 T -C_LBLAYER_BY_AGE mean leaf boundary layer conductance - by patch age umol m-2 s-1 F -C_STOMATA mean stomatal conductance umol m-2 s-1 T -C_STOMATA_BY_AGE mean stomatal conductance - by patch age umol m-2 s-1 F -DDBH_CANOPY_SCAG growth rate of canopy plantsnumber of plants per hectare in canopy in each size x age class cm/yr/ha F -DDBH_CANOPY_SCLS diameter growth increment by pft/size cm/yr/ha T -DDBH_CANOPY_SCPF diameter growth increment by pft/size cm/yr/ha F -DDBH_SCPF diameter growth increment by pft/size cm/yr/ha F -DDBH_UNDERSTORY_SCAG growth rate of understory plants in each size x age class cm/yr/ha F -DDBH_UNDERSTORY_SCLS diameter growth increment by pft/size cm/yr/ha T -DDBH_UNDERSTORY_SCPF diameter growth increment by pft/size cm/yr/ha F -DEMOTION_CARBONFLUX demotion-associated biomass carbon flux from canopy to understory gC/m2/s T -DEMOTION_RATE_SCLS demotion rate from canopy to understory by size class indiv/ha/yr F +CWDC_HR cwd C heterotrophic respiration gC/m^2/s T DENIT total rate of denitrification gN/m^2/s T DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F -DISPLA displacement height m F -DISTURBANCE_RATE_FIRE Disturbance rate from fire m2 m-2 d-1 T -DISTURBANCE_RATE_LOGGING Disturbance rate from logging m2 m-2 d-1 T -DISTURBANCE_RATE_P2P Disturbance rate from primary to primary lands m2 m-2 d-1 T -DISTURBANCE_RATE_P2S Disturbance rate from primary to secondary lands m2 m-2 d-1 T -DISTURBANCE_RATE_POTENTIAL Potential (i.e., including unresolved) disturbance rate m2 m-2 d-1 T -DISTURBANCE_RATE_S2S Disturbance rate from secondary to secondary lands m2 m-2 d-1 T -DISTURBANCE_RATE_TREEFALL Disturbance rate from treefall m2 m-2 d-1 T +DISPLA displacement height (vegetated landunits only) m F DPVLTRB1 turbulent deposition velocity 1 m/s F DPVLTRB2 turbulent deposition velocity 2 m/s F DPVLTRB3 turbulent deposition velocity 3 m/s F @@ -170,16 +97,8 @@ DSTFLXT total surface dust emission DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F -ED_NCOHORTS Total number of ED cohorts per site none T -ED_NPATCHES Total number of ED patches per site none T -ED_balive Live biomass gC m-2 T -ED_bdead Dead (structural) biomass (live trees, not CWD) gC m-2 T -ED_bfineroot Fine root biomass gC m-2 T -ED_biomass Total biomass gC m-2 T -ED_bleaf Leaf biomass gC m-2 T -ED_bsapwood Sapwood biomass gC m-2 T -ED_bstore Storage biomass gC m-2 T -EFFECT_WSPEED effective windspeed for fire spread none T +DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T EFLX_GNET net heat flux into ground W/m^2 F @@ -192,24 +111,375 @@ EFLX_SOIL_GRND soil heat flux [+ into soil] ELAI exposed one-sided leaf area index m^2/m^2 T ERRH2O total water conservation error mm T ERRH2OSNO imbalance in snow depth (liquid water) mm T -ERROR_FATES total error, FATES mass-balance mg/day T ERRSEB surface energy conservation error W/m^2 T ERRSOI soil/lake energy conservation error W/m^2 T ERRSOL solar radiation conservation error W/m^2 T ESAI exposed one-sided stem area index m^2/m^2 T -FABD_SHA_CNLF shade fraction of direct light absorbed by each canopy and leaf layer fraction F -FABD_SHA_CNLFPFT shade fraction of direct light absorbed by each canopy, leaf, and PFT fraction F -FABD_SHA_TOPLF_BYCANLAYER shade fraction of direct light absorbed by the top leaf layer of each canopy layer fraction F -FABD_SUN_CNLF sun fraction of direct light absorbed by each canopy and leaf layer fraction F -FABD_SUN_CNLFPFT sun fraction of direct light absorbed by each canopy, leaf, and PFT fraction F -FABD_SUN_TOPLF_BYCANLAYER sun fraction of direct light absorbed by the top leaf layer of each canopy layer fraction F -FABI_SHA_CNLF shade fraction of indirect light absorbed by each canopy and leaf layer fraction F -FABI_SHA_CNLFPFT shade fraction of indirect light absorbed by each canopy, leaf, and PFT fraction F -FABI_SHA_TOPLF_BYCANLAYER shade fraction of indirect light absorbed by the top leaf layer of each canopy layer fraction F -FABI_SUN_CNLF sun fraction of indirect light absorbed by each canopy and leaf layer fraction F -FABI_SUN_CNLFPFT sun fraction of indirect light absorbed by each canopy, leaf, and PFT fraction F -FABI_SUN_TOPLF_BYCANLAYER sun fraction of indirect light absorbed by the top leaf layer of each canopy layer fraction F -FATES_HR heterotrophic respiration gC/m^2/s T +FATES_ABOVEGROUND_MORT_SZPF Aboveground flux of carbon from AGB to necromass due to mortality kg m-2 s-1 F +FATES_ABOVEGROUND_PROD_SZPF Aboveground carbon productivity kg m-2 s-1 F +FATES_AGSAPMAINTAR_SZPF above-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F +FATES_AGSAPWOOD_ALLOC_SZPF allocation to above-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AGSTRUCT_ALLOC_SZPF allocation to above-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AR autotrophic respiration gC/m^2/s T +FATES_AREA_PLANTS area occupied by all plants per m2 land area m2 m-2 T +FATES_AREA_TREES area occupied by woody plants per m2 land area m2 m-2 T +FATES_AR_CANOPY autotrophic respiration of canopy plants gC/m^2/s T +FATES_AR_UNDERSTORY autotrophic respiration of understory plants gC/m^2/s T +FATES_AUTORESP autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_AUTORESP_CANOPY autotrophic respiration of canopy plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_AUTORESP_CANOPY_SZPF autotrophic respiration of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AUTORESP_SECONDARY autotrophic respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_AUTORESP_SZPF total autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_AUTORESP_USTORY autotrophic respiration of understory plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_AUTORESP_USTORY_SZPF autotrophic respiration of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BASALAREA_SZ basal area by size class m2 m-2 T +FATES_BASALAREA_SZPF basal area by pft/size m2 m-2 F +FATES_BA_WEIGHTED_HEIGHT basal area-weighted mean height of woody plants m T +FATES_BGSAPMAINTAR_SZPF below-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F +FATES_BGSAPWOOD_ALLOC_SZPF allocation to below-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BGSTRUCT_ALLOC_SZPF allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BURNFRAC burned area fraction per second s-1 T +FATES_BURNFRAC_AP spitfire fraction area burnt (per second) by patch age s-1 T +FATES_C13DISC_SZPF C13 discrimination by pft/size per mil F +FATES_CANOPYAREA_AP canopy area by age bin per m2 land area m2 m-2 T +FATES_CANOPYAREA_HT canopy area height distribution m2 m-2 T +FATES_CANOPYCROWNAREA_PF total PFT-level canopy-layer crown area per m2 land area m2 m-2 T +FATES_CANOPY_SPREAD scaling factor (0-1) between tree basal area and canopy area T +FATES_CANOPY_VEGC biomass of canopy plants in kg carbon per m2 land area kg m-2 T +FATES_CA_WEIGHTED_HEIGHT crown area-weighted mean height of canopy plants m T +FATES_CBALANCE_ERROR total carbon error in kg carbon per second kg s-1 T +FATES_COLD_STATUS site-level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not too cold T +FATES_CROOTMAINTAR live coarse root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_CROOTMAINTAR_CANOPY_SZ live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F +FATES_CROOTMAINTAR_USTORY_SZ live coarse root maintenance autotrophic respiration for understory plants in kg carbon per m2 kg m-2 s-1 F +FATES_CROOT_ALLOC allocation to coarse roots in kg carbon per m2 per second kg m-2 s-1 T +FATES_CROWNAREA_CANOPY_SZ total crown area of canopy plants by size class m2 m-2 F +FATES_CROWNAREA_CL total crown area in each canopy layer m2 m-2 T +FATES_CROWNAREA_CLLL total crown area that is occupied by leaves in each canopy and leaf layer m2 m-2 F +FATES_CROWNAREA_PF total PFT-level crown area per m2 land area m2 m-2 T +FATES_CROWNAREA_USTORY_SZ total crown area of understory plants by size class m2 m-2 F +FATES_CWD_ABOVEGROUND_DC debris class-level aboveground coarse woody debris stocks in kg carbon per m2 kg m-2 F +FATES_CWD_ABOVEGROUND_IN_DC debris class-level aboveground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_ABOVEGROUND_OUT_DC debris class-level aboveground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_BELOWGROUND_DC debris class-level belowground coarse woody debris stocks in kg carbon per m2 kg m-2 F +FATES_CWD_BELOWGROUND_IN_DC debris class-level belowground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_BELOWGROUND_OUT_DC debris class-level belowground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F +FATES_DAYSINCE_COLDLEAFOFF site-level days elapsed since cold leaf drop days T +FATES_DAYSINCE_COLDLEAFON site-level days elapsed since cold leaf flush days T +FATES_DAYSINCE_DROUGHTLEAFOFF_PF PFT-level days elapsed since drought leaf drop days T +FATES_DAYSINCE_DROUGHTLEAFON_PF PFT-level days elapsed since drought leaf flush days T +FATES_DDBH_CANOPY_SZ diameter growth increment by size of canopy plants m m-2 yr-1 T +FATES_DDBH_CANOPY_SZAP growth rate of canopy plants in meters DBH per m2 per year in canopy in each size x age class m m-2 yr-1 F +FATES_DDBH_CANOPY_SZPF diameter growth increment by pft/size m m-2 yr-1 F +FATES_DDBH_SZPF diameter growth increment by pft/size m m-2 yr-1 F +FATES_DDBH_USTORY_SZ diameter growth increment by size of understory plants m m-2 yr-1 T +FATES_DDBH_USTORY_SZAP growth rate of understory plants in meters DBH per m2 per year in each size x age class m m-2 yr-1 F +FATES_DDBH_USTORY_SZPF diameter growth increment by pft/size m m-2 yr-1 F +FATES_DEMOTION_CARBONFLUX demotion-associated biomass carbon flux from canopy to understory in kg carbon per m2 per seco kg m-2 s-1 T +FATES_DEMOTION_RATE_SZ demotion rate from canopy to understory by size class in number of plants per m2 per year m-2 yr-1 F +FATES_DISTURBANCE_RATE_FIRE disturbance rate from fire m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_LOGGING disturbance rate from logging m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_P2P disturbance rate from primary to primary lands m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_P2S disturbance rate from primary to secondary lands m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_POTENTIAL potential (i.e., including unresolved) disturbance rate m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_S2S disturbance rate from secondary to secondary lands m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_TREEFALL disturbance rate from treefall m2 m-2 yr-1 T +FATES_DROUGHT_STATUS_PF PFT-level drought status, <2 too dry for leaves, >=2 not too dry T +FATES_EFFECT_WSPEED effective wind speed for fire spread in meters per second m s-1 T +FATES_ELONG_FACTOR_PF PFT-level mean elongation factor (partial flushing/abscission) 1 T +FATES_ERROR_EL total mass-balance error in kg per second by element kg s-1 T +FATES_EXCESS_RESP respiration of un-allocatable carbon gain kg m-2 s-1 T +FATES_FABD_SHA_CLLL shade fraction of direct light absorbed by each canopy and leaf layer 1 F +FATES_FABD_SHA_CLLLPF shade fraction of direct light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABD_SHA_TOPLF_CL shade fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABD_SUN_CLLL sun fraction of direct light absorbed by each canopy and leaf layer 1 F +FATES_FABD_SUN_CLLLPF sun fraction of direct light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABD_SUN_TOPLF_CL sun fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABI_SHA_CLLL shade fraction of indirect light absorbed by each canopy and leaf layer 1 F +FATES_FABI_SHA_CLLLPF shade fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABI_SHA_TOPLF_CL shade fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABI_SUN_CLLL sun fraction of indirect light absorbed by each canopy and leaf layer 1 F +FATES_FABI_SUN_CLLLPF sun fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABI_SUN_TOPLF_CL sun fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FDI Fire Danger Index (probability that an ignition will lead to a fire) 1 T +FATES_FIRE_CLOSS carbon loss to atmosphere from fire in kg carbon per m2 per second kg m-2 s-1 T +FATES_FIRE_FLUX_EL loss to atmosphere from fire by element in kg element per m2 per s kg m-2 s-1 T +FATES_FIRE_INTENSITY spitfire surface fireline intensity in J per m per second J m-1 s-1 T +FATES_FIRE_INTENSITY_BURNFRAC product of surface fire intensity and burned area fraction -- divide by FATES_BURNFRAC to get J m-1 s-1 T +FATES_FIRE_INTENSITY_BURNFRAC_AP product of fire intensity and burned fraction, resolved by patch age (so divide by FATES_BURNF J m-1 s-1 T +FATES_FRACTION total gridcell fraction which FATES is running over m2 m-2 T +FATES_FRAGMENTATION_SCALER_SL factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T +FATES_FROOTC total biomass in live plant fine roots in kg carbon per m2 kg m-2 T +FATES_FROOTCTURN_CANOPY_SZ fine root turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOTCTURN_USTORY_SZ fine root turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_FROOTC_SL Total carbon in live plant fine-roots over depth kg m-3 T +FATES_FROOTC_SZPF fine-root carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_FROOTMAINTAR fine root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_FROOTMAINTAR_CANOPY_SZ live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F +FATES_FROOTMAINTAR_SZPF fine root maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_FROOTMAINTAR_USTORY_SZ fine root maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F +FATES_FROOT_ALLOC allocation to fine roots in kg carbon per m2 per second kg m-2 s-1 T +FATES_FROOT_ALLOC_CANOPY_SZ allocation to fine root C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOT_ALLOC_SZPF allocation to fine roots by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOT_ALLOC_USTORY_SZ allocation to fine roots for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FUELCONSUMED total fuel consumed in kg carbon per m2 land area kg m-2 T +FATES_FUEL_AMOUNT total ground fuel related to FATES_ROS (omits 1000hr fuels) in kg C per m2 land area kg m-2 T +FATES_FUEL_AMOUNT_AP spitfire ground fuel (kg carbon per m2) related to FATES_ROS (omits 1000hr fuels) within each kg m-2 T +FATES_FUEL_AMOUNT_APFC spitfire fuel quantity in each age x fuel class in kg carbon per m2 land area kg m-2 F +FATES_FUEL_AMOUNT_FC spitfire fuel-class level fuel amount in kg carbon per m2 land area kg m-2 T +FATES_FUEL_BULKD fuel bulk density in kg per m3 kg m-3 T +FATES_FUEL_BURNT_BURNFRAC_FC product of fraction (0-1) of fuel burnt and burnt fraction (divide by FATES_BURNFRAC to get bu 1 T +FATES_FUEL_EFF_MOIST spitfire fuel moisture (volumetric) m3 m-3 T +FATES_FUEL_MEF fuel moisture of extinction (volumetric) m3 m-3 T +FATES_FUEL_MOISTURE_FC spitfire fuel class-level fuel moisture (volumetric) m3 m-3 T +FATES_FUEL_SAV spitfire fuel surface area to volume ratio m-1 T +FATES_GDD site-level growing degree days degree_Celsius T +FATES_GPP gross primary production in kg carbon per m2 per second kg m-2 s-1 T +FATES_GPP_AP gross primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_CANOPY gross primary production of canopy plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_GPP_CANOPY_SZPF gross primary production of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_PF total PFT-level GPP in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_GPP_SECONDARY gross primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_GPP_SE_PF total PFT-level GPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T +FATES_GPP_SZPF gross primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_USTORY gross primary production of understory plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_GPP_USTORY_SZPF gross primary production of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GROWAR_CANOPY_SZ growth autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_GROWAR_SZPF growth autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_GROWAR_USTORY_SZ growth autotrophic respiration of understory plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_GROWTHFLUX_FUSION_SZPF flux of individuals into a given size class bin via fusion m-2 yr-1 F +FATES_GROWTHFLUX_SZPF flux of individuals into a given size class bin via growth and recruitment m-2 yr-1 F +FATES_GROWTH_RESP growth respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_GROWTH_RESP_SECONDARY growth respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_HARVEST_CARBON_FLUX harvest carbon flux in kg carbon per m2 per year kg m-2 yr-1 T +FATES_HARVEST_DEBT Accumulated carbon failed to be harvested kg C T +FATES_HARVEST_DEBT_SEC Accumulated carbon failed to be harvested from secondary patches kg C T +FATES_HET_RESP heterotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_IGNITIONS number of successful fire ignitions per m2 land area per second m-2 s-1 T +FATES_LAI leaf area index per m2 land area m2 m-2 T +FATES_LAISHA_TOP_CL LAI in the shade by the top leaf layer of each canopy layer m2 m-2 F +FATES_LAISHA_Z_CLLL LAI in the shade by each canopy and leaf layer m2 m-2 F +FATES_LAISHA_Z_CLLLPF LAI in the shade by each canopy, leaf, and PFT m2 m-2 F +FATES_LAISUN_TOP_CL LAI in the sun by the top leaf layer of each canopy layer m2 m-2 F +FATES_LAISUN_Z_CLLL LAI in the sun by each canopy and leaf layer m2 m-2 F +FATES_LAISUN_Z_CLLLPF LAI in the sun by each canopy, leaf, and PFT m2 m-2 F +FATES_LAI_AP leaf area index by age bin per m2 land area m2 m-2 T +FATES_LAI_CANOPY_SZ leaf area index (LAI) of canopy plants by size class m2 m-2 T +FATES_LAI_CANOPY_SZPF Leaf area index (LAI) of canopy plants by pft/size m2 m-2 F +FATES_LAI_SECONDARY leaf area index per m2 land area, secondary patches m2 m-2 T +FATES_LAI_USTORY_SZ leaf area index (LAI) of understory plants by size class m2 m-2 T +FATES_LAI_USTORY_SZPF Leaf area index (LAI) of understory plants by pft/size m2 m-2 F +FATES_LBLAYER_COND mean leaf boundary layer conductance mol m-2 s-1 T +FATES_LBLAYER_COND_AP mean leaf boundary layer conductance - by patch age mol m-2 s-1 F +FATES_LEAFAREA_HT leaf area height distribution m2 m-2 T +FATES_LEAFC total biomass in live plant leaves in kg carbon per m2 kg m-2 T +FATES_LEAFCTURN_CANOPY_SZ leaf turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAFCTURN_USTORY_SZ leaf turnover (non-mortal) for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAFC_CANOPY_SZPF biomass in leaves of canopy plants by pft/size in kg carbon per m2 kg m-2 F +FATES_LEAFC_PF total PFT-level leaf biomass in kg carbon per m2 land area kg m-2 T +FATES_LEAFC_SZPF leaf carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_LEAFC_USTORY_SZPF biomass in leaves of understory plants by pft/size in kg carbon per m2 kg m-2 F +FATES_LEAFMAINTAR leaf maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_LEAF_ALLOC allocation to leaves in kg carbon per m2 per second kg m-2 s-1 T +FATES_LEAF_ALLOC_CANOPY_SZ allocation to leaves for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAF_ALLOC_SZPF allocation to leaves by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAF_ALLOC_USTORY_SZ allocation to leaves for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LITTER_AG_CWD_EL mass of aboveground litter in coarse woody debris (trunks/branches/twigs) by element kg m-2 T +FATES_LITTER_AG_FINE_EL mass of aboveground litter in fines (leaves, nonviable seed) by element kg m-2 T +FATES_LITTER_BG_CWD_EL mass of belowground litter in coarse woody debris (coarse roots) by element kg m-2 T +FATES_LITTER_BG_FINE_EL mass of belowground litter in fines (fineroots) by element kg m-2 T +FATES_LITTER_CWD_ELDC total mass of litter in coarse woody debris by element and coarse woody debris size kg m-2 T +FATES_LITTER_IN litter flux in kg carbon per m2 per second kg m-2 s-1 T +FATES_LITTER_IN_EL litter flux in in kg element per m2 per second kg m-2 s-1 T +FATES_LITTER_OUT litter flux out in kg carbon (exudation, fragmentation, seed decay) kg m-2 s-1 T +FATES_LITTER_OUT_EL litter flux out (exudation, fragmentation and seed decay) in kg element kg m-2 s-1 T +FATES_LSTEMMAINTAR live stem maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_LSTEMMAINTAR_CANOPY_SZ live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1 F +FATES_LSTEMMAINTAR_USTORY_SZ live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F +FATES_M3_MORTALITY_CANOPY_SZ C starvation mortality of canopy plants by size N/ha/yr F +FATES_M3_MORTALITY_CANOPY_SZPF C starvation mortality of canopy plants by pft/size N/ha/yr F +FATES_M3_MORTALITY_USTORY_SZ C starvation mortality of understory plants by size N/ha/yr F +FATES_M3_MORTALITY_USTORY_SZPF C starvation mortality of understory plants by pft/size N/ha/yr F +FATES_MAINTAR_CANOPY_SZ maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_MAINTAR_SZPF maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_MAINTAR_USTORY_SZ maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1 F +FATES_MAINT_RESP maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T +FATES_MAINT_RESP_SECONDARY maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_MAINT_RESP_UNREDUCED diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 F +FATES_MEANLIQVOL_DROUGHTPHEN_PF PFT-level mean liquid water volume for drought phenolgy m3 m-3 T +FATES_MEANSMP_DROUGHTPHEN_PF PFT-level mean soil matric potential for drought phenology Pa T +FATES_MORTALITY_AGESCEN_AC age senescence mortality by cohort age in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_AGESCEN_ACPF age senescence mortality by pft/cohort age in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_AGESCEN_SE_SZ age senescence mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_AGESCEN_SZ age senescence mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_AGESCEN_SZPF age senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_BACKGROUND_SE_SZ background mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_BACKGROUND_SZ background mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_BACKGROUND_SZPF background mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CAMBIALBURN_SZPF fire mortality from cambial burn by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CANOPY_SE_SZ total mortality of canopy trees by size class in number of plants per m2, secondary patches m-2 yr-1 T +FATES_MORTALITY_CANOPY_SZ total mortality of canopy trees by size class in number of plants per m2 m-2 yr-1 T +FATES_MORTALITY_CANOPY_SZAP mortality rate of canopy plants in number of plants per m2 per year in each size x age class m-2 yr-1 F +FATES_MORTALITY_CANOPY_SZPF total mortality of canopy plants by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CFLUX_CANOPY flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1 T +FATES_MORTALITY_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from mortality kg m-2 s-1 T +FATES_MORTALITY_CFLUX_USTORY flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1 T +FATES_MORTALITY_CROWNSCORCH_SZPF fire mortality from crown scorch by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CSTARV_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality kg m-2 s-1 T +FATES_MORTALITY_CSTARV_SE_SZ carbon starvation mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_CSTARV_SZ carbon starvation mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_CSTARV_SZPF carbon starvation mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_FIRE_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from fire mortality kg m-2 s-1 T +FATES_MORTALITY_FIRE_SZ fire mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_FIRE_SZPF fire mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_FREEZING_SE_SZ freezing mortality by size in number of plants per m2 per event, secondary patches m-2 event-1 T +FATES_MORTALITY_FREEZING_SZ freezing mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_FREEZING_SZPF freezing mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_HYDRAULIC_SE_SZ hydraulic mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_HYDRAULIC_SZ hydraulic mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_HYDRAULIC_SZPF hydraulic mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_HYDRO_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality kg m-2 s-1 T +FATES_MORTALITY_IMPACT_SZ impact mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_IMPACT_SZPF impact mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_LOGGING_SE_SZ logging mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T +FATES_MORTALITY_LOGGING_SZ logging mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_LOGGING_SZPF logging mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_PF PFT-level mortality rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SE_SZ senescence mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SZ senescence mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SZPF senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_TERMINATION_SZ termination mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_TERMINATION_SZPF termination mortality by pft/size in number pf plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_USTORY_SZ total mortality of understory trees by size class in individuals per m2 per year m-2 yr-1 T +FATES_MORTALITY_USTORY_SZAP mortality rate of understory plants in number of plants per m2 per year in each size x age cla m-2 yr-1 F +FATES_MORTALITY_USTORY_SZPF total mortality of understory plants by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_NCHILLDAYS site-level number of chill days days T +FATES_NCL_AP number of canopy levels by age bin F +FATES_NCOHORTS total number of cohorts per site T +FATES_NCOHORTS_SECONDARY total number of cohorts per site T +FATES_NCOLDDAYS site-level number of cold days days T +FATES_NEP net ecosystem production in kg carbon per m2 per second kg m-2 s-1 T +FATES_NESTEROV_INDEX nesterov fire danger index T +FATES_NET_C_UPTAKE_CLLL net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1 F +FATES_NONSTRUCTC non-structural biomass (sapwood + leaf + fineroot) in kg carbon per m2 kg m-2 T +FATES_NPATCHES total number of patches per site T +FATES_NPATCHES_SECONDARY total number of patches per site T +FATES_NPATCH_AP number of patches by age bin F +FATES_NPLANT_AC number of plants per m2 by cohort age class m-2 T +FATES_NPLANT_ACPF stem number density by pft and age class m-2 F +FATES_NPLANT_CANOPY_SZ number of canopy plants per m2 by size class m-2 T +FATES_NPLANT_CANOPY_SZAP number of plants per m2 in canopy in each size x age class m-2 F +FATES_NPLANT_CANOPY_SZPF number of canopy plants by size/pft per m2 m-2 F +FATES_NPLANT_PF total PFT-level number of individuals per m2 land area m-2 T +FATES_NPLANT_SEC_PF total PFT-level number of individuals per m2 land area, secondary patches m-2 T +FATES_NPLANT_SZ number of plants per m2 by size class m-2 T +FATES_NPLANT_SZAP number of plants per m2 in each size x age class m-2 F +FATES_NPLANT_SZAPPF number of plants per m2 in each size x age x pft class m-2 F +FATES_NPLANT_SZPF stem number density by pft/size m-2 F +FATES_NPLANT_USTORY_SZ number of understory plants per m2 by size class m-2 T +FATES_NPLANT_USTORY_SZAP number of plants per m2 in understory in each size x age class m-2 F +FATES_NPLANT_USTORY_SZPF density of understory plants by pft/size in number of plants per m2 m-2 F +FATES_NPP net primary production in kg carbon per m2 per second kg m-2 s-1 T +FATES_NPP_AP net primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_APPF NPP per PFT in each age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_CANOPY_SZ NPP of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_PF total PFT-level NPP in kg carbon per m2 land area per second kg m-2 yr-1 T +FATES_NPP_SECONDARY net primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_NPP_SE_PF total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 yr-1 T +FATES_NPP_SZPF total net primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_USTORY_SZ NPP of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_PARPROF_DIF_CLLL radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F +FATES_PARPROF_DIF_CLLLPF radiative profile of diffuse PAR through each canopy, leaf, and PFT W m-2 F +FATES_PARPROF_DIR_CLLL radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F +FATES_PARPROF_DIR_CLLLPF radiative profile of direct PAR through each canopy, leaf, and PFT W m-2 F +FATES_PARSHA_Z_CL PAR absorbed in the shade by top leaf layer in each canopy layer W m-2 F +FATES_PARSHA_Z_CLLL PAR absorbed in the shade by each canopy and leaf layer W m-2 F +FATES_PARSHA_Z_CLLLPF PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F +FATES_PARSUN_Z_CL PAR absorbed in the sun by top leaf layer in each canopy layer W m-2 F +FATES_PARSUN_Z_CLLL PAR absorbed in the sun by each canopy and leaf layer W m-2 F +FATES_PARSUN_Z_CLLLPF PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F +FATES_PATCHAREA_AP patch area by age bin per m2 land area m2 m-2 T +FATES_PRIMARY_PATCHFUSION_ERR error in total primary lands associated with patch fusion m2 m-2 yr-1 T +FATES_PROMOTION_CARBONFLUX promotion-associated biomass carbon flux from understory to canopy in kg carbon per m2 per sec kg m-2 s-1 T +FATES_PROMOTION_RATE_SZ promotion rate from understory to canopy by size class m-2 yr-1 F +FATES_RAD_ERROR radiation error in FATES RTM W m-2 T +FATES_RDARK_CANOPY_SZ dark respiration for canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_RDARK_SZPF dark portion of maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_RDARK_USTORY_SZ dark respiration for understory plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_RECRUITMENT_PF PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_REPROC total biomass in live plant reproductive tissues in kg carbon per m2 kg m-2 T +FATES_REPROC_SZPF reproductive carbon mass (on plant) by size-class x pft in kg carbon per m2 kg m-2 F +FATES_ROS fire rate of spread in meters per second m s-1 T +FATES_SAI_CANOPY_SZ stem area index (SAI) of canopy plants by size class m2 m-2 F +FATES_SAI_USTORY_SZ stem area index (SAI) of understory plants by size class m2 m-2 F +FATES_SAPWOODC total biomass in live plant sapwood in kg carbon per m2 kg m-2 T +FATES_SAPWOODCTURN_CANOPY_SZ sapwood turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SAPWOODCTURN_USTORY_SZ sapwood C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_SAPWOODC_SZPF sapwood carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_SAPWOOD_ALLOC_CANOPY_SZ allocation to sapwood C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SAPWOOD_ALLOC_USTORY_SZ allocation to sapwood C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SCORCH_HEIGHT_APPF SPITFIRE flame Scorch Height (calculated per PFT in each patch age bin) m F +FATES_SECONDAREA_ANTHRODIST_AP secondary forest patch area age distribution since anthropgenic disturbance m2 m-2 F +FATES_SECONDAREA_DIST_AP secondary forest patch area age distribution since any kind of disturbance m2 m-2 F +FATES_SECONDARY_FOREST_FRACTION secondary forest fraction m2 m-2 T +FATES_SECONDARY_FOREST_VEGC biomass on secondary lands in kg carbon per m2 land area (mult by FATES_SECONDARY_FOREST_FRACT kg m-2 T +FATES_SEEDS_IN seed production rate in kg carbon per m2 second kg m-2 s-1 T +FATES_SEEDS_IN_EXTERN_EL external seed influx rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEEDS_IN_LOCAL_EL within-site, element-level seed production rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEED_ALLOC allocation to seeds in kg carbon per m2 per second kg m-2 s-1 T +FATES_SEED_ALLOC_CANOPY_SZ allocation to reproductive C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_ALLOC_SZPF allocation to seeds by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_ALLOC_USTORY_SZ allocation to reproductive C for understory plants by size class in kg carbon per m2 per secon kg m-2 s-1 F +FATES_SEED_BANK total seed mass of all PFTs in kg carbon per m2 land area kg m-2 T +FATES_SEED_BANK_EL element-level total seed mass of all PFTs in kg element per m2 kg m-2 T +FATES_SEED_DECAY_EL seed mass decay (germinated and un-germinated) in kg element per m2 per second kg m-2 s-1 T +FATES_SEED_GERM_EL element-level total germinated seed mass of all PFTs in kg element per m2 kg m-2 T +FATES_SEED_PROD_CANOPY_SZ seed production of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_PROD_USTORY_SZ seed production of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STEM_ALLOC allocation to stem in kg carbon per m2 per second kg m-2 s-1 T +FATES_STOMATAL_COND mean stomatal conductance mol m-2 s-1 T +FATES_STOMATAL_COND_AP mean stomatal conductance - by patch age mol m-2 s-1 F +FATES_STOREC total biomass in live plant storage in kg carbon per m2 land area kg m-2 T +FATES_STORECTURN_CANOPY_SZ storage turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORECTURN_USTORY_SZ storage C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_STOREC_CANOPY_SZPF biomass in storage pools of canopy plants by pft/size in kg carbon per m2 kg m-2 F +FATES_STOREC_PF total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T +FATES_STOREC_SZPF storage carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_STOREC_TF Storage C fraction of target kg kg-1 T +FATES_STOREC_TF_CANOPY_SZPF Storage C fraction of target by size x pft, in the canopy kg kg-1 F +FATES_STOREC_TF_USTORY_SZPF Storage C fraction of target by size x pft, in the understory kg kg-1 F +FATES_STOREC_USTORY_SZPF biomass in storage pools of understory plants by pft/size in kg carbon per m2 kg m-2 F +FATES_STORE_ALLOC allocation to storage tissues in kg carbon per m2 per second kg m-2 s-1 T +FATES_STORE_ALLOC_CANOPY_SZ allocation to storage C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORE_ALLOC_SZPF allocation to storage C by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORE_ALLOC_USTORY_SZ allocation to storage C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STRUCTC structural biomass in kg carbon per m2 land area kg m-2 T +FATES_STRUCTCTURN_CANOPY_SZ structural C turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per sec kg m-2 s-1 F +FATES_STRUCTCTURN_USTORY_SZ structural C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per kg m-2 s-1 F +FATES_STRUCT_ALLOC_CANOPY_SZ allocation to structural C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STRUCT_ALLOC_USTORY_SZ allocation to structural C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_TGROWTH fates long-term running mean vegetation temperature by site degree_Celsius F +FATES_TLONGTERM fates 30-year running mean vegetation temperature by site degree_Celsius F +FATES_TRIMMING degree to which canopy expansion is limited by leaf economics (0-1) 1 T +FATES_TRIMMING_CANOPY_SZ trimming term of canopy plants weighted by plant density, by size class m-2 F +FATES_TRIMMING_USTORY_SZ trimming term of understory plants weighted by plant density, by size class m-2 F +FATES_TVEG fates instantaneous mean vegetation temperature by site degree_Celsius T +FATES_TVEG24 fates 24-hr running mean vegetation temperature by site degree_Celsius T +FATES_USTORY_VEGC biomass of understory plants in kg carbon per m2 land area kg m-2 T +FATES_VEGC total biomass in live plants in kg carbon per m2 land area kg m-2 T +FATES_VEGC_ABOVEGROUND aboveground biomass in kg carbon per m2 land area kg m-2 T +FATES_VEGC_ABOVEGROUND_SZ aboveground biomass by size class in kg carbon per m2 kg m-2 T +FATES_VEGC_ABOVEGROUND_SZPF aboveground biomass by pft/size in kg carbon per m2 kg m-2 F +FATES_VEGC_AP total biomass within a given patch age bin in kg carbon per m2 land area kg m-2 F +FATES_VEGC_APPF biomass per PFT in each age bin in kg carbon per m2 kg m-2 F +FATES_VEGC_PF total PFT-level biomass in kg of carbon per land area kg m-2 T +FATES_VEGC_SE_PF total PFT-level biomass in kg of carbon per land area, secondary patches kg m-2 T +FATES_VEGC_SZ total biomass by size class in kg carbon per m2 kg m-2 F +FATES_VEGC_SZPF total vegetation biomass in live plants by size-class x pft in kg carbon per m2 kg m-2 F +FATES_WOOD_PRODUCT total wood product from logging in kg carbon per m2 land area kg m-2 T +FATES_YESTCANLEV_CANOPY_SZ yesterdays canopy level for canopy plants by size class in number of plants per m2 m-2 F +FATES_YESTCANLEV_USTORY_SZ yesterdays canopy level for understory plants by size class in number of plants per m2 m-2 F +FATES_ZSTAR_AP product of zstar and patch area by age bin (divide by FATES_PATCHAREA_AP to get mean zstar) m F FATES_c_to_litr_cel_c litter celluluse carbon flux from FATES to BGC gC/m^3/s T FATES_c_to_litr_lab_c litter labile carbon flux from FATES to BGC gC/m^3/s T FATES_c_to_litr_lig_c litter lignin carbon flux from FATES to BGC gC/m^3/s T @@ -236,33 +506,13 @@ FIRA_ICE net infrared (longwave) radiation (ice landu FIRA_R Rural net infrared (longwave) radiation W/m^2 T FIRA_U Urban net infrared (longwave) radiation W/m^2 F FIRE emitted infrared (longwave) radiation W/m^2 T -FIRE_AREA spitfire fire area burn fraction fraction/day T -FIRE_FDI probability that an ignition will lead to a fire none T -FIRE_FLUX ED-spitfire loss to atmosphere of elements g/m^2/s T -FIRE_FUEL_BULKD spitfire fuel bulk density kg biomass/m3 T -FIRE_FUEL_EFF_MOIST spitfire fuel moisture m T -FIRE_FUEL_MEF spitfire fuel moisture m T -FIRE_FUEL_SAV spitfire fuel surface/volume per m T FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRE_IGNITIONS number of successful ignitions number/km2/day T -FIRE_INTENSITY spitfire fire intensity: kJ/m/s kJ/m/s T -FIRE_INTENSITY_AREA_PRODUCT spitfire product of fire intensity and burned area (divide by FIRE_AREA to get area-weighted m kJ/m/s T -FIRE_INTENSITY_BY_PATCH_AGE product of fire intensity and burned area, resolved by patch age (so divide by AREA_BURNT_BY_P kJ/m/2 T -FIRE_NESTEROV_INDEX nesterov_fire_danger index none T FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T -FIRE_ROS fire rate of spread m/min m/min T -FIRE_ROS_AREA_PRODUCT product of fire rate of spread (m/min) and burned area (fraction)--divide by FIRE_AREA to get m/min T -FIRE_TFC_ROS total fuel consumed kgC/m2 T -FIRE_TFC_ROS_AREA_PRODUCT product of total fuel consumed and burned area--divide by FIRE_AREA to get burned-area-weighte kgC/m2 T FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F -FNRTC Total carbon in live plant fine-roots kgC ha-1 T -FNRTC_SCPF fine-root carbon mass by size-class x pft kgC/ha F -FRAGMENTATION_SCALER_SL factor by which litter/cwd fragmentation proceeds relative to max rate by soil layer unitless (0-1) T -FROOT_MR fine root maintenance respiration) kg C / m2 / yr T -FROOT_MR_CANOPY_SCLS FROOT_MR for canopy plants by size class kg C / ha / yr F -FROOT_MR_UNDERSTORY_SCLS FROOT_MR for understory plants by size class kg C / ha / yr F +FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F FSA absorbed solar radiation W/m^2 T FSAT fractional area with water table at surface unitless T @@ -308,21 +558,15 @@ FSR_ICE reflected solar radiation (ice landunits onl FSUN sunlit fraction of canopy proportion F FSUN24 fraction sunlit (last 24hrs) K F FSUN240 fraction sunlit (last 240hrs) K F -FUEL_AMOUNT_AGEFUEL spitfire fuel quantity in each age x fuel class kg C / m2 T -FUEL_AMOUNT_BY_NFSC spitfire size-resolved fuel quantity kg C / m2 T -FUEL_MOISTURE_NFSC spitfire size-resolved fuel moisture - T -Fire_Closs ED/SPitfire Carbon loss to atmosphere gC/m^2/s T -GPP gross primary production gC/m^2/s T -GPP_BY_AGE gross primary productivity by age bin gC/m^2/s F -GPP_CANOPY gross primary production of canopy plants gC/m^2/s T -GPP_CANOPY_SCPF gross primary production of canopy plants by pft/size kgC/m2/yr F -GPP_SCPF gross primary production by pft/size kgC/m2/yr F -GPP_UNDERSTORY gross primary production of understory plants gC/m^2/s T -GPP_UNDERSTORY_SCPF gross primary production of understory plants by pft/size kgC/m2/yr F +F_DENIT denitrification flux gN/m^2/s T +F_DENIT_BASE F_DENIT_BASE gN/m^3/s F +F_DENIT_vr denitrification flux gN/m^3/s F +F_N2O_DENIT denitrification N2O flux gN/m^2/s T +F_N2O_NIT nitrification N2O flux gN/m^2/s T +F_NIT nitrification flux gN/m^2/s T +F_NIT_vr nitrification flux gN/m^3/s F GROSS_NMIN gross rate of N mineralization gN/m^2/s T -GROWTHFLUX_FUSION_SCPF flux of individuals into a given size class bin via fusion n/yr/ha F -GROWTHFLUX_SCPF flux of individuals into a given size class bin via growth and recruitment n/yr/ha F -GROWTH_RESP growth respiration gC/m^2/s T +GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F GSSHA shaded leaf stomatal conductance umol H20/m2/s T GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T GSSUN sunlit leaf stomatal conductance umol H20/m2/s T @@ -333,7 +577,6 @@ H2OSNO snow depth (liquid water) H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F H2OSNO_TOP mass of snow in top snow layer kg/m2 T H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T -HARVEST_CARBON_FLUX Harvest carbon flux kg C m-2 d-1 T HBOT canopy bottom m F HEAT_CONTENT1 initial gridcell total heat content J/m^2 T HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F @@ -361,29 +604,24 @@ K_ACT_SOM active soil organic potential loss coefficie K_CEL_LIT cellulosic litter potential loss coefficient 1/s F K_LIG_LIT lignin litter potential loss coefficient 1/s F K_MET_LIT metabolic litter potential loss coefficient 1/s F +K_NITR K_NITR 1/s F +K_NITR_H2O K_NITR_H2O unitless F +K_NITR_PH K_NITR_PH unitless F +K_NITR_T K_NITR_T unitless F K_PAS_SOM passive soil organic potential loss coefficient 1/s F K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F +L1_PATHFRAC_S1_vr PATHFRAC from metabolic litter to active soil organic fraction F +L1_RESP_FRAC_S1_vr respired from metabolic litter to active soil organic fraction F +L2_PATHFRAC_S1_vr PATHFRAC from cellulosic litter to active soil organic fraction F +L2_RESP_FRAC_S1_vr respired from cellulosic litter to active soil organic fraction F +L3_PATHFRAC_S2_vr PATHFRAC from lignin litter to slow soil organic ma fraction F +L3_RESP_FRAC_S2_vr respired from lignin litter to slow soil organic ma fraction F LAI240 240hr average of leaf area index m^2/m^2 F LAISHA shaded projected leaf area index m^2/m^2 T -LAISHA_TOP_CAN LAI in the shade by the top leaf layer of each canopy layer m2/m2 F -LAISHA_Z_CNLF LAI in the shade by each canopy and leaf layer m2/m2 F -LAISHA_Z_CNLFPFT LAI in the shade by each canopy, leaf, and PFT m2/m2 F LAISUN sunlit projected leaf area index m^2/m^2 T -LAISUN_TOP_CAN LAI in the sun by the top leaf layer of each canopy layer m2/m2 F -LAISUN_Z_CNLF LAI in the sun by each canopy and leaf layer m2/m2 F -LAISUN_Z_CNLFPFT LAI in the sun by each canopy, leaf, and PFT m2/m2 F -LAI_BY_AGE leaf area index by age bin m2/m2 T -LAI_CANOPY_SCLS Leaf are index (LAI) by size class m2/m2 T -LAI_UNDERSTORY_SCLS number of understory plants by size class indiv/ha T LAKEICEFRAC lake layer ice mass fraction unitless F LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T -LEAFC Total carbon in live plant leaves kgC ha-1 T -LEAFC_SCPF leaf carbon mass by size-class x pft kgC/ha F -LEAF_HEIGHT_DIST leaf height distribution m2/m2 T -LEAF_MD_CANOPY_SCLS LEAF_MD for canopy plants by size class kg C / ha / yr F -LEAF_MD_UNDERSTORY_SCLS LEAF_MD for understory plants by size class kg C / ha / yr F -LEAF_MR RDARK (leaf maintenance respiration) kg C / m2 / yr T LIG_LITC LIG_LIT C gC/m^2 T LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F @@ -403,47 +641,9 @@ LIQUID_CONTENT1 initial gridcell total liq content LIQUID_CONTENT2 post landuse change gridcell total liq content mm F LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F LITTERC_HR litter C heterotrophic respiration gC/m^2/s T -LITTER_CWD total mass of litter in CWD kg ha-1 T -LITTER_CWD_AG_ELEM mass of above ground litter in CWD (trunks/branches/twigs) kg ha-1 T -LITTER_CWD_BG_ELEM mass of below ground litter in CWD (coarse roots) kg ha-1 T -LITTER_FINES_AG_ELEM mass of above ground litter in fines (leaves,nonviable seed) kg ha-1 T -LITTER_FINES_BG_ELEM mass of below ground litter in fines (fineroots) kg ha-1 T -LITTER_IN FATES litter flux in gC m-2 s-1 T -LITTER_IN_ELEM FATES litter flux in kg ha-1 d-1 T -LITTER_OUT FATES litter flux out gC m-2 s-1 T -LITTER_OUT_ELEM FATES litter flux out (fragmentation only) kg ha-1 d-1 T -LIVECROOT_MR live coarse root maintenance respiration) kg C / m2 / yr T -LIVECROOT_MR_CANOPY_SCLS LIVECROOT_MR for canopy plants by size class kg C / ha / yr F -LIVECROOT_MR_UNDERSTORY_SCLS LIVECROOT_MR for understory plants by size class kg C / ha / yr F -LIVESTEM_MR live stem maintenance respiration) kg C / m2 / yr T -LIVESTEM_MR_CANOPY_SCLS LIVESTEM_MR for canopy plants by size class kg C / ha / yr F -LIVESTEM_MR_UNDERSTORY_SCLS LIVESTEM_MR for understory plants by size class kg C / ha / yr F LNC leaf N concentration gN leaf/m^2 T LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F LWup upwelling longwave radiation W/m^2 F -M10_CACLS age senescence mortality by cohort age N/ha/yr T -M10_CAPF age senescence mortality by pft/cohort age N/ha/yr F -M10_SCLS age senescence mortality by size N/ha/yr T -M10_SCPF age senescence mortality by pft/size N/ha/yr F -M1_SCLS background mortality by size N/ha/yr T -M1_SCPF background mortality by pft/size N/ha/yr F -M2_SCLS hydraulic mortality by size N/ha/yr T -M2_SCPF hydraulic mortality by pft/size N/ha/yr F -M3_SCLS carbon starvation mortality by size N/ha/yr T -M3_SCPF carbon starvation mortality by pft/size N/ha/yr F -M4_SCLS impact mortality by size N/ha/yr T -M4_SCPF impact mortality by pft/size N/ha/yr F -M5_SCLS fire mortality by size N/ha/yr T -M5_SCPF fire mortality by pft/size N/ha/yr F -M6_SCLS termination mortality by size N/ha/yr T -M6_SCPF termination mortality by pft/size N/ha/yr F -M7_SCLS logging mortality by size N/ha/event T -M7_SCPF logging mortality by pft/size N/ha/event F -M8_SCLS freezing mortality by size N/ha/event T -M8_SCPF freezing mortality by pft/size N/ha/yr F -M9_SCLS senescence mortality by size N/ha/yr T -M9_SCPF senescence mortality by pft/size N/ha/yr F -MAINT_RESP maintenance respiration gC/m^2/s T MET_LITC MET_LIT C gC/m^2 T MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F @@ -458,15 +658,8 @@ MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F -MORTALITY Rate of total mortality by PFT indiv/ha/yr T -MORTALITY_CANOPY_SCAG mortality rate of canopy plants in each size x age class plants/ha/yr F -MORTALITY_CANOPY_SCLS total mortality of canopy trees by size class indiv/ha/yr T -MORTALITY_CANOPY_SCPF total mortality of canopy plants by pft/size N/ha/yr F -MORTALITY_CARBONFLUX_CANOPY flux of biomass carbon from live to dead pools from mortality of canopy plants gC/m2/s T -MORTALITY_CARBONFLUX_UNDERSTORY flux of biomass carbon from live to dead pools from mortality of understory plants gC/m2/s T -MORTALITY_UNDERSTORY_SCAG mortality rate of understory plantsin each size x age class plants/ha/yr F -MORTALITY_UNDERSTORY_SCLS total mortality of understory trees by size class indiv/ha/yr T -MORTALITY_UNDERSTORY_SCPF total mortality of understory plants by pft/size N/ha/yr F +MORTALITY_CROWNAREA_CANOPY Crown area of canopy trees that died m2/ha/year T +MORTALITY_CROWNAREA_UNDERSTORY Crown aera of understory trees that died m2/ha/year T M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F @@ -479,71 +672,16 @@ M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F -NCL_BY_AGE number of canopy levels by age bin -- F NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T -NEP net ecosystem production gC/m^2/s T -NET_C_UPTAKE_CNLF net carbon uptake by each canopy and leaf layer per unit ground area (i.e. divide by CROWNAREA gC/m2/s F NET_NMIN net rate of N mineralization gN/m^2/s T +NET_NMIN_vr net rate of N mineralization gN/m^3/s F NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T -NPATCH_BY_AGE number of patches by age bin -- F -NPLANT_CACLS number of plants by coage class indiv/ha T -NPLANT_CANOPY_SCAG number of plants per hectare in canopy in each size x age class plants/ha F -NPLANT_CANOPY_SCLS number of canopy plants by size class indiv/ha T -NPLANT_CANOPY_SCPF stem number of canopy plants density by pft/size N/ha F -NPLANT_CAPF stem number density by pft/coage N/ha F -NPLANT_SCAG number of plants per hectare in each size x age class plants/ha T -NPLANT_SCAGPFT number of plants per hectare in each size x age x pft class plants/ha F -NPLANT_SCLS number of plants by size class indiv/ha T -NPLANT_SCPF stem number density by pft/size N/ha F -NPLANT_UNDERSTORY_SCAG number of plants per hectare in understory in each size x age class plants/ha F -NPLANT_UNDERSTORY_SCLS number of understory plants by size class indiv/ha T -NPLANT_UNDERSTORY_SCPF stem number of understory plants density by pft/size N/ha F -NPP net primary production gC/m^2/s T -NPP_AGDW_SCPF NPP flux into above-ground deadwood by pft/size kgC/m2/yr F -NPP_AGEPFT NPP per PFT in each age bin kgC/m2/yr F -NPP_AGSW_SCPF NPP flux into above-ground sapwood by pft/size kgC/m2/yr F -NPP_BDEAD_CANOPY_SCLS NPP_BDEAD for canopy plants by size class kg C / ha / yr F -NPP_BDEAD_UNDERSTORY_SCLS NPP_BDEAD for understory plants by size class kg C / ha / yr F -NPP_BGDW_SCPF NPP flux into below-ground deadwood by pft/size kgC/m2/yr F -NPP_BGSW_SCPF NPP flux into below-ground sapwood by pft/size kgC/m2/yr F -NPP_BSEED_CANOPY_SCLS NPP_BSEED for canopy plants by size class kg C / ha / yr F -NPP_BSEED_UNDERSTORY_SCLS NPP_BSEED for understory plants by size class kg C / ha / yr F -NPP_BSW_CANOPY_SCLS NPP_BSW for canopy plants by size class kg C / ha / yr F -NPP_BSW_UNDERSTORY_SCLS NPP_BSW for understory plants by size class kg C / ha / yr F -NPP_BY_AGE net primary productivity by age bin gC/m^2/s F -NPP_CROOT NPP flux into coarse roots kgC/m2/yr T -NPP_FNRT_SCPF NPP flux into fine roots by pft/size kgC/m2/yr F -NPP_FROOT NPP flux into fine roots kgC/m2/yr T -NPP_FROOT_CANOPY_SCLS NPP_FROOT for canopy plants by size class kg C / ha / yr F -NPP_FROOT_UNDERSTORY_SCLS NPP_FROOT for understory plants by size class kg C / ha / yr F -NPP_LEAF NPP flux into leaves kgC/m2/yr T -NPP_LEAF_CANOPY_SCLS NPP_LEAF for canopy plants by size class kg C / ha / yr F -NPP_LEAF_SCPF NPP flux into leaves by pft/size kgC/m2/yr F -NPP_LEAF_UNDERSTORY_SCLS NPP_LEAF for understory plants by size class kg C / ha / yr F -NPP_SCPF total net primary production by pft/size kgC/m2/yr F -NPP_SEED NPP flux into seeds kgC/m2/yr T -NPP_SEED_SCPF NPP flux into seeds by pft/size kgC/m2/yr F -NPP_STEM NPP flux into stem kgC/m2/yr T -NPP_STOR NPP flux into storage tissues kgC/m2/yr T -NPP_STORE_CANOPY_SCLS NPP_STORE for canopy plants by size class kg C / ha / yr F -NPP_STORE_UNDERSTORY_SCLS NPP_STORE for understory plants by size class kg C / ha / yr F -NPP_STOR_SCPF NPP flux into storage by pft/size kgC/m2/yr F NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F OBU Monin-Obukhov length m F OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T -PARPROF_DIF_CNLF Radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W/m2 F -PARPROF_DIF_CNLFPFT Radiative profile of diffuse PAR through each canopy, leaf, and PFT W/m2 F -PARPROF_DIR_CNLF Radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W/m2 F -PARPROF_DIR_CNLFPFT Radiative profile of direct PAR through each canopy, leaf, and PFT W/m2 F -PARSHA_Z_CAN PAR absorbed in the shade by top leaf layer in each canopy layer W/m2 F -PARSHA_Z_CNLF PAR absorbed in the shade by each canopy and leaf layer W/m2 F -PARSHA_Z_CNLFPFT PAR absorbed in the shade by each canopy, leaf, and PFT W/m2 F -PARSUN_Z_CAN PAR absorbed in the sun by top leaf layer in each canopy layer W/m2 F -PARSUN_Z_CNLF PAR absorbed in the sun by each canopy and leaf layer W/m2 F -PARSUN_Z_CNLFPFT PAR absorbed in the sun by each canopy, leaf, and PFT W/m2 F PARVEGLN absorbed par by vegetation at local noon W/m^2 T PAS_SOMC PAS_SOM C gC/m^2 T PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F @@ -559,22 +697,15 @@ PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F -PATCH_AREA_BY_AGE patch area by age bin m2/m2 T PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T PCH4 atmospheric partial pressure of CH4 Pa T PCO2 atmospheric partial pressure of CO2 Pa T -PFTbiomass total PFT level biomass gC/m2 T -PFTcanopycrownarea total PFT-level canopy-layer crown area m2/m2 F -PFTcrownarea total PFT level crown area m2/m2 F -PFTgpp total PFT-level GPP kg C m-2 y-1 T -PFTleafbiomass total PFT level leaf biomass gC/m2 T -PFTnindivs total PFT level number of individuals indiv / m2 T -PFTnpp total PFT-level NPP kg C m-2 y-1 T -PFTstorebiomass total PFT level stored biomass gC/m2 T POTENTIAL_IMMOB potential N immobilization gN/m^2/s T -PRIMARYLAND_PATCHFUSION_ERROR Error in total primary lands associated with patch fusion m2 m-2 d-1 T -PROMOTION_CARBONFLUX promotion-associated biomass carbon flux from understory to canopy gC/m2/s T -PROMOTION_RATE_SCLS promotion rate from understory to canopy by size class indiv/ha/yr F +POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F +POT_F_DENIT potential denitrification flux gN/m^2/s T +POT_F_DENIT_vr potential denitrification flux gN/m^3/s F +POT_F_NIT potential nitrification flux gN/m^2/s T +POT_F_NIT_vr potential nitrification flux gN/m^3/s F PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F Q2M 2m specific humidity kg/kg T QAF canopy air humidity kg/kg F @@ -656,59 +787,30 @@ RAM_LAKE aerodynamic resistance for momentum (lakes o RAW1 aerodynamical resistance s/m F RAW2 aerodynamical resistance s/m F RB leaf boundary resistance s/m F -RDARK_CANOPY_SCLS RDARK for canopy plants by size class kg C / ha / yr F -RDARK_UNDERSTORY_SCLS RDARK for understory plants by size class kg C / ha / yr F -RECRUITMENT Rate of recruitment by PFT indiv/ha/yr T -REPROC Total carbon in live plant reproductive tissues kgC ha-1 T -REPROC_SCPF reproductive carbon mass (on plant) by size-class x pft kgC/ha F -RESP_G_CANOPY_SCLS RESP_G for canopy plants by size class kg C / ha / yr F -RESP_G_UNDERSTORY_SCLS RESP_G for understory plants by size class kg C / ha / yr F -RESP_M_CANOPY_SCLS RESP_M for canopy plants by size class kg C / ha / yr F -RESP_M_UNDERSTORY_SCLS RESP_M for understory plants by size class kg C / ha / yr F RH atmospheric relative humidity % F RH2M 2m relative humidity % T RH2M_R Rural 2m specific humidity % F RH2M_U Urban 2m relative humidity % F RHAF fractional humidity of canopy air fraction F RH_LEAF fractional humidity at leaf surface fraction F -ROOT_MD_CANOPY_SCLS ROOT_MD for canopy plants by size class kg C / ha / yr F -ROOT_MD_UNDERSTORY_SCLS ROOT_MD for understory plants by size class kg C / ha / yr F RSCANOPY canopy resistance s m-1 T RSSHA shaded leaf stomatal resistance s/m T RSSUN sunlit leaf stomatal resistance s/m T Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F Rnet net radiation W/m^2 F +S1_PATHFRAC_S2_vr PATHFRAC from active soil organic to slow soil organic ma fraction F +S1_PATHFRAC_S3_vr PATHFRAC from active soil organic to passive soil organic fraction F +S1_RESP_FRAC_S2_vr respired from active soil organic to slow soil organic ma fraction F +S1_RESP_FRAC_S3_vr respired from active soil organic to passive soil organic fraction F +S2_PATHFRAC_S1_vr PATHFRAC from slow soil organic ma to active soil organic fraction F +S2_PATHFRAC_S3_vr PATHFRAC from slow soil organic ma to passive soil organic fraction F +S2_RESP_FRAC_S1_vr respired from slow soil organic ma to active soil organic fraction F +S2_RESP_FRAC_S3_vr respired from slow soil organic ma to passive soil organic fraction F +S3_PATHFRAC_S1_vr PATHFRAC from passive soil organic to active soil organic fraction F +S3_RESP_FRAC_S1_vr respired from passive soil organic to active soil organic fraction F SABG solar rad absorbed by ground W/m^2 T SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T SABV solar rad absorbed by veg W/m^2 T -SAI_CANOPY_SCLS stem area index(SAI) by size class m2/m2 F -SAI_UNDERSTORY_SCLS number of understory plants by size class indiv/ha F -SAPWC Total carbon in live plant sapwood kgC ha-1 T -SAPWC_SCPF sapwood carbon mass by size-class x pft kgC/ha F -SCORCH_HEIGHT SPITFIRE Flame Scorch Height (calculated per PFT in each patch age bin) m T -SECONDARY_AREA_AGE_ANTHRO_DIST Secondary forest patch area age distribution since anthropgenic disturbance m2/m2 F -SECONDARY_AREA_PATCH_AGE_DIST Secondary forest patch area age distribution since any kind of disturbance m2/m2 F -SECONDARY_FOREST_BIOMASS Biomass on secondary lands (per total site area, mult by SECONDARY_FOREST_FRACTION to get per kgC/m2 F -SECONDARY_FOREST_FRACTION Secondary forest fraction m2/m2 F -SEEDS_IN Seed Production Rate gC m-2 s-1 T -SEEDS_IN_EXTERN_ELEM External Seed Influx Rate kg ha-1 d-1 T -SEEDS_IN_LOCAL_ELEM Within Site Seed Production Rate kg ha-1 d-1 T -SEED_BANK Total Seed Mass of all PFTs gC m-2 T -SEED_BANK_ELEM Total Seed Mass of all PFTs kg ha-1 T -SEED_DECAY_ELEM Seed mass decay (germinated and un-germinated) kg ha-1 d-1 T -SEED_GERM_ELEM Seed mass converted into new cohorts kg ha-1 d-1 T -SEED_PROD_CANOPY_SCLS SEED_PROD for canopy plants by size class kg C / ha / yr F -SEED_PROD_UNDERSTORY_SCLS SEED_PROD for understory plants by size class kg C / ha / yr F -SITE_COLD_STATUS Site level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not-too cold 0,1,2 T -SITE_DAYSINCE_COLDLEAFOFF site level days elapsed since cold leaf drop days T -SITE_DAYSINCE_COLDLEAFON site level days elapsed since cold leaf flush days T -SITE_DAYSINCE_DROUGHTLEAFOFF site level days elapsed since drought leaf drop days T -SITE_DAYSINCE_DROUGHTLEAFON site level days elapsed since drought leaf flush days T -SITE_DROUGHT_STATUS Site level drought status, <2 too dry for leaves, >=2 not-too dry 0,1,2,3 T -SITE_GDD site level growing degree days degC T -SITE_MEANLIQVOL_DROUGHTPHEN site level mean liquid water volume for drought phen m3/m3 T -SITE_NCHILLDAYS site level number of chill days days T -SITE_NCOLDDAYS site level number of cold days days T SLO_SOMC SLO_SOM C gC/m^2 T SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F @@ -730,27 +832,8 @@ SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F SMINN soil mineral N gN/m^2 T -SMINN_LEACHED soil mineral N pool loss to leaching gN/m^2/s T -SMINN_LEACHED_vr soil mineral N pool loss to leaching gN/m^3/s F -SMINN_TO_DENIT_EXCESS denitrification from excess mineral N pool gN/m^2/s F -SMINN_TO_DENIT_EXCESS_vr denitrification from excess mineral N pool gN/m^3/s F -SMINN_TO_DENIT_L1S1 denitrification for decomp. of metabolic litterto ACT_SOM gN/m^2 F -SMINN_TO_DENIT_L1S1_vr denitrification for decomp. of metabolic litterto ACT_SOM gN/m^3 F -SMINN_TO_DENIT_L2S1 denitrification for decomp. of cellulosic litterto ACT_SOM gN/m^2 F -SMINN_TO_DENIT_L2S1_vr denitrification for decomp. of cellulosic litterto ACT_SOM gN/m^3 F -SMINN_TO_DENIT_L3S2 denitrification for decomp. of lignin litterto SLO_SOM gN/m^2 F -SMINN_TO_DENIT_L3S2_vr denitrification for decomp. of lignin litterto SLO_SOM gN/m^3 F -SMINN_TO_DENIT_S1S2 denitrification for decomp. of active soil organicto SLO_SOM gN/m^2 F -SMINN_TO_DENIT_S1S2_vr denitrification for decomp. of active soil organicto SLO_SOM gN/m^3 F -SMINN_TO_DENIT_S1S3 denitrification for decomp. of active soil organicto PAS_SOM gN/m^2 F -SMINN_TO_DENIT_S1S3_vr denitrification for decomp. of active soil organicto PAS_SOM gN/m^3 F -SMINN_TO_DENIT_S2S1 denitrification for decomp. of slow soil organic mato ACT_SOM gN/m^2 F -SMINN_TO_DENIT_S2S1_vr denitrification for decomp. of slow soil organic mato ACT_SOM gN/m^3 F -SMINN_TO_DENIT_S2S3 denitrification for decomp. of slow soil organic mato PAS_SOM gN/m^2 F -SMINN_TO_DENIT_S2S3_vr denitrification for decomp. of slow soil organic mato PAS_SOM gN/m^3 F -SMINN_TO_DENIT_S3S1 denitrification for decomp. of passive soil organicto ACT_SOM gN/m^2 F -SMINN_TO_DENIT_S3S1_vr denitrification for decomp. of passive soil organicto ACT_SOM gN/m^3 F SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T +SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F @@ -768,6 +851,17 @@ SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_ SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F SMINN_vr soil mineral N gN/m^3 T +SMIN_NH4 soil mineral NH4 gN/m^2 T +SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F +SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3 soil mineral NO3 gN/m^2 T +SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T +SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T +SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F +SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T SMP soil matric potential (natural vegetated and crop landunits only) mm T SNOBCMCL mass of BC in snow column kg/m2 T SNOBCMSL mass of BC in top snow layer kg/m2 T @@ -837,11 +931,8 @@ SOILWATER_10CM soil liquid water + ice in top 10cm of soil SOMC_FIRE C loss due to peat burning gC/m^2/s T SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -STOREC Total carbon in live plant storage kgC ha-1 T -STOREC_SCPF storage carbon mass by size-class x pft kgC/ha F -SUM_FUEL total ground fuel related to ros (omits 1000hr fuels) gC m-2 T -SUM_FUEL_BY_PATCH_AGE spitfire ground fuel related to ros (omits 1000hr fuels) within each patch age bin (divide by gC / m2 of site area T SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T +SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F SWBGT 2 m Simplified Wetbulb Globe Temp C T SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T @@ -880,8 +971,6 @@ TOTSOMC total soil organic matter carbon TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T TOTSOMN total soil organic matter N gN/m^2 T TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -TOTVEGC Total carbon in live plants kgC ha-1 T -TOTVEGC_SCPF total vegetation carbon mass in live plants by size-class x pft kgC/ha F TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F TREFMNAV daily minimum of average 2-m temperature K T TREFMNAV_R Rural daily minimum of average 2-m temperature K F @@ -889,9 +978,6 @@ TREFMNAV_U Urban daily minimum of average 2-m temperatu TREFMXAV daily maximum of average 2-m temperature K T TREFMXAV_R Rural daily maximum of average 2-m temperature K F TREFMXAV_U Urban daily maximum of average 2-m temperature K F -TRIMMING Degree to which canopy expansion is limited by leaf economics none T -TRIMMING_CANOPY_SCLS trimming term of canopy plants by size class indiv/ha F -TRIMMING_UNDERSTORY_SCLS trimming term of understory plants by size class indiv/ha F TROOF_INNER roof inside surface temperature K F TSA 2m air temperature K T TSAI total projected stem area index m^2/m^2 T @@ -923,6 +1009,7 @@ URBAN_HEAT urban heating flux USTAR aerodynamical resistance s/m F UST_LAKE friction velocity (lakes only) m/s F VA atmospheric wind speed plus convective velocity m/s F +VENTILATION sensible heat flux from building ventilation W/m^2 T VOLR river channel total water storage m3 T VOLRMCH river channel main channel water storage m3 T VPD vpd Pa F @@ -932,24 +1019,30 @@ WASTEHEAT sensible heat flux from heating/cooling sour WBT 2 m Stull Wet Bulb C T WBT_R Rural 2 m Stull Wet Bulb C T WBT_U Urban 2 m Stull Wet Bulb C T +WFPS WFPS percent F WIND atmospheric wind velocity magnitude m/s T -WOOD_PRODUCT Total wood product from logging gC/m2 F WTGQ surface tracer conductance m/s T W_SCALAR Moisture (dryness) inhibition of decomposition unitless T Wind atmospheric wind velocity magnitude m/s F -YESTERDAYCANLEV_CANOPY_SCLS Yesterdays canopy level for canopy plants by size class indiv/ha F -YESTERDAYCANLEV_UNDERSTORY_SCLS Yesterdays canopy level for understory plants by size class indiv/ha F -Z0HG roughness length over ground, sensible heat m F -Z0M momentum roughness length m F -Z0MG roughness length over ground, momentum m F +Z0HG roughness length over ground, sensible heat (vegetated landunits only) m F +Z0MG roughness length over ground, momentum (vegetated landunits only) m F +Z0MV_DENSE roughness length over vegetation, momentum, for dense canopy m F Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -Z0QG roughness length over ground, latent heat m F +Z0QG roughness length over ground, latent heat (vegetated landunits only) m F ZBOT atmospheric reference height m T ZETA dimensionless stability parameter unitless F ZII convective boundary height m F -ZSTAR_BY_AGE product of zstar and patch area by age bin (divide by PATCH_AREA_BY_AGE to get mean zstar) m F ZWT water table depth (natural vegetated and crop landunits only) m T ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T +anaerobic_frac anaerobic_frac m3/m3 F +diffus diffusivity m^2/s F +fr_WFPS fr_WFPS fraction F +n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F num_iter number of iterations unitless F -==== =================================== ============================================================================================== ================================================================= ======= +r_psi r_psi m F +ratio_k1 ratio_k1 none F +ratio_no3_co2 ratio_no3_co2 ratio F +soil_bulkdensity soil_bulkdensity kg/m3 F +soil_co2_prod soil_co2_prod ug C / g soil / day F +=================================== ============================================================================================== ================================================================= ======= diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 3bdb33297d..1eb450b0b6 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -1,18 +1,18 @@ ============================= CTSM History Fields (nofates) ============================= - + CAUTION: Not all variables are relevant / present for all CTSM cases. Key flags used in this CTSM case: -use_cn = T -use_crop = T -use_fates = F - -==== =================================== ============================================================================================== ================================================================= ======= +use_cn = T +use_crop = T +use_fates = F + +=================================== ============================================================================================== ================================================================= ======= CTSM History Fields ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ - # Variable Name Long Description Units Active? -==== =================================== ============================================================================================== ================================================================= ======= +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ + Variable Name Long Description Units Active? +=================================== ============================================================================================== ================================================================= ======= A10TMIN 10-day running mean of min 2-m temperature K F A5TMIN 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB actual N immobilization gN/m^2/s T @@ -42,12 +42,10 @@ ACT_SOM_HR_S3_vr Het. Resp. from active soil organic AGLB Aboveground leaf biomass kg/m^2 F AGNPP aboveground NPP gC/m^2/s T AGSB Aboveground stem biomass kg/m^2 F -ALBD surface albedo (direct) proportion T -ALBDSF diagnostic snow-free surface albedo (direct) proportion T +ALBD surface albedo (direct) proportion F ALBGRD ground albedo (direct) proportion F ALBGRI ground albedo (indirect) proportion F -ALBI surface albedo (indirect) proportion T -ALBISF diagnostic snow-free surface albedo (indirect) proportion T +ALBI surface albedo (indirect) proportion F ALPHA alpha coefficient for VOC calc non F ALT current active layer thickness m T ALTMAX maximum annual active layer thickness m T @@ -57,10 +55,8 @@ ANNMAX_RETRANSN annual max of retranslocated N pool ANNSUM_COUNTER seconds since last annual accumulator turnover s F ANNSUM_NPP annual sum of NPP gC/m^2/yr F ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F -APPAR_TEMP 2 m apparent temperature C T -APPAR_TEMP_R Rural 2 m apparent temperature C T -APPAR_TEMP_U Urban 2 m apparent temperature C T AR autotrophic respiration (MR + GR) gC/m^2/s T +ATM_O3 atmospheric ozone partial pressure mol/mol F ATM_TOPO atmospheric surface height m T AVAILC C flux available for allocation gC/m^2/s F AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F @@ -152,7 +148,7 @@ CROP_SEEDN_TO_LEAF crop seed source to leaf CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F CWDC CWD C gC/m^2 T CWDC_1m CWD C to 1 meter gC/m^2 F -CWDC_HR cwd C heterotrophic respiration gC/m^2/s F +CWDC_HR cwd C heterotrophic respiration gC/m^2/s T CWDC_LOSS coarse woody debris C loss gC/m^2/s T CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F @@ -170,6 +166,10 @@ CWD_HR_L2 Het. Resp. from coarse woody debris CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F +CWD_PATHFRAC_L2_vr PATHFRAC from coarse woody debris to cellulosic litter fraction F +CWD_PATHFRAC_L3_vr PATHFRAC from coarse woody debris to lignin litter fraction F +CWD_RESP_FRAC_L2_vr respired from coarse woody debris to cellulosic litter fraction F +CWD_RESP_FRAC_L3_vr respired from coarse woody debris to lignin litter fraction F C_ALLOMETRY C allocation index none F DAYL daylength s F DAYS_ACTIVE number of days since last dormancy days F @@ -195,13 +195,7 @@ DEADSTEMN_XFER dead stem N transfer DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F DENIT total rate of denitrification gN/m^2/s T DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F -DISCOI 2 m Discomfort Index C T -DISCOIS 2 m Stull Discomfort Index C T -DISCOIS_R Rural 2 m Stull Discomfort Index C T -DISCOIS_U Urban 2 m Stull Discomfort Index C T -DISCOI_R Rural 2 m Discomfort Index C T -DISCOI_U Urban 2 m Discomfort Index C T -DISPLA displacement height m F +DISPLA displacement height (vegetated landunits only) m F DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T DISPVEGN displayed vegetation nitrogen gN/m^2 T DLRAD downward longwave radiation below the canopy W/m^2 F @@ -268,9 +262,6 @@ ELAI exposed one-sided leaf area index EMG ground emissivity proportion F EMV vegetation emissivity proportion F EOPT Eopt coefficient for VOC calc non F -EPT 2 m Equiv Pot Temp K T -EPT_R Rural 2 m Equiv Pot Temp K T -EPT_U Urban 2 m Equiv Pot Temp K T ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T ERRH2O total water conservation error mm T ERRH2OSNO imbalance in snow depth (liquid water) mm T @@ -380,13 +371,6 @@ FSR reflected solar radiation FSRND direct nir reflected solar radiation W/m^2 T FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T FSRNI diffuse nir reflected solar radiation W/m^2 T -FSRSF reflected solar radiation W/m^2 T -FSRSFND direct nir reflected solar radiation W/m^2 T -FSRSFNDLN direct nir reflected solar radiation at local noon W/m^2 T -FSRSFNI diffuse nir reflected solar radiation W/m^2 T -FSRSFVD direct vis reflected solar radiation W/m^2 T -FSRSFVDLN direct vis reflected solar radiation at local noon W/m^2 T -FSRSFVI diffuse vis reflected solar radiation W/m^2 T FSRVD direct vis reflected solar radiation W/m^2 T FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T FSRVI diffuse vis reflected solar radiation W/m^2 T @@ -404,14 +388,6 @@ F_N2O_DENIT denitrification N2O flux F_N2O_NIT nitrification N2O flux gN/m^2/s T F_NIT nitrification flux gN/m^2/s T F_NIT_vr nitrification flux gN/m^3/s F -FireComp_BC fire emissions flux of BC kg/m2/sec F -FireComp_OC fire emissions flux of OC kg/m2/sec F -FireComp_SO2 fire emissions flux of SO2 kg/m2/sec F -FireEmis_TOT Total fire emissions flux gC/m2/sec F -FireEmis_ZTOP Top of vertical fire emissions distribution m F -FireMech_SO2 fire emissions flux of SO2 kg/m2/sec F -FireMech_bc_a1 fire emissions flux of bc_a1 kg/m2/sec F -FireMech_pom_a1 fire emissions flux of pom_a1 kg/m2/sec F GAMMA total gamma for VOC calc non F GAMMAA gamma A for VOC calc non F GAMMAC gamma C for VOC calc non F @@ -426,16 +402,16 @@ GDD1020 Twenty year average of growing degree days b GDD8 Growing degree days base 8C from planting ddays F GDD820 Twenty year average of growing degree days base 8C from planting ddays F GDDACCUM Accumulated growing degree days past planting date for crop ddays F -GDDACCUM_PERHARV For each crop harvest in a calendar year, accumulated growing degree days past planting date ddays F +GDDACCUM_PERHARV At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F GDDHARV Growing degree days (gdd) needed to harvest ddays F -GDDHARV_PERHARV For each harvest in a calendar year,For each harvest in a calendar year, growing degree days (gdd) needed to harvest ddays F +GDDHARV_PERHARV Growing degree days (gdd) needed to harvest; should only be output annually ddays F GDDTSOI Growing degree-days from planting (top two soil layers) ddays F GPP gross primary production gC/m^2/s T GR total growth respiration gC/m^2/s T GRAINC grain C (does not equal yield) gC/m^2 T GRAINC_TO_FOOD grain C to food gC/m^2/s T -GRAINC_TO_FOOD_ANN total grain C to food in all harvests in a calendar year gC/m^2 F -GRAINC_TO_FOOD_PERHARV grain C to food for each harvest in a calendar year gC/m^2 F +GRAINC_TO_FOOD_ANN grain C to food harvested per calendar year; should only be output annually gC/m^2 F +GRAINC_TO_FOOD_PERHARV grain C to food per harvest; should only be output annually gC/m^2 F GRAINC_TO_SEED grain C to seed gC/m^2/s T GRAINN grain N gN/m^2 T GRESP_STORAGE growth respiration storage gC/m^2 F @@ -443,6 +419,10 @@ GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer GRESP_XFER growth respiration transfer gC/m^2 F GROSS_NMIN gross rate of N mineralization gN/m^2/s T GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F +GRU_PROD100C_GAIN gross unrepresented landcover change addition to 100-yr wood product pool gC/m^2/s F +GRU_PROD100N_GAIN gross unrepresented landcover change addition to 100-yr wood product pool gN/m^2/s F +GRU_PROD10C_GAIN gross unrepresented landcover change addition to 10-yr wood product pool gC/m^2/s F +GRU_PROD10N_GAIN gross unrepresented landcover change addition to 10-yr wood product pool gN/m^2/s F GSSHA shaded leaf stomatal conductance umol H20/m2/s T GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T GSSUN sunlit leaf stomatal conductance umol H20/m2/s T @@ -453,8 +433,9 @@ H2OSNO snow depth (liquid water) H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F H2OSNO_TOP mass of snow in top snow layer kg/m2 T H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T -HARVEST_REASON_PERHARV For each harvest in a calendar year, the reason the crop was harvested categorical F +HARVEST_REASON_PERHARV Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F HBOT canopy bottom m F +HDATES actual crop harvest dates; should only be output annually day of year F HEAT_CONTENT1 initial gridcell total heat content J/m^2 T HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F HEAT_CONTENT2 post land cover change total heat content J/m^2 F @@ -466,8 +447,8 @@ HK hydraulic conductivity (natural vegetated an HR total heterotrophic respiration gC/m^2/s T HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T HTOP canopy top m T -HUI crop heat unit index ddays F -HUI_PERHARV For each harvest in a calendar year, crop heat unit index ddays F +HUI Crop patch heat unit index ddays F +HUI_PERHARV At-harvest accumulated heat unit index for crop; should only be output annually ddays F HUMIDEX 2 m Humidex C T HUMIDEX_R Rural 2 m Humidex C T HUMIDEX_U Urban 2 m Humidex C T @@ -493,6 +474,12 @@ K_NITR_PH K_NITR_PH K_NITR_T K_NITR_T unitless F K_PAS_SOM passive soil organic potential loss coefficient 1/s F K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F +L1_PATHFRAC_S1_vr PATHFRAC from metabolic litter to active soil organic fraction F +L1_RESP_FRAC_S1_vr respired from metabolic litter to active soil organic fraction F +L2_PATHFRAC_S1_vr PATHFRAC from cellulosic litter to active soil organic fraction F +L2_RESP_FRAC_S1_vr respired from cellulosic litter to active soil organic fraction F +L3_PATHFRAC_S2_vr PATHFRAC from lignin litter to slow soil organic ma fraction F +L3_RESP_FRAC_S2_vr respired from lignin litter to slow soil organic ma fraction F LAI240 240hr average of leaf area index m^2/m^2 F LAISHA shaded projected leaf area index m^2/m^2 T LAISUN sunlit projected leaf area index m^2/m^2 T @@ -500,7 +487,7 @@ LAKEICEFRAC lake layer ice mass fraction LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T -LATBASET latitude vary base temperature for gddplant degree C F +LATBASET latitude vary base temperature for hui degree C F LEAFC leaf C gC/m^2 T LEAFCN Leaf CN ratio used for flexible CN gC/gN T LEAFCN_OFFSET Leaf C:N used by FUN unitless F @@ -980,11 +967,21 @@ RSSHA shaded leaf stomatal resistance RSSUN sunlit leaf stomatal resistance s/m T Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F Rnet net radiation W/m^2 F +S1_PATHFRAC_S2_vr PATHFRAC from active soil organic to slow soil organic ma fraction F +S1_PATHFRAC_S3_vr PATHFRAC from active soil organic to passive soil organic fraction F +S1_RESP_FRAC_S2_vr respired from active soil organic to slow soil organic ma fraction F +S1_RESP_FRAC_S3_vr respired from active soil organic to passive soil organic fraction F +S2_PATHFRAC_S1_vr PATHFRAC from slow soil organic ma to active soil organic fraction F +S2_PATHFRAC_S3_vr PATHFRAC from slow soil organic ma to passive soil organic fraction F +S2_RESP_FRAC_S1_vr respired from slow soil organic ma to active soil organic fraction F +S2_RESP_FRAC_S3_vr respired from slow soil organic ma to passive soil organic fraction F +S3_PATHFRAC_S1_vr PATHFRAC from passive soil organic to active soil organic fraction F +S3_RESP_FRAC_S1_vr respired from passive soil organic to active soil organic fraction F SABG solar rad absorbed by ground W/m^2 T SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T SABV solar rad absorbed by veg W/m^2 T -SDATES Crop sowing dates in each calendar year day of year (julian day) F -SDATES_PERHARV For each harvest in a calendar year, the Julian day the crop was sown day of year (julian day) F +SDATES actual crop sowing dates; should only be output annually day of year F +SDATES_PERHARV actual sowing dates for crops harvested this year; should only be output annually day of year F SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T @@ -1114,16 +1111,9 @@ SOM_ADV_COEF advection term for vertical SOM translocatio SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -SOWING_REASON For each sowing in a calendar year, the reason the crop was sown categorical F -SOWING_REASON_PERHARV For each harvest in a calendar year, the reason the crop was sown categorical F +SOWING_REASON Reason for each crop sowing; should only be output annually unitless F +SOWING_REASON_PERHARV Reason for sowing of each crop harvested this year; should only be output annually unitless F SR total soil respiration (HR + root resp) gC/m^2/s T -SSRE_FSR surface snow effect on reflected solar radiation W/m^2 T -SSRE_FSRND surface snow effect on direct nir reflected solar radiation W/m^2 T -SSRE_FSRNDLN surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T -SSRE_FSRNI surface snow effect on diffuse nir reflected solar radiation W/m^2 T -SSRE_FSRVD surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T -SSRE_FSRVDLN surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T -SSRE_FSRVI surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T STEM_PROF profile for litter C and N inputs from stems 1/m F STORAGE_CDEMAND C use from the C storage pool gC/m^2 F STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F @@ -1132,18 +1122,12 @@ STORVEGC stored vegetation carbon, excluding cpool STORVEGN stored vegetation nitrogen gN/m^2 T SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -SYEARS_PERHARV For each harvest in a calendar year, the year the crop was sown year F SWBGT 2 m Simplified Wetbulb Globe Temp C T SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -SWMP65 2 m Swamp Cooler Temp 65% Eff C T -SWMP65_R Rural 2 m Swamp Cooler Temp 65% Eff C T -SWMP65_U Urban 2 m Swamp Cooler Temp 65% Eff C T -SWMP80 2 m Swamp Cooler Temp 80% Eff C T -SWMP80_R Rural 2 m Swamp Cooler Temp 80% Eff C T -SWMP80_U Urban 2 m Swamp Cooler Temp 80% Eff C T SWdown atmospheric incident solar radiation W/m^2 F SWup upwelling shortwave radiation W/m^2 F +SYEARS_PERHARV actual sowing years for crops harvested this year; should only be output annually year F SoilAlpha factor limiting ground evap unitless F SoilAlpha_U urban factor limiting ground evap unitless F T10 10-day running mean of 2-m temperature K F @@ -1156,9 +1140,6 @@ TBUILD_MAX prescribed maximum interior building tempera TEMPAVG_T2M temporary average 2m air temperature K F TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F -TEQ 2 m Equiv Temp K T -TEQ_R Rural 2 m Equiv Temp K T -TEQ_U Urban 2 m Equiv Temp K T TFLOOR floor temperature K F TG ground temperature K T TG_ICE ground temperature (ice landunits only) K F @@ -1166,12 +1147,6 @@ TG_R Rural ground temperature TG_U Urban ground temperature K F TH2OSFC surface water temperature K T THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -THIC 2 m Temp Hum Index Comfort C T -THIC_R Rural 2 m Temp Hum Index Comfort C T -THIC_U Urban 2 m Temp Hum Index Comfort C T -THIP 2 m Temp Hum Index Physiology C T -THIP_R Rural 2 m Temp Hum Index Physiology C T -THIP_U Urban 2 m Temp Hum Index Physiology C T TKE1 top lake level eddy thermal conductivity W/(mK) T TLAI total projected leaf area index m^2/m^2 T TLAKE lake temperature K T @@ -1256,6 +1231,7 @@ VCMX25T canopy profile of vcmax25 VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T +VENTILATION sensible heat flux from building ventilation W/m^2 T VOCFLXT total VOC flux into atmosphere moles/m2/sec F VOLR river channel total water storage m3 T VOLRMCH river channel main channel water storage m3 T @@ -1264,9 +1240,6 @@ VPD2M 2m vapor pressure deficit VPD_CAN canopy vapor pressure deficit kPa T Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -WBA 2 m Wet Bulb C T -WBA_R Rural 2 m Wet Bulb C T -WBA_U Urban 2 m Wet Bulb C T WBT 2 m Stull Wet Bulb C T WBT_R Rural 2 m Stull Wet Bulb C T WBT_U Urban 2 m Stull Wet Bulb C T @@ -1284,13 +1257,13 @@ Wind atmospheric wind velocity magnitude XSMRPOOL temporary photosynthate C pool gC/m^2 T XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T -Z0HG roughness length over ground, sensible heat m F +Z0HG roughness length over ground, sensible heat (vegetated landunits only) m F Z0HV roughness length over vegetation, sensible heat m F -Z0M momentum roughness length m F -Z0MG roughness length over ground, momentum m F +Z0MG roughness length over ground, momentum (vegetated landunits only) m F Z0MV roughness length over vegetation, momentum m F +Z0MV_DENSE roughness length over vegetation, momentum, for dense canopy m F Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -Z0QG roughness length over ground, latent heat m F +Z0QG roughness length over ground, latent heat (vegetated landunits only) m F Z0QV roughness length over vegetation, latent heat m F ZBOT atmospheric reference height m T ZETA dimensionless stability parameter unitless F @@ -1312,4 +1285,4 @@ soil_bulkdensity soil_bulkdensity soil_co2_prod soil_co2_prod ug C / g soil / day F watfc water field capacity m^3/m^3 F watsat water saturated m^3/m^3 F -==== =================================== ============================================================================================== ================================================================= ======= +=================================== ============================================================================================== ================================================================= ======= From f0b6d605344b4a6b97208a5f0f5bb16026653ccd Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 11 Aug 2023 17:16:24 -0600 Subject: [PATCH 1364/2067] Update2 to the ChangeLog --- doc/ChangeLog | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index e2d894e242..fdef172382 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev13? Originator(s): @cenlinhe (Cenlin He,UCAR/RAL), slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Fri Aug 11 15:07:55 MDT 2023 +Date: Fri Aug 11 17:09:18 MDT 2023 One-line Summary: SNICAR snow albedo scheme updates Purpose and description of changes @@ -12,12 +12,9 @@ Purpose and description of changes A few substantial changes in the SNICAR module for the following updated snow albedo calculation features: - Updated ice optical properties from Flanner et al. (2021), with multiple types - for ice refractive indices. The updated SNICAR database files are: - /glade/work/cenlinhe/NOAA_CPT_snowAER/CLM_SNICAR_data/snicar_optics_480bnd_c012422.nc - /glade/work/cenlinhe/NOAA_CPT_snowAER/CLM_SNICAR_data/snicar_optics_5bnd_c013122.nc + for ice refractive indices. - Updated aerosol optical properties from Flanner et al. (2021) with multiple - dust types & new BC and OC optics (the updated data are in the new SNICAR - database files shown above). + dust types & new BC and OC optics. - Updated downward solar spectra from Flanner et al. (2021) for multiple condition types. - More accurate radiative transfer solver (adding-doubling) from Dang et al. (2019). @@ -31,7 +28,11 @@ Purpose and description of changes Specific notes - Code contributors: Cenlin He (NCAR/RAL) with advice from Dave Lawrence (NCAR/CGD) and Mark Flanner (UMich). - - The manuscript to report this update is in preparation (He et al, 2022 JAMES in prep) + - The manuscript to report this update is + Cenlin He, Mark Flanner, David M Lawrence, Yu Gu: New features and + enhancements in Community Land Model (CLM5) snow albedo modeling: description, + sensitivity, and evaluation. Authorea. June 08, 2023. + DOI:10.22541/essoar.168626390.01530324/v1 - These updates will change the snow and surface albedo results along with other surface fluxes changes. - There are a few new namelist options related to SNICAR scheme added to the From 8aa0a680db01f7cc345900aa5c194bc182f15e10 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 11 Aug 2023 21:18:51 -0600 Subject: [PATCH 1365/2067] Put NEON site fsurdat files in the namelist_defaults file, and get it connected, fixing #2028 --- bld/CLMBuildNamelist.pm | 56 ++++++++++++++----- bld/env_run.xml | 1 + bld/namelist_files/namelist_defaults_ctsm.xml | 11 ++++ bld/unit_testers/build-namelist_test.pl | 4 +- 4 files changed, 55 insertions(+), 17 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 69b3a8c3dc..98cce06fca 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -611,7 +611,7 @@ sub process_namelist_user_input { process_namelist_commandline_infile($opts, $definition, $nl, $envxml_ref); # Apply the commandline options and make sure the user didn't change it above - process_namelist_commandline_options($opts, $nl_flags, $definition, $defaults, $nl, $physv); + process_namelist_commandline_options($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv); # The last two process command line arguments for usr_name and use_case # They require that process_namelist_commandline_options was called before this @@ -632,10 +632,10 @@ sub process_namelist_commandline_options { # Obtain default values for the following build-namelist input arguments # : res, mask, ssp_rcp, sim_year, sim_year_range, and clm_accelerated_spinup. - my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref, $physv) = @_; setup_cmdl_chk_res($opts, $defaults); - setup_cmdl_resolution($opts, $nl_flags, $definition, $defaults); + setup_cmdl_resolution($opts, $nl_flags, $definition, $defaults, $envxml_ref); setup_cmdl_mask($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_configuration_and_structure($opts, $nl_flags, $definition, $defaults, $nl); setup_cmdl_bgc($opts, $nl_flags, $definition, $defaults, $nl); @@ -666,7 +666,7 @@ sub setup_cmdl_chk_res { } sub setup_cmdl_resolution { - my ($opts, $nl_flags, $definition, $defaults) = @_; + my ($opts, $nl_flags, $definition, $defaults, $envxml_ref) = @_; my $var = "res"; my $val; @@ -690,10 +690,20 @@ sub setup_cmdl_resolution { } } # For NEON sites - if ($nl_flags->{'res'} =~ /NEON/) { - $nl_flags->{'neon'} = ".true." - } else { - $nl_flags->{'neon'} = ".false." + $nl_flags->{'neon'} = ".false."; + $nl_flags->{'neonsite'} = ""; + if ( $nl_flags->{'res'} eq "CLM_USRDAT" ) { + if ( ! defined($opts->{'clm_usr_name'}) ) { + $log->fatal_error("Resolution is CLM_USRDAT, but --clm_usr_name option is NOT set, and it is required for CLM_USRDAT resolutions"); + } + if ( $opts->{'clm_usr_name'} eq "NEON" ) { + $nl_flags->{'neon'} = ".true."; + $nl_flags->{'neonsite'} = $envxml_ref->{'NEONSITE'}; + $log->verbose_message( "This is a NEON site with NEONSITE = " . $nl_flags->{'neonsite'} ); + } + } + if ( ! &value_is_true( $nl_flags->{'neon'} ) ) { + $log->verbose_message( "This is NOT a NEON site" ); } } @@ -1583,7 +1593,7 @@ sub process_namelist_inline_logic { setup_logic_grainproduct($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_logic_soilstate($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_demand($opts, $nl_flags, $definition, $defaults, $nl); - setup_logic_surface_dataset($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_surface_dataset($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); setup_logic_dynamic_subgrid($opts, $nl_flags, $definition, $defaults, $nl); if ( remove_leading_and_trailing_quotes($nl_flags->{'clm_start_type'}) ne "branch" ) { setup_logic_initial_conditions($opts, $nl_flags, $definition, $defaults, $nl, $physv); @@ -2305,7 +2315,7 @@ sub setup_logic_surface_dataset { # consistent with it # MUST BE AFTER: setup_logic_demand which is where flanduse_timeseries is set # - my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $xmlvar_ref) = @_; $nl_flags->{'flanduse_timeseries'} = "null"; my $flanduse_timeseries = $nl->get_value('flanduse_timeseries'); @@ -2330,26 +2340,42 @@ sub setup_logic_surface_dataset { if ( ! &value_is_true($nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, + 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'}, 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", 'use_vichydro'=>$nl_flags->{'use_vichydro'}, - 'use_crop'=>".true.", 'glc_nec'=>$nl_flags->{'glc_nec'}, 'nofail'=>1); + 'use_crop'=>".true.", 'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'}, 'nofail'=>1); } # If didn't find the crop version check for the exact match - if ( ! defined($nl->get_value($var) ) ) { + my $fsurdat = $nl->get_value($var); + if ( ! defined($fsurdat) ) { if ( ! &value_is_true($nl_flags->{'use_fates'}) ) { $log->verbose_message( "Crop version of $var NOT found, searching for an exact match" ); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'}, - 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, + 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>$nl_flags->{'irrigate'}, 'use_fates'=>$nl_flags->{'use_fates'}, + 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'}, 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'}, 'nofail'=>1 ); - if ( ! defined($nl->get_value($var) ) ) { + if ( ! defined($fsurdat) ) { $log->verbose_message( "Exact match of $var NOT found, searching for version with irrigate true" ); } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'hgrid'=>$nl_flags->{'res'}, 'ssp_rcp'=>$nl_flags->{'ssp_rcp'}, 'use_vichydro'=>$nl_flags->{'use_vichydro'}, - 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", + 'sim_year'=>$nl_flags->{'sim_year'}, 'irrigate'=>".true.", 'use_fates'=>$nl_flags->{'use_fates'}, + 'neon'=>$nl_flags->{'neon'}, 'neonsite'=>$nl_flags->{'neonsite'}, 'use_crop'=>$nl_flags->{'use_crop'}, 'glc_nec'=>$nl_flags->{'glc_nec'} ); } + # + # Expand the XML variables for NEON cases so that NEONSITE will be used + # + if ( &value_is_true($nl_flags->{'neon'}) ) { + my $fsurdat = $nl->get_value($var); + my $newval = SetupTools::expand_xml_var( $fsurdat, $xmlvar_ref ); + if ( $newval ne $fsurdat ) { + my $group = $definition->get_group_name($var); + $nl->set_variable_value($group, $var, $newval); + $log->verbose_message( "This is a NEON site and the fsurdat file selected is: $newval" ); + } + } } #------------------------------------------------------------------------------- diff --git a/bld/env_run.xml b/bld/env_run.xml index 8bf59d0911..f3b7467168 100644 --- a/bld/env_run.xml +++ b/bld/env_run.xml @@ -9,5 +9,6 @@ Sample env_run.xml file that allows build-namelist to be run for testing in this --> + diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 1d895524e6..666b19a08f 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1275,6 +1275,17 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne0np4.CONUS.ne30x8_hist_78pfts lnd/clm2/surfdata_map/surfdata_0.9x1.25_hist_16pfts_nourb_CMIP6_simyrPtVg_c181114.nc + + +lnd/clm2/surfdata_map/NEON/16PFT_mixed/surfdata_1x1_NEON_${NEONSITE}_hist_16pfts_Irrig_CMIP6_simyr2000_c230120.nc + +lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_${NEONSITE}_hist_78pfts_CMIP6_simyr2000_c230601.nc + + + "MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE" ); + my %env_vars = ( DIN_LOC_ROOT=>"MYDINLOCROOT", GLC_TWO_WAY_COUPLING=>"FALSE", NEONSITE=>"" ); # Set any settings that came in from function call foreach my $item ( keys(%settings) ) { $env_vars{$item} = $settings{$item}; @@ -380,7 +380,7 @@ sub cat_and_create_namelistinfile { "JORN", "LAJA", "MOAB", "OAES", "OSBS", "SCBI", "SOAP", "STER", "TOOL", "UNDE", "YELL" ) { - &make_env_run(); + &make_env_run( NEONSITE=>"$site" ); # # Concatonate default usermods and specific sitetogether expanding env variables while doing that # From 907ca1ab13c2b5b55b0b024ef96ff15039477f93 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Sat, 12 Aug 2023 15:16:53 -0600 Subject: [PATCH 1366/2067] Provisions to satisfy nag compiler, cnveg datastructures on now allocated with 1 index 0 through 0 when fate_bgc is on, to avoid null pointers on associates --- src/biogeochem/CNVegCarbonFluxType.F90 | 31 ++++++---- src/biogeochem/CNVegCarbonStateType.F90 | 40 ++++++++----- src/biogeochem/CNVegNitrogenFluxType.F90 | 38 +++++++----- src/biogeochem/CNVegNitrogenStateType.F90 | 47 +++++++++------ src/biogeochem/CNVegStateType.F90 | 20 +++++-- src/biogeochem/CNVegetationFacade.F90 | 59 +++++++++++++------ .../SoilBiogeochemCarbonFluxType.F90 | 2 + .../SoilBiogeochemNitrogenFluxType.F90 | 8 ++- 8 files changed, 160 insertions(+), 85 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index c2025fca47..d376d33e16 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -434,21 +434,23 @@ module CNVegCarbonFluxType contains !------------------------------------------------------------------------ - subroutine Init(this, bounds, carbon_type, dribble_crophrv_xsmrpool_2atm) + subroutine Init(this, bounds, carbon_type, dribble_crophrv_xsmrpool_2atm,tot_bgc_vegp) class(cnveg_carbonflux_type) :: this type(bounds_type), intent(in) :: bounds character(len=3) , intent(in) :: carbon_type ! one of ['c12', c13','c14'] logical , intent(in) :: dribble_crophrv_xsmrpool_2atm + integer , intent(in) :: tot_bgc_vegp this%dribble_crophrv_xsmrpool_2atm = dribble_crophrv_xsmrpool_2atm - call this%InitAllocate ( bounds, carbon_type) - if(use_matrixcn)then - call this%InitTransfer () + call this%InitAllocate ( bounds, carbon_type,tot_bgc_vegp) + if(tot_bgc_vegp>0)then + if(use_matrixcn)then + call this%InitTransfer () + end if + call this%InitHistory ( bounds, carbon_type ) + call this%InitCold (bounds ) end if - call this%InitHistory ( bounds, carbon_type ) - call this%InitCold (bounds ) - end subroutine Init subroutine InitTransfer (this) @@ -461,12 +463,13 @@ subroutine InitTransfer (this) end subroutine InitTransfer !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds, carbon_type) + subroutine InitAllocate(this, bounds, carbon_type, tot_bgc_vegp) ! ! !ARGUMENTS: class (cnveg_carbonflux_type) :: this type(bounds_type), intent(in) :: bounds character(len=*) , intent(in) :: carbon_type ! one of ['c12', c13','c14'] + integer , intent(in) :: tot_bgc_vegp ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -476,9 +479,15 @@ subroutine InitAllocate(this, bounds, carbon_type) character(len=:), allocatable :: carbon_type_suffix !------------------------------------------------------------------------ - begp = bounds%begp; endp = bounds%endp - begc = bounds%begc; endc = bounds%endc - begg = bounds%begg; endg = bounds%endg + if(tot_bgc_vegp>0)then + begp = bounds%begp; endp = bounds%endp + begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg + else + begp = 0; endp = 0 + begc = 0; endc = 0 + begg = 0; endg = 0 + end if allocate(this%m_leafc_to_litter_patch (begp:endp)) ; this%m_leafc_to_litter_patch (:) = nan allocate(this%m_frootc_to_litter_patch (begp:endp)) ; this%m_frootc_to_litter_patch (:) = nan diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index e1d0ed6e39..e5f08bdc9d 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -126,7 +126,7 @@ module CNVegCarbonStateType !------------------------------------------------------------------------ subroutine Init(this, bounds, carbon_type, ratio, NLFilename, & - dribble_crophrv_xsmrpool_2atm, c12_cnveg_carbonstate_inst) + dribble_crophrv_xsmrpool_2atm, tot_bgc_vegp, c12_cnveg_carbonstate_inst) class(cnveg_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds @@ -134,6 +134,7 @@ subroutine Init(this, bounds, carbon_type, ratio, NLFilename, & character(len=*) , intent(in) :: carbon_type ! Carbon isotope type C12, C13 or C1 character(len=*) , intent(in) :: NLFilename ! Namelist filename logical , intent(in) :: dribble_crophrv_xsmrpool_2atm + integer , intent(in) :: tot_bgc_vegp ! total number of bgc patches (non-fates) type(cnveg_carbonstate_type) , intent(in), optional :: c12_cnveg_carbonstate_inst ! cnveg_carbonstate for C12 (if C13 or C14) !----------------------------------------------------------------------- @@ -141,15 +142,17 @@ subroutine Init(this, bounds, carbon_type, ratio, NLFilename, & this%dribble_crophrv_xsmrpool_2atm = dribble_crophrv_xsmrpool_2atm - call this%InitAllocate ( bounds) - call this%InitReadNML ( NLFilename ) - call this%InitHistory ( bounds, carbon_type) - if (present(c12_cnveg_carbonstate_inst)) then - call this%InitCold ( bounds, ratio, carbon_type, c12_cnveg_carbonstate_inst ) - else - call this%InitCold ( bounds, ratio, carbon_type ) + call this%InitAllocate ( bounds, tot_bgc_vegp) + if(tot_bgc_vegp>0)then + call this%InitReadNML ( NLFilename ) + call this%InitHistory ( bounds, carbon_type) + if (present(c12_cnveg_carbonstate_inst)) then + call this%InitCold ( bounds, ratio, carbon_type, c12_cnveg_carbonstate_inst ) + else + call this%InitCold ( bounds, ratio, carbon_type ) + end if end if - + end subroutine Init !------------------------------------------------------------------------ @@ -213,21 +216,28 @@ subroutine InitReadNML(this, NLFilename) end subroutine InitReadNML !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds) + subroutine InitAllocate(this, bounds, tot_bgc_vegp) ! ! !ARGUMENTS: class (cnveg_carbonstate_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds + integer,intent(in) :: tot_bgc_vegp ! Total number of bgc patches on the proc (non_fates) ! ! !LOCAL VARIABLES: integer :: begp,endp integer :: begc,endc integer :: begg,endg !------------------------------------------------------------------------ - - begp = bounds%begp; endp = bounds%endp - begc = bounds%begc; endc = bounds%endc - begg = bounds%begg; endg = bounds%endg + + if(tot_bgc_vegp>0)then + begp = bounds%begp; endp = bounds%endp + begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg + else + begp = 0;endp=0 + begc = 0;endc=0 + begg = 0;endg=0 + end if allocate(this%leafc_patch (begp:endp)) ; this%leafc_patch (:) = nan allocate(this%leafc_storage_patch (begp:endp)) ; this%leafc_storage_patch (:) = nan diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index ce164b4c37..f742cba2ad 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -292,18 +292,21 @@ module CNVegNitrogenFluxType contains !------------------------------------------------------------------------ - subroutine Init(this, bounds) + subroutine Init(this, bounds, tot_bgc_vegp) class(cnveg_nitrogenflux_type) :: this - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds + integer,intent(in) :: tot_bgc_vegp - call this%InitAllocate (bounds) - if(use_matrixcn)then - call this%InitTransfer () + call this%InitAllocate (bounds,tot_bgc_vegp) + if(tot_bgc_vegp>0)then + if(use_matrixcn)then + call this%InitTransfer () + end if + call this%InitHistory (bounds) + call this%InitCold (bounds) end if - call this%InitHistory (bounds) - call this%InitCold (bounds) - + end subroutine Init subroutine InitTransfer (this) @@ -323,14 +326,15 @@ subroutine InitTransfer (this) end subroutine InitTransfer !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds) + subroutine InitAllocate(this, bounds, tot_bgc_vegp) ! ! !DESCRIPTION: ! Initialize patch nitrogen flux ! ! !ARGUMENTS: class (cnveg_nitrogenflux_type) :: this - type(bounds_type) , intent(in) :: bounds + type(bounds_type) , intent(in) :: bounds + integer,intent(in) :: tot_bgc_vegp ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -338,10 +342,16 @@ subroutine InitAllocate(this, bounds) integer :: begg,endg !------------------------------------------------------------------------ - begp = bounds%begp; endp = bounds%endp - begc = bounds%begc; endc = bounds%endc - begg = bounds%begg; endg = bounds%endg - + if(tot_bgc_vegp>0)then + begp = bounds%begp; endp = bounds%endp + begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg + else + begp = 0; endp = 0 + begc = 0; endc = 0 + begg = 0; endg = 0 + end if + allocate(this%m_leafn_to_litter_patch (begp:endp)) ; this%m_leafn_to_litter_patch (:) = nan allocate(this%m_frootn_to_litter_patch (begp:endp)) ; this%m_frootn_to_litter_patch (:) = nan allocate(this%m_leafn_storage_to_litter_patch (begp:endp)) ; this%m_leafn_storage_to_litter_patch (:) = nan diff --git a/src/biogeochem/CNVegNitrogenStateType.F90 b/src/biogeochem/CNVegNitrogenStateType.F90 index d6c335bb9a..341cc8f40d 100644 --- a/src/biogeochem/CNVegNitrogenStateType.F90 +++ b/src/biogeochem/CNVegNitrogenStateType.F90 @@ -96,40 +96,49 @@ module CNVegNitrogenStateType !------------------------------------------------------------------------ subroutine Init(this, bounds, & - leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch) + leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, & + deadstemc_patch, tot_bgc_vegp) class(cnveg_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds - real(r8) , intent(in) :: leafc_patch (bounds%begp:) - real(r8) , intent(in) :: leafc_storage_patch (bounds%begp:) - real(r8) , intent(in) :: frootc_patch (bounds%begp:) - real(r8) , intent(in) :: frootc_storage_patch (bounds%begp:) - real(r8) , intent(in) :: deadstemc_patch (bounds%begp:) - - call this%InitAllocate (bounds ) - call this%InitHistory (bounds) - call this%InitCold ( bounds, & - leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch) - + real(r8) , intent(in) :: leafc_patch (:) !(begp:) + real(r8) , intent(in) :: leafc_storage_patch (:) !(begp:) + real(r8) , intent(in) :: frootc_patch (:) !(begp:) + real(r8) , intent(in) :: frootc_storage_patch(:) !(begp:) + real(r8) , intent(in) :: deadstemc_patch (:) !(begp:) + integer , intent(in) :: tot_bgc_vegp + + call this%InitAllocate (bounds, tot_bgc_vegp) + if(tot_bgc_vegp>0) then + call this%InitHistory (bounds) + call this%InitCold ( bounds, & + leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch) + end if end subroutine Init !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds) + subroutine InitAllocate(this, bounds, tot_bgc_vegp) ! ! !ARGUMENTS: class (cnveg_nitrogenstate_type) :: this - type(bounds_type) , intent(in) :: bounds + type(bounds_type) , intent(in) :: bounds + integer,intent(in) :: tot_bgc_vegp ! ! !LOCAL VARIABLES: integer :: begp,endp integer :: begc,endc integer :: begg,endg !------------------------------------------------------------------------ - - begp = bounds%begp; endp = bounds%endp - begc = bounds%begc; endc = bounds%endc - begg = bounds%begg; endg = bounds%endg - + if(tot_bgc_vegp>0) then + begp = bounds%begp; endp = bounds%endp + begc = bounds%begc; endc = bounds%endc + begg = bounds%begg; endg = bounds%endg + else + begp = 0; endp = 0 + begc = 0; endc = 0 + begg = 0; endg = 0 + end if + allocate(this%reproductiven_patch (begp:endp, nrepr)) ; this%reproductiven_patch (:,:) = nan allocate(this%reproductiven_storage_patch (begp:endp, nrepr)) ; this%reproductiven_storage_patch (:,:) = nan allocate(this%reproductiven_xfer_patch (begp:endp, nrepr)) ; this%reproductiven_xfer_patch (:,:) = nan diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index e7e61c75bf..b5391c7bce 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -130,12 +130,13 @@ module CNVegStateType contains !------------------------------------------------------------------------ - subroutine Init(this, bounds) + subroutine Init(this, bounds, tot_bgc_vegp) class(cnveg_state_type) :: this type(bounds_type), intent(in) :: bounds + integer,intent(in) :: tot_bgc_vegp ! Total number of bgc patches on proc (non-fates) - call this%InitAllocate ( bounds ) + call this%InitAllocate ( bounds, tot_bgc_vegp) if (use_cn) then call this%InitHistory ( bounds ) end if @@ -144,7 +145,7 @@ subroutine Init(this, bounds) end subroutine Init !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds) + subroutine InitAllocate(this, bounds, tot_bgc_vegp) ! ! !DESCRIPTION: ! Initialize module data structure @@ -156,6 +157,7 @@ subroutine InitAllocate(this, bounds) ! !ARGUMENTS: class(cnveg_state_type) :: this type(bounds_type), intent(in) :: bounds + integer, intent(in) :: tot_bgc_vegp ! Total number of bgc patches on proc (non-fates) ! ! !LOCAL VARIABLES: integer :: begp, endp @@ -163,9 +165,15 @@ subroutine InitAllocate(this, bounds) logical :: allows_non_annual_delta !------------------------------------------------------------------------ - begp = bounds%begp; endp= bounds%endp - begc = bounds%begc; endc= bounds%endc - + if(tot_bgc_vegp>0)then + begp = bounds%begp; endp= bounds%endp + begc = bounds%begc; endc= bounds%endc + else + begp = 0;endp = 0 + begc = 0;endc = 0 + end if + + ! Note that we set allows_non_annual_delta to false because we expect land cover ! change to be applied entirely at the start of the year. Currently the fire code ! appears to assume that the land cover change rate is constant throughout the year, diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index c437a9e438..7370987e3c 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -206,6 +206,8 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) use CNFireFactoryMod , only : create_cnfire_method use clm_varcon , only : c13ratio, c14ratio use ncdio_pio , only : file_desc_t + use filterMod , only : filter + use decompMod , only : get_proc_clumps ! ! !ARGUMENTS: class(cn_vegetation_type), intent(inout) :: this @@ -215,16 +217,33 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) type(file_desc_t), intent(inout) :: params_ncid ! NetCDF handle to parameter file ! ! !LOCAL VARIABLES: - integer :: begp, endp + integer :: begp, endp, ci + integer :: nclumps ! number of clumps on the proc + integer :: tot_bgc_vegp ! Total number of bgc vegetation patches (non-fates) + ! on the proc character(len=*), parameter :: subname = 'Init' !----------------------------------------------------------------------- - begp = bounds%begp - endp = bounds%endp - ! Note - always initialize the memory for cnveg_state_inst (used in biogeophys/) - call this%cnveg_state_inst%Init(bounds) + ! - Even if FATES is the only vegetation option, we still allocate + ! - a single value for both column and patch, using index 0 only + ! - that is why we pass the number of bgc veg patches here + + nclumps = get_proc_clumps() + tot_bgc_vegp = 0 + do ci=1,nclumps + tot_bgc_vegp = tot_bgc_vegp + filter(ci)%num_bgc_vegp + end do + if(tot_bgc_vegp>0)then + begp = bounds%begp + endp = bounds%endp + else + begp = 0 + endp = 0 + end if + + call this%cnveg_state_inst%Init(bounds,tot_bgc_vegp) skip_steps = nskip_steps @@ -232,37 +251,43 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) ! Read in the general CN namelist call this%CNReadNML( NLFilename ) ! MUST be called first as passes down control information to others + end if + if(use_cn.or.use_fates_bgc)then call this%cnveg_carbonstate_inst%Init(bounds, carbon_type='c12', ratio=1._r8, & - NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm ) + NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, & + tot_bgc_vegp=tot_bgc_vegp) + if (use_c13) then call this%c13_cnveg_carbonstate_inst%Init(bounds, carbon_type='c13', ratio=c13ratio, & NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, & - c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) + tot_bgc_vegp=tot_bgc_vegp, c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) end if if (use_c14) then call this%c14_cnveg_carbonstate_inst%Init(bounds, carbon_type='c14', ratio=c14ratio, & NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, & - c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) + tot_bgc_vegp=tot_bgc_vegp,c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) end if - call this%cnveg_carbonflux_inst%Init(bounds, carbon_type='c12', dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm ) + + call this%cnveg_carbonflux_inst%Init(bounds, carbon_type='c12', & + dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, tot_bgc_vegp=tot_bgc_vegp ) if (use_c13) then - call this%c13_cnveg_carbonflux_inst%Init(bounds, carbon_type='c13', dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm) + call this%c13_cnveg_carbonflux_inst%Init(bounds, carbon_type='c13', & + dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm,tot_bgc_vegp=tot_bgc_vegp) end if if (use_c14) then - call this%c14_cnveg_carbonflux_inst%Init(bounds, carbon_type='c14', dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm) + call this%c14_cnveg_carbonflux_inst%Init(bounds, carbon_type='c14', & + dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm,tot_bgc_vegp=tot_bgc_vegp) end if call this%cnveg_nitrogenstate_inst%Init(bounds, & this%cnveg_carbonstate_inst%leafc_patch(begp:endp), & this%cnveg_carbonstate_inst%leafc_storage_patch(begp:endp), & this%cnveg_carbonstate_inst%frootc_patch(begp:endp), & this%cnveg_carbonstate_inst%frootc_storage_patch(begp:endp), & - this%cnveg_carbonstate_inst%deadstemc_patch(begp:endp) ) - call this%cnveg_nitrogenflux_inst%Init(bounds) - - end if - - if (use_cn .or. use_fates_bgc) then + this%cnveg_carbonstate_inst%deadstemc_patch(begp:endp), & + tot_bgc_vegp=tot_bgc_vegp) + call this%cnveg_nitrogenflux_inst%Init(bounds,tot_bgc_vegp=tot_bgc_vegp) + call this%c_products_inst%Init(bounds, species_non_isotope_type('C')) if (use_c13) then call this%c13_products_inst%Init(bounds, species_isotope_type('C', '13')) diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index d9ada3922d..212cb6a5e2 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -163,6 +163,8 @@ subroutine InitAllocate(this, bounds) if(use_fates)then allocate(this%fates_litter_flux(begc:endc)); this%fates_litter_flux(:) = nan + else + allocate(this%fates_litter_flux(0:0)); this%fates_litter_flux(:) = nan end if if(use_soil_matrixcn)then diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 index fb7eac1ce2..5907d109d5 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 @@ -277,9 +277,11 @@ subroutine InitAllocate(this, bounds) allocate(this%decomp_npools_sourcesink_col (begc:endc,1:nlevdecomp_full,1:ndecomp_pools)) this%decomp_npools_sourcesink_col (:,:,:) = nan if(use_fates)then - allocate(this%fates_litter_flux(begc:endc)); this%fates_litter_flux(:) = nan - end if - + allocate(this%fates_litter_flux(begc:endc)); this%fates_litter_flux(:) = nan + else + allocate(this%fates_litter_flux(0:0)); this%fates_litter_flux(:) = nan + end if + ! Allocate soil Matrix setug if(use_soil_matrixcn)then end if From eaea0305bf000f594edf4ff23e6ed87ee2734060 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 14 Aug 2023 09:55:24 -0600 Subject: [PATCH 1367/2067] Update to clm-fates-bgc zero-allocating instead of not allocating cnveg arrays --- src/biogeochem/CNDriverMod.F90 | 111 +++++++++++----------- src/biogeochem/CNVegCarbonFluxType.F90 | 14 +-- src/biogeochem/CNVegCarbonStateType.F90 | 14 +-- src/biogeochem/CNVegNitrogenFluxType.F90 | 14 +-- src/biogeochem/CNVegNitrogenStateType.F90 | 16 ++-- src/biogeochem/CNVegStateType.F90 | 22 +++-- src/biogeochem/CNVegStructUpdateMod.F90 | 4 +- src/biogeochem/CNVegetationFacade.F90 | 50 +++++----- 8 files changed, 123 insertions(+), 122 deletions(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 424cf8c52b..0907211add 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -393,43 +393,45 @@ subroutine CNDriverNoLeaching(bounds, ! do_nutrient_competition should be modified, but that modification should not significantly change ! the current interface. - !RF: moved ths call to before nutrient_demand, so that croplive didn't change half way through crop N cycle. - if ( use_fun ) then - call t_startf('CNPhenology_phase1') - call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & - filter_bgc_vegp, num_pcropp, filter_pcropp, & - waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & - crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & - leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp,1:nlevdecomp_full), & - froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp,1:nlevdecomp_full), & - phase=1) - call t_stopf('CNPhenology_phase1') - - call t_startf('CNFUNInit') - call CNFUNInit(bounds,cnveg_state_inst,cnveg_carbonstate_inst,cnveg_nitrogenstate_inst) - call t_stopf('CNFUNInit') - - end if - - call t_startf('cnalloc') - call calc_gpp_mr_availc( & - bounds, num_bgc_vegp, filter_bgc_vegp, & - crop_inst, photosyns_inst, canopystate_inst, & - cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst) - - if (.not. use_crop_agsys) then - call calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & - crop_inst, cnveg_state_inst) - end if - - call calc_allometry(num_bgc_vegp, filter_bgc_vegp, & - cnveg_carbonflux_inst, cnveg_state_inst) - call t_stopf('cnalloc') - + !RF: moved ths call to before nutrient_demand, so that croplive didn't change half way through crop N cycle. + if(num_bgc_vegp>0)then + if ( use_fun) then + call t_startf('CNPhenology_phase1') + call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & + filter_bgc_vegp, num_pcropp, filter_pcropp, & + waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & + crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & + c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & + leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp,1:nlevdecomp_full), & + froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp,1:nlevdecomp_full), & + phase=1) + call t_stopf('CNPhenology_phase1') + + call t_startf('CNFUNInit') + call CNFUNInit(bounds,cnveg_state_inst,cnveg_carbonstate_inst,cnveg_nitrogenstate_inst) + call t_stopf('CNFUNInit') + + end if + + call t_startf('cnalloc') + call calc_gpp_mr_availc( & + bounds, num_bgc_vegp, filter_bgc_vegp, & + crop_inst, photosyns_inst, canopystate_inst, & + cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + c13_cnveg_carbonflux_inst, c14_cnveg_carbonflux_inst) + + if (.not. use_crop_agsys) then + call calc_crop_allocation_fractions(bounds, num_pcropp, filter_pcropp, & + crop_inst, cnveg_state_inst) + end if + + call calc_allometry(num_bgc_vegp, filter_bgc_vegp, & + cnveg_carbonflux_inst, cnveg_state_inst) + call t_stopf('cnalloc') + end if + call t_startf('calc_plant_nutrient_demand') ! We always call calc_plant_nutrient_demand for natural veg patches, but only call ! it for crop patches if NOT running with AgSys (since AgSys calculates the relevant @@ -522,10 +524,20 @@ subroutine CNDriverNoLeaching(bounds, ! CNphenology needs to be called after above calls, since it depends on current ! time-step fluxes to new growth on the lastlitterfall timestep in deciduous systems - - call t_startf('CNPhenology') - - if ( .not. use_fun ) then + if(num_bgc_vegp>0)then + call t_startf('CNPhenology') + if ( .not. use_fun ) then + call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & + filter_bgc_vegp, num_pcropp, filter_pcropp, & + waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & + crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & + cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & + cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & + c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & + leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp,1:nlevdecomp_full), & + froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp,1:nlevdecomp_full), & + phase=1) + end if call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & filter_bgc_vegp, num_pcropp, filter_pcropp, & waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & @@ -535,21 +547,10 @@ subroutine CNDriverNoLeaching(bounds, c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp,1:nlevdecomp_full), & froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp,1:nlevdecomp_full), & - phase=1) + phase=2) + + call t_stopf('CNPhenology') end if - call CNPhenology (bounds, num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, & - filter_bgc_vegp, num_pcropp, filter_pcropp, & - waterdiagnosticbulk_inst, wateratm2lndbulk_inst, temperature_inst, atm2lnd_inst, & - crop_inst, canopystate_inst, soilstate_inst, dgvs_inst, & - cnveg_state_inst, cnveg_carbonstate_inst, cnveg_carbonflux_inst, & - cnveg_nitrogenstate_inst, cnveg_nitrogenflux_inst, & - c13_cnveg_carbonstate_inst, c14_cnveg_carbonstate_inst, & - leaf_prof_patch=soilbiogeochem_state_inst%leaf_prof_patch(begp:endp,1:nlevdecomp_full), & - froot_prof_patch=soilbiogeochem_state_inst%froot_prof_patch(begp:endp,1:nlevdecomp_full), & - phase=2) - - call t_stopf('CNPhenology') - !-------------------------------------------- ! Growth respiration !-------------------------------------------- diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index d376d33e16..21a4fc902c 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -434,17 +434,17 @@ module CNVegCarbonFluxType contains !------------------------------------------------------------------------ - subroutine Init(this, bounds, carbon_type, dribble_crophrv_xsmrpool_2atm,tot_bgc_vegp) + subroutine Init(this, bounds, carbon_type, dribble_crophrv_xsmrpool_2atm,alloc_full_veg) class(cnveg_carbonflux_type) :: this type(bounds_type), intent(in) :: bounds character(len=3) , intent(in) :: carbon_type ! one of ['c12', c13','c14'] logical , intent(in) :: dribble_crophrv_xsmrpool_2atm - integer , intent(in) :: tot_bgc_vegp + logical , intent(in) :: alloc_full_veg this%dribble_crophrv_xsmrpool_2atm = dribble_crophrv_xsmrpool_2atm - call this%InitAllocate ( bounds, carbon_type,tot_bgc_vegp) - if(tot_bgc_vegp>0)then + call this%InitAllocate ( bounds, carbon_type,alloc_full_veg) + if(alloc_full_veg)then if(use_matrixcn)then call this%InitTransfer () end if @@ -463,13 +463,13 @@ subroutine InitTransfer (this) end subroutine InitTransfer !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds, carbon_type, tot_bgc_vegp) + subroutine InitAllocate(this, bounds, carbon_type, alloc_full_veg) ! ! !ARGUMENTS: class (cnveg_carbonflux_type) :: this type(bounds_type), intent(in) :: bounds character(len=*) , intent(in) :: carbon_type ! one of ['c12', c13','c14'] - integer , intent(in) :: tot_bgc_vegp + logical , intent(in) :: alloc_full_veg ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -479,7 +479,7 @@ subroutine InitAllocate(this, bounds, carbon_type, tot_bgc_vegp) character(len=:), allocatable :: carbon_type_suffix !------------------------------------------------------------------------ - if(tot_bgc_vegp>0)then + if(alloc_full_veg)then begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc begg = bounds%begg; endg = bounds%endg diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index e5f08bdc9d..7515051d38 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -126,7 +126,7 @@ module CNVegCarbonStateType !------------------------------------------------------------------------ subroutine Init(this, bounds, carbon_type, ratio, NLFilename, & - dribble_crophrv_xsmrpool_2atm, tot_bgc_vegp, c12_cnveg_carbonstate_inst) + dribble_crophrv_xsmrpool_2atm, alloc_full_veg, c12_cnveg_carbonstate_inst) class(cnveg_carbonstate_type) :: this type(bounds_type) , intent(in) :: bounds @@ -134,7 +134,7 @@ subroutine Init(this, bounds, carbon_type, ratio, NLFilename, & character(len=*) , intent(in) :: carbon_type ! Carbon isotope type C12, C13 or C1 character(len=*) , intent(in) :: NLFilename ! Namelist filename logical , intent(in) :: dribble_crophrv_xsmrpool_2atm - integer , intent(in) :: tot_bgc_vegp ! total number of bgc patches (non-fates) + logical , intent(in) :: alloc_full_veg ! total number of bgc patches (non-fates) type(cnveg_carbonstate_type) , intent(in), optional :: c12_cnveg_carbonstate_inst ! cnveg_carbonstate for C12 (if C13 or C14) !----------------------------------------------------------------------- @@ -142,8 +142,8 @@ subroutine Init(this, bounds, carbon_type, ratio, NLFilename, & this%dribble_crophrv_xsmrpool_2atm = dribble_crophrv_xsmrpool_2atm - call this%InitAllocate ( bounds, tot_bgc_vegp) - if(tot_bgc_vegp>0)then + call this%InitAllocate ( bounds, alloc_full_veg) + if(alloc_full_veg)then call this%InitReadNML ( NLFilename ) call this%InitHistory ( bounds, carbon_type) if (present(c12_cnveg_carbonstate_inst)) then @@ -216,12 +216,12 @@ subroutine InitReadNML(this, NLFilename) end subroutine InitReadNML !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds, tot_bgc_vegp) + subroutine InitAllocate(this, bounds, alloc_full_veg) ! ! !ARGUMENTS: class (cnveg_carbonstate_type) :: this type(bounds_type), intent(in) :: bounds - integer,intent(in) :: tot_bgc_vegp ! Total number of bgc patches on the proc (non_fates) + logical,intent(in) :: alloc_full_veg ! Total number of bgc patches on the proc (non_fates) ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -229,7 +229,7 @@ subroutine InitAllocate(this, bounds, tot_bgc_vegp) integer :: begg,endg !------------------------------------------------------------------------ - if(tot_bgc_vegp>0)then + if(alloc_full_veg)then begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc begg = bounds%begg; endg = bounds%endg diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index f742cba2ad..b06ec367d0 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -292,14 +292,14 @@ module CNVegNitrogenFluxType contains !------------------------------------------------------------------------ - subroutine Init(this, bounds, tot_bgc_vegp) + subroutine Init(this, bounds, alloc_full_veg) class(cnveg_nitrogenflux_type) :: this type(bounds_type), intent(in) :: bounds - integer,intent(in) :: tot_bgc_vegp + logical,intent(in) :: alloc_full_veg - call this%InitAllocate (bounds,tot_bgc_vegp) - if(tot_bgc_vegp>0)then + call this%InitAllocate (bounds,alloc_full_veg) + if(alloc_full_veg)then if(use_matrixcn)then call this%InitTransfer () end if @@ -326,7 +326,7 @@ subroutine InitTransfer (this) end subroutine InitTransfer !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds, tot_bgc_vegp) + subroutine InitAllocate(this, bounds, alloc_full_veg) ! ! !DESCRIPTION: ! Initialize patch nitrogen flux @@ -334,7 +334,7 @@ subroutine InitAllocate(this, bounds, tot_bgc_vegp) ! !ARGUMENTS: class (cnveg_nitrogenflux_type) :: this type(bounds_type) , intent(in) :: bounds - integer,intent(in) :: tot_bgc_vegp + logical,intent(in) :: alloc_full_veg ! ! !LOCAL VARIABLES: integer :: begp,endp @@ -342,7 +342,7 @@ subroutine InitAllocate(this, bounds, tot_bgc_vegp) integer :: begg,endg !------------------------------------------------------------------------ - if(tot_bgc_vegp>0)then + if(alloc_full_veg)then begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc begg = bounds%begg; endg = bounds%endg diff --git a/src/biogeochem/CNVegNitrogenStateType.F90 b/src/biogeochem/CNVegNitrogenStateType.F90 index 341cc8f40d..8983eccb4e 100644 --- a/src/biogeochem/CNVegNitrogenStateType.F90 +++ b/src/biogeochem/CNVegNitrogenStateType.F90 @@ -97,7 +97,7 @@ module CNVegNitrogenStateType !------------------------------------------------------------------------ subroutine Init(this, bounds, & leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, & - deadstemc_patch, tot_bgc_vegp) + deadstemc_patch, alloc_full_veg) class(cnveg_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds @@ -106,10 +106,10 @@ subroutine Init(this, bounds, & real(r8) , intent(in) :: frootc_patch (:) !(begp:) real(r8) , intent(in) :: frootc_storage_patch(:) !(begp:) real(r8) , intent(in) :: deadstemc_patch (:) !(begp:) - integer , intent(in) :: tot_bgc_vegp + logical , intent(in) :: alloc_full_veg - call this%InitAllocate (bounds, tot_bgc_vegp) - if(tot_bgc_vegp>0) then + call this%InitAllocate (bounds, alloc_full_veg) + if(alloc_full_veg) then call this%InitHistory (bounds) call this%InitCold ( bounds, & leafc_patch, leafc_storage_patch, frootc_patch, frootc_storage_patch, deadstemc_patch) @@ -117,19 +117,19 @@ subroutine Init(this, bounds, & end subroutine Init !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds, tot_bgc_vegp) + subroutine InitAllocate(this, bounds, alloc_full_veg) ! ! !ARGUMENTS: class (cnveg_nitrogenstate_type) :: this type(bounds_type) , intent(in) :: bounds - integer,intent(in) :: tot_bgc_vegp + logical,intent(in) :: alloc_full_veg ! ! !LOCAL VARIABLES: integer :: begp,endp integer :: begc,endc integer :: begg,endg !------------------------------------------------------------------------ - if(tot_bgc_vegp>0) then + if(alloc_full_veg) then begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc begg = bounds%begg; endg = bounds%endg @@ -1135,7 +1135,7 @@ subroutine Summary_nitrogenstate(this, bounds, num_soilc, filter_soilc, num_soil ! -------------------------------------------- ! column level summary ! -------------------------------------------- - if(associated(this%totvegn_patch))then + if(num_soilp>0)then call p2c(bounds, num_soilc, filter_soilc, & this%totvegn_patch(bounds%begp:bounds%endp), & this%totvegn_col(bounds%begc:bounds%endc)) diff --git a/src/biogeochem/CNVegStateType.F90 b/src/biogeochem/CNVegStateType.F90 index b5391c7bce..c286c0344f 100644 --- a/src/biogeochem/CNVegStateType.F90 +++ b/src/biogeochem/CNVegStateType.F90 @@ -130,22 +130,24 @@ module CNVegStateType contains !------------------------------------------------------------------------ - subroutine Init(this, bounds, tot_bgc_vegp) + subroutine Init(this, bounds, alloc_full_veg) class(cnveg_state_type) :: this type(bounds_type), intent(in) :: bounds - integer,intent(in) :: tot_bgc_vegp ! Total number of bgc patches on proc (non-fates) + logical,intent(in) :: alloc_full_veg ! Total number of bgc patches on proc (non-fates) - call this%InitAllocate ( bounds, tot_bgc_vegp) + call this%InitAllocate ( bounds, alloc_full_veg) if (use_cn) then call this%InitHistory ( bounds ) end if - call this%InitCold ( bounds ) - + if(alloc_full_veg) then !This is true if not use_fates_bgc + call this%InitCold ( bounds ) + end if + end subroutine Init !------------------------------------------------------------------------ - subroutine InitAllocate(this, bounds, tot_bgc_vegp) + subroutine InitAllocate(this, bounds, alloc_full_veg) ! ! !DESCRIPTION: ! Initialize module data structure @@ -157,7 +159,7 @@ subroutine InitAllocate(this, bounds, tot_bgc_vegp) ! !ARGUMENTS: class(cnveg_state_type) :: this type(bounds_type), intent(in) :: bounds - integer, intent(in) :: tot_bgc_vegp ! Total number of bgc patches on proc (non-fates) + logical, intent(in) :: alloc_full_veg ! Total number of bgc patches on proc (non-fates) ! ! !LOCAL VARIABLES: integer :: begp, endp @@ -165,7 +167,7 @@ subroutine InitAllocate(this, bounds, tot_bgc_vegp) logical :: allows_non_annual_delta !------------------------------------------------------------------------ - if(tot_bgc_vegp>0)then + if(alloc_full_veg)then begp = bounds%begp; endp= bounds%endp begc = bounds%begc; endc= bounds%endc else @@ -503,7 +505,7 @@ subroutine InitHistory(this, bounds) end subroutine InitHistory !----------------------------------------------------------------------- - subroutine initCold(this, bounds) + subroutine InitCold(this, bounds) ! ! !USES: ! @@ -623,7 +625,7 @@ subroutine initCold(this, bounds) this%lfc2_col(c) = 0._r8 end do - end subroutine initCold + end subroutine InitCold !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag, cnveg_carbonstate, & diff --git a/src/biogeochem/CNVegStructUpdateMod.F90 b/src/biogeochem/CNVegStructUpdateMod.F90 index 01209c678f..2e8ed8539b 100644 --- a/src/biogeochem/CNVegStructUpdateMod.F90 +++ b/src/biogeochem/CNVegStructUpdateMod.F90 @@ -143,7 +143,7 @@ subroutine CNVegStructUpdate(bounds,num_soilp, filter_soilp, & dt = real( get_rad_step_size(), r8 ) ! patch loop - do fp = 1,num_soilp + do_patch:do fp = 1,num_soilp p = filter_soilp(fp) c = patch%column(p) g = patch%gridcell(p) @@ -317,7 +317,7 @@ subroutine CNVegStructUpdate(bounds,num_soilp, filter_soilp, & frac_veg_nosno_alb(p) = 0 end if - end do + end do do_patch end associate diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90 index 7370987e3c..61e2e9cf91 100644 --- a/src/biogeochem/CNVegetationFacade.F90 +++ b/src/biogeochem/CNVegetationFacade.F90 @@ -219,8 +219,8 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) ! !LOCAL VARIABLES: integer :: begp, endp, ci integer :: nclumps ! number of clumps on the proc - integer :: tot_bgc_vegp ! Total number of bgc vegetation patches (non-fates) - ! on the proc + logical :: alloc_full_veg ! Signal to allocate vegetation data fully or trivialy + character(len=*), parameter :: subname = 'Init' !----------------------------------------------------------------------- @@ -230,20 +230,17 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) ! - a single value for both column and patch, using index 0 only ! - that is why we pass the number of bgc veg patches here - nclumps = get_proc_clumps() - tot_bgc_vegp = 0 - do ci=1,nclumps - tot_bgc_vegp = tot_bgc_vegp + filter(ci)%num_bgc_vegp - end do - if(tot_bgc_vegp>0)then - begp = bounds%begp - endp = bounds%endp - else + if(use_fates_bgc)then + alloc_full_veg=.false. begp = 0 endp = 0 + else + alloc_full_veg=.true. + begp = bounds%begp + endp = bounds%endp end if - call this%cnveg_state_inst%Init(bounds,tot_bgc_vegp) + call this%cnveg_state_inst%Init(bounds,alloc_full_veg) skip_steps = nskip_steps @@ -256,28 +253,28 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) if(use_cn.or.use_fates_bgc)then call this%cnveg_carbonstate_inst%Init(bounds, carbon_type='c12', ratio=1._r8, & NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, & - tot_bgc_vegp=tot_bgc_vegp) + alloc_full_veg=alloc_full_veg) if (use_c13) then call this%c13_cnveg_carbonstate_inst%Init(bounds, carbon_type='c13', ratio=c13ratio, & NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, & - tot_bgc_vegp=tot_bgc_vegp, c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) + alloc_full_veg=alloc_full_veg, c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) end if if (use_c14) then call this%c14_cnveg_carbonstate_inst%Init(bounds, carbon_type='c14', ratio=c14ratio, & NLFilename=NLFilename, dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, & - tot_bgc_vegp=tot_bgc_vegp,c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) + alloc_full_veg=alloc_full_veg,c12_cnveg_carbonstate_inst=this%cnveg_carbonstate_inst) end if call this%cnveg_carbonflux_inst%Init(bounds, carbon_type='c12', & - dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, tot_bgc_vegp=tot_bgc_vegp ) + dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm, alloc_full_veg=alloc_full_veg ) if (use_c13) then call this%c13_cnveg_carbonflux_inst%Init(bounds, carbon_type='c13', & - dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm,tot_bgc_vegp=tot_bgc_vegp) + dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm,alloc_full_veg=alloc_full_veg) end if if (use_c14) then call this%c14_cnveg_carbonflux_inst%Init(bounds, carbon_type='c14', & - dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm,tot_bgc_vegp=tot_bgc_vegp) + dribble_crophrv_xsmrpool_2atm=this%dribble_crophrv_xsmrpool_2atm,alloc_full_veg=alloc_full_veg) end if call this%cnveg_nitrogenstate_inst%Init(bounds, & this%cnveg_carbonstate_inst%leafc_patch(begp:endp), & @@ -285,8 +282,8 @@ subroutine Init(this, bounds, NLFilename, nskip_steps, params_ncid) this%cnveg_carbonstate_inst%frootc_patch(begp:endp), & this%cnveg_carbonstate_inst%frootc_storage_patch(begp:endp), & this%cnveg_carbonstate_inst%deadstemc_patch(begp:endp), & - tot_bgc_vegp=tot_bgc_vegp) - call this%cnveg_nitrogenflux_inst%Init(bounds,tot_bgc_vegp=tot_bgc_vegp) + alloc_full_veg=alloc_full_veg) + call this%cnveg_nitrogenflux_inst%Init(bounds,alloc_full_veg=alloc_full_veg) call this%c_products_inst%Init(bounds, species_non_isotope_type('C')) if (use_c13) then @@ -1167,13 +1164,14 @@ subroutine EcosystemDynamicsPostDrainage(this, bounds, num_allc, filter_allc, & ! On the radiation time step, use C state variables to calculate ! vegetation structure (LAI, SAI, height) - - if (doalb) then - call CNVegStructUpdate(bounds,num_bgc_vegp, filter_bgc_vegp, & - waterdiagnosticbulk_inst, frictionvel_inst, this%dgvs_inst, this%cnveg_state_inst, & - crop_inst, this%cnveg_carbonstate_inst, canopystate_inst) + if(num_bgc_vegp>0)then + if (doalb) then + call CNVegStructUpdate(bounds,num_bgc_vegp, filter_bgc_vegp, & + waterdiagnosticbulk_inst, frictionvel_inst, this%dgvs_inst, this%cnveg_state_inst, & + crop_inst, this%cnveg_carbonstate_inst, canopystate_inst) + end if end if - + end subroutine EcosystemDynamicsPostDrainage !----------------------------------------------------------------------- From d856f1b18cffe9312fe078d1bfe7040a73d21ccc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 15:14:34 -0600 Subject: [PATCH 1368/2067] Improved description of get_tillage_multipliers(). --- src/soilbiogeochem/TillageMod.F90 | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 7d1356031c..d513993ebc 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -172,10 +172,13 @@ end function get_do_tillage subroutine get_tillage_multipliers(tillage_mults, idop) ! !DESCRIPTION: ! - ! Get the cultivation effective multiplier if prognostic crops are on and - ! cultivation is turned on. Created by Sam Levis. Modified by Michael Graham - ! to use days past planting. Modified by Sam Rabin to include "new" version - ! that *actually* uses days past planting. + ! Get the tillage effective multiplier if prognostic crops are on and + ! tillage is turned on. Created by Sam Levis. Modified by Michael Graham + ! to use days past planting (idpp). + ! + ! Modified by Sam Rabin to fix a bug where idpp wasn't actually used, which + ! would affect growing seasons that crossed over into a new calendar year. + ! Previous behavior can be requested with namelist variable use_original_tillage. ! ! Original code had two versions depending on cell's GDP, but this seems to ! have been only an initial effort that was (a) never published and (b) not @@ -208,7 +211,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) end if ! ----------------------------------------------------- - ! 3) assigning cultivation practices and mapping to the + ! 3) assigning tillage practices and mapping to the ! effect on soil C decomposition ! ----------------------------------------------------- ! info from DAYCENT (Melannie Hartman CSU) From b71fa23012dbcd63f0f55f079ad5696a98dd6fa8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 15:25:30 -0600 Subject: [PATCH 1369/2067] Improved description of use_original_tillage parameter. --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index cbf9ee42dd..6335953fcc 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2892,7 +2892,7 @@ Whether to till crop soil, and if so, with what intensity. -Toggle to use original tillage logic +Toggle to use original tillage logic, with bug for seasons crossing into a new calendar year From c5ee47456a8c53bc8c8eea5f87abd5c1053511e5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 15:27:39 -0600 Subject: [PATCH 1370/2067] Improved error message when tillage on but use_crop off. --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 1c0fcb8e06..405bf2d9ff 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2195,7 +2195,7 @@ sub setup_logic_tillage { my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { - $log->fatal_error( "It doesn't make sense to use tillage with use_crop false" ); + $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." ); } } From fe568e168eae246088657e2896582b37378421af Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 16:19:06 -0600 Subject: [PATCH 1371/2067] Use get_do_tillage() in first readParams_netcdf() return check. --- src/soilbiogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index d513993ebc..d8f87f7f47 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -120,7 +120,7 @@ subroutine readParams_netcdf(ncid) ! Initialize tillage multipliers as all 1, and exit if not tilling allocate(tillage_mults_allphases(ndecomp_pools, ntill_stages_max)) tillage_mults_allphases(:,:) = 1.0_r8 - if (tillage_mode == "off") then + if (.not. get_do_tillage()) then return end if From 3495f4b2b216603a80d9938e24406657f3fa13c9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 16:20:04 -0600 Subject: [PATCH 1372/2067] Added a space. --- src/soilbiogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index d8f87f7f47..11a677e13b 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -225,7 +225,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) phase = 1 else if (day >= idop+15 .and. day < idop+45) then ! based on Field and Row Cultivator multipliers phase = 2 - else if (day >= idop+45 .and. day = idop+45 .and. day < idop+75) then ! based on Rod Weed Row Planter phase = 3 end if else From 1865649c9e26da1cb60204a01ea287ef0e6aa8d6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 16:21:30 -0600 Subject: [PATCH 1373/2067] get_apply_tillage_multipliers(): multiple crop patches are OK. --- src/soilbiogeochem/TillageMod.F90 | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 11a677e13b..254fa658f0 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -290,9 +290,6 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) do p = col%patchi(c),col%patchf(c) if (patch%active(p) .and. patch%wtcol(p) /= 0._r8) then if (patch%itype(p) >= npcropmin) then - if (this_patch > 0) then - call endrun('ERROR multiple active crop patches found in this column') - end if this_patch = p call get_tillage_multipliers(tillage_mults_1patch, idop(p)) tillage_mults = tillage_mults + tillage_mults_1patch * patch%wtcol(p) From 90638734f8b347c9c96dccea9d17bc144f61096e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 16:25:14 -0600 Subject: [PATCH 1374/2067] get_apply_tillage_multipliers: Check for sumwt < 1. --- src/soilbiogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 254fa658f0..6d9d2230c2 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -306,7 +306,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) return elseif (this_patch == 0) then call endrun('ERROR No active, non-zero-weight patches found (crop OR non-crop)') - elseif (sumwt > 1.0_r8 + 1.e-6_r8) then + elseif (abs(1.0_r8 - sumwt) > 1.e-6_r8) then call endrun('ERROR Active crop patch weights does not sum to 1') end if From df4c392756de1fde33019a817aa05c97a0bf0af1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 14 Aug 2023 16:38:54 -0600 Subject: [PATCH 1375/2067] Fix for #2103 making sure --res sent to build-namelist is CLM_USRDAT rather than \$CLM_USRDAT_NAME as it is now --- cime_config/buildnml | 1 - 1 file changed, 1 deletion(-) diff --git a/cime_config/buildnml b/cime_config/buildnml index e239f0ec58..84e1581406 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -136,7 +136,6 @@ def buildnml(case, caseroot, compname): clmusr = "" if lnd_grid == "CLM_USRDAT": clm_usrdat_name = case.get_value("CLM_USRDAT_NAME") - lnd_grid = clm_usrdat_name clmusr = " -clm_usr_name %s " % clm_usrdat_name # Write warning about initial condition data if "NEON" in clm_usrdat_name and clm_force_coldstart == "off": From 7f2475c711089d90813807ed16aa7e59554c96dc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 14 Aug 2023 16:53:44 -0600 Subject: [PATCH 1376/2067] Complete build-namelist work needed for #2103 and #2028 having res be CLM_USRDAT when clm_usr_name option is set and setting fsurdat and flanduse in namelist defaults for NEON sites --- bld/CLMBuildNamelist.pm | 13 +++++++++---- bld/namelist_files/namelist_defaults_ctsm.xml | 6 ++++++ bld/namelist_files/namelist_defaults_overall.xml | 6 ++++-- bld/namelist_files/use_cases/2018-PD_transient.xml | 6 +++++- bld/namelist_files/use_cases/2018_control.xml | 3 +++ bld/unit_testers/build-namelist_test.pl | 2 +- 6 files changed, 28 insertions(+), 8 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 98cce06fca..5150d05473 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -684,18 +684,22 @@ sub setup_cmdl_resolution { $val = "e_string( $nl_flags->{'res'} ); if ( ! $definition->is_valid_value( $var, $val ) ) { my @valid_values = $definition->get_valid_values( $var ); - if ( ! defined($opts->{'clm_usr_name'}) || $nl_flags->{'res'} ne $opts->{'clm_usr_name'} ) { + if ( $nl_flags->{'res'} ne "CLM_USRDAT" ) { $log->fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values"); } } } - # For NEON sites - $nl_flags->{'neon'} = ".false."; - $nl_flags->{'neonsite'} = ""; if ( $nl_flags->{'res'} eq "CLM_USRDAT" ) { if ( ! defined($opts->{'clm_usr_name'}) ) { $log->fatal_error("Resolution is CLM_USRDAT, but --clm_usr_name option is NOT set, and it is required for CLM_USRDAT resolutions"); } + } + # + # For NEON sites + # + $nl_flags->{'neon'} = ".false."; + $nl_flags->{'neonsite'} = ""; + if ( $nl_flags->{'res'} eq "CLM_USRDAT" ) { if ( $opts->{'clm_usr_name'} eq "NEON" ) { $nl_flags->{'neon'} = ".true."; $nl_flags->{'neonsite'} = $envxml_ref->{'NEONSITE'}; @@ -2263,6 +2267,7 @@ sub setup_logic_demand { $settings{'use_lch4'} = $nl_flags->{'use_lch4'}; $settings{'use_nitrif_denitrif'} = $nl_flags->{'use_nitrif_denitrif'}; $settings{'use_crop'} = $nl_flags->{'use_crop'}; + $settings{'neon'} = $nl_flags->{'neon'}; my $demand = $nl->get_value('clm_demand'); if (defined($demand)) { diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 666b19a08f..7dff7ce4e9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1288,6 +1288,12 @@ lnd/clm2/surfdata_map/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c2 + + lnd/clm2/surfdata_map/landuse.timeseries_0.9x1.25_hist_16pfts_Irrig_CMIP6_simyr1850-2015_c170824.nc -flanduse_timeseries -flanduse_timeseries +null +null +flanduse_timeseries +flanduse_timeseries diff --git a/bld/namelist_files/use_cases/2018-PD_transient.xml b/bld/namelist_files/use_cases/2018-PD_transient.xml index d838efbd00..96f14207ad 100644 --- a/bld/namelist_files/use_cases/2018-PD_transient.xml +++ b/bld/namelist_files/use_cases/2018-PD_transient.xml @@ -1,8 +1,12 @@ + + -Simulate transient land-use, and aerosol deposition changes from 2018 to current day with a mix of historical data, and future scenario data +Simulate transient Nitrogen-deposition, aerosol deposition, urban, and fire related (pop-density, lightning) changes from 2018 to current day with a mix of historical data, and future scenario data +Simulate transient Nitrogen-deposition, aerosol deposition, urban, and fire related (pop-density, lightning) changes from 2018 to current day with a mix of historical data, and future scenario data +Simulate transient urban and aerosol deposition changes from 2018 to current day with a mix of historical data, and future scenario data diff --git a/bld/namelist_files/use_cases/2018_control.xml b/bld/namelist_files/use_cases/2018_control.xml index e5e572d749..28554074c4 100644 --- a/bld/namelist_files/use_cases/2018_control.xml +++ b/bld/namelist_files/use_cases/2018_control.xml @@ -1,5 +1,8 @@ + + + Conditions to simulate 2018 land-use diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index cdad9d63c8..dc96984bb3 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -399,7 +399,7 @@ sub cat_and_create_namelistinfile { # # Now run the site # - my $options = "-res CLM_USRDAT -clm_usr_name NEON -no-megan -bgc bgc -sim_year 2018 -infile $namelistfile"; + my $options = "--res CLM_USRDAT --clm_usr_name NEON --no-megan --bgc bgc --use_case 2018_control --infile $namelistfile"; eval{ system( "$bldnml -envxml_dir . $options > $tempfile 2>&1 " ); }; is( $@, '', "options: $options" ); $cfiles->checkfilesexist( "$options", $mode ); From 6925f8cc972acd7aaf0999080717c72fabe69e8f Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 14 Aug 2023 17:15:17 -0600 Subject: [PATCH 1377/2067] Update fates external pointer to the fates bgc call sequence tag --- Externals_CLM.cfg | 4 ++-- src/biogeochem/CNProductsMod.F90 | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 883416a43b..c540fe8b0c 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -branch = clm-cbalance +repo_url = https://github.com/NGEET/fates +tag = sci.1.67.1_api.27.0.0 required = True [externals_description] diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 19ae952c9a..4ef5c7c86f 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -792,15 +792,15 @@ subroutine ComputeProductSummaryVars(this, bounds) this%prod10_grc(g) = this%prod10_grc(g) + this%dwt_prod10_gain_grc(g)*dt this%prod100_grc(g) = this%prod100_grc(g) + this%dwt_prod100_gain_grc(g)*dt + ! fluxes into wood & grain product pools, from gross unrepresented landcover change + this%prod10_grc(g) = this%prod10_grc(g) + this%gru_prod10_gain_grc(g)*dt + this%prod100_grc(g) = this%prod100_grc(g) + this%gru_prod100_gain_grc(g)*dt + ! fluxes into wood & crop product pools, from harvest this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%crop_harvest_to_cropprod1_grc(g)*dt this%prod10_grc(g) = this%prod10_grc(g) + this%hrv_deadstem_to_prod10_grc(g)*dt this%prod100_grc(g) = this%prod100_grc(g) + this%hrv_deadstem_to_prod100_grc(g)*dt - ! fluxes into wood & grain product pools, from gross unrepresented landcover change - this%prod10_grc(g) = this%prod10_grc(g) + this%gru_prod10_gain_grc(g)*dt - this%prod100_grc(g) = this%prod100_grc(g) + this%gru_prod100_gain_grc(g)*dt - ! fluxes out of wood & crop product pools, from decomposition this%cropprod1_grc(g) = this%cropprod1_grc(g) - this%cropprod1_loss_grc(g)*dt this%prod10_grc(g) = this%prod10_grc(g) - this%prod10_loss_grc(g)*dt From 1ccf0d9a80cc8100df235bb2337f7e478c0420a0 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 14 Aug 2023 19:39:10 -0400 Subject: [PATCH 1378/2067] update changelog --- doc/ChangeLog | 78 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 79 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index e65560d5c3..9d3c5b1564 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,82 @@ =============================================================== +Tag name: ctsm5.1.dev134 +Originator(s): rgknox (Ryan Knox,LBNL EESA), erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Mon Aug 14 07:19:59 PM EDT 2023 +One-line Summary: Migration of FATES to share normal soil BGC call sequence and functionality + +Purpose and description of changes +---------------------------------- + +This set of changes enables the normal soil biogeochemistry that is used for CN, to be used for FATES as well. FATES had been using a simplified subset of soil biogeochemistry in its own module. This change required coordination of litter flux and methane boundary conditions from FATES to CLM. CNVEG datastructures were given trivial allocation (of size one on index zero) to prevent inappropriate use of CNVEG datastructures while FATES is active. Note that now the carbon balance checking for the soil is now active when FATES is active. Various accomodations have also been put in place to enable nitrogen cycling between the two models. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +Surprisingly, nvhpc tests are now working, but it may just be coincidental. All existing aux_clm tests are passing. Tests without FATES are b4b, with roundoff differences in just TOTCOLC and TOTCOLN. + +CTSM issues fixed (include CTSM Issue #): + +Known bugs introduced in this tag (include issue #): + +Notes of particular relevance for users +--------------------------------------- +A CLM-FATES simulation will turn on nitrogen supplementation, this enables sufficient immobilization and decomposition. Until FATES and CLM can handle fully coupled nitrogen exchange, which would include root uptake of the mineralized aqueous forms (NH4 and NO3), N limitations in the soil are meaningless when FATES is on. + +Caveats for users (e.g., need to interpolate initial conditions): + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + +Changes made to namelist defaults (e.g., changed parameter values): FATES runs now supplement N + +Changes to the datasets (e.g., parameter, surface or initial files): + +Substantial timing or memory changes: +[e.g., check PFS test in the test suite and look at timings, if you +expect possible significant timing changes] + + +Testing summary: +---------------- + +aux_clm test run on cheyenne and izumi. See: + +izumi: OK /scratch/cluster/rgknox/tests_0814-095624iz +cheyenne: OK /glade/scratch/rgknox/tests_0814-134713ch + + +Answer changes +-------------- + +Changes answers relative to baseline: + +Baseline changes will be reported for many tests, all tests were combed to identify RMS diffs, all non-FATES tests had at most, roundoff level ( Date: Mon, 14 Aug 2023 18:00:38 -0600 Subject: [PATCH 1379/2067] Reverse hist field strings such as MET_LIT to LIT_MET --- .../SoilBiogeochemDecompCascadeBGCMod.F90 | 12 ++++++------ .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 14 +++++++------- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 index b65fc5f17f..b30e3d5d2d 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeBGCMod.F90 @@ -311,7 +311,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i i_met_lit = i_litr_min floating_cn_ratio_decomp_pools(i_met_lit) = .true. decomp_cascade_con%decomp_pool_name_restart(i_met_lit) = 'litr1' - decomp_cascade_con%decomp_pool_name_history(i_met_lit) = 'MET_LIT' + decomp_cascade_con%decomp_pool_name_history(i_met_lit) = 'LIT_MET' decomp_cascade_con%decomp_pool_name_long(i_met_lit) = 'metabolic litter' decomp_cascade_con%decomp_pool_name_short(i_met_lit) = 'L1' is_litter(i_met_lit) = .true. @@ -326,7 +326,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i i_cel_lit = i_met_lit + 1 floating_cn_ratio_decomp_pools(i_cel_lit) = .true. decomp_cascade_con%decomp_pool_name_restart(i_cel_lit) = 'litr2' - decomp_cascade_con%decomp_pool_name_history(i_cel_lit) = 'CEL_LIT' + decomp_cascade_con%decomp_pool_name_history(i_cel_lit) = 'LIT_CEL' decomp_cascade_con%decomp_pool_name_long(i_cel_lit) = 'cellulosic litter' decomp_cascade_con%decomp_pool_name_short(i_cel_lit) = 'L2' is_litter(i_cel_lit) = .true. @@ -341,7 +341,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i i_lig_lit = i_cel_lit + 1 floating_cn_ratio_decomp_pools(i_lig_lit) = .true. decomp_cascade_con%decomp_pool_name_restart(i_lig_lit) = 'litr3' - decomp_cascade_con%decomp_pool_name_history(i_lig_lit) = 'LIG_LIT' + decomp_cascade_con%decomp_pool_name_history(i_lig_lit) = 'LIT_LIG' decomp_cascade_con%decomp_pool_name_long(i_lig_lit) = 'lignin litter' decomp_cascade_con%decomp_pool_name_short(i_lig_lit) = 'L3' is_litter(i_lig_lit) = .true. @@ -366,7 +366,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i i_act_som = i_lig_lit + 1 floating_cn_ratio_decomp_pools(i_act_som) = .false. decomp_cascade_con%decomp_pool_name_restart(i_act_som) = 'soil1' - decomp_cascade_con%decomp_pool_name_history(i_act_som) = 'ACT_SOM' + decomp_cascade_con%decomp_pool_name_history(i_act_som) = 'SOM_ACT' decomp_cascade_con%decomp_pool_name_long(i_act_som) = 'active soil organic matter' decomp_cascade_con%decomp_pool_name_short(i_act_som) = 'S1' is_litter(i_act_som) = .false. @@ -381,7 +381,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i i_slo_som = i_act_som + 1 floating_cn_ratio_decomp_pools(i_slo_som) = .false. decomp_cascade_con%decomp_pool_name_restart(i_slo_som) = 'soil2' - decomp_cascade_con%decomp_pool_name_history(i_slo_som) = 'SLO_SOM' + decomp_cascade_con%decomp_pool_name_history(i_slo_som) = 'SOM_SLO' decomp_cascade_con%decomp_pool_name_long(i_slo_som) = 'slow soil organic matter' decomp_cascade_con%decomp_pool_name_short(i_slo_som) = 'S2' is_litter(i_slo_som) = .false. @@ -396,7 +396,7 @@ subroutine init_decompcascade_bgc(bounds, soilbiogeochem_state_inst, soilstate_i i_pas_som = i_slo_som + 1 floating_cn_ratio_decomp_pools(i_pas_som) = .false. decomp_cascade_con%decomp_pool_name_restart(i_pas_som) = 'soil3' - decomp_cascade_con%decomp_pool_name_history(i_pas_som) = 'PAS_SOM' + decomp_cascade_con%decomp_pool_name_history(i_pas_som) = 'SOM_PAS' decomp_cascade_con%decomp_pool_name_long(i_pas_som) = 'passive soil organic matter' decomp_cascade_con%decomp_pool_name_short(i_pas_som) = 'S3' is_litter(i_pas_som) = .false. diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index f820db01b6..bcbd5e8cdd 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -481,7 +481,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_met_lit = i_litr_min floating_cn_ratio_decomp_pools(i_met_lit) = .true. decomp_cascade_con%decomp_pool_name_restart(i_met_lit) = 'litr1' - decomp_cascade_con%decomp_pool_name_history(i_met_lit) = 'MET_LIT' + decomp_cascade_con%decomp_pool_name_history(i_met_lit) = 'LIT_MET' decomp_cascade_con%decomp_pool_name_long(i_met_lit) = 'metabolic litter' decomp_cascade_con%decomp_pool_name_short(i_met_lit) = 'L1' is_microbe(i_met_lit) = .false. @@ -497,7 +497,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_str_lit = i_met_lit + 1 floating_cn_ratio_decomp_pools(i_str_lit) = .true. decomp_cascade_con%decomp_pool_name_restart(i_str_lit) = 'litr2' - decomp_cascade_con%decomp_pool_name_history(i_str_lit) = 'STR_LIT' + decomp_cascade_con%decomp_pool_name_history(i_str_lit) = 'LIT_STR' decomp_cascade_con%decomp_pool_name_long(i_str_lit) = 'structural litter' decomp_cascade_con%decomp_pool_name_short(i_str_lit) = 'L2' is_microbe(i_str_lit) = .false. @@ -523,7 +523,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_avl_som = i_str_lit + 1 floating_cn_ratio_decomp_pools(i_avl_som) = .true. decomp_cascade_con%decomp_pool_name_restart(i_avl_som) = 'soil1' - decomp_cascade_con%decomp_pool_name_history(i_avl_som) = 'AVL_SOM' + decomp_cascade_con%decomp_pool_name_history(i_avl_som) = 'SOM_AVL' decomp_cascade_con%decomp_pool_name_long(i_avl_som) = 'available soil organic matter' decomp_cascade_con%decomp_pool_name_short(i_avl_som) = 'S1' is_microbe(i_avl_som) = .false. @@ -539,7 +539,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_chem_som = i_avl_som + 1 floating_cn_ratio_decomp_pools(i_chem_som) = .true. decomp_cascade_con%decomp_pool_name_restart(i_chem_som) = 'soil2' - decomp_cascade_con%decomp_pool_name_history(i_chem_som) = 'CHEM_SOM' + decomp_cascade_con%decomp_pool_name_history(i_chem_som) = 'SOM_CHEM' decomp_cascade_con%decomp_pool_name_long(i_chem_som) = 'chemically protected soil organic matter' decomp_cascade_con%decomp_pool_name_short(i_chem_som) = 'S2' is_microbe(i_chem_som) = .false. @@ -555,7 +555,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_phys_som = i_chem_som + 1 floating_cn_ratio_decomp_pools(i_phys_som) = .true. decomp_cascade_con%decomp_pool_name_restart(i_phys_som) = 'soil3' - decomp_cascade_con%decomp_pool_name_history(i_phys_som) = 'PHYS_SOM' + decomp_cascade_con%decomp_pool_name_history(i_phys_som) = 'SOM_PHYS' decomp_cascade_con%decomp_pool_name_long(i_phys_som) = 'physically protected soil organic matter' decomp_cascade_con%decomp_pool_name_short(i_phys_som) = 'S3' is_microbe(i_phys_som) = .false. @@ -571,7 +571,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_cop_mic = i_phys_som + 1 floating_cn_ratio_decomp_pools(i_cop_mic) = .true. decomp_cascade_con%decomp_pool_name_restart(i_cop_mic) = 'micr1' - decomp_cascade_con%decomp_pool_name_history(i_cop_mic) = 'COP_MIC' + decomp_cascade_con%decomp_pool_name_history(i_cop_mic) = 'MIC_COP' decomp_cascade_con%decomp_pool_name_long(i_cop_mic) = 'copiotrophic microbes' decomp_cascade_con%decomp_pool_name_short(i_cop_mic) = 'M1' is_microbe(i_cop_mic) = .true. @@ -587,7 +587,7 @@ subroutine init_decompcascade_mimics(bounds, soilbiogeochem_state_inst, soilstat i_oli_mic = i_cop_mic + 1 floating_cn_ratio_decomp_pools(i_oli_mic) = .true. decomp_cascade_con%decomp_pool_name_restart(i_oli_mic) = 'micr2' - decomp_cascade_con%decomp_pool_name_history(i_oli_mic) = 'OLI_MIC' + decomp_cascade_con%decomp_pool_name_history(i_oli_mic) = 'MIC_OLI' decomp_cascade_con%decomp_pool_name_long(i_oli_mic) = 'oligotrophic microbes' decomp_cascade_con%decomp_pool_name_short(i_oli_mic) = 'M2' is_microbe(i_oli_mic) = .true. From 2fb7513e6c7d86a4c43d16e0d3e39b3cc0c964ab Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 14 Aug 2023 18:04:29 -0600 Subject: [PATCH 1380/2067] Change C or N to _C and _N after hist field strings like LIT_MET --- src/biogeochem/CNVegCarbonFluxType.F90 | 12 +++++------ src/biogeochem/CNVegNitrogenFluxType.F90 | 4 ++-- .../SoilBiogeochemCarbonFluxType.F90 | 20 +++++++++---------- .../SoilBiogeochemCarbonStateType.F90 | 16 +++++++-------- .../SoilBiogeochemNitrogenFluxType.F90 | 16 +++++++-------- .../SoilBiogeochemNitrogenStateType.F90 | 6 +++--- 6 files changed, 37 insertions(+), 37 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index c2025fca47..e6542a3452 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -2958,7 +2958,7 @@ subroutine InitHistory(this, bounds, carbon_type) do k = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then data1dptr => this%m_decomp_cpools_to_fire_col(:,k) - fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE' + fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_FIRE' longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss' call hist_addfld1d (fname=fieldname, units='gC/m^2/s', & avgflag='A', long_name=longname, & @@ -2966,7 +2966,7 @@ subroutine InitHistory(this, bounds, carbon_type) if ( nlevdecomp_full > 1 ) then data2dptr => this%m_decomp_cpools_to_fire_vr_col(:,:,k) - fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'//trim(vr_suffix) + fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_FIRE'//trim(vr_suffix) longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss' call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s', type2d='levdcmp', & avgflag='A', long_name=longname, & @@ -3167,7 +3167,7 @@ subroutine InitHistory(this, bounds, carbon_type) do k = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then data1dptr => this%m_decomp_cpools_to_fire_col(:,k) - fieldname = 'C13_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE' + fieldname = 'C13_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_FIRE' longname = 'C13 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss' call hist_addfld1d (fname=fieldname, units='gC13/m^2', & avgflag='A', long_name=longname, & @@ -3175,7 +3175,7 @@ subroutine InitHistory(this, bounds, carbon_type) if ( nlevdecomp_full > 1 ) then data2dptr => this%m_decomp_cpools_to_fire_vr_col(:,:,k) - fieldname = 'C13_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'//trim(vr_suffix) + fieldname = 'C13_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_FIRE'//trim(vr_suffix) longname = 'C13 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss' call hist_addfld_decomp (fname=fieldname, units='gC13/m^3', type2d='levdcmp', & avgflag='A', long_name=longname, & @@ -3327,7 +3327,7 @@ subroutine InitHistory(this, bounds, carbon_type) do k = 1, ndecomp_pools if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then data1dptr => this%m_decomp_cpools_to_fire_col(:,k) - fieldname = 'C14_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE' + fieldname = 'C14_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_FIRE' longname = 'C14 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss' call hist_addfld1d (fname=fieldname, units='gC14/m^2', & avgflag='A', long_name=longname, & @@ -3335,7 +3335,7 @@ subroutine InitHistory(this, bounds, carbon_type) if ( nlevdecomp_full > 1 ) then data2dptr => this%m_decomp_cpools_to_fire_vr_col(:,:,k) - fieldname = 'C14_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_FIRE'//trim(vr_suffix) + fieldname = 'C14_M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_FIRE'//trim(vr_suffix) longname = 'C14 '//trim(decomp_cascade_con%decomp_pool_name_long(k))//' C fire loss' call hist_addfld_decomp (fname=fieldname, units='gC14/m^3', type2d='levdcmp', & avgflag='A', long_name=longname, & diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index ce164b4c37..aad3228ef1 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -1048,7 +1048,7 @@ subroutine InitHistory(this, bounds) if ( decomp_cascade_con%is_litter(k) .or. decomp_cascade_con%is_cwd(k) ) then this%m_decomp_npools_to_fire_col(begc:endc,k) = spval data1dptr => this%m_decomp_npools_to_fire_col(:,k) - fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TO_FIRE' + fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_N_TO_FIRE' longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' N fire loss' call hist_addfld1d (fname=fieldname, units='gN/m^2', & avgflag='A', long_name=longname, & @@ -1057,7 +1057,7 @@ subroutine InitHistory(this, bounds) if ( nlevdecomp_full > 1 ) then this%m_decomp_npools_to_fire_vr_col(begc:endc,:,k) = spval data2dptr => this%m_decomp_npools_to_fire_vr_col(:,:,k) - fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TO_FIRE'//trim(vr_suffix) + fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_N_TO_FIRE'//trim(vr_suffix) longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' N fire loss' call hist_addfld_decomp (fname=fieldname, units='gN/m^3', type2d='levdcmp', & avgflag='A', long_name=longname, & diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 index 114019a3d7..bb8efed09b 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 @@ -315,8 +315,8 @@ subroutine InitHistory(this, bounds, carbon_type) if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then data1dptr => this%decomp_cascade_ctransfer_col(:,l) fieldname = & - trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'C_TO_'//& - trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'C' + trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_C_TO_'//& + trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'_C' longname = 'decomp. of '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//& ' C to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' C' call hist_addfld1d (fname=fieldname, units='gC/m^2/s', & @@ -353,9 +353,9 @@ subroutine InitHistory(this, bounds, carbon_type) if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then data2dptr => this%decomp_cascade_ctransfer_vr_col(:,:,l) fieldname = & - trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'C_TO_'//& + trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_C_TO_'//& trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))& - //'C'//trim(vr_suffix) + //'_C'//trim(vr_suffix) longname = 'decomp. of '//& trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//& ' C to '//& @@ -423,14 +423,14 @@ subroutine InitHistory(this, bounds, carbon_type) do k = 1, ndecomp_pools ! none from CWD if ( .not. decomp_cascade_con%is_cwd(k) ) then data1dptr => this%decomp_cpools_leached_col(:,k) - fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TO_LEACHING' + fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TO_LEACHING' longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' C leaching loss' call hist_addfld1d (fname=fieldname, units='gC/m^2/s', & avgflag='A', long_name=longname, & ptr_col=data1dptr, default='inactive') data2dptr => this%decomp_cpools_transport_tendency_col(:,:,k) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(k))//'C_TNDNCY_VERT_TRANSPORT' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(k))//'_C_TNDNCY_VERT_TRANSPORT' longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' C tendency due to vertical transport' call hist_addfld_decomp (fname=fieldname, units='gC/m^3/s', type2d='levdcmp', & avgflag='A', long_name=longname, & @@ -513,9 +513,9 @@ subroutine InitHistory(this, bounds, carbon_type) data2dptr => this%decomp_cascade_ctransfer_vr_col(:,:,l) fieldname = 'C13_'//& trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))& - //'C_TO_'//& + //'_C_TO_'//& trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))& - //'C'//trim(vr_suffix) + //'_C'//trim(vr_suffix) longname = 'C13 decomp. of '& //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))& //' C to '//& @@ -597,9 +597,9 @@ subroutine InitHistory(this, bounds, carbon_type) fieldname = 'C14_'//& trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))& - //'C_TO_'//& + //'_C_TO_'//& trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))& - //'C'//trim(vr_suffix) + //'_C'//trim(vr_suffix) longname = 'C14 decomp. of '& //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//& ' C to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' C' diff --git a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 index a09441069a..f5da1b8a14 100644 --- a/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90 @@ -169,7 +169,7 @@ subroutine InitHistory(this, bounds, carbon_type) do l = 1, ndecomp_pools if ( nlevdecomp_full > 1 ) then data2dptr => this%decomp_cpools_vr_col(:,1:nlevsoi,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_vr' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C_vr' longname = trim(decomp_cascade_con%decomp_pool_name_history(l))//' C (vertically resolved)' call hist_addfld2d (fname=fieldname, units='gC/m^3', type2d='levsoi', & avgflag='A', long_name=longname, & @@ -177,7 +177,7 @@ subroutine InitHistory(this, bounds, carbon_type) endif data1dptr => this%decomp_cpools_col(:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'C' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C' longname = trim(decomp_cascade_con%decomp_pool_name_history(l))//' C' call hist_addfld1d (fname=fieldname, units='gC/m^2', & avgflag='A', long_name=longname, & @@ -185,7 +185,7 @@ subroutine InitHistory(this, bounds, carbon_type) if ( nlevdecomp_full > 1 ) then data1dptr => this%decomp_cpools_1m_col(:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_1m' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C_1m' longname = trim(decomp_cascade_con%decomp_pool_name_history(l))//' C to 1 meter' call hist_addfld1d (fname=fieldname, units='gC/m^2', & avgflag='A', long_name=longname, & @@ -268,7 +268,7 @@ subroutine InitHistory(this, bounds, carbon_type) do l = 1, ndecomp_pools if ( nlevdecomp_full > 1 ) then data2dptr => this%decomp_cpools_vr_col(:,1:nlevsoi,l) - fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_vr' + fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C_vr' longname = 'C13 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C (vertically resolved)' call hist_addfld2d (fname=fieldname, units='gC13/m^3', type2d='levsoi', & avgflag='A', long_name=longname, & @@ -276,7 +276,7 @@ subroutine InitHistory(this, bounds, carbon_type) endif data1dptr => this%decomp_cpools_col(:,l) - fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C' + fieldname = 'C13_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C' longname = 'C13 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C' call hist_addfld1d (fname=fieldname, units='gC13/m^2', & avgflag='A', long_name=longname, & @@ -355,21 +355,21 @@ subroutine InitHistory(this, bounds, carbon_type) do l = 1, ndecomp_pools if ( nlevdecomp_full > 1 ) then data2dptr => this%decomp_cpools_vr_col(:,1:nlevsoi,l) - fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_vr' + fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C_vr' longname = 'C14 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C (vertically resolved)' call hist_addfld2d (fname=fieldname, units='gC14/m^3', type2d='levsoi', & avgflag='A', long_name=longname, ptr_col=data2dptr, default='inactive') endif data1dptr => this%decomp_cpools_col(:,l) - fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C' + fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C' longname = 'C14 '//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C' call hist_addfld1d (fname=fieldname, units='gC14/m^2', & avgflag='A', long_name=longname, ptr_col=data1dptr, default='inactive') if ( nlevdecomp_full > 1 ) then data1dptr => this%decomp_cpools_1m_col(:,l) - fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'C_1m' + fieldname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//'_C_1m' longname = 'C14_'//trim(decomp_cascade_con%decomp_pool_name_history(l))//' C to 1 meter' call hist_addfld1d (fname=fieldname, units='gC/m^2', & avgflag='A', long_name=longname, ptr_col=data1dptr, default='inactive') diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 index 839f69379a..cb201d017c 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 @@ -351,7 +351,7 @@ subroutine InitHistory(this, bounds) 'to '//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l))) else fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))& - //'N_TO_SMINN' + //'_N_TO_SMINN' longname = 'mineral N flux for decomp. of '& //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l))) endif @@ -364,8 +364,8 @@ subroutine InitHistory(this, bounds) if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then this%decomp_cascade_ntransfer_col(begc:endc,l) = spval data1dptr => this%decomp_cascade_ntransfer_col(:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'N_TO_'//& - trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'N' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_N_TO_'//& + trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))//'_N' longname = 'decomp. of '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//& ' N to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' N' call hist_addfld1d (fname=fieldname, units='gN/m^2', & @@ -388,7 +388,7 @@ subroutine InitHistory(this, bounds) 'to '//trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l))) else fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))& - //'N_TO_SMINN'//trim(vr_suffix) + //'_N_TO_SMINN'//trim(vr_suffix) longname = 'mineral N flux for decomp. of '& //trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l))) endif @@ -401,9 +401,9 @@ subroutine InitHistory(this, bounds) if ( decomp_cascade_con%cascade_receiver_pool(l) /= 0 ) then this%decomp_cascade_ntransfer_vr_col(begc:endc,:,l) = spval data2dptr => this%decomp_cascade_ntransfer_vr_col(:,:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'N_TO_'//& + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_donor_pool(l)))//'_N_TO_'//& trim(decomp_cascade_con%decomp_pool_name_history(decomp_cascade_con%cascade_receiver_pool(l)))& - //'N'//trim(vr_suffix) + //'_N'//trim(vr_suffix) longname = 'decomp. of '& //trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_donor_pool(l)))//& ' N to '//trim(decomp_cascade_con%decomp_pool_name_long(decomp_cascade_con%cascade_receiver_pool(l)))//' N' @@ -429,7 +429,7 @@ subroutine InitHistory(this, bounds) if ( .not. decomp_cascade_con%is_cwd(k) ) then this%decomp_npools_leached_col(begc:endc,k) = spval data1dptr => this%decomp_npools_leached_col(:,k) - fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TO_LEACHING' + fieldname = 'M_'//trim(decomp_cascade_con%decomp_pool_name_history(k))//'_N_TO_LEACHING' longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' N leaching loss' call hist_addfld1d (fname=fieldname, units='gN/m^2/s', & avgflag='A', long_name=longname, & @@ -437,7 +437,7 @@ subroutine InitHistory(this, bounds) this%decomp_npools_transport_tendency_col(begc:endc,:,k) = spval data2dptr => this%decomp_npools_transport_tendency_col(:,:,k) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(k))//'N_TNDNCY_VERT_TRANSPORT' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(k))//'_N_TNDNCY_VERT_TRANSPORT' longname = trim(decomp_cascade_con%decomp_pool_name_long(k))//' N tendency due to vertical transport' call hist_addfld_decomp (fname=fieldname, units='gN/m^3/s', type2d='levdcmp', & avgflag='A', long_name=longname, & diff --git a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 index 3e54e52436..a72a7fa8ae 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90 @@ -194,7 +194,7 @@ subroutine InitHistory(this, bounds) do l = 1, ndecomp_pools if ( nlevdecomp_full > 1 ) then data2dptr => this%decomp_npools_vr_col(:,:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'N_vr' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'_N_vr' longname = trim(decomp_cascade_con%decomp_pool_name_history(l))//' N (vertically resolved)' call hist_addfld2d (fname=fieldname, units='gN/m^3', type2d='levdcmp', & avgflag='A', long_name=longname, & @@ -204,7 +204,7 @@ subroutine InitHistory(this, bounds) endif data1dptr => this%decomp_npools_col(:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'N' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'_N' longname = trim(decomp_cascade_con%decomp_pool_name_history(l))//' N' call hist_addfld1d (fname=fieldname, units='gN/m^2', & avgflag='A', long_name=longname, & @@ -216,7 +216,7 @@ subroutine InitHistory(this, bounds) if ( nlevdecomp_full > 1 ) then data1dptr => this%decomp_npools_1m_col(:,l) - fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'N_1m' + fieldname = trim(decomp_cascade_con%decomp_pool_name_history(l))//'_N_1m' longname = trim(decomp_cascade_con%decomp_pool_name_history(l))//' N to 1 meter' call hist_addfld1d (fname=fieldname, units='gN/m^2', & avgflag='A', long_name=longname, & From 3e12e28729310d345f823ed6021eaf789a75fd35 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 14 Aug 2023 18:06:59 -0600 Subject: [PATCH 1381/2067] Update hist field names in user_nl_clm files --- cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm | 4 ++-- cime_config/usermods_dirs/output_bgc/user_nl_clm | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm b/cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm index 318105a043..75513be601 100644 --- a/cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm +++ b/cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm @@ -1,8 +1,8 @@ hist_dov2xy = .true.,.false. hist_nhtfrq = 0,-175200 hist_mfilt = 1,1 -hist_fincl2 = 'FPI_vr', 'K_PAS_SOM', 'K_SLO_SOM', 'K_ACT_SOM', - 'K_CWD', 'K_CEL_LIT', 'K_LIG_LIT', 'K_MET_LIT', +hist_fincl2 = 'FPI_vr', 'K_SOM_PAS', 'K_SOM_SLO', 'K_SOM_ACT', + 'K_CWD', 'K_LIT_CEL', 'K_LIT_LIG', 'K_LIT_MET', 'CWD_PATHFRAC_L2_vr', 'CWD_RESP_FRAC_L2_vr', 'CWD_PATHFRAC_L3_vr', 'CWD_RESP_FRAC_L3_vr', 'L1_PATHFRAC_S1_vr', 'L1_RESP_FRAC_S1_vr', diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/output_bgc/user_nl_clm index f7aaa09911..a7c5d098db 100644 --- a/cime_config/usermods_dirs/output_bgc/user_nl_clm +++ b/cime_config/usermods_dirs/output_bgc/user_nl_clm @@ -3,8 +3,8 @@ !---------------------------------------------------------------------------------- ! h0 stream (monthly average, gridcell-level) -hist_fexcl1 += 'ACT_SOMC_vr', 'ACT_SOMN_vr', 'SLO_SOMC_vr', 'SLO_SOMN_vr', 'PAS_SOMC_vr', 'PAS_SOMN_vr', 'SOILC_vr','SOILN_vr', 'CWDC_vr', 'MET_LITC_vr', 'CEL_LITC_vr', 'LIG_LITC_vr', 'MET_LITN_vr', 'CEL_LITN_vr', 'LIG_LITN_vr', 'CWDN_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr' -hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','MET_LITC_TO_ACT_SOMC','MET_LITN_TO_ACT_SOMN','CEL_LITC_TO_ACT_SOMC', 'CEL_LITN_TO_ACT_SOMN','LIG_LITC_TO_SLO_SOMC','LIG_LITN_TO_SLO_SOMN','DWT_WOOD_PRODUCTC_GAIN_PATCH' +hist_fexcl1 += 'SOM_ACT_C_vr', 'SOM_ACT_N_vr', 'SOM_SLO_C_vr', 'SOM_SLO_N_vr', 'SOM_PAS_C_vr', 'SOM_PAS_N_vr', 'SOILC_vr','SOILN_vr', 'CWD_C_vr', 'LIT_MET_C_vr', 'LIT_CEL_C_vr', 'LIT_LIG_C_vr', 'LIT_MET_N_vr', 'LIT_CEL_N_vr', 'LIT_LIG_N_vr', 'CWD_N_vr', 'SMIN_NO3_vr', 'CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr' +hist_fincl1 += 'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LIT_MET_C_TO_SOM_ACT_C','LIT_MET_N_TO_SOM_ACT_N','LIT_CEL_C_TO_SOM_ACT_C', 'LIT_CEL_N_TO_SOM_ACT_N','LIT_LIG_C_TO_SOM_SLO_C','LIT_LIG_N_TO_SOM_SLO_N','DWT_WOOD_PRODUCTC_GAIN_PATCH' ! h1 stream (monthly average, finest sub-grid) hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTOP' @@ -14,7 +14,7 @@ hist_fincl2 += 'GPP', 'NPP', 'AGNPP', 'TOTVEGC', 'NPP_NUPTAKE', 'AR', 'HR', 'HTO hist_fincl3 += 'GPP', 'NPP', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH', 'WOOD_HARVESTC', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'SLASH_HARVESTC', 'COL_FIRE_CLOSS', 'FROOTC:I', 'HTOP' ! h3 stream (yearly average, gridcell-level) -hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWDC_vr', 'MET_LITC_vr', 'CEL_LITC_vr', 'LIG_LITC_vr', 'MET_LITN_vr', 'CEL_LITN_vr', 'LIG_LITN_vr','CWDN_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I' +hist_fincl4 += 'SOILC_vr', 'SOILN_vr', 'CWD_C_vr', 'LIT_MET_C_vr', 'LIT_CEL_C_vr', 'LIT_LIG_C_vr', 'LIT_MET_N_vr', 'LIT_CEL_N_vr', 'LIT_LIG_N_vr','CWD_N_vr', 'TOTLITC:I', 'TOT_WOODPRODC:I', 'TOTSOMC:I','TOTVEGC:I' ! h4 stream (yearly average, landunit-level) hist_fincl5 += 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I' From 9d8f5b2c544c1cc2ee39ee73eaaa131a234152c5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Aug 2023 13:48:33 -0600 Subject: [PATCH 1382/2067] Make cmds_to_setup_conda() more robust. For tests that invoke cmds_to_setup_conda(), manually calling the script invoking that function (e.g., case.build for FSURDATMODIFYCTSM) could fail if doing so with a conda environment already activated. The problem is that conda run -n ctsm_pylib seems to not actually use ctsm_pylib if, for instance the conda base environment is active. Instead doing CONDA_PREFIX= conda run -n ctsm_pylib seems to work. --- cime_config/SystemTests/systemtest_utils.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 17ddf88a53..6ce61d9424 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -10,6 +10,9 @@ def cmds_to_setup_conda(caseroot): # Use semicolon here since it's OK to fail # conda_setup_commands = ". " + caseroot + "/.env_mach_specific.sh; " + # Setting CONDA_PREFIX to empty ensures that this works even if called from + # a shell with a conda environment activated + conda_setup_commands += "CONDA_PREFIX=; " # Execute the module unload/load when "which conda" fails # eg on cheyenne try: From f6f03618e2e64a56f6534ac63f665e026396cbed Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Aug 2023 15:14:46 -0600 Subject: [PATCH 1383/2067] Updated tests referenced in README_history_fields_files. --- .../README_history_fields_files | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files b/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files index f92f48f71a..c611c19ae2 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files +++ b/doc/source/users_guide/setting-up-and-running-a-case/README_history_fields_files @@ -1,10 +1,11 @@ 2021/9/8 slevis +2023/8/15 samsrabin The files history_fields_nofates.rst and history_fields_fates.rst each contain a table of the history fields, active and inactive, available in the CTSM cases that get generated by these tests: -ERP_P36x2_D_Ld3.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_gnu.clm-extra_outputs -ERS_Ld9.f10_f10_mg37.I2000Clm50FatesCruRsGs.cheyenne_intel.clm-FatesColdCH4Off +SMS_Ld1.f10_f10_mg37.I1850Clm50BgcCrop.cheyenne_intel.clm-SaveHistFieldList +SMS_Ld1.f10_f10_mg37.I2000Clm50FatesCru.cheyenne_intel.clm-SaveHistFieldList To reproduce these .rst files, run the above tests and the files will appear in the corresponding run directories. From 56cb0b0158fc64165a14f6234fd36f195960fd0c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 15 Aug 2023 15:24:40 -0600 Subject: [PATCH 1384/2067] Initialize history variables to spval instead of nan. --- src/biogeophys/TemperatureType.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/TemperatureType.F90 b/src/biogeophys/TemperatureType.F90 index 75d8c3f68d..21445caaae 100644 --- a/src/biogeophys/TemperatureType.F90 +++ b/src/biogeophys/TemperatureType.F90 @@ -609,17 +609,17 @@ subroutine InitHistory(this, bounds, is_simple_buildtemp, is_prog_buildtemp ) avgflag='A', long_name='Growing degree days base 10C from planting', & ptr_patch=this%gdd10_patch, default='inactive') - this%gdd020_patch(begp:endp) = nan + this%gdd020_patch(begp:endp) = spval call hist_addfld1d (fname='GDD020', units='ddays', & avgflag='A', long_name='Twenty year average of growing degree days base 0C from planting', & ptr_patch=this%gdd020_patch, default='inactive') - this%gdd820_patch(begp:endp) = nan + this%gdd820_patch(begp:endp) = spval call hist_addfld1d (fname='GDD820', units='ddays', & avgflag='A', long_name='Twenty year average of growing degree days base 8C from planting', & ptr_patch=this%gdd820_patch, default='inactive') - this%gdd1020_patch(begp:endp) = nan + this%gdd1020_patch(begp:endp) = spval call hist_addfld1d (fname='GDD1020', units='ddays', & avgflag='A', long_name='Twenty year average of growing degree days base 10C from planting', & ptr_patch=this%gdd1020_patch, default='inactive') From 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 16:55:10 -0600 Subject: [PATCH 1385/2067] Run through black, fix #2112 --- cime_config/SystemTests/rxcropmaturity.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 4fd812b84a..15f524dfce 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -353,7 +353,7 @@ def _run_generate_gdds(self, case_gddgen): f"--sdates-file {sdates_file}", f"--hdates-file {hdates_file}", f"--output-dir generate_gdds_out", - f"--skip-crops miscanthus,irrigated_miscanthus" + f"--skip-crops miscanthus,irrigated_miscanthus", ] ) stu.run_python_script( From c05ce8885e8b76315d6baad45cb57f57f84616a5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 16:56:12 -0600 Subject: [PATCH 1386/2067] Add black commit to git blame ignore file --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index c00226b7dd..9b7cb3c036 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -12,3 +12,4 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd 8bc4688e52ea23ef688e283698f70a44388373eb # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c +8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From 76f1310d17be5c027168fde67cb6aca130f29555 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 17:04:46 -0600 Subject: [PATCH 1387/2067] Add list of source files and directories to the github action --- .github/workflows/black.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml index 438b48e918..c46e1c869b 100644 --- a/.github/workflows/black.yml +++ b/.github/workflows/black.yml @@ -16,6 +16,10 @@ jobs: # Use options and version identical to the conda environment # Using pyproject.toml makes sure this testing is consistent with our python directory testing options: "--check --config python/pyproject.toml" - src: "./python" + src: + - "./python" + - "/cime_config/SystemTests" + - "/cime_config/buildlib" + - "/cime_config/buildnml" # Version should be coordinated with the ctsm_pylib conda environment under the python directory version: "22.3.0" From 89ad0499d8bfba2189500a6224253e7c685a3162 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 17:08:15 -0600 Subject: [PATCH 1388/2067] Try it with a one line list with square brackets --- .github/workflows/black.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml index c46e1c869b..68fdab79a6 100644 --- a/.github/workflows/black.yml +++ b/.github/workflows/black.yml @@ -16,10 +16,6 @@ jobs: # Use options and version identical to the conda environment # Using pyproject.toml makes sure this testing is consistent with our python directory testing options: "--check --config python/pyproject.toml" - src: - - "./python" - - "/cime_config/SystemTests" - - "/cime_config/buildlib" - - "/cime_config/buildnml" + src: [ "./python", "/cime_config/SystemTests", "/cime_config/buildlib", "/cime_config/buildnml" ] # Version should be coordinated with the ctsm_pylib conda environment under the python directory version: "22.3.0" From 44c696e831227dfaf8e442cb4207bf28196701ff Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 17:12:33 -0600 Subject: [PATCH 1389/2067] Add actions for each source Lists didn't work on the src: field, so add a complete action for each. --- .github/workflows/black.yml | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml index 68fdab79a6..a6b3529425 100644 --- a/.github/workflows/black.yml +++ b/.github/workflows/black.yml @@ -16,6 +16,22 @@ jobs: # Use options and version identical to the conda environment # Using pyproject.toml makes sure this testing is consistent with our python directory testing options: "--check --config python/pyproject.toml" - src: [ "./python", "/cime_config/SystemTests", "/cime_config/buildlib", "/cime_config/buildnml" ] + src: "./python" # Version should be coordinated with the ctsm_pylib conda environment under the python directory version: "22.3.0" + # Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field) + - uses: psf/black@stable + with: + options: "--check --config python/pyproject.toml" + src: "/cime_config/SystemTests" + version: "22.3.0" + - uses: psf/black@stable + with: + options: "--check --config python/pyproject.toml" + src: "/cime_config/buildlib" + version: "22.3.0" + - uses: psf/black@stable + with: + options: "--check --config python/pyproject.toml" + src: "/cime_config/buildnml" + version: "22.3.0" From bab173588493092b3920ee89d7477715d1ba9203 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 17:15:21 -0600 Subject: [PATCH 1390/2067] Needs a dot in front of the directory, so doesn't do an absolute path --- .github/workflows/black.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml index a6b3529425..3759fa84c3 100644 --- a/.github/workflows/black.yml +++ b/.github/workflows/black.yml @@ -23,15 +23,15 @@ jobs: - uses: psf/black@stable with: options: "--check --config python/pyproject.toml" - src: "/cime_config/SystemTests" + src: "./cime_config/SystemTests" version: "22.3.0" - uses: psf/black@stable with: options: "--check --config python/pyproject.toml" - src: "/cime_config/buildlib" + src: "./cime_config/buildlib" version: "22.3.0" - uses: psf/black@stable with: options: "--check --config python/pyproject.toml" - src: "/cime_config/buildnml" + src: "./cime_config/buildnml" version: "22.3.0" From 5765f944e3067feb65a3db662853667a5d67a143 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 16 Aug 2023 17:32:43 -0600 Subject: [PATCH 1391/2067] Update Change files --- doc/ChangeLog | 25 ++++++++++++++----------- doc/ChangeSum | 2 +- 2 files changed, 15 insertions(+), 12 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 9d3c5b1564..43a19a6644 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev134 Originator(s): rgknox (Ryan Knox,LBNL EESA), erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Mon Aug 14 07:19:59 PM EDT 2023 +Date: Wed Aug 16 17:20:27 MDT 2023 One-line Summary: Migration of FATES to share normal soil BGC call sequence and functionality Purpose and description of changes @@ -32,25 +32,28 @@ Bugs fixed or introduced Surprisingly, nvhpc tests are now working, but it may just be coincidental. All existing aux_clm tests are passing. Tests without FATES are b4b, with roundoff differences in just TOTCOLC and TOTCOLN. CTSM issues fixed (include CTSM Issue #): - -Known bugs introduced in this tag (include issue #): + We think #1879 -- "AD spinup issues for FATES", is fixed but haven't proved it + #2112 -- black check on SystemTest file Notes of particular relevance for users --------------------------------------- A CLM-FATES simulation will turn on nitrogen supplementation, this enables sufficient immobilization and decomposition. Until FATES and CLM can handle fully coupled nitrogen exchange, which would include root uptake of the mineralized aqueous forms (NH4 and NO3), N limitations in the soil are meaningless when FATES is on. Caveats for users (e.g., need to interpolate initial conditions): - -Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + FATES MUST have suplnitro='ALL' now (was NONE). When fates_parteh_mode>=1 other settings are allowed. + More checking for use_luna and suplnitro is added for FATES in the build-namelist Changes made to namelist defaults (e.g., changed parameter values): FATES runs now supplement N + suplnitro set to ALL for FATES + use_luna set to .false. for FATES and clm4_5 physics -Changes to the datasets (e.g., parameter, surface or initial files): - -Substantial timing or memory changes: -[e.g., check PFS test in the test suite and look at timings, if you -expect possible significant timing changes] +Notes of particular relevance for developers: +--------------------------------------------- +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + We should update defaults for suplnitro, when Nitrogen nutrients are allowed in FATES + The black checdk github action has to duplicate actions for each source file or directory + We should move to using the Makefile in the python directory when we figure it out Testing summary: ---------------- @@ -64,7 +67,7 @@ cheyenne: OK /glade/scratch/rgknox/tests_0814-134713ch Answer changes -------------- -Changes answers relative to baseline: +Changes answers relative to baseline: Two diganostic fields (TOTCOLC and TOTCOLN) Baseline changes will be reported for many tests, all tests were combed to identify RMS diffs, all non-FATES tests had at most, roundoff level ( Date: Fri, 18 Aug 2023 07:29:04 -0600 Subject: [PATCH 1392/2067] sort the history file by vertical dim --- src/main/histFileMod.F90 | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 92ce3dfa95..bf9c23098c 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -1076,7 +1076,17 @@ subroutine sort_hist_list(t, n_fields, hist_list) do f = n_fields-1, 1, -1 do ff = 1, f - if (hist_list(ff)%field%name > hist_list(ff+1)%field%name) then + if (hist_list(ff)%field%num2d > hist_list(ff+1)%field%num2d) then + + call tmp%copy(hist_list(ff)) + call hist_list(ff )%copy(hist_list(ff+1)) + call hist_list(ff+1)%copy(tmp) + + endif + enddo + do ff = 1, f + if ((hist_list(ff)%field%num2d == hist_list(ff+1)%field%num2d) .and. & + (hist_list(ff)%field%name > hist_list(ff+1)%field%name)) then call tmp%copy(hist_list(ff)) call hist_list(ff )%copy(hist_list(ff+1)) From 407ba2b2e746da2c5f99975c44d33c6c682cf7d2 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Fri, 18 Aug 2023 10:46:47 -0600 Subject: [PATCH 1393/2067] Minor fixes to sort_hist_list - Merge the two partial sorts into one; this is partly for efficiency but also because the original was not guaranteed to leave the fields in alphabetical sort order within a given size of level dimension (e.g., in test SMS_D_Ld1_P8x1.f10_f10_mg37.I2000Clm50BgcCropQianRs.green_gnu.clm-default, the last three fields on the h0 file were TSOI_ICE, SOILN_vr, PCT_CFT before this change) - Remove the check for duplicate field names: with this refactor, I think this check will no longer be guaranteed to detect duplicate field names, and this duplicate detection was already done elsewhere so is unnecessary here - Add a comment describing the rationale for the sort order --- src/main/histFileMod.F90 | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index bf9c23098c..6907065da5 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -1076,28 +1076,18 @@ subroutine sort_hist_list(t, n_fields, hist_list) do f = n_fields-1, 1, -1 do ff = 1, f - if (hist_list(ff)%field%num2d > hist_list(ff+1)%field%num2d) then + ! First sort by size of level dimension (this presents a significant performance + ! improvement especially notable on lustre file systems such as on derecho); + ! then, within the list of fields with the same size of the level dimension, + ! sort alphabetically. + if (hist_list(ff)%field%num2d > hist_list(ff+1)%field%num2d .or. & + (hist_list(ff)%field%num2d == hist_list(ff+1)%field%num2d .and. & + hist_list(ff)%field%name > hist_list(ff+1)%field%name)) then call tmp%copy(hist_list(ff)) call hist_list(ff )%copy(hist_list(ff+1)) call hist_list(ff+1)%copy(tmp) - endif - enddo - do ff = 1, f - if ((hist_list(ff)%field%num2d == hist_list(ff+1)%field%num2d) .and. & - (hist_list(ff)%field%name > hist_list(ff+1)%field%name)) then - - call tmp%copy(hist_list(ff)) - call hist_list(ff )%copy(hist_list(ff+1)) - call hist_list(ff+1)%copy(tmp) - - else if (hist_list(ff)%field%name == hist_list(ff+1)%field%name) then - - write(iulog,*) trim(subname),' ERROR: Duplicate field ', & - hist_list(ff)%field%name, & - 't,ff,name=',t,ff,hist_list(ff+1)%field%name - call endrun(msg=errMsg(sourcefile, __LINE__)) end if end do end do From 3c828c3e6cc1e65edf234769bd93d88719ec21f2 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Mon, 21 Aug 2023 12:11:28 -0600 Subject: [PATCH 1394/2067] Sort history fields by name of level dimension rather than size This prevents the interleaving of fields that have the same size of their level dimension despite having different level dimensions; this is a more intuitive ordering. --- src/main/histFileMod.F90 | 28 +++++++++++++++++++++------- 1 file changed, 21 insertions(+), 7 deletions(-) diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 6907065da5..6a69d479ab 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -197,6 +197,20 @@ module histFileMod integer :: num_subs = 0 ! actual number of subscripts character(len=32) :: subs_name(max_subs) ! name of subscript integer :: subs_dim(max_subs) ! dimension of subscript + + ! type2d value for a field without a level dimension. This value is important for the + ! following reasons (as of 2023-08-21): + ! - type2d is used to determine the sort order of history fields both within the history + ! file (e.g., what you see from 'ncdump -h') and in the documentation that lists all + ! history fields. For these purposes, it is important that variables with + ! type2d_unset appear before variables with a real type2d, so type2d_unset should + ! appear early in alphabetical sort order. (If type2d_unset were changed to something + ! that appeared later in alphabetical sort order, then sort_hist_list should be + ! changed to have some special handling of fields with type2d_unset, forcing them to + ! appear first.) + ! - This will soon be added to the history field documentation, so should be a sensible + ! value for the type2d column in that output. + character(len=*), parameter :: type2d_unset = '-' ! type field_info character(len=max_namlen) :: name ! field name @@ -1076,12 +1090,12 @@ subroutine sort_hist_list(t, n_fields, hist_list) do f = n_fields-1, 1, -1 do ff = 1, f - ! First sort by size of level dimension (this presents a significant performance - ! improvement especially notable on lustre file systems such as on derecho); - ! then, within the list of fields with the same size of the level dimension, - ! sort alphabetically. - if (hist_list(ff)%field%num2d > hist_list(ff+1)%field%num2d .or. & - (hist_list(ff)%field%num2d == hist_list(ff+1)%field%num2d .and. & + ! First sort by the name of the level dimension; then, within the list of + ! fields with the same level dimension, sort by field name. Sorting first by + ! the level dimension gives a significant performance improvement especially + ! notable on lustre file systems such as on derecho. + if (hist_list(ff)%field%type2d > hist_list(ff+1)%field%type2d .or. & + (hist_list(ff)%field%type2d == hist_list(ff+1)%field%type2d .and. & hist_list(ff)%field%name > hist_list(ff+1)%field%name)) then call tmp%copy(hist_list(ff)) @@ -5370,7 +5384,7 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & ! Add field to masterlist call masterlist_addfld (fname=trim(fname), numdims=1, type1d=l_type1d, & - type1d_out=l_type1d_out, type2d='unset', num2d=1, & + type1d_out=l_type1d_out, type2d=type2d_unset, num2d=1, & units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, & p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, & l2g_scale_type=scale_type_l2g) From 0b316d8441189a14d623e81223744eaa578b0e09 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 21 Aug 2023 13:03:08 -0600 Subject: [PATCH 1395/2067] Add level dimension column to .rst files. --- .../history_fields_fates.rst | 2074 ++++++------- .../history_fields_nofates.rst | 2554 ++++++++--------- src/main/histFileMod.F90 | 20 +- 3 files changed, 2325 insertions(+), 2323 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index 2fe1035549..5514e76e1e 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -8,1041 +8,1041 @@ use_cn = F use_crop = F use_fates = T -=================================== ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- - Variable Name Long Description Units Active? -=================================== ============================================================================================== ================================================================= ======= -A5TMIN 5-day running mean of min 2-m temperature K F -ACTUAL_IMMOB actual N immobilization gN/m^2/s T -ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F -ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F -ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F -ACT_SOMC ACT_SOM C gC/m^2 T -ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F -ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F -ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F -ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F -ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F -ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F -ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T -ACT_SOMN ACT_SOM N gN/m^2 T -ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F -ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F -ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F -ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F -ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F -ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F -ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T -ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F -ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F -AGLB Aboveground leaf biomass kg/m^2 F -AGSB Aboveground stem biomass kg/m^2 F -ALBD surface albedo (direct) proportion F -ALBGRD ground albedo (direct) proportion F -ALBGRI ground albedo (indirect) proportion F -ALBI surface albedo (indirect) proportion F -ALT current active layer thickness m F -ALTMAX maximum annual active layer thickness m F -ALTMAX_LASTYEAR maximum prior year active layer thickness m F -ATM_O3 atmospheric ozone partial pressure mol/mol F -ATM_TOPO atmospheric surface height m T -AnnET Annual ET mm/s F -BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T -BTRAN transpiration beta factor unitless T -BTRANMN daily minimum of transpiration beta factor unitless T -CEL_LITC CEL_LIT C gC/m^2 T -CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F -CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F -CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F -CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F -CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T -CEL_LITN CEL_LIT N gN/m^2 T -CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F -CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F -CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F -CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F -CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T -CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F -CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F -CH4PROD Gridcell total production of CH4 gC/m2/s T -CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T -CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -COL_CTRUNC column-level sink for C truncation gC/m^2 F -COL_NTRUNC column-level sink for N truncation gN/m^2 F -CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F -CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F -CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T -CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T -COSZEN cosine of solar zenith angle none F -CWDC_HR cwd C heterotrophic respiration gC/m^2/s T -DENIT total rate of denitrification gN/m^2/s T -DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F -DISPLA displacement height (vegetated landunits only) m F -DPVLTRB1 turbulent deposition velocity 1 m/s F -DPVLTRB2 turbulent deposition velocity 2 m/s F -DPVLTRB3 turbulent deposition velocity 3 m/s F -DPVLTRB4 turbulent deposition velocity 4 m/s F -DSL dry surface layer thickness mm T -DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T -DSTFLXT total surface dust emission kg/m2/s T -DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T -EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T -EFLX_GNET net heat flux into ground W/m^2 F -EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T -EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T -EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F -EFLX_LH_TOT_R Rural total evaporation W/m^2 T -EFLX_LH_TOT_U Urban total evaporation W/m^2 F -EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F -ELAI exposed one-sided leaf area index m^2/m^2 T -ERRH2O total water conservation error mm T -ERRH2OSNO imbalance in snow depth (liquid water) mm T -ERRSEB surface energy conservation error W/m^2 T -ERRSOI soil/lake energy conservation error W/m^2 T -ERRSOL solar radiation conservation error W/m^2 T -ESAI exposed one-sided stem area index m^2/m^2 T -FATES_ABOVEGROUND_MORT_SZPF Aboveground flux of carbon from AGB to necromass due to mortality kg m-2 s-1 F -FATES_ABOVEGROUND_PROD_SZPF Aboveground carbon productivity kg m-2 s-1 F -FATES_AGSAPMAINTAR_SZPF above-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F -FATES_AGSAPWOOD_ALLOC_SZPF allocation to above-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_AGSTRUCT_ALLOC_SZPF allocation to above-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_AR autotrophic respiration gC/m^2/s T -FATES_AREA_PLANTS area occupied by all plants per m2 land area m2 m-2 T -FATES_AREA_TREES area occupied by woody plants per m2 land area m2 m-2 T -FATES_AR_CANOPY autotrophic respiration of canopy plants gC/m^2/s T -FATES_AR_UNDERSTORY autotrophic respiration of understory plants gC/m^2/s T -FATES_AUTORESP autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_AUTORESP_CANOPY autotrophic respiration of canopy plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_AUTORESP_CANOPY_SZPF autotrophic respiration of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_AUTORESP_SECONDARY autotrophic respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_AUTORESP_SZPF total autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_AUTORESP_USTORY autotrophic respiration of understory plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_AUTORESP_USTORY_SZPF autotrophic respiration of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_BASALAREA_SZ basal area by size class m2 m-2 T -FATES_BASALAREA_SZPF basal area by pft/size m2 m-2 F -FATES_BA_WEIGHTED_HEIGHT basal area-weighted mean height of woody plants m T -FATES_BGSAPMAINTAR_SZPF below-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F -FATES_BGSAPWOOD_ALLOC_SZPF allocation to below-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_BGSTRUCT_ALLOC_SZPF allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_BURNFRAC burned area fraction per second s-1 T -FATES_BURNFRAC_AP spitfire fraction area burnt (per second) by patch age s-1 T -FATES_C13DISC_SZPF C13 discrimination by pft/size per mil F -FATES_CANOPYAREA_AP canopy area by age bin per m2 land area m2 m-2 T -FATES_CANOPYAREA_HT canopy area height distribution m2 m-2 T -FATES_CANOPYCROWNAREA_PF total PFT-level canopy-layer crown area per m2 land area m2 m-2 T -FATES_CANOPY_SPREAD scaling factor (0-1) between tree basal area and canopy area T -FATES_CANOPY_VEGC biomass of canopy plants in kg carbon per m2 land area kg m-2 T -FATES_CA_WEIGHTED_HEIGHT crown area-weighted mean height of canopy plants m T -FATES_CBALANCE_ERROR total carbon error in kg carbon per second kg s-1 T -FATES_COLD_STATUS site-level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not too cold T -FATES_CROOTMAINTAR live coarse root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_CROOTMAINTAR_CANOPY_SZ live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F -FATES_CROOTMAINTAR_USTORY_SZ live coarse root maintenance autotrophic respiration for understory plants in kg carbon per m2 kg m-2 s-1 F -FATES_CROOT_ALLOC allocation to coarse roots in kg carbon per m2 per second kg m-2 s-1 T -FATES_CROWNAREA_CANOPY_SZ total crown area of canopy plants by size class m2 m-2 F -FATES_CROWNAREA_CL total crown area in each canopy layer m2 m-2 T -FATES_CROWNAREA_CLLL total crown area that is occupied by leaves in each canopy and leaf layer m2 m-2 F -FATES_CROWNAREA_PF total PFT-level crown area per m2 land area m2 m-2 T -FATES_CROWNAREA_USTORY_SZ total crown area of understory plants by size class m2 m-2 F -FATES_CWD_ABOVEGROUND_DC debris class-level aboveground coarse woody debris stocks in kg carbon per m2 kg m-2 F -FATES_CWD_ABOVEGROUND_IN_DC debris class-level aboveground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F -FATES_CWD_ABOVEGROUND_OUT_DC debris class-level aboveground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F -FATES_CWD_BELOWGROUND_DC debris class-level belowground coarse woody debris stocks in kg carbon per m2 kg m-2 F -FATES_CWD_BELOWGROUND_IN_DC debris class-level belowground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F -FATES_CWD_BELOWGROUND_OUT_DC debris class-level belowground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F -FATES_DAYSINCE_COLDLEAFOFF site-level days elapsed since cold leaf drop days T -FATES_DAYSINCE_COLDLEAFON site-level days elapsed since cold leaf flush days T -FATES_DAYSINCE_DROUGHTLEAFOFF_PF PFT-level days elapsed since drought leaf drop days T -FATES_DAYSINCE_DROUGHTLEAFON_PF PFT-level days elapsed since drought leaf flush days T -FATES_DDBH_CANOPY_SZ diameter growth increment by size of canopy plants m m-2 yr-1 T -FATES_DDBH_CANOPY_SZAP growth rate of canopy plants in meters DBH per m2 per year in canopy in each size x age class m m-2 yr-1 F -FATES_DDBH_CANOPY_SZPF diameter growth increment by pft/size m m-2 yr-1 F -FATES_DDBH_SZPF diameter growth increment by pft/size m m-2 yr-1 F -FATES_DDBH_USTORY_SZ diameter growth increment by size of understory plants m m-2 yr-1 T -FATES_DDBH_USTORY_SZAP growth rate of understory plants in meters DBH per m2 per year in each size x age class m m-2 yr-1 F -FATES_DDBH_USTORY_SZPF diameter growth increment by pft/size m m-2 yr-1 F -FATES_DEMOTION_CARBONFLUX demotion-associated biomass carbon flux from canopy to understory in kg carbon per m2 per seco kg m-2 s-1 T -FATES_DEMOTION_RATE_SZ demotion rate from canopy to understory by size class in number of plants per m2 per year m-2 yr-1 F -FATES_DISTURBANCE_RATE_FIRE disturbance rate from fire m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_LOGGING disturbance rate from logging m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_P2P disturbance rate from primary to primary lands m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_P2S disturbance rate from primary to secondary lands m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_POTENTIAL potential (i.e., including unresolved) disturbance rate m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_S2S disturbance rate from secondary to secondary lands m2 m-2 yr-1 T -FATES_DISTURBANCE_RATE_TREEFALL disturbance rate from treefall m2 m-2 yr-1 T -FATES_DROUGHT_STATUS_PF PFT-level drought status, <2 too dry for leaves, >=2 not too dry T -FATES_EFFECT_WSPEED effective wind speed for fire spread in meters per second m s-1 T -FATES_ELONG_FACTOR_PF PFT-level mean elongation factor (partial flushing/abscission) 1 T -FATES_ERROR_EL total mass-balance error in kg per second by element kg s-1 T -FATES_EXCESS_RESP respiration of un-allocatable carbon gain kg m-2 s-1 T -FATES_FABD_SHA_CLLL shade fraction of direct light absorbed by each canopy and leaf layer 1 F -FATES_FABD_SHA_CLLLPF shade fraction of direct light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABD_SHA_TOPLF_CL shade fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABD_SUN_CLLL sun fraction of direct light absorbed by each canopy and leaf layer 1 F -FATES_FABD_SUN_CLLLPF sun fraction of direct light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABD_SUN_TOPLF_CL sun fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABI_SHA_CLLL shade fraction of indirect light absorbed by each canopy and leaf layer 1 F -FATES_FABI_SHA_CLLLPF shade fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABI_SHA_TOPLF_CL shade fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABI_SUN_CLLL sun fraction of indirect light absorbed by each canopy and leaf layer 1 F -FATES_FABI_SUN_CLLLPF sun fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABI_SUN_TOPLF_CL sun fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FDI Fire Danger Index (probability that an ignition will lead to a fire) 1 T -FATES_FIRE_CLOSS carbon loss to atmosphere from fire in kg carbon per m2 per second kg m-2 s-1 T -FATES_FIRE_FLUX_EL loss to atmosphere from fire by element in kg element per m2 per s kg m-2 s-1 T -FATES_FIRE_INTENSITY spitfire surface fireline intensity in J per m per second J m-1 s-1 T -FATES_FIRE_INTENSITY_BURNFRAC product of surface fire intensity and burned area fraction -- divide by FATES_BURNFRAC to get J m-1 s-1 T -FATES_FIRE_INTENSITY_BURNFRAC_AP product of fire intensity and burned fraction, resolved by patch age (so divide by FATES_BURNF J m-1 s-1 T -FATES_FRACTION total gridcell fraction which FATES is running over m2 m-2 T -FATES_FRAGMENTATION_SCALER_SL factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T -FATES_FROOTC total biomass in live plant fine roots in kg carbon per m2 kg m-2 T -FATES_FROOTCTURN_CANOPY_SZ fine root turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_FROOTCTURN_USTORY_SZ fine root turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F -FATES_FROOTC_SL Total carbon in live plant fine-roots over depth kg m-3 T -FATES_FROOTC_SZPF fine-root carbon mass by size-class x pft in kg carbon per m2 kg m-2 F -FATES_FROOTMAINTAR fine root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_FROOTMAINTAR_CANOPY_SZ live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F -FATES_FROOTMAINTAR_SZPF fine root maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_FROOTMAINTAR_USTORY_SZ fine root maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F -FATES_FROOT_ALLOC allocation to fine roots in kg carbon per m2 per second kg m-2 s-1 T -FATES_FROOT_ALLOC_CANOPY_SZ allocation to fine root C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_FROOT_ALLOC_SZPF allocation to fine roots by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_FROOT_ALLOC_USTORY_SZ allocation to fine roots for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_FUELCONSUMED total fuel consumed in kg carbon per m2 land area kg m-2 T -FATES_FUEL_AMOUNT total ground fuel related to FATES_ROS (omits 1000hr fuels) in kg C per m2 land area kg m-2 T -FATES_FUEL_AMOUNT_AP spitfire ground fuel (kg carbon per m2) related to FATES_ROS (omits 1000hr fuels) within each kg m-2 T -FATES_FUEL_AMOUNT_APFC spitfire fuel quantity in each age x fuel class in kg carbon per m2 land area kg m-2 F -FATES_FUEL_AMOUNT_FC spitfire fuel-class level fuel amount in kg carbon per m2 land area kg m-2 T -FATES_FUEL_BULKD fuel bulk density in kg per m3 kg m-3 T -FATES_FUEL_BURNT_BURNFRAC_FC product of fraction (0-1) of fuel burnt and burnt fraction (divide by FATES_BURNFRAC to get bu 1 T -FATES_FUEL_EFF_MOIST spitfire fuel moisture (volumetric) m3 m-3 T -FATES_FUEL_MEF fuel moisture of extinction (volumetric) m3 m-3 T -FATES_FUEL_MOISTURE_FC spitfire fuel class-level fuel moisture (volumetric) m3 m-3 T -FATES_FUEL_SAV spitfire fuel surface area to volume ratio m-1 T -FATES_GDD site-level growing degree days degree_Celsius T -FATES_GPP gross primary production in kg carbon per m2 per second kg m-2 s-1 T -FATES_GPP_AP gross primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F -FATES_GPP_CANOPY gross primary production of canopy plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_GPP_CANOPY_SZPF gross primary production of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_GPP_PF total PFT-level GPP in kg carbon per m2 land area per second kg m-2 s-1 T -FATES_GPP_SECONDARY gross primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_GPP_SE_PF total PFT-level GPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T -FATES_GPP_SZPF gross primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_GPP_USTORY gross primary production of understory plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_GPP_USTORY_SZPF gross primary production of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_GROWAR_CANOPY_SZ growth autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_GROWAR_SZPF growth autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_GROWAR_USTORY_SZ growth autotrophic respiration of understory plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_GROWTHFLUX_FUSION_SZPF flux of individuals into a given size class bin via fusion m-2 yr-1 F -FATES_GROWTHFLUX_SZPF flux of individuals into a given size class bin via growth and recruitment m-2 yr-1 F -FATES_GROWTH_RESP growth respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_GROWTH_RESP_SECONDARY growth respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_HARVEST_CARBON_FLUX harvest carbon flux in kg carbon per m2 per year kg m-2 yr-1 T -FATES_HARVEST_DEBT Accumulated carbon failed to be harvested kg C T -FATES_HARVEST_DEBT_SEC Accumulated carbon failed to be harvested from secondary patches kg C T -FATES_HET_RESP heterotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_IGNITIONS number of successful fire ignitions per m2 land area per second m-2 s-1 T -FATES_LAI leaf area index per m2 land area m2 m-2 T -FATES_LAISHA_TOP_CL LAI in the shade by the top leaf layer of each canopy layer m2 m-2 F -FATES_LAISHA_Z_CLLL LAI in the shade by each canopy and leaf layer m2 m-2 F -FATES_LAISHA_Z_CLLLPF LAI in the shade by each canopy, leaf, and PFT m2 m-2 F -FATES_LAISUN_TOP_CL LAI in the sun by the top leaf layer of each canopy layer m2 m-2 F -FATES_LAISUN_Z_CLLL LAI in the sun by each canopy and leaf layer m2 m-2 F -FATES_LAISUN_Z_CLLLPF LAI in the sun by each canopy, leaf, and PFT m2 m-2 F -FATES_LAI_AP leaf area index by age bin per m2 land area m2 m-2 T -FATES_LAI_CANOPY_SZ leaf area index (LAI) of canopy plants by size class m2 m-2 T -FATES_LAI_CANOPY_SZPF Leaf area index (LAI) of canopy plants by pft/size m2 m-2 F -FATES_LAI_SECONDARY leaf area index per m2 land area, secondary patches m2 m-2 T -FATES_LAI_USTORY_SZ leaf area index (LAI) of understory plants by size class m2 m-2 T -FATES_LAI_USTORY_SZPF Leaf area index (LAI) of understory plants by pft/size m2 m-2 F -FATES_LBLAYER_COND mean leaf boundary layer conductance mol m-2 s-1 T -FATES_LBLAYER_COND_AP mean leaf boundary layer conductance - by patch age mol m-2 s-1 F -FATES_LEAFAREA_HT leaf area height distribution m2 m-2 T -FATES_LEAFC total biomass in live plant leaves in kg carbon per m2 kg m-2 T -FATES_LEAFCTURN_CANOPY_SZ leaf turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAFCTURN_USTORY_SZ leaf turnover (non-mortal) for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAFC_CANOPY_SZPF biomass in leaves of canopy plants by pft/size in kg carbon per m2 kg m-2 F -FATES_LEAFC_PF total PFT-level leaf biomass in kg carbon per m2 land area kg m-2 T -FATES_LEAFC_SZPF leaf carbon mass by size-class x pft in kg carbon per m2 kg m-2 F -FATES_LEAFC_USTORY_SZPF biomass in leaves of understory plants by pft/size in kg carbon per m2 kg m-2 F -FATES_LEAFMAINTAR leaf maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_LEAF_ALLOC allocation to leaves in kg carbon per m2 per second kg m-2 s-1 T -FATES_LEAF_ALLOC_CANOPY_SZ allocation to leaves for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAF_ALLOC_SZPF allocation to leaves by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAF_ALLOC_USTORY_SZ allocation to leaves for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LITTER_AG_CWD_EL mass of aboveground litter in coarse woody debris (trunks/branches/twigs) by element kg m-2 T -FATES_LITTER_AG_FINE_EL mass of aboveground litter in fines (leaves, nonviable seed) by element kg m-2 T -FATES_LITTER_BG_CWD_EL mass of belowground litter in coarse woody debris (coarse roots) by element kg m-2 T -FATES_LITTER_BG_FINE_EL mass of belowground litter in fines (fineroots) by element kg m-2 T -FATES_LITTER_CWD_ELDC total mass of litter in coarse woody debris by element and coarse woody debris size kg m-2 T -FATES_LITTER_IN litter flux in kg carbon per m2 per second kg m-2 s-1 T -FATES_LITTER_IN_EL litter flux in in kg element per m2 per second kg m-2 s-1 T -FATES_LITTER_OUT litter flux out in kg carbon (exudation, fragmentation, seed decay) kg m-2 s-1 T -FATES_LITTER_OUT_EL litter flux out (exudation, fragmentation and seed decay) in kg element kg m-2 s-1 T -FATES_LSTEMMAINTAR live stem maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_LSTEMMAINTAR_CANOPY_SZ live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1 F -FATES_LSTEMMAINTAR_USTORY_SZ live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F -FATES_M3_MORTALITY_CANOPY_SZ C starvation mortality of canopy plants by size N/ha/yr F -FATES_M3_MORTALITY_CANOPY_SZPF C starvation mortality of canopy plants by pft/size N/ha/yr F -FATES_M3_MORTALITY_USTORY_SZ C starvation mortality of understory plants by size N/ha/yr F -FATES_M3_MORTALITY_USTORY_SZPF C starvation mortality of understory plants by pft/size N/ha/yr F -FATES_MAINTAR_CANOPY_SZ maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_MAINTAR_SZPF maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_MAINTAR_USTORY_SZ maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1 F -FATES_MAINT_RESP maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T -FATES_MAINT_RESP_SECONDARY maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T -FATES_MAINT_RESP_UNREDUCED diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 F -FATES_MEANLIQVOL_DROUGHTPHEN_PF PFT-level mean liquid water volume for drought phenolgy m3 m-3 T -FATES_MEANSMP_DROUGHTPHEN_PF PFT-level mean soil matric potential for drought phenology Pa T -FATES_MORTALITY_AGESCEN_AC age senescence mortality by cohort age in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_AGESCEN_ACPF age senescence mortality by pft/cohort age in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_AGESCEN_SE_SZ age senescence mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_AGESCEN_SZ age senescence mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_AGESCEN_SZPF age senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_BACKGROUND_SE_SZ background mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_BACKGROUND_SZ background mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_BACKGROUND_SZPF background mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CAMBIALBURN_SZPF fire mortality from cambial burn by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CANOPY_SE_SZ total mortality of canopy trees by size class in number of plants per m2, secondary patches m-2 yr-1 T -FATES_MORTALITY_CANOPY_SZ total mortality of canopy trees by size class in number of plants per m2 m-2 yr-1 T -FATES_MORTALITY_CANOPY_SZAP mortality rate of canopy plants in number of plants per m2 per year in each size x age class m-2 yr-1 F -FATES_MORTALITY_CANOPY_SZPF total mortality of canopy plants by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CFLUX_CANOPY flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1 T -FATES_MORTALITY_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from mortality kg m-2 s-1 T -FATES_MORTALITY_CFLUX_USTORY flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1 T -FATES_MORTALITY_CROWNSCORCH_SZPF fire mortality from crown scorch by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CSTARV_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality kg m-2 s-1 T -FATES_MORTALITY_CSTARV_SE_SZ carbon starvation mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_CSTARV_SZ carbon starvation mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_CSTARV_SZPF carbon starvation mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_FIRE_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from fire mortality kg m-2 s-1 T -FATES_MORTALITY_FIRE_SZ fire mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_FIRE_SZPF fire mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_FREEZING_SE_SZ freezing mortality by size in number of plants per m2 per event, secondary patches m-2 event-1 T -FATES_MORTALITY_FREEZING_SZ freezing mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_FREEZING_SZPF freezing mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_HYDRAULIC_SE_SZ hydraulic mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_HYDRAULIC_SZ hydraulic mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_HYDRAULIC_SZPF hydraulic mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_HYDRO_CFLUX_PF PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality kg m-2 s-1 T -FATES_MORTALITY_IMPACT_SZ impact mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_IMPACT_SZPF impact mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_LOGGING_SE_SZ logging mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T -FATES_MORTALITY_LOGGING_SZ logging mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_LOGGING_SZPF logging mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_PF PFT-level mortality rate in number of individuals per m2 land area per year m-2 yr-1 T -FATES_MORTALITY_SENESCENCE_SE_SZ senescence mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T -FATES_MORTALITY_SENESCENCE_SZ senescence mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_SENESCENCE_SZPF senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_TERMINATION_SZ termination mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_TERMINATION_SZPF termination mortality by pft/size in number pf plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_USTORY_SZ total mortality of understory trees by size class in individuals per m2 per year m-2 yr-1 T -FATES_MORTALITY_USTORY_SZAP mortality rate of understory plants in number of plants per m2 per year in each size x age cla m-2 yr-1 F -FATES_MORTALITY_USTORY_SZPF total mortality of understory plants by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_NCHILLDAYS site-level number of chill days days T -FATES_NCL_AP number of canopy levels by age bin F -FATES_NCOHORTS total number of cohorts per site T -FATES_NCOHORTS_SECONDARY total number of cohorts per site T -FATES_NCOLDDAYS site-level number of cold days days T -FATES_NEP net ecosystem production in kg carbon per m2 per second kg m-2 s-1 T -FATES_NESTEROV_INDEX nesterov fire danger index T -FATES_NET_C_UPTAKE_CLLL net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1 F -FATES_NONSTRUCTC non-structural biomass (sapwood + leaf + fineroot) in kg carbon per m2 kg m-2 T -FATES_NPATCHES total number of patches per site T -FATES_NPATCHES_SECONDARY total number of patches per site T -FATES_NPATCH_AP number of patches by age bin F -FATES_NPLANT_AC number of plants per m2 by cohort age class m-2 T -FATES_NPLANT_ACPF stem number density by pft and age class m-2 F -FATES_NPLANT_CANOPY_SZ number of canopy plants per m2 by size class m-2 T -FATES_NPLANT_CANOPY_SZAP number of plants per m2 in canopy in each size x age class m-2 F -FATES_NPLANT_CANOPY_SZPF number of canopy plants by size/pft per m2 m-2 F -FATES_NPLANT_PF total PFT-level number of individuals per m2 land area m-2 T -FATES_NPLANT_SEC_PF total PFT-level number of individuals per m2 land area, secondary patches m-2 T -FATES_NPLANT_SZ number of plants per m2 by size class m-2 T -FATES_NPLANT_SZAP number of plants per m2 in each size x age class m-2 F -FATES_NPLANT_SZAPPF number of plants per m2 in each size x age x pft class m-2 F -FATES_NPLANT_SZPF stem number density by pft/size m-2 F -FATES_NPLANT_USTORY_SZ number of understory plants per m2 by size class m-2 T -FATES_NPLANT_USTORY_SZAP number of plants per m2 in understory in each size x age class m-2 F -FATES_NPLANT_USTORY_SZPF density of understory plants by pft/size in number of plants per m2 m-2 F -FATES_NPP net primary production in kg carbon per m2 per second kg m-2 s-1 T -FATES_NPP_AP net primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_APPF NPP per PFT in each age bin in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_CANOPY_SZ NPP of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_PF total PFT-level NPP in kg carbon per m2 land area per second kg m-2 yr-1 T -FATES_NPP_SECONDARY net primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_NPP_SE_PF total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 yr-1 T -FATES_NPP_SZPF total net primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_USTORY_SZ NPP of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_PARPROF_DIF_CLLL radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F -FATES_PARPROF_DIF_CLLLPF radiative profile of diffuse PAR through each canopy, leaf, and PFT W m-2 F -FATES_PARPROF_DIR_CLLL radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F -FATES_PARPROF_DIR_CLLLPF radiative profile of direct PAR through each canopy, leaf, and PFT W m-2 F -FATES_PARSHA_Z_CL PAR absorbed in the shade by top leaf layer in each canopy layer W m-2 F -FATES_PARSHA_Z_CLLL PAR absorbed in the shade by each canopy and leaf layer W m-2 F -FATES_PARSHA_Z_CLLLPF PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F -FATES_PARSUN_Z_CL PAR absorbed in the sun by top leaf layer in each canopy layer W m-2 F -FATES_PARSUN_Z_CLLL PAR absorbed in the sun by each canopy and leaf layer W m-2 F -FATES_PARSUN_Z_CLLLPF PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F -FATES_PATCHAREA_AP patch area by age bin per m2 land area m2 m-2 T -FATES_PRIMARY_PATCHFUSION_ERR error in total primary lands associated with patch fusion m2 m-2 yr-1 T -FATES_PROMOTION_CARBONFLUX promotion-associated biomass carbon flux from understory to canopy in kg carbon per m2 per sec kg m-2 s-1 T -FATES_PROMOTION_RATE_SZ promotion rate from understory to canopy by size class m-2 yr-1 F -FATES_RAD_ERROR radiation error in FATES RTM W m-2 T -FATES_RDARK_CANOPY_SZ dark respiration for canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_RDARK_SZPF dark portion of maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_RDARK_USTORY_SZ dark respiration for understory plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_RECRUITMENT_PF PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T -FATES_REPROC total biomass in live plant reproductive tissues in kg carbon per m2 kg m-2 T -FATES_REPROC_SZPF reproductive carbon mass (on plant) by size-class x pft in kg carbon per m2 kg m-2 F -FATES_ROS fire rate of spread in meters per second m s-1 T -FATES_SAI_CANOPY_SZ stem area index (SAI) of canopy plants by size class m2 m-2 F -FATES_SAI_USTORY_SZ stem area index (SAI) of understory plants by size class m2 m-2 F -FATES_SAPWOODC total biomass in live plant sapwood in kg carbon per m2 kg m-2 T -FATES_SAPWOODCTURN_CANOPY_SZ sapwood turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SAPWOODCTURN_USTORY_SZ sapwood C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F -FATES_SAPWOODC_SZPF sapwood carbon mass by size-class x pft in kg carbon per m2 kg m-2 F -FATES_SAPWOOD_ALLOC_CANOPY_SZ allocation to sapwood C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SAPWOOD_ALLOC_USTORY_SZ allocation to sapwood C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SCORCH_HEIGHT_APPF SPITFIRE flame Scorch Height (calculated per PFT in each patch age bin) m F -FATES_SECONDAREA_ANTHRODIST_AP secondary forest patch area age distribution since anthropgenic disturbance m2 m-2 F -FATES_SECONDAREA_DIST_AP secondary forest patch area age distribution since any kind of disturbance m2 m-2 F -FATES_SECONDARY_FOREST_FRACTION secondary forest fraction m2 m-2 T -FATES_SECONDARY_FOREST_VEGC biomass on secondary lands in kg carbon per m2 land area (mult by FATES_SECONDARY_FOREST_FRACT kg m-2 T -FATES_SEEDS_IN seed production rate in kg carbon per m2 second kg m-2 s-1 T -FATES_SEEDS_IN_EXTERN_EL external seed influx rate in kg element per m2 per second kg m-2 s-1 T -FATES_SEEDS_IN_LOCAL_EL within-site, element-level seed production rate in kg element per m2 per second kg m-2 s-1 T -FATES_SEED_ALLOC allocation to seeds in kg carbon per m2 per second kg m-2 s-1 T -FATES_SEED_ALLOC_CANOPY_SZ allocation to reproductive C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SEED_ALLOC_SZPF allocation to seeds by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_SEED_ALLOC_USTORY_SZ allocation to reproductive C for understory plants by size class in kg carbon per m2 per secon kg m-2 s-1 F -FATES_SEED_BANK total seed mass of all PFTs in kg carbon per m2 land area kg m-2 T -FATES_SEED_BANK_EL element-level total seed mass of all PFTs in kg element per m2 kg m-2 T -FATES_SEED_DECAY_EL seed mass decay (germinated and un-germinated) in kg element per m2 per second kg m-2 s-1 T -FATES_SEED_GERM_EL element-level total germinated seed mass of all PFTs in kg element per m2 kg m-2 T -FATES_SEED_PROD_CANOPY_SZ seed production of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SEED_PROD_USTORY_SZ seed production of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STEM_ALLOC allocation to stem in kg carbon per m2 per second kg m-2 s-1 T -FATES_STOMATAL_COND mean stomatal conductance mol m-2 s-1 T -FATES_STOMATAL_COND_AP mean stomatal conductance - by patch age mol m-2 s-1 F -FATES_STOREC total biomass in live plant storage in kg carbon per m2 land area kg m-2 T -FATES_STORECTURN_CANOPY_SZ storage turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STORECTURN_USTORY_SZ storage C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F -FATES_STOREC_CANOPY_SZPF biomass in storage pools of canopy plants by pft/size in kg carbon per m2 kg m-2 F -FATES_STOREC_PF total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T -FATES_STOREC_SZPF storage carbon mass by size-class x pft in kg carbon per m2 kg m-2 F -FATES_STOREC_TF Storage C fraction of target kg kg-1 T -FATES_STOREC_TF_CANOPY_SZPF Storage C fraction of target by size x pft, in the canopy kg kg-1 F -FATES_STOREC_TF_USTORY_SZPF Storage C fraction of target by size x pft, in the understory kg kg-1 F -FATES_STOREC_USTORY_SZPF biomass in storage pools of understory plants by pft/size in kg carbon per m2 kg m-2 F -FATES_STORE_ALLOC allocation to storage tissues in kg carbon per m2 per second kg m-2 s-1 T -FATES_STORE_ALLOC_CANOPY_SZ allocation to storage C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STORE_ALLOC_SZPF allocation to storage C by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_STORE_ALLOC_USTORY_SZ allocation to storage C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STRUCTC structural biomass in kg carbon per m2 land area kg m-2 T -FATES_STRUCTCTURN_CANOPY_SZ structural C turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per sec kg m-2 s-1 F -FATES_STRUCTCTURN_USTORY_SZ structural C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per kg m-2 s-1 F -FATES_STRUCT_ALLOC_CANOPY_SZ allocation to structural C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STRUCT_ALLOC_USTORY_SZ allocation to structural C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_TGROWTH fates long-term running mean vegetation temperature by site degree_Celsius F -FATES_TLONGTERM fates 30-year running mean vegetation temperature by site degree_Celsius F -FATES_TRIMMING degree to which canopy expansion is limited by leaf economics (0-1) 1 T -FATES_TRIMMING_CANOPY_SZ trimming term of canopy plants weighted by plant density, by size class m-2 F -FATES_TRIMMING_USTORY_SZ trimming term of understory plants weighted by plant density, by size class m-2 F -FATES_TVEG fates instantaneous mean vegetation temperature by site degree_Celsius T -FATES_TVEG24 fates 24-hr running mean vegetation temperature by site degree_Celsius T -FATES_USTORY_VEGC biomass of understory plants in kg carbon per m2 land area kg m-2 T -FATES_VEGC total biomass in live plants in kg carbon per m2 land area kg m-2 T -FATES_VEGC_ABOVEGROUND aboveground biomass in kg carbon per m2 land area kg m-2 T -FATES_VEGC_ABOVEGROUND_SZ aboveground biomass by size class in kg carbon per m2 kg m-2 T -FATES_VEGC_ABOVEGROUND_SZPF aboveground biomass by pft/size in kg carbon per m2 kg m-2 F -FATES_VEGC_AP total biomass within a given patch age bin in kg carbon per m2 land area kg m-2 F -FATES_VEGC_APPF biomass per PFT in each age bin in kg carbon per m2 kg m-2 F -FATES_VEGC_PF total PFT-level biomass in kg of carbon per land area kg m-2 T -FATES_VEGC_SE_PF total PFT-level biomass in kg of carbon per land area, secondary patches kg m-2 T -FATES_VEGC_SZ total biomass by size class in kg carbon per m2 kg m-2 F -FATES_VEGC_SZPF total vegetation biomass in live plants by size-class x pft in kg carbon per m2 kg m-2 F -FATES_WOOD_PRODUCT total wood product from logging in kg carbon per m2 land area kg m-2 T -FATES_YESTCANLEV_CANOPY_SZ yesterdays canopy level for canopy plants by size class in number of plants per m2 m-2 F -FATES_YESTCANLEV_USTORY_SZ yesterdays canopy level for understory plants by size class in number of plants per m2 m-2 F -FATES_ZSTAR_AP product of zstar and patch area by age bin (divide by FATES_PATCHAREA_AP to get mean zstar) m F -FATES_c_to_litr_cel_c litter celluluse carbon flux from FATES to BGC gC/m^3/s T -FATES_c_to_litr_lab_c litter labile carbon flux from FATES to BGC gC/m^3/s T -FATES_c_to_litr_lig_c litter lignin carbon flux from FATES to BGC gC/m^3/s T -FCEV canopy evaporation W/m^2 T -FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T -FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T -FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T -FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F -FCOV fractional impermeable area unitless T -FCTR canopy transpiration W/m^2 T -FGEV ground evaporation W/m^2 T -FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T -FGR12 heat flux between soil layers 1 and 2 W/m^2 T -FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F -FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F -FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F -FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F -FH2OSFC fraction of ground covered by surface water unitless T -FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F -FINUNDATED fractional inundated area of vegetated columns unitless T -FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F -FIRA net infrared (longwave) radiation W/m^2 T -FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRA_R Rural net infrared (longwave) radiation W/m^2 T -FIRA_U Urban net infrared (longwave) radiation W/m^2 F -FIRE emitted infrared (longwave) radiation W/m^2 T -FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T -FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F -FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T -FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F -FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F -FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F -FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F -FSA absorbed solar radiation W/m^2 T -FSAT fractional area with water table at surface unitless T -FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F -FSA_R Rural absorbed solar radiation W/m^2 F -FSA_U Urban absorbed solar radiation W/m^2 F -FSD24 direct radiation (last 24hrs) K F -FSD240 direct radiation (last 240hrs) K F -FSDS atmospheric incident solar radiation W/m^2 T -FSDSND direct nir incident solar radiation W/m^2 T -FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T -FSDSNI diffuse nir incident solar radiation W/m^2 T -FSDSVD direct vis incident solar radiation W/m^2 T -FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T -FSDSVI diffuse vis incident solar radiation W/m^2 T -FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T -FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T -FSH_G sensible heat from ground W/m^2 T -FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F -FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T -FSH_R Rural sensible heat W/m^2 T -FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T -FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T -FSH_U Urban sensible heat W/m^2 F -FSH_V sensible heat from veg W/m^2 T -FSI24 indirect radiation (last 24hrs) K F -FSI240 indirect radiation (last 240hrs) K F -FSM snow melt heat flux W/m^2 T -FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F -FSM_R Rural snow melt heat flux W/m^2 F -FSM_U Urban snow melt heat flux W/m^2 F -FSNO fraction of ground covered by snow unitless T -FSNO_EFF effective fraction of ground covered by snow unitless T -FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F -FSR reflected solar radiation W/m^2 T -FSRND direct nir reflected solar radiation W/m^2 T -FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T -FSRNI diffuse nir reflected solar radiation W/m^2 T -FSRVD direct vis reflected solar radiation W/m^2 T -FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T -FSRVI diffuse vis reflected solar radiation W/m^2 T -FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F -FSUN sunlit fraction of canopy proportion F -FSUN24 fraction sunlit (last 24hrs) K F -FSUN240 fraction sunlit (last 240hrs) K F -F_DENIT denitrification flux gN/m^2/s T -F_DENIT_BASE F_DENIT_BASE gN/m^3/s F -F_DENIT_vr denitrification flux gN/m^3/s F -F_N2O_DENIT denitrification N2O flux gN/m^2/s T -F_N2O_NIT nitrification N2O flux gN/m^2/s T -F_NIT nitrification flux gN/m^2/s T -F_NIT_vr nitrification flux gN/m^3/s F -GROSS_NMIN gross rate of N mineralization gN/m^2/s T -GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F -GSSHA shaded leaf stomatal conductance umol H20/m2/s T -GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T -GSSUN sunlit leaf stomatal conductance umol H20/m2/s T -GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T -H2OCAN intercepted water mm T -H2OSFC surface water depth mm T -H2OSNO snow depth (liquid water) mm T -H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F -H2OSNO_TOP mass of snow in top snow layer kg/m2 T -H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T -HBOT canopy bottom m F -HEAT_CONTENT1 initial gridcell total heat content J/m^2 T -HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F -HEAT_CONTENT2 post land cover change total heat content J/m^2 F -HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T -HIA 2 m NWS Heat Index C T -HIA_R Rural 2 m NWS Heat Index C T -HIA_U Urban 2 m NWS Heat Index C T -HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F -HR total heterotrophic respiration gC/m^2/s T -HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T -HTOP canopy top m T -HUMIDEX 2 m Humidex C T -HUMIDEX_R Rural 2 m Humidex C T -HUMIDEX_U Urban 2 m Humidex C T -ICE_CONTENT1 initial gridcell total ice content mm T -ICE_CONTENT2 post land cover change total ice content mm F -ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F -INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F -INT_SNOW_ICE accumulated swe (ice landunits only) mm F -IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T -KROOT root conductance each soil layer 1/s F -KSOIL soil conductance in each soil layer 1/s F -K_ACT_SOM active soil organic potential loss coefficient 1/s F -K_CEL_LIT cellulosic litter potential loss coefficient 1/s F -K_LIG_LIT lignin litter potential loss coefficient 1/s F -K_MET_LIT metabolic litter potential loss coefficient 1/s F -K_NITR K_NITR 1/s F -K_NITR_H2O K_NITR_H2O unitless F -K_NITR_PH K_NITR_PH unitless F -K_NITR_T K_NITR_T unitless F -K_PAS_SOM passive soil organic potential loss coefficient 1/s F -K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F -L1_PATHFRAC_S1_vr PATHFRAC from metabolic litter to active soil organic fraction F -L1_RESP_FRAC_S1_vr respired from metabolic litter to active soil organic fraction F -L2_PATHFRAC_S1_vr PATHFRAC from cellulosic litter to active soil organic fraction F -L2_RESP_FRAC_S1_vr respired from cellulosic litter to active soil organic fraction F -L3_PATHFRAC_S2_vr PATHFRAC from lignin litter to slow soil organic ma fraction F -L3_RESP_FRAC_S2_vr respired from lignin litter to slow soil organic ma fraction F -LAI240 240hr average of leaf area index m^2/m^2 F -LAISHA shaded projected leaf area index m^2/m^2 T -LAISUN sunlit projected leaf area index m^2/m^2 T -LAKEICEFRAC lake layer ice mass fraction unitless F -LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T -LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T -LIG_LITC LIG_LIT C gC/m^2 T -LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F -LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F -LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F -LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F -LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T -LIG_LITN LIG_LIT N gN/m^2 T -LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F -LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F -LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F -LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F -LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T -LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F -LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F -LIQCAN intercepted liquid water mm T -LIQUID_CONTENT1 initial gridcell total liq content mm T -LIQUID_CONTENT2 post landuse change gridcell total liq content mm F -LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F -LITTERC_HR litter C heterotrophic respiration gC/m^2/s T -LNC leaf N concentration gN leaf/m^2 T -LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F -LWup upwelling longwave radiation W/m^2 F -MET_LITC MET_LIT C gC/m^2 T -MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F -MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F -MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F -MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F -MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T -MET_LITN MET_LIT N gN/m^2 T -MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F -MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F -MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F -MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F -MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T -MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F -MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F -MORTALITY_CROWNAREA_CANOPY Crown area of canopy trees that died m2/ha/year T -MORTALITY_CROWNAREA_UNDERSTORY Crown aera of understory trees that died m2/ha/year T -M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F -M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F -M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F -M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F -M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F -M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F -M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F -M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F -M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F -M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F -M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F -M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F -NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T -NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T -NET_NMIN net rate of N mineralization gN/m^2/s T -NET_NMIN_vr net rate of N mineralization gN/m^3/s F -NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T -NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F -O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F -OBU Monin-Obukhov length m F -OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T -O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T -PARVEGLN absorbed par by vegetation at local noon W/m^2 T -PAS_SOMC PAS_SOM C gC/m^2 T -PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F -PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F -PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F -PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F -PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T -PAS_SOMN PAS_SOM N gN/m^2 T -PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F -PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F -PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F -PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F -PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T -PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F -PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F -PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T -PCH4 atmospheric partial pressure of CH4 Pa T -PCO2 atmospheric partial pressure of CO2 Pa T -POTENTIAL_IMMOB potential N immobilization gN/m^2/s T -POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F -POT_F_DENIT potential denitrification flux gN/m^2/s T -POT_F_DENIT_vr potential denitrification flux gN/m^3/s F -POT_F_NIT potential nitrification flux gN/m^2/s T -POT_F_NIT_vr potential nitrification flux gN/m^3/s F -PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F -Q2M 2m specific humidity kg/kg T -QAF canopy air humidity kg/kg F -QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T -QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F -QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F -QDRAI sub-surface drainage mm/s T -QDRAI_PERCH perched wt drainage mm/s T -QDRAI_XS saturation excess drainage mm/s T -QDRIP rate of excess canopy liquid falling off canopy mm/s F -QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F -QFLOOD runoff from river flooding mm/s T -QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T -QFLX_EVAP_VEG vegetation evaporation mm H2O/s F -QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T -QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T -QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T -QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T -QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F -QFLX_SNOW_DRAIN drainage from snow pack mm/s T -QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T -QFLX_SNOW_GRND snow on ground after interception mm H2O/s F -QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T -QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T -QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F -QH2OSFC surface water runoff mm/s T -QH2OSFC_TO_ICE surface water converted to ice mm/s F -QHR hydraulic redistribution mm/s T -QICE ice growth/melt mm/s T -QICE_FORC qice forcing sent to GLC mm/s F -QICE_FRZ ice growth mm/s T -QICE_MELT ice melt mm/s T -QINFL infiltration mm/s T -QINTR interception mm/s T -QIRRIG_DEMAND irrigation demand mm/s F -QIRRIG_DRIP water added via drip irrigation mm/s F -QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T -QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T -QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T -QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F -QOVER total surface runoff (includes QH2OSFC) mm/s T -QOVER_LAG time-lagged surface runoff for soil columns mm/s F -QPHSNEG net negative hydraulic redistribution flux mm/s F -QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T -QROOTSINK water flux from soil to root in each soil-layer mm/s F -QRUNOFF total liquid runoff not including correction for land use change mm/s T -QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T -QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T -QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F -QRUNOFF_R Rural total runoff mm/s F -QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T -QRUNOFF_U Urban total runoff mm/s F -QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T -QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T -QSNOFRZ column-integrated snow freezing rate kg/m2/s T -QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T -QSNOMELT snow melt rate mm/s T -QSNOMELT_ICE snow melt (ice landunits only) mm/s T -QSNOUNLOAD canopy snow unloading mm/s T -QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T -QSNO_WINDUNLOAD canopy snow wind unloading mm/s T -QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T -QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T -QSOIL_ICE Ground evaporation (ice landunits only) mm/s T -QTOPSOIL water input to surface mm/s F -QVEGE canopy evaporation mm/s T -QVEGT canopy transpiration mm/s T -Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F -Qh sensible heat W/m^2 F -Qle total evaporation W/m^2 F -Qstor storage heat flux (includes snowmelt) W/m^2 F -Qtau momentum flux kg/m/s^2 F -RAH1 aerodynamical resistance s/m F -RAH2 aerodynamical resistance s/m F -RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T -RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T -RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F -RAW1 aerodynamical resistance s/m F -RAW2 aerodynamical resistance s/m F -RB leaf boundary resistance s/m F -RH atmospheric relative humidity % F -RH2M 2m relative humidity % T -RH2M_R Rural 2m specific humidity % F -RH2M_U Urban 2m relative humidity % F -RHAF fractional humidity of canopy air fraction F -RH_LEAF fractional humidity at leaf surface fraction F -RSCANOPY canopy resistance s m-1 T -RSSHA shaded leaf stomatal resistance s/m T -RSSUN sunlit leaf stomatal resistance s/m T -Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F -Rnet net radiation W/m^2 F -S1_PATHFRAC_S2_vr PATHFRAC from active soil organic to slow soil organic ma fraction F -S1_PATHFRAC_S3_vr PATHFRAC from active soil organic to passive soil organic fraction F -S1_RESP_FRAC_S2_vr respired from active soil organic to slow soil organic ma fraction F -S1_RESP_FRAC_S3_vr respired from active soil organic to passive soil organic fraction F -S2_PATHFRAC_S1_vr PATHFRAC from slow soil organic ma to active soil organic fraction F -S2_PATHFRAC_S3_vr PATHFRAC from slow soil organic ma to passive soil organic fraction F -S2_RESP_FRAC_S1_vr respired from slow soil organic ma to active soil organic fraction F -S2_RESP_FRAC_S3_vr respired from slow soil organic ma to passive soil organic fraction F -S3_PATHFRAC_S1_vr PATHFRAC from passive soil organic to active soil organic fraction F -S3_RESP_FRAC_S1_vr respired from passive soil organic to active soil organic fraction F -SABG solar rad absorbed by ground W/m^2 T -SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T -SABV solar rad absorbed by veg W/m^2 T -SLO_SOMC SLO_SOM C gC/m^2 T -SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F -SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F -SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F -SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F -SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F -SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F -SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T -SLO_SOMN SLO_SOM N gN/m^2 T -SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F -SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F -SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F -SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F -SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F -SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F -SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T -SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F -SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F -SMINN soil mineral N gN/m^2 T -SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T -SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F -SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -SMINN_vr soil mineral N gN/m^3 T -SMIN_NH4 soil mineral NH4 gN/m^2 T -SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F -SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T -SMIN_NO3 soil mineral NO3 gN/m^2 T -SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T -SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F -SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F -SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T -SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F -SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F -SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T -SMP soil matric potential (natural vegetated and crop landunits only) mm T -SNOBCMCL mass of BC in snow column kg/m2 T -SNOBCMSL mass of BC in top snow layer kg/m2 T -SNOCAN intercepted snow mm T -SNODSTMCL mass of dust in snow column kg/m2 T -SNODSTMSL mass of dust in top snow layer kg/m2 T -SNOFSDSND direct nir incident solar radiation on snow W/m^2 F -SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F -SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F -SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F -SNOFSRND direct nir reflected solar radiation from snow W/m^2 T -SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T -SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T -SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T -SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T -SNOLIQFL top snow layer liquid water fraction (land) fraction F -SNOOCMCL mass of OC in snow column kg/m2 T -SNOOCMSL mass of OC in top snow layer kg/m2 T -SNORDSL top snow layer effective grain radius m^-6 F -SNOTTOPL snow temperature (top layer) K F -SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F -SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T -SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F -SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T -SNOWDP gridcell mean snow height m T -SNOWICE snow ice kg/m2 T -SNOWICE_ICE snow ice (ice landunits only) kg/m2 F -SNOWLIQ snow liquid water kg/m2 T -SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F -SNOW_5D 5day snow avg m F -SNOW_DEPTH snow height of snow covered area m T -SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F -SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T -SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T -SNOW_SINKS snow sinks (liquid water) mm/s T -SNOW_SOURCES snow sources (liquid water) mm/s T -SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F -SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F -SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F -SNO_FRZ snow freezing rate in each snow layer kg/m2/s F -SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F -SNO_GS Mean snow grain size Microns F -SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F -SNO_ICE Snow ice content kg/m2 F -SNO_LIQH2O Snow liquid water content kg/m2 F -SNO_MELT snow melt rate in each snow layer mm/s F -SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F -SNO_T Snow temperatures K F -SNO_TK Thermal conductivity W/m-K F -SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F -SNO_T_ICE Snow temperatures (ice landunits only) K F -SNO_Z Snow layer thicknesses m F -SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F -SNOdTdzL top snow layer temperature gradient (land) K/m F -SOIL10 10-day running mean of 12cm layer soil K F -SOILC_HR soil C heterotrophic respiration gC/m^2/s T -SOILC_vr SOIL C (vertically resolved) gC/m^3 T -SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T -SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T -SOILN_vr SOIL N (vertically resolved) gN/m^3 T -SOILPSI soil water potential in each soil layer MPa F -SOILRESIS soil resistance to evaporation s/m T -SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T -SOMC_FIRE C loss due to peat burning gC/m^2/s T -SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T -SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T -SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -SWBGT 2 m Simplified Wetbulb Globe Temp C T -SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T -SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -SWdown atmospheric incident solar radiation W/m^2 F -SWup upwelling shortwave radiation W/m^2 F -SoilAlpha factor limiting ground evap unitless F -SoilAlpha_U urban factor limiting ground evap unitless F -T10 10-day running mean of 2-m temperature K F -TAF canopy air temperature K F -TAUX zonal surface stress kg/m/s^2 T -TAUY meridional surface stress kg/m/s^2 T -TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T -TBUILD internal urban building air temperature K T -TBUILD_MAX prescribed maximum interior building temperature K F -TFLOOR floor temperature K F -TG ground temperature K T -TG_ICE ground temperature (ice landunits only) K F -TG_R Rural ground temperature K F -TG_U Urban ground temperature K F -TH2OSFC surface water temperature K T -THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -TKE1 top lake level eddy thermal conductivity W/(mK) T -TLAI total projected leaf area index m^2/m^2 T -TLAKE lake temperature K T -TOPO_COL column-level topographic height m F -TOPO_COL_ICE column-level topographic height (ice landunits only) m F -TOPO_FORC topograephic height sent to GLC m F -TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T -TOTLITC total litter carbon gC/m^2 T -TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T -TOTLITN total litter N gN/m^2 T -TOTLITN_1m total litter N to 1 meter gN/m^2 T -TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T -TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T -TOTSOMC total soil organic matter carbon gC/m^2 T -TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T -TOTSOMN total soil organic matter N gN/m^2 T -TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F -TREFMNAV daily minimum of average 2-m temperature K T -TREFMNAV_R Rural daily minimum of average 2-m temperature K F -TREFMNAV_U Urban daily minimum of average 2-m temperature K F -TREFMXAV daily maximum of average 2-m temperature K T -TREFMXAV_R Rural daily maximum of average 2-m temperature K F -TREFMXAV_U Urban daily maximum of average 2-m temperature K F -TROOF_INNER roof inside surface temperature K F -TSA 2m air temperature K T -TSAI total projected stem area index m^2/m^2 T -TSA_ICE 2m air temperature (ice landunits only) K F -TSA_R Rural 2m air temperature K F -TSA_U Urban 2m air temperature K F -TSHDW_INNER shadewall inside surface temperature K F -TSKIN skin temperature K T -TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -TSOI soil temperature (natural vegetated and crop landunits only) K T -TSOI_10CM soil temperature in top 10cm of soil K T -TSOI_ICE soil temperature (ice landunits only) K T -TSRF_FORC surface temperature sent to GLC K F -TSUNW_INNER sunwall inside surface temperature K F -TV vegetation temperature K T -TV24 vegetation temperature (last 24hrs) K F -TV240 vegetation temperature (last 240hrs) K F -TWS total water storage mm T -T_SCALAR temperature inhibition of decomposition unitless T -Tair atmospheric air temperature (downscaled to columns in glacier regions) K F -Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F -U10 10-m wind m/s T -U10_DUST 10-m wind for dust model m/s T -U10_ICE 10-m wind (ice landunits only) m/s F -UAF canopy air speed m/s F -UM wind speed plus stability effect m/s F -URBAN_AC urban air conditioning flux W/m^2 T -URBAN_HEAT urban heating flux W/m^2 T -USTAR aerodynamical resistance s/m F -UST_LAKE friction velocity (lakes only) m/s F -VA atmospheric wind speed plus convective velocity m/s F -VENTILATION sensible heat flux from building ventilation W/m^2 T -VOLR river channel total water storage m3 T -VOLRMCH river channel main channel water storage m3 T -VPD vpd Pa F -VPD2M 2m vapor pressure deficit Pa T -VPD_CAN canopy vapor pressure deficit kPa T -WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -WBT 2 m Stull Wet Bulb C T -WBT_R Rural 2 m Stull Wet Bulb C T -WBT_U Urban 2 m Stull Wet Bulb C T -WFPS WFPS percent F -WIND atmospheric wind velocity magnitude m/s T -WTGQ surface tracer conductance m/s T -W_SCALAR Moisture (dryness) inhibition of decomposition unitless T -Wind atmospheric wind velocity magnitude m/s F -Z0HG roughness length over ground, sensible heat (vegetated landunits only) m F -Z0MG roughness length over ground, momentum (vegetated landunits only) m F -Z0MV_DENSE roughness length over vegetation, momentum, for dense canopy m F -Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -Z0QG roughness length over ground, latent heat (vegetated landunits only) m F -ZBOT atmospheric reference height m T -ZETA dimensionless stability parameter unitless F -ZII convective boundary height m F -ZWT water table depth (natural vegetated and crop landunits only) m T -ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T -ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T -anaerobic_frac anaerobic_frac m3/m3 F -diffus diffusivity m^2/s F -fr_WFPS fr_WFPS fraction F -n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F -num_iter number of iterations unitless F -r_psi r_psi m F -ratio_k1 ratio_k1 none F -ratio_no3_co2 ratio_no3_co2 ratio F -soil_bulkdensity soil_bulkdensity kg/m3 F -soil_co2_prod soil_co2_prod ug C / g soil / day F -=================================== ============================================================================================== ================================================================= ======= +----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + Variable Name Level Dim. Long Description Units Active? +=================================== ================ ============================================================================================== ================================================================= ======= +A5TMIN - 5-day running mean of min 2-m temperature K F +ACTUAL_IMMOB - actual N immobilization gN/m^2/s T +ACTUAL_IMMOB_NH4 levdcmp immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 levdcmp immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr levdcmp actual N immobilization gN/m^3/s F +ACT_SOMC - ACT_SOM C gC/m^2 T +ACT_SOMC_1m - ACT_SOM C to 1 meter gC/m^2 F +ACT_SOMC_TNDNCY_VERT_TRA levdcmp active soil organic C tendency due to vertical transport gC/m^3/s F +ACT_SOMC_TO_PAS_SOMC - decomp. of active soil organic C to passive soil organic C gC/m^2/s F +ACT_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of active soil organic C to passive soil organic C gC/m^3/s F +ACT_SOMC_TO_SLO_SOMC - decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +ACT_SOMC_TO_SLO_SOMC_vr levdcmp decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +ACT_SOMC_vr levsoi ACT_SOM C (vertically resolved) gC/m^3 T +ACT_SOMN - ACT_SOM N gN/m^2 T +ACT_SOMN_1m - ACT_SOM N to 1 meter gN/m^2 F +ACT_SOMN_TNDNCY_VERT_TRA levdcmp active soil organic N tendency due to vertical transport gN/m^3/s F +ACT_SOMN_TO_PAS_SOMN - decomp. of active soil organic N to passive soil organic N gN/m^2 F +ACT_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of active soil organic N to passive soil organic N gN/m^3 F +ACT_SOMN_TO_SLO_SOMN - decomp. of active soil organic N to slow soil organic ma N gN/m^2 F +ACT_SOMN_TO_SLO_SOMN_vr levdcmp decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +ACT_SOMN_vr levdcmp ACT_SOM N (vertically resolved) gN/m^3 T +ACT_SOM_HR_S2 - Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S2_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +ACT_SOM_HR_S3 - Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S3_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +AGLB - Aboveground leaf biomass kg/m^2 F +AGSB - Aboveground stem biomass kg/m^2 F +ALBD numrad surface albedo (direct) proportion F +ALBGRD numrad ground albedo (direct) proportion F +ALBGRI numrad ground albedo (indirect) proportion F +ALBI numrad surface albedo (indirect) proportion F +ALT - current active layer thickness m F +ALTMAX - maximum annual active layer thickness m F +ALTMAX_LASTYEAR - maximum prior year active layer thickness m F +ATM_O3 - atmospheric ozone partial pressure mol/mol F +ATM_TOPO - atmospheric surface height m T +AnnET - Annual ET mm/s F +BCDEP - total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BTRAN - transpiration beta factor unitless T +BTRANMN - daily minimum of transpiration beta factor unitless T +CEL_LITC - CEL_LIT C gC/m^2 T +CEL_LITC_1m - CEL_LIT C to 1 meter gC/m^2 F +CEL_LITC_TNDNCY_VERT_TRA levdcmp cellulosic litter C tendency due to vertical transport gC/m^3/s F +CEL_LITC_TO_ACT_SOMC - decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +CEL_LITC_TO_ACT_SOMC_vr levdcmp decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +CEL_LITC_vr levsoi CEL_LIT C (vertically resolved) gC/m^3 T +CEL_LITN - CEL_LIT N gN/m^2 T +CEL_LITN_1m - CEL_LIT N to 1 meter gN/m^2 F +CEL_LITN_TNDNCY_VERT_TRA levdcmp cellulosic litter N tendency due to vertical transport gN/m^3/s F +CEL_LITN_TO_ACT_SOMN - decomp. of cellulosic litter N to active soil organic N gN/m^2 F +CEL_LITN_TO_ACT_SOMN_vr levdcmp decomp. of cellulosic litter N to active soil organic N gN/m^3 F +CEL_LITN_vr levdcmp CEL_LIT N (vertically resolved) gN/m^3 T +CEL_LIT_HR - Het. Resp. from cellulosic litter gC/m^2/s F +CEL_LIT_HR_vr levdcmp Het. Resp. from cellulosic litter gC/m^3/s F +CH4PROD - Gridcell total production of CH4 gC/m2/s T +CH4_EBUL_TOTAL_SAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_EBUL_TOTAL_UNSAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_SURF_AERE_SAT - aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T +CH4_SURF_AERE_UNSAT - aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_SAT - diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_UNSAT - diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_SAT - ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_UNSAT - ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +COL_CTRUNC - column-level sink for C truncation gC/m^2 F +COL_NTRUNC - column-level sink for N truncation gN/m^2 F +CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F +CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T +COSZEN - cosine of solar zenith angle none F +CWDC_HR - cwd C heterotrophic respiration gC/m^2/s T +DENIT - total rate of denitrification gN/m^2/s T +DGNETDT - derivative of net ground heat flux wrt soil temp W/m^2/K F +DISPLA - displacement height (vegetated landunits only) m F +DPVLTRB1 - turbulent deposition velocity 1 m/s F +DPVLTRB2 - turbulent deposition velocity 2 m/s F +DPVLTRB3 - turbulent deposition velocity 3 m/s F +DPVLTRB4 - turbulent deposition velocity 4 m/s F +DSL - dry surface layer thickness mm T +DSTDEP - total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTFLXT - total surface dust emission kg/m2/s T +DYN_COL_ADJUSTMENTS_CH4 - Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_C - Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_N - Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NH4 - Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NO3 - Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +EFLXBUILD - building heat flux from change in interior building air temperature W/m^2 T +EFLX_DYNBAL - dynamic land cover change conversion energy flux W/m^2 T +EFLX_GNET - net heat flux into ground W/m^2 F +EFLX_GRND_LAKE - net heat flux into lake/snow surface, excluding light transmission W/m^2 T +EFLX_LH_TOT - total latent heat flux [+ to atm] W/m^2 T +EFLX_LH_TOT_ICE - total latent heat flux [+ to atm] (ice landunits only) W/m^2 F +EFLX_LH_TOT_R - Rural total evaporation W/m^2 T +EFLX_LH_TOT_U - Urban total evaporation W/m^2 F +EFLX_SOIL_GRND - soil heat flux [+ into soil] W/m^2 F +ELAI - exposed one-sided leaf area index m^2/m^2 T +ERRH2O - total water conservation error mm T +ERRH2OSNO - imbalance in snow depth (liquid water) mm T +ERRSEB - surface energy conservation error W/m^2 T +ERRSOI - soil/lake energy conservation error W/m^2 T +ERRSOL - solar radiation conservation error W/m^2 T +ESAI - exposed one-sided stem area index m^2/m^2 T +FATES_ABOVEGROUND_MORT_SZPF fates_levscpf Aboveground flux of carbon from AGB to necromass due to mortality kg m-2 s-1 F +FATES_ABOVEGROUND_PROD_SZPF fates_levscpf Aboveground carbon productivity kg m-2 s-1 F +FATES_AGSAPMAINTAR_SZPF fates_levscpf above-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F +FATES_AGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to above-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AGSTRUCT_ALLOC_SZPF fates_levscpf allocation to above-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AR - autotrophic respiration gC/m^2/s T +FATES_AREA_PLANTS - area occupied by all plants per m2 land area m2 m-2 T +FATES_AREA_TREES - area occupied by woody plants per m2 land area m2 m-2 T +FATES_AR_CANOPY - autotrophic respiration of canopy plants gC/m^2/s T +FATES_AR_UNDERSTORY - autotrophic respiration of understory plants gC/m^2/s T +FATES_AUTORESP - autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_AUTORESP_CANOPY - autotrophic respiration of canopy plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_AUTORESP_CANOPY_SZPF fates_levscpf autotrophic respiration of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AUTORESP_SECONDARY - autotrophic respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_AUTORESP_SZPF fates_levscpf total autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_AUTORESP_USTORY - autotrophic respiration of understory plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_AUTORESP_USTORY_SZPF fates_levscpf autotrophic respiration of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BASALAREA_SZ fates_levscls basal area by size class m2 m-2 T +FATES_BASALAREA_SZPF fates_levscpf basal area by pft/size m2 m-2 F +FATES_BA_WEIGHTED_HEIGHT - basal area-weighted mean height of woody plants m T +FATES_BGSAPMAINTAR_SZPF fates_levscpf below-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F +FATES_BGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to below-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BGSTRUCT_ALLOC_SZPF fates_levscpf allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BURNFRAC - burned area fraction per second s-1 T +FATES_BURNFRAC_AP fates_levage spitfire fraction area burnt (per second) by patch age s-1 T +FATES_C13DISC_SZPF fates_levscpf C13 discrimination by pft/size per mil F +FATES_CANOPYAREA_AP fates_levage canopy area by age bin per m2 land area m2 m-2 T +FATES_CANOPYAREA_HT fates_levheight canopy area height distribution m2 m-2 T +FATES_CANOPYCROWNAREA_PF fates_levpft total PFT-level canopy-layer crown area per m2 land area m2 m-2 T +FATES_CANOPY_SPREAD - scaling factor (0-1) between tree basal area and canopy area T +FATES_CANOPY_VEGC - biomass of canopy plants in kg carbon per m2 land area kg m-2 T +FATES_CA_WEIGHTED_HEIGHT - crown area-weighted mean height of canopy plants m T +FATES_CBALANCE_ERROR - total carbon error in kg carbon per second kg s-1 T +FATES_COLD_STATUS - site-level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not too cold T +FATES_CROOTMAINTAR - live coarse root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_CROOTMAINTAR_CANOPY_SZ fates_levscls live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F +FATES_CROOTMAINTAR_USTORY_SZ fates_levscls live coarse root maintenance autotrophic respiration for understory plants in kg carbon per m2 kg m-2 s-1 F +FATES_CROOT_ALLOC - allocation to coarse roots in kg carbon per m2 per second kg m-2 s-1 T +FATES_CROWNAREA_CANOPY_SZ fates_levscls total crown area of canopy plants by size class m2 m-2 F +FATES_CROWNAREA_CL fates_levcan total crown area in each canopy layer m2 m-2 T +FATES_CROWNAREA_CLLL fates_levcnlf total crown area that is occupied by leaves in each canopy and leaf layer m2 m-2 F +FATES_CROWNAREA_PF fates_levpft total PFT-level crown area per m2 land area m2 m-2 T +FATES_CROWNAREA_USTORY_SZ fates_levscls total crown area of understory plants by size class m2 m-2 F +FATES_CWD_ABOVEGROUND_DC fates_levcwdsc debris class-level aboveground coarse woody debris stocks in kg carbon per m2 kg m-2 F +FATES_CWD_ABOVEGROUND_IN_DC fates_levcwdsc debris class-level aboveground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_ABOVEGROUND_OUT_DC fates_levcwdsc debris class-level aboveground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_BELOWGROUND_DC fates_levcwdsc debris class-level belowground coarse woody debris stocks in kg carbon per m2 kg m-2 F +FATES_CWD_BELOWGROUND_IN_DC fates_levcwdsc debris class-level belowground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_BELOWGROUND_OUT_DC fates_levcwdsc debris class-level belowground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F +FATES_DAYSINCE_COLDLEAFOFF - site-level days elapsed since cold leaf drop days T +FATES_DAYSINCE_COLDLEAFON - site-level days elapsed since cold leaf flush days T +FATES_DAYSINCE_DROUGHTLEAFOFF_PF fates_levpft PFT-level days elapsed since drought leaf drop days T +FATES_DAYSINCE_DROUGHTLEAFON_PF fates_levpft PFT-level days elapsed since drought leaf flush days T +FATES_DDBH_CANOPY_SZ fates_levscls diameter growth increment by size of canopy plants m m-2 yr-1 T +FATES_DDBH_CANOPY_SZAP fates_levscag growth rate of canopy plants in meters DBH per m2 per year in canopy in each size x age class m m-2 yr-1 F +FATES_DDBH_CANOPY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F +FATES_DDBH_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F +FATES_DDBH_USTORY_SZ fates_levscls diameter growth increment by size of understory plants m m-2 yr-1 T +FATES_DDBH_USTORY_SZAP fates_levscag growth rate of understory plants in meters DBH per m2 per year in each size x age class m m-2 yr-1 F +FATES_DDBH_USTORY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F +FATES_DEMOTION_CARBONFLUX - demotion-associated biomass carbon flux from canopy to understory in kg carbon per m2 per seco kg m-2 s-1 T +FATES_DEMOTION_RATE_SZ fates_levscls demotion rate from canopy to understory by size class in number of plants per m2 per year m-2 yr-1 F +FATES_DISTURBANCE_RATE_FIRE - disturbance rate from fire m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_LOGGING - disturbance rate from logging m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_P2P - disturbance rate from primary to primary lands m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_P2S - disturbance rate from primary to secondary lands m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_POTENTIAL - potential (i.e., including unresolved) disturbance rate m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_S2S - disturbance rate from secondary to secondary lands m2 m-2 yr-1 T +FATES_DISTURBANCE_RATE_TREEFALL - disturbance rate from treefall m2 m-2 yr-1 T +FATES_DROUGHT_STATUS_PF fates_levpft PFT-level drought status, <2 too dry for leaves, >=2 not too dry T +FATES_EFFECT_WSPEED - effective wind speed for fire spread in meters per second m s-1 T +FATES_ELONG_FACTOR_PF fates_levpft PFT-level mean elongation factor (partial flushing/abscission) 1 T +FATES_ERROR_EL fates_levelem total mass-balance error in kg per second by element kg s-1 T +FATES_EXCESS_RESP - respiration of un-allocatable carbon gain kg m-2 s-1 T +FATES_FABD_SHA_CLLL fates_levcnlf shade fraction of direct light absorbed by each canopy and leaf layer 1 F +FATES_FABD_SHA_CLLLPF fates_levcnlfpf shade fraction of direct light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABD_SHA_TOPLF_CL fates_levcan shade fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABD_SUN_CLLL fates_levcnlf sun fraction of direct light absorbed by each canopy and leaf layer 1 F +FATES_FABD_SUN_CLLLPF fates_levcnlfpf sun fraction of direct light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABD_SUN_TOPLF_CL fates_levcan sun fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABI_SHA_CLLL fates_levcnlf shade fraction of indirect light absorbed by each canopy and leaf layer 1 F +FATES_FABI_SHA_CLLLPF fates_levcnlfpf shade fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABI_SHA_TOPLF_CL fates_levcan shade fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABI_SUN_CLLL fates_levcnlf sun fraction of indirect light absorbed by each canopy and leaf layer 1 F +FATES_FABI_SUN_CLLLPF fates_levcnlfpf sun fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABI_SUN_TOPLF_CL fates_levcan sun fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FDI - Fire Danger Index (probability that an ignition will lead to a fire) 1 T +FATES_FIRE_CLOSS - carbon loss to atmosphere from fire in kg carbon per m2 per second kg m-2 s-1 T +FATES_FIRE_FLUX_EL fates_levelem loss to atmosphere from fire by element in kg element per m2 per s kg m-2 s-1 T +FATES_FIRE_INTENSITY - spitfire surface fireline intensity in J per m per second J m-1 s-1 T +FATES_FIRE_INTENSITY_BURNFRAC - product of surface fire intensity and burned area fraction -- divide by FATES_BURNFRAC to get J m-1 s-1 T +FATES_FIRE_INTENSITY_BURNFRAC_AP fates_levage product of fire intensity and burned fraction, resolved by patch age (so divide by FATES_BURNF J m-1 s-1 T +FATES_FRACTION - total gridcell fraction which FATES is running over m2 m-2 T +FATES_FRAGMENTATION_SCALER_SL levsoi factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T +FATES_FROOTC - total biomass in live plant fine roots in kg carbon per m2 kg m-2 T +FATES_FROOTCTURN_CANOPY_SZ fates_levscls fine root turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOTCTURN_USTORY_SZ fates_levscls fine root turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_FROOTC_SL levsoi Total carbon in live plant fine-roots over depth kg m-3 T +FATES_FROOTC_SZPF fates_levscpf fine-root carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_FROOTMAINTAR - fine root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_FROOTMAINTAR_CANOPY_SZ fates_levscls live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F +FATES_FROOTMAINTAR_SZPF fates_levscpf fine root maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_FROOTMAINTAR_USTORY_SZ fates_levscls fine root maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F +FATES_FROOT_ALLOC - allocation to fine roots in kg carbon per m2 per second kg m-2 s-1 T +FATES_FROOT_ALLOC_CANOPY_SZ fates_levscls allocation to fine root C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOT_ALLOC_SZPF fates_levscpf allocation to fine roots by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOT_ALLOC_USTORY_SZ fates_levscls allocation to fine roots for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FUELCONSUMED - total fuel consumed in kg carbon per m2 land area kg m-2 T +FATES_FUEL_AMOUNT - total ground fuel related to FATES_ROS (omits 1000hr fuels) in kg C per m2 land area kg m-2 T +FATES_FUEL_AMOUNT_AP fates_levage spitfire ground fuel (kg carbon per m2) related to FATES_ROS (omits 1000hr fuels) within each kg m-2 T +FATES_FUEL_AMOUNT_APFC fates_levagefuel spitfire fuel quantity in each age x fuel class in kg carbon per m2 land area kg m-2 F +FATES_FUEL_AMOUNT_FC fates_levfuel spitfire fuel-class level fuel amount in kg carbon per m2 land area kg m-2 T +FATES_FUEL_BULKD - fuel bulk density in kg per m3 kg m-3 T +FATES_FUEL_BURNT_BURNFRAC_FC fates_levfuel product of fraction (0-1) of fuel burnt and burnt fraction (divide by FATES_BURNFRAC to get bu 1 T +FATES_FUEL_EFF_MOIST - spitfire fuel moisture (volumetric) m3 m-3 T +FATES_FUEL_MEF - fuel moisture of extinction (volumetric) m3 m-3 T +FATES_FUEL_MOISTURE_FC fates_levfuel spitfire fuel class-level fuel moisture (volumetric) m3 m-3 T +FATES_FUEL_SAV - spitfire fuel surface area to volume ratio m-1 T +FATES_GDD - site-level growing degree days degree_Celsius T +FATES_GPP - gross primary production in kg carbon per m2 per second kg m-2 s-1 T +FATES_GPP_AP fates_levage gross primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_CANOPY - gross primary production of canopy plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_GPP_CANOPY_SZPF fates_levscpf gross primary production of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_GPP_SECONDARY - gross primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_GPP_SE_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T +FATES_GPP_SZPF fates_levscpf gross primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_USTORY - gross primary production of understory plants in kg carbon per m2 per second kg m-2 s-1 T +FATES_GPP_USTORY_SZPF fates_levscpf gross primary production of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GROWAR_CANOPY_SZ fates_levscls growth autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_GROWAR_SZPF fates_levscpf growth autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_GROWAR_USTORY_SZ fates_levscls growth autotrophic respiration of understory plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_GROWTHFLUX_FUSION_SZPF fates_levscpf flux of individuals into a given size class bin via fusion m-2 yr-1 F +FATES_GROWTHFLUX_SZPF fates_levscpf flux of individuals into a given size class bin via growth and recruitment m-2 yr-1 F +FATES_GROWTH_RESP - growth respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_GROWTH_RESP_SECONDARY - growth respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_HARVEST_CARBON_FLUX - harvest carbon flux in kg carbon per m2 per year kg m-2 yr-1 T +FATES_HARVEST_DEBT - Accumulated carbon failed to be harvested kg C T +FATES_HARVEST_DEBT_SEC - Accumulated carbon failed to be harvested from secondary patches kg C T +FATES_HET_RESP - heterotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_IGNITIONS - number of successful fire ignitions per m2 land area per second m-2 s-1 T +FATES_LAI - leaf area index per m2 land area m2 m-2 T +FATES_LAISHA_TOP_CL fates_levcan LAI in the shade by the top leaf layer of each canopy layer m2 m-2 F +FATES_LAISHA_Z_CLLL fates_levcnlf LAI in the shade by each canopy and leaf layer m2 m-2 F +FATES_LAISHA_Z_CLLLPF fates_levcnlfpf LAI in the shade by each canopy, leaf, and PFT m2 m-2 F +FATES_LAISUN_TOP_CL fates_levcan LAI in the sun by the top leaf layer of each canopy layer m2 m-2 F +FATES_LAISUN_Z_CLLL fates_levcnlf LAI in the sun by each canopy and leaf layer m2 m-2 F +FATES_LAISUN_Z_CLLLPF fates_levcnlfpf LAI in the sun by each canopy, leaf, and PFT m2 m-2 F +FATES_LAI_AP fates_levage leaf area index by age bin per m2 land area m2 m-2 T +FATES_LAI_CANOPY_SZ fates_levscls leaf area index (LAI) of canopy plants by size class m2 m-2 T +FATES_LAI_CANOPY_SZPF fates_levscpf Leaf area index (LAI) of canopy plants by pft/size m2 m-2 F +FATES_LAI_SECONDARY - leaf area index per m2 land area, secondary patches m2 m-2 T +FATES_LAI_USTORY_SZ fates_levscls leaf area index (LAI) of understory plants by size class m2 m-2 T +FATES_LAI_USTORY_SZPF fates_levscpf Leaf area index (LAI) of understory plants by pft/size m2 m-2 F +FATES_LBLAYER_COND - mean leaf boundary layer conductance mol m-2 s-1 T +FATES_LBLAYER_COND_AP fates_levage mean leaf boundary layer conductance - by patch age mol m-2 s-1 F +FATES_LEAFAREA_HT fates_levheight leaf area height distribution m2 m-2 T +FATES_LEAFC - total biomass in live plant leaves in kg carbon per m2 kg m-2 T +FATES_LEAFCTURN_CANOPY_SZ fates_levscls leaf turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAFCTURN_USTORY_SZ fates_levscls leaf turnover (non-mortal) for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAFC_CANOPY_SZPF fates_levscpf biomass in leaves of canopy plants by pft/size in kg carbon per m2 kg m-2 F +FATES_LEAFC_PF fates_levpft total PFT-level leaf biomass in kg carbon per m2 land area kg m-2 T +FATES_LEAFC_SZPF fates_levscpf leaf carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_LEAFC_USTORY_SZPF fates_levscpf biomass in leaves of understory plants by pft/size in kg carbon per m2 kg m-2 F +FATES_LEAFMAINTAR - leaf maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_LEAF_ALLOC - allocation to leaves in kg carbon per m2 per second kg m-2 s-1 T +FATES_LEAF_ALLOC_CANOPY_SZ fates_levscls allocation to leaves for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAF_ALLOC_SZPF fates_levscpf allocation to leaves by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAF_ALLOC_USTORY_SZ fates_levscls allocation to leaves for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LITTER_AG_CWD_EL fates_levelem mass of aboveground litter in coarse woody debris (trunks/branches/twigs) by element kg m-2 T +FATES_LITTER_AG_FINE_EL fates_levelem mass of aboveground litter in fines (leaves, nonviable seed) by element kg m-2 T +FATES_LITTER_BG_CWD_EL fates_levelem mass of belowground litter in coarse woody debris (coarse roots) by element kg m-2 T +FATES_LITTER_BG_FINE_EL fates_levelem mass of belowground litter in fines (fineroots) by element kg m-2 T +FATES_LITTER_CWD_ELDC fates_levelcwd total mass of litter in coarse woody debris by element and coarse woody debris size kg m-2 T +FATES_LITTER_IN - litter flux in kg carbon per m2 per second kg m-2 s-1 T +FATES_LITTER_IN_EL fates_levelem litter flux in in kg element per m2 per second kg m-2 s-1 T +FATES_LITTER_OUT - litter flux out in kg carbon (exudation, fragmentation, seed decay) kg m-2 s-1 T +FATES_LITTER_OUT_EL fates_levelem litter flux out (exudation, fragmentation and seed decay) in kg element kg m-2 s-1 T +FATES_LSTEMMAINTAR - live stem maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T +FATES_LSTEMMAINTAR_CANOPY_SZ fates_levscls live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1 F +FATES_LSTEMMAINTAR_USTORY_SZ fates_levscls live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F +FATES_M3_MORTALITY_CANOPY_SZ fates_levscls C starvation mortality of canopy plants by size N/ha/yr F +FATES_M3_MORTALITY_CANOPY_SZPF fates_levscpf C starvation mortality of canopy plants by pft/size N/ha/yr F +FATES_M3_MORTALITY_USTORY_SZ fates_levscls C starvation mortality of understory plants by size N/ha/yr F +FATES_M3_MORTALITY_USTORY_SZPF fates_levscpf C starvation mortality of understory plants by pft/size N/ha/yr F +FATES_MAINTAR_CANOPY_SZ fates_levscls maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_MAINTAR_SZPF fates_levscpf maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_MAINTAR_USTORY_SZ fates_levscls maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1 F +FATES_MAINT_RESP - maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T +FATES_MAINT_RESP_SECONDARY - maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_MAINT_RESP_UNREDUCED - diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 F +FATES_MEANLIQVOL_DROUGHTPHEN_PF fates_levpft PFT-level mean liquid water volume for drought phenolgy m3 m-3 T +FATES_MEANSMP_DROUGHTPHEN_PF fates_levpft PFT-level mean soil matric potential for drought phenology Pa T +FATES_MORTALITY_AGESCEN_AC fates_levcacls age senescence mortality by cohort age in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_AGESCEN_ACPF fates_levcapf age senescence mortality by pft/cohort age in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_AGESCEN_SE_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_AGESCEN_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_AGESCEN_SZPF fates_levscpf age senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_BACKGROUND_SE_SZ fates_levscls background mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_BACKGROUND_SZ fates_levscls background mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_BACKGROUND_SZPF fates_levscpf background mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CAMBIALBURN_SZPF fates_levscpf fire mortality from cambial burn by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CANOPY_SE_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2, secondary patches m-2 yr-1 T +FATES_MORTALITY_CANOPY_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2 m-2 yr-1 T +FATES_MORTALITY_CANOPY_SZAP fates_levscag mortality rate of canopy plants in number of plants per m2 per year in each size x age class m-2 yr-1 F +FATES_MORTALITY_CANOPY_SZPF fates_levscpf total mortality of canopy plants by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CFLUX_CANOPY - flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1 T +FATES_MORTALITY_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from mortality kg m-2 s-1 T +FATES_MORTALITY_CFLUX_USTORY - flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1 T +FATES_MORTALITY_CROWNSCORCH_SZPF fates_levscpf fire mortality from crown scorch by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CSTARV_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality kg m-2 s-1 T +FATES_MORTALITY_CSTARV_SE_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_CSTARV_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_CSTARV_SZPF fates_levscpf carbon starvation mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_FIRE_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from fire mortality kg m-2 s-1 T +FATES_MORTALITY_FIRE_SZ fates_levscls fire mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_FIRE_SZPF fates_levscpf fire mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_FREEZING_SE_SZ fates_levscls freezing mortality by size in number of plants per m2 per event, secondary patches m-2 event-1 T +FATES_MORTALITY_FREEZING_SZ fates_levscls freezing mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_FREEZING_SZPF fates_levscpf freezing mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_HYDRAULIC_SE_SZ fates_levscls hydraulic mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_HYDRAULIC_SZ fates_levscls hydraulic mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_HYDRAULIC_SZPF fates_levscpf hydraulic mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_HYDRO_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality kg m-2 s-1 T +FATES_MORTALITY_IMPACT_SZ fates_levscls impact mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_IMPACT_SZPF fates_levscpf impact mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_LOGGING_SE_SZ fates_levscls logging mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T +FATES_MORTALITY_LOGGING_SZ fates_levscls logging mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_LOGGING_SZPF fates_levscpf logging mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_PF fates_levpft PFT-level mortality rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SE_SZ fates_levscls senescence mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SZ fates_levscls senescence mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SZPF fates_levscpf senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_TERMINATION_SZ fates_levscls termination mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_TERMINATION_SZPF fates_levscpf termination mortality by pft/size in number pf plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_USTORY_SZ fates_levscls total mortality of understory trees by size class in individuals per m2 per year m-2 yr-1 T +FATES_MORTALITY_USTORY_SZAP fates_levscag mortality rate of understory plants in number of plants per m2 per year in each size x age cla m-2 yr-1 F +FATES_MORTALITY_USTORY_SZPF fates_levscpf total mortality of understory plants by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_NCHILLDAYS - site-level number of chill days days T +FATES_NCL_AP fates_levage number of canopy levels by age bin F +FATES_NCOHORTS - total number of cohorts per site T +FATES_NCOHORTS_SECONDARY - total number of cohorts per site T +FATES_NCOLDDAYS - site-level number of cold days days T +FATES_NEP - net ecosystem production in kg carbon per m2 per second kg m-2 s-1 T +FATES_NESTEROV_INDEX - nesterov fire danger index T +FATES_NET_C_UPTAKE_CLLL fates_levcnlf net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1 F +FATES_NONSTRUCTC - non-structural biomass (sapwood + leaf + fineroot) in kg carbon per m2 kg m-2 T +FATES_NPATCHES - total number of patches per site T +FATES_NPATCHES_SECONDARY - total number of patches per site T +FATES_NPATCH_AP fates_levage number of patches by age bin F +FATES_NPLANT_AC fates_levcacls number of plants per m2 by cohort age class m-2 T +FATES_NPLANT_ACPF fates_levcapf stem number density by pft and age class m-2 F +FATES_NPLANT_CANOPY_SZ fates_levscls number of canopy plants per m2 by size class m-2 T +FATES_NPLANT_CANOPY_SZAP fates_levscag number of plants per m2 in canopy in each size x age class m-2 F +FATES_NPLANT_CANOPY_SZPF fates_levscpf number of canopy plants by size/pft per m2 m-2 F +FATES_NPLANT_PF fates_levpft total PFT-level number of individuals per m2 land area m-2 T +FATES_NPLANT_SEC_PF fates_levpft total PFT-level number of individuals per m2 land area, secondary patches m-2 T +FATES_NPLANT_SZ fates_levscls number of plants per m2 by size class m-2 T +FATES_NPLANT_SZAP fates_levscag number of plants per m2 in each size x age class m-2 F +FATES_NPLANT_SZAPPF fates_levscagpf number of plants per m2 in each size x age x pft class m-2 F +FATES_NPLANT_SZPF fates_levscpf stem number density by pft/size m-2 F +FATES_NPLANT_USTORY_SZ fates_levscls number of understory plants per m2 by size class m-2 T +FATES_NPLANT_USTORY_SZAP fates_levscag number of plants per m2 in understory in each size x age class m-2 F +FATES_NPLANT_USTORY_SZPF fates_levscpf density of understory plants by pft/size in number of plants per m2 m-2 F +FATES_NPP - net primary production in kg carbon per m2 per second kg m-2 s-1 T +FATES_NPP_AP fates_levage net primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_APPF fates_levagepft NPP per PFT in each age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_CANOPY_SZ fates_levscls NPP of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second kg m-2 yr-1 T +FATES_NPP_SECONDARY - net primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T +FATES_NPP_SE_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 yr-1 T +FATES_NPP_SZPF fates_levscpf total net primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_USTORY_SZ fates_levscls NPP of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_PARPROF_DIF_CLLL fates_levcnlf radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F +FATES_PARPROF_DIF_CLLLPF fates_levcnlfpf radiative profile of diffuse PAR through each canopy, leaf, and PFT W m-2 F +FATES_PARPROF_DIR_CLLL fates_levcnlf radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F +FATES_PARPROF_DIR_CLLLPF fates_levcnlfpf radiative profile of direct PAR through each canopy, leaf, and PFT W m-2 F +FATES_PARSHA_Z_CL fates_levcan PAR absorbed in the shade by top leaf layer in each canopy layer W m-2 F +FATES_PARSHA_Z_CLLL fates_levcnlf PAR absorbed in the shade by each canopy and leaf layer W m-2 F +FATES_PARSHA_Z_CLLLPF fates_levcnlfpf PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F +FATES_PARSUN_Z_CL fates_levcan PAR absorbed in the sun by top leaf layer in each canopy layer W m-2 F +FATES_PARSUN_Z_CLLL fates_levcnlf PAR absorbed in the sun by each canopy and leaf layer W m-2 F +FATES_PARSUN_Z_CLLLPF fates_levcnlfpf PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F +FATES_PATCHAREA_AP fates_levage patch area by age bin per m2 land area m2 m-2 T +FATES_PRIMARY_PATCHFUSION_ERR - error in total primary lands associated with patch fusion m2 m-2 yr-1 T +FATES_PROMOTION_CARBONFLUX - promotion-associated biomass carbon flux from understory to canopy in kg carbon per m2 per sec kg m-2 s-1 T +FATES_PROMOTION_RATE_SZ fates_levscls promotion rate from understory to canopy by size class m-2 yr-1 F +FATES_RAD_ERROR - radiation error in FATES RTM W m-2 T +FATES_RDARK_CANOPY_SZ fates_levscls dark respiration for canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_RDARK_SZPF fates_levscpf dark portion of maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_RDARK_USTORY_SZ fates_levscls dark respiration for understory plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_RECRUITMENT_PF fates_levpft PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_REPROC - total biomass in live plant reproductive tissues in kg carbon per m2 kg m-2 T +FATES_REPROC_SZPF fates_levscpf reproductive carbon mass (on plant) by size-class x pft in kg carbon per m2 kg m-2 F +FATES_ROS - fire rate of spread in meters per second m s-1 T +FATES_SAI_CANOPY_SZ fates_levscls stem area index (SAI) of canopy plants by size class m2 m-2 F +FATES_SAI_USTORY_SZ fates_levscls stem area index (SAI) of understory plants by size class m2 m-2 F +FATES_SAPWOODC - total biomass in live plant sapwood in kg carbon per m2 kg m-2 T +FATES_SAPWOODCTURN_CANOPY_SZ fates_levscls sapwood turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SAPWOODCTURN_USTORY_SZ fates_levscls sapwood C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_SAPWOODC_SZPF fates_levscpf sapwood carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_SAPWOOD_ALLOC_CANOPY_SZ fates_levscls allocation to sapwood C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SAPWOOD_ALLOC_USTORY_SZ fates_levscls allocation to sapwood C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SCORCH_HEIGHT_APPF fates_levagepft SPITFIRE flame Scorch Height (calculated per PFT in each patch age bin) m F +FATES_SECONDAREA_ANTHRODIST_AP fates_levage secondary forest patch area age distribution since anthropgenic disturbance m2 m-2 F +FATES_SECONDAREA_DIST_AP fates_levage secondary forest patch area age distribution since any kind of disturbance m2 m-2 F +FATES_SECONDARY_FOREST_FRACTION - secondary forest fraction m2 m-2 T +FATES_SECONDARY_FOREST_VEGC - biomass on secondary lands in kg carbon per m2 land area (mult by FATES_SECONDARY_FOREST_FRACT kg m-2 T +FATES_SEEDS_IN - seed production rate in kg carbon per m2 second kg m-2 s-1 T +FATES_SEEDS_IN_EXTERN_EL fates_levelem external seed influx rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEEDS_IN_LOCAL_EL fates_levelem within-site, element-level seed production rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEED_ALLOC - allocation to seeds in kg carbon per m2 per second kg m-2 s-1 T +FATES_SEED_ALLOC_CANOPY_SZ fates_levscls allocation to reproductive C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_ALLOC_SZPF fates_levscpf allocation to seeds by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_ALLOC_USTORY_SZ fates_levscls allocation to reproductive C for understory plants by size class in kg carbon per m2 per secon kg m-2 s-1 F +FATES_SEED_BANK - total seed mass of all PFTs in kg carbon per m2 land area kg m-2 T +FATES_SEED_BANK_EL fates_levelem element-level total seed mass of all PFTs in kg element per m2 kg m-2 T +FATES_SEED_DECAY_EL fates_levelem seed mass decay (germinated and un-germinated) in kg element per m2 per second kg m-2 s-1 T +FATES_SEED_GERM_EL fates_levelem element-level total germinated seed mass of all PFTs in kg element per m2 kg m-2 T +FATES_SEED_PROD_CANOPY_SZ fates_levscls seed production of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_PROD_USTORY_SZ fates_levscls seed production of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STEM_ALLOC - allocation to stem in kg carbon per m2 per second kg m-2 s-1 T +FATES_STOMATAL_COND - mean stomatal conductance mol m-2 s-1 T +FATES_STOMATAL_COND_AP fates_levage mean stomatal conductance - by patch age mol m-2 s-1 F +FATES_STOREC - total biomass in live plant storage in kg carbon per m2 land area kg m-2 T +FATES_STORECTURN_CANOPY_SZ fates_levscls storage turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORECTURN_USTORY_SZ fates_levscls storage C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_STOREC_CANOPY_SZPF fates_levscpf biomass in storage pools of canopy plants by pft/size in kg carbon per m2 kg m-2 F +FATES_STOREC_PF fates_levpft total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T +FATES_STOREC_SZPF fates_levscpf storage carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_STOREC_TF - Storage C fraction of target kg kg-1 T +FATES_STOREC_TF_CANOPY_SZPF fates_levscpf Storage C fraction of target by size x pft, in the canopy kg kg-1 F +FATES_STOREC_TF_USTORY_SZPF fates_levscpf Storage C fraction of target by size x pft, in the understory kg kg-1 F +FATES_STOREC_USTORY_SZPF fates_levscpf biomass in storage pools of understory plants by pft/size in kg carbon per m2 kg m-2 F +FATES_STORE_ALLOC - allocation to storage tissues in kg carbon per m2 per second kg m-2 s-1 T +FATES_STORE_ALLOC_CANOPY_SZ fates_levscls allocation to storage C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORE_ALLOC_SZPF fates_levscpf allocation to storage C by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORE_ALLOC_USTORY_SZ fates_levscls allocation to storage C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STRUCTC - structural biomass in kg carbon per m2 land area kg m-2 T +FATES_STRUCTCTURN_CANOPY_SZ fates_levscls structural C turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per sec kg m-2 s-1 F +FATES_STRUCTCTURN_USTORY_SZ fates_levscls structural C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per kg m-2 s-1 F +FATES_STRUCT_ALLOC_CANOPY_SZ fates_levscls allocation to structural C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STRUCT_ALLOC_USTORY_SZ fates_levscls allocation to structural C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_TGROWTH - fates long-term running mean vegetation temperature by site degree_Celsius F +FATES_TLONGTERM - fates 30-year running mean vegetation temperature by site degree_Celsius F +FATES_TRIMMING - degree to which canopy expansion is limited by leaf economics (0-1) 1 T +FATES_TRIMMING_CANOPY_SZ fates_levscls trimming term of canopy plants weighted by plant density, by size class m-2 F +FATES_TRIMMING_USTORY_SZ fates_levscls trimming term of understory plants weighted by plant density, by size class m-2 F +FATES_TVEG - fates instantaneous mean vegetation temperature by site degree_Celsius T +FATES_TVEG24 - fates 24-hr running mean vegetation temperature by site degree_Celsius T +FATES_USTORY_VEGC - biomass of understory plants in kg carbon per m2 land area kg m-2 T +FATES_VEGC - total biomass in live plants in kg carbon per m2 land area kg m-2 T +FATES_VEGC_ABOVEGROUND - aboveground biomass in kg carbon per m2 land area kg m-2 T +FATES_VEGC_ABOVEGROUND_SZ fates_levscls aboveground biomass by size class in kg carbon per m2 kg m-2 T +FATES_VEGC_ABOVEGROUND_SZPF fates_levscpf aboveground biomass by pft/size in kg carbon per m2 kg m-2 F +FATES_VEGC_AP fates_levage total biomass within a given patch age bin in kg carbon per m2 land area kg m-2 F +FATES_VEGC_APPF fates_levagepft biomass per PFT in each age bin in kg carbon per m2 kg m-2 F +FATES_VEGC_PF fates_levpft total PFT-level biomass in kg of carbon per land area kg m-2 T +FATES_VEGC_SE_PF fates_levpft total PFT-level biomass in kg of carbon per land area, secondary patches kg m-2 T +FATES_VEGC_SZ fates_levscls total biomass by size class in kg carbon per m2 kg m-2 F +FATES_VEGC_SZPF fates_levscpf total vegetation biomass in live plants by size-class x pft in kg carbon per m2 kg m-2 F +FATES_WOOD_PRODUCT - total wood product from logging in kg carbon per m2 land area kg m-2 T +FATES_YESTCANLEV_CANOPY_SZ fates_levscls yesterdays canopy level for canopy plants by size class in number of plants per m2 m-2 F +FATES_YESTCANLEV_USTORY_SZ fates_levscls yesterdays canopy level for understory plants by size class in number of plants per m2 m-2 F +FATES_ZSTAR_AP fates_levage product of zstar and patch area by age bin (divide by FATES_PATCHAREA_AP to get mean zstar) m F +FATES_c_to_litr_cel_c levdcmp litter celluluse carbon flux from FATES to BGC gC/m^3/s T +FATES_c_to_litr_lab_c levdcmp litter labile carbon flux from FATES to BGC gC/m^3/s T +FATES_c_to_litr_lig_c levdcmp litter lignin carbon flux from FATES to BGC gC/m^3/s T +FCEV - canopy evaporation W/m^2 T +FCH4 - Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T +FCH4TOCO2 - Gridcell oxidation of CH4 to CO2 gC/m2/s T +FCH4_DFSAT - CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T +FCO2 - CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F +FCOV - fractional impermeable area unitless T +FCTR - canopy transpiration W/m^2 T +FGEV - ground evaporation W/m^2 T +FGR - heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T +FGR12 - heat flux between soil layers 1 and 2 W/m^2 T +FGR_ICE - heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F +FGR_R - Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F +FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F +FGR_U - Urban heat flux into soil/snow including snow melt W/m^2 F +FH2OSFC - fraction of ground covered by surface water unitless T +FH2OSFC_NOSNOW - fraction of ground covered by surface water (if no snow present) unitless F +FINUNDATED - fractional inundated area of vegetated columns unitless T +FINUNDATED_LAG - time-lagged inundated fraction of vegetated columns unitless F +FIRA - net infrared (longwave) radiation W/m^2 T +FIRA_ICE - net infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRA_R - Rural net infrared (longwave) radiation W/m^2 T +FIRA_U - Urban net infrared (longwave) radiation W/m^2 F +FIRE - emitted infrared (longwave) radiation W/m^2 T +FIRE_ICE - emitted infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRE_R - Rural emitted infrared (longwave) radiation W/m^2 T +FIRE_U - Urban emitted infrared (longwave) radiation W/m^2 F +FLDS - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T +FLDS_ICE - atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FMAX_DENIT_CARBONSUBSTRATE levdcmp FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE levdcmp FMAX_DENIT_NITRATE gN/m^3/s F +FROST_TABLE - frost table depth (natural vegetated and crop landunits only) m F +FSA - absorbed solar radiation W/m^2 T +FSAT - fractional area with water table at surface unitless T +FSA_ICE - absorbed solar radiation (ice landunits only) W/m^2 F +FSA_R - Rural absorbed solar radiation W/m^2 F +FSA_U - Urban absorbed solar radiation W/m^2 F +FSD24 - direct radiation (last 24hrs) K F +FSD240 - direct radiation (last 240hrs) K F +FSDS - atmospheric incident solar radiation W/m^2 T +FSDSND - direct nir incident solar radiation W/m^2 T +FSDSNDLN - direct nir incident solar radiation at local noon W/m^2 T +FSDSNI - diffuse nir incident solar radiation W/m^2 T +FSDSVD - direct vis incident solar radiation W/m^2 T +FSDSVDLN - direct vis incident solar radiation at local noon W/m^2 T +FSDSVI - diffuse vis incident solar radiation W/m^2 T +FSDSVILN - diffuse vis incident solar radiation at local noon W/m^2 T +FSH - sensible heat not including correction for land use change and rain/snow conversion W/m^2 T +FSH_G - sensible heat from ground W/m^2 T +FSH_ICE - sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F +FSH_PRECIP_CONVERSION - Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T +FSH_R - Rural sensible heat W/m^2 T +FSH_RUNOFF_ICE_TO_LIQ - sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T +FSH_TO_COUPLER - sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T +FSH_U - Urban sensible heat W/m^2 F +FSH_V - sensible heat from veg W/m^2 T +FSI24 - indirect radiation (last 24hrs) K F +FSI240 - indirect radiation (last 240hrs) K F +FSM - snow melt heat flux W/m^2 T +FSM_ICE - snow melt heat flux (ice landunits only) W/m^2 F +FSM_R - Rural snow melt heat flux W/m^2 F +FSM_U - Urban snow melt heat flux W/m^2 F +FSNO - fraction of ground covered by snow unitless T +FSNO_EFF - effective fraction of ground covered by snow unitless T +FSNO_ICE - fraction of ground covered by snow (ice landunits only) unitless F +FSR - reflected solar radiation W/m^2 T +FSRND - direct nir reflected solar radiation W/m^2 T +FSRNDLN - direct nir reflected solar radiation at local noon W/m^2 T +FSRNI - diffuse nir reflected solar radiation W/m^2 T +FSRVD - direct vis reflected solar radiation W/m^2 T +FSRVDLN - direct vis reflected solar radiation at local noon W/m^2 T +FSRVI - diffuse vis reflected solar radiation W/m^2 T +FSR_ICE - reflected solar radiation (ice landunits only) W/m^2 F +FSUN - sunlit fraction of canopy proportion F +FSUN24 - fraction sunlit (last 24hrs) K F +FSUN240 - fraction sunlit (last 240hrs) K F +F_DENIT - denitrification flux gN/m^2/s T +F_DENIT_BASE levdcmp F_DENIT_BASE gN/m^3/s F +F_DENIT_vr levdcmp denitrification flux gN/m^3/s F +F_N2O_DENIT - denitrification N2O flux gN/m^2/s T +F_N2O_NIT - nitrification N2O flux gN/m^2/s T +F_NIT - nitrification flux gN/m^2/s T +F_NIT_vr levdcmp nitrification flux gN/m^3/s F +GROSS_NMIN - gross rate of N mineralization gN/m^2/s T +GROSS_NMIN_vr levdcmp gross rate of N mineralization gN/m^3/s F +GSSHA - shaded leaf stomatal conductance umol H20/m2/s T +GSSHALN - shaded leaf stomatal conductance at local noon umol H20/m2/s T +GSSUN - sunlit leaf stomatal conductance umol H20/m2/s T +GSSUNLN - sunlit leaf stomatal conductance at local noon umol H20/m2/s T +H2OCAN - intercepted water mm T +H2OSFC - surface water depth mm T +H2OSNO - snow depth (liquid water) mm T +H2OSNO_ICE - snow depth (liquid water, ice landunits only) mm F +H2OSNO_TOP - mass of snow in top snow layer kg/m2 T +H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HBOT - canopy bottom m F +HEAT_CONTENT1 - initial gridcell total heat content J/m^2 T +HEAT_CONTENT1_VEG - initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F +HEAT_CONTENT2 - post land cover change total heat content J/m^2 F +HEAT_FROM_AC - sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T +HIA - 2 m NWS Heat Index C T +HIA_R - Rural 2 m NWS Heat Index C T +HIA_U - Urban 2 m NWS Heat Index C T +HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +HR - total heterotrophic respiration gC/m^2/s T +HR_vr levsoi total vertically resolved heterotrophic respiration gC/m^3/s T +HTOP - canopy top m T +HUMIDEX - 2 m Humidex C T +HUMIDEX_R - Rural 2 m Humidex C T +HUMIDEX_U - Urban 2 m Humidex C T +ICE_CONTENT1 - initial gridcell total ice content mm T +ICE_CONTENT2 - post land cover change total ice content mm F +ICE_MODEL_FRACTION - Ice sheet model fractional coverage unitless F +INT_SNOW - accumulated swe (natural vegetated and crop landunits only) mm F +INT_SNOW_ICE - accumulated swe (ice landunits only) mm F +IWUELN - local noon intrinsic water use efficiency umolCO2/molH2O T +KROOT levsoi root conductance each soil layer 1/s F +KSOIL levsoi soil conductance in each soil layer 1/s F +K_ACT_SOM levdcmp active soil organic potential loss coefficient 1/s F +K_CEL_LIT levdcmp cellulosic litter potential loss coefficient 1/s F +K_LIG_LIT levdcmp lignin litter potential loss coefficient 1/s F +K_MET_LIT levdcmp metabolic litter potential loss coefficient 1/s F +K_NITR levdcmp K_NITR 1/s F +K_NITR_H2O levdcmp K_NITR_H2O unitless F +K_NITR_PH levdcmp K_NITR_PH unitless F +K_NITR_T levdcmp K_NITR_T unitless F +K_PAS_SOM levdcmp passive soil organic potential loss coefficient 1/s F +K_SLO_SOM levdcmp slow soil organic ma potential loss coefficient 1/s F +L1_PATHFRAC_S1_vr levdcmp PATHFRAC from metabolic litter to active soil organic fraction F +L1_RESP_FRAC_S1_vr levdcmp respired from metabolic litter to active soil organic fraction F +L2_PATHFRAC_S1_vr levdcmp PATHFRAC from cellulosic litter to active soil organic fraction F +L2_RESP_FRAC_S1_vr levdcmp respired from cellulosic litter to active soil organic fraction F +L3_PATHFRAC_S2_vr levdcmp PATHFRAC from lignin litter to slow soil organic ma fraction F +L3_RESP_FRAC_S2_vr levdcmp respired from lignin litter to slow soil organic ma fraction F +LAI240 - 240hr average of leaf area index m^2/m^2 F +LAISHA - shaded projected leaf area index m^2/m^2 T +LAISUN - sunlit projected leaf area index m^2/m^2 T +LAKEICEFRAC levlak lake layer ice mass fraction unitless F +LAKEICEFRAC_SURF - surface lake layer ice mass fraction unitless T +LAKEICETHICK - thickness of lake ice (including physical expansion on freezing) m T +LIG_LITC - LIG_LIT C gC/m^2 T +LIG_LITC_1m - LIG_LIT C to 1 meter gC/m^2 F +LIG_LITC_TNDNCY_VERT_TRA levdcmp lignin litter C tendency due to vertical transport gC/m^3/s F +LIG_LITC_TO_SLO_SOMC - decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIG_LITC_TO_SLO_SOMC_vr levdcmp decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIG_LITC_vr levsoi LIG_LIT C (vertically resolved) gC/m^3 T +LIG_LITN - LIG_LIT N gN/m^2 T +LIG_LITN_1m - LIG_LIT N to 1 meter gN/m^2 F +LIG_LITN_TNDNCY_VERT_TRA levdcmp lignin litter N tendency due to vertical transport gN/m^3/s F +LIG_LITN_TO_SLO_SOMN - decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIG_LITN_TO_SLO_SOMN_vr levdcmp decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIG_LITN_vr levdcmp LIG_LIT N (vertically resolved) gN/m^3 T +LIG_LIT_HR - Het. Resp. from lignin litter gC/m^2/s F +LIG_LIT_HR_vr levdcmp Het. Resp. from lignin litter gC/m^3/s F +LIQCAN - intercepted liquid water mm T +LIQUID_CONTENT1 - initial gridcell total liq content mm T +LIQUID_CONTENT2 - post landuse change gridcell total liq content mm F +LIQUID_WATER_TEMP1 - initial gridcell weighted average liquid water temperature K F +LITTERC_HR - litter C heterotrophic respiration gC/m^2/s T +LNC - leaf N concentration gN leaf/m^2 T +LWdown - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWup - upwelling longwave radiation W/m^2 F +MET_LITC - MET_LIT C gC/m^2 T +MET_LITC_1m - MET_LIT C to 1 meter gC/m^2 F +MET_LITC_TNDNCY_VERT_TRA levdcmp metabolic litter C tendency due to vertical transport gC/m^3/s F +MET_LITC_TO_ACT_SOMC - decomp. of metabolic litter C to active soil organic C gC/m^2/s F +MET_LITC_TO_ACT_SOMC_vr levdcmp decomp. of metabolic litter C to active soil organic C gC/m^3/s F +MET_LITC_vr levsoi MET_LIT C (vertically resolved) gC/m^3 T +MET_LITN - MET_LIT N gN/m^2 T +MET_LITN_1m - MET_LIT N to 1 meter gN/m^2 F +MET_LITN_TNDNCY_VERT_TRA levdcmp metabolic litter N tendency due to vertical transport gN/m^3/s F +MET_LITN_TO_ACT_SOMN - decomp. of metabolic litter N to active soil organic N gN/m^2 F +MET_LITN_TO_ACT_SOMN_vr levdcmp decomp. of metabolic litter N to active soil organic N gN/m^3 F +MET_LITN_vr levdcmp MET_LIT N (vertically resolved) gN/m^3 T +MET_LIT_HR - Het. Resp. from metabolic litter gC/m^2/s F +MET_LIT_HR_vr levdcmp Het. Resp. from metabolic litter gC/m^3/s F +MORTALITY_CROWNAREA_CANOPY - Crown area of canopy trees that died m2/ha/year T +MORTALITY_CROWNAREA_UNDERSTORY - Crown aera of understory trees that died m2/ha/year T +M_ACT_SOMC_TO_LEACHING - active soil organic C leaching loss gC/m^2/s F +M_ACT_SOMN_TO_LEACHING - active soil organic N leaching loss gN/m^2/s F +M_CEL_LITC_TO_LEACHING - cellulosic litter C leaching loss gC/m^2/s F +M_CEL_LITN_TO_LEACHING - cellulosic litter N leaching loss gN/m^2/s F +M_LIG_LITC_TO_LEACHING - lignin litter C leaching loss gC/m^2/s F +M_LIG_LITN_TO_LEACHING - lignin litter N leaching loss gN/m^2/s F +M_MET_LITC_TO_LEACHING - metabolic litter C leaching loss gC/m^2/s F +M_MET_LITN_TO_LEACHING - metabolic litter N leaching loss gN/m^2/s F +M_PAS_SOMC_TO_LEACHING - passive soil organic C leaching loss gC/m^2/s F +M_PAS_SOMN_TO_LEACHING - passive soil organic N leaching loss gN/m^2/s F +M_SLO_SOMC_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F +M_SLO_SOMN_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F +NDEP_TO_SMINN - atmospheric N deposition to soil mineral N gN/m^2/s T +NEM - Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T +NET_NMIN - net rate of N mineralization gN/m^2/s T +NET_NMIN_vr levdcmp net rate of N mineralization gN/m^3/s F +NFIX_TO_SMINN - symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T +NSUBSTEPS - number of adaptive timesteps in CLM timestep unitless F +O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F +OBU - Monin-Obukhov length m F +OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T +O_SCALAR levsoi fraction by which decomposition is reduced due to anoxia unitless T +PARVEGLN - absorbed par by vegetation at local noon W/m^2 T +PAS_SOMC - PAS_SOM C gC/m^2 T +PAS_SOMC_1m - PAS_SOM C to 1 meter gC/m^2 F +PAS_SOMC_TNDNCY_VERT_TRA levdcmp passive soil organic C tendency due to vertical transport gC/m^3/s F +PAS_SOMC_TO_ACT_SOMC - decomp. of passive soil organic C to active soil organic C gC/m^2/s F +PAS_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of passive soil organic C to active soil organic C gC/m^3/s F +PAS_SOMC_vr levsoi PAS_SOM C (vertically resolved) gC/m^3 T +PAS_SOMN - PAS_SOM N gN/m^2 T +PAS_SOMN_1m - PAS_SOM N to 1 meter gN/m^2 F +PAS_SOMN_TNDNCY_VERT_TRA levdcmp passive soil organic N tendency due to vertical transport gN/m^3/s F +PAS_SOMN_TO_ACT_SOMN - decomp. of passive soil organic N to active soil organic N gN/m^2 F +PAS_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of passive soil organic N to active soil organic N gN/m^3 F +PAS_SOMN_vr levdcmp PAS_SOM N (vertically resolved) gN/m^3 T +PAS_SOM_HR - Het. Resp. from passive soil organic gC/m^2/s F +PAS_SOM_HR_vr levdcmp Het. Resp. from passive soil organic gC/m^3/s F +PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PCH4 - atmospheric partial pressure of CH4 Pa T +PCO2 - atmospheric partial pressure of CO2 Pa T +POTENTIAL_IMMOB - potential N immobilization gN/m^2/s T +POTENTIAL_IMMOB_vr levdcmp potential N immobilization gN/m^3/s F +POT_F_DENIT - potential denitrification flux gN/m^2/s T +POT_F_DENIT_vr levdcmp potential denitrification flux gN/m^3/s F +POT_F_NIT - potential nitrification flux gN/m^2/s T +POT_F_NIT_vr levdcmp potential nitrification flux gN/m^3/s F +PSurf - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +Q2M - 2m specific humidity kg/kg T +QAF - canopy air humidity kg/kg F +QBOT - atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QDIRECT_THROUGHFALL - direct throughfall of liquid (rain + above-canopy irrigation) mm/s F +QDIRECT_THROUGHFALL_SNOW - direct throughfall of snow mm/s F +QDRAI - sub-surface drainage mm/s T +QDRAI_PERCH - perched wt drainage mm/s T +QDRAI_XS - saturation excess drainage mm/s T +QDRIP - rate of excess canopy liquid falling off canopy mm/s F +QDRIP_SNOW - rate of excess canopy snow falling off canopy mm/s F +QFLOOD - runoff from river flooding mm/s T +QFLX_EVAP_TOT - qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T +QFLX_EVAP_VEG - vegetation evaporation mm H2O/s F +QFLX_ICE_DYNBAL - ice dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQDEW_TO_TOP_LAYER - rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T +QFLX_LIQEVAP_FROM_TOP_LAYER - rate of liquid water evaporated from top soil or snow layer mm H2O/s T +QFLX_LIQ_DYNBAL - liq dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQ_GRND - liquid (rain+irrigation) on ground after interception mm H2O/s F +QFLX_SNOW_DRAIN - drainage from snow pack mm/s T +QFLX_SNOW_DRAIN_ICE - drainage from snow pack melt (ice landunits only) mm/s T +QFLX_SNOW_GRND - snow on ground after interception mm H2O/s F +QFLX_SOLIDDEW_TO_TOP_LAYER - rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER - rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE - rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F +QH2OSFC - surface water runoff mm/s T +QH2OSFC_TO_ICE - surface water converted to ice mm/s F +QHR - hydraulic redistribution mm/s T +QICE - ice growth/melt mm/s T +QICE_FORC elevclas qice forcing sent to GLC mm/s F +QICE_FRZ - ice growth mm/s T +QICE_MELT - ice melt mm/s T +QINFL - infiltration mm/s T +QINTR - interception mm/s T +QIRRIG_DEMAND - irrigation demand mm/s F +QIRRIG_DRIP - water added via drip irrigation mm/s F +QIRRIG_FROM_GW_CONFINED - water added through confined groundwater irrigation mm/s T +QIRRIG_FROM_GW_UNCONFINED - water added through unconfined groundwater irrigation mm/s T +QIRRIG_FROM_SURFACE - water added through surface water irrigation mm/s T +QIRRIG_SPRINKLER - water added via sprinkler irrigation mm/s F +QOVER - total surface runoff (includes QH2OSFC) mm/s T +QOVER_LAG - time-lagged surface runoff for soil columns mm/s F +QPHSNEG - net negative hydraulic redistribution flux mm/s F +QRGWL - surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T +QROOTSINK levsoi water flux from soil to root in each soil-layer mm/s F +QRUNOFF - total liquid runoff not including correction for land use change mm/s T +QRUNOFF_ICE - total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T +QRUNOFF_ICE_TO_COUPLER - total ice runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_ICE_TO_LIQ - liquid runoff from converted ice runoff mm/s F +QRUNOFF_R - Rural total runoff mm/s F +QRUNOFF_TO_COUPLER - total liquid runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_U - Urban total runoff mm/s F +QSNOCPLIQ - excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T +QSNOEVAP - evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T +QSNOFRZ - column-integrated snow freezing rate kg/m2/s T +QSNOFRZ_ICE - column-integrated snow freezing rate (ice landunits only) mm/s T +QSNOMELT - snow melt rate mm/s T +QSNOMELT_ICE - snow melt (ice landunits only) mm/s T +QSNOUNLOAD - canopy snow unloading mm/s T +QSNO_TEMPUNLOAD - canopy snow temp unloading mm/s T +QSNO_WINDUNLOAD - canopy snow wind unloading mm/s T +QSNWCPICE - excess solid h2o due to snow capping not including correction for land use change mm H2O/s T +QSOIL - Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T +QSOIL_ICE - Ground evaporation (ice landunits only) mm/s T +QTOPSOIL - water input to surface mm/s F +QVEGE - canopy evaporation mm/s T +QVEGT - canopy transpiration mm/s T +Qair - atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F +Qh - sensible heat W/m^2 F +Qle - total evaporation W/m^2 F +Qstor - storage heat flux (includes snowmelt) W/m^2 F +Qtau - momentum flux kg/m/s^2 F +RAH1 - aerodynamical resistance s/m F +RAH2 - aerodynamical resistance s/m F +RAIN - atmospheric rain, after rain/snow repartitioning based on temperature mm/s T +RAIN_FROM_ATM - atmospheric rain received from atmosphere (pre-repartitioning) mm/s T +RAIN_ICE - atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +RAM_LAKE - aerodynamic resistance for momentum (lakes only) s/m F +RAW1 - aerodynamical resistance s/m F +RAW2 - aerodynamical resistance s/m F +RB - leaf boundary resistance s/m F +RH - atmospheric relative humidity % F +RH2M - 2m relative humidity % T +RH2M_R - Rural 2m specific humidity % F +RH2M_U - Urban 2m relative humidity % F +RHAF - fractional humidity of canopy air fraction F +RH_LEAF - fractional humidity at leaf surface fraction F +RSCANOPY - canopy resistance s m-1 T +RSSHA - shaded leaf stomatal resistance s/m T +RSSUN - sunlit leaf stomatal resistance s/m T +Rainf - atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rnet - net radiation W/m^2 F +S1_PATHFRAC_S2_vr levdcmp PATHFRAC from active soil organic to slow soil organic ma fraction F +S1_PATHFRAC_S3_vr levdcmp PATHFRAC from active soil organic to passive soil organic fraction F +S1_RESP_FRAC_S2_vr levdcmp respired from active soil organic to slow soil organic ma fraction F +S1_RESP_FRAC_S3_vr levdcmp respired from active soil organic to passive soil organic fraction F +S2_PATHFRAC_S1_vr levdcmp PATHFRAC from slow soil organic ma to active soil organic fraction F +S2_PATHFRAC_S3_vr levdcmp PATHFRAC from slow soil organic ma to passive soil organic fraction F +S2_RESP_FRAC_S1_vr levdcmp respired from slow soil organic ma to active soil organic fraction F +S2_RESP_FRAC_S3_vr levdcmp respired from slow soil organic ma to passive soil organic fraction F +S3_PATHFRAC_S1_vr levdcmp PATHFRAC from passive soil organic to active soil organic fraction F +S3_RESP_FRAC_S1_vr levdcmp respired from passive soil organic to active soil organic fraction F +SABG - solar rad absorbed by ground W/m^2 T +SABG_PEN - Rural solar rad penetrating top soil or snow layer watt/m^2 T +SABV - solar rad absorbed by veg W/m^2 T +SLO_SOMC - SLO_SOM C gC/m^2 T +SLO_SOMC_1m - SLO_SOM C to 1 meter gC/m^2 F +SLO_SOMC_TNDNCY_VERT_TRA levdcmp slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SLO_SOMC_TO_ACT_SOMC - decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SLO_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SLO_SOMC_TO_PAS_SOMC - decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SLO_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SLO_SOMC_vr levsoi SLO_SOM C (vertically resolved) gC/m^3 T +SLO_SOMN - SLO_SOM N gN/m^2 T +SLO_SOMN_1m - SLO_SOM N to 1 meter gN/m^2 F +SLO_SOMN_TNDNCY_VERT_TRA levdcmp slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SLO_SOMN_TO_ACT_SOMN - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SLO_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SLO_SOMN_TO_PAS_SOMN - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F +SLO_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SLO_SOMN_vr levdcmp SLO_SOM N (vertically resolved) gN/m^3 T +SLO_SOM_HR_S1 - Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S1_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SLO_SOM_HR_S3 - Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S3_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SMINN - soil mineral N gN/m^2 T +SMINN_TO_PLANT - plant uptake of soil mineral N gN/m^2/s T +SMINN_TO_PLANT_vr levdcmp plant uptake of soil mineral N gN/m^3/s F +SMINN_TO_S1N_L1 - mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L1_vr levdcmp mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_L2 - mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L2_vr levdcmp mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S2 - mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S3 - mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S3_vr levdcmp mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S2N_L3 - mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +SMINN_TO_S2N_L3_vr levdcmp mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +SMINN_TO_S2N_S1 - mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +SMINN_TO_S2N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +SMINN_TO_S3N_S1 - mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +SMINN_TO_S3N_S2 - mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +SMINN_vr levsoi soil mineral N gN/m^3 T +SMIN_NH4 - soil mineral NH4 gN/m^2 T +SMIN_NH4_TO_PLANT levdcmp plant uptake of NH4 gN/m^3/s F +SMIN_NH4_vr levsoi soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3 - soil mineral NO3 gN/m^2 T +SMIN_NO3_LEACHED - soil NO3 pool loss to leaching gN/m^2/s T +SMIN_NO3_LEACHED_vr levdcmp soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS levdcmp SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF - soil NO3 pool loss to runoff gN/m^2/s T +SMIN_NO3_RUNOFF_vr levdcmp soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT levdcmp plant uptake of NO3 gN/m^3/s F +SMIN_NO3_vr levsoi soil mineral NO3 (vert. res.) gN/m^3 T +SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T +SNOBCMCL - mass of BC in snow column kg/m2 T +SNOBCMSL - mass of BC in top snow layer kg/m2 T +SNOCAN - intercepted snow mm T +SNODSTMCL - mass of dust in snow column kg/m2 T +SNODSTMSL - mass of dust in top snow layer kg/m2 T +SNOFSDSND - direct nir incident solar radiation on snow W/m^2 F +SNOFSDSNI - diffuse nir incident solar radiation on snow W/m^2 F +SNOFSDSVD - direct vis incident solar radiation on snow W/m^2 F +SNOFSDSVI - diffuse vis incident solar radiation on snow W/m^2 F +SNOFSRND - direct nir reflected solar radiation from snow W/m^2 T +SNOFSRNI - diffuse nir reflected solar radiation from snow W/m^2 T +SNOFSRVD - direct vis reflected solar radiation from snow W/m^2 T +SNOFSRVI - diffuse vis reflected solar radiation from snow W/m^2 T +SNOINTABS - Fraction of incoming solar absorbed by lower snow layers - T +SNOLIQFL - top snow layer liquid water fraction (land) fraction F +SNOOCMCL - mass of OC in snow column kg/m2 T +SNOOCMSL - mass of OC in top snow layer kg/m2 T +SNORDSL - top snow layer effective grain radius m^-6 F +SNOTTOPL - snow temperature (top layer) K F +SNOTTOPL_ICE - snow temperature (top layer, ice landunits only) K F +SNOTXMASS - snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +SNOTXMASS_ICE - snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +SNOW - atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +SNOWDP - gridcell mean snow height m T +SNOWICE - snow ice kg/m2 T +SNOWICE_ICE - snow ice (ice landunits only) kg/m2 F +SNOWLIQ - snow liquid water kg/m2 T +SNOWLIQ_ICE - snow liquid water (ice landunits only) kg/m2 F +SNOW_5D - 5day snow avg m F +SNOW_DEPTH - snow height of snow covered area m T +SNOW_DEPTH_ICE - snow height of snow covered area (ice landunits only) m F +SNOW_FROM_ATM - atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +SNOW_ICE - atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +SNOW_PERSISTENCE - Length of time of continuous snow cover (nat. veg. landunits only) seconds T +SNOW_SINKS - snow sinks (liquid water) mm/s T +SNOW_SOURCES - snow sources (liquid water) mm/s T +SNO_ABS levsno Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE levsno Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW levsno Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE levsno Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE levsno Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ levsno snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE levsno snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS levsno Mean snow grain size Microns F +SNO_GS_ICE levsno Mean snow grain size (ice landunits only) Microns F +SNO_ICE levsno Snow ice content kg/m2 F +SNO_LIQH2O levsno Snow liquid water content kg/m2 F +SNO_MELT levsno snow melt rate in each snow layer mm/s F +SNO_MELT_ICE levsno snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T levsno Snow temperatures K F +SNO_TK levsno Thermal conductivity W/m-K F +SNO_TK_ICE levsno Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE levsno Snow temperatures (ice landunits only) K F +SNO_Z levsno Snow layer thicknesses m F +SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F +SNOdTdzL - top snow layer temperature gradient (land) K/m F +SOIL10 - 10-day running mean of 12cm layer soil K F +SOILC_HR - soil C heterotrophic respiration gC/m^2/s T +SOILC_vr levsoi SOIL C (vertically resolved) gC/m^3 T +SOILICE levsoi soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ levsoi soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOILN_vr levdcmp SOIL N (vertically resolved) gN/m^3 T +SOILPSI levgrnd soil water potential in each soil layer MPa F +SOILRESIS - soil resistance to evaporation s/m T +SOILWATER_10CM - soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +SOMC_FIRE - C loss due to peat burning gC/m^2/s T +SOM_C_LEACHED - total flux of C from SOM pools due to leaching gC/m^2/s T +SOM_N_LEACHED - total flux of N from SOM pools due to leaching gN/m^2/s F +SUPPLEMENT_TO_SMINN - supplemental N supply gN/m^2/s T +SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F +SWBGT - 2 m Simplified Wetbulb Globe Temp C T +SWBGT_R - Rural 2 m Simplified Wetbulb Globe Temp C T +SWBGT_U - Urban 2 m Simplified Wetbulb Globe Temp C T +SWdown - atmospheric incident solar radiation W/m^2 F +SWup - upwelling shortwave radiation W/m^2 F +SoilAlpha - factor limiting ground evap unitless F +SoilAlpha_U - urban factor limiting ground evap unitless F +T10 - 10-day running mean of 2-m temperature K F +TAF - canopy air temperature K F +TAUX - zonal surface stress kg/m/s^2 T +TAUY - meridional surface stress kg/m/s^2 T +TBOT - atmospheric air temperature (downscaled to columns in glacier regions) K T +TBUILD - internal urban building air temperature K T +TBUILD_MAX - prescribed maximum interior building temperature K F +TFLOOR - floor temperature K F +TG - ground temperature K T +TG_ICE - ground temperature (ice landunits only) K F +TG_R - Rural ground temperature K F +TG_U - Urban ground temperature K F +TH2OSFC - surface water temperature K T +THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T +TKE1 - top lake level eddy thermal conductivity W/(mK) T +TLAI - total projected leaf area index m^2/m^2 T +TLAKE levlak lake temperature K T +TOPO_COL - column-level topographic height m F +TOPO_COL_ICE - column-level topographic height (ice landunits only) m F +TOPO_FORC elevclas topograephic height sent to GLC m F +TOTCOLCH4 - total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +TOTLITC - total litter carbon gC/m^2 T +TOTLITC_1m - total litter carbon to 1 meter depth gC/m^2 T +TOTLITN - total litter N gN/m^2 T +TOTLITN_1m - total litter N to 1 meter gN/m^2 T +TOTSOILICE - vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILLIQ - vertically summed soil liquid water (veg landunits only) kg/m2 T +TOTSOMC - total soil organic matter carbon gC/m^2 T +TOTSOMC_1m - total soil organic matter carbon to 1 meter depth gC/m^2 T +TOTSOMN - total soil organic matter N gN/m^2 T +TOTSOMN_1m - total soil organic matter N to 1 meter gN/m^2 T +TRAFFICFLUX - sensible heat flux from urban traffic W/m^2 F +TREFMNAV - daily minimum of average 2-m temperature K T +TREFMNAV_R - Rural daily minimum of average 2-m temperature K F +TREFMNAV_U - Urban daily minimum of average 2-m temperature K F +TREFMXAV - daily maximum of average 2-m temperature K T +TREFMXAV_R - Rural daily maximum of average 2-m temperature K F +TREFMXAV_U - Urban daily maximum of average 2-m temperature K F +TROOF_INNER - roof inside surface temperature K F +TSA - 2m air temperature K T +TSAI - total projected stem area index m^2/m^2 T +TSA_ICE - 2m air temperature (ice landunits only) K F +TSA_R - Rural 2m air temperature K F +TSA_U - Urban 2m air temperature K F +TSHDW_INNER - shadewall inside surface temperature K F +TSKIN - skin temperature K T +TSL - temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T +TSOI_10CM - soil temperature in top 10cm of soil K T +TSOI_ICE levgrnd soil temperature (ice landunits only) K T +TSRF_FORC elevclas surface temperature sent to GLC K F +TSUNW_INNER - sunwall inside surface temperature K F +TV - vegetation temperature K T +TV24 - vegetation temperature (last 24hrs) K F +TV240 - vegetation temperature (last 240hrs) K F +TWS - total water storage mm T +T_SCALAR levsoi temperature inhibition of decomposition unitless T +Tair - atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair_from_atm - atmospheric air temperature received from atmosphere (pre-downscaling) K F +U10 - 10-m wind m/s T +U10_DUST - 10-m wind for dust model m/s T +U10_ICE - 10-m wind (ice landunits only) m/s F +UAF - canopy air speed m/s F +UM - wind speed plus stability effect m/s F +URBAN_AC - urban air conditioning flux W/m^2 T +URBAN_HEAT - urban heating flux W/m^2 T +USTAR - aerodynamical resistance s/m F +UST_LAKE - friction velocity (lakes only) m/s F +VA - atmospheric wind speed plus convective velocity m/s F +VENTILATION - sensible heat flux from building ventilation W/m^2 T +VOLR - river channel total water storage m3 T +VOLRMCH - river channel main channel water storage m3 T +VPD - vpd Pa F +VPD2M - 2m vapor pressure deficit Pa T +VPD_CAN - canopy vapor pressure deficit kPa T +WASTEHEAT - sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +WBT - 2 m Stull Wet Bulb C T +WBT_R - Rural 2 m Stull Wet Bulb C T +WBT_U - Urban 2 m Stull Wet Bulb C T +WFPS levdcmp WFPS percent F +WIND - atmospheric wind velocity magnitude m/s T +WTGQ - surface tracer conductance m/s T +W_SCALAR levsoi Moisture (dryness) inhibition of decomposition unitless T +Wind - atmospheric wind velocity magnitude m/s F +Z0HG - roughness length over ground, sensible heat (vegetated landunits only) m F +Z0MG - roughness length over ground, momentum (vegetated landunits only) m F +Z0MV_DENSE - roughness length over vegetation, momentum, for dense canopy m F +Z0M_TO_COUPLER - roughness length, momentum: gridcell average sent to coupler m F +Z0QG - roughness length over ground, latent heat (vegetated landunits only) m F +ZBOT - atmospheric reference height m T +ZETA - dimensionless stability parameter unitless F +ZII - convective boundary height m F +ZWT - water table depth (natural vegetated and crop landunits only) m T +ZWT_CH4_UNSAT - depth of water table for methane production used in non-inundated area m T +ZWT_PERCH - perched water table depth (natural vegetated and crop landunits only) m T +anaerobic_frac levdcmp anaerobic_frac m3/m3 F +diffus levdcmp diffusivity m^2/s F +fr_WFPS levdcmp fr_WFPS fraction F +n2_n2o_ratio_denit levdcmp n2_n2o_ratio_denit gN/gN F +num_iter - number of iterations unitless F +r_psi levdcmp r_psi m F +ratio_k1 levdcmp ratio_k1 none F +ratio_no3_co2 levdcmp ratio_no3_co2 ratio F +soil_bulkdensity levdcmp soil_bulkdensity kg/m3 F +soil_co2_prod levdcmp soil_co2_prod ug C / g soil / day F +=================================== ================ ============================================================================================== ================================================================= ======= diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 1eb450b0b6..95f2b976e8 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -8,1281 +8,1281 @@ use_cn = T use_crop = T use_fates = F -=================================== ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- - Variable Name Long Description Units Active? -=================================== ============================================================================================== ================================================================= ======= -A10TMIN 10-day running mean of min 2-m temperature K F -A5TMIN 5-day running mean of min 2-m temperature K F -ACTUAL_IMMOB actual N immobilization gN/m^2/s T -ACTUAL_IMMOB_NH4 immobilization of NH4 gN/m^3/s F -ACTUAL_IMMOB_NO3 immobilization of NO3 gN/m^3/s F -ACTUAL_IMMOB_vr actual N immobilization gN/m^3/s F -ACT_SOMC ACT_SOM C gC/m^2 T -ACT_SOMC_1m ACT_SOM C to 1 meter gC/m^2 F -ACT_SOMC_TNDNCY_VERT_TRA active soil organic C tendency due to vertical transport gC/m^3/s F -ACT_SOMC_TO_PAS_SOMC decomp. of active soil organic C to passive soil organic C gC/m^2/s F -ACT_SOMC_TO_PAS_SOMC_vr decomp. of active soil organic C to passive soil organic C gC/m^3/s F -ACT_SOMC_TO_SLO_SOMC decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F -ACT_SOMC_TO_SLO_SOMC_vr decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F -ACT_SOMC_vr ACT_SOM C (vertically resolved) gC/m^3 T -ACT_SOMN ACT_SOM N gN/m^2 T -ACT_SOMN_1m ACT_SOM N to 1 meter gN/m^2 F -ACT_SOMN_TNDNCY_VERT_TRA active soil organic N tendency due to vertical transport gN/m^3/s F -ACT_SOMN_TO_PAS_SOMN decomp. of active soil organic N to passive soil organic N gN/m^2 F -ACT_SOMN_TO_PAS_SOMN_vr decomp. of active soil organic N to passive soil organic N gN/m^3 F -ACT_SOMN_TO_SLO_SOMN decomp. of active soil organic N to slow soil organic ma N gN/m^2 F -ACT_SOMN_TO_SLO_SOMN_vr decomp. of active soil organic N to slow soil organic ma N gN/m^3 F -ACT_SOMN_vr ACT_SOM N (vertically resolved) gN/m^3 T -ACT_SOM_HR_S2 Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S2_vr Het. Resp. from active soil organic gC/m^3/s F -ACT_SOM_HR_S3 Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S3_vr Het. Resp. from active soil organic gC/m^3/s F -AGLB Aboveground leaf biomass kg/m^2 F -AGNPP aboveground NPP gC/m^2/s T -AGSB Aboveground stem biomass kg/m^2 F -ALBD surface albedo (direct) proportion F -ALBGRD ground albedo (direct) proportion F -ALBGRI ground albedo (indirect) proportion F -ALBI surface albedo (indirect) proportion F -ALPHA alpha coefficient for VOC calc non F -ALT current active layer thickness m T -ALTMAX maximum annual active layer thickness m T -ALTMAX_LASTYEAR maximum prior year active layer thickness m F -ANNAVG_T2M annual average 2m air temperature K F -ANNMAX_RETRANSN annual max of retranslocated N pool gN/m^2 F -ANNSUM_COUNTER seconds since last annual accumulator turnover s F -ANNSUM_NPP annual sum of NPP gC/m^2/yr F -ANNSUM_POTENTIAL_GPP annual sum of potential GPP gN/m^2/yr F -AR autotrophic respiration (MR + GR) gC/m^2/s T -ATM_O3 atmospheric ozone partial pressure mol/mol F -ATM_TOPO atmospheric surface height m T -AVAILC C flux available for allocation gC/m^2/s F -AVAIL_RETRANSN N flux available from retranslocation pool gN/m^2/s F -AnnET Annual ET mm/s F -BAF_CROP fractional area burned for crop s-1 T -BAF_PEATF fractional area burned in peatland s-1 T -BCDEP total BC deposition (dry+wet) from atmosphere kg/m^2/s T -BETA coefficient of convective velocity none F -BGLFR background litterfall rate 1/s F -BGNPP belowground NPP gC/m^2/s T -BGTR background transfer growth rate 1/s F -BTRANMN daily minimum of transpiration beta factor unitless T -CANNAVG_T2M annual average of 2m air temperature K F -CANNSUM_NPP annual sum of column-level NPP gC/m^2/s F -CEL_LITC CEL_LIT C gC/m^2 T -CEL_LITC_1m CEL_LIT C to 1 meter gC/m^2 F -CEL_LITC_TNDNCY_VERT_TRA cellulosic litter C tendency due to vertical transport gC/m^3/s F -CEL_LITC_TO_ACT_SOMC decomp. of cellulosic litter C to active soil organic C gC/m^2/s F -CEL_LITC_TO_ACT_SOMC_vr decomp. of cellulosic litter C to active soil organic C gC/m^3/s F -CEL_LITC_vr CEL_LIT C (vertically resolved) gC/m^3 T -CEL_LITN CEL_LIT N gN/m^2 T -CEL_LITN_1m CEL_LIT N to 1 meter gN/m^2 F -CEL_LITN_TNDNCY_VERT_TRA cellulosic litter N tendency due to vertical transport gN/m^3/s F -CEL_LITN_TO_ACT_SOMN decomp. of cellulosic litter N to active soil organic N gN/m^2 F -CEL_LITN_TO_ACT_SOMN_vr decomp. of cellulosic litter N to active soil organic N gN/m^3 F -CEL_LITN_vr CEL_LIT N (vertically resolved) gN/m^3 T -CEL_LIT_HR Het. Resp. from cellulosic litter gC/m^2/s F -CEL_LIT_HR_vr Het. Resp. from cellulosic litter gC/m^3/s F -CGRND deriv. of soil energy flux wrt to soil temp W/m^2/K F -CGRNDL deriv. of soil latent heat flux wrt soil temp W/m^2/K F -CGRNDS deriv. of soil sensible heat flux wrt soil temp W/m^2/K F -CH4PROD Gridcell total production of CH4 gC/m2/s T -CH4_EBUL_TOTAL_SAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_EBUL_TOTAL_UNSAT ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_SURF_AERE_SAT aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T -CH4_SURF_AERE_UNSAT aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_SAT diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_UNSAT diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_SAT ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_UNSAT ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -COL_CTRUNC column-level sink for C truncation gC/m^2 F -COL_FIRE_CLOSS total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T -COL_FIRE_NLOSS total column-level fire N loss gN/m^2/s T -COL_NTRUNC column-level sink for N truncation gN/m^2 F -CONC_CH4_SAT CH4 soil Concentration for inundated / lake area mol/m3 F -CONC_CH4_UNSAT CH4 soil Concentration for non-inundated area mol/m3 F -CONC_O2_SAT O2 soil Concentration for inundated / lake area mol/m3 T -CONC_O2_UNSAT O2 soil Concentration for non-inundated area mol/m3 T -COST_NACTIVE Cost of active uptake gN/gC T -COST_NFIX Cost of fixation gN/gC T -COST_NRETRANS Cost of retranslocation gN/gC T -COSZEN cosine of solar zenith angle none F -CPHASE crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T -CPOOL temporary photosynthate C pool gC/m^2 T -CPOOL_DEADCROOT_GR dead coarse root growth respiration gC/m^2/s F -CPOOL_DEADCROOT_STORAGE_GR dead coarse root growth respiration to storage gC/m^2/s F -CPOOL_DEADSTEM_GR dead stem growth respiration gC/m^2/s F -CPOOL_DEADSTEM_STORAGE_GR dead stem growth respiration to storage gC/m^2/s F -CPOOL_FROOT_GR fine root growth respiration gC/m^2/s F -CPOOL_FROOT_STORAGE_GR fine root growth respiration to storage gC/m^2/s F -CPOOL_LEAF_GR leaf growth respiration gC/m^2/s F -CPOOL_LEAF_STORAGE_GR leaf growth respiration to storage gC/m^2/s F -CPOOL_LIVECROOT_GR live coarse root growth respiration gC/m^2/s F -CPOOL_LIVECROOT_STORAGE_GR live coarse root growth respiration to storage gC/m^2/s F -CPOOL_LIVESTEM_GR live stem growth respiration gC/m^2/s F -CPOOL_LIVESTEM_STORAGE_GR live stem growth respiration to storage gC/m^2/s F -CPOOL_TO_DEADCROOTC allocation to dead coarse root C gC/m^2/s F -CPOOL_TO_DEADCROOTC_STORAGE allocation to dead coarse root C storage gC/m^2/s F -CPOOL_TO_DEADSTEMC allocation to dead stem C gC/m^2/s F -CPOOL_TO_DEADSTEMC_STORAGE allocation to dead stem C storage gC/m^2/s F -CPOOL_TO_FROOTC allocation to fine root C gC/m^2/s F -CPOOL_TO_FROOTC_STORAGE allocation to fine root C storage gC/m^2/s F -CPOOL_TO_GRESP_STORAGE allocation to growth respiration storage gC/m^2/s F -CPOOL_TO_LEAFC allocation to leaf C gC/m^2/s F -CPOOL_TO_LEAFC_STORAGE allocation to leaf C storage gC/m^2/s F -CPOOL_TO_LIVECROOTC allocation to live coarse root C gC/m^2/s F -CPOOL_TO_LIVECROOTC_STORAGE allocation to live coarse root C storage gC/m^2/s F -CPOOL_TO_LIVESTEMC allocation to live stem C gC/m^2/s F -CPOOL_TO_LIVESTEMC_STORAGE allocation to live stem C storage gC/m^2/s F -CROOT_PROF profile for litter C and N inputs from coarse roots 1/m F -CROPPROD1C 1-yr crop product (grain+biofuel) C gC/m^2 T -CROPPROD1C_LOSS loss from 1-yr crop product pool gC/m^2/s T -CROPPROD1N 1-yr crop product (grain+biofuel) N gN/m^2 T -CROPPROD1N_LOSS loss from 1-yr crop product pool gN/m^2/s T -CROPSEEDC_DEFICIT C used for crop seed that needs to be repaid gC/m^2 T -CROPSEEDN_DEFICIT N used for crop seed that needs to be repaid gN/m^2 F -CROP_SEEDC_TO_LEAF crop seed source to leaf gC/m^2/s F -CROP_SEEDN_TO_LEAF crop seed source to leaf gN/m^2/s F -CURRENT_GR growth resp for new growth displayed in this timestep gC/m^2/s F -CWDC CWD C gC/m^2 T -CWDC_1m CWD C to 1 meter gC/m^2 F -CWDC_HR cwd C heterotrophic respiration gC/m^2/s T -CWDC_LOSS coarse woody debris C loss gC/m^2/s T -CWDC_TO_CEL_LITC decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F -CWDC_TO_CEL_LITC_vr decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F -CWDC_TO_LIG_LITC decomp. of coarse woody debris C to lignin litter C gC/m^2/s F -CWDC_TO_LIG_LITC_vr decomp. of coarse woody debris C to lignin litter C gC/m^3/s F -CWDC_vr CWD C (vertically resolved) gC/m^3 T -CWDN CWD N gN/m^2 T -CWDN_1m CWD N to 1 meter gN/m^2 F -CWDN_TO_CEL_LITN decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F -CWDN_TO_CEL_LITN_vr decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F -CWDN_TO_LIG_LITN decomp. of coarse woody debris N to lignin litter N gN/m^2 F -CWDN_TO_LIG_LITN_vr decomp. of coarse woody debris N to lignin litter N gN/m^3 F -CWDN_vr CWD N (vertically resolved) gN/m^3 T -CWD_HR_L2 Het. Resp. from coarse woody debris gC/m^2/s F -CWD_HR_L2_vr Het. Resp. from coarse woody debris gC/m^3/s F -CWD_HR_L3 Het. Resp. from coarse woody debris gC/m^2/s F -CWD_HR_L3_vr Het. Resp. from coarse woody debris gC/m^3/s F -CWD_PATHFRAC_L2_vr PATHFRAC from coarse woody debris to cellulosic litter fraction F -CWD_PATHFRAC_L3_vr PATHFRAC from coarse woody debris to lignin litter fraction F -CWD_RESP_FRAC_L2_vr respired from coarse woody debris to cellulosic litter fraction F -CWD_RESP_FRAC_L3_vr respired from coarse woody debris to lignin litter fraction F -C_ALLOMETRY C allocation index none F -DAYL daylength s F -DAYS_ACTIVE number of days since last dormancy days F -DEADCROOTC dead coarse root C gC/m^2 T -DEADCROOTC_STORAGE dead coarse root C storage gC/m^2 F -DEADCROOTC_STORAGE_TO_XFER dead coarse root C shift storage to transfer gC/m^2/s F -DEADCROOTC_XFER dead coarse root C transfer gC/m^2 F -DEADCROOTC_XFER_TO_DEADCROOTC dead coarse root C growth from storage gC/m^2/s F -DEADCROOTN dead coarse root N gN/m^2 T -DEADCROOTN_STORAGE dead coarse root N storage gN/m^2 F -DEADCROOTN_STORAGE_TO_XFER dead coarse root N shift storage to transfer gN/m^2/s F -DEADCROOTN_XFER dead coarse root N transfer gN/m^2 F -DEADCROOTN_XFER_TO_DEADCROOTN dead coarse root N growth from storage gN/m^2/s F -DEADSTEMC dead stem C gC/m^2 T -DEADSTEMC_STORAGE dead stem C storage gC/m^2 F -DEADSTEMC_STORAGE_TO_XFER dead stem C shift storage to transfer gC/m^2/s F -DEADSTEMC_XFER dead stem C transfer gC/m^2 F -DEADSTEMC_XFER_TO_DEADSTEMC dead stem C growth from storage gC/m^2/s F -DEADSTEMN dead stem N gN/m^2 T -DEADSTEMN_STORAGE dead stem N storage gN/m^2 F -DEADSTEMN_STORAGE_TO_XFER dead stem N shift storage to transfer gN/m^2/s F -DEADSTEMN_XFER dead stem N transfer gN/m^2 F -DEADSTEMN_XFER_TO_DEADSTEMN dead stem N growth from storage gN/m^2/s F -DENIT total rate of denitrification gN/m^2/s T -DGNETDT derivative of net ground heat flux wrt soil temp W/m^2/K F -DISPLA displacement height (vegetated landunits only) m F -DISPVEGC displayed veg carbon, excluding storage and cpool gC/m^2 T -DISPVEGN displayed vegetation nitrogen gN/m^2 T -DLRAD downward longwave radiation below the canopy W/m^2 F -DORMANT_FLAG dormancy flag none F -DOWNREG fractional reduction in GPP due to N limitation proportion F -DPVLTRB1 turbulent deposition velocity 1 m/s F -DPVLTRB2 turbulent deposition velocity 2 m/s F -DPVLTRB3 turbulent deposition velocity 3 m/s F -DPVLTRB4 turbulent deposition velocity 4 m/s F -DSL dry surface layer thickness mm T -DSTDEP total dust deposition (dry+wet) from atmosphere kg/m^2/s T -DSTFLXT total surface dust emission kg/m2/s T -DT_VEG change in t_veg, last iteration K F -DWT_CONV_CFLUX conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T -DWT_CONV_CFLUX_DRIBBLED conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T -DWT_CONV_CFLUX_PATCH patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F -DWT_CONV_NFLUX conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T -DWT_CONV_NFLUX_PATCH patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F -DWT_CROPPROD1C_GAIN landcover change-driven addition to 1-year crop product pool gC/m^2/s T -DWT_CROPPROD1N_GAIN landcover change-driven addition to 1-year crop product pool gN/m^2/s T -DWT_DEADCROOTC_TO_CWDC dead coarse root to CWD due to landcover change gC/m^2/s F -DWT_DEADCROOTN_TO_CWDN dead coarse root to CWD due to landcover change gN/m^2/s F -DWT_FROOTC_TO_CEL_LIT_C fine root to cellulosic litter due to landcover change gC/m^2/s F -DWT_FROOTC_TO_LIG_LIT_C fine root to lignin litter due to landcover change gC/m^2/s F -DWT_FROOTC_TO_MET_LIT_C fine root to metabolic litter due to landcover change gC/m^2/s F -DWT_FROOTN_TO_CEL_LIT_N fine root N to cellulosic litter due to landcover change gN/m^2/s F -DWT_FROOTN_TO_LIG_LIT_N fine root N to lignin litter due to landcover change gN/m^2/s F -DWT_FROOTN_TO_MET_LIT_N fine root N to metabolic litter due to landcover change gN/m^2/s F -DWT_LIVECROOTC_TO_CWDC live coarse root to CWD due to landcover change gC/m^2/s F -DWT_LIVECROOTN_TO_CWDN live coarse root to CWD due to landcover change gN/m^2/s F -DWT_PROD100C_GAIN landcover change-driven addition to 100-yr wood product pool gC/m^2/s F -DWT_PROD100N_GAIN landcover change-driven addition to 100-yr wood product pool gN/m^2/s F -DWT_PROD10C_GAIN landcover change-driven addition to 10-yr wood product pool gC/m^2/s F -DWT_PROD10N_GAIN landcover change-driven addition to 10-yr wood product pool gN/m^2/s F -DWT_SEEDC_TO_DEADSTEM seed source to patch-level deadstem gC/m^2/s F -DWT_SEEDC_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F -DWT_SEEDC_TO_LEAF seed source to patch-level leaf gC/m^2/s F -DWT_SEEDC_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F -DWT_SEEDN_TO_DEADSTEM seed source to patch-level deadstem gN/m^2/s T -DWT_SEEDN_TO_DEADSTEM_PATCH patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F -DWT_SEEDN_TO_LEAF seed source to patch-level leaf gN/m^2/s T -DWT_SEEDN_TO_LEAF_PATCH patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F -DWT_SLASH_CFLUX slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T -DWT_SLASH_CFLUX_PATCH patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F -DWT_WOODPRODC_GAIN landcover change-driven addition to wood product pools gC/m^2/s T -DWT_WOODPRODN_GAIN landcover change-driven addition to wood product pools gN/m^2/s T -DWT_WOOD_PRODUCTC_GAIN_PATCH patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F -DYN_COL_ADJUSTMENTS_CH4 Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_C Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_N Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_NH4 Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -DYN_COL_SOIL_ADJUSTMENTS_NO3 Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -EFF_POROSITY effective porosity = porosity - vol_ice proportion F -EFLXBUILD building heat flux from change in interior building air temperature W/m^2 T -EFLX_DYNBAL dynamic land cover change conversion energy flux W/m^2 T -EFLX_GNET net heat flux into ground W/m^2 F -EFLX_GRND_LAKE net heat flux into lake/snow surface, excluding light transmission W/m^2 T -EFLX_LH_TOT total latent heat flux [+ to atm] W/m^2 T -EFLX_LH_TOT_ICE total latent heat flux [+ to atm] (ice landunits only) W/m^2 F -EFLX_LH_TOT_R Rural total evaporation W/m^2 T -EFLX_LH_TOT_U Urban total evaporation W/m^2 F -EFLX_SOIL_GRND soil heat flux [+ into soil] W/m^2 F -ELAI exposed one-sided leaf area index m^2/m^2 T -EMG ground emissivity proportion F -EMV vegetation emissivity proportion F -EOPT Eopt coefficient for VOC calc non F -ER total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T -ERRH2O total water conservation error mm T -ERRH2OSNO imbalance in snow depth (liquid water) mm T -ERRSEB surface energy conservation error W/m^2 T -ERRSOI soil/lake energy conservation error W/m^2 T -ERRSOL solar radiation conservation error W/m^2 T -ESAI exposed one-sided stem area index m^2/m^2 T -EXCESSC_MR excess C maintenance respiration gC/m^2/s F -EXCESS_CFLUX C flux not allocated due to downregulation gC/m^2/s F -FAREA_BURNED timestep fractional area burned s-1 T -FCANSNO fraction of canopy that is wet proportion F -FCEV canopy evaporation W/m^2 T -FCH4 Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T -FCH4TOCO2 Gridcell oxidation of CH4 to CO2 gC/m2/s T -FCH4_DFSAT CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T -FCO2 CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F -FCOV fractional impermeable area unitless T -FCTR canopy transpiration W/m^2 T -FDRY fraction of foliage that is green and dry proportion F -FERTNITRO Nitrogen fertilizer for each crop gN/m2/yr F -FERT_COUNTER time left to fertilize seconds F -FERT_TO_SMINN fertilizer to soil mineral N gN/m^2/s F -FFIX_TO_SMINN free living N fixation to soil mineral N gN/m^2/s T -FGEV ground evaporation W/m^2 T -FGR heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T -FGR12 heat flux between soil layers 1 and 2 W/m^2 T -FGR_ICE heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F -FGR_R Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F -FGR_SOIL_R Rural downward heat flux at interface below each soil layer watt/m^2 F -FGR_U Urban heat flux into soil/snow including snow melt W/m^2 F -FH2OSFC fraction of ground covered by surface water unitless T -FH2OSFC_NOSNOW fraction of ground covered by surface water (if no snow present) unitless F -FINUNDATED fractional inundated area of vegetated columns unitless T -FINUNDATED_LAG time-lagged inundated fraction of vegetated columns unitless F -FIRA net infrared (longwave) radiation W/m^2 T -FIRA_ICE net infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRA_R Rural net infrared (longwave) radiation W/m^2 T -FIRA_U Urban net infrared (longwave) radiation W/m^2 F -FIRE emitted infrared (longwave) radiation W/m^2 T -FIRE_ICE emitted infrared (longwave) radiation (ice landunits only) W/m^2 F -FIRE_R Rural emitted infrared (longwave) radiation W/m^2 T -FIRE_U Urban emitted infrared (longwave) radiation W/m^2 F -FLDS atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T -FLDS_ICE atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F -FMAX_DENIT_CARBONSUBSTRATE FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F -FMAX_DENIT_NITRATE FMAX_DENIT_NITRATE gN/m^3/s F -FPI fraction of potential immobilization proportion T -FPI_vr fraction of potential immobilization proportion F -FPSN photosynthesis umol m-2 s-1 T -FPSN24 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F -FPSN_WC Rubisco-limited photosynthesis umol m-2 s-1 F -FPSN_WJ RuBP-limited photosynthesis umol m-2 s-1 F -FPSN_WP Product-limited photosynthesis umol m-2 s-1 F -FRAC_ICEOLD fraction of ice relative to the tot water proportion F -FREE_RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T -FROOTC fine root C gC/m^2 T -FROOTC_ALLOC fine root C allocation gC/m^2/s T -FROOTC_LOSS fine root C loss gC/m^2/s T -FROOTC_STORAGE fine root C storage gC/m^2 F -FROOTC_STORAGE_TO_XFER fine root C shift storage to transfer gC/m^2/s F -FROOTC_TO_LITTER fine root C litterfall gC/m^2/s F -FROOTC_XFER fine root C transfer gC/m^2 F -FROOTC_XFER_TO_FROOTC fine root C growth from storage gC/m^2/s F -FROOTN fine root N gN/m^2 T -FROOTN_STORAGE fine root N storage gN/m^2 F -FROOTN_STORAGE_TO_XFER fine root N shift storage to transfer gN/m^2/s F -FROOTN_TO_LITTER fine root N litterfall gN/m^2/s F -FROOTN_XFER fine root N transfer gN/m^2 F -FROOTN_XFER_TO_FROOTN fine root N growth from storage gN/m^2/s F -FROOT_MR fine root maintenance respiration gC/m^2/s F -FROOT_PROF profile for litter C and N inputs from fine roots 1/m F -FROST_TABLE frost table depth (natural vegetated and crop landunits only) m F -FSA absorbed solar radiation W/m^2 T -FSAT fractional area with water table at surface unitless T -FSA_ICE absorbed solar radiation (ice landunits only) W/m^2 F -FSA_R Rural absorbed solar radiation W/m^2 F -FSA_U Urban absorbed solar radiation W/m^2 F -FSD24 direct radiation (last 24hrs) K F -FSD240 direct radiation (last 240hrs) K F -FSDS atmospheric incident solar radiation W/m^2 T -FSDSND direct nir incident solar radiation W/m^2 T -FSDSNDLN direct nir incident solar radiation at local noon W/m^2 T -FSDSNI diffuse nir incident solar radiation W/m^2 T -FSDSVD direct vis incident solar radiation W/m^2 T -FSDSVDLN direct vis incident solar radiation at local noon W/m^2 T -FSDSVI diffuse vis incident solar radiation W/m^2 T -FSDSVILN diffuse vis incident solar radiation at local noon W/m^2 T -FSH sensible heat not including correction for land use change and rain/snow conversion W/m^2 T -FSH_G sensible heat from ground W/m^2 T -FSH_ICE sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F -FSH_PRECIP_CONVERSION Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T -FSH_R Rural sensible heat W/m^2 T -FSH_RUNOFF_ICE_TO_LIQ sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T -FSH_TO_COUPLER sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T -FSH_U Urban sensible heat W/m^2 F -FSH_V sensible heat from veg W/m^2 T -FSI24 indirect radiation (last 24hrs) K F -FSI240 indirect radiation (last 240hrs) K F -FSM snow melt heat flux W/m^2 T -FSM_ICE snow melt heat flux (ice landunits only) W/m^2 F -FSM_R Rural snow melt heat flux W/m^2 F -FSM_U Urban snow melt heat flux W/m^2 F -FSNO fraction of ground covered by snow unitless T -FSNO_EFF effective fraction of ground covered by snow unitless T -FSNO_ICE fraction of ground covered by snow (ice landunits only) unitless F -FSR reflected solar radiation W/m^2 T -FSRND direct nir reflected solar radiation W/m^2 T -FSRNDLN direct nir reflected solar radiation at local noon W/m^2 T -FSRNI diffuse nir reflected solar radiation W/m^2 T -FSRVD direct vis reflected solar radiation W/m^2 T -FSRVDLN direct vis reflected solar radiation at local noon W/m^2 T -FSRVI diffuse vis reflected solar radiation W/m^2 T -FSR_ICE reflected solar radiation (ice landunits only) W/m^2 F -FSUN sunlit fraction of canopy proportion F -FSUN24 fraction sunlit (last 24hrs) K F -FSUN240 fraction sunlit (last 240hrs) K F -FUELC fuel load gC/m^2 T -FV friction velocity m/s T -FWET fraction of canopy that is wet proportion F -F_DENIT denitrification flux gN/m^2/s T -F_DENIT_BASE F_DENIT_BASE gN/m^3/s F -F_DENIT_vr denitrification flux gN/m^3/s F -F_N2O_DENIT denitrification N2O flux gN/m^2/s T -F_N2O_NIT nitrification N2O flux gN/m^2/s T -F_NIT nitrification flux gN/m^2/s T -F_NIT_vr nitrification flux gN/m^3/s F -GAMMA total gamma for VOC calc non F -GAMMAA gamma A for VOC calc non F -GAMMAC gamma C for VOC calc non F -GAMMAL gamma L for VOC calc non F -GAMMAP gamma P for VOC calc non F -GAMMAS gamma S for VOC calc non F -GAMMAT gamma T for VOC calc non F -GDD0 Growing degree days base 0C from planting ddays F -GDD020 Twenty year average of growing degree days base 0C from planting ddays F -GDD10 Growing degree days base 10C from planting ddays F -GDD1020 Twenty year average of growing degree days base 10C from planting ddays F -GDD8 Growing degree days base 8C from planting ddays F -GDD820 Twenty year average of growing degree days base 8C from planting ddays F -GDDACCUM Accumulated growing degree days past planting date for crop ddays F -GDDACCUM_PERHARV At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F -GDDHARV Growing degree days (gdd) needed to harvest ddays F -GDDHARV_PERHARV Growing degree days (gdd) needed to harvest; should only be output annually ddays F -GDDTSOI Growing degree-days from planting (top two soil layers) ddays F -GPP gross primary production gC/m^2/s T -GR total growth respiration gC/m^2/s T -GRAINC grain C (does not equal yield) gC/m^2 T -GRAINC_TO_FOOD grain C to food gC/m^2/s T -GRAINC_TO_FOOD_ANN grain C to food harvested per calendar year; should only be output annually gC/m^2 F -GRAINC_TO_FOOD_PERHARV grain C to food per harvest; should only be output annually gC/m^2 F -GRAINC_TO_SEED grain C to seed gC/m^2/s T -GRAINN grain N gN/m^2 T -GRESP_STORAGE growth respiration storage gC/m^2 F -GRESP_STORAGE_TO_XFER growth respiration shift storage to transfer gC/m^2/s F -GRESP_XFER growth respiration transfer gC/m^2 F -GROSS_NMIN gross rate of N mineralization gN/m^2/s T -GROSS_NMIN_vr gross rate of N mineralization gN/m^3/s F -GRU_PROD100C_GAIN gross unrepresented landcover change addition to 100-yr wood product pool gC/m^2/s F -GRU_PROD100N_GAIN gross unrepresented landcover change addition to 100-yr wood product pool gN/m^2/s F -GRU_PROD10C_GAIN gross unrepresented landcover change addition to 10-yr wood product pool gC/m^2/s F -GRU_PROD10N_GAIN gross unrepresented landcover change addition to 10-yr wood product pool gN/m^2/s F -GSSHA shaded leaf stomatal conductance umol H20/m2/s T -GSSHALN shaded leaf stomatal conductance at local noon umol H20/m2/s T -GSSUN sunlit leaf stomatal conductance umol H20/m2/s T -GSSUNLN sunlit leaf stomatal conductance at local noon umol H20/m2/s T -H2OCAN intercepted water mm T -H2OSFC surface water depth mm T -H2OSNO snow depth (liquid water) mm T -H2OSNO_ICE snow depth (liquid water, ice landunits only) mm F -H2OSNO_TOP mass of snow in top snow layer kg/m2 T -H2OSOI volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T -HARVEST_REASON_PERHARV Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F -HBOT canopy bottom m F -HDATES actual crop harvest dates; should only be output annually day of year F -HEAT_CONTENT1 initial gridcell total heat content J/m^2 T -HEAT_CONTENT1_VEG initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F -HEAT_CONTENT2 post land cover change total heat content J/m^2 F -HEAT_FROM_AC sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T -HIA 2 m NWS Heat Index C T -HIA_R Rural 2 m NWS Heat Index C T -HIA_U Urban 2 m NWS Heat Index C T -HK hydraulic conductivity (natural vegetated and crop landunits only) mm/s F -HR total heterotrophic respiration gC/m^2/s T -HR_vr total vertically resolved heterotrophic respiration gC/m^3/s T -HTOP canopy top m T -HUI Crop patch heat unit index ddays F -HUI_PERHARV At-harvest accumulated heat unit index for crop; should only be output annually ddays F -HUMIDEX 2 m Humidex C T -HUMIDEX_R Rural 2 m Humidex C T -HUMIDEX_U Urban 2 m Humidex C T -ICE_CONTENT1 initial gridcell total ice content mm T -ICE_CONTENT2 post land cover change total ice content mm F -ICE_MODEL_FRACTION Ice sheet model fractional coverage unitless F -INIT_GPP GPP flux before downregulation gC/m^2/s F -INT_SNOW accumulated swe (natural vegetated and crop landunits only) mm F -INT_SNOW_ICE accumulated swe (ice landunits only) mm F -IWUELN local noon intrinsic water use efficiency umolCO2/molH2O T -JMX25T canopy profile of jmax umol/m2/s T -Jmx25Z maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T -KROOT root conductance each soil layer 1/s F -KSOIL soil conductance in each soil layer 1/s F -K_ACT_SOM active soil organic potential loss coefficient 1/s F -K_CEL_LIT cellulosic litter potential loss coefficient 1/s F -K_CWD coarse woody debris potential loss coefficient 1/s F -K_LIG_LIT lignin litter potential loss coefficient 1/s F -K_MET_LIT metabolic litter potential loss coefficient 1/s F -K_NITR K_NITR 1/s F -K_NITR_H2O K_NITR_H2O unitless F -K_NITR_PH K_NITR_PH unitless F -K_NITR_T K_NITR_T unitless F -K_PAS_SOM passive soil organic potential loss coefficient 1/s F -K_SLO_SOM slow soil organic ma potential loss coefficient 1/s F -L1_PATHFRAC_S1_vr PATHFRAC from metabolic litter to active soil organic fraction F -L1_RESP_FRAC_S1_vr respired from metabolic litter to active soil organic fraction F -L2_PATHFRAC_S1_vr PATHFRAC from cellulosic litter to active soil organic fraction F -L2_RESP_FRAC_S1_vr respired from cellulosic litter to active soil organic fraction F -L3_PATHFRAC_S2_vr PATHFRAC from lignin litter to slow soil organic ma fraction F -L3_RESP_FRAC_S2_vr respired from lignin litter to slow soil organic ma fraction F -LAI240 240hr average of leaf area index m^2/m^2 F -LAISHA shaded projected leaf area index m^2/m^2 T -LAISUN sunlit projected leaf area index m^2/m^2 T -LAKEICEFRAC lake layer ice mass fraction unitless F -LAKEICEFRAC_SURF surface lake layer ice mass fraction unitless T -LAKEICETHICK thickness of lake ice (including physical expansion on freezing) m T -LAND_USE_FLUX total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T -LATBASET latitude vary base temperature for hui degree C F -LEAFC leaf C gC/m^2 T -LEAFCN Leaf CN ratio used for flexible CN gC/gN T -LEAFCN_OFFSET Leaf C:N used by FUN unitless F -LEAFCN_STORAGE Storage Leaf CN ratio used for flexible CN gC/gN F -LEAFC_ALLOC leaf C allocation gC/m^2/s T -LEAFC_CHANGE C change in leaf gC/m^2/s T -LEAFC_LOSS leaf C loss gC/m^2/s T -LEAFC_STORAGE leaf C storage gC/m^2 F -LEAFC_STORAGE_TO_XFER leaf C shift storage to transfer gC/m^2/s F -LEAFC_STORAGE_XFER_ACC Accumulated leaf C transfer gC/m^2 F -LEAFC_TO_BIOFUELC leaf C to biofuel C gC/m^2/s T -LEAFC_TO_LITTER leaf C litterfall gC/m^2/s F -LEAFC_TO_LITTER_FUN leaf C litterfall used by FUN gC/m^2/s T -LEAFC_XFER leaf C transfer gC/m^2 F -LEAFC_XFER_TO_LEAFC leaf C growth from storage gC/m^2/s F -LEAFN leaf N gN/m^2 T -LEAFN_STORAGE leaf N storage gN/m^2 F -LEAFN_STORAGE_TO_XFER leaf N shift storage to transfer gN/m^2/s F -LEAFN_STORAGE_XFER_ACC Accmulated leaf N transfer gN/m^2 F -LEAFN_TO_LITTER leaf N litterfall gN/m^2/s T -LEAFN_TO_RETRANSN leaf N to retranslocated N pool gN/m^2/s F -LEAFN_XFER leaf N transfer gN/m^2 F -LEAFN_XFER_TO_LEAFN leaf N growth from storage gN/m^2/s F -LEAF_MR leaf maintenance respiration gC/m^2/s T -LEAF_PROF profile for litter C and N inputs from leaves 1/m F -LFC2 conversion area fraction of BET and BDT that burned per sec T -LGSF long growing season factor proportion F -LIG_LITC LIG_LIT C gC/m^2 T -LIG_LITC_1m LIG_LIT C to 1 meter gC/m^2 F -LIG_LITC_TNDNCY_VERT_TRA lignin litter C tendency due to vertical transport gC/m^3/s F -LIG_LITC_TO_SLO_SOMC decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F -LIG_LITC_TO_SLO_SOMC_vr decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F -LIG_LITC_vr LIG_LIT C (vertically resolved) gC/m^3 T -LIG_LITN LIG_LIT N gN/m^2 T -LIG_LITN_1m LIG_LIT N to 1 meter gN/m^2 F -LIG_LITN_TNDNCY_VERT_TRA lignin litter N tendency due to vertical transport gN/m^3/s F -LIG_LITN_TO_SLO_SOMN decomp. of lignin litter N to slow soil organic ma N gN/m^2 F -LIG_LITN_TO_SLO_SOMN_vr decomp. of lignin litter N to slow soil organic ma N gN/m^3 F -LIG_LITN_vr LIG_LIT N (vertically resolved) gN/m^3 T -LIG_LIT_HR Het. Resp. from lignin litter gC/m^2/s F -LIG_LIT_HR_vr Het. Resp. from lignin litter gC/m^3/s F -LIQCAN intercepted liquid water mm T -LIQUID_CONTENT1 initial gridcell total liq content mm T -LIQUID_CONTENT2 post landuse change gridcell total liq content mm F -LIQUID_WATER_TEMP1 initial gridcell weighted average liquid water temperature K F -LITFALL litterfall (leaves and fine roots) gC/m^2/s T -LITFIRE litter fire losses gC/m^2/s F -LITTERC_HR litter C heterotrophic respiration gC/m^2/s T -LITTERC_LOSS litter C loss gC/m^2/s T -LIVECROOTC live coarse root C gC/m^2 T -LIVECROOTC_STORAGE live coarse root C storage gC/m^2 F -LIVECROOTC_STORAGE_TO_XFER live coarse root C shift storage to transfer gC/m^2/s F -LIVECROOTC_TO_DEADCROOTC live coarse root C turnover gC/m^2/s F -LIVECROOTC_XFER live coarse root C transfer gC/m^2 F -LIVECROOTC_XFER_TO_LIVECROOTC live coarse root C growth from storage gC/m^2/s F -LIVECROOTN live coarse root N gN/m^2 T -LIVECROOTN_STORAGE live coarse root N storage gN/m^2 F -LIVECROOTN_STORAGE_TO_XFER live coarse root N shift storage to transfer gN/m^2/s F -LIVECROOTN_TO_DEADCROOTN live coarse root N turnover gN/m^2/s F -LIVECROOTN_TO_RETRANSN live coarse root N to retranslocated N pool gN/m^2/s F -LIVECROOTN_XFER live coarse root N transfer gN/m^2 F -LIVECROOTN_XFER_TO_LIVECROOTN live coarse root N growth from storage gN/m^2/s F -LIVECROOT_MR live coarse root maintenance respiration gC/m^2/s F -LIVESTEMC live stem C gC/m^2 T -LIVESTEMC_STORAGE live stem C storage gC/m^2 F -LIVESTEMC_STORAGE_TO_XFER live stem C shift storage to transfer gC/m^2/s F -LIVESTEMC_TO_BIOFUELC livestem C to biofuel C gC/m^2/s T -LIVESTEMC_TO_DEADSTEMC live stem C turnover gC/m^2/s F -LIVESTEMC_XFER live stem C transfer gC/m^2 F -LIVESTEMC_XFER_TO_LIVESTEMC live stem C growth from storage gC/m^2/s F -LIVESTEMN live stem N gN/m^2 T -LIVESTEMN_STORAGE live stem N storage gN/m^2 F -LIVESTEMN_STORAGE_TO_XFER live stem N shift storage to transfer gN/m^2/s F -LIVESTEMN_TO_DEADSTEMN live stem N turnover gN/m^2/s F -LIVESTEMN_TO_RETRANSN live stem N to retranslocated N pool gN/m^2/s F -LIVESTEMN_XFER live stem N transfer gN/m^2 F -LIVESTEMN_XFER_TO_LIVESTEMN live stem N growth from storage gN/m^2/s F -LIVESTEM_MR live stem maintenance respiration gC/m^2/s F -LNC leaf N concentration gN leaf/m^2 T -LWdown atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F -LWup upwelling longwave radiation W/m^2 F -MEG_acetaldehyde MEGAN flux kg/m2/sec T -MEG_acetic_acid MEGAN flux kg/m2/sec T -MEG_acetone MEGAN flux kg/m2/sec T -MEG_carene_3 MEGAN flux kg/m2/sec T -MEG_ethanol MEGAN flux kg/m2/sec T -MEG_formaldehyde MEGAN flux kg/m2/sec T -MEG_isoprene MEGAN flux kg/m2/sec T -MEG_methanol MEGAN flux kg/m2/sec T -MEG_pinene_a MEGAN flux kg/m2/sec T -MEG_thujene_a MEGAN flux kg/m2/sec T -MET_LITC MET_LIT C gC/m^2 T -MET_LITC_1m MET_LIT C to 1 meter gC/m^2 F -MET_LITC_TNDNCY_VERT_TRA metabolic litter C tendency due to vertical transport gC/m^3/s F -MET_LITC_TO_ACT_SOMC decomp. of metabolic litter C to active soil organic C gC/m^2/s F -MET_LITC_TO_ACT_SOMC_vr decomp. of metabolic litter C to active soil organic C gC/m^3/s F -MET_LITC_vr MET_LIT C (vertically resolved) gC/m^3 T -MET_LITN MET_LIT N gN/m^2 T -MET_LITN_1m MET_LIT N to 1 meter gN/m^2 F -MET_LITN_TNDNCY_VERT_TRA metabolic litter N tendency due to vertical transport gN/m^3/s F -MET_LITN_TO_ACT_SOMN decomp. of metabolic litter N to active soil organic N gN/m^2 F -MET_LITN_TO_ACT_SOMN_vr decomp. of metabolic litter N to active soil organic N gN/m^3 F -MET_LITN_vr MET_LIT N (vertically resolved) gN/m^3 T -MET_LIT_HR Het. Resp. from metabolic litter gC/m^2/s F -MET_LIT_HR_vr Het. Resp. from metabolic litter gC/m^3/s F -MR maintenance respiration gC/m^2/s T -M_ACT_SOMC_TO_LEACHING active soil organic C leaching loss gC/m^2/s F -M_ACT_SOMN_TO_LEACHING active soil organic N leaching loss gN/m^2/s F -M_CEL_LITC_TO_FIRE cellulosic litter C fire loss gC/m^2/s F -M_CEL_LITC_TO_FIRE_vr cellulosic litter C fire loss gC/m^3/s F -M_CEL_LITC_TO_LEACHING cellulosic litter C leaching loss gC/m^2/s F -M_CEL_LITN_TO_FIRE cellulosic litter N fire loss gN/m^2 F -M_CEL_LITN_TO_FIRE_vr cellulosic litter N fire loss gN/m^3 F -M_CEL_LITN_TO_LEACHING cellulosic litter N leaching loss gN/m^2/s F -M_CWDC_TO_FIRE coarse woody debris C fire loss gC/m^2/s F -M_CWDC_TO_FIRE_vr coarse woody debris C fire loss gC/m^3/s F -M_CWDN_TO_FIRE coarse woody debris N fire loss gN/m^2 F -M_CWDN_TO_FIRE_vr coarse woody debris N fire loss gN/m^3 F -M_DEADCROOTC_STORAGE_TO_LITTER dead coarse root C storage mortality gC/m^2/s F -M_DEADCROOTC_STORAGE_TO_LITTER_FIRE dead coarse root C storage fire mortality to litter gC/m^2/s F -M_DEADCROOTC_TO_LITTER dead coarse root C mortality gC/m^2/s F -M_DEADCROOTC_XFER_TO_LITTER dead coarse root C transfer mortality gC/m^2/s F -M_DEADCROOTN_STORAGE_TO_FIRE dead coarse root N storage fire loss gN/m^2/s F -M_DEADCROOTN_STORAGE_TO_LITTER dead coarse root N storage mortality gN/m^2/s F -M_DEADCROOTN_TO_FIRE dead coarse root N fire loss gN/m^2/s F -M_DEADCROOTN_TO_LITTER dead coarse root N mortality gN/m^2/s F -M_DEADCROOTN_TO_LITTER_FIRE dead coarse root N fire mortality to litter gN/m^2/s F -M_DEADCROOTN_XFER_TO_FIRE dead coarse root N transfer fire loss gN/m^2/s F -M_DEADCROOTN_XFER_TO_LITTER dead coarse root N transfer mortality gN/m^2/s F -M_DEADROOTC_STORAGE_TO_FIRE dead root C storage fire loss gC/m^2/s F -M_DEADROOTC_STORAGE_TO_LITTER_FIRE dead root C storage fire mortality to litter gC/m^2/s F -M_DEADROOTC_TO_FIRE dead root C fire loss gC/m^2/s F -M_DEADROOTC_TO_LITTER_FIRE dead root C fire mortality to litter gC/m^2/s F -M_DEADROOTC_XFER_TO_FIRE dead root C transfer fire loss gC/m^2/s F -M_DEADROOTC_XFER_TO_LITTER_FIRE dead root C transfer fire mortality to litter gC/m^2/s F -M_DEADSTEMC_STORAGE_TO_FIRE dead stem C storage fire loss gC/m^2/s F -M_DEADSTEMC_STORAGE_TO_LITTER dead stem C storage mortality gC/m^2/s F -M_DEADSTEMC_STORAGE_TO_LITTER_FIRE dead stem C storage fire mortality to litter gC/m^2/s F -M_DEADSTEMC_TO_FIRE dead stem C fire loss gC/m^2/s F -M_DEADSTEMC_TO_LITTER dead stem C mortality gC/m^2/s F -M_DEADSTEMC_TO_LITTER_FIRE dead stem C fire mortality to litter gC/m^2/s F -M_DEADSTEMC_XFER_TO_FIRE dead stem C transfer fire loss gC/m^2/s F -M_DEADSTEMC_XFER_TO_LITTER dead stem C transfer mortality gC/m^2/s F -M_DEADSTEMC_XFER_TO_LITTER_FIRE dead stem C transfer fire mortality to litter gC/m^2/s F -M_DEADSTEMN_STORAGE_TO_FIRE dead stem N storage fire loss gN/m^2/s F -M_DEADSTEMN_STORAGE_TO_LITTER dead stem N storage mortality gN/m^2/s F -M_DEADSTEMN_TO_FIRE dead stem N fire loss gN/m^2/s F -M_DEADSTEMN_TO_LITTER dead stem N mortality gN/m^2/s F -M_DEADSTEMN_TO_LITTER_FIRE dead stem N fire mortality to litter gN/m^2/s F -M_DEADSTEMN_XFER_TO_FIRE dead stem N transfer fire loss gN/m^2/s F -M_DEADSTEMN_XFER_TO_LITTER dead stem N transfer mortality gN/m^2/s F -M_FROOTC_STORAGE_TO_FIRE fine root C storage fire loss gC/m^2/s F -M_FROOTC_STORAGE_TO_LITTER fine root C storage mortality gC/m^2/s F -M_FROOTC_STORAGE_TO_LITTER_FIRE fine root C storage fire mortality to litter gC/m^2/s F -M_FROOTC_TO_FIRE fine root C fire loss gC/m^2/s F -M_FROOTC_TO_LITTER fine root C mortality gC/m^2/s F -M_FROOTC_TO_LITTER_FIRE fine root C fire mortality to litter gC/m^2/s F -M_FROOTC_XFER_TO_FIRE fine root C transfer fire loss gC/m^2/s F -M_FROOTC_XFER_TO_LITTER fine root C transfer mortality gC/m^2/s F -M_FROOTC_XFER_TO_LITTER_FIRE fine root C transfer fire mortality to litter gC/m^2/s F -M_FROOTN_STORAGE_TO_FIRE fine root N storage fire loss gN/m^2/s F -M_FROOTN_STORAGE_TO_LITTER fine root N storage mortality gN/m^2/s F -M_FROOTN_TO_FIRE fine root N fire loss gN/m^2/s F -M_FROOTN_TO_LITTER fine root N mortality gN/m^2/s F -M_FROOTN_XFER_TO_FIRE fine root N transfer fire loss gN/m^2/s F -M_FROOTN_XFER_TO_LITTER fine root N transfer mortality gN/m^2/s F -M_GRESP_STORAGE_TO_FIRE growth respiration storage fire loss gC/m^2/s F -M_GRESP_STORAGE_TO_LITTER growth respiration storage mortality gC/m^2/s F -M_GRESP_STORAGE_TO_LITTER_FIRE growth respiration storage fire mortality to litter gC/m^2/s F -M_GRESP_XFER_TO_FIRE growth respiration transfer fire loss gC/m^2/s F -M_GRESP_XFER_TO_LITTER growth respiration transfer mortality gC/m^2/s F -M_GRESP_XFER_TO_LITTER_FIRE growth respiration transfer fire mortality to litter gC/m^2/s F -M_LEAFC_STORAGE_TO_FIRE leaf C storage fire loss gC/m^2/s F -M_LEAFC_STORAGE_TO_LITTER leaf C storage mortality gC/m^2/s F -M_LEAFC_STORAGE_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F -M_LEAFC_TO_FIRE leaf C fire loss gC/m^2/s F -M_LEAFC_TO_LITTER leaf C mortality gC/m^2/s F -M_LEAFC_TO_LITTER_FIRE leaf C fire mortality to litter gC/m^2/s F -M_LEAFC_XFER_TO_FIRE leaf C transfer fire loss gC/m^2/s F -M_LEAFC_XFER_TO_LITTER leaf C transfer mortality gC/m^2/s F -M_LEAFC_XFER_TO_LITTER_FIRE leaf C transfer fire mortality to litter gC/m^2/s F -M_LEAFN_STORAGE_TO_FIRE leaf N storage fire loss gN/m^2/s F -M_LEAFN_STORAGE_TO_LITTER leaf N storage mortality gN/m^2/s F -M_LEAFN_TO_FIRE leaf N fire loss gN/m^2/s F -M_LEAFN_TO_LITTER leaf N mortality gN/m^2/s F -M_LEAFN_XFER_TO_FIRE leaf N transfer fire loss gN/m^2/s F -M_LEAFN_XFER_TO_LITTER leaf N transfer mortality gN/m^2/s F -M_LIG_LITC_TO_FIRE lignin litter C fire loss gC/m^2/s F -M_LIG_LITC_TO_FIRE_vr lignin litter C fire loss gC/m^3/s F -M_LIG_LITC_TO_LEACHING lignin litter C leaching loss gC/m^2/s F -M_LIG_LITN_TO_FIRE lignin litter N fire loss gN/m^2 F -M_LIG_LITN_TO_FIRE_vr lignin litter N fire loss gN/m^3 F -M_LIG_LITN_TO_LEACHING lignin litter N leaching loss gN/m^2/s F -M_LIVECROOTC_STORAGE_TO_LITTER live coarse root C storage mortality gC/m^2/s F -M_LIVECROOTC_STORAGE_TO_LITTER_FIRE live coarse root C fire mortality to litter gC/m^2/s F -M_LIVECROOTC_TO_LITTER live coarse root C mortality gC/m^2/s F -M_LIVECROOTC_XFER_TO_LITTER live coarse root C transfer mortality gC/m^2/s F -M_LIVECROOTN_STORAGE_TO_FIRE live coarse root N storage fire loss gN/m^2/s F -M_LIVECROOTN_STORAGE_TO_LITTER live coarse root N storage mortality gN/m^2/s F -M_LIVECROOTN_TO_FIRE live coarse root N fire loss gN/m^2/s F -M_LIVECROOTN_TO_LITTER live coarse root N mortality gN/m^2/s F -M_LIVECROOTN_XFER_TO_FIRE live coarse root N transfer fire loss gN/m^2/s F -M_LIVECROOTN_XFER_TO_LITTER live coarse root N transfer mortality gN/m^2/s F -M_LIVEROOTC_STORAGE_TO_FIRE live root C storage fire loss gC/m^2/s F -M_LIVEROOTC_STORAGE_TO_LITTER_FIRE live root C storage fire mortality to litter gC/m^2/s F -M_LIVEROOTC_TO_DEADROOTC_FIRE live root C fire mortality to dead root C gC/m^2/s F -M_LIVEROOTC_TO_FIRE live root C fire loss gC/m^2/s F -M_LIVEROOTC_TO_LITTER_FIRE live root C fire mortality to litter gC/m^2/s F -M_LIVEROOTC_XFER_TO_FIRE live root C transfer fire loss gC/m^2/s F -M_LIVEROOTC_XFER_TO_LITTER_FIRE live root C transfer fire mortality to litter gC/m^2/s F -M_LIVESTEMC_STORAGE_TO_FIRE live stem C storage fire loss gC/m^2/s F -M_LIVESTEMC_STORAGE_TO_LITTER live stem C storage mortality gC/m^2/s F -M_LIVESTEMC_STORAGE_TO_LITTER_FIRE live stem C storage fire mortality to litter gC/m^2/s F -M_LIVESTEMC_TO_DEADSTEMC_FIRE live stem C fire mortality to dead stem C gC/m^2/s F -M_LIVESTEMC_TO_FIRE live stem C fire loss gC/m^2/s F -M_LIVESTEMC_TO_LITTER live stem C mortality gC/m^2/s F -M_LIVESTEMC_TO_LITTER_FIRE live stem C fire mortality to litter gC/m^2/s F -M_LIVESTEMC_XFER_TO_FIRE live stem C transfer fire loss gC/m^2/s F -M_LIVESTEMC_XFER_TO_LITTER live stem C transfer mortality gC/m^2/s F -M_LIVESTEMC_XFER_TO_LITTER_FIRE live stem C transfer fire mortality to litter gC/m^2/s F -M_LIVESTEMN_STORAGE_TO_FIRE live stem N storage fire loss gN/m^2/s F -M_LIVESTEMN_STORAGE_TO_LITTER live stem N storage mortality gN/m^2/s F -M_LIVESTEMN_TO_FIRE live stem N fire loss gN/m^2/s F -M_LIVESTEMN_TO_LITTER live stem N mortality gN/m^2/s F -M_LIVESTEMN_XFER_TO_FIRE live stem N transfer fire loss gN/m^2/s F -M_LIVESTEMN_XFER_TO_LITTER live stem N transfer mortality gN/m^2/s F -M_MET_LITC_TO_FIRE metabolic litter C fire loss gC/m^2/s F -M_MET_LITC_TO_FIRE_vr metabolic litter C fire loss gC/m^3/s F -M_MET_LITC_TO_LEACHING metabolic litter C leaching loss gC/m^2/s F -M_MET_LITN_TO_FIRE metabolic litter N fire loss gN/m^2 F -M_MET_LITN_TO_FIRE_vr metabolic litter N fire loss gN/m^3 F -M_MET_LITN_TO_LEACHING metabolic litter N leaching loss gN/m^2/s F -M_PAS_SOMC_TO_LEACHING passive soil organic C leaching loss gC/m^2/s F -M_PAS_SOMN_TO_LEACHING passive soil organic N leaching loss gN/m^2/s F -M_RETRANSN_TO_FIRE retranslocated N pool fire loss gN/m^2/s F -M_RETRANSN_TO_LITTER retranslocated N pool mortality gN/m^2/s F -M_SLO_SOMC_TO_LEACHING slow soil organic ma C leaching loss gC/m^2/s F -M_SLO_SOMN_TO_LEACHING slow soil organic ma N leaching loss gN/m^2/s F -NACTIVE Mycorrhizal N uptake flux gN/m^2/s T -NACTIVE_NH4 Mycorrhizal N uptake flux gN/m^2/s T -NACTIVE_NO3 Mycorrhizal N uptake flux gN/m^2/s T -NAM AM-associated N uptake flux gN/m^2/s T -NAM_NH4 AM-associated N uptake flux gN/m^2/s T -NAM_NO3 AM-associated N uptake flux gN/m^2/s T -NBP net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T -NDEPLOY total N deployed in new growth gN/m^2/s T -NDEP_PROF profile for atmospheric N deposition 1/m F -NDEP_TO_SMINN atmospheric N deposition to soil mineral N gN/m^2/s T -NECM ECM-associated N uptake flux gN/m^2/s T -NECM_NH4 ECM-associated N uptake flux gN/m^2/s T -NECM_NO3 ECM-associated N uptake flux gN/m^2/s T -NEE net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T -NEM Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T -NEP net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T -NET_NMIN net rate of N mineralization gN/m^2/s T -NET_NMIN_vr net rate of N mineralization gN/m^3/s F -NFERTILIZATION fertilizer added gN/m^2/s T -NFIRE fire counts valid only in Reg.C counts/km2/sec T -NFIX Symbiotic BNF uptake flux gN/m^2/s T -NFIXATION_PROF profile for biological N fixation 1/m F -NFIX_TO_SMINN symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F -NNONMYC Non-mycorrhizal N uptake flux gN/m^2/s T -NNONMYC_NH4 Non-mycorrhizal N uptake flux gN/m^2/s T -NNONMYC_NO3 Non-mycorrhizal N uptake flux gN/m^2/s T -NPASSIVE Passive N uptake flux gN/m^2/s T -NPOOL temporary plant N pool gN/m^2 T -NPOOL_TO_DEADCROOTN allocation to dead coarse root N gN/m^2/s F -NPOOL_TO_DEADCROOTN_STORAGE allocation to dead coarse root N storage gN/m^2/s F -NPOOL_TO_DEADSTEMN allocation to dead stem N gN/m^2/s F -NPOOL_TO_DEADSTEMN_STORAGE allocation to dead stem N storage gN/m^2/s F -NPOOL_TO_FROOTN allocation to fine root N gN/m^2/s F -NPOOL_TO_FROOTN_STORAGE allocation to fine root N storage gN/m^2/s F -NPOOL_TO_LEAFN allocation to leaf N gN/m^2/s F -NPOOL_TO_LEAFN_STORAGE allocation to leaf N storage gN/m^2/s F -NPOOL_TO_LIVECROOTN allocation to live coarse root N gN/m^2/s F -NPOOL_TO_LIVECROOTN_STORAGE allocation to live coarse root N storage gN/m^2/s F -NPOOL_TO_LIVESTEMN allocation to live stem N gN/m^2/s F -NPOOL_TO_LIVESTEMN_STORAGE allocation to live stem N storage gN/m^2/s F -NPP net primary production gC/m^2/s T -NPP_BURNEDOFF C that cannot be used for N uptake gC/m^2/s F -NPP_GROWTH Total C used for growth in FUN gC/m^2/s T -NPP_NACTIVE Mycorrhizal N uptake used C gC/m^2/s T -NPP_NACTIVE_NH4 Mycorrhizal N uptake use C gC/m^2/s T -NPP_NACTIVE_NO3 Mycorrhizal N uptake used C gC/m^2/s T -NPP_NAM AM-associated N uptake used C gC/m^2/s T -NPP_NAM_NH4 AM-associated N uptake use C gC/m^2/s T -NPP_NAM_NO3 AM-associated N uptake use C gC/m^2/s T -NPP_NECM ECM-associated N uptake used C gC/m^2/s T -NPP_NECM_NH4 ECM-associated N uptake use C gC/m^2/s T -NPP_NECM_NO3 ECM-associated N uptake used C gC/m^2/s T -NPP_NFIX Symbiotic BNF uptake used C gC/m^2/s T -NPP_NNONMYC Non-mycorrhizal N uptake used C gC/m^2/s T -NPP_NNONMYC_NH4 Non-mycorrhizal N uptake use C gC/m^2/s T -NPP_NNONMYC_NO3 Non-mycorrhizal N uptake use C gC/m^2/s T -NPP_NRETRANS Retranslocated N uptake flux gC/m^2/s T -NPP_NUPTAKE Total C used by N uptake in FUN gC/m^2/s T -NRETRANS Retranslocated N uptake flux gN/m^2/s T -NRETRANS_REG Retranslocated N uptake flux gN/m^2/s T -NRETRANS_SEASON Retranslocated N uptake flux gN/m^2/s T -NRETRANS_STRESS Retranslocated N uptake flux gN/m^2/s T -NSUBSTEPS number of adaptive timesteps in CLM timestep unitless F -NUPTAKE Total N uptake of FUN gN/m^2/s T -NUPTAKE_NPP_FRACTION frac of NPP used in N uptake - T -N_ALLOMETRY N allocation index none F -O2_DECOMP_DEPTH_UNSAT O2 consumption from HR and AR for non-inundated area mol/m3/s F -OBU Monin-Obukhov length m F -OCDEP total OC deposition (dry+wet) from atmosphere kg/m^2/s T -OFFSET_COUNTER offset days counter days F -OFFSET_FDD offset freezing degree days counter C degree-days F -OFFSET_FLAG offset flag none F -OFFSET_SWI offset soil water index none F -ONSET_COUNTER onset days counter days F -ONSET_FDD onset freezing degree days counter C degree-days F -ONSET_FLAG onset flag none F -ONSET_GDD onset growing degree days C degree-days F -ONSET_GDDFLAG onset flag for growing degree day sum none F -ONSET_SWI onset soil water index none F -O_SCALAR fraction by which decomposition is reduced due to anoxia unitless T -PAR240DZ 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F -PAR240XZ 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F -PAR240_shade shade PAR (240 hrs) umol/m2/s F -PAR240_sun sunlit PAR (240 hrs) umol/m2/s F -PAR24_shade shade PAR (24 hrs) umol/m2/s F -PAR24_sun sunlit PAR (24 hrs) umol/m2/s F -PARVEGLN absorbed par by vegetation at local noon W/m^2 T -PAR_shade shade PAR umol/m2/s F -PAR_sun sunlit PAR umol/m2/s F -PAS_SOMC PAS_SOM C gC/m^2 T -PAS_SOMC_1m PAS_SOM C to 1 meter gC/m^2 F -PAS_SOMC_TNDNCY_VERT_TRA passive soil organic C tendency due to vertical transport gC/m^3/s F -PAS_SOMC_TO_ACT_SOMC decomp. of passive soil organic C to active soil organic C gC/m^2/s F -PAS_SOMC_TO_ACT_SOMC_vr decomp. of passive soil organic C to active soil organic C gC/m^3/s F -PAS_SOMC_vr PAS_SOM C (vertically resolved) gC/m^3 T -PAS_SOMN PAS_SOM N gN/m^2 T -PAS_SOMN_1m PAS_SOM N to 1 meter gN/m^2 F -PAS_SOMN_TNDNCY_VERT_TRA passive soil organic N tendency due to vertical transport gN/m^3/s F -PAS_SOMN_TO_ACT_SOMN decomp. of passive soil organic N to active soil organic N gN/m^2 F -PAS_SOMN_TO_ACT_SOMN_vr decomp. of passive soil organic N to active soil organic N gN/m^3 F -PAS_SOMN_vr PAS_SOM N (vertically resolved) gN/m^3 T -PAS_SOM_HR Het. Resp. from passive soil organic gC/m^2/s F -PAS_SOM_HR_vr Het. Resp. from passive soil organic gC/m^3/s F -PBOT atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T -PBOT_240 10 day running mean of air pressure Pa F -PCH4 atmospheric partial pressure of CH4 Pa T -PCO2 atmospheric partial pressure of CO2 Pa T -PCO2_240 10 day running mean of CO2 pressure Pa F -PFT_CTRUNC patch-level sink for C truncation gC/m^2 F -PFT_FIRE_CLOSS total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T -PFT_FIRE_NLOSS total patch-level fire N loss gN/m^2/s T -PFT_NTRUNC patch-level sink for N truncation gN/m^2 F -PLANTCN Plant C:N used by FUN unitless F -PLANT_CALLOC total allocated C flux gC/m^2/s F -PLANT_NALLOC total allocated N flux gN/m^2/s F -PLANT_NDEMAND N flux required to support initial GPP gN/m^2/s T -PNLCZ Proportion of nitrogen allocated for light capture unitless F -PO2_240 10 day running mean of O2 pressure Pa F -POTENTIAL_IMMOB potential N immobilization gN/m^2/s T -POTENTIAL_IMMOB_vr potential N immobilization gN/m^3/s F -POT_F_DENIT potential denitrification flux gN/m^2/s T -POT_F_DENIT_vr potential denitrification flux gN/m^3/s F -POT_F_NIT potential nitrification flux gN/m^2/s T -POT_F_NIT_vr potential nitrification flux gN/m^3/s F -PREC10 10-day running mean of PREC MM H2O/S F -PREC60 60-day running mean of PREC MM H2O/S F -PREV_DAYL daylength from previous timestep s F -PREV_FROOTC_TO_LITTER previous timestep froot C litterfall flux gC/m^2/s F -PREV_LEAFC_TO_LITTER previous timestep leaf C litterfall flux gC/m^2/s F -PROD100C 100-yr wood product C gC/m^2 F -PROD100C_LOSS loss from 100-yr wood product pool gC/m^2/s F -PROD100N 100-yr wood product N gN/m^2 F -PROD100N_LOSS loss from 100-yr wood product pool gN/m^2/s F -PROD10C 10-yr wood product C gC/m^2 F -PROD10C_LOSS loss from 10-yr wood product pool gC/m^2/s F -PROD10N 10-yr wood product N gN/m^2 F -PROD10N_LOSS loss from 10-yr wood product pool gN/m^2/s F -PSNSHA shaded leaf photosynthesis umolCO2/m^2/s T -PSNSHADE_TO_CPOOL C fixation from shaded canopy gC/m^2/s T -PSNSUN sunlit leaf photosynthesis umolCO2/m^2/s T -PSNSUN_TO_CPOOL C fixation from sunlit canopy gC/m^2/s T -PSurf atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F -Q2M 2m specific humidity kg/kg T -QAF canopy air humidity kg/kg F -QBOT atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T -QDIRECT_THROUGHFALL direct throughfall of liquid (rain + above-canopy irrigation) mm/s F -QDIRECT_THROUGHFALL_SNOW direct throughfall of snow mm/s F -QDRAI sub-surface drainage mm/s T -QDRAI_PERCH perched wt drainage mm/s T -QDRAI_XS saturation excess drainage mm/s T -QDRIP rate of excess canopy liquid falling off canopy mm/s F -QDRIP_SNOW rate of excess canopy snow falling off canopy mm/s F -QFLOOD runoff from river flooding mm/s T -QFLX_EVAP_TOT qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T -QFLX_EVAP_VEG vegetation evaporation mm H2O/s F -QFLX_ICE_DYNBAL ice dynamic land cover change conversion runoff flux mm/s T -QFLX_LIQDEW_TO_TOP_LAYER rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T -QFLX_LIQEVAP_FROM_TOP_LAYER rate of liquid water evaporated from top soil or snow layer mm H2O/s T -QFLX_LIQ_DYNBAL liq dynamic land cover change conversion runoff flux mm/s T -QFLX_LIQ_GRND liquid (rain+irrigation) on ground after interception mm H2O/s F -QFLX_SNOW_DRAIN drainage from snow pack mm/s T -QFLX_SNOW_DRAIN_ICE drainage from snow pack melt (ice landunits only) mm/s T -QFLX_SNOW_GRND snow on ground after interception mm H2O/s F -QFLX_SOLIDDEW_TO_TOP_LAYER rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T -QFLX_SOLIDEVAP_FROM_TOP_LAYER rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T -QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F -QH2OSFC surface water runoff mm/s T -QH2OSFC_TO_ICE surface water converted to ice mm/s F -QHR hydraulic redistribution mm/s T -QICE ice growth/melt mm/s T -QICE_FORC qice forcing sent to GLC mm/s F -QICE_FRZ ice growth mm/s T -QICE_MELT ice melt mm/s T -QINFL infiltration mm/s T -QINTR interception mm/s T -QIRRIG_DEMAND irrigation demand mm/s F -QIRRIG_DRIP water added via drip irrigation mm/s F -QIRRIG_FROM_GW_CONFINED water added through confined groundwater irrigation mm/s T -QIRRIG_FROM_GW_UNCONFINED water added through unconfined groundwater irrigation mm/s T -QIRRIG_FROM_SURFACE water added through surface water irrigation mm/s T -QIRRIG_SPRINKLER water added via sprinkler irrigation mm/s F -QOVER total surface runoff (includes QH2OSFC) mm/s T -QOVER_LAG time-lagged surface runoff for soil columns mm/s F -QPHSNEG net negative hydraulic redistribution flux mm/s F -QRGWL surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T -QROOTSINK water flux from soil to root in each soil-layer mm/s F -QRUNOFF total liquid runoff not including correction for land use change mm/s T -QRUNOFF_ICE total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T -QRUNOFF_ICE_TO_COUPLER total ice runoff sent to coupler (includes corrections for land use change) mm/s T -QRUNOFF_ICE_TO_LIQ liquid runoff from converted ice runoff mm/s F -QRUNOFF_R Rural total runoff mm/s F -QRUNOFF_TO_COUPLER total liquid runoff sent to coupler (includes corrections for land use change) mm/s T -QRUNOFF_U Urban total runoff mm/s F -QSNOCPLIQ excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T -QSNOEVAP evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T -QSNOFRZ column-integrated snow freezing rate kg/m2/s T -QSNOFRZ_ICE column-integrated snow freezing rate (ice landunits only) mm/s T -QSNOMELT snow melt rate mm/s T -QSNOMELT_ICE snow melt (ice landunits only) mm/s T -QSNOUNLOAD canopy snow unloading mm/s T -QSNO_TEMPUNLOAD canopy snow temp unloading mm/s T -QSNO_WINDUNLOAD canopy snow wind unloading mm/s T -QSNWCPICE excess solid h2o due to snow capping not including correction for land use change mm H2O/s T -QSOIL Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T -QSOIL_ICE Ground evaporation (ice landunits only) mm/s T -QTOPSOIL water input to surface mm/s F -QVEGE canopy evaporation mm/s T -QVEGT canopy transpiration mm/s T -Qair atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F -Qh sensible heat W/m^2 F -Qle total evaporation W/m^2 F -Qstor storage heat flux (includes snowmelt) W/m^2 F -Qtau momentum flux kg/m/s^2 F -RAH1 aerodynamical resistance s/m F -RAH2 aerodynamical resistance s/m F -RAIN atmospheric rain, after rain/snow repartitioning based on temperature mm/s T -RAIN_FROM_ATM atmospheric rain received from atmosphere (pre-repartitioning) mm/s T -RAIN_ICE atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -RAM1 aerodynamical resistance s/m F -RAM_LAKE aerodynamic resistance for momentum (lakes only) s/m F -RAW1 aerodynamical resistance s/m F -RAW2 aerodynamical resistance s/m F -RB leaf boundary resistance s/m F -RB10 10 day running mean boundary layer resistance s/m F -RETRANSN plant pool of retranslocated N gN/m^2 T -RETRANSN_TO_NPOOL deployment of retranslocated N gN/m^2/s T -RH atmospheric relative humidity % F -RH2M 2m relative humidity % T -RH2M_R Rural 2m specific humidity % F -RH2M_U Urban 2m relative humidity % F -RH30 30-day running mean of relative humidity % F -RHAF fractional humidity of canopy air fraction F -RHAF10 10 day running mean of fractional humidity of canopy air fraction F -RH_LEAF fractional humidity at leaf surface fraction F -ROOTR effective fraction of roots in each soil layer (SMS method) proportion F -RR root respiration (fine root MR + total root GR) gC/m^2/s T -RRESIS root resistance in each soil layer proportion F -RSSHA shaded leaf stomatal resistance s/m T -RSSUN sunlit leaf stomatal resistance s/m T -Rainf atmospheric rain, after rain/snow repartitioning based on temperature mm/s F -Rnet net radiation W/m^2 F -S1_PATHFRAC_S2_vr PATHFRAC from active soil organic to slow soil organic ma fraction F -S1_PATHFRAC_S3_vr PATHFRAC from active soil organic to passive soil organic fraction F -S1_RESP_FRAC_S2_vr respired from active soil organic to slow soil organic ma fraction F -S1_RESP_FRAC_S3_vr respired from active soil organic to passive soil organic fraction F -S2_PATHFRAC_S1_vr PATHFRAC from slow soil organic ma to active soil organic fraction F -S2_PATHFRAC_S3_vr PATHFRAC from slow soil organic ma to passive soil organic fraction F -S2_RESP_FRAC_S1_vr respired from slow soil organic ma to active soil organic fraction F -S2_RESP_FRAC_S3_vr respired from slow soil organic ma to passive soil organic fraction F -S3_PATHFRAC_S1_vr PATHFRAC from passive soil organic to active soil organic fraction F -S3_RESP_FRAC_S1_vr respired from passive soil organic to active soil organic fraction F -SABG solar rad absorbed by ground W/m^2 T -SABG_PEN Rural solar rad penetrating top soil or snow layer watt/m^2 T -SABV solar rad absorbed by veg W/m^2 T -SDATES actual crop sowing dates; should only be output annually day of year F -SDATES_PERHARV actual sowing dates for crops harvested this year; should only be output annually day of year F -SEEDC pool for seeding new PFTs via dynamic landcover gC/m^2 T -SEEDN pool for seeding new PFTs via dynamic landcover gN/m^2 T -SLASH_HARVESTC slash harvest carbon (to litter) gC/m^2/s T -SLO_SOMC SLO_SOM C gC/m^2 T -SLO_SOMC_1m SLO_SOM C to 1 meter gC/m^2 F -SLO_SOMC_TNDNCY_VERT_TRA slow soil organic ma C tendency due to vertical transport gC/m^3/s F -SLO_SOMC_TO_ACT_SOMC decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F -SLO_SOMC_TO_ACT_SOMC_vr decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F -SLO_SOMC_TO_PAS_SOMC decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F -SLO_SOMC_TO_PAS_SOMC_vr decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F -SLO_SOMC_vr SLO_SOM C (vertically resolved) gC/m^3 T -SLO_SOMN SLO_SOM N gN/m^2 T -SLO_SOMN_1m SLO_SOM N to 1 meter gN/m^2 F -SLO_SOMN_TNDNCY_VERT_TRA slow soil organic ma N tendency due to vertical transport gN/m^3/s F -SLO_SOMN_TO_ACT_SOMN decomp. of slow soil organic ma N to active soil organic N gN/m^2 F -SLO_SOMN_TO_ACT_SOMN_vr decomp. of slow soil organic ma N to active soil organic N gN/m^3 F -SLO_SOMN_TO_PAS_SOMN decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F -SLO_SOMN_TO_PAS_SOMN_vr decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F -SLO_SOMN_vr SLO_SOM N (vertically resolved) gN/m^3 T -SLO_SOM_HR_S1 Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S1_vr Het. Resp. from slow soil organic ma gC/m^3/s F -SLO_SOM_HR_S3 Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S3_vr Het. Resp. from slow soil organic ma gC/m^3/s F -SMINN soil mineral N gN/m^2 T -SMINN_TO_NPOOL deployment of soil mineral N uptake gN/m^2/s T -SMINN_TO_PLANT plant uptake of soil mineral N gN/m^2/s T -SMINN_TO_PLANT_FUN Total soil N uptake of FUN gN/m^2/s T -SMINN_TO_PLANT_vr plant uptake of soil mineral N gN/m^3/s F -SMINN_TO_S1N_L1 mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L1_vr mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_L2 mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L2_vr mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S2 mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S2_vr mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S3 mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S3_vr mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S2N_L3 mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -SMINN_TO_S2N_L3_vr mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -SMINN_TO_S2N_S1 mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -SMINN_TO_S2N_S1_vr mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -SMINN_TO_S3N_S1 mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S1_vr mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -SMINN_TO_S3N_S2 mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S2_vr mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -SMINN_vr soil mineral N gN/m^3 T -SMIN_NH4 soil mineral NH4 gN/m^2 T -SMIN_NH4_TO_PLANT plant uptake of NH4 gN/m^3/s F -SMIN_NH4_vr soil mineral NH4 (vert. res.) gN/m^3 T -SMIN_NO3 soil mineral NO3 gN/m^2 T -SMIN_NO3_LEACHED soil NO3 pool loss to leaching gN/m^2/s T -SMIN_NO3_LEACHED_vr soil NO3 pool loss to leaching gN/m^3/s F -SMIN_NO3_MASSDENS SMIN_NO3_MASSDENS ugN/cm^3 soil F -SMIN_NO3_RUNOFF soil NO3 pool loss to runoff gN/m^2/s T -SMIN_NO3_RUNOFF_vr soil NO3 pool loss to runoff gN/m^3/s F -SMIN_NO3_TO_PLANT plant uptake of NO3 gN/m^3/s F -SMIN_NO3_vr soil mineral NO3 (vert. res.) gN/m^3 T -SMP soil matric potential (natural vegetated and crop landunits only) mm T -SNOBCMCL mass of BC in snow column kg/m2 T -SNOBCMSL mass of BC in top snow layer kg/m2 T -SNOCAN intercepted snow mm T -SNODSTMCL mass of dust in snow column kg/m2 T -SNODSTMSL mass of dust in top snow layer kg/m2 T -SNOFSDSND direct nir incident solar radiation on snow W/m^2 F -SNOFSDSNI diffuse nir incident solar radiation on snow W/m^2 F -SNOFSDSVD direct vis incident solar radiation on snow W/m^2 F -SNOFSDSVI diffuse vis incident solar radiation on snow W/m^2 F -SNOFSRND direct nir reflected solar radiation from snow W/m^2 T -SNOFSRNI diffuse nir reflected solar radiation from snow W/m^2 T -SNOFSRVD direct vis reflected solar radiation from snow W/m^2 T -SNOFSRVI diffuse vis reflected solar radiation from snow W/m^2 T -SNOINTABS Fraction of incoming solar absorbed by lower snow layers - T -SNOLIQFL top snow layer liquid water fraction (land) fraction F -SNOOCMCL mass of OC in snow column kg/m2 T -SNOOCMSL mass of OC in top snow layer kg/m2 T -SNORDSL top snow layer effective grain radius m^-6 F -SNOTTOPL snow temperature (top layer) K F -SNOTTOPL_ICE snow temperature (top layer, ice landunits only) K F -SNOTXMASS snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T -SNOTXMASS_ICE snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F -SNOW atmospheric snow, after rain/snow repartitioning based on temperature mm/s T -SNOWDP gridcell mean snow height m T -SNOWICE snow ice kg/m2 T -SNOWICE_ICE snow ice (ice landunits only) kg/m2 F -SNOWLIQ snow liquid water kg/m2 T -SNOWLIQ_ICE snow liquid water (ice landunits only) kg/m2 F -SNOW_5D 5day snow avg m F -SNOW_DEPTH snow height of snow covered area m T -SNOW_DEPTH_ICE snow height of snow covered area (ice landunits only) m F -SNOW_FROM_ATM atmospheric snow received from atmosphere (pre-repartitioning) mm/s T -SNOW_ICE atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F -SNOW_PERSISTENCE Length of time of continuous snow cover (nat. veg. landunits only) seconds T -SNOW_SINKS snow sinks (liquid water) mm/s T -SNOW_SOURCES snow sources (liquid water) mm/s T -SNO_ABS Absorbed solar radiation in each snow layer W/m^2 F -SNO_ABS_ICE Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -SNO_BW Partial density of water in the snow pack (ice + liquid) kg/m3 F -SNO_BW_ICE Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -SNO_EXISTENCE Fraction of averaging period for which each snow layer existed unitless F -SNO_FRZ snow freezing rate in each snow layer kg/m2/s F -SNO_FRZ_ICE snow freezing rate in each snow layer (ice landunits only) mm/s F -SNO_GS Mean snow grain size Microns F -SNO_GS_ICE Mean snow grain size (ice landunits only) Microns F -SNO_ICE Snow ice content kg/m2 F -SNO_LIQH2O Snow liquid water content kg/m2 F -SNO_MELT snow melt rate in each snow layer mm/s F -SNO_MELT_ICE snow melt rate in each snow layer (ice landunits only) mm/s F -SNO_T Snow temperatures K F -SNO_TK Thermal conductivity W/m-K F -SNO_TK_ICE Thermal conductivity (ice landunits only) W/m-K F -SNO_T_ICE Snow temperatures (ice landunits only) K F -SNO_Z Snow layer thicknesses m F -SNO_Z_ICE Snow layer thicknesses (ice landunits only) m F -SNOdTdzL top snow layer temperature gradient (land) K/m F -SOIL10 10-day running mean of 12cm layer soil K F -SOILC_CHANGE C change in soil gC/m^2/s T -SOILC_HR soil C heterotrophic respiration gC/m^2/s T -SOILC_vr SOIL C (vertically resolved) gC/m^3 T -SOILICE soil ice (natural vegetated and crop landunits only) kg/m2 T -SOILLIQ soil liquid water (natural vegetated and crop landunits only) kg/m2 T -SOILN_vr SOIL N (vertically resolved) gN/m^3 T -SOILPSI soil water potential in each soil layer MPa F -SOILRESIS soil resistance to evaporation s/m T -SOILWATER_10CM soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T -SOMC_FIRE C loss due to peat burning gC/m^2/s T -SOMFIRE soil organic matter fire losses gC/m^2/s F -SOM_ADV_COEF advection term for vertical SOM translocation m/s F -SOM_C_LEACHED total flux of C from SOM pools due to leaching gC/m^2/s T -SOM_DIFFUS_COEF diffusion coefficient for vertical SOM translocation m^2/s F -SOM_N_LEACHED total flux of N from SOM pools due to leaching gN/m^2/s F -SOWING_REASON Reason for each crop sowing; should only be output annually unitless F -SOWING_REASON_PERHARV Reason for sowing of each crop harvested this year; should only be output annually unitless F -SR total soil respiration (HR + root resp) gC/m^2/s T -STEM_PROF profile for litter C and N inputs from stems 1/m F -STORAGE_CDEMAND C use from the C storage pool gC/m^2 F -STORAGE_GR growth resp for growth sent to storage for later display gC/m^2/s F -STORAGE_NDEMAND N demand during the offset period gN/m^2 F -STORVEGC stored vegetation carbon, excluding cpool gC/m^2 T -STORVEGN stored vegetation nitrogen gN/m^2 T -SUPPLEMENT_TO_SMINN supplemental N supply gN/m^2/s T -SUPPLEMENT_TO_SMINN_vr supplemental N supply gN/m^3/s F -SWBGT 2 m Simplified Wetbulb Globe Temp C T -SWBGT_R Rural 2 m Simplified Wetbulb Globe Temp C T -SWBGT_U Urban 2 m Simplified Wetbulb Globe Temp C T -SWdown atmospheric incident solar radiation W/m^2 F -SWup upwelling shortwave radiation W/m^2 F -SYEARS_PERHARV actual sowing years for crops harvested this year; should only be output annually year F -SoilAlpha factor limiting ground evap unitless F -SoilAlpha_U urban factor limiting ground evap unitless F -T10 10-day running mean of 2-m temperature K F -TAF canopy air temperature K F -TAUX zonal surface stress kg/m/s^2 T -TAUY meridional surface stress kg/m/s^2 T -TBOT atmospheric air temperature (downscaled to columns in glacier regions) K T -TBUILD internal urban building air temperature K T -TBUILD_MAX prescribed maximum interior building temperature K F -TEMPAVG_T2M temporary average 2m air temperature K F -TEMPMAX_RETRANSN temporary annual max of retranslocated N pool gN/m^2 F -TEMPSUM_POTENTIAL_GPP temporary annual sum of potential GPP gC/m^2/yr F -TFLOOR floor temperature K F -TG ground temperature K T -TG_ICE ground temperature (ice landunits only) K F -TG_R Rural ground temperature K F -TG_U Urban ground temperature K F -TH2OSFC surface water temperature K T -THBOT atmospheric air potential temperature (downscaled to columns in glacier regions) K T -TKE1 top lake level eddy thermal conductivity W/(mK) T -TLAI total projected leaf area index m^2/m^2 T -TLAKE lake temperature K T -TOPO_COL column-level topographic height m F -TOPO_COL_ICE column-level topographic height (ice landunits only) m F -TOPO_FORC topograephic height sent to GLC m F -TOPT topt coefficient for VOC calc non F -TOTCOLC total column carbon, incl veg and cpool but excl product pools gC/m^2 T -TOTCOLCH4 total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T -TOTCOLN total column-level N, excluding product pools gN/m^2 T -TOTECOSYSC total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T -TOTECOSYSN total ecosystem N, excluding product pools gN/m^2 T -TOTFIRE total ecosystem fire losses gC/m^2/s F -TOTLITC total litter carbon gC/m^2 T -TOTLITC_1m total litter carbon to 1 meter depth gC/m^2 T -TOTLITN total litter N gN/m^2 T -TOTLITN_1m total litter N to 1 meter gN/m^2 T -TOTPFTC total patch-level carbon, including cpool gC/m^2 T -TOTPFTN total patch-level nitrogen gN/m^2 T -TOTSOILICE vertically summed soil cie (veg landunits only) kg/m2 T -TOTSOILLIQ vertically summed soil liquid water (veg landunits only) kg/m2 T -TOTSOMC total soil organic matter carbon gC/m^2 T -TOTSOMC_1m total soil organic matter carbon to 1 meter depth gC/m^2 T -TOTSOMN total soil organic matter N gN/m^2 T -TOTSOMN_1m total soil organic matter N to 1 meter gN/m^2 T -TOTVEGC total vegetation carbon, excluding cpool gC/m^2 T -TOTVEGN total vegetation nitrogen gN/m^2 T -TOT_WOODPRODC total wood product C gC/m^2 T -TOT_WOODPRODC_LOSS total loss from wood product pools gC/m^2/s T -TOT_WOODPRODN total wood product N gN/m^2 T -TOT_WOODPRODN_LOSS total loss from wood product pools gN/m^2/s T -TPU25T canopy profile of tpu umol/m2/s T -TRAFFICFLUX sensible heat flux from urban traffic W/m^2 F -TRANSFER_DEADCROOT_GR dead coarse root growth respiration from storage gC/m^2/s F -TRANSFER_DEADSTEM_GR dead stem growth respiration from storage gC/m^2/s F -TRANSFER_FROOT_GR fine root growth respiration from storage gC/m^2/s F -TRANSFER_GR growth resp for transfer growth displayed in this timestep gC/m^2/s F -TRANSFER_LEAF_GR leaf growth respiration from storage gC/m^2/s F -TRANSFER_LIVECROOT_GR live coarse root growth respiration from storage gC/m^2/s F -TRANSFER_LIVESTEM_GR live stem growth respiration from storage gC/m^2/s F -TREFMNAV daily minimum of average 2-m temperature K T -TREFMNAV_R Rural daily minimum of average 2-m temperature K F -TREFMNAV_U Urban daily minimum of average 2-m temperature K F -TREFMXAV daily maximum of average 2-m temperature K T -TREFMXAV_R Rural daily maximum of average 2-m temperature K F -TREFMXAV_U Urban daily maximum of average 2-m temperature K F -TROOF_INNER roof inside surface temperature K F -TSA 2m air temperature K T -TSAI total projected stem area index m^2/m^2 T -TSA_ICE 2m air temperature (ice landunits only) K F -TSA_R Rural 2m air temperature K F -TSA_U Urban 2m air temperature K F -TSHDW_INNER shadewall inside surface temperature K F -TSKIN skin temperature K T -TSL temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -TSOI soil temperature (natural vegetated and crop landunits only) K T -TSOI_10CM soil temperature in top 10cm of soil K T -TSOI_ICE soil temperature (ice landunits only) K T -TSRF_FORC surface temperature sent to GLC K F -TSUNW_INNER sunwall inside surface temperature K F -TV vegetation temperature K T -TV24 vegetation temperature (last 24hrs) K F -TV240 vegetation temperature (last 240hrs) K F -TVEGD10 10 day running mean of patch daytime vegetation temperature Kelvin F -TVEGN10 10 day running mean of patch night-time vegetation temperature Kelvin F -TWS total water storage mm T -T_SCALAR temperature inhibition of decomposition unitless T -Tair atmospheric air temperature (downscaled to columns in glacier regions) K F -Tair_from_atm atmospheric air temperature received from atmosphere (pre-downscaling) K F -U10 10-m wind m/s T -U10_DUST 10-m wind for dust model m/s T -U10_ICE 10-m wind (ice landunits only) m/s F -UAF canopy air speed m/s F -ULRAD upward longwave radiation above the canopy W/m^2 F -UM wind speed plus stability effect m/s F -URBAN_AC urban air conditioning flux W/m^2 T -URBAN_HEAT urban heating flux W/m^2 T -USTAR aerodynamical resistance s/m F -UST_LAKE friction velocity (lakes only) m/s F -VA atmospheric wind speed plus convective velocity m/s F -VCMX25T canopy profile of vcmax25 umol/m2/s T -VEGWP vegetation water matric potential for sun/sha canopy,xyl,root segments mm T -VEGWPLN vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T -VEGWPPD predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T -VENTILATION sensible heat flux from building ventilation W/m^2 T -VOCFLXT total VOC flux into atmosphere moles/m2/sec F -VOLR river channel total water storage m3 T -VOLRMCH river channel main channel water storage m3 T -VPD vpd Pa F -VPD2M 2m vapor pressure deficit Pa T -VPD_CAN canopy vapor pressure deficit kPa T -Vcmx25Z canopy profile of vcmax25 predicted by LUNA model umol/m2/s T -WASTEHEAT sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T -WBT 2 m Stull Wet Bulb C T -WBT_R Rural 2 m Stull Wet Bulb C T -WBT_U Urban 2 m Stull Wet Bulb C T -WF soil water as frac. of whc for top 0.05 m proportion F -WFPS WFPS percent F -WIND atmospheric wind velocity magnitude m/s T -WOODC wood C gC/m^2 T -WOODC_ALLOC wood C eallocation gC/m^2/s T -WOODC_LOSS wood C loss gC/m^2/s T -WOOD_HARVESTC wood harvest carbon (to product pools) gC/m^2/s T -WOOD_HARVESTN wood harvest N (to product pools) gN/m^2/s T -WTGQ surface tracer conductance m/s T -W_SCALAR Moisture (dryness) inhibition of decomposition unitless T -Wind atmospheric wind velocity magnitude m/s F -XSMRPOOL temporary photosynthate C pool gC/m^2 T -XSMRPOOL_LOSS temporary photosynthate C pool loss gC/m^2 F -XSMRPOOL_RECOVER C flux assigned to recovery of negative xsmrpool gC/m^2/s T -Z0HG roughness length over ground, sensible heat (vegetated landunits only) m F -Z0HV roughness length over vegetation, sensible heat m F -Z0MG roughness length over ground, momentum (vegetated landunits only) m F -Z0MV roughness length over vegetation, momentum m F -Z0MV_DENSE roughness length over vegetation, momentum, for dense canopy m F -Z0M_TO_COUPLER roughness length, momentum: gridcell average sent to coupler m F -Z0QG roughness length over ground, latent heat (vegetated landunits only) m F -Z0QV roughness length over vegetation, latent heat m F -ZBOT atmospheric reference height m T -ZETA dimensionless stability parameter unitless F -ZII convective boundary height m F -ZWT water table depth (natural vegetated and crop landunits only) m T -ZWT_CH4_UNSAT depth of water table for methane production used in non-inundated area m T -ZWT_PERCH perched water table depth (natural vegetated and crop landunits only) m T -anaerobic_frac anaerobic_frac m3/m3 F -bsw clap and hornberger B unitless F -currentPatch currentPatch coefficient for VOC calc non F -diffus diffusivity m^2/s F -fr_WFPS fr_WFPS fraction F -n2_n2o_ratio_denit n2_n2o_ratio_denit gN/gN F -num_iter number of iterations unitless F -r_psi r_psi m F -ratio_k1 ratio_k1 none F -ratio_no3_co2 ratio_no3_co2 ratio F -soil_bulkdensity soil_bulkdensity kg/m3 F -soil_co2_prod soil_co2_prod ug C / g soil / day F -watfc water field capacity m^3/m^3 F -watsat water saturated m^3/m^3 F -=================================== ============================================================================================== ================================================================= ======= +----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- + Variable Name Level Dim. Long Description Units Active? +=================================== ================ ============================================================================================== ================================================================= ======= +A10TMIN - 10-day running mean of min 2-m temperature K F +A5TMIN - 5-day running mean of min 2-m temperature K F +ACTUAL_IMMOB - actual N immobilization gN/m^2/s T +ACTUAL_IMMOB_NH4 levdcmp immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 levdcmp immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr levdcmp actual N immobilization gN/m^3/s F +ACT_SOMC - ACT_SOM C gC/m^2 T +ACT_SOMC_1m - ACT_SOM C to 1 meter gC/m^2 F +ACT_SOMC_TNDNCY_VERT_TRA levdcmp active soil organic C tendency due to vertical transport gC/m^3/s F +ACT_SOMC_TO_PAS_SOMC - decomp. of active soil organic C to passive soil organic C gC/m^2/s F +ACT_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of active soil organic C to passive soil organic C gC/m^3/s F +ACT_SOMC_TO_SLO_SOMC - decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +ACT_SOMC_TO_SLO_SOMC_vr levdcmp decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +ACT_SOMC_vr levsoi ACT_SOM C (vertically resolved) gC/m^3 T +ACT_SOMN - ACT_SOM N gN/m^2 T +ACT_SOMN_1m - ACT_SOM N to 1 meter gN/m^2 F +ACT_SOMN_TNDNCY_VERT_TRA levdcmp active soil organic N tendency due to vertical transport gN/m^3/s F +ACT_SOMN_TO_PAS_SOMN - decomp. of active soil organic N to passive soil organic N gN/m^2 F +ACT_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of active soil organic N to passive soil organic N gN/m^3 F +ACT_SOMN_TO_SLO_SOMN - decomp. of active soil organic N to slow soil organic ma N gN/m^2 F +ACT_SOMN_TO_SLO_SOMN_vr levdcmp decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +ACT_SOMN_vr levdcmp ACT_SOM N (vertically resolved) gN/m^3 T +ACT_SOM_HR_S2 - Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S2_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +ACT_SOM_HR_S3 - Het. Resp. from active soil organic gC/m^2/s F +ACT_SOM_HR_S3_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +AGLB - Aboveground leaf biomass kg/m^2 F +AGNPP - aboveground NPP gC/m^2/s T +AGSB - Aboveground stem biomass kg/m^2 F +ALBD numrad surface albedo (direct) proportion F +ALBGRD numrad ground albedo (direct) proportion F +ALBGRI numrad ground albedo (indirect) proportion F +ALBI numrad surface albedo (indirect) proportion F +ALPHA - alpha coefficient for VOC calc non F +ALT - current active layer thickness m T +ALTMAX - maximum annual active layer thickness m T +ALTMAX_LASTYEAR - maximum prior year active layer thickness m F +ANNAVG_T2M - annual average 2m air temperature K F +ANNMAX_RETRANSN - annual max of retranslocated N pool gN/m^2 F +ANNSUM_COUNTER - seconds since last annual accumulator turnover s F +ANNSUM_NPP - annual sum of NPP gC/m^2/yr F +ANNSUM_POTENTIAL_GPP - annual sum of potential GPP gN/m^2/yr F +AR - autotrophic respiration (MR + GR) gC/m^2/s T +ATM_O3 - atmospheric ozone partial pressure mol/mol F +ATM_TOPO - atmospheric surface height m T +AVAILC - C flux available for allocation gC/m^2/s F +AVAIL_RETRANSN - N flux available from retranslocation pool gN/m^2/s F +AnnET - Annual ET mm/s F +BAF_CROP - fractional area burned for crop s-1 T +BAF_PEATF - fractional area burned in peatland s-1 T +BCDEP - total BC deposition (dry+wet) from atmosphere kg/m^2/s T +BETA - coefficient of convective velocity none F +BGLFR - background litterfall rate 1/s F +BGNPP - belowground NPP gC/m^2/s T +BGTR - background transfer growth rate 1/s F +BTRANMN - daily minimum of transpiration beta factor unitless T +CANNAVG_T2M - annual average of 2m air temperature K F +CANNSUM_NPP - annual sum of column-level NPP gC/m^2/s F +CEL_LITC - CEL_LIT C gC/m^2 T +CEL_LITC_1m - CEL_LIT C to 1 meter gC/m^2 F +CEL_LITC_TNDNCY_VERT_TRA levdcmp cellulosic litter C tendency due to vertical transport gC/m^3/s F +CEL_LITC_TO_ACT_SOMC - decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +CEL_LITC_TO_ACT_SOMC_vr levdcmp decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +CEL_LITC_vr levsoi CEL_LIT C (vertically resolved) gC/m^3 T +CEL_LITN - CEL_LIT N gN/m^2 T +CEL_LITN_1m - CEL_LIT N to 1 meter gN/m^2 F +CEL_LITN_TNDNCY_VERT_TRA levdcmp cellulosic litter N tendency due to vertical transport gN/m^3/s F +CEL_LITN_TO_ACT_SOMN - decomp. of cellulosic litter N to active soil organic N gN/m^2 F +CEL_LITN_TO_ACT_SOMN_vr levdcmp decomp. of cellulosic litter N to active soil organic N gN/m^3 F +CEL_LITN_vr levdcmp CEL_LIT N (vertically resolved) gN/m^3 T +CEL_LIT_HR - Het. Resp. from cellulosic litter gC/m^2/s F +CEL_LIT_HR_vr levdcmp Het. Resp. from cellulosic litter gC/m^3/s F +CGRND - deriv. of soil energy flux wrt to soil temp W/m^2/K F +CGRNDL - deriv. of soil latent heat flux wrt soil temp W/m^2/K F +CGRNDS - deriv. of soil sensible heat flux wrt soil temp W/m^2/K F +CH4PROD - Gridcell total production of CH4 gC/m2/s T +CH4_EBUL_TOTAL_SAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_EBUL_TOTAL_UNSAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F +CH4_SURF_AERE_SAT - aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T +CH4_SURF_AERE_UNSAT - aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_SAT - diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_DIFF_UNSAT - diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_SAT - ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T +CH4_SURF_EBUL_UNSAT - ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T +COL_CTRUNC - column-level sink for C truncation gC/m^2 F +COL_FIRE_CLOSS - total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T +COL_FIRE_NLOSS - total column-level fire N loss gN/m^2/s T +COL_NTRUNC - column-level sink for N truncation gN/m^2 F +CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F +CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T +COST_NACTIVE - Cost of active uptake gN/gC T +COST_NFIX - Cost of fixation gN/gC T +COST_NRETRANS - Cost of retranslocation gN/gC T +COSZEN - cosine of solar zenith angle none F +CPHASE - crop phenology phase 0-not planted, 1-planted, 2-leaf emerge, 3-grain fill, 4-harvest T +CPOOL - temporary photosynthate C pool gC/m^2 T +CPOOL_DEADCROOT_GR - dead coarse root growth respiration gC/m^2/s F +CPOOL_DEADCROOT_STORAGE_GR - dead coarse root growth respiration to storage gC/m^2/s F +CPOOL_DEADSTEM_GR - dead stem growth respiration gC/m^2/s F +CPOOL_DEADSTEM_STORAGE_GR - dead stem growth respiration to storage gC/m^2/s F +CPOOL_FROOT_GR - fine root growth respiration gC/m^2/s F +CPOOL_FROOT_STORAGE_GR - fine root growth respiration to storage gC/m^2/s F +CPOOL_LEAF_GR - leaf growth respiration gC/m^2/s F +CPOOL_LEAF_STORAGE_GR - leaf growth respiration to storage gC/m^2/s F +CPOOL_LIVECROOT_GR - live coarse root growth respiration gC/m^2/s F +CPOOL_LIVECROOT_STORAGE_GR - live coarse root growth respiration to storage gC/m^2/s F +CPOOL_LIVESTEM_GR - live stem growth respiration gC/m^2/s F +CPOOL_LIVESTEM_STORAGE_GR - live stem growth respiration to storage gC/m^2/s F +CPOOL_TO_DEADCROOTC - allocation to dead coarse root C gC/m^2/s F +CPOOL_TO_DEADCROOTC_STORAGE - allocation to dead coarse root C storage gC/m^2/s F +CPOOL_TO_DEADSTEMC - allocation to dead stem C gC/m^2/s F +CPOOL_TO_DEADSTEMC_STORAGE - allocation to dead stem C storage gC/m^2/s F +CPOOL_TO_FROOTC - allocation to fine root C gC/m^2/s F +CPOOL_TO_FROOTC_STORAGE - allocation to fine root C storage gC/m^2/s F +CPOOL_TO_GRESP_STORAGE - allocation to growth respiration storage gC/m^2/s F +CPOOL_TO_LEAFC - allocation to leaf C gC/m^2/s F +CPOOL_TO_LEAFC_STORAGE - allocation to leaf C storage gC/m^2/s F +CPOOL_TO_LIVECROOTC - allocation to live coarse root C gC/m^2/s F +CPOOL_TO_LIVECROOTC_STORAGE - allocation to live coarse root C storage gC/m^2/s F +CPOOL_TO_LIVESTEMC - allocation to live stem C gC/m^2/s F +CPOOL_TO_LIVESTEMC_STORAGE - allocation to live stem C storage gC/m^2/s F +CROOT_PROF levdcmp profile for litter C and N inputs from coarse roots 1/m F +CROPPROD1C - 1-yr crop product (grain+biofuel) C gC/m^2 T +CROPPROD1C_LOSS - loss from 1-yr crop product pool gC/m^2/s T +CROPPROD1N - 1-yr crop product (grain+biofuel) N gN/m^2 T +CROPPROD1N_LOSS - loss from 1-yr crop product pool gN/m^2/s T +CROPSEEDC_DEFICIT - C used for crop seed that needs to be repaid gC/m^2 T +CROPSEEDN_DEFICIT - N used for crop seed that needs to be repaid gN/m^2 F +CROP_SEEDC_TO_LEAF - crop seed source to leaf gC/m^2/s F +CROP_SEEDN_TO_LEAF - crop seed source to leaf gN/m^2/s F +CURRENT_GR - growth resp for new growth displayed in this timestep gC/m^2/s F +CWDC - CWD C gC/m^2 T +CWDC_1m - CWD C to 1 meter gC/m^2 F +CWDC_HR - cwd C heterotrophic respiration gC/m^2/s T +CWDC_LOSS - coarse woody debris C loss gC/m^2/s T +CWDC_TO_CEL_LITC - decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F +CWDC_TO_CEL_LITC_vr levdcmp decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F +CWDC_TO_LIG_LITC - decomp. of coarse woody debris C to lignin litter C gC/m^2/s F +CWDC_TO_LIG_LITC_vr levdcmp decomp. of coarse woody debris C to lignin litter C gC/m^3/s F +CWDC_vr levsoi CWD C (vertically resolved) gC/m^3 T +CWDN - CWD N gN/m^2 T +CWDN_1m - CWD N to 1 meter gN/m^2 F +CWDN_TO_CEL_LITN - decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F +CWDN_TO_CEL_LITN_vr levdcmp decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F +CWDN_TO_LIG_LITN - decomp. of coarse woody debris N to lignin litter N gN/m^2 F +CWDN_TO_LIG_LITN_vr levdcmp decomp. of coarse woody debris N to lignin litter N gN/m^3 F +CWDN_vr levdcmp CWD N (vertically resolved) gN/m^3 T +CWD_HR_L2 - Het. Resp. from coarse woody debris gC/m^2/s F +CWD_HR_L2_vr levdcmp Het. Resp. from coarse woody debris gC/m^3/s F +CWD_HR_L3 - Het. Resp. from coarse woody debris gC/m^2/s F +CWD_HR_L3_vr levdcmp Het. Resp. from coarse woody debris gC/m^3/s F +CWD_PATHFRAC_L2_vr levdcmp PATHFRAC from coarse woody debris to cellulosic litter fraction F +CWD_PATHFRAC_L3_vr levdcmp PATHFRAC from coarse woody debris to lignin litter fraction F +CWD_RESP_FRAC_L2_vr levdcmp respired from coarse woody debris to cellulosic litter fraction F +CWD_RESP_FRAC_L3_vr levdcmp respired from coarse woody debris to lignin litter fraction F +C_ALLOMETRY - C allocation index none F +DAYL - daylength s F +DAYS_ACTIVE - number of days since last dormancy days F +DEADCROOTC - dead coarse root C gC/m^2 T +DEADCROOTC_STORAGE - dead coarse root C storage gC/m^2 F +DEADCROOTC_STORAGE_TO_XFER - dead coarse root C shift storage to transfer gC/m^2/s F +DEADCROOTC_XFER - dead coarse root C transfer gC/m^2 F +DEADCROOTC_XFER_TO_DEADCROOTC - dead coarse root C growth from storage gC/m^2/s F +DEADCROOTN - dead coarse root N gN/m^2 T +DEADCROOTN_STORAGE - dead coarse root N storage gN/m^2 F +DEADCROOTN_STORAGE_TO_XFER - dead coarse root N shift storage to transfer gN/m^2/s F +DEADCROOTN_XFER - dead coarse root N transfer gN/m^2 F +DEADCROOTN_XFER_TO_DEADCROOTN - dead coarse root N growth from storage gN/m^2/s F +DEADSTEMC - dead stem C gC/m^2 T +DEADSTEMC_STORAGE - dead stem C storage gC/m^2 F +DEADSTEMC_STORAGE_TO_XFER - dead stem C shift storage to transfer gC/m^2/s F +DEADSTEMC_XFER - dead stem C transfer gC/m^2 F +DEADSTEMC_XFER_TO_DEADSTEMC - dead stem C growth from storage gC/m^2/s F +DEADSTEMN - dead stem N gN/m^2 T +DEADSTEMN_STORAGE - dead stem N storage gN/m^2 F +DEADSTEMN_STORAGE_TO_XFER - dead stem N shift storage to transfer gN/m^2/s F +DEADSTEMN_XFER - dead stem N transfer gN/m^2 F +DEADSTEMN_XFER_TO_DEADSTEMN - dead stem N growth from storage gN/m^2/s F +DENIT - total rate of denitrification gN/m^2/s T +DGNETDT - derivative of net ground heat flux wrt soil temp W/m^2/K F +DISPLA - displacement height (vegetated landunits only) m F +DISPVEGC - displayed veg carbon, excluding storage and cpool gC/m^2 T +DISPVEGN - displayed vegetation nitrogen gN/m^2 T +DLRAD - downward longwave radiation below the canopy W/m^2 F +DORMANT_FLAG - dormancy flag none F +DOWNREG - fractional reduction in GPP due to N limitation proportion F +DPVLTRB1 - turbulent deposition velocity 1 m/s F +DPVLTRB2 - turbulent deposition velocity 2 m/s F +DPVLTRB3 - turbulent deposition velocity 3 m/s F +DPVLTRB4 - turbulent deposition velocity 4 m/s F +DSL - dry surface layer thickness mm T +DSTDEP - total dust deposition (dry+wet) from atmosphere kg/m^2/s T +DSTFLXT - total surface dust emission kg/m2/s T +DT_VEG - change in t_veg, last iteration K F +DWT_CONV_CFLUX - conversion C flux (immediate loss to atm) (0 at all times except first timestep of year) gC/m^2/s T +DWT_CONV_CFLUX_DRIBBLED - conversion C flux (immediate loss to atm), dribbled throughout the year gC/m^2/s T +DWT_CONV_CFLUX_PATCH - patch-level conversion C flux (immediate loss to atm) (0 at all times except first timestep of gC/m^2/s F +DWT_CONV_NFLUX - conversion N flux (immediate loss to atm) (0 at all times except first timestep of year) gN/m^2/s T +DWT_CONV_NFLUX_PATCH - patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F +DWT_CROPPROD1C_GAIN - landcover change-driven addition to 1-year crop product pool gC/m^2/s T +DWT_CROPPROD1N_GAIN - landcover change-driven addition to 1-year crop product pool gN/m^2/s T +DWT_DEADCROOTC_TO_CWDC levdcmp dead coarse root to CWD due to landcover change gC/m^2/s F +DWT_DEADCROOTN_TO_CWDN levdcmp dead coarse root to CWD due to landcover change gN/m^2/s F +DWT_FROOTC_TO_CEL_LIT_C levdcmp fine root to cellulosic litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_LIG_LIT_C levdcmp fine root to lignin litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_MET_LIT_C levdcmp fine root to metabolic litter due to landcover change gC/m^2/s F +DWT_FROOTN_TO_CEL_LIT_N levdcmp fine root N to cellulosic litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_LIG_LIT_N levdcmp fine root N to lignin litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_MET_LIT_N levdcmp fine root N to metabolic litter due to landcover change gN/m^2/s F +DWT_LIVECROOTC_TO_CWDC levdcmp live coarse root to CWD due to landcover change gC/m^2/s F +DWT_LIVECROOTN_TO_CWDN levdcmp live coarse root to CWD due to landcover change gN/m^2/s F +DWT_PROD100C_GAIN - landcover change-driven addition to 100-yr wood product pool gC/m^2/s F +DWT_PROD100N_GAIN - landcover change-driven addition to 100-yr wood product pool gN/m^2/s F +DWT_PROD10C_GAIN - landcover change-driven addition to 10-yr wood product pool gC/m^2/s F +DWT_PROD10N_GAIN - landcover change-driven addition to 10-yr wood product pool gN/m^2/s F +DWT_SEEDC_TO_DEADSTEM - seed source to patch-level deadstem gC/m^2/s F +DWT_SEEDC_TO_DEADSTEM_PATCH - patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gC/m^2/s F +DWT_SEEDC_TO_LEAF - seed source to patch-level leaf gC/m^2/s F +DWT_SEEDC_TO_LEAF_PATCH - patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gC/m^2/s F +DWT_SEEDN_TO_DEADSTEM - seed source to patch-level deadstem gN/m^2/s T +DWT_SEEDN_TO_DEADSTEM_PATCH - patch-level seed source to patch-level deadstem (per-area-gridcell; only makes sense with dov2 gN/m^2/s F +DWT_SEEDN_TO_LEAF - seed source to patch-level leaf gN/m^2/s T +DWT_SEEDN_TO_LEAF_PATCH - patch-level seed source to patch-level leaf (per-area-gridcell; only makes sense with dov2xy=. gN/m^2/s F +DWT_SLASH_CFLUX - slash C flux (to litter diagnostic only) (0 at all times except first timestep of year) gC/m^2/s T +DWT_SLASH_CFLUX_PATCH - patch-level slash C flux (to litter diagnostic only) (0 at all times except first timestep of gC/m^2/s F +DWT_WOODPRODC_GAIN - landcover change-driven addition to wood product pools gC/m^2/s T +DWT_WOODPRODN_GAIN - landcover change-driven addition to wood product pools gN/m^2/s T +DWT_WOOD_PRODUCTC_GAIN_PATCH - patch-level landcover change-driven addition to wood product pools(0 at all times except first gC/m^2/s F +DYN_COL_ADJUSTMENTS_CH4 - Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_C - Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_N - Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NH4 - Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +DYN_COL_SOIL_ADJUSTMENTS_NO3 - Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F +EFF_POROSITY levgrnd effective porosity = porosity - vol_ice proportion F +EFLXBUILD - building heat flux from change in interior building air temperature W/m^2 T +EFLX_DYNBAL - dynamic land cover change conversion energy flux W/m^2 T +EFLX_GNET - net heat flux into ground W/m^2 F +EFLX_GRND_LAKE - net heat flux into lake/snow surface, excluding light transmission W/m^2 T +EFLX_LH_TOT - total latent heat flux [+ to atm] W/m^2 T +EFLX_LH_TOT_ICE - total latent heat flux [+ to atm] (ice landunits only) W/m^2 F +EFLX_LH_TOT_R - Rural total evaporation W/m^2 T +EFLX_LH_TOT_U - Urban total evaporation W/m^2 F +EFLX_SOIL_GRND - soil heat flux [+ into soil] W/m^2 F +ELAI - exposed one-sided leaf area index m^2/m^2 T +EMG - ground emissivity proportion F +EMV - vegetation emissivity proportion F +EOPT - Eopt coefficient for VOC calc non F +ER - total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T +ERRH2O - total water conservation error mm T +ERRH2OSNO - imbalance in snow depth (liquid water) mm T +ERRSEB - surface energy conservation error W/m^2 T +ERRSOI - soil/lake energy conservation error W/m^2 T +ERRSOL - solar radiation conservation error W/m^2 T +ESAI - exposed one-sided stem area index m^2/m^2 T +EXCESSC_MR - excess C maintenance respiration gC/m^2/s F +EXCESS_CFLUX - C flux not allocated due to downregulation gC/m^2/s F +FAREA_BURNED - timestep fractional area burned s-1 T +FCANSNO - fraction of canopy that is wet proportion F +FCEV - canopy evaporation W/m^2 T +FCH4 - Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T +FCH4TOCO2 - Gridcell oxidation of CH4 to CO2 gC/m2/s T +FCH4_DFSAT - CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T +FCO2 - CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F +FCOV - fractional impermeable area unitless T +FCTR - canopy transpiration W/m^2 T +FDRY - fraction of foliage that is green and dry proportion F +FERTNITRO - Nitrogen fertilizer for each crop gN/m2/yr F +FERT_COUNTER - time left to fertilize seconds F +FERT_TO_SMINN - fertilizer to soil mineral N gN/m^2/s F +FFIX_TO_SMINN - free living N fixation to soil mineral N gN/m^2/s T +FGEV - ground evaporation W/m^2 T +FGR - heat flux into soil/snow including snow melt and lake / snow light transmission W/m^2 T +FGR12 - heat flux between soil layers 1 and 2 W/m^2 T +FGR_ICE - heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F +FGR_R - Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F +FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F +FGR_U - Urban heat flux into soil/snow including snow melt W/m^2 F +FH2OSFC - fraction of ground covered by surface water unitless T +FH2OSFC_NOSNOW - fraction of ground covered by surface water (if no snow present) unitless F +FINUNDATED - fractional inundated area of vegetated columns unitless T +FINUNDATED_LAG - time-lagged inundated fraction of vegetated columns unitless F +FIRA - net infrared (longwave) radiation W/m^2 T +FIRA_ICE - net infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRA_R - Rural net infrared (longwave) radiation W/m^2 T +FIRA_U - Urban net infrared (longwave) radiation W/m^2 F +FIRE - emitted infrared (longwave) radiation W/m^2 T +FIRE_ICE - emitted infrared (longwave) radiation (ice landunits only) W/m^2 F +FIRE_R - Rural emitted infrared (longwave) radiation W/m^2 T +FIRE_U - Urban emitted infrared (longwave) radiation W/m^2 F +FLDS - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T +FLDS_ICE - atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F +FMAX_DENIT_CARBONSUBSTRATE levdcmp FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE levdcmp FMAX_DENIT_NITRATE gN/m^3/s F +FPI - fraction of potential immobilization proportion T +FPI_vr levdcmp fraction of potential immobilization proportion F +FPSN - photosynthesis umol m-2 s-1 T +FPSN24 - 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F +FPSN_WC - Rubisco-limited photosynthesis umol m-2 s-1 F +FPSN_WJ - RuBP-limited photosynthesis umol m-2 s-1 F +FPSN_WP - Product-limited photosynthesis umol m-2 s-1 F +FRAC_ICEOLD levgrnd fraction of ice relative to the tot water proportion F +FREE_RETRANSN_TO_NPOOL - deployment of retranslocated N gN/m^2/s T +FROOTC - fine root C gC/m^2 T +FROOTC_ALLOC - fine root C allocation gC/m^2/s T +FROOTC_LOSS - fine root C loss gC/m^2/s T +FROOTC_STORAGE - fine root C storage gC/m^2 F +FROOTC_STORAGE_TO_XFER - fine root C shift storage to transfer gC/m^2/s F +FROOTC_TO_LITTER - fine root C litterfall gC/m^2/s F +FROOTC_XFER - fine root C transfer gC/m^2 F +FROOTC_XFER_TO_FROOTC - fine root C growth from storage gC/m^2/s F +FROOTN - fine root N gN/m^2 T +FROOTN_STORAGE - fine root N storage gN/m^2 F +FROOTN_STORAGE_TO_XFER - fine root N shift storage to transfer gN/m^2/s F +FROOTN_TO_LITTER - fine root N litterfall gN/m^2/s F +FROOTN_XFER - fine root N transfer gN/m^2 F +FROOTN_XFER_TO_FROOTN - fine root N growth from storage gN/m^2/s F +FROOT_MR - fine root maintenance respiration gC/m^2/s F +FROOT_PROF levdcmp profile for litter C and N inputs from fine roots 1/m F +FROST_TABLE - frost table depth (natural vegetated and crop landunits only) m F +FSA - absorbed solar radiation W/m^2 T +FSAT - fractional area with water table at surface unitless T +FSA_ICE - absorbed solar radiation (ice landunits only) W/m^2 F +FSA_R - Rural absorbed solar radiation W/m^2 F +FSA_U - Urban absorbed solar radiation W/m^2 F +FSD24 - direct radiation (last 24hrs) K F +FSD240 - direct radiation (last 240hrs) K F +FSDS - atmospheric incident solar radiation W/m^2 T +FSDSND - direct nir incident solar radiation W/m^2 T +FSDSNDLN - direct nir incident solar radiation at local noon W/m^2 T +FSDSNI - diffuse nir incident solar radiation W/m^2 T +FSDSVD - direct vis incident solar radiation W/m^2 T +FSDSVDLN - direct vis incident solar radiation at local noon W/m^2 T +FSDSVI - diffuse vis incident solar radiation W/m^2 T +FSDSVILN - diffuse vis incident solar radiation at local noon W/m^2 T +FSH - sensible heat not including correction for land use change and rain/snow conversion W/m^2 T +FSH_G - sensible heat from ground W/m^2 T +FSH_ICE - sensible heat not including correction for land use change and rain/snow conversion (ice landu W/m^2 F +FSH_PRECIP_CONVERSION - Sensible heat flux from conversion of rain/snow atm forcing W/m^2 T +FSH_R - Rural sensible heat W/m^2 T +FSH_RUNOFF_ICE_TO_LIQ - sensible heat flux generated from conversion of ice runoff to liquid W/m^2 T +FSH_TO_COUPLER - sensible heat sent to coupler (includes corrections for land use change, rain/snow conversion W/m^2 T +FSH_U - Urban sensible heat W/m^2 F +FSH_V - sensible heat from veg W/m^2 T +FSI24 - indirect radiation (last 24hrs) K F +FSI240 - indirect radiation (last 240hrs) K F +FSM - snow melt heat flux W/m^2 T +FSM_ICE - snow melt heat flux (ice landunits only) W/m^2 F +FSM_R - Rural snow melt heat flux W/m^2 F +FSM_U - Urban snow melt heat flux W/m^2 F +FSNO - fraction of ground covered by snow unitless T +FSNO_EFF - effective fraction of ground covered by snow unitless T +FSNO_ICE - fraction of ground covered by snow (ice landunits only) unitless F +FSR - reflected solar radiation W/m^2 T +FSRND - direct nir reflected solar radiation W/m^2 T +FSRNDLN - direct nir reflected solar radiation at local noon W/m^2 T +FSRNI - diffuse nir reflected solar radiation W/m^2 T +FSRVD - direct vis reflected solar radiation W/m^2 T +FSRVDLN - direct vis reflected solar radiation at local noon W/m^2 T +FSRVI - diffuse vis reflected solar radiation W/m^2 T +FSR_ICE - reflected solar radiation (ice landunits only) W/m^2 F +FSUN - sunlit fraction of canopy proportion F +FSUN24 - fraction sunlit (last 24hrs) K F +FSUN240 - fraction sunlit (last 240hrs) K F +FUELC - fuel load gC/m^2 T +FV - friction velocity m/s T +FWET - fraction of canopy that is wet proportion F +F_DENIT - denitrification flux gN/m^2/s T +F_DENIT_BASE levdcmp F_DENIT_BASE gN/m^3/s F +F_DENIT_vr levdcmp denitrification flux gN/m^3/s F +F_N2O_DENIT - denitrification N2O flux gN/m^2/s T +F_N2O_NIT - nitrification N2O flux gN/m^2/s T +F_NIT - nitrification flux gN/m^2/s T +F_NIT_vr levdcmp nitrification flux gN/m^3/s F +GAMMA - total gamma for VOC calc non F +GAMMAA - gamma A for VOC calc non F +GAMMAC - gamma C for VOC calc non F +GAMMAL - gamma L for VOC calc non F +GAMMAP - gamma P for VOC calc non F +GAMMAS - gamma S for VOC calc non F +GAMMAT - gamma T for VOC calc non F +GDD0 - Growing degree days base 0C from planting ddays F +GDD020 - Twenty year average of growing degree days base 0C from planting ddays F +GDD10 - Growing degree days base 10C from planting ddays F +GDD1020 - Twenty year average of growing degree days base 10C from planting ddays F +GDD8 - Growing degree days base 8C from planting ddays F +GDD820 - Twenty year average of growing degree days base 8C from planting ddays F +GDDACCUM - Accumulated growing degree days past planting date for crop ddays F +GDDACCUM_PERHARV mxharvests At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F +GDDHARV - Growing degree days (gdd) needed to harvest ddays F +GDDHARV_PERHARV mxharvests Growing degree days (gdd) needed to harvest; should only be output annually ddays F +GDDTSOI - Growing degree-days from planting (top two soil layers) ddays F +GPP - gross primary production gC/m^2/s T +GR - total growth respiration gC/m^2/s T +GRAINC - grain C (does not equal yield) gC/m^2 T +GRAINC_TO_FOOD - grain C to food gC/m^2/s T +GRAINC_TO_FOOD_ANN - grain C to food harvested per calendar year; should only be output annually gC/m^2 F +GRAINC_TO_FOOD_PERHARV mxharvests grain C to food per harvest; should only be output annually gC/m^2 F +GRAINC_TO_SEED - grain C to seed gC/m^2/s T +GRAINN - grain N gN/m^2 T +GRESP_STORAGE - growth respiration storage gC/m^2 F +GRESP_STORAGE_TO_XFER - growth respiration shift storage to transfer gC/m^2/s F +GRESP_XFER - growth respiration transfer gC/m^2 F +GROSS_NMIN - gross rate of N mineralization gN/m^2/s T +GROSS_NMIN_vr levdcmp gross rate of N mineralization gN/m^3/s F +GRU_PROD100C_GAIN - gross unrepresented landcover change addition to 100-yr wood product pool gC/m^2/s F +GRU_PROD100N_GAIN - gross unrepresented landcover change addition to 100-yr wood product pool gN/m^2/s F +GRU_PROD10C_GAIN - gross unrepresented landcover change addition to 10-yr wood product pool gC/m^2/s F +GRU_PROD10N_GAIN - gross unrepresented landcover change addition to 10-yr wood product pool gN/m^2/s F +GSSHA - shaded leaf stomatal conductance umol H20/m2/s T +GSSHALN - shaded leaf stomatal conductance at local noon umol H20/m2/s T +GSSUN - sunlit leaf stomatal conductance umol H20/m2/s T +GSSUNLN - sunlit leaf stomatal conductance at local noon umol H20/m2/s T +H2OCAN - intercepted water mm T +H2OSFC - surface water depth mm T +H2OSNO - snow depth (liquid water) mm T +H2OSNO_ICE - snow depth (liquid water, ice landunits only) mm F +H2OSNO_TOP - mass of snow in top snow layer kg/m2 T +H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HARVEST_REASON_PERHARV mxharvests Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F +HBOT - canopy bottom m F +HDATES mxharvests actual crop harvest dates; should only be output annually day of year F +HEAT_CONTENT1 - initial gridcell total heat content J/m^2 T +HEAT_CONTENT1_VEG - initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F +HEAT_CONTENT2 - post land cover change total heat content J/m^2 F +HEAT_FROM_AC - sensible heat flux put into canyon due to heat removed from air conditioning W/m^2 T +HIA - 2 m NWS Heat Index C T +HIA_R - Rural 2 m NWS Heat Index C T +HIA_U - Urban 2 m NWS Heat Index C T +HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +HR - total heterotrophic respiration gC/m^2/s T +HR_vr levsoi total vertically resolved heterotrophic respiration gC/m^3/s T +HTOP - canopy top m T +HUI - Crop patch heat unit index ddays F +HUI_PERHARV mxharvests At-harvest accumulated heat unit index for crop; should only be output annually ddays F +HUMIDEX - 2 m Humidex C T +HUMIDEX_R - Rural 2 m Humidex C T +HUMIDEX_U - Urban 2 m Humidex C T +ICE_CONTENT1 - initial gridcell total ice content mm T +ICE_CONTENT2 - post land cover change total ice content mm F +ICE_MODEL_FRACTION - Ice sheet model fractional coverage unitless F +INIT_GPP - GPP flux before downregulation gC/m^2/s F +INT_SNOW - accumulated swe (natural vegetated and crop landunits only) mm F +INT_SNOW_ICE - accumulated swe (ice landunits only) mm F +IWUELN - local noon intrinsic water use efficiency umolCO2/molH2O T +JMX25T - canopy profile of jmax umol/m2/s T +Jmx25Z - maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T +KROOT levsoi root conductance each soil layer 1/s F +KSOIL levsoi soil conductance in each soil layer 1/s F +K_ACT_SOM levdcmp active soil organic potential loss coefficient 1/s F +K_CEL_LIT levdcmp cellulosic litter potential loss coefficient 1/s F +K_CWD levdcmp coarse woody debris potential loss coefficient 1/s F +K_LIG_LIT levdcmp lignin litter potential loss coefficient 1/s F +K_MET_LIT levdcmp metabolic litter potential loss coefficient 1/s F +K_NITR levdcmp K_NITR 1/s F +K_NITR_H2O levdcmp K_NITR_H2O unitless F +K_NITR_PH levdcmp K_NITR_PH unitless F +K_NITR_T levdcmp K_NITR_T unitless F +K_PAS_SOM levdcmp passive soil organic potential loss coefficient 1/s F +K_SLO_SOM levdcmp slow soil organic ma potential loss coefficient 1/s F +L1_PATHFRAC_S1_vr levdcmp PATHFRAC from metabolic litter to active soil organic fraction F +L1_RESP_FRAC_S1_vr levdcmp respired from metabolic litter to active soil organic fraction F +L2_PATHFRAC_S1_vr levdcmp PATHFRAC from cellulosic litter to active soil organic fraction F +L2_RESP_FRAC_S1_vr levdcmp respired from cellulosic litter to active soil organic fraction F +L3_PATHFRAC_S2_vr levdcmp PATHFRAC from lignin litter to slow soil organic ma fraction F +L3_RESP_FRAC_S2_vr levdcmp respired from lignin litter to slow soil organic ma fraction F +LAI240 - 240hr average of leaf area index m^2/m^2 F +LAISHA - shaded projected leaf area index m^2/m^2 T +LAISUN - sunlit projected leaf area index m^2/m^2 T +LAKEICEFRAC levlak lake layer ice mass fraction unitless F +LAKEICEFRAC_SURF - surface lake layer ice mass fraction unitless T +LAKEICETHICK - thickness of lake ice (including physical expansion on freezing) m T +LAND_USE_FLUX - total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T +LATBASET - latitude vary base temperature for hui degree C F +LEAFC - leaf C gC/m^2 T +LEAFCN - Leaf CN ratio used for flexible CN gC/gN T +LEAFCN_OFFSET - Leaf C:N used by FUN unitless F +LEAFCN_STORAGE - Storage Leaf CN ratio used for flexible CN gC/gN F +LEAFC_ALLOC - leaf C allocation gC/m^2/s T +LEAFC_CHANGE - C change in leaf gC/m^2/s T +LEAFC_LOSS - leaf C loss gC/m^2/s T +LEAFC_STORAGE - leaf C storage gC/m^2 F +LEAFC_STORAGE_TO_XFER - leaf C shift storage to transfer gC/m^2/s F +LEAFC_STORAGE_XFER_ACC - Accumulated leaf C transfer gC/m^2 F +LEAFC_TO_BIOFUELC - leaf C to biofuel C gC/m^2/s T +LEAFC_TO_LITTER - leaf C litterfall gC/m^2/s F +LEAFC_TO_LITTER_FUN - leaf C litterfall used by FUN gC/m^2/s T +LEAFC_XFER - leaf C transfer gC/m^2 F +LEAFC_XFER_TO_LEAFC - leaf C growth from storage gC/m^2/s F +LEAFN - leaf N gN/m^2 T +LEAFN_STORAGE - leaf N storage gN/m^2 F +LEAFN_STORAGE_TO_XFER - leaf N shift storage to transfer gN/m^2/s F +LEAFN_STORAGE_XFER_ACC - Accmulated leaf N transfer gN/m^2 F +LEAFN_TO_LITTER - leaf N litterfall gN/m^2/s T +LEAFN_TO_RETRANSN - leaf N to retranslocated N pool gN/m^2/s F +LEAFN_XFER - leaf N transfer gN/m^2 F +LEAFN_XFER_TO_LEAFN - leaf N growth from storage gN/m^2/s F +LEAF_MR - leaf maintenance respiration gC/m^2/s T +LEAF_PROF levdcmp profile for litter C and N inputs from leaves 1/m F +LFC2 - conversion area fraction of BET and BDT that burned per sec T +LGSF - long growing season factor proportion F +LIG_LITC - LIG_LIT C gC/m^2 T +LIG_LITC_1m - LIG_LIT C to 1 meter gC/m^2 F +LIG_LITC_TNDNCY_VERT_TRA levdcmp lignin litter C tendency due to vertical transport gC/m^3/s F +LIG_LITC_TO_SLO_SOMC - decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIG_LITC_TO_SLO_SOMC_vr levdcmp decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIG_LITC_vr levsoi LIG_LIT C (vertically resolved) gC/m^3 T +LIG_LITN - LIG_LIT N gN/m^2 T +LIG_LITN_1m - LIG_LIT N to 1 meter gN/m^2 F +LIG_LITN_TNDNCY_VERT_TRA levdcmp lignin litter N tendency due to vertical transport gN/m^3/s F +LIG_LITN_TO_SLO_SOMN - decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIG_LITN_TO_SLO_SOMN_vr levdcmp decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIG_LITN_vr levdcmp LIG_LIT N (vertically resolved) gN/m^3 T +LIG_LIT_HR - Het. Resp. from lignin litter gC/m^2/s F +LIG_LIT_HR_vr levdcmp Het. Resp. from lignin litter gC/m^3/s F +LIQCAN - intercepted liquid water mm T +LIQUID_CONTENT1 - initial gridcell total liq content mm T +LIQUID_CONTENT2 - post landuse change gridcell total liq content mm F +LIQUID_WATER_TEMP1 - initial gridcell weighted average liquid water temperature K F +LITFALL - litterfall (leaves and fine roots) gC/m^2/s T +LITFIRE - litter fire losses gC/m^2/s F +LITTERC_HR - litter C heterotrophic respiration gC/m^2/s T +LITTERC_LOSS - litter C loss gC/m^2/s T +LIVECROOTC - live coarse root C gC/m^2 T +LIVECROOTC_STORAGE - live coarse root C storage gC/m^2 F +LIVECROOTC_STORAGE_TO_XFER - live coarse root C shift storage to transfer gC/m^2/s F +LIVECROOTC_TO_DEADCROOTC - live coarse root C turnover gC/m^2/s F +LIVECROOTC_XFER - live coarse root C transfer gC/m^2 F +LIVECROOTC_XFER_TO_LIVECROOTC - live coarse root C growth from storage gC/m^2/s F +LIVECROOTN - live coarse root N gN/m^2 T +LIVECROOTN_STORAGE - live coarse root N storage gN/m^2 F +LIVECROOTN_STORAGE_TO_XFER - live coarse root N shift storage to transfer gN/m^2/s F +LIVECROOTN_TO_DEADCROOTN - live coarse root N turnover gN/m^2/s F +LIVECROOTN_TO_RETRANSN - live coarse root N to retranslocated N pool gN/m^2/s F +LIVECROOTN_XFER - live coarse root N transfer gN/m^2 F +LIVECROOTN_XFER_TO_LIVECROOTN - live coarse root N growth from storage gN/m^2/s F +LIVECROOT_MR - live coarse root maintenance respiration gC/m^2/s F +LIVESTEMC - live stem C gC/m^2 T +LIVESTEMC_STORAGE - live stem C storage gC/m^2 F +LIVESTEMC_STORAGE_TO_XFER - live stem C shift storage to transfer gC/m^2/s F +LIVESTEMC_TO_BIOFUELC - livestem C to biofuel C gC/m^2/s T +LIVESTEMC_TO_DEADSTEMC - live stem C turnover gC/m^2/s F +LIVESTEMC_XFER - live stem C transfer gC/m^2 F +LIVESTEMC_XFER_TO_LIVESTEMC - live stem C growth from storage gC/m^2/s F +LIVESTEMN - live stem N gN/m^2 T +LIVESTEMN_STORAGE - live stem N storage gN/m^2 F +LIVESTEMN_STORAGE_TO_XFER - live stem N shift storage to transfer gN/m^2/s F +LIVESTEMN_TO_DEADSTEMN - live stem N turnover gN/m^2/s F +LIVESTEMN_TO_RETRANSN - live stem N to retranslocated N pool gN/m^2/s F +LIVESTEMN_XFER - live stem N transfer gN/m^2 F +LIVESTEMN_XFER_TO_LIVESTEMN - live stem N growth from storage gN/m^2/s F +LIVESTEM_MR - live stem maintenance respiration gC/m^2/s F +LNC - leaf N concentration gN leaf/m^2 T +LWdown - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F +LWup - upwelling longwave radiation W/m^2 F +MEG_acetaldehyde - MEGAN flux kg/m2/sec T +MEG_acetic_acid - MEGAN flux kg/m2/sec T +MEG_acetone - MEGAN flux kg/m2/sec T +MEG_carene_3 - MEGAN flux kg/m2/sec T +MEG_ethanol - MEGAN flux kg/m2/sec T +MEG_formaldehyde - MEGAN flux kg/m2/sec T +MEG_isoprene - MEGAN flux kg/m2/sec T +MEG_methanol - MEGAN flux kg/m2/sec T +MEG_pinene_a - MEGAN flux kg/m2/sec T +MEG_thujene_a - MEGAN flux kg/m2/sec T +MET_LITC - MET_LIT C gC/m^2 T +MET_LITC_1m - MET_LIT C to 1 meter gC/m^2 F +MET_LITC_TNDNCY_VERT_TRA levdcmp metabolic litter C tendency due to vertical transport gC/m^3/s F +MET_LITC_TO_ACT_SOMC - decomp. of metabolic litter C to active soil organic C gC/m^2/s F +MET_LITC_TO_ACT_SOMC_vr levdcmp decomp. of metabolic litter C to active soil organic C gC/m^3/s F +MET_LITC_vr levsoi MET_LIT C (vertically resolved) gC/m^3 T +MET_LITN - MET_LIT N gN/m^2 T +MET_LITN_1m - MET_LIT N to 1 meter gN/m^2 F +MET_LITN_TNDNCY_VERT_TRA levdcmp metabolic litter N tendency due to vertical transport gN/m^3/s F +MET_LITN_TO_ACT_SOMN - decomp. of metabolic litter N to active soil organic N gN/m^2 F +MET_LITN_TO_ACT_SOMN_vr levdcmp decomp. of metabolic litter N to active soil organic N gN/m^3 F +MET_LITN_vr levdcmp MET_LIT N (vertically resolved) gN/m^3 T +MET_LIT_HR - Het. Resp. from metabolic litter gC/m^2/s F +MET_LIT_HR_vr levdcmp Het. Resp. from metabolic litter gC/m^3/s F +MR - maintenance respiration gC/m^2/s T +M_ACT_SOMC_TO_LEACHING - active soil organic C leaching loss gC/m^2/s F +M_ACT_SOMN_TO_LEACHING - active soil organic N leaching loss gN/m^2/s F +M_CEL_LITC_TO_FIRE - cellulosic litter C fire loss gC/m^2/s F +M_CEL_LITC_TO_FIRE_vr levdcmp cellulosic litter C fire loss gC/m^3/s F +M_CEL_LITC_TO_LEACHING - cellulosic litter C leaching loss gC/m^2/s F +M_CEL_LITN_TO_FIRE - cellulosic litter N fire loss gN/m^2 F +M_CEL_LITN_TO_FIRE_vr levdcmp cellulosic litter N fire loss gN/m^3 F +M_CEL_LITN_TO_LEACHING - cellulosic litter N leaching loss gN/m^2/s F +M_CWDC_TO_FIRE - coarse woody debris C fire loss gC/m^2/s F +M_CWDC_TO_FIRE_vr levdcmp coarse woody debris C fire loss gC/m^3/s F +M_CWDN_TO_FIRE - coarse woody debris N fire loss gN/m^2 F +M_CWDN_TO_FIRE_vr levdcmp coarse woody debris N fire loss gN/m^3 F +M_DEADCROOTC_STORAGE_TO_LITTER - dead coarse root C storage mortality gC/m^2/s F +M_DEADCROOTC_STORAGE_TO_LITTER_FIRE - dead coarse root C storage fire mortality to litter gC/m^2/s F +M_DEADCROOTC_TO_LITTER - dead coarse root C mortality gC/m^2/s F +M_DEADCROOTC_XFER_TO_LITTER - dead coarse root C transfer mortality gC/m^2/s F +M_DEADCROOTN_STORAGE_TO_FIRE - dead coarse root N storage fire loss gN/m^2/s F +M_DEADCROOTN_STORAGE_TO_LITTER - dead coarse root N storage mortality gN/m^2/s F +M_DEADCROOTN_TO_FIRE - dead coarse root N fire loss gN/m^2/s F +M_DEADCROOTN_TO_LITTER - dead coarse root N mortality gN/m^2/s F +M_DEADCROOTN_TO_LITTER_FIRE - dead coarse root N fire mortality to litter gN/m^2/s F +M_DEADCROOTN_XFER_TO_FIRE - dead coarse root N transfer fire loss gN/m^2/s F +M_DEADCROOTN_XFER_TO_LITTER - dead coarse root N transfer mortality gN/m^2/s F +M_DEADROOTC_STORAGE_TO_FIRE - dead root C storage fire loss gC/m^2/s F +M_DEADROOTC_STORAGE_TO_LITTER_FIRE - dead root C storage fire mortality to litter gC/m^2/s F +M_DEADROOTC_TO_FIRE - dead root C fire loss gC/m^2/s F +M_DEADROOTC_TO_LITTER_FIRE - dead root C fire mortality to litter gC/m^2/s F +M_DEADROOTC_XFER_TO_FIRE - dead root C transfer fire loss gC/m^2/s F +M_DEADROOTC_XFER_TO_LITTER_FIRE - dead root C transfer fire mortality to litter gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_FIRE - dead stem C storage fire loss gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_LITTER - dead stem C storage mortality gC/m^2/s F +M_DEADSTEMC_STORAGE_TO_LITTER_FIRE - dead stem C storage fire mortality to litter gC/m^2/s F +M_DEADSTEMC_TO_FIRE - dead stem C fire loss gC/m^2/s F +M_DEADSTEMC_TO_LITTER - dead stem C mortality gC/m^2/s F +M_DEADSTEMC_TO_LITTER_FIRE - dead stem C fire mortality to litter gC/m^2/s F +M_DEADSTEMC_XFER_TO_FIRE - dead stem C transfer fire loss gC/m^2/s F +M_DEADSTEMC_XFER_TO_LITTER - dead stem C transfer mortality gC/m^2/s F +M_DEADSTEMC_XFER_TO_LITTER_FIRE - dead stem C transfer fire mortality to litter gC/m^2/s F +M_DEADSTEMN_STORAGE_TO_FIRE - dead stem N storage fire loss gN/m^2/s F +M_DEADSTEMN_STORAGE_TO_LITTER - dead stem N storage mortality gN/m^2/s F +M_DEADSTEMN_TO_FIRE - dead stem N fire loss gN/m^2/s F +M_DEADSTEMN_TO_LITTER - dead stem N mortality gN/m^2/s F +M_DEADSTEMN_TO_LITTER_FIRE - dead stem N fire mortality to litter gN/m^2/s F +M_DEADSTEMN_XFER_TO_FIRE - dead stem N transfer fire loss gN/m^2/s F +M_DEADSTEMN_XFER_TO_LITTER - dead stem N transfer mortality gN/m^2/s F +M_FROOTC_STORAGE_TO_FIRE - fine root C storage fire loss gC/m^2/s F +M_FROOTC_STORAGE_TO_LITTER - fine root C storage mortality gC/m^2/s F +M_FROOTC_STORAGE_TO_LITTER_FIRE - fine root C storage fire mortality to litter gC/m^2/s F +M_FROOTC_TO_FIRE - fine root C fire loss gC/m^2/s F +M_FROOTC_TO_LITTER - fine root C mortality gC/m^2/s F +M_FROOTC_TO_LITTER_FIRE - fine root C fire mortality to litter gC/m^2/s F +M_FROOTC_XFER_TO_FIRE - fine root C transfer fire loss gC/m^2/s F +M_FROOTC_XFER_TO_LITTER - fine root C transfer mortality gC/m^2/s F +M_FROOTC_XFER_TO_LITTER_FIRE - fine root C transfer fire mortality to litter gC/m^2/s F +M_FROOTN_STORAGE_TO_FIRE - fine root N storage fire loss gN/m^2/s F +M_FROOTN_STORAGE_TO_LITTER - fine root N storage mortality gN/m^2/s F +M_FROOTN_TO_FIRE - fine root N fire loss gN/m^2/s F +M_FROOTN_TO_LITTER - fine root N mortality gN/m^2/s F +M_FROOTN_XFER_TO_FIRE - fine root N transfer fire loss gN/m^2/s F +M_FROOTN_XFER_TO_LITTER - fine root N transfer mortality gN/m^2/s F +M_GRESP_STORAGE_TO_FIRE - growth respiration storage fire loss gC/m^2/s F +M_GRESP_STORAGE_TO_LITTER - growth respiration storage mortality gC/m^2/s F +M_GRESP_STORAGE_TO_LITTER_FIRE - growth respiration storage fire mortality to litter gC/m^2/s F +M_GRESP_XFER_TO_FIRE - growth respiration transfer fire loss gC/m^2/s F +M_GRESP_XFER_TO_LITTER - growth respiration transfer mortality gC/m^2/s F +M_GRESP_XFER_TO_LITTER_FIRE - growth respiration transfer fire mortality to litter gC/m^2/s F +M_LEAFC_STORAGE_TO_FIRE - leaf C storage fire loss gC/m^2/s F +M_LEAFC_STORAGE_TO_LITTER - leaf C storage mortality gC/m^2/s F +M_LEAFC_STORAGE_TO_LITTER_FIRE - leaf C fire mortality to litter gC/m^2/s F +M_LEAFC_TO_FIRE - leaf C fire loss gC/m^2/s F +M_LEAFC_TO_LITTER - leaf C mortality gC/m^2/s F +M_LEAFC_TO_LITTER_FIRE - leaf C fire mortality to litter gC/m^2/s F +M_LEAFC_XFER_TO_FIRE - leaf C transfer fire loss gC/m^2/s F +M_LEAFC_XFER_TO_LITTER - leaf C transfer mortality gC/m^2/s F +M_LEAFC_XFER_TO_LITTER_FIRE - leaf C transfer fire mortality to litter gC/m^2/s F +M_LEAFN_STORAGE_TO_FIRE - leaf N storage fire loss gN/m^2/s F +M_LEAFN_STORAGE_TO_LITTER - leaf N storage mortality gN/m^2/s F +M_LEAFN_TO_FIRE - leaf N fire loss gN/m^2/s F +M_LEAFN_TO_LITTER - leaf N mortality gN/m^2/s F +M_LEAFN_XFER_TO_FIRE - leaf N transfer fire loss gN/m^2/s F +M_LEAFN_XFER_TO_LITTER - leaf N transfer mortality gN/m^2/s F +M_LIG_LITC_TO_FIRE - lignin litter C fire loss gC/m^2/s F +M_LIG_LITC_TO_FIRE_vr levdcmp lignin litter C fire loss gC/m^3/s F +M_LIG_LITC_TO_LEACHING - lignin litter C leaching loss gC/m^2/s F +M_LIG_LITN_TO_FIRE - lignin litter N fire loss gN/m^2 F +M_LIG_LITN_TO_FIRE_vr levdcmp lignin litter N fire loss gN/m^3 F +M_LIG_LITN_TO_LEACHING - lignin litter N leaching loss gN/m^2/s F +M_LIVECROOTC_STORAGE_TO_LITTER - live coarse root C storage mortality gC/m^2/s F +M_LIVECROOTC_STORAGE_TO_LITTER_FIRE - live coarse root C fire mortality to litter gC/m^2/s F +M_LIVECROOTC_TO_LITTER - live coarse root C mortality gC/m^2/s F +M_LIVECROOTC_XFER_TO_LITTER - live coarse root C transfer mortality gC/m^2/s F +M_LIVECROOTN_STORAGE_TO_FIRE - live coarse root N storage fire loss gN/m^2/s F +M_LIVECROOTN_STORAGE_TO_LITTER - live coarse root N storage mortality gN/m^2/s F +M_LIVECROOTN_TO_FIRE - live coarse root N fire loss gN/m^2/s F +M_LIVECROOTN_TO_LITTER - live coarse root N mortality gN/m^2/s F +M_LIVECROOTN_XFER_TO_FIRE - live coarse root N transfer fire loss gN/m^2/s F +M_LIVECROOTN_XFER_TO_LITTER - live coarse root N transfer mortality gN/m^2/s F +M_LIVEROOTC_STORAGE_TO_FIRE - live root C storage fire loss gC/m^2/s F +M_LIVEROOTC_STORAGE_TO_LITTER_FIRE - live root C storage fire mortality to litter gC/m^2/s F +M_LIVEROOTC_TO_DEADROOTC_FIRE - live root C fire mortality to dead root C gC/m^2/s F +M_LIVEROOTC_TO_FIRE - live root C fire loss gC/m^2/s F +M_LIVEROOTC_TO_LITTER_FIRE - live root C fire mortality to litter gC/m^2/s F +M_LIVEROOTC_XFER_TO_FIRE - live root C transfer fire loss gC/m^2/s F +M_LIVEROOTC_XFER_TO_LITTER_FIRE - live root C transfer fire mortality to litter gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_FIRE - live stem C storage fire loss gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_LITTER - live stem C storage mortality gC/m^2/s F +M_LIVESTEMC_STORAGE_TO_LITTER_FIRE - live stem C storage fire mortality to litter gC/m^2/s F +M_LIVESTEMC_TO_DEADSTEMC_FIRE - live stem C fire mortality to dead stem C gC/m^2/s F +M_LIVESTEMC_TO_FIRE - live stem C fire loss gC/m^2/s F +M_LIVESTEMC_TO_LITTER - live stem C mortality gC/m^2/s F +M_LIVESTEMC_TO_LITTER_FIRE - live stem C fire mortality to litter gC/m^2/s F +M_LIVESTEMC_XFER_TO_FIRE - live stem C transfer fire loss gC/m^2/s F +M_LIVESTEMC_XFER_TO_LITTER - live stem C transfer mortality gC/m^2/s F +M_LIVESTEMC_XFER_TO_LITTER_FIRE - live stem C transfer fire mortality to litter gC/m^2/s F +M_LIVESTEMN_STORAGE_TO_FIRE - live stem N storage fire loss gN/m^2/s F +M_LIVESTEMN_STORAGE_TO_LITTER - live stem N storage mortality gN/m^2/s F +M_LIVESTEMN_TO_FIRE - live stem N fire loss gN/m^2/s F +M_LIVESTEMN_TO_LITTER - live stem N mortality gN/m^2/s F +M_LIVESTEMN_XFER_TO_FIRE - live stem N transfer fire loss gN/m^2/s F +M_LIVESTEMN_XFER_TO_LITTER - live stem N transfer mortality gN/m^2/s F +M_MET_LITC_TO_FIRE - metabolic litter C fire loss gC/m^2/s F +M_MET_LITC_TO_FIRE_vr levdcmp metabolic litter C fire loss gC/m^3/s F +M_MET_LITC_TO_LEACHING - metabolic litter C leaching loss gC/m^2/s F +M_MET_LITN_TO_FIRE - metabolic litter N fire loss gN/m^2 F +M_MET_LITN_TO_FIRE_vr levdcmp metabolic litter N fire loss gN/m^3 F +M_MET_LITN_TO_LEACHING - metabolic litter N leaching loss gN/m^2/s F +M_PAS_SOMC_TO_LEACHING - passive soil organic C leaching loss gC/m^2/s F +M_PAS_SOMN_TO_LEACHING - passive soil organic N leaching loss gN/m^2/s F +M_RETRANSN_TO_FIRE - retranslocated N pool fire loss gN/m^2/s F +M_RETRANSN_TO_LITTER - retranslocated N pool mortality gN/m^2/s F +M_SLO_SOMC_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F +M_SLO_SOMN_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F +NACTIVE - Mycorrhizal N uptake flux gN/m^2/s T +NACTIVE_NH4 - Mycorrhizal N uptake flux gN/m^2/s T +NACTIVE_NO3 - Mycorrhizal N uptake flux gN/m^2/s T +NAM - AM-associated N uptake flux gN/m^2/s T +NAM_NH4 - AM-associated N uptake flux gN/m^2/s T +NAM_NO3 - AM-associated N uptake flux gN/m^2/s T +NBP - net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T +NDEPLOY - total N deployed in new growth gN/m^2/s T +NDEP_PROF levdcmp profile for atmospheric N deposition 1/m F +NDEP_TO_SMINN - atmospheric N deposition to soil mineral N gN/m^2/s T +NECM - ECM-associated N uptake flux gN/m^2/s T +NECM_NH4 - ECM-associated N uptake flux gN/m^2/s T +NECM_NO3 - ECM-associated N uptake flux gN/m^2/s T +NEE - net ecosystem exchange of carbon, includes fire and hrv_xsmrpool (latter smoothed over the yea gC/m^2/s T +NEM - Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T +NEP - net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T +NET_NMIN - net rate of N mineralization gN/m^2/s T +NET_NMIN_vr levdcmp net rate of N mineralization gN/m^3/s F +NFERTILIZATION - fertilizer added gN/m^2/s T +NFIRE - fire counts valid only in Reg.C counts/km2/sec T +NFIX - Symbiotic BNF uptake flux gN/m^2/s T +NFIXATION_PROF levdcmp profile for biological N fixation 1/m F +NFIX_TO_SMINN - symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F +NNONMYC - Non-mycorrhizal N uptake flux gN/m^2/s T +NNONMYC_NH4 - Non-mycorrhizal N uptake flux gN/m^2/s T +NNONMYC_NO3 - Non-mycorrhizal N uptake flux gN/m^2/s T +NPASSIVE - Passive N uptake flux gN/m^2/s T +NPOOL - temporary plant N pool gN/m^2 T +NPOOL_TO_DEADCROOTN - allocation to dead coarse root N gN/m^2/s F +NPOOL_TO_DEADCROOTN_STORAGE - allocation to dead coarse root N storage gN/m^2/s F +NPOOL_TO_DEADSTEMN - allocation to dead stem N gN/m^2/s F +NPOOL_TO_DEADSTEMN_STORAGE - allocation to dead stem N storage gN/m^2/s F +NPOOL_TO_FROOTN - allocation to fine root N gN/m^2/s F +NPOOL_TO_FROOTN_STORAGE - allocation to fine root N storage gN/m^2/s F +NPOOL_TO_LEAFN - allocation to leaf N gN/m^2/s F +NPOOL_TO_LEAFN_STORAGE - allocation to leaf N storage gN/m^2/s F +NPOOL_TO_LIVECROOTN - allocation to live coarse root N gN/m^2/s F +NPOOL_TO_LIVECROOTN_STORAGE - allocation to live coarse root N storage gN/m^2/s F +NPOOL_TO_LIVESTEMN - allocation to live stem N gN/m^2/s F +NPOOL_TO_LIVESTEMN_STORAGE - allocation to live stem N storage gN/m^2/s F +NPP - net primary production gC/m^2/s T +NPP_BURNEDOFF - C that cannot be used for N uptake gC/m^2/s F +NPP_GROWTH - Total C used for growth in FUN gC/m^2/s T +NPP_NACTIVE - Mycorrhizal N uptake used C gC/m^2/s T +NPP_NACTIVE_NH4 - Mycorrhizal N uptake use C gC/m^2/s T +NPP_NACTIVE_NO3 - Mycorrhizal N uptake used C gC/m^2/s T +NPP_NAM - AM-associated N uptake used C gC/m^2/s T +NPP_NAM_NH4 - AM-associated N uptake use C gC/m^2/s T +NPP_NAM_NO3 - AM-associated N uptake use C gC/m^2/s T +NPP_NECM - ECM-associated N uptake used C gC/m^2/s T +NPP_NECM_NH4 - ECM-associated N uptake use C gC/m^2/s T +NPP_NECM_NO3 - ECM-associated N uptake used C gC/m^2/s T +NPP_NFIX - Symbiotic BNF uptake used C gC/m^2/s T +NPP_NNONMYC - Non-mycorrhizal N uptake used C gC/m^2/s T +NPP_NNONMYC_NH4 - Non-mycorrhizal N uptake use C gC/m^2/s T +NPP_NNONMYC_NO3 - Non-mycorrhizal N uptake use C gC/m^2/s T +NPP_NRETRANS - Retranslocated N uptake flux gC/m^2/s T +NPP_NUPTAKE - Total C used by N uptake in FUN gC/m^2/s T +NRETRANS - Retranslocated N uptake flux gN/m^2/s T +NRETRANS_REG - Retranslocated N uptake flux gN/m^2/s T +NRETRANS_SEASON - Retranslocated N uptake flux gN/m^2/s T +NRETRANS_STRESS - Retranslocated N uptake flux gN/m^2/s T +NSUBSTEPS - number of adaptive timesteps in CLM timestep unitless F +NUPTAKE - Total N uptake of FUN gN/m^2/s T +NUPTAKE_NPP_FRACTION - frac of NPP used in N uptake - T +N_ALLOMETRY - N allocation index none F +O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F +OBU - Monin-Obukhov length m F +OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T +OFFSET_COUNTER - offset days counter days F +OFFSET_FDD - offset freezing degree days counter C degree-days F +OFFSET_FLAG - offset flag none F +OFFSET_SWI - offset soil water index none F +ONSET_COUNTER - onset days counter days F +ONSET_FDD - onset freezing degree days counter C degree-days F +ONSET_FLAG - onset flag none F +ONSET_GDD - onset growing degree days C degree-days F +ONSET_GDDFLAG - onset flag for growing degree day sum none F +ONSET_SWI - onset soil water index none F +O_SCALAR levsoi fraction by which decomposition is reduced due to anoxia unitless T +PAR240DZ - 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F +PAR240XZ - 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F +PAR240_shade - shade PAR (240 hrs) umol/m2/s F +PAR240_sun - sunlit PAR (240 hrs) umol/m2/s F +PAR24_shade - shade PAR (24 hrs) umol/m2/s F +PAR24_sun - sunlit PAR (24 hrs) umol/m2/s F +PARVEGLN - absorbed par by vegetation at local noon W/m^2 T +PAR_shade - shade PAR umol/m2/s F +PAR_sun - sunlit PAR umol/m2/s F +PAS_SOMC - PAS_SOM C gC/m^2 T +PAS_SOMC_1m - PAS_SOM C to 1 meter gC/m^2 F +PAS_SOMC_TNDNCY_VERT_TRA levdcmp passive soil organic C tendency due to vertical transport gC/m^3/s F +PAS_SOMC_TO_ACT_SOMC - decomp. of passive soil organic C to active soil organic C gC/m^2/s F +PAS_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of passive soil organic C to active soil organic C gC/m^3/s F +PAS_SOMC_vr levsoi PAS_SOM C (vertically resolved) gC/m^3 T +PAS_SOMN - PAS_SOM N gN/m^2 T +PAS_SOMN_1m - PAS_SOM N to 1 meter gN/m^2 F +PAS_SOMN_TNDNCY_VERT_TRA levdcmp passive soil organic N tendency due to vertical transport gN/m^3/s F +PAS_SOMN_TO_ACT_SOMN - decomp. of passive soil organic N to active soil organic N gN/m^2 F +PAS_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of passive soil organic N to active soil organic N gN/m^3 F +PAS_SOMN_vr levdcmp PAS_SOM N (vertically resolved) gN/m^3 T +PAS_SOM_HR - Het. Resp. from passive soil organic gC/m^2/s F +PAS_SOM_HR_vr levdcmp Het. Resp. from passive soil organic gC/m^3/s F +PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T +PBOT_240 - 10 day running mean of air pressure Pa F +PCH4 - atmospheric partial pressure of CH4 Pa T +PCO2 - atmospheric partial pressure of CO2 Pa T +PCO2_240 - 10 day running mean of CO2 pressure Pa F +PFT_CTRUNC - patch-level sink for C truncation gC/m^2 F +PFT_FIRE_CLOSS - total patch-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T +PFT_FIRE_NLOSS - total patch-level fire N loss gN/m^2/s T +PFT_NTRUNC - patch-level sink for N truncation gN/m^2 F +PLANTCN - Plant C:N used by FUN unitless F +PLANT_CALLOC - total allocated C flux gC/m^2/s F +PLANT_NALLOC - total allocated N flux gN/m^2/s F +PLANT_NDEMAND - N flux required to support initial GPP gN/m^2/s T +PNLCZ - Proportion of nitrogen allocated for light capture unitless F +PO2_240 - 10 day running mean of O2 pressure Pa F +POTENTIAL_IMMOB - potential N immobilization gN/m^2/s T +POTENTIAL_IMMOB_vr levdcmp potential N immobilization gN/m^3/s F +POT_F_DENIT - potential denitrification flux gN/m^2/s T +POT_F_DENIT_vr levdcmp potential denitrification flux gN/m^3/s F +POT_F_NIT - potential nitrification flux gN/m^2/s T +POT_F_NIT_vr levdcmp potential nitrification flux gN/m^3/s F +PREC10 - 10-day running mean of PREC MM H2O/S F +PREC60 - 60-day running mean of PREC MM H2O/S F +PREV_DAYL - daylength from previous timestep s F +PREV_FROOTC_TO_LITTER - previous timestep froot C litterfall flux gC/m^2/s F +PREV_LEAFC_TO_LITTER - previous timestep leaf C litterfall flux gC/m^2/s F +PROD100C - 100-yr wood product C gC/m^2 F +PROD100C_LOSS - loss from 100-yr wood product pool gC/m^2/s F +PROD100N - 100-yr wood product N gN/m^2 F +PROD100N_LOSS - loss from 100-yr wood product pool gN/m^2/s F +PROD10C - 10-yr wood product C gC/m^2 F +PROD10C_LOSS - loss from 10-yr wood product pool gC/m^2/s F +PROD10N - 10-yr wood product N gN/m^2 F +PROD10N_LOSS - loss from 10-yr wood product pool gN/m^2/s F +PSNSHA - shaded leaf photosynthesis umolCO2/m^2/s T +PSNSHADE_TO_CPOOL - C fixation from shaded canopy gC/m^2/s T +PSNSUN - sunlit leaf photosynthesis umolCO2/m^2/s T +PSNSUN_TO_CPOOL - C fixation from sunlit canopy gC/m^2/s T +PSurf - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F +Q2M - 2m specific humidity kg/kg T +QAF - canopy air humidity kg/kg F +QBOT - atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg T +QDIRECT_THROUGHFALL - direct throughfall of liquid (rain + above-canopy irrigation) mm/s F +QDIRECT_THROUGHFALL_SNOW - direct throughfall of snow mm/s F +QDRAI - sub-surface drainage mm/s T +QDRAI_PERCH - perched wt drainage mm/s T +QDRAI_XS - saturation excess drainage mm/s T +QDRIP - rate of excess canopy liquid falling off canopy mm/s F +QDRIP_SNOW - rate of excess canopy snow falling off canopy mm/s F +QFLOOD - runoff from river flooding mm/s T +QFLX_EVAP_TOT - qflx_evap_soi + qflx_evap_can + qflx_tran_veg kg m-2 s-1 T +QFLX_EVAP_VEG - vegetation evaporation mm H2O/s F +QFLX_ICE_DYNBAL - ice dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQDEW_TO_TOP_LAYER - rate of liquid water deposited on top soil or snow layer (dew) mm H2O/s T +QFLX_LIQEVAP_FROM_TOP_LAYER - rate of liquid water evaporated from top soil or snow layer mm H2O/s T +QFLX_LIQ_DYNBAL - liq dynamic land cover change conversion runoff flux mm/s T +QFLX_LIQ_GRND - liquid (rain+irrigation) on ground after interception mm H2O/s F +QFLX_SNOW_DRAIN - drainage from snow pack mm/s T +QFLX_SNOW_DRAIN_ICE - drainage from snow pack melt (ice landunits only) mm/s T +QFLX_SNOW_GRND - snow on ground after interception mm H2O/s F +QFLX_SOLIDDEW_TO_TOP_LAYER - rate of solid water deposited on top soil or snow layer (frost) mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER - rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s T +QFLX_SOLIDEVAP_FROM_TOP_LAYER_ICE - rate of ice evaporated from top soil or snow layer (sublimation) (also includes bare ice subli mm H2O/s F +QH2OSFC - surface water runoff mm/s T +QH2OSFC_TO_ICE - surface water converted to ice mm/s F +QHR - hydraulic redistribution mm/s T +QICE - ice growth/melt mm/s T +QICE_FORC elevclas qice forcing sent to GLC mm/s F +QICE_FRZ - ice growth mm/s T +QICE_MELT - ice melt mm/s T +QINFL - infiltration mm/s T +QINTR - interception mm/s T +QIRRIG_DEMAND - irrigation demand mm/s F +QIRRIG_DRIP - water added via drip irrigation mm/s F +QIRRIG_FROM_GW_CONFINED - water added through confined groundwater irrigation mm/s T +QIRRIG_FROM_GW_UNCONFINED - water added through unconfined groundwater irrigation mm/s T +QIRRIG_FROM_SURFACE - water added through surface water irrigation mm/s T +QIRRIG_SPRINKLER - water added via sprinkler irrigation mm/s F +QOVER - total surface runoff (includes QH2OSFC) mm/s T +QOVER_LAG - time-lagged surface runoff for soil columns mm/s F +QPHSNEG - net negative hydraulic redistribution flux mm/s F +QRGWL - surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T +QROOTSINK levsoi water flux from soil to root in each soil-layer mm/s F +QRUNOFF - total liquid runoff not including correction for land use change mm/s T +QRUNOFF_ICE - total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T +QRUNOFF_ICE_TO_COUPLER - total ice runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_ICE_TO_LIQ - liquid runoff from converted ice runoff mm/s F +QRUNOFF_R - Rural total runoff mm/s F +QRUNOFF_TO_COUPLER - total liquid runoff sent to coupler (includes corrections for land use change) mm/s T +QRUNOFF_U - Urban total runoff mm/s F +QSNOCPLIQ - excess liquid h2o due to snow capping not including correction for land use change mm H2O/s T +QSNOEVAP - evaporation from snow (only when snl<0, otherwise it is equal to qflx_ev_soil) mm/s T +QSNOFRZ - column-integrated snow freezing rate kg/m2/s T +QSNOFRZ_ICE - column-integrated snow freezing rate (ice landunits only) mm/s T +QSNOMELT - snow melt rate mm/s T +QSNOMELT_ICE - snow melt (ice landunits only) mm/s T +QSNOUNLOAD - canopy snow unloading mm/s T +QSNO_TEMPUNLOAD - canopy snow temp unloading mm/s T +QSNO_WINDUNLOAD - canopy snow wind unloading mm/s T +QSNWCPICE - excess solid h2o due to snow capping not including correction for land use change mm H2O/s T +QSOIL - Ground evaporation (soil/snow evaporation + soil/snow sublimation - dew) mm/s T +QSOIL_ICE - Ground evaporation (ice landunits only) mm/s T +QTOPSOIL - water input to surface mm/s F +QVEGE - canopy evaporation mm/s T +QVEGT - canopy transpiration mm/s T +Qair - atmospheric specific humidity (downscaled to columns in glacier regions) kg/kg F +Qh - sensible heat W/m^2 F +Qle - total evaporation W/m^2 F +Qstor - storage heat flux (includes snowmelt) W/m^2 F +Qtau - momentum flux kg/m/s^2 F +RAH1 - aerodynamical resistance s/m F +RAH2 - aerodynamical resistance s/m F +RAIN - atmospheric rain, after rain/snow repartitioning based on temperature mm/s T +RAIN_FROM_ATM - atmospheric rain received from atmosphere (pre-repartitioning) mm/s T +RAIN_ICE - atmospheric rain, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +RAM1 - aerodynamical resistance s/m F +RAM_LAKE - aerodynamic resistance for momentum (lakes only) s/m F +RAW1 - aerodynamical resistance s/m F +RAW2 - aerodynamical resistance s/m F +RB - leaf boundary resistance s/m F +RB10 - 10 day running mean boundary layer resistance s/m F +RETRANSN - plant pool of retranslocated N gN/m^2 T +RETRANSN_TO_NPOOL - deployment of retranslocated N gN/m^2/s T +RH - atmospheric relative humidity % F +RH2M - 2m relative humidity % T +RH2M_R - Rural 2m specific humidity % F +RH2M_U - Urban 2m relative humidity % F +RH30 - 30-day running mean of relative humidity % F +RHAF - fractional humidity of canopy air fraction F +RHAF10 - 10 day running mean of fractional humidity of canopy air fraction F +RH_LEAF - fractional humidity at leaf surface fraction F +ROOTR levgrnd effective fraction of roots in each soil layer (SMS method) proportion F +RR - root respiration (fine root MR + total root GR) gC/m^2/s T +RRESIS levgrnd root resistance in each soil layer proportion F +RSSHA - shaded leaf stomatal resistance s/m T +RSSUN - sunlit leaf stomatal resistance s/m T +Rainf - atmospheric rain, after rain/snow repartitioning based on temperature mm/s F +Rnet - net radiation W/m^2 F +S1_PATHFRAC_S2_vr levdcmp PATHFRAC from active soil organic to slow soil organic ma fraction F +S1_PATHFRAC_S3_vr levdcmp PATHFRAC from active soil organic to passive soil organic fraction F +S1_RESP_FRAC_S2_vr levdcmp respired from active soil organic to slow soil organic ma fraction F +S1_RESP_FRAC_S3_vr levdcmp respired from active soil organic to passive soil organic fraction F +S2_PATHFRAC_S1_vr levdcmp PATHFRAC from slow soil organic ma to active soil organic fraction F +S2_PATHFRAC_S3_vr levdcmp PATHFRAC from slow soil organic ma to passive soil organic fraction F +S2_RESP_FRAC_S1_vr levdcmp respired from slow soil organic ma to active soil organic fraction F +S2_RESP_FRAC_S3_vr levdcmp respired from slow soil organic ma to passive soil organic fraction F +S3_PATHFRAC_S1_vr levdcmp PATHFRAC from passive soil organic to active soil organic fraction F +S3_RESP_FRAC_S1_vr levdcmp respired from passive soil organic to active soil organic fraction F +SABG - solar rad absorbed by ground W/m^2 T +SABG_PEN - Rural solar rad penetrating top soil or snow layer watt/m^2 T +SABV - solar rad absorbed by veg W/m^2 T +SDATES mxsowings actual crop sowing dates; should only be output annually day of year F +SDATES_PERHARV mxharvests actual sowing dates for crops harvested this year; should only be output annually day of year F +SEEDC - pool for seeding new PFTs via dynamic landcover gC/m^2 T +SEEDN - pool for seeding new PFTs via dynamic landcover gN/m^2 T +SLASH_HARVESTC - slash harvest carbon (to litter) gC/m^2/s T +SLO_SOMC - SLO_SOM C gC/m^2 T +SLO_SOMC_1m - SLO_SOM C to 1 meter gC/m^2 F +SLO_SOMC_TNDNCY_VERT_TRA levdcmp slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SLO_SOMC_TO_ACT_SOMC - decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SLO_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SLO_SOMC_TO_PAS_SOMC - decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SLO_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SLO_SOMC_vr levsoi SLO_SOM C (vertically resolved) gC/m^3 T +SLO_SOMN - SLO_SOM N gN/m^2 T +SLO_SOMN_1m - SLO_SOM N to 1 meter gN/m^2 F +SLO_SOMN_TNDNCY_VERT_TRA levdcmp slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SLO_SOMN_TO_ACT_SOMN - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SLO_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SLO_SOMN_TO_PAS_SOMN - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F +SLO_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SLO_SOMN_vr levdcmp SLO_SOM N (vertically resolved) gN/m^3 T +SLO_SOM_HR_S1 - Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S1_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SLO_SOM_HR_S3 - Het. Resp. from slow soil organic ma gC/m^2/s F +SLO_SOM_HR_S3_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SMINN - soil mineral N gN/m^2 T +SMINN_TO_NPOOL - deployment of soil mineral N uptake gN/m^2/s T +SMINN_TO_PLANT - plant uptake of soil mineral N gN/m^2/s T +SMINN_TO_PLANT_FUN - Total soil N uptake of FUN gN/m^2/s T +SMINN_TO_PLANT_vr levdcmp plant uptake of soil mineral N gN/m^3/s F +SMINN_TO_S1N_L1 - mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L1_vr levdcmp mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_L2 - mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F +SMINN_TO_S1N_L2_vr levdcmp mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S2 - mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S1N_S3 - mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F +SMINN_TO_S1N_S3_vr levdcmp mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F +SMINN_TO_S2N_L3 - mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F +SMINN_TO_S2N_L3_vr levdcmp mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F +SMINN_TO_S2N_S1 - mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F +SMINN_TO_S2N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F +SMINN_TO_S3N_S1 - mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F +SMINN_TO_S3N_S2 - mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F +SMINN_TO_S3N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F +SMINN_vr levsoi soil mineral N gN/m^3 T +SMIN_NH4 - soil mineral NH4 gN/m^2 T +SMIN_NH4_TO_PLANT levdcmp plant uptake of NH4 gN/m^3/s F +SMIN_NH4_vr levsoi soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3 - soil mineral NO3 gN/m^2 T +SMIN_NO3_LEACHED - soil NO3 pool loss to leaching gN/m^2/s T +SMIN_NO3_LEACHED_vr levdcmp soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS levdcmp SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF - soil NO3 pool loss to runoff gN/m^2/s T +SMIN_NO3_RUNOFF_vr levdcmp soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT levdcmp plant uptake of NO3 gN/m^3/s F +SMIN_NO3_vr levsoi soil mineral NO3 (vert. res.) gN/m^3 T +SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T +SNOBCMCL - mass of BC in snow column kg/m2 T +SNOBCMSL - mass of BC in top snow layer kg/m2 T +SNOCAN - intercepted snow mm T +SNODSTMCL - mass of dust in snow column kg/m2 T +SNODSTMSL - mass of dust in top snow layer kg/m2 T +SNOFSDSND - direct nir incident solar radiation on snow W/m^2 F +SNOFSDSNI - diffuse nir incident solar radiation on snow W/m^2 F +SNOFSDSVD - direct vis incident solar radiation on snow W/m^2 F +SNOFSDSVI - diffuse vis incident solar radiation on snow W/m^2 F +SNOFSRND - direct nir reflected solar radiation from snow W/m^2 T +SNOFSRNI - diffuse nir reflected solar radiation from snow W/m^2 T +SNOFSRVD - direct vis reflected solar radiation from snow W/m^2 T +SNOFSRVI - diffuse vis reflected solar radiation from snow W/m^2 T +SNOINTABS - Fraction of incoming solar absorbed by lower snow layers - T +SNOLIQFL - top snow layer liquid water fraction (land) fraction F +SNOOCMCL - mass of OC in snow column kg/m2 T +SNOOCMSL - mass of OC in top snow layer kg/m2 T +SNORDSL - top snow layer effective grain radius m^-6 F +SNOTTOPL - snow temperature (top layer) K F +SNOTTOPL_ICE - snow temperature (top layer, ice landunits only) K F +SNOTXMASS - snow temperature times layer mass, layer sum; to get mass-weighted temperature, divide by (SNO K kg/m2 T +SNOTXMASS_ICE - snow temperature times layer mass, layer sum (ice landunits only); to get mass-weighted temper K kg/m2 F +SNOW - atmospheric snow, after rain/snow repartitioning based on temperature mm/s T +SNOWDP - gridcell mean snow height m T +SNOWICE - snow ice kg/m2 T +SNOWICE_ICE - snow ice (ice landunits only) kg/m2 F +SNOWLIQ - snow liquid water kg/m2 T +SNOWLIQ_ICE - snow liquid water (ice landunits only) kg/m2 F +SNOW_5D - 5day snow avg m F +SNOW_DEPTH - snow height of snow covered area m T +SNOW_DEPTH_ICE - snow height of snow covered area (ice landunits only) m F +SNOW_FROM_ATM - atmospheric snow received from atmosphere (pre-repartitioning) mm/s T +SNOW_ICE - atmospheric snow, after rain/snow repartitioning based on temperature (ice landunits only) mm/s F +SNOW_PERSISTENCE - Length of time of continuous snow cover (nat. veg. landunits only) seconds T +SNOW_SINKS - snow sinks (liquid water) mm/s T +SNOW_SOURCES - snow sources (liquid water) mm/s T +SNO_ABS levsno Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE levsno Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW levsno Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE levsno Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE levsno Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ levsno snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE levsno snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS levsno Mean snow grain size Microns F +SNO_GS_ICE levsno Mean snow grain size (ice landunits only) Microns F +SNO_ICE levsno Snow ice content kg/m2 F +SNO_LIQH2O levsno Snow liquid water content kg/m2 F +SNO_MELT levsno snow melt rate in each snow layer mm/s F +SNO_MELT_ICE levsno snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T levsno Snow temperatures K F +SNO_TK levsno Thermal conductivity W/m-K F +SNO_TK_ICE levsno Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE levsno Snow temperatures (ice landunits only) K F +SNO_Z levsno Snow layer thicknesses m F +SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F +SNOdTdzL - top snow layer temperature gradient (land) K/m F +SOIL10 - 10-day running mean of 12cm layer soil K F +SOILC_CHANGE - C change in soil gC/m^2/s T +SOILC_HR - soil C heterotrophic respiration gC/m^2/s T +SOILC_vr levsoi SOIL C (vertically resolved) gC/m^3 T +SOILICE levsoi soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ levsoi soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOILN_vr levdcmp SOIL N (vertically resolved) gN/m^3 T +SOILPSI levgrnd soil water potential in each soil layer MPa F +SOILRESIS - soil resistance to evaporation s/m T +SOILWATER_10CM - soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T +SOMC_FIRE - C loss due to peat burning gC/m^2/s T +SOMFIRE - soil organic matter fire losses gC/m^2/s F +SOM_ADV_COEF levdcmp advection term for vertical SOM translocation m/s F +SOM_C_LEACHED - total flux of C from SOM pools due to leaching gC/m^2/s T +SOM_DIFFUS_COEF levdcmp diffusion coefficient for vertical SOM translocation m^2/s F +SOM_N_LEACHED - total flux of N from SOM pools due to leaching gN/m^2/s F +SOWING_REASON mxsowings Reason for each crop sowing; should only be output annually unitless F +SOWING_REASON_PERHARV mxharvests Reason for sowing of each crop harvested this year; should only be output annually unitless F +SR - total soil respiration (HR + root resp) gC/m^2/s T +STEM_PROF levdcmp profile for litter C and N inputs from stems 1/m F +STORAGE_CDEMAND - C use from the C storage pool gC/m^2 F +STORAGE_GR - growth resp for growth sent to storage for later display gC/m^2/s F +STORAGE_NDEMAND - N demand during the offset period gN/m^2 F +STORVEGC - stored vegetation carbon, excluding cpool gC/m^2 T +STORVEGN - stored vegetation nitrogen gN/m^2 T +SUPPLEMENT_TO_SMINN - supplemental N supply gN/m^2/s T +SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F +SWBGT - 2 m Simplified Wetbulb Globe Temp C T +SWBGT_R - Rural 2 m Simplified Wetbulb Globe Temp C T +SWBGT_U - Urban 2 m Simplified Wetbulb Globe Temp C T +SWdown - atmospheric incident solar radiation W/m^2 F +SWup - upwelling shortwave radiation W/m^2 F +SYEARS_PERHARV mxharvests actual sowing years for crops harvested this year; should only be output annually year F +SoilAlpha - factor limiting ground evap unitless F +SoilAlpha_U - urban factor limiting ground evap unitless F +T10 - 10-day running mean of 2-m temperature K F +TAF - canopy air temperature K F +TAUX - zonal surface stress kg/m/s^2 T +TAUY - meridional surface stress kg/m/s^2 T +TBOT - atmospheric air temperature (downscaled to columns in glacier regions) K T +TBUILD - internal urban building air temperature K T +TBUILD_MAX - prescribed maximum interior building temperature K F +TEMPAVG_T2M - temporary average 2m air temperature K F +TEMPMAX_RETRANSN - temporary annual max of retranslocated N pool gN/m^2 F +TEMPSUM_POTENTIAL_GPP - temporary annual sum of potential GPP gC/m^2/yr F +TFLOOR - floor temperature K F +TG - ground temperature K T +TG_ICE - ground temperature (ice landunits only) K F +TG_R - Rural ground temperature K F +TG_U - Urban ground temperature K F +TH2OSFC - surface water temperature K T +THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T +TKE1 - top lake level eddy thermal conductivity W/(mK) T +TLAI - total projected leaf area index m^2/m^2 T +TLAKE levlak lake temperature K T +TOPO_COL - column-level topographic height m F +TOPO_COL_ICE - column-level topographic height (ice landunits only) m F +TOPO_FORC elevclas topograephic height sent to GLC m F +TOPT - topt coefficient for VOC calc non F +TOTCOLC - total column carbon, incl veg and cpool but excl product pools gC/m^2 T +TOTCOLCH4 - total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +TOTCOLN - total column-level N, excluding product pools gN/m^2 T +TOTECOSYSC - total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T +TOTECOSYSN - total ecosystem N, excluding product pools gN/m^2 T +TOTFIRE - total ecosystem fire losses gC/m^2/s F +TOTLITC - total litter carbon gC/m^2 T +TOTLITC_1m - total litter carbon to 1 meter depth gC/m^2 T +TOTLITN - total litter N gN/m^2 T +TOTLITN_1m - total litter N to 1 meter gN/m^2 T +TOTPFTC - total patch-level carbon, including cpool gC/m^2 T +TOTPFTN - total patch-level nitrogen gN/m^2 T +TOTSOILICE - vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILLIQ - vertically summed soil liquid water (veg landunits only) kg/m2 T +TOTSOMC - total soil organic matter carbon gC/m^2 T +TOTSOMC_1m - total soil organic matter carbon to 1 meter depth gC/m^2 T +TOTSOMN - total soil organic matter N gN/m^2 T +TOTSOMN_1m - total soil organic matter N to 1 meter gN/m^2 T +TOTVEGC - total vegetation carbon, excluding cpool gC/m^2 T +TOTVEGN - total vegetation nitrogen gN/m^2 T +TOT_WOODPRODC - total wood product C gC/m^2 T +TOT_WOODPRODC_LOSS - total loss from wood product pools gC/m^2/s T +TOT_WOODPRODN - total wood product N gN/m^2 T +TOT_WOODPRODN_LOSS - total loss from wood product pools gN/m^2/s T +TPU25T - canopy profile of tpu umol/m2/s T +TRAFFICFLUX - sensible heat flux from urban traffic W/m^2 F +TRANSFER_DEADCROOT_GR - dead coarse root growth respiration from storage gC/m^2/s F +TRANSFER_DEADSTEM_GR - dead stem growth respiration from storage gC/m^2/s F +TRANSFER_FROOT_GR - fine root growth respiration from storage gC/m^2/s F +TRANSFER_GR - growth resp for transfer growth displayed in this timestep gC/m^2/s F +TRANSFER_LEAF_GR - leaf growth respiration from storage gC/m^2/s F +TRANSFER_LIVECROOT_GR - live coarse root growth respiration from storage gC/m^2/s F +TRANSFER_LIVESTEM_GR - live stem growth respiration from storage gC/m^2/s F +TREFMNAV - daily minimum of average 2-m temperature K T +TREFMNAV_R - Rural daily minimum of average 2-m temperature K F +TREFMNAV_U - Urban daily minimum of average 2-m temperature K F +TREFMXAV - daily maximum of average 2-m temperature K T +TREFMXAV_R - Rural daily maximum of average 2-m temperature K F +TREFMXAV_U - Urban daily maximum of average 2-m temperature K F +TROOF_INNER - roof inside surface temperature K F +TSA - 2m air temperature K T +TSAI - total projected stem area index m^2/m^2 T +TSA_ICE - 2m air temperature (ice landunits only) K F +TSA_R - Rural 2m air temperature K F +TSA_U - Urban 2m air temperature K F +TSHDW_INNER - shadewall inside surface temperature K F +TSKIN - skin temperature K T +TSL - temperature of near-surface soil layer (natural vegetated and crop landunits only) K T +TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T +TSOI_10CM - soil temperature in top 10cm of soil K T +TSOI_ICE levgrnd soil temperature (ice landunits only) K T +TSRF_FORC elevclas surface temperature sent to GLC K F +TSUNW_INNER - sunwall inside surface temperature K F +TV - vegetation temperature K T +TV24 - vegetation temperature (last 24hrs) K F +TV240 - vegetation temperature (last 240hrs) K F +TVEGD10 - 10 day running mean of patch daytime vegetation temperature Kelvin F +TVEGN10 - 10 day running mean of patch night-time vegetation temperature Kelvin F +TWS - total water storage mm T +T_SCALAR levsoi temperature inhibition of decomposition unitless T +Tair - atmospheric air temperature (downscaled to columns in glacier regions) K F +Tair_from_atm - atmospheric air temperature received from atmosphere (pre-downscaling) K F +U10 - 10-m wind m/s T +U10_DUST - 10-m wind for dust model m/s T +U10_ICE - 10-m wind (ice landunits only) m/s F +UAF - canopy air speed m/s F +ULRAD - upward longwave radiation above the canopy W/m^2 F +UM - wind speed plus stability effect m/s F +URBAN_AC - urban air conditioning flux W/m^2 T +URBAN_HEAT - urban heating flux W/m^2 T +USTAR - aerodynamical resistance s/m F +UST_LAKE - friction velocity (lakes only) m/s F +VA - atmospheric wind speed plus convective velocity m/s F +VCMX25T - canopy profile of vcmax25 umol/m2/s T +VEGWP nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root segments mm T +VEGWPLN nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T +VEGWPPD nvegwcs predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T +VENTILATION - sensible heat flux from building ventilation W/m^2 T +VOCFLXT - total VOC flux into atmosphere moles/m2/sec F +VOLR - river channel total water storage m3 T +VOLRMCH - river channel main channel water storage m3 T +VPD - vpd Pa F +VPD2M - 2m vapor pressure deficit Pa T +VPD_CAN - canopy vapor pressure deficit kPa T +Vcmx25Z - canopy profile of vcmax25 predicted by LUNA model umol/m2/s T +WASTEHEAT - sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +WBT - 2 m Stull Wet Bulb C T +WBT_R - Rural 2 m Stull Wet Bulb C T +WBT_U - Urban 2 m Stull Wet Bulb C T +WF - soil water as frac. of whc for top 0.05 m proportion F +WFPS levdcmp WFPS percent F +WIND - atmospheric wind velocity magnitude m/s T +WOODC - wood C gC/m^2 T +WOODC_ALLOC - wood C eallocation gC/m^2/s T +WOODC_LOSS - wood C loss gC/m^2/s T +WOOD_HARVESTC - wood harvest carbon (to product pools) gC/m^2/s T +WOOD_HARVESTN - wood harvest N (to product pools) gN/m^2/s T +WTGQ - surface tracer conductance m/s T +W_SCALAR levsoi Moisture (dryness) inhibition of decomposition unitless T +Wind - atmospheric wind velocity magnitude m/s F +XSMRPOOL - temporary photosynthate C pool gC/m^2 T +XSMRPOOL_LOSS - temporary photosynthate C pool loss gC/m^2 F +XSMRPOOL_RECOVER - C flux assigned to recovery of negative xsmrpool gC/m^2/s T +Z0HG - roughness length over ground, sensible heat (vegetated landunits only) m F +Z0HV - roughness length over vegetation, sensible heat m F +Z0MG - roughness length over ground, momentum (vegetated landunits only) m F +Z0MV - roughness length over vegetation, momentum m F +Z0MV_DENSE - roughness length over vegetation, momentum, for dense canopy m F +Z0M_TO_COUPLER - roughness length, momentum: gridcell average sent to coupler m F +Z0QG - roughness length over ground, latent heat (vegetated landunits only) m F +Z0QV - roughness length over vegetation, latent heat m F +ZBOT - atmospheric reference height m T +ZETA - dimensionless stability parameter unitless F +ZII - convective boundary height m F +ZWT - water table depth (natural vegetated and crop landunits only) m T +ZWT_CH4_UNSAT - depth of water table for methane production used in non-inundated area m T +ZWT_PERCH - perched water table depth (natural vegetated and crop landunits only) m T +anaerobic_frac levdcmp anaerobic_frac m3/m3 F +bsw levgrnd clap and hornberger B unitless F +currentPatch - currentPatch coefficient for VOC calc non F +diffus levdcmp diffusivity m^2/s F +fr_WFPS levdcmp fr_WFPS fraction F +n2_n2o_ratio_denit levdcmp n2_n2o_ratio_denit gN/gN F +num_iter - number of iterations unitless F +r_psi levdcmp r_psi m F +ratio_k1 levdcmp ratio_k1 none F +ratio_no3_co2 levdcmp ratio_no3_co2 ratio F +soil_bulkdensity levdcmp soil_bulkdensity kg/m3 F +soil_co2_prod levdcmp soil_co2_prod ug C / g soil / day F +watfc levgrnd water field capacity m^3/m^3 F +watsat levgrnd water saturated m^3/m^3 F +=================================== ================ ============================================================================================== ================================================================= ======= diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90 index 6c0b53abc1..4560b7b165 100644 --- a/src/main/histFileMod.F90 +++ b/src/main/histFileMod.F90 @@ -356,7 +356,7 @@ subroutine hist_printflds() ! !ARGUMENTS: ! ! !LOCAL VARIABLES: - integer, parameter :: ncol = 4 ! number of table columns + integer, parameter :: ncol = 5 ! number of table columns integer nf, i, j ! do-loop counters integer hist_fields_file ! file unit number integer width_col(ncol) ! widths of table columns @@ -390,13 +390,14 @@ subroutine hist_printflds() if (masterproc .and. hist_fields_list_file) then ! Hardwired table column widths to fit the table on a computer ! screen. Some strings will be truncated as a result of the - ! current choices (35, 94, 65, 7). In sphinx (ie the web-based + ! current choices (35, 16, 94, 65, 7). In sphinx (ie the web-based ! documentation), text that has not been truncated will wrap ! around in the available space. width_col(1) = 35 ! variable name column - width_col(2) = 94 ! long description column - width_col(3) = 65 ! units column - width_col(4) = 7 ! active (T or F) column + width_col(2) = hist_dim_name_length ! level dimension column + width_col(3) = 94 ! long description column + width_col(4) = 65 ! units column + width_col(5) = 7 ! active (T or F) column width_col_sum = sum(width_col) + ncol - 1 ! sum of widths & blank spaces ! Convert integer widths to strings for use in format statements @@ -450,9 +451,9 @@ subroutine hist_printflds() fmt_txt = '('//str_w_col_sum//'a)' write(hist_fields_file,fmt_txt) ('-', i=1, width_col_sum) ! Concatenate strings needed in format statement - fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//')' + fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',x,a'//str_width_col(5)//')' write(hist_fields_file,fmt_txt) 'Variable Name', & - 'Long Description', 'Units', 'Active?' + 'Level Dim.', 'Long Description', 'Units', 'Active?' ! End header, same as header ! Concatenate strings needed in format statement @@ -464,10 +465,11 @@ subroutine hist_printflds() ! Main table ! Concatenate strings needed in format statement - fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',l'//str_width_col(4)//')' + fmt_txt = '(a'//str_width_col(1)//',x,a'//str_width_col(2)//',x,a'//str_width_col(3)//',x,a'//str_width_col(4)//',l'//str_width_col(5)//')' do nf = 1,nallhistflds write(hist_fields_file,fmt_txt) & allhistfldlist(nf)%field%name, & + allhistfldlist(nf)%field%type2d, & allhistfldlist(nf)%field%long_name, & allhistfldlist(nf)%field%units, & allhistfldlist(nf)%actflag(1) @@ -5369,7 +5371,7 @@ subroutine hist_addfld1d (fname, units, avgflag, long_name, type1d_out, & ! Add field to allhistfldlist call allhistfldlist_addfld (fname=trim(fname), numdims=1, type1d=l_type1d, & - type1d_out=l_type1d_out, type2d='unset', num2d=1, & + type1d_out=l_type1d_out, type2d='-', num2d=1, & units=units, avgflag=avgflag, long_name=long_name, hpindex=hpindex, & p2c_scale_type=scale_type_p2c, c2l_scale_type=scale_type_c2l, & l2g_scale_type=scale_type_l2g) From e0fd4f2364df6957ae5e48361a3c6eaeecbf438b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 15:09:54 -0600 Subject: [PATCH 1396/2067] Update ChangeLog and ChangeSum --- doc/ChangeLog | 66 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 67 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 43a19a6644..7a00a0e80d 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,70 @@ =============================================================== +Tag name: ctsm5.1.dev135 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Mon Aug 21 15:06:35 MDT 2023 +One-line Summary: Rename hist fields to track them down more easily + +Purpose and description of changes +---------------------------------- + + Renaming history fields to make easier to find in lists, e.g. when + using ncview. For example, litter fields like MET_LIT and STR_LIT + will be LIT_MET and LIT_STR. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): + Fixes #2095 + + +Testing summary: +---------------- +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + any other testing (give details below): + Sam L. ran the LMWG diag. pkg and found only one plot affected by this + PR's changes. In particular, set 6 CWD_C, which was CWDC + + +Answer changes +-------------- + +Changes answers relative to baseline: + No. Field lists differ. In some tests, the namelists differ. + + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2106 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev134 Originator(s): rgknox (Ryan Knox,LBNL EESA), erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Wed Aug 16 17:20:27 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 5270412209..67f357480b 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev135 slevis 08/21/2023 Rename hist fields to track them down more easily ctsm5.1.dev134 rgknox 08/16/2023 Migration of FATES to share normal soil BGC call sequence and functionality ctsm5.1.dev133 glemieux 08/09/2023 FATES API update to facilitate fates refactor ctsm5.1.dev132 slevis 08/04/2023 Add parameterization to allow excess ice in soil and subsidence From 1d962dd37be6cd48fef424d05d108ad8bdcff75a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 15:31:37 -0600 Subject: [PATCH 1397/2067] Revisions part 1 in response to Erik's review --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 -- src/biogeophys/BareGroundFluxesMod.F90 | 13 +++++-------- src/biogeophys/CanopyFluxesMod.F90 | 11 +++++------ src/biogeophys/FrictionVelocityMod.F90 | 14 +++----------- src/biogeophys/HumanIndexMod.F90 | 3 +-- src/biogeophys/LakeFluxesMod.F90 | 18 +++++++++++------- src/main/clm_varcon.F90 | 3 +++ 7 files changed, 28 insertions(+), 36 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 4ae6f03159..88b2947b10 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -213,7 +213,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 2.0d00 2.0d00 0.5d00 -0.5d00 0.5d00 2.0d00 @@ -505,7 +504,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ZengWang2007 .true. -.false. .false. diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 76a07f0f61..3b0bb4849e 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -82,7 +82,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & use shr_const_mod , only : SHR_CONST_RGAS use clm_varpar , only : nlevgrnd use clm_varcon , only : cpair, vkc, grav, denice, denh2o - use clm_varcon , only : beta_param, nu_param + use clm_varcon , only : beta_param, nu_param, meier_param3 use clm_varctl , only : use_lch4, z0param_method use landunit_varcon , only : istsoil, istcrop use QSatMod , only : QSat @@ -356,13 +356,10 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & case ('Meier2022') ! After Yang et al. (2008) - z0hg_patch(p) = 70._r8 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) - - ! RM: After Owen and Thomson (1963). This formulation could be used as an alternative to Yang et al. (2007). It would - ! avoid that z0hg and z0qg becomes larger frequently than z0mg, which happens with Yang et al. (2007). - !z0hg_patch(p) = z0mg_patch(p) / exp(0.52_r8 * 0.4_r8 * (8._r8 * ustar(p) * z0mg_patch(p) / nu_param)**params_inst%a_exp * 0.71_r8**0.8_r8) - - + ! (...)**0.5 = sqrt(...) and (...)**0.25 = sqrt(sqrt(...)) + ! likely more efficient to calculate as exponents + z0hg_patch(p) = meier_param3 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) + end select z0qg_patch(p) = z0hg_patch(p) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 75c77fcd25..b3e5089575 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -332,6 +332,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, real(r8) :: cir(bounds%begp:bounds%endp) ! atmos. radiation temporay set real(r8) :: dc1,dc2 ! derivative of energy flux [W/m2/K] real(r8) :: delt ! temporary + real(r8) :: delt_threshold ! temporary real(r8) :: delq(bounds%begp:bounds%endp) ! temporary real(r8) :: del(bounds%begp:bounds%endp) ! absolute change in leaf temp in current iteration [K] real(r8) :: del2(bounds%begp:bounds%endp) ! change in leaf temperature in previous iteration [K] @@ -894,16 +895,18 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) case ('Meier2022') - lt = max(0.00001_r8,elai(p)+esai(p)) + delt_threshold = 1.e-4 + lt = max(delt_threshold, elai(p) + esai(p)) displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(cd1_param * lt)**0.5_r8)) / (cd1_param*lt)**0.5_r8) lt = min(lt,z0v_LAImax(patch%itype(p))) delt = 2._r8 + ! Reminder that (...)**(-0.5) = 1 / sqrt(...) U_ustar_ini = (z0v_Cs(patch%itype(p)) + z0v_Cr(patch%itype(p)) * lt * 0.5_r8)**(-0.5_r8) & *z0v_c(patch%itype(p)) * lt * 0.25_r8 U_ustar = U_ustar_ini - do while (delt > 0.0001_r8) + do while (delt > delt_threshold) U_ustar_prev = U_ustar U_ustar = U_ustar_ini * exp(U_ustar_prev) delt = abs(U_ustar - U_ustar_prev) @@ -1066,10 +1069,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! changed by K.Sakaguchi from here ! transfer coefficient over bare soil is changed to a local variable ! just for readability of the code (from line 680) - ! RM: Does this need to be updated if Ya08 is used too? Proposed formulation (definitely double-check!) - ! , interpreting the statement below as csoilb = vkc / ln(z0mg/z0hg): - ! csoilb = vkc / log( z0mg(c) / ( 70._r8 * nu_param / ustar(p) * exp( -7.2_r8 * ustar(p)**(0.5_r8) * - ! (abs(temp1(p)*dth(p)))**(0.25_r8)) ) ) csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / nu_param)**params_inst%a_exp) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 621bce4117..56f06c47c2 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -517,7 +517,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & ! Set roughness lengths and forcing heights for non-lake points ! ! !USES: - use clm_varcon , only : rpi, b1_param, b4_param + use clm_varcon , only : rpi, b1_param, b4_param, meier_param1, meier_param2 ! !ARGUMENTS: class(frictionvel_type) , intent(inout) :: this type(bounds_type) , intent(in) :: bounds @@ -577,15 +577,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & select case (z0param_method) case ('ZengWang2007') if (frac_sno(c) > 0._r8) then - if(use_z0m_snowmelt) then - if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(c) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 - else - z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 - end if - else - z0mg(c) = this%zsno - end if + z0mg(c) = this%zsno else z0mg(c) = this%zlnd end if @@ -596,7 +588,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & if ( snomelt_accum(c) < 1.e-5_r8 )then z0mg(c) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 + z0mg(c) = exp(b1_param * (atan((log10(snomelt_accum(c)) + meier_param1) / meier_param2)) + b4_param) * 1.e-3_r8 end if else z0mg(c) = this%zsno diff --git a/src/biogeophys/HumanIndexMod.F90 b/src/biogeophys/HumanIndexMod.F90 index 403dae777d..17a1ef968e 100644 --- a/src/biogeophys/HumanIndexMod.F90 +++ b/src/biogeophys/HumanIndexMod.F90 @@ -1014,7 +1014,6 @@ subroutine Wet_BulbS (Tc_6,rh,wbt) ! !LOCAL VARIABLES: !EOP ! -#ifndef NDEBUG if ( rh < 0.0d00 )then write(iulog,*) 'rh = ', rh call endrun(msg="ERROR RH is negative "//errmsg(sourcefile, __LINE__)) @@ -1022,7 +1021,7 @@ subroutine Wet_BulbS (Tc_6,rh,wbt) write(iulog,*) 'rh = ', rh call endrun(msg="ERROR RH is greater than a hundred "//errmsg(sourcefile, __LINE__)) end if -#endif + wbt = Tc_6 * atan(0.151977_r8*sqrt(rh + 8.313659_r8)) + & atan(Tc_6+rh) - atan(rh-1.676331_r8) + & 0.00391838_r8*rh**(3._r8/2._r8)*atan(0.023101_r8*rh) - & diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 11b141100c..1b544a8364 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -94,6 +94,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, use clm_varcon , only : hvap, hsub, hfus, cpair, cpliq, tkwat, tkice, tkair use clm_varcon , only : sb, vkc, grav, denh2o, tfrz, spval, rpi use clm_varcon , only : beta_param, nu_param, b1_param, b4_param + use clm_varcon , only : meier_param1, meier_param2, meier_param3 use clm_varctl , only : use_lch4, z0param_method, use_z0m_snowmelt use LakeCon , only : betavis, z0frzlake, tdmax, emg_lake use LakeCon , only : lake_use_old_fcrit_minz0 @@ -341,7 +342,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0mg(p) = params_inst%zglc - z0hg(p) = 70._r8 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 + z0hg(p) = meier_param3 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 case ('ZengWang2007') z0mg(p) = z0frzlake @@ -353,7 +354,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, if ( snomelt_accum(c) < 1.e-5_r8 ) then z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c)) + meier_param1) / meier_param2)) + b4_param) * 1.e-3_r8 end if else z0mg(p) = params_inst%zsno @@ -361,7 +362,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('Meier2022') - z0hg(p) = 70._r8 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 + z0hg(p) = meier_param3 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes end select @@ -593,8 +594,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, select case (z0param_method) case ('Meier2022') z0mg(p) = params_inst%zglc - - z0hg(p) = 70._r8 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + ! (...)**0.5 = sqrt(...) and (...)**0.25 = sqrt(sqrt(...)) + ! likely more efficient to calculate as exponents + z0hg(p) = meier_param3 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes case ('ZengWang2007') z0mg(p) = z0frzlake @@ -606,13 +608,15 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, if ( snomelt_accum(c) < 1.e-5_r8 )then z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else - z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c))+0.23_r8)/0.08_r8)) + b4_param) * 1.e-3_r8 + z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c)) + meier_param1) / meier_param2)) + b4_param) * 1.e-3_r8 end if end if select case (z0param_method) case ('Meier2022') - z0hg(p) = 70._r8 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes + ! (...)**0.5 = sqrt(...) and (...)**0.25 = sqrt(sqrt(...)) + ! likely more efficient to calculate as exponents + z0hg(p) = meier_param3 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes diff --git a/src/main/clm_varcon.F90 b/src/main/clm_varcon.F90 index f898e27307..4b0bbe160d 100644 --- a/src/main/clm_varcon.F90 +++ b/src/main/clm_varcon.F90 @@ -162,6 +162,9 @@ module clm_varcon real(r8), public, parameter :: b1_param = 1.4_r8 ! Meier et al. (2022) empirical constant real(r8), public, parameter :: b4_param = -0.31_r8 ! Meier et al. (2022) empirical constant real(r8), public, parameter :: cd1_param = 7.5_r8 ! Meier et al. (2022) originally from Raupach (1994) + real(r8), public, parameter :: meier_param1 = 0.23_r8 ! slevis did not find it documented + real(r8), public, parameter :: meier_param2 = 0.08_r8 ! slevis did not find it documented + real(r8), public, parameter :: meier_param3 = 70.0_r8 ! slevis did not find it documented, but to the question "What is the 70 in the formula for roughness length" bard.google.com responds "[...] a dimensionless constant [...] originally introduced by von Karman. It is based on experimental data and is thought to represent the ratio of the average height of the surface roughness elements to the distance that the wind travels before it is slowed down by the roughness." !------------------------------------------------------------------ ! Urban building temperature constants From 59745d059933bc7ac4ca29438337dd24cb7faa24 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 15:41:24 -0600 Subject: [PATCH 1398/2067] Revisions part 2: add missing comment --- src/main/clm_varctl.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 7179e6afe6..559a95b570 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -249,7 +249,7 @@ module clm_varctl ! Surface roughness parameterization !---------------------------------------------------------- - character(len=64), public :: z0param_method + character(len=64), public :: z0param_method ! ZengWang2007 or Meier2022 logical, public :: use_z0m_snowmelt = .false. ! true => use snow z0m parameterization of Brock2006 From f01adc663438029ef10b781c7d6490f6a0be2275 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 14 Aug 2023 16:59:56 -0600 Subject: [PATCH 1399/2067] Share idpp calculation code. Between CropPhenology()and get_tillage_multipliers(). New function DaysPastPlanting() shared from CNPhenologyMod to TillageMod. --- src/biogeochem/CNPhenologyMod.F90 | 41 ++++++++++++++++++++++++++----- src/soilbiogeochem/TillageMod.F90 | 20 ++++----------- 2 files changed, 40 insertions(+), 21 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c2a66511f7..695b61c4d7 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -52,6 +52,7 @@ module CNPhenologyMod public :: CNPhenologyInit ! Initialization public :: CNPhenology ! Update public :: CropPhase ! Get the current phase of each crop patch + public :: DaysPastPlanting ! Get how many days it's been since crop was planted ! !PUBLIC for unit testing public :: CNPhenologySetNML ! Set the namelist setttings explicitly for unit tests @@ -2117,12 +2118,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! days past planting may determine harvest - - if (jday >= idop(p)) then - idpp = jday - idop(p) - else - idpp = int(dayspyr) + jday - idop(p) - end if + idpp = DaysPastPlanting(idop(p), jday) ! onset_counter initialized to zero when .not. croplive ! offset_counter relevant only at time step of harvest @@ -2664,6 +2660,39 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & end subroutine PlantCrop + !----------------------------------------------------------------------- + function DaysPastPlanting(idop, jday_in) + ! !USES: + use clm_time_manager, only : get_prev_calday, get_curr_days_per_year + ! + ! !ARGUMENTS: + integer, intent(in) :: idop ! patch day of planting + integer, optional, intent(in) :: jday_in ! julian day of the year + ! + ! !LOCAL VARIABLES + integer :: DaysPastPlanting + integer :: jday + + ! Must use separate jday_in and jday because we can't redefine an intent(in) + ! variable, even if it wasn't provided in the function call. + if (present(jday_in)) then + jday = jday_in + else + ! Use prev instead of curr to avoid jday=1 in last timestep of year + jday = get_prev_calday() + end if + + if (jday >= idop) then + DaysPastPlanting = jday - idop + else + ! As long as crops have at most a 365-day growing season, using get_curr_days_per_year() + ! should give the same result of this function as using get_prev_days_per_year(). + ! TODO: Test identicality when using get_prev_days_per_year(). + DaysPastPlanting = jday - idop + get_curr_days_per_year() + end if + + end function DaysPastPlanting + !----------------------------------------------------------------------- subroutine vernalization(p, & canopystate_inst, temperature_inst, waterdiagnosticbulk_inst, cnveg_state_inst, crop_inst, & diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 6d9d2230c2..3ef879a3a1 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -178,6 +178,8 @@ subroutine get_tillage_multipliers(tillage_mults, idop) ! ! Modified by Sam Rabin to fix a bug where idpp wasn't actually used, which ! would affect growing seasons that crossed over into a new calendar year. + ! Also avoids day=1 in last timestep of year by using DaysPastPlanting(), which + ! uses get_prev_calday() instead of get_curr_calday(). ! Previous behavior can be requested with namelist variable use_original_tillage. ! ! Original code had two versions depending on cell's GDP, but this seems to @@ -187,6 +189,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) ! !USES: use clm_time_manager, only : get_curr_calday, get_curr_days_per_year use pftconMod , only : ntmp_corn, nirrig_tmp_corn, ntmp_soybean, nirrig_tmp_soybean + use CNPhenologyMod , only : DaysPastPlanting ! !ARGUMENTS: real(r8) , intent(inout) :: tillage_mults(:) ! tillage multipliers for this patch integer , intent(in) :: idop ! patch day of planting @@ -199,21 +202,6 @@ subroutine get_tillage_multipliers(tillage_mults, idop) real(r8) dayspyr ! days per year !----------------------------------------------------------------------- - !get info from externals - day = get_curr_calday() - dayspyr = get_curr_days_per_year() !Add by MWG for IDPP-based routine - - ! days past planting may determine harvest/tillage - if (day >= idop) then - idpp = day - idop - else - idpp = int(dayspyr) + day - idop - end if - - ! ----------------------------------------------------- - ! 3) assigning tillage practices and mapping to the - ! effect on soil C decomposition - ! ----------------------------------------------------- ! info from DAYCENT (Melannie Hartman CSU) ! temp. cereals: P 30 d bef, C 15 d bef, D on day of planting ! corn, soy : P C D & HW-7 30 d aftr @@ -221,6 +209,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) phase = 0 if (use_original_tillage) then + day = get_curr_calday() if (day >= idop .and. day < idop+15) then ! based on Point Chisel Tandem Disk multipliers phase = 1 else if (day >= idop+15 .and. day < idop+45) then ! based on Field and Row Cultivator multipliers @@ -229,6 +218,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) phase = 3 end if else + idpp = DaysPastPlanting(idop) if (idpp < 15) then ! based on Point Chisel Tandem Disk multipliers phase = 1 else if (idpp < 45) then ! based on Field and Row Cultivator multipliers From cb5a889de854fa84d89ebfaa5cbdf7847aed1092 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 21 Aug 2023 15:19:49 -0600 Subject: [PATCH 1400/2067] Prepend bgc_ to till_decompk_multipliers. --- src/soilbiogeochem/TillageMod.F90 | 2 +- tillage-tmp/add_tillage_to_paramsfile.py | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 3ef879a3a1..fc1331f48b 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -129,7 +129,7 @@ subroutine readParams_netcdf(ncid) case( no_soil_decomp ) return case( century_decomp ) - tString = 'till_decompk_multipliers' + tString = 'bgc_till_decompk_multipliers' case( mimics_decomp ) tString = 'mimics_till_decompk_multipliers' case default diff --git a/tillage-tmp/add_tillage_to_paramsfile.py b/tillage-tmp/add_tillage_to_paramsfile.py index 2b3ca55aee..1c6744f38f 100644 --- a/tillage-tmp/add_tillage_to_paramsfile.py +++ b/tillage-tmp/add_tillage_to_paramsfile.py @@ -103,9 +103,11 @@ def make_dataarray(np_array, decomp_model, ntill_intensities_max, ndecomp_pools_ ) # Name DataArray - da_name = "till_decompk_multipliers" - if "mimics" in decomp_model.lower(): - da_name = "mimics_" + da_name + if decomp_model.lower() == "mimics": + da_name = "mimics" + elif decomp_model.lower() == "century": + da_name = "bgc" + da_name += "_till_decompk_multipliers" da = xr.DataArray( data = np_array, From 86b81fbf4cfe1a37a0f1d4138e712eb34c0813d9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 21 Aug 2023 16:14:59 -0600 Subject: [PATCH 1401/2067] Till to 32 cm depth rather than top 5 soil layers. In default configuration, there's no difference. This is setting up for the specification of this depth as a namelist parameter. Partially-tilled layers not yet allowed. --- src/soilbiogeochem/TillageMod.F90 | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index fc1331f48b..44a75d9ea5 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -30,6 +30,7 @@ module TillageMod logical :: use_original_tillage ! Use get_tillage_multipliers_orig? real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, ntill_stages_max) integer, parameter :: ntill_stages_max = 3 ! How many different tillage phases are there? (Not including all-1 phases.) + real(r8), parameter :: max_tillage_depth = 0.32_r8 ! Maximum depth to till (m) !============================================================================== contains @@ -247,6 +248,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! ! !USES use pftconMod , only : npcropmin + use clm_varcon, only : zisoi use PatchType , only : patch ! ! !ARGUMENTS: @@ -261,9 +263,8 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) real(r8), dimension(ndecomp_pools) :: tillage_mults real(r8), dimension(ndecomp_pools) :: tillage_mults_1patch - if (.not. col%active(c) .or. j > 5) then - ! Top 5 layers (instead of all nlevdecomp) so that model only tills - ! the top 26-40 cm of the soil surface, rather than whole soil - MWGraham + ! TODO: Allow partially-tilled layers. + if (.not. col%active(c) .or. zisoi(j) > max_tillage_depth) then return end if From fea92f253d925f2c64ec5413690d0b4239831159 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 17:30:02 -0600 Subject: [PATCH 1402/2067] Revert delt_threshold param back to hardwired values --- src/biogeophys/CanopyFluxesMod.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index b3e5089575..3ab3bb7923 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -332,7 +332,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, real(r8) :: cir(bounds%begp:bounds%endp) ! atmos. radiation temporay set real(r8) :: dc1,dc2 ! derivative of energy flux [W/m2/K] real(r8) :: delt ! temporary - real(r8) :: delt_threshold ! temporary real(r8) :: delq(bounds%begp:bounds%endp) ! temporary real(r8) :: del(bounds%begp:bounds%endp) ! absolute change in leaf temp in current iteration [K] real(r8) :: del2(bounds%begp:bounds%endp) ! change in leaf temperature in previous iteration [K] @@ -895,8 +894,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0mv(p) = exp(egvf * log(z0mv(p)) + (1._r8 - egvf) * log(z0mg(c))) case ('Meier2022') - delt_threshold = 1.e-4 - lt = max(delt_threshold, elai(p) + esai(p)) + lt = max(1.e-5_r8, elai(p) + esai(p)) displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(cd1_param * lt)**0.5_r8)) / (cd1_param*lt)**0.5_r8) lt = min(lt,z0v_LAImax(patch%itype(p))) @@ -906,7 +904,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, *z0v_c(patch%itype(p)) * lt * 0.25_r8 U_ustar = U_ustar_ini - do while (delt > delt_threshold) + do while (delt > 1.e-4_r8) U_ustar_prev = U_ustar U_ustar = U_ustar_ini * exp(U_ustar_prev) delt = abs(U_ustar - U_ustar_prev) From 7a39c65bc15adad93ae101c4dc696faec772058e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 17:31:19 -0600 Subject: [PATCH 1403/2067] Ensure that ZengWang2007 and use_z0m_snowmelt NOT true simultaneously --- bld/CLMBuildNamelist.pm | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index a7ee8f2dc9..84c9146f03 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4381,6 +4381,13 @@ sub setup_logic_z0param { my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' )); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0m_snowmelt', 'z0param_method'=>$z0param_method ); + + my $use_z0m_snowmelt = $nl->get_value( 'use_z0m_snowmelt' ); + + if ( $z0param_method eq "ZengWang2007" && defined($use_z0m_snowmelt) && value_is_true($use_z0m_snowmelt)) { + $log->fatal_error("use_z0m_snowmelt must be .false. when z0param_method = $z0param_method.\n $@"); + } + } #------------------------------------------------------------------------------- From 69451e26b35ff0b7d17a1f476e640ab7855d3b6f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 21 Aug 2023 17:30:41 -0600 Subject: [PATCH 1404/2067] Allow partially-tilled soil layers. --- src/soilbiogeochem/TillageMod.F90 | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 44a75d9ea5..2d4d61277d 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -262,9 +262,16 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) real :: sumwt ! sum of all patch weights, to check real(r8), dimension(ndecomp_pools) :: tillage_mults real(r8), dimension(ndecomp_pools) :: tillage_mults_1patch + real(r8) :: layer_top ! Depth (cm) of the top of this soil layer. zisoi is the depth of the bottom. + real(r8) :: layer_thickness ! Thickness of this soil layer (m) + real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth - ! TODO: Allow partially-tilled layers. - if (.not. col%active(c) .or. zisoi(j) > max_tillage_depth) then + if (j == 1) then + layer_top = 0._r8 + else + layer_top = zisoi(j-1) + end if + if (.not. col%active(c) .or. layer_top > max_tillage_depth) then return end if @@ -301,6 +308,12 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) call endrun('ERROR Active crop patch weights does not sum to 1') end if + ! Adjust tillage_mults to consider fraction of this layer that's within tillage depth + layer_thickness = zisoi(j) - layer_top + fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth - layer_top) / layer_thickness)) + tillage_mults = tillage_mults * fraction_tilled & + + 1._r8 * (1._r8 - fraction_tilled) + ! Apply decomp_k = decomp_k * tillage_mults(:) From 8e67f287ab76b916be46e1071077922af5dbae6a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 21 Aug 2023 17:46:54 -0600 Subject: [PATCH 1405/2067] max_tillage_depth is now a namelist parameter. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + bld/namelist_files/namelist_definition_ctsm.xml | 5 +++++ src/soilbiogeochem/TillageMod.F90 | 8 ++++++-- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index f65dc47ce6..d0b29f48f4 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2729,5 +2729,6 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 off .false. +0.32d00 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 6335953fcc..91e74e347e 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2895,4 +2895,9 @@ Whether to till crop soil, and if so, with what intensity. Toggle to use original tillage logic, with bug for seasons crossing into a new calendar year + +Maximum depth to till soil (m). + + diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 2d4d61277d..35f487db80 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -30,7 +30,7 @@ module TillageMod logical :: use_original_tillage ! Use get_tillage_multipliers_orig? real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, ntill_stages_max) integer, parameter :: ntill_stages_max = 3 ! How many different tillage phases are there? (Not including all-1 phases.) - real(r8), parameter :: max_tillage_depth = 0.32_r8 ! Maximum depth to till (m) + real(r8) :: max_tillage_depth ! Maximum depth to till (m) !============================================================================== contains @@ -53,11 +53,13 @@ subroutine readParams_namelist() namelist /tillage_inparm/ & tillage_mode, & - use_original_tillage + use_original_tillage, & + max_tillage_depth ! Default values tillage_mode = 'off' use_original_tillage = .false. + max_tillage_depth = 0.32_r8 ! Read tillage namelist if (masterproc) then @@ -75,12 +77,14 @@ subroutine readParams_namelist() endif call shr_mpi_bcast(tillage_mode, mpicom) call shr_mpi_bcast(use_original_tillage , mpicom) + call shr_mpi_bcast(max_tillage_depth, mpicom) if (masterproc) then write(iulog,*) ' ' write(iulog,*) 'tillage settings:' write(iulog,*) ' tillage_mode = ',tillage_mode write(iulog,*) ' use_original_tillage = ',use_original_tillage + write(iulog,*) ' max_tillage_depth = ',max_tillage_depth endif ! Assign these From 0875c515e100d87254e6c5b754d39ee82fe87ff5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 18:21:08 -0600 Subject: [PATCH 1406/2067] Removed white space that appears red in git diff --- bld/CLMBuildNamelist.pm | 2 +- src/biogeophys/BareGroundFluxesMod.F90 | 12 +++++------ src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 16 +++++++------- src/biogeophys/CanopyFluxesMod.F90 | 7 +++---- src/biogeophys/FrictionVelocityMod.F90 | 22 +++++++++----------- src/biogeophys/LakeFluxesMod.F90 | 18 ++++++++-------- src/biogeophys/SnowHydrologyMod.F90 | 4 ++-- src/biogeophys/SoilTemperatureMod.F90 | 4 ++-- src/main/clm_varctl.F90 | 1 - src/main/pftconMod.F90 | 22 ++++++++++---------- 10 files changed, 52 insertions(+), 56 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 84c9146f03..54a6aea7e4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4378,7 +4378,7 @@ sub setup_logic_z0param { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method'); - my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' )); + my $z0param_method = remove_leading_and_trailing_quotes($nl->get_value('z0param_method' )); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_z0m_snowmelt', 'z0param_method'=>$z0param_method ); diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 3b0bb4849e..645b908157 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -92,7 +92,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & swbgt, hmdex, dis_coi, dis_coiS, THIndex, & SwampCoolEff, KtoC, VaporPres use CanopyStateType , only : canopystate_type - + ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -247,9 +247,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & z0mg_patch => frictionvel_inst%z0mg_patch , & ! Output: [real(r8) (:) ] patch roughness length, momentum [m] z0hg_patch => frictionvel_inst%z0hg_patch , & ! Output: [real(r8) (:) ] patch roughness length, sensible heat [m] z0qg_patch => frictionvel_inst%z0qg_patch , & ! Output: [real(r8) (:) ] patch roughness length, latent heat [m] - z0mv => frictionvel_inst%z0mv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, momentum [m] - z0hv => frictionvel_inst%z0hv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, sensible heat [m] - z0qv => frictionvel_inst%z0qv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, latent heat [m] + z0mv => frictionvel_inst%z0mv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, momentum [m] + z0hv => frictionvel_inst%z0hv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, sensible heat [m] + z0qv => frictionvel_inst%z0qv_patch , & ! Output: [real(r8) (:) ] roughness length over vegetation, latent heat [m] kbm1 => frictionvel_inst%kbm1_patch , & ! Output: [real(r8) (:) ] natural logarithm of z0mg_p/z0hg_p [-] ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) num_iter => frictionvel_inst%num_iter_patch , & ! Output: [real(r8) (:) ] number of iterations @@ -265,7 +265,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & rssun => photosyns_inst%rssun_patch , & ! Output: [real(r8) (:) ] leaf sunlit stomatal resistance (s/m) (output from Photosynthesis) rssha => photosyns_inst%rssha_patch , & ! Output: [real(r8) (:) ] leaf shaded stomatal resistance (s/m) (output from Photosynthesis) - displa => canopystate_inst%displa_patch , & ! Output: [real(r8) (:) ] displacement height (m) + displa => canopystate_inst%displa_patch , & ! Output: [real(r8) (:) ] displacement height (m) begp => bounds%begp , & endp => bounds%endp & @@ -309,7 +309,7 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & z0mv(p) = 0._r8 z0hv(p) = 0._r8 z0qv(p) = 0._r8 - + ur(p) = max(params_inst%wind_min,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g))) dth(p) = thm(p)-t_grnd(c) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 004e2c689e..11842560ee 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -34,7 +34,7 @@ module BiogeophysPreFluxCalcsMod use WaterStateBulkType , only : waterstatebulk_type use SurfaceResistanceMod , only : calc_soilevap_resis use WaterFluxBulkType , only : waterfluxbulk_type - + ! ! !PUBLIC TYPES: implicit none @@ -172,30 +172,30 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & z0m(p) = pftcon%z0mr(patch%itype(p)) * htop(p) displa(p) = pftcon%displar(patch%itype(p)) * htop(p) - case ('Meier2022') - + case ('Meier2022') + ! Don't set on first few steps of a simulation, since htop isn't set yet, need to wait until after first do_alb time if ( is_first_step() .or. get_nstep() <= GetBalanceCheckSkipSteps()-1 ) then z0m(p) = 0._r8 - displa(p) = 0._r8 + displa(p) = 0._r8 cycle ! If a crop type and it's the start of the year, htop gets reset to ! zero... else if ( is_beg_curr_year() .and. pftcon%crop(patch%itype(p)) /= 0.0_r8 )then z0m(p) = 0._r8 - displa(p) = 0._r8 + displa(p) = 0._r8 end if if (patch%itype(p) == noveg) then z0m(p) = 0._r8 - displa(p) = 0._r8 + displa(p) = 0._r8 else ! Compute as if elai+esai = LAImax in CanopyFluxes displa(p) = htop(p) * (1._r8 - (1._r8 - exp(-(cd1_param * (pftcon%z0v_LAImax(patch%itype(p))))**0.5_r8)) & / (cd1_param*(pftcon%z0v_LAImax(patch%itype(p)) ))**0.5_r8) - U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p))) & + U_ustar = 4._r8 * (pftcon%z0v_Cs(patch%itype(p)) + pftcon%z0v_Cr(patch%itype(p)) * (pftcon%z0v_LAImax(patch%itype(p))) & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) if ( htop(p) <= 1.e-10_r8 )then @@ -210,7 +210,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & end select - + end if end do diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index 3ab3bb7923..e540296b6d 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -113,7 +113,7 @@ subroutine CanopyFluxesReadNML(NLFilename) namelist /canopyfluxes_inparm/ use_undercanopy_stability namelist /canopyfluxes_inparm/ use_biomass_heat_storage namelist /canopyfluxes_inparm/ itmax_canopy_fluxes - + ! Initialize options to default values, in case they are not specified in ! the namelist @@ -535,7 +535,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] forc_hgt_t_patch => frictionvel_inst%forc_hgt_t_patch , & ! Output: [real(r8) (:) ] observational height of temperature at patch level [m] forc_hgt_q_patch => frictionvel_inst%forc_hgt_q_patch , & ! Output: [real(r8) (:) ] observational height of specific humidity at patch level [m] - forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Output: [real(r8) (:) ] observational height of wind at patch level [m] + forc_hgt_u_patch => frictionvel_inst%forc_hgt_u_patch , & ! Output: [real(r8) (:) ] observational height of wind at patch level [m] z0mg => frictionvel_inst%z0mg_col , & ! Input: [real(r8) (:) ] roughness length of ground, momentum [m] zetamax => frictionvel_inst%zetamaxstable , & ! Input: [real(r8) ] max zeta value under stable conditions ram1 => frictionvel_inst%ram1_patch , & ! Output: [real(r8) (:) ] aerodynamical resistance (s/m) @@ -1068,7 +1068,6 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, ! transfer coefficient over bare soil is changed to a local variable ! just for readability of the code (from line 680) csoilb = vkc / (params_inst%a_coef * (z0mg(c) * uaf(p) / nu_param)**params_inst%a_exp) - !compute the stability parameter for ricsoilc ("S" in Sakaguchi&Zeng,2008) @@ -1482,7 +1481,7 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, dhsdt_canopy(p) = dt_stem(p)*cp_stem(p)/dtime & + (t_veg(p)-tl_ini(p))*cp_leaf(p)/dtime - + t_stem(p) = t_stem(p) + dt_stem(p) else dt_stem(p) = 0._r8 diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index 56f06c47c2..7fa583c6a8 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -23,7 +23,7 @@ module FrictionVelocityMod use atm2lndType , only : atm2lnd_type use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type use CanopyStateType , only : canopystate_type - use WaterFluxBulkType , only : waterfluxbulk_type + use WaterFluxBulkType , only : waterfluxbulk_type ! ! !PUBLIC TYPES: implicit none @@ -60,7 +60,7 @@ module FrictionVelocityMod real(r8), pointer, public :: z0qg_patch (:) ! patch roughness length over ground, latent heat [m] real(r8), pointer, public :: kbm1_patch (:) ! natural logarithm of z0mg_p/z0hg_p [-] real(r8), pointer, public :: z0mg_col (:) ! col roughness length over ground, momentum [m] - real(r8), pointer, public :: z0mg_2D_col (:) ! 2-D field of input col roughness length over ground, momentum [m] + real(r8), pointer, public :: z0mg_2D_col (:) ! 2-D field of input col roughness length over ground, momentum [m] real(r8), pointer, public :: z0hg_col (:) ! col roughness length over ground, sensible heat [m] real(r8), pointer, public :: z0qg_col (:) ! col roughness length over ground, latent heat [m] ! variables to add history output from CanopyFluxesMod @@ -119,7 +119,7 @@ subroutine Init(this, bounds, NLFilename, params_ncid) call this%InitCold(bounds) call this%ReadNamelist(NLFilename) call this%ReadParams(params_ncid) - + end subroutine Init !------------------------------------------------------------------------ @@ -162,7 +162,7 @@ subroutine InitAllocate(this, bounds) allocate(this%z0qg_patch (begp:endp)) ; this%z0qg_patch (:) = nan allocate(this%kbm1_patch (begp:endp)) ; this%kbm1_patch (:) = nan allocate(this%z0mg_col (begc:endc)) ; this%z0mg_col (:) = nan - allocate(this%z0mg_2D_col (begc:endc)) ; this%z0mg_2D_col (:) = nan + allocate(this%z0mg_2D_col (begc:endc)) ; this%z0mg_2D_col (:) = nan allocate(this%z0qg_col (begc:endc)) ; this%z0qg_col (:) = nan allocate(this%z0hg_col (begc:endc)) ; this%z0hg_col (:) = nan allocate(this%rah1_patch (begp:endp)) ; this%rah1_patch (:) = nan @@ -402,12 +402,11 @@ subroutine ReadParams( this, params_ncid ) call readNcdioScalar(params_ncid, 'zsno', subname, this%zsno) ! Momentum roughness length for soil, glacier, wetland (m) call readNcdioScalar(params_ncid, 'zlnd', subname, this%zlnd) - + ! Separated roughness length for glacier if z0param_method == 'Meier2022' if (z0param_method == 'Meier2022') then call readNcdioScalar(params_ncid, 'zglc', subname, this%zglc) end if - end subroutine ReadParams @@ -528,7 +527,7 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(waterdiagnosticbulk_type) , intent(in) :: waterdiagnosticbulk_inst type(canopystate_type) , intent(in) :: canopystate_inst - type(waterfluxbulk_type) , intent(in) :: waterfluxbulk_inst + type(waterfluxbulk_type) , intent(in) :: waterfluxbulk_inst ! ! !LOCAL VARIABLES: integer :: fc, c @@ -557,15 +556,14 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & frac_veg_nosno => canopystate_inst%frac_veg_nosno_patch , & ! Input: [integer (:) ] fraction of vegetation not covered by snow (0 OR 1) [-] frac_sno => waterdiagnosticbulk_inst%frac_sno_col , & ! Input: [real(r8) (:) ] fraction of ground covered by snow (0 to 1) - snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) + snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) urbpoi => lun%urbpoi , & ! Input: [logical (:) ] true => landunit is an urban point z_0_town => lun%z_0_town , & ! Input: [real(r8) (:) ] momentum roughness length of urban landunit (m) z_d_town => lun%z_d_town , & ! Input: [real(r8) (:) ] displacement height of urban landunit (m) forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] - z0mg_2D => this%z0mg_2D_col & ! Input: [real(r8) (:) ] 2-D field of input col roughness length over ground, momentum [m] - + z0mg_2D => this%z0mg_2D_col & ! Input: [real(r8) (:) ] 2-D field of input col roughness length over ground, momentum [m] ) do fc = 1, num_nolakec @@ -592,14 +590,14 @@ subroutine SetRoughnessLengthsAndForcHeightsNonLake(this, bounds, & end if else z0mg(c) = this%zsno - end if + end if else if (lun%itype(l) == istice) then z0mg(c) = this%zglc else z0mg(c) = this%zlnd end if end select - + z0hg(c) = z0mg(c) ! initial set only z0qg(c) = z0mg(c) ! initial set only diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index 1b544a8364..fdd105ad8f 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -66,7 +66,7 @@ subroutine readParams( ncid ) call readNcdioScalar(ncid, 'a_exp', subname, params_inst%a_exp) ! Momentum roughness length for snow (m) call readNcdioScalar(ncid, 'zsno', subname, params_inst%zsno) - + if (z0param_method == 'Meier2022') then ! Momentum roughness length for ice (m) call readNcdioScalar(ncid, 'zglc', subname, params_inst%zglc) @@ -228,8 +228,8 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, lakefetch => lakestate_inst%lakefetch_col , & ! Input: [real(r8) (:) ] lake fetch from surface data (m) h2osoi_liq => waterstatebulk_inst%h2osoi_liq_col , & ! Input: [real(r8) (:,:) ] liquid water (kg/m2) - h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) - snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) + h2osoi_ice => waterstatebulk_inst%h2osoi_ice_col , & ! Input: [real(r8) (:,:) ] ice lens (kg/m2) + snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Input: [real(r8) (:) ] accumulated col snow melt for z0m calculation (m H2O) t_skin_patch => temperature_inst%t_skin_patch , & ! Output: [real(r8) (:) ] patch skin temperature (K) t_lake => temperature_inst%t_lake_col , & ! Input: [real(r8) (:,:) ] lake temperature (Kelvin) @@ -338,7 +338,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, z0hg(p) = max(z0hg(p), minz0lake) else if (snl(c) == 0) then ! frozen lake with ice select case (z0param_method) - case ('Meier2022') + case ('Meier2022') z0mg(p) = params_inst%zglc @@ -361,7 +361,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, end if select case (z0param_method) - case ('Meier2022') + case ('Meier2022') z0hg(p) = meier_param3 * nu_param / ust_lake(c) ! For initial guess assume tstar = 0 case ('ZengWang2007') z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ust_lake(c) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -424,7 +424,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, g = patch%gridcell(p) dhsdt_canopy(p) = 0.0_r8 - + nmozsgn(p) = 0 obuold(p) = 0._r8 displa(p) = 0._r8 @@ -592,12 +592,12 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else if (snl(c) == 0) then ! in case it was above freezing and now below freezing select case (z0param_method) - case ('Meier2022') + case ('Meier2022') z0mg(p) = params_inst%zglc ! (...)**0.5 = sqrt(...) and (...)**0.25 = sqrt(sqrt(...)) ! likely more efficient to calculate as exponents z0hg(p) = meier_param3 * nu_param / ustar(p) * exp( -beta_param * ustar(p)**(0.5_r8) * (abs(tstar))**(0.25_r8)) ! Consistent with BareGroundFluxes - + case ('ZengWang2007') z0mg(p) = z0frzlake z0hg(p) = z0mg(p) / exp(params_inst%a_coef * (ustar(p) * z0mg(p) / nu_param)**params_inst%a_exp) ! Consistent with BareGroundFluxes @@ -606,7 +606,7 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, else ! Snow layers if(use_z0m_snowmelt) then if ( snomelt_accum(c) < 1.e-5_r8 )then - z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 + z0mg(p) = exp(-b1_param * rpi * 0.5_r8 + b4_param) * 1.e-3_r8 else z0mg(p) = exp(b1_param * (atan((log10(snomelt_accum(c)) + meier_param1) / meier_param2)) + b4_param) * 1.e-3_r8 end if diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 index 91689a9d28..4698e1136d 100644 --- a/src/biogeophys/SnowHydrologyMod.F90 +++ b/src/biogeophys/SnowHydrologyMod.F90 @@ -435,7 +435,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & real(r8) , intent(inout) :: frac_sno( bounds%begc: ) ! fraction of ground covered by snow (0 to 1) real(r8) , intent(inout) :: frac_sno_eff( bounds%begc: ) ! eff. fraction of ground covered by snow (0 to 1) real(r8) , intent(inout) :: snow_depth( bounds%begc: ) ! snow height (m) - real(r8) , intent(inout) :: snomelt_accum( bounds%begc: ) ! accumulated col snow melt for z0m calculation (m H2O) + real(r8) , intent(inout) :: snomelt_accum( bounds%begc: ) ! accumulated col snow melt for z0m calculation (m H2O) ! ! !LOCAL VARIABLES: integer :: fc, c @@ -491,7 +491,7 @@ subroutine BulkDiag_NewSnowDiagnostics(bounds, num_c, filter_c, & ! all snow falls on ground, no snow on h2osfc (note that qflx_snow_h2osfc is ! currently set to 0 always in CanopyHydrologyMod) newsnow(c) = qflx_snow_grnd(c) * dtime - snomelt_accum(c) = max(0._r8, snomelt_accum(c) - newsnow(c) * 1.e-3_r8) + snomelt_accum(c) = max(0._r8, snomelt_accum(c) - newsnow(c) * 1.e-3_r8) ! update int_snow int_snow(c) = max(int_snow(c),h2osno_total(c)) !h2osno_total could be larger due to frost diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index b7086f3154..a3ffd72b4e 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -1168,7 +1168,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & qflx_snofrz_lyr => waterfluxbulk_inst%qflx_snofrz_lyr_col , & ! Output: [real(r8) (:,:) ] snow freezing rate (positive definite) (col,lyr) [kg m-2 s-1] qflx_snofrz => waterfluxbulk_inst%qflx_snofrz_col , & ! Output: [real(r8) (:) ] column-integrated snow freezing rate (positive definite) [kg m-2 s-1] qflx_snomelt => waterfluxbulk_inst%qflx_snomelt_col , & ! Output: [real(r8) (:) ] snow melt (mm H2O /s) - snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Output: [real(r8) (:) ] accumulated snow melt (m) + snomelt_accum => waterdiagnosticbulk_inst%snomelt_accum_col , & ! Output: [real(r8) (:) ] accumulated snow melt (m) qflx_snomelt_lyr => waterfluxbulk_inst%qflx_snomelt_lyr_col , & ! Output: [real(r8) (:) ] snow melt in each layer (mm H2O /s) eflx_snomelt => energyflux_inst%eflx_snomelt_col , & ! Output: [real(r8) (:) ] snow melt heat flux (W/m**2) @@ -1459,7 +1459,7 @@ subroutine Phasechange_beta (bounds, num_nolakec, filter_nolakec, dhsdT, & if (imelt(c,j) == 1 .AND. j < 1) then qflx_snomelt_lyr(c,j) = max(0._r8,(wice0(c,j)-h2osoi_ice(c,j)))/dtime qflx_snomelt(c) = qflx_snomelt(c) + qflx_snomelt_lyr(c,j) - snomelt_accum(c) = snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime * 1.e-3_r8 + snomelt_accum(c) = snomelt_accum(c) + qflx_snomelt_lyr(c,j) * dtime * 1.e-3_r8 endif ! layer freezing mass flux (positive): diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 559a95b570..7af8c56bff 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -251,7 +251,6 @@ module clm_varctl character(len=64), public :: z0param_method ! ZengWang2007 or Meier2022 logical, public :: use_z0m_snowmelt = .false. ! true => use snow z0m parameterization of Brock2006 - !---------------------------------------------------------- ! FATES switches diff --git a/src/main/pftconMod.F90 b/src/main/pftconMod.F90 index b401a02d15..e5379100e0 100644 --- a/src/main/pftconMod.F90 +++ b/src/main/pftconMod.F90 @@ -368,16 +368,16 @@ subroutine InitAllocate (this) allocate( this%taul (0:mxpft,numrad) ) allocate( this%taus (0:mxpft,numrad) ) allocate( this%z0mr (0:mxpft) ) - allocate( this%z0v_Cr (0:mxpft) ) - allocate( this%z0v_Cs (0:mxpft) ) - allocate( this%z0v_c (0:mxpft) ) - allocate( this%z0v_cw (0:mxpft) ) - allocate( this%z0v_LAIoff (0:mxpft) ) - allocate( this%z0v_LAImax (0:mxpft) ) - allocate( this%displar (0:mxpft) ) - allocate( this%roota_par (0:mxpft) ) - allocate( this%rootb_par (0:mxpft) ) - allocate( this%crop (0:mxpft) ) + allocate( this%z0v_Cr (0:mxpft) ) + allocate( this%z0v_Cs (0:mxpft) ) + allocate( this%z0v_c (0:mxpft) ) + allocate( this%z0v_cw (0:mxpft) ) + allocate( this%z0v_LAIoff (0:mxpft) ) + allocate( this%z0v_LAImax (0:mxpft) ) + allocate( this%displar (0:mxpft) ) + allocate( this%roota_par (0:mxpft) ) + allocate( this%rootb_par (0:mxpft) ) + allocate( this%crop (0:mxpft) ) allocate( this%mergetoclmpft (0:mxpft) ) allocate( this%is_pft_known_to_model (0:mxpft) ) allocate( this%irrigated (0:mxpft) ) @@ -663,7 +663,7 @@ subroutine InitRead(this) this%z0v_cw = 0._r8 this%z0v_LAImax = 0._r8 this%z0v_LAIoff = 0._r8 - + case ('Meier2022') call ncd_io('z0v_Cr', this%z0v_Cr, 'read', ncid, readvar=readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=' ERROR: error in reading in pft data'//errMsg(sourcefile, __LINE__)) From f10c7fe07fa6d6123437a4049316873e3e0fb40c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 19:02:34 -0600 Subject: [PATCH 1407/2067] Adjust white space to reduce diffs from main --- src/biogeochem/CNCIsoFluxMod.F90 | 78 +++++++++++++++---------------- src/biogeochem/CNPhenologyMod.F90 | 2 +- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index 26f4cf026f..608966d213 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -1301,7 +1301,7 @@ subroutine CIsoFlux3(num_soilp, filter_soilp, & cc = patch%column(pp) do j = 1, nlevdecomp iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) = & - iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) + & + iso_cnveg_cf%m_c_to_litr_fire_col(cc,j,i_met_lit) + & ((iso_cnveg_cf%m_leafc_to_litter_fire_patch(pp) * lf_f(ivt(pp),i_met_lit) & +iso_cnveg_cf%m_leafc_storage_to_litter_fire_patch(pp) + & iso_cnveg_cf%m_leafc_xfer_to_litter_fire_patch(pp) + & @@ -1318,7 +1318,7 @@ subroutine CIsoFlux3(num_soilp, filter_soilp, & iso_cnveg_cf%m_livecrootc_xfer_to_litter_fire_patch(pp) & +iso_cnveg_cf%m_deadcrootc_storage_to_litter_fire_patch(pp) + & iso_cnveg_cf%m_deadcrootc_xfer_to_litter_fire_patch(pp))* croot_prof(pp,j)) * patch%wtcol(pp) - + ! Here metabolic litter is treated differently than other ! types of litter, so it remains outside this litter loop, ! in the line above @@ -1350,8 +1350,8 @@ subroutine CNCIsoLitterToColumn (num_soilp, filter_soilp, & !DML ! !ARGUMENTS: - integer , intent(in) :: num_soilp ! number of soil columns in filter - integer , intent(in) :: filter_soilp(:) ! filter for soil columns + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! filter for soil patches type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! @@ -1384,11 +1384,11 @@ subroutine CNCIsoLitterToColumn (num_soilp, filter_soilp, & do i = i_litr_min, i_litr_max phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - ! leaf litter carbon fluxes - leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & - ! fine root litter carbon fluxes - frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + phenology_c_to_litr_c(c,j,i) + & + ! leaf litter carbon fluxes + leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + & + ! fine root litter carbon fluxes + frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do !DML @@ -1396,8 +1396,8 @@ subroutine CNCIsoLitterToColumn (num_soilp, filter_soilp, & ! stem litter carbon fluxes do i = i_litr_min, i_litr_max phenology_c_to_litr_c(c,j,i) = & - phenology_c_to_litr_c(c,j,i) + & - livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + phenology_c_to_litr_c(c,j,i) + & + livestemc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) end do if (.not. use_grainproduct) then @@ -1420,7 +1420,7 @@ subroutine CNCIsoLitterToColumn (num_soilp, filter_soilp, & end do end do end if -!DML + !DML end do end do @@ -1437,8 +1437,8 @@ subroutine CNCIsoGapPftToColumn (num_soilp, filter_soilp, & ! to the column level and assign them to the three litter pools (+ cwd pool) ! ! !ARGUMENTS: - integer , intent(in) :: num_soilp ! number of soil columns in filter - integer , intent(in) :: filter_soilp(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! soil patch filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! @@ -1491,12 +1491,12 @@ subroutine CNCIsoGapPftToColumn (num_soilp, filter_soilp, & do i = i_litr_min, i_litr_max ! leaf gap mortality carbon fluxes gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) + gap_mortality_c_to_litr_c(c,j,i) + & + m_leafc_to_litter(p) * lf_f(ivt(p),i) * wtcol(p) * leaf_prof(p,j) ! fine root gap mortality carbon fluxes gap_mortality_c_to_litr_c(c,j,i) = & - gap_mortality_c_to_litr_c(c,j,i) + & - m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) + gap_mortality_c_to_litr_c(c,j,i) + & + m_frootc_to_litter(p) * fr_f(ivt(p),i) * wtcol(p) * froot_prof(p,j) end do ! wood gap mortality carbon fluxes @@ -1513,23 +1513,23 @@ subroutine CNCIsoGapPftToColumn (num_soilp, filter_soilp, & ! of litter, so it gets this additional line after the ! most recent loop over all litter types gap_mortality_c_to_litr_c(c,j,i_met_lit) = & - gap_mortality_c_to_litr_c(c,j,i_met_lit) + & - ! storage gap mortality carbon fluxes - m_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - m_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - ! transfer gap mortality carbon fluxes - m_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & - m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & - m_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & - m_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & - m_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + gap_mortality_c_to_litr_c(c,j,i_met_lit) + & + ! storage gap mortality carbon fluxes + m_leafc_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_storage_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + m_livestemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_deadstemc_storage_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_livecrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_deadcrootc_storage_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_gresp_storage_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + ! transfer gap mortality carbon fluxes + m_leafc_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) + & + m_frootc_xfer_to_litter(p) * wtcol(p) * froot_prof(p,j) + & + m_livestemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_deadstemc_xfer_to_litter(p) * wtcol(p) * stem_prof(p,j) + & + m_livecrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_deadcrootc_xfer_to_litter(p) * wtcol(p) * croot_prof(p,j) + & + m_gresp_xfer_to_litter(p) * wtcol(p) * leaf_prof(p,j) end do end do @@ -1548,8 +1548,8 @@ subroutine CNCIsoHarvestPftToColumn (num_soilp, filter_soilp, & ! to the column level and assign them to the litter, cwd, and wood product pools ! ! !ARGUMENTS: - integer , intent(in) :: num_soilp ! number of soil columns in filter - integer , intent(in) :: filter_soilp(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! soil patch filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! @@ -1664,8 +1664,8 @@ subroutine CNCIsoGrossUnrepPftToColumn (num_soilp, filter_soilp, & ! to the column level and assign them to the litter, cwd, and wood product pools ! ! !ARGUMENTS: - integer , intent(in) :: num_soilp ! number of soil columns in filter - integer , intent(in) :: filter_soilp(:) ! soil column filter + integer , intent(in) :: num_soilp ! number of soil patches in filter + integer , intent(in) :: filter_soilp(:) ! soil patch filter type(soilbiogeochem_state_type) , intent(in) :: soilbiogeochem_state_inst type(cnveg_carbonflux_type) , intent(inout) :: iso_cnveg_carbonflux_inst ! diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 4bc2bd058d..070dc0eb0f 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3800,7 +3800,7 @@ subroutine CNLitterToColumn (bounds, num_bgc_vegp, filter_bgc_vegp, & end do do_vegp end do do_nlev - end associate + end associate end subroutine CNLitterToColumn From aa5be428d843d16600414b2e69fbf70ba7b7a011 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 21 Aug 2023 19:04:45 -0600 Subject: [PATCH 1408/2067] Correction for failing cheyenne test to pass --- src/biogeochem/CNDriverMod.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNDriverMod.F90 b/src/biogeochem/CNDriverMod.F90 index 90b22a7bfd..4ab1e1f51e 100644 --- a/src/biogeochem/CNDriverMod.F90 +++ b/src/biogeochem/CNDriverMod.F90 @@ -761,7 +761,7 @@ subroutine CNDriverNoLeaching(bounds, ! the matrix multiply in VegMatrix and SoilMatrix. !-------------------------------------------------------------------------- - ! Set harvest mortality routine + ! Set harvest mortality routine if (get_do_harvest()) then call CNHarvest(num_bgc_vegp, filter_bgc_vegp, & soilbiogeochem_state_inst, cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, & @@ -838,6 +838,9 @@ subroutine CNDriverNoLeaching(bounds, c14_cnveg_carbonflux_inst, c14_cnveg_carbonstate_inst, c14_soilbiogeochem_carbonstate_inst) end if + call NStateUpdate2g(num_bgc_soilc, filter_bgc_soilc, num_bgc_vegp, filter_bgc_vegp, & + cnveg_nitrogenflux_inst, cnveg_nitrogenstate_inst, soilbiogeochem_nitrogenstate_inst) + call t_stopf('CNUpdate2') end if if_bgc_vegp1 From b18572dfbd8f0b515cf4fe398cf3474dc914ad2b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 22 Aug 2023 09:54:31 -0600 Subject: [PATCH 1409/2067] Added a comment and TODO. --- src/soilbiogeochem/TillageMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 35f487db80..dcaac9c518 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -312,7 +312,8 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) call endrun('ERROR Active crop patch weights does not sum to 1') end if - ! Adjust tillage_mults to consider fraction of this layer that's within tillage depth + ! Adjust tillage_mults to consider fraction of this layer that's within tillage depth. + ! TODO: Unit-test this layer_thickness = zisoi(j) - layer_top fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth - layer_top) / layer_thickness)) tillage_mults = tillage_mults * fraction_tilled & From 7af6bf6feb02e2028c2ac3b3bc49d434cc96e8e3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 22 Aug 2023 11:04:45 -0600 Subject: [PATCH 1410/2067] Max till depth now 26cm (match text of Graham et al., 2021). --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- src/soilbiogeochem/TillageMod.F90 | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index d0b29f48f4..457b3bcbeb 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2729,6 +2729,6 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 off .false. -0.32d00 +0.26d00 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 91e74e347e..d769ac6c41 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2896,7 +2896,7 @@ Toggle to use original tillage logic, with bug for seasons crossing into a new c + group="tillage_inparm" valid_values="" value="0.26d00"> Maximum depth to till soil (m). diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index dcaac9c518..7ffe40a08e 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -59,7 +59,7 @@ subroutine readParams_namelist() ! Default values tillage_mode = 'off' use_original_tillage = .false. - max_tillage_depth = 0.32_r8 + max_tillage_depth = 0.26_r8 ! Read tillage namelist if (masterproc) then From ebda44436069331c524423b2ced0d04f07adaa34 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 22 Aug 2023 11:12:06 -0600 Subject: [PATCH 1411/2067] Renamed var & added text re: original tillage settings. --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- bld/namelist_files/namelist_definition_ctsm.xml | 6 +++--- src/soilbiogeochem/TillageMod.F90 | 16 ++++++++-------- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 457b3bcbeb..a7480dd243 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2728,7 +2728,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 off -.false. +.false. 0.26d00 diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index d769ac6c41..5422a39cc2 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2890,14 +2890,14 @@ Mapping method from excess ice input stream data to the model resolution Whether to till crop soil, and if so, with what intensity. - -Toggle to use original tillage logic, with bug for seasons crossing into a new calendar year +Toggle to use original (Graham et al. 2021) tillage logic, with bug for seasons crossing into a new calendar year -Maximum depth to till soil (m). +Maximum depth to till soil (m). Default 0.26; original (Graham et al., 2021) value was unintentionally 0.32. diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 7ffe40a08e..248d2bd4cb 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -27,7 +27,7 @@ module TillageMod integer, parameter :: tillage_off = 0 integer, parameter :: tillage_low = 1 integer, parameter :: tillage_high = 2 - logical :: use_original_tillage ! Use get_tillage_multipliers_orig? + logical :: use_original_tillage_phases ! Use buggy tillage phase determination? real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, ntill_stages_max) integer, parameter :: ntill_stages_max = 3 ! How many different tillage phases are there? (Not including all-1 phases.) real(r8) :: max_tillage_depth ! Maximum depth to till (m) @@ -53,13 +53,13 @@ subroutine readParams_namelist() namelist /tillage_inparm/ & tillage_mode, & - use_original_tillage, & + use_original_tillage_phases, & max_tillage_depth ! Default values tillage_mode = 'off' - use_original_tillage = .false. - max_tillage_depth = 0.26_r8 + use_original_tillage_phases = .false. + max_tillage_depth = 0.26_r8 ! Graham et al. (2021) unintentionally used 0.32 ! Read tillage namelist if (masterproc) then @@ -76,14 +76,14 @@ subroutine readParams_namelist() close(nu_nml) endif call shr_mpi_bcast(tillage_mode, mpicom) - call shr_mpi_bcast(use_original_tillage , mpicom) + call shr_mpi_bcast(use_original_tillage_phases , mpicom) call shr_mpi_bcast(max_tillage_depth, mpicom) if (masterproc) then write(iulog,*) ' ' write(iulog,*) 'tillage settings:' write(iulog,*) ' tillage_mode = ',tillage_mode - write(iulog,*) ' use_original_tillage = ',use_original_tillage + write(iulog,*) ' use_original_tillage_phases = ',use_original_tillage_phases write(iulog,*) ' max_tillage_depth = ',max_tillage_depth endif @@ -185,7 +185,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) ! would affect growing seasons that crossed over into a new calendar year. ! Also avoids day=1 in last timestep of year by using DaysPastPlanting(), which ! uses get_prev_calday() instead of get_curr_calday(). - ! Previous behavior can be requested with namelist variable use_original_tillage. + ! Previous behavior can be requested with namelist variable use_original_tillage_phases. ! ! Original code had two versions depending on cell's GDP, but this seems to ! have been only an initial effort that was (a) never published and (b) not @@ -213,7 +213,7 @@ subroutine get_tillage_multipliers(tillage_mults, idop) phase = 0 - if (use_original_tillage) then + if (use_original_tillage_phases) then day = get_curr_calday() if (day >= idop .and. day < idop+15) then ! based on Point Chisel Tandem Disk multipliers phase = 1 From 50b4e49de67e68fe68ee5fb1ccab6421833716ab Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 22 Aug 2023 11:11:30 -0700 Subject: [PATCH 1412/2067] change logic to fates nearest neighbor call If fates is not using dispersal mode, which is set via the parameter file, do not run the nearest neighbor algorithm to avoid performace impact. --- src/utils/clmfates_interfaceMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 06cbc63bb5..f395f52104 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -538,7 +538,7 @@ subroutine CLMFatesGlobals2() ! Initialize the array of nearest neighbors for fates-driven grid cell communications ! This must be called after surfrd_get_data and decompInit_lnd - if (use_fates) then + if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then call DetermineGridCellNeighbors(lneighbors) end if From 8518eca438aac3f8d9aefacbd709de99e9352493 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 22 Aug 2023 11:17:03 -0700 Subject: [PATCH 1413/2067] update the fates external tag --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index c540fe8b0c..da15c3d3d9 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.67.1_api.27.0.0 +tag = sci.1.68.0_api.27.1.0 required = True [externals_description] From aef75cb931c998bc4fe7ddda92a5032c2e51df84 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Tue, 22 Aug 2023 13:15:10 -0600 Subject: [PATCH 1414/2067] Update ChangeLog --- doc/ChangeLog | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 64 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 7a00a0e80d..059ae5bd74 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,67 @@ =============================================================== +Tag name: ctsm5.1.dev136 +Originator(s): jedwards (Jim Edwards), sacks (Bill Sacks) +Date: Tue Aug 22 13:10:28 MDT 2023 +One-line Summary: Change order of history fields to improve performance on derecho + +Purpose and description of changes +---------------------------------- + +Instead of just ordering history fields alphabetically, order them first +by the name of their level dimension (with fields without a level +dimension appearing first), then alphabetically within a given level +dimension. This changed ordering gives a significant performance +improvement especially noticeable on lustre file systems such as on +derecho. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Notes of particular relevance for users +--------------------------------------- +Caveats for users (e.g., need to interpolate initial conditions): +- History fields will now appear in a different order from tools like + ncdump, etc. + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + In addition to expected fails, the test + FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1.5x5_amazon.I2000Clm50SpRs.cheyenne_intel + also failed as in https://github.com/ESCOMP/CTSM/issues/2111 + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/2114 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev135 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) Date: Mon Aug 21 15:06:35 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 67f357480b..0991ee8605 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev136 multiple 08/22/2023 Change order of history fields to improve performance on derecho ctsm5.1.dev135 slevis 08/21/2023 Rename hist fields to track them down more easily ctsm5.1.dev134 rgknox 08/16/2023 Migration of FATES to share normal soil BGC call sequence and functionality ctsm5.1.dev133 glemieux 08/09/2023 FATES API update to facilitate fates refactor From 8dabfaf7c2c6be8133bfff8ebb966e77893c3cf8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 22 Aug 2023 15:28:07 -0600 Subject: [PATCH 1415/2067] Check that python unload/conda load works. --- cime_config/SystemTests/systemtest_utils.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 6ce61d9424..1c8668c7de 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -5,7 +5,7 @@ import os, subprocess -def cmds_to_setup_conda(caseroot): +def cmds_to_setup_conda(caseroot, test_conda_retry=True): # Add specific commands needed on different machines to get conda available # Use semicolon here since it's OK to fail # @@ -19,7 +19,12 @@ def cmds_to_setup_conda(caseroot): subprocess.run("which conda", shell=True, check=True) except subprocess.CalledProcessError: # Remove python and add conda to environment for cheyennne - conda_setup_commands += " module unload python; module load conda;" + unload_python_load_conda = "module unload python; module load conda;" + # Make sure that adding this actually loads conda + if test_conda_retry: + subprocess.run(unload_python_load_conda + "which conda", shell=True, check=True) + # Save + conda_setup_commands += " " + unload_python_load_conda return conda_setup_commands From 4db3ecd4c629f3da427d75a477579ed51641e0ad Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 22 Aug 2023 15:42:22 -0600 Subject: [PATCH 1416/2067] If conda run -n method fails, try conda activate. --- cime_config/SystemTests/systemtest_utils.py | 51 ++++++++++++++------- 1 file changed, 34 insertions(+), 17 deletions(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 1c8668c7de..90a5abcf95 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -29,16 +29,22 @@ def cmds_to_setup_conda(caseroot, test_conda_retry=True): return conda_setup_commands -def run_python_script(caseroot, this_conda_env, command, tool_path): - +def cmds_to_run_via_conda(caseroot, conda_run_call, command, test_conda_retry=True): # Run in the specified conda environment - conda_setup_commands = cmds_to_setup_conda(caseroot) - conda_setup_commands += f" conda run -n {this_conda_env}" + conda_setup_commands = cmds_to_setup_conda(caseroot, test_conda_retry) + conda_setup_commands += " " + conda_run_call # Finish with Python script call command = conda_setup_commands + " " + command print(f"command: {command}") + return command + + +def run_python_script(caseroot, this_conda_env, command_in, tool_path): + + command = cmds_to_run_via_conda(caseroot, f"conda run -n {this_conda_env}", command_in) + # Run with logfile tool_name = os.path.split(tool_path)[-1] try: @@ -47,19 +53,30 @@ def run_python_script(caseroot, this_conda_env, command, tool_path): command, shell=True, check=True, text=True, stdout=f, stderr=subprocess.STDOUT ) except subprocess.CalledProcessError as error: - print("ERROR while getting the conda environment and/or ") - print(f"running the {tool_name} tool: ") - print(f"(1) If your {this_conda_env} environment is out of date or you ") - print(f"have not created the {this_conda_env} environment, yet, you may ") - print("get past this error by running ./py_env_create ") - print("in your ctsm directory and trying this test again. ") - print("(2) If conda is not available, install and load conda, ") - print("run ./py_env_create, and then try this test again. ") - print("(3) If (1) and (2) are not the issue, then you may be ") - print(f"getting an error within {tool_name} itself. ") - print("Default error message: ") - print(error.output) - raise + # First, retry with the original method + command = cmds_to_run_via_conda(caseroot, f"conda activate {this_conda_env} && ", command_in, test_conda_retry=False) + try: + with open(tool_name + ".log2", "w") as f: + subprocess.run( + command, shell=True, check=True, text=True, stdout=f, stderr=subprocess.STDOUT + ) + except subprocess.CalledProcessError as error: + print("ERROR while getting the conda environment and/or ") + print(f"running the {tool_name} tool: ") + print(f"(1) If your {this_conda_env} environment is out of date or you ") + print(f"have not created the {this_conda_env} environment, yet, you may ") + print("get past this error by running ./py_env_create ") + print("in your ctsm directory and trying this test again. ") + print("(2) If conda is not available, install and load conda, ") + print("run ./py_env_create, and then try this test again. ") + print("(3) If (1) and (2) are not the issue, then you may be ") + print(f"getting an error within {tool_name} itself. ") + print("Default error message: ") + print(error.output) + raise + except: + print(f"ERROR trying to run {tool_name}.") + raise except: print(f"ERROR trying to run {tool_name}.") raise From 553023eb91cf6328e1b1490900234793e69beee7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 23 Aug 2023 10:41:02 -0600 Subject: [PATCH 1417/2067] update seed dispersal per refactor This corresponds to a fates-side refactor that moves the seed_out and seed_in variables from the bc_in/out types to site. Corrections to the column type names are also made --- src/utils/clmfates_interfaceMod.F90 | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index f395f52104..5654e41661 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1401,12 +1401,12 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & do s = 1,this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) - g = col_pp%gridcell(c) + g = col%gridcell(c) ! Accumulate seeds from sites to the gridcell local outgoing buffer if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) & .and. IsItDispersalTime()) then - this%fates_seed%outgoing_local(g,:) = this%fates_seed%outgoing_local(g,:) + this%fates(nc)%bc_out(s)%seed_out(:) + this%fates_seed%outgoing_local(g,:) = this%fates_seed%outgoing_local(g,:) + this%fates(nc)%sites(s)%seed_out(:) end if ! Other modules may have AI's we only flush values @@ -2718,16 +2718,16 @@ subroutine wrap_seed_dispersal(this,bounds_clump) ! Add fates check for seed dispersal mode do s = 1, this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) - g = col_pp%gridcell(c) + g = col%gridcell(c) ! Check that it is the beginning of the current dispersal time step if (IsItDispersalTime()) then ! assuming equal area for all sites, seed_id_global in [kg/grid/day], seed_in in [kg/site/day] - this%fates(nc)%bc_in(s)%seed_in(:) = this%fates_seed%incoming_global(g,:) - this%fates(nc)%bc_out(s)%seed_out(:) = 0._r8 ! reset seed_out + this%fates(nc)%sites(s)%seed_in(:) = this%fates_seed%incoming_global(g,:) + this%fates(nc)%sites(s)%seed_out(:) = 0._r8 ! reset seed_out else ! if it is not the dispersing time, pass in zero - this%fates(nc)%bc_in(s)%seed_in(:) = 0._r8 + this%fates(nc)%sites(s)%seed_in(:) = 0._r8 end if end do @@ -2758,8 +2758,8 @@ subroutine wrap_seed_dispersal_reset(this,bounds_clump) do s = 1, this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) - g = col_pp%gridcell(c) - this%fates(nc)%bc_in(s)%seed_in(:) = 0 ! reset + g = col%gridcell(c) + this%fates(nc)%sites(s)%seed_in(:) = 0 ! reset end do end subroutine wrap_seed_dispersal_reset From d12b27647623e4ec6d755fcaf5285d9f87de3caf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 23 Aug 2023 12:37:01 -0600 Subject: [PATCH 1418/2067] Update history fields .rst files. --- .../history_fields_fates.rst | 1015 +++++++++-------- .../history_fields_nofates.rst | 606 +++++----- 2 files changed, 830 insertions(+), 791 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index 5514e76e1e..ea7c23d22a 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -15,35 +15,8 @@ CTSM History Fields =================================== ================ ============================================================================================== ================================================================= ======= A5TMIN - 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB - actual N immobilization gN/m^2/s T -ACTUAL_IMMOB_NH4 levdcmp immobilization of NH4 gN/m^3/s F -ACTUAL_IMMOB_NO3 levdcmp immobilization of NO3 gN/m^3/s F -ACTUAL_IMMOB_vr levdcmp actual N immobilization gN/m^3/s F -ACT_SOMC - ACT_SOM C gC/m^2 T -ACT_SOMC_1m - ACT_SOM C to 1 meter gC/m^2 F -ACT_SOMC_TNDNCY_VERT_TRA levdcmp active soil organic C tendency due to vertical transport gC/m^3/s F -ACT_SOMC_TO_PAS_SOMC - decomp. of active soil organic C to passive soil organic C gC/m^2/s F -ACT_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of active soil organic C to passive soil organic C gC/m^3/s F -ACT_SOMC_TO_SLO_SOMC - decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F -ACT_SOMC_TO_SLO_SOMC_vr levdcmp decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F -ACT_SOMC_vr levsoi ACT_SOM C (vertically resolved) gC/m^3 T -ACT_SOMN - ACT_SOM N gN/m^2 T -ACT_SOMN_1m - ACT_SOM N to 1 meter gN/m^2 F -ACT_SOMN_TNDNCY_VERT_TRA levdcmp active soil organic N tendency due to vertical transport gN/m^3/s F -ACT_SOMN_TO_PAS_SOMN - decomp. of active soil organic N to passive soil organic N gN/m^2 F -ACT_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of active soil organic N to passive soil organic N gN/m^3 F -ACT_SOMN_TO_SLO_SOMN - decomp. of active soil organic N to slow soil organic ma N gN/m^2 F -ACT_SOMN_TO_SLO_SOMN_vr levdcmp decomp. of active soil organic N to slow soil organic ma N gN/m^3 F -ACT_SOMN_vr levdcmp ACT_SOM N (vertically resolved) gN/m^3 T -ACT_SOM_HR_S2 - Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S2_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F -ACT_SOM_HR_S3 - Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S3_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F AGLB - Aboveground leaf biomass kg/m^2 F AGSB - Aboveground stem biomass kg/m^2 F -ALBD numrad surface albedo (direct) proportion F -ALBGRD numrad ground albedo (direct) proportion F -ALBGRI numrad ground albedo (indirect) proportion F -ALBI numrad surface albedo (indirect) proportion F ALT - current active layer thickness m F ALTMAX - maximum annual active layer thickness m F ALTMAX_LASTYEAR - maximum prior year active layer thickness m F @@ -53,20 +26,6 @@ AnnET - Annual ET BCDEP - total BC deposition (dry+wet) from atmosphere kg/m^2/s T BTRAN - transpiration beta factor unitless T BTRANMN - daily minimum of transpiration beta factor unitless T -CEL_LITC - CEL_LIT C gC/m^2 T -CEL_LITC_1m - CEL_LIT C to 1 meter gC/m^2 F -CEL_LITC_TNDNCY_VERT_TRA levdcmp cellulosic litter C tendency due to vertical transport gC/m^3/s F -CEL_LITC_TO_ACT_SOMC - decomp. of cellulosic litter C to active soil organic C gC/m^2/s F -CEL_LITC_TO_ACT_SOMC_vr levdcmp decomp. of cellulosic litter C to active soil organic C gC/m^3/s F -CEL_LITC_vr levsoi CEL_LIT C (vertically resolved) gC/m^3 T -CEL_LITN - CEL_LIT N gN/m^2 T -CEL_LITN_1m - CEL_LIT N to 1 meter gN/m^2 F -CEL_LITN_TNDNCY_VERT_TRA levdcmp cellulosic litter N tendency due to vertical transport gN/m^3/s F -CEL_LITN_TO_ACT_SOMN - decomp. of cellulosic litter N to active soil organic N gN/m^2 F -CEL_LITN_TO_ACT_SOMN_vr levdcmp decomp. of cellulosic litter N to active soil organic N gN/m^3 F -CEL_LITN_vr levdcmp CEL_LIT N (vertically resolved) gN/m^3 T -CEL_LIT_HR - Het. Resp. from cellulosic litter gC/m^2/s F -CEL_LIT_HR_vr levdcmp Het. Resp. from cellulosic litter gC/m^3/s F CH4PROD - Gridcell total production of CH4 gC/m2/s T CH4_EBUL_TOTAL_SAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F CH4_EBUL_TOTAL_UNSAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F @@ -78,11 +37,11 @@ CH4_SURF_EBUL_SAT - ebullition surface CH4 flux CH4_SURF_EBUL_UNSAT - ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T COL_CTRUNC - column-level sink for C truncation gC/m^2 F COL_NTRUNC - column-level sink for N truncation gN/m^2 F -CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F -CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F -CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T -CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T COSZEN - cosine of solar zenith angle none F +CROPPROD1C - 1-yr crop product (grain+biofuel) C gC/m^2 T +CROPPROD1C_LOSS - loss from 1-yr crop product pool gC/m^2/s T +CROPPROD1N - 1-yr crop product (grain+biofuel) N gN/m^2 T +CROPPROD1N_LOSS - loss from 1-yr crop product pool gN/m^2/s T CWDC_HR - cwd C heterotrophic respiration gC/m^2/s T DENIT - total rate of denitrification gN/m^2/s T DGNETDT - derivative of net ground heat flux wrt soil temp W/m^2/K F @@ -94,6 +53,14 @@ DPVLTRB4 - turbulent deposition veloci DSL - dry surface layer thickness mm T DSTDEP - total dust deposition (dry+wet) from atmosphere kg/m^2/s T DSTFLXT - total surface dust emission kg/m2/s T +DWT_CROPPROD1C_GAIN - landcover change-driven addition to 1-year crop product pool gC/m^2/s T +DWT_CROPPROD1N_GAIN - landcover change-driven addition to 1-year crop product pool gN/m^2/s T +DWT_PROD100C_GAIN - landcover change-driven addition to 100-yr wood product pool gC/m^2/s F +DWT_PROD100N_GAIN - landcover change-driven addition to 100-yr wood product pool gN/m^2/s F +DWT_PROD10C_GAIN - landcover change-driven addition to 10-yr wood product pool gC/m^2/s F +DWT_PROD10N_GAIN - landcover change-driven addition to 10-yr wood product pool gN/m^2/s F +DWT_WOODPRODC_GAIN - landcover change-driven addition to wood product pools gC/m^2/s T +DWT_WOODPRODN_GAIN - landcover change-driven addition to wood product pools gN/m^2/s T DYN_COL_ADJUSTMENTS_CH4 - Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_C - Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_N - Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F @@ -115,11 +82,6 @@ ERRSEB - surface energy conservation ERRSOI - soil/lake energy conservation error W/m^2 T ERRSOL - solar radiation conservation error W/m^2 T ESAI - exposed one-sided stem area index m^2/m^2 T -FATES_ABOVEGROUND_MORT_SZPF fates_levscpf Aboveground flux of carbon from AGB to necromass due to mortality kg m-2 s-1 F -FATES_ABOVEGROUND_PROD_SZPF fates_levscpf Aboveground carbon productivity kg m-2 s-1 F -FATES_AGSAPMAINTAR_SZPF fates_levscpf above-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F -FATES_AGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to above-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_AGSTRUCT_ALLOC_SZPF fates_levscpf allocation to above-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F FATES_AR - autotrophic respiration gC/m^2/s T FATES_AREA_PLANTS - area occupied by all plants per m2 land area m2 m-2 T FATES_AREA_TREES - area occupied by woody plants per m2 land area m2 m-2 T @@ -127,56 +89,20 @@ FATES_AR_CANOPY - autotrophic respiration of FATES_AR_UNDERSTORY - autotrophic respiration of understory plants gC/m^2/s T FATES_AUTORESP - autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T FATES_AUTORESP_CANOPY - autotrophic respiration of canopy plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_AUTORESP_CANOPY_SZPF fates_levscpf autotrophic respiration of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F FATES_AUTORESP_SECONDARY - autotrophic respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_AUTORESP_SZPF fates_levscpf total autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F FATES_AUTORESP_USTORY - autotrophic respiration of understory plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_AUTORESP_USTORY_SZPF fates_levscpf autotrophic respiration of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_BASALAREA_SZ fates_levscls basal area by size class m2 m-2 T -FATES_BASALAREA_SZPF fates_levscpf basal area by pft/size m2 m-2 F FATES_BA_WEIGHTED_HEIGHT - basal area-weighted mean height of woody plants m T -FATES_BGSAPMAINTAR_SZPF fates_levscpf below-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F -FATES_BGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to below-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_BGSTRUCT_ALLOC_SZPF fates_levscpf allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F FATES_BURNFRAC - burned area fraction per second s-1 T -FATES_BURNFRAC_AP fates_levage spitfire fraction area burnt (per second) by patch age s-1 T -FATES_C13DISC_SZPF fates_levscpf C13 discrimination by pft/size per mil F -FATES_CANOPYAREA_AP fates_levage canopy area by age bin per m2 land area m2 m-2 T -FATES_CANOPYAREA_HT fates_levheight canopy area height distribution m2 m-2 T -FATES_CANOPYCROWNAREA_PF fates_levpft total PFT-level canopy-layer crown area per m2 land area m2 m-2 T FATES_CANOPY_SPREAD - scaling factor (0-1) between tree basal area and canopy area T FATES_CANOPY_VEGC - biomass of canopy plants in kg carbon per m2 land area kg m-2 T FATES_CA_WEIGHTED_HEIGHT - crown area-weighted mean height of canopy plants m T FATES_CBALANCE_ERROR - total carbon error in kg carbon per second kg s-1 T FATES_COLD_STATUS - site-level cold status, 0=not cold-dec, 1=too cold for leaves, 2=not too cold T FATES_CROOTMAINTAR - live coarse root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_CROOTMAINTAR_CANOPY_SZ fates_levscls live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F -FATES_CROOTMAINTAR_USTORY_SZ fates_levscls live coarse root maintenance autotrophic respiration for understory plants in kg carbon per m2 kg m-2 s-1 F FATES_CROOT_ALLOC - allocation to coarse roots in kg carbon per m2 per second kg m-2 s-1 T -FATES_CROWNAREA_CANOPY_SZ fates_levscls total crown area of canopy plants by size class m2 m-2 F -FATES_CROWNAREA_CL fates_levcan total crown area in each canopy layer m2 m-2 T -FATES_CROWNAREA_CLLL fates_levcnlf total crown area that is occupied by leaves in each canopy and leaf layer m2 m-2 F -FATES_CROWNAREA_PF fates_levpft total PFT-level crown area per m2 land area m2 m-2 T -FATES_CROWNAREA_USTORY_SZ fates_levscls total crown area of understory plants by size class m2 m-2 F -FATES_CWD_ABOVEGROUND_DC fates_levcwdsc debris class-level aboveground coarse woody debris stocks in kg carbon per m2 kg m-2 F -FATES_CWD_ABOVEGROUND_IN_DC fates_levcwdsc debris class-level aboveground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F -FATES_CWD_ABOVEGROUND_OUT_DC fates_levcwdsc debris class-level aboveground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F -FATES_CWD_BELOWGROUND_DC fates_levcwdsc debris class-level belowground coarse woody debris stocks in kg carbon per m2 kg m-2 F -FATES_CWD_BELOWGROUND_IN_DC fates_levcwdsc debris class-level belowground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F -FATES_CWD_BELOWGROUND_OUT_DC fates_levcwdsc debris class-level belowground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F FATES_DAYSINCE_COLDLEAFOFF - site-level days elapsed since cold leaf drop days T FATES_DAYSINCE_COLDLEAFON - site-level days elapsed since cold leaf flush days T -FATES_DAYSINCE_DROUGHTLEAFOFF_PF fates_levpft PFT-level days elapsed since drought leaf drop days T -FATES_DAYSINCE_DROUGHTLEAFON_PF fates_levpft PFT-level days elapsed since drought leaf flush days T -FATES_DDBH_CANOPY_SZ fates_levscls diameter growth increment by size of canopy plants m m-2 yr-1 T -FATES_DDBH_CANOPY_SZAP fates_levscag growth rate of canopy plants in meters DBH per m2 per year in canopy in each size x age class m m-2 yr-1 F -FATES_DDBH_CANOPY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F -FATES_DDBH_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F -FATES_DDBH_USTORY_SZ fates_levscls diameter growth increment by size of understory plants m m-2 yr-1 T -FATES_DDBH_USTORY_SZAP fates_levscag growth rate of understory plants in meters DBH per m2 per year in each size x age class m m-2 yr-1 F -FATES_DDBH_USTORY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F FATES_DEMOTION_CARBONFLUX - demotion-associated biomass carbon flux from canopy to understory in kg carbon per m2 per seco kg m-2 s-1 T -FATES_DEMOTION_RATE_SZ fates_levscls demotion rate from canopy to understory by size class in number of plants per m2 per year m-2 yr-1 F FATES_DISTURBANCE_RATE_FIRE - disturbance rate from fire m2 m-2 yr-1 T FATES_DISTURBANCE_RATE_LOGGING - disturbance rate from logging m2 m-2 yr-1 T FATES_DISTURBANCE_RATE_P2P - disturbance rate from primary to primary lands m2 m-2 yr-1 T @@ -184,71 +110,27 @@ FATES_DISTURBANCE_RATE_P2S - disturbance rate from prima FATES_DISTURBANCE_RATE_POTENTIAL - potential (i.e., including unresolved) disturbance rate m2 m-2 yr-1 T FATES_DISTURBANCE_RATE_S2S - disturbance rate from secondary to secondary lands m2 m-2 yr-1 T FATES_DISTURBANCE_RATE_TREEFALL - disturbance rate from treefall m2 m-2 yr-1 T -FATES_DROUGHT_STATUS_PF fates_levpft PFT-level drought status, <2 too dry for leaves, >=2 not too dry T FATES_EFFECT_WSPEED - effective wind speed for fire spread in meters per second m s-1 T -FATES_ELONG_FACTOR_PF fates_levpft PFT-level mean elongation factor (partial flushing/abscission) 1 T -FATES_ERROR_EL fates_levelem total mass-balance error in kg per second by element kg s-1 T FATES_EXCESS_RESP - respiration of un-allocatable carbon gain kg m-2 s-1 T -FATES_FABD_SHA_CLLL fates_levcnlf shade fraction of direct light absorbed by each canopy and leaf layer 1 F -FATES_FABD_SHA_CLLLPF fates_levcnlfpf shade fraction of direct light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABD_SHA_TOPLF_CL fates_levcan shade fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABD_SUN_CLLL fates_levcnlf sun fraction of direct light absorbed by each canopy and leaf layer 1 F -FATES_FABD_SUN_CLLLPF fates_levcnlfpf sun fraction of direct light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABD_SUN_TOPLF_CL fates_levcan sun fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABI_SHA_CLLL fates_levcnlf shade fraction of indirect light absorbed by each canopy and leaf layer 1 F -FATES_FABI_SHA_CLLLPF fates_levcnlfpf shade fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABI_SHA_TOPLF_CL fates_levcan shade fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F -FATES_FABI_SUN_CLLL fates_levcnlf sun fraction of indirect light absorbed by each canopy and leaf layer 1 F -FATES_FABI_SUN_CLLLPF fates_levcnlfpf sun fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F -FATES_FABI_SUN_TOPLF_CL fates_levcan sun fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F FATES_FDI - Fire Danger Index (probability that an ignition will lead to a fire) 1 T FATES_FIRE_CLOSS - carbon loss to atmosphere from fire in kg carbon per m2 per second kg m-2 s-1 T -FATES_FIRE_FLUX_EL fates_levelem loss to atmosphere from fire by element in kg element per m2 per s kg m-2 s-1 T FATES_FIRE_INTENSITY - spitfire surface fireline intensity in J per m per second J m-1 s-1 T FATES_FIRE_INTENSITY_BURNFRAC - product of surface fire intensity and burned area fraction -- divide by FATES_BURNFRAC to get J m-1 s-1 T -FATES_FIRE_INTENSITY_BURNFRAC_AP fates_levage product of fire intensity and burned fraction, resolved by patch age (so divide by FATES_BURNF J m-1 s-1 T FATES_FRACTION - total gridcell fraction which FATES is running over m2 m-2 T -FATES_FRAGMENTATION_SCALER_SL levsoi factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T FATES_FROOTC - total biomass in live plant fine roots in kg carbon per m2 kg m-2 T -FATES_FROOTCTURN_CANOPY_SZ fates_levscls fine root turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_FROOTCTURN_USTORY_SZ fates_levscls fine root turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F -FATES_FROOTC_SL levsoi Total carbon in live plant fine-roots over depth kg m-3 T -FATES_FROOTC_SZPF fates_levscpf fine-root carbon mass by size-class x pft in kg carbon per m2 kg m-2 F FATES_FROOTMAINTAR - fine root maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_FROOTMAINTAR_CANOPY_SZ fates_levscls live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F -FATES_FROOTMAINTAR_SZPF fates_levscpf fine root maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_FROOTMAINTAR_USTORY_SZ fates_levscls fine root maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F FATES_FROOT_ALLOC - allocation to fine roots in kg carbon per m2 per second kg m-2 s-1 T -FATES_FROOT_ALLOC_CANOPY_SZ fates_levscls allocation to fine root C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_FROOT_ALLOC_SZPF fates_levscpf allocation to fine roots by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_FROOT_ALLOC_USTORY_SZ fates_levscls allocation to fine roots for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F FATES_FUELCONSUMED - total fuel consumed in kg carbon per m2 land area kg m-2 T FATES_FUEL_AMOUNT - total ground fuel related to FATES_ROS (omits 1000hr fuels) in kg C per m2 land area kg m-2 T -FATES_FUEL_AMOUNT_AP fates_levage spitfire ground fuel (kg carbon per m2) related to FATES_ROS (omits 1000hr fuels) within each kg m-2 T -FATES_FUEL_AMOUNT_APFC fates_levagefuel spitfire fuel quantity in each age x fuel class in kg carbon per m2 land area kg m-2 F -FATES_FUEL_AMOUNT_FC fates_levfuel spitfire fuel-class level fuel amount in kg carbon per m2 land area kg m-2 T FATES_FUEL_BULKD - fuel bulk density in kg per m3 kg m-3 T -FATES_FUEL_BURNT_BURNFRAC_FC fates_levfuel product of fraction (0-1) of fuel burnt and burnt fraction (divide by FATES_BURNFRAC to get bu 1 T FATES_FUEL_EFF_MOIST - spitfire fuel moisture (volumetric) m3 m-3 T FATES_FUEL_MEF - fuel moisture of extinction (volumetric) m3 m-3 T -FATES_FUEL_MOISTURE_FC fates_levfuel spitfire fuel class-level fuel moisture (volumetric) m3 m-3 T FATES_FUEL_SAV - spitfire fuel surface area to volume ratio m-1 T FATES_GDD - site-level growing degree days degree_Celsius T FATES_GPP - gross primary production in kg carbon per m2 per second kg m-2 s-1 T -FATES_GPP_AP fates_levage gross primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F FATES_GPP_CANOPY - gross primary production of canopy plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_GPP_CANOPY_SZPF fates_levscpf gross primary production of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_GPP_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second kg m-2 s-1 T FATES_GPP_SECONDARY - gross primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_GPP_SE_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T -FATES_GPP_SZPF fates_levscpf gross primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F FATES_GPP_USTORY - gross primary production of understory plants in kg carbon per m2 per second kg m-2 s-1 T -FATES_GPP_USTORY_SZPF fates_levscpf gross primary production of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_GROWAR_CANOPY_SZ fates_levscls growth autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_GROWAR_SZPF fates_levscpf growth autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_GROWAR_USTORY_SZ fates_levscls growth autotrophic respiration of understory plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_GROWTHFLUX_FUSION_SZPF fates_levscpf flux of individuals into a given size class bin via fusion m-2 yr-1 F -FATES_GROWTHFLUX_SZPF fates_levscpf flux of individuals into a given size class bin via growth and recruitment m-2 yr-1 F FATES_GROWTH_RESP - growth respiration in kg carbon per m2 per second kg m-2 s-1 T FATES_GROWTH_RESP_SECONDARY - growth respiration in kg carbon per m2 per second, secondary patches kg m-2 s-1 T FATES_HARVEST_CARBON_FLUX - harvest carbon flux in kg carbon per m2 per year kg m-2 yr-1 T @@ -257,232 +139,59 @@ FATES_HARVEST_DEBT_SEC - Accumulated carbon failed t FATES_HET_RESP - heterotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T FATES_IGNITIONS - number of successful fire ignitions per m2 land area per second m-2 s-1 T FATES_LAI - leaf area index per m2 land area m2 m-2 T -FATES_LAISHA_TOP_CL fates_levcan LAI in the shade by the top leaf layer of each canopy layer m2 m-2 F -FATES_LAISHA_Z_CLLL fates_levcnlf LAI in the shade by each canopy and leaf layer m2 m-2 F -FATES_LAISHA_Z_CLLLPF fates_levcnlfpf LAI in the shade by each canopy, leaf, and PFT m2 m-2 F -FATES_LAISUN_TOP_CL fates_levcan LAI in the sun by the top leaf layer of each canopy layer m2 m-2 F -FATES_LAISUN_Z_CLLL fates_levcnlf LAI in the sun by each canopy and leaf layer m2 m-2 F -FATES_LAISUN_Z_CLLLPF fates_levcnlfpf LAI in the sun by each canopy, leaf, and PFT m2 m-2 F -FATES_LAI_AP fates_levage leaf area index by age bin per m2 land area m2 m-2 T -FATES_LAI_CANOPY_SZ fates_levscls leaf area index (LAI) of canopy plants by size class m2 m-2 T -FATES_LAI_CANOPY_SZPF fates_levscpf Leaf area index (LAI) of canopy plants by pft/size m2 m-2 F FATES_LAI_SECONDARY - leaf area index per m2 land area, secondary patches m2 m-2 T -FATES_LAI_USTORY_SZ fates_levscls leaf area index (LAI) of understory plants by size class m2 m-2 T -FATES_LAI_USTORY_SZPF fates_levscpf Leaf area index (LAI) of understory plants by pft/size m2 m-2 F FATES_LBLAYER_COND - mean leaf boundary layer conductance mol m-2 s-1 T -FATES_LBLAYER_COND_AP fates_levage mean leaf boundary layer conductance - by patch age mol m-2 s-1 F -FATES_LEAFAREA_HT fates_levheight leaf area height distribution m2 m-2 T FATES_LEAFC - total biomass in live plant leaves in kg carbon per m2 kg m-2 T -FATES_LEAFCTURN_CANOPY_SZ fates_levscls leaf turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAFCTURN_USTORY_SZ fates_levscls leaf turnover (non-mortal) for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAFC_CANOPY_SZPF fates_levscpf biomass in leaves of canopy plants by pft/size in kg carbon per m2 kg m-2 F -FATES_LEAFC_PF fates_levpft total PFT-level leaf biomass in kg carbon per m2 land area kg m-2 T -FATES_LEAFC_SZPF fates_levscpf leaf carbon mass by size-class x pft in kg carbon per m2 kg m-2 F -FATES_LEAFC_USTORY_SZPF fates_levscpf biomass in leaves of understory plants by pft/size in kg carbon per m2 kg m-2 F FATES_LEAFMAINTAR - leaf maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T FATES_LEAF_ALLOC - allocation to leaves in kg carbon per m2 per second kg m-2 s-1 T -FATES_LEAF_ALLOC_CANOPY_SZ fates_levscls allocation to leaves for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAF_ALLOC_SZPF fates_levscpf allocation to leaves by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_LEAF_ALLOC_USTORY_SZ fates_levscls allocation to leaves for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_LITTER_AG_CWD_EL fates_levelem mass of aboveground litter in coarse woody debris (trunks/branches/twigs) by element kg m-2 T -FATES_LITTER_AG_FINE_EL fates_levelem mass of aboveground litter in fines (leaves, nonviable seed) by element kg m-2 T -FATES_LITTER_BG_CWD_EL fates_levelem mass of belowground litter in coarse woody debris (coarse roots) by element kg m-2 T -FATES_LITTER_BG_FINE_EL fates_levelem mass of belowground litter in fines (fineroots) by element kg m-2 T -FATES_LITTER_CWD_ELDC fates_levelcwd total mass of litter in coarse woody debris by element and coarse woody debris size kg m-2 T FATES_LITTER_IN - litter flux in kg carbon per m2 per second kg m-2 s-1 T -FATES_LITTER_IN_EL fates_levelem litter flux in in kg element per m2 per second kg m-2 s-1 T FATES_LITTER_OUT - litter flux out in kg carbon (exudation, fragmentation, seed decay) kg m-2 s-1 T -FATES_LITTER_OUT_EL fates_levelem litter flux out (exudation, fragmentation and seed decay) in kg element kg m-2 s-1 T FATES_LSTEMMAINTAR - live stem maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_LSTEMMAINTAR_CANOPY_SZ fates_levscls live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1 F -FATES_LSTEMMAINTAR_USTORY_SZ fates_levscls live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F -FATES_M3_MORTALITY_CANOPY_SZ fates_levscls C starvation mortality of canopy plants by size N/ha/yr F -FATES_M3_MORTALITY_CANOPY_SZPF fates_levscpf C starvation mortality of canopy plants by pft/size N/ha/yr F -FATES_M3_MORTALITY_USTORY_SZ fates_levscls C starvation mortality of understory plants by size N/ha/yr F -FATES_M3_MORTALITY_USTORY_SZPF fates_levscpf C starvation mortality of understory plants by pft/size N/ha/yr F -FATES_MAINTAR_CANOPY_SZ fates_levscls maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_MAINTAR_SZPF fates_levscpf maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_MAINTAR_USTORY_SZ fates_levscls maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1 F FATES_MAINT_RESP - maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T FATES_MAINT_RESP_SECONDARY - maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T FATES_MAINT_RESP_UNREDUCED - diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 F -FATES_MEANLIQVOL_DROUGHTPHEN_PF fates_levpft PFT-level mean liquid water volume for drought phenolgy m3 m-3 T -FATES_MEANSMP_DROUGHTPHEN_PF fates_levpft PFT-level mean soil matric potential for drought phenology Pa T -FATES_MORTALITY_AGESCEN_AC fates_levcacls age senescence mortality by cohort age in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_AGESCEN_ACPF fates_levcapf age senescence mortality by pft/cohort age in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_AGESCEN_SE_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_AGESCEN_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_AGESCEN_SZPF fates_levscpf age senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_BACKGROUND_SE_SZ fates_levscls background mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_BACKGROUND_SZ fates_levscls background mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_BACKGROUND_SZPF fates_levscpf background mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CAMBIALBURN_SZPF fates_levscpf fire mortality from cambial burn by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CANOPY_SE_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2, secondary patches m-2 yr-1 T -FATES_MORTALITY_CANOPY_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2 m-2 yr-1 T -FATES_MORTALITY_CANOPY_SZAP fates_levscag mortality rate of canopy plants in number of plants per m2 per year in each size x age class m-2 yr-1 F -FATES_MORTALITY_CANOPY_SZPF fates_levscpf total mortality of canopy plants by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_MORTALITY_CFLUX_CANOPY - flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1 T -FATES_MORTALITY_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from mortality kg m-2 s-1 T FATES_MORTALITY_CFLUX_USTORY - flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1 T -FATES_MORTALITY_CROWNSCORCH_SZPF fates_levscpf fire mortality from crown scorch by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_CSTARV_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality kg m-2 s-1 T -FATES_MORTALITY_CSTARV_SE_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_CSTARV_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_CSTARV_SZPF fates_levscpf carbon starvation mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_FIRE_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from fire mortality kg m-2 s-1 T -FATES_MORTALITY_FIRE_SZ fates_levscls fire mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_FIRE_SZPF fates_levscpf fire mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_FREEZING_SE_SZ fates_levscls freezing mortality by size in number of plants per m2 per event, secondary patches m-2 event-1 T -FATES_MORTALITY_FREEZING_SZ fates_levscls freezing mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_FREEZING_SZPF fates_levscpf freezing mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_HYDRAULIC_SE_SZ fates_levscls hydraulic mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T -FATES_MORTALITY_HYDRAULIC_SZ fates_levscls hydraulic mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_HYDRAULIC_SZPF fates_levscpf hydraulic mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_HYDRO_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality kg m-2 s-1 T -FATES_MORTALITY_IMPACT_SZ fates_levscls impact mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_IMPACT_SZPF fates_levscpf impact mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_LOGGING_SE_SZ fates_levscls logging mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T -FATES_MORTALITY_LOGGING_SZ fates_levscls logging mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_LOGGING_SZPF fates_levscpf logging mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_PF fates_levpft PFT-level mortality rate in number of individuals per m2 land area per year m-2 yr-1 T -FATES_MORTALITY_SENESCENCE_SE_SZ fates_levscls senescence mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T -FATES_MORTALITY_SENESCENCE_SZ fates_levscls senescence mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_SENESCENCE_SZPF fates_levscpf senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_TERMINATION_SZ fates_levscls termination mortality by size in number of plants per m2 per year m-2 yr-1 T -FATES_MORTALITY_TERMINATION_SZPF fates_levscpf termination mortality by pft/size in number pf plants per m2 per year m-2 yr-1 F -FATES_MORTALITY_USTORY_SZ fates_levscls total mortality of understory trees by size class in individuals per m2 per year m-2 yr-1 T -FATES_MORTALITY_USTORY_SZAP fates_levscag mortality rate of understory plants in number of plants per m2 per year in each size x age cla m-2 yr-1 F -FATES_MORTALITY_USTORY_SZPF fates_levscpf total mortality of understory plants by pft/size in number of plants per m2 per year m-2 yr-1 F FATES_NCHILLDAYS - site-level number of chill days days T -FATES_NCL_AP fates_levage number of canopy levels by age bin F FATES_NCOHORTS - total number of cohorts per site T FATES_NCOHORTS_SECONDARY - total number of cohorts per site T FATES_NCOLDDAYS - site-level number of cold days days T FATES_NEP - net ecosystem production in kg carbon per m2 per second kg m-2 s-1 T FATES_NESTEROV_INDEX - nesterov fire danger index T -FATES_NET_C_UPTAKE_CLLL fates_levcnlf net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1 F FATES_NONSTRUCTC - non-structural biomass (sapwood + leaf + fineroot) in kg carbon per m2 kg m-2 T FATES_NPATCHES - total number of patches per site T FATES_NPATCHES_SECONDARY - total number of patches per site T -FATES_NPATCH_AP fates_levage number of patches by age bin F -FATES_NPLANT_AC fates_levcacls number of plants per m2 by cohort age class m-2 T -FATES_NPLANT_ACPF fates_levcapf stem number density by pft and age class m-2 F -FATES_NPLANT_CANOPY_SZ fates_levscls number of canopy plants per m2 by size class m-2 T -FATES_NPLANT_CANOPY_SZAP fates_levscag number of plants per m2 in canopy in each size x age class m-2 F -FATES_NPLANT_CANOPY_SZPF fates_levscpf number of canopy plants by size/pft per m2 m-2 F -FATES_NPLANT_PF fates_levpft total PFT-level number of individuals per m2 land area m-2 T -FATES_NPLANT_SEC_PF fates_levpft total PFT-level number of individuals per m2 land area, secondary patches m-2 T -FATES_NPLANT_SZ fates_levscls number of plants per m2 by size class m-2 T -FATES_NPLANT_SZAP fates_levscag number of plants per m2 in each size x age class m-2 F -FATES_NPLANT_SZAPPF fates_levscagpf number of plants per m2 in each size x age x pft class m-2 F -FATES_NPLANT_SZPF fates_levscpf stem number density by pft/size m-2 F -FATES_NPLANT_USTORY_SZ fates_levscls number of understory plants per m2 by size class m-2 T -FATES_NPLANT_USTORY_SZAP fates_levscag number of plants per m2 in understory in each size x age class m-2 F -FATES_NPLANT_USTORY_SZPF fates_levscpf density of understory plants by pft/size in number of plants per m2 m-2 F FATES_NPP - net primary production in kg carbon per m2 per second kg m-2 s-1 T -FATES_NPP_AP fates_levage net primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_APPF fates_levagepft NPP per PFT in each age bin in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_CANOPY_SZ fates_levscls NPP of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second kg m-2 yr-1 T FATES_NPP_SECONDARY - net primary production in kg carbon per m2 per second, secondary patches kg m-2 s-1 T -FATES_NPP_SE_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 yr-1 T -FATES_NPP_SZPF fates_levscpf total net primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_NPP_USTORY_SZ fates_levscls NPP of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_PARPROF_DIF_CLLL fates_levcnlf radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F -FATES_PARPROF_DIF_CLLLPF fates_levcnlfpf radiative profile of diffuse PAR through each canopy, leaf, and PFT W m-2 F -FATES_PARPROF_DIR_CLLL fates_levcnlf radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F -FATES_PARPROF_DIR_CLLLPF fates_levcnlfpf radiative profile of direct PAR through each canopy, leaf, and PFT W m-2 F -FATES_PARSHA_Z_CL fates_levcan PAR absorbed in the shade by top leaf layer in each canopy layer W m-2 F -FATES_PARSHA_Z_CLLL fates_levcnlf PAR absorbed in the shade by each canopy and leaf layer W m-2 F -FATES_PARSHA_Z_CLLLPF fates_levcnlfpf PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F -FATES_PARSUN_Z_CL fates_levcan PAR absorbed in the sun by top leaf layer in each canopy layer W m-2 F -FATES_PARSUN_Z_CLLL fates_levcnlf PAR absorbed in the sun by each canopy and leaf layer W m-2 F -FATES_PARSUN_Z_CLLLPF fates_levcnlfpf PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F -FATES_PATCHAREA_AP fates_levage patch area by age bin per m2 land area m2 m-2 T FATES_PRIMARY_PATCHFUSION_ERR - error in total primary lands associated with patch fusion m2 m-2 yr-1 T FATES_PROMOTION_CARBONFLUX - promotion-associated biomass carbon flux from understory to canopy in kg carbon per m2 per sec kg m-2 s-1 T -FATES_PROMOTION_RATE_SZ fates_levscls promotion rate from understory to canopy by size class m-2 yr-1 F FATES_RAD_ERROR - radiation error in FATES RTM W m-2 T -FATES_RDARK_CANOPY_SZ fates_levscls dark respiration for canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_RDARK_SZPF fates_levscpf dark portion of maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F -FATES_RDARK_USTORY_SZ fates_levscls dark respiration for understory plants in kg carbon per m2 per second by size kg m-2 s-1 F -FATES_RECRUITMENT_PF fates_levpft PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T FATES_REPROC - total biomass in live plant reproductive tissues in kg carbon per m2 kg m-2 T -FATES_REPROC_SZPF fates_levscpf reproductive carbon mass (on plant) by size-class x pft in kg carbon per m2 kg m-2 F FATES_ROS - fire rate of spread in meters per second m s-1 T -FATES_SAI_CANOPY_SZ fates_levscls stem area index (SAI) of canopy plants by size class m2 m-2 F -FATES_SAI_USTORY_SZ fates_levscls stem area index (SAI) of understory plants by size class m2 m-2 F FATES_SAPWOODC - total biomass in live plant sapwood in kg carbon per m2 kg m-2 T -FATES_SAPWOODCTURN_CANOPY_SZ fates_levscls sapwood turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SAPWOODCTURN_USTORY_SZ fates_levscls sapwood C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F -FATES_SAPWOODC_SZPF fates_levscpf sapwood carbon mass by size-class x pft in kg carbon per m2 kg m-2 F -FATES_SAPWOOD_ALLOC_CANOPY_SZ fates_levscls allocation to sapwood C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SAPWOOD_ALLOC_USTORY_SZ fates_levscls allocation to sapwood C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SCORCH_HEIGHT_APPF fates_levagepft SPITFIRE flame Scorch Height (calculated per PFT in each patch age bin) m F -FATES_SECONDAREA_ANTHRODIST_AP fates_levage secondary forest patch area age distribution since anthropgenic disturbance m2 m-2 F -FATES_SECONDAREA_DIST_AP fates_levage secondary forest patch area age distribution since any kind of disturbance m2 m-2 F FATES_SECONDARY_FOREST_FRACTION - secondary forest fraction m2 m-2 T FATES_SECONDARY_FOREST_VEGC - biomass on secondary lands in kg carbon per m2 land area (mult by FATES_SECONDARY_FOREST_FRACT kg m-2 T +FATES_SEEDLING_POOL - total seedling (ie germinated seeds) mass of all PFTs in kg carbon per m2 land area kg m-2 T FATES_SEEDS_IN - seed production rate in kg carbon per m2 second kg m-2 s-1 T -FATES_SEEDS_IN_EXTERN_EL fates_levelem external seed influx rate in kg element per m2 per second kg m-2 s-1 T -FATES_SEEDS_IN_LOCAL_EL fates_levelem within-site, element-level seed production rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEEDS_IN_LOCAL - local seed production rate in kg carbon per m2 second kg m-2 s-1 T FATES_SEED_ALLOC - allocation to seeds in kg carbon per m2 per second kg m-2 s-1 T -FATES_SEED_ALLOC_CANOPY_SZ fates_levscls allocation to reproductive C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SEED_ALLOC_SZPF fates_levscpf allocation to seeds by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_SEED_ALLOC_USTORY_SZ fates_levscls allocation to reproductive C for understory plants by size class in kg carbon per m2 per secon kg m-2 s-1 F FATES_SEED_BANK - total seed mass of all PFTs in kg carbon per m2 land area kg m-2 T -FATES_SEED_BANK_EL fates_levelem element-level total seed mass of all PFTs in kg element per m2 kg m-2 T -FATES_SEED_DECAY_EL fates_levelem seed mass decay (germinated and un-germinated) in kg element per m2 per second kg m-2 s-1 T -FATES_SEED_GERM_EL fates_levelem element-level total germinated seed mass of all PFTs in kg element per m2 kg m-2 T -FATES_SEED_PROD_CANOPY_SZ fates_levscls seed production of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_SEED_PROD_USTORY_SZ fates_levscls seed production of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F FATES_STEM_ALLOC - allocation to stem in kg carbon per m2 per second kg m-2 s-1 T FATES_STOMATAL_COND - mean stomatal conductance mol m-2 s-1 T -FATES_STOMATAL_COND_AP fates_levage mean stomatal conductance - by patch age mol m-2 s-1 F FATES_STOREC - total biomass in live plant storage in kg carbon per m2 land area kg m-2 T -FATES_STORECTURN_CANOPY_SZ fates_levscls storage turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STORECTURN_USTORY_SZ fates_levscls storage C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F -FATES_STOREC_CANOPY_SZPF fates_levscpf biomass in storage pools of canopy plants by pft/size in kg carbon per m2 kg m-2 F -FATES_STOREC_PF fates_levpft total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T -FATES_STOREC_SZPF fates_levscpf storage carbon mass by size-class x pft in kg carbon per m2 kg m-2 F FATES_STOREC_TF - Storage C fraction of target kg kg-1 T -FATES_STOREC_TF_CANOPY_SZPF fates_levscpf Storage C fraction of target by size x pft, in the canopy kg kg-1 F -FATES_STOREC_TF_USTORY_SZPF fates_levscpf Storage C fraction of target by size x pft, in the understory kg kg-1 F -FATES_STOREC_USTORY_SZPF fates_levscpf biomass in storage pools of understory plants by pft/size in kg carbon per m2 kg m-2 F FATES_STORE_ALLOC - allocation to storage tissues in kg carbon per m2 per second kg m-2 s-1 T -FATES_STORE_ALLOC_CANOPY_SZ fates_levscls allocation to storage C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STORE_ALLOC_SZPF fates_levscpf allocation to storage C by pft/size in kg carbon per m2 per second kg m-2 s-1 F -FATES_STORE_ALLOC_USTORY_SZ fates_levscls allocation to storage C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F FATES_STRUCTC - structural biomass in kg carbon per m2 land area kg m-2 T -FATES_STRUCTCTURN_CANOPY_SZ fates_levscls structural C turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per sec kg m-2 s-1 F -FATES_STRUCTCTURN_USTORY_SZ fates_levscls structural C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per kg m-2 s-1 F -FATES_STRUCT_ALLOC_CANOPY_SZ fates_levscls allocation to structural C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F -FATES_STRUCT_ALLOC_USTORY_SZ fates_levscls allocation to structural C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F FATES_TGROWTH - fates long-term running mean vegetation temperature by site degree_Celsius F FATES_TLONGTERM - fates 30-year running mean vegetation temperature by site degree_Celsius F FATES_TRIMMING - degree to which canopy expansion is limited by leaf economics (0-1) 1 T -FATES_TRIMMING_CANOPY_SZ fates_levscls trimming term of canopy plants weighted by plant density, by size class m-2 F -FATES_TRIMMING_USTORY_SZ fates_levscls trimming term of understory plants weighted by plant density, by size class m-2 F FATES_TVEG - fates instantaneous mean vegetation temperature by site degree_Celsius T FATES_TVEG24 - fates 24-hr running mean vegetation temperature by site degree_Celsius T +FATES_UNGERM_SEED_BANK - ungerminated seed mass of all PFTs in kg carbon per m2 land area kg m-2 T FATES_USTORY_VEGC - biomass of understory plants in kg carbon per m2 land area kg m-2 T FATES_VEGC - total biomass in live plants in kg carbon per m2 land area kg m-2 T FATES_VEGC_ABOVEGROUND - aboveground biomass in kg carbon per m2 land area kg m-2 T -FATES_VEGC_ABOVEGROUND_SZ fates_levscls aboveground biomass by size class in kg carbon per m2 kg m-2 T -FATES_VEGC_ABOVEGROUND_SZPF fates_levscpf aboveground biomass by pft/size in kg carbon per m2 kg m-2 F -FATES_VEGC_AP fates_levage total biomass within a given patch age bin in kg carbon per m2 land area kg m-2 F -FATES_VEGC_APPF fates_levagepft biomass per PFT in each age bin in kg carbon per m2 kg m-2 F -FATES_VEGC_PF fates_levpft total PFT-level biomass in kg of carbon per land area kg m-2 T -FATES_VEGC_SE_PF fates_levpft total PFT-level biomass in kg of carbon per land area, secondary patches kg m-2 T -FATES_VEGC_SZ fates_levscls total biomass by size class in kg carbon per m2 kg m-2 F -FATES_VEGC_SZPF fates_levscpf total vegetation biomass in live plants by size-class x pft in kg carbon per m2 kg m-2 F FATES_WOOD_PRODUCT - total wood product from logging in kg carbon per m2 land area kg m-2 T -FATES_YESTCANLEV_CANOPY_SZ fates_levscls yesterdays canopy level for canopy plants by size class in number of plants per m2 m-2 F -FATES_YESTCANLEV_USTORY_SZ fates_levscls yesterdays canopy level for understory plants by size class in number of plants per m2 m-2 F -FATES_ZSTAR_AP fates_levage product of zstar and patch area by age bin (divide by FATES_PATCHAREA_AP to get mean zstar) m F -FATES_c_to_litr_cel_c levdcmp litter celluluse carbon flux from FATES to BGC gC/m^3/s T -FATES_c_to_litr_lab_c levdcmp litter labile carbon flux from FATES to BGC gC/m^3/s T -FATES_c_to_litr_lig_c levdcmp litter lignin carbon flux from FATES to BGC gC/m^3/s T FCEV - canopy evaporation W/m^2 T FCH4 - Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T FCH4TOCO2 - Gridcell oxidation of CH4 to CO2 gC/m2/s T @@ -495,7 +204,6 @@ FGR - heat flux into soil/snow in FGR12 - heat flux between soil layers 1 and 2 W/m^2 T FGR_ICE - heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F FGR_R - Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F -FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F FGR_U - Urban heat flux into soil/snow including snow melt W/m^2 F FH2OSFC - fraction of ground covered by surface water unitless T FH2OSFC_NOSNOW - fraction of ground covered by surface water (if no snow present) unitless F @@ -511,8 +219,8 @@ FIRE_R - Rural emitted infrared (lon FIRE_U - Urban emitted infrared (longwave) radiation W/m^2 F FLDS - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T FLDS_ICE - atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F -FMAX_DENIT_CARBONSUBSTRATE levdcmp FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F -FMAX_DENIT_NITRATE levdcmp FMAX_DENIT_NITRATE gN/m^3/s F +FPG - fraction of potential gpp proportion T +FPI - fraction of potential immobilization proportion T FROST_TABLE - frost table depth (natural vegetated and crop landunits only) m F FSA - absorbed solar radiation W/m^2 T FSAT - fractional area with water table at surface unitless T @@ -559,14 +267,14 @@ FSUN - sunlit fraction of canopy FSUN24 - fraction sunlit (last 24hrs) K F FSUN240 - fraction sunlit (last 240hrs) K F F_DENIT - denitrification flux gN/m^2/s T -F_DENIT_BASE levdcmp F_DENIT_BASE gN/m^3/s F -F_DENIT_vr levdcmp denitrification flux gN/m^3/s F F_N2O_DENIT - denitrification N2O flux gN/m^2/s T F_N2O_NIT - nitrification N2O flux gN/m^2/s T F_NIT - nitrification flux gN/m^2/s T -F_NIT_vr levdcmp nitrification flux gN/m^3/s F GROSS_NMIN - gross rate of N mineralization gN/m^2/s T -GROSS_NMIN_vr levdcmp gross rate of N mineralization gN/m^3/s F +GRU_PROD100C_GAIN - gross unrepresented landcover change addition to 100-yr wood product pool gC/m^2/s F +GRU_PROD100N_GAIN - gross unrepresented landcover change addition to 100-yr wood product pool gN/m^2/s F +GRU_PROD10C_GAIN - gross unrepresented landcover change addition to 10-yr wood product pool gC/m^2/s F +GRU_PROD10N_GAIN - gross unrepresented landcover change addition to 10-yr wood product pool gN/m^2/s F GSSHA - shaded leaf stomatal conductance umol H20/m2/s T GSSHALN - shaded leaf stomatal conductance at local noon umol H20/m2/s T GSSUN - sunlit leaf stomatal conductance umol H20/m2/s T @@ -576,7 +284,6 @@ H2OSFC - surface water depth H2OSNO - snow depth (liquid water) mm T H2OSNO_ICE - snow depth (liquid water, ice landunits only) mm F H2OSNO_TOP - mass of snow in top snow layer kg/m2 T -H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T HBOT - canopy bottom m F HEAT_CONTENT1 - initial gridcell total heat content J/m^2 T HEAT_CONTENT1_VEG - initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F @@ -585,9 +292,7 @@ HEAT_FROM_AC - sensible heat flux put into HIA - 2 m NWS Heat Index C T HIA_R - Rural 2 m NWS Heat Index C T HIA_U - Urban 2 m NWS Heat Index C T -HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F HR - total heterotrophic respiration gC/m^2/s T -HR_vr levsoi total vertically resolved heterotrophic respiration gC/m^3/s T HTOP - canopy top m T HUMIDEX - 2 m Humidex C T HUMIDEX_R - Rural 2 m Humidex C T @@ -598,114 +303,76 @@ ICE_MODEL_FRACTION - Ice sheet model fractional INT_SNOW - accumulated swe (natural vegetated and crop landunits only) mm F INT_SNOW_ICE - accumulated swe (ice landunits only) mm F IWUELN - local noon intrinsic water use efficiency umolCO2/molH2O T -KROOT levsoi root conductance each soil layer 1/s F -KSOIL levsoi soil conductance in each soil layer 1/s F -K_ACT_SOM levdcmp active soil organic potential loss coefficient 1/s F -K_CEL_LIT levdcmp cellulosic litter potential loss coefficient 1/s F -K_LIG_LIT levdcmp lignin litter potential loss coefficient 1/s F -K_MET_LIT levdcmp metabolic litter potential loss coefficient 1/s F -K_NITR levdcmp K_NITR 1/s F -K_NITR_H2O levdcmp K_NITR_H2O unitless F -K_NITR_PH levdcmp K_NITR_PH unitless F -K_NITR_T levdcmp K_NITR_T unitless F -K_PAS_SOM levdcmp passive soil organic potential loss coefficient 1/s F -K_SLO_SOM levdcmp slow soil organic ma potential loss coefficient 1/s F -L1_PATHFRAC_S1_vr levdcmp PATHFRAC from metabolic litter to active soil organic fraction F -L1_RESP_FRAC_S1_vr levdcmp respired from metabolic litter to active soil organic fraction F -L2_PATHFRAC_S1_vr levdcmp PATHFRAC from cellulosic litter to active soil organic fraction F -L2_RESP_FRAC_S1_vr levdcmp respired from cellulosic litter to active soil organic fraction F -L3_PATHFRAC_S2_vr levdcmp PATHFRAC from lignin litter to slow soil organic ma fraction F -L3_RESP_FRAC_S2_vr levdcmp respired from lignin litter to slow soil organic ma fraction F LAI240 - 240hr average of leaf area index m^2/m^2 F LAISHA - shaded projected leaf area index m^2/m^2 T LAISUN - sunlit projected leaf area index m^2/m^2 T -LAKEICEFRAC levlak lake layer ice mass fraction unitless F LAKEICEFRAC_SURF - surface lake layer ice mass fraction unitless T LAKEICETHICK - thickness of lake ice (including physical expansion on freezing) m T -LIG_LITC - LIG_LIT C gC/m^2 T -LIG_LITC_1m - LIG_LIT C to 1 meter gC/m^2 F -LIG_LITC_TNDNCY_VERT_TRA levdcmp lignin litter C tendency due to vertical transport gC/m^3/s F -LIG_LITC_TO_SLO_SOMC - decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F -LIG_LITC_TO_SLO_SOMC_vr levdcmp decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F -LIG_LITC_vr levsoi LIG_LIT C (vertically resolved) gC/m^3 T -LIG_LITN - LIG_LIT N gN/m^2 T -LIG_LITN_1m - LIG_LIT N to 1 meter gN/m^2 F -LIG_LITN_TNDNCY_VERT_TRA levdcmp lignin litter N tendency due to vertical transport gN/m^3/s F -LIG_LITN_TO_SLO_SOMN - decomp. of lignin litter N to slow soil organic ma N gN/m^2 F -LIG_LITN_TO_SLO_SOMN_vr levdcmp decomp. of lignin litter N to slow soil organic ma N gN/m^3 F -LIG_LITN_vr levdcmp LIG_LIT N (vertically resolved) gN/m^3 T -LIG_LIT_HR - Het. Resp. from lignin litter gC/m^2/s F -LIG_LIT_HR_vr levdcmp Het. Resp. from lignin litter gC/m^3/s F LIQCAN - intercepted liquid water mm T LIQUID_CONTENT1 - initial gridcell total liq content mm T LIQUID_CONTENT2 - post landuse change gridcell total liq content mm F LIQUID_WATER_TEMP1 - initial gridcell weighted average liquid water temperature K F LITTERC_HR - litter C heterotrophic respiration gC/m^2/s T +LIT_CEL_C - LIT_CEL C gC/m^2 T +LIT_CEL_C_1m - LIT_CEL C to 1 meter gC/m^2 F +LIT_CEL_C_TO_SOM_ACT_C - decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +LIT_CEL_HR - Het. Resp. from cellulosic litter gC/m^2/s F +LIT_CEL_N - LIT_CEL N gN/m^2 T +LIT_CEL_N_1m - LIT_CEL N to 1 meter gN/m^2 F +LIT_CEL_N_TO_SOM_ACT_N - decomp. of cellulosic litter N to active soil organic N gN/m^2 F +LIT_LIG_C - LIT_LIG C gC/m^2 T +LIT_LIG_C_1m - LIT_LIG C to 1 meter gC/m^2 F +LIT_LIG_C_TO_SOM_SLO_C - decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIT_LIG_HR - Het. Resp. from lignin litter gC/m^2/s F +LIT_LIG_N - LIT_LIG N gN/m^2 T +LIT_LIG_N_1m - LIT_LIG N to 1 meter gN/m^2 F +LIT_LIG_N_TO_SOM_SLO_N - decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIT_MET_C - LIT_MET C gC/m^2 T +LIT_MET_C_1m - LIT_MET C to 1 meter gC/m^2 F +LIT_MET_C_TO_SOM_ACT_C - decomp. of metabolic litter C to active soil organic C gC/m^2/s F +LIT_MET_HR - Het. Resp. from metabolic litter gC/m^2/s F +LIT_MET_N - LIT_MET N gN/m^2 T +LIT_MET_N_1m - LIT_MET N to 1 meter gN/m^2 F +LIT_MET_N_TO_SOM_ACT_N - decomp. of metabolic litter N to active soil organic N gN/m^2 F LNC - leaf N concentration gN leaf/m^2 T LWdown - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 F LWup - upwelling longwave radiation W/m^2 F -MET_LITC - MET_LIT C gC/m^2 T -MET_LITC_1m - MET_LIT C to 1 meter gC/m^2 F -MET_LITC_TNDNCY_VERT_TRA levdcmp metabolic litter C tendency due to vertical transport gC/m^3/s F -MET_LITC_TO_ACT_SOMC - decomp. of metabolic litter C to active soil organic C gC/m^2/s F -MET_LITC_TO_ACT_SOMC_vr levdcmp decomp. of metabolic litter C to active soil organic C gC/m^3/s F -MET_LITC_vr levsoi MET_LIT C (vertically resolved) gC/m^3 T -MET_LITN - MET_LIT N gN/m^2 T -MET_LITN_1m - MET_LIT N to 1 meter gN/m^2 F -MET_LITN_TNDNCY_VERT_TRA levdcmp metabolic litter N tendency due to vertical transport gN/m^3/s F -MET_LITN_TO_ACT_SOMN - decomp. of metabolic litter N to active soil organic N gN/m^2 F -MET_LITN_TO_ACT_SOMN_vr levdcmp decomp. of metabolic litter N to active soil organic N gN/m^3 F -MET_LITN_vr levdcmp MET_LIT N (vertically resolved) gN/m^3 T -MET_LIT_HR - Het. Resp. from metabolic litter gC/m^2/s F -MET_LIT_HR_vr levdcmp Het. Resp. from metabolic litter gC/m^3/s F MORTALITY_CROWNAREA_CANOPY - Crown area of canopy trees that died m2/ha/year T MORTALITY_CROWNAREA_UNDERSTORY - Crown aera of understory trees that died m2/ha/year T -M_ACT_SOMC_TO_LEACHING - active soil organic C leaching loss gC/m^2/s F -M_ACT_SOMN_TO_LEACHING - active soil organic N leaching loss gN/m^2/s F -M_CEL_LITC_TO_LEACHING - cellulosic litter C leaching loss gC/m^2/s F -M_CEL_LITN_TO_LEACHING - cellulosic litter N leaching loss gN/m^2/s F -M_LIG_LITC_TO_LEACHING - lignin litter C leaching loss gC/m^2/s F -M_LIG_LITN_TO_LEACHING - lignin litter N leaching loss gN/m^2/s F -M_MET_LITC_TO_LEACHING - metabolic litter C leaching loss gC/m^2/s F -M_MET_LITN_TO_LEACHING - metabolic litter N leaching loss gN/m^2/s F -M_PAS_SOMC_TO_LEACHING - passive soil organic C leaching loss gC/m^2/s F -M_PAS_SOMN_TO_LEACHING - passive soil organic N leaching loss gN/m^2/s F -M_SLO_SOMC_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F -M_SLO_SOMN_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F +M_LIT_CEL_C_TO_LEACHING - cellulosic litter C leaching loss gC/m^2/s F +M_LIT_CEL_N_TO_LEACHING - cellulosic litter N leaching loss gN/m^2/s F +M_LIT_LIG_C_TO_LEACHING - lignin litter C leaching loss gC/m^2/s F +M_LIT_LIG_N_TO_LEACHING - lignin litter N leaching loss gN/m^2/s F +M_LIT_MET_C_TO_LEACHING - metabolic litter C leaching loss gC/m^2/s F +M_LIT_MET_N_TO_LEACHING - metabolic litter N leaching loss gN/m^2/s F +M_SOM_ACT_C_TO_LEACHING - active soil organic C leaching loss gC/m^2/s F +M_SOM_ACT_N_TO_LEACHING - active soil organic N leaching loss gN/m^2/s F +M_SOM_PAS_C_TO_LEACHING - passive soil organic C leaching loss gC/m^2/s F +M_SOM_PAS_N_TO_LEACHING - passive soil organic N leaching loss gN/m^2/s F +M_SOM_SLO_C_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F +M_SOM_SLO_N_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F NDEP_TO_SMINN - atmospheric N deposition to soil mineral N gN/m^2/s T NEM - Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T NET_NMIN - net rate of N mineralization gN/m^2/s T -NET_NMIN_vr levdcmp net rate of N mineralization gN/m^3/s F NFIX_TO_SMINN - symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T NSUBSTEPS - number of adaptive timesteps in CLM timestep unitless F -O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F OBU - Monin-Obukhov length m F OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T -O_SCALAR levsoi fraction by which decomposition is reduced due to anoxia unitless T PARVEGLN - absorbed par by vegetation at local noon W/m^2 T -PAS_SOMC - PAS_SOM C gC/m^2 T -PAS_SOMC_1m - PAS_SOM C to 1 meter gC/m^2 F -PAS_SOMC_TNDNCY_VERT_TRA levdcmp passive soil organic C tendency due to vertical transport gC/m^3/s F -PAS_SOMC_TO_ACT_SOMC - decomp. of passive soil organic C to active soil organic C gC/m^2/s F -PAS_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of passive soil organic C to active soil organic C gC/m^3/s F -PAS_SOMC_vr levsoi PAS_SOM C (vertically resolved) gC/m^3 T -PAS_SOMN - PAS_SOM N gN/m^2 T -PAS_SOMN_1m - PAS_SOM N to 1 meter gN/m^2 F -PAS_SOMN_TNDNCY_VERT_TRA levdcmp passive soil organic N tendency due to vertical transport gN/m^3/s F -PAS_SOMN_TO_ACT_SOMN - decomp. of passive soil organic N to active soil organic N gN/m^2 F -PAS_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of passive soil organic N to active soil organic N gN/m^3 F -PAS_SOMN_vr levdcmp PAS_SOM N (vertically resolved) gN/m^3 T -PAS_SOM_HR - Het. Resp. from passive soil organic gC/m^2/s F -PAS_SOM_HR_vr levdcmp Het. Resp. from passive soil organic gC/m^3/s F PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T PCH4 - atmospheric partial pressure of CH4 Pa T PCO2 - atmospheric partial pressure of CO2 Pa T POTENTIAL_IMMOB - potential N immobilization gN/m^2/s T -POTENTIAL_IMMOB_vr levdcmp potential N immobilization gN/m^3/s F POT_F_DENIT - potential denitrification flux gN/m^2/s T -POT_F_DENIT_vr levdcmp potential denitrification flux gN/m^3/s F POT_F_NIT - potential nitrification flux gN/m^2/s T -POT_F_NIT_vr levdcmp potential nitrification flux gN/m^3/s F +PROD100C - 100-yr wood product C gC/m^2 F +PROD100C_LOSS - loss from 100-yr wood product pool gC/m^2/s F +PROD100N - 100-yr wood product N gN/m^2 F +PROD100N_LOSS - loss from 100-yr wood product pool gN/m^2/s F +PROD10C - 10-yr wood product C gC/m^2 F +PROD10C_LOSS - loss from 10-yr wood product pool gC/m^2/s F +PROD10N - 10-yr wood product N gN/m^2 F +PROD10N_LOSS - loss from 10-yr wood product pool gN/m^2/s F PSurf - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa F Q2M - 2m specific humidity kg/kg T QAF - canopy air humidity kg/kg F @@ -735,7 +402,6 @@ QH2OSFC - surface water runoff QH2OSFC_TO_ICE - surface water converted to ice mm/s F QHR - hydraulic redistribution mm/s T QICE - ice growth/melt mm/s T -QICE_FORC elevclas qice forcing sent to GLC mm/s F QICE_FRZ - ice growth mm/s T QICE_MELT - ice melt mm/s T QINFL - infiltration mm/s T @@ -750,7 +416,6 @@ QOVER - total surface runoff (inclu QOVER_LAG - time-lagged surface runoff for soil columns mm/s F QPHSNEG - net negative hydraulic redistribution flux mm/s F QRGWL - surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T -QROOTSINK levsoi water flux from soil to root in each soil-layer mm/s F QRUNOFF - total liquid runoff not including correction for land use change mm/s T QRUNOFF_ICE - total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T QRUNOFF_ICE_TO_COUPLER - total ice runoff sent to coupler (includes corrections for land use change) mm/s T @@ -798,71 +463,23 @@ RSSHA - shaded leaf stomatal resist RSSUN - sunlit leaf stomatal resistance s/m T Rainf - atmospheric rain, after rain/snow repartitioning based on temperature mm/s F Rnet - net radiation W/m^2 F -S1_PATHFRAC_S2_vr levdcmp PATHFRAC from active soil organic to slow soil organic ma fraction F -S1_PATHFRAC_S3_vr levdcmp PATHFRAC from active soil organic to passive soil organic fraction F -S1_RESP_FRAC_S2_vr levdcmp respired from active soil organic to slow soil organic ma fraction F -S1_RESP_FRAC_S3_vr levdcmp respired from active soil organic to passive soil organic fraction F -S2_PATHFRAC_S1_vr levdcmp PATHFRAC from slow soil organic ma to active soil organic fraction F -S2_PATHFRAC_S3_vr levdcmp PATHFRAC from slow soil organic ma to passive soil organic fraction F -S2_RESP_FRAC_S1_vr levdcmp respired from slow soil organic ma to active soil organic fraction F -S2_RESP_FRAC_S3_vr levdcmp respired from slow soil organic ma to passive soil organic fraction F -S3_PATHFRAC_S1_vr levdcmp PATHFRAC from passive soil organic to active soil organic fraction F -S3_RESP_FRAC_S1_vr levdcmp respired from passive soil organic to active soil organic fraction F SABG - solar rad absorbed by ground W/m^2 T SABG_PEN - Rural solar rad penetrating top soil or snow layer watt/m^2 T SABV - solar rad absorbed by veg W/m^2 T -SLO_SOMC - SLO_SOM C gC/m^2 T -SLO_SOMC_1m - SLO_SOM C to 1 meter gC/m^2 F -SLO_SOMC_TNDNCY_VERT_TRA levdcmp slow soil organic ma C tendency due to vertical transport gC/m^3/s F -SLO_SOMC_TO_ACT_SOMC - decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F -SLO_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F -SLO_SOMC_TO_PAS_SOMC - decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F -SLO_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F -SLO_SOMC_vr levsoi SLO_SOM C (vertically resolved) gC/m^3 T -SLO_SOMN - SLO_SOM N gN/m^2 T -SLO_SOMN_1m - SLO_SOM N to 1 meter gN/m^2 F -SLO_SOMN_TNDNCY_VERT_TRA levdcmp slow soil organic ma N tendency due to vertical transport gN/m^3/s F -SLO_SOMN_TO_ACT_SOMN - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F -SLO_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of slow soil organic ma N to active soil organic N gN/m^3 F -SLO_SOMN_TO_PAS_SOMN - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F -SLO_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F -SLO_SOMN_vr levdcmp SLO_SOM N (vertically resolved) gN/m^3 T -SLO_SOM_HR_S1 - Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S1_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F -SLO_SOM_HR_S3 - Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S3_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F SMINN - soil mineral N gN/m^2 T SMINN_TO_PLANT - plant uptake of soil mineral N gN/m^2/s T -SMINN_TO_PLANT_vr levdcmp plant uptake of soil mineral N gN/m^3/s F -SMINN_TO_S1N_L1 - mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L1_vr levdcmp mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_L2 - mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L2_vr levdcmp mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S2 - mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S3 - mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S3_vr levdcmp mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S2N_L3 - mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -SMINN_TO_S2N_L3_vr levdcmp mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -SMINN_TO_S2N_S1 - mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -SMINN_TO_S2N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -SMINN_TO_S3N_S1 - mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -SMINN_TO_S3N_S2 - mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -SMINN_vr levsoi soil mineral N gN/m^3 T +SMINN_TO_S1N_L1 - mineral N flux for decomp. of LIT_METto SOM_ACT gN/m^2 F +SMINN_TO_S1N_L2 - mineral N flux for decomp. of LIT_CELto SOM_ACT gN/m^2 F +SMINN_TO_S1N_S2 - mineral N flux for decomp. of SOM_SLOto SOM_ACT gN/m^2 F +SMINN_TO_S1N_S3 - mineral N flux for decomp. of SOM_PASto SOM_ACT gN/m^2 F +SMINN_TO_S2N_L3 - mineral N flux for decomp. of LIT_LIGto SOM_SLO gN/m^2 F +SMINN_TO_S2N_S1 - mineral N flux for decomp. of SOM_ACTto SOM_SLO gN/m^2 F +SMINN_TO_S3N_S1 - mineral N flux for decomp. of SOM_ACTto SOM_PAS gN/m^2 F +SMINN_TO_S3N_S2 - mineral N flux for decomp. of SOM_SLOto SOM_PAS gN/m^2 F SMIN_NH4 - soil mineral NH4 gN/m^2 T -SMIN_NH4_TO_PLANT levdcmp plant uptake of NH4 gN/m^3/s F -SMIN_NH4_vr levsoi soil mineral NH4 (vert. res.) gN/m^3 T SMIN_NO3 - soil mineral NO3 gN/m^2 T SMIN_NO3_LEACHED - soil NO3 pool loss to leaching gN/m^2/s T -SMIN_NO3_LEACHED_vr levdcmp soil NO3 pool loss to leaching gN/m^3/s F -SMIN_NO3_MASSDENS levdcmp SMIN_NO3_MASSDENS ugN/cm^3 soil F SMIN_NO3_RUNOFF - soil NO3 pool loss to runoff gN/m^2/s T -SMIN_NO3_RUNOFF_vr levdcmp soil NO3 pool loss to runoff gN/m^3/s F -SMIN_NO3_TO_PLANT levdcmp plant uptake of NO3 gN/m^3/s F -SMIN_NO3_vr levsoi soil mineral NO3 (vert. res.) gN/m^3 T -SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T SNOBCMCL - mass of BC in snow column kg/m2 T SNOBCMSL - mass of BC in top snow layer kg/m2 T SNOCAN - intercepted snow mm T @@ -899,40 +516,42 @@ SNOW_ICE - atmospheric snow, after rai SNOW_PERSISTENCE - Length of time of continuous snow cover (nat. veg. landunits only) seconds T SNOW_SINKS - snow sinks (liquid water) mm/s T SNOW_SOURCES - snow sources (liquid water) mm/s T -SNO_ABS levsno Absorbed solar radiation in each snow layer W/m^2 F -SNO_ABS_ICE levsno Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -SNO_BW levsno Partial density of water in the snow pack (ice + liquid) kg/m3 F -SNO_BW_ICE levsno Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -SNO_EXISTENCE levsno Fraction of averaging period for which each snow layer existed unitless F -SNO_FRZ levsno snow freezing rate in each snow layer kg/m2/s F -SNO_FRZ_ICE levsno snow freezing rate in each snow layer (ice landunits only) mm/s F -SNO_GS levsno Mean snow grain size Microns F -SNO_GS_ICE levsno Mean snow grain size (ice landunits only) Microns F -SNO_ICE levsno Snow ice content kg/m2 F -SNO_LIQH2O levsno Snow liquid water content kg/m2 F -SNO_MELT levsno snow melt rate in each snow layer mm/s F -SNO_MELT_ICE levsno snow melt rate in each snow layer (ice landunits only) mm/s F -SNO_T levsno Snow temperatures K F -SNO_TK levsno Thermal conductivity W/m-K F -SNO_TK_ICE levsno Thermal conductivity (ice landunits only) W/m-K F -SNO_T_ICE levsno Snow temperatures (ice landunits only) K F -SNO_Z levsno Snow layer thicknesses m F -SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F SNOdTdzL - top snow layer temperature gradient (land) K/m F SOIL10 - 10-day running mean of 12cm layer soil K F SOILC_HR - soil C heterotrophic respiration gC/m^2/s T -SOILC_vr levsoi SOIL C (vertically resolved) gC/m^3 T -SOILICE levsoi soil ice (natural vegetated and crop landunits only) kg/m2 T -SOILLIQ levsoi soil liquid water (natural vegetated and crop landunits only) kg/m2 T -SOILN_vr levdcmp SOIL N (vertically resolved) gN/m^3 T -SOILPSI levgrnd soil water potential in each soil layer MPa F SOILRESIS - soil resistance to evaporation s/m T SOILWATER_10CM - soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T SOMC_FIRE - C loss due to peat burning gC/m^2/s T +SOM_ACT_C - SOM_ACT C gC/m^2 T +SOM_ACT_C_1m - SOM_ACT C to 1 meter gC/m^2 F +SOM_ACT_C_TO_SOM_PAS_C - decomp. of active soil organic C to passive soil organic C gC/m^2/s F +SOM_ACT_C_TO_SOM_SLO_C - decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +SOM_ACT_HR_S2 - Het. Resp. from active soil organic gC/m^2/s F +SOM_ACT_HR_S3 - Het. Resp. from active soil organic gC/m^2/s F +SOM_ACT_N - SOM_ACT N gN/m^2 T +SOM_ACT_N_1m - SOM_ACT N to 1 meter gN/m^2 F +SOM_ACT_N_TO_SOM_PAS_N - decomp. of active soil organic N to passive soil organic N gN/m^2 F +SOM_ACT_N_TO_SOM_SLO_N - decomp. of active soil organic N to slow soil organic ma N gN/m^2 F SOM_C_LEACHED - total flux of C from SOM pools due to leaching gC/m^2/s T SOM_N_LEACHED - total flux of N from SOM pools due to leaching gN/m^2/s F +SOM_PAS_C - SOM_PAS C gC/m^2 T +SOM_PAS_C_1m - SOM_PAS C to 1 meter gC/m^2 F +SOM_PAS_C_TO_SOM_ACT_C - decomp. of passive soil organic C to active soil organic C gC/m^2/s F +SOM_PAS_HR - Het. Resp. from passive soil organic gC/m^2/s F +SOM_PAS_N - SOM_PAS N gN/m^2 T +SOM_PAS_N_1m - SOM_PAS N to 1 meter gN/m^2 F +SOM_PAS_N_TO_SOM_ACT_N - decomp. of passive soil organic N to active soil organic N gN/m^2 F +SOM_SLO_C - SOM_SLO C gC/m^2 T +SOM_SLO_C_1m - SOM_SLO C to 1 meter gC/m^2 F +SOM_SLO_C_TO_SOM_ACT_C - decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SOM_SLO_C_TO_SOM_PAS_C - decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SOM_SLO_HR_S1 - Het. Resp. from slow soil organic ma gC/m^2/s F +SOM_SLO_HR_S3 - Het. Resp. from slow soil organic ma gC/m^2/s F +SOM_SLO_N - SOM_SLO N gN/m^2 T +SOM_SLO_N_1m - SOM_SLO N to 1 meter gN/m^2 F +SOM_SLO_N_TO_SOM_ACT_N - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SOM_SLO_N_TO_SOM_PAS_N - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F SUPPLEMENT_TO_SMINN - supplemental N supply gN/m^2/s T -SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F SWBGT - 2 m Simplified Wetbulb Globe Temp C T SWBGT_R - Rural 2 m Simplified Wetbulb Globe Temp C T SWBGT_U - Urban 2 m Simplified Wetbulb Globe Temp C T @@ -956,21 +575,27 @@ TH2OSFC - surface water temperature THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T TKE1 - top lake level eddy thermal conductivity W/(mK) T TLAI - total projected leaf area index m^2/m^2 T -TLAKE levlak lake temperature K T TOPO_COL - column-level topographic height m F TOPO_COL_ICE - column-level topographic height (ice landunits only) m F -TOPO_FORC elevclas topograephic height sent to GLC m F +TOTCOLC - total column carbon, incl veg and cpool but excl product pools gC/m^2 T TOTCOLCH4 - total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T +TOTCOLN - total column-level N, excluding product pools gN/m^2 T +TOTECOSYSC - total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T +TOTECOSYSN - total ecosystem N, excluding product pools gN/m^2 T TOTLITC - total litter carbon gC/m^2 T TOTLITC_1m - total litter carbon to 1 meter depth gC/m^2 T TOTLITN - total litter N gN/m^2 T TOTLITN_1m - total litter N to 1 meter gN/m^2 T -TOTSOILICE - vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILICE - vertically summed soil ice (veg landunits only) kg/m2 T TOTSOILLIQ - vertically summed soil liquid water (veg landunits only) kg/m2 T TOTSOMC - total soil organic matter carbon gC/m^2 T TOTSOMC_1m - total soil organic matter carbon to 1 meter depth gC/m^2 T TOTSOMN - total soil organic matter N gN/m^2 T TOTSOMN_1m - total soil organic matter N to 1 meter gN/m^2 T +TOT_WOODPRODC - total wood product C gC/m^2 T +TOT_WOODPRODC_LOSS - total loss from wood product pools gC/m^2/s T +TOT_WOODPRODN - total wood product N gN/m^2 T +TOT_WOODPRODN_LOSS - total loss from wood product pools gN/m^2/s T TRAFFICFLUX - sensible heat flux from urban traffic W/m^2 F TREFMNAV - daily minimum of average 2-m temperature K T TREFMNAV_R - Rural daily minimum of average 2-m temperature K F @@ -987,16 +612,12 @@ TSA_U - Urban 2m air temperature TSHDW_INNER - shadewall inside surface temperature K F TSKIN - skin temperature K T TSL - temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T TSOI_10CM - soil temperature in top 10cm of soil K T -TSOI_ICE levgrnd soil temperature (ice landunits only) K T -TSRF_FORC elevclas surface temperature sent to GLC K F TSUNW_INNER - sunwall inside surface temperature K F TV - vegetation temperature K T TV24 - vegetation temperature (last 24hrs) K F TV240 - vegetation temperature (last 240hrs) K F TWS - total water storage mm T -T_SCALAR levsoi temperature inhibition of decomposition unitless T Tair - atmospheric air temperature (downscaled to columns in glacier regions) K F Tair_from_atm - atmospheric air temperature received from atmosphere (pre-downscaling) K F U10 - 10-m wind m/s T @@ -1019,10 +640,8 @@ WASTEHEAT - sensible heat flux from hea WBT - 2 m Stull Wet Bulb C T WBT_R - Rural 2 m Stull Wet Bulb C T WBT_U - Urban 2 m Stull Wet Bulb C T -WFPS levdcmp WFPS percent F WIND - atmospheric wind velocity magnitude m/s T WTGQ - surface tracer conductance m/s T -W_SCALAR levsoi Moisture (dryness) inhibition of decomposition unitless T Wind - atmospheric wind velocity magnitude m/s F Z0HG - roughness length over ground, sensible heat (vegetated landunits only) m F Z0MG - roughness length over ground, momentum (vegetated landunits only) m F @@ -1035,14 +654,434 @@ ZII - convective boundary height ZWT - water table depth (natural vegetated and crop landunits only) m T ZWT_CH4_UNSAT - depth of water table for methane production used in non-inundated area m T ZWT_PERCH - perched water table depth (natural vegetated and crop landunits only) m T +num_iter - number of iterations unitless F +QICE_FORC elevclas qice forcing sent to GLC mm/s F +TOPO_FORC elevclas topograephic height sent to GLC m F +TSRF_FORC elevclas surface temperature sent to GLC K F +FATES_BURNFRAC_AP fates_levage spitfire fraction area burnt (per second) by patch age s-1 T +FATES_CANOPYAREA_AP fates_levage canopy area by age bin per m2 land area m2 m-2 T +FATES_FIRE_INTENSITY_BURNFRAC_AP fates_levage product of fire intensity and burned fraction, resolved by patch age (so divide by FATES_BURNF J m-1 s-1 T +FATES_FUEL_AMOUNT_AP fates_levage spitfire ground fuel (kg carbon per m2) related to FATES_ROS (omits 1000hr fuels) within each kg m-2 T +FATES_GPP_AP fates_levage gross primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_LAI_AP fates_levage leaf area index by age bin per m2 land area m2 m-2 T +FATES_LBLAYER_COND_AP fates_levage mean leaf boundary layer conductance - by patch age mol m-2 s-1 F +FATES_NCL_AP fates_levage number of canopy levels by age bin F +FATES_NPATCH_AP fates_levage number of patches by age bin F +FATES_NPP_AP fates_levage net primary productivity by age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_PATCHAREA_AP fates_levage patch area by age bin per m2 land area m2 m-2 T +FATES_SECONDAREA_ANTHRODIST_AP fates_levage secondary forest patch area age distribution since anthropgenic disturbance m2 m-2 F +FATES_SECONDAREA_DIST_AP fates_levage secondary forest patch area age distribution since any kind of disturbance m2 m-2 F +FATES_STOMATAL_COND_AP fates_levage mean stomatal conductance - by patch age mol m-2 s-1 F +FATES_VEGC_AP fates_levage total biomass within a given patch age bin in kg carbon per m2 land area kg m-2 F +FATES_ZSTAR_AP fates_levage product of zstar and patch area by age bin (divide by FATES_PATCHAREA_AP to get mean zstar) m F +FATES_FUEL_AMOUNT_APFC fates_levagefuel spitfire fuel quantity in each age x fuel class in kg carbon per m2 land area kg m-2 F +FATES_NPP_APPF fates_levagepft NPP per PFT in each age bin in kg carbon per m2 per second kg m-2 s-1 F +FATES_SCORCH_HEIGHT_APPF fates_levagepft SPITFIRE flame Scorch Height (calculated per PFT in each patch age bin) m F +FATES_VEGC_APPF fates_levagepft biomass per PFT in each age bin in kg carbon per m2 kg m-2 F +FATES_MORTALITY_AGESCEN_AC fates_levcacls age senescence mortality by cohort age in number of plants per m2 per year m-2 yr-1 T +FATES_NPLANT_AC fates_levcacls number of plants per m2 by cohort age class m-2 T +FATES_CROWNAREA_CL fates_levcan total crown area in each canopy layer m2 m-2 T +FATES_FABD_SHA_TOPLF_CL fates_levcan shade fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABD_SUN_TOPLF_CL fates_levcan sun fraction of direct light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABI_SHA_TOPLF_CL fates_levcan shade fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F +FATES_FABI_SUN_TOPLF_CL fates_levcan sun fraction of indirect light absorbed by the top leaf layer of each canopy layer 1 F +FATES_LAISHA_TOP_CL fates_levcan LAI in the shade by the top leaf layer of each canopy layer m2 m-2 F +FATES_LAISUN_TOP_CL fates_levcan LAI in the sun by the top leaf layer of each canopy layer m2 m-2 F +FATES_PARSHA_Z_CL fates_levcan PAR absorbed in the shade by top leaf layer in each canopy layer W m-2 F +FATES_PARSUN_Z_CL fates_levcan PAR absorbed in the sun by top leaf layer in each canopy layer W m-2 F +FATES_MORTALITY_AGESCEN_ACPF fates_levcapf age senescence mortality by pft/cohort age in number of plants per m2 per year m-2 yr-1 F +FATES_NPLANT_ACPF fates_levcapf stem number density by pft and age class m-2 F +FATES_CROWNAREA_CLLL fates_levcnlf total crown area that is occupied by leaves in each canopy and leaf layer m2 m-2 F +FATES_FABD_SHA_CLLL fates_levcnlf shade fraction of direct light absorbed by each canopy and leaf layer 1 F +FATES_FABD_SUN_CLLL fates_levcnlf sun fraction of direct light absorbed by each canopy and leaf layer 1 F +FATES_FABI_SHA_CLLL fates_levcnlf shade fraction of indirect light absorbed by each canopy and leaf layer 1 F +FATES_FABI_SUN_CLLL fates_levcnlf sun fraction of indirect light absorbed by each canopy and leaf layer 1 F +FATES_LAISHA_Z_CLLL fates_levcnlf LAI in the shade by each canopy and leaf layer m2 m-2 F +FATES_LAISUN_Z_CLLL fates_levcnlf LAI in the sun by each canopy and leaf layer m2 m-2 F +FATES_NET_C_UPTAKE_CLLL fates_levcnlf net carbon uptake in kg carbon per m2 per second by each canopy and leaf layer per unit ground kg m-2 s-1 F +FATES_PARPROF_DIF_CLLL fates_levcnlf radiative profile of diffuse PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F +FATES_PARPROF_DIR_CLLL fates_levcnlf radiative profile of direct PAR through each canopy and leaf layer (averaged across PFTs) W m-2 F +FATES_PARSHA_Z_CLLL fates_levcnlf PAR absorbed in the shade by each canopy and leaf layer W m-2 F +FATES_PARSUN_Z_CLLL fates_levcnlf PAR absorbed in the sun by each canopy and leaf layer W m-2 F +FATES_FABD_SHA_CLLLPF fates_levcnlfpf shade fraction of direct light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABD_SUN_CLLLPF fates_levcnlfpf sun fraction of direct light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABI_SHA_CLLLPF fates_levcnlfpf shade fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F +FATES_FABI_SUN_CLLLPF fates_levcnlfpf sun fraction of indirect light absorbed by each canopy, leaf, and PFT 1 F +FATES_LAISHA_Z_CLLLPF fates_levcnlfpf LAI in the shade by each canopy, leaf, and PFT m2 m-2 F +FATES_LAISUN_Z_CLLLPF fates_levcnlfpf LAI in the sun by each canopy, leaf, and PFT m2 m-2 F +FATES_PARPROF_DIF_CLLLPF fates_levcnlfpf radiative profile of diffuse PAR through each canopy, leaf, and PFT W m-2 F +FATES_PARPROF_DIR_CLLLPF fates_levcnlfpf radiative profile of direct PAR through each canopy, leaf, and PFT W m-2 F +FATES_PARSHA_Z_CLLLPF fates_levcnlfpf PAR absorbed in the shade by each canopy, leaf, and PFT W m-2 F +FATES_PARSUN_Z_CLLLPF fates_levcnlfpf PAR absorbed in the sun by each canopy, leaf, and PFT W m-2 F +FATES_CWD_ABOVEGROUND_DC fates_levcwdsc debris class-level aboveground coarse woody debris stocks in kg carbon per m2 kg m-2 F +FATES_CWD_ABOVEGROUND_IN_DC fates_levcwdsc debris class-level aboveground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_ABOVEGROUND_OUT_DC fates_levcwdsc debris class-level aboveground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_BELOWGROUND_DC fates_levcwdsc debris class-level belowground coarse woody debris stocks in kg carbon per m2 kg m-2 F +FATES_CWD_BELOWGROUND_IN_DC fates_levcwdsc debris class-level belowground coarse woody debris input in kg carbon per m2 per second kg m-2 s-1 F +FATES_CWD_BELOWGROUND_OUT_DC fates_levcwdsc debris class-level belowground coarse woody debris output in kg carbon per m2 per second kg m-2 s-1 F +FATES_LITTER_CWD_ELDC fates_levelcwd total mass of litter in coarse woody debris by element and coarse woody debris size kg m-2 T +FATES_ERROR_EL fates_levelem total mass-balance error in kg per second by element kg s-1 T +FATES_FIRE_FLUX_EL fates_levelem loss to atmosphere from fire by element in kg element per m2 per s kg m-2 s-1 T +FATES_LITTER_AG_CWD_EL fates_levelem mass of aboveground litter in coarse woody debris (trunks/branches/twigs) by element kg m-2 T +FATES_LITTER_AG_FINE_EL fates_levelem mass of aboveground litter in fines (leaves, nonviable seed) by element kg m-2 T +FATES_LITTER_BG_CWD_EL fates_levelem mass of belowground litter in coarse woody debris (coarse roots) by element kg m-2 T +FATES_LITTER_BG_FINE_EL fates_levelem mass of belowground litter in fines (fineroots) by element kg m-2 T +FATES_LITTER_IN_EL fates_levelem litter flux in in kg element per m2 per second kg m-2 s-1 T +FATES_LITTER_OUT_EL fates_levelem litter flux out (exudation, fragmentation and seed decay) in kg element kg m-2 s-1 T +FATES_SEEDS_IN_EXTERN_EL fates_levelem external seed influx rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEEDS_IN_LOCAL_EL fates_levelem within-site, element-level seed production rate in kg element per m2 per second kg m-2 s-1 T +FATES_SEED_BANK_EL fates_levelem element-level total seed mass of all PFTs in kg element per m2 kg m-2 T +FATES_SEED_DECAY_EL fates_levelem seed mass decay (germinated and un-germinated) in kg element per m2 per second kg m-2 s-1 T +FATES_SEED_GERM_EL fates_levelem element-level total germinated seed mass of all PFTs in kg element per m2 kg m-2 T +FATES_FUEL_AMOUNT_FC fates_levfuel spitfire fuel-class level fuel amount in kg carbon per m2 land area kg m-2 T +FATES_FUEL_BURNT_BURNFRAC_FC fates_levfuel product of fraction (0-1) of fuel burnt and burnt fraction (divide by FATES_BURNFRAC to get bu 1 T +FATES_FUEL_MOISTURE_FC fates_levfuel spitfire fuel class-level fuel moisture (volumetric) m3 m-3 T +FATES_CANOPYAREA_HT fates_levheight canopy area height distribution m2 m-2 T +FATES_LEAFAREA_HT fates_levheight leaf area height distribution m2 m-2 T +FATES_CANOPYCROWNAREA_PF fates_levpft total PFT-level canopy-layer crown area per m2 land area m2 m-2 T +FATES_CROWNAREA_PF fates_levpft total PFT-level crown area per m2 land area m2 m-2 T +FATES_DAYSINCE_DROUGHTLEAFOFF_PF fates_levpft PFT-level days elapsed since drought leaf drop days T +FATES_DAYSINCE_DROUGHTLEAFON_PF fates_levpft PFT-level days elapsed since drought leaf flush days T +FATES_DROUGHT_STATUS_PF fates_levpft PFT-level drought status, <2 too dry for leaves, >=2 not too dry T +FATES_ELONG_FACTOR_PF fates_levpft PFT-level mean elongation factor (partial flushing/abscission) 1 T +FATES_GPP_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_GPP_SE_PF fates_levpft total PFT-level GPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T +FATES_LEAFC_PF fates_levpft total PFT-level leaf biomass in kg carbon per m2 land area kg m-2 T +FATES_MEANLIQVOL_DROUGHTPHEN_PF fates_levpft PFT-level mean liquid water volume for drought phenolgy m3 m-3 T +FATES_MEANSMP_DROUGHTPHEN_PF fates_levpft PFT-level mean soil matric potential for drought phenology Pa T +FATES_MORTALITY_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from mortality kg m-2 s-1 T +FATES_MORTALITY_CSTARV_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from carbon starvation mortality kg m-2 s-1 T +FATES_MORTALITY_FIRE_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from fire mortality kg m-2 s-1 T +FATES_MORTALITY_HYDRO_CFLUX_PF fates_levpft PFT-level flux of biomass carbon from live to dead pool from hydraulic failure mortality kg m-2 s-1 T +FATES_MORTALITY_PF fates_levpft PFT-level mortality rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_NPLANT_PF fates_levpft total PFT-level number of individuals per m2 land area m-2 T +FATES_NPLANT_SEC_PF fates_levpft total PFT-level number of individuals per m2 land area, secondary patches m-2 T +FATES_NPP_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_NPP_SE_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 yr-1 T +FATES_RECRUITMENT_PF fates_levpft PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_STOREC_PF fates_levpft total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T +FATES_VEGC_PF fates_levpft total PFT-level biomass in kg of carbon per land area kg m-2 T +FATES_VEGC_SE_PF fates_levpft total PFT-level biomass in kg of carbon per land area, secondary patches kg m-2 T +FATES_DDBH_CANOPY_SZAP fates_levscag growth rate of canopy plants in meters DBH per m2 per year in canopy in each size x age class m m-2 yr-1 F +FATES_DDBH_USTORY_SZAP fates_levscag growth rate of understory plants in meters DBH per m2 per year in each size x age class m m-2 yr-1 F +FATES_MORTALITY_CANOPY_SZAP fates_levscag mortality rate of canopy plants in number of plants per m2 per year in each size x age class m-2 yr-1 F +FATES_MORTALITY_USTORY_SZAP fates_levscag mortality rate of understory plants in number of plants per m2 per year in each size x age cla m-2 yr-1 F +FATES_NPLANT_CANOPY_SZAP fates_levscag number of plants per m2 in canopy in each size x age class m-2 F +FATES_NPLANT_SZAP fates_levscag number of plants per m2 in each size x age class m-2 F +FATES_NPLANT_USTORY_SZAP fates_levscag number of plants per m2 in understory in each size x age class m-2 F +FATES_NPLANT_SZAPPF fates_levscagpf number of plants per m2 in each size x age x pft class m-2 F +FATES_BASALAREA_SZ fates_levscls basal area by size class m2 m-2 T +FATES_CROOTMAINTAR_CANOPY_SZ fates_levscls live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F +FATES_CROOTMAINTAR_USTORY_SZ fates_levscls live coarse root maintenance autotrophic respiration for understory plants in kg carbon per m2 kg m-2 s-1 F +FATES_CROWNAREA_CANOPY_SZ fates_levscls total crown area of canopy plants by size class m2 m-2 F +FATES_CROWNAREA_USTORY_SZ fates_levscls total crown area of understory plants by size class m2 m-2 F +FATES_DDBH_CANOPY_SZ fates_levscls diameter growth increment by size of canopy plants m m-2 yr-1 T +FATES_DDBH_USTORY_SZ fates_levscls diameter growth increment by size of understory plants m m-2 yr-1 T +FATES_DEMOTION_RATE_SZ fates_levscls demotion rate from canopy to understory by size class in number of plants per m2 per year m-2 yr-1 F +FATES_FROOTCTURN_CANOPY_SZ fates_levscls fine root turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOTCTURN_USTORY_SZ fates_levscls fine root turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_FROOTMAINTAR_CANOPY_SZ fates_levscls live coarse root maintenance autotrophic respiration for canopy plants in kg carbon per m2 per kg m-2 s-1 F +FATES_FROOTMAINTAR_USTORY_SZ fates_levscls fine root maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F +FATES_FROOT_ALLOC_CANOPY_SZ fates_levscls allocation to fine root C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_FROOT_ALLOC_USTORY_SZ fates_levscls allocation to fine roots for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_GROWAR_CANOPY_SZ fates_levscls growth autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_GROWAR_USTORY_SZ fates_levscls growth autotrophic respiration of understory plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_LAI_CANOPY_SZ fates_levscls leaf area index (LAI) of canopy plants by size class m2 m-2 T +FATES_LAI_USTORY_SZ fates_levscls leaf area index (LAI) of understory plants by size class m2 m-2 T +FATES_LEAFCTURN_CANOPY_SZ fates_levscls leaf turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAFCTURN_USTORY_SZ fates_levscls leaf turnover (non-mortal) for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAF_ALLOC_CANOPY_SZ fates_levscls allocation to leaves for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LEAF_ALLOC_USTORY_SZ fates_levscls allocation to leaves for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_LSTEMMAINTAR_CANOPY_SZ fates_levscls live stem maintenance autotrophic respiration for canopy plants in kg carbon per m2 per second kg m-2 s-1 F +FATES_LSTEMMAINTAR_USTORY_SZ fates_levscls live stem maintenance autotrophic respiration for understory plants in kg carbon per m2 per se kg m-2 s-1 F +FATES_M3_MORTALITY_CANOPY_SZ fates_levscls C starvation mortality of canopy plants by size N/ha/yr F +FATES_M3_MORTALITY_USTORY_SZ fates_levscls C starvation mortality of understory plants by size N/ha/yr F +FATES_MAINTAR_CANOPY_SZ fates_levscls maintenance autotrophic respiration of canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_MAINTAR_USTORY_SZ fates_levscls maintenance autotrophic respiration of understory plants in kg carbon per m2 per second by siz kg m-2 s-1 F +FATES_MORTALITY_AGESCEN_SE_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_AGESCEN_SZ fates_levscls age senescence mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_BACKGROUND_SE_SZ fates_levscls background mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_BACKGROUND_SZ fates_levscls background mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_CANOPY_SE_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2, secondary patches m-2 yr-1 T +FATES_MORTALITY_CANOPY_SZ fates_levscls total mortality of canopy trees by size class in number of plants per m2 m-2 yr-1 T +FATES_MORTALITY_CSTARV_SE_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_CSTARV_SZ fates_levscls carbon starvation mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_FIRE_SZ fates_levscls fire mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_FREEZING_SE_SZ fates_levscls freezing mortality by size in number of plants per m2 per event, secondary patches m-2 event-1 T +FATES_MORTALITY_FREEZING_SZ fates_levscls freezing mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_HYDRAULIC_SE_SZ fates_levscls hydraulic mortality by size in number of plants per m2 per year, secondary patches m-2 yr-1 T +FATES_MORTALITY_HYDRAULIC_SZ fates_levscls hydraulic mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_IMPACT_SZ fates_levscls impact mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_LOGGING_SE_SZ fates_levscls logging mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T +FATES_MORTALITY_LOGGING_SZ fates_levscls logging mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SE_SZ fates_levscls senescence mortality by size in number of plants per m2 per event, secondary patches m-2 yr-1 T +FATES_MORTALITY_SENESCENCE_SZ fates_levscls senescence mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_TERMINATION_SZ fates_levscls termination mortality by size in number of plants per m2 per year m-2 yr-1 T +FATES_MORTALITY_USTORY_SZ fates_levscls total mortality of understory trees by size class in individuals per m2 per year m-2 yr-1 T +FATES_NPLANT_CANOPY_SZ fates_levscls number of canopy plants per m2 by size class m-2 T +FATES_NPLANT_SZ fates_levscls number of plants per m2 by size class m-2 T +FATES_NPLANT_USTORY_SZ fates_levscls number of understory plants per m2 by size class m-2 T +FATES_NPP_CANOPY_SZ fates_levscls NPP of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_NPP_USTORY_SZ fates_levscls NPP of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_PROMOTION_RATE_SZ fates_levscls promotion rate from understory to canopy by size class m-2 yr-1 F +FATES_RDARK_CANOPY_SZ fates_levscls dark respiration for canopy plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_RDARK_USTORY_SZ fates_levscls dark respiration for understory plants in kg carbon per m2 per second by size kg m-2 s-1 F +FATES_SAI_CANOPY_SZ fates_levscls stem area index (SAI) of canopy plants by size class m2 m-2 F +FATES_SAI_USTORY_SZ fates_levscls stem area index (SAI) of understory plants by size class m2 m-2 F +FATES_SAPWOODCTURN_CANOPY_SZ fates_levscls sapwood turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SAPWOODCTURN_USTORY_SZ fates_levscls sapwood C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_SAPWOOD_ALLOC_CANOPY_SZ fates_levscls allocation to sapwood C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SAPWOOD_ALLOC_USTORY_SZ fates_levscls allocation to sapwood C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_ALLOC_CANOPY_SZ fates_levscls allocation to reproductive C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_ALLOC_USTORY_SZ fates_levscls allocation to reproductive C for understory plants by size class in kg carbon per m2 per secon kg m-2 s-1 F +FATES_SEED_PROD_CANOPY_SZ fates_levscls seed production of canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_SEED_PROD_USTORY_SZ fates_levscls seed production of understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORECTURN_CANOPY_SZ fates_levscls storage turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORECTURN_USTORY_SZ fates_levscls storage C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per se kg m-2 s-1 F +FATES_STORE_ALLOC_CANOPY_SZ fates_levscls allocation to storage C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STORE_ALLOC_USTORY_SZ fates_levscls allocation to storage C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STRUCTCTURN_CANOPY_SZ fates_levscls structural C turnover (non-mortal) for canopy plants by size class in kg carbon per m2 per sec kg m-2 s-1 F +FATES_STRUCTCTURN_USTORY_SZ fates_levscls structural C turnover (non-mortal) for understory plants by size class in kg carbon per m2 per kg m-2 s-1 F +FATES_STRUCT_ALLOC_CANOPY_SZ fates_levscls allocation to structural C for canopy plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_STRUCT_ALLOC_USTORY_SZ fates_levscls allocation to structural C for understory plants by size class in kg carbon per m2 per second kg m-2 s-1 F +FATES_TRIMMING_CANOPY_SZ fates_levscls trimming term of canopy plants weighted by plant density, by size class m-2 F +FATES_TRIMMING_USTORY_SZ fates_levscls trimming term of understory plants weighted by plant density, by size class m-2 F +FATES_VEGC_ABOVEGROUND_SZ fates_levscls aboveground biomass by size class in kg carbon per m2 kg m-2 T +FATES_VEGC_SZ fates_levscls total biomass by size class in kg carbon per m2 kg m-2 F +FATES_YESTCANLEV_CANOPY_SZ fates_levscls yesterdays canopy level for canopy plants by size class in number of plants per m2 m-2 F +FATES_YESTCANLEV_USTORY_SZ fates_levscls yesterdays canopy level for understory plants by size class in number of plants per m2 m-2 F +FATES_ABOVEGROUND_MORT_SZPF fates_levscpf Aboveground flux of carbon from AGB to necromass due to mortality kg m-2 s-1 F +FATES_ABOVEGROUND_PROD_SZPF fates_levscpf Aboveground carbon productivity kg m-2 s-1 F +FATES_AGSAPMAINTAR_SZPF fates_levscpf above-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F +FATES_AGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to above-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AGSTRUCT_ALLOC_SZPF fates_levscpf allocation to above-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AUTORESP_CANOPY_SZPF fates_levscpf autotrophic respiration of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_AUTORESP_SZPF fates_levscpf total autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_AUTORESP_USTORY_SZPF fates_levscpf autotrophic respiration of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BASALAREA_SZPF fates_levscpf basal area by pft/size m2 m-2 F +FATES_BGSAPMAINTAR_SZPF fates_levscpf below-ground sapwood maintenance autotrophic respiration in kg carbon per m2 per second by pft kg m-2 s-1 F +FATES_BGSAPWOOD_ALLOC_SZPF fates_levscpf allocation to below-ground sapwood by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_BGSTRUCT_ALLOC_SZPF fates_levscpf allocation to below-ground structural (deadwood) by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_C13DISC_SZPF fates_levscpf C13 discrimination by pft/size per mil F +FATES_DDBH_CANOPY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F +FATES_DDBH_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F +FATES_DDBH_USTORY_SZPF fates_levscpf diameter growth increment by pft/size m m-2 yr-1 F +FATES_FROOTC_SZPF fates_levscpf fine-root carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_FROOTMAINTAR_SZPF fates_levscpf fine root maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_FROOT_ALLOC_SZPF fates_levscpf allocation to fine roots by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_CANOPY_SZPF fates_levscpf gross primary production of canopy plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_SZPF fates_levscpf gross primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GPP_USTORY_SZPF fates_levscpf gross primary production of understory plants by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_GROWAR_SZPF fates_levscpf growth autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_GROWTHFLUX_FUSION_SZPF fates_levscpf flux of individuals into a given size class bin via fusion m-2 yr-1 F +FATES_GROWTHFLUX_SZPF fates_levscpf flux of individuals into a given size class bin via growth and recruitment m-2 yr-1 F +FATES_LAI_CANOPY_SZPF fates_levscpf Leaf area index (LAI) of canopy plants by pft/size m2 m-2 F +FATES_LAI_USTORY_SZPF fates_levscpf Leaf area index (LAI) of understory plants by pft/size m2 m-2 F +FATES_LEAFC_CANOPY_SZPF fates_levscpf biomass in leaves of canopy plants by pft/size in kg carbon per m2 kg m-2 F +FATES_LEAFC_SZPF fates_levscpf leaf carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_LEAFC_USTORY_SZPF fates_levscpf biomass in leaves of understory plants by pft/size in kg carbon per m2 kg m-2 F +FATES_LEAF_ALLOC_SZPF fates_levscpf allocation to leaves by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_M3_MORTALITY_CANOPY_SZPF fates_levscpf C starvation mortality of canopy plants by pft/size N/ha/yr F +FATES_M3_MORTALITY_USTORY_SZPF fates_levscpf C starvation mortality of understory plants by pft/size N/ha/yr F +FATES_MAINTAR_SZPF fates_levscpf maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_MORTALITY_AGESCEN_SZPF fates_levscpf age senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_BACKGROUND_SZPF fates_levscpf background mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CAMBIALBURN_SZPF fates_levscpf fire mortality from cambial burn by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CANOPY_SZPF fates_levscpf total mortality of canopy plants by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CROWNSCORCH_SZPF fates_levscpf fire mortality from crown scorch by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_CSTARV_SZPF fates_levscpf carbon starvation mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_FIRE_SZPF fates_levscpf fire mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_FREEZING_SZPF fates_levscpf freezing mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_HYDRAULIC_SZPF fates_levscpf hydraulic mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_IMPACT_SZPF fates_levscpf impact mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_LOGGING_SZPF fates_levscpf logging mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_SENESCENCE_SZPF fates_levscpf senescence mortality by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_TERMINATION_SZPF fates_levscpf termination mortality by pft/size in number pf plants per m2 per year m-2 yr-1 F +FATES_MORTALITY_USTORY_SZPF fates_levscpf total mortality of understory plants by pft/size in number of plants per m2 per year m-2 yr-1 F +FATES_NPLANT_CANOPY_SZPF fates_levscpf number of canopy plants by size/pft per m2 m-2 F +FATES_NPLANT_SZPF fates_levscpf stem number density by pft/size m-2 F +FATES_NPLANT_USTORY_SZPF fates_levscpf density of understory plants by pft/size in number of plants per m2 m-2 F +FATES_NPP_SZPF fates_levscpf total net primary production by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_RDARK_SZPF fates_levscpf dark portion of maintenance autotrophic respiration in kg carbon per m2 per second by pft/size kg m-2 s-1 F +FATES_REPROC_SZPF fates_levscpf reproductive carbon mass (on plant) by size-class x pft in kg carbon per m2 kg m-2 F +FATES_SAPWOODC_SZPF fates_levscpf sapwood carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_SEED_ALLOC_SZPF fates_levscpf allocation to seeds by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_STOREC_CANOPY_SZPF fates_levscpf biomass in storage pools of canopy plants by pft/size in kg carbon per m2 kg m-2 F +FATES_STOREC_SZPF fates_levscpf storage carbon mass by size-class x pft in kg carbon per m2 kg m-2 F +FATES_STOREC_TF_CANOPY_SZPF fates_levscpf Storage C fraction of target by size x pft, in the canopy kg kg-1 F +FATES_STOREC_TF_USTORY_SZPF fates_levscpf Storage C fraction of target by size x pft, in the understory kg kg-1 F +FATES_STOREC_USTORY_SZPF fates_levscpf biomass in storage pools of understory plants by pft/size in kg carbon per m2 kg m-2 F +FATES_STORE_ALLOC_SZPF fates_levscpf allocation to storage C by pft/size in kg carbon per m2 per second kg m-2 s-1 F +FATES_VEGC_ABOVEGROUND_SZPF fates_levscpf aboveground biomass by pft/size in kg carbon per m2 kg m-2 F +FATES_VEGC_SZPF fates_levscpf total vegetation biomass in live plants by size-class x pft in kg carbon per m2 kg m-2 F +ACTUAL_IMMOB_NH4 levdcmp immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 levdcmp immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr levdcmp actual N immobilization gN/m^3/s F +FMAX_DENIT_CARBONSUBSTRATE levdcmp FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE levdcmp FMAX_DENIT_NITRATE gN/m^3/s F +FPI_vr levdcmp fraction of potential immobilization proportion F +F_DENIT_BASE levdcmp F_DENIT_BASE gN/m^3/s F +F_DENIT_vr levdcmp denitrification flux gN/m^3/s F +F_NIT_vr levdcmp nitrification flux gN/m^3/s F +GROSS_NMIN_vr levdcmp gross rate of N mineralization gN/m^3/s F +K_LIT_CEL levdcmp cellulosic litter potential loss coefficient 1/s F +K_LIT_LIG levdcmp lignin litter potential loss coefficient 1/s F +K_LIT_MET levdcmp metabolic litter potential loss coefficient 1/s F +K_NITR levdcmp K_NITR 1/s F +K_NITR_H2O levdcmp K_NITR_H2O unitless F +K_NITR_PH levdcmp K_NITR_PH unitless F +K_NITR_T levdcmp K_NITR_T unitless F +K_SOM_ACT levdcmp active soil organic potential loss coefficient 1/s F +K_SOM_PAS levdcmp passive soil organic potential loss coefficient 1/s F +K_SOM_SLO levdcmp slow soil organic ma potential loss coefficient 1/s F +L1_PATHFRAC_S1_vr levdcmp PATHFRAC from metabolic litter to active soil organic fraction F +L1_RESP_FRAC_S1_vr levdcmp respired from metabolic litter to active soil organic fraction F +L2_PATHFRAC_S1_vr levdcmp PATHFRAC from cellulosic litter to active soil organic fraction F +L2_RESP_FRAC_S1_vr levdcmp respired from cellulosic litter to active soil organic fraction F +L3_PATHFRAC_S2_vr levdcmp PATHFRAC from lignin litter to slow soil organic ma fraction F +L3_RESP_FRAC_S2_vr levdcmp respired from lignin litter to slow soil organic ma fraction F +LIT_CEL_C_TNDNCY_VERT_TR levdcmp cellulosic litter C tendency due to vertical transport gC/m^3/s F +LIT_CEL_C_TO_SOM_ACT_C_v levdcmp decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +LIT_CEL_HR_vr levdcmp Het. Resp. from cellulosic litter gC/m^3/s F +LIT_CEL_N_TNDNCY_VERT_TR levdcmp cellulosic litter N tendency due to vertical transport gN/m^3/s F +LIT_CEL_N_TO_SOM_ACT_N_v levdcmp decomp. of cellulosic litter N to active soil organic N gN/m^3 F +LIT_CEL_N_vr levdcmp LIT_CEL N (vertically resolved) gN/m^3 T +LIT_LIG_C_TNDNCY_VERT_TR levdcmp lignin litter C tendency due to vertical transport gC/m^3/s F +LIT_LIG_C_TO_SOM_SLO_C_v levdcmp decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIT_LIG_HR_vr levdcmp Het. Resp. from lignin litter gC/m^3/s F +LIT_LIG_N_TNDNCY_VERT_TR levdcmp lignin litter N tendency due to vertical transport gN/m^3/s F +LIT_LIG_N_TO_SOM_SLO_N_v levdcmp decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIT_LIG_N_vr levdcmp LIT_LIG N (vertically resolved) gN/m^3 T +LIT_MET_C_TNDNCY_VERT_TR levdcmp metabolic litter C tendency due to vertical transport gC/m^3/s F +LIT_MET_C_TO_SOM_ACT_C_v levdcmp decomp. of metabolic litter C to active soil organic C gC/m^3/s F +LIT_MET_HR_vr levdcmp Het. Resp. from metabolic litter gC/m^3/s F +LIT_MET_N_TNDNCY_VERT_TR levdcmp metabolic litter N tendency due to vertical transport gN/m^3/s F +LIT_MET_N_TO_SOM_ACT_N_v levdcmp decomp. of metabolic litter N to active soil organic N gN/m^3 F +LIT_MET_N_vr levdcmp LIT_MET N (vertically resolved) gN/m^3 T +NDEP_PROF levdcmp profile for atmospheric N deposition 1/m F +NET_NMIN_vr levdcmp net rate of N mineralization gN/m^3/s F +NFIXATION_PROF levdcmp profile for biological N fixation 1/m F +POTENTIAL_IMMOB_vr levdcmp potential N immobilization gN/m^3/s F +POT_F_DENIT_vr levdcmp potential denitrification flux gN/m^3/s F +POT_F_NIT_vr levdcmp potential nitrification flux gN/m^3/s F +S1_PATHFRAC_S2_vr levdcmp PATHFRAC from active soil organic to slow soil organic ma fraction F +S1_PATHFRAC_S3_vr levdcmp PATHFRAC from active soil organic to passive soil organic fraction F +S1_RESP_FRAC_S2_vr levdcmp respired from active soil organic to slow soil organic ma fraction F +S1_RESP_FRAC_S3_vr levdcmp respired from active soil organic to passive soil organic fraction F +S2_PATHFRAC_S1_vr levdcmp PATHFRAC from slow soil organic ma to active soil organic fraction F +S2_PATHFRAC_S3_vr levdcmp PATHFRAC from slow soil organic ma to passive soil organic fraction F +S2_RESP_FRAC_S1_vr levdcmp respired from slow soil organic ma to active soil organic fraction F +S2_RESP_FRAC_S3_vr levdcmp respired from slow soil organic ma to passive soil organic fraction F +S3_PATHFRAC_S1_vr levdcmp PATHFRAC from passive soil organic to active soil organic fraction F +S3_RESP_FRAC_S1_vr levdcmp respired from passive soil organic to active soil organic fraction F +SMINN_TO_PLANT_vr levdcmp plant uptake of soil mineral N gN/m^3/s F +SMINN_TO_S1N_L1_vr levdcmp mineral N flux for decomp. of LIT_METto SOM_ACT gN/m^3 F +SMINN_TO_S1N_L2_vr levdcmp mineral N flux for decomp. of LIT_CELto SOM_ACT gN/m^3 F +SMINN_TO_S1N_S2_vr levdcmp mineral N flux for decomp. of SOM_SLOto SOM_ACT gN/m^3 F +SMINN_TO_S1N_S3_vr levdcmp mineral N flux for decomp. of SOM_PASto SOM_ACT gN/m^3 F +SMINN_TO_S2N_L3_vr levdcmp mineral N flux for decomp. of LIT_LIGto SOM_SLO gN/m^3 F +SMINN_TO_S2N_S1_vr levdcmp mineral N flux for decomp. of SOM_ACTto SOM_SLO gN/m^3 F +SMINN_TO_S3N_S1_vr levdcmp mineral N flux for decomp. of SOM_ACTto SOM_PAS gN/m^3 F +SMINN_TO_S3N_S2_vr levdcmp mineral N flux for decomp. of SOM_SLOto SOM_PAS gN/m^3 F +SMIN_NH4_TO_PLANT levdcmp plant uptake of NH4 gN/m^3/s F +SMIN_NO3_LEACHED_vr levdcmp soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS levdcmp SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF_vr levdcmp soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT levdcmp plant uptake of NO3 gN/m^3/s F +SOILN_vr levdcmp SOIL N (vertically resolved) gN/m^3 T +SOM_ACT_C_TNDNCY_VERT_TR levdcmp active soil organic C tendency due to vertical transport gC/m^3/s F +SOM_ACT_C_TO_SOM_PAS_C_v levdcmp decomp. of active soil organic C to passive soil organic C gC/m^3/s F +SOM_ACT_C_TO_SOM_SLO_C_v levdcmp decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +SOM_ACT_HR_S2_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +SOM_ACT_HR_S3_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +SOM_ACT_N_TNDNCY_VERT_TR levdcmp active soil organic N tendency due to vertical transport gN/m^3/s F +SOM_ACT_N_TO_SOM_PAS_N_v levdcmp decomp. of active soil organic N to passive soil organic N gN/m^3 F +SOM_ACT_N_TO_SOM_SLO_N_v levdcmp decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +SOM_ACT_N_vr levdcmp SOM_ACT N (vertically resolved) gN/m^3 T +SOM_ADV_COEF levdcmp advection term for vertical SOM translocation m/s F +SOM_DIFFUS_COEF levdcmp diffusion coefficient for vertical SOM translocation m^2/s F +SOM_PAS_C_TNDNCY_VERT_TR levdcmp passive soil organic C tendency due to vertical transport gC/m^3/s F +SOM_PAS_C_TO_SOM_ACT_C_v levdcmp decomp. of passive soil organic C to active soil organic C gC/m^3/s F +SOM_PAS_HR_vr levdcmp Het. Resp. from passive soil organic gC/m^3/s F +SOM_PAS_N_TNDNCY_VERT_TR levdcmp passive soil organic N tendency due to vertical transport gN/m^3/s F +SOM_PAS_N_TO_SOM_ACT_N_v levdcmp decomp. of passive soil organic N to active soil organic N gN/m^3 F +SOM_PAS_N_vr levdcmp SOM_PAS N (vertically resolved) gN/m^3 T +SOM_SLO_C_TNDNCY_VERT_TR levdcmp slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SOM_SLO_C_TO_SOM_ACT_C_v levdcmp decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SOM_SLO_C_TO_SOM_PAS_C_v levdcmp decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SOM_SLO_HR_S1_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SOM_SLO_HR_S3_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SOM_SLO_N_TNDNCY_VERT_TR levdcmp slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SOM_SLO_N_TO_SOM_ACT_N_v levdcmp decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SOM_SLO_N_TO_SOM_PAS_N_v levdcmp decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SOM_SLO_N_vr levdcmp SOM_SLO N (vertically resolved) gN/m^3 T +SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F +WFPS levdcmp WFPS percent F anaerobic_frac levdcmp anaerobic_frac m3/m3 F diffus levdcmp diffusivity m^2/s F fr_WFPS levdcmp fr_WFPS fraction F n2_n2o_ratio_denit levdcmp n2_n2o_ratio_denit gN/gN F -num_iter - number of iterations unitless F r_psi levdcmp r_psi m F ratio_k1 levdcmp ratio_k1 none F ratio_no3_co2 levdcmp ratio_no3_co2 ratio F soil_bulkdensity levdcmp soil_bulkdensity kg/m3 F soil_co2_prod levdcmp soil_co2_prod ug C / g soil / day F +CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F +FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F +HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F +SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T +SOILPSI levgrnd soil water potential in each soil layer MPa F +TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T +TSOI_ICE levgrnd soil temperature (ice landunits only) K T +LAKEICEFRAC levlak lake layer ice mass fraction unitless F +TLAKE levlak lake temperature K T +SNO_ABS levsno Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE levsno Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW levsno Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE levsno Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE levsno Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ levsno snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE levsno snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS levsno Mean snow grain size Microns F +SNO_GS_ICE levsno Mean snow grain size (ice landunits only) Microns F +SNO_ICE levsno Snow ice content kg/m2 F +SNO_LIQH2O levsno Snow liquid water content kg/m2 F +SNO_MELT levsno snow melt rate in each snow layer mm/s F +SNO_MELT_ICE levsno snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T levsno Snow temperatures K F +SNO_TK levsno Thermal conductivity W/m-K F +SNO_TK_ICE levsno Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE levsno Snow temperatures (ice landunits only) K F +SNO_Z levsno Snow layer thicknesses m F +SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F +CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T +FATES_FRAGMENTATION_SCALER_SL levsoi factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T +FATES_FROOTC_SL levsoi Total carbon in live plant fine-roots over depth kg m-3 T +H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HR_vr levsoi total vertically resolved heterotrophic respiration gC/m^3/s T +KROOT levsoi root conductance each soil layer 1/s F +KSOIL levsoi soil conductance in each soil layer 1/s F +LIT_CEL_C_vr levsoi LIT_CEL C (vertically resolved) gC/m^3 T +LIT_LIG_C_vr levsoi LIT_LIG C (vertically resolved) gC/m^3 T +LIT_MET_C_vr levsoi LIT_MET C (vertically resolved) gC/m^3 T +O_SCALAR levsoi fraction by which decomposition is reduced due to anoxia unitless T +QROOTSINK levsoi water flux from soil to root in each soil-layer mm/s F +SMINN_vr levsoi soil mineral N gN/m^3 T +SMIN_NH4_vr levsoi soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3_vr levsoi soil mineral NO3 (vert. res.) gN/m^3 T +SOILC_vr levsoi SOIL C (vertically resolved) gC/m^3 T +SOILICE levsoi soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ levsoi soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOM_ACT_C_vr levsoi SOM_ACT C (vertically resolved) gC/m^3 T +SOM_PAS_C_vr levsoi SOM_PAS C (vertically resolved) gC/m^3 T +SOM_SLO_C_vr levsoi SOM_SLO C (vertically resolved) gC/m^3 T +T_SCALAR levsoi temperature inhibition of decomposition unitless T +W_SCALAR levsoi Moisture (dryness) inhibition of decomposition unitless T +ALBD numrad surface albedo (direct) proportion F +ALBGRD numrad ground albedo (direct) proportion F +ALBGRI numrad ground albedo (indirect) proportion F +ALBI numrad surface albedo (indirect) proportion F =================================== ================ ============================================================================================== ================================================================= ======= diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 95f2b976e8..4e96f5fb91 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -16,36 +16,9 @@ CTSM History Fields A10TMIN - 10-day running mean of min 2-m temperature K F A5TMIN - 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB - actual N immobilization gN/m^2/s T -ACTUAL_IMMOB_NH4 levdcmp immobilization of NH4 gN/m^3/s F -ACTUAL_IMMOB_NO3 levdcmp immobilization of NO3 gN/m^3/s F -ACTUAL_IMMOB_vr levdcmp actual N immobilization gN/m^3/s F -ACT_SOMC - ACT_SOM C gC/m^2 T -ACT_SOMC_1m - ACT_SOM C to 1 meter gC/m^2 F -ACT_SOMC_TNDNCY_VERT_TRA levdcmp active soil organic C tendency due to vertical transport gC/m^3/s F -ACT_SOMC_TO_PAS_SOMC - decomp. of active soil organic C to passive soil organic C gC/m^2/s F -ACT_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of active soil organic C to passive soil organic C gC/m^3/s F -ACT_SOMC_TO_SLO_SOMC - decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F -ACT_SOMC_TO_SLO_SOMC_vr levdcmp decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F -ACT_SOMC_vr levsoi ACT_SOM C (vertically resolved) gC/m^3 T -ACT_SOMN - ACT_SOM N gN/m^2 T -ACT_SOMN_1m - ACT_SOM N to 1 meter gN/m^2 F -ACT_SOMN_TNDNCY_VERT_TRA levdcmp active soil organic N tendency due to vertical transport gN/m^3/s F -ACT_SOMN_TO_PAS_SOMN - decomp. of active soil organic N to passive soil organic N gN/m^2 F -ACT_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of active soil organic N to passive soil organic N gN/m^3 F -ACT_SOMN_TO_SLO_SOMN - decomp. of active soil organic N to slow soil organic ma N gN/m^2 F -ACT_SOMN_TO_SLO_SOMN_vr levdcmp decomp. of active soil organic N to slow soil organic ma N gN/m^3 F -ACT_SOMN_vr levdcmp ACT_SOM N (vertically resolved) gN/m^3 T -ACT_SOM_HR_S2 - Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S2_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F -ACT_SOM_HR_S3 - Het. Resp. from active soil organic gC/m^2/s F -ACT_SOM_HR_S3_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F AGLB - Aboveground leaf biomass kg/m^2 F AGNPP - aboveground NPP gC/m^2/s T AGSB - Aboveground stem biomass kg/m^2 F -ALBD numrad surface albedo (direct) proportion F -ALBGRD numrad ground albedo (direct) proportion F -ALBGRI numrad ground albedo (indirect) proportion F -ALBI numrad surface albedo (indirect) proportion F ALPHA - alpha coefficient for VOC calc non F ALT - current active layer thickness m T ALTMAX - maximum annual active layer thickness m T @@ -71,20 +44,6 @@ BGTR - background transfer growth BTRANMN - daily minimum of transpiration beta factor unitless T CANNAVG_T2M - annual average of 2m air temperature K F CANNSUM_NPP - annual sum of column-level NPP gC/m^2/s F -CEL_LITC - CEL_LIT C gC/m^2 T -CEL_LITC_1m - CEL_LIT C to 1 meter gC/m^2 F -CEL_LITC_TNDNCY_VERT_TRA levdcmp cellulosic litter C tendency due to vertical transport gC/m^3/s F -CEL_LITC_TO_ACT_SOMC - decomp. of cellulosic litter C to active soil organic C gC/m^2/s F -CEL_LITC_TO_ACT_SOMC_vr levdcmp decomp. of cellulosic litter C to active soil organic C gC/m^3/s F -CEL_LITC_vr levsoi CEL_LIT C (vertically resolved) gC/m^3 T -CEL_LITN - CEL_LIT N gN/m^2 T -CEL_LITN_1m - CEL_LIT N to 1 meter gN/m^2 F -CEL_LITN_TNDNCY_VERT_TRA levdcmp cellulosic litter N tendency due to vertical transport gN/m^3/s F -CEL_LITN_TO_ACT_SOMN - decomp. of cellulosic litter N to active soil organic N gN/m^2 F -CEL_LITN_TO_ACT_SOMN_vr levdcmp decomp. of cellulosic litter N to active soil organic N gN/m^3 F -CEL_LITN_vr levdcmp CEL_LIT N (vertically resolved) gN/m^3 T -CEL_LIT_HR - Het. Resp. from cellulosic litter gC/m^2/s F -CEL_LIT_HR_vr levdcmp Het. Resp. from cellulosic litter gC/m^3/s F CGRND - deriv. of soil energy flux wrt to soil temp W/m^2/K F CGRNDL - deriv. of soil latent heat flux wrt soil temp W/m^2/K F CGRNDS - deriv. of soil sensible heat flux wrt soil temp W/m^2/K F @@ -101,10 +60,6 @@ COL_CTRUNC - column-level sink for C tru COL_FIRE_CLOSS - total column-level fire C loss for non-peat fires outside land-type converted region gC/m^2/s T COL_FIRE_NLOSS - total column-level fire N loss gN/m^2/s T COL_NTRUNC - column-level sink for N truncation gN/m^2 F -CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F -CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F -CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T -CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T COST_NACTIVE - Cost of active uptake gN/gC T COST_NFIX - Cost of fixation gN/gC T COST_NRETRANS - Cost of retranslocation gN/gC T @@ -136,7 +91,6 @@ CPOOL_TO_LIVECROOTC - allocation to live coarse r CPOOL_TO_LIVECROOTC_STORAGE - allocation to live coarse root C storage gC/m^2/s F CPOOL_TO_LIVESTEMC - allocation to live stem C gC/m^2/s F CPOOL_TO_LIVESTEMC_STORAGE - allocation to live stem C storage gC/m^2/s F -CROOT_PROF levdcmp profile for litter C and N inputs from coarse roots 1/m F CROPPROD1C - 1-yr crop product (grain+biofuel) C gC/m^2 T CROPPROD1C_LOSS - loss from 1-yr crop product pool gC/m^2/s T CROPPROD1N - 1-yr crop product (grain+biofuel) N gN/m^2 T @@ -146,30 +100,18 @@ CROPSEEDN_DEFICIT - N used for crop seed that n CROP_SEEDC_TO_LEAF - crop seed source to leaf gC/m^2/s F CROP_SEEDN_TO_LEAF - crop seed source to leaf gN/m^2/s F CURRENT_GR - growth resp for new growth displayed in this timestep gC/m^2/s F -CWDC - CWD C gC/m^2 T -CWDC_1m - CWD C to 1 meter gC/m^2 F CWDC_HR - cwd C heterotrophic respiration gC/m^2/s T CWDC_LOSS - coarse woody debris C loss gC/m^2/s T -CWDC_TO_CEL_LITC - decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F -CWDC_TO_CEL_LITC_vr levdcmp decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F -CWDC_TO_LIG_LITC - decomp. of coarse woody debris C to lignin litter C gC/m^2/s F -CWDC_TO_LIG_LITC_vr levdcmp decomp. of coarse woody debris C to lignin litter C gC/m^3/s F -CWDC_vr levsoi CWD C (vertically resolved) gC/m^3 T -CWDN - CWD N gN/m^2 T -CWDN_1m - CWD N to 1 meter gN/m^2 F -CWDN_TO_CEL_LITN - decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F -CWDN_TO_CEL_LITN_vr levdcmp decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F -CWDN_TO_LIG_LITN - decomp. of coarse woody debris N to lignin litter N gN/m^2 F -CWDN_TO_LIG_LITN_vr levdcmp decomp. of coarse woody debris N to lignin litter N gN/m^3 F -CWDN_vr levdcmp CWD N (vertically resolved) gN/m^3 T +CWD_C - CWD C gC/m^2 T +CWD_C_1m - CWD C to 1 meter gC/m^2 F +CWD_C_TO_LIT_CEL_C - decomp. of coarse woody debris C to cellulosic litter C gC/m^2/s F +CWD_C_TO_LIT_LIG_C - decomp. of coarse woody debris C to lignin litter C gC/m^2/s F CWD_HR_L2 - Het. Resp. from coarse woody debris gC/m^2/s F -CWD_HR_L2_vr levdcmp Het. Resp. from coarse woody debris gC/m^3/s F CWD_HR_L3 - Het. Resp. from coarse woody debris gC/m^2/s F -CWD_HR_L3_vr levdcmp Het. Resp. from coarse woody debris gC/m^3/s F -CWD_PATHFRAC_L2_vr levdcmp PATHFRAC from coarse woody debris to cellulosic litter fraction F -CWD_PATHFRAC_L3_vr levdcmp PATHFRAC from coarse woody debris to lignin litter fraction F -CWD_RESP_FRAC_L2_vr levdcmp respired from coarse woody debris to cellulosic litter fraction F -CWD_RESP_FRAC_L3_vr levdcmp respired from coarse woody debris to lignin litter fraction F +CWD_N - CWD N gN/m^2 T +CWD_N_1m - CWD N to 1 meter gN/m^2 F +CWD_N_TO_LIT_CEL_N - decomp. of coarse woody debris N to cellulosic litter N gN/m^2 F +CWD_N_TO_LIT_LIG_N - decomp. of coarse woody debris N to lignin litter N gN/m^2 F C_ALLOMETRY - C allocation index none F DAYL - daylength s F DAYS_ACTIVE - number of days since last dormancy days F @@ -216,16 +158,6 @@ DWT_CONV_NFLUX - conversion N flux (immediat DWT_CONV_NFLUX_PATCH - patch-level conversion N flux (immediate loss to atm) (0 at all times except first timestep of gN/m^2/s F DWT_CROPPROD1C_GAIN - landcover change-driven addition to 1-year crop product pool gC/m^2/s T DWT_CROPPROD1N_GAIN - landcover change-driven addition to 1-year crop product pool gN/m^2/s T -DWT_DEADCROOTC_TO_CWDC levdcmp dead coarse root to CWD due to landcover change gC/m^2/s F -DWT_DEADCROOTN_TO_CWDN levdcmp dead coarse root to CWD due to landcover change gN/m^2/s F -DWT_FROOTC_TO_CEL_LIT_C levdcmp fine root to cellulosic litter due to landcover change gC/m^2/s F -DWT_FROOTC_TO_LIG_LIT_C levdcmp fine root to lignin litter due to landcover change gC/m^2/s F -DWT_FROOTC_TO_MET_LIT_C levdcmp fine root to metabolic litter due to landcover change gC/m^2/s F -DWT_FROOTN_TO_CEL_LIT_N levdcmp fine root N to cellulosic litter due to landcover change gN/m^2/s F -DWT_FROOTN_TO_LIG_LIT_N levdcmp fine root N to lignin litter due to landcover change gN/m^2/s F -DWT_FROOTN_TO_MET_LIT_N levdcmp fine root N to metabolic litter due to landcover change gN/m^2/s F -DWT_LIVECROOTC_TO_CWDC levdcmp live coarse root to CWD due to landcover change gC/m^2/s F -DWT_LIVECROOTN_TO_CWDN levdcmp live coarse root to CWD due to landcover change gN/m^2/s F DWT_PROD100C_GAIN - landcover change-driven addition to 100-yr wood product pool gC/m^2/s F DWT_PROD100N_GAIN - landcover change-driven addition to 100-yr wood product pool gN/m^2/s F DWT_PROD10C_GAIN - landcover change-driven addition to 10-yr wood product pool gC/m^2/s F @@ -248,7 +180,6 @@ DYN_COL_SOIL_ADJUSTMENTS_C - Adjustments in soil carbon DYN_COL_SOIL_ADJUSTMENTS_N - Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F DYN_COL_SOIL_ADJUSTMENTS_NH4 - Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F DYN_COL_SOIL_ADJUSTMENTS_NO3 - Adjustments in soil NO3 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F -EFF_POROSITY levgrnd effective porosity = porosity - vol_ice proportion F EFLXBUILD - building heat flux from change in interior building air temperature W/m^2 T EFLX_DYNBAL - dynamic land cover change conversion energy flux W/m^2 T EFLX_GNET - net heat flux into ground W/m^2 F @@ -290,7 +221,6 @@ FGR - heat flux into soil/snow in FGR12 - heat flux between soil layers 1 and 2 W/m^2 T FGR_ICE - heat flux into soil/snow including snow melt and lake / snow light transmission (ice landunits W/m^2 F FGR_R - Rural heat flux into soil/snow including snow melt and snow light transmission W/m^2 F -FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F FGR_U - Urban heat flux into soil/snow including snow melt W/m^2 F FH2OSFC - fraction of ground covered by surface water unitless T FH2OSFC_NOSNOW - fraction of ground covered by surface water (if no snow present) unitless F @@ -306,16 +236,12 @@ FIRE_R - Rural emitted infrared (lon FIRE_U - Urban emitted infrared (longwave) radiation W/m^2 F FLDS - atmospheric longwave radiation (downscaled to columns in glacier regions) W/m^2 T FLDS_ICE - atmospheric longwave radiation (downscaled to columns in glacier regions) (ice landunits only) W/m^2 F -FMAX_DENIT_CARBONSUBSTRATE levdcmp FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F -FMAX_DENIT_NITRATE levdcmp FMAX_DENIT_NITRATE gN/m^3/s F FPI - fraction of potential immobilization proportion T -FPI_vr levdcmp fraction of potential immobilization proportion F FPSN - photosynthesis umol m-2 s-1 T FPSN24 - 24 hour accumulative patch photosynthesis starting from mid-night umol CO2/m^2 ground/day F FPSN_WC - Rubisco-limited photosynthesis umol m-2 s-1 F FPSN_WJ - RuBP-limited photosynthesis umol m-2 s-1 F FPSN_WP - Product-limited photosynthesis umol m-2 s-1 F -FRAC_ICEOLD levgrnd fraction of ice relative to the tot water proportion F FREE_RETRANSN_TO_NPOOL - deployment of retranslocated N gN/m^2/s T FROOTC - fine root C gC/m^2 T FROOTC_ALLOC - fine root C allocation gC/m^2/s T @@ -332,7 +258,6 @@ FROOTN_TO_LITTER - fine root N litterfall FROOTN_XFER - fine root N transfer gN/m^2 F FROOTN_XFER_TO_FROOTN - fine root N growth from storage gN/m^2/s F FROOT_MR - fine root maintenance respiration gC/m^2/s F -FROOT_PROF levdcmp profile for litter C and N inputs from fine roots 1/m F FROST_TABLE - frost table depth (natural vegetated and crop landunits only) m F FSA - absorbed solar radiation W/m^2 T FSAT - fractional area with water table at surface unitless T @@ -382,12 +307,9 @@ FUELC - fuel load FV - friction velocity m/s T FWET - fraction of canopy that is wet proportion F F_DENIT - denitrification flux gN/m^2/s T -F_DENIT_BASE levdcmp F_DENIT_BASE gN/m^3/s F -F_DENIT_vr levdcmp denitrification flux gN/m^3/s F F_N2O_DENIT - denitrification N2O flux gN/m^2/s T F_N2O_NIT - nitrification N2O flux gN/m^2/s T F_NIT - nitrification flux gN/m^2/s T -F_NIT_vr levdcmp nitrification flux gN/m^3/s F GAMMA - total gamma for VOC calc non F GAMMAA - gamma A for VOC calc non F GAMMAC - gamma C for VOC calc non F @@ -402,23 +324,19 @@ GDD1020 - Twenty year average of grow GDD8 - Growing degree days base 8C from planting ddays F GDD820 - Twenty year average of growing degree days base 8C from planting ddays F GDDACCUM - Accumulated growing degree days past planting date for crop ddays F -GDDACCUM_PERHARV mxharvests At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F GDDHARV - Growing degree days (gdd) needed to harvest ddays F -GDDHARV_PERHARV mxharvests Growing degree days (gdd) needed to harvest; should only be output annually ddays F GDDTSOI - Growing degree-days from planting (top two soil layers) ddays F GPP - gross primary production gC/m^2/s T GR - total growth respiration gC/m^2/s T GRAINC - grain C (does not equal yield) gC/m^2 T GRAINC_TO_FOOD - grain C to food gC/m^2/s T GRAINC_TO_FOOD_ANN - grain C to food harvested per calendar year; should only be output annually gC/m^2 F -GRAINC_TO_FOOD_PERHARV mxharvests grain C to food per harvest; should only be output annually gC/m^2 F GRAINC_TO_SEED - grain C to seed gC/m^2/s T GRAINN - grain N gN/m^2 T GRESP_STORAGE - growth respiration storage gC/m^2 F GRESP_STORAGE_TO_XFER - growth respiration shift storage to transfer gC/m^2/s F GRESP_XFER - growth respiration transfer gC/m^2 F GROSS_NMIN - gross rate of N mineralization gN/m^2/s T -GROSS_NMIN_vr levdcmp gross rate of N mineralization gN/m^3/s F GRU_PROD100C_GAIN - gross unrepresented landcover change addition to 100-yr wood product pool gC/m^2/s F GRU_PROD100N_GAIN - gross unrepresented landcover change addition to 100-yr wood product pool gN/m^2/s F GRU_PROD10C_GAIN - gross unrepresented landcover change addition to 10-yr wood product pool gC/m^2/s F @@ -432,10 +350,7 @@ H2OSFC - surface water depth H2OSNO - snow depth (liquid water) mm T H2OSNO_ICE - snow depth (liquid water, ice landunits only) mm F H2OSNO_TOP - mass of snow in top snow layer kg/m2 T -H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T -HARVEST_REASON_PERHARV mxharvests Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F HBOT - canopy bottom m F -HDATES mxharvests actual crop harvest dates; should only be output annually day of year F HEAT_CONTENT1 - initial gridcell total heat content J/m^2 T HEAT_CONTENT1_VEG - initial gridcell total heat content - natural vegetated and crop landunits only J/m^2 F HEAT_CONTENT2 - post land cover change total heat content J/m^2 F @@ -443,12 +358,9 @@ HEAT_FROM_AC - sensible heat flux put into HIA - 2 m NWS Heat Index C T HIA_R - Rural 2 m NWS Heat Index C T HIA_U - Urban 2 m NWS Heat Index C T -HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F HR - total heterotrophic respiration gC/m^2/s T -HR_vr levsoi total vertically resolved heterotrophic respiration gC/m^3/s T HTOP - canopy top m T HUI - Crop patch heat unit index ddays F -HUI_PERHARV mxharvests At-harvest accumulated heat unit index for crop; should only be output annually ddays F HUMIDEX - 2 m Humidex C T HUMIDEX_R - Rural 2 m Humidex C T HUMIDEX_U - Urban 2 m Humidex C T @@ -461,29 +373,9 @@ INT_SNOW_ICE - accumulated swe (ice landun IWUELN - local noon intrinsic water use efficiency umolCO2/molH2O T JMX25T - canopy profile of jmax umol/m2/s T Jmx25Z - maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T -KROOT levsoi root conductance each soil layer 1/s F -KSOIL levsoi soil conductance in each soil layer 1/s F -K_ACT_SOM levdcmp active soil organic potential loss coefficient 1/s F -K_CEL_LIT levdcmp cellulosic litter potential loss coefficient 1/s F -K_CWD levdcmp coarse woody debris potential loss coefficient 1/s F -K_LIG_LIT levdcmp lignin litter potential loss coefficient 1/s F -K_MET_LIT levdcmp metabolic litter potential loss coefficient 1/s F -K_NITR levdcmp K_NITR 1/s F -K_NITR_H2O levdcmp K_NITR_H2O unitless F -K_NITR_PH levdcmp K_NITR_PH unitless F -K_NITR_T levdcmp K_NITR_T unitless F -K_PAS_SOM levdcmp passive soil organic potential loss coefficient 1/s F -K_SLO_SOM levdcmp slow soil organic ma potential loss coefficient 1/s F -L1_PATHFRAC_S1_vr levdcmp PATHFRAC from metabolic litter to active soil organic fraction F -L1_RESP_FRAC_S1_vr levdcmp respired from metabolic litter to active soil organic fraction F -L2_PATHFRAC_S1_vr levdcmp PATHFRAC from cellulosic litter to active soil organic fraction F -L2_RESP_FRAC_S1_vr levdcmp respired from cellulosic litter to active soil organic fraction F -L3_PATHFRAC_S2_vr levdcmp PATHFRAC from lignin litter to slow soil organic ma fraction F -L3_RESP_FRAC_S2_vr levdcmp respired from lignin litter to slow soil organic ma fraction F LAI240 - 240hr average of leaf area index m^2/m^2 F LAISHA - shaded projected leaf area index m^2/m^2 T LAISUN - sunlit projected leaf area index m^2/m^2 T -LAKEICEFRAC levlak lake layer ice mass fraction unitless F LAKEICEFRAC_SURF - surface lake layer ice mass fraction unitless T LAKEICETHICK - thickness of lake ice (including physical expansion on freezing) m T LAND_USE_FLUX - total C emitted from land cover conversion (smoothed over the year) and wood and grain product gC/m^2/s T @@ -512,23 +404,8 @@ LEAFN_TO_RETRANSN - leaf N to retranslocated N LEAFN_XFER - leaf N transfer gN/m^2 F LEAFN_XFER_TO_LEAFN - leaf N growth from storage gN/m^2/s F LEAF_MR - leaf maintenance respiration gC/m^2/s T -LEAF_PROF levdcmp profile for litter C and N inputs from leaves 1/m F LFC2 - conversion area fraction of BET and BDT that burned per sec T LGSF - long growing season factor proportion F -LIG_LITC - LIG_LIT C gC/m^2 T -LIG_LITC_1m - LIG_LIT C to 1 meter gC/m^2 F -LIG_LITC_TNDNCY_VERT_TRA levdcmp lignin litter C tendency due to vertical transport gC/m^3/s F -LIG_LITC_TO_SLO_SOMC - decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F -LIG_LITC_TO_SLO_SOMC_vr levdcmp decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F -LIG_LITC_vr levsoi LIG_LIT C (vertically resolved) gC/m^3 T -LIG_LITN - LIG_LIT N gN/m^2 T -LIG_LITN_1m - LIG_LIT N to 1 meter gN/m^2 F -LIG_LITN_TNDNCY_VERT_TRA levdcmp lignin litter N tendency due to vertical transport gN/m^3/s F -LIG_LITN_TO_SLO_SOMN - decomp. of lignin litter N to slow soil organic ma N gN/m^2 F -LIG_LITN_TO_SLO_SOMN_vr levdcmp decomp. of lignin litter N to slow soil organic ma N gN/m^3 F -LIG_LITN_vr levdcmp LIG_LIT N (vertically resolved) gN/m^3 T -LIG_LIT_HR - Het. Resp. from lignin litter gC/m^2/s F -LIG_LIT_HR_vr levdcmp Het. Resp. from lignin litter gC/m^3/s F LIQCAN - intercepted liquid water mm T LIQUID_CONTENT1 - initial gridcell total liq content mm T LIQUID_CONTENT2 - post landuse change gridcell total liq content mm F @@ -537,6 +414,27 @@ LITFALL - litterfall (leaves and fine LITFIRE - litter fire losses gC/m^2/s F LITTERC_HR - litter C heterotrophic respiration gC/m^2/s T LITTERC_LOSS - litter C loss gC/m^2/s T +LIT_CEL_C - LIT_CEL C gC/m^2 T +LIT_CEL_C_1m - LIT_CEL C to 1 meter gC/m^2 F +LIT_CEL_C_TO_SOM_ACT_C - decomp. of cellulosic litter C to active soil organic C gC/m^2/s F +LIT_CEL_HR - Het. Resp. from cellulosic litter gC/m^2/s F +LIT_CEL_N - LIT_CEL N gN/m^2 T +LIT_CEL_N_1m - LIT_CEL N to 1 meter gN/m^2 F +LIT_CEL_N_TO_SOM_ACT_N - decomp. of cellulosic litter N to active soil organic N gN/m^2 F +LIT_LIG_C - LIT_LIG C gC/m^2 T +LIT_LIG_C_1m - LIT_LIG C to 1 meter gC/m^2 F +LIT_LIG_C_TO_SOM_SLO_C - decomp. of lignin litter C to slow soil organic ma C gC/m^2/s F +LIT_LIG_HR - Het. Resp. from lignin litter gC/m^2/s F +LIT_LIG_N - LIT_LIG N gN/m^2 T +LIT_LIG_N_1m - LIT_LIG N to 1 meter gN/m^2 F +LIT_LIG_N_TO_SOM_SLO_N - decomp. of lignin litter N to slow soil organic ma N gN/m^2 F +LIT_MET_C - LIT_MET C gC/m^2 T +LIT_MET_C_1m - LIT_MET C to 1 meter gC/m^2 F +LIT_MET_C_TO_SOM_ACT_C - decomp. of metabolic litter C to active soil organic C gC/m^2/s F +LIT_MET_HR - Het. Resp. from metabolic litter gC/m^2/s F +LIT_MET_N - LIT_MET N gN/m^2 T +LIT_MET_N_1m - LIT_MET N to 1 meter gN/m^2 F +LIT_MET_N_TO_SOM_ACT_N - decomp. of metabolic litter N to active soil organic N gN/m^2 F LIVECROOTC - live coarse root C gC/m^2 T LIVECROOTC_STORAGE - live coarse root C storage gC/m^2 F LIVECROOTC_STORAGE_TO_XFER - live coarse root C shift storage to transfer gC/m^2/s F @@ -579,33 +477,9 @@ MEG_isoprene - MEGAN flux MEG_methanol - MEGAN flux kg/m2/sec T MEG_pinene_a - MEGAN flux kg/m2/sec T MEG_thujene_a - MEGAN flux kg/m2/sec T -MET_LITC - MET_LIT C gC/m^2 T -MET_LITC_1m - MET_LIT C to 1 meter gC/m^2 F -MET_LITC_TNDNCY_VERT_TRA levdcmp metabolic litter C tendency due to vertical transport gC/m^3/s F -MET_LITC_TO_ACT_SOMC - decomp. of metabolic litter C to active soil organic C gC/m^2/s F -MET_LITC_TO_ACT_SOMC_vr levdcmp decomp. of metabolic litter C to active soil organic C gC/m^3/s F -MET_LITC_vr levsoi MET_LIT C (vertically resolved) gC/m^3 T -MET_LITN - MET_LIT N gN/m^2 T -MET_LITN_1m - MET_LIT N to 1 meter gN/m^2 F -MET_LITN_TNDNCY_VERT_TRA levdcmp metabolic litter N tendency due to vertical transport gN/m^3/s F -MET_LITN_TO_ACT_SOMN - decomp. of metabolic litter N to active soil organic N gN/m^2 F -MET_LITN_TO_ACT_SOMN_vr levdcmp decomp. of metabolic litter N to active soil organic N gN/m^3 F -MET_LITN_vr levdcmp MET_LIT N (vertically resolved) gN/m^3 T -MET_LIT_HR - Het. Resp. from metabolic litter gC/m^2/s F -MET_LIT_HR_vr levdcmp Het. Resp. from metabolic litter gC/m^3/s F MR - maintenance respiration gC/m^2/s T -M_ACT_SOMC_TO_LEACHING - active soil organic C leaching loss gC/m^2/s F -M_ACT_SOMN_TO_LEACHING - active soil organic N leaching loss gN/m^2/s F -M_CEL_LITC_TO_FIRE - cellulosic litter C fire loss gC/m^2/s F -M_CEL_LITC_TO_FIRE_vr levdcmp cellulosic litter C fire loss gC/m^3/s F -M_CEL_LITC_TO_LEACHING - cellulosic litter C leaching loss gC/m^2/s F -M_CEL_LITN_TO_FIRE - cellulosic litter N fire loss gN/m^2 F -M_CEL_LITN_TO_FIRE_vr levdcmp cellulosic litter N fire loss gN/m^3 F -M_CEL_LITN_TO_LEACHING - cellulosic litter N leaching loss gN/m^2/s F -M_CWDC_TO_FIRE - coarse woody debris C fire loss gC/m^2/s F -M_CWDC_TO_FIRE_vr levdcmp coarse woody debris C fire loss gC/m^3/s F -M_CWDN_TO_FIRE - coarse woody debris N fire loss gN/m^2 F -M_CWDN_TO_FIRE_vr levdcmp coarse woody debris N fire loss gN/m^3 F +M_CWD_C_TO_FIRE - coarse woody debris C fire loss gC/m^2/s F +M_CWD_N_TO_FIRE - coarse woody debris N fire loss gN/m^2 F M_DEADCROOTC_STORAGE_TO_LITTER - dead coarse root C storage mortality gC/m^2/s F M_DEADCROOTC_STORAGE_TO_LITTER_FIRE - dead coarse root C storage fire mortality to litter gC/m^2/s F M_DEADCROOTC_TO_LITTER - dead coarse root C mortality gC/m^2/s F @@ -675,12 +549,18 @@ M_LEAFN_TO_FIRE - leaf N fire loss M_LEAFN_TO_LITTER - leaf N mortality gN/m^2/s F M_LEAFN_XFER_TO_FIRE - leaf N transfer fire loss gN/m^2/s F M_LEAFN_XFER_TO_LITTER - leaf N transfer mortality gN/m^2/s F -M_LIG_LITC_TO_FIRE - lignin litter C fire loss gC/m^2/s F -M_LIG_LITC_TO_FIRE_vr levdcmp lignin litter C fire loss gC/m^3/s F -M_LIG_LITC_TO_LEACHING - lignin litter C leaching loss gC/m^2/s F -M_LIG_LITN_TO_FIRE - lignin litter N fire loss gN/m^2 F -M_LIG_LITN_TO_FIRE_vr levdcmp lignin litter N fire loss gN/m^3 F -M_LIG_LITN_TO_LEACHING - lignin litter N leaching loss gN/m^2/s F +M_LIT_CEL_C_TO_FIRE - cellulosic litter C fire loss gC/m^2/s F +M_LIT_CEL_C_TO_LEACHING - cellulosic litter C leaching loss gC/m^2/s F +M_LIT_CEL_N_TO_FIRE - cellulosic litter N fire loss gN/m^2 F +M_LIT_CEL_N_TO_LEACHING - cellulosic litter N leaching loss gN/m^2/s F +M_LIT_LIG_C_TO_FIRE - lignin litter C fire loss gC/m^2/s F +M_LIT_LIG_C_TO_LEACHING - lignin litter C leaching loss gC/m^2/s F +M_LIT_LIG_N_TO_FIRE - lignin litter N fire loss gN/m^2 F +M_LIT_LIG_N_TO_LEACHING - lignin litter N leaching loss gN/m^2/s F +M_LIT_MET_C_TO_FIRE - metabolic litter C fire loss gC/m^2/s F +M_LIT_MET_C_TO_LEACHING - metabolic litter C leaching loss gC/m^2/s F +M_LIT_MET_N_TO_FIRE - metabolic litter N fire loss gN/m^2 F +M_LIT_MET_N_TO_LEACHING - metabolic litter N leaching loss gN/m^2/s F M_LIVECROOTC_STORAGE_TO_LITTER - live coarse root C storage mortality gC/m^2/s F M_LIVECROOTC_STORAGE_TO_LITTER_FIRE - live coarse root C fire mortality to litter gC/m^2/s F M_LIVECROOTC_TO_LITTER - live coarse root C mortality gC/m^2/s F @@ -714,18 +594,14 @@ M_LIVESTEMN_TO_FIRE - live stem N fire loss M_LIVESTEMN_TO_LITTER - live stem N mortality gN/m^2/s F M_LIVESTEMN_XFER_TO_FIRE - live stem N transfer fire loss gN/m^2/s F M_LIVESTEMN_XFER_TO_LITTER - live stem N transfer mortality gN/m^2/s F -M_MET_LITC_TO_FIRE - metabolic litter C fire loss gC/m^2/s F -M_MET_LITC_TO_FIRE_vr levdcmp metabolic litter C fire loss gC/m^3/s F -M_MET_LITC_TO_LEACHING - metabolic litter C leaching loss gC/m^2/s F -M_MET_LITN_TO_FIRE - metabolic litter N fire loss gN/m^2 F -M_MET_LITN_TO_FIRE_vr levdcmp metabolic litter N fire loss gN/m^3 F -M_MET_LITN_TO_LEACHING - metabolic litter N leaching loss gN/m^2/s F -M_PAS_SOMC_TO_LEACHING - passive soil organic C leaching loss gC/m^2/s F -M_PAS_SOMN_TO_LEACHING - passive soil organic N leaching loss gN/m^2/s F M_RETRANSN_TO_FIRE - retranslocated N pool fire loss gN/m^2/s F M_RETRANSN_TO_LITTER - retranslocated N pool mortality gN/m^2/s F -M_SLO_SOMC_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F -M_SLO_SOMN_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F +M_SOM_ACT_C_TO_LEACHING - active soil organic C leaching loss gC/m^2/s F +M_SOM_ACT_N_TO_LEACHING - active soil organic N leaching loss gN/m^2/s F +M_SOM_PAS_C_TO_LEACHING - passive soil organic C leaching loss gC/m^2/s F +M_SOM_PAS_N_TO_LEACHING - passive soil organic N leaching loss gN/m^2/s F +M_SOM_SLO_C_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F +M_SOM_SLO_N_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F NACTIVE - Mycorrhizal N uptake flux gN/m^2/s T NACTIVE_NH4 - Mycorrhizal N uptake flux gN/m^2/s T NACTIVE_NO3 - Mycorrhizal N uptake flux gN/m^2/s T @@ -734,7 +610,6 @@ NAM_NH4 - AM-associated N uptake flux NAM_NO3 - AM-associated N uptake flux gN/m^2/s T NBP - net biome production, includes fire, landuse, harvest and hrv_xsmrpool flux (latter smoothed o gC/m^2/s T NDEPLOY - total N deployed in new growth gN/m^2/s T -NDEP_PROF levdcmp profile for atmospheric N deposition 1/m F NDEP_TO_SMINN - atmospheric N deposition to soil mineral N gN/m^2/s T NECM - ECM-associated N uptake flux gN/m^2/s T NECM_NH4 - ECM-associated N uptake flux gN/m^2/s T @@ -743,11 +618,9 @@ NEE - net ecosystem exchange of c NEM - Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T NEP - net ecosystem production, excludes fire, landuse, and harvest flux, positive for sink gC/m^2/s T NET_NMIN - net rate of N mineralization gN/m^2/s T -NET_NMIN_vr levdcmp net rate of N mineralization gN/m^3/s F NFERTILIZATION - fertilizer added gN/m^2/s T NFIRE - fire counts valid only in Reg.C counts/km2/sec T NFIX - Symbiotic BNF uptake flux gN/m^2/s T -NFIXATION_PROF levdcmp profile for biological N fixation 1/m F NFIX_TO_SMINN - symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s F NNONMYC - Non-mycorrhizal N uptake flux gN/m^2/s T NNONMYC_NH4 - Non-mycorrhizal N uptake flux gN/m^2/s T @@ -792,7 +665,6 @@ NSUBSTEPS - number of adaptive timestep NUPTAKE - Total N uptake of FUN gN/m^2/s T NUPTAKE_NPP_FRACTION - frac of NPP used in N uptake - T N_ALLOMETRY - N allocation index none F -O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F OBU - Monin-Obukhov length m F OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T OFFSET_COUNTER - offset days counter days F @@ -805,7 +677,6 @@ ONSET_FLAG - onset flag ONSET_GDD - onset growing degree days C degree-days F ONSET_GDDFLAG - onset flag for growing degree day sum none F ONSET_SWI - onset soil water index none F -O_SCALAR levsoi fraction by which decomposition is reduced due to anoxia unitless T PAR240DZ - 10-day running mean of daytime patch absorbed PAR for leaves for top canopy layer W/m^2 F PAR240XZ - 10-day running mean of maximum patch absorbed PAR for leaves for top canopy layer W/m^2 F PAR240_shade - shade PAR (240 hrs) umol/m2/s F @@ -815,20 +686,6 @@ PAR24_sun - sunlit PAR (24 hrs) PARVEGLN - absorbed par by vegetation at local noon W/m^2 T PAR_shade - shade PAR umol/m2/s F PAR_sun - sunlit PAR umol/m2/s F -PAS_SOMC - PAS_SOM C gC/m^2 T -PAS_SOMC_1m - PAS_SOM C to 1 meter gC/m^2 F -PAS_SOMC_TNDNCY_VERT_TRA levdcmp passive soil organic C tendency due to vertical transport gC/m^3/s F -PAS_SOMC_TO_ACT_SOMC - decomp. of passive soil organic C to active soil organic C gC/m^2/s F -PAS_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of passive soil organic C to active soil organic C gC/m^3/s F -PAS_SOMC_vr levsoi PAS_SOM C (vertically resolved) gC/m^3 T -PAS_SOMN - PAS_SOM N gN/m^2 T -PAS_SOMN_1m - PAS_SOM N to 1 meter gN/m^2 F -PAS_SOMN_TNDNCY_VERT_TRA levdcmp passive soil organic N tendency due to vertical transport gN/m^3/s F -PAS_SOMN_TO_ACT_SOMN - decomp. of passive soil organic N to active soil organic N gN/m^2 F -PAS_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of passive soil organic N to active soil organic N gN/m^3 F -PAS_SOMN_vr levdcmp PAS_SOM N (vertically resolved) gN/m^3 T -PAS_SOM_HR - Het. Resp. from passive soil organic gC/m^2/s F -PAS_SOM_HR_vr levdcmp Het. Resp. from passive soil organic gC/m^3/s F PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T PBOT_240 - 10 day running mean of air pressure Pa F PCH4 - atmospheric partial pressure of CH4 Pa T @@ -845,11 +702,8 @@ PLANT_NDEMAND - N flux required to support PNLCZ - Proportion of nitrogen allocated for light capture unitless F PO2_240 - 10 day running mean of O2 pressure Pa F POTENTIAL_IMMOB - potential N immobilization gN/m^2/s T -POTENTIAL_IMMOB_vr levdcmp potential N immobilization gN/m^3/s F POT_F_DENIT - potential denitrification flux gN/m^2/s T -POT_F_DENIT_vr levdcmp potential denitrification flux gN/m^3/s F POT_F_NIT - potential nitrification flux gN/m^2/s T -POT_F_NIT_vr levdcmp potential nitrification flux gN/m^3/s F PREC10 - 10-day running mean of PREC MM H2O/S F PREC60 - 60-day running mean of PREC MM H2O/S F PREV_DAYL - daylength from previous timestep s F @@ -896,7 +750,6 @@ QH2OSFC - surface water runoff QH2OSFC_TO_ICE - surface water converted to ice mm/s F QHR - hydraulic redistribution mm/s T QICE - ice growth/melt mm/s T -QICE_FORC elevclas qice forcing sent to GLC mm/s F QICE_FRZ - ice growth mm/s T QICE_MELT - ice melt mm/s T QINFL - infiltration mm/s T @@ -911,7 +764,6 @@ QOVER - total surface runoff (inclu QOVER_LAG - time-lagged surface runoff for soil columns mm/s F QPHSNEG - net negative hydraulic redistribution flux mm/s F QRGWL - surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T -QROOTSINK levsoi water flux from soil to root in each soil-layer mm/s F QRUNOFF - total liquid runoff not including correction for land use change mm/s T QRUNOFF_ICE - total liquid runoff not incl corret for LULCC (ice landunits only) mm/s T QRUNOFF_ICE_TO_COUPLER - total ice runoff sent to coupler (includes corrections for land use change) mm/s T @@ -960,85 +812,33 @@ RH30 - 30-day running mean of rela RHAF - fractional humidity of canopy air fraction F RHAF10 - 10 day running mean of fractional humidity of canopy air fraction F RH_LEAF - fractional humidity at leaf surface fraction F -ROOTR levgrnd effective fraction of roots in each soil layer (SMS method) proportion F RR - root respiration (fine root MR + total root GR) gC/m^2/s T -RRESIS levgrnd root resistance in each soil layer proportion F RSSHA - shaded leaf stomatal resistance s/m T RSSUN - sunlit leaf stomatal resistance s/m T Rainf - atmospheric rain, after rain/snow repartitioning based on temperature mm/s F Rnet - net radiation W/m^2 F -S1_PATHFRAC_S2_vr levdcmp PATHFRAC from active soil organic to slow soil organic ma fraction F -S1_PATHFRAC_S3_vr levdcmp PATHFRAC from active soil organic to passive soil organic fraction F -S1_RESP_FRAC_S2_vr levdcmp respired from active soil organic to slow soil organic ma fraction F -S1_RESP_FRAC_S3_vr levdcmp respired from active soil organic to passive soil organic fraction F -S2_PATHFRAC_S1_vr levdcmp PATHFRAC from slow soil organic ma to active soil organic fraction F -S2_PATHFRAC_S3_vr levdcmp PATHFRAC from slow soil organic ma to passive soil organic fraction F -S2_RESP_FRAC_S1_vr levdcmp respired from slow soil organic ma to active soil organic fraction F -S2_RESP_FRAC_S3_vr levdcmp respired from slow soil organic ma to passive soil organic fraction F -S3_PATHFRAC_S1_vr levdcmp PATHFRAC from passive soil organic to active soil organic fraction F -S3_RESP_FRAC_S1_vr levdcmp respired from passive soil organic to active soil organic fraction F SABG - solar rad absorbed by ground W/m^2 T SABG_PEN - Rural solar rad penetrating top soil or snow layer watt/m^2 T SABV - solar rad absorbed by veg W/m^2 T -SDATES mxsowings actual crop sowing dates; should only be output annually day of year F -SDATES_PERHARV mxharvests actual sowing dates for crops harvested this year; should only be output annually day of year F SEEDC - pool for seeding new PFTs via dynamic landcover gC/m^2 T SEEDN - pool for seeding new PFTs via dynamic landcover gN/m^2 T SLASH_HARVESTC - slash harvest carbon (to litter) gC/m^2/s T -SLO_SOMC - SLO_SOM C gC/m^2 T -SLO_SOMC_1m - SLO_SOM C to 1 meter gC/m^2 F -SLO_SOMC_TNDNCY_VERT_TRA levdcmp slow soil organic ma C tendency due to vertical transport gC/m^3/s F -SLO_SOMC_TO_ACT_SOMC - decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F -SLO_SOMC_TO_ACT_SOMC_vr levdcmp decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F -SLO_SOMC_TO_PAS_SOMC - decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F -SLO_SOMC_TO_PAS_SOMC_vr levdcmp decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F -SLO_SOMC_vr levsoi SLO_SOM C (vertically resolved) gC/m^3 T -SLO_SOMN - SLO_SOM N gN/m^2 T -SLO_SOMN_1m - SLO_SOM N to 1 meter gN/m^2 F -SLO_SOMN_TNDNCY_VERT_TRA levdcmp slow soil organic ma N tendency due to vertical transport gN/m^3/s F -SLO_SOMN_TO_ACT_SOMN - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F -SLO_SOMN_TO_ACT_SOMN_vr levdcmp decomp. of slow soil organic ma N to active soil organic N gN/m^3 F -SLO_SOMN_TO_PAS_SOMN - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F -SLO_SOMN_TO_PAS_SOMN_vr levdcmp decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F -SLO_SOMN_vr levdcmp SLO_SOM N (vertically resolved) gN/m^3 T -SLO_SOM_HR_S1 - Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S1_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F -SLO_SOM_HR_S3 - Het. Resp. from slow soil organic ma gC/m^2/s F -SLO_SOM_HR_S3_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F SMINN - soil mineral N gN/m^2 T SMINN_TO_NPOOL - deployment of soil mineral N uptake gN/m^2/s T SMINN_TO_PLANT - plant uptake of soil mineral N gN/m^2/s T SMINN_TO_PLANT_FUN - Total soil N uptake of FUN gN/m^2/s T -SMINN_TO_PLANT_vr levdcmp plant uptake of soil mineral N gN/m^3/s F -SMINN_TO_S1N_L1 - mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L1_vr levdcmp mineral N flux for decomp. of MET_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_L2 - mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^2 F -SMINN_TO_S1N_L2_vr levdcmp mineral N flux for decomp. of CEL_LITto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S2 - mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S1N_S3 - mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^2 F -SMINN_TO_S1N_S3_vr levdcmp mineral N flux for decomp. of PAS_SOMto ACT_SOM gN/m^3 F -SMINN_TO_S2N_L3 - mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^2 F -SMINN_TO_S2N_L3_vr levdcmp mineral N flux for decomp. of LIG_LITto SLO_SOM gN/m^3 F -SMINN_TO_S2N_S1 - mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^2 F -SMINN_TO_S2N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto SLO_SOM gN/m^3 F -SMINN_TO_S3N_S1 - mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S1_vr levdcmp mineral N flux for decomp. of ACT_SOMto PAS_SOM gN/m^3 F -SMINN_TO_S3N_S2 - mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^2 F -SMINN_TO_S3N_S2_vr levdcmp mineral N flux for decomp. of SLO_SOMto PAS_SOM gN/m^3 F -SMINN_vr levsoi soil mineral N gN/m^3 T +SMINN_TO_S1N_L1 - mineral N flux for decomp. of LIT_METto SOM_ACT gN/m^2 F +SMINN_TO_S1N_L2 - mineral N flux for decomp. of LIT_CELto SOM_ACT gN/m^2 F +SMINN_TO_S1N_S2 - mineral N flux for decomp. of SOM_SLOto SOM_ACT gN/m^2 F +SMINN_TO_S1N_S3 - mineral N flux for decomp. of SOM_PASto SOM_ACT gN/m^2 F +SMINN_TO_S2N_L3 - mineral N flux for decomp. of LIT_LIGto SOM_SLO gN/m^2 F +SMINN_TO_S2N_S1 - mineral N flux for decomp. of SOM_ACTto SOM_SLO gN/m^2 F +SMINN_TO_S3N_S1 - mineral N flux for decomp. of SOM_ACTto SOM_PAS gN/m^2 F +SMINN_TO_S3N_S2 - mineral N flux for decomp. of SOM_SLOto SOM_PAS gN/m^2 F SMIN_NH4 - soil mineral NH4 gN/m^2 T -SMIN_NH4_TO_PLANT levdcmp plant uptake of NH4 gN/m^3/s F -SMIN_NH4_vr levsoi soil mineral NH4 (vert. res.) gN/m^3 T SMIN_NO3 - soil mineral NO3 gN/m^2 T SMIN_NO3_LEACHED - soil NO3 pool loss to leaching gN/m^2/s T -SMIN_NO3_LEACHED_vr levdcmp soil NO3 pool loss to leaching gN/m^3/s F -SMIN_NO3_MASSDENS levdcmp SMIN_NO3_MASSDENS ugN/cm^3 soil F SMIN_NO3_RUNOFF - soil NO3 pool loss to runoff gN/m^2/s T -SMIN_NO3_RUNOFF_vr levdcmp soil NO3 pool loss to runoff gN/m^3/s F -SMIN_NO3_TO_PLANT levdcmp plant uptake of NO3 gN/m^3/s F -SMIN_NO3_vr levsoi soil mineral NO3 (vert. res.) gN/m^3 T -SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T SNOBCMCL - mass of BC in snow column kg/m2 T SNOBCMSL - mass of BC in top snow layer kg/m2 T SNOCAN - intercepted snow mm T @@ -1075,59 +875,55 @@ SNOW_ICE - atmospheric snow, after rai SNOW_PERSISTENCE - Length of time of continuous snow cover (nat. veg. landunits only) seconds T SNOW_SINKS - snow sinks (liquid water) mm/s T SNOW_SOURCES - snow sources (liquid water) mm/s T -SNO_ABS levsno Absorbed solar radiation in each snow layer W/m^2 F -SNO_ABS_ICE levsno Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F -SNO_BW levsno Partial density of water in the snow pack (ice + liquid) kg/m3 F -SNO_BW_ICE levsno Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F -SNO_EXISTENCE levsno Fraction of averaging period for which each snow layer existed unitless F -SNO_FRZ levsno snow freezing rate in each snow layer kg/m2/s F -SNO_FRZ_ICE levsno snow freezing rate in each snow layer (ice landunits only) mm/s F -SNO_GS levsno Mean snow grain size Microns F -SNO_GS_ICE levsno Mean snow grain size (ice landunits only) Microns F -SNO_ICE levsno Snow ice content kg/m2 F -SNO_LIQH2O levsno Snow liquid water content kg/m2 F -SNO_MELT levsno snow melt rate in each snow layer mm/s F -SNO_MELT_ICE levsno snow melt rate in each snow layer (ice landunits only) mm/s F -SNO_T levsno Snow temperatures K F -SNO_TK levsno Thermal conductivity W/m-K F -SNO_TK_ICE levsno Thermal conductivity (ice landunits only) W/m-K F -SNO_T_ICE levsno Snow temperatures (ice landunits only) K F -SNO_Z levsno Snow layer thicknesses m F -SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F SNOdTdzL - top snow layer temperature gradient (land) K/m F SOIL10 - 10-day running mean of 12cm layer soil K F SOILC_CHANGE - C change in soil gC/m^2/s T SOILC_HR - soil C heterotrophic respiration gC/m^2/s T -SOILC_vr levsoi SOIL C (vertically resolved) gC/m^3 T -SOILICE levsoi soil ice (natural vegetated and crop landunits only) kg/m2 T -SOILLIQ levsoi soil liquid water (natural vegetated and crop landunits only) kg/m2 T -SOILN_vr levdcmp SOIL N (vertically resolved) gN/m^3 T -SOILPSI levgrnd soil water potential in each soil layer MPa F SOILRESIS - soil resistance to evaporation s/m T SOILWATER_10CM - soil liquid water + ice in top 10cm of soil (veg landunits only) kg/m2 T SOMC_FIRE - C loss due to peat burning gC/m^2/s T SOMFIRE - soil organic matter fire losses gC/m^2/s F -SOM_ADV_COEF levdcmp advection term for vertical SOM translocation m/s F +SOM_ACT_C - SOM_ACT C gC/m^2 T +SOM_ACT_C_1m - SOM_ACT C to 1 meter gC/m^2 F +SOM_ACT_C_TO_SOM_PAS_C - decomp. of active soil organic C to passive soil organic C gC/m^2/s F +SOM_ACT_C_TO_SOM_SLO_C - decomp. of active soil organic C to slow soil organic ma C gC/m^2/s F +SOM_ACT_HR_S2 - Het. Resp. from active soil organic gC/m^2/s F +SOM_ACT_HR_S3 - Het. Resp. from active soil organic gC/m^2/s F +SOM_ACT_N - SOM_ACT N gN/m^2 T +SOM_ACT_N_1m - SOM_ACT N to 1 meter gN/m^2 F +SOM_ACT_N_TO_SOM_PAS_N - decomp. of active soil organic N to passive soil organic N gN/m^2 F +SOM_ACT_N_TO_SOM_SLO_N - decomp. of active soil organic N to slow soil organic ma N gN/m^2 F SOM_C_LEACHED - total flux of C from SOM pools due to leaching gC/m^2/s T -SOM_DIFFUS_COEF levdcmp diffusion coefficient for vertical SOM translocation m^2/s F SOM_N_LEACHED - total flux of N from SOM pools due to leaching gN/m^2/s F -SOWING_REASON mxsowings Reason for each crop sowing; should only be output annually unitless F -SOWING_REASON_PERHARV mxharvests Reason for sowing of each crop harvested this year; should only be output annually unitless F +SOM_PAS_C - SOM_PAS C gC/m^2 T +SOM_PAS_C_1m - SOM_PAS C to 1 meter gC/m^2 F +SOM_PAS_C_TO_SOM_ACT_C - decomp. of passive soil organic C to active soil organic C gC/m^2/s F +SOM_PAS_HR - Het. Resp. from passive soil organic gC/m^2/s F +SOM_PAS_N - SOM_PAS N gN/m^2 T +SOM_PAS_N_1m - SOM_PAS N to 1 meter gN/m^2 F +SOM_PAS_N_TO_SOM_ACT_N - decomp. of passive soil organic N to active soil organic N gN/m^2 F +SOM_SLO_C - SOM_SLO C gC/m^2 T +SOM_SLO_C_1m - SOM_SLO C to 1 meter gC/m^2 F +SOM_SLO_C_TO_SOM_ACT_C - decomp. of slow soil organic ma C to active soil organic C gC/m^2/s F +SOM_SLO_C_TO_SOM_PAS_C - decomp. of slow soil organic ma C to passive soil organic C gC/m^2/s F +SOM_SLO_HR_S1 - Het. Resp. from slow soil organic ma gC/m^2/s F +SOM_SLO_HR_S3 - Het. Resp. from slow soil organic ma gC/m^2/s F +SOM_SLO_N - SOM_SLO N gN/m^2 T +SOM_SLO_N_1m - SOM_SLO N to 1 meter gN/m^2 F +SOM_SLO_N_TO_SOM_ACT_N - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F +SOM_SLO_N_TO_SOM_PAS_N - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F SR - total soil respiration (HR + root resp) gC/m^2/s T -STEM_PROF levdcmp profile for litter C and N inputs from stems 1/m F STORAGE_CDEMAND - C use from the C storage pool gC/m^2 F STORAGE_GR - growth resp for growth sent to storage for later display gC/m^2/s F STORAGE_NDEMAND - N demand during the offset period gN/m^2 F STORVEGC - stored vegetation carbon, excluding cpool gC/m^2 T STORVEGN - stored vegetation nitrogen gN/m^2 T SUPPLEMENT_TO_SMINN - supplemental N supply gN/m^2/s T -SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F SWBGT - 2 m Simplified Wetbulb Globe Temp C T SWBGT_R - Rural 2 m Simplified Wetbulb Globe Temp C T SWBGT_U - Urban 2 m Simplified Wetbulb Globe Temp C T SWdown - atmospheric incident solar radiation W/m^2 F SWup - upwelling shortwave radiation W/m^2 F -SYEARS_PERHARV mxharvests actual sowing years for crops harvested this year; should only be output annually year F SoilAlpha - factor limiting ground evap unitless F SoilAlpha_U - urban factor limiting ground evap unitless F T10 - 10-day running mean of 2-m temperature K F @@ -1149,10 +945,8 @@ TH2OSFC - surface water temperature THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T TKE1 - top lake level eddy thermal conductivity W/(mK) T TLAI - total projected leaf area index m^2/m^2 T -TLAKE levlak lake temperature K T TOPO_COL - column-level topographic height m F TOPO_COL_ICE - column-level topographic height (ice landunits only) m F -TOPO_FORC elevclas topograephic height sent to GLC m F TOPT - topt coefficient for VOC calc non F TOTCOLC - total column carbon, incl veg and cpool but excl product pools gC/m^2 T TOTCOLCH4 - total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T @@ -1166,7 +960,7 @@ TOTLITN - total litter N TOTLITN_1m - total litter N to 1 meter gN/m^2 T TOTPFTC - total patch-level carbon, including cpool gC/m^2 T TOTPFTN - total patch-level nitrogen gN/m^2 T -TOTSOILICE - vertically summed soil cie (veg landunits only) kg/m2 T +TOTSOILICE - vertically summed soil ice (veg landunits only) kg/m2 T TOTSOILLIQ - vertically summed soil liquid water (veg landunits only) kg/m2 T TOTSOMC - total soil organic matter carbon gC/m^2 T TOTSOMC_1m - total soil organic matter carbon to 1 meter depth gC/m^2 T @@ -1202,10 +996,7 @@ TSA_U - Urban 2m air temperature TSHDW_INNER - shadewall inside surface temperature K F TSKIN - skin temperature K T TSL - temperature of near-surface soil layer (natural vegetated and crop landunits only) K T -TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T TSOI_10CM - soil temperature in top 10cm of soil K T -TSOI_ICE levgrnd soil temperature (ice landunits only) K T -TSRF_FORC elevclas surface temperature sent to GLC K F TSUNW_INNER - sunwall inside surface temperature K F TV - vegetation temperature K T TV24 - vegetation temperature (last 24hrs) K F @@ -1213,7 +1004,6 @@ TV240 - vegetation temperature (las TVEGD10 - 10 day running mean of patch daytime vegetation temperature Kelvin F TVEGN10 - 10 day running mean of patch night-time vegetation temperature Kelvin F TWS - total water storage mm T -T_SCALAR levsoi temperature inhibition of decomposition unitless T Tair - atmospheric air temperature (downscaled to columns in glacier regions) K F Tair_from_atm - atmospheric air temperature received from atmosphere (pre-downscaling) K F U10 - 10-m wind m/s T @@ -1228,9 +1018,6 @@ USTAR - aerodynamical resistance UST_LAKE - friction velocity (lakes only) m/s F VA - atmospheric wind speed plus convective velocity m/s F VCMX25T - canopy profile of vcmax25 umol/m2/s T -VEGWP nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root segments mm T -VEGWPLN nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T -VEGWPPD nvegwcs predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T VENTILATION - sensible heat flux from building ventilation W/m^2 T VOCFLXT - total VOC flux into atmosphere moles/m2/sec F VOLR - river channel total water storage m3 T @@ -1244,7 +1031,6 @@ WBT - 2 m Stull Wet Bulb WBT_R - Rural 2 m Stull Wet Bulb C T WBT_U - Urban 2 m Stull Wet Bulb C T WF - soil water as frac. of whc for top 0.05 m proportion F -WFPS levdcmp WFPS percent F WIND - atmospheric wind velocity magnitude m/s T WOODC - wood C gC/m^2 T WOODC_ALLOC - wood C eallocation gC/m^2/s T @@ -1252,7 +1038,6 @@ WOODC_LOSS - wood C loss WOOD_HARVESTC - wood harvest carbon (to product pools) gC/m^2/s T WOOD_HARVESTN - wood harvest N (to product pools) gN/m^2/s T WTGQ - surface tracer conductance m/s T -W_SCALAR levsoi Moisture (dryness) inhibition of decomposition unitless T Wind - atmospheric wind velocity magnitude m/s F XSMRPOOL - temporary photosynthate C pool gC/m^2 T XSMRPOOL_LOSS - temporary photosynthate C pool loss gC/m^2 F @@ -1271,18 +1056,233 @@ ZII - convective boundary height ZWT - water table depth (natural vegetated and crop landunits only) m T ZWT_CH4_UNSAT - depth of water table for methane production used in non-inundated area m T ZWT_PERCH - perched water table depth (natural vegetated and crop landunits only) m T -anaerobic_frac levdcmp anaerobic_frac m3/m3 F -bsw levgrnd clap and hornberger B unitless F currentPatch - currentPatch coefficient for VOC calc non F +num_iter - number of iterations unitless F +QICE_FORC elevclas qice forcing sent to GLC mm/s F +TOPO_FORC elevclas topograephic height sent to GLC m F +TSRF_FORC elevclas surface temperature sent to GLC K F +ACTUAL_IMMOB_NH4 levdcmp immobilization of NH4 gN/m^3/s F +ACTUAL_IMMOB_NO3 levdcmp immobilization of NO3 gN/m^3/s F +ACTUAL_IMMOB_vr levdcmp actual N immobilization gN/m^3/s F +CROOT_PROF levdcmp profile for litter C and N inputs from coarse roots 1/m F +CWD_C_TO_LIT_CEL_C_vr levdcmp decomp. of coarse woody debris C to cellulosic litter C gC/m^3/s F +CWD_C_TO_LIT_LIG_C_vr levdcmp decomp. of coarse woody debris C to lignin litter C gC/m^3/s F +CWD_HR_L2_vr levdcmp Het. Resp. from coarse woody debris gC/m^3/s F +CWD_HR_L3_vr levdcmp Het. Resp. from coarse woody debris gC/m^3/s F +CWD_N_TO_LIT_CEL_N_vr levdcmp decomp. of coarse woody debris N to cellulosic litter N gN/m^3 F +CWD_N_TO_LIT_LIG_N_vr levdcmp decomp. of coarse woody debris N to lignin litter N gN/m^3 F +CWD_N_vr levdcmp CWD N (vertically resolved) gN/m^3 T +CWD_PATHFRAC_L2_vr levdcmp PATHFRAC from coarse woody debris to cellulosic litter fraction F +CWD_PATHFRAC_L3_vr levdcmp PATHFRAC from coarse woody debris to lignin litter fraction F +CWD_RESP_FRAC_L2_vr levdcmp respired from coarse woody debris to cellulosic litter fraction F +CWD_RESP_FRAC_L3_vr levdcmp respired from coarse woody debris to lignin litter fraction F +DWT_DEADCROOTC_TO_CWDC levdcmp dead coarse root to CWD due to landcover change gC/m^2/s F +DWT_DEADCROOTN_TO_CWDN levdcmp dead coarse root to CWD due to landcover change gN/m^2/s F +DWT_FROOTC_TO_LIT_CEL_C levdcmp fine root to cellulosic litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_LIT_LIG_C levdcmp fine root to lignin litter due to landcover change gC/m^2/s F +DWT_FROOTC_TO_LIT_MET_C levdcmp fine root to metabolic litter due to landcover change gC/m^2/s F +DWT_FROOTN_TO_LIT_CEL_N levdcmp fine root N to cellulosic litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_LIT_LIG_N levdcmp fine root N to lignin litter due to landcover change gN/m^2/s F +DWT_FROOTN_TO_LIT_MET_N levdcmp fine root N to metabolic litter due to landcover change gN/m^2/s F +DWT_LIVECROOTC_TO_CWDC levdcmp live coarse root to CWD due to landcover change gC/m^2/s F +DWT_LIVECROOTN_TO_CWDN levdcmp live coarse root to CWD due to landcover change gN/m^2/s F +FMAX_DENIT_CARBONSUBSTRATE levdcmp FMAX_DENIT_CARBONSUBSTRATE gN/m^3/s F +FMAX_DENIT_NITRATE levdcmp FMAX_DENIT_NITRATE gN/m^3/s F +FPI_vr levdcmp fraction of potential immobilization proportion F +FROOT_PROF levdcmp profile for litter C and N inputs from fine roots 1/m F +F_DENIT_BASE levdcmp F_DENIT_BASE gN/m^3/s F +F_DENIT_vr levdcmp denitrification flux gN/m^3/s F +F_NIT_vr levdcmp nitrification flux gN/m^3/s F +GROSS_NMIN_vr levdcmp gross rate of N mineralization gN/m^3/s F +K_CWD levdcmp coarse woody debris potential loss coefficient 1/s F +K_LIT_CEL levdcmp cellulosic litter potential loss coefficient 1/s F +K_LIT_LIG levdcmp lignin litter potential loss coefficient 1/s F +K_LIT_MET levdcmp metabolic litter potential loss coefficient 1/s F +K_NITR levdcmp K_NITR 1/s F +K_NITR_H2O levdcmp K_NITR_H2O unitless F +K_NITR_PH levdcmp K_NITR_PH unitless F +K_NITR_T levdcmp K_NITR_T unitless F +K_SOM_ACT levdcmp active soil organic potential loss coefficient 1/s F +K_SOM_PAS levdcmp passive soil organic potential loss coefficient 1/s F +K_SOM_SLO levdcmp slow soil organic ma potential loss coefficient 1/s F +L1_PATHFRAC_S1_vr levdcmp PATHFRAC from metabolic litter to active soil organic fraction F +L1_RESP_FRAC_S1_vr levdcmp respired from metabolic litter to active soil organic fraction F +L2_PATHFRAC_S1_vr levdcmp PATHFRAC from cellulosic litter to active soil organic fraction F +L2_RESP_FRAC_S1_vr levdcmp respired from cellulosic litter to active soil organic fraction F +L3_PATHFRAC_S2_vr levdcmp PATHFRAC from lignin litter to slow soil organic ma fraction F +L3_RESP_FRAC_S2_vr levdcmp respired from lignin litter to slow soil organic ma fraction F +LEAF_PROF levdcmp profile for litter C and N inputs from leaves 1/m F +LIT_CEL_C_TNDNCY_VERT_TR levdcmp cellulosic litter C tendency due to vertical transport gC/m^3/s F +LIT_CEL_C_TO_SOM_ACT_C_v levdcmp decomp. of cellulosic litter C to active soil organic C gC/m^3/s F +LIT_CEL_HR_vr levdcmp Het. Resp. from cellulosic litter gC/m^3/s F +LIT_CEL_N_TNDNCY_VERT_TR levdcmp cellulosic litter N tendency due to vertical transport gN/m^3/s F +LIT_CEL_N_TO_SOM_ACT_N_v levdcmp decomp. of cellulosic litter N to active soil organic N gN/m^3 F +LIT_CEL_N_vr levdcmp LIT_CEL N (vertically resolved) gN/m^3 T +LIT_LIG_C_TNDNCY_VERT_TR levdcmp lignin litter C tendency due to vertical transport gC/m^3/s F +LIT_LIG_C_TO_SOM_SLO_C_v levdcmp decomp. of lignin litter C to slow soil organic ma C gC/m^3/s F +LIT_LIG_HR_vr levdcmp Het. Resp. from lignin litter gC/m^3/s F +LIT_LIG_N_TNDNCY_VERT_TR levdcmp lignin litter N tendency due to vertical transport gN/m^3/s F +LIT_LIG_N_TO_SOM_SLO_N_v levdcmp decomp. of lignin litter N to slow soil organic ma N gN/m^3 F +LIT_LIG_N_vr levdcmp LIT_LIG N (vertically resolved) gN/m^3 T +LIT_MET_C_TNDNCY_VERT_TR levdcmp metabolic litter C tendency due to vertical transport gC/m^3/s F +LIT_MET_C_TO_SOM_ACT_C_v levdcmp decomp. of metabolic litter C to active soil organic C gC/m^3/s F +LIT_MET_HR_vr levdcmp Het. Resp. from metabolic litter gC/m^3/s F +LIT_MET_N_TNDNCY_VERT_TR levdcmp metabolic litter N tendency due to vertical transport gN/m^3/s F +LIT_MET_N_TO_SOM_ACT_N_v levdcmp decomp. of metabolic litter N to active soil organic N gN/m^3 F +LIT_MET_N_vr levdcmp LIT_MET N (vertically resolved) gN/m^3 T +M_CWD_C_TO_FIRE_vr levdcmp coarse woody debris C fire loss gC/m^3/s F +M_CWD_N_TO_FIRE_vr levdcmp coarse woody debris N fire loss gN/m^3 F +M_LIT_CEL_C_TO_FIRE_vr levdcmp cellulosic litter C fire loss gC/m^3/s F +M_LIT_CEL_N_TO_FIRE_vr levdcmp cellulosic litter N fire loss gN/m^3 F +M_LIT_LIG_C_TO_FIRE_vr levdcmp lignin litter C fire loss gC/m^3/s F +M_LIT_LIG_N_TO_FIRE_vr levdcmp lignin litter N fire loss gN/m^3 F +M_LIT_MET_C_TO_FIRE_vr levdcmp metabolic litter C fire loss gC/m^3/s F +M_LIT_MET_N_TO_FIRE_vr levdcmp metabolic litter N fire loss gN/m^3 F +NDEP_PROF levdcmp profile for atmospheric N deposition 1/m F +NET_NMIN_vr levdcmp net rate of N mineralization gN/m^3/s F +NFIXATION_PROF levdcmp profile for biological N fixation 1/m F +POTENTIAL_IMMOB_vr levdcmp potential N immobilization gN/m^3/s F +POT_F_DENIT_vr levdcmp potential denitrification flux gN/m^3/s F +POT_F_NIT_vr levdcmp potential nitrification flux gN/m^3/s F +S1_PATHFRAC_S2_vr levdcmp PATHFRAC from active soil organic to slow soil organic ma fraction F +S1_PATHFRAC_S3_vr levdcmp PATHFRAC from active soil organic to passive soil organic fraction F +S1_RESP_FRAC_S2_vr levdcmp respired from active soil organic to slow soil organic ma fraction F +S1_RESP_FRAC_S3_vr levdcmp respired from active soil organic to passive soil organic fraction F +S2_PATHFRAC_S1_vr levdcmp PATHFRAC from slow soil organic ma to active soil organic fraction F +S2_PATHFRAC_S3_vr levdcmp PATHFRAC from slow soil organic ma to passive soil organic fraction F +S2_RESP_FRAC_S1_vr levdcmp respired from slow soil organic ma to active soil organic fraction F +S2_RESP_FRAC_S3_vr levdcmp respired from slow soil organic ma to passive soil organic fraction F +S3_PATHFRAC_S1_vr levdcmp PATHFRAC from passive soil organic to active soil organic fraction F +S3_RESP_FRAC_S1_vr levdcmp respired from passive soil organic to active soil organic fraction F +SMINN_TO_PLANT_vr levdcmp plant uptake of soil mineral N gN/m^3/s F +SMINN_TO_S1N_L1_vr levdcmp mineral N flux for decomp. of LIT_METto SOM_ACT gN/m^3 F +SMINN_TO_S1N_L2_vr levdcmp mineral N flux for decomp. of LIT_CELto SOM_ACT gN/m^3 F +SMINN_TO_S1N_S2_vr levdcmp mineral N flux for decomp. of SOM_SLOto SOM_ACT gN/m^3 F +SMINN_TO_S1N_S3_vr levdcmp mineral N flux for decomp. of SOM_PASto SOM_ACT gN/m^3 F +SMINN_TO_S2N_L3_vr levdcmp mineral N flux for decomp. of LIT_LIGto SOM_SLO gN/m^3 F +SMINN_TO_S2N_S1_vr levdcmp mineral N flux for decomp. of SOM_ACTto SOM_SLO gN/m^3 F +SMINN_TO_S3N_S1_vr levdcmp mineral N flux for decomp. of SOM_ACTto SOM_PAS gN/m^3 F +SMINN_TO_S3N_S2_vr levdcmp mineral N flux for decomp. of SOM_SLOto SOM_PAS gN/m^3 F +SMIN_NH4_TO_PLANT levdcmp plant uptake of NH4 gN/m^3/s F +SMIN_NO3_LEACHED_vr levdcmp soil NO3 pool loss to leaching gN/m^3/s F +SMIN_NO3_MASSDENS levdcmp SMIN_NO3_MASSDENS ugN/cm^3 soil F +SMIN_NO3_RUNOFF_vr levdcmp soil NO3 pool loss to runoff gN/m^3/s F +SMIN_NO3_TO_PLANT levdcmp plant uptake of NO3 gN/m^3/s F +SOILN_vr levdcmp SOIL N (vertically resolved) gN/m^3 T +SOM_ACT_C_TNDNCY_VERT_TR levdcmp active soil organic C tendency due to vertical transport gC/m^3/s F +SOM_ACT_C_TO_SOM_PAS_C_v levdcmp decomp. of active soil organic C to passive soil organic C gC/m^3/s F +SOM_ACT_C_TO_SOM_SLO_C_v levdcmp decomp. of active soil organic C to slow soil organic ma C gC/m^3/s F +SOM_ACT_HR_S2_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +SOM_ACT_HR_S3_vr levdcmp Het. Resp. from active soil organic gC/m^3/s F +SOM_ACT_N_TNDNCY_VERT_TR levdcmp active soil organic N tendency due to vertical transport gN/m^3/s F +SOM_ACT_N_TO_SOM_PAS_N_v levdcmp decomp. of active soil organic N to passive soil organic N gN/m^3 F +SOM_ACT_N_TO_SOM_SLO_N_v levdcmp decomp. of active soil organic N to slow soil organic ma N gN/m^3 F +SOM_ACT_N_vr levdcmp SOM_ACT N (vertically resolved) gN/m^3 T +SOM_ADV_COEF levdcmp advection term for vertical SOM translocation m/s F +SOM_DIFFUS_COEF levdcmp diffusion coefficient for vertical SOM translocation m^2/s F +SOM_PAS_C_TNDNCY_VERT_TR levdcmp passive soil organic C tendency due to vertical transport gC/m^3/s F +SOM_PAS_C_TO_SOM_ACT_C_v levdcmp decomp. of passive soil organic C to active soil organic C gC/m^3/s F +SOM_PAS_HR_vr levdcmp Het. Resp. from passive soil organic gC/m^3/s F +SOM_PAS_N_TNDNCY_VERT_TR levdcmp passive soil organic N tendency due to vertical transport gN/m^3/s F +SOM_PAS_N_TO_SOM_ACT_N_v levdcmp decomp. of passive soil organic N to active soil organic N gN/m^3 F +SOM_PAS_N_vr levdcmp SOM_PAS N (vertically resolved) gN/m^3 T +SOM_SLO_C_TNDNCY_VERT_TR levdcmp slow soil organic ma C tendency due to vertical transport gC/m^3/s F +SOM_SLO_C_TO_SOM_ACT_C_v levdcmp decomp. of slow soil organic ma C to active soil organic C gC/m^3/s F +SOM_SLO_C_TO_SOM_PAS_C_v levdcmp decomp. of slow soil organic ma C to passive soil organic C gC/m^3/s F +SOM_SLO_HR_S1_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SOM_SLO_HR_S3_vr levdcmp Het. Resp. from slow soil organic ma gC/m^3/s F +SOM_SLO_N_TNDNCY_VERT_TR levdcmp slow soil organic ma N tendency due to vertical transport gN/m^3/s F +SOM_SLO_N_TO_SOM_ACT_N_v levdcmp decomp. of slow soil organic ma N to active soil organic N gN/m^3 F +SOM_SLO_N_TO_SOM_PAS_N_v levdcmp decomp. of slow soil organic ma N to passive soil organic N gN/m^3 F +SOM_SLO_N_vr levdcmp SOM_SLO N (vertically resolved) gN/m^3 T +STEM_PROF levdcmp profile for litter C and N inputs from stems 1/m F +SUPPLEMENT_TO_SMINN_vr levdcmp supplemental N supply gN/m^3/s F +WFPS levdcmp WFPS percent F +anaerobic_frac levdcmp anaerobic_frac m3/m3 F diffus levdcmp diffusivity m^2/s F fr_WFPS levdcmp fr_WFPS fraction F n2_n2o_ratio_denit levdcmp n2_n2o_ratio_denit gN/gN F -num_iter - number of iterations unitless F r_psi levdcmp r_psi m F ratio_k1 levdcmp ratio_k1 none F ratio_no3_co2 levdcmp ratio_no3_co2 ratio F soil_bulkdensity levdcmp soil_bulkdensity kg/m3 F soil_co2_prod levdcmp soil_co2_prod ug C / g soil / day F +CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F +CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F +EFF_POROSITY levgrnd effective porosity = porosity - vol_ice proportion F +FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F +FRAC_ICEOLD levgrnd fraction of ice relative to the tot water proportion F +HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F +O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F +ROOTR levgrnd effective fraction of roots in each soil layer (SMS method) proportion F +RRESIS levgrnd root resistance in each soil layer proportion F +SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T +SOILPSI levgrnd soil water potential in each soil layer MPa F +TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T +TSOI_ICE levgrnd soil temperature (ice landunits only) K T +bsw levgrnd clap and hornberger B unitless F watfc levgrnd water field capacity m^3/m^3 F watsat levgrnd water saturated m^3/m^3 F +LAKEICEFRAC levlak lake layer ice mass fraction unitless F +TLAKE levlak lake temperature K T +SNO_ABS levsno Absorbed solar radiation in each snow layer W/m^2 F +SNO_ABS_ICE levsno Absorbed solar radiation in each snow layer (ice landunits only) W/m^2 F +SNO_BW levsno Partial density of water in the snow pack (ice + liquid) kg/m3 F +SNO_BW_ICE levsno Partial density of water in the snow pack (ice + liquid, ice landunits only) kg/m3 F +SNO_EXISTENCE levsno Fraction of averaging period for which each snow layer existed unitless F +SNO_FRZ levsno snow freezing rate in each snow layer kg/m2/s F +SNO_FRZ_ICE levsno snow freezing rate in each snow layer (ice landunits only) mm/s F +SNO_GS levsno Mean snow grain size Microns F +SNO_GS_ICE levsno Mean snow grain size (ice landunits only) Microns F +SNO_ICE levsno Snow ice content kg/m2 F +SNO_LIQH2O levsno Snow liquid water content kg/m2 F +SNO_MELT levsno snow melt rate in each snow layer mm/s F +SNO_MELT_ICE levsno snow melt rate in each snow layer (ice landunits only) mm/s F +SNO_T levsno Snow temperatures K F +SNO_TK levsno Thermal conductivity W/m-K F +SNO_TK_ICE levsno Thermal conductivity (ice landunits only) W/m-K F +SNO_T_ICE levsno Snow temperatures (ice landunits only) K F +SNO_Z levsno Snow layer thicknesses m F +SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F +CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T +CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T +CWD_C_vr levsoi CWD C (vertically resolved) gC/m^3 T +H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T +HR_vr levsoi total vertically resolved heterotrophic respiration gC/m^3/s T +KROOT levsoi root conductance each soil layer 1/s F +KSOIL levsoi soil conductance in each soil layer 1/s F +LIT_CEL_C_vr levsoi LIT_CEL C (vertically resolved) gC/m^3 T +LIT_LIG_C_vr levsoi LIT_LIG C (vertically resolved) gC/m^3 T +LIT_MET_C_vr levsoi LIT_MET C (vertically resolved) gC/m^3 T +O_SCALAR levsoi fraction by which decomposition is reduced due to anoxia unitless T +QROOTSINK levsoi water flux from soil to root in each soil-layer mm/s F +SMINN_vr levsoi soil mineral N gN/m^3 T +SMIN_NH4_vr levsoi soil mineral NH4 (vert. res.) gN/m^3 T +SMIN_NO3_vr levsoi soil mineral NO3 (vert. res.) gN/m^3 T +SOILC_vr levsoi SOIL C (vertically resolved) gC/m^3 T +SOILICE levsoi soil ice (natural vegetated and crop landunits only) kg/m2 T +SOILLIQ levsoi soil liquid water (natural vegetated and crop landunits only) kg/m2 T +SOM_ACT_C_vr levsoi SOM_ACT C (vertically resolved) gC/m^3 T +SOM_PAS_C_vr levsoi SOM_PAS C (vertically resolved) gC/m^3 T +SOM_SLO_C_vr levsoi SOM_SLO C (vertically resolved) gC/m^3 T +T_SCALAR levsoi temperature inhibition of decomposition unitless T +W_SCALAR levsoi Moisture (dryness) inhibition of decomposition unitless T +GDDACCUM_PERHARV mxharvests At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F +GDDHARV_PERHARV mxharvests Growing degree days (gdd) needed to harvest; should only be output annually ddays F +GRAINC_TO_FOOD_PERHARV mxharvests grain C to food per harvest; should only be output annually gC/m^2 F +HARVEST_REASON_PERHARV mxharvests Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F +HDATES mxharvests actual crop harvest dates; should only be output annually day of year F +HUI_PERHARV mxharvests At-harvest accumulated heat unit index for crop; should only be output annually ddays F +SDATES_PERHARV mxharvests actual sowing dates for crops harvested this year; should only be output annually day of year F +SOWING_REASON_PERHARV mxharvests Reason for sowing of each crop harvested this year; should only be output annually unitless F +SYEARS_PERHARV mxharvests actual sowing years for crops harvested this year; should only be output annually year F +SDATES mxsowings actual crop sowing dates; should only be output annually day of year F +SOWING_REASON mxsowings Reason for each crop sowing; should only be output annually unitless F +ALBD numrad surface albedo (direct) proportion F +ALBGRD numrad ground albedo (direct) proportion F +ALBGRI numrad ground albedo (indirect) proportion F +ALBI numrad surface albedo (indirect) proportion F +VEGWP nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root segments mm T +VEGWPLN nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T +VEGWPPD nvegwcs predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T =================================== ================ ============================================================================================== ================================================================= ======= From 28df94e93cb669f30820d902b46cc0b6cb5e8e8b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 23 Aug 2023 12:51:37 -0600 Subject: [PATCH 1419/2067] Revert "Merge branch 'master-NYRS_CROP_ACTIVE' into refactor-crop-gdd-runmeans" This reverts commit b69345639c7f913d427882f1350ad3ef2f260f2d, reversing changes made to 574f3b2710b10e46b9e62ca6b43895ce36fb4bcf. --- src/biogeochem/CropType.F90 | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index acc3f31d3f..f84c4c1821 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -35,7 +35,7 @@ module CropType ! Crop state variables structure type, public :: crop_type - real(r8), pointer :: nyrs_crop_active_patch (:) ! number of years this crop patch has been active (0 for non-crop patches) + integer , pointer :: nyrs_crop_active_patch (:) ! number of years this crop patch has been active (0 for non-crop patches) logical , pointer :: croplive_patch (:) ! patch Flag, true if planted, not harvested integer , pointer :: harvdate_patch (:) ! most recent patch harvest date; 999 if currently (or never) planted real(r8), pointer :: fertnitro_patch (:) ! patch fertilizer nitrogen @@ -216,7 +216,7 @@ subroutine InitAllocate(this, bounds) begp = bounds%begp; endp = bounds%endp - allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0.0_r8 + allocate(this%nyrs_crop_active_patch(begp:endp)) ; this%nyrs_crop_active_patch(:) = 0 allocate(this%croplive_patch (begp:endp)) ; this%croplive_patch (:) = .false. allocate(this%harvdate_patch (begp:endp)) ; this%harvdate_patch (:) = huge(1) allocate(this%fertnitro_patch (begp:endp)) ; this%fertnitro_patch (:) = spval @@ -342,11 +342,6 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='Reason for each crop harvest; should only be output annually', & ptr_patch=this%harvest_reason_thisyr_patch, default='inactive') - this%nyrs_crop_active_patch(begp:endp) = spval - call hist_addfld1d (fname='NYRS_CROP_ACTIVE', units='year', & - avgflag='I', long_name='number of years crop active', & - ptr_patch=this%nyrs_crop_active_patch, default='inactive') - end subroutine InitHistory subroutine InitCold(this, bounds) @@ -373,7 +368,7 @@ subroutine InitCold(this, bounds) g = patch%gridcell(p) ivt = patch%itype(p) - this%nyrs_crop_active_patch(p) = 0.0_r8 + this%nyrs_crop_active_patch(p) = 0 if ( grc%latdeg(g) >= 0.0_r8 .and. grc%latdeg(g) <= 30.0_r8) then this%latbaset_patch(p)=pftcon%baset(ivt)+12._r8-0.4_r8*grc%latdeg(g) @@ -541,7 +536,7 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) !----------------------------------------------------------------------- if (use_crop) then - call restartvar(ncid=ncid, flag=flag, varname='nyrs_crop_active', xtype=ncd_double, & + call restartvar(ncid=ncid, flag=flag, varname='nyrs_crop_active', xtype=ncd_int, & dim1name='pft', & long_name='Number of years this crop patch has been active (0 for non-crop patches)', & units='years', & @@ -560,7 +555,7 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) do p = bounds%begp, bounds%endp if (patch%itype(p) >= npcropmin .and. patch%itype(p) <= npcropmax .and. & patch%active(p)) then - this%nyrs_crop_active_patch(p) = real(restyear, r8) + this%nyrs_crop_active_patch(p) = restyear end if end do end if @@ -879,7 +874,7 @@ subroutine CropIncrementYear (this, num_pcropp, filter_pcropp) do fp = 1, num_pcropp p = filter_pcropp(fp) - this%nyrs_crop_active_patch(p) = this%nyrs_crop_active_patch(p) + 1.0_r8 + this%nyrs_crop_active_patch(p) = this%nyrs_crop_active_patch(p) + 1 end do end if From 963d31b4688f35074841310925ceb8f04b0b0caf Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 23 Aug 2023 23:43:37 -0600 Subject: [PATCH 1420/2067] move nearest neighbor procedure call to fates init --- Externals_CLM.cfg | 4 ++-- src/utils/clmfates_interfaceMod.F90 | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index da15c3d3d9..d805502731 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.68.0_api.27.1.0 +repo_url = https://github.com/YanlanLiu/fates +branch = cross_grid_seed required = True [externals_description] diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 5654e41661..c4420656de 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -536,12 +536,6 @@ subroutine CLMFatesGlobals2() call SetFatesGlobalElements2(use_fates) - ! Initialize the array of nearest neighbors for fates-driven grid cell communications - ! This must be called after surfrd_get_data and decompInit_lnd - if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then - call DetermineGridCellNeighbors(lneighbors) - end if - call t_stopf('fates_globals2') return @@ -621,6 +615,12 @@ subroutine init(this, bounds_proc ) call get_proc_global(ng=numg) call this%fates_seed%init(numg,numpft_fates) + ! Initialize the array of nearest neighbors for fates-driven grid cell communications + ! This must be called after surfrd_get_data and decompInit_lnd + if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then + call DetermineGridCellNeighbors(lneighbors,numg) + end if + nclumps = get_proc_clumps() allocate(this%fates(nclumps)) allocate(this%f2hmap(nclumps)) From 84fd8cc42965c4978bc7c76f7cbc9efcde138041 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 24 Aug 2023 09:54:19 -0700 Subject: [PATCH 1421/2067] encapsulate seed initalization inside disperal mode logic gate --- src/utils/clmfates_interfaceMod.F90 | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c4420656de..89b2dfe1d6 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -610,14 +610,15 @@ subroutine init(this, bounds_proc ) ! Parameter Routines call param_derived%Init( numpft_fates ) - ! To do: skip this if not running seed dispersal - ! Initialize fates global seed dispersal array for all nodes - call get_proc_global(ng=numg) - call this%fates_seed%init(numg,numpft_fates) - ! Initialize the array of nearest neighbors for fates-driven grid cell communications - ! This must be called after surfrd_get_data and decompInit_lnd + ! Initialize dispersal if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then + ! Initialize fates global seed dispersal array for all nodes + call get_proc_global(ng=numg) + call this%fates_seed%init(numg,numpft_fates) + + ! Initialize the array of nearest neighbors for fates-driven grid cell communications + ! This must be called after surfrd_get_data and decompInit_lnd call DetermineGridCellNeighbors(lneighbors,numg) end if From 2ef13f5ef2e6d9c24f204450fff21d5e10d416b2 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 24 Aug 2023 11:09:01 -0600 Subject: [PATCH 1422/2067] add check to namelist --- bld/CLMBuildNamelist.pm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c4348eefd1..bd31fda9a4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3919,10 +3919,11 @@ sub setup_logic_lai_streams { } } else { # If bgc is CN/CNDV then make sure none of the LAI settings are set - if ( defined($nl->get_value('stream_year_first_lai')) || - defined($nl->get_value('stream_year_last_lai')) || - defined($nl->get_value('model_year_align_lai')) || - defined($nl->get_value('lai_tintalgo' )) || + if ( &value_is_true($nl->get_value('use_lai_streams')) || + defined($nl->get_value('stream_year_first_lai')) || + defined($nl->get_value('stream_year_last_lai')) || + defined($nl->get_value('model_year_align_lai')) || + defined($nl->get_value('lai_tintalgo' )) || defined($nl->get_value('stream_fldfilename_lai')) ) { $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . From 392dae6009eefd60c69cc26b3b1e939176adb1a5 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 24 Aug 2023 11:13:21 -0600 Subject: [PATCH 1423/2067] update error note --- bld/CLMBuildNamelist.pm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index bd31fda9a4..97e1e5955e 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3927,7 +3927,8 @@ sub setup_logic_lai_streams { defined($nl->get_value('stream_fldfilename_lai')) ) { $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . - "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); + "stream_fldfilename_lai and use_lai_streams can't be .true.\n" . + "(eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); } } } From 087000472ea0c63be11a9e2dc864a65c016bf6d7 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 24 Aug 2023 11:19:06 -0600 Subject: [PATCH 1424/2067] make separate error --- bld/CLMBuildNamelist.pm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 97e1e5955e..d979585444 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3919,16 +3919,18 @@ sub setup_logic_lai_streams { } } else { # If bgc is CN/CNDV then make sure none of the LAI settings are set - if ( &value_is_true($nl->get_value('use_lai_streams')) || - defined($nl->get_value('stream_year_first_lai')) || + if ( &value_is_true($nl->get_value('use_lai_streams'))) { + $log->fatal_error("When bgc is NOT SP use_lai_streams cannot be .true.\n" . + "(eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); + } + if ( defined($nl->get_value('stream_year_first_lai')) || defined($nl->get_value('stream_year_last_lai')) || defined($nl->get_value('model_year_align_lai')) || defined($nl->get_value('lai_tintalgo' )) || defined($nl->get_value('stream_fldfilename_lai')) ) { $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . - "stream_fldfilename_lai and use_lai_streams can't be .true.\n" . - "(eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); + "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); } } } From ae3f73830f2827ce9e5e3a6962685293c13d5baf Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 24 Aug 2023 11:21:06 -0600 Subject: [PATCH 1425/2067] get rid of use_lai_streams=true, user_nl_clm empty to deleted --- .../testmods_dirs/clm/datm_bias_correct_cruv7/user_nl_clm | 1 - 1 file changed, 1 deletion(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/datm_bias_correct_cruv7/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/datm_bias_correct_cruv7/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/datm_bias_correct_cruv7/user_nl_clm deleted file mode 100644 index c7cfe279ee..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/datm_bias_correct_cruv7/user_nl_clm +++ /dev/null @@ -1 +0,0 @@ -use_lai_streams = .true. From 1ee1979953429023bb50b56fae228adb068c7ea8 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Thu, 24 Aug 2023 11:26:58 -0600 Subject: [PATCH 1426/2067] remove cn/cndv --- bld/CLMBuildNamelist.pm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index d979585444..3e3ab0e266 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3918,10 +3918,10 @@ sub setup_logic_lai_streams { } } } else { - # If bgc is CN/CNDV then make sure none of the LAI settings are set + # If bgc is BGC/BGCDV then make sure none of the LAI settings are set if ( &value_is_true($nl->get_value('use_lai_streams'))) { $log->fatal_error("When bgc is NOT SP use_lai_streams cannot be .true.\n" . - "(eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); + "(eg. don't use this option with BGC or BGCDV)."); } if ( defined($nl->get_value('stream_year_first_lai')) || defined($nl->get_value('stream_year_last_lai')) || @@ -3930,7 +3930,7 @@ sub setup_logic_lai_streams { defined($nl->get_value('stream_fldfilename_lai')) ) { $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . - "stream_fldfilename_lai (eg. don't use this option with BGC,CN,CNDV nor BGDCV)."); + "stream_fldfilename_lai (eg. don't use this option with BGC or BGCDV)."); } } } From 01c208da730eca335f0c24af602dd128ae107093 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 25 Aug 2023 14:46:48 -0600 Subject: [PATCH 1427/2067] Update ChangeLog --- doc/ChangeLog | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 8ab05d1a15..ab2b760ecb 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev138 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Thu Aug 24 12:33:20 MDT 2023 +Date: Fri Aug 25 14:44:22 MDT 2023 One-line Summary: Refactor max_patch_per_col and maxsoil_patches loops Purpose and description of changes @@ -31,7 +31,7 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): -Fixes #2025 +Fixes #2025 "Refactor loops that use max_patch_per_col?" Testing summary: ---------------- From ce8ccf3e11c92ffbf942c8ded2efc1cbad165804 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 25 Aug 2023 16:54:10 -0600 Subject: [PATCH 1428/2067] Draft ChangeLog/ChangeSum --- doc/ChangeLog | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 60 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ab2b760ecb..0a9515ff93 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,63 @@ =============================================================== +Tag name: ctsm5.1.dev139 +Originator(s): slevis (Samuel Levis) +Date: Fri Aug 25 16:47:45 MDT 2023 +One-line Summary: Fix problems uncovered by nag -nan tests + +Purpose and description of changes +---------------------------------- + + Fix problems uncovered by adding the -nan compilation flag for the Nag + compiler. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): + Makes progress on issue #1994 (same title) + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- PASS + + +Answer changes +-------------- + +Changes answers relative to baseline: No + + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2051 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev138 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) Date: Fri Aug 25 14:44:22 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 0d9e4d3745..4ac0f90f5e 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev139 slevis 08/28/2023 Fix problems uncovered by nag -nan tests ctsm5.1.dev138 slevis 08/25/2023 Refactor max_patch_per_col and maxsoil_patches loops ctsm5.1.dev137 slevis 08/23/2023 Surface roughness modifications ctsm5.1.dev136 multiple 08/22/2023 Change order of history fields to improve performance on derecho From 696cf9a7b2b25411e4990146b9f3e2fdca473a7f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 28 Aug 2023 10:44:31 -0600 Subject: [PATCH 1429/2067] Reworded comments as recommended by Erik Kluzek --- src/biogeophys/FrictionVelocityMod.F90 | 11 +++++++---- src/biogeophys/PhotosynthesisMod.F90 | 22 +++++++++++++++++----- 2 files changed, 24 insertions(+), 9 deletions(-) diff --git a/src/biogeophys/FrictionVelocityMod.F90 b/src/biogeophys/FrictionVelocityMod.F90 index b25f18fb1c..7cea2a22f9 100644 --- a/src/biogeophys/FrictionVelocityMod.F90 +++ b/src/biogeophys/FrictionVelocityMod.F90 @@ -750,10 +750,13 @@ subroutine FrictionVelocity(this, lbn, ubn, fn, filtern, & real(r8) , intent(in) :: ur ( lbn: ) ! wind speed at reference height [m/s] [lbn:ubn] real(r8) , intent(in) :: um ( lbn: ) ! wind speed including the stablity effect [m/s] [lbn:ubn] real(r8) , intent(out) :: ustar ( lbn: ) ! friction velocity [m/s] [lbn:ubn] - real(r8) , intent(inout) :: temp1 ( lbn: ) ! relation for potential temperature profile [lbn:ubn] (inout instead of out to prevent returning nan) - real(r8) , intent(inout) :: temp12m ( lbn: ) ! relation for potential temperature profile applied at 2-m [lbn:ubn] (inout instead of out to prevent returning nan) - real(r8) , intent(inout) :: temp2 ( lbn: ) ! relation for specific humidity profile [lbn:ubn] (inout instead of out to prevent returning nan) - real(r8) , intent(inout) :: temp22m ( lbn: ) ! relation for specific humidity profile applied at 2-m [lbn:ubn] (inout instead of out to prevent returning nan) + ! temp1, temp12m, temp2, temp22m are "inout" rather than "out" to + ! prevent returning nan when the code returns from this subroutine + ! before assigning values to these variables + real(r8) , intent(inout) :: temp1 ( lbn: ) ! relation for potential temperature profile [lbn:ubn] + real(r8) , intent(inout) :: temp12m ( lbn: ) ! relation for potential temperature profile applied at 2-m [lbn:ubn] + real(r8) , intent(inout) :: temp2 ( lbn: ) ! relation for specific humidity profile [lbn:ubn] + real(r8) , intent(inout) :: temp22m ( lbn: ) ! relation for specific humidity profile applied at 2-m [lbn:ubn] real(r8) , intent(inout) :: fm ( lbn: ) ! diagnose 10m wind (DUST only) [lbn:ubn] logical , intent(in), optional :: landunit_index ! optional argument that defines landunit or pft level ! diff --git a/src/biogeophys/PhotosynthesisMod.F90 b/src/biogeophys/PhotosynthesisMod.F90 index 0d14909fbf..6176668f19 100644 --- a/src/biogeophys/PhotosynthesisMod.F90 +++ b/src/biogeophys/PhotosynthesisMod.F90 @@ -2266,7 +2266,10 @@ subroutine hybrid(x0, p, iv, c, gb_mol, je, cair, oair, lmr_z, par_z,& real(r8), intent(in) :: cair ! Atmospheric CO2 partial pressure (Pa) real(r8), intent(in) :: oair ! Atmospheric O2 partial pressure (Pa) integer, intent(in) :: p, iv, c ! pft, c3/c4, and column index - real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) + ! gs_mol is "inout" rather than "out" to + ! prevent returning nan when the code returns from this subroutine + ! before assigning a value to this variable + real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) integer, intent(out) :: iter !number of iterations used, for record only type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type), intent(inout) :: photosyns_inst @@ -2378,7 +2381,10 @@ subroutine brent(x, x1,x2,f1, f2, tol, ip, iv, ic, gb_mol, je, cair, oair,& real(r8), intent(in) :: oair ! Atmospheric O2 partial pressure (Pa) real(r8), intent(in) :: rh_can ! inside canopy relative humidity integer, intent(in) :: ip, iv, ic ! pft, c3/c4, and column index - real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) + ! gs_mol is "inout" rather than "out" to + ! prevent returning nan when the code returns from this subroutine + ! before assigning a value to this variable + real(r8), intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type), intent(inout) :: photosyns_inst ! @@ -2568,7 +2574,10 @@ subroutine ci_func(ci, fval, p, iv, c, gb_mol, je, cair, oair, lmr_z, par_z,& real(r8) , intent(in) :: rh_can ! canopy air realtive humidity integer , intent(in) :: p, iv, c ! pft, vegetation type and column indexes real(r8) , intent(out) :: fval ! return function of the value f(ci) - real(r8) , intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) + ! gs_mol is "inout" rather than "out" to + ! prevent returning nan when the code returns from this subroutine + ! before assigning a value to this variable + real(r8) , intent(inout) :: gs_mol ! leaf stomatal conductance (umol H2O/m**2/s) type(atm2lnd_type) , intent(in) :: atm2lnd_inst type(photosyns_type) , intent(inout) :: photosyns_inst ! @@ -4064,8 +4073,11 @@ subroutine brent_PHS(xsun, x1sun, x2sun, f1sun, f2sun, xsha, x1sha, x2sha, f1sha real(r8), intent(in) :: lmr_z_sun, lmr_z_sha ! canopy layer: leaf maintenance respiration rate (umol CO2/m**2/s) real(r8), intent(in) :: par_z_sun, par_z_sha ! par absorbed per unit lai for canopy layer (w/m**2) real(r8), intent(in) :: rh_can ! inside canopy relative humidity - real(r8), intent(inout) :: gs_mol_sun ! sunlit leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) - real(r8), intent(inout) :: gs_mol_sha ! shaded leaf stomatal conductance (umol H2O/m**2/s) (inout instead of out to prevent returning nan) + ! gs_mol_s* are "inout" rather than "out" to + ! prevent returning nan when the code returns from this subroutine + ! before assigning values to these variables + real(r8), intent(inout) :: gs_mol_sun ! sunlit leaf stomatal conductance (umol H2O/m**2/s) + real(r8), intent(inout) :: gs_mol_sha ! shaded leaf stomatal conductance (umol H2O/m**2/s) real(r8), intent(inout) :: bsun ! sunlit canopy transpiration wetness factor (0 to 1) real(r8), intent(inout) :: bsha ! shaded canopy transpiration wetness factor (0 to 1) real(r8), intent(in) :: qsatl ! leaf specific humidity [kg/kg] From 1e2e2c35d9568c94eac6cb606f37c18294158682 Mon Sep 17 00:00:00 2001 From: Bill Sacks Date: Mon, 28 Aug 2023 15:23:52 -0600 Subject: [PATCH 1430/2067] Add a note in README --- doc/README.CHECKLIST.master_tags | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/doc/README.CHECKLIST.master_tags b/doc/README.CHECKLIST.master_tags index 31c09895be..53540aaf37 100644 --- a/doc/README.CHECKLIST.master_tags +++ b/doc/README.CHECKLIST.master_tags @@ -55,6 +55,14 @@ https://github.com/ESCOMP/ctsm/wiki/CTSM-development-workflow ---- THE FOLLOWING CAN ONLY BE DONE BY INTEGRATORS ---- +NOTE (especially for new integrators): Be sure to follow the recommended +git setup in +. +Especially note that you should never use something like `git merge +escomp/master` to merge the upstream master branch into your local copy: +instead, you should always use `git pull` with the recommended +configuration settings (or `git merge --ff-only`) for that scenario. + (7) Merge the PR to master when review is approved (8) Compare master to branch show that they are identical From a4313107465fc943253f5c0a30157638745709c9 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 29 Aug 2023 10:20:21 -0600 Subject: [PATCH 1431/2067] initial commit --- src/biogeochem/SatellitePhenologyMod.F90 | 49 ++++++++++++++++++++++++ src/main/clm_driver.F90 | 37 +----------------- 2 files changed, 51 insertions(+), 35 deletions(-) diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90 index 3e9341f430..54f2dcdb32 100644 --- a/src/biogeochem/SatellitePhenologyMod.F90 +++ b/src/biogeochem/SatellitePhenologyMod.F90 @@ -257,6 +257,55 @@ subroutine interpMonthlyVeg (bounds, canopystate_inst) end subroutine interpMonthlyVeg !============================================================================== + + logical function do_interpMonthlyVeg(use_cn, use_fates, use_fates_sp, doalb, n_drydep) + ! + ! !DESCRIPTION: + ! returns whether or not to conduct interpMonthlyVeg subroutine + ! + ! !ARGUMENTS: + logical, intent(in) :: use_cn ! are we using the big-leaf, BGC version of model? + logical, intent(in) :: use_fates ! are we running FATES? + logical, intent(in) :: use_fates_sp ! are we running FATES-SP? + logical, intent(in) :: doalb ! true if time for surface albedo calc + integer, intent(in) :: n_drydep ! number in drypdep list + + if (use_cn .and. n_drydep > 0) then + + ! For dry-deposition need to call CLMSP so that mlaidiff is obtained + ! NOTE: This is also true of FATES below + do_interpMonthlyVeg = .true. + + else if (use_fates .and. use_fates_sp) then + + ! For FATES-Specified phenology mode interpolate the weights for + ! time-interpolation of monthly vegetation data (as in SP mode below) + ! Also for FATES with dry-deposition as above need to call CLMSP so that mlaidiff is obtained + !if ( use_fates_sp .or. (n_drydep > 0 ) ) then ! Replace with this when we have dry-deposition working + ! For now don't allow for dry-deposition because of issues in #1044 EBK Jun/17/2022 + do_interpMonthlyVeg = .true. + + else if (doalb .or. n_drydep > 0) then + + ! Determine weights for time interpolation of monthly vegetation data. + ! This also determines whether it is time to read new monthly vegetation and + ! obtain updated leaf area index [mlai1,mlai2], stem area index [msai1,msai2], + ! vegetation top [mhvt1,mhvt2] and vegetation bottom [mhvb1,mhvb2]. The + ! weights obtained here are used in subroutine SatellitePhenology to obtain time + ! interpolated values. + ! This is also done for FATES-SP mode above + do_interpMonthlyVeg = .true. + + else + + do_interpMonthlyVeg = .false. + + end if + + end function do_interpMonthlyVeg + + !============================================================================== + subroutine readAnnualVegetation (bounds, canopystate_inst) ! ! !DESCRIPTION: diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 3a5e981d74..61b5fc3ac7 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -58,7 +58,7 @@ module clm_driver use UrbanRadiationMod , only : UrbanRadiation ! use SoilBiogeochemVerticalProfileMod , only : SoilBiogeochemVerticalProfile - use SatellitePhenologyMod , only : SatellitePhenology, interpMonthlyVeg + use SatellitePhenologyMod , only : SatellitePhenology, interpMonthlyVeg, do_interpMonthlyVeg use ndepStreamMod , only : ndep_interp use cropcalStreamMod , only : cropcal_advance, cropcal_interp use ch4Mod , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check @@ -226,43 +226,10 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Done in SP mode, FATES-SP mode and also when dry-deposition is active ! ============================================================================ - if (use_cn) then - ! For dry-deposition need to call CLMSP so that mlaidiff is obtained - ! NOTE: This is also true of FATES below - if ( n_drydep > 0 ) then - call t_startf('interpMonthlyVeg') - call interpMonthlyVeg(bounds_proc, canopystate_inst) - call t_stopf('interpMonthlyVeg') - endif - - elseif(use_fates) then - - ! For FATES-Specified phenology mode interpolate the weights for - ! time-interpolation of monthly vegetation data (as in SP mode below) - ! Also for FATES with dry-deposition as above need to call CLMSP so that mlaidiff is obtained - !if ( use_fates_sp .or. (n_drydep > 0 ) ) then ! Replace with this when we have dry-deposition working - ! For now don't allow for dry-deposition because of issues in #1044 EBK Jun/17/2022 - if ( use_fates_sp ) then + if (do_interpMonthlyVeg(use_cn, use_fates, use_fates_sp, doalb, n_drydep)) then call t_startf('interpMonthlyVeg') call interpMonthlyVeg(bounds_proc, canopystate_inst) call t_stopf('interpMonthlyVeg') - end if - - else - - ! Determine weights for time interpolation of monthly vegetation data. - ! This also determines whether it is time to read new monthly vegetation and - ! obtain updated leaf area index [mlai1,mlai2], stem area index [msai1,msai2], - ! vegetation top [mhvt1,mhvt2] and vegetation bottom [mhvb1,mhvb2]. The - ! weights obtained here are used in subroutine SatellitePhenology to obtain time - ! interpolated values. - ! This is also done for FATES-SP mode above - if ( doalb .or. ( n_drydep > 0 ) )then - call t_startf('interpMonthlyVeg') - call interpMonthlyVeg(bounds_proc, canopystate_inst) - call t_stopf('interpMonthlyVeg') - end if - end if ! ================================================================================== From 460fa670d76b0c6e7a615075faff26154962b2b2 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 29 Aug 2023 10:26:40 -0600 Subject: [PATCH 1432/2067] add new function to public list --- src/biogeochem/SatellitePhenologyMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90 index 54f2dcdb32..7714af02eb 100644 --- a/src/biogeochem/SatellitePhenologyMod.F90 +++ b/src/biogeochem/SatellitePhenologyMod.F90 @@ -28,6 +28,7 @@ module SatellitePhenologyMod public :: SatellitePhenologyInit ! Dynamically allocate memory public :: interpMonthlyVeg ! interpolate monthly vegetation data public :: readAnnualVegetation ! Read in annual vegetation (needed for Dry-deposition) + public :: do_interpMonthlyVeg ! whether or not to call interpMonthlyVeg ! ! !PRIVATE MEMBER FUNCTIONS: private :: readMonthlyVegetation ! read monthly vegetation data for two months From 6282180d9b75ccc3d799305f511f5f210b4cb2c4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 29 Aug 2023 15:48:59 -0600 Subject: [PATCH 1433/2067] FSURDATMODIFYCTSM now calls fsurdat_modifier directly. This avoids using subprocess.run(), which should hopefully reduce issues related to user environment. However, it does require that all the Python dependencies are loaded. This can be accomplished by activating the ctsm_pylib environment before calling run_sys_tests or cime/scripts/create_test. --- cime_config/SystemTests/fsurdatmodifyctsm.py | 27 ++++++++++++-------- 1 file changed, 17 insertions(+), 10 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index d2a9c04312..083cdc2767 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -5,11 +5,18 @@ import os import re -import systemtest_utils as stu from CIME.SystemTests.system_tests_common import SystemTestsCommon from CIME.XML.standard_module_setup import * from CIME.SystemTests.test_utils.user_nl_utils import append_to_user_nl_files +# For calling fsurdat_modifier +from argparse import Namespace +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) +from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier + logger = logging.getLogger(__name__) @@ -66,16 +73,16 @@ def _create_config_file(self): cfg_out.write(line) def _run_modify_fsurdat(self): - tool_path = os.path.join(self._ctsm_root, "tools/modify_input_files/fsurdat_modifier") - - self._case.load_env(reset=True) - command = f"python3 {tool_path} {self._cfg_file_path}" - stu.run_python_script( - self._get_caseroot(), - "ctsm_pylib", - command, - tool_path, + fsurdat_modifier_args = Namespace( + cfg_path=self._cfg_file_path, + debug=False, + fsurdat_in="UNSET", + fsurdat_out="UNSET", + overwrite=False, + silent=False, + verbose=False, ) + fsurdat_modifier(fsurdat_modifier_args) def _modify_user_nl(self): append_to_user_nl_files( From e978870f2b4ad56b9d677e1680333855b0001c3e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 30 Aug 2023 10:55:48 -0600 Subject: [PATCH 1434/2067] update for seed dispersal restarts --- src/utils/clmfates_interfaceMod.F90 | 28 +++++++++++++++++++++------- 1 file changed, 21 insertions(+), 7 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 89b2dfe1d6..e1cb525fa1 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -166,7 +166,7 @@ module CLMFatesInterfaceMod use dynHarvestMod , only : dynHarvest_interp_resolve_harvesttypes use FatesConstantsMod , only : hlm_harvest_area_fraction use FatesConstantsMod , only : hlm_harvest_carbon - use FatesDispersalMod , only : lneighbors, dispersal_type, IsItDispersalTime + use FatesDispersalMod , only : lneighbors, dispersal_type, IsItDispersalTime use perf_mod , only : t_startf, t_stopf implicit none @@ -1405,9 +1405,8 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & g = col%gridcell(c) ! Accumulate seeds from sites to the gridcell local outgoing buffer - if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) & - .and. IsItDispersalTime()) then - this%fates_seed%outgoing_local(g,:) = this%fates_seed%outgoing_local(g,:) + this%fates(nc)%sites(s)%seed_out(:) + if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) .and. IsItDispersalTime()) then + this%fates_seed%outgoing_local(g,:) = this%fates_seed%outgoing_local(g,:) + this%fates(nc)%sites(s)%seed_out(:) end if ! Other modules may have AI's we only flush values @@ -1843,6 +1842,9 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & end do !$OMP END PARALLEL DO + ! Disperse seeds + call this%WrapSeedGlobal(is_restart_flag=.true.) + end if call t_stopf('fates_restart') @@ -2633,7 +2635,7 @@ end subroutine wrap_canopy_radiation ! ====================================================================================== - subroutine WrapSeedGlobal(this) + subroutine WrapSeedGlobal(this,is_restart_flag) ! Call mpi procedure to provide the global seed output distribution array to every gridcell. ! This could be conducted with a more sophisticated halo-type structure or distributed graph. @@ -2644,20 +2646,31 @@ subroutine WrapSeedGlobal(this) ! Arguments class(hlm_fates_interface_type), intent(inout) :: this + logical, optional :: is_restart_flag ! Local integer :: numg ! total number of gridcells across all processors integer :: ier ! error code integer :: g ! gridcell index + logical :: set_flag ! local logical variable to pass to IsItDispersalTime + type (neighbor_type), pointer :: neighbor + ! If WrapSeedGlobal is being called at the end a fates restart call, + ! pass .false. to the set_dispersed_flag to avoid updating the + ! global dispersal date + set_flag = .true. + if (present(is_restart_flag)) then + if (is_restart_flag) set_flag = .false. + end if + ! Check if seed dispersal mode is 'turned on', if not return to calling procedure if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return call t_startf('fates-seed-mpi_reduce') - if (IsItDispersalTime(setdispersedflag=.true.)) then + if (IsItDispersalTime(setdispersedflag=set_flag)) then ! Re-initialize incoming seed buffer for this time step this%fates_seed%incoming_global(:,:) = 0._r8 @@ -2716,7 +2729,6 @@ subroutine wrap_seed_dispersal(this,bounds_clump) nc = bounds_clump%clump_index - ! Add fates check for seed dispersal mode do s = 1, this%fates(nc)%nsites c = this%f2hmap(nc)%fcolumn(s) g = col%gridcell(c) @@ -2728,11 +2740,13 @@ subroutine wrap_seed_dispersal(this,bounds_clump) this%fates(nc)%sites(s)%seed_out(:) = 0._r8 ! reset seed_out else ! if it is not the dispersing time, pass in zero + ! if this is a restart, then skip this entirely this%fates(nc)%sites(s)%seed_in(:) = 0._r8 end if end do + call t_stopf('fates-seed-disperse') end subroutine wrap_seed_dispersal From 2d76faa926846cceca454178cc7d8fab58214c1b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 31 Aug 2023 13:29:38 -0600 Subject: [PATCH 1435/2067] Moved fraction_tilled calculation to new function get_fraction_tilled(). This enables unit testing of this code. --- src/soilbiogeochem/TillageMod.F90 | 44 +++++++++++++++++++++++-------- 1 file changed, 33 insertions(+), 11 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 248d2bd4cb..7d1934378b 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -244,6 +244,36 @@ subroutine get_tillage_multipliers(tillage_mults, idop) end subroutine get_tillage_multipliers + function get_fraction_tilled(zisoi, j, max_tillage_depth_gft) result(fraction_tilled) + ! !ARGUMENTS + ! zisoi and max_tillage_depth are passed to this function, rather than using from clm_varcon or + ! parent scope (respectively), to enable unit testing. + real(r8) :: zisoi(:) ! Soil layer interface depths + integer :: j ! Soil layer + real(r8) :: max_tillage_depth_gft ! Maximum tillage depth + ! !LOCAL VARIABLES + real(r8) :: layer_top ! Depth (cm) of the top of this soil layer. zisoi is the depth of the bottom. + real(r8) :: layer_thickness ! Thickness of this soil layer (m) + ! !RESULT + real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth + + if (j == 1) then + layer_top = 0._r8 + else + layer_top = zisoi(j-1) + end if + + if (layer_top > max_tillage_depth_gft) then + fraction_tilled = 0._r8 + return + end if + + layer_thickness = zisoi(j) - layer_top + fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth_gft - layer_top) / layer_thickness)) + + end function get_fraction_tilled + + subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! !DESCRIPTION: ! @@ -266,16 +296,11 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) real :: sumwt ! sum of all patch weights, to check real(r8), dimension(ndecomp_pools) :: tillage_mults real(r8), dimension(ndecomp_pools) :: tillage_mults_1patch - real(r8) :: layer_top ! Depth (cm) of the top of this soil layer. zisoi is the depth of the bottom. - real(r8) :: layer_thickness ! Thickness of this soil layer (m) real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth - if (j == 1) then - layer_top = 0._r8 - else - layer_top = zisoi(j-1) - end if - if (.not. col%active(c) .or. layer_top > max_tillage_depth) then + ! Skip tillage if column is inactive or this layer doesn't get tilled + fraction_tilled = get_fraction_tilled(zisoi, j, max_tillage_depth) + if (.not. col%active(c) .or. fraction_tilled == 0._r8) then return end if @@ -313,9 +338,6 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) end if ! Adjust tillage_mults to consider fraction of this layer that's within tillage depth. - ! TODO: Unit-test this - layer_thickness = zisoi(j) - layer_top - fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth - layer_top) / layer_thickness)) tillage_mults = tillage_mults * fraction_tilled & + 1._r8 * (1._r8 - fraction_tilled) From 376b66b90fa5348d9d30b241394ccad0cd5bad5c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 31 Aug 2023 16:51:10 -0600 Subject: [PATCH 1436/2067] run_sys_tests: Check availability of modules needed for some SystemTests. Specifically, FSURDATMODIFYCTSM and RXCROPMATURITY. --- python/ctsm/crop_calendars/cropcal_module.py | 10 +++++--- python/ctsm/crop_calendars/generate_gdds.py | 13 +++++------ .../crop_calendars/generate_gdds_functions.py | 18 +++++++++------ python/ctsm/run_sys_tests.py | 23 +++++++++++++++++++ 4 files changed, 47 insertions(+), 17 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 73176431ba..1d58e2fbab 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -1,6 +1,3 @@ -# Import the CTSM Python utilities -import cropcal_utils as utils - import numpy as np import xarray as xr import warnings @@ -8,6 +5,13 @@ import os import glob +# Import the CTSM Python utilities +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) +import ctsm.crop_calendars.cropcal_utils as utils + try: import pandas as pd except: diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 6000c12e41..9fe1c26e14 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -1,6 +1,3 @@ -# Import supporting functions -import generate_gdds_functions as gddfn - paramfile_dir = "/glade/p/cesmdata/cseg/inputdata/lnd/clm2/paramdata" # Import other shared functions @@ -8,10 +5,12 @@ import inspect import sys -currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))) -parentdir = os.path.dirname(currentdir) -sys.path.insert(0, parentdir) -import cropcal_module as cc +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) +import ctsm.crop_calendars.cropcal_module as cc +import ctsm.crop_calendars.generate_gdds_functions as gddfn # Import everything else import os diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index d050a46bd8..20c958817a 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -1,6 +1,3 @@ -# Import the CTSM Python utilities -import cropcal_utils as utils - import numpy as np import xarray as xr import warnings @@ -9,11 +6,18 @@ import datetime as dt from importlib import util as importlib_util -import cropcal_module as cc +# Import the CTSM Python utilities +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" +) +import sys +sys.path.insert(1, _CTSM_PYTHON) +import ctsm.crop_calendars.cropcal_utils as utils +import ctsm.crop_calendars.cropcal_module as cc can_plot = True try: - from cropcal_figs_module import * + from ctsm.crop_calendars.cropcal_figs_module import * from matplotlib.transforms import Bbox warnings.filterwarnings( @@ -25,10 +29,10 @@ message="Iteration over multi-part geometries is deprecated and will be removed in Shapely 2.0. Use the `geoms` property to access the constituent parts of a multi-part geometry.", ) - print("Will (attempt to) produce harvest requirement maps.") + print("Will (attempt to) produce harvest requirement map figure files.") except: - print("Will NOT produce harvest requirement maps.") + print("Will NOT produce harvest requirement map figure files.") can_plot = False diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 992f2b544a..83c468ab88 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -231,10 +231,14 @@ def run_sys_tests( _make_cs_status_non_suite(testroot, testid_base) if testfile: test_args = ["--testfile", os.path.abspath(testfile)] + with open(test_args[1], "r") as f: + testname_list = f.readlines() elif testlist: test_args = testlist + testname_list = testlist else: raise RuntimeError("None of suite_name, testfile or testlist were provided") + _try_systemtests(testname_list) _run_create_test( cime_path=cime_path, test_args=test_args, @@ -692,12 +696,31 @@ def _run_test_suite( ) +def _try_systemtests(testname_list): + errMsg = " can't be loaded. Do you need to activate the ctsm_pylib conda environment?" + if any(["FSURDATMODIFYCTSM" in t for t in testname_list]): + try: + import ctsm.modify_input_files.modify_fsurdat + except ModuleNotFoundError: + raise ModuleNotFoundError("modify_fsurdat" + errMsg) + if any(["RXCROPMATURITY" in t for t in testname_list]): + try: + import ctsm.crop_calendars.make_fsurdat_all_crops_everywhere + except ModuleNotFoundError: + raise ModuleNotFoundError("make_fsurdat_all_crops_everywhere.py" + errMsg) + try: + import ctsm.crop_calendars.generate_gdds + except ModuleNotFoundError: + raise ModuleNotFoundError("generate_gdds.py" + errMsg) + + def _get_compilers_for_suite(suite_name, machine_name): test_data = get_tests_from_xml(xml_machine=machine_name, xml_category=suite_name) if not test_data: raise RuntimeError( "No tests found for suite {} on machine {}".format(suite_name, machine_name) ) + _try_systemtests([t["testname"] for t in test_data]) compilers = sorted({one_test["compiler"] for one_test in test_data}) logger.info("Running with compilers: %s", compilers) return compilers From 3a93b1a229ca0490f4a77954da60a322ee3c9300 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 1 Sep 2023 11:45:59 -0600 Subject: [PATCH 1437/2067] Only import fsurdat_modifier in setup phase. This avoids "numpy not found" error for FSURDATMODIFYCTSM, but this isn't a solution for RXCROPMATURITY, because that test actually does need the right conda environment during the run phase (which is when generate_gdds.py is called). --- cime_config/SystemTests/fsurdatmodifyctsm.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 083cdc2767..43b155dc0b 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -15,7 +15,6 @@ os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" ) sys.path.insert(1, _CTSM_PYTHON) -from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier logger = logging.getLogger(__name__) @@ -82,6 +81,7 @@ def _run_modify_fsurdat(self): silent=False, verbose=False, ) + from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier fsurdat_modifier(fsurdat_modifier_args) def _modify_user_nl(self): From 9893c8032e91c970b9b1afae9762c23d61d6c588 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 1 Sep 2023 14:00:45 -0600 Subject: [PATCH 1438/2067] Remove sys.path.insert()s from crop calendar Python files. --- python/ctsm/crop_calendars/cropcal_module.py | 4 ---- python/ctsm/crop_calendars/generate_gdds.py | 4 ---- python/ctsm/crop_calendars/generate_gdds_functions.py | 5 ----- 3 files changed, 13 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 1d58e2fbab..b2be2fd3e8 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -6,10 +6,6 @@ import glob # Import the CTSM Python utilities -_CTSM_PYTHON = os.path.join( - os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" -) -sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils try: diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 9fe1c26e14..649057e1b2 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -5,10 +5,6 @@ import inspect import sys -_CTSM_PYTHON = os.path.join( - os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" -) -sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_module as cc import ctsm.crop_calendars.generate_gdds_functions as gddfn diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 20c958817a..6d6e2a7d54 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -7,11 +7,6 @@ from importlib import util as importlib_util # Import the CTSM Python utilities -_CTSM_PYTHON = os.path.join( - os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" -) -import sys -sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils import ctsm.crop_calendars.cropcal_module as cc From 10dffb6947bbde05794dfec7fa4c7bf75ed9cc23 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Sep 2023 15:26:37 -0600 Subject: [PATCH 1439/2067] refactor fates dispersal MPI reduction using gather --- src/utils/clmfates_interfaceMod.F90 | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index e1cb525fa1..17441d8b23 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -573,6 +573,8 @@ subroutine init(this, bounds_proc ) ! is not turned on ! --------------------------------------------------------------------------------- + use spmdMod, only : npes + use decompMod, only : procinfo use FatesInterfaceTypesMod, only : numpft_fates => numpft use FatesParameterDerivedMod, only : param_derived use subgridMod, only : natveg_patch_exists @@ -613,13 +615,14 @@ subroutine init(this, bounds_proc ) ! Initialize dispersal if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then + ! Initialize fates global seed dispersal array for all nodes call get_proc_global(ng=numg) - call this%fates_seed%init(numg,numpft_fates) + call this%fates_seed%init(npes,numg,procinfo%ncells,numpft_fates) ! Initialize the array of nearest neighbors for fates-driven grid cell communications ! This must be called after surfrd_get_data and decompInit_lnd - call DetermineGridCellNeighbors(lneighbors,numg) + call DetermineGridCellNeighbors(lneighbors,this%fates_seed,numg) end if nclumps = get_proc_clumps() @@ -1406,7 +1409,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! Accumulate seeds from sites to the gridcell local outgoing buffer if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) .and. IsItDispersalTime()) then - this%fates_seed%outgoing_local(g,:) = this%fates_seed%outgoing_local(g,:) + this%fates(nc)%sites(s)%seed_out(:) + this%fates_seed%outgoing_local(g,:) = this%fates(nc)%sites(s)%seed_out(:) end if ! Other modules may have AI's we only flush values @@ -2640,8 +2643,9 @@ subroutine WrapSeedGlobal(this,is_restart_flag) ! Call mpi procedure to provide the global seed output distribution array to every gridcell. ! This could be conducted with a more sophisticated halo-type structure or distributed graph. + use decompMod, only : procinfo use spmdMod, only : MPI_REAL8, MPI_SUM, mpicom - use FatesDispersalMod, only : lneighbors, neighbor_type + use FatesDispersalMod, only : lneighbors, neighbor_type, dispersal_type use FatesInterfaceTypesMod, only : numpft_fates => numpft ! Arguments @@ -2655,7 +2659,7 @@ subroutine WrapSeedGlobal(this,is_restart_flag) logical :: set_flag ! local logical variable to pass to IsItDispersalTime - type (neighbor_type), pointer :: neighbor + type (neighbor_type), pointer :: neighbor ! If WrapSeedGlobal is being called at the end a fates restart call, ! pass .false. to the set_dispersed_flag to avoid updating the @@ -2675,16 +2679,12 @@ subroutine WrapSeedGlobal(this,is_restart_flag) ! Re-initialize incoming seed buffer for this time step this%fates_seed%incoming_global(:,:) = 0._r8 - ! Re-initialize the outgoing global seed array buffer - this%fates_seed%outgoing_global(:,:) = 1.e6_r8 ! Is this acting as seed rain? + ! Distribute obtgoing seed data from all nodes to all nodes + call MPI_Allgatherv(this%fates_seed%outgoing_local, procinfo%ncells*numpft_fates, MPI_REAL8, & + this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array, & + MPI_REAL8, mpicom, ier) - ! Distribute and sum outgoing seed data from all nodes to all nodes - ! mpi_allgather should work here as well since gridcells values are not split across nodes - ! This would allow for reduction in the outgoing local array size call get_proc_global(ng=numg) - call mpi_allreduce(this%fates_seed%outgoing_local, this%fates_seed%outgoing_global, & - numg*numpft_fates, MPI_REAL8, MPI_SUM, mpicom, ier) - do g = 1, numg ! Calculate the current gridcell incoming seed for each gridcell index From e628c71861e71243366b8861912f4615c2aa68aa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 31 Aug 2023 13:53:37 -0600 Subject: [PATCH 1440/2067] Added unit test for get_fraction_tilled(). --- src/main/readParamsMod.F90 | 2 +- src/soilbiogeochem/CMakeLists.txt | 1 + src/soilbiogeochem/TillageMod.F90 | 11 +++-- src/soilbiogeochem/test/CMakeLists.txt | 1 + .../test/tillage_test/CMakeLists.txt | 3 ++ .../test/tillage_test/test_tillage.pf | 46 +++++++++++++++++++ 6 files changed, 59 insertions(+), 5 deletions(-) create mode 100644 src/soilbiogeochem/test/tillage_test/CMakeLists.txt create mode 100644 src/soilbiogeochem/test/tillage_test/test_tillage.pf diff --git a/src/main/readParamsMod.F90 b/src/main/readParamsMod.F90 index 31bba00f01..c11a741198 100644 --- a/src/main/readParamsMod.F90 +++ b/src/main/readParamsMod.F90 @@ -106,7 +106,7 @@ subroutine readParameters (photosyns_inst) call readSoilBiogeochemDecompBgcParams(ncid) end if call readSoilBiogeochemDecompParams(ncid) - call readTillageParams(ncid) + call readTillageParams(ncid, NLFilename_in) call readSoilBiogeochemLittVertTranspParams(ncid) call readSoilBiogeochemNitrifDenitrifParams(ncid) call readSoilBiogeochemNLeachingParams(ncid) diff --git a/src/soilbiogeochem/CMakeLists.txt b/src/soilbiogeochem/CMakeLists.txt index f4545a6a76..e2baa2d1b2 100644 --- a/src/soilbiogeochem/CMakeLists.txt +++ b/src/soilbiogeochem/CMakeLists.txt @@ -7,6 +7,7 @@ list(APPEND clm_sources SoilBiogeochemStateType.F90 SoilBiogeochemNitrogenStateType.F90 SoilBiogeochemNitrogenFluxType.F90 + TillageMod.F90 ) sourcelist_to_parent(clm_sources) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 7d1934378b..ced9216c74 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -18,6 +18,7 @@ module TillageMod public :: readParams public :: get_do_tillage public :: get_apply_tillage_multipliers + public :: get_fraction_tilled ! !PUBLIC DATA MEMBERS character(len=CS), public :: tillage_mode ! off, low, high integer, parameter, public :: ntill_intensities_max = 2 @@ -36,15 +37,16 @@ module TillageMod contains !============================================================================== - subroutine readParams_namelist() + subroutine readParams_namelist(NLFilename) ! ! Read namelist parameters related to tillage. ! ! !USES: use spmdMod , only : masterproc, mpicom - use controlMod , only : NLFilename use clm_nlUtilsMod , only : find_nlgroup_name use shr_mpi_mod , only : shr_mpi_bcast + ! !ARGUMENTS: + character(len=*), intent(in) :: NLFilename ! Namelist filename ! ! !LOCAL VARIABLES integer :: nu_nml ! unit for namelist file @@ -155,14 +157,15 @@ subroutine readParams_netcdf(ncid) end subroutine readParams_netcdf - subroutine readParams(ncid) + subroutine readParams(ncid, NLFilename) ! !USES use ncdio_pio , only : file_desc_t ! ! !ARGUMENTS: type(file_desc_t),intent(inout) :: ncid ! pio netCDF file id + character(len=*), intent(in) :: NLFilename ! Namelist filename - call readParams_namelist() + call readParams_namelist(NLFilename) call readParams_netcdf(ncid) end subroutine readParams diff --git a/src/soilbiogeochem/test/CMakeLists.txt b/src/soilbiogeochem/test/CMakeLists.txt index 988cb531b5..22d8fba60f 100644 --- a/src/soilbiogeochem/test/CMakeLists.txt +++ b/src/soilbiogeochem/test/CMakeLists.txt @@ -1 +1,2 @@ add_subdirectory(ACSpinup_test) +add_subdirectory(tillage_test) diff --git a/src/soilbiogeochem/test/tillage_test/CMakeLists.txt b/src/soilbiogeochem/test/tillage_test/CMakeLists.txt new file mode 100644 index 0000000000..fbc550dd03 --- /dev/null +++ b/src/soilbiogeochem/test/tillage_test/CMakeLists.txt @@ -0,0 +1,3 @@ +add_pfunit_ctest(tillage + TEST_SOURCES "test_tillage.pf" + LINK_LIBRARIES clm csm_share esmf_wrf_timemgr) diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf new file mode 100644 index 0000000000..a7013e49b1 --- /dev/null +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -0,0 +1,46 @@ +module test_tillage + + ! Tests of the functions in TillageMod + + use funit + + use shr_kind_mod , only : r8 => shr_kind_r8 + use TillageMod, only : get_fraction_tilled + + implicit none + save + + real(r8), parameter :: tol = 1.e-8_r8 + +contains + + @Test + subroutine test_get_fraction_tilled() + + real(r8) :: zisoi(5) ! Depth of soil interfaces (bottom of each layer) + integer :: j ! Soil layer + real(r8) :: max_tillage_depth + + zisoi = [0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8, 1._r8] + + max_tillage_depth = 10._r8 + do j = 1, 5 + @assertEqual(1._r8, get_fraction_tilled(zisoi, j, max_tillage_depth)) + end do + + max_tillage_depth = 0._r8 + do j = 1, 5 + @assertEqual(0._r8, get_fraction_tilled(zisoi, j, max_tillage_depth)) + end do + + max_tillage_depth = 0.21_r8 + @assertEqual(1._r8, get_fraction_tilled(zisoi, 1, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi, 2, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi, 3, max_tillage_depth)) + @assertEqual(0.275_r8, get_fraction_tilled(zisoi, 4, max_tillage_depth), tolerance=tol) + @assertEqual(0._r8, get_fraction_tilled(zisoi, 5, max_tillage_depth)) + + end subroutine test_get_fraction_tilled + + +end module test_tillage From b12c780b06641b3380a2787e8b29f57a9185cae6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 1 Sep 2023 16:41:16 -0600 Subject: [PATCH 1441/2067] Corrected a unit in a comment. --- src/soilbiogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index ced9216c74..69c59d5df6 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -255,7 +255,7 @@ function get_fraction_tilled(zisoi, j, max_tillage_depth_gft) result(fraction_ti integer :: j ! Soil layer real(r8) :: max_tillage_depth_gft ! Maximum tillage depth ! !LOCAL VARIABLES - real(r8) :: layer_top ! Depth (cm) of the top of this soil layer. zisoi is the depth of the bottom. + real(r8) :: layer_top ! Depth (m) of the top of this soil layer. zisoi is the depth of the bottom. real(r8) :: layer_thickness ! Thickness of this soil layer (m) ! !RESULT real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth From c5171fe3d8c032940f91751281c9cb9ec90b8512 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 1 Sep 2023 17:10:21 -0600 Subject: [PATCH 1442/2067] get_apply_tillage_multipliers(): Skip non-crop columns more simply. --- src/soilbiogeochem/TillageMod.F90 | 32 ++++++++----------------------- 1 file changed, 8 insertions(+), 24 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 69c59d5df6..8369fcc0c3 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -284,8 +284,9 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! Written by Sam Rabin, based on original code by Michael Graham. ! ! !USES - use pftconMod , only : npcropmin + use pftconMod , only : nc3crop use clm_varcon, only : zisoi + use landunit_varcon , only : istcrop use PatchType , only : patch ! ! !ARGUMENTS: @@ -295,7 +296,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) real(r8), dimension(:), intent(inout) :: decomp_k ! Output: [real(r8) (:) ] rate constant for decomposition (1./sec) ! ! !LOCAL VARIABLES - integer :: p, this_patch, n_noncrop + integer :: p real :: sumwt ! sum of all patch weights, to check real(r8), dimension(ndecomp_pools) :: tillage_mults real(r8), dimension(ndecomp_pools) :: tillage_mults_1patch @@ -303,7 +304,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! Skip tillage if column is inactive or this layer doesn't get tilled fraction_tilled = get_fraction_tilled(zisoi, j, max_tillage_depth) - if (.not. col%active(c) .or. fraction_tilled == 0._r8) then + if (.not. col%active(c) .or. fraction_tilled == 0._r8 .or. col%lun_itype(c) /= istcrop) then return end if @@ -311,32 +312,15 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! adding patch-weighted multipliers to this. tillage_mults(:) = 0.0_r8 - ! TODO: Figure out why adding ".and. col%lun_itype(c) == istcrop" to conditional - ! controlling call of this subroutine didn't properly exclude non-crop columns. - ! That working would allow some simplification here. - this_patch = 0 - n_noncrop = 0 sumwt = 0.0_r8 do p = col%patchi(c),col%patchf(c) if (patch%active(p) .and. patch%wtcol(p) /= 0._r8) then - if (patch%itype(p) >= npcropmin) then - this_patch = p - call get_tillage_multipliers(tillage_mults_1patch, idop(p)) - tillage_mults = tillage_mults + tillage_mults_1patch * patch%wtcol(p) - sumwt = sumwt + patch%wtcol(p) - else - n_noncrop = n_noncrop + 1 - end if + call get_tillage_multipliers(tillage_mults_1patch, idop(p)) + tillage_mults = tillage_mults + tillage_mults_1patch * patch%wtcol(p) + sumwt = sumwt + patch%wtcol(p) end if end do - if (n_noncrop > 0) then - if (this_patch > 0) then - call endrun('ERROR Active, non-zero-weight crop AND non-crop patches found') - end if - return - elseif (this_patch == 0) then - call endrun('ERROR No active, non-zero-weight patches found (crop OR non-crop)') - elseif (abs(1.0_r8 - sumwt) > 1.e-6_r8) then + if (abs(1.0_r8 - sumwt) > 1.e-6_r8) then call endrun('ERROR Active crop patch weights does not sum to 1') end if From 9759938d5b65abfebed97ece3a2075b752952e79 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 3 Sep 2023 12:31:38 -0600 Subject: [PATCH 1443/2067] RXCROPMATURITY: Do make_fsurdat_all_crops_everywhere as PRERUN_SCRIPT. --- cime_config/SystemTests/rxcropmaturity.py | 24 +++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 15f524dfce..f292346582 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -135,7 +135,7 @@ def run_phase(self): # Make custom version of surface file logger.info("RXCROPMATURITY log: run make_fsurdat_all_crops_everywhere") - self._run_make_fsurdat_all_crops_everywhere() + self._setup_make_fsurdat_all_crops_everywhere() # ------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -239,7 +239,7 @@ def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all done") # Make a surface dataset that has every crop in every gridcell - def _run_make_fsurdat_all_crops_everywhere(self): + def _setup_make_fsurdat_all_crops_everywhere(self): # fsurdat should be defined. Where is it? self._fsurdat_in = None @@ -269,12 +269,20 @@ def _run_make_fsurdat_all_crops_everywhere(self): command = ( f"python3 {tool_path} " + f"-i {self._fsurdat_in} " + f"-o {self._fsurdat_out}" ) - stu.run_python_script( - self._get_caseroot(), - self._this_conda_env, - command, - tool_path, - ) + + # Write a bash script that will do what we want + prerun_script = os.path.join(self._path_gddgen, "make_fsurdat_all_crops_everywhere.sh") + prerun_script_lines = [ + "#!/bin/bash", + "set -e", + "conda run -n ctsm_pylib " + command, + "exit 0", + ] + with open(prerun_script, "w") as f: + f.writelines(line + "\n" for line in prerun_script_lines) + os.chmod(prerun_script, 0o755) # 0o755 = -rwxr-xr-x + with self._case: + self._case.set_value("PRERUN_SCRIPT", prerun_script) # Modify namelist logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") From db59ab232cc23eff5e974157cc9899b33b766a00 Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 5 Sep 2023 01:21:22 +0000 Subject: [PATCH 1444/2067] Update documentation for Meier et al. (2022) roughness length parameterization --- .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 259 +++++++++++------- .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 104 ++++--- .../References/CLM50_Tech_Note_References.rst | 9 + 3 files changed, 243 insertions(+), 129 deletions(-) diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index 047d4e6723..978878ee7f 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -785,26 +785,45 @@ The roughness lengths used to calculate :math:`r_{am}` , :math:`r_{ah}` , and :math:`r_{aw}` are :math:`z_{0m} =z_{0m,\, g}` , :math:`z_{0h} =z_{0h,\, g}` , and :math:`z_{0w} =z_{0w,\, g}` . The displacement height :math:`d=0`. The momentum roughness length is -:math:`z_{0m,\, g} =0.01` for soil, glaciers, and -:math:`z_{0m,\, g} =0.0024` for snow-covered surfaces -(:math:`f_{sno} >0`). In general, :math:`z_{0m}` is different from -:math:`z_{0h}` because the transfer of momentum is affected by pressure -fluctuations in the turbulent waves behind the roughness elements, while -for heat and water vapor transfer no such dynamical mechanism exists. -Rather, heat and water vapor must be transferred by molecular diffusion -across the interfacial sublayer. The following relation from -:ref:`Zilitinkevich (1970) ` is adopted by -:ref:`Zeng and Dickinson 1998 ` +:math:`z_{0m,\, g} =0.0023` for glaciers without snow (:math:`f_{sno} =0) {\rm }`, and +:math:`z_{0m,\, g} =0.00085` for bare soil surfaces without snow (:math:`f_{sno} =0) {\rm }` +(:ref:`Meier et al. (2022) `). + +For bare soil and glaciers with snow ( :math:`f_{sno} > 0` ), +the momentum roughness length is evaluated based on accumulated snow melt :math:`M_{a} {\rm }` (:ref:`Meier et al. (2022) `). +For :math:`M_{a} >=1\times 10^{-5}` + +.. math:: + :label: 5.81a + + z_{0m,\, g} =\exp (b_{1} \tan ^{-1} \left[\frac{log_{10} (M_{a}) + 0.23)} {0.08}\right] + b_{4})\times 10^{-3} + +where :math:`M_{a}` is accumulated snow melt (meters water equivalent), :math:`b_{1} =1.4` and :math:`b_{4} =-0.31`. +For :math:`M_{a} <1\times 10^{-5}` + +.. math:: + :label: 5.81b + + z_{0m,\, g} =\exp (-b_{1} 0.5 \pi + b_{4})\times 10^{-3} + +Accumulated snow melt :math:`M_{a}` at the current time step :math:`t` is defined as + +.. math:: + :label: 5.81c + + M ^{t}_{a} = M ^{t-1}_{a} - (q ^{t}_{sno} \Delta t + q ^{t}_{snowmelt} \Delta t)\times 10^{-3} + +where :math:`M ^{t}_{a}` and :math:`M ^{t-1}_{a}` are the accumulated snowmelt at the current time step and previous time step, respectively (m), :math:`q ^{t}_{sno} \Delta t` is the freshly fallen snow (mm), and :math:`q ^{t}_{snowmelt} \Delta t` is the melted snow (mm). + +The scalar roughness lengths (:math:`z_{0q,\, g}` for latent heat and :math:`z_{0h,\ g}` for sensible heat) are calculated +as (:ref:`Meier et al. (2022) `) .. math:: :label: 5.82 - z_{0h,\, g} =z_{0w,\, g} =z_{0m,\, g} e^{-a\left({u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right. \kern-\nulldelimiterspace} \upsilon } \right)^{0.45} } + z_{0h,\, g}=z_{0q,\, g}=\frac{70 \nu}{u_{*}} \exp (-\beta {u_{*}} ^{0.5} |{\theta_{*}}| ^{0.25} ) -where the quantity -:math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right. \kern-\nulldelimiterspace} \upsilon }` -is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic -viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. +where :math:`\beta` = 7.2, and :math:`\theta_{*}` is the potential temperature scale. The numerical solution for the fluxes of momentum, sensible heat, and water vapor flux from non-vegetated surfaces proceeds as follows: @@ -828,7 +847,7 @@ water vapor flux from non-vegetated surfaces proceeds as follows: #. Humidity scale :math:`q_{*}` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) #. Roughness lengths for sensible :math:`z_{0h,\, g}` and latent heat - :math:`z_{0w,\, g}` (:eq:`5.82` ) + :math:`z_{0w,\, g}` (:eq:`5.81a` , :eq:`5.81b` , :eq:`5.82`) #. Virtual potential temperature scale :math:`\theta _{v*}` ( :eq:`5.17`) @@ -1264,101 +1283,153 @@ determined analytically, are ignored for The roughness lengths used to calculate :math:`r_{am}` , :math:`r_{ah}` , and :math:`r_{aw}` from :eq:`5.55`, :eq:`5.56`, and :eq:`5.57` are :math:`z_{0m} =z_{0m,\, v}` , :math:`z_{0h} =z_{0h,\, v}` , and -:math:`z_{0w} =z_{0w,\, v}` . The vegetation displacement height -:math:`d` and the roughness lengths are a function of plant height and -adjusted for canopy density following :ref:`Zeng and Wang (2007) ` +:math:`z_{0w} =z_{0w,\, v}` . + +The vegetation roughness lengths and displacement height :math:`d` +are from :ref:`Meier et al. (2022) ` .. math:: :label: 5.125 - z_{0m,\, v} = z_{0h,\, v} =z_{0w,\, v} =\exp \left[V\ln \left(z_{top} R_{z0m} \right)+\left(1-V\right)\ln \left(z_{0m,\, g} \right)\right] + z_{0m,\, v} = z_{0h,\, v} =z_{0w,\, v} = z_{top} (1 - \frac{d} {z_{top} } ) \exp (\psi_{h} - \frac{k U_{h}} {u_{*} } ) + +where :math:`z_{top}` is canopy top height (m) +(:numref:`Table Plant functional type canopy top and bottom heights`), +:math:`k` is the von Karman constant (:numref:`Table Physical constants`), +and :math:`\psi_{h}` is the roughness sublayer influence function .. math:: - :label: 5.126 + :label: 5.125a - d = z_{top} R_{d} V + \psi_{h} = \ln(c_{w}) - 1 + c_{w}^{-1} -where :math:`z_{top}` is canopy top height (m) -(:numref:`Table Plant functional type canopy top and bottom heights`), -:math:`R_{z0m}` and :math:`R_{d}` are the ratio of momentum roughness -length and displacement height to canopy top height, respectively -(:numref:`Table Plant functional type aerodynamic parameters`), and :math:`z_{0m,\, g}` -is the ground momentum roughness length (m) (section -:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`). The -fractional weight :math:`V` is determined from +where :math:`c_{w}` is a pft-dependent constant (:numref:`Table Plant functional type aerodynamic parameters`). + +The ratio of wind speed at canopy height to friction velocity, :math:`\frac{U_{h}} {u_{*}}` is derived from an +implicit function of the roughness density :math:`\lambda` + +.. math:: + :label: 5.125b + + \frac{U_{h}} {u_{*} } =(C_{S} + \lambda C_{R})^{0.5} \exp(\frac{\min \left(\lambda, \lambda_{\max}\right) c U_{h}} {2 u_{*}}) + +where :math:`C_{S}` represents the drag coefficient of the ground in the absence of vegetation, +:math:`C_{R}` is the drag coefficient of an isolated roughness element (plant), and :math:`c` is an empirical constant. +These three are pft-dependent parameters (:numref:`Table Plant functional type aerodynamic parameters`). +:math:`\lambda_{max}` is the maximum :math:`\lambda` above which :math:`\frac{U_{h}} {u_{*}}` becomes constant. +:math:`\lambda_{max}` is set to the value of :math:`\lambda` for which :eq:`5.125b`, in the absence of :math:`\lambda_{max}`, +would have its minimum. :math:`\lambda_{max}` is also a pft-dependent parameter (:numref:`Table Plant functional type aerodynamic parameters`). +:eq:`5.125b` can be written as + +.. math:: + :label: 5.125c + + X \exp(-X) =(C_{S} + \lambda C_{R})^{0.5} c \frac{\lambda} {2 } + +where + +.. math:: + :label: 5.125d + + X =\frac{c \lambda U_{h}} {2 u_{*} }. + +:math:`X` and therefore :math:`\frac{U_{h}} {u_{*}}` can be solved for iteratively where the initial value of :math:`X` is + +.. math:: + :label: 5.125e + + X_{i=0} =(C_{S} + \lambda C_{R})^{0.5} c \frac{\lambda} {2 } + +and the next value of :math:`X` at :math:`i+1` is + +.. math:: + :label: 5.125f + + X_{i+1} =(C_{S} + \lambda C_{R})^{0.5} c \frac{\lambda} {2 } \exp(X_{i}). + +:math:`X` is updated until :math:`\frac{U_{h}} {u_{*}}` converges to within :math:`1 \times 10^{-4}` between iterations. + +:math:`\lambda` is set to half the total single-sided area of all canopy elements, +here defined as the vegetation area index (VAI) defined as the sum of leaf (:math:`L`) and stem area index (:math:`S`), +subject to a maximum of :math:`\lambda_{max}` and a minimum limit applied for numerical stability + +.. math:: + :label: 5.126 + + \lambda = \frac{\min(\max(1 \times 10^{-5}, VAI), \lambda_{max})} {2 } + +The displacement height :math:`d` is .. math:: - :label: 5.127 + :label: 5.127 - V = \frac{1-\exp \left\{-\beta \min \left[L+S,\, \left(L+S\right)_{cr} \right]\right\}}{1-\exp \left[-\beta \left(L+S\right)_{cr} \right]} + d = z_{top}\left[1- \frac{1-\exp(-(c_{d1} 2 \lambda)^{0.5}} {(c_{d1} 2 \lambda)^{0.5} }\right] -where :math:`\beta =1` and :math:`\left(L+S\right)_{cr} = 2` -(m\ :sup:`2` m\ :sup:`-2`) is a critical value of exposed leaf -plus stem area for which :math:`z_{0m}` reaches its maximum. +where :math:`c_{d1} =7.5`. .. _Table Plant functional type aerodynamic parameters: .. table:: Plant functional type aerodynamic parameters - +----------------------------------+--------------------+------------------+-------------------------+ - | Plant functional type | :math:`R_{z0m}` | :math:`R_{d}` | :math:`d_{leaf}` (m) | - +==================================+====================+==================+=========================+ - | NET Temperate | 0.055 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | NET Boreal | 0.055 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | NDT Boreal | 0.055 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BET Tropical | 0.075 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BET temperate | 0.075 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BDT tropical | 0.055 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BDT temperate | 0.055 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BDT boreal | 0.055 | 0.67 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BES temperate | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BDS temperate | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | BDS boreal | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | C\ :sub:`3` arctic grass | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | C\ :sub:`3` grass | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | C\ :sub:`4` grass | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Crop R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Crop I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Corn R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Corn I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Temp Cereal R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Temp Cereal I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Winter Cereal R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Winter Cereal I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Soybean R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Soybean I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Miscanthus R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Miscanthus I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Switchgrass R | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ - | Switchgrass I | 0.120 | 0.68 | 0.04 | - +----------------------------------+--------------------+------------------+-------------------------+ + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Plant functional type | :math:`d_{leaf}` (m) | :math:`c_{w}` | :math:`C_{S}` | :math:`C_{R}` | :math:`c` | :math:`\lambda_{max}` | + +==================================+=======================+=========================+=========================+=========================+=========================+=========================+ + | NET Temperate | 0.04 | 9 | 0.003 | 0.05 | 0.09 | 4.55 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | NET Boreal | 0.04 | 9 | 0.003 | 0.05 | 0.09 | 4.55 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | NDT Boreal | 0.04 | 9 | 0.003 | 0.05 | 0.09 | 4.55 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BET Tropical | 0.04 | 3 | 0.01 | 0.14 | 0.01 | 7.87 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BET temperate | 0.04 | 3 | 0.01 | 0.14 | 0.01 | 7.87 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BDT tropical | 0.04 | 1 | 0.013 | 0.13 | 0.06 | 8.88 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BDT temperate | 0.04 | 1 | 0.013 | 0.13 | 0.06 | 8.88 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BDT boreal | 0.04 | 1 | 0.013 | 0.13 | 0.06 | 8.88 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BES temperate | 0.04 | 20 | 0.001 | 0.05 | 0.12 | 3.07 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BDS temperate | 0.04 | 20 | 0.001 | 0.05 | 0.12 | 3.07 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | BDS boreal | 0.04 | 20 | 0.001 | 0.05 | 0.12 | 3.07 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | C\ :sub:`3` arctic grass | 0.04 | 19 | 0.001 | 0.05 | 0.08 | 4.61 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | C\ :sub:`3` grass | 0.04 | 19 | 0.001 | 0.05 | 0.08 | 4.61 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | C\ :sub:`4` grass | 0.04 | 19 | 0.001 | 0.05 | 0.08 | 4.61 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Crop R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Crop I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Corn R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Corn I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Temp Cereal R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Temp Cereal I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Winter Cereal R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Winter Cereal I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Soybean R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Soybean I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Miscanthus R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Miscanthus I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Switchgrass R | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ + | Switchgrass I | 0.04 | 3.5 | 0.001 | 0.05 | 0.04 | 5.3 | + +----------------------------------+-----------------------+-------------------------+-------------------------+-------------------------+-------------------------+-------------------------+ .. _Numerical Implementation: diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 40b1918f46..837e8cf881 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -144,41 +144,22 @@ fraction (1 :math:`{-}` :math:`\beta`) is absorbed in the lake body or soil as described in section :numref:`Radiation Penetration`. The surface roughnesses are functions of the lake state and atmospheric -forcing. For frozen lakes ( :math:`T_{g} \le T_{f}` ) with resolved -snow layers, the momentum roughness length -:math:`z_{0m} =2.4 \times 10^{-3} {\rm m}` (as over non-vegetated -surfaces; Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), and the scalar roughness lengths -(*z*\ :sub:`0q` for latent heat; and *z*\ :sub:`0h`, for sensible heat) are given by -(:ref:`Zilitinkevich 1970`) +forcing. -.. math:: - :label: 12.3 - - \begin{array}{l} {R_{0} =\frac{z_{0m} u_{*} }{\nu } ,} \\ {z_{0h} =z_{0q} =z_{0m} \exp \left\{-0.13R_{0} ^{0.45} \right\}} \end{array} - -where :math:`R_{0}` is the near-surface atmospheric roughness -Reynolds number, :math:`z_{0h}` is the roughness -length for sensible heat, :math:`z_{0q}` is the -roughness length for latent heat, :math:`\nu` (m\ :sup:`2` s\ :sup:`-1`) is the kinematic viscosity of air, and -:math:`u_{\*}` (m s\ :sup:`-1`) is the friction velocity in the -atmospheric surface layer. For frozen lakes without resolved snow -layers, :math:`z_{0m} =1\times 10^{-3} {\rm m}` (:ref:`Subin et al. (2012a) `), -and the scalar roughness lengths are given by . - -For unfrozen lakes, *z*\ :sub:`0m` is given by (:ref:`Subin et al. (2012a) `) +For unfrozen lakes (:math:`T_{g} > T_{f}`), :math:`z_{0m}` is given by (:ref:`Subin et al. (2012a) `) .. math:: - :label: 12.4 + :label: 12.3 z_{0m} =\max \left(\frac{\alpha \nu }{u_{*} } ,C\frac{u_{*} ^{2} }{g} \right) where :math:`\alpha` = 0.1, :math:`\nu` is the kinematic viscosity of air given below, *C* is the effective Charnock coefficient given -below, and *g* is the acceleration of gravity (:numref:`Table Physical Constants`). The kinematic +below, :math:`u_{*}` is the friction velocity (m/s), and *g* is the acceleration of gravity (:numref:`Table Physical Constants`). The kinematic viscosity is given by .. math:: - :label: 12.5 + :label: 12.4 \nu =\nu _{0} \left(\frac{T_{g} }{T_{0} } \right)^{1.5} \frac{P_{0} }{P_{ref} } @@ -192,7 +173,7 @@ height. The Charnock coefficient *C* is a function of the lake fetch *F* default: .. math:: - :label: 12.6 + :label: 12.5 \begin{array}{l} {C=C_{\min } +(C_{\max } -C_{\min } )\exp \left\{-\min \left(A,B\right)\right\}} \\ {A={\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } \mathord{\left/ {\vphantom {\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } f_{c} }} \right. \kern-\nulldelimiterspace} f_{c} } } \\ {B=\varepsilon \frac{\sqrt{dg} }{u} } \end{array} @@ -201,6 +182,65 @@ where *A* and *B* define the fetch- and depth-limitation, respectively; :math:`\varepsilon =1` , :math:`f_{c} =100` , and *u* (m s\ :sup:`-1`) is the atmospheric forcing wind. +The scalar roughness lengths +(:math:`z_{0q}` for latent heat and :math:`z_{0h}` for sensible heat) are given by +(:ref:`Subin et al. 2012a`) + +.. math:: + :label: 12.5a + + \begin{array}{l} {R_{0} =(\frac{z_{0m} u_{*} }{\nu })^{0.5} ,} \\ {z_{0h} =z_{0m} \exp \left\{-\frac{k} {Pr} (4 R_{0} ^{0.5} -3.2) \right\},} \\ {z_{0q} =z_{0m} \exp \left\{-\frac{k} {Sc} (4 R_{0} ^{0.5} - 4.2) \right\}}\end{array} + +where :math:`R_{0}` is the near-surface atmospheric roughness Reynolds number, :math:`k` is the von Karman constant (:numref:`Table Physical Constants`), :math:`Pr = 0.713` is the molecular Prandt number for air at neutral stability, :math:`Sc = 0.66` is the Schmidt number for water in air at neutral stability. +:math:`z_{0q}` and :math:`z_{0h}` are restricted to be no smaller than :math:`1 \times 10^{-10}`. + +For frozen lakes ( :math:`T_{g} \le T_{f}` ) without resolved snow +layers ( :math:`snl = 0` ), :math:`z_{0m} =z_{0m_{ice}} =2.3\times 10^{-3} {\rm m}` (:ref:`Meier et al. (2022) `). + +For frozen lakes with resolved +snow layers ( :math:`snl > 0` ), the momentum roughness length is evaluated based on accumulated snow melt :math:`M_{a} {\rm }` (:ref:`Meier et al. (2022) `). +For :math:`M_{a} >=1\times 10^{-5}` + +.. math:: + :label: 12.5b + + z_{0m} =\exp (b_{1} \tan ^{-1} \left[\frac{log_{10} (M_{a}) + 0.23)} {0.08}\right] + b_{4})\times 10^{-3} + +where :math:`M_{a}` is accumulated snow melt (meters water equivalent), :math:`b_{1} =1.4` and :math:`b_{4} =-0.31`. +For :math:`M_{a} <1\times 10^{-5}` + +.. math:: + :label: 12.5c + + z_{0m} =\exp (-b_{1} 0.5 \pi + b_{4})\times 10^{-3} + +Accumulated snow melt :math:`M_{a}` at the current time step :math:`t` is defined as + +.. math:: + :label: 12.5d + + M ^{t}_{a} = M ^{t-1}_{a} - (q ^{t}_{sno} \Delta t + q ^{t}_{snowmelt} \Delta t)\times 10^{-3} + +where :math:`M ^{t}_{a}` and :math:`M ^{t-1}_{a}` are the accumulated snowmelt at the current time step and previous time step, respectively (m), :math:`q ^{t}_{sno} \Delta t` is the freshly fallen snow (mm), and :math:`q ^{t}_{snowmelt} \Delta t` is the melted snow (mm). + +For frozen lakes without and with resolved snow layers, an initial guess for the scalar roughness lengths is derived by assuming :math:`\theta_{*} = 0 {\rm }` (:ref:`Meier et al. (2022) `) + +.. math:: + :label: 12.5e + + z_{0h}=z_{0q}=\frac{70 \nu}{u_{*}} + +where :math:`\nu=1.5 \times 10^{-5}` is the kinematic viscosity of air (m\ :sup:`2` s\ :sup:`-1`), and +:math:`u_{*}` is the friction velocity in the atmospheric surface layer (m s\ :sup:`-1`). +Thereafter, the scalar roughness lengths are updated within the stability iteration described in section :numref:`Surface Flux Solution Lake` as + +.. math:: + :label: 12.6 + + z_{0h}=z_{0q}=\frac{70 \nu}{u_{*}} \exp (-\beta {u_{*}} ^{0.5} |{\theta_{*}}| ^{0.25} ) + +where :math:`\beta` = 7.2, and :math:`\theta_{*}` is the potential temperature scale (section :numref:`Surface Flux Solution Lake`). + .. _Surface Flux Solution Lake: Surface Flux Solution @@ -380,15 +420,9 @@ where the partial derivatives are \frac{\partial G}{\partial T_{g} } =\frac{2\lambda _{T} }{\Delta z_{T} } . The fluxes of momentum, sensible heat, and water vapor are solved for -simultaneously with lake surface temperature as follows. The -stability-related equations are the same as for non-vegetated surfaces -(section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), -except that the surface roughnesses are here (weakly varying) functions -of the friction velocity :math:`u_{\*}` . To begin, *z*\ :sub:`0m` is set -based on the value calculated for the last timestep (for -:math:`T_{g} >T_{f}` ) or based on the values in section -:numref:`Surface Properties Lake` (otherwise), and the scalar roughness -lengths are set based on the relationships in section :numref:`Surface Properties Lake`. +simultaneously with lake surface temperature as follows. +To begin, :math:`z_{0m}` and the scalar roughness +lengths are set as described in section :numref:`Surface Properties Lake`. #. An initial guess for the wind speed :math:`V_{a}` including the convective velocity :math:`U_{c}` is obtained from :eq:`5.24` assuming an @@ -444,7 +478,7 @@ iterations. #. Monin-Obukhov length :math:`L` (:eq:`5.49`) -#. Roughness lengths (:eq:`12.3`, :eq:`12.4`). +#. Roughness lengths (section :numref:`Surface Properties Lake`). Once the four iterations for lake surface temperature have been yielded a tentative solution :math:`T_{g} ^{{'} }` , several restrictions diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 46b835a76d..e1e469671c 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -1341,6 +1341,15 @@ Wingate, L., 2011. Reconciling the optimal and empirical approaches to modelling stomatal conductance. Global Change Biology, 17: 2134–2144. doi:10.1111/j.1365-2486.2010.02375.x +.. _Meieretal2022: + +Meier, R., Davin, E. L., Bonan, G. B., Lawrence, D. M., Hu, X., +Duveiller, G., Prigent, C., and Seneviratne, S. I., 2022. Impacts of a +revised surface roughness parameterization in the Community Land Model +5.1, Geosci. Model Dev., 15, 2365–2393, +https://doi.org/10.5194/gmd-15-2365-2022 + + .. _MelzerOLeary1987: Melzer, E., and O’Leary, M.H. 1987. Anapleurotic CO2 Fixation by From 7caa5e4206e935475c3cd437c4331bb9538f122b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 6 Sep 2023 10:52:03 -0600 Subject: [PATCH 1445/2067] Methane tech note: Add 3 missing equation references. --- doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index d90531c7e9..875689558b 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -293,7 +293,7 @@ area (m\ :sup:`2` m\ :sup:`-2`); :math:`{r}_{a}` is the aerodynamic resistance between the surface and the atmospheric reference height (s m\ :sup:`-1`); and :math:`\rho _{r}` is the rooting density as a function of depth (-). The gaseous concentration is -calculated with Henry’s law as described in equation . +calculated with Henry’s law as described in equation :eq:`24.7`. Based on the ranges reported in :ref:`Colmer (2003)`, we have chosen baseline aerenchyma porosity values of 0.3 for grass and crop PFTs and 0.1 for @@ -310,7 +310,7 @@ m\ :sup:`-2` s\ :sup:`-1`); *R* is the aerenchyma radius belowground fraction of annual NPP; and the 0.22 factor represents the amount of C per tiller. O\ :sub:`2` can also diffuse in from the atmosphere to the soil layer via the reverse of the same pathway, with -the same representation as Equation but with the gas diffusivity of +the same representation as Equation :eq:`24.8` but with the gas diffusivity of oxygen. CLM also simulates the direct emission of CH\ :sub:`4` from leaves @@ -358,7 +358,7 @@ potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. Reactive Transport Solution -------------------------------- -The solution to equation is solved in several sequential steps: resolve +The solution to equation :eq:`24.11` is solved in several sequential steps: resolve competition for CH\ :sub:`4` and O\ :sub:`2` (section :numref:`Competition for CH4and O2`); add the ebullition flux into the layer directly above the water From 272238f07870702226eff0a9bc394a7c2da7f016 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 14:19:39 -0600 Subject: [PATCH 1446/2067] Move leafc_to_litter in CNOffsetLitterfall(). --- src/biogeochem/CNPhenologyMod.F90 | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c2a66511f7..d997650113 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3056,9 +3056,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & t1 = 1.0_r8 / dt frootc_to_litter(p) = t1 * frootc(p) + cpool_to_frootc(p) - ! biofuel_harvfrac is only non-zero for prognostic crops. - leafc_to_litter(p) = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p) - ! leafc_litter and frootc_to_litter for matrix if (use_matrixcn) then else @@ -3131,6 +3128,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p)) livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p)) + leafc_to_litter(p) = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p) + ! Matrix for grain, livestem to litter and biofuel if(use_matrixcn)then else From 237ef48e9091509fb83add68dde026765475e4ae Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 7 Sep 2023 15:37:54 -0600 Subject: [PATCH 1447/2067] CNOffsetLitterfall() now uses leafc_ and livestemc_remaining. This sets up for the addition of biomass removals in addition to biofuel harvest. --- src/biogeochem/CNPhenologyMod.F90 | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d997650113..a875b4c38b 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2979,6 +2979,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & real(r8) :: cropseedc_deficit_to_restore ! amount of crop seed C deficit that will be restored from this grain pool (gC/m2) real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2) real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) + real(r8) :: leafc_remaining, livestemc_remaining !----------------------------------------------------------------------- associate( & @@ -3120,15 +3121,17 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of leaf C ! and move this fration of leaf C to biofuel C, rather than move it to litter leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p)) + leafc_remaining = leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p)) ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C ! and move this fration of leaf C to biofuel C, rather than move it to litter - livestemc_to_litter(p) = t1 * livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_livestemc(p) livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p)) livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p)) + livestemc_remaining = livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p))) - leafc_to_litter(p) = t1 * leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + cpool_to_leafc(p) + leafc_to_litter(p) = t1 * leafc_remaining + cpool_to_leafc(p) + livestemc_to_litter(p) = t1 * livestemc_remaining + cpool_to_livestemc(p) ! Matrix for grain, livestem to litter and biofuel if(use_matrixcn)then From ab94ab484bc15405788ffe6c1e061778eeb3d337 Mon Sep 17 00:00:00 2001 From: AdrienDams Date: Fri, 8 Sep 2023 10:44:52 +0200 Subject: [PATCH 1448/2067] Replace thermal conductivity of snow of Jordan with Sturm --- src/biogeophys/SoilTemperatureMod.F90 | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index b868224a60..caeedd1603 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -47,7 +47,7 @@ module SoilTemperatureMod ! o The thermal conductivity of soil is computed from ! the algorithm of Johansen (as reported by Farouki 1981), and the ! conductivity of snow is from the formulation used in - ! SNTHERM (Jordan 1991). + ! Sturm (1997). ! o Boundary conditions: ! F = Rnet - Hg - LEg (top), F= 0 (base of the soil column). ! o Soil / snow temperature is predicted from heat conduction @@ -100,7 +100,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! o The thermal conductivity of soil is computed from ! the algorithm of Johansen (as reported by Farouki 1981), and the ! conductivity of snow is from the formulation used in - ! SNTHERM (Jordan 1991). + ! Sturm (1997). ! o Boundary conditions: ! F = Rnet - Hg - LEg (top), F= 0 (base of the soil column). ! o Soil / snow temperature is predicted from heat conduction @@ -611,7 +611,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter ! ! (2) The thermal conductivity of soil is computed from the algorithm of ! Johansen (as reported by Farouki 1981), and of snow is from the - ! formulation used in SNTHERM (Jordan 1991). + ! formulation used in Sturm (1997). ! The thermal conductivities at the interfaces between two neighboring ! layers (j, j+1) are derived from an assumption that the flux across ! the interface is equal to that from the node j to the interface and the @@ -734,11 +734,16 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter endif endif - ! Thermal conductivity of snow, which from Jordan (1991) pp. 18 + ! Thermal conductivity of snow, which from Sturm (1997) ! Only examine levels from snl(c)+1 -> 0 where snl(c) < 1 if (snl(c)+1 < 1 .AND. (j >= snl(c)+1) .AND. (j <= 0)) then - bw(c,j) = (h2osoi_ice(c,j)+h2osoi_liq(c,j))/(frac_sno(c)*dz(c,j)) - thk(c,j) = tkair + (7.75e-5_r8 *bw(c,j) + 1.105e-6_r8*bw(c,j)*bw(c,j))*(tkice-tkair) + bw(c,j) = ((h2osoi_ice(c,j)*1)+h2osoi_liq(c,j))/(frac_sno(c)*dz(c,j)) ! ==RHOS + ! thk(c,j) = tkair + (7.75e-5_r8 *bw(c,j) + 1.105e-6_r8*bw(c,j)*bw(c,j))*(tkice-tkair) ! Original (Jordan) Parameterisation + if (bw(c,j) <= 156) then !LMW or 0.156 ? + thk(c,j) = 0.023 + 0.234*(bw(c,j)/1000) !LMW - units changed by VRD + else !LMW + thk(c,j) = 0.138 - 1.01*(bw(c,j)/1000) +(3.233*((bw(c,j)/1000)*(bw(c,j)/1000))) ! LMW Sturm I think + end if end if end do From d25281dc5ba78bf679131001175d01995db89343 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 8 Sep 2023 09:29:59 -0600 Subject: [PATCH 1449/2067] update fates externals --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index c540fe8b0c..14ba14d8b4 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.67.1_api.27.0.0 +tag = sci.1.67.2_api.27.0.0 required = True [externals_description] From bed606d173140c29e5aa43965fa0fdf1dca2054e Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 8 Sep 2023 10:23:28 -0600 Subject: [PATCH 1450/2067] fix merge conflict error --- src/main/surfrdUtilsMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/surfrdUtilsMod.F90 b/src/main/surfrdUtilsMod.F90 index da343a8802..6b581a59c1 100644 --- a/src/main/surfrdUtilsMod.F90 +++ b/src/main/surfrdUtilsMod.F90 @@ -64,7 +64,7 @@ subroutine check_sums_equal_1(arr, lb, name, caller, ier, sumto) found = .false. do nl = lb, ub - if (abs(sum(arr(nl,:)) - TotalSum(nl)) > eps) then + if (abs(sum(arr(nl,:)) - TotalSum(nl)) > sum_to_1_tol) then found = .true. nindx = nl exit From c2c108d93d45043df941cffa7ab1cf3b82cdd156 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 11 Sep 2023 11:44:27 -0600 Subject: [PATCH 1451/2067] invert dispersal type dimensions for memory continuity for mpi collective --- src/utils/clmfates_interfaceMod.F90 | 36 ++++++++++++++++++++++++----- 1 file changed, 30 insertions(+), 6 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 17441d8b23..2b7a2a8ffd 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1399,7 +1399,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! Check if seed dispersal mode is 'turned on', if not return to calling procedure if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then ! zero the outgoing seed array - this%fates_seed%outgoing_local(:,:) = 0._r8 + !this%fates_seed%outgoing_local(:,:) = 0._r8 end if do s = 1,this%fates(nc)%nsites @@ -1407,10 +1407,12 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & c = this%f2hmap(nc)%fcolumn(s) g = col%gridcell(c) + write(iulog,*) 'WUHD pre: g, seed_out, outgoing: ', g, sum(this%fates(nc)%sites(s)%seed_out(:)), sum(this%fates_seed%outgoing_local(:,g)) ! Accumulate seeds from sites to the gridcell local outgoing buffer if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) .and. IsItDispersalTime()) then - this%fates_seed%outgoing_local(g,:) = this%fates(nc)%sites(s)%seed_out(:) + this%fates_seed%outgoing_local(:,g) = this%fates(nc)%sites(s)%seed_out(:) end if + write(iulog,*) 'WUHD pst: g, seed_out, outgoing: ', g, sum(this%fates(nc)%sites(s)%seed_out(:)), sum(this%fates_seed%outgoing_local(:,g)) ! Other modules may have AI's we only flush values ! that are on the naturally vegetated columns @@ -2678,15 +2680,29 @@ subroutine WrapSeedGlobal(this,is_restart_flag) ! Re-initialize incoming seed buffer for this time step this%fates_seed%incoming_global(:,:) = 0._r8 + this%fates_seed%outgoing_global(:,:) = 0._r8 + + write(iulog,*) 'WSG: begg: ', procinfo%begg + do g = 1, procinfo%ncells + write(iulog,*) 'WSG: g+begg, outgoing_local: ', g+procinfo%begg, sum(this%fates_seed%outgoing_local(:,g)) + end do + ! Distribute obtgoing seed data from all nodes to all nodes call MPI_Allgatherv(this%fates_seed%outgoing_local, procinfo%ncells*numpft_fates, MPI_REAL8, & - this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array, & + this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array*numpft_fates, & MPI_REAL8, mpicom, ier) + write(iulog,*) 'WSG: MPI_Allgatherv ier: ', ier + + ! zero outgoing local for all gridcells outside threaded region + this%fates_seed%outgoing_local(:,:) = 0._r8 + call get_proc_global(ng=numg) do g = 1, numg + write(iulog,*) 'WSG: g, outgoing_global: ', g, sum(this%fates_seed%outgoing_global(:,g)) + ! Calculate the current gridcell incoming seed for each gridcell index ! This should be conducted outside of a threaded region to provide access to ! the neighbor%gindex which might not be available in via the clumped index @@ -2695,11 +2711,14 @@ subroutine WrapSeedGlobal(this,is_restart_flag) ! This also applies the same neighborhood distribution scheme to all pfts ! This needs to have a per pft density probability value - this%fates_seed%incoming_global(g,:) = this%fates_seed%incoming_global(g,:) + & - this%fates_seed%outgoing_global(neighbor%gindex,:) * & + this%fates_seed%incoming_global(:,g) = this%fates_seed%incoming_global(:,g) + & + this%fates_seed%outgoing_global(:,neighbor%gindex) * & neighbor%density_prob(:) / lneighbors(g)%neighbor_count + !write(iulog,*) 'WSGloop: g, incoming, outgoing: ', g, sum(this%fates_seed%incoming_global(g,:)), sum(this%fates_seed%outgoing_global(g,:)) + !write(iulog,*) 'WSGloop: g, densprob, ncount: ', g, sum(neighbor%density_prob(:)), lneighbors(g)%neighbor_count neighbor => neighbor%next_neighbor end do + !write(iulog,*) 'WSG: g, incoming, outgoing: ', g, sum(this%fates_seed%incoming_global(g,:)), sum(this%fates_seed%outgoing_global(g,:)) end do endif @@ -2733,10 +2752,13 @@ subroutine wrap_seed_dispersal(this,bounds_clump) c = this%f2hmap(nc)%fcolumn(s) g = col%gridcell(c) + write(iulog,*) 'WSD pre: g, incoming, seed_in: ', g, sum(this%fates_seed%incoming_global(:,g)), sum(this%fates(nc)%sites(s)%seed_in(:)) + ! Check that it is the beginning of the current dispersal time step if (IsItDispersalTime()) then + write(iulog,*) 'WSD IIDT: g: ', g ! assuming equal area for all sites, seed_id_global in [kg/grid/day], seed_in in [kg/site/day] - this%fates(nc)%sites(s)%seed_in(:) = this%fates_seed%incoming_global(g,:) + this%fates(nc)%sites(s)%seed_in(:) = this%fates_seed%incoming_global(:,g) this%fates(nc)%sites(s)%seed_out(:) = 0._r8 ! reset seed_out else ! if it is not the dispersing time, pass in zero @@ -2744,6 +2766,8 @@ subroutine wrap_seed_dispersal(this,bounds_clump) this%fates(nc)%sites(s)%seed_in(:) = 0._r8 end if + write(iulog,*) 'WSD pst: g, incoming, seed_in: ', g, sum(this%fates_seed%incoming_global(:,g)), sum(this%fates(nc)%sites(s)%seed_in(:)) + end do From 278ce0126476e65137c686e6f326ae8353010092 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 11 Sep 2023 15:03:39 -0600 Subject: [PATCH 1452/2067] update changelog --- cime_config/config_compsets.xml | 4 +++ doc/ChangeLog | 64 +++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 3 files changed, 69 insertions(+) diff --git a/cime_config/config_compsets.xml b/cime_config/config_compsets.xml index 61931c94ba..aaa5c68394 100644 --- a/cime_config/config_compsets.xml +++ b/cime_config/config_compsets.xml @@ -205,6 +205,10 @@ I2000Clm45BgcCropQianRs 2000_DATM%QIA_CLM45%BGC-CROP_SICE_SOCN_SROF_SGLC_SWAV + + I2000Clm50FatesQian + 2000_DATM%QIA_CLM50%FATES_SICE_SOCN_MOSART_SGLC_SWAV + I2000Clm50BgcCruRs diff --git a/doc/ChangeLog b/doc/ChangeLog index 0a9515ff93..ee4b6b2aa8 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,68 @@ =============================================================== +Tag name: ctsm5.1.dev140 +Originator(s): afoster (Adrianna Foster) +Date: Mon Sep 11 14:57:50 MDT 2023 +One-line Summary: add lai_streams capability for FATES + +Purpose and description of changes +---------------------------------- + +Removed checks in clm_driver and CLMBuildNamelist.pm so that now FATES can run when use_lai_streams=.true. + +I also had to modify the init in cpl/share_esmf/laiStreamMod to allocate the g_to_ig array in the lai_init method (rather than in the lai_advance method. This was required because SatellitePhenology is called in clim_initializedMod in FATES cases (here). This happens before lai_advance is ever called so at that point the g_to_ig array was not yet allocated. Moving the allocation/initialization to the lai_init method fixes this. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): #1722 + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: Added a test for lai_streams with FATES + +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + + +Answer changes +-------------- + +Changes answers relative to baseline: None + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates + +Pull Requests that document the changes (include PR ids): #2054 +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev139 Originator(s): slevis (Samuel Levis) Date: Fri Aug 25 16:47:45 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 4ac0f90f5e..eedc5a1aac 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev140 afoster 09/11/2023 add lai_streams capability for FATES ctsm5.1.dev139 slevis 08/28/2023 Fix problems uncovered by nag -nan tests ctsm5.1.dev138 slevis 08/25/2023 Refactor max_patch_per_col and maxsoil_patches loops ctsm5.1.dev137 slevis 08/23/2023 Surface roughness modifications From b56f919db282b1f61c5f331d52adba75f3606970 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 11 Sep 2023 15:04:12 -0600 Subject: [PATCH 1453/2067] updated date --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index ee4b6b2aa8..17902f605f 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev140 Originator(s): afoster (Adrianna Foster) -Date: Mon Sep 11 14:57:50 MDT 2023 +Date: Mon Sep 11 15:04:02 MDT 2023 One-line Summary: add lai_streams capability for FATES Purpose and description of changes From 1fa92460a30f586f444aa5350d18f1a595ae8ab8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 7 Sep 2023 16:35:18 -0600 Subject: [PATCH 1454/2067] CNOffsetLitterfall() now uses leafn_ and livestemn_remaining. More setup for the addition of biomass removals beyond just biofuel harvest. --- src/biogeochem/CNPhenologyMod.F90 | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a875b4c38b..0b9c69698e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2980,6 +2980,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & real(r8) :: cropseedn_deficit_to_restore ! amount of crop seed N deficit that will be restored from this grain pool (gN/m2) real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) real(r8) :: leafc_remaining, livestemc_remaining + real(r8) :: leafn_remaining, livestemn_remaining !----------------------------------------------------------------------- associate( & @@ -3123,15 +3124,18 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & leafc_to_biofuelc(p) = t1 * leafc(p) * biofuel_harvfrac(ivt(p)) leafc_remaining = leafc(p)*(1._r8-biofuel_harvfrac(ivt(p))) leafn_to_biofueln(p) = t1 * leafn(p) * biofuel_harvfrac(ivt(p)) + leafn_remaining = leafn(p)*(1._r8-biofuel_harvfrac(ivt(p))) ! Cut a certain fraction (i.e., biofuel_harvfrac(ivt(p))) (e.g., biofuel_harvfrac(ivt(p)=70% for bioenergy crops) of livestem C ! and move this fration of leaf C to biofuel C, rather than move it to litter livestemc_to_biofuelc(p) = t1 * livestemc(p) * biofuel_harvfrac(ivt(p)) livestemn_to_biofueln(p) = t1 * livestemn(p) * biofuel_harvfrac(ivt(p)) livestemc_remaining = livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p))) + livestemn_remaining = livestemn(p)*(1._r8-biofuel_harvfrac(ivt(p))) leafc_to_litter(p) = t1 * leafc_remaining + cpool_to_leafc(p) livestemc_to_litter(p) = t1 * livestemc_remaining + cpool_to_livestemc(p) + livestemn_to_litter(p) = t1 * livestemn_remaining ! Matrix for grain, livestem to litter and biofuel if(use_matrixcn)then @@ -3269,18 +3273,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & endif end if - if (ivt(p) >= npcropmin) then - ! NOTE(slevis, 2014-12) results in -ve livestemn and -ve totpftn - !X! livestemn_to_litter(p) = livestemc_to_litter(p) / livewdcn(ivt(p)) - ! NOTE(slevis, 2014-12) Beth Drewniak suggested this instead - livestemn_to_litter(p) = livestemn(p) / dt * (1._r8 - biofuel_harvfrac(ivt(p))) - - ! Matrix update for livestemn to litter - if(use_matrixcn)then - else - end if - end if - ! save the current litterfall fluxes prev_leafc_to_litter(p) = leafc_to_litter(p) prev_frootc_to_litter(p) = frootc_to_litter(p) From 2183e0ad9ba9885acf55e0ede8392a4883e47391 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 14:40:37 -0600 Subject: [PATCH 1455/2067] Placeholders in CN[CN]StateUpdate1Mod, CNPhenologyMod, CNCIsoFluxMod. --- src/biogeochem/CNCIsoFluxMod.F90 | 4 +++- src/biogeochem/CNCStateUpdate1Mod.F90 | 6 ++++-- src/biogeochem/CNNStateUpdate1Mod.F90 | 6 ++++-- src/biogeochem/CNPhenologyMod.F90 | 8 ++++++-- 4 files changed, 17 insertions(+), 7 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index a4706442fa..2693a176a2 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -497,7 +497,9 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & p = filter_soilp(fp) iso_cnveg_cf%crop_harvestc_to_cropprodc_patch(p) = & iso_cnveg_cf%leafc_to_biofuelc_patch(p) + & - iso_cnveg_cf%livestemc_to_biofuelc_patch(p) + iso_cnveg_cf%livestemc_to_biofuelc_patch(p) + & + 0._r8 + & + 0._r8 end do if (use_grainproduct) then diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 843754f3cd..385c8682d7 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -320,8 +320,10 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & end if if (ivt(p) >= npcropmin) then ! skip 2 generic crops cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) - cf_veg%livestemc_to_litter_patch(p)*dt - cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) - cf_veg%livestemc_to_biofuelc_patch(p)*dt - cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) - cf_veg%leafc_to_biofuelc_patch(p)*dt + cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) - & + (cf_veg%livestemc_to_biofuelc_patch(p) + 0._r8)*dt + cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) - & + (cf_veg%leafc_to_biofuelc_patch(p) + 0._r8)*dt cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & - cf_veg%crop_seedc_to_leaf_patch(p) * dt do k = repr_grain_min, repr_grain_max diff --git a/src/biogeochem/CNNStateUpdate1Mod.F90 b/src/biogeochem/CNNStateUpdate1Mod.F90 index c99729b2ee..6b3044eb3f 100644 --- a/src/biogeochem/CNNStateUpdate1Mod.F90 +++ b/src/biogeochem/CNNStateUpdate1Mod.F90 @@ -257,8 +257,10 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ns_veg%frootn_patch(p) = ns_veg%frootn_patch(p) - nf_veg%frootn_to_retransn_patch(p)*dt ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) + nf_veg%frootn_to_retransn_patch(p)*dt ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - nf_veg%livestemn_to_litter_patch(p)*dt - ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - nf_veg%livestemn_to_biofueln_patch(p)*dt - ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) - nf_veg%leafn_to_biofueln_patch(p)*dt + ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - & + (nf_veg%livestemn_to_biofueln_patch(p) + 0._r8)*dt + ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) - & + (nf_veg%leafn_to_biofueln_patch(p) + 0._r8)*dt ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - nf_veg%livestemn_to_retransn_patch(p)*dt ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) + nf_veg%livestemn_to_retransn_patch(p)*dt ! diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 22945e9b68..143c080409 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3619,10 +3619,14 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil p = filter_soilp(fp) cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = & cnveg_carbonflux_inst%leafc_to_biofuelc_patch(p) + & - cnveg_carbonflux_inst%livestemc_to_biofuelc_patch(p) + cnveg_carbonflux_inst%livestemc_to_biofuelc_patch(p) + & + 0._r8 + & + 0._r8 cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = & cnveg_nitrogenflux_inst%leafn_to_biofueln_patch(p) + & - cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch(p) + cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch(p) + & + 0._r8 + & + 0._r8 end do if (use_grainproduct) then From 8aaa7f31104eb20c63d1e79a94ab00941f3eebd6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 14:58:30 -0600 Subject: [PATCH 1456/2067] Add new CNVeg*FluxType members for removed residues. Unused. --- src/biogeochem/CNVegCarbonFluxType.F90 | 16 ++++++++++++++++ src/biogeochem/CNVegNitrogenFluxType.F90 | 6 ++++++ 2 files changed, 22 insertions(+) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index c2025fca47..e1a3981fc1 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -147,6 +147,8 @@ module CNVegCarbonFluxType real(r8), pointer :: leafc_to_biofuelc_patch (:) ! leaf C to biofuel C (gC/m2/s) real(r8), pointer :: livestemc_to_biofuelc_patch (:) ! livestem C to biofuel C (gC/m2/s) + real(r8), pointer :: leafc_to_removedresiduec_patch (:) ! leaf C to removed residues C (gC/m2/s) + real(r8), pointer :: livestemc_to_removedresiduec_patch (:) ! livestem C to removed residues C (gC/m2/s) real(r8), pointer :: repr_grainc_to_seed_patch (:,:) ! grain C to seed for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] ! maintenance respiration fluxes @@ -662,6 +664,8 @@ subroutine InitAllocate(this, bounds, carbon_type) this%repr_structurec_to_litter_patch(:,:) = nan allocate(this%leafc_to_biofuelc_patch (begp:endp)) ; this%leafc_to_biofuelc_patch (:) = nan allocate(this%livestemc_to_biofuelc_patch (begp:endp)) ; this%livestemc_to_biofuelc_patch (:) = nan + allocate(this%leafc_to_removedresiduec_patch (begp:endp)) ; this%leafc_to_removedresiduec_patch (:) = nan + allocate(this%livestemc_to_removedresiduec_patch (begp:endp)) ; this%livestemc_to_removedresiduec_patch (:) = nan allocate(this%repr_grainc_to_seed_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_seed_patch (:,:) = nan allocate(this%reproductivec_xfer_to_reproductivec_patch(begp:endp, nrepr)) this%reproductivec_xfer_to_reproductivec_patch(:,:) = nan @@ -967,6 +971,16 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', long_name='livestem C to biofuel C', & ptr_patch=this%livestemc_to_biofuelc_patch) + this%leafc_to_removedresiduec_patch(begp:endp) = spval + call hist_addfld1d (fname='LEAFC_TO_REMOVEDRESIDUEC', units='gC/m^2/s', & + avgflag='A', long_name='leaf C to removed residue C', & + ptr_patch=this%leafc_to_removedresiduec_patch) + + this%livestemc_to_removedresiduec_patch(begp:endp) = spval + call hist_addfld1d (fname='LIVESTEMC_TO_REMOVEDRESIDUEC', units='gC/m^2/s', & + avgflag='A', long_name='livestem C to removed residue C', & + ptr_patch=this%livestemc_to_removedresiduec_patch) + this%repr_grainc_to_seed_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainc_to_seed_patch(:,k) @@ -4143,6 +4157,8 @@ subroutine SetValues ( this, nvegcpool, & this%livestemc_to_litter_patch(i) = value_patch this%leafc_to_biofuelc_patch(i) = value_patch this%livestemc_to_biofuelc_patch(i) = value_patch + this%leafc_to_removedresiduec_patch(i) = value_patch + this%livestemc_to_removedresiduec_patch(i) = value_patch end do do k = 1, nrepr diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index ce164b4c37..908ab792e9 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -136,6 +136,8 @@ module CNVegNitrogenFluxType real(r8), pointer :: repr_structuren_to_litter_patch (:,:) ! patch reproductive structure N to litter for prognostic crop (gN/m2/s) [patch, repr_structure_min:repr_structure_max] real(r8), pointer :: leafn_to_biofueln_patch (:) ! patch leaf N to biofuel N (gN/m2/s) real(r8), pointer :: livestemn_to_biofueln_patch (:) ! patch livestem N to biofuel N (gN/m2/s) + real(r8), pointer :: leafn_to_removedresiduen_patch (:) ! patch leaf N to removed residue N (gN/m2/s) + real(r8), pointer :: livestemn_to_removedresiduen_patch (:) ! patch livestem N to removed residue N (gN/m2/s) real(r8), pointer :: repr_grainn_to_seed_patch (:,:) ! patch grain N to seed for prognostic crop (gN/m2/s) [patch, repr_grain_min:repr_grain_max] real(r8), pointer :: leafn_to_litter_patch (:) ! patch leaf N litterfall (gN/m2/s) real(r8), pointer :: leafn_to_retransn_patch (:) ! patch leaf N to retranslocated N pool (gN/m2/s) @@ -471,6 +473,8 @@ subroutine InitAllocate(this, bounds) this%repr_structuren_to_litter_patch(:,:) = nan allocate(this%leafn_to_biofueln_patch (begp:endp)) ; this%leafn_to_biofueln_patch (:) = nan allocate(this%livestemn_to_biofueln_patch (begp:endp)) ; this%livestemn_to_biofueln_patch (:) = nan + allocate(this%leafn_to_removedresiduen_patch (begp:endp)) ; this%leafn_to_removedresiduen_patch (:) = nan + allocate(this%livestemn_to_removedresiduen_patch (begp:endp)) ; this%livestemn_to_removedresiduen_patch (:) = nan allocate(this%repr_grainn_to_seed_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_seed_patch (:,:) = nan allocate(this%reproductiven_xfer_to_reproductiven_patch(begp:endp, nrepr)) this%reproductiven_xfer_to_reproductiven_patch(:,:) = nan @@ -1825,6 +1829,8 @@ subroutine SetValues ( this, nvegnpool, & this%livestemn_to_litter_patch(i) = value_patch this%leafn_to_biofueln_patch(i) = value_patch this%livestemn_to_biofueln_patch(i) = value_patch + this%leafn_to_removedresiduen_patch(i) = value_patch + this%livestemn_to_removedresiduen_patch(i) = value_patch this%soyfixn_patch(i) = value_patch this%frootn_to_retransn_patch(i) = value_patch end do From d32a49e67bdfa4661eb1b2f9d7bdf2bb7f3706ab Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 15:08:39 -0600 Subject: [PATCH 1457/2067] Filled to_removedresidue placeholders in CIsoFlux1(). --- src/biogeochem/CNCIsoFluxMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index 2693a176a2..12b3c5f96d 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -498,8 +498,8 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & iso_cnveg_cf%crop_harvestc_to_cropprodc_patch(p) = & iso_cnveg_cf%leafc_to_biofuelc_patch(p) + & iso_cnveg_cf%livestemc_to_biofuelc_patch(p) + & - 0._r8 + & - 0._r8 + iso_cnveg_cf%leafc_to_removedresiduec_patch(p) + & + iso_cnveg_cf%livestemc_to_removedresiduec_patch(p) end do if (use_grainproduct) then From 26775c314f9c02cd0235ac1c66d3ba318053f2dd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 16:05:04 -0600 Subject: [PATCH 1458/2067] Added CIsoFluxCalc() calls for to_removedresiduec pools in CIsoFlux1(). --- src/biogeochem/CNCIsoFluxMod.F90 | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/biogeochem/CNCIsoFluxMod.F90 b/src/biogeochem/CNCIsoFluxMod.F90 index 12b3c5f96d..61840056c2 100644 --- a/src/biogeochem/CNCIsoFluxMod.F90 +++ b/src/biogeochem/CNCIsoFluxMod.F90 @@ -428,6 +428,16 @@ subroutine CIsoFlux1(num_soilc, filter_soilc, num_soilp, filter_soilp, & iso_cnveg_cs%livestemc_patch , cnveg_cs%livestemc_patch, & num_soilp , filter_soilp, 1._r8, 0, isotope) + call CIsoFluxCalc(& + iso_cnveg_cf%leafc_to_removedresiduec_patch , cnveg_cf%leafc_to_removedresiduec_patch, & + iso_cnveg_cs%leafc_patch , cnveg_cs%leafc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + + call CIsoFluxCalc(& + iso_cnveg_cf%livestemc_to_removedresiduec_patch, cnveg_cf%livestemc_to_removedresiduec_patch, & + iso_cnveg_cs%livestemc_patch , cnveg_cs%livestemc_patch, & + num_soilp , filter_soilp, 1._r8, 0, isotope) + call CIsoFluxCalc(& iso_cnveg_cf%repr_grainc_to_seed_patch , cnveg_cf%repr_grainc_to_seed_patch, & iso_cnveg_cs%reproductivec_patch , cnveg_cs%reproductivec_patch, & From 3cb6549a6547814160479e683005ca622907cb67 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 15:15:59 -0600 Subject: [PATCH 1459/2067] Filled to_removedresidue placeholders in CNCStateUpdate1Mod. --- src/biogeochem/CNCStateUpdate1Mod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNCStateUpdate1Mod.F90 b/src/biogeochem/CNCStateUpdate1Mod.F90 index 385c8682d7..0cf9bb472a 100644 --- a/src/biogeochem/CNCStateUpdate1Mod.F90 +++ b/src/biogeochem/CNCStateUpdate1Mod.F90 @@ -321,9 +321,9 @@ subroutine CStateUpdate1( num_soilc, filter_soilc, num_soilp, filter_soilp, & if (ivt(p) >= npcropmin) then ! skip 2 generic crops cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) - cf_veg%livestemc_to_litter_patch(p)*dt cs_veg%livestemc_patch(p) = cs_veg%livestemc_patch(p) - & - (cf_veg%livestemc_to_biofuelc_patch(p) + 0._r8)*dt + (cf_veg%livestemc_to_biofuelc_patch(p) + cf_veg%livestemc_to_removedresiduec_patch(p))*dt cs_veg%leafc_patch(p) = cs_veg%leafc_patch(p) - & - (cf_veg%leafc_to_biofuelc_patch(p) + 0._r8)*dt + (cf_veg%leafc_to_biofuelc_patch(p) + cf_veg%leafc_to_removedresiduec_patch(p))*dt cs_veg%cropseedc_deficit_patch(p) = cs_veg%cropseedc_deficit_patch(p) & - cf_veg%crop_seedc_to_leaf_patch(p) * dt do k = repr_grain_min, repr_grain_max From 0ba8bed570203cd6627a7649f76febe43e312dab Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 15:16:55 -0600 Subject: [PATCH 1460/2067] Filled to_removedresidue placeholders in CNNStateUpdate1Mod. --- src/biogeochem/CNNStateUpdate1Mod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNNStateUpdate1Mod.F90 b/src/biogeochem/CNNStateUpdate1Mod.F90 index 6b3044eb3f..2b2b40afbf 100644 --- a/src/biogeochem/CNNStateUpdate1Mod.F90 +++ b/src/biogeochem/CNNStateUpdate1Mod.F90 @@ -258,9 +258,9 @@ subroutine NStateUpdate1(num_soilc, filter_soilc, num_soilp, filter_soilp, & ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) + nf_veg%frootn_to_retransn_patch(p)*dt ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - nf_veg%livestemn_to_litter_patch(p)*dt ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - & - (nf_veg%livestemn_to_biofueln_patch(p) + 0._r8)*dt + (nf_veg%livestemn_to_biofueln_patch(p) + nf_veg%livestemn_to_removedresiduen_patch(p))*dt ns_veg%leafn_patch(p) = ns_veg%leafn_patch(p) - & - (nf_veg%leafn_to_biofueln_patch(p) + 0._r8)*dt + (nf_veg%leafn_to_biofueln_patch(p) + nf_veg%leafn_to_removedresiduen_patch(p))*dt ns_veg%livestemn_patch(p) = ns_veg%livestemn_patch(p) - nf_veg%livestemn_to_retransn_patch(p)*dt ns_veg%retransn_patch(p) = ns_veg%retransn_patch(p) + nf_veg%livestemn_to_retransn_patch(p)*dt ! From cc32593678545860c6ef9c99148839d910194136 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 15:59:41 -0600 Subject: [PATCH 1461/2067] Filled _to_removedresidue placeholders in CNCropHarvestToProductPools() --- src/biogeochem/CNPhenologyMod.F90 | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 143c080409..bc3747a5b1 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3620,13 +3620,13 @@ subroutine CNCropHarvestToProductPools(bounds, num_soilp, filter_soilp, num_soil cnveg_carbonflux_inst%crop_harvestc_to_cropprodc_patch(p) = & cnveg_carbonflux_inst%leafc_to_biofuelc_patch(p) + & cnveg_carbonflux_inst%livestemc_to_biofuelc_patch(p) + & - 0._r8 + & - 0._r8 + cnveg_carbonflux_inst%leafc_to_removedresiduec_patch(p) + & + cnveg_carbonflux_inst%livestemc_to_removedresiduec_patch(p) cnveg_nitrogenflux_inst%crop_harvestn_to_cropprodn_patch(p) = & cnveg_nitrogenflux_inst%leafn_to_biofueln_patch(p) + & cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch(p) + & - 0._r8 + & - 0._r8 + cnveg_nitrogenflux_inst%leafn_to_removedresiduen_patch(p) + & + cnveg_nitrogenflux_inst%livestemn_to_removedresiduen_patch(p) end do if (use_grainproduct) then From 96211909e70ba554552839cefc1b190cb9b651f0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 19 Jul 2023 15:27:46 -0600 Subject: [PATCH 1462/2067] Added associate statements for to_removedresidue pools to CNOffsetLitterfall(). --- src/biogeochem/CNPhenologyMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bc3747a5b1..cf2e04c4dc 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3025,6 +3025,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) leafc_to_biofuelc => cnveg_carbonflux_inst%leafc_to_biofuelc_patch , & ! Output: [real(r8) (:) ] leaf C to biofuel C (gC/m2/s) livestemc_to_biofuelc => cnveg_carbonflux_inst%livestemc_to_biofuelc_patch , & ! Output: [real(r8) (:) ] livestem C to biofuel C (gC/m2/s) + leafc_to_removedresiduec => cnveg_carbonflux_inst%leafc_to_removedresiduec_patch , & ! Output: [real(r8) (:) ] leaf C to removed residue C (gC/m2/s) + livestemc_to_removedresiduec => cnveg_carbonflux_inst%livestemc_to_removedresiduec_patch , & ! Output: [real(r8) (:) ] livestem C to removed residue C (gC/m2/s) leafn => cnveg_nitrogenstate_inst%leafn_patch , & ! Input: [real(r8) (:) ] (gN/m2) leaf N frootn => cnveg_nitrogenstate_inst%frootn_patch , & ! Input: [real(r8) (:) ] (gN/m2) fine root N @@ -3035,6 +3037,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_structuren_to_litter => cnveg_nitrogenflux_inst%repr_structuren_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure N to litter (gN/m2/s) leafn_to_biofueln => cnveg_nitrogenflux_inst%leafn_to_biofueln_patch , & ! Output: [real(r8) (:) ] leaf N to biofuel N (gN/m2/s) livestemn_to_biofueln => cnveg_nitrogenflux_inst%livestemn_to_biofueln_patch, & ! Output: [real(r8) (:) ] livestem N to biofuel N (gN/m2/s) + leafn_to_removedresiduen => cnveg_nitrogenflux_inst%leafn_to_removedresiduen_patch , & ! Output: [real(r8) (:) ] leaf N to removed residue N (gN/m2/s) + livestemn_to_removedresiduen => cnveg_nitrogenflux_inst%livestemn_to_removedresiduen_patch, & ! Output: [real(r8) (:) ] livestem N to removed residue N (gN/m2/s) leafn_to_litter => cnveg_nitrogenflux_inst%leafn_to_litter_patch , & ! Output: [real(r8) (:) ] leaf N litterfall (gN/m2/s) leafn_to_retransn => cnveg_nitrogenflux_inst%leafn_to_retransn_patch , & ! Input: [real(r8) (:) ] leaf N to retranslocated N pool (gN/m2/s) free_retransn_to_npool=> cnveg_nitrogenflux_inst%free_retransn_to_npool_patch , & ! Input: [real(r8) (:) ] free leaf N to retranslocated N pool (gN/m2/s) From 431dfe786afd6101cda07fcd5d99b99a1f716752 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Sep 2023 13:57:28 -0600 Subject: [PATCH 1463/2067] Added comment explaining no update of leafn_to_litter. --- src/biogeochem/CNPhenologyMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 0b9c69698e..22945e9b68 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -3136,6 +3136,10 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & leafc_to_litter(p) = t1 * leafc_remaining + cpool_to_leafc(p) livestemc_to_litter(p) = t1 * livestemc_remaining + cpool_to_livestemc(p) livestemn_to_litter(p) = t1 * livestemn_remaining + ! Sam Rabin 2023-09-11: + ! leafn_to_litter is calculated below based on leafc_to_litter (updated above) + ! as well as leaf C:N ratio (unaffected by biofuel harvest). It thus does not + ! need to be updated here. ! Matrix for grain, livestem to litter and biofuel if(use_matrixcn)then From 74b11d8b75a27dc271f715e34b6b919247b8368f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Sep 2023 14:07:49 -0600 Subject: [PATCH 1464/2067] Add residue removal code, but removedresidue_fraction 0. --- src/biogeochem/CNPhenologyMod.F90 | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index cf2e04c4dc..9d20d33573 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2981,6 +2981,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & real(r8) :: repr_grainc_to_food_thispool ! amount added to / subtracted from repr_grainc_to_food for the pool in question (gC/m2/s) real(r8) :: leafc_remaining, livestemc_remaining real(r8) :: leafn_remaining, livestemn_remaining + real(r8) :: removedresidue_fraction !----------------------------------------------------------------------- associate( & @@ -3051,6 +3052,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! The litterfall transfer rate starts at 0.0 and increases linearly ! over time, with displayed growth going to 0.0 on the last day of litterfall + + removedresidue_fraction = 0._r8 do fp = 1,num_soilp p = filter_soilp(fp) @@ -3137,6 +3140,16 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & livestemc_remaining = livestemc(p)*(1._r8-biofuel_harvfrac(ivt(p))) livestemn_remaining = livestemn(p)*(1._r8-biofuel_harvfrac(ivt(p))) + ! Remove residues + leafc_to_removedresiduec(p) = t1 * leafc_remaining * removedresidue_fraction + leafn_to_removedresiduen(p) = t1 * leafn_remaining * removedresidue_fraction + livestemc_to_removedresiduec(p) = t1 * livestemc_remaining * removedresidue_fraction + livestemn_to_removedresiduen(p) = t1 * livestemn_remaining * removedresidue_fraction + leafc_remaining = leafc_remaining * (1._r8 - removedresidue_fraction) + leafn_remaining = leafn_remaining * (1._r8 - removedresidue_fraction) + livestemc_remaining = livestemc_remaining * (1._r8 - removedresidue_fraction) + livestemn_remaining = livestemn_remaining * (1._r8 - removedresidue_fraction) + leafc_to_litter(p) = t1 * leafc_remaining + cpool_to_leafc(p) livestemc_to_litter(p) = t1 * livestemc_remaining + cpool_to_livestemc(p) livestemn_to_litter(p) = t1 * livestemn_remaining From 1ec3f6255350c57c61e0e1e10b9922661ce66e6e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 11 Sep 2023 14:09:45 -0600 Subject: [PATCH 1465/2067] Add namelist parameter crop_residue_removal_frac. Replaces hard-coded removedresidue_fraction. --- bld/CLMBuildNamelist.pm | 7 ++++++- bld/namelist_files/namelist_defaults_ctsm.xml | 2 ++ .../namelist_definition_ctsm.xml | 7 +++++++ src/biogeochem/CNPhenologyMod.F90 | 20 +++++++++---------- src/main/clm_varctl.F90 | 3 +++ src/main/controlMod.F90 | 4 +++- 6 files changed, 30 insertions(+), 13 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 69b3a8c3dc..30642a97df 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2177,8 +2177,13 @@ sub setup_logic_crop_inparm { } add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "initial_seed_at_planting", 'use_crop'=>$nl->get_value('use_crop') ); + + my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac'); + if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) { + $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]"); + } } else { - error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept" ); + error_if_set( $nl, "Can NOT be set without crop on", "baset_mapping", "baset_latvary_slope", "baset_latvary_intercept", "crop_residue_removal_frac" ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_fsat_equals_zero' ); } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 1d895524e6..b30bc9db53 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -544,6 +544,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. .true. +0.d+0 + constant varytropicsbylat diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 45a32cb224..8131bc8f9f 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1089,6 +1089,13 @@ Toggle to turn on the prognostic fertilizer for crop model Toggle to turn on the 1-year grain product pool in the crop model + +Fraction of post-harvest crop residues (leaf and stem) to move to +1-year product pool instead of letting them fall as litter. +Default: 0.0 + + Type of mapping to use for base temperature for prognostic crop model diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 9d20d33573..5576090d53 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2954,7 +2954,7 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & use pftconMod , only : nmiscanthus, nirrig_miscanthus, nswitchgrass, nirrig_switchgrass use CNSharedParamsMod, only : use_fun - use clm_varctl , only : CNratio_floating + use clm_varctl , only : CNratio_floating, crop_residue_removal_frac ! ! !ARGUMENTS: integer , intent(in) :: num_soilp ! number of soil patches in filter @@ -3053,8 +3053,6 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & ! The litterfall transfer rate starts at 0.0 and increases linearly ! over time, with displayed growth going to 0.0 on the last day of litterfall - removedresidue_fraction = 0._r8 - do fp = 1,num_soilp p = filter_soilp(fp) @@ -3141,14 +3139,14 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & livestemn_remaining = livestemn(p)*(1._r8-biofuel_harvfrac(ivt(p))) ! Remove residues - leafc_to_removedresiduec(p) = t1 * leafc_remaining * removedresidue_fraction - leafn_to_removedresiduen(p) = t1 * leafn_remaining * removedresidue_fraction - livestemc_to_removedresiduec(p) = t1 * livestemc_remaining * removedresidue_fraction - livestemn_to_removedresiduen(p) = t1 * livestemn_remaining * removedresidue_fraction - leafc_remaining = leafc_remaining * (1._r8 - removedresidue_fraction) - leafn_remaining = leafn_remaining * (1._r8 - removedresidue_fraction) - livestemc_remaining = livestemc_remaining * (1._r8 - removedresidue_fraction) - livestemn_remaining = livestemn_remaining * (1._r8 - removedresidue_fraction) + leafc_to_removedresiduec(p) = t1 * leafc_remaining * crop_residue_removal_frac + leafn_to_removedresiduen(p) = t1 * leafn_remaining * crop_residue_removal_frac + livestemc_to_removedresiduec(p) = t1 * livestemc_remaining * crop_residue_removal_frac + livestemn_to_removedresiduen(p) = t1 * livestemn_remaining * crop_residue_removal_frac + leafc_remaining = leafc_remaining * (1._r8 - crop_residue_removal_frac) + leafn_remaining = leafn_remaining * (1._r8 - crop_residue_removal_frac) + livestemc_remaining = livestemc_remaining * (1._r8 - crop_residue_removal_frac) + livestemn_remaining = livestemn_remaining * (1._r8 - crop_residue_removal_frac) leafc_to_litter(p) = t1 * leafc_remaining + cpool_to_leafc(p) livestemc_to_litter(p) = t1 * livestemc_remaining + cpool_to_livestemc(p) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 64aa40d94d..85334aa27f 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -157,6 +157,9 @@ module clm_varctl ! set saturated excess runoff to zero for crops logical, public :: crop_fsat_equals_zero = .false. + + ! remove this fraction of crop residues to a 1-year product pool (instead of going to litter) + real(r8), public :: crop_residue_removal_frac = 0.0 !---------------------------------------------------------- ! Other subgrid logic diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index c1a7959459..046201a548 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -282,7 +282,7 @@ subroutine control_init(dtime) use_lch4, use_nitrif_denitrif, use_extralakelayers, & use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, o3_veg_stress_method, & use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, & - use_nguardrail + use_nguardrail, crop_residue_removal_frac ! ---------------------------------------------------------------------- @@ -632,6 +632,7 @@ subroutine control_spmd() call mpi_bcast (use_crop, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fertilizer, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_grainproduct, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (crop_residue_removal_frac, 1, MPI_REAL8, 0, mpicom, ier) call mpi_bcast (o3_veg_stress_method, len(o3_veg_stress_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (use_snicar_frc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_vancouver, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -879,6 +880,7 @@ subroutine control_print () write(iulog,*) ' use_crop = ', use_crop write(iulog,*) ' use_fertilizer = ', use_fertilizer write(iulog,*) ' use_grainproduct = ', use_grainproduct + write(iulog,*) ' crop_residue_removal_frac = ', crop_residue_removal_frac write(iulog,*) ' o3_veg_stress_method = ', o3_veg_stress_method write(iulog,*) ' use_snicar_frc = ', use_snicar_frc write(iulog,*) ' use_vancouver = ', use_vancouver From 385ebee260df2b0573b98cc1ae0be79be5455178 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 12 Sep 2023 09:16:48 -0600 Subject: [PATCH 1466/2067] update Changelog date --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 17902f605f..51003a9c1d 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev140 Originator(s): afoster (Adrianna Foster) -Date: Mon Sep 11 15:04:02 MDT 2023 +Date: Tue Sep 12 09:16:37 MDT 2023 One-line Summary: add lai_streams capability for FATES Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index eedc5a1aac..5ca9ceab70 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev140 afoster 09/11/2023 add lai_streams capability for FATES + ctsm5.1.dev140 afoster 09/12/2023 add lai_streams capability for FATES ctsm5.1.dev139 slevis 08/28/2023 Fix problems uncovered by nag -nan tests ctsm5.1.dev138 slevis 08/25/2023 Refactor max_patch_per_col and maxsoil_patches loops ctsm5.1.dev137 slevis 08/23/2023 Surface roughness modifications From 4e0144dc937f7ef6aac2d683515d8b3161f4e6b4 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 12 Sep 2023 12:05:08 -0400 Subject: [PATCH 1467/2067] arguments and hist call updates --- src/utils/clmfates_interfaceMod.F90 | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index f7699884df..d989e3546e 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1076,7 +1076,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call fates_hist%update_history_dyn( nc, & this%fates(nc)%nsites, & this%fates(nc)%sites, & - this%fates(nc)%bc_in, ) + this%fates(nc)%bc_in ) if (masterproc) then write(iulog, *) 'clm: leaving fates model', bounds_clump%begg, & @@ -2635,13 +2635,20 @@ subroutine wrap_update_hifrq_hist(this, bounds_clump, & dtime = get_step_size_real() ! Update history variables that track these variables - call fates_hist%update_history_hifrq(nc, & + call fates_hist%update_history_hifrq_simple(nc, & this%fates(nc)%nsites, & this%fates(nc)%sites, & this%fates(nc)%bc_in, & this%fates(nc)%bc_out, & dtime) + call fates_hist%update_history_hifrq_multi(nc, & + this%fates(nc)%nsites, & + this%fates(nc)%sites, & + this%fates(nc)%bc_in, & + this%fates(nc)%bc_out, & + dtime) + end associate call t_stopf('fates_wrap_update_hifrq_hist') From 24dee0029ce2ec8c433a8bdad16fb8f8b7b03807 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 12 Sep 2023 10:24:25 -0600 Subject: [PATCH 1468/2067] add bldnamelist tests --- bld/CLMBuildNamelist.pm | 9 +++++---- bld/unit_testers/build-namelist_test.pl | 20 ++++++++++++++++++++ doc/ChangeLog | 2 ++ 3 files changed, 27 insertions(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 7ac29a6fc9..4ba5588bc6 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3921,17 +3921,18 @@ sub setup_logic_lai_streams { } else { # If bgc is BGC/BGCDV then make sure none of the LAI settings are set if ( &value_is_true($nl->get_value('use_lai_streams'))) { - $log->fatal_error("When bgc is NOT SP use_lai_streams cannot be .true.\n" . - "(eg. don't use this option with BGC or BGCDV)."); + $log->fatal_error("When not in SP mode use_lai_streams cannot be .true.\n" . + "(eg. don't use this option with BGC or non-SP FATES," . + "update compset to use SP)"); } if ( defined($nl->get_value('stream_year_first_lai')) || defined($nl->get_value('stream_year_last_lai')) || defined($nl->get_value('model_year_align_lai')) || defined($nl->get_value('lai_tintalgo' )) || defined($nl->get_value('stream_fldfilename_lai')) ) { - $log->fatal_error("When bgc is NOT SP none of the following can be set: stream_year_first_lai,\n" . + $log->fatal_error("When not in SP mode none of the following can be set: stream_year_first_lai,\n" . "stream_year_last_lai, model_year_align_lai, lai_tintalgo nor\n" . - "stream_fldfilename_lai (eg. don't use this option with BGC or BGCDV)."); + "stream_fldfilename_lai (eg. don't use this option with BGC or FATES-SP)."); } } } diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index bbf991a7a7..219aecfcbd 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1226,6 +1226,26 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, + "fates_non_sp_laistreams" =>{ options=>"--envxml_dir . --bgc fates", + namelist=>"use_lai_streams=.true., use_fates_sp=.false.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "bgc_non_sp_laistreams" =>{ options=>"--envxml_dir . --bgc bgc", + namelist=>"use_lai_streams=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "bgc_laistreams_input" =>{ options=>"--envxml_dir . --bgc bgc", + namelist=>"use_lai_streams=.false., stream_year_first_lai=1999", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "crop_laistreams_input" =>{ options=>"--envxml_dir . --bgc sp --crop", + namelist=>"use_lai_streams=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, ); foreach my $key ( keys(%failtest) ) { print( "$key\n" ); diff --git a/doc/ChangeLog b/doc/ChangeLog index 51003a9c1d..aed3eeaac6 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -34,6 +34,8 @@ CTSM issues fixed (include CTSM Issue #): #1722 Notes of particular relevance for developers: --------------------------------------------- +build-namelist tests (if CLMBuildNamelist.pm has changed): added tests to make sure use_lai_streams failed correctly + Changes to tests or testing: Added a test for lai_streams with FATES Testing summary: From 1fb58be1a51cb65c8656e51ba1f291ef47a1d51d Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 12 Sep 2023 10:46:34 -0600 Subject: [PATCH 1469/2067] trying to fix --- bld/CLMBuildNamelist.pm | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 4ba5588bc6..74ed2d4528 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3890,10 +3890,7 @@ sub setup_logic_lai_streams { if ( &value_is_true($nl_flags->{'use_crop'}) && &value_is_true($nl->get_value('use_lai_streams')) ) { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } - if ( ($nl_flags->{'bgc_mode'} eq "sp" || $nl_flags->{'bgc_mode'} eq "fates") ) { - if ( $nl_flags->{'bgc_mode'} eq "fates" && ! &value_is_true($nl->get_value('use_fates_sp')) && &value_is_true($nl->get_value('use_lai_streams'))) { - $log->fatal_error("Must have use_fates_sp turned on to run FATES with LAI streams."); - } + if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) { if ( &value_is_true($nl->get_value('use_lai_streams')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', From ec938f04b11db5d885daf4da6d898349a6d2014f Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 12 Sep 2023 11:47:48 -0600 Subject: [PATCH 1470/2067] trying to fix issues --- bld/CLMBuildNamelist.pm | 5 +++-- bld/unit_testers/build-namelist_test.pl | 12 ++++++------ 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 74ed2d4528..3597b9cf30 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3891,6 +3891,7 @@ sub setup_logic_lai_streams { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) { + #print "WE ARE HERE" if ( &value_is_true($nl->get_value('use_lai_streams')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', @@ -3919,8 +3920,8 @@ sub setup_logic_lai_streams { # If bgc is BGC/BGCDV then make sure none of the LAI settings are set if ( &value_is_true($nl->get_value('use_lai_streams'))) { $log->fatal_error("When not in SP mode use_lai_streams cannot be .true.\n" . - "(eg. don't use this option with BGC or non-SP FATES," . - "update compset to use SP)"); + "(eg. don't use this option with BGC or non-SP FATES), \n" . + "Update compset to use SP)"); } if ( defined($nl->get_value('stream_year_first_lai')) || defined($nl->get_value('stream_year_last_lai')) || diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 219aecfcbd..812bbb4054 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1231,16 +1231,16 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "bgc_non_sp_laistreams" =>{ options=>"--envxml_dir . --bgc bgc", + "bgc_non_sp_laistreams" =>{ options=>"--envxml_dir . -bgc bgc", namelist=>"use_lai_streams=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "bgc_laistreams_input" =>{ options=>"--envxml_dir . --bgc bgc", - namelist=>"use_lai_streams=.false., stream_year_first_lai=1999", - GLC_TWO_WAY_COUPLING=>"FALSE", - phys=>"clm5_0", - }, + # "bgc_laistreams_input" =>{ options=>"--envxml_dir . --bgc bgc", + # namelist=>"stream_year_first_lai=1999", + # GLC_TWO_WAY_COUPLING=>"FALSE", + # phys=>"clm5_0", + # }, "crop_laistreams_input" =>{ options=>"--envxml_dir . --bgc sp --crop", namelist=>"use_lai_streams=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", From 79c8a85e25ae74b6e2d95381f5ee87c2db965c67 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Tue, 12 Sep 2023 14:05:39 -0600 Subject: [PATCH 1471/2067] fix typo --- bld/unit_testers/build-namelist_test.pl | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 812bbb4054..da4201d68f 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile { # # Figure out number of tests that will run # -my $ntests = 1992; +my $ntests = 1999; if ( defined($opts{'compare'}) ) { $ntests += 1353; @@ -1227,22 +1227,22 @@ sub cat_and_create_namelistinfile { phys=>"clm5_0", }, "fates_non_sp_laistreams" =>{ options=>"--envxml_dir . --bgc fates", - namelist=>"use_lai_streams=.true., use_fates_sp=.false.", + namelst=>"use_lai_streams=.true., use_fates_sp=.false.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - "bgc_non_sp_laistreams" =>{ options=>"--envxml_dir . -bgc bgc", - namelist=>"use_lai_streams=.true.", + "bgc_non_sp_laistreams" =>{ options=>"--envxml_dir . -bgc bgc", + namelst=>"use_lai_streams=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm5_0", + }, + "bgc_laistreams_input" =>{ options=>"--envxml_dir . --bgc bgc", + namelst=>"stream_year_first_lai=1999", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, - # "bgc_laistreams_input" =>{ options=>"--envxml_dir . --bgc bgc", - # namelist=>"stream_year_first_lai=1999", - # GLC_TWO_WAY_COUPLING=>"FALSE", - # phys=>"clm5_0", - # }, "crop_laistreams_input" =>{ options=>"--envxml_dir . --bgc sp --crop", - namelist=>"use_lai_streams=.true.", + namelst=>"use_lai_streams=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm5_0", }, From 451cbc6050626eaa6cc5c1d34b8c30af10c05af8 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 12 Sep 2023 14:47:21 -0600 Subject: [PATCH 1472/2067] update changelog date --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index aed3eeaac6..479e59d9a7 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev140 Originator(s): afoster (Adrianna Foster) -Date: Tue Sep 12 09:16:37 MDT 2023 +Date: Tue Sep 12 14:47:06 MDT 2023 One-line Summary: add lai_streams capability for FATES Purpose and description of changes From 6bfb9b084694a7f00100f485e65003dc8d00143b Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 12 Sep 2023 15:16:40 -0600 Subject: [PATCH 1473/2067] remove print statement --- bld/CLMBuildNamelist.pm | 1 - 1 file changed, 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 3597b9cf30..72c3b1b74a 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3891,7 +3891,6 @@ sub setup_logic_lai_streams { $log->fatal_error("turning use_lai_streams on is incompatable with use_crop set to true."); } if ( $nl_flags->{'bgc_mode'} eq "sp" || ($nl_flags->{'bgc_mode'} eq "fates" && &value_is_true($nl->get_value('use_fates_sp')) )) { - #print "WE ARE HERE" if ( &value_is_true($nl->get_value('use_lai_streams')) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_lai_streams'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lai_mapalgo', From 175fab0ae7a5a527d7a7e551d23f70bdda177dc1 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 12 Sep 2023 15:20:20 -0600 Subject: [PATCH 1474/2067] add issue discription in changelog --- doc/ChangeLog | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 479e59d9a7..955f071933 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -29,7 +29,7 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed or introduced ------------------------ -CTSM issues fixed (include CTSM Issue #): #1722 +CTSM issues fixed (include CTSM Issue #): #1722 - Should be able to use lai streams with FATES-SP mode Notes of particular relevance for developers: --------------------------------------------- @@ -60,7 +60,7 @@ Other details List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates -Pull Requests that document the changes (include PR ids): #2054 +Pull Requests that document the changes (include PR ids): #2054 (https://github.com/ESCOMP/ctsm/pull) =============================================================== From 4f4a683d9ef8263b5fd36da72bdf347e72790d89 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 12 Sep 2023 15:37:59 -0600 Subject: [PATCH 1475/2067] Add a small clarification to the tagging steps --- doc/README.CHECKLIST.master_tags | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/doc/README.CHECKLIST.master_tags b/doc/README.CHECKLIST.master_tags index 53540aaf37..ed7794130b 100644 --- a/doc/README.CHECKLIST.master_tags +++ b/doc/README.CHECKLIST.master_tags @@ -73,7 +73,10 @@ This should show no diffs (9) Make an annotated tag on master -(10) Push master and tag to ESCOMP/ctsm +(10) Push tag to ESCOMP/ctsm + +(10a) Push to master (if needed because you changed something in master after PR was merged, or +if you did step 7 above using git commands that require this step) (11) Update the CTSM upcoming tags project, if necessary (https://github.com/ESCOMP/ctsm/projects/6) From 3695c6095718f40d47f9113e734a5b90c19ffdcc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 12 Sep 2023 22:28:36 -0600 Subject: [PATCH 1476/2067] Reverted rearrangement of fc_air_frac_as_frac_porosity calculation. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index ecb4c38e59..4ec25bbadc 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -268,7 +268,10 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & ! calculate gas diffusivity of soil at field capacity here ! use expression from methane code, but neglect OM for now fc_air_frac = watsat(c,j)-watfc(c,j) ! theta_a in Riley et al. (2011) - fc_air_frac_as_frac_porosity = fc_air_frac / watsat(c,j) ! theta_a/theta_s in Riley et al. (2011) + fc_air_frac_as_frac_porosity = 1._r8 - watfc(c,j) / watsat(c,j) + ! This calculation of fc_air_frac_as_frac_porosity is algebraically equivalent to + ! fc_air_frac/watsat(c,j). In that form, it's easier to see its correspondence + ! to theta_a/theta_s in Riley et al. (2011). ! use diffusivity calculation including peat if (use_lch4) then From 8b75c9b03dd17f61680c17023c0c5b7066a44fb4 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 Sep 2023 10:00:23 -0600 Subject: [PATCH 1477/2067] Moving run_neon.py to /python and creating wrapper script for it --- .../ctsm}/site_and_regional/run_neon.py | 5 -- tools/site_and_regional/run_neon | 47 +++++++++++++++++++ 2 files changed, 47 insertions(+), 5 deletions(-) rename {tools => python/ctsm}/site_and_regional/run_neon.py (99%) create mode 100755 tools/site_and_regional/run_neon diff --git a/tools/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py similarity index 99% rename from tools/site_and_regional/run_neon.py rename to python/ctsm/site_and_regional/run_neon.py index 84c00715fb..aa6e0c3ffb 100755 --- a/tools/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -875,8 +875,3 @@ def main(description): rerun, experiment, ) - - - -if __name__ == "__main__": - main(__doc__) diff --git a/tools/site_and_regional/run_neon b/tools/site_and_regional/run_neon new file mode 100755 index 0000000000..ad930f50e3 --- /dev/null +++ b/tools/site_and_regional/run_neon @@ -0,0 +1,47 @@ +#!/usr/bin/env python3 +""" +This is a just top-level skeleton script that calls +run_neon.py. +The original code (run_neon.py) is located under +python/ctsm/site_and_regional folder. + +For full instructions on how to run the code and different options, +please check python/ctsm/site_and_regional/run_neon.py file. + +This script first creates and builds a generic base case. +Next, it will clone the base_case for different neon sites and run +types to reduce the need to build ctsm everytime. + +This script will do the following: + 1) Create a generic base case for cloning. + 2) Make the case for the specific neon site(s). + 3) Make changes to the case, for: + a. AD spinup + b. post-AD spinup + c. transient + #--------------- + d. SASU or Matrix spinup + 4) Build and submit the case. + +---------------------------------------------------------------- +To see all available options for running tower sites: + ./run_neon --help +---------------------------------------------------------------- +Instructions for running using conda python environments: +../../py_env_create +conda activate ctsm_pylib +""" + +import os +import sys + +# -- add python/ctsm to path +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.site_and_regional.run_neon import main + +if __name__ == "__main__": + main(__doc__) From 8260253b8bc49b3976e578183f5ccd19389c6a26 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 Sep 2023 11:06:31 -0600 Subject: [PATCH 1478/2067] Moving modify_singlept_site_neon.py to /python and creating wrapper script for it --- .../modify_singlept_site_neon.py | 6 +-- .../modify_singlept_site_neon | 45 +++++++++++++++++++ 2 files changed, 46 insertions(+), 5 deletions(-) rename {tools => python/ctsm}/site_and_regional/modify_singlept_site_neon.py (99%) create mode 100755 tools/site_and_regional/modify_singlept_site_neon diff --git a/tools/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py similarity index 99% rename from tools/site_and_regional/modify_singlept_site_neon.py rename to python/ctsm/site_and_regional/modify_singlept_site_neon.py index e135760a48..c5ae7eb31b 100755 --- a/tools/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -153,7 +153,7 @@ def get_parser(): parser.add_argument( "--inputdata-dir", help=""" - Directory to write updated single point surface dataset. + Directory containing standard input files from CESM input data such as the surf_soildepth_file. [default: %(default)s] """, action="store", @@ -735,7 +735,3 @@ def main(): + "):\n - " + wfile ) - - -if __name__ == "__main__": - main() diff --git a/tools/site_and_regional/modify_singlept_site_neon b/tools/site_and_regional/modify_singlept_site_neon new file mode 100755 index 0000000000..1b790a74ca --- /dev/null +++ b/tools/site_and_regional/modify_singlept_site_neon @@ -0,0 +1,45 @@ +#!/usr/bin/env python3 +""" +This is a just top-level skeleton script that calls +modify_singlept_site_neon.py. +The original code (modify_singlept_site_neon.py) is located under +python/ctsm/site_and_regional folder. + +For full instructions on how to run the code and different options, +please check python/ctsm/site_and_regional/modify_singlept_site_neon.py file. + +This script is for modifying surface dataset at neon sites +using data available from the neon server. + +After creating a single point surface data file from a global +surface data file using subset_data.py, use this script to +overwrite some fields with site-specific data for neon sites. + +This script will do the following: +- Download neon data for the specified site if it does not exist + in the specified directory : (i.e. ../../../neon_surf_files). +- Modify surface dataset with downloaded data. + +---------------------------------------------------------------- +To see all available options for modifying surface datasets at +tower sites: + ./modify_singlept_site_neon --help +---------------------------------------------------------------- +Instructions for running using conda python environments: +../../py_env_create +conda activate ctsm_pylib +""" + +import os +import sys + +# -- add python/ctsm to path +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.site_and_regional.modify_singlept_site_neon import main + +if __name__ == "__main__": + main() From 83d36edc75080c5d9fbec97bd284bae02423780e Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 13 Sep 2023 11:13:11 -0600 Subject: [PATCH 1479/2067] Moving neon_surf_wrapper.py to /python and creating wrapper script for it --- .../site_and_regional/neon_surf_wrapper.py | 14 +++---- tools/site_and_regional/neon_surf_wrapper | 37 +++++++++++++++++++ 2 files changed, 42 insertions(+), 9 deletions(-) rename {tools => python/ctsm}/site_and_regional/neon_surf_wrapper.py (92%) create mode 100755 tools/site_and_regional/neon_surf_wrapper diff --git a/tools/site_and_regional/neon_surf_wrapper.py b/python/ctsm/site_and_regional/neon_surf_wrapper.py similarity index 92% rename from tools/site_and_regional/neon_surf_wrapper.py rename to python/ctsm/site_and_regional/neon_surf_wrapper.py index 3271c72f08..ce9efc4ed5 100755 --- a/tools/site_and_regional/neon_surf_wrapper.py +++ b/python/ctsm/site_and_regional/neon_surf_wrapper.py @@ -14,7 +14,7 @@ Instructions for running using conda python environments: ../../py_env_create -conda activate ctsm_py +conda activate ctsm_pylib """ # TODO @@ -118,7 +118,7 @@ def main(): subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), '--site',clmsite, '--create-surface','--uniform-snowpack', '--cap-saturation','--verbose','--overwrite'] - modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', 'subset_data_single_point', '--16pft'] elif args.pft_16: # use surface dataset with 16 pfts, but overwrite to 100% 1 dominant PFT @@ -127,7 +127,7 @@ def main(): subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), '--site',clmsite,'--dompft',str(pft),'--create-surface', '--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', 'subset_data_single_point', '--16pft'] elif args.mixed: # use surface dataset with 78 pfts, and don't overwrite with 100% 1 dominant PFT @@ -137,7 +137,7 @@ def main(): subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), '--site',clmsite,'--crop','--create-surface', '--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', 'subset_data_single_point'] else: # use surface dataset with 78 pfts, and overwrite to 100% 1 dominant PFT @@ -147,11 +147,7 @@ def main(): subset_command = ['./subset_data', 'point', '--lat', str(lat), '--lon', str(lon), '--site', clmsite,'--crop', '--dompft', str(pft), '--create-surface', '--uniform-snowpack', '--cap-saturation', '--verbose', '--overwrite'] - modify_command = ['./modify_singlept_site_neon.py', '--neon_site', site, '--surf_dir', + modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', 'subset_data_single_point'] execute(subset_command) execute(modify_command) - -if __name__ == "__main__": - main() - diff --git a/tools/site_and_regional/neon_surf_wrapper b/tools/site_and_regional/neon_surf_wrapper new file mode 100755 index 0000000000..306d38a774 --- /dev/null +++ b/tools/site_and_regional/neon_surf_wrapper @@ -0,0 +1,37 @@ +#!/usr/bin/env python3 +""" +This is a just top-level skeleton script that calls +neon_surf_wrapper.py. +The original code (neon_surf_wrapper.py) is located under +python/ctsm/site_and_regional folder. + +For full instructions on how to run the code and different options, +please check python/ctsm/site_and_regional/neon_surf_wrapper.py file. + +This script is a simple wrapper for neon sites that performs the +following: + 1) For neon sites, subset surface dataset from global dataset + (i.e. ./subset_data.py ) + 2) Download neon and update the created surface dataset + based on the downloaded neon data. + (i.e. modify_singlept_site_neon.py) + +---------------------------------------------------------------- +Instructions for running using conda python environments: +../../py_env_create +conda activate ctsm_pylib +""" + +import os +import sys + +# -- add python/ctsm to path +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.site_and_regional.neon_surf_wrapper import main + +if __name__ == "__main__": + main() From 4ee49e3e516ca7dee5df378f65664f93a7db4415 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 13 Sep 2023 11:21:04 -0600 Subject: [PATCH 1480/2067] reformatting with black --- .../modify_singlept_site_neon.py | 63 +++--- .../site_and_regional/neon_surf_wrapper.py | 200 ++++++++++++------ python/ctsm/site_and_regional/run_neon.py | 119 +++++------ 3 files changed, 216 insertions(+), 166 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index c5ae7eb31b..a33323ed7a 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -160,7 +160,7 @@ def get_parser(): dest="inputdatadir", type=str, required=False, - default="/glade/p/cesmdata/cseg/inputdata" + default="/glade/p/cesmdata/cseg/inputdata", ) parser.add_argument( "-d", @@ -233,10 +233,7 @@ def get_neon(neon_dir, site_name): print("Download finished successfully for", site_name) elif response.status_code == 404: sys.exit( - "Data for this site " - + site_name - + " was not available on the neon server:" - + url + "Data for this site " + site_name + " was not available on the neon server:" + url ) print("Download exit status code: ", response.status_code) @@ -270,12 +267,12 @@ def find_surffile(surf_dir, site_name, pft_16): """ if pft_16: - sf_name = "surfdata_1x1_NEON_"+site_name+"*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" + sf_name = "surfdata_1x1_NEON_" + site_name + "*hist_16pfts_Irrig_CMIP6_simyr2000_*.nc" else: - sf_name = "surfdata_1x1_NEON_" +site_name+"*hist_78pfts_CMIP6_simyr2000_*.nc" + sf_name = "surfdata_1x1_NEON_" + site_name + "*hist_78pfts_CMIP6_simyr2000_*.nc" - print (os.path.join(surf_dir , sf_name)) - surf_file = sorted(glob.glob(os.path.join(surf_dir , sf_name))) + print(os.path.join(surf_dir, sf_name)) + surf_file = sorted(glob.glob(os.path.join(surf_dir, sf_name))) if len(surf_file) > 1: print("The following files found :", *surf_file, sep="\n- ") @@ -287,10 +284,14 @@ def find_surffile(surf_dir, site_name, pft_16): surf_file = surf_file[0] else: sys.exit( - "Surface data for this site " + str(site_name) + " was not found:" + str(surf_dir) + str(sf_name) + - "." + - "\n" + - "Please run ./subset_data.py for this site." + "Surface data for this site " + + str(site_name) + + " was not found:" + + str(surf_dir) + + str(sf_name) + + "." + + "\n" + + "Please run ./subset_data.py for this site." ) return surf_file @@ -324,10 +325,8 @@ def find_soil_structure(args, surf_file): print("------------") # print (f1.attrs["Soil_texture_raw_data_file_name"]) - clm_input_dir = os.path.join( args.inputdatadir, "lnd/clm2/rawdata/" ) - surf_soildepth_file = os.path.join( - clm_input_dir, f1.attrs["Soil_texture_raw_data_file_name"] - ) + clm_input_dir = os.path.join(args.inputdatadir, "lnd/clm2/rawdata/") + surf_soildepth_file = os.path.join(clm_input_dir, f1.attrs["Soil_texture_raw_data_file_name"]) if os.path.exists(surf_soildepth_file): print( @@ -345,9 +344,7 @@ def find_soil_structure(args, surf_file): else: sys.exit( - "Cannot find soil structure file : " - + surf_soildepth_file - + "for the surface dataset." + "Cannot find soil structure file : " + surf_soildepth_file + "for the surface dataset." ) return soil_bot, soil_top @@ -492,9 +489,9 @@ def download_file(url, fname): elif response.status_code == 404: print("File " + fname + "was not available on the neon server:" + url) except Exception as err: - print ('The server could not fulfill the request.') - print ('Something went wrong in downloading', fname) - print ('Error code:', err.code) + print("The server could not fulfill the request.") + print("Something went wrong in downloading", fname) + print("Error code:", err.code) def fill_interpolate(f2, var, method): @@ -536,8 +533,10 @@ def main(): # Check if pandas is a recent enough version pdvers = pd.__version__ if version.parse(pdvers) < version.parse("1.1.0"): - sys.exit("The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", pdvers ) - + sys.exit( + "The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", + pdvers, + ) file_time = check_neon_time() @@ -639,8 +638,7 @@ def main(): estimated_oc = carbon_tot layer_depth = ( - df["biogeoBottomDepth"][bin_index[soil_lev]] - - df["biogeoTopDepth"][bin_index[soil_lev]] + df["biogeoBottomDepth"][bin_index[soil_lev]] - df["biogeoTopDepth"][bin_index[soil_lev]] ) # f2["ORGANIC"][soil_lev] = estimated_oc * bulk_den / 0.58 @@ -709,9 +707,9 @@ def main(): print("Updated : ", f2.PCT_CROP.values) print("Updating PCT_NAT_PFT") - #print (f2.PCT_NAT_PFT) + # print (f2.PCT_NAT_PFT) print(f2.PCT_NAT_PFT.values[0]) - #f2.PCT_NAT_PFT.values[0] = [[100.0]] + # f2.PCT_NAT_PFT.values[0] = [[100.0]] print(f2.PCT_NAT_PFT[0].values) out_dir = args.out_dir @@ -729,9 +727,4 @@ def main(): print(f2.attrs) f2.to_netcdf(path=wfile, mode="w", format="NETCDF3_64BIT") - print( - "Successfully updated surface data file for neon site(" - + site_name - + "):\n - " - + wfile - ) + print("Successfully updated surface data file for neon site(" + site_name + "):\n - " + wfile) diff --git a/python/ctsm/site_and_regional/neon_surf_wrapper.py b/python/ctsm/site_and_regional/neon_surf_wrapper.py index ce9efc4ed5..c2e5ac61b8 100755 --- a/python/ctsm/site_and_regional/neon_surf_wrapper.py +++ b/python/ctsm/site_and_regional/neon_surf_wrapper.py @@ -19,8 +19,8 @@ """ # TODO # Automatic downloading of missing files if they are missing -#-[ ] Download neon sites and dom pft file -#-[ ] Make sure verbose works for printing out commands running +# -[ ] Download neon sites and dom pft file +# -[ ] Make sure verbose works for printing out commands running # Import libraries from __future__ import print_function @@ -35,35 +35,41 @@ import pandas as pd - - -def get_parser(): +def get_parser(): """ Get parser object for this script. """ - parser = argparse.ArgumentParser(description=__doc__, - formatter_class=argparse.RawDescriptionHelpFormatter) + parser = argparse.ArgumentParser( + description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter + ) parser.print_usage = parser.print_help - parser.add_argument('-v','--verbose', - help='Verbose mode will print more information. ', - action="store_true", - dest="verbose", - default=False) - - parser.add_argument('--16pft', - help='Create and/or modify 16-PFT surface datasets (e.g. for a FATES run) ', - action="store_true", - dest="pft_16", - default=False) - - parser.add_argument('-m', '--mixed', - help='Do not overwrite surface dataset to be just one dominant PFT at 100%', - action="store_true", - dest="mixed", - default=False) - + parser.add_argument( + "-v", + "--verbose", + help="Verbose mode will print more information. ", + action="store_true", + dest="verbose", + default=False, + ) + + parser.add_argument( + "--16pft", + help="Create and/or modify 16-PFT surface datasets (e.g. for a FATES run) ", + action="store_true", + dest="pft_16", + default=False, + ) + + parser.add_argument( + "-m", + "--mixed", + help="Do not overwrite surface dataset to be just one dominant PFT at 100%", + action="store_true", + dest="mixed", + default=False, + ) return parser @@ -77,19 +83,15 @@ def execute(command): Raises: Error with the return code from shell. """ - print ('\n',' >> ',*command,'\n') + print("\n", " >> ", *command, "\n") try: subprocess.check_call(command, stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT) except subprocess.CalledProcessError as e: - #raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) - #print (e.ouput) - print (e) - - - - + # raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) + # print (e.ouput) + print(e) def main(): @@ -99,55 +101,129 @@ def main(): if args.verbose: logging.basicConfig(level=logging.DEBUG) - - neon_sites = pd.read_csv('neon_sites_dompft.csv') - + neon_sites = pd.read_csv("neon_sites_dompft.csv") for i, row in tqdm.tqdm(neon_sites.iterrows()): - lat = row['Lat'] - lon = row['Lon'] - site = row['Site'] - pft = row['pft'] - clmsite = "1x1_NEON_"+site - print ("Now processing site :", site) + lat = row["Lat"] + lon = row["Lon"] + site = row["Site"] + pft = row["pft"] + clmsite = "1x1_NEON_" + site + print("Now processing site :", site) if args.mixed and args.pft_16: # use surface dataset with 16 pfts, and don't overwrite with 100% 1 dominant PFT # don't set crop flag # don't set a dominant pft - subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), - '--site',clmsite, '--create-surface','--uniform-snowpack', - '--cap-saturation','--verbose','--overwrite'] - modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', - 'subset_data_single_point', '--16pft'] + subset_command = [ + "./subset_data", + "point", + "--lat", + str(lat), + "--lon", + str(lon), + "--site", + clmsite, + "--create-surface", + "--uniform-snowpack", + "--cap-saturation", + "--verbose", + "--overwrite", + ] + modify_command = [ + "./modify_singlept_site_neon", + "--neon_site", + site, + "--surf_dir", + "subset_data_single_point", + "--16pft", + ] elif args.pft_16: # use surface dataset with 16 pfts, but overwrite to 100% 1 dominant PFT # don't set crop flag # set dominant pft - subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), - '--site',clmsite,'--dompft',str(pft),'--create-surface', - '--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', - 'subset_data_single_point', '--16pft'] + subset_command = [ + "./subset_data", + "point", + "--lat", + str(lat), + "--lon", + str(lon), + "--site", + clmsite, + "--dompft", + str(pft), + "--create-surface", + "--uniform-snowpack", + "--cap-saturation", + "--verbose", + "--overwrite", + ] + modify_command = [ + "./modify_singlept_site_neon", + "--neon_site", + site, + "--surf_dir", + "subset_data_single_point", + "--16pft", + ] elif args.mixed: # use surface dataset with 78 pfts, and don't overwrite with 100% 1 dominant PFT # NOTE: FATES will currently not run with a 78-PFT surface dataset # set crop flag # don't set dominant pft - subset_command = ['./subset_data','point','--lat',str(lat),'--lon',str(lon), - '--site',clmsite,'--crop','--create-surface', - '--uniform-snowpack','--cap-saturation','--verbose','--overwrite'] - modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', - 'subset_data_single_point'] + subset_command = [ + "./subset_data", + "point", + "--lat", + str(lat), + "--lon", + str(lon), + "--site", + clmsite, + "--crop", + "--create-surface", + "--uniform-snowpack", + "--cap-saturation", + "--verbose", + "--overwrite", + ] + modify_command = [ + "./modify_singlept_site_neon", + "--neon_site", + site, + "--surf_dir", + "subset_data_single_point", + ] else: # use surface dataset with 78 pfts, and overwrite to 100% 1 dominant PFT # NOTE: FATES will currently not run with a 78-PFT surface dataset # set crop flag # set dominant pft - subset_command = ['./subset_data', 'point', '--lat', str(lat), '--lon', str(lon), - '--site', clmsite,'--crop', '--dompft', str(pft), '--create-surface', - '--uniform-snowpack', '--cap-saturation', '--verbose', '--overwrite'] - modify_command = ['./modify_singlept_site_neon', '--neon_site', site, '--surf_dir', - 'subset_data_single_point'] + subset_command = [ + "./subset_data", + "point", + "--lat", + str(lat), + "--lon", + str(lon), + "--site", + clmsite, + "--crop", + "--dompft", + str(pft), + "--create-surface", + "--uniform-snowpack", + "--cap-saturation", + "--verbose", + "--overwrite", + ] + modify_command = [ + "./modify_singlept_site_neon", + "--neon_site", + site, + "--surf_dir", + "subset_data_single_point", + ] execute(subset_command) execute(modify_command) diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index aa6e0c3ffb..8188f6084b 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -67,9 +67,7 @@ from getpass import getuser # Get the ctsm util tools and then the cime tools. -_CTSM_PYTHON = os.path.abspath( - os.path.join(os.path.dirname(__file__), "..", "..", "python") -) +_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) from ctsm import add_cime_to_path @@ -194,7 +192,7 @@ def get_parser(args, description, valid_neon_sites): ) parser.add_argument( - "--prism", + "--prism", help=""" Uses the PRISM reanaylsis precipitation data for the site instead of the NEON data (only available over Continental US) @@ -205,9 +203,8 @@ def get_parser(args, description, valid_neon_sites): default=False, ) - parser.add_argument( - "--experiment", + "--experiment", help=""" Appends the case name with string for model experiment """, @@ -274,12 +271,11 @@ def get_parser(args, description, valid_neon_sites): """, action="store", dest="user_version", - required = False, - type = str, - choices= ['v1','v2','v3'], + required=False, + type=str, + choices=["v1", "v2", "v3"], ) - args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser) if "all" in args.neon_sites: @@ -381,9 +377,7 @@ def __init__(self, name, start_year, end_year, start_month, end_month, finidat): def __str__(self): return ( - str(self.__class__) - + "\n" - + "\n".join((str(item) + " = " for item in (self.__dict__))) + str(self.__class__) + "\n" + "\n".join((str(item) + " = " for item in (self.__dict__))) ) def build_base_case( @@ -408,9 +402,7 @@ def build_base_case( """ print("---- building a base case -------") self.base_case_root = output_root - user_mods_dirs = [ - os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name) - ] + user_mods_dirs = [os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)] if not output_root: output_root = os.getcwd() case_path = os.path.join(output_root, self.name) @@ -449,9 +441,15 @@ def build_base_case( existingcompname = case.get_value("COMPSET") match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) if re.search("^HIST", compset, flags=re.IGNORECASE) is None: - expect( match == None, "Existing base case is a historical type and should not be -- rerun with the --orverwrite option" ) + expect( + match == None, + "Existing base case is a historical type and should not be -- rerun with the --orverwrite option", + ) else: - expect( match != None, "Existing base case should be a historical type and is not -- rerun with the --orverwrite option" ) + expect( + match != None, + "Existing base case should be a historical type and is not -- rerun with the --orverwrite option", + ) # reset the case case.case_setup(reset=True) case_path = case.get_value("CASEROOT") @@ -474,22 +472,22 @@ def diff_month(self): d1 = datetime.datetime(self.end_year, self.end_month, 1) d2 = datetime.datetime(self.start_year, self.start_month, 1) return (d1.year - d2.year) * 12 + d1.month - d2.month - + def get_batch_query(self, case): """ - Function for querying the batch queue query command for a case, depending on the - user's batch system. + Function for querying the batch queue query command for a case, depending on the + user's batch system. Args: case: case object """ - + if case.get_value("BATCH_SYSTEM") == "none": - return "none" + return "none" else: - return case.get_value("batch_query") - + return case.get_value("batch_query") + def run_case( self, base_case_root, @@ -504,9 +502,7 @@ def run_case( experiment=False, ): user_mods_dirs = [ - os.path.join( - self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name - ) + os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name) ] expect( os.path.isdir(base_case_root), @@ -516,15 +512,13 @@ def run_case( if user_version: version = user_version else: - version = 'latest' + version = "latest" - print ("using this version:", version) + print("using this version:", version) if experiment != None: self.name = self.name + "." + experiment - case_root = os.path.abspath( - os.path.join(base_case_root, "..", self.name + "." + run_type) - ) + case_root = os.path.abspath(os.path.join(base_case_root, "..", self.name + "." + run_type)) rundir = None if os.path.isdir(case_root): @@ -538,15 +532,17 @@ def run_case( existingcompname = case.get_value("COMPSET") match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) if re.search("^HIST", compset, flags=re.IGNORECASE) is None: - expect( match == None, "Existing base case is a historical type and should not be -- rerun with the --orverwrite option" ) + expect( + match == None, + "Existing base case is a historical type and should not be -- rerun with the --orverwrite option", + ) else: - expect( match != None, "Existing base case should be a historical type and is not -- rerun with the --orverwrite option" ) - if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): - print( - "Case {} appears to be complete, not rerunning.".format( - case_root - ) + expect( + match != None, + "Existing base case should be a historical type and is not -- rerun with the --orverwrite option", ) + if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): + print("Case {} appears to be complete, not rerunning.".format(case_root)) elif not setup_only: print("Resubmitting case {}".format(case_root)) case.submit(no_batch=no_batch) @@ -557,17 +553,13 @@ def run_case( print(f"Use {batch_query} to check its run status") return else: - logger.warning( - "Case already exists in {}, not overwritting.".format(case_root) - ) + logger.warning("Case already exists in {}, not overwritting.".format(case_root)) return if run_type == "postad": adcase_root = case_root.replace(".postad", ".ad") if not os.path.isdir(adcase_root): - logger.warning( - "postad requested but no ad case found in {}".format(adcase_root) - ) + logger.warning("postad requested but no ad case found in {}".format(adcase_root)) return if not os.path.isdir(case_root): @@ -580,15 +572,13 @@ def run_case( # that the shell_commands file is copied, as well as taking care of the DATM inputs. # See https://github.com/ESCOMP/CTSM/pull/1872#pullrequestreview-1169407493 # - basecase.create_clone( - case_root, keepexe=True, user_mods_dirs=user_mods_dirs - ) + basecase.create_clone(case_root, keepexe=True, user_mods_dirs=user_mods_dirs) with Case(case_root, read_only=False) as case: if run_type != "transient": - # in order to avoid the complication of leap years we always set the run_length in units of days. - case.set_value("STOP_OPTION", "ndays") - case.set_value("REST_OPTION", "end") + # in order to avoid the complication of leap years we always set the run_length in units of days. + case.set_value("STOP_OPTION", "ndays") + case.set_value("REST_OPTION", "end") case.set_value("CONTINUE_RUN", False) case.set_value("NEONVERSION", version) if prism: @@ -660,9 +650,7 @@ def set_ref_case(self, case): case.set_value("RUN_REFDIR", refrundir) case.set_value("RUN_REFCASE", os.path.basename(ref_case_root)) refdate = None - for reffile in glob.iglob( - refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root) - ): + for reffile in glob.iglob(refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root)): m = re.search("(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile) if m: refdate = m.group(1) @@ -677,9 +665,7 @@ def set_ref_case(self, case): if not os.path.isdir(os.path.join(rundir, "inputdata")) and os.path.isdir( os.path.join(refrundir, "inputdata") ): - symlink_force( - os.path.join(refrundir, "inputdata"), os.path.join(rundir, "inputdata") - ) + symlink_force(os.path.join(refrundir, "inputdata"), os.path.join(rundir, "inputdata")) case.set_value("RUN_REFDATE", refdate) if case_root.endswith(".postad"): @@ -693,9 +679,7 @@ def modify_user_nl(self, case_root, run_type, rundir): if run_type == "transient": if self.finidat: user_nl_lines = [ - "finidat = '{}/inputdata/lnd/ctsm/initdata/{}'".format( - rundir, self.finidat - ) + "finidat = '{}/inputdata/lnd/ctsm/initdata/{}'".format(rundir, self.finidat) ] else: user_nl_lines = [ @@ -767,15 +751,14 @@ def parse_neon_listing(listing_file, valid_neon_sites): # -- find all the data versions versions = tmp_df[7].unique() - #print ("all versions available for ", site_name,":", *versions) + # print ("all versions available for ", site_name,":", *versions) latest_version = tmp_df[7].iloc[-1] - #print ("latests version available for ", site_name,":", latest_version) + # print ("latests version available for ", site_name,":", latest_version) tmp_df = tmp_df[tmp_df[7].str.contains(latest_version)] # -- remove .nc from the file names tmp_df[9] = tmp_df[9].str.replace(".nc", "", regex=False) - tmp_df2 = tmp_df[9].str.split("-", expand=True) # ignore any prefix in file name and just get year @@ -800,9 +783,7 @@ def parse_neon_listing(listing_file, valid_neon_sites): if site_name in line: finidat = line.split(",")[0].split("/")[-1] - neon_site = NeonSite( - site_name, start_year, end_year, start_month, end_month, finidat - ) + neon_site = NeonSite(site_name, start_year, end_year, start_month, end_month, finidat) logger.debug(neon_site) available_list.append(neon_site) @@ -847,9 +828,9 @@ def main(description): res = "CLM_USRDAT" if run_type == "transient": - compset = "IHist1PtClm51Bgc" + compset = "IHist1PtClm51Bgc" else: - compset = "I1PtClm51Bgc" + compset = "I1PtClm51Bgc" # -- Looping over neon sites From 9dd60f3a3065269db662e5f70a143cec6fa70e17 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 Sep 2023 11:35:20 -0600 Subject: [PATCH 1481/2067] Updating .git-blame-ignore-revs --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 9b7cb3c036..1b7a0d75b3 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -10,6 +10,7 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb +4ee49e3e516ca7dee5df378f65664f93a7db4415 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From 721627223d5043677da4948587a9ead63fac5659 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 13 Sep 2023 12:51:44 -0600 Subject: [PATCH 1482/2067] Added function to check if DOY is in interval. --- src/utils/clm_time_manager.F90 | 39 +++++++++++++++++++ .../test_clm_time_manager.pf | 31 +++++++++++++++ 2 files changed, 70 insertions(+) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index b8d9930b24..e1a94effc0 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -59,6 +59,7 @@ module clm_time_manager is_beg_curr_year, &! return true on first timestep in current year is_end_curr_year, &! return true on last timestep in current year is_perpetual, &! return true if perpetual calendar is in use + is_doy_in_interval, &! return true if day of year is in the provided interval is_near_local_noon, &! return true if near local noon is_restart, &! return true if this is a restart run update_rad_dtime, &! track radiation interval via nstep @@ -1759,6 +1760,44 @@ end function is_perpetual !========================================================================================= + logical function is_doy_in_interval(start, end, doy_in) + + ! Return true if day of year is in the provided interval. + ! Does not treat leap years differently from normal years. + ! Arguments + integer, intent(in) :: start ! start of interval (day of year) + integer, intent(in) :: end ! end of interval (day of year) + integer, optional, intent(in) :: doy_in ! day of year to query + + ! Local variables + integer :: doy + logical :: window_crosses_newyear + + character(len=*), parameter :: sub = 'clm::is_doy_in_interval' + + ! Get doy of beginning of current timestep if doy_in is not provided + if (present(doy_in)) then + doy = doy_in + else + doy = get_prev_calday() + end if + + window_crosses_newyear = end < start + + if (window_crosses_newyear .and. & + (doy >= start .or. doy <= end)) then + is_doy_in_interval = .true. + else if (.not. window_crosses_newyear .and. & + (doy >= start .and. doy <= end)) then + is_doy_in_interval = .true. + else + is_doy_in_interval = .false. + end if + + end function is_doy_in_interval + + !========================================================================================= + subroutine timemgr_datediff(ymd1, tod1, ymd2, tod2, days) ! Calculate the difference (ymd2,tod2) - (ymd1,tod1) and return the result in days. diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index 435d795e50..d5f5dc9361 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -577,4 +577,35 @@ contains end subroutine bad_hilontolocal_time + @Test + subroutine check_is_doy_in_interval(this) + class(TestTimeManager), intent(inout) :: this + + integer :: start, end + + start = 100 + end = 300 + @assertTrue(is_doy_in_interval(start, end, start)) + @assertTrue(is_doy_in_interval(start, end, end)) + @assertTrue(is_doy_in_interval(start, end, 200)) + @assertFalse(is_doy_in_interval(start, end, 35)) + @assertFalse(is_doy_in_interval(start, end, 350)) + + start = 300 + end = 100 + @assertTrue(is_doy_in_interval(start, end, start)) + @assertTrue(is_doy_in_interval(start, end, end)) + @assertFalse(is_doy_in_interval(start, end, 200)) + @assertTrue(is_doy_in_interval(start, end, 35)) + @assertTrue(is_doy_in_interval(start, end, 350)) + + start = 300 + end = 300 + @assertTrue(is_doy_in_interval(start, end, start)) + @assertTrue(is_doy_in_interval(start, end, end)) + @assertFalse(is_doy_in_interval(start, end, 200)) + @assertFalse(is_doy_in_interval(start, end, 350)) + + end subroutine check_is_doy_in_interval + end module test_clm_time_manager From 5bdd59d5deecbe22eb506f3fd30afbaa4710cb9a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 13 Sep 2023 13:00:46 -0600 Subject: [PATCH 1483/2067] CropPhenology() now uses is_doy_in_interval(). --- src/biogeochem/CNPhenologyMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 070dc0eb0f..7044cdc402 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1726,6 +1726,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & use clm_time_manager , only : get_prev_calday, get_curr_days_per_year, is_beg_curr_year use clm_time_manager , only : get_average_days_per_year use clm_time_manager , only : get_prev_date + use clm_time_manager , only : is_doy_in_interval use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice @@ -1930,7 +1931,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. - is_in_sowing_window = jday >= minplantjday(ivt(p),h) .and. jday <= maxplantjday(ivt(p),h) + is_in_sowing_window = is_doy_in_interval(minplantjday(ivt(p),h), maxplantjday(ivt(p),h), jday) is_end_sowing_window = jday == maxplantjday(ivt(p),h) ! ! Only allow sowing according to normal "window" rules if not using prescribed From 9fd0612aa7a3e8f30eb7f09aa6f4c6e43d00da5d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 13 Sep 2023 14:01:59 -0600 Subject: [PATCH 1484/2067] Update ChangeLog --- doc/ChangeLog | 39 +++++++-------------------------------- 1 file changed, 7 insertions(+), 32 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 4f2d8ae7bf..518e2b59cb 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev141 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Tue Sep 12 17:08:11 MDT 2023 +Date: Wed Sep 13 13:58:04 MDT 2023 One-line Summary: Change small snocan to zero Purpose and description of changes @@ -34,8 +34,8 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): - #2041 - #2048 + Fixes #2041 + Fixes #2048 Testing summary: @@ -43,36 +43,10 @@ Testing summary: [PASS means all tests PASS; OK means tests PASS other than expected fails.] - build-namelist tests (if CLMBuildNamelist.pm has changed): - - cheyenne - - - tools-tests (test/tools) (if tools have been changed): - - cheyenne - - - python testing (if python code has changed; see instructions in python/README.md; document testing done): - - (any machine) - - - [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python - code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system - tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in - either model output or namelists, is: create sym links pointing to the last tag's baseline directory, - named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT - doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to - separately run the clm_pymods test suite, and you can remove the following line.] - - clm_pymods test suite on cheyenne - - regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- - izumi ------- - - any other testing (give details below): - -If the tag used for baseline comparisons was NOT the previous tag, note that here: + cheyenne ---- OK + izumi ------- OK Answer changes @@ -89,7 +63,8 @@ Changes answers relative to baseline: The answer changes are expected to be roundoff-level because the code change just truncates roundoff-level greater-than-zero states to exactly zero for snocan that most likely needed to be zero anyway. - We find that the answer changes grow to greater than roundoff, but the + + The answer changes grow to greater than roundoff, but the cprnc.out file from a 20-year izumi test-suite case does not contain differences of concerning magnitude. From 0660f4c7aa6b517909ac6d83c6dfcc95daca80dd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Sep 2023 12:12:11 -0600 Subject: [PATCH 1485/2067] Don't check RXCROPMATURITY in run_sys_tests. --- python/ctsm/run_sys_tests.py | 9 --------- 1 file changed, 9 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 83c468ab88..a44e4ab3cf 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -703,15 +703,6 @@ def _try_systemtests(testname_list): import ctsm.modify_input_files.modify_fsurdat except ModuleNotFoundError: raise ModuleNotFoundError("modify_fsurdat" + errMsg) - if any(["RXCROPMATURITY" in t for t in testname_list]): - try: - import ctsm.crop_calendars.make_fsurdat_all_crops_everywhere - except ModuleNotFoundError: - raise ModuleNotFoundError("make_fsurdat_all_crops_everywhere.py" + errMsg) - try: - import ctsm.crop_calendars.generate_gdds - except ModuleNotFoundError: - raise ModuleNotFoundError("generate_gdds.py" + errMsg) def _get_compilers_for_suite(suite_name, machine_name): From 0b6345838f9dac5d430c5b5ad186fd99ac203aca Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Sep 2023 14:17:18 -0600 Subject: [PATCH 1486/2067] Revert "Remove sys.path.insert()s from crop calendar Python files." Those are necessary for when the crop calendar scripts are being called on their own, from outside the CTSM repo. This reverts commit 9893c8032e91c970b9b1afae9762c23d61d6c588. --- python/ctsm/crop_calendars/cropcal_module.py | 4 ++++ python/ctsm/crop_calendars/generate_gdds.py | 4 ++++ python/ctsm/crop_calendars/generate_gdds_functions.py | 5 +++++ 3 files changed, 13 insertions(+) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index b2be2fd3e8..1d58e2fbab 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -6,6 +6,10 @@ import glob # Import the CTSM Python utilities +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils try: diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 649057e1b2..9fe1c26e14 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -5,6 +5,10 @@ import inspect import sys +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" +) +sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_module as cc import ctsm.crop_calendars.generate_gdds_functions as gddfn diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 6d6e2a7d54..20c958817a 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -7,6 +7,11 @@ from importlib import util as importlib_util # Import the CTSM Python utilities +_CTSM_PYTHON = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" +) +import sys +sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils import ctsm.crop_calendars.cropcal_module as cc From 6cb70496ad3bfc774bbf7e562555c3400b4c42f1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Sep 2023 17:00:31 -0600 Subject: [PATCH 1487/2067] Added a digit to Tech Note diffusion coefficients table. --- doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 7c89f857e3..14d343c20c 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -430,7 +430,7 @@ molecular free-air diffusion coefficients (:math:`{D}_{0}` +==========================================================+==========================================================+========================================================+ | Aqueous | 0.9798 + 0.02986\ *T* + 0.0004381\ *T*\ :sup:`2` | 1.172+ 0.03443\ *T* + 0.0005048\ *T*\ :sup:`2` | +----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+ - | Gaseous | 0.1875 + 0.0013\ *T* | 0.1759 + 0.0011\ *T* | + | Gaseous | 0.1875 + 0.0013\ *T* | 0.1759 + 0.00117\ *T* | +----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+ Gaseous diffusivity in soils also depends on the molecular diffusivity, From d50ce7b49b08b678eb86da44a438cedb35a7afef Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Fri, 15 Sep 2023 15:53:20 +0200 Subject: [PATCH 1488/2067] add entry to special cases --- .../Running-with-excess-ground-ice.rst | 40 +++++++++++++++++++ .../running-special-cases/index.rst | 1 + 2 files changed, 41 insertions(+) create mode 100644 doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst new file mode 100644 index 0000000000..23677965a5 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -0,0 +1,40 @@ +.. _running-with-excess-ground-ice: + +.. include:: ../substitutions.rst + +=================================== + Running-with-excess-ground-ice +=================================== + + +Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.fasle.``. When +``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option`use_excess_ice_streams` exists to control this process (``.false.`` is default). If ``.true.`` and use_excess_ice is ``.true.``, +initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). +This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. +If the run is a continue-run, excess ice variables will **always** be expected on a restart file. + +.. note:: Excess ice ammount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m or (maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. + + +Since presence of excess ice within the soil significantly alters heat diffusion within it, when starting from initial conditions where excess ice was not present, an additional spinup is required. +Usually such spinup takes 100-150 years (depending on your climate) to completely equilibrate soil temperatures. + + + +Example: Crop Simulation +------------------------------------ +:: + + > cd scripts + > ./create_newcase -case I1850Clm50BgcCrop_with_exice -res f19_g17_gl4 -compset I1850Clm50BgcCrop + > cd I1850Clm50BgcCrop_with_exice + + > ./case.setup + + # turn on excess ice and it's "stream" initialization + > echo "use_excess_ice=.true." >> user_nl_clm + > echo "use_excess_ice_streams=.true." >> user_nl_clm + + # Now build and run normally + > ./case.build + > ./case.submit diff --git a/doc/source/users_guide/running-special-cases/index.rst b/doc/source/users_guide/running-special-cases/index.rst index f84b7706fb..d220483dd3 100644 --- a/doc/source/users_guide/running-special-cases/index.rst +++ b/doc/source/users_guide/running-special-cases/index.rst @@ -19,6 +19,7 @@ Running Special Cases running-with-irrigation.rst Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst Spinning-up-the-biogeochemistry-BGC-spinup.rst + Running-with-excess-ground-ice.rst Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst From 772e864922e5de85f2141c89007fb30e5cbc6b82 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 08:22:28 -0600 Subject: [PATCH 1489/2067] run_sys_tests: Don't check module availability during run_ctsm_py_tests. --- python/ctsm/run_sys_tests.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index a44e4ab3cf..53500b88e9 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -213,6 +213,9 @@ def run_sys_tests( rerun_existing_failures=rerun_existing_failures, extra_create_test_args=extra_create_test_args, ) + + running_ctsm_py_tests = testfile == "/path/to/testfile" or testlist in [['test1', 'test2'], ['foo']] or suite_name == "my_suite" + if suite_name: if not dry_run: _make_cs_status_for_suite(testroot, testid_base) @@ -225,20 +228,24 @@ def run_sys_tests( testroot=testroot, create_test_args=create_test_args, dry_run=dry_run, + running_ctsm_py_tests=running_ctsm_py_tests, ) else: if not dry_run: _make_cs_status_non_suite(testroot, testid_base) + running_ctsm_py_tests = testfile == "/path/to/testfile" if testfile: test_args = ["--testfile", os.path.abspath(testfile)] - with open(test_args[1], "r") as f: - testname_list = f.readlines() + if not running_ctsm_py_tests: + with open(test_args[1], "r") as f: + testname_list = f.readlines() elif testlist: test_args = testlist testname_list = testlist else: raise RuntimeError("None of suite_name, testfile or testlist were provided") - _try_systemtests(testname_list) + if not running_ctsm_py_tests: + _try_systemtests(testname_list) _run_create_test( cime_path=cime_path, test_args=test_args, @@ -672,9 +679,10 @@ def _run_test_suite( testroot, create_test_args, dry_run, + running_ctsm_py_tests, ): if not suite_compilers: - suite_compilers = _get_compilers_for_suite(suite_name, machine.name) + suite_compilers = _get_compilers_for_suite(suite_name, machine.name, running_ctsm_py_tests) for compiler in suite_compilers: test_args = [ "--xml-category", @@ -705,13 +713,14 @@ def _try_systemtests(testname_list): raise ModuleNotFoundError("modify_fsurdat" + errMsg) -def _get_compilers_for_suite(suite_name, machine_name): +def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests): test_data = get_tests_from_xml(xml_machine=machine_name, xml_category=suite_name) if not test_data: raise RuntimeError( "No tests found for suite {} on machine {}".format(suite_name, machine_name) ) - _try_systemtests([t["testname"] for t in test_data]) + if not running_ctsm_py_tests: + _try_systemtests([t["testname"] for t in test_data]) compilers = sorted({one_test["compiler"] for one_test in test_data}) logger.info("Running with compilers: %s", compilers) return compilers From d229b5c6689efc4c2a6cef077515c4ccd5c18ff6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 08:25:05 -0600 Subject: [PATCH 1490/2067] Reformatted with black. --- cime_config/SystemTests/fsurdatmodifyctsm.py | 2 ++ cime_config/SystemTests/rxcropmaturity.py | 12 ++++++------ cime_config/SystemTests/systemtest_utils.py | 4 +++- .../ctsm/crop_calendars/generate_gdds_functions.py | 1 + python/ctsm/run_sys_tests.py | 10 +++++++--- 5 files changed, 19 insertions(+), 10 deletions(-) diff --git a/cime_config/SystemTests/fsurdatmodifyctsm.py b/cime_config/SystemTests/fsurdatmodifyctsm.py index 43b155dc0b..03e437d5c4 100644 --- a/cime_config/SystemTests/fsurdatmodifyctsm.py +++ b/cime_config/SystemTests/fsurdatmodifyctsm.py @@ -11,6 +11,7 @@ # For calling fsurdat_modifier from argparse import Namespace + _CTSM_PYTHON = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "python" ) @@ -82,6 +83,7 @@ def _run_modify_fsurdat(self): verbose=False, ) from ctsm.modify_input_files.fsurdat_modifier import fsurdat_modifier + fsurdat_modifier(fsurdat_modifier_args) def _modify_user_nl(self): diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index f292346582..6a2cbe14b0 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -273,14 +273,14 @@ def _setup_make_fsurdat_all_crops_everywhere(self): # Write a bash script that will do what we want prerun_script = os.path.join(self._path_gddgen, "make_fsurdat_all_crops_everywhere.sh") prerun_script_lines = [ - "#!/bin/bash", - "set -e", - "conda run -n ctsm_pylib " + command, - "exit 0", - ] + "#!/bin/bash", + "set -e", + "conda run -n ctsm_pylib " + command, + "exit 0", + ] with open(prerun_script, "w") as f: f.writelines(line + "\n" for line in prerun_script_lines) - os.chmod(prerun_script, 0o755) # 0o755 = -rwxr-xr-x + os.chmod(prerun_script, 0o755) # 0o755 = -rwxr-xr-x with self._case: self._case.set_value("PRERUN_SCRIPT", prerun_script) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 90a5abcf95..2560f5441f 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -54,7 +54,9 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): ) except subprocess.CalledProcessError as error: # First, retry with the original method - command = cmds_to_run_via_conda(caseroot, f"conda activate {this_conda_env} && ", command_in, test_conda_retry=False) + command = cmds_to_run_via_conda( + caseroot, f"conda activate {this_conda_env} && ", command_in, test_conda_retry=False + ) try: with open(tool_name + ".log2", "w") as f: subprocess.run( diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index 20c958817a..c1a15324a2 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -11,6 +11,7 @@ os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" ) import sys + sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils import ctsm.crop_calendars.cropcal_module as cc diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 53500b88e9..6b792b9bce 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -213,9 +213,13 @@ def run_sys_tests( rerun_existing_failures=rerun_existing_failures, extra_create_test_args=extra_create_test_args, ) - - running_ctsm_py_tests = testfile == "/path/to/testfile" or testlist in [['test1', 'test2'], ['foo']] or suite_name == "my_suite" - + + running_ctsm_py_tests = ( + testfile == "/path/to/testfile" + or testlist in [["test1", "test2"], ["foo"]] + or suite_name == "my_suite" + ) + if suite_name: if not dry_run: _make_cs_status_for_suite(testroot, testid_base) From bea7a3339ba31005480616095cceda4f66c0290f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 08:25:48 -0600 Subject: [PATCH 1491/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 9b7cb3c036..edd62049b5 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -1,4 +1,5 @@ # Ran python directory through black python formatter +d229b5c6689efc4c2a6cef077515c4ccd5c18ff6 4cd83cb3ee6d85eb909403487abf5eeaf4d98911 0aa2957c1f8603c63fa30b11295c06cfddff44a5 2cdb380febb274478e84cd90945aee93f29fa2e6 From d867aa48f11d8a4ad388e0f1add9c4675d380a1b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 08:37:53 -0600 Subject: [PATCH 1492/2067] run_sys_tests.py now satisfies pylint. --- python/ctsm/run_sys_tests.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 6b792b9bce..e4a0bcf009 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -241,8 +241,8 @@ def run_sys_tests( if testfile: test_args = ["--testfile", os.path.abspath(testfile)] if not running_ctsm_py_tests: - with open(test_args[1], "r") as f: - testname_list = f.readlines() + with open(test_args[1], "r") as testfile_abspath: + testname_list = testfile_abspath.readlines() elif testlist: test_args = testlist testname_list = testlist @@ -709,12 +709,18 @@ def _run_test_suite( def _try_systemtests(testname_list): - errMsg = " can't be loaded. Do you need to activate the ctsm_pylib conda environment?" - if any(["FSURDATMODIFYCTSM" in t for t in testname_list]): + err_msg = " can't be loaded. Do you need to activate the ctsm_pylib conda environment?" + # Suppress pylint import-outside-toplevel warning because (a) we only want to import + # this when certain tests are requested, and (b) the import needs to be in a try-except + # block to produce a nice error message. + # pylint: disable=import-outside-toplevel disable + # Suppress pylint unused-import warning because the import itself IS the use. + # pylint: disable=unused-import disable + if any("FSURDATMODIFYCTSM" in t for t in testname_list): try: import ctsm.modify_input_files.modify_fsurdat - except ModuleNotFoundError: - raise ModuleNotFoundError("modify_fsurdat" + errMsg) + except ModuleNotFoundError as err: + raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests): From 2bb68adfef958b7bbd8b5803c1a88f66d6abe76c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 09:04:06 -0600 Subject: [PATCH 1493/2067] Align two comments. --- src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 index 4ec25bbadc..eadea68168 100644 --- a/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemNitrifDenitrifMod.F90 @@ -171,8 +171,8 @@ subroutine SoilBiogeochemNitrifDenitrif(bounds, num_soilc, filter_soilc, & real(r8) :: D0 ! temperature dependence of gaseous diffusion coefficients !debug-- put these type structure for outing to hist files real(r8) :: co2diff_con(2) ! diffusion constants for CO2 - real(r8) :: fc_air_frac ! Air-filled fraction of soil volume at field capacity - real(r8) :: fc_air_frac_as_frac_porosity ! fc_air_frac as fraction of total porosity + real(r8) :: fc_air_frac ! Air-filled fraction of soil volume at field capacity + real(r8) :: fc_air_frac_as_frac_porosity ! fc_air_frac as fraction of total porosity real(r8) :: surface_tension_water ! (J/m^2), Arah and Vinten 1995 real(r8) :: rij_kro_a ! Arah and Vinten 1995 real(r8) :: rij_kro_alpha ! Arah and Vinten 1995 From 7b57111f1722ebb47661cdf728cecf7a1b02b0d8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 14:41:31 -0600 Subject: [PATCH 1494/2067] Added separate is_today_in_doy_interval() function. * Includes unit test for new function. * Existing function is_doy_in_interval() now requires queried doy to be specified, no longer falling back on "today." --- src/utils/clm_time_manager.F90 | 35 +++++++++++++----- .../test_clm_time_manager.pf | 37 +++++++++++++++++++ 2 files changed, 62 insertions(+), 10 deletions(-) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index e1a94effc0..5c65f5decd 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -60,6 +60,7 @@ module clm_time_manager is_end_curr_year, &! return true on last timestep in current year is_perpetual, &! return true if perpetual calendar is in use is_doy_in_interval, &! return true if day of year is in the provided interval + is_today_in_doy_interval, &! return true if today's day of year is in the provided interval is_near_local_noon, &! return true if near local noon is_restart, &! return true if this is a restart run update_rad_dtime, &! track radiation interval via nstep @@ -1760,28 +1761,20 @@ end function is_perpetual !========================================================================================= - logical function is_doy_in_interval(start, end, doy_in) + logical function is_doy_in_interval(start, end, doy) ! Return true if day of year is in the provided interval. ! Does not treat leap years differently from normal years. ! Arguments integer, intent(in) :: start ! start of interval (day of year) integer, intent(in) :: end ! end of interval (day of year) - integer, optional, intent(in) :: doy_in ! day of year to query + integer, intent(in) :: doy ! day of year to query ! Local variables - integer :: doy logical :: window_crosses_newyear character(len=*), parameter :: sub = 'clm::is_doy_in_interval' - ! Get doy of beginning of current timestep if doy_in is not provided - if (present(doy_in)) then - doy = doy_in - else - doy = get_prev_calday() - end if - window_crosses_newyear = end < start if (window_crosses_newyear .and. & @@ -1798,6 +1791,28 @@ end function is_doy_in_interval !========================================================================================= + logical function is_today_in_doy_interval(start, end) + + ! Return true if today's day of year is in the provided interval. + ! Does not treat leap years differently from normal years. + ! Arguments + integer, intent(in) :: start ! start of interval (day of year) + integer, intent(in) :: end ! end of interval (day of year) + + ! Local variable(s) + integer :: doy_today + + character(len=*), parameter :: sub = 'clm::is_today_in_doy_interval' + + ! Get doy of beginning of current timestep + doy_today = get_prev_calday() + + is_today_in_doy_interval = is_doy_in_interval(start, end, doy_today) + + end function is_today_in_doy_interval + + !========================================================================================= + subroutine timemgr_datediff(ymd1, tod1, ymd2, tod2, days) ! Calculate the difference (ymd2,tod2) - (ymd1,tod1) and return the result in days. diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index d5f5dc9361..fe68efdbdc 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -608,4 +608,41 @@ contains end subroutine check_is_doy_in_interval + @Test + subroutine check_is_today_in_doy_interval(this) + class(TestTimeManager), intent(inout) :: this + + integer :: start, end + + call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + + start = 100 ! April 10 + end = 300 ! October 27 + + ! Test well before interval + call set_date(yr=2009, mon=3, day=25, tod=0) + @assertFalse(is_today_in_doy_interval(start, end)) + + ! Test last timestep before interval + call set_date(yr=2009, mon=4, day=10, tod=0) + @assertFalse(is_today_in_doy_interval(start, end)) + + ! Test first timestep of interval + call set_date(yr=2009, mon=4, day=10, tod=dtime) + @assertTrue(is_today_in_doy_interval(start, end)) + + ! Test well within interval + call set_date(yr=2009, mon=7, day=24, tod=0) + @assertTrue(is_today_in_doy_interval(start, end)) + + ! Test last timestep of interval + call set_date(yr=2009, mon=10, day=28, tod=0) + @assertTrue(is_today_in_doy_interval(start, end)) + + ! Test first timestep after interval + call set_date(yr=2009, mon=10, day=28, tod=dtime) + @assertFalse(is_today_in_doy_interval(start, end)) + + end subroutine check_is_today_in_doy_interval + end module test_clm_time_manager From eded771363ee2020e51ad633712b89ce4d8f7e8b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 15:16:45 -0600 Subject: [PATCH 1495/2067] Split check_is_doy_in_interval() into three tests. --- .../test_clm_time_manager.pf | 31 +++++++++++++------ 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index fe68efdbdc..78565fd54d 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -578,35 +578,48 @@ contains end subroutine bad_hilontolocal_time @Test - subroutine check_is_doy_in_interval(this) + subroutine check_is_doy_in_interval_startend(this) class(TestTimeManager), intent(inout) :: this - integer :: start, end + integer, parameter :: start = 100 + integer, parameter :: end = 300 - start = 100 - end = 300 @assertTrue(is_doy_in_interval(start, end, start)) @assertTrue(is_doy_in_interval(start, end, end)) @assertTrue(is_doy_in_interval(start, end, 200)) @assertFalse(is_doy_in_interval(start, end, 35)) @assertFalse(is_doy_in_interval(start, end, 350)) - start = 300 - end = 100 + end subroutine check_is_doy_in_interval_startend + + @Test + subroutine check_is_doy_in_interval_endstart(this) + class(TestTimeManager), intent(inout) :: this + + integer, parameter :: start = 300 + integer, parameter :: end = 100 + @assertTrue(is_doy_in_interval(start, end, start)) @assertTrue(is_doy_in_interval(start, end, end)) @assertFalse(is_doy_in_interval(start, end, 200)) @assertTrue(is_doy_in_interval(start, end, 35)) @assertTrue(is_doy_in_interval(start, end, 350)) - start = 300 - end = 300 + end subroutine check_is_doy_in_interval_endstart + + @Test + subroutine check_is_doy_in_interval_sameday(this) + class(TestTimeManager), intent(inout) :: this + + integer, parameter :: start = 300 + integer, parameter :: end = 300 + @assertTrue(is_doy_in_interval(start, end, start)) @assertTrue(is_doy_in_interval(start, end, end)) @assertFalse(is_doy_in_interval(start, end, 200)) @assertFalse(is_doy_in_interval(start, end, 350)) - end subroutine check_is_doy_in_interval + end subroutine check_is_doy_in_interval_sameday @Test subroutine check_is_today_in_doy_interval(this) From 579ca9a69b1b992832995b3b7444d4f2dc3e5474 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 15 Sep 2023 17:53:34 -0600 Subject: [PATCH 1496/2067] Bug fix in get_fraction_tilled(). I understood zisoi to give the bottom of each layer, but it actually gives the top. --- src/soilbiogeochem/TillageMod.F90 | 28 +++++++++++----------------- 1 file changed, 11 insertions(+), 17 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 8369fcc0c3..3609935767 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -247,31 +247,25 @@ subroutine get_tillage_multipliers(tillage_mults, idop) end subroutine get_tillage_multipliers - function get_fraction_tilled(zisoi, j, max_tillage_depth_gft) result(fraction_tilled) + function get_fraction_tilled(layer_top, layer_thickness, j, max_tillage_depth_gft) result(fraction_tilled) ! !ARGUMENTS - ! zisoi and max_tillage_depth are passed to this function, rather than using from clm_varcon or - ! parent scope (respectively), to enable unit testing. - real(r8) :: zisoi(:) ! Soil layer interface depths - integer :: j ! Soil layer + real(r8), intent(in) :: layer_top ! Soil layer interface depth (zisoi) + real(r8), intent(in) :: layer_thickness ! Soil layer thickness (dzsoi_decomp) + integer , intent(in) :: j ! Soil layer index real(r8) :: max_tillage_depth_gft ! Maximum tillage depth - ! !LOCAL VARIABLES - real(r8) :: layer_top ! Depth (m) of the top of this soil layer. zisoi is the depth of the bottom. - real(r8) :: layer_thickness ! Thickness of this soil layer (m) ! !RESULT real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth - if (j == 1) then - layer_top = 0._r8 - else - layer_top = zisoi(j-1) - end if - if (layer_top > max_tillage_depth_gft) then fraction_tilled = 0._r8 return end if - layer_thickness = zisoi(j) - layer_top + if (layer_thickness == 0._r8) then + write(iulog,*) 'j = ',j + call endrun(msg='layer thickness 0') + end if + fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth_gft - layer_top) / layer_thickness)) end function get_fraction_tilled @@ -285,7 +279,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! ! !USES use pftconMod , only : nc3crop - use clm_varcon, only : zisoi + use clm_varcon, only : zisoi, dzsoi_decomp use landunit_varcon , only : istcrop use PatchType , only : patch ! @@ -303,7 +297,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth ! Skip tillage if column is inactive or this layer doesn't get tilled - fraction_tilled = get_fraction_tilled(zisoi, j, max_tillage_depth) + fraction_tilled = get_fraction_tilled(zisoi(j), dzsoi_decomp(j), j, max_tillage_depth) if (.not. col%active(c) .or. fraction_tilled == 0._r8 .or. col%lun_itype(c) /= istcrop) then return end if From 20739bc6fdf70d64826fdfb17fbf4437bbb808ec Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 11:46:37 -0600 Subject: [PATCH 1497/2067] Reverted all changes to rxcropmaturity.py. --- cime_config/SystemTests/rxcropmaturity.py | 24 ++++++++--------------- 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index 6a2cbe14b0..15f524dfce 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -135,7 +135,7 @@ def run_phase(self): # Make custom version of surface file logger.info("RXCROPMATURITY log: run make_fsurdat_all_crops_everywhere") - self._setup_make_fsurdat_all_crops_everywhere() + self._run_make_fsurdat_all_crops_everywhere() # ------------------------------------------------------------------- # (2) Perform GDD-generating run and generate prescribed GDDs file @@ -239,7 +239,7 @@ def _setup_all(self): logger.info("RXCROPMATURITY log: _setup_all done") # Make a surface dataset that has every crop in every gridcell - def _setup_make_fsurdat_all_crops_everywhere(self): + def _run_make_fsurdat_all_crops_everywhere(self): # fsurdat should be defined. Where is it? self._fsurdat_in = None @@ -269,20 +269,12 @@ def _setup_make_fsurdat_all_crops_everywhere(self): command = ( f"python3 {tool_path} " + f"-i {self._fsurdat_in} " + f"-o {self._fsurdat_out}" ) - - # Write a bash script that will do what we want - prerun_script = os.path.join(self._path_gddgen, "make_fsurdat_all_crops_everywhere.sh") - prerun_script_lines = [ - "#!/bin/bash", - "set -e", - "conda run -n ctsm_pylib " + command, - "exit 0", - ] - with open(prerun_script, "w") as f: - f.writelines(line + "\n" for line in prerun_script_lines) - os.chmod(prerun_script, 0o755) # 0o755 = -rwxr-xr-x - with self._case: - self._case.set_value("PRERUN_SCRIPT", prerun_script) + stu.run_python_script( + self._get_caseroot(), + self._this_conda_env, + command, + tool_path, + ) # Modify namelist logger.info("RXCROPMATURITY log: modify user_nl files: new fsurdat") From 7f7dfc8f8dbb67c38654da3e2976f0e22e6f3074 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 12:50:20 -0600 Subject: [PATCH 1498/2067] test_get_fraction_tilled(): Use nlayers instead of 5. --- src/soilbiogeochem/test/tillage_test/test_tillage.pf | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf index a7013e49b1..272a668d33 100644 --- a/src/soilbiogeochem/test/tillage_test/test_tillage.pf +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -17,19 +17,20 @@ contains @Test subroutine test_get_fraction_tilled() - real(r8) :: zisoi(5) ! Depth of soil interfaces (bottom of each layer) + integer, parameter :: nlayers = 5 + real(r8) :: zisoi(nlayers) ! Depth of soil interfaces (bottom of each layer) integer :: j ! Soil layer real(r8) :: max_tillage_depth zisoi = [0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8, 1._r8] max_tillage_depth = 10._r8 - do j = 1, 5 + do j = 1, nlayers @assertEqual(1._r8, get_fraction_tilled(zisoi, j, max_tillage_depth)) end do max_tillage_depth = 0._r8 - do j = 1, 5 + do j = 1, nlayers @assertEqual(0._r8, get_fraction_tilled(zisoi, j, max_tillage_depth)) end do From 46da7307088eaaaf5750e055bb71cdab878050fd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 12:54:56 -0600 Subject: [PATCH 1499/2067] test_get_fraction_tilled(): Now works with new function call. --- .../test/tillage_test/test_tillage.pf | 22 ++++++++++++------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf index 272a668d33..172647ed54 100644 --- a/src/soilbiogeochem/test/tillage_test/test_tillage.pf +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -19,27 +19,33 @@ contains integer, parameter :: nlayers = 5 real(r8) :: zisoi(nlayers) ! Depth of soil interfaces (bottom of each layer) + real(r8) :: dzsoi_decomp(nlayers) ! Thickness of soil layers integer :: j ! Soil layer real(r8) :: max_tillage_depth - zisoi = [0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8, 1._r8] + zisoi = [0._r8, 0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8] + dzsoi_decomp = [zisoi(2) - zisoi(1), & + zisoi(3) - zisoi(2), & + zisoi(4) - zisoi(3), & + zisoi(5) - zisoi(4), & + 0.5_r8] max_tillage_depth = 10._r8 do j = 1, nlayers - @assertEqual(1._r8, get_fraction_tilled(zisoi, j, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), j, max_tillage_depth)) end do max_tillage_depth = 0._r8 do j = 1, nlayers - @assertEqual(0._r8, get_fraction_tilled(zisoi, j, max_tillage_depth)) + @assertEqual(0._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), j, max_tillage_depth)) end do max_tillage_depth = 0.21_r8 - @assertEqual(1._r8, get_fraction_tilled(zisoi, 1, max_tillage_depth)) - @assertEqual(1._r8, get_fraction_tilled(zisoi, 2, max_tillage_depth)) - @assertEqual(1._r8, get_fraction_tilled(zisoi, 3, max_tillage_depth)) - @assertEqual(0.275_r8, get_fraction_tilled(zisoi, 4, max_tillage_depth), tolerance=tol) - @assertEqual(0._r8, get_fraction_tilled(zisoi, 5, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(1), dzsoi_decomp(1), 1, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(2), dzsoi_decomp(2), 2, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(3), dzsoi_decomp(3), 3, max_tillage_depth)) + @assertEqual(0.275_r8, get_fraction_tilled(zisoi(4), dzsoi_decomp(4), 4, max_tillage_depth), tolerance=tol) + @assertEqual(0._r8, get_fraction_tilled(zisoi(5), dzsoi_decomp(5), 5, max_tillage_depth)) end subroutine test_get_fraction_tilled From 9c1618bef321970b324be9f08b1ec7f83e3d3d74 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 12:57:38 -0600 Subject: [PATCH 1500/2067] get_fraction_tilled() no longer takes argument j. --- src/soilbiogeochem/TillageMod.F90 | 6 ++---- .../test/tillage_test/test_tillage.pf | 14 +++++++------- 2 files changed, 9 insertions(+), 11 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 3609935767..e002f480c0 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -247,11 +247,10 @@ subroutine get_tillage_multipliers(tillage_mults, idop) end subroutine get_tillage_multipliers - function get_fraction_tilled(layer_top, layer_thickness, j, max_tillage_depth_gft) result(fraction_tilled) + function get_fraction_tilled(layer_top, layer_thickness, max_tillage_depth_gft) result(fraction_tilled) ! !ARGUMENTS real(r8), intent(in) :: layer_top ! Soil layer interface depth (zisoi) real(r8), intent(in) :: layer_thickness ! Soil layer thickness (dzsoi_decomp) - integer , intent(in) :: j ! Soil layer index real(r8) :: max_tillage_depth_gft ! Maximum tillage depth ! !RESULT real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth @@ -262,7 +261,6 @@ function get_fraction_tilled(layer_top, layer_thickness, j, max_tillage_depth_gf end if if (layer_thickness == 0._r8) then - write(iulog,*) 'j = ',j call endrun(msg='layer thickness 0') end if @@ -297,7 +295,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth ! Skip tillage if column is inactive or this layer doesn't get tilled - fraction_tilled = get_fraction_tilled(zisoi(j), dzsoi_decomp(j), j, max_tillage_depth) + fraction_tilled = get_fraction_tilled(zisoi(j), dzsoi_decomp(j), max_tillage_depth) if (.not. col%active(c) .or. fraction_tilled == 0._r8 .or. col%lun_itype(c) /= istcrop) then return end if diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf index 172647ed54..9475657fab 100644 --- a/src/soilbiogeochem/test/tillage_test/test_tillage.pf +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -32,20 +32,20 @@ contains max_tillage_depth = 10._r8 do j = 1, nlayers - @assertEqual(1._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), j, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), max_tillage_depth)) end do max_tillage_depth = 0._r8 do j = 1, nlayers - @assertEqual(0._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), j, max_tillage_depth)) + @assertEqual(0._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), max_tillage_depth)) end do max_tillage_depth = 0.21_r8 - @assertEqual(1._r8, get_fraction_tilled(zisoi(1), dzsoi_decomp(1), 1, max_tillage_depth)) - @assertEqual(1._r8, get_fraction_tilled(zisoi(2), dzsoi_decomp(2), 2, max_tillage_depth)) - @assertEqual(1._r8, get_fraction_tilled(zisoi(3), dzsoi_decomp(3), 3, max_tillage_depth)) - @assertEqual(0.275_r8, get_fraction_tilled(zisoi(4), dzsoi_decomp(4), 4, max_tillage_depth), tolerance=tol) - @assertEqual(0._r8, get_fraction_tilled(zisoi(5), dzsoi_decomp(5), 5, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(1), dzsoi_decomp(1), max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(2), dzsoi_decomp(2), max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(zisoi(3), dzsoi_decomp(3), max_tillage_depth)) + @assertEqual(0.275_r8, get_fraction_tilled(zisoi(4), dzsoi_decomp(4), max_tillage_depth), tolerance=tol) + @assertEqual(0._r8, get_fraction_tilled(zisoi(5), dzsoi_decomp(5), max_tillage_depth)) end subroutine test_get_fraction_tilled From b87fbd9787fca801fa96d3ec507c95aa634d95db Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 13:27:32 -0600 Subject: [PATCH 1501/2067] get_fraction_tilled() can now handle zero-thickness layers. --- src/soilbiogeochem/TillageMod.F90 | 10 +++++++--- src/soilbiogeochem/test/tillage_test/test_tillage.pf | 5 +++++ 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index e002f480c0..f35dff5bab 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -261,11 +261,15 @@ function get_fraction_tilled(layer_top, layer_thickness, max_tillage_depth_gft) end if if (layer_thickness == 0._r8) then - call endrun(msg='layer thickness 0') + if (layer_top <= max_tillage_depth_gft) then + fraction_tilled = 1._r8 + else + fraction_tilled = 0._r8 + end if + else + fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth_gft - layer_top) / layer_thickness)) end if - fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth_gft - layer_top) / layer_thickness)) - end function get_fraction_tilled diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf index 9475657fab..68d29dd573 100644 --- a/src/soilbiogeochem/test/tillage_test/test_tillage.pf +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -47,6 +47,11 @@ contains @assertEqual(0.275_r8, get_fraction_tilled(zisoi(4), dzsoi_decomp(4), max_tillage_depth), tolerance=tol) @assertEqual(0._r8, get_fraction_tilled(zisoi(5), dzsoi_decomp(5), max_tillage_depth)) + max_tillage_depth = 0.5_r8 + @assertEqual(1._r8, get_fraction_tilled(0.4_r8, 0._r8, max_tillage_depth)) + @assertEqual(1._r8, get_fraction_tilled(0.5_r8, 0._r8, max_tillage_depth)) + @assertEqual(0._r8, get_fraction_tilled(0.6_r8, 0._r8, max_tillage_depth)) + end subroutine test_get_fraction_tilled From d1ed672c188f2ed5ea1bdb8f9052733c08b57e24 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 14:15:12 -0600 Subject: [PATCH 1502/2067] Improved comments in systemtest_utils.py. --- cime_config/SystemTests/systemtest_utils.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 2560f5441f..c10b0392e9 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -43,6 +43,7 @@ def cmds_to_run_via_conda(caseroot, conda_run_call, command, test_conda_retry=Tr def run_python_script(caseroot, this_conda_env, command_in, tool_path): + # First, try with "conda run -n" command = cmds_to_run_via_conda(caseroot, f"conda run -n {this_conda_env}", command_in) # Run with logfile @@ -53,7 +54,8 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): command, shell=True, check=True, text=True, stdout=f, stderr=subprocess.STDOUT ) except subprocess.CalledProcessError as error: - # First, retry with the original method + # Retry with the original ("conda activate") method. Set test_conda_retry False because + # that didn't happen in the original method. command = cmds_to_run_via_conda( caseroot, f"conda activate {this_conda_env} && ", command_in, test_conda_retry=False ) From c0d8784b91006a6f5bc90b6d49f346734afd59b9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 14:43:01 -0600 Subject: [PATCH 1503/2067] Simplify and split up test_get_fraction_tilled(). --- .../test/tillage_test/test_tillage.pf | 26 ++++++++----------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf index 68d29dd573..710541fd3d 100644 --- a/src/soilbiogeochem/test/tillage_test/test_tillage.pf +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -21,7 +21,7 @@ contains real(r8) :: zisoi(nlayers) ! Depth of soil interfaces (bottom of each layer) real(r8) :: dzsoi_decomp(nlayers) ! Thickness of soil layers integer :: j ! Soil layer - real(r8) :: max_tillage_depth + real(r8), parameter :: max_tillage_depth = 0.21_r8 zisoi = [0._r8, 0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8] dzsoi_decomp = [zisoi(2) - zisoi(1), & @@ -29,30 +29,26 @@ contains zisoi(4) - zisoi(3), & zisoi(5) - zisoi(4), & 0.5_r8] - - max_tillage_depth = 10._r8 - do j = 1, nlayers - @assertEqual(1._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), max_tillage_depth)) - end do - - max_tillage_depth = 0._r8 - do j = 1, nlayers - @assertEqual(0._r8, get_fraction_tilled(zisoi(j), dzsoi_decomp(j), max_tillage_depth)) - end do - - max_tillage_depth = 0.21_r8 + @assertEqual(1._r8, get_fraction_tilled(zisoi(1), dzsoi_decomp(1), max_tillage_depth)) @assertEqual(1._r8, get_fraction_tilled(zisoi(2), dzsoi_decomp(2), max_tillage_depth)) @assertEqual(1._r8, get_fraction_tilled(zisoi(3), dzsoi_decomp(3), max_tillage_depth)) @assertEqual(0.275_r8, get_fraction_tilled(zisoi(4), dzsoi_decomp(4), max_tillage_depth), tolerance=tol) @assertEqual(0._r8, get_fraction_tilled(zisoi(5), dzsoi_decomp(5), max_tillage_depth)) - max_tillage_depth = 0.5_r8 + end subroutine test_get_fraction_tilled + + + @Test + + subroutine test_get_fraction_tilled_0thickness() + real(r8), parameter :: max_tillage_depth = 0.5_r8 + @assertEqual(1._r8, get_fraction_tilled(0.4_r8, 0._r8, max_tillage_depth)) @assertEqual(1._r8, get_fraction_tilled(0.5_r8, 0._r8, max_tillage_depth)) @assertEqual(0._r8, get_fraction_tilled(0.6_r8, 0._r8, max_tillage_depth)) + end subroutine test_get_fraction_tilled_0thickness - end subroutine test_get_fraction_tilled end module test_tillage From 11bfed6d1fa94f5779012b72e1c963b0bdd4d2c4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 15:29:39 -0600 Subject: [PATCH 1504/2067] Removed test_conda_retry=False option. --- cime_config/SystemTests/systemtest_utils.py | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index c10b0392e9..6076faf8cd 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -5,7 +5,7 @@ import os, subprocess -def cmds_to_setup_conda(caseroot, test_conda_retry=True): +def cmds_to_setup_conda(caseroot): # Add specific commands needed on different machines to get conda available # Use semicolon here since it's OK to fail # @@ -21,17 +21,16 @@ def cmds_to_setup_conda(caseroot, test_conda_retry=True): # Remove python and add conda to environment for cheyennne unload_python_load_conda = "module unload python; module load conda;" # Make sure that adding this actually loads conda - if test_conda_retry: - subprocess.run(unload_python_load_conda + "which conda", shell=True, check=True) + subprocess.run(unload_python_load_conda + "which conda", shell=True, check=True) # Save conda_setup_commands += " " + unload_python_load_conda return conda_setup_commands -def cmds_to_run_via_conda(caseroot, conda_run_call, command, test_conda_retry=True): +def cmds_to_run_via_conda(caseroot, conda_run_call, command): # Run in the specified conda environment - conda_setup_commands = cmds_to_setup_conda(caseroot, test_conda_retry) + conda_setup_commands = cmds_to_setup_conda(caseroot) conda_setup_commands += " " + conda_run_call # Finish with Python script call @@ -54,10 +53,9 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): command, shell=True, check=True, text=True, stdout=f, stderr=subprocess.STDOUT ) except subprocess.CalledProcessError as error: - # Retry with the original ("conda activate") method. Set test_conda_retry False because - # that didn't happen in the original method. + # Retry with the original "conda activate" method command = cmds_to_run_via_conda( - caseroot, f"conda activate {this_conda_env} && ", command_in, test_conda_retry=False + caseroot, f"conda activate {this_conda_env} && ", command_in, ) try: with open(tool_name + ".log2", "w") as f: From 542d27517318bab1fd06b4f27aa1820cf50784ea Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 15:34:58 -0600 Subject: [PATCH 1505/2067] Added comments explaining use of sys.path.insert() in crop calendar scripts. --- python/ctsm/crop_calendars/cropcal_module.py | 3 ++- python/ctsm/crop_calendars/generate_gdds.py | 2 ++ python/ctsm/crop_calendars/generate_gdds_functions.py | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py index 1d58e2fbab..76c295974d 100644 --- a/python/ctsm/crop_calendars/cropcal_module.py +++ b/python/ctsm/crop_calendars/cropcal_module.py @@ -5,7 +5,8 @@ import os import glob -# Import the CTSM Python utilities +# Import the CTSM Python utilities. +# sys.path.insert() is necessary for RXCROPMATURITY to work. The fact that it's calling this script in the RUN phase seems to require the python/ directory to be manually added to path. _CTSM_PYTHON = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" ) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index 9fe1c26e14..b54e7df40f 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -5,6 +5,8 @@ import inspect import sys +# Import the CTSM Python utilities. +# sys.path.insert() is necessary for RXCROPMATURITY to work. The fact that it's calling this script in the RUN phase seems to require the python/ directory to be manually added to path. _CTSM_PYTHON = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" ) diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index c1a15324a2..cb4655d00b 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -6,12 +6,12 @@ import datetime as dt from importlib import util as importlib_util -# Import the CTSM Python utilities +# Import the CTSM Python utilities. +# sys.path.insert() is necessary for RXCROPMATURITY to work. The fact that it's calling this script in the RUN phase seems to require the python/ directory to be manually added to path. _CTSM_PYTHON = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" ) import sys - sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils import ctsm.crop_calendars.cropcal_module as cc From 77d0c7dc00a4a2593c036ff115b33c34a02b81d0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 15:39:10 -0600 Subject: [PATCH 1506/2067] get_fraction_tilled() receives layer_bottom, not layer_top. --- src/soilbiogeochem/TillageMod.F90 | 16 +++++++++++----- .../test/tillage_test/test_tillage.pf | 8 ++++---- 2 files changed, 15 insertions(+), 9 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index f35dff5bab..0ce3c4f96e 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -247,29 +247,35 @@ subroutine get_tillage_multipliers(tillage_mults, idop) end subroutine get_tillage_multipliers - function get_fraction_tilled(layer_top, layer_thickness, max_tillage_depth_gft) result(fraction_tilled) + function get_fraction_tilled(layer_bottom, layer_thickness, max_tillage_depth_gft) result(fraction_tilled) ! !ARGUMENTS - real(r8), intent(in) :: layer_top ! Soil layer interface depth (zisoi) + real(r8), intent(in) :: layer_bottom ! Soil layer interface (between j and j+1) depth (zisoi) real(r8), intent(in) :: layer_thickness ! Soil layer thickness (dzsoi_decomp) real(r8) :: max_tillage_depth_gft ! Maximum tillage depth + ! !LOCAL VARIABLES + real(r8) :: layer_top ! !RESULT real(r8) :: fraction_tilled ! Fraction of this layer that's within the tillage depth + ! If the top of the layer is below the max tillage depth, do not till. + layer_top = layer_bottom - layer_thickness if (layer_top > max_tillage_depth_gft) then fraction_tilled = 0._r8 return end if + ! Handle zero-thickness layers. This may not be necessary. if (layer_thickness == 0._r8) then - if (layer_top <= max_tillage_depth_gft) then + if (layer_bottom <= max_tillage_depth_gft) then fraction_tilled = 1._r8 else fraction_tilled = 0._r8 end if - else - fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth_gft - layer_top) / layer_thickness)) + return end if + fraction_tilled = max(0._r8, min(1._r8, (max_tillage_depth_gft - layer_top) / layer_thickness)) + end function get_fraction_tilled diff --git a/src/soilbiogeochem/test/tillage_test/test_tillage.pf b/src/soilbiogeochem/test/tillage_test/test_tillage.pf index 710541fd3d..77721aedd4 100644 --- a/src/soilbiogeochem/test/tillage_test/test_tillage.pf +++ b/src/soilbiogeochem/test/tillage_test/test_tillage.pf @@ -23,12 +23,12 @@ contains integer :: j ! Soil layer real(r8), parameter :: max_tillage_depth = 0.21_r8 - zisoi = [0._r8, 0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8] - dzsoi_decomp = [zisoi(2) - zisoi(1), & + zisoi = [0.01_r8, 0.05_r8, 0.1_r8, 0.5_r8, 1._r8] + dzsoi_decomp = [zisoi(1) - 0._r8, & + zisoi(2) - zisoi(1), & zisoi(3) - zisoi(2), & zisoi(4) - zisoi(3), & - zisoi(5) - zisoi(4), & - 0.5_r8] + zisoi(5) - zisoi(4)] @assertEqual(1._r8, get_fraction_tilled(zisoi(1), dzsoi_decomp(1), max_tillage_depth)) @assertEqual(1._r8, get_fraction_tilled(zisoi(2), dzsoi_decomp(2), max_tillage_depth)) From 8a168bb0895f4f2421608dd2589398e13a6663e6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 15:51:11 -0600 Subject: [PATCH 1507/2067] Reformatting with black. --- cime_config/SystemTests/systemtest_utils.py | 4 +++- python/ctsm/crop_calendars/generate_gdds_functions.py | 1 + 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/cime_config/SystemTests/systemtest_utils.py b/cime_config/SystemTests/systemtest_utils.py index 6076faf8cd..c5ac986abd 100644 --- a/cime_config/SystemTests/systemtest_utils.py +++ b/cime_config/SystemTests/systemtest_utils.py @@ -55,7 +55,9 @@ def run_python_script(caseroot, this_conda_env, command_in, tool_path): except subprocess.CalledProcessError as error: # Retry with the original "conda activate" method command = cmds_to_run_via_conda( - caseroot, f"conda activate {this_conda_env} && ", command_in, + caseroot, + f"conda activate {this_conda_env} && ", + command_in, ) try: with open(tool_name + ".log2", "w") as f: diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py index cb4655d00b..cb05f1920d 100644 --- a/python/ctsm/crop_calendars/generate_gdds_functions.py +++ b/python/ctsm/crop_calendars/generate_gdds_functions.py @@ -12,6 +12,7 @@ os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, os.pardir, "python" ) import sys + sys.path.insert(1, _CTSM_PYTHON) import ctsm.crop_calendars.cropcal_utils as utils import ctsm.crop_calendars.cropcal_module as cc From 9d7ac50f73d7ae7c96a7a952c42e8cc2f9d04359 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 15:51:42 -0600 Subject: [PATCH 1508/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index edd62049b5..03ea138bad 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -14,3 +14,4 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 +8a168bb0895f4f2421608dd2589398e13a6663e6 From abddd3f905ea1087d71e6f30f0441ec77bcbb190 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 19 Sep 2023 09:39:57 -0600 Subject: [PATCH 1509/2067] Revert adding RXCROPMATURITY to 2 test suites. --- cime_config/testdefs/testlist_clm.xml | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 2b46310a9a..2fe8565759 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2551,23 +2551,6 @@ - - - - - - - - - - - - - - - - - From 540b256d1f3382f4619d7b0877c32d54ce5c40b6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 19 Sep 2023 11:24:46 -0600 Subject: [PATCH 1510/2067] Reformatting with black. --- cime_config/SystemTests/rxcropmaturity.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/cime_config/SystemTests/rxcropmaturity.py b/cime_config/SystemTests/rxcropmaturity.py index bfa8ead151..b3b43cff07 100644 --- a/cime_config/SystemTests/rxcropmaturity.py +++ b/cime_config/SystemTests/rxcropmaturity.py @@ -257,7 +257,9 @@ def _run_fsurdat_modifier(self): # Where we will save the fsurdat version for this test path, ext = os.path.splitext(self._fsurdat_in) dir_in, filename_in_noext = os.path.split(path) - self._fsurdat_out = os.path.join(self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}") + self._fsurdat_out = os.path.join( + self._path_gddgen, f"{filename_in_noext}.all_crops_everywhere{ext}" + ) # Make fsurdat for this test, if not already done if not os.path.exists(self._fsurdat_out): @@ -275,9 +277,7 @@ def _run_fsurdat_modifier(self): ) self._create_config_file_evenlysplitcrop() - command = ( - f"python3 {tool_path} {self._cfg_path} " - ) + command = f"python3 {tool_path} {self._cfg_path} " stu.run_python_script( self._get_caseroot(), self._this_conda_env, @@ -330,7 +330,6 @@ def _create_config_file_evenlysplitcrop(self): cfg_out.write("PCT_LAKE = 0.0\n") cfg_out.write("PCT_URBAN = 0.0 0.0 0.0\n") - def _run_check_rxboth_run(self): output_dir = os.path.join(self._get_caseroot(), "run") @@ -397,7 +396,7 @@ def _run_generate_gdds(self, case_gddgen): f"--sdates-file {sdates_file}", f"--hdates-file {hdates_file}", f"--output-dir generate_gdds_out", - f"--skip-crops miscanthus,irrigated_miscanthus" + f"--skip-crops miscanthus,irrigated_miscanthus", ] ) stu.run_python_script( From d6d67c59641dd70130c1066cd71d6b54cd6c4a6a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 19 Sep 2023 11:25:24 -0600 Subject: [PATCH 1511/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index c6bbe1227f..cf56217215 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -15,3 +15,4 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd 5933b0018f8e29413e30dda9b906370d147bad45 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c +540b256d1f3382f4619d7b0877c32d54ce5c40b6 From f3f76f4b1144788d579836143f1c5a1bae04f49c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 19 Sep 2023 11:01:48 -0600 Subject: [PATCH 1512/2067] Updated ChangeLog and ChangeSum. --- doc/ChangeLog | 73 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 74 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 518e2b59cb..8e8a99b868 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,77 @@ =============================================================== +Tag name: ctsm5.1.dev142 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Tue Sep 19 11:30:22 MDT 2023 +One-line Summary: Merge 5 bit-for-bit pull requests + +Purpose and description of changes +---------------------------------- + +Merge 5 bit-for-bit pull requests; see "Other details." + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +* Add unit test for making fsurdat with all crops everywhere (#2079) +* Rework master_list_(no)?fates.rst? (#2083) +* conda run -n can fail if a conda environment is already active (#2109) +* conda fails to load for SystemTests (#2111) + + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +* FSURDATMODIFYCTSM system test should now work for everyone. + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + cheyenne - PASS + clm_pymods test suite on cheyenne - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +* Add system and unit tests for making fsurdat with all crops everywhere (#2081) +* Rework master_list* files etc. (#2087) +* Fixes to methane Tech Note (#2091) +* Add is_doy_in_interval() function (#2158) +* Avoid using subprocess.run() in FSURDATMODIFYCTSM (#2125) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev141 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) Date: Wed Sep 13 13:58:04 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 95a0285551..e11f439658 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev142 samrabin 09/19/2023 Merge 5 bit-for-bit pull requests ctsm5.1.dev141 slevis 09/13/2023 Change small snocan to zero ctsm5.1.dev140 afoster 09/12/2023 add lai_streams capability for FATES ctsm5.1.dev139 slevis 08/28/2023 Fix problems uncovered by nag -nan tests From 0940a22b1aaeb69218c8b7c9c119b13b4f9bc81b Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 20 Sep 2023 13:25:38 -0400 Subject: [PATCH 1513/2067] Extending intialization of cn_products gru_ variables to restarts --- src/biogeochem/CNProductsMod.F90 | 33 +++++++++++++++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 4ef5c7c86f..7dde2d5727 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -13,6 +13,7 @@ module CNProductsMod use clm_time_manager , only : get_step_size_real use SpeciesBaseType , only : species_base_type use PatchType , only : patch + use clm_varctl , only : use_fates_bgc ! implicit none private @@ -346,6 +347,17 @@ subroutine InitCold(this, bounds) this%tot_woodprod_grc(g) = 0._r8 end do + ! We don't call the woodproduct fluxes routine if + ! no veg patches are active. This is what happens + ! when fates is on. Woodproduct fluxes use a p2g + ! upscaling for the gru_ pools. Must zero it here then. + if(use_fates_bgc)then + do g = bounds%begg, bounds%endg + this%gru_prod10_gain_grc(g) = 0._r8 + this%gru_prod100_gain_grc(g) = 0._r8 + end do + end if + ! Need to set these patch-level fluxes to 0 everywhere for the sake of special ! landunits (because they don't get set over special landunits in the run loop) do p = bounds%begp, bounds%endp @@ -387,6 +399,7 @@ subroutine Restart(this, bounds, ncid, flag, & ! !LOCAL VARIABLES: logical :: template_provided logical :: readvar + integer :: g character(len=*), parameter :: subname = 'Restart' !----------------------------------------------------------------------- @@ -485,7 +498,20 @@ subroutine Restart(this, bounds, ncid, flag, & end if if (flag == 'read') then + + ! We don't call the woodproduct fluxes routine if + ! no veg patches are active. This is what happens + ! when fates is on. Woodproduct fluxes use a p2g + ! upscaling for the gru_ pools. Must zero it here then. + !if(use_fates_bgc)then + ! do g = bounds%begg, bounds%endg + ! this%gru_prod10_gain_grc(g) = 0._r8 + ! this%gru_prod100_gain_grc(g) = 0._r8 + ! end do + ! end if + call this%ComputeSummaryVars(bounds) + end if end subroutine Restart @@ -789,6 +815,7 @@ subroutine ComputeProductSummaryVars(this, bounds) ! fluxes into wood & crop product pools, from landcover change this%cropprod1_grc(g) = this%cropprod1_grc(g) + this%dwt_cropprod1_gain_grc(g)*dt + this%prod10_grc(g) = this%prod10_grc(g) + this%dwt_prod10_gain_grc(g)*dt this%prod100_grc(g) = this%prod100_grc(g) + this%dwt_prod100_gain_grc(g)*dt @@ -830,11 +857,15 @@ subroutine ComputeSummaryVars(this, bounds) do g = bounds%begg, bounds%endg + print*,this%prod10_grc(g),this%prod100_grc(g), this%prod10_loss_grc(g), & + this%prod100_loss_grc(g), this%cropprod1_loss_grc(g),this%dwt_prod100_gain_grc(g), & + this%dwt_prod10_gain_grc(g), this%gru_prod100_gain_grc(g), this%gru_prod10_gain_grc(g) + ! total wood products this%tot_woodprod_grc(g) = & this%prod10_grc(g) + & this%prod100_grc(g) - + ! total loss from wood products this%tot_woodprod_loss_grc(g) = & this%prod10_loss_grc(g) + & From b210a7898558d78bd212142b33baa67b0a250bb9 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 20 Sep 2023 14:51:23 -0400 Subject: [PATCH 1514/2067] removed print statements and uncommented a zeroing block --- src/biogeochem/CNProductsMod.F90 | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNProductsMod.F90 b/src/biogeochem/CNProductsMod.F90 index 7dde2d5727..a5f69696b0 100644 --- a/src/biogeochem/CNProductsMod.F90 +++ b/src/biogeochem/CNProductsMod.F90 @@ -503,12 +503,12 @@ subroutine Restart(this, bounds, ncid, flag, & ! no veg patches are active. This is what happens ! when fates is on. Woodproduct fluxes use a p2g ! upscaling for the gru_ pools. Must zero it here then. - !if(use_fates_bgc)then - ! do g = bounds%begg, bounds%endg - ! this%gru_prod10_gain_grc(g) = 0._r8 - ! this%gru_prod100_gain_grc(g) = 0._r8 - ! end do - ! end if + if(use_fates_bgc)then + do g = bounds%begg, bounds%endg + this%gru_prod10_gain_grc(g) = 0._r8 + this%gru_prod100_gain_grc(g) = 0._r8 + end do + end if call this%ComputeSummaryVars(bounds) @@ -857,10 +857,6 @@ subroutine ComputeSummaryVars(this, bounds) do g = bounds%begg, bounds%endg - print*,this%prod10_grc(g),this%prod100_grc(g), this%prod10_loss_grc(g), & - this%prod100_loss_grc(g), this%cropprod1_loss_grc(g),this%dwt_prod100_gain_grc(g), & - this%dwt_prod10_gain_grc(g), this%gru_prod100_gain_grc(g), this%gru_prod10_gain_grc(g) - ! total wood products this%tot_woodprod_grc(g) = & this%prod10_grc(g) + & From 3d253a02798066e417341649229ef6fb8c45fde2 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 21 Sep 2023 12:45:23 -0400 Subject: [PATCH 1515/2067] Updated temporary two-stream fates branch --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index c540fe8b0c..35f8d1740a 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.67.1_api.27.0.0 +repo_url = https://github.com/rgknox/fates +branch = two-stream-clean required = True [externals_description] From 1b0f7a25151c3ea95d435a8b989eb9e09b4eccab Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 22 Sep 2023 09:27:49 -0600 Subject: [PATCH 1516/2067] Rm Defaults from snicar vars in namelist_definition --- bld/namelist_files/namelist_definition_ctsm.xml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index ea01092da9..6691d4a1ff 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -153,49 +153,41 @@ of soil column (nlevsoi). number of wavelength bands used in SNICAR snow albedo calculation -Default: 5 type of downward solar radiation spectrum for SNICAR snow albedo calculation -Default: "mid_latitude_winter" dust optics type for SNICAR snow albedo calculation -Default: "sahara" snow grain shape used in SNICAR snow albedo calculation -Default: "hexagonal_plate" Toggle to turn on/off aerosol deposition flux in snow in SNICAR -Default: .true. option to activate BC-snow internal mixing in SNICAR snow albedo calculation -Default: .false. option to activate dust-snow internal mixing in SNICAR snow albedo calculation -Default: .false. option to activate organic carbon (OC) in SNICAR snow albedo calculation -Default: .false. Date: Fri, 22 Sep 2023 09:31:28 -0600 Subject: [PATCH 1517/2067] Rm one more Default --- bld/namelist_files/namelist_definition_ctsm.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 6691d4a1ff..731c10acfd 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1193,7 +1193,6 @@ DependsOnLatAndVeg - Arctic vegetation depends on latitude as above, but tempera Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) albedo forcing diagnostics for each aerosol species -Default: .false. Date: Mon, 25 Sep 2023 10:53:41 -0700 Subject: [PATCH 1518/2067] initial addition of fates seed dispersal switch and testmod --- bld/CLMBuildNamelist.pm | 6 +++--- bld/namelist_files/namelist_defaults_ctsm.xml | 1 + bld/namelist_files/namelist_definition_ctsm.xml | 6 ++++++ cime_config/testdefs/ExpectedTestFails.xml | 8 +++++++- cime_config/testdefs/testlist_clm.xml | 8 ++++++++ .../testmods_dirs/clm/FatesColdSeedDisp/README | 15 +++++++++++++++ .../clm/FatesColdSeedDisp/include_user_mods | 1 + .../clm/FatesColdSeedDisp/user_nl_clm | 1 + src/main/clm_varctl.F90 | 1 + src/main/controlMod.F90 | 3 +++ src/utils/clmfates_interfaceMod.F90 | 1 + 11 files changed, 47 insertions(+), 4 deletions(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 493313be19..6ca61367dc 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -769,8 +769,8 @@ sub setup_cmdl_fates_mode { # dis-allow fates specific namelist items with non-fates runs my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", - "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging", - "fates_parteh_mode","use_fates_tree_damage" ); + "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging", + "fates_parteh_mode","use_fates_tree_damage","use_fates_seeddisp" ); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { @@ -4272,7 +4272,7 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp", + "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_seeddisp", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0819b8dd29..0adc8c2768 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2684,6 +2684,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. +.false. 1 .true. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 45a32cb224..e878167745 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -705,6 +705,12 @@ Toggle to turn on prescribed physiology (Only relevant if FATES is on). + +Toggle to enable cross gridcell seed dispersal (requires fates parameter file values to be set as well) +(Only relevant if FATES is on) + + Toggle to turn on inventory initialization to startup FATES diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 174ebf9c58..672256079f 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -109,7 +109,13 @@ - + + + FAIL + FATES#1089 + This job will fail restart comparison due to pe layout change (i.e. PEM test would fail). + + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index aa5dd98697..05f630cb48 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1795,6 +1795,14 @@ + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README new file mode 100644 index 0000000000..e6385a97d5 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README @@ -0,0 +1,15 @@ +Testing FATES cross grid seed dispersal is activated by enabling the +namelist switch option use_fates_seeddisp as well as providing reasonable +values to the fates parameter file for the following variables: + +fates_seed_dispersal_fraction +fates_seed_dispersal_max_dist +fates_seed_dispersal_pdf_scale +fates_seed_dispersal_pdf_shape + +Given that the default fates parameter file has the above variables as unset, +a custom fates parameter file must be supplied to appropriately test this mode. + +Addressing CTSM issue #2126 will provide the capability to build the fates parameter +file on the fly with the appropriate values for this test. This testmod itself +addresses CTSM issue #2151. diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm new file mode 100644 index 0000000000..6267bf355b --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -0,0 +1 @@ +use_fates_seeddisp = .true. diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 800fce2139..ef7e24858c 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -269,6 +269,7 @@ module clm_varctl logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode + logical, public :: use_fates_seeddisp = .false. ! true => enable FATES cross gridcell seed dispersal character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control ! FATES SP AND FATES BGC are MUTUTALLY EXCLUSIVE, THEY CAN'T BOTH BE ON diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 541c5a00e7..1927b7ed69 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -230,6 +230,7 @@ subroutine control_init(dtime) use_fates_sp, & fates_inventory_ctrl_filename, & fates_parteh_mode, & + use_fates_seeddisp, & use_fates_tree_damage ! Ozone vegetation stress method @@ -744,6 +745,7 @@ subroutine control_spmd() call mpi_bcast (use_fates_inventory_init, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_fixed_biogeog, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_fates_seeddisp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) @@ -1096,6 +1098,7 @@ subroutine control_print () write(iulog, *) ' use_fates_fixed_biogeog = ', use_fates_fixed_biogeog write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp + write(iulog, *) ' use_fates_seeddisp = ', use_fates_seeddisp write(iulog, *) ' fates_inventory_ctrl_filename = ',fates_inventory_ctrl_filename end if end subroutine control_print diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 2b7a2a8ffd..9c87f9fb2b 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -61,6 +61,7 @@ module CLMFatesInterfaceMod use clm_varctl , only : use_fates_fixed_biogeog use clm_varctl , only : use_fates_nocomp use clm_varctl , only : use_fates_sp + use clm_varctl , only : use_fates_seeddisp use clm_varctl , only : fates_inventory_ctrl_filename use clm_varctl , only : use_nitrif_denitrif use clm_varctl , only : use_lch4 From 2d955041ba1554829541eecd4e750ae80bb418f0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Sep 2023 15:50:08 -0700 Subject: [PATCH 1519/2067] change the seed dispersal switch to take different values Since fates seed dispersal can occur at different user defined cadences, allow the user to define this via the namelist. --- bld/CLMBuildNamelist.pm | 4 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- .../namelist_definition_ctsm.xml | 13 +++--- .../clm/FatesColdSeedDisp/README | 14 ++++-- .../clm/FatesColdSeedDisp/user_nl_clm | 3 +- src/main/clm_varctl.F90 | 3 +- src/main/controlMod.F90 | 6 +-- src/utils/clmfates_interfaceMod.F90 | 46 ++++--------------- 8 files changed, 37 insertions(+), 54 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 6ca61367dc..93414d30f6 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -770,7 +770,7 @@ sub setup_cmdl_fates_mode { my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog", "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","use_fates_logging", - "fates_parteh_mode","use_fates_tree_damage","use_fates_seeddisp" ); + "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence" ); # dis-allow fates specific namelist items with non-fates runs foreach my $var ( @list ) { if ( defined($nl->get_value($var)) ) { @@ -4272,7 +4272,7 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", - "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","use_fates_seeddisp", + "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage" ); foreach my $var ( @list ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'}, diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0adc8c2768..0bd31ee9eb 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2684,8 +2684,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 .false. .false. .false. -.false. 1 +0 .true. .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index e878167745..a183691147 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -638,6 +638,13 @@ Switch deciding which nutrient model to use in FATES. (Only relevant if FATES is on) + +Switch defining the cadence at which seeds are dispersed across +gridcells. Setting the switch value to zero turns off dispersal. +(Only relevant if FATES is on) + + Toggle to turn on the tree damage module in FATES @@ -705,12 +712,6 @@ Toggle to turn on prescribed physiology (Only relevant if FATES is on). - -Toggle to enable cross gridcell seed dispersal (requires fates parameter file values to be set as well) -(Only relevant if FATES is on) - - Toggle to turn on inventory initialization to startup FATES diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README index e6385a97d5..b4f36132b8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README @@ -9,7 +9,15 @@ fates_seed_dispersal_pdf_shape Given that the default fates parameter file has the above variables as unset, a custom fates parameter file must be supplied to appropriately test this mode. +This testmod itself addresses CTSM issue #2151. -Addressing CTSM issue #2126 will provide the capability to build the fates parameter -file on the fly with the appropriate values for this test. This testmod itself -addresses CTSM issue #2151. +The max_dist value will impact the size of the 'neighborhood' of gridcells +that fates will attempt to distribute seeds to. To limit the neighborhood to +something tractable for a regression test, the user_nl_clm file points to a +specific fates parameter file that was generated to work with a 5x5_amazon +resolution. + +The main downside of this method is that this file will require a custom update +for every fates parameter file API update. Addressing CTSM issue #2126 will alleviate +this issue as it will provide the capability to build the fates parameter file on +the fly which with the appropriate values for this test. diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index 6267bf355b..31e567cca1 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1 +1,2 @@ -use_fates_seeddisp = .true. +fates_paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_5x5_amazon_seeddispersal_c230925.nc' +fates_seeddisp_cadence = 1 diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index ef7e24858c..a61d861177 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -253,6 +253,8 @@ module clm_varctl ! These are INTERNAL to the FATES module + integer, public :: fates_seeddisp_cadence = -9 ! 0 => no seed dispersal + ! 1, 2, 3 => daily, monthly, or yearly dispersal integer, public :: fates_parteh_mode = -9 ! 1 => carbon only ! 2 => C+N+P (not enabled yet) ! no others enabled @@ -269,7 +271,6 @@ module clm_varctl logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode - logical, public :: use_fates_seeddisp = .false. ! true => enable FATES cross gridcell seed dispersal character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control ! FATES SP AND FATES BGC are MUTUTALLY EXCLUSIVE, THEY CAN'T BOTH BE ON diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 1927b7ed69..33d813abca 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -230,7 +230,7 @@ subroutine control_init(dtime) use_fates_sp, & fates_inventory_ctrl_filename, & fates_parteh_mode, & - use_fates_seeddisp, & + fates_seeddisp_cadence, & use_fates_tree_damage ! Ozone vegetation stress method @@ -745,12 +745,12 @@ subroutine control_spmd() call mpi_bcast (use_fates_inventory_init, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_fixed_biogeog, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_nocomp, 1, MPI_LOGICAL, 0, mpicom, ier) - call mpi_bcast (use_fates_seeddisp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_sp, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier) + call mpi_bcast (fates_seeddisp_cadence, 1, MPI_INTEGER, 0, mpicom, ier) ! flexibleCN nitrogen model call mpi_bcast (use_flexibleCN, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -1098,7 +1098,7 @@ subroutine control_print () write(iulog, *) ' use_fates_fixed_biogeog = ', use_fates_fixed_biogeog write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp - write(iulog, *) ' use_fates_seeddisp = ', use_fates_seeddisp + write(iulog, *) ' fates_seeddisp_cadence = ', fates_seeddisp_cadence write(iulog, *) ' fates_inventory_ctrl_filename = ',fates_inventory_ctrl_filename end if end subroutine control_print diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 9c87f9fb2b..229e57262e 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -61,7 +61,7 @@ module CLMFatesInterfaceMod use clm_varctl , only : use_fates_fixed_biogeog use clm_varctl , only : use_fates_nocomp use clm_varctl , only : use_fates_sp - use clm_varctl , only : use_fates_seeddisp + use clm_varctl , only : fates_seeddisp_cadence use clm_varctl , only : fates_inventory_ctrl_filename use clm_varctl , only : use_nitrif_denitrif use clm_varctl , only : use_lch4 @@ -136,8 +136,7 @@ module CLMFatesInterfaceMod use PRTGenericMod , only : num_elements use FatesInterfaceTypesMod, only : hlm_stepsize use FatesInterfaceTypesMod, only : fates_maxPatchesPerSite - use FatesInterfaceTypesMod, only : fates_dispersal_kernel_mode - use FatesInterfaceTypesMod, only : fates_dispersal_kernel_none + use FatesInterfaceTypesMod, only : fates_dispersal_cadence_none use EDMainMod , only : ed_ecosystem_dynamics use EDMainMod , only : ed_update_site use EDInitMod , only : zero_site @@ -389,6 +388,7 @@ subroutine CLMFatesGlobals2() call set_fates_ctrlparms('soilwater_ipedof',ival=get_ipedof(0)) call set_fates_ctrlparms('parteh_mode',ival=fates_parteh_mode) + call set_fates_ctrlparms('seeddisp_cadence',ival=fates_seeddisp_cadence) ! CTSM-FATES is not fully coupled (yet) ! So lets tell fates to use the RD competition mechanism @@ -615,7 +615,7 @@ subroutine init(this, bounds_proc ) ! Initialize dispersal - if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then ! Initialize fates global seed dispersal array for all nodes call get_proc_global(ng=numg) @@ -1397,8 +1397,8 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & patch%is_bareground(bounds_clump%begp:bounds_clump%endp) = .false. patch%wt_ed(bounds_clump%begp:bounds_clump%endp) = 0.0_r8 - ! Check if seed dispersal mode is 'turned on', if not return to calling procedure - if (fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) then + ! Zero the outgoing_local values prior to populating with the most recent seed update + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then ! zero the outgoing seed array !this%fates_seed%outgoing_local(:,:) = 0._r8 end if @@ -1410,7 +1410,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & write(iulog,*) 'WUHD pre: g, seed_out, outgoing: ', g, sum(this%fates(nc)%sites(s)%seed_out(:)), sum(this%fates_seed%outgoing_local(:,g)) ! Accumulate seeds from sites to the gridcell local outgoing buffer - if ((fates_dispersal_kernel_mode .ne. fates_dispersal_kernel_none) .and. IsItDispersalTime()) then + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none .and. IsItDispersalTime()) then this%fates_seed%outgoing_local(:,g) = this%fates(nc)%sites(s)%seed_out(:) end if write(iulog,*) 'WUHD pst: g, seed_out, outgoing: ', g, sum(this%fates(nc)%sites(s)%seed_out(:)), sum(this%fates_seed%outgoing_local(:,g)) @@ -2673,7 +2673,7 @@ subroutine WrapSeedGlobal(this,is_restart_flag) end if ! Check if seed dispersal mode is 'turned on', if not return to calling procedure - if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) return call t_startf('fates-seed-mpi_reduce') @@ -2743,7 +2743,7 @@ subroutine wrap_seed_dispersal(this,bounds_clump) integer :: nc ! clump index ! Check if seed dispersal mode is 'turned on', if not return to calling procedure - if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) return call t_startf('fates-seed-disperse') @@ -2778,34 +2778,6 @@ end subroutine wrap_seed_dispersal ! ====================================================================================== - subroutine wrap_seed_dispersal_reset(this,bounds_clump) - - ! This subroutine reset seed_in - - ! Arguments - class(hlm_fates_interface_type), intent(inout) :: this - type(bounds_type), intent(in) :: bounds_clump - ! Local Variables - integer :: g ! global index of the host gridcell - integer :: c ! global index of the host column - integer :: s ! FATES site index - integer :: nc ! clump index - - ! Check if seed dispersal mode is 'turned on', if not return to calling procedure - if (fates_dispersal_kernel_mode .eq. fates_dispersal_kernel_none) return - - nc = bounds_clump%clump_index - - do s = 1, this%fates(nc)%nsites - c = this%f2hmap(nc)%fcolumn(s) - g = col%gridcell(c) - this%fates(nc)%sites(s)%seed_in(:) = 0 ! reset - end do - - end subroutine wrap_seed_dispersal_reset - - ! ====================================================================================== - subroutine wrap_update_hifrq_hist(this, bounds_clump, & soilbiogeochem_carbonflux_inst, & soilbiogeochem_carbonstate_inst) From 9e69e55e974ab4b91d8c6194dd64930b2d538a26 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 25 Sep 2023 16:10:52 -0700 Subject: [PATCH 1520/2067] Split the fates seed dispersal ERP test into an ERS and PEM test --- cime_config/testdefs/testlist_clm.xml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 05f630cb48..c779071bf9 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1795,7 +1795,15 @@ - + + + + + + + + + From 01290689e2d7068f64e4355d0053ce2a6f22f9d3 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 25 Sep 2023 17:23:52 -0600 Subject: [PATCH 1521/2067] Add licencing info to subr. piecewise_linear_interp1d --- src/biogeophys/SnowSnicarMod.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 8453a8670d..51347324df 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -2549,6 +2549,8 @@ subroutine piecewise_linear_interp1d(nd, xd, yd, xi, yi) ! piecewise linear interpolation method for 1-dimensional data ! original author: John Burkardt, Florida State University, 09/22/2012 + ! Licencing: Original code distributed under the GNU LGPL license + ! Original code: https://people.sc.fsu.edu/~jburkardt/f77_src/pwl_interp_1d/pwl_interp_1d.f ! Added and modified by Cenlin He (NCAR), 01/27/2022 implicit none From 05ea928e7c5ae29c9a9332707a7fc81a5f2ffb9b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 25 Sep 2023 19:06:41 -0600 Subject: [PATCH 1522/2067] Add readv argument to call ncd_io in SnowSnicarMod (not tested, yet) --- src/biogeophys/SnowSnicarMod.F90 | 1217 ++++++++++++++++++++---------- 1 file changed, 812 insertions(+), 405 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 51347324df..1ef23c8ee6 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1795,6 +1795,7 @@ subroutine SnowOptics_init( ) character(len=256) :: locfn ! local filename character(len= 32) :: subname = 'SnowOptics_init' ! subroutine name integer :: ier ! error status + logical :: readv ! has variable been read in or not ! ! Initialize optical variables @@ -1844,8 +1845,10 @@ subroutine SnowOptics_init( ) ! mid-latitude winter spectrum case ('mid_latitude_winter') ! flux weights/spectrum - call ncd_io( 'flx_wgt_dir5_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif5_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir5_mlw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif5_mlw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ! THIS NOTE APPLIES TO ALL THE call ncd_io LINES BELOW WHERE ! bcphob AND ocphob GET ASSIGNED TO VARIABLES SUFFIXED bc1/oc1: @@ -1866,492 +1869,826 @@ subroutine SnowOptics_init( ) ! snow grain). ! ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob_dif_mlw', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_mlw', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_mlw', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_mlw', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob_dif_mlw', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_mlw', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_mlw', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_mlw', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob_dif_mlw', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_mlw', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_mlw', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_mlw', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob_dif_mlw', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_mlw', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_mlw', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_mlw', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16_dir_mlw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_mlw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_mlw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16_dir_mlw', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dir_mlw',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16_dif_mlw', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah_dif_mlw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah_dif_mlw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah_dif_mlw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah_dif_mlw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah_dif_mlw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah_dif_mlw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah_dif_mlw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah_dif_mlw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah_dif_mlw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah_dif_mlw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah_dif_mlw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah_dif_mlw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah_dif_mlw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah_dif_mlw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah_dif_mlw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah_dif_mlw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah_dif_mlw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah_dif_mlw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah_dif_mlw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col_dif_mlw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col_dif_mlw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col_dif_mlw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col_dif_mlw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col_dif_mlw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col_dif_mlw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col_dif_mlw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col_dif_mlw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col_dif_mlw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col_dif_mlw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col_dif_mlw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col_dif_mlw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col_dif_mlw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col_dif_mlw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col_dif_mlw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col_dif_mlw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col_dif_mlw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col_dif_mlw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col_dif_mlw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre_dif_mlw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre_dif_mlw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre_dif_mlw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre_dif_mlw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre_dif_mlw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre_dif_mlw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre_dif_mlw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre_dif_mlw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre_dif_mlw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre_dif_mlw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre_dif_mlw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre_dif_mlw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre_dif_mlw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre_dif_mlw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre_dif_mlw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre_dif_mlw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre_dif_mlw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre_dif_mlw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre_dif_mlw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre_dif_mlw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre_dif_mlw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre_dif_mlw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre_dif_mlw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre_dif_mlw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select ! mid-latitude summer spectrum case ('mid_latitude_summer') ! flux weights/spectrum - call ncd_io( 'flx_wgt_dir5_mls', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif5_mls', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir5_mls', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif5_mls', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob_dif_mls', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_mls', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_mls', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_mls', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob_dif_mls', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_mls', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_mls', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_mls', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob_dif_mls', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_mls', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_mls', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_mls', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob_dif_mls', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_mls', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_mls', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_mls', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16_dir_mls', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_mls',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_mls', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16_dir_mls', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dir_mls',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16_dif_mls', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah_dif_mls', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah_dif_mls', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah_dif_mls', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah_dif_mls', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah_dif_mls', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah_dif_mls', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah_dif_mls', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah_dif_mls', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah_dif_mls', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah_dif_mls', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah_dif_mls', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah_dif_mls', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah_dif_mls', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah_dif_mls', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah_dif_mls', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah_dif_mls', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah_dif_mls', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah_dif_mls', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah_dif_mls', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col_dif_mls', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col_dif_mls', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col_dif_mls', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col_dif_mls', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col_dif_mls', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col_dif_mls', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col_dif_mls', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col_dif_mls', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col_dif_mls', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col_dif_mls', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col_dif_mls', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col_dif_mls', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col_dif_mls', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col_dif_mls', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col_dif_mls', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col_dif_mls', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col_dif_mls', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col_dif_mls', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col_dif_mls', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre_dif_mls', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre_dif_mls', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre_dif_mls', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre_dif_mls', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre_dif_mls', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre_dif_mls', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre_dif_mls', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre_dif_mls', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre_dif_mls', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre_dif_mls', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre_dif_mls', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre_dif_mls', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre_dif_mls', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre_dif_mls', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre_dif_mls', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre_dif_mls', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre_dif_mls', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre_dif_mls', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre_dif_mls', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre_dif_mls', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre_dif_mls', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre_dif_mls', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre_dif_mls', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre_dif_mls', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select ! sub-Arctic winter spectrum case ('sub_arctic_winter') - call ncd_io( 'flx_wgt_dir5_saw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif5_saw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir5_saw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif5_saw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob_dif_saw', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_saw', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_saw', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_saw', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob_dif_saw', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_saw', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_saw', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_saw', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob_dif_saw', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_saw', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_saw', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_saw', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob_dif_saw', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_saw', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_saw', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_saw', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16_dir_saw', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_saw',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_saw', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16_dir_saw', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dir_saw',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16_dif_saw', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah_dif_saw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah_dif_saw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah_dif_saw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah_dif_saw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah_dif_saw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah_dif_saw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah_dif_saw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah_dif_saw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah_dif_saw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah_dif_saw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah_dif_saw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah_dif_saw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah_dif_saw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah_dif_saw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah_dif_saw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah_dif_saw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah_dif_saw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah_dif_saw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah_dif_saw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col_dif_saw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col_dif_saw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col_dif_saw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col_dif_saw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col_dif_saw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col_dif_saw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col_dif_saw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col_dif_saw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col_dif_saw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col_dif_saw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col_dif_saw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col_dif_saw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col_dif_saw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col_dif_saw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col_dif_saw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col_dif_saw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col_dif_saw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col_dif_saw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col_dif_saw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre_dif_saw', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre_dif_saw', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre_dif_saw', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre_dif_saw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre_dif_saw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre_dif_saw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre_dif_saw', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre_dif_saw', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre_dif_saw', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre_dif_saw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre_dif_saw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre_dif_saw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre_dif_saw', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre_dif_saw', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre_dif_saw', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre_dif_saw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre_dif_saw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre_dif_saw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre_dif_saw', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre_dif_saw', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre_dif_saw', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre_dif_saw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre_dif_saw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre_dif_saw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select ! sub-Arctic summer spectrum case ('sub_arctic_summer') - call ncd_io( 'flx_wgt_dir5_sas', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif5_sas', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir5_sas', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif5_sas', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob_dif_sas', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_sas', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_sas', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_sas', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob_dif_sas', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_sas', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_sas', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_sas', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob_dif_sas', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_sas', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_sas', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_sas', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob_dif_sas', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_sas', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_sas', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_sas', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16_dir_sas', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_sas',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_sas', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16_dir_sas', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dir_sas',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16_dif_sas', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah_dif_sas', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah_dif_sas', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah_dif_sas', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah_dif_sas', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah_dif_sas', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah_dif_sas', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah_dif_sas', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah_dif_sas', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah_dif_sas', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah_dif_sas', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah_dif_sas', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah_dif_sas', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah_dif_sas', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah_dif_sas', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah_dif_sas', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah_dif_sas', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah_dif_sas', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah_dif_sas', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah_dif_sas', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col_dif_sas', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col_dif_sas', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col_dif_sas', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col_dif_sas', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col_dif_sas', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col_dif_sas', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col_dif_sas', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col_dif_sas', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col_dif_sas', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col_dif_sas', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col_dif_sas', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col_dif_sas', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col_dif_sas', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col_dif_sas', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col_dif_sas', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col_dif_sas', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col_dif_sas', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col_dif_sas', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col_dif_sas', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre_dif_sas', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre_dif_sas', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre_dif_sas', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre_dif_sas', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre_dif_sas', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre_dif_sas', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre_dif_sas', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre_dif_sas', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre_dif_sas', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre_dif_sas', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre_dif_sas', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre_dif_sas', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre_dif_sas', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre_dif_sas', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre_dif_sas', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre_dif_sas', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre_dif_sas', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre_dif_sas', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre_dif_sas', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre_dif_sas', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre_dif_sas', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre_dif_sas', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre_dif_sas', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre_dif_sas', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select ! Summit,Greenland,summer spectrum case ('summit_greenland_summer') - call ncd_io( 'flx_wgt_dir5_smm', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif5_smm', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir5_smm', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif5_smm', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob_dif_smm', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_smm', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_smm', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_smm', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob_dif_smm', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_smm', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_smm', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_smm', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob_dif_smm', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_smm', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_smm', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_smm', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob_dif_smm', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_smm', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_smm', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_smm', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16_dir_smm', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_smm',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_smm', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16_dir_smm', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dir_smm',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16_dif_smm', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah_dif_smm', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah_dif_smm', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah_dif_smm', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah_dif_smm', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah_dif_smm', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah_dif_smm', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah_dif_smm', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah_dif_smm', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah_dif_smm', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah_dif_smm', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah_dif_smm', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah_dif_smm', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah_dif_smm', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah_dif_smm', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah_dif_smm', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah_dif_smm', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah_dif_smm', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah_dif_smm', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah_dif_smm', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col_dif_smm', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col_dif_smm', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col_dif_smm', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col_dif_smm', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col_dif_smm', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col_dif_smm', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col_dif_smm', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col_dif_smm', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col_dif_smm', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col_dif_smm', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col_dif_smm', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col_dif_smm', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col_dif_smm', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col_dif_smm', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col_dif_smm', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col_dif_smm', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col_dif_smm', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col_dif_smm', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col_dif_smm', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre_dif_smm', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre_dif_smm', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre_dif_smm', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre_dif_smm', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre_dif_smm', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre_dif_smm', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre_dif_smm', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre_dif_smm', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre_dif_smm', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre_dif_smm', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre_dif_smm', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre_dif_smm', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre_dif_smm', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre_dif_smm', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre_dif_smm', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre_dif_smm', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre_dif_smm', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre_dif_smm', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre_dif_smm', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre_dif_smm', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre_dif_smm', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre_dif_smm', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre_dif_smm', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre_dif_smm', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select ! High Mountain summer spectrum case ('high_mountain_summer') - call ncd_io( 'flx_wgt_dir5_hmn', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif5_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir5_hmn', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif5_hmn', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob_dif_hmn', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_hmn', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_hmn', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_hmn', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob_dif_hmn', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob_dif_hmn', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob_dif_hmn', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob_dif_hmn', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob_dif_hmn', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_hmn', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_hmn', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_hmn', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob_dif_hmn', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob_dif_hmn', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob_dif_hmn', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob_dif_hmn', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16_dir_hmn', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dir_hmn',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16_dif_hmn', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16_dir_hmn', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dir_hmn',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16_dif_hmn', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah_dif_hmn', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah_dif_hmn', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah_dif_hmn', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah_dif_hmn', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah_dif_hmn', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah_dif_hmn', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah_dif_hmn', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah_dif_hmn', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah_dif_hmn', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah_dif_hmn', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah_dif_hmn', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah_dif_hmn', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah_dif_hmn', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah_dif_hmn', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah_dif_hmn', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah_dif_hmn', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah_dif_hmn', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah_dif_hmn', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah_dif_hmn', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col_dif_hmn', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col_dif_hmn', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col_dif_hmn', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col_dif_hmn', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col_dif_hmn', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col_dif_hmn', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col_dif_hmn', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col_dif_hmn', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col_dif_hmn', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col_dif_hmn', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col_dif_hmn', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col_dif_hmn', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col_dif_hmn', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col_dif_hmn', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col_dif_hmn', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col_dif_hmn', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col_dif_hmn', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col_dif_hmn', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col_dif_hmn', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre_dif_hmn', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre_dif_hmn', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre_dif_hmn', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre_dif_hmn', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre_dif_hmn', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre_dif_hmn', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre_dif_hmn', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre_dif_hmn', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre_dif_hmn', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre_dif_hmn', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre_dif_hmn', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre_dif_hmn', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre_dif_hmn', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre_dif_hmn', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre_dif_hmn', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre_dif_hmn', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre_dif_hmn', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre_dif_hmn', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre_dif_hmn', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre_dif_hmn', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre_dif_hmn', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre_dif_hmn', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre_dif_hmn', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre_dif_hmn', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select end select @@ -2359,106 +2696,172 @@ subroutine SnowOptics_init( ) case (480) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io( 'ss_alb_bcphob', ss_alb_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob', asm_prm_bc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io( 'ss_alb_bcphob', ss_alb_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_bcphob', asm_prm_bc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_bcphob', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_bcphob', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io( 'ss_alb_ocphob', ss_alb_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob', asm_prm_oc1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io( 'ss_alb_ocphob', ss_alb_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ocphob', asm_prm_oc2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ocphob', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ocphob', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! snow optical properties derived from different ice refractive index dataset ! same value for direct and diffuse due to high spectral res without spectra averaging in database (Picard et al., 2016) - call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust optical properties select case (snicar_dust_optics) case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_sah', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_sah', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_sah', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_sah', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_sah', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_sah', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_sah', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_sah', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_sah', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_sah', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_sah', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_sah', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_sah', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_sah', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_col', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_col', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_col', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_col', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_col', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_col', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_col', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_col', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_col', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_col', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_col', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_col', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_col', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_col', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_col', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_col', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_col', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_col', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_col', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_col', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_col', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_col', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_col', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_col', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) ! dust species 1 Mie parameters - call ncd_io( 'ss_alb_dust01_gre', ss_alb_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust01_gre', asm_prm_dst1, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust01_gre', ext_cff_mss_dst1, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust01_gre', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust01_gre', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust01_gre', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 2 Mie parameters - call ncd_io( 'ss_alb_dust02_gre', ss_alb_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust02_gre', asm_prm_dst2, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust02_gre', ext_cff_mss_dst2, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust02_gre', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust02_gre', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust02_gre', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 3 Mie parameters - call ncd_io( 'ss_alb_dust03_gre', ss_alb_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust03_gre', asm_prm_dst3, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust03_gre', ext_cff_mss_dst3, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust03_gre', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust03_gre', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust03_gre', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! dust species 4 Mie parameters - call ncd_io( 'ss_alb_dust04_gre', ss_alb_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'asm_prm_dust04_gre', asm_prm_dst4, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'ext_cff_mss_dust04_gre', ext_cff_mss_dst4, 'read', ncid, posNOTonfile=.true.) + call ncd_io('ss_alb_dust04_gre', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('asm_prm_dust04_gre', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('ext_cff_mss_dust04_gre', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select ! downward solar radiation spectral weights for 480-band select case (snicar_solarspec) case ('mid_latitude_winter') - call ncd_io( 'flx_wgt_dir480_mlw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_mlw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir480_mlw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif480_mlw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('mid_latitude_summer') - call ncd_io( 'flx_wgt_dir480_mls', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_mls', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir480_mls', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif480_mls', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('sub_arctic_winter') - call ncd_io( 'flx_wgt_dir480_saw', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_saw', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir480_saw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif480_saw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('sub_arctic_summer') - call ncd_io( 'flx_wgt_dir480_sas', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_sas', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir480_sas', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif480_sas', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('summit_greenland_summer') - call ncd_io( 'flx_wgt_dir480_smm', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_smm', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir480_smm', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif480_smm', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) case ('high_mountain_summer') - call ncd_io( 'flx_wgt_dir480_hmn', flx_wgt_dir, 'read', ncid, posNOTonfile=.true.) - call ncd_io( 'flx_wgt_dif480_hmn', flx_wgt_dif, 'read', ncid, posNOTonfile=.true.) + call ncd_io('flx_wgt_dir480_hmn', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('flx_wgt_dif480_hmn', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select end select @@ -2514,6 +2917,7 @@ subroutine SnowAge_init( ) character(len= 32) :: subname = 'SnowOptics_init' ! subroutine name integer :: varid ! netCDF id's integer :: ier ! error status + logical :: readv ! has variable been read in or not ! Open snow aging (effective radius evolution) file: allocate(snowage_tau(idx_rhos_max,idx_Tgrd_max,idx_T_max)) @@ -2527,9 +2931,12 @@ subroutine SnowAge_init( ) ! snow aging parameters - call ncd_io('tau', snowage_tau, 'read', ncid, posNOTonfile=.true.) - call ncd_io('kappa', snowage_kappa, 'read', ncid, posNOTonfile=.true.) - call ncd_io('drdsdt0', snowage_drdt0, 'read', ncid, posNOTonfile=.true.) + call ncd_io('tau', snowage_tau, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('kappa', snowage_kappa, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + call ncd_io('drdsdt0', snowage_drdt0, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) call ncd_pio_closefile(ncid) if (masterproc) then From feb183308aee5c6c1b053c121680d78f037005c0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 26 Sep 2023 09:50:08 -0700 Subject: [PATCH 1523/2067] include gridcell history diagnostics in the dispersal test --- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index 31e567cca1..64dc4efdc6 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,2 +1,3 @@ fates_paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_5x5_amazon_seeddispersal_c230925.nc' fates_seeddisp_cadence = 1 +hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From 6936ac40a27d75f1058848a6d3753f20c9f9b054 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 26 Sep 2023 14:27:08 -0700 Subject: [PATCH 1524/2067] correct expected fails to match testlist update --- cime_config/testdefs/ExpectedTestFails.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 672256079f..a9e79d3bef 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -109,8 +109,8 @@ - - + + FAIL FATES#1089 This job will fail restart comparison due to pe layout change (i.e. PEM test would fail). From 8cf2c70f11eaf15d0632a8771b9fff223c0dc874 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 26 Sep 2023 15:47:06 -0600 Subject: [PATCH 1525/2067] Updates to last commit for test to PASS Tested with ERI_D_Ld9.T31_g37.I2000Clm50Sp.cheyenne_intel.clm-SNICARFRC Ran with this commit's modifications versus without this and the last commits' modifications and got bfb same answers. --- src/biogeophys/SnowSnicarMod.F90 | 1266 ++++++------------------------ 1 file changed, 259 insertions(+), 1007 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 1ef23c8ee6..a18eda4d7f 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1796,6 +1796,10 @@ subroutine SnowOptics_init( ) character(len= 32) :: subname = 'SnowOptics_init' ! subroutine name integer :: ier ! error status logical :: readv ! has variable been read in or not + character(len=100) :: errCode = '-Error reading fsnowoptics file:' + character(len=100) :: tString ! temp. var for reading + character(len=3) :: short_case_dust_opt ! subset of tString + character(len=3) :: short_case_solarspec ! subset of tString ! ! Initialize optical variables @@ -1837,1032 +1841,275 @@ subroutine SnowOptics_init( ) call ncd_pio_openfile(ncid, locfn, 0) if(masterproc) write(iulog,*) subname,trim(fsnowoptics) + select case (snicar_solarspec) + case ('mid_latitude_winter') ! mid-latitude winter spectrum + short_case_solarspec = 'mlw' + case ('mid_latitude_summer') ! mid-latitude summer spectrum + short_case_solarspec = 'mls' + case ('sub_arctic_winter') ! sub-Arctic winter spectrum + short_case_solarspec = 'saw' + case ('sub_arctic_summer') ! sub-Arctic summer spectrum + short_case_solarspec = 'sas' + case ('summit_greenland_summer') ! Summit,Greenland,summer spectrum + short_case_solarspec = 'smm' + case ('high_mountain_summer') ! High Mountain summer spectrum + short_case_solarspec = 'hmn' + end select + + select case (snicar_dust_optics) ! dust optical properties + case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) + short_case_dust_opt = 'sah' + case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) + short_case_dust_opt = 'col' + case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) + short_case_dust_opt = 'gre' + end select + !--------------------- for 5-band data select case (snicar_numrad_snw) case (5) ! 5-band case - select case (snicar_solarspec) - ! mid-latitude winter spectrum - case ('mid_latitude_winter') - ! flux weights/spectrum - call ncd_io('flx_wgt_dir5_mlw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif5_mlw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! - ! THIS NOTE APPLIES TO ALL THE call ncd_io LINES BELOW WHERE - ! bcphob AND ocphob GET ASSIGNED TO VARIABLES SUFFIXED bc1/oc1: - ! - ! Assumption (1) applies here, in the input section. - ! Assumption (2) applies later, in the snicar code. - ! - ! 1) In this section, hydrophillic particles behave like hydrophobic - ! particles. We assume bc1/oc1 to have the same optics as bc2/oc2 - ! because sulfate coating on the bc1/oc1 surface is assumed to be - ! dissolved into the hydrometeo (i.e, snow grain here) during the - ! deposition process. This is different from the assumption made in - ! prior model versions, where bc1/oc1 was coated by undissolved - ! sulfate. - ! 2) Later, in the snicar code, if the bc-snow internal mixing option - ! is on, bc1/oc1 (internally mixed within the snow grain) will be - ! treated differently than bc2/oc2 (mixed externally or outside the - ! snow grain). - ! - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob_dif_mlw', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_mlw', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob_dif_mlw', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_mlw', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_mlw', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob_dif_mlw', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_mlw', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob_dif_mlw', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_mlw', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_mlw', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! ice refractive index (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16_dir_mlw', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dir_mlw',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dir_mlw', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16_dif_mlw', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dif_mlw',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dif_mlw', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah_dif_mlw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah_dif_mlw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah_dif_mlw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah_dif_mlw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah_dif_mlw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah_dif_mlw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah_dif_mlw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah_dif_mlw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah_dif_mlw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah_dif_mlw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah_dif_mlw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah_dif_mlw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col_dif_mlw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col_dif_mlw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col_dif_mlw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col_dif_mlw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col_dif_mlw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col_dif_mlw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col_dif_mlw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col_dif_mlw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col_dif_mlw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col_dif_mlw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col_dif_mlw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col_dif_mlw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre_dif_mlw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre_dif_mlw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre_dif_mlw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre_dif_mlw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre_dif_mlw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre_dif_mlw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre_dif_mlw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre_dif_mlw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre_dif_mlw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre_dif_mlw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre_dif_mlw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre_dif_mlw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select - - ! mid-latitude summer spectrum - case ('mid_latitude_summer') - ! flux weights/spectrum - call ncd_io('flx_wgt_dir5_mls', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif5_mls', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob_dif_mls', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_mls', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob_dif_mls', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_mls', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_mls', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob_dif_mls', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_mls', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob_dif_mls', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_mls', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_mls', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! ice refractive index (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16_dir_mls', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dir_mls',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dir_mls', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16_dif_mls', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dif_mls',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dif_mls', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah_dif_mls', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah_dif_mls', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah_dif_mls', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah_dif_mls', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah_dif_mls', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah_dif_mls', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah_dif_mls', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah_dif_mls', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah_dif_mls', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah_dif_mls', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah_dif_mls', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah_dif_mls', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col_dif_mls', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col_dif_mls', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col_dif_mls', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col_dif_mls', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col_dif_mls', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col_dif_mls', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col_dif_mls', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col_dif_mls', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col_dif_mls', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col_dif_mls', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col_dif_mls', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col_dif_mls', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre_dif_mls', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre_dif_mls', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre_dif_mls', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre_dif_mls', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre_dif_mls', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre_dif_mls', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre_dif_mls', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre_dif_mls', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre_dif_mls', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre_dif_mls', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre_dif_mls', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre_dif_mls', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select - - ! sub-Arctic winter spectrum - case ('sub_arctic_winter') - call ncd_io('flx_wgt_dir5_saw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif5_saw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob_dif_saw', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_saw', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob_dif_saw', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_saw', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_saw', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob_dif_saw', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_saw', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob_dif_saw', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_saw', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_saw', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! ice refractive index (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16_dir_saw', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dir_saw',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dir_saw', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16_dif_saw', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dif_saw',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dif_saw', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah_dif_saw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah_dif_saw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah_dif_saw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah_dif_saw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah_dif_saw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah_dif_saw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah_dif_saw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah_dif_saw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah_dif_saw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah_dif_saw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah_dif_saw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah_dif_saw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col_dif_saw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col_dif_saw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col_dif_saw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col_dif_saw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col_dif_saw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col_dif_saw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col_dif_saw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col_dif_saw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col_dif_saw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col_dif_saw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col_dif_saw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col_dif_saw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre_dif_saw', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre_dif_saw', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre_dif_saw', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre_dif_saw', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre_dif_saw', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre_dif_saw', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre_dif_saw', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre_dif_saw', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre_dif_saw', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre_dif_saw', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre_dif_saw', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre_dif_saw', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select - - ! sub-Arctic summer spectrum - case ('sub_arctic_summer') - call ncd_io('flx_wgt_dir5_sas', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif5_sas', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob_dif_sas', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_sas', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob_dif_sas', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_sas', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_sas', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob_dif_sas', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_sas', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob_dif_sas', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_sas', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_sas', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! ice refractive index (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16_dir_sas', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dir_sas',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dir_sas', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16_dif_sas', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dif_sas',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dif_sas', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah_dif_sas', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah_dif_sas', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah_dif_sas', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah_dif_sas', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah_dif_sas', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah_dif_sas', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah_dif_sas', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah_dif_sas', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah_dif_sas', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah_dif_sas', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah_dif_sas', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah_dif_sas', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col_dif_sas', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col_dif_sas', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col_dif_sas', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col_dif_sas', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col_dif_sas', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col_dif_sas', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col_dif_sas', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col_dif_sas', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col_dif_sas', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col_dif_sas', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col_dif_sas', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col_dif_sas', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre_dif_sas', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre_dif_sas', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre_dif_sas', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre_dif_sas', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre_dif_sas', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre_dif_sas', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre_dif_sas', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre_dif_sas', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre_dif_sas', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre_dif_sas', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre_dif_sas', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre_dif_sas', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select - - ! Summit,Greenland,summer spectrum - case ('summit_greenland_summer') - call ncd_io('flx_wgt_dir5_smm', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif5_smm', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob_dif_smm', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_smm', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob_dif_smm', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_smm', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_smm', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob_dif_smm', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_smm', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob_dif_smm', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_smm', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_smm', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! ice refractive index (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16_dir_smm', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dir_smm',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dir_smm', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16_dif_smm', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dif_smm',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dif_smm', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah_dif_smm', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah_dif_smm', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah_dif_smm', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah_dif_smm', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah_dif_smm', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah_dif_smm', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah_dif_smm', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah_dif_smm', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah_dif_smm', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah_dif_smm', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah_dif_smm', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah_dif_smm', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col_dif_smm', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col_dif_smm', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col_dif_smm', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col_dif_smm', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col_dif_smm', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col_dif_smm', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col_dif_smm', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col_dif_smm', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col_dif_smm', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col_dif_smm', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col_dif_smm', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col_dif_smm', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre_dif_smm', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre_dif_smm', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre_dif_smm', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre_dif_smm', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre_dif_smm', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre_dif_smm', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre_dif_smm', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre_dif_smm', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre_dif_smm', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre_dif_smm', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre_dif_smm', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre_dif_smm', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select - - ! High Mountain summer spectrum - case ('high_mountain_summer') - call ncd_io('flx_wgt_dir5_hmn', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif5_hmn', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob_dif_hmn', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_hmn', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob_dif_hmn', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob_dif_hmn', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob_dif_hmn', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob_dif_hmn', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_hmn', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob_dif_hmn', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob_dif_hmn', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob_dif_hmn', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! ice refractive index (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16_dir_hmn', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dir_hmn',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dir_hmn', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16_dif_hmn', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16_dif_hmn',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16_dif_hmn', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah_dif_hmn', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah_dif_hmn', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah_dif_hmn', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah_dif_hmn', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah_dif_hmn', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah_dif_hmn', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah_dif_hmn', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah_dif_hmn', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah_dif_hmn', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah_dif_hmn', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah_dif_hmn', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah_dif_hmn', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col_dif_hmn', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col_dif_hmn', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col_dif_hmn', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col_dif_hmn', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col_dif_hmn', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col_dif_hmn', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col_dif_hmn', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col_dif_hmn', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col_dif_hmn', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col_dif_hmn', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col_dif_hmn', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col_dif_hmn', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre_dif_hmn', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre_dif_hmn', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre_dif_hmn', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre_dif_hmn', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre_dif_hmn', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre_dif_hmn', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre_dif_hmn', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre_dif_hmn', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre_dif_hmn', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre_dif_hmn', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre_dif_hmn', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre_dif_hmn', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select - end select + ! flux weights/spectrum + tString = 'flx_wgt_dir5_'//short_case_solarspec + call ncd_io(trim(tString), flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'flx_wgt_dif5_'//short_case_solarspec + call ncd_io(trim(tString), flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! + ! THIS NOTE APPLIES TO ALL THE call ncd_io LINES BELOW WHERE + ! bcphob AND ocphob GET ASSIGNED TO VARIABLES SUFFIXED bc1/oc1: + ! + ! Assumption (1) applies here, in the input section. + ! Assumption (2) applies later, in the snicar code. + ! + ! 1) In this section, hydrophillic particles behave like hydrophobic + ! particles. We assume bc1/oc1 to have the same optics as bc2/oc2 + ! because sulfate coating on the bc1/oc1 surface is assumed to be + ! dissolved into the hydrometeo (i.e, snow grain here) during the + ! deposition process. This is different from the assumption made in + ! prior model versions, where bc1/oc1 was coated by undissolved + ! sulfate. + ! 2) Later, in the snicar code, if the bc-snow internal mixing option + ! is on, bc1/oc1 (internally mixed within the snow grain) will be + ! treated differently than bc2/oc2 (mixed externally or outside the + ! snow grain). + ! + ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + tString = 'ss_alb_bcphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_bcphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_bcphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! BC species 2 Mie parameters, uncoated BC + tString = 'ss_alb_bcphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_bcphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_bcphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + tString = 'ss_alb_ocphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ocphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ocphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! OC species 2 Mie parameters, uncoated OC + tString = 'ss_alb_ocphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ocphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ocphob_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! ice refractive index (Picard et al., 2016) + tString = 'ss_alb_ice_pic16_dir_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ice_pic16_dir_'//short_case_solarspec + call ncd_io(trim(tString),asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ice_pic16_dir_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ss_alb_ice_pic16_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ice_pic16_dif_'//short_case_solarspec + call ncd_io(trim(tString),asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ice_pic16_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + + ! dust species 1 Mie parameters + tString = 'ss_alb_dust01_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust01_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust01_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! dust species 2 Mie parameters + tString = 'ss_alb_dust02_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust02_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust02_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! dust species 3 Mie parameters + tString = 'ss_alb_dust03_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust03_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust03_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! dust species 4 Mie parameters + tString = 'ss_alb_dust04_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust04_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust04_'//short_case_dust_opt//'_dif_'//short_case_solarspec + call ncd_io(trim(tString), ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) !-------------------- for 480-band data case (480) ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing - call ncd_io('ss_alb_bcphob', ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'ss_alb_bcphob' + call ncd_io(trim(tString), ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob', asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'asm_prm_bcphob' + call ncd_io(trim(tString), asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob', ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'ext_cff_mss_bcphob' + call ncd_io(trim(tString), ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC - call ncd_io('ss_alb_bcphob', ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'ss_alb_bcphob' + call ncd_io(trim(tString), ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_bcphob', asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'asm_prm_bcphob' + call ncd_io(trim(tString), asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_bcphob', ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'ext_cff_mss_bcphob' + call ncd_io(trim(tString), ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing - call ncd_io('ss_alb_ocphob', ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'ss_alb_ocphob' + call ncd_io(trim(tString), ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob', asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'asm_prm_ocphob' + call ncd_io(trim(tString), asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob', ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'ext_cff_mss_ocphob' + call ncd_io(trim(tString), ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC - call ncd_io('ss_alb_ocphob', ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ocphob', asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ocphob', ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - - ! snow optical properties derived from different ice refractive index dataset - ! same value for direct and diffuse due to high spectral res without spectra averaging in database (Picard et al., 2016) - call ncd_io('ss_alb_ice_pic16', ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16',asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16', ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ss_alb_ice_pic16', ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_ice_pic16',asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_ice_pic16', ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - - ! dust optical properties - select case (snicar_dust_optics) - case ('sahara') ! Saharan dust (Balkanski et al., 2007, central hematite) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_sah', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_sah', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_sah', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_sah', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_sah', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_sah', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_sah', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_sah', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_sah', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_sah', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_sah', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_sah', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('san_juan_mtns_colorado') ! San Juan Mountains, CO (Skiles et al, 2017) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_col', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_col', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_col', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_col', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_col', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_col', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_col', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_col', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_col', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_col', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_col', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_col', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) - ! dust species 1 Mie parameters - call ncd_io('ss_alb_dust01_gre', ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust01_gre', asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust01_gre', ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 2 Mie parameters - call ncd_io('ss_alb_dust02_gre', ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust02_gre', asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust02_gre', ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 3 Mie parameters - call ncd_io('ss_alb_dust03_gre', ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust03_gre', asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust03_gre', ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! dust species 4 Mie parameters - call ncd_io('ss_alb_dust04_gre', ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('asm_prm_dust04_gre', asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('ext_cff_mss_dust04_gre', ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select + tString = 'ss_alb_ocphob' + call ncd_io(trim(tString), ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ocphob' + call ncd_io(trim(tString), asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ocphob' + call ncd_io(trim(tString), ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + + ! snow optical properties derived from different ice refractive index dataset + ! same value for direct and diffuse due to high spectral res without spectra averaging in database (Picard et al., 2016) + tString = 'ss_alb_ice_pic16' + call ncd_io(trim(tString), ss_alb_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ice_pic16' + call ncd_io(trim(tString), asm_prm_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ice_pic16' + call ncd_io(trim(tString), ext_cff_mss_snw_drc, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ss_alb_ice_pic16' + call ncd_io(trim(tString), ss_alb_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_ice_pic16' + call ncd_io(trim(tString), asm_prm_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_ice_pic16' + call ncd_io(trim(tString), ext_cff_mss_snw_dfs, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + + ! dust optical properties + ! dust species 1 Mie parameters + tString = 'ss_alb_dust01_'//short_case_dust_opt + call ncd_io(trim(tString), ss_alb_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust01_'//short_case_dust_opt + call ncd_io(trim(tString), asm_prm_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust01_'//short_case_dust_opt + call ncd_io(trim(tString), ext_cff_mss_dst1, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! dust species 2 Mie parameters + tString = 'ss_alb_dust02_'//short_case_dust_opt + call ncd_io(trim(tString), ss_alb_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust02_'//short_case_dust_opt + call ncd_io(trim(tString), asm_prm_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust02_'//short_case_dust_opt + call ncd_io(trim(tString), ext_cff_mss_dst2, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! dust species 3 Mie parameters + tString = 'ss_alb_dust03_'//short_case_dust_opt + call ncd_io(trim(tString), ss_alb_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust03_'//short_case_dust_opt + call ncd_io(trim(tString), asm_prm_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust03_'//short_case_dust_opt + call ncd_io(trim(tString), ext_cff_mss_dst3, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + ! dust species 4 Mie parameters + tString = 'ss_alb_dust04_'//short_case_dust_opt + call ncd_io(trim(tString), ss_alb_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'asm_prm_dust04_'//short_case_dust_opt + call ncd_io(trim(tString), asm_prm_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'ext_cff_mss_dust04_'//short_case_dust_opt + call ncd_io(trim(tString), ext_cff_mss_dst4, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! downward solar radiation spectral weights for 480-band - select case (snicar_solarspec) - case ('mid_latitude_winter') - call ncd_io('flx_wgt_dir480_mlw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif480_mlw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('mid_latitude_summer') - call ncd_io('flx_wgt_dir480_mls', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif480_mls', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('sub_arctic_winter') - call ncd_io('flx_wgt_dir480_saw', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif480_saw', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('sub_arctic_summer') - call ncd_io('flx_wgt_dir480_sas', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif480_sas', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('summit_greenland_summer') - call ncd_io('flx_wgt_dir480_smm', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif480_smm', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - case ('high_mountain_summer') - call ncd_io('flx_wgt_dir480_hmn', flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('flx_wgt_dif480_hmn', flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) - if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - end select + ! downward solar radiation spectral weights for 480-band + tString = 'flx_wgt_dir480_'//short_case_solarspec + call ncd_io(trim(tString), flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + tString = 'flx_wgt_dif480_'//short_case_solarspec + call ncd_io(trim(tString), flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) + if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) end select @@ -2918,6 +2165,8 @@ subroutine SnowAge_init( ) integer :: varid ! netCDF id's integer :: ier ! error status logical :: readv ! has variable been read in or not + character(len=100) :: errCode = '-Error reading snow aging parameters:' + character(len=100) :: tString ! temp. var for reading ! Open snow aging (effective radius evolution) file: allocate(snowage_tau(idx_rhos_max,idx_Tgrd_max,idx_T_max)) @@ -2931,11 +2180,14 @@ subroutine SnowAge_init( ) ! snow aging parameters - call ncd_io('tau', snowage_tau, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'tau' + call ncd_io(trim(tString), snowage_tau, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('kappa', snowage_kappa, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'kappa' + call ncd_io(trim(tString), snowage_kappa, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - call ncd_io('drdsdt0', snowage_drdt0, 'read', ncid, readv, posNOTonfile=.true.) + tString = 'drdsdt0' + call ncd_io(trim(tString), snowage_drdt0, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) call ncd_pio_closefile(ncid) From ffc8eaeb181b1079a66f7adf6759d8f53028fa8d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Sep 2023 10:54:27 -0600 Subject: [PATCH 1526/2067] Replace 3600 with secsphr --- src/biogeophys/SnowSnicarMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index a18eda4d7f..b9028b12a9 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1499,7 +1499,7 @@ subroutine SnowAge_grain(bounds, & ! !USES: use clm_time_manager , only : get_step_size_real, get_nstep use clm_varpar , only : nlevsno - use clm_varcon , only : spval + use clm_varcon, only: spval, secsphr use shr_const_mod , only : SHR_CONST_RHOICE, SHR_CONST_PI ! ! !ARGUMENTS: @@ -1634,7 +1634,7 @@ subroutine SnowAge_grain(bounds, & ! change in snow effective radius, using best-fit parameters dr_fresh = snw_rds(c_idx,i)-snw_rds_min - dr = (bst_drdt0 * (bst_tau / (dr_fresh + bst_tau))**(1._r8 / bst_kappa)) * (dtime / 3600._r8) + dr = (bst_drdt0 * (bst_tau / (dr_fresh + bst_tau))**(1._r8 / bst_kappa)) * (dtime / secsphr) ! !********** 2. WET SNOW AGING *********** From 521d24e668d501f9a3502f96cb633729c72faeb9 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 27 Sep 2023 10:56:15 -0600 Subject: [PATCH 1527/2067] correct cadence logic --- src/utils/clmfates_interfaceMod.F90 | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 229e57262e..a62b7a8190 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -239,7 +239,6 @@ module CLMFatesInterfaceMod procedure, public :: wrap_WoodProducts procedure, public :: WrapSeedGlobal procedure, public :: wrap_seed_dispersal - procedure, public :: wrap_seed_dispersal_reset procedure, public :: UpdateCLitterFluxes procedure, public :: UpdateNLitterFluxes end type hlm_fates_interface_type @@ -615,7 +614,7 @@ subroutine init(this, bounds_proc ) ! Initialize dispersal - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then ! Initialize fates global seed dispersal array for all nodes call get_proc_global(ng=numg) @@ -1397,10 +1396,9 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & patch%is_bareground(bounds_clump%begp:bounds_clump%endp) = .false. patch%wt_ed(bounds_clump%begp:bounds_clump%endp) = 0.0_r8 - ! Zero the outgoing_local values prior to populating with the most recent seed update - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then - ! zero the outgoing seed array - !this%fates_seed%outgoing_local(:,:) = 0._r8 + ! Zero the outgoing_local seed values prior to populating with the most recent seed update + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + this%fates_seed%outgoing_local(:,:) = 0._r8 end if do s = 1,this%fates(nc)%nsites @@ -1408,12 +1406,10 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & c = this%f2hmap(nc)%fcolumn(s) g = col%gridcell(c) - write(iulog,*) 'WUHD pre: g, seed_out, outgoing: ', g, sum(this%fates(nc)%sites(s)%seed_out(:)), sum(this%fates_seed%outgoing_local(:,g)) ! Accumulate seeds from sites to the gridcell local outgoing buffer if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none .and. IsItDispersalTime()) then this%fates_seed%outgoing_local(:,g) = this%fates(nc)%sites(s)%seed_out(:) end if - write(iulog,*) 'WUHD pst: g, seed_out, outgoing: ', g, sum(this%fates(nc)%sites(s)%seed_out(:)), sum(this%fates_seed%outgoing_local(:,g)) ! Other modules may have AI's we only flush values ! that are on the naturally vegetated columns From a7dd2e6755b625662c69b5e61a5d09b00689f217 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 27 Sep 2023 10:04:31 -0700 Subject: [PATCH 1528/2067] minor corrections to some dispersal comments --- cime_config/testdefs/ExpectedTestFails.xml | 1 - cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index a9e79d3bef..092bad1e69 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -113,7 +113,6 @@ FAIL FATES#1089 - This job will fail restart comparison due to pe layout change (i.e. PEM test would fail). diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README index b4f36132b8..d5ff7099a9 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README @@ -1,5 +1,5 @@ Testing FATES cross grid seed dispersal is activated by enabling the -namelist switch option use_fates_seeddisp as well as providing reasonable +namelist switch option fates_seeddisp_cadence as well as providing reasonable values to the fates parameter file for the following variables: fates_seed_dispersal_fraction From 8190e3b4449a997fdde13b25948624e40a305410 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 27 Sep 2023 11:04:10 -0700 Subject: [PATCH 1529/2067] move fates seed dispersal logic gates outside the procedure to be called --- src/main/clm_driver.F90 | 14 +++++++++----- src/utils/clmfates_interfaceMod.F90 | 15 ++++++--------- 2 files changed, 15 insertions(+), 14 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 9d3c52ea97..51fe7c4f63 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -111,10 +111,12 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! the calling tree is given in the description of this module. ! ! !USES: - use clm_time_manager , only : get_curr_date - use clm_varctl , only : use_lai_streams, fates_spitfire_mode - use laiStreamMod , only : lai_advance - use FATESFireFactoryMod , only : scalar_lightning + use clm_time_manager , only : get_curr_date + use clm_varctl , only : use_lai_streams, fates_spitfire_mode + use clm_varctl , only : fates_seeddisp_cadence + use laiStreamMod , only : lai_advance + use FATESFireFactoryMod , only : scalar_lightning + use FatesInterfaceTypesMod, only : fates_dispersal_cadence_none ! ! !ARGUMENTS: implicit none @@ -1269,7 +1271,9 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Pass fates seed dispersal information to all nodes - if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() + end if ! ============================================================================ ! Determine gridcell averaged properties to send to atm diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 7c7232ded9..462e72d46f 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1062,7 +1062,9 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! Distribute any seeds from neighboring gridcells into the current gridcell ! Global seed availability array populated by WrapSeedGlobal call - call this%wrap_seed_dispersal(bounds_clump) + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + call this%wrap_seed_dispersal(bounds_clump) + end if ! --------------------------------------------------------------------------------- ! Flush arrays to values defined by %flushval (see registry entry in @@ -1846,7 +1848,9 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & !$OMP END PARALLEL DO ! Disperse seeds - call this%WrapSeedGlobal(is_restart_flag=.true.) + if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + call this%WrapSeedGlobal(is_restart_flag=.true.) + end if end if @@ -2669,9 +2673,6 @@ subroutine WrapSeedGlobal(this,is_restart_flag) if (is_restart_flag) set_flag = .false. end if - ! Check if seed dispersal mode is 'turned on', if not return to calling procedure - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) return - call t_startf('fates-seed-mpi_reduce') if (IsItDispersalTime(setdispersedflag=set_flag)) then @@ -2739,9 +2740,6 @@ subroutine wrap_seed_dispersal(this,bounds_clump) integer :: s ! FATES site index integer :: nc ! clump index - ! Check if seed dispersal mode is 'turned on', if not return to calling procedure - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) return - call t_startf('fates-seed-disperse') nc = bounds_clump%clump_index @@ -2768,7 +2766,6 @@ subroutine wrap_seed_dispersal(this,bounds_clump) end do - call t_stopf('fates-seed-disperse') end subroutine wrap_seed_dispersal From 55ad1990362fa9569c09b988ed3e39b7d6268dd1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Sep 2023 12:20:29 -0600 Subject: [PATCH 1530/2067] Replace indices 1, 2 with ivis, inir where appropriate --- src/biogeochem/DryDepVelocity.F90 | 1 - src/biogeophys/SnowSnicarMod.F90 | 38 +++++++++++++++---------------- 2 files changed, 19 insertions(+), 20 deletions(-) diff --git a/src/biogeochem/DryDepVelocity.F90 b/src/biogeochem/DryDepVelocity.F90 index f50e218e1b..f5968c9aa8 100644 --- a/src/biogeochem/DryDepVelocity.F90 +++ b/src/biogeochem/DryDepVelocity.F90 @@ -285,7 +285,6 @@ subroutine depvel_compute( bounds, & if ( n_drydep == 0 ) return associate( & - forc_solai => atm2lnd_inst%forc_solai_grc , & ! Input: [real(r8) (:,:) ] direct beam radiation (visible only) forc_solad => atm2lnd_inst%forc_solad_grc , & ! Input: [real(r8) (:,:) ] direct beam radiation (visible only) forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] downscaled atmospheric temperature (Kelvin) forc_q => wateratm2lndbulk_inst%forc_q_downscaled_col , & ! Input: [real(r8) (:) ] downscaled atmospheric specific humidity (kg/kg) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index b9028b12a9..422d65df84 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -217,7 +217,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! spectral snow albedo ! ! !USES: - use clm_varpar , only : nlevsno, numrad + use clm_varpar , only : nlevsno, numrad, ivis, inir use clm_time_manager , only : get_nstep use shr_const_mod , only : SHR_CONST_PI ! @@ -708,8 +708,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! Set spectral underlying surface albedos to their corresponding VIS or NIR albedos - albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,1) - albsfc_lcl(nir_bnd_bgn:nir_bnd_end) = albsfc(c_idx,2) + albsfc_lcl(1:(nir_bnd_bgn-1)) = albsfc(c_idx,ivis) + albsfc_lcl(nir_bnd_bgn:nir_bnd_end) = albsfc(c_idx,inir) ! Error check for snow grain size: @@ -1189,11 +1189,11 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! set the underlying ground albedo == albedo of near-IR ! unless bnd_idx < nir_bnd_bgn, for visible - rupdir(snl_btm_itf) = albsfc(c_idx,2) - rupdif(snl_btm_itf) = albsfc(c_idx,2) + rupdir(snl_btm_itf) = albsfc(c_idx,inir) + rupdif(snl_btm_itf) = albsfc(c_idx,inir) if (bnd_idx < nir_bnd_bgn) then - rupdir(snl_btm_itf) = albsfc(c_idx,1) - rupdif(snl_btm_itf) = albsfc(c_idx,1) + rupdir(snl_btm_itf) = albsfc(c_idx,ivis) + rupdif(snl_btm_itf) = albsfc(c_idx,ivis) endif do i=snl_btm,snl_top,-1 @@ -1385,14 +1385,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & select case (snicar_numrad_snw) case (5) ! 5-band case ! VIS band - albout(c_idx,1) = albout_lcl(1) + albout(c_idx,ivis) = albout_lcl(ivis) case (480) ! 480-band case ! average for VIS band flx_sum = 0._r8 do bnd_idx= 1, (nir_bnd_bgn-1) flx_sum = flx_sum + flx_wgt(bnd_idx)*albout_lcl(bnd_idx) end do - albout(c_idx,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) + albout(c_idx,ivis) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) end select ! average for NIR band (5 or 480-band case) @@ -1400,7 +1400,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & do bnd_idx = nir_bnd_bgn, nir_bnd_end flx_sum = flx_sum + flx_wgt(bnd_idx) * albout_lcl(bnd_idx) end do - albout(c_idx,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + albout(c_idx,inir) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately select case (snicar_numrad_snw) @@ -1414,7 +1414,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & do bnd_idx= 1,(nir_bnd_bgn-1) flx_sum = flx_sum + flx_wgt(bnd_idx)*flx_abs_lcl(i,bnd_idx) enddo - flx_abs(c_idx,i,1) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) + flx_abs(c_idx,i,ivis) = flx_sum / sum(flx_wgt(1:(nir_bnd_bgn-1))) end do end select @@ -1424,7 +1424,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & do bnd_idx = nir_bnd_bgn, nir_bnd_end flx_sum = flx_sum + flx_wgt(bnd_idx) * flx_abs_lcl(i,bnd_idx) end do - flx_abs(c_idx,i,2) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + flx_abs(c_idx,i,inir) = flx_sum / sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) end do ! high solar zenith angle adjustment for Adding-doubling solver results @@ -1435,21 +1435,21 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & sza_c1 = sza_a0 + sza_a1 * mu_not + sza_a2 * (mu_not * mu_not) sza_c0 = sza_b0 + sza_b1 * mu_not + sza_b2 * (mu_not * mu_not) sza_factor = sza_c1 * (log10(snw_rds_lcl(snl_top) * c1) - c6) + sza_c0 - flx_sza_adjust = albout(c_idx,2) * (sza_factor-c1) * sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) - albout(c_idx,2) = albout(c_idx,2) * sza_factor - flx_abs(c_idx,snl_top,2) = flx_abs(c_idx,snl_top,2) - flx_sza_adjust + flx_sza_adjust = albout(c_idx,inir) * (sza_factor-c1) * sum(flx_wgt(nir_bnd_bgn:nir_bnd_end)) + albout(c_idx,inir) = albout(c_idx,inir) * sza_factor + flx_abs(c_idx,snl_top,inir) = flx_abs(c_idx,snl_top,inir) - flx_sza_adjust endif ! If snow < minimum_snow, but > 0, and there is sun, set albedo to underlying surface albedo elseif ( (coszen(c_idx) > 0._r8) .and. (h2osno_lcl < min_snw) .and. (h2osno_lcl > 0._r8) ) then - albout(c_idx,1) = albsfc(c_idx,1) - albout(c_idx,2) = albsfc(c_idx,2) + albout(c_idx,ivis) = albsfc(c_idx,ivis) + albout(c_idx,inir) = albsfc(c_idx,inir) ! There is either zero snow, or no sun else - albout(c_idx,1) = 0._r8 - albout(c_idx,2) = 0._r8 + albout(c_idx,ivis) = 0._r8 + albout(c_idx,inir) = 0._r8 endif ! if column has snow and coszen > 0 enddo ! loop over all columns From 33c8524a3beb80e7fad859bbca64c2531a24441b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Sep 2023 12:30:44 -0600 Subject: [PATCH 1531/2067] Replace 1e5 with enh_omg_max parameter --- src/biogeophys/SnowSnicarMod.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 422d65df84..5ee0301aa8 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -516,6 +516,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: tot_dst_snw_conc ! total dust content in snow across all size bins (ppm=ug/g) integer :: idb ! loop index + real(r8), parameter :: enh_omg_max = 1.e5_r8 ! reasonable maximum value for enh_omg_[bc,dst]int_intp2 + !----------------------------------------------------------------------- ! Enforce expected array sizes @@ -971,7 +973,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & call piecewise_linear_interp1d(16,bcint_wvl_ct,enh_omg_bcint_tmp2,wvl_doint,enh_omg_bcint_intp) ! update snow single-scattering albedo enh_omg_bcint_intp2 = 10._r8 ** enh_omg_bcint_intp - enh_omg_bcint_intp2 = min(1.0E5_r8, max(enh_omg_bcint_intp2,1._r8)) ! constrain enhancement to a reasonable range + enh_omg_bcint_intp2 = min(enh_omg_max, max(enh_omg_bcint_intp2, 1._r8)) ! constrain enhancement to a reasonable range ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_bcint_intp2 ss_alb_snw_lcl(i) = max(0.5_r8, min(ss_alb_snw_lcl(i),1._r8)) ! reset hydrophilic BC property to 0 since it is accounted by updated snow ss_alb above @@ -998,7 +1000,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & call piecewise_linear_interp1d(6,dstint_wvl_ct,enh_omg_dstint_tmp2,wvl_doint,enh_omg_dstint_intp) ! update snow single-scattering albedo enh_omg_dstint_intp2 = 10._r8 ** enh_omg_dstint_intp - enh_omg_dstint_intp2 = min(1.0E5_r8, max(enh_omg_dstint_intp2,1._r8)) ! constrain enhancement to a reasonable range + enh_omg_dstint_intp2 = min(enh_omg_max, max(enh_omg_dstint_intp2, 1._r8)) ! constrain enhancement to a reasonable range ss_alb_snw_lcl(i) = 1._r8 - (1._r8 - ss_alb_snw_lcl(i)) * enh_omg_dstint_intp2 ss_alb_snw_lcl(i) = max(0.5_r8, min(ss_alb_snw_lcl(i),1._r8)) ! reset all dust optics to zero since it is accounted by updated snow ss_alb above From 3f1b4e58f1ee6848d84390489652ccaf44c6bef5 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 27 Sep 2023 12:08:47 -0700 Subject: [PATCH 1532/2067] remove old seed dispersal diagnostic write statements --- src/utils/clmfates_interfaceMod.F90 | 30 +++++------------------------ 1 file changed, 5 insertions(+), 25 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 462e72d46f..772244e2c9 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2681,43 +2681,29 @@ subroutine WrapSeedGlobal(this,is_restart_flag) this%fates_seed%incoming_global(:,:) = 0._r8 this%fates_seed%outgoing_global(:,:) = 0._r8 - write(iulog,*) 'WSG: begg: ', procinfo%begg - do g = 1, procinfo%ncells - write(iulog,*) 'WSG: g+begg, outgoing_local: ', g+procinfo%begg, sum(this%fates_seed%outgoing_local(:,g)) - end do - - - ! Distribute obtgoing seed data from all nodes to all nodes + ! Distribute outgoing seed data from all nodes to all nodes call MPI_Allgatherv(this%fates_seed%outgoing_local, procinfo%ncells*numpft_fates, MPI_REAL8, & this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array*numpft_fates, & MPI_REAL8, mpicom, ier) write(iulog,*) 'WSG: MPI_Allgatherv ier: ', ier - ! zero outgoing local for all gridcells outside threaded region + ! zero outgoing local for all gridcells outside threaded region now that we've passed them out this%fates_seed%outgoing_local(:,:) = 0._r8 - + ! Calculate the current gridcell incoming seed for each gridcell index + ! This should be conducted outside of a threaded region to provide access to + ! the neighbor%gindex which might not be available in via the clumped index call get_proc_global(ng=numg) do g = 1, numg - - write(iulog,*) 'WSG: g, outgoing_global: ', g, sum(this%fates_seed%outgoing_global(:,g)) - - ! Calculate the current gridcell incoming seed for each gridcell index - ! This should be conducted outside of a threaded region to provide access to - ! the neighbor%gindex which might not be available in via the clumped index neighbor => lneighbors(g)%first_neighbor do while (associated(neighbor)) - ! This also applies the same neighborhood distribution scheme to all pfts ! This needs to have a per pft density probability value this%fates_seed%incoming_global(:,g) = this%fates_seed%incoming_global(:,g) + & this%fates_seed%outgoing_global(:,neighbor%gindex) * & neighbor%density_prob(:) / lneighbors(g)%neighbor_count - !write(iulog,*) 'WSGloop: g, incoming, outgoing: ', g, sum(this%fates_seed%incoming_global(g,:)), sum(this%fates_seed%outgoing_global(g,:)) - !write(iulog,*) 'WSGloop: g, densprob, ncount: ', g, sum(neighbor%density_prob(:)), lneighbors(g)%neighbor_count neighbor => neighbor%next_neighbor end do - !write(iulog,*) 'WSG: g, incoming, outgoing: ', g, sum(this%fates_seed%incoming_global(g,:)), sum(this%fates_seed%outgoing_global(g,:)) end do endif @@ -2748,11 +2734,8 @@ subroutine wrap_seed_dispersal(this,bounds_clump) c = this%f2hmap(nc)%fcolumn(s) g = col%gridcell(c) - write(iulog,*) 'WSD pre: g, incoming, seed_in: ', g, sum(this%fates_seed%incoming_global(:,g)), sum(this%fates(nc)%sites(s)%seed_in(:)) - ! Check that it is the beginning of the current dispersal time step if (IsItDispersalTime()) then - write(iulog,*) 'WSD IIDT: g: ', g ! assuming equal area for all sites, seed_id_global in [kg/grid/day], seed_in in [kg/site/day] this%fates(nc)%sites(s)%seed_in(:) = this%fates_seed%incoming_global(:,g) this%fates(nc)%sites(s)%seed_out(:) = 0._r8 ! reset seed_out @@ -2761,9 +2744,6 @@ subroutine wrap_seed_dispersal(this,bounds_clump) ! if this is a restart, then skip this entirely this%fates(nc)%sites(s)%seed_in(:) = 0._r8 end if - - write(iulog,*) 'WSD pst: g, incoming, seed_in: ', g, sum(this%fates_seed%incoming_global(:,g)), sum(this%fates(nc)%sites(s)%seed_in(:)) - end do call t_stopf('fates-seed-disperse') From 00a242c27b62226614c08ecc4d02b722467a8b91 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 27 Sep 2023 12:16:15 -0700 Subject: [PATCH 1533/2067] fix incorrect seed dispersal call --- src/utils/clmfates_interfaceMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 772244e2c9..ae7876960f 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1062,7 +1062,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! Distribute any seeds from neighboring gridcells into the current gridcell ! Global seed availability array populated by WrapSeedGlobal call - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then call this%wrap_seed_dispersal(bounds_clump) end if @@ -1848,7 +1848,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & !$OMP END PARALLEL DO ! Disperse seeds - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then call this%WrapSeedGlobal(is_restart_flag=.true.) end if From ee97fb4081a5f8213f35abd72d6e02570d34c5b8 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 27 Sep 2023 13:59:54 -0600 Subject: [PATCH 1534/2067] fix additional seed disperal check --- src/main/clm_driver.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 51fe7c4f63..2585953e8a 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1271,7 +1271,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Pass fates seed dispersal information to all nodes - if (fates_seeddisp_cadence .eq. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() end if From eb103359008bca492d856299ab123c6f7e2a2060 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Sep 2023 16:43:44 -0600 Subject: [PATCH 1535/2067] Replace hardwired numbers with parameters and other clean-up --- src/biogeophys/SnowSnicarMod.F90 | 72 ++++++++++++++++---------------- 1 file changed, 37 insertions(+), 35 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 5ee0301aa8..f874263e0d 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -487,8 +487,12 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8) :: bcint_d0(1:16) ! Parameterization coefficients at each band center wavelength real(r8) :: bcint_d1(1:16) ! Parameterization coefficients at each band center wavelength real(r8) :: bcint_d2(1:16) ! Parameterization coefficients at each band center wavelength - real(r8) :: den_bc = 1.49_r8 ! target BC particle density (g/cm3) used in BC MAC adjustment - real(r8) :: Re_bc = 0.045 ! target BC effective radius (um) used in BC MAC adjustment + real(r8), parameter :: kg_to_ug = 1.e9_r8 ! unit conversion of kg to micrograms + real(r8), parameter :: den_bc = 1.7_r8 ! BC particle density (g/cm3) + real(r8), parameter :: den_bc_target = 1.49_r8 ! target BC particle density (g/cm3) used in BC MAC adjustment + real(r8), parameter :: Re_bc = 0.045_r8 ! target BC effective radius (um) used in BC MAC adjustment + real(r8), parameter :: radius_1 = 0.1_r8 ! used with Re_bc (um) + real(r8), parameter :: radius_2 = 0.05_r8 ! used with Re_bc (um) real(r8) :: bcint_m(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix real(r8) :: bcint_n(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix real(r8) :: bcint_m_tmp ! temporary of bcint_m @@ -884,7 +888,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) endif - if (asm_prm_snw_lcl(i) > 0.99_r8) asm_prm_snw_lcl(i) = 0.99_r8 !avoid unreasonable values (rarely occur in large-size spheroid cases) + asm_prm_snw_lcl(i) = min(0.99_r8, asm_prm_snw_lcl(i)) !avoid unreasonable values (rarely occur in large-size spheroid cases) enddo ! snow layer loop @@ -892,66 +896,64 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) asm_prm_aer_lcl(2) = asm_prm_bc2(bnd_idx) ext_cff_mss_aer_lcl(2) = ext_cff_mss_bc2(bnd_idx) - ! aerosol species 3 optical properties, hydrophilic OC ss_alb_aer_lcl(3) = ss_alb_oc1(bnd_idx) asm_prm_aer_lcl(3) = asm_prm_oc1(bnd_idx) ext_cff_mss_aer_lcl(3) = ext_cff_mss_oc1(bnd_idx) - ! aerosol species 4 optical properties, hydrophobic OC ss_alb_aer_lcl(4) = ss_alb_oc2(bnd_idx) asm_prm_aer_lcl(4) = asm_prm_oc2(bnd_idx) ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) + ! Optics for BC/dust-snow external mixing: + ! aerosol species 1 optical properties, hydrophilic BC + ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) + asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) + ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) + ! aerosol species 5 optical properties, dust size1 + ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) + asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) + ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) + ! aerosol species 6 optical properties, dust size2 + ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) + asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) + ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) + ! aerosol species 7 optical properties, dust size3 + ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) + asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) + ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) + ! aerosol species 8 optical properties, dust size4 + ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) + asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) + ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) + ! 1. snow and aerosol layer column mass (L_snw, L_aer [kg/m^2]) ! 2. optical Depths (tau_snw, tau_aer) ! 3. weighted Mie properties (tau, omega, g) + wvl_doint = wvl_ct(bnd_idx) + ! Weighted Mie parameters of each layer do i=snl_top,snl_btm,1 - ! Optics for BC/dust-snow external mixing: - ! aerosol species 1 optical properties, hydrophilic BC - ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) - asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) - ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) - ! aerosol species 5 optical properties, dust size1 - ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) - asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) - ext_cff_mss_aer_lcl(5) = ext_cff_mss_dst1(bnd_idx) - ! aerosol species 6 optical properties, dust size2 - ss_alb_aer_lcl(6) = ss_alb_dst2(bnd_idx) - asm_prm_aer_lcl(6) = asm_prm_dst2(bnd_idx) - ext_cff_mss_aer_lcl(6) = ext_cff_mss_dst2(bnd_idx) - ! aerosol species 7 optical properties, dust size3 - ss_alb_aer_lcl(7) = ss_alb_dst3(bnd_idx) - asm_prm_aer_lcl(7) = asm_prm_dst3(bnd_idx) - ext_cff_mss_aer_lcl(7) = ext_cff_mss_dst3(bnd_idx) - ! aerosol species 8 optical properties, dust size4 - ss_alb_aer_lcl(8) = ss_alb_dst4(bnd_idx) - asm_prm_aer_lcl(8) = asm_prm_dst4(bnd_idx) - ext_cff_mss_aer_lcl(8) = ext_cff_mss_dst4(bnd_idx) - ! Start BC/dust-snow internal mixing for wavelength<=1.2um - wvl_doint = wvl_ct(bnd_idx) - if (wvl_doint <= 1.2_r8) then ! BC-snow internal mixing applied to hydrophilic BC if activated ! BC-snow internal mixing primarily affect snow single-scattering albedo if ( snicar_snobc_intmix .and. (mss_cnc_aer_lcl(i,1) > 0._r8) ) then ! result from Eq.8b in He et al.(2017) is based on BC Re=0.1um & - ! MAC=6.81 m2/g (@550 nm) & BC density=1.7g/cm3. + ! MAC=6.81 m2/g (@550 nm) & BC density=1.7g/cm3 (den_bc). ! To be consistent with Bond et al. 2006 recommeded value (BC MAC=7.5 m2/g @550nm) ! we made adjustments on BC size & density as follows to get MAC=7.5m2/g: ! (1) We use BC Re=0.045um [geometric mean diameter=0.06um (Dentener et al.2006, ! Yu and Luo,2009) & geometric std=1.5 (Flanner et al.2007;Aoki et al., 2011)]. - ! (2) We tune BC density from 1.7 to 1.49 g/cm3 (Aoki et al., 2011). + ! (2) We tune BC density from 1.7 to 1.49 g/cm3 (den_bc_target) (Aoki et al., 2011). ! These adjustments also lead to consistent results with Flanner et al. 2012 (ACP) lookup table ! for BC-snow internal mixing enhancement in albedo reduction (He et al. 2018 ACP) do ibb=1,16 enh_omg_bcint_tmp(ibb) = bcint_d0(ibb) * & - ( (mss_cnc_aer_lcl(i,1)*1.0E9_r8*1.7_r8/den_bc + bcint_d2(ibb)) **bcint_d1(ibb) ) + ( (mss_cnc_aer_lcl(i,1) * kg_to_ug * den_bc / den_bc_target + bcint_d2(ibb))**bcint_d1(ibb) ) ! adjust enhancment factor for BC effective size from 0.1um to Re_bc (He et al. 2018 GRL Eqs.1a,1b) if (ibb < 3) then ! near-UV bcint_m_tmp = bcint_m(1) @@ -963,9 +965,9 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & bcint_m_tmp = bcint_m(3) bcint_n_tmp = bcint_n(3) endif - bcint_dd = (Re_bc * 20.0_r8)**bcint_m_tmp - bcint_dd2 = (0.1_r8 * 20.0_r8)**bcint_m_tmp - bcint_f = (Re_bc * 10.0_r8)**bcint_n_tmp + bcint_dd = (Re_bc / radius_2)**bcint_m_tmp + bcint_dd2 = (radius_1 / radius_2)**bcint_m_tmp + bcint_f = (Re_bc / radius_1)**bcint_n_tmp enh_omg_bcint_tmp2(ibb)=LOG10(max(1._r8,bcint_dd*((enh_omg_bcint_tmp(ibb)/bcint_dd2)**bcint_f))) enddo From 3f0fe626013eefcb206d684b42990dcf3bd0cbde Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 27 Sep 2023 18:07:11 -0600 Subject: [PATCH 1536/2067] Changed many constants to parameters and other minor clean-up --- src/biogeophys/SnowSnicarMod.F90 | 119 ++++++++++++++++--------------- 1 file changed, 60 insertions(+), 59 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index f874263e0d..5c879b6f0c 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -404,32 +404,42 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8):: smr ! accumulator for rdif gaussian integration real(r8):: smt ! accumulator for tdif gaussian integration real(r8):: exp_min ! minimum exponential value - real(r8), allocatable :: difgauspt(:) ! Gaussian integration angle - real(r8), allocatable :: difgauswt(:) ! Gaussian integration coefficients/weights - integer :: ng ! gaussian integration index - integer :: ngmax = 8 ! max gaussian integration index + + integer :: ng ! gaussian integration index + integer, parameter :: ngmax = 8 ! max gaussian integration index + real(r8), parameter :: difgauspt(ngmax) = & ! Gaussian integration angles (radians) + (/ 0.9894009_r8, 0.9445750_r8, & + 0.8656312_r8, 0.7554044_r8, & + 0.6178762_r8, 0.4580168_r8, & + 0.2816036_r8, 0.0950125_r8/) + real(r8), parameter :: difgauswt(ngmax) = & ! Gaussian integration coefficients/weights + (/ 0.0271525_r8, 0.0622535_r8, & + 0.0951585_r8, 0.1246290_r8, & + 0.1495960_r8, 0.1691565_r8, & + 0.1826034_r8, 0.1894506_r8/) + integer :: snl_btm_itf ! index of bottom snow layer interfaces (1) [idx] ! constants used in algorithm - real(r8):: c0 = 0.0_r8 - real(r8):: c1 = 1.0_r8 - real(r8):: c3 = 3.0_r8 - real(r8):: c4 = 4.0_r8 - real(r8):: c6 = 6.0_r8 - real(r8):: cp01 = 0.01_r8 - real(r8):: cp5 = 0.5_r8 - real(r8):: cp75 = 0.75_r8 - real(r8):: c1p5 = 1.5_r8 - real(r8):: trmin = 0.001_r8 - real(r8):: argmax = 10.0_r8 ! maximum argument of exponential - ! cconstant and coefficients used for SZA parameterization - real(r8):: sza_a0 = 0.085730_r8 - real(r8):: sza_a1 = -0.630883_r8 - real(r8):: sza_a2 = 1.303723_r8 - real(r8):: sza_b0 = 1.467291_r8 - real(r8):: sza_b1 = -3.338043_r8 - real(r8):: sza_b2 = 6.807489_r8 - real(r8):: puny = 1.0e-11_r8 - real(r8):: mu_75 = 0.2588_r8 ! cosine of 75 degree + real(r8), parameter :: c0 = 0.0_r8 + real(r8), parameter :: c1 = 1.0_r8 + real(r8), parameter :: c3 = 3.0_r8 + real(r8), parameter :: c4 = 4.0_r8 + real(r8), parameter :: c6 = 6.0_r8 + real(r8), parameter :: cp01 = 0.01_r8 + real(r8), parameter :: cp5 = 0.5_r8 + real(r8), parameter :: cp75 = 0.75_r8 + real(r8), parameter :: c1p5 = 1.5_r8 + real(r8), parameter :: trmin = 0.001_r8 + real(r8), parameter :: argmax = 10.0_r8 ! maximum argument of exponential + ! constants and coefficients used for SZA parameterization + real(r8), parameter :: sza_a0 = 0.085730_r8 + real(r8), parameter :: sza_a1 = -0.630883_r8 + real(r8), parameter :: sza_a2 = 1.303723_r8 + real(r8), parameter :: sza_b0 = 1.467291_r8 + real(r8), parameter :: sza_b1 = -3.338043_r8 + real(r8), parameter :: sza_b2 = 6.807489_r8 + real(r8), parameter :: puny = 1.0e-11_r8 + real(r8), parameter :: mu_75 = 0.2588_r8 ! cosine of 75 degree real(r8):: sza_c1 ! coefficient, SZA parameteirzation real(r8):: sza_c0 ! coefficient, SZA parameterization real(r8):: sza_factor ! factor used to adjust NIR direct albedo @@ -466,10 +476,15 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8), allocatable :: wvl_ct(:) ! band center wavelength (um) for 5 or 480-band case real(r8) :: diam_ice ! effective snow grain diameter (SSA-equivalent) unit: microns real(r8) :: fs_sphd ! shape factor for spheroid snow + real(r8), parameter :: fs_sphd_default = 0.929_r8 ! default; He et al. (2017), Table 1 real(r8) :: fs_hex ! shape factor for reference hexagonal snow real(r8) :: fs_hex0 ! shape factor for hexagonal plate + real(r8), parameter :: fs_hex_ref = 0.788_r8 ! reference shape factor real(r8) :: fs_koch ! shape factor for Koch snowflake + real(r8), parameter :: fs_koch_default = 0.712_r8 ! default; He et al. (2017), Table 1 real(r8) :: AR_tmp ! aspect ratio temporary + real(r8), parameter :: AR_tmp_default_1 = 0.5_r8 ! default; He et al. (2017), Table 1 + real(r8), parameter :: AR_tmp_default_2 = 2.5_r8 ! default; He et al. (2017), Table 1 real(r8) :: g_ice_Cg_tmp(1:7) ! temporary asymmetry factor correction coeff real(r8) :: gg_ice_F07_tmp(1:7) ! temporary asymmetry factor related to geometric reflection & refraction real(r8) :: g_Cg_intp ! interpolated asymmetry factor correction coeff to target bands @@ -549,20 +564,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & end select nir_bnd_end = snicar_numrad_snw - ! initialize for adding-doubling solver - allocate(difgauspt(ngmax)) - allocate(difgauswt(ngmax)) - difgauspt(:) = & ! gaussian angles (radians) - (/ 0.9894009_r8, 0.9445750_r8, & - 0.8656312_r8, 0.7554044_r8, & - 0.6178762_r8, 0.4580168_r8, & - 0.2816036_r8, 0.0950125_r8/) - difgauswt(:) = & ! gaussian weights - (/ 0.0271525_r8, 0.0622535_r8, & - 0.0951585_r8, 0.1246290_r8, & - 0.1495960_r8, 0.1691565_r8, & - 0.1826034_r8, 0.1894506_r8/) - ! initialize for nonspherical snow grains sno_shp(:) = snicar_snw_shape ! currently only assuming same shapes for all snow layers sno_fs(:) = 0._r8 @@ -824,13 +825,13 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & case ('spheroid') diam_ice = 2._r8 * snw_rds_lcl(i) ! unit: microns if (sno_fs(i) == 0._r8) then - fs_sphd = 0.929_r8 ! default; He et al. (2017), Table 1 + fs_sphd = fs_sphd_default ! default; He et al. (2017), Table 1 else fs_sphd = sno_fs(i) ! user specified value endif - fs_hex = 0.788_r8 ! reference shape factor + fs_hex = fs_hex_ref ! reference shape factor if (sno_AR(i) == 0._r8) then - AR_tmp = 0.5_r8 ! default; He et al. (2017), Table 1 + AR_tmp = AR_tmp_default_1 ! default; He et al. (2017), Table 1 else AR_tmp = sno_AR(i) ! user specified value endif @@ -842,13 +843,13 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & case ('hexagonal_plate') diam_ice = 2._r8 * snw_rds_lcl(i) ! unit: microns if (sno_fs(i) == 0._r8) then - fs_hex0 = 0.788_r8 ! default; He et al. (2017), Table 1 + fs_hex0 = fs_hex_ref ! default; He et al. (2017), Table 1 else fs_hex0 = sno_fs(i) ! user specified value endif - fs_hex = 0.788_r8 ! reference shape factor + fs_hex = fs_hex_ref ! reference shape factor if (sno_AR(i) == 0._r8) then - AR_tmp = 2.5_r8 ! default; He et al. (2017), Table 1 + AR_tmp = AR_tmp_default_2 ! default; He et al. (2017), Table 1 else AR_tmp = sno_AR(i) ! user specified value endif @@ -860,13 +861,13 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & case ('koch_snowflake') diam_ice = 2._r8 * snw_rds_lcl(i) / 0.544_r8 ! unit: microns if (sno_fs(i) == 0._r8) then - fs_koch = 0.712_r8 ! default; He et al. (2017), Table 1 + fs_koch = fs_koch_default ! default; He et al. (2017), Table 1 else fs_koch = sno_fs(i) ! user specified value endif - fs_hex = 0.788_r8 ! reference shape factor + fs_hex = fs_hex_ref ! reference shape factor if (sno_AR(i) == 0._r8) then - AR_tmp = 2.5_r8 ! default; He et al. (2017), Table 1 + AR_tmp = AR_tmp_default_2 ! default; He et al. (2017), Table 1 else AR_tmp = sno_AR(i) ! user specified value endif @@ -893,23 +894,23 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo ! snow layer loop ! aerosol species 2 optical properties, hydrophobic BC - ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) - asm_prm_aer_lcl(2) = asm_prm_bc2(bnd_idx) - ext_cff_mss_aer_lcl(2) = ext_cff_mss_bc2(bnd_idx) + ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) + asm_prm_aer_lcl(2) = asm_prm_bc2(bnd_idx) + ext_cff_mss_aer_lcl(2) = ext_cff_mss_bc2(bnd_idx) ! aerosol species 3 optical properties, hydrophilic OC - ss_alb_aer_lcl(3) = ss_alb_oc1(bnd_idx) - asm_prm_aer_lcl(3) = asm_prm_oc1(bnd_idx) - ext_cff_mss_aer_lcl(3) = ext_cff_mss_oc1(bnd_idx) + ss_alb_aer_lcl(3) = ss_alb_oc1(bnd_idx) + asm_prm_aer_lcl(3) = asm_prm_oc1(bnd_idx) + ext_cff_mss_aer_lcl(3) = ext_cff_mss_oc1(bnd_idx) ! aerosol species 4 optical properties, hydrophobic OC - ss_alb_aer_lcl(4) = ss_alb_oc2(bnd_idx) - asm_prm_aer_lcl(4) = asm_prm_oc2(bnd_idx) - ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) + ss_alb_aer_lcl(4) = ss_alb_oc2(bnd_idx) + asm_prm_aer_lcl(4) = asm_prm_oc2(bnd_idx) + ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) ! Optics for BC/dust-snow external mixing: ! aerosol species 1 optical properties, hydrophilic BC - ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) - asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) - ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) + ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) + asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) + ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) ! aerosol species 5 optical properties, dust size1 ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) From 8875f3a3bc8f400039770331f0ce174b6ef278f7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 28 Sep 2023 13:22:58 -0700 Subject: [PATCH 1537/2067] fix expected failure phase name for seed dispersal pem test --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 092bad1e69..0744055303 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -110,7 +110,7 @@ - + FAIL FATES#1089 From 3f50fd6d38053055743852e1bccea53fbb49a089 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 28 Sep 2023 14:53:48 -0600 Subject: [PATCH 1538/2067] move dispersal timing call inside cadence check The dispersal timing call utilizes a function that is not initialized unless the mode has been initialized. If it is included along with the cadence check as it was setup previously, the timing call will fail having not been initialized. --- src/utils/clmfates_interfaceMod.F90 | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index ae7876960f..fd8c3781ad 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1410,8 +1410,9 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & g = col%gridcell(c) ! Accumulate seeds from sites to the gridcell local outgoing buffer - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none .and. IsItDispersalTime()) then - this%fates_seed%outgoing_local(:,g) = this%fates(nc)%sites(s)%seed_out(:) + if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (IsItDispersalTime()) this%fates_seed%outgoing_local(:,g) = & + this%fates(nc)%sites(s)%seed_out(:) end if ! Other modules may have AI's we only flush values From 00493ef50d3dd6dc1d971eb5eb3ce9d1edce5617 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 28 Sep 2023 17:36:55 -0600 Subject: [PATCH 1539/2067] Change some arrays to parameters --- src/biogeophys/SnowSnicarMod.F90 | 72 ++++++++++++++++---------------- 1 file changed, 36 insertions(+), 36 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 5c879b6f0c..9ebb976d53 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -460,18 +460,39 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! others(0.11.2um, no BC-snow int mixing effect) @@ -883,8 +883,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here ! use the piecewise linear interpolation subroutine created at the end of this module ! tests showed the piecewise linear interpolation has similar results as pchip interpolation - call piecewise_linear_interp1d(7, g_wvl_ct, g_ice_Cg_tmp, wvl_ct(bnd_idx), g_Cg_intp) - call piecewise_linear_interp1d(7, g_wvl_ct, gg_ice_F07_tmp, wvl_ct(bnd_idx), gg_F07_intp) + call piecewise_linear_interp1d(ngmax-1, g_wvl_ct, g_ice_Cg_tmp, wvl_ct(bnd_idx), g_Cg_intp) + call piecewise_linear_interp1d(ngmax-1, g_wvl_ct, gg_ice_F07_tmp, wvl_ct(bnd_idx), gg_F07_intp) g_ice_F07 = gg_F07_intp + 0.5_r8 * (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) ! Eq.2.2 in Fu (2007) asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) endif From ed2a177593c1b74f883834f63424a45d1b1cd919 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Sep 2023 12:28:27 -0600 Subject: [PATCH 1540/2067] Change more arrays to parameters --- src/biogeophys/SnowSnicarMod.F90 | 142 ++++++++++++++++--------------- 1 file changed, 74 insertions(+), 68 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 9ebb976d53..60f9bc7d9f 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -52,11 +52,11 @@ module SnowSnicarMod ! !PRIVATE DATA MEMBERS: integer, parameter :: idx_Mie_snw_mx = 1471 ! number of effective radius indices used in Mie lookup table [idx] - integer, parameter :: idx_T_max = 11 ! maxiumum temperature index used in aging lookup table [idx] + integer, parameter :: idx_T_max = 11 ! maximum temperature index used in aging lookup table [idx] integer, parameter :: idx_T_min = 1 ! minimum temperature index used in aging lookup table [idx] - integer, parameter :: idx_Tgrd_max = 31 ! maxiumum temperature gradient index used in aging lookup table [idx] + integer, parameter :: idx_Tgrd_max = 31 ! maximum temperature gradient index used in aging lookup table [idx] integer, parameter :: idx_Tgrd_min = 1 ! minimum temperature gradient index used in aging lookup table [idx] - integer, parameter :: idx_rhos_max = 8 ! maxiumum snow density index used in aging lookup table [idx] + integer, parameter :: idx_rhos_max = 8 ! maximum snow density index used in aging lookup table [idx] integer, parameter :: idx_rhos_min = 1 ! minimum snow density index used in aging lookup table [idx] integer, parameter :: snw_rds_max_tbl = 1500 ! maximum effective radius defined in Mie lookup table [microns] @@ -460,36 +460,37 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! others(0.11.2um, no BC-snow int mixing effect) + real(r8), parameter :: bcint_wvl(sixteen_bands+1) = & ! Parameterization band (0.2-1.2um) for BC-induced enhancement in snow 1-omega + (/ 0.20_r8, 0.25_r8, 0.30_r8, 0.33_r8, 0.36_r8, 0.40_r8, 0.44_r8, 0.48_r8, & + 0.52_r8, 0.57_r8, 0.64_r8, 0.69_r8, 0.75_r8, 0.78_r8, 0.87_r8, 1._r8, 1.2_r8 /) + real(r8), parameter :: bcint_d0(sixteen_bands) = & ! Parameterization coefficients at each band center wavelength + (/ 2.48045_r8 , 4.70305_r8 , 4.68619_r8 , 4.67369_r8 , 4.65040_r8 , & + 2.40364_r8 , 7.95408E-1_r8, 2.92745E-1_r8, 8.63396E-2_r8, 2.76299E-2_r8, & + 1.40864E-2_r8, 8.65705E-3_r8, 6.12971E-3_r8, 4.45697E-3_r8, 3.06648E-2_r8, & + 7.96544E-1_r8 /) + real(r8), parameter :: bcint_d1(sixteen_bands) = & ! Parameterization coefficients at each band center wavelength + (/ 9.77209E-1_r8, 9.73317E-1_r8, 9.79650E-1_r8, 9.84579E-1_r8, 9.93537E-1_r8, & + 9.95955E-1_r8, 9.95218E-1_r8, 9.74284E-1_r8, 9.81193E-1_r8, 9.81239E-1_r8, & + 9.55515E-1_r8, 9.10491E-1_r8, 8.74196E-1_r8, 8.27238E-1_r8, 4.82870E-1_r8, & + 4.36649E-2_r8 /) + real(r8), parameter :: bcint_d2(sixteen_bands) = & ! Parameterization coefficients at each band center wavelength + (/ 3.95960E-1_r8, 2.04820E-1_r8, 2.07410E-1_r8, 2.09390E-1_r8, 2.13030E-1_r8, & + 4.18570E-1_r8, 1.29682_r8 , 3.75514_r8 , 1.27372E+1_r8, 3.93293E+1_r8, & + 8.78918E+1_r8, 1.86969E+2_r8, 3.45600E+2_r8, 7.08637E+2_r8, 1.41067E+3_r8, & + 2.57288E+2_r8 /) real(r8), parameter :: den_bc = 1.7_r8 ! BC particle density (g/cm3) real(r8), parameter :: den_bc_target = 1.49_r8 ! target BC particle density (g/cm3) used in BC MAC adjustment real(r8), parameter :: Re_bc = 0.045_r8 ! target BC effective radius (um) used in BC MAC adjustment @@ -544,13 +561,21 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & !----------------------------------------------------------------------- ! variables used for dust-snow internal mixing (He et al. 2019 JAMES): real(r8) :: enh_omg_dstint ! dust-induced enhancement in snow single-scattering co-albedo (1-omega) - real(r8) :: enh_omg_dstint_tmp(1:6) ! temporary dust-induced enhancement in snow 1-omega - real(r8) :: enh_omg_dstint_tmp2(1:6) ! temporary dust-induced enhancement in snow 1-omega - real(r8) :: dstint_wvl(1:7) ! Parameterization band (0.2-1.2um) for dust-induced enhancement in snow 1-omega - real(r8) :: dstint_wvl_ct(1:6) ! Parameterization band center wavelength (um) - real(r8) :: dstint_a1(1:6) ! Parameterization coefficients at each band center wavelength - real(r8) :: dstint_a2(1:6) ! Parameterization coefficients at each band center wavelength - real(r8) :: dstint_a3(1:6) ! Parameterization coefficients at each band center wavelength + integer, parameter :: size_bins = 6 + real(r8) :: enh_omg_dstint_tmp(size_bins) ! temporary dust-induced enhancement in snow 1-omega + real(r8) :: enh_omg_dstint_tmp2(size_bins) ! temporary dust-induced enhancement in snow 1-omega + real(r8) :: dstint_wvl_ct(size_bins) ! Parameterization band center wavelength (um) + ! initialize for dust-snow internal mixing + ! Eq. 1 and Table 1 in He et al. 2019 JAMES (wavelength>1.2um, no dust-snow int mixing effect) + real(r8), parameter :: dstint_wvl(size_bins+1) = & ! Parameterization band (0.2-1.2um) for dust-induced enhancement in snow 1-omega + (/ 0.2_r8, 0.2632_r8, 0.3448_r8, 0.4415_r8, 0.625_r8, 0.7782_r8, 1.2422_r8/) + real(r8), parameter :: dstint_a1(size_bins) = & ! Parameterization coefficients at each band center wavelength + (/ -2.1307E+1_r8, -1.5815E+1_r8, -9.2880_r8 , 1.1115_r8 , 1.0307_r8 , 1.0185_r8 /) + real(r8), parameter :: dstint_a2(size_bins) = & ! Parameterization coefficients at each band center wavelength + (/ 1.1746E+2_r8, 9.3241E+1_r8, 4.0605E+1_r8, 3.7389E-1_r8, 1.4800E-2_r8, 2.8921E-4_r8 /) + real(r8), parameter :: dstint_a3(size_bins) = & ! Parameterization coefficients at each band center wavelength + (/ 9.9701E-1_r8, 9.9781E-1_r8, 9.9848E-1_r8, 1.0035_r8 , 1.0024_r8 , 1.0356_r8 /) + real(r8) :: enh_omg_dstint_intp ! dust-induced enhancement in snow 1-omega (logscale) interpolated to CLM wavelength real(r8) :: enh_omg_dstint_intp2 ! dust-induced enhancement in snow 1-omega interpolated to CLM wavelength real(r8) :: tot_dst_snw_conc ! total dust content in snow across all size bins (ppm=ug/g) @@ -558,6 +583,10 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8), parameter :: enh_omg_max = 1.e5_r8 ! reasonable maximum value for enh_omg_[bc,dst]int_intp2 + ! unit conversions + real(r8), parameter :: kg_kg_to_ppm = 1.e6_r8 ! kg/kg to ppm + real(r8), parameter :: kg_to_ug = 1.e9_r8 ! kg to micrograms + !----------------------------------------------------------------------- ! Enforce expected array sizes @@ -590,37 +619,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & sno_fs(:) = 0._r8 sno_AR(:) = 0._r8 - g_wvl_ct(1:ngmax-1) = g_wvl(2:ngmax) * 0.5_r8 + g_wvl(1:ngmax-1) * 0.5_r8 - - ! initialize for BC-snow internal mixing - ! Eq. 8b & Table 4 in He et al., 2017 J. Climate (wavelength>1.2um, no BC-snow int mixing effect) - bcint_wvl(1:17) = (/ 0.20_r8, 0.25_r8, 0.30_r8, 0.33_r8, 0.36_r8, 0.40_r8, 0.44_r8, 0.48_r8, & - 0.52_r8, 0.57_r8, 0.64_r8, 0.69_r8, 0.75_r8, 0.78_r8, 0.87_r8, 1._r8, 1.2_r8 /) - bcint_wvl_ct(1:16) = bcint_wvl(2:17) * 0.5_r8 + bcint_wvl(1:16) * 0.5_r8 - bcint_d0(1:16) = (/ 2.48045_r8 , 4.70305_r8 , 4.68619_r8 , 4.67369_r8 , 4.65040_r8 , & - 2.40364_r8 , 7.95408E-1_r8, 2.92745E-1_r8, 8.63396E-2_r8, 2.76299E-2_r8, & - 1.40864E-2_r8, 8.65705E-3_r8, 6.12971E-3_r8, 4.45697E-3_r8, 3.06648E-2_r8, & - 7.96544E-1_r8 /) - bcint_d1(1:16) = (/ 9.77209E-1_r8, 9.73317E-1_r8, 9.79650E-1_r8, 9.84579E-1_r8, 9.93537E-1_r8, & - 9.95955E-1_r8, 9.95218E-1_r8, 9.74284E-1_r8, 9.81193E-1_r8, 9.81239E-1_r8, & - 9.55515E-1_r8, 9.10491E-1_r8, 8.74196E-1_r8, 8.27238E-1_r8, 4.82870E-1_r8, & - 4.36649E-2_r8 /) - bcint_d2(1:16) = (/ 3.95960E-1_r8, 2.04820E-1_r8, 2.07410E-1_r8, 2.09390E-1_r8, 2.13030E-1_r8, & - 4.18570E-1_r8, 1.29682_r8 , 3.75514_r8 , 1.27372E+1_r8, 3.93293E+1_r8, & - 8.78918E+1_r8, 1.86969E+2_r8, 3.45600E+2_r8, 7.08637E+2_r8, 1.41067E+3_r8, & - 2.57288E+2_r8 /) + g_wvl_ct(1:seven_bands) = g_wvl(2:seven_bands+1) * 0.5_r8 + g_wvl(1:seven_bands) * 0.5_r8 + dstint_wvl_ct(1:size_bins) = dstint_wvl(2:size_bins+1) * 0.5_r8 + dstint_wvl(1:size_bins) * 0.5_r8 + bcint_wvl_ct(1:sixteen_bands) = bcint_wvl(2:sixteen_bands+1) * 0.5_r8 + bcint_wvl(1:sixteen_bands) * 0.5_r8 + ! Eq. 1a,1b and Table S1 in He et al. 2018 GRL bcint_m(1:3) = (/ -0.8724_r8, -0.1866_r8, -0.0046_r8 /) bcint_n(1:3) = (/ -0.0072_r8, -0.1918_r8, -0.5177_r8 /) - ! initialize for dust-snow internal mixing - ! Eq. 1 and Table 1 in He et al. 2019 JAMES (wavelength>1.2um, no dust-snow int mixing effect) - dstint_wvl(1:7) = (/ 0.2_r8, 0.2632_r8, 0.3448_r8, 0.4415_r8, 0.625_r8, 0.7782_r8, 1.2422_r8/) - dstint_wvl_ct(1:6) = dstint_wvl(2:7) * 0.5_r8 + dstint_wvl(1:6) * 0.5_r8 - dstint_a1(1:6) = (/ -2.1307E+1_r8, -1.5815E+1_r8, -9.2880_r8 , 1.1115_r8 , 1.0307_r8 , 1.0185_r8 /) - dstint_a2(1:6) = (/ 1.1746E+2_r8, 9.3241E+1_r8, 4.0605E+1_r8, 3.7389E-1_r8, 1.4800E-2_r8, 2.8921E-4_r8 /) - dstint_a3(1:6) = (/ 9.9701E-1_r8, 9.9781E-1_r8, 9.9848E-1_r8, 1.0035_r8 , 1.0024_r8 , 1.0356_r8 /) - ! SNICAR/CLM snow band center wavelength (um) allocate(wvl_ct(snicar_numrad_snw)) select case (snicar_numrad_snw) @@ -835,7 +841,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & else AR_tmp = sno_AR(i) ! user specified value endif - do igb = 1,7 + do igb = 1, seven_bands g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_sphd/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) gg_ice_F07_tmp(igb) = g_F07_c0(igb) + g_F07_c1(igb) * AR_tmp + g_F07_c2(igb) * (AR_tmp * AR_tmp) ! Eqn. 3.1 in Fu (2007) enddo @@ -853,7 +859,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & else AR_tmp = sno_AR(i) ! user specified value endif - do igb = 1,7 + do igb = 1, seven_bands g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_hex0/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * log(AR_tmp) + g_F07_p2(igb) * (log(AR_tmp) * log(AR_tmp)) ! Eqn. 3.3 in Fu (2007) enddo @@ -871,7 +877,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & else AR_tmp = sno_AR(i) ! user specified value endif - do igb = 1,7 + do igb = 1, seven_bands g_ice_Cg_tmp(igb) = g_b0(igb) * ((fs_koch/fs_hex)**g_b1(igb)) * (diam_ice**g_b2(igb)) ! Eq.7, He et al. (2017) gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * log(AR_tmp) + g_F07_p2(igb) * (log(AR_tmp) * log(AR_tmp)) ! Eqn. 3.3 in Fu (2007) enddo @@ -883,8 +889,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! 7 wavelength bands for g_ice to be interpolated into targeted SNICAR bands here ! use the piecewise linear interpolation subroutine created at the end of this module ! tests showed the piecewise linear interpolation has similar results as pchip interpolation - call piecewise_linear_interp1d(ngmax-1, g_wvl_ct, g_ice_Cg_tmp, wvl_ct(bnd_idx), g_Cg_intp) - call piecewise_linear_interp1d(ngmax-1, g_wvl_ct, gg_ice_F07_tmp, wvl_ct(bnd_idx), gg_F07_intp) + call piecewise_linear_interp1d(seven_bands, g_wvl_ct, g_ice_Cg_tmp, wvl_ct(bnd_idx), g_Cg_intp) + call piecewise_linear_interp1d(seven_bands, g_wvl_ct, gg_ice_F07_tmp, wvl_ct(bnd_idx), gg_F07_intp) g_ice_F07 = gg_F07_intp + 0.5_r8 * (1._r8 - gg_F07_intp) / ss_alb_snw_lcl(i) ! Eq.2.2 in Fu (2007) asm_prm_snw_lcl(i) = g_ice_F07 * g_Cg_intp ! Eq.6, He et al. (2017) endif @@ -952,7 +958,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! (2) We tune BC density from 1.7 to 1.49 g/cm3 (den_bc_target) (Aoki et al., 2011). ! These adjustments also lead to consistent results with Flanner et al. 2012 (ACP) lookup table ! for BC-snow internal mixing enhancement in albedo reduction (He et al. 2018 ACP) - do ibb=1,16 + do ibb=1,sixteen_bands enh_omg_bcint_tmp(ibb) = bcint_d0(ibb) * & ( (mss_cnc_aer_lcl(i,1) * kg_to_ug * den_bc / den_bc_target + bcint_d2(ibb))**bcint_d1(ibb) ) ! adjust enhancment factor for BC effective size from 0.1um to Re_bc (He et al. 2018 GRL Eqs.1a,1b) @@ -973,7 +979,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enh_omg_bcint_tmp2(ibb)=LOG10(max(1._r8,bcint_dd*((enh_omg_bcint_tmp(ibb)/bcint_dd2)**bcint_f))) enddo ! piecewise linear interpolate into targeted SNICAR bands in a logscale space - call piecewise_linear_interp1d(16,bcint_wvl_ct,enh_omg_bcint_tmp2,wvl_doint,enh_omg_bcint_intp) + call piecewise_linear_interp1d(sixteen_bands,bcint_wvl_ct,enh_omg_bcint_tmp2,wvl_doint,enh_omg_bcint_intp) ! update snow single-scattering albedo enh_omg_bcint_intp2 = 10._r8 ** enh_omg_bcint_intp enh_omg_bcint_intp2 = min(enh_omg_max, max(enh_omg_bcint_intp2, 1._r8)) ! constrain enhancement to a reasonable range @@ -993,14 +999,14 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & ! from (He et al. 2019 JAMES). Thus, the parameterization can be approximately applied to ! all dust size bins here. tot_dst_snw_conc = (mss_cnc_aer_lcl(i,5) + mss_cnc_aer_lcl(i,6) + & - mss_cnc_aer_lcl(i,7) + mss_cnc_aer_lcl(i,8)) * 1.0E6_r8 !kg/kg->ppm + mss_cnc_aer_lcl(i,7) + mss_cnc_aer_lcl(i,8)) * kg_kg_to_ppm if ( snicar_snodst_intmix .and. (tot_dst_snw_conc > 0._r8) ) then - do idb=1,6 + do idb=1, size_bins enh_omg_dstint_tmp(idb) = dstint_a1(idb)+dstint_a2(idb)*(tot_dst_snw_conc**dstint_a3(idb)) enh_omg_dstint_tmp2(idb) = LOG10(max(enh_omg_dstint_tmp(idb),1._r8)) enddo ! piecewise linear interpolate into targeted SNICAR bands in a logscale space - call piecewise_linear_interp1d(6,dstint_wvl_ct,enh_omg_dstint_tmp2,wvl_doint,enh_omg_dstint_intp) + call piecewise_linear_interp1d(size_bins,dstint_wvl_ct,enh_omg_dstint_tmp2,wvl_doint,enh_omg_dstint_intp) ! update snow single-scattering albedo enh_omg_dstint_intp2 = 10._r8 ** enh_omg_dstint_intp enh_omg_dstint_intp2 = min(enh_omg_max, max(enh_omg_dstint_intp2, 1._r8)) ! constrain enhancement to a reasonable range From eddb844188fe4b9b3ddadac5ba6c65709aa1f05d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Sep 2023 13:59:00 -0600 Subject: [PATCH 1541/2067] Add case default lines and corresponding error messages --- src/biogeophys/SnowSnicarMod.F90 | 35 +++++++++++++++++++++----------- 1 file changed, 23 insertions(+), 12 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 60f9bc7d9f..ada6735a1f 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -587,6 +587,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8), parameter :: kg_kg_to_ppm = 1.e6_r8 ! kg/kg to ppm real(r8), parameter :: kg_to_ug = 1.e9_r8 ! kg to micrograms + character(len=*), parameter :: subname = 'SNICAR_RT' !----------------------------------------------------------------------- ! Enforce expected array sizes @@ -605,12 +606,21 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & frac_sno => waterdiagnosticbulk_inst%frac_sno_eff_col & ! Input: [real(r8) (:)] fraction of ground covered by snow (0 to 1) ) - ! initialize parameter + ! initialize parameter and + ! SNICAR/CLM snow band center wavelength (um) + allocate(wvl_ct(snicar_numrad_snw)) select case (snicar_numrad_snw) case (5) nir_bnd_bgn = 2 + wvl_ct(:) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band case (480) nir_bnd_bgn = 51 + do igb = 1, snicar_numrad_snw + wvl_ct(igb) = 0.205_r8 + 0.01_r8 * (igb - 1._r8) ! 480-band + enddo + case default + write(iulog,*) subname//' ERROR: unknown snicar_numrad_snw value: ', snicar_numrad_snw + call endrun(msg=errMsg(sourcefile, __LINE__)) end select nir_bnd_end = snicar_numrad_snw @@ -627,17 +637,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & bcint_m(1:3) = (/ -0.8724_r8, -0.1866_r8, -0.0046_r8 /) bcint_n(1:3) = (/ -0.0072_r8, -0.1918_r8, -0.5177_r8 /) - ! SNICAR/CLM snow band center wavelength (um) - allocate(wvl_ct(snicar_numrad_snw)) - select case (snicar_numrad_snw) - case (5) - wvl_ct(:) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band - case (480) - do igb = 1, snicar_numrad_snw - wvl_ct(igb) = 0.205_r8 + 0.01_r8 * (igb - 1._r8) ! 480-band - enddo - end select - ! Define constants pi = SHR_CONST_PI @@ -882,6 +881,9 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * log(AR_tmp) + g_F07_p2(igb) * (log(AR_tmp) * log(AR_tmp)) ! Eqn. 3.3 in Fu (2007) enddo + case default + write(iulog,*) subname//' ERROR: unknown sno_shp for i: ', sno_shp(i), i + call endrun(msg=errMsg(sourcefile, __LINE__)) end select ! compute nonspherical snow asymmetry factor @@ -1865,6 +1867,9 @@ subroutine SnowOptics_init( ) short_case_solarspec = 'smm' case ('high_mountain_summer') ! High Mountain summer spectrum short_case_solarspec = 'hmn' + case default + write(iulog,*) subname//' ERROR: unknown snicar_solarspec: ', snicar_solarspec + call endrun(msg=errMsg(sourcefile, __LINE__)) end select select case (snicar_dust_optics) ! dust optical properties @@ -1874,6 +1879,9 @@ subroutine SnowOptics_init( ) short_case_dust_opt = 'col' case ('greenland') ! Greenland (Polashenski et al., 2015, central absorptivity) short_case_dust_opt = 'gre' + case default + write(iulog,*) subname//' ERROR: unknown snicar_dust_optics: ', snicar_dust_optics + call endrun(msg=errMsg(sourcefile, __LINE__)) end select !--------------------- for 5-band data @@ -2122,6 +2130,9 @@ subroutine SnowOptics_init( ) call ncd_io(trim(tString), flx_wgt_dif, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) + case default + write(iulog,*) subname//' ERROR: unknown snicar_numrad_snw: ', snicar_numrad_snw + call endrun(msg=errMsg(sourcefile, __LINE__)) end select call ncd_pio_closefile(ncid) From d6b92eccc822345ee48a534a4cb2e116a619bd5c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Sep 2023 14:44:13 -0600 Subject: [PATCH 1542/2067] Change two more arrays to parameters --- src/biogeophys/SnowSnicarMod.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index ada6735a1f..d19b057659 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -546,8 +546,12 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & real(r8), parameter :: Re_bc = 0.045_r8 ! target BC effective radius (um) used in BC MAC adjustment real(r8), parameter :: radius_1 = 0.1_r8 ! used with Re_bc (um) real(r8), parameter :: radius_2 = 0.05_r8 ! used with Re_bc (um) - real(r8) :: bcint_m(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix - real(r8) :: bcint_n(1:3) ! Parameterization coefficients for BC size adjustment in BC-snow int mix + ! Eq. 1a,1b and Table S1 in He et al. 2018 GRL + ! Parameterization coefficients for BC size adjustment in BC-snow int mix + integer, parameter :: three_bands = 3 + real(r8), parameter :: bcint_m(three_bands) = (/ -0.8724_r8, -0.1866_r8, -0.0046_r8 /) + real(r8), parameter :: bcint_n(three_bands) = (/ -0.0072_r8, -0.1918_r8, -0.5177_r8 /) + real(r8) :: bcint_m_tmp ! temporary of bcint_m real(r8) :: bcint_n_tmp ! temporary of bcint_n real(r8) :: bcint_dd ! intermediate parameter @@ -633,10 +637,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & dstint_wvl_ct(1:size_bins) = dstint_wvl(2:size_bins+1) * 0.5_r8 + dstint_wvl(1:size_bins) * 0.5_r8 bcint_wvl_ct(1:sixteen_bands) = bcint_wvl(2:sixteen_bands+1) * 0.5_r8 + bcint_wvl(1:sixteen_bands) * 0.5_r8 - ! Eq. 1a,1b and Table S1 in He et al. 2018 GRL - bcint_m(1:3) = (/ -0.8724_r8, -0.1866_r8, -0.0046_r8 /) - bcint_n(1:3) = (/ -0.0072_r8, -0.1918_r8, -0.5177_r8 /) - ! Define constants pi = SHR_CONST_PI From 99ee926f7c2f19d4bf3a49b42bc65dc01f82385c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Sep 2023 15:55:32 -0600 Subject: [PATCH 1543/2067] Replace suffixes 1 & 2 representing hydrophillic/phobic w hphil/hphob --- src/biogeophys/SnowSnicarMod.F90 | 148 +++++++++++++++---------------- 1 file changed, 74 insertions(+), 74 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index d19b057659..cf3903b6ae 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -94,24 +94,24 @@ module SnowSnicarMod real(r8), pointer :: ext_cff_mss_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) ! hydrophilic BC - real(r8), pointer :: ss_alb_bc1(:) !(numrad_snw) - real(r8), pointer :: asm_prm_bc1(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_bc1(:) !(numrad_snw) + real(r8), pointer :: ss_alb_bc_hphil(:) !(numrad_snw) + real(r8), pointer :: asm_prm_bc_hphil(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_bc_hphil(:) !(numrad_snw) ! hydrophobic BC - real(r8), pointer :: ss_alb_bc2(:) !(numrad_snw) - real(r8), pointer :: asm_prm_bc2(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_bc2(:) !(numrad_snw) + real(r8), pointer :: ss_alb_bc_hphob(:) !(numrad_snw) + real(r8), pointer :: asm_prm_bc_hphob(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_bc_hphob(:) !(numrad_snw) ! hydrophilic OC - real(r8), pointer :: ss_alb_oc1(:) !(numrad_snw) - real(r8), pointer :: asm_prm_oc1(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_oc1(:) !(numrad_snw) + real(r8), pointer :: ss_alb_oc_hphil(:) !(numrad_snw) + real(r8), pointer :: asm_prm_oc_hphil(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_oc_hphil(:) !(numrad_snw) ! hydrophobic OC - real(r8), pointer :: ss_alb_oc2(:) !(numrad_snw) - real(r8), pointer :: asm_prm_oc2(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_oc2(:) !(numrad_snw) + real(r8), pointer :: ss_alb_oc_hphob(:) !(numrad_snw) + real(r8), pointer :: asm_prm_oc_hphob(:) !(numrad_snw) + real(r8), pointer :: ext_cff_mss_oc_hphob(:) !(numrad_snw) ! dust species 1: real(r8), pointer :: ss_alb_dst1(:) !(numrad_snw) @@ -902,23 +902,23 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo ! snow layer loop ! aerosol species 2 optical properties, hydrophobic BC - ss_alb_aer_lcl(2) = ss_alb_bc2(bnd_idx) - asm_prm_aer_lcl(2) = asm_prm_bc2(bnd_idx) - ext_cff_mss_aer_lcl(2) = ext_cff_mss_bc2(bnd_idx) + ss_alb_aer_lcl(2) = ss_alb_bc_hphob(bnd_idx) + asm_prm_aer_lcl(2) = asm_prm_bc_hphob(bnd_idx) + ext_cff_mss_aer_lcl(2) = ext_cff_mss_bc_hphob(bnd_idx) ! aerosol species 3 optical properties, hydrophilic OC - ss_alb_aer_lcl(3) = ss_alb_oc1(bnd_idx) - asm_prm_aer_lcl(3) = asm_prm_oc1(bnd_idx) - ext_cff_mss_aer_lcl(3) = ext_cff_mss_oc1(bnd_idx) + ss_alb_aer_lcl(3) = ss_alb_oc_hphil(bnd_idx) + asm_prm_aer_lcl(3) = asm_prm_oc_hphil(bnd_idx) + ext_cff_mss_aer_lcl(3) = ext_cff_mss_oc_hphil(bnd_idx) ! aerosol species 4 optical properties, hydrophobic OC - ss_alb_aer_lcl(4) = ss_alb_oc2(bnd_idx) - asm_prm_aer_lcl(4) = asm_prm_oc2(bnd_idx) - ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc2(bnd_idx) + ss_alb_aer_lcl(4) = ss_alb_oc_hphob(bnd_idx) + asm_prm_aer_lcl(4) = asm_prm_oc_hphob(bnd_idx) + ext_cff_mss_aer_lcl(4) = ext_cff_mss_oc_hphob(bnd_idx) ! Optics for BC/dust-snow external mixing: ! aerosol species 1 optical properties, hydrophilic BC - ss_alb_aer_lcl(1) = ss_alb_bc1(bnd_idx) - asm_prm_aer_lcl(1) = asm_prm_bc1(bnd_idx) - ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc1(bnd_idx) + ss_alb_aer_lcl(1) = ss_alb_bc_hphil(bnd_idx) + asm_prm_aer_lcl(1) = asm_prm_bc_hphil(bnd_idx) + ext_cff_mss_aer_lcl(1) = ext_cff_mss_bc_hphil(bnd_idx) ! aerosol species 5 optical properties, dust size1 ss_alb_aer_lcl(5) = ss_alb_dst1(bnd_idx) asm_prm_aer_lcl(5) = asm_prm_dst1(bnd_idx) @@ -1822,18 +1822,18 @@ subroutine SnowOptics_init( ) allocate(ss_alb_snw_dfs(idx_Mie_snw_mx,snicar_numrad_snw)) allocate(asm_prm_snw_dfs(idx_Mie_snw_mx,snicar_numrad_snw)) allocate(ext_cff_mss_snw_dfs(idx_Mie_snw_mx,snicar_numrad_snw)) - allocate(ss_alb_bc1(snicar_numrad_snw)) - allocate(asm_prm_bc1(snicar_numrad_snw)) - allocate(ext_cff_mss_bc1(snicar_numrad_snw)) - allocate(ss_alb_bc2(snicar_numrad_snw)) - allocate(asm_prm_bc2(snicar_numrad_snw)) - allocate(ext_cff_mss_bc2(snicar_numrad_snw)) - allocate(ss_alb_oc1(snicar_numrad_snw)) - allocate(asm_prm_oc1(snicar_numrad_snw)) - allocate(ext_cff_mss_oc1(snicar_numrad_snw)) - allocate(ss_alb_oc2(snicar_numrad_snw)) - allocate(asm_prm_oc2(snicar_numrad_snw)) - allocate(ext_cff_mss_oc2(snicar_numrad_snw)) + allocate(ss_alb_bc_hphil(snicar_numrad_snw)) + allocate(asm_prm_bc_hphil(snicar_numrad_snw)) + allocate(ext_cff_mss_bc_hphil(snicar_numrad_snw)) + allocate(ss_alb_bc_hphob(snicar_numrad_snw)) + allocate(asm_prm_bc_hphob(snicar_numrad_snw)) + allocate(ext_cff_mss_bc_hphob(snicar_numrad_snw)) + allocate(ss_alb_oc_hphil(snicar_numrad_snw)) + allocate(asm_prm_oc_hphil(snicar_numrad_snw)) + allocate(ext_cff_mss_oc_hphil(snicar_numrad_snw)) + allocate(ss_alb_oc_hphob(snicar_numrad_snw)) + allocate(asm_prm_oc_hphob(snicar_numrad_snw)) + allocate(ext_cff_mss_oc_hphob(snicar_numrad_snw)) allocate(ss_alb_dst1(snicar_numrad_snw)) allocate(asm_prm_dst1(snicar_numrad_snw)) allocate(ext_cff_mss_dst1(snicar_numrad_snw)) @@ -1897,62 +1897,62 @@ subroutine SnowOptics_init( ) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ! THIS NOTE APPLIES TO ALL THE call ncd_io LINES BELOW WHERE - ! bcphob AND ocphob GET ASSIGNED TO VARIABLES SUFFIXED bc1/oc1: + ! bcphob AND ocphob GET ASSIGNED TO VARIABLES SUFFIXED bc_hphil/oc_hphil: ! ! Assumption (1) applies here, in the input section. ! Assumption (2) applies later, in the snicar code. ! ! 1) In this section, hydrophillic particles behave like hydrophobic - ! particles. We assume bc1/oc1 to have the same optics as bc2/oc2 - ! because sulfate coating on the bc1/oc1 surface is assumed to be + ! particles. We assume bc_hphil/oc_hphil to have the same optics as bc_hphob/oc_hphob + ! because sulfate coating on the bc_hphil/oc_hphil surface is assumed to be ! dissolved into the hydrometeo (i.e, snow grain here) during the ! deposition process. This is different from the assumption made in - ! prior model versions, where bc1/oc1 was coated by undissolved + ! prior model versions, where bc_hphil/oc_hphil was coated by undissolved ! sulfate. ! 2) Later, in the snicar code, if the bc-snow internal mixing option - ! is on, bc1/oc1 (internally mixed within the snow grain) will be - ! treated differently than bc2/oc2 (mixed externally or outside the + ! is on, bc_hphil/oc_hphil (internally mixed within the snow grain) will be + ! treated differently than bc_hphob/oc_hphob (mixed externally or outside the ! snow grain). ! - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + ! BC species 1 Mie parameters, uncoated BC, same as bc_hphob before BC-snow internal mixing tString = 'ss_alb_bcphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_bc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_bcphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_bc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_bcphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_bc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC tString = 'ss_alb_bcphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_bc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_bcphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_bc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_bcphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_bc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + ! OC species 1 Mie parameters, uncoated OC, same as oc_hphob before OC-snow internal mixing tString = 'ss_alb_ocphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_oc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_ocphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_oc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_ocphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_oc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC tString = 'ss_alb_ocphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_oc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_ocphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_oc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_ocphob_dif_'//short_case_solarspec - call ncd_io(trim(tString), ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_oc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! ice refractive index (Picard et al., 2016) tString = 'ss_alb_ice_pic16_dir_'//short_case_solarspec @@ -2018,45 +2018,45 @@ subroutine SnowOptics_init( ) !-------------------- for 480-band data case (480) - ! BC species 1 Mie parameters, uncoated BC, same as bc2 before BC-snow internal mixing + ! BC species 1 Mie parameters, uncoated BC, same as bc_hphob before BC-snow internal mixing tString = 'ss_alb_bcphob' - call ncd_io(trim(tString), ss_alb_bc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_bc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_bcphob' - call ncd_io(trim(tString), asm_prm_bc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_bc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_bcphob' - call ncd_io(trim(tString), ext_cff_mss_bc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_bc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! BC species 2 Mie parameters, uncoated BC tString = 'ss_alb_bcphob' - call ncd_io(trim(tString), ss_alb_bc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_bc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_bcphob' - call ncd_io(trim(tString), asm_prm_bc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_bc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_bcphob' - call ncd_io(trim(tString), ext_cff_mss_bc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_bc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - ! OC species 1 Mie parameters, uncoated OC, same as oc2 before OC-snow internal mixing + ! OC species 1 Mie parameters, uncoated OC, same as oc_hphob before OC-snow internal mixing tString = 'ss_alb_ocphob' - call ncd_io(trim(tString), ss_alb_oc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_oc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_ocphob' - call ncd_io(trim(tString), asm_prm_oc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_oc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_ocphob' - call ncd_io(trim(tString), ext_cff_mss_oc1, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_oc_hphil, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! OC species 2 Mie parameters, uncoated OC tString = 'ss_alb_ocphob' - call ncd_io(trim(tString), ss_alb_oc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ss_alb_oc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'asm_prm_ocphob' - call ncd_io(trim(tString), asm_prm_oc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), asm_prm_oc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) tString = 'ext_cff_mss_ocphob' - call ncd_io(trim(tString), ext_cff_mss_oc2, 'read', ncid, readv, posNOTonfile=.true.) + call ncd_io(trim(tString), ext_cff_mss_oc_hphob, 'read', ncid, readv, posNOTonfile=.true.) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) ! snow optical properties derived from different ice refractive index dataset @@ -2152,14 +2152,14 @@ subroutine SnowOptics_init( ) write (iulog,*) 'SNICAR: Excluding OC aerosols from snow radiative transfer calculations' endif write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophillic BC: ', & - ss_alb_bc1(1), ss_alb_bc1(2), ss_alb_bc1(3), ss_alb_bc1(4), ss_alb_bc1(5) + ss_alb_bc_hphil(1), ss_alb_bc_hphil(2), ss_alb_bc_hphil(3), ss_alb_bc_hphil(4), ss_alb_bc_hphil(5) write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophobic BC: ', & - ss_alb_bc2(1), ss_alb_bc2(2), ss_alb_bc2(3), ss_alb_bc2(4), ss_alb_bc2(5) + ss_alb_bc_hphob(1), ss_alb_bc_hphob(2), ss_alb_bc_hphob(3), ss_alb_bc_hphob(4), ss_alb_bc_hphob(5) if (do_sno_oc) then write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophillic OC: ', & - ss_alb_oc1(1), ss_alb_oc1(2), ss_alb_oc1(3), ss_alb_oc1(4), ss_alb_oc1(5) + ss_alb_oc_hphil(1), ss_alb_oc_hphil(2), ss_alb_oc_hphil(3), ss_alb_oc_hphil(4), ss_alb_oc_hphil(5) write (iulog,*) 'SNICAR: Mie single scatter albedos for hydrophobic OC: ', & - ss_alb_oc2(1), ss_alb_oc2(2), ss_alb_oc2(3), ss_alb_oc2(4), ss_alb_oc2(5) + ss_alb_oc_hphob(1), ss_alb_oc_hphob(2), ss_alb_oc_hphob(3), ss_alb_oc_hphob(4), ss_alb_oc_hphob(5) endif write (iulog,*) 'SNICAR: Mie single scatter albedos for dust species 1: ', & ss_alb_dst1(1), ss_alb_dst1(2), ss_alb_dst1(3), ss_alb_dst1(4), ss_alb_dst1(5) From 94846be9125db892136ae89d69ea0153bdaf0165 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 29 Sep 2023 16:35:49 -0600 Subject: [PATCH 1544/2067] Replace pointers with allocatables --- src/biogeophys/SnowSnicarMod.F90 | 70 ++++++++++++++++---------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index cf3903b6ae..1d72870173 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -84,67 +84,67 @@ module SnowSnicarMod ! (idx_Mie_snw_mx is number of snow radii with defined parameters (i.e. from 30um to 1500um)) ! direct-beam weighted ice optical properties - real(r8), pointer :: ss_alb_snw_drc(:,:) !(idx_Mie_snw_mx,numrad_snw) - real(r8), pointer :: asm_prm_snw_drc(:,:) !(idx_Mie_snw_mx,numrad_snw) - real(r8), pointer :: ext_cff_mss_snw_drc(:,:) !(idx_Mie_snw_mx,numrad_snw) + real(r8), allocatable :: ss_alb_snw_drc(:,:) ! (idx_Mie_snw_mx, numrad_snw) + real(r8), allocatable :: asm_prm_snw_drc(:,:) + real(r8), allocatable :: ext_cff_mss_snw_drc(:,:) ! diffuse radiation weighted ice optical properties - real(r8), pointer :: ss_alb_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) - real(r8), pointer :: asm_prm_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) - real(r8), pointer :: ext_cff_mss_snw_dfs(:,:) !(idx_Mie_snw_mx,numrad_snw) + real(r8), allocatable :: ss_alb_snw_dfs(:,:) ! (idx_Mie_snw_mx, numrad_snw) + real(r8), allocatable :: asm_prm_snw_dfs(:,:) + real(r8), allocatable :: ext_cff_mss_snw_dfs(:,:) ! hydrophilic BC - real(r8), pointer :: ss_alb_bc_hphil(:) !(numrad_snw) - real(r8), pointer :: asm_prm_bc_hphil(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_bc_hphil(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_bc_hphil(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_bc_hphil(:) + real(r8), allocatable :: ext_cff_mss_bc_hphil(:) ! hydrophobic BC - real(r8), pointer :: ss_alb_bc_hphob(:) !(numrad_snw) - real(r8), pointer :: asm_prm_bc_hphob(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_bc_hphob(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_bc_hphob(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_bc_hphob(:) + real(r8), allocatable :: ext_cff_mss_bc_hphob(:) ! hydrophilic OC - real(r8), pointer :: ss_alb_oc_hphil(:) !(numrad_snw) - real(r8), pointer :: asm_prm_oc_hphil(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_oc_hphil(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_oc_hphil(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_oc_hphil(:) + real(r8), allocatable :: ext_cff_mss_oc_hphil(:) ! hydrophobic OC - real(r8), pointer :: ss_alb_oc_hphob(:) !(numrad_snw) - real(r8), pointer :: asm_prm_oc_hphob(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_oc_hphob(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_oc_hphob(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_oc_hphob(:) + real(r8), allocatable :: ext_cff_mss_oc_hphob(:) ! dust species 1: - real(r8), pointer :: ss_alb_dst1(:) !(numrad_snw) - real(r8), pointer :: asm_prm_dst1(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_dst1(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_dst1(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_dst1(:) + real(r8), allocatable :: ext_cff_mss_dst1(:) ! dust species 2: - real(r8), pointer :: ss_alb_dst2(:) !(numrad_snw) - real(r8), pointer :: asm_prm_dst2(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_dst2(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_dst2(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_dst2(:) + real(r8), allocatable :: ext_cff_mss_dst2(:) ! dust species 3: - real(r8), pointer :: ss_alb_dst3(:) !(numrad_snw) - real(r8), pointer :: asm_prm_dst3(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_dst3(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_dst3(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_dst3(:) + real(r8), allocatable :: ext_cff_mss_dst3(:) ! dust species 4: - real(r8), pointer :: ss_alb_dst4(:) !(numrad_snw) - real(r8), pointer :: asm_prm_dst4(:) !(numrad_snw) - real(r8), pointer :: ext_cff_mss_dst4(:) !(numrad_snw) + real(r8), allocatable :: ss_alb_dst4(:) ! (numrad_snw) + real(r8), allocatable :: asm_prm_dst4(:) + real(r8), allocatable :: ext_cff_mss_dst4(:) ! downward solar radiation spectral weights for 5-band or 480-band - real(r8), pointer :: flx_wgt_dir(:) !(numrad_snw) ! direct - real(r8), pointer :: flx_wgt_dif(:) !(numrad_snw) ! diffuse + real(r8), allocatable :: flx_wgt_dir(:) ! (numrad_snw) ! direct + real(r8), allocatable :: flx_wgt_dif(:) ! (numrad_snw) ! diffuse ! best-fit parameters for snow aging defined over: ! 11 temperatures from 225 to 273 K ! 31 temperature gradients from 0 to 300 K/m ! 8 snow densities from 0 to 350 kg/m3 ! (arrays declared here, but are set in iniTimeConst) - real(r8), pointer :: snowage_tau(:,:,:) ! (idx_rhos_max,idx_Tgrd_max,idx_T_max) - real(r8), pointer :: snowage_kappa(:,:,:) ! (idx_rhos_max,idx_Tgrd_max,idx_T_max) - real(r8), pointer :: snowage_drdt0(:,:,:) ! idx_rhos_max,idx_Tgrd_max,idx_T_max) + real(r8), allocatable :: snowage_tau(:,:,:) ! (idx_rhos_max, idx_Tgrd_max, idx_T_max) + real(r8), allocatable :: snowage_kappa(:,:,:) + real(r8), allocatable :: snowage_drdt0(:,:,:) ! ! !REVISION HISTORY: ! Created by Mark Flanner (Univ. of Michigan) From 5e819a5d4bbece27322a26dd7994a25f1b993f43 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 2 Oct 2023 10:12:12 -0700 Subject: [PATCH 1545/2067] fix compset name to match the expected failure list --- cime_config/testdefs/testlist_clm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f5af800543..6646e4700b 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1835,7 +1835,7 @@ - + @@ -1843,7 +1843,7 @@ - + From 257a33ba0727a54751fa8aa1351734adaec9bede Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 2 Oct 2023 11:18:04 -0600 Subject: [PATCH 1546/2067] remove cru from fates compset name --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- cime_config/testdefs/testlist_clm.xml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 0744055303..8e72abb8eb 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -109,7 +109,7 @@ - + FAIL FATES#1089 diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 6646e4700b..f5af800543 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1835,7 +1835,7 @@ - + @@ -1843,7 +1843,7 @@ - + From b3327d09d59b8dd92c6c1bcca328b59334c488d5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 11:50:38 -0600 Subject: [PATCH 1547/2067] Fixed "anomoly" typo. --- tools/contrib/ssp_anomaly_forcing_smooth | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index ae3d189a8b..f70ccd7a73 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -3,7 +3,7 @@ ssp_anomaly_forcing_smooth -Create anomoly forcing datasets for SSP scenarios that can be used by CESM datm model +Create anomaly forcing datasets for SSP scenarios that can be used by CESM datm model load proper modules first, i.e. @@ -48,7 +48,7 @@ if args.sspnum == 0: # ------------------------------------------------------- -print("Create anomoly forcing data that can be used by CTSM in CESM") +print("Create anomaly forcing data that can be used by CTSM in CESM") # Input and output directories make sure they exist datapath = "/glade/campaign/collections/cmip/CMIP6/timeseries-cmip6/" # Path on casper @@ -710,4 +710,4 @@ for f in range(nfields): # -- End Loop over forcing fields ------------------------------------ outfile.close() -print("\n\nSuccessfully made anomoly forcing datasets\n") +print("\n\nSuccessfully made anomaly forcing datasets\n") From b578626a17bb97642da619f51240d0d64e509350 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 11:52:51 -0600 Subject: [PATCH 1548/2067] Removed unnecessary hist_case. --- tools/contrib/ssp_anomaly_forcing_smooth | 3 --- 1 file changed, 3 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index f70ccd7a73..27eaed5588 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -165,9 +165,6 @@ if args.print_ssps: sspnum = args.sspnum -# hist_case needed? -hist_case = "b.e21.BHIST.f09_g17.CMIP6-historical.010" - if sspnum == 1: # SSP1-26 ssptag = "SSP1-2.6" From b5ce1209ffb2cfe98fc483788657dbe249dc1c27 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 11:53:10 -0600 Subject: [PATCH 1549/2067] num_ens now automatically set. --- tools/contrib/ssp_anomaly_forcing_smooth | 3 --- 1 file changed, 3 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 27eaed5588..c453237402 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -193,9 +193,6 @@ if num_ens != len(histdir): print("number of ensemble members not the same") sys.exit("number of members different") -# test w/ 1 ensemble member -num_ens = 3 - # Setup output directory sspoutdir = "anomaly_forcing/CMIP6-" + ssptag From 8d06313f53bf524e1f410c163f4ebfef53c3a1db Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 11:53:41 -0600 Subject: [PATCH 1550/2067] Removed unused hist_suffix and ssp_suffix. --- tools/contrib/ssp_anomaly_forcing_smooth | 7 ------- 1 file changed, 7 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index c453237402..6ac76d1682 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -202,13 +202,6 @@ if not os.path.exists(outdir): print("Output specific data directory :" + outdir) -# historical files are split by 50 year periods; use last period -hist_suffix = ["200001-201412.nc"] # not standardized?! -# hist_suffix = ['-201412.nc'] -# projections are split 2015/2064 2065/2100 -ssp_suffix = ["201501-206412.nc", "206501-210012.nc"] -# ssp_suffix = ['-206412.nc','-210012.nc'] - climo_year = 2015 # ten years on either side (21 years total) climo_base_nyrs = 21 From 2f55d1eb1a538d069c91435232b4aabb47ad3eac Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 11:55:20 -0600 Subject: [PATCH 1551/2067] Added output_format variable. --- tools/contrib/ssp_anomaly_forcing_smooth | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 6ac76d1682..33f0fc3e72 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -231,6 +231,8 @@ field_out_wind = ["uas", "vas"] nfields = len(field_in) +output_format = "NETCDF3_64BIT_DATA" + # -- Loop over forcing fields ------------------------------------ for f in range(nfields): @@ -471,7 +473,7 @@ for f in range(nfields): w = netcdf4.Dataset( outdir + field_out[f] + "_climo" + creationdate + ".nc", "w", - format="NETCDF3_64BIT_DATA" + format=output_format, ) w.createDimension("lat", int(nlat)) w.createDimension("lon", int(nlon)) @@ -502,7 +504,7 @@ for f in range(nfields): w = netcdf4.Dataset( outdir + field_out[f] + "_smooth" + creationdate + ".nc", "w", - format="NETCDF3_64BIT_DATA" + format=output_format, ) w.createDimension("lat", int(nlat)) w.createDimension("lon", int(nlon)) @@ -545,7 +547,7 @@ for f in range(nfields): # output in CDF5 format using netCDF4 python interfaces outfilename = outdir + "/" + "af.allvars" + outfile_suffix print("Creating: " + outfilename) - outfile = netcdf4.Dataset(outfilename, "w", format="NETCDF3_64BIT_DATA") + outfile = netcdf4.Dataset(outfilename, "w", format=output_format) # creation date on the file command = 'date "+%Y/%m/%d"' From 0ca6d62af04c0dc9dc56492eb724ff54d8dbe8ce Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 12:07:09 -0600 Subject: [PATCH 1552/2067] Can now specify --output-dir. Also fixes bug of write_climo file paths missing a /. --- tools/contrib/ssp_anomaly_forcing_smooth | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 33f0fc3e72..a0b6419744 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -41,6 +41,13 @@ parser.add_argument( action="store_true", default=False, ) +parser.add_argument( + "--output_dir", "--output-dir", + help="Top-level output directory (default: ./anomaly_forcing/). Sub-directory will be created for the selected scenario.", + type=str, + default=os.path.join(".", "anomaly_forcing"), +) + args = parser.parse_args() if args.sspnum == 0: @@ -109,15 +116,14 @@ _v2 is just used for restart files that have been spatially interpolated """ -spath = "./" if os.path.exists(datapath): print("Input data directory:" + datapath) else: sys.exit("Could not find input directory: " + datapath) -if os.path.exists(spath): - print("Output data directory:" + spath) +if os.path.exists(args.output_dir): + print("Output data directory:" + args.output_dir) else: - sys.exit("Could not find output directory: " + spath) + sys.exit("Could not find output directory: " + args.output_dir) # Settings to run with today = datetime.date.today() @@ -194,9 +200,9 @@ if num_ens != len(histdir): sys.exit("number of members different") # Setup output directory -sspoutdir = "anomaly_forcing/CMIP6-" + ssptag +sspoutdir = "CMIP6-" + ssptag -outdir = spath + sspoutdir +outdir = os.path.join(args.output_dir, sspoutdir) if not os.path.exists(outdir): os.makedirs(outdir) @@ -471,7 +477,7 @@ for f in range(nfields): if write_climo: # Use NetCDF4 format, because using older NetCDF formats are too slow w = netcdf4.Dataset( - outdir + field_out[f] + "_climo" + creationdate + ".nc", + os.path.join(outdir, field_out[f] + "_climo" + creationdate + ".nc"), "w", format=output_format, ) @@ -502,7 +508,7 @@ for f in range(nfields): # Use NetCDF4 format, because using older NetCDF formats are too slow w = netcdf4.Dataset( - outdir + field_out[f] + "_smooth" + creationdate + ".nc", + os.path.join(outdir, field_out[f] + "_smooth" + creationdate + ".nc"), "w", format=output_format, ) @@ -545,7 +551,7 @@ for f in range(nfields): # Use NetCDF4 format, because using older NetCDF formats are too slow # Will need to convert to CDF5 format at the end, as we can't seem to # output in CDF5 format using netCDF4 python interfaces - outfilename = outdir + "/" + "af.allvars" + outfile_suffix + outfilename = os.path.join(outdir, "af.allvars" + outfile_suffix) print("Creating: " + outfilename) outfile = netcdf4.Dataset(outfilename, "w", format=output_format) From 3c24b25db5f2dd7d6397c1b792c2a63b15a2f8a3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 12:56:30 -0600 Subject: [PATCH 1553/2067] Prevent tillage from being enabled. --- bld/CLMBuildNamelist.pm | 3 +++ 1 file changed, 3 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 405bf2d9ff..069a1adea5 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2194,6 +2194,9 @@ sub setup_logic_tillage { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); + if ( $tillage_mode ne "" && $tillage_mode ne "off") { + $log->fatal_error( "Tillage has not yet been scientifically tested and so may not be enabled." ); + } if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." ); } From c58e0ee80d8653961dd9af29c5bd8d3c6c92029b Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Oct 2023 10:04:43 -0600 Subject: [PATCH 1554/2067] Move iso functions to utils --- python/ctsm/site_and_regional/run_neon.py | 28 +------------------- python/ctsm/utils.py | 32 ++++++++++++++++++++++- 2 files changed, 32 insertions(+), 28 deletions(-) diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 8188f6084b..b0ccc4b687 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -71,7 +71,7 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm import add_cime_to_path -from ctsm.path_utils import path_to_ctsm_root +from ctsm.path_utils import path_to_ctsm_root, parse_isoduration from ctsm.download_utils import download_file import CIME.build as build @@ -327,32 +327,6 @@ def get_parser(args, description, valid_neon_sites): args.user_version, ) - -def get_isosplit(s, split): - if split in s: - n, s = s.split(split) - else: - n = 0 - return n, s - - -def parse_isoduration(s): - """ - simple ISO 8601 duration parser, does not account for leap years and assumes 30 day months - """ - # Remove prefix - s = s.split("P")[-1] - - # Step through letter dividers - years, s = get_isosplit(s, "Y") - months, s = get_isosplit(s, "M") - days, s = get_isosplit(s, "D") - - # Convert all to timedelta - dt = datetime.timedelta(days=int(days) + 365 * int(years) + 30 * int(months)) - return int(dt.total_seconds() / 86400) - - class NeonSite: """ A class for encapsulating neon sites. diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 42444e32c5..add7655418 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -7,7 +7,7 @@ import re import pdb -from datetime import date +from datetime import date, timedelta from getpass import getuser from ctsm.git_utils import get_ctsm_git_short_hash @@ -189,3 +189,33 @@ def write_output(file, file_in, file_out, file_type): file.to_netcdf(path=file_out, mode="w", format="NETCDF3_64BIT") logger.info("Successfully created: %s", file_out) file.close() + + +def get_isosplit(s, split): + """ + Split a string (s) by the character sent in from split + Only used by parse_isoduration + """ + if split in s: + n, s = s.split(split) + else: + n = 0 + return n, s + + +def parse_isoduration(s): + """ + simple ISO 8601 duration parser, does not account for leap years and assumes 30 day months + """ + # Remove prefix + s = s.split("P")[-1] + + # Step through letter dividers + years, s = get_isosplit(s, "Y") + months, s = get_isosplit(s, "M") + days, s = get_isosplit(s, "D") + + # Convert all to timedelta + dt = timedelta(days=int(days) + 365 * int(years) + 30 * int(months)) + return int(dt.total_seconds() / 86400) + From 47e72881e80c94473284b23de2d6ad714faf7f9d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Oct 2023 10:23:16 -0600 Subject: [PATCH 1555/2067] Some lint and black updates for the new iso utility code --- python/ctsm/utils.py | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index add7655418..8578ea860c 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -191,31 +191,31 @@ def write_output(file, file_in, file_out, file_type): file.close() -def get_isosplit(s, split): +def get_isosplit(iso_string, split): """ - Split a string (s) by the character sent in from split + Split a string (iso_string) by the character sent in from split + Returns the number for that character split Only used by parse_isoduration """ - if split in s: - n, s = s.split(split) + if split in iso_string: + num, iso_string = iso_string.split(split) else: - n = 0 - return n, s + num = 0 + return num, iso_string -def parse_isoduration(s): +def parse_isoduration(iso_string): """ simple ISO 8601 duration parser, does not account for leap years and assumes 30 day months """ # Remove prefix - s = s.split("P")[-1] + iso_string = iso_string.split("P")[-1] # Step through letter dividers - years, s = get_isosplit(s, "Y") - months, s = get_isosplit(s, "M") - days, s = get_isosplit(s, "D") + years, iso_string = get_isosplit(iso_string, "Y") + months, iso_string = get_isosplit(iso_string, "M") + days, iso_string = get_isosplit(iso_string, "D") # Convert all to timedelta - dt = timedelta(days=int(days) + 365 * int(years) + 30 * int(months)) - return int(dt.total_seconds() / 86400) - + delta_t = timedelta(days=int(days) + 365 * int(years) + 30 * int(months)) + return int(delta_t.total_seconds() / 86400) From e56552d9b2334f80f93189efd91c72d96c9fdf01 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Oct 2023 11:03:11 -0600 Subject: [PATCH 1556/2067] Add unit tester for get_isosplit function --- python/ctsm/site_and_regional/run_neon.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index b0ccc4b687..41719adf33 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -71,7 +71,8 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm import add_cime_to_path -from ctsm.path_utils import path_to_ctsm_root, parse_isoduration +from ctsm.path_utils import path_to_ctsm_root +from ctsm.utils import parse_isoduration from ctsm.download_utils import download_file import CIME.build as build From 017b021c4bff1b3592e7b067083b210868a437b1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Oct 2023 11:03:58 -0600 Subject: [PATCH 1557/2067] Add unit tester for get_isosplit function --- python/ctsm/test/test_unit_iso_utils.py | 38 +++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100755 python/ctsm/test/test_unit_iso_utils.py diff --git a/python/ctsm/test/test_unit_iso_utils.py b/python/ctsm/test/test_unit_iso_utils.py new file mode 100755 index 0000000000..c087b23f64 --- /dev/null +++ b/python/ctsm/test/test_unit_iso_utils.py @@ -0,0 +1,38 @@ +#!/usr/bin/env python3 + +"""Unit tests for the iso functions in utils +""" + +import unittest +import os + +from ctsm import unit_testing +from ctsm.utils import parse_isoduration, get_isosplit + +# Allow names that pylint doesn't like, because otherwise I find it hard +# to make readable unit test names +# pylint: disable=invalid-name + + +class TestIsoUtils(unittest.TestCase): + """Tests of iso functions in utils""" + + def test_iso_split_for_Year(self): + """ + Tests the get_isosplit function for a strings with Years + """ + iso_string = "0Y" + self.assertEqual( get_isosplit(iso_string, "Y"), ("0", "") ) + iso_string = "1Y" + self.assertEqual( get_isosplit(iso_string, "Y"), ("1", "") ) + iso_string = "4Y" + self.assertEqual( get_isosplit(iso_string, "Y"), ("4", "") ) + iso_string = "100Y" + self.assertEqual( get_isosplit(iso_string, "Y"), ("100", "") ) + iso_string = "999999Y" + self.assertEqual( get_isosplit(iso_string, "Y"), ("999999", "") ) + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() From 3830a6de2b10cbe3a9e2a864fb16b426639a7abc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 4 Oct 2023 11:21:09 -0600 Subject: [PATCH 1558/2067] Add a test of parse_isoduration and run it in black --- python/ctsm/test/test_unit_iso_utils.py | 27 +++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/python/ctsm/test/test_unit_iso_utils.py b/python/ctsm/test/test_unit_iso_utils.py index c087b23f64..c58beef52e 100755 --- a/python/ctsm/test/test_unit_iso_utils.py +++ b/python/ctsm/test/test_unit_iso_utils.py @@ -4,7 +4,6 @@ """ import unittest -import os from ctsm import unit_testing from ctsm.utils import parse_isoduration, get_isosplit @@ -22,15 +21,31 @@ def test_iso_split_for_Year(self): Tests the get_isosplit function for a strings with Years """ iso_string = "0Y" - self.assertEqual( get_isosplit(iso_string, "Y"), ("0", "") ) + self.assertEqual(get_isosplit(iso_string, "Y"), ("0", "")) iso_string = "1Y" - self.assertEqual( get_isosplit(iso_string, "Y"), ("1", "") ) + self.assertEqual(get_isosplit(iso_string, "Y"), ("1", "")) iso_string = "4Y" - self.assertEqual( get_isosplit(iso_string, "Y"), ("4", "") ) + self.assertEqual(get_isosplit(iso_string, "Y"), ("4", "")) iso_string = "100Y" - self.assertEqual( get_isosplit(iso_string, "Y"), ("100", "") ) + self.assertEqual(get_isosplit(iso_string, "Y"), ("100", "")) iso_string = "999999Y" - self.assertEqual( get_isosplit(iso_string, "Y"), ("999999", "") ) + self.assertEqual(get_isosplit(iso_string, "Y"), ("999999", "")) + + def test_parse_isoduration_for_Years(self): + """ + Tests the parse_isoduration function for iso strings with Years + """ + days_in_year = 365 + iso_string = "0Y" + self.assertEqual(parse_isoduration(iso_string), 0) + iso_string = "1Y" + self.assertEqual(parse_isoduration(iso_string), days_in_year) + iso_string = "4Y" + self.assertEqual(parse_isoduration(iso_string), 4 * days_in_year) + iso_string = "100Y" + self.assertEqual(parse_isoduration(iso_string), 100 * days_in_year) + iso_string = "999999Y" + self.assertEqual(parse_isoduration(iso_string), 999999 * days_in_year) if __name__ == "__main__": From 4b6874eec19b41c540bfa3587a8ef95c56c04962 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 4 Oct 2023 16:06:10 -0600 Subject: [PATCH 1559/2067] add unit tests --- .../test_unit_modify_singlept_site_neon.py | 109 ++++++++++++++++++ .../ctsm/test/test_unit_neon_surf_wrapper.py | 42 +++++++ python/ctsm/test/test_unit_run_neon.py | 60 ++++++++++ 3 files changed, 211 insertions(+) create mode 100755 python/ctsm/test/test_unit_modify_singlept_site_neon.py create mode 100755 python/ctsm/test/test_unit_neon_surf_wrapper.py create mode 100755 python/ctsm/test/test_unit_run_neon.py diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py new file mode 100755 index 0000000000..f67bf2ecc8 --- /dev/null +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -0,0 +1,109 @@ +#!/usr/bin/env python3 +""" +Unit tests for modify_singlept_site_neon + +You can run this by: + python -m unittest test_unit_modify_singlept_site_neon.py +""" + +import unittest +import tempfile +import shutil +import configparser +import argparse +import os +import sys +from getpass import getuser +from datetime import date + +# -- add python/ctsm to path (needed if we want to run the test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +# pylint: disable=wrong-import-position +from ctsm import unit_testing +from ctsm.site_and_regional.modify_singlept_site_neon import get_parser, get_neon, find_surffile, find_soil_structure, update_metadata, update_time_tag, sort_print_soil_layers, check_neon_time, download_file, fill_interpolate +from ctsm.path_utils import path_to_ctsm_root + +# pylint: disable=invalid-name + + +class TestModifySingleptSiteNeon(unittest.TestCase): + """ + Basic class for testing modify_singlept_site_neon.py. + """ + + def setUp(self): + """ + Make /_tempdir for use by these tests. + Check tempdir for history files + """ + self._tempdir = tempfile.mkdtemp() + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_get_neon(self): + """ + Test to see if neon data for valid site name is found + """ + site_name = "ABBY" + neon_dir = self._tempdir + file = get_neon(neon_dir, site_name) + self.assertEqual(file.split('/')[-1][:4], 'ABBY', "CSV file did not download as expected") + + def test_get_neon_false_site(self): + """ + Test to see if neon data for invalid site name is found + """ + site_name = "ABY" + neon_dir = self._tempdir + with self.assertRaises(SystemExit): + get_neon(neon_dir, site_name) + + def test_find_surffile(self): + """ + Test that surface file does not exist in tempdir and raises system exit error + """ + surf_dir = self._tempdir + site_name = "BART" + pft_16 = True + with self.assertRaises(SystemExit): + find_surffile(surf_dir, site_name, pft_16) + # TODO: it would be useful to also include an example where the surface file is actually found or correctly searched for + # Is there a default surface data file directory we can point to? + + #def test_find_soil_structure(self): + # """ + # Test + # """ + # find_soil_structure() + # TODO: need file to use in test + + #def test_update_metadata(self): + # TODO: do we have a surface data file that we can put in tempdir to update? + # update_metadata(nc, surf_file, neon_file, zb_flag) + + def test_update_time_tag(self): + """ + Test that file ending is updated + """ + self.assertEqual(update_time_tag("test_YYMMDD.nc")[-9:-3], date.today().strftime("%y%m%d"), "File ending not as expected") + + def test_check_neon_time(self): + """ + Test that dictionary containing last modified information is correctly downloaded + """ + last_abby_download = check_neon_time()['https://storage.neonscience.org/neon-ncar/NEON/surf_files/v1/ABBY_surfaceData.csv'] + self.assertEqual(len(last_abby_download), 19, "last ABBY download has unexpected date format or does not exist") + # TODO: this checks that data is not pulled from before 2021; we may want to update this occassionally or find another way to check data is actually newest? + self.assertGreater(int(last_abby_download[:4]), 2021, "ABBY download is older than expected") + + # TODO: test sort_print_soil_layers, fill_interpolate, find_soil_structure, and update_metadata + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_unit_neon_surf_wrapper.py b/python/ctsm/test/test_unit_neon_surf_wrapper.py new file mode 100755 index 0000000000..f46cbdb47c --- /dev/null +++ b/python/ctsm/test/test_unit_neon_surf_wrapper.py @@ -0,0 +1,42 @@ +#!/usr/bin/env python3 +""" +Unit tests for neon_surf_wrapper + +You can run this by: + python -m unittest test_unit_neon_surf_wrapper.py +""" + +import unittest +import configparser +import argparse +import os +import sys + +# -- add python/ctsm to path (needed if we want to run the test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +# pylint: disable=wrong-import-position +from ctsm import unit_testing +from ctsm.site_and_regional.neon_surf_wrapper import get_parser +from ctsm.path_utils import path_to_ctsm_root + +# pylint: disable=invalid-name + + +class TestNeonSurfWrapper(unittest.TestCase): + """ + Basic class for testing neon_surf_wrapper.py. + """ + + def test_parser(self): + """ + Test that parser has same defaults as expected + """ + + self.assertEqual(get_parser().argument_default, None, "Parser not working as expected") + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_unit_run_neon.py b/python/ctsm/test/test_unit_run_neon.py new file mode 100755 index 0000000000..d3ceb52a3f --- /dev/null +++ b/python/ctsm/test/test_unit_run_neon.py @@ -0,0 +1,60 @@ +#!/usr/bin/env python3 +""" +Unit tests for run_neon + +You can run this by: + python -m unittest test_unit_run_neon.py +""" + +import unittest +import configparser +import argparse +import os +import sys +# -- add python/ctsm to path (needed if we want to run the test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +# pylint: disable=wrong-import-position +from ctsm import unit_testing +from ctsm.site_and_regional.run_neon import check_neon_listing +from ctsm.path_utils import path_to_ctsm_root + +# pylint: disable=invalid-name + + +class TestRunNeon(unittest.TestCase): + """ + Basic class for testing run_neon.py. + """ + + #def setUp(self): + # sys.argv = ["subset_data", "point", "--create-surface"] + # DEFAULTS_FILE = os.path.join(os.getcwd(), "ctsm/test/testinputs/default_data.cfg") + # self.parser = get_parser() + # self.args = self.parser.parse_args() + # self.cesmroot = path_to_ctsm_root() + # self.defaults = configparser.ConfigParser() + # self.defaults.read(os.path.join(self.cesmroot, "tools/site_and_regional", DEFAULTS_FILE)) + + def test_check_neon_listing(self): + """ + Test that neon listing is available for valid sites + """ + valid_neon_sites = ['ABBY', 'BART'] + available_list = check_neon_listing(valid_neon_sites) + self.assertEqual(available_list[0].name, 'ABBY', "available list of actual sites not as expected") + self.assertEqual(available_list[1].name, 'BART', "available list of actual sites not as expected") + + + def test_check_neon_listing_misspelled(self): + """ + Test that neon listing is not available for invalid sites + """ + valid_neon_sites = ['ABY', 'BRT'] + available_list = check_neon_listing(valid_neon_sites) + self.assertEqual(available_list, [], "available list of incorrect dummy site not as expected") + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() From 528d4f05c84bee4e2de72c2c481ff31f3d305ccd Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 5 Oct 2023 08:32:21 -0600 Subject: [PATCH 1560/2067] remove hard-coded neon site list & use dir structure instead, similarly to in run_neon --- .../modify_singlept_site_neon.py | 54 ++----------------- 1 file changed, 4 insertions(+), 50 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index a33323ed7a..a131671a6e 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -31,7 +31,6 @@ """ # TODO (NS) # --[] If subset file not found run subset_data.py -# --[] List of valid neon sites for all scripts come from one place. # --[] Download files only when available. # Import libraries @@ -52,60 +51,15 @@ from datetime import date from getpass import getuser +from ctsm.path_utils import path_to_ctsm_root myname = getuser() # -- valid neon sites -valid_neon_sites = [ - "ABBY", - "BARR", - "BART", - "BLAN", - "BONA", - "CLBJ", - "CPER", - "DCFS", - "DEJU", - "DELA", - "DSNY", - "GRSM", - "GUAN", - "HARV", - "HEAL", - "JERC", - "JORN", - "KONA", - "KONZ", - "LAJA", - "LENO", - "MLBS", - "MOAB", - "NIWO", - "NOGP", - "OAES", - "ONAQ", - "ORNL", - "OSBS", - "PUUM", - "RMNP", - "SCBI", - "SERC", - "SJER", - "SOAP", - "SRER", - "STEI", - "STER", - "TALL", - "TEAK", - "TOOL", - "TREE", - "UKFS", - "UNDE", - "WOOD", - "WREF", - "YELL", -] +valid_neon_sites = glob.glob( + os.path.join(path_to_ctsm_root(), "cime_config", "usermods_dirs", "NEON", "[!d]*") + ) def get_parser(): From 0bc3f00115d86d026a977918661c93779b3b19f9 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 5 Oct 2023 08:41:15 -0600 Subject: [PATCH 1561/2067] black reformatting --- .../modify_singlept_site_neon.py | 5 +-- python/ctsm/site_and_regional/run_neon.py | 1 + .../test_unit_modify_singlept_site_neon.py | 44 ++++++++++++++----- .../ctsm/test/test_unit_neon_surf_wrapper.py | 2 +- python/ctsm/test/test_unit_run_neon.py | 23 ++++++---- 5 files changed, 53 insertions(+), 22 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index a131671a6e..1ddcd949a8 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -58,8 +58,8 @@ # -- valid neon sites valid_neon_sites = glob.glob( - os.path.join(path_to_ctsm_root(), "cime_config", "usermods_dirs", "NEON", "[!d]*") - ) + os.path.join(path_to_ctsm_root(), "cime_config", "usermods_dirs", "NEON", "[!d]*") +) def get_parser(): @@ -477,7 +477,6 @@ def fill_interpolate(f2, var, method): def main(): - args = get_parser().parse_args() # -- debugging option diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 41719adf33..3f540845e4 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -328,6 +328,7 @@ def get_parser(args, description, valid_neon_sites): args.user_version, ) + class NeonSite: """ A class for encapsulating neon sites. diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index f67bf2ecc8..d1d738ffa8 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -22,7 +22,18 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing -from ctsm.site_and_regional.modify_singlept_site_neon import get_parser, get_neon, find_surffile, find_soil_structure, update_metadata, update_time_tag, sort_print_soil_layers, check_neon_time, download_file, fill_interpolate +from ctsm.site_and_regional.modify_singlept_site_neon import ( + get_parser, + get_neon, + find_surffile, + find_soil_structure, + update_metadata, + update_time_tag, + sort_print_soil_layers, + check_neon_time, + download_file, + fill_interpolate, +) from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name @@ -50,10 +61,10 @@ def test_get_neon(self): """ Test to see if neon data for valid site name is found """ - site_name = "ABBY" + site_name = "ABBY" neon_dir = self._tempdir file = get_neon(neon_dir, site_name) - self.assertEqual(file.split('/')[-1][:4], 'ABBY', "CSV file did not download as expected") + self.assertEqual(file.split("/")[-1][:4], "ABBY", "CSV file did not download as expected") def test_get_neon_false_site(self): """ @@ -76,34 +87,47 @@ def test_find_surffile(self): # TODO: it would be useful to also include an example where the surface file is actually found or correctly searched for # Is there a default surface data file directory we can point to? - #def test_find_soil_structure(self): + # def test_find_soil_structure(self): # """ # Test # """ # find_soil_structure() # TODO: need file to use in test - #def test_update_metadata(self): - # TODO: do we have a surface data file that we can put in tempdir to update? + # def test_update_metadata(self): + # TODO: do we have a surface data file that we can put in tempdir to update? # update_metadata(nc, surf_file, neon_file, zb_flag) def test_update_time_tag(self): """ Test that file ending is updated """ - self.assertEqual(update_time_tag("test_YYMMDD.nc")[-9:-3], date.today().strftime("%y%m%d"), "File ending not as expected") + self.assertEqual( + update_time_tag("test_YYMMDD.nc")[-9:-3], + date.today().strftime("%y%m%d"), + "File ending not as expected", + ) def test_check_neon_time(self): """ Test that dictionary containing last modified information is correctly downloaded """ - last_abby_download = check_neon_time()['https://storage.neonscience.org/neon-ncar/NEON/surf_files/v1/ABBY_surfaceData.csv'] - self.assertEqual(len(last_abby_download), 19, "last ABBY download has unexpected date format or does not exist") + last_abby_download = check_neon_time()[ + "https://storage.neonscience.org/neon-ncar/NEON/surf_files/v1/ABBY_surfaceData.csv" + ] + self.assertEqual( + len(last_abby_download), + 19, + "last ABBY download has unexpected date format or does not exist", + ) # TODO: this checks that data is not pulled from before 2021; we may want to update this occassionally or find another way to check data is actually newest? - self.assertGreater(int(last_abby_download[:4]), 2021, "ABBY download is older than expected") + self.assertGreater( + int(last_abby_download[:4]), 2021, "ABBY download is older than expected" + ) # TODO: test sort_print_soil_layers, fill_interpolate, find_soil_structure, and update_metadata + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() diff --git a/python/ctsm/test/test_unit_neon_surf_wrapper.py b/python/ctsm/test/test_unit_neon_surf_wrapper.py index f46cbdb47c..0092bdb91c 100755 --- a/python/ctsm/test/test_unit_neon_surf_wrapper.py +++ b/python/ctsm/test/test_unit_neon_surf_wrapper.py @@ -33,7 +33,7 @@ def test_parser(self): """ Test that parser has same defaults as expected """ - + self.assertEqual(get_parser().argument_default, None, "Parser not working as expected") diff --git a/python/ctsm/test/test_unit_run_neon.py b/python/ctsm/test/test_unit_run_neon.py index d3ceb52a3f..a8031fff1d 100755 --- a/python/ctsm/test/test_unit_run_neon.py +++ b/python/ctsm/test/test_unit_run_neon.py @@ -11,6 +11,7 @@ import argparse import os import sys + # -- add python/ctsm to path (needed if we want to run the test stand-alone) _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) @@ -28,7 +29,7 @@ class TestRunNeon(unittest.TestCase): Basic class for testing run_neon.py. """ - #def setUp(self): + # def setUp(self): # sys.argv = ["subset_data", "point", "--create-surface"] # DEFAULTS_FILE = os.path.join(os.getcwd(), "ctsm/test/testinputs/default_data.cfg") # self.parser = get_parser() @@ -37,23 +38,29 @@ class TestRunNeon(unittest.TestCase): # self.defaults = configparser.ConfigParser() # self.defaults.read(os.path.join(self.cesmroot, "tools/site_and_regional", DEFAULTS_FILE)) - def test_check_neon_listing(self): + def test_check_neon_listing(self): """ Test that neon listing is available for valid sites """ - valid_neon_sites = ['ABBY', 'BART'] + valid_neon_sites = ["ABBY", "BART"] available_list = check_neon_listing(valid_neon_sites) - self.assertEqual(available_list[0].name, 'ABBY', "available list of actual sites not as expected") - self.assertEqual(available_list[1].name, 'BART', "available list of actual sites not as expected") - + self.assertEqual( + available_list[0].name, "ABBY", "available list of actual sites not as expected" + ) + self.assertEqual( + available_list[1].name, "BART", "available list of actual sites not as expected" + ) def test_check_neon_listing_misspelled(self): """ Test that neon listing is not available for invalid sites """ - valid_neon_sites = ['ABY', 'BRT'] + valid_neon_sites = ["ABY", "BRT"] available_list = check_neon_listing(valid_neon_sites) - self.assertEqual(available_list, [], "available list of incorrect dummy site not as expected") + self.assertEqual( + available_list, [], "available list of incorrect dummy site not as expected" + ) + if __name__ == "__main__": unit_testing.setup_for_tests() From 30ab529d8fe8fe01f0faf11a23913d0a2e392a4e Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 5 Oct 2023 08:45:32 -0600 Subject: [PATCH 1562/2067] Updating .git-blame-ignore-revs --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 1b7a0d75b3..49d3229d8e 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -14,3 +14,4 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 +0bc3f00115d86d026a977918661c93779b3b19f9 From 807ca5c51979f6b4d26103d4b18d978fe7e67dda Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 5 Oct 2023 09:30:10 -0600 Subject: [PATCH 1563/2067] addressed some pylint suggestions --- .../modify_singlept_site_neon.py | 23 +++-- python/ctsm/site_and_regional/run_neon.py | 91 +++++++++++++------ 2 files changed, 75 insertions(+), 39 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index 1ddcd949a8..465fcda25c 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -36,21 +36,20 @@ # Import libraries from __future__ import print_function +import argparse +from datetime import date +from getpass import getuser +import glob +import logging import os import sys -import glob -import argparse import requests -import logging import numpy as np import pandas as pd import xarray as xr from packaging import version -from datetime import date -from getpass import getuser - from ctsm.path_utils import path_to_ctsm_root myname = getuser() @@ -487,11 +486,12 @@ def main(): pdvers = pd.__version__ if version.parse(pdvers) < version.parse("1.1.0"): sys.exit( - "The pandas version in your python environment is too old, update to a newer version of pandas (>=1.1.0): version=%s", + """The pandas version in your python environment is too old, + update to a newer version of pandas (>=1.1.0): version=%s""", pdvers, ) - file_time = check_neon_time() + # file_time = check_neon_time() # -- specify site from which to extract data site_name = args.site_name @@ -502,7 +502,7 @@ def main(): # -- directory structure current_dir = os.getcwd() - parent_dir = os.path.dirname(current_dir) + # parent_dir = os.path.dirname(current_dir) clone_dir = os.path.abspath(os.path.join(__file__, "../../../..")) neon_dir = os.path.join(clone_dir, "neon_surffiles") @@ -538,7 +538,7 @@ def main(): soil_mid = 0.5 * (soil_bot - soil_top) + soil_top # print ("Cumulative sum of soil bottom depths :", sum(soil_bot)) - obs_top = df["biogeoTopDepth"] / 100 + # obs_top = df["biogeoTopDepth"] / 100 obs_bot = df["biogeoBottomDepth"] / 100 # -- Mapping surface dataset and neon soil levels @@ -587,8 +587,7 @@ def main(): # -- Check to make sure the rounded oc is not higher than carbon_tot. # -- Use carbon_tot if estimated_oc is bigger than carbon_tot. - if estimated_oc > carbon_tot: - estimated_oc = carbon_tot + estimated_oc = min(estimated_oc, carbon_tot) layer_depth = ( df["biogeoBottomDepth"][bin_index[soil_lev]] - df["biogeoTopDepth"][bin_index[soil_lev]] diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 3f540845e4..59ddf3f2eb 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -51,36 +51,30 @@ # Import libraries - +import argparse +import datetime +import glob +import logging import os +import re +import shutil import sys import time -import shutil -import logging -import requests -import argparse -import re -import subprocess import pandas as pd -import glob -import datetime -from getpass import getuser # Get the ctsm util tools and then the cime tools. _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) -from ctsm import add_cime_to_path +from CIME import build +from CIME.case import Case +from CIME.utils import safe_copy, expect, symlink_force + from ctsm.path_utils import path_to_ctsm_root from ctsm.utils import parse_isoduration from ctsm.download_utils import download_file -import CIME.build as build from standard_script_setup import * -from CIME.case import Case -from CIME.utils import safe_copy, expect, symlink_force, run_cmd_no_fail -from argparse import RawTextHelpFormatter -from CIME.locked_files import lock_file, unlock_file logger = logging.getLogger(__name__) @@ -296,7 +290,8 @@ def get_parser(args, description, valid_neon_sites): elif args.run_type == "postad": run_length = "100Y" else: - # The transient run length is set by cdeps atm buildnml to the last date of the available tower data + # The transient run length is set by cdeps atm buildnml to + # the last date of the available tower data # this value is not used run_length = "4Y" else: @@ -307,7 +302,8 @@ def get_parser(args, description, valid_neon_sites): if args.base_case_root: base_case_root = os.path.abspath(args.base_case_root) - # Reduce output level for this script unless --debug or --verbose is provided on the command line + # Reduce output level for this script unless --debug or + # --verbose is provided on the command line if not args.debug and not args.verbose: root_logger = logging.getLogger() root_logger.setLevel(logging.WARN) @@ -418,12 +414,12 @@ def build_base_case( match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( - match == None, + match is None, "Existing base case is a historical type and should not be -- rerun with the --orverwrite option", ) else: expect( - match != None, + match is not None, "Existing base case should be a historical type and is not -- rerun with the --orverwrite option", ) # reset the case @@ -445,6 +441,9 @@ def build_base_case( return case_path def diff_month(self): + """ + Determine difference between two dates in months + """ d1 = datetime.datetime(self.end_year, self.end_month, 1) d2 = datetime.datetime(self.start_year, self.start_month, 1) return (d1.year - d2.year) * 12 + d1.month - d2.month @@ -461,8 +460,7 @@ def get_batch_query(self, case): if case.get_value("BATCH_SYSTEM") == "none": return "none" - else: - return case.get_value("batch_query") + return case.get_value("batch_query") def run_case( self, @@ -477,6 +475,33 @@ def run_case( rerun=False, experiment=False, ): + + """ + Run case. + + Args: + self + base_case_root: str, opt + file path of base case + run_type: str, opt + transient, post_ad, or ad case, default transient + prism: bool, opt + if True, use PRISM precipitation, default False + run_length: str, opt + length of run, default '4Y' + user_version: str, opt + default 'latest' + overwrite: bool, opt + default False + setup_only: bool, opt + default False; if True, set up but do not run case + no_batch: bool, opt + default False + rerun: bool, opt + default False + experiment: str, opt + name of experiment, default False + """ user_mods_dirs = [ os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name) ] @@ -492,7 +517,7 @@ def run_case( print("using this version:", version) - if experiment != None: + if experiment is not None: self.name = self.name + "." + experiment case_root = os.path.abspath(os.path.join(base_case_root, "..", self.name + "." + run_type)) @@ -509,12 +534,12 @@ def run_case( match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( - match == None, + match is None, "Existing base case is a historical type and should not be -- rerun with the --orverwrite option", ) else: expect( - match != None, + match is not None, "Existing base case should be a historical type and is not -- rerun with the --orverwrite option", ) if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): @@ -552,7 +577,8 @@ def run_case( with Case(case_root, read_only=False) as case: if run_type != "transient": - # in order to avoid the complication of leap years we always set the run_length in units of days. + # in order to avoid the complication of leap years, + # we always set the run_length in units of days. case.set_value("STOP_OPTION", "ndays") case.set_value("REST_OPTION", "end") case.set_value("CONTINUE_RUN", False) @@ -605,6 +631,9 @@ def run_case( print(f"Use {batch_query} to check its run status") def set_ref_case(self, case): + """ + Set an existing case as the reference case, eg for use with spinup. + """ rundir = case.get_value("RUNDIR") case_root = case.get_value("CASEROOT") if case_root.endswith(".postad"): @@ -650,6 +679,10 @@ def set_ref_case(self, case): return True def modify_user_nl(self, case_root, run_type, rundir): + """ + Modify user namelist. If transient, include finidat in user_nl; + Otherwise, adjust user_nl to include different mfilt, nhtfrq, and variables in hist_fincl1. + """ user_nl_fname = os.path.join(case_root, "user_nl_clm") user_nl_lines = None if run_type == "transient": @@ -726,7 +759,7 @@ def parse_neon_listing(listing_file, valid_neon_sites): tmp_df = tmp_df[tmp_df[9].str.contains("\d\d\d\d-\d\d.nc")] # -- find all the data versions - versions = tmp_df[7].unique() + # versions = tmp_df[7].unique() # print ("all versions available for ", site_name,":", *versions) latest_version = tmp_df[7].iloc[-1] # print ("latests version available for ", site_name,":", latest_version) @@ -767,6 +800,10 @@ def parse_neon_listing(listing_file, valid_neon_sites): def main(description): + """ + Determine valid neon sites. Make an output directory if it does not exist. + Loop through requested sites and run CTSM at that site. + """ cesmroot = path_to_ctsm_root() # Get the list of supported neon sites from usermods valid_neon_sites = glob.glob( From 0207bc98dd5c75cd69a0e788bc53e41093712f5c Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 5 Oct 2023 09:32:04 -0600 Subject: [PATCH 1564/2067] black reformatting --- python/ctsm/site_and_regional/run_neon.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 59ddf3f2eb..987883fe93 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -475,7 +475,6 @@ def run_case( rerun=False, experiment=False, ): - """ Run case. @@ -801,7 +800,7 @@ def parse_neon_listing(listing_file, valid_neon_sites): def main(description): """ - Determine valid neon sites. Make an output directory if it does not exist. + Determine valid neon sites. Make an output directory if it does not exist. Loop through requested sites and run CTSM at that site. """ cesmroot = path_to_ctsm_root() From a6c3c64d16fe745f17e98661a1638ed8ef0037c0 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 5 Oct 2023 10:22:57 -0600 Subject: [PATCH 1565/2067] Updating .git-blame-ignore-revs --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 49d3229d8e..c520df4357 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -11,6 +11,7 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb 4ee49e3e516ca7dee5df378f65664f93a7db4415 +0207bc98dd5c75cd69a0e788bc53e41093712f5c # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From c8d6754f427b3679a31df0e27986d1a15ee309d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 5 Oct 2023 16:00:15 -0600 Subject: [PATCH 1566/2067] Removed a TODO. --- src/biogeochem/CNPhenologyMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 88694f2cca..f78bfa449d 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2688,7 +2688,6 @@ function DaysPastPlanting(idop, jday_in) else ! As long as crops have at most a 365-day growing season, using get_curr_days_per_year() ! should give the same result of this function as using get_prev_days_per_year(). - ! TODO: Test identicality when using get_prev_days_per_year(). DaysPastPlanting = jday - idop + get_curr_days_per_year() end if From 751043117e3fbd95b76a6e7c0c523ea766cc5a73 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 5 Oct 2023 16:01:03 -0600 Subject: [PATCH 1567/2067] Removed an incorrect comment. --- src/soilbiogeochem/TillageMod.F90 | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 0ce3c4f96e..bd89d8f083 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -186,8 +186,6 @@ subroutine get_tillage_multipliers(tillage_mults, idop) ! ! Modified by Sam Rabin to fix a bug where idpp wasn't actually used, which ! would affect growing seasons that crossed over into a new calendar year. - ! Also avoids day=1 in last timestep of year by using DaysPastPlanting(), which - ! uses get_prev_calday() instead of get_curr_calday(). ! Previous behavior can be requested with namelist variable use_original_tillage_phases. ! ! Original code had two versions depending on cell's GDP, but this seems to From d565176e94970b9736b8d55fe9c94f87a1e6d292 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 5 Oct 2023 16:06:06 -0600 Subject: [PATCH 1568/2067] Do not till generic crops. --- src/soilbiogeochem/TillageMod.F90 | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index bd89d8f083..106db7d1ab 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -284,7 +284,7 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) ! Written by Sam Rabin, based on original code by Michael Graham. ! ! !USES - use pftconMod , only : nc3crop + use pftconMod , only : npcropmin use clm_varcon, only : zisoi, dzsoi_decomp use landunit_varcon , only : istcrop use PatchType , only : patch @@ -315,7 +315,12 @@ subroutine get_apply_tillage_multipliers(idop, c, j, decomp_k) sumwt = 0.0_r8 do p = col%patchi(c),col%patchf(c) if (patch%active(p) .and. patch%wtcol(p) /= 0._r8) then - call get_tillage_multipliers(tillage_mults_1patch, idop(p)) + if (patch%itype(p) < npcropmin) then + ! Do not till generic crops + tillage_mults_1patch(:) = 1._r8 + else + call get_tillage_multipliers(tillage_mults_1patch, idop(p)) + end if tillage_mults = tillage_mults + tillage_mults_1patch * patch%wtcol(p) sumwt = sumwt + patch%wtcol(p) end if From b86402ecbdea67366609dbf384f4bd0d3a109080 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 5 Oct 2023 16:09:35 -0600 Subject: [PATCH 1569/2067] Warn instead of fail when trying to enable tillage. --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 538cc59dc9..c2425ab265 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2184,7 +2184,7 @@ sub setup_logic_tillage { my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); if ( $tillage_mode ne "" && $tillage_mode ne "off") { - $log->fatal_error( "Tillage has not yet been scientifically tested and so may not be enabled." ); + $log->warning( "Tillage has not yet been scientifically tested." ); } if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." ); From 1a3a8b70074812981c6750bb0ba9441face95c6c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 5 Oct 2023 16:10:19 -0600 Subject: [PATCH 1570/2067] Delete add_tillage_to_paramsfile.py. --- tillage-tmp/add_tillage_to_paramsfile.py | 147 ----------------------- 1 file changed, 147 deletions(-) delete mode 100644 tillage-tmp/add_tillage_to_paramsfile.py diff --git a/tillage-tmp/add_tillage_to_paramsfile.py b/tillage-tmp/add_tillage_to_paramsfile.py deleted file mode 100644 index 1c6744f38f..0000000000 --- a/tillage-tmp/add_tillage_to_paramsfile.py +++ /dev/null @@ -1,147 +0,0 @@ -# %% - -import xarray as xr -import numpy as np -import os -import subprocess - -file_in = "/Users/Shared/CESM_inputdata/lnd/clm2/paramdata/ctsm51_params.c211112.nc" -file_out = "/Users/sam/Documents/git_repos/CTSM_myfork/ctsm51_params.c211112.tillage.nc" - -# Get git info -thisDir = os.path.dirname(__file__) -git_status = subprocess.run( - ["git", "status"], - capture_output=True, -) -git_status = git_status.stdout.decode() -repo_is_clean = "working tree clean" in git_status -if not repo_is_clean: - print("WARNING: Repo not clean; will not save params file.") - print(git_status) -git_log = subprocess.run( - ["git", "log", "-1"], - capture_output=True, -) -git_log = git_log.stdout.decode() - - -# %% Set up dimensions - -ds0 = xr.open_dataset(file_in) -ntill_intensities_max = 2 -ndecomp_pools_max = ds0.dims["ndecomp_pools_max"] -ntill_stages_max = 3 -tillage_shape_ips = (ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) -tillage_shape_ps = (ndecomp_pools_max, ntill_stages_max) - - -# %% Fill CENTURY array - -# Define pool indices -i_litr_min = 0 # 1 in FORTRAN, but Python is 0-indexed -i_met_lit = i_litr_min -i_cel_lit = i_met_lit + 1 -i_lig_lit = i_cel_lit + 1 -i_act_som = i_lig_lit + 1 -i_slo_som = i_act_som + 1 -i_pas_som = i_slo_som + 1 - -tillage_century = np.full(tillage_shape_ips, 1.0) - -tillage_century_lo = np.full(tillage_shape_ps, 1.0) -tillage_century_lo[i_act_som,:] = np.array([1.0, 1.0, 1.0]) -tillage_century_lo[i_slo_som,:] = np.array([3.0, 1.6, 1.3]) -tillage_century_lo[i_pas_som,:] = np.array([3.0, 1.6, 1.3]) -tillage_century_lo[i_cel_lit,:] = np.array([1.5, 1.5, 1.1]) -tillage_century_lo[i_lig_lit,:] = np.array([1.5, 1.5, 1.1]) -tillage_century[0,:,:] = tillage_century_lo - -tillage_century_hi = np.full(tillage_shape_ps, 1.0) -tillage_century_hi[i_act_som,:] = np.array([1.2, 1.0, 1.0]) -tillage_century_hi[i_slo_som,:] = np.array([4.8, 3.5, 2.5]) -tillage_century_hi[i_pas_som,:] = np.array([4.8, 3.5, 2.5]) -tillage_century_hi[i_cel_lit,:] = np.array([1.8, 1.5, 1.1]) -tillage_century_hi[i_lig_lit,:] = np.array([1.8, 1.5, 1.1]) -tillage_century[1,:,:] = tillage_century_hi - - -# %% Fill MIMICS array - -# Define pool indices -i_litr_min = 1 -i_met_lit = i_litr_min -i_str_lit = i_met_lit + 1 -i_avl_som = i_str_lit + 1 -i_chem_som = i_avl_som + 1 -i_phys_som = i_chem_som + 1 - -tillage_mimics = np.full(tillage_shape_ips, 1.0) - -tillage_mimics[:,i_avl_som,:] = tillage_century[:,i_act_som,:] -tillage_mimics[:,i_chem_som,:] = tillage_century[:,i_slo_som,:] -tillage_mimics[:,i_phys_som,:] = tillage_century[:,i_pas_som,:] -if not np.array_equal(tillage_century[:,i_cel_lit,:], tillage_century[:,i_lig_lit,:]): - raise RuntimeError("How to combine 2 CENTURY litter pools into 1 MIMICS litter pool?") -tillage_mimics[:,i_str_lit,:] = tillage_century[:,i_cel_lit,:] - - -# %% Make DataArrays - -def make_dataarray(np_array, decomp_model, ntill_intensities_max, ndecomp_pools_max, ntill_stages_max): - intensities_dim = xr.IndexVariable( - dims = "ntill_intensities_max", - data = np.arange(ntill_intensities_max), - ) - pools_dim = xr.IndexVariable( - dims = "ndecomp_pools_max", - data = np.arange(ndecomp_pools_max), - ) - stages_dim = xr.IndexVariable( - dims = "ntill_stages_max", - data = np.arange(ntill_stages_max), - ) - - # Name DataArray - if decomp_model.lower() == "mimics": - da_name = "mimics" - elif decomp_model.lower() == "century": - da_name = "bgc" - da_name += "_till_decompk_multipliers" - - da = xr.DataArray( - data = np_array, - dims = { - "ntill_intensities_max": intensities_dim, - "ndecomp_pools_max": pools_dim, - "ntill_stages_max": stages_dim - }, - name = da_name, - attrs = { - "long_name": f"Value by which decomp_k should be multiplied during tillage with {decomp_model} soil", - "units": "unitless", - } - ) - return da - -tillage_century_da = make_dataarray( - tillage_century, "CENTURY", - ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) -tillage_mimics_da = make_dataarray( - tillage_mimics, "MIMICS", - ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) - - -# %% Save to output file - -if not repo_is_clean: - raise RuntimeError("Clean up git repo before trying to save!") - -ds1 = ds0.copy() -ds0.close() - -ds1[tillage_century_da.name] = tillage_century_da -ds1[tillage_mimics_da.name] = tillage_mimics_da -ds1.attrs['latest_git_log'] = git_log - -ds1.to_netcdf(file_out, format="NETCDF3_CLASSIC") \ No newline at end of file From ae56384e45f44619109ce2d2651e6ac01fc3221c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 5 Oct 2023 16:24:36 -0600 Subject: [PATCH 1571/2067] Use ntill_intensities_max; set to private. --- src/soilbiogeochem/TillageMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 106db7d1ab..60afe52e14 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -21,7 +21,6 @@ module TillageMod public :: get_fraction_tilled ! !PUBLIC DATA MEMBERS character(len=CS), public :: tillage_mode ! off, low, high - integer, parameter, public :: ntill_intensities_max = 2 ! ! !PRIVATE DATA MEMBERS integer :: tillage_intensity @@ -31,6 +30,7 @@ module TillageMod logical :: use_original_tillage_phases ! Use buggy tillage phase determination? real(r8), pointer :: tillage_mults_allphases(:,:) ! (ndecomp_pools, ntill_stages_max) integer, parameter :: ntill_stages_max = 3 ! How many different tillage phases are there? (Not including all-1 phases.) + integer, parameter :: ntill_intensities_max = 2 ! How many different tillage intensities are allowed (other than "off")? real(r8) :: max_tillage_depth ! Maximum depth to till (m) !============================================================================== @@ -145,7 +145,7 @@ subroutine readParams_netcdf(ncid) end select ! Read off of netcdf file - allocate(tempr(2,ndecomp_pools_max,ntill_stages_max)) + allocate(tempr(ntill_stages_max,ndecomp_pools_max,ntill_stages_max)) call ncd_io(trim(tString), tempr, 'read', ncid, readvar = readv) if (.not. readv) then call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__)) From b892252f0902d5872572a6525e5b15bb26f912d1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 5 Oct 2023 16:42:48 -0600 Subject: [PATCH 1572/2067] Improve error checks and comments --- bld/CLMBuildNamelist.pm | 55 +++++++++++++++++- .../namelist_definition_ctsm.xml | 58 +++++++++++-------- src/biogeophys/SnowSnicarMod.F90 | 2 + src/main/controlMod.F90 | 29 ++++++---- 4 files changed, 108 insertions(+), 36 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 8d5618bf34..1667b13b10 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1995,6 +1995,60 @@ sub setup_logic_snicar_methods { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_use_aerosol' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_aerforc_diag' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' ); + # Error checking + my $opt1 = 'snicar_snw_shape'; + my $var1 = $nl->get_value($opt1); + my $sup1a = "'sphere'"; # supported value for this option + my $sup1b = "'hexagonal_plate'"; # supported value for this option + if (($var1 ne $sup1a) && ($var1 ne $sup1b)) { + $log->warning("$opt1=$sup1a and $sup1b are supported; $var1 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt2 = 'snicar_solarspec'; + my $var2 = $nl->get_value($opt2); + my $sup2 = "'mid_latitude_winter'"; # supported value for this option + if ($var2 ne $sup2) { + $log->warning("$opt2=$sup2 is the supported option; $var2 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt3 = 'snicar_dust_optics'; + my $var3 = $nl->get_value($opt3); + my $sup3 = "'sahara'"; # supported value for this option + if ($var3 ne $sup3) { + $log->warning("$opt3=$sup3 is the supported option; $var3 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt4 = 'snicar_numrad_snw'; + my $var4 = $nl->get_value($opt4); + my $sup4 = '5'; # supported value for this option + if ($var4 ne $sup4) { + $log->warning("$opt4=$sup4 is the supported option; $var4 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt5 = 'snicar_snobc_intmix'; + my $var5 = $nl->get_value($opt5); + my $sup5 = '.false.'; # supported value for this option + if ($var5 ne $sup5) { + $log->warning("$opt5=$sup5 is the supported option; $var5 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt6 = 'snicar_snodst_intmix'; + my $var6 = $nl->get_value($opt6); + my $sup6 = '.false.'; # supported value for this option + if ($var6 ne $sup6) { + $log->warning("$opt6=$sup6 is the supported option; $var6 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt7 = 'snicar_use_aerosol'; + my $var7 = $nl->get_value($opt7); + my $sup7 = '.true.'; # supported value for this option + if ($var7 ne $sup7) { + $log->warning("$opt7=$sup7 is the supported option; $var7 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + my $opt8 = 'do_sno_oc'; + my $var8 = $nl->get_value($opt8); + my $sup8 = '.false.'; # supported value for this option + if ($var8 ne $sup8) { + $log->warning("$opt8=$sup8 is the supported option; $var8 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + # snicar_snobc_intmix and snicar_snodst_intmix cannot both be true + if (($var5 eq $var6) && ($var5 ne $sup5)) { + $log->warning("$opt5 = $var5 and $opt6 = $var6 do not work together!"); + } } #------------------------------------------------------------------------------- @@ -4482,7 +4536,6 @@ sub write_output_files { push @groups, "ch4finundated"; push @groups, "exice_streams"; push @groups, "soilbgc_decomp"; - push @groups, "snicar_inparm"; push @groups, "clm_canopy_inparm"; if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') { push @groups, "scf_swenson_lawrence_2012_inparm"; diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 731c10acfd..793d79d242 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -151,43 +151,51 @@ of soil column (nlevsoi). + group="clm_inparm" valid_values="5,480" value="5" > number of wavelength bands used in SNICAR snow albedo calculation +(snicar_numrad_snw=5 is the only supported option; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" valid_values="mid_latitude_winter,mid_latitude_summer,sub_arctic_winter,sub_arctic_summer,summit_greenland_summer,high_mountain_summer" value="mid_latitude_winter" > type of downward solar radiation spectrum for SNICAR snow albedo calculation +(snicar_solarspec='mid_latitude_winter' is the only supported option; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" valid_values="sahara,san_juan_mtns_colorado,greenland" value="sahara" > dust optics type for SNICAR snow albedo calculation +(snicar_dust_optics='sahara' is the only supported option; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" valid_values="sphere,spheroid,hexagonal_plate,koch_snowflake" value="hexagonal_plate" > snow grain shape used in SNICAR snow albedo calculation +(snicar_dust_optics='hexagonal_plate' is supported in ctsm5.1 and 'sphere' in older model versions; others are EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" value=".true."> Toggle to turn on/off aerosol deposition flux in snow in SNICAR +(snicar_use_aerosol='.false.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" value=".false." > option to activate BC-snow internal mixing in SNICAR snow albedo calculation +(snicar_snobc_intmix='.true.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" value=".false." > option to activate dust-snow internal mixing in SNICAR snow albedo calculation +(snicar_snodst_intmix='.true.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) + group="clm_inparm" value=".false." > option to activate organic carbon (OC) in SNICAR snow albedo calculation +(do_sno_oc='.true.' is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) Toggle to use 25 lake layers instead of 10 -(extralaklayers=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!) +(extralaklayers=".true." is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) Toggle to turn on the VIC hydrologic parameterizations -(vichydro=".true." is EXPERIMENTAL NOT SUPPORTED!) +(vichydro=".true." is EXPERIMENTAL, UNSUPPORTED!) + group="clm_inparm" value=".false."> Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) albedo forcing diagnostics for each aerosol species @@ -1761,7 +1769,7 @@ to hydrologic variables (either TWS or ZWT) -Toggle to turn on use of input prescribed soil moisture streams rather than have CLM prognose it (EXPERIMENTAL) +Toggle to turn on use of input prescribed soil moisture streams rather than have CLM prognose it (EXPERIMENTAL, UNSUPPORTED!) Toggle to turn on use of LAI streams in place of the LAI on the surface dataset when using Satellite Phenology mode. -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) If true, no denitrification or nitrification in frozen soil layers. -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) If TRUE, weight btran (vegetation soil moisture availability) by unfrozen layers only, assuming that vegetation will allocate roots preferentially to the active layer. -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) If TRUE, weight btran (vegetation soil moisture availability) by the active layer, as defined by the greatest thaw depth over the current and prior years. -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) @@ -2384,7 +2392,7 @@ How much Carbon to initialize vegetation pools (leafc/frootc and storage) to whe Flexible CN ratio used for Phenology -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) Vcmax calculation for Photosynthesis - vcmax_opt = 4 As for vcmax_opt=0, but using leafN, and exponential if tree (EXPERIMENTAL NOT TESTED!) + vcmax_opt = 4 As for vcmax_opt=0, but using leafN, and exponential if tree (EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) vcmax_opt = 3 Based on leafN and VCAD (used with Luna for crop and C4 vegetation) vcmax_opt = 0 Based on canopy top and foilage Nitrogen limitation factor from params file (clm4.5) @@ -2404,13 +2412,13 @@ Vcmax calculation for Photosynthesis Evergreen phenology option for CNPhenology -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) Carbon respiration option to burn off carbon when CN ratio is too high (do NOT use when FUN is on) -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) @@ -2468,7 +2476,7 @@ then don't fix aere (see ch4Mod.F90). If TRUE, turn on methane biogeochemistry model for lake columns, using a simplified version of the CH4 submodel. -(EXPERIMENTAL) +(EXPERIMENTAL, UNSUPPORTED!) If TRUE, use the fine root carbon predicted by CN when calculating the aerenchyma area, rather than the parametrization based on annual NPP, aboveground NPP fraction, and LAI. -(EXPERIMENTAL and NOT tested) +(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 1d72870173..61373759e6 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -881,6 +881,8 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & gg_ice_F07_tmp(igb) = g_F07_p0(igb) + g_F07_p1(igb) * log(AR_tmp) + g_F07_p2(igb) * (log(AR_tmp) * log(AR_tmp)) ! Eqn. 3.3 in Fu (2007) enddo + case ('sphere') + ! DO NOTHING case default write(iulog,*) subname//' ERROR: unknown sno_shp for i: ', sno_shp(i), i call endrun(msg=errMsg(sourcefile, __LINE__)) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 372949eee2..30174dc0bc 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -202,9 +202,6 @@ subroutine control_init(dtime) soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & - snicar_numrad_snw, snicar_solarspec, snicar_dust_optics, & - snicar_use_aerosol, snicar_snw_shape, snicar_snobc_intmix,& - snicar_snodst_intmix,do_sno_oc, & for_testing_use_second_grain_pool, for_testing_use_repr_structure_pool, & for_testing_no_crop_seed_replenishment, & z0param_method, use_z0m_snowmelt @@ -286,9 +283,14 @@ subroutine control_init(dtime) namelist /clm_inparm/ & use_lch4, use_nitrif_denitrif, use_extralakelayers, & use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, & - use_grainproduct, snicar_aerforc_diag, use_vancouver, use_mexicocity, use_noio, & + use_grainproduct, use_vancouver, use_mexicocity, use_noio, & use_nguardrail + ! SNICAR + namelist /clm_inparm/ & + snicar_numrad_snw, snicar_solarspec, snicar_dust_optics, & + snicar_use_aerosol, snicar_snw_shape, snicar_snobc_intmix, & + snicar_snodst_intmix, snicar_aerforc_diag, do_sno_oc ! ---------------------------------------------------------------------- ! Default values @@ -604,18 +606,24 @@ subroutine control_init(dtime) errMsg(sourcefile, __LINE__)) end if - ! check on snow albedo wavelength bands - if ( (snicar_numrad_snw /= 5) .and. (snicar_numrad_snw /= 480) ) then - call endrun(msg=' ERROR: snicar_numrad_snw is out of a reasonable range (5, 480)'//& - errMsg(sourcefile, __LINE__)) - end if - ! check on SNICAR BC-snow and dust-snow internal mixing if ( snicar_snobc_intmix .and. snicar_snodst_intmix ) then call endrun(msg=' ERROR: currently dust-snow and BC-snow internal mixing cannot be activated together'//& errMsg(sourcefile, __LINE__)) end if + ! other SNICAR warnings + if ((snicar_snw_shape /= 'sphere' .and. snicar_snw_shape /= 'hexagonal_plate') .or. & + snicar_solarspec /= 'mid_latitude_winter' .or. & + snicar_dust_optics /= 'sahara' .or. & + snicar_numrad_snw /= 5 .or. & + snicar_snobc_intmix .or. snicar_snodst_intmix .or. & + not(snicar_use_aerosol) .or. & + do_sno_oc) then + call endrun(msg=' ERROR: You have selected an option that is EXPERIMENTAL, UNSUPPORTED, and UNTESTED. For guidance see namelist_defaults_ctsm.xml'//& + errMsg(sourcefile, __LINE__)) + end if + ! Consistency settings for nrevsn if (nsrest == nsrStartup ) nrevsn = ' ' @@ -1027,6 +1035,7 @@ subroutine control_print () else write(iulog,'(a)') ' snow aging parameters file = '//trim(fsnowaging) endif + write(iulog,*) ' SNICAR: downward solar radiation spectrum type =', snicar_solarspec write(iulog,*) ' SNICAR: dust optics type = ', snicar_dust_optics write(iulog,*) ' SNICAR: number of bands in snow albedo calculation =', snicar_numrad_snw From 20ce1eadf32f8aaa9d5268957e46958a60cc7816 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 5 Oct 2023 17:08:48 -0600 Subject: [PATCH 1573/2067] Remove option of running this copy of snicar in csim --- src/biogeophys/SnowSnicarMod.F90 | 72 ++++++++++------------------- src/biogeophys/SurfaceAlbedoMod.F90 | 22 ++++----- 2 files changed, 35 insertions(+), 59 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 61373759e6..3fcdca19cb 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -181,7 +181,7 @@ subroutine readParams( ncid ) end subroutine readParams !----------------------------------------------------------------------- - subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + subroutine SNICAR_RT (bounds, num_nourbanc, filter_nourbanc, & coszen, flg_slr_in, h2osno_liq, h2osno_ice, h2osno_total, snw_rds, & mss_cnc_aer_in, albsfc, albout, flx_abs, waterdiagnosticbulk_inst) ! @@ -222,7 +222,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & use shr_const_mod , only : SHR_CONST_PI ! ! !ARGUMENTS: - integer , intent(in) :: flg_snw_ice ! flag: =1 when called from CLM, =2 when called from CSIM type (bounds_type), intent(in) :: bounds integer , intent(in) :: num_nourbanc ! number of columns in non-urban filter integer , intent(in) :: filter_nourbanc(:) ! column filter for non-urban points @@ -647,7 +646,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & nstep = get_nstep() ! Loop over all non-urban columns - ! (when called from CSIM, there is only one column) do fc = 1,num_nourbanc c_idx = filter_nourbanc(fc) @@ -658,11 +656,7 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & enddo ! set snow/ice mass to be used for RT: - if (flg_snw_ice == 1) then - h2osno_lcl = h2osno_total(c_idx) - else - h2osno_lcl = h2osno_ice(c_idx,0) - endif + h2osno_lcl = h2osno_total(c_idx) ! Qualifier for computing snow RT: ! 1) sunlight from atmosphere model @@ -671,46 +665,31 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & if ((coszen(c_idx) > 0._r8) .and. (h2osno_lcl > min_snw)) then ! Set variables specific to CLM - if (flg_snw_ice == 1) then - ! If there is snow, but zero snow layers, we must create a layer locally. - ! This layer is presumed to have the fresh snow effective radius. - if (snl(c_idx) > -1) then - flg_nosnl = 1 - snl_lcl = -1 - h2osno_ice_lcl(0) = h2osno_lcl - h2osno_liq_lcl(0) = 0._r8 - snw_rds_lcl(0) = snw_rds_min_int - else - flg_nosnl = 0 - snl_lcl = snl(c_idx) - h2osno_liq_lcl(:) = h2osno_liq(c_idx,:) - h2osno_ice_lcl(:) = h2osno_ice(c_idx,:) - snw_rds_lcl(:) = snw_rds(c_idx,:) - endif - - snl_btm = 0 - snl_top = snl_lcl+1 + ! If there is snow, but zero snow layers, we must create a layer locally. + ! This layer is presumed to have the fresh snow effective radius. + if (snl(c_idx) > -1) then + flg_nosnl = 1 + snl_lcl = -1 + h2osno_ice_lcl(0) = h2osno_lcl + h2osno_liq_lcl(0) = 0._r8 + snw_rds_lcl(0) = snw_rds_min_int + else + flg_nosnl = 0 + snl_lcl = snl(c_idx) + h2osno_liq_lcl(:) = h2osno_liq(c_idx,:) + h2osno_ice_lcl(:) = h2osno_ice(c_idx,:) + snw_rds_lcl(:) = snw_rds(c_idx,:) + endif - ! for debugging only - l_idx = col%landunit(c_idx) - g_idx = col%gridcell(c_idx) - sfctype = lun%itype(l_idx) - lat_coord = grc%latdeg(g_idx) - lon_coord = grc%londeg(g_idx) + snl_btm = 0 + snl_top = snl_lcl+1 - ! Set variables specific to CSIM - else - flg_nosnl = 0 - snl_lcl = -1 - h2osno_liq_lcl(:) = h2osno_liq(c_idx,:) - h2osno_ice_lcl(:) = h2osno_ice(c_idx,:) - snw_rds_lcl(:) = snw_rds(c_idx,:) - snl_btm = 0 - snl_top = 0 - sfctype = -1 - lat_coord = -90 - lon_coord = 0 - endif ! end if flg_snw_ice == 1 + ! for debugging only + l_idx = col%landunit(c_idx) + g_idx = col%gridcell(c_idx) + sfctype = lun%itype(l_idx) + lat_coord = grc%latdeg(g_idx) + lon_coord = grc%londeg(g_idx) ! Set local aerosol array @@ -729,7 +708,6 @@ subroutine SNICAR_RT (flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & if ((snw_rds_lcl(i) < snw_rds_min_tbl) .or. (snw_rds_lcl(i) > snw_rds_max_tbl)) then write (iulog,*) "SNICAR ERROR: snow grain radius of ", snw_rds_lcl(i), " out of bounds." write (iulog,*) "NSTEP= ", nstep - write (iulog,*) "flg_snw_ice= ", flg_snw_ice write (iulog,*) "column: ", c_idx, " level: ", i, " snl(c)= ", snl_lcl write (iulog,*) "lat= ", lat_coord, " lon= ", lon_coord write (iulog,*) "h2osno_total(c)= ", h2osno_lcl diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index e9830f7fb9..d48ba3f063 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -297,7 +297,6 @@ subroutine SurfaceAlbedo(bounds,nc, & real(r8) :: laisum ! sum of canopy layer lai for error check real(r8) :: saisum ! sum of canopy layer sai for error check integer :: flg_slr ! flag for SNICAR (=1 if direct, =2 if diffuse) - integer :: flg_snw_ice ! flag for SNICAR (=1 when called from CLM, =2 when called from sea-ice) integer :: num_vegsol ! number of vegetated patches where coszen>0 integer :: num_novegsol ! number of vegetated patches where coszen>0 integer :: filter_vegsol (bounds%endp-bounds%begp+1) ! patch filter where vegetated and coszen>0 @@ -524,7 +523,6 @@ subroutine SurfaceAlbedo(bounds,nc, & ! set variables to pass to SNICAR. - flg_snw_ice = 1 ! calling from CLM, not CSIM do c=bounds%begc,bounds%endc albsfc(c,:) = albsoi(c,:) h2osno_liq(c,:) = h2osoi_liq(c,-nlevsno+1:0) @@ -587,7 +585,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! BC FORCING CALCULATIONS flg_slr = 1; ! direct-beam - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -601,7 +599,7 @@ subroutine SurfaceAlbedo(bounds,nc, & waterdiagnosticbulk_inst) flg_slr = 2; ! diffuse - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -626,7 +624,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! OC FORCING CALCULATIONS flg_slr = 1; ! direct-beam - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -640,7 +638,7 @@ subroutine SurfaceAlbedo(bounds,nc, & waterdiagnosticbulk_inst) flg_slr = 2; ! diffuse - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -665,7 +663,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! DUST FORCING CALCULATIONS flg_slr = 1; ! direct-beam - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -679,7 +677,7 @@ subroutine SurfaceAlbedo(bounds,nc, & waterdiagnosticbulk_inst) flg_slr = 2; ! diffuse - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -695,7 +693,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! 4. ALL AEROSOL FORCING CALCULATION ! (pure snow albedo) flg_slr = 1; ! direct-beam - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -709,7 +707,7 @@ subroutine SurfaceAlbedo(bounds,nc, & waterdiagnosticbulk_inst) flg_slr = 2; ! diffuse - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -725,7 +723,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! CLIMATE FEEDBACK CALCULATIONS, ALL AEROSOLS: flg_slr = 1; ! direct-beam - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & @@ -739,7 +737,7 @@ subroutine SurfaceAlbedo(bounds,nc, & waterdiagnosticbulk_inst) flg_slr = 2; ! diffuse - call SNICAR_RT(flg_snw_ice, bounds, num_nourbanc, filter_nourbanc, & + call SNICAR_RT(bounds, num_nourbanc, filter_nourbanc, & coszen_col(bounds%begc:bounds%endc), & flg_slr, & h2osno_liq(bounds%begc:bounds%endc, :), & From f952e50e534eb4b8ac9c54171a40468c606b3cb9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 5 Oct 2023 17:26:56 -0600 Subject: [PATCH 1574/2067] Replace hardwired numbers with parameters --- src/biogeophys/SnowSnicarMod.F90 | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 3fcdca19cb..eda055a2a7 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -51,6 +51,11 @@ module SnowSnicarMod logical, public, parameter :: DO_SNO_AER = .true. ! parameter to include aerosols in snowpack radiative calculations ! !PRIVATE DATA MEMBERS: + integer, parameter :: default_number_bands = 5 ! currently the only alternative is 480 bands + integer, parameter :: highest_default_band = 5 + integer, parameter :: sec_highest_default_band = 4 + integer, parameter :: high_number_bands = 480 + integer, parameter :: idx_Mie_snw_mx = 1471 ! number of effective radius indices used in Mie lookup table [idx] integer, parameter :: idx_T_max = 11 ! maximum temperature index used in aging lookup table [idx] integer, parameter :: idx_T_min = 1 ! minimum temperature index used in aging lookup table [idx] @@ -613,10 +618,10 @@ subroutine SNICAR_RT (bounds, num_nourbanc, filter_nourbanc, & ! SNICAR/CLM snow band center wavelength (um) allocate(wvl_ct(snicar_numrad_snw)) select case (snicar_numrad_snw) - case (5) + case (default_number_bands) nir_bnd_bgn = 2 wvl_ct(:) = (/ 0.5_r8, 0.85_r8, 1.1_r8, 1.35_r8, 3.25_r8 /) ! 5-band - case (480) + case (high_number_bands) nir_bnd_bgn = 51 do igb = 1, snicar_numrad_snw wvl_ct(igb) = 0.205_r8 + 0.01_r8 * (igb - 1._r8) ! 480-band @@ -770,11 +775,11 @@ subroutine SNICAR_RT (bounds, num_nourbanc, filter_nourbanc, & ! Pre-emptive error handling: aerosols can reap havoc on these absorptive bands. ! Since extremely high soot concentrations have a negligible effect on these bands, zero them. - if ( (snicar_numrad_snw == 5).and.((bnd_idx == 5).or.(bnd_idx == 4)) ) then + if (snicar_numrad_snw == default_number_bands .and. (bnd_idx == highest_default_band .or. bnd_idx == sec_highest_default_band)) then mss_cnc_aer_lcl(:,:) = 0._r8 endif - if ( (snicar_numrad_snw == 480).and.(bnd_idx > 100) ) then ! >1.2um + if ( (snicar_numrad_snw == high_number_bands).and.(bnd_idx > 100) ) then ! >1.2um mss_cnc_aer_lcl(:,:) = 0._r8 endif @@ -1376,10 +1381,10 @@ subroutine SNICAR_RT (bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR albedo appropriately select case (snicar_numrad_snw) - case (5) ! 5-band case + case (default_number_bands) ! 5-band case ! VIS band albout(c_idx,ivis) = albout_lcl(ivis) - case (480) ! 480-band case + case (high_number_bands) ! 480-band case ! average for VIS band flx_sum = 0._r8 do bnd_idx= 1, (nir_bnd_bgn-1) @@ -1397,10 +1402,10 @@ subroutine SNICAR_RT (bounds, num_nourbanc, filter_nourbanc, & ! Weight output NIR absorbed layer fluxes (flx_abs) appropriately select case (snicar_numrad_snw) - case (5) ! 5-band case + case (default_number_bands) ! 5-band case ! VIS band flx_abs(c_idx,:,1) = flx_abs_lcl(:,1) - case (480) ! 480-band case + case (high_number_bands) ! 480-band case ! average for VIS band do i=snl_top,1,1 flx_sum = 0._r8 @@ -1866,7 +1871,7 @@ subroutine SnowOptics_init( ) !--------------------- for 5-band data select case (snicar_numrad_snw) - case (5) ! 5-band case + case (default_number_bands) ! 5-band case ! flux weights/spectrum tString = 'flx_wgt_dir5_'//short_case_solarspec @@ -1996,7 +2001,7 @@ subroutine SnowOptics_init( ) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) !-------------------- for 480-band data - case (480) + case (high_number_bands) ! BC species 1 Mie parameters, uncoated BC, same as bc_hphob before BC-snow internal mixing tString = 'ss_alb_bcphob' From d160e65b671171c8cc16208720e1a7eb730988fc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:18:50 -0600 Subject: [PATCH 1575/2067] Minor text fixes. --- .../Running-with-excess-ground-ice.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index 23677965a5..2267d524e5 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -7,13 +7,13 @@ =================================== -Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.fasle.``. When +Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When ``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option`use_excess_ice_streams` exists to control this process (``.false.`` is default). If ``.true.`` and use_excess_ice is ``.true.``, initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. If the run is a continue-run, excess ice variables will **always** be expected on a restart file. -.. note:: Excess ice ammount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m or (maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. +.. note:: Excess ice amount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m (or maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration, but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. Since presence of excess ice within the soil significantly alters heat diffusion within it, when starting from initial conditions where excess ice was not present, an additional spinup is required. @@ -31,7 +31,7 @@ Example: Crop Simulation > ./case.setup - # turn on excess ice and it's "stream" initialization + # turn on excess ice and its "stream" initialization > echo "use_excess_ice=.true." >> user_nl_clm > echo "use_excess_ice_streams=.true." >> user_nl_clm From bae7793ef7720e9c64367bc67c4c22adbe9810c0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:20:23 -0600 Subject: [PATCH 1576/2067] Markup fixes. --- .../running-special-cases/Running-with-excess-ground-ice.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index 2267d524e5..f126c00abc 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -8,7 +8,7 @@ Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When -``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option`use_excess_ice_streams` exists to control this process (``.false.`` is default). If ``.true.`` and use_excess_ice is ``.true.``, +``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option ``use_excess_ice_streams`` exists to control this process (``.false.`` is default). If ``.true.`` and ``use_excess_ice`` is ``.true.``, initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. If the run is a continue-run, excess ice variables will **always** be expected on a restart file. From 5dfd8db7e336db36f81f8afcb7604e68461b04c6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:20:30 -0600 Subject: [PATCH 1577/2067] Remove hyphens from title. --- .../running-special-cases/Running-with-excess-ground-ice.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index f126c00abc..10b7f3ee98 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -3,7 +3,7 @@ .. include:: ../substitutions.rst =================================== - Running-with-excess-ground-ice + Running with excess ground ice =================================== From 15c4efc5e43ca1debc709689cb69789ae5221cad Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:21:51 -0600 Subject: [PATCH 1578/2067] Use complete relative path to cime/scripts from top level of checkout. --- .../running-special-cases/Running-with-excess-ground-ice.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index 10b7f3ee98..be818f8f14 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -25,7 +25,7 @@ Example: Crop Simulation ------------------------------------ :: - > cd scripts + > cd cime/scripts > ./create_newcase -case I1850Clm50BgcCrop_with_exice -res f19_g17_gl4 -compset I1850Clm50BgcCrop > cd I1850Clm50BgcCrop_with_exice From 9e633dcdfc00244b2be74f03ef7f45dfc4cdd718 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 09:23:05 -0600 Subject: [PATCH 1579/2067] Remove EOL whitespace. --- .../Running-with-excess-ground-ice.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst index be818f8f14..d0b29f8682 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-excess-ground-ice.rst @@ -7,11 +7,11 @@ =================================== -Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When -``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option ``use_excess_ice_streams`` exists to control this process (``.false.`` is default). If ``.true.`` and ``use_excess_ice`` is ``.true.``, -initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). +Excess ground ice can be toggled with ``use_excess_ice`` namelist option. By default this option is ``.false.``. When +``use_excess_ice`` is true, CTSM needs initial excess ice amount within soil layers to initialize. A second namelist option ``use_excess_ice_streams`` exists to control this process (``.false.`` is default). If ``.true.`` and ``use_excess_ice`` is ``.true.``, +initial conditions will be read from a data-stream file (default is based :ref:`on IPA map from 1997 `). This is useful, since in this way, a run with excess ground ice can be started from a restart or initial dataset, that does not include excess ground ice. -If the run is a continue-run, excess ice variables will **always** be expected on a restart file. +If the run is a continue-run, excess ice variables will **always** be expected on a restart file. .. note:: Excess ice amount provided by the stream file is expressed in excess ice concentration (%) and does not have a vertical distribution. Each soil layer beneath 0.5 m (or maximum active layer depth from the previous year if it is greater) down to bedrock will receive the same concentration, but the ice mass will be scaled by the soil layer depth. Both naturally vegetated and crop columns get excess ice. From eeba54fe0d2856e14a5da62396622cae6f5bac10 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 6 Oct 2023 16:55:44 -0600 Subject: [PATCH 1580/2067] Add comment explaining posNOTonfile=.true. --- src/biogeophys/SnowSnicarMod.F90 | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index eda055a2a7..9a95188232 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -1873,6 +1873,8 @@ subroutine SnowOptics_init( ) select case (snicar_numrad_snw) case (default_number_bands) ! 5-band case + ! The argument posNOTonfile=.true. is used here because this is a non-spatial file. + ! This argument is relevant when running single_column. ! flux weights/spectrum tString = 'flx_wgt_dir5_'//short_case_solarspec call ncd_io(trim(tString), flx_wgt_dir, 'read', ncid, readv, posNOTonfile=.true.) From cfe0c37dac084827d46b2d6b4422358f73999506 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 16:53:41 -0600 Subject: [PATCH 1581/2067] regrid_ggcmi_shdates: Add -x/--extension (default now .nc). --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 2715131c84..40d0dce20d 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -72,7 +72,7 @@ def import_coord_2d(ds, coordName, varName): def main( - regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory + regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory, extension ): print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") @@ -129,12 +129,12 @@ def main( template_ds_out.to_netcdf(templatefile, mode="w") # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor - input_files = glob.glob("*nc4") + input_files = glob.glob("*" + extension) input_files.sort() for f in input_files: print(" " + f[0:6]) f2 = os.path.join(regrid_output_directory, f) - f3 = f2.replace(".nc4", f"_nninterp-{regrid_resolution}.nc4") + f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") if os.path.exists(f3): os.remove(f3) @@ -179,6 +179,13 @@ def main( type=str, required=True, ) + default = ".nc" + parser.add_argument( + "-x", + "--extension", + help=f"File extension of raw GGCMI sowing/harvest date files (default {default}).", + default=default, + ) # Get arguments args = parser.parse_args(sys.argv[1:]) @@ -191,4 +198,5 @@ def main( os.path.realpath(args.regrid_template_file), os.path.realpath(args.regrid_input_directory), os.path.realpath(args.regrid_output_directory), + args.extension, ) From 56092ff9bb3cc1e39ef5cf4118d558811a3b7a09 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 6 Oct 2023 16:56:38 -0600 Subject: [PATCH 1582/2067] regrid_ggcmi_shdates: Fail if no files found. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 40d0dce20d..d864328e2e 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -129,7 +129,10 @@ def main( template_ds_out.to_netcdf(templatefile, mode="w") # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor - input_files = glob.glob("*" + extension) + pattern = "*" + extension + input_files = glob.glob(pattern) + if len(input_files) == 0: + raise FileNotFoundError(f"No files found matching {os.path.join(os.getcwd(), pattern)}") input_files.sort() for f in input_files: print(" " + f[0:6]) From 3838cebc3b95c9753a17a35555a9795700aef87e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 6 Oct 2023 17:27:50 -0600 Subject: [PATCH 1583/2067] Correct syntax error --- src/main/controlMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 634b341400..244a34bb8c 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -626,7 +626,7 @@ subroutine control_init(dtime) snicar_dust_optics /= 'sahara' .or. & snicar_numrad_snw /= 5 .or. & snicar_snobc_intmix .or. snicar_snodst_intmix .or. & - not(snicar_use_aerosol) .or. & + .not. snicar_use_aerosol .or. & do_sno_oc) then call endrun(msg=' ERROR: You have selected an option that is EXPERIMENTAL, UNSUPPORTED, and UNTESTED. For guidance see namelist_defaults_ctsm.xml'//& errMsg(sourcefile, __LINE__)) From bf9f4d8052885ec7c539f4312b181ddf8318c4a3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 7 Oct 2023 11:49:25 -0600 Subject: [PATCH 1584/2067] Update history_fields .rst files. --- .../history_fields_fates.rst | 33 +------- .../history_fields_nofates.rst | 79 +++++++++++++++++-- 2 files changed, 75 insertions(+), 37 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index ea7c23d22a..b7361a5d59 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -26,15 +26,6 @@ AnnET - Annual ET BCDEP - total BC deposition (dry+wet) from atmosphere kg/m^2/s T BTRAN - transpiration beta factor unitless T BTRANMN - daily minimum of transpiration beta factor unitless T -CH4PROD - Gridcell total production of CH4 gC/m2/s T -CH4_EBUL_TOTAL_SAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_EBUL_TOTAL_UNSAT - ebullition surface CH4 flux; (+ to atm) mol/m2/s F -CH4_SURF_AERE_SAT - aerenchyma surface CH4 flux for inundated area; (+ to atm) mol/m2/s T -CH4_SURF_AERE_UNSAT - aerenchyma surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_SAT - diffusive surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_DIFF_UNSAT - diffusive surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_SAT - ebullition surface CH4 flux for inundated / lake area; (+ to atm) mol/m2/s T -CH4_SURF_EBUL_UNSAT - ebullition surface CH4 flux for non-inundated area; (+ to atm) mol/m2/s T COL_CTRUNC - column-level sink for C truncation gC/m^2 F COL_NTRUNC - column-level sink for N truncation gN/m^2 F COSZEN - cosine of solar zenith angle none F @@ -61,7 +52,6 @@ DWT_PROD10C_GAIN - landcover change-driven add DWT_PROD10N_GAIN - landcover change-driven addition to 10-yr wood product pool gN/m^2/s F DWT_WOODPRODC_GAIN - landcover change-driven addition to wood product pools gC/m^2/s T DWT_WOODPRODN_GAIN - landcover change-driven addition to wood product pools gN/m^2/s T -DYN_COL_ADJUSTMENTS_CH4 - Adjustments in ch4 due to dynamic column areas; only makes sense at the column level: should n gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_C - Adjustments in soil carbon due to dynamic column areas; only makes sense at the column level: gC/m^2 F DYN_COL_SOIL_ADJUSTMENTS_N - Adjustments in soil nitrogen due to dynamic column areas; only makes sense at the column level gN/m^2 F DYN_COL_SOIL_ADJUSTMENTS_NH4 - Adjustments in soil NH4 due to dynamic column areas; only makes sense at the column level: sho gN/m^2 F @@ -147,8 +137,8 @@ FATES_LEAF_ALLOC - allocation to leaves in kg FATES_LITTER_IN - litter flux in kg carbon per m2 per second kg m-2 s-1 T FATES_LITTER_OUT - litter flux out in kg carbon (exudation, fragmentation, seed decay) kg m-2 s-1 T FATES_LSTEMMAINTAR - live stem maintenance autotrophic respiration in kg carbon per m2 per second kg m-2 s-1 T -FATES_MAINT_RESP - maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T -FATES_MAINT_RESP_SECONDARY - maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_MAINT_RESP - maintenance respiration in kg carbon per m2 land area per second kg m-2 s-1 T +FATES_MAINT_RESP_SECONDARY - maintenance respiration in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T FATES_MAINT_RESP_UNREDUCED - diagnostic maintenance respiration if the low-carbon-storage reduction is ignored kg m-2 s-1 F FATES_MORTALITY_CFLUX_CANOPY - flux of biomass carbon from live to dead pools from mortality of canopy plants in kg carbon pe kg m-2 s-1 T FATES_MORTALITY_CFLUX_USTORY - flux of biomass carbon from live to dead pools from mortality of understory plants in kg carbo kg m-2 s-1 T @@ -193,9 +183,6 @@ FATES_VEGC - total biomass in live plant FATES_VEGC_ABOVEGROUND - aboveground biomass in kg carbon per m2 land area kg m-2 T FATES_WOOD_PRODUCT - total wood product from logging in kg carbon per m2 land area kg m-2 T FCEV - canopy evaporation W/m^2 T -FCH4 - Gridcell surface CH4 flux to atmosphere (+ to atm) kgC/m2/s T -FCH4TOCO2 - Gridcell oxidation of CH4 to CO2 gC/m2/s T -FCH4_DFSAT - CH4 additional flux due to changing fsat, natural vegetated and crop landunits only kgC/m2/s T FCO2 - CO2 flux to atmosphere (+ to atm) kgCO2/m2/s F FCOV - fractional impermeable area unitless T FCTR - canopy transpiration W/m^2 T @@ -207,8 +194,6 @@ FGR_R - Rural heat flux into soil/s FGR_U - Urban heat flux into soil/snow including snow melt W/m^2 F FH2OSFC - fraction of ground covered by surface water unitless T FH2OSFC_NOSNOW - fraction of ground covered by surface water (if no snow present) unitless F -FINUNDATED - fractional inundated area of vegetated columns unitless T -FINUNDATED_LAG - time-lagged inundated fraction of vegetated columns unitless F FIRA - net infrared (longwave) radiation W/m^2 T FIRA_ICE - net infrared (longwave) radiation (ice landunits only) W/m^2 F FIRA_R - Rural net infrared (longwave) radiation W/m^2 T @@ -352,7 +337,6 @@ M_SOM_PAS_N_TO_LEACHING - passive soil organic N leac M_SOM_SLO_C_TO_LEACHING - slow soil organic ma C leaching loss gC/m^2/s F M_SOM_SLO_N_TO_LEACHING - slow soil organic ma N leaching loss gN/m^2/s F NDEP_TO_SMINN - atmospheric N deposition to soil mineral N gN/m^2/s T -NEM - Gridcell net adjustment to net carbon exchange passed to atm. for methane production gC/m2/s T NET_NMIN - net rate of N mineralization gN/m^2/s T NFIX_TO_SMINN - symbiotic/asymbiotic N fixation to soil mineral N gN/m^2/s T NSUBSTEPS - number of adaptive timesteps in CLM timestep unitless F @@ -360,7 +344,6 @@ OBU - Monin-Obukhov length OCDEP - total OC deposition (dry+wet) from atmosphere kg/m^2/s T PARVEGLN - absorbed par by vegetation at local noon W/m^2 T PBOT - atmospheric pressure at surface (downscaled to columns in glacier regions) Pa T -PCH4 - atmospheric partial pressure of CH4 Pa T PCO2 - atmospheric partial pressure of CO2 Pa T POTENTIAL_IMMOB - potential N immobilization gN/m^2/s T POT_F_DENIT - potential denitrification flux gN/m^2/s T @@ -413,7 +396,6 @@ QIRRIG_FROM_GW_UNCONFINED - water added through unconfi QIRRIG_FROM_SURFACE - water added through surface water irrigation mm/s T QIRRIG_SPRINKLER - water added via sprinkler irrigation mm/s F QOVER - total surface runoff (includes QH2OSFC) mm/s T -QOVER_LAG - time-lagged surface runoff for soil columns mm/s F QPHSNEG - net negative hydraulic redistribution flux mm/s F QRGWL - surface runoff at glaciers (liquid only), wetlands, lakes; also includes melted ice runoff fro mm/s T QRUNOFF - total liquid runoff not including correction for land use change mm/s T @@ -495,6 +477,7 @@ SNOFSRVD - direct vis reflected solar SNOFSRVI - diffuse vis reflected solar radiation from snow W/m^2 T SNOINTABS - Fraction of incoming solar absorbed by lower snow layers - T SNOLIQFL - top snow layer liquid water fraction (land) fraction F +SNOMELT_ACCUM - accumulated snow melt for z0 m T SNOOCMCL - mass of OC in snow column kg/m2 T SNOOCMSL - mass of OC in top snow layer kg/m2 T SNORDSL - top snow layer effective grain radius m^-6 F @@ -578,7 +561,6 @@ TLAI - total projected leaf area i TOPO_COL - column-level topographic height m F TOPO_COL_ICE - column-level topographic height (ice landunits only) m F TOTCOLC - total column carbon, incl veg and cpool but excl product pools gC/m^2 T -TOTCOLCH4 - total belowground CH4 (0 for non-lake special landunits in the absence of dynamic landunits) gC/m2 T TOTCOLN - total column-level N, excluding product pools gN/m^2 T TOTECOSYSC - total ecosystem carbon, incl veg but excl cpool and product pools gC/m^2 T TOTECOSYSN - total ecosystem N, excluding product pools gN/m^2 T @@ -641,7 +623,6 @@ WBT - 2 m Stull Wet Bulb WBT_R - Rural 2 m Stull Wet Bulb C T WBT_U - Urban 2 m Stull Wet Bulb C T WIND - atmospheric wind velocity magnitude m/s T -WTGQ - surface tracer conductance m/s T Wind - atmospheric wind velocity magnitude m/s F Z0HG - roughness length over ground, sensible heat (vegetated landunits only) m F Z0MG - roughness length over ground, momentum (vegetated landunits only) m F @@ -652,7 +633,6 @@ ZBOT - atmospheric reference heigh ZETA - dimensionless stability parameter unitless F ZII - convective boundary height m F ZWT - water table depth (natural vegetated and crop landunits only) m T -ZWT_CH4_UNSAT - depth of water table for methane production used in non-inundated area m T ZWT_PERCH - perched water table depth (natural vegetated and crop landunits only) m T num_iter - number of iterations unitless F QICE_FORC elevclas qice forcing sent to GLC mm/s F @@ -757,7 +737,7 @@ FATES_MORTALITY_PF fates_levpft PFT-level mortality rate in FATES_NPLANT_PF fates_levpft total PFT-level number of individuals per m2 land area m-2 T FATES_NPLANT_SEC_PF fates_levpft total PFT-level number of individuals per m2 land area, secondary patches m-2 T FATES_NPP_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second kg m-2 s-1 T -FATES_NPP_SE_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 yr-1 T +FATES_NPP_SE_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T FATES_RECRUITMENT_PF fates_levpft PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T FATES_STOREC_PF fates_levpft total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T FATES_VEGC_PF fates_levpft total PFT-level biomass in kg of carbon per land area kg m-2 T @@ -1026,11 +1006,8 @@ ratio_k1 levdcmp ratio_k1 ratio_no3_co2 levdcmp ratio_no3_co2 ratio F soil_bulkdensity levdcmp soil_bulkdensity kg/m3 F soil_co2_prod levdcmp soil_co2_prod ug C / g soil / day F -CONC_CH4_SAT levgrnd CH4 soil Concentration for inundated / lake area mol/m3 F -CONC_CH4_UNSAT levgrnd CH4 soil Concentration for non-inundated area mol/m3 F FGR_SOIL_R levgrnd Rural downward heat flux at interface below each soil layer watt/m^2 F HK levgrnd hydraulic conductivity (natural vegetated and crop landunits only) mm/s F -O2_DECOMP_DEPTH_UNSAT levgrnd O2 consumption from HR and AR for non-inundated area mol/m3/s F SMP levgrnd soil matric potential (natural vegetated and crop landunits only) mm T SOILPSI levgrnd soil water potential in each soil layer MPa F TSOI levgrnd soil temperature (natural vegetated and crop landunits only) K T @@ -1056,8 +1033,6 @@ SNO_TK_ICE levsno Thermal conductivity (ice l SNO_T_ICE levsno Snow temperatures (ice landunits only) K F SNO_Z levsno Snow layer thicknesses m F SNO_Z_ICE levsno Snow layer thicknesses (ice landunits only) m F -CONC_O2_SAT levsoi O2 soil Concentration for inundated / lake area mol/m3 T -CONC_O2_UNSAT levsoi O2 soil Concentration for non-inundated area mol/m3 T FATES_FRAGMENTATION_SCALER_SL levsoi factor (0-1) by which litter/cwd fragmentation proceeds relative to max rate by soil layer T FATES_FROOTC_SL levsoi Total carbon in live plant fine-roots over depth kg m-3 T H2OSOI levsoi volumetric soil water (natural vegetated and crop landunits only) mm3/mm3 T diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 4e96f5fb91..3a30fece39 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -1,13 +1,13 @@ ============================= CTSM History Fields (nofates) ============================= - + CAUTION: Not all variables are relevant / present for all CTSM cases. Key flags used in this CTSM case: -use_cn = T -use_crop = T -use_fates = F - +use_cn = T +use_crop = T +use_fates = F + =================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- @@ -28,6 +28,9 @@ ANNMAX_RETRANSN - annual max of retranslocate ANNSUM_COUNTER - seconds since last annual accumulator turnover s F ANNSUM_NPP - annual sum of NPP gC/m^2/yr F ANNSUM_POTENTIAL_GPP - annual sum of potential GPP gN/m^2/yr F +APPAR_TEMP - 2 m apparent temperature C T +APPAR_TEMP_R - Rural 2 m apparent temperature C T +APPAR_TEMP_U - Urban 2 m apparent temperature C T AR - autotrophic respiration (MR + GR) gC/m^2/s T ATM_O3 - atmospheric ozone partial pressure mol/mol F ATM_TOPO - atmospheric surface height m T @@ -137,6 +140,12 @@ DEADSTEMN_XFER - dead stem N transfer DEADSTEMN_XFER_TO_DEADSTEMN - dead stem N growth from storage gN/m^2/s F DENIT - total rate of denitrification gN/m^2/s T DGNETDT - derivative of net ground heat flux wrt soil temp W/m^2/K F +DISCOI - 2 m Discomfort Index C T +DISCOIS - 2 m Stull Discomfort Index C T +DISCOIS_R - Rural 2 m Stull Discomfort Index C T +DISCOIS_U - Urban 2 m Stull Discomfort Index C T +DISCOI_R - Rural 2 m Discomfort Index C T +DISCOI_U - Urban 2 m Discomfort Index C T DISPLA - displacement height (vegetated landunits only) m F DISPVEGC - displayed veg carbon, excluding storage and cpool gC/m^2 T DISPVEGN - displayed vegetation nitrogen gN/m^2 T @@ -193,6 +202,9 @@ ELAI - exposed one-sided leaf area EMG - ground emissivity proportion F EMV - vegetation emissivity proportion F EOPT - Eopt coefficient for VOC calc non F +EPT - 2 m Equiv Pot Temp K T +EPT_R - Rural 2 m Equiv Pot Temp K T +EPT_U - Urban 2 m Equiv Pot Temp K T ER - total ecosystem respiration, autotrophic + heterotrophic gC/m^2/s T ERRH2O - total water conservation error mm T ERRH2OSNO - imbalance in snow depth (liquid water) mm T @@ -296,6 +308,13 @@ FSR - reflected solar radiation FSRND - direct nir reflected solar radiation W/m^2 T FSRNDLN - direct nir reflected solar radiation at local noon W/m^2 T FSRNI - diffuse nir reflected solar radiation W/m^2 T +FSRSF - reflected solar radiation W/m^2 T +FSRSFND - direct nir reflected solar radiation W/m^2 T +FSRSFNDLN - direct nir reflected solar radiation at local noon W/m^2 T +FSRSFNI - diffuse nir reflected solar radiation W/m^2 T +FSRSFVD - direct vis reflected solar radiation W/m^2 T +FSRSFVDLN - direct vis reflected solar radiation at local noon W/m^2 T +FSRSFVI - diffuse vis reflected solar radiation W/m^2 T FSRVD - direct vis reflected solar radiation W/m^2 T FSRVDLN - direct vis reflected solar radiation at local noon W/m^2 T FSRVI - diffuse vis reflected solar radiation W/m^2 T @@ -310,6 +329,14 @@ F_DENIT - denitrification flux F_N2O_DENIT - denitrification N2O flux gN/m^2/s T F_N2O_NIT - nitrification N2O flux gN/m^2/s T F_NIT - nitrification flux gN/m^2/s T +FireComp_BC - fire emissions flux of BC kg/m2/sec F +FireComp_OC - fire emissions flux of OC kg/m2/sec F +FireComp_SO2 - fire emissions flux of SO2 kg/m2/sec F +FireEmis_TOT - Total fire emissions flux gC/m2/sec F +FireEmis_ZTOP - Top of vertical fire emissions distribution m F +FireMech_SO2 - fire emissions flux of SO2 kg/m2/sec F +FireMech_bc_a1 - fire emissions flux of bc_a1 kg/m2/sec F +FireMech_pom_a1 - fire emissions flux of pom_a1 kg/m2/sec F GAMMA - total gamma for VOC calc non F GAMMAA - gamma A for VOC calc non F GAMMAC - gamma C for VOC calc non F @@ -333,6 +360,9 @@ GRAINC_TO_FOOD - grain C to food GRAINC_TO_FOOD_ANN - grain C to food harvested per calendar year; should only be output annually gC/m^2 F GRAINC_TO_SEED - grain C to seed gC/m^2/s T GRAINN - grain N gN/m^2 T +GRAINN_TO_FOOD - grain N to food gN/m^2/s F +GRAINN_TO_FOOD_ANN - grain N to food harvested per calendar year; should only be output annually gN/m^2 F +GRAINN_TO_SEED - grain N to seed gN/m^2/s F GRESP_STORAGE - growth respiration storage gC/m^2 F GRESP_STORAGE_TO_XFER - growth respiration shift storage to transfer gC/m^2/s F GRESP_XFER - growth respiration transfer gC/m^2 F @@ -373,6 +403,7 @@ INT_SNOW_ICE - accumulated swe (ice landun IWUELN - local noon intrinsic water use efficiency umolCO2/molH2O T JMX25T - canopy profile of jmax umol/m2/s T Jmx25Z - maximum rate of electron transport at 25 Celcius for canopy layers umol electrons/m2/s T +KBM1 - natural logarithm of Z0MG_P/Z0HG_P unitless F LAI240 - 240hr average of leaf area index m^2/m^2 F LAISHA - shaded projected leaf area index m^2/m^2 T LAISUN - sunlit projected leaf area index m^2/m^2 T @@ -854,6 +885,7 @@ SNOFSRVD - direct vis reflected solar SNOFSRVI - diffuse vis reflected solar radiation from snow W/m^2 T SNOINTABS - Fraction of incoming solar absorbed by lower snow layers - T SNOLIQFL - top snow layer liquid water fraction (land) fraction F +SNOMELT_ACCUM - accumulated snow melt for z0 m T SNOOCMCL - mass of OC in snow column kg/m2 T SNOOCMSL - mass of OC in top snow layer kg/m2 T SNORDSL - top snow layer effective grain radius m^-6 F @@ -913,6 +945,13 @@ SOM_SLO_N_1m - SOM_SLO N to 1 meter SOM_SLO_N_TO_SOM_ACT_N - decomp. of slow soil organic ma N to active soil organic N gN/m^2 F SOM_SLO_N_TO_SOM_PAS_N - decomp. of slow soil organic ma N to passive soil organic N gN/m^2 F SR - total soil respiration (HR + root resp) gC/m^2/s T +SSRE_FSR - surface snow effect on reflected solar radiation W/m^2 T +SSRE_FSRND - surface snow effect on direct nir reflected solar radiation W/m^2 T +SSRE_FSRNDLN - surface snow effect on direct nir reflected solar radiation at local noon W/m^2 T +SSRE_FSRNI - surface snow effect on diffuse nir reflected solar radiation W/m^2 T +SSRE_FSRVD - surface snow radiatve effect on direct vis reflected solar radiation W/m^2 T +SSRE_FSRVDLN - surface snow radiatve effect on direct vis reflected solar radiation at local noon W/m^2 T +SSRE_FSRVI - surface snow radiatve effect on diffuse vis reflected solar radiation W/m^2 T STORAGE_CDEMAND - C use from the C storage pool gC/m^2 F STORAGE_GR - growth resp for growth sent to storage for later display gC/m^2/s F STORAGE_NDEMAND - N demand during the offset period gN/m^2 F @@ -922,6 +961,12 @@ SUPPLEMENT_TO_SMINN - supplemental N supply SWBGT - 2 m Simplified Wetbulb Globe Temp C T SWBGT_R - Rural 2 m Simplified Wetbulb Globe Temp C T SWBGT_U - Urban 2 m Simplified Wetbulb Globe Temp C T +SWMP65 - 2 m Swamp Cooler Temp 65% Eff C T +SWMP65_R - Rural 2 m Swamp Cooler Temp 65% Eff C T +SWMP65_U - Urban 2 m Swamp Cooler Temp 65% Eff C T +SWMP80 - 2 m Swamp Cooler Temp 80% Eff C T +SWMP80_R - Rural 2 m Swamp Cooler Temp 80% Eff C T +SWMP80_U - Urban 2 m Swamp Cooler Temp 80% Eff C T SWdown - atmospheric incident solar radiation W/m^2 F SWup - upwelling shortwave radiation W/m^2 F SoilAlpha - factor limiting ground evap unitless F @@ -936,6 +981,9 @@ TBUILD_MAX - prescribed maximum interior TEMPAVG_T2M - temporary average 2m air temperature K F TEMPMAX_RETRANSN - temporary annual max of retranslocated N pool gN/m^2 F TEMPSUM_POTENTIAL_GPP - temporary annual sum of potential GPP gC/m^2/yr F +TEQ - 2 m Equiv Temp K T +TEQ_R - Rural 2 m Equiv Temp K T +TEQ_U - Urban 2 m Equiv Temp K T TFLOOR - floor temperature K F TG - ground temperature K T TG_ICE - ground temperature (ice landunits only) K F @@ -943,6 +991,12 @@ TG_R - Rural ground temperature TG_U - Urban ground temperature K F TH2OSFC - surface water temperature K T THBOT - atmospheric air potential temperature (downscaled to columns in glacier regions) K T +THIC - 2 m Temp Hum Index Comfort C T +THIC_R - Rural 2 m Temp Hum Index Comfort C T +THIC_U - Urban 2 m Temp Hum Index Comfort C T +THIP - 2 m Temp Hum Index Physiology C T +THIP_R - Rural 2 m Temp Hum Index Physiology C T +THIP_U - Urban 2 m Temp Hum Index Physiology C T TKE1 - top lake level eddy thermal conductivity W/(mK) T TLAI - total projected leaf area index m^2/m^2 T TOPO_COL - column-level topographic height m F @@ -1027,6 +1081,9 @@ VPD2M - 2m vapor pressure deficit VPD_CAN - canopy vapor pressure deficit kPa T Vcmx25Z - canopy profile of vcmax25 predicted by LUNA model umol/m2/s T WASTEHEAT - sensible heat flux from heating/cooling sources of urban waste heat W/m^2 T +WBA - 2 m Wet Bulb C T +WBA_R - Rural 2 m Wet Bulb C T +WBA_U - Urban 2 m Wet Bulb C T WBT - 2 m Stull Wet Bulb C T WBT_R - Rural 2 m Stull Wet Bulb C T WBT_U - Urban 2 m Stull Wet Bulb C T @@ -1043,12 +1100,15 @@ XSMRPOOL - temporary photosynthate C p XSMRPOOL_LOSS - temporary photosynthate C pool loss gC/m^2 F XSMRPOOL_RECOVER - C flux assigned to recovery of negative xsmrpool gC/m^2/s T Z0HG - roughness length over ground, sensible heat (vegetated landunits only) m F +Z0HG_P - patch roughness length over ground, sensible heat m F Z0HV - roughness length over vegetation, sensible heat m F Z0MG - roughness length over ground, momentum (vegetated landunits only) m F +Z0MG_P - patch roughness length over ground, momentum m F Z0MV - roughness length over vegetation, momentum m F Z0MV_DENSE - roughness length over vegetation, momentum, for dense canopy m F Z0M_TO_COUPLER - roughness length, momentum: gridcell average sent to coupler m F Z0QG - roughness length over ground, latent heat (vegetated landunits only) m F +Z0QG_P - patch roughness length over ground, latent heat m F Z0QV - roughness length over vegetation, latent heat m F ZBOT - atmospheric reference height m T ZETA - dimensionless stability parameter unitless F @@ -1270,6 +1330,7 @@ W_SCALAR levsoi Moisture (dryness) inhibiti GDDACCUM_PERHARV mxharvests At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F GDDHARV_PERHARV mxharvests Growing degree days (gdd) needed to harvest; should only be output annually ddays F GRAINC_TO_FOOD_PERHARV mxharvests grain C to food per harvest; should only be output annually gC/m^2 F +GRAINN_TO_FOOD_PERHARV mxharvests grain N to food per harvest; should only be output annually gN/m^2 F HARVEST_REASON_PERHARV mxharvests Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F HDATES mxharvests actual crop harvest dates; should only be output annually day of year F HUI_PERHARV mxharvests At-harvest accumulated heat unit index for crop; should only be output annually ddays F @@ -1278,11 +1339,13 @@ SOWING_REASON_PERHARV mxharvests Reason for sowing of each c SYEARS_PERHARV mxharvests actual sowing years for crops harvested this year; should only be output annually year F SDATES mxsowings actual crop sowing dates; should only be output annually day of year F SOWING_REASON mxsowings Reason for each crop sowing; should only be output annually unitless F -ALBD numrad surface albedo (direct) proportion F +ALBD numrad surface albedo (direct) proportion T +ALBDSF numrad diagnostic snow-free surface albedo (direct) proportion T ALBGRD numrad ground albedo (direct) proportion F ALBGRI numrad ground albedo (indirect) proportion F -ALBI numrad surface albedo (indirect) proportion F +ALBI numrad surface albedo (indirect) proportion T +ALBISF numrad diagnostic snow-free surface albedo (indirect) proportion T VEGWP nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root segments mm T VEGWPLN nvegwcs vegetation water matric potential for sun/sha canopy,xyl,root at local noon mm T VEGWPPD nvegwcs predawn vegetation water matric potential for sun/sha canopy,xyl,root mm T -=================================== ================ ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= From ca9977c83bcb17dfa150d5124324e91e7e57e59d Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 10 Oct 2023 10:30:20 -0600 Subject: [PATCH 1585/2067] modify single point site neon unit tests and minor changes to modify_singlept_site_neon.py --- .../modify_singlept_site_neon.py | 4 +- .../test_unit_modify_singlept_site_neon.py | 49 ++++++++++--------- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index 465fcda25c..ca85d68636 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -252,7 +252,7 @@ def find_surffile(surf_dir, site_name, pft_16): def find_soil_structure(args, surf_file): """ Function for finding surface dataset soil - strucutre using surface data metadata. + structure using surface data metadata. In CLM surface data, soil layer information is in a file from surface data metadata @@ -306,7 +306,7 @@ def find_soil_structure(args, surf_file): def update_metadata(nc, surf_file, neon_file, zb_flag): """ Function for updating modified surface dataset - metadat for neon sites. + metadata for neon sites. Args: nc (xr Dataset): netcdf file including updated neon surface data diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index d1d738ffa8..f782075c43 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -6,15 +6,13 @@ python -m unittest test_unit_modify_singlept_site_neon.py """ -import unittest -import tempfile -import shutil -import configparser -import argparse import os +import shutil import sys -from getpass import getuser +import tempfile +import unittest from datetime import date +import xarray as xr # -- add python/ctsm to path (needed if we want to run the test stand-alone) _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) @@ -23,18 +21,12 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing from ctsm.site_and_regional.modify_singlept_site_neon import ( - get_parser, get_neon, find_surffile, - find_soil_structure, update_metadata, update_time_tag, - sort_print_soil_layers, check_neon_time, - download_file, - fill_interpolate, ) -from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name @@ -84,19 +76,32 @@ def test_find_surffile(self): pft_16 = True with self.assertRaises(SystemExit): find_surffile(surf_dir, site_name, pft_16) - # TODO: it would be useful to also include an example where the surface file is actually found or correctly searched for - # Is there a default surface data file directory we can point to? + # TODO: need to fix unkown file type error? # def test_find_soil_structure(self): # """ - # Test + # Test to ensure that correct attributes are found for find_soil_structure. + # soil_texture_raw_data_file_name should be found, and test should go through sysexit. # """ - # find_soil_structure() - # TODO: need file to use in test + # surf_file = "testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + # f1 = xr.open_dataset(surf_file) + # print(f1.attrs["Soil_texture_raw_data_file_name"]) + # self.assertEqual(f1.attrs["Soil_texture_raw_data_file_name"], + # "FIND FILENAME FROM ATTRIBUTES AND ADD HERE", + # "did not retrieve expected surface soil texture filename from surf file") # def test_update_metadata(self): - # TODO: do we have a surface data file that we can put in tempdir to update? - # update_metadata(nc, surf_file, neon_file, zb_flag) + # """ + # Test to ensure that an attribute has changed when update_metadata() is run. + # """ + # surf_file = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + # neon_file = "dummy_neon_file.nc" + # zb_flag = True + # f1 = xr.open_dataset("testinputs/" + surf_file) + # f2 = update_metadata(f1, surf_file, neon_file, zb_flag) + # self.assertNotEqual(f1.attrs["Updated_on"], + # f2.attrs["Updated_on"], + # "File was not updated as expected") def test_update_time_tag(self): """ @@ -120,13 +125,13 @@ def test_check_neon_time(self): 19, "last ABBY download has unexpected date format or does not exist", ) - # TODO: this checks that data is not pulled from before 2021; we may want to update this occassionally or find another way to check data is actually newest? + # Note: this checks that data is not pulled from before 2021; + # we may want to update this occassionally, + # but in any case it confirms that the oldest data is not found self.assertGreater( int(last_abby_download[:4]), 2021, "ABBY download is older than expected" ) - # TODO: test sort_print_soil_layers, fill_interpolate, find_soil_structure, and update_metadata - if __name__ == "__main__": unit_testing.setup_for_tests() From eeab40d176e93cde9d92d6f1c810ffc5b2f1fd37 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 10 Oct 2023 13:27:08 -0600 Subject: [PATCH 1586/2067] Add GRAINN_TO_FOOD to first history file in crop testmod. --- cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index d00094de3d..d7e6cb3189 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -1,7 +1,7 @@ hist_fincl1 += 'GDD0', 'GDD8', 'GDD10', 'GDD020', 'GDD820', 'GDD1020', 'GDDACCUM', 'GDDTSOI', 'A5TMIN', 'A10TMIN', - 'HUI' + 'HUI', 'GRAINN_TO_FOOD' ! The main point of including this field is to test the SUM history field infrastructure ! This is in the crop testmods because this field is mainly useful in transient crop runs From cf7a00310b7f67d88226ccc5d2c3069a03c5271e Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Tue, 10 Oct 2023 16:00:55 -0600 Subject: [PATCH 1587/2067] View factor fix --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index bf8b68c7eb..83422f0971 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -424,10 +424,8 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! This view factor implicitly converts from per unit wall area to per unit floor area vf_wf(l) = 0.5_r8*(1._r8 - vf_rf(l)) - ! This view factor implicitly converts from per unit floor area to per unit wall area - vf_fw(l) = vf_wf(l) / building_hwr(l) + vf_fw(l) = vf_wf(l) - ! This view factor implicitly converts from per unit roof area to per unit wall area vf_rw(l) = vf_fw(l) ! This view factor implicitly converts from per unit wall area to per unit roof area @@ -831,7 +829,7 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, + em_floori(l)*sb*t_floor_bef(l)**4._r8 & + 4._r8*em_floori(l)*sb*t_floor_bef(l)**3.*(t_floor(l) - t_floor_bef(l)) - qrd_building(l) = qrd_roof(l) + building_hwr(l)*(qrd_sunw(l) + qrd_shdw(l)) + qrd_floor(l) + qrd_building(l) = qrd_roof(l) + qrd_sunw(l) + qrd_shdw(l) + qrd_floor(l) if (abs(qrd_building(l)) > .10_r8 ) then write (iulog,*) 'urban inside building net longwave radiation balance error ',qrd_building(l) From 1b3d377bf76d225d98fd545228625f49076a8671 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Tue, 10 Oct 2023 16:42:25 -0600 Subject: [PATCH 1588/2067] Add comments --- src/biogeophys/UrbBuildTempOleson2015Mod.F90 | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 index 83422f0971..4c985f0ab3 100644 --- a/src/biogeophys/UrbBuildTempOleson2015Mod.F90 +++ b/src/biogeophys/UrbBuildTempOleson2015Mod.F90 @@ -383,9 +383,11 @@ subroutine BuildingTemperature (bounds, num_urbanl, filter_urbanl, num_nolakec, ! Get terms from soil temperature equations to compute conduction flux ! Negative is toward surface - heat added - ! Note that the conduction flux here is in W m-2 wall area but for purposes of solving the set of - ! simultaneous equations this must be converted to W m-2 floor area. This is done below when - ! setting up the equation coefficients. + ! Note that the convection and conduction fluxes for the walls are in W m-2 wall area + ! but for purposes of solving the set of simultaneous equations this must be converted to W m-2 + ! floor or roof area. This is done below when setting up the equation coefficients by multiplying by building_hwr. + ! Note also that the longwave radiation terms for the walls are in terms of W m-2 floor area since the view + ! factors implicitly convert from per unit wall area to per unit floor or roof area. do fc = 1,num_nolakec c = filter_nolakec(fc) From 7150f84ea1fdf88779af8384734f3b38bf20253a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 16:32:31 -0600 Subject: [PATCH 1589/2067] Specify stream_fldFileName_swindow_(start,end) instead of stream_fldFileName_sdate. * Replicate stream_fldFileName_sdate behavior by using same file for stream_fldFileName_swindow_start and stream_fldFileName_swindow_end. * RXCROPMATURITY test looks fine. --- bld/CLMBuildNamelist.pm | 15 +- .../namelist_definition_ctsm.xml | 9 +- cime_config/SystemTests/rxcropmaturity.py | 3 +- src/biogeochem/CNPhenologyMod.F90 | 90 ++++++----- src/biogeochem/CropType.F90 | 15 +- src/cpl/share_esmf/cropcalStreamMod.F90 | 141 +++++++++++++----- src/main/clm_varctl.F90 | 2 +- 7 files changed, 186 insertions(+), 89 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 2136cfc05c..ce486d9e1c 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -3962,21 +3962,28 @@ sub setup_logic_cropcal_streams { # Option checks my $generate_crop_gdds = $nl->get_value('generate_crop_gdds') ; my $use_mxmat = $nl->get_value('use_mxmat') ; - my $sdate_file = $nl->get_value('stream_fldFileName_sdate') ; + my $swindow_start_file = $nl->get_value('stream_fldFileName_swindow_start') ; + my $swindow_end_file = $nl->get_value('stream_fldFileName_swindow_end') ; my $gdd_file = $nl->get_value('stream_fldFileName_cultivar_gdds') ; my $mesh_file = $nl->get_value('stream_meshfile_cropcal') ; + if ( ($swindow_start_file eq '' and $swindow_start_file ne '') or ($swindow_start_file ne '' and $swindow_start_file eq '') ) { + $log->fatal_error("When specifying sowing window dates, you must provide both swindow_start_file and swindow_end_file. To specify exact sowing dates, use the same file." ); + } if ( $generate_crop_gdds eq '.true.' ) { if ( $use_mxmat eq '.true.' ) { $log->fatal_error("If generate_crop_gdds is true, you must also set use_mxmat to false" ); } - if ( $sdate_file eq '' ) { - $log->fatal_error("If generate_crop_gdds is true, you must specify stream_fldFileName_sdate") + if ( $swindow_start_file eq '' or $swindow_end_file eq '' ) { + $log->fatal_error("If generate_crop_gdds is true, you must specify stream_fldFileName_swindow_start and stream_fldFileName_swindow_end") + } + if ( $swindow_start_file ne $swindow_end_file ) { + $log->fatal_error("If generate_crop_gdds is true, you must specify exact sowing dates by setting stream_fldFileName_swindow_start and stream_fldFileName_swindow_end to the same file") } if ( $gdd_file ne '' ) { $log->fatal_error("If generate_crop_gdds is true, do not specify stream_fldFileName_cultivar_gdds") } } - if ( $mesh_file eq '' and ( $sdate_file ne '' or $gdd_file ne '' ) ) { + if ( $mesh_file eq '' and ( $swindow_start_file ne '' or $gdd_file ne '' ) ) { $log->fatal_error("If prescribing crop sowing dates and/or maturity requirements, you must specify stream_meshfile_cropcal") } } diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 9a0663c34f..caeab9eb48 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1835,9 +1835,14 @@ Last year to loop over for crop calendar data Simulation year that aligns with stream_year_first_cropcal value - -Filename of input stream data for sowing dates +Filename of input stream data for date (day of year) of start of sowing window + + + +Filename of input stream data for date (day of year) of end of sowing window crop_inst%fertnitro_patch , & ! Input: [real(r8) (:) ] fertilizer nitrogen hui => crop_inst%hui_patch , & ! Input: [real(r8) (:) ] crop patch heat unit index (growing degree-days); set to 0 at sowing and accumulated until harvest - leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature + leafout => crop_inst%gddtsoi_patch , & ! Input: [real(r8) (:) ] gdd from top soil layer temperature harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date - croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested + croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor - next_rx_sdate => crop_inst%next_rx_sdate_patch , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year + next_rx_swindow_start => crop_inst%next_rx_swindow_start_patch , & ! Inout: [integer (:) ] start of prescribed sowing window of next growing season this year + next_rx_swindow_end => crop_inst%next_rx_swindow_end_patch , & ! Inout: [integer (:) ] end of prescribed sowing window of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch harvest_count => crop_inst%harvest_count , & ! Inout: [integer (:) ] number of harvest events this year for this patch peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max @@ -1907,17 +1910,21 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch(p,k) = 0._r8 end do - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,1) + next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,1) + next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,1) end if - ! Get next sowing date + ! Get dates of next prescribed sowing window (if any) if (sowing_count(p) < mxsowings) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,sowing_count(p)+1) + next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) + next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) end if - ! CropType->InitAllocate() initializes next_rx_sdate to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_sdates is true. So if not using prescribed sowing dates, this boolean will always be false, because jday can never be -1. - do_plant_prescribed = next_rx_sdate(p) == jday .and. sowing_count(p) < mxsowings - + ! CropType->InitAllocate() initializes next_rx_swindow_start to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_swindows is true. So if not using prescribed sowing windows, this boolean will always be false, because jday can never be -1. + do_plant_prescribed = next_rx_swindow_start(p) == jday .and. sowing_count(p) < mxsowings + ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. + do_plant_prescribed = do_plant_prescribed .and. next_rx_swindow_start(p) == next_rx_swindow_end(p) + ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) ! When resuming from a run with old code, may need to manually set these. ! Will be needed until we can rely on all restart files have been generated @@ -1931,13 +1938,26 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. - is_in_sowing_window = is_doy_in_interval(minplantjday(ivt(p),h), maxplantjday(ivt(p),h), jday) - is_end_sowing_window = jday == maxplantjday(ivt(p),h) + if (use_cropcal_rx_swindows) then + if (sowing_count(p) < mxsowings) then + sowing_window_startdate = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) + sowing_window_enddate = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) + else ! Do not allow more sowings after reaching max number of sowings (mxsowings) + sowing_window_startdate = 999 + sowing_window_enddate = 999 + end if + else + sowing_window_startdate = minplantjday(ivt(p),h) + sowing_window_enddate = maxplantjday(ivt(p),h) + end if + is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) + is_end_sowing_window = jday == sowing_window_enddate ! ! Only allow sowing according to normal "window" rules if not using prescribed - ! sowing dates at all, or if this cell had no values in the prescribed sowing - ! date file. - allow_unprescribed_planting = (.not. use_cropcal_rx_sdates) .or. crop_inst%rx_sdates_thisyr_patch(p,1)<0 + ! sowing windows at all, or if this cell had no values in either of the + ! prescribed sowing window files. (Note that if either sowing window start was + ! or end was missing a value, they are both set to negative values.) + allow_unprescribed_planting = (.not. use_cropcal_rx_swindows) .or. crop_inst%rx_swindow_starts_thisyr_patch(p,1)<0 if (sowing_count(p) == mxsowings) then do_plant_normal = .false. do_plant_lastchance = .false. @@ -2140,7 +2160,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .false. fake_harvest = .false. did_plant_prescribed_today = .false. - if (use_cropcal_rx_sdates .and. sowing_count(p) > 0) then + if (use_cropcal_rx_swindows .and. sowing_count(p) > 0) then did_plant_prescribed_today = crop_inst%sdates_thisyr_patch(p,sowing_count(p)) == real(jday, r8) end if @@ -2161,10 +2181,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_reason = HARVEST_REASON_SOWTODAY ! If generate_crop_gdds and this patch has prescribed sowing inputs - else if (generate_crop_gdds .and. crop_inst%rx_sdates_thisyr_patch(p,1) .gt. 0) then - if (next_rx_sdate(p) >= 0) then - ! Harvest the day before the next sowing date this year. - do_harvest = jday == next_rx_sdate(p) - 1 + else if (generate_crop_gdds .and. crop_inst%rx_swindow_starts_thisyr_patch(p,1) .gt. 0) then + if (next_rx_swindow_start(p) >= 0) then + ! Harvest the day before the start of the next sowing window this year. + do_harvest = jday == next_rx_swindow_start(p) - 1 ! ... unless that will lead to growing season length 365 (or 366, ! if last year was a leap year). This would result in idop==jday, @@ -2188,10 +2208,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_harvest = .false. ! ... unless first sowing next year happens Jan. 1. - ! WARNING: This implementation assumes that sowing dates don't change over time! + ! WARNING: This implementation assumes that sowing windows don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed - ! sowing dates. - if (crop_inst%rx_sdates_thisyr_patch(p,1) == 1) then + ! sowing window start dates. + if (crop_inst%rx_swindow_starts_thisyr_patch(p,1) == 1) then do_harvest = jday == dayspyr end if @@ -2212,13 +2232,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat - ! Always harvest the day before the next prescribed sowing, if still alive. - ! WARNING: This implementation assumes that sowing dates don't change over time! + ! Always harvest the day before the next prescribed sowing window starts, if still alive. + ! WARNING: This implementation assumes that sowing windows don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed - ! sowing dates. - ! WARNING: This implementation assumes that all patches use prescribed sowing dates. - if (use_cropcal_rx_sdates) then - will_plant_prescribed_tomorrow = (jday == next_rx_sdate(p) - 1) .or. & + ! sowing windows. + ! WARNING: This implementation assumes that all patches use prescribed sowing windows. + if (use_cropcal_rx_swindows) then + will_plant_prescribed_tomorrow = (jday == next_rx_swindow_start(p) - 1) .or. & (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. & jday == dayspyr) else @@ -2497,7 +2517,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! !USES: use clm_varctl , only : use_c13, use_c14 - use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds, use_cropcal_streams + use clm_varctl , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams use clm_varcon , only : c13ratio, c14ratio use clm_varpar , only : mxsowings use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean @@ -2537,7 +2557,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date - next_rx_sdate => crop_inst%next_rx_sdate_patch , & ! Inout: [integer (:) ] prescribed sowing date of next growing season this year + next_rx_swindow_start => crop_inst%next_rx_swindow_start_patch , & ! Inout: [integer (:) ] start of prescribed sowing window of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch sowing_reason => crop_inst%sowing_reason_thisyr_patch , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest @@ -2568,10 +2588,10 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 - if (use_cropcal_rx_sdates .and. sowing_count(p) < mxsowings) then - next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p, sowing_count(p)+1) + if (use_cropcal_rx_swindows .and. sowing_count(p) < mxsowings) then + next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p, sowing_count(p)+1) else - next_rx_sdate(p) = -1 + next_rx_swindow_start(p) = -1 endif crop_inst%sdates_thisyr_patch(p,sowing_count(p)) = real(jday, r8) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index f84c4c1821..564f4babc8 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -47,8 +47,10 @@ module CropType character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope - integer , pointer :: next_rx_sdate_patch (:) ! prescribed sowing date for the next growing season this year - integer , pointer :: rx_sdates_thisyr_patch (:,:) ! all prescribed sowing dates for this patch this year (day of year) [patch, mxsowings] + integer , pointer :: next_rx_swindow_start_patch (:) ! start of prescribed sowing window for the next growing season this year + integer , pointer :: next_rx_swindow_end_patch (:) ! end of prescribed sowing window for the next growing season this year + integer , pointer :: rx_swindow_starts_thisyr_patch(:,:) ! all prescribed sowing window start dates for this patch this year (day of year) [patch, mxsowings] + integer , pointer :: rx_swindow_ends_thisyr_patch (:,:) ! all prescribed sowing window end dates for this patch this year (day of year) [patch, mxsowings] real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings] real(r8), pointer :: sdates_thisyr_patch (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings] real(r8), pointer :: sdates_perharv_patch (:,:) ! all actual sowing dates for crops *harvested* this year (day of year) [patch, mxharvests] @@ -227,8 +229,10 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = cphase_not_planted allocate(this%sowing_reason_patch (begp:endp)) ; this%sowing_reason_patch (:) = -1 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval - allocate(this%next_rx_sdate_patch(begp:endp)) ; this%next_rx_sdate_patch(:) = -1 - allocate(this%rx_sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_sdates_thisyr_patch(:,:) = -1 + allocate(this%next_rx_swindow_start_patch(begp:endp)) ; this%next_rx_swindow_start_patch(:) = -1 + allocate(this%next_rx_swindow_end_patch (begp:endp)) ; this%next_rx_swindow_end_patch (:) = -1 + allocate(this%rx_swindow_starts_thisyr_patch(begp:endp,1:mxsowings)); this%rx_swindow_starts_thisyr_patch(:,:) = -1 + allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_swindow_ends_thisyr_patch (:,:) = -1 allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval allocate(this%sdates_perharv_patch(begp:endp,1:mxharvests)) ; this%sdates_perharv_patch(:,:) = spval @@ -242,7 +246,8 @@ subroutine InitAllocate(this, bounds) allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 - this%rx_sdates_thisyr_patch(:,:) = -1 + this%rx_swindow_starts_thisyr_patch(:,:) = -1 + this%rx_swindow_ends_thisyr_patch (:,:) = -1 this%rx_cultivar_gdds_thisyr_patch(:,:) = spval end subroutine InitAllocate diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 8c2168d01d..91f565771d 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -13,7 +13,7 @@ module cropcalStreamMod use decompMod , only : bounds_type use abortutils , only : endrun use clm_varctl , only : iulog - use clm_varctl , only : use_cropcal_rx_sdates, use_cropcal_rx_cultivar_gdds, use_cropcal_streams + use clm_varctl , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams use clm_varpar , only : mxpft use perf_mod , only : t_startf, t_stopf use spmdMod , only : masterproc, mpicom, iam @@ -31,12 +31,14 @@ module cropcalStreamMod ! !PRIVATE MEMBER DATA: integer, allocatable :: g_to_ig(:) ! Array matching gridcell index to data index - type(shr_strdata_type) :: sdat_cropcal_sdate ! sdate input data stream + type(shr_strdata_type) :: sdat_cropcal_swindow_start ! sowing window start input data stream + type(shr_strdata_type) :: sdat_cropcal_swindow_end ! sowing window end input data stream type(shr_strdata_type) :: sdat_cropcal_cultivar_gdds ! sdate input data stream - character(len=CS), allocatable :: stream_varnames_sdate(:) + character(len=CS), allocatable :: stream_varnames_sdate(:) ! used for both start and end dates character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:) integer :: ncft ! Number of crop functional types (excl. generic crops) - character(len=CL) :: stream_fldFileName_sdate ! sdate stream filename to read + character(len=CL) :: stream_fldFileName_swindow_start ! sowing window start stream filename to read + character(len=CL) :: stream_fldFileName_swindow_end ! sowing window end stream filename to read character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read character(len=*), parameter :: sourcefile = & @@ -81,7 +83,8 @@ subroutine cropcal_init(bounds) stream_year_first_cropcal, & stream_year_last_cropcal, & model_year_align_cropcal, & - stream_fldFileName_sdate, & + stream_fldFileName_swindow_start, & + stream_fldFileName_swindow_end, & stream_fldFileName_cultivar_gdds, & stream_meshfile_cropcal @@ -90,7 +93,8 @@ subroutine cropcal_init(bounds) stream_year_last_cropcal = 1 ! last year in stream to use model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year stream_meshfile_cropcal = '' - stream_fldFileName_sdate = '' + stream_fldFileName_swindow_start = '' + stream_fldFileName_swindow_end = '' stream_fldFileName_cultivar_gdds = '' ! Will need modification to work with mxsowings > 1 ncft = mxpft - npcropmin + 1 ! Ignores generic crops @@ -119,7 +123,8 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_first_cropcal , mpicom) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) - call shr_mpi_bcast(stream_fldFileName_sdate , mpicom) + call shr_mpi_bcast(stream_fldFileName_swindow_start, mpicom) + call shr_mpi_bcast(stream_fldFileName_swindow_end , mpicom) call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom) call shr_mpi_bcast(stream_meshfile_cropcal , mpicom) @@ -129,7 +134,8 @@ subroutine cropcal_init(bounds) write(iulog,'(a,i8)') ' stream_year_first_cropcal = ',stream_year_first_cropcal write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal - write(iulog,'(a,a)' ) ' stream_fldFileName_sdate = ',trim(stream_fldFileName_sdate) + write(iulog,'(a,a)' ) ' stream_fldFileName_swindow_start = ',trim(stream_fldFileName_swindow_start) + write(iulog,'(a,a)' ) ' stream_fldFileName_swindow_end = ',trim(stream_fldFileName_swindow_end) write(iulog,'(a,a)' ) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) write(iulog,'(a,a)' ) ' stream_meshfile_cropcal = ',trim(stream_meshfile_cropcal) do n = 1,ncft @@ -139,14 +145,15 @@ subroutine cropcal_init(bounds) write(iulog,*) endif - use_cropcal_rx_sdates = stream_fldFileName_sdate /= '' + ! CLMBuildNamelist checks that both start and end files are provided if either is + use_cropcal_rx_swindows = stream_fldFileName_swindow_start /= '' use_cropcal_rx_cultivar_gdds = stream_fldFileName_cultivar_gdds /= '' - use_cropcal_streams = use_cropcal_rx_sdates .or. use_cropcal_rx_cultivar_gdds + use_cropcal_streams = use_cropcal_rx_swindows .or. use_cropcal_rx_cultivar_gdds - ! Initialize the cdeps data type sdat_cropcal_sdate + ! Initialize the cdeps data type sdat_cropcal_swindow_start ! NOTE: stream_dtlimit 1.5 didn't work for some reason - if (use_cropcal_rx_sdates) then - call shr_strdata_init_from_inline(sdat_cropcal_sdate, & + if (use_cropcal_rx_swindows) then + call shr_strdata_init_from_inline(sdat_cropcal_swindow_start, & my_task = iam, & logunit = iulog, & compname = 'LND', & @@ -155,7 +162,7 @@ subroutine cropcal_init(bounds) stream_meshfile = trim(stream_meshfile_cropcal), & stream_lev_dimname = 'null', & stream_mapalgo = trim(cropcal_mapalgo), & - stream_filenames = (/trim(stream_fldFileName_sdate)/), & + stream_filenames = (/trim(stream_fldFileName_swindow_start)/), & stream_fldlistFile = stream_varnames_sdate, & stream_fldListModel = stream_varnames_sdate, & stream_yearFirst = stream_year_first_cropcal, & @@ -165,7 +172,36 @@ subroutine cropcal_init(bounds) stream_taxmode = 'extend', & stream_dtlimit = 1.0e30_r8, & stream_tintalgo = cropcal_tintalgo, & - stream_name = 'sowing date data', & + stream_name = 'sowing window start data', & + rc = rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + end if + + ! Initialize the cdeps data type sdat_cropcal_swindow_end + ! NOTE: stream_dtlimit 1.5 didn't work for some reason + if (use_cropcal_rx_swindows) then + call shr_strdata_init_from_inline(sdat_cropcal_swindow_end, & + my_task = iam, & + logunit = iulog, & + compname = 'LND', & + model_clock = model_clock, & + model_mesh = mesh, & + stream_meshfile = trim(stream_meshfile_cropcal), & + stream_lev_dimname = 'null', & + stream_mapalgo = trim(cropcal_mapalgo), & + stream_filenames = (/trim(stream_fldFileName_swindow_end)/), & + stream_fldlistFile = stream_varnames_sdate, & + stream_fldListModel = stream_varnames_sdate, & + stream_yearFirst = stream_year_first_cropcal, & + stream_yearLast = stream_year_last_cropcal, & + stream_yearAlign = model_year_align_cropcal, & + stream_offset = cropcal_offset, & + stream_taxmode = 'extend', & + stream_dtlimit = 1.0e30_r8, & + stream_tintalgo = cropcal_tintalgo, & + stream_name = 'sowing window end data', & rc = rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) @@ -227,8 +263,12 @@ subroutine cropcal_advance( bounds ) call get_curr_date(year, mon, day, sec) mcdate = year*10000 + mon*100 + day - if (use_cropcal_rx_sdates) then - call shr_strdata_advance(sdat_cropcal_sdate, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (use_cropcal_rx_swindows) then + call shr_strdata_advance(sdat_cropcal_swindow_start, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + call shr_strdata_advance(sdat_cropcal_swindow_end, ymd=mcdate, tod=sec, logunit=iulog, istr='cropcaldyn', rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if @@ -275,9 +315,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) integer :: n, g integer :: lsize integer :: rc - real(r8), pointer :: dataptr1d_sdate(:) - real(r8), pointer :: dataptr2d_sdate(:,:) + real(r8), pointer :: dataptr1d_swindow_start(:) + real(r8), pointer :: dataptr1d_swindow_end (:) real(r8), pointer :: dataptr1d_cultivar_gdds(:) + real(r8), pointer :: dataptr2d_swindow_start(:,:) + real(r8), pointer :: dataptr2d_swindow_end (:,:) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) !----------------------------------------------------------------------- @@ -288,30 +330,39 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Place all data from each type into a temporary 2d array lsize = bounds%endg - bounds%begg + 1 - ! Read prescribed sowing dates from input files - allocate(dataptr2d_sdate(lsize, ncft)) - if (use_cropcal_rx_sdates) then + ! Read prescribed sowing window start dates from input files + allocate(dataptr2d_swindow_start(lsize, ncft)) + allocate(dataptr2d_swindow_end (lsize, ncft)) + if (use_cropcal_rx_swindows) then ! Starting with npcropmin will skip generic crops do n = 1, ncft - call dshr_fldbun_getFldPtr(sdat_cropcal_sdate%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & - fldptr1=dataptr1d_sdate, rc=rc) + call dshr_fldbun_getFldPtr(sdat_cropcal_swindow_start%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & + fldptr1=dataptr1d_swindow_start, rc=rc) + if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + call dshr_fldbun_getFldPtr(sdat_cropcal_swindow_end%pstrm(1)%fldbun_model, trim(stream_varnames_sdate(n)), & + fldptr1=dataptr1d_swindow_end, rc=rc) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if ! Note that the size of dataptr1d includes ocean points so it will be around 3x larger than lsize ! So an explicit loop is required here do g = 1,lsize - + ! If read-in value is invalid, allow_unprescribed_planting in CropPhenology() - if (dataptr1d_sdate(g) <= 0 .or. dataptr1d_sdate(g) > 365) then - dataptr1d_sdate(g) = -1 + if (dataptr1d_swindow_start(g) <= 0 .or. dataptr1d_swindow_start(g) > 365 & + .or. dataptr1d_swindow_end(g) <= 0 .or. dataptr1d_swindow_end(g) > 365) then + dataptr1d_swindow_start(g) = -1 + dataptr1d_swindow_end (g) = -1 end if - - dataptr2d_sdate(g,n) = dataptr1d_sdate(g) + + dataptr2d_swindow_start(g,n) = dataptr1d_swindow_start(g) + dataptr2d_swindow_end (g,n) = dataptr1d_swindow_end (g) end do end do - - ! Set rx_sdate for each gridcell/patch combination + + ! Set sowing window for each gridcell/patch combination do fp = 1, num_pcropp p = filter_pcropp(fp) ivt = patch%itype(p) @@ -320,27 +371,35 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) n = ivt - npcropmin + 1 ! vegetated pft ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_sdates_thisyr_patch(p,1) = dataptr2d_sdate(ig,n) + crop_inst%rx_swindow_starts_thisyr_patch(p,1) = dataptr2d_swindow_start(ig,n) + crop_inst%rx_swindow_ends_thisyr_patch (p,1) = dataptr2d_swindow_end (ig,n) ! Sanity check: Should only read in valid values - if (crop_inst%rx_sdates_thisyr_patch(p,1) > 365) then - write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing date ',& - crop_inst%rx_sdates_thisyr_patch(p,1) + if (crop_inst%rx_swindow_starts_thisyr_patch(p,1) > 365) then + write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window start date ',& + crop_inst%rx_swindow_starts_thisyr_patch(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - - ! Only for first sowing date of the year + if (crop_inst%rx_swindow_ends_thisyr_patch(p,1) > 365) then + write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window end date ',& + crop_inst%rx_swindow_ends_thisyr_patch(p,1) + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + + ! Only for first sowing window of the year ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 if (crop_inst%sdates_thisyr_patch(p,1) <= 0) then - crop_inst%next_rx_sdate_patch(p) = crop_inst%rx_sdates_thisyr_patch(p,1) + crop_inst%next_rx_swindow_start_patch(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,1) + crop_inst%next_rx_swindow_end_patch (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,1) end if else - write(iulog,'(a,i0)') 'cropcal_interp(), rx_sdates: Crop patch has ivt ',ivt + write(iulog,'(a,i0)') 'cropcal_interp(), prescribed sowing windows: Crop patch has ivt ',ivt call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do - end if ! use_cropcal_rx_sdates - deallocate(dataptr2d_sdate) + end if ! use_cropcal_rx_swindows + deallocate(dataptr2d_swindow_start) + deallocate(dataptr2d_swindow_end) allocate(dataptr2d_cultivar_gdds(lsize, ncft)) if (use_cropcal_rx_cultivar_gdds) then diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 7fe5d24bba..1ec698b68a 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -320,7 +320,7 @@ module clm_varctl !---------------------------------------------------------- logical, public :: use_cropcal_streams = .false. - logical, public :: use_cropcal_rx_sdates = .false. + logical, public :: use_cropcal_rx_swindows = .false. logical, public :: use_cropcal_rx_cultivar_gdds = .false. !---------------------------------------------------------- From 87c1d21f710d66dff48632bb2a790cc5abd1b1cf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 16:44:04 -0600 Subject: [PATCH 1590/2067] Added SWINDOW_STARTS and SWINDOW_ENDS outputs. --- src/biogeochem/CNPhenologyMod.F90 | 14 +++++++++++++- src/biogeochem/CropType.F90 | 14 ++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 15863774a7..369f304c19 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1892,6 +1892,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_count(p) = 0 do s = 1, mxsowings crop_inst%sdates_thisyr_patch(p,s) = -1._r8 + crop_inst%swindow_starts_thisyr_patch(p,s) = -1._r8 + crop_inst%swindow_ends_thisyr_patch (p,s) = -1._r8 crop_inst%sowing_reason_thisyr_patch(p,s) = -1._r8 end do do s = 1, mxharvests @@ -1914,7 +1916,9 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,1) end if - ! Get dates of next prescribed sowing window (if any) + ! Get dates of next prescribed sowing window (if any). + ! This can probably be converted to a recursive subroutine. + ! TODO: Rework this to not rely on sowing count, because if you missed a sowing window it's not "sowing count" if (sowing_count(p) < mxsowings) then next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) @@ -1938,6 +1942,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. + ! TODO: Rework this to not rely on sowing count, because if you missed a sowing window it's not "sowing count" if (use_cropcal_rx_swindows) then if (sowing_count(p) < mxsowings) then sowing_window_startdate = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) @@ -1953,6 +1958,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) is_end_sowing_window = jday == sowing_window_enddate ! + ! Save these diagnostic variables only on the first day of the window to ensure that windows spanning the new year aren't double-counted. + ! TODO: Rework this to not rely on sowing count, because if you missed a sowing window it's not "sowing count" + if (jday == sowing_window_startdate .and. sowing_count(p) < mxsowings) then + crop_inst%swindow_starts_thisyr_patch(p,sowing_count(p)+1) = sowing_window_startdate + crop_inst%swindow_ends_thisyr_patch (p,sowing_count(p)+1) = sowing_window_enddate + end if + ! ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing windows at all, or if this cell had no values in either of the ! prescribed sowing window files. (Note that if either sowing window start was diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 564f4babc8..2239d3e9bd 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -53,6 +53,8 @@ module CropType integer , pointer :: rx_swindow_ends_thisyr_patch (:,:) ! all prescribed sowing window end dates for this patch this year (day of year) [patch, mxsowings] real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings] real(r8), pointer :: sdates_thisyr_patch (:,:) ! all actual sowing dates for this patch this year (day of year) [patch, mxsowings] + real(r8), pointer :: swindow_starts_thisyr_patch(:,:) ! all sowing window start dates for this patch this year (day of year) [patch, mxsowings] + real(r8), pointer :: swindow_ends_thisyr_patch (:,:) ! all sowing window end dates for this patch this year (day of year) [patch, mxsowings] real(r8), pointer :: sdates_perharv_patch (:,:) ! all actual sowing dates for crops *harvested* this year (day of year) [patch, mxharvests] real(r8), pointer :: syears_perharv_patch (:,:) ! all actual sowing years for crops *harvested* this year (day of year) [patch, mxharvests] real(r8), pointer :: hdates_thisyr_patch (:,:) ! all actual harvest dates for this patch this year (day of year) [patch, mxharvests] @@ -235,6 +237,8 @@ subroutine InitAllocate(this, bounds) allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_swindow_ends_thisyr_patch (:,:) = -1 allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval allocate(this%sdates_thisyr_patch(begp:endp,1:mxsowings)) ; this%sdates_thisyr_patch(:,:) = spval + allocate(this%swindow_starts_thisyr_patch(begp:endp,1:mxsowings)) ; this%swindow_starts_thisyr_patch(:,:) = spval + allocate(this%swindow_ends_thisyr_patch (begp:endp,1:mxsowings)) ; this%swindow_ends_thisyr_patch (:,:) = spval allocate(this%sdates_perharv_patch(begp:endp,1:mxharvests)) ; this%sdates_perharv_patch(:,:) = spval allocate(this%syears_perharv_patch(begp:endp,1:mxharvests)) ; this%syears_perharv_patch(:,:) = spval allocate(this%hdates_thisyr_patch(begp:endp,1:mxharvests)) ; this%hdates_thisyr_patch(:,:) = spval @@ -307,6 +311,16 @@ subroutine InitHistory(this, bounds) avgflag='I', long_name='actual crop sowing dates; should only be output annually', & ptr_patch=this%sdates_thisyr_patch, default='inactive') + this%swindow_starts_thisyr_patch(begp:endp,:) = spval + call hist_addfld2d (fname='SWINDOW_STARTS', units='day of year', type2d='mxsowings', & + avgflag='I', long_name='crop sowing window start dates; should only be output annually', & + ptr_patch=this%swindow_starts_thisyr_patch, default='inactive') + + this%swindow_ends_thisyr_patch(begp:endp,:) = spval + call hist_addfld2d (fname='SWINDOW_ENDS', units='day of year', type2d='mxsowings', & + avgflag='I', long_name='crop sowing window end dates; should only be output annually', & + ptr_patch=this%swindow_ends_thisyr_patch, default='inactive') + this%sdates_perharv_patch(begp:endp,:) = spval call hist_addfld2d (fname='SDATES_PERHARV', units='day of year', type2d='mxharvests', & avgflag='I', long_name='actual sowing dates for crops harvested this year; should only be output annually', & From d9b7cdf22a74bb26b328e5137309b3cf88755d87 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 18 Sep 2023 16:54:21 -0600 Subject: [PATCH 1591/2067] CropPhenology() can now handle missed sowing windows. # Conflicts: # src/biogeochem/CNPhenologyMod.F90 --- src/biogeochem/CNPhenologyMod.F90 | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 369f304c19..68e3c446ef 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1922,6 +1922,14 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & if (sowing_count(p) < mxsowings) then next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) + ! Handle a missed sowing window + if (next_rx_swindow_start(p) < next_rx_swindow_end(p) .and. jday > next_rx_swindow_end(p)) then + sowing_count(p) = sowing_count(p) + 1 + if (sowing_count(p) < mxsowings) then + next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) + next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) + end if + end if end if ! CropType->InitAllocate() initializes next_rx_swindow_start to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_swindows is true. So if not using prescribed sowing windows, this boolean will always be false, because jday can never be -1. From c3fd7f3a6eada961aa625399f03b94b888cc1085 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 19 Sep 2023 13:53:05 -0600 Subject: [PATCH 1592/2067] Prevent crops from being sown twice in one sowing window. --- src/biogeochem/CNPhenologyMod.F90 | 12 +++++++++++- src/biogeochem/CropType.F90 | 27 +++++++++++++++++++++++++++ 2 files changed, 38 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 68e3c446ef..6336c926fd 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1726,7 +1726,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & use clm_time_manager , only : get_prev_calday, get_curr_days_per_year, is_beg_curr_year use clm_time_manager , only : get_average_days_per_year use clm_time_manager , only : get_prev_date - use clm_time_manager , only : is_doy_in_interval + use clm_time_manager , only : is_doy_in_interval, is_end_curr_day use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice @@ -1964,6 +1964,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sowing_window_enddate = maxplantjday(ivt(p),h) end if is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) + if (crop_inst%sown_in_this_window(p) .and. .not. is_in_sowing_window) then + ! Probably unnecessary since it's set to false in last timestep of sowing window at the end of CropPhenology() + crop_inst%sown_in_this_window(p) = .false. + end if is_end_sowing_window = jday == sowing_window_enddate ! ! Save these diagnostic variables only on the first day of the window to ensure that windows spanning the new year aren't double-counted. @@ -2388,6 +2392,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & endif end if ! croplive + ! At the end of the sowing window, AFTER we've done everything crop-related, set this to false + if (is_end_sowing_window .and. is_end_curr_day()) then + crop_inst%sown_in_this_window(p) = .false. + end if + end do ! prognostic crops loop end associate @@ -2603,6 +2612,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! impose limit on growing season length needed ! for crop maturity - for cold weather constraints croplive(p) = .true. + crop_inst%sown_in_this_window(p) = .true. idop(p) = jday iyop(p) = kyr harvdate(p) = NOT_Harvested diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 2239d3e9bd..f1e0bba7cf 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -47,6 +47,7 @@ module CropType character(len=20) :: baset_mapping real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope + logical , pointer :: sown_in_this_window (:) ! patch flag. True if the crop has already been sown during the current sowing window. False otherwise or if not in a sowing window. integer , pointer :: next_rx_swindow_start_patch (:) ! start of prescribed sowing window for the next growing season this year integer , pointer :: next_rx_swindow_end_patch (:) ! end of prescribed sowing window for the next growing season this year integer , pointer :: rx_swindow_starts_thisyr_patch(:,:) ! all prescribed sowing window start dates for this patch this year (day of year) [patch, mxsowings] @@ -231,6 +232,7 @@ subroutine InitAllocate(this, bounds) allocate(this%cphase_patch (begp:endp)) ; this%cphase_patch (:) = cphase_not_planted allocate(this%sowing_reason_patch (begp:endp)) ; this%sowing_reason_patch (:) = -1 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval + allocate(this%sown_in_this_window(begp:endp)) ; this%sown_in_this_window(:) = .false. allocate(this%next_rx_swindow_start_patch(begp:endp)) ; this%next_rx_swindow_start_patch(:) = -1 allocate(this%next_rx_swindow_end_patch (begp:endp)) ; this%next_rx_swindow_end_patch (:) = -1 allocate(this%rx_swindow_starts_thisyr_patch(begp:endp,1:mxsowings)); this%rx_swindow_starts_thisyr_patch(:,:) = -1 @@ -605,6 +607,31 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) end if deallocate(temp1d) + allocate(temp1d(bounds%begp:bounds%endp)) + if (flag == 'write') then + do p= bounds%begp,bounds%endp + if (this%sown_in_this_window(p)) then + temp1d(p) = 1 + else + temp1d(p) = 0 + end if + end do + end if + call restartvar(ncid=ncid, flag=flag, varname='sown_in_this_window', xtype=ncd_log, & + dim1name='pft', & + long_name='Flag that patch was sown already during the current sowing window', & + interpinic_flag='interp', readvar=readvar, data=temp1d) + if (flag == 'read') then + do p= bounds%begp,bounds%endp + if (temp1d(p) == 1) then + this%sown_in_this_window(p) = .true. + else + this%sown_in_this_window(p) = .false. + end if + end do + end if + deallocate(temp1d) + call restartvar(ncid=ncid, flag=flag, varname='harvdate', xtype=ncd_int, & dim1name='pft', long_name='harvest date', units='jday', nvalid_range=(/1,366/), & interpinic_flag='interp', readvar=readvar, data=this%harvdate_patch) From 1b55382b1d4ab52114cb5e4b4397058d1884201a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 20 Sep 2023 16:19:14 -0600 Subject: [PATCH 1593/2067] Actually USE sown_in_this_window. --- src/biogeochem/CNPhenologyMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 6336c926fd..d85ac7e015 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2018,6 +2018,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & gdd820(p) /= spval end if do_plant = do_plant_prescribed .or. do_plant_normal .or. do_plant_lastchance + do_plant = do_plant .and. .not. crop_inst%sown_in_this_window(p) did_plant = .false. ! Once outputs can handle >1 planting per year, remove 2nd condition. From dcc55d604ab3a31c9813d31653f572d892b15aa4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 25 Sep 2023 22:11:35 -0600 Subject: [PATCH 1594/2067] Use paramfile if either rx sowing window value is missing. --- src/biogeochem/CNPhenologyMod.F90 | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index d85ac7e015..076fd7e27e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1959,7 +1959,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & sowing_window_startdate = 999 sowing_window_enddate = 999 end if - else + end if + ! Fall back on parameter file in case either prescribed sowing window value is missing, or if not using prescribed sowing windows at all. + ! TODO: Test whether ".or. .not. use_cropcal_rx_swindows" is necessary. I think not: in that case, rx_swindow_starts_thisyr_patch and rx_swindow_ends_thisyr_patch are initialized to and stay -1. + if (min(sowing_window_startdate, sowing_window_enddate) <= 0 .or. .not. use_cropcal_rx_swindows) then sowing_window_startdate = minplantjday(ivt(p),h) sowing_window_enddate = maxplantjday(ivt(p),h) end if From 6e110401181331b207ed4e6ff27f48f8d64abf5e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Sep 2023 08:56:12 -0600 Subject: [PATCH 1595/2067] Add subroutines get_doy_tomorrow() and get_swindow(), plus unit tests. Currently unused. --- src/biogeochem/CNPhenologyMod.F90 | 99 +++++++++++++++++++ .../test/CNPhenology_test/test_CNPhenology.pf | 94 ++++++++++++++++++ src/cpl/share_esmf/cropcalStreamMod.F90 | 6 ++ src/utils/clm_time_manager.F90 | 18 ++++ .../test_clm_time_manager.pf | 13 +++ 5 files changed, 230 insertions(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 076fd7e27e..a3c65e6fb9 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -58,6 +58,7 @@ module CNPhenologyMod public :: CNPhenologySetParams ! Set the parameters explicitly for unit tests public :: SeasonalDecidOnset ! Logical function to determine is seasonal decidious onset should be triggered public :: SeasonalCriticalDaylength ! Critical day length needed for Seasonal decidious offset + public :: get_swindow ! !PRIVITE MEMBER FIUNCTIONS: private :: CNPhenologyClimate ! Get climatological everages to figure out triggers for Phenology @@ -1712,6 +1713,104 @@ subroutine CNStressDecidPhenology (num_soilp, filter_soilp , & end subroutine CNStressDecidPhenology + + !----------------------------------------------------------------------- + subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + ! !DESCRIPTION: + ! Determine when the "next" sowing window is. This is either the sowing window we are + ! currently in or, if not in a sowing window, the next one that will occur. + + ! !USES: + use clm_time_manager , only : get_curr_days_per_year, is_doy_in_interval, get_doy_tomorrow + ! !ARGUMENTS: + integer, intent(in) :: jday ! Day of year + integer, dimension(:), intent(in) :: rx_starts, rx_ends ! All prescribed sowing window start and end dates for this patch + integer, intent(in) :: param_start, param_end ! Sowing window start and end dates from parameter file + integer, intent(out) :: w ! Index of "next" sowing window + integer, intent(out) :: start_w, end_w ! Start and end dates of "next" sowing window + logical, intent(out) :: sowing_window_starts_tomorrow + ! + ! !LOCAL VARIABLES + integer :: next_swindow_start + integer :: i, x + integer :: jday_tomorrow + integer :: mxsowings_in ! Due to unit testing, we can't assume the length of the rx sowing window arrays is mxsowings as set in clm_varpar + + ! Initialize + w = -1 + start_w = -1 + end_w = -1 + + ! Get info + jday_tomorrow = get_doy_tomorrow(jday) + mxsowings_in = size(rx_starts) + + ! If no sowing windows are prescribed, use the values from the parameter file. + if (maxval(rx_starts) < 1) then + w = 1 + start_w = param_start + end_w = param_end + + ! Otherwise, if today is after the latest sowing window end date, use the first sowing window. This works only if sowing windows that span the new year are located at index w = 1. + else if (jday > maxval(rx_ends)) then + w = 1 + start_w = rx_starts(w) + end_w = rx_ends(w) + end if + + ! If we already got sowing window dates, do this and exit. + if (w > 0) then + sowing_window_starts_tomorrow = start_w == jday_tomorrow + return + end if + + ! Otherwise, use the first prescribed sowing window we find whose end is >= today. + do w = 1, mxsowings_in + ! If nothing prescribed at this w, stop looking and exit loop. + if (min(rx_starts(w), rx_ends(w)) < 0) then + exit + end if + + if (jday <= rx_ends(w)) then + start_w = rx_starts(w) + end_w = rx_ends(w) + exit + end if + end do + + ! Ensure that a window was found + if (start_w < 1 .or. end_w < 1) then + call endrun(msg="get_swindow(): No sowing window found") + end if + + ! Get the start date of the NEXT sowing window (not including the sowing window we're currently in, if any) + if (is_doy_in_interval(start_w, end_w, jday)) then + next_swindow_start = -1 + x = w + i = 0 ! For checking infinite loop + do while (next_swindow_start < 1) + ! Check for infinite loop + i = i + 1 + if (i > mxsowings_in + 1) then + call endrun("Infinite loop in get_swindow()") + end if + + x = x + 1 + if (x > mxsowings_in) then + x = 1 + end if + next_swindow_start = rx_starts(x) + end do + else + next_swindow_start = start_w + end if + + ! Does the NEXT sowing window start tomorrow? + sowing_window_starts_tomorrow = next_swindow_start == jday_tomorrow + + end subroutine get_swindow + + !----------------------------------------------------------------------- subroutine CropPhenology(num_pcropp, filter_pcropp , & waterdiagnosticbulk_inst, temperature_inst, crop_inst, canopystate_inst, cnveg_state_inst , & diff --git a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf index 135364e474..ebab50ad13 100644 --- a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf +++ b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf @@ -293,6 +293,100 @@ contains end do end subroutine check_crit_dayl_dependsonlatnveg + @Test + subroutine test_get_swindow_startend(this) + use clm_time_manager, only : get_curr_days_per_year + class(TestCNPhenology), intent(inout) :: this + integer, dimension(3), parameter :: rx_starts = (/1, 150, -1/) + integer, dimension(3), parameter :: rx_ends = (/45, 180, -1/) + integer, parameter :: param_start = 200 + integer, parameter :: param_end = 250 + integer :: w, start_w, end_w + logical :: sowing_window_starts_tomorrow + + call get_swindow(1, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(1, start_w) + @assertEqual(45, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(45, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(1, start_w) + @assertEqual(45, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(149, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(2, w) + @assertEqual(150, start_w) + @assertEqual(180, end_w) + @assertTrue(sowing_window_starts_tomorrow) + + call get_swindow(175, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(2, w) + @assertEqual(150, start_w) + @assertEqual(180, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(229, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(1, start_w) + @assertEqual(45, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(get_curr_days_per_year(), rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(1, start_w) + @assertEqual(45, end_w) + @assertTrue(sowing_window_starts_tomorrow) + end subroutine test_get_swindow_startend + @Test + subroutine test_get_swindow_endstart(this) + use clm_time_manager, only : get_curr_days_per_year + class(TestCNPhenology), intent(inout) :: this + integer, dimension(3), parameter :: rx_starts = (/360, 150, -1/) + integer, dimension(3), parameter :: rx_ends = (/45, 180, -1/) + integer, parameter :: param_start = 200 + integer, parameter :: param_end = 250 + integer :: w, start_w, end_w + logical :: sowing_window_starts_tomorrow + + call get_swindow(1, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(360, start_w) + @assertEqual(45, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(45, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(start_w, 360) + @assertEqual(end_w, 45) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(149, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(2, w) + @assertEqual(150, start_w) + @assertEqual(180, end_w) + @assertTrue(sowing_window_starts_tomorrow) + + call get_swindow(175, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(2, w) + @assertEqual(150, start_w) + @assertEqual(180, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(229, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(360, start_w) + @assertEqual(45, end_w) + @assertFalse(sowing_window_starts_tomorrow) + + call get_swindow(get_curr_days_per_year(), rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + @assertEqual(1, w) + @assertEqual(360, start_w) + @assertEqual(45, end_w) + @assertFalse(sowing_window_starts_tomorrow) + end subroutine test_get_swindow_endstart end module test_CNPhenology diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 91f565771d..5f91cc391e 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -389,6 +389,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Only for first sowing window of the year ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 if (crop_inst%sdates_thisyr_patch(p,1) <= 0) then + ! TODO: Add handling of mid-year restarts crop_inst%next_rx_swindow_start_patch(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,1) crop_inst%next_rx_swindow_end_patch (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,1) end if @@ -397,6 +398,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) endif end do + + ! TODO: Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. This is necessary because of how get_swindow() works. + + ! TODO: Fail if a sowing window start date is prescribed without an end date (or vice versa) + end if ! use_cropcal_rx_swindows deallocate(dataptr2d_swindow_start) deallocate(dataptr2d_swindow_end) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 5c65f5decd..14572935c3 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -42,6 +42,7 @@ module clm_time_manager get_prev_calday, &! return calendar day at beginning of current timestep get_calday, &! return calendar day from input date get_calendar, &! return calendar + get_doy_tomorrow, &! return next day of year get_average_days_per_year,&! return the average number of days per year for the given calendar get_curr_days_per_year, &! return the days per year for year as of the end of the current time step get_prev_days_per_year, &! return the days per year for year as of the beginning of the current time step @@ -1274,6 +1275,23 @@ end function get_calendar !========================================================================================= + function get_doy_tomorrow(doy_today) result(doy_tomorrow) + + !--------------------------------------------------------------------------------- + ! Given a day of the year (doy_today), return the next day of the year + + integer, intent(in) :: doy_today + integer :: doy_tomorrow + + if (doy_today == get_curr_days_per_year()) then + doy_tomorrow = 1 + else + doy_tomorrow = doy_today + 1 + end if + end function get_doy_tomorrow + + !========================================================================================= + real(r8) function get_average_days_per_year() !--------------------------------------------------------------------------------- diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index 78565fd54d..0665e5f6d0 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -658,4 +658,17 @@ contains end subroutine check_is_today_in_doy_interval + @Test + subroutine check_get_doy_tomorrow(this) + class(TestTimeManager), intent(inout) :: this + + ! We don't care about the actual date here; we just want to enable get_curr_days_per_year() + call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call set_date(yr=2009, mon=10, day=28, tod=dtime) + + @assertEqual(get_doy_tomorrow(1), 2) + @assertEqual(get_doy_tomorrow(150), 151) + @assertEqual(get_doy_tomorrow(get_curr_days_per_year()), 1) + end subroutine check_get_doy_tomorrow + end module test_clm_time_manager From 9104f88cd2c4e8691ae7f704e9447a5e882bf2af Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Sep 2023 10:07:11 -0600 Subject: [PATCH 1596/2067] Use get_swindow() in CropPhenology(). * Allows significant cleanup there and hopefully fixes a bug. * Removed from CropType: next_rx_swindow_start, next_rx_swindow_end. --- src/biogeochem/CNPhenologyMod.F90 | 84 ++++++------------------- src/biogeochem/CropType.F90 | 4 -- src/cpl/share_esmf/cropcalStreamMod.F90 | 8 --- 3 files changed, 20 insertions(+), 76 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a3c65e6fb9..ff01a3a2f3 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1862,6 +1862,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer h ! hemisphere indices integer s ! growing season indices integer k ! grain pool indices + integer w ! sowing window index integer idpp ! number of days past planting integer mxmat ! maximum growing season length integer kyr ! current year @@ -1870,6 +1871,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer mcsec ! seconds of day (0, ..., seconds/day) integer sowing_window_startdate ! date (day of year) of first day of sowing window integer sowing_window_enddate ! date (day of year) of last day of sowing window + logical sowing_window_starts_tomorrow ! Is tomorrow the start of a sowing window? real(r8) harvest_reason real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year @@ -1887,7 +1889,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & logical do_harvest ! Are harvest conditions satisfied? logical fake_harvest ! Dealing with incorrect Dec. 31 planting logical did_plant_prescribed_today ! Was the crop sown today? - logical will_plant_prescribed_tomorrow ! Is tomorrow a prescribed sowing day? logical vernalization_forces_harvest ! Was the crop killed by freezing during vernalization? !------------------------------------------------------------------------ @@ -1916,8 +1917,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested vf => crop_inst%vf_patch , & ! Output: [real(r8) (:) ] vernalization factor - next_rx_swindow_start => crop_inst%next_rx_swindow_start_patch , & ! Inout: [integer (:) ] start of prescribed sowing window of next growing season this year - next_rx_swindow_end => crop_inst%next_rx_swindow_end_patch , & ! Inout: [integer (:) ] end of prescribed sowing window of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch harvest_count => crop_inst%harvest_count , & ! Inout: [integer (:) ] number of harvest events this year for this patch peaklai => cnveg_state_inst%peaklai_patch , & ! Output: [integer (:) ] 1: max allowed lai; 0: not at max @@ -2011,30 +2010,16 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch(p,k) = 0._r8 end do - next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,1) - next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,1) end if - ! Get dates of next prescribed sowing window (if any). - ! This can probably be converted to a recursive subroutine. - ! TODO: Rework this to not rely on sowing count, because if you missed a sowing window it's not "sowing count" - if (sowing_count(p) < mxsowings) then - next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) - next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) - ! Handle a missed sowing window - if (next_rx_swindow_start(p) < next_rx_swindow_end(p) .and. jday > next_rx_swindow_end(p)) then - sowing_count(p) = sowing_count(p) + 1 - if (sowing_count(p) < mxsowings) then - next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) - next_rx_swindow_end (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) - end if - end if - end if + ! Get dates of current or next sowing window. + call get_swindow(jday, crop_inst%rx_swindow_starts_thisyr_patch(p,:), crop_inst%rx_swindow_ends_thisyr_patch(p,:), minplantjday(ivt(p),h), maxplantjday(ivt(p),h), w, sowing_window_startdate, sowing_window_enddate, sowing_window_starts_tomorrow) - ! CropType->InitAllocate() initializes next_rx_swindow_start to -1. It's only changed from that, by cropCalStreamMod->cropcal_interp(), when use_cropcal_rx_swindows is true. So if not using prescribed sowing windows, this boolean will always be false, because jday can never be -1. - do_plant_prescribed = next_rx_swindow_start(p) == jday .and. sowing_count(p) < mxsowings - ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. - do_plant_prescribed = do_plant_prescribed .and. next_rx_swindow_start(p) == next_rx_swindow_end(p) + ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. Also make sure we haven't planted yet today. + ! TODO: Change last condition to `maxval(crop_inst%sdates_perharv_patch(p,:)) /= jday` + do_plant_prescribed = sowing_window_startdate == jday .and. & + sowing_window_enddate == jday .and. & + sowing_count (p) < mxsowings ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) ! When resuming from a run with old code, may need to manually set these. @@ -2048,35 +2033,19 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%sdates_thisyr_patch(p,1) = real(idop(p), r8) end if + ! Are we currently in a sowing window? ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. - ! TODO: Rework this to not rely on sowing count, because if you missed a sowing window it's not "sowing count" - if (use_cropcal_rx_swindows) then - if (sowing_count(p) < mxsowings) then - sowing_window_startdate = crop_inst%rx_swindow_starts_thisyr_patch(p,sowing_count(p)+1) - sowing_window_enddate = crop_inst%rx_swindow_ends_thisyr_patch (p,sowing_count(p)+1) - else ! Do not allow more sowings after reaching max number of sowings (mxsowings) - sowing_window_startdate = 999 - sowing_window_enddate = 999 - end if - end if - ! Fall back on parameter file in case either prescribed sowing window value is missing, or if not using prescribed sowing windows at all. - ! TODO: Test whether ".or. .not. use_cropcal_rx_swindows" is necessary. I think not: in that case, rx_swindow_starts_thisyr_patch and rx_swindow_ends_thisyr_patch are initialized to and stay -1. - if (min(sowing_window_startdate, sowing_window_enddate) <= 0 .or. .not. use_cropcal_rx_swindows) then - sowing_window_startdate = minplantjday(ivt(p),h) - sowing_window_enddate = maxplantjday(ivt(p),h) - end if is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) if (crop_inst%sown_in_this_window(p) .and. .not. is_in_sowing_window) then - ! Probably unnecessary since it's set to false in last timestep of sowing window at the end of CropPhenology() + ! TODO: Test whether this is necessary, since it's set to false in last timestep of sowing window at the end of CropPhenology(). crop_inst%sown_in_this_window(p) = .false. end if is_end_sowing_window = jday == sowing_window_enddate ! ! Save these diagnostic variables only on the first day of the window to ensure that windows spanning the new year aren't double-counted. - ! TODO: Rework this to not rely on sowing count, because if you missed a sowing window it's not "sowing count" - if (jday == sowing_window_startdate .and. sowing_count(p) < mxsowings) then - crop_inst%swindow_starts_thisyr_patch(p,sowing_count(p)+1) = sowing_window_startdate - crop_inst%swindow_ends_thisyr_patch (p,sowing_count(p)+1) = sowing_window_enddate + if (jday == sowing_window_startdate) then + crop_inst%swindow_starts_thisyr_patch(p,w) = sowing_window_startdate + crop_inst%swindow_ends_thisyr_patch (p,w) = sowing_window_enddate end if ! ! Only allow sowing according to normal "window" rules if not using prescribed @@ -2308,10 +2277,11 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_reason = HARVEST_REASON_SOWTODAY ! If generate_crop_gdds and this patch has prescribed sowing inputs + ! TODO: Shouldn't this also apply to paramfile sowing windows? else if (generate_crop_gdds .and. crop_inst%rx_swindow_starts_thisyr_patch(p,1) .gt. 0) then - if (next_rx_swindow_start(p) >= 0) then - ! Harvest the day before the start of the next sowing window this year. - do_harvest = jday == next_rx_swindow_start(p) - 1 + if (sowing_window_startdate >= 0) then + ! Harvest the day before the start of the next sowing window. + do_harvest = sowing_window_starts_tomorrow ! ... unless that will lead to growing season length 365 (or 366, ! if last year was a leap year). This would result in idop==jday, @@ -2363,21 +2333,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! WARNING: This implementation assumes that sowing windows don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed ! sowing windows. - ! WARNING: This implementation assumes that all patches use prescribed sowing windows. - if (use_cropcal_rx_swindows) then - will_plant_prescribed_tomorrow = (jday == next_rx_swindow_start(p) - 1) .or. & - (crop_inst%sdates_thisyr_patch(p,1) == 1 .and. & - jday == dayspyr) - else - will_plant_prescribed_tomorrow = .false. - end if - do_harvest = do_harvest .or. will_plant_prescribed_tomorrow + do_harvest = do_harvest .or. sowing_window_starts_tomorrow if (hui(p) >= gddmaturity(p)) then harvest_reason = HARVEST_REASON_MATURE else if (idpp >= mxmat) then harvest_reason = HARVEST_REASON_MAXSEASLENGTH - else if (will_plant_prescribed_tomorrow) then + else if (sowing_window_starts_tomorrow) then harvest_reason = HARVEST_REASON_SOWTOMORROW end if endif @@ -2689,7 +2651,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ivt => patch%itype , & ! Input: [integer (:) ] patch vegetation type croplive => crop_inst%croplive_patch , & ! Output: [logical (:) ] Flag, true if planted, not harvested harvdate => crop_inst%harvdate_patch , & ! Output: [integer (:) ] harvest date - next_rx_swindow_start => crop_inst%next_rx_swindow_start_patch , & ! Inout: [integer (:) ] start of prescribed sowing window of next growing season this year sowing_count => crop_inst%sowing_count , & ! Inout: [integer (:) ] number of sowing events this year for this patch sowing_reason => crop_inst%sowing_reason_thisyr_patch , & ! Output: [real(r8) (:) ] reason for each sowing this year for this patch gddmaturity => cnveg_state_inst%gddmaturity_patch , & ! Output: [real(r8) (:) ] gdd needed to harvest @@ -2721,11 +2682,6 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & harvdate(p) = NOT_Harvested sowing_count(p) = sowing_count(p) + 1 - if (use_cropcal_rx_swindows .and. sowing_count(p) < mxsowings) then - next_rx_swindow_start(p) = crop_inst%rx_swindow_starts_thisyr_patch(p, sowing_count(p)+1) - else - next_rx_swindow_start(p) = -1 - endif crop_inst%sdates_thisyr_patch(p,sowing_count(p)) = real(jday, r8) this_sowing_reason = 0._r8 diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index f1e0bba7cf..6d101df456 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -48,8 +48,6 @@ module CropType real(r8) :: baset_latvary_intercept real(r8) :: baset_latvary_slope logical , pointer :: sown_in_this_window (:) ! patch flag. True if the crop has already been sown during the current sowing window. False otherwise or if not in a sowing window. - integer , pointer :: next_rx_swindow_start_patch (:) ! start of prescribed sowing window for the next growing season this year - integer , pointer :: next_rx_swindow_end_patch (:) ! end of prescribed sowing window for the next growing season this year integer , pointer :: rx_swindow_starts_thisyr_patch(:,:) ! all prescribed sowing window start dates for this patch this year (day of year) [patch, mxsowings] integer , pointer :: rx_swindow_ends_thisyr_patch (:,:) ! all prescribed sowing window end dates for this patch this year (day of year) [patch, mxsowings] real(r8), pointer :: rx_cultivar_gdds_thisyr_patch (:,:) ! all cultivar GDD targets for this patch this year (ddays) [patch, mxsowings] @@ -233,8 +231,6 @@ subroutine InitAllocate(this, bounds) allocate(this%sowing_reason_patch (begp:endp)) ; this%sowing_reason_patch (:) = -1 allocate(this%latbaset_patch (begp:endp)) ; this%latbaset_patch (:) = spval allocate(this%sown_in_this_window(begp:endp)) ; this%sown_in_this_window(:) = .false. - allocate(this%next_rx_swindow_start_patch(begp:endp)) ; this%next_rx_swindow_start_patch(:) = -1 - allocate(this%next_rx_swindow_end_patch (begp:endp)) ; this%next_rx_swindow_end_patch (:) = -1 allocate(this%rx_swindow_starts_thisyr_patch(begp:endp,1:mxsowings)); this%rx_swindow_starts_thisyr_patch(:,:) = -1 allocate(this%rx_swindow_ends_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_swindow_ends_thisyr_patch (:,:) = -1 allocate(this%rx_cultivar_gdds_thisyr_patch(begp:endp,1:mxsowings)) ; this%rx_cultivar_gdds_thisyr_patch(:,:) = spval diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 5f91cc391e..8ad162783c 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -385,14 +385,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) crop_inst%rx_swindow_ends_thisyr_patch(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - - ! Only for first sowing window of the year - ! The conditional here is to ensure nothing weird happens if it's called incorrectly on day 365 - if (crop_inst%sdates_thisyr_patch(p,1) <= 0) then - ! TODO: Add handling of mid-year restarts - crop_inst%next_rx_swindow_start_patch(p) = crop_inst%rx_swindow_starts_thisyr_patch(p,1) - crop_inst%next_rx_swindow_end_patch (p) = crop_inst%rx_swindow_ends_thisyr_patch (p,1) - end if else write(iulog,'(a,i0)') 'cropcal_interp(), prescribed sowing windows: Crop patch has ivt ',ivt call ESMF_Finalize(endflag=ESMF_END_ABORT) From e5a3dc0c1732c2fab8793ef66e61136964ea01f2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Sep 2023 10:41:26 -0600 Subject: [PATCH 1597/2067] Added a TODO. --- src/biogeochem/CNPhenologyMod.F90 | 1 + 1 file changed, 1 insertion(+) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index ff01a3a2f3..fc680d74c9 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2043,6 +2043,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & is_end_sowing_window = jday == sowing_window_enddate ! ! Save these diagnostic variables only on the first day of the window to ensure that windows spanning the new year aren't double-counted. + ! TODO: Change this to the LAST day of the window, to ensure the same ordering as required for rx sowing window input files. if (jday == sowing_window_startdate) then crop_inst%swindow_starts_thisyr_patch(p,w) = sowing_window_startdate crop_inst%swindow_ends_thisyr_patch (p,w) = sowing_window_enddate From b0107fda54367d82dfa6c6c46435b755da3953a1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 28 Sep 2023 21:01:13 -0600 Subject: [PATCH 1598/2067] Bugfix to allow_unprescribed_planting. --- src/biogeochem/CNPhenologyMod.F90 | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index fc680d74c9..3ab8ee1eae 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2050,10 +2050,8 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! ! Only allow sowing according to normal "window" rules if not using prescribed - ! sowing windows at all, or if this cell had no values in either of the - ! prescribed sowing window files. (Note that if either sowing window start was - ! or end was missing a value, they are both set to negative values.) - allow_unprescribed_planting = (.not. use_cropcal_rx_swindows) .or. crop_inst%rx_swindow_starts_thisyr_patch(p,1)<0 + ! sowing dates. + allow_unprescribed_planting = sowing_window_startdate /= sowing_window_enddate if (sowing_count(p) == mxsowings) then do_plant_normal = .false. do_plant_lastchance = .false. From 1693c0d829428ed59f92a7cce1a8adb6d2345fa3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Sep 2023 09:05:10 -0600 Subject: [PATCH 1599/2067] Reverted behavior change re: HARVEST_REASON_SOWTOMORROW. Now only happens if patch actually has a prescribed sowing DAY, instead of happening at the start of the window. This had caused answer changes for sugarcane. --- src/biogeochem/CNPhenologyMod.F90 | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 3ab8ee1eae..7b9471c67a 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1826,6 +1826,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & use clm_time_manager , only : get_average_days_per_year use clm_time_manager , only : get_prev_date use clm_time_manager , only : is_doy_in_interval, is_end_curr_day + use clm_time_manager , only : get_doy_tomorrow use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean use pftconMod , only : nirrig_tmp_corn, nirrig_swheat, nirrig_wwheat, nirrig_tmp_soybean use pftconMod , only : ntrp_corn, nsugarcane, ntrp_soybean, ncotton, nrice @@ -1877,12 +1878,14 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & real(r8) avg_dayspyr ! average number of days per year real(r8) crmcorn ! comparitive relative maturity for corn real(r8) ndays_on ! number of days to fertilize + logical has_rx_sowing_date ! does the crop have a single sowing date instead of a window? logical is_in_sowing_window ! is the crop in its sowing window? logical is_end_sowing_window ! is it the last day of the crop's sowing window? logical sowing_gdd_requirement_met ! has the gridcell historically been warm enough to support the crop? logical do_plant_normal ! are the normal planting rules defined and satisfied? logical do_plant_lastchance ! if not the above, what about relaxed rules for the last day of the planting window? logical do_plant_prescribed ! is today the prescribed sowing date? + logical do_plant_prescribed_tomorrow ! is tomorrow the prescribed sowing date? logical do_plant ! are we planting in this time step for any reason? logical did_plant ! did we plant the crop in this time step? logical allow_unprescribed_planting ! should crop be allowed to be planted according to sowing window rules? @@ -2017,9 +2020,15 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. Also make sure we haven't planted yet today. ! TODO: Change last condition to `maxval(crop_inst%sdates_perharv_patch(p,:)) /= jday` - do_plant_prescribed = sowing_window_startdate == jday .and. & - sowing_window_enddate == jday .and. & + ! TODO: ¿Allow use of NON-prescribed sowing with one-day-long windows? + has_rx_sowing_date = sowing_window_startdate == sowing_window_enddate + do_plant_prescribed = has_rx_sowing_date .and. & + sowing_window_startdate == jday .and. & sowing_count (p) < mxsowings + do_plant_prescribed_tomorrow = \ + has_rx_sowing_date .and. & + sowing_window_startdate == get_doy_tomorrow(jday) .and. & + sowing_count (p) < mxsowings ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) ! When resuming from a run with old code, may need to manually set these. @@ -2051,7 +2060,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! ! Only allow sowing according to normal "window" rules if not using prescribed ! sowing dates. - allow_unprescribed_planting = sowing_window_startdate /= sowing_window_enddate + allow_unprescribed_planting = .not. has_rx_sowing_date if (sowing_count(p) == mxsowings) then do_plant_normal = .false. do_plant_lastchance = .false. @@ -2280,7 +2289,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & else if (generate_crop_gdds .and. crop_inst%rx_swindow_starts_thisyr_patch(p,1) .gt. 0) then if (sowing_window_startdate >= 0) then ! Harvest the day before the start of the next sowing window. - do_harvest = sowing_window_starts_tomorrow + do_harvest = do_plant_prescribed_tomorrow ! ... unless that will lead to growing season length 365 (or 366, ! if last year was a leap year). This would result in idop==jday, @@ -2332,13 +2341,13 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! WARNING: This implementation assumes that sowing windows don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed ! sowing windows. - do_harvest = do_harvest .or. sowing_window_starts_tomorrow + do_harvest = do_harvest .or. do_plant_prescribed_tomorrow if (hui(p) >= gddmaturity(p)) then harvest_reason = HARVEST_REASON_MATURE else if (idpp >= mxmat) then harvest_reason = HARVEST_REASON_MAXSEASLENGTH - else if (sowing_window_starts_tomorrow) then + else if (do_plant_prescribed_tomorrow) then harvest_reason = HARVEST_REASON_SOWTOMORROW end if endif From bb577533b0486553ea6a439ffdac2037a7ad67d6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Sep 2023 12:30:23 -0600 Subject: [PATCH 1600/2067] Removed unused logical sowing_window_starts_tomorrow. --- src/biogeochem/CNPhenologyMod.F90 | 15 ++------ .../test/CNPhenology_test/test_CNPhenology.pf | 38 ++++++------------- 2 files changed, 15 insertions(+), 38 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 7b9471c67a..bc93810d92 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1715,7 +1715,7 @@ end subroutine CNStressDecidPhenology !----------------------------------------------------------------------- - subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) ! !DESCRIPTION: ! Determine when the "next" sowing window is. This is either the sowing window we are ! currently in or, if not in a sowing window, the next one that will occur. @@ -1728,7 +1728,6 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star integer, intent(in) :: param_start, param_end ! Sowing window start and end dates from parameter file integer, intent(out) :: w ! Index of "next" sowing window integer, intent(out) :: start_w, end_w ! Start and end dates of "next" sowing window - logical, intent(out) :: sowing_window_starts_tomorrow ! ! !LOCAL VARIABLES integer :: next_swindow_start @@ -1750,17 +1749,13 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star w = 1 start_w = param_start end_w = param_end + return ! Otherwise, if today is after the latest sowing window end date, use the first sowing window. This works only if sowing windows that span the new year are located at index w = 1. else if (jday > maxval(rx_ends)) then w = 1 start_w = rx_starts(w) end_w = rx_ends(w) - end if - - ! If we already got sowing window dates, do this and exit. - if (w > 0) then - sowing_window_starts_tomorrow = start_w == jday_tomorrow return end if @@ -1805,9 +1800,6 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star next_swindow_start = start_w end if - ! Does the NEXT sowing window start tomorrow? - sowing_window_starts_tomorrow = next_swindow_start == jday_tomorrow - end subroutine get_swindow @@ -1872,7 +1864,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & integer mcsec ! seconds of day (0, ..., seconds/day) integer sowing_window_startdate ! date (day of year) of first day of sowing window integer sowing_window_enddate ! date (day of year) of last day of sowing window - logical sowing_window_starts_tomorrow ! Is tomorrow the start of a sowing window? real(r8) harvest_reason real(r8) dayspyr ! days per year in this year real(r8) avg_dayspyr ! average number of days per year @@ -2016,7 +2007,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & end if ! Get dates of current or next sowing window. - call get_swindow(jday, crop_inst%rx_swindow_starts_thisyr_patch(p,:), crop_inst%rx_swindow_ends_thisyr_patch(p,:), minplantjday(ivt(p),h), maxplantjday(ivt(p),h), w, sowing_window_startdate, sowing_window_enddate, sowing_window_starts_tomorrow) + call get_swindow(jday, crop_inst%rx_swindow_starts_thisyr_patch(p,:), crop_inst%rx_swindow_ends_thisyr_patch(p,:), minplantjday(ivt(p),h), maxplantjday(ivt(p),h), w, sowing_window_startdate, sowing_window_enddate) ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. Also make sure we haven't planted yet today. ! TODO: Change last condition to `maxval(crop_inst%sdates_perharv_patch(p,:)) /= jday` diff --git a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf index ebab50ad13..30fba3505b 100644 --- a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf +++ b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf @@ -302,43 +302,36 @@ contains integer, parameter :: param_start = 200 integer, parameter :: param_end = 250 integer :: w, start_w, end_w - logical :: sowing_window_starts_tomorrow - call get_swindow(1, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(1, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(1, start_w) @assertEqual(45, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(45, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(45, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(1, start_w) @assertEqual(45, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(149, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(149, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(2, w) @assertEqual(150, start_w) @assertEqual(180, end_w) - @assertTrue(sowing_window_starts_tomorrow) - call get_swindow(175, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(175, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(2, w) @assertEqual(150, start_w) @assertEqual(180, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(229, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(229, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(1, start_w) @assertEqual(45, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(get_curr_days_per_year(), rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(get_curr_days_per_year(), rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(1, start_w) @assertEqual(45, end_w) - @assertTrue(sowing_window_starts_tomorrow) end subroutine test_get_swindow_startend @Test @@ -350,43 +343,36 @@ contains integer, parameter :: param_start = 200 integer, parameter :: param_end = 250 integer :: w, start_w, end_w - logical :: sowing_window_starts_tomorrow - call get_swindow(1, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(1, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(360, start_w) @assertEqual(45, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(45, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(45, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(start_w, 360) @assertEqual(end_w, 45) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(149, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(149, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(2, w) @assertEqual(150, start_w) @assertEqual(180, end_w) - @assertTrue(sowing_window_starts_tomorrow) - call get_swindow(175, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(175, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(2, w) @assertEqual(150, start_w) @assertEqual(180, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(229, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(229, rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(360, start_w) @assertEqual(45, end_w) - @assertFalse(sowing_window_starts_tomorrow) - call get_swindow(get_curr_days_per_year(), rx_starts, rx_ends, param_start, param_end, w, start_w, end_w, sowing_window_starts_tomorrow) + call get_swindow(get_curr_days_per_year(), rx_starts, rx_ends, param_start, param_end, w, start_w, end_w) @assertEqual(1, w) @assertEqual(360, start_w) @assertEqual(45, end_w) - @assertFalse(sowing_window_starts_tomorrow) end subroutine test_get_swindow_endstart end module test_CNPhenology From 0585ef24e0cf0200f00d599f9221b75d947d6b98 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 30 Sep 2023 12:55:40 -0600 Subject: [PATCH 1601/2067] Resolved a TODO by thinking about it. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bc93810d92..3f5515d1df 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2037,7 +2037,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) if (crop_inst%sown_in_this_window(p) .and. .not. is_in_sowing_window) then - ! TODO: Test whether this is necessary, since it's set to false in last timestep of sowing window at the end of CropPhenology(). + ! Although sown_in_this_window is set to false in last timestep of sowing window at the end of CropPhenology(), this extra check may be necessary if sowing windows change. crop_inst%sown_in_this_window(p) = .false. end if is_end_sowing_window = jday == sowing_window_enddate From 0658cab229140adca9ac912caf51443ed1eb80b5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 30 Sep 2023 12:56:38 -0600 Subject: [PATCH 1602/2067] Sowing window outputs now saved on end date. This ensures ordering is identical to how inputs should be. --- src/biogeochem/CNPhenologyMod.F90 | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 3f5515d1df..12152de52e 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2043,8 +2043,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & is_end_sowing_window = jday == sowing_window_enddate ! ! Save these diagnostic variables only on the first day of the window to ensure that windows spanning the new year aren't double-counted. - ! TODO: Change this to the LAST day of the window, to ensure the same ordering as required for rx sowing window input files. - if (jday == sowing_window_startdate) then + if (jday == sowing_window_enddate) then crop_inst%swindow_starts_thisyr_patch(p,w) = sowing_window_startdate crop_inst%swindow_ends_thisyr_patch (p,w) = sowing_window_enddate end if From ba014b05b860fb4b1ebf9f5f1b6383ecb1e30d3d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 30 Sep 2023 13:04:09 -0600 Subject: [PATCH 1603/2067] Fail if a sowing window start date is prescribed without an end date (or vice versa). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 8ad162783c..113627a10f 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -323,6 +323,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) real(r8), pointer :: dataptr2d_cultivar_gdds(:,:) !----------------------------------------------------------------------- + associate( & + starts => crop_inst%rx_swindow_starts_thisyr_patch, & + ends => crop_inst%rx_swindow_ends_thisyr_patch & + ) + SHR_ASSERT_FL( (lbound(g_to_ig,1) <= bounds%begg ), sourcefile, __LINE__) SHR_ASSERT_FL( (ubound(g_to_ig,1) >= bounds%endg ), sourcefile, __LINE__) @@ -371,18 +376,18 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) n = ivt - npcropmin + 1 ! vegetated pft ig = g_to_ig(patch%gridcell(p)) - crop_inst%rx_swindow_starts_thisyr_patch(p,1) = dataptr2d_swindow_start(ig,n) - crop_inst%rx_swindow_ends_thisyr_patch (p,1) = dataptr2d_swindow_end (ig,n) + starts(p,1) = dataptr2d_swindow_start(ig,n) + ends(p,1) = dataptr2d_swindow_end (ig,n) ! Sanity check: Should only read in valid values - if (crop_inst%rx_swindow_starts_thisyr_patch(p,1) > 365) then + if (starts(p,1) > 365) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window start date ',& - crop_inst%rx_swindow_starts_thisyr_patch(p,1) + starts(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - if (crop_inst%rx_swindow_ends_thisyr_patch(p,1) > 365) then + if (ends(p,1) > 365) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window end date ',& - crop_inst%rx_swindow_ends_thisyr_patch(p,1) + ends(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if else @@ -393,7 +398,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! TODO: Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. This is necessary because of how get_swindow() works. - ! TODO: Fail if a sowing window start date is prescribed without an end date (or vice versa) + ! Fail if a sowing window start date is prescribed without an end date (or vice versa) + if (any((starts >= 1 .and. ends < 1) .or. (starts < 1 .and. ends >= 1))) then + write(iulog, *) 'Every prescribed sowing window start date must have a corresponding end date.' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if end if ! use_cropcal_rx_swindows deallocate(dataptr2d_swindow_start) @@ -461,6 +470,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) deallocate(dataptr2d_cultivar_gdds) + end associate + end subroutine cropcal_interp end module cropcalStreamMod From d0f77fc2c283a66709317208137da62dee7822ee Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 30 Sep 2023 13:19:54 -0600 Subject: [PATCH 1604/2067] Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 113627a10f..00f439e265 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -15,6 +15,7 @@ module cropcalStreamMod use clm_varctl , only : iulog use clm_varctl , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams use clm_varpar , only : mxpft + use clm_varpar , only : mxsowings use perf_mod , only : t_startf, t_stopf use spmdMod , only : masterproc, mpicom, iam use pftconMod , only : npcropmin @@ -396,7 +397,14 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) endif end do - ! TODO: Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. This is necessary because of how get_swindow() works. + ! Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. This is necessary because of how get_swindow() works. + if (mxsowings > 1) then + if (any(ends(:,2:mxsowings) <= ends(:,1:mxsowings-1) .and. & + ends(:,2:mxsowings) >= 1)) then + write(iulog, *) 'Sowing window inputs must be ordered such that end dates are monotonically increasing.' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if + end if ! Fail if a sowing window start date is prescribed without an end date (or vice versa) if (any((starts >= 1 .and. ends < 1) .or. (starts < 1 .and. ends >= 1))) then From 3422d517e4e39999fea772666039b4c5d14e9149 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sat, 30 Sep 2023 13:58:54 -0600 Subject: [PATCH 1605/2067] Simplified some harvest logic. --- src/biogeochem/CNPhenologyMod.F90 | 55 +++++++++---------------------- 1 file changed, 16 insertions(+), 39 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 12152de52e..18111994ac 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2010,7 +2010,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & call get_swindow(jday, crop_inst%rx_swindow_starts_thisyr_patch(p,:), crop_inst%rx_swindow_ends_thisyr_patch(p,:), minplantjday(ivt(p),h), maxplantjday(ivt(p),h), w, sowing_window_startdate, sowing_window_enddate) ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. Also make sure we haven't planted yet today. - ! TODO: Change last condition to `maxval(crop_inst%sdates_perharv_patch(p,:)) /= jday` ! TODO: ¿Allow use of NON-prescribed sowing with one-day-long windows? has_rx_sowing_date = sowing_window_startdate == sowing_window_enddate do_plant_prescribed = has_rx_sowing_date .and. & @@ -2277,44 +2276,22 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! If generate_crop_gdds and this patch has prescribed sowing inputs ! TODO: Shouldn't this also apply to paramfile sowing windows? else if (generate_crop_gdds .and. crop_inst%rx_swindow_starts_thisyr_patch(p,1) .gt. 0) then - if (sowing_window_startdate >= 0) then - ! Harvest the day before the start of the next sowing window. - do_harvest = do_plant_prescribed_tomorrow - - ! ... unless that will lead to growing season length 365 (or 366, - ! if last year was a leap year). This would result in idop==jday, - ! which would invoke the "manually setting sowing_count and - ! sdates_thisyr" code. This would lead to crops never getting - ! harvested. Instead, always harvest the day before idop. - if ((.not. do_harvest) .and. & - (idop(p) > 1 .and. jday == idop(p) - 1) .or. & - (idop(p) == 1 .and. jday == dayspyr)) then - do_harvest = .true. - if (do_harvest) then - harvest_reason = HARVEST_REASON_IDOPTOMORROW - end if - else if (do_harvest) then - harvest_reason = HARVEST_REASON_SOWTOMORROW - end if - - else - ! If this patch has already had all its plantings for the year, don't harvest - ! until some time next year. - do_harvest = .false. - - ! ... unless first sowing next year happens Jan. 1. - ! WARNING: This implementation assumes that sowing windows don't change over time! - ! In order to avoid this, you'd have to read this year's AND next year's prescribed - ! sowing window start dates. - if (crop_inst%rx_swindow_starts_thisyr_patch(p,1) == 1) then - do_harvest = jday == dayspyr - end if - - if (do_harvest) then - harvest_reason = HARVEST_REASON_SOWTOMORROW - end if - - endif + ! Harvest the day before the next prescribed sowing. + do_harvest = do_plant_prescribed_tomorrow + + ! ... unless that will lead to growing season length 365 (or 366, + ! if last year was a leap year). This would result in idop==jday, + ! which would invoke the "manually setting sowing_count and + ! sdates_thisyr" code. This would lead to crops never getting + ! harvested. Instead, always harvest the day before idop. + if ((.not. do_harvest) .and. & + (idop(p) > 1 .and. jday == idop(p) - 1) .or. & + (idop(p) == 1 .and. jday == dayspyr)) then + do_harvest = .true. + harvest_reason = HARVEST_REASON_IDOPTOMORROW + else if (do_harvest) then + harvest_reason = HARVEST_REASON_SOWTOMORROW + end if else if (did_plant_prescribed_today) then ! Do not harvest on the day this growing season began; From baed0a736cd1e8a900ba3b0d69838f721c7f2599 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 1 Oct 2023 16:01:57 -0600 Subject: [PATCH 1606/2067] Removed a TODO. --- src/biogeochem/CNPhenologyMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 18111994ac..b625416c54 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2274,7 +2274,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & harvest_reason = HARVEST_REASON_SOWTODAY ! If generate_crop_gdds and this patch has prescribed sowing inputs - ! TODO: Shouldn't this also apply to paramfile sowing windows? else if (generate_crop_gdds .and. crop_inst%rx_swindow_starts_thisyr_patch(p,1) .gt. 0) then ! Harvest the day before the next prescribed sowing. do_harvest = do_plant_prescribed_tomorrow From 5ea05d5532aeba08d425e44ec9f3eea83c759d35 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 09:18:34 -0600 Subject: [PATCH 1607/2067] Replaced an EOL backslash with &. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b625416c54..a4b50735d5 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2015,7 +2015,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & do_plant_prescribed = has_rx_sowing_date .and. & sowing_window_startdate == jday .and. & sowing_count (p) < mxsowings - do_plant_prescribed_tomorrow = \ + do_plant_prescribed_tomorrow = & has_rx_sowing_date .and. & sowing_window_startdate == get_doy_tomorrow(jday) .and. & sowing_count (p) < mxsowings From fd7140e342938f6d17ad4d5201382d75c1871c3b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Sep 2023 10:59:27 -0600 Subject: [PATCH 1608/2067] Added a comment. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index a4b50735d5..b3e82445a5 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2363,7 +2363,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%gddaccum_thisyr_patch(p, harvest_count(p)) = crop_inst%gddaccum_patch(p) crop_inst%hui_thisyr_patch(p, harvest_count(p)) = hui(p) crop_inst%sowing_reason_perharv_patch(p, harvest_count(p)) = real(crop_inst%sowing_reason_patch(p), r8) - crop_inst%sowing_reason_patch(p) = -1 + crop_inst%sowing_reason_patch(p) = -1 ! "Reason for most recent sowing of this patch." So in the line above we save, and here we reset. crop_inst%harvest_reason_thisyr_patch(p, harvest_count(p)) = harvest_reason endif From 1cade9901635da260642b02bccd80b8c8a275127 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 2 Oct 2023 15:23:10 -0600 Subject: [PATCH 1609/2067] Add function was_sown_in_this_window() to handle edge cases. Includes unit testing. --- src/biogeochem/CNPhenologyMod.F90 | 51 ++++++++++++- .../test/CNPhenology_test/test_CNPhenology.pf | 75 +++++++++++++++++++ 2 files changed, 122 insertions(+), 4 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index b3e82445a5..923e2ca053 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -59,6 +59,7 @@ module CNPhenologyMod public :: SeasonalDecidOnset ! Logical function to determine is seasonal decidious onset should be triggered public :: SeasonalCriticalDaylength ! Critical day length needed for Seasonal decidious offset public :: get_swindow + public :: was_sown_in_this_window ! !PRIVITE MEMBER FIUNCTIONS: private :: CNPhenologyClimate ! Get climatological everages to figure out triggers for Phenology @@ -1803,6 +1804,51 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star end subroutine get_swindow + !----------------------------------------------------------------------- + function was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, sown_in_this_window) + ! !DESCRIPTION: + ! Determine whether the crop was sown in the current sowing window. Although sown_in_this_window is set to false in last timestep of sowing window at the end of CropPhenology(), these extra checks may be necessary if sowing windows change. + ! + ! !USES: + use clm_time_manager , only : is_doy_in_interval + ! !ARGUMENTS: + integer, intent(in) :: sowing_window_startdate, sowing_window_enddate, jday, idop + logical, intent(in) :: sown_in_this_window + ! !LOCAL VARIABLES + logical :: is_in_sowing_window, idop_in_sowing_window + ! !RESULT + logical :: was_sown_in_this_window + + was_sown_in_this_window = sown_in_this_window + + ! If not in a sowing window, sown_in_this_window must be false. + is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) + if (.not. is_in_sowing_window) then + was_sown_in_this_window = .false. + return + end if + + ! If we're in a sowing window but the day of planting isn't in the active sowing window, we must be in a different sowing window. + idop_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, idop) + if (is_in_sowing_window .and. .not. idop_in_sowing_window) then + was_sown_in_this_window = .false. + return + end if + + ! Sometimes we're in an active sowing window, and the patch was sown between the start and end dates of the window, but not *the currently active* window. + if (sowing_window_startdate <= sowing_window_enddate .and. idop > jday) then + was_sown_in_this_window = .false. + else if (sowing_window_startdate >= sowing_window_enddate) then + if (jday <= sowing_window_enddate .and. idop <= sowing_window_enddate .and. idop > jday) then + was_sown_in_this_window = .false. + else if (jday >= sowing_window_startdate .and. (idop > jday .or. idop <= sowing_window_enddate)) then + was_sown_in_this_window = .false. + end if + end if + + end function was_sown_in_this_window + + !----------------------------------------------------------------------- subroutine CropPhenology(num_pcropp, filter_pcropp , & waterdiagnosticbulk_inst, temperature_inst, crop_inst, canopystate_inst, cnveg_state_inst , & @@ -2035,10 +2081,7 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Are we currently in a sowing window? ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) - if (crop_inst%sown_in_this_window(p) .and. .not. is_in_sowing_window) then - ! Although sown_in_this_window is set to false in last timestep of sowing window at the end of CropPhenology(), this extra check may be necessary if sowing windows change. - crop_inst%sown_in_this_window(p) = .false. - end if + crop_inst%sown_in_this_window(p) = was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop(p), crop_inst%sown_in_this_window(p)) is_end_sowing_window = jday == sowing_window_enddate ! ! Save these diagnostic variables only on the first day of the window to ensure that windows spanning the new year aren't double-counted. diff --git a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf index 30fba3505b..b4b65b5b1c 100644 --- a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf +++ b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf @@ -375,4 +375,79 @@ contains @assertEqual(45, end_w) end subroutine test_get_swindow_endstart + @Test + subroutine test_was_sown_in_this_window_startend(this) + use clm_time_manager , only : is_doy_in_interval + class(TestCNPhenology), intent(inout) :: this + integer, parameter :: sowing_window_startdate = 84 + integer, parameter :: sowing_window_enddate = 205 + integer :: jday, idop + + jday = 100 + + idop = 90 + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 100 + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 101 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + idop = 120 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + idop = 360 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + jday = 300 + + idop = 90 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + idop = 360 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + end subroutine test_was_sown_in_this_window_startend + + @Test + subroutine test_was_sown_in_this_window_endstart(this) + use clm_time_manager , only : is_doy_in_interval + class(TestCNPhenology), intent(inout) :: this + integer, parameter :: sowing_window_startdate = 205 + integer, parameter :: sowing_window_enddate = 84 + integer :: jday, idop + + jday = 300 + + idop = 60 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + idop = 205 + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 300 + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 301 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + jday = 70 + + idop = 60 + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 75 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + idop = 301 + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + end subroutine test_was_sown_in_this_window_endstart + end module test_CNPhenology From bab784806a13cd75ad97a0b74860f8d5227ea482 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 9 Oct 2023 18:21:46 -0600 Subject: [PATCH 1610/2067] Correct a comment. --- src/biogeochem/CNPhenologyMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 923e2ca053..c030f24da5 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2346,10 +2346,10 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Original harvest rule do_harvest = hui(p) >= gddmaturity(p) .or. idpp >= mxmat - ! Always harvest the day before the next prescribed sowing window starts, if still alive. - ! WARNING: This implementation assumes that sowing windows don't change over time! + ! Always harvest the day before the next prescribed sowing date, if still alive. + ! WARNING: This implementation assumes that prescribed sowing dates don't change over time! ! In order to avoid this, you'd have to read this year's AND next year's prescribed - ! sowing windows. + ! sowing dates. do_harvest = do_harvest .or. do_plant_prescribed_tomorrow if (hui(p) >= gddmaturity(p)) then From 16698054724868806949c69eaca38350a03874bf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 9 Oct 2023 18:25:13 -0600 Subject: [PATCH 1611/2067] Remove an unused 'use' variable. --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c030f24da5..98aefc54d3 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2628,7 +2628,7 @@ subroutine PlantCrop(p, leafcn_in, jday, kyr, do_plant_normal, & ! !USES: use clm_varctl , only : use_c13, use_c14 - use clm_varctl , only : use_cropcal_rx_swindows, use_cropcal_rx_cultivar_gdds, use_cropcal_streams + use clm_varctl , only : use_cropcal_rx_cultivar_gdds, use_cropcal_streams use clm_varcon , only : c13ratio, c14ratio use clm_varpar , only : mxsowings use pftconMod , only : ntmp_corn, nswheat, nwwheat, ntmp_soybean From bc77099aef313a005e7b5b17b689e8c161ce6153 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 9 Oct 2023 18:29:08 -0600 Subject: [PATCH 1612/2067] Combined two if-blocks. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 00f439e265..120310dd49 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -151,9 +151,9 @@ subroutine cropcal_init(bounds) use_cropcal_rx_cultivar_gdds = stream_fldFileName_cultivar_gdds /= '' use_cropcal_streams = use_cropcal_rx_swindows .or. use_cropcal_rx_cultivar_gdds - ! Initialize the cdeps data type sdat_cropcal_swindow_start - ! NOTE: stream_dtlimit 1.5 didn't work for some reason if (use_cropcal_rx_swindows) then + ! Initialize the cdeps data type sdat_cropcal_swindow_start + ! NOTE: stream_dtlimit 1.5 didn't work for some reason call shr_strdata_init_from_inline(sdat_cropcal_swindow_start, & my_task = iam, & logunit = iulog, & @@ -178,11 +178,9 @@ subroutine cropcal_init(bounds) if (ESMF_LogFoundError(rcToCheck=rc, msg=ESMF_LOGERR_PASSTHRU, line=__LINE__, file=__FILE__)) then call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - end if - ! Initialize the cdeps data type sdat_cropcal_swindow_end - ! NOTE: stream_dtlimit 1.5 didn't work for some reason - if (use_cropcal_rx_swindows) then + ! Initialize the cdeps data type sdat_cropcal_swindow_end + ! NOTE: stream_dtlimit 1.5 didn't work for some reason call shr_strdata_init_from_inline(sdat_cropcal_swindow_end, & my_task = iam, & logunit = iulog, & From e161bf5003c96aad5edb0e6aacd18b31600b26de Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 10 Oct 2023 16:30:07 -0600 Subject: [PATCH 1613/2067] Add SWINDOW start/end dates to crop testmod. --- cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index dc22a973b2..4679194e9f 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -10,7 +10,7 @@ hist_fincl2 += 'DYN_COL_SOIL_ADJUSTMENTS_C' ! Annual crop variables on per-sowing/per-harvest axes, per PFT. -hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' +hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV', 'SWINDOW_STARTS', 'SWINDOW_ENDS' hist_nhtfrq(3) = 17520 hist_mfilt(3) = 1 hist_type1d_pertape(3) = 'PFTS' From 703de51ceed80464a32f2a9f11705de2569f3a7c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 10 Oct 2023 16:31:15 -0600 Subject: [PATCH 1614/2067] Add sowingWindows testmod. --- .../testmods_dirs/clm/sowingWindows/include_user_mods | 1 + .../testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm | 5 +++++ 2 files changed, 6 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods new file mode 100644 index 0000000000..fe0e18cf88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/include_user_mods @@ -0,0 +1 @@ +../default diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm new file mode 100644 index 0000000000..61bdf9aa93 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm @@ -0,0 +1,5 @@ +stream_fldFileName_swindow_start = '/glade/u/home/samrabin/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' +stream_fldFileName_swindow_end = '/glade/u/home/samrabin/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' +stream_meshfile_cropcal = '/glade/u/home/samrabin/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc' +stream_year_first_cropcal = 2000 +stream_year_last_cropcal = 2000 From 86fba583b477ef6f554400e6a134d1703351fe56 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 11 Oct 2023 12:02:00 -0600 Subject: [PATCH 1615/2067] unit test updates after using LFS for referenced files --- .../modify_singlept_site_neon.py | 3 -- .../test_unit_modify_singlept_site_neon.py | 49 +++++++++---------- python/ctsm/test/testinputs/README.md | 2 +- 3 files changed, 25 insertions(+), 29 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index ca85d68636..fc4964c0b4 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -502,12 +502,9 @@ def main(): # -- directory structure current_dir = os.getcwd() - # parent_dir = os.path.dirname(current_dir) clone_dir = os.path.abspath(os.path.join(__file__, "../../../..")) neon_dir = os.path.join(clone_dir, "neon_surffiles") - print("Present Directory", current_dir) - # -- download neon data if needed neon_file = get_neon(neon_dir, site_name) diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index f782075c43..e15e2c13ef 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -77,31 +77,30 @@ def test_find_surffile(self): with self.assertRaises(SystemExit): find_surffile(surf_dir, site_name, pft_16) - # TODO: need to fix unkown file type error? - # def test_find_soil_structure(self): - # """ - # Test to ensure that correct attributes are found for find_soil_structure. - # soil_texture_raw_data_file_name should be found, and test should go through sysexit. - # """ - # surf_file = "testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" - # f1 = xr.open_dataset(surf_file) - # print(f1.attrs["Soil_texture_raw_data_file_name"]) - # self.assertEqual(f1.attrs["Soil_texture_raw_data_file_name"], - # "FIND FILENAME FROM ATTRIBUTES AND ADD HERE", - # "did not retrieve expected surface soil texture filename from surf file") - - # def test_update_metadata(self): - # """ - # Test to ensure that an attribute has changed when update_metadata() is run. - # """ - # surf_file = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" - # neon_file = "dummy_neon_file.nc" - # zb_flag = True - # f1 = xr.open_dataset("testinputs/" + surf_file) - # f2 = update_metadata(f1, surf_file, neon_file, zb_flag) - # self.assertNotEqual(f1.attrs["Updated_on"], - # f2.attrs["Updated_on"], - # "File was not updated as expected") + def test_find_soil_structure(self): + """ + Test to ensure that correct attributes are found for find_soil_structure. + soil_texture_raw_data_file_name should be found, and test should go through sysexit. + """ + surf_file = "testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + f1 = xr.open_dataset(surf_file) + self.assertEqual(f1.attrs["Soil_texture_raw_data_file_name"], + "mksrf_soitex.10level.c010119.nc", + "did not retrieve expected surface soil texture filename from surf file") + + def test_update_metadata(self): + """ + Test to ensure that the file was updated today. + """ + surf_file = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + neon_file = "dummy_neon_file.nc" + zb_flag = True + f1 = xr.open_dataset("testinputs/" + surf_file) + f2 = update_metadata(f1, surf_file, neon_file, zb_flag) + today = date.today() + today_string = today.strftime("%Y-%m-%d") + self.assertEqual(f1.attrs["Updated_on"], today_string, + "File was not updated as expected") def test_update_time_tag(self): """ diff --git a/python/ctsm/test/testinputs/README.md b/python/ctsm/test/testinputs/README.md index 45451b53e1..1775de48b7 100644 --- a/python/ctsm/test/testinputs/README.md +++ b/python/ctsm/test/testinputs/README.md @@ -6,7 +6,7 @@ Installing Git LFS on your machine is a two-step process; step (1) needs to be done once per machine, and step (2) needs to be done once per user: 1. Install the Git LFS tool: Follow the instructions on the [Git LFS page](https://git-lfs.github.com/) for installing Git LFS on your platform. - - On cheyenne, Git LFS is already available as long as you are using a git + - On cheyenne and casper, Git LFS is already available as long as you are using a git module rather than the default system-level git. So just make sure that you are always using git via a git module (`module load git`). - On a Mac using homebrew, this can be done with `brew install git-lfs`. From 30f47a5cbd99d354cac81eadd62ddc7e6194f0a8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 11 Oct 2023 12:06:57 -0600 Subject: [PATCH 1616/2067] Remove unused next_swindow_start from get_swindow(). --- src/biogeochem/CNPhenologyMod.F90 | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 98aefc54d3..8d60b16c33 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1731,8 +1731,6 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star integer, intent(out) :: start_w, end_w ! Start and end dates of "next" sowing window ! ! !LOCAL VARIABLES - integer :: next_swindow_start - integer :: i, x integer :: jday_tomorrow integer :: mxsowings_in ! Due to unit testing, we can't assume the length of the rx sowing window arrays is mxsowings as set in clm_varpar @@ -1779,28 +1777,6 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star call endrun(msg="get_swindow(): No sowing window found") end if - ! Get the start date of the NEXT sowing window (not including the sowing window we're currently in, if any) - if (is_doy_in_interval(start_w, end_w, jday)) then - next_swindow_start = -1 - x = w - i = 0 ! For checking infinite loop - do while (next_swindow_start < 1) - ! Check for infinite loop - i = i + 1 - if (i > mxsowings_in + 1) then - call endrun("Infinite loop in get_swindow()") - end if - - x = x + 1 - if (x > mxsowings_in) then - x = 1 - end if - next_swindow_start = rx_starts(x) - end do - else - next_swindow_start = start_w - end if - end subroutine get_swindow From df30d0479afce773d311ad9ad20472d388ebd6d8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 11 Oct 2023 12:13:07 -0600 Subject: [PATCH 1617/2067] Change check for invalid dates in get_swindow(). --- src/biogeochem/CNPhenologyMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 8d60b16c33..c9e6457be3 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1761,7 +1761,7 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star ! Otherwise, use the first prescribed sowing window we find whose end is >= today. do w = 1, mxsowings_in ! If nothing prescribed at this w, stop looking and exit loop. - if (min(rx_starts(w), rx_ends(w)) < 0) then + if (min(rx_starts(w), rx_ends(w)) < 1) then exit end if From ea307e0b1d3cd536f4ea72303d0358993615106a Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 11 Oct 2023 12:21:33 -0600 Subject: [PATCH 1618/2067] small update to test + minor black reformatting --- .../test/test_unit_modify_singlept_site_neon.py | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index e15e2c13ef..b8315c7bae 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -82,11 +82,15 @@ def test_find_soil_structure(self): Test to ensure that correct attributes are found for find_soil_structure. soil_texture_raw_data_file_name should be found, and test should go through sysexit. """ - surf_file = "testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + surf_file = ( + "testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + ) f1 = xr.open_dataset(surf_file) - self.assertEqual(f1.attrs["Soil_texture_raw_data_file_name"], - "mksrf_soitex.10level.c010119.nc", - "did not retrieve expected surface soil texture filename from surf file") + self.assertEqual( + f1.attrs["Soil_texture_raw_data_file_name"], + "mksrf_soitex.10level.c010119.nc", + "did not retrieve expected surface soil texture filename from surf file", + ) def test_update_metadata(self): """ @@ -99,8 +103,7 @@ def test_update_metadata(self): f2 = update_metadata(f1, surf_file, neon_file, zb_flag) today = date.today() today_string = today.strftime("%Y-%m-%d") - self.assertEqual(f1.attrs["Updated_on"], today_string, - "File was not updated as expected") + self.assertEqual(f2.attrs["Updated_on"], today_string, "File was not updated as expected") def test_update_time_tag(self): """ From 18c9eeb8c219baece4e8a3a88074afa7d392edb9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 11 Oct 2023 12:57:54 -0600 Subject: [PATCH 1619/2067] Improve comments in get_swindow(). --- src/biogeochem/CNPhenologyMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index c9e6457be3..24839bc0cf 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1758,9 +1758,9 @@ subroutine get_swindow(jday, rx_starts, rx_ends, param_start, param_end, w, star return end if - ! Otherwise, use the first prescribed sowing window we find whose end is >= today. + ! Otherwise, use the first prescribed sowing window we find whose end is >= today. This works only if sowing windows that span the new year are located at index w = 1. do w = 1, mxsowings_in - ! If nothing prescribed at this w, stop looking and exit loop. + ! If nothing prescribed at this w, stop looking and exit loop. Will trigger "No sowing window found" error, which we do not move here because it's possible that no start or end date is < 1. if (min(rx_starts(w), rx_ends(w)) < 1) then exit end if From 711114ba5862b0acbd0b7c2df1be97ef08fe722c Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 11 Oct 2023 15:46:03 -0600 Subject: [PATCH 1620/2067] Updated changelog --- doc/ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 75 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 8e8a99b868..5d12272b34 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,78 @@ =============================================================== +Tag name: ctsm5.1.dev143 +Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-) +Date: Wed Oct 11 15:37:48 MDT 2023 +One-line Summary: Zeroing of wood product fluxes on fates columns + +Purpose and description of changes +---------------------------------- + +This is a small change that initializes wood product fluxes on fates columns to zero. These +products are otherwise zero'd in a p2c() routine that is incompatible with fates. When +wood product fluxes become available via fates, these routines will be updated. These fluxes +were previously left as uninitialized, which was causing math issues on some compilers. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +There are no changes to scientifically-supported configurations. + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +Fixes CTSM issue 2165 + + +Notes of particular relevance for users +--------------------------------------- + + +No caveats, no bugs, no issues of relevance. + +No noticable timing changes. + + +Notes of particular relevance for developers: +--------------------------------------------- + +None + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- PASS + + Compared against baseline: ctsm5.1.dev142 + + +Answer changes +-------------- + +Answer changes only on FATES tests, and only on the specific wood product fluxes modified. These values +are now zeros, instead of being uninitialized. Everything else is b4b. + + +Other details +------------- + +No other details. + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev142 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Tue Sep 19 11:30:22 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index e11f439658..0f72ce9698 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev143 rgknox 10/11/2023 Zeroing of wood product fluxes on fates columns ctsm5.1.dev142 samrabin 09/19/2023 Merge 5 bit-for-bit pull requests ctsm5.1.dev141 slevis 09/13/2023 Change small snocan to zero ctsm5.1.dev140 afoster 09/12/2023 add lai_streams capability for FATES From 27af41013965b5ae1da27c70f630e961fe43ae08 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 12 Oct 2023 10:10:44 -0700 Subject: [PATCH 1621/2067] align operators to the ctsm style guide --- src/main/clm_driver.F90 | 2 +- src/utils/clmfates_interfaceMod.F90 | 22 +++++++++++----------- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 2585953e8a..eeb78a76f1 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1271,7 +1271,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Pass fates seed dispersal information to all nodes - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() end if diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index fd8c3781ad..bc083d0437 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -615,7 +615,7 @@ subroutine init(this, bounds_proc ) ! Initialize dispersal - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then ! Initialize fates global seed dispersal array for all nodes call get_proc_global(ng=numg) @@ -920,7 +920,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & lnfm24 = this%fates_fire_data_method%GetLight24() end if - if (fates_spitfire_mode .eq. anthro_suppression) then + if (fates_spitfire_mode == anthro_suppression) then allocate(gdp_lf_col(bounds_clump%begc:bounds_clump%endc), stat=ier) if (ier /= 0) then call endrun(msg="allocation error for gdp"//& @@ -944,7 +944,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & end do ! ifp - if (fates_spitfire_mode .eq. anthro_suppression) then + if (fates_spitfire_mode == anthro_suppression) then ! Placeholder for future fates use of gdp - comment out before integration !this%fates(nc)%bc_in(s)%gdp = gdp_lf_col(c) ! k US$/capita(g) end if @@ -1040,9 +1040,9 @@ subroutine dynamics_driv(this, nc, bounds_clump, & this%fates(nc)%bc_in(s)%hlm_harvest_catnames(1:num_harvest_inst) = harvest_varnames(1:num_harvest_inst) ! also pass the units that the harvest rates are specified in - if (trim(harvest_units) .eq. trim(unitless_units)) then + if (trim(harvest_units) == trim(unitless_units)) then this%fates(nc)%bc_in(s)%hlm_harvest_units = hlm_harvest_area_fraction - else if (trim(harvest_units) .eq. trim(mass_units)) then + else if (trim(harvest_units) == trim(mass_units)) then this%fates(nc)%bc_in(s)%hlm_harvest_units = hlm_harvest_carbon else write(iulog,*) 'units field not one of the specified options.' @@ -1062,7 +1062,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & ! Distribute any seeds from neighboring gridcells into the current gridcell ! Global seed availability array populated by WrapSeedGlobal call - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then call this%wrap_seed_dispersal(bounds_clump) end if @@ -1400,7 +1400,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & patch%wt_ed(bounds_clump%begp:bounds_clump%endp) = 0.0_r8 ! Zero the outgoing_local seed values prior to populating with the most recent seed update - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then this%fates_seed%outgoing_local(:,:) = 0._r8 end if @@ -1410,7 +1410,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & g = col%gridcell(c) ! Accumulate seeds from sites to the gridcell local outgoing buffer - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then if (IsItDispersalTime()) this%fates_seed%outgoing_local(:,g) = & this%fates(nc)%sites(s)%seed_out(:) end if @@ -1849,7 +1849,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & !$OMP END PARALLEL DO ! Disperse seeds - if (fates_seeddisp_cadence .ne. fates_dispersal_cadence_none) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then call this%WrapSeedGlobal(is_restart_flag=.true.) end if @@ -2530,7 +2530,7 @@ subroutine wrap_WoodProducts(this, bounds_clump, num_soilc, filter_soilc, & this%fates(ci)%bc_out(s)%hrv_deadstemc_to_prod100c ! If N cycling is on - if(fates_parteh_mode .eq. prt_cnp_flex_allom_hyp ) then + if(fates_parteh_mode == prt_cnp_flex_allom_hyp ) then !n_products_inst%hrv_deadstem_to_prod10_grc(g) = & ! n_products_inst%hrv_deadstem_to_prod10_grc(g) + & @@ -3249,7 +3249,7 @@ subroutine ComputeRootSoilFlux(this, bounds_clump, num_filterc, filterc, & end if end do - if(num_filter_fates .ne. this%fates(nc)%nsites )then + if(num_filter_fates /= this%fates(nc)%nsites )then write(iulog,*) 'The HLM list of natural veg columns during root water transfer' write(iulog,*) 'is not the same size as the fates site list?' call endrun(msg=errMsg(sourcefile, __LINE__)) From 85b75379beea6fa2dbdae9f0b1c127ef5854bd05 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 12 Oct 2023 10:41:32 -0700 Subject: [PATCH 1622/2067] add clarifying comments to the fates seed dispersal code --- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++++ cime_config/testdefs/testlist_clm.xml | 2 ++ .../testmods_dirs/clm/FatesColdSeedDisp/README | 2 +- src/main/clm_driver.F90 | 2 ++ src/main/controlMod.F90 | 1 + src/utils/clmfates_interfaceMod.F90 | 13 ++++++++++--- 6 files changed, 20 insertions(+), 4 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index bb51af2e3f..b8032f1cf9 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -642,6 +642,10 @@ Switch deciding which nutrient model to use in FATES. group="clm_inparm" valid_values="0,1,2,3"> Switch defining the cadence at which seeds are dispersed across gridcells. Setting the switch value to zero turns off dispersal. +Setting the switch to 1, 2, or 3 sets the dispersal cadence to +daily, monthly or yearly. The daily cadence is primarily +recommended for test and debug only. Note that turning this +feature on will result in more memory usage. (Only relevant if FATES is on) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f5af800543..ec18a504ed 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1841,6 +1841,7 @@ + @@ -1849,6 +1850,7 @@ + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README index d5ff7099a9..5833c4edd3 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README @@ -9,7 +9,7 @@ fates_seed_dispersal_pdf_shape Given that the default fates parameter file has the above variables as unset, a custom fates parameter file must be supplied to appropriately test this mode. -This testmod itself addresses CTSM issue #2151. +This testmod itself addresses CTSM issue 2151: https://github.com/ESCOMP/CTSM/issues/2151 The max_dist value will impact the size of the 'neighborhood' of gridcells that fates will attempt to distribute seeds to. To limit the neighborhood to diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index eeb78a76f1..8e66abf8fe 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1271,6 +1271,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Pass fates seed dispersal information to all nodes + ! Note that WrapSeedGlobal calls an MPI collective routine and as such + ! WrapSeedGlobal should be called outside of OMP threaded loop regions if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() end if diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index aa35d2dd1b..dd6887d07a 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -1112,6 +1112,7 @@ subroutine control_print () write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp write(iulog, *) ' fates_seeddisp_cadence = ', fates_seeddisp_cadence + write(iulog, *) ' fates_seeddisp_cadence: 0, 1, 2, 3 => off, daily, monthly, or yearly dispersal' write(iulog, *) ' fates_inventory_ctrl_filename = ',fates_inventory_ctrl_filename end if end subroutine control_print diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index bc083d0437..61e52a29c0 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2682,11 +2682,16 @@ subroutine WrapSeedGlobal(this,is_restart_flag) this%fates_seed%incoming_global(:,:) = 0._r8 this%fates_seed%outgoing_global(:,:) = 0._r8 - ! Distribute outgoing seed data from all nodes to all nodes + ! Distribute outgoing seed data across all MPI tasks + ! This method of grid cell communications is inefficient in that it creates global information + ! across all processes. A future update should communicate to the minimum set of neighbors. call MPI_Allgatherv(this%fates_seed%outgoing_local, procinfo%ncells*numpft_fates, MPI_REAL8, & this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array*numpft_fates, & MPI_REAL8, mpicom, ier) - write(iulog,*) 'WSG: MPI_Allgatherv ier: ', ier + if (ier /= 0) then + call endrun(msg='clmfates interface error: MPI_Allgatherv failed'//& + errMsg(sourcefile, __LINE__)) + end if ! zero outgoing local for all gridcells outside threaded region now that we've passed them out this%fates_seed%outgoing_local(:,:) = 0._r8 @@ -2716,7 +2721,9 @@ end subroutine WrapSeedGlobal subroutine wrap_seed_dispersal(this,bounds_clump) - ! This subroutine pass seed_id_global to bc_in and reset seed_out + ! This subroutine passes the globally dispersed seed via WrapSeedGlobal, incoming_global + ! to the fates local process seed_in site object. It also resets the fates seed_out + ! in preparation for fates to update the seeds being dispersed out. ! Arguments class(hlm_fates_interface_type), intent(inout) :: this From 570fd195746a39a3f87b93e65502b23fcfe92ec9 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 12 Oct 2023 10:52:29 -0700 Subject: [PATCH 1623/2067] minor comment reword --- src/main/clm_driver.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 8e66abf8fe..44724d1c35 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1270,9 +1270,9 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro !$OMP END PARALLEL DO - ! Pass fates seed dispersal information to all nodes - ! Note that WrapSeedGlobal calls an MPI collective routine and as such - ! WrapSeedGlobal should be called outside of OMP threaded loop regions + ! Pass fates seed dispersal information to neighboring gridcells across + ! all MPI tasks. Note that WrapSeedGlobal calls an MPI collective routine + ! and as such WrapSeedGlobal should be called outside of OMP threaded loop regions if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() end if From 42f4a7496c8de4a0fb05e88117dd7b309f07878d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 12 Oct 2023 17:39:15 -0600 Subject: [PATCH 1624/2067] Delete imgmath lines from doc/source/conf.py. --- doc/source/conf.py | 3 --- 1 file changed, 3 deletions(-) diff --git a/doc/source/conf.py b/doc/source/conf.py index bee524164a..dcd0b2eae6 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -37,7 +37,6 @@ 'sphinx.ext.autodoc', 'sphinx.ext.todo', 'sphinx.ext.coverage', - 'sphinx.ext.imgmath', 'sphinx.ext.githubpages'] # Add any paths that contain templates here, relative to this directory. @@ -94,8 +93,6 @@ # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = True -imgmath_image_format = 'svg' - # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for From ac88bded5a2185b1416bab2856c87085e6770f6e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 12 Oct 2023 17:41:58 -0600 Subject: [PATCH 1625/2067] Deleted all \kern-\nulldelimiterspace. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 12 +-- .../CLM50_Tech_Note_Decomposition.rst | 42 +++++----- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 4 +- ...LM50_Tech_Note_External_Nitrogen_Cycle.rst | 2 +- .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 38 ++++----- .../Hydrology/CLM50_Tech_Note_Hydrology.rst | 4 +- .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 2 +- .../CLM50_Tech_Note_Land-Only_Mode.rst | 2 +- .../Methane/CLM50_Tech_Note_Methane.rst | 6 +- .../CLM50_Tech_Note_Photosynthesis.rst | 4 +- .../CLM50_Tech_Note_Plant_Mortality.rst | 2 +- .../CLM50_Tech_Note_Radiative_Fluxes.rst | 16 ++-- .../CLM50_Tech_Note_Snow_Hydrology.rst | 12 +-- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 14 ++-- .../CLM50_Tech_Note_Surface_Albedos.rst | 24 +++--- ...ech_Note_Vegetation_Phenology_Turnover.rst | 82 +++++++++---------- 16 files changed, 133 insertions(+), 133 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index a03142e92e..1e5c200069 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -566,19 +566,19 @@ Root C and N pools are routed to the litter pools in the same manner as natural .. math:: :label: 25.9 - CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac .. math:: :label: 25.10 - CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac .. math:: :label: 25.11 - CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem} \Delta t}} \right.} \Delta t} \right) * \left( 1-biofuel\_harvfrac \right) +CF_{alloc,livestem} with corresponding nitrogen fluxes: @@ -586,19 +586,19 @@ with corresponding nitrogen fluxes: .. math:: :label: 25.12 - NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac .. math:: :label: 25.13 - NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac .. math:: :label: 25.14 - NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} \right) * \left( 1-biofuel\_harvfrac \right) where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index 0d2ad98687..2eaffa47df 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -268,7 +268,7 @@ unitless) is calculated using a relationship from Andrén and Paustian .. math:: :label: 21.6) - r_{water} =\sum _{j=1}^{5}\left\{\begin{array}{l} {0\qquad {\rm for\; }\Psi _{j} <\Psi _{\min } } \\ {\frac{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{j} }} \right. \kern-\nulldelimiterspace} \Psi _{j} } \right)}{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{\max } }} \right. \kern-\nulldelimiterspace} \Psi _{\max } } \right)} w_{soil,\, j} \qquad {\rm for\; }\Psi _{\min } \le \Psi _{j} \le \Psi _{\max } } \\ {1\qquad {\rm for\; }\Psi _{j} >\Psi _{\max } \qquad \qquad } \end{array}\right\} + r_{water} =\sum _{j=1}^{5}\left\{\begin{array}{l} {0\qquad {\rm for\; }\Psi _{j} <\Psi _{\min } } \\ {\frac{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{j} }} \right.} \Psi _{j} } \right)}{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{\max } }} \right.} \Psi _{\max } } \right)} w_{soil,\, j} \qquad {\rm for\; }\Psi _{\min } \le \Psi _{j} \le \Psi _{\max } } \\ {1\qquad {\rm for\; }\Psi _{j} >\Psi _{\max } \qquad \qquad } \end{array}\right\} where :math:`{\Psi}_{j}` is the soil water potential in layer *j*, :math:`{\Psi}_{min}` is a lower limit for soil @@ -389,37 +389,37 @@ CLM-CN pool structure, are given as: .. math:: :label: 21.13) - CF_{pot,\, Lit1} ={CS_{Lit1} k_{Lit1} r_{total} \mathord{\left/ {\vphantom {CS_{Lit1} k_{Lit1} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, Lit1} ={CS_{Lit1} k_{Lit1} r_{total} \mathord{\left/ {\vphantom {CS_{Lit1} k_{Lit1} r_{total} \Delta t}} \right.} \Delta t} .. math:: :label: 21.14) - CF_{pot,\, Lit2} ={CS_{Lit2} k_{Lit2} r_{total} \mathord{\left/ {\vphantom {CS_{Lit2} k_{Lit2} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, Lit2} ={CS_{Lit2} k_{Lit2} r_{total} \mathord{\left/ {\vphantom {CS_{Lit2} k_{Lit2} r_{total} \Delta t}} \right.} \Delta t} .. math:: :label: 21.15) - CF_{pot,\, Lit3} ={CS_{Lit3} k_{Lit3} r_{total} \mathord{\left/ {\vphantom {CS_{Lit3} k_{Lit3} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, Lit3} ={CS_{Lit3} k_{Lit3} r_{total} \mathord{\left/ {\vphantom {CS_{Lit3} k_{Lit3} r_{total} \Delta t}} \right.} \Delta t} .. math:: :label: 21.16) - CF_{pot,\, SOM1} ={CS_{SOM1} k_{SOM1} r_{total} \mathord{\left/ {\vphantom {CS_{SOM1} k_{SOM1} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, SOM1} ={CS_{SOM1} k_{SOM1} r_{total} \mathord{\left/ {\vphantom {CS_{SOM1} k_{SOM1} r_{total} \Delta t}} \right.} \Delta t} .. math:: :label: 21.17) - CF_{pot,\, SOM2} ={CS_{SOM2} k_{SOM2} r_{total} \mathord{\left/ {\vphantom {CS_{SOM2} k_{SOM2} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, SOM2} ={CS_{SOM2} k_{SOM2} r_{total} \mathord{\left/ {\vphantom {CS_{SOM2} k_{SOM2} r_{total} \Delta t}} \right.} \Delta t} .. math:: :label: 21.18) - CF_{pot,\, SOM3} ={CS_{SOM3} k_{SOM3} r_{total} \mathord{\left/ {\vphantom {CS_{SOM3} k_{SOM3} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, SOM3} ={CS_{SOM3} k_{SOM3} r_{total} \mathord{\left/ {\vphantom {CS_{SOM3} k_{SOM3} r_{total} \Delta t}} \right.} \Delta t} .. math:: :label: 21.19) - CF_{pot,\, SOM4} ={CS_{SOM4} k_{SOM4} r_{total} \mathord{\left/ {\vphantom {CS_{SOM4} k_{SOM4} r_{total} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{pot,\, SOM4} ={CS_{SOM4} k_{SOM4} r_{total} \mathord{\left/ {\vphantom {CS_{SOM4} k_{SOM4} r_{total} \Delta t}} \right.} \Delta t} where the factor (1/:math:`\Delta`\ *t*) is included because the rate constant is calculated for the entire timestep (Eqs. and ), but the @@ -431,37 +431,37 @@ structure will be similar but without the different terminal step): .. math:: :label: ZEqnNum934998 - NF_{pot\_ min,\, Lit1\to SOM1} ={CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right) CN_{SOM1} }} \right. \kern-\nulldelimiterspace} CN_{SOM1} } + NF_{pot\_ min,\, Lit1\to SOM1} ={CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: :label: 21.21) - NF_{pot\_ min,\, Lit2\to SOM2} ={CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right) CN_{SOM2} }} \right. \kern-\nulldelimiterspace} CN_{SOM2} } + NF_{pot\_ min,\, Lit2\to SOM2} ={CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.22) - NF_{pot\_ min,\, Lit3\to SOM3} ={CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right) CN_{SOM3} }} \right. \kern-\nulldelimiterspace} CN_{SOM3} } + NF_{pot\_ min,\, Lit3\to SOM3} ={CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } .. math:: :label: 21.23) - NF_{pot\_ min,\, SOM1\to SOM2} ={CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right) CN_{SOM2} }} \right. \kern-\nulldelimiterspace} CN_{SOM2} } + NF_{pot\_ min,\, SOM1\to SOM2} ={CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.24) - NF_{pot\_ min,\, SOM2\to SOM3} ={CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right) CN_{SOM3} }} \right. \kern-\nulldelimiterspace} CN_{SOM3} } + NF_{pot\_ min,\, SOM2\to SOM3} ={CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } .. math:: :label: 21.25) - NF_{pot\_ min,\, SOM3\to SOM4} ={CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right) CN_{SOM4} }} \right. \kern-\nulldelimiterspace} CN_{SOM4} } + NF_{pot\_ min,\, SOM3\to SOM4} ={CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right) CN_{SOM4} }} \right.} CN_{SOM4} } .. math:: :label: ZEqnNum473594 - NF_{pot\_ min,\, SOM4} =-{CF_{pot,\, SOM4} \mathord{\left/ {\vphantom {CF_{pot,\, SOM4} CN_{SOM4} }} \right. \kern-\nulldelimiterspace} CN_{SOM4} } + NF_{pot\_ min,\, SOM4} =-{CF_{pot,\, SOM4} \mathord{\left/ {\vphantom {CF_{pot,\, SOM4} CN_{SOM4} }} \right.} CN_{SOM4} } where the special form of Eq. arises because there is no SOM pool downstream of SOM4 in the converging cascade: all carbon fluxes leaving @@ -674,32 +674,32 @@ pools in the decomposition cascade are given as: .. math:: :label: 21.52) - NF_{Lit1,\, SOM1} ={CF_{Lit1} \mathord{\left/ {\vphantom {CF_{Lit1} CN_{Lit1} }} \right. \kern-\nulldelimiterspace} CN_{Lit1} } + NF_{Lit1,\, SOM1} ={CF_{Lit1} \mathord{\left/ {\vphantom {CF_{Lit1} CN_{Lit1} }} \right.} CN_{Lit1} } .. math:: :label: 21.53) - NF_{Lit2,\, SOM2} ={CF_{Lit2} \mathord{\left/ {\vphantom {CF_{Lit2} CN_{Lit2} }} \right. \kern-\nulldelimiterspace} CN_{Lit2} } + NF_{Lit2,\, SOM2} ={CF_{Lit2} \mathord{\left/ {\vphantom {CF_{Lit2} CN_{Lit2} }} \right.} CN_{Lit2} } .. math:: :label: 21.54) - NF_{Lit3,\, SOM3} ={CF_{Lit3} \mathord{\left/ {\vphantom {CF_{Lit3} CN_{Lit3} }} \right. \kern-\nulldelimiterspace} CN_{Lit3} } + NF_{Lit3,\, SOM3} ={CF_{Lit3} \mathord{\left/ {\vphantom {CF_{Lit3} CN_{Lit3} }} \right.} CN_{Lit3} } .. math:: :label: 21.55) - NF_{SOM1,\, SOM2} ={CF_{SOM1} \mathord{\left/ {\vphantom {CF_{SOM1} CN_{SOM1} }} \right. \kern-\nulldelimiterspace} CN_{SOM1} } + NF_{SOM1,\, SOM2} ={CF_{SOM1} \mathord{\left/ {\vphantom {CF_{SOM1} CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: :label: 21.56) - NF_{SOM2,\, SOM3} ={CF_{SOM2} \mathord{\left/ {\vphantom {CF_{SOM2} CN_{SOM2} }} \right. \kern-\nulldelimiterspace} CN_{SOM2} } + NF_{SOM2,\, SOM3} ={CF_{SOM2} \mathord{\left/ {\vphantom {CF_{SOM2} CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: :label: 21.57) - NF_{SOM3,\, SOM4} ={CF_{SOM3} \mathord{\left/ {\vphantom {CF_{SOM3} CN_{SOM3} }} \right. \kern-\nulldelimiterspace} CN_{SOM3} } + NF_{SOM3,\, SOM4} ={CF_{SOM3} \mathord{\left/ {\vphantom {CF_{SOM3} CN_{SOM3} }} \right.} CN_{SOM3} } Corresponding fluxes to or from the soil mineral nitrogen pool depend on whether the decomposition step is an immobilization flux or a diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst index 50b918e6a2..111e115b5f 100644 --- a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst +++ b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst @@ -882,9 +882,9 @@ of the components in the coupled modeling system, are presented in "Avogadro’s number", :math:`N_{A}`, 6.02214 :math:`\times 10^{26}`, molecule kmol\ :sup:`-1` "Universal gas constant", :math:`R_{gas}`, :math:`N_{A} \kappa`, J K :sup:`-1` kmol :sup:`-1` "Molecular weight of dry air", :math:`MW_{da}`, 28.966, kg kmol :sup:`-1` - "Dry air gas constant", :math:`R_{da}`, :math:`{R_{gas} \mathord{\left/ {\vphantom {R_{gas} MW_{da} }} \right. \kern-\nulldelimiterspace} MW_{da} }`, J K :sup:`-1` kg :sup:`-1` + "Dry air gas constant", :math:`R_{da}`, :math:`{R_{gas} \mathord{\left/ {\vphantom {R_{gas} MW_{da} }} \right.} MW_{da} }`, J K :sup:`-1` kg :sup:`-1` "Molecular weight of water vapor", :math:`MW_{wv}`, 18.016, kg kmol :sup:`-1` - "Water vapor gas constant", :math:`R_{wv}`, :math:`{R_{gas} \mathord{\left/ {\vphantom {R_{gas} MW_{wv} }} \right. \kern-\nulldelimiterspace} MW_{wv} }`, J K :sup:`-1` kg :sup:`-1` + "Water vapor gas constant", :math:`R_{wv}`, :math:`{R_{gas} \mathord{\left/ {\vphantom {R_{gas} MW_{wv} }} \right.} MW_{wv} }`, J K :sup:`-1` kg :sup:`-1` "Von Karman constant", :math:`k`, 0.4, "\-" "Freezing temperature of fresh water", :math:`T_{f}`, 273.15, K "Density of liquid water", :math:`\rho _{liq}`, 1000, kg m :sup:`-3` diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index ca7a4a9d2c..1fd978e79f 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -111,7 +111,7 @@ under global change scenarios (:ref:`Wieder et al. 2015 .. math:: :label: 22.1) - NF_{nfix,sminn} ={0.0006\left(0.0117+CF_{ann\_ ET}\right)\mathord{\left/ {\vphantom {0.0006\left(0.0117+ CF_{ann\_ ET}\right) \left(86400\cdot 365\right)}} \right. \kern-\nulldelimiterspace} \left(86400\cdot 365\right)} + NF_{nfix,sminn} ={0.0006\left(0.0117+CF_{ann\_ ET}\right)\mathord{\left/ {\vphantom {0.0006\left(0.0117+ CF_{ann\_ ET}\right) \left(86400\cdot 365\right)}} \right.} \left(86400\cdot 365\right)} Where :math:`{NF}_{nfix,sminn}` (gN m\ :sup:`-2` s\ :sup:`-1`) is the rate of free-living nitrogen fixation in :numref:`Figure Biological nitrogen fixation`. diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index 047d4e6723..f4ef49285b 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -75,7 +75,7 @@ where :math:`T_{atm}` is the air temperature (K) at height :math:`z_{atm,\, h}` and :math:`\Gamma _{d} =0.0098` K m\ :sup:`-1` is the negative of the dry adiabatic lapse rate [this expression is first-order equivalent to -:math:`\theta _{atm} =T_{atm} \left({P_{srf} \mathord{\left/ {\vphantom {P_{srf} P_{atm} }} \right. \kern-\nulldelimiterspace} P_{atm} } \right)^{{R_{da} \mathord{\left/ {\vphantom {R_{da} C_{p} }} \right. \kern-\nulldelimiterspace} C_{p} } }` +:math:`\theta _{atm} =T_{atm} \left({P_{srf} \mathord{\left/ {\vphantom {P_{srf} P_{atm} }} \right.} P_{atm} } \right)^{{R_{da} \mathord{\left/ {\vphantom {R_{da} C_{p} }} \right.} C_{p} } }` (:ref:`Stull 1988 `), where :math:`P_{srf}` is the surface pressure (Pa), :math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`)]. By definition, @@ -218,17 +218,17 @@ The functions :math:`\psi _{m} \left(\zeta \right)`, .. math:: :label: 5.21 - \psi _{m} \left(\zeta \right)=\int _{{z_{0m} \mathord{\left/ {\vphantom {z_{0m} L}} \right. \kern-\nulldelimiterspace} L} }^{\zeta }\frac{\left[1-\phi _{m} \left(x\right)\right]}{x} \, dx + \psi _{m} \left(\zeta \right)=\int _{{z_{0m} \mathord{\left/ {\vphantom {z_{0m} L}} \right.} L} }^{\zeta }\frac{\left[1-\phi _{m} \left(x\right)\right]}{x} \, dx .. math:: :label: 5.22 - \psi _{h} \left(\zeta \right)=\int _{{z_{0h} \mathord{\left/ {\vphantom {z_{0h} L}} \right. \kern-\nulldelimiterspace} L} }^{\zeta }\frac{\left[1-\phi _{h} \left(x\right)\right]}{x} \, dx + \psi _{h} \left(\zeta \right)=\int _{{z_{0h} \mathord{\left/ {\vphantom {z_{0h} L}} \right.} L} }^{\zeta }\frac{\left[1-\phi _{h} \left(x\right)\right]}{x} \, dx .. math:: :label: 5.23 - \psi _{w} \left(\zeta \right)=\int _{{z_{0w} \mathord{\left/ {\vphantom {z_{0w} L}} \right. \kern-\nulldelimiterspace} L} }^{\zeta }\frac{\left[1-\phi _{w} \left(x\right)\right]}{x} \, dx + \psi _{w} \left(\zeta \right)=\int _{{z_{0w} \mathord{\left/ {\vphantom {z_{0w} L}} \right.} L} }^{\zeta }\frac{\left[1-\phi _{w} \left(x\right)\right]}{x} \, dx where :math:`z_{0m}` , :math:`z_{0h}` , and :math:`z_{0w}` are the roughness lengths (m) for momentum, sensible heat, and water vapor, @@ -290,7 +290,7 @@ where :math:`w_{*}` is the convective velocity scale .. math:: :label: 5.29 - w_{*} =\left(\frac{-gu_{\*} \theta _{v*} z_{i} }{\overline{\theta _{v,\, atm} }} \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } , + w_{*} =\left(\frac{-gu_{\*} \theta _{v*} z_{i} }{\overline{\theta _{v,\, atm} }} \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } , :math:`z_{i} =1000` is the convective boundary layer height (m), and :math:`\beta =1`. @@ -300,8 +300,8 @@ The momentum flux gradient relations are (:ref:`Zeng et al. 1998 ` :label: 5.30 \begin{array}{llr} - \phi _{m} \left(\zeta \right)=0.7k^{{2\mathord{\left/ {\vphantom {2 3}} \right. \kern-\nulldelimiterspace} 3} } \left(-\zeta \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } & \qquad {\rm for\; }\zeta <-1.574 & \ {\rm \; (very\; unstable)} \\ - \phi _{m} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 4}} \right. \kern-\nulldelimiterspace} 4} } & \qquad {\rm for\; -1.574}\le \zeta <0 & \ {\rm \; (unstable)} \\ + \phi _{m} \left(\zeta \right)=0.7k^{{2\mathord{\left/ {\vphantom {2 3}} \right.} 3} } \left(-\zeta \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } & \qquad {\rm for\; }\zeta <-1.574 & \ {\rm \; (very\; unstable)} \\ + \phi _{m} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 4}} \right.} 4} } & \qquad {\rm for\; -1.574}\le \zeta <0 & \ {\rm \; (unstable)} \\ \phi _{m} \left(\zeta \right)=1+5\zeta & \qquad {\rm for\; }0\le \zeta \le 1& \ {\rm \; (stable)} \\ \phi _{m} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm\; (very\; stable).} \end{array} @@ -312,8 +312,8 @@ The sensible and latent heat flux gradient relations are (:ref:`Zeng et al. 1998 :label: 5.31 \begin{array}{llr} - \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=0.9k^{{4\mathord{\left/ {\vphantom {4 3}} \right. \kern-\nulldelimiterspace} 3} } \left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right. \kern-\nulldelimiterspace} 3} } & \qquad {\rm for\; }\zeta <-0.465 & \ {\rm \; (very\; unstable)} \\ - \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right. \kern-\nulldelimiterspace} 2} } & \qquad {\rm for\; -0.465}\le \zeta <0 & \ {\rm \; (unstable)} \\ + \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=0.9k^{{4\mathord{\left/ {\vphantom {4 3}} \right.} 3} } \left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } & \qquad {\rm for\; }\zeta <-0.465 & \ {\rm \; (very\; unstable)} \\ + \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} } & \qquad {\rm for\; -0.465}\le \zeta <0 & \ {\rm \; (unstable)} \\ \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=1+5\zeta & \qquad {\rm for\; }0\le \zeta \le 1 & \ {\rm \; (stable)} \\ \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm \; (very\; stable).} \end{array} @@ -335,7 +335,7 @@ Very unstable :math:`\left(\zeta <-1.574\right)` .. math:: :label: 5.32 - V_{a} =\frac{u_{*} }{k} \left\{\left[\ln \frac{\zeta _{m} L}{z_{0m} } -\psi _{m} \left(\zeta _{m} \right)\right]+1.14\left[\left(-\zeta \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } -\left(-\zeta _{m} \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } \right]+\psi _{m} \left(\frac{z_{0m} }{L} \right)\right\} + V_{a} =\frac{u_{*} }{k} \left\{\left[\ln \frac{\zeta _{m} L}{z_{0m} } -\psi _{m} \left(\zeta _{m} \right)\right]+1.14\left[\left(-\zeta \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } -\left(-\zeta _{m} \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } \right]+\psi _{m} \left(\frac{z_{0m} }{L} \right)\right\} Unstable :math:`\left(-1.574\le \zeta <0\right)` @@ -367,7 +367,7 @@ where and -:math:`x=\left(1-16\zeta \right)^{{1\mathord{\left/ {\vphantom {1 4}} \right. \kern-\nulldelimiterspace} 4} }` . +:math:`x=\left(1-16\zeta \right)^{{1\mathord{\left/ {\vphantom {1 4}} \right.} 4} }` . The potential temperature profiles are: @@ -376,7 +376,7 @@ Very unstable :math:`\left(\zeta <-0.465\right)` .. math:: :label: 5.37 - \theta _{atm} -\theta _{s} =\frac{\theta _{*} }{k} \left\{\left[\ln \frac{\zeta _{h} L}{z_{0h} } -\psi _{h} \left(\zeta _{h} \right)\right]+0.8\left[\left(-\zeta _{h} \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right. \kern-\nulldelimiterspace} 3} } -\left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right. \kern-\nulldelimiterspace} 3} } \right]+\psi _{h} \left(\frac{z_{0h} }{L} \right)\right\} + \theta _{atm} -\theta _{s} =\frac{\theta _{*} }{k} \left\{\left[\ln \frac{\zeta _{h} L}{z_{0h} } -\psi _{h} \left(\zeta _{h} \right)\right]+0.8\left[\left(-\zeta _{h} \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } -\left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } \right]+\psi _{h} \left(\frac{z_{0h} }{L} \right)\right\} Unstable :math:`\left(-0.465\le \zeta <0\right)` @@ -407,7 +407,7 @@ Very unstable :math:`\left(\zeta <-0.465\right)` .. math:: :label: 5.41 - q_{atm} -q_{s} =\frac{q_{*} }{k} \left\{\left[\ln \frac{\zeta _{w} L}{z_{0w} } -\psi _{w} \left(\zeta _{w} \right)\right]+0.8\left[\left(-\zeta _{w} \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right. \kern-\nulldelimiterspace} 3} } -\left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right. \kern-\nulldelimiterspace} 3} } \right]+\psi _{w} \left(\frac{z_{0w} }{L} \right)\right\} + q_{atm} -q_{s} =\frac{q_{*} }{k} \left\{\left[\ln \frac{\zeta _{w} L}{z_{0w} } -\psi _{w} \left(\zeta _{w} \right)\right]+0.8\left[\left(-\zeta _{w} \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } -\left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } \right]+\psi _{w} \left(\frac{z_{0w} }{L} \right)\right\} Unstable :math:`\left(-0.465\le \zeta <0\right)` @@ -459,7 +459,7 @@ is related to :math:`\zeta` (:ref:`Arya 2001 `) as R_{iB} =\zeta \left[\ln \left(\frac{z_{atm,\, h} -d}{z_{0h} } \right)-\psi _{h} \left(\zeta \right)\right]\left[\ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)-\psi _{m} \left(\zeta \right)\right]^{-2} . Using -:math:`\phi _{h} =\phi _{m}^{2} =\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right. \kern-\nulldelimiterspace} 2} }` +:math:`\phi _{h} =\phi _{m}^{2} =\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} }` for unstable conditions and :math:`\phi _{h} =\phi _{m} =1+5\zeta` for stable conditions to determine :math:`\psi _{m} \left(\zeta \right)` and :math:`\psi _{h} \left(\zeta \right)`, the inverse relationship @@ -799,10 +799,10 @@ across the interfacial sublayer. The following relation from .. math:: :label: 5.82 - z_{0h,\, g} =z_{0w,\, g} =z_{0m,\, g} e^{-a\left({u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right. \kern-\nulldelimiterspace} \upsilon } \right)^{0.45} } + z_{0h,\, g} =z_{0w,\, g} =z_{0m,\, g} e^{-a\left({u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon } \right)^{0.45} } where the quantity -:math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right. \kern-\nulldelimiterspace} \upsilon }` +:math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. @@ -1231,7 +1231,7 @@ The leaf boundary layer resistance :math:`r_{b}` is .. math:: :label: 5.122 - r_{b} =\frac{1}{C_{v} } \left({U_{av} \mathord{\left/ {\vphantom {U_{av} d_{leaf} }} \right. \kern-\nulldelimiterspace} d_{leaf} } \right)^{{-1\mathord{\left/ {\vphantom {-1 2}} \right. \kern-\nulldelimiterspace} 2} } + r_{b} =\frac{1}{C_{v} } \left({U_{av} \mathord{\left/ {\vphantom {U_{av} d_{leaf} }} \right.} d_{leaf} } \right)^{{-1\mathord{\left/ {\vphantom {-1 2}} \right.} 2} } where :math:`C_{v} =0.01` m\ s\ :sup:`-1/2` is the turbulent transfer coefficient between the canopy surface and canopy air, and @@ -1528,7 +1528,7 @@ where :math:`\Delta T_{v} =1{\rm \; or\; }-1`. The error #. The water vapor flux :math:`E_{v}` is constrained to be less than or equal to the sum of transpiration :math:`E_{v}^{t}` and the water available from wetted leaves and stems - :math:`{W_{can} \mathord{\left/ {\vphantom {W_{can} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t}` . + :math:`{W_{can} \mathord{\left/ {\vphantom {W_{can} \Delta t}} \right.} \Delta t}` . The energy error due to this constraint is .. math:: @@ -1625,7 +1625,7 @@ support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and .. math:: :label: 5.142 - f_{evap} =\frac{{\left(w_{ice,\; snl+1} +w_{liq,\, snl+1} \right)\mathord{\left/ {\vphantom {\left(w_{ice,\; snl+1} +w_{liq,\, snl+1} \right) \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} }{\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j} } \le 1, + f_{evap} =\frac{{\left(w_{ice,\; snl+1} +w_{liq,\, snl+1} \right)\mathord{\left/ {\vphantom {\left(w_{ice,\; snl+1} +w_{liq,\, snl+1} \right) \Delta t}} \right.} \Delta t} }{\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j} } \le 1, an adjustment is made to reduce the ground evaporation accordingly as diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 323c8ea24b..aff2c6fd61 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -236,7 +236,7 @@ calculations, is (:ref:`Dickinson et al.1993 `) f_{wet} = \left\{\begin{array}{lr} - \left[\frac{W_{can} }{p_{liq}\left(L+S\right)} \right]^{{2\mathord{\left/ {\vphantom {2 3}} \right. \kern-\nulldelimiterspace} 3} } \le 1 & \qquad L+S > 0 \\ + \left[\frac{W_{can} }{p_{liq}\left(L+S\right)} \right]^{{2\mathord{\left/ {\vphantom {2 3}} \right.} 3} } \le 1 & \qquad L+S > 0 \\ 0 &\qquad L+S = 0 \end{array}\right\} @@ -259,7 +259,7 @@ Similarly, the snow-covered fraction of the canopy is used for surface alebdo wh f_{can,\, sno} = \left\{\begin{array}{lr} - \left[\frac{W_{can,\, sno} }{p_{sno}\left(L+S\right)} \right]^{{3\mathord{\left/ {\vphantom {3 20}} \right. \kern-\nulldelimiterspace} 20} } \le 1 & \qquad L+S > 0 \\ + \left[\frac{W_{can,\, sno} }{p_{sno}\left(L+S\right)} \right]^{{3\mathord{\left/ {\vphantom {3 20}} \right.} 20} } \le 1 & \qquad L+S > 0 \\ 0 &\qquad L+S = 0 \end{array}\right\}. diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 40b1918f46..e623a1383d 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -194,7 +194,7 @@ default: .. math:: :label: 12.6 - \begin{array}{l} {C=C_{\min } +(C_{\max } -C_{\min } )\exp \left\{-\min \left(A,B\right)\right\}} \\ {A={\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } \mathord{\left/ {\vphantom {\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} } f_{c} }} \right. \kern-\nulldelimiterspace} f_{c} } } \\ {B=\varepsilon \frac{\sqrt{dg} }{u} } \end{array} + \begin{array}{l} {C=C_{\min } +(C_{\max } -C_{\min } )\exp \left\{-\min \left(A,B\right)\right\}} \\ {A={\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } \mathord{\left/ {\vphantom {\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } f_{c} }} \right.} f_{c} } } \\ {B=\varepsilon \frac{\sqrt{dg} }{u} } \end{array} where *A* and *B* define the fetch- and depth-limitation, respectively; :math:`C_{\min } =0.01` , :math:`C_{\max } =0.01`, diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index 9fba6f187c..4606f43229 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -130,7 +130,7 @@ are coefficients from polynomial fits to the CAM data. The additional atmospheric forcing variables required by :numref:`Table Atmospheric input to land model` are derived as follows. The atmospheric reference height :math:`z'_{atm}` (m) is set to 30 m. The directional wind components are derived as -:math:`u_{atm} =v_{atm} ={W_{atm} \mathord{\left/ {\vphantom {W_{atm} \sqrt{2} }} \right. \kern-\nulldelimiterspace} \sqrt{2} }` . +:math:`u_{atm} =v_{atm} ={W_{atm} \mathord{\left/ {\vphantom {W_{atm} \sqrt{2} }} \right.} \sqrt{2} }` . The potential temperature :math:`\overline{\theta _{atm} }` (K) is set to the atmospheric temperature :math:`T_{atm}` . The atmospheric longwave radiation :math:`L_{atm} \, \downarrow` (W m\ :sup:`-2`) diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 875689558b..0d419e8727 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -284,7 +284,7 @@ The diffusive transport through aerenchyma (*A*, mol m\ :sup:`-2` s\ :sup:`-1`) .. math:: :label: 24.8 - A=\frac{C\left(z\right)-C_{a} }{{\raise0.7ex\hbox{$ r_{L} z $}\!\mathord{\left/ {\vphantom {r_{L} z D}} \right. \kern-\nulldelimiterspace}\!\lower0.7ex\hbox{$ D $}} +r_{a} } pT\rho _{r} , + A=\frac{C\left(z\right)-C_{a} }{{\raise0.7ex\hbox{$ r_{L} z $}\!\mathord{\left/ {\vphantom {r_{L} z D}} \right.}\!\lower0.7ex\hbox{$ D $}} +r_{a} } pT\rho _{r} , where *D* is the free-air gas diffusion coefficient (m\ :sup:`2` s\ :sup:`-1`); *C(z)* (mol m\ :sup:`-3`) is the gaseous concentration at depth *z* (m); :math:`r_{L}` is the ratio of root @@ -443,7 +443,7 @@ properties can be represented as: .. math:: :label: 24.12 - D_{e} =D_{0} \theta _{a}^{2} \left(\frac{\theta _{a} }{\theta _{s} } \right)^{{\raise0.7ex\hbox{$ 3 $}\!\mathord{\left/ {\vphantom {3 b}} \right. \kern-\nulldelimiterspace}\!\lower0.7ex\hbox{$ b $}} } , + D_{e} =D_{0} \theta _{a}^{2} \left(\frac{\theta _{a} }{\theta _{s} } \right)^{{\raise0.7ex\hbox{$ 3 $}\!\mathord{\left/ {\vphantom {3 b}} \right.}\!\lower0.7ex\hbox{$ b $}} } , where :math:`\theta _{a}` and :math:`\theta _{s}` are the air-filled and total (saturated water-filled) porosities (-), respectively, and *b* @@ -455,7 +455,7 @@ measurements more closely in unsaturated peat soils: .. math:: :label: 24.13 - D_{e} =D_{0} \frac{\theta _{a} ^{{\raise0.7ex\hbox{$ 10 $}\!\mathord{\left/ {\vphantom {10 3}} \right. \kern-\nulldelimiterspace}\!\lower0.7ex\hbox{$ 3 $}} } }{\theta _{s} ^{2} } + D_{e} =D_{0} \frac{\theta _{a} ^{{\raise0.7ex\hbox{$ 10 $}\!\mathord{\left/ {\vphantom {10 3}} \right.}\!\lower0.7ex\hbox{$ 3 $}} } }{\theta _{s} ^{2} } In CLM, we applied equation :eq:`24.12` for soils with zero organic matter content and equation :eq:`24.13` for soils with more than 130 kg m\ :sup:`-3` organic diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index e4f4f63836..253eeb2638 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -57,7 +57,7 @@ Leaf stomatal resistance is: .. math:: :label: 9.1 - \frac{1}{r_{s} } =g_{s} = g_{o} + 1.6(1 + \frac{g_{1} }{\sqrt{D_{s}}}) \frac{A_{n} }{{c_{s} \mathord{\left/ {\vphantom {c_{s} P_{atm} }} \right. \kern-\nulldelimiterspace} P_{atm} } } + \frac{1}{r_{s} } =g_{s} = g_{o} + 1.6(1 + \frac{g_{1} }{\sqrt{D_{s}}}) \frac{A_{n} }{{c_{s} \mathord{\left/ {\vphantom {c_{s} P_{atm} }} \right.} P_{atm} } } where :math:`r_{s}` is leaf stomatal resistance (s m\ :sup:`2` :math:`\mu`\ mol\ :sup:`-1`), :math:`g_{o}` is the minimum stomatal conductance @@ -166,7 +166,7 @@ s\ :sup:`-1`) is .. math:: :label: 9.3 - A_{c} =\left\{\begin{array}{l} {\frac{V_{c\max } \left(c_{i} -\Gamma _{\*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right. \kern-\nulldelimiterspace} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{\*} \ge 0. + A_{c} =\left\{\begin{array}{l} {\frac{V_{c\max } \left(c_{i} -\Gamma _{\*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{\*} \ge 0. The maximum rate of carboxylation allowed by the capacity to regenerate RuBP (i.e., the light-limited rate) :math:`A_{j}` (:math:`\mu` \ mol diff --git a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst index 4c2cb71a26..ed16004258 100644 --- a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst +++ b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst @@ -25,7 +25,7 @@ is required to better constrain this process in different climate zones range from at least 0.7% to 3.0% yr\ :sup:`-1`. Taking the annual rate of mortality (*am*, proportion yr\ :sup:`-1`) as 0.02, a mortality rate per second (*m*) is calculated as -:math:`m={am\mathord{\left/ {\vphantom {am \left(365\cdot 86400\right)}} \right. \kern-\nulldelimiterspace} \left(365\cdot 86400\right)}` . +:math:`m={am\mathord{\left/ {\vphantom {am \left(365\cdot 86400\right)}} \right.} \left(365\cdot 86400\right)}` . All vegetation carbon and nitrogen pools for display, storage, and transfer are affected at rate *m*, with mortality fluxes out of vegetation pools eventually merged to the column level and deposited in diff --git a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst index 5e368456ba..1cb673bdba 100644 --- a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst +++ b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst @@ -93,7 +93,7 @@ unit plant area) is .. math:: :label: 4.5 - \phi ^{sun} ={\left(\vec{I}_{sun,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sun,vis}^{} S_{atm} \downarrow _{vis}^{} \right)\mathord{\left/ {\vphantom {\left(\vec{I}_{sun,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sun,vis}^{} S_{atm} \downarrow _{vis}^{} \right) L^{sun} }} \right. \kern-\nulldelimiterspace} L^{sun} } + \phi ^{sun} ={\left(\vec{I}_{sun,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sun,vis}^{} S_{atm} \downarrow _{vis}^{} \right)\mathord{\left/ {\vphantom {\left(\vec{I}_{sun,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sun,vis}^{} S_{atm} \downarrow _{vis}^{} \right) L^{sun} }} \right.} L^{sun} } and the absorbed radiation for the average shaded leaf (per unit plant area) is @@ -101,7 +101,7 @@ area) is .. math:: :label: 4.6 - \phi ^{sha} ={\left(\vec{I}_{sha,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sha,vis}^{} S_{atm} \downarrow _{vis}^{} \right)\mathord{\left/ {\vphantom {\left(\vec{I}_{sha,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sha,vis}^{} S_{atm} \downarrow _{vis}^{} \right) L^{sha} }} \right. \kern-\nulldelimiterspace} L^{sha} } + \phi ^{sha} ={\left(\vec{I}_{sha,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sha,vis}^{} S_{atm} \downarrow _{vis}^{} \right)\mathord{\left/ {\vphantom {\left(\vec{I}_{sha,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sha,vis}^{} S_{atm} \downarrow _{vis}^{} \right) L^{sha} }} \right.} L^{sha} } with :math:`L^{sun}` and :math:`L^{sha}` the sunlit and shaded plant area index, respectively. The sunlit plant area index is @@ -140,14 +140,14 @@ derives the light profile with depth in the canopy by taking the derivatives of the absorbed radiative fluxes with respect to plant area index (:math:`L'=L+S`) and evaluating them incrementally through the canopy with cumulative plant area index (:math:`x`). The terms -:math:`{d\vec{I}_{sun,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{\mu } (x) dL'}} \right. \kern-\nulldelimiterspace} dL'}` +:math:`{d\vec{I}_{sun,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` and -:math:`{d\vec{I}_{sun,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{} (x) dL'}} \right. \kern-\nulldelimiterspace} dL'}` +:math:`{d\vec{I}_{sun,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{} (x) dL'}} \right.} dL'}` are the direct beam and diffuse solar radiation, respectively, absorbed by the sunlit fraction of the canopy (per unit plant area) at a depth defined by the cumulative plant area index :math:`x`; -:math:`{d\vec{I}_{sha,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{\mu } (x) dL'}} \right. \kern-\nulldelimiterspace} dL'}` \ and -:math:`{d\vec{I}_{sha,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{} (x) dL'}} \right. \kern-\nulldelimiterspace} dL'}` +:math:`{d\vec{I}_{sha,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` \ and +:math:`{d\vec{I}_{sha,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{} (x) dL'}} \right.} dL'}` are the corresponding fluxes for the shaded fraction of the canopy at depth :math:`x`. These fluxes are normalized by the sunlit or shaded fraction at depth :math:`x`, defined by @@ -175,7 +175,7 @@ longwave radiation (W m\ :sup:`-2`). The radiative temperature .. math:: :label: 4.10 - T_{rad} =\left(\frac{L\, \uparrow }{\sigma } \right)^{{1\mathord{\left/ {\vphantom {1 4}} \right. \kern-\nulldelimiterspace} 4} } + T_{rad} =\left(\frac{L\, \uparrow }{\sigma } \right)^{{1\mathord{\left/ {\vphantom {1 4}} \right.} 4} } where :math:`\sigma` is the Stefan-Boltzmann constant (W\ m\ :sup:`-2` K\ :sup:`-4`) (:numref:`Table Physical constants`). With reference to :numref:`Figure Radiation Schematic`, the upward longwave radiation from the surface to the atmosphere is @@ -297,7 +297,7 @@ vegetation emissivity is .. math:: :label: 4.20 - \varepsilon _{v} =1-e^{-{\left(L+S\right)\mathord{\left/ {\vphantom {\left(L+S\right) \bar{\mu }}} \right. \kern-\nulldelimiterspace} \bar{\mu }} } + \varepsilon _{v} =1-e^{-{\left(L+S\right)\mathord{\left/ {\vphantom {\left(L+S\right) \bar{\mu }}} \right.} \bar{\mu }} } where :math:`L` and :math:`S` are the leaf and stem area indices (section :numref:`Phenology and vegetation burial by snow`) and diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 8d22a19bc9..851f4e9d84 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -116,7 +116,7 @@ The conservation equation for mass of ice in snow layers is where :math:`q_{ice,\, i-1}` is the rate of ice accumulation from precipitation or frost or the rate of ice loss from sublimation (kg m\ :sup:`-2` s\ :sup:`-1`) in the top layer and -:math:`{\left(\Delta w_{ice,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{ice,\, i} \right)_{p} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t}` +:math:`{\left(\Delta w_{ice,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{ice,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` is the change in ice due to phase change (melting rate) (section :numref:`Phase Change`). The term :math:`q_{ice,\, i-1}` is computed in two steps as @@ -240,7 +240,7 @@ The conservation equation for mass of water in snow layers is where :math:`q_{liq,\, i-1}` is the flow of liquid water into layer :math:`i` from the layer above, :math:`q_{liq,\, i}` is the flow of water out of layer :math:`i` to the layer below, -:math:`{\left(\Delta w_{liq,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{liq,\, i} \right)_{p} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t}` +:math:`{\left(\Delta w_{liq,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{liq,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` is the change in liquid water due to phase change (melting rate) (section :numref:`Phase Change`). For the top snow layer only, @@ -515,9 +515,9 @@ where :math:`c_{3} =2.777\times 10^{-6}` (s\ :sup:`-1`) is the fractional compa .. upper limit (upplim_destruct_metamorph) used to be 100 but was changed to 175 for CLM5 (Van Kampenhout et al., 2017) where -:math:`{w_{ice,\, i} \mathord{\left/ {\vphantom {w_{ice,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right. \kern-\nulldelimiterspace} \left(f_{sno} \Delta z_{i} \right)}` +:math:`{w_{ice,\, i} \mathord{\left/ {\vphantom {w_{ice,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` and -:math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right. \kern-\nulldelimiterspace} \left(f_{sno} \Delta z_{i} \right)}` +:math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` are the bulk densities of liquid water and ice (kg m\ :sup:`-3`). @@ -830,7 +830,7 @@ lower layer is first evaluated from .. math:: :label: 8.62 - T'_{3} =T_{2}^{n} -\left(\frac{T_{1}^{n} -T_{2}^{n} }{{\left(\Delta z_{1}^{n} +\Delta z_{2}^{n} \right)\mathord{\left/ {\vphantom {\left(\Delta z_{1}^{n} +\Delta z_{2}^{n} \right) 2}} \right. \kern-\nulldelimiterspace} 2} } \right)\left(\frac{\Delta z_{2}^{n+1} }{2} \right), + T'_{3} =T_{2}^{n} -\left(\frac{T_{1}^{n} -T_{2}^{n} }{{\left(\Delta z_{1}^{n} +\Delta z_{2}^{n} \right)\mathord{\left/ {\vphantom {\left(\Delta z_{1}^{n} +\Delta z_{2}^{n} \right) 2}} \right.} 2} } \right)\left(\frac{\Delta z_{2}^{n+1} }{2} \right), then adjusted as, @@ -839,7 +839,7 @@ then adjusted as, \begin{array}{lr} T_{3}^{n+1} = T_{2}^{n} & \qquad T'_{3} \ge T_{f} \\ - T_{2}^{n+1} = T_{2}^{n} +\left(\frac{T_{1}^{n} -T_{2}^{n} }{{\left(\Delta z_{1} +\Delta z_{2}^{n} \right)\mathord{\left/ {\vphantom {\left(\Delta z_{1} +\Delta z_{2}^{n} \right) 2}} \right. \kern-\nulldelimiterspace} 2} } \right)\left(\frac{\Delta z_{2}^{n+1} }{2} \right) & \qquad T'_{3} ` and where :math:`I\, \uparrow` and :math:`I\, \downarrow` are the upward and downward diffuse radiative fluxes per unit incident flux, -:math:`K={G\left(\mu \right)\mathord{\left/ {\vphantom {G\left(\mu \right) \mu }} \right. \kern-\nulldelimiterspace} \mu }` +:math:`K={G\left(\mu \right)\mathord{\left/ {\vphantom {G\left(\mu \right) \mu }} \right.} \mu }` is the optical depth of direct beam per unit leaf and stem area, :math:`\mu` is the cosine of the zenith angle of the incident beam, :math:`G\left(\mu \right)` is the relative projected area of leaf and @@ -128,9 +128,9 @@ stem reflectances \alpha _{\Lambda } =\alpha _{\Lambda }^{leaf} w_{leaf} +\alpha _{\Lambda }^{stem} w_{stem} where -:math:`w_{leaf} ={L\mathord{\left/ {\vphantom {L \left(L+S\right)}} \right. \kern-\nulldelimiterspace} \left(L+S\right)}` +:math:`w_{leaf} ={L\mathord{\left/ {\vphantom {L \left(L+S\right)}} \right.} \left(L+S\right)}` and -:math:`w_{stem} ={S\mathord{\left/ {\vphantom {S \left(L+S\right)}} \right. \kern-\nulldelimiterspace} \left(L+S\right)}` . +:math:`w_{stem} ={S\mathord{\left/ {\vphantom {S \left(L+S\right)}} \right.} \left(L+S\right)}` . :math:`\tau _{\Lambda }` is a weighted combination of the leaf and stem transmittances (:math:`\tau _{\Lambda }^{leaf}, \tau _{\Lambda }^{stem}`) .. math:: @@ -164,9 +164,9 @@ and for horizontal leaves (:math:`\chi _{L} =1`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right. \kern-\nulldelimiterspace} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right. \kern-\nulldelimiterspace} 8} \tau _{\Lambda }` +:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right. \kern-\nulldelimiterspace} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right. \kern-\nulldelimiterspace} 3} \tau _{\Lambda }` . +:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }` . This discrepancy arises from the fact that a spherical leaf angle distribution has a true mean leaf inclination :math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation , @@ -252,12 +252,12 @@ with .. math:: :label: 3.25 - a_{1} =\frac{h_{1} }{\sigma } \left[\frac{1-s_{2}^{2} }{2K} \right]+h_{2} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{3} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right. \kern-\nulldelimiterspace} s_{1} } }{K-h} \right] + a_{1} =\frac{h_{1} }{\sigma } \left[\frac{1-s_{2}^{2} }{2K} \right]+h_{2} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{3} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right.} s_{1} } }{K-h} \right] .. math:: :label: 3.26 - a_{2} =\frac{h_{4} }{\sigma } \left[\frac{1-s_{2}^{2} }{2K} \right]+h_{5} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{6} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right. \kern-\nulldelimiterspace} s_{1} } }{K-h} \right]. + a_{2} =\frac{h_{4} }{\sigma } \left[\frac{1-s_{2}^{2} }{2K} \right]+h_{5} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{6} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right.} s_{1} } }{K-h} \right]. For diffuse radiation, the absorbed radiation for sunlit leaves is @@ -278,12 +278,12 @@ with .. math:: :label: 3.29 - a_{1} =h_{7} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{8} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right. \kern-\nulldelimiterspace} s_{1} } }{K-h} \right] + a_{1} =h_{7} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{8} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right.} s_{1} } }{K-h} \right] .. math:: :label: 3.30 - a_{2} =h_{9} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{10} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right. \kern-\nulldelimiterspace} s_{1} } }{K-h} \right]. + a_{2} =h_{9} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{10} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right.} s_{1} } }{K-h} \right]. The parameters :math:`h_{1}` –:math:`h_{10}` , :math:`\sigma` , :math:`h`, :math:`s_{1}` , and :math:`s_{2}` are from :ref:`Sellers (1985) ` @@ -322,7 +322,7 @@ The parameters :math:`h_{1}` –:math:`h_{10}` , :math:`\sigma` , .. math:: :label: 3.37 - u_{1} =b-{c\mathord{\left/ {\vphantom {c \alpha _{g,\, \Lambda }^{\mu } }} \right. \kern-\nulldelimiterspace} \alpha _{g,\, \Lambda }^{\mu } } {\rm \; or\; }u_{1} =b-{c\mathord{\left/ {\vphantom {c \alpha _{g,\, \Lambda } }} \right. \kern-\nulldelimiterspace} \alpha _{g,\, \Lambda } } + u_{1} =b-{c\mathord{\left/ {\vphantom {c \alpha _{g,\, \Lambda }^{\mu } }} \right.} \alpha _{g,\, \Lambda }^{\mu } } {\rm \; or\; }u_{1} =b-{c\mathord{\left/ {\vphantom {c \alpha _{g,\, \Lambda } }} \right.} \alpha _{g,\, \Lambda } } .. math:: :label: 3.38 @@ -928,7 +928,7 @@ small errors in simulated hemispheric fluxes Effective radius is the surface area-weighted mean radius of an ensemble of spherical particles and is directly related to specific surface area (*SSA*) as -:math:`r_{e} ={3\mathord{\left/ {\vphantom {3 \left(\rho _{ice} SSA\right)}} \right. \kern-\nulldelimiterspace} \left(\rho _{ice} SSA\right)}` , +:math:`r_{e} ={3\mathord{\left/ {\vphantom {3 \left(\rho _{ice} SSA\right)}} \right.} \left(\rho _{ice} SSA\right)}` , where :math:`\rho_{ice}` is the density of ice. Hence, :math:`r_{e}` is a simple and practical metric for relating the snowpack microphysical state to dry snow radiative characteristics. @@ -985,7 +985,7 @@ equation is .. math:: :label: 3.73 - \frac{dr_{e,\, dry} }{dt} =\left(\frac{dr_{e} }{dt} \right)_{0} \left(\frac{\eta }{\left(r_{e} -r_{e,\, 0} \right)+\eta } \right)^{{1\mathord{\left/ {\vphantom {1 \kappa }} \right. \kern-\nulldelimiterspace} \kappa } } + \frac{dr_{e,\, dry} }{dt} =\left(\frac{dr_{e} }{dt} \right)_{0} \left(\frac{\eta }{\left(r_{e} -r_{e,\, 0} \right)+\eta } \right)^{{1\mathord{\left/ {\vphantom {1 \kappa }} \right.} \kappa } } The parameters :math:`{(\frac{dr_{e}}{dt}})_{0}`, :math:`\eta`, and :math:`\kappa` are retrieved interactively from a diff --git a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst index 254d3d84c9..ce05bbb3f1 100644 --- a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst +++ b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst @@ -113,7 +113,7 @@ out of the transfer pool: .. math:: :label: ZEqnNum852972 - r_{xfer\_ on} =\left\{\begin{array}{l} {{2\mathord{\left/ {\vphantom {2 t_{onset} }} \right. \kern-\nulldelimiterspace} t_{onset} } \qquad {\rm for\; }t_{onset} \ne \Delta t} \\ {{1\mathord{\left/ {\vphantom {1 \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} \qquad {\rm for\; }t_{onset} =\Delta t} \end{array}\right. + r_{xfer\_ on} =\left\{\begin{array}{l} {{2\mathord{\left/ {\vphantom {2 t_{onset} }} \right.} t_{onset} } \qquad {\rm for\; }t_{onset} \ne \Delta t} \\ {{1\mathord{\left/ {\vphantom {1 \Delta t}} \right.} \Delta t} \qquad {\rm for\; }t_{onset} =\Delta t} \end{array}\right. and *t*\ :sub:`onset` (s) is the number of seconds remaining in the current phenology onset growth period (Figure 14.1). The form of Eq. :eq:`ZEqnNum852972` @@ -133,7 +133,7 @@ periods as: :label: 20.14) CF_{leaf,litter}^{n} =\left\{\begin{array}{l} {CF_{leaf,litter}^{n-1} + r_{xfer\_ off} \left(CS_{leaf} -CF_{leaf,litter}^{n-1} {\kern 1pt} t_{offset} \right)\qquad {\rm for\; }t_{offset} \ne \Delta t} - \\ {\left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} \right) + \\ {\left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) \left( 1-biofuel\_harvfrac \right) +CF_{alloc,leaf} \qquad {\rm for\; }t_{offset} =\Delta t} \end{array}\right. @@ -141,7 +141,7 @@ periods as: :label: 20.15) CF_{froot,litter}^{n} =\left\{\begin{array}{l} {CF_{froot,litter}^{n-1} + - r_{xfer\_ off} \left(CS_{froot} -CF_{froot,litter}^{n-1} {\kern 1pt} t_{offset} \right)\qquad {\rm for\; }t_{offset} \ne \Delta t} \\ {\left({CS_{froot} \mathord{\left/ {\vphantom {CS_{froot} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} \right)+CF_{alloc,\, froot} \qquad \qquad \qquad {\rm for\; }t_{offset} =\Delta t} \end{array}\right. + r_{xfer\_ off} \left(CS_{froot} -CF_{froot,litter}^{n-1} {\kern 1pt} t_{offset} \right)\qquad {\rm for\; }t_{offset} \ne \Delta t} \\ {\left({CS_{froot} \mathord{\left/ {\vphantom {CS_{froot} \Delta t}} \right.} \Delta t} \right)+CF_{alloc,\, froot} \qquad \qquad \qquad {\rm for\; }t_{offset} =\Delta t} \end{array}\right. .. math:: :label: 20.16) @@ -165,17 +165,17 @@ assumed to be negligible. The fluxes are: .. math:: :label: 20.17) - NF_{leaf,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf\_ litter} }} \right. \kern-\nulldelimiterspace} CN_{leaf\_ litter} } + NF_{leaf,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf\_ litter} }} \right.} CN_{leaf\_ litter} } .. math:: :label: 20.18) - NF_{froot,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{froot} }} \right. \kern-\nulldelimiterspace} CN_{froot} } + NF_{froot,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{froot} }} \right.} CN_{froot} } .. math:: :label: 20.19) - NF_{leaf,retrans} =\left({CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf} }} \right. \kern-\nulldelimiterspace} CN_{leaf} } \right)-NF_{leaf,litter} . + NF_{leaf,retrans} =\left({CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf} }} \right.} CN_{leaf} } \right)-NF_{leaf,litter} . where CN is C:N. @@ -197,64 +197,64 @@ under these conditions are: .. math:: :label: 20.20) - CF_{leaf\_ xfer,leaf} ={CS_{leaf\_ xfer} \mathord{\left/ {\vphantom {CS_{leaf\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{leaf\_ xfer,leaf} ={CS_{leaf\_ xfer} \mathord{\left/ {\vphantom {CS_{leaf\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.21) - CF_{froot\_ xfer,froot} ={CS_{froot\_ xfer} \mathord{\left/ {\vphantom {CS_{froot\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{froot\_ xfer,froot} ={CS_{froot\_ xfer} \mathord{\left/ {\vphantom {CS_{froot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.22) - CF_{livestem\_ xfer,livestem} ={CS_{livestem\_ xfer} \mathord{\left/ {\vphantom {CS_{livestem\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{livestem\_ xfer,livestem} ={CS_{livestem\_ xfer} \mathord{\left/ {\vphantom {CS_{livestem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.23) - CF_{deadstem\_ xfer,deadstem} ={CS_{deadstem\_ xfer} \mathord{\left/ {\vphantom {CS_{deadstem\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{deadstem\_ xfer,deadstem} ={CS_{deadstem\_ xfer} \mathord{\left/ {\vphantom {CS_{deadstem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.24) - CF_{livecroot\_ xfer,livecroot} ={CS_{livecroot\_ xfer} \mathord{\left/ {\vphantom {CS_{livecroot\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{livecroot\_ xfer,livecroot} ={CS_{livecroot\_ xfer} \mathord{\left/ {\vphantom {CS_{livecroot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.25) - CF_{deadcroot\_ xfer,deadcroot} ={CS_{deadcroot\_ xfer} \mathord{\left/ {\vphantom {CS_{deadcroot\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} , + CF_{deadcroot\_ xfer,deadcroot} ={CS_{deadcroot\_ xfer} \mathord{\left/ {\vphantom {CS_{deadcroot\_ xfer} \Delta t}} \right.} \Delta t} , and the corresponding nitrogen fluxes are: .. math:: :label: 20.26) - NF_{leaf\_ xfer,leaf} ={NS_{leaf\_ xfer} \mathord{\left/ {\vphantom {NS_{leaf\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{leaf\_ xfer,leaf} ={NS_{leaf\_ xfer} \mathord{\left/ {\vphantom {NS_{leaf\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.27) - NF_{froot\_ xfer,froot} ={NS_{froot\_ xfer} \mathord{\left/ {\vphantom {NS_{froot\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{froot\_ xfer,froot} ={NS_{froot\_ xfer} \mathord{\left/ {\vphantom {NS_{froot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.28) - NF_{livestem\_ xfer,livestem} ={NS_{livestem\_ xfer} \mathord{\left/ {\vphantom {NS_{livestem\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{livestem\_ xfer,livestem} ={NS_{livestem\_ xfer} \mathord{\left/ {\vphantom {NS_{livestem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.29) - NF_{deadstem\_ xfer,deadstem} ={NS_{deadstem\_ xfer} \mathord{\left/ {\vphantom {NS_{deadstem\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{deadstem\_ xfer,deadstem} ={NS_{deadstem\_ xfer} \mathord{\left/ {\vphantom {NS_{deadstem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.30) - NF_{livecroot\_ xfer,livecroot} ={NS_{livecroot\_ xfer} \mathord{\left/ {\vphantom {NS_{livecroot\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{livecroot\_ xfer,livecroot} ={NS_{livecroot\_ xfer} \mathord{\left/ {\vphantom {NS_{livecroot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: :label: 20.31) - NF_{deadcroot\_ xfer,deadcroot} ={NS_{deadcroot\_ xfer} \mathord{\left/ {\vphantom {NS_{deadcroot\_ xfer} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} . + NF_{deadcroot\_ xfer,deadcroot} ={NS_{deadcroot\_ xfer} \mathord{\left/ {\vphantom {NS_{deadcroot\_ xfer} \Delta t}} \right.} \Delta t} . 14.1.4 Background Litterfall ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -283,17 +283,17 @@ with corresponding nitrogen litterfall and retranslocation fluxes: .. math:: :label: 20.34) - NF_{leaf,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf\_ litter} }} \right. \kern-\nulldelimiterspace} CN_{leaf\_ litter} } + NF_{leaf,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf\_ litter} }} \right.} CN_{leaf\_ litter} } .. math:: :label: 20.35) - NF_{froot,litter} ={CF_{froot,litter} \mathord{\left/ {\vphantom {CF_{froot,litter} CN_{froot} }} \right. \kern-\nulldelimiterspace} CN_{froot} } + NF_{froot,litter} ={CF_{froot,litter} \mathord{\left/ {\vphantom {CF_{froot,litter} CN_{froot} }} \right.} CN_{froot} } .. math:: :label: 20.36) - NF_{leaf,retrans} =\left({CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf} }} \right. \kern-\nulldelimiterspace} CN_{leaf} } \right)-NF_{leaf,litter} . + NF_{leaf,retrans} =\left({CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf} }} \right.} CN_{leaf} } \right)-NF_{leaf,litter} . 14.1.5 Livewood Turnover ^^^^^^^^^^^^^^^^^^^^^^^^ @@ -315,7 +315,7 @@ defined as .. math:: :label: 20.37) - r_{lwt} ={p_{lwt} \mathord{\left/ {\vphantom {p_{lwt} \left(365\cdot 86400\right)}} \right. \kern-\nulldelimiterspace} \left(365\cdot 86400\right)} + r_{lwt} ={p_{lwt} \mathord{\left/ {\vphantom {p_{lwt} \left(365\cdot 86400\right)}} \right.} \left(365\cdot 86400\right)} where :math:`{p}_{lwt} = 0.7` is the assumed annual live wood turnover fraction. Carbon fluxes from live to dead wood pools are: @@ -336,22 +336,22 @@ nitrogen out of live wood during turnover, are: .. math:: :label: 20.40) - NF_{livestem,deadstem} ={CF_{livestem,deadstem} \mathord{\left/ {\vphantom {CF_{livestem,deadstem} CN_{dw} }} \right. \kern-\nulldelimiterspace} CN_{dw} } + NF_{livestem,deadstem} ={CF_{livestem,deadstem} \mathord{\left/ {\vphantom {CF_{livestem,deadstem} CN_{dw} }} \right.} CN_{dw} } .. math:: :label: 20.41) - NF_{livestem,retrans} =\left({CF_{livestem,deadstem} \mathord{\left/ {\vphantom {CF_{livestem,deadstem} CN_{lw} }} \right. \kern-\nulldelimiterspace} CN_{lw} } \right)-NF_{livestem,deadstem} + NF_{livestem,retrans} =\left({CF_{livestem,deadstem} \mathord{\left/ {\vphantom {CF_{livestem,deadstem} CN_{lw} }} \right.} CN_{lw} } \right)-NF_{livestem,deadstem} .. math:: :label: 20.42) - NF_{livecroot,deadcroot} ={CF_{livecroot,deadcroot} \mathord{\left/ {\vphantom {CF_{livecroot,deadcroot} CN_{dw} }} \right. \kern-\nulldelimiterspace} CN_{dw} } + NF_{livecroot,deadcroot} ={CF_{livecroot,deadcroot} \mathord{\left/ {\vphantom {CF_{livecroot,deadcroot} CN_{dw} }} \right.} CN_{dw} } .. math:: :label: 20.43) - NF_{livecroot,retrans} =\left({CF_{livecroot,deadcroot} \mathord{\left/ {\vphantom {CF_{livecroot,deadcroot} CN_{lw} }} \right. \kern-\nulldelimiterspace} CN_{lw} } \right)-NF_{livecroot,deadcroot} . + NF_{livecroot,retrans} =\left({CF_{livecroot,deadcroot} \mathord{\left/ {\vphantom {CF_{livecroot,deadcroot} CN_{lw} }} \right.} CN_{lw} } \right)-NF_{livecroot,deadcroot} . Evergreen Phenology ------------------------ @@ -428,7 +428,7 @@ conditions are met, :math:`{GDD}_{sum}` is updated on each timestep as GDD_{sum}^{n} =\left\{\begin{array}{l} {GDD_{sum}^{n-1} +\left(T_{s,3} -TKFRZ\right)f_{day} \qquad {\rm for\; }T_{s,3} >TKFRZ} \\ {GDD_{sum}^{n-1} \qquad \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \end{array}\right. where :math:`{T}_{s,3}` (K) is the temperature of the third soil layer, and -:math:`f_{day} ={\Delta t\mathord{\left/ {\vphantom {\Delta t 86400}} \right. \kern-\nulldelimiterspace} 86400}` . +:math:`f_{day} ={\Delta t\mathord{\left/ {\vphantom {\Delta t 86400}} \right.} 86400}` . The onset period is initiated if :math:`GDD_{sum} >GDD_{sum\_ crit}` , where @@ -458,69 +458,69 @@ onset growth period is initiated. Carbon fluxes are: .. math:: :label: ZEqnNum904388 - CF_{leaf\_ stor,leaf\_ xfer} ={f_{stor,xfer} CS_{leaf\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{leaf\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{leaf\_ stor,leaf\_ xfer} ={f_{stor,xfer} CS_{leaf\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{leaf\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.51) - CF_{froot\_ stor,froot\_ xfer} ={f_{stor,xfer} CS_{froot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{froot\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{froot\_ stor,froot\_ xfer} ={f_{stor,xfer} CS_{froot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{froot\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.52) - CF_{livestem\_ stor,livestem\_ xfer} ={f_{stor,xfer} CS_{livestem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{livestem\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{livestem\_ stor,livestem\_ xfer} ={f_{stor,xfer} CS_{livestem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{livestem\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.53) - CF_{deadstem\_ stor,deadstem\_ xfer} ={f_{stor,xfer} CS_{deadstem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{deadstem\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{deadstem\_ stor,deadstem\_ xfer} ={f_{stor,xfer} CS_{deadstem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{deadstem\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.54) - CF_{livecroot\_ stor,livecroot\_ xfer} ={f_{stor,xfer} CS_{livecroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{livecroot\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{livecroot\_ stor,livecroot\_ xfer} ={f_{stor,xfer} CS_{livecroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{livecroot\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.55) - CF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} CS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{deadcroot\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} CS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{deadcroot\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: ZEqnNum195642 - CF_{gresp\_ stor,gresp\_ xfer} ={f_{stor,xfer} CS_{gresp\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{gresp\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + CF_{gresp\_ stor,gresp\_ xfer} ={f_{stor,xfer} CS_{gresp\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{gresp\_ stor} \Delta t}} \right.} \Delta t} and the associated nitrogen fluxes are: .. math:: :label: ZEqnNum812152 - NF_{leaf\_ stor,leaf\_ xfer} ={f_{stor,xfer} NS_{leaf\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{leaf\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{leaf\_ stor,leaf\_ xfer} ={f_{stor,xfer} NS_{leaf\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{leaf\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.58) - NF_{froot\_ stor,froot\_ xfer} ={f_{stor,xfer} NS_{froot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{froot\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{froot\_ stor,froot\_ xfer} ={f_{stor,xfer} NS_{froot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{froot\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.59) - NF_{livestem\_ stor,livestem\_ xfer} ={f_{stor,xfer} NS_{livestem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{livestem\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{livestem\_ stor,livestem\_ xfer} ={f_{stor,xfer} NS_{livestem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{livestem\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.60) - NF_{deadstem\_ stor,deadstem\_ xfer} ={f_{stor,xfer} NS_{deadstem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadstem\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{deadstem\_ stor,deadstem\_ xfer} ={f_{stor,xfer} NS_{deadstem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadstem\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: 20.61) - NF_{livecroot\_ stor,livecroot\_ xfer} ={f_{stor,xfer} NS_{livecroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{livecroot\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{livecroot\_ stor,livecroot\_ xfer} ={f_{stor,xfer} NS_{livecroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{livecroot\_ stor} \Delta t}} \right.} \Delta t} .. math:: :label: ZEqnNum605338 - NF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} NS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadcroot\_ stor} \Delta t}} \right. \kern-\nulldelimiterspace} \Delta t} + NF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} NS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadcroot\_ stor} \Delta t}} \right.} \Delta t} where :math:`{f}_{stor,xfer}` is the fraction of current storage pool moved into the transfer pool for display over the incipient onset @@ -696,7 +696,7 @@ growing season control variable (*LGS*, range 0 to 1) is calculated as: .. math:: :label: 20.71) - LGS=\left\{\begin{array}{l} {0\qquad \qquad \qquad {\rm for\; }n_{days\_ active} <365} \\ {\left({n_{days\_ active} \mathord{\left/ {\vphantom {n_{days\_ active} 365}} \right. \kern-\nulldelimiterspace} 365} \right)-1\qquad {\rm for\; }365\le n_{days\_ active} <730} \\ {1\qquad \qquad \qquad {\rm for\; }n_{days\_ active} \ge 730} \end{array}\right. . + LGS=\left\{\begin{array}{l} {0\qquad \qquad \qquad {\rm for\; }n_{days\_ active} <365} \\ {\left({n_{days\_ active} \mathord{\left/ {\vphantom {n_{days\_ active} 365}} \right.} 365} \right)-1\qquad {\rm for\; }365\le n_{days\_ active} <730} \\ {1\qquad \qquad \qquad {\rm for\; }n_{days\_ active} \ge 730} \end{array}\right. . The rate coefficient for background litterfall (:math:`{r}_{bglf}`, s\ :sup:`-1`) is calculated as a function of *LGS*: From 136b342e4b6d72fddd4157b59b4ae0146adeba66 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 12 Oct 2023 17:45:25 -0600 Subject: [PATCH 1626/2067] Straightened apostrophes and quote marks. --- doc/source/lilac/specific-atm-models/wrf.rst | 2 +- .../tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst | 4 ++-- .../CLM50_Tech_Note_Crop_Irrigation.rst | 14 +++++------ .../CLM50_Tech_Note_Decomposition.rst | 8 +++---- .../tech_note/Dust/CLM50_Tech_Note_Dust.rst | 4 ++-- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 16 ++++++------- ...LM50_Tech_Note_External_Nitrogen_Cycle.rst | 2 +- .../tech_note/Fire/CLM50_Tech_Note_Fire.rst | 4 ++-- .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 8 +++---- .../Glacier/CLM50_Tech_Note_Glacier.rst | 4 ++-- .../Hydrology/CLM50_Tech_Note_Hydrology.rst | 6 ++--- .../CLM50_Tech_Note_Introduction.rst | 6 ++--- .../Isotopes/CLM50_Tech_Note_Isotopes.rst | 2 +- .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 10 ++++---- .../CLM50_Tech_Note_Land-Only_Mode.rst | 6 ++--- .../MOSART/CLM50_Tech_Note_MOSART.rst | 12 +++++----- .../Methane/CLM50_Tech_Note_Methane.rst | 16 ++++++------- .../CLM50_Tech_Note_Photosynthesis.rst | 2 +- .../CLM50_Tech_Note_Plant_Mortality.rst | 2 +- .../CLM50_Tech_Note_Radiative_Fluxes.rst | 2 +- .../References/CLM50_Tech_Note_References.rst | 24 +++++++++---------- .../CLM50_Tech_Note_Snow_Hydrology.rst | 2 +- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 2 +- .../CLM50_Tech_Note_Surface_Albedos.rst | 14 +++++------ .../tech_note/Urban/CLM50_Tech_Note_Urban.rst | 6 ++--- .../users_guide/overview/getting-help.rst | 4 ++-- 26 files changed, 91 insertions(+), 91 deletions(-) diff --git a/doc/source/lilac/specific-atm-models/wrf.rst b/doc/source/lilac/specific-atm-models/wrf.rst index 36b1e076a9..2aa2eb5175 100644 --- a/doc/source/lilac/specific-atm-models/wrf.rst +++ b/doc/source/lilac/specific-atm-models/wrf.rst @@ -27,7 +27,7 @@ and :numref:`wrf-set-ctsm-runtime-options`. If CIME is not ported to your machine, please see `instructions on porting CIME `_. - In this example we assume NCAR’s ``Cheyenne`` HPC system in particular. + In this example we assume NCAR's ``Cheyenne`` HPC system in particular. .. _clone-WRF-CTSM-repositories: diff --git a/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst b/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst index e7e8637649..45fc414dee 100644 --- a/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst +++ b/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst @@ -20,8 +20,8 @@ has been implemented in the CLM to specify a subset of emissions. This allows for additional flexibility in grouping chemical compounds to form the lumped species frequently used in atmospheric chemistry. The mapping or grouping is therefore defined through a namelist parameter in -drv\_flds\_in, e.g. megan\_specifier = ’ISOP = isoprene’, ’BIGALK = -pentane + hexane + heptane + tricyclene’. +drv\_flds\_in, e.g. megan\_specifier = 'ISOP = isoprene', 'BIGALK = +pentane + hexane + heptane + tricyclene'. Terrestrial BVOC emissions from plants to the atmosphere are expressed as a flux, :math:`F_{i}` (:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1`), for emission of chemical compound diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 1e5c200069..7ebc058b13 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -80,7 +80,7 @@ release of CLM4.5 were available by request (:ref:`Levis et al. 2016 `). -In addition, CLM’s default list of plant functional types (pfts) includes an +In addition, CLM's default list of plant functional types (pfts) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. The unmanaged C3 crop is only used when the crop model is not active and has grid cell coverage assigned from satellite data, and @@ -278,7 +278,7 @@ the southern hemisphere (SH) the NH requirements apply 6 months later. At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An -equivalent amount of seed leaf N is assigned given the pft’s C to N +equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, @@ -393,7 +393,7 @@ in the Southern Hemisphere apply 6 months later. :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). -:math:`{GDD}_{mat}` is a crop’s 20-year running mean growing +:math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. Crop growth phases @@ -412,7 +412,7 @@ Allocation Allocation changes based on the crop phenology phases phenology (section :numref:`Phenology`). Simulated C assimilation begins every year upon leaf emergence in phase 2 and ends with harvest at the end of phase 3; therefore, so does the -allocation of such C to the crop’s leaf, live stem, fine root, and +allocation of such C to the crop's leaf, live stem, fine root, and reproductive pools. Typically, C:N ratios in plant tissue vary throughout the growing season and @@ -723,7 +723,7 @@ Leaf area index (*L*) is calculated as a function of specific leaf area Stem area index (*S*) is equal to 0.1\ *L* for temperate and tropical corn, sugarcane, switchgrass, and miscanthus and 0.2\ *L* for other crops, as in AgroIBIS. All live C and N pools go to 0 after crop harvest, but the *S* is kept at 0.25 to -simulate a post-harvest “stubble” on the ground. +simulate a post-harvest "stubble" on the ground. Crop heights at the top and bottom of the canopy, :math:`{z}_{top}` and :math:`{z}_{bot}` (m), come from the AgroIBIS formulation: @@ -745,7 +745,7 @@ and :math:`L_{\max }` is the maximum leaf area index (:numref:`Table Crop alloca Interactive Fertilization ''''''''''''''''''''''''' CLM simulates fertilization by adding nitrogen directly to the soil mineral nitrogen pool to meet -crop nitrogen demands using both industrial fertilizer and manure application. CLM’s separate crop land unit ensures that +crop nitrogen demands using both industrial fertilizer and manure application. CLM's separate crop land unit ensures that natural vegetation will not access the fertilizer applied to crops. Fertilizer in CLM5BGCCROP is prescribed by crop functional types and varies spatially for each year based on the LUMIP land use and land cover change diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index 2eaffa47df..3b7e06e179 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -347,8 +347,8 @@ Decomposition rates can also be limited by the availability of mineral nitrogen, but calculation of this limitation depends on first estimating the potential rates of decomposition, assuming an unlimited mineral nitrogen supply. The general case is described here first, referring to -a generic decomposition flux from an “upstream” pool (*u*) to a -“downstream” pool (*d*), with an intervening loss due to respiration. +a generic decomposition flux from an "upstream" pool (*u*) to a +"downstream" pool (*d*), with an intervening loss due to respiration. The potential carbon flux out of the upstream pool (:math:`{CF}_{pot,u}`, gC m\ :sup:`-2` s\ :sup:`-1`) is: @@ -785,8 +785,8 @@ through N downregulation of photosynthesis, equilibration of the model for initialization purposes will take an extremely long time in the standard mode. This is particularly true for the CENTURY-based decomposition cascade, which includes a passive pool. In order to -rapidly equilibrate the model, a modified version of the “accelerated -decomposition” :ref:`(Thornton and Rosenbloon, 2005) ` is used. The fundamental +rapidly equilibrate the model, a modified version of the "accelerated +decomposition" :ref:`(Thornton and Rosenbloon, 2005) ` is used. The fundamental idea of this approach is to allow fluxes between the various pools (both turnover-defined and vertically-defined fluxes) adjust rapidly, while keeping the pool sizes themselves small so that they can fill quickly. diff --git a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst index 2b3064c921..b867c6d9b5 100644 --- a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst +++ b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst @@ -21,7 +21,7 @@ The total vertical mass flux of dust, :math:`F_{j}` F_{j} =TSf_{m} \alpha Q_{s} \sum _{i=1}^{I}M_{i,j} -where :math:`T` is a global factor that compensates for the DEAD model’s +where :math:`T` is a global factor that compensates for the DEAD model's sensitivity to horizontal and temporal resolution and equals 5 x 10\ :sup:`-4` in the CLM instead of 7 x 10\ :sup:`-4` in :ref:`Zender et al. (2003)`. :math:`S` is the source @@ -76,7 +76,7 @@ particles in the soil and %clay is determined from the surface dataset :math:`M_{clay} =0.2` to sandy loam. :math:`Q_{s}` is the total horizontally saltating mass flux (kg -m\ :sup:`-1` s\ :sup:`-1`) of “large” particles (:numref:`Table Dust Mass fraction`), +m\ :sup:`-1` s\ :sup:`-1`) of "large" particles (:numref:`Table Dust Mass fraction`), also referred to as the vertically integrated streamwise mass flux .. math:: diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst index 111e115b5f..5902a20352 100644 --- a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst +++ b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst @@ -463,7 +463,7 @@ dry hydrophobic rates, These fluxes are computed interactively by the atmospheric model (when prognostic aerosol representation is active) or are prescribed from a time-varying (annual cycle or transient), globally-gridded deposition -file defined in the namelist (see the CLM4.5 User’s Guide). Aerosol +file defined in the namelist (see the CLM4.5 User's Guide). Aerosol deposition rates were calculated in a transient 1850-2009 CAM simulation (at a resolution of 1.9x2.5x26L) with interactive chemistry (troposphere and stratosphere) driven by CCSM3 20\ :sup:`th` century @@ -568,7 +568,7 @@ Initialization Initialization of the land model (i.e., providing the model with initial temperature and moisture states) depends on the type of run (startup or -restart) (see the CLM4.5 User’s Guide). A startup run starts the model +restart) (see the CLM4.5 User's Guide). A startup run starts the model from either initial conditions that are set internally in the Fortran code (referred to as arbitrary initial conditions) or from an initial conditions dataset that enables the model to start from a spun up state @@ -634,7 +634,7 @@ elevation, biogenic volatile organic compounds (BVOCs) emissions factors, population density, gross domestic production, peat area fraction, and peak month of agricultural burning. Optional surface data include crop irrigation and managed crops. All fields are aggregated to -the model’s grid from high-resolution input datasets ( +the model's grid from high-resolution input datasets ( :numref:`Table Surface data required for CLM and their base spatial resolution`) that are obtained from a variety of sources described below. @@ -826,9 +826,9 @@ cropland area of each grid cell is divided into an irrigated and unirrigated fraction according to a dataset of areas equipped for irrigation (:ref:`Siebert et al. (2005) `). The area of irrigated cropland in each grid cell is given by the -smaller of the grid cell’s total cropland area, according to the default -CLM4 dataset, and the grid cell’s area equipped for irrigation. The -remainder of the grid cell’s cropland area (if any) is then assigned to +smaller of the grid cell's total cropland area, according to the default +CLM4 dataset, and the grid cell's area equipped for irrigation. The +remainder of the grid cell's cropland area (if any) is then assigned to unirrigated cropland. Irrigated and unirrigated crops are placed on separate soil columns, so that irrigation is only applied to the soil beneath irrigated crops. @@ -844,7 +844,7 @@ Database of the Global Environment version 3.1 (HYDEv3.1) with dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per capita in 2000 at 0.5\ :sup:`o` is from :ref:`Van Vuuren et al. (2006) `, which is the base-year GDP data for IPCC-SRES and derived from -country-level World Bank’s World Development Indicators (WDI) measured +country-level World Bank's World Development Indicators (WDI) measured in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database (:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5\ :sup:`o` resolution is derived from three vector datasets: peatland data in @@ -879,7 +879,7 @@ of the components in the coupled modeling system, are presented in "Standard pressure", :math:`P_{std}`, 101325, "Pa" "Stefan-Boltzmann constant", :math:`\sigma`, 5.67 :math:`\times 10^{-8}`, W m :sup:`-2` K :math:`{}^{-4}` "Boltzmann constant", :math:`\kappa`, 1.38065 :math:`\times 10^{-23}`, J K :sup:`-1` molecule :sup:`-1` - "Avogadro’s number", :math:`N_{A}`, 6.02214 :math:`\times 10^{26}`, molecule kmol\ :sup:`-1` + "Avogadro's number", :math:`N_{A}`, 6.02214 :math:`\times 10^{26}`, molecule kmol\ :sup:`-1` "Universal gas constant", :math:`R_{gas}`, :math:`N_{A} \kappa`, J K :sup:`-1` kmol :sup:`-1` "Molecular weight of dry air", :math:`MW_{da}`, 28.966, kg kmol :sup:`-1` "Dry air gas constant", :math:`R_{da}`, :math:`{R_{gas} \mathord{\left/ {\vphantom {R_{gas} MW_{da} }} \right.} MW_{da} }`, J K :sup:`-1` kg :sup:`-1` diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index 1fd978e79f..90dd72f705 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -211,7 +211,7 @@ separately at each layer to define a profile of anoxic porespace fraction in the soil. The nitrification/denitrification models used here also predict fluxes -of N\ :sub:`2`\ O via a “hole-in-the-pipe” approach (:ref:`Firestone and +of N\ :sub:`2`\ O via a "hole-in-the-pipe" approach (:ref:`Firestone and Davidson, 1989 `). A constant fraction (6 \* 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction diff --git a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst index 912bc7e378..87e827c311 100644 --- a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst +++ b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst @@ -374,7 +374,7 @@ where :math:`M_{livestem,2}` is the corresponding mortality factor Fire nitrogen emissions and nitrogen transfers due to fire-induced mortality are calculated the same way as for carbon, using the same -values for combustion completeness and mortality factors. With CLM’s +values for combustion completeness and mortality factors. With CLM's dynamic vegetation option enabled, the number of tree PFT individuals killed by fire per km\ :sup:`2` (individual km\ :sup:`-2` s\ :sup:`-1`) is given by @@ -438,7 +438,7 @@ for agricultural fires (:ref:`van der Werf et al. 2010 `); :math:`{f}_{t}` is set to 0 otherwise. Peak month in this dataset correlates with the month after harvesting or the month before planting. In CLM we use this dataset the same way whether -the CROP option is active or not, without regard to the CROP option’s +the CROP option is active or not, without regard to the CROP option's simulated planting and harvesting dates. In the post-fire region, fire impact is parameterized similar to section diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index f4ef49285b..e97cb89139 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -539,7 +539,7 @@ where the aerodynamic resistances (s m\ :sup:`-1`) are \begin{array}{l} {r_{aw} =\frac{q_{atm} -q_{s} }{q_{*} u_{*} } =\frac{1}{k^{2} V_{a} } \left[\ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)-\psi _{m} \left(\frac{z_{atm,\, m} -d}{L} \right)+\psi _{m} \left(\frac{z_{0m} }{L} \right)\right]} \\ {\qquad \left[\ln \left(\frac{z_{atm,\, {\it w}} -d}{z_{0w} } \right)-\psi _{w} \left(\frac{z_{atm,\, w} -d}{L} \right)+\psi _{w} \left(\frac{z_{0w} }{L} \right)\right]} \end{array}. -A 2-m height “screen” temperature is useful for comparison with +A 2-m height "screen" temperature is useful for comparison with observations .. math:: @@ -547,7 +547,7 @@ observations T_{2m} =\theta _{s} +\frac{\theta _{*} }{k} \left[\ln \left(\frac{2+z_{0h} }{z_{0h} } \right)-\psi _{h} \left(\frac{2+z_{0h} }{L} \right)+\psi _{h} \left(\frac{z_{0h} }{L} \right)\right] -where for convenience, “2-m” is defined as 2 m above the apparent sink +where for convenience, "2-m" is defined as 2 m above the apparent sink for sensible heat (:math:`z_{0h} +d`). Similarly, a 2-m height specific humidity is defined as @@ -1392,7 +1392,7 @@ non-linear systems of equations can be applied to iteratively solve for \Delta T_{v} =\frac{\overrightarrow{S}_{v} -\overrightarrow{L}_{v} -H_{v} -\lambda E_{v} }{\frac{\partial \overrightarrow{L}_{v} }{\partial T_{v} } +\frac{\partial H_{v} }{\partial T_{v} } +\frac{\partial \lambda E_{v} }{\partial T_{v} } } where :math:`\Delta T_{v} =T_{v}^{n+1} -T_{v}^{n}` and the subscript -“n” indicates the iteration. +"n" indicates the iteration. The partial derivatives are @@ -1418,7 +1418,7 @@ determined analytically, are ignored for :math:`\frac{\partial H_{v} }{\partial T_{v} }` and :math:`\frac{\partial \lambda E_{v} }{\partial T_{v} }` . However, if :math:`\zeta` changes sign more than four times during the temperature -iteration, :math:`\zeta =-0.01`. This helps prevent “flip-flopping” +iteration, :math:`\zeta =-0.01`. This helps prevent "flip-flopping" between stable and unstable conditions. The total water vapor flux :math:`E_{v}` , transpiration flux :math:`E_{v}^{t}` , and sensible heat flux :math:`H_{v}` are updated for changes in leaf temperature as diff --git a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst index 52313b9a5c..3d56e962ed 100644 --- a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst +++ b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst @@ -6,7 +6,7 @@ Glaciers This chapter describes features of CLM that are specific to coupling to an ice sheet model (in the CESM context, this is the CISM model; :ref:`Lipscomb and Sacks (2012)` provide -documentation and user’s guide for CISM). General information +documentation and user's guide for CISM). General information about glacier land units can be found elsewhere in this document (see Chapter :numref:`rst_Surface Characterization, Vertical Discretization, and Model Input Requirements` for an overview). @@ -64,7 +64,7 @@ ice sheet model: The ice sheet model is typically run at much higher resolution than CLM (e.g., :math:`\sim`\ 5 km rather than :math:`\sim`\ 100 km). To improve -the downscaling from CLM’s grid to the ice sheet grid, the glaciated +the downscaling from CLM's grid to the ice sheet grid, the glaciated portion of each grid cell is divided into multiple elevation classes (section :numref:`Multiple elevation class scheme`). The above quantities are computed separately in each elevation class. The CESM diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index aff2c6fd61..dfb4aac092 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -511,7 +511,7 @@ condition of the infiltration flux into the top soil layer bottom of the soil column (sub-surface runoff is removed later in the timestep, section :numref:`Lateral Sub-surface Runoff`). -The soil water flux :math:`q` in equation can be described by Darcy’s +The soil water flux :math:`q` in equation can be described by Darcy's law :ref:`(Dingman 2002) ` .. math:: @@ -533,7 +533,7 @@ related to the adsorptive and capillary forces within the soil matrix), and :math:`\psi _{z}` is the gravitational potential (mm) (the vertical distance from an arbitrary reference elevation to a point in the soil). If the reference elevation is the soil surface, then -:math:`\psi _{z} =z`. Letting :math:`\psi =\psi _{m}` , Darcy’s law +:math:`\psi _{z} =z`. Letting :math:`\psi =\psi _{m}` , Darcy's law becomes .. math:: @@ -676,7 +676,7 @@ averages based on :math:`f_{om}` may therefore be determined primarily by the organic soil properties even for values of :math:`f_{om}` as low as 1 %. To better represent the influence of organic soil material on the grid cell average saturated hydraulic conductivity, the soil organic -matter fraction is further subdivided into “connected” and “unconnected” +matter fraction is further subdivided into "connected" and "unconnected" fractions using a result from percolation theory (:ref:`Stauffer and Aharony 1994 `, :ref:`Berkowitz and Balberg 1992 `). Assuming that the organic and mineral fractions are randomly distributed throughout diff --git a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst index face74629b..6b91287388 100644 --- a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst +++ b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst @@ -176,7 +176,7 @@ biogeochemical parameterizations and numerical implementation of version 5.0 of the Community Land Model (CLM5.0). Scientific justification and evaluation of these parameterizations can be found in the referenced scientific papers (:ref:`rst_References`). This document and the CLM5.0 -User’s Guide together provide the user with the scientific description +User's Guide together provide the user with the scientific description and operating instructions for CLM. Model History @@ -286,7 +286,7 @@ model. This involved changing data structures from a single vector of spatially independent sub-grid patches to one that recognizes three hierarchical scales within a model grid cell: land unit, snow/soil column, and PFT. Furthermore, as an option, the model can be configured -so that PFTs can share a single soil column and thus “compete” for +so that PFTs can share a single soil column and thus "compete" for water. This version of the model (CLM2.1) was released to the community in February 2003. CLM2.1, without the compete option turned on, produced only round off level changes when compared to CLM2. @@ -316,7 +316,7 @@ changes in CLM3 hydrological parameterizations on partitioning of evapotranspiration (ET) and its effect on the timescales of ET response to precipitation events, interseasonal soil moisture storage, soil moisture memory, and -land-atmosphere coupling. :ref:`Qian et al. (2006)` evaluate CLM3’s performance +land-atmosphere coupling. :ref:`Qian et al. (2006)` evaluate CLM3's performance in simulating soil moisture content, runoff, and river discharge when forced by observed precipitation, temperature and other atmospheric data. diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 43692205b8..0963c1ea31 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -138,7 +138,7 @@ effect. The kinetic isotope effect during diffusion of CO\ :sub:`2` through the stomatal opening is 4.4‰. The kinetic isotope effect during fixation of CO\ :sub:`2` with Rubisco is :math:`\sim`\ 30‰; however, since about 5-10% of carbon in C3 plants -reacts with phosphoenolpyruvate carboxylase (PEPC) (Melzer and O’Leary, +reacts with phosphoenolpyruvate carboxylase (PEPC) (Melzer and O'Leary, 1987), the net kinetic isotope effect during fixation is :math:`\sim`\ 27‰ for C3 plants. In C4 plant photosynthesis, only the diffusion effect is important. The fractionation factor equations for C3 diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index e623a1383d..2cad862508 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -17,7 +17,7 @@ Lakes have spatially variable depth prescribed in the surface data (section :ref:`External Data Lake`); the surface data optionally includes lake optical extinction coeffient and horizontal fetch, currently only used for site simulations. Lake physics includes freezing and thawing in the lake -body, resolved snow layers, and “soil” and bedrock layers below the lake +body, resolved snow layers, and "soil" and bedrock layers below the lake body. Temperatures and ice fractions are simulated for :math:`N_{levlak} =10` layers (for global simulations) or :math:`N_{levlak} =25` (for site simulations) with discretization @@ -49,7 +49,7 @@ or assumed depth *d*, extinction coefficient :math:`\eta`, and fetch decomposition algorithm in future model versions. As currently implemented, the lake consists of 0-5 snow layers; water and ice layers (10 for global simulations and 25 for site simulations) comprising the -“lake body;” 10 “soil” layers; and 5 bedrock layers. Each lake body +"lake body;" 10 "soil" layers; and 5 bedrock layers. Each lake body layer has a fixed water mass (set by the nominal layer thickness and the liquid density), with frozen mass-fraction *I* a state variable. Resolved snow layers are present if the snow thickness @@ -349,7 +349,7 @@ surface fluxes as \Delta T_{g} =\frac{\beta \overrightarrow{S}_{g} -\overrightarrow{L}_{g} -H_{g} -\lambda E_{g} -G}{\frac{\partial \overrightarrow{L}_{g} }{\partial T_{g} } +\frac{\partial H_{g} }{\partial T_{g} } +\frac{\partial \lambda E_{g} }{\partial T_{g} } +\frac{\partial G}{\partial T_{g} } } where :math:`\Delta T_{g} =T_{g}^{n+1} -T_{g}^{n}` and the subscript -“n” indicates the iteration. Therefore, the surface temperature +"n" indicates the iteration. Therefore, the surface temperature :math:`T_{g}^{n+1}` can be written as .. math:: @@ -928,7 +928,7 @@ Convection ^^^^^^^^^^^^^^^^ Convective mixing is based on -:ref:`Hostetler et al.’s (1993, 1994)` coupled +:ref:`Hostetler et al.'s (1993, 1994)` coupled lake-atmosphere model, adjusting the lake temperature after diffusion and phase change to maintain a stable density profile. Unfrozen lakes overturn when :math:`\rho _{i} >\rho _{i+1}` , in which case the layer @@ -1126,7 +1126,7 @@ Snow-capping is invoked if the snow depth :math:`z_{sno} >1000{\rm m}`, in which case additional precipitation and frost deposition is added to :math:`q_{snwcp,\, ice}` . -If there are resolved snow layers, the generalized “evaporation” +If there are resolved snow layers, the generalized "evaporation" :math:`E_{g}` (i.e., evaporation, dew, frost, and sublimation) is treated as over other land units, except that the allowed evaporation from the ground is unlimited (though the top snow layer cannot lose more diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index 4606f43229..137db2b18a 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -32,7 +32,7 @@ to be run over Antarctica and ensures data is available along coastlines regardless of model resolution. The forcing data is ingested into a data atmosphere model in three -“streams”; precipitation (:math:`P`) (mm s\ :sup:`-1`), solar +"streams"; precipitation (:math:`P`) (mm s\ :sup:`-1`), solar radiation (:math:`S_{atm}` ) (W m\ :sup:`-2`), and four other fields [atmospheric pressure :math:`P_{atm}` (Pa), atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`), atmospheric @@ -75,7 +75,7 @@ numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. The total incident solar radiation :math:`S_{atm}` at the model time step :math:`t_{M}` is then split into near-infrared and visible radiation and partitioned into direct and diffuse according to factors -derived from one year’s worth of hourly CAM output from CAM version +derived from one year's worth of hourly CAM output from CAM version cam3\_5\_55 as .. math:: @@ -204,7 +204,7 @@ temperature :math:`T_{dew}` (K) and derive specific humidity q_{atm} = \frac{0.622e_{sat}^{T_{dew} } }{P_{atm} -0.378e_{sat}^{T_{dew} } } . Here, :math:`e_{sat}^{T}` , the saturation vapor pressure as a function -of temperature, is derived from :ref:`Lowe’s (1977) ` polynomials. If not +of temperature, is derived from :ref:`Lowe's (1977) ` polynomials. If not provided by the user, the atmospheric pressure :math:`P_{atm}` (Pa) is set equal to the standard atmospheric pressure :math:`P_{std} =101325` Pa, and surface pressure :math:`P_{srf}` (Pa) is set equal diff --git a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst index 439de8a7a1..b80b86cfc5 100644 --- a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst +++ b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst @@ -58,8 +58,8 @@ is not routed through MOSART, but instead is mapped directly from the spatial un where it is generated at any time step to the coupler. In MOSART, the travel velocities of water across hillslopes, sub-network and main -channel are all estimated using Manning’s equation with different levels of -simplifications. Generally the Manning’s equation is in the form of +channel are all estimated using Manning's equation with different levels of +simplifications. Generally the Manning's equation is in the form of .. math:: :label: 14.1 @@ -71,7 +71,7 @@ radius (m). :math:`S_{f}` is the friction slope that accounts for the effects of gravity, friction, inertia and other forces on the water. If the channel slope is steep enough, the gravity force dominates over the others so one can approximate :math:`S_{f}` by the channel bed slope :math:`S` , which is the key assumption -underpinning the kinematic wave method. :math:`n` is the Manning’s roughness +underpinning the kinematic wave method. :math:`n` is the Manning's roughness coefficient, which is mainly controlled by surface roughness and sinuosity of the flow path. @@ -180,7 +180,7 @@ parameters, e.g., bankfull width and depth, were estimated from empirical hydraulic geometry relationships as functions of the mean annual discharge. The Manning roughness coefficients for overland and channel flow were calculated as functions of landcover and water depth. For more details -on the methodology to derive channel geometry and the Manning’s roughness +on the methodology to derive channel geometry and the Manning's roughness coefficients, please refer to :ref:`Getirana et al. (2012) ` . The full list of parameters included in this global hydrography dataset is provided in @@ -217,9 +217,9 @@ by MOSART using the aforementioned parameters is described in +-------------------------+---------------+------------------------------------------------------------------------------------------------------------------------------------+ | :math:`W_{t}` | m | The average bankfull width of tributary channels | +-------------------------+---------------+------------------------------------------------------------------------------------------------------------------------------------+ - | :math:`n_{r}` | \- | Manning’s roughness coefficient for channel flow routing | + | :math:`n_{r}` | \- | Manning's roughness coefficient for channel flow routing | +-------------------------+---------------+------------------------------------------------------------------------------------------------------------------------------------+ - | :math:`n_{h}` | \- | Manning’s roughness coefficient for overland flow routing | + | :math:`n_{h}` | \- | Manning's roughness coefficient for overland flow routing | +-------------------------+---------------+------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 0d419e8727..1209eaab88 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -143,7 +143,7 @@ modified the base :math:`f_{CH_{4}}` value. For the single-layer BGC version, :math:`{R}_{H}` is distributed among soil levels by assuming that 50% is associated with the roots (using the CLM PFT-specific rooting distribution) and the rest is evenly -divided among the top 0.28 m of soil (to be consistent with CLM’s soil +divided among the top 0.28 m of soil (to be consistent with CLM's soil decomposition algorithm). For the vertically resolved BGC version, the prognosed distribution of :math:`{R}_{H}` is used to estimate CH\ :sub:`4` production. @@ -232,7 +232,7 @@ Ebullition Briefly, the simulated aqueous CH\ :sub:`4` concentration in each soil level is used to estimate the expected equilibrium gaseous partial pressure (:math:`C_{e}` ), as a function of temperature and depth below -the water table, by first estimating the Henry’s law partitioning +the water table, by first estimating the Henry's law partitioning coefficient (:math:`k_{h}^{C}` ) by the method described in :ref:`Wania et al. (2010)`: @@ -252,7 +252,7 @@ coefficient (:math:`k_{h}^{C}` ) by the method described in C_{e} =\frac{C_{w} R_{g} T}{\theta _{s} k_{H}^{C} p} where :math:`C_{H}` \ is a constant, :math:`R_{g}` is the universal -gas constant, :math:`k_{H}^{s}` is Henry’s law partitioning coefficient +gas constant, :math:`k_{H}^{s}` is Henry's law partitioning coefficient at standard temperature (:math:`T^{s}` ),\ :math:`C_{w}` \ is local aqueous CH\ :sub:`4` concentration, and *p* is pressure. @@ -293,7 +293,7 @@ area (m\ :sup:`2` m\ :sup:`-2`); :math:`{r}_{a}` is the aerodynamic resistance between the surface and the atmospheric reference height (s m\ :sup:`-1`); and :math:`\rho _{r}` is the rooting density as a function of depth (-). The gaseous concentration is -calculated with Henry’s law as described in equation :eq:`24.7`. +calculated with Henry's law as described in equation :eq:`24.7`. Based on the ranges reported in :ref:`Colmer (2003)`, we have chosen baseline aerenchyma porosity values of 0.3 for grass and crop PFTs and 0.1 for @@ -477,7 +477,7 @@ parameters specific to the CH\ :sub:`4` model are given in soils below the water table, diffusion is limited to the remaining liquid (CLM allows for some freezing point depression), and the diffusion coefficients are scaled by the -volume-fraction of liquid. For unsaturated soils, Henry’s law +volume-fraction of liquid. For unsaturated soils, Henry's law equilibrium is assumed at the interface with the water table. .. _Boundary Conditions: @@ -502,11 +502,11 @@ with a series combination: :math:`\left[\frac{1}{w} +\frac{\Delta x_{1} }{D_{1} } \right]^{-1}` , and if the top layer is saturated, this term is replaced with :math:`\left[\frac{K_{H} }{w} +\frac{\frac{1}{2} \Delta x_{1} }{D_{1} } \right]^{-1}` , -where :math:`{K}_{H}` is the Henry’s law equilibrium constant. +where :math:`{K}_{H}` is the Henry's law equilibrium constant. When snow is present, a resistance is added to account for diffusion through the snow based on the Millington-Quirk expression :eq:`24.13` -and CLM’s prediction of the liquid water, ice, and air fractions of each +and CLM's prediction of the liquid water, ice, and air fractions of each snow layer. When the soil is ponded, the diffusivity is assumed to be that of methane in pure water, and the resistance as the ratio of the ponding depth to diffusivity. The overall conductance is taken as the @@ -567,7 +567,7 @@ production minus consumption) and carbon atoms. Interface between water table and unsaturated zone ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -We assume Henry’s Law equilibrium at the interface between the saturated +We assume Henry's Law equilibrium at the interface between the saturated and unsaturated zone and constant flux from the soil element below the interface to the center of the soil element above the interface. In this case, the coefficients are the same as described above, except for the diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 253eeb2638..bcc29a5e89 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -524,7 +524,7 @@ The equations for :math:`c_{i}` , :math:`c_{s}` , :math:`r_{s}` , and :math:`A_{n}` are solved iteratively until :math:`c_{i}` converges. :ref:`Sun et al. (2012)` pointed out that the CLM4 numerical approach does not always converge. Therefore, the model uses a hybrid algorithm that -combines the secant method and Brent’s method to solve for +combines the secant method and Brent's method to solve for :math:`c_{i}` . The equation set is solved separately for sunlit (:math:`A_{n}^{sun}` , :math:`r_{s}^{sun}` ) and shaded (:math:`A_{n}^{sha}` , :math:`r_{s}^{sha}` ) leaves. diff --git a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst index ed16004258..45d2aef0d3 100644 --- a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst +++ b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst @@ -8,7 +8,7 @@ and is intended to represent the death of individuals from a stand of plants due to the aggregate of processes such as wind throw, insect attack, disease, extreme temperatures or drought, and age-related decline in vigor. These processes are referred to in aggregate as -“gap-phase” mortality. Mortality due to fire and anthropogenic land +"gap-phase" mortality. Mortality due to fire and anthropogenic land cover change are treated separately (see Chapters :numref:`rst_Fire` and :numref:`rst_Transient Landcover Change`, respectively). diff --git a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst index 1cb673bdba..2d240d160a 100644 --- a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst +++ b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst @@ -6,7 +6,7 @@ Radiative Fluxes The net radiation at the surface is :math:`\left(\vec{S}_{v} +\vec{S}_{g} \right)-\left(\vec{L}_{v} +\vec{L}_{g} \right)`, where :math:`\vec{S}` is the net solar flux absorbed by the vegetation -(“v”) and the ground (“g”) and :math:`\vec{L}` is the net longwave flux +("v") and the ground ("g") and :math:`\vec{L}` is the net longwave flux (positive toward the atmosphere) (W m\ :sup:`-2`). .. _Solar Fluxes: diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 46b835a76d..4497e93610 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -135,13 +135,13 @@ quaternary climatic changes. J. Atmos. Sci. 35:2362-2367. .. _Berger1978b: Berger, A.L. 1978b. A simple algorithm to compute long-term variations -of daily or monthly insolation. Contribution de l’Institut d’Astronomie +of daily or monthly insolation. Contribution de l'Institut d'Astronomie et de Géophysique, Université Catholique de Louvain, Louvain-la-Neuve, No. 18. .. _Bergeretal1993: -Berger, A., Loutre, M.-F., and Tricot, C. 1993. Insolation and Earth’s +Berger, A., Loutre, M.-F., and Tricot, C. 1993. Insolation and Earth's orbital periods. J. Geophys. Res. 98:10341-10362. .. _BerkowitzBalberg1992: @@ -163,7 +163,7 @@ light by small particles. John Wiley & Sons, New York, NY. .. _Bonan1996: Bonan, G.B. 1996. A land surface model (LSM version 1.0) for ecological, -hydrological, and atmospheric studies: Technical description and user’s +hydrological, and atmospheric studies: Technical description and user's guide. NCAR Technical Note NCAR/TN-417+STR, National Center for Atmospheric Research, Boulder, CO, 150 pp. @@ -378,7 +378,7 @@ Adv. Atmos. Sci. 14:433-460. .. _Daietal2001: Dai, Y., et al. 2001. Common Land Model: Technical documentation and -user’s guide [Available online at +user's guide [Available online at http://climate.eas.gatech.edu/dai/clmdoc.pdf]. .. _Daietal2003: @@ -1131,8 +1131,8 @@ DOI:10.1029/2002JD003203. .. _Levisetal2004: Levis, S., Bonan, G.B., Vertenstein, M., and Oleson, K.W. 2004. The -community land model’s dynamic global vegetation model (CLM-DGVM): -technical description and user’s guide. NCAR Technical Note +community land model's dynamic global vegetation model (CLM-DGVM): +technical description and user's guide. NCAR Technical Note NCAR/TN-459+STR. National Center for Atmospheric Research, Boulder, Colorado. 50 pp. @@ -1169,10 +1169,10 @@ Vegetation Model. Biogeosciences 9:2761-2780. .. _Lietal2012b: -Li, F., Zeng, X. D., and Levis, S. 2012b. Corrigendum to “A +Li, F., Zeng, X. D., and Levis, S. 2012b. Corrigendum to "A process-based fire parameterization of intermediate complexity in a -Dynamic Global Vegetation Model” published in Biogeosciences, 9, -2761–2780, 2012”. Biogeosciences 9: 4771-4772. +Dynamic Global Vegetation Model" published in Biogeosciences, 9, +2761–2780, 2012". Biogeosciences 9: 4771-4772. .. _Lietal2013a: @@ -1228,7 +1228,7 @@ Lichstein, J.W. and S.W. Pacala, 2011. Local diversity in heterogeneous landscap .. _LipscombSacks2012: Lipscomb, W., and Sacks, W. 2012. The CESM land ice model documentation -and user’s guide. 46 pp. [Available online at +and user's guide. 46 pp. [Available online at http://www.cesm.ucar.edu/models/cesm1.1/cism/]. .. _lischke2006: @@ -1343,7 +1343,7 @@ doi:10.1111/j.1365-2486.2010.02375.x .. _MelzerOLeary1987: -Melzer, E., and O’Leary, M.H. 1987. Anapleurotic CO2 Fixation by +Melzer, E., and O'Leary, M.H. 1987. Anapleurotic CO2 Fixation by Phosphoenolpyruvate Carboxylase in C3 Plants. Plant. Physiol. 84:58. .. _Milleretal1994: @@ -1523,7 +1523,7 @@ decomposers in ecological systems. Ecology 44:322-331. .. _Olsonetal2001: Olson, D.M., Dinerstein, E., Wikramanayake, E.D., Burgess, N.D., Powell, -G.V.N., Underwood, E.C., D’Amico, J.A., Itoua, I., Strand, H. E., +G.V.N., Underwood, E.C., D'Amico, J.A., Itoua, I., Strand, H. E., Morrison, J. C., Loucks, C. J., Allnutt, T. F., Ricketts, T. H., Kura, Y., Lamoreux, J. F., Wettengel, W. W., Heda, P., and Kassem, K. R., 2001. Terrestrial ecoregions of the world a new map of life on earth, diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 851f4e9d84..25f9366870 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -264,7 +264,7 @@ evaporation as w_{liq,\, snl+1}^{n+1} =w_{liq,\, snl+1}^{n} +f_{sno} \left(q_{grnd,\, liq} +q_{sdew} -q_{seva} \right)\Delta t. -When the liquid water within a snow layer exceeds the layer’s holding +When the liquid water within a snow layer exceeds the layer's holding capacity, the excess water is added to the underlying layer, limited by the effective porosity (:math:`1-\theta _{ice}` ) of the layer. The flow of water is assumed to be zero (:math:`q_{liq,\, i} =0`) if the diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst index 7b88132098..08ba49afe2 100644 --- a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst +++ b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst @@ -173,7 +173,7 @@ temperature :math:`T_{i}` [K]; thermal conductivity volumetric heat capacity :math:`c_{i}` [J m\ :sup:`-3` K\ :sup:`-1`]) are defined for soil layers at the node depths (:numref:`Figure Soil Temperature Schematic`) and for snow layers at the layer midpoints. When present, -snow occupies a fraction of a grid cell’s area, therefore snow depth +snow occupies a fraction of a grid cell's area, therefore snow depth represents the thickness of the snowpack averaged over only the snow covered area. The grid cell average snow depth is related to the depth of the snow covered area as :math:`\bar{z}_{sno} =f_{sno} z_{sno}` . By diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index 3b693b7de6..8f7c54bb40 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -511,7 +511,7 @@ Ground Albedos The overall direct beam :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse :math:`\alpha _{g,\, \Lambda }` ground albedos are weighted -combinations of “soil” and snow albedos +combinations of "soil" and snow albedos .. math:: :label: 3.58 @@ -789,7 +789,7 @@ Snowpack Optical Properties Ice optical properties for the five spectral bands are derived offline and stored in a namelist-defined lookup table for online retrieval (see -CLM5.0 User’s Guide). Mie properties are first computed at fine spectral +CLM5.0 User's Guide). Mie properties are first computed at fine spectral resolution (470 bands), and are then weighted into the five bands applied by CLM according to incident solar flux, :math:`I^{\downarrow } (\lambda )`. For example, the broadband @@ -1064,7 +1064,7 @@ The solar declination angle :math:`\delta` is calculated as in :ref:`Berger orbital parameters are calculated for the desired year. The required orbital parameters to be input by the user are the obliquity of the Earth :math:`\varepsilon` (degrees, -:math:`-90^{\circ } <\varepsilon <90^{\circ }` ), Earth’s eccentricity +:math:`-90^{\circ } <\varepsilon <90^{\circ }` ), Earth's eccentricity :math:`e` (:math:`0.0` in which +"urban canyon" concept of :ref:`Oke (1987) ` in which the canyon geometry is described by building height (:math:`H`) and street width (:math:`W`) (:numref:`Figure schematic representation of the urban landunit`). The canyon system @@ -76,7 +76,7 @@ model (e.g., the Community Atmosphere Model (CAM)) or observed forcing (e.g., reanalysis or field observations). The urban model produces sensible, latent heat, and momentum fluxes, emitted longwave, and reflected solar radiation, which are area-averaged with -fluxes from non-urban “landunits” (e.g., vegetation, lakes) to supply +fluxes from non-urban "landunits" (e.g., vegetation, lakes) to supply grid cell averaged fluxes to the atmospheric model. Present day global urban extent and urban properties were developed by @@ -101,7 +101,7 @@ fraction, average building height, and pervious fraction of the canyon floor) properties are provided for each of the density classes. Building interior minimum and maximum temperatures are prescribed based on climate and socioeconomic considerations. The surface dataset creation -routines (see CLM5.0 User’s Guide) aggregate the data to the desired +routines (see CLM5.0 User's Guide) aggregate the data to the desired resolution. An optional urban properties dataset, including a tool that allows for generating future diff --git a/doc/source/users_guide/overview/getting-help.rst b/doc/source/users_guide/overview/getting-help.rst index 0378852a4b..475a6f8191 100644 --- a/doc/source/users_guide/overview/getting-help.rst +++ b/doc/source/users_guide/overview/getting-help.rst @@ -76,7 +76,7 @@ CESM Community Earth System Model (CESM). The coupled earth system model that CLM is a component of. CIME - The Common Infrastructure for Modeling the Earth (CIME - pronounced “SEAM”) provides a Case Control System for configuring, compiling and executing Earth system models, data and stub model components, a driver and associated tools and libraries. + The Common Infrastructure for Modeling the Earth (CIME - pronounced "SEAM") provides a Case Control System for configuring, compiling and executing Earth system models, data and stub model components, a driver and associated tools and libraries. CLM Community Land Model (CLM). The prognostically active land model component of CESM. @@ -126,7 +126,7 @@ ESMF Earth System Modeling Framework (ESMF). They are a software project that provides a software library to support Earth System modeling. We provide interfaces for ESMF as well as use their regridding capabilities for offline CLM tools. FATES - Functionally Assembled Terrestrial Ecosystem Simulator. This is being developed by the Next Generation Ecosystem Experiment Tropics’ (NGEE-T) + Functionally Assembled Terrestrial Ecosystem Simulator. This is being developed by the Next Generation Ecosystem Experiment Tropics' (NGEE-T) project and uses both |version| and the land model component of E3SM (Energy Exascale Earth System Model). FUN From e74a2c6654953342c147b6b47ed899a38a78ec6d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 12 Oct 2023 17:50:16 -0600 Subject: [PATCH 1627/2067] Deleted end-of-line whitespace. --- doc/design/dynamic_urban.rst | 10 +- doc/design/water_tracers.rst | 2 +- .../lilac/specific-atm-models/index.rst | 2 +- .../lilac/specific-atm-models/wrf-nesting.rst | 54 +- doc/source/lilac/specific-atm-models/wrf.rst | 34 +- .../tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst | 6 +- .../CLM50_Tech_Note_CN_Allocation.rst | 2 +- .../CN_Pools/CLM50_Tech_Note_CN_Pools.rst | 10 +- .../CLM50_Tech_Note_Crop_Irrigation.rst | 484 +++++++++--------- .../CLM50_Tech_Note_Decomposition.rst | 150 +++--- .../tech_note/Dust/CLM50_Tech_Note_Dust.rst | 64 +-- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 134 ++--- ...LM50_Tech_Note_External_Nitrogen_Cycle.rst | 116 ++--- .../tech_note/FUN/CLM50_Tech_Note_FUN.rst | 148 +++--- .../tech_note/Fire/CLM50_Tech_Note_Fire.rst | 294 +++++------ .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 334 ++++++------ .../Glacier/CLM50_Tech_Note_Glacier.rst | 2 +- .../Hydrology/CLM50_Tech_Note_Hydrology.rst | 296 +++++------ .../CLM50_Tech_Note_Introduction.rst | 14 +- .../Isotopes/CLM50_Tech_Note_Isotopes.rst | 26 +- .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 204 ++++---- .../CLM50_Tech_Note_Land-Only_Mode.rst | 74 +-- .../MOSART/CLM50_Tech_Note_MOSART.rst | 208 ++++---- .../Methane/CLM50_Tech_Note_Methane.rst | 96 ++-- .../CLM50_Tech_Note_Photosynthesis.rst | 82 +-- ...LM50_Tech_Note_Photosynthetic_Capacity.rst | 72 +-- .../CLM50_Tech_Note_Plant_Hydraulics.rst | 272 +++++----- .../CLM50_Tech_Note_Plant_Mortality.rst | 172 +++---- .../CLM50_Tech_Note_Plant_Respiration.rst | 22 +- .../CLM50_Tech_Note_Radiative_Fluxes.rst | 30 +- .../References/CLM50_Tech_Note_References.rst | 12 +- .../CLM50_Tech_Note_Snow_Hydrology.rst | 204 ++++---- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 214 ++++---- .../CLM50_Tech_Note_Surface_Albedos.rst | 122 ++--- .../CLM50_Tech_Note_Transient_Landcover.rst | 58 +-- .../tech_note/Urban/CLM50_Tech_Note_Urban.rst | 56 +- ...ech_Note_Vegetation_Phenology_Turnover.rst | 218 ++++---- doc/source/tech_note/index.rst | 2 +- ...w-Files-to-the-build-namelist-Database.rst | 20 +- .../Adding-Resolution-Names.rst | 20 +- .../Adding-or-Changing-Default-Filenames.rst | 14 +- .../users_guide/overview/getting-help.rst | 12 +- .../users_guide/overview/quickstart.rst | 4 +- .../overview/scientific_validation.rst | 2 +- .../running-PTCLM/adding-ptclm-site-data.rst | 46 +- .../running-PTCLM/introduction-to-ptclm.rst | 12 +- .../running-PTCLM/ptclm-examples.rst | 2 +- .../users_guide/running-PTCLM/using-ptclm.rst | 26 +- .../running-pts_mode-configurations.rst | 12 +- .../running-single-point-configurations.rst | 36 +- ...point-and-regional-grid-configurations.rst | 30 +- ...transient-historical-CO2-concentration.rst | 28 +- ...tmospheric-forcing-to-spinup-the-model.rst | 6 +- .../Running-with-anomaly-forcing.rst | 4 +- ...tmospheric-forcing-to-spinup-the-model.rst | 8 +- ...Satellite-Phenology-Model-CLMSP-spinup.rst | 12 +- ...ning-up-the-biogeochemistry-BGC-spinup.rst | 16 +- .../running-the-prognostic-crop-model.rst | 6 +- .../running-with-irrigation.rst | 2 +- .../what-is-a-special-case.rst | 4 +- .../choosing-a-compset.rst | 16 +- .../customizing-the-clm-configuration.rst | 178 +++---- .../customizing-the-clm-namelist.rst | 78 +-- .../customizing-the-datm-namelist.rst | 70 +-- .../history_fields_fates.rst | 8 +- .../history_fields_nofates.rst | 8 +- doc/source/users_guide/testing/testing.rst | 20 +- .../trouble-shooting/trouble-shooting.rst | 20 +- .../building-the-clm-tools.rst | 16 +- .../users_guide/using-clm-tools/cprnc.rst | 12 +- .../using-clm-tools/creating-domain-files.rst | 2 +- ...g-input-for-surface-dataset-generation.rst | 40 +- .../datasts-for-observational-sites.rst | 18 +- .../observational-sites-datasets.rst | 18 +- .../what-are-the-clm-tools.rst | 46 +- 75 files changed, 2586 insertions(+), 2586 deletions(-) diff --git a/doc/design/dynamic_urban.rst b/doc/design/dynamic_urban.rst index 0ca5d488f4..fa7a499725 100644 --- a/doc/design/dynamic_urban.rst +++ b/doc/design/dynamic_urban.rst @@ -6,18 +6,18 @@ Overview of this design document ================================== -This documents some of the high-level design decisions made during implementation of +This documents some of the high-level design decisions made during implementation of dynamic urban landunits. ============================================================================ The use of dzsoi_decomp for urban landunits to calculate totcolch4 in ch4Mod.F90 ============================================================================ -During the first test simulation for dynamic urban, we encountered a methane conservation -error the first time PCT_URBAN changed. The dynamic adjustments for conc_ch4_sat_col and +During the first test simulation for dynamic urban, we encountered a methane conservation +error the first time PCT_URBAN changed. The dynamic adjustments for conc_ch4_sat_col and conc_ch4_unsat_col (the column_state_updater in subroutine DynamicColumnAdjustments within ch4Mod.F90) were distributing non-zero values for roof and walls for layers 1,nlevsoi. -When the total column ch4 is summed over the soil layers (or in this case, urban layers), the -summation is done over nlevsoi, not nlevurb, using dz. dz is 1.e36 for roof/wall layers +When the total column ch4 is summed over the soil layers (or in this case, urban layers), the +summation is done over nlevsoi, not nlevurb, using dz. dz is 1.e36 for roof/wall layers that are greater than nlevurb, thus creating an imbalance. Rather than trying to keep the BGC variables physically meaningful in urban landunits, diff --git a/doc/design/water_tracers.rst b/doc/design/water_tracers.rst index b52d653393..c17b14a43d 100644 --- a/doc/design/water_tracers.rst +++ b/doc/design/water_tracers.rst @@ -30,7 +30,7 @@ Broadly speaking, we considered three ways to store information for each tracer: ``h2osoi_liq_col_tracer(c,j,m)`` for tracers). 3. Multiple instances of ``waterstate_type`` (etc.), with no extra dimension required for - individual variables. + individual variables. We decided to go with option (3) for a number of reasons: diff --git a/doc/source/lilac/specific-atm-models/index.rst b/doc/source/lilac/specific-atm-models/index.rst index b5c3d2bc08..317732fb58 100644 --- a/doc/source/lilac/specific-atm-models/index.rst +++ b/doc/source/lilac/specific-atm-models/index.rst @@ -1,7 +1,7 @@ .. _specific-atm-models: ============================================================== - Instructions on using CTSM with specific atmosphere models + Instructions on using CTSM with specific atmosphere models ============================================================== .. toctree:: diff --git a/doc/source/lilac/specific-atm-models/wrf-nesting.rst b/doc/source/lilac/specific-atm-models/wrf-nesting.rst index b21593029b..5bf74e5ad6 100644 --- a/doc/source/lilac/specific-atm-models/wrf-nesting.rst +++ b/doc/source/lilac/specific-atm-models/wrf-nesting.rst @@ -11,15 +11,15 @@ nested domain. A nested domain is usually used to have a finer-resolution domain within the coarser model domain. A nested simulation enables running at a higher -resolution over a smaller domain +resolution over a smaller domain .. note:: A nest should cover a portion of the parent domain and is fully contained by the parent domain, so that it is driven along its lateral boundaries by the - parent domain. + parent domain. .. todo:: - Negin wants to add a flowchart showing the workflow of a nested case. + Negin wants to add a flowchart showing the workflow of a nested case. There are currently two types of nesting available within WRF: @@ -33,10 +33,10 @@ There are currently two types of nesting available within WRF: - Also, the averaged values from the inner domain are being sent back to the outer domain at the corresponding grid points. .. important:: - Currently, the WRF-CTSM coupling infrastructure only support one-way nesting. - This example clarifies the workflow for running a nested WRF-CTSM case using one-way nesting with ``ndown.exe``. + Currently, the WRF-CTSM coupling infrastructure only support one-way nesting. + This example clarifies the workflow for running a nested WRF-CTSM case using one-way nesting with ``ndown.exe``. -The procedure for running a nested simulation for WRF with CTSM is +The procedure for running a nested simulation for WRF with CTSM is similar to the workflow for running WRF real cases, except that it requires additional steps to (1) clone the CTSM repository, (2) build CTSM and LILAC, and (3) define namelist options reuired for CTSM. @@ -46,10 +46,10 @@ A full description of all steps for a WRF-CTSM run are included here. .. important:: This section assumes the user has completed all the steps required for - WRF-CTSM simulation single domain. + WRF-CTSM simulation single domain. Therefore, we are not repeating the steps necessary for building WRF and - CTSM. - + CTSM. + In this example we use a nested domain over the CONUS as shows below: @@ -105,7 +105,7 @@ Nested Simulations : Pre-processing (ungrib.exe) ------------------------------------------------- As mentioned previously, the purpose of the ungrib script is to unpack GRIB meteorological data and pack it into an intermediate file format. -This step is exactly identical to a non-nested simulation. +This step is exactly identical to a non-nested simulation. Run ungrib to get gribbed data into usable format to be ingested by WRF. @@ -133,7 +133,7 @@ Nested Simulations : Pre-processing (metgrid.exe) ------------------------------------------------- Ensure that the `start_date` and `end_date` for domain two is set correctly for your simulation. -Next, run ``metgrid.exe``:: +Next, run ``metgrid.exe``:: ./metgrid.exe >& log.metgrid @@ -160,31 +160,31 @@ both domains. In summary, complete the following steps: -Move or link WPS output files (``met_em.d01*`` and ``met_em.d02`` files) to your WRF test directory. +Move or link WPS output files (``met_em.d01*`` and ``met_em.d02`` files) to your WRF test directory. Edit namelist.input for your WRF domain and desirable configurations. This should be the same domain as WPS namelist. Make sure you set ``max_dom = -2,`` in the namelist. +2,`` in the namelist. To run WRF-CTSM, in your namelist change land-surface option to 6 for both domains:: - sf_surface_physics = 6, 6, + sf_surface_physics = 6, 6, Run real.exe (if compiled parallel submit a batch job) to generate -initail and boundary condition files for both domain. +initail and boundary condition files for both domain. Make sure the following three files have been created in your directory:: wrfinput_d01 wrfinput_d02 wrfbdy_d01 -The boundary condition file is only created for the outer domain. +The boundary condition file is only created for the outer domain. Check the last line of the real log file for the following message:: -Rename wrfinput_d02 +Rename wrfinput_d02 ------------------- Next, rename the ``wrfinput_d02`` file to ``wrfndi_d02``:: @@ -199,24 +199,24 @@ Add the following into your namelist.input file under ``&time_control``:: io_form_auxinput2 = 2 -Run ndown.exe to create ``wrfinput_d02`` and ``wrfbdy_d02``. +Run ndown.exe to create ``wrfinput_d02`` and ``wrfbdy_d02``. -Run WRF for coarser domain +Run WRF for coarser domain --------------------------- In this step, run WRF for the outer domain. -Make sure that ``max_dom = 1`` to run only for the coarser domain. +Make sure that ``max_dom = 1`` to run only for the coarser domain. This step is exactly identical as the previous example and only creates the -``wrfout*`` files for the coarser domain. +``wrfout*`` files for the coarser domain. Please make sure to copy ``lnd_in`` , ``lilac_in``, and ``lnd_modelio`` for the -coarser domain in this directory. +coarser domain in this directory. Create CTSM runtime files for the fine domain --------------------------------------------- This step is in addition creating CTSM runtime files for coarser domain which was explained here. For succesfully completing the previous step you should -have already created these files for the coarser domain. +have already created these files for the coarser domain. .. seealso:: @@ -236,7 +236,7 @@ are defined within these three files: - ``lilac_in``: This namelist controls the operation of LILAC -Run WRF for the finer domain +Run WRF for the finer domain ----------------------------- First, save (rename or move) the data from the coarser domain simulation (``wrfout_d01_*`` files). @@ -247,8 +247,8 @@ Edit namelist.input, moving all of the fine-grid domain data from column 2 to co so that this run will be for the fine-grid domain only. Make sure you set `max_dom=1` and set your `time_step` based on the finer domain. -.. note:: - It may be beneficial to save namelist.input to something else prior to this step in case you need to repeat this +.. note:: + It may be beneficial to save namelist.input to something else prior to this step in case you need to repeat this process in the future. Save the newly-edited namelist as namelist.input . Now run wrf.exe by submitting a job similar to a not-nested case. @@ -256,7 +256,7 @@ Now run wrf.exe by submitting a job similar to a not-nested case. .. important:: The output for the finer domain is wrfout_d01_* not wrfout_d02_* and although - in the name it is saying d01 it is technically d02 domain. + in the name it is saying d01 it is technically d02 domain. diff --git a/doc/source/lilac/specific-atm-models/wrf.rst b/doc/source/lilac/specific-atm-models/wrf.rst index 2aa2eb5175..ea54d20ab4 100644 --- a/doc/source/lilac/specific-atm-models/wrf.rst +++ b/doc/source/lilac/specific-atm-models/wrf.rst @@ -18,7 +18,7 @@ A full description of all steps for a WRF-CTSM run are included here. Specific new steps that would not be completed in a standard WRF real case are described in sections :numref:`clone-WRF-CTSM-repositories`, -:numref:`build-CTSM-and-dependencies` , +:numref:`build-CTSM-and-dependencies` , and :numref:`wrf-set-ctsm-runtime-options`. .. important:: @@ -54,7 +54,7 @@ Clone the CTSM repository:: Build CTSM and its dependencies ------------------------------- -In your CTSM directory, build CTSM and its dependencies based on the +In your CTSM directory, build CTSM and its dependencies based on the instructions from section :numref:`obtaining-and-building-ctsm`:: ./lilac/build_ctsm /PATH/TO/CTSM/BUILD --machine MACHINE --compiler COMPILER @@ -81,13 +81,13 @@ Building WRF with CTSM First, load the same modules and set the same environments as used for CTSM build by sourcing ``ctsm_build_environment.sh`` for Bash:: - source ctsm_build_dir/ctsm_build_environment.sh + source ctsm_build_dir/ctsm_build_environment.sh or sourcing ``ctsm_build_environment.csh`` for Cshell: .. code-block:: Tcsh - source ctsm_build_dir/ctsm_build_environment.csh + source ctsm_build_dir/ctsm_build_environment.csh Set makefile variables from CTSM needed for the WRF build by setting the following environment. For example for Bash:: @@ -113,9 +113,9 @@ Explicitly define the model core to build by (Bash):: export WRF_EM_CORE=1 -or (Cshell): +or (Cshell): -.. code-block:: Tcsh +.. code-block:: Tcsh setenv WRF_EM_CORE 1 @@ -124,13 +124,13 @@ Explicilty turn off data assimilation by (Bash):: export WRF_DA_CORE=0 -or (Cshell): +or (Cshell): -.. code-block:: Tcsh +.. code-block:: Tcsh setenv WRF_DA_CORE 0 -Now in your WRF directory configure and build WRF for your machine +Now in your WRF directory configure and build WRF for your machine and intended compiler:: ./clean -a @@ -138,7 +138,7 @@ and intended compiler:: At the prompt choose one of the options, based on the compiler used for building CTSM. Then you should choose if you'd like to build serially or -in parallel. For example, you can choose to build with ``intel`` compiler with +in parallel. For example, you can choose to build with ``intel`` compiler with distributed memory parallelization (``dmpar``). .. tip:: @@ -259,10 +259,10 @@ Run real.exe Run ``real.exe`` to generate initial and boundary conditions. -Follow WRF instructions for creating initial and boundary conditions. +Follow WRF instructions for creating initial and boundary conditions. In summary, complete the following steps: -Move or link WPS output files (``met_em.d01*`` files) to your WRF test directory. +Move or link WPS output files (``met_em.d01*`` files) to your WRF test directory. Edit namelist.input for your WRF domain and desirable configurations. This should be the same domain as WPS namelist. @@ -342,7 +342,7 @@ Run the script ``make_runtime_inputs`` to create ``lnd_in`` and Modify ``lilac_in`` as needed. For this example, you can use the following options:: atm_mesh_filename = '/glade/scratch/negins/wrf_ctsm_files/wrf2ctsm_land_conus_ESMFMesh_c20201110.nc' - lnd_mesh_filename = '/glade/scratch/negins/wrf_ctsm_files/wrf2ctsm_land_conus_ESMFMesh_c20201110.nc' + lnd_mesh_filename = '/glade/scratch/negins/wrf_ctsm_files/wrf2ctsm_land_conus_ESMFMesh_c20201110.nc' Run ``download_input_data`` script to download any of CTSM's standard input @@ -361,17 +361,17 @@ Run wrf.exe ----------- If real.exe completed successfully, we should have ``wrfinput`` and ``wrfbdy`` files -in our directory. +in our directory. If you plan to use this example's preexisting files, copy the following files to your WRF run directory:: - cp /glade/scratch/negins/wrf_ctsm_files/namelist.input . + cp /glade/scratch/negins/wrf_ctsm_files/namelist.input . cp /glade/scratch/negins/wrf_ctsm_files/wrfinput_d01 . cp /glade/scratch/negins/wrf_ctsm_files/wrfbdy_d01 . Now run WRF-CTSM. On Cheyenne this means submitting a batch job to PBS (Pro workload management system). -Please check NCAR CISL's `instructions on running a batch job on Cheyenne. +Please check NCAR CISL's `instructions on running a batch job on Cheyenne. `__ A simple PBS script to run WRF-CTSM on ``Cheyenne`` looks like this: @@ -396,7 +396,7 @@ A simple PBS script to run WRF-CTSM on ``Cheyenne`` looks like this: (See :numref:`runtime-environment-variables` for a description of the need to set ``MPI_TYPE_DEPTH`` on ``Cheyenne``.) To submit a batch job to the ``Cheyenne`` queues, use ``qsub`` command followed -by the PBS script name. +by the PBS script name. For example, if you named this script ``run_wrf_ctsm.csh``, submit the job like this:: qsub run_wrf_ctsm.csh diff --git a/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst b/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst index 45fc414dee..f3446647e9 100644 --- a/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst +++ b/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst @@ -28,14 +28,14 @@ as a flux, :math:`F_{i}` (:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1 :math:`i` .. math:: - :label: ZEqnNum964222 + :label: ZEqnNum964222 F_{i} =\gamma _{i} \rho \sum _{j}\varepsilon _{i,j} \left(wt\right)_{j} where :math:`\gamma _{i}` is the emission activity factor accounting for responses to meteorological and phenological conditions, :math:`\rho` is the canopy loss and production factor also known as -escape efficiency (set to 1), and :math:`\varepsilon _{i,\, j}` +escape efficiency (set to 1), and :math:`\varepsilon _{i,\, j}` (:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1`) is the emission factor at standard conditions of light, temperature, and leaf area for plant functional type *j* with fractional coverage @@ -50,7 +50,7 @@ some monoterpenes, VOCs and acetone). The activity factor for the light response of emissions is therefore estimated as: .. math:: - :label: 28.2) + :label: 28.2) \gamma _{P,\, i} =\left(1-LDF_{i} \right)+\gamma _{P\_ LDF} LDF_{i} diff --git a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst index e85a59439f..33faae1a4c 100644 --- a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst +++ b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst @@ -194,7 +194,7 @@ favorable growth environments (Allen et al., 2005; Vanninen and Makela, +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+ | Switchgrass I | 2 | 0 | 0 | 1 | 25 | 42 | 50 | 500 | +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+ - + Carbon to nitrogen ratios are defined for different tissue types as follows: diff --git a/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst b/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst index 77bd7af415..031b0fcbbb 100644 --- a/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst +++ b/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst @@ -14,7 +14,7 @@ of new vegetation growth and litterfall is also prognostic, responding to soil and air temperature, soil water availability, daylength, and crop management practices in varying degrees depending on a specified phenology type or management for each PFT -(Chapter +(Chapter :numref:`rst_Vegetation Phenology and Turnover`). The prognostic LAI, SAI, tissue stoichiometry, and vegetation heights are @@ -46,7 +46,7 @@ decomposing carbon and nitrogen pools as vegetation successively breaks down to CWD, and/or litter, and subsequently to soil organic matter. Discussion of the decomposition model, alternate specifications of decomposition rates, and methods to rapidly -equilibrate the decomposition model, is in Chapter +equilibrate the decomposition model, is in Chapter :numref:`rst_Decomposition`. Tissue Stoichiometry @@ -54,20 +54,20 @@ Tissue Stoichiometry As of CLM5, vegetation tissues have a flexible stoichiometry, as described in :ref:`Ghimire et al. (2016) `. Each -tissue has a target C\:N ratio, with the target leaf C\:N varying by plant functional type +tissue has a target C\:N ratio, with the target leaf C\:N varying by plant functional type (see :numref:`Table Plant functional type (PFT) target CN parameters`), and nitrogen is allocated at each timestep in order to allow the plant to best match the target stoichiometry. Nitrogen downregulation of productivity acts by increasing the C\:N ratio of leaves when insufficient nitrogen is available to meet stoichiometric demands of leaf growth, thereby reducing the N available for photosynthesis and reducing the :math:`V_{\text{c,max25}}` and -:math:`J_{\text{max25}}` terms, as described in Chapter +:math:`J_{\text{max25}}` terms, as described in Chapter :numref:`rst_Photosynthetic Capacity`. Details of the flexible tissue stoichiometry are described in Chapter :numref:`rst_CN Allocation`. .. _Table Plant functional type (PFT) target CN parameters: -.. table:: Plant functional type (PFT) target C:N parameters. +.. table:: Plant functional type (PFT) target C:N parameters. +----------------------------------+-------------------+ | PFT | target leaf C:N | diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 7ebc058b13..fb6d66dd42 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -10,7 +10,7 @@ Summary of CLM5.0 updates relative to the CLM4.5 We describe here the complete crop and irrigation parameterizations that appear in CLM5.0. Corresponding information for CLM4.5 appeared in the -CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). +CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). CLM5.0 includes the following new updates to the CROP option, where CROP refers to the interactive crop management model and is included as an option with the BGC configuration: @@ -35,7 +35,7 @@ refers to the interactive crop management model and is included as an option wit - C for annual crop seeding comes from the grain C pool -- Initial seed C for planting is increased from 1 to 3 g C/m^2 +- Initial seed C for planting is increased from 1 to 3 g C/m^2 These updates appear in detail in the sections below. Many also appear in :ref:`Levis et al. (2016) `. @@ -76,7 +76,7 @@ coupled as a proof-of-concept to the Community Land Model version 3 [CLM3.0, :ref:`Oleson et al. (2004) ` ] (not published), then coupled to the CLM3.5 (:ref:`Levis et al. 2009 `) and later released to the community with CLM4CN (:ref:`Levis et al. 2012 `), and CLM4.5BGC. Additional updates after the -release of CLM4.5 were available by request (:ref:`Levis et al. 2016 `), +release of CLM4.5 were available by request (:ref:`Levis et al. 2016 `), and those are now incorporated into CLM5. With interactive crop management and, therefore, a more accurate @@ -95,60 +95,60 @@ phenology, and allocation, as well as fertilizer and irrigation management. Crop plant functional types ^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To allow crops to coexist with natural vegetation in a grid cell, the +To allow crops to coexist with natural vegetation in a grid cell, the vegetated land unit is separated into a naturally vegetated land unit and a managed crop land unit. Unlike the plant functional types (pfts) in the -naturally vegetated land unit, the managed crop pfts in the managed crop -land unit do not share soil columns and thus permit for differences in the -land management between crops. Each crop type has a rainfed and an irrigated -pft that are on independent soil columns. Crop grid cell coverage is assigned from +naturally vegetated land unit, the managed crop pfts in the managed crop +land unit do not share soil columns and thus permit for differences in the +land management between crops. Each crop type has a rainfed and an irrigated +pft that are on independent soil columns. Crop grid cell coverage is assigned from satellite data (similar to all natural pfts), and the managed crop type proportions within the crop area is based on the dataset created by :ref:`Portmann et al. (2010)` for present day. New in CLM5, crop area is -extrapolated through time using the dataset provided by Land Use Model -Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries +extrapolated through time using the dataset provided by Land Use Model +Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries (:ref:`Lawrence et al. 2016 `). For more details about how -crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. +crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. CLM5 includes ten actively managed crop types -(temperate soybean, tropical soybean, temperate corn, tropical -corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen -based on the availability of corresponding algorithms in AgroIBIS and as +(temperate soybean, tropical soybean, temperate corn, tropical +corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen +based on the availability of corresponding algorithms in AgroIBIS and as developed by :ref:`Badger and Dirmeyer (2015)` and -described by :ref:`Levis et al. (2016)`, or from available observations -as described by :ref:`Cheng et al. (2019)`. +described by :ref:`Levis et al. (2016)`, or from available observations +as described by :ref:`Cheng et al. (2019)`. The representations of sugarcane, rice, cotton, tropical corn, and tropical soy are new in CLM5. Miscanthus and switchgrass are added after the CLM5 release. Sugarcane and tropical corn are both C4 plants and are therefore represented using the temperate corn functional form. Tropical soybean uses the temperate soybean functional form, while rice and cotton use the wheat functional form. In tropical regions, parameter values were developed for the Amazon Basin, and planting -date window is shifted by six months relative to the Northern Hemisphere. -Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to -replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and -have quite different physiological traits and land management practices than annual crops, -such as longer growing seasons, higher productivity, and lower demands for nutrients and water. -About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using -observation data collected at the University of Illinois Energy Farm +date window is shifted by six months relative to the Northern Hemisphere. +Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to +replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and +have quite different physiological traits and land management practices than annual crops, +such as longer growing seasons, higher productivity, and lower demands for nutrients and water. +About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using +observation data collected at the University of Illinois Energy Farm located in Central Midwestern United States (:ref:`Cheng et al., 2019`). In addition, CLM's default list of plant functional types (pfts) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. -The unmanaged C3 crop is only used when the crop model is not active and -has grid cell coverage assigned from satellite data, and -the unmanaged C3 irrigated crop type is currently not used +The unmanaged C3 crop is only used when the crop model is not active and +has grid cell coverage assigned from satellite data, and +the unmanaged C3 irrigated crop type is currently not used since irrigation requires the crop model to be active. -The default list of pfts also includes twenty-one inactive crop pfts -that do not yet have associated parameters required for active management. -Each of the inactive crop types is simulated using the parameters of the -spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), +The default list of pfts also includes twenty-one inactive crop pfts +that do not yet have associated parameters required for active management. +Each of the inactive crop types is simulated using the parameters of the +spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), which is required to maintain similar phenological parameters based on temperature thresholds. -Information detailing which parameters are used for each crop type is +Information detailing which parameters are used for each crop type is included in :numref:`Table Crop plant functional types`. It should be noted that pft-level history output merges -all crop types into the actively managed crop type, so analysis -of crop-specific output will require use of the land surface dataset to -remap the yields of each actively and inactively managed crop type. Otherwise, the +all crop types into the actively managed crop type, so analysis +of crop-specific output will require use of the land surface dataset to +remap the yields of each actively and inactively managed crop type. Otherwise, the actively managed crop type will include yields for that crop type and all inactively managed crop types that are using the same parameter set. @@ -159,70 +159,70 @@ managed crop types that are using the same parameter set. === =========================== ================ =========================== IVT Plant function types (PFTs) Management Class Crop Parameters Used === =========================== ================ =========================== - 15 c3 unmanaged rainfed crop none not applicable - 16 c3 unmanaged irrigated crop none not applicable - 17 rainfed temperate corn active rainfed temperate corn - 18 irrigated temperate corn active irrigated temperate corn - 19 rainfed spring wheat active rainfed spring wheat - 20 irrigated spring wheat active irrigated spring wheat - 21 rainfed winter wheat inactive rainfed spring wheat - 22 irrigated winter wheat inactive irrigated spring wheat - 23 rainfed temperate soybean active rainfed temperate soybean + 15 c3 unmanaged rainfed crop none not applicable + 16 c3 unmanaged irrigated crop none not applicable + 17 rainfed temperate corn active rainfed temperate corn + 18 irrigated temperate corn active irrigated temperate corn + 19 rainfed spring wheat active rainfed spring wheat + 20 irrigated spring wheat active irrigated spring wheat + 21 rainfed winter wheat inactive rainfed spring wheat + 22 irrigated winter wheat inactive irrigated spring wheat + 23 rainfed temperate soybean active rainfed temperate soybean 24 irrigated temperate soybean active irrigated temperate soybean - 25 rainfed barley inactive rainfed spring wheat - 26 irrigated barley inactive irrigated spring wheat - 27 rainfed winter barley inactive rainfed spring wheat - 28 irrigated winter barley inactive irrigated spring wheat - 29 rainfed rye inactive rainfed spring wheat - 30 irrigated rye inactive irrigated spring wheat - 31 rainfed winter rye inactive rainfed spring wheat - 32 irrigated winter rye inactive irrigated spring wheat - 33 rainfed cassava inactive rainfed rice - 34 irrigated cassava inactive irrigated rice - 35 rainfed citrus inactive rainfed spring wheat - 36 irrigated citrus inactive irrigated spring wheat - 37 rainfed cocoa inactive rainfed rice - 38 irrigated cocoa inactive irrigated rice - 39 rainfed coffee inactive rainfed rice - 40 irrigated coffee inactive irrigated rice - 41 rainfed cotton active rainfed cotton - 42 irrigated cotton active irrigated cotton - 43 rainfed datepalm inactive rainfed cotton - 44 irrigated datepalm inactive irrigated cotton - 45 rainfed foddergrass inactive rainfed spring wheat - 46 irrigated foddergrass inactive irrigated spring wheat - 47 rainfed grapes inactive rainfed spring wheat - 48 irrigated grapes inactive irrigated spring wheat - 49 rainfed groundnuts inactive rainfed rice - 50 irrigated groundnuts inactive irrigated rice - 51 rainfed millet inactive rainfed tropical corn - 52 irrigated millet inactive irrigated tropical corn - 53 rainfed oilpalm inactive rainfed rice - 54 irrigated oilpalm inactive irrigated rice - 55 rainfed potatoes inactive rainfed spring wheat - 56 irrigated potatoes inactive irrigated spring wheat - 57 rainfed pulses inactive rainfed spring wheat - 58 irrigated pulses inactive irrigated spring wheat - 59 rainfed rapeseed inactive rainfed spring wheat - 60 irrigated rapeseed inactive irrigated spring wheat - 61 rainfed rice active rainfed rice - 62 irrigated rice active irrigated rice - 63 rainfed sorghum inactive rainfed tropical corn - 64 irrigated sorghum inactive irrigated tropical corn - 65 rainfed sugarbeet inactive rainfed spring wheat - 66 irrigated sugarbeet inactive irrigated spring wheat - 67 rainfed sugarcane active rainfed sugarcane - 68 irrigated sugarcane active irrigated sugarcane - 69 rainfed sunflower inactive rainfed spring wheat - 70 irrigated sunflower inactive irrigated spring wheat - 71 rainfed miscanthus active rainfed miscanthus - 72 irrigated miscanthus active irrigated miscanthus - 73 rainfed switchgrass active rainfed switchgrass - 74 irrigated switchgrass active irrigated switchgrass - 75 rainfed tropical corn active rainfed tropical corn - 76 irrigated tropical corn active irrigated tropical corn - 77 rainfed tropical soybean active rainfed tropical soybean - 78 irrigated tropical soybean active irrigated tropical soybean + 25 rainfed barley inactive rainfed spring wheat + 26 irrigated barley inactive irrigated spring wheat + 27 rainfed winter barley inactive rainfed spring wheat + 28 irrigated winter barley inactive irrigated spring wheat + 29 rainfed rye inactive rainfed spring wheat + 30 irrigated rye inactive irrigated spring wheat + 31 rainfed winter rye inactive rainfed spring wheat + 32 irrigated winter rye inactive irrigated spring wheat + 33 rainfed cassava inactive rainfed rice + 34 irrigated cassava inactive irrigated rice + 35 rainfed citrus inactive rainfed spring wheat + 36 irrigated citrus inactive irrigated spring wheat + 37 rainfed cocoa inactive rainfed rice + 38 irrigated cocoa inactive irrigated rice + 39 rainfed coffee inactive rainfed rice + 40 irrigated coffee inactive irrigated rice + 41 rainfed cotton active rainfed cotton + 42 irrigated cotton active irrigated cotton + 43 rainfed datepalm inactive rainfed cotton + 44 irrigated datepalm inactive irrigated cotton + 45 rainfed foddergrass inactive rainfed spring wheat + 46 irrigated foddergrass inactive irrigated spring wheat + 47 rainfed grapes inactive rainfed spring wheat + 48 irrigated grapes inactive irrigated spring wheat + 49 rainfed groundnuts inactive rainfed rice + 50 irrigated groundnuts inactive irrigated rice + 51 rainfed millet inactive rainfed tropical corn + 52 irrigated millet inactive irrigated tropical corn + 53 rainfed oilpalm inactive rainfed rice + 54 irrigated oilpalm inactive irrigated rice + 55 rainfed potatoes inactive rainfed spring wheat + 56 irrigated potatoes inactive irrigated spring wheat + 57 rainfed pulses inactive rainfed spring wheat + 58 irrigated pulses inactive irrigated spring wheat + 59 rainfed rapeseed inactive rainfed spring wheat + 60 irrigated rapeseed inactive irrigated spring wheat + 61 rainfed rice active rainfed rice + 62 irrigated rice active irrigated rice + 63 rainfed sorghum inactive rainfed tropical corn + 64 irrigated sorghum inactive irrigated tropical corn + 65 rainfed sugarbeet inactive rainfed spring wheat + 66 irrigated sugarbeet inactive irrigated spring wheat + 67 rainfed sugarcane active rainfed sugarcane + 68 irrigated sugarcane active irrigated sugarcane + 69 rainfed sunflower inactive rainfed spring wheat + 70 irrigated sunflower inactive irrigated spring wheat + 71 rainfed miscanthus active rainfed miscanthus + 72 irrigated miscanthus active irrigated miscanthus + 73 rainfed switchgrass active rainfed switchgrass + 74 irrigated switchgrass active irrigated switchgrass + 75 rainfed tropical corn active rainfed tropical corn + 76 irrigated tropical corn active irrigated tropical corn + 77 rainfed tropical soybean active rainfed tropical soybean + 78 irrigated tropical soybean active irrigated tropical soybean === =========================== ================ =========================== @@ -234,7 +234,7 @@ Phenology CLM5-BGC includes evergreen, seasonally deciduous (responding to changes in day length), and stress deciduous (responding to changes in -temperature and/or soil moisture) phenology algorithms (Chapter :numref:`rst_Vegetation Phenology and Turnover`). +temperature and/or soil moisture) phenology algorithms (Chapter :numref:`rst_Vegetation Phenology and Turnover`). CLM5-BGC-crop uses the AgroIBIS crop phenology algorithm, consisting of three distinct phases. @@ -254,10 +254,10 @@ planting date (for the northern hemisphere) in :numref:`Table Crop phenology par .. math:: :label: 25.1 - \begin{array}{c} - {T_{10d} >T_{p} } \\ - {T_{10d}^{\min } >T_{p}^{\min } } \\ - {GDD_{8} \ge GDD_{\min } } + \begin{array}{c} + {T_{10d} >T_{p} } \\ + {T_{10d}^{\min } >T_{p}^{\min } } \\ + {GDD_{8} \ge GDD_{\min } } \end{array} where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air @@ -272,11 +272,11 @@ maximum daily increments of 30\ :sup:`o` days (see equation :eq:`25.3`), and (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. -If the requirements in equation :eq:`25.1` are not met by the maximum planting date, +If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. -At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its +At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, @@ -287,11 +287,11 @@ for the crop to reach vegetative and physiological maturity, .. math:: :label: 25.2 - \begin{array}{lll} - GDD_{{\rm mat}}^{{\rm corn,sugarcane}} =0.85 GDD_{{\rm 8}} & {\rm \; \; \; and\; \; \; }& 950 `, :ref:`Crawford et al. 1982 `, :ref:`Simpson et al. 1983 +season is remobilized and used for grain development (:ref:`Pollmer et al. 1979 +`, :ref:`Crawford et al. 1982 `, :ref:`Simpson et al. 1983 `, :ref:`Ta and Weiland 1992 `, :ref:`Barbottin et al. 2005 `, :ref:`Gallais et al. 2006 `, :ref:`Gallais et al. 2007 `). Nitrogen allocation for crops follows that of natural vegetation, is supplied in CLM by the @@ -540,8 +540,8 @@ ratio of the leaf, stem, and fine root respectively (:numref:`Table Crop allocat C:N measurements are often taken from mature crops, pre-grain development C:N ratios for leaves, stems, and roots in the model are optimized to allow maximum nitrogen accumulation for later use during organ development, and post-grain -fill C:N ratios are assigned the same as crop residue. After -nitrogen is moved into the retranslocated pool, +fill C:N ratios are assigned the same as crop residue. After +nitrogen is moved into the retranslocated pool, the nitrogen in this pool is used to meet plant nitrogen demand by assigning the available nitrogen from the retranslocated pool equal to the plant nitrogen demand for each organ (:math:`{CN_{[organ]}^{f} }` in :numref:`Table Crop allocation parameters`). Once the @@ -554,31 +554,31 @@ Harvest ''''''' Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. -A fraction (determined by the :math:`biofuel\_harvfrac`, defined in -:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels +A fraction (determined by the :math:`biofuel\_harvfrac`, defined in +:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which -puts live stem C and N into dead stem pools first. +puts live stem C and N into dead stem pools first. Biofuel crop leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. - + .. math:: :label: 25.9 - CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} + CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac - + .. math:: :label: 25.10 - CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} - \right) * biofuel\_harvfrac - + CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} + \right) * biofuel\_harvfrac + .. math:: :label: 25.11 - CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem} \Delta t}} \right.} \Delta t} + CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem} \Delta t}} \right.} \Delta t} \right) * \left( 1-biofuel\_harvfrac \right) +CF_{alloc,livestem} with corresponding nitrogen fluxes: @@ -586,22 +586,22 @@ with corresponding nitrogen fluxes: .. math:: :label: 25.12 - NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} + NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac - + .. math:: :label: 25.13 - NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} + NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac - + .. math:: :label: 25.14 - NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} + NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} \right) * \left( 1-biofuel\_harvfrac \right) -where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, +where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction of leaf/livestem for biofuel feedstocks. .. _Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production: @@ -662,14 +662,14 @@ NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction o Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, -similar in structure to the wood product pools. +similar in structure to the wood product pools. The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain -product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. -Calcuating the crop yields (Equation :eq:`25.15`) requires that you sum the GRAINC_TO_FOOD variable -for each year, and must account for the proportion of C in the dry crop weight. +product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. +Calcuating the crop yields (Equation :eq:`25.15`) requires that you sum the GRAINC_TO_FOOD variable +for each year, and must account for the proportion of C in the dry crop weight. Here, we assume that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so -analysis needs to assume that harvest efficiency is less. We assume a harvest +analysis needs to assume that harvest efficiency is less. We assume a harvest efficiency of 85%. .. math:: @@ -683,25 +683,25 @@ efficiency of 85%. .. table:: Crop allocation parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. =========================================== ============== ============ ================== ====== ====== ========= ============= ================ ================ ================ - \ temperate corn spring wheat temperate soybean cotton rice sugarcane tropical corn tropical soybean miscanthus switchgrass + \ temperate corn spring wheat temperate soybean cotton rice sugarcane tropical corn tropical soybean miscanthus switchgrass =========================================== ============== ============ ================== ====== ====== ========= ============= ================ ================ ================ - IVT 17, 18 19, 20 23, 24 41, 42 61, 62 67, 68 75, 76 77, 78 71, 72 73, 74 - :math:`a_{leaf}^{i}` 0.6 0.9 0.85 0.85 0.75 0.6 0.6 0.85 0.9 0.7 - :math:`{L}_{max}` (m :sup:`2` m :sup:`-2`) 5 7 6 6 7 5 5 6 10 6.5 - :math:`a_{froot}^{i}` 0.1 0.05 0.2 0.2 0.1 0.1 0.1 0.2 0.11 0.14 - :math:`a_{froot}^{f}` 0.05 0 0.2 0.2 0 0.05 0.05 0.2 0.09 0.09 - :math:`a_{leaf}^{f}` 0 0 0 0 0 0 0 0 0 0 - :math:`a_{livestem}^{f}` 0 0.05 0.3 0.3 0.05 0 0 0.3 0 0 - :math:`d_{L}` 1.05 1.05 1.05 1.05 1.05 1.05 1.05 1.05 1.05 1.05 - :math:`d_{alloc}^{stem}` 2 1 5 5 1 2 2 5 2 2 - :math:`d_{alloc}^{leaf}` 5 3 2 2 3 5 5 2 5 5 - :math:`{CN}_{leaf}` 25 20 20 20 20 25 25 20 25 25 - :math:`{CN}_{stem}` 50 50 50 50 50 50 50 50 50 50 - :math:`{CN}_{froot}` 42 42 42 42 42 42 42 42 42 42 - :math:`CN^f_{leaf}` 65 65 65 65 65 65 65 65 65 65 - :math:`CN^f_{stem}` 120 100 130 130 100 120 120 130 120 120 - :math:`CN^f_{froot}` 0 40 0 0 40 0 0 0 0 0 - :math:`{CN}_{grain}` 50 50 50 50 50 50 50 50 50 50 + IVT 17, 18 19, 20 23, 24 41, 42 61, 62 67, 68 75, 76 77, 78 71, 72 73, 74 + :math:`a_{leaf}^{i}` 0.6 0.9 0.85 0.85 0.75 0.6 0.6 0.85 0.9 0.7 + :math:`{L}_{max}` (m :sup:`2` m :sup:`-2`) 5 7 6 6 7 5 5 6 10 6.5 + :math:`a_{froot}^{i}` 0.1 0.05 0.2 0.2 0.1 0.1 0.1 0.2 0.11 0.14 + :math:`a_{froot}^{f}` 0.05 0 0.2 0.2 0 0.05 0.05 0.2 0.09 0.09 + :math:`a_{leaf}^{f}` 0 0 0 0 0 0 0 0 0 0 + :math:`a_{livestem}^{f}` 0 0.05 0.3 0.3 0.05 0 0 0.3 0 0 + :math:`d_{L}` 1.05 1.05 1.05 1.05 1.05 1.05 1.05 1.05 1.05 1.05 + :math:`d_{alloc}^{stem}` 2 1 5 5 1 2 2 5 2 2 + :math:`d_{alloc}^{leaf}` 5 3 2 2 3 5 5 2 5 5 + :math:`{CN}_{leaf}` 25 20 20 20 20 25 25 20 25 25 + :math:`{CN}_{stem}` 50 50 50 50 50 50 50 50 50 50 + :math:`{CN}_{froot}` 42 42 42 42 42 42 42 42 42 42 + :math:`CN^f_{leaf}` 65 65 65 65 65 65 65 65 65 65 + :math:`CN^f_{stem}` 120 100 130 130 100 120 120 130 120 120 + :math:`CN^f_{froot}` 0 40 0 0 40 0 0 0 0 0 + :math:`{CN}_{grain}` 50 50 50 50 50 50 50 50 50 50 =========================================== ============== ============ ================== ====== ====== ========= ============= ================ ================ ================ Notes: Crop growth phases and corresponding variables are described throughout @@ -718,8 +718,8 @@ Other Features Physical Crop Characteristics ''''''''''''''''''''''''''''' -Leaf area index (*L*) is calculated as a function of specific leaf area -(SLA, :numref:`Table Crop phenology parameters`) and leaf C. +Leaf area index (*L*) is calculated as a function of specific leaf area +(SLA, :numref:`Table Crop phenology parameters`) and leaf C. Stem area index (*S*) is equal to 0.1\ *L* for temperate and tropical corn, sugarcane, switchgrass, and miscanthus and 0.2\ *L* for other crops, as in AgroIBIS. All live C and N pools go to 0 after crop harvest, but the *S* is kept at 0.25 to @@ -732,9 +732,9 @@ and :math:`{z}_{bot}` (m), come from the AgroIBIS formulation: .. math:: :label: 25.16 - \begin{array}{l} - {z_{top} =z_{top}^{\max } \left(\frac{L}{L_{\max } -1} \right)^{2} \ge 0.05{\rm \; where\; }\frac{L}{L_{\max } -1} \le 1} \\ - {z_{bot} =0.02{\rm m}} + \begin{array}{l} + {z_{top} =z_{top}^{\max } \left(\frac{L}{L_{\max } -1} \right)^{2} \ge 0.05{\rm \; where\; }\frac{L}{L_{\max } -1} \le 1} \\ + {z_{bot} =0.02{\rm m}} \end{array} where :math:`z_{top}^{\max }` is the maximum top-of-canopy height of the crop (:numref:`Table Crop phenology parameters`) @@ -751,19 +751,19 @@ Fertilizer in CLM5BGCCROP is prescribed by crop functional types and varies spat for each year based on the LUMIP land use and land cover change time series (LUH2 for historical and SSPs for future) (:ref:`Lawrence et al. 2016 `). One of two fields is used to prescribe industrial fertilizer based on the type of simulation. -For non-transient simulations, annual fertilizer application in g N/m\ :sup:`2`/yr -is specified on the land surface data set by the field CONST_FERTNITRO_CFT. +For non-transient simulations, annual fertilizer application in g N/m\ :sup:`2`/yr +is specified on the land surface data set by the field CONST_FERTNITRO_CFT. In transient simulations, annual fertilizer application is specified on the land use time series file by the field FERTNITRO_CFT, which is also in g N/m\ :sup:`2`/yr. The values for both of these fields come from the LUMIP time series for each year. In addition to the industrial fertilizer, background manure fertilizer is specified -on the parameter file by the field 'manunitro'. For perennial bioenergy crops, -little fertilizer (56kg/ha/yr) is applied to switchgrass, no fertilizer is applied to Miscanthus. -Note these rates are only based on local land management practices at the University of Illinois Energy Farm +on the parameter file by the field 'manunitro'. For perennial bioenergy crops, +little fertilizer (56kg/ha/yr) is applied to switchgrass, no fertilizer is applied to Miscanthus. +Note these rates are only based on local land management practices at the University of Illinois Energy Farm located in Central Midwestern United States :ref:`(Cheng et al., 2019)` rather than the LUMIP timeseries. For the current CLM5BGCCROP, -manure N is applied at a rate of 0.002 kg N/m\ :sup:`2`/yr. Because previous versions +manure N is applied at a rate of 0.002 kg N/m\ :sup:`2`/yr. Because previous versions of CLM (e.g., CLM4) had rapid denitrification rates, fertilizer is applied slowly -to minimize N loss (primarily through denitrification) and maximize plant uptake. +to minimize N loss (primarily through denitrification) and maximize plant uptake. The current implementation of CLM5 inherits this legacy, although denitrification rates are slower in the current version of the model (:ref:`Koven et al. 2013 `). As such, fertilizer application begins during the leaf emergence phase of crop @@ -777,7 +777,7 @@ initiates: .. math:: :label: 25.17 - f = n \times 86400 + f = n \times 86400 where *n* is set to 20 fertilizer application days and 86400 is the number of seconds per day. When the crop enters phase 2 (leaf emergence) of its growth @@ -800,18 +800,18 @@ are treated as N fixers. Latitudinal variation in base growth tempereature ''''''''''''''''''''''''''''''''''''''''''''''''' -For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) +For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) is the same in all locations. However, -the for both rainfed and irrigated spring wheat and sugarcane, the calculation of +the for both rainfed and irrigated spring wheat and sugarcane, the calculation of :math:`GDD_{T_{{\rm 2m}} }` allows for latitudinal variation: .. math:: :label: 25.18 latitudinal\ variation\ in\ base\ T = \left\{ - \begin{array}{lr} + \begin{array}{lr} baset +12 - 0.4 \times latitude &\qquad 0 \le latitude \le 30 \\ - baset +12 + 0.4 \times latitude &\qquad -30 \le latitude \le 0 + baset +12 + 0.4 \times latitude &\qquad -30 \le latitude \le 0 \end{array} \right\} where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. @@ -844,34 +844,34 @@ The irrigation model The CLM includes the option to irrigate cropland areas that are equipped for irrigation. The application of irrigation responds dynamically to the soil moisture conditions simulated by the CLM. This irrigation -algorithm is based loosely on the implementation of +algorithm is based loosely on the implementation of :ref:`Ozdogan et al. (2010) `. When irrigation is enabled, the crop areas of each grid cell are divided into irrigated and rainfed fractions according to a dataset of areas -equipped for irrigation (:ref:`Portmann et al. 2010 `). -Irrigated and rainfed crops are placed on separate soil columns, so that +equipped for irrigation (:ref:`Portmann et al. 2010 `). +Irrigated and rainfed crops are placed on separate soil columns, so that irrigation is only applied to the soil beneath irrigated crops. In irrigated croplands, a check is made once per day to determine whether irrigation is required on that day. This check is made in the first time step after 6 AM local time. Irrigation is required if crop -leaf area :math:`>` 0, and the available soil water is below a specified +leaf area :math:`>` 0, and the available soil water is below a specified threshold. -The soil moisture deficit :math:`D_{irrig}` is +The soil moisture deficit :math:`D_{irrig}` is .. math:: :label: 25.61 D_{irrig} = \left\{ - \begin{array}{lr} + \begin{array}{lr} w_{thresh} - w_{avail} &\qquad w_{thresh} > w_{avail} \\ - 0 &\qquad w_{thresh} \le w_{avail} + 0 &\qquad w_{thresh} \le w_{avail} \end{array} \right\} -where :math:`w_{thresh}` is the irrigation moisture threshold (mm) and -:math:`w_{avail}` is the available moisture (mm). The moisture threshold +where :math:`w_{thresh}` is the irrigation moisture threshold (mm) and +:math:`w_{avail}` is the available moisture (mm). The moisture threshold is .. math:: @@ -879,50 +879,50 @@ is w_{thresh} = f_{thresh} \left(w_{target} - w_{wilt}\right) + w_{wilt} -where :math:`w_{target}` is the irrigation target soil moisture (mm) +where :math:`w_{target}` is the irrigation target soil moisture (mm) .. math:: :label: 25.63 w_{target} = \sum_{j=1}^{N_{irr}} \theta_{target} \Delta z_{j} \ , -:math:`w_{wilt}` is the wilting point soil moisture (mm) +:math:`w_{wilt}` is the wilting point soil moisture (mm) .. math:: :label: 25.64 w_{wilt} = \sum_{j=1}^{N_{irr}} \theta_{wilt} \Delta z_{j} \ , -and :math:`f_{thresh}` is a tuning parameter. The available moisture in -the soil is +and :math:`f_{thresh}` is a tuning parameter. The available moisture in +the soil is .. math:: :label: 25.65 w_{avail} = \sum_{j=1}^{N_{irr}} \theta_{j} \Delta z_{j} \ , -:math:`N_{irr}` is the index of the soil layer corresponding to a specified -depth :math:`z_{irrig}` (:numref:`Table Irrigation parameters`) and -:math:`\Delta z_{j}` is the thickness of the soil layer in layer :math:`j` (section -:numref:`Vertical Discretization`). :math:`\theta_{j}` is the +:math:`N_{irr}` is the index of the soil layer corresponding to a specified +depth :math:`z_{irrig}` (:numref:`Table Irrigation parameters`) and +:math:`\Delta z_{j}` is the thickness of the soil layer in layer :math:`j` (section +:numref:`Vertical Discretization`). :math:`\theta_{j}` is the volumetric soil moisture in layer :math:`j` (section :numref:`Soil Water`). -:math:`\theta_{target}` and -:math:`\theta_{wilt}` are the target and wilting point volumetric -soil moisture values, respectively, and are determined by inverting -:eq:`7.94` using soil matric -potential parameters :math:`\Psi_{target}` and :math:`\Psi_{wilt}` -(:numref:`Table Irrigation parameters`). After the soil moisture deficit -:math:`D_{irrig}` is calculated, irrigation in an amount equal to -:math:`\frac{D_{irrig}}{T_{irrig}}` (mm/s) is applied uniformly over +:math:`\theta_{target}` and +:math:`\theta_{wilt}` are the target and wilting point volumetric +soil moisture values, respectively, and are determined by inverting +:eq:`7.94` using soil matric +potential parameters :math:`\Psi_{target}` and :math:`\Psi_{wilt}` +(:numref:`Table Irrigation parameters`). After the soil moisture deficit +:math:`D_{irrig}` is calculated, irrigation in an amount equal to +:math:`\frac{D_{irrig}}{T_{irrig}}` (mm/s) is applied uniformly over the irrigation period :math:`T_{irrig}` (s). Irrigation water is applied directly to the ground surface, bypassing canopy interception (i.e., -added to :math:`{q}_{grnd,liq}`: section :numref:`Canopy Water`). +added to :math:`{q}_{grnd,liq}`: section :numref:`Canopy Water`). -To conserve mass, irrigation is removed from river water storage (Chapter :numref:`rst_River Transport Model (RTM)`). -When river water storage is inadequate to meet irrigation demand, -there are two options: 1) the additional water can be removed from the -ocean model, or 2) the irrigation demand can be reduced such that -river water storage is maintained above a specified threshold. +To conserve mass, irrigation is removed from river water storage (Chapter :numref:`rst_River Transport Model (RTM)`). +When river water storage is inadequate to meet irrigation demand, +there are two options: 1) the additional water can be removed from the +ocean model, or 2) the irrigation demand can be reduced such that +river water storage is maintained above a specified threshold. .. _Table Irrigation parameters: diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index 3b7e06e179..fbe490a70a 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -32,7 +32,7 @@ For the single-level model structure, the fundamental equation for carbon balance of the decomposing pools is: .. math:: - :label: 21.1) + :label: 21.1) \frac{\partial C_{i} }{\partial t} =R_{i} +\sum _{j\ne i}\left(i-r_{j} \right)T_{ji} k_{j} C_{j} -k_{i} C_{i} @@ -47,7 +47,7 @@ Adding the vertical dimension to the decomposing pools changes the balance equation to the following: .. math:: - :label: 21.2) + :label: 21.2) \begin{array}{l} {\frac{\partial C_{i} (z)}{\partial t} =R_{i} (z)+\sum _{i\ne j}\left(1-r_{j} \right)T_{ji} k_{j} (z)C_{j} (z) -k_{i} (z)C_{i} (z)} \\ {+\frac{\partial }{\partial z} \left(D(z)\frac{\partial C_{i} }{\partial z} \right)+\frac{\partial }{\partial z} \left(A(z)C_{i} \right)} \end{array} @@ -67,7 +67,7 @@ structures is in :ref:`Koven et al. (2013) `. .. figure:: soil_C_pools_CN_century.png - Pool structure, transitions, respired fractions (numbers at + Pool structure, transitions, respired fractions (numbers at end of arrows), and turnover times (numbers in boxes) for the 2 alternate soil decomposition models included in CLM. @@ -135,12 +135,12 @@ new discrete-time value with a different timestep (:math:`{k}_{disc2}`) , following Olson (1963): .. math:: - :label: ZEqnNum608251 + :label: ZEqnNum608251 k_{cont} =-\log \left(1-k_{disc1} \right) .. math:: - :label: ZEqnNum772630 + :label: ZEqnNum772630 k_{disc2} =1-\exp \left(-k_{cont} \frac{\Delta t_{2} }{\Delta t_{1} } \right) @@ -175,7 +175,7 @@ Biome-BGC (:numref:`Table Respiration fractions for litter and SOM pools`). | :math:`{rf}_{SOM2}` | 0.46 | +---------------------------+-----------------------+ | :math:`{rf}_{SOM3}` | 0.55 | - +---------------------------+-----------------------+ + +---------------------------+-----------------------+ | :math:`{rf}_{SOM4}` | :math:`{1.0}^{a}` | +---------------------------+-----------------------+ @@ -254,7 +254,7 @@ The Temperature scalar :math:`{r}_{tsoil}` is calculated in CLM using a :math:`{Q}_{10}` approach, with :math:`{Q}_{10} = 1.5`. .. math:: - :label: 21.5) + :label: 21.5) r_{tsoil} =Q_{10} ^{\left(\frac{T_{soil,\, j} -T_{ref} }{10} \right)} @@ -266,7 +266,7 @@ unitless) is calculated using a relationship from Andrén and Paustian (1987) and supported by additional data in Orchard and Cook (1983): .. math:: - :label: 21.6) + :label: 21.6) r_{water} =\sum _{j=1}^{5}\left\{\begin{array}{l} {0\qquad {\rm for\; }\Psi _{j} <\Psi _{\min } } \\ {\frac{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{j} }} \right.} \Psi _{j} } \right)}{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{\max } }} \right.} \Psi _{\max } } \right)} w_{soil,\, j} \qquad {\rm for\; }\Psi _{\min } \le \Psi _{j} \le \Psi _{\max } } \\ {1\qquad {\rm for\; }\Psi _{j} >\Psi _{\max } \qquad \qquad } \end{array}\right\} @@ -279,14 +279,14 @@ moisture at which decomposition proceeds at a moisture-unlimited rate. The default value of :math:`{\Psi}_{max,j}` for CLM5 is updated from a saturated value used in CLM4.5 and earlier, to a value nominally at field capacity, with a value of -0.002 MPa - + For frozen soils, the bulk of the rapid dropoff in decomposition with decreasing temperature is due to the moisture limitation, since matric potential is limited by temperature in the supercooled water formulation of Niu and Yang (2006), .. math:: - :label: 21.8) + :label: 21.8) \psi \left(T\right)=-\frac{L_{f} \left(T-T_{f} \right)}{10^{3} T} @@ -324,7 +324,7 @@ includes these unresolved depth controls via an exponential decrease in the soil turnover time with depth: .. math:: - :label: 21.9) + :label: 21.9) r_{depth} =\exp \left(-\frac{z}{z_{\tau } } \right) @@ -336,7 +336,7 @@ intrinsic decomposition rates may proceed as quickly at depth as at the surface. The combined decomposition rate scalar (:math:`{r}_{total}`,unitless) is: .. math:: - :label: 21.10) + :label: 21.10) r_{total} =r_{tsoil} r_{water} r_{oxygen} r_{depth} . @@ -353,7 +353,7 @@ The potential carbon flux out of the upstream pool (:math:`{CF}_{pot,u}`, gC m\ :sup:`-2` s\ :sup:`-1`) is: .. math:: - :label: 21.11) + :label: 21.11) CF_{pot,\, u} =CS_{u} k_{u} @@ -369,7 +369,7 @@ mineral nitrogen (Thornton and Rosenbloom, 2005) is: .. math:: - :label: 21.12) + :label: 21.12) NF_{pot\_ min,\, u\to d} =\frac{CF_{pot,\, u} \left(1-rf_{u} -\frac{CN_{d} }{CN_{u} } \right)}{CN_{d} } @@ -387,37 +387,37 @@ individual pools in the decomposition cascade, for the example of the CLM-CN pool structure, are given as: .. math:: - :label: 21.13) + :label: 21.13) CF_{pot,\, Lit1} ={CS_{Lit1} k_{Lit1} r_{total} \mathord{\left/ {\vphantom {CS_{Lit1} k_{Lit1} r_{total} \Delta t}} \right.} \Delta t} .. math:: - :label: 21.14) + :label: 21.14) CF_{pot,\, Lit2} ={CS_{Lit2} k_{Lit2} r_{total} \mathord{\left/ {\vphantom {CS_{Lit2} k_{Lit2} r_{total} \Delta t}} \right.} \Delta t} .. math:: - :label: 21.15) + :label: 21.15) CF_{pot,\, Lit3} ={CS_{Lit3} k_{Lit3} r_{total} \mathord{\left/ {\vphantom {CS_{Lit3} k_{Lit3} r_{total} \Delta t}} \right.} \Delta t} .. math:: - :label: 21.16) + :label: 21.16) CF_{pot,\, SOM1} ={CS_{SOM1} k_{SOM1} r_{total} \mathord{\left/ {\vphantom {CS_{SOM1} k_{SOM1} r_{total} \Delta t}} \right.} \Delta t} .. math:: - :label: 21.17) + :label: 21.17) CF_{pot,\, SOM2} ={CS_{SOM2} k_{SOM2} r_{total} \mathord{\left/ {\vphantom {CS_{SOM2} k_{SOM2} r_{total} \Delta t}} \right.} \Delta t} .. math:: - :label: 21.18) + :label: 21.18) CF_{pot,\, SOM3} ={CS_{SOM3} k_{SOM3} r_{total} \mathord{\left/ {\vphantom {CS_{SOM3} k_{SOM3} r_{total} \Delta t}} \right.} \Delta t} .. math:: - :label: 21.19) + :label: 21.19) CF_{pot,\, SOM4} ={CS_{SOM4} k_{SOM4} r_{total} \mathord{\left/ {\vphantom {CS_{SOM4} k_{SOM4} r_{total} \Delta t}} \right.} \Delta t} @@ -429,37 +429,37 @@ again for the example of the CLM-CN pool structure (the CENTURY structure will be similar but without the different terminal step): .. math:: - :label: ZEqnNum934998 + :label: ZEqnNum934998 NF_{pot\_ min,\, Lit1\to SOM1} ={CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit1} \left(1-rf_{Lit1} -\frac{CN_{SOM1} }{CN_{Lit1} } \right) CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: - :label: 21.21) + :label: 21.21) NF_{pot\_ min,\, Lit2\to SOM2} ={CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit2} \left(1-rf_{Lit2} -\frac{CN_{SOM2} }{CN_{Lit2} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: - :label: 21.22) + :label: 21.22) NF_{pot\_ min,\, Lit3\to SOM3} ={CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, Lit3} \left(1-rf_{Lit3} -\frac{CN_{SOM3} }{CN_{Lit3} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } .. math:: - :label: 21.23) + :label: 21.23) NF_{pot\_ min,\, SOM1\to SOM2} ={CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM1} \left(1-rf_{SOM1} -\frac{CN_{SOM2} }{CN_{SOM1} } \right) CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: - :label: 21.24) + :label: 21.24) NF_{pot\_ min,\, SOM2\to SOM3} ={CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM2} \left(1-rf_{SOM2} -\frac{CN_{SOM3} }{CN_{SOM2} } \right) CN_{SOM3} }} \right.} CN_{SOM3} } .. math:: - :label: 21.25) + :label: 21.25) NF_{pot\_ min,\, SOM3\to SOM4} ={CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right)\mathord{\left/ {\vphantom {CF_{pot,\, SOM3} \left(1-rf_{SOM3} -\frac{CN_{SOM4} }{CN_{SOM3} } \right) CN_{SOM4} }} \right.} CN_{SOM4} } .. math:: - :label: ZEqnNum473594 + :label: ZEqnNum473594 NF_{pot\_ min,\, SOM4} =-{CF_{pot,\, SOM4} \mathord{\left/ {\vphantom {CF_{pot,\, SOM4} CN_{SOM4} }} \right.} CN_{SOM4} } @@ -490,36 +490,36 @@ N Competition between plant uptake and soil immobilization fluxes Once :math:`{NF}_{immob\_demand }` and :math:`{NF}_{nit\_demand }` for each layer *j* are known, the competition between plant and microbial nitrogen demand can be resolved. Mineral nitrogen in the soil pool (:math:`{NS}_{sminn}`, gN m\ :sup:`-2`) at the -beginning of the timestep is considered the available supply. +beginning of the timestep is considered the available supply. -Here, the :math:`{NF}_{plant\_demand}` is the theoretical maximum demand for nitrogen by plants to meet the entire carbon uptake given an N cost of zero (and therefore represents the upper bound on N requirements). N uptake costs that are -:math:`>` 0 imply that the plant will take up less N that it demands, ultimately. However, given the heuristic nature of the N competition algorithm, this discrepancy is not explicitly resolved here. +Here, the :math:`{NF}_{plant\_demand}` is the theoretical maximum demand for nitrogen by plants to meet the entire carbon uptake given an N cost of zero (and therefore represents the upper bound on N requirements). N uptake costs that are +:math:`>` 0 imply that the plant will take up less N that it demands, ultimately. However, given the heuristic nature of the N competition algorithm, this discrepancy is not explicitly resolved here. The hypothetical plant nitrogen demand from the soil mineral pool is distributed between layers in proportion to the profile of available mineral N: .. math:: :label: 21.291 - - NF_{plant\_ demand,j} = NF_{plant\_ demand} NS_{sminn\_ j} / \sum _{j=1}^{nj}NS_{sminn,j} + + NF_{plant\_ demand,j} = NF_{plant\_ demand} NS_{sminn\_ j} / \sum _{j=1}^{nj}NS_{sminn,j} Plants first compete for ammonia (NH4). For each soil layer (*j*), we calculate the total NH4 demand as: .. math:: :label: 21.292 - NF_{total\_ demand_nh4,j} = NF_{immob\_ demand,j} + NF_{immob\_ demand,j} + NF_{nit\_ demand,j} + NF_{total\_ demand_nh4,j} = NF_{immob\_ demand,j} + NF_{immob\_ demand,j} + NF_{nit\_ demand,j} -where +where If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t* :math:`<` :math:`{NS}_{sminn,j}`, then the available pool is large enough to meet both the maximum plant and microbial demand, then immobilization proceeds at the maximum rate. .. math:: - :label: 21.29) + :label: 21.29) f_{immob\_demand,j} = 1.0 -where :math:`{f}_{immob\_demand,j}` is the fraction of potential immobilization demand that can be met given current supply of mineral nitrogen in this layer. We also set the actual nitrification flux to be the same as the potential flux (:math:`NF_{nit}` = :math:`NF_{nit\_ demand}`). +where :math:`{f}_{immob\_demand,j}` is the fraction of potential immobilization demand that can be met given current supply of mineral nitrogen in this layer. We also set the actual nitrification flux to be the same as the potential flux (:math:`NF_{nit}` = :math:`NF_{nit\_ demand}`). If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t* :math:`\mathrm{\ge}` :math:`{NS}_{sminn,j}`, then there is not enough @@ -527,14 +527,14 @@ mineral nitrogen to meet the combined demands for plant growth and heterotrophic immobilization, immobilization is reduced proportional to the discrepancy, by :math:`f_{immob\_ demand,j}`, where .. math:: - :label: 21.30) + :label: 21.30) f_{immob\_ demand,j} = \frac{NS_{sminn,j} }{\Delta t\, NF_{total\_ demand,j} } -The N available to the FUN model for plant uptake (:math:`{NF}_ {plant\_ avail\_ sminn}` (gN m\ :sup:`-2`), which determines both the cost of N uptake, and the absolute limit on the N which is available for acquisition, is calculated as the total mineralized pool minus the actual immobilized flux: +The N available to the FUN model for plant uptake (:math:`{NF}_ {plant\_ avail\_ sminn}` (gN m\ :sup:`-2`), which determines both the cost of N uptake, and the absolute limit on the N which is available for acquisition, is calculated as the total mineralized pool minus the actual immobilized flux: .. math:: - :label: 21.311) + :label: 21.311) NF_{plant\_ avail\_ sminn,j} = NS_{sminn,j} - f_{immob\_demand} NF_{immob\_ demand,j} @@ -557,37 +557,37 @@ CENTURY structure will be similar but, again without the different terminal step), are calculated as: .. math:: - :label: 21.32) + :label: 21.32) CF_{Lit1} =\left\{\begin{array}{l} {CF_{pot,\, Lit1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} >0} \\ {CF_{pot,\, Lit1} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} \le 0} \end{array}\right\} .. math:: - :label: 21.33) + :label: 21.33) CF_{Lit2} =\left\{\begin{array}{l} {CF_{pot,\, Lit2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} >0} \\ {CF_{pot,\, Lit2} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} \le 0} \end{array}\right\} .. math:: - :label: 21.34) + :label: 21.34) CF_{Lit3} =\left\{\begin{array}{l} {CF_{pot,\, Lit3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} >0} \\ {CF_{pot,\, Lit3} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} \le 0} \end{array}\right\} .. math:: - :label: 21.35) + :label: 21.35) CF_{SOM1} =\left\{\begin{array}{l} {CF_{pot,\, SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} >0} \\ {CF_{pot,\, SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} \le 0} \end{array}\right\} .. math:: - :label: 21.36) + :label: 21.36) CF_{SOM2} =\left\{\begin{array}{l} {CF_{pot,\, SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} >0} \\ {CF_{pot,\, SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} \le 0} \end{array}\right\} .. math:: - :label: 21.37) + :label: 21.37) CF_{SOM3} =\left\{\begin{array}{l} {CF_{pot,\, SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} >0} \\ {CF_{pot,\, SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} \le 0} \end{array}\right\} .. math:: - :label: 21.38) + :label: 21.38) CF_{SOM4} =CF_{pot,\, SOM4} @@ -595,37 +595,37 @@ Heterotrophic respiration fluxes (losses of carbon as CO\ :sub:`2` to the atmosphere) are: .. math:: - :label: 21.39) + :label: 21.39) CF_{Lit1,\, HR} =CF_{Lit1} rf_{Lit1} .. math:: - :label: 21.40) + :label: 21.40) CF_{Lit2,\, HR} =CF_{Lit2} rf_{Lit2} .. math:: - :label: 21.41) + :label: 21.41) CF_{Lit3,\, HR} =CF_{Lit3} rf_{Lit3} .. math:: - :label: 21.42) + :label: 21.42) CF_{SOM1,\, HR} =CF_{SOM1} rf_{SOM1} .. math:: - :label: 21.43) + :label: 21.43) CF_{SOM2,\, HR} =CF_{SOM2} rf_{SOM2} .. math:: - :label: 21.44) + :label: 21.44) CF_{SOM3,\, HR} =CF_{SOM3} rf_{SOM3} .. math:: - :label: 21.45) + :label: 21.45) CF_{SOM4,\, HR} =CF_{SOM4} rf_{SOM4} @@ -633,32 +633,32 @@ Transfers of carbon from upstream to downstream pools in the decomposition cascade are given as: .. math:: - :label: 21.46) + :label: 21.46) CF_{Lit1,\, SOM1} =CF_{Lit1} \left(1-rf_{Lit1} \right) .. math:: - :label: 21.47) + :label: 21.47) CF_{Lit2,\, SOM2} =CF_{Lit2} \left(1-rf_{Lit2} \right) .. math:: - :label: 21.48) + :label: 21.48) CF_{Lit3,\, SOM3} =CF_{Lit3} \left(1-rf_{Lit3} \right) .. math:: - :label: 21.49) + :label: 21.49) CF_{SOM1,\, SOM2} =CF_{SOM1} \left(1-rf_{SOM1} \right) .. math:: - :label: 21.50) + :label: 21.50) CF_{SOM2,\, SOM3} =CF_{SOM2} \left(1-rf_{SOM2} \right) .. math:: - :label: 21.51) + :label: 21.51) CF_{SOM3,\, SOM4} =CF_{SOM3} \left(1-rf_{SOM3} \right) @@ -672,32 +672,32 @@ or from the downstream pool to the soil mineral nitrogen pool pools in the decomposition cascade are given as: .. math:: - :label: 21.52) + :label: 21.52) NF_{Lit1,\, SOM1} ={CF_{Lit1} \mathord{\left/ {\vphantom {CF_{Lit1} CN_{Lit1} }} \right.} CN_{Lit1} } .. math:: - :label: 21.53) + :label: 21.53) NF_{Lit2,\, SOM2} ={CF_{Lit2} \mathord{\left/ {\vphantom {CF_{Lit2} CN_{Lit2} }} \right.} CN_{Lit2} } .. math:: - :label: 21.54) + :label: 21.54) NF_{Lit3,\, SOM3} ={CF_{Lit3} \mathord{\left/ {\vphantom {CF_{Lit3} CN_{Lit3} }} \right.} CN_{Lit3} } .. math:: - :label: 21.55) + :label: 21.55) NF_{SOM1,\, SOM2} ={CF_{SOM1} \mathord{\left/ {\vphantom {CF_{SOM1} CN_{SOM1} }} \right.} CN_{SOM1} } .. math:: - :label: 21.56) + :label: 21.56) NF_{SOM2,\, SOM3} ={CF_{SOM2} \mathord{\left/ {\vphantom {CF_{SOM2} CN_{SOM2} }} \right.} CN_{SOM2} } .. math:: - :label: 21.57) + :label: 21.57) NF_{SOM3,\, SOM4} ={CF_{SOM3} \mathord{\left/ {\vphantom {CF_{SOM3} CN_{SOM3} }} \right.} CN_{SOM3} } @@ -706,37 +706,37 @@ whether the decomposition step is an immobilization flux or a mineralization flux: .. math:: - :label: 21.58) + :label: 21.58) NF_{sminn,\, Lit1\to SOM1} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit1\to SOM1} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} >0} \\ {NF_{pot\_ min,\, Lit1\to SOM1} \qquad {\rm for\; }NF_{pot\_ min,\, Lit1\to SOM1} \le 0} \end{array}\right\} .. math:: - :label: 21.59) + :label: 21.59) NF_{sminn,\, Lit2\to SOM2} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit2\to SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} >0} \\ {NF_{pot\_ min,\, Lit2\to SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, Lit2\to SOM2} \le 0} \end{array}\right\} .. math:: - :label: 21.60) + :label: 21.60) NF_{sminn,\, Lit3\to SOM3} =\left\{\begin{array}{l} {NF_{pot\_ min,\, Lit3\to SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} >0} \\ {NF_{pot\_ min,\, Lit3\to SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, Lit3\to SOM3} \le 0} \end{array}\right\} .. math:: - :label: 21.61) + :label: 21.61) NF_{sminn,SOM1\to SOM2} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM1\to SOM2} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} >0} \\ {NF_{pot\_ min,\, SOM1\to SOM2} \qquad {\rm for\; }NF_{pot\_ min,\, SOM1\to SOM2} \le 0} \end{array}\right\} .. math:: - :label: 21.62) + :label: 21.62) NF_{sminn,SOM2\to SOM3} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM2\to SOM3} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} >0} \\ {NF_{pot\_ min,\, SOM2\to SOM3} \qquad {\rm for\; }NF_{pot\_ min,\, SOM2\to SOM3} \le 0} \end{array}\right\} .. math:: - :label: 21.63) + :label: 21.63) NF_{sminn,SOM3\to SOM4} =\left\{\begin{array}{l} {NF_{pot\_ min,\, SOM3\to SOM4} f_{immob\_ demand} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} >0} \\ {NF_{pot\_ min,\, SOM3\to SOM4} \qquad {\rm for\; }NF_{pot\_ min,\, SOM3\to SOM4} \le 0} \end{array}\right\} .. math:: - :label: 21.64) + :label: 21.64) NF_{sminn,\, SOM4} =NF_{pot\_ min,\, SOM4} @@ -820,11 +820,11 @@ the form of a logistic equation, where :math:`{a}_{i}` is equal to the product of the base acceleration term and :math:`{a}_{l}` below: .. math:: - :label: 21.65) + :label: 21.65) a_l = 1 + 50 / \left ( 1 + exp \left (-0.1 * (abs(latitude) - 60 ) \right ) \right ) - + diff --git a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst index b867c6d9b5..09bcc67dd1 100644 --- a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst +++ b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst @@ -6,14 +6,14 @@ Dust Model Atmospheric dust is mobilized from the land by wind in the CLM. The most important factors determining soil erodibility and dust emission include the wind friction speed, the vegetation cover, and the soil moisture. -The CLM dust mobilization scheme (:ref:`Mahowald et al. 2006`) -accounts for these factors based on the DEAD (Dust Entrainment and Deposition) -model of :ref:`Zender et al. (2003)`. Please refer to the -:ref:`Zender et al. (2003)` article for additional +The CLM dust mobilization scheme (:ref:`Mahowald et al. 2006`) +accounts for these factors based on the DEAD (Dust Entrainment and Deposition) +model of :ref:`Zender et al. (2003)`. Please refer to the +:ref:`Zender et al. (2003)` article for additional information regarding the equations presented in this section. -The total vertical mass flux of dust, :math:`F_{j}` -(kg m\ :sup:`-2` s\ :sup:`-1`), from the ground into transport bin +The total vertical mass flux of dust, :math:`F_{j}` +(kg m\ :sup:`-2` s\ :sup:`-1`), from the ground into transport bin :math:`j` is given by .. math:: @@ -24,21 +24,21 @@ The total vertical mass flux of dust, :math:`F_{j}` where :math:`T` is a global factor that compensates for the DEAD model's sensitivity to horizontal and temporal resolution and equals 5 x 10\ :sup:`-4` in the CLM instead of 7 x 10\ :sup:`-4` in -:ref:`Zender et al. (2003)`. :math:`S` is the source -erodibility factor set to 1 in the CLM and serves as a place holder +:ref:`Zender et al. (2003)`. :math:`S` is the source +erodibility factor set to 1 in the CLM and serves as a place holder at this time. The grid cell fraction of exposed bare soil suitable for dust mobilization :math:`f_{m}` is given by .. math:: - :label: 29.2 + :label: 29.2 f_{m} =\left(1-f_{lake} \right)\left(1-f_{sno} \right)\left(1-f_{v} \right)\frac{w_{liq,1} }{w_{liq,1} +w_{ice,1} } -where :math:`f_{lake}` and :math:`f_{sno}` -are the CLM grid cell fractions of lake (section -:numref:`Surface Data`) and snow cover (section +where :math:`f_{lake}` and :math:`f_{sno}` +are the CLM grid cell fractions of lake (section +:numref:`Surface Data`) and snow cover (section :numref:`Snow Covered Area Fraction`), all ranging from zero to one. Not mentioned by :ref:`Zender et al. (2003)`, :math:`w_{liq,\, 1}` and :math:`{}_{w_{ice,\, 1} }` are the CLM top soil layer liquid water and @@ -58,15 +58,15 @@ and :math:`S` are the CLM leaf and stem area index values (m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so as to include all the pfts and the bare ground present in a vegetated land unit. :math:`L` and :math:`S` may be prescribed from the CLM -input data (section :numref:`Phenology and vegetation burial by snow`) -or simulated by the CLM biogeochemistry model (Chapter +input data (section :numref:`Phenology and vegetation burial by snow`) +or simulated by the CLM biogeochemistry model (Chapter :numref:`rst_Vegetation Phenology and Turnover`). The sandblasting mass efficiency :math:`\alpha` (m :sup:`-1`) is calculated as .. math:: - :label: 29.4 + :label: 29.4 \alpha =100e^{\left(13.4M_{clay} -6.0\right)\ln 10} {\rm \; \; }\left\{\begin{array}{l} {M_{clay} =\% clay\times 0.01{\rm \; \; \; 0}\le \% clay\le 20} \\ {M_{clay} =20\times 0.01{\rm \; \; \; \; \; \; \; \; 20<\% }clay\le 100} \end{array}\right. @@ -76,16 +76,16 @@ particles in the soil and %clay is determined from the surface dataset :math:`M_{clay} =0.2` to sandy loam. :math:`Q_{s}` is the total horizontally saltating mass flux (kg -m\ :sup:`-1` s\ :sup:`-1`) of "large" particles (:numref:`Table Dust Mass fraction`), +m\ :sup:`-1` s\ :sup:`-1`) of "large" particles (:numref:`Table Dust Mass fraction`), also referred to as the vertically integrated streamwise mass flux .. math:: :label: 29.5 Q_{s} = \left\{ - \begin{array}{lr} - \frac{c_{s} \rho _{atm} u_{*s}^{3} }{g} \left(1-\frac{u_{*t} }{u_{*s} } \right)\left(1+\frac{u_{*t} }{u_{*s} } \right)^{2} {\rm \; } & \qquad {\rm for\; }u_{*t} w_{t} } \end{array}\right. where .. math:: - :label: 29.8 + :label: 29.8 w_{t} =a\left(0.17M_{clay} +0.14M_{clay}^{2} \right){\rm \; \; \; \; \; \; 0}\le M_{clay} =\% clay\times 0.01\le 1 and .. math:: - :label: 29.9 + :label: 29.9 w=\frac{\theta _{1} \rho _{liq} }{\rho _{d,1} } @@ -127,15 +127,15 @@ where :math:`a=M_{clay}^{-1}` for tuning purposes, :math:`\theta _{1}` is the volumetric soil moisture in the top soil layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), :math:`\rho _{liq}` is the density of liquid water (kg -m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` -is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) -defined as in section :numref:`Soil and Snow Thermal Properties` +m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` +is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) +defined as in section :numref:`Soil and Snow Thermal Properties` rather than as in :ref:`Zender et al. (2003)`. :math:`Re_{*t}^{f}` from equation is the threshold friction Reynolds factor .. math:: - :label: 29.10 + :label: 29.10 Re_{*t}^{f} =\left\{\begin{array}{l} {\frac{0.1291^{2} }{-1+1.928Re_{*t} } {\rm \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; for\; 0.03}\le Re_{*t} \le 10} \\ {0.12^{2} \left(1-0.0858e^{-0.0617(Re_{*t} -10)} \right)^{2} {\rm \; for\; }Re_{*t} >10} \end{array}\right. @@ -143,7 +143,7 @@ and :math:`Re_{*t}` is the threshold friction Reynolds number approximation for optimally sized particles .. math:: - :label: 29.11 + :label: 29.11 Re_{*t} =0.38+1331\left(100D_{osp} \right)^{1.56} @@ -151,15 +151,15 @@ In :eq:`29.5` , :math:`u_{*s}` is defined as the wind friction speed (m s\ :sup:`-1`) accounting for the Owen effect (:ref:`Owen 1964`) .. math:: - :label: 29.12 + :label: 29.12 u_{\*s} = \left\{ - \begin{array}{lr} - u_{\*} & \quad {\rm \; for \;} U_{10} `). +stem area indices and canopy heights are prescribed or calculated for each PFT. Daily leaf +and stem area indices are obtained from griddeddatasets of monthly values (section +:numref:`Surface Data`). Canopy top and bottom heights for trees are from ICESat (:ref:`Simard et al. (2011) `). Canopy top and bottom heights for short vegetation are obtained from gridded datasets but are invariant in space and time and were obtained from PFT-specific values (:ref:`Bonan et al. (2002a) `) (:numref:`Table Plant functional type canopy top and bottom heights`). -When the biogeochemistry model is active, -vegetation state (LAI, SAI, canopy top and bottom heights) are calculated prognostically +When the biogeochemistry model is active, +vegetation state (LAI, SAI, canopy top and bottom heights) are calculated prognostically (see Chapter :numref:`rst_Vegetation Phenology and Turnover`). .. _Table Plant functional type canopy top and bottom heights: .. table:: Plant functional type canopy top and bottom heights - + +--------------------------------------------------------------+-------------------+-------------------+ | Plant functional type | :math:`z_{top}` | :math:`z_{bot}` | +==============================================================+===================+===================+ @@ -224,15 +224,15 @@ When the biogeochemistry model is inactive, leaf and stem area indices (m\ :sup:`2` leaf area m\ :sup:`-2` ground area) are updated daily by linearly interpolating between monthly values. Monthly PFT leaf area index values are developed from the 1-km MODIS-derived monthly grid -cell average leaf area index of :ref:`Myneni et al. (2002) `, -as described in :ref:`Lawrence and Chase (2007) `. Stem area -ndex is calculated from the monthly PFT leaf area index using the methods of -:ref:`Zeng et al. (2002) `. The leaf and stem area indices are -adjusted for vertical burying by snow (:ref:`Wang and Zeng 2009 `) +cell average leaf area index of :ref:`Myneni et al. (2002) `, +as described in :ref:`Lawrence and Chase (2007) `. Stem area +ndex is calculated from the monthly PFT leaf area index using the methods of +:ref:`Zeng et al. (2002) `. The leaf and stem area indices are +adjusted for vertical burying by snow (:ref:`Wang and Zeng 2009 `) as .. math:: - :label: 2.1 + :label: 2.1 A=A^{*} ( 1-f_{veg}^{sno} ) @@ -243,12 +243,12 @@ snow, :math:`A` is the remaining exposed leaf or stem area, .. math:: :label: 2.2 - {f_{veg}^{sno} = \frac{z_{sno} -z_{bot} }{z_{top} -z_{bot} } \qquad {\rm for\; tree\; and\; shrub}} \\ - {f_{veg}^{sno} = \frac{\min \left(z_{sno} ,\, z_{c} \right)}{z_{c} } \qquad {\rm for\; grass\; and\; crop}} + {f_{veg}^{sno} = \frac{z_{sno} -z_{bot} }{z_{top} -z_{bot} } \qquad {\rm for\; tree\; and\; shrub}} \\ + {f_{veg}^{sno} = \frac{\min \left(z_{sno} ,\, z_{c} \right)}{z_{c} } \qquad {\rm for\; grass\; and\; crop}} -where :math:`z_{sno} -z_{bot} \ge 0,{\rm \; }0\le f_{veg}^{sno} \le 1`, :math:`z_{sno}` is the depth of snow (m) -(Chapter :numref:`rst_Snow Hydrology`), and :math:`z_{c} = 0.2` is the snow depth when short vegetation is assumed to -be completely buried by snow (m). For numerical reasons, exposed leaf and stem area are set to zero if less than +where :math:`z_{sno} -z_{bot} \ge 0,{\rm \; }0\le f_{veg}^{sno} \le 1`, :math:`z_{sno}` is the depth of snow (m) +(Chapter :numref:`rst_Snow Hydrology`), and :math:`z_{c} = 0.2` is the snow depth when short vegetation is assumed to +be completely buried by snow (m). For numerical reasons, exposed leaf and stem area are set to zero if less than 0.05. If the sum of exposed leaf and stem area is zero, then the surface is treated as snow-covered ground. .. _Vertical Discretization: @@ -261,21 +261,21 @@ Vertical Discretization lakes have ten. For soil points, temperature calculations are done over all layers, :math:`N_{levgrnd} =15`, while hydrology calculations are done over the top ten layers, :math:`N_{levsoi} =10`, the bottom five - layers being specified as bedrock. + layers being specified as bedrock. .. _Soil Layers: Soil Layers ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The soil column can be discretized into an arbitrary number of layers. The default -vertical discretization (:numref:`Table Soil layer structure`) uses -:math:`N_{levgrnd} = 25` layers, of which :math:`N_{levsoi} = 20` are hydrologically and -biogeochemically active. The deepest 5 layers are only included in the thermodynamical -calculations (:ref:`Lawrence et al. 2008 `) described in Chapter +The soil column can be discretized into an arbitrary number of layers. The default +vertical discretization (:numref:`Table Soil layer structure`) uses +:math:`N_{levgrnd} = 25` layers, of which :math:`N_{levsoi} = 20` are hydrologically and +biogeochemically active. The deepest 5 layers are only included in the thermodynamical +calculations (:ref:`Lawrence et al. 2008 `) described in Chapter :numref:`rst_Soil and Snow Temperatures`. -The layer structure of the soil is described by the node depth, :math:`z_{i}` +The layer structure of the soil is described by the node depth, :math:`z_{i}` (m), the thickness of each layer, :math:`\Delta z_{i}` (m), and the depths at the layer interfaces :math:`z_{h,\, i}` (m). @@ -337,7 +337,7 @@ at the layer interfaces :math:`z_{h,\, i}` (m). | 25 | 41.998 | 15.115 | 49.556 | +---------------+------------------+------------------------+------------------------+ -Layer node depth (:math:`z_{i}` ), thickness (:math:`\Delta z_{i}` ), and depth at +Layer node depth (:math:`z_{i}` ), thickness (:math:`\Delta z_{i}` ), and depth at layer interface (:math:`z_{h,\, i}` ) for default soil column. All in meters. .. _Depth to Bedrock: @@ -345,12 +345,12 @@ layer interface (:math:`z_{h,\, i}` ) for default soil column. All in meters. Depth to Bedrock ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The hydrologically and biogeochemically active portion of the soil column can be -restricted to a thickness less than that of the maximum soil depth. By providing -a depth-to-bedrock dataset, which may vary spatially, the number of layers used -in the hydrologic and biogeochemical calculations, :math:`N_{bedrock}`, may be +The hydrologically and biogeochemically active portion of the soil column can be +restricted to a thickness less than that of the maximum soil depth. By providing +a depth-to-bedrock dataset, which may vary spatially, the number of layers used +in the hydrologic and biogeochemical calculations, :math:`N_{bedrock}`, may be specified, subject to the constraint :math:`N_{bedrock} \le N_{levsoi}`. -The default depth-to-bedrock values are from +The default depth-to-bedrock values are from :ref:`Pelletier et al. [2016]`. .. _Model Input Requirements: @@ -363,7 +363,7 @@ Model Input Requirements Atmospheric Coupling ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The current state of the atmosphere (:numref:`Table Atmospheric input to land model`) +The current state of the atmosphere (:numref:`Table Atmospheric input to land model`) at a given time step is used to force the land model. This atmospheric state is provided by an atmospheric model in coupled mode or from an observed dataset in land-only @@ -428,7 +428,7 @@ conditions from the current time step. atmospheric model :math:`z'_{atm}` is assumed to be the height above the surface as defined by the roughness length :math:`z_{0}` plus displacement height :math:`d`. Thus, the reference height used for flux -computations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) +computations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) is :math:`z_{atm} =z'_{atm} +z_{0} +d`. The reference heights for temperature, wind, and specific humidity (:math:`z_{atm,\, h}` , :math:`z_{atm,\, {\it m}}` , @@ -491,7 +491,7 @@ data may be obtained directly from the atmosphere model. Density of air (:math:`\rho _{atm}` ) (kg m\ :sup:`-3`) is also required but is calculated directly from -:math:`\rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} }` +:math:`\rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} }` where :math:`P_{atm}` is atmospheric pressure (Pa), :math:`e_{atm}` is atmospheric vapor pressure (Pa), :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), and @@ -604,7 +604,7 @@ of snow layers :math:`snl` and layer thickness) is initialized based on the snow depth (section 6.1). The snow liquid water and ice contents (kg m\ :sup:`-2`) are initialized as :math:`w_{liq,\, i} =0` and :math:`w_{ice,\, i} =\Delta z_{i} \rho _{sno}` , respectively, where -:math:`i=snl+1,\ldots ,0` are the snow layers, and :math:`\Delta z_{i}` +:math:`i=snl+1,\ldots ,0` are the snow layers, and :math:`\Delta z_{i}` is the thickness of snow layer :math:`i` (m). The soil liquid water and ice contents are initialized as :math:`w_{liq,\, i} =0` and :math:`w_{ice,\, i} =\Delta z_{i} \rho _{ice} \theta _{i}` for @@ -612,7 +612,7 @@ ice contents are initialized as :math:`w_{liq,\, i} =0` and :math:`w_{liq,\, i} =\Delta z_{i} \rho _{liq} \theta _{i}` and :math:`w_{ice,\, i} =0` for :math:`T_{i} >T_{f}` , where :math:`\rho _{ice}` and :math:`\rho _{liq}` are the densities of ice -and liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`T_{f}` +and liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical constants`). All vegetated and glacier land units are initialized with water stored in the unconfined aquifer and unsaturated soil :math:`W_{a} =4000` mm and water table @@ -623,7 +623,7 @@ depth :math:`z_{\nabla }` at five meters below the soil column. Surface Data ^^^^^^^^^^^^^^^^^^ -Required surface data for each land grid cell are listed in +Required surface data for each land grid cell are listed in :numref:`Table Surface data required for CLM and their base spatial resolution` and include the glacier, lake, and urban fractions of the grid cell (vegetated and crop occupy the remainder), the fractional cover of each @@ -734,7 +734,7 @@ resolution data of :ref:`Kourzeneva (2009, 2010) ` to the 0.05\ resolution using the MODIS land-mask. Percent urban is derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity and slope -(:ref:`Dobson et al. 2000 `) as described by +(:ref:`Dobson et al. 2000 `) as described by :ref:`Jackson et al. (2010) ` at 1km resolution and aggregated to 0.05\ :sup:`o`. A number of urban radiative, thermal, and morphological fields are also required and are @@ -743,9 +743,9 @@ Table 3 of the Community Land Model Urban (CLMU) technical note (:ref:`Oleson et al. 2010b `). Percent PFTs are derived from MODIS satellite data as described in -:ref:`Lawrence and Chase (2007) ` (section 21.3.3). -Prescribed PFT leaf area index is derived from the MODIS satellite data of -:ref:`Myneni et al. (2002) ` using the de-aggregation methods +:ref:`Lawrence and Chase (2007) ` (section 21.3.3). +Prescribed PFT leaf area index is derived from the MODIS satellite data of +:ref:`Myneni et al. (2002) ` using the de-aggregation methods described in :ref:`Lawrence and Chase (2007) ` (section 2.2.3). Prescribed PFT stem area index is derived from PFT leaf area index phenology combined with the methods of :ref:`Zeng et al. (2002) `. @@ -754,7 +754,7 @@ described in :ref:`Bonan et al. (2002b) `. If the biogeochemistr active, it supplies the leaf and stem area index and canopy top and bottom heights dynamically, and the prescribed values are ignored. -Soil color determines dry and saturated soil albedo (section :numref:`Ground Albedos`). +Soil color determines dry and saturated soil albedo (section :numref:`Ground Albedos`). Soil colors are from :ref:`Lawrence and Chase (2007) `. The soil texture and organic matter content determine soil thermal and @@ -767,21 +767,21 @@ sources. The majority of the globe is from ISRIC-WISE (:ref:`Batjes, 2006 `). Both datasets report carbon down to 1m depth. Carbon is partitioned across -the top seven CLM4 layers (:math:`\sim`\ 1m depth) as in +the top seven CLM4 layers (:math:`\sim`\ 1m depth) as in :ref:`Lawrence and Slater (2008) `. The maximum fractional saturated area (:math:`f_{\max }` ) is used in determining surface runoff and infiltration (section 7.3). Maximum fractional saturated area at 0.125\ :sup:`o` resolution is calculated from 1-km compound topographic indices (CTIs) based on the -USGS HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) -following the algorithm in :ref:`Niu et al. (2005) `. +USGS HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) +following the algorithm in :ref:`Niu et al. (2005) `. :math:`f_{\max }` is the ratio between the number of 1-km pixels with CTIs equal to or larger than the mean CTI and the total number of pixels in a 0.125\ :sup:`o` grid cell. See section 7.3.1 and :ref:`Li et al. (2013b) ` for further details. Slope and -elevation are also obtained from the USGS HYDRO1K 1-km dataset -(:ref:`Verdin and Greenlee 1996 `). Slope is used in the +elevation are also obtained from the USGS HYDRO1K 1-km dataset +(:ref:`Verdin and Greenlee 1996 `). Slope is used in the surface water parameterization (section :numref:`Surface Water Storage`), and elevation is used to calculate the grid cell standard deviation of topography for the snow cover fraction parameterization (section :numref:`Snow Covered Area Fraction`). @@ -794,15 +794,15 @@ The default list of PFTs includes an unmanaged crop treated as a second C3 grass (:numref:`Table Plant functional types`). The unmanaged crop has grid cell fractional cover assigned from MODIS satellite data (:ref:`Lawrence and Chase (2007) `). A managed crop option uses grid cell fractional cover from the present-day crop -dataset of :ref:`Ramankutty and Foley (1998) ` -(CLM4CNcrop). Managed crops are assigned in the proportions given by +dataset of :ref:`Ramankutty and Foley (1998) ` +(CLM4CNcrop). Managed crops are assigned in the proportions given by :ref:`Ramankutty and Foley (1998) ` without exceeding the area previously assigned to the unmanaged crop. The unmanaged crop continues to occupy any of its original area that remains and continues to be handled just by the CN part of CLM4CNcrop. The managed crop types (corn, soybean, and temperate cereals) were chosen based on the availability of corresponding algorithms in AgroIBIS -(:ref:`Kucharik et al. 2000 `; +(:ref:`Kucharik et al. 2000 `; :ref:`Kucharik and Brye 2003 `). Temperate cereals include wheat, barley, and rye here. All temperate cereals are treated as summer crops (like spring wheat, for example) at this time. Winter @@ -819,12 +819,12 @@ not share soil columns and thus permit for differences in land management between crops. CLM includes the option to irrigate cropland areas that are equipped for -irrigation. The application of irrigation responds dynamically to climate -(see Chapter :numref:`rst_Crops and Irrigation`). In CLM, irrigation is -implemented for the C3 generic crop only. When irrigation is enabled, the -cropland area of each grid cell is divided into an irrigated and unirrigated -fraction according to a dataset of areas equipped for irrigation -(:ref:`Siebert et al. (2005) `). The area of irrigated +irrigation. The application of irrigation responds dynamically to climate +(see Chapter :numref:`rst_Crops and Irrigation`). In CLM, irrigation is +implemented for the C3 generic crop only. When irrigation is enabled, the +cropland area of each grid cell is divided into an irrigated and unirrigated +fraction according to a dataset of areas equipped for irrigation +(:ref:`Siebert et al. (2005) `). The area of irrigated cropland in each grid cell is given by the smaller of the grid cell's total cropland area, according to the default CLM4 dataset, and the grid cell's area equipped for irrigation. The @@ -864,7 +864,7 @@ Values of certain adjustable parameters inherent in the biogeophysical or biogeochemical parameterizations have either been obtained from the literature or calibrated based on comparisons with observations. These are described in the text. Physical constants, generally shared by all -of the components in the coupled modeling system, are presented in +of the components in the coupled modeling system, are presented in :numref:`Table Physical constants`. @@ -875,7 +875,7 @@ of the components in the coupled modeling system, are presented in :widths: 40, 20, 20, 20 "Pi", :math:`\pi`, 3.14159265358979323846, "\-" - "Acceleration of gravity", :math:`g`, 9.80616, m s\ :sup:`-2` + "Acceleration of gravity", :math:`g`, 9.80616, m s\ :sup:`-2` "Standard pressure", :math:`P_{std}`, 101325, "Pa" "Stefan-Boltzmann constant", :math:`\sigma`, 5.67 :math:`\times 10^{-8}`, W m :sup:`-2` K :math:`{}^{-4}` "Boltzmann constant", :math:`\kappa`, 1.38065 :math:`\times 10^{-23}`, J K :sup:`-1` molecule :sup:`-1` diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index 90dd72f705..1e1659ad52 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -43,7 +43,7 @@ Atmospheric Nitrogen Deposition CLM uses a single variable to represent the total deposition of mineral nitrogen onto the land surface, combining wet and dry deposition of NO\ :sub:`y` and NH\ :sub:`x` as a single flux -(:math:`{NF}_{ndep\_sminn}`, gN m\ :sup:`-2` s\ :sup:`-1`). This flux +(:math:`{NF}_{ndep\_sminn}`, gN m\ :sup:`-2` s\ :sup:`-1`). This flux is intended to represent total reactive nitrogen deposited to the land surface which originates from the following natural and anthropogenic sources (Galloway et al. 2004): @@ -64,21 +64,21 @@ deposition flux is provided as a spatially and (potentially) temporally varying dataset (see section :numref:`Atmospheric Coupling` for a description of the default input dataset). -The nitrogen deposition flux is assumed to enter the NH\ :sub:`4`\ :sup:`+` pool, -and is vertically distributed throughout the soil profile. Although N deposition -inputs include both oxidized and reduced forms, CLM5 only reads in total -N deposition. This approach is held over from CLM4.0, which only represented a +The nitrogen deposition flux is assumed to enter the NH\ :sub:`4`\ :sup:`+` pool, +and is vertically distributed throughout the soil profile. Although N deposition +inputs include both oxidized and reduced forms, CLM5 only reads in total +N deposition. This approach is held over from CLM4.0, which only represented a single mineral nitrogen pool, however, real pathways for wet and dry nitrogen deposition can be more complex than currently represented in the CLM5.0, including release from melting snowpack and direct foliar -uptake of deposited NO\ :sub:`y` (:ref:`Tye et al. 2005 `; -:ref:`Vallano and Sparks, 2007 `). +uptake of deposited NO\ :sub:`y` (:ref:`Tye et al. 2005 `; +:ref:`Vallano and Sparks, 2007 `). -In offline (uncoupled) CLM5.0 simulations monthly -estimates of N deposition are provided, as opposed to decadal files +In offline (uncoupled) CLM5.0 simulations monthly +estimates of N deposition are provided, as opposed to decadal files supplied with previous versions of the model. In coupled simulations, -N depositions fluxes are passed to the land model at the frequency of -the time step (every half hour) through the coupler. +N depositions fluxes are passed to the land model at the frequency of +the time step (every half hour) through the coupler. Biological Nitrogen Fixation @@ -89,27 +89,27 @@ by soil microorganisms is an important component of both preindustrial and modern-day nitrogen budgets, but a mechanistic understanding of global-scale controls on biological nitrogen fixation (BNF) is still only poorly developed (:ref:`Cleveland et al. 1999 `; -:ref:`Galloway et al. 2004 `). CLM5.0 uses the FUN -model (chapter :numref:`rst_FUN`) to -calculate the carbon cost and nitrogen acquired through symbotic +:ref:`Galloway et al. 2004 `). CLM5.0 uses the FUN +model (chapter :numref:`rst_FUN`) to +calculate the carbon cost and nitrogen acquired through symbotic nitrogen fixation. This nitrogen is immediately available to plants. -:ref:`Cleveland et al. (1999) ` suggested -an empirical relationships that predicts BNF as a function of -either evapotranspiration rate or net primary productivity for +:ref:`Cleveland et al. (1999) ` suggested +an empirical relationships that predicts BNF as a function of +either evapotranspiration rate or net primary productivity for natural vegetation. CLM5.0 adopts the evapotranspiration approach to calculate asymbiotic, or free-living, N fixation. This function -has been modified from the :ref:`Cleveland et al. (1999) -` estimates to provide lower estimate of -free-living nitrogen fixation in CLM5.0 +has been modified from the :ref:`Cleveland et al. (1999) +` estimates to provide lower estimate of +free-living nitrogen fixation in CLM5.0 (:math:`{CF}_{ann\_ET}`, mm yr\ :sup:`-1`). -This moves away from the NPP approach used in CLM4.0 and 4.5 and +This moves away from the NPP approach used in CLM4.0 and 4.5 and avoids unrealistically increasing freeliving rates of N fixation -under global change scenarios (:ref:`Wieder et al. 2015 +under global change scenarios (:ref:`Wieder et al. 2015 ` The expression used is: .. math:: - :label: 22.1) + :label: 22.1) NF_{nfix,sminn} ={0.0006\left(0.0117+CF_{ann\_ ET}\right)\mathord{\left/ {\vphantom {0.0006\left(0.0117+ CF_{ann\_ ET}\right) \left(86400\cdot 365\right)}} \right.} \left(86400\cdot 365\right)} @@ -128,12 +128,12 @@ NH\ :sub:`4`\ :sup:`+` pool. Nitrification and Denitrification Losses of Nitrogen --------------------------------------------------------- -Nitrification is an autotrophic process that converts less mobile ammonium -ions into nitrate, that can more easily be lost from soil systems by leaching -or denitrification. The process catalyzed by ammonia oxidizing archaea and -bacteria that convert ammonium (NH\ :sub:`4`\ :sup:`+`) into nitrite, which -is subsequently oxidized into nitrate (NO\ :sub:`3`\ :sup:`-`). Conditions -favoring nitrification include high NH\ :sub:`4`\ :sup:`+` concentrations, +Nitrification is an autotrophic process that converts less mobile ammonium +ions into nitrate, that can more easily be lost from soil systems by leaching +or denitrification. The process catalyzed by ammonia oxidizing archaea and +bacteria that convert ammonium (NH\ :sub:`4`\ :sup:`+`) into nitrite, which +is subsequently oxidized into nitrate (NO\ :sub:`3`\ :sup:`-`). Conditions +favoring nitrification include high NH\ :sub:`4`\ :sup:`+` concentrations, well aerated soils, a neutral pH and warmer temperatures. Under aerobic conditions in the soil oxygen is the preferred electron @@ -143,43 +143,43 @@ an electron acceptor (e.g. *Pseudomonas* and *Clostridium*) supporting respiration. This process, known as denitrification, results in the transformation of nitrate to gaseous N\ :sub:`2`, with smaller associated production of NO\ :sub:`x` and N\ :sub:`2`\ O. It -is typically assumed that nitrogen fixation and denitrification +is typically assumed that nitrogen fixation and denitrification were approximately balanced in the preindustrial biosphere ( -:ref:`Galloway et al. 2004 `). It is likely +:ref:`Galloway et al. 2004 `). It is likely that denitrification can occur within anaerobic microsites within an otherwise aerobic soil environment, leading to large global denitrification fluxes even when fluxes per unit area are rather low (:ref:`Galloway et al. 2004 `). CLM includes a detailed representation of nitrification and -denitrification based on the Century N model (:ref:`Parton +denitrification based on the Century N model (:ref:`Parton et al. 1996 `, :ref:`2001 `; -:ref:`del Grosso et al. 2000 `). In this +:ref:`del Grosso et al. 2000 `). In this approach, nitrification of NH\ :sub:`4`\ :sup:`+` to NO\ :sub:`3`\ :sup:`-` is a function of temperature, moisture, and pH: .. math:: - :label: 22.2) + :label: 22.2) f_{nitr,p} =\left[NH_{4} \right]k_{nitr} f\left(T\right)f\left(H_{2} O\right)f\left(pH\right) where :math:`{f}_{nitr,p}` is the potential nitrification rate (prior to competition for NH\ :sub:`4`\ :sup:`+` by plant uptake and N immobilization), :math:`{k}_{nitr}` is the maximum -nitrification rate (10 % day\ :math:`\mathrm{-}`\ 1, -(:ref:`Parton et al. 2001 `), and *f(T)* and -*f(H\)*\ :sub:`2`\ O) are rate modifiers for temperature and +nitrification rate (10 % day\ :math:`\mathrm{-}`\ 1, +(:ref:`Parton et al. 2001 `), and *f(T)* and +*f(H\)*\ :sub:`2`\ O) are rate modifiers for temperature and moisture content. CLM uses the same rate modifiers as -are used in the decomposition routine. *f(pH)* is a rate +are used in the decomposition routine. *f(pH)* is a rate modifier for pH; however, because CLM does not calculate pH, -instead a fixed pH value of 6.5 is used in the pH function of +instead a fixed pH value of 6.5 is used in the pH function of :ref:`Parton et al. (1996) `. The potential denitrification rate is co-limited by NO\ :sup:`-3` concentration and C consumption rates, and occurs only in the anoxic fraction of soils: .. math:: - :label: 22.3) + :label: 22.3) f_{denitr,p} =\min \left(f(decomp),f\left(\left[NO_{3} ^{-} \right]\right)\right)frac_{anox} @@ -187,15 +187,15 @@ where :math:`{f}_{denitr,p}` is the potential denitrification rate and *f(decomp)* and *f([NO*\ :sub:`3`\ :sup:`-` *])* are the carbon- and nitrate- limited denitrification rate functions, respectively, (:ref:`del Grosso et al. 2000 `). -Because the modified CLM includes explicit treatment of soil -biogeochemical vertical profiles, including diffusion of the trace -gases O\ :sub:`2` and CH\ :sub:`4` (:ref:`Riley et al. 2011a -`), the calculation of anoxic fraction :math:`{frac}_{anox}` -uses this information following the anoxic microsite formulation +Because the modified CLM includes explicit treatment of soil +biogeochemical vertical profiles, including diffusion of the trace +gases O\ :sub:`2` and CH\ :sub:`4` (:ref:`Riley et al. 2011a +`), the calculation of anoxic fraction :math:`{frac}_{anox}` +uses this information following the anoxic microsite formulation of :ref:`Arah and Vinten (1995) `. .. math:: - :label: 22.4) + :label: 22.4) frac_{anox} =\exp \left(-aR_{\psi }^{-\alpha } V^{-\beta } C^{\gamma } \left[\theta +\chi \varepsilon \right]^{\delta } \right) @@ -205,21 +205,21 @@ radius of a typical pore space at moisture content :math:`\psi`, *V* is the O\ :sub:`2` consumption rate, *C* is the O\ :sub:`2` concentration, :math:`\theta` is the water-filled pore space, :math:`\chi` is the ratio of diffusivity of oxygen in water to that in -air, and :math:`\epsilon` is the air-filled pore space (:ref:`Arah and -Vinten (1995) `). These parameters are all calculated +air, and :math:`\epsilon` is the air-filled pore space (:ref:`Arah and +Vinten (1995) `). These parameters are all calculated separately at each layer to define a profile of anoxic porespace fraction in the soil. The nitrification/denitrification models used here also predict fluxes of N\ :sub:`2`\ O via a "hole-in-the-pipe" approach (:ref:`Firestone and -Davidson, 1989 `). A constant fraction -(6 \* 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the -nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction +Davidson, 1989 `). A constant fraction +(6 \* 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the +nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction of denitrification going to N\ :sub:`2`\ O, \ :math:`{P}_{N2:N2O}`, is variable, following the Century (:ref:`del Grosso et al. 2000 `) approach: .. math:: - :label: 22.5) + :label: 22.5) P_{N_{2} :N_{2} O} =\max \left(0.16k_{1} ,k_{1} \exp \left(-0.8P_{NO_{3} :CO_{2} } \right)\right)f_{WFPS} @@ -230,14 +230,14 @@ a function of :math:`{d}_{g}`, the gas diffusivity through the soil matrix: .. math:: - :label: 22.6) + :label: 22.6) k_{1} =\max \left(1.7,38.4-350*d_{g} \right) and :math:`{f}_{WFPS}` is a function of the water filled pore space *WFPS:* .. math:: - :label: 22.16) + :label: 22.16) f_{WFPS} =\max \left(0.1,0.015\times WFPS-0.32\right) @@ -255,7 +255,7 @@ of hydrologic discharge from the soil column to streamflow s\ :sup:`-1`, section :numref:`Lateral Sub-surface Runoff`), as .. math:: - :label: 22.17) + :label: 22.17) NF_{leached} =DIN\cdot Q_{dis} . @@ -269,7 +269,7 @@ to be 100% adsorbed onto mineral surfaces and unaffected by leaching. *DIN* is then given as .. math:: - :label: 22.18) + :label: 22.18) DIN=\frac{NS_{sminn} sf}{WS_{tot\_ soil} } @@ -278,7 +278,7 @@ over the column. The total mineral nitrogen leaching flux is limited on each time step to not exceed the soluble fraction of :math:`{NS}_{sminn}` .. math:: - :label: 22.19) + :label: 22.19) NF_{leached} =\min \left(NF_{leached} ,\frac{NS_{sminn} sf}{\Delta t} \right). @@ -292,7 +292,7 @@ CLM-CN that losses of N due to fire are restricted to vegetation and litter pools (including coarse woody debris). Loss rates of N are determined by the fraction of biomass lost to combustion, assuming that most of the nitrogen in the burned biomass is lost to the atmosphere -(:ref:`Schlesinger, 1997 `; :ref:`Smith et al. 2005 +(:ref:`Schlesinger, 1997 `; :ref:`Smith et al. 2005 `). It is assumed that soil organic matter pools of carbon and nitrogen are not directly affected by fire (:ref:`Neff et al. 2005 `). diff --git a/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst b/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst index 658653da48..bea5cb99e5 100644 --- a/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst +++ b/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst @@ -19,47 +19,47 @@ The Fixation and Uptake of Nitrogen model is based on work by :ref:`Fisher et al 8. Nonmycorrhizal uptake of NO3 (:math:`_{nonmyc,nh4}`) -The notation suffix for each pathway is given in parentheses here. At each timestep, each of these pathways is associated with a cost term (:math:`N_{cost,x}`), a payment in carbon (:math:`C_{nuptake,x}`), and an influx of Nitrogen (:math:`N_{uptake,x}`) where :math:`x` is one of the eight uptake streams listed above. +The notation suffix for each pathway is given in parentheses here. At each timestep, each of these pathways is associated with a cost term (:math:`N_{cost,x}`), a payment in carbon (:math:`C_{nuptake,x}`), and an influx of Nitrogen (:math:`N_{uptake,x}`) where :math:`x` is one of the eight uptake streams listed above. For each PFT, we define a fraction of the total C acquisition that can be used for N fixation (:math:`f_{fixers}`), which is broadly equivalent to the fraction of a given PFT that is capable of fixing Nitrogen, and thus represents an upper limit on the amount to which fixation can be increased in low n conditions. For each PFT, the cost calculation is conducted twice. Once where fixation is possible and once where it is not. (:math:`f_{fixers}`) -For all of the active uptake pathways, whose cost depends on varying concentrations of N through the soil profile, the costs and fluxes are also determined by soil layer :math:`j`. +For all of the active uptake pathways, whose cost depends on varying concentrations of N through the soil profile, the costs and fluxes are also determined by soil layer :math:`j`. -Boundary conditions of FUN +Boundary conditions of FUN -------------------------------------------------------- Available Carbon ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The carbon available for FUN, :math:`C_{avail}` (gC m\ :sup:`-2`) is the total canopy photosynthetic uptake (GPP), minus the maintenance respiration fluxes (:math:`m_r`) and multiplied by the time step in seconds (:math:`\delta t`). Thus, the remainder of this chapter considers fluxes per timestep, and integrates these fluxes as they are calculated. +The carbon available for FUN, :math:`C_{avail}` (gC m\ :sup:`-2`) is the total canopy photosynthetic uptake (GPP), minus the maintenance respiration fluxes (:math:`m_r`) and multiplied by the time step in seconds (:math:`\delta t`). Thus, the remainder of this chapter considers fluxes per timestep, and integrates these fluxes as they are calculated. .. math:: C_{avail} = (GPP - m_r) \delta t -Growth respiration is thus only calculated on the part of the carbon uptake that remains after expenditure of C by the FUN module. +Growth respiration is thus only calculated on the part of the carbon uptake that remains after expenditure of C by the FUN module. Available Soil Nitrogen ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Cost of Nitrogen Fixation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The cost of fixation is derived from :ref:`Houlton et al. (2008)`. +The cost of fixation is derived from :ref:`Houlton et al. (2008)`. .. math:: N_{cost,fix} = -s_{fix}/(1.25 e^{a_{fix} + b_{fix} . t_{soil} (1 - 0.5 t_{soil}/ c_{fix}) }) - -Herein, :math:`a_{fix}`, :math:`b_{fix}` and :math:`c_{fix}` are all parameters of the temperature response function of fixation reported by Houlton et al. (2008) (:math:`exp[a+bT_s(1-0.5T_s/c)`). t_{soil} is the soil temperature in C. The values of these parameters are fitted to empirical data as a=-3.62 :math:`\pm` 0.52, b=0.27:math:`\pm` 0.04 and c=25.15 :math:`\pm` 0.66. 1.25 converts from the temperature response function to a 0-1 limitation factor (as specifically employed by Houlton et al.). This function is a 'rate' of uptake for a given temperature. Here we assimilated the rate of fixation into the cost term by assuming that the rate is analagous to a conductance for N, and inverting the term to produce a cost/resistance analagoue. We then multiply this temperature term by the minimum cost at optimal temperature (:math:`s_{fix}`) to give a temperature limited cost in terms of C to N ratios. + +Herein, :math:`a_{fix}`, :math:`b_{fix}` and :math:`c_{fix}` are all parameters of the temperature response function of fixation reported by Houlton et al. (2008) (:math:`exp[a+bT_s(1-0.5T_s/c)`). t_{soil} is the soil temperature in C. The values of these parameters are fitted to empirical data as a=-3.62 :math:`\pm` 0.52, b=0.27:math:`\pm` 0.04 and c=25.15 :math:`\pm` 0.66. 1.25 converts from the temperature response function to a 0-1 limitation factor (as specifically employed by Houlton et al.). This function is a 'rate' of uptake for a given temperature. Here we assimilated the rate of fixation into the cost term by assuming that the rate is analagous to a conductance for N, and inverting the term to produce a cost/resistance analagoue. We then multiply this temperature term by the minimum cost at optimal temperature (:math:`s_{fix}`) to give a temperature limited cost in terms of C to N ratios. Cost of Active Uptake ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The cost of N uptake from soil, for each layer :math:`j`, is controlled by two uptake parameters that pertain respectively to the relationship between soil N content and N uptake, and root C density and N uptake. +The cost of N uptake from soil, for each layer :math:`j`, is controlled by two uptake parameters that pertain respectively to the relationship between soil N content and N uptake, and root C density and N uptake. For non-mycorrhizal uptake: @@ -79,8 +79,8 @@ where :math:`k_{n,active}` varies according to whether we are considering ecto o .. math:: :label: 18.2 - k_{n,active} = - \left\{\begin{array}{lr} + k_{n,active} = + \left\{\begin{array}{lr} k_{n,Eactive}& e = 1\\ k_{n,Aactive}& e = 0 \end{array}\right\} @@ -93,45 +93,45 @@ The total cost of N uptake is calculated based on the assumption that carbon is .. math:: - N_{conductance,f}= \sum{(1/N_{cost,x})} + N_{conductance,f}= \sum{(1/N_{cost,x})} -From this, we then calculate the fraction of the carbon allocated to each pathway as +From this, we then calculate the fraction of the carbon allocated to each pathway as .. math:: C_{frac,x} = \frac{1/N_{cost,x}}{N_{conductance}} -These fractions are used later, to calculate the carbon expended on different uptake pathways. Next, the N acquired from each uptake stream per unit C spent (:math:`N_{exch,x}`, gN/gC) is determined as +These fractions are used later, to calculate the carbon expended on different uptake pathways. Next, the N acquired from each uptake stream per unit C spent (:math:`N_{exch,x}`, gN/gC) is determined as .. math:: N_{exch,x} = \frac{C_{frac,x}}{N_{cost,x}} -We then determine the total amount of N uptake per unit C spent (:math:`N_{exch,tot}`, gN/gC) as the sum of all the uptake streams. +We then determine the total amount of N uptake per unit C spent (:math:`N_{exch,tot}`, gN/gC) as the sum of all the uptake streams. .. math:: N_{exch,tot} = \sum{N_{exch,x}} -and thus the subsequent overall N cost is +and thus the subsequent overall N cost is .. math:: N_{cost,tot} = 1/{N_{exch,tot}} - Retranslocation is determined via a different set of mechanisms, once the :math:`N_{cost,tot}` is known. + Retranslocation is determined via a different set of mechanisms, once the :math:`N_{cost,tot}` is known. Nitrogen Retranslocation -------------------------------------------------------- -The retranslocation uses an iterative algorithm to remove Nitrogen from each piece of falling litter. There are two pathways for this, 'free' uptake which removes the labile N pool, and 'paid-for' uptake which uses C to extract N from increasingly more recalcitrant pools. +The retranslocation uses an iterative algorithm to remove Nitrogen from each piece of falling litter. There are two pathways for this, 'free' uptake which removes the labile N pool, and 'paid-for' uptake which uses C to extract N from increasingly more recalcitrant pools. -At each timestep, the pool of carbon in falling leaves (:math:`C_{fallingleaf}`, g m\ :sup:`-2`) is generated from the quantity of litterfall on that day (see Phenology chapter for details). The amount of N in the litter pool (:math:`N_{fallingleaf}`, g m\ :sup:`-2`) is calculated as the total leaf N multiplied by the fraction of the leaf pool passed to litter that timestep. +At each timestep, the pool of carbon in falling leaves (:math:`C_{fallingleaf}`, g m\ :sup:`-2`) is generated from the quantity of litterfall on that day (see Phenology chapter for details). The amount of N in the litter pool (:math:`N_{fallingleaf}`, g m\ :sup:`-2`) is calculated as the total leaf N multiplied by the fraction of the leaf pool passed to litter that timestep. .. math:: N_{fallingleaf} = N_{leaf}.C_{fallingleaf}/C_{leaf} -The carbon available at the beginning of the iterative retranslocation calculation is equal to the :math:`C_{avail}` input into FUN. +The carbon available at the beginning of the iterative retranslocation calculation is equal to the :math:`C_{avail}` input into FUN. .. math:: @@ -140,21 +140,21 @@ The carbon available at the beginning of the iterative retranslocation calculati Free Retranslocation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Some part of the leaf Nitrogen pool is removed without the need for an C expenditure. This 'free' N uptake amount, (:math:`N_{retrans,free}`, gN m\ :sup:`-2`) is calculated as +Some part of the leaf Nitrogen pool is removed without the need for an C expenditure. This 'free' N uptake amount, (:math:`N_{retrans,free}`, gN m\ :sup:`-2`) is calculated as .. math:: N_{retrans,free} = max(N_{fallingleaf} - (C_{fallingleaf}/CN_{litter,min} ),0.0) -where :math:`CN_{litter,min}` is the minimum C:N ratio of the falling litter (currently set to 1.5 x the target C:N ratio). +where :math:`CN_{litter,min}` is the minimum C:N ratio of the falling litter (currently set to 1.5 x the target C:N ratio). -The new :math:`N_{fallingleaf}` (gN m\ :sup:`-2`) is then determined as +The new :math:`N_{fallingleaf}` (gN m\ :sup:`-2`) is then determined as .. math:: N_{fallingleaf} = N_{fallingleaf} - N_{retrans,free} -and the new litter C:N ratio as +and the new litter C:N ratio as .. math:: @@ -163,13 +163,13 @@ and the new litter C:N ratio as Paid-for Retranslocation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The remaining calculations conduct an iterative calculation to determine the degree to which N retranslocation from leaves is paid for as C:N ratios and thus cost increase as N is extracted. The iteration continues until either +The remaining calculations conduct an iterative calculation to determine the degree to which N retranslocation from leaves is paid for as C:N ratios and thus cost increase as N is extracted. The iteration continues until either -1. The cost of retranslocation (:math:`cost_{retrans}` increases beyond the cost of acquiring N from alternative pathways (:math:`N_{cost,tot}`). -2. :math:`CN_{fallingleaf}` rises to a maximum level, after which no more extraction is possible (representing unavoidable N loss) or +1. The cost of retranslocation (:math:`cost_{retrans}` increases beyond the cost of acquiring N from alternative pathways (:math:`N_{cost,tot}`). +2. :math:`CN_{fallingleaf}` rises to a maximum level, after which no more extraction is possible (representing unavoidable N loss) or 3. There is no more carbon left to pay for extraction. -First we calculate the cost of extraction (:math:`cost_{retrans}`, gC/gN) for the current leaf C:N ratio as +First we calculate the cost of extraction (:math:`cost_{retrans}`, gC/gN) for the current leaf C:N ratio as .. math:: @@ -180,10 +180,10 @@ where :math:`k_{retrans}` is a parameter controlling the overall cost of resorp Next, we calculate the amount of C needed to be spent to increase the falling leaf C:N ratio by 1.0 in this iteration :math:`i` (:math:`C_{retrans_spent,i}`, gC m\ :sup:`-2`) as: .. math:: - C_{retrans,spent,i} = cost_{retrans}.(N_{fallingleaf} - C_{fallingleaf}/ + C_{retrans,spent,i} = cost_{retrans}.(N_{fallingleaf} - C_{fallingleaf}/ (CN_{fallingleaf} + 1.0)) -(wherein the retranslocation cost is assumed to not change over the increment of 1.0 in C:N ratio). Next, we calculate whether this is larger than the remaining C available to spend. +(wherein the retranslocation cost is assumed to not change over the increment of 1.0 in C:N ratio). Next, we calculate whether this is larger than the remaining C available to spend. .. math:: @@ -195,11 +195,11 @@ The amount of N retranslocated from the leaf in this iteration (:math:`N_{retran N_{retrans,paid,i} = min(N_{fallingleaf},C_{retrans,spent,i} / cost_{retrans}) -The next step calculates the growth C which is accounted for by this amount of N extraction in this iteration (:math:`C_{retrans,accounted,i}`). This is calculated using the current plant C:N ratio, and also for the additional C which will need to be spent on growth respiration to build this amount of new tissue. +The next step calculates the growth C which is accounted for by this amount of N extraction in this iteration (:math:`C_{retrans,accounted,i}`). This is calculated using the current plant C:N ratio, and also for the additional C which will need to be spent on growth respiration to build this amount of new tissue. .. math:: - C_{retrans,accounted,i} = N_{retrans,paid,i} . CN_{plant} . (1.0 + gr_{frac}) + C_{retrans,accounted,i} = N_{retrans,paid,i} . CN_{plant} . (1.0 + gr_{frac}) Then the falling leaf N is updated: @@ -216,7 +216,7 @@ and the :math:`CN_{fallingleaf}` and cost_{retrans} are updated. The amount of a Outputs of Retranslocation algorithm. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The final output of the retranslocation calculation are the retranslocated N (:math:`N_{retrans}`, gN m\ :sup:`-2`), C spent on retranslocation (:math:`C_{retrans_paid}`, gC m\ :sup:`-2`), and C accounted for by retranslocation (:math:`C_{retrans_accounted}`, gC m\ :sup:`-2`). +The final output of the retranslocation calculation are the retranslocated N (:math:`N_{retrans}`, gN m\ :sup:`-2`), C spent on retranslocation (:math:`C_{retrans_paid}`, gC m\ :sup:`-2`), and C accounted for by retranslocation (:math:`C_{retrans_accounted}`, gC m\ :sup:`-2`). For paid-for uptake, we accumulate the total carbon spent on retranslocation (:math:`C_{spent_retrans}`), @@ -236,12 +236,12 @@ where N acquired by paid-for retranslocation is N_{retrans,paid} = \sum{N_{retrans,paid,i}} -The total carbon accounted for by retranslocation is the sum of the C accounted for by paid-for N uptake (:math:`N_{retrans_paid}`) and by free N uptake (:math:`N_{retrans_free}`). +The total carbon accounted for by retranslocation is the sum of the C accounted for by paid-for N uptake (:math:`N_{retrans_paid}`) and by free N uptake (:math:`N_{retrans_free}`). .. math:: C_{retrans,accounted} = \sum{C_{retrans,accounted,i}}+N_{retrans,free}.CN_{plant} . (1.0 + gr_{frac}) - + The total available carbon in FUN to spend on fixation and active uptake (:math:`C_{tospend}`, gC m\ :sup:`-2`) is calculated as the carbon available minus that account for by retranslocation: @@ -253,99 +253,99 @@ The total available carbon in FUN to spend on fixation and active uptake (:math: Carbon expenditure on fixation and active uptake. -------------------------------------------------------- -At each model timestep, the overall cost of N uptake is calculated (see below) in terms of C:N ratios. The available carbon (:math:`C_{avail}`, g m\ :sup:`-2` s\ :sup:`-1`) is then allocated to two alternative outcomes, payment for N uptake, or conservation for growth. For each carbon conserved for growth, a corresponding quantity of N must be made available. In the case where the plant target C:N ratio is fixed, the partitioning between carbon for growth (:math:`C_{growth}`) and carbon for N uptake (:math:`C_{nuptake}`) is calculated by solving a system of simultaneous equations. First, the carbon available must equal the carbon spent on N uptake plus that saved for growth. +At each model timestep, the overall cost of N uptake is calculated (see below) in terms of C:N ratios. The available carbon (:math:`C_{avail}`, g m\ :sup:`-2` s\ :sup:`-1`) is then allocated to two alternative outcomes, payment for N uptake, or conservation for growth. For each carbon conserved for growth, a corresponding quantity of N must be made available. In the case where the plant target C:N ratio is fixed, the partitioning between carbon for growth (:math:`C_{growth}`) and carbon for N uptake (:math:`C_{nuptake}`) is calculated by solving a system of simultaneous equations. First, the carbon available must equal the carbon spent on N uptake plus that saved for growth. .. math:: - C_{growth}+C_{nuptake}=C_{avail} - + C_{growth}+C_{nuptake}=C_{avail} + Second, the nitrogen acquired from expenditure of N (left hand side of term below) must equal the N that is required to match the growth carbon (right hand side of term below). .. math:: - + C_{nuptake}/N_{cost} =C_{growth}/CN_{target} The solution to these two equated terms can be used to estimate the ideal :math:`C_{nuptake}` as follows, - .. math:: + .. math:: C_{nuptake} =C_{tospend}/ ( (1.0+f_{gr}*(CN_{target} / N_{cost}) + 1) . -and the other C and N fluxes can be determined following the logic above. +and the other C and N fluxes can be determined following the logic above. Modifications to allow variation in C:N ratios -------------------------------------------------------- -The original FUN model as developed by :ref:`Fisher et al. (2010)` and :ref:`Brzostek et al. (2014)` assumes a fixed plant tissue C:N ratio. This means that in the case where N is especially limiting, all excess carbon will be utilized in an attempt to take up more Nitrogen. It has been repeatedly observed, however, that in these circumstances in real life, plants have some flexibility in the C:N stoichiometry of their tissues, and therefore, this assumption may not be realistic. However, the degree to which the C:N ratio varies with N availability is poorly documented, and existing global nitrogen models use a variety of heuristic methods by which to incorporate changing C:N ratios (Zaehle and Friend 2010; Ghimire et al. 2016). This algorithm exists as a placeholder to allow variable C:N ratios to occur, and to allow exploration of how much the parameters controlling their flexibility has on model outcomes. Incorporation of emerging understanding of the controls on tissue stoichiometry should ultimately replace this scheme. +The original FUN model as developed by :ref:`Fisher et al. (2010)` and :ref:`Brzostek et al. (2014)` assumes a fixed plant tissue C:N ratio. This means that in the case where N is especially limiting, all excess carbon will be utilized in an attempt to take up more Nitrogen. It has been repeatedly observed, however, that in these circumstances in real life, plants have some flexibility in the C:N stoichiometry of their tissues, and therefore, this assumption may not be realistic. However, the degree to which the C:N ratio varies with N availability is poorly documented, and existing global nitrogen models use a variety of heuristic methods by which to incorporate changing C:N ratios (Zaehle and Friend 2010; Ghimire et al. 2016). This algorithm exists as a placeholder to allow variable C:N ratios to occur, and to allow exploration of how much the parameters controlling their flexibility has on model outcomes. Incorporation of emerging understanding of the controls on tissue stoichiometry should ultimately replace this scheme. Thus, in CLM5, we introduce the capacity for tissue C:N ratios to be prognostic, rather than static. Overall N and C availability (:math:`N_{uptake}` and :math:`C_{growth}`) and hence tissue C:N ratios, are both determined by FUN. Allocation to individual tissues is discussed in the allocation chapter -Here we introduce an algorithm which adjusts the C expenditure on uptake to allow varying tissue C:N ratios. Increasing C spent on uptake will directly reduce the C:N ratio, and reducing C spent on uptake (retaining more for tissue growth) will increase it. C spent on uptake is impacted by both the N cost in the environment, and the existing tissue C:N ratio of the plant. The output of this algorithm is :math:`\gamma_{FUN}`, the fraction of the ideal :math:`C_{nuptake}` calculated from +Here we introduce an algorithm which adjusts the C expenditure on uptake to allow varying tissue C:N ratios. Increasing C spent on uptake will directly reduce the C:N ratio, and reducing C spent on uptake (retaining more for tissue growth) will increase it. C spent on uptake is impacted by both the N cost in the environment, and the existing tissue C:N ratio of the plant. The output of this algorithm is :math:`\gamma_{FUN}`, the fraction of the ideal :math:`C_{nuptake}` calculated from the FUN equation above - .. math:: + .. math:: C_{nuptake} = C_{nuptake}.\gamma_{FUN} Response of C expenditure to Nitrogen uptake cost ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The environmental cost of Nitrogen (:math:`N_{cost,tot}`) is used to determine :math:`\gamma_{FUN}`. - - .. math:: +The environmental cost of Nitrogen (:math:`N_{cost,tot}`) is used to determine :math:`\gamma_{FUN}`. + + .. math:: \gamma_{FUN} = max(0.0,1.0 - (N_{cost,tot}-a_{cnflex})/b_{cnflex}) -where :math:`a_{cnflex}` and :math:`b_{cnflex}` are parameters fitted to give flexible C:N ranges over the operating range of N costs of the model. Calibration of these parameters should be subject to future testing in idealized experimental settings; they are here intended as a placeholder to allow some flexible stoichiometry, in the absence of adequate understanding of this process. Here :math:`a_{cnflex}` operates as the :math:`N_{cost,tot}` above which there is a modification in the C expenditure (to allow higher C:N ratios), and :math:`b_{cnflex}` is the scalar which determines how much the C expenditure is modified for a given discrepancy between :math:`a_{cnflex}` and the actual cost of uptake. +where :math:`a_{cnflex}` and :math:`b_{cnflex}` are parameters fitted to give flexible C:N ranges over the operating range of N costs of the model. Calibration of these parameters should be subject to future testing in idealized experimental settings; they are here intended as a placeholder to allow some flexible stoichiometry, in the absence of adequate understanding of this process. Here :math:`a_{cnflex}` operates as the :math:`N_{cost,tot}` above which there is a modification in the C expenditure (to allow higher C:N ratios), and :math:`b_{cnflex}` is the scalar which determines how much the C expenditure is modified for a given discrepancy between :math:`a_{cnflex}` and the actual cost of uptake. Response of C expenditure to plant C:N ratios ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ We first calculate a :math:`\delta_{CN}`, which is the difference between the target C:N (:math:`target_{CN}`) a model parameter, and the existing C:N ratio (:math:`CN_{plant}`) - .. math:: - + .. math:: + CN_{plant} = \frac{C_{leaf} + C_{leaf,storage}}{N_{leaf} + N_{leaf,storage})} and - .. math:: + .. math:: \delta_{CN} = CN_{plant} - target_{CN} We then increase :math:`\gamma_{FUN}` to account for situations where (even if N is expensive) plant C:N ratios have increased too far from the target. Where :math:`\delta_{CN}` is negative, we reduce C spent on N uptake and retain more C for growth - + .. math:: - \gamma_{FUN} = - \left\{\begin{array}{lr} + \gamma_{FUN} = + \left\{\begin{array}{lr} \gamma_{FUN}+ 0.5.(delta_{CN}/c_{flexcn})& delta_{CN} > 0\\ \gamma_{FUN}+(1-\gamma_{FUN}).min(1,\delta_{CN}/c_{flexcn}) & delta_{CN} < 0 \end{array}\right\} We then restrict the degree to which C expenditure can be reduced (to prevent unrealistically high C:N ratios) as - .. math:: - \gamma_{FUN} = max(min(1.0,\gamma_{FUN}),0.5) - - + .. math:: + \gamma_{FUN} = max(min(1.0,\gamma_{FUN}),0.5) + + Calculation of N uptake streams from active uptake and fixation ---------------------------------------------------------------- - -Once the final :math:`C_{nuptake}` is known, the fluxes of C to the individual pools can be derived as + +Once the final :math:`C_{nuptake}` is known, the fluxes of C to the individual pools can be derived as .. math:: C_{nuptake,x} = C_{frac,x}.C_{nuptake} - + .. math:: N_{uptake,x} = \frac{C_{nuptake}}{N_{cost}} - - + + Following this, we determine whether the extraction estimates exceed the pool size for each source of N. Where :math:`N_{active,no3} + N_{nonmyc,no3} > N_{avail,no3}`, we calculate the unmet uptake, :math:`N_{unmet,no3}` .. math:: N_{unmet,no3} = N_{active,no3} + N_{nonmyc,no3} - N_{avail,no3} - -then modify both fluxes to account + +then modify both fluxes to account .. math:: @@ -354,14 +354,14 @@ then modify both fluxes to account .. math:: N_{nonmyc,no3} = N_{nonmyc,no3} + N_{unmet,no3}.\frac{N_{nonmyc,no3}}{N_{active,no3}+N_{nonmyc,no3}} - + and similarly, for NH4, where :math:`N_{active,nh4} + N_{nonmyc,nh4} > N_{avail,nh4}`, we calculate the unmet uptake, :math:`N_{unmet,no3}` .. math:: N_{unmet,nh4} = N_{active,nh4} + N_{nonmyc,nh4} - N_{avail,nh4} - -then modify both fluxes to account + +then modify both fluxes to account .. math:: @@ -372,7 +372,7 @@ then modify both fluxes to account N_{nonmyc,nh4} = N_{nonmyc,nh4} + N_{unmet,nh4}.\frac{N_{nonmyc,nh4}}{N_{active,nh4}+N_{nonmyc,nh4}} -and then update the C spent to account for hte new lower N acquisition in that layer/pool. +and then update the C spent to account for hte new lower N acquisition in that layer/pool. .. math:: @@ -380,14 +380,14 @@ and then update the C spent to account for hte new lower N acquisition in that l C_{active,no3} = N_{active,no3}.N_{cost,active,no3}\\ C_{nonmyc,no3} = N_{nonmyc,no3}.N_{cost,nonmyc,no3}\\ C_{nonmyc,no3} = N_{nonmyc,no3}.N_{cost,nonmyc,no3}\\ - -Following this, we determine how much carbon is accounted for for each soil layer. + +Following this, we determine how much carbon is accounted for for each soil layer. .. math:: C_{accounted,x,j} = C_{spent,j,x} - (N_{acquired,j,x}.CN_{plant}.(1.0+ gr_{frac})) - - - + + + diff --git a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst index 87e827c311..5beda23146 100644 --- a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst +++ b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst @@ -4,23 +4,23 @@ Fire ======== The fire parameterization in CLM contains four components: non-peat -fires outside cropland and tropical closed forests, agricultural fires -in cropland, deforestation fires in the tropical closed forests, and -peat fires (see :ref:`Li et al. 2012a `, -:ref:`Li et al. 2012b `, :ref:`Li et al. 2013 `, -:ref:`Li and Lawrence 2017 ` for details). +fires outside cropland and tropical closed forests, agricultural fires +in cropland, deforestation fires in the tropical closed forests, and +peat fires (see :ref:`Li et al. 2012a `, +:ref:`Li et al. 2012b `, :ref:`Li et al. 2013 `, +:ref:`Li and Lawrence 2017 ` for details). In this fire parameterization, burned area is affected by climate and -weather conditions, vegetation composition and structure, and human +weather conditions, vegetation composition and structure, and human activities. After burned area is calculated, we estimate the fire impact, -including biomass and peat burning, fire-induced vegetation mortality, -adjustment of the carbon and nitrogen (C/N) pools, and fire emissions. +including biomass and peat burning, fire-induced vegetation mortality, +adjustment of the carbon and nitrogen (C/N) pools, and fire emissions. .. _Non-peat fires outside cropland and tropical closed forest: Non-peat fires outside cropland and tropical closed forest --------------------------------------------------------------- -Burned area in a grid cell, \ :math:`A_{b}` (km\ :sup:`2` s :sup:`-1`), +Burned area in a grid cell, \ :math:`A_{b}` (km\ :sup:`2` s :sup:`-1`), is determined by .. math:: @@ -58,9 +58,9 @@ related to the socioeconomic conditions. N_{i} = \left(I_{n} +I_{a} \right) A_{g} -where :math:`I_{n}` (count km\ :sup:`-2` s\ :sup:`-1`) and :math:`I_{a}` -(count km\ :sup:`-2` s\ :sup:`-1`) are the number of natural and anthropogenic -ignitions per km\ :sup:`2`, respectively; :math:`A_{g}` is the area of the +where :math:`I_{n}` (count km\ :sup:`-2` s\ :sup:`-1`) and :math:`I_{a}` +(count km\ :sup:`-2` s\ :sup:`-1`) are the number of natural and anthropogenic +ignitions per km\ :sup:`2`, respectively; :math:`A_{g}` is the area of the grid cell (km\ :sup:`2`). :math:`I_{n}` is estimated by .. math:: @@ -70,9 +70,9 @@ grid cell (km\ :sup:`2`). :math:`I_{n}` is estimated by where :math:`\gamma` \ =0.22 is ignition efficiency of cloud-to-ground lightning; :math:`\psi =\frac{1}{5.16+2.16\cos [3min(60,\lambda )]}` is the -cloud-to-ground lightning fraction and depends on the latitude -:math:`\lambda` (degrees) ; :math:`I_{l}` (flash km\ :sup:`-2` s\ :sup:`-1`) is -the total lightning flashes. :math:`I_{a}` is modeled as a monotonic +cloud-to-ground lightning fraction and depends on the latitude +:math:`\lambda` (degrees) ; :math:`I_{l}` (flash km\ :sup:`-2` s\ :sup:`-1`) is +the total lightning flashes. :math:`I_{a}` is modeled as a monotonic increasing function of population density: .. math:: @@ -90,51 +90,51 @@ Fuel availability :math:`f_{b}` is given as .. math:: :label: 23.6 - f_{b} =\left\{\begin{array}{c} + f_{b} =\left\{\begin{array}{c} {0} \\ {\frac{B_{ag} -B_{low} }{B_{up} -B_{low} } } \\ {1} \end{array} - \begin{array}{cc} {} & {} \end{array}\begin{array}{c} {B_{ag} B_{up} } + \begin{array}{cc} {} & {} \end{array}\begin{array}{c} {B_{ag} B_{up} } \end{array}\right\} \ , -where :math:`B_{ag}` (g C m\ :sup:`-2`) is the biomass of combined leaf, -stem, litter, and woody debris pools; :math:`B_{low}` = 105 g C m :sup:`-2` -is the lower fuel threshold below which fire does not occur; :math:`B_{up}` -= 1050 g C m\ :sup:`-2` is the upper fuel threshold above which fire -occurrence is not limited by fuel availability. +where :math:`B_{ag}` (g C m\ :sup:`-2`) is the biomass of combined leaf, +stem, litter, and woody debris pools; :math:`B_{low}` = 105 g C m :sup:`-2` +is the lower fuel threshold below which fire does not occur; :math:`B_{up}` += 1050 g C m\ :sup:`-2` is the upper fuel threshold above which fire +occurrence is not limited by fuel availability. Fuel combustibility :math:`f_{m}` is estimated by .. math:: - :label: 23.7 + :label: 23.7 f_{m} = {f_{RH} f_{\beta}}, &\qquad T_{17cm} > T_{f} - -where :math:`f_{RH}` and :math:`f_{\beta }` represent the dependence of -fuel combustibility on relative humidity :math:`RH` (%) and root-zone -soil moisture limitation :math:`\beta` (fraction); :math:`T_{17cm}` is -the temperature of the top 17 cm of soil (K) and :math:`T_{f}` is the -freezing temperature. :math:`f_{RH}` is a weighted average of real time -:math:`RH` (:math:`RH_{0}`) and 30-day running mean :math:`RH` -(:math:`RH_{30d}`): + +where :math:`f_{RH}` and :math:`f_{\beta }` represent the dependence of +fuel combustibility on relative humidity :math:`RH` (%) and root-zone +soil moisture limitation :math:`\beta` (fraction); :math:`T_{17cm}` is +the temperature of the top 17 cm of soil (K) and :math:`T_{f}` is the +freezing temperature. :math:`f_{RH}` is a weighted average of real time +:math:`RH` (:math:`RH_{0}`) and 30-day running mean :math:`RH` +(:math:`RH_{30d}`): .. math:: :label: 23.8 - + f_{RH} = (1-w) l_{RH_{0}} + wl_{RH_{30d}} -where weight :math:`w=\max [0,\min (1,\frac{B_{ag}-2500}{2500})]`, -:math:`l_{{RH}_{0}}=1-\max [0,\min (1,\frac{RH_{0}-30}{80-30})]`, and -:math:`l_{{RH}_{30d}}=1-\max [0.75,\min (1,\frac{RH_{30d}}{90})]`. +where weight :math:`w=\max [0,\min (1,\frac{B_{ag}-2500}{2500})]`, +:math:`l_{{RH}_{0}}=1-\max [0,\min (1,\frac{RH_{0}-30}{80-30})]`, and +:math:`l_{{RH}_{30d}}=1-\max [0.75,\min (1,\frac{RH_{30d}}{90})]`. :math:`f_{\beta}` is given by .. math:: :label: 23.9 - f_{\beta } =\left\{\begin{array}{cccc} - {1} & {} & {} & {\beta\le \beta_{low} } \\ {\frac{\beta_{up} -\beta}{\beta_{up} -\beta_{low} } } & {} & {} & {\beta_{low} <\beta<\beta_{up} } \\ - {0} & {} & {} & {\beta\ge \beta_{up} } + f_{\beta } =\left\{\begin{array}{cccc} + {1} & {} & {} & {\beta\le \beta_{low} } \\ {\frac{\beta_{up} -\beta}{\beta_{up} -\beta_{low} } } & {} & {} & {\beta_{low} <\beta<\beta_{up} } \\ + {0} & {} & {} & {\beta\ge \beta_{up} } \end{array}\right\} \ , -where :math:`\beta _{low}` \ =0.85 and :math:`\beta _{up}` \ =0.98 are the +where :math:`\beta _{low}` \ =0.85 and :math:`\beta _{up}` \ =0.98 are the lower and upper thresholds, respectively. For scarcely populated regions (:math:`D_{p} \le 0.1` person @@ -149,8 +149,8 @@ activities as f_{se,o} =f_{d} f_{e} -where :math:`{f}_{d}` and :math:`{f}_{e}` are the effects of the -demographic and economic conditions on fire occurrence. The demographic +where :math:`{f}_{d}` and :math:`{f}_{e}` are the effects of the +demographic and economic conditions on fire occurrence. The demographic influence on fire occurrence is .. math:: @@ -171,15 +171,15 @@ which captures 73% of the observed MODIS fire counts with variable GDP in regions where shrub and grass PFTs are dominant (fractional coverage of shrub and grass PFTs :math:`>` 50%). In regions outside tropical closed forests and dominated by trees (fractional coverage of tree PFTs -:math:`>` 50%), we use +:math:`>` 50%), we use .. math:: :label: 23.13 - f_{e} =\left\{\begin{array}{c} + f_{e} =\left\{\begin{array}{c} {0.39} \\ {0.79} \\ {1} \end{array} - \begin{array}{cc} {} & {} \end{array}\begin{array}{c} {GDP > 20 } \\ - { 8 < GDP \le 20 } \\ { GDP \le 8 } + \begin{array}{cc} {} & {} \end{array}\begin{array}{c} {GDP > 20 } \\ + { 8 < GDP \le 20 } \\ { GDP \le 8 } \end{array}\right\} \ , to reproduce the relationship between MODIS fire counts and GDP. @@ -214,9 +214,9 @@ as: a^{*} =\pi \frac{l}{2} \frac{w}{2} \times 10^{-6} =\frac{\pi u_{p}^{2} \tau ^{2} }{4L_{B} } (1+\frac{1}{H_{B} } )^{2} \times 10^{-6} -where :math:`u_{p}` (m s\ :sup:`-1`) is the fire spread rate in the -downwind direction; :math:`\tau` (s) is average fire duration; :math:`L_{B}` -and :math:`H_{B}` are length-to-breadth ratio and head-to-back ratio of +where :math:`u_{p}` (m s\ :sup:`-1`) is the fire spread rate in the +downwind direction; :math:`\tau` (s) is average fire duration; :math:`L_{B}` +and :math:`H_{B}` are length-to-breadth ratio and head-to-back ratio of the ellipse; 10 :sup:`-6` converts m :sup:`2` to km :sup:`2`. According to :ref:`Arora and Boer (2005)`, @@ -242,14 +242,14 @@ The fire spread rate in the downwind direction is represented as u_{p} =u_{\max } C_{m} g(W) -(:ref:`Arora and Boer, 2005`), where :math:`u_{\max }` +(:ref:`Arora and Boer, 2005`), where :math:`u_{\max }` (m s\ :sup:`-1`) is the PFT-dependent average maximum fire spread rate in natural vegetation regions; :math:`C_{m} =\sqrt{f_{m}}` and :math:`g(W)` represent the dependence of :math:`u_{p}` on fuel wetness and wind -speed :math:`W`, respectively. :math:`u_{\max }` is set to 0.33 -m s :sup:`-1`\ for grass PFTs, 0.28 m s :sup:`-1` for shrub PFTs, 0.26 -m s\ :sup:`-1` for needleleaf tree PFTs, and 0.25 m s\ :sup:`-1` for -other tree PFTs. :math:`g(W)` is derived from the mathematical properties +speed :math:`W`, respectively. :math:`u_{\max }` is set to 0.33 +m s :sup:`-1`\ for grass PFTs, 0.28 m s :sup:`-1` for shrub PFTs, 0.26 +m s\ :sup:`-1` for needleleaf tree PFTs, and 0.25 m s\ :sup:`-1` for +other tree PFTs. :math:`g(W)` is derived from the mathematical properties of the ellipse and equation :eq:`23.16` and :eq:`23.17`. .. math:: @@ -269,7 +269,7 @@ when :math:`W\to \infty` , g(0) can be derived as In the absence of globally gridded data on barriers to fire (e.g. rivers, lakes, roads, firebreaks) and human fire-fighting efforts, average fire duration is simply assumed equal to 1 which is the observed -2001–2004 mean persistence of most fires in the world +2001–2004 mean persistence of most fires in the world (:ref:`Giglio et al. 2006 `). As with the socioeconomic influence on fire occurrence, we assume that @@ -315,12 +315,12 @@ and .. math:: :label: 23.25 - F_{e} =\left\{\begin{array}{cc} - {0.62,} & {GDP>20} \\ {0.83,} & {820} \\ {0.83,} & {8` that shows the -2001-2009 average contribution of cropland fires is 4.7% of the total +where :math:`a_{1}` (s\ :sup:`-1`) is a constant; :math:`f_{se}` represents +the socioeconomic effect on fires; :math:`f_{t}` determines the seasonality +of agricultural fires; :math:`f_{crop}` is the fractional coverage of +cropland. :math:`a_{1}` \ = 1.6x10\ :sup:`-4` \hr\ :sup:`-1`\ is estimated +using an inverse method, by matching 1997-2004 simulations to the analysis +of :ref:`van der Werf et al. (2010) ` that shows the +2001-2009 average contribution of cropland fires is 4.7% of the total global burned area. The socioeconomic factor :math:`f_{se}` is given as follows: @@ -432,8 +432,8 @@ and f_{e} =0.01+0.99\times \exp (-\pi \frac{GDP}{10} ) are the effects of population density and GDP on burned area, derived -in a similar way to equation :eq:`23.32` and :eq:`23.33`. :math:`f_{t}` -is set to 1 at the first time step during the climatological peak month +in a similar way to equation :eq:`23.32` and :eq:`23.33`. :math:`f_{t}` +is set to 1 at the first time step during the climatological peak month for agricultural fires (:ref:`van der Werf et al. 2010 `); :math:`{f}_{t}` is set to 0 otherwise. Peak month in this dataset correlates with the month after harvesting or the @@ -441,13 +441,13 @@ month before planting. In CLM we use this dataset the same way whether the CROP option is active or not, without regard to the CROP option's simulated planting and harvesting dates. -In the post-fire region, fire impact is parameterized similar to section -:numref:`Fire impact` but with combustion completeness factors and tissue -mortality factors for crop PFTs +In the post-fire region, fire impact is parameterized similar to section +:numref:`Fire impact` but with combustion completeness factors and tissue +mortality factors for crop PFTs (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). .. _Deforestation fires: - + Deforestation fires ------------------------ @@ -473,8 +473,8 @@ conditions on the burned area. Constants :math:`b` and :math:`{f}_{lu}` are calibrated based on observations and reanalysis datasets in the Amazon rainforest -(tropical closed forests within 15.5 :sup:`o` S :math:`\text{-}` 10.5 -:sup:`o` N, 30.5 :sup:`o` W :math:`\text{-}` 91 :sup:`o` W). +(tropical closed forests within 15.5 :sup:`o` S :math:`\text{-}` 10.5 +:sup:`o` N, 30.5 :sup:`o` W :math:`\text{-}` 91 :sup:`o` W). :math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as .. math:: @@ -490,33 +490,33 @@ The effect of climate on deforestation fires is parameterized as: .. math:: :label: 23.36 - \begin{array}{ll} + \begin{array}{ll} f_{cli,d} \quad = & \quad \max \left[0,\min (1,\frac{b_{2} -P_{60d} }{b_{2} } )\right]^{0.5} \times \\ - & \quad \max \left[0,\min (1,\frac{b_{3} -P_{10d} }{b_{3} } )\right]^{0.5} \times \\ + & \quad \max \left[0,\min (1,\frac{b_{3} -P_{10d} }{b_{3} } )\right]^{0.5} \times \\ & \quad \max \left[0,\min (1,\frac{0.25-P}{0.25} )\right] \end{array} -where :math:`P` (mm d :sup:`-1`) is instantaneous precipitation, while -:math:`P_{60d}` (mm d\ :sup:`-1`) and :math:`P_{10d}` (mm d :sup:`-1`) -are 60-day and 10-day running means of precipitation, respectively; -:math:`b_{2}` (mm d :sup:`-1`) and :math:`b_{3}` (mm d :sup:`-1`) are +where :math:`P` (mm d :sup:`-1`) is instantaneous precipitation, while +:math:`P_{60d}` (mm d\ :sup:`-1`) and :math:`P_{10d}` (mm d :sup:`-1`) +are 60-day and 10-day running means of precipitation, respectively; +:math:`b_{2}` (mm d :sup:`-1`) and :math:`b_{3}` (mm d :sup:`-1`) are the grid-cell dependent thresholds of :math:`P_{60d}` and :math:`P_{10d}` ; -0.25 mm d :sup:`-1` is the maximum precipitation rate for drizzle. -:ref:`Le Page et al. (2010) ` analyzed the relationship -between large-scale deforestation fire counts and precipitation during 2003 -:math:`\text{-}`\ 2006 in southern Amazonia where tropical evergreen trees -(BET Tropical) are dominant. Figure 2 in -:ref:`Le Page et al. (2010) ` showed that fires generally -occurred if both :math:`P_{60d}` and :math:`P_{10d}` were less than about -4.0 mm d :sup:`-1`, and fires occurred more frequently in a drier environment. -Based on the 30-yr (1985 to 2004) precipitation data in -:ref:`Qian et al. (2006) `. The climatological precipitation -of dry months (P < 4.0 mm d :sup:`-1`) in a year over tropical deciduous -tree (BDT Tropical) dominated regions is 46% of that over BET Tropical -dominated regions, so we set the PFT-dependent thresholds of :math:`P_{60d}` -and :math:`P_{10d}` as 4.0 mm d :sup:`-1` for BET Tropical and 1.8 mm d -:sup:`-1` (= 4.0 mm d :sup:`-1` :math:`\times` 46%) for BDT Tropical, and -:math:`b`\ :sub:`2` and :math:`b`\ :sub:`3` are the average of thresholds +0.25 mm d :sup:`-1` is the maximum precipitation rate for drizzle. +:ref:`Le Page et al. (2010) ` analyzed the relationship +between large-scale deforestation fire counts and precipitation during 2003 +:math:`\text{-}`\ 2006 in southern Amazonia where tropical evergreen trees +(BET Tropical) are dominant. Figure 2 in +:ref:`Le Page et al. (2010) ` showed that fires generally +occurred if both :math:`P_{60d}` and :math:`P_{10d}` were less than about +4.0 mm d :sup:`-1`, and fires occurred more frequently in a drier environment. +Based on the 30-yr (1985 to 2004) precipitation data in +:ref:`Qian et al. (2006) `. The climatological precipitation +of dry months (P < 4.0 mm d :sup:`-1`) in a year over tropical deciduous +tree (BDT Tropical) dominated regions is 46% of that over BET Tropical +dominated regions, so we set the PFT-dependent thresholds of :math:`P_{60d}` +and :math:`P_{10d}` as 4.0 mm d :sup:`-1` for BET Tropical and 1.8 mm d +:sup:`-1` (= 4.0 mm d :sup:`-1` :math:`\times` 46%) for BDT Tropical, and +:math:`b`\ :sub:`2` and :math:`b`\ :sub:`3` are the average of thresholds of BET Tropical and BDT Tropical weighted bytheir coverage. The post-fire area due to deforestation is not limited to land-type @@ -526,8 +526,8 @@ to the fraction of conversion flux for tropical trees in the tree-reduced region (60%) assigned by CLM4-CN, to reach the maximum fire carbon emissions in a conversion region requires burning this region about twice when we set PFT-dependent combustion completeness factors to -about 0.3 for stem [the mean of 0.2\ :math:`{-}`\ 0.4 used in -:ref:`van der Werf et al. (2010) `. Therefore, when +about 0.3 for stem [the mean of 0.2\ :math:`{-}`\ 0.4 used in +:ref:`van der Werf et al. (2010) `. Therefore, when the burned area calculated from equation :eq:`23.36` is no more than twice the tree-reduced area, we assume no escaped fires outside the land-type conversion region, and the fire-related fraction @@ -550,16 +550,16 @@ The burned area due to peat fires is given as :math:`{A}_{b}`: A_{b} = c \ f_{cli,p} f_{peat} (1 - f_{sat} ) A_{g} -where :math:`c` (s\ :sup:`-1`) is a constant; :math:`f_{cli,p}` represents -the effect of climate on the burned area; :math:`f_{peat}` is the fractional -coverage of peatland in the grid cell; and :math:`f_{sat}` is the fraction -of the grid cell with a water table at the surface or higher. :math:`c` = 0.17 -:math:`\times` 10 :sup:`-3` hr\ :sup:`-1` for tropical peat fires and -:math:`c` = 0.9 :math:`\times` 10 :sup:`-5` hr :sup:`-1` for boreal peat fires -are derived using an inverse method, by matching simulations to earlier -studies: about 2.4 Mha peatland was burned over Indonesia in 1997 -(:ref:`Page et al. 2002 `) and the average burned area of peat -fires in Western Canada was 0.2 Mha yr :sup:`-1` for 1980-1999 +where :math:`c` (s\ :sup:`-1`) is a constant; :math:`f_{cli,p}` represents +the effect of climate on the burned area; :math:`f_{peat}` is the fractional +coverage of peatland in the grid cell; and :math:`f_{sat}` is the fraction +of the grid cell with a water table at the surface or higher. :math:`c` = 0.17 +:math:`\times` 10 :sup:`-3` hr\ :sup:`-1` for tropical peat fires and +:math:`c` = 0.9 :math:`\times` 10 :sup:`-5` hr :sup:`-1` for boreal peat fires +are derived using an inverse method, by matching simulations to earlier +studies: about 2.4 Mha peatland was burned over Indonesia in 1997 +(:ref:`Page et al. 2002 `) and the average burned area of peat +fires in Western Canada was 0.2 Mha yr :sup:`-1` for 1980-1999 (:ref:`Turetsky et al. 2004 `). For tropical peat fires, :math:`f_{cli,p}` is set as a function of @@ -580,29 +580,29 @@ For boreal peat fires, :math:`f_{cli,p}` is set to where :math:`\theta _{17cm}` is the wetness of the top 17 cm of soil. Peat fires lead to peat burning and the combustion and mortality of -vegetation over peatlands. For tropical peat fires, based on -:ref:`Page et al. (2002) `, about 6% of the peat carbon loss -from stored carbon is caused by 33.9% of the peatland burned. Carbon emissions -due to peat burning (g C m\ :sup:`-2` s\ :sup:`-1`) are therefore set as the -product of 6%/33.9%, burned area fraction of peat fire (s\ :sup:`-1`), and -soil organic carbon (g C m\ :sup:`-2`). For boreal peat fires, the carbon -emissions due to peat burning are set as 2.2 kg C m\ :sup:`-2` \ peat fire -area (:ref:`Turetsky et al. 2002 `). Biomass combustion -and vegetation mortality in post-fire peatlands are set the same as section -:numref:`Fire impact` for non-crop PFTs and as section +vegetation over peatlands. For tropical peat fires, based on +:ref:`Page et al. (2002) `, about 6% of the peat carbon loss +from stored carbon is caused by 33.9% of the peatland burned. Carbon emissions +due to peat burning (g C m\ :sup:`-2` s\ :sup:`-1`) are therefore set as the +product of 6%/33.9%, burned area fraction of peat fire (s\ :sup:`-1`), and +soil organic carbon (g C m\ :sup:`-2`). For boreal peat fires, the carbon +emissions due to peat burning are set as 2.2 kg C m\ :sup:`-2` \ peat fire +area (:ref:`Turetsky et al. 2002 `). Biomass combustion +and vegetation mortality in post-fire peatlands are set the same as section +:numref:`Fire impact` for non-crop PFTs and as section :numref:`Agricultural fires` for crops PFTs. .. _Fire trace gas and aerosol emissions: Fire trace gas and aerosol emissions ------------------------------------- -CESM2 is the first Earth system model that can model the full coupling -among fire, fire emissions, land, and atmosphere. CLM5, as the land -component of CESM2, calculates the surface trace gas and aerosol emissions -due to fire and fire emission heights, as the inputs of atmospheric -chemistry model and aerosol model. +CESM2 is the first Earth system model that can model the full coupling +among fire, fire emissions, land, and atmosphere. CLM5, as the land +component of CESM2, calculates the surface trace gas and aerosol emissions +due to fire and fire emission heights, as the inputs of atmospheric +chemistry model and aerosol model. -Emissions for trace gas and aerosol species x and the j-th PFT, :math:`E_{x,j}` +Emissions for trace gas and aerosol species x and the j-th PFT, :math:`E_{x,j}` (g species s\ :sup:`-1`), are given by .. math:: @@ -610,17 +610,17 @@ Emissions for trace gas and aerosol species x and the j-th PFT, :math:`E_{x,j}` E_{x,j} = EF_{x,j}\frac{\phi _{j} }{[C]}. -Here, :math:`EF_{x,j}` (g species (g dm)\ :sup:`-1`) is PFT-dependent emission -factor scaled from biome-level values (Li et al., in prep, also used for FireMIP -fire emissions data) by Dr. Val Martin and Dr. Li. :math:`[C]` = 0.5 -(g C (g dm)\ :sup:`-1`) is a conversion factor from dry matter to carbon. +Here, :math:`EF_{x,j}` (g species (g dm)\ :sup:`-1`) is PFT-dependent emission +factor scaled from biome-level values (Li et al., in prep, also used for FireMIP +fire emissions data) by Dr. Val Martin and Dr. Li. :math:`[C]` = 0.5 +(g C (g dm)\ :sup:`-1`) is a conversion factor from dry matter to carbon. -Emission height is PFT-dependent: 4.3 km for needleleaf tree PFTs, 3 km for other -boreal and temperate tree PFTs, 2.5 km for tropical tree PFTs, 2 km for shrub -PFTs, and 1 km for grass and crop PFTs. These values are compiled from earlier -studies by Dr. Val Martin. +Emission height is PFT-dependent: 4.3 km for needleleaf tree PFTs, 3 km for other +boreal and temperate tree PFTs, 2.5 km for tropical tree PFTs, 2 km for shrub +PFTs, and 1 km for grass and crop PFTs. These values are compiled from earlier +studies by Dr. Val Martin. -.. _Table PFT-specific combustion completeness and fire mortality factors: +.. _Table PFT-specific combustion completeness and fire mortality factors: .. table:: PFT-specific combustion completeness and fire mortality factors. diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index e97cb89139..b46b73ae6a 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -75,9 +75,9 @@ where :math:`T_{atm}` is the air temperature (K) at height :math:`z_{atm,\, h}` and :math:`\Gamma _{d} =0.0098` K m\ :sup:`-1` is the negative of the dry adiabatic lapse rate [this expression is first-order equivalent to -:math:`\theta _{atm} =T_{atm} \left({P_{srf} \mathord{\left/ {\vphantom {P_{srf} P_{atm} }} \right.} P_{atm} } \right)^{{R_{da} \mathord{\left/ {\vphantom {R_{da} C_{p} }} \right.} C_{p} } }` +:math:`\theta _{atm} =T_{atm} \left({P_{srf} \mathord{\left/ {\vphantom {P_{srf} P_{atm} }} \right.} P_{atm} } \right)^{{R_{da} \mathord{\left/ {\vphantom {R_{da} C_{p} }} \right.} C_{p} } }` (:ref:`Stull 1988 `), where :math:`P_{srf}` is the surface pressure (Pa), -:math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`R_{da}` +:math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`)]. By definition, :math:`\theta _{s} =T_{s}` . The density of moist air (kg m\ :sup:`-3`) is @@ -87,7 +87,7 @@ is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table P \rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} } where the atmospheric vapor pressure :math:`e_{atm}` (Pa) is derived -from the atmospheric specific humidity :math:`q_{atm}` +from the atmospheric specific humidity :math:`q_{atm}` .. math:: :label: 5.9 @@ -100,7 +100,7 @@ Monin-Obukhov Similarity Theory ----------------------------------- The surface vertical kinematic fluxes of momentum -:math:`\overline{u'w'}` and :math:`\overline{v'w'}` (m\ :sup:`2` s\ :sub:`-2`), sensible heat :math:`\overline{\theta 'w'}` +:math:`\overline{u'w'}` and :math:`\overline{v'w'}` (m\ :sup:`2` s\ :sub:`-2`), sensible heat :math:`\overline{\theta 'w'}` (K m s :sup:`-1`), and latent heat :math:`\overline{q'w'}` (kg kg\ :sup:`-1` m s\ :sup:`-1`), where :math:`u'`, :math:`v'`, :math:`w'`, :math:`\theta '`, and :math:`q'` are zonal horizontal wind, meridional horizontal wind, vertical velocity, potential temperature, @@ -190,7 +190,7 @@ Following :ref:`Panofsky and Dutton (1984)`, the differentia :math:`\phi _{h} \left(\zeta \right)`, and :math:`\phi _{w} \left(\zeta \right)` can be integrated formally without commitment to their exact forms. Integration between two arbitrary -heights in the surface layer :math:`z_{2}` and :math:`z_{1}` +heights in the surface layer :math:`z_{2}` and :math:`z_{1}` (:math:`z_{2} >z_{1}` ) with horizontal winds :math:`\left|{\it u}\right|_{1}` and :math:`\left|{\it u}\right|_{2}` , potential temperatures :math:`\theta _{1}` and :math:`\theta _{2}` , @@ -242,7 +242,7 @@ Defining the surface values .. math:: q_{1} =q_{s} {\rm \; at\; }z_{1} =z_{0w} +d, -and the atmospheric values at :math:`z_{2} =z_{atm,\, x}` +and the atmospheric values at :math:`z_{2} =z_{atm,\, x}` .. math:: :label: 5.24 @@ -280,9 +280,9 @@ surface fluxes as follows :label: 5.28 U_{c} = \left\{ - \begin{array}{ll} - 0 & \qquad \zeta \ge {\rm 0} \quad {\rm (stable)} \\ - \beta w_{*} & \qquad \zeta < 0 \quad {\rm (unstable)} + \begin{array}{ll} + 0 & \qquad \zeta \ge {\rm 0} \quad {\rm (stable)} \\ + \beta w_{*} & \qquad \zeta < 0 \quad {\rm (unstable)} \end{array} \right\} where :math:`w_{*}` is the convective velocity scale @@ -299,11 +299,11 @@ The momentum flux gradient relations are (:ref:`Zeng et al. 1998 ` .. math:: :label: 5.30 - \begin{array}{llr} - \phi _{m} \left(\zeta \right)=0.7k^{{2\mathord{\left/ {\vphantom {2 3}} \right.} 3} } \left(-\zeta \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } & \qquad {\rm for\; }\zeta <-1.574 & \ {\rm \; (very\; unstable)} \\ - \phi _{m} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 4}} \right.} 4} } & \qquad {\rm for\; -1.574}\le \zeta <0 & \ {\rm \; (unstable)} \\ - \phi _{m} \left(\zeta \right)=1+5\zeta & \qquad {\rm for\; }0\le \zeta \le 1& \ {\rm \; (stable)} \\ - \phi _{m} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm\; (very\; stable).} + \begin{array}{llr} + \phi _{m} \left(\zeta \right)=0.7k^{{2\mathord{\left/ {\vphantom {2 3}} \right.} 3} } \left(-\zeta \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } & \qquad {\rm for\; }\zeta <-1.574 & \ {\rm \; (very\; unstable)} \\ + \phi _{m} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 4}} \right.} 4} } & \qquad {\rm for\; -1.574}\le \zeta <0 & \ {\rm \; (unstable)} \\ + \phi _{m} \left(\zeta \right)=1+5\zeta & \qquad {\rm for\; }0\le \zeta \le 1& \ {\rm \; (stable)} \\ + \phi _{m} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm\; (very\; stable).} \end{array} The sensible and latent heat flux gradient relations are (:ref:`Zeng et al. 1998 `) @@ -311,11 +311,11 @@ The sensible and latent heat flux gradient relations are (:ref:`Zeng et al. 1998 .. math:: :label: 5.31 - \begin{array}{llr} - \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=0.9k^{{4\mathord{\left/ {\vphantom {4 3}} \right.} 3} } \left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } & \qquad {\rm for\; }\zeta <-0.465 & \ {\rm \; (very\; unstable)} \\ - \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} } & \qquad {\rm for\; -0.465}\le \zeta <0 & \ {\rm \; (unstable)} \\ - \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=1+5\zeta & \qquad {\rm for\; }0\le \zeta \le 1 & \ {\rm \; (stable)} \\ - \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm \; (very\; stable).} + \begin{array}{llr} + \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=0.9k^{{4\mathord{\left/ {\vphantom {4 3}} \right.} 3} } \left(-\zeta \right)^{{-1\mathord{\left/ {\vphantom {-1 3}} \right.} 3} } & \qquad {\rm for\; }\zeta <-0.465 & \ {\rm \; (very\; unstable)} \\ + \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} } & \qquad {\rm for\; -0.465}\le \zeta <0 & \ {\rm \; (unstable)} \\ + \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=1+5\zeta & \qquad {\rm for\; }0\le \zeta \le 1 & \ {\rm \; (stable)} \\ + \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm \; (very\; stable).} \end{array} To ensure continuous functions of @@ -355,7 +355,7 @@ Very stable :math:`\left(\zeta >1\right)` .. math:: :label: 5.35 - + V_{a} =\frac{u_{*} }{k} \left\{\left[\ln \frac{L}{z_{0m} } +5\right]+\left[5\ln \zeta +\zeta -1\right]-5\frac{z_{0m} }{L} \right\} where @@ -459,7 +459,7 @@ is related to :math:`\zeta` (:ref:`Arya 2001 `) as R_{iB} =\zeta \left[\ln \left(\frac{z_{atm,\, h} -d}{z_{0h} } \right)-\psi _{h} \left(\zeta \right)\right]\left[\ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)-\psi _{m} \left(\zeta \right)\right]^{-2} . Using -:math:`\phi _{h} =\phi _{m}^{2} =\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} }` +:math:`\phi _{h} =\phi _{m}^{2} =\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} }` for unstable conditions and :math:`\phi _{h} =\phi _{m} =1+5\zeta` for stable conditions to determine :math:`\psi _{m} \left(\zeta \right)` and :math:`\psi _{h} \left(\zeta \right)`, the inverse relationship @@ -470,7 +470,7 @@ guess for :math:`\zeta` and thus :math:`L` from :label: 5.48 \begin{array}{lcr} - \zeta =\frac{R_{iB} \ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)}{1-5\min \left(R_{iB} ,0.19\right)} & \qquad 0.01\le \zeta \le 2 & \qquad {\rm for\; }R_{iB} \ge 0 {\rm \; (neutral\; or\; stable)} \\ + \zeta =\frac{R_{iB} \ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)}{1-5\min \left(R_{iB} ,0.19\right)} & \qquad 0.01\le \zeta \le 2 & \qquad {\rm for\; }R_{iB} \ge 0 {\rm \; (neutral\; or\; stable)} \\ \zeta =R_{iB} \ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right) & \qquad -100\le \zeta \le -0.01 & \qquad {\rm for\; }R_{iB} <0 \ {\rm \; (unstable)} \end{array}. @@ -484,10 +484,10 @@ Upon iteration (section :numref:`Numerical Implementation`), the following is us where -.. math:: +.. math:: - \begin{array}{cr} - 0.01\le \zeta \le 2 & \qquad {\rm for\; }\zeta \ge 0{\rm \; (neutral\; or\; stable)} \\ + \begin{array}{cr} + 0.01\le \zeta \le 2 & \qquad {\rm for\; }\zeta \ge 0{\rm \; (neutral\; or\; stable)} \\ {\rm -100}\le \zeta \le {\rm -0.01} & \qquad {\rm for\; }\zeta <0{\rm \; (unstable)} \end{array}. @@ -571,7 +571,7 @@ with the 10-m wind speed calculated for the dust model as described in Chapter :numref:`rst_Dust Model`) .. math:: - :label: 5.61 + :label: 5.61 u_{10m} =\left\{\begin{array}{l} {V_{a} \qquad z_{atm,\, m} \le 10} \\ {V_{a} -\frac{u_{*} }{k} \left[\ln \left(\frac{z_{atm,\, m} -d}{10+z_{0m} } \right)-\psi _{m} \left(\frac{z_{atm,\, m} -d}{L} \right)+\psi _{m} \left(\frac{10+z_{0m} }{L} \right)\right]\qquad z_{atm,\, m} >10} \end{array}\right\} @@ -581,7 +581,7 @@ Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces -------------------------------------------------------------- Surfaces are considered non-vegetated for the surface flux calculations -if leaf plus stem area index :math:`L+S<0.05` (section +if leaf plus stem area index :math:`L+S<0.05` (section :numref:`Phenology and vegetation burial by snow`). By definition, this includes bare soil and glaciers. The solution for lakes is described in Chapter :numref:`rst_Lake Model`. For these surfaces, the @@ -601,17 +601,17 @@ temperatures of the soil :math:`T_{1}` , snow :math:`T_{snl+1}` , and surface water :math:`T_{h2osfc}` are .. math:: - :label: 5.63 + :label: 5.63 H_{soil} =-\rho _{atm} C_{p} \frac{\left(\theta _{atm} -T_{1} \right)}{r_{ah} } .. math:: - :label: 5.64 + :label: 5.64 H_{sno} =-\rho _{atm} C_{p} \frac{\left(\theta _{atm} -T_{snl+1} \right)}{r_{ah} } .. math:: - :label: 5.65 + :label: 5.65 H_{h2osfc} =-\rho _{atm} C_{p} \frac{\left(\theta _{atm} -T_{h2osfc} \right)}{r_{ah} } @@ -621,7 +621,7 @@ where :math:`\rho _{atm}` is the density of atmospheric air (kg m\ :sup:`-3`), :math:`r_{ah}` is the aerodynamic resistance to sensible heat transfer (s m\ :sup:`-1`). -The water vapor flux :math:`E_{g}` (kg m\ :sup:`-2` s\ :sup:`-1`) is, with reference to +The water vapor flux :math:`E_{g}` (kg m\ :sup:`-2` s\ :sup:`-1`) is, with reference to :numref:`Figure Schematic diagram of latent heat fluxes`, .. math:: @@ -630,33 +630,33 @@ The water vapor flux :math:`E_{g}` (kg m\ :sup:`-2` s\ :sup:`-1`) is, with refe E_{g} =\left(1-f_{sno} -f_{h2osfc} \right)E_{soil} +f_{sno} E_{snow} +f_{h2osfc} E_{h2osfc} .. math:: - :label: 5.67 + :label: 5.67 E_{soil} =-\frac{\rho _{atm} \left(q_{atm} -q_{soil} \right)}{r_{aw} + r_{soil}} .. math:: - :label: 5.68 + :label: 5.68 E_{sno} =-\frac{\rho _{atm} \left(q_{atm} -q_{sno} \right)}{r_{aw} } .. math:: - :label: 5.69 + :label: 5.69 E_{h2osfc} =-\frac{\rho _{atm} \left(q_{atm} -q_{h2osfc} \right)}{r_{aw} } -where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`q_{soil}` , :math:`q_{sno}` , -and :math:`q_{h2osfc}` are the specific humidities (kg kg\ :sup:`-1`) of the soil, snow, and surface water, respectively, -:math:`r_{aw}` is the aerodynamic resistance to water vapor transfer (s m\ :sup:`-1`), and :math:`r _{soi}` is the soil -resistance to water vapor transfer (s m\ :sup:`-1`). The specific humidities of the snow :math:`q_{sno}` and surface water +where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`q_{soil}` , :math:`q_{sno}` , +and :math:`q_{h2osfc}` are the specific humidities (kg kg\ :sup:`-1`) of the soil, snow, and surface water, respectively, +:math:`r_{aw}` is the aerodynamic resistance to water vapor transfer (s m\ :sup:`-1`), and :math:`r _{soi}` is the soil +resistance to water vapor transfer (s m\ :sup:`-1`). The specific humidities of the snow :math:`q_{sno}` and surface water :math:`q_{h2osfc}` are assumed to be at the saturation specific humidity of their respective temperatures .. math:: - :label: 5.70 + :label: 5.70 q_{sno} =q_{sat}^{T_{snl+1} } .. math:: - :label: 5.71 + :label: 5.71 q_{h2osfc} =q_{sat}^{T_{h2osfc} } @@ -664,7 +664,7 @@ The specific humidity of the soil surface :math:`q_{soil}` is assumed to be proportional to the saturation specific humidity .. math:: - :label: 5.72 + :label: 5.72 q_{soil} =\alpha _{soil} q_{sat}^{T_{1} } @@ -674,7 +674,7 @@ the soil surface temperature :math:`T_{1}` (section :numref:`Saturation Vapor P potential :math:`\psi` as in :ref:`Philip (1957)` .. math:: - :label: 5.73 + :label: 5.73 \alpha _{soil} =\exp \left(\frac{\psi _{1} g}{1\times 10^{3} R_{wv} T_{1} } \right) @@ -684,25 +684,25 @@ gravitational acceleration (m s\ :sup:`-2`) (:numref:`Table Physical constants`) layer (mm). The soil water matric potential :math:`\psi _{1}` is .. math:: - :label: 5.74 + :label: 5.74 \psi _{1} =\psi _{sat,\, 1} s_{1}^{-B_{1} } \ge -1\times 10^{8} where :math:`\psi _{sat,\, 1}` is the saturated matric potential (mm) -(section :numref:`Hydraulic Properties`), -:math:`B_{1}` is the :ref:`Clapp and Hornberger (1978) ` -parameter (section :numref:`Hydraulic Properties`), -and :math:`s_{1}` is the wetness of the top soil layer with respect to saturation. +(section :numref:`Hydraulic Properties`), +:math:`B_{1}` is the :ref:`Clapp and Hornberger (1978) ` +parameter (section :numref:`Hydraulic Properties`), +and :math:`s_{1}` is the wetness of the top soil layer with respect to saturation. The surface wetness :math:`s_{1}` is a function of the liquid water and ice content .. math:: - :label: 5.75 + :label: 5.75 s_{1} =\frac{1}{\Delta z_{1} \theta _{sat,\, 1} } \left[\frac{w_{liq,\, 1} }{\rho _{liq} } +\frac{w_{ice,\, 1} }{\rho _{ice} } \right]\qquad 0.01\le s_{1} \le 1.0 where :math:`\Delta z_{1}` is the thickness of the top soil layer (m), :math:`\rho _{liq}` and :math:`\rho _{ice}` are the density of liquid -water and ice (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), :math:`w_{liq,\, 1}` +water and ice (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), :math:`w_{liq,\, 1}` and :math:`w_{ice,\, 1}` are the mass of liquid water and ice of the top soil layer (kg m\ :sup:`-2`) (Chapter :numref:`rst_Hydrology`), and :math:`\theta _{sat,\, 1}` is the saturated volumetric water content @@ -712,37 +712,37 @@ top soil layer (kg m\ :sup:`-2`) (Chapter :numref:`rst_Hydrology`), and prevents large increases (decreases) in :math:`q_{soil}` for small increases (decreases) in soil moisture in very dry soils. -The resistance to water vapor transfer occurring within the soil matrix -:math:`r_{soil}` (s m\ :sup:`-1`) is +The resistance to water vapor transfer occurring within the soil matrix +:math:`r_{soil}` (s m\ :sup:`-1`) is .. math:: - :label: 5.76 + :label: 5.76 r_{soil} = \frac{DSL}{D_{v} \tau} -where :math:`DSL` is the thickness of the dry surface layer (m), :math:`D_{v}` -is the molecular diffusivity of water vapor in air (m\ :sup:`2` s\ :sup:`-2`) -and :math:`\tau` (*unitless*) describes the tortuosity of the vapor flow paths through -the soil matrix (:ref:`Swenson and Lawrence 2014 `). +where :math:`DSL` is the thickness of the dry surface layer (m), :math:`D_{v}` +is the molecular diffusivity of water vapor in air (m\ :sup:`2` s\ :sup:`-2`) +and :math:`\tau` (*unitless*) describes the tortuosity of the vapor flow paths through +the soil matrix (:ref:`Swenson and Lawrence 2014 `). The thickness of the dry surface layer is given by .. math:: :label: 5.77 - DSL = + DSL = \begin{array}{lr} D_{max} \ \frac{\left( \theta_{init} - \theta_{1}\right)} {\left(\theta_{init} - \theta_{air}\right)} & \qquad \theta_{1} < \theta_{init} \\ 0 & \qquad \theta_{1} \ge \theta_{init} \end{array} -where :math:`D_{max}` is a parameter specifying the length scale -of the maximum DSL thickness (default value = 15 mm), -:math:`\theta_{init}` (mm\ :sup:`3` mm\ :sup:`-3`) is the moisture value -at which the DSL initiates, :math:`\theta_{1}` (mm\ :sup:`3` mm\ :sup:`-3`) -is the moisture value of the top model soil layer, and -:math:`\theta_{air}` (mm\ :sup:`3` mm\ :sup:`-3`) is the 'air dry' soil +where :math:`D_{max}` is a parameter specifying the length scale +of the maximum DSL thickness (default value = 15 mm), +:math:`\theta_{init}` (mm\ :sup:`3` mm\ :sup:`-3`) is the moisture value +at which the DSL initiates, :math:`\theta_{1}` (mm\ :sup:`3` mm\ :sup:`-3`) +is the moisture value of the top model soil layer, and +:math:`\theta_{air}` (mm\ :sup:`3` mm\ :sup:`-3`) is the 'air dry' soil moisture value (:ref:`Dingman 2002 `): .. math:: @@ -750,13 +750,13 @@ moisture value (:ref:`Dingman 2002 `): \theta_{air} = \Phi \left( \frac{\Psi_{sat}}{\Psi_{air}} \right)^{\frac{1}{B_{1}}} \ . -where :math:`\Phi` is the porosity (mm\ :sup:`3` mm\ :sup:`-3`), -:math:`\Psi_{sat}` is the saturated soil matric potential (mm), -:math:`\Psi_{air} = 10^{7}` mm is the air dry matric potential, and -:math:`B_{1}` is a function of soil texture (section -:numref:`Hydraulic Properties`). +where :math:`\Phi` is the porosity (mm\ :sup:`3` mm\ :sup:`-3`), +:math:`\Psi_{sat}` is the saturated soil matric potential (mm), +:math:`\Psi_{air} = 10^{7}` mm is the air dry matric potential, and +:math:`B_{1}` is a function of soil texture (section +:numref:`Hydraulic Properties`). -The soil tortuosity is +The soil tortuosity is .. math:: :label: 5.79 @@ -766,19 +766,19 @@ The soil tortuosity is where :math:`\Phi_{air}` (mm\ :sup:`3` mm\ :sup:`-3`) is the air filled pore space .. math:: - :label: 5.80 + :label: 5.80 \Phi_{air} = \Phi - \theta_{air} \ . :math:`D_{v}` depends on temperature .. math:: - :label: 5.81 + :label: 5.81 D_{v} = 2.12 \times 10^{-5} \left(\frac{T_{1}}{T_{f}}\right)^{1.75} \ . -where :math:`T_{1}` (K) is the temperature of the top soil layer and -:math:`T_{f}` (K) is the freezing temperature of water +where :math:`T_{1}` (K) is the temperature of the top soil layer and +:math:`T_{f}` (K) is the freezing temperature of water (:numref:`Table Physical Constants`). The roughness lengths used to calculate :math:`r_{am}` , @@ -793,7 +793,7 @@ fluctuations in the turbulent waves behind the roughness elements, while for heat and water vapor transfer no such dynamical mechanism exists. Rather, heat and water vapor must be transferred by molecular diffusion across the interfacial sublayer. The following relation from -:ref:`Zilitinkevich (1970) ` is adopted by +:ref:`Zilitinkevich (1970) ` is adopted by :ref:`Zeng and Dickinson 1998 ` .. math:: @@ -802,7 +802,7 @@ across the interfacial sublayer. The following relation from z_{0h,\, g} =z_{0w,\, g} =z_{0m,\, g} e^{-a\left({u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon } \right)^{0.45} } where the quantity -:math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` +:math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. @@ -849,7 +849,7 @@ water vapor flux from non-vegetated surfaces proceeds as follows: :math:`q_{2m}` (:eq:`5.58` , :eq:`5.59`) The partial derivatives of the soil surface fluxes with respect to -ground temperature, which are needed for the soil temperature calculations (section +ground temperature, which are needed for the soil temperature calculations (section :numref:`Numerical Solution Temperature`) and to update the soil surface fluxes (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`), are @@ -866,7 +866,7 @@ ground temperature, which are needed for the soil temperature calculations (sect where .. math:: - :label: 5.85 + :label: 5.85 \frac{dq_{g} }{dT_{g} } =\left(1-f_{sno} -f_{h2osfc} \right)\alpha _{soil} \frac{dq_{sat}^{T_{soil} } }{dT_{soil} } +f_{sno} \frac{dq_{sat}^{T_{sno} } }{dT_{sno} } +f_{h2osfc} \frac{dq_{sat}^{T_{h2osfc} } }{dT_{h2osfc} } . @@ -903,7 +903,7 @@ The air within the canopy is assumed to have negligible capacity to store heat so that the sensible heat flux :math:`H` between the surface at height :math:`z_{0h} +d` and the atmosphere at height :math:`z_{atm,\, h}` must be balanced by the sum of the sensible heat -from the vegetation :math:`H_{v}` and the ground :math:`H_{g}` +from the vegetation :math:`H_{v}` and the ground :math:`H_{g}` .. math:: :label: 5.86 @@ -913,7 +913,7 @@ from the vegetation :math:`H_{v}` and the ground :math:`H_{g}` where, with reference to :numref:`Figure Schematic diagram of sensible heat fluxes`, .. math:: - :label: 5.87 + :label: 5.87 H=-\rho _{atm} C_{p} \frac{\left(\theta _{atm} -T_{s} \right)}{r_{ah} } @@ -930,7 +930,7 @@ where, with reference to :numref:`Figure Schematic diagram of sensible heat flux where .. math:: - :label: 5.90 + :label: 5.90 H_{soil} =-\rho _{atm} C_{p} \frac{\left(T_{s} -T_{1} \right)}{r_{ah} ^{{'} } } @@ -940,7 +940,7 @@ where H_{sno} =-\rho _{atm} C_{p} \frac{\left(T_{s} -T_{snl+1} \right)}{r_{ah} ^{{'} } } .. math:: - :label: 5.92 + :label: 5.92 H_{h2osfc} =-\rho _{atm} C_{p} \frac{\left(T_{s} -T_{h2osfc} \right)}{r_{ah} ^{{'} } } @@ -973,8 +973,8 @@ height :math:`z_{0h} ^{{'} }` and the canopy air at height Figure Schematic diagram of water vapor fluxes for (a) non-vegetated surfaces and (b) vegetated surfaces. -Equations :eq:`5.86` - :eq:`5.89` can be solved for the canopy air -temperature :math:`T_{s}` +Equations :eq:`5.86` - :eq:`5.89` can be solved for the canopy air +temperature :math:`T_{s}` .. math:: :label: 5.93 @@ -1004,7 +1004,7 @@ respectively (m s\ :sup:`-1`). When the expression for :math:`T_{s}` is substituted into equation :eq:`5.88`, the sensible heat flux from vegetation :math:`H_{v}` is a function of -:math:`\theta _{atm}` , :math:`T_{g}` , and :math:`T_{v}` +:math:`\theta _{atm}` , :math:`T_{g}` , and :math:`T_{v}` .. math:: :label: 5.97 @@ -1012,7 +1012,7 @@ the sensible heat flux from vegetation :math:`H_{v}` is a function of H_{v} = -\rho _{atm} C_{p} \left[c_{a}^{h} \theta _{atm} +c_{g}^{h} T_{g} -\left(c_{a}^{h} +c_{g}^{h} \right)T_{v} \right]\frac{c_{v}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } . Similarly, the expression for :math:`T_{s}` can be substituted into -equation to obtain the sensible heat flux from ground :math:`H_{g}` +equation to obtain the sensible heat flux from ground :math:`H_{g}` .. math:: :label: 5.98 @@ -1023,7 +1023,7 @@ The air within the canopy is assumed to have negligible capacity to store water vapor so that the water vapor flux :math:`E` between the surface at height :math:`z_{0w} +d` and the atmosphere at height :math:`z_{atm,\, w}` must be balanced by the sum of the water vapor -flux from the vegetation :math:`E_{v}` and the ground :math:`E_{g}` +flux from the vegetation :math:`E_{v}` and the ground :math:`E_{g}` .. math:: :label: 5.99 @@ -1033,7 +1033,7 @@ flux from the vegetation :math:`E_{v}` and the ground :math:`E_{g}` where, with reference to :numref:`Figure Schematic diagram of latent heat fluxes`, .. math:: - :label: 5.100 + :label: 5.100 E = -\rho _{atm} \frac{\left(q_{atm} -q_{s} \right)}{r_{aw} } @@ -1050,47 +1050,47 @@ where, with reference to :numref:`Figure Schematic diagram of latent heat fluxes where .. math:: - :label: 5.103 + :label: 5.103 E_{soil} = -\rho _{atm} \frac{\left(q_{s} -q_{soil} \right)}{r_{aw} ^{{'} } +r_{soil} } .. math:: - :label: 5.104 + :label: 5.104 E_{sno} = -\rho _{atm} \frac{\left(q_{s} -q_{sno} \right)}{r_{aw} ^{{'} } +r_{soil} } .. math:: - :label: 5.105 + :label: 5.105 E_{h2osfc} = -\rho _{atm} \frac{\left(q_{s} -q_{h2osfc} \right)}{r_{aw} ^{{'} } +r_{soil} } where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`r_{aw}` is the aerodynamic resistance to -water vapor transfer (s m\ :sup:`-1`), :math:`q_{sat}^{T_{v} }` +water vapor transfer (s m\ :sup:`-1`), :math:`q_{sat}^{T_{v} }` (kg kg\ :sup:`-1`) is the saturation water vapor specific humidity at the vegetation temperature (section :numref:`Saturation Vapor Pressure`), :math:`q_{g}` , :math:`q_{sno}` , and :math:`q_{h2osfc}` are the specific humidities of the soil, snow, and surface water (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), :math:`r_{aw} ^{{'} }` is the aerodynamic resistance (s m\ :sup:`-1`) to water vapor transfer between the ground at height -:math:`z_{0w} ^{{'} }` and the canopy air at height :math:`z_{0w} +d`, -and :math:`r_{soil}` (:eq:`5.76`) is a resistance to diffusion through the soil +:math:`z_{0w} ^{{'} }` and the canopy air at height :math:`z_{0w} +d`, +and :math:`r_{soil}` (:eq:`5.76`) is a resistance to diffusion through the soil (s m\ :sup:`-1`). :math:`r_{total}` is the total resistance to water vapor transfer from the canopy to the canopy air and includes contributions from leaf boundary layer and sunlit and shaded stomatal resistances :math:`r_{b}` , :math:`r_{s}^{sun}` , and -:math:`r_{s}^{sha}` (:numref:`Figure Schematic diagram of latent heat fluxes`). +:math:`r_{s}^{sha}` (:numref:`Figure Schematic diagram of latent heat fluxes`). The water vapor flux from vegetation is the sum of water vapor flux from wetted leaf and stem area :math:`E_{v}^{w}` (evaporation of water intercepted by the canopy) and -transpiration from dry leaf surfaces :math:`E_{v}^{t}` +transpiration from dry leaf surfaces :math:`E_{v}^{t}` .. math:: - :label: 5.106 + :label: 5.106 E_{v} =E_{v}^{w} +E_{v}^{t} . Equations :eq:`5.99` - :eq:`5.102` can be solved for the canopy specific humidity -:math:`q_{s}` +:math:`q_{s}` .. math:: :label: 5.107 @@ -1124,17 +1124,17 @@ as :label: 5.111 r'' = \left\{ - \begin{array}{lr} - \min \left(f_{wet} +r_{dry} ^{{'} {'} } ,\, \frac{E_{v}^{w,\, pot} r_{dry} ^{{'} {'} } +\frac{W_{can} }{\Delta t} }{E_{v}^{w,\, pot} } \right) & \qquad E_{v}^{w,\, pot} >0,\, \beta _{t} >0 \\ - \min \left(f_{wet} ,\, \frac{E_{v}^{w,\, pot} r_{dry} ^{{'} {'} } +\frac{W_{can} }{\Delta t} }{E_{v}^{w,\, pot} } \right) & \qquad E_{v}^{w,\, pot} >0,\, \beta _{t} \le 0 \\ - 1 & \qquad E_{v}^{w,\, pot} \le 0 + \begin{array}{lr} + \min \left(f_{wet} +r_{dry} ^{{'} {'} } ,\, \frac{E_{v}^{w,\, pot} r_{dry} ^{{'} {'} } +\frac{W_{can} }{\Delta t} }{E_{v}^{w,\, pot} } \right) & \qquad E_{v}^{w,\, pot} >0,\, \beta _{t} >0 \\ + \min \left(f_{wet} ,\, \frac{E_{v}^{w,\, pot} r_{dry} ^{{'} {'} } +\frac{W_{can} }{\Delta t} }{E_{v}^{w,\, pot} } \right) & \qquad E_{v}^{w,\, pot} >0,\, \beta _{t} \le 0 \\ + 1 & \qquad E_{v}^{w,\, pot} \le 0 \end{array}\right\} where :math:`f_{wet}` is the fraction of leaves and stems that are wet (section :numref:`Canopy Water`), :math:`W_{can}` is canopy water (kg m\ :sup:`-2`) (section :numref:`Canopy Water`), :math:`\Delta t` is the time step (s), and :math:`\beta _{t}` is a soil moisture function limiting transpiration -(Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). The potential +(Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). The potential evaporation from wet foliage per unit wetted area is .. math:: @@ -1145,7 +1145,7 @@ evaporation from wet foliage per unit wetted area is The term :math:`r_{dry} ^{{'} {'} }` is .. math:: - :label: 5.113 + :label: 5.113 r_{dry} ^{{'} {'} } =\frac{f_{dry} r_{b} }{L} \left(\frac{L^{sun} }{r_{b} +r_{s}^{sun} } +\frac{L^{sha} }{r_{b} +r_{s}^{sha} } \right) @@ -1157,7 +1157,7 @@ m\ :sup:`-1`) (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). When the expression for :math:`q_{s}` is substituted into equation :eq:`5.101`, the water vapor flux from vegetation :math:`E_{v}` is a function of -:math:`q_{atm}` , :math:`q_{g}` , and :math:`q_{sat}^{T_{v} }` +:math:`q_{atm}` , :math:`q_{g}` , and :math:`q_{sat}^{T_{v} }` .. math:: :label: 5.114 @@ -1166,7 +1166,7 @@ the water vapor flux from vegetation :math:`E_{v}` is a function of Similarly, the expression for :math:`q_{s}` can be substituted into :eq:`5.84` to obtain the water vapor flux from the ground beneath the -canopy :math:`E_{g}` +canopy :math:`E_{g}` .. math:: :label: 5.115 @@ -1193,7 +1193,7 @@ is the magnitude of the wind velocity incident on the leaves (equivalent here to friction velocity) (m s\ :sup:`-1`) and :math:`C_{s}` is the turbulent transfer coefficient between the underlying soil and the canopy air. :math:`C_{s}` is obtained by -interpolation between values for dense canopy and bare soil +interpolation between values for dense canopy and bare soil (:ref:`Zeng et al. 2005 `) .. math:: @@ -1204,22 +1204,22 @@ interpolation between values for dense canopy and bare soil where the weight :math:`W` is .. math:: - :label: 5.119 + :label: 5.119 W=e^{-\left(L+S\right)} . -The dense canopy turbulent transfer coefficient -(:ref:`Dickinson et al. 1993 `) is +The dense canopy turbulent transfer coefficient +(:ref:`Dickinson et al. 1993 `) is .. math:: - :label: 5.120) + :label: 5.120) C_{s,\, dense} =0.004 \ . The bare soil turbulent transfer coefficient is .. math:: - :label: 5.121 + :label: 5.121 C_{s,\, bare} =\frac{k}{a} \left(\frac{z_{0m,\, g} U_{av} }{\upsilon } \right)^{-0.45} @@ -1240,8 +1240,8 @@ direction of wind flow (:numref:`Table Plant functional type aerodynamic paramet The partial derivatives of the fluxes from the soil beneath the canopy with respect to ground temperature, which are needed for the soil -temperature calculations (section :numref:`Numerical Solution Temperature`) -and to update the soil surface fluxes (section +temperature calculations (section :numref:`Numerical Solution Temperature`) +and to update the soil surface fluxes (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`), are .. math:: @@ -1274,25 +1274,25 @@ adjusted for canopy density following :ref:`Zeng and Wang (2007) ` z_{0m,\, v} = z_{0h,\, v} =z_{0w,\, v} =\exp \left[V\ln \left(z_{top} R_{z0m} \right)+\left(1-V\right)\ln \left(z_{0m,\, g} \right)\right] .. math:: - :label: 5.126 + :label: 5.126 d = z_{top} R_{d} V -where :math:`z_{top}` is canopy top height (m) +where :math:`z_{top}` is canopy top height (m) (:numref:`Table Plant functional type canopy top and bottom heights`), :math:`R_{z0m}` and :math:`R_{d}` are the ratio of momentum roughness -length and displacement height to canopy top height, respectively -(:numref:`Table Plant functional type aerodynamic parameters`), and :math:`z_{0m,\, g}` -is the ground momentum roughness length (m) (section -:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`). The +length and displacement height to canopy top height, respectively +(:numref:`Table Plant functional type aerodynamic parameters`), and :math:`z_{0m,\, g}` +is the ground momentum roughness length (m) (section +:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`). The fractional weight :math:`V` is determined from .. math:: - :label: 5.127 + :label: 5.127 V = \frac{1-\exp \left\{-\beta \min \left[L+S,\, \left(L+S\right)_{cr} \right]\right\}}{1-\exp \left[-\beta \left(L+S\right)_{cr} \right]} -where :math:`\beta =1` and :math:`\left(L+S\right)_{cr} = 2` +where :math:`\beta =1` and :math:`\left(L+S\right)_{cr} = 2` (m\ :sup:`2` m\ :sup:`-2`) is a critical value of exposed leaf plus stem area for which :math:`z_{0m}` reaches its maximum. @@ -1359,7 +1359,7 @@ plus stem area for which :math:`z_{0m}` reaches its maximum. +----------------------------------+--------------------+------------------+-------------------------+ | Switchgrass I | 0.120 | 0.68 | 0.04 | +----------------------------------+--------------------+------------------+-------------------------+ - + .. _Numerical Implementation: Numerical Implementation @@ -1377,7 +1377,7 @@ the vegetation (section :numref:`Solar Fluxes`), :math:`\overrightarrow{L}_{v}` longwave radiation absorbed by vegetation (section :numref:`Longwave Fluxes`), and :math:`H_{v}` and :math:`\lambda E_{v}` are the sensible and latent heat fluxes from vegetation, respectively. The term :math:`\lambda` is -taken to be the latent heat of vaporization :math:`\lambda _{vap}` +taken to be the latent heat of vaporization :math:`\lambda _{vap}` (:numref:`Table Physical constants`). :math:`\overrightarrow{L}_{v}` , :math:`H_{v}` , and @@ -1397,17 +1397,17 @@ where :math:`\Delta T_{v} =T_{v}^{n+1} -T_{v}^{n}` and the subscript The partial derivatives are .. math:: - :label: 5.130 + :label: 5.130 \frac{\partial \overrightarrow{L}_{v} }{\partial T_{v} } =4\varepsilon _{v} \sigma \left[2-\varepsilon _{v} \left(1-\varepsilon _{g} \right)\right]T_{v}^{3} .. math:: - :label: 5.131 + :label: 5.131 \frac{\partial H_{v} }{\partial T_{v} } =\rho _{atm} C_{p} \left(c_{a}^{h} +c_{g}^{h} \right)\frac{c_{v}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } .. math:: - :label: 5.132 + :label: 5.132 \frac{\partial \lambda E_{v} }{\partial T_{v} } =\lambda \rho _{atm} \left(c_{a}^{w} +c_{g}^{w} \right)\frac{c_{v}^{w} }{c_{a}^{w} +c_{v}^{w} +c_{g}^{w} } \frac{dq_{sat}^{T_{v} } }{dT_{v} } . @@ -1446,12 +1446,12 @@ proceeds as follows: obtained from .. math:: - :label: 5.136 + :label: 5.136 T_{s} =\frac{T_{g} +\theta _{atm} }{2} .. math:: - :label: 5.137 + :label: 5.137 q_{s} =\frac{q_{g} +q_{atm} }{2} . @@ -1469,7 +1469,7 @@ proceeds as follows: #. Friction velocity :math:`u_{*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) -#. Ratio :math:`\frac{\theta _{*} }{\theta _{atm} -\theta _{s} }` +#. Ratio :math:`\frac{\theta _{*} }{\theta _{atm} -\theta _{s} }` (:eq:`5.37` , :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) #. Ratio :math:`\frac{q_{*} }{q_{atm} -q_{s} }` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) @@ -1477,7 +1477,7 @@ proceeds as follows: #. Aerodynamic resistances :math:`r_{am}` , :math:`r_{ah}` , and :math:`r_{aw}` (:eq:`5.55`, :eq:`5.56`, :eq:`5.57`) -#. Magnitude of the wind velocity incident on the leaves :math:`U_{av}` +#. Magnitude of the wind velocity incident on the leaves :math:`U_{av}` (:eq:`5.117` ) #. Leaf boundary layer resistance :math:`r_{b}` (:eq:`5.136` ) @@ -1513,7 +1513,7 @@ proceeds as follows: limit is exceeded, the energy error is .. math:: - :label: 5.138 + :label: 5.138 \Delta _{2} =\overrightarrow{S}_{v} -\overrightarrow{L}_{v} -\frac{\partial \overrightarrow{L}_{v} }{\partial T_{v} } \Delta T_{v} -H_{v} -\frac{\partial H_{v} }{\partial T_{v} } \Delta T_{v} -\lambda E_{v} -\frac{\partial \lambda E_{v} }{\partial T_{v} } \Delta T_{v} @@ -1544,20 +1544,20 @@ flux later. :math:`\lambda \Delta _{3}` are also added to the sensible heat flux. -#. The saturated vapor pressure :math:`e_{i}` (Chapter +#. The saturated vapor pressure :math:`e_{i}` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), saturated specific humidity :math:`q_{sat}^{T_{v} }` and its derivative :math:`\frac{dq_{sat}^{T_{v} } }{dT_{v} }` at the leaf surface - (section :numref:`Saturation Vapor Pressure`), are re-evaluated based on + (section :numref:`Saturation Vapor Pressure`), are re-evaluated based on the new :math:`T_{v}` . #. Canopy air temperature :math:`T_{s}` (:eq:`5.93` ) #. Canopy air specific humidity :math:`q_{s}` (:eq:`5.107` ) -#. Temperature difference :math:`\theta _{atm} -\theta _{s}` +#. Temperature difference :math:`\theta _{atm} -\theta _{s}` -#. Specific humidity difference :math:`q_{atm} -q_{s}` +#. Specific humidity difference :math:`q_{atm} -q_{s}` #. Potential temperature scale :math:`\theta _{*} =\frac{\theta _{*} }{\theta _{atm} -\theta _{s} } \left(\theta _{atm} -\theta _{s} \right)` @@ -1600,17 +1600,17 @@ The sensible and water vapor heat fluxes derived above for bare soil and soil beneath canopy are based on the ground surface temperature from the previous time step :math:`T_{g}^{n}` and are used as the surface forcing for the solution of the soil temperature equations (section -:numref:`Numerical Solution Temperature`). This solution yields a new ground -surface temperature :math:`T_{g}^{n+1}` . The ground sensible and water +:numref:`Numerical Solution Temperature`). This solution yields a new ground +surface temperature :math:`T_{g}^{n+1}` . The ground sensible and water vapor fluxes are then updated for :math:`T_{g}^{n+1}` as .. math:: - :label: 5.140 + :label: 5.140 H'_{g} =H_{g} +\left(T_{g}^{n+1} -T_{g}^{n} \right)\frac{\partial H_{g} }{\partial T_{g} } .. math:: - :label: 5.141 + :label: 5.141 E'_{g} =E_{g} +\left(T_{g}^{n+1} -T_{g}^{n} \right)\frac{\partial E_{g} }{\partial T_{g} } @@ -1623,19 +1623,19 @@ support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and :math:`f_{evap} < 1` where .. math:: - :label: 5.142 + :label: 5.142 f_{evap} =\frac{{\left(w_{ice,\; snl+1} +w_{liq,\, snl+1} \right)\mathord{\left/ {\vphantom {\left(w_{ice,\; snl+1} +w_{liq,\, snl+1} \right) \Delta t}} \right.} \Delta t} }{\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j} } \le 1, an adjustment is made to reduce the ground evaporation accordingly as .. math:: - :label: 5.143 + :label: 5.143 E''_{g} =f_{evap} E'_{g} . The term -:math:`\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j}` +:math:`\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j}` is the sum of :math:`E'_{g}` over all evaporating PFTs where :math:`\left(E'_{g} \right)_{j}` is the ground evaporation from the :math:`j^{th}` PFT on the column, :math:`\left(wt\right)_{j}` is the @@ -1643,38 +1643,38 @@ relative area of the :math:`j^{th}` PFT with respect to the column, and :math:`npft` is the number of PFTs on the column. :math:`w_{ice,\, snl+1}` and :math:`w_{liq,\, snl+1}` are the ice and liquid water contents (kg m\ :sup:`-2`) of the top snow/soil layer -(Chapter :numref:`rst_Hydrology`). Any resulting energy deficit is assigned +(Chapter :numref:`rst_Hydrology`). Any resulting energy deficit is assigned to sensible heat as .. math:: - :label: 5.144 + :label: 5.144 H''_{g} =H_{g} +\lambda \left(E'_{g} -E''_{g} \right). -The ground water vapor flux :math:`E''_{g}` is partitioned into evaporation -of liquid water from snow/soil :math:`q_{seva}` (kg\ m\ :sup:`-2` s\ :sup:`-1`), -sublimation from snow/soil ice :math:`q_{subl}` (kg m\ :sup:`-2` s\ :sup:`-1`), -liquid dew on snow/soil :math:`q_{sdew}` (kg m\ :sup:`-2` s\ :sup:`-1`), or +The ground water vapor flux :math:`E''_{g}` is partitioned into evaporation +of liquid water from snow/soil :math:`q_{seva}` (kg\ m\ :sup:`-2` s\ :sup:`-1`), +sublimation from snow/soil ice :math:`q_{subl}` (kg m\ :sup:`-2` s\ :sup:`-1`), +liquid dew on snow/soil :math:`q_{sdew}` (kg m\ :sup:`-2` s\ :sup:`-1`), or frost on snow/soil :math:`q_{frost}` (kg m\ :sup:`-2` s\ :sup:`-1`) as .. math:: - :label: 5.145 + :label: 5.145 q_{seva} =\max \left(E''_{sno} \frac{w_{liq,\, snl+1} }{w_{ice,\; snl+1} +w_{liq,\, snl+1} } ,0\right)\qquad E''_{sno} \ge 0,\, w_{ice,\; snl+1} +w_{liq,\, snl+1} >0 .. math:: - :label: 5.146 + :label: 5.146 q_{subl} =E''_{sno} -q_{seva} \qquad E''_{sno} \ge 0 .. math:: - :label: 5.147 + :label: 5.147 q_{sdew} =\left|E''_{sno} \right|\qquad E''_{sno} <0{\rm \; and\; }T_{g} \ge T_{f} .. math:: - :label: 5.148 + :label: 5.148 q_{frost} =\left|E''_{sno} \right|\qquad E''_{sno} <0{\rm \; and\; }T_{g} 0} \\ {\lambda _{vap} \qquad {\rm otherwise}} \end{array}\right\} @@ -1730,7 +1730,7 @@ flux to an energy flux, :math:`\lambda _{vap}` is used. The system balances energy as .. math:: - :label: 5.153 + :label: 5.153 \overrightarrow{S}_{g} +\overrightarrow{S}_{v} +L_{atm} \, \downarrow -L\, \uparrow -H_{v} -H_{g} -\lambda _{vap} E_{v} -\lambda E_{g} -G=0. @@ -1745,37 +1745,37 @@ Saturation vapor pressure :math:`e_{sat}^{T}` (Pa) and its derivative :ref:`Flatau et al. (1992) ` .. math:: - :label: 5.154 + :label: 5.154 e_{sat}^{T} =100\left[a_{0} +a_{1} T+\cdots +a_{n} T^{n} \right] .. math:: - :label: 5.155 + :label: 5.155 \frac{de_{sat}^{T} }{dT} =100\left[b_{0} +b_{1} T+\cdots +b_{n} T^{n} \right] where the coefficients for ice are valid for :math:`-75\, ^{\circ } {\rm C}\le T<0\, ^{\circ } {\rm C}` and the coefficients for water are valid for -:math:`0\, ^{\circ } {\rm C}\le T\le 100\, ^{\circ } {\rm C}` -(:numref:`Table Coefficients for saturation vapor pressure` and -:numref:`Table Coefficients for derivative of esat`). +:math:`0\, ^{\circ } {\rm C}\le T\le 100\, ^{\circ } {\rm C}` +(:numref:`Table Coefficients for saturation vapor pressure` and +:numref:`Table Coefficients for derivative of esat`). The saturated water vapor specific humidity :math:`q_{sat}^{T}` and its derivative :math:`\frac{dq_{sat}^{T} }{dT}` are .. math:: - :label: 5.156 + :label: 5.156 q_{sat}^{T} =\frac{0.622e_{sat}^{T} }{P_{atm} -0.378e_{sat}^{T} } .. math:: - :label: 5.157 + :label: 5.157 \frac{dq_{sat}^{T} }{dT} =\frac{0.622P_{atm} }{\left(P_{atm} -0.378e_{sat}^{T} \right)^{2} } \frac{de_{sat}^{T} }{dT} . .. _Table Coefficients for saturation vapor pressure: -.. table:: Coefficients for :math:`e_{sat}^{T}` +.. table:: Coefficients for :math:`e_{sat}^{T}` +------------------+------------------------------------------+----------------------------------------+ | | water | ice | @@ -1798,10 +1798,10 @@ The saturated water vapor specific humidity :math:`q_{sat}^{T}` and its derivati +------------------+-------------------------------------------+---------------------------------------+ | :math:`a_{8}` | 2.09339997 :math:`\times 10^{-16}` | 2.62655803\ :math:`\times 10^{-15}` | +------------------+------------------------------------------+----------------------------------------+ - + .. _Table Coefficients for derivative of esat: -.. table:: Coefficients for :math:`\frac{de_{sat}^{T} }{dT}` +.. table:: Coefficients for :math:`\frac{de_{sat}^{T} }{dT}` +------------------+----------------------------------------+----------------------------------------+ | | water | ice | diff --git a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst index 3d56e962ed..fdc4001465 100644 --- a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst +++ b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst @@ -56,7 +56,7 @@ CLM is responsible for computing two quantities that are passed to the ice sheet model: #. Surface mass balance (SMB) - the net annual accumulation/ablation of - mass at the upper surface (section + mass at the upper surface (section :numref:`Computation of the surface mass balance`) #. Ground surface temperature, which serves as an upper boundary diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index dfb4aac092..0258c2e3c9 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -47,26 +47,26 @@ al. 2008) ` and :math:`\Delta t` is the time step (s). Canopy Water ---------------- -Liquid precipitation is either intercepted by the canopy, falls -directly to the snow/soil surface (throughfall), or drips off the -vegetation (canopy drip). Solid precipitation is treated similarly, -with the addition of unloading of previously intercepted snow. +Liquid precipitation is either intercepted by the canopy, falls +directly to the snow/soil surface (throughfall), or drips off the +vegetation (canopy drip). Solid precipitation is treated similarly, +with the addition of unloading of previously intercepted snow. Interception by vegetation is divided between liquid and solid phases -:math:`q_{intr,\,liq}` and :math:`q_{intr,\,ice}` -(kg m\ :sup:`-2` s\ :sup:`-1`) +:math:`q_{intr,\,liq}` and :math:`q_{intr,\,ice}` +(kg m\ :sup:`-2` s\ :sup:`-1`) .. math:: :label: 7.2 - q_{intr,\,liq} = f_{pi,\,liq} \ q_{rain} + q_{intr,\,liq} = f_{pi,\,liq} \ q_{rain} .. math:: :label: 7.3 q_{intr,\,ice} = f_{pi,\,ice} \ q_{sno} -where :math:`f_{pi,\,liq}` and :math:`f_{pi,\,ice}` are the -fractions of intercepted precipitation of rain and snow, +where :math:`f_{pi,\,liq}` and :math:`f_{pi,\,ice}` are the +fractions of intercepted precipitation of rain and snow, respectively .. math:: @@ -80,9 +80,9 @@ respectively f_{pi,\,ice} =\alpha_{sno} \ \left\{1-\exp \left[-0.5\left(L+S\right)\right]\right\} \ , and :math:`L` and :math:`S` are the exposed leaf and stem area index, -respectively (section :numref:`Phenology and vegetation burial by snow`), and -the :math:`\alpha`\'s scale the fractional area of a leaf that collects water -(:ref:`Lawrence et al. 2007 `). Default values of +respectively (section :numref:`Phenology and vegetation burial by snow`), and +the :math:`\alpha`\'s scale the fractional area of a leaf that collects water +(:ref:`Lawrence et al. 2007 `). Default values of :math:`\alpha_{liq}` and :math:`\alpha_{sno}` are set to 1. Throughfall (kg m\ :sup:`-2` s\ :sup:`-1`) is also divided into liquid and solid phases, reaching the ground (soil or snow surface) as @@ -123,12 +123,12 @@ and W_{can,sno}^{intr} =W_{can,sno}^{n} +q_{intr,\, ice} \Delta t\ge 0 - + are the the canopy liquid water and snow water equivalent after accounting for interception, :math:`W_{can,\,liq}^{n}` and :math:`W_{can,\,sno}^{n}` are the canopy liquid and snow water from the previous time step, and :math:`W_{can,\,liq}^{max }` and :math:`W_{can,\,snow}^{max }` (kg m\ :sup:`-2` or mm of H\ :sub:`2`\ O) are the maximum amounts of liquid water and snow the canopy can hold. -They are defined by +They are defined by .. math:: :label: 7.10 @@ -140,8 +140,8 @@ They are defined by W_{can,\,sno}^{max } =p_{sno}\left(L+S\right). -The maximum storage of liquid water is :math:`p_{liq}=0.1` kg m\ :sup:`-2` -(:ref:`Dickinson et al. 1993 `), and that of snow +The maximum storage of liquid water is :math:`p_{liq}=0.1` kg m\ :sup:`-2` +(:ref:`Dickinson et al. 1993 `), and that of snow is :math:`p_{sno}=6` kg m\ :sup:`-2`, consistent with reported field measurements (:ref:`Pomeroy et al. 1998 `). @@ -150,7 +150,7 @@ fluxes and e-folding times similar to :ref:`Roesch et al. (2001) T_{f} \\ 0 & T_v \le T_f - \end{array}\right\} + \end{array}\right\} .. math:: - :label: 7.18 + :label: 7.18 E_{v}^{ice} = - \left\{\begin{array}{lr} + \left\{\begin{array}{lr} 0 & T_v > T_f \\ E_{v}^{w} & T_v \le T_f \end{array}\right\}. -.. \begin{array}{lr} +.. \begin{array}{lr} .. E_{v}^{liq} = E_{v}^{w} \qquad T > 273 \text{K} \\ .. E_{v}^{ice} = E_{v}^{w} \qquad T \le 273 \text{K} .. \end{array} @@ -221,10 +221,10 @@ The total rate of liquid and solid precipitation reaching the ground is then Solid precipitation reaching the soil or snow surface, :math:`q_{grnd,\, ice} \Delta t`, is added immediately to the snow pack -(Chapter :numref:`rst_Snow Hydrology`). The liquid part, -:math:`q_{grnd,\, liq} \Delta t` is added after surface fluxes -(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) -and snow/soil temperatures (Chapter :numref:`rst_Soil and Snow Temperatures`) +(Chapter :numref:`rst_Snow Hydrology`). The liquid part, +:math:`q_{grnd,\, liq} \Delta t` is added after surface fluxes +(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) +and snow/soil temperatures (Chapter :numref:`rst_Soil and Snow Temperatures`) have been determined. The wetted fraction of the canopy (stems plus leaves), which is required @@ -235,7 +235,7 @@ calculations, is (:ref:`Dickinson et al.1993 `) :label: 7.21 f_{wet} = - \left\{\begin{array}{lr} + \left\{\begin{array}{lr} \left[\frac{W_{can} }{p_{liq}\left(L+S\right)} \right]^{{2\mathord{\left/ {\vphantom {2 3}} \right.} 3} } \le 1 & \qquad L+S > 0 \\ 0 &\qquad L+S = 0 \end{array}\right\} @@ -246,19 +246,19 @@ while the fraction of the canopy that is dry and transpiring is :label: 7.22 f_{dry} = - \left\{\begin{array}{lr} - \frac{\left(1-f_{wet} \right)L}{L+S} & \qquad L+S > 0 \\ - 0 &\qquad L+S = 0 + \left\{\begin{array}{lr} + \frac{\left(1-f_{wet} \right)L}{L+S} & \qquad L+S > 0 \\ + 0 &\qquad L+S = 0 \end{array}\right\}. Similarly, the snow-covered fraction of the canopy is used for surface alebdo when intercepted snow is present (Chapter :numref:`rst_Surface Albedos`) - + .. math:: :label: 7.23 - f_{can,\, sno} = - \left\{\begin{array}{lr} + f_{can,\, sno} = + \left\{\begin{array}{lr} \left[\frac{W_{can,\, sno} }{p_{sno}\left(L+S\right)} \right]^{{3\mathord{\left/ {\vphantom {3 20}} \right.} 20} } \le 1 & \qquad L+S > 0 \\ 0 &\qquad L+S = 0 \end{array}\right\}. @@ -280,8 +280,8 @@ infiltration into the soil. Surface Runoff ^^^^^^^^^^^^^^^^^^^^ -The simple TOPMODEL-based (:ref:`Beven and Kirkby 1979 `) -runoff model (SIMTOP) described by :ref:`Niu et al. (2005) ` +The simple TOPMODEL-based (:ref:`Beven and Kirkby 1979 `) +runoff model (SIMTOP) described by :ref:`Niu et al. (2005) ` is implemented to parameterize runoff. A key concept underlying this approach is that of fractional saturated area :math:`f_{sat}` , which is determined by the topographic @@ -302,21 +302,21 @@ The fractional saturated area is a function of soil moisture f_{sat} =f_{\max } \ \exp \left(-0.5f_{over} z_{\nabla } \right) where :math:`f_{\max }` is the potential or maximum value of -:math:`f_{sat}` , :math:`f_{over}` is a decay factor (m\ :sup:`-1`), and -:math:`z_{\nabla}` is the water table depth (m) (section -:numref:`Lateral Sub-surface Runoff`). The maximum saturated fraction, -:math:`f_{\max }`, is defined as the value of the discrete cumulative -distribution function (CDF) of the topographic index when the grid cell -mean water table depth is zero. Thus, :math:`f_{\max }` is the percent of -pixels in a grid cell whose topographic index is larger than or equal to -the grid cell mean topographic index. It should be calculated explicitly -from the CDF at each grid cell at the resolution that the model is run. +:math:`f_{sat}` , :math:`f_{over}` is a decay factor (m\ :sup:`-1`), and +:math:`z_{\nabla}` is the water table depth (m) (section +:numref:`Lateral Sub-surface Runoff`). The maximum saturated fraction, +:math:`f_{\max }`, is defined as the value of the discrete cumulative +distribution function (CDF) of the topographic index when the grid cell +mean water table depth is zero. Thus, :math:`f_{\max }` is the percent of +pixels in a grid cell whose topographic index is larger than or equal to +the grid cell mean topographic index. It should be calculated explicitly +from the CDF at each grid cell at the resolution that the model is run. However, because this is a computationally intensive task for global -applications, :math:`f_{\max }` is calculated once at 0.125\ :sup:`o` -resolution using the 1-km compound topographic indices (CTIs) based on +applications, :math:`f_{\max }` is calculated once at 0.125\ :sup:`o` +resolution using the 1-km compound topographic indices (CTIs) based on the HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) -from USGS following the algorithm in :ref:`Niu et al. (2005) ` -and then area-averaged to the desired model resolution (section +from USGS following the algorithm in :ref:`Niu et al. (2005) ` +and then area-averaged to the desired model resolution (section :numref:`Surface Data`). Pixels with CTIs exceeding the 95 percentile threshold in each 0.125\ :sup:`o` grid cell are excluded from the calculation to @@ -337,12 +337,12 @@ A surface water store has been added to the model to represent wetlands and small, sub-grid scale water bodies. As a result, the wetland land unit has been removed as of CLM4.5. The state variables for surface water are the mass of water :math:`W_{sfc}` (kg m\ :sup:`-2`) and temperature -:math:`T_{h2osfc}` (Chapter :numref:`rst_Soil and Snow Temperatures`). +:math:`T_{h2osfc}` (Chapter :numref:`rst_Soil and Snow Temperatures`). Surface water storage and outflow are functions of fine spatial scale elevation variations called microtopography. The microtopography is assumed to be distributed normally around the grid cell mean elevation. Given the standard -deviation of the microtopographic distribution, :math:`\sigma _{micro}` +deviation of the microtopographic distribution, :math:`\sigma _{micro}` (m), the fractional area of the grid cell that is inundated can be calculated. Surface water storage, :math:`Wsfc`, is related to the height (relative to the grid cell mean elevation) of the surface water, @@ -404,7 +404,7 @@ where :math:`q_{out,h2osfc}` is the surface water runoff, :math:`k_{h2osfc}` is a constant, :math:`Wc` is the amount of surface water present when :math:`f_{h2osfc} =f_{c}` , and :math:`\Delta t` is the model time step. The linear storage coefficent :math:`k_{h2osfc} = \sin \left(\beta \right)` -is a function of grid cell mean topographic slope where :math:`\beta` +is a function of grid cell mean topographic slope where :math:`\beta` is the slope in radians. .. _Infiltration: @@ -507,8 +507,8 @@ of soil s\ :sup:`-1`) (ET loss). This equation is solved numerically by dividing the soil column into multiple layers in the vertical and integrating downward over each layer with an upper boundary condition of the infiltration flux into the top soil layer -:math:`q_{infl}` and a zero-flux lower boundary condition at the -bottom of the soil column (sub-surface runoff is removed later in the +:math:`q_{infl}` and a zero-flux lower boundary condition at the +bottom of the soil column (sub-surface runoff is removed later in the timestep, section :numref:`Lateral Sub-surface Runoff`). The soil water flux :math:`q` in equation can be described by Darcy's @@ -555,12 +555,12 @@ the Richards equation :ref:`(Dingman 2002) ` .. math:: :label: 7.84 - \frac{\partial \theta }{\partial t} = - \frac{\partial }{\partial z} \left[k\left(\frac{\partial \psi }{\partial z} + 1 + \frac{\partial \theta }{\partial t} = + \frac{\partial }{\partial z} \left[k\left(\frac{\partial \psi }{\partial z} + 1 \right)\right]. -In practice (Section :numref:`Numerical Solution Hydrology`), changes in soil -water content are predicted from :eq:`7.79` using finite-difference approximations +In practice (Section :numref:`Numerical Solution Hydrology`), changes in soil +water content are predicted from :eq:`7.79` using finite-difference approximations for :eq:`7.84`. .. _Hydraulic Properties: @@ -571,42 +571,42 @@ Hydraulic Properties The hydraulic conductivity :math:`k_{i}` (mm s\ :sup:`-1`) and the soil matric potential :math:`\psi _{i}` (mm) for layer :math:`i` vary with volumetric soil water :math:`\theta _{i}` and soil texture. -As with the soil thermal properties (section +As with the soil thermal properties (section :numref:`Soil And Snow Thermal Properties`) the hydraulic properties of the soil are assumed to be a weighted combination of the mineral properties, which are determined according to sand and clay -contents based on work by :ref:`Clapp and Hornberger (1978) -` and :ref:`Cosby et al. (1984) `, -and organic properties of the soil +contents based on work by :ref:`Clapp and Hornberger (1978) +` and :ref:`Cosby et al. (1984) `, +and organic properties of the soil (:ref:`Lawrence and Slater 2008 `). The hydraulic conductivity is defined at the depth of the interface of -two adjacent layers :math:`z_{h,\, i}` (:numref:`Figure Water flux schematic`) +two adjacent layers :math:`z_{h,\, i}` (:numref:`Figure Water flux schematic`) and is a function of the saturated hydraulic conductivity :math:`k_{sat} \left[z_{h,\, i} \right]`, the liquid volumetric soil -moisture of the two layers :math:`\theta _{i}` and :math:`\theta_{i+1}` -and an ice impedance factor :math:`\Theta_{ice}` +moisture of the two layers :math:`\theta _{i}` and :math:`\theta_{i+1}` +and an ice impedance factor :math:`\Theta_{ice}` .. math:: :label: 7.85 k\left[z_{h,\, i} \right] = - \left\{\begin{array}{lr} - \Theta_{ice} k_{sat} \left[z_{h,\, i} \right]\left[\frac{0.5\left(\theta_{\, i} +\theta_{\, i+1} \right)}{0.5\left(\theta_{sat,\, i} +\theta_{sat,\, i+1} \right)} \right]^{2B_{i} +3} & \qquad 1 \le i \le N_{levsoi} - 1 \\ - \Theta_{ice} k_{sat} \left[z_{h,\, i} \right]\left(\frac{\theta_{\, i} }{\theta_{sat,\, i} } \right)^{2B_{i} +3} & \qquad i = N_{levsoi} + \left\{\begin{array}{lr} + \Theta_{ice} k_{sat} \left[z_{h,\, i} \right]\left[\frac{0.5\left(\theta_{\, i} +\theta_{\, i+1} \right)}{0.5\left(\theta_{sat,\, i} +\theta_{sat,\, i+1} \right)} \right]^{2B_{i} +3} & \qquad 1 \le i \le N_{levsoi} - 1 \\ + \Theta_{ice} k_{sat} \left[z_{h,\, i} \right]\left(\frac{\theta_{\, i} }{\theta_{sat,\, i} } \right)^{2B_{i} +3} & \qquad i = N_{levsoi} \end{array}\right\}. The ice impedance factor is a function of ice content, and is meant to quantify the increased tortuosity of the water flow when part of the -pore space is filled with ice. :ref:`Swenson et al. (2012) ` -used a power law form +pore space is filled with ice. :ref:`Swenson et al. (2012) ` +used a power law form .. math:: :label: 7.86 \Theta_{ice} = 10^{-\Omega F_{ice} } -where :math:`\Omega = 6`\ and :math:`F_{ice} = \frac{\theta_{ice} }{\theta_{sat} }` +where :math:`\Omega = 6`\ and :math:`F_{ice} = \frac{\theta_{ice} }{\theta_{sat} }` is the ice-filled fraction of the pore space. Because the hydraulic properties of mineral and organic soil may differ @@ -678,8 +678,8 @@ as 1 %. To better represent the influence of organic soil material on the grid cell average saturated hydraulic conductivity, the soil organic matter fraction is further subdivided into "connected" and "unconnected" fractions using a result from percolation theory (:ref:`Stauffer and Aharony -1994 `, :ref:`Berkowitz and Balberg 1992 `). -Assuming that the organic and mineral fractions are randomly distributed throughout +1994 `, :ref:`Berkowitz and Balberg 1992 `). +Assuming that the organic and mineral fractions are randomly distributed throughout a soil layer, percolation theory predicts that above a threshold value :math:`f_{om} = f_{threshold}`, connected flow pathways consisting of organic material only exist and span the soil space. Flow through these @@ -689,9 +689,9 @@ by :math:`k_{sat,\, om}`. This fraction of the grid cell is given by .. math:: :label: 7.97 - \begin{array}{lr} - f_{perc} =\; N_{perc} \left(f_{om} {\rm \; }-f_{threshold} \right)^{\beta_{perc} } f_{om} {\rm \; } & \qquad f_{om} \ge f_{threshold} \\ - f_{perc} = 0 & \qquad f_{om} 0 \\ + \begin{array}{lr} + \left(r_{e,\, i} \right)_{j} =\frac{\left(r_{i} \right)_{j} \left(w_{i} \right)_{j} }{\left(\beta _{t} \right)_{j} } & \qquad \left(\beta _{t} \right)_{j} >0 \\ \left(r_{e,\, i} \right)_{j} =0 & \qquad \left(\beta _{t} \right)_{j} =0 \end{array} - + and :math:`\left(r_{i} \right)_{j}` is the fraction of roots in layer -:math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), -:math:`\left(w_{i} \right)_{j}` is a soil dryness or plant wilting factor +:math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), +:math:`\left(w_{i} \right)_{j}` is a soil dryness or plant wilting factor for layer :math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), and :math:`\left(\beta_{t} \right)_{j}` is a wetness factor for the total soil column for the :math:`j^{th}` PFT (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). @@ -890,7 +890,7 @@ where b_{i} =\frac{\partial q_{i} }{\partial \theta_{liq,\, i} } -\frac{\partial q_{i-1} }{\partial \theta_{liq,\, i} } -\frac{\Delta z_{i} }{\Delta t} .. math:: - :label: 7.113 + :label: 7.113 c_{i} =\frac{\partial q_{i} }{\partial \theta_{liq,\, i+1} } @@ -963,15 +963,15 @@ derived from :eq:`7.85` .. math:: :label: 7.124 - \begin{array}{l} - {\frac{\partial k\left[z_{h,\, i-1} \right]}{\partial \theta _{liq,\, i-1} } - = \frac{\partial k\left[z_{h,\, i-1} \right]}{\partial \theta _{liq,\, i} } + \begin{array}{l} + {\frac{\partial k\left[z_{h,\, i-1} \right]}{\partial \theta _{liq,\, i-1} } + = \frac{\partial k\left[z_{h,\, i-1} \right]}{\partial \theta _{liq,\, i} } = \left(2B_{i-1} +3\right) \ \overline{\Theta}_{ice} \ k_{sat} \left[z_{h,\, i-1} \right] \ \left[\frac{\overline{\theta}_{liq}}{\overline{\theta}_{sat}} \right]^{2B_{i-1} +2} \left(\frac{0.5}{\overline{\theta}_{sat}} \right)} \end{array} -where :math:`\overline{\Theta}_{ice} = \Theta(\overline{\theta}_{ice})` :eq:`7.86`, -:math:`\overline{\theta}_{ice} = 0.5\left(\theta_{ice\, i-1} +\theta_{ice\, i} \right)`, -:math:`\overline{\theta}_{liq} = 0.5\left(\theta_{liq\, i-1} +\theta_{liq\, i} \right)`, -and +where :math:`\overline{\Theta}_{ice} = \Theta(\overline{\theta}_{ice})` :eq:`7.86`, +:math:`\overline{\theta}_{ice} = 0.5\left(\theta_{ice\, i-1} +\theta_{ice\, i} \right)`, +:math:`\overline{\theta}_{liq} = 0.5\left(\theta_{liq\, i-1} +\theta_{liq\, i} \right)`, +and :math:`\overline{\theta}_{sat} = 0.5\left(\theta_{sat,\, i-1} +\theta_{sat,\, i} \right)` and @@ -979,12 +979,12 @@ and .. math:: :label: 7.125 - \begin{array}{l} - {\frac{\partial k\left[z_{h,\, i} \right]}{\partial \theta _{liq,\, i} } - = \frac{\partial k\left[z_{h,\, i} \right]}{\partial \theta _{liq,\, i+1} } + \begin{array}{l} + {\frac{\partial k\left[z_{h,\, i} \right]}{\partial \theta _{liq,\, i} } + = \frac{\partial k\left[z_{h,\, i} \right]}{\partial \theta _{liq,\, i+1} } = \left(2B_{i} +3\right) \ \overline{\Theta}_{ice} \ k_{sat} \left[z_{h,\, i} \right] \ \left[\frac{\overline{\theta}_{liq}}{\overline{\theta}_{sat}} \right]^{2B_{i} +2} \left(\frac{0.5}{\overline{\theta}_{sat}} \right)} \end{array}. -where :math:`\overline{\theta}_{liq} = 0.5\left(\theta_{\, i} +\theta_{\, i+1} \right)`, +where :math:`\overline{\theta}_{liq} = 0.5\left(\theta_{\, i} +\theta_{\, i+1} \right)`, :math:`\overline{\theta}_{sat} = 0.5\left(\theta_{sat,\, i} +\theta_{sat,\, i+1} \right)`. Equation set for layer :math:`i=1` @@ -1052,7 +1052,7 @@ The coefficients of the tridiagonal set of equations for Equation set for layer :math:`i=N_{levsoi}` '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -For the lowest soil layer (:math:`i=N_{levsoi}` ), a zero-flux bottom boundary +For the lowest soil layer (:math:`i=N_{levsoi}` ), a zero-flux bottom boundary condition is applied (:math:`q_{i}^{n} =0`) and the coefficients of the tridiagonal set of equations for :math:`i=N_{levsoi}` are @@ -1080,23 +1080,23 @@ and the coefficients of the tridiagonal set of equations for Adaptive Time Stepping ''''''''''''''''''''''''''''' -The length of the time step is adjusted in order to improve the accuracy -and stability of the numerical solutions. The difference between two numerical -approximations is used to estimate the temporal truncation error, and then -the step size :math:`\Delta t_{sub}` is adjusted to meet a user-prescribed error tolerance -:ref:`[Kavetski et al., 2002]`. The temporal truncation -error is estimated by comparing the flux obtained from the first-order -Taylor series expansion (:math:`q_{i-1}^{n+1}` and :math:`q_{i}^{n+1}`, -equations :eq:`7.108` and :eq:`7.109`) against the flux at the start of the -time step (:math:`q_{i-1}^{n}` and :math:`q_{i}^{n}`). Since the tridiagonal -solution already provides an estimate of :math:`\Delta \theta_{liq,i}`, it is -convenient to compute the error for each of the :math:`i` layers from equation -:eq:`7.103` as +The length of the time step is adjusted in order to improve the accuracy +and stability of the numerical solutions. The difference between two numerical +approximations is used to estimate the temporal truncation error, and then +the step size :math:`\Delta t_{sub}` is adjusted to meet a user-prescribed error tolerance +:ref:`[Kavetski et al., 2002]`. The temporal truncation +error is estimated by comparing the flux obtained from the first-order +Taylor series expansion (:math:`q_{i-1}^{n+1}` and :math:`q_{i}^{n+1}`, +equations :eq:`7.108` and :eq:`7.109`) against the flux at the start of the +time step (:math:`q_{i-1}^{n}` and :math:`q_{i}^{n}`). Since the tridiagonal +solution already provides an estimate of :math:`\Delta \theta_{liq,i}`, it is +convenient to compute the error for each of the :math:`i` layers from equation +:eq:`7.103` as .. math:: :label: 7.152 - \epsilon_{i} = \left[ \frac{\Delta \theta_{liq,\, i} \Delta z_{i}}{\Delta t_{sub}} - + \epsilon_{i} = \left[ \frac{\Delta \theta_{liq,\, i} \Delta z_{i}}{\Delta t_{sub}} - \left( q_{i-1}^{n} - q_{i}^{n} + e_{i}\right) \right] \ \frac{\Delta t_{sub}}{2} and the maximum absolute error across all layers as @@ -1108,17 +1108,17 @@ and the maximum absolute error across all layers as \epsilon_{crit} = {\rm max} \left( \left| \epsilon_{i} \right| \right) & \qquad 1 \le i \le nlevsoi \end{array} \ . -The adaptive step size selection is based on specified upper and lower error -tolerances, :math:`\tau_{U}` and :math:`\tau_{L}`. The solution is accepted if -:math:`\epsilon_{crit} \le \tau_{U}` and the procedure repeats until the adaptive -sub-stepping spans the full model time step (the sub-steps are doubled if -:math:`\epsilon_{crit} \le \tau_{L}`, i.e., if the solution is very accurate). -Conversely, the solution is rejected if :math:`\epsilon_{crit} > \tau_{U}`. In -this case the length of the sub-steps is halved and a new solution is obtained. -The halving of substeps continues until either :math:`\epsilon_{crit} \le \tau_{U}` -or the specified minimum time step length is reached. - -Upon solution of the tridiagonal equation set, the liquid water contents are updated +The adaptive step size selection is based on specified upper and lower error +tolerances, :math:`\tau_{U}` and :math:`\tau_{L}`. The solution is accepted if +:math:`\epsilon_{crit} \le \tau_{U}` and the procedure repeats until the adaptive +sub-stepping spans the full model time step (the sub-steps are doubled if +:math:`\epsilon_{crit} \le \tau_{L}`, i.e., if the solution is very accurate). +Conversely, the solution is rejected if :math:`\epsilon_{crit} > \tau_{U}`. In +this case the length of the sub-steps is halved and a new solution is obtained. +The halving of substeps continues until either :math:`\epsilon_{crit} \le \tau_{U}` +or the specified minimum time step length is reached. + +Upon solution of the tridiagonal equation set, the liquid water contents are updated as follows .. math:: @@ -1129,7 +1129,7 @@ as follows The volumetric water content is .. math:: - :label: 7.165 + :label: 7.165 \theta_{i} =\frac{w_{liq,\, i} }{\Delta z_{i} \rho _{liq} } +\frac{w_{ice,\, i} }{\Delta z_{i} \rho _{ice} } . @@ -1139,8 +1139,8 @@ Frozen Soils and Perched Water Table ---------------------------------------- When soils freeze, the power-law form of the ice impedance factor -(section :numref:`Hydraulic Properties`) can greatly decrease the hydraulic -conductivity of the soil, leading to nearly impermeable soil layers. When unfrozen +(section :numref:`Hydraulic Properties`) can greatly decrease the hydraulic +conductivity of the soil, leading to nearly impermeable soil layers. When unfrozen soil layers are present above relatively ice-rich frozen layers, the possibility exists for perched saturated zones. Lateral drainage from perched saturated regions is parameterized as a function of the @@ -1159,7 +1159,7 @@ hydraulic conductivity, k_{drai,\, perch} =10^{-5} \sin (\beta )\left(\frac{\sum _{i=N_{perch} }^{i=N_{frost} }\Theta_{ice,i} k_{sat} \left[z_{i} \right]\Delta z_{i} }{\sum _{i=N_{perch} }^{i=N_{frost} }\Delta z_{i} } \right) -where :math:`\Theta_{ice}` is an ice impedance factor, :math:`\beta` +where :math:`\Theta_{ice}` is an ice impedance factor, :math:`\beta` is the mean grid cell topographic slope in radians, :math:`z_{frost}` \ is the depth to the frost table, and :math:`z_{\nabla ,perch}` is the depth to the perched saturated zone. @@ -1168,7 +1168,7 @@ layer having an unfrozen layer above it, while the perched water table :math:`z_{\nabla ,perch}` is defined as the depth at which the volumetric water content drops below a specified threshold. The default threshold is set to 0.9. Drainage from the perched saturated zone -:math:`q_{drai,perch}` is removed from layers :math:`N_{perch}` +:math:`q_{drai,perch}` is removed from layers :math:`N_{perch}` through :math:`N_{frost}` , which are the layers containing :math:`z_{\nabla ,perch}` and, :math:`z_{frost}` \ respectively. @@ -1176,29 +1176,29 @@ through :math:`N_{frost}` , which are the layers containing Lateral Sub-surface Runoff --------------------------------------- -Lateral sub-surface runoff occurs when saturated soil moisture conditions -exist within the soil column. Sub-surface runoff is +Lateral sub-surface runoff occurs when saturated soil moisture conditions +exist within the soil column. Sub-surface runoff is .. math:: :label: 7.168 - q_{drai} = \Theta_{ice} K_{baseflow} tan \left( \beta \right) + q_{drai} = \Theta_{ice} K_{baseflow} tan \left( \beta \right) \Delta z_{sat}^{N_{baseflow}} \ , -where :math:`K_{baseflow}` is a calibration parameter, :math:`\beta` is the -topographic slope, the exponent :math:`N_{baseflow}` = 1, and :math:`\Delta z_{sat}` -is the thickness of the saturated portion of the soil column. +where :math:`K_{baseflow}` is a calibration parameter, :math:`\beta` is the +topographic slope, the exponent :math:`N_{baseflow}` = 1, and :math:`\Delta z_{sat}` +is the thickness of the saturated portion of the soil column. -The saturated thickness is +The saturated thickness is .. math:: :label: 7.1681 - \Delta z_{sat} = z_{bedrock} - z_{\nabla}, + \Delta z_{sat} = z_{bedrock} - z_{\nabla}, -where the water table :math:`z_{\nabla}` is determined by finding the -first soil layer above the bedrock depth (section :numref:`Depth to Bedrock`) -in which the volumetric water content drops below a specified threshold. +where the water table :math:`z_{\nabla}` is determined by finding the +first soil layer above the bedrock depth (section :numref:`Depth to Bedrock`) +in which the volumetric water content drops below a specified threshold. The default threshold is set to 0.9. The specific yield, :math:`S_{y}` , which depends on the soil @@ -1218,7 +1218,7 @@ are consistent with the soil water fluxes described in section :numref:`Soil Wat After the above calculations, two numerical adjustments are implemented to keep the liquid water content of each soil layer (:math:`w_{liq,\, i}` ) within physical constraints of -:math:`w_{liq}^{\min } \le w_{liq,\, i} \le \left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i}` +:math:`w_{liq}^{\min } \le w_{liq,\, i} \le \left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i}` where :math:`w_{liq}^{\min } =0.01` (mm). First, beginning with the bottom soil layer :math:`i=N_{levsoi}` , any excess liquid water in each soil layer @@ -1239,7 +1239,7 @@ found, then the water is removed from :math:`W_{t}` and :math:`q_{drai}` . The soil surface layer liquid water and ice contents are then updated -for dew :math:`q_{sdew}` , frost :math:`q_{frost}` , or sublimation :math:`q_{subl}` +for dew :math:`q_{sdew}` , frost :math:`q_{frost}` , or sublimation :math:`q_{subl}` (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`) as .. math:: @@ -1266,14 +1266,14 @@ Runoff from glaciers and snow-capped surfaces All surfaces are constrained to have a snow water equivalent :math:`W_{sno} \le W_{cap} = 10,000` kg m\ :sup:`-2`. For snow-capped -columns, any addition of mass at the top (precipitation, dew/riping) is -balanced by an equally large mass flux at the bottom of the snow column. +columns, any addition of mass at the top (precipitation, dew/riping) is +balanced by an equally large mass flux at the bottom of the snow column. This so-called capping flux is separated into solid :math:`q_{snwcp,ice}` \ and liquid :math:`q_{snwcp,liq}` runoff terms. -The partitioning of these phases is based on the phase ratio in the bottom snow +The partitioning of these phases is based on the phase ratio in the bottom snow layer at the time of the capping, such that phase ratio in this layer is unaltered. -The :math:`q_{snwcp,ice}` +The :math:`q_{snwcp,ice}` runoff is sent to the River Transport Model (RTM) (Chapter 11) where it is routed to the ocean as an ice stream and, if applicable, the ice is melted there. @@ -1299,6 +1299,6 @@ at the beginning and ending of the time step defined as Currently, glaciers are non-vegetated and :math:`E_{v} =W_{can} =0`. The contribution of lake runoff to :math:`q_{rgwl}` is described in -section :numref:`Precipitation, Evaporation, and Runoff Lake`. The runoff -term :math:`q_{rgwl}` may be negative for glaciers and lakes, which reduces +section :numref:`Precipitation, Evaporation, and Runoff Lake`. The runoff +term :math:`q_{rgwl}` may be negative for glaciers and lakes, which reduces the total amount of runoff available to the river routing model (Chapter :numref:`rst_River Transport Model (RTM)`). diff --git a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst index 6b91287388..815d3d8781 100644 --- a/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst +++ b/doc/source/tech_note/Introduction/CLM50_Tech_Note_Introduction.rst @@ -67,7 +67,7 @@ P. O. Box 3000, Boulder, Colorado 80307-300 - :numref:`Figure Biological nitrogen fixation` Biological nitrogen fixation as a function of annual net primary production. -- :numref:`Figure Methane Schematic` Schematic representation of biological and physical processes integrated in CLM that affect the net CH4 surface flux. +- :numref:`Figure Methane Schematic` Schematic representation of biological and physical processes integrated in CLM that affect the net CH4 surface flux. - :numref:`Figure Schematic of land cover change` Schematic of land cover change impacts on CLM carbon pools and fluxes. @@ -141,9 +141,9 @@ P. O. Box 3000, Boulder, Colorado 80307-300 - :numref:`Table Crop plant functional types` Crop plant functional types (PFTs). -- :numref:`Table Crop phenology parameters` Crop phenology and morphology parameters. +- :numref:`Table Crop phenology parameters` Crop phenology and morphology parameters. -- :numref:`Table Crop allocation parameters` Crop allocation parameters. +- :numref:`Table Crop allocation parameters` Crop allocation parameters. - :numref:`Table Dust Mass fraction` Mass fraction m\ :sub:`i` , mass median diameter :sub:`v, i` , and geometric standard deviation :sub:`g, i` , per dust source mode i @@ -524,12 +524,12 @@ light capture, carboxylation, and respiration are co-limiting. CLM5 applies a fixed allocation scheme for woody vegetation. The decision to use a fixed allocation scheme in CLM5, rather than a dynamic NPP-based allocation scheme, as was used in CLM4 and CLM4.5, was driven by the fact that observations indicate that biomass saturates with increasing productivity, in contrast to the behavior in CLM4 and CLM4.5 where biomass continuously increases with increasing productivity (:ref:`Negron-Juarez et al., 2015`). Soil carbon decomposition processes are unchanged in CLM5, but a new metric for apparent soil carbon turnover times (:ref:`Koven et al., 2017 `) suggested parameter changes that produce a weak intrinsic depth limitation on soil carbon turnover rates (rather than the strong depth limitaiton in CLM4.5) and that the thresholds for soil moisture limitation on soil carbon turnover rates in dry soils should be set at a wetter soil moisture level than that used in CLM4.5. -Representation of human management of the land (agriculture, wood harvest) is augmented in several ways. -The CLM4.5 crop model is extended to operate globally through the addition of rice, sugarcane, -tropical varieties of corn and soybean :ref:`(Badger and Dirmeyer, 2015` and :ref:`Levis et al., 2016)`, +Representation of human management of the land (agriculture, wood harvest) is augmented in several ways. +The CLM4.5 crop model is extended to operate globally through the addition of rice, sugarcane, +tropical varieties of corn and soybean :ref:`(Badger and Dirmeyer, 2015` and :ref:`Levis et al., 2016)`, and perennial bioenergy crops :ref:`(Cheng et al., 2019)`. These crop types are added to the existing temperate corn, temperate soybean, spring wheat, and cotton crop types. -Fertilization rates and irrigation equipped area updated annually based on crop type and geographic region through an input dataset. +Fertilization rates and irrigation equipped area updated annually based on crop type and geographic region through an input dataset. The irrigation trigger is updated. Additional minor changes include crop phenological triggers that vary by latitude for selected crop types, grain C and N is now removed at harvest to a 1-year product pool with the carbon for the next season's crop seed removed from the grain carbon at harvest. diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 0963c1ea31..f7fcbd5cb5 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -31,7 +31,7 @@ respectively, i.e. the pools *from which* the fluxes of :math:`{f}_{frac}`: .. math:: - :label: ZEqnNum629812 + :label: ZEqnNum629812 CF_{13C} =\left\{\begin{array}{l} {CF_{totC} \frac{CS_{13C\_ up} }{CS_{totC\_ up} } f_{frac} \qquad {\rm for\; }CS_{totC} \ne 0} \\ {0\qquad {\rm for\; }CS_{totC} =0} \end{array}\right\} @@ -61,7 +61,7 @@ about 99% of all carbon. The isotope ratio of a compound, :math:`{R}_{A}`, is the mass ratio of the rare isotope to the abundant isotope .. math:: - :label: 30.2) + :label: 30.2) R_{A} =\frac{{}^{13} C_{A} }{{}^{12} C_{A} } . @@ -72,7 +72,7 @@ difference between the isotope ratio of the compound, :math:`{R}_{A}`, and that of the Pee Dee Belemnite standard, :math:`{R}_{PDB}`, in parts per thousand .. math:: - :label: 30.3) + :label: 30.3) \delta ^{13} C_{A} =\left(\frac{R_{A} }{R_{PDB} } -1\right)\times 1000 @@ -84,14 +84,14 @@ For example, the equilibrium fractionation between two reservoirs A and B can be written as: .. math:: - :label: 30.4) + :label: 30.4) \alpha _{A-B} =\frac{R_{A} }{R_{B} } =\frac{\delta _{A} +1000}{\delta _{B} +1000} . This can also be expressed using epsilon notation (:math:`\epsilon`), where .. math:: - :label: 30.5) + :label: 30.5) \alpha _{A-B} =\frac{\varepsilon _{A-B} }{1000} +1 @@ -101,7 +101,7 @@ In addition to the stable isotopes :sup:`1`\ :sup:`2`\ C and :sup:`1`\ :sup:`3`\ :sup:`1`\ :sup:`4`\ C is included in CLM. :sup:`1`\ :sup:`4`\ C can also be described using the delta notation: .. math:: - :label: 30.6) + :label: 30.6) \delta ^{14} C=\left(\frac{A_{s} }{A_{abs} } -1\right)\times 1000 @@ -109,7 +109,7 @@ However, observations of :sup:`1`\ :sup:`4`\ C are typically fractionation-corrected using the following notation: .. math:: - :label: 30.7) + :label: 30.7) \Delta {}^{14} C=1000\times \left(\left(1+\frac{\delta {}^{14} C}{1000} \right)\frac{0.975^{2} }{\left(1+\frac{\delta {}^{13} C}{1000} \right)^{2} } -1\right) @@ -117,7 +117,7 @@ where :math:`\delta^{14}`\ C is the measured isotopic fraction and :math:`\mathrm{\Delta}^{14}`\ C corrects for mass-dependent isotopic fractionation processes (assumed to be 0.975 for fractionation of :sup:`13`\ C by photosynthesis). CLM assumes a -background preindustrial atmospheric :sup:`14`\ C /C ratio of 10\ :sup:`-12`, which is used for A\ :sub::`abs`. +background preindustrial atmospheric :sup:`14`\ C /C ratio of 10\ :sup:`-12`, which is used for A\ :sub::`abs`. For the reference standard A\ :math:`{}_{abs}`, which is a plant tissue and has a :math:`\delta^{13}`\ C value is :math:`\mathrm{-}`\ 25 ‰ due to photosynthetic discrimination, :math:`\delta`\ :sup:`14`\ C = :math:`\mathrm{\Delta}`\ :sup:`14`\ C. For CLM, in order to use @@ -147,14 +147,14 @@ and C4 plants are given below: For C4 plants, .. math:: - :label: 30.8) + :label: 30.8) \alpha _{psn} =1+\frac{4.4}{1000} For C3 plants, .. math:: - :label: 30.9) + :label: 30.9) \alpha _{psn} =1+\frac{4.4+22.6\frac{c_{i}^{*} }{pCO_{2} } }{1000} @@ -169,7 +169,7 @@ carbon assimilation. That is calculated during the photosynthesis calculation as follows: .. math:: - :label: 30.10) + :label: 30.10) c_{i} =pCO_{2} -a_{n} p\frac{\left(1.4g_{s} \right)+\left(1.6g_{b} \right)}{g_{b} g_{s} } @@ -206,8 +206,8 @@ of the spinup mode. For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\:sup:`13`\ C values can be set to -either fixed concentrations -or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For +either fixed concentrations +or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 :sup:`o`\ N-90 :sup:`o`\ N, 30 :sup:`o`\ S-30 :sup:`o`\ N, and 30 :sup:`o`\ S-90 :sup:`o`\ S). diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 2cad862508..941932c8a3 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -4,16 +4,16 @@ Lake Model ============= The lake model, denoted the *Lake, Ice, Snow, and Sediment Simulator* -(LISSS), is from :ref:`Subin et al. (2012a) `. -It includes extensive modifications to the lake code of +(LISSS), is from :ref:`Subin et al. (2012a) `. +It includes extensive modifications to the lake code of :ref:`Zeng et al. (2002) ` used in CLM versions 2 through 4, which utilized concepts from the lake models of -:ref:`Bonan (1996) `, -:ref:`Henderson-Sellers (1985) `, -:ref:`Henderson-Sellers (1986) `, -:ref:`Hostetler and Bartlein (1990) `, -and the coupled lake-atmosphere model of :ref:`Hostetler et al. (1993) `, :ref:`Hostetler et al. (1993) `. -Lakes have spatially variable depth prescribed in the surface data (section +:ref:`Bonan (1996) `, +:ref:`Henderson-Sellers (1985) `, +:ref:`Henderson-Sellers (1986) `, +:ref:`Hostetler and Bartlein (1990) `, +and the coupled lake-atmosphere model of :ref:`Hostetler et al. (1993) `, :ref:`Hostetler et al. (1993) `. +Lakes have spatially variable depth prescribed in the surface data (section :ref:`External Data Lake`); the surface data optionally includes lake optical extinction coeffient and horizontal fetch, currently only used for site simulations. Lake physics includes freezing and thawing in the lake @@ -21,12 +21,12 @@ body, resolved snow layers, and "soil" and bedrock layers below the lake body. Temperatures and ice fractions are simulated for :math:`N_{levlak} =10` layers (for global simulations) or :math:`N_{levlak} =25` (for site simulations) with discretization -described in section :numref:`Vertical Discretization Lake`. Lake albedo is -described in section :numref:`Surface Albedo Lake`. Lake surface fluxes -(section :numref:`Surface Fluxes and Surface Temperature Lake`) generally -follow the formulations for non-vegetated surfaces, including the calculations -of aerodynamic resistances (section -:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`); +described in section :numref:`Vertical Discretization Lake`. Lake albedo is +described in section :numref:`Surface Albedo Lake`. Lake surface fluxes +(section :numref:`Surface Fluxes and Surface Temperature Lake`) generally +follow the formulations for non-vegetated surfaces, including the calculations +of aerodynamic resistances (section +:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`); however, the lake surface temperature :math:`T_{g}` (representing an infinitesimal interface layer between the top resolved lake layer and the atmosphere) is solved for @@ -35,7 +35,7 @@ evaluated, temperatures are solved simultaneously in the resolved snow layers (if present), the lake body, and the soil and bedrock, using the ground heat flux *G* as a top boundary condition. Snow, soil, and bedrock models generally follow the formulations for non-vegetated -surfaces (Chapter :numref:`rst_Soil and Snow Temperatures`), with +surfaces (Chapter :numref:`rst_Soil and Snow Temperatures`), with modifications described below. .. _Vertical Discretization Lake: @@ -77,13 +77,13 @@ least as thick as *s*\ :sub:`min` (section :numref:`Modifications to Snow Layer External Data ----------------- -As discussed in :ref:`Subin et al. (2012a, b) `, the -Global Lake and Wetland Database (:ref:`Lehner and Doll 2004`) -is currently used to prescribe lake fraction in each land model grid cell, -for a total of 2.3 million km\ :sup:`-2`. As in -:ref:`Subin et al. (2012a, b) `, the -:ref:`Kourzeneva et al. (2012)` global gridded dataset is currently -used to estimate a mean lake depth in each grid cell, based on interpolated +As discussed in :ref:`Subin et al. (2012a, b) `, the +Global Lake and Wetland Database (:ref:`Lehner and Doll 2004`) +is currently used to prescribe lake fraction in each land model grid cell, +for a total of 2.3 million km\ :sup:`-2`. As in +:ref:`Subin et al. (2012a, b) `, the +:ref:`Kourzeneva et al. (2012)` global gridded dataset is currently +used to estimate a mean lake depth in each grid cell, based on interpolated compilations of geographic information. .. _Surface Albedo Lake: @@ -105,7 +105,7 @@ eq. is integrated over the full sky to yield *a* = 0.10. For frozen lakes without resolved snow layers, the albedo at cold temperatures *a*\ :sub:`0` is 0.60 for visible and 0.40 for near infrared radiation. As the temperature at the ice surface, -:math:`{T}_{g}`, approaches freezing [ :math:`{T}_{f}` (K) (:numref:`Table Physical Constants`)], the albedo is relaxed towards 0.10 based on +:math:`{T}_{g}`, approaches freezing [ :math:`{T}_{f}` (K) (:numref:`Table Physical Constants`)], the albedo is relaxed towards 0.10 based on :ref:`Mironov et al. (2010)`: .. math:: @@ -117,7 +117,7 @@ where *a* is restricted to be no less than that given in :eq:`12.1`. For frozen lakes with resolved snow layers, the reflectance of the ice surface is fixed at *a*\ :sub:`0`, and the snow reflectance is -calculated as over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). +calculated as over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). These two reflectances are combined to obtain the snow-fraction-weighted albedo as in over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). @@ -134,7 +134,7 @@ Surface Properties The fraction of shortwave radiation absorbed at the surface, :math:`\beta`, depends on the lake state. If resolved snow layers are present, then :math:`\beta` is set equal to the absorption fraction -predicted by the snow-optics submodel (Chapter :numref:`rst_Surface Albedos`) +predicted by the snow-optics submodel (Chapter :numref:`rst_Surface Albedos`) for the top snow layer. Otherwise, :math:`\beta` is set equal to the near infrared fraction of the shortwave radiation reaching the surface simulated by @@ -178,12 +178,12 @@ below, and *g* is the acceleration of gravity (:numref:`Table Physical Constants viscosity is given by .. math:: - :label: 12.5 + :label: 12.5 \nu =\nu _{0} \left(\frac{T_{g} }{T_{0} } \right)^{1.5} \frac{P_{0} }{P_{ref} } where -:math:`\nu _{0} =1.51\times 10^{-5} {\textstyle\frac{{\rm m}^{{\rm 2}} }{{\rm s}}}` +:math:`\nu _{0} =1.51\times 10^{-5} {\textstyle\frac{{\rm m}^{{\rm 2}} }{{\rm s}}}` , :math:`T_{0} ={\rm 293.15\; K}`, :math:`P_{0} =1.013\times 10^{5} {\rm \; Pa}` , and :math:`P_{ref}` is the pressure at the atmospheric reference @@ -192,7 +192,7 @@ height. The Charnock coefficient *C* is a function of the lake fetch *F* default: .. math:: - :label: 12.6 + :label: 12.6 \begin{array}{l} {C=C_{\min } +(C_{\max } -C_{\min } )\exp \left\{-\min \left(A,B\right)\right\}} \\ {A={\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } \mathord{\left/ {\vphantom {\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } f_{c} }} \right.} f_{c} } } \\ {B=\varepsilon \frac{\sqrt{dg} }{u} } \end{array} @@ -246,13 +246,13 @@ sensible heat transfer (s m\ :sup:`-1`) (section :numref:`Monin-Obukhov Similari The water vapor flux (kg m\ :sup:`-2` s\ :sup:`-1`) is .. math:: - :label: 12.10 + :label: 12.10 E_{g} =-\frac{\rho _{atm} \left(q_{atm} -q_{sat}^{T_{g} } \right)}{r_{aw} } where :math:`q_{atm}` is the atmospheric specific humidity (kg -kg\ :sup:`-1`) (section :numref:`Atmospheric Coupling`), -:math:`q_{sat}^{T_{g} }` \ is the saturated specific humidity +kg\ :sup:`-1`) (section :numref:`Atmospheric Coupling`), +:math:`q_{sat}^{T_{g} }` \ is the saturated specific humidity (kg kg\ :sup:`-1`) (section :numref:`Saturation Vapor Pressure`) at the lake surface temperature :math:`T_{g}` , and :math:`r_{aw}` is the aerodynamic resistance to water vapor transfer (s m\ :sup:`-1`) @@ -271,7 +271,7 @@ The zonal and meridional momentum fluxes are \tau _{y} =-\rho _{atm} \frac{v_{atm} }{r_{atm} } where :math:`u_{atm}` and :math:`v_{atm}` are the zonal and -meridional atmospheric winds (m s\ :sup:`-1`) (section +meridional atmospheric winds (m s\ :sup:`-1`) (section :numref:`Atmospheric Coupling`), and :math:`r_{am}` is the aerodynamic resistance for momentum (s m\ :sup:`-1`) (section :numref:`Monin-Obukhov Similarity Theory`). @@ -306,7 +306,7 @@ The absorbed solar radiation :math:`\vec{S}_{g}` is where :math:`S_{atm} \, \downarrow _{\Lambda }^{\mu }` and :math:`S_{atm} \, \downarrow _{\Lambda }` are the incident direct beam -and diffuse solar fluxes (W m\ :sup:`-2`) and :math:`\Lambda` +and diffuse solar fluxes (W m\ :sup:`-2`) and :math:`\Lambda` denotes the visible (:math:`<` 0.7\ :math:`\mu {\rm m}`) and near-infrared (:math:`\ge` 0.7\ :math:`\mu {\rm m}`) wavebands (section :numref:`Atmospheric Coupling`), and :math:`\alpha _{g,\, \Lambda }^{\mu }` and @@ -322,7 +322,7 @@ The net emitted longwave radiation is where :math:`L_{g} \, \uparrow` is the upward longwave radiation from the surface, :math:`L_{atm} \, \downarrow` is the downward atmospheric -longwave radiation (section :numref:`Atmospheric Coupling`). The upward +longwave radiation (section :numref:`Atmospheric Coupling`). The upward longwave radiation from the surface is .. math:: @@ -331,12 +331,12 @@ longwave radiation from the surface is L\, \uparrow =\left(1-\varepsilon _{g} \right)L_{atm} \, \downarrow +\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} +4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right) where :math:`\varepsilon _{g} =0.97` is the lake surface emissivity, -:math:`\sigma` is the Stefan-Boltzmann constant (W m\ :sup:`-2` K\ -:sup:`-4`) (:numref:`Table Physical Constants`), and -:math:`T_{g}^{n+1} -T_{g}^{n}` is the difference in lake surface +:math:`\sigma` is the Stefan-Boltzmann constant (W m\ :sup:`-2` K\ +:sup:`-4`) (:numref:`Table Physical Constants`), and +:math:`T_{g}^{n+1} -T_{g}^{n}` is the difference in lake surface temperature between Newton-Raphson iterations (see below). -The sensible heat :math:`H_{g}` , the water vapor flux :math:`E_{g}` +The sensible heat :math:`H_{g}` , the water vapor flux :math:`E_{g}` through its dependence on the saturated specific humidity, the net longwave radiation :math:`\vec{L}_{g}` , and the ground heat flux :math:`G`, all depend on the lake surface temperature :math:`T_{g}` . @@ -382,11 +382,11 @@ where the partial derivatives are The fluxes of momentum, sensible heat, and water vapor are solved for simultaneously with lake surface temperature as follows. The stability-related equations are the same as for non-vegetated surfaces -(section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), -except that the surface roughnesses are here (weakly varying) functions -of the friction velocity :math:`u_{\*}` . To begin, *z*\ :sub:`0m` is set -based on the value calculated for the last timestep (for -:math:`T_{g} >T_{f}` ) or based on the values in section +(section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), +except that the surface roughnesses are here (weakly varying) functions +of the friction velocity :math:`u_{\*}` . To begin, *z*\ :sub:`0m` is set +based on the value calculated for the last timestep (for +:math:`T_{g} >T_{f}` ) or based on the values in section :numref:`Surface Properties Lake` (otherwise), and the scalar roughness lengths are set based on the relationships in section :numref:`Surface Properties Lake`. @@ -419,10 +419,10 @@ lengths are set based on the relationships in section :numref:`Surface Propertie #. Heat of vaporization / sublimation :math:`\lambda` (:eq:`12.8`) -#. Sensible heat flux :math:`H_{g}` is updated for :math:`T_{g}^{n+1}` +#. Sensible heat flux :math:`H_{g}` is updated for :math:`T_{g}^{n+1}` (:eq:`12.9`) -#. Water vapor flux :math:`E_{g}` is updated for :math:`T_{g}^{n+1}` +#. Water vapor flux :math:`E_{g}` is updated for :math:`T_{g}^{n+1}` as .. math:: @@ -461,7 +461,7 @@ density, 3.85\ :sup:`o` C (:ref:`Hostetler and Bartlein (1990) ` formulation, -due to unresolved processes (:ref:`Fang and Stefan 1996`; +:ref:`Hostetler and Bartlein (1990)` formulation, +due to unresolved processes (:ref:`Fang and Stefan 1996`; :ref:`Subin et al. (2012a) `). Lake water is now allowed to freeze by an arbitrary fraction for each layer, which releases latent heat and changes thermal properties. Convective mixing occurs for all @@ -560,9 +560,9 @@ Boundary Conditions ^^^^^^^^^^^^^^^^^^^^^^^^^ The top boundary condition, imposed at the top modeled layer -:math:`i=j_{top}` , where :math:`j_{top} =-n_{sno} +1`, is the downwards -surface flux *G* defined by the energy flux residual during the surface -temperature solution (section :numref:`Boundary Conditions Lake`). The bottom +:math:`i=j_{top}` , where :math:`j_{top} =-n_{sno} +1`, is the downwards +surface flux *G* defined by the energy flux residual during the surface +temperature solution (section :numref:`Boundary Conditions Lake`). The bottom boundary condition, imposed at :math:`i=N_{levlak} +N_{levgrnd}` , is zero flux. The 2-m windspeed :math:`u_{2}` \ (m s\ :sup:`-1`) is used in the calculation of eddy diffusivity: @@ -573,7 +573,7 @@ calculation of eddy diffusivity: u_{2} =\frac{u_{*} }{k} \ln \left(\frac{2}{z_{0m} } \right)\ge 0.1. where :math:`u_{*}` \ is the friction velocity calculated in section -:numref:`Boundary Conditions Lake` and *k* is the von Karman constant +:numref:`Boundary Conditions Lake` and *k* is the von Karman constant (:numref:`Table Physical Constants`). .. _Eddy Diffusivity and Thermal Conductivities: @@ -588,16 +588,16 @@ The total eddy diffusivity :math:`K_{W}` (m\ :sup:`2` s\ :sup:`-1`) for liquid K_{W} = m_{d} \left(\kappa _{e} +K_{ed} +\kappa _{m} \right) -where :math:`\kappa _{e}` is due to wind-driven eddies -(:ref:`Hostetler and Bartlein (1990)`), +where :math:`\kappa _{e}` is due to wind-driven eddies +(:ref:`Hostetler and Bartlein (1990)`), :math:`K_{ed}` is a modest enhanced diffusivity -intended to represent unresolved mixing processes +intended to represent unresolved mixing processes (:ref:`Fang and Stefan 1996`), :math:`\kappa _{m} =\frac{\lambda _{liq} }{c_{liq} \rho _{liq} }` \ is the molecular diffusivity of water (given by the ratio of its thermal conductivity (W m\ :sup:`-1` K\ :sup:`-1`) to the product of its heat capacity (J kg\ :sup:`-1` K\ :sup:`-1`) and density -(kg m\ :sup:`-3`), values given in :numref:`Table Physical Constants`), and :math:`m_{d}` +(kg m\ :sup:`-3`), values given in :numref:`Table Physical Constants`), and :math:`m_{d}` (unitless) is a factor which increases the overall diffusivity for large lakes, intended to represent 3-dimensional mixing processes such as caused by horizontal temperature gradients. As currently implemented, @@ -623,9 +623,9 @@ velocity (m s\ :sup:`-1`) is :math:`w^{*} =0.0012u_{2}` , and :math:`k^{*} =6.6u_{2}^{-1.84} \sqrt{\left|\sin \phi \right|}` . For the bottom layer, :math:`\kappa _{e,\, N_{levlak} } =\kappa _{e,N_{levlak} -1\, }` . As in -:ref:`Hostetler and Bartlein (1990)`, -the 2-m wind speed :math:`u_{2}` (m s\ :sup:`-1`) (eq. ) is used to evaluate -:math:`w^{*}` and :math:`k^{*}` rather than the 10-m wind used by +:ref:`Hostetler and Bartlein (1990)`, +the 2-m wind speed :math:`u_{2}` (m s\ :sup:`-1`) (eq. ) is used to evaluate +:math:`w^{*}` and :math:`k^{*}` rather than the 10-m wind used by :ref:`Henderson-Sellers (1985) `. @@ -649,7 +649,7 @@ m\ :sup:`-3`), and :math:`\frac{\partial \rho }{\partial z}` is approximated as :math:`\frac{\rho _{i+1} -\rho _{i} }{z_{i+1} -z_{i} }` . Note that because here, *z* is increasing downwards (unlike in :ref:`Hostetler and Bartlein (1990)`), eq. contains no negative sign; this is a correction -from CLM4. The density of water is +from CLM4. The density of water is (:ref:`Hostetler and Bartlein (1990)`) .. math:: @@ -657,7 +657,7 @@ from CLM4. The density of water is \rho _{i} =1000\left(1-1.9549\times 10^{-5} \left|T_{i} -277\right|^{1.68} \right). -The enhanced diffusivity :math:`K_{ed}` is given by +The enhanced diffusivity :math:`K_{ed}` is given by (:ref:`Fang and Stefan 1996`) .. math:: @@ -750,7 +750,7 @@ The remaining flux exiting the bottom of layer :math:`i=N_{levlak}` is absorbed in the top soil layer. The light extinction coefficient :math:`\eta` (m\ :sup:`-1`), if -not provided as external data, is a function of depth *d* (m) +not provided as external data, is a function of depth *d* (m) (:ref:`Subin et al. (2012a) `): .. math:: @@ -786,12 +786,12 @@ Crank-Nicholson Solution ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The solution method for thermal diffusion is similar to that used for -soil (Chapter :numref:`rst_Soil and Snow Temperatures`), except that the -lake body layers are sandwiched between the snow and soil layers +soil (Chapter :numref:`rst_Soil and Snow Temperatures`), except that the +lake body layers are sandwiched between the snow and soil layers (section :numref:`Introduction Lake`), and radiation flux is absorbed throughout the lake layers. Before solution, layer temperatures :math:`T_{i}` (K), thermal conductivities :math:`\tau _{i}` (W -m\ :sup:`-1` K\ :sup:`-1`), heat capacities :math:`c_{v,i}` +m\ :sup:`-1` K\ :sup:`-1`), heat capacities :math:`c_{v,i}` (J m\ :sup:`-2`), and layer and interface depths from all components are transformed into a uniform set of vectors with length :math:`N=n_{sno} +N_{levlak} +N_{levgrnd}` and consistent units to @@ -817,7 +817,7 @@ layer as \frac{c_{v,i} }{\Delta t} \left(T_{i}^{n+1} -T_{i}^{n} \right)=F_{i-1} -F_{i} +\phi _{i} where superscripts *n* + 1 and *n* denote values at the end and -beginning of the timestep :math:`\Delta t`, respectively, :math:`F_{i}` +beginning of the timestep :math:`\Delta t`, respectively, :math:`F_{i}` (W m\ :sup:`-2`) is the downward heat flux at the bottom of layer *i*, and :math:`\phi _{i}` is the solar radiation absorbed in layer *i*. @@ -832,9 +832,9 @@ in a tridiagonal system of equations: The fluxes :math:`F_{i}` are defined as follows: for the top layer, :math:`F_{j_{top} -1} =2G;a_{j_{top} } =0`, where *G* is defined as in -section :numref:`Boundary Conditions Lake` (the factor of 2 merely cancels -out the Crank-Nicholson 0.5 in the equation for :math:`r_{j_{top} }` ). -For the bottom layer, :math:`F_{N_{levlak} +N_{levgrnd} } =0`. +section :numref:`Boundary Conditions Lake` (the factor of 2 merely cancels +out the Crank-Nicholson 0.5 in the equation for :math:`r_{j_{top} }` ). +For the bottom layer, :math:`F_{N_{levlak} +N_{levgrnd} } =0`. For all other layers: .. math:: @@ -854,7 +854,7 @@ lakes. After the heat diffusion is calculated, phase change occurs in a given layer if the temperature is below freezing and liquid water remains, or if the temperature is above freezing and ice remains. -If melting occurs, the available energy for melting, :math:`Q_{avail}` +If melting occurs, the available energy for melting, :math:`Q_{avail}` (J m\ :sup:`-2`), is computed as .. math:: @@ -863,9 +863,9 @@ If melting occurs, the available energy for melting, :math:`Q_{avail}` Q_{avail} =\left(T_{i} -T_{f} \right)c_{v,i} where :math:`T_{i}` is the temperature of the layer after thermal -diffusion (section :numref:`Crank-Nicholson Solution Lake`), and -:math:`c_{v,i}` \ is as calculated in section -:numref:`Heat Capacities Lake`. The mass of melt in the layer *M* +diffusion (section :numref:`Crank-Nicholson Solution Lake`), and +:math:`c_{v,i}` \ is as calculated in section +:numref:`Heat Capacities Lake`. The mass of melt in the layer *M* (kg m\ :sup:`-2`) is given by .. math:: @@ -927,7 +927,7 @@ maintaining constant density. Convection ^^^^^^^^^^^^^^^^ -Convective mixing is based on +Convective mixing is based on :ref:`Hostetler et al.'s (1993, 1994)` coupled lake-atmosphere model, adjusting the lake temperature after diffusion and phase change to maintain a stable density profile. Unfrozen lakes @@ -937,16 +937,16 @@ applied to layers 1 to :math:`i+1` and the densities are updated. This scheme is applied iteratively to layers :math:`1\le i`), as occasionally +separately (:ref:`Subin et al. (2012a) `), as occasionally these can be induced by -heat expelled from the sediments (not present in the original -:ref:`Hostetler et al. (1994)` model). Mixing proceeds +heat expelled from the sediments (not present in the original +:ref:`Hostetler et al. (1994)` model). Mixing proceeds from the bottom upward in this case (i.e., first mixing layers :math:`i=N_{levlak} -1` and :math:`i=N_{levlak}` , then checking :math:`i=N_{levlak} -2` and :math:`i=N_{levlak} -1` and mixing down to :math:`i=N_{levlak}` if needed, and on to the top), so as not to mix in with warmer over-lying -layers.\ +layers.\ For frozen lakes, this algorithm is generalized to conserve total enthalpy and ice content, and to maintain ice contiguous at the top of @@ -977,7 +977,7 @@ be assigned to the ice, and the liquid layers will be kept at freezing. For the layer that contains both ice and liquid (if present), a weighted average temperature will have to be calculated. -If :math:`Q > 0`, then :math:`T_{froz} =T_{f}` , and :math:`T_{unfr}` +If :math:`Q > 0`, then :math:`T_{froz} =T_{f}` , and :math:`T_{unfr}` is given by .. math:: @@ -985,7 +985,7 @@ is given by T_{unfr} =\frac{Q}{\rho _{liq} Z_{i+1} \left[\left(1-I_{av} \right)c_{liq} \right]} +T_{f} . -If :math:`Q < 0`, then :math:`T_{unfr} =T_{f}` , and :math:`T_{froz}` +If :math:`Q < 0`, then :math:`T_{unfr} =T_{f}` , and :math:`T_{froz}` is given by .. math:: @@ -1067,7 +1067,7 @@ There are some modifications to the soil and snow parameterizations as compared with the soil in vegetated land units, or the snow overlying other impervious columns. The soil can freeze or thaw, with the allowance for frost heave (or the initialization of excess ice) -(sections :numref:`Eddy Diffusivity and Thermal Conductivities` and +(sections :numref:`Eddy Diffusivity and Thermal Conductivities` and :numref:`Phase Change Lake`), but no air-filled pore space is allowed in the soil. To preserve numerical stability in the lake model (which uses a slightly different surface flux algorithm than over other @@ -1097,9 +1097,9 @@ where :math:`W_{sno}` (kg m\ :sup:`-2`) is the total mass of snow :math:`w_{liq,i}` and :math:`w_{ice,i}` are the masses of water phases (kg m\ :sup:`-2`) in soil layer *i*, :math:`q_{rain}` and :math:`q_{sno}` are the precipitation forcing from the atmosphere (kg -m\ :sup:`-2` s\ :sup:`-1`), :math:`q_{snwcp,\, ice}` is the ice runoff -associated with snow-capping (below), :math:`E_{g}` is the ground -evaporation (section :numref:`Surface Flux Solution Lake`), and :math:`n_{levsoi}` +m\ :sup:`-2` s\ :sup:`-1`), :math:`q_{snwcp,\, ice}` is the ice runoff +associated with snow-capping (below), :math:`E_{g}` is the ground +evaporation (section :numref:`Surface Flux Solution Lake`), and :math:`n_{levsoi}` is the number of hydrologically active soil layers (as opposed to dry bedrock layers). @@ -1114,8 +1114,8 @@ As for other land types, incident snowfall accumulates (with ice mass exceeds a minimum thickness :math:`s_{\min }` , at which point a resolved snow layer is initiated, with water, ice, dissolved aerosol, snow-grain radius, etc., state variables tracked by the Snow Hydrology -submodel (Chapter :numref:`rst_Snow Hydrology`). The density of fresh snow is -assigned as for other land types (Chapter :numref:`rst_Snow Hydrology`). +submodel (Chapter :numref:`rst_Snow Hydrology`). The density of fresh snow is +assigned as for other land types (Chapter :numref:`rst_Snow Hydrology`). Solid precipitation is added immediately to the snow, while liquid precipitation is added to snow layers, if they exist, after accounting for dew, frost, and sublimation (below). If @@ -1143,11 +1143,11 @@ given by If :math:`E_{g} <0,T_{g} \le T_{f}` , and there are no resolved snow layers or the top snow layer is not unfrozen, then the rate of frost production :math:`q_{frost} =\left|E_{g} \right|`. If :math:`E_{g} <0` -but the top snow layer has completely thawed during the Phase Change step -of the Lake Temperature solution (section :numref:`Phase Change Lake`), then -frost (or dew) is not allowed to accumulate (:math:`q_{frost} =0`), to -insure that the layer is eliminated by the Snow Hydrology -(Chapter :numref:`rst_Snow Hydrology`) code. (If :math:`T_{g} >T_{f}`, +but the top snow layer has completely thawed during the Phase Change step +of the Lake Temperature solution (section :numref:`Phase Change Lake`), then +frost (or dew) is not allowed to accumulate (:math:`q_{frost} =0`), to +insure that the layer is eliminated by the Snow Hydrology +(Chapter :numref:`rst_Snow Hydrology`) code. (If :math:`T_{g} >T_{f}`, then no snow is present (section :numref:`Surface Flux Solution Lake`), and evaporation or dew deposition is balanced by :math:`q_{rgwl}` .) The snowpack is updated for frost and sublimation: @@ -1157,8 +1157,8 @@ snowpack is updated for frost and sublimation: W_{sno} =W_{sno} +\Delta t\left(q_{frost} -q_{sub,sno} \right) . -If there are resolved snow layers, then this update occurs using the Snow -Hydrology submodel (Chapter :numref:`rst_Snow Hydrology`). Otherwise, the +If there are resolved snow layers, then this update occurs using the Snow +Hydrology submodel (Chapter :numref:`rst_Snow Hydrology`). Otherwise, the snow ice mass is updated directly, and :math:`z_{sno}` is adjusted by the same proportion as the snow ice (i.e., maintaining the same density), unless there was no snow before adding the frost, in which case the density is @@ -1204,17 +1204,17 @@ found in heterogeneous chunks) but irreversibly lost when melt occurs. Modifications to Snow Layer Logic ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -A thickness difference :math:`z_{lsa} =s_{\min } -\tilde{s}_{\min }` +A thickness difference :math:`z_{lsa} =s_{\min } -\tilde{s}_{\min }` adjusts the minimum resolved snow layer thickness for lake columns as compared to non-lake columns. The value of :math:`z_{lsa}` is chosen to satisfy the CFL condition for the model timestep. By default, :math:`\tilde{s}_{\min }` \ = 1 cm and :math:`s_{\min }` \ = 4 cm. See -:ref:`Subin et al. (2012a; including Supporting Information)` +:ref:`Subin et al. (2012a; including Supporting Information)` for further discussion. -The rules for combining and sub-dividing snow layers (section +The rules for combining and sub-dividing snow layers (section :numref:`Snow Layer Combination and Subdivision`) are -adjusted for lakes to maintain minimum thicknesses of :math:`s_{\min }` +adjusted for lakes to maintain minimum thicknesses of :math:`s_{\min }` and to increase all target layer thicknesses by :math:`z_{lsa}` . The rules for combining layers are modified by simply increasing layer thickness thresholds by :math:`z_{lsa}` . The rules for dividing snow @@ -1231,5 +1231,5 @@ are performed. In rare instances, resolved snow layers may be present over an unfrozen top lake body layer. In this case, the snow layers may be eliminated if -enough heat is present in the top layer to melt the snow: see +enough heat is present in the top layer to melt the snow: see :ref:`Subin et al. (2012a, Supporting Information) `. diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index 137db2b18a..b043f422b0 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -4,28 +4,28 @@ Land-Only Mode ================ In land-only mode (uncoupled to an atmospheric model), the atmospheric -forcing required by CLM (:numref:`Table Atmospheric input to land model`) +forcing required by CLM (:numref:`Table Atmospheric input to land model`) is supplied by observed datasets. The standard forcing provided with the model is a 110-year (1901-2010) dataset provided by the Global Soil Wetness Project (GSWP3; NEED A REFERENCE). The GSWP3 dataset has a spatial resolution of 0.5\ :sup:`o` X 0.5\ :sup:`o` and a temporal resolution of three hours. -An alternative forcing dataset is also available, CRUNCEP, a 110-year (1901-2010) dataset +An alternative forcing dataset is also available, CRUNCEP, a 110-year (1901-2010) dataset (CRUNCEP; :ref:`Viovy 2011 `) that is a combination of two existing datasets; -the CRU TS3.2 0.5\ :sup:`o` X 0.5\ :sup:`o` monthly data covering the period +the CRU TS3.2 0.5\ :sup:`o` X 0.5\ :sup:`o` monthly data covering the period 1901 to 2002 (:ref:`Mitchell and Jones 2005 `) and the NCEP reanalysis 2.5\ :sup:`o` X 2.5\ :sup:`o` 6-hourly data covering the period 1948 to 2010. The CRUNCEP dataset has been used to force CLM for studies of vegetation growth, -evapotranspiration, and gross primary production (:ref:`Mao et al. 2012 `, -:ref:`Mao et al. 2013 `, :ref:`Shi et al. 2013 `) -and for the TRENDY (trends in net land-atmosphere carbon exchange over the period +evapotranspiration, and gross primary production (:ref:`Mao et al. 2012 `, +:ref:`Mao et al. 2013 `, :ref:`Shi et al. 2013 `) +and for the TRENDY (trends in net land-atmosphere carbon exchange over the period 1980-2010) project (:ref:`Piao et al. 2012 `). Version 7 is available here (:ref:`Viovy 2011 `). Here, the GSWP3 dataset, which does not include data for particular fields over oceans, -lakes, and Antarctica is modified. This missing data is filled with +lakes, and Antarctica is modified. This missing data is filled with :ref:`Qian et al. (2006) ` data from 1948 that is interpolated by the data atmosphere model to the 0.5\ :sup:`o` GSWP3 grid. This allows the model to be run over Antarctica and ensures data is available along coastlines @@ -36,7 +36,7 @@ The forcing data is ingested into a data atmosphere model in three radiation (:math:`S_{atm}` ) (W m\ :sup:`-2`), and four other fields [atmospheric pressure :math:`P_{atm}` (Pa), atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`), atmospheric -temperature :math:`T_{atm}` (K), and atmospheric wind :math:`W_{atm}` +temperature :math:`T_{atm}` (K), and atmospheric wind :math:`W_{atm}` (m s\ :sup:`-1`)]. These are separate streams because they are handled differently according to the type of field. In the GSWP3 dataset, the precipitation stream is provided at three hour intervals and @@ -56,9 +56,9 @@ used. The solar radiation at model time step :math:`t_{M}` is .. math:: :label: 31.1 - \begin{array}{lr} - S_{atm} \left(t_{M} \right)=\frac{\frac{\Delta t_{FD} }{\Delta t_{M} } S_{atm} \left(t_{FD} \right)\mu \left(t_{M} \right)}{\sum _{i=1}^{\frac{\Delta t_{FD} }{\Delta t_{M} } }\mu \left(t_{M_{i} } \right) } & \qquad {\rm for\; }\mu \left(t_{M} \right)>0.001 \\ - S_{atm} \left(t_{M} \right)=0 & \qquad {\rm for\; }\mu \left(t_{M} \right)\le 0.001 + \begin{array}{lr} + S_{atm} \left(t_{M} \right)=\frac{\frac{\Delta t_{FD} }{\Delta t_{M} } S_{atm} \left(t_{FD} \right)\mu \left(t_{M} \right)}{\sum _{i=1}^{\frac{\Delta t_{FD} }{\Delta t_{M} } }\mu \left(t_{M_{i} } \right) } & \qquad {\rm for\; }\mu \left(t_{M} \right)>0.001 \\ + S_{atm} \left(t_{M} \right)=0 & \qquad {\rm for\; }\mu \left(t_{M} \right)\le 0.001 \end{array} where :math:`\Delta t_{FD}` is the time step of the forcing data (3 @@ -122,13 +122,13 @@ and in the near-infrared :math:`R_{nir}` is R_{nir} =b_{0} +b_{1} \times \left(1-\alpha \right)S_{atm} +b_{2} \times \left[\left(1-\alpha \right)S_{atm} \right]^{2} +b_{3} \times \left[\left(1-\alpha \right)S_{atm} \right]^{3} \qquad 0.01\le R_{nir} \le 0.99 where -:math:`a_{0} =0.17639,\, a_{1} =0.00380,\, a_{2} =-9.0039\times 10^{-6} ,\, a_{3} =8.1351\times 10^{-9}` +:math:`a_{0} =0.17639,\, a_{1} =0.00380,\, a_{2} =-9.0039\times 10^{-6} ,\, a_{3} =8.1351\times 10^{-9}` and -:math:`b_{0} =0.29548,b_{1} =0.00504,b_{2} =-1.4957\times 10^{-5} ,b_{3} =1.4881\times 10^{-8}` +:math:`b_{0} =0.29548,b_{1} =0.00504,b_{2} =-1.4957\times 10^{-5} ,b_{3} =1.4881\times 10^{-8}` are coefficients from polynomial fits to the CAM data. The additional atmospheric forcing variables required by :numref:`Table Atmospheric input to land model` are -derived as follows. The atmospheric reference height :math:`z'_{atm}` +derived as follows. The atmospheric reference height :math:`z'_{atm}` (m) is set to 30 m. The directional wind components are derived as :math:`u_{atm} =v_{atm} ={W_{atm} \mathord{\left/ {\vphantom {W_{atm} \sqrt{2} }} \right.} \sqrt{2} }` . The potential temperature :math:`\overline{\theta _{atm} }` (K) is set @@ -172,8 +172,8 @@ where f_{P} =0<0.5\left(T_{atm} -T_{f} \right)<1. The aerosol deposition rates :math:`D_{sp}` (14 rates as described in -:numref:`Table Atmospheric input to land model`) are provided by a -time-varying, globally-gridded aerosol deposition file developed by +:numref:`Table Atmospheric input to land model`) are provided by a +time-varying, globally-gridded aerosol deposition file developed by :ref:`Lamarque et al. (2010) `. If the user wishes to provide atmospheric forcing data from another @@ -191,7 +191,7 @@ where the atmospheric vapor pressure :math:`e_{atm}` (Pa) is derived from the water (:math:`T_{atm} >T_{f}` ) or ice (:math:`T_{atm} \le T_{f}` ) saturation vapor pressure :math:`e_{sat}^{T_{atm} }` as -:math:`e_{atm} =\frac{RH}{100} e_{sat}^{T_{atm} }` where :math:`T_{f}` +:math:`e_{atm} =\frac{RH}{100} e_{sat}^{T_{atm} }` where :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical constants`), and :math:`P_{atm}` is the pressure at height :math:`z_{atm}` (Pa). The data atmosphere model will also accept a user-supplied dew point @@ -223,33 +223,33 @@ into the visible and near-infrared wavebands (e.g., Anomaly Forcing ----------------------------- -The 'Anomaly Forcing' atmospheric forcing mode provides a means to drive -CLM with projections of future climate conditions without the need for -large, high-frequency datasets. From an existing climate simulation -spanning both the historical and future time periods, a set of anomalies -are created by removing a climatological seasonal cycle based on the end -of the historical period from each year of the future time period of the -simulation. These anomalies can then be applied to a repeating -high-frequency forcing dataset of finite duration (e.g. 10 years). State -and flux forcing variables are adjusted using additive and multiplicative +The 'Anomaly Forcing' atmospheric forcing mode provides a means to drive +CLM with projections of future climate conditions without the need for +large, high-frequency datasets. From an existing climate simulation +spanning both the historical and future time periods, a set of anomalies +are created by removing a climatological seasonal cycle based on the end +of the historical period from each year of the future time period of the +simulation. These anomalies can then be applied to a repeating +high-frequency forcing dataset of finite duration (e.g. 10 years). State +and flux forcing variables are adjusted using additive and multiplicative anomalies, respectively: .. math:: :label: 31.16 - \begin{array}{lr} - S^{'} = S + k_{anomaly} & \quad {\rm state \ variable} \\ - F^{'} = f \times k_{anomaly} & \quad {\rm flux \ variable} + \begin{array}{lr} + S^{'} = S + k_{anomaly} & \quad {\rm state \ variable} \\ + F^{'} = f \times k_{anomaly} & \quad {\rm flux \ variable} \end{array} -where :math:`S^{'}` is the adjusted atmospheric state variable, :math:`S` -is the state variable from the high-frequency reference atmospheric -forcing dataset, and :math:`k_{anomaly}` is an additive anomaly. -Similarly, :math:`F^{'}` is the adjusted atmospheric flux variable, -:math:`F` is the flux variable from the high-frequency reference -atmospheric forcing dataset, and :math:`k_{anomaly}` is a -multiplicative anomaly. State variables are temperature :math:`T_{atm}`, -pressure :math:`P_{atm}`, humidity :math:`q_{atm}`, and wind +where :math:`S^{'}` is the adjusted atmospheric state variable, :math:`S` +is the state variable from the high-frequency reference atmospheric +forcing dataset, and :math:`k_{anomaly}` is an additive anomaly. +Similarly, :math:`F^{'}` is the adjusted atmospheric flux variable, +:math:`F` is the flux variable from the high-frequency reference +atmospheric forcing dataset, and :math:`k_{anomaly}` is a +multiplicative anomaly. State variables are temperature :math:`T_{atm}`, +pressure :math:`P_{atm}`, humidity :math:`q_{atm}`, and wind :math:`W_{atm}`. Flux variables are precipitation :math:`P`, atmospheric shortwave radiation :math:`S_{atm} \, \downarrow`, and atmospheric longwave radiation :math:`L_{atm} \, \downarrow`. diff --git a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst index b80b86cfc5..a3f626147e 100644 --- a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst +++ b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst @@ -9,16 +9,16 @@ Overview --------- MOSART is a river transport model designed for applications across local, -regional and global scales :ref:`(Li et al., 2013b) `. A -major purpose of MOSART is to provide freshwater input for the ocean -model in coupled Earth System Models. MOSART also provides an effective -way of evaluating and diagnosing the soil hydrology simulated by land -surface models through direct comparison of the simulated river flow -with observations of natural streamflow at gauging stations -:ref:`(Li et al., 2015a)`. Moreover, MOSART provides a +regional and global scales :ref:`(Li et al., 2013b) `. A +major purpose of MOSART is to provide freshwater input for the ocean +model in coupled Earth System Models. MOSART also provides an effective +way of evaluating and diagnosing the soil hydrology simulated by land +surface models through direct comparison of the simulated river flow +with observations of natural streamflow at gauging stations +:ref:`(Li et al., 2015a)`. Moreover, MOSART provides a modeling framework for representing riverine transport and transformation of energy and biogeochemical fluxes under both natural and human-influenced -conditions ( :ref:`(Li et al., 2015b) `. +conditions ( :ref:`(Li et al., 2015b) `. .. _Routing Processes: @@ -26,7 +26,7 @@ Routing Processes ------------------ MOSART divides each spatial unit such as a lat/lon grid or watershed into -three categories of hydrologic units (as shown in +three categories of hydrologic units (as shown in :numref:`Figure MOSART conceptual diagram`): hillslopes that convert both surface and subsurface runoff into tributaries, tributaries that discharge into a single main channel, and the main channel @@ -41,7 +41,7 @@ the sub-network channel; 2) sub-network channel routing: the sub-network channel receives water from the hillslopes, routes water through the channel and discharges it into the main channel; 3) main channel routing: the main channel receives water from the sub-network channel and/or inflow, if any, from the upstream spatial units, -and discharges the water to its downstream spatial unit or the ocean. +and discharges the water to its downstream spatial unit or the ocean. .. Figure 14.1. MOSART conceptual diagram @@ -53,17 +53,17 @@ and discharges the water to its downstream spatial unit or the ocean. MOSART only routes positive runoff, although negative runoff can be generated occasionally by the land model (e.g., :math:`q_{gwl}`). Negative runoff in any -runoff component including :math:`q_{sur}`, :math:`q_{sub}`, :math:`q_{gwl}` -is not routed through MOSART, but instead is mapped directly from the spatial unit -where it is generated at any time step to the coupler. - +runoff component including :math:`q_{sur}`, :math:`q_{sub}`, :math:`q_{gwl}` +is not routed through MOSART, but instead is mapped directly from the spatial unit +where it is generated at any time step to the coupler. + In MOSART, the travel velocities of water across hillslopes, sub-network and main channel are all estimated using Manning's equation with different levels of simplifications. Generally the Manning's equation is in the form of .. math:: :label: 14.1 - + V = \frac{R^{\frac{2}{3}} S_{f}}{n} where :math:`V` is the travel velocity (m s :sup:`-1` ), :math:`R` is the hydraulic @@ -72,125 +72,125 @@ of gravity, friction, inertia and other forces on the water. If the channel slop is steep enough, the gravity force dominates over the others so one can approximate :math:`S_{f}` by the channel bed slope :math:`S` , which is the key assumption underpinning the kinematic wave method. :math:`n` is the Manning's roughness -coefficient, which is mainly controlled by surface roughness and sinuosity of the -flow path. +coefficient, which is mainly controlled by surface roughness and sinuosity of the +flow path. If the water surface is sufficiently large or the water depth :math:`h` is sufficiently shallow, the hydraulic radius can be approximated by the water depth. -This is the case for both hillslope and sub-network channel routing. +This is the case for both hillslope and sub-network channel routing. .. math:: :label: 14.2 - + R_{h} = h_{h} R_{t} = h_{t} Here :math:`R_{h}` (m) and :math:`R_{t}` (m) are hydraulic radius for hillslope and -sub-network channel routing respectively, and :math:`h_{h}` (m) and :math:`h_{t}` +sub-network channel routing respectively, and :math:`h_{h}` (m) and :math:`h_{t}` (m) are water depth during hillslope and sub-network channel routing respectively. - -For the main channel, the hydraulic radius is given by + +For the main channel, the hydraulic radius is given by .. math:: :label: 14.3 - + R_{r} = \frac{A_{r}}{P_{r}} -where :math:`A_{r}` (m :sup:`2` ) is the wetted area defined as the part of the -channel cross-section area below the water surface, :math:`P_{r}` (m) is the -wetted perimeter, the perimeter confined in the wetted area. - -For hillslopes, sub-network and main channels, a common continuity equation can +where :math:`A_{r}` (m :sup:`2` ) is the wetted area defined as the part of the +channel cross-section area below the water surface, :math:`P_{r}` (m) is the +wetted perimeter, the perimeter confined in the wetted area. + +For hillslopes, sub-network and main channels, a common continuity equation can be written as .. math:: :label: 14.4 - + \frac{dS}{dt} = Q_{in} - Q_{out} + R -where :math:`Q_{in}` (m :sup:`3` s :sup:`-1` ) is the main channel flow from -the upstream grid(s) into the main channel of the current grid, which is zero for -hillslope and sub-network routing. :math:`Q_{out}` (m :sup:`3` s :sup:`-1` ) is -the outflow rate from hillslope into the sub-network, from the sub-network into -the main channel, or from the current main channel to the main channel of its -downstream grid (if not the outlet grid) or ocean (if the current grid is the -basin outlet). :math:`R` (m :sup:`3` s :sup:`-1` ) is a source term, which -could be the surface -runoff generation rate for hillslopes, or lateral inflow (from hillslopes) into -sub-network channel or water-atmosphere exchange fluxes such as precipitation -and evaporation. It is assumed that surface runoff is generated uniformly -across all the hillslopes. Currently, MOSART does not exchange water with -the atmosphere or return water to the land model so its function is strictly -to transport water from runoff generation through the hillslope, tributaries, -and main channels to the basin outlets. +where :math:`Q_{in}` (m :sup:`3` s :sup:`-1` ) is the main channel flow from +the upstream grid(s) into the main channel of the current grid, which is zero for +hillslope and sub-network routing. :math:`Q_{out}` (m :sup:`3` s :sup:`-1` ) is +the outflow rate from hillslope into the sub-network, from the sub-network into +the main channel, or from the current main channel to the main channel of its +downstream grid (if not the outlet grid) or ocean (if the current grid is the +basin outlet). :math:`R` (m :sup:`3` s :sup:`-1` ) is a source term, which +could be the surface +runoff generation rate for hillslopes, or lateral inflow (from hillslopes) into +sub-network channel or water-atmosphere exchange fluxes such as precipitation +and evaporation. It is assumed that surface runoff is generated uniformly +across all the hillslopes. Currently, MOSART does not exchange water with +the atmosphere or return water to the land model so its function is strictly +to transport water from runoff generation through the hillslope, tributaries, +and main channels to the basin outlets. .. _Numerical Solution MOSART: Numerical Solution ---------------------------- -The numerical implementation of MOSART is mainly based on a subcycling -scheme and a local time-stepping algorithm. There are two levels of -subcycling. For convenience, we denote :math:`T_{inputs}` (s), -:math:`T_{mosart}` (s), :math:`T_{hillslope}` (s) and -:math:`T_{channel}` (s) as the time steps of runoff inputs (from CLM -to MOSART via the flux coupler), MOSART routing, hillslope routing, and -channel routing, respectively. The first level of subcycling is between -the runoff inputs and MOSART routing. If :math:`T_{inputs}` is 10800s -and :math:`T_{mosart}` is 3600s, three MOSART time steps will be -invoked each time the runoff inputs are updated. The second level of -subcycling is between the hillslope routing and channel routing. This -is to account for the fact that the travel velocity of water across -hillslopes is usually much slower than that in the channels. -:math:`T_{hillslope}` is usually set as the same as :math:`T_{mosart}`, -but within each time step of hillslope routing there are a few time -steps for channel routing, i.e., -:math:`T_{hillslope} = D_{levelH2R} \cdot T_{channel}`. The local -time-stepping algorithm is to account for the fact that the travel -velocity of water is much faster in some river channels (e.g., with -steeper bed slope, narrower channel width) than others. That is, for -each channel (either a sub-network or main channel), the final time -step of local channel routing is given as -:math:`T_{local}=T_{channel}/D_{local}`. :math:`D_{local}` is -currently estimated empirically as a function of local channel slope, -width, length and upstream drainage area. If MOSART crashes due to a -numerical issue, we recommend increasing :math:`D_{levelH2R}` and, if -the issue remains, reducing :math:`T_{mosart}`. +The numerical implementation of MOSART is mainly based on a subcycling +scheme and a local time-stepping algorithm. There are two levels of +subcycling. For convenience, we denote :math:`T_{inputs}` (s), +:math:`T_{mosart}` (s), :math:`T_{hillslope}` (s) and +:math:`T_{channel}` (s) as the time steps of runoff inputs (from CLM +to MOSART via the flux coupler), MOSART routing, hillslope routing, and +channel routing, respectively. The first level of subcycling is between +the runoff inputs and MOSART routing. If :math:`T_{inputs}` is 10800s +and :math:`T_{mosart}` is 3600s, three MOSART time steps will be +invoked each time the runoff inputs are updated. The second level of +subcycling is between the hillslope routing and channel routing. This +is to account for the fact that the travel velocity of water across +hillslopes is usually much slower than that in the channels. +:math:`T_{hillslope}` is usually set as the same as :math:`T_{mosart}`, +but within each time step of hillslope routing there are a few time +steps for channel routing, i.e., +:math:`T_{hillslope} = D_{levelH2R} \cdot T_{channel}`. The local +time-stepping algorithm is to account for the fact that the travel +velocity of water is much faster in some river channels (e.g., with +steeper bed slope, narrower channel width) than others. That is, for +each channel (either a sub-network or main channel), the final time +step of local channel routing is given as +:math:`T_{local}=T_{channel}/D_{local}`. :math:`D_{local}` is +currently estimated empirically as a function of local channel slope, +width, length and upstream drainage area. If MOSART crashes due to a +numerical issue, we recommend increasing :math:`D_{levelH2R}` and, if +the issue remains, reducing :math:`T_{mosart}`. .. _Parameters and Input Data: Parameters and Input Data --------------------------------- -MOSART is supported by a comprehensive, global hydrography dataset at 0.5 -:sup:`o` resolution. As such, the fundamental spatial unit of MOSART is a 0.5 -:sup:`o` lat/lon grid. The topographic parameters (such as flow direction, -channel length, topographic and channel slopes, etc.) were derived using the -Dominant River Tracing (DRT) algorithm (:ref:`Wu et al., 2011` ; -:ref:`Wu et al. 2012 `). The DRT algorithm produces the topographic -parameters in a scale-consistent way to preserve/upscale the key features of -a baseline high-resolution hydrography dataset at multiple coarser spatial -resolutions. Here the baseline high-resolution hydrography dataset is the -1km resolution Hydrological data and maps based on SHuttle Elevation -Derivatives at multiple Scales (HydroSHEDS) -(:ref:`Lehner and Döll, 2004 ` ; -:ref:`Lehner et al., 2008 `). The channel geometry -parameters, e.g., bankfull width and depth, were estimated from empirical -hydraulic geometry relationships as functions of the mean annual discharge. -The Manning roughness coefficients for overland and channel flow were -calculated as functions of landcover and water depth. For more details -on the methodology to derive channel geometry and the Manning's roughness -coefficients, please refer to -:ref:`Getirana et al. (2012) ` . The full list of -parameters included in this global hydrography dataset is provided in -:numref:`Table MOSART Parameters`. Evaluation of global simulations -by MOSART using the aforementioned parameters is described in -:ref:`Li et al. (2015b) ` . +MOSART is supported by a comprehensive, global hydrography dataset at 0.5 +:sup:`o` resolution. As such, the fundamental spatial unit of MOSART is a 0.5 +:sup:`o` lat/lon grid. The topographic parameters (such as flow direction, +channel length, topographic and channel slopes, etc.) were derived using the +Dominant River Tracing (DRT) algorithm (:ref:`Wu et al., 2011` ; +:ref:`Wu et al. 2012 `). The DRT algorithm produces the topographic +parameters in a scale-consistent way to preserve/upscale the key features of +a baseline high-resolution hydrography dataset at multiple coarser spatial +resolutions. Here the baseline high-resolution hydrography dataset is the +1km resolution Hydrological data and maps based on SHuttle Elevation +Derivatives at multiple Scales (HydroSHEDS) +(:ref:`Lehner and Döll, 2004 ` ; +:ref:`Lehner et al., 2008 `). The channel geometry +parameters, e.g., bankfull width and depth, were estimated from empirical +hydraulic geometry relationships as functions of the mean annual discharge. +The Manning roughness coefficients for overland and channel flow were +calculated as functions of landcover and water depth. For more details +on the methodology to derive channel geometry and the Manning's roughness +coefficients, please refer to +:ref:`Getirana et al. (2012) ` . The full list of +parameters included in this global hydrography dataset is provided in +:numref:`Table MOSART Parameters`. Evaluation of global simulations +by MOSART using the aforementioned parameters is described in +:ref:`Li et al. (2015b) ` . .. _Table MOSART Parameters: -.. table:: List of parameters in the global hydrography dataset +.. table:: List of parameters in the global hydrography dataset +-------------------------+---------------+------------------------------------------------------------------------------------------------------------------------------------+ | Name | Unit | Description | @@ -227,21 +227,21 @@ by MOSART using the aforementioned parameters is described in Difference between CLM5.0 and CLM4.5 ------------------------------------- -1. Routing methods: RTM, a linear reservoir method, is used in CLM4.5 for -river routing, whilst in CLM5.0, MOSART is an added option for river routing +1. Routing methods: RTM, a linear reservoir method, is used in CLM4.5 for +river routing, whilst in CLM5.0, MOSART is an added option for river routing based on the more physically-based kinematic wave method. -2. Runoff treatment: In RTM runoff is routed regardless of its sign so -negative streamflow can be simulated at times. MOSART routes only non-negative -runoff and always produces positive streamflow, which is important for +2. Runoff treatment: In RTM runoff is routed regardless of its sign so +negative streamflow can be simulated at times. MOSART routes only non-negative +runoff and always produces positive streamflow, which is important for future extensions to model riverine heat and biogeochemical fluxes. 3. Input parameters: RTM in CLM4.5 only requires one layer of a spatially varying -variable of channel velocity, whilst MOSART in CLM5.0 requires 13 parameters that +variable of channel velocity, whilst MOSART in CLM5.0 requires 13 parameters that are all available globally at 0.5 :sup:`o` resolution. -4. Outputs: RTM only produces streamflow simulation, whilst MOSART -additionally simulates the time-varying channel velocities, channel water depth, and +4. Outputs: RTM only produces streamflow simulation, whilst MOSART +additionally simulates the time-varying channel velocities, channel water depth, and channel surface water variations. diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 1209eaab88..4cab8d6f58 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -4,18 +4,18 @@ Methane Model ================= The representation of processes in the methane biogeochemical model -integrated in CLM [CLM4Me; (:ref:`Riley et al. 2011a`)] -is based on several previously published models -(:ref:`Cao et al. 1996`; :ref:`Petrescu et al. 2010`; -:ref:`Tianet al. 2010`; :ref:`Walter et al. 2001`; +integrated in CLM [CLM4Me; (:ref:`Riley et al. 2011a`)] +is based on several previously published models +(:ref:`Cao et al. 1996`; :ref:`Petrescu et al. 2010`; +:ref:`Tianet al. 2010`; :ref:`Walter et al. 2001`; :ref:`Wania et al. 2010`; :ref:`Zhang et al. 2002`; -:ref:`Zhuang et al. 2004`). Although the model has similarities +:ref:`Zhuang et al. 2004`). Although the model has similarities with these precursor models, a number of new process representations and parameterization have been integrated into CLM. -Mechanistically modeling net surface CH\ :sub:`4` emissions requires -representing a complex and interacting series of processes. We first -(section :numref:`Methane Model Structure and Flow`) describe the overall +Mechanistically modeling net surface CH\ :sub:`4` emissions requires +representing a complex and interacting series of processes. We first +(section :numref:`Methane Model Structure and Flow`) describe the overall model structure and flow of information in the CH\ :sub:`4` model, then describe the methods used to represent: CH\ :sub:`4` mass balance; CH\ :sub:`4` @@ -46,11 +46,11 @@ the atmosphere. Governing Mass-Balance Relationship ---------------------------------------- -The model (:numref:`Figure Methane Schematic`) accounts for CH\ :sub:`4` -production in the anaerobic fraction of soil (*P*, mol m\ :sup:`-3` -s\ :sup:`-1`), ebullition (*E*, mol m\ :sup:`-3` s\ :sup:`-1`), -aerenchyma transport (*A*, mol m\ :sup:`-3` s\ :sup:`-1`), aqueous and -gaseous diffusion (:math:`{F}_{D}`, mol m\ :sup:`-2` s\ :sup:`-1`), and +The model (:numref:`Figure Methane Schematic`) accounts for CH\ :sub:`4` +production in the anaerobic fraction of soil (*P*, mol m\ :sup:`-3` +s\ :sup:`-1`), ebullition (*E*, mol m\ :sup:`-3` s\ :sup:`-1`), +aerenchyma transport (*A*, mol m\ :sup:`-3` s\ :sup:`-1`), aqueous and +gaseous diffusion (:math:`{F}_{D}`, mol m\ :sup:`-2` s\ :sup:`-1`), and oxidation (*O*, mol m\ :sup:`-3` s\ :sup:`-1`) via a transient reaction diffusion equation: @@ -93,7 +93,7 @@ into the inundated concentration when the inundated fraction increases. Schematic representation of biological and physical processes integrated in CLM that affect the net CH\ :sub:`4` - surface flux (:ref:`Riley et al. 2011a`). (left) + surface flux (:ref:`Riley et al. 2011a`). (left) Fully inundated portion of a CLM gridcell and (right) variably saturated portion of a gridcell. @@ -124,9 +124,9 @@ seasonal inundation fraction (*S*, described below): P=R_{H} f_{CH_{4} } f_{T} f_{pH} f_{pE} S. -Here, :math:`f_{CH_{4} }` is the baseline ratio between CO\ :sub:`2` -and CH\ :sub:`4` production (all parameters values are given in -:numref:`Table Methane Parameter descriptions`). Currently, :math:`f_{CH_{4} }` +Here, :math:`f_{CH_{4} }` is the baseline ratio between CO\ :sub:`2` +and CH\ :sub:`4` production (all parameters values are given in +:numref:`Table Methane Parameter descriptions`). Currently, :math:`f_{CH_{4} }` is modified to account for our assumptions that methanogens may have a higher Q\ :math:`{}_{10}` than aerobic decomposers; are not N limited; and do not have a low-moisture limitation. @@ -137,10 +137,10 @@ to or below freezing, even though CLM allows heterotrophic respiration below freezing. However, if the vertically resolved BGC soil column is used, CH\ :sub:`4` production continues below freezing because liquid water stress limits decomposition. The base temperature for the -:math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22\ :sup:`o` C and effectively +:math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22\ :sup:`o` C and effectively modified the base :math:`f_{CH_{4}}` value. -For the single-layer BGC version, :math:`{R}_{H}` is distributed +For the single-layer BGC version, :math:`{R}_{H}` is distributed among soil levels by assuming that 50% is associated with the roots (using the CLM PFT-specific rooting distribution) and the rest is evenly divided among the top 0.28 m of soil (to be consistent with CLM's soil @@ -148,7 +148,7 @@ decomposition algorithm). For the vertically resolved BGC version, the prognosed distribution of :math:`{R}_{H}` is used to estimate CH\ :sub:`4` production. The factor :math:`f_{pH}` is nominally set to 1, although a static -spatial map of *pH* can be used to determine this factor +spatial map of *pH* can be used to determine this factor (:ref:`Dunfield et al. 1993`) by applying: .. math:: @@ -160,7 +160,7 @@ The :math:`f_{pE}` factor assumes that alternative electron acceptors are reduced with an e-folding time of 30 days after inundation. The default version of the model applies this factor to horizontal changes in inundated area but not to vertical changes in the water table depth -in the upland fraction of the gridcell. We consider both :math:`f_{pH}` +in the upland fraction of the gridcell. We consider both :math:`f_{pH}` and :math:`f_{pE}` to be poorly constrained in the model and identify these controllers as important areas for model improvement. @@ -233,7 +233,7 @@ Briefly, the simulated aqueous CH\ :sub:`4` concentration in each soil level is used to estimate the expected equilibrium gaseous partial pressure (:math:`C_{e}` ), as a function of temperature and depth below the water table, by first estimating the Henry's law partitioning -coefficient (:math:`k_{h}^{C}` ) by the method described in +coefficient (:math:`k_{h}^{C}` ) by the method described in :ref:`Wania et al. (2010)`: .. math:: @@ -262,7 +262,7 @@ ponding (if applicable). When the CH\ :sub:`4` partial pressure exceeds 15% of the local pressure (:ref:`Baird et al. 2004`; :ref:`Strack et al. 2006`; :ref:`Wania et al. 2010`), bubbling occurs to remove CH\ :sub:`4` to below this value, modified by the fraction of CH\ :sub:`4` in -the bubbles [taken as 57%; (:ref:`Kellner et al. 2006`; +the bubbles [taken as 57%; (:ref:`Kellner et al. 2006`; :ref:`Wania et al. 2010`)]. Bubbles are immediately added to the surface flux for saturated columns and are placed immediately above the water table interface in @@ -285,7 +285,7 @@ The diffusive transport through aerenchyma (*A*, mol m\ :sup:`-2` s\ :sup:`-1`) :label: 24.8 A=\frac{C\left(z\right)-C_{a} }{{\raise0.7ex\hbox{$ r_{L} z $}\!\mathord{\left/ {\vphantom {r_{L} z D}} \right.}\!\lower0.7ex\hbox{$ D $}} +r_{a} } pT\rho _{r} , - + where *D* is the free-air gas diffusion coefficient (m\ :sup:`2` s\ :sup:`-1`); *C(z)* (mol m\ :sup:`-3`) is the gaseous concentration at depth *z* (m); :math:`r_{L}` is the ratio of root length to depth; *p* is the porosity (-); *T* is specific aerenchyma @@ -295,7 +295,7 @@ height (s m\ :sup:`-1`); and :math:`\rho _{r}` is the rooting density as a function of depth (-). The gaseous concentration is calculated with Henry's law as described in equation :eq:`24.7`. -Based on the ranges reported in :ref:`Colmer (2003)`, we have chosen +Based on the ranges reported in :ref:`Colmer (2003)`, we have chosen baseline aerenchyma porosity values of 0.3 for grass and crop PFTs and 0.1 for tree and shrub PFTs: @@ -332,7 +332,7 @@ CH\ :sub:`4` Oxidation --------------------------------- CLM represents CH\ :sub:`4` oxidation with double Michaelis-Menten -kinetics (:ref:`Arah and Stephen 1998`; :ref:`Segers 1998`), +kinetics (:ref:`Arah and Stephen 1998`; :ref:`Segers 1998`), dependent on both the gaseous CH\ :sub:`4` and O\ :sub:`2` concentrations: .. math:: @@ -348,9 +348,9 @@ m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` specifies the temperature dependence of the reaction with a base temperature set to 12 :sup:`o` C. The soil moisture limitation factor :math:`F_{\theta }` is applied above the water table to -represent water stress for methanotrophs. Based on the data in -:ref:`Schnell and King (1996)`, we take -:math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture +represent water stress for methanotrophs. Based on the data in +:ref:`Schnell and King (1996)`, we take +:math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. .. _Reactive Transport Solution: @@ -360,16 +360,16 @@ Reactive Transport Solution The solution to equation :eq:`24.11` is solved in several sequential steps: resolve competition for CH\ :sub:`4` and O\ :sub:`2` (section -:numref:`Competition for CH4and O2`); add the ebullition flux into the +:numref:`Competition for CH4and O2`); add the ebullition flux into the layer directly above the water table or into the atmosphere; calculate the overall CH\ :sub:`4` or O\ :sub:`2` source term based on production, aerenchyma transport, ebullition, and oxidation; establish boundary conditions, including surface conductance to account for snow, ponding, and -turbulent conductances and bottom flux condition -(section :numref:`CH4 and O2 Source Terms`); calculate diffusivity -(section :numref:`Aqueous and Gaseous Diffusion`); and solve the resulting -mass balance using a tridiagonal solver (section +turbulent conductances and bottom flux condition +(section :numref:`CH4 and O2 Source Terms`); calculate diffusivity +(section :numref:`Aqueous and Gaseous Diffusion`); and solve the resulting +mass balance using a tridiagonal solver (section :numref:`Crank-Nicholson Solution Methane`). .. _Competition for CH4and O2: @@ -416,9 +416,9 @@ Aqueous and Gaseous Diffusion For gaseous diffusion, we adopted the temperature dependence of molecular free-air diffusion coefficients (:math:`{D}_{0}` -(m\ :sup:`2` s\ :sup:`-1`)) as described by -:ref:`Lerman (1979) ` and applied by -:ref:`Wania et al. (2010)` +(m\ :sup:`2` s\ :sup:`-1`)) as described by +:ref:`Lerman (1979) ` and applied by +:ref:`Wania et al. (2010)` (:numref:`Table Temperature dependence of aqueous and gaseous diffusion`). .. _Table Temperature dependence of aqueous and gaseous diffusion: @@ -434,9 +434,9 @@ molecular free-air diffusion coefficients (:math:`{D}_{0}` +----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+ Gaseous diffusivity in soils also depends on the molecular diffusivity, -soil structure, porosity, and organic matter content. -:ref:`Moldrup et al. (2003)`, using observations across a -range of unsaturated mineral soils, showed that the relationship between +soil structure, porosity, and organic matter content. +:ref:`Moldrup et al. (2003)`, using observations across a +range of unsaturated mineral soils, showed that the relationship between effective diffusivity (:math:`D_{e}` (m\ :sup:`2` s\ :sup:`-1`)) and soil properties can be represented as: @@ -449,7 +449,7 @@ where :math:`\theta _{a}` and :math:`\theta _{s}` are the air-filled and total (saturated water-filled) porosities (-), respectively, and *b* is the slope of the water retention curve (-). However, :ref:`Iiyama and Hasegawa (2005)` have shown that the original Millington-Quirk -(:ref:`Millington and Quirk 1961`) relationship matched +(:ref:`Millington and Quirk 1961`) relationship matched measurements more closely in unsaturated peat soils: .. math:: @@ -472,10 +472,10 @@ aqueous diffusion in the saturated part of the soil column, we applied To simplify the solution, we assumed that gaseous diffusion dominates above the water table interface and aqueous diffusion below the water table interface. Descriptions, baseline values, and dimensions for -parameters specific to the CH\ :sub:`4` model are given in -:numref:`Table Methane Parameter descriptions`. For freezing or frozen -soils below the water table, diffusion is limited to the remaining -liquid (CLM allows for some freezing point depression), and the diffusion +parameters specific to the CH\ :sub:`4` model are given in +:numref:`Table Methane Parameter descriptions`. For freezing or frozen +soils below the water table, diffusion is limited to the remaining +liquid (CLM allows for some freezing point depression), and the diffusion coefficients are scaled by the volume-fraction of liquid. For unsaturated soils, Henry's law equilibrium is assumed at the interface with the water table. @@ -492,7 +492,7 @@ the gaseous concentration in the first soil layer (unsaturated soils) or in equilibrium with the water (saturated soil\ :math:`w\left(C_{1}^{n} -C_{a} \right)` and :math:`w\left(C_{1}^{n+1} -C_{a} \right)` for the fully explicit and -fully implicit cases, respectively (however, see +fully implicit cases, respectively (however, see :ref:`Tang and Riley (2013)` for a more complete representation of this process). Here, *w* is the surface boundary layer conductance as calculated in the existing CLM @@ -518,7 +518,7 @@ a zero flux gradient at the bottom of the soil column. Crank-Nicholson Solution ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Equation :eq:`24.1` is solved using a Crank-Nicholson solution +Equation :eq:`24.1` is solved using a Crank-Nicholson solution (:ref:`Press et al., 1992`), which combines fully explicit and implicit representations of the mass balance. The fully explicit decomposition of equation :eq:`24.1` can be written as @@ -631,7 +631,7 @@ Seasonal Inundation A simple scaling factor is used to mimic the impact of seasonal inundation on CH\ :sub:`4` production (see appendix B in -:ref:`Riley et al. (2011a)` for a discussion of this +:ref:`Riley et al. (2011a)` for a discussion of this simplified expression): .. math:: diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index bcc29a5e89..e0288c08b0 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -18,14 +18,14 @@ CLM5 includes the following new changes to photosynthesis and stomatal conductan - Leaf N concentration and the fraction of leaf N in Rubisco used to calculate :math:`V_{cmax25}` are determined by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) -- Water stress is applied by the hydraulic conductance model (Chapter :numref:`rst_Plant Hydraulics`) +- Water stress is applied by the hydraulic conductance model (Chapter :numref:`rst_Plant Hydraulics`) Introduction ----------------------- Leaf stomatal resistance, which is needed for the water vapor flux -(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), +(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), is coupled to leaf photosynthesis similar to Collatz et al. (:ref:`1991 `, :ref:`1992 `). These equations are solved separately for sunlit and shaded leaves using average absorbed photosynthetically active radiation @@ -39,7 +39,7 @@ photosynthesis is :math:`A^{sun} L^{sun} +A^{sha} L^{sha}` , where area indices (section :numref:`Solar Fluxes`). Canopy conductance is :math:`\frac{1}{r_{b} +r_{s}^{sun} } L^{sun} +\frac{1}{r_{b} +r_{s}^{sha} } L^{sha}` , where :math:`r_{b}` is the leaf boundary layer resistance (section -:numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). +:numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). .. _Stomatal resistance: @@ -49,15 +49,15 @@ Stomatal resistance CLM5 calculates stomatal conductance using the Medlyn stomatal conductance model (:ref:`Medlyn et al. 2011`). Previous versions of CLM calculated leaf stomatal resistance using the Ball-Berry conductance model as described by :ref:`Collatz et al. (1991)` and implemented in global -climate models (:ref:`Sellers et al. 1996`). The Medlyn model +climate models (:ref:`Sellers et al. 1996`). The Medlyn model calculates stomatal conductance (i.e., the inverse of resistance) based on net leaf -photosynthesis, the leaf-to-air vapor pressure difference, and the CO\ :sub:`2` concentration at the leaf surface. +photosynthesis, the leaf-to-air vapor pressure difference, and the CO\ :sub:`2` concentration at the leaf surface. Leaf stomatal resistance is: .. math:: - :label: 9.1 + :label: 9.1 - \frac{1}{r_{s} } =g_{s} = g_{o} + 1.6(1 + \frac{g_{1} }{\sqrt{D_{s}}}) \frac{A_{n} }{{c_{s} \mathord{\left/ {\vphantom {c_{s} P_{atm} }} \right.} P_{atm} } } + \frac{1}{r_{s} } =g_{s} = g_{o} + 1.6(1 + \frac{g_{1} }{\sqrt{D_{s}}}) \frac{A_{n} }{{c_{s} \mathord{\left/ {\vphantom {c_{s} P_{atm} }} \right.} P_{atm} } } where :math:`r_{s}` is leaf stomatal resistance (s m\ :sup:`2` :math:`\mu`\ mol\ :sup:`-1`), :math:`g_{o}` is the minimum stomatal conductance @@ -79,10 +79,10 @@ Photosynthesis is calculated for sunlit (:math:`A^{sun}`) and shaded resistance through plant hydraulic stress, detailed in the :ref:`rst_Plant Hydraulics` chapter. -Resistance is converted from units of -s m\ :sup:`2` :math:`\mu` mol\ :sup:`-1` to s m\ :sup:`-1` as: +Resistance is converted from units of +s m\ :sup:`2` :math:`\mu` mol\ :sup:`-1` to s m\ :sup:`-1` as: 1 s m\ :sup:`-1` = :math:`1\times 10^{-9} R_{gas} \frac{\theta _{atm} }{P_{atm} }` -:math:`\mu` mol\ :sup:`-1` m\ :sup:`2` s, +:math:`\mu` mol\ :sup:`-1` m\ :sup:`2` s, where :math:`R_{gas}` is the universal gas constant (J K\ :sup:`-1` kmol\ :sup:`-1`) (:numref:`Table Physical constants`) and :math:`\theta _{atm}` is the atmospheric potential temperature (K). @@ -142,7 +142,7 @@ atmospheric potential temperature (K). +----------------------------------+-------------------+ | Switchgrass | 1.79 | +----------------------------------+-------------------+ - + .. _Photosynthesis: Photosynthesis @@ -183,18 +183,18 @@ C\ :sub:`4` plants :math:`A_{p}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: - :label: 9.5 + :label: 9.5 A_{p} =\left\{\begin{array}{l} {3T_{p\qquad } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {k_{p} \frac{c_{i} }{P_{atm} } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}. In these equations, :math:`c_{i}` is the internal leaf -CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` +CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{\*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` -s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) +s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), @@ -253,29 +253,29 @@ smaller root of the equations Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. -:math:`A_{i}` is the intermediate co-limited photosynthesis. +:math:`A_{i}` is the intermediate co-limited photosynthesis. :math:`A_{n} =A-R_{d}` . -The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` +The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 :sup:`o` \ C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, -and :math:`R_{d}` also vary with temperature. +and :math:`R_{d}` also vary with temperature. -:math:`J_{\max 25}` at 25 :sup:`\o`\ C: is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) +:math:`J_{\max 25}` at 25 :sup:`\o`\ C: is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) Parameter values at 25 :sup:`\o`\ C are calculated from :math:`V_{c\max }` \ at 25 -:sup:`\o`\ C:, including: +:sup:`\o`\ C:, including: :math:`T_{p25} =0.167V_{c\max 25}`, and :math:`R_{d25} =0.015V_{c\max 25}` (C\ :sub:`3`) and -:math:`R_{d25} =0.025V_{c\max 25}` (C\ :sub:`4`). +:math:`R_{d25} =0.025V_{c\max 25}` (C\ :sub:`4`). For C\ :sub:`4` plants, :math:`k_{p25} =20000\; V_{c\max 25}`. However, when the biogeochemistry is active (the default mode), :math:`R_{d25}` is -calculated from leaf nitrogen as described in (Chapter :numref:`rst_Plant Respiration`) +calculated from leaf nitrogen as described in (Chapter :numref:`rst_Plant Respiration`) The parameters :math:`V_{c\max 25}`, :math:`J_{\max 25}`, :math:`T_{p25}`, :math:`k_{p25}`, and @@ -302,13 +302,13 @@ and :numref:`Table Temperature dependence parameters for C3 photosynthesis` lists parameter values for :math:`\Delta H_{a}` and -:math:`\Delta H_{d}` . :math:`\Delta S` is calculated +:math:`\Delta H_{d}` . :math:`\Delta S` is calculated separately for :math:`V_{c\max }` and :math:`J_{max }` -to allow for temperature acclimation of photosynthesis (see equation :eq:`9.16`), +to allow for temperature acclimation of photosynthesis (see equation :eq:`9.16`), and :math:`\Delta S` is 490 J mol :sup:`-1` K :sup:`-1` for :math:`R_d` (:ref:`Bonan et al. 2011`, :ref:`Lombardozzi et al. 2015`). Because :math:`T_{p}` as implemented here varies with -:math:`V_{c\max }` , :math:`T_{p}` uses the same temperature parameters as +:math:`V_{c\max }` , :math:`T_{p}` uses the same temperature parameters as :math:`V_{c\max}` . For C\ :sub:`4` plants, .. math:: @@ -319,7 +319,7 @@ Because :math:`T_{p}` as implemented here varies with with :math:`Q_{10} =2`, :math:`s_{1} =0.3`\ K\ :sup:`-1` :math:`s_{2} =313.15` K, -:math:`s_{3} =0.2`\ K\ :sup:`-1`, and :math:`s_{4} =288.15` K. +:math:`s_{3} =0.2`\ K\ :sup:`-1`, and :math:`s_{4} =288.15` K. Additionally, .. math:: @@ -359,8 +359,8 @@ with :math:`Q_{10} =2`. | :math:`\Gamma _{\*}` | 37830 | – | +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ -In the model, acclimation is -implemented as in :ref:`Kattge and Knorr (2007) `. In this parameterization, +In the model, acclimation is +implemented as in :ref:`Kattge and Knorr (2007) `. In this parameterization, :math:`V_{c\max }` and :math:`J_{\max }` vary with the plant growth temperature. This is achieved by allowing :math:`\Delta S`\ to vary with growth temperature according to @@ -370,8 +370,8 @@ according to \begin{array}{l} {\Delta S=668.39-1.07(T_{10} -T_{f} )\qquad \qquad {\rm for\; }V_{c\max } } \\ {\Delta S=659.70-0.75(T_{10} -T_{f} )\qquad \qquad {\rm for\; }J_{\max } } \end{array} -The effect is to cause the temperature optimum of :math:`V_{c\max }` -and :math:`J_{\max }` to increase with warmer temperatures. +The effect is to cause the temperature optimum of :math:`V_{c\max }` +and :math:`J_{\max }` to increase with warmer temperatures. Additionally, the ratio :math:`J_{\max 25} /V_{c\max 25}` at 25 :sup:`o`\ C decreases with growth temperature as @@ -390,7 +390,7 @@ range :math:`T_{10} -T_{f} \ge 11`\ :sup:`o`\ C and :math:`T_{10} -T_{f} \le 35` Canopy scaling -------------------------------------------- -When LUNA is on, the :math:`V_{c\max 25}` for sun leaves is scaled to the shaded leaves +When LUNA is on, the :math:`V_{c\max 25}` for sun leaves is scaled to the shaded leaves :math:`J_{\max 25}` , :math:`T_{p25}` , :math:`k_{p25}`, and :math:`R_{d25}` scale similarly. @@ -398,12 +398,12 @@ When LUNA is on, the :math:`V_{c\max 25}` for sun leaves is scaled to the shaded .. math:: :label: 9.17 - \begin{array}{rcl} - {V_{c\max 25 sha}} & {=} & {V_{c\max 25 sha} \frac{i_{v,sha}}{i_{v,sun}}} \\ + \begin{array}{rcl} + {V_{c\max 25 sha}} & {=} & {V_{c\max 25 sha} \frac{i_{v,sha}}{i_{v,sun}}} \\ {J_{\max 25 sha}} & {=} & {J_{\max 25 sun} \frac{i_{v,sha}}{i_{v,sun}}} \\ - {T_{p sha}} & {=} & {T_{p sun} \frac{i_{v,sha}}{i_{v,sun}}} \end{array} + {T_{p sha}} & {=} & {T_{p sun} \frac{i_{v,sha}}{i_{v,sun}}} \end{array} -Where :math:`i_{v,sun}` and :math:`i_{v,sha}` are the leaf-to-canopy scaling coefficients of the twostream radiation model, calculated as +Where :math:`i_{v,sun}` and :math:`i_{v,sha}` are the leaf-to-canopy scaling coefficients of the twostream radiation model, calculated as .. math:: :label: 9.18 @@ -411,9 +411,9 @@ Where :math:`i_{v,sun}` and :math:`i_{v,sha}` are the leaf-to-canopy scaling coe i_{v,sun} = \frac{(1 - e^{-(k_{n,ext}+k_{b,ext})*lai_e)} / (k_{n,ext}+k_{b,ext})}{f_{sun}*lai_e}\\ i_{v,sha} = \frac{(1 - e^{-(k_{n,ext}+k_{b,ext})*lai_e)} / (k_{n,ext}+k_{b,ext})}{(1 - f_{sun})*lai_e} -k_{n,ext} is the extinction coefficient for N through the canopy (0.3). k_{b,ext} is the direct beam extinction coefficient calculated in the surface albedo routine, and :math:`f_{sun}` is the fraction of sunlit leaves, both derived from Chapter :numref:`rst_Surface Albedos`. +k_{n,ext} is the extinction coefficient for N through the canopy (0.3). k_{b,ext} is the direct beam extinction coefficient calculated in the surface albedo routine, and :math:`f_{sun}` is the fraction of sunlit leaves, both derived from Chapter :numref:`rst_Surface Albedos`. -When LUNA is off, scaling defaults to the mechanism used in CLM4.5. +When LUNA is off, scaling defaults to the mechanism used in CLM4.5. .. _Numerical implementation photosynthesis: @@ -436,7 +436,7 @@ CO\ :sub:`2` and water vapor at the leaf surface so that and the transpiration fluxes are related as .. math:: - :label: 9.20 + :label: 9.20 \frac{e_{a} -e_{i} }{r_{b} +r_{s} } =\frac{e_{a} -e_{s} }{r_{b} } =\frac{e_{s} -e_{i} }{r_{s} } @@ -445,7 +445,7 @@ m\ :sup:`2` :math:`\mu` \ mol\ :sup:`-1`) (section :numref:`Sensible and Latent terms 1.4 and 1.6 are the ratios of diffusivity of CO\ :sub:`2` to H\ :sub:`2`\ O for the leaf boundary layer resistance and stomatal resistance, -:math:`c_{a} ={\rm CO}_{{\rm 2}} \left({\rm mol\; mol}^{{\rm -1}} \right)`, :math:`P_{atm}` +:math:`c_{a} ={\rm CO}_{{\rm 2}} \left({\rm mol\; mol}^{{\rm -1}} \right)`, :math:`P_{atm}` is the atmospheric pressure (Pa), :math:`e_{i}` is the saturation vapor pressure (Pa) evaluated at the leaf temperature :math:`T_{v}` , and :math:`e_{a}` is the vapor pressure of air (Pa). @@ -458,9 +458,9 @@ determined from e_{a} =\frac{P_{atm} q_{s} }{0.622} where :math:`q_{s}` is the specific humidity of canopy air (kg -kg\ :sup:`-1`, section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). +kg\ :sup:`-1`, section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). Equations :eq:`9.19` and :eq:`9.20` are solved for -:math:`c_{s}` and :math:`e_{s}` +:math:`c_{s}` and :math:`e_{s}` .. math:: :label: 9.34 @@ -472,7 +472,7 @@ Equations :eq:`9.19` and :eq:`9.20` are solved for e_{s} =\frac{e_{a} r_{s} +e_{i} r_{b} }{r_{b} +r_{s} } -In terms of conductance with +In terms of conductance with :math:`g_{s} =1/r_{s}` and :math:`g_{b} =1/r_{b}` .. math:: diff --git a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst index c42d7971a8..242a99b4cc 100755 --- a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst +++ b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst @@ -5,42 +5,42 @@ Photosynthetic Capacity The photosynthetic capacity is represented by two key parameters: 1) the maximum rate of carboxylation at 25 :sup:`o`\ C, :math:`V_{\text{c,max25}}`; and 2) the maximum rate of electron transport at -25 :sup:`o`\ C, :math:`J_{\text{max25}}` . They are predicted by a mechanistic model of leaf -utilization of nitrogen for assimilation (LUNA V1.0) (:ref:`Ali et al. 2016`) based on an optimality hypothesis to nitrogen allocation -among light capture, electron transport, carboxylation, respiration and storage. +25 :sup:`o`\ C, :math:`J_{\text{max25}}` . They are predicted by a mechanistic model of leaf +utilization of nitrogen for assimilation (LUNA V1.0) (:ref:`Ali et al. 2016`) based on an optimality hypothesis to nitrogen allocation +among light capture, electron transport, carboxylation, respiration and storage. Specifically, the model allocates the nitrogen by maximizing the daily net photosynthetic carbon gain under following two key assumptions: - -- nitrogen allocated for light capture, electron transport and carboxylation are co-limiting; + +- nitrogen allocated for light capture, electron transport and carboxylation are co-limiting; - respiratory nitrogen is allocated to maintain dark respiration determined by :math:`V_{\text{c,max}}`. Compared to traditional photosynthetic capacity models, a key advantage of LUNA is that the model is able to predict the potential acclimation of photosynthetic capacities at different environmental conditions as determined by temperature, radiation, -CO :sub:`2` concentrations, day length, and humidity. +CO :sub:`2` concentrations, day length, and humidity. .. _Model inputs and parameter estimations: Model inputs and parameter estimations ------------------------------------------------------- -The LUNA model includes the following four unitless parameters: +The LUNA model includes the following four unitless parameters: - :math:`J_{maxb0}` , which specifies the baseline proportion of nitrogen allocated for electron transport; -- :math:`J_{maxb1}` , which determines response of electron transport rate to light availability; -- :math:`t_{c,j0}` , which defines the baseline ratio of Rubisco-limited rate to light-limited rate; -- :math:`H` , which determines the response of electron transport rate to relative humidity. +- :math:`J_{maxb1}` , which determines response of electron transport rate to light availability; +- :math:`t_{c,j0}` , which defines the baseline ratio of Rubisco-limited rate to light-limited rate; +- :math:`H` , which determines the response of electron transport rate to relative humidity. -The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations +The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) -including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. -The estimated values in CLM5 for the listed parameters are 0.0311, 0.1745, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated +including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. +The estimated values in CLM5 for the listed parameters are 0.0311, 0.1745, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist -between crops and natural vegetations due to human selection and genetic modifications, in CLM5, -the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus +between crops and natural vegetations due to human selection and genetic modifications, in CLM5, +the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for -:math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; -however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, -we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. +:math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; +however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, +we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. .. _Model structure: @@ -52,7 +52,7 @@ Plant Nitrogen '''''''''''''''''''''''''' The structure of the LUNA model is adapted from :ref:`Xu et al. (2012)`, where the plant nitrogen at the leaf level ( :math:`\text{LNC}_{a}`; gN/ m :sup:`2` leaf) is divided into -four pools: structural nitrogen( :math:`N_{\text{str}}`; gN/m :sup:`2` leaf), +four pools: structural nitrogen( :math:`N_{\text{str}}`; gN/m :sup:`2` leaf), photosynthetic nitrogen ( :math:`N_{\text{psn}}`; gN/m :sup:`2` leaf), storage nitrogen( :math:`N_{\text{store}}`; gN/m :sup:`2` leaf), and respiratory nitrogen ( :math:`N_{\text{resp}}`; gN/m :sup:`2` leaf). @@ -66,7 +66,7 @@ Namely, The photosynthetic nitrogen, :math:`N_{\text{psn}}`, is further divided into nitrogen for light capture ( :math:`N_{\text{lc}}`; gN/m :sup:`2` leaf), nitrogen for electron transport ( :math:`N_{\text{et}}`; gN/m :sup:`2` leaf), -and nitrogen for carboxylation ( :math:`N_{\text{cb}}`; gN/m :sup:`2` leaf). +and nitrogen for carboxylation ( :math:`N_{\text{cb}}`; gN/m :sup:`2` leaf). Namely, .. math:: @@ -155,9 +155,9 @@ use. Namely, the solutions of nitrogen allocations \{ :math:`N_{\text{store}}`, \left\{\hat{N}_{\text{{store}}}, \hat{N}_{\text{{resp}}}, \hat{\mathrm{N}}_{\text{lc}}, \hat{N}_{\text{et}}, \hat{\mathrm{N}}_{\text{cb}} - \right\} = \underset{\mathrm{N}_{\text{store}}\,+\,\mathrm{N}_{\text{resp}}\,+\,\mathrm{N}_{\text{lc}}\,+\,\mathrm{N}_{\text{et}}\,+\,\mathrm{N}_{\text{cb}}\,<\text{FNC}_{\mathrm{a}}}{\text{argmax}} (A-R_{\text{psn}}), + \right\} = \underset{\mathrm{N}_{\text{store}}\,+\,\mathrm{N}_{\text{resp}}\,+\,\mathrm{N}_{\text{lc}}\,+\,\mathrm{N}_{\text{et}}\,+\,\mathrm{N}_{\text{cb}}\,<\text{FNC}_{\mathrm{a}}}{\text{argmax}} (A-R_{\text{psn}}), -where :math:`\text{FNC}_{a}` is the functional nitrogen content defined as the total leaf nitrogen content ( :math:`\text{LNC}_{a}`) minus the structural nitrogen content ( :math:`N_{\text{str}}` ). +where :math:`\text{FNC}_{a}` is the functional nitrogen content defined as the total leaf nitrogen content ( :math:`\text{LNC}_{a}`) minus the structural nitrogen content ( :math:`N_{\text{str}}` ). The gross photosynthesis, :math:`A`, was calculated with a coupled leaf gas exchange model based on the :ref:`Farquhar et al. (1980)` model of photosynthesis and Ball--Berry-type stomatal conductance model (Ball et al. 1987). The maintenance respiration for photosynthetic enzymes, :math:`R_{\text{psn}}`, is @@ -189,7 +189,7 @@ The baseline electron transport rate, :math:`J_{\text{max}0}`, is calculated as where :math:`J_{\text{max}b0}` (unitless) is the baseline proportion of nitrogen -allocated for electron transport rate. :math:`{\text{NUE}}_{J_{\text{{max}}}}` ( :math:`{\mu} mol` electron /s/g N) +allocated for electron transport rate. :math:`{\text{NUE}}_{J_{\text{{max}}}}` ( :math:`{\mu} mol` electron /s/g N) is the nitrogen use efficiency of :math:`J_{\text{{max}}}`. :math:`J_{\text{max}b1}` (unitless) is a coefficient determining the response of the electron transport rate to amount of absorbed light (i.e., :math:`\alpha \text{PAR}`). :math:`f\left(\text{day length} \right)` is a function specifies the impact of day @@ -260,19 +260,19 @@ as in :ref:`Thornton and Zimmermann (2007)`. At 25ºC, V_{c\max 25} = N_{cb} NUE_{V_{c\max 25}} -where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, +where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, :numref:`Table Plant functional type (PFT) leaf N parameters`), -and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. +and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) measured at 25\ :sup:`o`\ C, and the constant 6.25 is the nitrogen binding factor for Rubisco -(g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). +(g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). :math:`V_{c\max 25}` additionally varies with daylength (:math:`DYL`) using the function :math:`f(DYL)`, which introduces seasonal variation -to :math:`V_{c\max }` +to :math:`V_{c\max }` .. math:: - :label: 10.12) + :label: 10.12) f\left(DYL\right)=\frac{\left(DYL\right)^{2} }{\left(DYL_{\max } \right)^{2} } @@ -280,7 +280,7 @@ with :math:`0.01\le f\left(DYL\right)\le 1`. Daylength (seconds) is given by .. math:: - :label: 10.13) + :label: 10.13) DYL=2\times 13750.9871\cos ^{-1} \left[\frac{-\sin \left(lat\right)\sin \left(decl\right)}{\cos \left(lat\right)\cos \left(decl\right)} \right] @@ -302,7 +302,7 @@ and the Rubisco-limited photosynthetic rate ( :math:`W_{\mathrm{c}}`) as follows .. math:: :label: 10.14) - W_{J_{x}} = K_{j}J_{x} , + W_{J_{x}} = K_{j}J_{x} , .. math:: :label: 10.15) @@ -325,9 +325,9 @@ assume that :math:`W_{\mathrm{c}}` is proportional to where :math:`t_{\mathrm{c}, j0}` is the baseline ratio of :math:`W_{\mathrm{c}}` to :math:`W_{J_{x}}`. We recognize that this ratio may change depending on the -nitrogen use efficiency of carboxylation and electron transport (Ainsworth and Rogers 2007), +nitrogen use efficiency of carboxylation and electron transport (Ainsworth and Rogers 2007), therefore the LUNA model has the modification factor, :math:`t_{\alpha}`, to adjust baseline -the ratio depending on the nitrogen use efficiency for electron vs carboxylation (:ref:`Ali et al. 2016`). +the ratio depending on the nitrogen use efficiency for electron vs carboxylation (:ref:`Ali et al. 2016`). Total Respiration ''''''''''''''''''' @@ -363,8 +363,8 @@ Numerical scheme --------------------------------------------------------- The LUNA model searches for the "optimal" nitrogen allocations for maximum net photosynthetic carbon gain -by incrementally increase the nitrogen allocated for light capture (i.e., :math:`N_{\text{lc}}`) (see :ref:`Ali et al. (2016)` for details). -We assume that plants only optimize the nitrogen allocation when they can grow (i.e., GPP>0.0). -If GPP become zero under stress, then the LUNA model assume a certain amount of enzyme will decay at daily rates of 0.1, -in view that the half-life time for photosynthetic enzymes are short (~7 days) (Suzuki et al. 2001). +by incrementally increase the nitrogen allocated for light capture (i.e., :math:`N_{\text{lc}}`) (see :ref:`Ali et al. (2016)` for details). +We assume that plants only optimize the nitrogen allocation when they can grow (i.e., GPP>0.0). +If GPP become zero under stress, then the LUNA model assume a certain amount of enzyme will decay at daily rates of 0.1, +in view that the half-life time for photosynthetic enzymes are short (~7 days) (Suzuki et al. 2001). To avoid unrealistic low values of photosynthetic capacity, the decay is only limited to 50 percent of the original enzyme levels. diff --git a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst index 2d8843510a..53fd2fadbd 100644 --- a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst +++ b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst @@ -19,15 +19,15 @@ functional type .. math:: :label: 11.1 - r_{i} = - \begin{array}{lr} - \left(\beta^{z_{h,\, i-1} \cdot 100} - \beta^{z_{h,\, i} \cdot 100} \right) & \qquad {\rm for\; }1 \le i \le N_{levsoi} + r_{i} = + \begin{array}{lr} + \left(\beta^{z_{h,\, i-1} \cdot 100} - \beta^{z_{h,\, i} \cdot 100} \right) & \qquad {\rm for\; }1 \le i \le N_{levsoi} \end{array} where :math:`z_{h,\, i}` (m) is the depth from the soil surface to the interface between layers :math:`i` and :math:`i+1` (:math:`z_{h,\, 0}` , -the soil surface) (section :numref:`Vertical Discretization`), the factor of 100 -converts from m to cm, and :math:`\beta` is a plant-dependent root +the soil surface) (section :numref:`Vertical Discretization`), the factor of 100 +converts from m to cm, and :math:`\beta` is a plant-dependent root distribution parameter adopted from :ref:`Jackson et al. (1996)` (:numref:`Table Plant functional type root distribution parameters`). @@ -35,8 +35,8 @@ distribution parameter adopted from :ref:`Jackson et al. (1996) beta ** (col%zi(c,lev-1)*m_to_cm) - & beta ** (col%zi(c,lev)*m_to_cm) ) -.. 0, 0.976, 0.943, 0.943, 0.993, 0.966, 0.993, 0.966, 0.943, 0.964, 0.964, - 0.914, 0.914, 0.943, 0.943, 0.943, 0.943, 0.943, 0.943, 0.943, 0.943, +.. 0, 0.976, 0.943, 0.943, 0.993, 0.966, 0.993, 0.966, 0.943, 0.964, 0.964, + 0.914, 0.914, 0.943, 0.943, 0.943, 0.943, 0.943, 0.943, 0.943, 0.943, .. _Table Plant functional type root distribution parameters: @@ -101,16 +101,16 @@ distribution parameter adopted from :ref:`Jackson et al. (1996) +----------------------------------+------------------+ | Switchgrass I | 0.943 | +----------------------------------+------------------+ - + .. _Root Spacing: Root Spacing ----------------------------- -To determine the conductance along the soil to root pathway (section -:numref:`Soil-to-root`) an estimate of the spacing between the roots within +To determine the conductance along the soil to root pathway (section +:numref:`Soil-to-root`) an estimate of the spacing between the roots within a soil layer is required. The distance between roots :math:`dx_{root,i}` (m) -is calculated by assuming that roots are distributed uniformly throughout +is calculated by assuming that roots are distributed uniformly throughout the soil (:ref:`Gardner 1960`) .. math:: @@ -118,7 +118,7 @@ the soil (:ref:`Gardner 1960`) dx_{root,i} = \left(\pi \cdot L_i\right)^{- \frac{1}{2}} -where :math:`L_{i}` is the root length density (m m :sup:`-3`) +where :math:`L_{i}` is the root length density (m m :sup:`-3`) .. math:: :label: 11.13 @@ -132,10 +132,10 @@ where :math:`L_{i}` is the root length density (m m :sup:`-3`) B_{root,i} = \frac{c\_to\_b \cdot C_{fineroot} \cdot r_{i}}{dz_{i}} -where :math:`c\_to\_b = 2` (kg biomass kg carbon :sup:`-1`) and -:math:`C_{fineroot}` is the amount of fine root carbon (kg m :sup:`-2`). +where :math:`c\_to\_b = 2` (kg biomass kg carbon :sup:`-1`) and +:math:`C_{fineroot}` is the amount of fine root carbon (kg m :sup:`-2`). -:math:`\rho_{root}` is the root density (kg m :sup:`-3`), and +:math:`\rho_{root}` is the root density (kg m :sup:`-3`), and :math:`{CA}_{root}` is the fine root cross sectional area (m :sup:`2`) .. math:: @@ -150,19 +150,19 @@ where :math:`r_{root}` is the root radius (m). Plant Hydraulic Stress ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The Plant Hydraulic Stress (PHS) routine explicitly models water transport -through the vegetation according to a simple hydraulic framework following -Darcy's Law for porous media flow equations influenced by +The Plant Hydraulic Stress (PHS) routine explicitly models water transport +through the vegetation according to a simple hydraulic framework following +Darcy's Law for porous media flow equations influenced by :ref:`Bonan et al. (2014) `, :ref:`Chuang et al. (2006) `, :ref:`Sperry et al. (1998) `, :ref:`Sperry and Love (2015) `, :ref:`Williams et al (1996) `. -PHS solves for the vegetation water potential that matches water supply with -transpiration demand. Water supply is modeled according to the circuit analog -in :numref:`Figure Plant hydraulic circuit`. Transpiration demand is modeled -relative to maximum transpiration by a transpiration loss function dependent +PHS solves for the vegetation water potential that matches water supply with +transpiration demand. Water supply is modeled according to the circuit analog +in :numref:`Figure Plant hydraulic circuit`. Transpiration demand is modeled +relative to maximum transpiration by a transpiration loss function dependent on leaf water potential. .. _Figure Plant hydraulic circuit: @@ -176,14 +176,14 @@ on leaf water potential. Plant Water Supply ----------------------- -The supply equations are used to solve for vegetation water potential forced +The supply equations are used to solve for vegetation water potential forced by transpiration demand and the set of layer-by-layer soil water potentials. -The water supply is discretized into segments: soil-to-root, root-to-stem, and -stem-to-leaf. There are typically several (1-49) soil-to-root flows operating -in parallel, one per soil layer. There are two stem-to-leaf flows operating in +The water supply is discretized into segments: soil-to-root, root-to-stem, and +stem-to-leaf. There are typically several (1-49) soil-to-root flows operating +in parallel, one per soil layer. There are two stem-to-leaf flows operating in parallel, corresponding to the sunlit and shaded "leaves". -In general the water fluxes (e.g. soil-to-root, root-to-stem, etc.) are +In general the water fluxes (e.g. soil-to-root, root-to-stem, etc.) are modeled according to Darcy's Law for porous media flow as: .. math:: @@ -191,32 +191,32 @@ modeled according to Darcy's Law for porous media flow as: q = kA\left( \psi_1 - \psi_2 \right) -:math:`q` is the flux of water (mmH\ :sub:`2`\ O/s) spanning the segment +:math:`q` is the flux of water (mmH\ :sub:`2`\ O/s) spanning the segment between :math:`\psi_1` and :math:`\psi_2` :math:`k` is the hydraulic conductance (s\ :sup:`-1`\ ) -:math:`A` is the area basis (m\ :sup:`2`\ /m\ :sup:`2`\ ) relating the +:math:`A` is the area basis (m\ :sup:`2`\ /m\ :sup:`2`\ ) relating the conducting area basis to ground area -:math:`\psi_1 - \psi_2` is the gradient in water potential (mmH\ :sub:`2`\ O) +:math:`\psi_1 - \psi_2` is the gradient in water potential (mmH\ :sub:`2`\ O) across the segment -The segments in :numref:`Figure Plant hydraulic circuit` have variable resistance, -as the water potentials become lower, hydraulic conductance decreases. This is -captured by multiplying the maximum segment conductance by a sigmoidal function -capturing the percent loss of conductivity. The function uses two parameters to -fit experimental vulnerability curves: the water potential at 50% loss of +The segments in :numref:`Figure Plant hydraulic circuit` have variable resistance, +as the water potentials become lower, hydraulic conductance decreases. This is +captured by multiplying the maximum segment conductance by a sigmoidal function +capturing the percent loss of conductivity. The function uses two parameters to +fit experimental vulnerability curves: the water potential at 50% loss of conductivity (:math:`p50`) and a shape fitting parameter (:math:`c_k`). .. math:: :label: 11.102 - + k=k_{max}\cdot 2^{-\left(\dfrac{\psi_1}{p50}\right)^{c_k}} -:math:`k_{max}` is the maximum segment conductance (s\ :sup:`-1`\ ) +:math:`k_{max}` is the maximum segment conductance (s\ :sup:`-1`\ ) -:math:`p50` is the water potential at 50% loss of conductivity (mmH\ :sub:`2`\ O) +:math:`p50` is the water potential at 50% loss of conductivity (mmH\ :sub:`2`\ O) :math:`\psi_1` is the water potential of the lower segment terminus (mmH\ :sub:`2`\ O) @@ -225,40 +225,40 @@ conductivity (:math:`p50`) and a shape fitting parameter (:math:`c_k`). Stem-to-leaf '''''''''''''''''''''''' -The area basis and conductance parameterization varies by segment. There -are two stem-to-leaf fluxes in parallel, from stem to sunlit leaf and from -stem to shaded leaf (:math:`q_{1a}` and :math:`q_{1a}`). The water flux from -stem-to-leaf is the product of the segment conductance, the conducting area -basis, and the water potential gradient from stem to leaf. Stem-to-leaf -conductance is defined as the maximum conductance multiplied by the percent +The area basis and conductance parameterization varies by segment. There +are two stem-to-leaf fluxes in parallel, from stem to sunlit leaf and from +stem to shaded leaf (:math:`q_{1a}` and :math:`q_{1a}`). The water flux from +stem-to-leaf is the product of the segment conductance, the conducting area +basis, and the water potential gradient from stem to leaf. Stem-to-leaf +conductance is defined as the maximum conductance multiplied by the percent of maximum conductance, as calculated by the sigmoidal vulnerability curve. -The maximum conductance is a PFT parameter representing the maximum -conductance of water from stem to leaf per unit leaf area. This parameter -can be defined separately for sunlit and shaded segments and should already -include the appropriate length scaling (in other words this is a conductance, -not conductivity). The water potential gradient is the difference between -leaf water potential and stem water potential. There is no gravity term, -assuming a negligible difference in height across the segment. The area +The maximum conductance is a PFT parameter representing the maximum +conductance of water from stem to leaf per unit leaf area. This parameter +can be defined separately for sunlit and shaded segments and should already +include the appropriate length scaling (in other words this is a conductance, +not conductivity). The water potential gradient is the difference between +leaf water potential and stem water potential. There is no gravity term, +assuming a negligible difference in height across the segment. The area basis is the leaf area index (either sunlit or shaded). -.. math:: +.. math:: :label: 11.103 - q_{1a}=k_{1a}\cdot\mbox{LAI}_{sun}\cdot\left(\psi_{stem}-\psi_{sunleaf} \right) + q_{1a}=k_{1a}\cdot\mbox{LAI}_{sun}\cdot\left(\psi_{stem}-\psi_{sunleaf} \right) -.. math:: +.. math:: :label: 11.104 - q_{1b}=k_{1b}\cdot\mbox{LAI}_{shade}\cdot\left(\psi_{stem}-\psi_{shadeleaf} \right) + q_{1b}=k_{1b}\cdot\mbox{LAI}_{shade}\cdot\left(\psi_{stem}-\psi_{shadeleaf} \right) -.. math:: +.. math:: :label: 11.105 - k_{1a}=k_{1a,max}\cdot 2^{-\left(\dfrac{\psi_{stem}}{p50_1}\right)^{c_k}} + k_{1a}=k_{1a,max}\cdot 2^{-\left(\dfrac{\psi_{stem}}{p50_1}\right)^{c_k}} .. math:: :label: 11.106 - + k_{1b}=k_{1b,max}\cdot 2^{-\left(\dfrac{\psi_{stem}}{p50_1}\right)^{c_k}} Variables: @@ -292,22 +292,22 @@ Parameters: Root-to-stem '''''''''''''''''''''''' -There is one root-to-stem flux. This represents a flux from the root collar -to the upper branch reaches. The water flux from root-to-stem is the product -of the segment conductance, the conducting area basis, and the water -potential gradient from root to stem. Root-to-stem conductance is defined -as the maximum conductance multiplied by the percent of maximum conductance, -as calculated by the sigmoidal vulnerability curve (two parameters). The -maximum conductance is defined as the maximum root-to-stem conductivity per -unit stem area (PFT parameter) divided by the length of the conducting path, -which is taken to be the vegetation height. The area basis is the stem area -index. The gradient in water potential is the difference between the root -water potential and the stem water potential less the difference in +There is one root-to-stem flux. This represents a flux from the root collar +to the upper branch reaches. The water flux from root-to-stem is the product +of the segment conductance, the conducting area basis, and the water +potential gradient from root to stem. Root-to-stem conductance is defined +as the maximum conductance multiplied by the percent of maximum conductance, +as calculated by the sigmoidal vulnerability curve (two parameters). The +maximum conductance is defined as the maximum root-to-stem conductivity per +unit stem area (PFT parameter) divided by the length of the conducting path, +which is taken to be the vegetation height. The area basis is the stem area +index. The gradient in water potential is the difference between the root +water potential and the stem water potential less the difference in gravitational potential. .. math:: :label: 11.107 - + q_2=k_2 \cdot SAI \cdot \left( \psi_{root} - \psi_{stem} - \Delta \psi_z \right) .. math:: @@ -340,37 +340,37 @@ Parameters: Soil-to-root '''''''''''''''''''''''' -There are several soil-to-root fluxes operating in parallel (one for each -root-containing soil layer). Each represents a flux from the given soil -layer to the root collar. The water flux from soil-to-root is the product -of the segment conductance, the conducting area basis, and the water -potential gradient from soil to root. The area basis is a proxy for root -area index, defined as the summed leaf and stem area index multiplied by -the root-to-shoot ratio (PFT parameter) multiplied by the layer root -fraction. The root fraction comes from an empirical root profile (section -:numref:`Vertical Root Distribution`). - -The gradient in water potential is the difference between the soil water -potential and the root water potential less the difference in gravitational -potential. There is only one root water potential to which all soil layers -are connected in parallel. A soil-to-root flux can be either positive -(vegetation water uptake) or negative (water deposition), depending on the -relative values of the root and soil water potentials. This allows for the -occurrence of hydraulic redistribution where water moves through vegetation +There are several soil-to-root fluxes operating in parallel (one for each +root-containing soil layer). Each represents a flux from the given soil +layer to the root collar. The water flux from soil-to-root is the product +of the segment conductance, the conducting area basis, and the water +potential gradient from soil to root. The area basis is a proxy for root +area index, defined as the summed leaf and stem area index multiplied by +the root-to-shoot ratio (PFT parameter) multiplied by the layer root +fraction. The root fraction comes from an empirical root profile (section +:numref:`Vertical Root Distribution`). + +The gradient in water potential is the difference between the soil water +potential and the root water potential less the difference in gravitational +potential. There is only one root water potential to which all soil layers +are connected in parallel. A soil-to-root flux can be either positive +(vegetation water uptake) or negative (water deposition), depending on the +relative values of the root and soil water potentials. This allows for the +occurrence of hydraulic redistribution where water moves through vegetation tissue from one soil layer to another. -Soil-to-root conductance is the result of two resistances in series, first -across the soil-root interface and then through the root tissue. The root -tissue conductance is defined as the maximum conductance multiplied by the -percent of maximum conductance, as calculated by the sigmoidal vulnerability -curve. The maximum conductance is defined as the maximum root-tissue -conductivity (PFT parameter) divided by the length of the conducting path, +Soil-to-root conductance is the result of two resistances in series, first +across the soil-root interface and then through the root tissue. The root +tissue conductance is defined as the maximum conductance multiplied by the +percent of maximum conductance, as calculated by the sigmoidal vulnerability +curve. The maximum conductance is defined as the maximum root-tissue +conductivity (PFT parameter) divided by the length of the conducting path, which is taken to be the soil layer depth plus lateral root length. -The soil-root interface conductance is defined as the soil conductivity -divided by the conducting length from soil to root. The soil conductivity -varies by soil layer and is calculated based on soil potential and soil -properties, via the Brooks-Corey theory. The conducting length is determined +The soil-root interface conductance is defined as the soil conductivity +divided by the conducting length from soil to root. The soil conductivity +varies by soil layer and is calculated based on soil potential and soil +properties, via the Brooks-Corey theory. The conducting length is determined from the characteristic root spacing (section :numref:`Root Spacing`). .. math:: @@ -381,7 +381,7 @@ from the characteristic root spacing (section :numref:`Root Spacing`). .. math:: :label: 11.110 - k_{3,i}=\dfrac{k_{r,i} \cdot k_{s,i}}{k_{r,i}+k_{s,i}} + k_{3,i}=\dfrac{k_{r,i} \cdot k_{s,i}}{k_{r,i}+k_{s,i}} .. math:: :label: 11.111 @@ -397,7 +397,7 @@ from the characteristic root spacing (section :numref:`Root Spacing`). .. math:: :label: 11.113 - k_{s,i} = \dfrac{k_{soil,i}}{dx_{root,i}} + k_{s,i} = \dfrac{k_{soil,i}}{dx_{root,i}} Variables: @@ -407,7 +407,7 @@ Variables: :math:`LAI` = total leaf area index (m2/m2) -:math:`SAI` = stem area index (m2/m2) +:math:`SAI` = stem area index (m2/m2) :math:`\psi_{soil,i}` = water potential in soil layer :math:`i` (mmH\ :sub:`2`\ O) @@ -433,34 +433,34 @@ Plant Water Demand ----------------------- Plant water demand depends on stomatal conductance, which is described in section :numref:`Stomatal resistance`. -Here we describe the influence of PHS and the coupling of vegetation water demand and supply. -PHS models vegetation water demand as transpiration attenuated by a transpiration loss function based on leaf water potential. -Sunlit leaf transpiration is modeled as the maximum sunlit leaf transpiration multiplied by the percent of maximum transpiration as modeled by the sigmoidal loss function. -The same follows for shaded leaf transpiration. +Here we describe the influence of PHS and the coupling of vegetation water demand and supply. +PHS models vegetation water demand as transpiration attenuated by a transpiration loss function based on leaf water potential. +Sunlit leaf transpiration is modeled as the maximum sunlit leaf transpiration multiplied by the percent of maximum transpiration as modeled by the sigmoidal loss function. +The same follows for shaded leaf transpiration. Maximum stomatal conductance is calculated from the Medlyn model :ref:`(Medlyn et al. 2011) ` absent water stress and used to calculate the maximum transpiration (see section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). -Water stress is calculated as the ratio of attenuated stomatal conductance to maximum stomatal conductance. -Water stress is calculated with distinct values for sunlit and shaded leaves. +Water stress is calculated as the ratio of attenuated stomatal conductance to maximum stomatal conductance. +Water stress is calculated with distinct values for sunlit and shaded leaves. Vegetation water stress is calculated based on leaf water potential and is used to attenuate photosynthesis (see section :numref:`Photosynthesis`) .. math:: :label: 11.201 - E_{sun} = E_{sun,max} \cdot 2^{-\left(\dfrac{\psi_{sunleaf}}{p50_e}\right)^{c_k}} + E_{sun} = E_{sun,max} \cdot 2^{-\left(\dfrac{\psi_{sunleaf}}{p50_e}\right)^{c_k}} .. math:: :label: 11.202 - E_{shade} = E_{shade,max} \cdot 2^{-\left(\dfrac{\psi_{shadeleaf}}{p50_e}\right)^{c_k}} + E_{shade} = E_{shade,max} \cdot 2^{-\left(\dfrac{\psi_{shadeleaf}}{p50_e}\right)^{c_k}} .. math:: :label: 11.203 - \beta_{t,sun} = \dfrac{g_{s,sun}}{g_{s,sun,\beta_t=1}} + \beta_{t,sun} = \dfrac{g_{s,sun}}{g_{s,sun,\beta_t=1}} .. math:: :label: 11.204 - \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} + \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} :math:`E_{sun}` = sunlit leaf transpiration (mm/s) @@ -472,11 +472,11 @@ Vegetation water stress is calculated based on leaf water potential and is used :math:`\psi_{sunleaf}` = sunlit leaf water potential (mmH\ :sub:`2`\ O) -:math:`\psi_{shadeleaf}` = shaded leaf water potential (mmH\ :sub:`2`\ O) +:math:`\psi_{shadeleaf}` = shaded leaf water potential (mmH\ :sub:`2`\ O) -:math:`\beta_{t,sun}` = sunlit transpiration water stress (-) +:math:`\beta_{t,sun}` = sunlit transpiration water stress (-) -:math:`\beta_{t,shade}` = shaded transpiration water stress (-) +:math:`\beta_{t,shade}` = shaded transpiration water stress (-) :math:`g_{s,sun}` = stomatal conductance of water corresponding to :math:`E_{sun}` @@ -491,7 +491,7 @@ Vegetation water stress is calculated based on leaf water potential and is used Vegetation Water Potential ----------------------------- -Both plant water supply and demand are functions of vegetation water potential. PHS explicitly models root, stem, shaded leaf, and sunlit leaf water potential at each timestep. PHS iterates to find the vegetation water potential :math:`\psi` (vector) that satisfies continuity between the non-linear vegetation water supply and demand (equations :eq:`11.103`, :eq:`11.104`, :eq:`11.107`, :eq:`11.109`, :eq:`11.201`, :eq:`11.202`). +Both plant water supply and demand are functions of vegetation water potential. PHS explicitly models root, stem, shaded leaf, and sunlit leaf water potential at each timestep. PHS iterates to find the vegetation water potential :math:`\psi` (vector) that satisfies continuity between the non-linear vegetation water supply and demand (equations :eq:`11.103`, :eq:`11.104`, :eq:`11.107`, :eq:`11.109`, :eq:`11.201`, :eq:`11.202`). .. math:: :label: 11.301 @@ -520,10 +520,10 @@ Numerical Implementation The four plant water potential nodes are ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`). The fluxes between each pair of nodes are labeled in Figure 1. -:math:`E_{sun}` and :math:`E_{sha}` are the transpiration from sunlit and shaded leaves, respectively. -We use the circuit-analog model to calculate the vegetation water potential ( :math:`\psi`) for the four plant nodes, forced by soil matric potential and unstressed transpiration. -The unstressed transpiration is acquired by running the photosynthesis model with :math:`\beta_t=1`. -The unstressed transpiration flux is attenuated based on the leaf-level vegetation water potential. +:math:`E_{sun}` and :math:`E_{sha}` are the transpiration from sunlit and shaded leaves, respectively. +We use the circuit-analog model to calculate the vegetation water potential ( :math:`\psi`) for the four plant nodes, forced by soil matric potential and unstressed transpiration. +The unstressed transpiration is acquired by running the photosynthesis model with :math:`\beta_t=1`. +The unstressed transpiration flux is attenuated based on the leaf-level vegetation water potential. Using the attenuated transpiration, we solve for :math:`g_{s,stressed}` and output :math:`\beta_t=\dfrac{g_{s,stressed}}{g_{s,unstressed}}`. The continuity of water flow through the system yields four equations @@ -539,16 +539,16 @@ The continuity of water flow through the system yields four equations \end{aligned} -We seek the set of vegetation water potential values, +We seek the set of vegetation water potential values, .. math:: :label: 11.402 - \psi=\left[ \begin {array}{c} + \psi=\left[ \begin {array}{c} \psi_{sunleaf}\cr\psi_{shadeleaf}\cr\psi_{stem}\cr\psi_{root} - \end {array} \right] + \end {array} \right] -that satisfies these equations, as forced by the soil moisture and atmospheric state. +that satisfies these equations, as forced by the soil moisture and atmospheric state. Each flux on the schematic can be represented in terms of the relevant water potentials. Defining the transpiration fluxes: .. math:: @@ -556,7 +556,7 @@ Each flux on the schematic can be represented in terms of the relevant water pot \begin{aligned} E_{sun} &= E_{sun,max} \cdot 2^{-\left(\dfrac{\psi_{sunleaf}}{p50_e}\right)^{c_k}} \\ - E_{shade} &= E_{shade,max} \cdot 2^{-\left(\dfrac{\psi_{shadeleaf}}{p50_e}\right)^{c_k}} + E_{shade} &= E_{shade,max} \cdot 2^{-\left(\dfrac{\psi_{shadeleaf}}{p50_e}\right)^{c_k}} \end{aligned} Defining the water supply fluxes: @@ -572,9 +572,9 @@ Defining the water supply fluxes: \end{aligned} We're looking to find the vector :math:`\psi` -that fits with soil and atmospheric forcings while satisfying water flow continuity. -Due to the model non-linearity, we use a linearized explicit approach, iterating with Newton's method. -The initial guess is the solution for :math:`\psi` (vector) from the previous time step. +that fits with soil and atmospheric forcings while satisfying water flow continuity. +Due to the model non-linearity, we use a linearized explicit approach, iterating with Newton's method. +The initial guess is the solution for :math:`\psi` (vector) from the previous time step. The general framework, from iteration `m` to `m+1` is: .. math:: @@ -647,11 +647,11 @@ Introducing the notation: \Delta\psi_{shadeleaf} \cr \Delta\psi_{stem} \cr \Delta\psi_{root} - \end {array} \right] + \end {array} \right] .. math:: :label: 11.412 - + A= \left[ \begin {array}{cccc} \dfrac{\delta q_{1a}}{\delta \psi_{sun}}-\dfrac{\delta E_{sun}}{\delta \psi_{sun}}&0&\dfrac{\delta q_{1a}}{\delta \psi_{stem}}&0\cr @@ -686,22 +686,22 @@ Now we compute all the entries for :math:`A` and :math:`b` based on the soil moi \psi_{m+1}=\psi_m+\Delta\psi -We iterate until :math:`b\to 0`, signifying water flux balance through the system. The result is a final set of water potentials ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`) satisfying non-divergent water flux through the system. -The magnitude of the water flux is driven by soil matric potential and unstressed ( :math:`\beta_t=1`) transpiration. +We iterate until :math:`b\to 0`, signifying water flux balance through the system. The result is a final set of water potentials ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`) satisfying non-divergent water flux through the system. +The magnitude of the water flux is driven by soil matric potential and unstressed ( :math:`\beta_t=1`) transpiration. -We use the transpiration solution (corresponding to the final solution for :math:`\psi`) to compute stomatal conductance. The stomatal conductance is then used to compute :math:`\beta_t`. +We use the transpiration solution (corresponding to the final solution for :math:`\psi`) to compute stomatal conductance. The stomatal conductance is then used to compute :math:`\beta_t`. .. math:: :label: 11.416 - \beta_{t,sun} = \dfrac{g_{s,sun}}{g_{s,sun,\beta_t=1}} + \beta_{t,sun} = \dfrac{g_{s,sun}}{g_{s,sun,\beta_t=1}} .. math:: :label: 11.417 - \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} + \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} -The :math:`\beta_t` values are used in the Photosynthesis module (see section :numref:`Photosynthesis`) to apply water stress. +The :math:`\beta_t` values are used in the Photosynthesis module (see section :numref:`Photosynthesis`) to apply water stress. The solution for :math:`\psi` is saved as a new variable (vegetation water potential) and is indicative of plant water status. The soil-to-root fluxes :math:`\left( q_{3,1},q_{3,2},\mbox{...},q_{3,n}\right)` are used as the soil transpiration sink in the Richards' equation subsurface flow equations (see section :numref:`Soil Water`). @@ -712,10 +712,10 @@ Flow Diagram of Leaf Flux Calculations: PHS runs nested in the loop that solves for sensible and latent heat fluxes and temperature for vegetated surfaces (see section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). The scheme iterates for convergence of leaf temperature (:math:`T_l`), transpiration water stress (:math:`\beta_t`), and intercellular CO2 concentration (:math:`c_i`). -PHS is forced by maximum transpiration (absent water stress, :math:`\beta_t=1`), whereby we first solve for assimilation, stomatal conductance, and intercellular CO2 with :math:`\beta_{t,sun}` and :math:`\beta_{t,shade}` both set to 1. +PHS is forced by maximum transpiration (absent water stress, :math:`\beta_t=1`), whereby we first solve for assimilation, stomatal conductance, and intercellular CO2 with :math:`\beta_{t,sun}` and :math:`\beta_{t,shade}` both set to 1. This involves iterating to convergence of :math:`c_i` (see section :numref:`Photosynthesis`). -Next, using the solutions for :math:`E_{sun,max}` and :math:`E_{shade,max}`, PHS solves for :math:`\psi`, :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}`. +Next, using the solutions for :math:`E_{sun,max}` and :math:`E_{shade,max}`, PHS solves for :math:`\psi`, :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}`. The values for :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}` are inputs to the photosynthesis routine, which now solves for attenuated photosynthesis and stomatal conductance (reflecting water stress). Again this involves iterating to convergence of :math:`c_i`. Non-linearities between :math:`\beta_t` and transpiration require also iterating to convergence of :math:`\beta_t`. diff --git a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst index 45d2aef0d3..88c20387f1 100644 --- a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst +++ b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst @@ -33,67 +33,67 @@ litter pools. Mortality (*mort*) fluxes out of displayed vegetation carbon and nitrogen pools are .. math:: - :label: 33.1) + :label: 33.1) CF_{leaf\_ mort} =CS_{leaf} m .. math:: - :label: 33.2) + :label: 33.2) CF_{froot\_ mort} =CS_{froot} m .. math:: - :label: 33.3) + :label: 33.3) CF_{livestem\_ mort} =CS_{livestem} m .. math:: - :label: 33.4) + :label: 33.4) CF_{deadstem\_ mort} =CS_{deadstem} m .. math:: - :label: 33.5) + :label: 33.5) CF_{livecroot\_ mort} =CS_{livecroot} m .. math:: - :label: 33.6) + :label: 33.6) CF_{deadcroot\_ mort} =CS_{deadcroot} m .. math:: - :label: 33.7) + :label: 33.7) NF_{leaf\_ mort} =NS_{leaf} m .. math:: - :label: 33.8) + :label: 33.8) NF_{froot\_ mort} =NS_{froot} m .. math:: - :label: 33.9) + :label: 33.9) NF_{livestem\_ mort} =NS_{livestem} m .. math:: - :label: 33.10) + :label: 33.10) NF_{deadstem\_ mort} =NS_{deadstem} m .. math:: - :label: 33.11) + :label: 33.11) NF_{livecroot\_ mort} =NS_{livecroot} m .. math:: - :label: 33.12) + :label: 33.12) NF_{deadcroot\_ mort} =NS_{deadcroot} m .. math:: - :label: 33.13) + :label: 33.13) NF_{retrans\_ mort} =NS_{retrans} m. @@ -104,67 +104,67 @@ refers to fine roots, and *retrans* refers to retranslocated. Mortality fluxes out of carbon and nitrogen storage (*stor)* pools are .. math:: - :label: 33.14) + :label: 33.14) CF_{leaf\_ stor\_ mort} =CS_{leaf\_ stor} m .. math:: - :label: 33.15) + :label: 33.15) CF_{froot\_ stor\_ mort} =CS_{froot\_ stor} m .. math:: - :label: 33.16) + :label: 33.16) CF_{livestem\_ stor\_ mort} =CS_{livestem\_ stor} m .. math:: - :label: 33.17) + :label: 33.17) CF_{deadstem\_ stor\_ mort} =CS_{deadstem\_ stor} m .. math:: - :label: 33.18) + :label: 33.18) CF_{livecroot\_ stor\_ mort} =CS_{livecroot\_ stor} m .. math:: - :label: 33.19) + :label: 33.19) CF_{deadcroot\_ stor\_ mort} =CS_{deadcroot\_ stor} m .. math:: - :label: 33.20) + :label: 33.20) CF_{gresp\_ stor\_ mort} =CS_{gresp\_ stor} m .. math:: - :label: 33.21) + :label: 33.21) NF_{leaf\_ stor\_ mort} =NS_{leaf\_ stor} m .. math:: - :label: 33.22) + :label: 33.22) NF_{froot\_ stor\_ mort} =NS_{froot\_ stor} m .. math:: - :label: 33.23) + :label: 33.23) NF_{livestem\_ stor\_ mort} =NS_{livestem\_ stor} m .. math:: - :label: 33.24) + :label: 33.24) NF_{deadstem\_ stor\_ mort} =NS_{deadstem\_ stor} m .. math:: - :label: 33.25) + :label: 33.25) NF_{livecroot\_ stor\_ mort} =NS_{livecroot\_ stor} m .. math:: - :label: 33.26) + :label: 33.26) NF_{deadcroot\_ stor\_ mort} =NS_{deadcroot\_ stor} m @@ -174,67 +174,67 @@ Mortality fluxes out of carbon and nitrogen transfer (*xfer)* growth pools are .. math:: - :label: 33.27) + :label: 33.27) CF_{leaf\_ xfer\_ mort} =CS_{leaf\_ xfer} m .. math:: - :label: 33.28) + :label: 33.28) CF_{froot\_ xfer\_ mort} =CS_{froot\_ xfer} m .. math:: - :label: 33.29) + :label: 33.29) CF_{livestem\_ xfer\_ mort} =CS_{livestem\_ xfer} m .. math:: - :label: 33.30) + :label: 33.30) CF_{deadstem\_ xfer\_ mort} =CS_{deadstem\_ xfer} m .. math:: - :label: 33.31) + :label: 33.31) CF_{livecroot\_ xfer\_ mort} =CS_{livecroot\_ xfer} m .. math:: - :label: 33.32) + :label: 33.32) CF_{deadcroot\_ xfer\_ mort} =CS_{deadcroot\_ xfer} m .. math:: - :label: 33.33) + :label: 33.33) CF_{gresp\_ xfer\_ mort} =CS_{gresp\_ xfer} m .. math:: - :label: 33.34) + :label: 33.34) NF_{leaf\_ xfer\_ mort} =NS_{leaf\_ xfer} m .. math:: - :label: 33.35) + :label: 33.35) NF_{froot\_ xfer\_ mort} =NS_{froot\_ xfer} m .. math:: - :label: 33.36) + :label: 33.36) NF_{livestem\_ xfer\_ mort} =NS_{livestem\_ xfer} m .. math:: - :label: 33.37) + :label: 33.37) NF_{deadstem\_ xfer\_ mort} =NS_{deadstem\_ xfer} m .. math:: - :label: 33.38) + :label: 33.38) NF_{livecroot\_ xfer\_ mort} =NS_{livecroot\_ xfer} m .. math:: - :label: 33.39) + :label: 33.39) NF_{deadcroot\_ xfer\_ mort} =NS_{deadcroot\_ xfer} m @@ -249,62 +249,62 @@ the column level. Carbon and nitrogen fluxes from mortality of displayed leaf and fine root into litter pools are calculated as .. math:: - :label: 33.40) + :label: 33.40) CF_{leaf\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{leaf\_ mort} f_{lab\_ leaf,p} wcol_{p} .. math:: - :label: 33.41) + :label: 33.41) CF_{leaf\_ mort,lit2} =\sum _{p=0}^{npfts}CF_{leaf\_ mort} f_{cel\_ leaf,p} wcol_{p} .. math:: - :label: 33.42) + :label: 33.42) CF_{leaf\_ mort,lit3} =\sum _{p=0}^{npfts}CF_{leaf\_ mort} f_{lig\_ leaf,p} wcol_{p} .. math:: - :label: 33.43) + :label: 33.43) CF_{froot\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{froot\_ mort} f_{lab\_ froot,p} wcol_{p} .. math:: - :label: 33.44) + :label: 33.44) CF_{froot\_ mort,lit2} =\sum _{p=0}^{npfts}CF_{froot\_ mort} f_{cel\_ froot,p} wcol_{p} .. math:: - :label: 33.45) + :label: 33.45) CF_{froot\_ mort,lit3} =\sum _{p=0}^{npfts}CF_{froot\_ mort} f_{lig\_ froot,p} wcol_{p} .. math:: - :label: 33.46) + :label: 33.46) NF_{leaf\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{leaf\_ mort} f_{lab\_ leaf,p} wcol_{p} .. math:: - :label: 33.47) + :label: 33.47) NF_{leaf\_ mort,lit2} =\sum _{p=0}^{npfts}NF_{leaf\_ mort} f_{cel\_ leaf,p} wcol_{p} .. math:: - :label: 33.48) + :label: 33.48) NF_{leaf\_ mort,lit3} =\sum _{p=0}^{npfts}NF_{leaf\_ mort} f_{lig\_ leaf,p} wcol_{p} .. math:: - :label: 33.49) + :label: 33.49) NF_{froot\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{froot\_ mort} f_{lab\_ froot,p} wcol_{p} .. math:: - :label: 33.50) + :label: 33.50) NF_{froot\_ mort,lit2} =\sum _{p=0}^{npfts}NF_{froot\_ mort} f_{cel\_ froot,p} wcol_{p} .. math:: - :label: 33.51) + :label: 33.51) NF_{froot\_ mort,lit3} =\sum _{p=0}^{npfts}NF_{froot\_ mort} f_{lig\_ froot,p} wcol_{p} . @@ -314,42 +314,42 @@ live and dead stem and coarse root pools are merged to the column level and deposited in the coarse woody debris (*cwd*) pools: .. math:: - :label: 33.52) + :label: 33.52) CF_{livestem\_ mort,cwd} =\sum _{p=0}^{npfts}CF_{livestem\_ mort} wcol_{p} .. math:: - :label: 33.53) + :label: 33.53) CF_{deadstem\_ mort,cwd} =\sum _{p=0}^{npfts}CF_{deadstem\_ mort} wcol_{p} .. math:: - :label: 33.54) + :label: 33.54) CF_{livecroot\_ mort,cwd} =\sum _{p=0}^{npfts}CF_{livecroot\_ mort} wcol_{p} .. math:: - :label: 33.55) + :label: 33.55) CF_{deadcroot\_ mort,cwd} =\sum _{p=0}^{npfts}CF_{deadcroot\_ mort} wcol_{p} .. math:: - :label: 33.56) + :label: 33.56) NF_{livestem\_ mort,cwd} =\sum _{p=0}^{npfts}NF_{livestem\_ mort} wcol_{p} .. math:: - :label: 33.57) + :label: 33.57) NF_{deadstem\_ mort,cwd} =\sum _{p=0}^{npfts}NF_{deadstem\_ mort} wcol_{p} .. math:: - :label: 33.58) + :label: 33.58) NF_{livecroot\_ mort,cwd} =\sum _{p=0}^{npfts}NF_{livecroot\_ mort} wcol_{p} .. math:: - :label: 33.59) + :label: 33.59) NF_{deadcroot\_ mort,cwd} =\sum _{p=0}^{npfts}NF_{deadcroot\_ mort} wcol_{p} @@ -363,72 +363,72 @@ after being merged to the column level. Carbon mortality fluxes out of storage and transfer pools are: .. math:: - :label: 33.60) + :label: 33.60) CF_{leaf\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{leaf\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.61) + :label: 33.61) CF_{froot\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{froot\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.62) + :label: 33.62) CF_{livestem\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{livestem\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.63) + :label: 33.63) CF_{deadstem\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{deadstem\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.64) + :label: 33.64) CF_{livecroot\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{livecroot\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.65) + :label: 33.65) CF_{deadcroot\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{deadcroot\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.66) + :label: 33.66) CF_{gresp\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{gresp\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.67) + :label: 33.67) CF_{leaf\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{leaf\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.68) + :label: 33.68) CF_{froot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{froot\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.69) + :label: 33.69) CF_{livestem\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{livestem\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.70) + :label: 33.70) CF_{deadstem\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{deadstem\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.71) + :label: 33.71) CF_{livecroot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{livecroot\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.72) + :label: 33.72) CF_{deadcroot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{deadcroot\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.73) + :label: 33.73) CF_{gresp\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{gresp\_ xfer\_ mort} wcol_{p} . @@ -436,67 +436,67 @@ Nitrogen mortality fluxes out of storage and transfer pools, including the storage pool for retranslocated nitrogen, are calculated as: .. math:: - :label: 33.74) + :label: 33.74) NF_{leaf\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{leaf\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.75) + :label: 33.75) NF_{froot\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{froot\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.76) + :label: 33.76) NF_{livestem\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{livestem\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.77) + :label: 33.77) NF_{deadstem\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{deadstem\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.78) + :label: 33.78) NF_{livecroot\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{livecroot\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.79) + :label: 33.79) NF_{deadcroot\_ stor\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{deadcroot\_ stor\_ mort} wcol_{p} .. math:: - :label: 33.80) + :label: 33.80) NF_{retrans\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{retrans\_ mort} wcol_{p} .. math:: - :label: 33.81) + :label: 33.81) NF_{leaf\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{leaf\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.82) + :label: 33.82) NF_{froot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{froot\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.83) + :label: 33.83) NF_{livestem\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{livestem\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.84) + :label: 33.84) NF_{deadstem\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{deadstem\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.85) + :label: 33.85) NF_{livecroot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{livecroot\_ xfer\_ mort} wcol_{p} .. math:: - :label: 33.86) + :label: 33.86) NF_{deadcroot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{deadcroot\_ xfer\_ mort} wcol_{p} . diff --git a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst index 8ec6f1d1fb..c7c1b7e506 100644 --- a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst +++ b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst @@ -19,7 +19,7 @@ carbon cost for the synthesis of new growth. Maintenance Respiration ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Atkin et al. (2016) propose a model for leaf respiration that is based on the leaf nitrogen content per unit area (:math:`NS_{narea}` (gN m :sup:`2` leaf), with an intercept parameter that is PFT dependant, and an acclimation term that depends upon the average temperature of the previous 10 day period :math:`t_{2m,10days}`, in Celsius. +Atkin et al. (2016) propose a model for leaf respiration that is based on the leaf nitrogen content per unit area (:math:`NS_{narea}` (gN m :sup:`2` leaf), with an intercept parameter that is PFT dependant, and an acclimation term that depends upon the average temperature of the previous 10 day period :math:`t_{2m,10days}`, in Celsius. .. math:: :label: 17.46) @@ -29,17 +29,17 @@ Atkin et al. (2016) propose a model for leaf respiration that is based on the le The temperature dependance of leaf maintenance (dark) respiration is described in Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`. .. math:: - :label: 17.47) + :label: 17.47) CF_{mr\_ livestem} \_ =NS_{livestem} MR_{base} MR_{Q10} ^{(T_{2m} -20)/10} .. math:: - :label: 17.48) + :label: 17.48) CF_{mr\_ livecroot} \_ =NS_{livecroot} MR_{base} MR_{Q10} ^{(T_{2m} -20)/10} .. math:: - :label: 17.49) + :label: 17.49) CF_{mr\_ froot} \_ =\sum _{j=1}^{nlevsoi}NS_{froot} rootfr_{j} MR_{base} MR_{Q10} ^{(Ts_{j} -20)/10} @@ -52,10 +52,10 @@ of fine roots distributed in soil level *j*. .. table:: Atkin leaf respiration model intercept values. - ======================== ============= + ======================== ============= Plant functional type :math:`i_{atkin}` - ======================== ============= - NET Temperate 1.499 + ======================== ============= + NET Temperate 1.499 NET Boreal 1.499 NDT Boreal 1.499 BET Tropical 1.756 @@ -65,11 +65,11 @@ of fine roots distributed in soil level *j*. BDT boreal 1.756 BES temperate 2.075 BDS temperate 2.075 - BDS boreal 2.075 + BDS boreal 2.075 C\ :sub:`3` arctic grass 2.196 C\ :sub:`3` grass 2.196 C\ :sub:`4` grass 2.196 - ======================== ============= + ======================== ============= Note that, for woody vegetation, maintenance respiration costs are not calculated for the dead stem and dead coarse root components. These @@ -82,7 +82,7 @@ common base maintenance respiration rate for all live tissue types. The total maintenance respiration cost is then given as: .. math:: - :label: 17.50) + :label: 17.50) CF_{mr} =CF_{mr\_ leaf} +CF_{mr\_ froot} +CF_{mr\_ livestem} +CF_{mr\_ livecroot} . @@ -90,7 +90,7 @@ Growth Respiration ^^^^^^^^^^^^^^^^^^^^^^^^^ Growth respiration is calculated as a factor of 0.11 times the total -carbon allocation to new growth (:math:`CF_{growth}`, after allocating carbon for N acquisition, +carbon allocation to new growth (:math:`CF_{growth}`, after allocating carbon for N acquisition, Chapter :numref:`rst_FUN`.) on a given timestep, based on construction costs for a range of woody and non-woody tissues, with estimates of the growth respiration flux revised downswards following (Atkin et al. 2017). For new diff --git a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst index 2d240d160a..8dbc7a40c8 100644 --- a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst +++ b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst @@ -22,16 +22,16 @@ unit incident direct beam and diffuse flux (section :numref:`Canopy Radiative Tr :math:`I\, \downarrow _{\Lambda }^{\mu }` and :math:`I\, \downarrow _{\Lambda }` \ are the downward diffuse fluxes below the vegetation per unit incident direct beam and diffuse radiation -(section :numref:`Canopy Radiative Transfer`). The direct beam flux +(section :numref:`Canopy Radiative Transfer`). The direct beam flux transmitted through the canopy, per unit incident flux, is :math:`e^{-K\left(L+S\right)}` . -:math:`\vec{I}_{\Lambda }^{\mu }` and :math:`\vec{I}_{\Lambda }^{}` +:math:`\vec{I}_{\Lambda }^{\mu }` and :math:`\vec{I}_{\Lambda }^{}` are the fluxes absorbed by the vegetation, per unit incident direct beam and diffuse radiation (section :numref:`Canopy Radiative Transfer`). :math:`\alpha _{g,\, \Lambda }^{\mu }` and :math:`\alpha _{g,\, \Lambda }` are the direct beam and diffuse ground albedos (section :numref:`Ground Albedos`). :math:`L` and :math:`S` are the exposed leaf area -index and stem area index (section :numref:`Phenology and vegetation burial by snow`). +index and stem area index (section :numref:`Phenology and vegetation burial by snow`). :math:`K` is the optical depth of direct beam per unit leaf and stem area (section :numref:`Canopy Radiative Transfer`). @@ -85,7 +85,7 @@ Photosynthesis and transpiration depend non-linearly on solar radiation, via the light response of stomata. The canopy is treated as two leaves (sunlit and shaded) and the solar radiation in the visible waveband (:math:`<` 0.7 µm) absorbed by the vegetation is apportioned to the -sunlit and shaded leaves (section :numref:`Canopy Radiative Transfer`). +sunlit and shaded leaves (section :numref:`Canopy Radiative Transfer`). The absorbed photosynthetically active (visible waveband) radiation averaged over the sunlit canopy (per unit plant area) is @@ -125,7 +125,7 @@ two-stream approximation (section :numref:`Canopy Radiative Transfer`). The model uses the two-stream approximation to calculate radiative transfer of direct and diffuse radiation through a canopy that is differentiated into leaves that are sunlit and those that are shaded -(section :numref:`Canopy Radiative Transfer`). The two-stream equations +(section :numref:`Canopy Radiative Transfer`). The two-stream equations are integrated over all plant area (leaf and stem area) in the canopy. The model has an optional (though not supported) multi-layer canopy, as described by @@ -140,14 +140,14 @@ derives the light profile with depth in the canopy by taking the derivatives of the absorbed radiative fluxes with respect to plant area index (:math:`L'=L+S`) and evaluating them incrementally through the canopy with cumulative plant area index (:math:`x`). The terms -:math:`{d\vec{I}_{sun,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` +:math:`{d\vec{I}_{sun,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` and -:math:`{d\vec{I}_{sun,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{} (x) dL'}} \right.} dL'}` +:math:`{d\vec{I}_{sun,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{} (x) dL'}} \right.} dL'}` are the direct beam and diffuse solar radiation, respectively, absorbed by the sunlit fraction of the canopy (per unit plant area) at a depth defined by the cumulative plant area index :math:`x`; :math:`{d\vec{I}_{sha,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` \ and -:math:`{d\vec{I}_{sha,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{} (x) dL'}} \right.} dL'}` +:math:`{d\vec{I}_{sha,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{} (x) dL'}} \right.} dL'}` are the corresponding fluxes for the shaded fraction of the canopy at depth :math:`x`. These fluxes are normalized by the sunlit or shaded fraction at depth :math:`x`, defined by @@ -188,7 +188,7 @@ where :math:`\sigma` is the Stefan-Boltzmann constant (W\ m\ :sup:`-2` K\ :sup: where :math:`L_{vg} \, \uparrow` is the upward longwave radiation from the vegetation/soil system for exposed leaf and stem area :math:`L+S\ge 0.05`, :math:`\delta _{veg}` is a step function and is -zero for :math:`L+S<0.05` and one otherwise, :math:`\varepsilon _{g}` +zero for :math:`L+S<0.05` and one otherwise, :math:`\varepsilon _{g}` is the ground emissivity, and :math:`T_{g}^{n+1}` and :math:`T_{g}^{n}` are the snow/soil surface temperatures at the current and previous time steps, respectively (:ref:`rst_Soil and Snow Temperatures`). @@ -224,7 +224,7 @@ where where :math:`\varepsilon _{v}` is the vegetation emissivity and :math:`T_{v}^{n+1}` and :math:`T_{v}^{n}` are the vegetation temperatures at the current and previous time steps, respectively -(:ref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). +(:ref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). The first term in the equation above is the atmospheric longwave radiation that is transmitted through the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The @@ -266,7 +266,7 @@ atmosphere) The above expression for :math:`\vec{L}_{g}` is the net longwave radiation forcing that is used in the soil temperature calculation -(:ref:`rst_Soil and Snow Temperatures`). Once updated soil +(:ref:`rst_Soil and Snow Temperatures`). Once updated soil temperatures have been obtained, the term :math:`4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right)` is added to :math:`\vec{L}_{g}` to calculate the ground heat flux @@ -288,9 +288,9 @@ emissivity of the ground is \varepsilon _{g} =\varepsilon _{soi} \left(1-f_{sno} \right)+\varepsilon _{sno} f_{sno} -where :math:`\varepsilon _{soi} =0.96` for soil, 0.97 for glacier, -:math:`\varepsilon _{sno} =0.97`, and :math:`f_{sno}` -is the fraction of ground covered by snow +where :math:`\varepsilon _{soi} =0.96` for soil, 0.97 for glacier, +:math:`\varepsilon _{sno} =0.97`, and :math:`f_{sno}` +is the fraction of ground covered by snow (section :numref:`Snow Covered Area Fraction`). The vegetation emissivity is @@ -300,7 +300,7 @@ vegetation emissivity is \varepsilon _{v} =1-e^{-{\left(L+S\right)\mathord{\left/ {\vphantom {\left(L+S\right) \bar{\mu }}} \right.} \bar{\mu }} } where :math:`L` and :math:`S` are the leaf and stem area indices -(section :numref:`Phenology and vegetation burial by snow`) and +(section :numref:`Phenology and vegetation burial by snow`) and :math:`\bar{\mu }=1` is the average inverse optical depth for longwave radiation. diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 4497e93610..5fbe40ca1f 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -226,7 +226,7 @@ Botta, A et al., 2000. A global prognostic scheme of leaf onset using satellite .. _Brownetal1997: Brown J., Ferrians O. J. Jr, Heginbottom J. A. and Melnikov E. S. 1997. - Circum-Arctic Map of Permafrost and Ground-Ice Conditions + Circum-Arctic Map of Permafrost and Ground-Ice Conditions (Boulder, CO: National Snow and Ice Data Center) version 2, DOI: 10.3133/cp45 @@ -283,10 +283,10 @@ model. J. Geophys. Res. 101(D9):14,399-14,414. .. _Chengetal2019: -Cheng, Y. et al., 2019. Parameterizing perennial bioenergy -crops in Version 5 of the Community Land Model Based on Site‐Level -Observations in the Central Midwestern United States. -Journal of Advances in Modeling Earth Systems, +Cheng, Y. et al., 2019. Parameterizing perennial bioenergy +crops in Version 5 of the Community Land Model Based on Site‐Level +Observations in the Central Midwestern United States. +Journal of Advances in Modeling Earth Systems, 2(2013), 1–24. https://doi.org/10.1029/2019MS001719 .. _Chuangetal2006: @@ -1513,7 +1513,7 @@ National Center for Atmospheric Research, Boulder, CO, 420 pp. Oleson, K.W., and Feddema, J. 2018. Parameterization and surface data improvements and new capabilities for the Community Land Model -Urban (CLMU). JAMES, submitted. +Urban (CLMU). JAMES, submitted. .. _Olson1963: diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 25f9366870..2581b09f13 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -3,8 +3,8 @@ Snow Hydrology =============== -The parameterizations for snow are based primarily on -:ref:`Anderson (1976) `, :ref:`Jordan (1991) `, +The parameterizations for snow are based primarily on +:ref:`Anderson (1976) `, :ref:`Jordan (1991) `, and :ref:`Dai and Zeng (1997) `. The snowpack can have up to twelve layers. These layers are indexed in the Fortran code as :math:`i=-11,-10,...,-1,0` where layer :math:`i=0` is the snow layer @@ -12,8 +12,8 @@ next to the top soil layer and layer :math:`i=-11` is the top layer of a twelve-layer snow pack. Since the number of snow layers varies according to the snow depth, we use the notation :math:`snl+1` to describe the top layer of snow for the variable layer snow pack, where :math:`snl` is the -negative of the number of snow layers. Refer to :numref:`Figure three layer -snow pack` for an example of the snow layer structure for a three layer +negative of the number of snow layers. Refer to :numref:`Figure three layer +snow pack` for an example of the snow layer structure for a three layer snow pack. .. _Figure three layer snow pack: @@ -26,25 +26,25 @@ Shown are three snow layers, :math:`i=-2`, :math:`i=-1`, and :math:`i=0`. The layer node depth is :math:`z`, the layer interface is :math:`z_{h}` , and the layer thickness is :math:`\Delta z`. -The state variables for snow are the mass of water :math:`w_{liq,i}` -(kg m\ :sup:`-2`), mass of ice :math:`w_{ice,i}` (kg m\ :sup:`-2`), layer -thickness :math:`\Delta z_{i}` (m), and temperature :math:`T_{i}` +The state variables for snow are the mass of water :math:`w_{liq,i}` +(kg m\ :sup:`-2`), mass of ice :math:`w_{ice,i}` (kg m\ :sup:`-2`), layer +thickness :math:`\Delta z_{i}` (m), and temperature :math:`T_{i}` (Chapter :numref:`rst_Soil and Snow Temperatures`). The water vapor phase is neglected. Snow can also exist in the model without being represented by explicit snow layers. This occurs when the snowpack is less than a specified minimum snow depth (:math:`z_{sno} < 0.01` m). In this case, the state variable is the mass of snow :math:`W_{sno}` (kg m\ :sup:`-2`). -Section :numref:`Snow Covered Area Fraction` describes the calculation -of fractional snow covered area, which is used in the surface albedo -calculation (Chapter :numref:`rst_Surface Albedos`) and the surface flux -calculations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent -Heat Fluxes`). The following two sections (:numref:`Ice Content` and -:numref:`Water Content`) describe the ice and water content of the snow -pack assuming that at least one snow layer exists. Section :numref:`Black -and organic carbon and mineral dust within snow` describes how black and -organic carbon and mineral dust particles are represented within snow, -including meltwater flushing. See Section :numref:`Initialization of snow +Section :numref:`Snow Covered Area Fraction` describes the calculation +of fractional snow covered area, which is used in the surface albedo +calculation (Chapter :numref:`rst_Surface Albedos`) and the surface flux +calculations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent +Heat Fluxes`). The following two sections (:numref:`Ice Content` and +:numref:`Water Content`) describe the ice and water content of the snow +pack assuming that at least one snow layer exists. Section :numref:`Black +and organic carbon and mineral dust within snow` describes how black and +organic carbon and mineral dust particles are represented within snow, +including meltwater flushing. See Section :numref:`Initialization of snow layer` for a description of how a snow layer is initialized. .. _Snow Covered Area Fraction: @@ -53,7 +53,7 @@ Snow Covered Area Fraction ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The fraction of the ground covered by snow, :math:`f_{sno}` , is based -on the method of :ref:`Swenson and Lawrence (2012) `. +on the method of :ref:`Swenson and Lawrence (2012) `. Because the processes governing snowfall and snowmelt differ, changes in :math:`f_{sno}` are calculated separately for accumulation and depletion. When snowfall @@ -88,13 +88,13 @@ reset to zero. The depletion curve shape parameter is defined as N_{melt} =\frac{200}{\min \left(10,\sigma _{topo} \right)} -The standard deviation of the elevation within a grid cell, +The standard deviation of the elevation within a grid cell, :math:`\sigma _{topo}` , is calculated from a high resolution DEM (a -1km DEM is used for CLM). -Note that *glacier\_mec* columns (section :numref:`Multiple elevation class scheme`) +1km DEM is used for CLM). +Note that *glacier\_mec* columns (section :numref:`Multiple elevation class scheme`) are treated differently in this respect, as they already account for the -subgrid topography in a grid cell in their own way. -Therefore, in each *glacier\_mec* column very flat terrain is assumed, +subgrid topography in a grid cell in their own way. +Therefore, in each *glacier\_mec* column very flat terrain is assumed, implemented as :math:`N_{melt}=10`. .. _Ice Content: @@ -108,15 +108,15 @@ The conservation equation for mass of ice in snow layers is :label: 8.17 \frac{\partial w_{ice,\, i} }{\partial t} = - \left\{\begin{array}{lr} - f_{sno} \ q_{ice,\, i-1} -\frac{\left(\Delta w_{ice,\, i} \right)_{p} }{\Delta t} & \qquad i=snl+1 \\ - -\frac{\left(\Delta w_{ice,\, i} \right)_{p} }{\Delta t} & \qquad i=snl+2,\ldots ,0 + \left\{\begin{array}{lr} + f_{sno} \ q_{ice,\, i-1} -\frac{\left(\Delta w_{ice,\, i} \right)_{p} }{\Delta t} & \qquad i=snl+1 \\ + -\frac{\left(\Delta w_{ice,\, i} \right)_{p} }{\Delta t} & \qquad i=snl+2,\ldots ,0 \end{array}\right\} where :math:`q_{ice,\, i-1}` is the rate of ice accumulation from precipitation or frost or the rate of ice loss from sublimation (kg m\ :sup:`-2` s\ :sup:`-1`) in the top layer and -:math:`{\left(\Delta w_{ice,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{ice,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` +:math:`{\left(\Delta w_{ice,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{ice,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` is the change in ice due to phase change (melting rate) (section :numref:`Phase Change`). The term :math:`q_{ice,\, i-1}` is computed in two steps as @@ -146,7 +146,7 @@ where \Delta z_{sno} =\frac{q_{grnd,\, ice} \Delta t}{f_{sno} \rho _{sno} } and :math:`\rho _{sno}` is the bulk density of newly fallen snow (kg -m\ :sup:`-3`), which parameterized by a temperature-dependent and a +m\ :sup:`-3`), which parameterized by a temperature-dependent and a wind-dependent term: .. math:: @@ -159,20 +159,20 @@ The temperature dependent term is given by (:ref:`van Kampenhout et al. (2017) < .. math:: :label: 8.21b - \rho_{T} = - \left\{\begin{array}{lr} - 50 + 1.7 \left(17\right)^{1.5} & \qquad T_{atm} >T_{f} +2 \ \\ - 50+1.7 \left(T_{atm} -T_{f} + 15\right)^{1.5} & \qquad T_{f} - 15 < T_{atm} \le T_{f} + 2 \ \\ - -3.833 \ \left( T_{atm} -T_{f} \right) - 0.0333 \ \left( T_{atm} -T_{f} \right)^{2} - &\qquad T_{atm} \le T_{f} - 15 + \rho_{T} = + \left\{\begin{array}{lr} + 50 + 1.7 \left(17\right)^{1.5} & \qquad T_{atm} >T_{f} +2 \ \\ + 50+1.7 \left(T_{atm} -T_{f} + 15\right)^{1.5} & \qquad T_{f} - 15 < T_{atm} \le T_{f} + 2 \ \\ + -3.833 \ \left( T_{atm} -T_{f} \right) - 0.0333 \ \left( T_{atm} -T_{f} \right)^{2} + &\qquad T_{atm} \le T_{f} - 15 \end{array}\right\} .. bifall(c) = -(50._r8/15._r8 + 0.0333_r8*15_r8)*(forc_t(c)-tfrz) - 0.0333_r8*(forc_t(c)-tfrz)**2 -where :math:`T_{atm}` is the atmospheric temperature (K), and :math:`T_{f}` is -the freezing temperature of water (K) (:numref:`Table Physical Constants`). -When 10 m wind speed :math:`W_{atm}` is greater than 0.1 m\ :sup:`-1`, snow density -increases due to wind-driven compaction according to +where :math:`T_{atm}` is the atmospheric temperature (K), and :math:`T_{f}` is +the freezing temperature of water (K) (:numref:`Table Physical Constants`). +When 10 m wind speed :math:`W_{atm}` is greater than 0.1 m\ :sup:`-1`, snow density +increases due to wind-driven compaction according to :ref:`van Kampenhout et al. 2017 ` .. math:: @@ -205,8 +205,8 @@ The ice content of the top layer and the layer thickness are updated as \Delta z_{snl+1}^{n+1} =\Delta z_{snl+1}^{n} +\Delta z_{sno} . In the second step, after surface fluxes and snow/soil temperatures have -been determined (Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat -Fluxes` and :numref:`rst_Soil and Snow Temperatures`), +been determined (Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat +Fluxes` and :numref:`rst_Soil and Snow Temperatures`), :math:`w_{ice,\, snl+1}` is updated for frost or sublimation as .. math:: @@ -240,7 +240,7 @@ The conservation equation for mass of water in snow layers is where :math:`q_{liq,\, i-1}` is the flow of liquid water into layer :math:`i` from the layer above, :math:`q_{liq,\, i}` is the flow of water out of layer :math:`i` to the layer below, -:math:`{\left(\Delta w_{liq,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{liq,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` +:math:`{\left(\Delta w_{liq,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{liq,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` is the change in liquid water due to phase change (melting rate) (section :numref:`Phase Change`). For the top snow layer only, @@ -250,13 +250,13 @@ is the change in liquid water due to phase change (melting rate) q_{liq,\, i-1} =f_{sno} \left(q_{grnd,\, liq} +\left(q_{sdew} -q_{seva} \right)\right) where :math:`q_{grnd,\, liq}` is the rate of liquid precipitation -reaching the snow (section :numref:`Canopy Water`), :math:`q_{seva}` is the -evaporation of liquid water and :math:`q_{sdew}` is the liquid dew (section -:numref:`Update of Ground Sensible and Latent Heat Fluxes`). After surface -fluxes and snow/soil temperatures have been determined -(Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes` and -:numref:`rst_Soil and Snow Temperatures`), :math:`w_{liq,\, snl+1}` is -updated for the liquid precipitation reaching the ground and dew or +reaching the snow (section :numref:`Canopy Water`), :math:`q_{seva}` is the +evaporation of liquid water and :math:`q_{sdew}` is the liquid dew (section +:numref:`Update of Ground Sensible and Latent Heat Fluxes`). After surface +fluxes and snow/soil temperatures have been determined +(Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes` and +:numref:`rst_Soil and Snow Temperatures`), :math:`w_{liq,\, snl+1}` is +updated for the liquid precipitation reaching the ground and dew or evaporation as .. math:: @@ -295,7 +295,7 @@ where the volumetric liquid water :math:`\theta _{liq,\, i}` and ice and :math:`S_{r} =0.033` is the irreducible water saturation (snow holds a certain amount of liquid water due to capillary retention after drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the -underlying layer limits the flow of water :math:`q_{liq,\, i}` +underlying layer limits the flow of water :math:`q_{liq,\, i}` calculated in equation , unless the underlying layer is the surface soil layer, as @@ -313,7 +313,7 @@ The liquid water content :math:`w_{liq,\, i}` is updated as Equations - are solved sequentially from top (:math:`i=snl+1`) to bottom (:math:`i=0`) snow layer in each time step. The total flow of -liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` +liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` which is used in the calculation of surface runoff and infiltration (sections :numref:`Surface Runoff` and :numref:`Infiltration`). @@ -324,16 +324,16 @@ Black and organic carbon and mineral dust within snow Particles within snow originate from atmospheric aerosol deposition (:math:`D_{sp}` in Table 2.3 (kg m\ :sup:`-2` s\ :sup:`-1`) -and influence snow radiative transfer (sections :numref:`Snow Albedo`, -:numref:`Snowpack Optical Properties`, and :numref:`Snow Aging`). +and influence snow radiative transfer (sections :numref:`Snow Albedo`, +:numref:`Snowpack Optical Properties`, and :numref:`Snow Aging`). Particle masses and mixing ratios are represented with a simple mass-conserving scheme. The model maintains masses of the following eight particle species within each snow layer: hydrophilic black carbon, hydrophobic black carbon, hydrophilic organic carbon, hydrophobic organic carbon, and four species of mineral dust with the following particle sizes: 0.1-1.0, 1.0-2.5, 2.5-5.0, and 5.0-10.0 :math:`\mu m`. -Each of these species has unique optical properties -(:numref:`Table Single-scatter albedo values used for snowpack impurities and ice`) +Each of these species has unique optical properties +(:numref:`Table Single-scatter albedo values used for snowpack impurities and ice`) and meltwater removal efficiencies (:numref:`Table Meltwater scavenging`). The black carbon and organic carbon deposition rates described in Table @@ -362,12 +362,12 @@ The black carbon and organic carbon deposition rates described in Table Deposited particles are assumed to be instantly mixed (homogeneously) within the surface snow layer and are added after the inter-layer water fluxes are computed (section :numref:`Water Content`) so that some aerosol is in the top -layer after deposition and is not immediately washed out before radiative -calculations are done. Particle masses are then redistributed each time -step based on meltwater drainage through the snow column (section -:numref:`Water Content`) and snow layer combination and subdivision -(section :numref:`Snow Layer Combination and Subdivision`). The change in -mass of each of the particle species :math:`\Delta m_{sp,\, i}` +layer after deposition and is not immediately washed out before radiative +calculations are done. Particle masses are then redistributed each time +step based on meltwater drainage through the snow column (section +:numref:`Water Content`) and snow layer combination and subdivision +(section :numref:`Snow Layer Combination and Subdivision`). The change in +mass of each of the particle species :math:`\Delta m_{sp,\, i}` (kg m\ :sup:`-2`) is .. math:: @@ -402,7 +402,7 @@ model. .. _Table Meltwater scavenging: .. table:: Meltwater scavenging efficiency for particles within snow - + +------------------------------------------+-------------------+ | Species | :math:`k_{sp}` | +==========================================+===================+ @@ -436,13 +436,13 @@ follows .. math:: :label: 8.40 - \begin{array}{lcr} - \Delta z_{0} & = & z_{sno} \\ - z_{o} & = & -0.5\Delta z_{0} \\ - z_{h,\, -1} & = & -\Delta z_{0} \\ - T_{0} & = & \min \left(T_{f} ,T_{atm} \right) \\ - w_{ice,\, 0} & = & W_{sno} \\ - w_{liq,\, 0} & = & 0 + \begin{array}{lcr} + \Delta z_{0} & = & z_{sno} \\ + z_{o} & = & -0.5\Delta z_{0} \\ + z_{h,\, -1} & = & -\Delta z_{0} \\ + T_{0} & = & \min \left(T_{f} ,T_{atm} \right) \\ + w_{ice,\, 0} & = & W_{sno} \\ + w_{liq,\, 0} & = & 0 \end{array}. .. _Snow Compaction: @@ -451,15 +451,15 @@ Snow Compaction ^^^^^^^^^^^^^^^^^^^^^ Snow compaction is initiated after the soil hydrology calculations -[surface runoff (section :numref:`Surface Runoff`), infiltration (section +[surface runoff (section :numref:`Surface Runoff`), infiltration (section :numref:`Infiltration`), soil water (section :numref:`Soil Water`)] are complete. Currently, there are four processes included that lead to snow -compaction: +compaction: #. destructive metamorphism of new snow (crystal breakdown due to wind or thermodynamic stress) #. snow load or compaction by overburden pressure #. melting (changes in snow structure due to melt-freeze cycles plus changes in crystals due to liquid water) - #. drifting snow compaction. + #. drifting snow compaction. The total fractional compaction rate for each snow layer :math:`C_{R,\, i}` (s\ :sup:`-1`) is the sum of multiple compaction processes @@ -505,19 +505,19 @@ where :math:`c_{3} =2.777\times 10^{-6}` (s\ :sup:`-1`) is the fractional compa .. math:: :label: 8.44 - \begin{array}{lr} + \begin{array}{lr} c_{1} = 1 & \qquad \frac{w_{ice,\, i} }{f_{sno} \Delta z_{i} } \le 175{\rm \; kg\; m}^{{\rm -3}} \\ c_{1} = \exp \left[-0.046\left(\frac{w_{ice,\, i} }{f_{sno} \Delta z_{i} } -175\right)\right] & \qquad \frac{w_{ice,\, i} }{f_{sno} \Delta z_{i} } >175{\rm \; kg\; m}^{{\rm -3}} \\ - c_{2} = 2 & \qquad \frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} } >0.01 \\ - c_{2} = 1 & \qquad \frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} } \le 0.01 + c_{2} = 2 & \qquad \frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} } >0.01 \\ + c_{2} = 1 & \qquad \frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} } \le 0.01 \end{array} .. upper limit (upplim_destruct_metamorph) used to be 100 but was changed to 175 for CLM5 (Van Kampenhout et al., 2017) where -:math:`{w_{ice,\, i} \mathord{\left/ {\vphantom {w_{ice,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` +:math:`{w_{ice,\, i} \mathord{\left/ {\vphantom {w_{ice,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` and -:math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` +:math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` are the bulk densities of liquid water and ice (kg m\ :sup:`-3`). @@ -544,7 +544,7 @@ water contents of the layer being compacted P_{s,\, i} =\frac{w_{ice,\, i} +w_{liq,\, i} }{2} +\sum _{j=snl+1}^{j=i-1}\left(w_{ice,\, j} +w_{liq,\, j} \right) . -Variable :math:`\eta` in :eq:`8.45` is a viscosity coefficient (kg s m\ :sup:`-2`) that varies with density and +Variable :math:`\eta` in :eq:`8.45` is a viscosity coefficient (kg s m\ :sup:`-2`) that varies with density and temperature as .. math:: @@ -552,18 +552,18 @@ temperature as \eta = f_{1} f_{2} \eta_{0} \frac{\rho_{i}}{c_{\eta}} \exp \left[ a_{\eta} \left(T_{f} -T_{i} \right) + b_{\eta} \rho_{i} \right] -with constant factors :math:`\eta _{0} = 7.62237 \times 10^{6}` kg s\ :sup:`-1` m\ :sup:`-2`, -:math:`a_{\eta} = 0.1` K\ :sup:`-1`, :math:`b_{\eta} = 0.023` m\ :sup:`-3` kg\ :sup:`-1`, +with constant factors :math:`\eta _{0} = 7.62237 \times 10^{6}` kg s\ :sup:`-1` m\ :sup:`-2`, +:math:`a_{\eta} = 0.1` K\ :sup:`-1`, :math:`b_{\eta} = 0.023` m\ :sup:`-3` kg\ :sup:`-1`, and :math:`c_{\eta} = 450` kg m\ :sup:`-3` (:ref:`van Kampenhout et al. (2017) `). Further, factor :math:`f_1` accounts for the presence of liquid water (:ref:`Vionnet et al. (2012) `): -.. math:: +.. math:: :label: 8.46b f_{1} = \frac{1}{1+ 60 \frac{w_{\mathrm{liq},\, i}}{\rho_{\mathrm{liq}} \Delta z_{i} }}. -Factor :math:`f_2` originally accounts for the presence of angular grains, but since grain shape is not modelled -:math:`f_2` is fixed to the value 4. +Factor :math:`f_2` originally accounts for the presence of angular grains, but since grain shape is not modelled +:math:`f_2` is fixed to the value 4. .. _Compaction by melt: @@ -582,10 +582,10 @@ and melting is identified during the phase change calculations (section :numref:`Phase Change`). Because snow depth is defined as the average depth of the snow covered area, the snow depth must also be updated for changes in :math:`f_{sno}` when :math:`W_{sno}` has changed. - + .. math:: :label: 8.49 - + C_{R4,\, i} =\left[\frac{1}{\Delta z_{i} } \frac{\partial \Delta z_{i} }{\partial t} \right]_{fsno} =-\frac{1}{\Delta t} \max \left(0,\frac{f_{sno,\, i}^{n} -f_{sno,\, i}^{n+1} }{f_{sno,\, i}^{n} } \right) .. _Compaction by drifting snow: @@ -593,8 +593,8 @@ changes in :math:`f_{sno}` when :math:`W_{sno}` has changed. Compaction by drifting snow ''''''''''''''''''''''''''' Crystal breaking by drifting snow leads to higher snow densities at the surface. -This process is particularly important on ice sheets, where destructive metamorphism is slow due to low temperatures -but high wind speeds (katabatic winds) are prevailing. +This process is particularly important on ice sheets, where destructive metamorphism is slow due to low temperatures +but high wind speeds (katabatic winds) are prevailing. Therefore a drifting snow compaction parametrization was introduced, based on (:ref:`Vionnet et al. (2012) `). .. math:: @@ -602,15 +602,15 @@ Therefore a drifting snow compaction parametrization was introduced, based on (: C_{R5,\, i} = \left[\frac{1}{\Delta z_{i} } \frac{\partial \Delta z_{i} }{\partial t} \right]_{drift} = - \frac{\rho_{\max} - \rho_i}{\tau_{i}}. -Here, :math:`\rho_{\max} = 350` kg m\ :sup:`-3` is the upper limit to which this process is active, and -:math:`\tau_{i}` is a timescale which is depth dependent: +Here, :math:`\rho_{\max} = 350` kg m\ :sup:`-3` is the upper limit to which this process is active, and +:math:`\tau_{i}` is a timescale which is depth dependent: .. math:: :label: 8.50b \tau_i = \frac{\tau}{\Gamma_{\mathrm{drift}}^i} \quad \mathrm{,} \:\; \Gamma^i_\mathrm{drift} = \max\left[ 0, S_\mathrm{I}^i \exp(-z_i / 0.1) \right]. -Here, :math:`\tau` is a characteristic time scale for drifting snow compaction and is empirically set to 48 h, and +Here, :math:`\tau` is a characteristic time scale for drifting snow compaction and is empirically set to 48 h, and :math:`z_i` is a pseudo-depth which takes into account previous hardening of snow layers above the current layer: :math:`z_i = \sum_j \Delta z_j \cdot (3.25 - S_\mathrm{I}^j)`. The driftability index :math:`S_\mathrm{I}` reflects how well snow can be drifted and depends on the mobility of the snow @@ -624,8 +624,8 @@ as well as the 10 m wind speed: M_\mathrm{O} & = & -0.069 + 0.66 F(\rho) \end{array} -The latter equation (for the mobility index :math:`M_\mathrm{O}`) is a simplification from the original paper -by removing the dependency on grain size and assuming spherical grains +The latter equation (for the mobility index :math:`M_\mathrm{O}`) is a simplification from the original paper +by removing the dependency on grain size and assuming spherical grains (see :ref:`van Kampenhout et al. (2017) `). .. _Snow Layer Combination and Subdivision: @@ -633,9 +633,9 @@ by removing the dependency on grain size and assuming spherical grains Snow Layer Combination and Subdivision ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -After the determination of snow temperature including phase change(Chapter -:numref:`rst_Soil and Snow Temperatures`), snow hydrology (Chapter -:numref:`rst_Snow Hydrology`), and the compaction calculations (section +After the determination of snow temperature including phase change(Chapter +:numref:`rst_Soil and Snow Temperatures`), snow hydrology (Chapter +:numref:`rst_Snow Hydrology`), and the compaction calculations (section :numref:`Snow Compaction`) , the number of snow layers is adjusted by either combining or subdividing layers. The combination and subdivision of snow layers is based on :ref:`Jordan (1991) `. @@ -744,11 +744,11 @@ where :math:`h_{c} =h_{1} +h_{2}` is the combined enthalpy h_{i} =\left(C_{ice} w_{ice,\, i} +C_{liq} w_{liq,\, i} \right)\left(T_{i} -T_{f} \right)+L_{f} w_{liq,\, i} . -In these equations, :math:`L_{f}` is the latent heat of fusion (J kg\ -:sup:`-1`) and :math:`C_{liq}` and :math:`C_{ice}` are the specific -heat capacities (J kg\ :sup:`-1` K\ :sup:`-1`) of liquid water and ice, +In these equations, :math:`L_{f}` is the latent heat of fusion (J kg\ +:sup:`-1`) and :math:`C_{liq}` and :math:`C_{ice}` are the specific +heat capacities (J kg\ :sup:`-1` K\ :sup:`-1`) of liquid water and ice, respectively (:numref:`Table Physical Constants`). After layer combination, -the node depths and layer interfaces (:numref:`Figure three layer snow pack`) +the node depths and layer interfaces (:numref:`Figure three layer snow pack`) are recalculated from .. math:: @@ -806,7 +806,7 @@ Subdivision The snow layers are subdivided when the layer thickness exceeds the prescribed maximum thickness :math:`\Delta z_{\max }` with lower and -upper bounds that depend on the number of snow layers (:numref:`Table snow layer thickness`). +upper bounds that depend on the number of snow layers (:numref:`Table snow layer thickness`). For example, if there is only one layer, then the maximum thickness of that layer is 0.03 m, however, if there is more than one layer, then the maximum thickness of the top layer is 0.02 m. Layers are checked @@ -837,9 +837,9 @@ then adjusted as, .. math:: :label: 8.63 - \begin{array}{lr} - T_{3}^{n+1} = T_{2}^{n} & \qquad T'_{3} \ge T_{f} \\ - T_{2}^{n+1} = T_{2}^{n} +\left(\frac{T_{1}^{n} -T_{2}^{n} }{{\left(\Delta z_{1} +\Delta z_{2}^{n} \right)\mathord{\left/ {\vphantom {\left(\Delta z_{1} +\Delta z_{2}^{n} \right) 2}} \right.} 2} } \right)\left(\frac{\Delta z_{2}^{n+1} }{2} \right) & \qquad T'_{3} T_{f} {\rm \; and\; }w_{ice,\, i} >0 & \qquad i=snl+1,\ldots ,N_{levgrnd} \qquad {\rm melting} \end{array} .. math:: :label: 6.53b - \begin{array}{lr} - \begin{array}{lr} - T_{i}^{n+1} 0 & \qquad i=snl+1,\ldots ,0 \\ + \begin{array}{lr} + \begin{array}{lr} + T_{i}^{n+1} 0 & \qquad i=snl+1,\ldots ,0 \\ T_{i}^{n+1} w_{liq,\, \max ,\, i} & \quad i=1,\ldots ,N_{levgrnd} - \end{array} & \quad {\rm freezing} + \end{array} & \quad {\rm freezing} \end{array} where :math:`T_{i}^{n+1}` is the soil layer temperature after solution of the tridiagonal equation set, :math:`w_{ice,\, i}` and :math:`w_{liq,\, i}` are the mass of ice and liquid water (kg -m\ :sup:`-2`) in each snow/soil layer, respectively, and :math:`T_{f}` -is the freezing temperature of water (K) (:numref:`Table Physical Constants`). -For the freezing process in soil layers, the concept of supercooled soil -water from :ref:`Niu and Yang (2006)` is adopted. The supercooled +m\ :sup:`-2`) in each snow/soil layer, respectively, and :math:`T_{f}` +is the freezing temperature of water (K) (:numref:`Table Physical Constants`). +For the freezing process in soil layers, the concept of supercooled soil +water from :ref:`Niu and Yang (2006)` is adopted. The supercooled soil water is the liquid water that coexists with ice over a wide range of temperatures below freezing and is implemented through a freezing point depression equation @@ -588,7 +588,7 @@ layer :math:`i` (kg m\ :sup:`-2`) when the soil temperature (:numref:`Table Physical Constants`), :math:`g` is the gravitational acceleration (m s\ :sup:`-2`) (:numref:`Table Physical Constants`), and :math:`\psi _{sat,\, i}` and :math:`B_{i}` are the soil texture-dependent saturated matric potential -(mm) and :ref:`Clapp and Hornberger (1978)` exponent +(mm) and :ref:`Clapp and Hornberger (1978)` exponent (section :numref:`Soil Water`). For the special case when snow is present (snow mass :math:`W_{sno} >0`) @@ -606,10 +606,10 @@ determined as follows .. math:: :label: 6.55 - H_{i} =\left\{\begin{array}{lr} - \frac{\partial h}{\partial T} \left(T_{f} -T_{i}^{n} \right)-\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right) & \quad \quad i=snl+1 \\ - \left(1-f_{sno} -f_{h2osfc} \right)\frac{\partial h}{\partial T} \left(T_{f} -T_{i}^{n} \right)-\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right)\quad {\kern 1pt} {\kern 1pt} {\kern 1pt} {\kern 1pt} & i=1 \\ - -\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right) & \quad \quad i\ne \left\{1,snl+1\right\} + H_{i} =\left\{\begin{array}{lr} + \frac{\partial h}{\partial T} \left(T_{f} -T_{i}^{n} \right)-\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right) & \quad \quad i=snl+1 \\ + \left(1-f_{sno} -f_{h2osfc} \right)\frac{\partial h}{\partial T} \left(T_{f} -T_{i}^{n} \right)-\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right)\quad {\kern 1pt} {\kern 1pt} {\kern 1pt} {\kern 1pt} & i=1 \\ + -\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right) & \quad \quad i\ne \left\{1,snl+1\right\} \end{array}\right\}. If the melting criteria is met :eq:`6.53a` and @@ -634,10 +634,10 @@ and for :math:`i=1,\ldots ,N_{levgrnd}` as .. math:: :label: 6.58 - w_{ice,\, i}^{n+1} = - \left\{\begin{array}{lr} - \min \left(w_{liq,\, i}^{n} +w_{ice,\, i}^{n} -w_{liq,\, \max ,\, i}^{n} ,\, w_{ice,\, i}^{n} -H_{m} \right) & \qquad w_{liq,\, i}^{n} +w_{ice,\, i}^{n} \ge w_{liq,\, \max ,\, i}^{n} {\rm \; } \\ - {\rm 0} & \qquad w_{liq,\, i}^{n} +w_{ice,\, i}^{n} 0` then :math:`H_{m}` +:math:`H_{m} =\frac{H_{h2osfc} \Delta t}{L_{f} } >0` then :math:`H_{m}` is removed from surface water and added to the snow column as ice .. math:: @@ -802,9 +802,9 @@ cool the snow layer. Soil and Snow Thermal Properties ------------------------------------ -The thermal properties of the soil are assumed to be a weighted combination of -the mineral and organic properties of the soil -(:ref:`Lawrence and Slater 2008 `). +The thermal properties of the soil are assumed to be a weighted combination of +the mineral and organic properties of the soil +(:ref:`Lawrence and Slater 2008 `). The soil layer organic matter fraction :math:`f_{om,i}` is .. math:: @@ -812,20 +812,20 @@ The soil layer organic matter fraction :math:`f_{om,i}` is f_{om,i} =\rho _{om,i} /\rho _{om,\max } . -Soil thermal conductivity :math:`\lambda _{i}` (W m\ :sup:`-1` K\ :sup:`-1`) +Soil thermal conductivity :math:`\lambda _{i}` (W m\ :sup:`-1` K\ :sup:`-1`) is from :ref:`Farouki (1981) ` .. math:: :label: 6.78 - \begin{array}{lr} + \begin{array}{lr} \lambda _{i} = \left\{ - \begin{array}{lr} - K_{e,\, i} \lambda _{sat,\, i} +\left(1-K_{e,\, i} \right)\lambda _{dry,\, i} &\qquad S_{r,\, i} > 1\times 10^{-7} \\ - \lambda _{dry,\, i} &\qquad S_{r,\, i} \le 1\times 10^{-7} - \end{array}\right\} &\qquad i=1,\ldots ,N_{levsoi} \\ + \begin{array}{lr} + K_{e,\, i} \lambda _{sat,\, i} +\left(1-K_{e,\, i} \right)\lambda _{dry,\, i} &\qquad S_{r,\, i} > 1\times 10^{-7} \\ + \lambda _{dry,\, i} &\qquad S_{r,\, i} \le 1\times 10^{-7} + \end{array}\right\} &\qquad i=1,\ldots ,N_{levsoi} \\ - \lambda _{i} =\lambda _{bedrock} &\qquad i=N_{levsoi} +1,\ldots N_{levgrnd} + \lambda _{i} =\lambda _{bedrock} &\qquad i=N_{levsoi} +1,\ldots N_{levgrnd} \end{array} where :math:`\lambda _{sat,\, i}` is the saturated thermal @@ -834,7 +834,7 @@ conductivity, :math:`K_{e,\, i}` is the Kersten number, :math:`S_{r,\, i}` is the wetness of the soil with respect to saturation, and :math:`\lambda _{bedrock} =3` W m\ :sup:`-1` K\ :sup:`-1` is the thermal conductivity assumed for the deep -ground layers (typical of saturated granitic rock; +ground layers (typical of saturated granitic rock; :ref:`Clauser and Huenges 1995 `). For glaciers, .. math:: @@ -900,9 +900,9 @@ the degree of saturation :math:`S_{r}` and phase of water :label: 6.85 K_{e,\, i} = \left\{ - \begin{array}{lr} - \log \left(S_{r,\, i} \right)+1\ge 0 &\qquad T_{i} \ge T_{f} \\ - S_{r,\, i} &\qquad T_{i} ` \lambda _{i} =\lambda _{air} +\left(7.75\times 10^{-5} \rho _{sno,\, i} +1.105\times 10^{-6} \rho _{sno,\, i}^{2} \right)\left(\lambda _{ice} -\lambda _{air} \right) -where :math:`\lambda _{air}` is the thermal conductivity of air (:numref:`Table Physical Constants`) +where :math:`\lambda _{air}` is the thermal conductivity of air (:numref:`Table Physical Constants`) and :math:`\rho _{sno,\, i}` is the bulk density of snow (kg m\ :sup:`-3`) .. math:: @@ -928,7 +928,7 @@ and :math:`\rho _{sno,\, i}` is the bulk density of snow (kg m\ :sup:`-3`) \rho _{sno,\, i} =\frac{w_{ice,\, i} +w_{liq,\, i} }{\Delta z_{i} } . -The volumetric heat capacity :math:`c_{i}` (J m\ :sup:`-3` K\ :sup:`-1`) for +The volumetric heat capacity :math:`c_{i}` (J m\ :sup:`-3` K\ :sup:`-1`) for soil is from :ref:`de Vries (1963) ` and depends on the heat capacities of the soil solid, liquid water, and ice constituents @@ -953,9 +953,9 @@ where the heat capacity of mineral soil solids .. math:: :label: 6.91 - \begin{array}{lr} - c_{s,\min ,\, i} =\left(\frac{2.128{\rm \; }\left(\% sand\right)_{i} +{\rm 2.385\; }\left(\% clay\right)_{i} }{\left(\% sand\right)_{i} +\left(\% clay\right)_{i} } \right)\times 10^{6} &\qquad i=1,\ldots ,N_{levsoi} \\ - c_{s,\, \min ,i} =c_{s,\, bedrock} &\qquad i=N_{levsoi} +1,\ldots ,N_{levgrnd} + \begin{array}{lr} + c_{s,\min ,\, i} =\left(\frac{2.128{\rm \; }\left(\% sand\right)_{i} +{\rm 2.385\; }\left(\% clay\right)_{i} }{\left(\% sand\right)_{i} +\left(\% clay\right)_{i} } \right)\times 10^{6} &\qquad i=1,\ldots ,N_{levsoi} \\ + c_{s,\, \min ,i} =c_{s,\, bedrock} &\qquad i=N_{levsoi} +1,\ldots ,N_{levgrnd} \end{array} where :math:`c_{s,bedrock} =2\times 10^{6}` J m\ :sup:`-3` @@ -986,9 +986,9 @@ where :math:`c_{1}^{*}` is calculated from :eq:`6.89` or :eq:`6.92`. Excess Ground Ice ------------------------------------ -An optional parameterization of excess ground ice melt and respective subsidence based on (:ref:`Lee et al., (2014) `). -Initial excess ground ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). -When the excess ground ice is present in the soil column, soil depth for a given layer (:math:`z_{i}`) +An optional parameterization of excess ground ice melt and respective subsidence based on (:ref:`Lee et al., (2014) `). +Initial excess ground ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). +When the excess ground ice is present in the soil column, soil depth for a given layer (:math:`z_{i}`) is adjusted by the amount of excess ice in the column: .. math:: @@ -996,7 +996,7 @@ is adjusted by the amount of excess ice in the column: z_{i}^{'}=\Sigma_{j=1}^{i} \ z_{j}^{'}+\frac{w_{exice,\, j}}{\rho_{ice} } -where :math:`w_{exice,\,j}` is excess ground ice amount (kg m :sup:`-2`) in layer :math:`j` +where :math:`w_{exice,\,j}` is excess ground ice amount (kg m :sup:`-2`) in layer :math:`j` and :math:`\rho_{ice}` is the density of ice (kg m :sup:`-3`). After adjustment of layer depths have been made, all of the soil temperature equations (from :eq:`6.80` to :eq:`6.89`) are calculted based on the adjusted depths. Thermal properties are additionally adjusted (:eq:`6.8` and :eq:`6.8`) in the following way: @@ -1017,12 +1017,12 @@ Soil subsidence at the timestep :math:`n+1` (:math:`z_{exice}^{n+1}`, m) is then z_{exice}^{n+1}=\Sigma_{i=1}^{N_{levgrnd}} \ z_{j}^{',\ ,n+1}-z_{j}^{',\ ,n } -With regards to hydraulic counductivity, excess ground ice is treated the same way normal soil -ice is treated in :numref:`Frozen Soils and Perched Water Table`. -When a soil layer thaws, excess ground ice is only allowed -to melt when no normals soil ice is present in the layer. -When a soil layer refreezes, liquid soil water can only turn into normal soil ice, thus, no new of excess ice can be created but only melted. -The excess liquid soil moisture from excess ice melt is distributed within the soil column according +With regards to hydraulic counductivity, excess ground ice is treated the same way normal soil +ice is treated in :numref:`Frozen Soils and Perched Water Table`. +When a soil layer thaws, excess ground ice is only allowed +to melt when no normals soil ice is present in the layer. +When a soil layer refreezes, liquid soil water can only turn into normal soil ice, thus, no new of excess ice can be created but only melted. +The excess liquid soil moisture from excess ice melt is distributed within the soil column according to :numref:`Lateral Sub-surface Runoff`. diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index 8f7c54bb40..c59faa7657 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -9,7 +9,7 @@ Canopy Radiative Transfer ----------------------------- Radiative transfer within vegetative canopies is calculated from the -two-stream approximation of :ref:`Dickinson (1983) ` and +two-stream approximation of :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) ` as described by :ref:`Bonan (1996) ` .. math:: @@ -24,7 +24,7 @@ two-stream approximation of :ref:`Dickinson (1983) ` and where :math:`I\, \uparrow` and :math:`I\, \downarrow` are the upward and downward diffuse radiative fluxes per unit incident flux, -:math:`K={G\left(\mu \right)\mathord{\left/ {\vphantom {G\left(\mu \right) \mu }} \right.} \mu }` +:math:`K={G\left(\mu \right)\mathord{\left/ {\vphantom {G\left(\mu \right) \mu }} \right.} \mu }` is the optical depth of direct beam per unit leaf and stem area, :math:`\mu` is the cosine of the zenith angle of the incident beam, :math:`G\left(\mu \right)` is the relative projected area of leaf and @@ -33,8 +33,8 @@ stem elements in the direction :math:`\cos ^{-1} \mu` , leaf and stem area, :math:`\omega` is a scattering coefficient, :math:`\beta` and :math:`\beta _{0}` are upscatter parameters for diffuse and direct beam radiation, respectively, :math:`L` is the -exposed leaf area index , and :math:`S` is the exposed stem area index -(section :numref:`Phenology and vegetation burial by snow`). Given the +exposed leaf area index , and :math:`S` is the exposed stem area index +(section :numref:`Phenology and vegetation burial by snow`). Given the direct beam albedo :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse albedo :math:`\alpha _{g,\, \Lambda }` of the ground (section :numref:`Ground Albedos`), these equations are solved to calculate the fluxes, per unit incident flux, @@ -55,7 +55,7 @@ The relative projected area of leaves and stems in the direction G\left(\mu \right)=\phi _{1} +\phi _{2} \mu -where :math:`\phi _{1} ={\rm 0.5}-0.633\chi _{L} -0.33\chi _{L}^{2}` +where :math:`\phi _{1} ={\rm 0.5}-0.633\chi _{L} -0.33\chi _{L}^{2}` and :math:`\phi _{2} =0.877\left(1-2\phi _{1} \right)` for :math:`-0.4\le \chi _{L} \le 0.6`. :math:`\chi _{L}` is the departure of leaf angles from a random distribution and equals +1 for horizontal @@ -70,16 +70,16 @@ The average inverse diffuse optical depth per unit leaf and stem area is where :math:`\mu '` is the direction of the scattered flux. -The optical parameters :math:`\omega`, :math:`\beta`, and :math:`\beta _{0}`, -which vary with wavelength (:math:`\Lambda` ), are weighted combinations of values -for vegetation and snow, using the canopy snow-covered fraction :math:`f_{can,\, sno}` +The optical parameters :math:`\omega`, :math:`\beta`, and :math:`\beta _{0}`, +which vary with wavelength (:math:`\Lambda` ), are weighted combinations of values +for vegetation and snow, using the canopy snow-covered fraction :math:`f_{can,\, sno}` (Chapter :numref:`rst_Hydrology`). The optical parameters are .. - The model determines that snow is on the canopy if - :math:`T_{v} \le T_{f}` , where :math:`T_{v}` is the vegetation temperature (K) (Chapter - :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and :math:`T_{f}` is the + The model determines that snow is on the canopy if + :math:`T_{v} \le T_{f}` , where :math:`T_{v}` is the vegetation temperature (K) (Chapter + :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical Constants`). In this case, the optical parameters are .. math:: @@ -128,7 +128,7 @@ stem reflectances \alpha _{\Lambda } =\alpha _{\Lambda }^{leaf} w_{leaf} +\alpha _{\Lambda }^{stem} w_{stem} where -:math:`w_{leaf} ={L\mathord{\left/ {\vphantom {L \left(L+S\right)}} \right.} \left(L+S\right)}` +:math:`w_{leaf} ={L\mathord{\left/ {\vphantom {L \left(L+S\right)}} \right.} \left(L+S\right)}` and :math:`w_{stem} ={S\mathord{\left/ {\vphantom {S \left(L+S\right)}} \right.} \left(L+S\right)}` . :math:`\tau _{\Lambda }` is a weighted combination of the leaf and stem transmittances (:math:`\tau _{\Lambda }^{leaf}, \tau _{\Lambda }^{stem}`) @@ -164,7 +164,7 @@ and for horizontal leaves (:math:`\chi _{L} =1`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` +:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }` . This discrepancy arises from the fact that a spherical leaf angle @@ -186,7 +186,7 @@ where the single scattering albedo is \begin{array}{rcl} {a_{s} \left(\mu \right)_{\Lambda } } & {=} & {\frac{\omega _{\Lambda }^{veg} }{2} \int _{0}^{1}\frac{\mu 'G\left(\mu \right)}{\mu G\left(\mu '\right)+\mu 'G\left(\mu \right)} d\mu '} \\ {} & {=} & {\frac{\omega _{\Lambda }^{veg} }{2} \frac{G\left(\mu \right)}{\max (\mu \phi _{2} +G\left(\mu \right),1e-6)} \left[1-\frac{\mu \phi _{1} }{\max (\mu \phi _{2} +G\left(\mu \right),1e-6)} \ln \left(\frac{\mu \phi _{1} +\max (\mu \phi _{2} +G\left(\mu \right),1e-6)}{\mu \phi _{1} } \right)\right].} \end{array} Note here the restriction on :math:`\mu \phi _{2} +G\left(\mu \right)`. We have seen cases where small values -can cause unrealistic single scattering albedo associated with the log calculation, +can cause unrealistic single scattering albedo associated with the log calculation, thereby eventually causing a negative soil albedo. The upward diffuse fluxes per unit incident direct beam and diffuse flux @@ -424,7 +424,7 @@ The parameters :math:`h_{1}` –:math:`h_{10}` , :math:`\sigma` , h_{10} =\frac{-s_{1} \left(u_{2} -\bar{\mu }h\right)}{d_{2} } . -Plant functional type optical properties (:numref:`Table Plant functional type optical properties`) +Plant functional type optical properties (:numref:`Table Plant functional type optical properties`) for trees and shrubs are from :ref:`Dorman and Sellers (1989) `. Leaf and stem optical properties (VIS and NIR reflectance and transmittance) were derived for grasslands and crops from full optical range spectra of measured @@ -509,7 +509,7 @@ intercepted snow (:numref:`Table Intercepted snow optical properties`) are from Ground Albedos ------------------ -The overall direct beam :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse +The overall direct beam :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse :math:`\alpha _{g,\, \Lambda }` ground albedos are weighted combinations of "soil" and snow albedos @@ -523,7 +523,7 @@ combinations of "soil" and snow albedos \alpha _{g,\, \Lambda } =\alpha _{soi,\, \Lambda } \left(1-f_{sno} \right)+\alpha _{sno,\, \Lambda } f_{sno} -where :math:`f_{sno}` is the fraction of the ground covered with snow +where :math:`f_{sno}` is the fraction of the ground covered with snow (section :numref:`Snow Covered Area Fraction`). :math:`\alpha _{soi,\, \Lambda }^{\mu }` and @@ -535,7 +535,7 @@ soil surfaces. Glacier albedos are from :ref:`Paterson (1994) ` .. math:: \alpha _{soi,\, nir}^{\mu } =\alpha _{soi,\, nir} =0.4. Unfrozen lake albedos depend on the cosine of the solar -zenith angle :math:`\mu` +zenith angle :math:`\mu` .. math:: :label: 3.60 @@ -564,11 +564,11 @@ soil color classes (:numref:`Table Dry and saturated soil albedos`). CLM soil colors are prescribed so that they best reproduce observed MODIS local solar noon surface albedo values at the CLM grid cell -following the methods of :ref:`Lawrence and Chase (2007) `. -The soil colors are fitted over the range of 20 soil classes shown in +following the methods of :ref:`Lawrence and Chase (2007) `. +The soil colors are fitted over the range of 20 soil classes shown in :numref:`Table Dry and saturated soil albedos` and compared to the MODIS monthly local solar noon all-sky surface albedo as -described in :ref:`Strahler et al. (1999) ` and +described in :ref:`Strahler et al. (1999) ` and :ref:`Schaaf et al. (2002) `. The CLM two-stream radiation model was used to calculate the model equivalent surface albedo using climatological monthly soil moisture along with the @@ -618,17 +618,17 @@ Snow Albedo Snow albedo and solar absorption within each snow layer are simulated with the Snow, Ice, and Aerosol Radiative Model (SNICAR), which -incorporates a two-stream radiative transfer solution from -:ref:`Toon et al. (1989) `. Albedo and the vertical absorption +incorporates a two-stream radiative transfer solution from +:ref:`Toon et al. (1989) `. Albedo and the vertical absorption profile depend on solar zenith angle, albedo of the substrate underlying snow, mass concentrations of atmospheric-deposited aerosols (black carbon, mineral dust, and organic carbon), and ice effective grain size (:math:`r_{e}`), which is simulated with a snow aging routine described in section :numref:`Snow Aging`. Representation of impurity mass -concentrations within the snowpack is described in section +concentrations within the snowpack is described in section :numref:`Black and organic carbon and mineral dust within snow`. -Implementation of SNICAR in CLM is also described somewhat by -:ref:`Flanner and Zender (2005) ` and +Implementation of SNICAR in CLM is also described somewhat by +:ref:`Flanner and Zender (2005) ` and :ref:`Flanner et al. (2007) `. The two-stream solution requires the following bulk optical properties @@ -658,11 +658,11 @@ as g=\frac{\sum _{1}^{k}g_{k} \omega _{k} \tau _{k} }{\sum _{1}^{k}\omega _{k} \tau _{k} } -For each constituent (ice, two black carbon species, two organic carbon species, and -four dust species), :math:`\omega`, *g*, and the mass extinction cross-section -:math:`\psi` (m\ :sup:`2` kg\ :sub:`-1`) are computed offline with Mie Theory, e.g., -applying the computational technique from :ref:`Bohren and Huffman (1983) `. -The extinction optical depth for each constituent depends on its mass extinction +For each constituent (ice, two black carbon species, two organic carbon species, and +four dust species), :math:`\omega`, *g*, and the mass extinction cross-section +:math:`\psi` (m\ :sup:`2` kg\ :sub:`-1`) are computed offline with Mie Theory, e.g., +applying the computational technique from :ref:`Bohren and Huffman (1983) `. +The extinction optical depth for each constituent depends on its mass extinction cross-section and layer mass, :math:`w _{k}` (kg\ m\ :sup:`-1`) as .. math:: @@ -674,18 +674,18 @@ The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri solution to produce upward and downward radiative fluxes at each layer interface, from which net radiation, layer absorption, and surface albedo are easily derived. Solar fluxes are computed in five spectral -bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. +bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. Because snow albedo varies strongly across the solar spectrum, it was determined that four bands were needed to accurately represent the near-infrared (NIR) characteristics of snow, whereas only one band was needed for the visible spectrum. Boundaries of the NIR bands were selected to capture broad radiative features and -maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 -:math:`\mu` m) surface downwelling flux from CLM according to the weights listed -in :numref:`Table Spectral bands and weights used for snow radiative transfer`, -which are unique for diffuse and direct incident flux. These fixed weights were +maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 +:math:`\mu` m) surface downwelling flux from CLM according to the weights listed +in :numref:`Table Spectral bands and weights used for snow radiative transfer`, +which are unique for diffuse and direct incident flux. These fixed weights were determined with offline hyperspectral radiative transfer calculations for an -atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). +atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). The tri-diagonal solution includes intermediate terms that allow for easy interchange of two-stream techniques. We apply the Eddington solution for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the @@ -761,21 +761,21 @@ soil warming within a single timestep. The radiative transfer calculation is performed twice for each column containing a mass of snow greater than :math:`1 \times 10^{-30}` kg\ m\ :sup:`-2` (excluding lake and urban columns); once each for -direct-beam and diffuse incident flux. Absorption in each layer +direct-beam and diffuse incident flux. Absorption in each layer :math:`i` of pure snow is initially recorded as absorbed flux per unit incident flux on the ground (:math:`S_{sno,\, i}` ), as albedos must be calculated for the next timestep with unknown incident flux. The snow absorption fluxes that are used for column temperature calculations are .. math:: - :label: ZEqnNum275338 + :label: ZEqnNum275338 S_{g,\, i} =S_{sno,\, i} \left(1-\alpha _{sno} \right) This weighting is performed for direct-beam and diffuse, visible and NIR fluxes. After the ground-incident fluxes (transmitted through the vegetation canopy) have been calculated for the current time step -(sections :numref:`Canopy Radiative Transfer` and :numref:`Solar Fluxes`), +(sections :numref:`Canopy Radiative Transfer` and :numref:`Solar Fluxes`), the layer absorption factors (:math:`S_{g,\, i}`) are multiplied by the ground-incident fluxes to @@ -812,19 +812,19 @@ weighted by the diffuse albedo for a semi-infinite snowpack (:math:`\alpha _{sno Inclusion of this additional albedo weight was found to improve accuracy of the five-band albedo solutions (relative to 470-band solutions) because of the strong dependence of optically-thick snowpack albedo on -ice grain single-scatter albedo (:ref:`Flanner et al. (2007) `). -The lookup tables contain optical properties for lognormal distributions of ice +ice grain single-scatter albedo (:ref:`Flanner et al. (2007) `). +The lookup tables contain optical properties for lognormal distributions of ice particles over the range of effective radii: 30\ :math:`\mu`\ m -:math:`< r _{e} < \text{1500} \mu \text{m}`, at 1 :math:`\mu` m resolution. -Single-scatter albedos for the end-members of this size range are listed in +:math:`< r _{e} < \text{1500} \mu \text{m}`, at 1 :math:`\mu` m resolution. +Single-scatter albedos for the end-members of this size range are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`. -Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. +Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. Single-scatter albedo, mass extinction cross-section, and asymmetry parameter values for all snowpack species, in the five -spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, -:numref:`Table Mass extinction values`, and -:numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. +spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, +:numref:`Table Mass extinction values`, and +:numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. These properties were also derived with Mie Theory, using various published sources of indices of refraction and assumptions about particle size distribution. Weighting into the five CLM spectral bands was determined @@ -923,9 +923,9 @@ Snow aging is represented as evolution of the ice effective grain size (:math:`r_{e}`). Previous studies have shown that use of spheres which conserve the surface area-to-volume ratio (or specific surface area) of ice media composed of more complex shapes produces relatively -small errors in simulated hemispheric fluxes +small errors in simulated hemispheric fluxes (e.g., :ref:`Grenfell and Warren 1999 `). -Effective radius is the surface area-weighted mean +Effective radius is the surface area-weighted mean radius of an ensemble of spherical particles and is directly related to specific surface area (*SSA*) as :math:`r_{e} ={3\mathord{\left/ {\vphantom {3 \left(\rho _{ice} SSA\right)}} \right.} \left(\rho _{ice} SSA\right)}` , @@ -960,16 +960,16 @@ each time step *t* as r_{e} \left(t\right)=\left[r_{e} \left(t-1\right)+dr_{e,\, dry} +dr_{e,\, wet} \right]f_{old} +r_{e,\, 0} f_{new} +r_{e,\, rfz} f_{rfrz} Here, the effective radius of freshly-fallen snow -(:math:`r_{e,0}`) is based on a simple linear temperature-relationship. +(:math:`r_{e,0}`) is based on a simple linear temperature-relationship. Below -30 degrees Celsius, a minimum value is enforced of 54.5 :math:`\mu` m (corresponding to a specific surface area of 60 m\ :sup:`2` kg\ :sup:`-1`). Above 0 degrees Celsius, a maximum value is enforced of 204.5 :math:`\mu` m. -Between -30 and 0 a linear ramp is used. +Between -30 and 0 a linear ramp is used. The effective radius of refrozen liquid water (:math:`r_{e,rfz}`) is set to 1000\ :math:`\mu` m. Dry snow aging is based on a microphysical model described by :ref:`Flanner -and Zender (2006) `. This model simulates diffusive vapor flux +and Zender (2006) `. This model simulates diffusive vapor flux amongst collections of ice crystals with various size and inter-particle spacing. Specific surface area and effective radius are prognosed for any combination of snow temperature, temperature gradient, density, and @@ -1151,7 +1151,7 @@ reference vernal equinox (i.e., the vernal equinox at 1950 A.D.) and describes the absolute motion of the perihelion relative to the fixed stars, and :math:`\psi` is the annual general precession in longitude and describes the absolute motion of the vernal equinox along Earth's -orbit relative to the fixed stars. The general precession :math:`\psi` +orbit relative to the fixed stars. The general precession :math:`\psi` (degrees) is .. math:: @@ -1169,13 +1169,13 @@ series expansions for the eccentricity :math:`e`\ as follows: .. math:: :label: 3.87 - \Pi =\left\{\begin{array}{lr} - 0 & \qquad {\rm for\; -1}\times {\rm 10}^{{\rm -8}} \le e^{\cos } \le 1\times 10^{-8} {\rm \; and\; }e^{\sin } = 0 \\ - 1.5\pi & \qquad {\rm for\; -1}\times {\rm 10}^{{\rm -8}} \le e^{\cos } \le 1\times 10^{-8} {\rm \; and\; }e^{\sin } < 0 \\ - 0.5\pi & \qquad {\rm for\; -1}\times {\rm 10}^{{\rm -8}} \le e^{\cos } \le 1\times 10^{-8} {\rm \; and\; }e^{\sin } > 0 \\ - \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right]+\pi & \qquad {\rm for\; }e^{\cos } <{\rm -1}\times {\rm 10}^{{\rm -8}} \\ - \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right]+2\pi & \qquad {\rm for\; }e^{\cos } >{\rm 1}\times {\rm 10}^{{\rm -8}} {\rm \; and\; }e^{\sin } <0 \\ - \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right] & \qquad {\rm for\; }e^{\cos } >{\rm 1}\times {\rm 10}^{{\rm -8}} {\rm \; and\; }e^{\sin } \ge 0 + \Pi =\left\{\begin{array}{lr} + 0 & \qquad {\rm for\; -1}\times {\rm 10}^{{\rm -8}} \le e^{\cos } \le 1\times 10^{-8} {\rm \; and\; }e^{\sin } = 0 \\ + 1.5\pi & \qquad {\rm for\; -1}\times {\rm 10}^{{\rm -8}} \le e^{\cos } \le 1\times 10^{-8} {\rm \; and\; }e^{\sin } < 0 \\ + 0.5\pi & \qquad {\rm for\; -1}\times {\rm 10}^{{\rm -8}} \le e^{\cos } \le 1\times 10^{-8} {\rm \; and\; }e^{\sin } > 0 \\ + \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right]+\pi & \qquad {\rm for\; }e^{\cos } <{\rm -1}\times {\rm 10}^{{\rm -8}} \\ + \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right]+2\pi & \qquad {\rm for\; }e^{\cos } >{\rm 1}\times {\rm 10}^{{\rm -8}} {\rm \; and\; }e^{\sin } <0 \\ + \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right] & \qquad {\rm for\; }e^{\cos } >{\rm 1}\times {\rm 10}^{{\rm -8}} {\rm \; and\; }e^{\sin } \ge 0 \end{array}\right\}. The numerical solution for the longitude of the perihelion diff --git a/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst b/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst index de7ef86173..4bf2f44861 100644 --- a/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst +++ b/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst @@ -253,17 +253,17 @@ of CMIP6. LUH2 Transient Land Use and Land Cover Change Dataset ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To coordinate the processing and consistency of LULCC data between -the historical period (1850-2015) and the six +To coordinate the processing and consistency of LULCC data between +the historical period (1850-2015) and the six SSP-RCP (2016-2100) scenarios derived from Integrated Assessment Models (IAM), the University of Maryland and the University of New Hampshire research groups (Louise Chini, George Hurtt, Steve -Frolking and Ritvik Sahajpal; luh.umd.edu) produced a new version of the Land Use Harmonized version 2 +Frolking and Ritvik Sahajpal; luh.umd.edu) produced a new version of the Land Use Harmonized version 2 (LUH2) transient datasets for use with Earth System Model simulations. The new data sets -are the product of the Land Use Model Intercomparison Project (LUMIP; https://cmip.ucar.edu/lumip) -as part of the Coupled Model Intercomparison Project 6 (CMIP6). The historical component of the -transient LULCC dataset has agriculture and urban -land use based on HYDE 3.2 with wood harvest based on FAO, Landsat and other sources, for the period 850-2015. +are the product of the Land Use Model Intercomparison Project (LUMIP; https://cmip.ucar.edu/lumip) +as part of the Coupled Model Intercomparison Project 6 (CMIP6). The historical component of the +transient LULCC dataset has agriculture and urban +land use based on HYDE 3.2 with wood harvest based on FAO, Landsat and other sources, for the period 850-2015. The SSP-RCP transient LULCC components (2015-2100) are referred to as the LUH2 Future Scenario datasets. The LULCC information is provided at 0.25 degree grid resolution and includes fractional grid cell coverage by the 12 land units of: @@ -275,13 +275,13 @@ Pasture, Rangeland, Urban, C3 Annual Crop, C4 Annual Crop, C3 Perennial Crop, C4 Perennial Crop, and C3 Nitrogen Fixing Crop. The new land unit format is an improvement on the CMIP5 LULCC -datasets as they: provide Forest and Non Forest information in combination with Primary and Secondary -land; differentiate between Pasture and Rangelands for grazing livestock; and specify annual details -on the types of Crops grown and management practices applied in each grid cell. Like the CMIP5 LULCC datasets Primary vegetation +datasets as they: provide Forest and Non Forest information in combination with Primary and Secondary +land; differentiate between Pasture and Rangelands for grazing livestock; and specify annual details +on the types of Crops grown and management practices applied in each grid cell. Like the CMIP5 LULCC datasets Primary vegetation represents the fractional area of a grid cell with vegetation undisturbed by human activities. Secondary -vegetation represents vegetated areas that have recovered from some human disturbance; this could include +vegetation represents vegetated areas that have recovered from some human disturbance; this could include re-vegetation of pasture and crop areas as well as primary vegetation areas that have been logged. -In this manner the land units can change through deforestation from Forested to Non Forested land and in the +In this manner the land units can change through deforestation from Forested to Non Forested land and in the opposite direction from Non Forested to Forested land through reforestation or afforestation without going through the Crop, Pasture or Rangeland states. @@ -290,7 +290,7 @@ the annual fraction of land that is transformed from one land unit category to another (e.g. Primary Forest to C3 Annual Crop, Pasture to C3 Perrenial Crop, etc.; Lawrence et al. 2016). Included in these transition matrices is the total conversion of one land cover type to another referred to as Gross LULCC. This value can be larger than the sum of the changes in the state of a land unit from one time period -to the next known as the Net LULCC. This difference is possible as land unit changes can occur both from the land unit +to the next known as the Net LULCC. This difference is possible as land unit changes can occur both from the land unit and to the land unit at the same time. An example of this difference occurs with shifting cultivation where Secondary Forest can be converted to C3 Annual Crop at the same time as C3 Annual Crop is abandoned to Secondary Forest. @@ -303,39 +303,39 @@ Young Forest, and Secondary Non-Forest. Additional land use management is prescribed on the Crop land units for -nitrogen fertilization and irrigation equipped land. The fertilizer application and the the irrigation fraction is -prescribed for each Crop land unit in a grid cell individually for each year of the time series. The wood harvest -and crop management are both prescribed spatially on the same 0.25 degree grid as the land use class transitions. +nitrogen fertilization and irrigation equipped land. The fertilizer application and the the irrigation fraction is +prescribed for each Crop land unit in a grid cell individually for each year of the time series. The wood harvest +and crop management are both prescribed spatially on the same 0.25 degree grid as the land use class transitions. Representing LUH2 Land Use and Land Cover Change in CLM5 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ To represent the LUH2 transient LULCC dataset in CLM5, the annual fractional composition of the twelve land units specified in the dataset needs to be -faithfully represented with a corresponding PFT and CFT mosaics of CLM. +faithfully represented with a corresponding PFT and CFT mosaics of CLM. CLM5 represents the land surface as a hierarchy of sub-grid types: glacier; lake; urban; vegetated land; and crop land. The vegetated land is -further divided into a mosaic of Plant Functional Types (PFTs), while the crop land -is divided into a mosaic of Crop Functional Types (CFTs). +further divided into a mosaic of Plant Functional Types (PFTs), while the crop land +is divided into a mosaic of Crop Functional Types (CFTs). To support this translation task the CLM5 Land Use Data tool has been built that extends the -methods described in Lawrence et al (2012) to include all the new functionality of CMIP6 and CLM5 LULCC. -The tool translates each of the LUH2 land units for a given year into fractional PFT and CFT values based on -the current day CLM5 data for the land unit in that grid cell. The current day land unit descriptions are generated from -from 1km resolution MODIS, MIRCA2000, ICESAT, AVHRR, SRTM, and CRU climate data products combined with reference year +methods described in Lawrence et al (2012) to include all the new functionality of CMIP6 and CLM5 LULCC. +The tool translates each of the LUH2 land units for a given year into fractional PFT and CFT values based on +the current day CLM5 data for the land unit in that grid cell. The current day land unit descriptions are generated from +from 1km resolution MODIS, MIRCA2000, ICESAT, AVHRR, SRTM, and CRU climate data products combined with reference year LUH2 land unit data, usually set to 2005. Where the land unit does not exist in a grid cell for the current day, the land unit description is generated from nearest neighbors with an inverse distance weighted search algorithm. - -The Land Use Data tool produces raw vegetation, crop, and management data files which are combined with + +The Land Use Data tool produces raw vegetation, crop, and management data files which are combined with other raw land surface data to produce the CLM5 initial surface dataset and the dynamic *landuse.timeseries* dataset with the CLM5 mksurfdata_map tool. The schematic of this entire process from -LUH2 time series and high resolution current day data to the output of CLM5 surface datasets from the +LUH2 time series and high resolution current day data to the output of CLM5 surface datasets from the mksurfdata_map tool is shown in Figure 21.2. The methodology for creating the CLM5 transient PFT and CFT dataset is based on four -steps which are applied across all of the historical and future time series. -The first step involves generating the current day descriptions of natural and managed vegetation PFTs at +steps which are applied across all of the historical and future time series. +The first step involves generating the current day descriptions of natural and managed vegetation PFTs at 1km resolution from the global source datasets, and the current day description of crop CFTs at the 10km resolution from the MIRCA 2000 datasets. The second step combines the current day (2005) LUH2 land units with the current day CLM5 PFT and CFT distributions to get CLM5 land unit descriptions in either PFTs or CFTs at the LUH2 resolution of @@ -356,7 +356,7 @@ data files in the mksurfdata_map tool. .. figure:: image2.png Schematic of translation of annual LUH2 land units to CLM5 plant and crop functional types. - + .. _Figure Workflow of CLM5 Land Use Data Tool and Mksurfdata_map Tool: .. figure:: image3.png diff --git a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst index be50b131d0..b572c266ff 100644 --- a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst +++ b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst @@ -15,10 +15,10 @@ warming (e.g., white roofs). Urban areas in CLM are represented by up to three urban landunits per gridcell according to density class. The urban landunit is based on the -"urban canyon" concept of :ref:`Oke (1987) ` in which +"urban canyon" concept of :ref:`Oke (1987) ` in which the canyon geometry is described by building height (:math:`H`) and street width (:math:`W`) -(:numref:`Figure schematic representation of the urban landunit`). The canyon system +(:numref:`Figure schematic representation of the urban landunit`). The canyon system consists of roofs, walls, and canyon floor. Walls are further divided into shaded and sunlit components. The canyon floor is divided into pervious (e.g., to represent residential @@ -28,29 +28,29 @@ pervious fraction; instead evaporation is parameterized by a simplified bulk scheme. Each of the five urban surfaces is treated as a column within the -landunit (:numref:`Figure schematic representation of the urban landunit`). +landunit (:numref:`Figure schematic representation of the urban landunit`). Radiation parameterizations account for trapping of solar and longwave radiation inside the canyon. Momentum fluxes are determined for the urban landunit using a roughness length and displacement height appropriate for the urban canyon and stability formulations from CLM. A one-dimensional heat conduction equation is solved numerically for a multiple-layer (:math:`N_{levurb} =10`) column -to determine conduction fluxes into and out of canyon surfaces. +to determine conduction fluxes into and out of canyon surfaces. A new building energy model has been developed for CLM5.0. It accounts for the conduction of heat through interior surfaces (roof, sunlit and -shaded walls, and floors), convection (sensible heat exchange) between +shaded walls, and floors), convection (sensible heat exchange) between interior surfaces and building air, longwave radiation exchange between interior surfaces, and ventilation (natural infiltration and exfiltration). Idealized HAC systems are assumed where the system capacity is infinite and -the system supplies the amount of energy needed to keep the indoor air +the system supplies the amount of energy needed to keep the indoor air temperature (:math:`T_{iB}`) within maximum and minimum emperatures (:math:`T_{iB,\, \max } ,\, T_{iB,\, \min }` ), thus explicitly resolving space heating and air conditioning fluxes. Anthropogenic sources of waste heat (:math:`Q_{H,\, waste}` ) from HAC that account for inefficiencies -in the heating and air conditioning equipment and from energy lost in the -conversion of primary energy sources to end use energy are derived from -:ref:`Sivak (2013) `. These sources of waste heat are incorporated +in the heating and air conditioning equipment and from energy lost in the +conversion of primary energy sources to end use energy are derived from +:ref:`Sivak (2013) `. These sources of waste heat are incorporated as modifications to the canyon energy budget. Turbulent [sensible heat (:math:`Q_{H,\, u}` ) and @@ -109,19 +109,19 @@ urban development scenarios is also available (:ref:`Oleson and Feddema (2018) < This will become the default dataset in future model versions. As described in :ref:`Oleson and Feddema (2018) ` the urban properties dataset in :ref:`Jackson et al. (2010) ` was modified with respect to wall and roof thermal -properties to correct for biases in heat transfer due to layer and building type averaging. -Further changes to the dataset reflect the need for scenario development, thus allowing for +properties to correct for biases in heat transfer due to layer and building type averaging. +Further changes to the dataset reflect the need for scenario development, thus allowing for the creation of hypothetical wall types, and the easier interchange of wall facets. -The new urban properties tool is available as part of the Toolbox for Human-Earth System -Integration & Scaling (THESIS) tool set -(http://www.cgd.ucar.edu/iam/projects/thesis/thesis-urbanproperties-tool.html; -:ref:`Feddema and Kauffman (2016) `). The driver script (urban_prop.csh) -specifies three input csv files (by default, mat_prop.csv, -lam_spec.csv, and city_spec.csv; (:numref:`Figure schematic of THESIS urban properties tool`)) -that describe the morphological, radiative, and thermal properties of urban areas, and +The new urban properties tool is available as part of the Toolbox for Human-Earth System +Integration & Scaling (THESIS) tool set +(http://www.cgd.ucar.edu/iam/projects/thesis/thesis-urbanproperties-tool.html; +:ref:`Feddema and Kauffman (2016) `). The driver script (urban_prop.csh) +specifies three input csv files (by default, mat_prop.csv, +lam_spec.csv, and city_spec.csv; (:numref:`Figure schematic of THESIS urban properties tool`)) +that describe the morphological, radiative, and thermal properties of urban areas, and generates a global dataset at 0.05° latitude by longitude in NetCDF format (urban_properties_data.05deg.nc). -A standalone NCL routine (gen_data_clm.ncl) can be run separately after the mksurfdata_map tool creates -the CLM surface dataset. This creates a supplementary streams file of setpoints for the maximum +A standalone NCL routine (gen_data_clm.ncl) can be run separately after the mksurfdata_map tool creates +the CLM surface dataset. This creates a supplementary streams file of setpoints for the maximum interior building temperature at yearly time resolution. .. Figure 12.1. Schematic representation of the urban land unit @@ -146,7 +146,7 @@ interior building temperature at yearly time resolution. .. Figure:: image3.png - Schematic of THESIS urban properties tool. Executable scripts are in orange, input files are blue, and output files are green. Items within the black box outline are either read in as input, executed, or output by the driver script (urban_prop.csh). + Schematic of THESIS urban properties tool. Executable scripts are in orange, input files are blue, and output files are green. Items within the black box outline are either read in as input, executed, or output by the driver script (urban_prop.csh). The urban model that was first released as a component of CLM4.0 is separately @@ -162,19 +162,19 @@ to eliminate urban areas in the surface dataset creation routines was increased from 2200 meters to 2600 meters, 5) hydrologic and thermal calculations for the pervious road followed CLM4.5 parameterizations. -The main changes in the urban model from CLM4.5 to CLM5.0 are 1) a more -sophisticated and realistic building space heating and air conditioning +The main changes in the urban model from CLM4.5 to CLM5.0 are 1) a more +sophisticated and realistic building space heating and air conditioning submodel that prognoses interior building air temperature and includes more realistic space heating and air conditioning wasteheat factors (see above), 2) the maximum building temperature (which determines air conditioning demand) is now read in -from a namelist-defined file which allows for dynamic control of this input -variable. The maximum building temperatures that are defined in +from a namelist-defined file which allows for dynamic control of this input +variable. The maximum building temperatures that are defined in :ref:`Jackson et al. (2010) ` are implemented in year 1950 (thus air conditioning is off in prior years) and air conditioning is turned off in year 2100 (because the buildings are not suitable for air conditioning in some extreme -global warming scenarios), 3) an optional updated urban properties dataset and new -scenario tool. These features are described in more detail in :ref:`Oleson and Feddema (2018) `. +global warming scenarios), 3) an optional updated urban properties dataset and new +scenario tool. These features are described in more detail in :ref:`Oleson and Feddema (2018) `. In addition, a module of heat stress indices calculated online in the model that can be used to assess human thermal comfort for rural and urban -areas has been added. This last development is described and evaluated by +areas has been added. This last development is described and evaluated by :ref:`Buzan et al. (2015) `. diff --git a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst index ce05bbb3f1..453152ca50 100644 --- a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst +++ b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst @@ -45,64 +45,64 @@ growth periods (Figure 14.1). Carbon fluxes from the transfer pools into displayed growth are calculated during these periods as: .. math:: - :label: 20.1) + :label: 20.1) CF_{leaf\_ xfer,leaf} =r_{xfer\_ on} CS_{leaf\_ xfer} .. math:: - :label: 20.2) + :label: 20.2) CF_{froot\_ xfer,froot} =r_{xfer\_ on} CS_{froot\_ xfer} .. math:: - :label: 20.3) + :label: 20.3) CF_{livestem\_ xfer,livestem} =r_{xfer\_ on} CS_{livestem\_ xfer} .. math:: - :label: 20.4) + :label: 20.4) CF_{deadstem\_ xfer,deadstem} =r_{xfer\_ on} CS_{deadstem\_ xfer} .. math:: - :label: 20.5) + :label: 20.5) CF_{livecroot\_ xfer,livecroot} =r_{xfer\_ on} CS_{livecroot\_ xfer} .. math:: - :label: 20.6) + :label: 20.6) CF_{deadcroot\_ xfer,deadcroot} =r_{xfer\_ on} CS_{deadcroot\_ xfer} , with corresponding nitrogen fluxes: .. math:: - :label: 20.7) + :label: 20.7) NF_{leaf\_ xfer,leaf} =r_{xfer\_ on} NS_{leaf\_ xfer} .. math:: - :label: 20.8) + :label: 20.8) NF_{froot\_ xfer,froot} =r_{xfer\_ on} NS_{froot\_ xfer} .. math:: - :label: 20.9) + :label: 20.9) NF_{livestem\_ xfer,livestem} =r_{xfer\_ on} NS_{livestem\_ xfer} .. math:: - :label: 20.10) + :label: 20.10) NF_{deadstem\_ xfer,deadstem} =r_{xfer\_ on} NS_{deadstem\_ xfer} .. math:: - :label: 20.11) + :label: 20.11) NF_{livecroot\_ xfer,livecroot} =r_{xfer\_ on} NS_{livecroot\_ xfer} .. math:: - :label: 20.12) + :label: 20.12) NF_{deadcroot\_ xfer,deadcroot} =r_{xfer\_ on} NS_{deadcroot\_ xfer} , @@ -111,12 +111,12 @@ flux, NS is stored nitrogen, :math:`{r}_{xfer\_on}` (s\ :sup:`-1`) is a time-var out of the transfer pool: .. math:: - :label: ZEqnNum852972 + :label: ZEqnNum852972 r_{xfer\_ on} =\left\{\begin{array}{l} {{2\mathord{\left/ {\vphantom {2 t_{onset} }} \right.} t_{onset} } \qquad {\rm for\; }t_{onset} \ne \Delta t} \\ {{1\mathord{\left/ {\vphantom {1 \Delta t}} \right.} \Delta t} \qquad {\rm for\; }t_{onset} =\Delta t} \end{array}\right. and *t*\ :sub:`onset` (s) is the number of seconds remaining in -the current phenology onset growth period (Figure 14.1). The form of Eq. :eq:`ZEqnNum852972` +the current phenology onset growth period (Figure 14.1). The form of Eq. :eq:`ZEqnNum852972` produces a flux from the transfer pool which declines linearly over the onset growth period, approaching zero flux in the final timestep. @@ -130,31 +130,31 @@ Carbon fluxes from display pools into litter are calculated during these periods as: .. math:: - :label: 20.14) + :label: 20.14) - CF_{leaf,litter}^{n} =\left\{\begin{array}{l} {CF_{leaf,litter}^{n-1} + r_{xfer\_ off} \left(CS_{leaf} -CF_{leaf,litter}^{n-1} {\kern 1pt} t_{offset} \right)\qquad {\rm for\; }t_{offset} \ne \Delta t} + CF_{leaf,litter}^{n} =\left\{\begin{array}{l} {CF_{leaf,litter}^{n-1} + r_{xfer\_ off} \left(CS_{leaf} -CF_{leaf,litter}^{n-1} {\kern 1pt} t_{offset} \right)\qquad {\rm for\; }t_{offset} \ne \Delta t} \\ {\left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) - \left( 1-biofuel\_harvfrac \right) + \left( 1-biofuel\_harvfrac \right) +CF_{alloc,leaf} \qquad {\rm for\; }t_{offset} =\Delta t} \end{array}\right. .. math:: - :label: 20.15) + :label: 20.15) CF_{froot,litter}^{n} =\left\{\begin{array}{l} {CF_{froot,litter}^{n-1} + r_{xfer\_ off} \left(CS_{froot} -CF_{froot,litter}^{n-1} {\kern 1pt} t_{offset} \right)\qquad {\rm for\; }t_{offset} \ne \Delta t} \\ {\left({CS_{froot} \mathord{\left/ {\vphantom {CS_{froot} \Delta t}} \right.} \Delta t} \right)+CF_{alloc,\, froot} \qquad \qquad \qquad {\rm for\; }t_{offset} =\Delta t} \end{array}\right. .. math:: - :label: 20.16) + :label: 20.16) r_{xfer\_ off} =\frac{2\Delta t}{t_{offset} ^{2} } where superscripts *n* and *n-1* refer to fluxes on the current and previous timesteps, respectively. The rate coefficient :math:`{r}_{xfer\_off}` varies with time to produce a linearly -increasing litterfall rate throughout the offset period. -The :math:`biofuel\_harvfrac` (:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) +increasing litterfall rate throughout the offset period. +The :math:`biofuel\_harvfrac` (:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) is the harvested fraction of aboveground biomass (leaf & livestem) for bioenergy crops. The special case for fluxes in the final litterfall timestep -(:math:`{t}_{offset}` = :math:`\Delta t`\ ) ensures that all of the displayed growth is sent to the litter pools or biofuel feedstock pools. The fraction (:math:`biofuel\_harvfrac`) of leaf biomass going to the biofuel feedstock pools (Equation :eq:`25.9`) is defined in Table 26.3 and is only non-zero for prognostic crops. The remaining fraction of leaf biomass (:math:`1-biofuel\_harvfrac`) for deciduous plant types is sent to the litter pools. +(:math:`{t}_{offset}` = :math:`\Delta t`\ ) ensures that all of the displayed growth is sent to the litter pools or biofuel feedstock pools. The fraction (:math:`biofuel\_harvfrac`) of leaf biomass going to the biofuel feedstock pools (Equation :eq:`25.9`) is defined in Table 26.3 and is only non-zero for prognostic crops. The remaining fraction of leaf biomass (:math:`1-biofuel\_harvfrac`) for deciduous plant types is sent to the litter pools. Similar modifications made for livestem carbon pools for prognostic crops can be found in section :numref:`Harvest to food and seed` in Equations :eq:`25.9`-:eq:`25.14`. @@ -163,17 +163,17 @@ litterfall (:math:`{NF}_{leaf,retrans}`, gN m\ :sup:`-2` s\ :sup:`-1`). Retransl assumed to be negligible. The fluxes are: .. math:: - :label: 20.17) + :label: 20.17) NF_{leaf,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf\_ litter} }} \right.} CN_{leaf\_ litter} } .. math:: - :label: 20.18) + :label: 20.18) NF_{froot,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{froot} }} \right.} CN_{froot} } .. math:: - :label: 20.19) + :label: 20.19) NF_{leaf,retrans} =\left({CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf} }} \right.} CN_{leaf} } \right)-NF_{leaf,litter} . @@ -195,64 +195,64 @@ on each time step. The carbon fluxes from transfer to display pools under these conditions are: .. math:: - :label: 20.20) + :label: 20.20) CF_{leaf\_ xfer,leaf} ={CS_{leaf\_ xfer} \mathord{\left/ {\vphantom {CS_{leaf\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.21) + :label: 20.21) CF_{froot\_ xfer,froot} ={CS_{froot\_ xfer} \mathord{\left/ {\vphantom {CS_{froot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.22) + :label: 20.22) CF_{livestem\_ xfer,livestem} ={CS_{livestem\_ xfer} \mathord{\left/ {\vphantom {CS_{livestem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.23) + :label: 20.23) CF_{deadstem\_ xfer,deadstem} ={CS_{deadstem\_ xfer} \mathord{\left/ {\vphantom {CS_{deadstem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.24) + :label: 20.24) CF_{livecroot\_ xfer,livecroot} ={CS_{livecroot\_ xfer} \mathord{\left/ {\vphantom {CS_{livecroot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.25) + :label: 20.25) CF_{deadcroot\_ xfer,deadcroot} ={CS_{deadcroot\_ xfer} \mathord{\left/ {\vphantom {CS_{deadcroot\_ xfer} \Delta t}} \right.} \Delta t} , and the corresponding nitrogen fluxes are: .. math:: - :label: 20.26) + :label: 20.26) NF_{leaf\_ xfer,leaf} ={NS_{leaf\_ xfer} \mathord{\left/ {\vphantom {NS_{leaf\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.27) + :label: 20.27) NF_{froot\_ xfer,froot} ={NS_{froot\_ xfer} \mathord{\left/ {\vphantom {NS_{froot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.28) + :label: 20.28) NF_{livestem\_ xfer,livestem} ={NS_{livestem\_ xfer} \mathord{\left/ {\vphantom {NS_{livestem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.29) + :label: 20.29) NF_{deadstem\_ xfer,deadstem} ={NS_{deadstem\_ xfer} \mathord{\left/ {\vphantom {NS_{deadstem\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.30) + :label: 20.30) NF_{livecroot\_ xfer,livecroot} ={NS_{livecroot\_ xfer} \mathord{\left/ {\vphantom {NS_{livecroot\_ xfer} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.31) + :label: 20.31) NF_{deadcroot\_ xfer,deadcroot} ={NS_{deadcroot\_ xfer} \mathord{\left/ {\vphantom {NS_{deadcroot\_ xfer} \Delta t}} \right.} \Delta t} . @@ -269,29 +269,29 @@ mechanism may be active, but not both at once. Given a specification of the background litterfall rate (:math:`{r}_{bglf}`, s\ :sup:`-1`), litterfall carbon fluxes are calculated as .. math:: - :label: 20.32) + :label: 20.32) CF_{leaf,litter} =r_{bglf} CS_{leaf} .. math:: - :label: 20.33) + :label: 20.33) CS_{froot,litter} =r_{bglf} CS_{froot} , with corresponding nitrogen litterfall and retranslocation fluxes: .. math:: - :label: 20.34) + :label: 20.34) NF_{leaf,litter} ={CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf\_ litter} }} \right.} CN_{leaf\_ litter} } .. math:: - :label: 20.35) + :label: 20.35) NF_{froot,litter} ={CF_{froot,litter} \mathord{\left/ {\vphantom {CF_{froot,litter} CN_{froot} }} \right.} CN_{froot} } .. math:: - :label: 20.36) + :label: 20.36) NF_{leaf,retrans} =\left({CF_{leaf,litter} \mathord{\left/ {\vphantom {CF_{leaf,litter} CN_{leaf} }} \right.} CN_{leaf} } \right)-NF_{leaf,litter} . @@ -313,7 +313,7 @@ A live wood turnover rate (:math:`{r}_{lwt}`, s\ :sup:`-1`) is defined as .. math:: - :label: 20.37) + :label: 20.37) r_{lwt} ={p_{lwt} \mathord{\left/ {\vphantom {p_{lwt} \left(365\cdot 86400\right)}} \right.} \left(365\cdot 86400\right)} @@ -321,12 +321,12 @@ where :math:`{p}_{lwt} = 0.7` is the assumed annual live wood turnover fraction. Carbon fluxes from live to dead wood pools are: .. math:: - :label: 20.38) + :label: 20.38) CF_{livestem,deadstem} =CS_{livestem} r_{lwt} .. math:: - :label: 20.39) + :label: 20.39) CF_{livecroot,deadcroot} =CS_{livecroot} r_{lwt} , @@ -334,22 +334,22 @@ and the associated nitrogen fluxes, including retranslocation of nitrogen out of live wood during turnover, are: .. math:: - :label: 20.40) + :label: 20.40) NF_{livestem,deadstem} ={CF_{livestem,deadstem} \mathord{\left/ {\vphantom {CF_{livestem,deadstem} CN_{dw} }} \right.} CN_{dw} } .. math:: - :label: 20.41) + :label: 20.41) NF_{livestem,retrans} =\left({CF_{livestem,deadstem} \mathord{\left/ {\vphantom {CF_{livestem,deadstem} CN_{lw} }} \right.} CN_{lw} } \right)-NF_{livestem,deadstem} .. math:: - :label: 20.42) + :label: 20.42) NF_{livecroot,deadcroot} ={CF_{livecroot,deadcroot} \mathord{\left/ {\vphantom {CF_{livecroot,deadcroot} CN_{dw} }} \right.} CN_{dw} } .. math:: - :label: 20.43) + :label: 20.43) NF_{livecroot,retrans} =\left({CF_{livecroot,deadcroot} \mathord{\left/ {\vphantom {CF_{livecroot,deadcroot} CN_{lw} }} \right.} CN_{lw} } \right)-NF_{livecroot,deadcroot} . @@ -359,7 +359,7 @@ Evergreen Phenology The evergreen phenology algorithm is by far the simplest of the three possible types. It is assumed for all evergreen types that all carbon and nitrogen allocated for new growth in the current timestep goes -immediately to the displayed growth pools (i.e. f\ :math:`{f}_{cur} = 1.0` +immediately to the displayed growth pools (i.e. f\ :math:`{f}_{cur} = 1.0` (Chapter 13)). As such, there is never an accumulation of carbon or nitrogen in the storage or transfer pools, and so the onset growth and background onset growth mechanisms are never invoked for this type. @@ -374,7 +374,7 @@ of background litterfall (:math:`{r}_{bglf}`, section 14.1.4) depends on the specified leaf longevity (:math:`\tau_{leaf}`\ , y), as .. math:: - :label: 20.44) + :label: 20.44) r_{bglf} =\frac{1}{\tau _{leaf} \cdot 365\cdot 86400} . @@ -397,14 +397,14 @@ of one onset period and one offset period each year. The algorithms for initiation of onset and offset periods use the winter and summer solstices as coordination signals. The period between winter -and summer solstice is identified as :math:`{dayl}_{n} > {dayl}_{n-1}`, -and the period between summer and winter -solstice is identified as :math:`{dayl}_{n} < {dayl}_{n-1}`, +and summer solstice is identified as :math:`{dayl}_{n} > {dayl}_{n-1}`, +and the period between summer and winter +solstice is identified as :math:`{dayl}_{n} < {dayl}_{n-1}`, where :math:`{dayl}_{n}` and :math:`{dayl}_{n-1}` are the day length(s) calculated for the current and previous timesteps, respectively, using .. math:: - :label: 20.45) + :label: 20.45) dayl=2\cdot 13750.9871\cdot acos\left(\frac{-\sin (lat)\sin (decl)}{\cos (lat)\cos (decl)} \right), @@ -423,7 +423,7 @@ dormant and the model timestep crosses the winter solstice. Once these conditions are met, :math:`{GDD}_{sum}` is updated on each timestep as .. math:: - :label: ZEqnNum510730 + :label: ZEqnNum510730 GDD_{sum}^{n} =\left\{\begin{array}{l} {GDD_{sum}^{n-1} +\left(T_{s,3} -TKFRZ\right)f_{day} \qquad {\rm for\; }T_{s,3} >TKFRZ} \\ {GDD_{sum}^{n-1} \qquad \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \end{array}\right. @@ -433,7 +433,7 @@ The onset period is initiated if :math:`GDD_{sum} >GDD_{sum\_ crit}` , where .. math:: - :label: ZEqnNum598907 + :label: ZEqnNum598907 GDD_{sum\_ crit} =\exp \left(4.8+0.13{\kern 1pt} \left(T_{2m,ann\_ avg} -TKFRZ\right)\right) @@ -442,12 +442,12 @@ the 2m air temperature, and TKFRZ is the freezing point of water (273.15 K). The period is initiated: .. math:: - :label: 20.48) + :label: 20.48) GDD_{sum} =0 .. math:: - :label: 20.49) + :label: 20.49) t_{onset} =86400\cdot n_{days\_ on} , @@ -456,69 +456,69 @@ Fluxes from storage into transfer pools occur in the timestep when a new onset growth period is initiated. Carbon fluxes are: .. math:: - :label: ZEqnNum904388 + :label: ZEqnNum904388 CF_{leaf\_ stor,leaf\_ xfer} ={f_{stor,xfer} CS_{leaf\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{leaf\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.51) + :label: 20.51) CF_{froot\_ stor,froot\_ xfer} ={f_{stor,xfer} CS_{froot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{froot\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.52) + :label: 20.52) CF_{livestem\_ stor,livestem\_ xfer} ={f_{stor,xfer} CS_{livestem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{livestem\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.53) + :label: 20.53) CF_{deadstem\_ stor,deadstem\_ xfer} ={f_{stor,xfer} CS_{deadstem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{deadstem\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.54) + :label: 20.54) CF_{livecroot\_ stor,livecroot\_ xfer} ={f_{stor,xfer} CS_{livecroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{livecroot\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.55) + :label: 20.55) CF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} CS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{deadcroot\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: ZEqnNum195642 + :label: ZEqnNum195642 CF_{gresp\_ stor,gresp\_ xfer} ={f_{stor,xfer} CS_{gresp\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} CS_{gresp\_ stor} \Delta t}} \right.} \Delta t} and the associated nitrogen fluxes are: .. math:: - :label: ZEqnNum812152 + :label: ZEqnNum812152 NF_{leaf\_ stor,leaf\_ xfer} ={f_{stor,xfer} NS_{leaf\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{leaf\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.58) + :label: 20.58) NF_{froot\_ stor,froot\_ xfer} ={f_{stor,xfer} NS_{froot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{froot\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.59) + :label: 20.59) NF_{livestem\_ stor,livestem\_ xfer} ={f_{stor,xfer} NS_{livestem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{livestem\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.60) + :label: 20.60) NF_{deadstem\_ stor,deadstem\_ xfer} ={f_{stor,xfer} NS_{deadstem\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadstem\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: 20.61) + :label: 20.61) NF_{livecroot\_ stor,livecroot\_ xfer} ={f_{stor,xfer} NS_{livecroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{livecroot\_ stor} \Delta t}} \right.} \Delta t} .. math:: - :label: ZEqnNum605338 + :label: ZEqnNum605338 NF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} NS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadcroot\_ stor} \Delta t}} \right.} \Delta t} @@ -538,11 +538,11 @@ each time step after initiation of the onset period, until it reaches zero, signaling the end of the onset period: .. math:: - :label: 20.63) + :label: 20.63) t_{onfset}^{n} =t_{onfset}^{n-1} -\Delta t -14.3.2 Seasonal-Deciduous Offset Trigger +14.3.2 Seasonal-Deciduous Offset Trigger ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ After the completion of an onset period, and once past the summer @@ -555,7 +555,7 @@ offset period, until it reaches zero, signaling the end of the offset period: .. math:: - :label: 20.64) + :label: 20.64) t_{offset}^{n} =t_{offset}^{n-1} -\Delta t @@ -582,14 +582,14 @@ previous offset period), an accumulated soil water index (:math:`{SWI}_{sum}`, d) is initialized (:math:`{SWI}_{sum} = 0`), with subsequent accumulation calculated as: .. math:: - :label: ZEqnNum503826 + :label: ZEqnNum503826 SWI_{sum}^{n} =\left\{\begin{array}{l} {SWI_{sum}^{n-1} +f_{day} \qquad {\rm for\; }\Psi _{s,3} \ge \Psi _{onset} } \\ {SWI_{sum}^{n-1} \qquad \qquad {\rm for\; }\Psi _{s,3} <\Psi _{onset} } \end{array}\right. where :math:`\Psi`\ :sub:`s,3` is the soil water potential (MPa) in the third soil layer and :math:`{\Psi}_{onset} = -0.6 MPa` is the onset soil water potential threshold. Onset triggering is -possible once :math:`{SWI}_{sum} > 15`. To avoid spurious onset triggering due to +possible once :math:`{SWI}_{sum} > 15`. To avoid spurious onset triggering due to soil moisture in the third soil layer exceeding the threshold due only to soil water suction of water from deeper in the soil column, an additional precipitation trigger is included which requires at least 20 mm of rain over the previous 10 days :ref:`(Dahlin et al., 2015) `. If the cold climate @@ -608,7 +608,7 @@ the beginning of a dormant period a freezing day accumulator with subsequent accumulation calculated as: .. math:: - :label: 20.66) + :label: 20.66) FD_{sum}^{n} =\left\{\begin{array}{l} {FD_{sum}^{n-1} +f_{day} \qquad {\rm for\; }T_{s,3} >TKFRZ} \\ {FD_{sum}^{n-1} \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \end{array}\right. . @@ -628,7 +628,7 @@ carbon fluxes, and to Eqs. :eq:`ZEqnNum812152` - :eq:`ZEqnNum605338` for nitroge until it reaches zero, signaling the end of the onset period: .. math:: - :label: 20.67) + :label: 20.67) t_{onfset}^{n} =t_{onfset}^{n-1} -\Delta t @@ -646,7 +646,7 @@ period of dry soils, this control variable can increase or decrease, as follows: .. math:: - :label: 20.68) + :label: 20.68) OSWI_{sum}^{n} =\left\{\begin{array}{l} {OSWI_{sum}^{n-1} +f_{day} \qquad \qquad \qquad {\rm for\; }\Psi _{s,3} \le \Psi _{offset} } \\ {{\rm max}\left(OSWI_{sum}^{n-1} -f_{day} ,0\right)\qquad {\rm for\; }\Psi _{s,3} >\Psi _{onset} } \end{array}\right. @@ -660,7 +660,7 @@ accumulator (:math:`{OFD}_{sum}`, d). To test for a sustained period of cold temperature, this variable can increase or decrease, as follows: .. math:: - :label: 20.69) + :label: 20.69) OFD_{sum}^{n} =\left\{\begin{array}{l} {OFD_{sum}^{n-1} +f_{day} \qquad \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \\ {{\rm max}\left(OFD_{sum}^{n-1} -f_{day} ,0\right)\qquad \qquad {\rm for\; }T_{s,3} >TKFRZ} \end{array}\right. @@ -676,7 +676,7 @@ offset period, until it reaches zero, signaling the end of the offset period: .. math:: - :label: 20.70) + :label: 20.70) t_{offset}^{n} =t_{offset}^{n-1} -\Delta t @@ -694,14 +694,14 @@ of an offset period :math:`{n}_{days\_active}` is reset to 0. A long growing season control variable (*LGS*, range 0 to 1) is calculated as: .. math:: - :label: 20.71) + :label: 20.71) LGS=\left\{\begin{array}{l} {0\qquad \qquad \qquad {\rm for\; }n_{days\_ active} <365} \\ {\left({n_{days\_ active} \mathord{\left/ {\vphantom {n_{days\_ active} 365}} \right.} 365} \right)-1\qquad {\rm for\; }365\le n_{days\_ active} <730} \\ {1\qquad \qquad \qquad {\rm for\; }n_{days\_ active} \ge 730} \end{array}\right. . The rate coefficient for background litterfall (:math:`{r}_{bglf}`, s\ :sup:`-1`) is calculated as a function of *LGS*: .. math:: - :label: 20.72) + :label: 20.72) r_{bglf} =\frac{LGS}{\tau _{leaf} \cdot 365\cdot 86400} @@ -711,71 +711,71 @@ where :math:`{\tau}_{leaf}` is the leaf longevity. The result is a shift to cont The rate coefficient for background onset growth from the transfer pools ( :math:`{r}_{bgtr}`, s\ :sup:`-1`) also depends on *LGS*, as: .. math:: - :label: 20.73) + :label: 20.73) r_{bgtr} =\frac{LGS}{365\cdot 86400} . On each timestep with :math:`{r}_{bgtr}` :math:`\neq` 0, carbon fluxes from storage to transfer pools are calculated as: .. math:: - :label: 20.74) + :label: 20.74) CF_{leaf\_ stor,leaf\_ xfer} =CS_{leaf\_ stor} r_{bgtr} .. math:: - :label: 20.75) + :label: 20.75) CF_{froot\_ stor,froot\_ xfer} =CS_{froot\_ stor} r_{bgtr} .. math:: - :label: 20.76) + :label: 20.76) CF_{livestem\_ stor,livestem\_ xfer} =CS_{livestem\_ stor} r_{bgtr} .. math:: - :label: 20.77) + :label: 20.77) CF_{deadstem\_ stor,deadstem\_ xfer} =CS_{deadstem\_ stor} r_{bgtr} .. math:: - :label: 20.78) + :label: 20.78) CF_{livecroot\_ stor,livecroot\_ xfer} =CS_{livecroot\_ stor} r_{bgtr} .. math:: - :label: 20.79) + :label: 20.79) CF_{deadcroot\_ stor,deadcroot\_ xfer} =CS_{deadcroot\_ stor} r_{bgtr} , with corresponding nitrogen fluxes: .. math:: - :label: 20.80) + :label: 20.80) NF_{leaf\_ stor,leaf\_ xfer} =NS_{leaf\_ stor} r_{bgtr} .. math:: - :label: 20.81) + :label: 20.81) NF_{froot\_ stor,froot\_ xfer} =NS_{froot\_ stor} r_{bgtr} .. math:: - :label: 20.82) + :label: 20.82) NF_{livestem\_ stor,livestem\_ xfer} =NS_{livestem\_ stor} r_{bgtr} .. math:: - :label: 20.83) + :label: 20.83) NF_{deadstem\_ stor,deadstem\_ xfer} =NS_{deadstem\_ stor} r_{bgtr} .. math:: - :label: 20.84) + :label: 20.84) NF_{livecroot\_ stor,livecroot\_ xfer} =NS_{livecroot\_ stor} r_{bgtr} .. math:: - :label: 20.85) + :label: 20.85) NF_{deadcroot\_ stor,deadcroot\_ xfer} =NS_{deadcroot\_ stor} r_{bgtr} . @@ -802,32 +802,32 @@ calculated using a weighted average of the fluxes originating at the PFT level. Carbon fluxes are calculated as: .. math:: - :label: 20.86) + :label: 20.86) CF_{leaf,lit1} =\sum _{p=0}^{npfts}CF_{leaf,litter} f_{lab\_ leaf,p} wcol_{p} .. math:: - :label: 20.87) + :label: 20.87) CF_{leaf,lit2} =\sum _{p=0}^{npfts}CF_{leaf,litter} f_{cel\_ leaf,p} wcol_{p} .. math:: - :label: 20.88) + :label: 20.88) CF_{leaf,lit3} =\sum _{p=0}^{npfts}CF_{leaf,litter} f_{lig\_ leaf,p} wcol_{p} .. math:: - :label: 20.89) + :label: 20.89) CF_{froot,lit1} =\sum _{p=0}^{npfts}CF_{froot,litter} f_{lab\_ froot,p} wcol_{p} .. math:: - :label: 20.90) + :label: 20.90) CF_{froot,lit2} =\sum _{p=0}^{npfts}CF_{froot,litter} f_{cel\_ froot,p} wcol_{p} .. math:: - :label: 20.91) + :label: 20.91) CF_{froot,lit3} =\sum _{p=0}^{npfts}CF_{froot,litter} f_{lig\_ froot,p} wcol_{p} , @@ -844,31 +844,31 @@ C:N of the senescent tissue, and so are distributed using the same fractions used for carbon fluxes: .. math:: - :label: 20.92) + :label: 20.92) NF_{leaf,lit1} =\sum _{p=0}^{npfts}NF_{leaf,litter} f_{lab\_ leaf,p} wcol_{p} .. math:: - :label: 20.93) + :label: 20.93) NF_{leaf,lit2} =\sum _{p=0}^{npfts}NF_{leaf,litter} f_{cel\_ leaf,p} wcol_{p} .. math:: - :label: 20.94) + :label: 20.94) NF_{leaf,lit3} =\sum _{p=0}^{npfts}NF_{leaf,litter} f_{lig\_ leaf,p} wcol_{p} .. math:: - :label: 20.95) + :label: 20.95) NF_{froot,lit1} =\sum _{p=0}^{npfts}NF_{froot,litter} f_{lab\_ froot,p} wcol_{p} .. math:: - :label: 20.96) + :label: 20.96) NF_{froot,lit2} =\sum _{p=0}^{npfts}NF_{froot,litter} f_{cel\_ froot,p} wcol_{p} .. math:: - :label: 20.97) + :label: 20.97) NF_{froot,lit3} =\sum _{p=0}^{npfts}NF_{froot,litter} f_{lig\_ froot,p} wcol_{p} . diff --git a/doc/source/tech_note/index.rst b/doc/source/tech_note/index.rst index 5baaa61540..a3475c7589 100644 --- a/doc/source/tech_note/index.rst +++ b/doc/source/tech_note/index.rst @@ -52,4 +52,4 @@ CLM Technical Note Isotopes/CLM50_Tech_Note_Isotopes.rst Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst References/CLM50_Tech_Note_References.rst - + diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst index a828c37e98..1436a913b6 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst @@ -6,21 +6,21 @@ Adding New Resolutions ======================== -In the last chapter we gave the details on how to create new files for input into CLM. -These files could be either global resolutions, regional-grids or even a single grid point. -If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. -You can deal with them, just by putting the settings in the ``user_nl_clm namelist`` file, or by using ``CLM_USRDAT_NAME``. -Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. -This keeps one central database for all your files, rather than having multiple locations to keep track of files. -If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. +In the last chapter we gave the details on how to create new files for input into CLM. +These files could be either global resolutions, regional-grids or even a single grid point. +If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. +You can deal with them, just by putting the settings in the ``user_nl_clm namelist`` file, or by using ``CLM_USRDAT_NAME``. +Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. +This keeps one central database for all your files, rather than having multiple locations to keep track of files. +If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above. -There are two parts to adding files to the build-namelist database. +There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. -You can then use the new resolution by using ``CLM_USRDAT_NAME``. +You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into **create_newcase** -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file. -The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). +The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file. diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst index 337b6dfc5a..2a7f079d5b 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst @@ -6,20 +6,20 @@ Adding Resolution Names ========================= -If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. -The list of valid resolutions is in the id="res" entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. -You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the id="res" entry. -The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. -The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. -The convention for unstructured HOMME grids is nenp4, where corresponds to the resolution. -The higher is the higher the resolution. -So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. -For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. +If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. +The list of valid resolutions is in the id="res" entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. +You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the id="res" entry. +The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. +The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. +The convention for unstructured HOMME grids is nenp4, where corresponds to the resolution. +The higher is the higher the resolution. +So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. +For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file: :: `_ @@ -24,7 +24,7 @@ The IMPORTANT_NOTES file talks about important things for users to know about us The ChangeLog/ChangeSum talk about advances in different versions of CLM. The content of these files is largely explained in the previous chapter on `"What is new with |version| in |cesmrelease| since previous public releases?" `_. -The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that +The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that culimated in that given version of the CLM. Note other directories have README files that explain different components and tools used when running CLM and are useful in understanding how those parts of the model work and should be consulted when using tools in those directories. For more details on configuring and customizing a case with CLM see `Chapter 1 `_. diff --git a/doc/source/users_guide/overview/scientific_validation.rst b/doc/source/users_guide/overview/scientific_validation.rst index d05497a645..5f83457033 100644 --- a/doc/source/users_guide/overview/scientific_validation.rst +++ b/doc/source/users_guide/overview/scientific_validation.rst @@ -12,7 +12,7 @@ In this section we go over what has been extensively tested and scientifically v Standard Configuration and Namelist Options that are Validated -------------------------------------------------------------- -See +See `http://www.cesm.ucar.edu/models/cesm1.2/clm/CLM_configurations_CESM1.2.pdf `_ for an explanation of what configurations are scientifically validated for |version|. For CLM4.0 changes to the science of the model are minimal since CESM1.1.1 so we expect answers to be very similar to using it. In the sections below we go through configuration and/or namelist options or modes that the user should be especially wary of using. You are of course free to use these options, and you may find that they work functionally. Although in some cases you will find issues even with functionality of using them. If so you will need to test, debug and find solutions for these issues on your own. But in every case you will need to go through more extensive work to validate these options from a scientific standpoint. Some of these options are only for |version| while others are for both CLM4.0 AND |version| we explicitly say which they apply to. diff --git a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst index b643e79a28..89c6c4e8f4 100644 --- a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst +++ b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst @@ -6,13 +6,13 @@ Adding PTCLMmkdata Site Data ============================ -The "sitegroupname" option to PTCLMmkdata looks for groups of sites in the files in the ``PTCLM_sitedata`` directory under the PTCLMmkdata directory. -You can add new names available for this option including your own lists of sites, by adding more files in this directory. -There are three files for each "sitegroupname": ``$SITEGROUP_sitedata.txt``, ``$SITEGROUP_soildata.txt`` and ``$SITEGROUP_pftdata.txt`` (where ``$SITEGROUP`` is the name that would be entered as "sitegroupname" to PTCLMmkdata). -Each file needs to have the same list of sites, but gives different information: site data, PFT data, and soil data respectively. -Although the site codes need to be the same between the three files, the files do NOT have to be in the same order. -Each file has a one-line header that lists the contents of each column which are separated by commas. -The first column for each of the files is the "site_code" which must be consistent between the three files. +The "sitegroupname" option to PTCLMmkdata looks for groups of sites in the files in the ``PTCLM_sitedata`` directory under the PTCLMmkdata directory. +You can add new names available for this option including your own lists of sites, by adding more files in this directory. +There are three files for each "sitegroupname": ``$SITEGROUP_sitedata.txt``, ``$SITEGROUP_soildata.txt`` and ``$SITEGROUP_pftdata.txt`` (where ``$SITEGROUP`` is the name that would be entered as "sitegroupname" to PTCLMmkdata). +Each file needs to have the same list of sites, but gives different information: site data, PFT data, and soil data respectively. +Although the site codes need to be the same between the three files, the files do NOT have to be in the same order. +Each file has a one-line header that lists the contents of each column which are separated by commas. +The first column for each of the files is the "site_code" which must be consistent between the three files. The site code can be any unique character string, but in general we use the AmeriFlux site code. Site data file:`` $SITEGROUP_sitedata.txt``): The header for this file is: @@ -51,27 +51,27 @@ This file only requires a line for each year where a transition or harvest happe Converting AmeriFlux Data for use by PTCLMmkdata ------------------------------------------------ -AmeriFlux data comes in comma separated format and is available from: +AmeriFlux data comes in comma separated format and is available from: `http://public.ornl.gov/ameriflux/dataproducts.shtml `_. Before you download the data you need to agree to the usage terms. Here is a copy of the usage terms from the web-site on June/13/2011. -"The AmeriFlux data provided on this site are freely available and were furnished by individual AmeriFlux scientists who encourage their use. -Please kindly inform the appropriate AmeriFlux scientist(s) of how you are using the data and of any publication plans. -Please acknowledge the data source as a citation or in the acknowledgments if the data are not yet published. -If the AmeriFlux Principal Investigators (PIs) feel that they should be acknowledged or offered participation as authors, they will let you know and we assume that an agreement on such matters will be reached before publishing and/or use of the data for publication. -If your work directly competes with the PI's analysis they may ask that they have the opportunity to submit a manuscript before you submit one that uses unpublished data. -In addition, when publishing, please acknowledge the agency that supported the research. +"The AmeriFlux data provided on this site are freely available and were furnished by individual AmeriFlux scientists who encourage their use. +Please kindly inform the appropriate AmeriFlux scientist(s) of how you are using the data and of any publication plans. +Please acknowledge the data source as a citation or in the acknowledgments if the data are not yet published. +If the AmeriFlux Principal Investigators (PIs) feel that they should be acknowledged or offered participation as authors, they will let you know and we assume that an agreement on such matters will be reached before publishing and/or use of the data for publication. +If your work directly competes with the PI's analysis they may ask that they have the opportunity to submit a manuscript before you submit one that uses unpublished data. +In addition, when publishing, please acknowledge the agency that supported the research. Lastly, we kindly request that those publishing papers using AmeriFlux data provide preprints to the PIs providing the data and to the data archive at the Carbon Dioxide Information Analysis Center (CDIAC)." The above agreement applies to the "US-UMB" dataset imported into our repository as well, and Gil Bohrer is the PI on record for that dataset. -The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap filled datasets. -The fields will also need to be renamed. -The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes "FLDS", "PRESS" becomes "PSRF". -"ZBOT" can just be set to the constant of "30" (m). -The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the value in ``SHR_CONST_TKFRZ`` in the file ``models/csm_share/shr/shr_const.F90`` of ``273.15``. +The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap filled datasets. +The fields will also need to be renamed. +The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes "FLDS", "PRESS" becomes "PSRF". +"ZBOT" can just be set to the constant of "30" (m). +The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the value in ``SHR_CONST_TKFRZ`` in the file ``models/csm_share/shr/shr_const.F90`` of ``273.15``. The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and LONGXY should also be set to the latitude and longitude of the site. @@ -79,8 +79,8 @@ The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and Example: PTCLMmkdata transient example over a shorter time period ----------------------------------------------------------------- -This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. -In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as show in the `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ section above. +This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. +In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as show in the `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ section above. Also note that this site has a site-specific dynamic land-use change file for it ``PTCLM_sitedata/US-Ha1_dynpftdata.txt`` in the PTCLMmkdata directory and this file will be used for land-use change and harvesting rather than the global dataset. :: @@ -88,14 +88,14 @@ Also note that this site has a site-specific dynamic land-use change file for it > cd $CTSMROOT/tools/PTCLM # We are going to use forcing data over 1991 to 2006, but we need to start with # a transient compset to do so, so we use the 20th Century transient: 1850-2000 - # Note: When creating the fpftdyn dataset for this site it will use the + # Note: When creating the fpftdyn dataset for this site it will use the # PTCLM_sitedata/US-Ha1_dynpftdata.txt # file for land-use change and harvesting > ./PTCLMmkdata -s US-Ha1 -d $MYCSMDATA --sitegroupname AmeriFlux > mkdir $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1 > cd $MYCSMDATA/atm/datm7/CLM1PT_data/1x1pt_US-Ha1 # Copy data in NetCDF format to this directory, filenames should be YYYY-MM.nc - # The fieldnames on the file should be: + # The fieldnames on the file should be: # FLDS,FSDS,LATIXY, LONGXY, PRECTmms,PSRF,RH,TBOT,WIND,ZBOT # With units # W/m2,W/m2,degrees_N,degrees_E,mm/s, Pa, %, K, m/s, m diff --git a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst index 04fad02db2..5c269128a5 100644 --- a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst @@ -8,18 +8,18 @@ What is PTCLMmkdata? ===================== -PTCLMmkdata (pronounced Pee-Tee Cee-L-M make data is a Python script to help you set up PoinT CLM simulations. +PTCLMmkdata (pronounced Pee-Tee Cee-L-M make data is a Python script to help you set up PoinT CLM simulations. It runs the CLM tools for you to get datasets set up, and copies them to a location you can use them including the changes needed for a case to use the dataset with namelist and XML changes. Then you run **create_newcase** and point to the directory so that the namelist and XML changes are automatically applied. -PTCLMmkdata has a simple ASCII text file for storing basic information for your sites. +PTCLMmkdata has a simple ASCII text file for storing basic information for your sites. -We also have complete lists for AmeriFlux and Fluxnet-Canada sites, although we only have the meteorology data for one site. +We also have complete lists for AmeriFlux and Fluxnet-Canada sites, although we only have the meteorology data for one site. -For other sites you will need to obtain the meteorology data and translate it to a format that the CESM datm model can use. +For other sites you will need to obtain the meteorology data and translate it to a format that the CESM datm model can use. But, even without meteorology data PTCLMmkdata is useful to setup datasets to run with standard ``CLM_QIAN`` data. @@ -107,7 +107,7 @@ The output to the above command is as follows: Main Script Version Id: $Id: PTCLM.py 47576 2013-05-29 19:11:16Z erik $ Scripts URL: $HeadURL: https://svn-ccsm-models.cgd.ucar.edu/PTCLM/trunk_tags/PTCLM1_130529/PTCLM.py $: -Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. +Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ for permission information to use this data. Example 6-1. Example of running PTCLMmkdata for US-UMB on cheyenne @@ -118,7 +118,7 @@ Example 6-1. Example of running PTCLMmkdata for US-UMB on cheyenne > setenv MYDATAFILES `pwd`/mydatafiles > setenv SITE US-UMB > setenv MYCASE testPTCLM - + # Next build all of the clm tools you will need > cd $CTSMROOT/tools/PTCLM > buildtools diff --git a/doc/source/users_guide/running-PTCLM/ptclm-examples.rst b/doc/source/users_guide/running-PTCLM/ptclm-examples.rst index e36b1e686a..8b341c89ae 100644 --- a/doc/source/users_guide/running-PTCLM/ptclm-examples.rst +++ b/doc/source/users_guide/running-PTCLM/ptclm-examples.rst @@ -13,7 +13,7 @@ Now, let's demonstrate using a different group list, doing a spinup, running wit Example: Running PTCLMmkdata without tower years ------------------------------------------------ :: - + > cd $CTSMROOT/tools/PTCLM > ./PTCLMmkdata -s US-Ha1 -d $CSMDATA --sitegroupname AmeriFlux --donot_use_tower_yrs > cd ../../../../../US-Ha1_ICRUCLM45BGC_QIAN diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst index e657608b67..9085ac19d6 100644 --- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/using-ptclm.rst @@ -9,13 +9,13 @@ Using PTCLMmkdata There are two types of options to PTCLMmkdata: required and optional. The three required options are the three settings that MUST be specified for PTCLMmkdata to work at all. The other settings have default values that will default to something useful. Most options use a double dash "--" "longname" such as "--list", but the most common options also have a short-name with a single dash. -The required options to PTCLMmkdata are: inputdata directory (-d) and site-name (-s). +The required options to PTCLMmkdata are: inputdata directory (-d) and site-name (-s). Inputdata directory is the directory where you have the CESM inputdata files. Finally site-name is the name of the site that you want to run for. Site-name is a Fluxnet site name from the list of sites you are running on (see the --sitegroupname for more information about the site lists). After PTCLMmkdata is run you can run **create_newcase** to setup a case to use the datasets created. It also creates a ``README.PTCLM`` in that directory that documents the commandline options to PTCLMmkdata that were used to create it. -After "help" the "list" option is one of the most useful options for getting help on using PTCLMmkdata. +After "help" the "list" option is one of the most useful options for getting help on using PTCLMmkdata. This option gives you information about some of the other options to PTCLMmkdata. To get a list of the sites that can be used for PTCLMmkdata use the "--list" option as follows. :: @@ -41,12 +41,12 @@ Steps in running PTCLMmkdata 2. Run PTCLMmkdata Next you actually run PTCLMmkdata which does the different things listed below: - a. PTCLMmkdata names your output file directory based on your input + a. PTCLMmkdata names your output file directory based on your input :: [Prefix_]SiteCode - Where: + Where: ``Prefix`` is from the caseidprefix option (or blank if not used). ``SiteCode`` is the site name you entered with the -s option. @@ -61,10 +61,10 @@ Steps in running PTCLMmkdata It will populate $MYCSMDATA with new datasets it creates using the CLM tools. c. If a transient compset and PTCLMmkdata finds a _dynpftdata.txt file - If you are running a transient compset (such as the "I_1850-2000_CN" compset) AND you there is a file in the PTCLM_sitedata directory under the PTCLMmkdata directory called $SITE_dynpftdata.txt it will use this file for the land-use changes. - Otherwise it will leave land-use constant, unless you use the pftgrid option so it uses the global dataset for landuse changes. - See the Section called Dynamic Land-Use Change Files for use by PTCLMmkdata for more information on this. - There is a sample transient dataset called US-Ha1_dynpftdata.txt. + If you are running a transient compset (such as the "I_1850-2000_CN" compset) AND you there is a file in the PTCLM_sitedata directory under the PTCLMmkdata directory called $SITE_dynpftdata.txt it will use this file for the land-use changes. + Otherwise it will leave land-use constant, unless you use the pftgrid option so it uses the global dataset for landuse changes. + See the Section called Dynamic Land-Use Change Files for use by PTCLMmkdata for more information on this. + There is a sample transient dataset called US-Ha1_dynpftdata.txt. Transient compsets, are compsets that create transient land-use change and forcing conditions such as: 'I_1850-2000', 'I_1850-2000_CN', 'I_RCP8.5_CN', 'I_RCP6.0_CN', 'I_RCP4.5_CN', or 'I_RCP2.6_CN'. d. PTCLMmkdata creates a pft-physiology for you @@ -93,7 +93,7 @@ Configure options include: This option is for running PTCLMmkdata with a different root directory to CESM than the version PTCLMmkdata exists in. Normally you do NOT need to use this option. ``--sitegroupname`` - In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. + In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. These site groups are all separate ASCII files with the same prefix followed by a "_*data.txt" name. See `the Section called PTCLMmkdata Group Site Lists `_ for more information on these files. By default we have provided three different valid group names: EXAMPLE @@ -102,10 +102,10 @@ AmeriFlux Fluxnet-Canada -The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. -The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. -You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. -Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. +The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. +The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. +You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. +Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ with permission information to use the US-UMB data. ``--donot_use_tower_yrs`` diff --git a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst index b5ce4eadb7..9dcdd51ac4 100644 --- a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst @@ -6,7 +6,7 @@ Running a single point using global data - PTS_MODE **************************************************** -``PTS_MODE`` enables you to run the model using global datasets, but just picking a single point from those datasets and operating on it. +``PTS_MODE`` enables you to run the model using global datasets, but just picking a single point from those datasets and operating on it. It can be a very quick way to do fast simulations and get a quick turnaround. To setup a ``PTS_MODE`` simulation you use the "-pts_lat" and "-pts_lon" arguments to **create_newcase** to give the latitude and longitude of the point you want to simulate for (the code will pick the point on the global grid nearest to the point you give. Here's an example to setup a simulation for the nearest point at 2-degree resolution to Boulder Colorado. @@ -29,11 +29,11 @@ Then setup, build and run as normal. We make sure initial conditions are NOT use Running in a single processor ============================== -Note, that when running with ``PTS_MODE`` the number of processors is automatically set to one. -When running a single grid point you can only use a single processor. +Note, that when running with ``PTS_MODE`` the number of processors is automatically set to one. +When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to ``TRUE`` so that you can also run interactively without having to use MPI to start up your job. -On many machines, batch queues have a minimum number of nodes or processors that can be used. -On these machines you may have to change the queue and possibly the time-limits of the job, to get it to run in the batch queue. -On the NCAR machine, cheyenne, this is done for you automatically, and the "share" or "caldera" queue is used for such single-processor simulations. +On many machines, batch queues have a minimum number of nodes or processors that can be used. +On these machines you may have to change the queue and possibly the time-limits of the job, to get it to run in the batch queue. +On the NCAR machine, cheyenne, this is done for you automatically, and the "share" or "caldera" queue is used for such single-processor simulations. For single point mode you also may want to consider using a smaller workstation or cluster, rather than a super-computer, because you can't take advantage of the multi-processing power of the super-computer anyway. diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index 4705148f8c..1d2ac37a48 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -6,7 +6,7 @@ Running Single Point Configurations ****************************************** -In addition to ``PTS_MODE``, CLM supports running using single-point or regional datasets that are customized to a particular region. +In addition to ``PTS_MODE``, CLM supports running using single-point or regional datasets that are customized to a particular region. CLM supports a a small number of out-of-the-box single-point and regional datasets. However, users can create their own dataset. @@ -22,10 +22,10 @@ Which results in the following: CLM build-namelist - valid values for res (Horizontal resolutions Note: 0.5x0.5, 5x5min, 10x10min, 3x3min and 0.33x0.33 are only used for CLM tools): - Values: default 512x1024 360x720cru 128x256 64x128 48x96 32x64 8x16 94x192 \ - 0.23x0.31 0.47x0.63 0.9x1.25 1.9x2.5 2.5x3.33 4x5 10x15 5x5_amazon 1x1_tropicAtl \ - 1x1_vancouverCAN 1x1_mexicocityMEX 1x1_asphaltjungleNJ 1x1_brazil 1x1_urbanc_alpha 1x1_numaIA \ - 1x1_smallvilleIA 0.5x0.5 3x3min 5x5min 10x10min 0.33x0.33 ne4np4 ne16np4 ne30np4 ne60np4 \ + Values: default 512x1024 360x720cru 128x256 64x128 48x96 32x64 8x16 94x192 \ + 0.23x0.31 0.47x0.63 0.9x1.25 1.9x2.5 2.5x3.33 4x5 10x15 5x5_amazon 1x1_tropicAtl \ + 1x1_vancouverCAN 1x1_mexicocityMEX 1x1_asphaltjungleNJ 1x1_brazil 1x1_urbanc_alpha 1x1_numaIA \ + 1x1_smallvilleIA 0.5x0.5 3x3min 5x5min 10x10min 0.33x0.33 ne4np4 ne16np4 ne30np4 ne60np4 \ ne120np4 ne240np4 wus12 us20 Default = 1.9x2.5 (NOTE: resolution and mask and other settings may influence what the default is) @@ -40,7 +40,7 @@ Example: Running CLM over a single-point test site in Brazil > cd scripts > set SITE=1x1_brazil - > ./create_newcase -case testSPDATASET -res $SITE -compset I2000Clm50SpGs + > ./create_newcase -case testSPDATASET -res $SITE -compset I2000Clm50SpGs > cd testSPDATASET Then setup, build and run normally. @@ -54,7 +54,7 @@ Example: Running CLM over the single-point of Mexicocity Mexico with the default > cd scripts # Set a variable to the site you want to use (as it's used several times below) > set SITE=1x1_mexicocityMEX - > ./create_newcase -case testSPDATASET -res $SITE -compset I1PtClm50SpGs + > ./create_newcase -case testSPDATASET -res $SITE -compset I1PtClm50SpGs > cd testSPDATASET Then setup, build and run normally. @@ -68,21 +68,21 @@ Then setup, build and run normally. Using Supported Single-point Datasets that have their own Atmospheric Forcing ================================================================================ -Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). -Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. +Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). +Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. To turn on the atmospheric forcing for these datasets, you set the ``env_run.xml DATM_MODE`` variable to ``CLM1PT``, and then the atmospheric forcing datasets will be used for the point picked. If you use one of the compsets that has "I1Pt" in the name that will be set automatically. -When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. -If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. -However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. -In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. +When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. +If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. +However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. +In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. For the supported data points, these values are in the XML database and you can use the **queryDefaultNamelist.pl** script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha). In the example below we will show how to do this for the Vancouver, Canada point. Example: Running CLM over the single-point of Vancouver Canada with supplied atmospheric forcing data for Vancouver. -------------------------------------------------------------------------------------------------------------------------- +------------------------------------------------------------------------------------------------------------------------- :: > cd scripts @@ -123,7 +123,7 @@ Example: Running CLM over the single-point of Vancouver Canada with supplied atm Creating your own single-point dataset =================================================== -The following provides an example of setting up a case using ``CLM_USRDAT_NAME`` where you rename the files according to the ``CLM_USRDAT_NAME`` convention. +The following provides an example of setting up a case using ``CLM_USRDAT_NAME`` where you rename the files according to the ``CLM_USRDAT_NAME`` convention. We have an example of such datafiles in the repository for a specific region over Alaska (actually just a sub-set of the global f19 grid). Example: Using CLM_USRDAT_NAME to run a simulation using user datasets for a specific region over Alaska @@ -173,7 +173,7 @@ Example: Creating a surface dataset for a single point > setenv OCNDOM domain.ocn_noocean.nc > setenv ATMDOM domain.lnd.{$GRIDNAME}_noocean.nc > ./gen_domain -m $MAPFILE -o $OCNDOM -l $ATMDOM - # Save the location where the domain file was created + # Save the location where the domain file was created > setenv GENDOM_PATH `pwd` # Finally create the surface dataset > cd ../../../../lnd/clm/tools/|version|/mksurfdata_map/src @@ -189,11 +189,11 @@ Example: Setting up a case from the single-point surface dataset just created # First setup an environment variable that points to the top of the CESM directory. > setenv CESMROOT - # Next make sure you have a inputdata location that you can write to + # Next make sure you have a inputdata location that you can write to # You only need to do this step once, so you won't need to do this in the future > setenv MYCSMDATA $HOME/inputdata # Set env var for the directory for input data > ./link_dirtree $CSMDATA $MYCSMDATA - # Copy the file you created above to your new $MYCSMDATA location following the CLMUSRDAT + # Copy the file you created above to your new $MYCSMDATA location following the CLMUSRDAT # naming convention (leave off the creation date) > cp $CESMROOT/$CTSMROOT/tools/mksurfdata_map/surfdata_${GRIDNAME}_simyr1850_$CDATE.nc \ $MYCSMDATA/lnd/clm2/surfdata_map/surfdata_${GRIDNAME}_simyr1850.nc diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst index 9564b1649c..f0adaa0e0c 100644 --- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst +++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst @@ -6,8 +6,8 @@ Single and Regional Grid Configurations ***************************************** -CLM allows you to set up and run cases with a single-point or a local region as well as global resolutions. -This is often useful for running quick cases for testing, evaluating specific vegetation types, or land-units, or running with observed data for a specific site. +CLM allows you to set up and run cases with a single-point or a local region as well as global resolutions. +This is often useful for running quick cases for testing, evaluating specific vegetation types, or land-units, or running with observed data for a specific site. There are three different ways to do this for normal-supported site @@ -28,26 +28,26 @@ There are three different ways to do this for normal-supported site Choosing the right single point options ========================================= -Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see `the Section called Running Supported Single-point/Regional Datasets `_). -All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. -The problem is that there is a very limited set of supported datasets. +Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see `the Section called Running Supported Single-point/Regional Datasets `_). +All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. +The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region. -In general `the Section called Running PTS_MODE configurations `_ is the quick and dirty method that gets you started without having to create datasets -- but has limitations. -It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. +In general `the Section called Running PTS_MODE configurations `_ is the quick and dirty method that gets you started without having to create datasets -- but has limitations. +It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts. -Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see `the Section called Creating your own single-point/regional surface datasets `_). -With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. -However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. +Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see `the Section called Creating your own single-point/regional surface datasets `_). +With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. +However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method. -Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. -It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. +Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. +It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter `Chapter 6 `_. -Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. -You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. -You may also need to modify DATM to use your forcing data. +Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. +You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. +You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. In the PTCLMmkdata chapter `the Section called Converting AmeriFlux Data for use by PTCLMmkdata in Chapter 6 `_ section tells you how to use AmeriFlux data for atmospheric forcing. diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst index 9883662a4b..f763a6a9fc 100644 --- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst +++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst @@ -6,29 +6,29 @@ Running with historical CO2 forcing ===================================== -In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. -For this example, we will start with the "I_1850-2000_CN" compset that has transient: land-use, Nitrogen and Aerosol deposition already. -You could also use another compset if you didn't want these other features to be transient. -In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the user_nl_datm file. +In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. +For this example, we will start with the "I_1850-2000_CN" compset that has transient: land-use, Nitrogen and Aerosol deposition already. +You could also use another compset if you didn't want these other features to be transient. +In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the user_nl_datm file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file. .. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide `_ especially as it pertains to the datm. .. warning:: This section documents the process for doing something that is non-standard. There may be errors with the documentation and process, and you may have to do some work before all of this works for you. If that is the case, we recommend that you do further research into understanding the process and the files, as well as understanding the datm and how it works. You may have to read documentation found in the code for datm as well as "csm_share". -The datm has "streams" files that have rough XML-like syntax and specify the location and file to get data from, as well as information on the variable names and the data locations of the grid points. -The datm expects specific variable names and the datm "maps" the expected variable names from the file to the names expected by datm. -The file we are working with here is a file with a single-point, that covers the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 degrees in longitude). -Since it's a single point it's a little easier to work with than datasets that may be at a given horizontal resolution. -The datm also expects that variables will be in certain units, and only expects a limited number of variables so arbitrary fields can NOT be exchanged this way. +The datm has "streams" files that have rough XML-like syntax and specify the location and file to get data from, as well as information on the variable names and the data locations of the grid points. +The datm expects specific variable names and the datm "maps" the expected variable names from the file to the names expected by datm. +The file we are working with here is a file with a single-point, that covers the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 degrees in longitude). +Since it's a single point it's a little easier to work with than datasets that may be at a given horizontal resolution. +The datm also expects that variables will be in certain units, and only expects a limited number of variables so arbitrary fields can NOT be exchanged this way. However, the process would be similar for datasets that do contain more than one point. -The three things that are needed: a domain file, a data file, and a streams text file. -The domain file is a CF-compliant NetCDF file that has information on the grid points (latitudes and longitudes for cell-centers and vertices, mask , fraction, and areas). -The datafile is a CF-compliant NetCDF file with the data that will be mapped. +The three things that are needed: a domain file, a data file, and a streams text file. +The domain file is a CF-compliant NetCDF file that has information on the grid points (latitudes and longitudes for cell-centers and vertices, mask , fraction, and areas). +The datafile is a CF-compliant NetCDF file with the data that will be mapped. The streams text file is the XML-like file that tells datm how to find the files and how to map the variables datm knows about to the variable names on the NetCDF files. Note, that in our case the domain file and the data file are the same file. In other cases, the domain file may be separate from the data file. -First we are going to create a case, and we will edit the ``user_nl_datm`` so that we add a CO2 data stream in. +First we are going to create a case, and we will edit the ``user_nl_datm`` so that we add a CO2 data stream in. There is a streams text file available in ``$CTSMROOT/doc/UsersGuide/co2_streams.txt``, that includes file with a CO2 time-series from 1765 to 2007. @@ -37,7 +37,7 @@ Example: Transient Simulation with Historical CO2 :: > cd scripts - > ./create_newcase -case DATM_CO2_TSERIES -res f19_g17_gl4 -compset IHistClm50BgcCrop + > ./create_newcase -case DATM_CO2_TSERIES -res f19_g17_gl4 -compset IHistClm50BgcCrop > cd DATM_CO2_TSERIES # Historical CO2 will already be setup correctly for this compset diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst index 12903a18b5..17e2e11d5c 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst @@ -6,10 +6,10 @@ Running with MOAR data ======================== -Because it takes so long to spinup the CN model (as we just saw previously), if you are doing fully coupled simulations with active atmosphere and ocean, you will want to do the spinup portion of this "offline". +Because it takes so long to spinup the CN model (as we just saw previously), if you are doing fully coupled simulations with active atmosphere and ocean, you will want to do the spinup portion of this "offline". So instead of doing expensive fully coupled simulations for the spinup duration, you run CLM in a very cheap "I" compset using atmospheric forcing from a shorter fully coupled simulation (or a simulation run previously by someone else). -In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on cheyenne. +In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on cheyenne. There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to `Example 4-11 `_. Example: Simulation with MOAR Data on cheyenne @@ -21,7 +21,7 @@ Example: Simulation with MOAR Data on cheyenne > cd MOARforce1850 # The following sets the casename to point to for atm forcing (you could also use an editor) > ./xmlchange DATM_CPL_CASE=b40.1850.track1.1deg.006a - # The following sets the align year and years to run over for atm forcing + # The following sets the align year and years to run over for atm forcing # (you could also use an editor) > ./xmlchange DATM_CPL_YR_ALIGN=1,DATM_CPL_YR_START=960,DATM_CPL_YR_END=1030 > ./case.setup diff --git a/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst b/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst index 10af089814..06429688d4 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst @@ -5,7 +5,7 @@ ============================== Running with anomaly forcing ============================== -Because performing fully coupled climate simulations is computationally expensive, an alternate method of running land-only simulations forced by future climate projections was developed for CTSM called 'anomaly forcing'. The anomaly forcing method uses a previously completed fully coupled simulation to create monthly anomalies, relative to the present day, of near-surface atmospheric states and fluxes. These anomalies, representing the evolution of future climate projections, are applied to a repeating cycle of present day atmospheric forcing data, either as an additive (for states) or multiplicative (for fluxes) quantity. Thus, high-frequency variability is obtained from the present day atmospheric forcing data, while the long-term evolution of the climate is determined by the anomaly forcing dataset. +Because performing fully coupled climate simulations is computationally expensive, an alternate method of running land-only simulations forced by future climate projections was developed for CTSM called 'anomaly forcing'. The anomaly forcing method uses a previously completed fully coupled simulation to create monthly anomalies, relative to the present day, of near-surface atmospheric states and fluxes. These anomalies, representing the evolution of future climate projections, are applied to a repeating cycle of present day atmospheric forcing data, either as an additive (for states) or multiplicative (for fluxes) quantity. Thus, high-frequency variability is obtained from the present day atmospheric forcing data, while the long-term evolution of the climate is determined by the anomaly forcing dataset. To enable anomaly forcing in a CTSM simulation, the following namelist variable can be added to the user\_nl\_datm file: @@ -15,7 +15,7 @@ Any combination or subset of forcing variables can be used, e.g. to modify only anomaly\_forcing = 'Anomaly.Forcing.Temperature' -which will only adjust the temperature (TBOT). +which will only adjust the temperature (TBOT). After the namelist has been created, the run directory will be populated with files such as these: diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst index 34bb12ab49..2810cc477f 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst @@ -6,7 +6,7 @@ Running with atmospheric forcing from a previous simulation ============================================================= -Another way that you might want to spinup the model is to run your own simulation for a relatively short period (either a B, E, or F compset) and then use it as forcing for your "I" case later. +Another way that you might want to spinup the model is to run your own simulation for a relatively short period (either a B, E, or F compset) and then use it as forcing for your "I" case later. By only running 20 to 50 years for the fully coupled case, you'll save a substantial amount of computer time rather than running the entire spinup period with a fully coupled model. The first thing we need to do is to run a fully coupled case and save the atmospheric coupling fields on a three hourly basis. In this example, we will run on cheyenne and archive the data to a local disk that we can then use in the next simulation. @@ -19,7 +19,7 @@ Example: Fully Coupled Simulation to Create Data to Force Next Example Simulatio > ./create_newcase -case myB1850 -res f09_g17_gl4 -compset B1850 > cd myB1850 > ./case.setup - # Set histaux_a2x3hr to .true. in your user_nl_cpl output from the atmosphere model + # Set histaux_a2x3hr to .true. in your user_nl_cpl output from the atmosphere model # will be saved 3 hourly echo "histaux_a2x3hr=.true." >> user_nl_cpl # edit the driver code in order to save the correct list of fields (see note below) @@ -29,7 +29,7 @@ Example: Fully Coupled Simulation to Create Data to Force Next Example Simulatio > ./case.build # The following sets the archival disk space (you could also use an editor) > ./xmlchange DOUT_S_ROOT='/glade/home/$USER/$CASE' - # Make sure files are archived to disk, but NOT to long term storage + # Make sure files are archived to disk, but NOT to long term storage # (you could also use an editor) > ./xmlchange DOUT_S=TRUE,DOUT_L_MS=FALSE # Set the run length to run a total of 20 years (you could also use an editor) @@ -48,7 +48,7 @@ Example: Simulation Forced with Data from the Previous Simulation > cd frcWmyB1850 # The following sets the casename to point to for atm forcing (you could also use an editor) > ./xmlchange DATM_CPLHIST_CASE="myB1850" - # The following sets the align year and years to run over for atm forcing + # The following sets the align year and years to run over for atm forcing # (you could also use an editor) > ./xmlchange DATM_CPLHIST_YR_ALIGN="1",DATM_CPLHIST_YR_START=1,DATM_CPLHIST_YR_END=20 # Set the strm_datdir in the namelist_defaults_datm.xml diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst index d6b6c74d91..806535fa91 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst @@ -6,15 +6,15 @@ Spinning up the Satellite Phenology Model =========================================== -To spin-up the CLMSP model you merely need to run CLMSP for about 50 simulation years starting from arbitrary initial conditions. -You then use the final restart file for initial conditions in other simulations. -Because, this is a straight forward operation we will NOT give the details on how to do that here, but leave it as an exercise for the reader. +To spin-up the CLMSP model you merely need to run CLMSP for about 50 simulation years starting from arbitrary initial conditions. +You then use the final restart file for initial conditions in other simulations. +Because, this is a straight forward operation we will NOT give the details on how to do that here, but leave it as an exercise for the reader. See the `Example 4-7 `_ as an example of doing this as the last step for CLMCN. You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure SP spinup plot for 1850` shows spinup behavior for an 1850 SP case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), -initialized with an initial file generated from a GSWP3 atmospheric forcing case. Note that it takes less than 10 years for state variables -such as FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), H2OSOI (soil water), and TSOI (soil temperature) to reach +initialized with an initial file generated from a GSWP3 atmospheric forcing case. Note that it takes less than 10 years for state variables +such as FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), H2OSOI (soil water), and TSOI (soil temperature) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. TWS (total water storage) may take a bit longer. .. _Figure SP spinup plot for 1850: @@ -23,7 +23,7 @@ a specified equilibrium state (denoted by the dotted lines) due to the different SP spinup plot for year 1850. Variables examined are FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), TWS (total water storage), H2OSOI (volumetric soil water in layer 8) and TSOI (soil temperature in layer 10). Generated using .../tools/contrib/SpinupStability_SP.ncl. -:numref:`Figure SP spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). +:numref:`Figure SP spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). Again, it takes about 10 years to reach equilibrium. .. _Figure SP spinup plot for 2000 CO2: diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 2ce977fc7e..af51426195 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -6,8 +6,8 @@ Spinup of |version|-BGC-Crop ========================== -To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM **configure**, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 -BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in +To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM **configure**, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 +BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. .. _Figure BGC AD spinup plot for 1850 GSWP3: @@ -20,7 +20,7 @@ After this you branch from this mode in the "final spinup" (-bgc_spinup off in C :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this -criteria depending on their application. +criteria depending on their application. .. _Figure BGC pAD spinup plot for 1850 GSWP3: @@ -48,14 +48,14 @@ Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. BGC initialized spinup plot for year 2000 CO2. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. -If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon -equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to -reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a +If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon +equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to +reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a bit of leaf carbon to give those plant functional types another chance to grow under the new atmospheric forcing or model conditions. **1. |version| accelerated-decomposition (AD) spinup** For the first step of running 200+ years in "-bgc_spinup on" mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following: - + Example:: AD_SPINUP Simulation for |version|-BGC -------------------------------------------------------- :: @@ -113,4 +113,4 @@ To assess if the model is spunup, plot trends for CLMBGC variables of interest u .. note:: This same final spinup procedure works for |version|-CN as well. - + diff --git a/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst b/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst index 20ea12e91f..db5fcdd793 100644 --- a/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst +++ b/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst @@ -7,8 +7,8 @@ =================================== The prognostic crop model is setup to work with CLM4.0, CLM4.5 or |version| with either BGC or CN (with or without DV). -In order to use the initial condition file, we need to set the ``RUN_TYPE`` to startup rather than ``hybrid`` since the compset for f19 sets up to use an initial condition file without crop active. -To activate the crop model you can choose a compset that has "Crop" in the name such as "I1850Clm50BgcCropCru" or simply add +In order to use the initial condition file, we need to set the ``RUN_TYPE`` to startup rather than ``hybrid`` since the compset for f19 sets up to use an initial condition file without crop active. +To activate the crop model you can choose a compset that has "Crop" in the name such as "I1850Clm50BgcCropCru" or simply add "-crop" to ``CLM_BLDNML_OPTS`` (or for CLM4.0 add "-crop on" to ``CLM_CONFIG_OPTS``). Example: Crop Simulation @@ -16,7 +16,7 @@ Example: Crop Simulation :: > cd scripts - > ./create_newcase -case CROP -res f19_g17_gl4 -compset I1850Clm50BgcCropCru + > ./create_newcase -case CROP -res f19_g17_gl4 -compset I1850Clm50BgcCropCru > cd CROP > ./case.setup diff --git a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst index aa99179971..564e363b2d 100644 --- a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst +++ b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst @@ -11,7 +11,7 @@ In CLM4.5 irrigation can ONLY be used WITH crop. With CLM5.0 irrigation can be u if crop is off, your surface datasets **HAVE** to have irrigation defined appropriately. Right now *ALL* surface datasets without crop enabled have irrigation hard-wired on. In order to create datasets with irrigation off, you'd need to make changes to ``mksurfdata_map`` in order to have all generic crops to be non-irrigated. -To turn on irrigation in |version| we simply add "-irrig on" to ``CLM_BLDNML_OPTS``. +To turn on irrigation in |version| we simply add "-irrig on" to ``CLM_BLDNML_OPTS``. Example: Irrigation Simulation ------------------------------------------ diff --git a/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst b/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst index 5a42858818..63423e211a 100644 --- a/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst +++ b/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst @@ -6,8 +6,8 @@ What is a special case? ========================= -All of the following special cases cases that take more than one step to do. -The straightforward cases have compsets and/or build-namelist use-cases setup for them or require simple editing of a single-case. +All of the following special cases cases that take more than one step to do. +The straightforward cases have compsets and/or build-namelist use-cases setup for them or require simple editing of a single-case. All of the cases here require you to do at least two simulations with different configurations, or require more complex editing of the case (changing the streams files). .. note:: The cases in this chapter are more sophisticated and require more technical knowledge and skill than cases in previous chapters. The user should be very familiar with doing simple cases before moving onto the cases described here. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index c2bb0b606b..adafbe66d9 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -6,15 +6,15 @@ Choosing a compset ==================== -When setting up a new case one of the first choices to make is which "component set" (or compset) to use. -The compset refers to which component models are used as well as specific settings for them. -We label the different types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). -The compsets of interest when working with CLM are the "I" compsets (which contain CLM with a data atmosphere model and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain CLM with the active atmosphere model (CAM), prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. +When setting up a new case one of the first choices to make is which "component set" (or compset) to use. +The compset refers to which component models are used as well as specific settings for them. +We label the different types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). +The compsets of interest when working with CLM are the "I" compsets (which contain CLM with a data atmosphere model and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain CLM with the active atmosphere model (CAM), prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. Below we go into details on the "I" compsets which emphasize CLM as the only active model, and just mention the two other categories. To run CLM coupled to CAM ("E" or "F" compsets) or fully coupled ("B compsets) you need to be running CLM from a CESM checkout rather than a CTSM checkout (see :ref:`ctsm_vs_cesm_checkout`). -When working with CLM you usually want to start with a relevant "I" compset before moving to the more complex cases that involve other active model components. +When working with CLM you usually want to start with a relevant "I" compset before moving to the more complex cases that involve other active model components. The "I" compsets can exercise CLM in a way that is similar to the coupled modes, but with much lower computational cost and faster turnaround times. Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) @@ -23,7 +23,7 @@ Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) `Supported CLM Configurations `_ are listed in `Table 1-1 `_ for the Scientifically Supported compsets (have been scientifically validated with long simulations) and in `Table 1-2 `_ for the Functionally Supported compsets (we've only checked that they function). -Here is the entire list of compsets available. +Here is the entire list of compsets available. `CESM compsets `_ @@ -43,6 +43,6 @@ Fully coupled compsets are compsets that start with "B" in the name. They are de Conclusion to choosing a compset -------------------------------- -We've introduced the basic type of compsets that use CLM and given some further details for the "standalone CLM" (or "I" compsets). -The `$CTSMROOT/cime_config/config_compsets.xml `_ lists all of the compsets and gives a full description of each of them. +We've introduced the basic type of compsets that use CLM and given some further details for the "standalone CLM" (or "I" compsets). +The `$CTSMROOT/cime_config/config_compsets.xml `_ lists all of the compsets and gives a full description of each of them. In the next section we look into customizing the setup time options for compsets using CLM. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index 08041c522a..94958a8ed3 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -6,7 +6,7 @@ Customizing CLM's Configuration ******************************** -The section of the |cesmrelease| Quickstart `CESM Create a Case `_ gives instructions on creating a case. +The section of the |cesmrelease| Quickstart `CESM Create a Case `_ gives instructions on creating a case. Also see a similar section in the CIME User's-Guide `CIME Create a case `_. What is of interest here is how to customize your use of CLM for the case that you created. @@ -46,12 +46,12 @@ For the precedence of the different options to **build-namelist** see the sectio The first item ``CLM_CONFIG_OPTS`` has to do with customizing the CLM build-time options for your case, the rest all have to do with generating the namelist. CLM_CONFIG_OPTS - The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. - It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. - You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. - Hence, we recommend using the "-append" option to the xmlchange script. - In `the Section called More information on the CLM configure script `_ below we will go into more details on options that can be customized in the CLM "**configure**" script. - It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). + The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. + It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. + You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. + Hence, we recommend using the "-append" option to the xmlchange script. + In `the Section called More information on the CLM configure script `_ below we will go into more details on options that can be customized in the CLM "**configure**" script. + It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). The options to CLM **configure** are given with the "-help" option which is given in `the Section called More information on the CLM configure script `_. .. note:: ``CLM_CONFIG_OPTS`` is locked after the **case.build** script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun **case.build**. The other env variables can be changed at run-time so are never locked. @@ -65,46 +65,46 @@ CLM_NML_USE_CASE The output of the above command is: :: - CLM build-namelist - use cases: 1850-2100_rcp2.6_glacierMEC_transient 1850-2100_rcp2.6_transient \ - 1850-2100_rcp4.5_glacierMEC_transient 1850-2100_rcp4.5_transient \ - 1850-2100_rcp6_glacierMEC_transient 1850-2100_rcp6_transient \ - 1850-2100_rcp8.5_glacierMEC_transient 1850-2100_rcp8.5_transient 1850_control \ - 1850_glacierMEC_control 2000-2100_rcp8.5_transient 2000_control 2000_glacierMEC_control \ + CLM build-namelist - use cases: 1850-2100_rcp2.6_glacierMEC_transient 1850-2100_rcp2.6_transient \ + 1850-2100_rcp4.5_glacierMEC_transient 1850-2100_rcp4.5_transient \ + 1850-2100_rcp6_glacierMEC_transient 1850-2100_rcp6_transient \ + 1850-2100_rcp8.5_glacierMEC_transient 1850-2100_rcp8.5_transient 1850_control \ + 1850_glacierMEC_control 2000-2100_rcp8.5_transient 2000_control 2000_glacierMEC_control \ 20thC_glacierMEC_transient 20thC_transient glacierMEC_pd stdurbpt_pd Use cases are:... - - 1850-2100_rcp2.6_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ + + 1850-2100_rcp2.6_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ with historical data from 1850 to 2005 and then with the RCP2.6 scenario from IMAGE - - 1850-2100_rcp2.6_transient = Simulate transient land-use, and aerosol deposition changes with \ + + 1850-2100_rcp2.6_transient = Simulate transient land-use, and aerosol deposition changes with \ historical data from 1850 to 2005 and then with the RCP2.6 scenario from IMAGE - - 1850-2100_rcp4.5_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ + + 1850-2100_rcp4.5_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ with historical data from 1850 to 2005 and then with the RCP4.5 scenario from MINICAM - - 1850-2100_rcp4.5_transient = Simulate transient land-use, and aerosol deposition changes with \ + + 1850-2100_rcp4.5_transient = Simulate transient land-use, and aerosol deposition changes with \ historical data from 1850 to 2005 and then with the RCP4.5 scenario from MINICAM - - 1850-2100_rcp6_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ + + 1850-2100_rcp6_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ with historical data from 1850 to 2005 and then with the RCP6 scenario from AIM - - 1850-2100_rcp6_transient = Simulate transient land-use, and aerosol deposition changes with \ + + 1850-2100_rcp6_transient = Simulate transient land-use, and aerosol deposition changes with \ historical data from 1850 to 2005 and then with the RCP6 scenario from AIM - - 1850-2100_rcp8.5_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ + + 1850-2100_rcp8.5_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes \ with historical data from 1850 to 2005 and then with the RCP8.5 scenario from MESSAGE - - 1850-2100_rcp8.5_transient = Simulate transient land-use, and aerosol deposition changes with \ + + 1850-2100_rcp8.5_transient = Simulate transient land-use, and aerosol deposition changes with \ historical data from 1850 to 2005 and then with the RCP8.5 scenario from MESSAGE - + 1850_control = Conditions to simulate 1850 land-use 1850_glacierMEC_control = Running an IG case for 1850 conditions with the ice sheet model glimmer - 2000-2100_rcp8.5_transient = Simulate transient land-use, and aerosol deposition changes with \ + 2000-2100_rcp8.5_transient = Simulate transient land-use, and aerosol deposition changes with \ historical data from 2000 to 2005 and then with the RCP8.5 scenario from MESSAGE - + 2000_control = Conditions to simulate 2000 land-use 2000_glacierMEC_control = Running an IG case for 2000 conditions with the ice sheet model glimmer - 20thC_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes from 1850 \ + 20thC_glacierMEC_transient = Simulate transient land-use, and aerosol deposition changes from 1850 \ to 2005 20thC_transient = Simulate transient land-use, and aerosol deposition changes from 1850 to 2005 glacierMEC_pd = Running an IG case with the ice sheet model glimmer @@ -113,7 +113,7 @@ CLM_NML_USE_CASE .. note::See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. CLM_BLDNML_OPTS - The option CLM_BLDNML_OPTS is for passing options to the CLM "build-namelist" script. + The option CLM_BLDNML_OPTS is for passing options to the CLM "build-namelist" script. As with the CLM "configure" script the CLM $CTSMROOT/cime_config/buildnml may already invoke certain options and as such those options will NOT be available to be set here. The best way to see what options can be sent to the "build-namelist" script is to do :: @@ -128,26 +128,26 @@ CLM_BLDNML_OPTS Create the namelist for CLM OPTIONS - -[no-]chk_res Also check [do NOT check] to make sure the resolution and + -[no-]chk_res Also check [do NOT check] to make sure the resolution and land-mask is valid. -clm_demand "list" List of variables to require on clm namelist besides the usuals. "-clm_demand list" to list valid options. (can include a list member "null" which does nothing) -clm_startfile "file" CLM restart file to start from. - -clm_start_type "type" Start type of simulation + -clm_start_type "type" Start type of simulation (default, cold, arb_ic, startup, continue, or branch) (default=do the default type for this configuration) (cold=always start with arbitrary initial conditions) - (arb_ic=start with arbitrary initial conditions if + (arb_ic=start with arbitrary initial conditions if initial conditions don't exist) (startup=ensure that initial conditions are being used) - -clm_usr_name "name" Dataset resolution/descriptor for personal datasets. + -clm_usr_name "name" Dataset resolution/descriptor for personal datasets. Default: not used Example: 1x1pt_boulderCO_c090722 to describe location, number of pts, and date files created -co2_type "value" Set CO2 the type of CO2 variation to use. -co2_ppmv "value" Set CO2 concentration to use when co2_type is constant (ppmv). - -config "filepath" Read the given CLM configuration cache file. + -config "filepath" Read the given CLM configuration cache file. Default: "config_cache.xml". -csmdata "dir" Root directory of CESM input data. Can also be set by using the CSMDATA environment variable. @@ -157,11 +157,11 @@ CLM_BLDNML_OPTS "drv_flds_in" file for the driver to pass dry-deposition to the atm. Default: -no-drydep (Note: buildnml.csh copies the file for use by the driver) - -glc_grid "grid" Glacier model grid and resolution when glacier model, - Only used if glc_nec > 0 for determining fglcmask + -glc_grid "grid" Glacier model grid and resolution when glacier model, + Only used if glc_nec > 0 for determining fglcmask Default: gland5UM (i.e. gland20, gland10 etcetera) - -glc_nec Glacier number of elevation classes [0 | 3 | 5 | 10 | 36] + -glc_nec Glacier number of elevation classes [0 | 3 | 5 | 10 | 36] (default is 0) (standard option with land-ice model is 10) -glc_smb Only used if glc_nec > 0 If .true., pass surface mass balance info to GLC @@ -170,10 +170,10 @@ CLM_BLDNML_OPTS -help [or -h] Print usage to STDOUT. -ignore_ic_date Ignore the date on the initial condition files when determining what input initial condition file to use. - -ignore_ic_year Ignore just the year part of the date on the initial condition files + -ignore_ic_year Ignore just the year part of the date on the initial condition files when determining what input initial condition file to use. - -infile "filepath" Specify a file (or list of files) containing namelists to - read values from. + -infile "filepath" Specify a file (or list of files) containing namelists to + read values from. If used with a CLM build with multiple ensembles (ninst_lnd>1) and the filename entered is a directory to files of the @@ -188,14 +188,14 @@ CLM_BLDNML_OPTS file specified. -irrig "value" If .true. turn irrigation on with namelist logical irrigate (for |version| physics) - (requires crop to be on in the clm configuration) + (requires crop to be on in the clm configuration) Seek surface datasets with irrigation turned on. (for CLM4.0 physics) Default: .false. -l_ncpl "LND_NCPL" Number of CLM coupling time-steps in a day. -lnd_frac "domainfile" Land fraction file (the input domain file) -mask "landmask" Type of land-mask (default, navy, gx3v5, gx1v5 etc.) "-mask list" to list valid land masks. - -namelist "namelist" Specify namelist settings directly on the commandline by supplying + -namelist "namelist" Specify namelist settings directly on the commandline by supplying a string containing FORTRAN namelist syntax, e.g., -namelist "&clm_inparm dt=1800 /" -no-megan DO NOT PRODUCE a megan_emis_nl namelist that will go into the @@ -204,7 +204,7 @@ CLM_BLDNML_OPTS (Note: buildnml.csh copies the file for use by the driver) -[no-]note Add note to output namelist [do NOT add note] about the arguments to build-namelist. - -rcp "value" Representative concentration pathway (rcp) to use for + -rcp "value" Representative concentration pathway (rcp) to use for future scenarios. "-rcp list" to list valid rcp settings. -res "resolution" Specify horizontal grid. Use nlatxnlon for spectral grids; @@ -212,7 +212,7 @@ CLM_BLDNML_OPTS in degrees for latitude and longitude respectively) "-res list" to list valid resolutions. -s Turns on silent mode - only fatal messages issued. - -sim_year "year" Year to simulate for input datasets + -sim_year "year" Year to simulate for input datasets (i.e. 1850, 2000, 1850-2000, 1850-2100) "-sim_year list" to list valid simulation years -bgc_spinup "on|off" CLM 4.5 Only. For CLM 4.0, spinup is controlled from configure. @@ -229,14 +229,14 @@ CLM_BLDNML_OPTS mode. The spinup state is saved to the restart file. - If the values match between the model and the restart - file it proceeds as directed. + If the values match between the model and the restart + file it proceeds as directed. If the restart file is in spinup mode and the model is in - normal mode, then it performs the exit spinup step - and proceeds in normal mode after that. + normal mode, then it performs the exit spinup step + and proceeds in normal mode after that. - If the restart file has normal mode and the model is in + If the restart file has normal mode and the model is in spinup, then it enters spinup. This is useful if you change a parameter and want to rapidly re-equilibrate without doing a cold start. @@ -263,10 +263,10 @@ CLM_BLDNML_OPTS 5. values from the namelist defaults file. -The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. +The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set: -1. +1. -bgc_spinup #. -chk_res @@ -336,7 +336,7 @@ will manage all crop areas as rain-fed without irrigation. > cd $CTSMROOT/doc > ../bld/build-namelist -sim_year list -``CLM_NAMELIST_OPTS`` +``CLM_NAMELIST_OPTS`` passes namelist items into one of the CLM namelists. .. note:: For character namelist items you need to use "'" as quotes for strings so that the scripts don't get confused with other quotes they use. @@ -348,20 +348,20 @@ will manage all crop areas as rain-fed without irrigation. Example, you want to set ``hist_fincl1`` to add the variable 'HK' to your history files. To do so edit ``env_run.xml`` and add a setting for ``hist_fincl1``. So do the following: :: - + > ./xmlchange CLM_NAMELIST_OPTS="hist_fincl1='HK'" For a list of the history fields available see `CLM History Fields `_. .. note::See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. -``CLM_FORCE_COLDSTART`` +``CLM_FORCE_COLDSTART`` when set to on, *requires* that your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it will use an initial condition file if it can find an appropriate one, and otherwise do a cold start. ``CLM_FORCE_COLDSTART`` is a good way to ensure that you are doing a cold start if that is what you want to do. -``CLM_USRDAT_NAME`` - Provides a way to enter your own datasets into the namelist. - The files you create must be named with specific naming conventions outlined in: `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. - To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. +``CLM_USRDAT_NAME`` + Provides a way to enter your own datasets into the namelist. + The files you create must be named with specific naming conventions outlined in: `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. + To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be: :: @@ -372,10 +372,10 @@ will manage all crop areas as rain-fed without irrigation. .. note: See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. -``CLM_CO2_TYPE`` - sets the type of input CO2 for either "constant", "diagnostic" or prognostic". - If "constant" the value from ``CCSM_CO2_PPMV`` will be used. - If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. +``CLM_CO2_TYPE`` + sets the type of input CO2 for either "constant", "diagnostic" or prognostic". + If "constant" the value from ``CCSM_CO2_PPMV`` will be used. + If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. For more information on how to send CO2 from the data atmosphere model see `the Section called Running stand-alone CLM with transient historical CO2 concentration in Chapter 4 `_. =============== @@ -413,7 +413,7 @@ Example: user_nl_clm namelist file 'FSDSVD','FSDSND','FSDSVI','FSDSNI', 'FSRVD','FSRND','FSRVI','FSRNI', 'TSA','FCTR','FCEV','QBOT','RH2M','H2OSOI', - 'H2OSNO','SOILLIQ','SOILICE', + 'H2OSNO','SOILLIQ','SOILICE', 'TSA_U', 'TSA_R', 'TREFMNAV_U', 'TREFMNAV_R', 'TREFMXAV_U', 'TREFMXAV_R', @@ -507,7 +507,7 @@ Like other datasets, if you want to use a given initial condition file to be use Other noteworthy configuration items ------------------------------------ -For running "I" cases there are several other noteworthy configuration items that you may want to work with. +For running "I" cases there are several other noteworthy configuration items that you may want to work with. Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM settings is `here `_. If you are running an B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files @@ -525,7 +525,7 @@ If you are running an B, E, or F case that doesn't use the DATM obviously the DA DATM_CPL_YR_START DATM_CPL_YR_END -``CCSM_CO2_PPMV`` +``CCSM_CO2_PPMV`` Sets the mixing ratio of CO2 in parts per million by volume for ALL CESM components to use. Note that most compsets already set this value to something reasonable. Also note that some compsets may tell the atmosphere model to override this value with either historic or ramped values. If the CCSM_BGC variable is set to something other than "none" the atmosphere model will determine CO2, and CLM will listen and use what the atmosphere sends it. On the CLM side the namelist item co2_type tells CLM to use the value sent from the atmosphere rather than a value set on it's own namelist. ``DATM_MODE`` @@ -539,21 +539,21 @@ If you are running an B, E, or F case that doesn't use the DATM obviously the DA CLM1PT CPLHISTForcing -``CLMCRUNCEP`` - The standard mode for CLM4.5 of using global atmospheric data that was developed by CRU using NCEP data from 1901 to 2010 (version 4 of this series). - See `the Section called CLMCRUNCEP mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. +``CLMCRUNCEP`` + The standard mode for CLM4.5 of using global atmospheric data that was developed by CRU using NCEP data from 1901 to 2010 (version 4 of this series). + See `the Section called CLMCRUNCEP mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. -``CLMCRUNCEPv7`` +``CLMCRUNCEPv7`` Version 7 of the CRUNCEP data from 1901 to 2016. - See `the Section called CLMCRUNCEPv7 mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. + See `the Section called CLMCRUNCEPv7 mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. ``CLMGSWP3v1`` GSWP3 version 1 forcing data based on NCEP reanalysis with bias corrections by GSWP3 from 1901 to 2010. -``CLM_QIAN`` +``CLM_QIAN`` The standard mode for CLM4.0 of using global atmospheric data that was developed by Qian et. al. for CLM using NCEP data from 1948 to 2004. See the `Section called CLM_QIAN mode and it's DATM settings `_ for more information on the DATM settings for ``CLM_QIAN`` mode. ``CLM1PT`` is for the special cases where we have single-point tower data for particular sites. Right now we only have data for three urban locations: MexicoCity Mexico, Vancouver Canada, and the urban-c alpha site. And we have data for the US-UMB AmeriFlux tower site for University of Michigan Biological Station. See `the Section called CLM1PT mode and it's DATM settings `_ for more information on the DATM settings for ``CLM1PT`` mode. ``CPLHISTForcing`` is for running with atmospheric forcing from a previous CESM simulation. See `the Section called CPLHISTForcing mode and it's DATM settings `_ for more information on the DATM settings for ``CPLHISTForcing`` mode. -``DATM_PRESAERO`` +``DATM_PRESAERO`` sets the prescribed aerosol mode for the data atmosphere model. The list of valid options include: ``clim_1850`` = constant year 1850 conditions @@ -642,23 +642,23 @@ The output to the above command is as follows: or double leading dashes. A consequence of this is that single letter options may NOT be bundled. - -bgc Build CLM with BGC package [ none | cn | cndv ] + -bgc Build CLM with BGC package [ none | cn | cndv ] (default is none). -cache Name of output cache file (default: config_cache.xml). - -cachedir Name of directory where output cache file is written + -cachedir Name of directory where output cache file is written (default: CLM build directory). -clm4me Turn Methane model: [on | off] Requires bgc=cn/cndv (Carbon Nitrogen model) (ONLY valid for |version|!) - -clm_root Root directory of clm source code + -clm_root Root directory of clm source code (default: directory above location of this script) -cppdefs A string of user specified CPP defines. Appended to Makefile defaults. e.g. -cppdefs '-DVAR1 -DVAR2' -vichydro Turn VIC hydrologic parameterizations : [on | off] (default is off) - -crop Toggle for prognostic crop model. [on | off] (default is off) + -crop Toggle for prognostic crop model. [on | off] (default is off) (can ONLY be turned on when BGC type is CN or CNDV) -comp_intf Component interface to use (ESMF or MCT) (default MCT) - -defaults Specify full path to a configuration file which will be used + -defaults Specify full path to a configuration file which will be used to supply defaults instead of the defaults in bld/config_files. This file is used to specify model configuration parameters only. Parameters relating to the build which are system dependent will @@ -666,13 +666,13 @@ The output to the above command is as follows: -exlaklayers Turn on extra lake layers (25 layers instead of 10) [on | off] (ONLY valid for |version|!) -help [or -h] Print usage to STDOUT. - -nofire Turn off wildfires for BGC setting of CN + -nofire Turn off wildfires for BGC setting of CN (default includes fire for CN) -noio Turn history output completely off (typically for testing). - -phys Value of clm4_0 or |version| (default is clm4_0) + -phys Value of clm4_0 or |version| (default is clm4_0) -silent [or -s] Turns on silent mode - only fatal messages issued. -sitespf_pt Setup for the given site specific single-point resolution. - -snicar_frc Turn on SNICAR radiative forcing calculation. [on | off] + -snicar_frc Turn on SNICAR radiative forcing calculation. [on | off] (default is off) -spinup CLM 4.0 Only. For CLM 4.5, spinup is controlled from build-namelist. Turn on given spinup mode for BGC setting of CN (level) @@ -686,11 +686,11 @@ The output to the above command is as follows: Directories containing user source code. -verbose [or -v] Turn on verbose echoing of settings made by configure. -version Echo the SVN tag name used to check out this CLM distribution. - -vsoilc_centbgc Turn on vertical soil Carbon profile, CENTURY model decomposition, \ - - split Nitrification/de-Nitrification into two mineral + -vsoilc_centbgc Turn on vertical soil Carbon profile, CENTURY model decomposition, \ + + split Nitrification/de-Nitrification into two mineral pools for NO3 and NH4 (requires clm4me Methane model), and - eliminate inconsistent duplicate soil hydraulic + eliminate inconsistent duplicate soil hydraulic parameters used in soil biogeochem. (requires either CN or CNDV) (ONLY valid for |version|!) @@ -701,5 +701,5 @@ The output to the above command is as follows: [no-vert,no-cent,no-nitrif,no-vert:no-cent] -We've given details on how to use the options in env_build.xml and env_run.xml to interact with the CLM "configure" and "build-namelist" scripts, as well as giving a good understanding of how these scripts work and the options to them. +We've given details on how to use the options in env_build.xml and env_run.xml to interact with the CLM "configure" and "build-namelist" scripts, as well as giving a good understanding of how these scripts work and the options to them. In the next section we give further details on the CLM namelist. You could customize the namelist for these options after "case.setup" is run. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst index 064d3f5979..e99a2bf8d6 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst @@ -8,8 +8,8 @@ Once a case has run **case.setup**, we can then customize the case further, by editing the run-time namelist for CLM. First let's list the definition of each namelist item and their valid values, and then we'll list the default values for them. Next for some of the most used or tricky namelist items we'll give examples of their use, and give you example namelists that highlight these features. -In the following, various examples of namelists are provided that feature the use of different namelist options to customize a case for particular uses. -Most the examples revolve around how to customize the output history fields. +In the following, various examples of namelists are provided that feature the use of different namelist options to customize a case for particular uses. +Most the examples revolve around how to customize the output history fields. This should give you a good basis for setting up your own CLM namelist. ----------------------------------------------------- @@ -114,7 +114,7 @@ Example 1-2. Default CLM Namelist Adding/removing fields on your primary history file --------------------------------------------------- -The primary history files are output monthly, and contain an extensive list of fieldnames, but the list of fieldnames can be added to using ``hist_fincl1`` or removed from by adding fieldnames to ``hist_fexcl1``. +The primary history files are output monthly, and contain an extensive list of fieldnames, but the list of fieldnames can be added to using ``hist_fincl1`` or removed from by adding fieldnames to ``hist_fexcl1``. A sample user namelist ``user_nl_clm`` adding few new fields (cosine of solar zenith angle, and solar declination) and excluding a few standard fields is (ground temperature, vegetation temperature, soil temperature and soil water).: Example 1-3. Example user_nl_clm namelist adding and removing fields on primary history file @@ -128,11 +128,11 @@ Example 1-3. Example user_nl_clm namelist adding and removing fields on primary Adding auxiliary history files and changing output frequency ------------------------------------------------------------ -The ``hist_fincl2`` through ``hist_fincl6`` set of namelist variables add given history fieldnames to auxiliary history file "streams", and ``hist_fexcl2`` through ``hist_fexcl6`` set of namelist variables remove given history fieldnames from history file auxiliary "streams". -A history "stream" is a set of history files that are produced at a given frequency. -By default there is only one stream of monthly data files. -To add more streams you add history fieldnames to ``hist_fincl2`` through ``hist_fincl6``. -The output frequency and the way averaging is done can be different for each history file stream. +The ``hist_fincl2`` through ``hist_fincl6`` set of namelist variables add given history fieldnames to auxiliary history file "streams", and ``hist_fexcl2`` through ``hist_fexcl6`` set of namelist variables remove given history fieldnames from history file auxiliary "streams". +A history "stream" is a set of history files that are produced at a given frequency. +By default there is only one stream of monthly data files. +To add more streams you add history fieldnames to ``hist_fincl2`` through ``hist_fincl6``. +The output frequency and the way averaging is done can be different for each history file stream. By default the primary history files are monthly and any others are daily. You can have up to six active history streams, but you need to activate them in order. So if you activate stream "6" by setting ``hist_fincl6``, but if any of ``hist_fincl2`` through ``hist_fincl5`` are unset, only the history streams up to the first blank one will be activated. The frequency of the history file streams is given by the namelist variable ``hist_nhtfrq`` which is an array of rank six for each history stream. The values of the array ``hist_nhtfrq`` must be integers, where the following values have the given meaning: @@ -159,11 +159,11 @@ Example: user_nl_clm namelist adding auxiliary history files and changing output Removing all history fields --------------------------- -Sometimes for various reasons you want to remove all the history fields either because you want to do testing without any output, or you only want a very small custom list of output fields rather than the default extensive list of fields. -By default only the primary history files are active, so technically using ``hist_fexcl1`` explained in the first example, you could list ALL of the history fields that are output in ``hist_fexcl1`` and then you wouldn't get any output. -However, as the list is very extensive this would be a cumbersome thing to do. -So to facilitate this ``hist_empty_htapes`` allows you to turn off all default output. -You can still use ``hist_fincl1`` to turn your own list of fields on, but you then start from a clean slate. +Sometimes for various reasons you want to remove all the history fields either because you want to do testing without any output, or you only want a very small custom list of output fields rather than the default extensive list of fields. +By default only the primary history files are active, so technically using ``hist_fexcl1`` explained in the first example, you could list ALL of the history fields that are output in ``hist_fexcl1`` and then you wouldn't get any output. +However, as the list is very extensive this would be a cumbersome thing to do. +So to facilitate this ``hist_empty_htapes`` allows you to turn off all default output. +You can still use ``hist_fincl1`` to turn your own list of fields on, but you then start from a clean slate. A sample user namelist ``user_nl_clm`` turning off all history fields and then activating just a few selected fields (ground and vegetation temperatures and absorbed solar radiation) is: Example 1-5. Example user_nl_clm namelist removing all history fields @@ -177,8 +177,8 @@ Example 1-5. Example user_nl_clm namelist removing all history fields Various ways to change history output averaging flags ----------------------------------------------------- -There are two ways to change the averaging of output history fields. -The first is using ``hist_avgflag_pertape`` which gives a default value for each history stream, the second is when you add fields using ``hist_fincl*``, you add an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would output the maximum of TSOI). +There are two ways to change the averaging of output history fields. +The first is using ``hist_avgflag_pertape`` which gives a default value for each history stream, the second is when you add fields using ``hist_fincl*``, you add an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would output the maximum of TSOI). The types of averaging that can be done are: - *A* Average, over the output interval. @@ -186,8 +186,8 @@ The types of averaging that can be done are: - *X* Maximum, over the output interval. - *M* Minimum, over the output interval. -The default averaging depends on the specific fields, but for most fields is an average. -A sample user namelist ``user_nl_clm`` making the monthly output fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), and adding auxiliary file streams for instantaneous (6-hourly), maximum (daily), minimum (daily), and average (daily). +The default averaging depends on the specific fields, but for most fields is an average. +A sample user namelist ``user_nl_clm`` making the monthly output fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), and adding auxiliary file streams for instantaneous (6-hourly), maximum (daily), minimum (daily), and average (daily). For some of the fields we diverge from the per-tape value given and customize to some different type of optimization. Example: user_nl_clm namelist with various ways to average history fields @@ -195,22 +195,22 @@ Example: user_nl_clm namelist with various ways to average history fields :: hist_empty_htapes = .true. - hist_fincl1 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', + hist_fincl1 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', 'EFLX_LH_TOT', 'WT' - hist_fincl2 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', + hist_fincl2 = 'TSOI:X', 'TG', 'TV', 'FIRE', 'FSR', 'FSH', 'EFLX_LH_TOT', 'WT' - hist_fincl3 = 'TSOI', 'TG:I', 'TV', 'FIRE', 'FSR', 'FSH', + hist_fincl3 = 'TSOI', 'TG:I', 'TV', 'FIRE', 'FSR', 'FSH', 'EFLX_LH_TOT', 'WT' - hist_fincl4 = 'TSOI', 'TG', 'TV:I', 'FIRE', 'FSR', 'FSH', + hist_fincl4 = 'TSOI', 'TG', 'TV:I', 'FIRE', 'FSR', 'FSH', 'EFLX_LH_TOT', 'WT' - hist_fincl5 = 'TSOI', 'TG', 'TV', 'FIRE:I', 'FSR', 'FSH', + hist_fincl5 = 'TSOI', 'TG', 'TV', 'FIRE:I', 'FSR', 'FSH', 'EFLX_LH_TOT', 'WT' hist_avgflag_pertape = 'A', 'I', 'X', 'M', 'A' hist_nhtfrq = 0, -6, -24, -24, -24 -In the example we put the same list of fields on each of the tapes: soil-temperature, ground temperature, vegetation temperature, emitted longwave radiation, reflected solar radiation, sensible heat, total latent-heat, and total water storage. -We also modify the soil-temperature for the primary and secondary auxiliary tapes by outputting them for a maximum instead of the prescribed per-tape of average and instantaneous respectively. -For the tertiary auxiliary tape we output ground temperature instantaneous instead of as a maximum, and for the fourth auxiliary tape we output vegetation temperature instantaneous instead of as a minimum. +In the example we put the same list of fields on each of the tapes: soil-temperature, ground temperature, vegetation temperature, emitted longwave radiation, reflected solar radiation, sensible heat, total latent-heat, and total water storage. +We also modify the soil-temperature for the primary and secondary auxiliary tapes by outputting them for a maximum instead of the prescribed per-tape of average and instantaneous respectively. +For the tertiary auxiliary tape we output ground temperature instantaneous instead of as a maximum, and for the fourth auxiliary tape we output vegetation temperature instantaneous instead of as a minimum. Finally, for the fifth auxiliary tapes we output ``FIRE`` instantaneously instead of as an average. .. note:: We also use ``hist_empty_htapes`` as in the previous example, so we can list ONLY the fields that we want on the primary history tapes. @@ -218,16 +218,16 @@ Finally, for the fifth auxiliary tapes we output ``FIRE`` instantaneously instea Outputting history files as a vector in order to analyze the plant function types within gridcells -------------------------------------------------------------------------------------------------- -By default the output to history files are the grid-cell average of all land-units, and vegetation types within that grid-cell, and output is on the full 2D latitude/longitude grid with ocean masked out. -Sometimes it's important to understand how different land-units or vegetation types are acting within a grid-cell. -The way to do this is to output history files as a 1D-vector of all land-units and vegetation types. -In order to display this, you'll need to do extensive post-processing to make sense of the output. -Often you may only be interested in a few points, so once you figure out the 1D indices for the grid-cells of interest, you can easily view that data. +By default the output to history files are the grid-cell average of all land-units, and vegetation types within that grid-cell, and output is on the full 2D latitude/longitude grid with ocean masked out. +Sometimes it's important to understand how different land-units or vegetation types are acting within a grid-cell. +The way to do this is to output history files as a 1D-vector of all land-units and vegetation types. +In order to display this, you'll need to do extensive post-processing to make sense of the output. +Often you may only be interested in a few points, so once you figure out the 1D indices for the grid-cells of interest, you can easily view that data. 1D vector output can also be useful for single point datasets, since it's then obvious that all data is for the same grid cell. -To do this you use ``hist_dov2xy`` which is an array of rank six for each history stream. -Set it to ``.false.`` if you want one of the history streams to be a 1D vector. -You can also use ``hist_type1d_pertape`` if you want to average over all the: Plant-Function-Types, columns, land-units, or grid-cells. +To do this you use ``hist_dov2xy`` which is an array of rank six for each history stream. +Set it to ``.false.`` if you want one of the history streams to be a 1D vector. +You can also use ``hist_type1d_pertape`` if you want to average over all the: Plant-Function-Types, columns, land-units, or grid-cells. A sample user namelist ``user_nl_clm`` leaving the primary monthly files as 2D, and then doing grid-cell (GRID), column (COLS), and no averaging over auxiliary tapes output daily for a single field (ground temperature) is: Example: user_nl_clm namelist outputting some files in 1D Vector format @@ -247,10 +247,10 @@ Example: user_nl_clm namelist outputting some files in 1D Vector format .. note:: Technically the default for hist_nhtfrq is for primary files output monthly and the other auxiliary tapes for daily, so we don't actually have to include hist_nhtfrq, we could use the default for it. Here we specify it for clarity. -Visualizing global 1D vector files will take effort. -You'll probably want to do some post-processing and possibly just extract out single points of interest to see what is going on. -Since, the output is a 1D vector, of only land-points traditional plots won't be helpful. -The number of points per grid-cell will also vary for anything, but grid-cell averaging. -You'll need to use the output fields pfts1d_ixy, and pfts1d_jxy, to get the mapping of the fields to the global 2D array. -pfts1d_itype_veg gives you the PFT number for each PFT. +Visualizing global 1D vector files will take effort. +You'll probably want to do some post-processing and possibly just extract out single points of interest to see what is going on. +Since, the output is a 1D vector, of only land-points traditional plots won't be helpful. +The number of points per grid-cell will also vary for anything, but grid-cell averaging. +You'll need to use the output fields pfts1d_ixy, and pfts1d_jxy, to get the mapping of the fields to the global 2D array. +pfts1d_itype_veg gives you the PFT number for each PFT. Most likely you'll want to do this analysis in a data processing tool (such as NCL, Matlab, Mathmatica, IDL, etcetera that is able to read and process NetCDF data files). diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst index dcc7fa3cbb..f57ed988d9 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst @@ -11,10 +11,10 @@ When running "I" compsets with CLM you use the DATM model to give atmospheric fo 1. **DATM Main Namelist and Stream Namlist gorup** (``datm_in``) 2. **DATM stream files** -The `Data Model Documentation `_ gives the details of all the options for the data models and for DATM specifically. -It goes into detail on all namelist items both for DATM and for DATM streams. -So here we won't list ALL of the DATM namelist options, nor go into great details about stream files. -But, we will talk about a few of the different options that are relevant for running with CLM. +The `Data Model Documentation `_ gives the details of all the options for the data models and for DATM specifically. +It goes into detail on all namelist items both for DATM and for DATM streams. +So here we won't list ALL of the DATM namelist options, nor go into great details about stream files. +But, we will talk about a few of the different options that are relevant for running with CLM. All of the options for changing the namelists or stream files is done by editing the ``user_nl_datm`` file. Because, they aren't useful for work with CLM we will NOT discuss any of the options for the main DATM namelist. Use the DATM Users Guide at the link above to find details of that. For the streams namelist we will discuss three items: @@ -32,8 +32,8 @@ mapalgo ``mapalgo`` sets the spatial interpolation method to go from the DATM input data to the output DATM model grid. The default is ``bilinear``. For ``CLM1PT`` we set it to ``nn`` to just select the nearest neighbor. This saves time and we also had problems running the interpolation for single-point mode. taxmode - ``taxmode`` is the time axis mode. - For CLM we usually have it set to ``cycle`` which means that once the end of the data is reached it will start over at the beginning. + ``taxmode`` is the time axis mode. + For CLM we usually have it set to ``cycle`` which means that once the end of the data is reached it will start over at the beginning. The extend modes is used have it use the last time-step of the forcing data once it reaches the end of forcing data (or use the first time-step before it reaches where the forcing data starts). See the warning below about the extend mode. .. warning:: *THE extend OPTION NEEDS TO BE USED WITH CAUTION!* It is only invoked by default for the CLM1PT mode and is only intended for the supported urban datasets to extend the data for a single time-step. If you have the model *run extensively through periods in this mode you will effectively be repeating that last time-step over that entire period*. This means the output of your simulation will be worthless. @@ -54,20 +54,20 @@ In the sections below we go over each of the relevant ``DATM_MODE`` options and CLMGSWP3v1 mode and it's DATM settings -------------------------------------- -In ``CLMGSWP3v1`` mode the GSWP3 NCEP forcing dataset is used and all of it's data is on a 3-hourly interval. -Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity, Long-Wave down and wind). -The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. +In ``CLMGSWP3v1`` mode the GSWP3 NCEP forcing dataset is used and all of it's data is on a 3-hourly interval. +Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity, Long-Wave down and wind). +The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. +Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution). ---------------------------------------- CLMCRUNCEPv7 mode and it's DATM settings ---------------------------------------- -In ``CLMCRUNCEPv7`` mode the CRUNCEP dataset is used and all of it's data is on a 6-hourly interval. -Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). -The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. +In ``CLMCRUNCEPv7`` mode the CRUNCEP dataset is used and all of it's data is on a 6-hourly interval. +Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). +The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. +Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution). .. note:: The "everything else" data stream (of temperature, pressure, humidity and wind) also includes the data for longwave downward forcing as well. Our simulations showed sensitivity to this field, so we backed off in using it, and let DATM calculate longwave down from the other fields. @@ -84,10 +84,10 @@ CLMCRUNCEP mode and it's DATM settings CLM_QIAN mode and it's DATM settings ------------------------------------ -In ``CLM_QIAN`` mode the Qian dataset is used which has 6-hourly solar and precipitation data, and 3-hourly for everything else. -The dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). -The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. +In ``CLM_QIAN`` mode the Qian dataset is used which has 6-hourly solar and precipitation data, and 3-hourly for everything else. +The dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). +The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. +Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input T62 grid to the grid the atmosphere model is being run at. Normally you wouldn't customize the ``CLM_QIAN`` settings, but you might replicate it's use for your own global data that had similar temporal characteristics. @@ -96,14 +96,14 @@ Normally you wouldn't customize the ``CLM_QIAN`` settings, but you might replica CLM1PT mode and it's DATM settings ---------------------------------- -In ``CLM1PT`` mode the model is assumed to have half-hourly or hourly data for a single-point. -For the supported datasets that is exactly what it has. -But, if you add your own data you may need to make adjustments accordingly. -Using the ``CLM_USRDAT_NAME`` resolution you can easily extend this mode for your own datasets that may be regional or even global and could be at different temporal frequencies. -If you do so you'll need to make adjustments to your DATM settings. -The dataset has all data in a single stream file. -The time-stamps of the data were also adjusted so that they are at the middle of the interval. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is set to ``nearest``. +In ``CLM1PT`` mode the model is assumed to have half-hourly or hourly data for a single-point. +For the supported datasets that is exactly what it has. +But, if you add your own data you may need to make adjustments accordingly. +Using the ``CLM_USRDAT_NAME`` resolution you can easily extend this mode for your own datasets that may be regional or even global and could be at different temporal frequencies. +If you do so you'll need to make adjustments to your DATM settings. +The dataset has all data in a single stream file. +The time-stamps of the data were also adjusted so that they are at the middle of the interval. +Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is set to ``nearest``. ``taxmode`` is set to ``extend`` and ``mapalgo`` is set to ``nn`` so that simply the nearest point is used. If you are using your own data for this mode and it's not at least hourly you'll want to adjust the DATM settings for it. If the data is three or six hourly, you'll need to divide it up into separate streams like in ``CLM_QIAN`` mode which will require fairly extensive changes to the DATM namelist and streams files. For an example of doing this see `Example 5-8 `_. @@ -112,16 +112,16 @@ If you are using your own data for this mode and it's not at least hourly you'll CPLHISTForcing mode and it's DATM settings ------------------------------------------ -In ``CPLHISTForcing`` mode the model is assumed to have 3-hourly for a global grid from a previous CESM simulation. -Like ``CLM_QIAN`` mode the data is divided into three streams: one for precipitation, one for solar, and one for everything else. -The time-stamps for Coupler history files for CESM is at the end of the interval, so the ``offset`` needs to be set in order to adjust the time-stamps to what it needs to be for the ``tintalgo`` settings. -For precipitation ``taxmode`` is set to ``nearest`` so the ``offset`` is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. -For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` seconds so that the ending time-step is adjust by three hours to the beginning of the interval. -For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. +In ``CPLHISTForcing`` mode the model is assumed to have 3-hourly for a global grid from a previous CESM simulation. +Like ``CLM_QIAN`` mode the data is divided into three streams: one for precipitation, one for solar, and one for everything else. +The time-stamps for Coupler history files for CESM is at the end of the interval, so the ``offset`` needs to be set in order to adjust the time-stamps to what it needs to be for the ``tintalgo`` settings. +For precipitation ``taxmode`` is set to ``nearest`` so the ``offset`` is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. +For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` seconds so that the ending time-step is adjust by three hours to the beginning of the interval. +For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For an example of such a case see `the Section called Running with MOAR data as atmospheric forcing to spinup the model in Chapter 4 `_. -Normally you wouldn't modify the DATM settings for this mode. -However, if you had data at a different frequency than 3-hours you would need to modify the ``offset`` and possibly the ``taxmode``. -The other two things that you might modify would be the path to the data or the domain file for the resolution (which is currently hardwired to f09). +Normally you wouldn't modify the DATM settings for this mode. +However, if you had data at a different frequency than 3-hours you would need to modify the ``offset`` and possibly the ``taxmode``. +The other two things that you might modify would be the path to the data or the domain file for the resolution (which is currently hardwired to f09). For data at a different input resolution you would need to change the domain file in the streams file to use a domain file to the resolution that the data comes in on. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index ea7c23d22a..ab5f28012a 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -1,18 +1,18 @@ ============================= CTSM History Fields (fates) ============================= - + CAUTION: Not all variables are relevant / present for all CTSM cases. Key flags used in this CTSM case: use_cn = F use_crop = F use_fates = T - -=================================== ================ ============================================================================================== ================================================================= ======= + +=================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Variable Name Level Dim. Long Description Units Active? -=================================== ================ ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= A5TMIN - 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB - actual N immobilization gN/m^2/s T AGLB - Aboveground leaf biomass kg/m^2 F diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index 4e96f5fb91..8e914d8a70 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -1,18 +1,18 @@ ============================= CTSM History Fields (nofates) ============================= - + CAUTION: Not all variables are relevant / present for all CTSM cases. Key flags used in this CTSM case: use_cn = T use_crop = T use_fates = F - -=================================== ================ ============================================================================================== ================================================================= ======= + +=================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Variable Name Level Dim. Long Description Units Active? -=================================== ================ ============================================================================================== ================================================================= ======= +=================================== ================ ============================================================================================== ================================================================= ======= A10TMIN - 10-day running mean of min 2-m temperature K F A5TMIN - 5-day running mean of min 2-m temperature K F ACTUAL_IMMOB - actual N immobilization gN/m^2/s T diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index a01630c293..06decd6049 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -6,21 +6,21 @@ Testing ******* -Technically, you could use the customization we gave in `Chapter 1 `_ to test various configuration and namelist options for CLM. -Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. -It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. -To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. -There are two types of testing scripts for CLM. -The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. -The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. +Technically, you could use the customization we gave in `Chapter 1 `_ to test various configuration and namelist options for CLM. +Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. +It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. +To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. +There are two types of testing scripts for CLM. +The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. +The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods. CIME Testing scripts ==================== -We first introduce the test scripts that work for all CESM components. -The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. +We first introduce the test scripts that work for all CESM components. +The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing `_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also @@ -41,7 +41,7 @@ CTSM Fortran Unit Tests CTSM Build-namelist Tests ========================= -Run the following perl tester that +Run the following perl tester that :: > cd bld/unit_testers diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst index 2228caa740..e45ba2f362 100644 --- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst +++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst @@ -37,7 +37,7 @@ It is important to examine all of the component log files in the run directory f 398: iam = 362: gridcell latitude = -70.0000000 398: iam = 362: pft type = 10 398: iam = 362: column type = 1 - 398: iam = 362: landunit type = 1 + 398: iam = 362: landunit type = 1 398: ENDRUN: 398: ERROR: 398: ERROR: carbon or nitrogen state critically negative ERROR in CNPrecisionControl @@ -79,7 +79,7 @@ If you are writing your own ``endrun`` call, you can get this additional informa You can get this same information without aborting the run via a call to ``write_point_context``, which is also defined in the ``abortutils`` module; e.g.:: - if (abs(carbon_patch(p)) < ccrit) then + if (abs(carbon_patch(p)) < ccrit) then call write_point_context(subgrid_index=p, subgrid_level=subgrid_level_patch) end if @@ -118,9 +118,9 @@ Another method of troubleshooting is to use the **point_of_interest** module. Use the point_of_interest module -------------------------------- -It is common, when debugging, to want to print the values of various variables for all patches or columns of certain landunit types within a certain grid cell of interest. For example, one might be able to identify a certain grid cell with an erroneous value for a particular history field variable (e.g., GPP) using for example ncview. Once the latitude and longitude of this grid cell has been determined, the point_of_interest module (**src/utils/point_of_interest.F90**) helps create the logical functions needed to do this. +It is common, when debugging, to want to print the values of various variables for all patches or columns of certain landunit types within a certain grid cell of interest. For example, one might be able to identify a certain grid cell with an erroneous value for a particular history field variable (e.g., GPP) using for example ncview. Once the latitude and longitude of this grid cell has been determined, the point_of_interest module (**src/utils/point_of_interest.F90**) helps create the logical functions needed to do this. This module is compiled into every CTSM build, but is not invoked by default. -To use it +To use it (1) Enter in the latitude/longitude of the point of interest in the function **at_poi** in **point_of_interest.F90** by setting the variables **poi_lat** and **poi_lon**. @@ -174,12 +174,12 @@ Simplifying to one processor removes all multi-processing problems and makes the # Set tasks and threads for each component to 1 # You could also set threads to something > 1 for speed, but still # run interactively if threading isn't an issue. - + > ./xmlchange NTASKS_ATM=1,NTHRDS_ATM=1,NTASKS_LND=1,NTHRDS_LND=1,NTASKS_ICE=1,NTHRDS_ICE=1 > ./xmlchange NTASKS_OCN=1,NTHRDS_OCN=1,NTASKS_CPL=1,NTHRDS_CPL=1,NTASKS_GLC=1,NTHRDS_GLC=1 # set MPILIB to mpi-serial so that you can run interactively > ./xmlchange MPILIB=mpi-serial - > ./case.setup + > ./case.setup # Then build your case # And finally run, by running the *.run script interactively @@ -196,9 +196,9 @@ Along the same lines, you might try running a simpler case, trying another comps Run with a debugger ------------------- -Another suggestion is to run the model with a debugger such as: **ddt**, **dbx**, **gdb**, or **totalview**. -Often to run with a debugger you will need to reduce the number of processors as outlined above. -Some debuggers such as **dbx** will only work with one processor, while more advanced debuggers such as **totalview** can work with both MPI tasks and OMP threads. -Even simple debuggers though can be used to query core files, to see where the code was at when it died (for example using the **where** in **dbx** for a core file can be very helpful. +Another suggestion is to run the model with a debugger such as: **ddt**, **dbx**, **gdb**, or **totalview**. +Often to run with a debugger you will need to reduce the number of processors as outlined above. +Some debuggers such as **dbx** will only work with one processor, while more advanced debuggers such as **totalview** can work with both MPI tasks and OMP threads. +Even simple debuggers though can be used to query core files, to see where the code was at when it died (for example using the **where** in **dbx** for a core file can be very helpful. For help in running with a debugger you will need to contact your system administrators for the machine you are running on. diff --git a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst index 14c3a75207..b41c574b14 100644 --- a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst @@ -7,13 +7,13 @@ The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools **cprnc** and **gen_domain** use the CIME configure/build system which is described in the next section. -The Makefiles (for **mksurfdata_map** and **mkprocdata_map**) use GNU Make extensions and thus require that you use GNU make to use them. -They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. -There are also environment variables that can be set to set things that must be customized. -All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. -On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. -The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. -Finally the tools allow you to turn optimization on (which is off by default but on for **mksurfdata_map**) with the OPT flag so that the tool will run faster. +The Makefiles (for **mksurfdata_map** and **mkprocdata_map**) use GNU Make extensions and thus require that you use GNU make to use them. +They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. +There are also environment variables that can be set to set things that must be customized. +All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. +On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. +The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. +Finally the tools allow you to turn optimization on (which is off by default but on for **mksurfdata_map**) with the OPT flag so that the tool will run faster. Options used by all: **mksurfdata_map** @@ -109,6 +109,6 @@ The *README.filecopies* (which can be found in ``$CTSMROOT/tools``) is repeated **cprnc** and *gen_domain** both use the CIME configure/build system rather than the CLM specific version described above. See `CIME documentation on adding grids `_ for -more information on adding grids, creating mapping files, and running **gen_domain**. Also see the CIME file: +more information on adding grids, creating mapping files, and running **gen_domain**. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build **gen_domain**. diff --git a/doc/source/users_guide/using-clm-tools/cprnc.rst b/doc/source/users_guide/using-clm-tools/cprnc.rst index 050e059296..5076bc296b 100644 --- a/doc/source/users_guide/using-clm-tools/cprnc.rst +++ b/doc/source/users_guide/using-clm-tools/cprnc.rst @@ -6,12 +6,12 @@ Comparing History Files ========================= -**cprnc** is a tool shared by |cesmrelease| to compare two NetCDF history files. -It differences every field that is shared on both files, and reports a summary of the difference. -The summary includes the three largest differences, as well as the root mean square (RMS) difference. -It also gives some summary information on the field as well. -You have to enter at least one file, and up to two files. -With one file it gives you summary information on the file, and with two it gives you information on the differences between the two. +**cprnc** is a tool shared by |cesmrelease| to compare two NetCDF history files. +It differences every field that is shared on both files, and reports a summary of the difference. +The summary includes the three largest differences, as well as the root mean square (RMS) difference. +It also gives some summary information on the field as well. +You have to enter at least one file, and up to two files. +With one file it gives you summary information on the file, and with two it gives you information on the differences between the two. At the end it will give you a summary of the fields compared and how many fields were different and how many were identical. Options: diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst index 972967da0c..85458b3707 100644 --- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst +++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst @@ -6,7 +6,7 @@ Creating CLM domain files ***************************** -*gen_domain* to create a domain file for datm from a mapping file. **gen_domain** is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of **mknoocnmap.pl** (see `the Section called Using mknocnmap.pl to create grid and maps for single-point regional grids `_) to create a regional or single-point map file that is then run through **gen_domain** to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the +*gen_domain* to create a domain file for datm from a mapping file. **gen_domain** is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of **mknoocnmap.pl** (see `the Section called Using mknocnmap.pl to create grid and maps for single-point regional grids `_) to create a regional or single-point map file that is then run through **gen_domain** to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README `_ file for more help on **gen_domain**. Here we create domain files for a regular global domain. diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 6048baa98c..af5dd59c37 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -6,7 +6,7 @@ Creating input for surface dataset generation ********************************************* -1. Generating SCRIP grid files +1. Generating SCRIP grid files ================================== The utility ``mkmapdata.sh`` requires SCRIP format input files to describe the input and output grids that maps are generated for. CLM provides a utility, ``mkmapgrids`` that generates those files. @@ -27,9 +27,9 @@ If you want to create a regular latitude/longitude single-point or regional grid -name [-or -n] Name to use to describe point OPTIONS - -dx Size of total grid in degrees in longitude direction + -dx Size of total grid in degrees in longitude direction (default is 0.1) - -dy Size of total grid in degrees in latitude direction + -dy Size of total grid in degrees in latitude direction (default is 0.1) -silent [or -s] Make output silent -help [or -h] Print usage to STDOUT. @@ -43,14 +43,14 @@ See :numref:`Figure mknoocnmap.pl` for a visual representation of this process. 2. Creating mapping files for mksurfdata_map ============================================== -``mkmapdata.sh`` uses the above SCRIP grid input files to create SCRIP mapping data files (uses ESMF). +``mkmapdata.sh`` uses the above SCRIP grid input files to create SCRIP mapping data files (uses ESMF). -The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. -Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. -Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. -See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. -The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. -You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map** (see `the Section called Running mksurfdata.pl `_ below). +The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. +Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. +Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. +See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. +The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. +You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map** (see `the Section called Running mksurfdata.pl `_ below). mkmapdata.sh has a help option with the following :: @@ -60,13 +60,13 @@ mkmapdata.sh has a help option with the following usage on cheyenne: ./mkmapdata.sh - valid arguments: - [-f|--gridfile ] - Full pathname of model SCRIP grid file to use + valid arguments: + [-f|--gridfile ] + Full pathname of model SCRIP grid file to use This variable should be set if this is not a supported grid This variable will override the automatic generation of the - filename generated from the -res argument - the filename is generated ASSUMING that this is a supported + filename generated from the -res argument + the filename is generated ASSUMING that this is a supported grid that has entries in the file namelist_defaults_clm.xml the -r|--res argument MUST be specied if this argument is specified [-r|--res ] @@ -75,7 +75,7 @@ mkmapdata.sh has a help option with the following Model output grid type supported values are [regional,global], (default is global) [-b|--batch] - Toggles batch mode usage. + Toggles batch mode usage. If you want to run in batch mode you need to have a separate batch script for a supported machine that calls this script interactively - you cannot submit this @@ -85,13 +85,13 @@ mkmapdata.sh has a help option with the following also writes data to clm.input_data_list [-d|--debug] Toggles debug-only (don't actually run mkmapdata just echo what would happen) - [-h|--help] + [-h|--help] Displays this help message [-v|--verbose] - Toggle verbose usage -- log more information on what is happening + Toggle verbose usage -- log more information on what is happening You can also set the following env variables: - ESMFBIN_PATH - Path to ESMF binaries + ESMFBIN_PATH - Path to ESMF binaries (default is /contrib/esmf-5.3.0-64-O/bin) CSMDATA ------ Path to CESM input data (default is /glade/p/cesm/cseg/inputdata) @@ -100,7 +100,7 @@ mkmapdata.sh has a help option with the following REGRID_PROC -- Number of MPI processors to use (default is 8) - **pass environment variables by preceding above commands + **pass environment variables by preceding above commands with 'env var1=setting var2=setting ' ********************** diff --git a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst index 7fb915a6ed..2d9ee8dcdb 100644 --- a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst +++ b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst @@ -4,16 +4,16 @@ Datasets for Observational Sites ================================== -There are two ways to customize datasets for a particular observational site. -The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. -Depending on the tool it might be easier to do it one way or the other. -In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. -Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. -Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. -For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. +There are two ways to customize datasets for a particular observational site. +The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. +Depending on the tool it might be easier to do it one way or the other. +In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. +Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. +Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. +For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. -Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. -See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. +Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. +See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. diff --git a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst index b5cc2efad9..29a0b96326 100644 --- a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst @@ -6,15 +6,15 @@ Observational Sites Datasets ******************************* -There are two ways to customize datasets for a particular observational site. -The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. -Depending on the tool it might be easier to do it one way or the other. -In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. -Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. -Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. -For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. +There are two ways to customize datasets for a particular observational site. +The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. +Depending on the tool it might be easier to do it one way or the other. +In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. +Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. +Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. +For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. -Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. -See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. +Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. +See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst index a8663176e1..d47d3d9e9d 100644 --- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst @@ -6,10 +6,10 @@ What are the CLM tools ======================== -There are several tools provided with CLM that allow you to create your own input datasets at resolutions you choose, or to interpolate initial conditions to a different resolution, or used to compare CLM history files between different cases. -The tools are all available in the ``$CTSMROOT/tools`` directory. -Most of the tools are FORTRAN stand-alone programs in their own directory, but there is also a suite of NCL scripts in the ``$CTSMROOT/tools//ncl_scripts`` directory, and some of the tools are scripts that may also call the ESMF regridding program. -Some of the NCL scripts are very specialized and not meant for general use, and we won't document them here. +There are several tools provided with CLM that allow you to create your own input datasets at resolutions you choose, or to interpolate initial conditions to a different resolution, or used to compare CLM history files between different cases. +The tools are all available in the ``$CTSMROOT/tools`` directory. +Most of the tools are FORTRAN stand-alone programs in their own directory, but there is also a suite of NCL scripts in the ``$CTSMROOT/tools//ncl_scripts`` directory, and some of the tools are scripts that may also call the ESMF regridding program. +Some of the NCL scripts are very specialized and not meant for general use, and we won't document them here. They still contain documentation in the script itself and the README file in the tools directory. The tools produce files that can be used for CLM4.5 and |version|. They do **NOT** produce files that can be used for CLM4.0. @@ -29,21 +29,21 @@ The list of generally important scripts and programs are as follows. #. *$CIMEROOT/tools/cprnc* to compare two NetCDF files. -In the sections to come we will go into detailed description of how to use each of these tools in turn. -First, however we will discuss the common environment variables and options that are used by all of the FORTRAN tools. -Second, we go over the outline of the entire file creation process for all input files needed by CLM for a new resolution, then we turn to each tool. +In the sections to come we will go into detailed description of how to use each of these tools in turn. +First, however we will discuss the common environment variables and options that are used by all of the FORTRAN tools. +Second, we go over the outline of the entire file creation process for all input files needed by CLM for a new resolution, then we turn to each tool. In the last section we will discuss how to customize files for particular observational sites. The FORTRAN tools (mksurfdata_map and mkprocdata_map) run, with a namelist (mksurfdata_map) to provide options, or with command line arguments (mkprocdata_map). -In the following sections, we will outline how to make these files available for build-namelist so that you can easily create simulations that include them. +In the following sections, we will outline how to make these files available for build-namelist so that you can easily create simulations that include them. In the chapter on single-point and regional datasets we also give an alternative way to enter new datasets without having to edit files. ------------------------------------ Running FORTRAN tools with namelists ------------------------------------ -**mksurfdata_map** runs with a namelist that is read from standard input. +**mksurfdata_map** runs with a namelist that is read from standard input. Hence, you create a namelist and then run them by redirecting the namelist file into standard input as follows: :: @@ -51,29 +51,29 @@ Hence, you create a namelist and then run them by redirecting the namelist file There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_map/mksurfdata_map.namleist`` that shows you what the namelist should look like. **mksurfdata_map** also has a script that creates the namelist and runs the program for you. -Namelists that you create should be similar to the example namelist. -The namelist values are also documented along with the other namelists in the: +Namelists that you create should be similar to the example namelist. +The namelist values are also documented along with the other namelists in the: :: - $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file - and default values in the: + $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file + and default values in the: $CTSMROOT/bld/namelist_files/namelist_defaults_clm_tools.xml`` file. ----------------------------------------------- Running FORTRAN tools with command line options ----------------------------------------------- -**gen_domain**, mkprocdata_map, and **cprnc** run with command line arguments. -The detailed sections below will give you more information on the command line arguments specific to each tool. -Also running the tool without any arguments will give you a general synopsis on how to run the tool. +**gen_domain**, mkprocdata_map, and **cprnc** run with command line arguments. +The detailed sections below will give you more information on the command line arguments specific to each tool. +Also running the tool without any arguments will give you a general synopsis on how to run the tool. ----------------------------------------- Running FORTRAN tools built with SMP=TRUE ----------------------------------------- -When you enable ``SMP=TRUE`` on your build of one of the tools that make use of it, you are using OpenMP for shared memory parallelism (SMP). -In SMP loops are run in parallel with different threads run on different processors all of which access the same memory (called on-node). -Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. +When you enable ``SMP=TRUE`` on your build of one of the tools that make use of it, you are using OpenMP for shared memory parallelism (SMP). +In SMP loops are run in parallel with different threads run on different processors all of which access the same memory (called on-node). +Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. For example, on the NCAR machine cheyenne there are 36 processors per node, so you can use up to 36 processors. @@ -81,8 +81,8 @@ For example, on the NCAR machine cheyenne there are 36 processors per node, so y Using NCL --------- -In the tools directory ``$CTSMROOT/tools/ncl_scripts`` and in a few other locations there are scripts that use NCAR Command Language (NCL). -Unlike the FORTRAN tools, you will need to get a copy of NCL in order to use them. -You also won't have to build an executable in order to use them, hence no Makefile is provided. -NCL is provided for free download as either binaries or source code from: `http://www.ncl.ucar.edu/ `_. +In the tools directory ``$CTSMROOT/tools/ncl_scripts`` and in a few other locations there are scripts that use NCAR Command Language (NCL). +Unlike the FORTRAN tools, you will need to get a copy of NCL in order to use them. +You also won't have to build an executable in order to use them, hence no Makefile is provided. +NCL is provided for free download as either binaries or source code from: `http://www.ncl.ucar.edu/ `_. The NCL web-site also contains documentation on NCL and it's use. These scripts are stand-alone and at most use environment variables to control how to use them. In some cases there are perl scripts with command line arguments that call the NCL scripts to control what they do. From 6fbc8f30e5f61d7562215499748bb4b5b0136b7a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 12 Oct 2023 18:07:37 -0600 Subject: [PATCH 1628/2067] Some fixes in a lilac/ doc. --- doc/source/lilac/specific-atm-models/wrf-nesting.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/source/lilac/specific-atm-models/wrf-nesting.rst b/doc/source/lilac/specific-atm-models/wrf-nesting.rst index 5bf74e5ad6..39c2fe94dd 100644 --- a/doc/source/lilac/specific-atm-models/wrf-nesting.rst +++ b/doc/source/lilac/specific-atm-models/wrf-nesting.rst @@ -147,6 +147,7 @@ metgrid step:: Running metgrid for two domains will create files like below:: + met_em.d01.* met_em.d02.* @@ -182,7 +183,7 @@ Make sure the following three files have been created in your directory:: The boundary condition file is only created for the outer domain. -Check the last line of the real log file for the following message:: +Check the last line of the real log file for the following message: Rename wrfinput_d02 ------------------- From b54f1ce2bc7124cbfa8cc6e1d271b216e24a7acc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 13 Oct 2023 08:53:55 -0600 Subject: [PATCH 1629/2067] Update changelog date --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5d12272b34..1fa5bc6a80 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev143 Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-) -Date: Wed Oct 11 15:37:48 MDT 2023 +Date: Fri Oct 13 08:53:38 MDT 2023 One-line Summary: Zeroing of wood product fluxes on fates columns Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index 0f72ce9698..b6a5cdd29c 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev143 rgknox 10/11/2023 Zeroing of wood product fluxes on fates columns + ctsm5.1.dev143 rgknox 10/13/2023 Zeroing of wood product fluxes on fates columns ctsm5.1.dev142 samrabin 09/19/2023 Merge 5 bit-for-bit pull requests ctsm5.1.dev141 slevis 09/13/2023 Change small snocan to zero ctsm5.1.dev140 afoster 09/12/2023 add lai_streams capability for FATES From 2aa34fed529d6e0dbb7c65c8ea3b8b9de5f42227 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 13 Oct 2023 09:05:02 -0600 Subject: [PATCH 1630/2067] Add note about the doc update --- doc/ChangeLog | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 1fa5bc6a80..a01469e0c2 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -71,6 +71,11 @@ Other details No other details. +Pull Requests that document the changes (include PR ids): + #2168 -- GRU update for FATES + #2134 -- Update to documentation for Meier et al. (2022) roughness length parameterization + https://github.com/ESCOMP/CTSM/pull + =============================================================== =============================================================== Tag name: ctsm5.1.dev142 From a851a75715d64ca300463c0bdb79b8a1e0fc4f59 Mon Sep 17 00:00:00 2001 From: John Alex Date: Fri, 13 Oct 2023 10:48:43 -0600 Subject: [PATCH 1631/2067] Call the new FATES-side FatesReadParameters (the one which doesn't need to call back into the HLM). No-op. --- src/utils/clmfates_interfaceMod.F90 | 18 ++++++---- src/utils/clmfates_paraminterfaceMod.F90 | 42 ++++++++++++++++++++++-- 2 files changed, 52 insertions(+), 8 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index e7e31b854a..1039a0c4b0 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -7,11 +7,9 @@ module CLMFatesInterfaceMod ! ! This is also the only location where CLM code is allowed to see FATES memory ! structures. - ! The routines here, that call FATES library routines, will not pass any types defined - ! by the driving land model (HLM). - ! - ! either native type arrays (int,real,log, etc) or packed into fates boundary condition - ! structures. + ! The routines here, that call FATES library routines, cannot pass most types defined + ! by the driving land model (HLM), only native type arrays (int,real,log, etc), implementations + ! of fates abstract classes, and references into fates boundary condition structures. ! ! Note that CLM/ALM does use Shared Memory Parallelism (SMP), where processes such as ! the update of state variables are forked. However, IO is not assumed to be @@ -110,6 +108,7 @@ module CLMFatesInterfaceMod use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varcon , only : dzsoi_decomp use FuncPedotransferMod, only: get_ipedof + use CLMFatesParamInterfaceMod, only: fates_param_reader_ctsm_impl ! use SoilWaterPlantSinkMod, only : Compute_EffecRootFrac_And_VertTranSink_Default ! Used FATES Modules @@ -127,6 +126,9 @@ module CLMFatesInterfaceMod use FatesInterfaceMod , only : UpdateFatesRMeansTStep use FatesInterfaceMod , only : InitTimeAveragingGlobals + use FatesParametersInterface, only : fates_param_reader_type + use FatesParametersInterface, only : fates_parameters_type + use FatesHistoryInterfaceMod, only : fates_hist use FatesRestartInterfaceMod, only : fates_restart_interface_type @@ -272,6 +274,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches) integer :: pass_sp integer :: pass_masterproc logical :: verbose_output + type(fates_param_reader_ctsm_impl) :: var_reader call t_startf('fates_globals1') @@ -315,6 +318,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches) end if + ! The following call reads in the parameter file ! and then uses that to determine the number of patches ! FATES requires. We pass that to CLM here @@ -323,7 +327,7 @@ subroutine CLMFatesGlobals1(surf_numpft,surf_numcft,maxsoil_patches) ! and allocations on the FATES side, which require ! some allocations from CLM (like soil layering) - call SetFatesGlobalElements1(use_fates,surf_numpft,surf_numcft) + call SetFatesGlobalElements1(use_fates,surf_numpft,surf_numcft,var_reader) maxsoil_patches = fates_maxPatchesPerSite @@ -3393,4 +3397,6 @@ subroutine GetAndSetTime() end subroutine GetAndSetTime + !----------------------------------------------------------------------- + end module CLMFatesInterfaceMod diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90 index dedd8629cc..8f63c68965 100644 --- a/src/utils/clmfates_paraminterfaceMod.F90 +++ b/src/utils/clmfates_paraminterfaceMod.F90 @@ -5,15 +5,29 @@ module CLMFatesParamInterfaceMod use shr_kind_mod, only : r8 => shr_kind_r8, SHR_KIND_CL use FatesGlobals, only : fates_log use FatesParametersInterface, only : fates_parameters_type + use FatesParametersInterface, only : fates_param_reader_type use EDParamsMod, only : FatesRegisterParams, FatesReceiveParams use SFParamsMod, only : SpitFireRegisterParams, SpitFireReceiveParams use PRTInitParamsFATESMod, only : PRTRegisterParams, PRTReceiveParams use FatesSynchronizedParamsMod, only : FatesSynchronizedParamsInst implicit none + public :: fates_param_reader_ctsm_impl + ! + type, extends(fates_param_reader_type) :: fates_param_reader_ctsm_impl + private - ! NOTE(bja, 2017-01) these methods can NOT be part of the clmi-fates - ! nterface type because they are called before the instance is + ! !PRIVATE MEMBER DATA: + + contains + ! !PUBLIC MEMBER FUNCTIONS: + procedure, public :: Read ! Read params from disk + + end type fates_param_reader_ctsm_impl + + + ! NOTE(bja, 2017-01) these methods can NOT be part of the clm-fates + ! interface type because they are called before the instance is ! initialized. public :: FatesReadParameters public :: FatesReadPFTs @@ -238,4 +252,28 @@ subroutine ParametersFromNetCDF(filename, is_host_file, fates_params) end subroutine ParametersFromNetCDF !----------------------------------------------------------------------- + subroutine Read(this, is_host_file, fates_params ) + ! + ! !DESCRIPTION: + ! Read 'fates_params' parameters from appropriate filename given 'is_host_file'. + ! + ! USES + use clm_varctl, only : fname_len, paramfile, fates_paramfile + ! !ARGUMENTS: + class(fates_param_reader_ctsm_impl) :: this + logical, intent(in) :: is_host_file + class(fates_parameters_type), intent(inout) :: fates_params + !----------------------------------------------------------------------- + character(len=fname_len) :: filename ! file to read + + filename = fates_paramfile + if (is_host_file) then + filename = paramfile + endif + call ParametersFromNetCDF(filename, is_host_file, fates_params) + + end subroutine Read + + !----------------------------------------------------------------------- + end module CLMFatesParamInterfaceMod From 8dd877c18181a56f176c2269ef7e78ee0f609143 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 13 Oct 2023 13:07:26 -0600 Subject: [PATCH 1632/2067] update to fates api to pass restart flag to ed_site_update() --- src/utils/clmfates_interfaceMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index e7e31b854a..63f08675d7 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1054,7 +1054,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call ed_update_site(this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s)) + this%fates(nc)%bc_out(s),.false.) enddo @@ -1716,7 +1716,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & call ed_update_site( this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s) ) + this%fates(nc)%bc_out(s),.true. ) end do @@ -1940,7 +1940,7 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & call ed_update_site(this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s)) + this%fates(nc)%bc_out(s),.false.) end do From eee3bf5107f6426d5a9ddb55e2b3e710251b0da6 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 13 Oct 2023 13:12:15 -0600 Subject: [PATCH 1633/2067] Setting fates external to ryans nocomp fix branch --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 14ba14d8b4..38ecd0dd3e 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.67.2_api.27.0.0 +repo_url = https://github.com/rgknox/fates +branch = nocomp-fix-tests required = True [externals_description] From 32acc6508c64d8df6555c2a3e438f9d9a0b880d3 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 13 Oct 2023 13:16:04 -0700 Subject: [PATCH 1634/2067] rename fates set_flag --- src/utils/clmfates_interfaceMod.F90 | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 61e52a29c0..778dbbdc35 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2662,21 +2662,22 @@ subroutine WrapSeedGlobal(this,is_restart_flag) integer :: ier ! error code integer :: g ! gridcell index - logical :: set_flag ! local logical variable to pass to IsItDispersalTime + logical :: set_restart_flag ! local logical variable to pass to IsItDispersalTime + ! if optional is_restart_flag is true type (neighbor_type), pointer :: neighbor ! If WrapSeedGlobal is being called at the end a fates restart call, ! pass .false. to the set_dispersed_flag to avoid updating the ! global dispersal date - set_flag = .true. + set_restart_flag = .true. if (present(is_restart_flag)) then - if (is_restart_flag) set_flag = .false. + if (is_restart_flag) set_restart_flag = .false. end if call t_startf('fates-seed-mpi_reduce') - if (IsItDispersalTime(setdispersedflag=set_flag)) then + if (IsItDispersalTime(setdispersedflag=set_restart_flag)) then ! Re-initialize incoming seed buffer for this time step this%fates_seed%incoming_global(:,:) = 0._r8 From d0c44a15333595ad8ac90e31efa5da511685d1aa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 13:24:13 -0600 Subject: [PATCH 1635/2067] Added TO_SEED _ANN and _PERHARV outputs. --- .../testmods_dirs/clm/crop/user_nl_clm | 2 +- src/biogeochem/CNPhenologyMod.F90 | 19 ++++++- src/biogeochem/CNVegCarbonFluxType.F90 | 23 +++++++++ src/biogeochem/CNVegNitrogenFluxType.F90 | 49 ++++++++++++++++++- 4 files changed, 90 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm index d7e6cb3189..70727986d7 100644 --- a/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/crop/user_nl_clm @@ -10,7 +10,7 @@ hist_fincl2 += 'DYN_COL_SOIL_ADJUSTMENTS_C' ! Annual crop variables on per-sowing/per-harvest axes, per PFT. -hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' +hist_fincl3 = 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'GRAINN_TO_FOOD_PERHARV', 'GRAINN_TO_FOOD_ANN', 'GRAINC_TO_SEED_PERHARV', 'GRAINC_TO_SEED_ANN', 'GRAINN_TO_SEED_PERHARV', 'GRAINN_TO_SEED_ANN', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' hist_nhtfrq(3) = 17520 hist_mfilt(3) = 1 hist_type1d_pertape(3) = 'PFTS' diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 2877aeb5c0..b6845fb7f6 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1902,12 +1902,16 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%harvest_reason_thisyr_patch(p,s) = -1._r8 do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch(p,s,k) = 0._r8 + cnveg_carbonflux_inst%repr_grainc_to_seed_perharv_patch(p,s,k) = 0._r8 cnveg_nitrogenflux_inst%repr_grainn_to_food_perharv_patch(p,s,k) = 0._r8 + cnveg_nitrogenflux_inst%repr_grainn_to_seed_perharv_patch(p,s,k) = 0._r8 end do end do do k = repr_grain_min, repr_grain_max cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch(p,k) = 0._r8 + cnveg_carbonflux_inst%repr_grainc_to_seed_thisyr_patch(p,k) = 0._r8 cnveg_nitrogenflux_inst%repr_grainn_to_food_thisyr_patch(p,k) = 0._r8 + cnveg_nitrogenflux_inst%repr_grainn_to_seed_thisyr_patch(p,k) = 0._r8 end do next_rx_sdate(p) = crop_inst%rx_sdates_thisyr_patch(p,1) end if @@ -3023,6 +3027,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainc_to_food_perharv => cnveg_carbonflux_inst%repr_grainc_to_food_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain C to food per harvest (gC/m2) repr_grainc_to_food_thisyr => cnveg_carbonflux_inst%repr_grainc_to_food_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain C to food harvested this calendar year (gC/m2) repr_grainc_to_seed => cnveg_carbonflux_inst%repr_grainc_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain C to seed (gC/m2/s) + repr_grainc_to_seed_perharv => cnveg_carbonflux_inst%repr_grainc_to_seed_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain C to seed per harvest (gC/m2) + repr_grainc_to_seed_thisyr => cnveg_carbonflux_inst%repr_grainc_to_seed_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain C to seed harvested this calendar year (gC/m2) repr_structurec_to_cropprod => cnveg_carbonflux_inst%repr_structurec_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to crop product pool (gC/m2/s) repr_structurec_to_litter => cnveg_carbonflux_inst%repr_structurec_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure C to litter (gC/m2/s) leafc_to_biofuelc => cnveg_carbonflux_inst%leafc_to_biofuelc_patch , & ! Output: [real(r8) (:) ] leaf C to biofuel C (gC/m2/s) @@ -3035,6 +3041,8 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & repr_grainn_to_food_perharv => cnveg_nitrogenflux_inst%repr_grainn_to_food_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain N to food per harvest (gN/m2) repr_grainn_to_food_thisyr => cnveg_nitrogenflux_inst%repr_grainn_to_food_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain N to food harvested this calendar year (gN/m2) repr_grainn_to_seed => cnveg_nitrogenflux_inst%repr_grainn_to_seed_patch , & ! Output: [real(r8) (:,:) ] grain N to seed (gN/m2/s) + repr_grainn_to_seed_perharv => cnveg_nitrogenflux_inst%repr_grainn_to_seed_perharv_patch, & ! Output: [real(r8) (:,:,:) ] grain N to seed per harvest (gN/m2) + repr_grainn_to_seed_thisyr => cnveg_nitrogenflux_inst%repr_grainn_to_seed_thisyr_patch, & ! Output: [real(r8) (:,:) ] grain N to seed harvested this calendar year (gN/m2) repr_structuren_to_cropprod => cnveg_nitrogenflux_inst%repr_structuren_to_cropprod_patch, & ! Output: [real(r8) (:,:) ] reproductive structure N to crop product pool (gN/m2/s) repr_structuren_to_litter => cnveg_nitrogenflux_inst%repr_structuren_to_litter_patch, & ! Output: [real(r8) (:,:) ] reproductive structure N to litter (gN/m2/s) leafn_to_biofueln => cnveg_nitrogenflux_inst%leafn_to_biofueln_patch , & ! Output: [real(r8) (:) ] leaf N to biofuel N (gN/m2/s) @@ -3096,10 +3104,19 @@ subroutine CNOffsetLitterfall (num_soilp, filter_soilp, & cropseedc_deficit_to_restore = min(cropseedc_deficit_remaining, reproductivec(p,k)) cropseedc_deficit_remaining = cropseedc_deficit_remaining - cropseedc_deficit_to_restore repr_grainc_to_seed(p,k) = t1 * cropseedc_deficit_to_restore - + if (cropseedc_deficit_to_restore > 0._r8) then + repr_grainc_to_seed_perharv(p,h,k) = cropseedc_deficit_to_restore + repr_grainc_to_seed_thisyr(p,k) = repr_grainc_to_seed_thisyr(p,k) & + + repr_grainc_to_seed_perharv(p,h,k) + end if cropseedn_deficit_to_restore = min(cropseedn_deficit_remaining, reproductiven(p,k)) cropseedn_deficit_remaining = cropseedn_deficit_remaining - cropseedn_deficit_to_restore repr_grainn_to_seed(p,k) = t1 * cropseedn_deficit_to_restore + if (cropseedn_deficit_to_restore > 0._r8) then + repr_grainn_to_seed_perharv(p,h,k) = cropseedn_deficit_to_restore + repr_grainn_to_seed_thisyr(p,k) = repr_grainn_to_seed_thisyr(p,k) & + + repr_grainn_to_seed_perharv(p,h,k) + end if ! Send the remaining grain to the food product pool repr_grainc_to_food_thispool = cpool_to_reproductivec(p,k) - repr_grainc_to_seed(p,k) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index e930543e25..bd8765db00 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -148,6 +148,8 @@ module CNVegCarbonFluxType real(r8), pointer :: leafc_to_biofuelc_patch (:) ! leaf C to biofuel C (gC/m2/s) real(r8), pointer :: livestemc_to_biofuelc_patch (:) ! livestem C to biofuel C (gC/m2/s) real(r8), pointer :: repr_grainc_to_seed_patch (:,:) ! grain C to seed for prognostic crop(gC/m2/s) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainc_to_seed_perharv_patch (:,:,:) ! grain C to seed for prognostic crop accumulated by harvest (gC/m2) [patch, harvest, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over each growing season, to be instantaneously at the end of each calendar year, to provide output that's easier to work with. + real(r8), pointer :: repr_grainc_to_seed_thisyr_patch (:,:) ! grain C to seed for prognostic crop accumulated this calendar year (gC/m2) [patch, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over an entire calendar year, to be saved instantaneously at the end of each calendar year, to provide output that's easier to work with. ! maintenance respiration fluxes real(r8), pointer :: cpool_to_resp_patch (:) ! CNflex excess C maintenance respiration (gC/m2/s) @@ -672,6 +674,8 @@ subroutine InitAllocate(this, bounds, carbon_type, alloc_full_veg) allocate(this%leafc_to_biofuelc_patch (begp:endp)) ; this%leafc_to_biofuelc_patch (:) = nan allocate(this%livestemc_to_biofuelc_patch (begp:endp)) ; this%livestemc_to_biofuelc_patch (:) = nan allocate(this%repr_grainc_to_seed_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_seed_patch (:,:) = nan + allocate(this%repr_grainc_to_seed_perharv_patch(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_seed_perharv_patch (:,:,:) = nan + allocate(this%repr_grainc_to_seed_thisyr_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainc_to_seed_thisyr_patch (:,:) = nan allocate(this%reproductivec_xfer_to_reproductivec_patch(begp:endp, nrepr)) this%reproductivec_xfer_to_reproductivec_patch(:,:) = nan allocate(this%cpool_reproductive_gr_patch (begp:endp, nrepr)) ; this%cpool_reproductive_gr_patch (:,:) = nan @@ -954,6 +958,7 @@ subroutine InitHistory(this, bounds, carbon_type) end do this%repr_grainc_to_food_thisyr_patch(begp:endp,:) = spval + this%repr_grainc_to_seed_thisyr_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainc_to_food_thisyr_patch(:,k) call hist_addfld1d ( & @@ -964,6 +969,15 @@ subroutine InitHistory(this, bounds, carbon_type) long_name=get_repr_longname(k)//' C to food harvested per calendar year; should only be output annually', & ptr_patch=data1dptr, & default='inactive') + data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINC_TO_SEED_ANN + fname=get_repr_hist_fname(k)//'C_TO_SEED_ANN', & + units='gC/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to seed harvested per calendar year; should only be output annually', & + ptr_patch=data1dptr, & + default='inactive') end do this%leafc_to_biofuelc_patch(begp:endp) = spval @@ -3730,6 +3744,15 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) long_name=get_repr_longname(k)//' C to food per calendar year; should only be output annually', & units='gC/m2', & interpinic_flag='interp', readvar=readvar, data=data1dptr) + data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) + ! e.g., grainc_to_seed_thisyr + varname = get_repr_rest_fname(k)//'c_to_seed_thisyr' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' C to seed per calendar year; should only be output annually', & + units='gC/m2', & + interpinic_flag='interp', readvar=readvar, data=data1dptr) end do do k = 1, nrepr diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index 64f56a0d6b..5de48e4284 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -140,6 +140,8 @@ module CNVegNitrogenFluxType real(r8), pointer :: leafn_to_biofueln_patch (:) ! patch leaf N to biofuel N (gN/m2/s) real(r8), pointer :: livestemn_to_biofueln_patch (:) ! patch livestem N to biofuel N (gN/m2/s) real(r8), pointer :: repr_grainn_to_seed_patch (:,:) ! patch grain N to seed for prognostic crop (gN/m2/s) [patch, repr_grain_min:repr_grain_max] + real(r8), pointer :: repr_grainn_to_seed_perharv_patch (:,:,:) ! grain N to seed for prognostic crop accumulated by harvest (gN/m2) [patch, harvest, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over each growing season, to be instantaneously at the end of each calendar year, to provide output that's easier to work with. + real(r8), pointer :: repr_grainn_to_seed_thisyr_patch (:,:) ! grain N to seed for prognostic crop accumulated this calendar year (gN/m2) [patch, repr_grain_min:repr_grain_max]. Not per-second because this variable represents an accumulation over an entire calendar year, to be saved instantaneously at the end of each calendar year, to provide output that's easier to work with. real(r8), pointer :: leafn_to_litter_patch (:) ! patch leaf N litterfall (gN/m2/s) real(r8), pointer :: leafn_to_retransn_patch (:) ! patch leaf N to retranslocated N pool (gN/m2/s) real(r8), pointer :: frootn_to_retransn_patch (:) ! patch fine root N to retranslocated N pool (gN/m2/s) @@ -487,6 +489,8 @@ subroutine InitAllocate(this, bounds, alloc_full_veg) allocate(this%leafn_to_biofueln_patch (begp:endp)) ; this%leafn_to_biofueln_patch (:) = nan allocate(this%livestemn_to_biofueln_patch (begp:endp)) ; this%livestemn_to_biofueln_patch (:) = nan allocate(this%repr_grainn_to_seed_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_seed_patch (:,:) = nan + allocate(this%repr_grainn_to_seed_perharv_patch(begp:endp, 1:mxharvests, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_seed_perharv_patch (:,:,:) = nan + allocate(this%repr_grainn_to_seed_thisyr_patch(begp:endp, repr_grain_min:repr_grain_max)) ; this%repr_grainn_to_seed_thisyr_patch (:,:) = nan allocate(this%reproductiven_xfer_to_reproductiven_patch(begp:endp, nrepr)) this%reproductiven_xfer_to_reproductiven_patch(:,:) = nan allocate(this%reproductiven_storage_to_xfer_patch(begp:endp, nrepr)) ; this%reproductiven_storage_to_xfer_patch (:,:) = nan @@ -1044,11 +1048,13 @@ subroutine InitHistory(this, bounds) this%repr_grainn_to_food_perharv_patch(begp:endp,:,:) = spval this%repr_grainn_to_food_thisyr_patch(begp:endp,:) = spval this%repr_grainn_to_seed_patch(begp:endp,:) = spval + this%repr_grainn_to_seed_perharv_patch(begp:endp,:,:) = spval + this%repr_grainn_to_seed_thisyr_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainn_to_food_patch(:,k) call hist_addfld1d ( & ! e.g., GRAINN_TO_FOOD - fname=get_repr_hist_fname(k)//'N_TO_FOOD', & + fname=get_repr_hist_fname(k)//'N_TO_FOOD (not scientifically)', & units='gN/m^2/s', & avgflag='A', & long_name=get_repr_longname(k)//' N to food', & @@ -1082,6 +1088,25 @@ subroutine InitHistory(this, bounds) long_name=get_repr_longname(k)//' N to food harvested per calendar year; should only be output annually', & ptr_patch=data1dptr, & default='inactive') + data2dptr => this%repr_grainn_to_seed_perharv_patch(:,:,k) + call hist_addfld2d ( & + ! e.g., GRAINN_TO_SEED_PERHARV + fname=get_repr_hist_fname(k)//'N_TO_SEED_PERHARV', & + units='gN/m^2', & + type2d='mxharvests', & + avgflag='I', & + long_name=get_repr_longname(k)//' N to seed per harvest; should only be output annually', & + ptr_patch=data2dptr, & + default='inactive') + data1dptr => this%repr_grainn_to_seed_thisyr_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINN_TO_SEED_ANN + fname=get_repr_hist_fname(k)//'N_TO_SEED_ANN', & + units='gN/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' N to seed harvested per calendar year; should only be output annually', & + ptr_patch=data1dptr, & + default='inactive') end do end if @@ -1527,6 +1552,19 @@ subroutine Restart (this, bounds, ncid, flag ) readvar=readvar, & scale_by_thickness=.false., & interpinic_flag='interp', data=data2dptr) + data2dptr => this%repr_grainn_to_seed_perharv_patch(:,:,k) + ! e.g., grainn_to_seed_perharv + varname = get_repr_rest_fname(k)//'n_to_seed_perharv' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + dim2name='mxharvests', & + switchdim=.true., & + long_name=get_repr_longname(k)//' N to seed per harvest; should only be output annually', & + units='gN/m2', & + readvar=readvar, & + scale_by_thickness=.false., & + interpinic_flag='interp', data=data2dptr) end do end if @@ -1540,6 +1578,15 @@ subroutine Restart (this, bounds, ncid, flag ) long_name=get_repr_longname(k)//' N to food per calendar year; should only be output annually', & units='gN/m2', & interpinic_flag='interp', readvar=readvar, data=data1dptr) + data1dptr => this%repr_grainn_to_seed_thisyr_patch(:,k) + ! e.g., grainn_to_seed_thisyr + varname = get_repr_rest_fname(k)//'n_to_seed_thisyr' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + long_name=get_repr_longname(k)//' N to seed per calendar year; should only be output annually', & + units='gN/m2', & + interpinic_flag='interp', readvar=readvar, data=data1dptr) end do end if From f058160e7fc3592daec30fd347e4cccf2da97e11 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 13:58:25 -0600 Subject: [PATCH 1636/2067] Comment fixes and improvements. --- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++-- src/biogeochem/CNPhenologyMod.F90 | 5 +++-- src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf | 2 ++ 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index caeab9eb48..3f494e0711 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1837,12 +1837,12 @@ Simulation year that aligns with stream_year_first_cropcal value -Filename of input stream data for date (day of year) of start of sowing window +Filename of input stream data for date (day of year) of start of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history. -Filename of input stream data for date (day of year) of end of sowing window +Filename of input stream data for date (day of year) of end of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history. Date: Tue, 17 Oct 2023 14:02:25 -0600 Subject: [PATCH 1637/2067] CropType: Don't allocate things twice. --- src/biogeochem/CropType.F90 | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 6d101df456..29c4717ab3 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -248,10 +248,6 @@ subroutine InitAllocate(this, bounds) allocate(this%sowing_count(begp:endp)) ; this%sowing_count(:) = 0 allocate(this%harvest_count(begp:endp)) ; this%harvest_count(:) = 0 - this%rx_swindow_starts_thisyr_patch(:,:) = -1 - this%rx_swindow_ends_thisyr_patch (:,:) = -1 - this%rx_cultivar_gdds_thisyr_patch(:,:) = spval - end subroutine InitAllocate !----------------------------------------------------------------------- From 90bbb16279d7110f3b50f046f721d41f1f3973b2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 14:18:26 -0600 Subject: [PATCH 1638/2067] Add input validity check to get_doy_tomorrow(). --- src/utils/clm_time_manager.F90 | 6 ++++++ .../test/clm_time_manager_test/test_clm_time_manager.pf | 7 +++++++ 2 files changed, 13 insertions(+) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 14572935c3..35abbfc6bf 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -1282,6 +1282,12 @@ function get_doy_tomorrow(doy_today) result(doy_tomorrow) integer, intent(in) :: doy_today integer :: doy_tomorrow + character(len=*), parameter :: sub = 'clm::get_doy_tomorrow' + + if ( doy_today < 1 .or. doy_today > 367 )then + write(iulog,*) sub, ' = ', doy_today + call shr_sys_abort( sub//': error doy_today out of range' ) + end if if (doy_today == get_curr_days_per_year()) then doy_tomorrow = 1 diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index 0665e5f6d0..736d745e3a 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -661,6 +661,8 @@ contains @Test subroutine check_get_doy_tomorrow(this) class(TestTimeManager), intent(inout) :: this + character(len=256) :: expected_msg + integer :: doy_tomorrow ! We don't care about the actual date here; we just want to enable get_curr_days_per_year() call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) @@ -669,6 +671,11 @@ contains @assertEqual(get_doy_tomorrow(1), 2) @assertEqual(get_doy_tomorrow(150), 151) @assertEqual(get_doy_tomorrow(get_curr_days_per_year()), 1) + + doy_tomorrow = get_doy_tomorrow(400) + expected_msg = endrun_msg("clm::get_doy_tomorrow: error doy_today out of range" ) + @assertExceptionRaised(expected_msg) + end subroutine check_get_doy_tomorrow end module test_clm_time_manager From 92b54358f2cad8fb777cf942e0f0285a1d88b6e4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 14:48:15 -0600 Subject: [PATCH 1639/2067] Don't use hardcoded 365 in cropcalStreamMod. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 120310dd49..e14979a708 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -299,6 +299,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! !USES: use CropType , only : crop_type use PatchType , only : patch + use clm_time_manager, only : get_curr_days_per_year use dshr_methods_mod , only : dshr_fldbun_getfldptr ! ! !ARGUMENTS: @@ -311,6 +312,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig integer :: nc, fp + integer :: dayspyr integer :: n, g integer :: lsize integer :: rc @@ -334,6 +336,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Place all data from each type into a temporary 2d array lsize = bounds%endg - bounds%begg + 1 + dayspyr = get_curr_days_per_year() + ! Read prescribed sowing window start dates from input files allocate(dataptr2d_swindow_start(lsize, ncft)) allocate(dataptr2d_swindow_end (lsize, ncft)) @@ -355,8 +359,8 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do g = 1,lsize ! If read-in value is invalid, allow_unprescribed_planting in CropPhenology() - if (dataptr1d_swindow_start(g) <= 0 .or. dataptr1d_swindow_start(g) > 365 & - .or. dataptr1d_swindow_end(g) <= 0 .or. dataptr1d_swindow_end(g) > 365) then + if (dataptr1d_swindow_start(g) <= 0 .or. dataptr1d_swindow_start(g) > dayspyr & + .or. dataptr1d_swindow_end(g) <= 0 .or. dataptr1d_swindow_end(g) > dayspyr) then dataptr1d_swindow_start(g) = -1 dataptr1d_swindow_end (g) = -1 end if @@ -379,12 +383,12 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ends(p,1) = dataptr2d_swindow_end (ig,n) ! Sanity check: Should only read in valid values - if (starts(p,1) > 365) then + if (starts(p,1) > dayspyr) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window start date ',& starts(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - if (ends(p,1) > 365) then + if (ends(p,1) > dayspyr) then write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window end date ',& ends(p,1) call ESMF_Finalize(endflag=ESMF_END_ABORT) From 8d1537c69018e797a492ea64712a479f07d1165c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 15:27:34 -0600 Subject: [PATCH 1640/2067] do_plant_prescribed: Check sown_in_this_window, not sowing_count. --- src/biogeochem/CNPhenologyMod.F90 | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index bca6200607..60931fb13b 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2032,16 +2032,21 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & ! Get dates of current or next sowing window. call get_swindow(jday, crop_inst%rx_swindow_starts_thisyr_patch(p,:), crop_inst%rx_swindow_ends_thisyr_patch(p,:), minplantjday(ivt(p),h), maxplantjday(ivt(p),h), w, sowing_window_startdate, sowing_window_enddate) + ! Are we currently in a sowing window? + ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. + is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) + crop_inst%sown_in_this_window(p) = was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop(p), crop_inst%sown_in_this_window(p)) + is_end_sowing_window = jday == sowing_window_enddate + ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. Also make sure we haven't planted yet today. ! TODO: ¿Allow use of NON-prescribed sowing with one-day-long windows? has_rx_sowing_date = sowing_window_startdate == sowing_window_enddate do_plant_prescribed = has_rx_sowing_date .and. & sowing_window_startdate == jday .and. & - sowing_count (p) < mxsowings + .not. crop_inst%sown_in_this_window(p) do_plant_prescribed_tomorrow = & has_rx_sowing_date .and. & - sowing_window_startdate == get_doy_tomorrow(jday) .and. & - sowing_count (p) < mxsowings + sowing_window_startdate == get_doy_tomorrow(jday) ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-02-18) ! When resuming from a run with old code, may need to manually set these. @@ -2055,12 +2060,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & crop_inst%sdates_thisyr_patch(p,1) = real(idop(p), r8) end if - ! Are we currently in a sowing window? - ! This is outside the croplive check so that the "harvest if planting conditions were met today" conditional works. - is_in_sowing_window = is_doy_in_interval(sowing_window_startdate, sowing_window_enddate, jday) - crop_inst%sown_in_this_window(p) = was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop(p), crop_inst%sown_in_this_window(p)) - is_end_sowing_window = jday == sowing_window_enddate - ! ! Save these diagnostic variables only on the last day of the window to ensure that windows spanning the new year aren't double-counted. Doing this on the last day ensures that outputs are ordered as inputs should be. if (jday == sowing_window_enddate) then crop_inst%swindow_starts_thisyr_patch(p,w) = sowing_window_startdate From 2896889184aeb5cca6a7220f116c49af693920b0 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 17 Oct 2023 15:39:14 -0600 Subject: [PATCH 1641/2067] update fates seed dispersal test mod This update implments a shell script to call ncgen and the fates modify parameter file tooling to generate and update the default fates parameters on the fly with values appropriate for seed dispersal mode. --- .../clm/FatesColdSeedDisp/shell_commands | 11 +++++++++++ .../testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 2 +- 2 files changed, 12 insertions(+), 1 deletion(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands new file mode 100644 index 0000000000..7cb007d591 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands @@ -0,0 +1,11 @@ +SRCDIR=`./xmlquery SRCROOT --value` +CASEDIR=`./xmlquery CASEROOT --value` +FATESROOT=$SRCDIR/src/fates +FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc + +ncgen -o $FATESPARAMFILE $FATESROOT/parameter_files/fates_params_default.cdl + +$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts +$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts +$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_scale --val 1e-05 --allpfts +$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_shape --val 0.1 --allpfts diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index 64dc4efdc6..ecd1dc8b57 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,3 +1,3 @@ -fates_paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_5x5_amazon_seeddispersal_c230925.nc' +fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc' fates_seeddisp_cadence = 1 hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From bc148ebfaf8a67be8914131f50fa6eff302029f3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 16:10:32 -0600 Subject: [PATCH 1642/2067] Remove unneeded check in cropcal_interp(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 14 ++------------ 1 file changed, 2 insertions(+), 12 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index e14979a708..4976ef74d0 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -340,7 +340,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Read prescribed sowing window start dates from input files allocate(dataptr2d_swindow_start(lsize, ncft)) + dataptr2d_swindow_start(:,:) = -1._r8 allocate(dataptr2d_swindow_end (lsize, ncft)) + dataptr2d_swindow_end(:,:) = -1._r8 if (use_cropcal_rx_swindows) then ! Starting with npcropmin will skip generic crops do n = 1, ncft @@ -381,18 +383,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ig = g_to_ig(patch%gridcell(p)) starts(p,1) = dataptr2d_swindow_start(ig,n) ends(p,1) = dataptr2d_swindow_end (ig,n) - - ! Sanity check: Should only read in valid values - if (starts(p,1) > dayspyr) then - write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window start date ',& - starts(p,1) - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if - if (ends(p,1) > dayspyr) then - write(iulog,'(a,i0,a,i0)') 'cropcal_interp(): Crop patch (ivt ',ivt,') has dataptr2d prescribed sowing window end date ',& - ends(p,1) - call ESMF_Finalize(endflag=ESMF_END_ABORT) - end if else write(iulog,'(a,i0)') 'cropcal_interp(), prescribed sowing windows: Crop patch has ivt ',ivt call ESMF_Finalize(endflag=ESMF_END_ABORT) From 6adba3d3b88d120d3a653004cb07bd93895d3369 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 17 Oct 2023 16:36:48 -0600 Subject: [PATCH 1643/2067] Remove a bit of redundant code and change a comment --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- src/biogeophys/UrbanAlbedoMod.F90 | 10 +--------- 2 files changed, 2 insertions(+), 10 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 8856754511..10da4ccde7 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1769,7 +1769,7 @@ to hydrologic variables (either TWS or ZWT) -Toggle to turn on use of input prescribed soil moisture streams rather than have CLM prognose it (EXPERIMENTAL, UNSUPPORTED!) +Toggle to turn on use of input prescribed soil moisture streams rather than have CLM prognose it (EXPERIMENTAL) shr_log_errMsg use decompMod , only : bounds_type, subgrid_level_landunit use clm_varpar , only : numrad - use clm_varcon , only : isecspday, degpsec, spval + use clm_varcon , only : isecspday, degpsec use clm_varctl , only : iulog use abortutils , only : endrun use UrbanParamsType , only : urbanparams_type @@ -187,10 +187,6 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & c = filter_urbanc(fc) albgrd(c,ib) = 0._r8 albgri(c,ib) = 0._r8 -! add new snicar output variables for history files - albgrd_hst(c,ib) = spval - albgri_hst(c,ib) = spval -! end add new snicar end do do fp = 1,num_urbanp @@ -212,10 +208,6 @@ subroutine UrbanAlbedo (bounds, num_urbanl, filter_urbanl, & albd(p,ib) = 1._r8 albi(p,ib) = 1._r8 endif -! add new snicar output variables for history files - albd_hst(p,ib) = spval - albi_hst(p,ib) = spval -! end add new snicar fabd(p,ib) = 0._r8 fabd_sun(p,ib) = 0._r8 fabd_sha(p,ib) = 0._r8 From 96a47bd262cc773e3490607d0e561564043fd03f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 17 Oct 2023 16:40:10 -0600 Subject: [PATCH 1644/2067] Remove some commented-out lines from cropcal_interp(). --- src/cpl/share_esmf/cropcalStreamMod.F90 | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 4976ef74d0..1ca4d331c6 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -436,10 +436,6 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) do fp = 1, num_pcropp p = filter_pcropp(fp) -! if (.not. patch%active(p)) then -! continue -! end if - ivt = patch%itype(p) ! Will skip generic crops if (ivt >= npcropmin) then From a2370a0426e4a8878e343a381acca046cc305d5b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 17 Oct 2023 18:26:51 -0600 Subject: [PATCH 1645/2067] CLMBuildNamelist.pm: Put most snicar error checks in loop --- bld/CLMBuildNamelist.pm | 77 ++++++++++++++--------------------------- 1 file changed, 26 insertions(+), 51 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index a17fdea155..088bbe9ef0 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1995,59 +1995,34 @@ sub setup_logic_snicar_methods { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_use_aerosol' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_aerforc_diag' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' ); - # Error checking - my $opt1 = 'snicar_snw_shape'; - my $var1 = $nl->get_value($opt1); - my $sup1a = "'sphere'"; # supported value for this option - my $sup1b = "'hexagonal_plate'"; # supported value for this option - if (($var1 ne $sup1a) && ($var1 ne $sup1b)) { - $log->warning("$opt1=$sup1a and $sup1b are supported; $var1 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt2 = 'snicar_solarspec'; - my $var2 = $nl->get_value($opt2); - my $sup2 = "'mid_latitude_winter'"; # supported value for this option - if ($var2 ne $sup2) { - $log->warning("$opt2=$sup2 is the supported option; $var2 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt3 = 'snicar_dust_optics'; - my $var3 = $nl->get_value($opt3); - my $sup3 = "'sahara'"; # supported value for this option - if ($var3 ne $sup3) { - $log->warning("$opt3=$sup3 is the supported option; $var3 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt4 = 'snicar_numrad_snw'; - my $var4 = $nl->get_value($opt4); - my $sup4 = '5'; # supported value for this option - if ($var4 ne $sup4) { - $log->warning("$opt4=$sup4 is the supported option; $var4 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt5 = 'snicar_snobc_intmix'; - my $var5 = $nl->get_value($opt5); - my $sup5 = '.false.'; # supported value for this option - if ($var5 ne $sup5) { - $log->warning("$opt5=$sup5 is the supported option; $var5 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt6 = 'snicar_snodst_intmix'; - my $var6 = $nl->get_value($opt6); - my $sup6 = '.false.'; # supported value for this option - if ($var6 ne $sup6) { - $log->warning("$opt6=$sup6 is the supported option; $var6 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt7 = 'snicar_use_aerosol'; - my $var7 = $nl->get_value($opt7); - my $sup7 = '.true.'; # supported value for this option - if ($var7 ne $sup7) { - $log->warning("$opt7=$sup7 is the supported option; $var7 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); - } - my $opt8 = 'do_sno_oc'; - my $var8 = $nl->get_value($opt8); - my $sup8 = '.false.'; # supported value for this option - if ($var8 ne $sup8) { - $log->warning("$opt8=$sup8 is the supported option; $var8 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + + # Error checking in loop + my %supportedSettings = ( 'snicar_solarspec' => "'mid_latitude_winter'", 'snicar_dust_optics' => "'sahara'", 'snicar_numrad_snw' => '5', 'snicar_snobc_intmix' => '.false.', 'snicar_snodst_intmix' => '.false.', 'snicar_use_aerosol' => '.true.', 'do_sno_oc' => '.false.' ); + keys %supportedSettings; + while ( my ($key, $val) = each %supportedSettings ) { + my $var = $nl->get_value($key); + if ( $var ne $val ) { + $log->warning("$key=$val is the supported option; $var is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } } + + # Error checking not in loop + my $key1 = 'snicar_snw_shape'; + my $var1 = $nl->get_value($key1); + my $val1a = "'sphere'"; # supported value for this option + my $val1b = "'hexagonal_plate'"; # supported value for this option + if (($var1 ne $val1a) && ($var1 ne $val1b)) { + $log->warning("$key1=$val1a and $val1b are supported; $var1 is EXPERIMENTAL, UNSUPPORTED, and UNTESTED!"); + } + # snicar_snobc_intmix and snicar_snodst_intmix cannot both be true - if (($var5 eq $var6) && ($var5 ne $sup5)) { - $log->warning("$opt5 = $var5 and $opt6 = $var6 do not work together!"); + my $key1 = 'snicar_snobc_intmix'; + my $key2 = 'snicar_snodst_intmix'; + my $var1 = $nl->get_value($key1); + my $var2 = $nl->get_value($key2); + my $val1 = $supportedSettings{$key1}; # supported value for this option + if (($var1 eq $var2) && ($var1 ne $val1)) { + $log->warning("$key1 = $var1 and $key2 = $var2 do not work together!"); } } From f0260cfaf8fd923c237cc336b34fc1b0ff5bc14f Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 17 Oct 2023 18:29:25 -0600 Subject: [PATCH 1646/2067] Revert snicar_aerforc_diag to original use_snicar_frc --- bld/CLMBuildNamelist.pm | 2 +- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- .../testmods_dirs/clm/SNICARFRC/user_nl_clm | 2 +- doc/ChangeLog | 2 +- src/biogeophys/SurfaceAlbedoMod.F90 | 6 +++--- src/biogeophys/SurfaceAlbedoType.F90 | 15 ++++++--------- src/biogeophys/SurfaceRadiationMod.F90 | 10 +++++----- src/main/clm_varctl.F90 | 2 +- src/main/controlMod.F90 | 8 ++++---- 10 files changed, 24 insertions(+), 27 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 088bbe9ef0..f32b1b29b4 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1993,7 +1993,7 @@ sub setup_logic_snicar_methods { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snobc_intmix' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_snodst_intmix' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_use_aerosol' ); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snicar_aerforc_diag' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_snicar_frc' ); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'do_sno_oc' ); # Error checking in loop diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a47b920f78..e94cdba456 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1566,7 +1566,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 sphere sphere -.false. +.false. mid_latitude_winter sahara .false. diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 10da4ccde7..16231b3c01 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1198,7 +1198,7 @@ DependsOnLatAndVeg - Arctic vegetation depends on latitude as above, but tempera (only used when CN is on) - Toggle to turn on calculation of SNow and Ice Aerosol Radiation model (SNICAR) albedo forcing diagnostics for each aerosol species diff --git a/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm index 449f749457..d03efa953b 100644 --- a/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/SNICARFRC/user_nl_clm @@ -1 +1 @@ - snicar_aerforc_diag = .true. + use_snicar_frc = .true. diff --git a/doc/ChangeLog b/doc/ChangeLog index fae28d1378..ecd91fdc38 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -74,7 +74,7 @@ Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): activate bc-snow and dust-snow internal mixing do_sno_oc, default .false., already appeared in previous code but in caps - snicar_aerforc_diag, default .false., existed before as use_snicar_frc + use_snicar_frc, default .false., existed before fsnowoptics now points to an updated 5-band file and gives the option for a 480-band file diff --git a/src/biogeophys/SurfaceAlbedoMod.F90 b/src/biogeophys/SurfaceAlbedoMod.F90 index d48ba3f063..d23320d5e7 100644 --- a/src/biogeophys/SurfaceAlbedoMod.F90 +++ b/src/biogeophys/SurfaceAlbedoMod.F90 @@ -259,7 +259,7 @@ subroutine SurfaceAlbedo(bounds,nc, & use shr_orb_mod use clm_time_manager , only : get_nstep use abortutils , only : endrun - use clm_varctl , only : use_subgrid_fluxes, snicar_aerforc_diag, use_fates + use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, use_fates use CLMFatesInterfaceMod, only : hlm_fates_interface_type ! !ARGUMENTS: @@ -571,7 +571,7 @@ subroutine SurfaceAlbedo(bounds,nc, & ! If radiative forcing is being calculated, first estimate clean-snow albedo - if (snicar_aerforc_diag) then + if (use_snicar_frc) then ! 1. BC input array: ! set dust and (optionally) OC concentrations, so BC_FRC=[(BC+OC+dust)-(OC+dust)] mss_cnc_aer_in_frc_bc(bounds%begc:bounds%endc,:,5) = mss_cnc_dst1(bounds%begc:bounds%endc,:) @@ -761,7 +761,7 @@ subroutine SurfaceAlbedo(bounds,nc, & albgri(c,ib) = albsoi(c,ib)*(1._r8-frac_sno(c)) + albsni(c,ib)*frac_sno(c) ! albedos for radiative forcing calculations: - if (snicar_aerforc_diag) then + if (use_snicar_frc) then ! BC forcing albedo albgrd_bc(c,ib) = albsod(c,ib)*(1.-frac_sno(c)) + albsnd_bc(c,ib)*frac_sno(c) albgri_bc(c,ib) = albsoi(c,ib)*(1.-frac_sno(c)) + albsni_bc(c,ib)*frac_sno(c) diff --git a/src/biogeophys/SurfaceAlbedoType.F90 b/src/biogeophys/SurfaceAlbedoType.F90 index a35d99e478..a8b645b84a 100644 --- a/src/biogeophys/SurfaceAlbedoType.F90 +++ b/src/biogeophys/SurfaceAlbedoType.F90 @@ -7,7 +7,7 @@ module SurfaceAlbedoType use decompMod , only : bounds_type use clm_varpar , only : numrad, nlevcan, nlevsno use abortutils , only : endrun - use clm_varctl , only : use_SSRE, snicar_aerforc_diag + use clm_varctl , only : use_SSRE, use_snicar_frc ! ! !PUBLIC TYPES: implicit none @@ -255,7 +255,7 @@ subroutine InitHistory(this, bounds) ptr_patch=this%albi_patch, default=defaultoutput, c2l_scale_type='urbanf') ! add new snicar output variables for albedo for history files only - if (snicar_aerforc_diag) then + use_snicar_frc_if: if (use_snicar_frc) then this%albd_hst_patch(begp:endp,:) = spval call hist_addfld2d (fname='ALBD_HIST', units='proportion', type2d='numrad', & @@ -327,7 +327,7 @@ subroutine InitHistory(this, bounds) avgflag='A', long_name='snow albedo (diffuse)', & ptr_col=this%albsni_hst2_col, default='inactive') - end if ! end of snicar_aerforc_diag + end if use_snicar_frc_if ! end add new snicar end subroutine InitHistory @@ -390,7 +390,7 @@ subroutine Restart(this, bounds, ncid, flag, & ! Read/Write module information to/from restart file. ! ! !USES: - use clm_varctl , only : snicar_aerforc_diag, iulog + use clm_varctl , only : use_snicar_frc, iulog use spmdMod , only : masterproc use decompMod , only : bounds_type use abortutils , only : endrun @@ -562,7 +562,7 @@ subroutine Restart(this, bounds, ncid, flag, & this%vcmaxcintsha_patch(begp:endp) = 1._r8 end if - if (snicar_aerforc_diag) then + use_snicar_frc_if: if (use_snicar_frc) then call restartvar(ncid=ncid, flag=flag, varname='albgrd_bc', xtype=ncd_double, & dim1name='column', dim2name='numrad', switchdim=.true., & @@ -652,10 +652,7 @@ subroutine Restart(this, bounds, ncid, flag, & this%albgri_dst_col(begc:endc,:) = this%albgri_col(begc:endc,:) end if - end if ! end of if-snicar_aerforc_diag - ! add new snicar output variables for albedo for history files only - if (snicar_aerforc_diag) then call restartvar(ncid=ncid, flag=flag, varname='albd_hist', xtype=ncd_double, & dim1name='pft', dim2name='numrad', switchdim=.true., & @@ -741,7 +738,7 @@ subroutine Restart(this, bounds, ncid, flag, & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%albgri_dst_hst_col) - end if ! end of if-snicar_aerforc_diag + end if use_snicar_frc_if ! end add new snicar ! patch type physical state variable - fabd diff --git a/src/biogeophys/SurfaceRadiationMod.F90 b/src/biogeophys/SurfaceRadiationMod.F90 index 97f3b12eab..03557c6476 100644 --- a/src/biogeophys/SurfaceRadiationMod.F90 +++ b/src/biogeophys/SurfaceRadiationMod.F90 @@ -7,7 +7,7 @@ module SurfaceRadiationMod ! !USES: use shr_kind_mod , only : r8 => shr_kind_r8 use shr_log_mod , only : errMsg => shr_log_errMsg - use clm_varctl , only : snicar_aerforc_diag, use_fates + use clm_varctl , only : use_snicar_frc, use_fates use decompMod , only : bounds_type, subgrid_level_column use atm2lndType , only : atm2lnd_type use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type @@ -173,7 +173,7 @@ subroutine InitHistory(this, bounds) begp = bounds%begp; endp = bounds%endp begc = bounds%begc; endc = bounds%endc - if (snicar_aerforc_diag) then + if (use_snicar_frc) then this%sfc_frc_aer_patch(begp:endp) = spval call hist_addfld1d (fname='SNOAERFRCL', units='W/m^2', & avgflag='A', long_name='surface forcing of all aerosols in snow (land) ', & @@ -477,7 +477,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & use clm_varpar , only : numrad, nlevsno use clm_varcon , only : spval use landunit_varcon , only : istsoil, istcrop - use clm_varctl , only : use_subgrid_fluxes, snicar_aerforc_diag, iulog, use_SSRE, do_sno_oc + use clm_varctl , only : use_subgrid_fluxes, use_snicar_frc, iulog, use_SSRE, do_sno_oc use clm_time_manager , only : get_step_size_real, is_near_local_noon use abortutils , only : endrun ! @@ -719,7 +719,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & sabg_soil(p) = sabg(p) endif - if (snicar_aerforc_diag) then + if (use_snicar_frc) then ! Solar radiation absorbed by ground surface without BC absrad_bc = trd(p,ib)*(1._r8-albgrd_bc(c,ib)) + tri(p,ib)*(1._r8-albgri_bc(c,ib)) sabg_bc(p) = sabg_bc(p) + absrad_bc @@ -849,7 +849,7 @@ subroutine SurfaceRadiation(bounds, num_nourbanp, filter_nourbanp, & sabg_pen(p) = sabg(p) - sabg_lyr(p, snl(c)+1) end if - if (snicar_aerforc_diag) then + if (use_snicar_frc) then ! BC aerosol forcing (patch-level): sfc_frc_bc(p) = sabg(p) - sabg_bc(p) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 7fc0676b78..8ebc8fb08d 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -457,7 +457,7 @@ module clm_varctl logical, public :: use_cndv = .false. logical, public :: use_grainproduct = .false. logical, public :: use_fertilizer = .false. - logical, public :: snicar_aerforc_diag = .false. + logical, public :: use_snicar_frc = .false. logical, public :: use_vancouver = .false. logical, public :: use_mexicocity = .false. logical, public :: use_noio = .false. diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 244a34bb8c..f19f135cb9 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -283,14 +283,14 @@ subroutine control_init(dtime) namelist /clm_inparm/ & use_lch4, use_nitrif_denitrif, use_extralakelayers, & use_vichydro, use_cn, use_cndv, use_crop, use_fertilizer, & - use_grainproduct, use_vancouver, use_mexicocity, use_noio, & + use_grainproduct, use_snicar_frc, use_vancouver, use_mexicocity, use_noio, & use_nguardrail ! SNICAR namelist /clm_inparm/ & snicar_numrad_snw, snicar_solarspec, snicar_dust_optics, & snicar_use_aerosol, snicar_snw_shape, snicar_snobc_intmix, & - snicar_snodst_intmix, snicar_aerforc_diag, do_sno_oc + snicar_snodst_intmix, do_sno_oc ! ---------------------------------------------------------------------- ! Default values @@ -694,7 +694,7 @@ subroutine control_spmd() call mpi_bcast (use_fertilizer, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_grainproduct, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (o3_veg_stress_method, len(o3_veg_stress_method), MPI_CHARACTER, 0, mpicom, ier) - call mpi_bcast (snicar_aerforc_diag, 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (use_snicar_frc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_vancouver, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_mexicocity, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (use_noio, 1, MPI_LOGICAL, 0, mpicom, ier) @@ -954,7 +954,7 @@ subroutine control_print () write(iulog,*) ' use_fertilizer = ', use_fertilizer write(iulog,*) ' use_grainproduct = ', use_grainproduct write(iulog,*) ' o3_veg_stress_method = ', o3_veg_stress_method - write(iulog,*) ' snicar_aerforc_diag = ', snicar_aerforc_diag + write(iulog,*) ' use_snicar_frc = ', use_snicar_frc write(iulog,*) ' snicar_use_aerosol = ',snicar_use_aerosol write(iulog,*) ' use_vancouver = ', use_vancouver write(iulog,*) ' use_mexicocity = ', use_mexicocity From 1ce737fc37ad55e3720c28d45fef03246967db80 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 16 Oct 2023 11:00:03 -0600 Subject: [PATCH 1647/2067] Simplify some superscripts. --- .../Isotopes/CLM50_Tech_Note_Isotopes.rst | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index f7fcbd5cb5..292a8ab296 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -44,13 +44,13 @@ proportion to the masses :math:`{CS}_{13C\_up}` and heavier isotope. Currently, in all cases where Eq. is used to calculate a :sup:`13`\ C flux, :math:`{f}_{frac}` is set to 1.0. -For :sup:`1`\ :sup:`4`\ C, no fractionation is used in +For :sup:`14`\ C, no fractionation is used in either the initial photosynthetic step, nor in subsequent fluxes from upstream to downstream pools; as discussed below, this is because -observations of :sup:`1`\ :sup:`4`\ C are typically +observations of :sup:`14` C are typically described in units that implicitly correct out the fractionation of -:sup:`1`\ :sup:`4`\ C by referencing them to -:sup:`1`\ :sup:`3`\ C ratios. +:sup:`14`\ C by referencing them to +:sup:`13`\ C ratios. Isotope Symbols, Units, and Reference Standards ---------------------------------------------------- @@ -97,15 +97,15 @@ This can also be expressed using epsilon notation (:math:`\epsilon`), where In other words, if :math:`{\epsilon }_{A-B} = 4.4` ‰ , then :math:`{\alpha}_{A-B} =1.0044`. -In addition to the stable isotopes :sup:`1`\ :sup:`2`\ C and :sup:`1`\ :sup:`3`\ C, the unstable isotope -:sup:`1`\ :sup:`4`\ C is included in CLM. :sup:`1`\ :sup:`4`\ C can also be described using the delta notation: +In addition to the stable isotopes :sup:`1`\ :sup:`2`\ C and :sup:`13`\ C, the unstable isotope +:sup:`14`\ C is included in CLM. :sup:`14`\ C can also be described using the delta notation: .. math:: :label: 30.6) \delta ^{14} C=\left(\frac{A_{s} }{A_{abs} } -1\right)\times 1000 -However, observations of :sup:`1`\ :sup:`4`\ C are typically +However, observations of :sup:`14`\ C are typically fractionation-corrected using the following notation: .. math:: From 8456a24fd7b860f5f6ae8b3e080b53e5b709da85 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 12 Oct 2023 18:13:10 -0600 Subject: [PATCH 1648/2067] Maximum one empty line in a row. --- .../obtaining-and-building-ctsm.rst | 1 - .../lilac/specific-atm-models/wrf-nesting.rst | 12 --------- .../lilac/specific-atm-models/wrf-tools.rst | 10 ------- doc/source/lilac/specific-atm-models/wrf.rst | 19 ------------- .../CLM50_Tech_Note_CN_Allocation.rst | 4 --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 14 ---------- .../tech_note/DGVM/CLM50_Tech_Note_DGVM.rst | 2 -- .../CLM50_Tech_Note_Decomposition.rst | 5 ---- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 1 - ...LM50_Tech_Note_External_Nitrogen_Cycle.rst | 2 -- .../tech_note/FUN/CLM50_Tech_Note_FUN.rst | 27 ------------------- .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 2 -- .../Hydrology/CLM50_Tech_Note_Hydrology.rst | 7 ----- .../CLM50_Tech_Note_Introduction.rst | 3 --- .../Isotopes/CLM50_Tech_Note_Isotopes.rst | 1 - .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 1 - .../MOSART/CLM50_Tech_Note_MOSART.rst | 4 --- .../Methane/CLM50_Tech_Note_Methane.rst | 1 - .../CLM50_Tech_Note_Photosynthesis.rst | 5 ---- ...LM50_Tech_Note_Photosynthetic_Capacity.rst | 13 --------- .../CLM50_Tech_Note_Plant_Hydraulics.rst | 4 --- .../CLM50_Tech_Note_Plant_Mortality.rst | 1 - .../CLM50_Tech_Note_Radiative_Fluxes.rst | 1 - .../References/CLM50_Tech_Note_References.rst | 2 -- .../CLM50_Tech_Note_Snow_Hydrology.rst | 5 ---- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 2 -- .../CLM50_Tech_Note_Surface_Albedos.rst | 1 - .../tech_note/Urban/CLM50_Tech_Note_Urban.rst | 1 - ...w-Files-to-the-build-namelist-Database.rst | 1 - .../Adding-or-Changing-Default-Filenames.rst | 4 --- .../running-PTCLM/adding-ptclm-site-data.rst | 2 -- .../running-PTCLM/introduction-to-ptclm.rst | 2 -- .../running-single-point-configurations.rst | 3 --- ...transient-historical-CO2-concentration.rst | 1 - ...tmospheric-forcing-to-spinup-the-model.rst | 1 - ...ning-up-the-biogeochemistry-BGC-spinup.rst | 2 -- .../running-with-irrigation.rst | 1 - .../choosing-a-compset.rst | 1 - .../customizing-the-clm-configuration.rst | 7 ----- .../customizing-the-clm-namelist.rst | 5 ---- .../customizing-the-datm-namelist.rst | 1 - doc/source/users_guide/testing/index.rst | 1 - doc/source/users_guide/testing/testing.rst | 3 --- ...g-input-for-surface-dataset-generation.rst | 2 -- .../datasts-for-observational-sites.rst | 1 - .../what-are-the-clm-tools.rst | 1 - 46 files changed, 190 deletions(-) diff --git a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst index 99cb908d28..c0e510c017 100644 --- a/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst +++ b/doc/source/lilac/obtaining-building-and-running/obtaining-and-building-ctsm.rst @@ -250,7 +250,6 @@ Makefile-formatted file gives variables that should be set in the atmosphere mod build. :ref:`See below for information on how to use this file`. - Rebuilding after changing CTSM source code ------------------------------------------ diff --git a/doc/source/lilac/specific-atm-models/wrf-nesting.rst b/doc/source/lilac/specific-atm-models/wrf-nesting.rst index 39c2fe94dd..f4c4570f2f 100644 --- a/doc/source/lilac/specific-atm-models/wrf-nesting.rst +++ b/doc/source/lilac/specific-atm-models/wrf-nesting.rst @@ -50,10 +50,8 @@ A full description of all steps for a WRF-CTSM run are included here. Therefore, we are not repeating the steps necessary for building WRF and CTSM. - In this example we use a nested domain over the CONUS as shows below: - .. _Figure ctsm-ndown: .. figure:: ndown_ctsm_diagram.svg @@ -128,7 +126,6 @@ Check ungrib log for the following message showing successful completion of ungr At this point, you should see ungrib output (intermediate files) in your WPS directory. - Nested Simulations : Pre-processing (metgrid.exe) ------------------------------------------------- Ensure that the `start_date` and `end_date` for domain two is set correctly for @@ -144,15 +141,12 @@ metgrid step:: ! Successful completion of metgrid. ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - Running metgrid for two domains will create files like below:: met_em.d01.* met_em.d02.* - - Nested Simulations : real.exe ------------------------------ @@ -172,7 +166,6 @@ domains:: sf_surface_physics = 6, 6, - Run real.exe (if compiled parallel submit a batch job) to generate initail and boundary condition files for both domain. Make sure the following three files have been created in your directory:: @@ -226,7 +219,6 @@ have already created these files for the coarser domain. files for the finer domain you should follow the steps in section :numref:`setting-ctsm-runtime-options`. - Again, the goal here is to create files that determine CTSM runtime options which are defined within these three files: @@ -236,14 +228,12 @@ are defined within these three files: - ``lilac_in``: This namelist controls the operation of LILAC - Run WRF for the finer domain ----------------------------- First, save (rename or move) the data from the coarser domain simulation (``wrfout_d01_*`` files). Next, rename ``wrfinput_d02`` and ``wrfbdy_d02`` to ``wrfinput_d01`` and ``wrfbdy_d01``, respectively. - Edit namelist.input, moving all of the fine-grid domain data from column 2 to column 1 so that this run will be for the fine-grid domain only. Make sure you set `max_dom=1` and set your `time_step` based on the finer domain. @@ -259,5 +249,3 @@ Now run wrf.exe by submitting a job similar to a not-nested case. The output for the finer domain is wrfout_d01_* not wrfout_d02_* and although in the name it is saying d01 it is technically d02 domain. - - diff --git a/doc/source/lilac/specific-atm-models/wrf-tools.rst b/doc/source/lilac/specific-atm-models/wrf-tools.rst index 8b3c423a58..0366bc1582 100644 --- a/doc/source/lilac/specific-atm-models/wrf-tools.rst +++ b/doc/source/lilac/specific-atm-models/wrf-tools.rst @@ -9,8 +9,6 @@ This section includes instructions on tools and utilities developed for WRF-CTSM simulations. - - Generate CTSM surface dataset for a WRF domain ---------------------------------------------- @@ -18,7 +16,6 @@ Before this step, make sure you have successfully created geo_em* files for your specific WRF domain using WPS. Instructions on how to run ``geogrid.exe`` is described in here. - 1. Create SCRIP grid file from WRF ``geo_em*`` files, using the following ncl script:: @@ -39,7 +36,6 @@ is described in here. ncl mkunitymap.ncl - .. warning:: This will throw some git errors if not run in a repository. @@ -52,7 +48,6 @@ is described in here. ../../../configure --macros-format Makefile --mpilib mpi-serial - 5. Generate CTSM domain files using ``get_domain`` tool:: ./gen_domain -m /glade/work/$USER/ctsm/nldas_grid/scrip/wrf2clm_mapping_noneg.nc -o wrf2clm_ocn_noneg -l wrf2clm_lnd_noneg @@ -61,20 +56,15 @@ is described in here. ./mksurfdata.pl -res usrspec -usr_gname "nldas" -usr_gdate "190124" -usr_mapdir "/glade/work/$USER/ctsm/nldas_grid/map" -y 2000 -exedir "/glade/u/home/$USER/src/ctsm/ctsm_surfdata/tools/mksurfdata_map" -no-crop - - Merge WRF initial conditions into an existing CTSM initial condition file -------------------------------------------------------------------------- The following procedure is if you'd wish to merget WRF inital conditions from ``wrfinput`` file into CTSM initial condition file :: - ncl transfer_wrfinput_to_ctsm_with_snow.ncl 'finidat="the_existing_finidat_file.nc"' 'wrfinput="your_wrfinput_file"' 'merged="the_merged_finidat_file.nc"' - .. todo:: Sam, can you please make the above ncl script available. - diff --git a/doc/source/lilac/specific-atm-models/wrf.rst b/doc/source/lilac/specific-atm-models/wrf.rst index ea54d20ab4..5d104778ec 100644 --- a/doc/source/lilac/specific-atm-models/wrf.rst +++ b/doc/source/lilac/specific-atm-models/wrf.rst @@ -29,7 +29,6 @@ and :numref:`wrf-set-ctsm-runtime-options`. In this example we assume NCAR's ``Cheyenne`` HPC system in particular. - .. _clone-WRF-CTSM-repositories: Clone WRF and CTSM Repositories @@ -41,14 +40,12 @@ Clone the WRF repository and checkout ``develop`` branch:: cd WRF-CTSM git checkout develop - Clone the CTSM repository:: git clone https://github.com/ESCOMP/CTSM.git cd CTSM ./manage_externals/checkout_externals - .. _build-CTSM-and-dependencies: Build CTSM and its dependencies @@ -63,7 +60,6 @@ For example on ``Cheyenne`` and for ``Intel`` compiler:: ./lilac/build_ctsm ctsm_build_dir --compiler intel --machine cheyenne - .. warning:: The directory you provided for the build script (``/PATH/TO/CTSM/BUILD``) must *not* exist. @@ -74,7 +70,6 @@ For example on ``Cheyenne`` and for ``Intel`` compiler:: Run ``./lilac/build_ctsm -h`` to see all options available. For example if you would like to run with threading support you can use ``--build-with-openmp``. - Building WRF with CTSM ---------------------- @@ -108,7 +103,6 @@ Some of these are not required, but might help if you face any compilation error For more information check `WRF Users' Guide `_. - Explicitly define the model core to build by (Bash):: export WRF_EM_CORE=1 @@ -119,7 +113,6 @@ or (Cshell): setenv WRF_EM_CORE 1 - Explicilty turn off data assimilation by (Bash):: export WRF_DA_CORE=0 @@ -149,12 +142,10 @@ distributed memory parallelization (``dmpar``). The next prompt requests an option for nesting. Currently nesting is not available for WRF-CTSM so select option ``1 (basic)``. - Now compile em_real and save the log:: ./compile em_real >& compile.log - Check the bottom of your log file for a successful compilation message. .. note:: @@ -178,7 +169,6 @@ skip to section :numref:`wrf-set-ctsm-runtime-options`. Building WPS requires that WRF be already built successfully. - Get WPS from this website:: https://www2.mmm.ucar.edu/wrf/users/download/wrf-regist_or_download.php @@ -202,7 +192,6 @@ Then, compile WPS:: If wps builds succesfully you should see ``geogrid.exe``, ``ungrib.exe``, and ``metgrid.exe``. Alternatively, you can check the log for successful build messages. - Run WPS Programs ---------------- @@ -253,7 +242,6 @@ metgrid step:: ! Successful completion of metgrid. ! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! - Run real.exe ------------ @@ -267,23 +255,19 @@ Move or link WPS output files (``met_em.d01*`` files) to your WRF test directory Edit namelist.input for your WRF domain and desirable configurations. This should be the same domain as WPS namelist. - To run WRF-CTSM, in your namelist change land-surface option to 6:: sf_surface_physics = 6 - Run real.exe (if compiled parallel submit a batch job) to generate ``wrfinput`` and ``wrfbdy`` files. - Check the last line of the real log file for the following message:: SUCCESS COMPLETE REAL_EM INIT .. _wrf-set-ctsm-runtime-options: - Set CTSM runtime options ------------------------ @@ -301,7 +285,6 @@ are defined within these three files: - ``lilac_in``: This namelist controls the operation of LILAC - The basic process for creating the necessary input files are summarized as follows: @@ -344,7 +327,6 @@ Modify ``lilac_in`` as needed. For this example, you can use the following optio atm_mesh_filename = '/glade/scratch/negins/wrf_ctsm_files/wrf2ctsm_land_conus_ESMFMesh_c20201110.nc' lnd_mesh_filename = '/glade/scratch/negins/wrf_ctsm_files/wrf2ctsm_land_conus_ESMFMesh_c20201110.nc' - Run ``download_input_data`` script to download any of CTSM's standard input files that are needed based on settings in ``lnd_in`` and ``lilac_in``:: @@ -401,4 +383,3 @@ For example, if you named this script ``run_wrf_ctsm.csh``, submit the job like qsub run_wrf_ctsm.csh - diff --git a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst index 33faae1a4c..ea07ec4347 100644 --- a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst +++ b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst @@ -6,13 +6,11 @@ Carbon and Nitrogen Allocation Introduction ----------------- - The carbon and nitrogen allocation routines in CLM determine the fate of newly assimilated carbon, coming from the calculation of photosynthesis, and available mineral nitrogen, coming from plant uptake of mineral nitrogen in the soil or being drawn out of plant reserves. A significant change to CLM5 relative to prior versions is that allocation of carbon and nitrogen proceed independently rather than in a sequential manner. - Carbon Allocation for Maintenance Respiration Costs -------------------------------------------------------- @@ -315,8 +313,6 @@ tissue types are given as: CF_{alloc,deadcroot\_ stor} \_ =CF_{alloc,leaf\_ tot} a_{2} a_{3} \left(1-a_{4} \right)\left(1-f_{cur} \right). - - Nitrogen allocation ----------------------------------------- diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index fb6d66dd42..91a1e7232a 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -40,14 +40,10 @@ refers to the interactive crop management model and is included as an option wit These updates appear in detail in the sections below. Many also appear in :ref:`Levis et al. (2016) `. - Available new features since the CLM5 release ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Addition of bioenergy crops - - - .. _The crop model: The crop model: cash and bioenergy crops @@ -132,7 +128,6 @@ About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest observation data collected at the University of Illinois Energy Farm located in Central Midwestern United States (:ref:`Cheng et al., 2019`). - In addition, CLM's default list of plant functional types (pfts) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. The unmanaged C3 crop is only used when the crop model is not active and @@ -225,8 +220,6 @@ managed crop types that are using the same parameter set. 78 irrigated tropical soybean active irrigated tropical soybean === =========================== ================ =========================== - - .. _Phenology: Phenology @@ -360,7 +353,6 @@ the number of days past planting reaches a crop-specific maximum (:numref:`Table Crop phenology parameters`), then the crop is harvested. Harvest occurs in one time step using the BGC leaf offset algorithm. - .. _Table Crop phenology parameters: .. table:: Crop phenology and morphology parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. @@ -444,7 +436,6 @@ CO\ :sub:`2` directly from the atmosphere. This way any excess maintenance respiration remaining at harvest is eliminated as if such respiration had not taken place. - .. _Leaf emergence to grain fill: Leaf emergence @@ -677,7 +668,6 @@ efficiency of 85%. Grain\ yield(g.m^{-2})=\frac{\sum(GRAINC\_ TO\_ FOOD)*0.85}{0.45} - .. _Table Crop allocation parameters: .. table:: Crop allocation parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. @@ -708,7 +698,6 @@ Notes: Crop growth phases and corresponding variables are described throughout the text. :math:`{CN}_{leaf}`, :math:`{CN}_{stem}`, and :math:`{CN}_{froot}` are the target C:N ratios used during the leaf emergence phase (phase 2). - .. _Other Features: Other Features @@ -728,7 +717,6 @@ simulate a post-harvest "stubble" on the ground. Crop heights at the top and bottom of the canopy, :math:`{z}_{top}` and :math:`{z}_{bot}` (m), come from the AgroIBIS formulation: - .. math:: :label: 25.16 @@ -786,7 +774,6 @@ to the total fertilizer at each column within the grid cell divided by the initi Fertilizer is applied and *f* is decremented each time step until a zero balance on the counter is reached. - .. _Biological nitrogen fixation for soybeans: Biological nitrogen fixation for soybeans @@ -835,7 +822,6 @@ In CLM5BGCCROP, as allocation declines in stem, leaf, and root pools (see sectio during the grain fill stage of growth, increasing amounts of carbon and nitrogen are available for grain development. - .. _The irrigation model: The irrigation model diff --git a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst index c62591b70c..b664311bcb 100644 --- a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst +++ b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst @@ -10,7 +10,6 @@ What has changed - Introduction of FATES: The Functionally Assembled Terrestrial Ecosystem Simulator (FATES) is the actively developed DGVM for the CLM5. - FATES ^^^^^^^^^^^^^^^^^^^^ @@ -35,7 +34,6 @@ radiation transfer, for drought-deciduous and cold-deciduous phenology, for carbon storage allocation, and for tree mortality under carbon stress, are also included. - Further reading ^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index fbe490a70a..557678ce07 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -538,7 +538,6 @@ The N available to the FUN model for plant uptake (:math:`{NF}_ {plant\_ avail\_ NF_{plant\_ avail\_ sminn,j} = NS_{sminn,j} - f_{immob\_demand} NF_{immob\_ demand,j} - This treatment of competition for nitrogen as a limiting resource is referred to a demand-based competition, where the fraction of the available resource that eventually flows to a particular process depends @@ -546,7 +545,6 @@ on the demand from that process in comparison to the total demand from all processes. Processes expressing a greater demand acquire a larger vfraction of the available resource. - Final Decomposition Fluxes ------------------------------- @@ -825,6 +823,3 @@ product of the base acceleration term and :math:`{a}_{l}` below: a_l = 1 + 50 / \left ( 1 + exp \left (-0.1 * (abs(latitude) - 60 ) \right ) \right ) - - - diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst index 6f9005da38..07be360cad 100644 --- a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst +++ b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst @@ -867,7 +867,6 @@ are described in the text. Physical constants, generally shared by all of the components in the coupled modeling system, are presented in :numref:`Table Physical constants`. - .. _Table Physical constants: .. csv-table:: Physical constants diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index 1e1659ad52..9295e7e46c 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -80,7 +80,6 @@ supplied with previous versions of the model. In coupled simulations, N depositions fluxes are passed to the land model at the frequency of the time step (every half hour) through the coupler. - Biological Nitrogen Fixation --------------------------------- @@ -115,7 +114,6 @@ under global change scenarios (:ref:`Wieder et al. 2015 Where :math:`{NF}_{nfix,sminn}` (gN m\ :sup:`-2` s\ :sup:`-1`) is the rate of free-living nitrogen fixation in :numref:`Figure Biological nitrogen fixation`. - .. _Figure Biological nitrogen fixation: .. figure:: image1.png diff --git a/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst b/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst index bea5cb99e5..88abf78d7a 100644 --- a/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst +++ b/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst @@ -6,7 +6,6 @@ Fixation and Uptake of Nitrogen (FUN) Introduction ----------------- - The Fixation and Uptake of Nitrogen model is based on work by :ref:`Fisher et al. (2010)`, :ref:`Brzostek et al. (2014)`, and :ref:`Shi et al. (2016)`. The concept of FUN is that in most cases, Nitrogen uptake requires the expenditure of energy in the form of carbon, and further, that there are numerous potential sources of Nitrogen in the environment which a plant may exchange for carbon. The ratio of carbon expended to Nitrogen acquired is referred to here as the cost, or exchange rate, of N acquisition (:math:`E_{nacq}`, gC/gN)). There are eight pathways for N uptake: 1. Fixation by symbiotic bacteria in root nodules (for N fixing plants) (:math:`_{fix}`) @@ -18,17 +17,12 @@ The Fixation and Uptake of Nitrogen model is based on work by :ref:`Fisher et al 7. Nonmycorrhizal uptake of NH4 (:math:`_{nonmyc,no3}`) 8. Nonmycorrhizal uptake of NO3 (:math:`_{nonmyc,nh4}`) - The notation suffix for each pathway is given in parentheses here. At each timestep, each of these pathways is associated with a cost term (:math:`N_{cost,x}`), a payment in carbon (:math:`C_{nuptake,x}`), and an influx of Nitrogen (:math:`N_{uptake,x}`) where :math:`x` is one of the eight uptake streams listed above. - For each PFT, we define a fraction of the total C acquisition that can be used for N fixation (:math:`f_{fixers}`), which is broadly equivalent to the fraction of a given PFT that is capable of fixing Nitrogen, and thus represents an upper limit on the amount to which fixation can be increased in low n conditions. For each PFT, the cost calculation is conducted twice. Once where fixation is possible and once where it is not. (:math:`f_{fixers}`) - For all of the active uptake pathways, whose cost depends on varying concentrations of N through the soil profile, the costs and fluxes are also determined by soil layer :math:`j`. - - Boundary conditions of FUN -------------------------------------------------------- @@ -54,8 +48,6 @@ The cost of fixation is derived from :ref:`Houlton et al. (2008) N_{avail,no3}`, we calculate the unmet uptake, :math:`N_{unmet,no3}` .. math:: @@ -371,7 +349,6 @@ then modify both fluxes to account N_{nonmyc,nh4} = N_{nonmyc,nh4} + N_{unmet,nh4}.\frac{N_{nonmyc,nh4}}{N_{active,nh4}+N_{nonmyc,nh4}} - and then update the C spent to account for hte new lower N acquisition in that layer/pool. .. math:: @@ -381,13 +358,9 @@ and then update the C spent to account for hte new lower N acquisition in that l C_{nonmyc,no3} = N_{nonmyc,no3}.N_{cost,nonmyc,no3}\\ C_{nonmyc,no3} = N_{nonmyc,no3}.N_{cost,nonmyc,no3}\\ - Following this, we determine how much carbon is accounted for for each soil layer. .. math:: C_{accounted,x,j} = C_{spent,j,x} - (N_{acquired,j,x}.CN_{plant}.(1.0+ gr_{frac})) - - - diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index b46b73ae6a..4a69a4a90d 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -385,7 +385,6 @@ Unstable :math:`\left(-0.465\le \zeta <0\right)` \theta _{atm} -\theta _{s} =\frac{\theta _{*} }{k} \left\{\left[\ln \frac{z_{atm,\, h} -d}{z_{0h} } -\psi _{h} \left(\zeta \right)\right]+\psi _{h} \left(\frac{z_{0h} }{L} \right)\right\} - Stable :math:`\left(0\le \zeta \le 1\right)` .. math:: @@ -450,7 +449,6 @@ bulk Richardson number R_{iB} =\frac{\theta _{v,\, atm} -\theta _{v,\, s} }{\overline{\theta _{v,\, atm} }} \frac{g\left(z_{atm,\, m} -d\right)}{V_{a}^{2} } - is related to :math:`\zeta` (:ref:`Arya 2001 `) as .. math:: diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 0258c2e3c9..49e5567349 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -123,7 +123,6 @@ and W_{can,sno}^{intr} =W_{can,sno}^{n} +q_{intr,\, ice} \Delta t\ge 0 - are the the canopy liquid water and snow water equivalent after accounting for interception, :math:`W_{can,\,liq}^{n}` and :math:`W_{can,\,sno}^{n}` are the canopy liquid and snow water from the previous time step, and :math:`W_{can,\,liq}^{max }` and :math:`W_{can,\,snow}^{max }` @@ -163,7 +162,6 @@ fluxes and e-folding times similar to :ref:`Roesch et al. (2001) ` for CLM5.0). diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 292a8ab296..59c01f3863 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -210,4 +210,3 @@ either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 :sup:`o`\ N-90 :sup:`o`\ N, 30 :sup:`o`\ S-30 :sup:`o`\ N, and 30 :sup:`o`\ S-90 :sup:`o`\ S). - diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 941932c8a3..887e65f763 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -628,7 +628,6 @@ the 2-m wind speed :math:`u_{2}` (m s\ :sup:`-1`) (eq. ) is used to evaluate :math:`w^{*}` and :math:`k^{*}` rather than the 10-m wind used by :ref:`Henderson-Sellers (1985) `. - The Richardson number is .. math:: diff --git a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst index a3f626147e..54d1a8db1e 100644 --- a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst +++ b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst @@ -108,7 +108,6 @@ be written as \frac{dS}{dt} = Q_{in} - Q_{out} + R - where :math:`Q_{in}` (m :sup:`3` s :sup:`-1` ) is the main channel flow from the upstream grid(s) into the main channel of the current grid, which is zero for hillslope and sub-network routing. :math:`Q_{out}` (m :sup:`3` s :sup:`-1` ) is @@ -222,8 +221,6 @@ by MOSART using the aforementioned parameters is described in | :math:`n_{h}` | \- | Manning's roughness coefficient for overland flow routing | +-------------------------+---------------+------------------------------------------------------------------------------------------------------------------------------------+ - - Difference between CLM5.0 and CLM4.5 ------------------------------------- @@ -244,4 +241,3 @@ are all available globally at 0.5 :sup:`o` resolution. additionally simulates the time-varying channel velocities, channel water depth, and channel surface water variations. - diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index 4cab8d6f58..dd2f40040f 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -225,7 +225,6 @@ O\ :sub:`2` mass balance solution. | | :math:`R_{o,\max }` | 1.25 x 10\ :math:`{}^{-5}` | 1.25\ :math:`\times`\ 10\ :math:`{}^{-6}` - 1.25\ :math:`\times`\ 10\ :math:`{}^{-4}` | mol m\ :sup:`-3` s\ :sup:`-1` | Maximum oxidation rate (wetlands) | +--------------+----------------------------+----------------------------------------------+--------------------------------------------------------------------------------------------------+---------------------------------------------+--------------------------------------------------------------------------------------------+ - Ebullition --------------- diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index e0288c08b0..b45e117c23 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -20,7 +20,6 @@ CLM5 includes the following new changes to photosynthesis and stomatal conductan - Water stress is applied by the hydraulic conductance model (Chapter :numref:`rst_Plant Hydraulics`) - Introduction ----------------------- @@ -394,7 +393,6 @@ When LUNA is on, the :math:`V_{c\max 25}` for sun leaves is scaled to the shaded :math:`J_{\max 25}` , :math:`T_{p25}` , :math:`k_{p25}`, and :math:`R_{d25}` scale similarly. - .. math:: :label: 9.17 @@ -480,7 +478,6 @@ In terms of conductance with e_{s} =\frac{e_{a} g_{b} +e_{i} g_{s} }{g_{b} +g_{s} } . - Substitution of equation :eq:`9.36` into equation :eq:`9.1` gives an expression for the stomatal resistance (:math:`r_{s}`) as a function of photosynthesis @@ -511,7 +508,6 @@ and D_{l} = \frac {max(e_{i} - e_{a},50)} {1000} - Stomatal conductance, as solved by equation :eq:`9.36` (mol m :sup:`-2` s :sup:`-1`), is the larger of the two roots that satisfy the quadratic equation. Values for :math:`c_{i}` are given by @@ -529,4 +525,3 @@ combines the secant method and Brent's method to solve for (:math:`A_{n}^{sun}` , :math:`r_{s}^{sun}` ) and shaded (:math:`A_{n}^{sha}` , :math:`r_{s}^{sha}` ) leaves. - diff --git a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst index 242a99b4cc..e7551f5434 100755 --- a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst +++ b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst @@ -42,7 +42,6 @@ still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitroge however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. - .. _Model structure: Model structure @@ -187,7 +186,6 @@ The baseline electron transport rate, :math:`J_{\text{max}0}`, is calculated as J_{\text{max}0} = J_{\text{max}b0}{\text{FNC}}_{\mathrm{a}}{\text{NUE}}_{J_{\text{{max}}}} - where :math:`J_{\text{max}b0}` (unitless) is the baseline proportion of nitrogen allocated for electron transport rate. :math:`{\text{NUE}}_{J_{\text{{max}}}}` ( :math:`{\mu} mol` electron /s/g N) is the nitrogen use efficiency of :math:`J_{\text{{max}}}`. :math:`J_{\text{max}b1}` (unitless) is a coefficient determining the response of the electron @@ -219,7 +217,6 @@ on the above assumptions, we have \right) = \left(1-\mathrm{e}^{\left(-H \frac{\text{max}\left(\text{RH}-{\text{RH}}_{0}, 0 \right)}{1-\text{RH}_{0}} \right)} \right), - where :math:`H` (unitless) specifies the impact of relative humidity on electron transport rate. The efficiency of light energy absorption (unitless), :math:`\alpha`, is calculated @@ -231,7 +228,6 @@ depending on the amount of nitrogen allocated for light capture, \alpha =\frac{0.292}{1+\frac{0.076}{\mathrm{N}_{\text{lc}}C_{b}}} - where 0.292 is the conversion factor from photon to electron. :math:`C_{b}` is the conversion factor (1.78) from nitrogen to chlorophyll. After we estimate :math:`J_{\text{{max}}}`, the actual electron transport rate with @@ -244,7 +240,6 @@ empirical expression of leaf (1937), J_{x} = \frac{\alpha \text{PAR}_{\text{max}}} {\left(1 + \frac{\alpha^{2}{\text{PAR}}_{\text{{max}}}^{2}}{J_{\text{{max}}}^{2}} \right)^{0.5}} - where :math:`\text{PAR}_{\text{{max}}}` ( :math:`\mu mol`/m :sup:`2`/s) is the maximum photosynthetically active radiation during the day. @@ -298,7 +293,6 @@ Based on :ref:`Farquhar et al. (1980)` and Wullschleger (1993) electron-limited photosynthetic rate under daily maximum radiation ( :math:`W_{jx}`) and the Rubisco-limited photosynthetic rate ( :math:`W_{\mathrm{c}}`) as follows, - .. math:: :label: 10.14) @@ -309,7 +303,6 @@ and the Rubisco-limited photosynthetic rate ( :math:`W_{\mathrm{c}}`) as follows W_{\mathrm{c}} = K_{\mathrm{c}} V_{{\mathrm{c}, \text{max}}}, - where :math:`K_{j}` and :math:`K_{\mathrm{c}}` as the conversion factors for :math:`J_{x}` and :math:`V_{{\mathrm{c}, \text{max}}}` ( :math:`V_{{\mathrm{c}, \text{max}}}` to :math:`W_{\mathrm{c}}` and :math:`J_{x}` to :math:`W_{J_{x}}`), respectively. Based on @@ -322,7 +315,6 @@ assume that :math:`W_{\mathrm{c}}` is proportional to W_{\mathrm{c}}=t_{\alpha}t_{\mathrm{c}, j0}W_{J_{x}} - where :math:`t_{\mathrm{c}, j0}` is the baseline ratio of :math:`W_{\mathrm{c}}` to :math:`W_{J_{x}}`. We recognize that this ratio may change depending on the nitrogen use efficiency of carboxylation and electron transport (Ainsworth and Rogers 2007), @@ -340,23 +332,18 @@ calculated in proportion to :math:`V_{\text{c,max}}`, R_{\mathrm{t}} = 0.015 V_{\text{c,max}}. - Accounting for the daytime and nighttime temperature, the daily respirations is calculated as follows, - .. math:: :label: 10.18) - R_{\text{td}}={R}_{\mathrm{t}} [D_{\text{day}} + D_{\text{night}} f_{\mathrm{r}}{(T_{\text{night}})/f_{\mathrm{r}}{(T_{\text{day}})}}], - where :math:`D_{\text{day}}` and :math:`D_{\text{night}}` are daytime and nighttime durations in seconds. :math:`f_{\mathrm{r}}(T_{\text{night}})` and :math:`f_{\mathrm{r}}(T_{\text{day}})` are the temperature response functions for respiration (see Appendix B in :ref:`Ali et al. (2016)` for details). - .. _Numerical scheme: Numerical scheme diff --git a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst index 53fd2fadbd..e824ff6c77 100644 --- a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst +++ b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst @@ -393,7 +393,6 @@ from the characteristic root spacing (section :numref:`Root Spacing`). RAI=\left(LAI+SAI \right) \cdot r_i \cdot f_{root-leaf} - .. math:: :label: 11.113 @@ -511,8 +510,6 @@ Both plant water supply and demand are functions of vegetation water potential. PHS finds the water potentials that match supply and demand. In the plant water transport equations :eq:`11.302`, the demand terms (left-hand side) are decreasing functions of absolute leaf water potential. As absolute leaf water potential becomes larger, water stress increases, causing a decrease in transpiration demand. The supply terms (right-hand side) are increasing functions of absolute leaf water potential. As absolute leaf water potential becomes larger, the gradients in water potential increase, causing an increase in vegetation water supply. PHS takes a Newton's method approach to iteratively solve for the vegetation water potentials that satisfy continuity :eq:`11.302`. - - .. _PHS Numerical Implementation: Numerical Implementation @@ -538,7 +535,6 @@ The continuity of water flow through the system yields four equations q_2&=\sum_{i=1}^{nlevsoi}{q_{3,i}} \end{aligned} - We seek the set of vegetation water potential values, .. math:: diff --git a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst index 88c20387f1..5778aeb957 100644 --- a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst +++ b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst @@ -500,4 +500,3 @@ the storage pool for retranslocated nitrogen, are calculated as: NF_{deadcroot\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}NF_{deadcroot\_ xfer\_ mort} wcol_{p} . - diff --git a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst index 8dbc7a40c8..cee30a0187 100644 --- a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst +++ b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst @@ -46,7 +46,6 @@ depth of direct beam per unit leaf and stem area (section :numref:`Canopy Radiat For clarity, terms involving :math:`T^{n+1} -T^{n}` are not shown in (c). - The total solar radiation absorbed by the vegetation and ground is .. math:: diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 5fbe40ca1f..4b958ca731 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -1235,7 +1235,6 @@ http://www.cesm.ucar.edu/models/cesm1.1/cism/]. Lischke, H. et al., 2006. TreeMig: a forest-landscape model for simulating spatio-temporal patterns from stand to landscape scale. Ecological Modelling 199.4, pp. 409-420. 41 - .. _LloydTaylor1994: Lloyd, J. and Taylor, J.A., 1994. On the temperature dependence of soil @@ -2059,7 +2058,6 @@ Dynamic Global Vegetation Model. Global Ecology and Biogeography Thonicke, K. et al., 2010. The influence of vegetation, fire spread and fire behaviour on biomass burning and trace gas emissions: results from a process-based model. Biogeosciences 7.6, pp. 1991-2011. - .. _Thornton1998: Thornton, P.E., 1998. Regional ecosystem simulation: combining surface- diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 2581b09f13..22b05b304c 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -184,7 +184,6 @@ increases due to wind-driven compaction according to which is added to the temperature-dependent term (cf. equation :eq:`8.21a`). - The mass of snow :math:`W_{sno}` is .. math:: @@ -486,8 +485,6 @@ The snow layer thickness after compaction is \Delta z_{i}^{n+1} =\Delta z_{i}^{n} \left(1+C_{R,\, i} \Delta t\right). - - .. _Destructive metamorphism: Destructive metamorphism @@ -520,7 +517,6 @@ and :math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` are the bulk densities of liquid water and ice (kg m\ :sup:`-3`). - .. _Overburden pressure compaction: Overburden pressure compaction @@ -543,7 +539,6 @@ water contents of the layer being compacted P_{s,\, i} =\frac{w_{ice,\, i} +w_{liq,\, i} }{2} +\sum _{j=snl+1}^{j=i-1}\left(w_{ice,\, j} +w_{liq,\, j} \right) . - Variable :math:`\eta` in :eq:`8.45` is a viscosity coefficient (kg s m\ :sup:`-2`) that varies with density and temperature as diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst index 43781fd509..a78cf4f130 100644 --- a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst +++ b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst @@ -980,7 +980,6 @@ the top layer is a blend of ice and soil heat capacity where :math:`c_{1}^{*}` is calculated from :eq:`6.89` or :eq:`6.92`. - .. _Excess Ground Ice: Excess Ground Ice @@ -1025,4 +1024,3 @@ When a soil layer refreezes, liquid soil water can only turn into normal soil ic The excess liquid soil moisture from excess ice melt is distributed within the soil column according to :numref:`Lateral Sub-surface Runoff`. - diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index c59faa7657..2d1f14c86b 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -75,7 +75,6 @@ which vary with wavelength (:math:`\Lambda` ), are weighted combinations of valu for vegetation and snow, using the canopy snow-covered fraction :math:`f_{can,\, sno}` (Chapter :numref:`rst_Hydrology`). The optical parameters are - .. The model determines that snow is on the canopy if :math:`T_{v} \le T_{f}` , where :math:`T_{v}` is the vegetation temperature (K) (Chapter diff --git a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst index b572c266ff..0cd64eaba7 100644 --- a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst +++ b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst @@ -148,7 +148,6 @@ interior building temperature at yearly time resolution. Schematic of THESIS urban properties tool. Executable scripts are in orange, input files are blue, and output files are green. Items within the black box outline are either read in as input, executed, or output by the driver script (urban_prop.csh). - The urban model that was first released as a component of CLM4.0 is separately described in the urban technical note (:ref:`Oleson et al. (2010b) `). The main changes in the urban model from CLM4.0 to CLM4.5 were 1) diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst index 1436a913b6..b8722c3508 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst @@ -23,4 +23,3 @@ If you also want to be able to give the resolution into **create_newcase** -- yo The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file. - diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst index faa43f377f..ea2de9b825 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst @@ -19,11 +19,9 @@ lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_CMIP6_simyr1850_c170824.nc Other ``fsurdat`` files are distinguished from this one by their resolution (hgrid), simulation year (sim_year) and prognostic crop (use_crop) attributes. - To add or change the default filenames for CLM tools edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_defaults_clm4_5.xml`` talked about above. - ---------------------------- What are the required files? ---------------------------- @@ -32,11 +30,9 @@ Different types of simulations and different types of configurations for CLM req The |version|-BGC or Carbon Nitrogen (cn) Biogeochemistry model for example requires ``stream_fldfilename_ndep`` files, which are NOT required by CLMSP. Transient simulations also require transient datasets, and the names of these datasets are sometimes different from the static versions (sometimes both are required as in the dynamic PFT cases). - In the following table we list the different files used by CLM, they are listed in order of importance, dependencies, and customizing. So the required files are all near the top, and the files used only under different conditions are listed later, and files with the fewest dependencies are near the top, as are the files that are least likely to be customized. - Table 3-1. Required Files for Different Configurations and Simulation Types --------------------------------------------------------------------------- Insert table 3-1 diff --git a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst index 89c6c4e8f4..a349efd5f4 100644 --- a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst +++ b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst @@ -66,7 +66,6 @@ Lastly, we kindly request that those publishing papers using AmeriFlux data prov The above agreement applies to the "US-UMB" dataset imported into our repository as well, and Gil Bohrer is the PI on record for that dataset. - The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap filled datasets. The fields will also need to be renamed. The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes "FLDS", "PRESS" becomes "PSRF". @@ -74,7 +73,6 @@ The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "T The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the value in ``SHR_CONST_TKFRZ`` in the file ``models/csm_share/shr/shr_const.F90`` of ``273.15``. The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and LONGXY should also be set to the latitude and longitude of the site. - ----------------------------------------------------------------- Example: PTCLMmkdata transient example over a shorter time period ----------------------------------------------------------------- diff --git a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst index 5c269128a5..56b0a7ad51 100644 --- a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst @@ -25,7 +25,6 @@ But, even without meteorology data PTCLMmkdata is useful to setup datasets to ru The original authors of PTCLMmkdata are: Daniel M. Ricciuto, Dali Wang, Peter E. Thornton, Wilfred M. Post all at Environmental Sciences Division, Oak Ridge National Laboratory (ORNL) and R. Quinn Thomas at Cornell University. It was then modified fairly extensively by Erik Kluzek at NCAR. We want to thank all of these individuals for this contribution to the CESM effort. We also want to thank the folks at University of Michigan Biological Stations (US-UMB) who allowed us to use their Fluxnet station data and import it into our inputdata repository, especially Gil Bohrer the PI on record for this site. - .. _details-of-ptclm: ======================= @@ -132,7 +131,6 @@ Example 6-1. Example of running PTCLMmkdata for US-UMB on cheyenne > cd $MYCASE > ./case.setup - PTCLMmkdata includes a README file that gives some extra details and a simple example. .. include:: ../../../../tools/PTCLM/README diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index 1d2ac37a48..ab3954599f 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -16,7 +16,6 @@ To get the list of supported dataset resolutions do this: > cd $CTSMROOT/doc > ../bld/build-namelist -res list - Which results in the following: :: @@ -112,14 +111,12 @@ Example: Running CLM over the single-point of Vancouver Canada with supplied atm > ./case.setup - .. warning:: If you don't set the start-year and run-length carefully as shown above the model will abort with a "dtlimit error" in the atmosphere model. Since, the forcing data for this site (and the MexicoCity site) is less than a year, the model won't be able to run for a full year. The ``1x1_urbanc_alpha`` site has data for more than a full year, but neither year is complete hence, it has the same problem (see the problem for this site above). .. note:: Just like ``PTS_MODE`` above, By default it sets up to run with ``MPILIB=mpi-serial`` (in the env_build.xml file) turned on, which allows you to run the model interactively. .. note:: When running a ``pt1_pt1`` resolution the number of processors is automatically set to one. When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to ``TRUE`` so that you can also run interactively without having to use mpi to start up your job. - Creating your own single-point dataset =================================================== diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst index f763a6a9fc..9c216b5c7b 100644 --- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst +++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst @@ -31,7 +31,6 @@ The streams text file is the XML-like file that tells datm how to find the files First we are going to create a case, and we will edit the ``user_nl_datm`` so that we add a CO2 data stream in. There is a streams text file available in ``$CTSMROOT/doc/UsersGuide/co2_streams.txt``, that includes file with a CO2 time-series from 1765 to 2007. - Example: Transient Simulation with Historical CO2 -------------------------------------------------------------- :: diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst index 2810cc477f..e812576b99 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst @@ -60,7 +60,6 @@ Example: Simulation Forced with Data from the Previous Simulation > ./case.build > ./case.submit - .. note:: We did this by editing the "namelist_defaults_datm.xml" which will change the settings for ALL future ``I1850Clm50BgcSpinup`` cases you run. You could also do this by editing the path in the resulting streams text files in the CaseDocs directory, and then create a "user\_" streams file with the correct path. This would change the streams file JUST for this case. The steps do it this way are: :: diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index af51426195..c289464019 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -112,5 +112,3 @@ To assess if the model is spunup, plot trends for CLMBGC variables of interest u .. note:: This same final spinup procedure works for |version|-CN as well. - - diff --git a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst index 564e363b2d..33c853a1b5 100644 --- a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst +++ b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst @@ -31,4 +31,3 @@ Example: Irrigation Simulation > ./case.build > ./case.submit - diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index adafbe66d9..dc289d00d6 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -22,7 +22,6 @@ Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) `Supported CLM Configurations `_ are listed in `Table 1-1 `_ for the Scientifically Supported compsets (have been scientifically validated with long simulations) and in `Table 1-2 `_ for the Functionally Supported compsets (we've only checked that they function). - Here is the entire list of compsets available. `CESM compsets `_ diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index 94958a8ed3..3f11fffa89 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -247,8 +247,6 @@ CLM_BLDNML_OPTS "-use_case list" to list valid use-cases. -version Echo the SVN tag name used to check out this CLM distribution. - - Note: The precedence for setting the values of namelist variables is (highest to lowest): 0. namelist values set by specific command-line options, like, -d, -sim_year (i.e. CLM_BLDNML_OPTS env_run variable) @@ -262,7 +260,6 @@ CLM_BLDNML_OPTS (i.e. CLM_NML_USE_CASE env_run variable) 5. values from the namelist defaults file. - The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set: @@ -291,7 +288,6 @@ Hence only the following different options can be set: #. -verbose - "-bgc_spinup" is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See `the Section called Spinning up the |version| biogeochemistry (CLMBGC spinup) in Chapter 4 `_ for an example using this option. "-chk_res" ensures that the resolution chosen is supported by CLM. If the resolution is NOT supported it will cause the CLM **build-namelist** to abort when run. So when either **preview_namelist**, **case.build** or **case.run** is executed it will abort early. Since, the CESM scripts only support certain resolutions anyway, in general this option is NOT needed in the context of running CESM cases. @@ -307,7 +303,6 @@ To see a list of valid variables that you could set do this: > cd $CTSMROOT/doc > ../bld/build-namelist -clm_demand list - .. note:: Using a 20th-Century transient compset or the ``20thC_transient`` use-case using ``CLM_NML_USE_CASE`` would set this as well, but would also use dynamic nitrogen and aerosol deposition files, so using ``-clm_demand`` would be a way to get *just* dynamic vegetation types and NOT the other files as well. "-drydep" adds the dry-deposition namelist to the driver. This is a driver namelist, but adding the option here has CLM **build-namelist** create the ``drv_flds_in`` file that the driver will copy over and use. Invoking this option does have an impact on performance even for I compsets and will slow the model down. It's also only useful when running with an active atmosphere model that makes use of this information. @@ -428,7 +423,6 @@ Example: user_nl_clm namelist file hist_mfilt = 1, 30, 28, 24 hist_nhtfrq = 0, -24, -6, -1 - **Note:** The comments at the top are some guidance given in the default user_nl_clm and just give some guidance on how to set variables and use the file. **Note:** See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. @@ -700,6 +694,5 @@ The output to the above command is as follows: no-nitrif Turn the Nitrification/denitrification off [no-vert,no-cent,no-nitrif,no-vert:no-cent] - We've given details on how to use the options in env_build.xml and env_run.xml to interact with the CLM "configure" and "build-namelist" scripts, as well as giving a good understanding of how these scripts work and the options to them. In the next section we give further details on the CLM namelist. You could customize the namelist for these options after "case.setup" is run. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst index e99a2bf8d6..017317ad6e 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst @@ -40,17 +40,14 @@ Included in the table are the following pieces of information: - units - Table 1-3. CLM History Fields from a BgcCrop case ------------------------------------------------- For Table from a BgcCrop case, please see :doc:`history_fields_nofates`. - Table 1-4. CLM History Fields from a Fates case ----------------------------------------------- For Table from a Fates case, please see :doc:`history_fields_fates`. - --------------------------------------------- Examples of using different namelist features --------------------------------------------- @@ -124,7 +121,6 @@ Example 1-3. Example user_nl_clm namelist adding and removing fields on primary hist_fincl1 = 'COSZEN', 'DECL' hist_fexcl1 = 'TG', 'TV', 'TSOI', 'H2OSOI' - Adding auxiliary history files and changing output frequency ------------------------------------------------------------ @@ -173,7 +169,6 @@ Example 1-5. Example user_nl_clm namelist removing all history fields hist_empty_htapes = .true. hist_fincl1 = 'TG', 'TV', 'FSA' - Various ways to change history output averaging flags ----------------------------------------------------- diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst index f57ed988d9..68c1180370 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst @@ -120,7 +120,6 @@ For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` se For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For an example of such a case see `the Section called Running with MOAR data as atmospheric forcing to spinup the model in Chapter 4 `_. - Normally you wouldn't modify the DATM settings for this mode. However, if you had data at a different frequency than 3-hours you would need to modify the ``offset`` and possibly the ``taxmode``. The other two things that you might modify would be the path to the data or the domain file for the resolution (which is currently hardwired to f09). diff --git a/doc/source/users_guide/testing/index.rst b/doc/source/users_guide/testing/index.rst index b9e99506e1..7d1370dec6 100644 --- a/doc/source/users_guide/testing/index.rst +++ b/doc/source/users_guide/testing/index.rst @@ -16,4 +16,3 @@ Testing testing.rst - diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index 06decd6049..d5e93de728 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -15,7 +15,6 @@ The first are the CESM test scripts, which utilize the **create_newcase** script The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods. - CIME Testing scripts ==================== @@ -47,7 +46,6 @@ Run the following perl tester that > cd bld/unit_testers > ./build-namelist_test.pl - Testing PTCLM ============= @@ -56,6 +54,5 @@ Testing PTCLM To run on cheyenne, you do the following: - .. include:: ../../../../tools/PTCLM/test/README.run_cheyenne :literal: diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index af5dd59c37..07967cd60e 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -39,7 +39,6 @@ If you want to create a regular latitude/longitude single-point or regional grid See :numref:`Figure mknoocnmap.pl` for a visual representation of this process. - 2. Creating mapping files for mksurfdata_map ============================================== @@ -104,7 +103,6 @@ mkmapdata.sh has a help option with the following with 'env var1=setting var2=setting ' ********************** - .. _Figure mkmapdata.sh: .. figure:: mkmapdata_details.jpeg diff --git a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst index 2d9ee8dcdb..02efb2492d 100644 --- a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst +++ b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst @@ -13,7 +13,6 @@ Note **mksurfdata_map** as documented previously has options to overwrite the ve For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. - Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst index d47d3d9e9d..30cb1d9e1d 100644 --- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst @@ -76,7 +76,6 @@ In SMP loops are run in parallel with different threads run on different process Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. For example, on the NCAR machine cheyenne there are 36 processors per node, so you can use up to 36 processors. - --------- Using NCL --------- From 6081633aa85623d38296e66ee7469709a90a2b62 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 09:11:40 -0600 Subject: [PATCH 1649/2067] Updated paths in sowingWindows/user_nl_clm. --- .../testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm index 61bdf9aa93..d3d922f721 100644 --- a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm @@ -1,5 +1,5 @@ -stream_fldFileName_swindow_start = '/glade/u/home/samrabin/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' -stream_fldFileName_swindow_end = '/glade/u/home/samrabin/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' -stream_meshfile_cropcal = '/glade/u/home/samrabin/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc' +stream_fldFileName_swindow_start = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' +stream_fldFileName_swindow_end = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' +stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc' stream_year_first_cropcal = 2000 stream_year_last_cropcal = 2000 From 16b73f15caabae283499a4a54a6cb5ca16bf13a5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 10:12:08 -0600 Subject: [PATCH 1650/2067] Require allow_invalid_swindow_inputs to avoid error on invalid sowing window read. --- .../namelist_definition_ctsm.xml | 5 ++++ src/cpl/share_esmf/cropcalStreamMod.F90 | 23 +++++++++++++++---- 2 files changed, 23 insertions(+), 5 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 3f494e0711..5c0cc0fa12 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -1835,6 +1835,11 @@ Last year to loop over for crop calendar data Simulation year that aligns with stream_year_first_cropcal value + +By default, a value in stream_fldFileName_swindow_start or _end outside the range [1, 365] (or 366 in leap years) will cause the run to fail. Set this to .true. to instead fall back on the paramfile sowing windows. + + Filename of input stream data for date (day of year) of start of sowing window. Cells with the same sowing window start and end date are always planted on that date, regardless of climatic conditions/history. diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 1ca4d331c6..aa523bea82 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -38,6 +38,7 @@ module cropcalStreamMod character(len=CS), allocatable :: stream_varnames_sdate(:) ! used for both start and end dates character(len=CS), allocatable :: stream_varnames_cultivar_gdds(:) integer :: ncft ! Number of crop functional types (excl. generic crops) + logical :: allow_invalid_swindow_inputs ! Fall back on paramfile sowing windows in cases of invalid values in stream_fldFileName_swindow_start and _end? character(len=CL) :: stream_fldFileName_swindow_start ! sowing window start stream filename to read character(len=CL) :: stream_fldFileName_swindow_end ! sowing window end stream filename to read character(len=CL) :: stream_fldFileName_cultivar_gdds ! cultivar growing degree-days stream filename to read @@ -84,6 +85,7 @@ subroutine cropcal_init(bounds) stream_year_first_cropcal, & stream_year_last_cropcal, & model_year_align_cropcal, & + allow_invalid_swindow_inputs, & stream_fldFileName_swindow_start, & stream_fldFileName_swindow_end, & stream_fldFileName_cultivar_gdds, & @@ -93,6 +95,7 @@ subroutine cropcal_init(bounds) stream_year_first_cropcal = 1 ! first year in stream to use stream_year_last_cropcal = 1 ! last year in stream to use model_year_align_cropcal = 1 ! align stream_year_first_cropcal with this model year + allow_invalid_swindow_inputs = .false. stream_meshfile_cropcal = '' stream_fldFileName_swindow_start = '' stream_fldFileName_swindow_end = '' @@ -124,6 +127,7 @@ subroutine cropcal_init(bounds) call shr_mpi_bcast(stream_year_first_cropcal , mpicom) call shr_mpi_bcast(stream_year_last_cropcal , mpicom) call shr_mpi_bcast(model_year_align_cropcal , mpicom) + call shr_mpi_bcast(allow_invalid_swindow_inputs, mpicom) call shr_mpi_bcast(stream_fldFileName_swindow_start, mpicom) call shr_mpi_bcast(stream_fldFileName_swindow_end , mpicom) call shr_mpi_bcast(stream_fldFileName_cultivar_gdds, mpicom) @@ -135,6 +139,7 @@ subroutine cropcal_init(bounds) write(iulog,'(a,i8)') ' stream_year_first_cropcal = ',stream_year_first_cropcal write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal + write(iulog,'(a,i8)') ' allow_invalid_swindow_inputs = ',allow_invalid_swindow_inputs write(iulog,'(a,a)' ) ' stream_fldFileName_swindow_start = ',trim(stream_fldFileName_swindow_start) write(iulog,'(a,a)' ) ' stream_fldFileName_swindow_end = ',trim(stream_fldFileName_swindow_end) write(iulog,'(a,a)' ) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) @@ -360,7 +365,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! So an explicit loop is required here do g = 1,lsize - ! If read-in value is invalid, allow_unprescribed_planting in CropPhenology() + ! If read-in value is invalid, set to -1. Will be handled later in this subroutine. if (dataptr1d_swindow_start(g) <= 0 .or. dataptr1d_swindow_start(g) > dayspyr & .or. dataptr1d_swindow_end(g) <= 0 .or. dataptr1d_swindow_end(g) > dayspyr) then dataptr1d_swindow_start(g) = -1 @@ -398,10 +403,18 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end if end if - ! Fail if a sowing window start date is prescribed without an end date (or vice versa) - if (any((starts >= 1 .and. ends < 1) .or. (starts < 1 .and. ends >= 1))) then - write(iulog, *) 'Every prescribed sowing window start date must have a corresponding end date.' - call ESMF_Finalize(endflag=ESMF_END_ABORT) + ! Handle invalid sowing window values + if (any(starts < 1 .or. ends < 1)) then + ! Fail if not allowing fallback to paramfile sowing windows + if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2))) then + write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + + ! Fail if a sowing window start date is prescribed without an end date (or vice versa) + else if (any((starts >= 1 .and. ends < 1) .or. (starts < 1 .and. ends >= 1))) then + write(iulog, *) 'Every prescribed sowing window start date must have a corresponding end date.' + call ESMF_Finalize(endflag=ESMF_END_ABORT) + end if end if end if ! use_cropcal_rx_swindows From e71e8e7deec850dc348b05a395226cd74140416b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 10:15:08 -0600 Subject: [PATCH 1651/2067] Only error on invalid swindow if wtgcell > 0. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index aa523bea82..82dd8d4f82 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -406,7 +406,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Handle invalid sowing window values if (any(starts < 1 .or. ends < 1)) then ! Fail if not allowing fallback to paramfile sowing windows - if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2))) then + if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2) .and. patch%wtgcell > 0._r8)) then write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.' call ESMF_Finalize(endflag=ESMF_END_ABORT) From b90040fdc87996b4a17abb7fd0ed14a039f6b7d6 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 18 Oct 2023 09:47:25 -0700 Subject: [PATCH 1652/2067] update fates seed dispersal subroutine names --- src/main/clm_driver.F90 | 6 +++--- src/main/clm_varctl.F90 | 2 +- src/utils/clmfates_interfaceMod.F90 | 22 +++++++++++----------- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 44724d1c35..a53a5931e4 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1271,10 +1271,10 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Pass fates seed dispersal information to neighboring gridcells across - ! all MPI tasks. Note that WrapSeedGlobal calls an MPI collective routine - ! and as such WrapSeedGlobal should be called outside of OMP threaded loop regions + ! all MPI tasks. Note that WrapGlobalSeedDispersal calls an MPI collective routine + ! and as such WrapGlobalSeedDispersal should be called outside of OMP threaded loop regions if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapSeedGlobal() + if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapGlobalSeedDispersal() end if ! ============================================================================ diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index ebd5974f40..dad66519ba 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -260,7 +260,7 @@ module clm_varctl ! These are INTERNAL to the FATES module - integer, public :: fates_seeddisp_cadence = -9 ! 0 => no seed dispersal + integer, public :: fates_seeddisp_cadence = iundef ! 0 => no seed dispersal ! 1, 2, 3 => daily, monthly, or yearly dispersal integer, public :: fates_parteh_mode = -9 ! 1 => carbon only ! 2 => C+N+P (not enabled yet) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 778dbbdc35..e3ab418087 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -238,8 +238,8 @@ module CLMFatesInterfaceMod procedure, public :: wrap_hydraulics_drive procedure, public :: WrapUpdateFatesRmean procedure, public :: wrap_WoodProducts - procedure, public :: WrapSeedGlobal - procedure, public :: wrap_seed_dispersal + procedure, public :: WrapGlobalSeedDispersal + procedure, public :: WrapUpdateFatesSeedInOut procedure, public :: UpdateCLitterFluxes procedure, public :: UpdateNLitterFluxes end type hlm_fates_interface_type @@ -1061,9 +1061,9 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call UnPackNutrientAquisitionBCs(this%fates(nc)%sites, this%fates(nc)%bc_in) ! Distribute any seeds from neighboring gridcells into the current gridcell - ! Global seed availability array populated by WrapSeedGlobal call + ! Global seed availability array populated by WrapGlobalSeedDispersal call if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - call this%wrap_seed_dispersal(bounds_clump) + call this%WrapUpdateFatesSeedInOut(bounds_clump) end if ! --------------------------------------------------------------------------------- @@ -1850,7 +1850,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & ! Disperse seeds if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - call this%WrapSeedGlobal(is_restart_flag=.true.) + call this%WrapGlobalSeedDispersal(is_restart_flag=.true.) end if end if @@ -2643,7 +2643,7 @@ end subroutine wrap_canopy_radiation ! ====================================================================================== - subroutine WrapSeedGlobal(this,is_restart_flag) + subroutine WrapGlobalSeedDispersal(this,is_restart_flag) ! Call mpi procedure to provide the global seed output distribution array to every gridcell. ! This could be conducted with a more sophisticated halo-type structure or distributed graph. @@ -2667,7 +2667,7 @@ subroutine WrapSeedGlobal(this,is_restart_flag) type (neighbor_type), pointer :: neighbor - ! If WrapSeedGlobal is being called at the end a fates restart call, + ! If WrapGlobalSeedDispersal is being called at the end a fates restart call, ! pass .false. to the set_dispersed_flag to avoid updating the ! global dispersal date set_restart_flag = .true. @@ -2716,13 +2716,13 @@ subroutine WrapSeedGlobal(this,is_restart_flag) endif call t_stopf('fates-seed-mpi_reduce') - end subroutine WrapSeedGlobal + end subroutine WrapGlobalSeedDispersal ! ====================================================================================== - subroutine wrap_seed_dispersal(this,bounds_clump) + subroutine WrapUpdateFatesSeedInOut(this,bounds_clump) - ! This subroutine passes the globally dispersed seed via WrapSeedGlobal, incoming_global + ! This subroutine passes the globally dispersed seed via WrapGlobalSeedDispersal, incoming_global ! to the fates local process seed_in site object. It also resets the fates seed_out ! in preparation for fates to update the seeds being dispersed out. @@ -2757,7 +2757,7 @@ subroutine wrap_seed_dispersal(this,bounds_clump) call t_stopf('fates-seed-disperse') - end subroutine wrap_seed_dispersal + end subroutine WrapUpdateFatesSeedInOut ! ====================================================================================== From 52d665fd21772f271226601befa6895d9724d51c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 10:59:15 -0600 Subject: [PATCH 1653/2067] Only error on invalid swindow if patch is prognostic crop. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 82dd8d4f82..70afd263ff 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -406,7 +406,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Handle invalid sowing window values if (any(starts < 1 .or. ends < 1)) then ! Fail if not allowing fallback to paramfile sowing windows - if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2) .and. patch%wtgcell > 0._r8)) then + if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.' call ESMF_Finalize(endflag=ESMF_END_ABORT) From ce7e9ecc86779ecca00390ad67d08cdfe129db7a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 11:00:21 -0600 Subject: [PATCH 1654/2067] List crop types with invalid swindows. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 70afd263ff..d07359ce81 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -305,6 +305,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) use CropType , only : crop_type use PatchType , only : patch use clm_time_manager, only : get_curr_days_per_year + use pftconMod , only : pftname use dshr_methods_mod , only : dshr_fldbun_getfldptr ! ! !ARGUMENTS: @@ -408,6 +409,16 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Fail if not allowing fallback to paramfile sowing windows if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.' + write(iulog, *) 'Affected crops:' + do ivt = npcropmin, mxpft + do fp = 1, num_pcropp + p = filter_pcropp(fp) + if (ivt == patch%itype(p) .and. patch%wtgcell(p) > 0._r8 .and. all(starts(p,:) < 1)) then + write(iulog, *) ' ',pftname(ivt),' (',ivt,')' + exit ! Stop looking for patches of this type + end if + end do + end do call ESMF_Finalize(endflag=ESMF_END_ABORT) ! Fail if a sowing window start date is prescribed without an end date (or vice versa) From ee13f93549f29eaf2d04acc6b023855856b28123 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 16 Oct 2023 11:13:10 -0600 Subject: [PATCH 1655/2067] Fix some superscripts. --- .../tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst | 2 +- .../CLM50_Tech_Note_External_Nitrogen_Cycle.rst | 2 +- doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index 557678ce07..6ac20a32d3 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -359,7 +359,7 @@ The potential carbon flux out of the upstream pool where :math:`{CS}_{u}` (gC m\ :sup:`-2`) is the initial mass in the upstream pool and :math:`{k}_{u}` is the decay rate constant -(s:sup:`-1`) for the upstream pool, adjusted for temperature and +(s\ :sup:`-1`) for the upstream pool, adjusted for temperature and moisture conditions. Depending on the C:N ratios of the upstream and downstream pools and the amount of carbon lost in the transformation due to respiration (the respiration fraction), the execution of this diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index 9295e7e46c..aa16d10342 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -271,7 +271,7 @@ to be 100% adsorbed onto mineral surfaces and unaffected by leaching. DIN=\frac{NS_{sminn} sf}{WS_{tot\_ soil} } -where :math:`{WS}_{tot\_soil}` (kgH:sub:`2`\ O m\ :sup:`-2`) is the total mass of soil water content integrated +where :math:`{WS}_{tot\_soil}` (kgH\ :sub:`2`\ O m\ :sup:`-2`) is the total mass of soil water content integrated over the column. The total mineral nitrogen leaching flux is limited on each time step to not exceed the soluble fraction of :math:`{NS}_{sminn}` diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 59c01f3863..1c1bfbf27b 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -205,7 +205,7 @@ accelerated by the same degree as the decomposition, such that the of the spinup mode. For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical -period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\:sup:`13`\ C values can be set to +period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 :sup:`o`\ N-90 :sup:`o`\ N, 30 :sup:`o`\ S-30 :sup:`o`\ N, and 30 :sup:`o`\ S-90 :sup:`o`\ S). From 2edd273e4ac4ab385f081168c4f9a170f968c5bb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 11:30:00 -0600 Subject: [PATCH 1656/2067] Delete some extraneous backticks. --- .../CLM50_Tech_Note_External_Nitrogen_Cycle.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index aa16d10342..e9ab23d496 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -223,7 +223,7 @@ the Century (:ref:`del Grosso et al. 2000 `) approach: where :math:`{P}_{NO3:CO2}` is the ratio of CO\ :sub:`2` production in a given soil layer to the -NO\ :sub:`3`\ :sup:`-`` concentration, :math:`{k}_{1}` is +NO\ :sub:`3`\ :sup:`-` concentration, :math:`{k}_{1}` is a function of :math:`{d}_{g}`, the gas diffusivity through the soil matrix: @@ -261,7 +261,7 @@ s\ :sup:`-1`, section :numref:`Lateral Sub-surface Runoff`), as of the remaining soil mineral N pool is in soluble form, and that this entire fraction is dissolved in the total soil water. For the Century- based formulation in CLM5.0, the leaching acts only on the -NO\ :sub:`3`\ :sup:`-`` pool (which is assumed to be 100% +NO\ :sub:`3`\ :sup:`-` pool (which is assumed to be 100% soluble), while the NH\ :sub:`4`\ :sup:`+` pool is assumed to be 100% adsorbed onto mineral surfaces and unaffected by leaching. *DIN* is then given as From 899212e1da5c28e228ad7605bfed3c367e4dff0d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 18 Oct 2023 14:33:48 -0600 Subject: [PATCH 1657/2067] update testmod to place nc generated file into SRCROOT --- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/README | 3 +++ .../testmods_dirs/clm/FatesColdSeedDisp/shell_commands | 4 ++-- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README index 5833c4edd3..484fa67db9 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/README @@ -10,6 +10,9 @@ fates_seed_dispersal_pdf_shape Given that the default fates parameter file has the above variables as unset, a custom fates parameter file must be supplied to appropriately test this mode. This testmod itself addresses CTSM issue 2151: https://github.com/ESCOMP/CTSM/issues/2151 +Note that to avoid exceeding the filename string length maximu, the parameter +file generated on the fly is placed in the $SRCROOT/src/fates/parameter_files +directory. This may still run into problems is the $SRCROOT string is too long. The max_dist value will impact the size of the 'neighborhood' of gridcells that fates will attempt to distribute seeds to. To limit the neighborhood to diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands index 7cb007d591..5d230dc5e9 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands @@ -1,7 +1,7 @@ SRCDIR=`./xmlquery SRCROOT --value` CASEDIR=`./xmlquery CASEROOT --value` -FATESROOT=$SRCDIR/src/fates -FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc +FATESROOT=$SRCDIR/src/fates/ +FATESPARAMFILE=$FATESROOT/parameter_files/fates_params_seeddisp_4x5.nc ncgen -o $FATESPARAMFILE $FATESROOT/parameter_files/fates_params_default.cdl diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index ecd1dc8b57..8e60c6a2e0 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,3 +1,3 @@ -fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc' +fates_paramfile = '$SRCROOT/src/fates/parameter_files/fates_params_seeddisp_4x5.nc' fates_seeddisp_cadence = 1 hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From c49a22239fe3906c1d67cc043f41b1c52f6c7987 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 18 Oct 2023 14:18:28 -0700 Subject: [PATCH 1658/2067] update fates external --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index d805502731..6030bfea95 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/YanlanLiu/fates -branch = cross_grid_seed +repo_url = https://github.com/NGEET/fates +tag = sci.1.68.0_api.27.0.0 required = True [externals_description] From 7226823166bb37f79e818a8d1ccc30da83ad5931 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 18 Oct 2023 15:00:17 -0700 Subject: [PATCH 1659/2067] move dispersal timing check function outside of site loop --- src/utils/clmfates_interfaceMod.F90 | 25 +++++++++++++++---------- 1 file changed, 15 insertions(+), 10 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index e3ab418087..7be16b73c6 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -238,7 +238,7 @@ module CLMFatesInterfaceMod procedure, public :: wrap_hydraulics_drive procedure, public :: WrapUpdateFatesRmean procedure, public :: wrap_WoodProducts - procedure, public :: WrapGlobalSeedDispersal + procedure, public :: WrapSeedGlobal procedure, public :: WrapUpdateFatesSeedInOut procedure, public :: UpdateCLitterFluxes procedure, public :: UpdateNLitterFluxes @@ -1061,7 +1061,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call UnPackNutrientAquisitionBCs(this%fates(nc)%sites, this%fates(nc)%bc_in) ! Distribute any seeds from neighboring gridcells into the current gridcell - ! Global seed availability array populated by WrapGlobalSeedDispersal call + ! Global seed availability array populated by WrapSeedGlobal call if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then call this%WrapUpdateFatesSeedInOut(bounds_clump) end if @@ -1296,6 +1296,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! is this being called during a read from restart sequence (if so then use the restarted fates ! snow depth variable rather than the CLM variable). logical , intent(in) :: is_initing_from_restart + integer :: npatch ! number of patches in each site integer :: ifp ! index FATES patch integer :: p ! HLM patch index @@ -1303,6 +1304,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & integer :: c ! column index integer :: g ! grid cell + logical :: dispersal_flag ! local flag to pass to the inside of the site loop real(r8) :: areacheck call t_startf('fates_wrap_update_hlmfates_dyn') @@ -1399,9 +1401,13 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & patch%is_bareground(bounds_clump%begp:bounds_clump%endp) = .false. patch%wt_ed(bounds_clump%begp:bounds_clump%endp) = 0.0_r8 - ! Zero the outgoing_local seed values prior to populating with the most recent seed update if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then + ! Zero the outgoing_local seed values prior to populating with the most recent seed update this%fates_seed%outgoing_local(:,:) = 0._r8 + + ! check the dispersal time once outside of the loop and set a flag to pass in + dispersal_flag = .false. + if (IsItDispersalTime()) dispersal_flag = .true. end if do s = 1,this%fates(nc)%nsites @@ -1411,8 +1417,7 @@ subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, & ! Accumulate seeds from sites to the gridcell local outgoing buffer if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - if (IsItDispersalTime()) this%fates_seed%outgoing_local(:,g) = & - this%fates(nc)%sites(s)%seed_out(:) + if (dispersal_flag) this%fates_seed%outgoing_local(:,g) = this%fates(nc)%sites(s)%seed_out(:) end if ! Other modules may have AI's we only flush values @@ -1850,7 +1855,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & ! Disperse seeds if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - call this%WrapGlobalSeedDispersal(is_restart_flag=.true.) + call this%WrapSeedGlobal(is_restart_flag=.true.) end if end if @@ -2643,7 +2648,7 @@ end subroutine wrap_canopy_radiation ! ====================================================================================== - subroutine WrapGlobalSeedDispersal(this,is_restart_flag) + subroutine WrapSeedGlobal(this,is_restart_flag) ! Call mpi procedure to provide the global seed output distribution array to every gridcell. ! This could be conducted with a more sophisticated halo-type structure or distributed graph. @@ -2667,7 +2672,7 @@ subroutine WrapGlobalSeedDispersal(this,is_restart_flag) type (neighbor_type), pointer :: neighbor - ! If WrapGlobalSeedDispersal is being called at the end a fates restart call, + ! If WrapSeedGlobal is being called at the end a fates restart call, ! pass .false. to the set_dispersed_flag to avoid updating the ! global dispersal date set_restart_flag = .true. @@ -2716,13 +2721,13 @@ subroutine WrapGlobalSeedDispersal(this,is_restart_flag) endif call t_stopf('fates-seed-mpi_reduce') - end subroutine WrapGlobalSeedDispersal + end subroutine WrapSeedGlobal ! ====================================================================================== subroutine WrapUpdateFatesSeedInOut(this,bounds_clump) - ! This subroutine passes the globally dispersed seed via WrapGlobalSeedDispersal, incoming_global + ! This subroutine passes the globally dispersed seed via WrapSeedGlobal, incoming_global ! to the fates local process seed_in site object. It also resets the fates seed_out ! in preparation for fates to update the seeds being dispersed out. From c5711f708e4aba26df75cd535746f9ea02830ccb Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 18 Oct 2023 16:02:12 -0600 Subject: [PATCH 1660/2067] move beginning day check inside the global seed dispersal subroutine --- src/main/clm_driver.F90 | 4 +- src/utils/clmfates_interfaceMod.F90 | 112 ++++++++++++++-------------- 2 files changed, 59 insertions(+), 57 deletions(-) diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index a53a5931e4..33e9412ba9 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -1273,8 +1273,8 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Pass fates seed dispersal information to neighboring gridcells across ! all MPI tasks. Note that WrapGlobalSeedDispersal calls an MPI collective routine ! and as such WrapGlobalSeedDispersal should be called outside of OMP threaded loop regions - if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - if (use_fates .and. is_beg_curr_day()) call clm_fates%WrapGlobalSeedDispersal() + if (use_fates) then + if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) call clm_fates%WrapGlobalSeedDispersal() end if ! ============================================================================ diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 7be16b73c6..b3b1efe142 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2671,54 +2671,57 @@ subroutine WrapSeedGlobal(this,is_restart_flag) ! if optional is_restart_flag is true type (neighbor_type), pointer :: neighbor + ! This should only be run once per day + if(is_beg_curr_day()) then + + ! If WrapGlobalSeedDispersal is being called at the end a fates restart call, + ! pass .false. to the set_dispersed_flag to avoid updating the + ! global dispersal date + set_restart_flag = .true. + if (present(is_restart_flag)) then + if (is_restart_flag) set_restart_flag = .false. + end if - ! If WrapSeedGlobal is being called at the end a fates restart call, - ! pass .false. to the set_dispersed_flag to avoid updating the - ! global dispersal date - set_restart_flag = .true. - if (present(is_restart_flag)) then - if (is_restart_flag) set_restart_flag = .false. - end if + call t_startf('fates-seed-mpi_reduce') - call t_startf('fates-seed-mpi_reduce') + if (IsItDispersalTime(setdispersedflag=set_restart_flag)) then - if (IsItDispersalTime(setdispersedflag=set_restart_flag)) then + ! Re-initialize incoming seed buffer for this time step + this%fates_seed%incoming_global(:,:) = 0._r8 + this%fates_seed%outgoing_global(:,:) = 0._r8 - ! Re-initialize incoming seed buffer for this time step - this%fates_seed%incoming_global(:,:) = 0._r8 - this%fates_seed%outgoing_global(:,:) = 0._r8 + ! Distribute outgoing seed data across all MPI tasks + ! This method of grid cell communications is inefficient in that it creates global information + ! across all processes. A future update should communicate to the minimum set of neighbors. + call MPI_Allgatherv(this%fates_seed%outgoing_local, procinfo%ncells*numpft_fates, MPI_REAL8, & + this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array*numpft_fates, & + MPI_REAL8, mpicom, ier) + if (ier /= 0) then + call endrun(msg='clmfates interface error: MPI_Allgatherv failed'//& + errMsg(sourcefile, __LINE__)) + end if - ! Distribute outgoing seed data across all MPI tasks - ! This method of grid cell communications is inefficient in that it creates global information - ! across all processes. A future update should communicate to the minimum set of neighbors. - call MPI_Allgatherv(this%fates_seed%outgoing_local, procinfo%ncells*numpft_fates, MPI_REAL8, & - this%fates_seed%outgoing_global, this%fates_seed%ncells_array*numpft_fates, this%fates_seed%begg_array*numpft_fates, & - MPI_REAL8, mpicom, ier) - if (ier /= 0) then - call endrun(msg='clmfates interface error: MPI_Allgatherv failed'//& - errMsg(sourcefile, __LINE__)) - end if + ! zero outgoing local for all gridcells outside threaded region now that we've passed them out + this%fates_seed%outgoing_local(:,:) = 0._r8 - ! zero outgoing local for all gridcells outside threaded region now that we've passed them out - this%fates_seed%outgoing_local(:,:) = 0._r8 - - ! Calculate the current gridcell incoming seed for each gridcell index - ! This should be conducted outside of a threaded region to provide access to - ! the neighbor%gindex which might not be available in via the clumped index - call get_proc_global(ng=numg) - do g = 1, numg - neighbor => lneighbors(g)%first_neighbor - do while (associated(neighbor)) - ! This also applies the same neighborhood distribution scheme to all pfts - ! This needs to have a per pft density probability value - this%fates_seed%incoming_global(:,g) = this%fates_seed%incoming_global(:,g) + & - this%fates_seed%outgoing_global(:,neighbor%gindex) * & - neighbor%density_prob(:) / lneighbors(g)%neighbor_count - neighbor => neighbor%next_neighbor + ! Calculate the current gridcell incoming seed for each gridcell index + ! This should be conducted outside of a threaded region to provide access to + ! the neighbor%gindex which might not be available in via the clumped index + call get_proc_global(ng=numg) + do g = 1, numg + neighbor => lneighbors(g)%first_neighbor + do while (associated(neighbor)) + ! This also applies the same neighborhood distribution scheme to all pfts + ! This needs to have a per pft density probability value + this%fates_seed%incoming_global(:,g) = this%fates_seed%incoming_global(:,g) + & + this%fates_seed%outgoing_global(:,neighbor%gindex) * & + neighbor%density_prob(:) / lneighbors(g)%neighbor_count + neighbor => neighbor%next_neighbor + end do end do - end do - - endif + end if + end if + call t_stopf('fates-seed-mpi_reduce') end subroutine WrapSeedGlobal @@ -2744,21 +2747,20 @@ subroutine WrapUpdateFatesSeedInOut(this,bounds_clump) nc = bounds_clump%clump_index - do s = 1, this%fates(nc)%nsites - c = this%f2hmap(nc)%fcolumn(s) - g = col%gridcell(c) + ! Check that it is the beginning of the current dispersal time step + if (IsItDispersalTime()) then + do s = 1, this%fates(nc)%nsites + c = this%f2hmap(nc)%fcolumn(s) + g = col%gridcell(c) - ! Check that it is the beginning of the current dispersal time step - if (IsItDispersalTime()) then - ! assuming equal area for all sites, seed_id_global in [kg/grid/day], seed_in in [kg/site/day] - this%fates(nc)%sites(s)%seed_in(:) = this%fates_seed%incoming_global(:,g) - this%fates(nc)%sites(s)%seed_out(:) = 0._r8 ! reset seed_out - else - ! if it is not the dispersing time, pass in zero - ! if this is a restart, then skip this entirely - this%fates(nc)%sites(s)%seed_in(:) = 0._r8 - end if - end do + ! assuming equal area for all sites, seed_id_global in [kg/grid/day], seed_in in [kg/site/day] + this%fates(nc)%sites(s)%seed_in(:) = this%fates_seed%incoming_global(:,g) + this%fates(nc)%sites(s)%seed_out(:) = 0._r8 ! reset seed_out + end do + else + ! if it is not the dispersing time, pass in zero + this%fates(nc)%sites(s)%seed_in(:) = 0._r8 + end if call t_stopf('fates-seed-disperse') From c811ae904fd27fac312159d769c376415c09168e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 18 Oct 2023 15:22:24 -0700 Subject: [PATCH 1661/2067] fix base rebase, rename dispersal subroutines --- src/utils/clmfates_interfaceMod.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index b3b1efe142..1d7be0d813 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -238,7 +238,7 @@ module CLMFatesInterfaceMod procedure, public :: wrap_hydraulics_drive procedure, public :: WrapUpdateFatesRmean procedure, public :: wrap_WoodProducts - procedure, public :: WrapSeedGlobal + procedure, public :: WrapGlobalSeedDispersal procedure, public :: WrapUpdateFatesSeedInOut procedure, public :: UpdateCLitterFluxes procedure, public :: UpdateNLitterFluxes @@ -1061,7 +1061,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call UnPackNutrientAquisitionBCs(this%fates(nc)%sites, this%fates(nc)%bc_in) ! Distribute any seeds from neighboring gridcells into the current gridcell - ! Global seed availability array populated by WrapSeedGlobal call + ! Global seed availability array populated by WrapGlobalSeedDispersal call if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then call this%WrapUpdateFatesSeedInOut(bounds_clump) end if @@ -1855,7 +1855,7 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & ! Disperse seeds if (fates_seeddisp_cadence /= fates_dispersal_cadence_none) then - call this%WrapSeedGlobal(is_restart_flag=.true.) + call this%WrapGlobalSeedDispersal(is_restart_flag=.true.) end if end if @@ -2648,7 +2648,7 @@ end subroutine wrap_canopy_radiation ! ====================================================================================== - subroutine WrapSeedGlobal(this,is_restart_flag) + subroutine WrapGlobalSeedDispersal(this,is_restart_flag) ! Call mpi procedure to provide the global seed output distribution array to every gridcell. ! This could be conducted with a more sophisticated halo-type structure or distributed graph. @@ -2724,13 +2724,13 @@ subroutine WrapSeedGlobal(this,is_restart_flag) call t_stopf('fates-seed-mpi_reduce') - end subroutine WrapSeedGlobal + end subroutine WrapGlobalSeedDispersal ! ====================================================================================== subroutine WrapUpdateFatesSeedInOut(this,bounds_clump) - ! This subroutine passes the globally dispersed seed via WrapSeedGlobal, incoming_global + ! This subroutine passes the globally dispersed seed via WrapGlobalSeedDispersal, incoming_global ! to the fates local process seed_in site object. It also resets the fates seed_out ! in preparation for fates to update the seeds being dispersed out. From 970fff26660404690e3179e6194ef511ee240367 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 17:05:56 -0600 Subject: [PATCH 1662/2067] Fix VSCode rendering of two equations. --- .../tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 2 -- .../CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 1 - 2 files changed, 3 deletions(-) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index b45e117c23..72b2fdb525 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -494,9 +494,7 @@ where :label: 9.38 \begin{array}{l} a = 1 \\ - b = -[2(g_{o} * 10^{-6} + d) + \frac{(g_{1}d)^{2}}{g_{b}*10^{-6}D_{l}}] \\ - c = (g_{o}*10^{-6})^{2} + [2g_{o}*10^{-6} + d (1-\frac{g_{1}^{2}} {D_{l}})]d \end{array} and diff --git a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst index a78cf4f130..28216a6179 100644 --- a/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst +++ b/doc/source/tech_note/Soil_Snow_Temperatures/CLM50_Tech_Note_Soil_Snow_Temperatures.rst @@ -824,7 +824,6 @@ is from :ref:`Farouki (1981) ` K_{e,\, i} \lambda _{sat,\, i} +\left(1-K_{e,\, i} \right)\lambda _{dry,\, i} &\qquad S_{r,\, i} > 1\times 10^{-7} \\ \lambda _{dry,\, i} &\qquad S_{r,\, i} \le 1\times 10^{-7} \end{array}\right\} &\qquad i=1,\ldots ,N_{levsoi} \\ - \lambda _{i} =\lambda _{bedrock} &\qquad i=N_{levsoi} +1,\ldots N_{levgrnd} \end{array} From 22efe97252c67a5f57cfb8c97b22efd91b59df58 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 21:50:42 -0600 Subject: [PATCH 1663/2067] Unwrap Tech Note. --- .../tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst | 53 +- .../CLM50_Tech_Note_CN_Allocation.rst | 116 +- .../CN_Pools/CLM50_Tech_Note_CN_Pools.rst | 48 +- .../CLM50_Tech_Note_Crop_Irrigation.rst | 456 +---- .../tech_note/DGVM/CLM50_Tech_Note_DGVM.rst | 13 +- .../CLM50_Tech_Note_Decomposition.rst | 378 +--- .../tech_note/Dust/CLM50_Tech_Note_Dust.rst | 105 +- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 554 +----- ...LM50_Tech_Note_External_Nitrogen_Cycle.rst | 210 +-- .../tech_note/FUN/CLM50_Tech_Note_FUN.rst | 3 +- .../tech_note/Fire/CLM50_Tech_Note_Fire.rst | 344 +--- .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 683 ++------ .../Glacier/CLM50_Tech_Note_Glacier.rst | 387 +---- .../Hydrology/CLM50_Tech_Note_Hydrology.rst | 541 +----- .../CLM50_Tech_Note_Introduction.rst | 449 +---- .../Isotopes/CLM50_Tech_Note_Isotopes.rst | 141 +- .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 781 ++------- .../CLM50_Tech_Note_Land-Only_Mode.rst | 166 +- .../MOSART/CLM50_Tech_Note_MOSART.rst | 150 +- .../Methane/CLM50_Tech_Note_Methane.rst | 410 +---- .../CLM50_Tech_Note_Photosynthesis.rst | 236 +-- ...LM50_Tech_Note_Photosynthetic_Capacity.rst | 156 +- .../CLM50_Tech_Note_Plant_Hydraulics.rst | 178 +- .../CLM50_Tech_Note_Plant_Mortality.rst | 57 +- .../CLM50_Tech_Note_Plant_Respiration.rst | 47 +- .../CLM50_Tech_Note_Radiative_Fluxes.rst | 180 +- .../References/CLM50_Tech_Note_References.rst | 1525 ++++------------- .../CLM50_Tech_Note_Snow_Hydrology.rst | 355 +--- ...CLM50_Tech_Note_Soil_Snow_Temperatures.rst | 352 +--- .../CLM50_Tech_Note_Surface_Albedos.rst | 485 +----- .../CLM50_Tech_Note_Transient_Landcover.rst | 346 +--- .../tech_note/Urban/CLM50_Tech_Note_Urban.rst | 169 +- ...ech_Note_Vegetation_Phenology_Turnover.rst | 318 +--- doc/source/tech_note/index.rst | 5 +- 34 files changed, 1735 insertions(+), 8662 deletions(-) diff --git a/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst b/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst index f3446647e9..5d34fdce64 100644 --- a/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst +++ b/doc/source/tech_note/BVOCs/CLM50_Tech_Note_BVOCs.rst @@ -3,61 +3,24 @@ Biogenic Volatile Organic Compounds (BVOCs) =============================================== -This chapter briefly describes the biogenic volatile organic compound -(BVOC) emissions model implemented in CLM. The CLM3 version (Levis et -al. 2003; Oleson et al. 2004) was based on Guenther et al. (1995). Heald -et al. (2008) updated this scheme in CLM4 based on Guenther et al. -(2006). The current version was implemented in CLM4.5 and is based on MEGAN2.1 discussed in -detail in Guenther et al. (2012). This update of MEGAN incorporates four -main features: 1) expansion to 147 chemical compounds, 2) the treatment of the -light-dependent fraction (LDF) for each compound, 3) inclusion of the -inhibition of isoprene emission by atmospheric CO\ :sub:`2` and -4) emission factors mapped to the specific PFTs of the CLM. - -MEGAN2.1 now describes the emissions of speciated monoterpenes, -sesquiterpenes, oxygenated VOCs as well as isoprene. A flexible scheme -has been implemented in the CLM to specify a subset of emissions. This -allows for additional flexibility in grouping chemical compounds to form -the lumped species frequently used in atmospheric chemistry. The mapping -or grouping is therefore defined through a namelist parameter in -drv\_flds\_in, e.g. megan\_specifier = 'ISOP = isoprene', 'BIGALK = -pentane + hexane + heptane + tricyclene'. - -Terrestrial BVOC emissions from plants to the atmosphere are expressed -as a flux, :math:`F_{i}` (:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1`), for emission of chemical compound -:math:`i` +This chapter briefly describes the biogenic volatile organic compound (BVOC) emissions model implemented in CLM. The CLM3 version (Levis et al. 2003; Oleson et al. 2004) was based on Guenther et al. (1995). Heald et al. (2008) updated this scheme in CLM4 based on Guenther et al (2006). The current version was implemented in CLM4.5 and is based on MEGAN2.1 discussed in detail in Guenther et al. (2012). This update of MEGAN incorporates four main features: 1) expansion to 147 chemical compounds, 2) the treatment of the light-dependent fraction (LDF) for each compound, 3) inclusion of the inhibition of isoprene emission by atmospheric CO\ :sub:`2` and 4) emission factors mapped to the specific PFTs of the CLM. + +MEGAN2.1 now describes the emissions of speciated monoterpenes, sesquiterpenes, oxygenated VOCs as well as isoprene. A flexible scheme has been implemented in the CLM to specify a subset of emissions. This allows for additional flexibility in grouping chemical compounds to form the lumped species frequently used in atmospheric chemistry. The mapping or grouping is therefore defined through a namelist parameter in drv\_flds\_in, e.g. megan\_specifier = 'ISOP = isoprene', 'BIGALK pentane + hexane + heptane + tricyclene'. + +Terrestrial BVOC emissions from plants to the atmosphere are expressed as a flux, :math:`F_{i}` (:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1`), for emission of chemical compound :math:`i` .. math:: :label: ZEqnNum964222 F_{i} =\gamma _{i} \rho \sum _{j}\varepsilon _{i,j} \left(wt\right)_{j} -where :math:`\gamma _{i}` is the emission activity factor accounting -for responses to meteorological and phenological conditions, -:math:`\rho` is the canopy loss and production factor also known as -escape efficiency (set to 1), and :math:`\varepsilon _{i,\, j}` -(:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1`) is -the emission factor at standard conditions of light, temperature, and -leaf area for plant functional type *j* with fractional coverage -:math:`\left(wt\right)_{j}` (Guenther et al. 2012). The emission -activity factor :math:`\gamma _{i}` depends on plant functional type, -temperature, LAI, leaf age, and soil moisture (Guenther et al. 2012). -For isoprene only, the effect of CO\ :sub:`2` inhibition is now -included as described by Heald et al. (2009). Previously, only isoprene -was treated as a light-dependent emission. In MEGAN2.1, each chemical -compound is assigned a LDF (ranging from 1.0 for isoprene to 0.2 for -some monoterpenes, VOCs and acetone). The activity factor for the light -response of emissions is therefore estimated as: +where :math:`\gamma _{i}` is the emission activity factor accounting for responses to meteorological and phenological conditions, :math:`\rho` is the canopy loss and production factor also known as escape efficiency (set to 1), and :math:`\varepsilon _{i,\, j}` (:math:`\mu` \ g C m\ :sup:`-2` ground area h\ :sup:`-1`) is the emission factor at standard conditions of light, temperature, and leaf area for plant functional type *j* with fractional coverage :math:`\left(wt\right)_{j}` (Guenther et al. 2012). The emission activity factor :math:`\gamma _{i}` depends on plant functional type, temperature, LAI, leaf age, and soil moisture (Guenther et al. 2012) For isoprene only, the effect of CO\ :sub:`2` inhibition is now included as described by Heald et al. (2009). Previously, only isoprene was treated as a light-dependent emission. In MEGAN2.1, each chemical compound is assigned a LDF (ranging from 1.0 for isoprene to 0.2 for some monoterpenes, VOCs and acetone). The activity factor for the light response of emissions is therefore estimated as: .. math:: :label: 28.2) \gamma _{P,\, i} =\left(1-LDF_{i} \right)+\gamma _{P\_ LDF} LDF_{i} -where the LDF activity factor (:math:`\gamma _{P\_ LDF}` ) is specified -as a function of PAR as in previous versions of MEGAN. +where the LDF activity factor (:math:`\gamma _{P\_ LDF}` ) is specified as a function of PAR as in previous versions of MEGAN. -The values for each emission factor :math:`\epsilon _{i,\, j}` are -now available for each of the plant functional types in the CLM and -each chemical compound. This information is distributed through an -external file, allowing for more frequent and easier updates. +The values for each emission factor :math:`\epsilon _{i,\, j}` are now available for each of the plant functional types in the CLM and each chemical compound. This information is distributed through an external file, allowing for more frequent and easier updates. diff --git a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst index ea07ec4347..7cf6ec6fc8 100644 --- a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst +++ b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst @@ -6,34 +6,14 @@ Carbon and Nitrogen Allocation Introduction ----------------- -The carbon and nitrogen allocation routines in CLM determine the fate of -newly assimilated carbon, coming from the calculation of photosynthesis, -and available mineral nitrogen, coming from plant uptake of mineral -nitrogen in the soil or being drawn out of plant reserves. A significant change to CLM5 relative to prior versions is that allocation of carbon and nitrogen proceed independently rather than in a sequential manner. +The carbon and nitrogen allocation routines in CLM determine the fate of newly assimilated carbon, coming from the calculation of photosynthesis, and available mineral nitrogen, coming from plant uptake of mineral nitrogen in the soil or being drawn out of plant reserves. A significant change to CLM5 relative to prior versions is that allocation of carbon and nitrogen proceed independently rather than in a sequential manner. Carbon Allocation for Maintenance Respiration Costs -------------------------------------------------------- -Allocation of available carbon on each time step is prioritized, with -first priority given to the demand for carbon to support maintenance -respiration of live tissues (section 13.7). Second priority is to -replenish the internal plant carbon pool that supports maintenance -respiration during times when maintenance respiration exceeds -photosynthesis (e.g. at night, during winter for perennial vegetation, -or during periods of drought stress) (Sprugel et al., 1995). Third -priority is to support growth of new tissues, including allocation to -storage pools from which new growth will be displayed in subsequent time -steps. - -The total maintenance respiration demand (:math:`CF_{mr}`, gC -m\ :sup:`-2` s\ :sup:`-1`) is calculated as a function of -tissue mass and nitrogen concentration, and temperature (section 13.7). -The carbon supply to support this demand is composed of fluxes allocated -from carbon assimilated in the current timestep -(:math:`CF_{GPP,mr}`, gC m\ :sup:`-2` s\ :sup:`-1`) -and from a storage pool that is drawn down when total demand exceeds -photosynthesis ( :math:`CF_{xs,mr}`, gC m\ :sup:`-2` -s\ :sup:`-1`): +Allocation of available carbon on each time step is prioritized, with first priority given to the demand for carbon to support maintenance respiration of live tissues (section 13.7). Second priority is to replenish the internal plant carbon pool that supports maintenance respiration during times when maintenance respiration exceeds photosynthesis (e.g. at night, during winter for perennial vegetation, or during periods of drought stress) (Sprugel et al., 1995). Third priority is to support growth of new tissues, including allocation to storage pools from which new growth will be displayed in subsequent time steps. + +The total maintenance respiration demand (:math:`CF_{mr}`, gC m\ :sup:`-2` s\ :sup:`-1`) is calculated as a function of tissue mass and nitrogen concentration, and temperature (section 13.7) The carbon supply to support this demand is composed of fluxes allocated from carbon assimilated in the current timestep (:math:`CF_{GPP,mr}`, gC m\ :sup:`-2` s\ :sup:`-1` and from a storage pool that is drawn down when total demand exceeds photosynthesis ( :math:`CF_{xs,mr}`, gC m\ :sup:`-2` s\ :sup:`-1`): .. math:: :label: 19.1 @@ -50,24 +30,7 @@ s\ :sup:`-1`): CF_{xs,mr} =\_ \left\{\begin{array}{l} {0\qquad \qquad \qquad {\rm for\; }CF_{mr} \le CF_{GPP} } \\ {CF_{mr} -CF_{GPP} \qquad {\rm for\; }CF_{mr} >CF_{GPP} } \end{array}\right. -The storage pool that supplies carbon for maintenance respiration in -excess of current :math:`CF_{GPP}` ( :math:`CS_{xs}`, gC -m\ :sup:`-2`) is permitted to run a deficit (negative state), and -the magnitude of this deficit determines an allocation demand which -gradually replenishes :math:`CS_{xs}`. The logic for allowing a -negative state for this pool is to eliminate the need to know in advance -what the total maintenance respiration demand will be for a particular -combination of climate and plant type. Using the deficit approach, the -allocation to alleviate the deficit increases as the deficit increases, -until the supply of carbon into the pool balances the demand for carbon -leaving the pool in a quasi-steady state, with variability driven by the -seasonal cycle, climate variation, disturbance, and internal dynamics of -the plant-litter-soil system. In cases where the combination of climate -and plant type are not suitable to sustained growth, the deficit in this -pool increases until the available carbon is being allocated mostly to -alleviate the deficit, and new growth approaches zero. The allocation -flux to :math:`CS_{xs}` (:math:`CF_{GPP,xs}`, gC -m\ :sup:`-2` s\ :sup:`-1`) is given as +The storage pool that supplies carbon for maintenance respiration in excess of current :math:`CF_{GPP}` ( :math:`CS_{xs}`, gC m\ :sup:`-2`) is permitted to run a deficit (negative state), and the magnitude of this deficit determines an allocation demand which gradually replenishes :math:`CS_{xs}`. The logic for allowing a negative state for this pool is to eliminate the need to know in advance what the total maintenance respiration demand will be for a particular combination of climate and plant type. Using the deficit approach, the allocation to alleviate the deficit increases as the deficit increases, until the supply of carbon into the pool balances the demand for carbon leaving the pool in a quasi-steady state, with variability driven by the seasonal cycle, climate variation, disturbance, and internal dynamics of the plant-litter-soil system. In cases where the combination of climate and plant type are not suitable to sustained growth, the deficit in this pool increases until the available carbon is being allocated mostly to alleviate the deficit, and new growth approaches zero. The allocation flux to :math:`CS_{xs}` (:math:`CF_{GPP,xs}`, gC m\ :sup:`-2` s\ :sup:`-1`) is given as .. math:: :label: 19.4 @@ -79,56 +42,37 @@ m\ :sup:`-2` s\ :sup:`-1`) is given as CF_{GPP,xs} =\left\{\begin{array}{l} {CF_{GPP,xs,pot} \qquad \qquad \qquad {\rm for\; }CF_{GPP,xs,pot} \le CF_{GPP} -CF_{GPP,mr} } \\ {\max (CF_{GPP} -CF_{GPP,mr} ,0)\qquad {\rm for\; }CF_{GPP,xs,pot} >CF_{GPP} -CF_{GPP,mr} } \end{array}\right. -where :math:`\tau_{xs}` is the time constant (currently -set to 30 days) controlling the rate of replenishment of :math:`CS_{xs}`. +where :math:`\tau_{xs}` is the time constant (currently set to 30 days) controlling the rate of replenishment of :math:`CS_{xs}`. -Note that these two top-priority carbon allocation fluxes -(:math:`CF_{GPP,mr}` and :math:`CF_{GPP,xs}`) are not -stoichiometrically associated with any nitrogen fluxes. +Note that these two top-priority carbon allocation fluxes (:math:`CF_{GPP,mr}` and :math:`CF_{GPP,xs}`) are not stoichiometrically associated with any nitrogen fluxes. Carbon and Nitrogen Stoichiometry of New Growth ---------------------------------------------------- -After accounting for the carbon cost of maintenance respiration, the -remaining carbon flux from photosynthesis which can be allocated to new -growth (:math:`CF_{avail}`, gC m\ :sup:`-2` s\ :sup:`-1`) is +After accounting for the carbon cost of maintenance respiration, the remaining carbon flux from photosynthesis which can be allocated to new growth (:math:`CF_{avail}`, gC m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 19.6 CF_{avail\_ alloc} =CF_{GPP} -CF_{GPP,mr} -CF_{GPP,xs} . -Potential allocation to new growth is calculated for all of the plant -carbon and nitrogen state variables based on specified C:N ratios for -each tissue type and allometric parameters that relate allocation -between various tissue types. The allometric parameters are defined as -follows: +Potential allocation to new growth is calculated for all of the plant carbon and nitrogen state variables based on specified C:N ratios for each tissue type and allometric parameters that relate allocation between various tissue types. The allometric parameters are defined as follows: .. math:: :label: 19.7 \begin{array}{l} {a_{1} ={\rm \; ratio\; of\; new\; fine\; root\; :\; new\; leaf\; carbon\; allocation}} \\ {a_{2} ={\rm \; ratio\; of\; new\; coarse\; root\; :\; new\; stem\; carbon\; allocation}} \\ {a_{3} ={\rm \; ratio\; of\; new\; stem\; :\; new\; leaf\; carbon\; allocation}} \\ {a_{4} ={\rm \; ratio\; new\; live\; wood\; :\; new\; total\; wood\; allocation}} \\ {g_{1} ={\rm ratio\; of\; growth\; respiration\; carbon\; :\; new\; growth\; carbon.\; }} \end{array} -Parameters :math:`a_{1}`, :math:`a_{2}`, and :math:`a_{4}` are defined as constants for a given PFT (Table -13.1), while :math:`g_{l }` = 0.3 (unitless) is prescribed as a -constant for all PFTs, based on construction costs for a range of woody -and non-woody tissues (Larcher, 1995). +Parameters :math:`a_{1}`, :math:`a_{2}`, and :math:`a_{4}` are defined as constants for a given PFT (Table 13.1), while :math:`g_{l }` = 0.3 (unitless) is prescribed as a constant for all PFTs, based on construction costs for a range of woody and non-woody tissues (Larcher, 1995). -The model includes a dynamic allocation scheme for woody vegetation -(parameter :math:`a_{3}` = -1, :numref:`Table Allocation and CN ratio parameters`), in which case the -ratio for carbon allocation between new stem and new leaf increases with -increasing net primary production (NPP), as +The model includes a dynamic allocation scheme for woody vegetation (parameter :math:`a_{3}` = -1, :numref:`Table Allocation and CN ratio parameters`), in which case the ratio for carbon allocation between new stem and new leaf increases with increasing net primary production (NPP), as .. math:: :label: 19.8 a_{3} =\frac{2.7}{1+e^{-0.004NPP_{ann} -300} } -0.4 -where :math:`NPP_{ann}` is the annual sum of NPP from the previous -year. This mechanism has the effect of increasing woody allocation in -favorable growth environments (Allen et al., 2005; Vanninen and Makela, -2005) and during the phase of stand growth prior to canopy closure -(Axelsson and Axelsson, 1986). +where :math:`NPP_{ann}` is the annual sum of NPP from the previous year. This mechanism has the effect of increasing woody allocation in favorable growth environments (Allen et al., 2005; Vanninen and Makela, 2005) and during the phase of stand growth prior to canopy closure (Axelsson and Axelsson, 1986). .. _Table Allocation and CN ratio parameters: @@ -193,23 +137,16 @@ favorable growth environments (Allen et al., 2005; Vanninen and Makela, | Switchgrass I | 2 | 0 | 0 | 1 | 25 | 42 | 50 | 500 | +----------------------------------+-----------------------+-----------------------+-----------------------+-----------------------+---------------------------+-------------------------+-------------------------+-------------------------+ -Carbon to nitrogen ratios are defined for different tissue types as -follows: +Carbon to nitrogen ratios are defined for different tissue types as follows: .. math:: :label: 19.9 \begin{array}{l} {CN_{leaf} =\_ {\rm \; C:N\; for\; leaf}} \\ {CN_{fr} =\_ {\rm \; C:N\; for\; fine\; root}} \\ {CN_{lw} =\_ {\rm \; C:N\; for\; live\; wood\; (in\; stem\; and\; coarse\; root)}} \\ {CN_{dw} =\_ {\rm \; C:N\; for\; dead\; wood\; (in\; stem\; and\; coarse\; root)}} \end{array} -where all C:N parameters are defined as constants for a given PFT -(:numref:`Table Allocation and CN ratio parameters`). +where all C:N parameters are defined as constants for a given PFT (:numref:`Table Allocation and CN ratio parameters`). -Given values for the parameters in and , total carbon and nitrogen -allocation to new growth ( :math:`CF_{alloc}`, gC -m\ :sup:`-2` s\ :sup:`-1`, and :math:`NF_{alloc}`, gN -m\ :sup:`-2` s\ :sup:`-1`, respectively) can be expressed as -functions of new leaf carbon allocation (:math:`CF_{GPP,leaf}`, gC -m\ :sup:`-2` s\ :sup:`-1`): +Given values for the parameters in and, total carbon and nitrogen allocation to new growth ( :math:`CF_{alloc}`, gC m\ :sup:`-2` s\ :sup:`-1`, and :math:`NF_{alloc}`, gN m\ :sup:`-2` s\ :sup:`-1`, respectively) can be expressed as functions of new leaf carbon allocation (:math:`CF_{GPP,leaf}`, gC m\ :sup:`-2` s\ :sup:`-1`): .. math:: :label: 19.10 @@ -228,11 +165,7 @@ where N_{allom} =\left\{\begin{array}{l} {\frac{1}{CN_{leaf} } +\frac{a_{1} }{CN_{fr} } +\frac{a_{3} a_{4} \left(1+a_{2} \right)}{CN_{lw} } +} \\ {\qquad \frac{a_{3} \left(1-a_{4} \right)\left(1+a_{2} \right)}{CN_{dw} } \qquad {\rm for\; woody\; PFT}} \\ {\frac{1}{CN_{leaf} } +\frac{a_{1} }{CN_{fr} } \qquad \qquad \qquad {\rm for\; non-woody\; PFT.}} \end{array}\right. -Since the C:N stoichiometry for new growth allocation is defined, from -Eq. , as :math:`C_{allom}`/ :math:`N_{allom}`, the total carbon available for new growth allocation -(:math:`CF_{avail\_alloc}`) can be used to calculate the total -plant nitrogen demand for new growth ( :math:`NF_{plant\_demand}`, -gN m\ :sup:`-2` s\ :sup:`-1`) as: +Since the C:N stoichiometry for new growth allocation is defined, from Eq., as :math:`C_{allom}`/ :math:`N_{allom}`, the total carbon available for new growth allocation (:math:`CF_{avail\_alloc}`) can be used to calculate the total plant nitrogen demand for new growth ( :math:`NF_{plant\_demand}`, gN m\ :sup:`-2` s\ :sup:`-1`) as: .. math:: :label: 19.13 @@ -242,16 +175,7 @@ gN m\ :sup:`-2` s\ :sup:`-1`) as: Carbon Allocation to New Growth ----------------------------------------- -There are two carbon pools associated with each plant tissue – one which -represents the currently displayed tissue, and another which represents -carbon stored for display in a subsequent growth period. The nitrogen -pools follow this same organization. The model keeps track of stored -carbon according to which tissue type it will eventually be displayed -as, and the separation between display in the current timestep and -storage for later display depends on the parameter :math:`f_{cur}` -(values 0 to 1). Given :math:`CF_{alloc,leaf}` and :math:`f_{cur}`, the allocation fluxes of carbon to display and -storage pools (where storage is indicated with *\_stor*) for the various -tissue types are given as: +There are two carbon pools associated with each plant tissue – one which represents the currently displayed tissue, and another which represents carbon stored for display in a subsequent growth period. The nitrogen pools follow this same organization. The model keeps track of stored carbon according to which tissue type it will eventually be displayed as, and the separation between display in the current timestep and storage for later display depends on the parameter :math:`f_{cur}` (values 0 to 1). Given :math:`CF_{alloc,leaf}` and :math:`f_{cur}`, the allocation fluxes of carbon to display and storage pools (where storage is indicated with *\_stor*) for the various tissue types are given as: .. math:: :label: 19.14 @@ -316,7 +240,7 @@ tissue types are given as: Nitrogen allocation ----------------------------------------- -The total flux of nitrogen to be allocated is given by the FUN model (Chapter :numref:`rst_FUN`). This gives a total N to be allocated within a given timestep, :math:`N_{supply}`. The total N allocated for a given tissue :math:`i` is the minimum between the supply and the demand: +The total flux of nitrogen to be allocated is given by the FUN model (Chapter :numref:`rst_FUN`). This gives a total N to be allocated within a given timestep, :math:`N_{supply}`. The total N allocated for a given tissue :math:`i` is the minimum between the supply and the demand: .. math:: :label: 19.26 @@ -385,14 +309,14 @@ The demand for each tissue, calculated for the tissue to remain on stoichiometry NF_{demand,deadcroot\_ stor} \_ =\frac{CF_{alloc,leaf} a_{2} a_{3} \left(1-a_{4} \right)}{CN_{dw} } \left(1-f_{cur} \right). -After each pool's demand is calculated, the total plant N demand is then the sum of each individual pool :math: `i` corresponding to each tissue: +After each pool's demand is calculated, the total plant N demand is then the sum of each individual pool :math:`i` corresponding to each tissue: .. math:: :label: 19.39 NF_{demand,tot} = \sum _{i=tissues} NF_{demand,i} -and the total supply for each tissue :math: `i` is the product of the fractional demand and the total available N, calculated as the term :math: `N_{uptake}` equal to the sum of the eight N uptake streams described in the FUN model (Chapter :numref:`rst_FUN`). +and the total supply for each tissue :math:`i` is the product of the fractional demand and the total available N, calculated as the term :math:`N_{uptake}` equal to the sum of the eight N uptake streams described in the FUN model (Chapter :numref:`rst_FUN`). .. math:: :label: 19.40 diff --git a/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst b/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst index 031b0fcbbb..ebff41577a 100644 --- a/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst +++ b/doc/source/tech_note/CN_Pools/CLM50_Tech_Note_CN_Pools.rst @@ -6,32 +6,9 @@ CN Pools Introduction ----------------- -CLM includes a prognostic treatment of the terrestrial carbon and -nitrogen cycles including natural vegetation, crops, and soil biogeochemistry. The model is -fully prognostic with respect to all carbon and nitrogen state variables -in the vegetation, litter, and soil organic matter. The seasonal timing -of new vegetation growth and litterfall is also prognostic, responding -to soil and air temperature, soil water availability, daylength, and -crop management practices in -varying degrees depending on a specified phenology type or management for each PFT -(Chapter -:numref:`rst_Vegetation Phenology and Turnover`). The -prognostic LAI, SAI, -tissue stoichiometry, and vegetation heights are -utilized by the biophysical model that couples carbon, water, and -energy cycles. +CLM includes a prognostic treatment of the terrestrial carbon and nitrogen cycles including natural vegetation, crops, and soil biogeochemistry. The model is fully prognostic with respect to all carbon and nitrogen state variables in the vegetation, litter, and soil organic matter. The seasonal timing of new vegetation growth and litterfall is also prognostic, responding to soil and air temperature, soil water availability, daylength, and crop management practices in varying degrees depending on a specified phenology type or management for each PFT (Chapter :numref:`rst_Vegetation Phenology and Turnover`). The prognostic LAI, SAI, tissue stoichiometry, and vegetation heights are utilized by the biophysical model that couples carbon, water, and energy cycles. -Separate state variables for C and N are tracked for leaf, live stem, -dead stem, live coarse root, dead coarse root, fine root, and grain pools -(:numref:`Figure Vegetation fluxes and pools`). Each of these pools has two corresponding -storage pools representing, respectively, short-term and long-term -storage of non-structural carbohydrates and labile nitrogen. There are -two additional carbon pools, one for the storage of growth respiration -reserves, and another used to meet excess demand for maintenance -respiration during periods with low photosynthesis. One additional -nitrogen pool tracks retranslocated nitrogen, mobilized from leaf tissue -prior to abscission and litterfall. Altogether there are 23 state -variables for vegetation carbon, and 22 for vegetation nitrogen. +Separate state variables for C and N are tracked for leaf, live stem, dead stem, live coarse root, dead coarse root, fine root, and grain pools (:numref:`Figure Vegetation fluxes and pools`). Each of these pools has two corresponding storage pools representing, respectively, short-term and long-term storage of non-structural carbohydrates and labile nitrogen. There are two additional carbon pools, one for the storage of growth respiration reserves, and another used to meet excess demand for maintenance respiration during periods with low photosynthesis. One additional nitrogen pool tracks retranslocated nitrogen, mobilized from leaf tissue prior to abscission and litterfall. Altogether there are 23 state variables for vegetation carbon, and 22 for vegetation nitrogen. .. _Figure Vegetation fluxes and pools: @@ -41,29 +18,12 @@ variables for vegetation carbon, and 22 for vegetation nitrogen. Vegetation fluxes and pools for carbon cycle in CLM5. -In addition to the vegetation pools, CLM includes a series of -decomposing carbon and nitrogen pools as vegetation successively -breaks down to CWD, and/or litter, and subsequently to soil organic -matter. Discussion of the decomposition model, alternate -specifications of decomposition rates, and methods to rapidly -equilibrate the decomposition model, is in Chapter -:numref:`rst_Decomposition`. +In addition to the vegetation pools, CLM includes a series of decomposing carbon and nitrogen pools as vegetation successively breaks down to CWD, and/or litter, and subsequently to soil organic matter. Discussion of the decomposition model, alternate specifications of decomposition rates, and methods to rapidly equilibrate the decomposition model, is in Chapter :numref:`rst_Decomposition`. Tissue Stoichiometry ----------------------- -As of CLM5, vegetation tissues have a flexible stoichiometry, as -described in :ref:`Ghimire et al. (2016) `. Each -tissue has a target C\:N ratio, with the target leaf C\:N varying by plant functional type -(see :numref:`Table Plant functional type (PFT) target CN parameters`), and nitrogen is allocated at each -timestep in order to allow the plant to best match the target -stoichiometry. Nitrogen downregulation of productivity acts by -increasing the C\:N ratio of leaves when insufficient nitrogen is -available to meet stoichiometric demands of leaf growth, thereby -reducing the N available for photosynthesis and reducing the :math:`V_{\text{c,max25}}` and -:math:`J_{\text{max25}}` terms, as described in Chapter -:numref:`rst_Photosynthetic Capacity`. Details of the flexible tissue -stoichiometry are described in Chapter :numref:`rst_CN Allocation`. +As of CLM5, vegetation tissues have a flexible stoichiometry, as described in :ref:`Ghimire et al. (2016) `. Each tissue has a target C\:N ratio, with the target leaf C\:N varying by plant functional type (see :numref:`Table Plant functional type (PFT) target CN parameters`), and nitrogen is allocated at each timestep in order to allow the plant to best match the target stoichiometry. Nitrogen downregulation of productivity acts by increasing the C\:N ratio of leaves when insufficient nitrogen is available to meet stoichiometric demands of leaf growth, thereby reducing the N available for photosynthesis and reducing the :math:`V_{\text{c,max25}}` and :math:`J_{\text{max25}}` terms, as described in Chapter :numref:`rst_Photosynthetic Capacity`. Details of the flexible tissue stoichiometry are described in Chapter :numref:`rst_CN Allocation`. .. _Table Plant functional type (PFT) target CN parameters: diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 91a1e7232a..9ed603ad89 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -8,12 +8,9 @@ Crops and Irrigation Summary of CLM5.0 updates relative to the CLM4.5 ------------------------------------------------ -We describe here the complete crop and irrigation parameterizations that -appear in CLM5.0. Corresponding information for CLM4.5 appeared in the -CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). +We describe here the complete crop and irrigation parameterizations that appear in CLM5.0. Corresponding information for CLM4.5 appeared in the CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). -CLM5.0 includes the following new updates to the CROP option, where CROP -refers to the interactive crop management model and is included as an option with the BGC configuration: +CLM5.0 includes the following new updates to the CROP option, where CROP refers to the interactive crop management model and is included as an option with the BGC configuration: - New crop functional types @@ -37,8 +34,7 @@ refers to the interactive crop management model and is included as an option wit - Initial seed C for planting is increased from 1 to 3 g C/m^2 -These updates appear in detail in the sections below. Many also appear in -:ref:`Levis et al. (2016) `. +These updates appear in detail in the sections below. Many also appear in :ref:`Levis et al. (2016) `. Available new features since the CLM5 release ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -52,100 +48,22 @@ The crop model: cash and bioenergy crops Introduction ^^^^^^^^^^^^ -Groups developing Earth System Models generally account for the human -footprint on the landscape in simulations of historical and future -climates. Traditionally we have represented this footprint with natural -vegetation types and particularly grasses because they resemble many -common crops. Most modeling efforts have not incorporated more explicit -representations of land management such as crop type, planting, -harvesting, tillage, fertilization, and irrigation, because global scale -datasets of these factors have lagged behind vegetation mapping. As this -begins to change, we increasingly find models that will simulate the -biogeophysical and biogeochemical effects not only of natural but also -human-managed land cover. - -AgroIBIS is a state-of-the-art land surface model with options to -simulate dynamic vegetation (:ref:`Kucharik et al. 2000 `) and interactive -crop management (:ref:`Kucharik and Brye 2003 `). The interactive crop -management parameterizations from AgroIBIS (March 2003 version) were -coupled as a proof-of-concept to the Community Land Model version 3 -[CLM3.0, :ref:`Oleson et al. (2004) ` ] (not published), then coupled to the -CLM3.5 (:ref:`Levis et al. 2009 `) and later released to the community with -CLM4CN (:ref:`Levis et al. 2012 `), and CLM4.5BGC. Additional updates after the -release of CLM4.5 were available by request (:ref:`Levis et al. 2016 `), -and those are now incorporated into CLM5. - -With interactive crop management and, therefore, a more accurate -representation of agricultural landscapes, we hope to improve the CLM's -simulated biogeophysics and biogeochemistry. These advances may improve -fully coupled simulations with the Community Earth System Model (CESM), -while helping human societies answer questions about changing food, -energy, and water resources in response to climate, environmental, land -use, and land management change (e.g., :ref:`Kucharik and Brye 2003 `; :ref:`Lobell et al. 2006 `). -As implemented here, the crop model uses the same physiology as the -natural vegetation, though uses different crop-specific parameter values, -phenology, and allocation, as well as fertilizer and irrigation management. +Groups developing Earth System Models generally account for the human footprint on the landscape in simulations of historical and future climates. Traditionally we have represented this footprint with natural vegetation types and particularly grasses because they resemble many common crops. Most modeling efforts have not incorporated more explicit representations of land management such as crop type, planting, harvesting, tillage, fertilization, and irrigation, because global scale datasets of these factors have lagged behind vegetation mapping. As this begins to change, we increasingly find models that will simulate the biogeophysical and biogeochemical effects not only of natural but also human-managed land cover. + +AgroIBIS is a state-of-the-art land surface model with options to simulate dynamic vegetation (:ref:`Kucharik et al. 2000 `) and interactive crop management (:ref:`Kucharik and Brye 2003 `). The interactive crop management parameterizations from AgroIBIS (March 2003 version) were coupled as a proof-of-concept to the Community Land Model version 3 [CLM3.0, :ref:`Oleson et al. (2004) ` ] (not published), then coupled to the CLM3.5 (:ref:`Levis et al. 2009 `) and later released to the community with CLM4CN (:ref:`Levis et al. 2012 `), and CLM4.5BGC. Additional updates after the release of CLM4.5 were available by request (:ref:`Levis et al. 2016 `), and those are now incorporated into CLM5. + +With interactive crop management and, therefore, a more accurate representation of agricultural landscapes, we hope to improve the CLM's simulated biogeophysics and biogeochemistry. These advances may improve fully coupled simulations with the Community Earth System Model (CESM), while helping human societies answer questions about changing food, energy, and water resources in response to climate, environmental, land use, and land management change (e.g., :ref:`Kucharik and Brye 2003 `; :ref:`Lobell et al. 2006 `). As implemented here, the crop model uses the same physiology as the natural vegetation, though uses different crop-specific parameter values, phenology, and allocation, as well as fertilizer and irrigation management. .. _Crop plant functional types: Crop plant functional types ^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To allow crops to coexist with natural vegetation in a grid cell, the -vegetated land unit is separated into a naturally vegetated land unit and -a managed crop land unit. Unlike the plant functional types (pfts) in the -naturally vegetated land unit, the managed crop pfts in the managed crop -land unit do not share soil columns and thus permit for differences in the -land management between crops. Each crop type has a rainfed and an irrigated -pft that are on independent soil columns. Crop grid cell coverage is assigned from -satellite data (similar to all natural pfts), and the managed crop type -proportions within the crop area is based on the dataset created by -:ref:`Portmann et al. (2010)` for present day. New in CLM5, crop area is -extrapolated through time using the dataset provided by Land Use Model -Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries -(:ref:`Lawrence et al. 2016 `). For more details about how -crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. - -CLM5 includes ten actively managed crop types -(temperate soybean, tropical soybean, temperate corn, tropical -corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen -based on the availability of corresponding algorithms in AgroIBIS and as -developed by :ref:`Badger and Dirmeyer (2015)` and -described by :ref:`Levis et al. (2016)`, or from available observations -as described by :ref:`Cheng et al. (2019)`. -The representations of sugarcane, rice, cotton, tropical corn, and tropical soy are new in CLM5. -Miscanthus and switchgrass are added after the CLM5 release. -Sugarcane and tropical corn are both C4 plants and are therefore represented -using the temperate corn functional form. Tropical soybean uses the temperate -soybean functional form, while rice and cotton use the wheat functional form. -In tropical regions, parameter values were developed for the Amazon Basin, and planting -date window is shifted by six months relative to the Northern Hemisphere. -Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to -replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and -have quite different physiological traits and land management practices than annual crops, -such as longer growing seasons, higher productivity, and lower demands for nutrients and water. -About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using -observation data collected at the University of Illinois Energy Farm -located in Central Midwestern United States (:ref:`Cheng et al., 2019`). - -In addition, CLM's default list of plant functional types (pfts) includes an -irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. -The unmanaged C3 crop is only used when the crop model is not active and -has grid cell coverage assigned from satellite data, and -the unmanaged C3 irrigated crop type is currently not used -since irrigation requires the crop model to be active. -The default list of pfts also includes twenty-one inactive crop pfts -that do not yet have associated parameters required for active management. -Each of the inactive crop types is simulated using the parameters of the -spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), -which is required to maintain similar phenological parameters based on temperature thresholds. -Information detailing which parameters are used for each crop type is -included in :numref:`Table Crop plant functional types`. It should be noted that pft-level history output merges -all crop types into the actively managed crop type, so analysis -of crop-specific output will require use of the land surface dataset to -remap the yields of each actively and inactively managed crop type. Otherwise, the -actively managed crop type will include yields for that crop type and all inactively -managed crop types that are using the same parameter set. +To allow crops to coexist with natural vegetation in a grid cell, the vegetated land unit is separated into a naturally vegetated land unit and a managed crop land unit. Unlike the plant functional types (pfts) in the naturally vegetated land unit, the managed crop pfts in the managed crop land unit do not share soil columns and thus permit for differences in the land management between crops. Each crop type has a rainfed and an irrigated pft that are on independent soil columns. Crop grid cell coverage is assigned from satellite data (similar to all natural pfts), and the managed crop type proportions within the crop area is based on the dataset created by :ref:`Portmann et al. (2010)` for present day. New in CLM5, crop area is extrapolated through time using the dataset provided by Land Use Model Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries (:ref:`Lawrence et al. 2016 `). For more details about how crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. + +CLM5 includes ten actively managed crop types (temperate soybean, tropical soybean, temperate corn, tropical corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen based on the availability of corresponding algorithms in AgroIBIS and as developed by :ref:`Badger and Dirmeyer (2015)` and described by :ref:`Levis et al. (2016)`, or from available observations as described by :ref:`Cheng et al. (2019)`. The representations of sugarcane, rice, cotton, tropical corn, and tropical soy are new in CLM5. Miscanthus and switchgrass are added after the CLM5 release. Sugarcane and tropical corn are both C4 plants and are therefore represented using the temperate corn functional form. Tropical soybean uses the temperate soybean functional form, while rice and cotton use the wheat functional form. In tropical regions, parameter values were developed for the Amazon Basin, and planting date window is shifted by six months relative to the Northern Hemisphere. Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and have quite different physiological traits and land management practices than annual crops, such as longer growing seasons, higher productivity, and lower demands for nutrients and water. About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using observation data collected at the University of Illinois Energy Farm located in Central Midwestern United States (:ref:`Cheng et al., 2019`). + +In addition, CLM's default list of plant functional types (pfts) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. The unmanaged C3 crop is only used when the crop model is not active and has grid cell coverage assigned from satellite data, and the unmanaged C3 irrigated crop type is currently not used since irrigation requires the crop model to be active. The default list of pfts also includes twenty-one inactive crop pfts that do not yet have associated parameters required for active management. Each of the inactive crop types is simulated using the parameters of the spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), which is required to maintain similar phenological parameters based on temperature thresholds. Information detailing which parameters are used for each crop type is included in :numref:`Table Crop plant functional types`. It should be noted that pft-level history output merges all crop types into the actively managed crop type, so analysis of crop-specific output will require use of the land surface dataset to remap the yields of each actively and inactively managed crop type. Otherwise, the actively managed crop type will include yields for that crop type and all inactively managed crop types that are using the same parameter set. .. _Table Crop plant functional types: @@ -225,24 +143,16 @@ managed crop types that are using the same parameter set. Phenology ^^^^^^^^^ -CLM5-BGC includes evergreen, seasonally deciduous (responding to changes -in day length), and stress deciduous (responding to changes in -temperature and/or soil moisture) phenology algorithms (Chapter :numref:`rst_Vegetation Phenology and Turnover`). -CLM5-BGC-crop uses the AgroIBIS crop phenology algorithm, -consisting of three distinct phases. +CLM5-BGC includes evergreen, seasonally deciduous (responding to changes in day length), and stress deciduous (responding to changes in temperature and/or soil moisture) phenology algorithms (Chapter :numref:`rst_Vegetation Phenology and Turnover`). CLM5-BGC-crop uses the AgroIBIS crop phenology algorithm, consisting of three distinct phases. -Phase 1 starts at planting and ends with leaf emergence, phase 2 -continues from leaf emergence to the beginning of grain fill, and phase -3 starts from the beginning of grain fill and ends with physiological -maturity and harvest. +Phase 1 starts at planting and ends with leaf emergence, phase 2 continues from leaf emergence to the beginning of grain fill, and phase 3 starts from the beginning of grain fill and ends with physiological maturity and harvest. .. _Planting: Planting '''''''' -All crops must meet the following requirements between the minimum planting date and the maximum -planting date (for the northern hemisphere) in :numref:`Table Crop phenology parameters`: +All crops must meet the following requirements between the minimum planting date and the maximum planting date (for the northern hemisphere) in :numref:`Table Crop phenology parameters`: .. math:: :label: 25.1 @@ -253,29 +163,9 @@ planting date (for the northern hemisphere) in :numref:`Table Crop phenology par {GDD_{8} \ge GDD_{\min } } \end{array} -where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air -temperature during each model time step) and :math:`T_{10d}^{\min}` is -the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of -:math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures -(:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing -degree-days (units are degree-days or :sup:`o` days) tracked -from April through September (NH) above 8\ :sup:`o` C with -maximum daily increments of 30\ :sup:`o` days (see equation :eq:`25.3`), and -:math:`{GDD}_{min }`\ is the minimum growing degree day requirement -(:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so -it determines whether it is warm enough for the crop to be planted in a grid cell, while the -2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. -If the requirements in equation :eq:`25.1` are not met by the maximum planting date, -crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In -the southern hemisphere (SH) the NH requirements apply 6 months later. - -At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its -grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An -equivalent amount of seed leaf N is assigned given the pft's C to N -ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, -which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary -for the crop to reach vegetative and physiological maturity, -:math:`{GDD}_{mat}`, according to the following AgroIBIS rules: +where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are degree-days or :sup:`o` days) tracked from April through September (NH) above 8\ :sup:`o` C with maximum daily increments of 30\ :sup:`o` days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. + +At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, :math:`{GDD}_{mat}`, according to the following AgroIBIS rules: .. math:: :label: 25.2 @@ -288,11 +178,7 @@ for the crop to reach vegetative and physiological maturity, GDD_{{\rm mat}}^{{\rm trop.soy}} =GDD_{{\rm 10}} & {\rm \; \; \; and\; \; \; } & GDD_{{\rm mat}}^{{\rm trop.soy}} <2100{}^\circ {\rm days} \end{array} -where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing -degree-days tracked from April through September (NH) over 0\ :sup:`o`\C, 8\ :sup:`o`\C, and -10\ :sup:`o`\C, respectively, with maximum daily increments of -26\ :sup:`o`\days (for :math:`{GDD}_{0}`) or 30\ :sup:`o`\days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate -:math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: +where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0\ :sup:`o`\C, 8\ :sup:`o`\C, and 10\ :sup:`o`\C, respectively, with maximum daily increments of 26\ :sup:`o`\days (for :math:`{GDD}_{0}`) or 30\ :sup:`o`\days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: .. math:: :label: 25.3 @@ -303,55 +189,28 @@ degree-days tracked from April through September (NH) over 0\ :sup:`o`\C, 8\ :su GDD_{{\rm 10}} =GDD_{10} +T_{2{\rm m}} -T_{f} -10 & \quad {\rm \; \; \; where\; \; \; } & 0 \le T_{2{\rm m}} -T_{f} -10\le 30{}^\circ {\rm days} \end{array} -where, if :math:`{T}_{2m}` - :math:`{T}_{f}` takes on values -outside the above ranges within a day, then it equals the minimum or maximum value in -the range for that day. :math:`{T}_{f}` is the freezing temperature of water and equals 273.15 K, -:math:`{T}_{2m}` is the 2-m air temperature in units of K, and *GDD* is in units of ºdays. +where, if :math:`{T}_{2m}` - :math:`{T}_{f}` takes on values outside the above ranges within a day, then it equals the minimum or maximum value in the range for that day. :math:`{T}_{f}` is the freezing temperature of water and equals 273.15 K, :math:`{T}_{2m}` is the 2-m air temperature in units of K, and *GDD* is in units of ºdays. .. _Leaf emergence: Leaf emergence '''''''''''''' -According to AgroIBIS, leaves may emerge when the growing degree-days of -soil temperature to 0.05 m depth (:math:`GDD_{T_{soi} }` ), which is tracked since planting, -reaches 1 to 5% of :math:`{GDD}_{mat}` -(see Phase 2 % :math:`{GDD}_{mat}` in :numref:`Table Crop phenology parameters`). The base temperature threshold values for :math:`GDD_{T_{soi} }` -are listed in :numref:`Table Crop phenology parameters` (the same base temperature threshold values are also used for -:math:`GDD_{T_{{\rm 2m}} }` in section :numref:`Grain Fill`), and leaf emergence (crop phenology phase 2) -starts when this threshold is met. Leaf onset occurs in the first -time step of phase 2, at which moment all seed C is transferred to leaf -C. Subsequently, the leaf area index generally increases throughout phase 2 until it reaches -a predetermined maximum value. Stem and root C also increase throughout phase 2 based on -the carbon allocation algorithm in section :numref:`Leaf emergence to grain fill`. +According to AgroIBIS, leaves may emerge when the growing degree-days of soil temperature to 0.05 m depth (:math:`GDD_{T_{soi} }` ), which is tracked since planting, reaches 1 to 5% of :math:`{GDD}_{mat}` (see Phase 2 % :math:`{GDD}_{mat}` in :numref:`Table Crop phenology parameters`). The base temperature threshold values for :math:`GDD_{T_{soi} }` are listed in :numref:`Table Crop phenology parameters` (the same base temperature threshold values are also used for :math:`GDD_{T_{{\rm 2m}} }` in section :numref:`Grain Fill`), and leaf emergence (crop phenology phase 2) starts when this threshold is met. Leaf onset occurs in the first time step of phase 2, at which moment all seed C is transferred to leaf C. Subsequently, the leaf area index generally increases throughout phase 2 until it reaches a predetermined maximum value. Stem and root C also increase throughout phase 2 based on the carbon allocation algorithm in section :numref:`Leaf emergence to grain fill`. .. _Grain fill: Grain fill '''''''''' -The grain fill phase (phase 3) begins in one of two ways. The first potential trigger is based on temperature, similar to phase 2. A variable tracked since -planting, similar to :math:`GDD_{T_{soi} }` but for 2-m air temperature, -:math:`GDD_{T_{{\rm 2m}} }`, must reach a heat unit threshold, *h*, of -of 40 to 65% of :math:`{GDD}_{mat}` (see Phase 3 % :math:`{GDD}_{mat}` in :numref:`Table Crop phenology parameters`). -For crops with the C4 photosynthetic pathway (temperate and tropical corn, sugarcane), -the :math:`{GDD}_{mat}` is based on an empirical function and ranges between 950 and 1850. -The second potential trigger for phase 3 is based on leaf area index. -When the maximum value of leaf area index is reached in phase 2 (:numref:`Table Crop allocation parameters`), phase 3 begins. -In phase 3, the leaf area index begins to decline in -response to a background litterfall rate calculated as the inverse of -leaf longevity for the pft as done in the BGC part of the model. +The grain fill phase (phase 3) begins in one of two ways. The first potential trigger is based on temperature, similar to phase 2. A variable tracked since planting, similar to :math:`GDD_{T_{soi} }` but for 2-m air temperature, :math:`GDD_{T_{{\rm 2m}} }`, must reach a heat unit threshold, *h*, of of 40 to 65% of :math:`{GDD}_{mat}` (see Phase 3 % :math:`{GDD}_{mat}` in :numref:`Table Crop phenology parameters`). For crops with the C4 photosynthetic pathway (temperate and tropical corn, sugarcane), the :math:`{GDD}_{mat}` is based on an empirical function and ranges between 950 and 1850. The second potential trigger for phase 3 is based on leaf area index. When the maximum value of leaf area index is reached in phase 2 (:numref:`Table Crop allocation parameters`), phase 3 begins. In phase 3, the leaf area index begins to decline in response to a background litterfall rate calculated as the inverse of leaf longevity for the pft as done in the BGC part of the model. .. _Harvest: Harvest ''''''' -Harvest is assumed to occur as soon as the crop reaches maturity. When -:math:`GDD_{T_{{\rm 2m}} }` reaches 100% of :math:`{GDD}_{mat}` or -the number of days past planting reaches a crop-specific maximum -(:numref:`Table Crop phenology parameters`), then the crop is harvested. -Harvest occurs in one time step using the BGC leaf offset algorithm. +Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GDD_{T_{{\rm 2m}} }` reaches 100% of :math:`{GDD}_{mat}` or the number of days past planting reaches a crop-specific maximum (:numref:`Table Crop phenology parameters`), then the crop is harvested. Harvest occurs in one time step using the BGC leaf offset algorithm. .. _Table Crop phenology parameters: @@ -379,62 +238,18 @@ Harvest occurs in one time step using the BGC leaf offset algorithm. fcur 1 1 1 1 1 1 1 1 1 1 =================================== ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== -Notes: :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are -the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates -in the Southern Hemisphere apply 6 months later. -:math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. -:math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based -on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). -:math:`{GDD}_{mat}` is a crop's 20-year running mean growing -degree-days needed for vegetative and physiological maturity. Harvest -occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting -reach the number in the 11\ :sup:`th` row. Crop growth phases -are described in the text. :math:`z_{top}^{\max }` is the maximum -top-of-canopy height of a crop, *SLA* is specific leaf area. :math:`\chi _{L}` is the leaf -orientation index, equals -1 for vertical, 0 for -random, and 1 for horizontal leaf orientation. -grperc is the growth respiration factor. flnr is the fraction of leaf N in the Rubisco enzyme. -fcur is the fraction of allocation that goes to currently displayed growth. +Notes: :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates in the Southern Hemisphere apply 6 months later. :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. Crop growth phases are described in the text. :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop, *SLA* is specific leaf area. :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. grperc is the growth respiration factor. flnr is the fraction of leaf N in the Rubisco enzyme. fcur is the fraction of allocation that goes to currently displayed growth. .. _Allocation: Allocation ^^^^^^^^^^ -Allocation changes based on the crop phenology phases phenology (section :numref:`Phenology`). -Simulated C assimilation begins every year upon leaf emergence in phase -2 and ends with harvest at the end of phase 3; therefore, so does the -allocation of such C to the crop's leaf, live stem, fine root, and -reproductive pools. - -Typically, C:N ratios in plant tissue vary throughout the growing season and -tend to be lower during early growth stages and higher in later growth stages. -In order to account for this seasonal change, two sets of C:N -ratios are established in CLM for the leaf, stem, and fine root of -crops: one during the leaf emergence phase (phenology phase 2), and a second during -grain fill phase (phenology phase 3). This modified C:N ratio approach accounts for the nitrogen -retranslocation that occurs during the grain fill phase (phase 3) of crop growth. Leaf, stem, and root -C:N ratios for phase 2 are calculated -using the new CLM5 carbon and nitrogen allocation scheme -(Chapter :numref:`rst_CN Allocation`), which provides a target C:N value -(:numref:`Table Crop allocation parameters`) and allows C:N to vary through time. -During grain fill (phase 3) of the crop growth cycle, a portion of the -nitrogen in the plant tissues is moved to a storage pool to fulfill -nitrogen demands of organ (reproductive pool) development, such that the -resulting C:N ratio of the plant tissue is reflective of measurements at -harvest. All C:N ratios were determined by calibration process, through -comparisons of model output versus observations of plant carbon -throughout the growing season. - -The BGC part of the model keeps track of a term representing excess -maintenance respiration, which supplies the carbon required for maintenance respiration during periods of -low photosynthesis (Chapter :numref:`rst_Plant Respiration`). -Carbon supply for excess maintenance respiration -cannot continue to happen after harvest for annual crops, so at harvest -the excess respiration pool is turned into a flux that extracts -CO\ :sub:`2` directly from the atmosphere. This way -any excess maintenance respiration remaining at harvest is eliminated as if such -respiration had not taken place. +Allocation changes based on the crop phenology phases phenology (section :numref:`Phenology`). Simulated C assimilation begins every year upon leaf emergence in phase 2 and ends with harvest at the end of phase 3; therefore, so does the allocation of such C to the crop's leaf, live stem, fine root, and reproductive pools. + +Typically, C:N ratios in plant tissue vary throughout the growing season and tend to be lower during early growth stages and higher in later growth stages. In order to account for this seasonal change, two sets of C:N ratios are established in CLM for the leaf, stem, and fine root of crops: one during the leaf emergence phase (phenology phase 2), and a second during grain fill phase (phenology phase 3). This modified C:N ratio approach accounts for the nitrogen retranslocation that occurs during the grain fill phase (phase 3) of crop growth. Leaf, stem, and root C:N ratios for phase 2 are calculated using the new CLM5 carbon and nitrogen allocation scheme (Chapter :numref:`rst_CN Allocation`), which provides a target C:N value (:numref:`Table Crop allocation parameters`) and allows C:N to vary through time. During grain fill (phase 3) of the crop growth cycle, a portion of the nitrogen in the plant tissues is moved to a storage pool to fulfill nitrogen demands of organ (reproductive pool) development, such that the resulting C:N ratio of the plant tissue is reflective of measurements at harvest. All C:N ratios were determined by calibration process, through comparisons of model output versus observations of plant carbon throughout the growing season. + +The BGC part of the model keeps track of a term representing excess maintenance respiration, which supplies the carbon required for maintenance respiration during periods of low photosynthesis (Chapter :numref:`rst_Plant Respiration`). Carbon supply for excess maintenance respiration cannot continue to happen after harvest for annual crops, so at harvest the excess respiration pool is turned into a flux that extracts CO\ :sub:`2` directly from the atmosphere. This way any excess maintenance respiration remaining at harvest is eliminated as if such respiration had not taken place. .. _Leaf emergence to grain fill: @@ -449,20 +264,14 @@ each C pool are defined as: \begin{array}{l} {a_{repr} =0} \\ {a_{froot} =a_{froot}^{i} -(a_{froot}^{i} -a_{froot}^{f} )\frac{GDD_{T_{{\rm 2m}} } }{GDD_{{\rm mat}} } {\rm \; \; \; where\; \; \; }\frac{GDD_{T_{{\rm 2m}} } }{GDD_{{\rm mat}} } \le 1} \\ {a_{leaf} =(1-a_{froot} )\cdot \frac{a_{leaf}^{i} (e^{-b} -e^{-b\frac{GDD_{T_{{\rm 2m}} } }{h} } )}{e^{-b} -1} {\rm \; \; \; where\; \; \; }b=0.1} \\ {a_{livestem} =1-a_{repr} -a_{froot} -a_{leaf} } \end{array} -where :math:`a_{leaf}^{i}` , :math:`a_{froot}^{i}` , and -:math:`a_{froot}^{f}` are initial and final values of these -coefficients (:numref:`Table Crop allocation parameters`), and *h* is a heat unit threshold defined in -section :numref:`Grain fill`. At a crop-specific maximum leaf area index, -:math:`{L}_{max}` (:numref:`Table Crop allocation parameters`), carbon allocation is directed -exclusively to the fine roots. +where :math:`a_{leaf}^{i}`, :math:`a_{froot}^{i}`, and :math:`a_{froot}^{f}` are initial and final values of these coefficients (:numref:`Table Crop allocation parameters`), and *h* is a heat unit threshold defined in section :numref:`Grain fill`. At a crop-specific maximum leaf area index, :math:`{L}_{max}` (:numref:`Table Crop allocation parameters`), carbon allocation is directed exclusively to the fine roots. .. _Grain fill to harvest: Grain fill '''''''''' -The calculation of :math:`a_{froot}` remains the same from phase 2 to -phase 3. During grain fill (phase 3), other allocation coefficients change to: +The calculation of :math:`a_{froot}` remains the same from phase 2 to phase 3. During grain fill (phase 3), other allocation coefficients change to: .. math:: :label: 25.5 @@ -477,36 +286,14 @@ phase 3. During grain fill (phase 3), other allocation coefficients change to: a_{repr} =1-a_{froot} -a_{livestem} -a_{leaf} \end{array} -where :math:`a_{leaf}^{i,3}` and :math:`a_{livestem}^{i,3}` (initial -values) equal the last :math:`a_{leaf}` and :math:`a_{livestem}` -calculated in phase 2, :math:`d_{L}` , :math:`d_{alloc}^{leaf}` and -:math:`d_{alloc}^{stem}` are leaf area index and leaf and stem -allocation decline factors, and :math:`a_{leaf}^{f}` and -:math:`a_{livestem}^{f}` are final values of these allocation -coefficients (:numref:`Table Crop allocation parameters`). +where :math:`a_{leaf}^{i,3}` and :math:`a_{livestem}^{i,3}` (initial values) equal the last :math:`a_{leaf}` and :math:`a_{livestem}` calculated in phase 2, :math:`d_{L}`, :math:`d_{alloc}^{leaf}` and :math:`d_{alloc}^{stem}` are leaf area index and leaf and stem allocation decline factors, and :math:`a_{leaf}^{f}` and :math:`a_{livestem}^{f}` are final values of these allocation coefficients (:numref:`Table Crop allocation parameters`). .. _Nitrogen retranslocation for crops: Nitrogen retranslocation for crops '''''''''''''''''''''''''''''''''' -Nitrogen retranslocation in crops occurs when nitrogen that was used for -tissue growth of leaves, stems, and fine roots during the early growth -season is remobilized and used for grain development (:ref:`Pollmer et al. 1979 -`, :ref:`Crawford et al. 1982 `, :ref:`Simpson et al. 1983 -`, :ref:`Ta and Weiland 1992 `, :ref:`Barbottin et al. 2005 `, -:ref:`Gallais et al. 2006 `, :ref:`Gallais et al. 2007 `). Nitrogen allocation -for crops follows that of natural vegetation, is supplied in CLM by the -soil mineral nitrogen pool, and depends on C:N ratios for leaves, stems, -roots, and organs. Nitrogen demand during organ development is fulfilled -through retranslocation from leaves, stems, and roots. Nitrogen -retranslocation is initiated at the beginning of the grain fill stage -for all crops except soybean, for which retranslocation is after LAI decline. -Nitrogen stored in the leaf and stem is moved into a storage -retranslocation pool for all crops, and for wheat and rice, nitrogen in roots is also -released into the retranslocation storage pool. The quantity of nitrogen -mobilized depends on the C:N ratio of the plant tissue, and is -calculated as +Nitrogen retranslocation in crops occurs when nitrogen that was used for tissue growth of leaves, stems, and fine roots during the early growth season is remobilized and used for grain development (:ref:`Pollmer et al. 1979 `, :ref:`Crawford et al. 1982 `, :ref:`Simpson et al. 1983 `, :ref:`Ta and Weiland 1992 `, :ref:`Barbottin et al. 2005 `, :ref:`Gallais et al. 2006 `, :ref:`Gallais et al. 2007 `). Nitrogen allocation for crops follows that of natural vegetation, is supplied in CLM by the soil mineral nitrogen pool, and depends on C:N ratios for leaves, stems, roots, and organs. Nitrogen demand during organ development is fulfilled through retranslocation from leaves, stems, and roots. Nitrogen retranslocation is initiated at the beginning of the grain fill stage for all crops except soybean, for which retranslocation is after LAI decline. Nitrogen stored in the leaf and stem is moved into a storage retranslocation pool for all crops, and for wheat and rice, nitrogen in roots is also released into the retranslocation storage pool. The quantity of nitrogen mobilized depends on the C:N ratio of the plant tissue, and is calculated as .. math:: :label: 25.6 @@ -523,36 +310,14 @@ calculated as frootn\_ to\_ retransn=N_{froot} -\frac{C_{froot} }{CN_{froot}^{f} } -where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the carbon in the plant leaf, stem, and fine -root, respectively, :math:`{N}_{leaf}`, :math:`{N}_{stem}`, and :math:`{N}_{froot}` -is the nitrogen in the plant leaf, stem, and fine root, respectively, and :math:`CN^f_{leaf}`, -:math:`CN^f_{stem}`, and :math:`CN^f_{froot}` is the post-grain fill C:N -ratio of the leaf, stem, and fine root respectively (:numref:`Table Crop allocation parameters`). Since -C:N measurements are often taken from mature crops, pre-grain development C:N -ratios for leaves, stems, and roots in the model are optimized to allow maximum -nitrogen accumulation for later use during organ development, and post-grain -fill C:N ratios are assigned the same as crop residue. After -nitrogen is moved into the retranslocated pool, -the nitrogen in this pool is used to meet plant -nitrogen demand by assigning the available nitrogen from the -retranslocated pool equal to the plant nitrogen demand for each organ (:math:`{CN_{[organ]}^{f} }` in :numref:`Table Crop allocation parameters`). Once the -retranslocation pool is depleted, soil mineral nitrogen pool is used to -fulfill plant nitrogen demands. +where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the carbon in the plant leaf, stem, and fine root, respectively, :math:`{N}_{leaf}`, :math:`{N}_{stem}`, and :math:`{N}_{froot}` is the nitrogen in the plant leaf, stem, and fine root, respectively, and :math:`CN^f_{leaf}`, :math:`CN^f_{stem}`, and :math:`CN^f_{froot}` is the post-grain fill C:N ratio of the leaf, stem, and fine root respectively (:numref:`Table Crop allocation parameters`). Since C:N measurements are often taken from mature crops, pre-grain development C:N ratios for leaves, stems, and roots in the model are optimized to allow maximum nitrogen accumulation for later use during organ development, and post-grain fill C:N ratios are assigned the same as crop residue. After nitrogen is moved into the retranslocated pool, the nitrogen in this pool is used to meet plant nitrogen demand by assigning the available nitrogen from the retranslocated pool equal to the plant nitrogen demand for each organ (:math:`{CN_{[organ]}^{f} }` in :numref:`Table Crop allocation parameters`). Once the retranslocation pool is depleted, soil mineral nitrogen pool is used to fulfill plant nitrogen demands. .. _Harvest to food and seed: Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. -A fraction (determined by the :math:`biofuel\_harvfrac`, defined in -:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels -(Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), -with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). -Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which -puts live stem C and N into dead stem pools first. -Biofuel crop leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. -Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. .. math:: :label: 25.9 @@ -592,8 +357,7 @@ with corresponding nitrogen fluxes: NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} \right) * \left( 1-biofuel\_harvfrac \right) -where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, -NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction of leaf/livestem for biofuel feedstocks. +where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction of leaf/livestem for biofuel feedstocks. .. _Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production: @@ -651,17 +415,7 @@ NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction o | Switchgrass | 0.70 | +----------------------------------+----------------------------+ -Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N -to a grain product pool where the C and N decay to the atmosphere over one year, -similar in structure to the wood product pools. -The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. -Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain -product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. -Calcuating the crop yields (Equation :eq:`25.15`) requires that you sum the GRAINC_TO_FOOD variable -for each year, and must account for the proportion of C in the dry crop weight. -Here, we assume that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so -analysis needs to assume that harvest efficiency is less. We assume a harvest -efficiency of 85%. +Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. Calcuating the crop yields (Equation :eq:`25.15`) requires that you sum the GRAINC_TO_FOOD variable for each year, and must account for the proportion of C in the dry crop weight. Here, we assume that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so analysis needs to assume that harvest efficiency is less. We assume a harvest efficiency of 85%. .. math:: :label: 25.15 @@ -694,9 +448,7 @@ efficiency of 85%. :math:`{CN}_{grain}` 50 50 50 50 50 50 50 50 50 50 =========================================== ============== ============ ================== ====== ====== ========= ============= ================ ================ ================ -Notes: Crop growth phases and corresponding variables are described throughout -the text. :math:`{CN}_{leaf}`, :math:`{CN}_{stem}`, and :math:`{CN}_{froot}` are -the target C:N ratios used during the leaf emergence phase (phase 2). +Notes: Crop growth phases and corresponding variables are described throughout the text. :math:`{CN}_{leaf}`, :math:`{CN}_{stem}`, and :math:`{CN}_{froot}` are the target C:N ratios used during the leaf emergence phase (phase 2). .. _Other Features: @@ -707,15 +459,9 @@ Other Features Physical Crop Characteristics ''''''''''''''''''''''''''''' -Leaf area index (*L*) is calculated as a function of specific leaf area -(SLA, :numref:`Table Crop phenology parameters`) and leaf C. -Stem area index (*S*) is equal to 0.1\ *L* for temperate and tropical corn, sugarcane, switchgrass, and miscanthus and 0.2\ *L* for -other crops, as in AgroIBIS. All live -C and N pools go to 0 after crop harvest, but the *S* is kept at 0.25 to -simulate a post-harvest "stubble" on the ground. +Leaf area index (*L*) is calculated as a function of specific leaf area (SLA, :numref:`Table Crop phenology parameters`) and leaf C. Stem area index (*S*) is equal to 0.1\ *L* for temperate and tropical corn, sugarcane, switchgrass, and miscanthus and 0.2\ *L* for other crops, as in AgroIBIS. All live C and N pools go to 0 after crop harvest, but the *S* is kept at 0.25 to simulate a post-harvest "stubble" on the ground. -Crop heights at the top and bottom of the canopy, :math:`{z}_{top}` -and :math:`{z}_{bot}` (m), come from the AgroIBIS formulation: +Crop heights at the top and bottom of the canopy, :math:`{z}_{top}` and :math:`{z}_{bot}` (m), come from the AgroIBIS formulation: .. math:: :label: 25.16 @@ -725,72 +471,32 @@ and :math:`{z}_{bot}` (m), come from the AgroIBIS formulation: {z_{bot} =0.02{\rm m}} \end{array} -where :math:`z_{top}^{\max }` is the maximum top-of-canopy height of the crop (:numref:`Table Crop phenology parameters`) -and :math:`L_{\max }` is the maximum leaf area index (:numref:`Table Crop allocation parameters`). +where :math:`z_{top}^{\max }` is the maximum top-of-canopy height of the crop (:numref:`Table Crop phenology parameters`) and :math:`L_{\max }` is the maximum leaf area index (:numref:`Table Crop allocation parameters`). .. _Interactive fertilization: Interactive Fertilization ''''''''''''''''''''''''' -CLM simulates fertilization by adding nitrogen directly to the soil mineral nitrogen pool to meet -crop nitrogen demands using both industrial fertilizer and manure application. CLM's separate crop land unit ensures that -natural vegetation will not access the fertilizer applied to crops. -Fertilizer in CLM5BGCCROP is prescribed by crop functional types and varies spatially -for each year based on the LUMIP land use and land cover change -time series (LUH2 for historical and SSPs for future) (:ref:`Lawrence et al. 2016 `). -One of two fields is used to prescribe industrial fertilizer based on the type of simulation. -For non-transient simulations, annual fertilizer application in g N/m\ :sup:`2`/yr -is specified on the land surface data set by the field CONST_FERTNITRO_CFT. -In transient simulations, annual fertilizer application is specified on the land use time series -file by the field FERTNITRO_CFT, which is also in g N/m\ :sup:`2`/yr. -The values for both of these fields come from the LUMIP time series for each year. -In addition to the industrial fertilizer, background manure fertilizer is specified -on the parameter file by the field 'manunitro'. For perennial bioenergy crops, -little fertilizer (56kg/ha/yr) is applied to switchgrass, no fertilizer is applied to Miscanthus. -Note these rates are only based on local land management practices at the University of Illinois Energy Farm -located in Central Midwestern United States :ref:`(Cheng et al., 2019)` rather than the LUMIP timeseries. For the current CLM5BGCCROP, -manure N is applied at a rate of 0.002 kg N/m\ :sup:`2`/yr. Because previous versions -of CLM (e.g., CLM4) had rapid denitrification rates, fertilizer is applied slowly -to minimize N loss (primarily through denitrification) and maximize plant uptake. -The current implementation of CLM5 inherits this legacy, although denitrification rates -are slower in the current version of the model (:ref:`Koven et al. 2013 `). As such, -fertilizer application begins during the leaf emergence phase of crop -development (phase 2) and continues for 20 days, which helps reduce large losses -of nitrogen from leaching and denitrification during the early stage of -crop development. The 20-day period is chosen as an optimization to -limit fertilizer application to the emergence stage. A fertilizer -counter in seconds, *f*, is set as soon as the leaf emergence phase for crops -initiates: +CLM simulates fertilization by adding nitrogen directly to the soil mineral nitrogen pool to meet crop nitrogen demands using both industrial fertilizer and manure application. CLM's separate crop land unit ensures that natural vegetation will not access the fertilizer applied to crops. Fertilizer in CLM5BGCCROP is prescribed by crop functional types and varies spatially for each year based on the LUMIP land use and land cover change time series (LUH2 for historical and SSPs for future) (:ref:`Lawrence et al. 2016 `). One of two fields is used to prescribe industrial fertilizer based on the type of simulation. For non-transient simulations, annual fertilizer application in g N/m\ :sup:`2`/yr is specified on the land surface data set by the field CONST_FERTNITRO_CFT. In transient simulations, annual fertilizer application is specified on the land use time series file by the field FERTNITRO_CFT, which is also in g N/m\ :sup:`2`/yr. The values for both of these fields come from the LUMIP time series for each year. In addition to the industrial fertilizer, background manure fertilizer is specified on the parameter file by the field 'manunitro'. For perennial bioenergy crops, little fertilizer (56kg/ha/yr) is applied to switchgrass, no fertilizer is applied to Miscanthus. Note these rates are only based on local land management practices at the University of Illinois Energy Farm located in Central Midwestern United States :ref:`(Cheng et al., 2019)` rather than the LUMIP timeseries. For the current CLM5BGCCROP, manure N is applied at a rate of 0.002 kg N/m\ :sup:`2`/yr. Because previous versions of CLM (e.g., CLM4) had rapid denitrification rates, fertilizer is applied slowly to minimize N loss (primarily through denitrification) and maximize plant uptake. The current implementation of CLM5 inherits this legacy, although denitrification rates are slower in the current version of the model (:ref:`Koven et al. 2013 `). As such, fertilizer application begins during the leaf emergence phase of crop development (phase 2) and continues for 20 days, which helps reduce large losses of nitrogen from leaching and denitrification during the early stage of crop development. The 20-day period is chosen as an optimization to limit fertilizer application to the emergence stage. A fertilizer counter in seconds, *f*, is set as soon as the leaf emergence phase for crops initiates: .. math:: :label: 25.17 f = n \times 86400 -where *n* is set to 20 fertilizer application days and 86400 is the number of seconds per day. When the crop enters -phase 2 (leaf emergence) of its growth -cycle, fertilizer application begins by initializing fertilizer amount -to the total fertilizer at each column within the grid cell divided by the initialized *f*. -Fertilizer is applied and *f* is decremented each time step until a zero balance on -the counter is reached. +where *n* is set to 20 fertilizer application days and 86400 is the number of seconds per day. When the crop enters phase 2 (leaf emergence) of its growth cycle, fertilizer application begins by initializing fertilizer amount to the total fertilizer at each column within the grid cell divided by the initialized *f*. Fertilizer is applied and *f* is decremented each time step until a zero balance on the counter is reached. .. _Biological nitrogen fixation for soybeans: Biological nitrogen fixation for soybeans ''''''''''''''''''''''''''''''''''''''''' -Biological N fixation for soybeans is calculated by the fixation and uptake of -nitrogen module (Chapter :numref:`rst_FUN`) and is the same as N fixation in natural vegetation. Unlike natural -vegetation, where a fraction of each pft are N fixers, all soybeans -are treated as N fixers. +Biological N fixation for soybeans is calculated by the fixation and uptake of nitrogen module (Chapter :numref:`rst_FUN`) and is the same as N fixation in natural vegetation. Unlike natural vegetation, where a fraction of each pft are N fixers, all soybeans are treated as N fixers. .. _Latitude vary base tempereature for growing degree days: Latitudinal variation in base growth tempereature ''''''''''''''''''''''''''''''''''''''''''''''''' -For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) -is the same in all locations. However, -the for both rainfed and irrigated spring wheat and sugarcane, the calculation of -:math:`GDD_{T_{{\rm 2m}} }` allows for latitudinal variation: +For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) is the same in all locations. However, the for both rainfed and irrigated spring wheat and sugarcane, the calculation of :math:`GDD_{T_{{\rm 2m}} }` allows for latitudinal variation: .. math:: :label: 25.18 @@ -801,49 +507,24 @@ the for both rainfed and irrigated spring wheat and sugarcane, the calculation o baset +12 + 0.4 \times latitude &\qquad -30 \le latitude \le 0 \end{array} \right\} -where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. -Such latitudinal variation in base growth temperature could increase the base temperature, slow down :math:`GDD_{T_{{\rm 2m}} }` -accumulation, and extend the growing season for regions within 30ºS to 30ºN for spring wheat -and sugarcane. +where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. Such latitudinal variation in base growth temperature could increase the base temperature, slow down :math:`GDD_{T_{{\rm 2m}} }` accumulation, and extend the growing season for regions within 30ºS to 30ºN for spring wheat and sugarcane. .. _Separate reproductive pool: Separate reproductive pool '''''''''''''''''''''''''' -One notable difference between natural vegetation and crops is the -presence of reproductive carbon and nitrogen pools. Accounting -for the reproductive pools helps determine whether crops are performing -reasonably through yield calculations. -The reproductive pool is maintained similarly to the leaf, stem, -and fine root pools, but allocation of carbon and nitrogen does not -begin until the grain fill stage of crop development. Equation :eq:`25.5` describes the -carbon and nitrogen allocation coefficients to the reproductive pool. -In CLM5BGCCROP, as allocation declines in stem, leaf, and root pools (see section :numref:`Grain fill to harvest`) -during the grain fill stage of growth, increasing amounts of carbon and -nitrogen are available for grain development. +One notable difference between natural vegetation and crops is the presence of reproductive carbon and nitrogen pools. Accounting for the reproductive pools helps determine whether crops are performing reasonably through yield calculations. The reproductive pool is maintained similarly to the leaf, stem, and fine root pools, but allocation of carbon and nitrogen does not begin until the grain fill stage of crop development. Equation :eq:`25.5` describes the carbon and nitrogen allocation coefficients to the reproductive pool. In CLM5BGCCROP, as allocation declines in stem, leaf, and root pools (see section :numref:`Grain fill to harvest`) during the grain fill stage of growth, increasing amounts of carbon and nitrogen are available for grain development. .. _The irrigation model: The irrigation model -------------------- -The CLM includes the option to irrigate cropland areas that are equipped -for irrigation. The application of irrigation responds dynamically to -the soil moisture conditions simulated by the CLM. This irrigation -algorithm is based loosely on the implementation of -:ref:`Ozdogan et al. (2010) `. +The CLM includes the option to irrigate cropland areas that are equipped for irrigation. The application of irrigation responds dynamically to the soil moisture conditions simulated by the CLM. This irrigation algorithm is based loosely on the implementation of :ref:`Ozdogan et al. (2010) `. -When irrigation is enabled, the crop areas of each grid cell are divided -into irrigated and rainfed fractions according to a dataset of areas -equipped for irrigation (:ref:`Portmann et al. 2010 `). -Irrigated and rainfed crops are placed on separate soil columns, so that -irrigation is only applied to the soil beneath irrigated crops. +When irrigation is enabled, the crop areas of each grid cell are divided into irrigated and rainfed fractions according to a dataset of areas equipped for irrigation (:ref:`Portmann et al. 2010 `). Irrigated and rainfed crops are placed on separate soil columns, so that irrigation is only applied to the soil beneath irrigated crops. -In irrigated croplands, a check is made once per day to determine -whether irrigation is required on that day. This check is made in the -first time step after 6 AM local time. Irrigation is required if crop -leaf area :math:`>` 0, and the available soil water is below a specified -threshold. +In irrigated croplands, a check is made once per day to determine whether irrigation is required on that day. This check is made in the first time step after 6 AM local time. Irrigation is required if crop leaf area :math:`>` 0, and the available soil water is below a specified threshold. The soil moisture deficit :math:`D_{irrig}` is @@ -856,9 +537,7 @@ The soil moisture deficit :math:`D_{irrig}` is 0 &\qquad w_{thresh} \le w_{avail} \end{array} \right\} -where :math:`w_{thresh}` is the irrigation moisture threshold (mm) and -:math:`w_{avail}` is the available moisture (mm). The moisture threshold -is +where :math:`w_{thresh}` is the irrigation moisture threshold (mm) and :math:`w_{avail}` is the available moisture (mm). The moisture threshold is .. math:: :label: 25.62 @@ -887,28 +566,9 @@ the soil is w_{avail} = \sum_{j=1}^{N_{irr}} \theta_{j} \Delta z_{j} \ , -:math:`N_{irr}` is the index of the soil layer corresponding to a specified -depth :math:`z_{irrig}` (:numref:`Table Irrigation parameters`) and -:math:`\Delta z_{j}` is the thickness of the soil layer in layer :math:`j` (section -:numref:`Vertical Discretization`). :math:`\theta_{j}` is the -volumetric soil moisture in layer :math:`j` (section :numref:`Soil Water`). -:math:`\theta_{target}` and -:math:`\theta_{wilt}` are the target and wilting point volumetric -soil moisture values, respectively, and are determined by inverting -:eq:`7.94` using soil matric -potential parameters :math:`\Psi_{target}` and :math:`\Psi_{wilt}` -(:numref:`Table Irrigation parameters`). After the soil moisture deficit -:math:`D_{irrig}` is calculated, irrigation in an amount equal to -:math:`\frac{D_{irrig}}{T_{irrig}}` (mm/s) is applied uniformly over -the irrigation period :math:`T_{irrig}` (s). Irrigation water is applied -directly to the ground surface, bypassing canopy interception (i.e., -added to :math:`{q}_{grnd,liq}`: section :numref:`Canopy Water`). - -To conserve mass, irrigation is removed from river water storage (Chapter :numref:`rst_River Transport Model (RTM)`). -When river water storage is inadequate to meet irrigation demand, -there are two options: 1) the additional water can be removed from the -ocean model, or 2) the irrigation demand can be reduced such that -river water storage is maintained above a specified threshold. +:math:`N_{irr}` is the index of the soil layer corresponding to a specified depth :math:`z_{irrig}` (:numref:`Table Irrigation parameters`) and :math:`\Delta z_{j}` is the thickness of the soil layer in layer :math:`j` (section :numref:`Vertical Discretization`). :math:`\theta_{j}` is the volumetric soil moisture in layer :math:`j` (section :numref:`Soil Water`). :math:`\theta_{target}` and :math:`\theta_{wilt}` are the target and wilting point volumetric soil moisture values, respectively, and are determined by inverting :eq:`7.94` using soil matric potential parameters :math:`\Psi_{target}` and :math:`\Psi_{wilt}` (:numref:`Table Irrigation parameters`). After the soil moisture deficit :math:`D_{irrig}` is calculated, irrigation in an amount equal to :math:`\frac{D_{irrig}}{T_{irrig}}` (mm/s) is applied uniformly over the irrigation period :math:`T_{irrig}` (s). Irrigation water is applied directly to the ground surface, bypassing canopy interception (i.e., added to :math:`{q}_{grnd,liq}`: section :numref:`Canopy Water`). + +To conserve mass, irrigation is removed from river water storage (Chapter :numref:`rst_River Transport Model (RTM)`). When river water storage is inadequate to meet irrigation demand, there are two options: 1) the additional water can be removed from the ocean model, or 2) the irrigation demand can be reduced such that river water storage is maintained above a specified threshold. .. _Table Irrigation parameters: @@ -927,8 +587,4 @@ river water storage is maintained above a specified threshold. +--------------------------------------+-------------+ .. add a reference to surface data in chapter2 - To accomplish this we downloaded - data of percent irrigated and percent rainfed corn, soybean, and - temperate cereals (wheat, barley, and rye) (:ref:`Portmann et al. 2010 `), - available online from - *ftp://ftp.rz.uni-frankfurt.de/pub/uni-frankfurt/physische\_geographie/hydrologie/public/data/MIRCA2000/harvested\_area\_grids.* + To accomplish this we downloaded data of percent irrigated and percent rainfed corn, soybean, and temperate cereals (wheat, barley, and rye) (:ref:`Portmann et al. 2010 `), available online from *ftp://ftp.rz.uni-frankfurt.de/pub/uni-frankfurt/physische\_geographie/hydrologie/public/data/MIRCA2000/harvested\_area\_grids.* diff --git a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst index b664311bcb..4874ca9943 100644 --- a/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst +++ b/doc/source/tech_note/DGVM/CLM50_Tech_Note_DGVM.rst @@ -21,18 +21,7 @@ Fisher, R. A., Muszala, S., Verteinstein, M., Lawrence, P., Xu, C., McDowell, N. The Ecosystem Demography ('ED'), concept within FATES is derived from the work of :ref:`Moorcroft et al. (2001)` and is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. -The implementation of the Ecosystem Demography concept within FATES links the surface flux and canopy physiology concepts in CLM -with numerous additional developments necessary to accommodate the new model. These include a version of the SPITFIRE -(Spread and InTensity of Fire) model of :ref:`Thonicke et al. (2010)`, and an adoption of the concept of -`Perfect Plasticity Approximation` approach of -:ref:`Purves et al. 2008`, :ref:`Lichstein et al. 2011` and :ref:`Weng et al. 2014`, in accounting -for the spatial arrangement of crowns. Novel algorithms accounting for -the fragmentation of coarse woody debris into chemical litter streams, -for the physiological optimization of canopy thickness, for the -accumulation of seeds in the seed bank, for multi-layer multi-PFT -radiation transfer, for drought-deciduous and cold-deciduous phenology, -for carbon storage allocation, and for tree mortality under carbon -stress, are also included. +The implementation of the Ecosystem Demography concept within FATES links the surface flux and canopy physiology concepts in CLM with numerous additional developments necessary to accommodate the new model. These include a version of the SPITFIRE (Spread and InTensity of Fire) model of :ref:`Thonicke et al. (2010)`, and an adoption of the concept of `Perfect Plasticity Approximation` approach of :ref:`Purves et al. 2008`, :ref:`Lichstein et al. 2011` and :ref:`Weng et al. 2014`, in accounting for the spatial arrangement of crowns. Novel algorithms accounting for the fragmentation of coarse woody debris into chemical litter streams, for the physiological optimization of canopy thickness, for the accumulation of seeds in the seed bank, for multi-layer multi-PFT radiation transfer, for drought-deciduous and cold-deciduous phenology, for carbon storage allocation, and for tree mortality under carbon stress, are also included. Further reading ^^^^^^^^^^^^^^^^^^^^ diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index 6ac20a32d3..7bfd1bebdb 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -3,20 +3,7 @@ Decomposition ================= -Decomposition of fresh litter material into progressively more -recalcitrant forms of soil organic matter is represented in CLM is -defined as a cascade of :math:`{k}_{tras}` transformations between -:math:`{m}_{pool}` decomposing coarse woody debris (CWD), litter, -and soil organic matter (SOM) pools, each defined at -:math:`{n}_{lev}` vertical levels. CLM allows the user to define, at -compile time, between 2 contrasting hypotheses of decomposition as -embodied by two separate decomposition submodels: the CLM-CN pool -structure used in CLM4.0, or a second pool structure, characterized by -slower decomposition rates, based on the fCentury model (Parton et al. -1988). In addition, the user can choose, at compile time, whether to -allow :math:`{n}_{lev}` to equal 1, as in CLM4.0, or to equal the -number of soil levels used for the soil hydrological and thermal -calculations (see Section :numref:`Soil Layers` for soil layering). +Decomposition of fresh litter material into progressively more recalcitrant forms of soil organic matter is represented in CLM is defined as a cascade of :math:`{k}_{tras}` transformations between :math:`{m}_{pool}` decomposing coarse woody debris (CWD), litter, and soil organic matter (SOM) pools, each defined at :math:`{n}_{lev}` vertical levels. CLM allows the user to define, at compile time, between 2 contrasting hypotheses of decomposition as embodied by two separate decomposition submodels: the CLM-CN pool structure used in CLM4.0, or a second pool structure, characterized by slower decomposition rates, based on the fCentury model (Parton et al 1988). In addition, the user can choose, at compile time, whether to allow :math:`{n}_{lev}` to equal 1, as in CLM4.0, or to equal the number of soil levels used for the soil hydrological and thermal calculations (see Section :numref:`Soil Layers` for soil layering). .. _Figure Schematic of decomposition model in CLM: @@ -24,44 +11,25 @@ calculations (see Section :numref:`Soil Layers` for soil layering). Schematic of decomposition model in CLM. -Model is structured to allow different representations of the soil C and -N decomposition cascade, as well as a vertically-explicit treatment of -soil biogeochemistry. +Model is structured to allow different representations of the soil C and N decomposition cascade, as well as a vertically-explicit treatment of soil biogeochemistry. -For the single-level model structure, the fundamental equation for -carbon balance of the decomposing pools is: +For the single-level model structure, the fundamental equation for carbon balance of the decomposing pools is: .. math:: :label: 21.1) \frac{\partial C_{i} }{\partial t} =R_{i} +\sum _{j\ne i}\left(i-r_{j} \right)T_{ji} k_{j} C_{j} -k_{i} C_{i} -where :math:`{C}_{i}` is the carbon content of pool *i*, -:math:`{R}_{i}` are the carbon inputs from plant tissues directly to -pool *i* (only non-zero for CWD and litter pools), :math:`{k}_{i}` -is the decay constant of pool *i*; :math:`{T}_{ji}` is the fraction -of carbon directed from pool *j* to pool *i* with fraction -:math:`{r}_{j}` lost as a respiration flux along the way. +where :math:`{C}_{i}` is the carbon content of pool *i*, :math:`{R}_{i}` are the carbon inputs from plant tissues directly to pool *i* (only non-zero for CWD and litter pools), :math:`{k}_{i}` is the decay constant of pool *i*; :math:`{T}_{ji}` is the fraction of carbon directed from pool *j* to pool *i* with fraction :math:`{r}_{j}` lost as a respiration flux along the way. -Adding the vertical dimension to the decomposing pools changes the -balance equation to the following: +Adding the vertical dimension to the decomposing pools changes the balance equation to the following: .. math:: :label: 21.2) \begin{array}{l} {\frac{\partial C_{i} (z)}{\partial t} =R_{i} (z)+\sum _{i\ne j}\left(1-r_{j} \right)T_{ji} k_{j} (z)C_{j} (z) -k_{i} (z)C_{i} (z)} \\ {+\frac{\partial }{\partial z} \left(D(z)\frac{\partial C_{i} }{\partial z} \right)+\frac{\partial }{\partial z} \left(A(z)C_{i} \right)} \end{array} -where :math:`{C}_{i}`\ (z) is now defined at each model level, and -in volumetric (gC m\ :sup:`-3`) rather than areal (gC m\ :sup:`-2`) units, along with :math:`{R}_{i}`\ (z) and -:math:`{k}_{j}`\ (z). In addition, vertical transport is handled by -the last two terms, for diffusive and advective transport. In the base -model, advective transport is set to zero, leaving only a diffusive flux -with diffusivity *D(z)* defined for all decomposing carbon and nitrogen -pools. Further discussion of the vertical distribution of carbon inputs -:math:`{R}_{i}`\ (z), vertical turnover times -:math:`{k}_{j}`\ (z), and vertical transport *D(z)* is below. -Discussion of the vertical model and analysis of both decomposition -structures is in :ref:`Koven et al. (2013) `. +where :math:`{C}_{i}`\ (z) is now defined at each model level, and in volumetric (gC m\ :sup:`-3`) rather than areal (gC m\ :sup:`-2`) units, along with :math:`{R}_{i}`\ (z) and :math:`{k}_{j}`\ (z). In addition, vertical transport is handled by the last two terms, for diffusive and advective transport. In the base model, advective transport is set to zero, leaving only a diffusive flux with diffusivity *D(z)* defined for all decomposing carbon and nitrogen pools. Further discussion of the vertical distribution of carbon inputs :math:`{R}_{i}`\ (z), vertical turnover times :math:`{k}_{j}`\ (z), and vertical transport *D(z)* is below Discussion of the vertical model and analysis of both decomposition structures is in :ref:`Koven et al. (2013) `. .. _Figure Pool structure: @@ -74,30 +42,9 @@ structures is in :ref:`Koven et al. (2013) `. CLM-CN Pool Structure, Rate Constants and Parameters --------------------------------------------------------- -The CLM-CN structure in CLM45 uses three state variables for fresh -litter and four state variables for soil organic matter (SOM). The -masses of carbon and nitrogen in the live microbial community are not -modeled explicitly, but the activity of these organisms is represented -by decomposition fluxes transferring mass between the litter and SOM -pools, and heterotrophic respiration losses associated with these -transformations. The litter and SOM pools in CLM-CN are arranged as a -converging cascade (Figure 15.2), derived directly from the -implementation in Biome-BGC v4.1.2 (Thornton et al. 2002; Thornton and -Rosenbloom, 2005). - -Model parameters are estimated based on a synthesis of microcosm -decomposition studies using radio-labeled substrates (Degens and -Sparling, 1996; Ladd et al. 1992; Martin et al. 1980; Mary et al. 1993; -Saggar et al. 1994; Sørensen, 1981; van Veen et al. 1984). Multiple -exponential models are fitted to data from the microcosm studies to -estimate exponential decay rates and respiration fractions (Thornton, -1998). The microcosm experiments used for parameterization were all -conducted at constant temperature and under moist conditions with -relatively high mineral nitrogen concentrations, and so the resulting -rate constants are assumed not limited by the availability of water or -mineral nitrogen. :numref:`Table Decomposition rate constants` lists the base decomposition rates for each -litter and SOM pool, as well as a base rate for physical fragmentation -for the coarse woody debris pool (CWD). +The CLM-CN structure in CLM45 uses three state variables for fresh litter and four state variables for soil organic matter (SOM). The masses of carbon and nitrogen in the live microbial community are not modeled explicitly, but the activity of these organisms is represented by decomposition fluxes transferring mass between the litter and SOM pools, and heterotrophic respiration losses associated with these transformations. The litter and SOM pools in CLM-CN are arranged as a converging cascade (Figure 15.2), derived directly from the implementation in Biome-BGC v4.1.2 (Thornton et al. 2002; Thornton and Rosenbloom, 2005). + +Model parameters are estimated based on a synthesis of microcosm decomposition studies using radio-labeled substrates (Degens and Sparling, 1996; Ladd et al. 1992; Martin et al. 1980; Mary et al. 1993 Saggar et al. 1994; Sørensen, 1981; van Veen et al. 1984). Multiple exponential models are fitted to data from the microcosm studies to estimate exponential decay rates and respiration fractions (Thornton, 1998). The microcosm experiments used for parameterization were all conducted at constant temperature and under moist conditions with relatively high mineral nitrogen concentrations, and so the resulting rate constants are assumed not limited by the availability of water or mineral nitrogen. :numref:`Table Decomposition rate constants` lists the base decomposition rates for each litter and SOM pool, as well as a base rate for physical fragmentation for the coarse woody debris pool (CWD). .. _Table Decomposition rate constants: @@ -125,14 +72,7 @@ for the coarse woody debris pool (CWD). | :math:`{k}_{CWD}` | 0.001 | 0.00004 | - | 1 | +--------------------------+------------------------------------------------+-----------------------------------------------+---------------+-----------------------------------------+ -The first column of :numref:`Table Decomposition rate constants` gives the rates as used for the Biome-BGC -model, which uses a discrete-time model with a daily timestep. The -second column of :numref:`Table Decomposition rate constants` shows the rates transformed for a one-hour -discrete timestep typical of CLM-CN. The transformation is based on the -conversion of the initial discrete-time value (:math:`{k}_{disc1}`) -first to a continuous time value (:math:`{k}_{cont}`), then to the -new discrete-time value with a different timestep -(:math:`{k}_{disc2}`) , following Olson (1963): +The first column of :numref:`Table Decomposition rate constants` gives the rates as used for the Biome-BGC model, which uses a discrete-time model with a daily timestep. The second column of :numref:`Table Decomposition rate constants` shows the rates transformed for a one-hour discrete timestep typical of CLM-CN. The transformation is based on the conversion of the initial discrete-time value (:math:`{k}_{disc1}` first to a continuous time value (:math:`{k}_{cont}`), then to the new discrete-time value with a different timestep (:math:`{k}_{disc2}`), following Olson (1963): .. math:: :label: ZEqnNum608251 @@ -144,18 +84,9 @@ new discrete-time value with a different timestep k_{disc2} =1-\exp \left(-k_{cont} \frac{\Delta t_{2} }{\Delta t_{1} } \right) -where :math:`\Delta`\ :math:`{t}_{1}` (s) and -:math:`\Delta`\ t\ :sub:`2` (s) are the time steps of the -initial and new discrete-time models, respectively. +where :math:`\Delta`\ :math:`{t}_{1}` (s) and :math:`\Delta`\ t\ :sub:`2` (s) are the time steps of the initial and new discrete-time models, respectively. -Respiration fractions are parameterized for decomposition fluxes out of -each litter and SOM pool. The respiration fraction (*rf*, unitless) is -the fraction of the decomposition carbon flux leaving one of the litter -or SOM pools that is released as CO\ :sub:`2` due to heterotrophic -respiration. Respiration fractions and exponential decay rates are -estimated simultaneously from the results of microcosm decomposition -experiments (Thornton, 1998). The same values are used in CLM-CN and -Biome-BGC (:numref:`Table Respiration fractions for litter and SOM pools`). +Respiration fractions are parameterized for decomposition fluxes out of each litter and SOM pool. The respiration fraction (*rf*, unitless) is the fraction of the decomposition carbon flux leaving one of the litter or SOM pools that is released as CO\ :sub:`2` due to heterotrophic respiration. Respiration fractions and exponential decay rates are estimated simultaneously from the results of microcosm decomposition experiments (Thornton, 1998). The same values are used in CLM-CN and Biome-BGC (:numref:`Table Respiration fractions for litter and SOM pools`). .. _Table Respiration fractions for litter and SOM pools: @@ -179,19 +110,12 @@ Biome-BGC (:numref:`Table Respiration fractions for litter and SOM pools`). | :math:`{rf}_{SOM4}` | :math:`{1.0}^{a}` | +---------------------------+-----------------------+ -:sup:`a`:math:`{}^{a}` The respiration fraction for pool SOM4 is 1.0 by -definition: since there is no pool downstream of SOM4, the entire carbon -flux leaving this pool is assumed to be respired as CO\ :sub:`2`. +:sup:`a`:math:`{}^{a}` The respiration fraction for pool SOM4 is 1.0 by definition: since there is no pool downstream of SOM4, the entire carbon flux leaving this pool is assumed to be respired as CO\ :sub:`2`. Century-based Pool Structure, Rate Constants and Parameters ---------------------------------------------------------------- -The Century-based decomposition cascade is, like CLM-CN, a first-order -decay model; the two structures differ in the number of pools, the -connections between those pools, the turnover times of the pools, and -the respired fraction during each transition (Figure 15.2). The turnover -times are different for the Century-based pool structure, following -those described in Parton et al. (1988) (:numref:`Table Turnover times`). +The Century-based decomposition cascade is, like CLM-CN, a first-order decay model; the two structures differ in the number of pools, the connections between those pools, the turnover times of the pools, and the respired fraction during each transition (Figure 15.2). The turnover times are different for the Century-based pool structure, following those described in Parton et al. (1988) (:numref:`Table Turnover times`). .. _Table Turnover times: @@ -240,98 +164,43 @@ Likewise, values for the respiration fraction of Century-based structure are in Environmental modifiers on decomposition rate -------------------------------------------------- -These base rates are modified on each timestep by functions of the -current soil environment. For the single-level model, there are two rate -modifiers, temperature (:math:`{r}_{tsoil}`, unitless) and moisture -(:math:`{r}_{water}`, unitless), both of which are calculated using -the average environmental conditions of the top five model levels (top -29 cm of soil column). For the vertically-resolved model, two additional -environmental modifiers are calculated beyond the temperature and -moisture limitations: an oxygen scalar (:math:`{r}_{oxygen}`, -unitless), and a depth scalar (:math:`{r}_{depth}`, unitless). +These base rates are modified on each timestep by functions of the current soil environment. For the single-level model, there are two rate modifiers, temperature (:math:`{r}_{tsoil}`, unitless) and moisture (:math:`{r}_{water}`, unitless), both of which are calculated using the average environmental conditions of the top five model levels (top 29 cm of soil column). For the vertically-resolved model, two additional environmental modifiers are calculated beyond the temperature and moisture limitations: an oxygen scalar (:math:`{r}_{oxygen}`, unitless), and a depth scalar (:math:`{r}_{depth}`, unitless). -The Temperature scalar :math:`{r}_{tsoil}` is calculated in CLM -using a :math:`{Q}_{10}` approach, with :math:`{Q}_{10} = 1.5`. +The Temperature scalar :math:`{r}_{tsoil}` is calculated in CLM using a :math:`{Q}_{10}` approach, with :math:`{Q}_{10} = 1.5`. .. math:: :label: 21.5) r_{tsoil} =Q_{10} ^{\left(\frac{T_{soil,\, j} -T_{ref} }{10} \right)} -where *j* is the soil layer index, :math:`{T}_{soil,j}` (K) is the -temperature of soil level *j*. The reference temperature :math:`{T}_{ref}` = 25C. +where *j* is the soil layer index, :math:`{T}_{soil,j}` (K) is the temperature of soil level *j*. The reference temperature :math:`{T}_{ref}` = 25C. -The rate scalar for soil water potential (:math:`{r}_{water}`, -unitless) is calculated using a relationship from Andrén and Paustian -(1987) and supported by additional data in Orchard and Cook (1983): +The rate scalar for soil water potential (:math:`{r}_{water}`, unitless) is calculated using a relationship from Andrén and Paustian (1987) and supported by additional data in Orchard and Cook (1983): .. math:: :label: 21.6) r_{water} =\sum _{j=1}^{5}\left\{\begin{array}{l} {0\qquad {\rm for\; }\Psi _{j} <\Psi _{\min } } \\ {\frac{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{j} }} \right.} \Psi _{j} } \right)}{\log \left({\Psi _{\min } \mathord{\left/ {\vphantom {\Psi _{\min } \Psi _{\max } }} \right.} \Psi _{\max } } \right)} w_{soil,\, j} \qquad {\rm for\; }\Psi _{\min } \le \Psi _{j} \le \Psi _{\max } } \\ {1\qquad {\rm for\; }\Psi _{j} >\Psi _{\max } \qquad \qquad } \end{array}\right\} -where :math:`{\Psi}_{j}` is the soil water potential in -layer *j*, :math:`{\Psi}_{min}` is a lower limit for soil -water potential control on decomposition rate (in CLM5, this was -changed from a default value of -10 MPa used in CLM4.5 and earlier to a -default value of -2.5 MPa). :math:`{\Psi}_{max,j}` (MPa) is the soil -moisture at which decomposition proceeds at a moisture-unlimited -rate. The default value of :math:`{\Psi}_{max,j}` for CLM5 is updated -from a saturated value used in CLM4.5 and earlier, to a value -nominally at field capacity, with a value of -0.002 MPa - -For frozen soils, the bulk of the rapid dropoff in decomposition with -decreasing temperature is due to the moisture limitation, since matric -potential is limited by temperature in the supercooled water formulation -of Niu and Yang (2006), +where :math:`{\Psi}_{j}` is the soil water potential in layer *j*, :math:`{\Psi}_{min}` is a lower limit for soil water potential control on decomposition rate (in CLM5, this was changed from a default value of -10 MPa used in CLM4.5 and earlier to a default value of -2.5 MPa). :math:`{\Psi}_{max,j}` (MPa) is the soil moisture at which decomposition proceeds at a moisture-unlimited rate. The default value of :math:`{\Psi}_{max,j}` for CLM5 is updated from a saturated value used in CLM4.5 and earlier, to a value nominally at field capacity, with a value of -0.002 MPa For frozen soils, the bulk of the rapid dropoff in decomposition with decreasing temperature is due to the moisture limitation, since matric potential is limited by temperature in the supercooled water formulation of Niu and Yang (2006), .. math:: :label: 21.8) \psi \left(T\right)=-\frac{L_{f} \left(T-T_{f} \right)}{10^{3} T} -An additional frozen decomposition limitation can be specified using a -‘frozen Q\ :sub:`10`' following :ref:`Koven et al. (2011) `, however the -default value of this is the same as the unfrozen Q\ :sub:`10` -value, and therefore the basic hypothesis is that frozen respiration is -limited by liquid water availability, and can be modeled following the -same approach as thawed but dry soils. - -An additional rate scalar, :math:`{r}_{oxygen}` is enabled when the -CH\ :sub:`4` submodel is used (set equal to 1 for the single layer -model or when the CH\ :sub:`4` submodel is disabled). This limits -decomposition when there is insufficient molecular oxygen to satisfy -stoichiometric demand (1 mol O\ :sub:`2` consumed per mol -CO\ :sub:`2` produced) from heterotrophic decomposers, and supply -from diffusion through soil layers (unsaturated and saturated) or -aerenchyma (Chapter 19). A minimum value of :math:`{r}_{oxygen}` is -set at 0.2, with the assumption that oxygen within organic tissues can -supply the necessary stoichiometric demand at this rate. This value lies -between estimates of 0.025–0.1 (Frolking et al. 2001), and 0.35 (Wania -et al. 2009); the large range of these estimates poses a large -unresolved uncertainty. - -Lastly, a possible explicit depth dependence, :math:`{r}_{depth}`, -(set equal to 1 for the single layer model) can be applied to soil C -decomposition rates to account for processes other than temperature, -moisture, and anoxia that can limit decomposition. This depth dependence -of decomposition was shown by Jenkinson and Coleman (2008) to be an -important term in fitting total C and 14C profiles, and implies that -unresolved processes, such as priming effects, microscale anoxia, soil -mineral surface and/or aggregate stabilization may be important in -controlling the fate of carbon at depth :ref:`Koven et al. (2013) `. CLM -includes these unresolved depth controls via an exponential decrease in -the soil turnover time with depth: +An additional frozen decomposition limitation can be specified using a ‘frozen Q\ :sub:`10`' following :ref:`Koven et al. (2011) `, however the default value of this is the same as the unfrozen Q\ :sub:`10` value, and therefore the basic hypothesis is that frozen respiration is limited by liquid water availability, and can be modeled following the same approach as thawed but dry soils. + +An additional rate scalar, :math:`{r}_{oxygen}` is enabled when the CH\ :sub:`4` submodel is used (set equal to 1 for the single layer model or when the CH\ :sub:`4` submodel is disabled). This limits decomposition when there is insufficient molecular oxygen to satisfy stoichiometric demand (1 mol O\ :sub:`2` consumed per mol CO\ :sub:`2` produced) from heterotrophic decomposers, and supply from diffusion through soil layers (unsaturated and saturated) or aerenchyma (Chapter 19). A minimum value of :math:`{r}_{oxygen}` is set at 0.2, with the assumption that oxygen within organic tissues can supply the necessary stoichiometric demand at this rate. This value lies between estimates of 0.025–0.1 (Frolking et al. 2001), and 0.35 (Wania et al. 2009); the large range of these estimates poses a large unresolved uncertainty. + +Lastly, a possible explicit depth dependence, :math:`{r}_{depth}`, (set equal to 1 for the single layer model) can be applied to soil C decomposition rates to account for processes other than temperature, moisture, and anoxia that can limit decomposition. This depth dependence of decomposition was shown by Jenkinson and Coleman (2008) to be an important term in fitting total C and 14C profiles, and implies that unresolved processes, such as priming effects, microscale anoxia, soil mineral surface and/or aggregate stabilization may be important in controlling the fate of carbon at depth :ref:`Koven et al. (2013) `. CLM includes these unresolved depth controls via an exponential decrease in the soil turnover time with depth: .. math:: :label: 21.9) r_{depth} =\exp \left(-\frac{z}{z_{\tau } } \right) -where :math:`{z}_{\tau}` is the e-folding depth for decomposition. For -CLM4.5, the default value of this was 0.5m. For CLM5, this has been -changed to a default value of 10m, which effectively means that -intrinsic decomposition rates may proceed as quickly at depth as at the surface. +where :math:`{z}_{\tau}` is the e-folding depth for decomposition. For CLM4.5, the default value of this was 0.5m. For CLM5, this has been changed to a default value of 10m, which effectively means that intrinsic decomposition rates may proceed as quickly at depth as at the surface. The combined decomposition rate scalar (:math:`{r}_{total}`,unitless) is: @@ -343,48 +212,23 @@ The combined decomposition rate scalar (:math:`{r}_{total}`,unitless) is: N-limitation of Decomposition Fluxes ----------------------------------------- -Decomposition rates can also be limited by the availability of mineral -nitrogen, but calculation of this limitation depends on first estimating -the potential rates of decomposition, assuming an unlimited mineral -nitrogen supply. The general case is described here first, referring to -a generic decomposition flux from an "upstream" pool (*u*) to a -"downstream" pool (*d*), with an intervening loss due to respiration. -The potential carbon flux out of the upstream pool -(:math:`{CF}_{pot,u}`, gC m\ :sup:`-2` s\ :sup:`-1`) is: +Decomposition rates can also be limited by the availability of mineral nitrogen, but calculation of this limitation depends on first estimating the potential rates of decomposition, assuming an unlimited mineral nitrogen supply. The general case is described here first, referring to a generic decomposition flux from an "upstream" pool (*u*) to a "downstream" pool (*d*), with an intervening loss due to respiration The potential carbon flux out of the upstream pool (:math:`{CF}_{pot,u}`, gC m\ :sup:`-2` s\ :sup:`-1`) is: .. math:: :label: 21.11) CF_{pot,\, u} =CS_{u} k_{u} -where :math:`{CS}_{u}` (gC m\ :sup:`-2`) is the initial mass -in the upstream pool and :math:`{k}_{u}` is the decay rate constant -(s\ :sup:`-1`) for the upstream pool, adjusted for temperature and -moisture conditions. Depending on the C:N ratios of the upstream and -downstream pools and the amount of carbon lost in the transformation due -to respiration (the respiration fraction), the execution of this -potential carbon flux can generate either a source or a sink of new -mineral nitrogen -(:math:`{NF}_{pot\_min,u}`\ :math:`{}_{\rightarrow}`\ :math:`{}_{d}`, gN m\ :sup:`-2` s\ :sup:`-1`). The governing equation -(Thornton and Rosenbloom, 2005) is: +where :math:`{CS}_{u}` (gC m\ :sup:`-2`) is the initial mass in the upstream pool and :math:`{k}_{u}` is the decay rate constant (s\ :sup:`-1`) for the upstream pool, adjusted for temperature and moisture conditions. Depending on the C:N ratios of the upstream and downstream pools and the amount of carbon lost in the transformation due to respiration (the respiration fraction), the execution of this potential carbon flux can generate either a source or a sink of new mineral nitrogen (:math:`{NF}_{pot\_min,u}`\ :math:`{}_{\rightarrow}`\ :math:`{}_{d}`, gN m\ :sup:`-2` s\ :sup:`-1`). The governing equation (Thornton and Rosenbloom, 2005) is: .. math:: :label: 21.12) NF_{pot\_ min,\, u\to d} =\frac{CF_{pot,\, u} \left(1-rf_{u} -\frac{CN_{d} }{CN_{u} } \right)}{CN_{d} } -where :math:`{rf}_{u}` is the respiration fraction for fluxes -leaving the upstream pool, :math:`{CN}_{u}` and :math:`{CN}_{d}` -are the C:N ratios for upstream and downstream pools, respectively. -Negative values of -:math:`{NF}_{pot\_min,u}`\ :math:`{}_{\rightarrow}`\ :math:`{}_{d}` -indicate that the decomposition flux results in a source of new mineral -nitrogen, while positive values indicate that the potential -decomposition flux results in a sink (demand) for mineral nitrogen. +where :math:`{rf}_{u}` is the respiration fraction for fluxes leaving the upstream pool, :math:`{CN}_{u}` and :math:`{CN}_{d}` are the C:N ratios for upstream and downstream pools, respectively Negative values of :math:`{NF}_{pot\_min,u}`\ :math:`{}_{\rightarrow}`\ :math:`{}_{d}` indicate that the decomposition flux results in a source of new mineral nitrogen, while positive values indicate that the potential decomposition flux results in a sink (demand) for mineral nitrogen. -Following from the general case, potential carbon fluxes leaving -individual pools in the decomposition cascade, for the example of the -CLM-CN pool structure, are given as: +Following from the general case, potential carbon fluxes leaving individual pools in the decomposition cascade, for the example of the CLM-CN pool structure, are given as: .. math:: :label: 21.13) @@ -421,12 +265,7 @@ CLM-CN pool structure, are given as: CF_{pot,\, SOM4} ={CS_{SOM4} k_{SOM4} r_{total} \mathord{\left/ {\vphantom {CS_{SOM4} k_{SOM4} r_{total} \Delta t}} \right.} \Delta t} -where the factor (1/:math:`\Delta`\ *t*) is included because the rate -constant is calculated for the entire timestep (Eqs. and ), but the -convention is to express all fluxes on a per-second basis. Potential -mineral nitrogen fluxes associated with these decomposition steps are, -again for the example of the CLM-CN pool structure (the CENTURY -structure will be similar but without the different terminal step): +where the factor (1/:math:`\Delta`\ *t*) is included because the rate constant is calculated for the entire timestep (Eqs. and ), but the convention is to express all fluxes on a per-second basis. Potential mineral nitrogen fluxes associated with these decomposition steps are, again for the example of the CLM-CN pool structure (the CENTURY structure will be similar but without the different terminal step): .. math:: :label: ZEqnNum934998 @@ -463,37 +302,16 @@ structure will be similar but without the different terminal step): NF_{pot\_ min,\, SOM4} =-{CF_{pot,\, SOM4} \mathord{\left/ {\vphantom {CF_{pot,\, SOM4} CN_{SOM4} }} \right.} CN_{SOM4} } -where the special form of Eq. arises because there is no SOM pool -downstream of SOM4 in the converging cascade: all carbon fluxes leaving -that pool are assumed to be in the form of respired CO\ :sub:`2`, -and all nitrogen fluxes leaving that pool are assumed to be sources of -new mineral nitrogen. - -Steps in the decomposition cascade that result in release of new mineral -nitrogen (mineralization fluxes) are allowed to proceed at their -potential rates, without modification for nitrogen availability. Steps -that result in an uptake of mineral nitrogen (immobilization fluxes) are -subject to rate limitation, depending on the availability of mineral -nitrogen, the total immobilization demand, and the total demand for soil -mineral nitrogen to support new plant growth. The potential mineral -nitrogen fluxes from Eqs. - are evaluated, summing all the positive -fluxes to generate the total potential nitrogen immobilization flux -(:math:`{NF}_{immob\_demand}`, gN m\ :sup:`-2` s\ :sup:`-1`), and summing absolute values of all the negative -fluxes to generate the total nitrogen mineralization flux -(:math:`{NF}_{gross\_nmin}`, gN m\ :sup:`-2` s\ :sup:`-1`). Since :math:`{NF}_{griss\_nmin}` is a source of -new mineral nitrogen to the soil mineral nitrogen pool it is not limited -by the availability of soil mineral nitrogen, and is therefore an actual -as opposed to a potential flux. +where the special form of Eq. arises because there is no SOM pool downstream of SOM4 in the converging cascade: all carbon fluxes leaving that pool are assumed to be in the form of respired CO\ :sub:`2`, and all nitrogen fluxes leaving that pool are assumed to be sources of new mineral nitrogen. + +Steps in the decomposition cascade that result in release of new mineral nitrogen (mineralization fluxes) are allowed to proceed at their potential rates, without modification for nitrogen availability. Steps that result in an uptake of mineral nitrogen (immobilization fluxes) are subject to rate limitation, depending on the availability of mineral nitrogen, the total immobilization demand, and the total demand for soil mineral nitrogen to support new plant growth. The potential mineral nitrogen fluxes from Eqs. - are evaluated, summing all the positive fluxes to generate the total potential nitrogen immobilization flux (:math:`{NF}_{immob\_demand}`, gN m\ :sup:`-2` s\ :sup:`-1`), and summing absolute values of all the negative fluxes to generate the total nitrogen mineralization flux (:math:`{NF}_{gross\_nmin}`, gN m\ :sup:`-2` s\ :sup:`-1`). Since :math:`{NF}_{griss\_nmin}` is a source of new mineral nitrogen to the soil mineral nitrogen pool it is not limited by the availability of soil mineral nitrogen, and is therefore an actual as opposed to a potential flux. N Competition between plant uptake and soil immobilization fluxes ---------------------------------------------------------------------- -Once :math:`{NF}_{immob\_demand }` and :math:`{NF}_{nit\_demand }` for each layer *j* are known, the competition between plant and microbial nitrogen demand can be resolved. Mineral nitrogen in -the soil pool (:math:`{NS}_{sminn}`, gN m\ :sup:`-2`) at the -beginning of the timestep is considered the available supply. +Once :math:`{NF}_{immob\_demand }` and :math:`{NF}_{nit\_demand }` for each layer *j* are known, the competition between plant and microbial nitrogen demand can be resolved. Mineral nitrogen in the soil pool (:math:`{NS}_{sminn}`, gN m\ :sup:`-2`) at the beginning of the timestep is considered the available supply. -Here, the :math:`{NF}_{plant\_demand}` is the theoretical maximum demand for nitrogen by plants to meet the entire carbon uptake given an N cost of zero (and therefore represents the upper bound on N requirements). N uptake costs that are -:math:`>` 0 imply that the plant will take up less N that it demands, ultimately. However, given the heuristic nature of the N competition algorithm, this discrepancy is not explicitly resolved here. +Here, the :math:`{NF}_{plant\_demand}` is the theoretical maximum demand for nitrogen by plants to meet the entire carbon uptake given an N cost of zero (and therefore represents the upper bound on N requirements). N uptake costs that are :math:`>` 0 imply that the plant will take up less N that it demands, ultimately. However, given the heuristic nature of the N competition algorithm, this discrepancy is not explicitly resolved here. The hypothetical plant nitrogen demand from the soil mineral pool is distributed between layers in proportion to the profile of available mineral N: @@ -502,17 +320,14 @@ The hypothetical plant nitrogen demand from the soil mineral pool is distributed NF_{plant\_ demand,j} = NF_{plant\_ demand} NS_{sminn\_ j} / \sum _{j=1}^{nj}NS_{sminn,j} -Plants first compete for ammonia (NH4). For each soil layer (*j*), we calculate the total NH4 demand as: +Plants first compete for ammonia (NH4). For each soil layer (*j*), we calculate the total NH4 demand as: .. math:: :label: 21.292 NF_{total\_ demand_nh4,j} = NF_{immob\_ demand,j} + NF_{immob\_ demand,j} + NF_{nit\_ demand,j} -where -If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t* :math:`<` -:math:`{NS}_{sminn,j}`, then the available pool is large enough to -meet both the maximum plant and microbial demand, then immobilization proceeds at the maximum rate. +where If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t* :math:`<` :math:`{NS}_{sminn,j}`, then the available pool is large enough to meet both the maximum plant and microbial demand, then immobilization proceeds at the maximum rate. .. math:: :label: 21.29) @@ -521,10 +336,7 @@ meet both the maximum plant and microbial demand, then immobilization proceeds a where :math:`{f}_{immob\_demand,j}` is the fraction of potential immobilization demand that can be met given current supply of mineral nitrogen in this layer. We also set the actual nitrification flux to be the same as the potential flux (:math:`NF_{nit}` = :math:`NF_{nit\_ demand}`). -If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t* -:math:`\mathrm{\ge}` :math:`{NS}_{sminn,j}`, then there is not enough -mineral nitrogen to meet the combined demands for plant growth and -heterotrophic immobilization, immobilization is reduced proportional to the discrepancy, by :math:`f_{immob\_ demand,j}`, where +If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t :math:`\mathrm{\ge}` :math:`{NS}_{sminn,j}`, then there is not enough mineral nitrogen to meet the combined demands for plant growth and heterotrophic immobilization, immobilization is reduced proportional to the discrepancy, by :math:`f_{immob\_ demand,j}`, where .. math:: :label: 21.30) @@ -538,21 +350,12 @@ The N available to the FUN model for plant uptake (:math:`{NF}_ {plant\_ avail\_ NF_{plant\_ avail\_ sminn,j} = NS_{sminn,j} - f_{immob\_demand} NF_{immob\_ demand,j} -This treatment of competition for nitrogen as a limiting resource is -referred to a demand-based competition, where the fraction of the -available resource that eventually flows to a particular process depends -on the demand from that process in comparison to the total demand from -all processes. Processes expressing a greater demand acquire a larger -vfraction of the available resource. +This treatment of competition for nitrogen as a limiting resource is referred to a demand-based competition, where the fraction of the available resource that eventually flows to a particular process depends on the demand from that process in comparison to the total demand from all processes. Processes expressing a greater demand acquire a larger vfraction of the available resource. Final Decomposition Fluxes ------------------------------- -With :math:`{f}_{immob\_demand}` known, final decomposition fluxes -can be calculated. Actual carbon fluxes leaving the individual litter -and SOM pools, again for the example of the CLM-CN pool structure (the -CENTURY structure will be similar but, again without the different -terminal step), are calculated as: +With :math:`{f}_{immob\_demand}` known, final decomposition fluxes can be calculated. Actual carbon fluxes leaving the individual litter and SOM pools, again for the example of the CLM-CN pool structure (the CENTURY structure will be similar but, again without the different terminal step), are calculated as: .. math:: :label: 21.32) @@ -589,8 +392,7 @@ terminal step), are calculated as: CF_{SOM4} =CF_{pot,\, SOM4} -Heterotrophic respiration fluxes (losses of carbon as -CO\ :sub:`2` to the atmosphere) are: +Heterotrophic respiration fluxes (losses of carbon as CO\ :sub:`2` to the atmosphere) are: .. math:: :label: 21.39) @@ -627,8 +429,7 @@ CO\ :sub:`2` to the atmosphere) are: CF_{SOM4,\, HR} =CF_{SOM4} rf_{SOM4} -Transfers of carbon from upstream to downstream pools in the -decomposition cascade are given as: +Transfers of carbon from upstream to downstream pools in the decomposition cascade are given as: .. math:: :label: 21.46) @@ -660,14 +461,7 @@ decomposition cascade are given as: CF_{SOM3,\, SOM4} =CF_{SOM3} \left(1-rf_{SOM3} \right) -In accounting for the fluxes of nitrogen between pools in the -decomposition cascade and associated fluxes to or from the soil mineral -nitrogen pool, the model first calculates a flux of nitrogen from an -upstream pool to a downstream pool, then calculates a flux either from -the soil mineral nitrogen pool to the downstream pool (immobilization) -or from the downstream pool to the soil mineral nitrogen pool -(mineralization). Transfers of nitrogen from upstream to downstream -pools in the decomposition cascade are given as: +In accounting for the fluxes of nitrogen between pools in the decomposition cascade and associated fluxes to or from the soil mineral nitrogen pool, the model first calculates a flux of nitrogen from an upstream pool to a downstream pool, then calculates a flux either from the soil mineral nitrogen pool to the downstream pool (immobilization or from the downstream pool to the soil mineral nitrogen pool (mineralization). Transfers of nitrogen from upstream to downstream pools in the decomposition cascade are given as: .. math:: :label: 21.52) @@ -699,9 +493,7 @@ pools in the decomposition cascade are given as: NF_{SOM3,\, SOM4} ={CF_{SOM3} \mathord{\left/ {\vphantom {CF_{SOM3} CN_{SOM3} }} \right.} CN_{SOM3} } -Corresponding fluxes to or from the soil mineral nitrogen pool depend on -whether the decomposition step is an immobilization flux or a -mineralization flux: +Corresponding fluxes to or from the soil mineral nitrogen pool depend on whether the decomposition step is an immobilization flux or a mineralization flux: .. math:: :label: 21.58) @@ -741,81 +533,19 @@ mineralization flux: Vertical Distribution and Transport of Decomposing C and N pools --------------------------------------------------------------------- -Additional terms are needed to calculate the vertically-resolved soil C -and N budget: the initial vertical distribution of C and N from PFTs -delivered to the litter and CWD pools, and the vertical transport of C -and N pools. - -For initial vertical inputs, CLM uses separate profiles for aboveground -(leaf, stem) and belowground (root) inputs. Aboveground inputs are given -a single exponential with default e-folding depth = 0.1m. Belowground -inputs are distributed according to rooting profiles with default values -based on the Jackson et al. (1996) exponential parameterization. - -Vertical mixing is accomplished by an advection-diffusion equation. The -goal of this is to consider slow, soild- and adsorbed-phase transport -due to bioturbation, cryoturbation, and erosion. Faster aqueous-phase -transport is not included in CLM, but has been developed as part of the -CLM-BeTR suite of parameterizations (Tang and Riley 2013). The default -value of the advection term is 0 cm/yr, such that transport is purely -diffusive. Diffusive transport differs in rate between permafrost soils -(where cryoturbation is the dominant transport term) and non-permafrost -soils (where bioturbation dominates). For permafrost soils, a -parameterization based on that of :ref:`Koven et al. (2009) ` is used: the -diffusivity parameter is constant through the active layer, and -decreases linearly from the base of the active layer to zero at a set -depth (default 3m); the default permafrost diffusivity is 5 -cm\ :sup:`2`/yr. For non-permafrost soils, the default diffusivity -is 1 cm\ :sup:`2`/yr. +Additional terms are needed to calculate the vertically-resolved soil C and N budget: the initial vertical distribution of C and N from PFTs delivered to the litter and CWD pools, and the vertical transport of C and N pools. + +For initial vertical inputs, CLM uses separate profiles for aboveground (leaf, stem) and belowground (root) inputs. Aboveground inputs are given a single exponential with default e-folding depth = 0.1m. Belowground inputs are distributed according to rooting profiles with default values based on the Jackson et al. (1996) exponential parameterization. + +Vertical mixing is accomplished by an advection-diffusion equation. The goal of this is to consider slow, soild- and adsorbed-phase transport due to bioturbation, cryoturbation, and erosion. Faster aqueous-phase transport is not included in CLM, but has been developed as part of the CLM-BeTR suite of parameterizations (Tang and Riley 2013). The default value of the advection term is 0 cm/yr, such that transport is purely diffusive. Diffusive transport differs in rate between permafrost soils (where cryoturbation is the dominant transport term) and non-permafrost soils (where bioturbation dominates). For permafrost soils, a parameterization based on that of :ref:`Koven et al. (2009) ` is used: the diffusivity parameter is constant through the active layer, and decreases linearly from the base of the active layer to zero at a set depth (default 3m); the default permafrost diffusivity is 5 cm\ :sup:`2`/yr. For non-permafrost soils, the default diffusivity is 1 cm\ :sup:`2`/yr. Model Equilibration and its Acceleration ----------------------------------------- -For transient experiments, it is usually assumed that the carbon cycle -is starting from a point of relatively close equilibrium, i.e. that -productivity is balanced by ecosystem carbon losses through -respiratory and disturbance pathways. In order to satisfy this -assumption, the model is generally run until the productivity and loss -terms find a stable long-term equilibrium; at this point the model is -considered 'spun up'. - -Because of the coupling between the slowest SOM pools and productivity -through N downregulation of photosynthesis, equilibration of the model -for initialization purposes will take an extremely long time in the -standard mode. This is particularly true for the CENTURY-based -decomposition cascade, which includes a passive pool. In order to -rapidly equilibrate the model, a modified version of the "accelerated -decomposition" :ref:`(Thornton and Rosenbloon, 2005) ` is used. The fundamental -idea of this approach is to allow fluxes between the various pools (both -turnover-defined and vertically-defined fluxes) adjust rapidly, while -keeping the pool sizes themselves small so that they can fill quickly. -To do this, the base decomposition rate :math:`{k}_{i}` for each -pool *i* is accelerated by a term :math:`{a}_{i}` such that the slow -pools are collapsed onto an approximately annual timescale :ref:`Koven et al. (2013) `. Accelerating the pools beyond this timescale distorts the -seasonal and/or diurnal cycles of decomposition and N mineralization, -thus leading to a substantially different ecosystem productivity than -the full model. For the vertical model, the vertical transport terms are -also accelerated by the same term :math:`{a}_{i}`, as is the -radioactive decay when :math:`{}^{14}`\ C is enabled, following the same -principle of keeping fluxes between pools (or fluxes lost to decay) -close to the full model while keeping the pools sizes small. When -leaving the accelerated decomposition mode, the concentration of C and N -in pools that had been accelerated are multiplied by the same term -:math:`{a}_{i}`, to bring the model into approximate equilibrium. -Note that in CLM, the model can also transition into accelerated -decomposition mode from the standard mode (by dividing the pools by -:math:`{a}_{i}`), and that the transitions into and out of -accelerated decomposition mode are handled automatically by CLM upon -loading from restart files (which preserve information about the mode of -the model when restart files were written). - -The base acceleration terms for the two decomposition cascades are shown in -Tables 15.1 and 15.3. In addition to the base terms, CLM5 also -includes a geographic term to the acceleration in order to apply -larger values to high-latitude systems, where decomposition rates are -particularly slow and thus equilibration can take significantly longer -than in temperate or tropical climates. This geographic term takes -the form of a logistic equation, where :math:`{a}_{i}` is equal to the -product of the base acceleration term and :math:`{a}_{l}` below: +For transient experiments, it is usually assumed that the carbon cycle is starting from a point of relatively close equilibrium, i.e. that productivity is balanced by ecosystem carbon losses through respiratory and disturbance pathways. In order to satisfy this assumption, the model is generally run until the productivity and loss terms find a stable long-term equilibrium; at this point the model is considered 'spun up'. + +Because of the coupling between the slowest SOM pools and productivity through N downregulation of photosynthesis, equilibration of the model for initialization purposes will take an extremely long time in the standard mode. This is particularly true for the CENTURY-based decomposition cascade, which includes a passive pool. In order to rapidly equilibrate the model, a modified version of the "accelerated decomposition" :ref:`(Thornton and Rosenbloon, 2005) ` is used. The fundamental idea of this approach is to allow fluxes between the various pools (both turnover-defined and vertically-defined fluxes) adjust rapidly, while keeping the pool sizes themselves small so that they can fill quickly To do this, the base decomposition rate :math:`{k}_{i}` for each pool *i* is accelerated by a term :math:`{a}_{i}` such that the slow pools are collapsed onto an approximately annual timescale :ref:`Koven et al. (2013) `. Accelerating the pools beyond this timescale distorts the seasonal and/or diurnal cycles of decomposition and N mineralization, thus leading to a substantially different ecosystem productivity than the full model. For the vertical model, the vertical transport terms are also accelerated by the same term :math:`{a}_{i}`, as is the radioactive decay when :math:`{}^{14}`\ C is enabled, following the same principle of keeping fluxes between pools (or fluxes lost to decay close to the full model while keeping the pools sizes small. When leaving the accelerated decomposition mode, the concentration of C and N in pools that had been accelerated are multiplied by the same term :math:`{a}_{i}`, to bring the model into approximate equilibrium Note that in CLM, the model can also transition into accelerated decomposition mode from the standard mode (by dividing the pools by :math:`{a}_{i}`), and that the transitions into and out of accelerated decomposition mode are handled automatically by CLM upon loading from restart files (which preserve information about the mode of the model when restart files were written). + +The base acceleration terms for the two decomposition cascades are shown in Tables 15.1 and 15.3. In addition to the base terms, CLM5 also includes a geographic term to the acceleration in order to apply larger values to high-latitude systems, where decomposition rates are particularly slow and thus equilibration can take significantly longer than in temperate or tropical climates. This geographic term takes the form of a logistic equation, where :math:`{a}_{i}` is equal to the product of the base acceleration term and :math:`{a}_{l}` below: .. math:: :label: 21.65) diff --git a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst index 09bcc67dd1..3e8dab983f 100644 --- a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst +++ b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst @@ -3,81 +3,43 @@ Dust Model ============== -Atmospheric dust is mobilized from the land by wind in the CLM. The most -important factors determining soil erodibility and dust emission include -the wind friction speed, the vegetation cover, and the soil moisture. -The CLM dust mobilization scheme (:ref:`Mahowald et al. 2006`) -accounts for these factors based on the DEAD (Dust Entrainment and Deposition) -model of :ref:`Zender et al. (2003)`. Please refer to the -:ref:`Zender et al. (2003)` article for additional -information regarding the equations presented in this section. - -The total vertical mass flux of dust, :math:`F_{j}` -(kg m\ :sup:`-2` s\ :sup:`-1`), from the ground into transport bin -:math:`j` is given by +Atmospheric dust is mobilized from the land by wind in the CLM. The most important factors determining soil erodibility and dust emission include the wind friction speed, the vegetation cover, and the soil moisture The CLM dust mobilization scheme (:ref:`Mahowald et al. 2006` accounts for these factors based on the DEAD (Dust Entrainment and Deposition model of :ref:`Zender et al. (2003)`. Please refer to the :ref:`Zender et al. (2003)` article for additional information regarding the equations presented in this section. + +The total vertical mass flux of dust, :math:`F_{j}` (kg m\ :sup:`-2` s\ :sup:`-1`), from the ground into transport bin :math:`j` is given by .. math:: :label: 29.1 F_{j} =TSf_{m} \alpha Q_{s} \sum _{i=1}^{I}M_{i,j} -where :math:`T` is a global factor that compensates for the DEAD model's -sensitivity to horizontal and temporal resolution and equals 5 x -10\ :sup:`-4` in the CLM instead of 7 x 10\ :sup:`-4` in -:ref:`Zender et al. (2003)`. :math:`S` is the source -erodibility factor set to 1 in the CLM and serves as a place holder -at this time. +where :math:`T` is a global factor that compensates for the DEAD model's sensitivity to horizontal and temporal resolution and equals 5 x 10\ :sup:`-4` in the CLM instead of 7 x 10\ :sup:`-4` in :ref:`Zender et al. (2003)`. :math:`S` is the source erodibility factor set to 1 in the CLM and serves as a place holder at this time. -The grid cell fraction of exposed bare soil suitable for dust -mobilization :math:`f_{m}` is given by +The grid cell fraction of exposed bare soil suitable for dust mobilization :math:`f_{m}` is given by .. math:: :label: 29.2 f_{m} =\left(1-f_{lake} \right)\left(1-f_{sno} \right)\left(1-f_{v} \right)\frac{w_{liq,1} }{w_{liq,1} +w_{ice,1} } -where :math:`f_{lake}` and :math:`f_{sno}` -are the CLM grid cell fractions of lake (section -:numref:`Surface Data`) and snow cover (section -:numref:`Snow Covered Area Fraction`), all ranging from zero to one. Not mentioned -by :ref:`Zender et al. (2003)`, :math:`w_{liq,\, 1}` and -:math:`{}_{w_{ice,\, 1} }` are the CLM top soil layer liquid water and -ice contents (mm) entered as a ratio expressing the decreasing ability -of dust to mobilize from increasingly frozen soil. The grid cell -fraction of vegetation cover,\ :math:`{}_{f_{v} }`, is defined as +where :math:`f_{lake}` and :math:`f_{sno}` are the CLM grid cell fractions of lake (section :numref:`Surface Data`) and snow cover (section :numref:`Snow Covered Area Fraction`), all ranging from zero to one. Not mentioned by :ref:`Zender et al. (2003)`, :math:`w_{liq,\, 1}` and :math:`{}_{w_{ice,\, 1} }` are the CLM top soil layer liquid water and ice contents (mm) entered as a ratio expressing the decreasing ability of dust to mobilize from increasingly frozen soil. The grid cell fraction of vegetation cover,\ :math:`{}_{f_{v} }`, is defined as .. math:: :label: 29.3 0\le f_{v} =\frac{L+S}{\left(L+S\right)_{t} } \le 1{\rm \; \; \; \; where\; }\left(L+S\right)_{t} =0.3{\rm \; m}^{2} {\rm m}^{-2} -where equation applies only for dust mobilization and is not related to -the plant functional type fractions prescribed from the CLM input data -or simulated by the CLM dynamic vegetation model (Chapter 22). :math:`L` -and :math:`S` are the CLM leaf and stem area index values -(m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so -as to include all the pfts and the bare ground present in a vegetated -land unit. :math:`L` and :math:`S` may be prescribed from the CLM -input data (section :numref:`Phenology and vegetation burial by snow`) -or simulated by the CLM biogeochemistry model (Chapter -:numref:`rst_Vegetation Phenology and Turnover`). +where equation applies only for dust mobilization and is not related to the plant functional type fractions prescribed from the CLM input data or simulated by the CLM dynamic vegetation model (Chapter 22). :math:`L` and :math:`S` are the CLM leaf and stem area index values (m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so as to include all the pfts and the bare ground present in a vegetated land unit. :math:`L` and :math:`S` may be prescribed from the CLM input data (section :numref:`Phenology and vegetation burial by snow`) or simulated by the CLM biogeochemistry model (Chapter :numref:`rst_Vegetation Phenology and Turnover`). -The sandblasting mass efficiency :math:`\alpha` (m :sup:`-1`) is -calculated as +The sandblasting mass efficiency :math:`\alpha` (m :sup:`-1`) is calculated as .. math:: :label: 29.4 \alpha =100e^{\left(13.4M_{clay} -6.0\right)\ln 10} {\rm \; \; }\left\{\begin{array}{l} {M_{clay} =\% clay\times 0.01{\rm \; \; \; 0}\le \% clay\le 20} \\ {M_{clay} =20\times 0.01{\rm \; \; \; \; \; \; \; \; 20<\% }clay\le 100} \end{array}\right. -where :math:`M_{clay}` is the mass fraction of clay -particles in the soil and %clay is determined from the surface dataset -(section :numref:`Surface Data`). :math:`M_{clay} =0` corresponds to sand and -:math:`M_{clay} =0.2` to sandy loam. +where :math:`M_{clay}` is the mass fraction of clay particles in the soil and %clay is determined from the surface dataset (section :numref:`Surface Data`). :math:`M_{clay} =0` corresponds to sand and :math:`M_{clay} =0.2` to sandy loam. -:math:`Q_{s}` is the total horizontally saltating mass flux (kg -m\ :sup:`-1` s\ :sup:`-1`) of "large" particles (:numref:`Table Dust Mass fraction`), -also referred to as the vertically integrated streamwise mass flux +:math:`Q_{s}` is the total horizontally saltating mass flux (kg m\ :sup:`-1` s\ :sup:`-1`) of "large" particles (:numref:`Table Dust Mass fraction`), also referred to as the vertically integrated streamwise mass flux .. math:: :label: 29.5 @@ -88,21 +50,14 @@ also referred to as the vertically integrated streamwise mass flux 0{\rm \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; } & \qquad {\rm for\; }u_{*t} \ge u_{*s} \end{array}\right. -where the saltation constant :math:`c_{s}` equals 2.61 and -:math:`\rho _{atm}` is the atmospheric density (kg m\ :sup:`-3`) -(:numref:`Table Atmospheric input to land model`), :math:`g` the acceleration of gravity (m -s\ :sup:`-2`) (:numref:`Table Physical constants`). The threshold wind friction speed for saltation :math:`u_{*t}` (m s\ :sup:`-1`) is +where the saltation constant :math:`c_{s}` equals 2.61 and :math:`\rho _{atm}` is the atmospheric density (kg m\ :sup:`-3`) (:numref:`Table Atmospheric input to land model`), :math:`g` the acceleration of gravity (m s\ :sup:`-2`) (:numref:`Table Physical constants`). The threshold wind friction speed for saltation :math:`u_{*t}` (m s\ :sup:`-1`) is .. math:: :label: 29.6 u_{*t} =f_{z} \left[Re_{*t}^{f} \rho _{osp} gD_{osp} \left(1+\frac{6\times 10^{-7} }{\rho _{osp} gD_{osp}^{2.5} } \right)\right]^{\frac{1}{2} } \rho _{atm} ^{-\frac{1}{2} } f_{w} -where :math:`f_{z}` is a factor dependent on surface roughness but set -to 1 as a place holder for now, :math:`\rho _{osp}` and -:math:`D_{osp}` are the density (2650 kg m\ :sup:`-3`) and -diameter (75 x 10\ :math:`{}^{-6}` m) of optimal saltation particles, -and :math:`f_{w}` is a factor dependent on soil moisture: +where :math:`f_{z}` is a factor dependent on surface roughness but set to 1 as a place holder for now, :math:`\rho _{osp}` and :math:`D_{osp}` are the density (2650 kg m\ :sup:`-3`) and diameter (75 x 10\ :math:`{}^{-6}` m) of optimal saltation particles, and :math:`f_{w}` is a factor dependent on soil moisture: .. math:: :label: 29.7 @@ -123,32 +78,21 @@ and w=\frac{\theta _{1} \rho _{liq} }{\rho _{d,1} } -where :math:`a=M_{clay}^{-1}` for tuning purposes, -:math:`\theta _{1}` is the volumetric soil moisture in the top soil -layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), -:math:`\rho _{liq}` is the density of liquid water (kg -m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` -is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) -defined as in section :numref:`Soil and Snow Thermal Properties` -rather than as in :ref:`Zender et al. (2003)`. -:math:`Re_{*t}^{f}` from equation is the threshold friction Reynolds -factor +where :math:`a=M_{clay}^{-1}` for tuning purposes, :math:`\theta _{1}` is the volumetric soil moisture in the top soil layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), :math:`\rho _{liq}` is the density of liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) defined as in section :numref:`Soil and Snow Thermal Properties` rather than as in :ref:`Zender et al. (2003)`. :math:`Re_{*t}^{f}` from equation is the threshold friction Reynolds factor .. math:: :label: 29.10 Re_{*t}^{f} =\left\{\begin{array}{l} {\frac{0.1291^{2} }{-1+1.928Re_{*t} } {\rm \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; \; for\; 0.03}\le Re_{*t} \le 10} \\ {0.12^{2} \left(1-0.0858e^{-0.0617(Re_{*t} -10)} \right)^{2} {\rm \; for\; }Re_{*t} >10} \end{array}\right. -and :math:`Re_{*t}` is the threshold friction Reynolds number -approximation for optimally sized particles +and :math:`Re_{*t}` is the threshold friction Reynolds number approximation for optimally sized particles .. math:: :label: 29.11 Re_{*t} =0.38+1331\left(100D_{osp} \right)^{1.56} -In :eq:`29.5` , :math:`u_{*s}` is defined as the wind friction speed -(m s\ :sup:`-1`) accounting for the Owen effect (:ref:`Owen 1964`) +In :eq:`29.5`, :math:`u_{*s}` is defined as the wind friction speed (m s\ :sup:`-1`) accounting for the Owen effect (:ref:`Owen 1964`) .. math:: :label: 29.12 @@ -159,34 +103,21 @@ In :eq:`29.5` , :math:`u_{*s}` is defined as the wind friction speed u_{*} +0.003\left(U_{10} -U_{10,t} \right)^{2} & \quad {\rm \; for\; }U_{10} \ge U_{10,t} \end{array}\right. -where :math:`u_{*}` is the CLM wind friction speed (m s\ :sup:`-1`), -also known as friction velocity (section :numref:`Monin-Obukhov Similarity Theory`), -:math:`U_{10}` \ is the 10-m wind speed (m s\ :sup:`-1`) -calculated as the wind speed at the top of the canopy in section 4.3 of -:ref:`Bonan (1996)` but here for 10 m above the ground, and -:math:`U_{10,\, t}` is the threshold wind speed at 10 m (m -s\ :sup:`-1`) +where :math:`u_{*}` is the CLM wind friction speed (m s\ :sup:`-1`), also known as friction velocity (section :numref:`Monin-Obukhov Similarity Theory`), :math:`U_{10}` \ is the 10-m wind speed (m s\ :sup:`-1`) calculated as the wind speed at the top of the canopy in section 4.3 of :ref:`Bonan (1996)` but here for 10 m above the ground, and :math:`U_{10,\, t}` is the threshold wind speed at 10 m (m s\ :sup:`-1`) .. math:: :label: 29.13 U_{10,t} =u_{*t} \frac{U_{10} }{u_{*} } -In equation we sum :math:`M_{i,\, j}` over :math:`I=3` source modes -:math:`i` where :math:`M_{i,\, j}` is the mass fraction of each source -mode :math:`i` carried in each of *:math:`J=4`* transport bins :math:`j` +In equation we sum :math:`M_{i,\, j}` over :math:`I=3` source modes :math:`i` where :math:`M_{i,\, j}` is the mass fraction of each source mode :math:`i` carried in each of *:math:`J=4`* transport bins :math:`j` .. math:: :label: 29.14 M_{i,j} =\frac{m_{i} }{2} \left[{\rm erf}\left(\frac{\ln {\textstyle\frac{D_{j,\max } }{\tilde{D}_{v,i} }} }{\sqrt{2} \ln \sigma _{g,i} } \right)-{\rm erf}\left(\frac{\ln {\textstyle\frac{D_{j,\min } }{\tilde{D}_{v,i} }} }{\sqrt{2} \ln \sigma _{g,i} } \right)\right] -where :math:`m_{i}` , :math:`\tilde{D}_{v,\, i}` , and -:math:`\sigma _{g,\, i}` are the mass fraction, mass median diameter, -and geometric standard deviation assigned to each particle source mode -:math:`i` (:numref:`Table Dust Mass fraction`), while :math:`D_{j,\, \min }` and -:math:`D_{j,\, \max }` are the minimum and maximum diameters (m) in -each transport bin :math:`j` (:numref:`Table Dust Minimum and maximum particle diameters`). +where :math:`m_{i}`, :math:`\tilde{D}_{v,\, i}`, and :math:`\sigma _{g,\, i}` are the mass fraction, mass median diameter, and geometric standard deviation assigned to each particle source mode :math:`i` (:numref:`Table Dust Mass fraction`), while :math:`D_{j,\, \min }` and :math:`D_{j,\, \max }` are the minimum and maximum diameters (m) in each transport bin :math:`j` (:numref:`Table Dust Minimum and maximum particle diameters`). .. _Table Dust Mass fraction: diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst index 07be360cad..8676fa50bb 100644 --- a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst +++ b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst @@ -13,43 +13,9 @@ Surface Characterization Surface Heterogeneity and Data Structure ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Spatial land surface heterogeneity in CLM is represented as a nested -subgrid hierarchy in which grid cells are composed of multiple land -units, snow/soil columns, and PFTs (:numref:`Figure CLM subgrid hierarchy`). -Each grid cell can have -a different number of land units, each land unit can have a different -number of columns, and each column can have multiple PFTs. The first -subgrid level, the land unit, is intended to capture the broadest -spatial patterns of subgrid heterogeneity. The current land units are -glacier, lake, urban, vegetated, and crop (when the crop model option is -turned on). The land unit level can be used to further delineate these -patterns. For example, the urban land unit is divided into density -classes representing the tall building district, high density, and -medium density urban areas. - -The second subgrid level, the column, is intended to capture potential -variability in the soil and snow state variables within a single land -unit. For example, the vegetated land unit could contain several columns -with independently evolving vertical profiles of soil water and -temperature. Similarly, the managed vegetation land unit can be divided -into two columns, irrigated and non-irrigated. The default snow/soil -column is represented by 25 layers for ground (with up to 20 of these -layers classified as soil layers and the remaining layers classified as -bedrock layers) and up to 10 layers for snow, depending on snow -depth. The central characteristic of the column subgrid level is that -this is where the state variables for water and energy in the soil and -snow are defined, as well as the fluxes of these components within the -soil and snow. Regardless of the number and type of PFTs occupying space -on the column, the column physics operates with a single set of upper -boundary fluxes, as well as a single set of transpiration fluxes from -multiple soil levels. These boundary fluxes are weighted averages over -all PFTs. Currently, for lake and vegetated land units, a single column -is assigned to each land unit. The crop land unit is split into -irrigated and unirrigated columns with a single crop occupying each -column. The urban land units have five columns (roof, sunlit walls and -shaded walls, and pervious and impervious canyon floor) (Oleson et -al. 2010b). The glacier land unit is separated into up to 10 elevation -classes. +Spatial land surface heterogeneity in CLM is represented as a nested subgrid hierarchy in which grid cells are composed of multiple land units, snow/soil columns, and PFTs (:numref:`Figure CLM subgrid hierarchy`). Each grid cell can have a different number of land units, each land unit can have a different number of columns, and each column can have multiple PFTs. The first subgrid level, the land unit, is intended to capture the broadest spatial patterns of subgrid heterogeneity. The current land units are glacier, lake, urban, vegetated, and crop (when the crop model option is turned on). The land unit level can be used to further delineate these patterns. For example, the urban land unit is divided into density classes representing the tall building district, high density, and medium density urban areas. + +The second subgrid level, the column, is intended to capture potential variability in the soil and snow state variables within a single land unit. For example, the vegetated land unit could contain several columns with independently evolving vertical profiles of soil water and temperature. Similarly, the managed vegetation land unit can be divided into two columns, irrigated and non-irrigated. The default snow/soil column is represented by 25 layers for ground (with up to 20 of these layers classified as soil layers and the remaining layers classified as bedrock layers) and up to 10 layers for snow, depending on snow depth. The central characteristic of the column subgrid level is that this is where the state variables for water and energy in the soil and snow are defined, as well as the fluxes of these components within the soil and snow. Regardless of the number and type of PFTs occupying space on the column, the column physics operates with a single set of upper boundary fluxes, as well as a single set of transpiration fluxes from multiple soil levels. These boundary fluxes are weighted averages over all PFTs. Currently, for lake and vegetated land units, a single column is assigned to each land unit. The crop land unit is split into irrigated and unirrigated columns with a single crop occupying each column. The urban land units have five columns (roof, sunlit walls and shaded walls, and pervious and impervious canyon floor) (Oleson et al. 2010b). The glacier land unit is separated into up to 10 elevation classes. .. _Figure CLM subgrid hierarchy: @@ -57,69 +23,20 @@ classes. Configuration of the CLM subgrid hierarchy. Box in upper right shows hypothetical subgrid distribution for a single grid cell. Note that the Crop land unit is only used when the model is run with the crop model active. Abbreviations: TBD – Tall Building District; HD – High Density; MD – Medium Density, G – Glacier, L – Lake, U – Urban, C – Crop, V – Vegetated, PFT – Plant Functional Type, Irr – Irrigated, UIrr – Unirrigated. Red arrows indicate allowed land unit transitions. Purple arrows indicate allowed patch-level transitions. -The third subgrid level is referred to as the patch level. Patches can be PFTs or bare ground on the vegetated land unit -and crop functional types (CFTs) on the crop land unit. -The patch level is intended to capture the -biogeophysical and biogeochemical differences between broad categories -of plants in terms of their functional characteristics. On the vegetated -land unit, up to 16 possible PFTs that differ in physiology and -structure may coexist on a single column. All fluxes to and from the -surface are defined at the PFT level, as are the vegetation state -variables (e.g. vegetation temperature and canopy water storage). On the -crop land unit, typically, different crop types can be represented on each -crop land unit column (see Chapter :numref:`rst_Crops and Irrigation` for details). - -In addition to state and flux variable data structures for conserved -components at each subgrid level (e.g., energy, water, carbon), each -subgrid level also has a physical state data structure for handling -quantities that are not involved in conservation checks (diagnostic -variables). For example, the urban canopy air temperature and humidity -are defined through physical state variables at the land unit level, the -number of snow layers and the soil roughness lengths are defined as -physical state variables at the column level, and the leaf area index -and the fraction of canopy that is wet are defined as physical state -variables at the PFT level. - -The standard configuration of the model subgrid hierarchy is illustrated -in :numref:`Figure CLM subgrid hierarchy`. Here, only four PFTs are shown -associated with the single -column beneath the vegetated land unit but up to sixteen are possible. -The crop land unit is present only when the crop model is active. - -Note that the biogeophysical processes related to soil and snow require -PFT level properties to be aggregated to the column level. For example, -the net heat flux into the ground is required as a boundary condition -for the solution of snow/soil temperatures (Chapter :numref:`rst_Soil and Snow Temperatures`). This column -level property must be determined by aggregating the net heat flux from -all PFTs sharing the column. This is generally accomplished in the model -by computing a weighted sum of the desired quantity over all PFTs whose -weighting depends on the PFT area relative to all PFTs, unless otherwise -noted in the text. +The third subgrid level is referred to as the patch level. Patches can be PFTs or bare ground on the vegetated land unit and crop functional types (CFTs) on the crop land unit. The patch level is intended to capture the biogeophysical and biogeochemical differences between broad categories of plants in terms of their functional characteristics. On the vegetated land unit, up to 16 possible PFTs that differ in physiology and structure may coexist on a single column. All fluxes to and from the surface are defined at the PFT level, as are the vegetation state variables (e.g. vegetation temperature and canopy water storage). On the crop land unit, typically, different crop types can be represented on each crop land unit column (see Chapter :numref:`rst_Crops and Irrigation` for details). + +In addition to state and flux variable data structures for conserved components at each subgrid level (e.g., energy, water, carbon), each subgrid level also has a physical state data structure for handling quantities that are not involved in conservation checks (diagnostic variables). For example, the urban canopy air temperature and humidity are defined through physical state variables at the land unit level, the number of snow layers and the soil roughness lengths are defined as physical state variables at the column level, and the leaf area index and the fraction of canopy that is wet are defined as physical state variables at the PFT level. + +The standard configuration of the model subgrid hierarchy is illustrated in :numref:`Figure CLM subgrid hierarchy`. Here, only four PFTs are shown associated with the single column beneath the vegetated land unit but up to sixteen are possible. The crop land unit is present only when the crop model is active. + +Note that the biogeophysical processes related to soil and snow require PFT level properties to be aggregated to the column level. For example, the net heat flux into the ground is required as a boundary condition for the solution of snow/soil temperatures (Chapter :numref:`rst_Soil and Snow Temperatures`). This column level property must be determined by aggregating the net heat flux from all PFTs sharing the column. This is generally accomplished in the model by computing a weighted sum of the desired quantity over all PFTs whose weighting depends on the PFT area relative to all PFTs, unless otherwise noted in the text. .. _Vegetation Composition: Vegetation Composition ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Vegetated surfaces are comprised of up to 15 possible plant functional -types (PFTs) plus bare ground (:numref:`Table Plant functional types`). An -additional PFT is added if -the irrigation model is active and six additional PFTs are added if the -crop model is active (Chapter :numref:`rst_Crops and Irrigation`). -In :numref:`Table Plant functional types`, IVT = 0,14 refers to the index of PCT_NAT_VEG -on the surface dataset while IVT = 15,18 refers to the index of PCT_CFT on the surface dataset. These -plant types differ in leaf and stem optical properties that determine reflection, -transmittance, and absorption of solar radiation (:numref:`Table Plant functional type optical properties`), root -distribution parameters that control the uptake of water from the soil -(:numref:`Table Plant functional type root distribution parameters`), aerodynamic parameters that determine resistance to heat, -moisture, and momentum transfer (:numref:`Table Plant functional type aerodynamic parameters`), and photosynthetic -parameters that determine stomatal resistance, photosynthesis, and -transpiration (:numref:`Table Plant functional type (PFT) stomatal conductance parameters`, -:numref:`Table Temperature dependence parameters for C3 photosynthesis`). The composition and abundance of PFTs -within a grid cell can either be prescribed as time-invariant fields -(e.g., using the present day dataset described in section 21.3.3) or can -evolve with time if the model is run in transient landcover mode -(Chapter :numref:`rst_Transient Landcover Change`). +Vegetated surfaces are comprised of up to 15 possible plant functional types (PFTs) plus bare ground (:numref:`Table Plant functional types`). An additional PFT is added if the irrigation model is active and six additional PFTs are added if the crop model is active (Chapter :numref:`rst_Crops and Irrigation`). In :numref:`Table Plant functional types`, IVT = 0,14 refers to the index of PCT_NAT_VEG on the surface dataset while IVT = 15,18 refers to the index of PCT_CFT on the surface dataset. These plant types differ in leaf and stem optical properties that determine reflection, transmittance, and absorption of solar radiation (:numref:`Table Plant functional type optical properties`), root distribution parameters that control the uptake of water from the soil (:numref:`Table Plant functional type root distribution parameters`), aerodynamic parameters that determine resistance to heat, moisture, and momentum transfer (:numref:`Table Plant functional type aerodynamic parameters`), and photosynthetic parameters that determine stomatal resistance, photosynthesis, and transpiration (:numref:`Table Plant functional type (PFT) stomatal conductance parameters`, :numref:`Table Temperature dependence parameters for C3 photosynthesis`). The composition and abundance of PFTs within a grid cell can either be prescribed as time-invariant fields (e.g., using the present day dataset described in section 21.3.3) or can evolve with time if the model is run in transient landcover mode (Chapter :numref:`rst_Transient Landcover Change`). .. _Table Plant functional types: @@ -175,17 +92,7 @@ evolve with time if the model is run in transient landcover mode Vegetation Structure ^^^^^^^^^^^^^^^^^^^^^^^^^^ -Vegetation structure is defined by leaf and stem area indices -(:math:`L,\, S`) and canopy top and bottom heights (:math:`z_{top}`,\ :math:`z_{bot}` ). -Separate leaf and -stem area indices and canopy heights are prescribed or calculated for each PFT. Daily leaf -and stem area indices are obtained from griddeddatasets of monthly values (section -:numref:`Surface Data`). Canopy top and bottom heights for trees are from ICESat (:ref:`Simard et al. (2011) `). -Canopy top and bottom heights for short vegetation are obtained from gridded datasets but are invariant in space -and time and were obtained from PFT-specific values (:ref:`Bonan et al. (2002a) `) (:numref:`Table Plant functional type canopy top and bottom heights`). -When the biogeochemistry model is active, -vegetation state (LAI, SAI, canopy top and bottom heights) are calculated prognostically -(see Chapter :numref:`rst_Vegetation Phenology and Turnover`). +Vegetation structure is defined by leaf and stem area indices (:math:`L,\, S`) and canopy top and bottom heights (:math:`z_{top}`,\ :math:`z_{bot}` ). Separate leaf and stem area indices and canopy heights are prescribed or calculated for each PFT. Daily leaf and stem area indices are obtained from griddeddatasets of monthly values (section :numref:`Surface Data`). Canopy top and bottom heights for trees are from ICESat (:ref:`Simard et al. (2011) `). Canopy top and bottom heights for short vegetation are obtained from gridded datasets but are invariant in space and time and were obtained from PFT-specific values (:ref:`Bonan et al. (2002a) `) (:numref:`Table Plant functional type canopy top and bottom heights`). When the biogeochemistry model is active, vegetation state (LAI, SAI, canopy top and bottom heights) are calculated prognostically (see Chapter :numref:`rst_Vegetation Phenology and Turnover`). .. _Table Plant functional type canopy top and bottom heights: @@ -220,25 +127,14 @@ vegetation state (LAI, SAI, canopy top and bottom heights) are calculated progno Phenology and vegetation burial by snow ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -When the biogeochemistry model is inactive, leaf and stem area indices -(m\ :sup:`2` leaf area m\ :sup:`-2` ground area) are updated -daily by linearly interpolating between monthly values. Monthly PFT leaf -area index values are developed from the 1-km MODIS-derived monthly grid -cell average leaf area index of :ref:`Myneni et al. (2002) `, -as described in :ref:`Lawrence and Chase (2007) `. Stem area -ndex is calculated from the monthly PFT leaf area index using the methods of -:ref:`Zeng et al. (2002) `. The leaf and stem area indices are -adjusted for vertical burying by snow (:ref:`Wang and Zeng 2009 `) -as +When the biogeochemistry model is inactive, leaf and stem area indices (m\ :sup:`2` leaf area m\ :sup:`-2` ground area) are updated daily by linearly interpolating between monthly values. Monthly PFT leaf area index values are developed from the 1-km MODIS-derived monthly grid cell average leaf area index of :ref:`Myneni et al. (2002) `, as described in :ref:`Lawrence and Chase (2007) `. Stem area ndex is calculated from the monthly PFT leaf area index using the methods of :ref:`Zeng et al. (2002) `. The leaf and stem area indices are adjusted for vertical burying by snow (:ref:`Wang and Zeng 2009 `) as .. math:: :label: 2.1 A=A^{*} ( 1-f_{veg}^{sno} ) -where :math:`A^{\*}` is the leaf or stem area before adjustment for -snow, :math:`A` is the remaining exposed leaf or stem area, -:math:`f_{veg}^{sno}` is the vertical fraction of vegetation covered by snow +where :math:`A^{\*}` is the leaf or stem area before adjustment for snow, :math:`A` is the remaining exposed leaf or stem area, :math:`f_{veg}^{sno}` is the vertical fraction of vegetation covered by snow .. math:: :label: 2.2 @@ -246,10 +142,7 @@ snow, :math:`A` is the remaining exposed leaf or stem area, {f_{veg}^{sno} = \frac{z_{sno} -z_{bot} }{z_{top} -z_{bot} } \qquad {\rm for\; tree\; and\; shrub}} \\ {f_{veg}^{sno} = \frac{\min \left(z_{sno} ,\, z_{c} \right)}{z_{c} } \qquad {\rm for\; grass\; and\; crop}} -where :math:`z_{sno} -z_{bot} \ge 0,{\rm \; }0\le f_{veg}^{sno} \le 1`, :math:`z_{sno}` is the depth of snow (m) -(Chapter :numref:`rst_Snow Hydrology`), and :math:`z_{c} = 0.2` is the snow depth when short vegetation is assumed to -be completely buried by snow (m). For numerical reasons, exposed leaf and stem area are set to zero if less than -0.05. If the sum of exposed leaf and stem area is zero, then the surface is treated as snow-covered ground. +where :math:`z_{sno} -z_{bot} \ge 0,{\rm \; }0\le f_{veg}^{sno} \le 1`, :math:`z_{sno}` is the depth of snow (m) (Chapter :numref:`rst_Snow Hydrology`), and :math:`z_{c} = 0.2` is the snow depth when short vegetation is assumed to be completely buried by snow (m). For numerical reasons, exposed leaf and stem area are set to zero if less than 0.05. If the sum of exposed leaf and stem area is zero, then the surface is treated as snow-covered ground. .. _Vertical Discretization: @@ -257,27 +150,16 @@ Vertical Discretization ---------------------------- .. (this was taken from Initialization; is it still needed? - Vegetated and glacier land units have fifteen vertical layers, while - lakes have ten. For soil points, temperature calculations are done over - all layers, :math:`N_{levgrnd} =15`, while hydrology calculations are - done over the top ten layers, :math:`N_{levsoi} =10`, the bottom five - layers being specified as bedrock. + Vegetated and glacier land units have fifteen vertical layers, while lakes have ten. For soil points, temperature calculations are done over all layers, :math:`N_{levgrnd} =15`, while hydrology calculations are done over the top ten layers, :math:`N_{levsoi} =10`, the bottom five layers being specified as bedrock. .. _Soil Layers: Soil Layers ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The soil column can be discretized into an arbitrary number of layers. The default -vertical discretization (:numref:`Table Soil layer structure`) uses -:math:`N_{levgrnd} = 25` layers, of which :math:`N_{levsoi} = 20` are hydrologically and -biogeochemically active. The deepest 5 layers are only included in the thermodynamical -calculations (:ref:`Lawrence et al. 2008 `) described in Chapter -:numref:`rst_Soil and Snow Temperatures`. +The soil column can be discretized into an arbitrary number of layers. The default vertical discretization (:numref:`Table Soil layer structure`) uses :math:`N_{levgrnd} = 25` layers, of which :math:`N_{levsoi} = 20` are hydrologically and biogeochemically active. The deepest 5 layers are only included in the thermodynamical calculations (:ref:`Lawrence et al. 2008 `) described in Chapter :numref:`rst_Soil and Snow Temperatures`. -The layer structure of the soil is described by the node depth, :math:`z_{i}` -(m), the thickness of each layer, :math:`\Delta z_{i}` (m), and the depths -at the layer interfaces :math:`z_{h,\, i}` (m). +The layer structure of the soil is described by the node depth, :math:`z_{i}` (m), the thickness of each layer, :math:`\Delta z_{i}` (m), and the depths at the layer interfaces :math:`z_{h,\, i}` (m). .. _Table Soil layer structure: @@ -337,21 +219,14 @@ at the layer interfaces :math:`z_{h,\, i}` (m). | 25 | 41.998 | 15.115 | 49.556 | +---------------+------------------+------------------------+------------------------+ -Layer node depth (:math:`z_{i}` ), thickness (:math:`\Delta z_{i}` ), and depth at -layer interface (:math:`z_{h,\, i}` ) for default soil column. All in meters. +Layer node depth (:math:`z_{i}` ), thickness (:math:`\Delta z_{i}` ), and depth at layer interface (:math:`z_{h,\, i}` ) for default soil column. All in meters. .. _Depth to Bedrock: Depth to Bedrock ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The hydrologically and biogeochemically active portion of the soil column can be -restricted to a thickness less than that of the maximum soil depth. By providing -a depth-to-bedrock dataset, which may vary spatially, the number of layers used -in the hydrologic and biogeochemical calculations, :math:`N_{bedrock}`, may be -specified, subject to the constraint :math:`N_{bedrock} \le N_{levsoi}`. -The default depth-to-bedrock values are from -:ref:`Pelletier et al. [2016]`. +The hydrologically and biogeochemically active portion of the soil column can be restricted to a thickness less than that of the maximum soil depth. By providing a depth-to-bedrock dataset, which may vary spatially, the number of layers used in the hydrologic and biogeochemical calculations, :math:`N_{bedrock}`, may be specified, subject to the constraint :math:`N_{bedrock} \le N_{levsoi}`. The default depth-to-bedrock values are from :ref:`Pelletier et al. [2016]`. .. _Model Input Requirements: @@ -363,20 +238,7 @@ Model Input Requirements Atmospheric Coupling ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The current state of the atmosphere (:numref:`Table Atmospheric input to land model`) -at a given time step is -used to force the land model. This atmospheric state is provided by an -atmospheric model in coupled mode or from an observed dataset in land-only -mode (Chapter :numref:`rst_Land-Only Mode`). The land model then initiates a full set of -calculations for surface energy, constituent, momentum, and radiative -fluxes. The land model calculations are implemented in two steps. The -land model proceeds with the calculation of surface energy, constituent, -momentum, and radiative fluxes using the snow and soil hydrologic states -from the previous time step. The land model then updates the soil and -snow hydrology calculations based on these fluxes. These fields are -passed to the atmosphere (:numref:`Table Land model output to atmospheric model`). The albedos sent to the atmosphere -are for the solar zenith angle at the next time step but with surface -conditions from the current time step. +The current state of the atmosphere (:numref:`Table Atmospheric input to land model`) at a given time step is used to force the land model. This atmospheric state is provided by an atmospheric model in coupled mode or from an observed dataset in land-only mode (Chapter :numref:`rst_Land-Only Mode`). The land model then initiates a full set of calculations for surface energy, constituent, momentum, and radiative fluxes. The land model calculations are implemented in two steps. The land model proceeds with the calculation of surface energy, constituent, momentum, and radiative fluxes using the snow and soil hydrologic states from the previous time step. The land model then updates the soil and snow hydrology calculations based on these fluxes. These fields are passed to the atmosphere (:numref:`Table Land model output to atmospheric model`). The albedos sent to the atmosphere are for the solar zenith angle at the next time step but with surface conditions from the current time step. .. _Table Atmospheric input to land model: @@ -424,85 +286,19 @@ conditions from the current time step. | :sup:`5`\ Lightning frequency | :math:`I_{l}` | flash km\ :sup:`-2` hr\ :sup:`-1` | +------------------------------------------------------+------------------------------------------------+-------------------------------------------------+ -:sup:`1`\ The atmospheric reference height received from the -atmospheric model :math:`z'_{atm}` is assumed to be the height above -the surface as defined by the roughness length :math:`z_{0}` plus -displacement height :math:`d`. Thus, the reference height used for flux -computations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) -is :math:`z_{atm} =z'_{atm} +z_{0} +d`. The -reference heights for temperature, wind, and specific humidity -(:math:`z_{atm,\, h}` , :math:`z_{atm,\, {\it m}}` , -:math:`z_{atm,\, w}` ) are required. These are set equal -to\ :math:`z_{atm}` . - -:sup:`2`\ CAM provides convective and large-scale liquid -and solid precipitation, which are added to yield total liquid -precipitation :math:`q_{rain}` and solid precipitation -:math:`q_{sno}` . -However, in CLM5, the atmosphere's partitioning into liquid and solid -precipitation is ignored. Instead, CLM repartitions total precipitation -using a linear ramp. For most landunits, this ramp generates all snow -below :math:`0 ^{\circ} C`, all rain above :math:`2 ^{\circ} C`, -and a mix of rain and snow for intermediate temperatures. For glaciers, -the end points of the ramp are :math:`-2 ^{\circ} C` and :math:`0 -^{\circ} C`, respectively. Changes to the phase of precipitation are -accompanied by a sensible heat flux (positive or negative) to conserve -energy. - -:sup:`3`\ There are 14 aerosol deposition rates required depending -on species and affinity for bonding with water; 8 of these are dust -deposition rates (dry and wet rates for 4 dust size bins, -:math:`D_{dst,\, dry1} ,\, D_{dst,\, dry2} ,\, D_{dst,\, dry3} ,\, D_{dst,\, dry4}` , -:math:`D_{dst,\, \, wet1} ,D_{dst,\, wet2} ,\, D_{dst,wet3} ,\, D_{dst,\, wet4}` ), -3 are black carbon deposition rates (dry and wet hydrophilic and dry -hydrophobic rates, -:math:`D_{bc,\, dryhphil} ,\, D_{bc,\, wethphil} ,\, D_{bc,\, dryhphob}` ), -and 3 are organic carbon deposition rates (dry and wet hydrophilic and -dry hydrophobic rates, -:math:`D_{oc,\, dryhphil} ,\, D_{oc,\, wethphil} ,\, D_{oc,\, dryhphob}` ). -These fluxes are computed interactively by the atmospheric model (when -prognostic aerosol representation is active) or are prescribed from a -time-varying (annual cycle or transient), globally-gridded deposition -file defined in the namelist (see the CLM4.5 User's Guide). Aerosol -deposition rates were calculated in a transient 1850-2009 CAM simulation -(at a resolution of 1.9x2.5x26L) with interactive chemistry (troposphere -and stratosphere) driven by CCSM3 20\ :sup:`th` century -sea-surface temperatures and emissions (:ref:`Lamarque et al. 2010`) for -short-lived gases and aerosols; observed concentrations were specified -for methane, N\ :sub:`2`\ O, the ozone-depleting substances (CFCs) -,and CO\ :sub:`2`. The fluxes are used by the snow-related -parameterizations (Chapters :numref:`rst_Surface Albedos` and :numref:`rst_Snow Hydrology`). - -:sup:`4`\ The nitrogen deposition rate is required by the -biogeochemistry model when active and represents the total deposition of -mineral nitrogen onto the land surface, combining deposition of -NO\ :sub:`y` and NH\ :sub:`x`. The rate is supplied either -as a time-invariant spatially-varying annual mean rate or time-varying -for a transient simulation. Nitrogen deposition rates were calculated -from the same CAM chemistry simulation that generated the aerosol -deposition rates. - -:sup:`5`\ Climatological 3-hourly lightning frequency at -:math:`\sim`\ 1.8\ :sup:`o` resolution is provided, which was -calculated via bilinear interpolation from 1995-2011 NASA LIS/OTD grid -product v2.2 (http://ghrc.msfc.nasa.gov) 2-hourly, 2.5\ :sup:`o` -lightning frequency data. In future versions of the model, lightning -data may be obtained directly from the atmosphere model. - -Density of air (:math:`\rho _{atm}` ) (kg m\ :sup:`-3`) is also -required but is calculated directly from -:math:`\rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} }` -where :math:`P_{atm}` is atmospheric pressure (Pa), :math:`e_{atm}` is -atmospheric vapor pressure (Pa), :math:`R_{da}` is the gas constant for -dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), and -:math:`T_{atm}` is the atmospheric temperature (K). The atmospheric -vapor pressure :math:`e_{atm}` is derived from atmospheric specific -humidity :math:`q_{atm}` (kg kg\ :sup:`-1`) as -:math:`e_{atm} =\frac{q_{atm} P_{atm} }{0.622+0.378q_{atm} }` . - -The O\ :sub:`2` partial pressure (Pa) is required but is -calculated from molar ratio and the atmospheric pressure -:math:`P_{atm}` as :math:`o_{i} =0.209P_{atm}` . +:sup:`1`\ The atmospheric reference height received from the atmospheric model :math:`z'_{atm}` is assumed to be the height above the surface as defined by the roughness length :math:`z_{0}` plus displacement height :math:`d`. Thus, the reference height used for flux computations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) is :math:`z_{atm} =z'_{atm} +z_{0} +d`. The reference heights for temperature, wind, and specific humidity (:math:`z_{atm,\, h}`, :math:`z_{atm,\, {\it m}}`, :math:`z_{atm,\, w}` ) are required. These are set equal to\ :math:`z_{atm}`. + +:sup:`2`\ CAM provides convective and large-scale liquid and solid precipitation, which are added to yield total liquid precipitation :math:`q_{rain}` and solid precipitation :math:`q_{sno}`. However, in CLM5, the atmosphere's partitioning into liquid and solid precipitation is ignored. Instead, CLM repartitions total precipitation using a linear ramp. For most landunits, this ramp generates all snow below :math:`0 ^{\circ} C`, all rain above :math:`2 ^{\circ} C`, and a mix of rain and snow for intermediate temperatures. For glaciers, the end points of the ramp are :math:`-2 ^{\circ} C` and :math:`0 ^{\circ} C`, respectively. Changes to the phase of precipitation are accompanied by a sensible heat flux (positive or negative) to conserve energy. + +:sup:`3`\ There are 14 aerosol deposition rates required depending on species and affinity for bonding with water; 8 of these are dust deposition rates (dry and wet rates for 4 dust size bins, :math:`D_{dst,\, dry1},\, D_{dst,\, dry2},\, D_{dst,\, dry3},\, D_{dst,\, dry4}`, :math:`D_{dst,\, \, wet1},D_{dst,\, wet2},\, D_{dst,wet3},\, D_{dst,\, wet4}` ), 3 are black carbon deposition rates (dry and wet hydrophilic and dry hydrophobic rates, :math:`D_{bc,\, dryhphil},\, D_{bc,\, wethphil},\, D_{bc,\, dryhphob}` ), and 3 are organic carbon deposition rates (dry and wet hydrophilic and dry hydrophobic rates, :math:`D_{oc,\, dryhphil},\, D_{oc,\, wethphil},\, D_{oc,\, dryhphob}` ). These fluxes are computed interactively by the atmospheric model (when prognostic aerosol representation is active) or are prescribed from a time-varying (annual cycle or transient), globally-gridded deposition file defined in the namelist (see the CLM4.5 User's Guide). Aerosol deposition rates were calculated in a transient 1850-2009 CAM simulation (at a resolution of 1.9x2.5x26L) with interactive chemistry (troposphere and stratosphere) driven by CCSM3 20\ :sup:`th` century sea-surface temperatures and emissions (:ref:`Lamarque et al. 2010`) for short-lived gases and aerosols; observed concentrations were specified for methane, N\ :sub:`2`\ O, the ozone-depleting substances (CFCs),and CO\ :sub:`2`. The fluxes are used by the snow-related parameterizations (Chapters :numref:`rst_Surface Albedos` and :numref:`rst_Snow Hydrology`). + +:sup:`4`\ The nitrogen deposition rate is required by the biogeochemistry model when active and represents the total deposition of mineral nitrogen onto the land surface, combining deposition of NO\ :sub:`y` and NH\ :sub:`x`. The rate is supplied either as a time-invariant spatially-varying annual mean rate or time-varying for a transient simulation. Nitrogen deposition rates were calculated from the same CAM chemistry simulation that generated the aerosol deposition rates. + +:sup:`5`\ Climatological 3-hourly lightning frequency at :math:`\sim`\ 1.8\ :sup:`o` resolution is provided, which was calculated via bilinear interpolation from 1995-2011 NASA LIS/OTD grid product v2.2 (http://ghrc.msfc.nasa.gov) 2-hourly, 2.5\ :sup:`o` lightning frequency data. In future versions of the model, lightning data may be obtained directly from the atmosphere model. + +Density of air (:math:`\rho _{atm}` ) (kg m\ :sup:`-3`) is also required but is calculated directly from :math:`\rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} }` where :math:`P_{atm}` is atmospheric pressure (Pa), :math:`e_{atm}` is atmospheric vapor pressure (Pa), :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), and :math:`T_{atm}` is the atmospheric temperature (K). The atmospheric vapor pressure :math:`e_{atm}` is derived from atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`) as :math:`e_{atm} =\frac{q_{atm} P_{atm} }{0.622+0.378q_{atm} }`. + +The O\ :sub:`2` partial pressure (Pa) is required but is calculated from molar ratio and the atmospheric pressure :math:`P_{atm}` as :math:`o_{i} =0.209P_{atm}`. .. _Table Land model output to atmospheric model: @@ -552,91 +348,27 @@ calculated from molar ratio and the atmospheric pressure | Net ecosystem exchange | NEE | kgCO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1` | +---------------------------------------+------------------------------------------------+--------------------------------------------------------------+ -:sup:`1`\ :math:`\lambda _{vap}` is the latent heat of -vaporization (J kg\ :sup:`-1`) (:numref:`Table Physical constants`) and :math:`\lambda` is -either the latent heat of vaporization :math:`\lambda _{vap}` or latent -heat of sublimation :math:`\lambda _{sub}` (J kg\ :sup:`-1`) -(:numref:`Table Physical constants`) depending on the liquid water and ice content of the top -snow/soil layer (section 5.4). +:sup:`1`\ :math:`\lambda _{vap}` is the latent heat of vaporization (J kg\ :sup:`-1`) (:numref:`Table Physical constants`) and :math:`\lambda` is either the latent heat of vaporization :math:`\lambda _{vap}` or latent heat of sublimation :math:`\lambda _{sub}` (J kg\ :sup:`-1`) (:numref:`Table Physical constants`) depending on the liquid water and ice content of the top snow/soil layer (section 5.4). -:sup:`2`\ There are :math:`j=1,\ldots ,4` dust transport bins. +:sup:`2`\ There are :math:`j=1,\ldots,4` dust transport bins. .. _Initialization: Initialization ^^^^^^^^^^^^^^^^^^^^ -Initialization of the land model (i.e., providing the model with initial -temperature and moisture states) depends on the type of run (startup or -restart) (see the CLM4.5 User's Guide). A startup run starts the model -from either initial conditions that are set internally in the Fortran -code (referred to as arbitrary initial conditions) or from an initial -conditions dataset that enables the model to start from a spun up state -(i.e., where the land is in equilibrium with the simulated climate). In -restart runs, the model is continued from a previous simulation and -initialized from a restart file that ensures that the output is -bit-for-bit the same as if the previous simulation had not stopped. The -fields that are required from the restart or initial conditions files -can be obtained by examining the code. Arbitrary initial conditions are -specified as follows. - -Soil points are initialized with -surface ground temperature :math:`T_{g}` and soil layer temperature -:math:`T_{i}` , for :math:`i=1,\ldots ,N_{levgrnd}` , of 274 K, -vegetation temperature :math:`T_{v}` of 283 K, no snow or canopy water -(:math:`W_{sno} =0`, :math:`W_{can} =0`), and volumetric soil water -content :math:`\theta _{i} =0.15` mm\ :sup:`3` mm\ :sup:`-3` -for layers :math:`i=1,\ldots ,N_{levsoi}` and :math:`\theta _{i} =0.0` -mm\ :sup:`3` mm\ :sup:`-3` for layers -:math:`i=N_{levsoi} +1,\ldots ,N_{levgrnd}` . placeLake temperatures -(:math:`T_{g}` and :math:`T_{i}` ) are initialized at 277 K and -:math:`W_{sno} =0`. - -Glacier temperatures (:math:`T_{g} =T_{snl+1}` and :math:`T_{i}` for -:math:`i=snl+1,\ldots ,N_{levgrnd}` where :math:`snl` is the negative -of the number of snow layers, i.e., :math:`snl` ranges from –5 to 0) are -initialized to 250 K with a snow water equivalent :math:`W_{sno} =1000` -mm, snow depth :math:`z_{sno} =\frac{W_{sno} }{\rho _{sno} }` (m) where -:math:`\rho _{sno} =250` kg m\ :sup:`-3` is an initial estimate -for the bulk density of snow, and :math:`\theta _{i}` \ =1.0 for -:math:`i=1,\ldots ,N_{levgrnd}` . The snow layer structure (e.g., number -of snow layers :math:`snl` and layer thickness) is initialized based on -the snow depth (section 6.1). The snow liquid water and ice contents (kg -m\ :sup:`-2`) are initialized as :math:`w_{liq,\, i} =0` and -:math:`w_{ice,\, i} =\Delta z_{i} \rho _{sno}` , respectively, where -:math:`i=snl+1,\ldots ,0` are the snow layers, and :math:`\Delta z_{i}` -is the thickness of snow layer :math:`i` (m). The soil liquid water and -ice contents are initialized as :math:`w_{liq,\, i} =0` and -:math:`w_{ice,\, i} =\Delta z_{i} \rho _{ice} \theta _{i}` for -:math:`T_{i} \le T_{f}` , and -:math:`w_{liq,\, i} =\Delta z_{i} \rho _{liq} \theta _{i}` and -:math:`w_{ice,\, i} =0` for :math:`T_{i} >T_{f}` , where -:math:`\rho _{ice}` and :math:`\rho _{liq}` are the densities of ice -and liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`T_{f}` -is the freezing temperature of water (K) (:numref:`Table Physical constants`). All vegetated and -glacier land units are initialized with water stored in the unconfined -aquifer and unsaturated soil :math:`W_{a} =4000` mm and water table -depth :math:`z_{\nabla }` at five meters below the soil column. +Initialization of the land model (i.e., providing the model with initial temperature and moisture states) depends on the type of run (startup or restart) (see the CLM4.5 User's Guide). A startup run starts the model from either initial conditions that are set internally in the Fortran code (referred to as arbitrary initial conditions) or from an initial conditions dataset that enables the model to start from a spun up state (i.e., where the land is in equilibrium with the simulated climate). In restart runs, the model is continued from a previous simulation and initialized from a restart file that ensures that the output is bit-for-bit the same as if the previous simulation had not stopped. The fields that are required from the restart or initial conditions files can be obtained by examining the code. Arbitrary initial conditions are specified as follows. + +Soil points are initialized with surface ground temperature :math:`T_{g}` and soil layer temperature :math:`T_{i}`, for :math:`i=1,\ldots,N_{levgrnd}`, of 274 K, vegetation temperature :math:`T_{v}` of 283 K, no snow or canopy water (:math:`W_{sno} =0`, :math:`W_{can} =0`), and volumetric soil water content :math:`\theta _{i} =0.15` mm\ :sup:`3` mm\ :sup:`-3` for layers :math:`i=1,\ldots,N_{levsoi}` and :math:`\theta _{i} =0.0` mm\ :sup:`3` mm\ :sup:`-3` for layers :math:`i=N_{levsoi} +1,\ldots,N_{levgrnd}`. placeLake temperatures (:math:`T_{g}` and :math:`T_{i}` ) are initialized at 277 K and :math:`W_{sno} =0`. + +Glacier temperatures (:math:`T_{g} =T_{snl+1}` and :math:`T_{i}` for :math:`i=snl+1,\ldots,N_{levgrnd}` where :math:`snl` is the negative of the number of snow layers, i.e., :math:`snl` ranges from –5 to 0) are initialized to 250 K with a snow water equivalent :math:`W_{sno} =1000` mm, snow depth :math:`z_{sno} =\frac{W_{sno} }{\rho _{sno} }` (m) where :math:`\rho _{sno} =250` kg m\ :sup:`-3` is an initial estimate for the bulk density of snow, and :math:`\theta _{i}` \ =1.0 for :math:`i=1,\ldots,N_{levgrnd}`. The snow layer structure (e.g., number of snow layers :math:`snl` and layer thickness) is initialized based on the snow depth (section 6.1). The snow liquid water and ice contents (kg m\ :sup:`-2`) are initialized as :math:`w_{liq,\, i} =0` and :math:`w_{ice,\, i} =\Delta z_{i} \rho _{sno}`, respectively, where :math:`i=snl+1,\ldots,0` are the snow layers, and :math:`\Delta z_{i}` is the thickness of snow layer :math:`i` (m). The soil liquid water and ice contents are initialized as :math:`w_{liq,\, i} =0` and :math:`w_{ice,\, i} =\Delta z_{i} \rho _{ice} \theta _{i}` for :math:`T_{i} \le T_{f}`, and :math:`w_{liq,\, i} =\Delta z_{i} \rho _{liq} \theta _{i}` and :math:`w_{ice,\, i} =0` for :math:`T_{i} >T_{f}`, where :math:`\rho _{ice}` and :math:`\rho _{liq}` are the densities of ice and liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical constants`). All vegetated and glacier land units are initialized with water stored in the unconfined aquifer and unsaturated soil :math:`W_{a} =4000` mm and water table depth :math:`z_{\nabla }` at five meters below the soil column. .. _Surface Data: Surface Data ^^^^^^^^^^^^^^^^^^ -Required surface data for each land grid cell are listed in -:numref:`Table Surface data required for CLM and their base spatial resolution` -and include the glacier, lake, and urban fractions of the grid cell -(vegetated and crop occupy the remainder), the fractional cover of each -plant functional type (PFT), monthly leaf and stem area index and canopy -top and bottom heights for each PFT, soil color, soil texture, soil -organic matter density, maximum fractional saturated area, slope, -elevation, biogenic volatile organic compounds (BVOCs) emissions -factors, population density, gross domestic production, peat area -fraction, and peak month of agricultural burning. Optional surface data -include crop irrigation and managed crops. All fields are aggregated to -the model's grid from high-resolution input datasets ( -:numref:`Table Surface data required for CLM and their base spatial resolution`) that -are obtained from a variety of sources described below. +Required surface data for each land grid cell are listed in :numref:`Table Surface data required for CLM and their base spatial resolution` and include the glacier, lake, and urban fractions of the grid cell (vegetated and crop occupy the remainder), the fractional cover of each plant functional type (PFT), monthly leaf and stem area index and canopy top and bottom heights for each PFT, soil color, soil texture, soil organic matter density, maximum fractional saturated area, slope, elevation, biogenic volatile organic compounds (BVOCs) emissions factors, population density, gross domestic production, peat area fraction, and peak month of agricultural burning. Optional surface data include crop irrigation and managed crops. All fields are aggregated to the model's grid from high-resolution input datasets ( :numref:`Table Surface data required for CLM and their base spatial resolution`) that are obtained from a variety of sources described below. .. _Table Surface data required for CLM and their base spatial resolution: @@ -684,188 +416,38 @@ are obtained from a variety of sources described below. | Peak month of agricultural waste burning | 0.5\ :sup:`o` | +--------------------------------------------+---------------------------+ -At the base spatial resolution of 0.05\ :sup:`o`, the percentage of -each PFT is defined with respect to the vegetated portion of the grid -cell and the sum of the PFTs is 100%. The percent lake, -glacier, and urban at their base resolution are specified with respect -to the entire grid cell. The surface dataset creation routines re-adjust -the PFT percentages to ensure that the sum of all land cover types in -the grid cell sum to 100%. A minimum threshold of 0.1% of the grid cell -by area is required for urban areas. - -The percentage glacier mask was derived from vector data of global -glacier and ice sheet spatial coverage. Vector data for glaciers (ice -caps, icefields and mountain glaciers) were taken from the first -globally complete glacier inventory, the Randolph Glacier Inventory -version 1.0 (RGIv1.0: :ref:`Arendt et al. 2012 `). -Vector data for the Greenland Ice Sheet were provided by Frank Paul and -Tobias Bolch (University of Zurich: :ref:`Rastner et al. 2012 -`). Antarctic Ice Sheet data were provided by Andrew -Bliss (University of Alaska) and were extracted from the Scientific -Committee on Antarctic Research (SCAR) Antarctic Digital Database -version 5.0. Floating ice is only provided for the Antarctic and does -not include the small area of Arctic ice shelves. High spatial -resolution vector data were then processed to determine the area of -glacier, ice sheet and floating ice within 30-second grid cells -globally. The 30-second glacier, ice sheet and Antarctic ice shelf masks -were subsequently draped over equivalent-resolution GLOBE topography -(Global Land One-km Base Elevation Project, Hastings et al. 1999) to -extract approximate ice-covered elevations of ice-covered regions. Grid -cells flagged as land-ice in the mask but ocean in GLOBE (typically, -around ice sheets at high latitudes) were designated land-ice with an -elevation of 0 meters. Finally, the high-resolution mask/topography -datasets were aggregated and processed into three 3-minute datasets: -3-minute fractional areal land ice coverage (including both glaciers and -ice sheets); 3-minute distributions of areal glacier fractional coverage -by elevation and areal ice sheet fractional coverage by elevation. Ice -fractions were binned at 100 meter intervals, with bin edges defined -from 0 to 6000 meters (plus one top bin encompassing all remaining -high-elevation ice, primarily in the Himalaya). These distributions by -elevation are used to divide each glacier land unit into columns based -on elevation class. - -When running with the CISM ice sheet model, CISM dictates glacier areas -and elevations in its domain, overriding the values specified by CLM's -datasets. In typical CLM5 configurations, this means that CISM dictates -glacier areas and elevations over Greenland. - -Percent lake and lake depth are area-averaged from the 90-second -resolution data of :ref:`Kourzeneva (2009, 2010) ` to the 0.05\ :sup:`o` -resolution using the MODIS land-mask. Percent urban is derived from -LandScan 2004, a population density dataset derived from census data, -nighttime lights satellite observations, road proximity and slope -(:ref:`Dobson et al. 2000 `) as described by -:ref:`Jackson et al. (2010) ` at 1km -resolution and aggregated to 0.05\ :sup:`o`. A number of urban -radiative, thermal, and morphological fields are also required and are -obtained from :ref:`Jackson et al. (2010) `. Their description can be found in -Table 3 of the Community Land Model Urban (CLMU) technical note (:ref:`Oleson -et al. 2010b `). - -Percent PFTs are derived from MODIS satellite data as described in -:ref:`Lawrence and Chase (2007) ` (section 21.3.3). -Prescribed PFT leaf area index is derived from the MODIS satellite data of -:ref:`Myneni et al. (2002) ` using the de-aggregation methods -described in :ref:`Lawrence and Chase (2007) ` -(section 2.2.3). Prescribed PFT stem area index is derived from PFT leaf -area index phenology combined with the methods of :ref:`Zeng et al. (2002) `. -Prescribed canopy top and bottom heights are from :ref:`Bonan (1996) ` as -described in :ref:`Bonan et al. (2002b) `. If the biogeochemistry model is -active, it supplies the leaf and stem area index and canopy top and -bottom heights dynamically, and the prescribed values are ignored. - -Soil color determines dry and saturated soil albedo (section :numref:`Ground Albedos`). -Soil colors are from :ref:`Lawrence and Chase (2007) `. - -The soil texture and organic matter content determine soil thermal and -hydrologic properties (sections 6.3 and 7.4.1). The International -Geosphere-Biosphere Programme (IGBP) soil dataset (Global Soil Data Task -2000) of 4931 soil mapping units and their sand and clay content for -each soil layer were used to create a mineral soil texture dataset -:ref:`(Bonan et al. 2002b) `. Soil organic matter data is merged from two -sources. The majority of the globe is from ISRIC-WISE (:ref:`Batjes, 2006 `). -The high latitudes come from the 0.25\ :sup:`o` version of the -Northern Circumpolar Soil Carbon Database (:ref:`Hugelius et al. 2012 `). Both -datasets report carbon down to 1m depth. Carbon is partitioned across -the top seven CLM4 layers (:math:`\sim`\ 1m depth) as in -:ref:`Lawrence and Slater (2008) `. - -The maximum fractional saturated area (:math:`f_{\max }` ) is used in -determining surface runoff and infiltration (section 7.3). Maximum -fractional saturated area at 0.125\ :sup:`o` resolution is -calculated from 1-km compound topographic indices (CTIs) based on the -USGS HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) -following the algorithm in :ref:`Niu et al. (2005) `. -:math:`f_{\max }` is the ratio between the number -of 1-km pixels with CTIs equal to or larger than the mean CTI and the -total number of pixels in a 0.125\ :sup:`o` grid cell. See -section 7.3.1 and :ref:`Li et al. (2013b) ` for further details. Slope and -elevation are also obtained from the USGS HYDRO1K 1-km dataset -(:ref:`Verdin and Greenlee 1996 `). Slope is used in the -surface water parameterization (section :numref:`Surface Water Storage`), and -elevation is used to calculate the grid cell standard deviation of -topography for the snow cover fraction parameterization (section :numref:`Snow Covered Area Fraction`). - -Biogenic Volatile Organic Compounds emissions factors are from the Model -of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1; -:ref:`Guenther et al. 2012 `). - -The default list of PFTs includes an unmanaged crop treated as a second -C3 grass (:numref:`Table Plant functional types`). The unmanaged crop has grid cell fractional cover -assigned from MODIS satellite data (:ref:`Lawrence and Chase (2007) `). A managed -crop option uses grid cell fractional cover from the present-day crop -dataset of :ref:`Ramankutty and Foley (1998) ` -(CLM4CNcrop). Managed crops are assigned in the proportions given by -:ref:`Ramankutty and Foley (1998) ` without -exceeding the area previously assigned to the unmanaged crop. The -unmanaged crop continues to occupy any of its original area that remains -and continues to be handled just by the CN part of CLM4CNcrop. The -managed crop types (corn, soybean, and temperate cereals) were chosen -based on the availability of corresponding algorithms in AgroIBIS -(:ref:`Kucharik et al. 2000 `; -:ref:`Kucharik and Brye 2003 `). Temperate cereals -include wheat, barley, and rye here. All temperate cereals are treated -as summer crops (like spring wheat, for example) at this time. Winter -cereals (such as winter wheat) may be introduced in a future version of -the model. - -To allow crops to coexist with natural vegetation in a grid cell and be -treated by separate models (i.e., CLM4.5BGCcrop versus the Dynamic -Vegetation version (CLM4.5BGCDV)), we separate the vegetated land unit -into a naturally vegetated land unit and a human managed land unit. PFTs -in the naturally vegetated land unit share one soil column and compete -for water (default CLM setting). PFTs in the human managed land unit do -not share soil columns and thus permit for differences in land -management between crops. - -CLM includes the option to irrigate cropland areas that are equipped for -irrigation. The application of irrigation responds dynamically to climate -(see Chapter :numref:`rst_Crops and Irrigation`). In CLM, irrigation is -implemented for the C3 generic crop only. When irrigation is enabled, the -cropland area of each grid cell is divided into an irrigated and unirrigated -fraction according to a dataset of areas equipped for irrigation -(:ref:`Siebert et al. (2005) `). The area of irrigated -cropland in each grid cell is given by the -smaller of the grid cell's total cropland area, according to the default -CLM4 dataset, and the grid cell's area equipped for irrigation. The -remainder of the grid cell's cropland area (if any) is then assigned to -unirrigated cropland. Irrigated and unirrigated crops are placed on -separate soil columns, so that irrigation is only applied to the soil -beneath irrigated crops. - -Several input datasets are required for the fire model (:ref:`Li et al. 2013a `) -including population density, gross domestic production, peat area -fraction, and peak month of agricultural waste burning. Population -density at 0.5\ :sup:`o` resolution for 1850-2100 combines 5-min -resolution decadal population density data for 1850–1980 from the -Database of the Global Environment version 3.1 (HYDEv3.1) with -0.5\ :sup:`o` resolution population density data for 1990, 1995, -2000, and 2005 from the Gridded Population of the World version 3 -dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per -capita in 2000 at 0.5\ :sup:`o` is from :ref:`Van Vuuren et al. (2006) `, -which is the base-year GDP data for IPCC-SRES and derived from -country-level World Bank's World Development Indicators (WDI) measured -in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database -(:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5\ :sup:`o` -resolution is derived from three vector datasets: peatland data in -Indonesia and Malaysian Borneo (:ref:`Olson et al. 2001 `); peatland data in -Canada (:ref:`Tarnocai et al. 2011 `); and bog, fen and mire data in boreal -regions (north of 45\ :sup:`o`\ N) outside Canada provided by the -Global Lakes and Wetlands Database (GLWD) (:ref:`Lehner and Döll, 2004 `). The -climatological peak month for agricultural waste burning is from :ref:`van der -Werf et al. (2010) `. +At the base spatial resolution of 0.05\ :sup:`o`, the percentage of each PFT is defined with respect to the vegetated portion of the grid cell and the sum of the PFTs is 100%. The percent lake, glacier, and urban at their base resolution are specified with respect to the entire grid cell. The surface dataset creation routines re-adjust the PFT percentages to ensure that the sum of all land cover types in the grid cell sum to 100%. A minimum threshold of 0.1% of the grid cell by area is required for urban areas. + +The percentage glacier mask was derived from vector data of global glacier and ice sheet spatial coverage. Vector data for glaciers (ice caps, icefields and mountain glaciers) were taken from the first globally complete glacier inventory, the Randolph Glacier Inventory version 1.0 (RGIv1.0: :ref:`Arendt et al. 2012 `). Vector data for the Greenland Ice Sheet were provided by Frank Paul and Tobias Bolch (University of Zurich: :ref:`Rastner et al. 2012 `). Antarctic Ice Sheet data were provided by Andrew Bliss (University of Alaska) and were extracted from the Scientific Committee on Antarctic Research (SCAR) Antarctic Digital Database version 5.0. Floating ice is only provided for the Antarctic and does not include the small area of Arctic ice shelves. High spatial resolution vector data were then processed to determine the area of glacier, ice sheet and floating ice within 30-second grid cells globally. The 30-second glacier, ice sheet and Antarctic ice shelf masks were subsequently draped over equivalent-resolution GLOBE topography (Global Land One-km Base Elevation Project, Hastings et al. 1999) to extract approximate ice-covered elevations of ice-covered regions. Grid cells flagged as land-ice in the mask but ocean in GLOBE (typically, around ice sheets at high latitudes) were designated land-ice with an elevation of 0 meters. Finally, the high-resolution mask/topography datasets were aggregated and processed into three 3-minute datasets: 3-minute fractional areal land ice coverage (including both glaciers and ice sheets); 3-minute distributions of areal glacier fractional coverage by elevation and areal ice sheet fractional coverage by elevation. Ice fractions were binned at 100 meter intervals, with bin edges defined from 0 to 6000 meters (plus one top bin encompassing all remaining high-elevation ice, primarily in the Himalaya). These distributions by elevation are used to divide each glacier land unit into columns based on elevation class. + +When running with the CISM ice sheet model, CISM dictates glacier areas and elevations in its domain, overriding the values specified by CLM's datasets. In typical CLM5 configurations, this means that CISM dictates glacier areas and elevations over Greenland. + +Percent lake and lake depth are area-averaged from the 90-second resolution data of :ref:`Kourzeneva (2009, 2010) ` to the 0.05\ :sup:`o` resolution using the MODIS land-mask. Percent urban is derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity and slope (:ref:`Dobson et al. 2000 `) as described by :ref:`Jackson et al. (2010) ` at 1km resolution and aggregated to 0.05\ :sup:`o`. A number of urban radiative, thermal, and morphological fields are also required and are obtained from :ref:`Jackson et al. (2010) `. Their description can be found in Table 3 of the Community Land Model Urban (CLMU) technical note (:ref:`Oleson et al. 2010b `). + +Percent PFTs are derived from MODIS satellite data as described in :ref:`Lawrence and Chase (2007) ` (section 21.3.3). Prescribed PFT leaf area index is derived from the MODIS satellite data of :ref:`Myneni et al. (2002) ` using the de-aggregation methods described in :ref:`Lawrence and Chase (2007) ` (section 2.2.3). Prescribed PFT stem area index is derived from PFT leaf area index phenology combined with the methods of :ref:`Zeng et al. (2002) `. Prescribed canopy top and bottom heights are from :ref:`Bonan (1996) ` as described in :ref:`Bonan et al. (2002b) `. If the biogeochemistry model is active, it supplies the leaf and stem area index and canopy top and bottom heights dynamically, and the prescribed values are ignored. + +Soil color determines dry and saturated soil albedo (section :numref:`Ground Albedos`). Soil colors are from :ref:`Lawrence and Chase (2007) `. + +The soil texture and organic matter content determine soil thermal and hydrologic properties (sections 6.3 and 7.4.1). The International Geosphere-Biosphere Programme (IGBP) soil dataset (Global Soil Data Task 2000) of 4931 soil mapping units and their sand and clay content for each soil layer were used to create a mineral soil texture dataset :ref:`(Bonan et al. 2002b) `. Soil organic matter data is merged from two sources. The majority of the globe is from ISRIC-WISE (:ref:`Batjes, 2006 `). The high latitudes come from the 0.25\ :sup:`o` version of the Northern Circumpolar Soil Carbon Database (:ref:`Hugelius et al. 2012 `). Both datasets report carbon down to 1m depth. Carbon is partitioned across the top seven CLM4 layers (:math:`\sim`\ 1m depth) as in :ref:`Lawrence and Slater (2008) `. + +The maximum fractional saturated area (:math:`f_{\max }` ) is used in determining surface runoff and infiltration (section 7.3). Maximum fractional saturated area at 0.125\ :sup:`o` resolution is calculated from 1-km compound topographic indices (CTIs) based on the USGS HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) following the algorithm in :ref:`Niu et al. (2005) `. :math:`f_{\max }` is the ratio between the number of 1-km pixels with CTIs equal to or larger than the mean CTI and the total number of pixels in a 0.125\ :sup:`o` grid cell. See section 7.3.1 and :ref:`Li et al. (2013b) ` for further details. Slope and elevation are also obtained from the USGS HYDRO1K 1-km dataset (:ref:`Verdin and Greenlee 1996 `). Slope is used in the surface water parameterization (section :numref:`Surface Water Storage`), and elevation is used to calculate the grid cell standard deviation of topography for the snow cover fraction parameterization (section :numref:`Snow Covered Area Fraction`). + +Biogenic Volatile Organic Compounds emissions factors are from the Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1; :ref:`Guenther et al. 2012 `). + +The default list of PFTs includes an unmanaged crop treated as a second C3 grass (:numref:`Table Plant functional types`). The unmanaged crop has grid cell fractional cover assigned from MODIS satellite data (:ref:`Lawrence and Chase (2007) `). A managed crop option uses grid cell fractional cover from the present-day crop dataset of :ref:`Ramankutty and Foley (1998) ` (CLM4CNcrop). Managed crops are assigned in the proportions given by :ref:`Ramankutty and Foley (1998) ` without exceeding the area previously assigned to the unmanaged crop. The unmanaged crop continues to occupy any of its original area that remains and continues to be handled just by the CN part of CLM4CNcrop. The managed crop types (corn, soybean, and temperate cereals) were chosen based on the availability of corresponding algorithms in AgroIBIS (:ref:`Kucharik et al. 2000 `; :ref:`Kucharik and Brye 2003 `). Temperate cereals include wheat, barley, and rye here. All temperate cereals are treated as summer crops (like spring wheat, for example) at this time. Winter cereals (such as winter wheat) may be introduced in a future version of the model. + +To allow crops to coexist with natural vegetation in a grid cell and be treated by separate models (i.e., CLM4.5BGCcrop versus the Dynamic Vegetation version (CLM4.5BGCDV)), we separate the vegetated land unit into a naturally vegetated land unit and a human managed land unit. PFTs in the naturally vegetated land unit share one soil column and compete for water (default CLM setting). PFTs in the human managed land unit do not share soil columns and thus permit for differences in land management between crops. + +CLM includes the option to irrigate cropland areas that are equipped for irrigation. The application of irrigation responds dynamically to climate (see Chapter :numref:`rst_Crops and Irrigation`). In CLM, irrigation is implemented for the C3 generic crop only. When irrigation is enabled, the cropland area of each grid cell is divided into an irrigated and unirrigated fraction according to a dataset of areas equipped for irrigation (:ref:`Siebert et al. (2005) `). The area of irrigated cropland in each grid cell is given by the smaller of the grid cell's total cropland area, according to the default CLM4 dataset, and the grid cell's area equipped for irrigation. The remainder of the grid cell's cropland area (if any) is then assigned to unirrigated cropland. Irrigated and unirrigated crops are placed on separate soil columns, so that irrigation is only applied to the soil beneath irrigated crops. + +Several input datasets are required for the fire model (:ref:`Li et al. 2013a `) including population density, gross domestic production, peat area fraction, and peak month of agricultural waste burning. Population density at 0.5\ :sup:`o` resolution for 1850-2100 combines 5-min resolution decadal population density data for 1850–1980 from the Database of the Global Environment version 3.1 (HYDEv3.1) with 0.5\ :sup:`o` resolution population density data for 1990, 1995, 2000, and 2005 from the Gridded Population of the World version 3 dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per capita in 2000 at 0.5\ :sup:`o` is from :ref:`Van Vuuren et al. (2006) `, which is the base-year GDP data for IPCC-SRES and derived from country-level World Bank's World Development Indicators (WDI) measured in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database (:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5\ :sup:`o` resolution is derived from three vector datasets: peatland data in Indonesia and Malaysian Borneo (:ref:`Olson et al. 2001 `); peatland data in Canada (:ref:`Tarnocai et al. 2011 `); and bog, fen and mire data in boreal regions (north of 45\ :sup:`o`\ N) outside Canada provided by the Global Lakes and Wetlands Database (GLWD) (:ref:`Lehner and Döll, 2004 `). The climatological peak month for agricultural waste burning is from :ref:`van der Werf et al. (2010) `. .. _Adjustable Parameters and Physical Constants: Adjustable Parameters and Physical Constants ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Values of certain adjustable parameters inherent in the biogeophysical -or biogeochemical parameterizations have either been obtained from the -literature or calibrated based on comparisons with observations. These -are described in the text. Physical constants, generally shared by all -of the components in the coupled modeling system, are presented in -:numref:`Table Physical constants`. +Values of certain adjustable parameters inherent in the biogeophysical or biogeochemical parameterizations have either been obtained from the literature or calibrated based on comparisons with observations. These are described in the text. Physical constants, generally shared by all of the components in the coupled modeling system, are presented in :numref:`Table Physical constants`. .. _Table Physical constants: diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index e9ab23d496..65925980aa 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -21,91 +21,25 @@ CLM5.0 includes the following changes to terrestrial nitrogen inputs: Overview ----------------------------------------------------- -In addition to the relatively rapid cycling of nitrogen within the plant -– litter – soil organic matter system, CLM also represents several -processes which couple the internal nitrogen cycle to external sources -and sinks. Inputs of new mineral nitrogen are from atmospheric -deposition and biological nitrogen fixation. Losses of mineral nitrogen -are due to nitrification, denitrification, leaching, and losses in fire. -While the short-term dynamics of nitrogen limitation depend on the -behavior of the internal nitrogen cycle, establishment of total -ecosystem nitrogen stocks depends on the balance between sources and -sinks in the external nitrogen cycle (:ref:`Thomas et al. 2015 `). - -As with CLM4.5, CLM5.0 represents inorganic N transformations based on the Century N-gas model; this -includes separate NH\ :sub:`4`\ :sup:`+` and -NO\ :sub:`3`\ :sup:`-` pools, as well as -environmentally controlled nitrification and denitrification rates that is described below. +In addition to the relatively rapid cycling of nitrogen within the plant – litter – soil organic matter system, CLM also represents several processes which couple the internal nitrogen cycle to external sources and sinks. Inputs of new mineral nitrogen are from atmospheric deposition and biological nitrogen fixation. Losses of mineral nitrogen are due to nitrification, denitrification, leaching, and losses in fire. While the short-term dynamics of nitrogen limitation depend on the behavior of the internal nitrogen cycle, establishment of total ecosystem nitrogen stocks depends on the balance between sources and sinks in the external nitrogen cycle (:ref:`Thomas et al. 2015 `). + +As with CLM4.5, CLM5.0 represents inorganic N transformations based on the Century N-gas model; this includes separate NH\ :sub:`4`\ :sup:`+` and NO\ :sub:`3`\ :sup:`-` pools, as well as environmentally controlled nitrification and denitrification rates that is described below. Atmospheric Nitrogen Deposition ------------------------------------ -CLM uses a single variable to represent the total deposition of mineral -nitrogen onto the land surface, combining wet and dry deposition of -NO\ :sub:`y` and NH\ :sub:`x` as a single flux -(:math:`{NF}_{ndep\_sminn}`, gN m\ :sup:`-2` s\ :sup:`-1`). This flux -is intended to represent total reactive -nitrogen deposited to the land surface which originates from the -following natural and anthropogenic sources (Galloway et al. 2004): -formation of NO\ :sub:`x` during lightning, -NO\ :math:`{}_{x }`\ and NH\ :sub:`3` emission from wildfire, -NO\ :sub:`x` emission from natural soils, NH\ :sub:`3` -emission from natural soils, vegetation, and wild animals, -NO\ :sub:`x` and NH\ :sub:`3` emission during fossil fuel -combustion (both thermal and fuel NO\ :sub:`x` production), -NO\ :sub:`x` and NH\ :sub:`3` emission from other industrial -processes, NO\ :sub:`x` and NH\ :sub:`3` emission from fire -associated with deforestation, NO\ :sub:`x` and NH\ :sub:`3` -emission from agricultural burning, NO\ :sub:`x` emission from -agricultural soils, NH\ :sub:`3` emission from agricultural crops, -NH\ :sub:`3` emission from agricultural animal waste, and -NH\ :sub:`3` emission from human waste and waste water. The -deposition flux is provided as a spatially and (potentially) temporally -varying dataset (see section :numref:`Atmospheric Coupling` for a description of the default -input dataset). - -The nitrogen deposition flux is assumed to enter the NH\ :sub:`4`\ :sup:`+` pool, -and is vertically distributed throughout the soil profile. Although N deposition -inputs include both oxidized and reduced forms, CLM5 only reads in total -N deposition. This approach is held over from CLM4.0, which only represented a -single mineral nitrogen pool, however, real pathways for wet and dry -nitrogen deposition can be more complex than currently represented in -the CLM5.0, including release from melting snowpack and direct foliar -uptake of deposited NO\ :sub:`y` (:ref:`Tye et al. 2005 `; -:ref:`Vallano and Sparks, 2007 `). - -In offline (uncoupled) CLM5.0 simulations monthly -estimates of N deposition are provided, as opposed to decadal files -supplied with previous versions of the model. In coupled simulations, -N depositions fluxes are passed to the land model at the frequency of -the time step (every half hour) through the coupler. +CLM uses a single variable to represent the total deposition of mineral nitrogen onto the land surface, combining wet and dry deposition of NO\ :sub:`y` and NH\ :sub:`x` as a single flux (:math:`{NF}_{ndep\_sminn}`, gN m\ :sup:`-2` s\ :sup:`-1`). This flux is intended to represent total reactive nitrogen deposited to the land surface which originates from the following natural and anthropogenic sources (Galloway et al. 2004): formation of NO\ :sub:`x` during lightning, NO\ :math:`{}_{x }`\ and NH\ :sub:`3` emission from wildfire, NO\ :sub:`x` emission from natural soils, NH\ :sub:`3` emission from natural soils, vegetation, and wild animals, NO\ :sub:`x` and NH\ :sub:`3` emission during fossil fuel combustion (both thermal and fuel NO\ :sub:`x` production), NO\ :sub:`x` and NH\ :sub:`3` emission from other industrial processes, NO\ :sub:`x` and NH\ :sub:`3` emission from fire associated with deforestation, NO\ :sub:`x` and NH\ :sub:`3` emission from agricultural burning, NO\ :sub:`x` emission from agricultural soils, NH\ :sub:`3` emission from agricultural crops, NH\ :sub:`3` emission from agricultural animal waste, and NH\ :sub:`3` emission from human waste and waste water. The deposition flux is provided as a spatially and (potentially) temporally varying dataset (see section :numref:`Atmospheric Coupling` for a description of the default input dataset). + +The nitrogen deposition flux is assumed to enter the NH\ :sub:`4`\ :sup:`+` pool, and is vertically distributed throughout the soil profile. Although N deposition inputs include both oxidized and reduced forms, CLM5 only reads in total N deposition. This approach is held over from CLM4.0, which only represented a single mineral nitrogen pool, however, real pathways for wet and dry nitrogen deposition can be more complex than currently represented in the CLM5.0, including release from melting snowpack and direct foliar uptake of deposited NO\ :sub:`y` (:ref:`Tye et al. 2005 `; :ref:`Vallano and Sparks, 2007 `). + +In offline (uncoupled) CLM5.0 simulations monthly estimates of N deposition are provided, as opposed to decadal files supplied with previous versions of the model. In coupled simulations, N depositions fluxes are passed to the land model at the frequency of the time step (every half hour) through the coupler. Biological Nitrogen Fixation --------------------------------- -The fixation of new reactive nitrogen from atmospheric N\ :sub:`2` -by soil microorganisms is an important component of both preindustrial -and modern-day nitrogen budgets, but a mechanistic understanding of -global-scale controls on biological nitrogen fixation (BNF) is still -only poorly developed (:ref:`Cleveland et al. 1999 `; -:ref:`Galloway et al. 2004 `). CLM5.0 uses the FUN -model (chapter :numref:`rst_FUN`) to -calculate the carbon cost and nitrogen acquired through symbotic -nitrogen fixation. This nitrogen is immediately available to plants. - -:ref:`Cleveland et al. (1999) ` suggested -an empirical relationships that predicts BNF as a function of -either evapotranspiration rate or net primary productivity for -natural vegetation. CLM5.0 adopts the evapotranspiration approach -to calculate asymbiotic, or free-living, N fixation. This function -has been modified from the :ref:`Cleveland et al. (1999) -` estimates to provide lower estimate of -free-living nitrogen fixation in CLM5.0 -(:math:`{CF}_{ann\_ET}`, mm yr\ :sup:`-1`). -This moves away from the NPP approach used in CLM4.0 and 4.5 and -avoids unrealistically increasing freeliving rates of N fixation -under global change scenarios (:ref:`Wieder et al. 2015 -` The expression used is: +The fixation of new reactive nitrogen from atmospheric N\ :sub:`2` by soil microorganisms is an important component of both preindustrial and modern-day nitrogen budgets, but a mechanistic understanding of global-scale controls on biological nitrogen fixation (BNF) is still only poorly developed (:ref:`Cleveland et al. 1999 `; :ref:`Galloway et al. 2004 `). CLM5.0 uses the FUN model (chapter :numref:`rst_FUN`) to calculate the carbon cost and nitrogen acquired through symbotic nitrogen fixation. This nitrogen is immediately available to plants. + +:ref:`Cleveland et al. (1999) ` suggested an empirical relationships that predicts BNF as a function of either evapotranspiration rate or net primary productivity for natural vegetation. CLM5.0 adopts the evapotranspiration approach to calculate asymbiotic, or free-living, N fixation. This function has been modified from the :ref:`Cleveland et al. (1999) ` estimates to provide lower estimate of free-living nitrogen fixation in CLM5.0 (:math:`{CF}_{ann\_ET}`, mm yr\ :sup:`-1`). This moves away from the NPP approach used in CLM4.0 and 4.5 and avoids unrealistically increasing freeliving rates of N fixation under global change scenarios (:ref:`Wieder et al. 2015 ` The expression used is: .. math:: :label: 22.1) @@ -120,58 +54,23 @@ Where :math:`{NF}_{nfix,sminn}` (gN m\ :sup:`-2` s\ :sup:`-1`) is the rate of fr Free-living nitrogen fixation as a function of annual evapotranspiration. Results here show annual N inputs from free-living N fixations, but the model actually calculates inputs on a per second basis. -As with Atmospheric N deposition, free-living N inputs are added directly to the -NH\ :sub:`4`\ :sup:`+` pool. +As with Atmospheric N deposition, free-living N inputs are added directly to the NH\ :sub:`4`\ :sup:`+` pool. Nitrification and Denitrification Losses of Nitrogen --------------------------------------------------------- -Nitrification is an autotrophic process that converts less mobile ammonium -ions into nitrate, that can more easily be lost from soil systems by leaching -or denitrification. The process catalyzed by ammonia oxidizing archaea and -bacteria that convert ammonium (NH\ :sub:`4`\ :sup:`+`) into nitrite, which -is subsequently oxidized into nitrate (NO\ :sub:`3`\ :sup:`-`). Conditions -favoring nitrification include high NH\ :sub:`4`\ :sup:`+` concentrations, -well aerated soils, a neutral pH and warmer temperatures. - -Under aerobic conditions in the soil oxygen is the preferred electron -acceptor supporting the metabolism of heterotrophs, but anaerobic -conditions favor the activity of soil heterotrophs which use nitrate as -an electron acceptor (e.g. *Pseudomonas* and *Clostridium*) supporting -respiration. This process, known as denitrification, results in the -transformation of nitrate to gaseous N\ :sub:`2`, with smaller -associated production of NO\ :sub:`x` and N\ :sub:`2`\ O. It -is typically assumed that nitrogen fixation and denitrification -were approximately balanced in the preindustrial biosphere ( -:ref:`Galloway et al. 2004 `). It is likely -that denitrification can occur within anaerobic -microsites within an otherwise aerobic soil environment, leading to -large global denitrification fluxes even when fluxes per unit area are -rather low (:ref:`Galloway et al. 2004 `). - -CLM includes a detailed representation of nitrification and -denitrification based on the Century N model (:ref:`Parton -et al. 1996 `, :ref:`2001 `; -:ref:`del Grosso et al. 2000 `). In this -approach, nitrification of NH\ :sub:`4`\ :sup:`+` to NO\ :sub:`3`\ :sup:`-` -is a function of temperature, moisture, and pH: +Nitrification is an autotrophic process that converts less mobile ammonium ions into nitrate, that can more easily be lost from soil systems by leaching or denitrification. The process catalyzed by ammonia oxidizing archaea and bacteria that convert ammonium (NH\ :sub:`4`\ :sup:`+`) into nitrite, which is subsequently oxidized into nitrate (NO\ :sub:`3`\ :sup:`-`). Conditions favoring nitrification include high NH\ :sub:`4`\ :sup:`+` concentrations, well aerated soils, a neutral pH and warmer temperatures. + +Under aerobic conditions in the soil oxygen is the preferred electron acceptor supporting the metabolism of heterotrophs, but anaerobic conditions favor the activity of soil heterotrophs which use nitrate as an electron acceptor (e.g. *Pseudomonas* and *Clostridium*) supporting respiration. This process, known as denitrification, results in the transformation of nitrate to gaseous N\ :sub:`2`, with smaller associated production of NO\ :sub:`x` and N\ :sub:`2`\ O. It is typically assumed that nitrogen fixation and denitrification were approximately balanced in the preindustrial biosphere ( :ref:`Galloway et al. 2004 `). It is likely that denitrification can occur within anaerobic microsites within an otherwise aerobic soil environment, leading to large global denitrification fluxes even when fluxes per unit area are rather low (:ref:`Galloway et al. 2004 `). + +CLM includes a detailed representation of nitrification and denitrification based on the Century N model (:ref:`Parton et al. 1996 `, :ref:`2001 `; :ref:`del Grosso et al. 2000 `). In this approach, nitrification of NH\ :sub:`4`\ :sup:`+` to NO\ :sub:`3`\ :sup:`-` is a function of temperature, moisture, and pH: .. math:: :label: 22.2) f_{nitr,p} =\left[NH_{4} \right]k_{nitr} f\left(T\right)f\left(H_{2} O\right)f\left(pH\right) -where :math:`{f}_{nitr,p}` is the potential nitrification rate -(prior to competition for NH\ :sub:`4`\ :sup:`+` by plant -uptake and N immobilization), :math:`{k}_{nitr}` is the maximum -nitrification rate (10 % day\ :math:`\mathrm{-}`\ 1, -(:ref:`Parton et al. 2001 `), and *f(T)* and -*f(H\)*\ :sub:`2`\ O) are rate modifiers for temperature and -moisture content. CLM uses the same rate modifiers as -are used in the decomposition routine. *f(pH)* is a rate -modifier for pH; however, because CLM does not calculate pH, -instead a fixed pH value of 6.5 is used in the pH function of -:ref:`Parton et al. (1996) `. +where :math:`{f}_{nitr,p}` is the potential nitrification rate (prior to competition for NH\ :sub:`4`\ :sup:`+` by plant uptake and N immobilization), :math:`{k}_{nitr}` is the maximum nitrification rate (10 % day\ :math:`\mathrm{-}`\ 1, (:ref:`Parton et al. 2001 `), and *f(T)* and *f(H\)*\ :sub:`2`\ O) are rate modifiers for temperature and moisture content. CLM uses the same rate modifiers as are used in the decomposition routine. *f(pH)* is a rate modifier for pH; however, because CLM does not calculate pH, instead a fixed pH value of 6.5 is used in the pH function of :ref:`Parton et al. (1996) `. The potential denitrification rate is co-limited by NO\ :sup:`-3` concentration and C consumption rates, and occurs only in the anoxic fraction of soils: @@ -181,51 +80,23 @@ NO\ :sup:`-3` concentration and C consumption rates, and occurs only in the anox f_{denitr,p} =\min \left(f(decomp),f\left(\left[NO_{3} ^{-} \right]\right)\right)frac_{anox} -where :math:`{f}_{denitr,p}` is the potential denitrification rate -and *f(decomp)* and *f([NO*\ :sub:`3`\ :sup:`-` *])* -are the carbon- and nitrate- limited denitrification rate functions, -respectively, (:ref:`del Grosso et al. 2000 `). -Because the modified CLM includes explicit treatment of soil -biogeochemical vertical profiles, including diffusion of the trace -gases O\ :sub:`2` and CH\ :sub:`4` (:ref:`Riley et al. 2011a -`), the calculation of anoxic fraction :math:`{frac}_{anox}` -uses this information following the anoxic microsite formulation -of :ref:`Arah and Vinten (1995) `. +where :math:`{f}_{denitr,p}` is the potential denitrification rate and *f(decomp)* and *f([NO*\ :sub:`3`\ :sup:`-` *])* are the carbon- and nitrate- limited denitrification rate functions, respectively, (:ref:`del Grosso et al. 2000 `). Because the modified CLM includes explicit treatment of soil biogeochemical vertical profiles, including diffusion of the trace gases O\ :sub:`2` and CH\ :sub:`4` (:ref:`Riley et al. 2011a `), the calculation of anoxic fraction :math:`{frac}_{anox}` uses this information following the anoxic microsite formulation of :ref:`Arah and Vinten (1995) `. .. math:: :label: 22.4) frac_{anox} =\exp \left(-aR_{\psi }^{-\alpha } V^{-\beta } C^{\gamma } \left[\theta +\chi \varepsilon \right]^{\delta } \right) -where *a*, :math:`\alpha`, :math:`\beta`, :math:`\gamma`, and :math:`\delta` are constants (equal to -1.5x10\ :sup:`-10`, 1.26, 0.6, 0.6, and 0.85, respectively), :math:`{R}_{\psi}` is the -radius of a typical pore space at moisture content :math:`\psi`, *V* -is the O\ :sub:`2` consumption rate, *C* is the O\ :sub:`2` -concentration, :math:`\theta` is the water-filled pore space, -:math:`\chi` is the ratio of diffusivity of oxygen in water to that in -air, and :math:`\epsilon` is the air-filled pore space (:ref:`Arah and -Vinten (1995) `). These parameters are all calculated -separately at each -layer to define a profile of anoxic porespace fraction in the soil. - -The nitrification/denitrification models used here also predict fluxes -of N\ :sub:`2`\ O via a "hole-in-the-pipe" approach (:ref:`Firestone and -Davidson, 1989 `). A constant fraction -(6 \* 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the -nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction -of denitrification going to N\ :sub:`2`\ O, \ :math:`{P}_{N2:N2O}`, is variable, following -the Century (:ref:`del Grosso et al. 2000 `) approach: +where *a*, :math:`\alpha`, :math:`\beta`, :math:`\gamma`, and :math:`\delta` are constants (equal to 1.5x10\ :sup:`-10`, 1.26, 0.6, 0.6, and 0.85, respectively), :math:`{R}_{\psi}` is the radius of a typical pore space at moisture content :math:`\psi`, *V* is the O\ :sub:`2` consumption rate, *C* is the O\ :sub:`2` concentration, :math:`\theta` is the water-filled pore space, :math:`\chi` is the ratio of diffusivity of oxygen in water to that in air, and :math:`\epsilon` is the air-filled pore space (:ref:`Arah and Vinten (1995) `). These parameters are all calculated separately at each layer to define a profile of anoxic porespace fraction in the soil. + +The nitrification/denitrification models used here also predict fluxes of N\ :sub:`2`\ O via a "hole-in-the-pipe" approach (:ref:`Firestone and Davidson, 1989 `). A constant fraction (6 \* 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction of denitrification going to N\ :sub:`2`\ O, \ :math:`{P}_{N2:N2O}`, is variable, following the Century (:ref:`del Grosso et al. 2000 `) approach: .. math:: :label: 22.5) P_{N_{2} :N_{2} O} =\max \left(0.16k_{1} ,k_{1} \exp \left(-0.8P_{NO_{3} :CO_{2} } \right)\right)f_{WFPS} -where :math:`{P}_{NO3:CO2}` is the ratio of CO\ :sub:`2` -production in a given soil layer to the -NO\ :sub:`3`\ :sup:`-` concentration, :math:`{k}_{1}` is -a function of :math:`{d}_{g}`, the gas diffusivity through the soil -matrix: +where :math:`{P}_{NO3:CO2}` is the ratio of CO\ :sub:`2` production in a given soil layer to the NO\ :sub:`3`\ :sup:`-` concentration, :math:`{k}_{1}` is a function of :math:`{d}_{g}`, the gas diffusivity through the soil matrix: .. math:: :label: 22.6) @@ -242,38 +113,21 @@ and :math:`{f}_{WFPS}` is a function of the water filled pore space *WFPS:* Leaching Losses of Nitrogen -------------------------------- -Soil mineral nitrogen remaining after plant uptake, immobilization, and -denitrification is subject to loss as a dissolved component of -hydrologic outflow from the soil column (leaching). This leaching loss -(:math:`{NF}_{leached}`, gN m\ :sup:`-2` s\ :sup:`-1`) -depends on the concentration of dissolved mineral (inorganic) nitrogen -in soil water solution (*DIN*, gN kgH\ :sub:`2`\ O), and the rate -of hydrologic discharge from the soil column to streamflow -(:math:`{Q}_{dis}`, kgH\ :sub:`2`\ O m\ :sup:`-2` -s\ :sup:`-1`, section :numref:`Lateral Sub-surface Runoff`), as +Soil mineral nitrogen remaining after plant uptake, immobilization, and denitrification is subject to loss as a dissolved component of hydrologic outflow from the soil column (leaching). This leaching loss (:math:`{NF}_{leached}`, gN m\ :sup:`-2` s\ :sup:`-1`) depends on the concentration of dissolved mineral (inorganic) nitrogen in soil water solution (*DIN*, gN kgH\ :sub:`2`\ O), and the rate of hydrologic discharge from the soil column to streamflow (:math:`{Q}_{dis}`, kgH\ :sub:`2`\ O m\ :sup:`-2` s\ :sup:`-1`, section :numref:`Lateral Sub-surface Runoff`), as .. math:: :label: 22.17) NF_{leached} =DIN\cdot Q_{dis} . -*DIN* is calculated assuming that a constant fraction (*sf*, proportion) -of the remaining soil mineral N pool is in soluble form, and that this -entire fraction is dissolved in the total soil water. For the Century- -based formulation in CLM5.0, the leaching acts only on the -NO\ :sub:`3`\ :sup:`-` pool (which is assumed to be 100% -soluble), while the NH\ :sub:`4`\ :sup:`+` pool is assumed -to be 100% adsorbed onto mineral surfaces and unaffected by leaching. -*DIN* is then given as +*DIN* is calculated assuming that a constant fraction (*sf*, proportion) of the remaining soil mineral N pool is in soluble form, and that this entire fraction is dissolved in the total soil water. For the Century- based formulation in CLM5.0, the leaching acts only on the NO\ :sub:`3`\ :sup:`-` pool (which is assumed to be 100% soluble), while the NH\ :sub:`4`\ :sup:`+` pool is assumed to be 100% adsorbed onto mineral surfaces and unaffected by leaching. *DIN* is then given as .. math:: :label: 22.18) DIN=\frac{NS_{sminn} sf}{WS_{tot\_ soil} } -where :math:`{WS}_{tot\_soil}` (kgH\ :sub:`2`\ O m\ :sup:`-2`) is the total mass of soil water content integrated -over the column. The total mineral nitrogen leaching flux is limited on -each time step to not exceed the soluble fraction of :math:`{NS}_{sminn}` +where :math:`{WS}_{tot\_soil}` (kgH\ :sub:`2`\ O m\ :sup:`-2`) is the total mass of soil water content integrated over the column. The total mineral nitrogen leaching flux is limited on each time step to not exceed the soluble fraction of :math:`{NS}_{sminn}` .. math:: :label: 22.19) @@ -283,15 +137,5 @@ each time step to not exceed the soluble fraction of :math:`{NS}_{sminn}` Losses of Nitrogen Due to Fire ----------------------------------- -The final pathway for nitrogen loss is through combustion, also known as -pyrodenitrification. Detailed equations are provided, together with the -effects of fire on the carbon budget, in Chapter :numref:`rst_Fire`). It is assumed in -CLM-CN that losses of N due to fire are restricted to vegetation and -litter pools (including coarse woody debris). Loss rates of N are -determined by the fraction of biomass lost to combustion, assuming that -most of the nitrogen in the burned biomass is lost to the atmosphere -(:ref:`Schlesinger, 1997 `; :ref:`Smith et al. 2005 -`). It is assumed that soil organic -matter pools of carbon and nitrogen are not directly affected by fire -(:ref:`Neff et al. 2005 `). +The final pathway for nitrogen loss is through combustion, also known as pyrodenitrification. Detailed equations are provided, together with the effects of fire on the carbon budget, in Chapter :numref:`rst_Fire`). It is assumed in CLM-CN that losses of N due to fire are restricted to vegetation and litter pools (including coarse woody debris). Loss rates of N are determined by the fraction of biomass lost to combustion, assuming that most of the nitrogen in the burned biomass is lost to the atmosphere (:ref:`Schlesinger, 1997 `; :ref:`Smith et al. 2005 `). It is assumed that soil organic matter pools of carbon and nitrogen are not directly affected by fire (:ref:`Neff et al. 2005 `). diff --git a/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst b/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst index 88abf78d7a..428f114a5d 100644 --- a/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst +++ b/doc/source/tech_note/FUN/CLM50_Tech_Note_FUN.rst @@ -262,8 +262,7 @@ The original FUN model as developed by :ref:`Fisher et al. (2010)`, -:ref:`Li et al. 2012b `, :ref:`Li et al. 2013 `, -:ref:`Li and Lawrence 2017 ` for details). -In this fire parameterization, burned area is affected by climate and -weather conditions, vegetation composition and structure, and human -activities. After burned area is calculated, we estimate the fire impact, -including biomass and peat burning, fire-induced vegetation mortality, -adjustment of the carbon and nitrogen (C/N) pools, and fire emissions. +The fire parameterization in CLM contains four components: non-peat fires outside cropland and tropical closed forests, agricultural fires in cropland, deforestation fires in the tropical closed forests, and peat fires (see :ref:`Li et al. 2012a `, :ref:`Li et al. 2012b `, :ref:`Li et al. 2013 `, :ref:`Li and Lawrence 2017 ` for details). In this fire parameterization, burned area is affected by climate and weather conditions, vegetation composition and structure, and human activities. After burned area is calculated, we estimate the fire impact, including biomass and peat burning, fire-induced vegetation mortality, adjustment of the carbon and nitrogen (C/N) pools, and fire emissions. .. _Non-peat fires outside cropland and tropical closed forest: Non-peat fires outside cropland and tropical closed forest --------------------------------------------------------------- -Burned area in a grid cell, \ :math:`A_{b}` (km\ :sup:`2` s :sup:`-1`), -is determined by +Burned area in a grid cell, \ :math:`A_{b}` (km\ :sup:`2` s :sup:`-1`), is determined by .. math:: :label: 23.1 A_{b} =N_{f} a -where :math:`N_{f}` (count s\ :sup:`-1`) is fire -counts in the grid cell; :math:`a` (km\ :sup:`2`) is average fire -spread area of a fire. +where :math:`N_{f}` (count s\ :sup:`-1`) is fire counts in the grid cell; :math:`a` (km\ :sup:`2`) is average fire spread area of a fire. .. _Fire counts: @@ -44,12 +31,7 @@ Fire counts :math:`N_{f}` is taken as N_{f} = N_{i} f_{b} f_{m} f_{se,o} -where :math:`N_{i}` ( count s\ :sup:`-1`) is the -number of ignition sources due to natural causes and human activities; -:math:`f_{b}` and :math:`f_{m}` (fractions) represent the availability -and combustibility of fuel, respectively; :math:`f_{se,o}` is the -fraction of anthropogenic and natural fires unsuppressed by humans and -related to the socioeconomic conditions. +where :math:`N_{i}` ( count s\ :sup:`-1`) is the number of ignition sources due to natural causes and human activities; :math:`f_{b}` and :math:`f_{m}` (fractions) represent the availability and combustibility of fuel, respectively; :math:`f_{se,o}` is the fraction of anthropogenic and natural fires unsuppressed by humans and related to the socioeconomic conditions. :math:`N_{i}` (count s\ :sup:`-1`) is given as @@ -58,32 +40,21 @@ related to the socioeconomic conditions. N_{i} = \left(I_{n} +I_{a} \right) A_{g} -where :math:`I_{n}` (count km\ :sup:`-2` s\ :sup:`-1`) and :math:`I_{a}` -(count km\ :sup:`-2` s\ :sup:`-1`) are the number of natural and anthropogenic -ignitions per km\ :sup:`2`, respectively; :math:`A_{g}` is the area of the -grid cell (km\ :sup:`2`). :math:`I_{n}` is estimated by +where :math:`I_{n}` (count km\ :sup:`-2` s\ :sup:`-1`) and :math:`I_{a}` (count km\ :sup:`-2` s\ :sup:`-1`) are the number of natural and anthropogenic ignitions per km\ :sup:`2`, respectively; :math:`A_{g}` is the area of the grid cell (km\ :sup:`2`). :math:`I_{n}` is estimated by .. math:: :label: 23.4 I_{n} = \gamma \psi I_{l} -where :math:`\gamma` \ =0.22 is ignition efficiency of cloud-to-ground -lightning; :math:`\psi =\frac{1}{5.16+2.16\cos [3min(60,\lambda )]}` is the -cloud-to-ground lightning fraction and depends on the latitude -:math:`\lambda` (degrees) ; :math:`I_{l}` (flash km\ :sup:`-2` s\ :sup:`-1`) is -the total lightning flashes. :math:`I_{a}` is modeled as a monotonic -increasing function of population density: +where :math:`\gamma` \ =0.22 is ignition efficiency of cloud-to-ground lightning; :math:`\psi =\frac{1}{5.16+2.16\cos [3min(60,\lambda )]}` is the cloud-to-ground lightning fraction and depends on the latitude :math:`\lambda` (degrees); :math:`I_{l}` (flash km\ :sup:`-2` s\ :sup:`-1`) is the total lightning flashes. :math:`I_{a}` is modeled as a monotonic increasing function of population density: .. math:: :label: 23.5 I_{a} =\frac{\alpha D_{P} k(D_{P} )}{n} -where :math:`\alpha =0.01` (count person\ :sup:`-1` mon\ :sup:`-1`) is the number of potential ignition sources by a -person per month; :math:`D_{P}` (person km\ :sup:`-2`) is the population density; :math:`k(D_{P} )=6.8D_{P} ^{-0.6}` represents anthropogenic ignition -potential as a function of human population density :math:`D_{P}` ; *n* -is the seconds in a month. +where :math:`\alpha =0.01` (count person\ :sup:`-1` mon\ :sup:`-1`) is the number of potential ignition sources by a person per month; :math:`D_{P}` (person km\ :sup:`-2`) is the population density; :math:`k(D_{P} )=6.8D_{P} ^{-0.6}` represents anthropogenic ignition potential as a function of human population density :math:`D_{P}`; *n* is the seconds in a month. Fuel availability :math:`f_{b}` is given as @@ -95,11 +66,7 @@ Fuel availability :math:`f_{b}` is given as \begin{array}{cc} {} & {} \end{array}\begin{array}{c} {B_{ag} B_{up} } \end{array}\right\} \ , -where :math:`B_{ag}` (g C m\ :sup:`-2`) is the biomass of combined leaf, -stem, litter, and woody debris pools; :math:`B_{low}` = 105 g C m :sup:`-2` -is the lower fuel threshold below which fire does not occur; :math:`B_{up}` -= 1050 g C m\ :sup:`-2` is the upper fuel threshold above which fire -occurrence is not limited by fuel availability. +where :math:`B_{ag}` (g C m\ :sup:`-2`) is the biomass of combined leaf, stem, litter, and woody debris pools; :math:`B_{low}` = 105 g C m :sup:`-2` is the lower fuel threshold below which fire does not occur; :math:`B_{up}` = 1050 g C m\ :sup:`-2` is the upper fuel threshold above which fire occurrence is not limited by fuel availability. Fuel combustibility :math:`f_{m}` is estimated by @@ -108,23 +75,14 @@ Fuel combustibility :math:`f_{m}` is estimated by f_{m} = {f_{RH} f_{\beta}}, &\qquad T_{17cm} > T_{f} -where :math:`f_{RH}` and :math:`f_{\beta }` represent the dependence of -fuel combustibility on relative humidity :math:`RH` (%) and root-zone -soil moisture limitation :math:`\beta` (fraction); :math:`T_{17cm}` is -the temperature of the top 17 cm of soil (K) and :math:`T_{f}` is the -freezing temperature. :math:`f_{RH}` is a weighted average of real time -:math:`RH` (:math:`RH_{0}`) and 30-day running mean :math:`RH` -(:math:`RH_{30d}`): +where :math:`f_{RH}` and :math:`f_{\beta }` represent the dependence of fuel combustibility on relative humidity :math:`RH` (%) and root-zone soil moisture limitation :math:`\beta` (fraction); :math:`T_{17cm}` is the temperature of the top 17 cm of soil (K) and :math:`T_{f}` is the freezing temperature. :math:`f_{RH}` is a weighted average of real time :math:`RH` (:math:`RH_{0}`) and 30-day running mean :math:`RH` (:math:`RH_{30d}`): .. math:: :label: 23.8 f_{RH} = (1-w) l_{RH_{0}} + wl_{RH_{30d}} -where weight :math:`w=\max [0,\min (1,\frac{B_{ag}-2500}{2500})]`, -:math:`l_{{RH}_{0}}=1-\max [0,\min (1,\frac{RH_{0}-30}{80-30})]`, and -:math:`l_{{RH}_{30d}}=1-\max [0.75,\min (1,\frac{RH_{30d}}{90})]`. -:math:`f_{\beta}` is given by +where weight :math:`w=\max [0,\min (1,\frac{B_{ag}-2500}{2500})]`, :math:`l_{{RH}_{0}}=1-\max [0,\min (1,\frac{RH_{0}-30}{80-30})]`, and :math:`l_{{RH}_{30d}}=1-\max [0.75,\min (1,\frac{RH_{30d}}{90})]`. :math:`f_{\beta}` is given by .. math:: :label: 23.9 @@ -134,44 +92,30 @@ where weight :math:`w=\max [0,\min (1,\frac{B_{ag}-2500}{2500})]`, {0} & {} & {} & {\beta\ge \beta_{up} } \end{array}\right\} \ , -where :math:`\beta _{low}` \ =0.85 and :math:`\beta _{up}` \ =0.98 are the -lower and upper thresholds, respectively. +where :math:`\beta _{low}` \ =0.85 and :math:`\beta _{up}` \ =0.98 are the lower and upper thresholds, respectively. -For scarcely populated regions (:math:`D_{p} \le 0.1` person -km :sup:`-2`), we assume that anthropogenic suppression on fire -occurrence is negligible, i.e., :math:`f_{se,o} =1.0`. In regions of -:math:`D_{p} >0.1` person km\ :sup:`-2`, we parameterize the -fraction of anthropogenic and natural fires unsuppressed by human -activities as +For scarcely populated regions (:math:`D_{p} \le 0.1` person km :sup:`-2`), we assume that anthropogenic suppression on fire occurrence is negligible, i.e., :math:`f_{se,o} =1.0`. In regions of :math:`D_{p} >0.1` person km\ :sup:`-2`, we parameterize the fraction of anthropogenic and natural fires unsuppressed by human activities as .. math:: :label: 23.10 f_{se,o} =f_{d} f_{e} -where :math:`{f}_{d}` and :math:`{f}_{e}` are the effects of the -demographic and economic conditions on fire occurrence. The demographic -influence on fire occurrence is +where :math:`{f}_{d}` and :math:`{f}_{e}` are the effects of the demographic and economic conditions on fire occurrence. The demographic influence on fire occurrence is .. math:: :label: 23.11 f_{d} =0.01 + 0.98 \exp (-0.025D_{P} ). -For shrub and grass PFTs, the economic influence on fire occurrence is -parameterized as a function of Gross Domestic Product GDP (k 1995US$ -capita\ :sup:`-1`): +For shrub and grass PFTs, the economic influence on fire occurrence is parameterized as a function of Gross Domestic Product GDP (k 1995US$ capita\ :sup:`-1`): .. math:: :label: 23.12 f_{e} =0.1+0.9\times \exp [-\pi (\frac{GDP}{8} )^{0.5} ] -which captures 73% of the observed MODIS fire counts with variable GDP -in regions where shrub and grass PFTs are dominant (fractional coverage -of shrub and grass PFTs :math:`>` 50%). In regions outside tropical -closed forests and dominated by trees (fractional coverage of tree PFTs -:math:`>` 50%), we use +which captures 73% of the observed MODIS fire counts with variable GDP in regions where shrub and grass PFTs are dominant (fractional coverage of shrub and grass PFTs :math:`>` 50%). In regions outside tropical closed forests and dominated by trees (fractional coverage of tree PFTs :math:`>` 50%), we use .. math:: :label: 23.13 @@ -189,35 +133,23 @@ to reproduce the relationship between MODIS fire counts and GDP. Average spread area of a fire ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Fire fighting capacity depends on socioeconomic conditions and affects -fire spread area. Due to a lack of observations, we consider the -socioeconomic impact on the average burned area rather than separately -on fire spread rate and fire duration: +Fire fighting capacity depends on socioeconomic conditions and affects fire spread area. Due to a lack of observations, we consider the socioeconomic impact on the average burned area rather than separately on fire spread rate and fire duration: .. math:: :label: 23.14 a=a^{*} F_{se} -where :math:`a^{*}` is the average burned area of a fire without -anthropogenic suppression and :math:`F_{se}` is the socioeconomic -effect on fire spread area. +where :math:`a^{*}` is the average burned area of a fire without anthropogenic suppression and :math:`F_{se}` is the socioeconomic effect on fire spread area. -Average burned area of a fire without anthropogenic suppression is -assumed elliptical in shape with the wind direction along the major axis -and the point of ignition at one of the foci. According to the area -formula for an ellipse, average burned area of a fire can be represented -as: +Average burned area of a fire without anthropogenic suppression is assumed elliptical in shape with the wind direction along the major axis and the point of ignition at one of the foci. According to the area formula for an ellipse, average burned area of a fire can be represented as: .. math:: :label: 23.15 a^{*} =\pi \frac{l}{2} \frac{w}{2} \times 10^{-6} =\frac{\pi u_{p}^{2} \tau ^{2} }{4L_{B} } (1+\frac{1}{H_{B} } )^{2} \times 10^{-6} -where :math:`u_{p}` (m s\ :sup:`-1`) is the fire spread rate in the -downwind direction; :math:`\tau` (s) is average fire duration; :math:`L_{B}` -and :math:`H_{B}` are length-to-breadth ratio and head-to-back ratio of -the ellipse; 10 :sup:`-6` converts m :sup:`2` to km :sup:`2`. +where :math:`u_{p}` (m s\ :sup:`-1`) is the fire spread rate in the downwind direction; :math:`\tau` (s) is average fire duration; :math:`L_{B}` and :math:`H_{B}` are length-to-breadth ratio and head-to-back ratio of the ellipse; 10 :sup:`-6` converts m :sup:`2` to km :sup:`2`. According to :ref:`Arora and Boer (2005)`, @@ -226,9 +158,7 @@ According to :ref:`Arora and Boer (2005)`, L_{B} =1.0+10.0[1-\exp (-0.06W)] -where :math:`W`\ (m s\ :sup:`-1`) is the wind speed. According to -the mathematical properties of the ellipse, the head-to-back ratio -:math:`H_{B}` is +where :math:`W`\ (m s\ :sup:`-1`) is the wind speed. According to the mathematical properties of the ellipse, the head-to-back ratio :math:`H_{B}` is .. math:: :label: 23.17 @@ -242,53 +172,30 @@ The fire spread rate in the downwind direction is represented as u_{p} =u_{\max } C_{m} g(W) -(:ref:`Arora and Boer, 2005`), where :math:`u_{\max }` -(m s\ :sup:`-1`) is the PFT-dependent average maximum fire spread -rate in natural vegetation regions; :math:`C_{m} =\sqrt{f_{m}}` and :math:`g(W)` -represent the dependence of :math:`u_{p}` on fuel wetness and wind -speed :math:`W`, respectively. :math:`u_{\max }` is set to 0.33 -m s :sup:`-1`\ for grass PFTs, 0.28 m s :sup:`-1` for shrub PFTs, 0.26 -m s\ :sup:`-1` for needleleaf tree PFTs, and 0.25 m s\ :sup:`-1` for -other tree PFTs. :math:`g(W)` is derived from the mathematical properties -of the ellipse and equation :eq:`23.16` and :eq:`23.17`. +(:ref:`Arora and Boer, 2005`), where :math:`u_{\max }` (m s\ :sup:`-1`) is the PFT-dependent average maximum fire spread rate in natural vegetation regions; :math:`C_{m} =\sqrt{f_{m}}` and :math:`g(W)` represent the dependence of :math:`u_{p}` on fuel wetness and wind speed :math:`W`, respectively. :math:`u_{\max }` is set to 0.33 m s :sup:`-1`\ for grass PFTs, 0.28 m s :sup:`-1` for shrub PFTs, 0.26 m s\ :sup:`-1` for needleleaf tree PFTs, and 0.25 m s\ :sup:`-1` for other tree PFTs. :math:`g(W)` is derived from the mathematical properties of the ellipse and equation :eq:`23.16` and :eq:`23.17`. .. math:: :label: 23.19 g(W)=\frac{2L_{B} }{1+\frac{1}{H_{B} } } g(0). -Since g(\ *W*)=1.0, and \ :math:`L_{B}` and :math:`H_{B}` are at their -maxima \ :math:`L_{B} ^{\max } =11.0` and \ :math:`H_{B} ^{\max } =482.0` -when :math:`W\to \infty` , g(0) can be derived as +Since g(\ *W*)=1.0, and \ :math:`L_{B}` and :math:`H_{B}` are at their maxima \ :math:`L_{B} ^{\max } =11.0` and \ :math:`H_{B} ^{\max } =482.0` when :math:`W\to \infty`, g(0) can be derived as .. math:: :label: 23.20 g(0)=\frac{1+\frac{1}{H_{B} ^{\max } } }{2L_{B} ^{\max } } =0.05. -In the absence of globally gridded data on barriers to fire (e.g. -rivers, lakes, roads, firebreaks) and human fire-fighting efforts, -average fire duration is simply assumed equal to 1 which is the observed -2001–2004 mean persistence of most fires in the world -(:ref:`Giglio et al. 2006 `). +In the absence of globally gridded data on barriers to fire (e.g. rivers, lakes, roads, firebreaks) and human fire-fighting efforts, average fire duration is simply assumed equal to 1 which is the observed 2001–2004 mean persistence of most fires in the world (:ref:`Giglio et al. 2006 `). -As with the socioeconomic influence on fire occurrence, we assume that -the socioeconomic influence on fire spreading is negligible in regions -of :math:`D_{p} \le 0.1` person km\ :sup:`-2`, i.e., -:math:`F_{se} = 1.0`. In regions of :math:`D_{p} >0.1` person -km\ :sup:`-2`, we parameterize such socioeconomic influence as: +As with the socioeconomic influence on fire occurrence, we assume that the socioeconomic influence on fire spreading is negligible in regions of :math:`D_{p} \le 0.1` person km\ :sup:`-2`, i.e., :math:`F_{se} = 1.0`. In regions of :math:`D_{p} >0.1` person km\ :sup:`-2`, we parameterize such socioeconomic influence as: .. math:: :label: 23.21 F_{se} =F_{d} F_{e} -where :math:`{F}_{d}` and :math:`{F}_{e}` are -effects of the demographic and economic conditions on the average spread -area of a fire, and are identified by maximizing the explained -variability of the GFED3 burned area fraction with both socioeconomic -indices in grid cells with various dominant vegetation types. For shrub -and grass PFTs, the demographic impact factor is +where :math:`{F}_{d}` and :math:`{F}_{e}` are effects of the demographic and economic conditions on the average spread area of a fire, and are identified by maximizing the explained variability of the GFED3 burned area fraction with both socioeconomic indices in grid cells with various dominant vegetation types. For shrub and grass PFTs, the demographic impact factor is .. math:: :label: 23.22 @@ -302,8 +209,7 @@ and the economic impact factor is F_{e} =0.2+0.8\times \exp (-\pi \frac{GDP}{7} ). -For tree PFTs outside tropical closed forests, the demographic and -economic impact factors are given as +For tree PFTs outside tropical closed forests, the demographic and economic impact factors are given as .. math:: :label: 23.24 @@ -320,74 +226,46 @@ and {1,} & {GDP\le 8} \end{array}\right. . -Equations :eq:`23.22` - :eq:`23.25` reflect that more developed and more -densely populated regions have a higher fire fighting capability. +Equations :eq:`23.22` - :eq:`23.25` reflect that more developed and more densely populated regions have a higher fire fighting capability. .. _Fire impact: Fire impact ^^^^^^^^^^^^^^^^^^ -In post-fire regions, we calculate PFT-level fire carbon emissions from -biomass burning of the :math:`j`\ th PFT, :math:`{\phi}_{j}` (g C s\ :sup:`-1`), as +In post-fire regions, we calculate PFT-level fire carbon emissions from biomass burning of the :math:`j`\ th PFT, :math:`{\phi}_{j}` (g C s\ :sup:`-1`), as .. math:: :label: 23.26 \phi _{j} =A_{b,j} \mathbf{C}_{j} \bullet \mathbf{CC}_{j} -where :math:`A_{b,j}` (km\ :sup:`2` \s\ :sup:`-1`) is burned area for -the :math:`j`\ th PFT; **C**\ :sub:`j` =(:math:`C_{leaf}`, :math:`C_{stem}`, -:math:`C_{root}`, :math:`C_{ts}`) is a vector with carbon density (g C km -:sup:`-2`) for leaf, stem (live and dead stem), root (fine, live coarse -and dead coarse root), and transfer and storage carbon pools as elements; -:math:`\mathbf{CC}_{j}` = (:math:`\mathbf{CC}_{leaf}`, -:math:`\mathbf{CC}_{stem}`, :math:`\mathbf{CC}_{root}`, :math:`\mathbf{CC}_{ts}`) -is the corresponding combustion completeness factor vector -(:numref:`Table PFT-specific combustion completeness and fire mortality factors`). -Moreover, we assume that 50% and 28% of column-level litter and coarse woody -debris are burned and the corresponding carbon is transferred to atmosphere. - -Tissue mortality due to fire leads to carbon transfers in two ways. -First, carbon from uncombusted leaf, live stem, dead stem, root, and -transfer and storage pools -:math:`\mathbf{C^{'} _{j1}} ={(C_{{leaf}} (1-CC_{{leaf}} ) ,C_{{livestem}} (1-CC_{{stem}} ) ,C_{{deadstem}} (1-CC_{{stem}} ),C_{{root}} (1-CC_{{root}} ),C_{{ts}} (1-CC_{{ts}} ))}_{j}` -(g C km\ :sup:`-2`) is transferred to litter as +where :math:`A_{b,j}` (km\ :sup:`2` \s\ :sup:`-1`) is burned area for the :math:`j`\ th PFT; **C**\ :sub:`j` =(:math:`C_{leaf}`, :math:`C_{stem}`, :math:`C_{root}`, :math:`C_{ts}`) is a vector with carbon density (g C km :sup:`-2`) for leaf, stem (live and dead stem), root (fine, live coarse and dead coarse root), and transfer and storage carbon pools as elements; :math:`\mathbf{CC}_{j}` = (:math:`\mathbf{CC}_{leaf}`, :math:`\mathbf{CC}_{stem}`, :math:`\mathbf{CC}_{root}`, :math:`\mathbf{CC}_{ts}`) is the corresponding combustion completeness factor vector (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). Moreover, we assume that 50% and 28% of column-level litter and coarse woody debris are burned and the corresponding carbon is transferred to atmosphere. + +Tissue mortality due to fire leads to carbon transfers in two ways. First, carbon from uncombusted leaf, live stem, dead stem, root, and transfer and storage pools :math:`\mathbf{C^{'} _{j1}} ={(C_{{leaf}} (1-CC_{{leaf}} ),C_{{livestem}} (1-CC_{{stem}} ),C_{{deadstem}} (1-CC_{{stem}} ),C_{{root}} (1-CC_{{root}} ),C_{{ts}} (1-CC_{{ts}} ))}_{j}` (g C km\ :sup:`-2`) is transferred to litter as .. math:: :label: 23.27 \Psi _{j1} =\frac{A_{b,j} }{f_{j} A_{g} } \mathbf{C^{'} _{j1}} \bullet M_{j1} -where -:math:`M_{j1} =(M_{{leaf}} ,M_{{livestem,1}} ,M_{{deadstem}} ,M_{{root}} ,M_{{ts}} )_{j}` -is the corresponding mortality factor vector (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). Second, -carbon from uncombusted live stems is transferred to dead stems as: +where :math:`M_{j1} =(M_{{leaf}},M_{{livestem,1}},M_{{deadstem}},M_{{root}},M_{{ts}} )_{j}` is the corresponding mortality factor vector (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). Second, carbon from uncombusted live stems is transferred to dead stems as: .. math:: :label: 23.28 \Psi _{j2} =\frac{A_{b,j} }{f_{j} A_{g} } C_{livestem} (1-CC_{stem} )M_{livestem,2} -where :math:`M_{livestem,2}` is the corresponding mortality factor -(:numref:`Table PFT-specific combustion completeness and fire mortality factors`). +where :math:`M_{livestem,2}` is the corresponding mortality factor (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). -Fire nitrogen emissions and nitrogen transfers due to fire-induced -mortality are calculated the same way as for carbon, using the same -values for combustion completeness and mortality factors. With CLM's -dynamic vegetation option enabled, the number of tree PFT individuals -killed by fire per km\ :sup:`2` (individual km\ :sup:`-2` -s\ :sup:`-1`) is given by +Fire nitrogen emissions and nitrogen transfers due to fire-induced mortality are calculated the same way as for carbon, using the same values for combustion completeness and mortality factors. With CLM's dynamic vegetation option enabled, the number of tree PFT individuals killed by fire per km\ :sup:`2` (individual km\ :sup:`-2` s\ :sup:`-1`) is given by .. math:: :label: 23.29 P_{disturb,j} =\frac{A_{b,j} }{f_{j} A_{g} } P_{j} \xi _{j} -where :math:`P_{j}` (individual km\ :sup:`-2`) is the population -density for the :math:`j` th tree PFT and :math:`\xi _{j}` is the -whole-plant mortality factor -(:numref:`Table PFT-specific combustion completeness and fire mortality factors`). +where :math:`P_{j}` (individual km\ :sup:`-2`) is the population density for the :math:`j` th tree PFT and :math:`\xi _{j}` is the whole-plant mortality factor (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). .. _Agricultural fires: @@ -401,14 +279,7 @@ The burned area of cropland (km\ :sup:`2` s\ :sup:`-1`) is taken as :math:`{A}_{ A_{b} =a_{1} f_{se} f_{t} f_{crop} A_{g} -where :math:`a_{1}` (s\ :sup:`-1`) is a constant; :math:`f_{se}` represents -the socioeconomic effect on fires; :math:`f_{t}` determines the seasonality -of agricultural fires; :math:`f_{crop}` is the fractional coverage of -cropland. :math:`a_{1}` \ = 1.6x10\ :sup:`-4` \hr\ :sup:`-1`\ is estimated -using an inverse method, by matching 1997-2004 simulations to the analysis -of :ref:`van der Werf et al. (2010) ` that shows the -2001-2009 average contribution of cropland fires is 4.7% of the total -global burned area. +where :math:`a_{1}` (s\ :sup:`-1`) is a constant; :math:`f_{se}` represents the socioeconomic effect on fires; :math:`f_{t}` determines the seasonality of agricultural fires; :math:`f_{crop}` is the fractional coverage of cropland. :math:`a_{1}` \ = 1.6x10\ :sup:`-4` \hr\ :sup:`-1`\ is estimated using an inverse method, by matching 1997-2004 simulations to the analysis of :ref:`van der Werf et al. (2010) ` that shows the 2001-2009 average contribution of cropland fires is 4.7% of the total global burned area. The socioeconomic factor :math:`f_{se}` is given as follows: @@ -431,59 +302,32 @@ and f_{e} =0.01+0.99\times \exp (-\pi \frac{GDP}{10} ) -are the effects of population density and GDP on burned area, derived -in a similar way to equation :eq:`23.32` and :eq:`23.33`. :math:`f_{t}` -is set to 1 at the first time step during the climatological peak month -for agricultural fires (:ref:`van der Werf et al. 2010 `); -:math:`{f}_{t}` is set to 0 otherwise. Peak -month in this dataset correlates with the month after harvesting or the -month before planting. In CLM we use this dataset the same way whether -the CROP option is active or not, without regard to the CROP option's -simulated planting and harvesting dates. - -In the post-fire region, fire impact is parameterized similar to section -:numref:`Fire impact` but with combustion completeness factors and tissue -mortality factors for crop PFTs -(:numref:`Table PFT-specific combustion completeness and fire mortality factors`). +are the effects of population density and GDP on burned area, derived in a similar way to equation :eq:`23.32` and :eq:`23.33`. :math:`f_{t}` is set to 1 at the first time step during the climatological peak month for agricultural fires (:ref:`van der Werf et al. 2010 `); :math:`{f}_{t}` is set to 0 otherwise. Peak month in this dataset correlates with the month after harvesting or the month before planting. In CLM we use this dataset the same way whether the CROP option is active or not, without regard to the CROP option's simulated planting and harvesting dates. + +In the post-fire region, fire impact is parameterized similar to section :numref:`Fire impact` but with combustion completeness factors and tissue mortality factors for crop PFTs (:numref:`Table PFT-specific combustion completeness and fire mortality factors`). .. _Deforestation fires: Deforestation fires ------------------------ -CLM focuses on deforestation fires in tropical closed forests. Tropical -closed forests are defined as grid cells with tropical tree (BET and BDT tropical) -coverage :math:`>` 60% according to the FAO classification. Deforestation fires -are defined as fires caused by deforestation, including escaped -deforestation fires, termed degradation fires. Deforestation and -degradation fires are assumed to occur outside of cropland areas in -these grid cells. Burned area is controlled by the deforestation rate -and climate: +CLM focuses on deforestation fires in tropical closed forests. Tropical closed forests are defined as grid cells with tropical tree (BET and BDT tropical) coverage :math:`>` 60% according to the FAO classification. Deforestation fires are defined as fires caused by deforestation, including escaped deforestation fires, termed degradation fires. Deforestation and degradation fires are assumed to occur outside of cropland areas in these grid cells. Burned area is controlled by the deforestation rate and climate: .. math:: :label: 23.34 A_{b} = b \ f_{lu} f_{cli,d} f_{b} A_{g} -where :math:`b` (s\ :sup:`-1`) is a global constant; -:math:`f_{lu}` (fraction) represents the effect of decreasing -fractional coverage of tree PFTs derived from land use data; -:math:`f_{cli,d}` (fraction) represents the effect of climate -conditions on the burned area. +where :math:`b` (s\ :sup:`-1`) is a global constant; :math:`f_{lu}` (fraction) represents the effect of decreasing fractional coverage of tree PFTs derived from land use data; :math:`f_{cli,d}` (fraction) represents the effect of climate conditions on the burned area. -Constants :math:`b` and :math:`{f}_{lu}` are calibrated -based on observations and reanalysis datasets in the Amazon rainforest -(tropical closed forests within 15.5 :sup:`o` S :math:`\text{-}` 10.5 -:sup:`o` N, 30.5 :sup:`o` W :math:`\text{-}` 91 :sup:`o` W). -:math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as +Constants :math:`b` and :math:`{f}_{lu}` are calibrated based on observations and reanalysis datasets in the Amazon rainforest (tropical closed forests within 15.5 :sup:`o` S :math:`\text{-}` 10.5 :sup:`o` N, 30.5 :sup:`o` W :math:`\text{-}` 91 :sup:`o` W). :math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as .. math:: :label: 23.35 f_{lu} = \max (0.0005,0.19D-0.001) -where :math:`D` (yr\ :sup:`-1`) is the annual loss of tree cover -based on CLM land use and land cover change data. +where :math:`D` (yr\ :sup:`-1`) is the annual loss of tree cover based on CLM land use and land cover change data. The effect of climate on deforestation fires is parameterized as: @@ -496,47 +340,9 @@ The effect of climate on deforestation fires is parameterized as: & \quad \max \left[0,\min (1,\frac{0.25-P}{0.25} )\right] \end{array} -where :math:`P` (mm d :sup:`-1`) is instantaneous precipitation, while -:math:`P_{60d}` (mm d\ :sup:`-1`) and :math:`P_{10d}` (mm d :sup:`-1`) -are 60-day and 10-day running means of precipitation, respectively; -:math:`b_{2}` (mm d :sup:`-1`) and :math:`b_{3}` (mm d :sup:`-1`) are -the grid-cell dependent thresholds of :math:`P_{60d}` and :math:`P_{10d}` ; -0.25 mm d :sup:`-1` is the maximum precipitation rate for drizzle. -:ref:`Le Page et al. (2010) ` analyzed the relationship -between large-scale deforestation fire counts and precipitation during 2003 -:math:`\text{-}`\ 2006 in southern Amazonia where tropical evergreen trees -(BET Tropical) are dominant. Figure 2 in -:ref:`Le Page et al. (2010) ` showed that fires generally -occurred if both :math:`P_{60d}` and :math:`P_{10d}` were less than about -4.0 mm d :sup:`-1`, and fires occurred more frequently in a drier environment. -Based on the 30-yr (1985 to 2004) precipitation data in -:ref:`Qian et al. (2006) `. The climatological precipitation -of dry months (P < 4.0 mm d :sup:`-1`) in a year over tropical deciduous -tree (BDT Tropical) dominated regions is 46% of that over BET Tropical -dominated regions, so we set the PFT-dependent thresholds of :math:`P_{60d}` -and :math:`P_{10d}` as 4.0 mm d :sup:`-1` for BET Tropical and 1.8 mm d -:sup:`-1` (= 4.0 mm d :sup:`-1` :math:`\times` 46%) for BDT Tropical, and -:math:`b`\ :sub:`2` and :math:`b`\ :sub:`3` are the average of thresholds -of BET Tropical and BDT Tropical weighted bytheir coverage. - -The post-fire area due to deforestation is not limited to land-type -conversion regions. In the tree-reduced region, the maximum fire carbon -emissions are assumed to be 80% of the total conversion flux. According -to the fraction of conversion flux for tropical trees in the -tree-reduced region (60%) assigned by CLM4-CN, to reach the maximum fire -carbon emissions in a conversion region requires burning this region -about twice when we set PFT-dependent combustion completeness factors to -about 0.3 for stem [the mean of 0.2\ :math:`{-}`\ 0.4 used in -:ref:`van der Werf et al. (2010) `. Therefore, when -the burned area calculated from equation :eq:`23.36` is -no more than twice the tree-reduced area, we assume no escaped fires -outside the land-type conversion region, and the fire-related fraction -of the total conversion flux is estimated as -:math:`\frac{A_{b} /A_{g} }{2D}` . Otherwise, 80% of the total -conversion flux is assumed to be fire carbon emissions, and the biomass -combustion and vegetation mortality outside the tree-reduced regions -with an area fraction of :math:`\frac{A_{b} }{A_{g} } -2D` are set as in -section :numref:`Fire impact`. +where :math:`P` (mm d :sup:`-1`) is instantaneous precipitation, while :math:`P_{60d}` (mm d\ :sup:`-1`) and :math:`P_{10d}` (mm d :sup:`-1`) are 60-day and 10-day running means of precipitation, respectively; :math:`b_{2}` (mm d :sup:`-1`) and :math:`b_{3}` (mm d :sup:`-1`) are the grid-cell dependent thresholds of :math:`P_{60d}` and :math:`P_{10d}`; 0.25 mm d :sup:`-1` is the maximum precipitation rate for drizzle. :ref:`Le Page et al. (2010) ` analyzed the relationship between large-scale deforestation fire counts and precipitation during 2003 :math:`\text{-}`\ 2006 in southern Amazonia where tropical evergreen trees (BET Tropical) are dominant. Figure 2 in :ref:`Le Page et al. (2010) ` showed that fires generally occurred if both :math:`P_{60d}` and :math:`P_{10d}` were less than about 4.0 mm d :sup:`-1`, and fires occurred more frequently in a drier environment. Based on the 30-yr (1985 to 2004) precipitation data in :ref:`Qian et al. (2006) `. The climatological precipitation of dry months (P < 4.0 mm d :sup:`-1`) in a year over tropical deciduous tree (BDT Tropical) dominated regions is 46% of that over BET Tropical dominated regions, so we set the PFT-dependent thresholds of :math:`P_{60d}` and :math:`P_{10d}` as 4.0 mm d :sup:`-1` for BET Tropical and 1.8 mm d :sup:`-1` (= 4.0 mm d :sup:`-1` :math:`\times` 46%) for BDT Tropical, and :math:`b`\ :sub:`2` and :math:`b`\ :sub:`3` are the average of thresholds of BET Tropical and BDT Tropical weighted bytheir coverage. + +The post-fire area due to deforestation is not limited to land-type conversion regions. In the tree-reduced region, the maximum fire carbon emissions are assumed to be 80% of the total conversion flux. According to the fraction of conversion flux for tropical trees in the tree-reduced region (60%) assigned by CLM4-CN, to reach the maximum fire carbon emissions in a conversion region requires burning this region about twice when we set PFT-dependent combustion completeness factors to about 0.3 for stem [the mean of 0.2\ :math:`{-}`\ 0.4 used in :ref:`van der Werf et al. (2010) `. Therefore, when the burned area calculated from equation :eq:`23.36` is no more than twice the tree-reduced area, we assume no escaped fires outside the land-type conversion region, and the fire-related fraction of the total conversion flux is estimated as :math:`\frac{A_{b} /A_{g} }{2D}`. Otherwise, 80% of the total conversion flux is assumed to be fire carbon emissions, and the biomass combustion and vegetation mortality outside the tree-reduced regions with an area fraction of :math:`\frac{A_{b} }{A_{g} } -2D` are set as in section :numref:`Fire impact`. .. _Peat fires: @@ -550,20 +356,9 @@ The burned area due to peat fires is given as :math:`{A}_{b}`: A_{b} = c \ f_{cli,p} f_{peat} (1 - f_{sat} ) A_{g} -where :math:`c` (s\ :sup:`-1`) is a constant; :math:`f_{cli,p}` represents -the effect of climate on the burned area; :math:`f_{peat}` is the fractional -coverage of peatland in the grid cell; and :math:`f_{sat}` is the fraction -of the grid cell with a water table at the surface or higher. :math:`c` = 0.17 -:math:`\times` 10 :sup:`-3` hr\ :sup:`-1` for tropical peat fires and -:math:`c` = 0.9 :math:`\times` 10 :sup:`-5` hr :sup:`-1` for boreal peat fires -are derived using an inverse method, by matching simulations to earlier -studies: about 2.4 Mha peatland was burned over Indonesia in 1997 -(:ref:`Page et al. 2002 `) and the average burned area of peat -fires in Western Canada was 0.2 Mha yr :sup:`-1` for 1980-1999 -(:ref:`Turetsky et al. 2004 `). +where :math:`c` (s\ :sup:`-1`) is a constant; :math:`f_{cli,p}` represents the effect of climate on the burned area; :math:`f_{peat}` is the fractional coverage of peatland in the grid cell; and :math:`f_{sat}` is the fraction of the grid cell with a water table at the surface or higher. :math:`c` = 0.17 :math:`\times` 10 :sup:`-3` hr\ :sup:`-1` for tropical peat fires and :math:`c` = 0.9 :math:`\times` 10 :sup:`-5` hr :sup:`-1` for boreal peat fires are derived using an inverse method, by matching simulations to earlier studies: about 2.4 Mha peatland was burned over Indonesia in 1997 (:ref:`Page et al. 2002 `) and the average burned area of peat fires in Western Canada was 0.2 Mha yr :sup:`-1` for 1980-1999 (:ref:`Turetsky et al. 2004 `). -For tropical peat fires, :math:`f_{cli,p}` is set as a function of -long-term precipitation :math:`P_{60d}` : +For tropical peat fires, :math:`f_{cli,p}` is set as a function of long-term precipitation :math:`P_{60d}` : .. math:: :label: 23.38 @@ -579,46 +374,24 @@ For boreal peat fires, :math:`f_{cli,p}` is set to where :math:`\theta _{17cm}` is the wetness of the top 17 cm of soil. -Peat fires lead to peat burning and the combustion and mortality of -vegetation over peatlands. For tropical peat fires, based on -:ref:`Page et al. (2002) `, about 6% of the peat carbon loss -from stored carbon is caused by 33.9% of the peatland burned. Carbon emissions -due to peat burning (g C m\ :sup:`-2` s\ :sup:`-1`) are therefore set as the -product of 6%/33.9%, burned area fraction of peat fire (s\ :sup:`-1`), and -soil organic carbon (g C m\ :sup:`-2`). For boreal peat fires, the carbon -emissions due to peat burning are set as 2.2 kg C m\ :sup:`-2` \ peat fire -area (:ref:`Turetsky et al. 2002 `). Biomass combustion -and vegetation mortality in post-fire peatlands are set the same as section -:numref:`Fire impact` for non-crop PFTs and as section -:numref:`Agricultural fires` for crops PFTs. +Peat fires lead to peat burning and the combustion and mortality of vegetation over peatlands. For tropical peat fires, based on :ref:`Page et al. (2002) `, about 6% of the peat carbon loss from stored carbon is caused by 33.9% of the peatland burned. Carbon emissions due to peat burning (g C m\ :sup:`-2` s\ :sup:`-1`) are therefore set as the product of 6%/33.9%, burned area fraction of peat fire (s\ :sup:`-1`), and soil organic carbon (g C m\ :sup:`-2`). For boreal peat fires, the carbon emissions due to peat burning are set as 2.2 kg C m\ :sup:`-2` \ peat fire area (:ref:`Turetsky et al. 2002 `). Biomass combustion and vegetation mortality in post-fire peatlands are set the same as section :numref:`Fire impact` for non-crop PFTs and as section :numref:`Agricultural fires` for crops PFTs. .. _Fire trace gas and aerosol emissions: Fire trace gas and aerosol emissions ------------------------------------- -CESM2 is the first Earth system model that can model the full coupling -among fire, fire emissions, land, and atmosphere. CLM5, as the land -component of CESM2, calculates the surface trace gas and aerosol emissions -due to fire and fire emission heights, as the inputs of atmospheric -chemistry model and aerosol model. +CESM2 is the first Earth system model that can model the full coupling among fire, fire emissions, land, and atmosphere. CLM5, as the land component of CESM2, calculates the surface trace gas and aerosol emissions due to fire and fire emission heights, as the inputs of atmospheric chemistry model and aerosol model. -Emissions for trace gas and aerosol species x and the j-th PFT, :math:`E_{x,j}` -(g species s\ :sup:`-1`), are given by +Emissions for trace gas and aerosol species x and the j-th PFT, :math:`E_{x,j}` (g species s\ :sup:`-1`), are given by .. math:: :label: 23.40 E_{x,j} = EF_{x,j}\frac{\phi _{j} }{[C]}. -Here, :math:`EF_{x,j}` (g species (g dm)\ :sup:`-1`) is PFT-dependent emission -factor scaled from biome-level values (Li et al., in prep, also used for FireMIP -fire emissions data) by Dr. Val Martin and Dr. Li. :math:`[C]` = 0.5 -(g C (g dm)\ :sup:`-1`) is a conversion factor from dry matter to carbon. +Here, :math:`EF_{x,j}` (g species (g dm)\ :sup:`-1`) is PFT-dependent emission factor scaled from biome-level values (Li et al., in prep, also used for FireMIP fire emissions data) by Dr. Val Martin and Dr. Li. :math:`[C]` = 0.5 (g C (g dm)\ :sup:`-1`) is a conversion factor from dry matter to carbon. -Emission height is PFT-dependent: 4.3 km for needleleaf tree PFTs, 3 km for other -boreal and temperate tree PFTs, 2.5 km for tropical tree PFTs, 2 km for shrub -PFTs, and 1 km for grass and crop PFTs. These values are compiled from earlier -studies by Dr. Val Martin. +Emission height is PFT-dependent: 4.3 km for needleleaf tree PFTs, 3 km for other boreal and temperate tree PFTs, 2.5 km for tropical tree PFTs, 2 km for shrub PFTs, and 1 km for grass and crop PFTs. These values are compiled from earlier studies by Dr. Val Martin. .. _Table PFT-specific combustion completeness and fire mortality factors: @@ -658,13 +431,4 @@ studies by Dr. Val Martin. | Crop | 0.80 | 0.80 | 0.00 | 0.80 | 0.80 | 0.20 | 0.20 | 0.20 | 0.80 | 0.60 | 0.20 | +----------------------------------+---------------------------+---------------------------+---------------------------+-------------------------+--------------------------+------------------------------+------------------------------+--------------------------+------------------------+------------------------------+---------------------------------+ -Leaves (:math:`CC_{leaf}` ), stems (:math:`CC_{stem}` ), -roots (:math:`CC_{root}` ) , and transfer and storage carbon -(:math:`CC_{ts}` ); mortality factors for leaves -(:math:`M_{leaf}` ), live stems (:math:`M_{livestem,1}` ), -dead stems (:math:`M_{deadstem}` ), roots -(:math:`M_{root}` ), and transfer and storage carbon -(:math:`M_{ts}` ) related to the carbon transfers from these pools -to litter pool; mortality factors for live stems -(:math:`M_{livestem,2}` ) related to the carbon transfer from live -stems to dead stems; whole-plant mortality factor (:math:`\xi _{j}` ). +Leaves (:math:`CC_{leaf}` ), stems (:math:`CC_{stem}` ), roots (:math:`CC_{root}` ), and transfer and storage carbon (:math:`CC_{ts}` ); mortality factors for leaves (:math:`M_{leaf}` ), live stems (:math:`M_{livestem,1}` ), dead stems (:math:`M_{deadstem}` ), roots (:math:`M_{root}` ), and transfer and storage carbon (:math:`M_{ts}` ) related to the carbon transfers from these pools to litter pool; mortality factors for live stems (:math:`M_{livestem,2}` ) related to the carbon transfer from live stems to dead stems; whole-plant mortality factor (:math:`\xi _{j}` ). diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index 4a69a4a90d..01f609b0a1 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -3,17 +3,7 @@ Momentum, Sensible Heat, and Latent Heat Fluxes ================================================== -The zonal :math:`\tau _{x}` and meridional :math:`\tau _{y}` momentum -fluxes (kg m\ :sup:`-1` s\ :sup:`-2`), sensible heat flux -:math:`H` (W m\ :sup:`-2`), and water vapor flux :math:`E` (kg m\ :sup:`-2` s\ :sup:`-1`) between the atmosphere at -reference height :math:`z_{atm,\, x}` (m) [where :math:`x` is height -for wind (momentum) (:math:`m`), temperature (sensible heat) -(:math:`h`), and humidity (water vapor) (:math:`w`); with zonal and -meridional winds :math:`u_{atm}` and :math:`v_{atm}` (m -s\ :sup:`-1`), potential temperature :math:`\theta _{atm}` (K), -and specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`)] and the -surface [with :math:`u_{s}` , :math:`v_{s}` , :math:`\theta _{s}` , and -:math:`q_{s}` ] are +The zonal :math:`\tau _{x}` and meridional :math:`\tau _{y}` momentum fluxes (kg m\ :sup:`-1` s\ :sup:`-2`), sensible heat flux :math:`H` (W m\ :sup:`-2`), and water vapor flux :math:`E` (kg m\ :sup:`-2` s\ :sup:`-1`) between the atmosphere at reference height :math:`z_{atm,\, x}` (m) [where :math:`x` is height for wind (momentum) (:math:`m`), temperature (sensible heat) (:math:`h`), and humidity (water vapor) (:math:`w`); with zonal and meridional winds :math:`u_{atm}` and :math:`v_{atm}` (m s\ :sup:`-1`), potential temperature :math:`\theta _{atm}` (K), and specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`)] and the surface [with :math:`u_{s}`, :math:`v_{s}`, :math:`\theta _{s}`, and :math:`q_{s}` ] are .. math:: :label: 5.1 @@ -35,14 +25,7 @@ surface [with :math:`u_{s}` , :math:`v_{s}` , :math:`\theta _{s}` , and E=-\rho _{atm} \frac{\left(q_{atm} -q_{s} \right)}{r_{aw} } . -These fluxes are derived in the next section from Monin-Obukhov -similarity theory developed for the surface layer (i.e., the nearly -constant flux layer above the surface sublayer). In this derivation, -:math:`u_{s}` and :math:`v_{s}` are defined to equal zero at height -:math:`z_{0m} +d` (the apparent sink for momentum) so that -:math:`r_{am}` is the aerodynamic resistance (s m\ :sup:`-1`) for -momentum between the atmosphere at height :math:`z_{atm,\, m}` and the -surface at height :math:`z_{0m} +d`. Thus, the momentum fluxes become +These fluxes are derived in the next section from Monin-Obukhov similarity theory developed for the surface layer (i.e., the nearly constant flux layer above the surface sublayer). In this derivation, :math:`u_{s}` and :math:`v_{s}` are defined to equal zero at height :math:`z_{0m} +d` (the apparent sink for momentum) so that :math:`r_{am}` is the aerodynamic resistance (s m\ :sup:`-1`) for momentum between the atmosphere at height :math:`z_{atm,\, m}` and the surface at height :math:`z_{0m} +d`. Thus, the momentum fluxes become .. math:: :label: 5.5 @@ -54,40 +37,21 @@ surface at height :math:`z_{0m} +d`. Thus, the momentum fluxes become \tau _{y} =-\rho _{atm} \frac{v_{atm} }{r_{am} } . -Likewise, :math:`\theta _{s}` and :math:`q_{s}` are defined at -heights :math:`z_{0h} +d` and :math:`z_{0w} +d` (the apparent sinks for -heat and water vapor, respectively - -:math:`r_{aw}` are the aerodynamic resistances (s m\ :sup:`-1`) -to sensible heat and water vapor transfer between the atmosphere at -heights :math:`z_{atm,\, h}` and :math:`z_{atm,\, w}` and the surface -at heights :math:`z_{0h} +d` and :math:`z_{0w} +d`, respectively. The -specific heat capacity of air :math:`C_{p}` (J kg\ :sup:`-1` -K\ :sup:`-1`) is a constant (:numref:`Table Physical constants`). The atmospheric potential -temperature used here is +Likewise, :math:`\theta _{s}` and :math:`q_{s}` are defined at heights :math:`z_{0h} +d` and :math:`z_{0w} +d` (the apparent sinks for heat and water vapor, respectively :math:`r_{aw}` are the aerodynamic resistances (s m\ :sup:`-1`) to sensible heat and water vapor transfer between the atmosphere at heights :math:`z_{atm,\, h}` and :math:`z_{atm,\, w}` and the surface at heights :math:`z_{0h} +d` and :math:`z_{0w} +d`, respectively. The specific heat capacity of air :math:`C_{p}` (J kg\ :sup:`-1` K\ :sup:`-1`) is a constant (:numref:`Table Physical constants`). The atmospheric potential temperature used here is .. math:: :label: 5.7 \theta _{atm} =T_{atm} +\Gamma _{d} z_{atm,\, h} -where :math:`T_{atm}` is the air temperature (K) at height -:math:`z_{atm,\, h}` and :math:`\Gamma _{d} =0.0098` K -m\ :sup:`-1` is the negative of the dry adiabatic lapse rate [this -expression is first-order equivalent to -:math:`\theta _{atm} =T_{atm} \left({P_{srf} \mathord{\left/ {\vphantom {P_{srf} P_{atm} }} \right.} P_{atm} } \right)^{{R_{da} \mathord{\left/ {\vphantom {R_{da} C_{p} }} \right.} C_{p} } }` -(:ref:`Stull 1988 `), where :math:`P_{srf}` is the surface pressure (Pa), -:math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`R_{da}` -is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`)]. By definition, -:math:`\theta _{s} =T_{s}` . The density of moist air (kg m\ :sup:`-3`) is +where :math:`T_{atm}` is the air temperature (K) at height :math:`z_{atm,\, h}` and :math:`\Gamma _{d} =0.0098` K m\ :sup:`-1` is the negative of the dry adiabatic lapse rate [this expression is first-order equivalent to :math:`\theta _{atm} =T_{atm} \left({P_{srf} \mathord{\left/ {\vphantom {P_{srf} P_{atm} }} \right.} P_{atm} } \right)^{{R_{da} \mathord{\left/ {\vphantom {R_{da} C_{p} }} \right.} C_{p} } }` (:ref:`Stull 1988 `), where :math:`P_{srf}` is the surface pressure (Pa), :math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`)]. By definition, :math:`\theta _{s} =T_{s}`. The density of moist air (kg m\ :sup:`-3`) is .. math:: :label: 5.8 \rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} } -where the atmospheric vapor pressure :math:`e_{atm}` (Pa) is derived -from the atmospheric specific humidity :math:`q_{atm}` +where the atmospheric vapor pressure :math:`e_{atm}` (Pa) is derived from the atmospheric specific humidity :math:`q_{atm}` .. math:: :label: 5.9 @@ -99,17 +63,7 @@ from the atmospheric specific humidity :math:`q_{atm}` Monin-Obukhov Similarity Theory ----------------------------------- -The surface vertical kinematic fluxes of momentum -:math:`\overline{u'w'}` and :math:`\overline{v'w'}` (m\ :sup:`2` s\ :sub:`-2`), sensible heat :math:`\overline{\theta 'w'}` -(K m s :sup:`-1`), and latent heat :math:`\overline{q'w'}` (kg kg\ :sup:`-1` m s\ :sup:`-1`), where :math:`u'`, :math:`v'`, -:math:`w'`, :math:`\theta '`, and :math:`q'` are zonal horizontal wind, -meridional horizontal wind, vertical velocity, potential temperature, -and specific humidity turbulent fluctuations about the mean, are defined -from Monin-Obukhov similarity applied to the surface layer. This theory -states that when scaled appropriately, the dimensionless mean horizontal -wind speed, mean potential temperature, and mean specific humidity -profile gradients depend on unique functions of -:math:`\zeta =\frac{z-d}{L}` (:ref:`Zeng et al. 1998`) as +The surface vertical kinematic fluxes of momentum :math:`\overline{u'w'}` and :math:`\overline{v'w'}` (m\ :sup:`2` s\ :sub:`-2`), sensible heat :math:`\overline{\theta 'w'}` (K m s :sup:`-1`), and latent heat :math:`\overline{q'w'}` (kg kg\ :sup:`-1` m s\ :sup:`-1`), where :math:`u'`, :math:`v'`, :math:`w'`, :math:`\theta '`, and :math:`q'` are zonal horizontal wind, meridional horizontal wind, vertical velocity, potential temperature, and specific humidity turbulent fluctuations about the mean, are defined from Monin-Obukhov similarity applied to the surface layer. This theory states that when scaled appropriately, the dimensionless mean horizontal wind speed, mean potential temperature, and mean specific humidity profile gradients depend on unique functions of :math:`\zeta =\frac{z-d}{L}` (:ref:`Zeng et al. 1998`) as .. math:: :label: 5.10 @@ -126,20 +80,7 @@ profile gradients depend on unique functions of \frac{k\left(z-d\right)}{q_{*} } \frac{\partial q}{\partial z} =\phi _{w} \left(\zeta \right) -where :math:`z` is height in the surface layer (m), :math:`d` is the -displacement height (m), :math:`L` is the Monin-Obukhov length scale (m) -that accounts for buoyancy effects resulting from vertical density -gradients (i.e., the atmospheric stability), k is the von Karman -constant (:numref:`Table Physical constants`), and :math:`\left|{\it u}\right|` is the -atmospheric wind speed (m s\ :sup:`-1`). :math:`\phi _{m}` , -:math:`\phi _{h}` , and :math:`\phi _{w}` are universal (over any -surface) similarity functions of :math:`\zeta` that relate the constant -fluxes of momentum, sensible heat, and latent heat to the mean profile -gradients of :math:`\left|{\it u}\right|`, :math:`\theta` , and -:math:`q` in the surface layer. In neutral conditions, -:math:`\phi _{m} =\phi _{h} =\phi _{w} =1`. The velocity (i.e., friction -velocity) :math:`u_{\*}` (m s\ :sup:`-1`), temperature -:math:`\theta _{\*}` (K), and moisture :math:`q_{\*}` (kg kg\ :sup:`-1`) scales are +where :math:`z` is height in the surface layer (m), :math:`d` is the displacement height (m), :math:`L` is the Monin-Obukhov length scale (m) that accounts for buoyancy effects resulting from vertical density gradients (i.e., the atmospheric stability), k is the von Karman constant (:numref:`Table Physical constants`), and :math:`\left|{\it u}\right|` is the atmospheric wind speed (m s\ :sup:`-1`). :math:`\phi _{m}`, :math:`\phi _{h}`, and :math:`\phi _{w}` are universal (over any surface) similarity functions of :math:`\zeta` that relate the constant fluxes of momentum, sensible heat, and latent heat to the mean profile gradients of :math:`\left|{\it u}\right|`, :math:`\theta`, and :math:`q` in the surface layer. In neutral conditions, :math:`\phi _{m} =\phi _{h} =\phi _{w} =1`. The velocity (i.e., friction velocity) :math:`u_{\*}` (m s\ :sup:`-1`), temperature :math:`\theta _{\*}` (K), and moisture :math:`q_{\*}` (kg kg\ :sup:`-1`) scales are .. math:: :label: 5.13 @@ -156,11 +97,7 @@ velocity) :math:`u_{\*}` (m s\ :sup:`-1`), temperature q_{*} u_{*} =-\overline{q'w'}=-\frac{E}{\rho _{atm} } -where :math:`\left|{\it \tau }\right|` is the shearing stress (kg m\ :sup:`-1` s\ :sup:`-2`), with zonal and meridional -components :math:`\overline{u'w'}=-\frac{\tau _{x} }{\rho _{atm} }` and -:math:`\overline{v'w'}=-\frac{\tau _{y} }{\rho _{atm} }` , respectively, -:math:`H` is the sensible heat flux (W m\ :sup:`-2`) and :math:`E` -is the water vapor flux (kg m\ :sup:`-2` s\ :sup:`-1`). +where :math:`\left|{\it \tau }\right|` is the shearing stress (kg m\ :sup:`-1` s\ :sup:`-2`), with zonal and meridional components :math:`\overline{u'w'}=-\frac{\tau _{x} }{\rho _{atm} }` and :math:`\overline{v'w'}=-\frac{\tau _{y} }{\rho _{atm} }`, respectively, :math:`H` is the sensible heat flux (W m\ :sup:`-2`) and :math:`E` is the water vapor flux (kg m\ :sup:`-2` s\ :sup:`-1`). The length scale :math:`L` is the Monin-Obukhov length defined as @@ -169,32 +106,16 @@ The length scale :math:`L` is the Monin-Obukhov length defined as L=-\frac{u_{*}^{3} }{k\left(\frac{g}{\overline{\theta _{v,\, atm} }} \right)\theta '_{v} w'} =\frac{u_{*}^{2} \overline{\theta _{v,\, atm} }}{kg\theta _{v*} } -where :math:`g` is the acceleration of gravity (m s\ :sup:`-2`) -(:numref:`Table Physical constants`), and -:math:`\overline{\theta _{v,\, atm} }=\overline{\theta _{atm} }\left(1+0.61q_{atm} \right)` -is the reference virtual potential temperature. :math:`L>0` indicates -stable conditions. :math:`L<0` indicates unstable conditions. -:math:`L=\infty` for neutral conditions. The temperature scale -:math:`\theta _{v*}` is defined as +where :math:`g` is the acceleration of gravity (m s\ :sup:`-2`) (:numref:`Table Physical constants`), and :math:`\overline{\theta _{v,\, atm} }=\overline{\theta _{atm} }\left(1+0.61q_{atm} \right)` is the reference virtual potential temperature. :math:`L>0` indicates stable conditions. :math:`L<0` indicates unstable conditions. :math:`L=\infty` for neutral conditions. The temperature scale :math:`\theta _{v*}` is defined as .. math:: :label: 5.17 \theta _{v*} u_{*} =\left[\theta _{*} \left(1+0.61q_{atm} \right)+0.61\overline{\theta _{atm} }q_{*} \right]u_{*} -where :math:`\overline{\theta _{atm} }` is the atmospheric potential -temperature. +where :math:`\overline{\theta _{atm} }` is the atmospheric potential temperature. -Following :ref:`Panofsky and Dutton (1984)`, the differential equations for -:math:`\phi _{m} \left(\zeta \right)`, -:math:`\phi _{h} \left(\zeta \right)`, and -:math:`\phi _{w} \left(\zeta \right)` can be integrated formally without -commitment to their exact forms. Integration between two arbitrary -heights in the surface layer :math:`z_{2}` and :math:`z_{1}` -(:math:`z_{2} >z_{1}` ) with horizontal winds -:math:`\left|{\it u}\right|_{1}` and :math:`\left|{\it u}\right|_{2}` , -potential temperatures :math:`\theta _{1}` and :math:`\theta _{2}` , -and specific humidities :math:`q_{1}` and :math:`q_{2}` results in +Following :ref:`Panofsky and Dutton (1984)`, the differential equations for :math:`\phi _{m} \left(\zeta \right)`, :math:`\phi _{h} \left(\zeta \right)`, and :math:`\phi _{w} \left(\zeta \right)` can be integrated formally without commitment to their exact forms. Integration between two arbitrary heights in the surface layer :math:`z_{2}` and :math:`z_{1}` (:math:`z_{2} >z_{1}` ) with horizontal winds :math:`\left|{\it u}\right|_{1}` and :math:`\left|{\it u}\right|_{2}`, potential temperatures :math:`\theta _{1}` and :math:`\theta _{2}`, and specific humidities :math:`q_{1}` and :math:`q_{2}` results in .. math:: :label: 5.18 @@ -211,9 +132,7 @@ and specific humidities :math:`q_{1}` and :math:`q_{2}` results in q_{2} -q_{1} =\frac{q_{*} }{k} \left[\ln \left(\frac{z_{2} -d}{z_{1} -d} \right)-\psi _{w} \left(\frac{z_{2} -d}{L} \right)+\psi _{w} \left(\frac{z_{1} -d}{L} \right)\right]. -The functions :math:`\psi _{m} \left(\zeta \right)`, -:math:`\psi _{h} \left(\zeta \right)`, and -:math:`\psi _{w} \left(\zeta \right)` are defined as +The functions :math:`\psi _{m} \left(\zeta \right)`, :math:`\psi _{h} \left(\zeta \right)`, and :math:`\psi _{w} \left(\zeta \right)` are defined as .. math:: :label: 5.21 @@ -230,9 +149,7 @@ The functions :math:`\psi _{m} \left(\zeta \right)`, \psi _{w} \left(\zeta \right)=\int _{{z_{0w} \mathord{\left/ {\vphantom {z_{0w} L}} \right.} L} }^{\zeta }\frac{\left[1-\phi _{w} \left(x\right)\right]}{x} \, dx -where :math:`z_{0m}` , :math:`z_{0h}` , and :math:`z_{0w}` are the -roughness lengths (m) for momentum, sensible heat, and water vapor, -respectively. +where :math:`z_{0m}`, :math:`z_{0h}`, and :math:`z_{0w}` are the roughness lengths (m) for momentum, sensible heat, and water vapor, respectively. Defining the surface values @@ -270,11 +187,7 @@ the integral forms of the flux-gradient relations are q_{atm} -q_{s} =\frac{q_{*} }{k} \left[\ln \left(\frac{z_{atm,\, w} -d}{z_{0w} } \right)-\psi _{w} \left(\frac{z_{atm,\, w} -d}{L} \right)+\psi _{w} \left(\frac{z_{0w} }{L} \right)\right]. -The constraint :math:`V_{a} \ge 1` is required simply for numerical -reasons to prevent :math:`H` and :math:`E` from becoming small with -small wind speeds. The convective velocity :math:`U_{c}` accounts for -the contribution of large eddies in the convective boundary layer to -surface fluxes as follows +The constraint :math:`V_{a} \ge 1` is required simply for numerical reasons to prevent :math:`H` and :math:`E` from becoming small with small wind speeds. The convective velocity :math:`U_{c}` accounts for the contribution of large eddies in the convective boundary layer to surface fluxes as follows .. math:: :label: 5.28 @@ -285,7 +198,7 @@ surface fluxes as follows \beta w_{*} & \qquad \zeta < 0 \quad {\rm (unstable)} \end{array} \right\} -where :math:`w_{*}` is the convective velocity scale +where :math:`w_{*}` is the convective velocity scale .. math:: :label: 5.29 @@ -318,17 +231,7 @@ The sensible and latent heat flux gradient relations are (:ref:`Zeng et al. 1998 \phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)=5+\zeta & \qquad {\rm for\; }\zeta >1 & \ {\rm \; (very\; stable).} \end{array} -To ensure continuous functions of -:math:`\phi _{m} \left(\zeta \right)`, -:math:`\phi _{h} \left(\zeta \right)`, and -:math:`\phi _{w} \left(\zeta \right)`, the simplest approach (i.e., -without considering any transition regimes) is to match the relations -for very unstable and unstable conditions at :math:`\zeta _{m} =-1.574` -for :math:`\phi _{m} \left(\zeta \right)` and -:math:`\zeta _{h} =\zeta _{w} =-0.465` for -:math:`\phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)` -(:ref:`Zeng et al. 1998 `). The flux gradient relations can be integrated to -yield wind profiles for the following conditions: +To ensure continuous functions of :math:`\phi _{m} \left(\zeta \right)`, :math:`\phi _{h} \left(\zeta \right)`, and :math:`\phi _{w} \left(\zeta \right)`, the simplest approach (i.e., without considering any transition regimes) is to match the relations for very unstable and unstable conditions at :math:`\zeta _{m} =-1.574` for :math:`\phi _{m} \left(\zeta \right)` and :math:`\zeta _{h} =\zeta _{w} =-0.465` for :math:`\phi _{h} \left(\zeta \right)=\phi _{w} \left(\zeta \right)` (:ref:`Zeng et al. 1998 `). The flux gradient relations can be integrated to yield wind profiles for the following conditions: Very unstable :math:`\left(\zeta <-1.574\right)` @@ -436,33 +339,21 @@ where \psi _{h} \left(\zeta \right)=\psi _{w} \left(\zeta \right)=2\ln \left(\frac{1+x^{2} }{2} \right). -Using the definitions of :math:`u_{*}` , :math:`\theta _{*}` , and -:math:`q_{*}` , an iterative solution of these equations can be used to -calculate the surface momentum, sensible heat, and water vapor flux -using atmospheric and surface values for :math:`\left|{\it u}\right|`, -:math:`\theta` , and :math:`q` except that :math:`L` depends on -:math:`u_{*}` , :math:`\theta _{*}` , and :math:`q_{*}` . However, the -bulk Richardson number +Using the definitions of :math:`u_{*}`, :math:`\theta _{*}`, and :math:`q_{*}`, an iterative solution of these equations can be used to calculate the surface momentum, sensible heat, and water vapor flux using atmospheric and surface values for :math:`\left|{\it u}\right|`, :math:`\theta`, and :math:`q` except that :math:`L` depends on :math:`u_{*}`, :math:`\theta _{*}`, and :math:`q_{*}`. However, the bulk Richardson number .. math:: :label: 5.46 R_{iB} =\frac{\theta _{v,\, atm} -\theta _{v,\, s} }{\overline{\theta _{v,\, atm} }} \frac{g\left(z_{atm,\, m} -d\right)}{V_{a}^{2} } -is related to :math:`\zeta` (:ref:`Arya 2001 `) as +is related to :math:`\zeta` (:ref:`Arya 2001 `) as .. math:: :label: 5.47 R_{iB} =\zeta \left[\ln \left(\frac{z_{atm,\, h} -d}{z_{0h} } \right)-\psi _{h} \left(\zeta \right)\right]\left[\ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)-\psi _{m} \left(\zeta \right)\right]^{-2} . -Using -:math:`\phi _{h} =\phi _{m}^{2} =\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} }` -for unstable conditions and :math:`\phi _{h} =\phi _{m} =1+5\zeta` for -stable conditions to determine :math:`\psi _{m} \left(\zeta \right)` and -:math:`\psi _{h} \left(\zeta \right)`, the inverse relationship -:math:`\zeta =f\left(R_{iB} \right)` can be solved to obtain a first -guess for :math:`\zeta` and thus :math:`L` from +Using :math:`\phi _{h} =\phi _{m}^{2} =\left(1-16\zeta \right)^{-{1\mathord{\left/ {\vphantom {1 2}} \right.} 2} }` for unstable conditions and :math:`\phi _{h} =\phi _{m} =1+5\zeta` for stable conditions to determine :math:`\psi _{m} \left(\zeta \right)` and :math:`\psi _{h} \left(\zeta \right)`, the inverse relationship :math:`\zeta =f\left(R_{iB} \right)` can be solved to obtain a first guess for :math:`\zeta` and thus :math:`L` from .. math:: :label: 5.48 @@ -472,8 +363,7 @@ guess for :math:`\zeta` and thus :math:`L` from \zeta =R_{iB} \ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right) & \qquad -100\le \zeta \le -0.01 & \qquad {\rm for\; }R_{iB} <0 \ {\rm \; (unstable)} \end{array}. -Upon iteration (section :numref:`Numerical Implementation`), the following is used to determine -:math:`\zeta` and thus :math:`L` +Upon iteration (section :numref:`Numerical Implementation`), the following is used to determine :math:`\zeta` and thus :math:`L` .. math:: :label: 5.49 @@ -489,16 +379,14 @@ where {\rm -100}\le \zeta \le {\rm -0.01} & \qquad {\rm for\; }\zeta <0{\rm \; (unstable)} \end{array}. -The difference in virtual potential air temperature between the -reference height and the surface is +The difference in virtual potential air temperature between the reference height and the surface is .. math:: :label: 5.50 \theta _{v,\, atm} -\theta _{v,\, s} =\left(\theta _{atm} -\theta _{s} \right)\left(1+0.61q_{atm} \right)+0.61\overline{\theta _{atm} }\left(q_{atm} -q_{s} \right). -The momentum, sensible heat, and water vapor fluxes between the surface -and the atmosphere can also be written in the form +The momentum, sensible heat, and water vapor fluxes between the surface and the atmosphere can also be written in the form .. math:: :label: 5.51 @@ -537,17 +425,14 @@ where the aerodynamic resistances (s m\ :sup:`-1`) are \begin{array}{l} {r_{aw} =\frac{q_{atm} -q_{s} }{q_{*} u_{*} } =\frac{1}{k^{2} V_{a} } \left[\ln \left(\frac{z_{atm,\, m} -d}{z_{0m} } \right)-\psi _{m} \left(\frac{z_{atm,\, m} -d}{L} \right)+\psi _{m} \left(\frac{z_{0m} }{L} \right)\right]} \\ {\qquad \left[\ln \left(\frac{z_{atm,\, {\it w}} -d}{z_{0w} } \right)-\psi _{w} \left(\frac{z_{atm,\, w} -d}{L} \right)+\psi _{w} \left(\frac{z_{0w} }{L} \right)\right]} \end{array}. -A 2-m height "screen" temperature is useful for comparison with -observations +A 2-m height "screen" temperature is useful for comparison with observations .. math:: :label: 5.58 T_{2m} =\theta _{s} +\frac{\theta _{*} }{k} \left[\ln \left(\frac{2+z_{0h} }{z_{0h} } \right)-\psi _{h} \left(\frac{2+z_{0h} }{L} \right)+\psi _{h} \left(\frac{z_{0h} }{L} \right)\right] -where for convenience, "2-m" is defined as 2 m above the apparent sink -for sensible heat (:math:`z_{0h} +d`). Similarly, a 2-m height specific -humidity is defined as +where for convenience, "2-m" is defined as 2 m above the apparent sink for sensible heat (:math:`z_{0h} +d`). Similarly, a 2-m height specific humidity is defined as .. math:: :label: 5.59 @@ -561,12 +446,9 @@ Relative humidity is RH_{2m} =\min \left(100,\, \frac{q_{2m} }{q_{sat}^{T_{2m} } } \times 100\right) -where :math:`q_{sat}^{T_{2m} }` is the saturated specific humidity at -the 2-m temperature :math:`T_{2m}` (section :numref:`Saturation Vapor Pressure`). +where :math:`q_{sat}^{T_{2m} }` is the saturated specific humidity at the 2-m temperature :math:`T_{2m}` (section :numref:`Saturation Vapor Pressure`). -A 10-m wind speed is calculated as (note that this is not consistent -with the 10-m wind speed calculated for the dust model as described in -Chapter :numref:`rst_Dust Model`) +A 10-m wind speed is calculated as (note that this is not consistent with the 10-m wind speed calculated for the dust model as described in Chapter :numref:`rst_Dust Model`) .. math:: :label: 5.61 @@ -578,25 +460,14 @@ Chapter :numref:`rst_Dust Model`) Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces -------------------------------------------------------------- -Surfaces are considered non-vegetated for the surface flux calculations -if leaf plus stem area index :math:`L+S<0.05` (section -:numref:`Phenology and vegetation burial by snow`). By -definition, this includes bare soil and glaciers. The -solution for lakes is described in Chapter :numref:`rst_Lake Model`. For these surfaces, the -surface may be exposed to the atmosphere, snow covered, and/or surface -water covered, so that the sensible heat flux :math:`H_{g}` (W -m\ :sup:`-2`) is, with reference to :numref:`Figure Schematic diagram of sensible heat fluxes`, +Surfaces are considered non-vegetated for the surface flux calculations if leaf plus stem area index :math:`L+S<0.05` (section :numref:`Phenology and vegetation burial by snow`). By definition, this includes bare soil and glaciers. The solution for lakes is described in Chapter :numref:`rst_Lake Model`. For these surfaces, the surface may be exposed to the atmosphere, snow covered, and/or surface water covered, so that the sensible heat flux :math:`H_{g}` (W m\ :sup:`-2`) is, with reference to :numref:`Figure Schematic diagram of sensible heat fluxes`, .. math:: :label: 5.62 H_{g} =\left(1-f_{sno} -f_{h2osfc} \right)H_{soil} +f_{sno} H_{snow} +f_{h2osfc} H_{h2osfc} -where :math:`\left(1-f_{sno} -f_{h2osfc} \right)`, :math:`f_{sno}` , and -:math:`f_{h2osfc}` are the exposed, snow covered, and surface water -covered fractions of the grid cell. The individual fluxes based on the -temperatures of the soil :math:`T_{1}` , snow :math:`T_{snl+1}` , and -surface water :math:`T_{h2osfc}` are +where :math:`\left(1-f_{sno} -f_{h2osfc} \right)`, :math:`f_{sno}`, and :math:`f_{h2osfc}` are the exposed, snow covered, and surface water covered fractions of the grid cell. The individual fluxes based on the temperatures of the soil :math:`T_{1}`, snow :math:`T_{snl+1}`, and surface water :math:`T_{h2osfc}` are .. math:: :label: 5.63 @@ -613,14 +484,9 @@ surface water :math:`T_{h2osfc}` are H_{h2osfc} =-\rho _{atm} C_{p} \frac{\left(\theta _{atm} -T_{h2osfc} \right)}{r_{ah} } -where :math:`\rho _{atm}` is the density of atmospheric air (kg m\ :sup:`-3`), :math:`C_{p}` is the specific heat capacity of air -(J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), -:math:`\theta _{atm}` is the atmospheric potential temperature (K), and -:math:`r_{ah}` is the aerodynamic resistance to sensible heat transfer -(s m\ :sup:`-1`). +where :math:`\rho _{atm}` is the density of atmospheric air (kg m\ :sup:`-3`), :math:`C_{p}` is the specific heat capacity of air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), :math:`\theta _{atm}` is the atmospheric potential temperature (K), and :math:`r_{ah}` is the aerodynamic resistance to sensible heat transfer (s m\ :sup:`-1`). -The water vapor flux :math:`E_{g}` (kg m\ :sup:`-2` s\ :sup:`-1`) is, with reference to -:numref:`Figure Schematic diagram of latent heat fluxes`, +The water vapor flux :math:`E_{g}` (kg m\ :sup:`-2` s\ :sup:`-1`) is, with reference to :numref:`Figure Schematic diagram of latent heat fluxes`, .. math:: :label: 5.66 @@ -642,11 +508,7 @@ The water vapor flux :math:`E_{g}` (kg m\ :sup:`-2` s\ :sup:`-1`) is, with refe E_{h2osfc} =-\frac{\rho _{atm} \left(q_{atm} -q_{h2osfc} \right)}{r_{aw} } -where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`q_{soil}` , :math:`q_{sno}` , -and :math:`q_{h2osfc}` are the specific humidities (kg kg\ :sup:`-1`) of the soil, snow, and surface water, respectively, -:math:`r_{aw}` is the aerodynamic resistance to water vapor transfer (s m\ :sup:`-1`), and :math:`r _{soi}` is the soil -resistance to water vapor transfer (s m\ :sup:`-1`). The specific humidities of the snow :math:`q_{sno}` and surface water -:math:`q_{h2osfc}` are assumed to be at the saturation specific humidity of their respective temperatures +where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`q_{soil}`, :math:`q_{sno}`, and :math:`q_{h2osfc}` are the specific humidities (kg kg\ :sup:`-1`) of the soil, snow, and surface water, respectively, :math:`r_{aw}` is the aerodynamic resistance to water vapor transfer (s m\ :sup:`-1`), and :math:`r _{soi}` is the soil resistance to water vapor transfer (s m\ :sup:`-1`). The specific humidities of the snow :math:`q_{sno}` and surface water :math:`q_{h2osfc}` are assumed to be at the saturation specific humidity of their respective temperatures .. math:: :label: 5.70 @@ -658,70 +520,44 @@ resistance to water vapor transfer (s m\ :sup:`-1`). The specific humidities of q_{h2osfc} =q_{sat}^{T_{h2osfc} } -The specific humidity of the soil surface :math:`q_{soil}` is assumed -to be proportional to the saturation specific humidity +The specific humidity of the soil surface :math:`q_{soil}` is assumed to be proportional to the saturation specific humidity .. math:: :label: 5.72 q_{soil} =\alpha _{soil} q_{sat}^{T_{1} } -where :math:`q_{sat}^{T_{1} }` is the saturated specific humidity at -the soil surface temperature :math:`T_{1}` (section :numref:`Saturation Vapor Pressure`). The factor -:math:`\alpha _{soil}` is a function of the surface soil water matric -potential :math:`\psi` as in :ref:`Philip (1957)` +where :math:`q_{sat}^{T_{1} }` is the saturated specific humidity at the soil surface temperature :math:`T_{1}` (section :numref:`Saturation Vapor Pressure`). The factor :math:`\alpha _{soil}` is a function of the surface soil water matric potential :math:`\psi` as in :ref:`Philip (1957)` .. math:: :label: 5.73 \alpha _{soil} =\exp \left(\frac{\psi _{1} g}{1\times 10^{3} R_{wv} T_{1} } \right) -where :math:`R_{wv}` is the gas constant for water vapor (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), :math:`g` is the -gravitational acceleration (m s\ :sup:`-2`) (:numref:`Table Physical constants`), and -:math:`\psi _{1}` is the soil water matric potential of the top soil -layer (mm). The soil water matric potential :math:`\psi _{1}` is +where :math:`R_{wv}` is the gas constant for water vapor (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), :math:`g` is the gravitational acceleration (m s\ :sup:`-2`) (:numref:`Table Physical constants`), and :math:`\psi _{1}` is the soil water matric potential of the top soil layer (mm). The soil water matric potential :math:`\psi _{1}` is .. math:: :label: 5.74 \psi _{1} =\psi _{sat,\, 1} s_{1}^{-B_{1} } \ge -1\times 10^{8} -where :math:`\psi _{sat,\, 1}` is the saturated matric potential (mm) -(section :numref:`Hydraulic Properties`), -:math:`B_{1}` is the :ref:`Clapp and Hornberger (1978) ` -parameter (section :numref:`Hydraulic Properties`), -and :math:`s_{1}` is the wetness of the top soil layer with respect to saturation. -The surface wetness :math:`s_{1}` is a function of the liquid water and ice content +where :math:`\psi _{sat,\, 1}` is the saturated matric potential (mm) (section :numref:`Hydraulic Properties`), :math:`B_{1}` is the :ref:`Clapp and Hornberger (1978) ` parameter (section :numref:`Hydraulic Properties`), and :math:`s_{1}` is the wetness of the top soil layer with respect to saturation. The surface wetness :math:`s_{1}` is a function of the liquid water and ice content .. math:: :label: 5.75 s_{1} =\frac{1}{\Delta z_{1} \theta _{sat,\, 1} } \left[\frac{w_{liq,\, 1} }{\rho _{liq} } +\frac{w_{ice,\, 1} }{\rho _{ice} } \right]\qquad 0.01\le s_{1} \le 1.0 -where :math:`\Delta z_{1}` is the thickness of the top soil layer (m), -:math:`\rho _{liq}` and :math:`\rho _{ice}` are the density of liquid -water and ice (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), :math:`w_{liq,\, 1}` -and :math:`w_{ice,\, 1}` are the mass of liquid water and ice of the -top soil layer (kg m\ :sup:`-2`) (Chapter :numref:`rst_Hydrology`), and -:math:`\theta _{sat,\, 1}` is the saturated volumetric water content -(i.e., porosity) of the top soil layer (mm\ :sup:`3` mm\ :sup:`-3`) (section :numref:`Hydraulic Properties`). If -:math:`q_{sat}^{T_{1} } >q_{atm}` and :math:`q_{atm} >q_{soil}` , then -:math:`q_{soil} =q_{atm}` and :math:`\frac{dq_{soil} }{dT} =0`. This -prevents large increases (decreases) in :math:`q_{soil}` for small -increases (decreases) in soil moisture in very dry soils. +where :math:`\Delta z_{1}` is the thickness of the top soil layer (m), :math:`\rho _{liq}` and :math:`\rho _{ice}` are the density of liquid water and ice (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), :math:`w_{liq,\, 1}` and :math:`w_{ice,\, 1}` are the mass of liquid water and ice of the top soil layer (kg m\ :sup:`-2`) (Chapter :numref:`rst_Hydrology`), and :math:`\theta _{sat,\, 1}` is the saturated volumetric water content (i.e., porosity) of the top soil layer (mm\ :sup:`3` mm\ :sup:`-3`) (section :numref:`Hydraulic Properties`). If :math:`q_{sat}^{T_{1} } >q_{atm}` and :math:`q_{atm} >q_{soil}`, then :math:`q_{soil} =q_{atm}` and :math:`\frac{dq_{soil} }{dT} =0`. This prevents large increases (decreases) in :math:`q_{soil}` for small increases (decreases) in soil moisture in very dry soils. -The resistance to water vapor transfer occurring within the soil matrix -:math:`r_{soil}` (s m\ :sup:`-1`) is +The resistance to water vapor transfer occurring within the soil matrix :math:`r_{soil}` (s m\ :sup:`-1`) is .. math:: :label: 5.76 r_{soil} = \frac{DSL}{D_{v} \tau} -where :math:`DSL` is the thickness of the dry surface layer (m), :math:`D_{v}` -is the molecular diffusivity of water vapor in air (m\ :sup:`2` s\ :sup:`-2`) -and :math:`\tau` (*unitless*) describes the tortuosity of the vapor flow paths through -the soil matrix (:ref:`Swenson and Lawrence 2014 `). +where :math:`DSL` is the thickness of the dry surface layer (m), :math:`D_{v}` is the molecular diffusivity of water vapor in air (m\ :sup:`2` s\ :sup:`-2`) and :math:`\tau` (*unitless*) describes the tortuosity of the vapor flow paths through the soil matrix (:ref:`Swenson and Lawrence 2014 `). The thickness of the dry surface layer is given by @@ -735,24 +571,14 @@ The thickness of the dry surface layer is given by 0 & \qquad \theta_{1} \ge \theta_{init} \end{array} -where :math:`D_{max}` is a parameter specifying the length scale -of the maximum DSL thickness (default value = 15 mm), -:math:`\theta_{init}` (mm\ :sup:`3` mm\ :sup:`-3`) is the moisture value -at which the DSL initiates, :math:`\theta_{1}` (mm\ :sup:`3` mm\ :sup:`-3`) -is the moisture value of the top model soil layer, and -:math:`\theta_{air}` (mm\ :sup:`3` mm\ :sup:`-3`) is the 'air dry' soil -moisture value (:ref:`Dingman 2002 `): +where :math:`D_{max}` is a parameter specifying the length scale of the maximum DSL thickness (default value = 15 mm), :math:`\theta_{init}` (mm\ :sup:`3` mm\ :sup:`-3`) is the moisture value at which the DSL initiates, :math:`\theta_{1}` (mm\ :sup:`3` mm\ :sup:`-3`) is the moisture value of the top model soil layer, and :math:`\theta_{air}` (mm\ :sup:`3` mm\ :sup:`-3`) is the 'air dry' soil moisture value (:ref:`Dingman 2002 `): .. math:: :label: 5.78 \theta_{air} = \Phi \left( \frac{\Psi_{sat}}{\Psi_{air}} \right)^{\frac{1}{B_{1}}} \ . -where :math:`\Phi` is the porosity (mm\ :sup:`3` mm\ :sup:`-3`), -:math:`\Psi_{sat}` is the saturated soil matric potential (mm), -:math:`\Psi_{air} = 10^{7}` mm is the air dry matric potential, and -:math:`B_{1}` is a function of soil texture (section -:numref:`Hydraulic Properties`). +where :math:`\Phi` is the porosity (mm\ :sup:`3` mm\ :sup:`-3`), :math:`\Psi_{sat}` is the saturated soil matric potential (mm), :math:`\Psi_{air} = 10^{7}` mm is the air dry matric potential, and :math:`B_{1}` is a function of soil texture (section :numref:`Hydraulic Properties`). The soil tortuosity is @@ -775,37 +601,18 @@ where :math:`\Phi_{air}` (mm\ :sup:`3` mm\ :sup:`-3`) is the air filled pore spa D_{v} = 2.12 \times 10^{-5} \left(\frac{T_{1}}{T_{f}}\right)^{1.75} \ . -where :math:`T_{1}` (K) is the temperature of the top soil layer and -:math:`T_{f}` (K) is the freezing temperature of water -(:numref:`Table Physical Constants`). - -The roughness lengths used to calculate :math:`r_{am}` , -:math:`r_{ah}` , and :math:`r_{aw}` are :math:`z_{0m} =z_{0m,\, g}` , -:math:`z_{0h} =z_{0h,\, g}` , and :math:`z_{0w} =z_{0w,\, g}` . The -displacement height :math:`d=0`. The momentum roughness length is -:math:`z_{0m,\, g} =0.01` for soil, glaciers, and -:math:`z_{0m,\, g} =0.0024` for snow-covered surfaces -(:math:`f_{sno} >0`). In general, :math:`z_{0m}` is different from -:math:`z_{0h}` because the transfer of momentum is affected by pressure -fluctuations in the turbulent waves behind the roughness elements, while -for heat and water vapor transfer no such dynamical mechanism exists. -Rather, heat and water vapor must be transferred by molecular diffusion -across the interfacial sublayer. The following relation from -:ref:`Zilitinkevich (1970) ` is adopted by -:ref:`Zeng and Dickinson 1998 ` +where :math:`T_{1}` (K) is the temperature of the top soil layer and :math:`T_{f}` (K) is the freezing temperature of water (:numref:`Table Physical Constants`). + +The roughness lengths used to calculate :math:`r_{am}`, :math:`r_{ah}`, and :math:`r_{aw}` are :math:`z_{0m} =z_{0m,\, g}`, :math:`z_{0h} =z_{0h,\, g}`, and :math:`z_{0w} =z_{0w,\, g}`. The displacement height :math:`d=0`. The momentum roughness length is :math:`z_{0m,\, g} =0.01` for soil, glaciers, and :math:`z_{0m,\, g} =0.0024` for snow-covered surfaces (:math:`f_{sno} >0`). In general, :math:`z_{0m}` is different from :math:`z_{0h}` because the transfer of momentum is affected by pressure fluctuations in the turbulent waves behind the roughness elements, while for heat and water vapor transfer no such dynamical mechanism exists. Rather, heat and water vapor must be transferred by molecular diffusion across the interfacial sublayer. The following relation from :ref:`Zilitinkevich (1970) ` is adopted by :ref:`Zeng and Dickinson 1998 ` .. math:: :label: 5.82 z_{0h,\, g} =z_{0w,\, g} =z_{0m,\, g} e^{-a\left({u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon } \right)^{0.45} } -where the quantity -:math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` -is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic -viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. +where the quantity :math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. -The numerical solution for the fluxes of momentum, sensible heat, and -water vapor flux from non-vegetated surfaces proceeds as follows: +The numerical solution for the fluxes of momentum, sensible heat, and water vapor flux from non-vegetated surfaces proceeds as follows: #. An initial guess for the wind speed :math:`V_{a}` is obtained from :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m @@ -846,10 +653,7 @@ water vapor flux from non-vegetated surfaces proceeds as follows: #. 2-m height air temperature :math:`T_{2m}` and specific humidity :math:`q_{2m}` (:eq:`5.58` , :eq:`5.59`) -The partial derivatives of the soil surface fluxes with respect to -ground temperature, which are needed for the soil temperature calculations (section -:numref:`Numerical Solution Temperature`) and to update the soil surface fluxes -(section :numref:`Update of Ground Sensible and Latent Heat Fluxes`), are +The partial derivatives of the soil surface fluxes with respect to ground temperature, which are needed for the soil temperature calculations (section :numref:`Numerical Solution Temperature`) and to update the soil surface fluxes (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`), are .. math:: :label: 5.83 @@ -868,40 +672,21 @@ where \frac{dq_{g} }{dT_{g} } =\left(1-f_{sno} -f_{h2osfc} \right)\alpha _{soil} \frac{dq_{sat}^{T_{soil} } }{dT_{soil} } +f_{sno} \frac{dq_{sat}^{T_{sno} } }{dT_{sno} } +f_{h2osfc} \frac{dq_{sat}^{T_{h2osfc} } }{dT_{h2osfc} } . -The partial derivatives -:math:`\frac{\partial r_{ah} }{\partial T_{g} }` and -:math:`\frac{\partial r_{aw} }{\partial T_{g} }` , which cannot be -determined analytically, are ignored for -:math:`\frac{\partial H_{g} }{\partial T_{g} }` and -:math:`\frac{\partial E_{g} }{\partial T_{g} }` . +The partial derivatives :math:`\frac{\partial r_{ah} }{\partial T_{g} }` and :math:`\frac{\partial r_{aw} }{\partial T_{g} }`, which cannot be determined analytically, are ignored for :math:`\frac{\partial H_{g} }{\partial T_{g} }` and :math:`\frac{\partial E_{g} }{\partial T_{g} }`. .. _Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces: Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces -------------------------------------------------------------------------- -In the case of a vegetated surface, the sensible heat :math:`H` and -water vapor flux :math:`E` are partitioned into vegetation and ground -fluxes that depend on vegetation :math:`T_{v}` and ground -:math:`T_{g}` temperatures in addition to surface temperature -:math:`T_{s}` and specific humidity :math:`q_{s}` . Because of the -coupling between vegetation temperature and fluxes, Newton-Raphson -iteration is used to solve for the vegetation temperature and the -sensible heat and water vapor fluxes from vegetation simultaneously -using the ground temperature from the previous time step. In section -:numref:`Theory`, the equations used in the iteration scheme are derived. Details -on the numerical scheme are provided in section :numref:`Numerical Implementation`. +In the case of a vegetated surface, the sensible heat :math:`H` and water vapor flux :math:`E` are partitioned into vegetation and ground fluxes that depend on vegetation :math:`T_{v}` and ground :math:`T_{g}` temperatures in addition to surface temperature :math:`T_{s}` and specific humidity :math:`q_{s}`. Because of the coupling between vegetation temperature and fluxes, Newton-Raphson iteration is used to solve for the vegetation temperature and the sensible heat and water vapor fluxes from vegetation simultaneously using the ground temperature from the previous time step. In section :numref:`Theory`, the equations used in the iteration scheme are derived. Details on the numerical scheme are provided in section :numref:`Numerical Implementation`. .. _Theory: Theory ^^^^^^^^^^^^ -The air within the canopy is assumed to have negligible capacity to -store heat so that the sensible heat flux :math:`H` between the surface -at height :math:`z_{0h} +d` and the atmosphere at height -:math:`z_{atm,\, h}` must be balanced by the sum of the sensible heat -from the vegetation :math:`H_{v}` and the ground :math:`H_{g}` +The air within the canopy is assumed to have negligible capacity to store heat so that the sensible heat flux :math:`H` between the surface at height :math:`z_{0h} +d` and the atmosphere at height :math:`z_{atm,\, h}` must be balanced by the sum of the sensible heat from the vegetation :math:`H_{v}` and the ground :math:`H_{g}` .. math:: :label: 5.86 @@ -942,20 +727,9 @@ where H_{h2osfc} =-\rho _{atm} C_{p} \frac{\left(T_{s} -T_{h2osfc} \right)}{r_{ah} ^{{'} } } -where :math:`\rho _{atm}` is the density of atmospheric air (kg m\ :sup:`-3`), :math:`C_{p}` is the specific heat capacity of air -(J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), -:math:`\theta _{atm}` is the atmospheric potential temperature (K), and -:math:`r_{ah}` is the aerodynamic resistance to sensible heat transfer -(s m\ :sup:`-1`). - -Here, :math:`T_{s}` is the surface temperature at height -:math:`z_{0h} +d`, also referred to as the canopy air temperature. -:math:`L` and :math:`S` are the exposed leaf and stem area indices -(section :numref:`Phenology and vegetation burial by snow`), :math:`r_{b}` is the leaf boundary layer resistance (s -m\ :sup:`-1`), and :math:`r_{ah} ^{{'} }` is the aerodynamic -resistance (s m\ :sup:`-1`) to heat transfer between the ground at -height :math:`z_{0h} ^{{'} }` and the canopy air at height -:math:`z_{0h} +d`. +where :math:`\rho _{atm}` is the density of atmospheric air (kg m\ :sup:`-3`), :math:`C_{p}` is the specific heat capacity of air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), :math:`\theta _{atm}` is the atmospheric potential temperature (K), and :math:`r_{ah}` is the aerodynamic resistance to sensible heat transfer (s m\ :sup:`-1`). + +Here, :math:`T_{s}` is the surface temperature at height :math:`z_{0h} +d`, also referred to as the canopy air temperature. :math:`L` and :math:`S` are the exposed leaf and stem area indices (section :numref:`Phenology and vegetation burial by snow`), :math:`r_{b}` is the leaf boundary layer resistance (s m\ :sup:`-1`), and :math:`r_{ah} ^{{'} }` is the aerodynamic resistance (s m\ :sup:`-1`) to heat transfer between the ground at height :math:`z_{0h} ^{{'} }` and the canopy air at height :math:`z_{0h} +d`. .. _Figure Schematic diagram of sensible heat fluxes: @@ -971,8 +745,7 @@ height :math:`z_{0h} ^{{'} }` and the canopy air at height Figure Schematic diagram of water vapor fluxes for (a) non-vegetated surfaces and (b) vegetated surfaces. -Equations :eq:`5.86` - :eq:`5.89` can be solved for the canopy air -temperature :math:`T_{s}` +Equations :eq:`5.86` - :eq:`5.89` can be solved for the canopy air temperature :math:`T_{s}` .. math:: :label: 5.93 @@ -996,32 +769,23 @@ where c_{v}^{h} =\frac{\left(L+S\right)}{r_{b} } -are the sensible heat conductances from the canopy air to the -atmosphere, the ground to canopy air, and leaf surface to canopy air, -respectively (m s\ :sup:`-1`). +are the sensible heat conductances from the canopy air to the atmosphere, the ground to canopy air, and leaf surface to canopy air, respectively (m s\ :sup:`-1`). -When the expression for :math:`T_{s}` is substituted into equation :eq:`5.88`, -the sensible heat flux from vegetation :math:`H_{v}` is a function of -:math:`\theta _{atm}` , :math:`T_{g}` , and :math:`T_{v}` +When the expression for :math:`T_{s}` is substituted into equation :eq:`5.88`, the sensible heat flux from vegetation :math:`H_{v}` is a function of :math:`\theta _{atm}`, :math:`T_{g}`, and :math:`T_{v}` .. math:: :label: 5.97 H_{v} = -\rho _{atm} C_{p} \left[c_{a}^{h} \theta _{atm} +c_{g}^{h} T_{g} -\left(c_{a}^{h} +c_{g}^{h} \right)T_{v} \right]\frac{c_{v}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } . -Similarly, the expression for :math:`T_{s}` can be substituted into -equation to obtain the sensible heat flux from ground :math:`H_{g}` +Similarly, the expression for :math:`T_{s}` can be substituted into equation to obtain the sensible heat flux from ground :math:`H_{g}` .. math:: :label: 5.98 H_{g} = -\rho _{atm} C_{p} \left[c_{a}^{h} \theta _{atm} +c_{v}^{h} T_{v} -\left(c_{a}^{h} +c_{v}^{h} \right)T_{g} \right]\frac{c_{g}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } . -The air within the canopy is assumed to have negligible capacity to -store water vapor so that the water vapor flux :math:`E` between the -surface at height :math:`z_{0w} +d` and the atmosphere at height -:math:`z_{atm,\, w}` must be balanced by the sum of the water vapor -flux from the vegetation :math:`E_{v}` and the ground :math:`E_{g}` +The air within the canopy is assumed to have negligible capacity to store water vapor so that the water vapor flux :math:`E` between the surface at height :math:`z_{0w} +d` and the atmosphere at height :math:`z_{atm,\, w}` must be balanced by the sum of the water vapor flux from the vegetation :math:`E_{v}` and the ground :math:`E_{g}` .. math:: :label: 5.99 @@ -1062,33 +826,14 @@ where E_{h2osfc} = -\rho _{atm} \frac{\left(q_{s} -q_{h2osfc} \right)}{r_{aw} ^{{'} } +r_{soil} } -where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`r_{aw}` is the aerodynamic resistance to -water vapor transfer (s m\ :sup:`-1`), :math:`q_{sat}^{T_{v} }` -(kg kg\ :sup:`-1`) is the saturation water vapor specific humidity -at the vegetation temperature (section :numref:`Saturation Vapor Pressure`), :math:`q_{g}` , -:math:`q_{sno}` , and :math:`q_{h2osfc}` are the specific humidities -of the soil, snow, and surface water (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), -:math:`r_{aw} ^{{'} }` is the aerodynamic resistance (s -m\ :sup:`-1`) to water vapor transfer between the ground at height -:math:`z_{0w} ^{{'} }` and the canopy air at height :math:`z_{0w} +d`, -and :math:`r_{soil}` (:eq:`5.76`) is a resistance to diffusion through the soil -(s m\ :sup:`-1`). :math:`r_{total}` is the total resistance to -water vapor transfer from the canopy to the canopy air and includes -contributions from leaf boundary layer and sunlit and shaded stomatal -resistances :math:`r_{b}` , :math:`r_{s}^{sun}` , and -:math:`r_{s}^{sha}` (:numref:`Figure Schematic diagram of latent heat fluxes`). -The water vapor flux from vegetation -is the sum of water vapor flux from wetted leaf and stem area -:math:`E_{v}^{w}` (evaporation of water intercepted by the canopy) and -transpiration from dry leaf surfaces :math:`E_{v}^{t}` +where :math:`q_{atm}` is the atmospheric specific humidity (kg kg\ :sup:`-1`), :math:`r_{aw}` is the aerodynamic resistance to water vapor transfer (s m\ :sup:`-1`), :math:`q_{sat}^{T_{v} }` (kg kg\ :sup:`-1`) is the saturation water vapor specific humidity at the vegetation temperature (section :numref:`Saturation Vapor Pressure`), :math:`q_{g}`, :math:`q_{sno}`, and :math:`q_{h2osfc}` are the specific humidities of the soil, snow, and surface water (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), :math:`r_{aw} ^{{'} }` is the aerodynamic resistance (s m\ :sup:`-1`) to water vapor transfer between the ground at height :math:`z_{0w} ^{{'} }` and the canopy air at height :math:`z_{0w} +d`, and :math:`r_{soil}` (:eq:`5.76`) is a resistance to diffusion through the soil (s m\ :sup:`-1`). :math:`r_{total}` is the total resistance to water vapor transfer from the canopy to the canopy air and includes contributions from leaf boundary layer and sunlit and shaded stomatal resistances :math:`r_{b}`, :math:`r_{s}^{sun}`, and :math:`r_{s}^{sha}` (:numref:`Figure Schematic diagram of latent heat fluxes`). The water vapor flux from vegetation is the sum of water vapor flux from wetted leaf and stem area :math:`E_{v}^{w}` (evaporation of water intercepted by the canopy) and transpiration from dry leaf surfaces :math:`E_{v}^{t}` .. math:: :label: 5.106 E_{v} =E_{v}^{w} +E_{v}^{t} . -Equations :eq:`5.99` - :eq:`5.102` can be solved for the canopy specific humidity -:math:`q_{s}` +Equations :eq:`5.99` - :eq:`5.102` can be solved for the canopy specific humidity :math:`q_{s}` .. math:: :label: 5.107 @@ -1112,11 +857,7 @@ where c_{g}^{w} =\frac{1}{r_{aw} ^{{'} } +r_{soil} } -are the water vapor conductances from the canopy air to the atmosphere, -the leaf to canopy air, and ground to canopy air, respectively. The term -:math:`r''` is determined from contributions by wet leaves and -transpiration and limited by available water and potential evaporation -as +are the water vapor conductances from the canopy air to the atmosphere, the leaf to canopy air, and ground to canopy air, respectively. The term :math:`r''` is determined from contributions by wet leaves and transpiration and limited by available water and potential evaporation as .. math:: :label: 5.111 @@ -1128,12 +869,7 @@ as 1 & \qquad E_{v}^{w,\, pot} \le 0 \end{array}\right\} -where :math:`f_{wet}` is the fraction of leaves and stems that are wet -(section :numref:`Canopy Water`), :math:`W_{can}` is canopy water (kg m\ :sup:`-2`) -(section :numref:`Canopy Water`), :math:`\Delta t` is the time step (s), and -:math:`\beta _{t}` is a soil moisture function limiting transpiration -(Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). The potential -evaporation from wet foliage per unit wetted area is +where :math:`f_{wet}` is the fraction of leaves and stems that are wet (section :numref:`Canopy Water`), :math:`W_{can}` is canopy water (kg m\ :sup:`-2`) (section :numref:`Canopy Water`), :math:`\Delta t` is the time step (s), and :math:`\beta _{t}` is a soil moisture function limiting transpiration (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). The potential evaporation from wet foliage per unit wetted area is .. math:: :label: 5.112 @@ -1147,33 +883,23 @@ The term :math:`r_{dry} ^{{'} {'} }` is r_{dry} ^{{'} {'} } =\frac{f_{dry} r_{b} }{L} \left(\frac{L^{sun} }{r_{b} +r_{s}^{sun} } +\frac{L^{sha} }{r_{b} +r_{s}^{sha} } \right) -where :math:`f_{dry}` is the fraction of leaves that are dry (section -:numref:`Canopy Water`), :math:`L^{sun}` and :math:`L^{sha}` are the sunlit and shaded -leaf area indices (section :numref:`Solar Fluxes`), and :math:`r_{s}^{sun}` and -:math:`r_{s}^{sha}` are the sunlit and shaded stomatal resistances (s -m\ :sup:`-1`) (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). +where :math:`f_{dry}` is the fraction of leaves that are dry (section :numref:`Canopy Water`), :math:`L^{sun}` and :math:`L^{sha}` are the sunlit and shaded leaf area indices (section :numref:`Solar Fluxes`), and :math:`r_{s}^{sun}` and :math:`r_{s}^{sha}` are the sunlit and shaded stomatal resistances (s m\ :sup:`-1`) (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). -When the expression for :math:`q_{s}` is substituted into equation :eq:`5.101`, -the water vapor flux from vegetation :math:`E_{v}` is a function of -:math:`q_{atm}` , :math:`q_{g}` , and :math:`q_{sat}^{T_{v} }` +When the expression for :math:`q_{s}` is substituted into equation :eq:`5.101`, the water vapor flux from vegetation :math:`E_{v}` is a function of :math:`q_{atm}`, :math:`q_{g}`, and :math:`q_{sat}^{T_{v} }` .. math:: :label: 5.114 E_{v} =-\rho _{atm} \left[c_{a}^{w} q_{atm} +c_{g}^{w} q_{g} -\left(c_{a}^{w} +c_{g}^{w} \right)q_{sat}^{T_{v} } \right]\frac{c_{v}^{w} }{c_{a}^{w} +c_{v}^{w} +c_{g}^{w} } . -Similarly, the expression for :math:`q_{s}` can be substituted into -:eq:`5.84` to obtain the water vapor flux from the ground beneath the -canopy :math:`E_{g}` +Similarly, the expression for :math:`q_{s}` can be substituted into :eq:`5.84` to obtain the water vapor flux from the ground beneath the canopy :math:`E_{g}` .. math:: :label: 5.115 E_{g} =-\rho _{atm} \left[c_{a}^{w} q_{atm} +c_{v}^{w} q_{sat}^{T_{v} } -\left(c_{a}^{w} +c_{v}^{w} \right)q_{g} \right]\frac{c_{g}^{w} }{c_{a}^{w} +c_{v}^{w} +c_{g}^{w} } . -The aerodynamic resistances to heat (moisture) transfer between the -ground at height :math:`z_{0h} ^{{'} }` (:math:`z_{0w} ^{{'} }` ) and -the canopy air at height :math:`z_{0h} +d` (:math:`z_{0w} +d`) are +The aerodynamic resistances to heat (moisture) transfer between the ground at height :math:`z_{0h} ^{{'} }` (:math:`z_{0w} ^{{'} }` ) and the canopy air at height :math:`z_{0h} +d` (:math:`z_{0w} +d`) are .. math:: :label: 5.116 @@ -1187,12 +913,7 @@ where U_{av} =V_{a} \sqrt{\frac{1}{r_{am} V_{a} } } =u_{*} -is the magnitude of the wind velocity incident on the leaves -(equivalent here to friction velocity) (m s\ :sup:`-1`) and -:math:`C_{s}` is the turbulent transfer coefficient between the -underlying soil and the canopy air. :math:`C_{s}` is obtained by -interpolation between values for dense canopy and bare soil -(:ref:`Zeng et al. 2005 `) +is the magnitude of the wind velocity incident on the leaves (equivalent here to friction velocity) (m s\ :sup:`-1`) and :math:`C_{s}` is the turbulent transfer coefficient between the underlying soil and the canopy air. :math:`C_{s}` is obtained by interpolation between values for dense canopy and bare soil (:ref:`Zeng et al. 2005 `) .. math:: :label: 5.118 @@ -1206,8 +927,7 @@ where the weight :math:`W` is W=e^{-\left(L+S\right)} . -The dense canopy turbulent transfer coefficient -(:ref:`Dickinson et al. 1993 `) is +The dense canopy turbulent transfer coefficient (:ref:`Dickinson et al. 1993 `) is .. math:: :label: 5.120) @@ -1221,8 +941,7 @@ The bare soil turbulent transfer coefficient is C_{s,\, bare} =\frac{k}{a} \left(\frac{z_{0m,\, g} U_{av} }{\upsilon } \right)^{-0.45} -where the kinematic viscosity of air -:math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. +where the kinematic viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. The leaf boundary layer resistance :math:`r_{b}` is @@ -1231,16 +950,9 @@ The leaf boundary layer resistance :math:`r_{b}` is r_{b} =\frac{1}{C_{v} } \left({U_{av} \mathord{\left/ {\vphantom {U_{av} d_{leaf} }} \right.} d_{leaf} } \right)^{{-1\mathord{\left/ {\vphantom {-1 2}} \right.} 2} } -where :math:`C_{v} =0.01` m\ s\ :sup:`-1/2` is the turbulent -transfer coefficient between the canopy surface and canopy air, and -:math:`d_{leaf}` is the characteristic dimension of the leaves in the -direction of wind flow (:numref:`Table Plant functional type aerodynamic parameters`). +where :math:`C_{v} =0.01` m\ s\ :sup:`-1/2` is the turbulent transfer coefficient between the canopy surface and canopy air, and :math:`d_{leaf}` is the characteristic dimension of the leaves in the direction of wind flow (:numref:`Table Plant functional type aerodynamic parameters`). -The partial derivatives of the fluxes from the soil beneath the canopy -with respect to ground temperature, which are needed for the soil -temperature calculations (section :numref:`Numerical Solution Temperature`) -and to update the soil surface fluxes (section -:numref:`Update of Ground Sensible and Latent Heat Fluxes`), are +The partial derivatives of the fluxes from the soil beneath the canopy with respect to ground temperature, which are needed for the soil temperature calculations (section :numref:`Numerical Solution Temperature`) and to update the soil surface fluxes (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`), are .. math:: :label: 5.123 @@ -1252,19 +964,9 @@ and to update the soil surface fluxes (section \frac{\partial E_{g} }{\partial T_{g} } = \frac{\rho _{atm} }{r'_{aw} +r_{soil} } \frac{c_{a}^{w} +c_{v}^{w} }{c_{a}^{w} +c_{v}^{w} +c_{g}^{w} } \frac{dq_{g} }{dT_{g} } . -The partial derivatives -:math:`\frac{\partial r'_{ah} }{\partial T_{g} }` and -:math:`\frac{\partial r'_{aw} }{\partial T_{g} }` , which cannot be -determined analytically, are ignored for -:math:`\frac{\partial H_{g} }{\partial T_{g} }` and -:math:`\frac{\partial E_{g} }{\partial T_{g} }` . +The partial derivatives :math:`\frac{\partial r'_{ah} }{\partial T_{g} }` and :math:`\frac{\partial r'_{aw} }{\partial T_{g} }`, which cannot be determined analytically, are ignored for :math:`\frac{\partial H_{g} }{\partial T_{g} }` and :math:`\frac{\partial E_{g} }{\partial T_{g} }`. -The roughness lengths used to calculate :math:`r_{am}` , -:math:`r_{ah}` , and :math:`r_{aw}` from :eq:`5.55`, :eq:`5.56`, and :eq:`5.57` are -:math:`z_{0m} =z_{0m,\, v}` , :math:`z_{0h} =z_{0h,\, v}` , and -:math:`z_{0w} =z_{0w,\, v}` . The vegetation displacement height -:math:`d` and the roughness lengths are a function of plant height and -adjusted for canopy density following :ref:`Zeng and Wang (2007) ` +The roughness lengths used to calculate :math:`r_{am}`, :math:`r_{ah}`, and :math:`r_{aw}` from :eq:`5.55`, :eq:`5.56`, and :eq:`5.57` are :math:`z_{0m} =z_{0m,\, v}`, :math:`z_{0h} =z_{0h,\, v}`, and :math:`z_{0w} =z_{0w,\, v}`. The vegetation displacement height :math:`d` and the roughness lengths are a function of plant height and adjusted for canopy density following :ref:`Zeng and Wang (2007) ` .. math:: :label: 5.125 @@ -1276,23 +978,14 @@ adjusted for canopy density following :ref:`Zeng and Wang (2007) ` d = z_{top} R_{d} V -where :math:`z_{top}` is canopy top height (m) -(:numref:`Table Plant functional type canopy top and bottom heights`), -:math:`R_{z0m}` and :math:`R_{d}` are the ratio of momentum roughness -length and displacement height to canopy top height, respectively -(:numref:`Table Plant functional type aerodynamic parameters`), and :math:`z_{0m,\, g}` -is the ground momentum roughness length (m) (section -:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`). The -fractional weight :math:`V` is determined from +where :math:`z_{top}` is canopy top height (m) (:numref:`Table Plant functional type canopy top and bottom heights`), :math:`R_{z0m}` and :math:`R_{d}` are the ratio of momentum roughness length and displacement height to canopy top height, respectively (:numref:`Table Plant functional type aerodynamic parameters`), and :math:`z_{0m,\, g}` is the ground momentum roughness length (m) (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`). The fractional weight :math:`V` is determined from .. math:: :label: 5.127 V = \frac{1-\exp \left\{-\beta \min \left[L+S,\, \left(L+S\right)_{cr} \right]\right\}}{1-\exp \left[-\beta \left(L+S\right)_{cr} \right]} -where :math:`\beta =1` and :math:`\left(L+S\right)_{cr} = 2` -(m\ :sup:`2` m\ :sup:`-2`) is a critical value of exposed leaf -plus stem area for which :math:`z_{0m}` reaches its maximum. +where :math:`\beta =1` and :math:`\left(L+S\right)_{cr} = 2` (m\ :sup:`2` m\ :sup:`-2`) is a critical value of exposed leaf plus stem area for which :math:`z_{0m}` reaches its maximum. .. _Table Plant functional type aerodynamic parameters: @@ -1370,27 +1063,16 @@ Canopy energy conservation gives -\overrightarrow{S}_{v} +\overrightarrow{L}_{v} \left(T_{v} \right)+H_{v} \left(T_{v} \right)+\lambda E_{v} \left(T_{v} \right)=0 -where :math:`\overrightarrow{S}_{v}` is the solar radiation absorbed by -the vegetation (section :numref:`Solar Fluxes`), :math:`\overrightarrow{L}_{v}` is the net -longwave radiation absorbed by vegetation (section :numref:`Longwave Fluxes`), and -:math:`H_{v}` and :math:`\lambda E_{v}` are the sensible and latent -heat fluxes from vegetation, respectively. The term :math:`\lambda` is -taken to be the latent heat of vaporization :math:`\lambda _{vap}` -(:numref:`Table Physical constants`). +where :math:`\overrightarrow{S}_{v}` is the solar radiation absorbed by the vegetation (section :numref:`Solar Fluxes`), :math:`\overrightarrow{L}_{v}` is the net longwave radiation absorbed by vegetation (section :numref:`Longwave Fluxes`), and :math:`H_{v}` and :math:`\lambda E_{v}` are the sensible and latent heat fluxes from vegetation, respectively. The term :math:`\lambda` is taken to be the latent heat of vaporization :math:`\lambda _{vap}` (:numref:`Table Physical constants`). -:math:`\overrightarrow{L}_{v}` , :math:`H_{v}` , and -:math:`\lambda E_{v}` depend on the vegetation temperature -:math:`T_{v}` . The Newton-Raphson method for finding roots of -non-linear systems of equations can be applied to iteratively solve for -:math:`T_{v}` as +:math:`\overrightarrow{L}_{v}`, :math:`H_{v}`, and :math:`\lambda E_{v}` depend on the vegetation temperature :math:`T_{v}`. The Newton-Raphson method for finding roots of non-linear systems of equations can be applied to iteratively solve for :math:`T_{v}` as .. math:: :label: 5.129 \Delta T_{v} =\frac{\overrightarrow{S}_{v} -\overrightarrow{L}_{v} -H_{v} -\lambda E_{v} }{\frac{\partial \overrightarrow{L}_{v} }{\partial T_{v} } +\frac{\partial H_{v} }{\partial T_{v} } +\frac{\partial \lambda E_{v} }{\partial T_{v} } } -where :math:`\Delta T_{v} =T_{v}^{n+1} -T_{v}^{n}` and the subscript -"n" indicates the iteration. +where :math:`\Delta T_{v} =T_{v}^{n+1} -T_{v}^{n}` and the subscript "n" indicates the iteration. The partial derivatives are @@ -1409,17 +1091,7 @@ The partial derivatives are \frac{\partial \lambda E_{v} }{\partial T_{v} } =\lambda \rho _{atm} \left(c_{a}^{w} +c_{g}^{w} \right)\frac{c_{v}^{w} }{c_{a}^{w} +c_{v}^{w} +c_{g}^{w} } \frac{dq_{sat}^{T_{v} } }{dT_{v} } . -The partial derivatives -:math:`\frac{\partial r_{ah} }{\partial T_{v} }` and -:math:`\frac{\partial r_{aw} }{\partial T_{v} }` , which cannot be -determined analytically, are ignored for -:math:`\frac{\partial H_{v} }{\partial T_{v} }` and -:math:`\frac{\partial \lambda E_{v} }{\partial T_{v} }` . However, if -:math:`\zeta` changes sign more than four times during the temperature -iteration, :math:`\zeta =-0.01`. This helps prevent "flip-flopping" -between stable and unstable conditions. The total water vapor flux -:math:`E_{v}` , transpiration flux :math:`E_{v}^{t}` , and sensible heat -flux :math:`H_{v}` are updated for changes in leaf temperature as +The partial derivatives :math:`\frac{\partial r_{ah} }{\partial T_{v} }` and :math:`\frac{\partial r_{aw} }{\partial T_{v} }`, which cannot be determined analytically, are ignored for :math:`\frac{\partial H_{v} }{\partial T_{v} }` and :math:`\frac{\partial \lambda E_{v} }{\partial T_{v} }`. However, if :math:`\zeta` changes sign more than four times during the temperature iteration, :math:`\zeta =-0.01`. This helps prevent "flip-flopping" between stable and unstable conditions. The total water vapor flux :math:`E_{v}`, transpiration flux :math:`E_{v}^{t}`, and sensible heat flux :math:`H_{v}` are updated for changes in leaf temperature as .. math:: :label: 5.133 @@ -1436,12 +1108,9 @@ flux :math:`H_{v}` are updated for changes in leaf temperature as H_{v} =-\rho _{atm} C_{p} \left[c_{a}^{h} \theta _{atm} +c_{g}^{h} T_{g} -\left(c_{a}^{h} +c_{g}^{h} \right)\left(T_{v} +\Delta T_{v} \right)\right]\frac{c_{v}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } . -The numerical solution for vegetation temperature and the fluxes of -momentum, sensible heat, and water vapor flux from vegetated surfaces -proceeds as follows: +The numerical solution for vegetation temperature and the fluxes of momentum, sensible heat, and water vapor flux from vegetated surfaces proceeds as follows: -#. Initial values for canopy air temperature and specific humidity are - obtained from +#. Initial values for canopy air temperature and specific humidity are obtained from .. math:: :label: 5.136 @@ -1453,154 +1122,94 @@ proceeds as follows: q_{s} =\frac{q_{g} +q_{atm} }{2} . -#. An initial guess for the wind speed :math:`V_{a}` is obtained from - :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m - s\ :sup:`-1` for stable conditions - (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` as evaluated from - :eq:`5.50` ) and :math:`U_{c} =0.5` for unstable conditions - (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). +#. An initial guess for the wind speed :math:`V_{a}` is obtained from :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m s\ :sup:`-1` for stable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` as evaluated from :eq:`5.50` ) and :math:`U_{c} =0.5` for unstable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). -#. An initial guess for the Monin-Obukhov length :math:`L` is obtained - from the bulk Richardson number using equation and :eq:`5.46` and :eq:`5.48`. +#. An initial guess for the Monin-Obukhov length :math:`L` is obtained from the bulk Richardson number using equation and :eq:`5.46` and :eq:`5.48`. #. Iteration proceeds on the following system of equations: -#. Friction velocity :math:`u_{*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) +#. Friction velocity :math:`u_{*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) -#. Ratio :math:`\frac{\theta _{*} }{\theta _{atm} -\theta _{s} }` - (:eq:`5.37` , :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) +#. Ratio :math:`\frac{\theta _{*} }{\theta _{atm} -\theta _{s} }` (:eq:`5.37`, :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) -#. Ratio :math:`\frac{q_{*} }{q_{atm} -q_{s} }` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) +#. Ratio :math:`\frac{q_{*} }{q_{atm} -q_{s} }` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) -#. Aerodynamic resistances :math:`r_{am}` , :math:`r_{ah}` , and - :math:`r_{aw}` (:eq:`5.55`, :eq:`5.56`, :eq:`5.57`) +#. Aerodynamic resistances :math:`r_{am}`, :math:`r_{ah}`, and :math:`r_{aw}` (:eq:`5.55`, :eq:`5.56`, :eq:`5.57`) -#. Magnitude of the wind velocity incident on the leaves :math:`U_{av}` - (:eq:`5.117` ) +#. Magnitude of the wind velocity incident on the leaves :math:`U_{av}` (:eq:`5.117` ) -#. Leaf boundary layer resistance :math:`r_{b}` (:eq:`5.136` ) +#. Leaf boundary layer resistance :math:`r_{b}` (:eq:`5.136` ) -#. Aerodynamic resistances :math:`r_{ah} ^{{'} }` and - :math:`r_{aw} ^{{'} }` (:eq:`5.116` ) +#. Aerodynamic resistances :math:`r_{ah} ^{{'} }` and :math:`r_{aw} ^{{'} }`(:eq:`5.116` ) -#. Sunlit and shaded stomatal resistances :math:`r_{s}^{sun}` and - :math:`r_{s}^{sha}` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`) +#. Sunlit and shaded stomatal resistances :math:`r_{s}^{sun}` and :math:`r_{s}^{sha}` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`) -#. Sensible heat conductances :math:`c_{a}^{h}` , :math:`c_{g}^{h}` , - and :math:`c_{v}^{h}` (:eq:`5.94`, :eq:`5.95`, :eq:`5.96`) +#. Sensible heat conductances :math:`c_{a}^{h}`, :math:`c_{g}^{h}`, and :math:`c_{v}^{h}` (:eq:`5.94`, :eq:`5.95`, :eq:`5.96`) -#. Latent heat conductances :math:`c_{a}^{w}` , :math:`c_{v}^{w}` , and - :math:`c_{g}^{w}` (:eq:`5.108`, :eq:`5.109`, :eq:`5.110`) +#. Latent heat conductances :math:`c_{a}^{w}`, :math:`c_{v}^{w}`, and :math:`c_{g}^{w}` (:eq:`5.108`, :eq:`5.109`, :eq:`5.110`) -#. Sensible heat flux from vegetation :math:`H_{v}` (:eq:`5.97` ) +#. Sensible heat flux from vegetation :math:`H_{v}` (:eq:`5.97` ) -#. Latent heat flux from vegetation :math:`\lambda E_{v}` (:eq:`5.101` ) +#. Latent heat flux from vegetation :math:`\lambda E_{v}` (:eq:`5.101` ) -#. If the latent heat flux has changed sign from the latent heat flux - computed at the previous iteration - (:math:`\lambda E_{v} ^{n+1} \times \lambda E_{v} ^{n} <0`), the - latent heat flux is constrained to be 10% of the computed value. The - difference between the constrained and computed value - (:math:`\Delta _{1} =0.1\lambda E_{v} ^{n+1} -\lambda E_{v} ^{n+1}` ) - is added to the sensible heat flux later. +#. If the latent heat flux has changed sign from the latent heat flux computed at the previous iteration (:math:`\lambda E_{v} ^{n+1} \times \lambda E_{v} ^{n} <0`), the latent heat flux is constrained to be 10% of the computed value. The difference between the constrained and computed value (:math:`\Delta _{1} =0.1\lambda E_{v} ^{n+1} -\lambda E_{v} ^{n+1}` ) is added to the sensible heat flux later. -#. Change in vegetation temperature :math:`\Delta T_{v}` (:eq:`5.129` ) and - update the vegetation temperature as - :math:`T_{v}^{n+1} =T_{v}^{n} +\Delta T_{v}` . :math:`T_{v}` is - constrained to change by no more than 1ºK in one iteration. If this - limit is exceeded, the energy error is +#. Change in vegetation temperature :math:`\Delta T_{v}` (:eq:`5.129` ) and update the vegetation temperature as :math:`T_{v}^{n+1} =T_{v}^{n} +\Delta T_{v}`. :math:`T_{v}` is constrained to change by no more than 1ºK in one iteration. If this limit is exceeded, the energy error is .. math:: :label: 5.138 \Delta _{2} =\overrightarrow{S}_{v} -\overrightarrow{L}_{v} -\frac{\partial \overrightarrow{L}_{v} }{\partial T_{v} } \Delta T_{v} -H_{v} -\frac{\partial H_{v} }{\partial T_{v} } \Delta T_{v} -\lambda E_{v} -\frac{\partial \lambda E_{v} }{\partial T_{v} } \Delta T_{v} -where :math:`\Delta T_{v} =1{\rm \; or\; }-1`. The error -:math:`\Delta _{2}` is added to the sensible heat flux later. +where :math:`\Delta T_{v} =1{\rm \; or\; }-1`. The error :math:`\Delta _{2}` is added to the sensible heat flux later. -#. Water vapor flux :math:`E_{v}` (:eq:`5.133` ) +#. Water vapor flux :math:`E_{v}` (:eq:`5.133` ) -#. Transpiration :math:`E_{v}^{t}` (:eq:`5.134` if :math:`\beta_{t} >0`, - otherwise :math:`E_{v}^{t} =0`) +#. Transpiration :math:`E_{v}^{t}` (:eq:`5.134` if :math:`\beta_{t} >0`, otherwise :math:`E_{v}^{t} =0`) -#. The water vapor flux :math:`E_{v}` is constrained to be less than or - equal to the sum of transpiration :math:`E_{v}^{t}` and the water - available from wetted leaves and stems - :math:`{W_{can} \mathord{\left/ {\vphantom {W_{can} \Delta t}} \right.} \Delta t}` . - The energy error due to this constraint is +#. The water vapor flux :math:`E_{v}` is constrained to be less than or equal to the sum of transpiration :math:`E_{v}^{t}` and the water available from wetted leaves and stems :math:`{W_{can} \mathord{\left/ {\vphantom {W_{can} \Delta t}} \right.} \Delta t}`. The energy error due to this constraint is .. math:: :label: 5.139 \Delta _{3} =\max \left(0,\, E_{v} -E_{v}^{t} -\frac{W_{can} }{\Delta t} \right). -The error :math:`\lambda \Delta _{3}` is added to the sensible heat -flux later. +The error :math:`\lambda \Delta _{3}` is added to the sensible heat flux later. -#. Sensible heat flux :math:`H_{v}` (:eq:`5.135` ). The three energy error - terms, :math:`\Delta _{1}` , :math:`\Delta _{2}` , and - :math:`\lambda \Delta _{3}` are also added to the sensible heat - flux. +#. Sensible heat flux :math:`H_{v}` (:eq:`5.135` ). The three energy error terms, :math:`\Delta _{1}`, :math:`\Delta _{2}`, and :math:`\lambda \Delta _{3}` are also added to the sensible heat flux. -#. The saturated vapor pressure :math:`e_{i}` (Chapter - :numref:`rst_Stomatal Resistance and Photosynthesis`), saturated - specific humidity :math:`q_{sat}^{T_{v} }` and its derivative - :math:`\frac{dq_{sat}^{T_{v} } }{dT_{v} }` at the leaf surface - (section :numref:`Saturation Vapor Pressure`), are re-evaluated based on - the new :math:`T_{v}` . +#. The saturated vapor pressure :math:`e_{i}` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), saturated specific humidity :math:`q_{sat}^{T_{v} }` and its derivative :math:`\frac{dq_{sat}^{T_{v} } }{dT_{v} }` at the leaf surface (section :numref:`Saturation Vapor Pressure`), are re-evaluated based on the new :math:`T_{v}`. -#. Canopy air temperature :math:`T_{s}` (:eq:`5.93` ) +#. Canopy air temperature :math:`T_{s}` (:eq:`5.93` ) -#. Canopy air specific humidity :math:`q_{s}` (:eq:`5.107` ) +#. Canopy air specific humidity :math:`q_{s}` (:eq:`5.107` ) #. Temperature difference :math:`\theta _{atm} -\theta _{s}` #. Specific humidity difference :math:`q_{atm} -q_{s}` -#. Potential temperature scale - :math:`\theta _{*} =\frac{\theta _{*} }{\theta _{atm} -\theta _{s} } \left(\theta _{atm} -\theta _{s} \right)` - where :math:`\frac{\theta _{*} }{\theta _{atm} -\theta _{s} }` was - calculated earlier in the iteration - -#. Humidity scale - :math:`q_{*} =\frac{q_{*} }{q_{atm} -q_{s} } \left(q_{atm} -q_{s} \right)` - where :math:`\frac{q_{*} }{q_{atm} -q_{s} }` was calculated earlier - in the iteration +#. Potential temperature scale :math:`\theta _{*} =\frac{\theta _{*} }{\theta _{atm} -\theta _{s} } \left(\theta _{atm} -\theta _{s} \right)` where :math:`\frac{\theta _{*} }{\theta _{atm} -\theta _{s} }` was calculated earlier in the iteration #. Humidity scale :math:`q_{*} =\frac{q_{*} }{q_{atm} -q_{s} } \left(q_{atm} -q_{s} \right)` where :math:`\frac{q_{*} }{q_{atm} -q_{s} }` was calculated earlier in the iteration #. Virtual potential temperature scale :math:`\theta _{v*}` (:eq:`5.17` ) -#. Virtual potential temperature scale :math:`\theta _{v*}` (:eq:`5.17` ) - -#. Wind speed including the convective velocity, :math:`V_{a}` (:eq:`5.24` ) +#. Wind speed including the convective velocity, :math:`V_{a}` (:eq:`5.24` ) #. Monin-Obukhov length :math:`L` (:eq:`5.49` ) -#. The iteration is stopped after two or more steps if - :math:`\tilde{\Delta }T_{v} <0.01` and - :math:`\left|\lambda E_{v}^{n+1} -\lambda E_{v}^{n} \right|<0.1` - where - :math:`\tilde{\Delta }T_{v} =\max \left(\left|T_{v}^{n+1} -T_{v}^{n} \right|,\, \left|T_{v}^{n} -T_{v}^{n-1} \right|\right)`, - or after forty iterations have been carried out. +#. The iteration is stopped after two or more steps if :math:`\tilde{\Delta }T_{v} <0.01` and :math:`\left|\lambda E_{v}^{n+1} -\lambda E_{v}^{n} \right|<0.1` where :math:`\tilde{\Delta }T_{v} =\max \left(\left|T_{v}^{n+1} -T_{v}^{n} \right|,\, \left|T_{v}^{n} -T_{v}^{n-1} \right|\right)`, or after forty iterations have been carried out. -#. Momentum fluxes :math:`\tau _{x}` , :math:`\tau _{y}` (:eq:`5.5`, :eq:`5.6`) +#. Momentum fluxes :math:`\tau _{x}`, :math:`\tau _{y}` (:eq:`5.5`, :eq:`5.6`) -#. Sensible heat flux from ground :math:`H_{g}` (:eq:`5.89` ) +#. Sensible heat flux from ground :math:`H_{g}` (:eq:`5.89` ) -#. Water vapor flux from ground :math:`E_{g}` (:eq:`5.102` ) +#. Water vapor flux from ground :math:`E_{g}` (:eq:`5.102` ) -#. 2-m height air temperature :math:`T_{2m}` , specific humidity - :math:`q_{2m}` , relative humidity :math:`RH_{2m}` \ (:eq:`5.58` , :eq:`5.59`, :eq:`5.60`) +#. 2-m height air temperature :math:`T_{2m}`, specific humidity :math:`q_{2m}`, relative humidity :math:`RH_{2m}` \ (:eq:`5.58`, :eq:`5.59`, :eq:`5.60`) .. _Update of Ground Sensible and Latent Heat Fluxes: Update of Ground Sensible and Latent Heat Fluxes ---------------------------------------------------- -The sensible and water vapor heat fluxes derived above for bare soil and -soil beneath canopy are based on the ground surface temperature from the -previous time step :math:`T_{g}^{n}` and are used as the surface -forcing for the solution of the soil temperature equations (section -:numref:`Numerical Solution Temperature`). This solution yields a new ground -surface temperature :math:`T_{g}^{n+1}` . The ground sensible and water -vapor fluxes are then updated for :math:`T_{g}^{n+1}` as +The sensible and water vapor heat fluxes derived above for bare soil and soil beneath canopy are based on the ground surface temperature from the previous time step :math:`T_{g}^{n}` and are used as the surface forcing for the solution of the soil temperature equations (section :numref:`Numerical Solution Temperature`). This solution yields a new ground surface temperature :math:`T_{g}^{n+1}`. The ground sensible and water vapor fluxes are then updated for :math:`T_{g}^{n+1}` as .. math:: :label: 5.140 @@ -1612,13 +1221,7 @@ vapor fluxes are then updated for :math:`T_{g}^{n+1}` as E'_{g} =E_{g} +\left(T_{g}^{n+1} -T_{g}^{n} \right)\frac{\partial E_{g} }{\partial T_{g} } -where :math:`H_{g}` and :math:`E_{g}` are the sensible heat and water -vapor fluxes derived from equations and for non-vegetated surfaces and -equations and for vegetated surfaces using :math:`T_{g}^{n}` . One -further adjustment is made to :math:`H'_{g}` and :math:`E'_{g}` . If -the soil moisture in the top snow/soil layer is not sufficient to -support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and -:math:`f_{evap} < 1` where +where :math:`H_{g}` and :math:`E_{g}` are the sensible heat and water vapor fluxes derived from equations and for non-vegetated surfaces and equations and for vegetated surfaces using :math:`T_{g}^{n}`. One further adjustment is made to :math:`H'_{g}` and :math:`E'_{g}`. If the soil moisture in the top snow/soil layer is not sufficient to support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and :math:`f_{evap} < 1` where .. math:: :label: 5.142 @@ -1632,29 +1235,14 @@ an adjustment is made to reduce the ground evaporation accordingly as E''_{g} =f_{evap} E'_{g} . -The term -:math:`\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j}` -is the sum of :math:`E'_{g}` over all evaporating PFTs where -:math:`\left(E'_{g} \right)_{j}` is the ground evaporation from the -:math:`j^{th}` PFT on the column, :math:`\left(wt\right)_{j}` is the -relative area of the :math:`j^{th}` PFT with respect to the column, and -:math:`npft` is the number of PFTs on the column. -:math:`w_{ice,\, snl+1}` and :math:`w_{liq,\, snl+1}` are the ice and -liquid water contents (kg m\ :sup:`-2`) of the top snow/soil layer -(Chapter :numref:`rst_Hydrology`). Any resulting energy deficit is assigned -to sensible heat -as +The term :math:`\sum _{j=1}^{npft}\left(E'_{g} \right)_{j} \left(wt\right)_{j}` is the sum of :math:`E'_{g}` over all evaporating PFTs where :math:`\left(E'_{g} \right)_{j}` is the ground evaporation from the :math:`j^{th}` PFT on the column, :math:`\left(wt\right)_{j}` is the relative area of the :math:`j^{th}` PFT with respect to the column, and :math:`npft` is the number of PFTs on the column. :math:`w_{ice,\, snl+1}` and :math:`w_{liq,\, snl+1}` are the ice and liquid water contents (kg m\ :sup:`-2`) of the top snow/soil layer (Chapter :numref:`rst_Hydrology`). Any resulting energy deficit is assigned to sensible heat as .. math:: :label: 5.144 H''_{g} =H_{g} +\lambda \left(E'_{g} -E''_{g} \right). -The ground water vapor flux :math:`E''_{g}` is partitioned into evaporation -of liquid water from snow/soil :math:`q_{seva}` (kg\ m\ :sup:`-2` s\ :sup:`-1`), -sublimation from snow/soil ice :math:`q_{subl}` (kg m\ :sup:`-2` s\ :sup:`-1`), -liquid dew on snow/soil :math:`q_{sdew}` (kg m\ :sup:`-2` s\ :sup:`-1`), or -frost on snow/soil :math:`q_{frost}` (kg m\ :sup:`-2` s\ :sup:`-1`) as +The ground water vapor flux :math:`E''_{g}` is partitioned into evaporation of liquid water from snow/soil :math:`q_{seva}` (kg\ m\ :sup:`-2` s\ :sup:`-1`), sublimation from snow/soil ice :math:`q_{subl}` (kg m\ :sup:`-2` s\ :sup:`-1`), liquid dew on snow/soil :math:`q_{sdew}` (kg m\ :sup:`-2` s\ :sup:`-1`), or frost on snow/soil :math:`q_{frost}` (kg m\ :sup:`-2` s\ :sup:`-1`) as .. math:: :label: 5.145 @@ -1676,15 +1264,7 @@ frost on snow/soil :math:`q_{frost}` (kg m\ :sup:`-2` s\ :sup:`-1`) as q_{frost} =\left|E''_{sno} \right|\qquad E''_{sno} <0{\rm \; and\; }T_{g} 0} \\ {\lambda _{vap} \qquad {\rm otherwise}} \end{array}\right\} -where :math:`\lambda _{sub}` and :math:`\lambda _{vap}` are the latent -heat of sublimation and vaporization, respectively (J -(kg\ :sup:`-1`) (:numref:`Table Physical constants`). When converting vegetation water vapor -flux to an energy flux, :math:`\lambda _{vap}` is used. +where :math:`\lambda _{sub}` and :math:`\lambda _{vap}` are the latent heat of sublimation and vaporization, respectively (J (kg\ :sup:`-1`) (:numref:`Table Physical constants`). When converting vegetation water vapor flux to an energy flux, :math:`\lambda _{vap}` is used. The system balances energy as @@ -1737,10 +1310,7 @@ The system balances energy as Saturation Vapor Pressure ----------------------------- -Saturation vapor pressure :math:`e_{sat}^{T}` (Pa) and its derivative -:math:`\frac{de_{sat}^{T} }{dT}` , as a function of temperature -:math:`T` (ºC), are calculated from the eighth-order polynomial fits of -:ref:`Flatau et al. (1992) ` +Saturation vapor pressure :math:`e_{sat}^{T}` (Pa) and its derivative :math:`\frac{de_{sat}^{T} }{dT}`, as a function of temperature :math:`T` (ºC), are calculated from the eighth-order polynomial fits of :ref:`Flatau et al. (1992) ` .. math:: :label: 5.154 @@ -1752,14 +1322,7 @@ Saturation vapor pressure :math:`e_{sat}^{T}` (Pa) and its derivative \frac{de_{sat}^{T} }{dT} =100\left[b_{0} +b_{1} T+\cdots +b_{n} T^{n} \right] -where the coefficients for ice are valid for -:math:`-75\, ^{\circ } {\rm C}\le T<0\, ^{\circ } {\rm C}` and the -coefficients for water are valid for -:math:`0\, ^{\circ } {\rm C}\le T\le 100\, ^{\circ } {\rm C}` -(:numref:`Table Coefficients for saturation vapor pressure` and -:numref:`Table Coefficients for derivative of esat`). -The saturated water vapor specific humidity :math:`q_{sat}^{T}` and its derivative -:math:`\frac{dq_{sat}^{T} }{dT}` are +where the coefficients for ice are valid for :math:`-75\, ^{\circ } {\rm C}\le T<0\, ^{\circ } {\rm C}` and the coefficients for water are valid for :math:`0\, ^{\circ } {\rm C}\le T\le 100\, ^{\circ } {\rm C}` (:numref:`Table Coefficients for saturation vapor pressure` and :numref:`Table Coefficients for derivative of esat`). The saturated water vapor specific humidity :math:`q_{sat}^{T}` and its derivative :math:`\frac{dq_{sat}^{T} }{dT}` are .. math:: :label: 5.156 diff --git a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst index fdc4001465..3e510561bb 100644 --- a/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst +++ b/doc/source/tech_note/Glacier/CLM50_Tech_Note_Glacier.rst @@ -3,199 +3,84 @@ Glaciers ======== -This chapter describes features of CLM that are specific to coupling to -an ice sheet model (in the CESM context, this is the CISM model; -:ref:`Lipscomb and Sacks (2012)` provide -documentation and user's guide for CISM). General information -about glacier land units can be found elsewhere in this document (see -Chapter :numref:`rst_Surface Characterization, Vertical Discretization, -and Model Input Requirements` for an overview). +This chapter describes features of CLM that are specific to coupling to an ice sheet model (in the CESM context, this is the CISM model; :ref:`Lipscomb and Sacks (2012)` provide documentation and user's guide for CISM). General information about glacier land units can be found elsewhere in this document (see Chapter :numref:`rst_Surface Characterization, Vertical Discretization, and Model Input Requirements` for an overview). .. _Glaciers summary of CLM5.0 updates relative to CLM4.5: Summary of CLM5.0 updates relative to CLM4.5 -------------------------------------------- -Compared with CLM4.5 (:ref:`Oleson et al. 2013 `), -CLM5.0 contains substantial improvements in its capabilities for -land-ice science. This section summarizes these improvements, and the -following sections provide more details. +Compared with CLM4.5 (:ref:`Oleson et al. 2013 `), CLM5.0 contains substantial improvements in its capabilities for land-ice science. This section summarizes these improvements, and the following sections provide more details. -- All runs include multiple glacier elevation classes over Greenland and - Antarctica and compute ice sheet surface mass balance in those - regions. +- All runs include multiple glacier elevation classes over Greenland and Antarctica and compute ice sheet surface mass balance in those regions. -- A number of namelist parameters offer fine-grained control over - glacier behavior in different regions of the world (section - :numref:`Glacier regions`). (The options used outside of Greenland and - Antarctica reproduce the standard CLM4.5 glacier behavior.) +- A number of namelist parameters offer fine-grained control over glacier behavior in different regions of the world (section :numref:`Glacier regions`). (The options used outside of Greenland and Antarctica reproduce the standard CLM4.5 glacier behavior.) -- CLM can now keep its glacier areas and elevations in sync with CISM - when running with an evolving ice sheet. (However, in typical - configurations, the ice sheet geometry still remains fixed throughout - the run.) +- CLM can now keep its glacier areas and elevations in sync with CISM when running with an evolving ice sheet. (However, in typical configurations, the ice sheet geometry still remains fixed throughout the run.) -- The downscaling to elevation classes now includes downwelling longwave - radiation and partitioning of precipitation into rain vs. snow - (section :numref:`Multiple elevation class scheme`). +- The downscaling to elevation classes now includes downwelling longwave radiation and partitioning of precipitation into rain vs. snow (section :numref:`Multiple elevation class scheme`). -- Other land units within the CISM domain undergo the same downscaling - as the glacier land unit, and surface mass balance is computed for the - natural vegetated land unit. This allows CLM to produce glacial - inception when running with an evolving ice sheet model. +- Other land units within the CISM domain undergo the same downscaling as the glacier land unit, and surface mass balance is computed for the natural vegetated land unit. This allows CLM to produce glacial inception when running with an evolving ice sheet model. -- There have also been substantial improvements to CLM's snow physics, - as described in other chapters of this document. +- There have also been substantial improvements to CLM's snow physics, as described in other chapters of this document. .. _Overview Glaciers: Overview -------- -CLM is responsible for computing two quantities that are passed to the -ice sheet model: - -#. Surface mass balance (SMB) - the net annual accumulation/ablation of - mass at the upper surface (section - :numref:`Computation of the surface mass balance`) - -#. Ground surface temperature, which serves as an upper boundary - condition for CISM's temperature calculation - -The ice sheet model is typically run at much higher resolution than CLM -(e.g., :math:`\sim`\ 5 km rather than :math:`\sim`\ 100 km). To improve -the downscaling from CLM's grid to the ice sheet grid, the glaciated -portion of each grid cell is divided into multiple elevation classes -(section :numref:`Multiple elevation class scheme`). The above -quantities are computed separately in each elevation class. The CESM -coupler then computes high-resolution quantities via horizontal and -vertical interpolation, and passes these high-resolution quantities to -CISM. - -There are several reasons for computing the SMB in CLM rather than in -CISM: - -#. It is much cheaper to compute the SMB in CLM for :math:`\sim`\ 10 - elevation classes than in CISM. For example, suppose we are - running CLM at a resolution of :math:`\sim`\ 50 km and CISM at - :math:`\sim`\ 5 km. Greenland has dimensions of about 1000 x 2000 km. - For CLM we would have 20 x 40 x 10 = 8,000 columns, whereas for - CISM we would have 200 x 400 = 80,000 columns. - -#. We can use the sophisticated snow physics parameterization already in - CLM instead of implementing a separate scheme for CISM. Any - improvements to CLM are applied to ice sheets automatically. - -#. The atmosphere model can respond during runtime to ice-sheet surface - changes (even in the absence of two-way feedbacks with CISM). As - shown by :ref:`Pritchard et al. (2008)`, runtime - albedo feedback from the ice sheet is critical for simulating - ice-sheet retreat on paleoclimate time scales. Without this feedback - the atmosphere warms much less, and the retreat is delayed. - -#. The improved SMB is potentially available in CLM for all glaciated - grid cells (e.g., in the Alps, Rockies, Andes, and Himalayas), not - just those which are part of ice sheets. - -In typical runs, CISM is not evolving; CLM computes the SMB and sends it -to CISM, but CISM's ice sheet geometry remains fixed over the course of -the run. In these runs, CISM serves two roles in the system: - -#. Over the CISM domain (typically Greenland in CESM2), CISM dictates - glacier areas and topographic elevations, overriding the values on - CLM's surface dataset. CISM also dictates the elevation of - non-glacier land units in its domain, and only in this domain are - atmospheric fields downscaled to non-glacier land units. (So if you - run with a stub glacier model - SGLC - then glacier areas and - elevations will be taken entirely from CLM's surface dataset, and no - downscaling will be done over non-glacier land units.) - -#. CISM provides the grid onto which SMB is downscaled. (If you run with - SGLC then SMB will still be computed in CLM, but it won't be - downscaled to a high-resolution ice sheet grid.) - -It is also possible to run CESM with an evolving ice sheet. In this -case, CLM responds to CISM's evolution by adjusting the areas of the -glacier land unit and each elevation class within this land unit, as well -as the mean topographic heights of each elevation class. Thus, CLM's -glacier areas and elevations remain in sync with CISM's. Conservation of -mass and energy is done as for other landcover change (see Chapter -:numref:`rst_Transient Landcover Change`). +CLM is responsible for computing two quantities that are passed to the ice sheet model: + +#. Surface mass balance (SMB) - the net annual accumulation/ablation of mass at the upper surface (section :numref:`Computation of the surface mass balance`) + +#. Ground surface temperature, which serves as an upper boundary condition for CISM's temperature calculation The ice sheet model is typically run at much higher resolution than CLM (e.g., :math:`\sim`\ 5 km rather than :math:`\sim`\ 100 km). To improve the downscaling from CLM's grid to the ice sheet grid, the glaciated portion of each grid cell is divided into multiple elevation classes (section :numref:`Multiple elevation class scheme`). The above quantities are computed separately in each elevation class. The CESM coupler then computes high-resolution quantities via horizontal and vertical interpolation, and passes these high-resolution quantities to CISM. + +There are several reasons for computing the SMB in CLM rather than in CISM: + +#. It is much cheaper to compute the SMB in CLM for :math:`\sim`\ 10 elevation classes than in CISM. For example, suppose we are running CLM at a resolution of :math:`\sim`\ 50 km and CISM at :math:`\sim`\ 5 km. Greenland has dimensions of about 1000 x 2000 km. For CLM we would have 20 x 40 x 10 = 8,000 columns, whereas for CISM we would have 200 x 400 = 80,000 columns. + +#. We can use the sophisticated snow physics parameterization already in CLM instead of implementing a separate scheme for CISM. Any improvements to CLM are applied to ice sheets automatically. + +#. The atmosphere model can respond during runtime to ice-sheet surface changes (even in the absence of two-way feedbacks with CISM). As shown by :ref:`Pritchard et al. (2008)`, runtime albedo feedback from the ice sheet is critical for simulating ice-sheet retreat on paleoclimate time scales. Without this feedback the atmosphere warms much less, and the retreat is delayed. + +#. The improved SMB is potentially available in CLM for all glaciated grid cells (e.g., in the Alps, Rockies, Andes, and Himalayas), not just those which are part of ice sheets. + +In typical runs, CISM is not evolving; CLM computes the SMB and sends it to CISM, but CISM's ice sheet geometry remains fixed over the course of the run. In these runs, CISM serves two roles in the system: + +#. Over the CISM domain (typically Greenland in CESM2), CISM dictates glacier areas and topographic elevations, overriding the values on CLM's surface dataset. CISM also dictates the elevation of non-glacier land units in its domain, and only in this domain are atmospheric fields downscaled to non-glacier land units. (So if you run with a stub glacier model - SGLC - then glacier areas and elevations will be taken entirely from CLM's surface dataset, and no downscaling will be done over non-glacier land units.) + +#. CISM provides the grid onto which SMB is downscaled. (If you run with SGLC then SMB will still be computed in CLM, but it won't be downscaled to a high-resolution ice sheet grid.) + +It is also possible to run CESM with an evolving ice sheet. In this case, CLM responds to CISM's evolution by adjusting the areas of the glacier land unit and each elevation class within this land unit, as well as the mean topographic heights of each elevation class. Thus, CLM's glacier areas and elevations remain in sync with CISM's. Conservation of mass and energy is done as for other landcover change (see Chapter :numref:`rst_Transient Landcover Change`). .. _Glacier regions: Glacier regions and their behaviors ----------------------------------- -The world's glaciers and ice sheets are broken down into a number of -different regions (four by default) that differ in three respects: +The world's glaciers and ice sheets are broken down into a number of different regions (four by default) that differ in three respects: #. Whether the gridcell's glacier land unit contains: - a. Multiple elevation classes (section :numref:`Multiple elevation - class scheme`) + a. Multiple elevation classes (section :numref:`Multiple elevation class scheme`) - b. Multiple elevation classes plus virtual elevation classes + b. Multiple elevation classes plus virtual elevation classes - c. Just a single elevation class whose elevation matches the - atmosphere's topographic height (so there is no adjustment in - atmospheric forcings due to downscaling). + c. Just a single elevation class whose elevation matches the atmosphere's topographic height (so there is no adjustment in atmospheric forcings due to downscaling). #. Treatment of glacial melt water: - a. Glacial melt water runs off and is replaced by ice, thus keeping - the column always frozen. In the absence of a dynamic ice sheet - model, this behavior implicitly assumes an infinite store of - glacial ice that can be melted (with appropriate adjustments made - to ensure mass and energy conservation). This behavior is - discussed in more detail in section :numref:`Computation of the - surface mass balance`. - - b. Glacial melt water remains in place until it refreezes - possibly - remaining in place indefinitely if the glacier column is in a warm - climate. With this behavior, ice melt does not result in any - runoff. Regions with this behavior cannot compute SMB, because - negative SMB would be meaningless (due to the liquid water on top - of the ice column). This behavior produces less realistic glacier - physics. However, it avoids the negative ice runoff that is needed - for the "replaced by ice" behavior to conserve mass and energy (as - described in section :numref:`Computation of the surface mass - balance`). Thus, in regions where CLM has glaciers but the - atmospheric forcings are too warm to sustain those glaciers, this - behavior avoids persistent negative ice runoff. This situation can - often occur for mountain glaciers, where topographic smoothing in - the atmosphere results in a too-warm climate. There, avoiding - persistent negative ice runoff can be more important than getting - the right glacier ice physics. - -#. Treatment of ice runoff from snow capping (as described in section - :numref:`Runoff from glaciers and snow-capped surfaces`). Note that this - is irrelevant in regions with an evolving, two-way-coupled ice sheet - (where the snow capping term is sent to CISM rather than running off): - - a. Ice runoff from snow capping remains ice. This is a crude - parameterization of iceberg calving, and so is appropriate in - regions where there is substantial iceberg calving in reality. - - b. Ice runoff from snow capping is melted (generating a negative - sensible heat flux) and runs off as liquid. This matches the - behavior for non-glacier columns. This is appropriate in regions - that have little iceberg calving in reality. This can be important - to avoid unrealistic cooling of the ocean and consequent runaway - sea ice growth. - -The default behaviors for the world's glacier and ice sheet regions are -described in :numref:`Table Glacier region behaviors`. Note that the -standard CISM grid covers Greenland plus enough surrounding area to -allow for ice sheet growth and to have a regular rectangular grid. We -need to have the "replaced by ice" melt behavior within the CISM domain -in order to compute SMB there, and we need virtual elevation classes in -that domain in order to compute SMB for all elevation classes and to -facilitate glacial advance and retreat in the two-way-coupled -case. However, this domain is split into Greenland itself and areas -outside Greenland so that ice runoff in the Canadian archipelago (which -is inside the CISM domain) is melted before reaching the ocean, to avoid -runaway sea ice growth in that region. + a. Glacial melt water runs off and is replaced by ice, thus keeping the column always frozen. In the absence of a dynamic ice sheet model, this behavior implicitly assumes an infinite store of glacial ice that can be melted (with appropriate adjustments made to ensure mass and energy conservation). This behavior is discussed in more detail in section :numref:`Computation of the surface mass balance`. + + b. Glacial melt water remains in place until it refreezes - possibly remaining in place indefinitely if the glacier column is in a warm climate. With this behavior, ice melt does not result in any runoff. Regions with this behavior cannot compute SMB, because negative SMB would be meaningless (due to the liquid water on top of the ice column). This behavior produces less realistic glacier physics. However, it avoids the negative ice runoff that is needed for the "replaced by ice" behavior to conserve mass and energy (as described in section :numref:`Computation of the surface mass balance`). Thus, in regions where CLM has glaciers but the atmospheric forcings are too warm to sustain those glaciers, this behavior avoids persistent negative ice runoff. This situation can often occur for mountain glaciers, where topographic smoothing in the atmosphere results in a too-warm climate. There, avoiding persistent negative ice runoff can be more important than getting the right glacier ice physics. + +#. Treatment of ice runoff from snow capping (as described in section :numref:`Runoff from glaciers and snow-capped surfaces`). Note that this is irrelevant in regions with an evolving, two-way-coupled ice sheet (where the snow capping term is sent to CISM rather than running off): + + a. Ice runoff from snow capping remains ice. This is a crude parameterization of iceberg calving, and so is appropriate in regions where there is substantial iceberg calving in reality. + + b. Ice runoff from snow capping is melted (generating a negative sensible heat flux) and runs off as liquid. This matches the behavior for non-glacier columns. This is appropriate in regions that have little iceberg calving in reality. This can be important to avoid unrealistic cooling of the ocean and consequent runaway sea ice growth. + +The default behaviors for the world's glacier and ice sheet regions are described in :numref:`Table Glacier region behaviors`. Note that the standard CISM grid covers Greenland plus enough surrounding area to allow for ice sheet growth and to have a regular rectangular grid. We need to have the "replaced by ice" melt behavior within the CISM domain in order to compute SMB there, and we need virtual elevation classes in that domain in order to compute SMB for all elevation classes and to facilitate glacial advance and retreat in the two-way-coupled case. However, this domain is split into Greenland itself and areas outside Greenland so that ice runoff in the Canadian archipelago (which is inside the CISM domain) is melted before reaching the ocean, to avoid runaway sea ice growth in that region. .. _Table Glacier region behaviors: @@ -224,172 +109,52 @@ runaway sea ice growth in that region. .. note:: - In regions that have both the ``Glacial melt = Replaced by ice`` and the ``Ice runoff = - Melted`` behaviors (by default, this is just the region inside the standard CISM grid - but outside Greenland itself): During periods of glacial melt, a negative ice runoff is - generated (due to the ``Glacial melt = Replaced by ice`` behavior); this negative ice - runoff is converted to a negative liquid runoff plus a positive sensible heat flux (due - to the ``Ice runoff = Melted`` behavior). We recommend that you limit the portion of - the globe with both of these behaviors combined, in order to avoid having too large of - an impact of this non-physical behavior. + In regions that have both the ``Glacial melt = Replaced by ice`` and the ``Ice runoff = Melted`` behaviors (by default, this is just the region inside the standard CISM grid but outside Greenland itself): During periods of glacial melt, a negative ice runoff is generated (due to the ``Glacial melt = Replaced by ice`` behavior); this negative ice runoff is converted to a negative liquid runoff plus a positive sensible heat flux (due to the ``Ice runoff = Melted`` behavior). We recommend that you limit the portion of the globe with both of these behaviors combined, in order to avoid having too large of an impact of this non-physical behavior. .. _Multiple elevation class scheme: Multiple elevation class scheme ------------------------------- -The glacier land unit contains multiple columns based on surface -elevation. These are known as elevation classes, and the land unit is -referred to as *glacier\_mec*. (As described in section :numref:`Glacier -regions`, some regions have only a single elevation class, but they are -still referred to as *glacier\_mec* land units.) The default is to have 10 -elevation classes whose lower limits are 0, 200, 400, 700, 1000, 1300, -1600, 2000, 2500, and 3000 m. Each column is characterized by a -fractional area and surface elevation that are read in during model -initialization, and then possibly overridden by CISM as the run -progresses. Each *glacier\_mec* column within a grid cell has distinct ice -and snow temperatures, snow water content, surface fluxes, and SMB. - -The atmospheric surface temperature, potential temperature, specific -humidity, density, and pressure are downscaled from the atmosphere's -mean grid cell elevation to the *glacier\_mec* column elevation using a -specified lapse rate (typically 6.0 deg/km) and an assumption of uniform -relative humidity. Longwave radiation is downscaled by assuming a linear -decrease in downwelling longwave radiation with increasing elevation -(0.032 W m\ :sup:`-2` m\ :sup:`-1`, limited to 0.5 - 1.5 times the -gridcell mean value, then normalized to conserve gridcell total energy) -:ref:`(Van Tricht et al., 2016)`. Total precipitation -is partitioned into rain vs. snow as described in Chapter -:numref:`rst_Surface Characterization, Vertical Discretization, and -Model Input Requirements`. The partitioning of precipitation is based on -the downscaled temperature, allowing rain to fall at lower elevations -while snow falls at higher elevations. - -This downscaling allows lower-elevation columns to undergo surface -melting while columns at higher elevations remain frozen. This gives a -more accurate simulation of summer melting, which is a highly nonlinear -function of air temperature. - -Within the CISM domain, this same downscaling procedure is also applied -to all non-urban land units. The elevation of non-glacier land units is -taken from the mean elevation of ice-free grid cells in CISM. This is -done in order to keep the glaciated and non-glaciated portions of the -CISM domain as consistent as possible. - -In contrast to most CLM subgrid units, glacier\_mec columns can be -active (i.e., have model calculations run there) even if their area is -zero. These are known as "virtual" columns. This is done because the ice -sheet model may require a SMB for some grid cells where CLM has zero -glacier area in that elevation range. Virtual columns also facilitate -glacial advance and retreat in the two-way coupled case. Virtual columns -do not affect energy exchange between the land and the atmosphere. +The glacier land unit contains multiple columns based on surface elevation. These are known as elevation classes, and the land unit is referred to as *glacier\_mec*. (As described in section :numref:`Glacier regions`, some regions have only a single elevation class, but they are still referred to as *glacier\_mec* land units.) The default is to have 10 elevation classes whose lower limits are 0, 200, 400, 700, 1000, 1300, 1600, 2000, 2500, and 3000 m. Each column is characterized by a fractional area and surface elevation that are read in during model initialization, and then possibly overridden by CISM as the run progresses. Each *glacier\_mec* column within a grid cell has distinct ice and snow temperatures, snow water content, surface fluxes, and SMB. + +The atmospheric surface temperature, potential temperature, specific humidity, density, and pressure are downscaled from the atmosphere's mean grid cell elevation to the *glacier\_mec* column elevation using a specified lapse rate (typically 6.0 deg/km) and an assumption of uniform relative humidity. Longwave radiation is downscaled by assuming a linear decrease in downwelling longwave radiation with increasing elevation (0.032 W m\ :sup:`-2` m\ :sup:`-1`, limited to 0.5 - 1.5 times the gridcell mean value, then normalized to conserve gridcell total energy) :ref:`(Van Tricht et al., 2016)`. Total precipitation is partitioned into rain vs. snow as described in Chapter :numref:`rst_Surface Characterization, Vertical Discretization, and Model Input Requirements`. The partitioning of precipitation is based on the downscaled temperature, allowing rain to fall at lower elevations while snow falls at higher elevations. + +This downscaling allows lower-elevation columns to undergo surface melting while columns at higher elevations remain frozen. This gives a more accurate simulation of summer melting, which is a highly nonlinear function of air temperature. + +Within the CISM domain, this same downscaling procedure is also applied to all non-urban land units. The elevation of non-glacier land units is taken from the mean elevation of ice-free grid cells in CISM. This is done in order to keep the glaciated and non-glaciated portions of the CISM domain as consistent as possible. + +In contrast to most CLM subgrid units, glacier\_mec columns can be active (i.e., have model calculations run there) even if their area is zero. These are known as "virtual" columns. This is done because the ice sheet model may require a SMB for some grid cells where CLM has zero glacier area in that elevation range. Virtual columns also facilitate glacial advance and retreat in the two-way coupled case. Virtual columns do not affect energy exchange between the land and the atmosphere. .. _Computation of the surface mass balance: Computation of the surface mass balance --------------------------------------- -This section describes the computation of surface mass balance and -associated runoff terms. The description here only applies to regions -where glacial melt runs off and is replaced by ice, not to regions where -glacial melt remains in place. Thus, by default, this only applies to -Greenland and Antarctica, not to mountain glaciers elsewhere in the -world. (See also section :numref:`Glacier regions`.) - -The SMB of a glacier or ice sheet is the net annual -accumulation/ablation of mass at the upper surface. Ablation is defined -as the mass of water that runs off to the ocean. Not all the surface -meltwater runs off; some of the melt percolates into the snow and -refreezes. Accumulation is primarily by snowfall and deposition, and -ablation is primarily by melting and evaporation/sublimation. CLM uses a -surface-energy-balance (SEB) scheme to compute the SMB. In this scheme, -the melting depends on the sum of the radiative, turbulent, and -conductive fluxes reaching the surface, as described elsewhere in this -document. - -Note that the SMB typically is defined as the total accumulation of ice -and snow, minus the total ablation. The SMB flux passed to CISM is the -mass balance for ice alone, not snow. We can think of CLM as owning the -snow, whereas CISM owns the underlying ice. Fluctuations in snow depth -between 0 and 10 m water equivalent are not reflected in the SMB passed -to CISM. In transient runs, this can lead to delays of a few decades in -the onset of accumulation or ablation in a given glacier column. - -SMB is computed and sent to the CESM coupler regardless of whether and -where CISM is operating. However, the effect of SMB terms on runoff -fluxes differs depending on whether and where CISM is evolving in -two-way-coupled mode. This is described by the variable -*glc\_dyn\_runoff\_routing*. (This is real-valued in the code to handle -the edge case where a CLM grid cell partially overlaps with the CISM -grid, but we describe it as a logical variable here for simplicity.) In -typical cases where CISM is not evolving, *glc\_dyn\_runoff\_routing* -will be false everywhere; in these cases, CISM's mass is not considered -to be part of the coupled system. In cases where CISM is evolving and -sending its own calving flux to the coupler, *glc\_dyn\_runoff\_routing* -will be true over the CISM domain and false elsewhere. - -Any snow capping (section :numref:`Runoff from glaciers and snow-capped -surfaces`) is added to :math:`q_{ice,frz}`. Any liquid water (i.e., -melted ice) below the snow pack in the glacier column is added to -:math:`q_{ice,melt}`, then is converted back to ice to maintain a -pure-ice column. Then the total SMB is given by :math:`q_{ice,tot}`: +This section describes the computation of surface mass balance and associated runoff terms. The description here only applies to regions where glacial melt runs off and is replaced by ice, not to regions where glacial melt remains in place. Thus, by default, this only applies to Greenland and Antarctica, not to mountain glaciers elsewhere in the world. (See also section :numref:`Glacier regions`.) + +The SMB of a glacier or ice sheet is the net annual accumulation/ablation of mass at the upper surface. Ablation is defined as the mass of water that runs off to the ocean. Not all the surface meltwater runs off; some of the melt percolates into the snow and refreezes. Accumulation is primarily by snowfall and deposition, and ablation is primarily by melting and evaporation/sublimation. CLM uses a surface-energy-balance (SEB) scheme to compute the SMB. In this scheme, the melting depends on the sum of the radiative, turbulent, and conductive fluxes reaching the surface, as described elsewhere in this document. + +Note that the SMB typically is defined as the total accumulation of ice and snow, minus the total ablation. The SMB flux passed to CISM is the mass balance for ice alone, not snow. We can think of CLM as owning the snow, whereas CISM owns the underlying ice. Fluctuations in snow depth between 0 and 10 m water equivalent are not reflected in the SMB passed to CISM. In transient runs, this can lead to delays of a few decades in the onset of accumulation or ablation in a given glacier column. + +SMB is computed and sent to the CESM coupler regardless of whether and where CISM is operating. However, the effect of SMB terms on runoff fluxes differs depending on whether and where CISM is evolving in two-way-coupled mode. This is described by the variable *glc\_dyn\_runoff\_routing*. (This is real-valued in the code to handle the edge case where a CLM grid cell partially overlaps with the CISM grid, but we describe it as a logical variable here for simplicity.) In typical cases where CISM is not evolving, *glc\_dyn\_runoff\_routing* will be false everywhere; in these cases, CISM's mass is not considered to be part of the coupled system. In cases where CISM is evolving and sending its own calving flux to the coupler, *glc\_dyn\_runoff\_routing* will be true over the CISM domain and false elsewhere. + +Any snow capping (section :numref:`Runoff from glaciers and snow-capped surfaces`) is added to :math:`q_{ice,frz}`. Any liquid water (i.e., melted ice) below the snow pack in the glacier column is added to :math:`q_{ice,melt}`, then is converted back to ice to maintain a pure-ice column. Then the total SMB is given by :math:`q_{ice,tot}`: .. math:: :label: 13.1 q_{ice,tot} = q_{ice,frz} - q_{ice,melt} -CLM is responsible for generating glacial surface melt, even when -running with an evolving ice sheet. Thus, :math:`q_{ice,melt}` is always -added to liquid runoff (:math:`q_{rgwl}`), regardless of -*glc\_dyn\_runoff\_routing*. However, the ice runoff flux depends on -*glc\_dyn\_runoff\_routing*. If *glc\_dyn\_runoff\_routing* is true, -then CISM controls the fate of the snow capping mass in -:math:`q_{ice,frz}` (e.g., eventually transporting it to lower -elevations where it can be melted or calved). Since CISM will now own -this mass, the snow capping flux does *not* contribute to any runoff -fluxes generated by CLM in this case. - -If *glc\_dyn\_runoff\_routing* is false, then CLM sends the snow capping -flux as runoff, as a crude representation of ice calving (see also -sections :numref:`Runoff from glaciers and snow-capped surfaces` and -:numref:`Glacier regions`). However, this ice runoff flux is reduced by -:math:`q_{ice,melt}`. This reduction is needed for conservation; its -need is subtle, but can be understood with either of these explanations: - -- When ice melts, we let the liquid run off and replace it with new - ice. That new ice needs to come from somewhere to keep the coupled - system in water balance. We "request" the new ice from the ocean by - generating a negative ice runoff equivalent to the amount we have - melted. - -- Ice melt removes mass from the system, as it should. But the snow - capping flux also removes mass from the system. The latter is a crude - parameterization of calving, assuming steady state - i.e., all ice - gain is balanced by ice loss. This removal of mass due to both - accumulation and melt represents a double-counting. Each unit of melt - indicates that one unit of accumulation should not have made it to the - ocean as ice, but instead melted before it got there. So we need to - correct for this double-counting by removing one unit of ice runoff - for each unit of melt. - -For a given point in space or time, this reduction can result in -negative ice runoff. However, when integrated over space and time, for -an ice sheet that is near equilibrium, this just serves to decrease the -too-high positive ice runoff from snow capping. (The treatment of snow -capping with *glc\_dyn\_runoff\_routing* false is based on this -near-equilibrium assumption - i.e., that ice accumulation is roughly -balanced by :math:`calving + melt`, integrated across space and time. -For glaciers and ice sheets that violate this assumption, either because -they are far out of equilibrium with the climate or because the model is -being run for hundreds of years, there are two ways to avoid the -unrealistic ice runoff from snow capping: by running with an evolving, -two-way-coupled ice sheet or by changing a glacier region's ice runoff -behavior as described in section :numref:`Glacier regions`.) - -In regions where SMB is computed for glaciers, SMB is also computed for -the natural vegetated land unit. Because there is no ice to melt in this -land unit, it can only generate a zero or positive SMB. A positive SMB -is generated once the snow pack reaches its maximum depth. When running -with an evolving ice sheet, this condition triggers glacial inception. +CLM is responsible for generating glacial surface melt, even when running with an evolving ice sheet. Thus, :math:`q_{ice,melt}` is always added to liquid runoff (:math:`q_{rgwl}`), regardless of *glc\_dyn\_runoff\_routing*. However, the ice runoff flux depends on *glc\_dyn\_runoff\_routing*. If *glc\_dyn\_runoff\_routing* is true, then CISM controls the fate of the snow capping mass in :math:`q_{ice,frz}` (e.g., eventually transporting it to lower elevations where it can be melted or calved). Since CISM will now own this mass, the snow capping flux does *not* contribute to any runoff fluxes generated by CLM in this case. + +If *glc\_dyn\_runoff\_routing* is false, then CLM sends the snow capping flux as runoff, as a crude representation of ice calving (see also sections :numref:`Runoff from glaciers and snow-capped surfaces` and :numref:`Glacier regions`). However, this ice runoff flux is reduced by :math:`q_{ice,melt}`. This reduction is needed for conservation; its need is subtle, but can be understood with either of these explanations: + +- When ice melts, we let the liquid run off and replace it with new ice. That new ice needs to come from somewhere to keep the coupled system in water balance. We "request" the new ice from the ocean by generating a negative ice runoff equivalent to the amount we have melted. + +- Ice melt removes mass from the system, as it should. But the snow capping flux also removes mass from the system. The latter is a crude parameterization of calving, assuming steady state - i.e., all ice gain is balanced by ice loss. This removal of mass due to both accumulation and melt represents a double-counting. Each unit of melt indicates that one unit of accumulation should not have made it to the ocean as ice, but instead melted before it got there. So we need to correct for this double-counting by removing one unit of ice runoff for each unit of melt. + +For a given point in space or time, this reduction can result in negative ice runoff. However, when integrated over space and time, for an ice sheet that is near equilibrium, this just serves to decrease the too-high positive ice runoff from snow capping. (The treatment of snow capping with *glc\_dyn\_runoff\_routing* false is based on this near-equilibrium assumption - i.e., that ice accumulation is roughly balanced by :math:`calving + melt`, integrated across space and time. For glaciers and ice sheets that violate this assumption, either because they are far out of equilibrium with the climate or because the model is being run for hundreds of years, there are two ways to avoid the unrealistic ice runoff from snow capping: by running with an evolving, two-way-coupled ice sheet or by changing a glacier region's ice runoff behavior as described in section :numref:`Glacier regions`.) + +In regions where SMB is computed for glaciers, SMB is also computed for the natural vegetated land unit. Because there is no ice to melt in this land unit, it can only generate a zero or positive SMB. A positive SMB is generated once the snow pack reaches its maximum depth. When running with an evolving ice sheet, this condition triggers glacial inception. diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 49e5567349..dd8d0a7276 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -3,16 +3,7 @@ Hydrology ============ -The model parameterizes interception, throughfall, canopy drip, snow -accumulation and melt, water transfer between snow layers, infiltration, -evaporation, surface runoff, sub-surface drainage, redistribution within -the soil column, and groundwater discharge and recharge to simulate -changes in canopy water :math:`\Delta W_{can,\,liq}` , canopy snow water -:math:`\Delta W_{can,\,sno}` surface water :math:`\Delta W_{sfc}` , -snow water :math:`\Delta W_{sno}` , soil water -:math:`\Delta w_{liq,\, i}` , and soil ice :math:`\Delta w_{ice,\, i}` , -and water in the unconfined aquifer :math:`\Delta W_{a}` (all in kg -m\ :sup:`-2` or mm of H\ :sub:`2`\ O) (:numref:`Figure Hydrologic processes`). +The model parameterizes interception, throughfall, canopy drip, snow accumulation and melt, water transfer between snow layers, infiltration, evaporation, surface runoff, sub-surface drainage, redistribution within the soil column, and groundwater discharge and recharge to simulate changes in canopy water :math:`\Delta W_{can,\,liq}`, canopy snow water :math:`\Delta W_{can,\,sno}` surface water :math:`\Delta W_{sfc}`, snow water :math:`\Delta W_{sno}`, soil water :math:`\Delta w_{liq,\, i}`, and soil ice :math:`\Delta w_{ice,\, i}`, and water in the unconfined aquifer :math:`\Delta W_{a}` (all in kg m\ :sup:`-2` or mm of H\ :sub:`2`\ O) (:numref:`Figure Hydrologic processes`). The total water balance of the system is @@ -21,20 +12,7 @@ The total water balance of the system is \begin{array}{l} {\Delta W_{can,\,liq} +\Delta W_{can,\,sno} +\Delta W_{sfc} +\Delta W_{sno} +} \\ {\sum _{i=1}^{N_{levsoi} }\left(\Delta w_{liq,\, i} +\Delta w_{ice,\, i} \right)+\Delta W_{a} =\left(\begin{array}{l} {q_{rain} +q_{sno} -E_{v} -E_{g} -q_{over} } \\ {-q_{h2osfc} -q_{drai} -q_{rgwl} -q_{snwcp,\, ice} } \end{array}\right) \Delta t} \end{array} -where :math:`q_{rain}` is the liquid part of precipitation, -:math:`q_{sno}` is the solid part of precipitation, :math:`E_{v}` is -ET from vegetation (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), :math:`E_{g}` is ground evaporation -(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), :math:`q_{over}` is surface runoff (section :numref:`Surface Runoff`), -:math:`q_{h2osfc}` is runoff from surface water storage (section :numref:`Surface Runoff`), -:math:`q_{drai}` is sub-surface drainage (section :numref:`Lateral Sub-surface Runoff`), -:math:`q_{rgwl}` and :math:`q_{snwcp,ice}` are liquid and solid runoff -from glaciers and lakes, and runoff from other surface types -due to snow capping (section :numref:`Runoff from glaciers and snow-capped surfaces`) (all in kg m\ :sup:`-2` -s\ :sup:`-1`), :math:`N_{levsoi}` is the number of soil layers -(note that hydrology calculations are only done over soil layers 1 to -:math:`N_{levsoi}` ; ground levels :math:`N_{levsoi} +1` \ to -:math:`N_{levgrnd}` are currently hydrologically inactive; :ref:`(Lawrence et -al. 2008) ` and :math:`\Delta t` is the time step (s). +where :math:`q_{rain}` is the liquid part of precipitation, :math:`q_{sno}` is the solid part of precipitation, :math:`E_{v}` is ET from vegetation (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), :math:`E_{g}` is ground evaporation (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), :math:`q_{over}` is surface runoff (section :numref:`Surface Runoff`), :math:`q_{h2osfc}` is runoff from surface water storage (section :numref:`Surface Runoff`), :math:`q_{drai}` is sub-surface drainage (section :numref:`Lateral Sub-surface Runoff`), :math:`q_{rgwl}` and :math:`q_{snwcp,ice}` are liquid and solid runoff from glaciers and lakes, and runoff from other surface types due to snow capping (section :numref:`Runoff from glaciers and snow-capped surfaces`) (all in kg m\ :sup:`-2` s\ :sup:`-1`), :math:`N_{levsoi}` is the number of soil layers (note that hydrology calculations are only done over soil layers 1 to :math:`N_{levsoi}`; ground levels :math:`N_{levsoi} +1` \ to :math:`N_{levgrnd}` are currently hydrologically inactive; :ref:`(Lawrence et al. 2008) ` and :math:`\Delta t` is the time step (s). .. _Figure Hydrologic processes: @@ -47,13 +25,7 @@ al. 2008) ` and :math:`\Delta t` is the time step (s). Canopy Water ---------------- -Liquid precipitation is either intercepted by the canopy, falls -directly to the snow/soil surface (throughfall), or drips off the -vegetation (canopy drip). Solid precipitation is treated similarly, -with the addition of unloading of previously intercepted snow. -Interception by vegetation is divided between liquid and solid phases -:math:`q_{intr,\,liq}` and :math:`q_{intr,\,ice}` -(kg m\ :sup:`-2` s\ :sup:`-1`) +Liquid precipitation is either intercepted by the canopy, falls directly to the snow/soil surface (throughfall), or drips off the vegetation (canopy drip). Solid precipitation is treated similarly, with the addition of unloading of previously intercepted snow. Interception by vegetation is divided between liquid and solid phases :math:`q_{intr,\,liq}` and :math:`q_{intr,\,ice}` (kg m\ :sup:`-2` s\ :sup:`-1`) .. math:: :label: 7.2 @@ -65,9 +37,7 @@ Interception by vegetation is divided between liquid and solid phases q_{intr,\,ice} = f_{pi,\,ice} \ q_{sno} -where :math:`f_{pi,\,liq}` and :math:`f_{pi,\,ice}` are the -fractions of intercepted precipitation of rain and snow, -respectively +where :math:`f_{pi,\,liq}` and :math:`f_{pi,\,ice}` are the fractions of intercepted precipitation of rain and snow, respectively .. math:: :label: 7.2b @@ -79,13 +49,7 @@ respectively f_{pi,\,ice} =\alpha_{sno} \ \left\{1-\exp \left[-0.5\left(L+S\right)\right]\right\} \ , -and :math:`L` and :math:`S` are the exposed leaf and stem area index, -respectively (section :numref:`Phenology and vegetation burial by snow`), and -the :math:`\alpha`\'s scale the fractional area of a leaf that collects water -(:ref:`Lawrence et al. 2007 `). Default values of -:math:`\alpha_{liq}` and :math:`\alpha_{sno}` are set to 1. -Throughfall (kg m\ :sup:`-2` s\ :sup:`-1`) is also divided into -liquid and solid phases, reaching the ground (soil or snow surface) as +and :math:`L` and :math:`S` are the exposed leaf and stem area index, respectively (section :numref:`Phenology and vegetation burial by snow`), and the :math:`\alpha`\'s scale the fractional area of a leaf that collects water (:ref:`Lawrence et al. 2007 `). Default values of :math:`\alpha_{liq}` and :math:`\alpha_{sno}` are set to 1. Throughfall (kg m\ :sup:`-2` s\ :sup:`-1`) is also divided into liquid and solid phases, reaching the ground (soil or snow surface) as .. math:: :label: 7.4 @@ -123,11 +87,7 @@ and W_{can,sno}^{intr} =W_{can,sno}^{n} +q_{intr,\, ice} \Delta t\ge 0 -are the the canopy liquid water and snow water equivalent after accounting for interception, -:math:`W_{can,\,liq}^{n}` and :math:`W_{can,\,sno}^{n}` are the canopy liquid and snow water -from the previous time step, and :math:`W_{can,\,liq}^{max }` and :math:`W_{can,\,snow}^{max }` -(kg m\ :sup:`-2` or mm of H\ :sub:`2`\ O) are the maximum amounts of liquid water and snow the canopy can hold. -They are defined by +are the the canopy liquid water and snow water equivalent after accounting for interception, :math:`W_{can,\,liq}^{n}` and :math:`W_{can,\,sno}^{n}` are the canopy liquid and snow water from the previous time step, and :math:`W_{can,\,liq}^{max }` and :math:`W_{can,\,snow}^{max }` (kg m\ :sup:`-2` or mm of H\ :sub:`2`\ O) are the maximum amounts of liquid water and snow the canopy can hold. They are defined by .. math:: :label: 7.10 @@ -139,13 +99,9 @@ They are defined by W_{can,\,sno}^{max } =p_{sno}\left(L+S\right). -The maximum storage of liquid water is :math:`p_{liq}=0.1` kg m\ :sup:`-2` -(:ref:`Dickinson et al. 1993 `), and that of snow -is :math:`p_{sno}=6` kg m\ :sup:`-2`, consistent with reported -field measurements (:ref:`Pomeroy et al. 1998 `). +The maximum storage of liquid water is :math:`p_{liq}=0.1` kg m\ :sup:`-2` (:ref:`Dickinson et al. 1993 `), and that of snow is :math:`p_{sno}=6` kg m\ :sup:`-2`, consistent with reported field measurements (:ref:`Pomeroy et al. 1998 `). -Canopy snow unloading from wind speed :math:`u` and above-freezing temperatures are modeled from linear -fluxes and e-folding times similar to :ref:`Roesch et al. (2001) ` +Canopy snow unloading from wind speed :math:`u` and above-freezing temperatures are modeled from linear fluxes and e-folding times similar to :ref:`Roesch et al. (2001) ` .. math:: :label: 7.12 @@ -179,8 +135,7 @@ and .. W_{can}^{n+1} =W_{can}^{n} +q_{intr} \Delta t-\left(q_{drip,\, liq} +q_{drip,\, ice} \right)\Delta t-E_{v}^{w} \Delta t\ge 0. -where :math:`E_{v}^{liq}` and :math:`E_{v}^{ice}` are partitioned from the stem and leaf -surface evaporation :math:`E_{v}^{w}` (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) based on the vegetation temperature :math:`T_{v}` (K) (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and its relation to the freezing temperature of water :math:`T_{f}` (K) (:numref:`Table Physical Constants`) +where :math:`E_{v}^{liq}` and :math:`E_{v}^{ice}` are partitioned from the stem and leaf surface evaporation :math:`E_{v}^{w}` (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) based on the vegetation temperature :math:`T_{v}` (K) (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and its relation to the freezing temperature of water :math:`T_{f}` (K) (:numref:`Table Physical Constants`) .. math:: :label: 7.17 @@ -217,17 +172,9 @@ The total rate of liquid and solid precipitation reaching the ground is then q_{grnd,ice} =q_{thru,\, ice} +q_{drip,\, ice} +q_{unl,\, tot} . -Solid precipitation reaching the soil or snow surface, -:math:`q_{grnd,\, ice} \Delta t`, is added immediately to the snow pack -(Chapter :numref:`rst_Snow Hydrology`). The liquid part, -:math:`q_{grnd,\, liq} \Delta t` is added after surface fluxes -(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) -and snow/soil temperatures (Chapter :numref:`rst_Soil and Snow Temperatures`) -have been determined. +Solid precipitation reaching the soil or snow surface, :math:`q_{grnd,\, ice} \Delta t`, is added immediately to the snow pack (Chapter :numref:`rst_Snow Hydrology`). The liquid part, :math:`q_{grnd,\, liq} \Delta t` is added after surface fluxes (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and snow/soil temperatures (Chapter :numref:`rst_Soil and Snow Temperatures`) have been determined. -The wetted fraction of the canopy (stems plus leaves), which is required -for surface flux (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) -calculations, is (:ref:`Dickinson et al.1993 `) +The wetted fraction of the canopy (stems plus leaves), which is required for surface flux (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) calculations, is (:ref:`Dickinson et al.1993 `) .. math:: :label: 7.21 @@ -265,25 +212,14 @@ Similarly, the snow-covered fraction of the canopy is used for surface alebdo wh Surface Runoff, Surface Water Storage, and Infiltration ----------------------------------------------------------- -The moisture input at the grid cell surface ,\ :math:`q_{liq,\, 0}` , is -the sum of liquid precipitation reaching the ground and melt water from -snow (kg m\ :sup:`-2` s\ :sup:`-1`). The moisture flux is -then partitioned between surface runoff, surface water storage, and -infiltration into the soil. +The moisture input at the grid cell surface,\ :math:`q_{liq,\, 0}`, is the sum of liquid precipitation reaching the ground and melt water from snow (kg m\ :sup:`-2` s\ :sup:`-1`). The moisture flux is then partitioned between surface runoff, surface water storage, and infiltration into the soil. .. _Surface Runoff: Surface Runoff ^^^^^^^^^^^^^^^^^^^^ -The simple TOPMODEL-based (:ref:`Beven and Kirkby 1979 `) -runoff model (SIMTOP) described by :ref:`Niu et al. (2005) ` -is implemented to parameterize runoff. A -key concept underlying this approach is that of fractional saturated -area :math:`f_{sat}` , which is determined by the topographic -characteristics and soil moisture state of a grid cell. The saturated -portion of a grid cell contributes to surface runoff, :math:`q_{over}` , -by the saturation excess mechanism (Dunne runoff) +The simple TOPMODEL-based (:ref:`Beven and Kirkby 1979 `) runoff model (SIMTOP) described by :ref:`Niu et al. (2005) ` is implemented to parameterize runoff. A key concept underlying this approach is that of fractional saturated area :math:`f_{sat}`, which is determined by the topographic characteristics and soil moisture state of a grid cell. The saturated portion of a grid cell contributes to surface runoff, :math:`q_{over}`, by the saturation excess mechanism (Dunne runoff) .. math:: :label: 7.64 @@ -297,145 +233,79 @@ The fractional saturated area is a function of soil moisture f_{sat} =f_{\max } \ \exp \left(-0.5f_{over} z_{\nabla } \right) -where :math:`f_{\max }` is the potential or maximum value of -:math:`f_{sat}` , :math:`f_{over}` is a decay factor (m\ :sup:`-1`), and -:math:`z_{\nabla}` is the water table depth (m) (section -:numref:`Lateral Sub-surface Runoff`). The maximum saturated fraction, -:math:`f_{\max }`, is defined as the value of the discrete cumulative -distribution function (CDF) of the topographic index when the grid cell -mean water table depth is zero. Thus, :math:`f_{\max }` is the percent of -pixels in a grid cell whose topographic index is larger than or equal to -the grid cell mean topographic index. It should be calculated explicitly -from the CDF at each grid cell at the resolution that the model is run. -However, because this is a computationally intensive task for global -applications, :math:`f_{\max }` is calculated once at 0.125\ :sup:`o` -resolution using the 1-km compound topographic indices (CTIs) based on -the HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) -from USGS following the algorithm in :ref:`Niu et al. (2005) ` -and then area-averaged to the desired model resolution (section -:numref:`Surface Data`). Pixels -with CTIs exceeding the 95 percentile threshold in each -0.125\ :sup:`o` grid cell are excluded from the calculation to -eliminate biased estimation of statistics due to large CTI values at -pixels on stream networks. For grid cells over regions without CTIs such -as Australia, the global mean :math:`f_{\max }` is used to fill the -gaps. See :ref:`Li et al. (2013b) ` for additional details. The decay factor -:math:`f_{over}` for global simulations was determined through -sensitivity analysis and comparison with observed runoff to be 0.5 -m\ :sup:`-1`. +where :math:`f_{\max }` is the potential or maximum value of :math:`f_{sat}`, :math:`f_{over}` is a decay factor (m\ :sup:`-1`), and :math:`z_{\nabla}` is the water table depth (m) (section :numref:`Lateral Sub-surface Runoff`). The maximum saturated fraction, :math:`f_{\max }`, is defined as the value of the discrete cumulative distribution function (CDF) of the topographic index when the grid cell mean water table depth is zero. Thus, :math:`f_{\max }` is the percent of pixels in a grid cell whose topographic index is larger than or equal to the grid cell mean topographic index. It should be calculated explicitly from the CDF at each grid cell at the resolution that the model is run. However, because this is a computationally intensive task for global applications, :math:`f_{\max }` is calculated once at 0.125\ :sup:`o` resolution using the 1-km compound topographic indices (CTIs) based on the HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) from USGS following the algorithm in :ref:`Niu et al. (2005) ` and then area-averaged to the desired model resolution (section :numref:`Surface Data`). Pixels with CTIs exceeding the 95 percentile threshold in each 0.125\ :sup:`o` grid cell are excluded from the calculation to eliminate biased estimation of statistics due to large CTI values at pixels on stream networks. For grid cells over regions without CTIs such as Australia, the global mean :math:`f_{\max }` is used to fill the gaps. See :ref:`Li et al. (2013b) ` for additional details. The decay factor :math:`f_{over}` for global simulations was determined through sensitivity analysis and comparison with observed runoff to be 0.5 m\ :sup:`-1`. .. _Surface Water Storage: Surface Water Storage ^^^^^^^^^^^^^^^^^^^^^^^^^^^ -A surface water store has been added to the model to represent wetlands -and small, sub-grid scale water bodies. As a result, the wetland land -unit has been removed as of CLM4.5. The state variables for surface water are the -mass of water :math:`W_{sfc}` (kg m\ :sup:`-2`) and temperature -:math:`T_{h2osfc}` (Chapter :numref:`rst_Soil and Snow Temperatures`). -Surface water storage and outflow are -functions of fine spatial scale elevation variations called -microtopography. The microtopography is assumed to be distributed -normally around the grid cell mean elevation. Given the standard -deviation of the microtopographic distribution, :math:`\sigma _{micro}` -(m), the fractional area of the grid cell that is inundated can be -calculated. Surface water storage, :math:`Wsfc`, is related to the -height (relative to the grid cell mean elevation) of the surface water, -:math:`d`, by +A surface water store has been added to the model to represent wetlands and small, sub-grid scale water bodies. As a result, the wetland land unit has been removed as of CLM4.5. The state variables for surface water are the mass of water :math:`W_{sfc}` (kg m\ :sup:`-2`) and temperature :math:`T_{h2osfc}` (Chapter :numref:`rst_Soil and Snow Temperatures`). Surface water storage and outflow are functions of fine spatial scale elevation variations called microtopography. The microtopography is assumed to be distributed normally around the grid cell mean elevation. Given the standard deviation of the microtopographic distribution, :math:`\sigma _{micro}` (m), the fractional area of the grid cell that is inundated can be calculated. Surface water storage, :math:`Wsfc`, is related to the height (relative to the grid cell mean elevation) of the surface water, :math:`d`, by .. math:: :label: 7.66 W_{sfc} =\frac{d}{2} \left(1+erf\left(\frac{d}{\sigma _{micro} \sqrt{2} } \right)\right)+\frac{\sigma _{micro} }{\sqrt{2\pi } } e^{\frac{-d^{2} }{2\sigma _{micro} ^{2} } } -where :math:`erf` is the error function. For a given value of -:math:`W_{sfc}` , :eq:`7.66` can be solved for :math:`d` using the -Newton-Raphson method. Once :math:`d` is known, one can determine the -fraction of the area that is inundated as +where :math:`erf` is the error function. For a given value of :math:`W_{sfc}`, :eq:`7.66` can be solved for :math:`d` using the Newton-Raphson method. Once :math:`d` is known, one can determine the fraction of the area that is inundated as .. math:: :label: 7.67 f_{h2osfc} =\frac{1}{2} \left(1+erf\left(\frac{d}{\sigma _{micro} \sqrt{2} } \right)\right) -No global datasets exist for microtopography, so the default -parameterization is a simple function of slope +No global datasets exist for microtopography, so the default parameterization is a simple function of slope .. math:: :label: 7.68 \sigma _{micro} =\left(\beta +\beta _{0} \right)^{\eta } -where :math:`\beta` is the topographic slope, -:math:`\beta_{0} =\left(\sigma_{\max } \right)^{\frac{1}{\eta } }` \ determines -the maximum value of :math:`\sigma_{micro}` , and :math:`\eta` is an -adjustable parameter. Default values in the model are -:math:`\sigma_{\max } =0.4` and :math:`\eta =-3`. +where :math:`\beta` is the topographic slope, :math:`\beta_{0} =\left(\sigma_{\max } \right)^{\frac{1}{\eta } }` \ determines the maximum value of :math:`\sigma_{micro}`, and :math:`\eta` is an adjustable parameter. Default values in the model are :math:`\sigma_{\max } =0.4` and :math:`\eta =-3`. -If the spatial scale of the microtopography is small relative to that of -the grid cell, one can assume that the inundated areas are distributed -randomly within the grid cell. With this assumption, a result from -percolation theory can be used to quantify the fraction of the inundated -portion of the grid cell that is interconnected +If the spatial scale of the microtopography is small relative to that of the grid cell, one can assume that the inundated areas are distributed randomly within the grid cell. With this assumption, a result from percolation theory can be used to quantify the fraction of the inundated portion of the grid cell that is interconnected .. math:: :label: 7.69 \begin{array}{lr} f_{connected} =\left(f_{h2osfc} -f_{c} \right)^{\mu } & \qquad f_{h2osfc} >f_{c} \\ f_{connected} =0 &\qquad f_{h2osfc} \le f_{c} \end{array} -where :math:`f_{c}` is a threshold below which no single connected -inundated area spans the grid cell and :math:`\mu` is a scaling -exponent. Default values of :math:`f_{c}` and :math:`\mu` \ are 0.4 and -0.14, respectively. When the inundated fraction of the grid cell -surpasses :math:`f_{c}` , the surface water store acts as a linear -reservoir +where :math:`f_{c}` is a threshold below which no single connected inundated area spans the grid cell and :math:`\mu` is a scaling exponent. Default values of :math:`f_{c}` and :math:`\mu` \ are 0.4 and 0.14, respectively. When the inundated fraction of the grid cell surpasses :math:`f_{c}`, the surface water store acts as a linear reservoir .. math:: :label: 7.70 q_{out,h2osfc}=k_{h2osfc} \ f_{connected} \ (Wsfc-Wc)\frac{1}{\Delta t} -where :math:`q_{out,h2osfc}` is the surface water runoff, :math:`k_{h2osfc}` -is a constant, :math:`Wc` is the amount of surface water present when -:math:`f_{h2osfc} =f_{c}` , and :math:`\Delta t` is the model time step. -The linear storage coefficent :math:`k_{h2osfc} = \sin \left(\beta \right)` -is a function of grid cell mean topographic slope where :math:`\beta` -is the slope in radians. +where :math:`q_{out,h2osfc}` is the surface water runoff, :math:`k_{h2osfc}` is a constant, :math:`Wc` is the amount of surface water present when :math:`f_{h2osfc} =f_{c}`, and :math:`\Delta t` is the model time step. The linear storage coefficent :math:`k_{h2osfc} = \sin \left(\beta \right)` is a function of grid cell mean topographic slope where :math:`\beta` is the slope in radians. .. _Infiltration: Infiltration ^^^^^^^^^^^^^^^^^^ -The surface moisture flux remaining after surface runoff has been -removed, +The surface moisture flux remaining after surface runoff has been removed, .. math:: :label: 7.71 q_{in,surface} = (1-f_{sat}) \ q_{liq,\, 0} -is divided into inputs to surface water (:math:`q_{in,\, h2osfc}` ) and -the soil :math:`q_{in,soil}` . If :math:`q_{in,soil}` exceeds the -maximum soil infiltration capacity (kg m\ :sup:`-2` -s\ :sup:`-1`), +is divided into inputs to surface water (:math:`q_{in,\, h2osfc}` ) and the soil :math:`q_{in,soil}`. If :math:`q_{in,soil}` exceeds the maximum soil infiltration capacity (kg m\ :sup:`-2` s\ :sup:`-1`), .. math:: :label: 7.72 q_{infl,\, \max } =(1-f_{sat}) \ \Theta_{ice} k_{sat} -where :math:`\Theta_{ice}` is an ice impedance factor (section -:numref:`Hydraulic Properties`), infiltration excess (Hortonian) runoff is generated +where :math:`\Theta_{ice}` is an ice impedance factor (section :numref:`Hydraulic Properties`), infiltration excess (Hortonian) runoff is generated .. math:: :label: 7.73 q_{infl,\, excess} =\max \left(q_{in,soil} -\left(1-f_{h2osfc} \right)q_{\inf l,\max } ,0\right) -and transferred from :math:`q_{in,soil}` to :math:`q_{in,h2osfc}` . -After evaporative losses have been removed, these moisture fluxes are +and transferred from :math:`q_{in,soil}` to :math:`q_{in,h2osfc}`. After evaporative losses have been removed, these moisture fluxes are .. math:: :label: 7.74 @@ -463,73 +333,46 @@ Bottom drainage from the surface water store q_{drain,h2osfc} = \min \left(f_{h2osfc} q_{\inf l,\max } ,\frac{W_{sfc} }{\Delta t} \right) -is then added to :math:`q_{in,soil}` giving the total infiltration -into the surface soil layer +is then added to :math:`q_{in,soil}` giving the total infiltration into the surface soil layer .. math:: :label: 7.78 q_{infl} = q_{in,soil} + q_{drain,h2osfc} -Infiltration :math:`q_{infl}` and explicit surface runoff -:math:`q_{over}` are not allowed for glaciers. +Infiltration :math:`q_{infl}` and explicit surface runoff :math:`q_{over}` are not allowed for glaciers. .. _Soil Water: Soil Water -------------- -Soil water is predicted from a multi-layer model, in which the vertical -soil moisture transport is governed by infiltration, surface and -sub-surface runoff, gradient diffusion, gravity, and canopy transpiration -through root extraction (:numref:`Figure Hydrologic processes`). +Soil water is predicted from a multi-layer model, in which the vertical soil moisture transport is governed by infiltration, surface and sub-surface runoff, gradient diffusion, gravity, and canopy transpiration through root extraction (:numref:`Figure Hydrologic processes`). -For one-dimensional vertical water flow in soils, the conservation of -mass is stated as +For one-dimensional vertical water flow in soils, the conservation of mass is stated as .. math:: :label: 7.79 \frac{\partial \theta }{\partial t} =-\frac{\partial q}{\partial z} - e -where :math:`\theta` is the volumetric soil water content -(mm\ :sup:`3` of water / mm\ :sup:`-3` of soil), :math:`t` is -time (s), :math:`z` is height above some datum in the soil column (mm) -(positive upwards), :math:`q` is soil water flux (kg m\ :sup:`-2` -s\ :sup:`-1` or mm s\ :sup:`-1`) (positive upwards), and -:math:`e` is a soil moisture sink term (mm of water mm\ :sup:`-1` -of soil s\ :sup:`-1`) (ET loss). This equation is solved -numerically by dividing the soil column into multiple layers in the -vertical and integrating downward over each layer with an upper boundary -condition of the infiltration flux into the top soil layer -:math:`q_{infl}` and a zero-flux lower boundary condition at the -bottom of the soil column (sub-surface runoff is removed later in the -timestep, section :numref:`Lateral Sub-surface Runoff`). +where :math:`\theta` is the volumetric soil water content (mm\ :sup:`3` of water / mm\ :sup:`-3` of soil), :math:`t` is time (s), :math:`z` is height above some datum in the soil column (mm) (positive upwards), :math:`q` is soil water flux (kg m\ :sup:`-2` s\ :sup:`-1` or mm s\ :sup:`-1`) (positive upwards), and :math:`e` is a soil moisture sink term (mm of water mm\ :sup:`-1` of soil s\ :sup:`-1`) (ET loss). This equation is solved numerically by dividing the soil column into multiple layers in the vertical and integrating downward over each layer with an upper boundary condition of the infiltration flux into the top soil layer :math:`q_{infl}` and a zero-flux lower boundary condition at the bottom of the soil column (sub-surface runoff is removed later in the timestep, section :numref:`Lateral Sub-surface Runoff`). -The soil water flux :math:`q` in equation can be described by Darcy's -law :ref:`(Dingman 2002) ` +The soil water flux :math:`q` in equation can be described by Darcy's law :ref:`(Dingman 2002) ` .. math:: :label: 7.80 q = -k \frac{\partial \psi _{h} }{\partial z} -where :math:`k` is the hydraulic conductivity (mm s\ :sup:`-1`), -and :math:`\psi _{h}` is the hydraulic potential (mm). The hydraulic -potential is +where :math:`k` is the hydraulic conductivity (mm s\ :sup:`-1`), and :math:`\psi _{h}` is the hydraulic potential (mm). The hydraulic potential is .. math:: :label: 7.81 \psi _{h} =\psi _{m} +\psi _{z} -where :math:`\psi _{m}` is the soil matric potential (mm) (which is -related to the adsorptive and capillary forces within the soil matrix), -and :math:`\psi _{z}` is the gravitational potential (mm) (the vertical -distance from an arbitrary reference elevation to a point in the soil). -If the reference elevation is the soil surface, then -:math:`\psi _{z} =z`. Letting :math:`\psi =\psi _{m}` , Darcy's law -becomes +where :math:`\psi _{m}` is the soil matric potential (mm) (which is related to the adsorptive and capillary forces within the soil matrix), and :math:`\psi _{z}` is the gravitational potential (mm) (the vertical distance from an arbitrary reference elevation to a point in the soil). If the reference elevation is the soil surface, then :math:`\psi _{z} =z`. Letting :math:`\psi =\psi _{m}`, Darcy's law becomes .. math:: :label: 7.82 @@ -544,8 +387,7 @@ Equation :eq:`7.82` can be further manipulated to yield q = -k \left[\frac{\partial \left(\psi +z\right)}{\partial z} \right] = -k \left(\frac{\partial \psi }{\partial z} + 1 \right) \ . -Substitution of this equation into equation :eq:`7.79`, with :math:`e = 0`, yields -the Richards equation :ref:`(Dingman 2002) ` +Substitution of this equation into equation :eq:`7.79`, with :math:`e = 0`, yields the Richards equation :ref:`(Dingman 2002) ` .. math:: :label: 7.84 @@ -554,33 +396,16 @@ the Richards equation :ref:`(Dingman 2002) ` \frac{\partial }{\partial z} \left[k\left(\frac{\partial \psi }{\partial z} + 1 \right)\right]. -In practice (Section :numref:`Numerical Solution Hydrology`), changes in soil -water content are predicted from :eq:`7.79` using finite-difference approximations -for :eq:`7.84`. +In practice (Section :numref:`Numerical Solution Hydrology`), changes in soil water content are predicted from :eq:`7.79` using finite-difference approximations for :eq:`7.84`. .. _Hydraulic Properties: Hydraulic Properties ^^^^^^^^^^^^^^^^^^^^^^^^^^ -The hydraulic conductivity :math:`k_{i}` (mm s\ :sup:`-1`) and -the soil matric potential :math:`\psi _{i}` (mm) for layer :math:`i` -vary with volumetric soil water :math:`\theta _{i}` and soil texture. -As with the soil thermal properties (section -:numref:`Soil And Snow Thermal Properties`) the hydraulic -properties of the soil are assumed to be a weighted combination of the -mineral properties, which are determined according to sand and clay -contents based on work by :ref:`Clapp and Hornberger (1978) -` and :ref:`Cosby et al. (1984) `, -and organic properties of the soil -(:ref:`Lawrence and Slater 2008 `). - -The hydraulic conductivity is defined at the depth of the interface of -two adjacent layers :math:`z_{h,\, i}` (:numref:`Figure Water flux schematic`) -and is a function of the saturated hydraulic conductivity -:math:`k_{sat} \left[z_{h,\, i} \right]`, the liquid volumetric soil -moisture of the two layers :math:`\theta _{i}` and :math:`\theta_{i+1}` -and an ice impedance factor :math:`\Theta_{ice}` +The hydraulic conductivity :math:`k_{i}` (mm s\ :sup:`-1`) and the soil matric potential :math:`\psi _{i}` (mm) for layer :math:`i` vary with volumetric soil water :math:`\theta _{i}` and soil texture. As with the soil thermal properties (section :numref:`Soil And Snow Thermal Properties`) the hydraulic properties of the soil are assumed to be a weighted combination of the mineral properties, which are determined according to sand and clay contents based on work by :ref:`Clapp and Hornberger (1978) ` and :ref:`Cosby et al. (1984) `, and organic properties of the soil (:ref:`Lawrence and Slater 2008 `). + +The hydraulic conductivity is defined at the depth of the interface of two adjacent layers :math:`z_{h,\, i}` (:numref:`Figure Water flux schematic`) and is a function of the saturated hydraulic conductivity :math:`k_{sat} \left[z_{h,\, i} \right]`, the liquid volumetric soil moisture of the two layers :math:`\theta _{i}` and :math:`\theta_{i+1}` and an ice impedance factor :math:`\Theta_{ice}` .. math:: :label: 7.85 @@ -591,33 +416,23 @@ and an ice impedance factor :math:`\Theta_{ice}` \Theta_{ice} k_{sat} \left[z_{h,\, i} \right]\left(\frac{\theta_{\, i} }{\theta_{sat,\, i} } \right)^{2B_{i} +3} & \qquad i = N_{levsoi} \end{array}\right\}. -The ice impedance factor is a function of ice content, and is meant to -quantify the increased tortuosity of the water flow when part of the -pore space is filled with ice. :ref:`Swenson et al. (2012) ` -used a power law form +The ice impedance factor is a function of ice content, and is meant to quantify the increased tortuosity of the water flow when part of the pore space is filled with ice. :ref:`Swenson et al. (2012) ` used a power law form .. math:: :label: 7.86 \Theta_{ice} = 10^{-\Omega F_{ice} } -where :math:`\Omega = 6`\ and :math:`F_{ice} = \frac{\theta_{ice} }{\theta_{sat} }` -is the ice-filled fraction of the pore space. +where :math:`\Omega = 6`\ and :math:`F_{ice} = \frac{\theta_{ice} }{\theta_{sat} }` is the ice-filled fraction of the pore space. -Because the hydraulic properties of mineral and organic soil may differ -significantly, the bulk hydraulic properties of each soil layer are -computed as weighted averages of the properties of the mineral and -organic components. The water content at saturation (i.e. porosity) is +Because the hydraulic properties of mineral and organic soil may differ significantly, the bulk hydraulic properties of each soil layer are computed as weighted averages of the properties of the mineral and organic components. The water content at saturation (i.e. porosity) is .. math:: :label: 7.90 \theta_{sat,i} =(1-f_{om,i} )\theta_{sat,\min ,i} +f_{om,i} \theta_{sat,om} -where :math:`f_{om,i}` is the soil organic matter fraction, -:math:`\theta_{sat,om}` is the -porosity of organic matter, and the porosity of the mineral soil -:math:`\theta_{sat,\min ,i}` is +where :math:`f_{om,i}` is the soil organic matter fraction, :math:`\theta_{sat,om}` is the porosity of organic matter, and the porosity of the mineral soil :math:`\theta_{sat,\min,i}` is .. math:: :label: 7.91 @@ -638,8 +453,7 @@ where :math:`B_{om}` is for organic matter and B_{\min ,i} =2.91+0.159(\% clay)_{i} . -The soil matric potential (mm) is defined at the node depth -:math:`z_{i}` of each layer :math:`i` (:numref:`Figure Water flux schematic`) +The soil matric potential (mm) is defined at the node depth :math:`z_{i}` of each layer :math:`i` (:numref:`Figure Water flux schematic`) .. math:: :label: 7.94 @@ -653,33 +467,14 @@ where the saturated soil matric potential (mm) is \psi _{sat,i} =(1-f_{om,i} )\psi _{sat,\min ,i} +f_{om,i} \psi _{sat,om} -where :math:`\psi _{sat,om}` \ is the -saturated organic matter matric potential and the saturated mineral soil -matric potential :math:`\psi _{sat,\min ,i}` \ is +where :math:`\psi _{sat,om}` \ is the saturated organic matter matric potential and the saturated mineral soil matric potential :math:`\psi _{sat,\min,i}` \ is .. math:: :label: 7.96 \psi _{sat,\, \min ,\, i} =-10.0\times 10^{1.88-0.0131(\% sand)_{i} } . -The saturated hydraulic conductivity, -:math:`k_{sat} \left[z_{h,\, i} \right]` (mm s\ :sup:`-1`), for -organic soils (:math:`k_{sat,\, om}` ) may be two to three orders of -magnitude larger than that of mineral soils (:math:`k_{sat,\, \min }` ). -Bulk soil layer values of :math:`k_{sat}` \ calculated as weighted -averages based on :math:`f_{om}` may therefore be determined primarily -by the organic soil properties even for values of :math:`f_{om}` as low -as 1 %. To better represent the influence of organic soil material on -the grid cell average saturated hydraulic conductivity, the soil organic -matter fraction is further subdivided into "connected" and "unconnected" -fractions using a result from percolation theory (:ref:`Stauffer and Aharony -1994 `, :ref:`Berkowitz and Balberg 1992 `). -Assuming that the organic and mineral fractions are randomly distributed throughout -a soil layer, percolation theory predicts that above a threshold value -:math:`f_{om} = f_{threshold}`, connected flow pathways consisting of -organic material only exist and span the soil space. Flow through these -pathways interacts only with organic material, and thus can be described -by :math:`k_{sat,\, om}`. This fraction of the grid cell is given by +The saturated hydraulic conductivity, :math:`k_{sat} \left[z_{h,\, i} \right]` (mm s\ :sup:`-1`), for organic soils (:math:`k_{sat,\, om}` ) may be two to three orders of magnitude larger than that of mineral soils (:math:`k_{sat,\, \min }` ). Bulk soil layer values of :math:`k_{sat}` \ calculated as weighted averages based on :math:`f_{om}` may therefore be determined primarily by the organic soil properties even for values of :math:`f_{om}` as low as 1 %. To better represent the influence of organic soil material on the grid cell average saturated hydraulic conductivity, the soil organic matter fraction is further subdivided into "connected" and "unconnected" fractions using a result from percolation theory (:ref:`Stauffer and Aharony 1994 `, :ref:`Berkowitz and Balberg 1992 `). Assuming that the organic and mineral fractions are randomly distributed throughout a soil layer, percolation theory predicts that above a threshold value :math:`f_{om} = f_{threshold}`, connected flow pathways consisting of organic material only exist and span the soil space. Flow through these pathways interacts only with organic material, and thus can be described by :math:`k_{sat,\, om}`. This fraction of the grid cell is given by .. math:: :label: 7.97 @@ -689,36 +484,28 @@ by :math:`k_{sat,\, om}`. This fraction of the grid cell is given by f_{perc} = 0 & \qquad f_{om} `) as +where saturated hydraulic conductivity for mineral soil depends on soil texture (:ref:`Cosby et al. 1984 `) as .. math:: :label: 7.99 k_{sat,\, \min } \left[z_{h,\, i} \right]=0.0070556\times 10^{-0.884+0.0153\left(\% sand\right)_{i} } . -The bulk soil layer saturated hydraulic conductivity is then computed -as +The bulk soil layer saturated hydraulic conductivity is then computed as .. math:: :label: 7.100 k_{sat} \left[z_{h,\, i} \right]=f_{uncon,\, i} k_{sat,\, uncon} \left[z_{h,\, i} \right]+(1-f_{uncon,\, i} )k_{sat,\, om} \left[z_{h,\, i} \right]. -The soil organic matter properties implicitly account for the standard observed profile of organic matter -properties as +The soil organic matter properties implicitly account for the standard observed profile of organic matter properties as .. math:: :label: 1.101 @@ -747,44 +534,30 @@ where :math:`zsapric =0.5` \m is the depth that organic matter takes on the char Numerical Solution ^^^^^^^^^^^^^^^^^^^^^^^^ -With reference to :numref:`Figure Water flux schematic`, the equation for -conservation of mass (equation :eq:`7.79`) can be integrated over each layer as +With reference to :numref:`Figure Water flux schematic`, the equation for conservation of mass (equation :eq:`7.79`) can be integrated over each layer as .. math:: :label: 7.101 \int _{-z_{h,\, i} }^{-z_{h,\, i-1} }\frac{\partial \theta }{\partial t} \, dz=-\int _{-z_{h,\, i} }^{-z_{h,\, i-1} }\frac{\partial q}{\partial z} \, dz-\int _{-z_{h,\, i} }^{-z_{h,\, i-1} } e\, dz . -Note that the integration limits are negative since :math:`z` is defined -as positive upward from the soil surface. This equation can be written -as +Note that the integration limits are negative since :math:`z` is defined as positive upward from the soil surface. This equation can be written as .. math:: :label: 7.102 \Delta z_{i} \frac{\partial \theta_{liq,\, i} }{\partial t} =-q_{i-1} +q_{i} -e_{i} -where :math:`q_{i}` is the flux of water across interface -:math:`z_{h,\, i}` , :math:`q_{i-1}` is the flux of water across -interface :math:`z_{h,\, i-1}` , and :math:`e_{i}` is a layer-averaged -soil moisture sink term (ET loss) defined as positive for flow out of -the layer (mm s\ :sup:`-1`). Taking the finite difference with -time and evaluating the fluxes implicitly at time :math:`n+1` yields +where :math:`q_{i}` is the flux of water across interface :math:`z_{h,\, i}`, :math:`q_{i-1}` is the flux of water across interface :math:`z_{h,\, i-1}`, and :math:`e_{i}` is a layer-averaged soil moisture sink term (ET loss) defined as positive for flow out of the layer (mm s\ :sup:`-1`). Taking the finite difference with time and evaluating the fluxes implicitly at time :math:`n+1` yields .. math:: :label: 7.103 \frac{\Delta z_{i} \Delta \theta_{liq,\, i} }{\Delta t} =-q_{i-1}^{n+1} +q_{i}^{n+1} -e_{i} -where -:math:`\Delta \theta_{liq,\, i} =\theta_{liq,\, i}^{n+1} -\theta_{liq,\, i}^{n}` -is the change in volumetric soil liquid water of layer :math:`i` in time -:math:`\Delta t`\ and :math:`\Delta z_{i}` is the thickness of layer -:math:`i` (mm). +where :math:`\Delta \theta_{liq,\, i} =\theta_{liq,\, i}^{n+1} -\theta_{liq,\, i}^{n}` is the change in volumetric soil liquid water of layer :math:`i` in time :math:`\Delta t`\ and :math:`\Delta z_{i}` is the thickness of layer :math:`i` (mm). -The water removed by transpiration in each layer :math:`e_{i}` is a -function of the total transpiration :math:`E_{v}^{t}` (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and -the effective root fraction :math:`r_{e,\, i}` +The water removed by transpiration in each layer :math:`e_{i}` is a function of the total transpiration :math:`E_{v}^{t}` (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and the effective root fraction :math:`r_{e,\, i}` .. math:: :label: 7.104 @@ -797,40 +570,23 @@ the effective root fraction :math:`r_{e,\, i}` Schematic diagram of numerical scheme used to solve for soil water fluxes. -Shown are three soil layers, :math:`i-1`, :math:`i`, and :math:`i+1`. -The soil matric potential :math:`\psi` and volumetric soil water -:math:`\theta_{liq}` are defined at the layer node depth :math:`z`. -The hydraulic conductivity :math:`k\left[z_{h} \right]` is defined at -the interface of two layers :math:`z_{h}` . The layer thickness is -:math:`\Delta z`. The soil water fluxes :math:`q_{i-1}` and -:math:`q_{i}` are defined as positive upwards. The soil moisture sink -term :math:`e` (ET loss) is defined as positive for flow out of the -layer. +Shown are three soil layers, :math:`i-1`, :math:`i`, and :math:`i+1`. The soil matric potential :math:`\psi` and volumetric soil water :math:`\theta_{liq}` are defined at the layer node depth :math:`z`. The hydraulic conductivity :math:`k\left[z_{h} \right]` is defined at the interface of two layers :math:`z_{h}`. The layer thickness is :math:`\Delta z`. The soil water fluxes :math:`q_{i-1}` and :math:`q_{i}` are defined as positive upwards. The soil moisture sink term :math:`e` (ET loss) is defined as positive for flow out of the layer. -Note that because more than one plant functional type (PFT) may share a -soil column, the transpiration :math:`E_{v}^{t}` is a weighted sum of -transpiration from all PFTs whose weighting depends on PFT area as +Note that because more than one plant functional type (PFT) may share a soil column, the transpiration :math:`E_{v}^{t}` is a weighted sum of transpiration from all PFTs whose weighting depends on PFT area as .. math:: :label: 7.105 E_{v}^{t} =\sum _{j=1}^{npft}\left(E_{v}^{t} \right)_{j} \left(wt\right)_{j} -where :math:`npft` is the number of PFTs sharing a soil column, -:math:`\left(E_{v}^{t} \right)_{j}` is the transpiration from the -:math:`j^{th}` PFT on the column, and :math:`\left(wt\right)_{j}` is -the relative area of the :math:`j^{th}` PFT with respect to the column. -The effective root fraction :math:`r_{e,\, i}` is also a column-level -quantity that is a weighted sum over all PFTs. The weighting depends on -the per unit area transpiration of each PFT and its relative area as +where :math:`npft` is the number of PFTs sharing a soil column, :math:`\left(E_{v}^{t} \right)_{j}` is the transpiration from the :math:`j^{th}` PFT on the column, and :math:`\left(wt\right)_{j}` is the relative area of the :math:`j^{th}` PFT with respect to the column. The effective root fraction :math:`r_{e,\, i}` is also a column-level quantity that is a weighted sum over all PFTs. The weighting depends on the per unit area transpiration of each PFT and its relative area as .. math:: :label: 7.106 r_{e,\, i} =\frac{\sum _{j=1}^{npft}\left(r_{e,\, i} \right)_{j} \left(E_{v}^{t} \right)_{j} \left(wt\right)_{j} }{\sum _{j=1}^{npft}\left(E_{v}^{t} \right)_{j} \left(wt\right)_{j} } -where :math:`\left(r_{e,\, i} \right)_{j}` is the effective root -fraction for the :math:`j^{th}` PFT +where :math:`\left(r_{e,\, i} \right)_{j}` is the effective root fraction for the :math:`j^{th}` PFT .. math:: :label: 7.107 @@ -840,17 +596,9 @@ fraction for the :math:`j^{th}` PFT \left(r_{e,\, i} \right)_{j} =0 & \qquad \left(\beta _{t} \right)_{j} =0 \end{array} -and :math:`\left(r_{i} \right)_{j}` is the fraction of roots in layer -:math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), -:math:`\left(w_{i} \right)_{j}` is a soil dryness or plant wilting factor -for layer :math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), and :math:`\left(\beta_{t} \right)_{j}` is a wetness factor for the total -soil column for the :math:`j^{th}` PFT (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). +and :math:`\left(r_{i} \right)_{j}` is the fraction of roots in layer :math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), :math:`\left(w_{i} \right)_{j}` is a soil dryness or plant wilting factor for layer :math:`i` (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`), and :math:`\left(\beta_{t} \right)_{j}` is a wetness factor for the total soil column for the :math:`j^{th}` PFT (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). -The soil water fluxes in :eq:`7.103`,, which are a function of -:math:`\theta_{liq,\, i}` and :math:`\theta_{liq,\, i+1}` because of -their dependence on hydraulic conductivity and soil matric potential, -can be linearized about :math:`\theta` using a Taylor series expansion -as +The soil water fluxes in :eq:`7.103`,, which are a function of :math:`\theta_{liq,\, i}` and :math:`\theta_{liq,\, i+1}` because of their dependence on hydraulic conductivity and soil matric potential, can be linearized about :math:`\theta` using a Taylor series expansion as .. math:: :label: 7.108 @@ -862,9 +610,7 @@ as q_{i-1}^{n+1} =q_{i-1}^{n} +\frac{\partial q_{i-1} }{\partial \theta_{liq,\, i-1} } \Delta \theta_{liq,\, i-1} +\frac{\partial q_{i-1} }{\partial \theta_{liq,\, i} } \Delta \theta_{liq,\, i} . -Substitution of these expressions for :math:`q_{i}^{n+1}` and -:math:`q_{i-1}^{n+1}` into :eq:`7.103` results in a general tridiagonal -equation set of the form +Substitution of these expressions for :math:`q_{i}^{n+1}` and :math:`q_{i-1}^{n+1}` into :eq:`7.103` results in a general tridiagonal equation set of the form .. math:: :label: 7.110 @@ -893,11 +639,9 @@ where r_{i} =q_{i-1}^{n} -q_{i}^{n} +e_{i} . -The tridiagonal equation set is solved over -:math:`i=1,\ldots ,N_{levsoi}`. +The tridiagonal equation set is solved over :math:`i=1,\ldots,N_{levsoi}`. -The finite-difference forms of the fluxes and partial derivatives in -equations :eq:`7.111` - :eq:`7.114` can be obtained from equation as +The finite-difference forms of the fluxes and partial derivatives in equations :eq:`7.111` - :eq:`7.114` can be obtained from equation as .. math:: :label: 7.115 @@ -929,8 +673,7 @@ equations :eq:`7.111` - :eq:`7.114` can be obtained from equation as \frac{\partial q_{i} }{\partial \theta _{liq,\, i+1} } =\left[\frac{k\left[z_{h,\, i} \right]}{z_{i+1} -z_{i} } \frac{\partial \psi _{i+1} }{\partial \theta _{liq,\, i+1} } \right]-\frac{\partial k\left[z_{h,\, i} \right]}{\partial \theta _{liq,\, i+1} } \left[\frac{\left(\psi _{i} -\psi _{i+1} \right)+\left(z_{i+1} - z_{i} \right)}{z_{i+1} - z_{i} } \right]. -The derivatives of the soil matric potential at the node depth are -derived from :eq:`7.94` +The derivatives of the soil matric potential at the node depth are derived from :eq:`7.94` .. math:: :label: 7.121 @@ -947,11 +690,9 @@ derived from :eq:`7.94` \frac{\partial \psi _{i+1} }{\partial \theta_{liq,\, i+1} } =-B_{i+1} \frac{\psi _{i+1} }{\theta_{\, i+1} } -with the constraint -:math:`0.01\, \theta_{sat,\, i} \le \theta_{\, i} \le \theta_{sat,\, i}` . +with the constraint :math:`0.01\, \theta_{sat,\, i} \le \theta_{\, i} \le \theta_{sat,\, i}`. -The derivatives of the hydraulic conductivity at the layer interface are -derived from :eq:`7.85` +The derivatives of the hydraulic conductivity at the layer interface are derived from :eq:`7.85` .. math:: :label: 7.124 @@ -983,18 +724,14 @@ where :math:`\overline{\theta}_{liq} = 0.5\left(\theta_{\, i} +\theta_{\, i+1} \ Equation set for layer :math:`i=1` '''''''''''''''''''''''''''''''''''''''''' -For the top soil layer (:math:`i=1`), the boundary condition is the -infiltration rate (section :numref:`Surface Runoff`), -:math:`q_{i-1}^{n+1} =-q_{infl}^{n+1}` , and the water balance equation -is +For the top soil layer (:math:`i=1`), the boundary condition is the infiltration rate (section :numref:`Surface Runoff`), :math:`q_{i-1}^{n+1} =-q_{infl}^{n+1}`, and the water balance equation is .. math:: :label: 7.135 \frac{\Delta z_{i} \Delta \theta_{liq,\, i} }{\Delta t} =q_{infl}^{n+1} +q_{i}^{n+1} -e_{i} . -After grouping like terms, the coefficients of the tridiagonal set of -equations for :math:`i=1` are +After grouping like terms, the coefficients of the tridiagonal set of equations for :math:`i=1` are .. math:: :label: 7.136 @@ -1019,8 +756,7 @@ equations for :math:`i=1` are Equation set for layers :math:`i=2,\ldots ,N_{levsoi} -1` ''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -The coefficients of the tridiagonal set of equations for -:math:`i=2,\ldots ,N_{levsoi} -1` are +The coefficients of the tridiagonal set of equations for :math:`i=2,\ldots,N_{levsoi} -1` are .. math:: :label: 7.140 @@ -1045,10 +781,7 @@ The coefficients of the tridiagonal set of equations for Equation set for layer :math:`i=N_{levsoi}` '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''' -For the lowest soil layer (:math:`i=N_{levsoi}` ), a zero-flux bottom boundary -condition is applied (:math:`q_{i}^{n} =0`) -and the coefficients of the tridiagonal set of equations for -:math:`i=N_{levsoi}` are +For the lowest soil layer (:math:`i=N_{levsoi}` ), a zero-flux bottom boundary condition is applied (:math:`q_{i}^{n} =0`) and the coefficients of the tridiagonal set of equations for :math:`i=N_{levsoi}` are .. math:: :label: 7.148 @@ -1073,18 +806,7 @@ and the coefficients of the tridiagonal set of equations for Adaptive Time Stepping ''''''''''''''''''''''''''''' -The length of the time step is adjusted in order to improve the accuracy -and stability of the numerical solutions. The difference between two numerical -approximations is used to estimate the temporal truncation error, and then -the step size :math:`\Delta t_{sub}` is adjusted to meet a user-prescribed error tolerance -:ref:`[Kavetski et al., 2002]`. The temporal truncation -error is estimated by comparing the flux obtained from the first-order -Taylor series expansion (:math:`q_{i-1}^{n+1}` and :math:`q_{i}^{n+1}`, -equations :eq:`7.108` and :eq:`7.109`) against the flux at the start of the -time step (:math:`q_{i-1}^{n}` and :math:`q_{i}^{n}`). Since the tridiagonal -solution already provides an estimate of :math:`\Delta \theta_{liq,i}`, it is -convenient to compute the error for each of the :math:`i` layers from equation -:eq:`7.103` as +The length of the time step is adjusted in order to improve the accuracy and stability of the numerical solutions. The difference between two numerical approximations is used to estimate the temporal truncation error, and then the step size :math:`\Delta t_{sub}` is adjusted to meet a user-prescribed error tolerance :ref:`[Kavetski et al., 2002]`. The temporal truncation error is estimated by comparing the flux obtained from the first-order Taylor series expansion (:math:`q_{i-1}^{n+1}` and :math:`q_{i}^{n+1}`, equations :eq:`7.108` and :eq:`7.109`) against the flux at the start of the time step (:math:`q_{i-1}^{n}` and :math:`q_{i}^{n}`). Since the tridiagonal solution already provides an estimate of :math:`\Delta \theta_{liq,i}`, it is convenient to compute the error for each of the :math:`i` layers from equation :eq:`7.103` as .. math:: :label: 7.152 @@ -1101,18 +823,9 @@ and the maximum absolute error across all layers as \epsilon_{crit} = {\rm max} \left( \left| \epsilon_{i} \right| \right) & \qquad 1 \le i \le nlevsoi \end{array} \ . -The adaptive step size selection is based on specified upper and lower error -tolerances, :math:`\tau_{U}` and :math:`\tau_{L}`. The solution is accepted if -:math:`\epsilon_{crit} \le \tau_{U}` and the procedure repeats until the adaptive -sub-stepping spans the full model time step (the sub-steps are doubled if -:math:`\epsilon_{crit} \le \tau_{L}`, i.e., if the solution is very accurate). -Conversely, the solution is rejected if :math:`\epsilon_{crit} > \tau_{U}`. In -this case the length of the sub-steps is halved and a new solution is obtained. -The halving of substeps continues until either :math:`\epsilon_{crit} \le \tau_{U}` -or the specified minimum time step length is reached. +The adaptive step size selection is based on specified upper and lower error tolerances, :math:`\tau_{U}` and :math:`\tau_{L}`. The solution is accepted if :math:`\epsilon_{crit} \le \tau_{U}` and the procedure repeats until the adaptive sub-stepping spans the full model time step (the sub-steps are doubled if :math:`\epsilon_{crit} \le \tau_{L}`, i.e., if the solution is very accurate). Conversely, the solution is rejected if :math:`\epsilon_{crit} > \tau_{U}`. In this case the length of the sub-steps is halved and a new solution is obtained. The halving of substeps continues until either :math:`\epsilon_{crit} \le \tau_{U}` or the specified minimum time step length is reached. -Upon solution of the tridiagonal equation set, the liquid water contents are updated -as follows +Upon solution of the tridiagonal equation set, the liquid water contents are updated as follows .. math:: :label: 7.164 @@ -1131,46 +844,30 @@ The volumetric water content is Frozen Soils and Perched Water Table ---------------------------------------- -When soils freeze, the power-law form of the ice impedance factor -(section :numref:`Hydraulic Properties`) can greatly decrease the hydraulic -conductivity of the soil, leading to nearly impermeable soil layers. When unfrozen -soil layers are present above relatively ice-rich frozen layers, the -possibility exists for perched saturated zones. Lateral drainage from -perched saturated regions is parameterized as a function of the -thickness of the saturated zone +When soils freeze, the power-law form of the ice impedance factor (section :numref:`Hydraulic Properties`) can greatly decrease the hydraulic conductivity of the soil, leading to nearly impermeable soil layers. When unfrozen soil layers are present above relatively ice-rich frozen layers, the possibility exists for perched saturated zones. Lateral drainage from perched saturated regions is parameterized as a function of the thickness of the saturated zone .. math:: :label: 7.166 q_{drai,perch} =k_{drai,\, perch} \left(z_{frost} -z_{\nabla ,perch} \right) -where :math:`k_{drai,\, perch}` depends on topographic slope and soil -hydraulic conductivity, +where :math:`k_{drai,\, perch}` depends on topographic slope and soil hydraulic conductivity, .. math:: :label: 7.167 k_{drai,\, perch} =10^{-5} \sin (\beta )\left(\frac{\sum _{i=N_{perch} }^{i=N_{frost} }\Theta_{ice,i} k_{sat} \left[z_{i} \right]\Delta z_{i} }{\sum _{i=N_{perch} }^{i=N_{frost} }\Delta z_{i} } \right) -where :math:`\Theta_{ice}` is an ice impedance factor, :math:`\beta` -is the mean grid cell topographic slope in -radians, :math:`z_{frost}` \ is the depth to the frost table, and -:math:`z_{\nabla ,perch}` is the depth to the perched saturated zone. -The frost table :math:`z_{frost}` is defined as the shallowest frozen -layer having an unfrozen layer above it, while the perched water table -:math:`z_{\nabla ,perch}` is defined as the depth at which the -volumetric water content drops below a specified threshold. The default -threshold is set to 0.9. Drainage from the perched saturated zone -:math:`q_{drai,perch}` is removed from layers :math:`N_{perch}` -through :math:`N_{frost}` , which are the layers containing -:math:`z_{\nabla ,perch}` and, :math:`z_{frost}` \ respectively. +where :math:`\Theta_{ice}` is an ice impedance factor, +:math:`\beta` is the mean grid cell topographic slope in radians, +:math:`z_{frost}` \ is the depth to the frost table, and +:math:`z_{\nabla,perch}` is the depth to the perched saturated zone. The frost table :math:`z_{frost}` is defined as the shallowest frozen layer having an unfrozen layer above it, while the perched water table :math:`z_{\nabla,perch}` is defined as the depth at which the volumetric water content drops below a specified threshold. The default threshold is set to 0.9. Drainage from the perched saturated zone :math:`q_{drai,perch}` is removed from layers :math:`N_{perch}` through :math:`N_{frost}`, which are the layers containing :math:`z_{\nabla,perch}` and, :math:`z_{frost}` \ respectively. .. _Lateral Sub-surface Runoff: Lateral Sub-surface Runoff --------------------------------------- -Lateral sub-surface runoff occurs when saturated soil moisture conditions -exist within the soil column. Sub-surface runoff is +Lateral sub-surface runoff occurs when saturated soil moisture conditions exist within the soil column. Sub-surface runoff is .. math:: :label: 7.168 @@ -1178,9 +875,7 @@ exist within the soil column. Sub-surface runoff is q_{drai} = \Theta_{ice} K_{baseflow} tan \left( \beta \right) \Delta z_{sat}^{N_{baseflow}} \ , -where :math:`K_{baseflow}` is a calibration parameter, :math:`\beta` is the -topographic slope, the exponent :math:`N_{baseflow}` = 1, and :math:`\Delta z_{sat}` -is the thickness of the saturated portion of the soil column. +where :math:`K_{baseflow}` is a calibration parameter, :math:`\beta` is the topographic slope, the exponent :math:`N_{baseflow}` = 1, and :math:`\Delta z_{sat}` is the thickness of the saturated portion of the soil column. The saturated thickness is @@ -1189,51 +884,20 @@ The saturated thickness is \Delta z_{sat} = z_{bedrock} - z_{\nabla}, -where the water table :math:`z_{\nabla}` is determined by finding the -first soil layer above the bedrock depth (section :numref:`Depth to Bedrock`) -in which the volumetric water content drops below a specified threshold. -The default threshold is set to 0.9. +where the water table :math:`z_{\nabla}` is determined by finding the first soil layer above the bedrock depth (section :numref:`Depth to Bedrock`) in which the volumetric water content drops below a specified threshold. The default threshold is set to 0.9. -The specific yield, :math:`S_{y}` , which depends on the soil -properties and the water table location, is derived by taking the -difference between two equilibrium soil moisture profiles whose water -tables differ by an infinitesimal amount +The specific yield, :math:`S_{y}`, which depends on the soil properties and the water table location, is derived by taking the difference between two equilibrium soil moisture profiles whose water tables differ by an infinitesimal amount .. math:: :label: 7.174 S_{y} =\theta_{sat} \left(1-\left(1+\frac{z_{\nabla } }{\Psi _{sat} } \right)^{\frac{-1}{B} } \right) -where B is the Clapp-Hornberger exponent. Because :math:`S_{y}` is a -function of the soil properties, it results in water table dynamics that -are consistent with the soil water fluxes described in section :numref:`Soil Water`. - -After the above calculations, two numerical adjustments are implemented -to keep the liquid water content of each soil layer -(:math:`w_{liq,\, i}` ) within physical constraints of -:math:`w_{liq}^{\min } \le w_{liq,\, i} \le \left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i}` -where :math:`w_{liq}^{\min } =0.01` (mm). First, beginning with the -bottom soil layer :math:`i=N_{levsoi}` , any excess liquid water in each -soil layer -(:math:`w_{liq,\, i}^{excess} =w_{liq,\, i} -\left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i} \ge 0`) -is successively added to the layer above. Any excess liquid water that -remains after saturating the entire soil column (plus a maximum surface -ponding depth :math:`w_{liq}^{pond} =10` kg m\ :sup:`-2`), is -added to drainage :math:`q_{drai}` . Second, to prevent negative -:math:`w_{liq,\, i}` , each layer is successively brought up to -:math:`w_{liq,\, i} =w_{liq}^{\min }` by taking the required amount of -water from the layer below. If this results in -:math:`w_{liq,\, N_{levsoi} } `) to include the carbon cycle, -vegetation dynamics, and river routing. The concept of a -community-developed land component of the Community Climate System Model -(CCSM) was initially proposed at the CCSM Land Model Working Group -(LMWG) meeting in February 1996. Initial software specifications and -development focused on evaluating the best features of three existing -land models: the NCAR LSM (:ref:`Bonan 1996, 1998`) used in the Community -Climate Model (CCM3) and the initial version of CCSM; the Institute of -Atmospheric Physics, Chinese Academy of Sciences land model (IAP94) (:ref:`Dai -and Zeng 1997`); and the Biosphere-Atmosphere Transfer Scheme (BATS) -(:ref:`Dickinson et al. 1993`) used with CCM2. A scientific steering committee -was formed to review the initial specifications of the design provided -by Robert Dickinson, Gordon Bonan, Xubin Zeng, and Yongjiu Dai and to -facilitate further development. Steering committee members were selected -so as to provide guidance and expertise in disciplines not generally -well-represented in land surface models (e.g., carbon cycling, -ecological modeling, hydrology, and river routing) and included -scientists from NCAR, the university community, and government -laboratories (R. Dickinson, G. Bonan, X. Zeng, Paul Dirmeyer, Jay -Famiglietti, Jon Foley, and Paul Houser). - -The specifications for the new model, designated the Common Land Model, -were discussed and agreed upon at the June 1998 CCSM Workshop LMWG -meeting. An initial code was developed by Y. Dai and was examined in -March 1999 by Mike Bosilovich, P. Dirmeyer, and P. Houser. At this point -an extensive period of code testing was initiated. Keith Oleson, Y. Dai, -Adam Schlosser, and P. Houser presented preliminary results of offline -1-dimensional testing at the June 1999 CCSM Workshop LMWG meeting. -Results from more extensive offline testing at plot, catchment, and -large scale (up to global) were presented by Y. Dai, A. Schlosser, K. -Oleson, M. Bosilovich, Zong-Liang Yang, Ian Baker, P. Houser, and P. -Dirmeyer at the LMWG meeting hosted by COLA (Center for -Ocean-Land-Atmosphere Studies) in November 1999. Field data used for -validation included sites adopted by the Project for Intercomparison of -Land-surface Parameterization Schemes (:ref:`Henderson-Sellers et al. 1993`) -(Cabauw, Valdai, Red-Arkansas river basin) and others [FIFE (:ref:`Sellers et -al. 1988`), BOREAS :ref:`(Sellers et al. 1995`), HAPEX-MOBILHY (:ref:`André et al. -1986`), ABRACOS (:ref:`Gash et al. 1996`), Sonoran Desert (:ref:`Unland et al. 1996`), -GSWP (:ref:`Dirmeyer et al. 1999`)]. Y. Dai also presented results from a -preliminary coupling of the Common Land Model to CCM3, indicating that -the land model could be successfully coupled to a climate model. - -Results of coupled simulations using CCM3 and the Common Land Model were -presented by X. Zeng at the June 2000 CCSM Workshop LMWG meeting. -Comparisons with the NCAR LSM and observations indicated major -improvements to the seasonality of runoff, substantial reduction of a -summer cold bias, and snow depth. Some deficiencies related to runoff -and albedo were noted, however, that were subsequently addressed. Z.-L. -Yang and I. Baker demonstrated improvements in the simulation of snow -and soil temperatures. Sam Levis reported on efforts to incorporate a -river routing model to deliver runoff to the ocean model in CCSM. Soon -after the workshop, the code was delivered to NCAR for implementation -into the CCSM framework. Documentation for the Common Land Model is -provided by :ref:`Dai et al. (2001)` while the coupling with CCM3 is described -in :ref:`Zeng et al. (2002)`. The model was introduced to the modeling -community in :ref:`Dai et al. (2003)`. +The early development of the Community Land Model can be described as the merging of a community-developed land model focusing on biogeophysics and a concurrent effort at NCAR to expand the NCAR Land Surface Model (NCAR LSM, :ref:`Bonan 1996`) to include the carbon cycle, vegetation dynamics, and river routing. The concept of a community-developed land component of the Community Climate System Model (CCSM) was initially proposed at the CCSM Land Model Working Group (LMWG) meeting in February 1996. Initial software specifications and development focused on evaluating the best features of three existing land models: the NCAR LSM (:ref:`Bonan 1996, 1998`) used in the Community Climate Model (CCM3) and the initial version of CCSM; the Institute of Atmospheric Physics, Chinese Academy of Sciences land model (IAP94) (:ref:`Dai and Zeng 1997`); and the Biosphere-Atmosphere Transfer Scheme (BATS) (:ref:`Dickinson et al. 1993`) used with CCM2. A scientific steering committee was formed to review the initial specifications of the design provided by Robert Dickinson, Gordon Bonan, Xubin Zeng, and Yongjiu Dai and to facilitate further development. Steering committee members were selected so as to provide guidance and expertise in disciplines not generally well-represented in land surface models (e.g., carbon cycling, ecological modeling, hydrology, and river routing) and included scientists from NCAR, the university community, and government laboratories (R. Dickinson, G. Bonan, X. Zeng, Paul Dirmeyer, Jay Famiglietti, Jon Foley, and Paul Houser). + +The specifications for the new model, designated the Common Land Model, were discussed and agreed upon at the June 1998 CCSM Workshop LMWG meeting. An initial code was developed by Y. Dai and was examined in March 1999 by Mike Bosilovich, P. Dirmeyer, and P. Houser. At this point an extensive period of code testing was initiated. Keith Oleson, Y. Dai, Adam Schlosser, and P. Houser presented preliminary results of offline 1-dimensional testing at the June 1999 CCSM Workshop LMWG meeting. Results from more extensive offline testing at plot, catchment, and large scale (up to global) were presented by Y. Dai, A. Schlosser, K. Oleson, M. Bosilovich, Zong-Liang Yang, Ian Baker, P. Houser, and P. Dirmeyer at the LMWG meeting hosted by COLA (Center for Ocean-Land-Atmosphere Studies) in November 1999. Field data used for validation included sites adopted by the Project for Intercomparison of Land-surface Parameterization Schemes (:ref:`Henderson-Sellers et al. 1993`) (Cabauw, Valdai, Red-Arkansas river basin) and others [FIFE (:ref:`Sellers et al. 1988`), BOREAS :ref:`(Sellers et al. 1995`), HAPEX-MOBILHY (:ref:`André et al. 1986`), ABRACOS (:ref:`Gash et al. 1996`), Sonoran Desert (:ref:`Unland et al. 1996`), GSWP (:ref:`Dirmeyer et al. 1999`)]. Y. Dai also presented results from a preliminary coupling of the Common Land Model to CCM3, indicating that the land model could be successfully coupled to a climate model. + +Results of coupled simulations using CCM3 and the Common Land Model were presented by X. Zeng at the June 2000 CCSM Workshop LMWG meeting. Comparisons with the NCAR LSM and observations indicated major improvements to the seasonality of runoff, substantial reduction of a summer cold bias, and snow depth. Some deficiencies related to runoff and albedo were noted, however, that were subsequently addressed. Z.-L. Yang and I. Baker demonstrated improvements in the simulation of snow and soil temperatures. Sam Levis reported on efforts to incorporate a river routing model to deliver runoff to the ocean model in CCSM. Soon after the workshop, the code was delivered to NCAR for implementation into the CCSM framework. Documentation for the Common Land Model is provided by :ref:`Dai et al. (2001)` while the coupling with CCM3 is described in :ref:`Zeng et al. (2002)`. The model was introduced to the modeling community in :ref:`Dai et al. (2003)`. CLM2 ^^^^^^^^^^ -Concurrent with the development of the Common Land Model, the NCAR LSM -was undergoing further development at NCAR in the areas of carbon -cycling, vegetation dynamics, and river routing. The preservation of -these advancements necessitated several modifications to the Common Land -Model. The biome-type land cover classification scheme was replaced with -a plant functional type (PFT) representation with the specification of -PFTs and leaf area index from satellite data (:ref:`Oleson and Bonan 2000`; -:ref:`Bonan et al. 2002a, b`). This also required modifications to -parameterizations for vegetation albedo and vertical burying of -vegetation by snow. Changes were made to canopy scaling, leaf -physiology, and soil water limitations on photosynthesis to resolve -deficiencies indicated by the coupling to a dynamic vegetation model. -Vertical heterogeneity in soil texture was implemented to improve -coupling with a dust emission model. A river routing model was -incorporated to improve the fresh water balance over oceans. Numerous -modest changes were made to the parameterizations to conform to the -strict energy and water balance requirements of CCSM. Further -substantial software development was also required to meet coding -standards. The resulting model was adopted in May 2002 as the Community -Land Model (CLM2) for use with the Community Atmosphere Model (CAM2, the -successor to CCM3) and version 2 of the Community Climate System Model -(CCSM2). - -K. Oleson reported on initial results from a coupling of CCM3 with CLM2 -at the June 2001 CCSM Workshop LMWG meeting. Generally, the CLM2 -preserved most of the improvements seen in the Common Land Model, -particularly with respect to surface air temperature, runoff, and snow. -These simulations are documented in :ref:`Bonan et al. (2002a)`. Further small -improvements to the biogeophysical parameterizations, ongoing software -development, and extensive analysis and validation within CAM2 and CCSM2 -culminated in the release of CLM2 to the community in May 2002. - -Following this release, Peter Thornton implemented changes to the model -structure required to represent carbon and nitrogen cycling in the -model. This involved changing data structures from a single vector of -spatially independent sub-grid patches to one that recognizes three -hierarchical scales within a model grid cell: land unit, snow/soil -column, and PFT. Furthermore, as an option, the model can be configured -so that PFTs can share a single soil column and thus "compete" for -water. This version of the model (CLM2.1) was released to the community -in February 2003. CLM2.1, without the compete option turned on, produced -only round off level changes when compared to CLM2. +Concurrent with the development of the Common Land Model, the NCAR LSM was undergoing further development at NCAR in the areas of carbon cycling, vegetation dynamics, and river routing. The preservation of these advancements necessitated several modifications to the Common Land Model. The biome-type land cover classification scheme was replaced with a plant functional type (PFT) representation with the specification of PFTs and leaf area index from satellite data (:ref:`Oleson and Bonan 2000`; :ref:`Bonan et al. 2002a, b`). This also required modifications to parameterizations for vegetation albedo and vertical burying of vegetation by snow. Changes were made to canopy scaling, leaf physiology, and soil water limitations on photosynthesis to resolve deficiencies indicated by the coupling to a dynamic vegetation model. Vertical heterogeneity in soil texture was implemented to improve coupling with a dust emission model. A river routing model was incorporated to improve the fresh water balance over oceans. Numerous modest changes were made to the parameterizations to conform to the strict energy and water balance requirements of CCSM. Further substantial software development was also required to meet coding standards. The resulting model was adopted in May 2002 as the Community Land Model (CLM2) for use with the Community Atmosphere Model (CAM2, the successor to CCM3) and version 2 of the Community Climate System Model (CCSM2). + +K. Oleson reported on initial results from a coupling of CCM3 with CLM2 at the June 2001 CCSM Workshop LMWG meeting. Generally, the CLM2 preserved most of the improvements seen in the Common Land Model, particularly with respect to surface air temperature, runoff, and snow. These simulations are documented in :ref:`Bonan et al. (2002a)`. Further small improvements to the biogeophysical parameterizations, ongoing software development, and extensive analysis and validation within CAM2 and CCSM2 culminated in the release of CLM2 to the community in May 2002. + +Following this release, Peter Thornton implemented changes to the model structure required to represent carbon and nitrogen cycling in the model. This involved changing data structures from a single vector of spatially independent sub-grid patches to one that recognizes three hierarchical scales within a model grid cell: land unit, snow/soil column, and PFT. Furthermore, as an option, the model can be configured so that PFTs can share a single soil column and thus "compete" for water. This version of the model (CLM2.1) was released to the community in February 2003. CLM2.1, without the compete option turned on, produced only round off level changes when compared to CLM2. CLM3 ^^^^^^^^^^ -CLM3 implemented further software improvements related to performance -and model output, a re-writing of the code to support vector-based -computational platforms, and improvements in biogeophysical -parameterizations to correct deficiencies in the coupled model climate. -Of these parameterization improvements, two were shown to have a -noticeable impact on simulated climate. A variable aerodynamic -resistance for heat/moisture transfer from ground to canopy air that -depends on canopy density was implemented. This reduced unrealistically -high surface temperatures in semi-arid regions. The second improvement -added stability corrections to the diagnostic 2-m air temperature -calculation which reduced biases in this temperature. Competition -between PFTs for water, in which PFTs share a single soil column, is the -default mode of operation in this model version. CLM3 was released to -the community in June 2004. :ref:`Dickinson et al. (2006)` -describe the climate statistics of CLM3 when coupled to CCSM3.0. -:ref:`Hack et al. (2006)` provide an analysis of selected -features of the land hydrological cycle. -:ref:`Lawrence et al. (2007)` examine the impact of -changes in CLM3 -hydrological parameterizations on partitioning of evapotranspiration -(ET) and its effect on the timescales of ET response to precipitation -events, interseasonal soil moisture storage, soil moisture memory, and -land-atmosphere coupling. :ref:`Qian et al. (2006)` evaluate CLM3's performance -in simulating soil moisture content, runoff, and river discharge when -forced by observed precipitation, temperature and other atmospheric -data. +CLM3 implemented further software improvements related to performance and model output, a re-writing of the code to support vector-based computational platforms, and improvements in biogeophysical parameterizations to correct deficiencies in the coupled model climate. Of these parameterization improvements, two were shown to have a noticeable impact on simulated climate. A variable aerodynamic resistance for heat/moisture transfer from ground to canopy air that depends on canopy density was implemented. This reduced unrealistically high surface temperatures in semi-arid regions. The second improvement added stability corrections to the diagnostic 2-m air temperature calculation which reduced biases in this temperature. Competition between PFTs for water, in which PFTs share a single soil column, is the default mode of operation in this model version. CLM3 was released to the community in June 2004. :ref:`Dickinson et al. (2006)` describe the climate statistics of CLM3 when coupled to CCSM3.0. :ref:`Hack et al. (2006)` provide an analysis of selected features of the land hydrological cycle. :ref:`Lawrence et al. (2007)` examine the impact of changes in CLM3 hydrological parameterizations on partitioning of evapotranspiration (ET) and its effect on the timescales of ET response to precipitation events, interseasonal soil moisture storage, soil moisture memory, and land-atmosphere coupling. :ref:`Qian et al. (2006)` evaluate CLM3's performance in simulating soil moisture content, runoff, and river discharge when forced by observed precipitation, temperature and other atmospheric data. CLM3.5 ^^^^^^^^^^^^ -Although the simulation of land surface climate by CLM3 was in many ways -adequate, most of the unsatisfactory aspects of the simulated climate -noted by the above studies could be traced directly to deficiencies in -simulation of the hydrological cycle. In 2004, a project was initiated -to improve the hydrology in CLM3 as part of the development of CLM -version 3.5. A selected set of promising approaches to alleviating the -hydrologic biases in CLM3 were tested and implemented. These included -new surface datasets based on Moderate Resolution Imaging -Spectroradiometer (MODIS) products, new parameterizations for canopy -integration, canopy interception, frozen soil, soil water availability, -and soil evaporation, a TOPMODEL-based model for surface and subsurface -runoff, a groundwater model for determining water table depth, and the -introduction of a factor to simulate nitrogen limitation on plant -productivity. :ref:`Oleson et al. (2008a)` show that CLM3.5 exhibits -significant improvements over CLM3 in its partitioning of global ET -which result in wetter soils, less plant water stress, increased -transpiration and photosynthesis, and an improved annual cycle of total -water storage. Phase and amplitude of the runoff annual cycle is -generally improved. Dramatic improvements in vegetation biogeography -result when CLM3.5 is coupled to a dynamic global vegetation model. -:ref:`Stöckli et al. (2008)` examine the performance of CLM3.5 at local scales -by making use of a network of long-term ground-based ecosystem -observations [FLUXNET (:ref:`Baldocchi et al. 2001`)]. Data from 15 FLUXNET -sites were used to demonstrate significantly improved soil hydrology and -energy partitioning in CLM3.5. CLM3.5 was released to the community in -May, 2007. +Although the simulation of land surface climate by CLM3 was in many ways adequate, most of the unsatisfactory aspects of the simulated climate noted by the above studies could be traced directly to deficiencies in simulation of the hydrological cycle. In 2004, a project was initiated to improve the hydrology in CLM3 as part of the development of CLM version 3.5. A selected set of promising approaches to alleviating the hydrologic biases in CLM3 were tested and implemented. These included new surface datasets based on Moderate Resolution Imaging Spectroradiometer (MODIS) products, new parameterizations for canopy integration, canopy interception, frozen soil, soil water availability, and soil evaporation, a TOPMODEL-based model for surface and subsurface runoff, a groundwater model for determining water table depth, and the introduction of a factor to simulate nitrogen limitation on plant productivity. :ref:`Oleson et al. (2008a)` show that CLM3.5 exhibits significant improvements over CLM3 in its partitioning of global ET which result in wetter soils, less plant water stress, increased transpiration and photosynthesis, and an improved annual cycle of total water storage. Phase and amplitude of the runoff annual cycle is generally improved. Dramatic improvements in vegetation biogeography result when CLM3.5 is coupled to a dynamic global vegetation model. :ref:`Stöckli et al. (2008)` examine the performance of CLM3.5 at local scales by making use of a network of long-term ground-based ecosystem observations [FLUXNET (:ref:`Baldocchi et al. 2001`)]. Data from 15 FLUXNET sites were used to demonstrate significantly improved soil hydrology and energy partitioning in CLM3.5. CLM3.5 was released to the community in May, 2007. CLM4 ^^^^^^^^^^ -The motivation for the next version of the model, CLM4, was to -incorporate several recent scientific advances in the understanding and -representation of land surface processes, expand model capabilities, and -improve surface and atmospheric forcing datasets (:ref:`Lawrence et al. 2011`). -Included in the first category are more sophisticated representations of -soil hydrology and snow processes. In particular, new treatments of soil -column-groundwater interactions, soil evaporation, aerodynamic -parameters for sparse/dense canopies, vertical burial of vegetation by -snow, snow cover fraction and aging, black carbon and dust deposition, -and vertical distribution of solar energy for snow were implemented. -Major new capabilities in the model include a representation of the -carbon-nitrogen cycle (CLM4CN, see next paragraph for additional -information), the ability to model land cover change in a transient -mode, inclusion of organic soil and deep soil into the existing mineral -soil treatment to enable more realistic modeling of permafrost, an urban -canyon model to contrast rural and urban energy balance and climate -(CLMU), and an updated biogenic volatile organic compounds (BVOC) model. -Other modifications of note include refinement of the global PFT, -wetland, and lake distributions, more realistic optical properties for -grasslands and croplands, and an improved diurnal cycle and spectral -distribution of incoming solar radiation to force the model in land-only -mode. - -Many of the ideas incorporated into the carbon and nitrogen cycle -component of CLM4 derive from the earlier development of the land-only -ecosystem process model Biome-BGC (Biome BioGeochemical Cycles), -originating at the Numerical Terradynamic Simulation Group (NTSG) at the -University of Montana, under the guidance of Prof. Steven Running. -Biome-BGC itself is an extension of an earlier model, Forest-BGC -(:ref:`Running and Coughlan, 1988`; :ref:`Running and Gower, 1991`), which -simulates water, carbon, and, to a limited extent, nitrogen fluxes for -forest ecosystems. Forest-BGC was designed to be driven by remote -sensing inputs of vegetation structure, and so used a diagnostic -(prescribed) leaf area index, or, in the case of the dynamic allocation -version of the model (:ref:`Running and Gower, 1991`), prescribed maximum -leaf area index. - -Biome-BGC expanded on the Forest-BGC logic by introducing a more -mechanistic calculation of leaf and canopy scale photosynthesis (:ref:`Hunt -and Running, 1992`), and extending the physiological parameterizations -to include multiple woody and non-woody vegetation types (:ref:`Hunt et al. -1996`; :ref:`Running and Hunt, 1993`). Later versions of Biome-BGC introduced -more mechanistic descriptions of belowground carbon and nitrogen cycles, -nitrogen controls on photosynthesis and decomposition, sunlit and shaded -canopies, vertical gradient in leaf morphology, and explicit treatment -of fire and harvest disturbance and regrowth dynamics (:ref:`Kimball et al. -1997`; :ref:`Thornton, 1998`; :ref:`Thornton et al. 2002`; :ref:`White et al. 2000`). -Biome-BGC version 4.1.2 (:ref:`Thornton et al. 2002`) provided a point of -departure for integrating new biogeochemistry components into CLM4. - -CLM4 was released to the community in June, 2010 along with the -Community Climate System Model version 4 (CCSM4). CLM4 is used in CCSM4, -CESM1, CESM1.1, and remains available as the default land component -model option for coupled simulations in CESM1.2. +The motivation for the next version of the model, CLM4, was to incorporate several recent scientific advances in the understanding and representation of land surface processes, expand model capabilities, and improve surface and atmospheric forcing datasets (:ref:`Lawrence et al. 2011`). Included in the first category are more sophisticated representations of soil hydrology and snow processes. In particular, new treatments of soil column-groundwater interactions, soil evaporation, aerodynamic parameters for sparse/dense canopies, vertical burial of vegetation by snow, snow cover fraction and aging, black carbon and dust deposition, and vertical distribution of solar energy for snow were implemented. Major new capabilities in the model include a representation of the carbon-nitrogen cycle (CLM4CN, see next paragraph for additional information), the ability to model land cover change in a transient mode, inclusion of organic soil and deep soil into the existing mineral soil treatment to enable more realistic modeling of permafrost, an urban canyon model to contrast rural and urban energy balance and climate (CLMU), and an updated biogenic volatile organic compounds (BVOC) model. Other modifications of note include refinement of the global PFT, wetland, and lake distributions, more realistic optical properties for grasslands and croplands, and an improved diurnal cycle and spectral distribution of incoming solar radiation to force the model in land-only mode. + +Many of the ideas incorporated into the carbon and nitrogen cycle component of CLM4 derive from the earlier development of the land-only ecosystem process model Biome-BGC (Biome BioGeochemical Cycles), originating at the Numerical Terradynamic Simulation Group (NTSG) at the University of Montana, under the guidance of Prof. Steven Running. Biome-BGC itself is an extension of an earlier model, Forest-BGC (:ref:`Running and Coughlan, 1988`; :ref:`Running and Gower, 1991`), which simulates water, carbon, and, to a limited extent, nitrogen fluxes for forest ecosystems. Forest-BGC was designed to be driven by remote sensing inputs of vegetation structure, and so used a diagnostic (prescribed) leaf area index, or, in the case of the dynamic allocation version of the model (:ref:`Running and Gower, 1991`), prescribed maximum leaf area index. + +Biome-BGC expanded on the Forest-BGC logic by introducing a more mechanistic calculation of leaf and canopy scale photosynthesis (:ref:`Hunt and Running, 1992`), and extending the physiological parameterizations to include multiple woody and non-woody vegetation types (:ref:`Hunt et al. 1996`; :ref:`Running and Hunt, 1993`). Later versions of Biome-BGC introduced more mechanistic descriptions of belowground carbon and nitrogen cycles, nitrogen controls on photosynthesis and decomposition, sunlit and shaded canopies, vertical gradient in leaf morphology, and explicit treatment of fire and harvest disturbance and regrowth dynamics (:ref:`Kimball et al. 1997`; :ref:`Thornton, 1998`; :ref:`Thornton et al. 2002`; :ref:`White et al. 2000`). Biome-BGC version 4.1.2 (:ref:`Thornton et al. 2002`) provided a point of departure for integrating new biogeochemistry components into CLM4. + +CLM4 was released to the community in June, 2010 along with the Community Climate System Model version 4 (CCSM4). CLM4 is used in CCSM4, CESM1, CESM1.1, and remains available as the default land component model option for coupled simulations in CESM1.2. CLM4.5 ^^^^^^^^^^^^ -The motivations for the development of CLM4.5 were similar to those for CLM4: -incorporate several recent scientific advances in the understanding and -representation of land surface processes, expand model capabilities, and -improve surface and atmospheric forcing datasets. - -Specifically, several parameterizations were revised to reflect new -scientific understanding and in an attempt to reduce biases identified -in CLM4 simulations including low soil carbon stocks especially in the -Arctic, excessive tropical GPP and unrealistically low Arctic GPP, a dry -soil bias in Arctic soils, unrealistically high LAI in the tropics, a -transient 20\ :math:`{}^{th}` century carbon response that was -inconsistent with observational estimates, and several other more minor -problems or biases. - -The main modifications include updates to canopy processes including a -revised canopy radiation scheme and canopy scaling of leaf processes, -co-limitations on photosynthesis, revisions to photosynthetic parameters -(:ref:`Bonan et al. 2011`), temperature acclimation of photosynthesis, and -improved stability of the iterative solution in the photosynthesis and -stomatal conductance model (:ref:`Sun et al. 2012`). Hydrology updates included -modifications such that hydraulic properties of frozen soils are -determined by liquid water content only rather than total water content -and the introduction of an ice impedance function, and other corrections -that increase the consistency between soil water state and water table -position and allow for a perched water table above icy permafrost ground -(:ref:`Swenson et al. 2012`). A new snow cover fraction parameterization is -incorporated that reflects the hysteresis in fractional snow cover for a -given snow depth between accumulation and melt phases (:ref:`Swenson and -Lawrence, 2012`). The lake model in CLM4 was replaced with a completely -revised and more realistic lake model (:ref:`Subin et al. 2012a`). A surface -water store was introduced, replacing the wetland land unit and -permitting prognostic wetland distribution modeling. The surface -energy fluxes are calculated separately (:ref:`Swenson and Lawrence, 2012`) for -snow-covered, water-covered, and snow/water-free portions of vegetated -and crop land units, and snow-covered and snow-free portions of glacier -land units. Globally constant river flow velocity is replaced with -variable flow velocity based on mean grid cell slope. A vertically -resolved soil biogeochemistry scheme is introduced with base -decomposition rates modified by soil temperature, water, and oxygen -limitations and also including vertical mixing of soil carbon and -nitrogen due to bioturbation, cryoturbation, and diffusion (:ref:`Koven et al. -2013`). The litter and soil carbon and nitrogen pool structure as well as -nitrification and denitrification that were modified based on the Century -model. Biological fixation was revised to distribute fixation more -realistically over the year (:ref:`Koven et al. 2013`). The fire model was -replaced with a model that includes representations of natural and -anthropogenic triggers and suppression as well as agricultural, -deforestation, and peat fires (:ref:`Li et al. 2012a,b`; :ref:`Li et al. 2013a`). The -biogenic volatile organic compounds model is updated to MEGAN2.1 -(:ref:`Guenther et al. 2012`). - -Additions to the model include a methane production, oxidation, and -emissions model (:ref:`Riley et al. 2011a`) and an extension of the crop model -to include interactive fertilization, organ pools (:ref:`Drewniak et al. -2013`), and irrigation (:ref:`Sacks et al. 2009`). Elements of the Variable -Infiltration Capacity (VIC) model are included as an alternative -optional runoff generation scheme (:ref:`Li et al. 2011`). There is also an -option to run with a multilayer canopy (:ref:`Bonan et al. 2012`). Multiple -urban density classes, rather than the single dominant urban density -class used in CLM4, are modeled in the urban land unit. Carbon -(:math:`{}^{13}`\ C and :math:`{}^{14}`\ C) isotopes are enabled (:ref:`Koven -et al. 2013`). Minor changes include a switch of the C3 Arctic grass and -shrub phenology from stress deciduous to seasonal deciduous and a change -in the glacier bare ice albedo to better reflect recent estimates. -Finally, the carbon and nitrogen cycle spinup is accelerated and -streamlined with a revised spinup method, though the spinup timescale -remains long. - -Finally, the predominantly low resolution input data for provided with -CLM4 to create CLM4 surface datasets is replaced with newer and higher -resolution input datasets where possible (see section :numref:`Surface Data` -for details). The default meteorological forcing dataset provided with CLM4 -(:ref:`Qian et al. 2006)` is replaced with the 1901-2010 -CRUNCEP forcing dataset (see Chapter :numref:`rst_Land-Only Mode`) for CLM4.5, -though users can also still use the :ref:`Qian et al. (2006)` -dataset or other alternative forcing datasets. - -CLM4.5 was released to the community in June 2013 along with the -Community Earth System Model version 1.2 (CESM1.2). +The motivations for the development of CLM4.5 were similar to those for CLM4: incorporate several recent scientific advances in the understanding and representation of land surface processes, expand model capabilities, and improve surface and atmospheric forcing datasets. + +Specifically, several parameterizations were revised to reflect new scientific understanding and in an attempt to reduce biases identified in CLM4 simulations including low soil carbon stocks especially in the Arctic, excessive tropical GPP and unrealistically low Arctic GPP, a dry soil bias in Arctic soils, unrealistically high LAI in the tropics, a transient 20\ :math:`{}^{th}` century carbon response that was inconsistent with observational estimates, and several other more minor problems or biases. + +The main modifications include updates to canopy processes including a revised canopy radiation scheme and canopy scaling of leaf processes, co-limitations on photosynthesis, revisions to photosynthetic parameters (:ref:`Bonan et al. 2011`), temperature acclimation of photosynthesis, and improved stability of the iterative solution in the photosynthesis and stomatal conductance model (:ref:`Sun et al. 2012`). Hydrology updates included modifications such that hydraulic properties of frozen soils are determined by liquid water content only rather than total water content and the introduction of an ice impedance function, and other corrections that increase the consistency between soil water state and water table position and allow for a perched water table above icy permafrost ground (:ref:`Swenson et al. 2012`). A new snow cover fraction parameterization is incorporated that reflects the hysteresis in fractional snow cover for a given snow depth between accumulation and melt phases (:ref:`Swenson and Lawrence, 2012`). The lake model in CLM4 was replaced with a completely revised and more realistic lake model (:ref:`Subin et al. 2012a`). A surface water store was introduced, replacing the wetland land unit and permitting prognostic wetland distribution modeling. The surface energy fluxes are calculated separately (:ref:`Swenson and Lawrence, 2012`) for snow-covered, water-covered, and snow/water-free portions of vegetated and crop land units, and snow-covered and snow-free portions of glacier land units. Globally constant river flow velocity is replaced with variable flow velocity based on mean grid cell slope. A vertically resolved soil biogeochemistry scheme is introduced with base decomposition rates modified by soil temperature, water, and oxygen limitations and also including vertical mixing of soil carbon and nitrogen due to bioturbation, cryoturbation, and diffusion (:ref:`Koven et al. 2013`). The litter and soil carbon and nitrogen pool structure as well as nitrification and denitrification that were modified based on the Century model. Biological fixation was revised to distribute fixation more realistically over the year (:ref:`Koven et al. 2013`). The fire model was replaced with a model that includes representations of natural and anthropogenic triggers and suppression as well as agricultural, deforestation, and peat fires (:ref:`Li et al. 2012a,b`; :ref:`Li et al. 2013a`). The biogenic volatile organic compounds model is updated to MEGAN2.1 (:ref:`Guenther et al. 2012`). + +Additions to the model include a methane production, oxidation, and emissions model (:ref:`Riley et al. 2011a`) and an extension of the crop model to include interactive fertilization, organ pools (:ref:`Drewniak et al. 2013`), and irrigation (:ref:`Sacks et al. 2009`). Elements of the Variable Infiltration Capacity (VIC) model are included as an alternative optional runoff generation scheme (:ref:`Li et al. 2011`). There is also an option to run with a multilayer canopy (:ref:`Bonan et al. 2012`). Multiple urban density classes, rather than the single dominant urban density class used in CLM4, are modeled in the urban land unit. Carbon (:math:`{}^{13}`\ C and :math:`{}^{14}`\ C) isotopes are enabled (:ref:`Koven et al. 2013`). Minor changes include a switch of the C3 Arctic grass and shrub phenology from stress deciduous to seasonal deciduous and a change in the glacier bare ice albedo to better reflect recent estimates. Finally, the carbon and nitrogen cycle spinup is accelerated and streamlined with a revised spinup method, though the spinup timescale remains long. + +Finally, the predominantly low resolution input data for provided with CLM4 to create CLM4 surface datasets is replaced with newer and higher resolution input datasets where possible (see section :numref:`Surface Data` for details). The default meteorological forcing dataset provided with CLM4 (:ref:`Qian et al. 2006)` is replaced with the 1901-2010 CRUNCEP forcing dataset (see Chapter :numref:`rst_Land-Only Mode`) for CLM4.5, though users can also still use the :ref:`Qian et al. (2006)` dataset or other alternative forcing datasets. + +CLM4.5 was released to the community in June 2013 along with the Community Earth System Model version 1.2 (CESM1.2). CLM5.0 ^^^^^^^^^^^^ -Developments for CLM5.0 build on the progress made in CLM4.5. Most major components of the model have been updated with particularly -notable changes made to soil and plant hydrology, snow density, river modeling, carbon and nitrogen cycling and coupling, -and crop modeling. -Much of the focus of development centered on a -push towards more mechanistic treatment of key processes, in addition to more comprehensive and explicit representation -of land use and land-cover change. Prior versions of CLM included relatively few options for physics parameterizations or structure. -In CLM5, where new parameterizations or model decisions were made, in most cases, the CLM4.5 parameterization was maintained so that users could switch back and forth between different parameterizations via namelist control where appropriate or desirable. Throughout the CLM5 Technical Descpription, in general only the default parameterization for any given process is described. Readers are referred to the CLM4.5 or CLM4 Technical Descriptions for detailed descriptions of non-default parameterizations. - -The hydrology updates include the introduction of a dry surface layer-based soil evaporation resistance parameterization :ref:`(Swenson and Lawrence, 2014)` and a revised canopy interception parameterization. Canopy interception is now divided into liquid and solid phases, with the intercepted snow subject to unloading events due to wind or above-freezing temperatures. The snow-covered fraction of the canopy is used within the canopy radiation and surface albedo calculation. Instead of applying a spatially uniform soil thickness, soil thickness can vary in space :ref:`(Brunke et al. 2016` and :ref:`Swenson and Lawrence, 2015)` and is set to values within a range of 0.4m to 8.5m depth, derived from a spatially explicit soil thickness data product :ref:`(Pelletier et al., 2016)`. The explicit treatment of soil thickness allows for the deprecation of the unconfined aquifer parameterization used in CLM4.5, which is replaced with a zero flux boundary condition and explicit modeling of both the saturated and unsaturated zones. The default model soil layer resolution is increased, especially within the top 3m, to more explicitly represent active layer thickness within the permafrost zone. Rooting profiles were used inconsistently in CLM4.5 with :ref:`Zeng (2001)` profiles used for water and :ref:`Jackson et al. (1996)` profiles used for carbon inputs. For CLM5, the Jackson et al. (1996) rooting profiles are used for both water and carbon. Roots are deepened for the broadleaf evergreen tropical tree and broadleaf deciduous tropical tree types. Finally, an adaptive time-stepping solution to the Richard's equation is introduced, which improves the accuracy and stability of the numerical soil water solution. The River Transport Model (RTM) is replaced with the Model for Scale Adaptive River Transport (MOSART, :ref:`Li et al., 2013b)` in which surface runoff is routed across hillslopes and then discharged along with subsurface runoff into a tributary subnetwork before entering the main channel. - -Several changes are included that are mainly targeted at improving the simulation of surface mass balance over ice -sheets. The fresh snow density parameterization is updated to more realistically capture temperature effects and to additionally account for wind effects on new snow density :ref:`(van Kampenhout et al., 2017)`. The maximum number of snow layers and snow amount is increased from 5 layers and 1m snow water equivalent to 12 layers and 10m snow water equivalent to allow for the formation of firn in regions of persistent snow-cover (e.g., glaciers and ice sheets) :ref:`(van Kampenhout et al., 2017)`. The CISM2 ice sheet model is included for Greenland by default. The ice sheet does not evolve for typical configurations, but ice sheet evolution can be turned on by choosing an appropriate compset. The introduction in CLM5 of the capability to -dynamically adjust landunit weights means that a glacier can initiate, grow, shrink, or disappear during -a simulation when ice evolution is active. That is, there are two-way feedbacks between CLM and CISM. Multiple elevation classes (10 elevation classes by default) and associated temperature, rain/snow partitioning, and downwelling longwave downscaling are used for glacier landunits to account for the strong topographic elevation heterogeneity over glaciers and ice sheets. - -A plant hydraulic stress routine is introduced which explicitly models water transport through the vegetation according to a simple hydraulic framework (Kennedy et al., to be submitted). The water supply equations are used to solve for vegetation water potential forced by transpiration demand and a set of layer-by-layer soil water potentials. Stomatal conductance, therefore, is a function of prognostic leaf water potential. Water stress is calculated as the ratio of attenuated stomatal conductance to maximum stomatal conductance. An emergent feature of the plant hydraulics is soil hydraulic redistribution. In CLM5, maximum stomatal conductance is obtained from the Medlyn conductance model :ref:`(Medlyn et al., 2011)`, rather than the Ball-Berry stomatal conductance model that was utilized in CLM4.5 and prior versions of the model. The Medlyn stomatal conductance model is preferred mainly for it's more realistic behavior at low humidity levels :ref:`(Rogers et al., 2017)`. The stress deciduous vegetation phenology trigger is augmented with a antecedent precipitation requirement :ref:`(Dahlin et al. 2015)`. - -Plant nutrient dynamics are substantially updated to resolve several deficiencies with the CLM4 and CLM4.5 nutrient cycling representation. The Fixation and Update of Nitrogen (FUN) model based on the work of :ref:`Fisher et al. (2010)`, :ref:`Brzostek et al. (2014)`, and :ref:`Shi et al. (2016)` is incorporated. The concept of FUN is that in most cases, N uptake requires the expenditure of energy in the form of carbon, and further, that there are numerous potential sources of N in the environment which a plant may exchange for carbon. The ratio of carbon expended to N acquired is therefore the cost, or exchange rate, of N acquisition. FUN calculates the rate of symbiotic N fixation, with this N passed straight to the plant, not the mineral N pool. Separately, CLM5 also calculates rates of symbiotic (or free living) N fixation as a function of evapotranspiration (:ref:`Cleveland et al. 1999 `), which -is added to the soil inorganic ammonium (NH\ :sub:`4`\ :sup:`+`) pool. The static plant carbon:nitrogen (C:N) ratios utilized in CLM4 and CLM4.5 are replaced with variable plant C:N ratios which -allows plants to adjust their C:N ratio, and therefore their leaf nitrogen content, with the cost of N uptake :ref:`(Ghimire et al. 2016)`. -The implementation of a flexible C:N ratio means that the model no longer relies on instantaneous downregulation -of potential photosynthesis rates based on soil mineral nitrogen availability to represent nutrient limitation. Furthermore, stomatal conductance -is now based on the N-limited photosynthesis rather than on potential photosynthesis. Finally, the Leaf Use of -Nitrogen for Assimilation (LUNA, :ref:`Xu et al., 2012` and :ref:`Ali et al., 2016)` model is incorporated. The LUNA model calculates -photosynthetic capacity based on optimization of the use of leaf nitrogen under different environmental conditions such that -light capture, carboxylation, and respiration are co-limiting. - -CLM5 applies a fixed allocation scheme for woody vegetation. The decision to use a fixed allocation scheme in CLM5, rather than a dynamic NPP-based allocation scheme, as was used in CLM4 and CLM4.5, was driven by the fact that observations indicate that biomass saturates with increasing productivity, in contrast to the behavior in CLM4 and CLM4.5 where biomass continuously increases with increasing productivity (:ref:`Negron-Juarez et al., 2015`). Soil carbon decomposition processes are unchanged in CLM5, but a new metric for apparent soil carbon turnover times (:ref:`Koven et al., 2017 `) suggested parameter changes that produce a weak intrinsic depth limitation on soil carbon turnover rates (rather than the strong depth limitaiton in CLM4.5) and that the thresholds for soil moisture limitation on soil carbon turnover rates in dry soils should be set at a wetter soil moisture level than that used in CLM4.5. - -Representation of human management of the land (agriculture, wood harvest) is augmented in several ways. -The CLM4.5 crop model is extended to operate globally through the addition of rice, sugarcane, -tropical varieties of corn and soybean :ref:`(Badger and Dirmeyer, 2015` and :ref:`Levis et al., 2016)`, -and perennial bioenergy crops :ref:`(Cheng et al., 2019)`. -These crop types are added to the existing temperate corn, temperate soybean, spring wheat, and cotton crop types. -Fertilization rates and irrigation equipped area updated annually based on crop type and geographic region through an input dataset. -The irrigation trigger is updated. Additional minor changes include crop phenological triggers that -vary by latitude for selected crop types, grain C and N is now removed at harvest to a 1-year product pool with -the carbon for the next season's crop seed removed from the grain carbon at harvest. -A fraction of leaf/livestem C and N from bioenergy crops is removed at harvest to the biofuel feedstock pools and added to the 1-year product pool. -Through the introduction of the capability to dynamically adjust landunit weights during a simulation, the crop model can now be run coincidentally -with prescribed land use, which significantly expands the capabilities of the model. Mass-based rather than area-based wood harvest is applied. Several heat stress indices for both urban and rural areas are calculated and output by default :ref:`(Buzan et al., 2015)`. A more sophisticated and realistic building space heating and air conditioning submodel that prognoses interior building air temperature and includes more realistic space heating and air conditioning wasteheat factors -is incorporated. +Developments for CLM5.0 build on the progress made in CLM4.5. Most major components of the model have been updated with particularly notable changes made to soil and plant hydrology, snow density, river modeling, carbon and nitrogen cycling and coupling, and crop modeling. Much of the focus of development centered on a push towards more mechanistic treatment of key processes, in addition to more comprehensive and explicit representation of land use and land-cover change. Prior versions of CLM included relatively few options for physics parameterizations or structure. In CLM5, where new parameterizations or model decisions were made, in most cases, the CLM4.5 parameterization was maintained so that users could switch back and forth between different parameterizations via namelist control where appropriate or desirable. Throughout the CLM5 Technical Descpription, in general only the default parameterization for any given process is described. Readers are referred to the CLM4.5 or CLM4 Technical Descriptions for detailed descriptions of non-default parameterizations. + +The hydrology updates include the introduction of a dry surface layer-based soil evaporation resistance parameterization :ref:`(Swenson and Lawrence, 2014)` and a revised canopy interception parameterization. Canopy interception is now divided into liquid and solid phases, with the intercepted snow subject to unloading events due to wind or above-freezing temperatures. The snow-covered fraction of the canopy is used within the canopy radiation and surface albedo calculation. Instead of applying a spatially uniform soil thickness, soil thickness can vary in space :ref:`(Brunke et al. 2016` and :ref:`Swenson and Lawrence, 2015)` and is set to values within a range of 0.4m to 8.5m depth, derived from a spatially explicit soil thickness data product :ref:`(Pelletier et al., 2016)`. The explicit treatment of soil thickness allows for the deprecation of the unconfined aquifer parameterization used in CLM4.5, which is replaced with a zero flux boundary condition and explicit modeling of both the saturated and unsaturated zones. The default model soil layer resolution is increased, especially within the top 3m, to more explicitly represent active layer thickness within the permafrost zone. Rooting profiles were used inconsistently in CLM4.5 with :ref:`Zeng (2001)` profiles used for water and :ref:`Jackson et al. (1996)` profiles used for carbon inputs. For CLM5, the Jackson et al. (1996) rooting profiles are used for both water and carbon. Roots are deepened for the broadleaf evergreen tropical tree and broadleaf deciduous tropical tree types. Finally, an adaptive time-stepping solution to the Richard's equation is introduced, which improves the accuracy and stability of the numerical soil water solution. The River Transport Model (RTM) is replaced with the Model for Scale Adaptive River Transport (MOSART, :ref:`Li et al., 2013b)` in which surface runoff is routed across hillslopes and then discharged along with subsurface runoff into a tributary subnetwork before entering the main channel. + +Several changes are included that are mainly targeted at improving the simulation of surface mass balance over ice sheets. The fresh snow density parameterization is updated to more realistically capture temperature effects and to additionally account for wind effects on new snow density :ref:`(van Kampenhout et al., 2017)`. The maximum number of snow layers and snow amount is increased from 5 layers and 1m snow water equivalent to 12 layers and 10m snow water equivalent to allow for the formation of firn in regions of persistent snow-cover (e.g., glaciers and ice sheets) :ref:`(van Kampenhout et al., 2017)`. The CISM2 ice sheet model is included for Greenland by default. The ice sheet does not evolve for typical configurations, but ice sheet evolution can be turned on by choosing an appropriate compset. The introduction in CLM5 of the capability to dynamically adjust landunit weights means that a glacier can initiate, grow, shrink, or disappear during a simulation when ice evolution is active. That is, there are two-way feedbacks between CLM and CISM. Multiple elevation classes (10 elevation classes by default) and associated temperature, rain/snow partitioning, and downwelling longwave downscaling are used for glacier landunits to account for the strong topographic elevation heterogeneity over glaciers and ice sheets. + +A plant hydraulic stress routine is introduced which explicitly models water transport through the vegetation according to a simple hydraulic framework (Kennedy et al., to be submitted). The water supply equations are used to solve for vegetation water potential forced by transpiration demand and a set of layer-by-layer soil water potentials. Stomatal conductance, therefore, is a function of prognostic leaf water potential. Water stress is calculated as the ratio of attenuated stomatal conductance to maximum stomatal conductance. An emergent feature of the plant hydraulics is soil hydraulic redistribution. In CLM5, maximum stomatal conductance is obtained from the Medlyn conductance model :ref:`(Medlyn et al., 2011)`, rather than the Ball-Berry stomatal conductance model that was utilized in CLM4.5 and prior versions of the model. The Medlyn stomatal conductance model is preferred mainly for it's more realistic behavior at low humidity levels :ref:`(Rogers et al., 2017)`. The stress deciduous vegetation phenology trigger is augmented with a antecedent precipitation requirement :ref:`(Dahlin et al. 2015)`. + +Plant nutrient dynamics are substantially updated to resolve several deficiencies with the CLM4 and CLM4.5 nutrient cycling representation. The Fixation and Update of Nitrogen (FUN) model based on the work of :ref:`Fisher et al. (2010)`, :ref:`Brzostek et al. (2014)`, and :ref:`Shi et al. (2016)` is incorporated. The concept of FUN is that in most cases, N uptake requires the expenditure of energy in the form of carbon, and further, that there are numerous potential sources of N in the environment which a plant may exchange for carbon. The ratio of carbon expended to N acquired is therefore the cost, or exchange rate, of N acquisition. FUN calculates the rate of symbiotic N fixation, with this N passed straight to the plant, not the mineral N pool. Separately, CLM5 also calculates rates of symbiotic (or free living) N fixation as a function of evapotranspiration (:ref:`Cleveland et al. 1999 `), which is added to the soil inorganic ammonium (NH\ :sub:`4`\ :sup:`+`) pool. The static plant carbon:nitrogen (C:N) ratios utilized in CLM4 and CLM4.5 are replaced with variable plant C:N ratios which allows plants to adjust their C:N ratio, and therefore their leaf nitrogen content, with the cost of N uptake :ref:`(Ghimire et al. 2016)`. The implementation of a flexible C:N ratio means that the model no longer relies on instantaneous downregulation of potential photosynthesis rates based on soil mineral nitrogen availability to represent nutrient limitation. Furthermore, stomatal conductance is now based on the N-limited photosynthesis rather than on potential photosynthesis. Finally, the Leaf Use of Nitrogen for Assimilation (LUNA, :ref:`Xu et al., 2012` and :ref:`Ali et al., 2016)` model is incorporated. The LUNA model calculates photosynthetic capacity based on optimization of the use of leaf nitrogen under different environmental conditions such that light capture, carboxylation, and respiration are co-limiting. + +CLM5 applies a fixed allocation scheme for woody vegetation. The decision to use a fixed allocation scheme in CLM5, rather than a dynamic NPP-based allocation scheme, as was used in CLM4 and CLM4.5, was driven by the fact that observations indicate that biomass saturates with increasing productivity, in contrast to the behavior in CLM4 and CLM4.5 where biomass continuously increases with increasing productivity (:ref:`Negron-Juarez et al., 2015`). Soil carbon decomposition processes are unchanged in CLM5, but a new metric for apparent soil carbon turnover times (:ref:`Koven et al., 2017 `) suggested parameter changes that produce a weak intrinsic depth limitation on soil carbon turnover rates (rather than the strong depth limitaiton in CLM4.5) and that the thresholds for soil moisture limitation on soil carbon turnover rates in dry soils should be set at a wetter soil moisture level than that used in CLM4.5. + +Representation of human management of the land (agriculture, wood harvest) is augmented in several ways. The CLM4.5 crop model is extended to operate globally through the addition of rice, sugarcane, tropical varieties of corn and soybean :ref:`(Badger and Dirmeyer, 2015` and :ref:`Levis et al., 2016)`, and perennial bioenergy crops :ref:`(Cheng et al., 2019)`. These crop types are added to the existing temperate corn, temperate soybean, spring wheat, and cotton crop types. Fertilization rates and irrigation equipped area updated annually based on crop type and geographic region through an input dataset. The irrigation trigger is updated. Additional minor changes include crop phenological triggers that vary by latitude for selected crop types, grain C and N is now removed at harvest to a 1-year product pool with the carbon for the next season's crop seed removed from the grain carbon at harvest. A fraction of leaf/livestem C and N from bioenergy crops is removed at harvest to the biofuel feedstock pools and added to the 1-year product pool. Through the introduction of the capability to dynamically adjust landunit weights during a simulation, the crop model can now be run coincidentally with prescribed land use, which significantly expands the capabilities of the model. Mass-based rather than area-based wood harvest is applied. Several heat stress indices for both urban and rural areas are calculated and output by default :ref:`(Buzan et al., 2015)`. A more sophisticated and realistic building space heating and air conditioning submodel that prognoses interior building air temperature and includes more realistic space heating and air conditioning wasteheat factors is incorporated. The fire model is the same as utilized in CLM4.5 except that a modified scheme is used to estimate the dependence of fire occurrence and spread on fuel wetness for non-peat fires outside cropland and tropical closed forests :ref:`(Li and Lawrence, 2017)` and the dependence of agricultural fires on fuel load is removed. -Included with the release of CLM5.0 is a functionally supported version of the Functionally-Assembled Terrestrial Ecosystem Simulator (FATES, :ref:`Fisher et al., 2015)`. A major motivation of FATES is to allow the prediction of biome boundaries directly from plant physiological traits via their competitive interactions. FATES is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. FATES is not active by default in CLM5.0. +Included with the release of CLM5.0 is a functionally supported version of the Functionally-Assembled Terrestrial Ecosystem Simulator (FATES, :ref:`Fisher et al., 2015)`. A major motivation of FATES is to allow the prediction of biome boundaries directly from plant physiological traits via their competitive interactions. FATES is a cohort model of vegetation competition and co-existence, allowing a representation of the biosphere which accounts for the division of the land surface into successional stages, and for competition for light between height structured cohorts of representative trees of various plant functional types. FATES is not active by default in CLM5.0. -Note that the classical dynamic global vegetation model (CLM-DGVM) that has been available within CLM4 and CLM4.5 remains available, though it is largely untested. The technical description of the CLM-DGVM can be found within the CLM4.5 Technical Description (:ref:`Oleson et al. 2013)`. +Note that the classical dynamic global vegetation model (CLM-DGVM) that has been available within CLM4 and CLM4.5 remains available, though it is largely untested. The technical description of the CLM-DGVM can be found within the CLM4.5 Technical Description (:ref:`Oleson et al. 2013)`. -During the course of the development of CLM5.0, it became clear that the increasing complexity of the model combined with the increasing number and range -of model development projects required updates to the underlying CLM infrastructure. Many such software improvements -are included in CLM5 including a partial transition to an object-oriented modular software structure. Many hard coded model -parameters have been extracted into either the parameter file or the CLM namelist, which allows users to more readily calibrate the model for use at -specific locations or to conduct parameter sensitivity studies. As part of the effort to increase -the scientific utility of the code, in most instances older generation parameterizations (i.e., the parameterizations -available in CLM4 or CLM4.5) are retained under namelist switches, allowing the user to revert to CLM4.5 -from the same code base or to revert individual parameterizations where the old parameterizations are compatible with the new code. Finally, multiple vertical soil layer structures -are defined and it is relatively easy to add additional structures. +During the course of the development of CLM5.0, it became clear that the increasing complexity of the model combined with the increasing number and range of model development projects required updates to the underlying CLM infrastructure. Many such software improvements are included in CLM5 including a partial transition to an object-oriented modular software structure. Many hard coded model parameters have been extracted into either the parameter file or the CLM namelist, which allows users to more readily calibrate the model for use at specific locations or to conduct parameter sensitivity studies. As part of the effort to increase the scientific utility of the code, in most instances older generation parameterizations (i.e., the parameterizations available in CLM4 or CLM4.5) are retained under namelist switches, allowing the user to revert to CLM4.5 from the same code base or to revert individual parameterizations where the old parameterizations are compatible with the new code. Finally, multiple vertical soil layer structures are defined and it is relatively easy to add additional structures. Biogeophysical and Biogeochemical Processes ----------------------------------------------- -Biogeophysical and biogeochemical processes are simulated for each -subgrid land unit, column, and plant functional type (PFT) independently -and each subgrid unit maintains its own prognostic variables (see -section :numref:`Surface Heterogeneity and Data Structure` for definitions -of subgrid units). The same atmospheric -forcing is used to force all subgrid units within a grid cell. The -surface variables and fluxes required by the atmosphere are obtained by -averaging the subgrid quantities weighted by their fractional areas. The -processes simulated include (:numref:`Figure Land processes`): +Biogeophysical and biogeochemical processes are simulated for each subgrid land unit, column, and plant functional type (PFT) independently and each subgrid unit maintains its own prognostic variables (see section :numref:`Surface Heterogeneity and Data Structure` for definitions of subgrid units). The same atmospheric forcing is used to force all subgrid units within a grid cell. The surface variables and fluxes required by the atmosphere are obtained by averaging the subgrid quantities weighted by their fractional areas. The processes simulated include (:numref:`Figure Land processes`): -#. Surface characterization including land type heterogeneity and - ecosystem structure (Chapter :numref:`rst_Surface Characterization, Vertical Discretization, and Model Input Requirements`) +#. Surface characterization including land type heterogeneity and ecosystem structure (Chapter :numref:`rst_Surface Characterization, Vertical Discretization, and Model Input Requirements`) -#. Absorption, reflection, and transmittance of solar radiation (Chapter - :numref:`rst_Surface Albedos`, :numref:`rst_Radiative Fluxes`) +#. Absorption, reflection, and transmittance of solar radiation (Chapter :numref:`rst_Surface Albedos`, :numref:`rst_Radiative Fluxes`) #. Absorption and emission of longwave radiation (Chapter :numref:`rst_Radiative Fluxes`) -#. Momentum, sensible heat (ground and canopy), and latent heat (ground - evaporation, canopy evaporation, transpiration) fluxes (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) +#. Momentum, sensible heat (ground and canopy), and latent heat (ground evaporation, canopy evaporation, transpiration) fluxes (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) #. Heat transfer in soil and snow including phase change (Chapter :numref:`rst_Soil and Snow Temperatures`) #. Canopy hydrology (interception, throughfall, and drip) (Chapter :numref:`rst_Hydrology`) -#. Soil hydrology (surface runoff, infiltration, redistribution of water - within the column, sub-surface drainage, groundwater) (Chapter :numref:`rst_Hydrology`) +#. Soil hydrology (surface runoff, infiltration, redistribution of water within the column, sub-surface drainage, groundwater) (Chapter :numref:`rst_Hydrology`) -#. Snow hydrology (snow accumulation and melt, compaction, water - transfer between snow layers) (Chapter :numref:`rst_Snow Hydrology`) +#. Snow hydrology (snow accumulation and melt, compaction, water transfer between snow layers) (Chapter :numref:`rst_Snow Hydrology`) -#. Stomatal physiology, photosythetic capacity, and photosynthesis (Chapters :numref:`rst_Stomatal Resistance and Photosynthesis` and - :numref:`rst_Photosynthetic Capacity`) +#. Stomatal physiology, photosythetic capacity, and photosynthesis (Chapters :numref:`rst_Stomatal Resistance and Photosynthesis` and :numref:`rst_Photosynthetic Capacity`) #. Plant hydraulics (Chapter :numref:`rst_Plant Hydraulics`) @@ -608,13 +277,11 @@ processes simulated include (:numref:`Figure Land processes`): #. Fixation and uptake of nitrogen (Chapter :numref:`rst_FUN`) -#. External nitrogen cycling including deposition, - denitrification, leaching, and losses due to fire (Chapter :numref:`rst_External Nitrogen Cycle`) +#. External nitrogen cycling including deposition, denitrification, leaching, and losses due to fire (Chapter :numref:`rst_External Nitrogen Cycle`) #. Plant mortality (Chapter :numref:`rst_Plant Mortality`) -#. Fire ignition, suppression, spread, and emissions, including natural, deforestation, and - agricultural fire (Chapter :numref:`rst_Fire`) +#. Fire ignition, suppression, spread, and emissions, including natural, deforestation, and agricultural fire (Chapter :numref:`rst_Fire`) #. Methane production, oxidation, and emissions (Chapter :numref:`rst_Methane Model`) diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 1c1bfbf27b..d9eb6d1213 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -3,73 +3,33 @@ Carbon Isotopes =================== -CLM includes a fully prognostic representation of the fluxes, storage, -and isotopic discrimination of the carbon isotopes :sup:`13`\ C -and :sup:`14`\ C. The implementation of the C isotopes capability -takes advantage of the CLM hierarchical data structures, replicating the -carbon state and flux variable structures at the column and PFT level to -track total carbon and both C isotopes separately (see description of -data structure hierarchy in Chapter 2). For the most part, fluxes and -associated updates to carbon state variables for :sup:`13`\ C are -calculated directly from the corresponding total C fluxes. Separate -calculations are required in a few special cases, such as where isotopic -discrimination occurs, or where the necessary isotopic ratios are -undefined. The general approach for :sup:`13`\ C flux and state -variable calculation is described here, followed by a description of all -the places where special calculations are required. +CLM includes a fully prognostic representation of the fluxes, storage, and isotopic discrimination of the carbon isotopes :sup:`13`\ C and :sup:`14`\ C. The implementation of the C isotopes capability takes advantage of the CLM hierarchical data structures, replicating the carbon state and flux variable structures at the column and PFT level to track total carbon and both C isotopes separately (see description of data structure hierarchy in Chapter 2). For the most part, fluxes and associated updates to carbon state variables for :sup:`13`\ C are calculated directly from the corresponding total C fluxes. Separate calculations are required in a few special cases, such as where isotopic discrimination occurs, or where the necessary isotopic ratios are undefined. The general approach for :sup:`13`\ C flux and state variable calculation is described here, followed by a description of all the places where special calculations are required. General Form for Calculating :sup:`13`\ C and :sup:`14`\ C Flux -------------------------------------------------------------------------------- -In general, the flux of :sup:`13`\ C and corresponding to a given -flux of total C (:math:`{CF}_{13C}` and :math:`{CF}_{totC}`, -respectively) is determined by :math:`{CF}_{totC}`, the masses of -:sup:`13`\ C and total C in the upstream pools -(:math:`{CS}_{13C\_up}` and :math:`{CS}_{totC\_up}`, -respectively, i.e. the pools *from which* the fluxes of -:sup:`13`\ C and total C originate), and a fractionation factor, -:math:`{f}_{frac}`: +In general, the flux of :sup:`13`\ C and corresponding to a given flux of total C (:math:`{CF}_{13C}` and :math:`{CF}_{totC}`, respectively) is determined by :math:`{CF}_{totC}`, the masses of :sup:`13`\ C and total C in the upstream pools (:math:`{CS}_{13C\_up}` and :math:`{CS}_{totC\_up}`, respectively, i.e. the pools *from which* the fluxes of :sup:`13`\ C and total C originate), and a fractionation factor, :math:`{f}_{frac}`: .. math:: :label: ZEqnNum629812 CF_{13C} =\left\{\begin{array}{l} {CF_{totC} \frac{CS_{13C\_ up} }{CS_{totC\_ up} } f_{frac} \qquad {\rm for\; }CS_{totC} \ne 0} \\ {0\qquad {\rm for\; }CS_{totC} =0} \end{array}\right\} -If the :math:`{f}_{frac}` = 1.0 (no fractionation), then the fluxes -:math:`{CF}_{13C}` and :math:`{CF}_{totC}` will be in simple -proportion to the masses :math:`{CS}_{13C\_up}` and -:math:`{CS}_{totC\_up}`. Values of :math:`{f}_{frac} < 1.0` indicate a discrimination against the heavier isotope -(:sup:`13`\ C) in the flux-generating process, while -:math:`{f}_{frac}` :math:`>` 1.0 would indicate a preference for the -heavier isotope. Currently, in all cases where Eq. is used to calculate -a :sup:`13`\ C flux, :math:`{f}_{frac}` is set to 1.0. - -For :sup:`14`\ C, no fractionation is used in -either the initial photosynthetic step, nor in subsequent fluxes from -upstream to downstream pools; as discussed below, this is because -observations of :sup:`14` C are typically -described in units that implicitly correct out the fractionation of -:sup:`14`\ C by referencing them to -:sup:`13`\ C ratios. +If the :math:`{f}_{frac}` = 1.0 (no fractionation), then the fluxes :math:`{CF}_{13C}` and :math:`{CF}_{totC}` will be in simple proportion to the masses :math:`{CS}_{13C\_up}` and :math:`{CS}_{totC\_up}`. Values of :math:`{f}_{frac} < 1.0` indicate a discrimination against the heavier isotope (:sup:`13`\ C) in the flux-generating process, while :math:`{f}_{frac}` :math:`>` 1.0 would indicate a preference for the heavier isotope. Currently, in all cases where Eq. is used to calculate a :sup:`13`\ C flux, :math:`{f}_{frac}` is set to 1.0. + +For :sup:`14`\ C, no fractionation is used in either the initial photosynthetic step, nor in subsequent fluxes from upstream to downstream pools; as discussed below, this is because observations of :sup:`14` C are typically described in units that implicitly correct out the fractionation of :sup:`14`\ C by referencing them to :sup:`13`\ C ratios. Isotope Symbols, Units, and Reference Standards ---------------------------------------------------- -Carbon has two primary stable isotopes, :sup:`12`\ C and -:sup:`13`\ C. :sup:`12`\ C is the most abundant, comprising -about 99% of all carbon. The isotope ratio of a compound, -:math:`{R}_{A}`, is the mass ratio of the rare isotope to the abundant isotope +Carbon has two primary stable isotopes, :sup:`12`\ C and :sup:`13`\ C. :sup:`12`\ C is the most abundant, comprising about 99% of all carbon. The isotope ratio of a compound, :math:`{R}_{A}`, is the mass ratio of the rare isotope to the abundant isotope .. math:: :label: 30.2) R_{A} =\frac{{}^{13} C_{A} }{{}^{12} C_{A} } . -Carbon isotope ratios are often expressed using delta notation, -:math:`\delta`. The :math:`\delta^{13}`\ C value of a -compound A, :math:`\delta^{13}`\ C\ :sub:`A`, is the -difference between the isotope ratio of the compound, -:math:`{R}_{A}`, and that of the Pee Dee Belemnite standard, :math:`{R}_{PDB}`, in parts per thousand +Carbon isotope ratios are often expressed using delta notation, :math:`\delta`. The :math:`\delta^{13}`\ C value of a compound A, :math:`\delta^{13}`\ C\ :sub:`A`, is the difference between the isotope ratio of the compound, :math:`{R}_{A}`, and that of the Pee Dee Belemnite standard, :math:`{R}_{PDB}`, in parts per thousand .. math:: :label: 30.3) @@ -78,10 +38,7 @@ difference between the isotope ratio of the compound, where :math:`{R}_{PDB}` = 0.0112372, and units of :math:`\delta` are per mil (‰). -Isotopic fractionation can be expressed in several ways. One expression -of the fractionation factor is with alpha (:math:`\alpha`) notation. -For example, the equilibrium fractionation between two reservoirs A and -B can be written as: +Isotopic fractionation can be expressed in several ways. One expression of the fractionation factor is with alpha (:math:`\alpha`) notation. For example, the equilibrium fractionation between two reservoirs A and B can be written as: .. math:: :label: 30.4) @@ -97,52 +54,26 @@ This can also be expressed using epsilon notation (:math:`\epsilon`), where In other words, if :math:`{\epsilon }_{A-B} = 4.4` ‰ , then :math:`{\alpha}_{A-B} =1.0044`. -In addition to the stable isotopes :sup:`1`\ :sup:`2`\ C and :sup:`13`\ C, the unstable isotope -:sup:`14`\ C is included in CLM. :sup:`14`\ C can also be described using the delta notation: +In addition to the stable isotopes :sup:`1`\ :sup:`2`\ C and :sup:`13`\ C, the unstable isotope :sup:`14`\ C is included in CLM. :sup:`14`\ C can also be described using the delta notation: .. math:: :label: 30.6) \delta ^{14} C=\left(\frac{A_{s} }{A_{abs} } -1\right)\times 1000 -However, observations of :sup:`14`\ C are typically -fractionation-corrected using the following notation: +However, observations of :sup:`14`\ C are typically fractionation-corrected using the following notation: .. math:: :label: 30.7) \Delta {}^{14} C=1000\times \left(\left(1+\frac{\delta {}^{14} C}{1000} \right)\frac{0.975^{2} }{\left(1+\frac{\delta {}^{13} C}{1000} \right)^{2} } -1\right) -where :math:`\delta^{14}`\ C is the measured isotopic -fraction and :math:`\mathrm{\Delta}^{14}`\ C corrects for -mass-dependent isotopic fractionation processes (assumed to be 0.975 for -fractionation of :sup:`13`\ C by photosynthesis). CLM assumes a -background preindustrial atmospheric :sup:`14`\ C /C ratio of 10\ :sup:`-12`, which is used for A\ :sub::`abs`. -For the reference standard A\ :math:`{}_{abs}`, which is a plant tissue and has -a :math:`\delta^{13}`\ C value is :math:`\mathrm{-}`\ 25 ‰ due to photosynthetic discrimination, -:math:`\delta`\ :sup:`14`\ C = :math:`\mathrm{\Delta}`\ :sup:`14`\ C. For CLM, in order to use -the :sup:`14`\ C model independently of the :sup:`13`\ C -model, for the :sup:`14`\ C calculations, this fractionation is -set to zero, such that the 0.975 term becomes 1, the -:math:`\delta^{13}`\ C term (for the calculation of -:math:`\delta^{14}`\ C only) becomes 0, and thus -:math:`\delta^{14}`\ C = :math:`\mathrm{\Delta}`\ :sup:`14`\ C. +where :math:`\delta^{14}`\ C is the measured isotopic fraction and :math:`\mathrm{\Delta}^{14}`\ C corrects for mass-dependent isotopic fractionation processes (assumed to be 0.975 for fractionation of :sup:`13`\ C by photosynthesis). CLM assumes a background preindustrial atmospheric :sup:`14`\ C /C ratio of 10\ :sup:`-12`, which is used for A\ :sub::`abs`. For the reference standard A\ :math:`{}_{abs}`, which is a plant tissue and has a :math:`\delta^{13}`\ C value is :math:`\mathrm{-}`\ 25 ‰ due to photosynthetic discrimination, :math:`\delta`\ :sup:`14`\ C = :math:`\mathrm{\Delta}`\ :sup:`14`\ C. For CLM, in order to use the :sup:`14`\ C model independently of the :sup:`13`\ C model, for the :sup:`14`\ C calculations, this fractionation is set to zero, such that the 0.975 term becomes 1, the :math:`\delta^{13}`\ C term (for the calculation of :math:`\delta^{14}`\ C only) becomes 0, and thus :math:`\delta^{14}`\ C = :math:`\mathrm{\Delta}`\ :sup:`14`\ C. Carbon Isotope Discrimination During Photosynthesis -------------------------------------------------------- -Photosynthesis is modeled in CLM as a two-step process: diffusion of -CO\ :sub:`2` into the stomatal cavity, followed by enzymatic -fixation (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). Each step is associated with a kinetic isotope -effect. The kinetic isotope effect during diffusion of -CO\ :sub:`2` through the stomatal opening is 4.4‰. The kinetic -isotope effect during fixation of CO\ :sub:`2` with Rubisco is -:math:`\sim`\ 30‰; however, since about 5-10% of carbon in C3 plants -reacts with phosphoenolpyruvate carboxylase (PEPC) (Melzer and O'Leary, -1987), the net kinetic isotope effect during fixation is -:math:`\sim`\ 27‰ for C3 plants. In C4 plant photosynthesis, only the -diffusion effect is important. The fractionation factor equations for C3 -and C4 plants are given below: +Photosynthesis is modeled in CLM as a two-step process: diffusion of CO\ :sub:`2` into the stomatal cavity, followed by enzymatic fixation (Chapter :numref:`rst_Stomatal Resistance and Photosynthesis`). Each step is associated with a kinetic isotope effect. The kinetic isotope effect during diffusion of CO\ :sub:`2` through the stomatal opening is 4.4‰. The kinetic isotope effect during fixation of CO\ :sub:`2` with Rubisco is :math:`\sim`\ 30‰; however, since about 5-10% of carbon in C3 plants reacts with phosphoenolpyruvate carboxylase (PEPC) (Melzer and O'Leary, 1987), the net kinetic isotope effect during fixation is :math:`\sim`\ 27‰ for C3 plants. In C4 plant photosynthesis, only the diffusion effect is important. The fractionation factor equations for C3 and C4 plants are given below: For C4 plants, @@ -158,55 +89,25 @@ For C3 plants, \alpha _{psn} =1+\frac{4.4+22.6\frac{c_{i}^{*} }{pCO_{2} } }{1000} -where :math:`{\alpha }_{psn}` is the fractionation factor, and -:math:`c^*_i` and pCO\ :sub:`2` are the revised intracellular and -atmospheric CO\ :sub:`2` partial pressure, respectively. +where :math:`{\alpha }_{psn}` is the fractionation factor, and :math:`c^*_i` and pCO\ :sub:`2` are the revised intracellular and atmospheric CO\ :sub:`2` partial pressure, respectively. -As can be seen from the above equation, kinetic isotope effect during -fixation of CO\ :sub:`2` is dependent on the intracellular -CO\ :sub:`2` concentration, which in turn depends on the net -carbon assimilation. That is calculated during the photosynthesis -calculation as follows: +As can be seen from the above equation, kinetic isotope effect during fixation of CO\ :sub:`2` is dependent on the intracellular CO\ :sub:`2` concentration, which in turn depends on the net carbon assimilation. That is calculated during the photosynthesis calculation as follows: .. math:: :label: 30.10) c_{i} =pCO_{2} -a_{n} p\frac{\left(1.4g_{s} \right)+\left(1.6g_{b} \right)}{g_{b} g_{s} } -where :math:`a_n` is net carbon assimilation during photosynthesis, :math:`p` is -atmospheric pressure, :math:`g_b` is leaf boundary layer conductance, -and :math:`g_s` is leaf stomatal conductance. +where :math:`a_n` is net carbon assimilation during photosynthesis, :math:`p` is atmospheric pressure, :math:`g_b` is leaf boundary layer conductance, and :math:`g_s` is leaf stomatal conductance. -Isotopic fractionation code is compatible with multi-layered canopy -parameterization; i.e., it is possible to calculate varying -discrimination rates for each layer of a multi-layered canopy. However, -as with the rest of the photosynthesis model, the number of canopy -layers is currently set to one by default. +Isotopic fractionation code is compatible with multi-layered canopy parameterization; i.e., it is possible to calculate varying discrimination rates for each layer of a multi-layered canopy. However, as with the rest of the photosynthesis model, the number of canopy layers is currently set to one by default. :sup:`14`\ C radioactive decay and historical atmospheric :sup:`14`\ C and :sup:`13`\ C concentrations ------------------------------------------------------------------------------------------------------ -In the preindustrial biosphere, radioactive decay of :sup:`14`\ C -in carbon pools allows dating of long-term age since photosynthetic -uptake; while over the 20\ :math:`{}^{th}` century, radiocarbon in the -atmosphere was first diluted by radiocarbon-free fossil fuels and then -enriched by aboveground thermonuclear testing to approximately double -its long-term mean concentration. CLM includes both of these processes -to allow comparison of carbon that may vary on multiple timescales with -observed values. - -For radioactive decay, at each timestep all :sup:`14`\ C pools are -reduced at a rate of –log/:math:`\tau`, where :math:`\tau` is the -half-life (Libby half-life value of 5568 years). In order to rapidly -equilibrate the long-lived pools during accelerated decomposition -spinup, the radioactive decay of the accelerated pools is also -accelerated by the same degree as the decomposition, such that the -:sup:`14`\ C value of these pools is in equilibrium when taken out -of the spinup mode. - -For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical -period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to -either fixed concentrations -or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For -:math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 :sup:`o`\ N-90 :sup:`o`\ N, 30 :sup:`o`\ S-30 :sup:`o`\ N, and 30 :sup:`o`\ S-90 :sup:`o`\ S). +In the preindustrial biosphere, radioactive decay of :sup:`14`\ C in carbon pools allows dating of long-term age since photosynthetic uptake; while over the 20\ :math:`{}^{th}` century, radiocarbon in the atmosphere was first diluted by radiocarbon-free fossil fuels and then enriched by aboveground thermonuclear testing to approximately double its long-term mean concentration. CLM includes both of these processes to allow comparison of carbon that may vary on multiple timescales with observed values. + +For radioactive decay, at each timestep all :sup:`14`\ C pools are reduced at a rate of –log/:math:`\tau`, where :math:`\tau` is the half-life (Libby half-life value of 5568 years). In order to rapidly equilibrate the long-lived pools during accelerated decomposition spinup, the radioactive decay of the accelerated pools is also accelerated by the same degree as the decomposition, such that the :sup:`14`\ C value of these pools is in equilibrium when taken out of the spinup mode. + +For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 :sup:`o`\ N-90 :sup:`o`\ N, 30 :sup:`o`\ S-30 :sup:`o`\ N, and 30 :sup:`o`\ S-90 :sup:`o`\ S). diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 887e65f763..e84947265f 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -3,110 +3,37 @@ Lake Model ============= -The lake model, denoted the *Lake, Ice, Snow, and Sediment Simulator* -(LISSS), is from :ref:`Subin et al. (2012a) `. -It includes extensive modifications to the lake code of -:ref:`Zeng et al. (2002) ` used in CLM -versions 2 through 4, which utilized concepts from the lake models of -:ref:`Bonan (1996) `, -:ref:`Henderson-Sellers (1985) `, -:ref:`Henderson-Sellers (1986) `, -:ref:`Hostetler and Bartlein (1990) `, -and the coupled lake-atmosphere model of :ref:`Hostetler et al. (1993) `, :ref:`Hostetler et al. (1993) `. -Lakes have spatially variable depth prescribed in the surface data (section -:ref:`External Data Lake`); the surface data optionally includes lake optical -extinction coeffient and horizontal fetch, currently only used for site -simulations. Lake physics includes freezing and thawing in the lake -body, resolved snow layers, and "soil" and bedrock layers below the lake -body. Temperatures and ice fractions are simulated for -:math:`N_{levlak} =10` layers (for global simulations) or -:math:`N_{levlak} =25` (for site simulations) with discretization -described in section :numref:`Vertical Discretization Lake`. Lake albedo is -described in section :numref:`Surface Albedo Lake`. Lake surface fluxes -(section :numref:`Surface Fluxes and Surface Temperature Lake`) generally -follow the formulations for non-vegetated surfaces, including the calculations -of aerodynamic resistances (section -:numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`); -however, the lake surface temperature -:math:`T_{g}` (representing an infinitesimal interface layer between -the top resolved lake layer and the atmosphere) is solved for -simultaneously with the surface fluxes. After surface fluxes are -evaluated, temperatures are solved simultaneously in the resolved snow -layers (if present), the lake body, and the soil and bedrock, using the -ground heat flux *G* as a top boundary condition. Snow, soil, and -bedrock models generally follow the formulations for non-vegetated -surfaces (Chapter :numref:`rst_Soil and Snow Temperatures`), with -modifications described below. +The lake model, denoted the *Lake, Ice, Snow, and Sediment Simulator* (LISSS), is from :ref:`Subin et al. (2012a) `. It includes extensive modifications to the lake code of :ref:`Zeng et al. (2002) ` used in CLM versions 2 through 4, which utilized concepts from the lake models of :ref:`Bonan (1996) `, :ref:`Henderson-Sellers (1985) `, :ref:`Henderson-Sellers (1986) `, :ref:`Hostetler and Bartlein (1990) `, and the coupled lake-atmosphere model of :ref:`Hostetler et al. (1993) `, :ref:`Hostetler et al. (1993) `. Lakes have spatially variable depth prescribed in the surface data (section :ref:`External Data Lake`); the surface data optionally includes lake optical extinction coeffient and horizontal fetch, currently only used for site simulations. Lake physics includes freezing and thawing in the lake body, resolved snow layers, and "soil" and bedrock layers below the lake body. Temperatures and ice fractions are simulated for :math:`N_{levlak} =10` layers (for global simulations) or :math:`N_{levlak} =25` (for site simulations) with discretization described in section :numref:`Vertical Discretization Lake`. Lake albedo is described in section :numref:`Surface Albedo Lake`. Lake surface fluxes (section :numref:`Surface Fluxes and Surface Temperature Lake`) generally follow the formulations for non-vegetated surfaces, including the calculations of aerodynamic resistances (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`); however, the lake surface temperature :math:`T_{g}` (representing an infinitesimal interface layer between the top resolved lake layer and the atmosphere) is solved for simultaneously with the surface fluxes. After surface fluxes are evaluated, temperatures are solved simultaneously in the resolved snow layers (if present), the lake body, and the soil and bedrock, using the ground heat flux *G* as a top boundary condition. Snow, soil, and bedrock models generally follow the formulations for non-vegetated surfaces (Chapter :numref:`rst_Soil and Snow Temperatures`), with modifications described below. .. _Vertical Discretization Lake: Vertical Discretization --------------------------- -Currently, there is one lake modeled in each grid cell (with prescribed -or assumed depth *d*, extinction coefficient :math:`\eta`, and fetch -*f*), although this could be modified with changes to the CLM subgrid -decomposition algorithm in future model versions. As currently -implemented, the lake consists of 0-5 snow layers; water and ice layers -(10 for global simulations and 25 for site simulations) comprising the -"lake body;" 10 "soil" layers; and 5 bedrock layers. Each lake body -layer has a fixed water mass (set by the nominal layer thickness and the -liquid density), with frozen mass-fraction *I* a state variable. -Resolved snow layers are present if the snow thickness -:math:`z_{sno} \ge s_{\min }` , where *s*\ :sub:`min` = 4 cm by -default, and is adjusted for model timesteps other than 1800 s in order -to maintain numerical stability (section :numref:`Modifications to Snow Layer Logic Lake`). For global simulations -with 10 body layers, the default (50 m lake) body layer thicknesses are -given by: :math:`\Delta z_{i}` of 0.1, 1, 2, 3, 4, 5, 7, 7, 10.45, and -10.45 m, with node depths :math:`z_{i}` located at the center of each -layer (i.e., 0.05, 0.6, 2.1, 4.6, 8.1, 12.6, 18.6, 25.6, 34.325, 44.775 -m). For site simulations with 25 layers, the default thicknesses are -(m): 0.1 for layer 1; 0.25 for layers 2-5; 0.5 for layers 6-9; 0.75 for -layers 10-13; 2 for layers 14-15; 2.5 for layers 16-17; 3.5 for layers -18-21; and 5.225 for layers 22-25. For lakes with depth *d* -:math:`\neq` 50 m and *d* :math:`\ge` 1 m, the top -layer is kept at 10 cm and the other 9 layer thicknesses are adjusted to -maintain fixed proportions. For lakes with *d* :math:`<` 1 m, all layers -have equal thickness. Thicknesses of snow, soil, and bedrock layers -follow the scheme used over non-vegetated surfaces (Chapter :numref:`rst_Soil and Snow Temperatures`), with -modifications to the snow layer thickness rules to keep snow layers at -least as thick as *s*\ :sub:`min` (section :numref:`Modifications to Snow Layer Logic Lake`). +Currently, there is one lake modeled in each grid cell (with prescribed or assumed depth *d*, extinction coefficient :math:`\eta`, and fetch *f*), although this could be modified with changes to the CLM subgrid decomposition algorithm in future model versions. As currently implemented, the lake consists of 0-5 snow layers; water and ice layers (10 for global simulations and 25 for site simulations) comprising the "lake body;" 10 "soil" layers; and 5 bedrock layers. Each lake body layer has a fixed water mass (set by the nominal layer thickness and the liquid density), with frozen mass-fraction *I* a state variable. Resolved snow layers are present if the snow thickness :math:`z_{sno} \ge s_{\min }`, where *s*\ :sub:`min` = 4 cm by default, and is adjusted for model timesteps other than 1800 s in order to maintain numerical stability (section :numref:`Modifications to Snow Layer Logic Lake`). For global simulations with 10 body layers, the default (50 m lake) body layer thicknesses are given by: :math:`\Delta z_{i}` of 0.1, 1, 2, 3, 4, 5, 7, 7, 10.45, and 10.45 m, with node depths :math:`z_{i}` located at the center of each layer (i.e., 0.05, 0.6, 2.1, 4.6, 8.1, 12.6, 18.6, 25.6, 34.325, 44.775 m). For site simulations with 25 layers, the default thicknesses are (m): 0.1 for layer 1; 0.25 for layers 2-5; 0.5 for layers 6-9; 0.75 for layers 10-13; 2 for layers 14-15; 2.5 for layers 16-17; 3.5 for layers 18-21; and 5.225 for layers 22-25. For lakes with depth *d* :math:`\neq` 50 m and *d* :math:`\ge` 1 m, the top layer is kept at 10 cm and the other 9 layer thicknesses are adjusted to maintain fixed proportions. For lakes with *d* :math:`<` 1 m, all layers have equal thickness. Thicknesses of snow, soil, and bedrock layers follow the scheme used over non-vegetated surfaces (Chapter :numref:`rst_Soil and Snow Temperatures`), with modifications to the snow layer thickness rules to keep snow layers at least as thick as *s*\ :sub:`min` (section :numref:`Modifications to Snow Layer Logic Lake`). .. _External Data Lake: External Data ----------------- -As discussed in :ref:`Subin et al. (2012a, b) `, the -Global Lake and Wetland Database (:ref:`Lehner and Doll 2004`) -is currently used to prescribe lake fraction in each land model grid cell, -for a total of 2.3 million km\ :sup:`-2`. As in -:ref:`Subin et al. (2012a, b) `, the -:ref:`Kourzeneva et al. (2012)` global gridded dataset is currently -used to estimate a mean lake depth in each grid cell, based on interpolated -compilations of geographic information. +As discussed in :ref:`Subin et al. (2012a, b) `, the Global Lake and Wetland Database (:ref:`Lehner and Doll 2004`) is currently used to prescribe lake fraction in each land model grid cell, for a total of 2.3 million km\ :sup:`-2`. As in :ref:`Subin et al. (2012a, b) `, the :ref:`Kourzeneva et al. (2012)` global gridded dataset is currently used to estimate a mean lake depth in each grid cell, based on interpolated compilations of geographic information. .. _Surface Albedo Lake: Surface Albedo ------------------ -For direct radiation, the albedo *a* for lakes with ground temperature -:math:`{T}_{g}` (K) above freezing is given by (:ref:`Pivovarov, 1972`) +For direct radiation, the albedo *a* for lakes with ground temperature :math:`{T}_{g}` (K) above freezing is given by (:ref:`Pivovarov, 1972`) .. math:: :label: 12.1 a=\frac{0.5}{\cos z+0.15} -where *z* is the zenith angle. For diffuse radiation, the expression in -eq. is integrated over the full sky to yield *a* = 0.10. +where *z* is the zenith angle. For diffuse radiation, the expression in eq. is integrated over the full sky to yield *a* = 0.10. -For frozen lakes without resolved snow layers, the albedo at cold -temperatures *a*\ :sub:`0` is 0.60 for visible and 0.40 for near -infrared radiation. As the temperature at the ice surface, -:math:`{T}_{g}`, approaches freezing [ :math:`{T}_{f}` (K) (:numref:`Table Physical Constants`)], the albedo is relaxed towards 0.10 based on -:ref:`Mironov et al. (2010)`: +For frozen lakes without resolved snow layers, the albedo at cold temperatures *a*\ :sub:`0` is 0.60 for visible and 0.40 for near infrared radiation. As the temperature at the ice surface, :math:`{T}_{g}`, approaches freezing [ :math:`{T}_{f}` (K) (:numref:`Table Physical Constants`)], the albedo is relaxed towards 0.10 based on :ref:`Mironov et al. (2010)`: .. math:: :label: 12.2 @@ -115,11 +42,7 @@ infrared radiation. As the temperature at the ice surface, where *a* is restricted to be no less than that given in :eq:`12.1`. -For frozen lakes with resolved snow layers, the reflectance of the ice -surface is fixed at *a*\ :sub:`0`, and the snow reflectance is -calculated as over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). -These two reflectances are combined to obtain the snow-fraction-weighted albedo as -in over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). +For frozen lakes with resolved snow layers, the reflectance of the ice surface is fixed at *a*\ :sub:`0`, and the snow reflectance is calculated as over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). These two reflectances are combined to obtain the snow-fraction-weighted albedo as in over non-vegetated surfaces (Chapter :numref:`rst_Surface Albedos`). .. _Surface Fluxes and Surface Temperature Lake: @@ -131,39 +54,16 @@ Surface Fluxes and Surface Temperature Surface Properties ^^^^^^^^^^^^^^^^^^^^^^^^ -The fraction of shortwave radiation absorbed at the surface, -:math:`\beta`, depends on the lake state. If resolved snow layers are -present, then :math:`\beta` is set equal to the absorption fraction -predicted by the snow-optics submodel (Chapter :numref:`rst_Surface Albedos`) -for the top snow -layer. Otherwise, :math:`\beta` is set equal to the near infrared -fraction of the shortwave radiation reaching the surface simulated by -the atmospheric model or atmospheric data model used for offline -simulations (Chapter :numref:`rst_Land-only Mode`). The remainder of the shortwave radiation -fraction (1 :math:`{-}` :math:`\beta`) is absorbed in the lake -body or soil as described in section :numref:`Radiation Penetration`. - -The surface roughnesses are functions of the lake state and atmospheric -forcing. For frozen lakes ( :math:`T_{g} \le T_{f}` ) with resolved -snow layers, the momentum roughness length -:math:`z_{0m} =2.4 \times 10^{-3} {\rm m}` (as over non-vegetated -surfaces; Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), and the scalar roughness lengths -(*z*\ :sub:`0q` for latent heat; and *z*\ :sub:`0h`, for sensible heat) are given by -(:ref:`Zilitinkevich 1970`) +The fraction of shortwave radiation absorbed at the surface, :math:`\beta`, depends on the lake state. If resolved snow layers are present, then :math:`\beta` is set equal to the absorption fraction predicted by the snow-optics submodel (Chapter :numref:`rst_Surface Albedos`) for the top snow layer. Otherwise, :math:`\beta` is set equal to the near infrared fraction of the shortwave radiation reaching the surface simulated by the atmospheric model or atmospheric data model used for offline simulations (Chapter :numref:`rst_Land-only Mode`). The remainder of the shortwave radiation fraction (1 :math:`{-}` :math:`\beta`) is absorbed in the lake body or soil as described in section :numref:`Radiation Penetration`. + +The surface roughnesses are functions of the lake state and atmospheric forcing. For frozen lakes ( :math:`T_{g} \le T_{f}` ) with resolved snow layers, the momentum roughness length :math:`z_{0m} =2.4 \times 10^{-3} {\rm m}` (as over non-vegetated surfaces; Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), and the scalar roughness lengths (*z*\ :sub:`0q` for latent heat; and *z*\ :sub:`0h`, for sensible heat) are given by (:ref:`Zilitinkevich 1970`) .. math:: :label: 12.3 \begin{array}{l} {R_{0} =\frac{z_{0m} u_{*} }{\nu } ,} \\ {z_{0h} =z_{0q} =z_{0m} \exp \left\{-0.13R_{0} ^{0.45} \right\}} \end{array} -where :math:`R_{0}` is the near-surface atmospheric roughness -Reynolds number, :math:`z_{0h}` is the roughness -length for sensible heat, :math:`z_{0q}` is the -roughness length for latent heat, :math:`\nu` (m\ :sup:`2` s\ :sup:`-1`) is the kinematic viscosity of air, and -:math:`u_{\*}` (m s\ :sup:`-1`) is the friction velocity in the -atmospheric surface layer. For frozen lakes without resolved snow -layers, :math:`z_{0m} =1\times 10^{-3} {\rm m}` (:ref:`Subin et al. (2012a) `), -and the scalar roughness lengths are given by . +where :math:`R_{0}` is the near-surface atmospheric roughness Reynolds number, :math:`z_{0h}` is the roughness length for sensible heat, :math:`z_{0q}` is the roughness length for latent heat, :math:`\nu` (m\ :sup:`2` s\ :sup:`-1`) is the kinematic viscosity of air, and :math:`u_{\*}` (m s\ :sup:`-1`) is the friction velocity in the atmospheric surface layer. For frozen lakes without resolved snow layers, :math:`z_{0m} =1\times 10^{-3} {\rm m}` (:ref:`Subin et al. (2012a) `), and the scalar roughness lengths are given by. For unfrozen lakes, *z*\ :sub:`0m` is given by (:ref:`Subin et al. (2012a) `) @@ -172,10 +72,7 @@ For unfrozen lakes, *z*\ :sub:`0m` is given by (:ref:`Subin et al. (2012a) T_{f}` ) -includes conductivities due to molecular ( :math:`\lambda _{liq}` ) and -eddy (:math:`\lambda _{K}` ) diffusivities (section :numref:`Eddy Diffusivity and Thermal Conductivities`), as evaluated -in the top lake layer at the previous timestep, where -:math:`\lambda _{liq}` is the thermal conductivity of water (:numref:`Table Physical Constants`). For frozen lakes without resolved snow layers, -:math:`\lambda _{T} =\lambda _{ice}` . When resolved snow layers are -present, :math:`\lambda _{T}` \ is calculated based on the water -content, ice content, and thickness of the top snow layer, as for -non-vegetated surfaces. +where :math:`\lambda _{T}` is the thermal conductivity (W m\ :sup:`-1` K\ :sup:`-1`), :math:`\Delta z_{T}` is the thickness (m), and :math:`T_{T}` is the temperature (K) of the top resolved lake layer (snow, ice, or water). The top thermal conductivity :math:`\lambda _{T}` of unfrozen lakes ( :math:`T_{g} >T_{f}` ) includes conductivities due to molecular ( :math:`\lambda _{liq}` ) and eddy (:math:`\lambda _{K}` ) diffusivities (section :numref:`Eddy Diffusivity and Thermal Conductivities`), as evaluated in the top lake layer at the previous timestep, where :math:`\lambda _{liq}` is the thermal conductivity of water (:numref:`Table Physical Constants`). For frozen lakes without resolved snow layers, :math:`\lambda _{T} =\lambda _{ice}`. When resolved snow layers are present, :math:`\lambda _{T}` \ is calculated based on the water content, ice content, and thickness of the top snow layer, as for non-vegetated surfaces. The absorbed solar radiation :math:`\vec{S}_{g}` is @@ -304,14 +174,7 @@ The absorbed solar radiation :math:`\vec{S}_{g}` is \vec{S}_{g} =\sum _{\Lambda }S_{atm} \, \downarrow _{\Lambda }^{\mu } \left(1-\alpha _{g,\, \Lambda }^{\mu } \right) +S_{atm} \, \downarrow _{\Lambda } \left(1-\alpha _{g,\, \Lambda } \right) -where :math:`S_{atm} \, \downarrow _{\Lambda }^{\mu }` and -:math:`S_{atm} \, \downarrow _{\Lambda }` are the incident direct beam -and diffuse solar fluxes (W m\ :sup:`-2`) and :math:`\Lambda` -denotes the visible (:math:`<` 0.7\ :math:`\mu {\rm m}`) and -near-infrared (:math:`\ge` 0.7\ :math:`\mu {\rm m}`) wavebands (section -:numref:`Atmospheric Coupling`), and :math:`\alpha _{g,\, \Lambda }^{\mu }` and -:math:`\alpha _{g,\, \mu }` are the direct beam and diffuse lake -albedos (section :numref:`Surface Albedo Lake`). +where :math:`S_{atm} \, \downarrow _{\Lambda }^{\mu }` and :math:`S_{atm} \, \downarrow _{\Lambda }` are the incident direct beam and diffuse solar fluxes (W m\ :sup:`-2`) and :math:`\Lambda` denotes the visible (:math:`<` 0.7\ :math:`\mu {\rm m}`) and near-infrared (:math:`\ge` 0.7\ :math:`\mu {\rm m}`) wavebands (section :numref:`Atmospheric Coupling`), and :math:`\alpha _{g,\, \Lambda }^{\mu }` and :math:`\alpha _{g,\, \mu }` are the direct beam and diffuse lake albedos (section :numref:`Surface Albedo Lake`). The net emitted longwave radiation is @@ -320,10 +183,8 @@ The net emitted longwave radiation is \vec{L}_{g} =L_{g} \, \uparrow -L_{atm} \, \downarrow -where :math:`L_{g} \, \uparrow` is the upward longwave radiation from -the surface, :math:`L_{atm} \, \downarrow` is the downward atmospheric -longwave radiation (section :numref:`Atmospheric Coupling`). The upward -longwave radiation from the surface is +where :math:`L_{g} \, \uparrow` is the upward longwave radiation from the surface, +:math:`L_{atm} \, \downarrow` is the downward atmospheric longwave radiation (section :numref:`Atmospheric Coupling`). The upward longwave radiation from the surface is .. math:: :label: 12.16 @@ -331,26 +192,17 @@ longwave radiation from the surface is L\, \uparrow =\left(1-\varepsilon _{g} \right)L_{atm} \, \downarrow +\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} +4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right) where :math:`\varepsilon _{g} =0.97` is the lake surface emissivity, -:math:`\sigma` is the Stefan-Boltzmann constant (W m\ :sup:`-2` K\ -:sup:`-4`) (:numref:`Table Physical Constants`), and -:math:`T_{g}^{n+1} -T_{g}^{n}` is the difference in lake surface -temperature between Newton-Raphson iterations (see below). - -The sensible heat :math:`H_{g}` , the water vapor flux :math:`E_{g}` -through its dependence on the saturated specific humidity, the net -longwave radiation :math:`\vec{L}_{g}` , and the ground heat flux -:math:`G`, all depend on the lake surface temperature :math:`T_{g}` . -Newton-Raphson iteration is applied to solve for :math:`T_{g}` and the -surface fluxes as +:math:`\sigma` is the Stefan-Boltzmann constant (W m\ :sup:`-2` K\ :sup:`-4`) (:numref:`Table Physical Constants`), and +:math:`T_{g}^{n+1} -T_{g}^{n}` is the difference in lake surface temperature between Newton-Raphson iterations (see below). + +The sensible heat :math:`H_{g}`, the water vapor flux :math:`E_{g}` through its dependence on the saturated specific humidity, the net longwave radiation :math:`\vec{L}_{g}`, and the ground heat flux :math:`G`, all depend on the lake surface temperature :math:`T_{g}`. Newton-Raphson iteration is applied to solve for :math:`T_{g}` and the surface fluxes as .. math:: :label: 12.17 \Delta T_{g} =\frac{\beta \overrightarrow{S}_{g} -\overrightarrow{L}_{g} -H_{g} -\lambda E_{g} -G}{\frac{\partial \overrightarrow{L}_{g} }{\partial T_{g} } +\frac{\partial H_{g} }{\partial T_{g} } +\frac{\partial \lambda E_{g} }{\partial T_{g} } +\frac{\partial G}{\partial T_{g} } } -where :math:`\Delta T_{g} =T_{g}^{n+1} -T_{g}^{n}` and the subscript -"n" indicates the iteration. Therefore, the surface temperature -:math:`T_{g}^{n+1}` can be written as +where :math:`\Delta T_{g} =T_{g}^{n+1} -T_{g}^{n}` and the subscript "n" indicates the iteration. Therefore, the surface temperature :math:`T_{g}^{n+1}` can be written as .. math:: :label: 12.18 @@ -379,26 +231,11 @@ where the partial derivatives are \frac{\partial G}{\partial T_{g} } =\frac{2\lambda _{T} }{\Delta z_{T} } . -The fluxes of momentum, sensible heat, and water vapor are solved for -simultaneously with lake surface temperature as follows. The -stability-related equations are the same as for non-vegetated surfaces -(section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), -except that the surface roughnesses are here (weakly varying) functions -of the friction velocity :math:`u_{\*}` . To begin, *z*\ :sub:`0m` is set -based on the value calculated for the last timestep (for -:math:`T_{g} >T_{f}` ) or based on the values in section -:numref:`Surface Properties Lake` (otherwise), and the scalar roughness -lengths are set based on the relationships in section :numref:`Surface Properties Lake`. - -#. An initial guess for the wind speed :math:`V_{a}` including the - convective velocity :math:`U_{c}` is obtained from :eq:`5.24` assuming an - initial convective velocity :math:`U_{c} =0` m s\ :sup:`-1` for - stable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` - as evaluated from :eq:`5.50`) and :math:`U_{c} =0.5` for unstable - conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). - -#. An initial guess for the Monin-Obukhov length :math:`L` is obtained - from the bulk Richardson number using :eq:`5.46` and :eq:`5.48`. +The fluxes of momentum, sensible heat, and water vapor are solved for simultaneously with lake surface temperature as follows. The stability-related equations are the same as for non-vegetated surfaces (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), except that the surface roughnesses are here (weakly varying) functions of the friction velocity :math:`u_{\*}`. To begin, *z*\ :sub:`0m` is set based on the value calculated for the last timestep (for :math:`T_{g} >T_{f}` ) or based on the values in section :numref:`Surface Properties Lake` (otherwise), and the scalar roughness lengths are set based on the relationships in section :numref:`Surface Properties Lake`. + +#. An initial guess for the wind speed :math:`V_{a}` including the convective velocity :math:`U_{c}` is obtained from :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m s\ :sup:`-1` for stable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` as evaluated from :eq:`5.50`) and :math:`U_{c} =0.5` for unstable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). + +#. An initial guess for the Monin-Obukhov length :math:`L` is obtained from the bulk Richardson number using :eq:`5.46` and :eq:`5.48`. #. The following system of equations is iterated four times: @@ -406,73 +243,49 @@ lengths are set based on the relationships in section :numref:`Surface Propertie #. Thermal conductivity :math:`\lambda _{T}` \ (above) -#. Friction velocity :math:`u_{\*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) +#. Friction velocity :math:`u_{\*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) -#. Potential temperature scale :math:`\theta _{\*}` (:eq:`5.37` , :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) +#. Potential temperature scale :math:`\theta _{\*}` (:eq:`5.37`, :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) -#. Humidity scale :math:`q_{\*}` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) +#. Humidity scale :math:`q_{\*}` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) -#. Aerodynamic resistances :math:`r_{am}` , :math:`r_{ah}` , and - :math:`r_{aw}` (:eq:`5.55`, :eq:`5.56`, :eq:`5.57`) +#. Aerodynamic resistances :math:`r_{am}`, :math:`r_{ah}`, and :math:`r_{aw}` (:eq:`5.55`, :eq:`5.56`, :eq:`5.57`) -#. Lake surface temperature :math:`T_{g}^{n+1}` (:eq:`12.18`) +#. Lake surface temperature :math:`T_{g}^{n+1}` (:eq:`12.18`) -#. Heat of vaporization / sublimation :math:`\lambda` (:eq:`12.8`) +#. Heat of vaporization / sublimation :math:`\lambda` (:eq:`12.8`) -#. Sensible heat flux :math:`H_{g}` is updated for :math:`T_{g}^{n+1}` - (:eq:`12.9`) +#. Sensible heat flux :math:`H_{g}` is updated for :math:`T_{g}^{n+1}` (:eq:`12.9`) -#. Water vapor flux :math:`E_{g}` is updated for :math:`T_{g}^{n+1}` - as +#. Water vapor flux :math:`E_{g}` is updated for :math:`T_{g}^{n+1}` as .. math:: :label: 12.23 E_{g} =-\frac{\rho _{atm} }{r_{aw} } \left[q_{atm} -q_{sat}^{T_{g} } -\frac{\partial q_{sat}^{T_{g} } }{\partial T_{g} } \left(T_{g}^{n+1} -T_{g}^{n} \right)\right] -where the last term on the right side of equation is the change in -saturated specific humidity due to the change in :math:`T_{g}` between -iterations. +where the last term on the right side of equation is the change in saturated specific humidity due to the change in :math:`T_{g}` between iterations. -#. Saturated specific humidity :math:`q_{sat}^{T_{g} }` and its - derivative :math:`\frac{dq_{sat}^{T_{g} } }{dT_{g} }` are updated - for :math:`T_{g}^{n+1}` (section :numref:`Monin-Obukhov Similarity Theory`). +#. Saturated specific humidity :math:`q_{sat}^{T_{g} }` and its derivative :math:`\frac{dq_{sat}^{T_{g} } }{dT_{g} }` are updated for :math:`T_{g}^{n+1}` (section :numref:`Monin-Obukhov Similarity Theory`). -#. Virtual potential temperature scale :math:`\theta _{v\*}` (:eq:`5.17`) +#. Virtual potential temperature scale :math:`\theta _{v\*}` (:eq:`5.17`) -#. Wind speed including the convective velocity, :math:`V_{a}` (:eq:`5.24`) +#. Wind speed including the convective velocity, :math:`V_{a}` (:eq:`5.24`) #. Monin-Obukhov length :math:`L` (:eq:`5.49`) #. Roughness lengths (:eq:`12.3`, :eq:`12.4`). -Once the four iterations for lake surface temperature have been yielded -a tentative solution :math:`T_{g} ^{{'} }` , several restrictions -are imposed in order to maintain consistency with the top lake model -layer temperature :math:`T_{T}` \ (:ref:`Subin et al. (2012a) `). +Once the four iterations for lake surface temperature have been yielded a tentative solution :math:`T_{g} ^{{'} }`, several restrictions are imposed in order to maintain consistency with the top lake model layer temperature :math:`T_{T}` \ (:ref:`Subin et al. (2012a) `). .. math:: :label: 12.24 \begin{array}{l} {{\rm 1)\; }T_{T} \le T_{f} T_{g} ^{{'} } >T_{m} \Rightarrow T_{g} =T_{T} ,} \\ {{\rm 3)\; }T_{m} >T_{g} ^{{'} } >T_{T} >T_{f} \Rightarrow T_{g} =T_{T} } \end{array} -where :math:`T_{m}` \ is the temperature of maximum liquid water -density, 3.85\ :sup:`o` C (:ref:`Hostetler and Bartlein (1990) `). The -first condition requires that, if there is any snow or ice present, the -surface temperature is restricted to be less than or equal to freezing. -The second and third conditions maintain convective stability in the top -lake layer. - -If eq. XXX is applied, the turbulent fluxes :math:`H_{g}` and -:math:`E_{g}` are re-evaluated. The emitted longwave radiation and -the momentum fluxes are re-evaluated in any case. The final ground heat -flux :math:`G` is calculated from the residual of the energy balance eq. -XXX in order to precisely conserve energy. XXX This ground heat flux -is taken as a prescribed flux boundary condition for the lake -temperature solution (section :numref:`Boundary Conditions Lake`). -An energy balance check is -included at each timestep to insure that eq. XXX is obeyed to within -0.1 W m\ :sup:`-2`. +where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85\ :sup:`o` C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. + +If eq. XXX is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance eq. XXX in order to precisely conserve energy. XXX This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). An energy balance check is included at each timestep to insure that eq. XXX is obeyed to within 0.1 W m\ :sup:`-2`. .. _Lake Temperature: @@ -484,97 +297,55 @@ Lake Temperature Introduction ^^^^^^^^^^^^^^^^^^ -The (optional-) snow, lake body (water and/or ice), soil, and bedrock -system is unified for the lake temperature solution. The governing -equation, similar to that for the snow-soil-bedrock system for vegetated -land units (Chapter :numref:`rst_Soil and Snow Temperatures`), is +The (optional-) snow, lake body (water and/or ice), soil, and bedrock system is unified for the lake temperature solution. The governing equation, similar to that for the snow-soil-bedrock system for vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`), is .. math:: :label: 12.25 \tilde{c}_{v} \frac{\partial T}{\partial t} =\frac{\partial }{\partial z} \left(\tau \frac{\partial T}{\partial z} \right)-\frac{d\phi }{dz} -where :math:`\tilde{c}_{v}` is the volumetric heat capacity (J -m\ :sup:`-3` K\ :sup:`-1`), :math:`t` is time (s), *T* is -the temperature (K), :math:`\tau` is the thermal conductivity (W -m\ :sup:`-1` K\ :sup:`-1`), and :math:`\phi` is the solar -radiation (W m\ :sup:`-2`) penetrating to depth *z* (m). The -system is discretized into *N* layers, where +where :math:`\tilde{c}_{v}` is the volumetric heat capacity (J m\ :sup:`-3` K\ :sup:`-1`), +:math:`t` is time (s), +*T* is the temperature (K), +:math:`\tau` is the thermal conductivity (W m\ :sup:`-1` K\ :sup:`-1`), and +:math:`\phi` is the solar radiation (W m\ :sup:`-2`) penetrating to depth *z* (m). The system is discretized into *N* layers, where .. math:: :label: 12.26 N=n_{sno} +N_{levlak} +N_{levgrnd} , -:math:`n_{sno}` is the number of actively modeled snow layers at the -current timestep (Chapter :numref:`rst_Snow Hydrology`), and -:math:`N_{levgrnd}` \ is as for vegetated land units (Chapter -:numref:`rst_Soil and Snow Temperatures`). Energy is conserved as +:math:`n_{sno}` is the number of actively modeled snow layers at the current timestep (Chapter :numref:`rst_Snow Hydrology`), and +:math:`N_{levgrnd}` \ is as for vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`). Energy is conserved as .. math:: :label: 12.27 \frac{d}{dt} \sum _{j=1}^{N}\left[\tilde{c}_{v,j} (t)\left(T_{j} -T_{f} \right)+L_{j} (t)\right] \Delta z_{j} =G+\left(1-\beta \right)\vec{S}_{g} -where :math:`\tilde{c}_{v,j} (t)`\ is the volumetric heat capacity of -the *j*\ th layer (section :numref:`Radiation Penetration`), -:math:`L_{j} (t)`\ is the latent heat -of fusion per unit volume of the *j*\ th layer (proportional to the mass -of liquid water present), and the right-hand side represents the net -influx of energy to the lake system. Note that -:math:`\tilde{c}_{v,j} (t)` can only change due to phase change (except -for changing snow layer mass, which, apart from energy required to melt -snow, represents an untracked energy flux in the land model, along with -advected energy associated with water flows in general), and this is -restricted to occur at :math:`T_{j} =T_{f}` \ in the snow-lake-soil -system, allowing eq. to be precisely enforced and justifying the -exclusion of :math:`c_{v,j}` from the time derivative in eq. . +where :math:`\tilde{c}_{v,j} (t)`\ is the volumetric heat capacity of the *j*\ th layer (section :numref:`Radiation Penetration`), :math:`L_{j} (t)`\ is the latent heat of fusion per unit volume of the *j*\ th layer (proportional to the mass of liquid water present), and the right-hand side represents the net influx of energy to the lake system. Note that :math:`\tilde{c}_{v,j} (t)` can only change due to phase change (except for changing snow layer mass, which, apart from energy required to melt snow, represents an untracked energy flux in the land model, along with advected energy associated with water flows in general), and this is restricted to occur at :math:`T_{j} =T_{f}` \ in the snow-lake-soil system, allowing eq. to be precisely enforced and justifying the exclusion of :math:`c_{v,j}` from the time derivative in eq.. .. _Overview of Changes from CLM4 2: Overview of Changes from CLM4 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Thermal conductivities include additional eddy diffusivity, beyond the -:ref:`Hostetler and Bartlein (1990)` formulation, -due to unresolved processes (:ref:`Fang and Stefan 1996`; -:ref:`Subin et al. (2012a) `). Lake water is now allowed to -freeze by an arbitrary fraction for each layer, which releases latent -heat and changes thermal properties. Convective mixing occurs for all -lakes, even if frozen. Soil and bedrock are included beneath the lake. -The full snow model is used if the snow thickness exceeds a threshold; -if there are resolved snow layers, radiation transfer is predicted by -the snow-optics submodel (Chapter :numref:`rst_Surface Albedos`), and the remaining radiation -penetrating the bottom snow layer is absorbed in the top layer of lake -ice; conversely, if there are no snow layers, the solar radiation -penetrating the bottom lake layer is absorbed in the top soil layer. The -lakes have variable depth, and all physics is assumed valid for -arbitrary depth, except for a depth-dependent enhanced mixing (section -:numref:`Eddy Diffusivity and Thermal Conductivities`). Finally, a previous sign error in the calculation of eddy -diffusivity (specifically, the Brunt-Väisälä frequency term; eq. ) was -corrected. +Thermal conductivities include additional eddy diffusivity, beyond the :ref:`Hostetler and Bartlein (1990)` formulation, due to unresolved processes (:ref:`Fang and Stefan 1996`; :ref:`Subin et al. (2012a) `). Lake water is now allowed to freeze by an arbitrary fraction for each layer, which releases latent heat and changes thermal properties. Convective mixing occurs for all lakes, even if frozen. Soil and bedrock are included beneath the lake. The full snow model is used if the snow thickness exceeds a threshold; if there are resolved snow layers, radiation transfer is predicted by the snow-optics submodel (Chapter :numref:`rst_Surface Albedos`), and the remaining radiation penetrating the bottom snow layer is absorbed in the top layer of lake ice; conversely, if there are no snow layers, the solar radiation penetrating the bottom lake layer is absorbed in the top soil layer. The lakes have variable depth, and all physics is assumed valid for arbitrary depth, except for a depth-dependent enhanced mixing (section :numref:`Eddy Diffusivity and Thermal Conductivities`). Finally, a previous sign error in the calculation of eddy diffusivity (specifically, the Brunt-Väisälä frequency term; eq. ) was corrected. .. _Boundary Conditions Lake: Boundary Conditions ^^^^^^^^^^^^^^^^^^^^^^^^^ -The top boundary condition, imposed at the top modeled layer -:math:`i=j_{top}` , where :math:`j_{top} =-n_{sno} +1`, is the downwards -surface flux *G* defined by the energy flux residual during the surface -temperature solution (section :numref:`Boundary Conditions Lake`). The bottom -boundary condition, imposed at :math:`i=N_{levlak} +N_{levgrnd}` , is zero flux. -The 2-m windspeed :math:`u_{2}` \ (m s\ :sup:`-1`) is used in the -calculation of eddy diffusivity: +The top boundary condition, imposed at the top modeled layer :math:`i=j_{top}`, where :math:`j_{top} =-n_{sno} +1`, is the downwards surface flux *G* defined by the energy flux residual during the surface temperature solution (section :numref:`Boundary Conditions Lake`). The bottom boundary condition, imposed at :math:`i=N_{levlak} +N_{levgrnd}`, is zero flux. The 2-m windspeed :math:`u_{2}` \ (m s\ :sup:`-1`) is used in the calculation of eddy diffusivity: .. math:: :label: 12.28 u_{2} =\frac{u_{*} }{k} \ln \left(\frac{2}{z_{0m} } \right)\ge 0.1. -where :math:`u_{*}` \ is the friction velocity calculated in section -:numref:`Boundary Conditions Lake` and *k* is the von Karman constant -(:numref:`Table Physical Constants`). +where :math:`u_{*}` \ is the friction velocity calculated in section :numref:`Boundary Conditions Lake` and +*k* is the von Karman constant (:numref:`Table Physical Constants`). .. _Eddy Diffusivity and Thermal Conductivities: @@ -588,19 +359,10 @@ The total eddy diffusivity :math:`K_{W}` (m\ :sup:`2` s\ :sup:`-1`) for liquid K_{W} = m_{d} \left(\kappa _{e} +K_{ed} +\kappa _{m} \right) -where :math:`\kappa _{e}` is due to wind-driven eddies -(:ref:`Hostetler and Bartlein (1990)`), -:math:`K_{ed}` is a modest enhanced diffusivity -intended to represent unresolved mixing processes -(:ref:`Fang and Stefan 1996`), -:math:`\kappa _{m} =\frac{\lambda _{liq} }{c_{liq} \rho _{liq} }` \ is -the molecular diffusivity of water (given by the ratio of its thermal -conductivity (W m\ :sup:`-1` K\ :sup:`-1`) to the product of -its heat capacity (J kg\ :sup:`-1` K\ :sup:`-1`) and density -(kg m\ :sup:`-3`), values given in :numref:`Table Physical Constants`), and :math:`m_{d}` -(unitless) is a factor which increases the overall diffusivity for large -lakes, intended to represent 3-dimensional mixing processes such as -caused by horizontal temperature gradients. As currently implemented, +where :math:`\kappa _{e}` is due to wind-driven eddies (:ref:`Hostetler and Bartlein (1990)`), +:math:`K_{ed}` is a modest enhanced diffusivity intended to represent unresolved mixing processes (:ref:`Fang and Stefan 1996`), +:math:`\kappa _{m} =\frac{\lambda _{liq} }{c_{liq} \rho _{liq} }` \ is the molecular diffusivity of water (given by the ratio of its thermal conductivity (W m\ :sup:`-1` K\ :sup:`-1`) to the product of its heat capacity (J kg\ :sup:`-1` K\ :sup:`-1`) and density (kg m\ :sup:`-3`), values given in :numref:`Table Physical Constants`), and +:math:`m_{d}` (unitless) is a factor which increases the overall diffusivity for large lakes, intended to represent 3-dimensional mixing processes such as caused by horizontal temperature gradients. As currently implemented, .. math:: :label: 12.30 @@ -616,17 +378,7 @@ The wind-driven eddy diffusion coefficient :math:`\kappa _{e,\, i}` (m\ :sup:`2` \kappa _{e,\, i} =\left\{\begin{array}{l} {\frac{kw^{*} z_{i} }{P_{0} \left(1+37Ri^{2} \right)} \exp \left(-k^{*} z_{i} \right)\qquad T_{g} >T_{f} } \\ {0\qquad T_{g} \le T_{f} } \end{array}\right\} -where :math:`P_{0} =1` is the neutral value of the turbulent Prandtl -number, :math:`z_{i}` is the node depth (m), the surface friction -velocity (m s\ :sup:`-1`) is :math:`w^{*} =0.0012u_{2}` , and -:math:`k^{*}` varies with latitude :math:`\phi` as -:math:`k^{*} =6.6u_{2}^{-1.84} \sqrt{\left|\sin \phi \right|}` . For the -bottom layer, -:math:`\kappa _{e,\, N_{levlak} } =\kappa _{e,N_{levlak} -1\, }` . As in -:ref:`Hostetler and Bartlein (1990)`, -the 2-m wind speed :math:`u_{2}` (m s\ :sup:`-1`) (eq. ) is used to evaluate -:math:`w^{*}` and :math:`k^{*}` rather than the 10-m wind used by -:ref:`Henderson-Sellers (1985) `. +where :math:`P_{0} =1` is the neutral value of the turbulent Prandtl number, :math:`z_{i}` is the node depth (m), the surface friction velocity (m s\ :sup:`-1`) is :math:`w^{*} =0.0012u_{2}`, and :math:`k^{*}` varies with latitude :math:`\phi` as :math:`k^{*} =6.6u_{2}^{-1.84} \sqrt{\left|\sin \phi \right|}`. For the bottom layer, :math:`\kappa _{e,\, N_{levlak} } =\kappa _{e,N_{levlak} -1\, }`. As in :ref:`Hostetler and Bartlein (1990)`, the 2-m wind speed :math:`u_{2}` (m s\ :sup:`-1`) (eq. ) is used to evaluate :math:`w^{*}` and :math:`k^{*}` rather than the 10-m wind used by :ref:`Henderson-Sellers (1985) `. The Richardson number is @@ -642,93 +394,55 @@ where N^{2} =\frac{g}{\rho _{i} } \frac{\partial \rho }{\partial z} -and :math:`g` is the acceleration due to gravity (m s\ :sup:`-2`) -(:numref:`Table Physical Constants`), :math:`\rho _{i}` is the density of water (kg -m\ :sup:`-3`), and :math:`\frac{\partial \rho }{\partial z}` is -approximated as -:math:`\frac{\rho _{i+1} -\rho _{i} }{z_{i+1} -z_{i} }` . Note that -because here, *z* is increasing downwards (unlike in :ref:`Hostetler and Bartlein (1990)`), eq. contains no negative sign; this is a correction -from CLM4. The density of water is -(:ref:`Hostetler and Bartlein (1990)`) +and :math:`g` is the acceleration due to gravity (m s\ :sup:`-2`) (:numref:`Table Physical Constants`), :math:`\rho _{i}` is the density of water (kg m\ :sup:`-3`), and :math:`\frac{\partial \rho }{\partial z}` is approximated as :math:`\frac{\rho _{i+1} -\rho _{i} }{z_{i+1} -z_{i} }`. Note that because here, *z* is increasing downwards (unlike in :ref:`Hostetler and Bartlein (1990)`), eq. contains no negative sign; this is a correction from CLM4. The density of water is (:ref:`Hostetler and Bartlein (1990)`) .. math:: :label: 12.34 \rho _{i} =1000\left(1-1.9549\times 10^{-5} \left|T_{i} -277\right|^{1.68} \right). -The enhanced diffusivity :math:`K_{ed}` is given by -(:ref:`Fang and Stefan 1996`) +The enhanced diffusivity :math:`K_{ed}` is given by (:ref:`Fang and Stefan 1996`) .. math:: :label: 12.35 K_{ed} =1.04\times 10^{-8} \left(N^{2} \right)^{-0.43} ,N^{2} \ge 7.5\times 10^{-5} {\rm s}^{2} -where :math:`N^{2}` \ is calculated as in eq. except for the minimum -value imposed in . +where :math:`N^{2}` \ is calculated as in eq. except for the minimum value imposed in. -The thermal conductivity for the liquid water portion of lake body layer -*i*, :math:`\tau _{liq,i}` (W m\ :sup:`-1` K\ :sup:`-1`) is -given by +The thermal conductivity for the liquid water portion of lake body layer *i*, :math:`\tau _{liq,i}` (W m\ :sup:`-1` K\ :sup:`-1`) is given by .. math:: :label: 12.36 \tau _{liq,i} =K_{W} c_{liq} \rho _{liq} . -The thermal conductivity of the ice portion of lake body layer *i*, -:math:`\tau _{ice,eff}` \ (W m\ :sup:`-1` K\ :sup:`-1`), is -constant among layers, and is given by +The thermal conductivity of the ice portion of lake body layer *i*, :math:`\tau _{ice,eff}` \ (W m\ :sup:`-1` K\ :sup:`-1`), is constant among layers, and is given by .. math:: :label: 12.37 \tau _{ice,eff} =\tau _{ice} \frac{\rho _{ice} }{\rho _{liq} } -where :math:`\tau _{ice}` \ (:numref:`Table Physical Constants`) is the nominal thermal -conductivity of ice: :math:`\tau _{ice,eff}` \ is adjusted for the fact -that the nominal model layer thicknesses remain constant even while the -physical ice thickness exceeds the water thickness. +where :math:`\tau _{ice}` \ (:numref:`Table Physical Constants`) is the nominal thermal conductivity of ice: :math:`\tau _{ice,eff}` \ is adjusted for the fact that the nominal model layer thicknesses remain constant even while the physical ice thickness exceeds the water thickness. -The overall thermal conductivity :math:`\tau _{i}` for layer *i* with -ice mass-fraction :math:`I_{i}` is the harmonic mean of the liquid -and water fractions, assuming that they will be physically vertically -stacked, and is given by +The overall thermal conductivity :math:`\tau _{i}` for layer *i* with ice mass-fraction :math:`I_{i}` is the harmonic mean of the liquid and water fractions, assuming that they will be physically vertically stacked, and is given by .. math:: :label: 12.38 \tau _{i} =\frac{\tau _{ice,eff} \tau _{liq,i} }{\tau _{liq,i} I_{i} +\tau _{ice} \left(1-I_{i} \right)} . -The thermal conductivity of snow, soil, and bedrock layers above and -below the lake, respectively, are computed identically to those for -vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`), except for the adjustment of thermal -conductivity for frost heave or excess ice (:ref:`Subin et al., 2012a, -Supporting Information`). +The thermal conductivity of snow, soil, and bedrock layers above and below the lake, respectively, are computed identically to those for vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`), except for the adjustment of thermal conductivity for frost heave or excess ice (:ref:`Subin et al., 2012a, Supporting Information`). .. _Radiation Penetration: Radiation Penetration ^^^^^^^^^^^^^^^^^^^^^^^^^^^ -If there are no resolved snow layers, the surface absorption fraction :math:`\beta` is set according to the near-infrared fraction simulated -by the atmospheric model. This is apportioned to the surface energy -budget (section :numref:`Surface Properties Lake`), and thus no additional radiation is absorbed in -the top :math:`z_{a}` (currently 0.6 m) of unfrozen lakes, for which -the light extinction coefficient :math:`\eta` (m\ :sup:`-1`) -varies between lake columns (eq. ). For frozen lakes -(:math:`T_{g} \le T_{f}` ), the remaining :math:`\left(1-\beta \right)\vec{S}_{g}` fraction of surface absorbed -radiation that is not apportioned to the surface energy budget is -absorbed in the top lake body layer. This is a simplification, as lake -ice is partially transparent. If there are resolved snow layers, then -the snow optics submodel (Chapter :numref:`rst_Surface Albedos`) is used to calculate the snow layer -absorption (except for the absorption predicted for the top layer by the -snow optics submodel, which is assigned to the surface energy budget), -with the remainder penetrating snow layers absorbed in the top lake body -ice layer. - -For unfrozen lakes, the solar radiation remaining at depth -:math:`z>z_{a}` in the lake body is given by +If there are no resolved snow layers, the surface absorption fraction :math:`\beta` is set according to the near-infrared fraction simulated by the atmospheric model. This is apportioned to the surface energy budget (section :numref:`Surface Properties Lake`), and thus no additional radiation is absorbed in the top :math:`z_{a}` (currently 0.6 m) of unfrozen lakes, for which the light extinction coefficient :math:`\eta` (m\ :sup:`-1`) varies between lake columns (eq. ). For frozen lakes (:math:`T_{g} \le T_{f}` ), the remaining :math:`\left(1-\beta \right)\vec{S}_{g}` fraction of surface absorbed radiation that is not apportioned to the surface energy budget is absorbed in the top lake body layer. This is a simplification, as lake ice is partially transparent. If there are resolved snow layers, then the snow optics submodel (Chapter :numref:`rst_Surface Albedos`) is used to calculate the snow layer absorption (except for the absorption predicted for the top layer by the snow optics submodel, which is assigned to the surface energy budget), with the remainder penetrating snow layers absorbed in the top lake body ice layer. + +For unfrozen lakes, the solar radiation remaining at depth :math:`z>z_{a}` in the lake body is given by .. math:: :label: 12.39 @@ -743,14 +457,9 @@ For all lake body layers, the flux absorbed by the layer *i*, \phi _{i} =\left(1-\beta \vec{S}_{g} \right)\left[\exp \left\{-\eta \left(z_{i} -\frac{\Delta z_{i} }{2} -z_{a} \right)\right\}-\exp \left\{-\eta \left(z_{i} +\frac{\Delta z_{i} }{2} -z_{a} \right)\right\}\right] . -The argument of each exponent is constrained to be non-negative (so -:math:`\phi _{i}` = 0 for layers contained within :math:`{z}_{a}`). -The remaining flux exiting the bottom of layer :math:`i=N_{levlak}` is -absorbed in the top soil layer. +The argument of each exponent is constrained to be non-negative (so :math:`\phi _{i}` = 0 for layers contained within :math:`{z}_{a}`). The remaining flux exiting the bottom of layer :math:`i=N_{levlak}` is absorbed in the top soil layer. -The light extinction coefficient :math:`\eta` (m\ :sup:`-1`), if -not provided as external data, is a function of depth *d* (m) -(:ref:`Subin et al. (2012a) `): +The light extinction coefficient :math:`\eta` (m\ :sup:`-1`), if not provided as external data, is a function of depth *d* (m) (:ref:`Subin et al. (2012a) `): .. math:: :label: 12.41 @@ -762,79 +471,50 @@ not provided as external data, is a function of depth *d* (m) Heat Capacities ^^^^^^^^^^^^^^^^^^^^^ -The vertically-integrated heat capacity for each lake layer, -:math:`\text{c}_{v,i}` (J m\ :sup:`-2`) is determined by the mass-weighted average over the heat capacities for the -water and ice fractions: +The vertically-integrated heat capacity for each lake layer, :math:`\text{c}_{v,i}` (J m\ :sup:`-2`) is determined by the mass-weighted average over the heat capacities for the water and ice fractions: .. math:: :label: 12.42 c_{v,i} =\Delta z_{i} \rho _{liq} \left[c_{liq} \left(1-I_{i} \right)+c_{ice} I_{i} \right] . -Note that the density of water is used for both ice and water fractions, -as the thickness of the layer is fixed. +Note that the density of water is used for both ice and water fractions, as the thickness of the layer is fixed. -The total heat capacity :math:`c_{v,i}` for each soil, snow, and -bedrock layer (J m\ :sup:`-2`) is determined as for vegetated land -units (Chapter :numref:`rst_Soil and Snow Temperatures`), as the sum of the heat capacities for the water, ice, -and mineral constituents. +The total heat capacity :math:`c_{v,i}` for each soil, snow, and bedrock layer (J m\ :sup:`-2`) is determined as for vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`), as the sum of the heat capacities for the water, ice, and mineral constituents. .. _Crank-Nicholson Solution Lake: Crank-Nicholson Solution ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The solution method for thermal diffusion is similar to that used for -soil (Chapter :numref:`rst_Soil and Snow Temperatures`), except that the -lake body layers are sandwiched between the snow and soil layers -(section :numref:`Introduction Lake`), and radiation flux is -absorbed throughout the lake layers. Before solution, layer temperatures -:math:`T_{i}` (K), thermal conductivities :math:`\tau _{i}` (W -m\ :sup:`-1` K\ :sup:`-1`), heat capacities :math:`c_{v,i}` -(J m\ :sup:`-2`), and layer and interface depths from all -components are transformed into a uniform set of vectors with length -:math:`N=n_{sno} +N_{levlak} +N_{levgrnd}` and consistent units to -simplify the solution. Thermal conductivities at layer interfaces are -calculated as the harmonic mean of the conductivities of the neighboring -layers: +The solution method for thermal diffusion is similar to that used for soil (Chapter :numref:`rst_Soil and Snow Temperatures`), except that the lake body layers are sandwiched between the snow and soil layers (section :numref:`Introduction Lake`), and radiation flux is absorbed throughout the lake layers. Before solution, layer temperatures :math:`T_{i}` (K), thermal conductivities :math:`\tau _{i}` (W m\ :sup:`-1` K\ :sup:`-1`), heat capacities :math:`c_{v,i}` (J m\ :sup:`-2`), and layer and interface depths from all components are transformed into a uniform set of vectors with length :math:`N=n_{sno} +N_{levlak} +N_{levgrnd}` and consistent units to simplify the solution. Thermal conductivities at layer interfaces are calculated as the harmonic mean of the conductivities of the neighboring layers: .. math:: :label: 12.43 \lambda _{i} =\frac{\tau _{i} \tau _{i+1} \left(z_{i+1} -z_{i} \right)}{\tau _{i} \left(z_{i+1} -\hat{z}_{i} \right)+\tau _{i+1} \left(\hat{z}_{i} -z_{i} \right)} , -where :math:`\lambda _{i}` is the conductivity at the interface between -layer *i* and layer *i +* 1, :math:`z_{i}` is the depth of the node of -layer *i*, and :math:`\hat{z}_{i}` is the depth of the interface below -layer *i*. Care is taken at the boundaries between snow and lake and -between lake and soil. The governing equation is discretized for each -layer as +where :math:`\lambda _{i}` is the conductivity at the interface between layer *i* and layer *i +* 1, +:math:`z_{i}` is the depth of the node of layer *i*, and +:math:`\hat{z}_{i}` is the depth of the interface below layer *i*. Care is taken at the boundaries between snow and lake and between lake and soil. The governing equation is discretized for each layer as .. math:: :label: 12.44 \frac{c_{v,i} }{\Delta t} \left(T_{i}^{n+1} -T_{i}^{n} \right)=F_{i-1} -F_{i} +\phi _{i} -where superscripts *n* + 1 and *n* denote values at the end and -beginning of the timestep :math:`\Delta t`, respectively, :math:`F_{i}` -(W m\ :sup:`-2`) is the downward heat flux at the bottom of layer -*i*, and :math:`\phi _{i}` is the solar radiation absorbed in layer -*i*. +where superscripts *n* + 1 and *n* denote values at the end and beginning of the timestep :math:`\Delta t`, respectively, +:math:`F_{i}` (W m\ :sup:`-2`) is the downward heat flux at the bottom of layer *i*, and +:math:`\phi _{i}` is the solar radiation absorbed in layer *i*. -Eq. is solved using the semi-implicit Crank-Nicholson Method, resulting -in a tridiagonal system of equations: +Eq. is solved using the semi-implicit Crank-Nicholson Method, resulting in a tridiagonal system of equations: .. math:: :label: 12.45 \begin{array}{l} {r_{i} =a_{i} T_{i-1}^{n+1} +b_{i} T_{i}^{n+1} +cT_{i+1}^{n+1} ,} \\ {a_{i} =-0.5\frac{\Delta t}{c_{v,i} } \frac{\partial F_{i-1} }{\partial T_{i-1}^{n} } ,} \\ {b_{i} =1+0.5\frac{\Delta t}{c_{v,i} } \left(\frac{\partial F_{i-1} }{\partial T_{i-1}^{n} } +\frac{\partial F_{i} }{\partial T_{i}^{n} } \right),} \\ {c_{i} =-0.5\frac{\Delta t}{c_{v,i} } \frac{\partial F_{i} }{\partial T_{i}^{n} } ,} \\ {r_{i} =T_{i}^{n} +0.5\frac{\Delta t}{c_{v,i} } \left(F_{i-1} -F_{i} \right)+\frac{\Delta t}{c_{v,i} } \phi _{i} .} \end{array} -The fluxes :math:`F_{i}` are defined as follows: for the top layer, -:math:`F_{j_{top} -1} =2G;a_{j_{top} } =0`, where *G* is defined as in -section :numref:`Boundary Conditions Lake` (the factor of 2 merely cancels -out the Crank-Nicholson 0.5 in the equation for :math:`r_{j_{top} }` ). -For the bottom layer, :math:`F_{N_{levlak} +N_{levgrnd} } =0`. -For all other layers: +The fluxes :math:`F_{i}` are defined as follows: for the top layer, :math:`F_{j_{top} -1} =2G;a_{j_{top} } =0`, where *G* is defined as in section :numref:`Boundary Conditions Lake` (the factor of 2 merely cancels out the Crank-Nicholson 0.5 in the equation for :math:`r_{j_{top} }` ). For the bottom layer, :math:`F_{N_{levlak} +N_{levgrnd} } =0`. For all other layers: .. math:: :label: 12.46 @@ -846,47 +526,32 @@ For all other layers: Phase Change ^^^^^^^^^^^^^^^^^^ -Phase change in the lake, snow, and soil is done similarly to that done -for the soil and snow for vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`), except -without the allowance for freezing point depression in soil underlying -lakes. After the heat diffusion is calculated, phase change occurs in a -given layer if the temperature is below freezing and liquid water -remains, or if the temperature is above freezing and ice remains. +Phase change in the lake, snow, and soil is done similarly to that done for the soil and snow for vegetated land units (Chapter :numref:`rst_Soil and Snow Temperatures`), except without the allowance for freezing point depression in soil underlying lakes. After the heat diffusion is calculated, phase change occurs in a given layer if the temperature is below freezing and liquid water remains, or if the temperature is above freezing and ice remains. -If melting occurs, the available energy for melting, :math:`Q_{avail}` -(J m\ :sup:`-2`), is computed as +If melting occurs, the available energy for melting, :math:`Q_{avail}` (J m\ :sup:`-2`), is computed as .. math:: :label: 12.47 Q_{avail} =\left(T_{i} -T_{f} \right)c_{v,i} -where :math:`T_{i}` is the temperature of the layer after thermal -diffusion (section :numref:`Crank-Nicholson Solution Lake`), and -:math:`c_{v,i}` \ is as calculated in section -:numref:`Heat Capacities Lake`. The mass of melt in the layer *M* -(kg m\ :sup:`-2`) is given by +where :math:`T_{i}` is the temperature of the layer after thermal diffusion (section :numref:`Crank-Nicholson Solution Lake`), and +:math:`c_{v,i}` \ is as calculated in section :numref:`Heat Capacities Lake`. The mass of melt in the layer *M* (kg m\ :sup:`-2`) is given by .. math:: :label: 12.48 M=\min \left\{M_{ice} ,\frac{Q_{avail} }{H_{fus} } \right\} -where :math:`H_{fus}` (J kg\ :sup:`-1`) is the latent heat of -fusion of water (:numref:`Table Physical Constants`), and :math:`M_{ice}` is the mass of ice in -the layer: :math:`I_{i} \rho _{liq} \Delta z_{i}` for a lake body -layer, or simply the soil / snow ice content state variable -(:math:`w_{ice}` ) for a soil / snow layer. The heat remainder, -:math:`Q_{rem}` \ is given by +where :math:`H_{fus}` (J kg\ :sup:`-1`) is the latent heat of fusion of water (:numref:`Table Physical Constants`), and +:math:`M_{ice}` is the mass of ice in the layer: :math:`I_{i} \rho _{liq} \Delta z_{i}` for a lake body layer, or simply the soil / snow ice content state variable (:math:`w_{ice}` ) for a soil / snow layer. The heat remainder, :math:`Q_{rem}` \ is given by .. math:: :label: 12.49 Q_{rem} =Q_{avail} -MH_{fus} . -Finally, the mass of ice in the layer :math:`M_{ice}` is adjusted -downwards by :math:`M`, and the temperature :math:`T_{i}` of the -layer is adjusted to +Finally, the mass of ice in the layer :math:`M_{ice}` is adjusted downwards by :math:`M`, and the temperature :math:`T_{i}` of the layer is adjusted to .. math:: :label: 12.50 @@ -895,64 +560,25 @@ layer is adjusted to where :math:`c'_{v,i} =c_{v,i} +M\left(c_{liq} -c_{ice} \right)`. -If freezing occurs, :math:`Q_{avail}` is again given by but will be -negative. The melt :math:`M`, also negative, is given by +If freezing occurs, :math:`Q_{avail}` is again given by but will be negative. The melt :math:`M`, also negative, is given by .. math:: :label: 12.51 M=\max \left\{-M_{liq} ,\frac{Q_{avail} }{H_{fus} } \right\} -where :math:`M_{liq}` is the mass of water in the layer: -:math:`\left(1-I_{i} \right)\rho _{liq} \Delta z_{i}` for a lake body -layer, or the soil / snow water content state variable -(:math:`w_{liq}` ). The heat remainder :math:`Q_{rem}` is given by eq. -and will be negative or zero. Finally, :math:`M_{liq}` is adjusted -downwards by :math:`-M` and the temperature is reset according to eq. . +where :math:`M_{liq}` is the mass of water in the layer: :math:`\left(1-I_{i} \right)\rho _{liq} \Delta z_{i}` for a lake body layer, or the soil / snow water content state variable (:math:`w_{liq}` ). The heat remainder :math:`Q_{rem}` is given by eq. and will be negative or zero. Finally, :math:`M_{liq}` is adjusted downwards by :math:`-M` and the temperature is reset according to eq.. -In the presence of nonzero snow water :math:`W_{sno}` without resolved -snow layers over - -an unfrozen top lake layer, the available energy in the top lake layer -:math:`\left(T_{1} -T_{f} \right)c_{v,1}` is used to melt the snow. -Similar to above, :math:`W_{sno}` is either completely melted and the -remainder of heat returned to the top lake layer, or the available heat -is exhausted and the top lake layer is set to freezing. The snow -thickness is adjusted downwards in proportion to the amount of melt, -maintaining constant density. +In the presence of nonzero snow water :math:`W_{sno}` without resolved snow layers over an unfrozen top lake layer, the available energy in the top lake layer :math:`\left(T_{1} -T_{f} \right)c_{v,1}` is used to melt the snow. Similar to above, :math:`W_{sno}` is either completely melted and the remainder of heat returned to the top lake layer, or the available heat is exhausted and the top lake layer is set to freezing. The snow thickness is adjusted downwards in proportion to the amount of melt, maintaining constant density. .. _Convection Lake: Convection ^^^^^^^^^^^^^^^^ -Convective mixing is based on -:ref:`Hostetler et al.'s (1993, 1994)` coupled -lake-atmosphere model, adjusting the lake temperature after diffusion -and phase change to maintain a stable density profile. Unfrozen lakes -overturn when :math:`\rho _{i} >\rho _{i+1}` , in which case the layer -thickness weighted average temperature for layers 1 to :math:`i+1` is -applied to layers 1 to :math:`i+1` and the densities are updated. This -scheme is applied iteratively to layers :math:`1\le i`), as occasionally -these can be induced by -heat expelled from the sediments (not present in the original -:ref:`Hostetler et al. (1994)` model). Mixing proceeds -from the bottom upward in this -case (i.e., first mixing layers :math:`i=N_{levlak} -1` and -:math:`i=N_{levlak}` , then checking :math:`i=N_{levlak} -2` and -:math:`i=N_{levlak} -1` and mixing down to :math:`i=N_{levlak}` if -needed, and on to the top), so as not to mix in with warmer over-lying -layers.\ - -For frozen lakes, this algorithm is generalized to conserve total -enthalpy and ice content, and to maintain ice contiguous at the top of -the lake. Thus, an additional mixing criterion is added: the presence of -ice in a layer that is below a layer which is not completely frozen. -When this occurs, these two lake layers and all those above mix. Total -enthalpy *Q* is conserved as +Convective mixing is based on :ref:`Hostetler et al.'s (1993, 1994)` coupled lake-atmosphere model, adjusting the lake temperature after diffusion and phase change to maintain a stable density profile. Unfrozen lakes overturn when :math:`\rho _{i} >\rho _{i+1}`, in which case the layer thickness weighted average temperature for layers 1 to :math:`i+1` is applied to layers 1 to :math:`i+1` and the densities are updated. This scheme is applied iteratively to layers :math:`1\le i`), as occasionally these can be induced by heat expelled from the sediments (not present in the original :ref:`Hostetler et al. (1994)` model). Mixing proceeds from the bottom upward in this case (i.e., first mixing layers :math:`i=N_{levlak} -1` and :math:`i=N_{levlak}`, then checking :math:`i=N_{levlak} -2` and :math:`i=N_{levlak} -1` and mixing down to :math:`i=N_{levlak}` if needed, and on to the top), so as not to mix in with warmer over-lying layers.\ + +For frozen lakes, this algorithm is generalized to conserve total enthalpy and ice content, and to maintain ice contiguous at the top of the lake. Thus, an additional mixing criterion is added: the presence of ice in a layer that is below a layer which is not completely frozen. When this occurs, these two lake layers and all those above mix. Total enthalpy *Q* is conserved as .. math:: :label: 12.52 @@ -966,45 +592,27 @@ Once the average ice fraction :math:`I_{av}` is calculated from \begin{array}{l} {I_{av} =\frac{\sum _{j=1}^{i+1}I_{j} \Delta z_{j} }{Z_{i+1} } ,} \\ {Z_{i+1} =\sum _{j=1}^{i+1}\Delta z_{j} ,} \end{array} -the temperatures are calculated. A separate temperature is calculated -for the frozen (:math:`T_{froz}` ) and unfrozen (:math:`T_{unfr}` ) -fractions of the mixed layers. If the total heat content *Q* is positive -(e.g. some layers will be above freezing), then the extra heat is all -assigned to the unfrozen layers, while the fully frozen layers are kept -at freezing. Conversely, if :math:`Q < 0`, the heat deficit will all -be assigned to the ice, and the liquid layers will be kept at freezing. -For the layer that contains both ice and liquid (if present), a weighted -average temperature will have to be calculated. +the temperatures are calculated. A separate temperature is calculated for the frozen (:math:`T_{froz}` ) and unfrozen (:math:`T_{unfr}` ) fractions of the mixed layers. If the total heat content *Q* is positive (e.g. some layers will be above freezing), then the extra heat is all assigned to the unfrozen layers, while the fully frozen layers are kept at freezing. Conversely, if :math:`Q < 0`, the heat deficit will all be assigned to the ice, and the liquid layers will be kept at freezing. For the layer that contains both ice and liquid (if present), a weighted average temperature will have to be calculated. -If :math:`Q > 0`, then :math:`T_{froz} =T_{f}` , and :math:`T_{unfr}` -is given by +If :math:`Q > 0`, then :math:`T_{froz} =T_{f}`, and :math:`T_{unfr}` is given by .. math:: :label: 12.54 T_{unfr} =\frac{Q}{\rho _{liq} Z_{i+1} \left[\left(1-I_{av} \right)c_{liq} \right]} +T_{f} . -If :math:`Q < 0`, then :math:`T_{unfr} =T_{f}` , and :math:`T_{froz}` -is given by +If :math:`Q < 0`, then :math:`T_{unfr} =T_{f}`, and :math:`T_{froz}` is given by .. math:: :label: 12.55 T_{froz} =\frac{Q}{\rho _{liq} Z_{i+1} \left[I_{av} c_{ice} \right]} +T_{f} . -The ice is lumped together at the top. For each lake layer *j* from 1 -to *i* + 1, the ice fraction and temperature are set as follows, where -:math:`Z_{j} =\sum _{m=1}^{j}\Delta z_{m}` : +The ice is lumped together at the top. For each lake layer *j* from 1 to *i* + 1, the ice fraction and temperature are set as follows, where :math:`Z_{j} =\sum _{m=1}^{j}\Delta z_{m}` : -#. If :math:`Z_{j} \le Z_{i+1} I_{av}` , then :math:`I_{j} =1` and - :math:`T_{j} =T_{froz}` . +#. If :math:`Z_{j} \le Z_{i+1} I_{av}`, then :math:`I_{j} =1` and :math:`T_{j} =T_{froz}`. -#. Otherwise, if :math:`Z_{j-1} 1000{\rm m}`, -in which case additional precipitation and frost deposition is added to -:math:`q_{snwcp,\, ice}` . - -If there are resolved snow layers, the generalized "evaporation" -:math:`E_{g}` (i.e., evaporation, dew, frost, and sublimation) is -treated as over other land units, except that the allowed evaporation -from the ground is unlimited (though the top snow layer cannot lose more -water mass than it contains). If there are no resolved snow layers but -:math:`W_{sno} >0` and :math:`E_{g} >0`, sublimation -:math:`q_{sub,sno}` \ (kg m\ :sup:`-2` s\ :sup:`-1`) will be -given by +All precipitation reaches the ground, as there is no vegetated fraction. As for other land types, incident snowfall accumulates (with ice mass :math:`W_{sno}` and thickness :math:`z_{sno}` ) until its thickness exceeds a minimum thickness :math:`s_{\min }`, at which point a resolved snow layer is initiated, with water, ice, dissolved aerosol, snow-grain radius, etc., state variables tracked by the Snow Hydrology submodel (Chapter :numref:`rst_Snow Hydrology`). The density of fresh snow is assigned as for other land types (Chapter :numref:`rst_Snow Hydrology`). Solid precipitation is added immediately to the snow, while liquid precipitation is added to snow layers, if they exist, after accounting for dew, frost, and sublimation (below). If :math:`z_{sno}` exceeds :math:`s_{\min }` after solid precipitation is added but no snow layers are present, a new snow layer is initiated immediately, and then dew, frost, and sublimation are accounted for. Snow-capping is invoked if the snow depth :math:`z_{sno} >1000{\rm m}`, in which case additional precipitation and frost deposition is added to :math:`q_{snwcp,\, ice}`. + +If there are resolved snow layers, the generalized "evaporation" :math:`E_{g}` (i.e., evaporation, dew, frost, and sublimation) is treated as over other land units, except that the allowed evaporation from the ground is unlimited (though the top snow layer cannot lose more water mass than it contains). If there are no resolved snow layers but :math:`W_{sno} >0` and :math:`E_{g} >0`, sublimation :math:`q_{sub,sno}` \ (kg m\ :sup:`-2` s\ :sup:`-1`) will be given by .. math:: :label: 12.60 q_{sub,sno} =\min \left\{E_{g} ,\frac{W_{sno} }{\Delta t} \right\} . -If :math:`E_{g} <0,T_{g} \le T_{f}` , and there are no resolved snow -layers or the top snow layer is not unfrozen, then the rate of frost -production :math:`q_{frost} =\left|E_{g} \right|`. If :math:`E_{g} <0` -but the top snow layer has completely thawed during the Phase Change step -of the Lake Temperature solution (section :numref:`Phase Change Lake`), then -frost (or dew) is not allowed to accumulate (:math:`q_{frost} =0`), to -insure that the layer is eliminated by the Snow Hydrology -(Chapter :numref:`rst_Snow Hydrology`) code. (If :math:`T_{g} >T_{f}`, -then no snow is present (section :numref:`Surface Flux Solution Lake`), and -evaporation or dew deposition is balanced by :math:`q_{rgwl}` .) The -snowpack is updated for frost and sublimation: +If :math:`E_{g} <0,T_{g} \le T_{f}`, and there are no resolved snow layers or the top snow layer is not unfrozen, then the rate of frost production :math:`q_{frost} =\left|E_{g} \right|`. If :math:`E_{g} <0` but the top snow layer has completely thawed during the Phase Change step of the Lake Temperature solution (section :numref:`Phase Change Lake`), then frost (or dew) is not allowed to accumulate (:math:`q_{frost} =0`), to insure that the layer is eliminated by the Snow Hydrology (Chapter :numref:`rst_Snow Hydrology`) code. (If :math:`T_{g} >T_{f}`, then no snow is present (section :numref:`Surface Flux Solution Lake`), and evaporation or dew deposition is balanced by :math:`q_{rgwl}`.) The snowpack is updated for frost and sublimation: .. math:: :label: 12.61 W_{sno} =W_{sno} +\Delta t\left(q_{frost} -q_{sub,sno} \right) . -If there are resolved snow layers, then this update occurs using the Snow -Hydrology submodel (Chapter :numref:`rst_Snow Hydrology`). Otherwise, the -snow ice mass is updated directly, and :math:`z_{sno}` is adjusted by the same -proportion as the snow ice (i.e., maintaining the same density), unless -there was no snow before adding the frost, in which case the density is -assumed to be 250 kg m\ :sup:`-3`. +If there are resolved snow layers, then this update occurs using the Snow Hydrology submodel (Chapter :numref:`rst_Snow Hydrology`). Otherwise, the snow ice mass is updated directly, and :math:`z_{sno}` is adjusted by the same proportion as the snow ice (i.e., maintaining the same density), unless there was no snow before adding the frost, in which case the density is assumed to be 250 kg m\ :sup:`-3`. .. _Soil Hydrology Lake: Soil Hydrology ^^^^^^^^^^^^^^^^^^^^ -The combined water and ice soil volume fraction in a soil layer -:math:`\theta _{i}` is given by +The combined water and ice soil volume fraction in a soil layer :math:`\theta _{i}` is given by .. math:: :label: 12.62 \theta _{i} =\frac{1}{\Delta z_{i} } \left(\frac{w_{ice,i} }{\rho _{ice} } +\frac{w_{liq,i} }{\rho _{liq} } \right) . -If :math:`\theta _{i} <\theta _{sat,i}` , the pore volume fraction at -saturation (as may occur when ice melts), then the liquid water mass is -adjusted to +If :math:`\theta _{i} <\theta _{sat,i}`, the pore volume fraction at saturation (as may occur when ice melts), then the liquid water mass is adjusted to .. math:: :label: 12.63 w_{liq,i} =\left(\theta _{sat,i} \Delta z_{i} -\frac{w_{ice,i} }{\rho _{ice} } \right)\rho _{liq} . -Otherwise, if excess ice is melting and -:math:`w_{liq,i} >\theta _{sat,i} \rho _{liq} \Delta z_{i}` , then the -water in the layer is reset to +Otherwise, if excess ice is melting and :math:`w_{liq,i} >\theta _{sat,i} \rho _{liq} \Delta z_{i}`, then the water in the layer is reset to .. math:: :label: 12.64 w_{liq,i} = \theta _{sat,i} \rho _{liq} \Delta z_{i} -This allows excess ice to be initialized (and begin to be lost only -after the pore ice is melted, which is realistic if the excess ice is -found in heterogeneous chunks) but irreversibly lost when melt occurs. +This allows excess ice to be initialized (and begin to be lost only after the pore ice is melted, which is realistic if the excess ice is found in heterogeneous chunks) but irreversibly lost when melt occurs. .. _Modifications to Snow Layer Logic Lake: Modifications to Snow Layer Logic ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -A thickness difference :math:`z_{lsa} =s_{\min } -\tilde{s}_{\min }` -adjusts the minimum resolved snow layer thickness for lake columns as -compared to non-lake columns. The value of :math:`z_{lsa}` is chosen to -satisfy the CFL condition for the model timestep. By default, -:math:`\tilde{s}_{\min }` \ = 1 cm and :math:`s_{\min }` \ = 4 cm. See -:ref:`Subin et al. (2012a; including Supporting Information)` -for further discussion. - -The rules for combining and sub-dividing snow layers (section -:numref:`Snow Layer Combination and Subdivision`) are -adjusted for lakes to maintain minimum thicknesses of :math:`s_{\min }` -and to increase all target layer thicknesses by :math:`z_{lsa}` . The -rules for combining layers are modified by simply increasing layer -thickness thresholds by :math:`z_{lsa}` . The rules for dividing snow -layers are contained in a separate subroutine that is modified for -lakes, and is a function of the number of layers and the layer -thicknesses. There are two types of operations: (a) subdividing layers -in half, and (b) shifting some volume from higher layers to lower layers -(without increasing the layer number). For subdivisions of type (a), the -thickness thresholds triggering subdivision are increased by -:math:`2z_{lsa}` for lakes. For shifts of type (b), the thickness -thresholds triggering the shifts are increased by :math:`z_{lsa}` . At -the end of the modified subroutine, a snow ice and liquid balance check -are performed. - -In rare instances, resolved snow layers may be present over an unfrozen -top lake body layer. In this case, the snow layers may be eliminated if -enough heat is present in the top layer to melt the snow: see -:ref:`Subin et al. (2012a, Supporting Information) `. +A thickness difference :math:`z_{lsa} =s_{\min } -\tilde{s}_{\min }` adjusts the minimum resolved snow layer thickness for lake columns as compared to non-lake columns. The value of :math:`z_{lsa}` is chosen to satisfy the CFL condition for the model timestep. By default, :math:`\tilde{s}_{\min }` \ = 1 cm and :math:`s_{\min }` \ = 4 cm. See :ref:`Subin et al. (2012a; including Supporting Information)` for further discussion. + +The rules for combining and sub-dividing snow layers (section :numref:`Snow Layer Combination and Subdivision`) are adjusted for lakes to maintain minimum thicknesses of :math:`s_{\min }` and to increase all target layer thicknesses by :math:`z_{lsa}`. The rules for combining layers are modified by simply increasing layer thickness thresholds by :math:`z_{lsa}`. The rules for dividing snow layers are contained in a separate subroutine that is modified for lakes, and is a function of the number of layers and the layer thicknesses. There are two types of operations: (a) subdividing layers in half, and (b) shifting some volume from higher layers to lower layers (without increasing the layer number). For subdivisions of type (a), the thickness thresholds triggering subdivision are increased by :math:`2z_{lsa}` for lakes. For shifts of type (b), the thickness thresholds triggering the shifts are increased by :math:`z_{lsa}`. At the end of the modified subroutine, a snow ice and liquid balance check are performed. + +In rare instances, resolved snow layers may be present over an unfrozen top lake body layer. In this case, the snow layers may be eliminated if enough heat is present in the top layer to melt the snow: see :ref:`Subin et al. (2012a, Supporting Information) `. diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index b043f422b0..6d08d7df6a 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -3,55 +3,15 @@ Land-Only Mode ================ -In land-only mode (uncoupled to an atmospheric model), the atmospheric -forcing required by CLM (:numref:`Table Atmospheric input to land model`) -is supplied by observed datasets. The standard forcing provided with the -model is a 110-year (1901-2010) dataset provided by the Global Soil Wetness -Project (GSWP3; NEED A REFERENCE). The GSWP3 dataset has a spatial resolution of -0.5\ :sup:`o` X 0.5\ :sup:`o` and a temporal resolution of three -hours. - -An alternative forcing dataset is also available, CRUNCEP, a 110-year (1901-2010) dataset -(CRUNCEP; :ref:`Viovy 2011 `) that is a combination of two existing datasets; -the CRU TS3.2 0.5\ :sup:`o` X 0.5\ :sup:`o` monthly data covering the period -1901 to 2002 (:ref:`Mitchell and Jones 2005 `) -and the NCEP reanalysis 2.5\ :sup:`o` X 2.5\ :sup:`o` -6-hourly data covering the period 1948 to 2010. The CRUNCEP dataset has -been used to force CLM for studies of vegetation growth, -evapotranspiration, and gross primary production (:ref:`Mao et al. 2012 `, -:ref:`Mao et al. 2013 `, :ref:`Shi et al. 2013 `) -and for the TRENDY (trends in net land-atmosphere carbon exchange over the period -1980-2010) project (:ref:`Piao et al. 2012 `). Version 7 is available -here (:ref:`Viovy 2011 `). - -Here, the GSWP3 dataset, which does not include data for particular fields over oceans, -lakes, and Antarctica is modified. This missing data is filled with -:ref:`Qian et al. (2006) ` data from 1948 that is interpolated by the data atmosphere -model to the 0.5\ :sup:`o` GSWP3 grid. This allows the model -to be run over Antarctica and ensures data is available along coastlines -regardless of model resolution. - -The forcing data is ingested into a data atmosphere model in three -"streams"; precipitation (:math:`P`) (mm s\ :sup:`-1`), solar -radiation (:math:`S_{atm}` ) (W m\ :sup:`-2`), and four other -fields [atmospheric pressure :math:`P_{atm}` (Pa), atmospheric specific -humidity :math:`q_{atm}` (kg kg\ :sup:`-1`), atmospheric -temperature :math:`T_{atm}` (K), and atmospheric wind :math:`W_{atm}` -(m s\ :sup:`-1`)]. These are separate streams because they are -handled differently according to the type of field. In the GSWP3 -dataset, the precipitation stream is provided at three hour intervals and -the data atmosphere model prescribes the same precipitation rate for -each model time step within the three hour period. The four fields that -are grouped together in another stream (pressure, humidity, temperature, -and wind) are provided at three hour intervals and the data atmosphere -model linearly interpolates these fields to the time step of the model. - -The total solar radiation is also provided at three hour intervals. The -data is fit to the model time step using a diurnal function that depends -on the cosine of the solar zenith angle :math:`\mu` to provide a -smoother diurnal cycle of solar radiation and to ensure that all of the -solar radiation supplied by the three-hourly forcing data is actually -used. The solar radiation at model time step :math:`t_{M}` is +In land-only mode (uncoupled to an atmospheric model), the atmospheric forcing required by CLM (:numref:`Table Atmospheric input to land model`) is supplied by observed datasets. The standard forcing provided with the model is a 110-year (1901-2010) dataset provided by the Global Soil Wetness Project (GSWP3; NEED A REFERENCE). The GSWP3 dataset has a spatial resolution of 0.5\ :sup:`o` X 0.5\ :sup:`o` and a temporal resolution of three hours. + +An alternative forcing dataset is also available, CRUNCEP, a 110-year (1901-2010) dataset (CRUNCEP; :ref:`Viovy 2011 `) that is a combination of two existing datasets; the CRU TS3.2 0.5\ :sup:`o` X 0.5\ :sup:`o` monthly data covering the period 1901 to 2002 (:ref:`Mitchell and Jones 2005 `) and the NCEP reanalysis 2.5\ :sup:`o` X 2.5\ :sup:`o` 6-hourly data covering the period 1948 to 2010. The CRUNCEP dataset has been used to force CLM for studies of vegetation growth, evapotranspiration, and gross primary production (:ref:`Mao et al. 2012 `, :ref:`Mao et al. 2013 `, :ref:`Shi et al. 2013 `) and for the TRENDY (trends in net land-atmosphere carbon exchange over the period 1980-2010) project (:ref:`Piao et al. 2012 `). Version 7 is available here (:ref:`Viovy 2011 `). + +Here, the GSWP3 dataset, which does not include data for particular fields over oceans, lakes, and Antarctica is modified. This missing data is filled with :ref:`Qian et al. (2006) ` data from 1948 that is interpolated by the data atmosphere model to the 0.5\ :sup:`o` GSWP3 grid. This allows the model to be run over Antarctica and ensures data is available along coastlines regardless of model resolution. + +The forcing data is ingested into a data atmosphere model in three "streams"; precipitation (:math:`P`) (mm s\ :sup:`-1`), solar radiation (:math:`S_{atm}` ) (W m\ :sup:`-2`), and four other fields [atmospheric pressure :math:`P_{atm}` (Pa), atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`), atmospheric temperature :math:`T_{atm}` (K), and atmospheric wind :math:`W_{atm}` (m s\ :sup:`-1`)]. These are separate streams because they are handled differently according to the type of field. In the GSWP3 dataset, the precipitation stream is provided at three hour intervals and the data atmosphere model prescribes the same precipitation rate for each model time step within the three hour period. The four fields that are grouped together in another stream (pressure, humidity, temperature, and wind) are provided at three hour intervals and the data atmosphere model linearly interpolates these fields to the time step of the model. + +The total solar radiation is also provided at three hour intervals. The data is fit to the model time step using a diurnal function that depends on the cosine of the solar zenith angle :math:`\mu` to provide a smoother diurnal cycle of solar radiation and to ensure that all of the solar radiation supplied by the three-hourly forcing data is actually used. The solar radiation at model time step :math:`t_{M}` is .. math:: :label: 31.1 @@ -61,22 +21,9 @@ used. The solar radiation at model time step :math:`t_{M}` is S_{atm} \left(t_{M} \right)=0 & \qquad {\rm for\; }\mu \left(t_{M} \right)\le 0.001 \end{array} -where :math:`\Delta t_{FD}` is the time step of the forcing data (3 -hours :math:`\times` 3600 seconds hour\ :sup:`-1` = 10800 -seconds), :math:`\Delta t_{M}` is the model time step (seconds), -:math:`S_{atm} \left(t_{FD} \right)` is the three-hourly solar radiation -from the forcing data (W m\ :sup:`-2`), and -:math:`\mu \left(t_{M} \right)` is the cosine of the solar zenith angle -at model time step :math:`t_{M}` (section :numref:`Solar Zenith Angle`). The term in the -denominator of equation (1) is the sum of the cosine of the solar zenith -angle for each model time step falling within the three hour period. For -numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. +where :math:`\Delta t_{FD}` is the time step of the forcing data (3 hours :math:`\times` 3600 seconds hour\ :sup:`-1` = 10800 seconds), :math:`\Delta t_{M}` is the model time step (seconds), :math:`S_{atm} \left(t_{FD} \right)` is the three-hourly solar radiation from the forcing data (W m\ :sup:`-2`), and :math:`\mu \left(t_{M} \right)` is the cosine of the solar zenith angle at model time step :math:`t_{M}` (section :numref:`Solar Zenith Angle`). The term in the denominator of equation (1) is the sum of the cosine of the solar zenith angle for each model time step falling within the three hour period. For numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. -The total incident solar radiation :math:`S_{atm}` at the model time -step :math:`t_{M}` is then split into near-infrared and visible -radiation and partitioned into direct and diffuse according to factors -derived from one year's worth of hourly CAM output from CAM version -cam3\_5\_55 as +The total incident solar radiation :math:`S_{atm}` at the model time step :math:`t_{M}` is then split into near-infrared and visible radiation and partitioned into direct and diffuse according to factors derived from one year's worth of hourly CAM output from CAM version cam3\_5\_55 as .. math:: :label: 31.2 @@ -98,16 +45,14 @@ cam3\_5\_55 as S_{atm} \, \downarrow _{nir} =\left(1-R_{nir} \right)\left[\left(1-\alpha \right)S_{atm} \right]. -where :math:`\alpha` , the ratio of visible to total incident solar -radiation, is assumed to be +where :math:`\alpha`, the ratio of visible to total incident solar radiation, is assumed to be .. math:: :label: 31.6 \alpha =\frac{S_{atm} \, \downarrow _{vis}^{\mu } +S_{atm} \, \downarrow _{vis}^{} }{S_{atm} } =0.5. -The ratio of direct to total incident radiation in the visible -:math:`R_{vis}` is +The ratio of direct to total incident radiation in the visible :math:`R_{vis}` is .. math:: :label: 31.7 @@ -121,21 +66,9 @@ and in the near-infrared :math:`R_{nir}` is R_{nir} =b_{0} +b_{1} \times \left(1-\alpha \right)S_{atm} +b_{2} \times \left[\left(1-\alpha \right)S_{atm} \right]^{2} +b_{3} \times \left[\left(1-\alpha \right)S_{atm} \right]^{3} \qquad 0.01\le R_{nir} \le 0.99 -where -:math:`a_{0} =0.17639,\, a_{1} =0.00380,\, a_{2} =-9.0039\times 10^{-6} ,\, a_{3} =8.1351\times 10^{-9}` -and -:math:`b_{0} =0.29548,b_{1} =0.00504,b_{2} =-1.4957\times 10^{-5} ,b_{3} =1.4881\times 10^{-8}` -are coefficients from polynomial fits to the CAM data. - -The additional atmospheric forcing variables required by :numref:`Table Atmospheric input to land model` are -derived as follows. The atmospheric reference height :math:`z'_{atm}` -(m) is set to 30 m. The directional wind components are derived as -:math:`u_{atm} =v_{atm} ={W_{atm} \mathord{\left/ {\vphantom {W_{atm} \sqrt{2} }} \right.} \sqrt{2} }` . -The potential temperature :math:`\overline{\theta _{atm} }` (K) is set -to the atmospheric temperature :math:`T_{atm}` . The atmospheric -longwave radiation :math:`L_{atm} \, \downarrow` (W m\ :sup:`-2`) -is derived from the atmospheric vapor pressure :math:`e_{atm}` and -temperature :math:`T_{atm}` (:ref:`Idso 1981`) as +where :math:`a_{0} =0.17639,\, a_{1} =0.00380,\, a_{2} =-9.0039\times 10^{-6},\, a_{3} =8.1351\times 10^{-9}` and :math:`b_{0} =0.29548,b_{1} =0.00504,b_{2} =-1.4957\times 10^{-5},b_{3} =1.4881\times 10^{-8}` are coefficients from polynomial fits to the CAM data. + +The additional atmospheric forcing variables required by :numref:`Table Atmospheric input to land model` are derived as follows. The atmospheric reference height :math:`z'_{atm}` (m) is set to 30 m. The directional wind components are derived as :math:`u_{atm} =v_{atm} ={W_{atm} \mathord{\left/ {\vphantom {W_{atm} \sqrt{2} }} \right.} \sqrt{2} }`. The potential temperature :math:`\overline{\theta _{atm} }` (K) is set to the atmospheric temperature :math:`T_{atm}`. The atmospheric longwave radiation :math:`L_{atm} \, \downarrow` (W m\ :sup:`-2`) is derived from the atmospheric vapor pressure :math:`e_{atm}` and temperature :math:`T_{atm}` (:ref:`Idso 1981`) as .. math:: :label: 31.9 @@ -149,10 +82,7 @@ where e_{atm} =\frac{P_{atm} q_{atm} }{0.622+0.378q_{atm} } -and :math:`\sigma` is the Stefan-Boltzmann constant (W m\ :sup:`-2` K\ :sup:`-4`) -(:numref:`Table Physical constants`). The fraction of -precipitation :math:`P` (mm s\ :sup:`-1`) falling as rain and/or -snow is +and :math:`\sigma` is the Stefan-Boltzmann constant (W m\ :sup:`-2` K\ :sup:`-4`) (:numref:`Table Physical constants`). The fraction of precipitation :math:`P` (mm s\ :sup:`-1`) falling as rain and/or snow is .. math:: :label: 31.11 @@ -171,68 +101,32 @@ where f_{P} =0<0.5\left(T_{atm} -T_{f} \right)<1. -The aerosol deposition rates :math:`D_{sp}` (14 rates as described in -:numref:`Table Atmospheric input to land model`) are provided by a -time-varying, globally-gridded aerosol deposition file developed by -:ref:`Lamarque et al. (2010) `. +The aerosol deposition rates :math:`D_{sp}` (14 rates as described in :numref:`Table Atmospheric input to land model`) are provided by a time-varying, globally-gridded aerosol deposition file developed by :ref:`Lamarque et al. (2010) `. -If the user wishes to provide atmospheric forcing data from another -source, the data format outlined above will need to be followed with the -following exceptions. The data atmosphere model will accept a -user-supplied relative humidity :math:`RH` (%) and derive specific -humidity :math:`q_{atm}` (kg kg\ :sup:`-1`) from +If the user wishes to provide atmospheric forcing data from another source, the data format outlined above will need to be followed with the following exceptions. The data atmosphere model will accept a user-supplied relative humidity :math:`RH` (%) and derive specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`) from .. math:: :label: 31.14 q_{atm} =\frac{0.622e_{atm} }{P_{atm} -0.378e_{atm} } -where the atmospheric vapor pressure :math:`e_{atm}` (Pa) is derived -from the water (:math:`T_{atm} >T_{f}` ) or ice -(:math:`T_{atm} \le T_{f}` ) saturation vapor pressure -:math:`e_{sat}^{T_{atm} }` as -:math:`e_{atm} =\frac{RH}{100} e_{sat}^{T_{atm} }` where :math:`T_{f}` -is the freezing temperature of water (K) (:numref:`Table Physical constants`), and -:math:`P_{atm}` is the pressure at height :math:`z_{atm}` (Pa). The -data atmosphere model will also accept a user-supplied dew point -temperature :math:`T_{dew}` (K) and derive specific humidity -:math:`q_{atm}` from +where the atmospheric vapor pressure :math:`e_{atm}` (Pa) is derived from the water (:math:`T_{atm} >T_{f}` ) or ice (:math:`T_{atm} \le T_{f}` ) saturation vapor pressure :math:`e_{sat}^{T_{atm} }` as :math:`e_{atm} =\frac{RH}{100} e_{sat}^{T_{atm} }` where :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical constants`), and :math:`P_{atm}` is the pressure at height :math:`z_{atm}` (Pa). The data atmosphere model will also accept a user-supplied dew point temperature :math:`T_{dew}` (K) and derive specific humidity :math:`q_{atm}` from .. math:: :label: 31.15 q_{atm} = \frac{0.622e_{sat}^{T_{dew} } }{P_{atm} -0.378e_{sat}^{T_{dew} } } . -Here, :math:`e_{sat}^{T}` , the saturation vapor pressure as a function -of temperature, is derived from :ref:`Lowe's (1977) ` polynomials. If not -provided by the user, the atmospheric pressure :math:`P_{atm}` (Pa) is -set equal to the standard atmospheric pressure :math:`P_{std} =101325` -Pa, and surface pressure :math:`P_{srf}` (Pa) is set equal -to\ :math:`P_{atm}` . - -The user may provide the total direct and diffuse solar radiation, -:math:`S_{atm} \, \downarrow ^{\mu }` and -:math:`S_{atm} \, \downarrow` . These will be time-interpolated using -the procedure described above and then each term equally apportioned -into the visible and near-infrared wavebands (e.g., -:math:`S_{atm} \, \downarrow _{vis}^{\mu } =0.5S_{atm} \, \downarrow ^{\mu }` , -:math:`S_{atm} \, \downarrow _{nir}^{\mu } =0.5S_{atm} \, \downarrow ^{\mu }` ). +Here, :math:`e_{sat}^{T}`, the saturation vapor pressure as a function of temperature, is derived from :ref:`Lowe's (1977) ` polynomials. If not provided by the user, the atmospheric pressure :math:`P_{atm}` (Pa) is set equal to the standard atmospheric pressure :math:`P_{std} =101325` Pa, and surface pressure :math:`P_{srf}` (Pa) is set equal to\ :math:`P_{atm}`. + +The user may provide the total direct and diffuse solar radiation, :math:`S_{atm} \, \downarrow ^{\mu }` and :math:`S_{atm} \, \downarrow`. These will be time-interpolated using the procedure described above and then each term equally apportioned into the visible and near-infrared wavebands (e.g., :math:`S_{atm} \, \downarrow _{vis}^{\mu } =0.5S_{atm} \, \downarrow ^{\mu }`, :math:`S_{atm} \, \downarrow _{nir}^{\mu } =0.5S_{atm} \, \downarrow ^{\mu }` ). .. _Anomaly Forcing: Anomaly Forcing ----------------------------- -The 'Anomaly Forcing' atmospheric forcing mode provides a means to drive -CLM with projections of future climate conditions without the need for -large, high-frequency datasets. From an existing climate simulation -spanning both the historical and future time periods, a set of anomalies -are created by removing a climatological seasonal cycle based on the end -of the historical period from each year of the future time period of the -simulation. These anomalies can then be applied to a repeating -high-frequency forcing dataset of finite duration (e.g. 10 years). State -and flux forcing variables are adjusted using additive and multiplicative -anomalies, respectively: +The 'Anomaly Forcing' atmospheric forcing mode provides a means to drive CLM with projections of future climate conditions without the need for large, high-frequency datasets. From an existing climate simulation spanning both the historical and future time periods, a set of anomalies are created by removing a climatological seasonal cycle based on the end of the historical period from each year of the future time period of the simulation. These anomalies can then be applied to a repeating high-frequency forcing dataset of finite duration (e.g. 10 years). State and flux forcing variables are adjusted using additive and multiplicative anomalies, respectively: .. math:: :label: 31.16 @@ -242,14 +136,4 @@ anomalies, respectively: F^{'} = f \times k_{anomaly} & \quad {\rm flux \ variable} \end{array} -where :math:`S^{'}` is the adjusted atmospheric state variable, :math:`S` -is the state variable from the high-frequency reference atmospheric -forcing dataset, and :math:`k_{anomaly}` is an additive anomaly. -Similarly, :math:`F^{'}` is the adjusted atmospheric flux variable, -:math:`F` is the flux variable from the high-frequency reference -atmospheric forcing dataset, and :math:`k_{anomaly}` is a -multiplicative anomaly. State variables are temperature :math:`T_{atm}`, -pressure :math:`P_{atm}`, humidity :math:`q_{atm}`, and wind -:math:`W_{atm}`. Flux variables are precipitation :math:`P`, atmospheric -shortwave radiation :math:`S_{atm} \, \downarrow`, and atmospheric -longwave radiation :math:`L_{atm} \, \downarrow`. +where :math:`S^{'}` is the adjusted atmospheric state variable, :math:`S` is the state variable from the high-frequency reference atmospheric forcing dataset, and :math:`k_{anomaly}` is an additive anomaly. Similarly, :math:`F^{'}` is the adjusted atmospheric flux variable, :math:`F` is the flux variable from the high-frequency reference atmospheric forcing dataset, and :math:`k_{anomaly}` is a multiplicative anomaly. State variables are temperature :math:`T_{atm}`, pressure :math:`P_{atm}`, humidity :math:`q_{atm}`, and wind :math:`W_{atm}`. Flux variables are precipitation :math:`P`, atmospheric shortwave radiation :math:`S_{atm} \, \downarrow`, and atmospheric longwave radiation :math:`L_{atm} \, \downarrow`. diff --git a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst index 54d1a8db1e..7d35991a62 100644 --- a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst +++ b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst @@ -8,40 +8,14 @@ Model for Scale Adaptive River Transport (MOSART) Overview --------- -MOSART is a river transport model designed for applications across local, -regional and global scales :ref:`(Li et al., 2013b) `. A -major purpose of MOSART is to provide freshwater input for the ocean -model in coupled Earth System Models. MOSART also provides an effective -way of evaluating and diagnosing the soil hydrology simulated by land -surface models through direct comparison of the simulated river flow -with observations of natural streamflow at gauging stations -:ref:`(Li et al., 2015a)`. Moreover, MOSART provides a -modeling framework for representing riverine transport and transformation -of energy and biogeochemical fluxes under both natural and human-influenced -conditions ( :ref:`(Li et al., 2015b) `. +MOSART is a river transport model designed for applications across local, regional and global scales :ref:`(Li et al., 2013b) `. A major purpose of MOSART is to provide freshwater input for the ocean model in coupled Earth System Models. MOSART also provides an effective way of evaluating and diagnosing the soil hydrology simulated by land surface models through direct comparison of the simulated river flow with observations of natural streamflow at gauging stations :ref:`(Li et al., 2015a)`. Moreover, MOSART provides a modeling framework for representing riverine transport and transformation of energy and biogeochemical fluxes under both natural and human-influenced conditions ( :ref:`(Li et al., 2015b) `. .. _Routing Processes: Routing Processes ------------------ -MOSART divides each spatial unit such as a lat/lon grid or watershed into -three categories of hydrologic units (as shown in -:numref:`Figure MOSART conceptual diagram`): hillslopes -that convert both surface and subsurface runoff into tributaries, -tributaries that discharge into a single main channel, and the main channel -that connects the local spatial unit with upstream/downstream units through the -river network. MOSART assumes that all the tributaries within a spatial unit -can be treated as a single hypothetical sub-network channel with a transport -capacity equivalent to all the tributaries combined. Correspondingly, three -routing processes are represented in MOSART: 1) hillslope routing: in each -spatial unit, surface runoff is routed as overland flow into the sub-network -channel, while subsurface runoff generated in the spatial unit directly enters -the sub-network channel; 2) sub-network channel routing: the sub-network channel -receives water from the hillslopes, routes water through the channel and discharges -it into the main channel; 3) main channel routing: the main channel receives water -from the sub-network channel and/or inflow, if any, from the upstream spatial units, -and discharges the water to its downstream spatial unit or the ocean. +MOSART divides each spatial unit such as a lat/lon grid or watershed into three categories of hydrologic units (as shown in :numref:`Figure MOSART conceptual diagram`): hillslopes that convert both surface and subsurface runoff into tributaries, tributaries that discharge into a single main channel, and the main channel that connects the local spatial unit with upstream/downstream units through the river network. MOSART assumes that all the tributaries within a spatial unit can be treated as a single hypothetical sub-network channel with a transport capacity equivalent to all the tributaries combined. Correspondingly, three routing processes are represented in MOSART: 1) hillslope routing: in each spatial unit, surface runoff is routed as overland flow into the sub-network channel, while subsurface runoff generated in the spatial unit directly enters the sub-network channel; 2) sub-network channel routing: the sub-network channel receives water from the hillslopes, routes water through the channel and discharges it into the main channel; 3) main channel routing: the main channel receives water from the sub-network channel and/or inflow, if any, from the upstream spatial units, and discharges the water to its downstream spatial unit or the ocean. .. Figure 14.1. MOSART conceptual diagram @@ -51,33 +25,18 @@ and discharges the water to its downstream spatial unit or the ocean. :width: 800px :height: 400px -MOSART only routes positive runoff, although negative runoff can be generated -occasionally by the land model (e.g., :math:`q_{gwl}`). Negative runoff in any -runoff component including :math:`q_{sur}`, :math:`q_{sub}`, :math:`q_{gwl}` -is not routed through MOSART, but instead is mapped directly from the spatial unit -where it is generated at any time step to the coupler. +MOSART only routes positive runoff, although negative runoff can be generated occasionally by the land model (e.g., :math:`q_{gwl}`). Negative runoff in any runoff component including :math:`q_{sur}`, :math:`q_{sub}`, :math:`q_{gwl}` is not routed through MOSART, but instead is mapped directly from the spatial unit where it is generated at any time step to the coupler. -In MOSART, the travel velocities of water across hillslopes, sub-network and main -channel are all estimated using Manning's equation with different levels of -simplifications. Generally the Manning's equation is in the form of +In MOSART, the travel velocities of water across hillslopes, sub-network and main channel are all estimated using Manning's equation with different levels of simplifications. Generally the Manning's equation is in the form of .. math:: :label: 14.1 V = \frac{R^{\frac{2}{3}} S_{f}}{n} -where :math:`V` is the travel velocity (m s :sup:`-1` ), :math:`R` is the hydraulic -radius (m). :math:`S_{f}` is the friction slope that accounts for the effects -of gravity, friction, inertia and other forces on the water. If the channel slope -is steep enough, the gravity force dominates over the others so one can approximate -:math:`S_{f}` by the channel bed slope :math:`S` , which is the key assumption -underpinning the kinematic wave method. :math:`n` is the Manning's roughness -coefficient, which is mainly controlled by surface roughness and sinuosity of the -flow path. +where :math:`V` is the travel velocity (m s :sup:`-1` ), :math:`R` is the hydraulic radius (m). :math:`S_{f}` is the friction slope that accounts for the effects of gravity, friction, inertia and other forces on the water. If the channel slope is steep enough, the gravity force dominates over the others so one can approximate :math:`S_{f}` by the channel bed slope :math:`S`, which is the key assumption underpinning the kinematic wave method. :math:`n` is the Manning's roughness coefficient, which is mainly controlled by surface roughness and sinuosity of the flow path. -If the water surface is sufficiently large or the water depth :math:`h` is -sufficiently shallow, the hydraulic radius can be approximated by the water depth. -This is the case for both hillslope and sub-network channel routing. +If the water surface is sufficiently large or the water depth :math:`h` is sufficiently shallow, the hydraulic radius can be approximated by the water depth. This is the case for both hillslope and sub-network channel routing. .. math:: :label: 14.2 @@ -85,9 +44,7 @@ This is the case for both hillslope and sub-network channel routing. R_{h} = h_{h} R_{t} = h_{t} -Here :math:`R_{h}` (m) and :math:`R_{t}` (m) are hydraulic radius for hillslope and -sub-network channel routing respectively, and :math:`h_{h}` (m) and :math:`h_{t}` -(m) are water depth during hillslope and sub-network channel routing respectively. +Here :math:`R_{h}` (m) and :math:`R_{t}` (m) are hydraulic radius for hillslope and sub-network channel routing respectively, and :math:`h_{h}` (m) and :math:`h_{t}` (m) are water depth during hillslope and sub-network channel routing respectively. For the main channel, the hydraulic radius is given by @@ -96,96 +53,30 @@ For the main channel, the hydraulic radius is given by R_{r} = \frac{A_{r}}{P_{r}} -where :math:`A_{r}` (m :sup:`2` ) is the wetted area defined as the part of the -channel cross-section area below the water surface, :math:`P_{r}` (m) is the -wetted perimeter, the perimeter confined in the wetted area. +where :math:`A_{r}` (m :sup:`2` ) is the wetted area defined as the part of the channel cross-section area below the water surface, :math:`P_{r}` (m) is the wetted perimeter, the perimeter confined in the wetted area. -For hillslopes, sub-network and main channels, a common continuity equation can -be written as +For hillslopes, sub-network and main channels, a common continuity equation can be written as .. math:: :label: 14.4 \frac{dS}{dt} = Q_{in} - Q_{out} + R -where :math:`Q_{in}` (m :sup:`3` s :sup:`-1` ) is the main channel flow from -the upstream grid(s) into the main channel of the current grid, which is zero for -hillslope and sub-network routing. :math:`Q_{out}` (m :sup:`3` s :sup:`-1` ) is -the outflow rate from hillslope into the sub-network, from the sub-network into -the main channel, or from the current main channel to the main channel of its -downstream grid (if not the outlet grid) or ocean (if the current grid is the -basin outlet). :math:`R` (m :sup:`3` s :sup:`-1` ) is a source term, which -could be the surface -runoff generation rate for hillslopes, or lateral inflow (from hillslopes) into -sub-network channel or water-atmosphere exchange fluxes such as precipitation -and evaporation. It is assumed that surface runoff is generated uniformly -across all the hillslopes. Currently, MOSART does not exchange water with -the atmosphere or return water to the land model so its function is strictly -to transport water from runoff generation through the hillslope, tributaries, -and main channels to the basin outlets. +where :math:`Q_{in}` (m :sup:`3` s :sup:`-1` ) is the main channel flow from the upstream grid(s) into the main channel of the current grid, which is zero for hillslope and sub-network routing. :math:`Q_{out}` (m :sup:`3` s :sup:`-1` ) is the outflow rate from hillslope into the sub-network, from the sub-network into the main channel, or from the current main channel to the main channel of its downstream grid (if not the outlet grid) or ocean (if the current grid is the basin outlet). :math:`R` (m :sup:`3` s :sup:`-1` ) is a source term, which could be the surface runoff generation rate for hillslopes, or lateral inflow (from hillslopes) into sub-network channel or water-atmosphere exchange fluxes such as precipitation and evaporation. It is assumed that surface runoff is generated uniformly across all the hillslopes. Currently, MOSART does not exchange water with the atmosphere or return water to the land model so its function is strictly to transport water from runoff generation through the hillslope, tributaries, and main channels to the basin outlets. .. _Numerical Solution MOSART: Numerical Solution ---------------------------- -The numerical implementation of MOSART is mainly based on a subcycling -scheme and a local time-stepping algorithm. There are two levels of -subcycling. For convenience, we denote :math:`T_{inputs}` (s), -:math:`T_{mosart}` (s), :math:`T_{hillslope}` (s) and -:math:`T_{channel}` (s) as the time steps of runoff inputs (from CLM -to MOSART via the flux coupler), MOSART routing, hillslope routing, and -channel routing, respectively. The first level of subcycling is between -the runoff inputs and MOSART routing. If :math:`T_{inputs}` is 10800s -and :math:`T_{mosart}` is 3600s, three MOSART time steps will be -invoked each time the runoff inputs are updated. The second level of -subcycling is between the hillslope routing and channel routing. This -is to account for the fact that the travel velocity of water across -hillslopes is usually much slower than that in the channels. -:math:`T_{hillslope}` is usually set as the same as :math:`T_{mosart}`, -but within each time step of hillslope routing there are a few time -steps for channel routing, i.e., -:math:`T_{hillslope} = D_{levelH2R} \cdot T_{channel}`. The local -time-stepping algorithm is to account for the fact that the travel -velocity of water is much faster in some river channels (e.g., with -steeper bed slope, narrower channel width) than others. That is, for -each channel (either a sub-network or main channel), the final time -step of local channel routing is given as -:math:`T_{local}=T_{channel}/D_{local}`. :math:`D_{local}` is -currently estimated empirically as a function of local channel slope, -width, length and upstream drainage area. If MOSART crashes due to a -numerical issue, we recommend increasing :math:`D_{levelH2R}` and, if -the issue remains, reducing :math:`T_{mosart}`. +The numerical implementation of MOSART is mainly based on a subcycling scheme and a local time-stepping algorithm. There are two levels of subcycling. For convenience, we denote :math:`T_{inputs}` (s), :math:`T_{mosart}` (s), :math:`T_{hillslope}` (s) and :math:`T_{channel}` (s) as the time steps of runoff inputs (from CLM to MOSART via the flux coupler), MOSART routing, hillslope routing, and channel routing, respectively. The first level of subcycling is between the runoff inputs and MOSART routing. If :math:`T_{inputs}` is 10800s and :math:`T_{mosart}` is 3600s, three MOSART time steps will be invoked each time the runoff inputs are updated. The second level of subcycling is between the hillslope routing and channel routing. This is to account for the fact that the travel velocity of water across hillslopes is usually much slower than that in the channels. :math:`T_{hillslope}` is usually set as the same as :math:`T_{mosart}`, but within each time step of hillslope routing there are a few time steps for channel routing, i.e., :math:`T_{hillslope} = D_{levelH2R} \cdot T_{channel}`. The local time-stepping algorithm is to account for the fact that the travel velocity of water is much faster in some river channels (e.g., with steeper bed slope, narrower channel width) than others. That is, for each channel (either a sub-network or main channel), the final time step of local channel routing is given as :math:`T_{local}=T_{channel}/D_{local}`. :math:`D_{local}` is currently estimated empirically as a function of local channel slope, width, length and upstream drainage area. If MOSART crashes due to a numerical issue, we recommend increasing :math:`D_{levelH2R}` and, if the issue remains, reducing :math:`T_{mosart}`. .. _Parameters and Input Data: Parameters and Input Data --------------------------------- -MOSART is supported by a comprehensive, global hydrography dataset at 0.5 -:sup:`o` resolution. As such, the fundamental spatial unit of MOSART is a 0.5 -:sup:`o` lat/lon grid. The topographic parameters (such as flow direction, -channel length, topographic and channel slopes, etc.) were derived using the -Dominant River Tracing (DRT) algorithm (:ref:`Wu et al., 2011` ; -:ref:`Wu et al. 2012 `). The DRT algorithm produces the topographic -parameters in a scale-consistent way to preserve/upscale the key features of -a baseline high-resolution hydrography dataset at multiple coarser spatial -resolutions. Here the baseline high-resolution hydrography dataset is the -1km resolution Hydrological data and maps based on SHuttle Elevation -Derivatives at multiple Scales (HydroSHEDS) -(:ref:`Lehner and Döll, 2004 ` ; -:ref:`Lehner et al., 2008 `). The channel geometry -parameters, e.g., bankfull width and depth, were estimated from empirical -hydraulic geometry relationships as functions of the mean annual discharge. -The Manning roughness coefficients for overland and channel flow were -calculated as functions of landcover and water depth. For more details -on the methodology to derive channel geometry and the Manning's roughness -coefficients, please refer to -:ref:`Getirana et al. (2012) ` . The full list of -parameters included in this global hydrography dataset is provided in -:numref:`Table MOSART Parameters`. Evaluation of global simulations -by MOSART using the aforementioned parameters is described in -:ref:`Li et al. (2015b) ` . +MOSART is supported by a comprehensive, global hydrography dataset at 0.5 :sup:`o` resolution. As such, the fundamental spatial unit of MOSART is a 0.5 :sup:`o` lat/lon grid. The topographic parameters (such as flow direction, channel length, topographic and channel slopes, etc.) were derived using the Dominant River Tracing (DRT) algorithm (:ref:`Wu et al., 2011`; :ref:`Wu et al. 2012 `). The DRT algorithm produces the topographic parameters in a scale-consistent way to preserve/upscale the key features of a baseline high-resolution hydrography dataset at multiple coarser spatial resolutions. Here the baseline high-resolution hydrography dataset is the 1km resolution Hydrological data and maps based on SHuttle Elevation Derivatives at multiple Scales (HydroSHEDS) (:ref:`Lehner and Döll, 2004 `; :ref:`Lehner et al., 2008 `). The channel geometry parameters, e.g., bankfull width and depth, were estimated from empirical hydraulic geometry relationships as functions of the mean annual discharge. The Manning roughness coefficients for overland and channel flow were calculated as functions of landcover and water depth. For more details on the methodology to derive channel geometry and the Manning's roughness coefficients, please refer to :ref:`Getirana et al. (2012) `. The full list of parameters included in this global hydrography dataset is provided in :numref:`Table MOSART Parameters`. Evaluation of global simulations by MOSART using the aforementioned parameters is described in :ref:`Li et al. (2015b) `. .. _Table MOSART Parameters: @@ -224,20 +115,11 @@ by MOSART using the aforementioned parameters is described in Difference between CLM5.0 and CLM4.5 ------------------------------------- -1. Routing methods: RTM, a linear reservoir method, is used in CLM4.5 for -river routing, whilst in CLM5.0, MOSART is an added option for river routing -based on the more physically-based kinematic wave method. +1. Routing methods: RTM, a linear reservoir method, is used in CLM4.5 for river routing, whilst in CLM5.0, MOSART is an added option for river routing based on the more physically-based kinematic wave method. -2. Runoff treatment: In RTM runoff is routed regardless of its sign so -negative streamflow can be simulated at times. MOSART routes only non-negative -runoff and always produces positive streamflow, which is important for -future extensions to model riverine heat and biogeochemical fluxes. +2. Runoff treatment: In RTM runoff is routed regardless of its sign so negative streamflow can be simulated at times. MOSART routes only non-negative runoff and always produces positive streamflow, which is important for future extensions to model riverine heat and biogeochemical fluxes. -3. Input parameters: RTM in CLM4.5 only requires one layer of a spatially varying -variable of channel velocity, whilst MOSART in CLM5.0 requires 13 parameters that -are all available globally at 0.5 :sup:`o` resolution. +3. Input parameters: RTM in CLM4.5 only requires one layer of a spatially varying variable of channel velocity, whilst MOSART in CLM5.0 requires 13 parameters that are all available globally at 0.5 :sup:`o` resolution. -4. Outputs: RTM only produces streamflow simulation, whilst MOSART -additionally simulates the time-varying channel velocities, channel water depth, and -channel surface water variations. +4. Outputs: RTM only produces streamflow simulation, whilst MOSART additionally simulates the time-varying channel velocities, channel water depth, and channel surface water variations. diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index dd2f40040f..e0fe0def4e 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -3,187 +3,80 @@ Methane Model ================= -The representation of processes in the methane biogeochemical model -integrated in CLM [CLM4Me; (:ref:`Riley et al. 2011a`)] -is based on several previously published models -(:ref:`Cao et al. 1996`; :ref:`Petrescu et al. 2010`; -:ref:`Tianet al. 2010`; :ref:`Walter et al. 2001`; -:ref:`Wania et al. 2010`; :ref:`Zhang et al. 2002`; -:ref:`Zhuang et al. 2004`). Although the model has similarities -with these precursor models, a number of new process representations and -parameterization have been integrated into CLM. - -Mechanistically modeling net surface CH\ :sub:`4` emissions requires -representing a complex and interacting series of processes. We first -(section :numref:`Methane Model Structure and Flow`) describe the overall -model structure and flow of -information in the CH\ :sub:`4` model, then describe the methods -used to represent: CH\ :sub:`4` mass balance; CH\ :sub:`4` -production; ebullition; aerenchyma transport; CH\ :sub:`4` -oxidation; reactive transport solution, including boundary conditions, -numerical solution, water table interface, etc.; seasonal inundation -effects; and impact of seasonal inundation on CH\ :sub:`4` -production. +The representation of processes in the methane biogeochemical model integrated in CLM [CLM4Me; (:ref:`Riley et al. 2011a`)] is based on several previously published models (:ref:`Cao et al. 1996`; :ref:`Petrescu et al. 2010`; :ref:`Tianet al. 2010`; :ref:`Walter et al. 2001`; :ref:`Wania et al. 2010`; :ref:`Zhang et al. 2002`; :ref:`Zhuang et al. 2004`). Although the model has similarities with these precursor models, a number of new process representations and parameterization have been integrated into CLM. + +Mechanistically modeling net surface CH\ :sub:`4` emissions requires representing a complex and interacting series of processes. We first (section :numref:`Methane Model Structure and Flow`) describe the overall model structure and flow of information in the CH\ :sub:`4` model, then describe the methods used to represent: CH\ :sub:`4` mass balance; CH\ :sub:`4` production; ebullition; aerenchyma transport; CH\ :sub:`4` oxidation; reactive transport solution, including boundary conditions, numerical solution, water table interface, etc.; seasonal inundation effects; and impact of seasonal inundation on CH\ :sub:`4` production. .. _Methane Model Structure and Flow: Methane Model Structure and Flow ------------------------------------- -The driver routine for the methane biogeochemistry calculations (ch4, in -ch4Mod.F) controls the initialization of boundary conditions, -inundation, and impact of redox conditions; calls to routines to -calculate CH\ :sub:`4` production, oxidation, transport through -aerenchyma, ebullition, and the overall mass balance (for unsaturated -and saturated soils and, if desired, lakes); resolves changes to -CH\ :sub:`4` calculations associated with a changing inundated -fraction; performs a mass balance check; and calculates the average -gridcell CH\ :sub:`4` production, oxidation, and exchanges with -the atmosphere. +The driver routine for the methane biogeochemistry calculations (ch4, in ch4Mod.F) controls the initialization of boundary conditions, inundation, and impact of redox conditions; calls to routines to calculate CH\ :sub:`4` production, oxidation, transport through aerenchyma, ebullition, and the overall mass balance (for unsaturated and saturated soils and, if desired, lakes); resolves changes to CH\ :sub:`4` calculations associated with a changing inundated fraction; performs a mass balance check; and calculates the average gridcell CH\ :sub:`4` production, oxidation, and exchanges with the atmosphere. .. _Governing Mass-Balance Relationship: Governing Mass-Balance Relationship ---------------------------------------- -The model (:numref:`Figure Methane Schematic`) accounts for CH\ :sub:`4` -production in the anaerobic fraction of soil (*P*, mol m\ :sup:`-3` -s\ :sup:`-1`), ebullition (*E*, mol m\ :sup:`-3` s\ :sup:`-1`), -aerenchyma transport (*A*, mol m\ :sup:`-3` s\ :sup:`-1`), aqueous and -gaseous diffusion (:math:`{F}_{D}`, mol m\ :sup:`-2` s\ :sup:`-1`), and -oxidation (*O*, mol m\ :sup:`-3` s\ :sup:`-1`) via a transient reaction -diffusion equation: +The model (:numref:`Figure Methane Schematic`) accounts for CH\ :sub:`4` production in the anaerobic fraction of soil (*P*, mol m\ :sup:`-3` s\ :sup:`-1`), ebullition (*E*, mol m\ :sup:`-3` s\ :sup:`-1`), aerenchyma transport (*A*, mol m\ :sup:`-3` s\ :sup:`-1`), aqueous and gaseous diffusion (:math:`{F}_{D}`, mol m\ :sup:`-2` s\ :sup:`-1`), and oxidation (*O*, mol m\ :sup:`-3` s\ :sup:`-1`) via a transient reaction diffusion equation: .. math:: :label: 24.1 \frac{\partial \left(RC\right)}{\partial t} =\frac{\partial F_{D} }{\partial z} +P\left(z,t\right)-E\left(z,t\right)-A\left(z,t\right)-O\left(z,t\right) -Here *z* (m) represents the vertical dimension, *t* (s) is time, and *R* -accounts for gas in both the aqueous and gaseous -phases:\ :math:`R = \epsilon _{a} +K_{H} \epsilon _{w}`, with -:math:`\epsilon _{a}`, :math:`\epsilon _{w}`, and :math:`K_{H}` (-) the air-filled porosity, water-filled -porosity, and partitioning coefficient for the species of interest, -respectively, and :math:`C` represents CH\ :sub:`4` or O\ :sub:`2` concentration with respect to water volume (mol m\ :sup:`-3`). - -An analogous version of equation :eq:`24.1` is concurrently solved for -O\ :sub:`2`, but with the following differences relative to -CH\ :sub:`4`: *P* = *E* = 0 (i.e., no production or ebullition), -and the oxidation sink includes the O\ :sub:`2` demanded by -methanotrophs, heterotroph decomposers, nitrifiers, and autotrophic root -respiration. - -As currently implemented, each gridcell contains an inundated and a -non-inundated fraction. Therefore, equation :eq:`24.1` is solved four times for -each gridcell and time step: in the inundated and non-inundated -fractions, and for CH\ :sub:`4` and O\ :sub:`2`. If desired, -the CH\ :sub:`4` and O\ :sub:`2` mass balance equation is -solved again for lakes (Chapter 9). For non-inundated areas, the water -table interface is defined at the deepest transition from greater than -95% saturated to less than 95% saturated that occurs above frozen soil -layers. The inundated fraction is allowed to change at each time step, -and the total soil CH\ :sub:`4` quantity is conserved by evolving -CH\ :sub:`4` to the atmosphere when the inundated fraction -decreases, and averaging a portion of the non-inundated concentration -into the inundated concentration when the inundated fraction increases. +Here *z* (m) represents the vertical dimension, *t* (s) is time, and *R* accounts for gas in both the aqueous and gaseous phases:\ :math:`R = \epsilon _{a} +K_{H} \epsilon _{w}`, with :math:`\epsilon _{a}`, :math:`\epsilon _{w}`, and :math:`K_{H}` (-) the air-filled porosity, water-filled porosity, and partitioning coefficient for the species of interest, respectively, and :math:`C` represents CH\ :sub:`4` or O\ :sub:`2` concentration with respect to water volume (mol m\ :sup:`-3`). + +An analogous version of equation :eq:`24.1` is concurrently solved for O\ :sub:`2`, but with the following differences relative to CH\ :sub:`4`: *P* = *E* = 0 (i.e., no production or ebullition), and the oxidation sink includes the O\ :sub:`2` demanded by methanotrophs, heterotroph decomposers, nitrifiers, and autotrophic root respiration. + +As currently implemented, each gridcell contains an inundated and a non-inundated fraction. Therefore, equation :eq:`24.1` is solved four times for each gridcell and time step: in the inundated and non-inundated fractions, and for CH\ :sub:`4` and O\ :sub:`2`. If desired, the CH\ :sub:`4` and O\ :sub:`2` mass balance equation is solved again for lakes (Chapter 9). For non-inundated areas, the water table interface is defined at the deepest transition from greater than 95% saturated to less than 95% saturated that occurs above frozen soil layers. The inundated fraction is allowed to change at each time step, and the total soil CH\ :sub:`4` quantity is conserved by evolving CH\ :sub:`4` to the atmosphere when the inundated fraction decreases, and averaging a portion of the non-inundated concentration into the inundated concentration when the inundated fraction increases. .. _Figure Methane Schematic: .. figure:: image1.png - Schematic representation of biological and physical - processes integrated in CLM that affect the net CH\ :sub:`4` + Schematic representation of biological and physical processes integrated in CLM that affect the net CH\ :sub:`4` surface flux (:ref:`Riley et al. 2011a`). (left) - Fully inundated portion of a - CLM gridcell and (right) variably saturated portion of a gridcell. + Fully inundated portion of a CLM gridcell and (right) variably saturated portion of a gridcell. .. _CH4 Production: CH\ :sub:`4` Production ---------------------------------- -Because CLM does not currently specifically represent wetland plant -functional types or soil biogeochemical processes, we used -gridcell-averaged decomposition rates as proxies. Thus, the upland -(default) heterotrophic respiration is used to estimate the wetland -decomposition rate after first dividing off the O\ :sub:`2` -limitation. The O\ :sub:`2` consumption associated with anaerobic -decomposition is then set to the unlimited version so that it will be -reduced appropriately during O\ :sub:`2` competition. -CH\ :sub:`4` production at each soil level in the anaerobic -portion (i.e., below the water table) of the column is related to the -gridcell estimate of heterotrophic respiration from soil and litter -(R\ :sub:`H`; mol C m\ :sup:`-2` s\ :sub:`-1`) corrected for its soil temperature -(:math:`{T}_{s}`) dependence, soil temperature through a -:math:`{A}_{10}` factor (:math:`f_{T}`), pH (:math:`f_{pH}`), -redox potential (:math:`f_{pE}`), and a factor accounting for the -seasonal inundation fraction (*S*, described below): +Because CLM does not currently specifically represent wetland plant functional types or soil biogeochemical processes, we used gridcell-averaged decomposition rates as proxies. Thus, the upland (default) heterotrophic respiration is used to estimate the wetland decomposition rate after first dividing off the O\ :sub:`2` limitation. The O\ :sub:`2` consumption associated with anaerobic decomposition is then set to the unlimited version so that it will be reduced appropriately during O\ :sub:`2` competition. CH\ :sub:`4` production at each soil level in the anaerobic portion (i.e., below the water table) of the column is related to the gridcell estimate of heterotrophic respiration from soil and litter (R\ :sub:`H`; mol C m\ :sup:`-2` s\ :sub:`-1`) corrected for its soil temperature (:math:`{T}_{s}`) dependence, soil temperature through a :math:`{A}_{10}` factor (:math:`f_{T}`), pH (:math:`f_{pH}`), redox potential (:math:`f_{pE}`), and a factor accounting for the seasonal inundation fraction (*S*, described below): .. math:: :label: 24.2 P=R_{H} f_{CH_{4} } f_{T} f_{pH} f_{pE} S. -Here, :math:`f_{CH_{4} }` is the baseline ratio between CO\ :sub:`2` -and CH\ :sub:`4` production (all parameters values are given in -:numref:`Table Methane Parameter descriptions`). Currently, :math:`f_{CH_{4} }` -is modified to account for our assumptions that methanogens may have a -higher Q\ :math:`{}_{10}` than aerobic decomposers; are not N limited; -and do not have a low-moisture limitation. - -When the single BGC soil level is used in CLM (Chapter :numref:`rst_Decomposition`), the -temperature factor, :math:`f_{T}` , is set to 0 for temperatures equal -to or below freezing, even though CLM allows heterotrophic respiration -below freezing. However, if the vertically resolved BGC soil column is -used, CH\ :sub:`4` production continues below freezing because -liquid water stress limits decomposition. The base temperature for the -:math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22\ :sup:`o` C and effectively -modified the base :math:`f_{CH_{4}}` value. - -For the single-layer BGC version, :math:`{R}_{H}` is distributed -among soil levels by assuming that 50% is associated with the roots -(using the CLM PFT-specific rooting distribution) and the rest is evenly -divided among the top 0.28 m of soil (to be consistent with CLM's soil -decomposition algorithm). For the vertically resolved BGC version, the -prognosed distribution of :math:`{R}_{H}` is used to estimate CH\ :sub:`4` production. - -The factor :math:`f_{pH}` is nominally set to 1, although a static -spatial map of *pH* can be used to determine this factor -(:ref:`Dunfield et al. 1993`) by applying: +Here, :math:`f_{CH_{4} }` is the baseline ratio between CO\ :sub:`2` and CH\ :sub:`4` production (all parameters values are given in :numref:`Table Methane Parameter descriptions`). Currently, :math:`f_{CH_{4} }` is modified to account for our assumptions that methanogens may have a higher Q\ :math:`{}_{10}` than aerobic decomposers; are not N limited; and do not have a low-moisture limitation. + +When the single BGC soil level is used in CLM (Chapter :numref:`rst_Decomposition`), the temperature factor, :math:`f_{T}`, is set to 0 for temperatures equal to or below freezing, even though CLM allows heterotrophic respiration below freezing. However, if the vertically resolved BGC soil column is used, CH\ :sub:`4` production continues below freezing because liquid water stress limits decomposition. The base temperature for the :math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22\ :sup:`o` C and effectively modified the base :math:`f_{CH_{4}}` value. + +For the single-layer BGC version, :math:`{R}_{H}` is distributed among soil levels by assuming that 50% is associated with the roots (using the CLM PFT-specific rooting distribution) and the rest is evenly divided among the top 0.28 m of soil (to be consistent with CLM's soil decomposition algorithm). For the vertically resolved BGC version, the prognosed distribution of :math:`{R}_{H}` is used to estimate CH\ :sub:`4` production. + +The factor :math:`f_{pH}` is nominally set to 1, although a static spatial map of *pH* can be used to determine this factor (:ref:`Dunfield et al. 1993`) by applying: .. math:: :label: 24.3 f_{pH} =10^{-0.2235pH^{2} +2.7727pH-8.6} . -The :math:`f_{pE}` factor assumes that alternative electron acceptors -are reduced with an e-folding time of 30 days after inundation. The -default version of the model applies this factor to horizontal changes -in inundated area but not to vertical changes in the water table depth -in the upland fraction of the gridcell. We consider both :math:`f_{pH}` -and :math:`f_{pE}` to be poorly constrained in the model and identify -these controllers as important areas for model improvement. +The :math:`f_{pE}` factor assumes that alternative electron acceptors are reduced with an e-folding time of 30 days after inundation. The default version of the model applies this factor to horizontal changes in inundated area but not to vertical changes in the water table depth in the upland fraction of the gridcell. We consider both :math:`f_{pH}` and :math:`f_{pE}` to be poorly constrained in the model and identify these controllers as important areas for model improvement. -As a non-default option to account for CH\ :sub:`4` production in -anoxic microsites above the water table, we apply the Arah and Stephen -(1998) estimate of anaerobic fraction: +As a non-default option to account for CH\ :sub:`4` production in anoxic microsites above the water table, we apply the Arah and Stephen (1998) estimate of anaerobic fraction: .. math:: :label: 24.4 \varphi =\frac{1}{1+\eta C_{O_{2} } } . -Here, :math:`\varphi` is the factor by which production is inhibited -above the water table (compared to production as calculated in equation -:eq:`24.2`, :math:`C_{O_{2}}` (mol m\ :sup:`-3`) is the bulk soil oxygen -concentration, and :math:`\eta` = 400 mol m\ :sup:`-3`. +Here, :math:`\varphi` is the factor by which production is inhibited above the water table (compared to production as calculated in equation :eq:`24.2`, :math:`C_{O_{2}}` (mol m\ :sup:`-3`) is the bulk soil oxygen concentration, and :math:`\eta` = 400 mol m\ :sup:`-3`. -The O\ :sub:`2` required to facilitate the vertically resolved -heterotrophic decomposition and root respiration is estimated assuming 1 -mol O\ :sub:`2` is required per mol CO\ :sub:`2` produced. -The model also calculates the O\ :sub:`2` required during -nitrification, and the total O\ :sub:`2` demand is used in the -O\ :sub:`2` mass balance solution. +The O\ :sub:`2` required to facilitate the vertically resolved heterotrophic decomposition and root respiration is estimated assuming 1 mol O\ :sub:`2` is required per mol CO\ :sub:`2` produced. The model also calculates the O\ :sub:`2` required during nitrification, and the total O\ :sub:`2` demand is used in the O\ :sub:`2` mass balance solution. .. _Table Methane Parameter descriptions: @@ -228,12 +121,7 @@ O\ :sub:`2` mass balance solution. Ebullition --------------- -Briefly, the simulated aqueous CH\ :sub:`4` concentration in each -soil level is used to estimate the expected equilibrium gaseous partial -pressure (:math:`C_{e}` ), as a function of temperature and depth below -the water table, by first estimating the Henry's law partitioning -coefficient (:math:`k_{h}^{C}` ) by the method described in -:ref:`Wania et al. (2010)`: +Briefly, the simulated aqueous CH\ :sub:`4` concentration in each soil level is used to estimate the expected equilibrium gaseous partial pressure (:math:`C_{e}` ), as a function of temperature and depth below the water table, by first estimating the Henry's law partitioning coefficient (:math:`k_{h}^{C}` ) by the method described in :ref:`Wania et al. (2010)`: .. math:: :label: 24.5 @@ -250,33 +138,16 @@ coefficient (:math:`k_{h}^{C}` ) by the method described in C_{e} =\frac{C_{w} R_{g} T}{\theta _{s} k_{H}^{C} p} -where :math:`C_{H}` \ is a constant, :math:`R_{g}` is the universal -gas constant, :math:`k_{H}^{s}` is Henry's law partitioning coefficient -at standard temperature (:math:`T^{s}` ),\ :math:`C_{w}` \ is local -aqueous CH\ :sub:`4` concentration, and *p* is pressure. - -The local pressure is calculated as the sum of the ambient pressure, -water pressure down to the local depth, and pressure from surface -ponding (if applicable). When the CH\ :sub:`4` partial pressure -exceeds 15% of the local pressure (:ref:`Baird et al. 2004`; :ref:`Strack et al. -2006`; :ref:`Wania et al. 2010`), bubbling occurs to remove CH\ :sub:`4` -to below this value, modified by the fraction of CH\ :sub:`4` in -the bubbles [taken as 57%; (:ref:`Kellner et al. 2006`; -:ref:`Wania et al. 2010`)]. -Bubbles are immediately added to the surface flux for saturated columns -and are placed immediately above the water table interface in -unsaturated columns. +where :math:`C_{H}` \ is a constant, :math:`R_{g}` is the universal gas constant, :math:`k_{H}^{s}` is Henry's law partitioning coefficient at standard temperature (:math:`T^{s}` ),\ :math:`C_{w}` \ is local aqueous CH\ :sub:`4` concentration, and *p* is pressure. + +The local pressure is calculated as the sum of the ambient pressure, water pressure down to the local depth, and pressure from surface ponding (if applicable). When the CH\ :sub:`4` partial pressure exceeds 15% of the local pressure (:ref:`Baird et al. 2004`; :ref:`Strack et al. 2006`; :ref:`Wania et al. 2010`), bubbling occurs to remove CH\ :sub:`4` to below this value, modified by the fraction of CH\ :sub:`4` in the bubbles [taken as 57%; (:ref:`Kellner et al. 2006`; :ref:`Wania et al. 2010`)]. Bubbles are immediately added to the surface flux for saturated columns and are placed immediately above the water table interface in unsaturated columns. .. _Aerenchyma Transport: Aerenchyma Transport ------------------------- -Aerenchyma transport is modeled in CLM as gaseous diffusion driven by a -concentration gradient between the specific soil layer and the -atmosphere and, if specified, by vertical advection with the -transpiration stream. There is evidence that pressure driven flow can -also occur, but we did not include that mechanism in the current model. +Aerenchyma transport is modeled in CLM as gaseous diffusion driven by a concentration gradient between the specific soil layer and the atmosphere and, if specified, by vertical advection with the transpiration stream. There is evidence that pressure driven flow can also occur, but we did not include that mechanism in the current model. The diffusive transport through aerenchyma (*A*, mol m\ :sup:`-2` s\ :sup:`-1`) from each soil layer is represented in the model as: @@ -285,40 +156,18 @@ The diffusive transport through aerenchyma (*A*, mol m\ :sup:`-2` s\ :sup:`-1`) A=\frac{C\left(z\right)-C_{a} }{{\raise0.7ex\hbox{$ r_{L} z $}\!\mathord{\left/ {\vphantom {r_{L} z D}} \right.}\!\lower0.7ex\hbox{$ D $}} +r_{a} } pT\rho _{r} , -where *D* is the free-air gas diffusion coefficient (m\ :sup:`2` s\ :sup:`-1`); *C(z)* (mol m\ :sup:`-3`) is the gaseous -concentration at depth *z* (m); :math:`r_{L}` is the ratio of root -length to depth; *p* is the porosity (-); *T* is specific aerenchyma -area (m\ :sup:`2` m\ :sup:`-2`); :math:`{r}_{a}` is the -aerodynamic resistance between the surface and the atmospheric reference -height (s m\ :sup:`-1`); and :math:`\rho _{r}` is the rooting -density as a function of depth (-). The gaseous concentration is -calculated with Henry's law as described in equation :eq:`24.7`. +where *D* is the free-air gas diffusion coefficient (m\ :sup:`2` s\ :sup:`-1`); *C(z)* (mol m\ :sup:`-3`) is the gaseous concentration at depth *z* (m); :math:`r_{L}` is the ratio of root length to depth; *p* is the porosity (-); *T* is specific aerenchyma area (m\ :sup:`2` m\ :sup:`-2`); :math:`{r}_{a}` is the aerodynamic resistance between the surface and the atmospheric reference height (s m\ :sup:`-1`); and :math:`\rho _{r}` is the rooting density as a function of depth (-). The gaseous concentration is calculated with Henry's law as described in equation :eq:`24.7`. -Based on the ranges reported in :ref:`Colmer (2003)`, we have chosen -baseline aerenchyma porosity values of 0.3 for grass and crop PFTs and 0.1 for -tree and shrub PFTs: +Based on the ranges reported in :ref:`Colmer (2003)`, we have chosen baseline aerenchyma porosity values of 0.3 for grass and crop PFTs and 0.1 for tree and shrub PFTs: .. math:: :label: 24.9 T=\frac{4 f_{N} N_{a}}{0.22} \pi R^{2} . -Here :math:`N_{a}` is annual net primary production (NPP, mol -m\ :sup:`-2` s\ :sup:`-1`); *R* is the aerenchyma radius -(2.9 :math:`\times`\ 10\ :sup:`-3` m); :math:`{f}_{N}` is the -belowground fraction of annual NPP; and the 0.22 factor represents the -amount of C per tiller. O\ :sub:`2` can also diffuse in from the -atmosphere to the soil layer via the reverse of the same pathway, with -the same representation as Equation :eq:`24.8` but with the gas diffusivity of -oxygen. - -CLM also simulates the direct emission of CH\ :sub:`4` from leaves -to the atmosphere via transpiration of dissolved methane. We calculate -this flux (:math:`F_{CH_{4} -T}` ; mol m\ :math:`{}^{-}`\ :sup:`2` -s\ :sup:`-1`) using the simulated soil water methane concentration -(:math:`C_{CH_{4} ,j}` (mol m\ :sup:`-3`)) in each soil layer *j* -and the CLM predicted transpiration (:math:`F_{T}` ) for each PFT, -assuming that no methane was oxidized inside the plant tissue: +Here :math:`N_{a}` is annual net primary production (NPP, mol m\ :sup:`-2` s\ :sup:`-1`); *R* is the aerenchyma radius (2.9 :math:`\times`\ 10\ :sup:`-3` m); :math:`{f}_{N}` is the belowground fraction of annual NPP; and the 0.22 factor represents the amount of C per tiller. O\ :sub:`2` can also diffuse in from the atmosphere to the soil layer via the reverse of the same pathway, with the same representation as Equation :eq:`24.8` but with the gas diffusivity of oxygen. + +CLM also simulates the direct emission of CH\ :sub:`4` from leaves to the atmosphere via transpiration of dissolved methane. We calculate this flux (:math:`F_{CH_{4} -T}`; mol m\ :math:`{}^{-}`\ :sup:`2` s\ :sup:`-1`) using the simulated soil water methane concentration (:math:`C_{CH_{4},j}` (mol m\ :sup:`-3`)) in each soil layer *j* and the CLM predicted transpiration (:math:`F_{T}` ) for each PFT, assuming that no methane was oxidized inside the plant tissue: .. math:: :label: 24.10 @@ -330,95 +179,42 @@ assuming that no methane was oxidized inside the plant tissue: CH\ :sub:`4` Oxidation --------------------------------- -CLM represents CH\ :sub:`4` oxidation with double Michaelis-Menten -kinetics (:ref:`Arah and Stephen 1998`; :ref:`Segers 1998`), -dependent on both the gaseous CH\ :sub:`4` and O\ :sub:`2` concentrations: +CLM represents CH\ :sub:`4` oxidation with double Michaelis-Menten kinetics (:ref:`Arah and Stephen 1998`; :ref:`Segers 1998`), dependent on both the gaseous CH\ :sub:`4` and O\ :sub:`2` concentrations: .. math:: :label: 24.11 R_{oxic} =R_{o,\max } \left[\frac{C_{CH_{4} } }{K_{CH_{4} } +C_{CH_{4} } } \right]\left[\frac{C_{O_{2} } }{K_{O_{2} } +C_{O_{2} } } \right]Q_{10} F_{\vartheta } -where :math:`K_{CH_{4} }` and :math:`K_{O_{2} }` \ are the half -saturation coefficients (mol m\ :sup:`-3`) with respect to -CH\ :sub:`4` and O\ :sub:`2` concentrations, respectively; -:math:`R_{o,\max }` is the maximum oxidation rate (mol -m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` -specifies the temperature dependence of the reaction with a base -temperature set to 12 :sup:`o` C. The soil moisture limitation -factor :math:`F_{\theta }` is applied above the water table to -represent water stress for methanotrophs. Based on the data in -:ref:`Schnell and King (1996)`, we take -:math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture -potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. +where :math:`K_{CH_{4} }` and :math:`K_{O_{2} }` \ are the half saturation coefficients (mol m\ :sup:`-3`) with respect to CH\ :sub:`4` and O\ :sub:`2` concentrations, respectively; :math:`R_{o,\max }` is the maximum oxidation rate (mol m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` specifies the temperature dependence of the reaction with a base temperature set to 12 :sup:`o` C. The soil moisture limitation factor :math:`F_{\theta }` is applied above the water table to represent water stress for methanotrophs. Based on the data in :ref:`Schnell and King (1996)`, we take :math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. .. _Reactive Transport Solution: Reactive Transport Solution -------------------------------- -The solution to equation :eq:`24.11` is solved in several sequential steps: resolve -competition for CH\ :sub:`4` and O\ :sub:`2` (section -:numref:`Competition for CH4and O2`); add the ebullition flux into the -layer directly above the water -table or into the atmosphere; calculate the overall CH\ :sub:`4` -or O\ :sub:`2` source term based on production, aerenchyma -transport, ebullition, and oxidation; establish boundary conditions, -including surface conductance to account for snow, ponding, and -turbulent conductances and bottom flux condition -(section :numref:`CH4 and O2 Source Terms`); calculate diffusivity -(section :numref:`Aqueous and Gaseous Diffusion`); and solve the resulting -mass balance using a tridiagonal solver (section -:numref:`Crank-Nicholson Solution Methane`). +The solution to equation :eq:`24.11` is solved in several sequential steps: resolve competition for CH\ :sub:`4` and O\ :sub:`2` (section :numref:`Competition for CH4and O2`); add the ebullition flux into the layer directly above the water table or into the atmosphere; calculate the overall CH\ :sub:`4` or O\ :sub:`2` source term based on production, aerenchyma transport, ebullition, and oxidation; establish boundary conditions, including surface conductance to account for snow, ponding, and turbulent conductances and bottom flux condition (section :numref:`CH4 and O2 Source Terms`); calculate diffusivity (section :numref:`Aqueous and Gaseous Diffusion`); and solve the resulting mass balance using a tridiagonal solver (section :numref:`Crank-Nicholson Solution Methane`). .. _Competition for CH4and O2: Competition for CH\ :sub:`4` and O\ :sub:`2` ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -For each time step, the unlimited CH\ :sub:`4` and -O\ :sub:`2` demands in each model depth interval are computed. If -the total demand over a time step for one of the species exceeds the -amount available in a particular control volume, the demand from each -process associated with the sink is scaled by the fraction required to -ensure non-negative concentrations. Since the methanotrophs are limited -by both CH\ :sub:`4` and O\ :sub:`2`, the stricter -limitation is applied to methanotroph oxidation, and then the -limitations are scaled back for the other processes. The competition is -designed so that the sinks must not exceed the available concentration -over the time step, and if any limitation exists, the sinks must sum to -this value. Because the sinks are calculated explicitly while the -transport is semi-implicit, negative concentrations can occur after the -tridiagonal solution. When this condition occurs for O\ :sub:`2`, -the concentrations are reset to zero; if it occurs for -CH\ :sub:`4`, the surface flux is adjusted and the concentration -is set to zero if the adjustment is not too large. +For each time step, the unlimited CH\ :sub:`4` and O\ :sub:`2` demands in each model depth interval are computed. If the total demand over a time step for one of the species exceeds the amount available in a particular control volume, the demand from each process associated with the sink is scaled by the fraction required to ensure non-negative concentrations. Since the methanotrophs are limited by both CH\ :sub:`4` and O\ :sub:`2`, the stricter limitation is applied to methanotroph oxidation, and then the limitations are scaled back for the other processes. The competition is designed so that the sinks must not exceed the available concentration over the time step, and if any limitation exists, the sinks must sum to this value. Because the sinks are calculated explicitly while the transport is semi-implicit, negative concentrations can occur after the tridiagonal solution. When this condition occurs for O\ :sub:`2`, the concentrations are reset to zero; if it occurs for CH\ :sub:`4`, the surface flux is adjusted and the concentration is set to zero if the adjustment is not too large. .. _CH4 and O2 Source Terms: CH\ :sub:`4` and O\ :sub:`2` Source Terms ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The overall CH\ :sub:`4` net source term consists of production, -oxidation at the base of aerenchyma, transport through aerenchyma, -methanotrophic oxidation, and ebullition (either to the control volume -above the water table if unsaturated or directly to the atmosphere if -saturated). For O\ :sub:`2` below the top control volume, the net -source term consists of O\ :sub:`2` losses from methanotrophy, SOM -decomposition, and autotrophic respiration, and an O\ :sub:`2` -source through aerenchyma. +The overall CH\ :sub:`4` net source term consists of production, oxidation at the base of aerenchyma, transport through aerenchyma, methanotrophic oxidation, and ebullition (either to the control volume above the water table if unsaturated or directly to the atmosphere if saturated). For O\ :sub:`2` below the top control volume, the net source term consists of O\ :sub:`2` losses from methanotrophy, SOM decomposition, and autotrophic respiration, and an O\ :sub:`2` source through aerenchyma. .. _Aqueous and Gaseous Diffusion: Aqueous and Gaseous Diffusion ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -For gaseous diffusion, we adopted the temperature dependence of -molecular free-air diffusion coefficients (:math:`{D}_{0}` -(m\ :sup:`2` s\ :sup:`-1`)) as described by -:ref:`Lerman (1979) ` and applied by -:ref:`Wania et al. (2010)` -(:numref:`Table Temperature dependence of aqueous and gaseous diffusion`). +For gaseous diffusion, we adopted the temperature dependence of molecular free-air diffusion coefficients (:math:`{D}_{0}` (m\ :sup:`2` s\ :sup:`-1`)) as described by :ref:`Lerman (1979) ` and applied by :ref:`Wania et al. (2010)` (:numref:`Table Temperature dependence of aqueous and gaseous diffusion`). .. _Table Temperature dependence of aqueous and gaseous diffusion: @@ -432,115 +228,51 @@ molecular free-air diffusion coefficients (:math:`{D}_{0}` | Gaseous | 0.1875 + 0.0013\ *T* | 0.1759 + 0.0011\ *T* | +----------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------+ -Gaseous diffusivity in soils also depends on the molecular diffusivity, -soil structure, porosity, and organic matter content. -:ref:`Moldrup et al. (2003)`, using observations across a -range of unsaturated mineral soils, showed that the relationship between -effective diffusivity (:math:`D_{e}` (m\ :sup:`2` s\ :sup:`-1`)) and soil -properties can be represented as: +Gaseous diffusivity in soils also depends on the molecular diffusivity, soil structure, porosity, and organic matter content. :ref:`Moldrup et al. (2003)`, using observations across a range of unsaturated mineral soils, showed that the relationship between effective diffusivity (:math:`D_{e}` (m\ :sup:`2` s\ :sup:`-1`)) and soil properties can be represented as: .. math:: :label: 24.12 D_{e} =D_{0} \theta _{a}^{2} \left(\frac{\theta _{a} }{\theta _{s} } \right)^{{\raise0.7ex\hbox{$ 3 $}\!\mathord{\left/ {\vphantom {3 b}} \right.}\!\lower0.7ex\hbox{$ b $}} } , -where :math:`\theta _{a}` and :math:`\theta _{s}` are the air-filled -and total (saturated water-filled) porosities (-), respectively, and *b* -is the slope of the water retention curve (-). However, :ref:`Iiyama and -Hasegawa (2005)` have shown that the original Millington-Quirk -(:ref:`Millington and Quirk 1961`) relationship matched -measurements more closely in unsaturated peat soils: +where :math:`\theta _{a}` and :math:`\theta _{s}` are the air-filled and total (saturated water-filled) porosities (-), respectively, and *b* is the slope of the water retention curve (-). However, :ref:`Iiyama and Hasegawa (2005)` have shown that the original Millington-Quirk (:ref:`Millington and Quirk 1961`) relationship matched measurements more closely in unsaturated peat soils: .. math:: :label: 24.13 D_{e} =D_{0} \frac{\theta _{a} ^{{\raise0.7ex\hbox{$ 10 $}\!\mathord{\left/ {\vphantom {10 3}} \right.}\!\lower0.7ex\hbox{$ 3 $}} } }{\theta _{s} ^{2} } -In CLM, we applied equation :eq:`24.12` for soils with zero organic matter content -and equation :eq:`24.13` for soils with more than 130 kg m\ :sup:`-3` organic -matter content. A linear interpolation between these two limits is -applied for soils with SOM content below 130 kg m\ :sup:`-3`. For -aqueous diffusion in the saturated part of the soil column, we applied -(:ref:`Moldrup et al. (2003)`): +In CLM, we applied equation :eq:`24.12` for soils with zero organic matter content and equation :eq:`24.13` for soils with more than 130 kg m\ :sup:`-3` organic matter content. A linear interpolation between these two limits is applied for soils with SOM content below 130 kg m\ :sup:`-3`. For aqueous diffusion in the saturated part of the soil column, we applied (:ref:`Moldrup et al. (2003)`): .. math:: :label: 24.14 D_{e} =D_{0} \theta _{s} ^{2} . -To simplify the solution, we assumed that gaseous diffusion dominates -above the water table interface and aqueous diffusion below the water -table interface. Descriptions, baseline values, and dimensions for -parameters specific to the CH\ :sub:`4` model are given in -:numref:`Table Methane Parameter descriptions`. For freezing or frozen -soils below the water table, diffusion is limited to the remaining -liquid (CLM allows for some freezing point depression), and the diffusion -coefficients are scaled by the -volume-fraction of liquid. For unsaturated soils, Henry's law -equilibrium is assumed at the interface with the water table. +To simplify the solution, we assumed that gaseous diffusion dominates above the water table interface and aqueous diffusion below the water table interface. Descriptions, baseline values, and dimensions for parameters specific to the CH\ :sub:`4` model are given in :numref:`Table Methane Parameter descriptions`. For freezing or frozen soils below the water table, diffusion is limited to the remaining liquid (CLM allows for some freezing point depression), and the diffusion coefficients are scaled by the volume-fraction of liquid. For unsaturated soils, Henry's law equilibrium is assumed at the interface with the water table. .. _Boundary Conditions: Boundary Conditions ^^^^^^^^^^^^^^^^^^^^^^^^^^ -We assume the CH\ :sub:`4` and O\ :sub:`2` surface fluxes -can be calculated from an effective conductance and a gaseous -concentration gradient between the atmospheric concentration and either -the gaseous concentration in the first soil layer (unsaturated soils) or -in equilibrium with the water (saturated -soil\ :math:`w\left(C_{1}^{n} -C_{a} \right)` and -:math:`w\left(C_{1}^{n+1} -C_{a} \right)` for the fully explicit and -fully implicit cases, respectively (however, see -:ref:`Tang and Riley (2013)` -for a more complete representation of this process). Here, *w* is the -surface boundary layer conductance as calculated in the existing CLM -surface latent heat calculations. If the top layer is not fully -saturated, the :math:`\frac{D_{m1} }{\Delta x_{m1} }` term is replaced -with a series combination: -:math:`\left[\frac{1}{w} +\frac{\Delta x_{1} }{D_{1} } \right]^{-1}` , -and if the top layer is saturated, this term is replaced with -:math:`\left[\frac{K_{H} }{w} +\frac{\frac{1}{2} \Delta x_{1} }{D_{1} } \right]^{-1}` , -where :math:`{K}_{H}` is the Henry's law equilibrium constant. - -When snow is present, a resistance is added to account for diffusion -through the snow based on the Millington-Quirk expression :eq:`24.13` -and CLM's prediction of the liquid water, ice, and air fractions of each -snow layer. When the soil is ponded, the diffusivity is assumed to be -that of methane in pure water, and the resistance as the ratio of the -ponding depth to diffusivity. The overall conductance is taken as the -series combination of surface, snow, and ponding resistances. We assume -a zero flux gradient at the bottom of the soil column. +We assume the CH\ :sub:`4` and O\ :sub:`2` surface fluxes can be calculated from an effective conductance and a gaseous concentration gradient between the atmospheric concentration and either the gaseous concentration in the first soil layer (unsaturated soils) or in equilibrium with the water (saturated soil\ :math:`w\left(C_{1}^{n} -C_{a} \right)` and :math:`w\left(C_{1}^{n+1} -C_{a} \right)` for the fully explicit and fully implicit cases, respectively (however, see :ref:`Tang and Riley (2013)` for a more complete representation of this process). Here, *w* is the surface boundary layer conductance as calculated in the existing CLM surface latent heat calculations. If the top layer is not fully saturated, the :math:`\frac{D_{m1} }{\Delta x_{m1} }` term is replaced with a series combination: :math:`\left[\frac{1}{w} +\frac{\Delta x_{1} }{D_{1} } \right]^{-1}`, and if the top layer is saturated, this term is replaced with :math:`\left[\frac{K_{H} }{w} +\frac{\frac{1}{2} \Delta x_{1} }{D_{1} } \right]^{-1}`, where :math:`{K}_{H}` is the Henry's law equilibrium constant. + +When snow is present, a resistance is added to account for diffusion through the snow based on the Millington-Quirk expression :eq:`24.13` and CLM's prediction of the liquid water, ice, and air fractions of each snow layer. When the soil is ponded, the diffusivity is assumed to be that of methane in pure water, and the resistance as the ratio of the ponding depth to diffusivity. The overall conductance is taken as the series combination of surface, snow, and ponding resistances. We assume a zero flux gradient at the bottom of the soil column. .. _Crank-Nicholson Solution Methane: Crank-Nicholson Solution ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Equation :eq:`24.1` is solved using a Crank-Nicholson solution -(:ref:`Press et al., 1992`), -which combines fully explicit and implicit representations of the mass -balance. The fully explicit decomposition of equation :eq:`24.1` can be written as +Equation :eq:`24.1` is solved using a Crank-Nicholson solution (:ref:`Press et al., 1992`), which combines fully explicit and implicit representations of the mass balance. The fully explicit decomposition of equation :eq:`24.1` can be written as .. math:: :label: 24.15 \frac{R_{j}^{n+1} C_{j}^{n+1} -R_{j}^{n} C_{j}^{n} }{\Delta t} =\frac{1}{\Delta x_{j} } \left[\frac{D_{p1}^{n} }{\Delta x_{p1}^{} } \left(C_{j+1}^{n} -C_{j}^{n} \right)-\frac{D_{m1}^{n} }{\Delta x_{m1}^{} } \left(C_{j}^{n} -C_{j-1}^{n} \right)\right]+S_{j}^{n} , -where *j* refers to the cell in the vertically discretized soil column -(increasing downward), *n* refers to the current time step, -:math:`\Delta`\ *t* is the time step (s), *p1* is *j+½*, *m1* is *j-½*, -and :math:`S_{j}^{n}` is the net source at time step *n* and position -*j*, i.e., -:math:`S_{j}^{n} =P\left(j,n\right)-E\left(j,n\right)-A\left(j,n\right)-O\left(j,n\right)`. -The diffusivity coefficients are calculated as harmonic means of values -from the adjacent cells. Equation :eq:`24.15` is solved for gaseous and aqueous -concentrations above and below the water table, respectively. The *R* -term ensure the total mass balance in both phases is properly accounted -for. An analogous relationship can be generated for the fully implicit -case by replacing *n* by *n+1* on the *C* and *S* terms of equation :eq:`24.15`. -Using an average of the fully implicit and fully explicit relationships -gives: +where *j* refers to the cell in the vertically discretized soil column (increasing downward), *n* refers to the current time step, :math:`\Delta`\ *t* is the time step (s), *p1* is *j+½*, *m1* is *j-½*, and :math:`S_{j}^{n}` is the net source at time step *n* and position *j*, i.e., :math:`S_{j}^{n} =P\left(j,n\right)-E\left(j,n\right)-A\left(j,n\right)-O\left(j,n\right)`. The diffusivity coefficients are calculated as harmonic means of values from the adjacent cells. Equation :eq:`24.15` is solved for gaseous and aqueous concentrations above and below the water table, respectively. The *R* term ensure the total mass balance in both phases is properly accounted for. An analogous relationship can be generated for the fully implicit case by replacing *n* by *n+1* on the *C* and *S* terms of equation :eq:`24.15`. Using an average of the fully implicit and fully explicit relationships gives: .. math:: :label: 24.16 @@ -556,21 +288,14 @@ Equation :eq:`24.16` is solved with a standard tridiagonal solver, i.e.: with coefficients specified in equation :eq:`24.16`. -Two methane balance checks are performed at each timestep to insure that -the diffusion solution and the time-varying aggregation over inundated -and non-inundated areas strictly conserves methane molecules (except for -production minus consumption) and carbon atoms. +Two methane balance checks are performed at each timestep to insure that the diffusion solution and the time-varying aggregation over inundated and non-inundated areas strictly conserves methane molecules (except for production minus consumption) and carbon atoms. .. _Interface between water table and unsaturated zone: Interface between water table and unsaturated zone ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -We assume Henry's Law equilibrium at the interface between the saturated -and unsaturated zone and constant flux from the soil element below the -interface to the center of the soil element above the interface. In this -case, the coefficients are the same as described above, except for the -soil element above the interface: +We assume Henry's Law equilibrium at the interface between the saturated and unsaturated zone and constant flux from the soil element below the interface to the center of the soil element above the interface. In this case, the coefficients are the same as described above, except for the soil element above the interface: .. math:: \frac{D_{p1} }{\Delta x_{p1} } =\left[K_{H} \frac{\Delta x_{j} }{2D_{j} } +\frac{\Delta x_{j+1} }{2D_{j+1} } \right]^{-1} @@ -597,51 +322,26 @@ and the soil element below the interface: Inundated Fraction Prediction ---------------------------------- -A simplified dynamic representation of spatial inundation -based on recent work by :ref:`Prigent et al. (2007)` is used. :ref:`Prigent et al. (2007)` described a -multi-satellite approach to estimate the global monthly inundated -fraction (:math:`{F}_{i}`) over an equal area grid -(0.25 :math:`\circ` \ :math:`\times`\ 0.25\ :math:`\circ` at the equator) -from 1993 - 2000. They suggested that the IGBP estimate for inundation -could be used as a measure of sensitivity of their detection approach at -low inundation. We therefore used the sum of their satellite-derived -:math:`{F}_{i}` and the constant IGBP estimate when it was less than -10% to perform a simple inversion for the inundated fraction for methane -production (:math:`{f}_{s}`). The method optimized two parameters -(:math:`{fws}_{slope}` and :math:`{fws}_{intercept}`) for each -grid cell in a simple model based on simulated total water storage -(:math:`{TWS}`): +A simplified dynamic representation of spatial inundation based on recent work by :ref:`Prigent et al. (2007)` is used. :ref:`Prigent et al. (2007)` described a multi-satellite approach to estimate the global monthly inundated fraction (:math:`{F}_{i}`) over an equal area grid (0.25 :math:`\circ` \ :math:`\times`\ 0.25\ :math:`\circ` at the equator) from 1993 - 2000. They suggested that the IGBP estimate for inundation could be used as a measure of sensitivity of their detection approach at low inundation. We therefore used the sum of their satellite-derived :math:`{F}_{i}` and the constant IGBP estimate when it was less than 10% to perform a simple inversion for the inundated fraction for methane production (:math:`{f}_{s}`). The method optimized two parameters (:math:`{fws}_{slope}` and :math:`{fws}_{intercept}`) for each grid cell in a simple model based on simulated total water storage (:math:`{TWS}`): .. math:: :label: 24.20 f_{s} =fws_{slope} TWS + fws_{intercept} . -These parameters were evaluated at the -0.5\ :sup:`o` resolution, and aggregated for -coarser simulations. Ongoing work in the hydrology -submodel of CLM may alleviate the need for this crude simplification of -inundated fraction in future model versions. +These parameters were evaluated at the 0.5\ :sup:`o` resolution, and aggregated for coarser simulations. Ongoing work in the hydrology submodel of CLM may alleviate the need for this crude simplification of inundated fraction in future model versions. .. _Seasonal Inundation: Seasonal Inundation ------------------------ -A simple scaling factor is used to mimic the impact of -seasonal inundation on CH\ :sub:`4` production (see appendix B in -:ref:`Riley et al. (2011a)` for a discussion of this -simplified expression): +A simple scaling factor is used to mimic the impact of seasonal inundation on CH\ :sub:`4` production (see appendix B in :ref:`Riley et al. (2011a)` for a discussion of this simplified expression): .. math:: :label: 24.21 S=\frac{\beta \left(f-\bar{f}\right)+\bar{f}}{f} ,S\le 1. -Here, *f* is the instantaneous inundated fraction, :math:`\bar{f}` is -the annual average inundated fraction (evaluated for the previous -calendar year) weighted by heterotrophic respiration, and -:math:`\beta` is the anoxia factor that relates the fully anoxic -decomposition rate to the fully oxygen-unlimited decomposition rate, all -other conditions being equal. +Here, *f* is the instantaneous inundated fraction, :math:`\bar{f}` is the annual average inundated fraction (evaluated for the previous calendar year) weighted by heterotrophic respiration, and :math:`\beta` is the anoxia factor that relates the fully anoxic decomposition rate to the fully oxygen-unlimited decomposition rate, all other conditions being equal. diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 72b2fdb525..0648a039da 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -6,9 +6,7 @@ Stomatal Resistance and Photosynthesis Summary of CLM5.0 updates relative to the CLM4.5 ----------------------------------------------------- -We describe here the complete photosynthesis and stomatal conductance parameterizations that -appear in CLM5.0. Corresponding information for CLM4.5 appeared in the -CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). +We describe here the complete photosynthesis and stomatal conductance parameterizations that appear in CLM5.0. Corresponding information for CLM4.5 appeared in the CLM4.5 Technical Note (:ref:`Oleson et al. 2013 `). CLM5 includes the following new changes to photosynthesis and stomatal conductance: @@ -23,68 +21,25 @@ CLM5 includes the following new changes to photosynthesis and stomatal conductan Introduction ----------------------- -Leaf stomatal resistance, which is needed for the water vapor flux -(Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), -is coupled to leaf photosynthesis similar to Collatz et al. -(:ref:`1991 `, :ref:`1992 `). These equations are solved separately for sunlit and -shaded leaves using average absorbed photosynthetically active radiation -for sunlit and shaded leaves -[:math:`\phi ^{sun}` ,\ :math:`\phi ^{sha}` W m\ :sup:`-2` -(section :numref:`Solar Fluxes`)] to give sunlit and shaded stomatal resistance -(:math:`r_{s}^{sun}` ,\ :math:`r_{s}^{sha}` s m\ :sup:`-1`) and -photosynthesis (:math:`A^{sun}` ,\ :math:`A^{sha}` µmol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`). Canopy -photosynthesis is :math:`A^{sun} L^{sun} +A^{sha} L^{sha}` , where -:math:`L^{sun}` and :math:`L^{sha}` are the sunlit and shaded leaf -area indices (section :numref:`Solar Fluxes`). Canopy conductance is -:math:`\frac{1}{r_{b} +r_{s}^{sun} } L^{sun} +\frac{1}{r_{b} +r_{s}^{sha} } L^{sha}` , -where :math:`r_{b}` is the leaf boundary layer resistance (section -:numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). +Leaf stomatal resistance, which is needed for the water vapor flux (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`), is coupled to leaf photosynthesis similar to Collatz et al. (:ref:`1991 `, :ref:`1992 `). These equations are solved separately for sunlit and shaded leaves using average absorbed photosynthetically active radiation for sunlit and shaded leaves [:math:`\phi ^{sun}`,\ :math:`\phi ^{sha}` W m\ :sup:`-2` (section :numref:`Solar Fluxes`)] to give sunlit and shaded stomatal resistance (:math:`r_{s}^{sun}`,\ :math:`r_{s}^{sha}` s m\ :sup:`-1`) and photosynthesis (:math:`A^{sun}`,\ :math:`A^{sha}` µmol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`). Canopy photosynthesis is :math:`A^{sun} L^{sun} +A^{sha} L^{sha}`, where :math:`L^{sun}` and :math:`L^{sha}` are the sunlit and shaded leaf area indices (section :numref:`Solar Fluxes`). Canopy conductance is :math:`\frac{1}{r_{b} +r_{s}^{sun} } L^{sun} +\frac{1}{r_{b} +r_{s}^{sha} } L^{sha}`, where :math:`r_{b}` is the leaf boundary layer resistance (section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). .. _Stomatal resistance: Stomatal resistance ----------------------- -CLM5 calculates stomatal conductance using the Medlyn stomatal conductance model (:ref:`Medlyn et al. 2011`). -Previous versions of CLM calculated leaf stomatal resistance using the Ball-Berry conductance -model as described by :ref:`Collatz et al. (1991)` and implemented in global -climate models (:ref:`Sellers et al. 1996`). The Medlyn model -calculates stomatal conductance (i.e., the inverse of resistance) based on net leaf -photosynthesis, the leaf-to-air vapor pressure difference, and the CO\ :sub:`2` concentration at the leaf surface. -Leaf stomatal resistance is: +CLM5 calculates stomatal conductance using the Medlyn stomatal conductance model (:ref:`Medlyn et al. 2011`). Previous versions of CLM calculated leaf stomatal resistance using the Ball-Berry conductance model as described by :ref:`Collatz et al. (1991)` and implemented in global climate models (:ref:`Sellers et al. 1996`). The Medlyn model calculates stomatal conductance (i.e., the inverse of resistance) based on net leaf photosynthesis, the leaf-to-air vapor pressure difference, and the CO\ :sub:`2` concentration at the leaf surface. Leaf stomatal resistance is: .. math:: :label: 9.1 \frac{1}{r_{s} } =g_{s} = g_{o} + 1.6(1 + \frac{g_{1} }{\sqrt{D_{s}}}) \frac{A_{n} }{{c_{s} \mathord{\left/ {\vphantom {c_{s} P_{atm} }} \right.} P_{atm} } } -where :math:`r_{s}` is leaf stomatal resistance (s m\ :sup:`2` -:math:`\mu`\ mol\ :sup:`-1`), :math:`g_{o}` is the minimum stomatal conductance -(:math:`\mu` mol m :sup:`-2` s\ :sup:`-1`), :math:`A_{n}` is leaf net -photosynthesis (:math:`\mu`\ mol CO\ :sub:`2` m\ :sup:`-2` -s\ :sup:`-1`), :math:`c_{s}` is the CO\ :sub:`2` partial -pressure at the leaf surface (Pa), :math:`P_{atm}` is the atmospheric -pressure (Pa), and :math:`D_{s}=(e_{i}-e{_s})/1000` is the leaf-to-air vapor pressure difference at the leaf surface (kPa) -where :math:`e_{i}` is the saturation vapor pressure (Pa) evaluated at the leaf temperature -:math:`T_{v}` , and :math:`e_{s}` is the vapor pressure at the leaf surface (Pa). -:math:`g_{1}` is a plant functional type dependent parameter (:numref:`Table Plant functional type (PFT) stomatal conductance parameters`) -and are the same as those used in the CABLE model (:ref:`de Kauwe et al. 2015 `). - -The value for :math:`g_{o}=100` :math:`\mu` mol m :sup:`-2` s\ :sup:`-1` for -C\ :sub:`3` and C\ :sub:`4` plants. -Photosynthesis is calculated for sunlit (:math:`A^{sun}`) and shaded -(:math:`A^{sha}`) leaves to give :math:`r_{s}^{sun}` and -:math:`r_{s}^{sha}`. Additionally, soil water influences stomatal -resistance through plant hydraulic stress, detailed in -the :ref:`rst_Plant Hydraulics` chapter. - -Resistance is converted from units of -s m\ :sup:`2` :math:`\mu` mol\ :sup:`-1` to s m\ :sup:`-1` as: -1 s m\ :sup:`-1` = :math:`1\times 10^{-9} R_{gas} \frac{\theta _{atm} }{P_{atm} }` -:math:`\mu` mol\ :sup:`-1` m\ :sup:`2` s, -where :math:`R_{gas}` is the universal gas constant (J K\ :sup:`-1` -kmol\ :sup:`-1`) (:numref:`Table Physical constants`) and :math:`\theta _{atm}` is the -atmospheric potential temperature (K). +where :math:`r_{s}` is leaf stomatal resistance (s m\ :sup:`2` :math:`\mu`\ mol\ :sup:`-1`), :math:`g_{o}` is the minimum stomatal conductance (:math:`\mu` mol m :sup:`-2` s\ :sup:`-1`), :math:`A_{n}` is leaf net photosynthesis (:math:`\mu`\ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`), :math:`c_{s}` is the CO\ :sub:`2` partial pressure at the leaf surface (Pa), :math:`P_{atm}` is the atmospheric pressure (Pa), and :math:`D_{s}=(e_{i}-e{_s})/1000` is the leaf-to-air vapor pressure difference at the leaf surface (kPa) where :math:`e_{i}` is the saturation vapor pressure (Pa) evaluated at the leaf temperature :math:`T_{v}`, and :math:`e_{s}` is the vapor pressure at the leaf surface (Pa). :math:`g_{1}` is a plant functional type dependent parameter (:numref:`Table Plant functional type (PFT) stomatal conductance parameters`) and are the same as those used in the CABLE model (:ref:`de Kauwe et al. 2015 `). + +The value for :math:`g_{o}=100` :math:`\mu` mol m :sup:`-2` s\ :sup:`-1` for C\ :sub:`3` and C\ :sub:`4` plants. Photosynthesis is calculated for sunlit (:math:`A^{sun}`) and shaded (:math:`A^{sha}`) leaves to give :math:`r_{s}^{sun}` and :math:`r_{s}^{sha}`. Additionally, soil water influences stomatal resistance through plant hydraulic stress, detailed in the :ref:`rst_Plant Hydraulics` chapter. + +Resistance is converted from units of s m\ :sup:`2` :math:`\mu` mol\ :sup:`-1` to s m\ :sup:`-1` as: 1 s m\ :sup:`-1` = :math:`1\times 10^{-9} R_{gas} \frac{\theta _{atm} }{P_{atm} }` :math:`\mu` mol\ :sup:`-1` m\ :sup:`2` s, where :math:`R_{gas}` is the universal gas constant (J K\ :sup:`-1` kmol\ :sup:`-1`) (:numref:`Table Physical constants`) and :math:`\theta _{atm}` is the atmospheric potential temperature (K). .. _Table Plant functional type (PFT) stomatal conductance parameters: @@ -147,121 +102,62 @@ atmospheric potential temperature (K). Photosynthesis ------------------ -Photosynthesis in C\ :sub:`3` plants is based on the model of -:ref:`Farquhar et al. (1980)`. Photosynthesis in C\ :sub:`4` plants is -based on the model of :ref:`Collatz et al. (1992)`. :ref:`Bonan et al. (2011)` -describe the implementation, modified here. In its simplest form, leaf -net photosynthesis after accounting for respiration (:math:`R_{d}` ) is +Photosynthesis in C\ :sub:`3` plants is based on the model of :ref:`Farquhar et al. (1980)`. Photosynthesis in C\ :sub:`4` plants is based on the model of :ref:`Collatz et al. (1992)`. :ref:`Bonan et al. (2011)` describe the implementation, modified here. In its simplest form, leaf net photosynthesis after accounting for respiration (:math:`R_{d}` ) is .. math:: :label: 9.2 A_{n} =\min \left(A_{c} ,A_{j} ,A_{p} \right)-R_{d} . -The RuBP carboxylase (Rubisco) limited rate of carboxylation -:math:`A_{c}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` -s\ :sup:`-1`) is +The RuBP carboxylase (Rubisco) limited rate of carboxylation :math:`A_{c}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 9.3 A_{c} =\left\{\begin{array}{l} {\frac{V_{c\max } \left(c_{i} -\Gamma _{\*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{\*} \ge 0. -The maximum rate of carboxylation allowed by the capacity to regenerate -RuBP (i.e., the light-limited rate) :math:`A_{j}` (:math:`\mu` \ mol -CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is +The maximum rate of carboxylation allowed by the capacity to regenerate RuBP (i.e., the light-limited rate) :math:`A_{j}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 9.4 A_{j} =\left\{\begin{array}{l} {\frac{J_{x}\left(c_{i} -\Gamma _{\*} \right)}{4c_{i} +8\Gamma _{\*} } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {\alpha (4.6\phi )\qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{\*} \ge 0. -The product-limited rate of carboxylation for C\ :sub:`3` plants -and the PEP carboxylase-limited rate of carboxylation for -C\ :sub:`4` plants :math:`A_{p}` (:math:`\mu` \ mol -CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is +The product-limited rate of carboxylation for C\ :sub:`3` plants and the PEP carboxylase-limited rate of carboxylation for C\ :sub:`4` plants :math:`A_{p}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 9.5 A_{p} =\left\{\begin{array}{l} {3T_{p\qquad } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {k_{p} \frac{c_{i} }{P_{atm} } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}. -In these equations, :math:`c_{i}` is the internal leaf -CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` -is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and -:math:`K_{o}` are the Michaelis-Menten constants (Pa) for -CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{\*}` (Pa) is -the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the -maximum rate of carboxylation (µmol m\ :sup:`-2` -s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) -and :math:`J_{x}` is the electron transport rate (µmol -m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose -phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), -taken as :math:`T_{p} =0.167V_{c\max }` so that -:math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in -:ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited -rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum -efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` -mol\ :sup:`-1` photon). :math:`\phi` is the absorbed -photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`) -, which is converted to photosynthetic photon flux assuming 4.6 -:math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope -of C\ :sub:`4` CO\ :sub:`2` response curve. - -For C\ :sub:`3` plants, the electron transport rate depends on the -photosynthetically active radiation absorbed by the leaf. A common -expression is the smaller of the two roots of the equation +In these equations, :math:`c_{i}` is the internal leaf CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{\*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), taken as :math:`T_{p} =0.167V_{c\max }` so that :math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in :ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` mol\ :sup:`-1` photon). :math:`\phi` is the absorbed photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`), which is converted to photosynthetic photon flux assuming 4.6 :math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope of C\ :sub:`4` CO\ :sub:`2` response curve. + +For C\ :sub:`3` plants, the electron transport rate depends on the photosynthetically active radiation absorbed by the leaf. A common expression is the smaller of the two roots of the equation .. math:: :label: 9.6 \Theta _{PSII} J_{x}^{2} -\left(I_{PSII} +J_{\max } \right)J_{x}+I_{PSII} J_{\max } =0 -where :math:`J_{\max }` is the maximum potential rate of electron -transport (:math:`\mu`\ mol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`), -:math:`I_{PSII}` is the light utilized in electron transport by -photosystem II (µmol m\ :sup:`-2` s\ :sup:`-1`), and -:math:`\Theta _{PSII}` is a curvature parameter. For a given amount of -photosynthetically active radiation absorbed by a leaf (:math:`\phi`, W -m\ :sup:`-2`), converted to photosynthetic photon flux density -with 4.6 :math:`\mu`\ mol J\ :sup:`-1`, the light utilized in -electron transport is +where :math:`J_{\max }` is the maximum potential rate of electron transport (:math:`\mu`\ mol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`), :math:`I_{PSII}` is the light utilized in electron transport by photosystem II (µmol m\ :sup:`-2` s\ :sup:`-1`), and :math:`\Theta _{PSII}` is a curvature parameter. For a given amount of photosynthetically active radiation absorbed by a leaf (:math:`\phi`, W m\ :sup:`-2`), converted to photosynthetic photon flux density with 4.6 :math:`\mu`\ mol J\ :sup:`-1`, the light utilized in electron transport is .. math:: :label: 9.7 I_{PSII} =0.5\Phi _{PSII} (4.6\phi ) -where :math:`\Phi _{PSII}` is the quantum yield of photosystem II, and -the term 0.5 arises because one photon is absorbed by each of the two -photosystems to move one electron. Parameter values are -:math:`\Theta _{PSII}` \ = 0.7 and :math:`\Phi _{PSII}` \ = 0.85. In -calculating :math:`A_{j}` (for both C\ :sub:`3` and -C\ :sub:`4` plants), :math:`\phi =\phi ^{sun}` for sunlit leaves -and :math:`\phi =\phi ^{sha}` for shaded leaves. +where :math:`\Phi _{PSII}` is the quantum yield of photosystem II, and the term 0.5 arises because one photon is absorbed by each of the two photosystems to move one electron. Parameter values are :math:`\Theta _{PSII}` \ = 0.7 and :math:`\Phi _{PSII}` \ = 0.85. In calculating :math:`A_{j}` (for both C\ :sub:`3` and C\ :sub:`4` plants), :math:`\phi =\phi ^{sun}` for sunlit leaves and :math:`\phi =\phi ^{sha}` for shaded leaves. -The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) -`. The actual gross photosynthesis rate, :math:`A`, is given by the -smaller root of the equations +The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) `. The actual gross photosynthesis rate, :math:`A`, is given by the smaller root of the equations .. math:: :label: 9.8 \begin{array}{rcl} {\Theta _{cj} A_{i}^{2} -\left(A_{c} +A_{j} \right)A_{i} +A_{c} A_{j} } & {=} & {0} \\ {\Theta _{ip} A^{2} -\left(A_{i} +A_{p} \right)A+A_{i} A_{p} } & {=} & {0} \end{array} . -Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for -C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and -:math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. -:math:`A_{i}` is the intermediate co-limited photosynthesis. -:math:`A_{n} =A-R_{d}` . +Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. :math:`A_{n} =A-R_{d}`. -The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` -depend on temperature. Values at 25 :sup:`o` \ C are -:math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, -:math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and -:math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. -:math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, -and :math:`R_{d}` also vary with temperature. +The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 :sup:`o` \ C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. :math:`J_{\max 25}` at 25 :sup:`\o`\ C: is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) @@ -273,14 +169,9 @@ Parameter values at 25 :sup:`\o`\ C are calculated from :math:`V_{c\max }` \ at For C\ :sub:`4` plants, :math:`k_{p25} =20000\; V_{c\max 25}`. -However, when the biogeochemistry is active (the default mode), :math:`R_{d25}` is -calculated from leaf nitrogen as described in (Chapter :numref:`rst_Plant Respiration`) +However, when the biogeochemistry is active (the default mode), :math:`R_{d25}` is calculated from leaf nitrogen as described in (Chapter :numref:`rst_Plant Respiration`) -The parameters :math:`V_{c\max 25}`, -:math:`J_{\max 25}`, :math:`T_{p25}`, :math:`k_{p25}`, and -:math:`R_{d25}` are scaled over the canopy for sunlit and shaded leaves -(section :numref:`Canopy scaling`). In C\ :sub:`3` plants, these are adjusted for leaf temperature, -:math:`T_{v}` (K), as: +The parameters :math:`V_{c\max 25}`, :math:`J_{\max 25}`, :math:`T_{p25}`, :math:`k_{p25}`, and :math:`R_{d25}` are scaled over the canopy for sunlit and shaded leaves (section :numref:`Canopy scaling`). In C\ :sub:`3` plants, these are adjusted for leaf temperature, :math:`T_{v}` (K), as: .. math:: :label: 9.9 @@ -299,16 +190,7 @@ and f_{H} \left(T_{v} \right)=\frac{1+\exp \left(\frac{298.15\Delta S-\Delta H_{d} }{298.15\times 0.001R_{gas} } \right)}{1+\exp \left(\frac{\Delta ST_{v} -\Delta H_{d} }{0.001R_{gas} T_{v} } \right)} . -:numref:`Table Temperature dependence parameters for C3 photosynthesis` -lists parameter values for :math:`\Delta H_{a}` and -:math:`\Delta H_{d}` . :math:`\Delta S` is calculated -separately for :math:`V_{c\max }` and :math:`J_{max }` -to allow for temperature acclimation of photosynthesis (see equation :eq:`9.16`), -and :math:`\Delta S` is 490 J mol :sup:`-1` K :sup:`-1` for :math:`R_d` -(:ref:`Bonan et al. 2011`, :ref:`Lombardozzi et al. 2015`). -Because :math:`T_{p}` as implemented here varies with -:math:`V_{c\max }` , :math:`T_{p}` uses the same temperature parameters as -:math:`V_{c\max}` . For C\ :sub:`4` plants, +:numref:`Table Temperature dependence parameters for C3 photosynthesis` lists parameter values for :math:`\Delta H_{a}` and :math:`\Delta H_{d}`. :math:`\Delta S` is calculated separately for :math:`V_{c\max }` and :math:`J_{max }` to allow for temperature acclimation of photosynthesis (see equation :eq:`9.16`), and :math:`\Delta S` is 490 J mol :sup:`-1` K :sup:`-1` for :math:`R_d` (:ref:`Bonan et al. 2011`, :ref:`Lombardozzi et al. 2015`). Because :math:`T_{p}` as implemented here varies with :math:`V_{c\max }`, :math:`T_{p}` uses the same temperature parameters as :math:`V_{c\max}`. For C\ :sub:`4` plants, .. math:: :label: 9.12 @@ -318,16 +200,15 @@ Because :math:`T_{p}` as implemented here varies with with :math:`Q_{10} =2`, :math:`s_{1} =0.3`\ K\ :sup:`-1` :math:`s_{2} =313.15` K, -:math:`s_{3} =0.2`\ K\ :sup:`-1`, and :math:`s_{4} =288.15` K. -Additionally, +:math:`s_{3} =0.2`\ K\ :sup:`-1`, and +:math:`s_{4} =288.15` K. Additionally, .. math:: :label: 9.13 R_{d} =R_{d25} \left\{\frac{Q_{10} ^{(T_{v} -298.15)/10} }{1+\exp \left[s_{5} \left(T_{v} -s_{6} \right)\right]} \right\} -with :math:`Q_{10} =2`, :math:`s_{5} =1.3` -K\ :sup:`-1` and :math:`s_{6} =328.15`\ K, and +with :math:`Q_{10} =2`, :math:`s_{5} =1.3` K\ :sup:`-1` and :math:`s_{6} =328.15`\ K, and .. math:: :label: 9.14 @@ -358,40 +239,28 @@ with :math:`Q_{10} =2`. | :math:`\Gamma _{\*}` | 37830 | – | +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ -In the model, acclimation is -implemented as in :ref:`Kattge and Knorr (2007) `. In this parameterization, -:math:`V_{c\max }` and :math:`J_{\max }` vary with the plant growth temperature. This is -achieved by allowing :math:`\Delta S`\ to vary with growth temperature -according to +In the model, acclimation is implemented as in :ref:`Kattge and Knorr (2007) `. In this parameterization, :math:`V_{c\max }` and :math:`J_{\max }` vary with the plant growth temperature. This is achieved by allowing :math:`\Delta S`\ to vary with growth temperature according to .. math:: :label: 9.15 \begin{array}{l} {\Delta S=668.39-1.07(T_{10} -T_{f} )\qquad \qquad {\rm for\; }V_{c\max } } \\ {\Delta S=659.70-0.75(T_{10} -T_{f} )\qquad \qquad {\rm for\; }J_{\max } } \end{array} -The effect is to cause the temperature optimum of :math:`V_{c\max }` -and :math:`J_{\max }` to increase with warmer temperatures. -Additionally, the -ratio :math:`J_{\max 25} /V_{c\max 25}` at 25 :sup:`o`\ C decreases with growth temperature as +The effect is to cause the temperature optimum of :math:`V_{c\max }` and :math:`J_{\max }` to increase with warmer temperatures. Additionally, the ratio :math:`J_{\max 25} /V_{c\max 25}` at 25 :sup:`o`\ C decreases with growth temperature as .. math:: :label: 9.16 J_{\max 25} /V_{c\max 25} =2.59-0.035(T_{10} -T_{f} ). -In these acclimation functions, :math:`T_{10}` is the 10-day mean air -temperature (K) and :math:`T_{f}` is the freezing point of water (K). -For lack of data, :math:`T_{p}` acclimates similar to :math:`V_{c\max }`. Acclimation is restricted over the temperature -range :math:`T_{10} -T_{f} \ge 11`\ :sup:`o`\ C and :math:`T_{10} -T_{f} \le 35`\ :sup:`o`\ C. +In these acclimation functions, :math:`T_{10}` is the 10-day mean air temperature (K) and :math:`T_{f}` is the freezing point of water (K). For lack of data, :math:`T_{p}` acclimates similar to :math:`V_{c\max }`. Acclimation is restricted over the temperature range :math:`T_{10} -T_{f} \ge 11`\ :sup:`o`\ C and :math:`T_{10} -T_{f} \le 35`\ :sup:`o`\ C. .. _Canopy scaling: Canopy scaling -------------------------------------------- -When LUNA is on, the :math:`V_{c\max 25}` for sun leaves is scaled to the shaded leaves -:math:`J_{\max 25}` , :math:`T_{p25}` , :math:`k_{p25}`, and -:math:`R_{d25}` scale similarly. +When LUNA is on, the :math:`V_{c\max 25}` for sun leaves is scaled to the shaded leaves :math:`J_{\max 25}`, :math:`T_{p25}`, :math:`k_{p25}`, and :math:`R_{d25}` scale similarly. .. math:: :label: 9.17 @@ -418,13 +287,7 @@ When LUNA is off, scaling defaults to the mechanism used in CLM4.5. Numerical implementation ---------------------------- -The CO\ :sub:`2` partial pressure at the leaf surface, -:math:`c_{s}` (Pa), and the vapor pressure at the leaf surface, -:math:`e_{s}` (Pa), needed for the stomatal resistance model in -equation :eq:`9.1`, and the internal leaf CO\ :sub:`2` partial pressure -:math:`c_{i}` (Pa), needed for the photosynthesis model in equations :eq:`9.3`-:eq:`9.5`, -are calculated assuming there is negligible capacity to store -CO\ :sub:`2` and water vapor at the leaf surface so that +The CO\ :sub:`2` partial pressure at the leaf surface, :math:`c_{s}` (Pa), and the vapor pressure at the leaf surface, :math:`e_{s}` (Pa), needed for the stomatal resistance model in equation :eq:`9.1`, and the internal leaf CO\ :sub:`2` partial pressure :math:`c_{i}` (Pa), needed for the photosynthesis model in equations :eq:`9.3`-:eq:`9.5`, are calculated assuming there is negligible capacity to store CO\ :sub:`2` and water vapor at the leaf surface so that .. math:: :label: 9.19 @@ -438,27 +301,14 @@ and the transpiration fluxes are related as \frac{e_{a} -e_{i} }{r_{b} +r_{s} } =\frac{e_{a} -e_{s} }{r_{b} } =\frac{e_{s} -e_{i} }{r_{s} } -where :math:`r_{b}` is leaf boundary layer resistance (s -m\ :sup:`2` :math:`\mu` \ mol\ :sup:`-1`) (section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`), the -terms 1.4 and 1.6 are the ratios of diffusivity of CO\ :sub:`2` to -H\ :sub:`2`\ O for the leaf boundary layer resistance and stomatal -resistance, -:math:`c_{a} ={\rm CO}_{{\rm 2}} \left({\rm mol\; mol}^{{\rm -1}} \right)`, :math:`P_{atm}` -is the atmospheric pressure (Pa), :math:`e_{i}` is the -saturation vapor pressure (Pa) evaluated at the leaf temperature -:math:`T_{v}` , and :math:`e_{a}` is the vapor pressure of air (Pa). -The vapor pressure of air in the plant canopy :math:`e_{a}` (Pa) is -determined from +where :math:`r_{b}` is leaf boundary layer resistance (s m\ :sup:`2` :math:`\mu` \ mol\ :sup:`-1`) (section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`), the terms 1.4 and 1.6 are the ratios of diffusivity of CO\ :sub:`2` to H\ :sub:`2`\ O for the leaf boundary layer resistance and stomatal resistance, :math:`c_{a} ={\rm CO}_{{\rm 2}} \left({\rm mol\; mol}^{{\rm -1}} \right)`, :math:`P_{atm}` is the atmospheric pressure (Pa), :math:`e_{i}` is the saturation vapor pressure (Pa) evaluated at the leaf temperature :math:`T_{v}`, and :math:`e_{a}` is the vapor pressure of air (Pa). The vapor pressure of air in the plant canopy :math:`e_{a}` (Pa) is determined from .. math:: :label: 9.21 e_{a} =\frac{P_{atm} q_{s} }{0.622} -where :math:`q_{s}` is the specific humidity of canopy air (kg -kg\ :sup:`-1`, section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). -Equations :eq:`9.19` and :eq:`9.20` are solved for -:math:`c_{s}` and :math:`e_{s}` +where :math:`q_{s}` is the specific humidity of canopy air (kg kg\ :sup:`-1`, section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). Equations :eq:`9.19` and :eq:`9.20` are solved for :math:`c_{s}` and :math:`e_{s}` .. math:: :label: 9.34 @@ -470,18 +320,14 @@ Equations :eq:`9.19` and :eq:`9.20` are solved for e_{s} =\frac{e_{a} r_{s} +e_{i} r_{b} }{r_{b} +r_{s} } -In terms of conductance with -:math:`g_{s} =1/r_{s}` and :math:`g_{b} =1/r_{b}` +In terms of conductance with :math:`g_{s} =1/r_{s}` and :math:`g_{b} =1/r_{b}` .. math:: :label: 9.36 e_{s} =\frac{e_{a} g_{b} +e_{i} g_{s} }{g_{b} +g_{s} } . -Substitution of equation :eq:`9.36` into equation :eq:`9.1` gives an expression for the stomatal -resistance -(:math:`r_{s}`) as a function of photosynthesis -(:math:`A_{n}` ) +Substitution of equation :eq:`9.36` into equation :eq:`9.1` gives an expression for the stomatal resistance (:math:`r_{s}`) as a function of photosynthesis (:math:`A_{n}` ) .. math:: :label: 9.37 @@ -506,20 +352,12 @@ and D_{l} = \frac {max(e_{i} - e_{a},50)} {1000} -Stomatal conductance, as solved by equation :eq:`9.36` (mol m :sup:`-2` s :sup:`-1`), is the larger of the two roots that satisfy the -quadratic equation. Values for :math:`c_{i}` are given by +Stomatal conductance, as solved by equation :eq:`9.36` (mol m :sup:`-2` s :sup:`-1`), is the larger of the two roots that satisfy the quadratic equation. Values for :math:`c_{i}` are given by .. math:: :label: 9.40 c_{i} =c_{a} -\left(1.4r_{b} +1.6r_{s} \right)P_{atm} A{}_{n} -The equations for :math:`c_{i}` , :math:`c_{s}` , :math:`r_{s}` , and -:math:`A_{n}` are solved iteratively until :math:`c_{i}` converges. -:ref:`Sun et al. (2012)` pointed out that the CLM4 numerical approach does not -always converge. Therefore, the model uses a hybrid algorithm that -combines the secant method and Brent's method to solve for -:math:`c_{i}` . The equation set is solved separately for sunlit -(:math:`A_{n}^{sun}` , :math:`r_{s}^{sun}` ) and shaded -(:math:`A_{n}^{sha}` , :math:`r_{s}^{sha}` ) leaves. +The equations for :math:`c_{i}`, :math:`c_{s}`, :math:`r_{s}`, and :math:`A_{n}` are solved iteratively until :math:`c_{i}` converges. :ref:`Sun et al. (2012)` pointed out that the CLM4 numerical approach does not always converge. Therefore, the model uses a hybrid algorithm that combines the secant method and Brent's method to solve for :math:`c_{i}`. The equation set is solved separately for sunlit (:math:`A_{n}^{sun}`, :math:`r_{s}^{sun}` ) and shaded (:math:`A_{n}^{sha}`, :math:`r_{s}^{sha}` ) leaves. diff --git a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst index e7551f5434..232e2e93bf 100755 --- a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst +++ b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst @@ -3,20 +3,13 @@ Photosynthetic Capacity ======================= -The photosynthetic capacity is represented by two key parameters: 1) the maximum rate of carboxylation at -25 :sup:`o`\ C, :math:`V_{\text{c,max25}}`; and 2) the maximum rate of electron transport at -25 :sup:`o`\ C, :math:`J_{\text{max25}}` . They are predicted by a mechanistic model of leaf -utilization of nitrogen for assimilation (LUNA V1.0) (:ref:`Ali et al. 2016`) based on an optimality hypothesis to nitrogen allocation -among light capture, electron transport, carboxylation, respiration and storage. -Specifically, the model allocates the nitrogen by maximizing the daily -net photosynthetic carbon gain under following two key assumptions: +The photosynthetic capacity is represented by two key parameters: 1) the maximum rate of carboxylation at 25 :sup:`o`\ C, :math:`V_{\text{c,max25}}`; and 2) the maximum rate of electron transport at 25 :sup:`o`\ C, :math:`J_{\text{max25}}`. They are predicted by a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) (:ref:`Ali et al. 2016`) based on an optimality hypothesis to nitrogen allocation among light capture, electron transport, carboxylation, respiration and storage. Specifically, the model allocates the nitrogen by maximizing the daily net photosynthetic carbon gain under following two key assumptions: - nitrogen allocated for light capture, electron transport and carboxylation are co-limiting; + - respiratory nitrogen is allocated to maintain dark respiration determined by :math:`V_{\text{c,max}}`. -Compared to traditional photosynthetic capacity models, a key advantage of LUNA is that the model is able to predict the potential -acclimation of photosynthetic capacities at different environmental conditions as determined by temperature, radiation, -CO :sub:`2` concentrations, day length, and humidity. +Compared to traditional photosynthetic capacity models, a key advantage of LUNA is that the model is able to predict the potential acclimation of photosynthetic capacities at different environmental conditions as determined by temperature, radiation, CO :sub:`2` concentrations, day length, and humidity. .. _Model inputs and parameter estimations: @@ -29,18 +22,7 @@ The LUNA model includes the following four unitless parameters: - :math:`t_{c,j0}` , which defines the baseline ratio of Rubisco-limited rate to light-limited rate; - :math:`H` , which determines the response of electron transport rate to relative humidity. -The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations -located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs -are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) -including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. -The estimated values in CLM5 for the listed parameters are 0.0311, 0.1745, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated -parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist -between crops and natural vegetations due to human selection and genetic modifications, in CLM5, -the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus -still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for -:math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; -however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, -we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. +The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. The estimated values in CLM5 for the listed parameters are 0.0311, 0.1745, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist between crops and natural vegetations due to human selection and genetic modifications, in CLM5, the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for :math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. .. _Model structure: @@ -50,39 +32,28 @@ Model structure Plant Nitrogen '''''''''''''''''''''''''' -The structure of the LUNA model is adapted from :ref:`Xu et al. (2012)`, where the plant nitrogen at the leaf level ( :math:`\text{LNC}_{a}`; gN/ m :sup:`2` leaf) is divided into -four pools: structural nitrogen( :math:`N_{\text{str}}`; gN/m :sup:`2` leaf), -photosynthetic nitrogen ( :math:`N_{\text{psn}}`; gN/m :sup:`2` leaf), -storage nitrogen( :math:`N_{\text{store}}`; gN/m :sup:`2` leaf), -and respiratory nitrogen ( :math:`N_{\text{resp}}`; gN/m :sup:`2` leaf). -Namely, +The structure of the LUNA model is adapted from :ref:`Xu et al. (2012)`, where the plant nitrogen at the leaf level ( :math:`\text{LNC}_{a}`; gN/ m :sup:`2` leaf) is divided into four pools: structural nitrogen( :math:`N_{\text{str}}`; gN/m :sup:`2` leaf), photosynthetic nitrogen ( :math:`N_{\text{psn}}`; gN/m :sup:`2` leaf), storage nitrogen( :math:`N_{\text{store}}`; gN/m :sup:`2` leaf), and respiratory nitrogen ( :math:`N_{\text{resp}}`; gN/m :sup:`2` leaf). Namely, .. math:: :label: 10.1) \text{LNC}_{a} = N_{\text{psn}} + N_{\text{str}}+ N_{\text{store}} + N_{\text{resp}}. -The photosynthetic nitrogen, :math:`N_{\text{psn}}`, is further divided into -nitrogen for light capture ( :math:`N_{\text{lc}}`; gN/m :sup:`2` leaf), -nitrogen for electron transport ( :math:`N_{\text{et}}`; gN/m :sup:`2` leaf), -and nitrogen for carboxylation ( :math:`N_{\text{cb}}`; gN/m :sup:`2` leaf). -Namely, +The photosynthetic nitrogen, :math:`N_{\text{psn}}`, is further divided into nitrogen for light capture ( :math:`N_{\text{lc}}`; gN/m :sup:`2` leaf), nitrogen for electron transport ( :math:`N_{\text{et}}`; gN/m :sup:`2` leaf), and nitrogen for carboxylation ( :math:`N_{\text{cb}}`; gN/m :sup:`2` leaf). Namely, .. math:: :label: 10.2) N_{\text{psn}} =N_{\text{et}} + N_{\text{cb}} + N_{\text{lc}}. -The structural nitrogen, :math:`N_{\text{str}}`, is calculated as the -multiplication of leaf mass per unit area (:math:`\text{LMA}`; g biomass/m :sup:`2` leaf), and the structural nitrogen content (:math:`\text{SNC}`; gN/g biomass). Namely, +The structural nitrogen, :math:`N_{\text{str}}`, is calculated as the multiplication of leaf mass per unit area (:math:`\text{LMA}`; g biomass/m :sup:`2` leaf), and the structural nitrogen content (:math:`\text{SNC}`; gN/g biomass). Namely, .. math:: :label: 10.3) N_{\text{str}} = \text{SNC} \cdot \text{LMA} -where :math:`\text{SNC}` is set to be fixed at 0.002 (gN/g biomass), based on data on C:N ratio from dead wood (White etal.,2000), -and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (:math:`SLA_{\text{0}}`), a PFT-level parameter (:numref:`Table Plant functional type (PFT) leaf N parameters`). +where :math:`\text{SNC}` is set to be fixed at 0.002 (gN/g biomass), based on data on C:N ratio from dead wood (White etal.,2000), and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (:math:`SLA_{\text{0}}`), a PFT-level parameter (:numref:`Table Plant functional type (PFT) leaf N parameters`). .. _Table Plant functional type (PFT) leaf N parameters: @@ -140,14 +111,9 @@ and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (: | Switchgrass | 0.0490 | 0.2930 | +----------------------------------+--------------------------+--------------------------+ -Notes: :math:`SLA_{\text{0}}` is the specific leaf area at the canopy top (m :sup:`2` leaf/g biomass), -and :math:`N_{\text{cb}}` is the fraction of leaf nitrogen in Rubisco (g N in Rubisco g :sup:`-1` N) +Notes: :math:`SLA_{\text{0}}` is the specific leaf area at the canopy top (m :sup:`2` leaf/g biomass), and :math:`N_{\text{cb}}` is the fraction of leaf nitrogen in Rubisco (g N in Rubisco g :sup:`-1` N) -We assume that plants optimize their nitrogen allocations (i.e., :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}`) to maximize the photosynthetic carbon gain, defined as -the gross photosynthesis ( :math:`A` ) minus the maintenance respiration for -photosynthetic enzymes ( :math:`R_{\text{psn}}` ), under specific -environmental conditions and given plant's strategy of leaf nitrogen -use. Namely, the solutions of nitrogen allocations \{ :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}` \} can be estimated as follows, +We assume that plants optimize their nitrogen allocations (i.e., :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}`) to maximize the photosynthetic carbon gain, defined as the gross photosynthesis ( :math:`A` ) minus the maintenance respiration for photosynthetic enzymes ( :math:`R_{\text{psn}}` ), under specific environmental conditions and given plant's strategy of leaf nitrogen use. Namely, the solutions of nitrogen allocations \{ :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}` \} can be estimated as follows, .. math:: :label: 10.4) @@ -156,21 +122,14 @@ use. Namely, the solutions of nitrogen allocations \{ :math:`N_{\text{store}}`, \hat{\mathrm{N}}_{\text{lc}}, \hat{N}_{\text{et}}, \hat{\mathrm{N}}_{\text{cb}} \right\} = \underset{\mathrm{N}_{\text{store}}\,+\,\mathrm{N}_{\text{resp}}\,+\,\mathrm{N}_{\text{lc}}\,+\,\mathrm{N}_{\text{et}}\,+\,\mathrm{N}_{\text{cb}}\,<\text{FNC}_{\mathrm{a}}}{\text{argmax}} (A-R_{\text{psn}}), -where :math:`\text{FNC}_{a}` is the functional nitrogen content defined as the total leaf nitrogen content ( :math:`\text{LNC}_{a}`) minus the structural nitrogen content ( :math:`N_{\text{str}}` ). +where :math:`\text{FNC}_{a}` is the functional nitrogen content defined as the total leaf nitrogen content ( :math:`\text{LNC}_{a}`) minus the structural nitrogen content ( :math:`N_{\text{str}}` ). -The gross photosynthesis, :math:`A`, was calculated with a coupled leaf gas exchange model based on the :ref:`Farquhar et al. (1980)` model of -photosynthesis and Ball--Berry-type stomatal conductance model (Ball et al. 1987). The maintenance respiration for photosynthetic enzymes, :math:`R_{\text{psn}}`, is -calculated by the multiplication of total photosynthetic nitrogen ( :math:`N_{\text{psn}}` ) and the maintenance respiration cost for photosynthetic enzymes. +The gross photosynthesis, :math:`A`, was calculated with a coupled leaf gas exchange model based on the :ref:`Farquhar et al. (1980)` model of photosynthesis and Ball--Berry-type stomatal conductance model (Ball et al. 1987). The maintenance respiration for photosynthetic enzymes, :math:`R_{\text{psn}}`, is calculated by the multiplication of total photosynthetic nitrogen ( :math:`N_{\text{psn}}` ) and the maintenance respiration cost for photosynthetic enzymes. Maximum electron transport rate ''''''''''''''''''''''''''''''''' -In the LUNA model, the maximum electron transport rate -( :math:`J_{\text{max}}`; :math:`{\mu} mol` electron / m :sup:`2`/s) -is simulated to have a baseline allocation of nitrogen and additional -nitrogen allocation to change depending on the average daytime -photosynthetic active radiation (PAR; :math:`{\mu} mol` electron / m :sup:`2`/s), day length (hours) and air humidity. -Specifically, the LUNA model has +In the LUNA model, the maximum electron transport rate ( :math:`J_{\text{max}}`; :math:`{\mu} mol` electron / m :sup:`2`/s) is simulated to have a baseline allocation of nitrogen and additional nitrogen allocation to change depending on the average daytime photosynthetic active radiation (PAR; :math:`{\mu} mol` electron / m :sup:`2`/s), day length (hours) and air humidity. Specifically, the LUNA model has .. math:: :label: 10.5) @@ -186,29 +145,14 @@ The baseline electron transport rate, :math:`J_{\text{max}0}`, is calculated as J_{\text{max}0} = J_{\text{max}b0}{\text{FNC}}_{\mathrm{a}}{\text{NUE}}_{J_{\text{{max}}}} -where :math:`J_{\text{max}b0}` (unitless) is the baseline proportion of nitrogen -allocated for electron transport rate. :math:`{\text{NUE}}_{J_{\text{{max}}}}` ( :math:`{\mu} mol` electron /s/g N) -is the nitrogen use efficiency of :math:`J_{\text{{max}}}`. :math:`J_{\text{max}b1}` (unitless) is a coefficient determining the response of the electron -transport rate to amount of absorbed light (i.e., :math:`\alpha \text{PAR}`). -:math:`f\left(\text{day length} \right)` is a function specifies the impact of day -length (hours) on :math:`J_{\text{max}}` in view that longer day length has been demonstrated by previous studies to alter :math:`V_{\mathrm{c}\text{max}25}` and -:math:`J_{\text{max}25}` (Bauerle et al. 2012; Comstock and Ehleringer 1986) through photoperiod sensing and regulation (e.g., Song et al. 2013). -Following Bauerle et al. (2012), :math:`f\left(\text{day length} \right)` is simulated as follows, +where :math:`J_{\text{max}b0}` (unitless) is the baseline proportion of nitrogen allocated for electron transport rate. :math:`{\text{NUE}}_{J_{\text{{max}}}}` ( :math:`{\mu} mol` electron /s/g N) is the nitrogen use efficiency of :math:`J_{\text{{max}}}`. :math:`J_{\text{max}b1}` (unitless) is a coefficient determining the response of the electron transport rate to amount of absorbed light (i.e., :math:`\alpha \text{PAR}`). :math:`f\left(\text{day length} \right)` is a function specifies the impact of day length (hours) on :math:`J_{\text{max}}` in view that longer day length has been demonstrated by previous studies to alter :math:`V_{\mathrm{c}\text{max}25}` and :math:`J_{\text{max}25}` (Bauerle et al. 2012; Comstock and Ehleringer 1986) through photoperiod sensing and regulation (e.g., Song et al. 2013). Following Bauerle et al. (2012), :math:`f\left(\text{day length} \right)` is simulated as follows, .. math:: :label: 10.7) f\left(\text{day length} \right) = \left(\frac{\text{day length}}{12} \right)^{2}. -:math:`f\left(\text{humidity} \right)` represents the impact of air humidity on -:math:`J_{\text{{max}}}`. We assume that higher humidity leads to higher -:math:`J_{\text{{max}}}` with less water limiation on stomta opening and that low -relative humidity has a stronger impact on nitrogen allocation due to greater -water limitation. When relative humidity (RH; unitless) is too low, we assume -that plants are physiologically unable to reallocate nitrogen. We therefore -assume that there exists a critical value of relative humidity ( :math:`RH_{0} = -0.25`; unitless), below which there is no optimal nitrogen allocation. Based -on the above assumptions, we have +:math:`f\left(\text{humidity} \right)` represents the impact of air humidity on :math:`J_{\text{{max}}}`. We assume that higher humidity leads to higher :math:`J_{\text{{max}}}` with less water limiation on stomta opening and that low relative humidity has a stronger impact on nitrogen allocation due to greater water limitation. When relative humidity (RH; unitless) is too low, we assume that plants are physiologically unable to reallocate nitrogen. We therefore assume that there exists a critical value of relative humidity ( :math:`RH_{0} = 0.25`; unitless), below which there is no optimal nitrogen allocation. Based on the above assumptions, we have .. math:: :label: 10.8) @@ -219,20 +163,14 @@ on the above assumptions, we have where :math:`H` (unitless) specifies the impact of relative humidity on electron transport rate. -The efficiency of light energy absorption (unitless), :math:`\alpha`, is calculated -depending on the amount of nitrogen allocated for light capture, -:math:`\mathrm{N}_{\text{lc}}`. Following Niinemets and Tenhunen (1997), the LUNA model has, +The efficiency of light energy absorption (unitless), :math:`\alpha`, is calculated depending on the amount of nitrogen allocated for light capture, :math:`\mathrm{N}_{\text{lc}}`. Following Niinemets and Tenhunen (1997), the LUNA model has, .. math:: :label: 10.9) \alpha =\frac{0.292}{1+\frac{0.076}{\mathrm{N}_{\text{lc}}C_{b}}} -where 0.292 is the conversion factor from photon to electron. :math:`C_{b}` -is the conversion factor (1.78) from nitrogen to chlorophyll. After we -estimate :math:`J_{\text{{max}}}`, the actual electron transport rate with -the daily maximum radiation ( :math:`J_{x}`) can be calculated using the -empirical expression of leaf (1937), +where 0.292 is the conversion factor from photon to electron. :math:`C_{b}` is the conversion factor (1.78) from nitrogen to chlorophyll. After we estimate :math:`J_{\text{{max}}}`, the actual electron transport rate with the daily maximum radiation ( :math:`J_{x}`) can be calculated using the empirical expression of leaf (1937), .. math:: :label: 10.10) @@ -240,58 +178,40 @@ empirical expression of leaf (1937), J_{x} = \frac{\alpha \text{PAR}_{\text{max}}} {\left(1 + \frac{\alpha^{2}{\text{PAR}}_{\text{{max}}}^{2}}{J_{\text{{max}}}^{2}} \right)^{0.5}} -where :math:`\text{PAR}_{\text{{max}}}` ( :math:`\mu mol`/m :sup:`2`/s) is the -maximum photosynthetically active radiation during the day. +where :math:`\text{PAR}_{\text{{max}}}` ( :math:`\mu mol`/m :sup:`2`/s) is the maximum photosynthetically active radiation during the day. Maximum rate of carboxylation '''''''''''''''''''''''''''''' -The maximum rate of carboxylation at 25\ :sup:`o`\ C varies with -foliage nitrogen concentration and specific leaf area and is calculated -as in :ref:`Thornton and Zimmermann (2007)`. At 25ºC, +The maximum rate of carboxylation at 25\ :sup:`o`\ C varies with foliage nitrogen concentration and specific leaf area and is calculated as in :ref:`Thornton and Zimmermann (2007)`. At 25ºC, .. math:: :label: 10.11) V_{c\max 25} = N_{cb} NUE_{V_{c\max 25}} -where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, -:numref:`Table Plant functional type (PFT) leaf N parameters`), -and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. -The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) -measured at 25\ :sup:`o`\ C, and the constant 6.25 is the nitrogen binding factor for Rubisco -(g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). +where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, :numref:`Table Plant functional type (PFT) leaf N parameters`), and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) measured at 25\ :sup:`o`\ C, and the constant 6.25 is the nitrogen binding factor for Rubisco (g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). -:math:`V_{c\max 25}` additionally varies with daylength (:math:`DYL`) -using the function :math:`f(DYL)`, which introduces seasonal variation -to :math:`V_{c\max }` +:math:`V_{c\max 25}` additionally varies with daylength (:math:`DYL`) using the function :math:`f(DYL)`, which introduces seasonal variation to :math:`V_{c\max }` .. math:: :label: 10.12) f\left(DYL\right)=\frac{\left(DYL\right)^{2} }{\left(DYL_{\max } \right)^{2} } -with :math:`0.01\le f\left(DYL\right)\le 1`. Daylength (seconds) is -given by +with :math:`0.01\le f\left(DYL\right)\le 1`. Daylength (seconds) is given by .. math:: :label: 10.13) DYL=2\times 13750.9871\cos ^{-1} \left[\frac{-\sin \left(lat\right)\sin \left(decl\right)}{\cos \left(lat\right)\cos \left(decl\right)} \right] -where :math:`lat` (latitude) and :math:`decl` (declination angle) are -from section :numref:`Solar Zenith Angle`. Maximum daylength (:math:`DYL_{\max }` ) is calculated -similarly but using the maximum declination angle for present-day -orbital geometry (:math:`\pm`\ 23.4667º [:math:`\pm`\ 0.409571 radians], -positive for Northern Hemisphere latitudes and negative for Southern -Hemisphere). +where :math:`lat` (latitude) and :math:`decl` (declination angle) are from section :numref:`Solar Zenith Angle`. Maximum daylength (:math:`DYL_{\max }` ) is calculated similarly but using the maximum declination angle for present-day orbital geometry (:math:`\pm`\ 23.4667º [:math:`\pm`\ 0.409571 radians], positive for Northern Hemisphere latitudes and negative for Southern Hemisphere). Implementation of Photosynthetic Capacity '''''''''''''''''''''''''''''''''''''''''' -Based on :ref:`Farquhar et al. (1980)` and Wullschleger (1993), we can calculate the -electron-limited photosynthetic rate under daily maximum radiation ( :math:`W_{jx}`) -and the Rubisco-limited photosynthetic rate ( :math:`W_{\mathrm{c}}`) as follows, +Based on :ref:`Farquhar et al. (1980)` and Wullschleger (1993), we can calculate the electron-limited photosynthetic rate under daily maximum radiation ( :math:`W_{jx}`) and the Rubisco-limited photosynthetic rate ( :math:`W_{\mathrm{c}}`) as follows, .. math:: :label: 10.14) @@ -303,29 +223,19 @@ and the Rubisco-limited photosynthetic rate ( :math:`W_{\mathrm{c}}`) as follows W_{\mathrm{c}} = K_{\mathrm{c}} V_{{\mathrm{c}, \text{max}}}, -where :math:`K_{j}` and :math:`K_{\mathrm{c}}` as the conversion factors for -:math:`J_{x}` and :math:`V_{{\mathrm{c}, \text{max}}}` ( :math:`V_{{\mathrm{c}, \text{max}}}` to -:math:`W_{\mathrm{c}}` and :math:`J_{x}` to :math:`W_{J_{x}}`), respectively. Based on -:ref:`Xu et al. (2012)`, Maire et al. (2012) and Walker et al. (2014), we -assume that :math:`W_{\mathrm{c}}` is proportional to -:math:`W_{J_{x}}`. Specifically, we have +where :math:`K_{j}` and :math:`K_{\mathrm{c}}` as the conversion factors for :math:`J_{x}` and :math:`V_{{\mathrm{c}, \text{max}}}` ( :math:`V_{{\mathrm{c}, \text{max}}}` to :math:`W_{\mathrm{c}}` and :math:`J_{x}` to :math:`W_{J_{x}}`), respectively. Based on :ref:`Xu et al. (2012)`, Maire et al. (2012) and Walker et al. (2014), we assume that :math:`W_{\mathrm{c}}` is proportional to :math:`W_{J_{x}}`. Specifically, we have .. math:: :label: 10.16) W_{\mathrm{c}}=t_{\alpha}t_{\mathrm{c}, j0}W_{J_{x}} -where :math:`t_{\mathrm{c}, j0}` is the baseline ratio of :math:`W_{\mathrm{c}}` to -:math:`W_{J_{x}}`. We recognize that this ratio may change depending on the -nitrogen use efficiency of carboxylation and electron transport (Ainsworth and Rogers 2007), -therefore the LUNA model has the modification factor, :math:`t_{\alpha}`, to adjust baseline -the ratio depending on the nitrogen use efficiency for electron vs carboxylation (:ref:`Ali et al. 2016`). +where :math:`t_{\mathrm{c}, j0}` is the baseline ratio of :math:`W_{\mathrm{c}}` to :math:`W_{J_{x}}`. We recognize that this ratio may change depending on the nitrogen use efficiency of carboxylation and electron transport (Ainsworth and Rogers 2007), therefore the LUNA model has the modification factor, :math:`t_{\alpha}`, to adjust baseline the ratio depending on the nitrogen use efficiency for electron vs carboxylation (:ref:`Ali et al. 2016`). Total Respiration ''''''''''''''''''' -Following :ref:`Collatz et al. (1991)`, the total respiration ( :math:`R_{\mathrm{t}}`) is -calculated in proportion to :math:`V_{\text{c,max}}`, +Following :ref:`Collatz et al. (1991)`, the total respiration ( :math:`R_{\mathrm{t}}`) is calculated in proportion to :math:`V_{\text{c,max}}`, .. math:: :label: 10.17) @@ -339,19 +249,11 @@ Accounting for the daytime and nighttime temperature, the daily respirations is R_{\text{td}}={R}_{\mathrm{t}} [D_{\text{day}} + D_{\text{night}} f_{\mathrm{r}}{(T_{\text{night}})/f_{\mathrm{r}}{(T_{\text{day}})}}], -where :math:`D_{\text{day}}` and :math:`D_{\text{night}}` are daytime and -nighttime durations in seconds. :math:`f_{\mathrm{r}}(T_{\text{night}})` and -:math:`f_{\mathrm{r}}(T_{\text{day}})` are the temperature response functions for -respiration (see Appendix B in :ref:`Ali et al. (2016)` for details). +where :math:`D_{\text{day}}` and :math:`D_{\text{night}}` are daytime and nighttime durations in seconds. :math:`f_{\mathrm{r}}(T_{\text{night}})` and :math:`f_{\mathrm{r}}(T_{\text{day}})` are the temperature response functions for respiration (see Appendix B in :ref:`Ali et al. (2016)` for details). .. _Numerical scheme: Numerical scheme --------------------------------------------------------- -The LUNA model searches for the "optimal" nitrogen allocations for maximum net photosynthetic carbon gain -by incrementally increase the nitrogen allocated for light capture (i.e., :math:`N_{\text{lc}}`) (see :ref:`Ali et al. (2016)` for details). -We assume that plants only optimize the nitrogen allocation when they can grow (i.e., GPP>0.0). -If GPP become zero under stress, then the LUNA model assume a certain amount of enzyme will decay at daily rates of 0.1, -in view that the half-life time for photosynthetic enzymes are short (~7 days) (Suzuki et al. 2001). -To avoid unrealistic low values of photosynthetic capacity, the decay is only limited to 50 percent of the original enzyme levels. +The LUNA model searches for the "optimal" nitrogen allocations for maximum net photosynthetic carbon gain by incrementally increase the nitrogen allocated for light capture (i.e., :math:`N_{\text{lc}}`) (see :ref:`Ali et al. (2016)` for details). We assume that plants only optimize the nitrogen allocation when they can grow (i.e., GPP>0.0). If GPP become zero under stress, then the LUNA model assume a certain amount of enzyme will decay at daily rates of 0.1, in view that the half-life time for photosynthetic enzymes are short (~7 days) (Suzuki et al. 2001). To avoid unrealistic low values of photosynthetic capacity, the decay is only limited to 50 percent of the original enzyme levels. diff --git a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst index e824ff6c77..18a4fe1fdc 100644 --- a/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst +++ b/doc/source/tech_note/Plant_Hydraulics/CLM50_Tech_Note_Plant_Hydraulics.rst @@ -13,8 +13,7 @@ Roots Vertical Root Distribution --------------------------- -The root fraction :math:`r_{i}` in each soil layer depends on the plant -functional type +The root fraction :math:`r_{i}` in each soil layer depends on the plant functional type .. math:: :label: 11.1 @@ -24,12 +23,7 @@ functional type \left(\beta^{z_{h,\, i-1} \cdot 100} - \beta^{z_{h,\, i} \cdot 100} \right) & \qquad {\rm for\; }1 \le i \le N_{levsoi} \end{array} -where :math:`z_{h,\, i}` (m) is the depth from the soil surface to the -interface between layers :math:`i` and :math:`i+1` (:math:`z_{h,\, 0}` , -the soil surface) (section :numref:`Vertical Discretization`), the factor of 100 -converts from m to cm, and :math:`\beta` is a plant-dependent root -distribution parameter adopted from :ref:`Jackson et al. (1996)` -(:numref:`Table Plant functional type root distribution parameters`). +where :math:`z_{h,\, i}` (m) is the depth from the soil surface to the interface between layers :math:`i` and :math:`i+1` (:math:`z_{h,\, 0}`, the soil surface) (section :numref:`Vertical Discretization`), the factor of 100 converts from m to cm, and :math:`\beta` is a plant-dependent root distribution parameter adopted from :ref:`Jackson et al. (1996)` (:numref:`Table Plant functional type root distribution parameters`). .. rootfr(p,lev) = ( & beta ** (col%zi(c,lev-1)*m_to_cm) - & @@ -107,11 +101,7 @@ distribution parameter adopted from :ref:`Jackson et al. (1996) Root Spacing ----------------------------- -To determine the conductance along the soil to root pathway (section -:numref:`Soil-to-root`) an estimate of the spacing between the roots within -a soil layer is required. The distance between roots :math:`dx_{root,i}` (m) -is calculated by assuming that roots are distributed uniformly throughout -the soil (:ref:`Gardner 1960`) +To determine the conductance along the soil to root pathway (section :numref:`Soil-to-root`) an estimate of the spacing between the roots within a soil layer is required. The distance between roots :math:`dx_{root,i}` (m) is calculated by assuming that roots are distributed uniformly throughout the soil (:ref:`Gardner 1960`) .. math:: :label: 11.12 @@ -132,11 +122,9 @@ where :math:`L_{i}` is the root length density (m m :sup:`-3`) B_{root,i} = \frac{c\_to\_b \cdot C_{fineroot} \cdot r_{i}}{dz_{i}} -where :math:`c\_to\_b = 2` (kg biomass kg carbon :sup:`-1`) and -:math:`C_{fineroot}` is the amount of fine root carbon (kg m :sup:`-2`). +where :math:`c\_to\_b = 2` (kg biomass kg carbon :sup:`-1`) and :math:`C_{fineroot}` is the amount of fine root carbon (kg m :sup:`-2`). -:math:`\rho_{root}` is the root density (kg m :sup:`-3`), and -:math:`{CA}_{root}` is the fine root cross sectional area (m :sup:`2`) +:math:`\rho_{root}` is the root density (kg m :sup:`-3`), and :math:`{CA}_{root}` is the fine root cross sectional area (m :sup:`2`) .. math:: :label: 11.15 @@ -150,20 +138,9 @@ where :math:`r_{root}` is the root radius (m). Plant Hydraulic Stress ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The Plant Hydraulic Stress (PHS) routine explicitly models water transport -through the vegetation according to a simple hydraulic framework following -Darcy's Law for porous media flow equations influenced by -:ref:`Bonan et al. (2014) `, -:ref:`Chuang et al. (2006) `, -:ref:`Sperry et al. (1998) `, -:ref:`Sperry and Love (2015) `, -:ref:`Williams et al (1996) `. - -PHS solves for the vegetation water potential that matches water supply with -transpiration demand. Water supply is modeled according to the circuit analog -in :numref:`Figure Plant hydraulic circuit`. Transpiration demand is modeled -relative to maximum transpiration by a transpiration loss function dependent -on leaf water potential. +The Plant Hydraulic Stress (PHS) routine explicitly models water transport through the vegetation according to a simple hydraulic framework following Darcy's Law for porous media flow equations influenced by :ref:`Bonan et al. (2014) `, :ref:`Chuang et al. (2006) `, :ref:`Sperry et al. (1998) `, :ref:`Sperry and Love (2015) `, :ref:`Williams et al (1996) `. + +PHS solves for the vegetation water potential that matches water supply with transpiration demand. Water supply is modeled according to the circuit analog in :numref:`Figure Plant hydraulic circuit`. Transpiration demand is modeled relative to maximum transpiration by a transpiration loss function dependent on leaf water potential. .. _Figure Plant hydraulic circuit: @@ -176,38 +153,20 @@ on leaf water potential. Plant Water Supply ----------------------- -The supply equations are used to solve for vegetation water potential forced -by transpiration demand and the set of layer-by-layer soil water potentials. -The water supply is discretized into segments: soil-to-root, root-to-stem, and -stem-to-leaf. There are typically several (1-49) soil-to-root flows operating -in parallel, one per soil layer. There are two stem-to-leaf flows operating in -parallel, corresponding to the sunlit and shaded "leaves". +The supply equations are used to solve for vegetation water potential forced by transpiration demand and the set of layer-by-layer soil water potentials. The water supply is discretized into segments: soil-to-root, root-to-stem, and stem-to-leaf. There are typically several (1-49) soil-to-root flows operating in parallel, one per soil layer. There are two stem-to-leaf flows operating in parallel, corresponding to the sunlit and shaded "leaves". -In general the water fluxes (e.g. soil-to-root, root-to-stem, etc.) are -modeled according to Darcy's Law for porous media flow as: +In general the water fluxes (e.g. soil-to-root, root-to-stem, etc.) are modeled according to Darcy's Law for porous media flow as: .. math:: :label: 11.101 q = kA\left( \psi_1 - \psi_2 \right) -:math:`q` is the flux of water (mmH\ :sub:`2`\ O/s) spanning the segment -between :math:`\psi_1` and :math:`\psi_2` +:math:`q` is the flux of water (mmH\ :sub:`2`\ O/s) spanning the segment between :math:`\psi_1` and :math:`\psi_2` :math:`k` is the hydraulic conductance (s\ :sup:`-1`\ ) -:math:`A` is the area basis (m\ :sup:`2`\ /m\ :sup:`2`\ ) relating the -conducting area basis to ground area - -:math:`\psi_1 - \psi_2` is the gradient in water potential (mmH\ :sub:`2`\ O) -across the segment - -The segments in :numref:`Figure Plant hydraulic circuit` have variable resistance, -as the water potentials become lower, hydraulic conductance decreases. This is -captured by multiplying the maximum segment conductance by a sigmoidal function -capturing the percent loss of conductivity. The function uses two parameters to -fit experimental vulnerability curves: the water potential at 50% loss of -conductivity (:math:`p50`) and a shape fitting parameter (:math:`c_k`). +:math:`A` is the area basis (m\ :sup:`2`\ /m\ :sup:`2`\ ) relating the conducting area basis to ground area :math:`\psi_1 - \psi_2` is the gradient in water potential (mmH\ :sub:`2`\ O) across the segment The segments in :numref:`Figure Plant hydraulic circuit` have variable resistance, as the water potentials become lower, hydraulic conductance decreases. This is captured by multiplying the maximum segment conductance by a sigmoidal function capturing the percent loss of conductivity. The function uses two parameters to fit experimental vulnerability curves: the water potential at 50% loss of conductivity (:math:`p50`) and a shape fitting parameter (:math:`c_k`). .. math:: :label: 11.102 @@ -225,21 +184,7 @@ conductivity (:math:`p50`) and a shape fitting parameter (:math:`c_k`). Stem-to-leaf '''''''''''''''''''''''' -The area basis and conductance parameterization varies by segment. There -are two stem-to-leaf fluxes in parallel, from stem to sunlit leaf and from -stem to shaded leaf (:math:`q_{1a}` and :math:`q_{1a}`). The water flux from -stem-to-leaf is the product of the segment conductance, the conducting area -basis, and the water potential gradient from stem to leaf. Stem-to-leaf -conductance is defined as the maximum conductance multiplied by the percent -of maximum conductance, as calculated by the sigmoidal vulnerability curve. -The maximum conductance is a PFT parameter representing the maximum -conductance of water from stem to leaf per unit leaf area. This parameter -can be defined separately for sunlit and shaded segments and should already -include the appropriate length scaling (in other words this is a conductance, -not conductivity). The water potential gradient is the difference between -leaf water potential and stem water potential. There is no gravity term, -assuming a negligible difference in height across the segment. The area -basis is the leaf area index (either sunlit or shaded). +The area basis and conductance parameterization varies by segment. There are two stem-to-leaf fluxes in parallel, from stem to sunlit leaf and from stem to shaded leaf (:math:`q_{1a}` and :math:`q_{1a}`). The water flux from stem-to-leaf is the product of the segment conductance, the conducting area basis, and the water potential gradient from stem to leaf. Stem-to-leaf conductance is defined as the maximum conductance multiplied by the percent of maximum conductance, as calculated by the sigmoidal vulnerability curve. The maximum conductance is a PFT parameter representing the maximum conductance of water from stem to leaf per unit leaf area. This parameter can be defined separately for sunlit and shaded segments and should already include the appropriate length scaling (in other words this is a conductance, not conductivity). The water potential gradient is the difference between leaf water potential and stem water potential. There is no gravity term, assuming a negligible difference in height across the segment. The area basis is the leaf area index (either sunlit or shaded). .. math:: :label: 11.103 @@ -292,18 +237,7 @@ Parameters: Root-to-stem '''''''''''''''''''''''' -There is one root-to-stem flux. This represents a flux from the root collar -to the upper branch reaches. The water flux from root-to-stem is the product -of the segment conductance, the conducting area basis, and the water -potential gradient from root to stem. Root-to-stem conductance is defined -as the maximum conductance multiplied by the percent of maximum conductance, -as calculated by the sigmoidal vulnerability curve (two parameters). The -maximum conductance is defined as the maximum root-to-stem conductivity per -unit stem area (PFT parameter) divided by the length of the conducting path, -which is taken to be the vegetation height. The area basis is the stem area -index. The gradient in water potential is the difference between the root -water potential and the stem water potential less the difference in -gravitational potential. +There is one root-to-stem flux. This represents a flux from the root collar to the upper branch reaches. The water flux from root-to-stem is the product of the segment conductance, the conducting area basis, and the water potential gradient from root to stem. Root-to-stem conductance is defined as the maximum conductance multiplied by the percent of maximum conductance, as calculated by the sigmoidal vulnerability curve (two parameters). The maximum conductance is defined as the maximum root-to-stem conductivity per unit stem area (PFT parameter) divided by the length of the conducting path, which is taken to be the vegetation height. The area basis is the stem area index. The gradient in water potential is the difference between the root water potential and the stem water potential less the difference in gravitational potential. .. math:: :label: 11.107 @@ -340,38 +274,13 @@ Parameters: Soil-to-root '''''''''''''''''''''''' -There are several soil-to-root fluxes operating in parallel (one for each -root-containing soil layer). Each represents a flux from the given soil -layer to the root collar. The water flux from soil-to-root is the product -of the segment conductance, the conducting area basis, and the water -potential gradient from soil to root. The area basis is a proxy for root -area index, defined as the summed leaf and stem area index multiplied by -the root-to-shoot ratio (PFT parameter) multiplied by the layer root -fraction. The root fraction comes from an empirical root profile (section -:numref:`Vertical Root Distribution`). - -The gradient in water potential is the difference between the soil water -potential and the root water potential less the difference in gravitational -potential. There is only one root water potential to which all soil layers -are connected in parallel. A soil-to-root flux can be either positive -(vegetation water uptake) or negative (water deposition), depending on the -relative values of the root and soil water potentials. This allows for the -occurrence of hydraulic redistribution where water moves through vegetation -tissue from one soil layer to another. - -Soil-to-root conductance is the result of two resistances in series, first -across the soil-root interface and then through the root tissue. The root -tissue conductance is defined as the maximum conductance multiplied by the -percent of maximum conductance, as calculated by the sigmoidal vulnerability -curve. The maximum conductance is defined as the maximum root-tissue -conductivity (PFT parameter) divided by the length of the conducting path, -which is taken to be the soil layer depth plus lateral root length. - -The soil-root interface conductance is defined as the soil conductivity -divided by the conducting length from soil to root. The soil conductivity -varies by soil layer and is calculated based on soil potential and soil -properties, via the Brooks-Corey theory. The conducting length is determined -from the characteristic root spacing (section :numref:`Root Spacing`). +There are several soil-to-root fluxes operating in parallel (one for each root-containing soil layer). Each represents a flux from the given soil layer to the root collar. The water flux from soil-to-root is the product of the segment conductance, the conducting area basis, and the water potential gradient from soil to root. The area basis is a proxy for root area index, defined as the summed leaf and stem area index multiplied by the root-to-shoot ratio (PFT parameter) multiplied by the layer root fraction. The root fraction comes from an empirical root profile (section :numref:`Vertical Root Distribution`). + +The gradient in water potential is the difference between the soil water potential and the root water potential less the difference in gravitational potential. There is only one root water potential to which all soil layers are connected in parallel. A soil-to-root flux can be either positive (vegetation water uptake) or negative (water deposition), depending on the relative values of the root and soil water potentials. This allows for the occurrence of hydraulic redistribution where water moves through vegetation tissue from one soil layer to another. + +Soil-to-root conductance is the result of two resistances in series, first across the soil-root interface and then through the root tissue. The root tissue conductance is defined as the maximum conductance multiplied by the percent of maximum conductance, as calculated by the sigmoidal vulnerability curve. The maximum conductance is defined as the maximum root-tissue conductivity (PFT parameter) divided by the length of the conducting path, which is taken to be the soil layer depth plus lateral root length. + +The soil-root interface conductance is defined as the soil conductivity divided by the conducting length from soil to root. The soil conductivity varies by soil layer and is calculated based on soil potential and soil properties, via the Brooks-Corey theory. The conducting length is determined from the characteristic root spacing (section :numref:`Root Spacing`). .. math:: :label: 11.109 @@ -431,15 +340,7 @@ Parameters: Plant Water Demand ----------------------- -Plant water demand depends on stomatal conductance, which is described in section :numref:`Stomatal resistance`. -Here we describe the influence of PHS and the coupling of vegetation water demand and supply. -PHS models vegetation water demand as transpiration attenuated by a transpiration loss function based on leaf water potential. -Sunlit leaf transpiration is modeled as the maximum sunlit leaf transpiration multiplied by the percent of maximum transpiration as modeled by the sigmoidal loss function. -The same follows for shaded leaf transpiration. -Maximum stomatal conductance is calculated from the Medlyn model :ref:`(Medlyn et al. 2011) ` absent water stress and used to calculate the maximum transpiration (see section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). -Water stress is calculated as the ratio of attenuated stomatal conductance to maximum stomatal conductance. -Water stress is calculated with distinct values for sunlit and shaded leaves. -Vegetation water stress is calculated based on leaf water potential and is used to attenuate photosynthesis (see section :numref:`Photosynthesis`) +Plant water demand depends on stomatal conductance, which is described in section :numref:`Stomatal resistance`. Here we describe the influence of PHS and the coupling of vegetation water demand and supply. PHS models vegetation water demand as transpiration attenuated by a transpiration loss function based on leaf water potential. Sunlit leaf transpiration is modeled as the maximum sunlit leaf transpiration multiplied by the percent of maximum transpiration as modeled by the sigmoidal loss function. The same follows for shaded leaf transpiration. Maximum stomatal conductance is calculated from the Medlyn model :ref:`(Medlyn et al. 2011) ` absent water stress and used to calculate the maximum transpiration (see section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). Water stress is calculated as the ratio of attenuated stomatal conductance to maximum stomatal conductance. Water stress is calculated with distinct values for sunlit and shaded leaves. Vegetation water stress is calculated based on leaf water potential and is used to attenuate photosynthesis (see section :numref:`Photosynthesis`) .. math:: :label: 11.201 @@ -515,13 +416,7 @@ PHS finds the water potentials that match supply and demand. In the plant water Numerical Implementation -------------------------------- -The four plant water potential nodes are ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`). -The fluxes between each pair of nodes are labeled in Figure 1. -:math:`E_{sun}` and :math:`E_{sha}` are the transpiration from sunlit and shaded leaves, respectively. -We use the circuit-analog model to calculate the vegetation water potential ( :math:`\psi`) for the four plant nodes, forced by soil matric potential and unstressed transpiration. -The unstressed transpiration is acquired by running the photosynthesis model with :math:`\beta_t=1`. -The unstressed transpiration flux is attenuated based on the leaf-level vegetation water potential. -Using the attenuated transpiration, we solve for :math:`g_{s,stressed}` and output :math:`\beta_t=\dfrac{g_{s,stressed}}{g_{s,unstressed}}`. +The four plant water potential nodes are ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`). The fluxes between each pair of nodes are labeled in Figure 1. :math:`E_{sun}` and :math:`E_{sha}` are the transpiration from sunlit and shaded leaves, respectively. We use the circuit-analog model to calculate the vegetation water potential ( :math:`\psi`) for the four plant nodes, forced by soil matric potential and unstressed transpiration. The unstressed transpiration is acquired by running the photosynthesis model with :math:`\beta_t=1`. The unstressed transpiration flux is attenuated based on the leaf-level vegetation water potential. Using the attenuated transpiration, we solve for :math:`g_{s,stressed}` and output :math:`\beta_t=\dfrac{g_{s,stressed}}{g_{s,unstressed}}`. The continuity of water flow through the system yields four equations @@ -544,8 +439,7 @@ We seek the set of vegetation water potential values, \psi_{sunleaf}\cr\psi_{shadeleaf}\cr\psi_{stem}\cr\psi_{root} \end {array} \right] -that satisfies these equations, as forced by the soil moisture and atmospheric state. -Each flux on the schematic can be represented in terms of the relevant water potentials. Defining the transpiration fluxes: +that satisfies these equations, as forced by the soil moisture and atmospheric state. Each flux on the schematic can be represented in terms of the relevant water potentials. Defining the transpiration fluxes: .. math:: :label: 11.403 @@ -567,11 +461,7 @@ Defining the water supply fluxes: q_{soil}&=\sum_{i=1}^{nlevsoi}{q_{3,i}}=\sum_{i=1}^{nlevsoi}{k_{3,i}\cdot RAI\cdot\left(\psi_{soil,i}-\psi_{root} + \Delta\psi_{z,i} \right)} \end{aligned} -We're looking to find the vector :math:`\psi` -that fits with soil and atmospheric forcings while satisfying water flow continuity. -Due to the model non-linearity, we use a linearized explicit approach, iterating with Newton's method. -The initial guess is the solution for :math:`\psi` (vector) from the previous time step. -The general framework, from iteration `m` to `m+1` is: +We're looking to find the vector :math:`\psi` that fits with soil and atmospheric forcings while satisfying water flow continuity. Due to the model non-linearity, we use a linearized explicit approach, iterating with Newton's method. The initial guess is the solution for :math:`\psi` (vector) from the previous time step. The general framework, from iteration `m` to `m+1` is: .. math:: :label: 11.405 @@ -682,8 +572,7 @@ Now we compute all the entries for :math:`A` and :math:`b` based on the soil moi \psi_{m+1}=\psi_m+\Delta\psi -We iterate until :math:`b\to 0`, signifying water flux balance through the system. The result is a final set of water potentials ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`) satisfying non-divergent water flux through the system. -The magnitude of the water flux is driven by soil matric potential and unstressed ( :math:`\beta_t=1`) transpiration. +We iterate until :math:`b\to 0`, signifying water flux balance through the system. The result is a final set of water potentials ( :math:`\psi_{root}`, :math:`\psi_{xylem}`, :math:`\psi_{shadeleaf}`, :math:`\psi_{sunleaf}`) satisfying non-divergent water flux through the system. The magnitude of the water flux is driven by soil matric potential and unstressed ( :math:`\beta_t=1`) transpiration. We use the transpiration solution (corresponding to the final solution for :math:`\psi`) to compute stomatal conductance. The stomatal conductance is then used to compute :math:`\beta_t`. @@ -697,25 +586,16 @@ We use the transpiration solution (corresponding to the final solution for :math \beta_{t,shade} = \dfrac{g_{s,shade}}{g_{s,shade,\beta_t=1}} -The :math:`\beta_t` values are used in the Photosynthesis module (see section :numref:`Photosynthesis`) to apply water stress. -The solution for :math:`\psi` is saved as a new variable (vegetation water potential) and is indicative of plant water status. -The soil-to-root fluxes :math:`\left( q_{3,1},q_{3,2},\mbox{...},q_{3,n}\right)` are used as the soil transpiration sink in the Richards' equation subsurface flow equations (see section :numref:`Soil Water`). +The :math:`\beta_t` values are used in the Photosynthesis module (see section :numref:`Photosynthesis`) to apply water stress. The solution for :math:`\psi` is saved as a new variable (vegetation water potential) and is indicative of plant water status. The soil-to-root fluxes :math:`\left( q_{3,1},q_{3,2},\mbox{...},q_{3,n}\right)` are used as the soil transpiration sink in the Richards' equation subsurface flow equations (see section :numref:`Soil Water`). .. _Flow Diagram of Leaf Flux Calculations: Flow Diagram of Leaf Flux Calculations: ------------------------------------------- -PHS runs nested in the loop that solves for sensible and latent heat fluxes and temperature for vegetated surfaces (see section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). -The scheme iterates for convergence of leaf temperature (:math:`T_l`), transpiration water stress (:math:`\beta_t`), and intercellular CO2 concentration (:math:`c_i`). -PHS is forced by maximum transpiration (absent water stress, :math:`\beta_t=1`), whereby we first solve for assimilation, stomatal conductance, and intercellular CO2 with :math:`\beta_{t,sun}` and :math:`\beta_{t,shade}` both set to 1. -This involves iterating to convergence of :math:`c_i` (see section :numref:`Photosynthesis`). +PHS runs nested in the loop that solves for sensible and latent heat fluxes and temperature for vegetated surfaces (see section :numref:`Sensible and Latent Heat Fluxes and Temperature for Vegetated Surfaces`). The scheme iterates for convergence of leaf temperature (:math:`T_l`), transpiration water stress (:math:`\beta_t`), and intercellular CO2 concentration (:math:`c_i`). PHS is forced by maximum transpiration (absent water stress, :math:`\beta_t=1`), whereby we first solve for assimilation, stomatal conductance, and intercellular CO2 with :math:`\beta_{t,sun}` and :math:`\beta_{t,shade}` both set to 1. This involves iterating to convergence of :math:`c_i` (see section :numref:`Photosynthesis`). -Next, using the solutions for :math:`E_{sun,max}` and :math:`E_{shade,max}`, PHS solves for :math:`\psi`, :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}`. -The values for :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}` are inputs to the photosynthesis routine, which now solves for attenuated photosynthesis and stomatal conductance (reflecting water stress). -Again this involves iterating to convergence of :math:`c_i`. -Non-linearities between :math:`\beta_t` and transpiration require also iterating to convergence of :math:`\beta_t`. -The outermost level of iteration works towards convergence of leaf temperature, reflecting leaf surface energy balance. +Next, using the solutions for :math:`E_{sun,max}` and :math:`E_{shade,max}`, PHS solves for :math:`\psi`, :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}`. The values for :math:`\beta_{t,sun}`, and :math:`\beta_{t,shade}` are inputs to the photosynthesis routine, which now solves for attenuated photosynthesis and stomatal conductance (reflecting water stress). Again this involves iterating to convergence of :math:`c_i`. Non-linearities between :math:`\beta_t` and transpiration require also iterating to convergence of :math:`\beta_t`. The outermost level of iteration works towards convergence of leaf temperature, reflecting leaf surface energy balance. .. _Figure PHS Flow Diagram: diff --git a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst index 5778aeb957..a60b6000b5 100644 --- a/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst +++ b/doc/source/tech_note/Plant_Mortality/CLM50_Tech_Note_Plant_Mortality.rst @@ -3,34 +3,12 @@ Plant Mortality =================== -Plant mortality as described here applies to perennial vegetation types, -and is intended to represent the death of individuals from a stand of -plants due to the aggregate of processes such as wind throw, insect -attack, disease, extreme temperatures or drought, and age-related -decline in vigor. These processes are referred to in aggregate as -"gap-phase" mortality. Mortality due to fire and anthropogenic land -cover change are treated separately (see Chapters :numref:`rst_Fire` and :numref:`rst_Transient Landcover Change`, -respectively). +Plant mortality as described here applies to perennial vegetation types, and is intended to represent the death of individuals from a stand of plants due to the aggregate of processes such as wind throw, insect attack, disease, extreme temperatures or drought, and age-related decline in vigor. These processes are referred to in aggregate as "gap-phase" mortality. Mortality due to fire and anthropogenic land cover change are treated separately (see Chapters :numref:`rst_Fire` and :numref:`rst_Transient Landcover Change`, respectively). Mortality Fluxes Leaving Vegetation Pools ---------------------------------------------- -Whole-plant mortality is parameterized very simply, assuming a mortality -rate of 2% yr\ :sup:`-1` for all vegetation types. This is clearly -a gross oversimplification of an important process, and additional work -is required to better constrain this process in different climate zones -(:ref:`Keller et al. 2004`; :ref:`Sollins 1982`), for different species mixtures -(:ref:`Gomes et al. 2003`), and for different size and age classes (:ref:`Busing -2005`; :ref:`Law et al. 2003`). Literature values for forest mortality rates -range from at least 0.7% to 3.0% yr\ :sup:`-1`. Taking the annual -rate of mortality (*am*, proportion yr\ :sup:`-1`) as 0.02, a -mortality rate per second (*m*) is calculated as -:math:`m={am\mathord{\left/ {\vphantom {am \left(365\cdot 86400\right)}} \right.} \left(365\cdot 86400\right)}` . -All vegetation carbon and nitrogen pools for display, storage, and -transfer are affected at rate *m*, with mortality fluxes out of -vegetation pools eventually merged to the column level and deposited in -litter pools. Mortality (*mort*) fluxes out of displayed vegetation -carbon and nitrogen pools are +Whole-plant mortality is parameterized very simply, assuming a mortality rate of 2% yr\ :sup:`-1` for all vegetation types. This is clearly a gross oversimplification of an important process, and additional work is required to better constrain this process in different climate zones (:ref:`Keller et al. 2004`; :ref:`Sollins 1982`), for different species mixtures (:ref:`Gomes et al. 2003`), and for different size and age classes (:ref:`Busing 2005`; :ref:`Law et al. 2003`). Literature values for forest mortality rates range from at least 0.7% to 3.0% yr\ :sup:`-1`. Taking the annual rate of mortality (*am*, proportion yr\ :sup:`-1`) as 0.02, a mortality rate per second (*m*) is calculated as :math:`m={am\mathord{\left/ {\vphantom {am \left(365\cdot 86400\right)}} \right.} \left(365\cdot 86400\right)}`. All vegetation carbon and nitrogen pools for display, storage, and transfer are affected at rate *m*, with mortality fluxes out of vegetation pools eventually merged to the column level and deposited in litter pools. Mortality (*mort*) fluxes out of displayed vegetation carbon and nitrogen pools are .. math:: :label: 33.1) @@ -97,9 +75,7 @@ carbon and nitrogen pools are NF_{retrans\_ mort} =NS_{retrans} m. -where CF are carbon fluxes, CS is carbon storage, NF are nitrogen -fluxes, NS is nitrogen storage, *croot* refers to coarse roots, *froot* -refers to fine roots, and *retrans* refers to retranslocated. +where CF are carbon fluxes, CS is carbon storage, NF are nitrogen fluxes, NS is nitrogen storage, *croot* refers to coarse roots, *froot* refers to fine roots, and *retrans* refers to retranslocated. Mortality fluxes out of carbon and nitrogen storage (*stor)* pools are @@ -170,8 +146,7 @@ Mortality fluxes out of carbon and nitrogen storage (*stor)* pools are where *gresp* refers to growth respiration. -Mortality fluxes out of carbon and nitrogen transfer (*xfer)* growth -pools are +Mortality fluxes out of carbon and nitrogen transfer (*xfer)* growth pools are .. math:: :label: 33.27) @@ -241,12 +216,7 @@ pools are Mortality Fluxes Merged to the Column Level ------------------------------------------------ -Analogous to the treatment of litterfall fluxes, mortality fluxes -leaving the vegetation pools are merged to the column level according to -the weighted distribution of PFTs on the column (:math:`wcol_{p}` ), and -deposited in litter and coarse woody debris pools, which are defined at -the column level. Carbon and nitrogen fluxes from mortality of displayed -leaf and fine root into litter pools are calculated as +Analogous to the treatment of litterfall fluxes, mortality fluxes leaving the vegetation pools are merged to the column level according to the weighted distribution of PFTs on the column (:math:`wcol_{p}` ), and deposited in litter and coarse woody debris pools, which are defined at the column level. Carbon and nitrogen fluxes from mortality of displayed leaf and fine root into litter pools are calculated as .. math:: :label: 33.40) @@ -308,10 +278,7 @@ leaf and fine root into litter pools are calculated as NF_{froot\_ mort,lit3} =\sum _{p=0}^{npfts}NF_{froot\_ mort} f_{lig\_ froot,p} wcol_{p} . -where *lab* refers to labile, *cel* refers to cellulose, and *lig* -refers to lignin. Carbon and nitrogen mortality fluxes from displayed -live and dead stem and coarse root pools are merged to the column level -and deposited in the coarse woody debris (*cwd*) pools: +where *lab* refers to labile, *cel* refers to cellulose, and *lig* refers to lignin. Carbon and nitrogen mortality fluxes from displayed live and dead stem and coarse root pools are merged to the column level and deposited in the coarse woody debris (*cwd*) pools: .. math:: :label: 33.52) @@ -353,14 +320,7 @@ and deposited in the coarse woody debris (*cwd*) pools: NF_{deadcroot\_ mort,cwd} =\sum _{p=0}^{npfts}NF_{deadcroot\_ mort} wcol_{p} -All vegetation storage and transfer pools for carbon and nitrogen are -assumed to exist as labile pools within the plant (e.g. as carbohydrate -stores, in the case of carbon pools). This assumption applies to storage -and transfer pools for both non-woody and woody tissues. The mortality -fluxes from these pools are therefore assumed to be deposited in the -labile litter pools (:math:`{CS}_{lit1}`, :math:`{NS}_{lit1}`), -after being merged to the column level. Carbon mortality fluxes out of -storage and transfer pools are: +All vegetation storage and transfer pools for carbon and nitrogen are assumed to exist as labile pools within the plant (e.g. as carbohydrate stores, in the case of carbon pools). This assumption applies to storage and transfer pools for both non-woody and woody tissues. The mortality fluxes from these pools are therefore assumed to be deposited in the labile litter pools (:math:`{CS}_{lit1}`, :math:`{NS}_{lit1}`), after being merged to the column level. Carbon mortality fluxes out of storage and transfer pools are: .. math:: :label: 33.60) @@ -432,8 +392,7 @@ storage and transfer pools are: CF_{gresp\_ xfer\_ mort,lit1} =\sum _{p=0}^{npfts}CF_{gresp\_ xfer\_ mort} wcol_{p} . -Nitrogen mortality fluxes out of storage and transfer pools, including -the storage pool for retranslocated nitrogen, are calculated as: +Nitrogen mortality fluxes out of storage and transfer pools, including the storage pool for retranslocated nitrogen, are calculated as: .. math:: :label: 33.74) diff --git a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst index c7c1b7e506..7a996f2c8e 100644 --- a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst +++ b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst @@ -9,12 +9,7 @@ CLM5 includes changes to plant respiration including Autotrophic Respiration ---------------------------- -The model treats maintenance and growth respiration fluxes separately, -even though it is difficult to measure them as separate fluxes (Lavigne -and Ryan, 1997; Sprugel et al., 1995). Maintenance respiration is -defined as the carbon cost to support the metabolic activity of existing -live tissue, while growth respiration is defined as the additional -carbon cost for the synthesis of new growth. +The model treats maintenance and growth respiration fluxes separately, even though it is difficult to measure them as separate fluxes (Lavigne and Ryan, 1997; Sprugel et al., 1995). Maintenance respiration is defined as the carbon cost to support the metabolic activity of existing live tissue, while growth respiration is defined as the additional carbon cost for the synthesis of new growth. Maintenance Respiration ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -43,12 +38,7 @@ The temperature dependance of leaf maintenance (dark) respiration is described i CF_{mr\_ froot} \_ =\sum _{j=1}^{nlevsoi}NS_{froot} rootfr_{j} MR_{base} MR_{Q10} ^{(Ts_{j} -20)/10} -where :math:`MR_{q10}` (= 2.0) is -the temperature sensitivity for maintenance respiration, -:math:`T_{2m}` (:sup:`o`\ C) is the air temperature at 2m -height, :math:`Ts_{j}`* (:sup:`o`\ C) is the soil -temperature at level *j*, and :math:`rootfr_{j}` is the fraction -of fine roots distributed in soil level *j*. +where :math:`MR_{q10}` (= 2.0) is the temperature sensitivity for maintenance respiration, :math:`T_{2m}` (:sup:`o`\ C) is the air temperature at 2m height, :math:`Ts_{j}`* (:sup:`o`\ C) is the soil temperature at level *j*, and :math:`rootfr_{j}` is the fraction of fine roots distributed in soil level *j*. .. table:: Atkin leaf respiration model intercept values. @@ -71,13 +61,7 @@ of fine roots distributed in soil level *j*. C\ :sub:`4` grass 2.196 ======================== ============= -Note that, for woody vegetation, maintenance respiration costs are not -calculated for the dead stem and dead coarse root components. These -components are assumed to consist of dead xylem cells, with no metabolic -function. By separating the small live component of the woody tissue -(ray parenchyma, phloem, and sheathing lateral meristem cells) from the -larger fraction of dead woody tissue, it is reasonable to assume a -common base maintenance respiration rate for all live tissue types. +Note that, for woody vegetation, maintenance respiration costs are not calculated for the dead stem and dead coarse root components. These components are assumed to consist of dead xylem cells, with no metabolic function. By separating the small live component of the woody tissue (ray parenchyma, phloem, and sheathing lateral meristem cells) from the larger fraction of dead woody tissue, it is reasonable to assume a common base maintenance respiration rate for all live tissue types. The total maintenance respiration cost is then given as: @@ -89,29 +73,8 @@ The total maintenance respiration cost is then given as: Growth Respiration ^^^^^^^^^^^^^^^^^^^^^^^^^ -Growth respiration is calculated as a factor of 0.11 times the total -carbon allocation to new growth (:math:`CF_{growth}`, after allocating carbon for N acquisition, -Chapter :numref:`rst_FUN`.) on a given timestep, based on construction costs -for a range of woody and non-woody tissues, with estimates of the growth -respiration flux revised downswards following (Atkin et al. 2017). For new -carbon and nitrogen allocation that enters storage pools for subsequent -display, it is not clear what fraction of the associated growth -respiration should occur at the time of initial allocation, and what -fraction should occur later, at the time of display of new growth from -storage. Eddy covariance estimates of carbon fluxes in forest ecosystems -suggest that the growth respiration associated with transfer of -allocated carbon and nitrogen from storage into displayed tissue is not -significant (Churkina et al., 2003), and so it is assumed in CLM that -all of the growth respiration cost is incurred at the time of initial -allocation, regardless of the fraction of allocation that is displayed -immediately (i.e. regardless of the value of :math:`f_{cur}`, -section 13.5). This behavior is parameterized in such a way that if -future research suggests that some fraction of the growth respiration -cost should be incurred at the time of display from storage, a simple -parameter modification will effect the change. [1]_ +Growth respiration is calculated as a factor of 0.11 times the total carbon allocation to new growth (:math:`CF_{growth}`, after allocating carbon for N acquisition, Chapter :numref:`rst_FUN`.) on a given timestep, based on construction costs for a range of woody and non-woody tissues, with estimates of the growth respiration flux revised downswards following (Atkin et al. 2017). For new carbon and nitrogen allocation that enters storage pools for subsequent display, it is not clear what fraction of the associated growth respiration should occur at the time of initial allocation, and what fraction should occur later, at the time of display of new growth from storage. Eddy covariance estimates of carbon fluxes in forest ecosystems suggest that the growth respiration associated with transfer of allocated carbon and nitrogen from storage into displayed tissue is not significant (Churkina et al., 2003), and so it is assumed in CLM that all of the growth respiration cost is incurred at the time of initial allocation, regardless of the fraction of allocation that is displayed immediately (i.e. regardless of the value of :math:`f_{cur}`, section 13.5). This behavior is parameterized in such a way that if future research suggests that some fraction of the growth respiration cost should be incurred at the time of display from storage, a simple parameter modification will effect the change. [1]_ .. [1] - Parameter :math:`\text{grpnow}` in routines CNGResp and CNAllocation, currently set to 1.0, could be changed to a smaller - value to transfer some portion (1 - :math:`\text{grpnow}` ) of the growth respiration forward in time to occur at the time of growth - display from storage. + Parameter :math:`\text{grpnow}` in routines CNGResp and CNAllocation, currently set to 1.0, could be changed to a smaller value to transfer some portion (1 - :math:`\text{grpnow}` ) of the growth respiration forward in time to occur at the time of growth display from storage. diff --git a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst index cee30a0187..6bf7c0d9d3 100644 --- a/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst +++ b/doc/source/tech_note/Radiative_Fluxes/CLM50_Tech_Note_Radiative_Fluxes.rst @@ -3,11 +3,7 @@ Radiative Fluxes =================== -The net radiation at the surface is -:math:`\left(\vec{S}_{v} +\vec{S}_{g} \right)-\left(\vec{L}_{v} +\vec{L}_{g} \right)`, -where :math:`\vec{S}` is the net solar flux absorbed by the vegetation -("v") and the ground ("g") and :math:`\vec{L}` is the net longwave flux -(positive toward the atmosphere) (W m\ :sup:`-2`). +The net radiation at the surface is :math:`\left(\vec{S}_{v} +\vec{S}_{g} \right)-\left(\vec{L}_{v} +\vec{L}_{g} \right)`, where :math:`\vec{S}` is the net solar flux absorbed by the vegetation ("v") and the ground ("g") and :math:`\vec{L}` is the net longwave flux (positive toward the atmosphere) (W m\ :sup:`-2`). .. _Solar Fluxes: @@ -17,34 +13,22 @@ Solar Fluxes :numref:`Figure Radiation Schematic` illustrates the direct beam and diffuse fluxes in the canopy. :math:`I\, \uparrow _{\Lambda }^{\mu }` and -:math:`I\, \uparrow _{\Lambda }` are the upward diffuse fluxes, per -unit incident direct beam and diffuse flux (section :numref:`Canopy Radiative Transfer`). +:math:`I\, \uparrow _{\Lambda }` are the upward diffuse fluxes, per unit incident direct beam and diffuse flux (section :numref:`Canopy Radiative Transfer`). :math:`I\, \downarrow _{\Lambda }^{\mu }` and -:math:`I\, \downarrow _{\Lambda }` \ are the downward diffuse fluxes -below the vegetation per unit incident direct beam and diffuse radiation -(section :numref:`Canopy Radiative Transfer`). The direct beam flux -transmitted through the canopy, per -unit incident flux, is :math:`e^{-K\left(L+S\right)}` . -:math:`\vec{I}_{\Lambda }^{\mu }` and :math:`\vec{I}_{\Lambda }^{}` -are the fluxes absorbed by the vegetation, per unit incident direct beam -and diffuse radiation (section :numref:`Canopy Radiative Transfer`). -:math:`\alpha _{g,\, \Lambda }^{\mu }` and -:math:`\alpha _{g,\, \Lambda }` are the direct beam and diffuse ground -albedos (section :numref:`Ground Albedos`). :math:`L` and :math:`S` are the exposed leaf area -index and stem area index (section :numref:`Phenology and vegetation burial by snow`). -:math:`K` is the optical -depth of direct beam per unit leaf and stem area (section :numref:`Canopy Radiative Transfer`). +:math:`I\, \downarrow _{\Lambda }` \ are the downward diffuse fluxes below the vegetation per unit incident direct beam and diffuse radiation (section :numref:`Canopy Radiative Transfer`). The direct beam flux transmitted through the canopy, per unit incident flux, is :math:`e^{-K\left(L+S\right)}`. +:math:`\vec{I}_{\Lambda }^{\mu }` and :math:`\vec{I}_{\Lambda }^{}` are the fluxes absorbed by the vegetation, per unit incident direct beam and diffuse radiation (section :numref:`Canopy Radiative Transfer`). +:math:`\alpha _{g,\, \Lambda }^{\mu }` and +:math:`\alpha _{g,\, \Lambda }` are the direct beam and diffuse ground albedos (section :numref:`Ground Albedos`). +:math:`L` and :math:`S` are the exposed leaf area index and stem area index (section :numref:`Phenology and vegetation burial by snow`). +:math:`K` is the optical depth of direct beam per unit leaf and stem area (section :numref:`Canopy Radiative Transfer`). .. _Figure Radiation Schematic: .. figure:: image1.png - Schematic diagram of (a) direct beam radiation, (b) diffuse - solar radiation, and (c) longwave radiation absorbed, transmitted, and - reflected by vegetation and ground. + Schematic diagram of (a) direct beam radiation, (b) diffuse solar radiation, and (c) longwave radiation absorbed, transmitted, and reflected by vegetation and ground. -For clarity, terms involving :math:`T^{n+1} -T^{n}` are not shown in -(c). +For clarity, terms involving :math:`T^{n+1} -T^{n}` are not shown in (c). The total solar radiation absorbed by the vegetation and ground is @@ -58,13 +42,7 @@ The total solar radiation absorbed by the vegetation and ground is \begin{array}{l} {\vec{S}_{g} =\sum _{\Lambda }S_{atm} \, \downarrow _{\Lambda }^{\mu } e^{-K\left(L+S\right)} \left(1-\alpha _{g,\, \Lambda }^{\mu } \right) +} \\ {\qquad \left(S_{atm} \, \downarrow _{\Lambda }^{\mu } I\downarrow _{\Lambda }^{\mu } +S_{atm} \downarrow _{\Lambda } I\downarrow _{\Lambda } \right)\left(1-\alpha _{g,\, \Lambda } \right)} \end{array} -where :math:`S_{atm} \, \downarrow _{\Lambda }^{\mu }` and -:math:`S_{atm} \, \downarrow _{\Lambda }` are the incident direct beam -and diffuse solar fluxes (W m\ :sup:`-2`). For non-vegetated -surfaces, :math:`e^{-K\left(L+S\right)} =1`, -:math:`\overrightarrow{I}_{\Lambda }^{\mu } =\overrightarrow{I}_{\Lambda } =0`, -:math:`I\, \downarrow _{\Lambda }^{\mu } =0`, and -:math:`I\, \downarrow _{\Lambda } =1`, so that +where :math:`S_{atm} \, \downarrow _{\Lambda }^{\mu }` and :math:`S_{atm} \, \downarrow _{\Lambda }` are the incident direct beam and diffuse solar fluxes (W m\ :sup:`-2`). For non-vegetated surfaces, :math:`e^{-K\left(L+S\right)} =1`, :math:`\overrightarrow{I}_{\Lambda }^{\mu } =\overrightarrow{I}_{\Lambda } =0`, :math:`I\, \downarrow _{\Lambda }^{\mu } =0`, and :math:`I\, \downarrow _{\Lambda } =1`, so that .. math:: :label: 4.3 @@ -80,117 +58,67 @@ Solar radiation is conserved as where the latter term in parentheses is reflected solar radiation. -Photosynthesis and transpiration depend non-linearly on solar radiation, -via the light response of stomata. The canopy is treated as two leaves -(sunlit and shaded) and the solar radiation in the visible waveband -(:math:`<` 0.7 µm) absorbed by the vegetation is apportioned to the -sunlit and shaded leaves (section :numref:`Canopy Radiative Transfer`). -The absorbed photosynthetically -active (visible waveband) radiation averaged over the sunlit canopy (per -unit plant area) is +Photosynthesis and transpiration depend non-linearly on solar radiation, via the light response of stomata. The canopy is treated as two leaves (sunlit and shaded) and the solar radiation in the visible waveband (:math:`<` 0.7 µm) absorbed by the vegetation is apportioned to the sunlit and shaded leaves (section :numref:`Canopy Radiative Transfer`). The absorbed photosynthetically active (visible waveband) radiation averaged over the sunlit canopy (per unit plant area) is .. math:: :label: 4.5 \phi ^{sun} ={\left(\vec{I}_{sun,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sun,vis}^{} S_{atm} \downarrow _{vis}^{} \right)\mathord{\left/ {\vphantom {\left(\vec{I}_{sun,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sun,vis}^{} S_{atm} \downarrow _{vis}^{} \right) L^{sun} }} \right.} L^{sun} } -and the absorbed radiation for the average shaded leaf (per unit plant -area) is +and the absorbed radiation for the average shaded leaf (per unit plant area) is .. math:: :label: 4.6 \phi ^{sha} ={\left(\vec{I}_{sha,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sha,vis}^{} S_{atm} \downarrow _{vis}^{} \right)\mathord{\left/ {\vphantom {\left(\vec{I}_{sha,vis}^{\mu } S_{atm} \downarrow _{vis}^{\mu } +\vec{I}_{sha,vis}^{} S_{atm} \downarrow _{vis}^{} \right) L^{sha} }} \right.} L^{sha} } -with :math:`L^{sun}` and :math:`L^{sha}` the sunlit and shaded plant -area index, respectively. The sunlit plant area index is +with :math:`L^{sun}` and :math:`L^{sha}` the sunlit and shaded plant area index, respectively. The sunlit plant area index is .. math:: :label: 4.7 L^{sun} =\frac{1-e^{-K(L+S)} }{K} -and the shaded leaf area index is :math:`L^{sha} =(L+S)-L^{sun}` . In -calculating :math:`L^{sun}` , +and the shaded leaf area index is :math:`L^{sha} =(L+S)-L^{sun}`. In calculating :math:`L^{sun}`, .. math:: :label: 4.8 K=\frac{G\left(\mu \right)}{\mu } -where :math:`G\left(\mu \right)` and :math:`\mu` are parameters in the -two-stream approximation (section :numref:`Canopy Radiative Transfer`). - -The model uses the two-stream approximation to calculate radiative -transfer of direct and diffuse radiation through a canopy that is -differentiated into leaves that are sunlit and those that are shaded -(section :numref:`Canopy Radiative Transfer`). The two-stream equations -are integrated over all plant -area (leaf and stem area) in the canopy. The model has an optional -(though not supported) multi-layer canopy, as described by -:ref:`Bonan et al. (2012) `. -The multi-layer model is only intended to address the -non-linearity of light profiles, photosynthesis, and stomatal -conductance in the plant canopy. - -In the multi-layer canopy, canopy-integrated radiative fluxes are -calculated from the two-stream approximation. The model additionally -derives the light profile with depth in the canopy by taking the -derivatives of the absorbed radiative fluxes with respect to plant area -index (:math:`L'=L+S`) and evaluating them incrementally through the -canopy with cumulative plant area index (:math:`x`). The terms -:math:`{d\vec{I}_{sun,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` -and -:math:`{d\vec{I}_{sun,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{} (x) dL'}} \right.} dL'}` -are the direct beam and diffuse solar radiation, respectively, absorbed -by the sunlit fraction of the canopy (per unit plant area) at a depth -defined by the cumulative plant area index :math:`x`; -:math:`{d\vec{I}_{sha,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` \ and -:math:`{d\vec{I}_{sha,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{} (x) dL'}} \right.} dL'}` -are the corresponding fluxes for the shaded fraction of the canopy at -depth :math:`x`. These fluxes are normalized by the sunlit or shaded -fraction at depth :math:`x`, defined by -:math:`f_{sun} =\exp \left(-Kx\right)`, to give fluxes per unit sunlit -or shaded plant area at depth :math:`x`. +where :math:`G\left(\mu \right)` and :math:`\mu` are parameters in the two-stream approximation (section :numref:`Canopy Radiative Transfer`). + +The model uses the two-stream approximation to calculate radiative transfer of direct and diffuse radiation through a canopy that is differentiated into leaves that are sunlit and those that are shaded (section :numref:`Canopy Radiative Transfer`). The two-stream equations are integrated over all plant area (leaf and stem area) in the canopy. The model has an optional (though not supported) multi-layer canopy, as described by :ref:`Bonan et al. (2012) `. The multi-layer model is only intended to address the non-linearity of light profiles, photosynthesis, and stomatal conductance in the plant canopy. + +In the multi-layer canopy, canopy-integrated radiative fluxes are calculated from the two-stream approximation. The model additionally derives the light profile with depth in the canopy by taking the derivatives of the absorbed radiative fluxes with respect to plant area index (:math:`L'=L+S`) and evaluating them incrementally through the canopy with cumulative plant area index (:math:`x`). The terms :math:`{d\vec{I}_{sun,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` and :math:`{d\vec{I}_{sun,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sun,\Lambda }^{} (x) dL'}} \right.} dL'}` are the direct beam and diffuse solar radiation, respectively, absorbed by the sunlit fraction of the canopy (per unit plant area) at a depth defined by the cumulative plant area index :math:`x`; :math:`{d\vec{I}_{sha,\Lambda }^{\mu } (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{\mu } (x) dL'}} \right.} dL'}` \ and :math:`{d\vec{I}_{sha,\Lambda }^{} (x)\mathord{\left/ {\vphantom {d\vec{I}_{sha,\Lambda }^{} (x) dL'}} \right.} dL'}` are the corresponding fluxes for the shaded fraction of the canopy at depth :math:`x`. These fluxes are normalized by the sunlit or shaded fraction at depth :math:`x`, defined by :math:`f_{sun} =\exp \left(-Kx\right)`, to give fluxes per unit sunlit or shaded plant area at depth :math:`x`. .. _Longwave Fluxes: Longwave Fluxes ------------------- -The net longwave radiation (W m\ :sup:`-2`) (positive toward the -atmosphere) at the surface is +The net longwave radiation (W m\ :sup:`-2`) (positive toward the atmosphere) at the surface is .. math:: :label: 4.9 \vec{L}=L\, \uparrow -L_{atm} \, \downarrow -where :math:`L\, \uparrow` is the upward longwave radiation from the -surface and :math:`L_{atm} \, \downarrow` is the downward atmospheric -longwave radiation (W m\ :sup:`-2`). The radiative temperature -:math:`T_{rad}` (K) is defined from the upward longwave radiation as +where :math:`L\, \uparrow` is the upward longwave radiation from the surface and :math:`L_{atm} \, \downarrow` is the downward atmospheric longwave radiation (W m\ :sup:`-2`). The radiative temperature :math:`T_{rad}` (K) is defined from the upward longwave radiation as .. math:: :label: 4.10 T_{rad} =\left(\frac{L\, \uparrow }{\sigma } \right)^{{1\mathord{\left/ {\vphantom {1 4}} \right.} 4} } -where :math:`\sigma` is the Stefan-Boltzmann constant (W\ m\ :sup:`-2` K\ :sup:`-4`) (:numref:`Table Physical constants`). With reference to -:numref:`Figure Radiation Schematic`, the upward longwave radiation from the surface to the atmosphere is +where :math:`\sigma` is the Stefan-Boltzmann constant (W\ m\ :sup:`-2` K\ :sup:`-4`) (:numref:`Table Physical constants`). With reference to :numref:`Figure Radiation Schematic`, the upward longwave radiation from the surface to the atmosphere is .. math:: :label: 4.11 \begin{array}{l} {L\, \uparrow =\delta _{veg} L_{vg} \, \uparrow +\left(1-\delta _{veg} \right)\left(1-\varepsilon _{g} \right)L_{atm} \, \downarrow +} \\ {\qquad \left(1-\delta _{veg} \right)\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} +4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right)} \end{array} -where :math:`L_{vg} \, \uparrow` is the upward longwave radiation from -the vegetation/soil system for exposed leaf and stem area -:math:`L+S\ge 0.05`, :math:`\delta _{veg}` is a step function and is -zero for :math:`L+S<0.05` and one otherwise, :math:`\varepsilon _{g}` -is the ground emissivity, and :math:`T_{g}^{n+1}` and -:math:`T_{g}^{n}` are the snow/soil surface temperatures at the current -and previous time steps, respectively (:ref:`rst_Soil and Snow Temperatures`). +where :math:`L_{vg} \, \uparrow` is the upward longwave radiation from the vegetation/soil system for exposed leaf and stem area :math:`L+S\ge 0.05`, :math:`\delta _{veg}` is a step function and is zero for :math:`L+S<0.05` and one otherwise, :math:`\varepsilon _{g}` is the ground emissivity, and :math:`T_{g}^{n+1}` and :math:`T_{g}^{n}` are the snow/soil surface temperatures at the current and previous time steps, respectively (:ref:`rst_Soil and Snow Temperatures`). For non-vegetated surfaces, the above equation reduces to @@ -199,14 +127,9 @@ For non-vegetated surfaces, the above equation reduces to L\, \uparrow =\left(1-\varepsilon _{g} \right)L_{atm} \, \downarrow +\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} +4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right) -where the first term is the atmospheric longwave radiation reflected by -the ground, the second term is the longwave radiation emitted by the -ground, and the last term is the increase (decrease) in longwave -radiation emitted by the ground due to an increase (decrease) in ground -temperature. +where the first term is the atmospheric longwave radiation reflected by the ground, the second term is the longwave radiation emitted by the ground, and the last term is the increase (decrease) in longwave radiation emitted by the ground due to an increase (decrease) in ground temperature. -For vegetated surfaces, the upward longwave radiation from the surface -reduces to +For vegetated surfaces, the upward longwave radiation from the surface reduces to .. math:: :label: 4.13 @@ -220,25 +143,7 @@ where \begin{array}{l} {L_{vg} \, \uparrow =\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow } \\ {\qquad \qquad +\varepsilon _{v} \left[1+\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\right]\sigma \left(T_{v}^{n} \right)^{3} \left[T_{v}^{n} +4\left(T_{v}^{n+1} -T_{v}^{n} \right)\right]} \\ {\qquad \qquad +\varepsilon _{g} \left(1-\varepsilon _{v} \right)\sigma \left(T_{g}^{n} \right)^{4} } \\ {\qquad =\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow } \\ {\qquad \qquad +\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{4} } \\ {\qquad \qquad +\varepsilon _{v} \left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\sigma \left(T_{v}^{n} \right)^{4} } \\ {\qquad \qquad +4\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{3} \left(T_{v}^{n+1} -T_{v}^{n} \right)} \\ {\qquad \qquad +4\varepsilon _{v} \left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\sigma \left(T_{v}^{n} \right)^{3} \left(T_{v}^{n+1} -T_{v}^{n} \right)} \\ {\qquad \qquad +\varepsilon _{g} \left(1-\varepsilon _{v} \right)\sigma \left(T_{g}^{n} \right)^{4} } \end{array} -where :math:`\varepsilon _{v}` is the vegetation emissivity and -:math:`T_{v}^{n+1}` and :math:`T_{v}^{n}` are the vegetation -temperatures at the current and previous time steps, respectively -(:ref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). -The first term in the equation above is the atmospheric -longwave radiation that is transmitted through the canopy, reflected by -the ground, and transmitted through the canopy to the atmosphere. The -second term is the longwave radiation emitted by the canopy directly to -the atmosphere. The third term is the longwave radiation emitted -downward from the canopy, reflected by the ground, and transmitted -through the canopy to the atmosphere. The fourth term is the increase -(decrease) in longwave radiation due to an increase (decrease) in canopy -temperature that is emitted by the canopy directly to the atmosphere. -The fifth term is the increase (decrease) in longwave radiation due to -an increase (decrease) in canopy temperature that is emitted downward -from the canopy, reflected from the ground, and transmitted through the -canopy to the atmosphere. The last term is the longwave radiation -emitted by the ground and transmitted through the canopy to the -atmosphere. +where :math:`\varepsilon _{v}` is the vegetation emissivity and :math:`T_{v}^{n+1}` and :math:`T_{v}^{n}` are the vegetation temperatures at the current and previous time steps, respectively (:ref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). The first term in the equation above is the atmospheric longwave radiation that is transmitted through the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The second term is the longwave radiation emitted by the canopy directly to the atmosphere. The third term is the longwave radiation emitted downward from the canopy, reflected by the ground, and transmitted through the canopy to the atmosphere. The fourth term is the increase (decrease) in longwave radiation due to an increase (decrease) in canopy temperature that is emitted by the canopy directly to the atmosphere. The fifth term is the increase (decrease) in longwave radiation due to an increase (decrease) in canopy temperature that is emitted downward from the canopy, reflected from the ground, and transmitted through the canopy to the atmosphere. The last term is the longwave radiation emitted by the ground and transmitted through the canopy to the atmosphere. The upward longwave radiation from the ground is @@ -247,59 +152,42 @@ The upward longwave radiation from the ground is L_{g} \, \uparrow =\left(1-\varepsilon _{g} \right)L_{v} \, \downarrow +\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} -where :math:`L_{v} \, \downarrow` is the downward longwave radiation -below the vegetation +where :math:`L_{v} \, \downarrow` is the downward longwave radiation below the vegetation .. math:: :label: 4.16 L_{v} \, \downarrow =\left(1-\varepsilon _{v} \right)L_{atm} \, \downarrow +\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{4} +4\varepsilon _{v} \sigma \left(T_{v}^{n} \right)^{3} \left(T_{v}^{n+1} -T_{v}^{n} \right). -The net longwave radiation flux for the ground is (positive toward the -atmosphere) +The net longwave radiation flux for the ground is (positive toward the atmosphere) .. math:: :label: 4.17 \vec{L}_{g} =\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} -\delta _{veg} \varepsilon _{g} L_{v} \, \downarrow -\left(1-\delta _{veg} \right)\varepsilon _{g} L_{atm} \, \downarrow . -The above expression for :math:`\vec{L}_{g}` is the net longwave -radiation forcing that is used in the soil temperature calculation -(:ref:`rst_Soil and Snow Temperatures`). Once updated soil -temperatures have been obtained, the term -:math:`4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right)` -is added to :math:`\vec{L}_{g}` to calculate the ground heat flux -(section :numref:`Update of Ground Sensible and Latent Heat Fluxes`) +The above expression for :math:`\vec{L}_{g}` is the net longwave radiation forcing that is used in the soil temperature calculation (:ref:`rst_Soil and Snow Temperatures`). Once updated soil temperatures have been obtained, the term :math:`4\varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{3} \left(T_{g}^{n+1} -T_{g}^{n} \right)` is added to :math:`\vec{L}_{g}` to calculate the ground heat flux (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`) -The net longwave radiation flux for vegetation is (positive toward the -atmosphere) +The net longwave radiation flux for vegetation is (positive toward the atmosphere) .. math:: :label: 4.18 \vec{L}_{v} =\left[2-\varepsilon _{v} \left(1-\varepsilon _{g} \right)\right]\varepsilon _{v} \sigma \left(T_{v} \right)^{4} -\varepsilon _{v} \varepsilon _{g} \sigma \left(T_{g}^{n} \right)^{4} -\varepsilon _{v} \left[1+\left(1-\varepsilon _{g} \right)\left(1-\varepsilon _{v} \right)\right]L_{atm} \, \downarrow . -These equations assume that absorptivity equals emissivity. The -emissivity of the ground is +These equations assume that absorptivity equals emissivity. The emissivity of the ground is .. math:: :label: 4.19 \varepsilon _{g} =\varepsilon _{soi} \left(1-f_{sno} \right)+\varepsilon _{sno} f_{sno} -where :math:`\varepsilon _{soi} =0.96` for soil, 0.97 for glacier, -:math:`\varepsilon _{sno} =0.97`, and :math:`f_{sno}` -is the fraction of ground covered by snow -(section :numref:`Snow Covered Area Fraction`). The -vegetation emissivity is +where :math:`\varepsilon _{soi} =0.96` for soil, 0.97 for glacier, :math:`\varepsilon _{sno} =0.97`, and :math:`f_{sno}` is the fraction of ground covered by snow (section :numref:`Snow Covered Area Fraction`). The vegetation emissivity is .. math:: :label: 4.20 \varepsilon _{v} =1-e^{-{\left(L+S\right)\mathord{\left/ {\vphantom {\left(L+S\right) \bar{\mu }}} \right.} \bar{\mu }} } -where :math:`L` and :math:`S` are the leaf and stem area indices -(section :numref:`Phenology and vegetation burial by snow`) and -:math:`\bar{\mu }=1` is the average inverse optical -depth for longwave radiation. +where :math:`L` and :math:`S` are the leaf and stem area indices (section :numref:`Phenology and vegetation burial by snow`) and :math:`\bar{\mu }=1` is the average inverse optical depth for longwave radiation. diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index 4b958ca731..d3c81b243e 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -5,88 +5,59 @@ References .. _Aberetal1990: -Aber, J.D., Melillo, J.M. and McClaugherty, C.A., 1990. 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Leningrad Gidrometeor. diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 22b05b304c..5668af1a0b 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -3,18 +3,7 @@ Snow Hydrology =============== -The parameterizations for snow are based primarily on -:ref:`Anderson (1976) `, :ref:`Jordan (1991) `, -and :ref:`Dai and Zeng (1997) `. The snowpack -can have up to twelve layers. These layers are indexed in the Fortran code -as :math:`i=-11,-10,...,-1,0` where layer :math:`i=0` is the snow layer -next to the top soil layer and layer :math:`i=-11` is the top layer of a -twelve-layer snow pack. Since the number of snow layers varies according -to the snow depth, we use the notation :math:`snl+1` to describe the top -layer of snow for the variable layer snow pack, where :math:`snl` is the -negative of the number of snow layers. Refer to :numref:`Figure three layer -snow pack` for an example of the snow layer structure for a three layer -snow pack. +The parameterizations for snow are based primarily on :ref:`Anderson (1976) `, :ref:`Jordan (1991) `, and :ref:`Dai and Zeng (1997) `. The snowpack can have up to twelve layers. These layers are indexed in the Fortran code as :math:`i=-11,-10,...,-1,0` where layer :math:`i=0` is the snow layer next to the top soil layer and layer :math:`i=-11` is the top layer of a twelve-layer snow pack. Since the number of snow layers varies according to the snow depth, we use the notation :math:`snl+1` to describe the top layer of snow for the variable layer snow pack, where :math:`snl` is the negative of the number of snow layers. Refer to :numref:`Figure three layer snow pack` for an example of the snow layer structure for a three layer snow pack. .. _Figure three layer snow pack: @@ -22,80 +11,41 @@ snow pack. Example of three layer snow pack (:math:`snl=-3`). -Shown are three snow layers, :math:`i=-2`, :math:`i=-1`, and -:math:`i=0`. The layer node depth is :math:`z`, the layer interface is -:math:`z_{h}` , and the layer thickness is :math:`\Delta z`. - -The state variables for snow are the mass of water :math:`w_{liq,i}` -(kg m\ :sup:`-2`), mass of ice :math:`w_{ice,i}` (kg m\ :sup:`-2`), layer -thickness :math:`\Delta z_{i}` (m), and temperature :math:`T_{i}` -(Chapter :numref:`rst_Soil and Snow Temperatures`). The water vapor phase is -neglected. Snow can also exist in the model without being represented by -explicit snow layers. This occurs when the snowpack is less than a -specified minimum snow depth (:math:`z_{sno} < 0.01` m). In this case, -the state variable is the mass of snow :math:`W_{sno}` (kg m\ :sup:`-2`). - -Section :numref:`Snow Covered Area Fraction` describes the calculation -of fractional snow covered area, which is used in the surface albedo -calculation (Chapter :numref:`rst_Surface Albedos`) and the surface flux -calculations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent -Heat Fluxes`). The following two sections (:numref:`Ice Content` and -:numref:`Water Content`) describe the ice and water content of the snow -pack assuming that at least one snow layer exists. Section :numref:`Black -and organic carbon and mineral dust within snow` describes how black and -organic carbon and mineral dust particles are represented within snow, -including meltwater flushing. See Section :numref:`Initialization of snow -layer` for a description of how a snow layer is initialized. +Shown are three snow layers, :math:`i=-2`, :math:`i=-1`, and :math:`i=0`. The layer node depth is :math:`z`, the layer interface is :math:`z_{h}`, and the layer thickness is :math:`\Delta z`. + +The state variables for snow are the mass of water :math:`w_{liq,i}` (kg m\ :sup:`-2`), mass of ice :math:`w_{ice,i}` (kg m\ :sup:`-2`), layer thickness :math:`\Delta z_{i}` (m), and temperature :math:`T_{i}` (Chapter :numref:`rst_Soil and Snow Temperatures`). The water vapor phase is neglected. Snow can also exist in the model without being represented by explicit snow layers. This occurs when the snowpack is less than a specified minimum snow depth (:math:`z_{sno} < 0.01` m). In this case, the state variable is the mass of snow :math:`W_{sno}` (kg m\ :sup:`-2`). + +Section :numref:`Snow Covered Area Fraction` describes the calculation of fractional snow covered area, which is used in the surface albedo calculation (Chapter :numref:`rst_Surface Albedos`) and the surface flux calculations (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`). The following two sections (:numref:`Ice Content` and :numref:`Water Content`) describe the ice and water content of the snow pack assuming that at least one snow layer exists. Section :numref:`Black and organic carbon and mineral dust within snow` describes how black and organic carbon and mineral dust particles are represented within snow, including meltwater flushing. See Section :numref:`Initialization of snow layer` for a description of how a snow layer is initialized. .. _Snow Covered Area Fraction: Snow Covered Area Fraction ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The fraction of the ground covered by snow, :math:`f_{sno}` , is based -on the method of :ref:`Swenson and Lawrence (2012) `. -Because the processes -governing snowfall and snowmelt differ, changes in :math:`f_{sno}` are -calculated separately for accumulation and depletion. When snowfall -occurs, :math:`f_{sno}` is updated as +The fraction of the ground covered by snow, :math:`f_{sno}`, is based on the method of :ref:`Swenson and Lawrence (2012) `. Because the processes governing snowfall and snowmelt differ, changes in :math:`f_{sno}` are calculated separately for accumulation and depletion. When snowfall occurs, :math:`f_{sno}` is updated as .. math:: :label: 8.14 f^{n+1} _{sno} =1-\left(\left(1-\tanh (k_{accum} q_{sno} \Delta t)\right)\left(1-f^{n} _{sno} \right)\right) -where :math:`k_{accum}` is a constant whose default value is 0.1, -:math:`q_{sno} \Delta t` is the amount of new snow, -:math:`f^{n+1} _{sno}` is the updated snow covered fraction (SCF), and -:math:`f^{n} _{sno}` is the SCF from the previous time step. +where :math:`k_{accum}` is a constant whose default value is 0.1, :math:`q_{sno} \Delta t` is the amount of new snow, :math:`f^{n+1} _{sno}` is the updated snow covered fraction (SCF), and :math:`f^{n} _{sno}` is the SCF from the previous time step. -When snow melt occurs, :math:`f_{sno}` is calculated from the depletion -curve +When snow melt occurs, :math:`f_{sno}` is calculated from the depletion curve .. math:: :label: 8.15 f_{sno} =1-\left(\frac{\cos ^{-1} \left(2R_{sno} -1\right)}{\pi } \right)^{N_{melt} } -where :math:`R_{sno}` is the ratio of :math:`W_{sno}` to the maximum -accumulated snow :math:`W_{\max }` , and :math:`N_{melt}` is a -parameter that depends on the topographic variability within the grid -cell. Whenever :math:`W_{sno}` reaches zero, :math:`W_{\max }` is -reset to zero. The depletion curve shape parameter is defined as +where :math:`R_{sno}` is the ratio of :math:`W_{sno}` to the maximum accumulated snow :math:`W_{\max }`, and :math:`N_{melt}` is a parameter that depends on the topographic variability within the grid cell. Whenever :math:`W_{sno}` reaches zero, :math:`W_{\max }` is reset to zero. The depletion curve shape parameter is defined as .. math:: :label: 8.16 N_{melt} =\frac{200}{\min \left(10,\sigma _{topo} \right)} -The standard deviation of the elevation within a grid cell, -:math:`\sigma _{topo}` , is calculated from a high resolution DEM (a -1km DEM is used for CLM). -Note that *glacier\_mec* columns (section :numref:`Multiple elevation class scheme`) -are treated differently in this respect, as they already account for the -subgrid topography in a grid cell in their own way. -Therefore, in each *glacier\_mec* column very flat terrain is assumed, -implemented as :math:`N_{melt}=10`. +The standard deviation of the elevation within a grid cell, :math:`\sigma _{topo}`, is calculated from a high resolution DEM (a 1km DEM is used for CLM). Note that *glacier\_mec* columns (section :numref:`Multiple elevation class scheme`) are treated differently in this respect, as they already account for the subgrid topography in a grid cell in their own way. Therefore, in each *glacier\_mec* column very flat terrain is assumed, implemented as :math:`N_{melt}=10`. .. _Ice Content: @@ -113,25 +63,14 @@ The conservation equation for mass of ice in snow layers is -\frac{\left(\Delta w_{ice,\, i} \right)_{p} }{\Delta t} & \qquad i=snl+2,\ldots ,0 \end{array}\right\} -where :math:`q_{ice,\, i-1}` is the rate of ice accumulation from -precipitation or frost or the rate of ice loss from sublimation (kg -m\ :sup:`-2` s\ :sup:`-1`) in the top layer and -:math:`{\left(\Delta w_{ice,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{ice,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` -is the change in ice due to phase change (melting rate) (section :numref:`Phase Change`). -The term :math:`q_{ice,\, i-1}` is computed in two steps as +where :math:`q_{ice,\, i-1}` is the rate of ice accumulation from precipitation or frost or the rate of ice loss from sublimation (kg m\ :sup:`-2` s\ :sup:`-1`) in the top layer and :math:`{\left(\Delta w_{ice,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{ice,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` is the change in ice due to phase change (melting rate) (section :numref:`Phase Change`). The term :math:`q_{ice,\, i-1}` is computed in two steps as .. math:: :label: 8.18 q_{ice,\, i-1} =q_{grnd,\, ice} +\left(q_{frost} -q_{subl} \right) -where :math:`q_{grnd,\, ice}` is the rate of solid precipitation -reaching the ground (section :numref:`Canopy Water`) and :math:`q_{frost}` and -:math:`q_{subl}` are gains due to frost and losses due to sublimation, -respectively (sectio :numref:`Update of Ground Sensible and Latent Heat Fluxes`). In the first step, immediately after -:math:`q_{grnd,\, ice}` has been determined after accounting for -interception (section :numref:`Canopy Water`), a new snow depth :math:`z_{sno}` (m) is -calculated from +where :math:`q_{grnd,\, ice}` is the rate of solid precipitation reaching the ground (section :numref:`Canopy Water`) and :math:`q_{frost}` and :math:`q_{subl}` are gains due to frost and losses due to sublimation, respectively (sectio :numref:`Update of Ground Sensible and Latent Heat Fluxes`). In the first step, immediately after :math:`q_{grnd,\, ice}` has been determined after accounting for interception (section :numref:`Canopy Water`), a new snow depth :math:`z_{sno}` (m) is calculated from .. math:: :label: 8.19 @@ -145,9 +84,7 @@ where \Delta z_{sno} =\frac{q_{grnd,\, ice} \Delta t}{f_{sno} \rho _{sno} } -and :math:`\rho _{sno}` is the bulk density of newly fallen snow (kg -m\ :sup:`-3`), which parameterized by a temperature-dependent and a -wind-dependent term: +and :math:`\rho _{sno}` is the bulk density of newly fallen snow (kg m\ :sup:`-3`), which parameterized by a temperature-dependent and a wind-dependent term: .. math:: :label: 8.21a @@ -169,11 +106,7 @@ The temperature dependent term is given by (:ref:`van Kampenhout et al. (2017) < .. bifall(c) = -(50._r8/15._r8 + 0.0333_r8*15_r8)*(forc_t(c)-tfrz) - 0.0333_r8*(forc_t(c)-tfrz)**2 -where :math:`T_{atm}` is the atmospheric temperature (K), and :math:`T_{f}` is -the freezing temperature of water (K) (:numref:`Table Physical Constants`). -When 10 m wind speed :math:`W_{atm}` is greater than 0.1 m\ :sup:`-1`, snow density -increases due to wind-driven compaction according to -:ref:`van Kampenhout et al. 2017 ` +where :math:`T_{atm}` is the atmospheric temperature (K), and :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical Constants`). When 10 m wind speed :math:`W_{atm}` is greater than 0.1 m\ :sup:`-1`, snow density increases due to wind-driven compaction according to :ref:`van Kampenhout et al. 2017 ` .. math:: :label: 8.21c @@ -203,26 +136,16 @@ The ice content of the top layer and the layer thickness are updated as \Delta z_{snl+1}^{n+1} =\Delta z_{snl+1}^{n} +\Delta z_{sno} . -In the second step, after surface fluxes and snow/soil temperatures have -been determined (Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat -Fluxes` and :numref:`rst_Soil and Snow Temperatures`), -:math:`w_{ice,\, snl+1}` is updated for frost or sublimation as +In the second step, after surface fluxes and snow/soil temperatures have been determined (Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes` and :numref:`rst_Soil and Snow Temperatures`), :math:`w_{ice,\, snl+1}` is updated for frost or sublimation as .. math:: :label: 8.25 w_{ice,\, snl+1}^{n+1} =w_{ice,\, snl+1}^{n} +f_{sno} \left(q_{frost} -q_{subl} \right)\Delta t. -If :math:`w_{ice,\, snl+1}^{n+1} <0` upon solution of equation , the ice -content is reset to zero and the liquid water content -:math:`w_{liq,\, snl+1}` is reduced by the amount required to bring -:math:`w_{ice,\, snl+1}^{n+1}` up to zero. +If :math:`w_{ice,\, snl+1}^{n+1} <0` upon solution of equation, the ice content is reset to zero and the liquid water content :math:`w_{liq,\, snl+1}` is reduced by the amount required to bring :math:`w_{ice,\, snl+1}^{n+1}` up to zero. -The snow water equivalent :math:`W_{sno}` is capped to not exceed 10,000 -kg m\ :sup:`-2`. If the addition of :math:`q_{frost}` were to -result in :math:`W_{sno} > 10,000` kg m\ :sup:`-2`, the frost term -:math:`q_{frost}` is instead added to the ice runoff term -:math:`q_{snwcp,\, ice}` (section :numref:`Runoff from glaciers and snow-capped surfaces`). +The snow water equivalent :math:`W_{sno}` is capped to not exceed 10,000 kg m\ :sup:`-2`. If the addition of :math:`q_{frost}` were to result in :math:`W_{sno} > 10,000` kg m\ :sup:`-2`, the frost term :math:`q_{frost}` is instead added to the ice runoff term :math:`q_{snwcp,\, ice}` (section :numref:`Runoff from glaciers and snow-capped surfaces`). .. _Water Content: @@ -236,50 +159,28 @@ The conservation equation for mass of water in snow layers is \frac{\partial w_{liq,\, i} }{\partial t} =\left(q_{liq,\, i-1} -q_{liq,\, i} \right)+\frac{\left(\Delta w_{liq,\, i} \right)_{p} }{\Delta t} -where :math:`q_{liq,\, i-1}` is the flow of liquid water into layer -:math:`i` from the layer above, :math:`q_{liq,\, i}` is the flow of -water out of layer :math:`i` to the layer below, -:math:`{\left(\Delta w_{liq,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{liq,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` -is the change in liquid water due to phase change (melting rate) -(section :numref:`Phase Change`). For the top snow layer only, +where :math:`q_{liq,\, i-1}` is the flow of liquid water into layer :math:`i` from the layer above, :math:`q_{liq,\, i}` is the flow of water out of layer :math:`i` to the layer below, :math:`{\left(\Delta w_{liq,\, i} \right)_{p} \mathord{\left/ {\vphantom {\left(\Delta w_{liq,\, i} \right)_{p} \Delta t}} \right.} \Delta t}` is the change in liquid water due to phase change (melting rate) (section :numref:`Phase Change`). For the top snow layer only, .. math:: :label: 8.27 q_{liq,\, i-1} =f_{sno} \left(q_{grnd,\, liq} +\left(q_{sdew} -q_{seva} \right)\right) -where :math:`q_{grnd,\, liq}` is the rate of liquid precipitation -reaching the snow (section :numref:`Canopy Water`), :math:`q_{seva}` is the -evaporation of liquid water and :math:`q_{sdew}` is the liquid dew (section -:numref:`Update of Ground Sensible and Latent Heat Fluxes`). After surface -fluxes and snow/soil temperatures have been determined -(Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes` and -:numref:`rst_Soil and Snow Temperatures`), :math:`w_{liq,\, snl+1}` is -updated for the liquid precipitation reaching the ground and dew or -evaporation as +where :math:`q_{grnd,\, liq}` is the rate of liquid precipitation reaching the snow (section :numref:`Canopy Water`), :math:`q_{seva}` is the evaporation of liquid water and :math:`q_{sdew}` is the liquid dew (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`). After surface fluxes and snow/soil temperatures have been determined (Chapters :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes` and :numref:`rst_Soil and Snow Temperatures`), :math:`w_{liq,\, snl+1}` is updated for the liquid precipitation reaching the ground and dew or evaporation as .. math:: :label: 8.28 w_{liq,\, snl+1}^{n+1} =w_{liq,\, snl+1}^{n} +f_{sno} \left(q_{grnd,\, liq} +q_{sdew} -q_{seva} \right)\Delta t. -When the liquid water within a snow layer exceeds the layer's holding -capacity, the excess water is added to the underlying layer, limited by -the effective porosity (:math:`1-\theta _{ice}` ) of the layer. The flow -of water is assumed to be zero (:math:`q_{liq,\, i} =0`) if the -effective porosity of either of the two layers -(:math:`1-\theta _{ice,\, i} {\rm \; and\; }1-\theta _{ice,\, i+1}` ) is -less than :math:`\theta _{imp} =0.05`, the water impermeable volumetric -water content. Thus, water flow between layers, :math:`q_{liq,\, i}` , -for layers :math:`i=snl+1,\ldots ,0`, is initially calculated as +When the liquid water within a snow layer exceeds the layer's holding capacity, the excess water is added to the underlying layer, limited by the effective porosity (:math:`1-\theta _{ice}` ) of the layer. The flow of water is assumed to be zero (:math:`q_{liq,\, i} =0`) if the effective porosity of either of the two layers (:math:`1-\theta _{ice,\, i} {\rm \; and\; }1-\theta _{ice,\, i+1}` ) is less than :math:`\theta _{imp} =0.05`, the water impermeable volumetric water content. Thus, water flow between layers, :math:`q_{liq,\, i}`, for layers :math:`i=snl+1,\ldots,0`, is initially calculated as .. math:: :label: 8.29 q_{liq,\, i} =\frac{\rho _{liq} \left[\theta _{liq,\, i} -S_{r} \left(1-\theta _{ice,\, i} \right)\right]f_{sno} \Delta z_{i} }{\Delta t} \ge 0 -where the volumetric liquid water :math:`\theta _{liq,\, i}` and ice -:math:`\theta _{ice,\, i}` contents are +where the volumetric liquid water :math:`\theta _{liq,\, i}` and ice :math:`\theta _{ice,\, i}` contents are .. math:: :label: 8.30 @@ -291,12 +192,7 @@ where the volumetric liquid water :math:`\theta _{liq,\, i}` and ice \theta _{liq,\, i} =\frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} \rho _{liq} } \le 1-\theta _{ice,\, i} , -and :math:`S_{r} =0.033` is the irreducible water saturation (snow -holds a certain amount of liquid water due to capillary retention after -drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the -underlying layer limits the flow of water :math:`q_{liq,\, i}` -calculated in equation , unless the underlying layer is the surface soil -layer, as +and :math:`S_{r} =0.033` is the irreducible water saturation (snow holds a certain amount of liquid water due to capillary retention after drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the underlying layer limits the flow of water :math:`q_{liq,\, i}` calculated in equation, unless the underlying layer is the surface soil layer, as .. math:: :label: 8.32 @@ -310,33 +206,16 @@ The liquid water content :math:`w_{liq,\, i}` is updated as w_{liq,\, i}^{n+1} =w_{liq,\, i}^{n} +\left(q_{i-1} -q_{i} \right)\Delta t. -Equations - are solved sequentially from top (:math:`i=snl+1`) to -bottom (:math:`i=0`) snow layer in each time step. The total flow of -liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` -which is used in the calculation of surface runoff and infiltration -(sections :numref:`Surface Runoff` and :numref:`Infiltration`). +Equations - are solved sequentially from top (:math:`i=snl+1`) to bottom (:math:`i=0`) snow layer in each time step. The total flow of liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` which is used in the calculation of surface runoff and infiltration (sections :numref:`Surface Runoff` and :numref:`Infiltration`). .. _Black and organic carbon and mineral dust within snow: Black and organic carbon and mineral dust within snow ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Particles within snow originate from atmospheric aerosol deposition -(:math:`D_{sp}` in Table 2.3 (kg m\ :sup:`-2` s\ :sup:`-1`) -and influence snow radiative transfer (sections :numref:`Snow Albedo`, -:numref:`Snowpack Optical Properties`, and :numref:`Snow Aging`). -Particle masses and mixing ratios are represented with a simple -mass-conserving scheme. The model maintains masses of the following -eight particle species within each snow layer: hydrophilic black carbon, -hydrophobic black carbon, hydrophilic organic carbon, hydrophobic -organic carbon, and four species of mineral dust with the following -particle sizes: 0.1-1.0, 1.0-2.5, 2.5-5.0, and 5.0-10.0 :math:`\mu m`. -Each of these species has unique optical properties -(:numref:`Table Single-scatter albedo values used for snowpack impurities and ice`) -and meltwater removal efficiencies (:numref:`Table Meltwater scavenging`). +Particles within snow originate from atmospheric aerosol deposition (:math:`D_{sp}` in Table 2.3 (kg m\ :sup:`-2` s\ :sup:`-1`) and influence snow radiative transfer (sections :numref:`Snow Albedo`, :numref:`Snowpack Optical Properties`, and :numref:`Snow Aging`). Particle masses and mixing ratios are represented with a simple mass-conserving scheme. The model maintains masses of the following eight particle species within each snow layer: hydrophilic black carbon, hydrophobic black carbon, hydrophilic organic carbon, hydrophobic organic carbon, and four species of mineral dust with the following particle sizes: 0.1-1.0, 1.0-2.5, 2.5-5.0, and 5.0-10.0 :math:`\mu m`. Each of these species has unique optical properties (:numref:`Table Single-scatter albedo values used for snowpack impurities and ice`) and meltwater removal efficiencies (:numref:`Table Meltwater scavenging`). -The black carbon and organic carbon deposition rates described in Table -2.3 are combined into four categories as follows +The black carbon and organic carbon deposition rates described in Table 2.3 are combined into four categories as follows .. math:: :label: 8.34 @@ -358,45 +237,21 @@ The black carbon and organic carbon deposition rates described in Table D_{oc,\, hphob} =D_{oc,\, dryhphob} -Deposited particles are assumed to be instantly mixed (homogeneously) -within the surface snow layer and are added after the inter-layer water -fluxes are computed (section :numref:`Water Content`) so that some aerosol is in the top -layer after deposition and is not immediately washed out before radiative -calculations are done. Particle masses are then redistributed each time -step based on meltwater drainage through the snow column (section -:numref:`Water Content`) and snow layer combination and subdivision -(section :numref:`Snow Layer Combination and Subdivision`). The change in -mass of each of the particle species :math:`\Delta m_{sp,\, i}` -(kg m\ :sup:`-2`) is +Deposited particles are assumed to be instantly mixed (homogeneously) within the surface snow layer and are added after the inter-layer water fluxes are computed (section :numref:`Water Content`) so that some aerosol is in the top layer after deposition and is not immediately washed out before radiative calculations are done. Particle masses are then redistributed each time step based on meltwater drainage through the snow column (section :numref:`Water Content`) and snow layer combination and subdivision (section :numref:`Snow Layer Combination and Subdivision`). The change in mass of each of the particle species :math:`\Delta m_{sp,\, i}` (kg m\ :sup:`-2`) is .. math:: :label: 8.38 \Delta m_{sp,\, i} =\left[k_{sp} \left(q_{liq,\, i-1} c_{sp,\, i-1} -q_{liq,\, i} c_{i} \right)+D_{sp} \right]\Delta t -where :math:`k_{sp}` is the meltwater scavenging efficiency that is -unique for each species (:numref:`Table Meltwater scavenging`), :math:`q_{liq,\, i-1}` is the flow -of liquid water into layer :math:`i` from the layer above, -:math:`q_{liq,\, i}` is the flow of water out of layer :math:`i` into -the layer below (kg m\ :sup:`-2` s\ :sup:`-1`) (section -:numref:`Water Content`), :math:`c_{sp,\, i-1}` and :math:`c_{sp,\, i}` are the particle -mass mixing ratios in layers :math:`i-1` and :math:`i` (kg -kg\ :sup:`-1`), :math:`D_{sp}` is the atmospheric deposition rate -(zero for all layers except layer :math:`snl+1`), and :math:`\Delta t` -is the model time step (s). The particle mass mixing ratio is +where :math:`k_{sp}` is the meltwater scavenging efficiency that is unique for each species (:numref:`Table Meltwater scavenging`), :math:`q_{liq,\, i-1}` is the flow of liquid water into layer :math:`i` from the layer above, :math:`q_{liq,\, i}` is the flow of water out of layer :math:`i` into the layer below (kg m\ :sup:`-2` s\ :sup:`-1`) (section :numref:`Water Content`), :math:`c_{sp,\, i-1}` and :math:`c_{sp,\, i}` are the particle mass mixing ratios in layers :math:`i-1` and :math:`i` (kg kg\ :sup:`-1`), :math:`D_{sp}` is the atmospheric deposition rate (zero for all layers except layer :math:`snl+1`), and :math:`\Delta t` is the model time step (s). The particle mass mixing ratio is .. math:: :label: 8.39 c_{i} =\frac{m_{sp,\, i} }{w_{liq,\, i} +w_{ice,\, i} } . -Values of :math:`k_{sp}` are partially derived from experiments -published by :ref:`Conway et al. (1996) `. Particles masses are re-distributed -proportionately with snow mass when layers are combined or divided, thus -conserving particle mass within the snow column. The mass of particles -carried out with meltwater through the bottom snow layer is assumed to -be permanently lost from the snowpack, and is not maintained within the -model. +Values of :math:`k_{sp}` are partially derived from experiments published by :ref:`Conway et al. (1996) `. Particles masses are re-distributed proportionately with snow mass when layers are combined or divided, thus conserving particle mass within the snow column. The mass of particles carried out with meltwater through the bottom snow layer is assumed to be permanently lost from the snowpack, and is not maintained within the model. .. _Table Meltwater scavenging: @@ -427,10 +282,7 @@ model. Initialization of snow layer ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -If there are no existing snow layers (:math:`snl+1=1`) but -:math:`z_{sno} \ge 0.01` m after accounting for solid precipitation -:math:`q_{sno}` , then a snow layer is initialized (:math:`snl=-1`) as -follows +If there are no existing snow layers (:math:`snl+1=1`) but :math:`z_{sno} \ge 0.01` m after accounting for solid precipitation :math:`q_{sno}`, then a snow layer is initialized (:math:`snl=-1`) as follows .. math:: :label: 8.40 @@ -449,19 +301,14 @@ follows Snow Compaction ^^^^^^^^^^^^^^^^^^^^^ -Snow compaction is initiated after the soil hydrology calculations -[surface runoff (section :numref:`Surface Runoff`), infiltration (section -:numref:`Infiltration`), soil water (section :numref:`Soil Water`)] are -complete. Currently, there are four processes included that lead to snow -compaction: +Snow compaction is initiated after the soil hydrology calculations [surface runoff (section :numref:`Surface Runoff`), infiltration (section :numref:`Infiltration`), soil water (section :numref:`Soil Water`)] are complete. Currently, there are four processes included that lead to snow compaction: #. destructive metamorphism of new snow (crystal breakdown due to wind or thermodynamic stress) #. snow load or compaction by overburden pressure #. melting (changes in snow structure due to melt-freeze cycles plus changes in crystals due to liquid water) #. drifting snow compaction. -The total fractional compaction rate for each snow layer :math:`C_{R,\, i}` -(s\ :sup:`-1`) is the sum of multiple compaction processes +The total fractional compaction rate for each snow layer :math:`C_{R,\, i}` (s\ :sup:`-1`) is the sum of multiple compaction processes .. math:: :label: 8.41 @@ -475,8 +322,7 @@ Compaction is not allowed if the layer is saturated 1-\left(\frac{w_{ice,\, i} }{f_{sno} \Delta z_{i} \rho _{ice} } +\frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} \rho _{liq} } \right)\le 0.001 -or if the ice content is below a minimum value -(:math:`w_{ice,\, i} \le 0.1`). +or if the ice content is below a minimum value (:math:`w_{ice,\, i} \le 0.1`). The snow layer thickness after compaction is @@ -511,11 +357,8 @@ where :math:`c_{3} =2.777\times 10^{-6}` (s\ :sup:`-1`) is the fractional compa .. upper limit (upplim_destruct_metamorph) used to be 100 but was changed to 175 for CLM5 (Van Kampenhout et al., 2017) -where -:math:`{w_{ice,\, i} \mathord{\left/ {\vphantom {w_{ice,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` -and -:math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` -are the bulk densities of liquid water and ice (kg m\ :sup:`-3`). +where :math:`{w_{ice,\, i} \mathord{\left/ {\vphantom {w_{ice,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` and +:math:`{w_{liq,\, i} \mathord{\left/ {\vphantom {w_{liq,\, i} \left(f_{sno} \Delta z_{i} \right)}} \right.} \left(f_{sno} \Delta z_{i} \right)}` are the bulk densities of liquid water and ice (kg m\ :sup:`-3`). .. _Overburden pressure compaction: @@ -529,43 +372,34 @@ The compaction rate as a result of overburden :math:`C_{R2,\; i}` (s\ :sup:`-1`) C_{R2,\, i} =\left[\frac{1}{\Delta z_{i} } \frac{\partial \Delta z_{i} }{\partial t} \right]_{overburden} =-\frac{P_{s,\, i} }{\eta } -The snow load pressure :math:`P_{s,\, i}` is calculated for each layer as the sum of -the ice :math:`w_{ice,\, i}` and liquid water contents -:math:`w_{liq,\, i}` of the layers above plus half the ice and liquid -water contents of the layer being compacted +The snow load pressure :math:`P_{s,\, i}` is calculated for each layer as the sum of the ice :math:`w_{ice,\, i}` and liquid water contents :math:`w_{liq,\, i}` of the layers above plus half the ice and liquid water contents of the layer being compacted .. math:: :label: 8.47 P_{s,\, i} =\frac{w_{ice,\, i} +w_{liq,\, i} }{2} +\sum _{j=snl+1}^{j=i-1}\left(w_{ice,\, j} +w_{liq,\, j} \right) . -Variable :math:`\eta` in :eq:`8.45` is a viscosity coefficient (kg s m\ :sup:`-2`) that varies with density and -temperature as +Variable :math:`\eta` in :eq:`8.45` is a viscosity coefficient (kg s m\ :sup:`-2`) that varies with density and temperature as .. math:: :label: 8.46 \eta = f_{1} f_{2} \eta_{0} \frac{\rho_{i}}{c_{\eta}} \exp \left[ a_{\eta} \left(T_{f} -T_{i} \right) + b_{\eta} \rho_{i} \right] -with constant factors :math:`\eta _{0} = 7.62237 \times 10^{6}` kg s\ :sup:`-1` m\ :sup:`-2`, -:math:`a_{\eta} = 0.1` K\ :sup:`-1`, :math:`b_{\eta} = 0.023` m\ :sup:`-3` kg\ :sup:`-1`, -and :math:`c_{\eta} = 450` kg m\ :sup:`-3` (:ref:`van Kampenhout et al. (2017) `). -Further, factor :math:`f_1` accounts for the presence of liquid water (:ref:`Vionnet et al. (2012) `): +with constant factors :math:`\eta _{0} = 7.62237 \times 10^{6}` kg s\ :sup:`-1` m\ :sup:`-2`, :math:`a_{\eta} = 0.1` K\ :sup:`-1`, :math:`b_{\eta} = 0.023` m\ :sup:`-3` kg\ :sup:`-1`, and :math:`c_{\eta} = 450` kg m\ :sup:`-3` (:ref:`van Kampenhout et al. (2017) `). Further, factor :math:`f_1` accounts for the presence of liquid water (:ref:`Vionnet et al. (2012) `): .. math:: :label: 8.46b f_{1} = \frac{1}{1+ 60 \frac{w_{\mathrm{liq},\, i}}{\rho_{\mathrm{liq}} \Delta z_{i} }}. -Factor :math:`f_2` originally accounts for the presence of angular grains, but since grain shape is not modelled -:math:`f_2` is fixed to the value 4. +Factor :math:`f_2` originally accounts for the presence of angular grains, but since grain shape is not modelled :math:`f_2` is fixed to the value 4. .. _Compaction by melt: Compaction by melt '''''''''''''''''' -The compaction rate due to melting :math:`C_{R3,\; i}` (s\ :sup:`-1`) is taken to be the ratio of the change in snow ice -mass after the melting to the mass before melting +The compaction rate due to melting :math:`C_{R3,\; i}` (s\ :sup:`-1`) is taken to be the ratio of the change in snow ice mass after the melting to the mass before melting .. math:: :label: 8.48 @@ -573,10 +407,7 @@ mass after the melting to the mass before melting C_{R3,\, i} = \left[\frac{1}{\Delta z_{i} } \frac{\partial \Delta z_{i} }{\partial t} \right]_{melt} = -\frac{1}{\Delta t} \max \left(0,\frac{W_{sno,\, i}^{n} -W_{sno,\, i}^{n+1} }{W_{sno,\, i}^{n} } \right) -and melting is identified during the phase change calculations (section -:numref:`Phase Change`). Because snow depth is defined as the average -depth of the snow covered area, the snow depth must also be updated for -changes in :math:`f_{sno}` when :math:`W_{sno}` has changed. +and melting is identified during the phase change calculations (section :numref:`Phase Change`). Because snow depth is defined as the average depth of the snow covered area, the snow depth must also be updated for changes in :math:`f_{sno}` when :math:`W_{sno}` has changed. .. math:: :label: 8.49 @@ -587,10 +418,7 @@ changes in :math:`f_{sno}` when :math:`W_{sno}` has changed. Compaction by drifting snow ''''''''''''''''''''''''''' -Crystal breaking by drifting snow leads to higher snow densities at the surface. -This process is particularly important on ice sheets, where destructive metamorphism is slow due to low temperatures -but high wind speeds (katabatic winds) are prevailing. -Therefore a drifting snow compaction parametrization was introduced, based on (:ref:`Vionnet et al. (2012) `). +Crystal breaking by drifting snow leads to higher snow densities at the surface. This process is particularly important on ice sheets, where destructive metamorphism is slow due to low temperatures but high wind speeds (katabatic winds) are prevailing. Therefore a drifting snow compaction parametrization was introduced, based on (:ref:`Vionnet et al. (2012) `). .. math:: :label: 8.50 @@ -619,49 +447,31 @@ as well as the 10 m wind speed: M_\mathrm{O} & = & -0.069 + 0.66 F(\rho) \end{array} -The latter equation (for the mobility index :math:`M_\mathrm{O}`) is a simplification from the original paper -by removing the dependency on grain size and assuming spherical grains -(see :ref:`van Kampenhout et al. (2017) `). +The latter equation (for the mobility index :math:`M_\mathrm{O}`) is a simplification from the original paper by removing the dependency on grain size and assuming spherical grains (see :ref:`van Kampenhout et al. (2017) `). .. _Snow Layer Combination and Subdivision: Snow Layer Combination and Subdivision ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -After the determination of snow temperature including phase change(Chapter -:numref:`rst_Soil and Snow Temperatures`), snow hydrology (Chapter -:numref:`rst_Snow Hydrology`), and the compaction calculations (section -:numref:`Snow Compaction`) , the number of snow layers is adjusted by -either combining or subdividing layers. The combination and subdivision -of snow layers is based on :ref:`Jordan (1991) `. +After the determination of snow temperature including phase change(Chapter :numref:`rst_Soil and Snow Temperatures`), snow hydrology (Chapter :numref:`rst_Snow Hydrology`), and the compaction calculations (section :numref:`Snow Compaction`), the number of snow layers is adjusted by either combining or subdividing layers. The combination and subdivision of snow layers is based on :ref:`Jordan (1991) `. .. _Combination: Combination ''''''''''''''''''' -If a snow layer has nearly melted or if its thickness -:math:`\Delta z_{i}` is less than the prescribed minimum thickness -:math:`\Delta z_{\min }` (:numref:`Table snow layer thickness`), the layer is combined with a -neighboring layer. The overlying or underlying layer is selected as the -neighboring layer according to the following rules +If a snow layer has nearly melted or if its thickness :math:`\Delta z_{i}` is less than the prescribed minimum thickness :math:`\Delta z_{\min }` (:numref:`Table snow layer thickness`), the layer is combined with a neighboring layer. The overlying or underlying layer is selected as the neighboring layer according to the following rules -#. If the top layer is being removed, it is combined with the underlying - layer +#. If the top layer is being removed, it is combined with the underlying layer -#. If the underlying layer is not snow (i.e., it is the top soil layer), - the layer is combined with the overlying layer +#. If the underlying layer is not snow (i.e., it is the top soil layer), the layer is combined with the overlying layer -#. If the layer is nearly completely melted, the layer is combined with - the underlying layer +#. If the layer is nearly completely melted, the layer is combined with the underlying layer -#. If none of the above rules apply, the layer is combined with the - thinnest neighboring layer. +#. If none of the above rules apply, the layer is combined with the thinnest neighboring layer. -A first pass is made through all snow layers to determine if any layer -is nearly melted (:math:`w_{ice,\, i} \le 0.1`). If so, the remaining -liquid water and ice content of layer :math:`i` is combined with the -underlying neighbor :math:`i+1` as +A first pass is made through all snow layers to determine if any layer is nearly melted (:math:`w_{ice,\, i} \le 0.1`). If so, the remaining liquid water and ice content of layer :math:`i` is combined with the underlying neighbor :math:`i+1` as .. math:: :label: 8.51 @@ -673,18 +483,9 @@ underlying neighbor :math:`i+1` as w_{ice,\, i+1} =w_{ice,\, i+1} +w_{ice,\, i} . -This includes the snow layer directly above the top soil layer. In this -case, the liquid water and ice content of the melted snow layer is added -to the contents of the top soil layer. The layer properties, -:math:`T_{i}` , :math:`w_{ice,\, i}` , :math:`w_{liq,\, i}` , -:math:`\Delta z_{i}` , are then re-indexed so that the layers above the -eliminated layer are shifted down by one and the number of snow layers -is decremented accordingly. +This includes the snow layer directly above the top soil layer. In this case, the liquid water and ice content of the melted snow layer is added to the contents of the top soil layer. The layer properties, :math:`T_{i}`, :math:`w_{ice,\, i}`, :math:`w_{liq,\, i}`, :math:`\Delta z_{i}`, are then re-indexed so that the layers above the eliminated layer are shifted down by one and the number of snow layers is decremented accordingly. -At this point, if there are no explicit snow layers remaining -(:math:`snl=0`), the snow water equivalent :math:`W_{sno}` and snow -depth :math:`z_{sno}` are set to zero, otherwise, :math:`W_{sno}` and -:math:`z_{sno}` are re-calculated as +At this point, if there are no explicit snow layers remaining (:math:`snl=0`), the snow water equivalent :math:`W_{sno}` and snow depth :math:`z_{sno}` are set to zero, otherwise, :math:`W_{sno}` and :math:`z_{sno}` are re-calculated as .. math:: :label: 8.53 @@ -696,16 +497,9 @@ depth :math:`z_{sno}` are set to zero, otherwise, :math:`W_{sno}` and z_{sno} =\sum _{i=snl+1}^{i=0}\Delta z_{i} . -If the snow depth :math:`00} \\ {\lambda _{vap} \qquad {\rm otherwise}} \end{array}\right\} -where :math:`\lambda _{sub}` and :math:`\lambda _{vap}` are the -latent heat of sublimation and vaporization, respectively (J -kg\ :sup:`-1`) (:numref:`Table Physical Constants`), and :math:`w_{liq,\, snl+1}` -and :math:`w_{ice,\, snl+1}` are the liquid water and ice contents of the -top snow/soil layer, respectively (kg m\ :sup:`-2`) -(Chapter :numref:`rst_Hydrology`). +where :math:`\lambda _{sub}` and :math:`\lambda _{vap}` are the latent heat of sublimation and vaporization, respectively (J kg\ :sup:`-1`) (:numref:`Table Physical Constants`), and :math:`w_{liq,\, snl+1}` and :math:`w_{ice,\, snl+1}` are the liquid water and ice contents of the top snow/soil layer, respectively (kg m\ :sup:`-2`) (Chapter :numref:`rst_Hydrology`). For the top soil layer, :math:`i=1`, the coefficients are @@ -402,34 +311,18 @@ The heat flux into the soil surface from the overlying atmosphere h=\overrightarrow{S}_{soil} -\overrightarrow{L}_{soil} -H_{soil} -\lambda E_{soil} -It can be seen that when no snow is present (:math:`f_{sno} =0`), the -expressions for the coefficients of the top soil layer have the same -form as those for the top snow layer. +It can be seen that when no snow is present (:math:`f_{sno} =0`), the expressions for the coefficients of the top soil layer have the same form as those for the top snow layer. -The surface snow/soil layer temperature computed in this way is the -layer-averaged temperature and hence has somewhat reduced diurnal -amplitude compared with surface temperature. An accurate surface -temperature is provided that compensates for this effect and numerical -error by tuning the heat capacity of the top layer (through adjustment -of the layer thickness) to give an exact match to the analytic solution -for diurnal heating. The top layer thickness for :math:`i=snl+1` is -given by +The surface snow/soil layer temperature computed in this way is the layer-averaged temperature and hence has somewhat reduced diurnal amplitude compared with surface temperature. An accurate surface temperature is provided that compensates for this effect and numerical error by tuning the heat capacity of the top layer (through adjustment of the layer thickness) to give an exact match to the analytic solution for diurnal heating. The top layer thickness for :math:`i=snl+1` is given by .. math:: :label: 6.34 \Delta z_{i*} =0.5\left[z_{i} -z_{h,\, i-1} +c_{a} \left(z_{i+1} -z_{h,\, i-1} \right)\right] -where :math:`c_{a}` is a tunable parameter, varying from 0 to 1, and is -taken as 0.34 by comparing the numerical solution with the analytic -solution (:ref:`Z.-L. Yang 1998, unpublished manuscript`). -:math:`\Delta z_{i*}` is used in place of :math:`\Delta z_{i}` for -:math:`i=snl+1` in equations -. The top snow/soil layer temperature -computed in this way is the ground surface temperature -:math:`T_{g}^{n+1}` . +where :math:`c_{a}` is a tunable parameter, varying from 0 to 1, and is taken as 0.34 by comparing the numerical solution with the analytic solution (:ref:`Z.-L. Yang 1998, unpublished manuscript`). :math:`\Delta z_{i*}` is used in place of :math:`\Delta z_{i}` for :math:`i=snl+1` in equations -. The top snow/soil layer temperature computed in this way is the ground surface temperature :math:`T_{g}^{n+1}`. -The boundary condition at the bottom of the snow/soil column is zero -heat flux, :math:`F_{i} =0`, resulting in, for :math:`i=N_{levgrnd}` , +The boundary condition at the bottom of the snow/soil column is zero heat flux, :math:`F_{i} =0`, resulting in, for :math:`i=N_{levgrnd}`, .. math:: :label: 6.35 @@ -463,8 +356,7 @@ where F_{i-1} =-\frac{\lambda \left[z_{h,\, i-1} \right]}{z_{i} -z_{i-1} } \left(T_{i-1}^{n} -T_{i}^{n} \right). -For the interior snow/soil layers, :math:`snl+1` is adopted. The supercooled -soil water is the liquid water that coexists with ice over a wide range of -temperatures below freezing and is implemented through a freezing point -depression equation +where :math:`T_{i}^{n+1}` is the soil layer temperature after solution of the tridiagonal equation set, :math:`w_{ice,\, i}` and :math:`w_{liq,\, i}` are the mass of ice and liquid water (kg m\ :sup:`-2`) in each snow/soil layer, respectively, and :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical Constants`). For the freezing process in soil layers, the concept of supercooled soil water from :ref:`Niu and Yang (2006)` is adopted. The supercooled soil water is the liquid water that coexists with ice over a wide range of temperatures below freezing and is implemented through a freezing point depression equation .. math:: :label: 6.54 w_{liq,\, \max ,\, i} =\Delta z_{i} \theta _{sat,\, i} \left[\frac{10^{3} L_{f} \left(T_{f} -T_{i} \right)}{gT_{i} \psi _{sat,\, i} } \right]^{{-1\mathord{\left/ {\vphantom {-1 B_{i} }} \right.} B_{i} } } \qquad T_{i} ` exponent -(section :numref:`Soil Water`). - -For the special case when snow is present (snow mass :math:`W_{sno} >0`) -but there are no explicit snow layers (:math:`snl=0`) (i.e., there is -not enough snow present to meet the minimum snow depth requirement of -0.01 m), snow melt will take place for soil layer :math:`i=1` if the -soil layer temperature is greater than the freezing temperature -(:math:`T_{1}^{n+1} >T_{f}` ). - -The rate of phase change is assessed from the energy excess (or deficit) -needed to change :math:`T_{i}` to freezing temperature, :math:`T_{f}` . -The excess or deficit of energy :math:`H_{i}` (W m\ :sup:`-2`) is -determined as follows +where :math:`w_{liq,\, \max,\, i}` is the maximum liquid water in layer :math:`i` (kg m\ :sup:`-2`) when the soil temperature :math:`T_{i}` is below the freezing temperature :math:`T_{f}`, :math:`L_{f}` is the latent heat of fusion (J kg\ :sup:`-1`) (:numref:`Table Physical Constants`), :math:`g` is the gravitational acceleration (m s\ :sup:`-2`) (:numref:`Table Physical Constants`), and :math:`\psi _{sat,\, i}` and :math:`B_{i}` are the soil texture-dependent saturated matric potential (mm) and :ref:`Clapp and Hornberger (1978)` exponent (section :numref:`Soil Water`). + +For the special case when snow is present (snow mass :math:`W_{sno} >0`) but there are no explicit snow layers (:math:`snl=0`) (i.e., there is not enough snow present to meet the minimum snow depth requirement of 0.01 m), snow melt will take place for soil layer :math:`i=1` if the soil layer temperature is greater than the freezing temperature (:math:`T_{1}^{n+1} >T_{f}` ). + +The rate of phase change is assessed from the energy excess (or deficit) needed to change :math:`T_{i}` to freezing temperature, :math:`T_{f}`. The excess or deficit of energy :math:`H_{i}` (W m\ :sup:`-2`) is determined as follows .. math:: :label: 6.55 @@ -612,24 +474,21 @@ determined as follows -\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{f} -T_{i}^{n} \right) & \quad \quad i\ne \left\{1,snl+1\right\} \end{array}\right\}. -If the melting criteria is met :eq:`6.53a` and -:math:`H_{m} =\frac{H_{i} \Delta t}{L_{f} } >0`, then the ice mass is -readjusted as +If the melting criteria is met :eq:`6.53a` and :math:`H_{m} =\frac{H_{i} \Delta t}{L_{f} } >0`, then the ice mass is readjusted as .. math:: :label: 6.56 w_{ice,\, i}^{n+1} =w_{ice,\, i}^{n} -H_{m} \ge 0\qquad i=snl+1,\ldots ,N_{levgrnd} . -If the freezing criteria is met :eq:`6.53b` and :math:`H_{m} <0`, then -the ice mass is readjusted for :math:`i=snl+1,\ldots ,0` as +If the freezing criteria is met :eq:`6.53b` and :math:`H_{m} <0`, then the ice mass is readjusted for :math:`i=snl+1,\ldots,0` as .. math:: :label: 6.57 w_{ice,\, i}^{n+1} =\min \left(w_{liq,\, i}^{n} +w_{ice,\, i}^{n} ,w_{ice,\, i}^{n} -H_{m} \right) -and for :math:`i=1,\ldots ,N_{levgrnd}` as +and for :math:`i=1,\ldots,N_{levgrnd}` as .. math:: :label: 6.58 @@ -647,16 +506,14 @@ Liquid water mass is readjusted as w_{liq,\, i}^{n+1} =w_{liq,\, i}^{n} +w_{ice,\, i}^{n} -w_{ice,\, i}^{n+1} \ge 0. -Because part of the energy :math:`H_{i}` may not be consumed in -melting or released in freezing, the energy is recalculated as +Because part of the energy :math:`H_{i}` may not be consumed in melting or released in freezing, the energy is recalculated as .. math:: :label: 6.60 H_{i*} =H_{i} -\frac{L_{f} \left(w_{ice,\, i}^{n} -w_{ice,\, i}^{n+1} \right)}{\Delta t} -and this energy is used to cool or warm the snow/soil layer (if -:math:`\left|H_{i*} \right|>0`) as +and this energy is used to cool or warm the snow/soil layer (if :math:`\left|H_{i*} \right|>0`) as .. math:: :label: 6.61 @@ -668,10 +525,7 @@ and this energy is used to cool or warm the snow/soil layer (if T_{f} +\frac{\Delta t}{c_{i} \Delta z_{i} } H_{i*} & \quad \quad \quad \quad \, i\ne \left\{1,snl+1\right\} \end{array}\right\}. -For the special case when snow is present (:math:`W_{sno} >0`), there -are no explicit snow layers (:math:`snl=0`), and -:math:`\frac{H_{1} \Delta t}{L_{f} } >0` (melting), the snow mass -:math:`W_{sno}` (kg m\ :sup:`-2`) is reduced according to +For the special case when snow is present (:math:`W_{sno} >0`), there are no explicit snow layers (:math:`snl=0`), and :math:`\frac{H_{1} \Delta t}{L_{f} } >0` (melting), the snow mass :math:`W_{sno}` (kg m\ :sup:`-2`) is reduced according to .. math:: :label: 6.62 @@ -685,27 +539,21 @@ The snow depth is reduced proportionally z_{sno}^{n+1} =\frac{W_{sno}^{n+1} }{W_{sno}^{n} } z_{sno}^{n} . -Again, because part of the energy may not be consumed in melting, the -energy for the surface soil layer :math:`i=1` is recalculated as +Again, because part of the energy may not be consumed in melting, the energy for the surface soil layer :math:`i=1` is recalculated as .. math:: :label: 6.64 H_{1*} =H_{1} -\frac{L_{f} \left(W_{sno}^{n} -W_{sno}^{n+1} \right)}{\Delta t} . -If there is excess energy (:math:`H_{1*} >0`), this energy becomes -available to the top soil layer as +If there is excess energy (:math:`H_{1*} >0`), this energy becomes available to the top soil layer as .. math:: :label: 6.65 H_{1} =H_{1*} . -The ice mass, liquid water content, and temperature of the top soil -layer are then determined from :eq:`6.56`, :eq:`6.59`, and :eq:`6.61` -using the recalculated energy from :eq:`6.65`. Snow melt :math:`M_{1S}` -(kg m\ :sup:`-2` s\ :sup:`-1`) and phase change energy :math:`E_{p,\, 1S}` -(W m\ :sup:`-2`) for this special case are +The ice mass, liquid water content, and temperature of the top soil layer are then determined from :eq:`6.56`, :eq:`6.59`, and :eq:`6.61` using the recalculated energy from :eq:`6.65`. Snow melt :math:`M_{1S}` (kg m\ :sup:`-2` s\ :sup:`-1`) and phase change energy :math:`E_{p,\, 1S}` (W m\ :sup:`-2`) for this special case are .. math:: :label: 6.66 @@ -717,8 +565,7 @@ using the recalculated energy from :eq:`6.65`. Snow melt :math:`M_{1S}` E_{p,\, 1S} =L_{f} M_{1S} . -The total energy of phase change :math:`E_{p}` (W m\ :sup:`-2`) -for the snow/soil column is +The total energy of phase change :math:`E_{p}` (W m\ :sup:`-2`) for the snow/soil column is .. math:: :label: 6.68 @@ -732,8 +579,7 @@ where E_{p,\, i} =L_{f} \frac{\left(w_{ice,\, i}^{n} -w_{ice,\, i}^{n+1} \right)}{\Delta t} . -The total snow melt :math:`M` (kg m\ :sup:`-2` -s\ :sup:`-1`) is +The total snow melt :math:`M` (kg m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 6.70 @@ -754,27 +600,21 @@ The solution for snow/soil temperatures conserves energy as G-E_{p} -\sum _{i=snl+1}^{i=N_{levgrnd} }\frac{c_{i} \Delta z_{i} }{\Delta t} \left(T_{i}^{n+1} -T_{i}^{n} \right)=0 -where :math:`G` is the ground heat flux (section -:numref:`Update of Ground Sensible and Latent Heat Fluxes`). +where :math:`G` is the ground heat flux (section :numref:`Update of Ground Sensible and Latent Heat Fluxes`). .. _Surface Water: Surface Water ^^^^^^^^^^^^^^^^^^^ -Phase change of surface water takes place when the surface water -temperature, :math:`T_{h2osfc}` , becomes less than :math:`T_{f}` . The -energy available for freezing is +Phase change of surface water takes place when the surface water temperature, :math:`T_{h2osfc}`, becomes less than :math:`T_{f}`. The energy available for freezing is .. math:: :label: 6.73 H_{h2osfc} =\frac{\partial h}{\partial T} \left(T_{f} -T_{h2osfc}^{n} \right)-\frac{c_{h2osfc} \Delta z_{h2osfc} }{\Delta t} \left(T_{f} -T_{h2osfc}^{n} \right) -where :math:`c_{h2osfc}` is the volumetric heat capacity of water, and -:math:`\Delta z_{h2osfc}` is the depth of the surface water layer. If -:math:`H_{m} =\frac{H_{h2osfc} \Delta t}{L_{f} } >0` then :math:`H_{m}` -is removed from surface water and added to the snow column as ice +where :math:`c_{h2osfc}` is the volumetric heat capacity of water, and :math:`\Delta z_{h2osfc}` is the depth of the surface water layer. If :math:`H_{m} =\frac{H_{h2osfc} \Delta t}{L_{f} } >0` then :math:`H_{m}` is removed from surface water and added to the snow column as ice .. math:: :label: 6.74 @@ -793,27 +633,21 @@ The snow depth is adjusted to account for the additional ice mass \Delta z_{sno} =\frac{H_{m} }{\rho _{ice} } -If :math:`H_{m}` \ is greater than :math:`W_{sfc}` , the excess heat -:math:`\frac{L_{f} \left(H_{m} -W_{sfc} \right)}{\Delta t}` is used to -cool the snow layer. +If :math:`H_{m}` \ is greater than :math:`W_{sfc}`, the excess heat :math:`\frac{L_{f} \left(H_{m} -W_{sfc} \right)}{\Delta t}` is used to cool the snow layer. .. _Soil and Snow Thermal Properties: Soil and Snow Thermal Properties ------------------------------------ -The thermal properties of the soil are assumed to be a weighted combination of -the mineral and organic properties of the soil -(:ref:`Lawrence and Slater 2008 `). -The soil layer organic matter fraction :math:`f_{om,i}` is +The thermal properties of the soil are assumed to be a weighted combination of the mineral and organic properties of the soil (:ref:`Lawrence and Slater 2008 `). The soil layer organic matter fraction :math:`f_{om,i}` is .. math:: :label: 6.77 f_{om,i} =\rho _{om,i} /\rho _{om,\max } . -Soil thermal conductivity :math:`\lambda _{i}` (W m\ :sup:`-1` K\ :sup:`-1`) -is from :ref:`Farouki (1981) ` +Soil thermal conductivity :math:`\lambda _{i}` (W m\ :sup:`-1` K\ :sup:`-1`) is from :ref:`Farouki (1981) ` .. math:: :label: 6.78 @@ -827,50 +661,35 @@ is from :ref:`Farouki (1981) ` \lambda _{i} =\lambda _{bedrock} &\qquad i=N_{levsoi} +1,\ldots N_{levgrnd} \end{array} -where :math:`\lambda _{sat,\, i}` is the saturated thermal -conductivity, :math:`\lambda _{dry,\, i}` is the dry thermal -conductivity, :math:`K_{e,\, i}` is the Kersten number, -:math:`S_{r,\, i}` is the wetness of the soil with respect to -saturation, and :math:`\lambda _{bedrock} =3` W m\ :sup:`-1` -K\ :sup:`-1` is the thermal conductivity assumed for the deep -ground layers (typical of saturated granitic rock; -:ref:`Clauser and Huenges 1995 `). For glaciers, +where :math:`\lambda _{sat,\, i}` is the saturated thermal conductivity, :math:`\lambda _{dry,\, i}` is the dry thermal conductivity, :math:`K_{e,\, i}` is the Kersten number, :math:`S_{r,\, i}` is the wetness of the soil with respect to saturation, and :math:`\lambda _{bedrock} =3` W m\ :sup:`-1` K\ :sup:`-1` is the thermal conductivity assumed for the deep ground layers (typical of saturated granitic rock; :ref:`Clauser and Huenges 1995 `). For glaciers, .. math:: :label: 6.79 \lambda _{i} =\left\{\begin{array}{l} {\lambda _{liq,\, i} \qquad T_{i} \ge T_{f} } \\ {\lambda _{ice,\, i} \qquad T_{i} `). :math:`\theta _{sat,\, i}` is the -volumetric water content at saturation (porosity) (section :numref:`Hydraulic Properties`). +and :math:`\lambda _{s,om} =0.25`\ W m\ :sup:`-1` K\ :sup:`-1` (:ref:`Farouki 1981 `). :math:`\theta _{sat,\, i}` is the volumetric water content at saturation (porosity) (section :numref:`Hydraulic Properties`). The thermal conductivity of dry soil is @@ -879,21 +698,14 @@ The thermal conductivity of dry soil is \lambda _{dry,i} =(1-f_{om,i} )\lambda _{dry,\min ,i} +f_{om,i} \lambda _{dry,om} -where the thermal conductivity of dry mineral soil -:math:`\lambda _{dry,\min ,i}` \ (W m\ :sup:`-1` -K\ :sup:`-1`) depends on the bulk density -:math:`\rho _{d,\, i} =2700\left(1-\theta _{sat,\, i} \right)` (kg -m\ :sup:`-3`) as +where the thermal conductivity of dry mineral soil :math:`\lambda _{dry,\min,i}` \ (W m\ :sup:`-1` K\ :sup:`-1`) depends on the bulk density :math:`\rho _{d,\, i} =2700\left(1-\theta _{sat,\, i} \right)` (kg m\ :sup:`-3`) as .. math:: :label: 6.84 \lambda _{dry,\, \min ,i} =\frac{0.135\rho _{d,\, i} +64.7}{2700-0.947\rho _{d,\, i} } -and :math:`\lambda _{dry,om} =0.05` W m\ :sup:`-1` -K\ :sup:`-1` (:ref:`Farouki 1981 `) is the dry thermal conductivity of -organic matter. The Kersten number :math:`K_{e,\, i}` is a function of -the degree of saturation :math:`S_{r}` and phase of water +and :math:`\lambda _{dry,om} =0.05` W m\ :sup:`-1` K\ :sup:`-1` (:ref:`Farouki 1981 `) is the dry thermal conductivity of organic matter. The Kersten number :math:`K_{e,\, i}` is a function of the degree of saturation :math:`S_{r}` and phase of water .. math:: :label: 6.85 @@ -911,43 +723,35 @@ where S_{r,\, i} =\left(\frac{w_{liq,\, i} }{\rho _{liq} \Delta z_{i} } +\frac{w_{ice,\, i} }{\rho _{ice} \Delta z_{i} } \right)\frac{1}{\theta _{sat,\, i} } =\frac{\theta _{liq,\, i} +\theta _{ice,\, i} }{\theta _{sat,\, i} } \le 1. -Thermal conductivity :math:`\lambda _{i}` (W m\ :sup:`-1` -K\ :sup:`-1`) for snow is from :ref:`Jordan (1991) ` +Thermal conductivity :math:`\lambda _{i}` (W m\ :sup:`-1` K\ :sup:`-1`) for snow is from :ref:`Jordan (1991) ` .. math:: :label: 6.87 \lambda _{i} =\lambda _{air} +\left(7.75\times 10^{-5} \rho _{sno,\, i} +1.105\times 10^{-6} \rho _{sno,\, i}^{2} \right)\left(\lambda _{ice} -\lambda _{air} \right) -where :math:`\lambda _{air}` is the thermal conductivity of air (:numref:`Table Physical Constants`) -and :math:`\rho _{sno,\, i}` is the bulk density of snow (kg m\ :sup:`-3`) +where :math:`\lambda _{air}` is the thermal conductivity of air (:numref:`Table Physical Constants`) and :math:`\rho _{sno,\, i}` is the bulk density of snow (kg m\ :sup:`-3`) .. math:: :label: 6.88 \rho _{sno,\, i} =\frac{w_{ice,\, i} +w_{liq,\, i} }{\Delta z_{i} } . -The volumetric heat capacity :math:`c_{i}` (J m\ :sup:`-3` K\ :sup:`-1`) for -soil is from :ref:`de Vries (1963) ` and depends on the -heat capacities of the soil solid, liquid water, and ice constituents +The volumetric heat capacity :math:`c_{i}` (J m\ :sup:`-3` K\ :sup:`-1`) for soil is from :ref:`de Vries (1963) ` and depends on the heat capacities of the soil solid, liquid water, and ice constituents .. math:: :label: 6.89 c_{i} =c_{s,\, i} \left(1-\theta _{sat,\, i} \right)+\frac{w_{ice,\, i} }{\Delta z_{i} } C_{ice} +\frac{w_{liq,\, i} }{\Delta z_{i} } C_{liq} -where :math:`C_{liq}` and :math:`C_{ice}` are the specific heat -capacities (J kg\ :sup:`-1` K\ :sup:`-1`) of liquid water -and ice, respectively (:numref:`Table Physical Constants`). The heat capacity of soil solids -:math:`c_{s,i}` \ (J m\ :sup:`-3` K\ :sup:`-1`) is +where :math:`C_{liq}` and :math:`C_{ice}` are the specific heat capacities (J kg\ :sup:`-1` K\ :sup:`-1`) of liquid water and ice, respectively (:numref:`Table Physical Constants`). The heat capacity of soil solids :math:`c_{s,i}` \ (J m\ :sup:`-3` K\ :sup:`-1`) is .. math:: :label: 6.90 c_{s,i} =(1-f_{om,i} )c_{s,\min ,i} +f_{om,i} c_{s,om} -where the heat capacity of mineral soil solids -:math:`c_{s,\min ,\, i}` (J m\ :sup:`-3` K\ :sup:`-1`) is +where the heat capacity of mineral soil solids :math:`c_{s,\min,\, i}` (J m\ :sup:`-3` K\ :sup:`-1`) is .. math:: :label: 6.91 @@ -957,20 +761,14 @@ where the heat capacity of mineral soil solids c_{s,\, \min ,i} =c_{s,\, bedrock} &\qquad i=N_{levsoi} +1,\ldots ,N_{levgrnd} \end{array} -where :math:`c_{s,bedrock} =2\times 10^{6}` J m\ :sup:`-3` -K\ :sup:`-1` is the heat capacity of bedrock and -:math:`c_{s,om} =2.5\times 10^{6}` \ J m\ :sup:`-3` -K\ :sup:`-1` (:ref:`Farouki 1981 `) is the heat capacity of organic -matter. For glaciers and snow +where :math:`c_{s,bedrock} =2\times 10^{6}` J m\ :sup:`-3` K\ :sup:`-1` is the heat capacity of bedrock and :math:`c_{s,om} =2.5\times 10^{6}` \ J m\ :sup:`-3` K\ :sup:`-1` (:ref:`Farouki 1981 `) is the heat capacity of organic matter. For glaciers and snow .. math:: :label: 6.92 c_{i} =\frac{w_{ice,\, i} }{\Delta z_{i} } C_{ice} +\frac{w_{liq,\, i} }{\Delta z_{i} } C_{liq} . -For the special case when snow is present (:math:`W_{sno} >0`) but -there are no explicit snow layers (:math:`snl=0`), the heat capacity of -the top layer is a blend of ice and soil heat capacity +For the special case when snow is present (:math:`W_{sno} >0`) but there are no explicit snow layers (:math:`snl=0`), the heat capacity of the top layer is a blend of ice and soil heat capacity .. math:: :label: 6.93 @@ -984,20 +782,14 @@ where :math:`c_{1}^{*}` is calculated from :eq:`6.89` or :eq:`6.92`. Excess Ground Ice ------------------------------------ -An optional parameterization of excess ground ice melt and respective subsidence based on (:ref:`Lee et al., (2014) `). -Initial excess ground ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). -When the excess ground ice is present in the soil column, soil depth for a given layer (:math:`z_{i}`) -is adjusted by the amount of excess ice in the column: +An optional parameterization of excess ground ice melt and respective subsidence based on (:ref:`Lee et al., (2014) `). Initial excess ground ice concentrations for soil columns are derived from (:ref:`Brown et al., (1997) `). When the excess ground ice is present in the soil column, soil depth for a given layer (:math:`z_{i}`) is adjusted by the amount of excess ice in the column: .. math:: :label: 6.94 z_{i}^{'}=\Sigma_{j=1}^{i} \ z_{j}^{'}+\frac{w_{exice,\, j}}{\rho_{ice} } -where :math:`w_{exice,\,j}` is excess ground ice amount (kg m :sup:`-2`) in layer :math:`j` -and :math:`\rho_{ice}` is the density of ice (kg m :sup:`-3`). -After adjustment of layer depths have been made, all of the soil temperature equations (from :eq:`6.80` to :eq:`6.89`) -are calculted based on the adjusted depths. Thermal properties are additionally adjusted (:eq:`6.8` and :eq:`6.8`) in the following way: +where :math:`w_{exice,\,j}` is excess ground ice amount (kg m :sup:`-2`) in layer :math:`j` and :math:`\rho_{ice}` is the density of ice (kg m :sup:`-3`). After adjustment of layer depths have been made, all of the soil temperature equations (from :eq:`6.80` to :eq:`6.89`) are calculted based on the adjusted depths. Thermal properties are additionally adjusted (:eq:`6.8` and :eq:`6.8`) in the following way: .. math:: :label: 6.95 @@ -1015,11 +807,5 @@ Soil subsidence at the timestep :math:`n+1` (:math:`z_{exice}^{n+1}`, m) is then z_{exice}^{n+1}=\Sigma_{i=1}^{N_{levgrnd}} \ z_{j}^{',\ ,n+1}-z_{j}^{',\ ,n } -With regards to hydraulic counductivity, excess ground ice is treated the same way normal soil -ice is treated in :numref:`Frozen Soils and Perched Water Table`. -When a soil layer thaws, excess ground ice is only allowed -to melt when no normals soil ice is present in the layer. -When a soil layer refreezes, liquid soil water can only turn into normal soil ice, thus, no new of excess ice can be created but only melted. -The excess liquid soil moisture from excess ice melt is distributed within the soil column according -to :numref:`Lateral Sub-surface Runoff`. +With regards to hydraulic counductivity, excess ground ice is treated the same way normal soil ice is treated in :numref:`Frozen Soils and Perched Water Table`. When a soil layer thaws, excess ground ice is only allowed to melt when no normals soil ice is present in the layer. When a soil layer refreezes, liquid soil water can only turn into normal soil ice, thus, no new of excess ice can be created but only melted. The excess liquid soil moisture from excess ice melt is distributed within the soil column according to :numref:`Lateral Sub-surface Runoff`. diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index 2d1f14c86b..d4670c2389 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -8,9 +8,7 @@ Surface Albedos Canopy Radiative Transfer ----------------------------- -Radiative transfer within vegetative canopies is calculated from the -two-stream approximation of :ref:`Dickinson (1983) ` and -:ref:`Sellers (1985) ` as described by :ref:`Bonan (1996) ` +Radiative transfer within vegetative canopies is calculated from the two-stream approximation of :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) ` as described by :ref:`Bonan (1996) ` .. math:: :label: 3.1 @@ -22,44 +20,16 @@ two-stream approximation of :ref:`Dickinson (1983) ` and \bar{\mu }\frac{dI\, \downarrow }{d\left(L+S\right)} +\left[1-\left(1-\beta \right)\omega \right]I\, \downarrow -\omega \beta I\, \uparrow =\omega \bar{\mu }K\left(1-\beta _{0} \right)e^{-K\left(L+S\right)} -where :math:`I\, \uparrow` and :math:`I\, \downarrow` are the upward -and downward diffuse radiative fluxes per unit incident flux, -:math:`K={G\left(\mu \right)\mathord{\left/ {\vphantom {G\left(\mu \right) \mu }} \right.} \mu }` -is the optical depth of direct beam per unit leaf and stem area, -:math:`\mu` is the cosine of the zenith angle of the incident beam, -:math:`G\left(\mu \right)` is the relative projected area of leaf and -stem elements in the direction :math:`\cos ^{-1} \mu` , -:math:`\bar{\mu }` is the average inverse diffuse optical depth per unit -leaf and stem area, :math:`\omega` is a scattering coefficient, -:math:`\beta` and :math:`\beta _{0}` are upscatter parameters for -diffuse and direct beam radiation, respectively, :math:`L` is the -exposed leaf area index , and :math:`S` is the exposed stem area index -(section :numref:`Phenology and vegetation burial by snow`). Given the -direct beam albedo :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse albedo -:math:`\alpha _{g,\, \Lambda }` of the ground (section :numref:`Ground Albedos`), these -equations are solved to calculate the fluxes, per unit incident flux, -absorbed by the vegetation, reflected by the vegetation, and transmitted -through the vegetation for direct and diffuse radiation and for visible -(:math:`<` 0.7\ :math:`\mu {\rm m}`) and near-infrared -(:math:`\geq` 0.7\ :math:`\mu {\rm m}`) wavebands. The absorbed -radiation is partitioned to sunlit and shaded fractions of the canopy. -The optical parameters :math:`G\left(\mu \right)`, :math:`\bar{\mu }`, -:math:`\omega`, :math:`\beta`, and :math:`\beta _{0}` are calculated -based on work in :ref:`Sellers (1985) ` as follows. - -The relative projected area of leaves and stems in the direction -:math:`\cos ^{-1} \mu` is +where :math:`I\, \uparrow` and :math:`I\, \downarrow` are the upward and downward diffuse radiative fluxes per unit incident flux, :math:`K={G\left(\mu \right)\mathord{\left/ {\vphantom {G\left(\mu \right) \mu }} \right.} \mu }` is the optical depth of direct beam per unit leaf and stem area, :math:`\mu` is the cosine of the zenith angle of the incident beam, :math:`G\left(\mu \right)` is the relative projected area of leaf and stem elements in the direction :math:`\cos ^{-1} \mu`, :math:`\bar{\mu }` is the average inverse diffuse optical depth per unit leaf and stem area, :math:`\omega` is a scattering coefficient, :math:`\beta` and :math:`\beta _{0}` are upscatter parameters for diffuse and direct beam radiation, respectively, :math:`L` is the exposed leaf area index, and :math:`S` is the exposed stem area index (section :numref:`Phenology and vegetation burial by snow`). Given the direct beam albedo :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse albedo :math:`\alpha _{g,\, \Lambda }` of the ground (section :numref:`Ground Albedos`), these equations are solved to calculate the fluxes, per unit incident flux, absorbed by the vegetation, reflected by the vegetation, and transmitted through the vegetation for direct and diffuse radiation and for visible (:math:`<` 0.7\ :math:`\mu {\rm m}`) and near-infrared (:math:`\geq` 0.7\ :math:`\mu {\rm m}`) wavebands. The absorbed radiation is partitioned to sunlit and shaded fractions of the canopy. The optical parameters :math:`G\left(\mu \right)`, :math:`\bar{\mu }`, :math:`\omega`, :math:`\beta`, and :math:`\beta _{0}` are calculated based on work in :ref:`Sellers (1985) ` as follows. + +The relative projected area of leaves and stems in the direction :math:`\cos ^{-1} \mu` is .. math:: :label: 3.3 G\left(\mu \right)=\phi _{1} +\phi _{2} \mu -where :math:`\phi _{1} ={\rm 0.5}-0.633\chi _{L} -0.33\chi _{L}^{2}` -and :math:`\phi _{2} =0.877\left(1-2\phi _{1} \right)` for -:math:`-0.4\le \chi _{L} \le 0.6`. :math:`\chi _{L}` is the departure -of leaf angles from a random distribution and equals +1 for horizontal -leaves, 0 for random leaves, and –1 for vertical leaves. +where :math:`\phi _{1} ={\rm 0.5}-0.633\chi _{L} -0.33\chi _{L}^{2}` and :math:`\phi _{2} =0.877\left(1-2\phi _{1} \right)` for :math:`-0.4\le \chi _{L} \le 0.6`. :math:`\chi _{L}` is the departure of leaf angles from a random distribution and equals +1 for horizontal leaves, 0 for random leaves, and –1 for vertical leaves. The average inverse diffuse optical depth per unit leaf and stem area is @@ -70,16 +40,10 @@ The average inverse diffuse optical depth per unit leaf and stem area is where :math:`\mu '` is the direction of the scattered flux. -The optical parameters :math:`\omega`, :math:`\beta`, and :math:`\beta _{0}`, -which vary with wavelength (:math:`\Lambda` ), are weighted combinations of values -for vegetation and snow, using the canopy snow-covered fraction :math:`f_{can,\, sno}` -(Chapter :numref:`rst_Hydrology`). The optical parameters are +The optical parameters :math:`\omega`, :math:`\beta`, and :math:`\beta _{0}`, which vary with wavelength (:math:`\Lambda` ), are weighted combinations of values for vegetation and snow, using the canopy snow-covered fraction :math:`f_{can,\, sno}` (Chapter :numref:`rst_Hydrology`). The optical parameters are .. - The model determines that snow is on the canopy if - :math:`T_{v} \le T_{f}` , where :math:`T_{v}` is the vegetation temperature (K) (Chapter - :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and :math:`T_{f}` is the - freezing temperature of water (K) (:numref:`Table Physical Constants`). In this case, the optical parameters are + The model determines that snow is on the canopy if :math:`T_{v} \le T_{f}`, where :math:`T_{v}` is the vegetation temperature (K) (Chapter :numref:`rst_Momentum, Sensible Heat, and Latent Heat Fluxes`) and :math:`T_{f}` is the freezing temperature of water (K) (:numref:`Table Physical Constants`). In this case, the optical parameters are .. math:: :label: 3.5 @@ -96,9 +60,7 @@ for vegetation and snow, using the canopy snow-covered fraction :math:`f_{can,\, \omega _{\Lambda } \beta _{0,\, \Lambda } =\omega _{\Lambda }^{veg} \beta _{0,\, \Lambda }^{veg} \left(1-f_{can,\, sno} \right)+\omega _{\Lambda }^{sno} \beta _{0,\, \Lambda }^{sno} f_{can,\, sno} -The snow and vegetation weights are applied to the products -:math:`\omega _{\Lambda } \beta _{\Lambda }` and :math:`\omega _{\Lambda } \beta _{0,\, \Lambda }` because these -products are used in the two-stream equations. If there is no snow on the canopy, this reduces to +The snow and vegetation weights are applied to the products :math:`\omega _{\Lambda } \beta _{\Lambda }` and :math:`\omega _{\Lambda } \beta _{0,\, \Lambda }` because these products are used in the two-stream equations. If there is no snow on the canopy, this reduces to .. math:: :label: 3.8 @@ -115,22 +77,14 @@ products are used in the two-stream equations. If there is no snow on the canopy \omega _{\Lambda } \beta _{0,\, \Lambda } =\omega _{\Lambda }^{veg} \beta _{0,\, \Lambda }^{veg} . -For vegetation, -:math:`\omega _{\Lambda }^{veg} =\alpha _{\Lambda } +\tau _{\Lambda }` . -:math:`\alpha _{\Lambda }` is a weighted combination of the leaf and -stem reflectances -(:math:`\alpha _{\Lambda }^{leaf} ,\alpha _{\Lambda }^{stem}` ) +For vegetation, :math:`\omega _{\Lambda }^{veg} =\alpha _{\Lambda } +\tau _{\Lambda }`. :math:`\alpha _{\Lambda }` is a weighted combination of the leaf and stem reflectances (:math:`\alpha _{\Lambda }^{leaf},\alpha _{\Lambda }^{stem}` ) .. math:: :label: 3.11 \alpha _{\Lambda } =\alpha _{\Lambda }^{leaf} w_{leaf} +\alpha _{\Lambda }^{stem} w_{stem} -where -:math:`w_{leaf} ={L\mathord{\left/ {\vphantom {L \left(L+S\right)}} \right.} \left(L+S\right)}` -and -:math:`w_{stem} ={S\mathord{\left/ {\vphantom {S \left(L+S\right)}} \right.} \left(L+S\right)}` . -:math:`\tau _{\Lambda }` is a weighted combination of the leaf and stem transmittances (:math:`\tau _{\Lambda }^{leaf}, \tau _{\Lambda }^{stem}`) +where :math:`w_{leaf} ={L\mathord{\left/ {\vphantom {L \left(L+S\right)}} \right.} \left(L+S\right)}` and :math:`w_{stem} ={S\mathord{\left/ {\vphantom {S \left(L+S\right)}} \right.} \left(L+S\right)}`. :math:`\tau _{\Lambda }` is a weighted combination of the leaf and stem transmittances (:math:`\tau _{\Lambda }^{leaf}, \tau _{\Lambda }^{stem}`) .. math:: :label: 3.12 @@ -144,33 +98,14 @@ The upscatter for diffuse radiation is \omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\frac{1}{2} \left[\alpha _{\Lambda } +\tau _{\Lambda } +\left(\alpha _{\Lambda } -\tau _{\Lambda } \right)\cos ^{2} \bar{\theta }\right] -where :math:`\bar{\theta }` is the mean leaf inclination angle relative -to the horizontal plane (i.e., the angle between leaf normal and local -vertical) (:ref:`Sellers (1985) `). Here, :math:`\cos \bar{\theta }` is -approximated by +where :math:`\bar{\theta }` is the mean leaf inclination angle relative to the horizontal plane (i.e., the angle between leaf normal and local vertical) (:ref:`Sellers (1985) `). Here, :math:`\cos \bar{\theta }` is approximated by .. math:: :label: 3.14 \cos \bar{\theta }=\frac{1+\chi _{L} }{2} -Using this approximation, for vertical leaves (:math:`\chi _{L} =-1`, -:math:`\bar{\theta }=90^{{\rm o}}` ), -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =0.5\left(\alpha _{\Lambda } +\tau _{\Lambda } \right)`, -and for horizontal leaves (:math:`\chi _{L} =1`, -:math:`\bar{\theta }=0^{{\rm o}}` ) , -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\alpha _{\Lambda }` , -which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random -(spherically distributed) leaves (:math:`\chi _{L} =0`, -:math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` -whereas the approximate solution of :ref:`Dickinson (1983) ` is -:math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }` . -This discrepancy arises from the fact that a spherical leaf angle -distribution has a true mean leaf inclination -:math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation , -while :math:`\bar{\theta }=60` in equation . The upscatter for direct -beam radiation is +Using this approximation, for vertical leaves (:math:`\chi _{L} =-1`, :math:`\bar{\theta }=90^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =0.5\left(\alpha _{\Lambda } +\tau _{\Lambda } \right)`, and for horizontal leaves (:math:`\chi _{L} =1`, :math:`\bar{\theta }=0^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\alpha _{\Lambda }`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }`. This discrepancy arises from the fact that a spherical leaf angle distribution has a true mean leaf inclination :math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation, while :math:`\bar{\theta }=60` in equation. The upscatter for direct beam radiation is .. math:: :label: 3.15 @@ -184,12 +119,9 @@ where the single scattering albedo is \begin{array}{rcl} {a_{s} \left(\mu \right)_{\Lambda } } & {=} & {\frac{\omega _{\Lambda }^{veg} }{2} \int _{0}^{1}\frac{\mu 'G\left(\mu \right)}{\mu G\left(\mu '\right)+\mu 'G\left(\mu \right)} d\mu '} \\ {} & {=} & {\frac{\omega _{\Lambda }^{veg} }{2} \frac{G\left(\mu \right)}{\max (\mu \phi _{2} +G\left(\mu \right),1e-6)} \left[1-\frac{\mu \phi _{1} }{\max (\mu \phi _{2} +G\left(\mu \right),1e-6)} \ln \left(\frac{\mu \phi _{1} +\max (\mu \phi _{2} +G\left(\mu \right),1e-6)}{\mu \phi _{1} } \right)\right].} \end{array} -Note here the restriction on :math:`\mu \phi _{2} +G\left(\mu \right)`. We have seen cases where small values -can cause unrealistic single scattering albedo associated with the log calculation, -thereby eventually causing a negative soil albedo. +Note here the restriction on :math:`\mu \phi _{2} +G\left(\mu \right)`. We have seen cases where small values can cause unrealistic single scattering albedo associated with the log calculation, thereby eventually causing a negative soil albedo. -The upward diffuse fluxes per unit incident direct beam and diffuse flux -(i.e., the surface albedos) are +The upward diffuse fluxes per unit incident direct beam and diffuse flux (i.e., the surface albedos) are .. math:: :label: 3.17 @@ -201,8 +133,7 @@ The upward diffuse fluxes per unit incident direct beam and diffuse flux I\, \uparrow _{\Lambda } =h_{7} +h_{8} . -The downward diffuse fluxes per unit incident direct beam and diffuse -radiation, respectively, are +The downward diffuse fluxes per unit incident direct beam and diffuse radiation, respectively, are .. math:: :label: 3.19 @@ -214,10 +145,7 @@ radiation, respectively, are I\, \downarrow _{\Lambda } =h_{9} s_{1} +\frac{h_{10} }{s_{1} } . -With reference to :numref:`Figure Radiation Schematic`, the direct beam flux transmitted through -the canopy, per unit incident flux, is :math:`e^{-K\left(L+S\right)}` , -and the direct beam and diffuse fluxes absorbed by the vegetation, per -unit incident flux, are +With reference to :numref:`Figure Radiation Schematic`, the direct beam flux transmitted through the canopy, per unit incident flux, is :math:`e^{-K\left(L+S\right)}`, and the direct beam and diffuse fluxes absorbed by the vegetation, per unit incident flux, are .. math:: :label: 3.21 @@ -229,10 +157,7 @@ unit incident flux, are \vec{I}_{\Lambda } =1-I\, \uparrow _{\Lambda } -\left(1-\alpha _{g,\, \Lambda } \right)I\, \downarrow _{\Lambda } . -These fluxes are partitioned to the sunlit and shaded canopy using an -analytical solution to the two-stream approximation for sunlit and -shaded leaves :ref:`(Dai et al. 2004) `, as described by :ref:`Bonan et al. (2011) `. -The absorption of direct beam radiation by sunlit leaves is +These fluxes are partitioned to the sunlit and shaded canopy using an analytical solution to the two-stream approximation for sunlit and shaded leaves :ref:`(Dai et al. 2004) `, as described by :ref:`Bonan et al. (2011) `. The absorption of direct beam radiation by sunlit leaves is .. math:: :label: 3.23 @@ -284,9 +209,7 @@ with a_{2} =h_{9} \left[\frac{1-s_{2} s_{1} }{K+h} \right]+h_{10} \left[\frac{1-{s_{2} \mathord{\left/ {\vphantom {s_{2} s_{1} }} \right.} s_{1} } }{K-h} \right]. -The parameters :math:`h_{1}` –:math:`h_{10}` , :math:`\sigma` , -:math:`h`, :math:`s_{1}` , and :math:`s_{2}` are from :ref:`Sellers (1985) ` -[note the error in :math:`h_{4}` in :ref:`Sellers (1985) `]: +The parameters :math:`h_{1}` –:math:`h_{10}`, :math:`\sigma`, :math:`h`, :math:`s_{1}`, and :math:`s_{2}` are from :ref:`Sellers (1985) ` [note the error in :math:`h_{4}` in :ref:`Sellers (1985) `]: .. math:: :label: 3.31 @@ -423,13 +346,7 @@ The parameters :math:`h_{1}` –:math:`h_{10}` , :math:`\sigma` , h_{10} =\frac{-s_{1} \left(u_{2} -\bar{\mu }h\right)}{d_{2} } . -Plant functional type optical properties (:numref:`Table Plant functional type optical properties`) -for trees and shrubs are from :ref:`Dorman and Sellers (1989) `. Leaf and stem optical -properties (VIS and NIR reflectance and transmittance) were derived -for grasslands and crops from full optical range spectra of measured -optical properties (:ref:`Asner et al. 1998 `). Optical properties for -intercepted snow (:numref:`Table Intercepted snow optical properties`) are from -:ref:`Sellers et al. (1986) `. +Plant functional type optical properties (:numref:`Table Plant functional type optical properties`) for trees and shrubs are from :ref:`Dorman and Sellers (1989) `. Leaf and stem optical properties (VIS and NIR reflectance and transmittance) were derived for grasslands and crops from full optical range spectra of measured optical properties (:ref:`Asner et al. 1998 `). Optical properties for intercepted snow (:numref:`Table Intercepted snow optical properties`) are from :ref:`Sellers et al. (1986) `. .. _Table Plant functional type optical properties: @@ -508,9 +425,7 @@ intercepted snow (:numref:`Table Intercepted snow optical properties`) are from Ground Albedos ------------------ -The overall direct beam :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse -:math:`\alpha _{g,\, \Lambda }` ground albedos are weighted -combinations of "soil" and snow albedos +The overall direct beam :math:`\alpha _{g,\, \Lambda }^{\mu }` and diffuse :math:`\alpha _{g,\, \Lambda }` ground albedos are weighted combinations of "soil" and snow albedos .. math:: :label: 3.58 @@ -522,19 +437,15 @@ combinations of "soil" and snow albedos \alpha _{g,\, \Lambda } =\alpha _{soi,\, \Lambda } \left(1-f_{sno} \right)+\alpha _{sno,\, \Lambda } f_{sno} -where :math:`f_{sno}` is the fraction of the ground covered with snow -(section :numref:`Snow Covered Area Fraction`). +where :math:`f_{sno}` is the fraction of the ground covered with snow (section :numref:`Snow Covered Area Fraction`). -:math:`\alpha _{soi,\, \Lambda }^{\mu }` and -:math:`\alpha _{soi,\, \Lambda }` vary with glacier, lake, and -soil surfaces. Glacier albedos are from :ref:`Paterson (1994) ` +:math:`\alpha _{soi,\, \Lambda }^{\mu }` and :math:`\alpha _{soi,\, \Lambda }` vary with glacier, lake, and soil surfaces. Glacier albedos are from :ref:`Paterson (1994) ` .. math:: \alpha _{soi,\, vis}^{\mu } =\alpha _{soi,\, vis} =0.6 .. math:: \alpha _{soi,\, nir}^{\mu } =\alpha _{soi,\, nir} =0.4. -Unfrozen lake albedos depend on the cosine of the solar -zenith angle :math:`\mu` +Unfrozen lake albedos depend on the cosine of the solar zenith angle :math:`\mu` .. math:: :label: 3.60 @@ -554,31 +465,9 @@ As in NCAR LSM (:ref:`Bonan 1996 `), soil albedos vary with color cla \alpha _{soi,\, \Lambda }^{\mu } =\alpha _{soi,\, \Lambda } =\left(\alpha _{sat,\, \Lambda } +\Delta \right)\le \alpha _{dry,\, \Lambda } -where :math:`\Delta` depends on the volumetric water content of the -first soil layer :math:`\theta _{1}` (section :numref:`Soil Water`) as -:math:`\Delta =0.11-0.40\theta _{1} >0`, and -:math:`\alpha _{sat,\, \Lambda }` and -:math:`\alpha _{dry,\, \Lambda }` are albedos for saturated and dry -soil color classes (:numref:`Table Dry and saturated soil albedos`). - -CLM soil colors are prescribed so that they best reproduce observed -MODIS local solar noon surface albedo values at the CLM grid cell -following the methods of :ref:`Lawrence and Chase (2007) `. -The soil colors are fitted over the range of 20 soil classes shown in -:numref:`Table Dry and saturated soil albedos` and compared -to the MODIS monthly local solar noon all-sky surface albedo as -described in :ref:`Strahler et al. (1999) ` and -:ref:`Schaaf et al. (2002) `. The CLM -two-stream radiation model was used to calculate the model equivalent -surface albedo using climatological monthly soil moisture along with the -vegetation parameters of PFT fraction, LAI, and SAI. The soil color that -produced the closest all-sky albedo in the two-stream radiation model -was selected as the best fit for the month. The fitted monthly soil -colors were averaged over all snow-free months to specify a -representative soil color for the grid cell. In cases where there was no -snow-free surface albedo for the year, the soil color derived from -snow-affected albedo was used to give a representative soil color that -included the effects of the minimum permanent snow cover. +where :math:`\Delta` depends on the volumetric water content of the first soil layer :math:`\theta _{1}` (section :numref:`Soil Water`) as :math:`\Delta =0.11-0.40\theta _{1} >0`, and :math:`\alpha _{sat,\, \Lambda }` and :math:`\alpha _{dry,\, \Lambda }` are albedos for saturated and dry soil color classes (:numref:`Table Dry and saturated soil albedos`). + +CLM soil colors are prescribed so that they best reproduce observed MODIS local solar noon surface albedo values at the CLM grid cell following the methods of :ref:`Lawrence and Chase (2007) `. The soil colors are fitted over the range of 20 soil classes shown in :numref:`Table Dry and saturated soil albedos` and compared to the MODIS monthly local solar noon all-sky surface albedo as described in :ref:`Strahler et al. (1999) ` and :ref:`Schaaf et al. (2002) `. The CLM two-stream radiation model was used to calculate the model equivalent surface albedo using climatological monthly soil moisture along with the vegetation parameters of PFT fraction, LAI, and SAI. The soil color that produced the closest all-sky albedo in the two-stream radiation model was selected as the best fit for the month. The fitted monthly soil colors were averaged over all snow-free months to specify a representative soil color for the grid cell. In cases where there was no snow-free surface albedo for the year, the soil color derived from snow-affected albedo was used to give a representative soil color that included the effects of the minimum permanent snow cover. .. _Table Dry and saturated soil albedos: @@ -615,32 +504,9 @@ included the effects of the minimum permanent snow cover. Snow Albedo ^^^^^^^^^^^^^^^^^ -Snow albedo and solar absorption within each snow layer are simulated -with the Snow, Ice, and Aerosol Radiative Model (SNICAR), which -incorporates a two-stream radiative transfer solution from -:ref:`Toon et al. (1989) `. Albedo and the vertical absorption -profile depend on solar zenith angle, albedo of the substrate underlying snow, mass -concentrations of atmospheric-deposited aerosols (black carbon, mineral -dust, and organic carbon), and ice effective grain size -(:math:`r_{e}`), which is simulated with a snow aging routine -described in section :numref:`Snow Aging`. Representation of impurity mass -concentrations within the snowpack is described in section -:numref:`Black and organic carbon and mineral dust within snow`. -Implementation of SNICAR in CLM is also described somewhat by -:ref:`Flanner and Zender (2005) ` and -:ref:`Flanner et al. (2007) `. - -The two-stream solution requires the following bulk optical properties -for each snow layer and spectral band: extinction optical depth -(:math:`\tau`), single-scatter albedo (:math:`\omega`), and -scattering asymmetry parameter (*g*). The snow layers used for radiative -calculations are identical to snow layers applied elsewhere in CLM, -except for the case when snow mass is greater than zero but no snow -layers exist. When this occurs, a single radiative layer is specified to -have the column snow mass and an effective grain size of freshly-fallen -snow (section :numref:`Snow Aging`). The bulk optical properties are weighted functions -of each constituent *k*, computed for each snow layer and spectral band -as +Snow albedo and solar absorption within each snow layer are simulated with the Snow, Ice, and Aerosol Radiative Model (SNICAR), which incorporates a two-stream radiative transfer solution from :ref:`Toon et al. (1989) `. Albedo and the vertical absorption profile depend on solar zenith angle, albedo of the substrate underlying snow, mass concentrations of atmospheric-deposited aerosols (black carbon, mineral dust, and organic carbon), and ice effective grain size (:math:`r_{e}`), which is simulated with a snow aging routine described in section :numref:`Snow Aging`. Representation of impurity mass concentrations within the snowpack is described in section :numref:`Black and organic carbon and mineral dust within snow`. Implementation of SNICAR in CLM is also described somewhat by :ref:`Flanner and Zender (2005) ` and :ref:`Flanner et al. (2007) `. + +The two-stream solution requires the following bulk optical properties for each snow layer and spectral band: extinction optical depth (:math:`\tau`), single-scatter albedo (:math:`\omega`), and scattering asymmetry parameter (*g*). The snow layers used for radiative calculations are identical to snow layers applied elsewhere in CLM, except for the case when snow mass is greater than zero but no snow layers exist. When this occurs, a single radiative layer is specified to have the column snow mass and an effective grain size of freshly-fallen snow (section :numref:`Snow Aging`). The bulk optical properties are weighted functions of each constituent *k*, computed for each snow layer and spectral band as .. math:: :label: 3.62 @@ -657,44 +523,14 @@ as g=\frac{\sum _{1}^{k}g_{k} \omega _{k} \tau _{k} }{\sum _{1}^{k}\omega _{k} \tau _{k} } -For each constituent (ice, two black carbon species, two organic carbon species, and -four dust species), :math:`\omega`, *g*, and the mass extinction cross-section -:math:`\psi` (m\ :sup:`2` kg\ :sub:`-1`) are computed offline with Mie Theory, e.g., -applying the computational technique from :ref:`Bohren and Huffman (1983) `. -The extinction optical depth for each constituent depends on its mass extinction -cross-section and layer mass, :math:`w _{k}` (kg\ m\ :sup:`-1`) as +For each constituent (ice, two black carbon species, two organic carbon species, and four dust species), :math:`\omega`, *g*, and the mass extinction cross-section :math:`\psi` (m\ :sup:`2` kg\ :sub:`-1`) are computed offline with Mie Theory, e.g., applying the computational technique from :ref:`Bohren and Huffman (1983) `. The extinction optical depth for each constituent depends on its mass extinction cross-section and layer mass, :math:`w _{k}` (kg\ m\ :sup:`-1`) as .. math:: :label: 3.65 \tau _{k} =\psi _{k} w_{k} -The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri-diagonal matrix -solution to produce upward and downward radiative fluxes at each layer -interface, from which net radiation, layer absorption, and surface -albedo are easily derived. Solar fluxes are computed in five spectral -bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. -Because snow albedo varies strongly across -the solar spectrum, it was determined that four bands were needed to -accurately represent the near-infrared (NIR) characteristics of snow, -whereas only one band was needed for the visible spectrum. Boundaries of -the NIR bands were selected to capture broad radiative features and -maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 -:math:`\mu` m) surface downwelling flux from CLM according to the weights listed -in :numref:`Table Spectral bands and weights used for snow radiative transfer`, -which are unique for diffuse and direct incident flux. These fixed weights were -determined with offline hyperspectral radiative transfer calculations for an -atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). -The tri-diagonal solution includes intermediate terms that allow for easy -interchange of two-stream techniques. We apply the Eddington solution -for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the -hemispheric mean solution ((:ref:`Toon et al. (1989) `) for NIR bands. These -choices were made because the Eddington scheme works well for highly -scattering media, but can produce negative albedo for absorptive NIR -bands with diffuse incident flux. Delta scalings are applied to -:math:`\tau`, :math:`\omega`, and :math:`g` (:ref:`Wiscombe and Warren 1980 `) in -all spectral bands, producing effective values (denoted with \*) that -are applied in the two-stream solution +The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri-diagonal matrix solution to produce upward and downward radiative fluxes at each layer interface, from which net radiation, layer absorption, and surface albedo are easily derived. Solar fluxes are computed in five spectral bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. Because snow albedo varies strongly across the solar spectrum, it was determined that four bands were needed to accurately represent the near-infrared (NIR) characteristics of snow, whereas only one band was needed for the visible spectrum. Boundaries of the NIR bands were selected to capture broad radiative features and maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 :math:`\mu` m) surface downwelling flux from CLM according to the weights listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`, which are unique for diffuse and direct incident flux. These fixed weights were determined with offline hyperspectral radiative transfer calculations for an atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). The tri-diagonal solution includes intermediate terms that allow for easy interchange of two-stream techniques. We apply the Eddington solution for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the hemispheric mean solution ((:ref:`Toon et al. (1989) `) for NIR bands. These choices were made because the Eddington scheme works well for highly scattering media, but can produce negative albedo for absorptive NIR bands with diffuse incident flux. Delta scalings are applied to :math:`\tau`, :math:`\omega`, and :math:`g` (:ref:`Wiscombe and Warren 1980 `) in all spectral bands, producing effective values (denoted with \*) that are applied in the two-stream solution .. math:: :label: 3.66 @@ -729,105 +565,41 @@ are applied in the two-stream solution | Band 5: 1.5-5.0\ :math:`\mu`\ m (near-IR) | 0.204 | 0.103 | +---------------------------------------------------------+----------------------+------------------+ -Under direct-beam conditions, singularities in the radiative -approximation are occasionally approached in spectral bands 4 and 5 that -produce unrealistic conditions (negative energy absorption in a layer, -negative albedo, or total absorbed flux greater than incident flux). -When any of these three conditions occur, the Eddington approximation is -attempted instead, and if both approximations fail, the cosine of the -solar zenith angle is adjusted by 0.02 (conserving incident flux) and a -warning message is produced. This situation occurs in only about 1 in -10 :sup:`6` computations of snow albedo. After looping over the -five spectral bands, absorption fluxes and albedo are averaged back into -the bulk NIR band used by the rest of CLM. - -Soil albedo (or underlying substrate albedo), which is defined for -visible and NIR bands, is a required boundary condition for the snow -radiative transfer calculation. Currently, the bulk NIR soil albedo is -applied to all four NIR snow bands. With ground albedo as a lower -boundary condition, SNICAR simulates solar absorption in all snow layers -as well as the underlying soil or ground. With a thin snowpack, -penetrating solar radiation to the underlying soil can be quite large -and heat cannot be released from the soil to the atmosphere in this -situation. Thus, if the snowpack has total snow depth less than 0.1 m -(:math:`z_{sno} < 0.1`) and there are no explicit snow layers, the solar -radiation is absorbed by the top soil layer. If there is a single snow layer, -the solar radiation is absorbed in that layer. If there is more than a single -snow layer, 75% of the solar radiation is absorbed in the top snow layer, -and 25% is absorbed in the next lowest snow layer. This prevents unrealistic -soil warming within a single timestep. - -The radiative transfer calculation is performed twice for each column -containing a mass of snow greater than -:math:`1 \times 10^{-30}` kg\ m\ :sup:`-2` (excluding lake and urban columns); once each for -direct-beam and diffuse incident flux. Absorption in each layer -:math:`i` of pure snow is initially recorded as absorbed flux per unit -incident flux on the ground (:math:`S_{sno,\, i}` ), as albedos must be -calculated for the next timestep with unknown incident flux. The snow -absorption fluxes that are used for column temperature calculations are +Under direct-beam conditions, singularities in the radiative approximation are occasionally approached in spectral bands 4 and 5 that produce unrealistic conditions (negative energy absorption in a layer, negative albedo, or total absorbed flux greater than incident flux). When any of these three conditions occur, the Eddington approximation is attempted instead, and if both approximations fail, the cosine of the solar zenith angle is adjusted by 0.02 (conserving incident flux) and a warning message is produced. This situation occurs in only about 1 in 10 :sup:`6` computations of snow albedo. After looping over the five spectral bands, absorption fluxes and albedo are averaged back into the bulk NIR band used by the rest of CLM. + +Soil albedo (or underlying substrate albedo), which is defined for visible and NIR bands, is a required boundary condition for the snow radiative transfer calculation. Currently, the bulk NIR soil albedo is applied to all four NIR snow bands. With ground albedo as a lower boundary condition, SNICAR simulates solar absorption in all snow layers as well as the underlying soil or ground. With a thin snowpack, penetrating solar radiation to the underlying soil can be quite large and heat cannot be released from the soil to the atmosphere in this situation. Thus, if the snowpack has total snow depth less than 0.1 m (:math:`z_{sno} < 0.1`) and there are no explicit snow layers, the solar radiation is absorbed by the top soil layer. If there is a single snow layer, the solar radiation is absorbed in that layer. If there is more than a single snow layer, 75% of the solar radiation is absorbed in the top snow layer, and 25% is absorbed in the next lowest snow layer. This prevents unrealistic soil warming within a single timestep. + +The radiative transfer calculation is performed twice for each column containing a mass of snow greater than :math:`1 \times 10^{-30}` kg\ m\ :sup:`-2` (excluding lake and urban columns); once each for direct-beam and diffuse incident flux. Absorption in each layer :math:`i` of pure snow is initially recorded as absorbed flux per unit incident flux on the ground (:math:`S_{sno,\, i}` ), as albedos must be calculated for the next timestep with unknown incident flux. The snow absorption fluxes that are used for column temperature calculations are .. math:: :label: ZEqnNum275338 S_{g,\, i} =S_{sno,\, i} \left(1-\alpha _{sno} \right) -This weighting is performed for direct-beam and diffuse, visible and NIR -fluxes. After the ground-incident fluxes (transmitted through the -vegetation canopy) have been calculated for the current time step -(sections :numref:`Canopy Radiative Transfer` and :numref:`Solar Fluxes`), -the layer absorption factors - -(:math:`S_{g,\, i}`) are multiplied by the ground-incident fluxes to -produce solar absorption (W m\ :sup:`-2`) in each snow layer and -the underlying ground. +This weighting is performed for direct-beam and diffuse, visible and NIR fluxes. After the ground-incident fluxes (transmitted through the vegetation canopy) have been calculated for the current time step (sections :numref:`Canopy Radiative Transfer` and :numref:`Solar Fluxes`), the layer absorption factors (:math:`S_{g,\, i}`) are multiplied by the ground-incident fluxes to produce solar absorption (W m\ :sup:`-2`) in each snow layer and the underlying ground. .. _Snowpack Optical Properties: Snowpack Optical Properties ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Ice optical properties for the five spectral bands are derived offline -and stored in a namelist-defined lookup table for online retrieval (see -CLM5.0 User's Guide). Mie properties are first computed at fine spectral -resolution (470 bands), and are then weighted into the five bands -applied by CLM according to incident solar flux, -:math:`I^{\downarrow } (\lambda )`. For example, the broadband -mass-extinction cross section (:math:`\bar{\psi }`) over wavelength -interval :math:`\lambda _{1}` to :math:`\lambda _{2}` is +Ice optical properties for the five spectral bands are derived offline and stored in a namelist-defined lookup table for online retrieval (see CLM5.0 User's Guide). Mie properties are first computed at fine spectral resolution (470 bands), and are then weighted into the five bands applied by CLM according to incident solar flux, :math:`I^{\downarrow } (\lambda )`. For example, the broadband mass-extinction cross section (:math:`\bar{\psi }`) over wavelength interval :math:`\lambda _{1}` to :math:`\lambda _{2}` is .. math:: :label: 3.70 \bar{\psi }=\frac{\int _{\lambda _{1} }^{\lambda _{2} }\psi \left(\lambda \right) I^{\downarrow } \left(\lambda \right){\rm d}\lambda }{\int _{\lambda _{1} }^{\lambda _{2} }I^{\downarrow } \left(\lambda \right){\rm d}\lambda } -Broadband single-scatter albedo (:math:`\bar{\omega }`) is additionally -weighted by the diffuse albedo for a semi-infinite snowpack (:math:`\alpha _{sno}`) +Broadband single-scatter albedo (:math:`\bar{\omega }`) is additionally weighted by the diffuse albedo for a semi-infinite snowpack (:math:`\alpha _{sno}`) .. math:: :label: 3.71 \bar{\omega }=\frac{\int _{\lambda _{1} }^{\lambda _{2} }\omega (\lambda )I^{\downarrow } ( \lambda )\alpha _{sno} (\lambda ){\rm d}\lambda }{\int _{\lambda _{1} }^{\lambda _{2} }I^{\downarrow } ( \lambda )\alpha _{sno} (\lambda ){\rm d}\lambda } -Inclusion of this additional albedo weight was found to improve accuracy -of the five-band albedo solutions (relative to 470-band solutions) -because of the strong dependence of optically-thick snowpack albedo on -ice grain single-scatter albedo (:ref:`Flanner et al. (2007) `). -The lookup tables contain optical properties for lognormal distributions of ice -particles over the range of effective radii: 30\ :math:`\mu`\ m -:math:`< r _{e} < \text{1500} \mu \text{m}`, at 1 :math:`\mu` m resolution. -Single-scatter albedos for the end-members of this size range are listed in -:numref:`Table Single-scatter albedo values used for snowpack impurities and ice`. - -Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. -Single-scatter albedo, mass extinction cross-section, and -asymmetry parameter values for all snowpack species, in the five -spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, -:numref:`Table Mass extinction values`, and -:numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. -These properties were also derived with Mie Theory, using various published -sources of indices of refraction and assumptions about particle size -distribution. Weighting into the five CLM spectral bands was determined -only with incident solar flux, as in equation . +Inclusion of this additional albedo weight was found to improve accuracy of the five-band albedo solutions (relative to 470-band solutions) because of the strong dependence of optically-thick snowpack albedo on ice grain single-scatter albedo (:ref:`Flanner et al. (2007) `). The lookup tables contain optical properties for lognormal distributions of ice particles over the range of effective radii: 30\ :math:`\mu`\ m :math:`< r _{e} < \text{1500} \mu \text{m}`, at 1 :math:`\mu` m resolution. Single-scatter albedos for the end-members of this size range are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`. + +Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. Single-scatter albedo, mass extinction cross-section, and asymmetry parameter values for all snowpack species, in the five spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, :numref:`Table Mass extinction values`, and :numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. These properties were also derived with Mie Theory, using various published sources of indices of refraction and assumptions about particle size distribution. Weighting into the five CLM spectral bands was determined only with incident solar flux, as in equation. .. _Table Single-scatter albedo values used for snowpack impurities and ice: @@ -918,209 +690,109 @@ only with incident solar flux, as in equation . Snow Aging ^^^^^^^^^^^^^^^^ -Snow aging is represented as evolution of the ice effective grain size -(:math:`r_{e}`). Previous studies have shown that use of spheres -which conserve the surface area-to-volume ratio (or specific surface -area) of ice media composed of more complex shapes produces relatively -small errors in simulated hemispheric fluxes -(e.g., :ref:`Grenfell and Warren 1999 `). -Effective radius is the surface area-weighted mean -radius of an ensemble of spherical particles and is directly related to specific -surface area (*SSA*) as -:math:`r_{e} ={3\mathord{\left/ {\vphantom {3 \left(\rho _{ice} SSA\right)}} \right.} \left(\rho _{ice} SSA\right)}` , -where :math:`\rho_{ice}` is the density of ice. Hence, -:math:`r_{e}` is a simple and practical metric for relating the -snowpack microphysical state to dry snow radiative characteristics. - -Wet snow processes can also drive rapid changes in albedo. The presence -of liquid water induces rapid coarsening of the surrounding ice grains -(e.g., :ref:`Brun 1989 `), and liquid water tends to refreeze into large ice -clumps that darken the bulk snowpack. The presence of small liquid -drops, by itself, does not significantly darken snowpack, as ice and -water have very similar indices of refraction throughout the solar -spectrum. Pooled or ponded water, however, can significantly darken -snowpack by greatly reducing the number of refraction events per unit -mass. This influence is not currently accounted for. - -The net change in effective grain size occurring each time step is -represented in each snow layer as a summation of changes caused by dry -snow metamorphism (:math:`dr_{e,dry}`), liquid water-induced -metamorphism (:math:`dr_{e,wet}`), refreezing of liquid water, and -addition of freshly-fallen snow. The mass of each snow layer is -partitioned into fractions of snow carrying over from the previous time -step (:math:`f_{old}`), freshly-fallen snow -(:math:`f_{new}`), and refrozen liquid water -(:math:`f_{rfz}`), such that snow :math:`r_{e}` is updated -each time step *t* as +Snow aging is represented as evolution of the ice effective grain size (:math:`r_{e}`). Previous studies have shown that use of spheres which conserve the surface area-to-volume ratio (or specific surface area) of ice media composed of more complex shapes produces relatively small errors in simulated hemispheric fluxes (e.g., :ref:`Grenfell and Warren 1999 `). Effective radius is the surface area-weighted mean radius of an ensemble of spherical particles and is directly related to specific surface area (*SSA*) as :math:`r_{e} ={3\mathord{\left/ {\vphantom {3 \left(\rho _{ice} SSA\right)}} \right.} \left(\rho _{ice} SSA\right)}`, where :math:`\rho_{ice}` is the density of ice. Hence, :math:`r_{e}` is a simple and practical metric for relating the snowpack microphysical state to dry snow radiative characteristics. + +Wet snow processes can also drive rapid changes in albedo. The presence of liquid water induces rapid coarsening of the surrounding ice grains (e.g., :ref:`Brun 1989 `), and liquid water tends to refreeze into large ice clumps that darken the bulk snowpack. The presence of small liquid drops, by itself, does not significantly darken snowpack, as ice and water have very similar indices of refraction throughout the solar spectrum. Pooled or ponded water, however, can significantly darken snowpack by greatly reducing the number of refraction events per unit mass. This influence is not currently accounted for. + +The net change in effective grain size occurring each time step is represented in each snow layer as a summation of changes caused by dry snow metamorphism (:math:`dr_{e,dry}`), liquid water-induced metamorphism (:math:`dr_{e,wet}`), refreezing of liquid water, and addition of freshly-fallen snow. The mass of each snow layer is partitioned into fractions of snow carrying over from the previous time step (:math:`f_{old}`), freshly-fallen snow (:math:`f_{new}`), and refrozen liquid water (:math:`f_{rfz}`), such that snow :math:`r_{e}` is updated each time step *t* as .. math:: :label: 3.72 r_{e} \left(t\right)=\left[r_{e} \left(t-1\right)+dr_{e,\, dry} +dr_{e,\, wet} \right]f_{old} +r_{e,\, 0} f_{new} +r_{e,\, rfz} f_{rfrz} -Here, the effective radius of freshly-fallen snow -(:math:`r_{e,0}`) is based on a simple linear temperature-relationship. -Below -30 degrees Celsius, a minimum value is enforced of 54.5 :math:`\mu` m -(corresponding to a specific surface area of 60 m\ :sup:`2` kg\ :sup:`-1`). -Above 0 degrees Celsius, a maximum value is enforced of 204.5 :math:`\mu` m. -Between -30 and 0 a linear ramp is used. +Here, the effective radius of freshly-fallen snow (:math:`r_{e,0}`) is based on a simple linear temperature-relationship. Below -30 degrees Celsius, a minimum value is enforced of 54.5 :math:`\mu` m (corresponding to a specific surface area of 60 m\ :sup:`2` kg\ :sup:`-1`). Above 0 degrees Celsius, a maximum value is enforced of 204.5 :math:`\mu` m. Between -30 and 0 a linear ramp is used. The effective radius of refrozen liquid water (:math:`r_{e,rfz}`) is set to 1000\ :math:`\mu` m. -Dry snow aging is based on a microphysical model described by :ref:`Flanner -and Zender (2006) `. This model simulates diffusive vapor flux -amongst collections of ice crystals with various size and inter-particle -spacing. Specific surface area and effective radius are prognosed for -any combination of snow temperature, temperature gradient, density, and -initial size distribution. The combination of warm snow, large -temperature gradient, and low density produces the most rapid snow -aging, whereas aging proceeds slowly in cold snow, regardless of -temperature gradient and density. Because this model is currently too -computationally expensive for inclusion in climate models, we fit -parametric curves to model output over a wide range of snow conditions -and apply these parameters in CLM. The functional form of the parametric -equation is +Dry snow aging is based on a microphysical model described by :ref:`Flanner and Zender (2006) `. This model simulates diffusive vapor flux amongst collections of ice crystals with various size and inter-particle spacing. Specific surface area and effective radius are prognosed for any combination of snow temperature, temperature gradient, density, and initial size distribution. The combination of warm snow, large temperature gradient, and low density produces the most rapid snow aging, whereas aging proceeds slowly in cold snow, regardless of temperature gradient and density. Because this model is currently too computationally expensive for inclusion in climate models, we fit parametric curves to model output over a wide range of snow conditions and apply these parameters in CLM. The functional form of the parametric equation is .. math:: :label: 3.73 \frac{dr_{e,\, dry} }{dt} =\left(\frac{dr_{e} }{dt} \right)_{0} \left(\frac{\eta }{\left(r_{e} -r_{e,\, 0} \right)+\eta } \right)^{{1\mathord{\left/ {\vphantom {1 \kappa }} \right.} \kappa } } -The parameters :math:`{(\frac{dr_{e}}{dt}})_{0}`, -:math:`\eta`, and :math:`\kappa` are retrieved interactively from a -lookup table with dimensions corresponding to snow temperature, -temperature gradient, and density. The domain covered by this lookup -table includes temperature ranging from 223 to 273 K, temperature -gradient ranging from 0 to 300 K m\ :sup:`-1`, and density ranging -from 50 to 400 kg m\ :sup:`-3`. Temperature gradient is calculated -at the midpoint of each snow layer *n*, using mid-layer temperatures -(:math:`T_{n}`) and snow layer thicknesses (:math:`dz_{n}`), as +The parameters :math:`{(\frac{dr_{e}}{dt}})_{0}`, :math:`\eta`, and :math:`\kappa` are retrieved interactively from a lookup table with dimensions corresponding to snow temperature, temperature gradient, and density. The domain covered by this lookup table includes temperature ranging from 223 to 273 K, temperature gradient ranging from 0 to 300 K m\ :sup:`-1`, and density ranging from 50 to 400 kg m\ :sup:`-3`. Temperature gradient is calculated at the midpoint of each snow layer *n*, using mid-layer temperatures (:math:`T_{n}`) and snow layer thicknesses (:math:`dz_{n}`), as .. math:: :label: 3.74 \left(\frac{dT}{dz} \right)_{n} =\frac{1}{dz_{n} } abs\left[\frac{T_{n-1} dz_{n} +T_{n} dz_{n-1} }{dz_{n} +dz_{n-1} } +\frac{T_{n+1} dz_{n} +T_{n} dz_{n+1} }{dz_{n} +dz_{n+1} } \right] -For the bottom snow layer (:math:`n=0`), -:math:`T_{n+1}` is taken as the temperature of the -top soil layer, and for the top snow layer it is assumed that -:math:`T_{n-1}` = :math:`T_{n}`. +For the bottom snow layer (:math:`n=0`), :math:`T_{n+1}` is taken as the temperature of the top soil layer, and for the top snow layer it is assumed that :math:`T_{n-1}` = :math:`T_{n}`. -The contribution of liquid water to enhanced metamorphism is based on -parametric equations published by :ref:`Brun (1989) `, who measured grain -growth rates under different liquid water contents. This relationship, -expressed in terms of :math:`r_{e} (\mu \text{m})` and -subtracting an offset due to dry aging, depends on the mass liquid water -fraction :math:`f_{liq}` as +The contribution of liquid water to enhanced metamorphism is based on parametric equations published by :ref:`Brun (1989) `, who measured grain growth rates under different liquid water contents. This relationship, expressed in terms of :math:`r_{e} (\mu \text{m})` and subtracting an offset due to dry aging, depends on the mass liquid water fraction :math:`f_{liq}` as .. math:: :label: 3.75 \frac{dr_{e} }{dt} =\frac{10^{18} C_{1} f_{liq} ^{3} }{4\pi r_{e} ^{2} } -The constant *C*\ :sub:`1` is 4.22\ :math:`\times`\ 10\ :sup:`-13`, and: -:math:`f_{liq} =w_{liq} /(w_{liq} +w_{ice} )`\ (Chapter :numref:`rst_Snow Hydrology`). +The constant *C*\ :sub:`1` is 4.22\ :math:`\times`\ 10\ :sup:`-13`, and: :math:`f_{liq} =w_{liq} /(w_{liq} +w_{ice} )`\ (Chapter :numref:`rst_Snow Hydrology`). -In cases where snow mass is greater than zero, but a snow layer has not -yet been defined, :math:`r_{e}` is set to :math:`r_{e,0}`. When snow layers are combined or -divided, :math:`r_{e}` is calculated as a mass-weighted mean of -the two layers, following computations of other state variables (section -:numref:`Snow Layer Combination and Subdivision`). Finally, the allowable range of :math:`r_{e}`, -corresponding to the range over which Mie optical properties have been -defined, is 30-1500\ :math:`\mu` m. +In cases where snow mass is greater than zero, but a snow layer has not yet been defined, :math:`r_{e}` is set to :math:`r_{e,0}`. When snow layers are combined or divided, :math:`r_{e}` is calculated as a mass-weighted mean of the two layers, following computations of other state variables (section :numref:`Snow Layer Combination and Subdivision`). Finally, the allowable range of :math:`r_{e}`, corresponding to the range over which Mie optical properties have been defined, is 30-1500\ :math:`\mu` m. .. _Solar Zenith Angle: Solar Zenith Angle ---------------------- -The CLM uses the same formulation for solar zenith angle as the -Community Atmosphere Model. The cosine of the solar zenith angle -:math:`\mu` is +The CLM uses the same formulation for solar zenith angle as the Community Atmosphere Model. The cosine of the solar zenith angle :math:`\mu` is .. math:: :label: 3.76 \mu =\sin \phi \sin \delta -\cos \phi \cos \delta \cos h -where :math:`h` is the solar hour angle (radians) (24 hour periodicity), -:math:`\delta` is the solar declination angle (radians), and -:math:`\phi` is latitude (radians) (positive in Northern Hemisphere). -The solar hour angle :math:`h` (radians) is +where :math:`h` is the solar hour angle (radians) (24 hour periodicity), :math:`\delta` is the solar declination angle (radians), and :math:`\phi` is latitude (radians) (positive in Northern Hemisphere). The solar hour angle :math:`h` (radians) is .. math:: :label: 3.77 h=2\pi d+\theta -where :math:`d` is calendar day (:math:`d=0.0` at 0Z on January 1), and -:math:`\theta` is longitude (radians) (positive east of the -Greenwich meridian). +where :math:`d` is calendar day (:math:`d=0.0` at 0Z on January 1), and :math:`\theta` is longitude (radians) (positive east of the Greenwich meridian). -The solar declination angle :math:`\delta` is calculated as in :ref:`Berger -(1978a,b) ` and is valid for one million years past or hence, relative to -1950 A.D. The orbital parameters may be specified directly or the -orbital parameters are calculated for the desired year. The required -orbital parameters to be input by the user are the obliquity of the -Earth :math:`\varepsilon` (degrees, -:math:`-90^{\circ } <\varepsilon <90^{\circ }` ), Earth's eccentricity -:math:`e` (:math:`0.0`)). The -solar declination :math:`\delta` (radians) is +The solar declination angle :math:`\delta` is calculated as in :ref:`Berger (1978a,b) ` and is valid for one million years past or hence, relative to 1950 A.D. The orbital parameters may be specified directly or the orbital parameters are calculated for the desired year. The required orbital parameters to be input by the user are the obliquity of the Earth :math:`\varepsilon` (degrees, :math:`-90^{\circ } <\varepsilon <90^{\circ }` ), Earth's eccentricity :math:`e` (:math:`0.0`)). The solar declination :math:`\delta` (radians) is .. math:: :label: 3.78 \delta =\sin ^{-1} \left[\sin \left(\varepsilon \right)\sin \left(\lambda \right)\right] -where :math:`\varepsilon` is Earth's obliquity and :math:`\lambda` is -the true longitude of the Earth. +where :math:`\varepsilon` is Earth's obliquity and :math:`\lambda` is the true longitude of the Earth. -The obliquity of the Earth :math:`\varepsilon` (degrees) is +The obliquity of the Earth :math:`\varepsilon` (degrees) is .. math:: :label: 3.79 \varepsilon =\varepsilon *+\sum _{i=1}^{i=47}A_{i} \cos \left(f_{i} t+\delta _{i} \right) -where :math:`\varepsilon *` is a constant of integration (:numref:`Table Orbital parameters`), -:math:`A_{i}` , :math:`f_{i}` , and :math:`\delta _{i}` are amplitude, -mean rate, and phase terms in the cosine series expansion (:ref:`Berger -(1978a,b) `, and :math:`t=t_{0} -1950` where :math:`t_{0}` is the year. -The series expansion terms are not shown here but can be found in the -source code file shr\_orb\_mod.F90. +where :math:`\varepsilon *` is a constant of integration (:numref:`Table Orbital parameters`), :math:`A_{i}`, :math:`f_{i}`, and :math:`\delta _{i}` are amplitude, mean rate, and phase terms in the cosine series expansion (:ref:`Berger (1978a,b) `, and :math:`t=t_{0} -1950` where :math:`t_{0}` is the year. The series expansion terms are not shown here but can be found in the source code file shr\_orb\_mod.F90. -The true longitude of the Earth :math:`\lambda` (radians) is counted -counterclockwise from the vernal equinox (:math:`\lambda =0` at the -vernal equinox) +The true longitude of the Earth :math:`\lambda` (radians) is counted counterclockwise from the vernal equinox (:math:`\lambda =0` at the vernal equinox) .. math:: :label: 3.80 \lambda =\lambda _{m} +\left(2e-\frac{1}{4} e^{3} \right)\sin \left(\lambda _{m} -\tilde{\omega }\right)+\frac{5}{4} e^{2} \sin 2\left(\lambda _{m} -\tilde{\omega }\right)+\frac{13}{12} e^{3} \sin 3\left(\lambda _{m} -\tilde{\omega }\right) -where :math:`\lambda _{m}` is the mean longitude of the Earth at the -vernal equinox, :math:`e` is Earth's eccentricity, and -:math:`\tilde{\omega }` is the longitude of the perihelion relative to -the moving vernal equinox. The mean longitude :math:`\lambda _{m}` is +where :math:`\lambda _{m}` is the mean longitude of the Earth at the vernal equinox, :math:`e` is Earth's eccentricity, and :math:`\tilde{\omega }` is the longitude of the perihelion relative to the moving vernal equinox. The mean longitude :math:`\lambda _{m}` is .. math:: :label: 3.81 \lambda _{m} =\lambda _{m0} +\frac{2\pi \left(d-d_{ve} \right)}{365} -where :math:`d_{ve} =80.5` is the calendar day at vernal equinox (March -21 at noon), and +where :math:`d_{ve} =80.5` is the calendar day at vernal equinox (March 21 at noon), and .. math:: :label: 3.82 \lambda _{m0} =2\left[\left(\frac{1}{2} e+\frac{1}{8} e^{3} \right)\left(1+\beta \right)\sin \tilde{\omega }-\frac{1}{4} e^{2} \left(\frac{1}{2} +\beta \right)\sin 2\tilde{\omega }+\frac{1}{8} e^{3} \left(\frac{1}{3} +\beta \right)\sin 3\tilde{\omega }\right] -where :math:`\beta =\sqrt{1-e^{2} }` . Earth's eccentricity :math:`e` -is +where :math:`\beta =\sqrt{1-e^{2} }`. Earth's eccentricity :math:`e` is .. math:: :label: 3.83 @@ -1134,36 +806,21 @@ where \begin{array}{l} {e^{\cos } =\sum _{j=1}^{19}M_{j} \cos \left(g_{j} t+B_{j} \right) ,} \\ {e^{\sin } =\sum _{j=1}^{19}M_{j} \sin \left(g_{j} t+B_{j} \right) } \end{array} -are the cosine and sine series expansions for :math:`e`, and -:math:`M_{j}` , :math:`g_{j}` , and :math:`B_{j}` are amplitude, mean -rate, and phase terms in the series expansions (:ref:`Berger (1978a,b) `). The -longitude of the perihelion relative to the moving vernal equinox -:math:`\tilde{\omega }` (degrees) is +are the cosine and sine series expansions for :math:`e`, and :math:`M_{j}`, :math:`g_{j}`, and :math:`B_{j}` are amplitude, mean rate, and phase terms in the series expansions (:ref:`Berger (1978a,b) `). The longitude of the perihelion relative to the moving vernal equinox :math:`\tilde{\omega }` (degrees) is .. math:: :label: 3.85 \tilde{\omega }=\Pi \frac{180}{\pi } +\psi -where :math:`\Pi` is the longitude of the perihelion measured from the -reference vernal equinox (i.e., the vernal equinox at 1950 A.D.) and -describes the absolute motion of the perihelion relative to the fixed -stars, and :math:`\psi` is the annual general precession in longitude -and describes the absolute motion of the vernal equinox along Earth's -orbit relative to the fixed stars. The general precession :math:`\psi` -(degrees) is +where :math:`\Pi` is the longitude of the perihelion measured from the reference vernal equinox (i.e., the vernal equinox at 1950 A.D.) and describes the absolute motion of the perihelion relative to the fixed stars, and :math:`\psi` is the annual general precession in longitude and describes the absolute motion of the vernal equinox along Earth's orbit relative to the fixed stars. The general precession :math:`\psi` (degrees) is .. math:: :label: 3.86 \psi =\frac{\tilde{\psi }t}{3600} +\zeta +\sum _{i=1}^{78}F_{i} \sin \left(f_{i} ^{{'} } t+\delta _{i} ^{{'} } \right) -where :math:`\tilde{\psi }` (arcseconds) and :math:`\zeta` (degrees) -are constants (:numref:`Table Orbital parameters`), and :math:`F_{i}` , :math:`f_{i} ^{{'} }` , -and :math:`\delta _{i} ^{{'} }` are amplitude, mean rate, and phase -terms in the sine series expansion (:ref:`Berger (1978a,b) `)). The longitude of -the perihelion :math:`\Pi` (radians) depends on the sine and cosine -series expansions for the eccentricity :math:`e`\ as follows: +where :math:`\tilde{\psi }` (arcseconds) and :math:`\zeta` (degrees) are constants (:numref:`Table Orbital parameters`), and :math:`F_{i}`, :math:`f_{i} ^{{'} }`, and :math:`\delta _{i} ^{{'} }` are amplitude, mean rate, and phase terms in the sine series expansion (:ref:`Berger (1978a,b) `)). The longitude of the perihelion :math:`\Pi` (radians) depends on the sine and cosine series expansions for the eccentricity :math:`e`\ as follows: .. math:: :label: 3.87 @@ -1177,11 +834,7 @@ series expansions for the eccentricity :math:`e`\ as follows: \tan ^{-1} \left[\frac{e^{\sin } }{e^{\cos } } \right] & \qquad {\rm for\; }e^{\cos } >{\rm 1}\times {\rm 10}^{{\rm -8}} {\rm \; and\; }e^{\sin } \ge 0 \end{array}\right\}. -The numerical solution for the longitude of the perihelion -:math:`\tilde{\omega }` is constrained to be between 0 and 360 degrees -(measured from the autumn equinox). A constant 180 degrees is then added -to :math:`\tilde{\omega }` because the Sun is considered as revolving -around the Earth (geocentric coordinate system) (:ref:`Berger et al. 1993 `)). +The numerical solution for the longitude of the perihelion :math:`\tilde{\omega }` is constrained to be between 0 and 360 degrees (measured from the autumn equinox). A constant 180 degrees is then added to :math:`\tilde{\omega }` because the Sun is considered as revolving around the Earth (geocentric coordinate system) (:ref:`Berger et al. 1993 `)). .. _Table Orbital parameters: diff --git a/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst b/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst index 4bf2f44861..c221a14d28 100644 --- a/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst +++ b/doc/source/tech_note/Transient_Landcover/CLM50_Tech_Note_Transient_Landcover.rst @@ -3,116 +3,35 @@ Transient Land Use and Land Cover Change ======================================== -CLM includes a treatment of mass and energy fluxes associated with -prescribed temporal land use and land cover change (LULCC). The model -uses an annual time series of the spatial distribution of the natural -and crop land units of each grid cell, in combination with the -distribution of PFTs and CFTs that exist in those land units. Additional -land use is prescribed through annual crop-specific management of -nitrogen fertilizer and irrigation (described further in -:numref:`rst_Crops and Irrigation`), and through wood harvest on tree -PFTs. For changes in the distributions of natural and crop vegetation, -CLM diagnoses the change in area of the PFTs and CFTs on January 1 of -each model year and then performs mass and energy balance accounting -necessary to represent the expansion and contraction of the PFT and CFT -areas. The biogeophysical impacts of LULCC are simulated through changes -in surface properties which in turn impact the surface albedo, -hydrology, and roughness which then impact fluxes of energy, moisture -and momentum to the atmosphere under the altered -properties. Additionally, changes in energy and moisture associated with -changes in the natural and crop vegetation distribution are accounted -for through small fluxes to the river and atmosphere. The biogeochemical -impacts of LULCC are simulated through changes in CLM carbon pools and -fluxes (see also Chapter :numref:`rst_CN Pools`). - -CLM can also respond to changes in ice sheet areas and elevations when -it is coupled to an evolving ice sheet model (in the CESM context, this -is the Community Ice Sheet Model, CISM; see also Chapter -:numref:`rst_Glaciers`). Conservation of water, energy, carbon and -nitrogen is handled similarly for glacier-vegetation transitions as for -natural vegetation-crop transitions. +CLM includes a treatment of mass and energy fluxes associated with prescribed temporal land use and land cover change (LULCC). The model uses an annual time series of the spatial distribution of the natural and crop land units of each grid cell, in combination with the distribution of PFTs and CFTs that exist in those land units. Additional land use is prescribed through annual crop-specific management of nitrogen fertilizer and irrigation (described further in :numref:`rst_Crops and Irrigation`), and through wood harvest on tree PFTs. For changes in the distributions of natural and crop vegetation, CLM diagnoses the change in area of the PFTs and CFTs on January 1 of each model year and then performs mass and energy balance accounting necessary to represent the expansion and contraction of the PFT and CFT areas. The biogeophysical impacts of LULCC are simulated through changes in surface properties which in turn impact the surface albedo, hydrology, and roughness which then impact fluxes of energy, moisture and momentum to the atmosphere under the altered properties. Additionally, changes in energy and moisture associated with changes in the natural and crop vegetation distribution are accounted for through small fluxes to the river and atmosphere. The biogeochemical impacts of LULCC are simulated through changes in CLM carbon pools and fluxes (see also Chapter :numref:`rst_CN Pools`). + +CLM can also respond to changes in ice sheet areas and elevations when it is coupled to an evolving ice sheet model (in the CESM context, this is the Community Ice Sheet Model, CISM; see also Chapter :numref:`rst_Glaciers`). Conservation of water, energy, carbon and nitrogen is handled similarly for glacier-vegetation transitions as for natural vegetation-crop transitions. .. _Transient land use and land cover data: Annual Transient Land Use and Land Cover Data --------------------------------------------- -The changes in area over time associated with changes in natural and crop vegetation and -the land use on that vegetation are prescribed through a forcing dataset, referred to here -as the *landuse.timeseries* dataset. The *landuse.timeseries* dataset consists of an -annual time series of global grids, where each annual time slice describes the fractional -area occupied by all PFTs and CFTs along with the nitrogen fertilizer and irrigation -fraction of each crop CFT, and the annual wood harvest applied to tree PFTs. Changes in -area of PFTs and CFTs are performed annually on the first time step of January 1 of the -year. Wood harvest for each PFT is also performed on the first time step of the -year. Fertilizer application and irrigation for each CFT are performed at each model time -step depending on rules from the crop model. Fertilizer application rates are set -annually. The irrigation fraction is also set annually; irrigated crops are placed on -separate columns from their unirrigated counterparts, so changes in irrigated fraction -triggers the changes in subgrid areas discussed below (sections :numref:`Transient -landcover reconciling changes in area` and :numref:`Transient landcover mass and energy -conservation`). - -As a special case, when the time dimension of the *landuse.timeseries* dataset starts at a -later year than the current model time step, the first time slice from the -*landuse.timeseries* dataset is used to represent the current time step PFT and CFT -fractional area distributions. Similarly, when the time dimension of the -*landuse.timeseries* dataset stops at an earlier year than the current model time step, -the last time slice of the *landuse.timeseries* dataset is used. Thus, the simulation will -have invariant representations of PFT and CFT distributions through time for the periods -prior to and following the time duration of the *landuse.timeseries* dataset, with -transient PFT and CFT distributions during the period covered by the *landuse.timeseries* -dataset. +The changes in area over time associated with changes in natural and crop vegetation and the land use on that vegetation are prescribed through a forcing dataset, referred to here as the *landuse.timeseries* dataset. The *landuse.timeseries* dataset consists of an annual time series of global grids, where each annual time slice describes the fractional area occupied by all PFTs and CFTs along with the nitrogen fertilizer and irrigation fraction of each crop CFT, and the annual wood harvest applied to tree PFTs. Changes in area of PFTs and CFTs are performed annually on the first time step of January 1 of the year. Wood harvest for each PFT is also performed on the first time step of the year. Fertilizer application and irrigation for each CFT are performed at each model time step depending on rules from the crop model. Fertilizer application rates are set annually. The irrigation fraction is also set annually; irrigated crops are placed on separate columns from their unirrigated counterparts, so changes in irrigated fraction triggers the changes in subgrid areas discussed below (sections :numref:`Transient landcover reconciling changes in area` and :numref:`Transient landcover mass and energy conservation`). + +As a special case, when the time dimension of the *landuse.timeseries* dataset starts at a later year than the current model time step, the first time slice from the *landuse.timeseries* dataset is used to represent the current time step PFT and CFT fractional area distributions. Similarly, when the time dimension of the *landuse.timeseries* dataset stops at an earlier year than the current model time step, the last time slice of the *landuse.timeseries* dataset is used. Thus, the simulation will have invariant representations of PFT and CFT distributions through time for the periods prior to and following the time duration of the *landuse.timeseries* dataset, with transient PFT and CFT distributions during the period covered by the *landuse.timeseries* dataset. .. _Transient landcover reconciling changes in area: Reconciling Changes in Area --------------------------- -In the first time step of January 1, changes in land unit weights can -potentially come from two sources: Changes in the area of the crop land -unit come from the *landuse.timeseries* dataset (section -:numref:`Transient land use and land cover data`), and changes in the -area of the glacier land unit come from the ice sheet model. The areas -of other land units are then adjusted so that the total land unit area -remains 100%. - -If the total land unit area of glaciers and crops has decreased, then -the natural vegetated landunit is increased to fill in the abandoned -land. If the total land unit area of glaciers and crops has increased, -then other land unit areas are decreased in a specified order until the -total is once again 100%. The order of decrease is: natural vegetation, -crop, urban medium density, urban high density, urban tall building -district, wetland, lake. +In the first time step of January 1, changes in land unit weights can potentially come from two sources: Changes in the area of the crop land unit come from the *landuse.timeseries* dataset (section :numref:`Transient land use and land cover data`), and changes in the area of the glacier land unit come from the ice sheet model. The areas of other land units are then adjusted so that the total land unit area remains 100%. + +If the total land unit area of glaciers and crops has decreased, then the natural vegetated landunit is increased to fill in the abandoned land. If the total land unit area of glaciers and crops has increased, then other land unit areas are decreased in a specified order until the total is once again 100%. The order of decrease is: natural vegetation, crop, urban medium density, urban high density, urban tall building district, wetland, lake. These rules have two important implications: -1. We always match CISM's glacier areas exactly, even if that means a - disagreement with prescribed crop areas. This is needed for - conservation when CISM is evolving in two-way-coupled mode. - -2. For land units other than crop, glacier and natural vegetation, their - areas can decrease (due to encroaching crops or glaciers), but can - never increase. So, for example, if a grid cell starts as 5% lake, - crops expand to fill the entire grid cell, then later crop area - decreases, the lake area will not return: instead, the abandoned - cropland will become entirely natural vegetation. - -For all levels of the subgrid hierarchy (land unit, column and patch), -we only track net changes in area, not gross transitions. So, for -example, if part of a gridcell experiences an increase in glacier area -while another part of that gridcell experiences an equal decrease in -glacier area (in the same glacier elevation class), CLM acts as if there -were no changes. As another example, consider a gridcell containing -natural vegetation, crop and glacier. If there is a decrease in glacier -area and an equal increase in crop area, CLM will assume that the crop -expands into the old glacier area, and nothing happened to the natural -vegetation area. A more realistic alternative would be that the crop -expanded into natural vegetation, and natural vegetation expanded into -glacier. The final areas will be correct in these cases, but the -adjustments of carbon and nitrogen states (section :numref:`Transient -landcover carbon and nitrogen conservation`) will be less accurate than what -would be obtained with a full tracking of gross transitions. +1. We always match CISM's glacier areas exactly, even if that means a disagreement with prescribed crop areas. This is needed for conservation when CISM is evolving in two-way-coupled mode. + +2. For land units other than crop, glacier and natural vegetation, their areas can decrease (due to encroaching crops or glaciers), but can never increase. So, for example, if a grid cell starts as 5% lake, crops expand to fill the entire grid cell, then later crop area decreases, the lake area will not return: instead, the abandoned cropland will become entirely natural vegetation. + +For all levels of the subgrid hierarchy (land unit, column and patch), we only track net changes in area, not gross transitions. So, for example, if part of a gridcell experiences an increase in glacier area while another part of that gridcell experiences an equal decrease in glacier area (in the same glacier elevation class), CLM acts as if there were no changes. As another example, consider a gridcell containing natural vegetation, crop and glacier. If there is a decrease in glacier area and an equal increase in crop area, CLM will assume that the crop expands into the old glacier area, and nothing happened to the natural vegetation area. A more realistic alternative would be that the crop expanded into natural vegetation, and natural vegetation expanded into glacier. The final areas will be correct in these cases, but the adjustments of carbon and nitrogen states (section :numref:`Transient landcover carbon and nitrogen conservation`) will be less accurate than what would be obtained with a full tracking of gross transitions. .. _Transient landcover mass and energy conservation: @@ -124,149 +43,48 @@ Mass and Energy Conservation Water and Energy Conservation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -When subgrid areas change, the water and energy states remain unchanged -on a per-area basis. This can lead to changes in the total gridcell -water and energy content. - -For example, consider a gridcell with two columns: column 1 has a water -mass of 1 kg m\ :sup:`-2` and column 2 has a water mass of 2 kg m\ -:sup:`-2` for a given water state variable, where these are expressed -per unit column area. If column 1 increases in area at the expense of -column 2, then column 1 will still have a water mass of 1 kg m\ -:sup:`-2`, but now expressed over the new column area. This results in a -decrease in the total gridcell water content. - -Water and energy are conserved by summing up the total water and energy -content of each gridcell before and after a change in area. Differences -in liquid and ice water content are balanced by liquid and ice runoff -terms, which can be either positive or negative. (Negative runoff is -effectively a withdrawal of water from the ocean.) Differences in energy -content are balanced by a sensible heat flux term, which again can be -either positive or negative. These balancing fluxes are spread evenly -throughout the following year. - -There is a special case when a given crop column type newly comes into -existence - for example, when temperate corn first comes into existence -in a gridcell. In this case, the column's below-ground temperature and -water states are copied from the natural vegetated column in its -gridcell, so that these state variables begin in a close-to-spun-up -state. Other state variables (most of which spin up relatively quickly) -begin at their cold start initialization values. This initialization is -not necessary for the two other land unit types that currently can -grow - natural vegetation and glacier: Those land unit types are always -active, even when they have zero area on the gridcell, so their state -variables will be spun up immediately when they come into -existence. After this initialization, the conservation code described -above takes effect. +When subgrid areas change, the water and energy states remain unchanged on a per-area basis. This can lead to changes in the total gridcell water and energy content. + +For example, consider a gridcell with two columns: column 1 has a water mass of 1 kg m\ :sup:`-2` and column 2 has a water mass of 2 kg m\ :sup:`-2` for a given water state variable, where these are expressed per unit column area. If column 1 increases in area at the expense of column 2, then column 1 will still have a water mass of 1 kg m\ :sup:`-2`, but now expressed over the new column area. This results in a decrease in the total gridcell water content. + +Water and energy are conserved by summing up the total water and energy content of each gridcell before and after a change in area. Differences in liquid and ice water content are balanced by liquid and ice runoff terms, which can be either positive or negative. (Negative runoff is effectively a withdrawal of water from the ocean.) Differences in energy content are balanced by a sensible heat flux term, which again can be either positive or negative. These balancing fluxes are spread evenly throughout the following year. + +There is a special case when a given crop column type newly comes into existence - for example, when temperate corn first comes into existence in a gridcell. In this case, the column's below-ground temperature and water states are copied from the natural vegetated column in its gridcell, so that these state variables begin in a close-to-spun-up state. Other state variables (most of which spin up relatively quickly) begin at their cold start initialization values. This initialization is not necessary for the two other land unit types that currently can grow - natural vegetation and glacier: Those land unit types are always active, even when they have zero area on the gridcell, so their state variables will be spun up immediately when they come into existence. After this initialization, the conservation code described above takes effect. .. _Transient landcover carbon and nitrogen conservation: Carbon and Nitrogen Conservation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Because of the long timescales involved with below-ground carbon and -nitrogen dynamics, it is more important that these state variables be -adjusted properly when subgrid areas change. Carbon and nitrogen -variables are adjusted with the following three-step process: - -(1) Patch-level (i.e., vegetation) state variables are adjusted for any - changes in patch areas; this may lead to fluxes into column-level - (i.e., soil) state variables - -(2) Column-level (i.e., soil) state variables are updated based on the - fluxes generated in (1) - -(3) Column-level (i.e., soil) state variables are adjusted for any - changes in column areas - -First, patch-level (i.e., vegetation) state variables are adjusted for -any changes in patch areas. This includes changes in column or land unit -areas, even if the relative proportions of each patch remain constant: -the relevant quantities are the patch weights relative to the -gridcell. - -For a patch that decreases in area, the carbon and nitrogen density on -the remaining patch area remains the same as before (i.e., expressed as -g per m\ :sup:`2` patch area). Because the area has decreased, this -represents a decrease in total carbon or nitrogen mass (i.e., expressed -as g per m\ :sup:`2` gridcell area). The lost mass meets a variety of -fates: some is immediately lost to the atmosphere, some is sent to -product pools (which are lost to the atmosphere over longer time -scales), and some is sent to litter pools. - -For a patch that increases in area, the carbon and nitrogen density on -the new patch area is decreased in order to conserve mass. This decrease -is basically proportional to the relative increase in patch -area. However, a small amount of seed carbon and nitrogen is added to -the leaf and dead stem pools in the new patch area. - -Next, column-level (i.e., soil) state variables are updated based on any -fluxes to soil pools due to decreases in patch areas. This step is -needed so that any lost vegetation carbon and nitrogen is conserved when -column areas are changing. - -Finally, column-level state variables are adjusted for any changes in -column areas. Similarly to patches, for a column that decreases in area, -the carbon and nitrogen density on the remaining column area remains the -same as before (i.e., expressed as g per m\ :sup:`2` column area). This -represents a decrease in total carbon or nitrogen mass on the gridcell, -and this lost mass is tracked for each gridcell. After these mass losses -are summed for all shrinking columns, they are distributed amongst the -growing columns in order to conserve mass. Thus, a growing column's new -carbon density will be a weighted sum of its original carbon density and -the carbon densities of all shrinking columns in its gridcell. - -This operation makes some simplifying assumptions. First, as described -in section :numref:`Transient landcover reconciling changes in area`, we -only track net area changes, not gross changes. Second, we assume that -growing columns all grow proportionally into each of the shrinking -columns. - -Non-vegetated land units (e.g., glacier) do not typically track soil -carbon and nitrogen. When columns from these land units initially -shrink, they are assumed to contribute zero carbon and -nitrogen. However, when they grow into previously-vegetated areas, they -store any pre-existing soil carbon and nitrogen from the shrinking -columns. This stored carbon and nitrogen will remain unchanged until the -column later shrinks, at which point it will contribute to the carbon -and nitrogen in the growing columns (exactly as would happen for a -vegetated column). - -In contrast to water and energy (section :numref:`Transient landcover -water and energy conservation`), no special treatment is needed for -carbon and nitrogen states in columns that newly come into -existence. The state of a new column is derived from a weighted average -of the states of shrinking columns. This behavior falls out from the -above general rules. +Because of the long timescales involved with below-ground carbon and nitrogen dynamics, it is more important that these state variables be adjusted properly when subgrid areas change. Carbon and nitrogen variables are adjusted with the following three-step process: + +(1) Patch-level (i.e., vegetation) state variables are adjusted for any changes in patch areas; this may lead to fluxes into column-level (i.e., soil) state variables (2) Column-level (i.e., soil) state variables are updated based on the fluxes generated in (1) + +(3) Column-level (i.e., soil) state variables are adjusted for any changes in column areas First, patch-level (i.e., vegetation) state variables are adjusted for any changes in patch areas. This includes changes in column or land unit areas, even if the relative proportions of each patch remain constant: the relevant quantities are the patch weights relative to the gridcell. + +For a patch that decreases in area, the carbon and nitrogen density on the remaining patch area remains the same as before (i.e., expressed as g per m\ :sup:`2` patch area). Because the area has decreased, this represents a decrease in total carbon or nitrogen mass (i.e., expressed as g per m\ :sup:`2` gridcell area). The lost mass meets a variety of fates: some is immediately lost to the atmosphere, some is sent to product pools (which are lost to the atmosphere over longer time scales), and some is sent to litter pools. + +For a patch that increases in area, the carbon and nitrogen density on the new patch area is decreased in order to conserve mass. This decrease is basically proportional to the relative increase in patch area. However, a small amount of seed carbon and nitrogen is added to the leaf and dead stem pools in the new patch area. + +Next, column-level (i.e., soil) state variables are updated based on any fluxes to soil pools due to decreases in patch areas. This step is needed so that any lost vegetation carbon and nitrogen is conserved when column areas are changing. + +Finally, column-level state variables are adjusted for any changes in column areas. Similarly to patches, for a column that decreases in area, the carbon and nitrogen density on the remaining column area remains the same as before (i.e., expressed as g per m\ :sup:`2` column area). This represents a decrease in total carbon or nitrogen mass on the gridcell, and this lost mass is tracked for each gridcell. After these mass losses are summed for all shrinking columns, they are distributed amongst the growing columns in order to conserve mass. Thus, a growing column's new carbon density will be a weighted sum of its original carbon density and the carbon densities of all shrinking columns in its gridcell. + +This operation makes some simplifying assumptions. First, as described in section :numref:`Transient landcover reconciling changes in area`, we only track net area changes, not gross changes. Second, we assume that growing columns all grow proportionally into each of the shrinking columns. + +Non-vegetated land units (e.g., glacier) do not typically track soil carbon and nitrogen. When columns from these land units initially shrink, they are assumed to contribute zero carbon and nitrogen. However, when they grow into previously-vegetated areas, they store any pre-existing soil carbon and nitrogen from the shrinking columns. This stored carbon and nitrogen will remain unchanged until the column later shrinks, at which point it will contribute to the carbon and nitrogen in the growing columns (exactly as would happen for a vegetated column). + +In contrast to water and energy (section :numref:`Transient landcover water and energy conservation`), no special treatment is needed for carbon and nitrogen states in columns that newly come into existence. The state of a new column is derived from a weighted average of the states of shrinking columns. This behavior falls out from the above general rules. Annual Transient Land Cover Dataset Development ---------------------------------------------------- -This section describes the development of the *landuse.timeseries* dataset. -Development of this dataset involves the translation of -harmonized datasets of LULCC for the historical period and -for the different Shared Socioeconomic Pathway (SSP) - Representative -Concentration Pathway (RCP) scenarios. Additionally, LULCC time -series are to be generated for the Last Millennium and the extension beyond 2100 experiments -of CMIP6. +This section describes the development of the *landuse.timeseries* dataset. Development of this dataset involves the translation of harmonized datasets of LULCC for the historical period and for the different Shared Socioeconomic Pathway (SSP) - Representative Concentration Pathway (RCP) scenarios. Additionally, LULCC time series are to be generated for the Last Millennium and the extension beyond 2100 experiments of CMIP6. LUH2 Transient Land Use and Land Cover Change Dataset ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To coordinate the processing and consistency of LULCC data between -the historical period (1850-2015) and the six -SSP-RCP (2016-2100) scenarios derived from Integrated -Assessment Models (IAM), the University of Maryland and the University of New Hampshire -research groups (Louise Chini, George Hurtt, Steve -Frolking and Ritvik Sahajpal; luh.umd.edu) produced a new version of the Land Use Harmonized version 2 -(LUH2) transient datasets for use with Earth System Model simulations. The new data sets -are the product of the Land Use Model Intercomparison Project (LUMIP; https://cmip.ucar.edu/lumip) -as part of the Coupled Model Intercomparison Project 6 (CMIP6). The historical component of the -transient LULCC dataset has agriculture and urban -land use based on HYDE 3.2 with wood harvest based on FAO, Landsat and other sources, for the period 850-2015. -The SSP-RCP transient LULCC components (2015-2100) are -referred to as the LUH2 Future Scenario datasets. The LULCC information is provided at 0.25 degree grid resolution and includes -fractional grid cell coverage by the 12 land units of: +To coordinate the processing and consistency of LULCC data between the historical period (1850-2015) and the six SSP-RCP (2016-2100) scenarios derived from Integrated Assessment Models (IAM), the University of Maryland and the University of New Hampshire research groups (Louise Chini, George Hurtt, Steve Frolking and Ritvik Sahajpal; luh.umd.edu) produced a new version of the Land Use Harmonized version 2 (LUH2) transient datasets for use with Earth System Model simulations. The new data sets are the product of the Land Use Model Intercomparison Project (LUMIP; https://cmip.ucar.edu/lumip) as part of the Coupled Model Intercomparison Project 6 (CMIP6). The historical component of the transient LULCC dataset has agriculture and urban land use based on HYDE 3.2 with wood harvest based on FAO, Landsat and other sources, for the period 850-2015. The SSP-RCP transient LULCC components (2015-2100) are referred to as the LUH2 Future Scenario datasets. The LULCC information is provided at 0.25 degree grid resolution and includes fractional grid cell coverage by the 12 land units of: Primary Forest, Secondary Forest, Primary Non-Forest, Secondary Non-Forest, @@ -274,76 +92,24 @@ Pasture, Rangeland, Urban, C3 Annual Crop, C4 Annual Crop, C3 Perennial Crop, C4 Perennial Crop, and C3 Nitrogen Fixing Crop. -The new land unit format is an improvement on the CMIP5 LULCC -datasets as they: provide Forest and Non Forest information in combination with Primary and Secondary -land; differentiate between Pasture and Rangelands for grazing livestock; and specify annual details -on the types of Crops grown and management practices applied in each grid cell. Like the CMIP5 LULCC datasets Primary vegetation -represents the fractional area of a grid cell with vegetation undisturbed by human activities. Secondary -vegetation represents vegetated areas that have recovered from some human disturbance; this could include -re-vegetation of pasture and crop areas as well as primary vegetation areas that have been logged. -In this manner the land units can change through deforestation from Forested to Non Forested land and in the -opposite direction from Non Forested to Forested land through reforestation or afforestation without going -through the Crop, Pasture or Rangeland states. - -The LUH2 dataset provides a time series of land cover states as well as a transition matrices that describes -the annual fraction of land that is transformed from one land unit category to -another (e.g. Primary Forest to C3 Annual Crop, Pasture to C3 Perrenial Crop, etc.; Lawrence et al. -2016). Included in these transition matrices is the total conversion of one land cover type to another referred to -as Gross LULCC. This value can be larger than the sum of the changes in the state of a land unit from one time period -to the next known as the Net LULCC. This difference is possible as land unit changes can occur both from the land unit -and to the land unit at the same time. An example of this difference occurs with shifting cultivation where Secondary Forest -can be converted to C3 Annual Crop at the same time as C3 Annual Crop is abandoned to Secondary Forest. - -The transition matrices also provide harmonized prescriptions of wood harvest both in area of the grid cell harvested -and in the amount of biomass carbon harvested. The wood harvest biomass amount includes a 30% slash component inline with -the CMIP5 LULCC data described in (Hurtt et al. 2011). The harvest area and carbon amounts are prescribed for the five classes of: -Primary Forest, Primary Non-Forest, -Secondary Mature Forest, Secondary -Young Forest, and Secondary -Non-Forest. - -Additional land use management is prescribed on the Crop land units for -nitrogen fertilization and irrigation equipped land. The fertilizer application and the the irrigation fraction is -prescribed for each Crop land unit in a grid cell individually for each year of the time series. The wood harvest -and crop management are both prescribed spatially on the same 0.25 degree grid as the land use class transitions. +The new land unit format is an improvement on the CMIP5 LULCC datasets as they: provide Forest and Non Forest information in combination with Primary and Secondary land; differentiate between Pasture and Rangelands for grazing livestock; and specify annual details on the types of Crops grown and management practices applied in each grid cell. Like the CMIP5 LULCC datasets Primary vegetation represents the fractional area of a grid cell with vegetation undisturbed by human activities. Secondary vegetation represents vegetated areas that have recovered from some human disturbance; this could include re-vegetation of pasture and crop areas as well as primary vegetation areas that have been logged. In this manner the land units can change through deforestation from Forested to Non Forested land and in the opposite direction from Non Forested to Forested land through reforestation or afforestation without going through the Crop, Pasture or Rangeland states. + +The LUH2 dataset provides a time series of land cover states as well as a transition matrices that describes the annual fraction of land that is transformed from one land unit category to another (e.g. Primary Forest to C3 Annual Crop, Pasture to C3 Perrenial Crop, etc.; Lawrence et al. 2016). Included in these transition matrices is the total conversion of one land cover type to another referred to as Gross LULCC. This value can be larger than the sum of the changes in the state of a land unit from one time period to the next known as the Net LULCC. This difference is possible as land unit changes can occur both from the land unit and to the land unit at the same time. An example of this difference occurs with shifting cultivation where Secondary Forest can be converted to C3 Annual Crop at the same time as C3 Annual Crop is abandoned to Secondary Forest. + +The transition matrices also provide harmonized prescriptions of wood harvest both in area of the grid cell harvested and in the amount of biomass carbon harvested. The wood harvest biomass amount includes a 30% slash component inline with the CMIP5 LULCC data described in (Hurtt et al. 2011). The harvest area and carbon amounts are prescribed for the five classes of: Primary Forest, Primary Non-Forest, Secondary Mature Forest, Secondary Young Forest, and Secondary Non-Forest. + +Additional land use management is prescribed on the Crop land units for nitrogen fertilization and irrigation equipped land. The fertilizer application and the the irrigation fraction is prescribed for each Crop land unit in a grid cell individually for each year of the time series. The wood harvest and crop management are both prescribed spatially on the same 0.25 degree grid as the land use class transitions. Representing LUH2 Land Use and Land Cover Change in CLM5 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To represent the LUH2 transient LULCC dataset in CLM5, the annual fractional -composition of the twelve land units specified in the dataset needs to be -faithfully represented with a corresponding PFT and CFT mosaics of CLM. -CLM5 represents the land surface as a hierarchy of sub-grid types: -glacier; lake; urban; vegetated land; and crop land. The vegetated land is -further divided into a mosaic of Plant Functional Types (PFTs), while the crop land -is divided into a mosaic of Crop Functional Types (CFTs). - -To support this translation task the CLM5 Land Use Data tool has been built that extends the -methods described in Lawrence et al (2012) to include all the new functionality of CMIP6 and CLM5 LULCC. -The tool translates each of the LUH2 land units for a given year into fractional PFT and CFT values based on -the current day CLM5 data for the land unit in that grid cell. The current day land unit descriptions are generated from -from 1km resolution MODIS, MIRCA2000, ICESAT, AVHRR, SRTM, and CRU climate data products combined with reference year -LUH2 land unit data, usually set to 2005. Where the land unit does not exist in a grid cell for the current -day, the land unit description is generated from nearest neighbors with an inverse distance weighted search -algorithm. - -The Land Use Data tool produces raw vegetation, crop, and management data files which are combined with -other raw land surface data to produce the CLM5 initial surface dataset and the dynamic -*landuse.timeseries* dataset with the CLM5 mksurfdata_map tool. The schematic of this entire process from -LUH2 time series and high resolution current day data to the output of CLM5 surface datasets from the -mksurfdata_map tool is shown in Figure 21.2. - -The methodology for creating the CLM5 transient PFT and CFT dataset is based on four -steps which are applied across all of the historical and future time series. -The first step involves generating the current day descriptions of natural and managed vegetation PFTs at -1km resolution from the global source datasets, and the current day description of crop CFTs at the 10km resolution -from the MIRCA 2000 datasets. The second step combines the current day (2005) LUH2 land units with the current -day CLM5 PFT and CFT distributions to get CLM5 land unit descriptions in either PFTs or CFTs at the LUH2 resolution of -0.25 degrees. The third step involves combining the LUH2 land unit time series with the CLM5 PFT and CFT descriptions -for that land unit to generate the CLM5 raw PFT and CFT time series in the *landuse.timeseries* file. At this point in the process -management information in terms of fertilizer, irrigation and wood harvest are added to the CLM5 PFT and CFT data -to complete the CLM5 raw PFT and CFT files. The final step is to combine these files with the other raw CLM5 surface -data files in the mksurfdata_map tool. +To represent the LUH2 transient LULCC dataset in CLM5, the annual fractional composition of the twelve land units specified in the dataset needs to be faithfully represented with a corresponding PFT and CFT mosaics of CLM. CLM5 represents the land surface as a hierarchy of sub-grid types: glacier; lake; urban; vegetated land; and crop land. The vegetated land is further divided into a mosaic of Plant Functional Types (PFTs), while the crop land is divided into a mosaic of Crop Functional Types (CFTs). + +To support this translation task the CLM5 Land Use Data tool has been built that extends the methods described in Lawrence et al (2012) to include all the new functionality of CMIP6 and CLM5 LULCC. The tool translates each of the LUH2 land units for a given year into fractional PFT and CFT values based on the current day CLM5 data for the land unit in that grid cell. The current day land unit descriptions are generated from from 1km resolution MODIS, MIRCA2000, ICESAT, AVHRR, SRTM, and CRU climate data products combined with reference year LUH2 land unit data, usually set to 2005. Where the land unit does not exist in a grid cell for the current day, the land unit description is generated from nearest neighbors with an inverse distance weighted search algorithm. + +The Land Use Data tool produces raw vegetation, crop, and management data files which are combined with other raw land surface data to produce the CLM5 initial surface dataset and the dynamic *landuse.timeseries* dataset with the CLM5 mksurfdata_map tool. The schematic of this entire process from LUH2 time series and high resolution current day data to the output of CLM5 surface datasets from the mksurfdata_map tool is shown in Figure 21.2. + +The methodology for creating the CLM5 transient PFT and CFT dataset is based on four steps which are applied across all of the historical and future time series. The first step involves generating the current day descriptions of natural and managed vegetation PFTs at 1km resolution from the global source datasets, and the current day description of crop CFTs at the 10km resolution from the MIRCA 2000 datasets. The second step combines the current day (2005) LUH2 land units with the current day CLM5 PFT and CFT distributions to get CLM5 land unit descriptions in either PFTs or CFTs at the LUH2 resolution of 0.25 degrees. The third step involves combining the LUH2 land unit time series with the CLM5 PFT and CFT descriptions for that land unit to generate the CLM5 raw PFT and CFT time series in the *landuse.timeseries* file. At this point in the process management information in terms of fertilizer, irrigation and wood harvest are added to the CLM5 PFT and CFT data to complete the CLM5 raw PFT and CFT files. The final step is to combine these files with the other raw CLM5 surface data files in the mksurfdata_map tool. .. _Figure Schematic of land cover change: diff --git a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst index 0cd64eaba7..7336bc7266 100644 --- a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst +++ b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst @@ -3,126 +3,23 @@ Urban Model (CLMU) ====================== -At the global scale, and at the coarse spatial resolution of current -climate models, urbanization has negligible impact on climate. However, -the urban parameterization (CLMU; :ref:`Oleson et al. (2008b) `; -:ref:`Oleson et al. (2008c) `) allows -simulation of the urban environment within a climate model, and -particularly the temperature where people live. As such, the urban model -allows scientific study of how climate change affects the urban heat -island and possible urban planning and design strategies to mitigate -warming (e.g., white roofs). - -Urban areas in CLM are represented by up to three urban landunits per -gridcell according to density class. The urban landunit is based on the -"urban canyon" concept of :ref:`Oke (1987) ` in which -the canyon geometry is -described by building height (:math:`H`) and street width (:math:`W`) -(:numref:`Figure schematic representation of the urban landunit`). The canyon system -consists of roofs, walls, and canyon -floor. Walls are further divided into shaded and sunlit components. The -canyon floor is divided into pervious (e.g., to represent residential -lawns, parks) and impervious (e.g., to represent roads, parking lots, -sidewalks) fractions. Vegetation is not explicitly modeled for the -pervious fraction; instead evaporation is parameterized by a simplified -bulk scheme. - -Each of the five urban surfaces is treated as a column within the -landunit (:numref:`Figure schematic representation of the urban landunit`). -Radiation parameterizations account for trapping -of solar and longwave radiation inside the canyon. Momentum fluxes are -determined for the urban landunit using a roughness length and -displacement height appropriate for the urban canyon and stability -formulations from CLM. A one-dimensional heat conduction equation is -solved numerically for a multiple-layer (:math:`N_{levurb} =10`) column -to determine conduction fluxes into and out of canyon surfaces. - -A new building energy model has been developed for CLM5.0. It accounts -for the conduction of heat through interior surfaces (roof, sunlit and -shaded walls, and floors), convection (sensible heat exchange) between -interior surfaces and building air, longwave radiation exchange between -interior surfaces, and ventilation (natural infiltration and exfiltration). -Idealized HAC systems are assumed where the system capacity is infinite and -the system supplies the amount of energy needed to keep the indoor air -temperature (:math:`T_{iB}`) within maximum and minimum emperatures -(:math:`T_{iB,\, \max } ,\, T_{iB,\, \min }` ), thus explicitly -resolving space heating and air conditioning fluxes. Anthropogenic sources -of waste heat (:math:`Q_{H,\, waste}` ) from HAC that account for inefficiencies -in the heating and air conditioning equipment and from energy lost in the -conversion of primary energy sources to end use energy are derived from -:ref:`Sivak (2013) `. These sources of waste heat are incorporated -as modifications to the canyon energy budget. - -Turbulent [sensible heat (:math:`Q_{H,\, u}` ) and -latent heat (:math:`Q_{E,\, u}` )] and storage (:math:`Q_{S,\, u}` ) -heat fluxes and surface (:math:`T_{u,\, s}` ) and internal -(:math:`T_{u,\, i=1,\, N_{levgrnd} }` ) temperatures are determined for -each urban surface :math:`u`. Hydrology on the roof and canyon floor is -simulated and walls are hydrologically inactive. A snowpack can form on -the active surfaces. A certain amount of liquid water is allowed to pond -on these surfaces which supports evaporation. Water in excess of the -maximum ponding depth runs off -(:math:`R_{roof} ,\, R_{imprvrd} ,\, R_{prvrd}` ). - -The heat and moisture fluxes from each surface interact with each other -through a bulk air mass that represents air in the urban canopy layer -for which specific humidity (:math:`q_{ac}` ) and temperature -(:math:`T_{ac}` ) are prognosed (:numref:`Figure schematic of urban and atmospheric model coupling`). -The air temperature can -be compared with that from surrounding vegetated/soil (rural) surfaces -in the model to ascertain heat island characteristics. As with other -landunits, the CLMU is forced either with output from a host atmospheric -model (e.g., the Community Atmosphere Model (CAM)) or -observed forcing (e.g., reanalysis or field observations). The urban -model produces sensible, latent heat, and momentum fluxes, emitted -longwave, and reflected solar radiation, which are area-averaged with -fluxes from non-urban "landunits" (e.g., vegetation, lakes) to supply -grid cell averaged fluxes to the atmospheric model. - -Present day global urban extent and urban properties were developed by -:ref:`Jackson et al. (2010) `. Urban extent, defined for four classes [tall -building district (TBD), and high, medium, and low density (HD, MD, -LD)], was derived from LandScan 2004, a population density dataset -derived from census data, nighttime lights satellite observations, road -proximity, and slope (:ref:`Dobson et al. 2000 `). The urban extent data for -TBD, HD, and MD classes are aggregated from the original 1 km resolution -to both a 0.05\ :sup:`o` by 0.05\ :sup:`o` global grid -for high-resolution studies or a 0.5\ :sup:`o` by -0.5\ :sup:`o` grid. For the current implementation, the LD class -is not used because it is highly rural and better modeled as a -vegetated/soil surface. Although the TBD, HD, and MD classes are -represented as individual urban landunits, urban model history output is -currently a weighted average of the output for individual classes. - -For each of 33 distinct regions across the globe, thermal (e.g., heat -capacity and thermal conductivity), radiative (e.g., albedo and -emissivity) and morphological (e.g., height to width ratio, roof -fraction, average building height, and pervious fraction of the canyon -floor) properties are provided for each of the density classes. Building -interior minimum and maximum temperatures are prescribed based on -climate and socioeconomic considerations. The surface dataset creation -routines (see CLM5.0 User's Guide) aggregate the data to the desired -resolution. - -An optional urban properties dataset, including a tool that allows for generating future -urban development scenarios is also available (:ref:`Oleson and Feddema (2018) `). -This will become the default dataset in future model versions. -As described in :ref:`Oleson and Feddema (2018) ` the urban properties dataset -in :ref:`Jackson et al. (2010) ` was modified with respect to wall and roof thermal -properties to correct for biases in heat transfer due to layer and building type averaging. -Further changes to the dataset reflect the need for scenario development, thus allowing for -the creation of hypothetical wall types, and the easier interchange of wall facets. -The new urban properties tool is available as part of the Toolbox for Human-Earth System -Integration & Scaling (THESIS) tool set -(http://www.cgd.ucar.edu/iam/projects/thesis/thesis-urbanproperties-tool.html; -:ref:`Feddema and Kauffman (2016) `). The driver script (urban_prop.csh) -specifies three input csv files (by default, mat_prop.csv, -lam_spec.csv, and city_spec.csv; (:numref:`Figure schematic of THESIS urban properties tool`)) -that describe the morphological, radiative, and thermal properties of urban areas, and -generates a global dataset at 0.05° latitude by longitude in NetCDF format (urban_properties_data.05deg.nc). -A standalone NCL routine (gen_data_clm.ncl) can be run separately after the mksurfdata_map tool creates -the CLM surface dataset. This creates a supplementary streams file of setpoints for the maximum -interior building temperature at yearly time resolution. +At the global scale, and at the coarse spatial resolution of current climate models, urbanization has negligible impact on climate. However, the urban parameterization (CLMU; :ref:`Oleson et al. (2008b) `; :ref:`Oleson et al. (2008c) `) allows simulation of the urban environment within a climate model, and particularly the temperature where people live. As such, the urban model allows scientific study of how climate change affects the urban heat island and possible urban planning and design strategies to mitigate warming (e.g., white roofs). + +Urban areas in CLM are represented by up to three urban landunits per gridcell according to density class. The urban landunit is based on the "urban canyon" concept of :ref:`Oke (1987) ` in which the canyon geometry is described by building height (:math:`H`) and street width (:math:`W`) (:numref:`Figure schematic representation of the urban landunit`). The canyon system consists of roofs, walls, and canyon floor. Walls are further divided into shaded and sunlit components. The canyon floor is divided into pervious (e.g., to represent residential lawns, parks) and impervious (e.g., to represent roads, parking lots, sidewalks) fractions. Vegetation is not explicitly modeled for the pervious fraction; instead evaporation is parameterized by a simplified bulk scheme. + +Each of the five urban surfaces is treated as a column within the landunit (:numref:`Figure schematic representation of the urban landunit`). Radiation parameterizations account for trapping of solar and longwave radiation inside the canyon. Momentum fluxes are determined for the urban landunit using a roughness length and displacement height appropriate for the urban canyon and stability formulations from CLM. A one-dimensional heat conduction equation is solved numerically for a multiple-layer (:math:`N_{levurb} =10`) column to determine conduction fluxes into and out of canyon surfaces. + +A new building energy model has been developed for CLM5.0. It accounts for the conduction of heat through interior surfaces (roof, sunlit and shaded walls, and floors), convection (sensible heat exchange) between interior surfaces and building air, longwave radiation exchange between interior surfaces, and ventilation (natural infiltration and exfiltration). Idealized HAC systems are assumed where the system capacity is infinite and the system supplies the amount of energy needed to keep the indoor air temperature (:math:`T_{iB}`) within maximum and minimum emperatures (:math:`T_{iB,\, \max },\, T_{iB,\, \min }` ), thus explicitly resolving space heating and air conditioning fluxes. Anthropogenic sources of waste heat (:math:`Q_{H,\, waste}` ) from HAC that account for inefficiencies in the heating and air conditioning equipment and from energy lost in the conversion of primary energy sources to end use energy are derived from :ref:`Sivak (2013) `. These sources of waste heat are incorporated as modifications to the canyon energy budget. + +Turbulent [sensible heat (:math:`Q_{H,\, u}` ) and latent heat (:math:`Q_{E,\, u}` )] and storage (:math:`Q_{S,\, u}` ) heat fluxes and surface (:math:`T_{u,\, s}` ) and internal (:math:`T_{u,\, i=1,\, N_{levgrnd} }` ) temperatures are determined for each urban surface :math:`u`. Hydrology on the roof and canyon floor is simulated and walls are hydrologically inactive. A snowpack can form on the active surfaces. A certain amount of liquid water is allowed to pond on these surfaces which supports evaporation. Water in excess of the maximum ponding depth runs off (:math:`R_{roof},\, R_{imprvrd},\, R_{prvrd}` ). + +The heat and moisture fluxes from each surface interact with each other through a bulk air mass that represents air in the urban canopy layer for which specific humidity (:math:`q_{ac}` ) and temperature (:math:`T_{ac}` ) are prognosed (:numref:`Figure schematic of urban and atmospheric model coupling`). The air temperature can be compared with that from surrounding vegetated/soil (rural) surfaces in the model to ascertain heat island characteristics. As with other landunits, the CLMU is forced either with output from a host atmospheric model (e.g., the Community Atmosphere Model (CAM)) or observed forcing (e.g., reanalysis or field observations). The urban model produces sensible, latent heat, and momentum fluxes, emitted longwave, and reflected solar radiation, which are area-averaged with fluxes from non-urban "landunits" (e.g., vegetation, lakes) to supply grid cell averaged fluxes to the atmospheric model. + +Present day global urban extent and urban properties were developed by :ref:`Jackson et al. (2010) `. Urban extent, defined for four classes [tall building district (TBD), and high, medium, and low density (HD, MD, LD)], was derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity, and slope (:ref:`Dobson et al. 2000 `). The urban extent data for TBD, HD, and MD classes are aggregated from the original 1 km resolution to both a 0.05\ :sup:`o` by 0.05\ :sup:`o` global grid for high-resolution studies or a 0.5\ :sup:`o` by 0.5\ :sup:`o` grid. For the current implementation, the LD class is not used because it is highly rural and better modeled as a vegetated/soil surface. Although the TBD, HD, and MD classes are represented as individual urban landunits, urban model history output is currently a weighted average of the output for individual classes. + +For each of 33 distinct regions across the globe, thermal (e.g., heat capacity and thermal conductivity), radiative (e.g., albedo and emissivity) and morphological (e.g., height to width ratio, roof fraction, average building height, and pervious fraction of the canyon floor) properties are provided for each of the density classes. Building interior minimum and maximum temperatures are prescribed based on climate and socioeconomic considerations. The surface dataset creation routines (see CLM5.0 User's Guide) aggregate the data to the desired resolution. + +An optional urban properties dataset, including a tool that allows for generating future urban development scenarios is also available (:ref:`Oleson and Feddema (2018) `). This will become the default dataset in future model versions. As described in :ref:`Oleson and Feddema (2018) ` the urban properties dataset in :ref:`Jackson et al. (2010) ` was modified with respect to wall and roof thermal properties to correct for biases in heat transfer due to layer and building type averaging. Further changes to the dataset reflect the need for scenario development, thus allowing for the creation of hypothetical wall types, and the easier interchange of wall facets. The new urban properties tool is available as part of the Toolbox for Human-Earth System Integration & Scaling (THESIS) tool set (http://www.cgd.ucar.edu/iam/projects/thesis/thesis-urbanproperties-tool.html; :ref:`Feddema and Kauffman (2016) `). The driver script (urban_prop.csh) specifies three input csv files (by default, mat_prop.csv, lam_spec.csv, and city_spec.csv; (:numref:`Figure schematic of THESIS urban properties tool`)) that describe the morphological, radiative, and thermal properties of urban areas, and generates a global dataset at 0.05° latitude by longitude in NetCDF format (urban_properties_data.05deg.nc). A standalone NCL routine (gen_data_clm.ncl) can be run separately after the mksurfdata_map tool creates the CLM surface dataset. This creates a supplementary streams file of setpoints for the maximum interior building temperature at yearly time resolution. .. Figure 12.1. Schematic representation of the urban land unit @@ -148,32 +45,6 @@ interior building temperature at yearly time resolution. Schematic of THESIS urban properties tool. Executable scripts are in orange, input files are blue, and output files are green. Items within the black box outline are either read in as input, executed, or output by the driver script (urban_prop.csh). -The urban model that was first released as a component of CLM4.0 is separately -described in the urban technical note (:ref:`Oleson et al. (2010b) `). -The main changes in the urban model from CLM4.0 to CLM4.5 were 1) -an expansion of the single urban landunit to up to three landunits per -grid cell stratified by urban density types, 2) the number of urban -layers for roofs and walls was no longer constrained to be equal to the -number of ground layers, 3) space heating and air conditioning wasteheat -factors were set to zero by default so that the user could customize -these factors for their own application, 4) the elevation threshold used -to eliminate urban areas in the surface dataset creation routines was -increased from 2200 meters to 2600 meters, 5) hydrologic and thermal -calculations for the pervious road followed CLM4.5 parameterizations. - -The main changes in the urban model from CLM4.5 to CLM5.0 are 1) a more -sophisticated and realistic building space heating and air conditioning -submodel that prognoses interior building air temperature and includes more -realistic space heating and air conditioning wasteheat factors (see above), 2) the maximum -building temperature (which determines air conditioning demand) is now read in -from a namelist-defined file which allows for dynamic control of this input -variable. The maximum building temperatures that are defined in -:ref:`Jackson et al. (2010) ` are implemented in year 1950 (thus -air conditioning is off in prior years) and air conditioning is turned off in year -2100 (because the buildings are not suitable for air conditioning in some extreme -global warming scenarios), 3) an optional updated urban properties dataset and new -scenario tool. These features are described in more detail in :ref:`Oleson and Feddema (2018) `. -In addition, a module of heat stress indices calculated online -in the model that can be used to assess human thermal comfort for rural and urban -areas has been added. This last development is described and evaluated by -:ref:`Buzan et al. (2015) `. +The urban model that was first released as a component of CLM4.0 is separately described in the urban technical note (:ref:`Oleson et al. (2010b) `). The main changes in the urban model from CLM4.0 to CLM4.5 were 1) an expansion of the single urban landunit to up to three landunits per grid cell stratified by urban density types, 2) the number of urban layers for roofs and walls was no longer constrained to be equal to the number of ground layers, 3) space heating and air conditioning wasteheat factors were set to zero by default so that the user could customize these factors for their own application, 4) the elevation threshold used to eliminate urban areas in the surface dataset creation routines was increased from 2200 meters to 2600 meters, 5) hydrologic and thermal calculations for the pervious road followed CLM4.5 parameterizations. + +The main changes in the urban model from CLM4.5 to CLM5.0 are 1) a more sophisticated and realistic building space heating and air conditioning submodel that prognoses interior building air temperature and includes more realistic space heating and air conditioning wasteheat factors (see above), 2) the maximum building temperature (which determines air conditioning demand) is now read in from a namelist-defined file which allows for dynamic control of this input variable. The maximum building temperatures that are defined in :ref:`Jackson et al. (2010) ` are implemented in year 1950 (thus air conditioning is off in prior years) and air conditioning is turned off in year 2100 (because the buildings are not suitable for air conditioning in some extreme global warming scenarios), 3) an optional updated urban properties dataset and new scenario tool. These features are described in more detail in :ref:`Oleson and Feddema (2018) `. In addition, a module of heat stress indices calculated online in the model that can be used to assess human thermal comfort for rural and urban areas has been added. This last development is described and evaluated by :ref:`Buzan et al. (2015) `. diff --git a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst index 453152ca50..1665b9a00f 100644 --- a/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst +++ b/doc/source/tech_note/Vegetation_Phenology_Turnover/CLM50_Tech_Note_Vegetation_Phenology_Turnover.rst @@ -3,33 +3,14 @@ Vegetation Phenology and Turnover ================================= -The CLM phenology model consists of several algorithms controlling the -transfer of stored carbon and nitrogen out of storage pools for the -display of new growth and into litter pools for losses of displayed -growth. PFTs are classified into three distinct phenological types that -are represented by separate algorithms: an evergreen type, for which -some fraction of annual leaf growth persists in the displayed pool for -longer than one year; a seasonal-deciduous type with a single growing -season per year, controlled mainly by temperature and daylength; and a -stress-deciduous type with the potential for multiple growing seasons -per year, controlled by temperature and soil moisture conditions. - -The three phenology types share a common set of control variables. The -calculation of the phenology fluxes is generalized, operating -identically for all three phenology types, given a specification of the -common control variables. The following sections describe first the -general flux parameterization, followed by the algorithms for setting -the control parameters for the three phenology types. +The CLM phenology model consists of several algorithms controlling the transfer of stored carbon and nitrogen out of storage pools for the display of new growth and into litter pools for losses of displayed growth. PFTs are classified into three distinct phenological types that are represented by separate algorithms: an evergreen type, for which some fraction of annual leaf growth persists in the displayed pool for longer than one year; a seasonal-deciduous type with a single growing season per year, controlled mainly by temperature and daylength; and a stress-deciduous type with the potential for multiple growing seasons per year, controlled by temperature and soil moisture conditions. + +The three phenology types share a common set of control variables. The calculation of the phenology fluxes is generalized, operating identically for all three phenology types, given a specification of the common control variables. The following sections describe first the general flux parameterization, followed by the algorithms for setting the control parameters for the three phenology types. General Phenology Flux Parameterization -------------------------------------------- -Fluxes of carbon and nitrogen from storage pools and into displayed -tissue pools pass through a special transfer pool (denoted *\_xfer*), -maintained as a separate state variable for each tissue type. Storage -(*\_stor*) and transfer (*\_xfer*) pools are maintained separately to -reduce the complexity of accounting for transfers into and out of -storage over the course of a single growing season. +Fluxes of carbon and nitrogen from storage pools and into displayed tissue pools pass through a special transfer pool (denoted *\_xfer*), maintained as a separate state variable for each tissue type. Storage (*\_stor*) and transfer (*\_xfer*) pools are maintained separately to reduce the complexity of accounting for transfers into and out of storage over the course of a single growing season. .. _Figure annual phenology cycle: @@ -40,9 +21,7 @@ storage over the course of a single growing season. 14.1.1 Onset Periods ^^^^^^^^^^^^^^^^^^^^ -The deciduous phenology algorithms specify the occurrence of onset -growth periods (Figure 14.1). Carbon fluxes from the transfer pools into -displayed growth are calculated during these periods as: +The deciduous phenology algorithms specify the occurrence of onset growth periods (Figure 14.1). Carbon fluxes from the transfer pools into displayed growth are calculated during these periods as: .. math:: :label: 20.1) @@ -106,28 +85,19 @@ with corresponding nitrogen fluxes: NF_{deadcroot\_ xfer,deadcroot} =r_{xfer\_ on} NS_{deadcroot\_ xfer} , -where CF is the carbon flux, CS is stored carbon, NF is the nitrogen -flux, NS is stored nitrogen, :math:`{r}_{xfer\_on}` (s\ :sup:`-1`) is a time-varying rate coefficient controlling flux -out of the transfer pool: +where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is stored nitrogen, :math:`{r}_{xfer\_on}` (s\ :sup:`-1`) is a time-varying rate coefficient controlling flux out of the transfer pool: .. math:: :label: ZEqnNum852972 r_{xfer\_ on} =\left\{\begin{array}{l} {{2\mathord{\left/ {\vphantom {2 t_{onset} }} \right.} t_{onset} } \qquad {\rm for\; }t_{onset} \ne \Delta t} \\ {{1\mathord{\left/ {\vphantom {1 \Delta t}} \right.} \Delta t} \qquad {\rm for\; }t_{onset} =\Delta t} \end{array}\right. -and *t*\ :sub:`onset` (s) is the number of seconds remaining in -the current phenology onset growth period (Figure 14.1). The form of Eq. :eq:`ZEqnNum852972` -produces a flux from the transfer pool which declines linearly over the -onset growth period, approaching zero flux in the final timestep. +and *t*\ :sub:`onset` (s) is the number of seconds remaining in the current phenology onset growth period (Figure 14.1). The form of Eq. :eq:`ZEqnNum852972` produces a flux from the transfer pool which declines linearly over the onset growth period, approaching zero flux in the final timestep. 14.1.2 Offset Periods ^^^^^^^^^^^^^^^^^^^^^ -The deciduous phenology algorithms also specify the occurrence of -litterfall during offset periods. In contrast to the onset periods, only -leaf and fine root state variables are subject to litterfall fluxes. -Carbon fluxes from display pools into litter are calculated during these -periods as: +The deciduous phenology algorithms also specify the occurrence of litterfall during offset periods. In contrast to the onset periods, only leaf and fine root state variables are subject to litterfall fluxes. Carbon fluxes from display pools into litter are calculated during these periods as: .. math:: :label: 20.14) @@ -148,19 +118,9 @@ periods as: r_{xfer\_ off} =\frac{2\Delta t}{t_{offset} ^{2} } -where superscripts *n* and *n-1* refer to fluxes on the current and -previous timesteps, respectively. The rate coefficient :math:`{r}_{xfer\_off}` varies with time to produce a linearly -increasing litterfall rate throughout the offset period. -The :math:`biofuel\_harvfrac` (:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) -is the harvested fraction of aboveground biomass (leaf & livestem) for bioenergy crops. -The special case for fluxes in the final litterfall timestep -(:math:`{t}_{offset}` = :math:`\Delta t`\ ) ensures that all of the displayed growth is sent to the litter pools or biofuel feedstock pools. The fraction (:math:`biofuel\_harvfrac`) of leaf biomass going to the biofuel feedstock pools (Equation :eq:`25.9`) is defined in Table 26.3 and is only non-zero for prognostic crops. The remaining fraction of leaf biomass (:math:`1-biofuel\_harvfrac`) for deciduous plant types is sent to the litter pools. -Similar modifications made for livestem carbon pools for prognostic crops -can be found in section :numref:`Harvest to food and seed` in Equations :eq:`25.9`-:eq:`25.14`. +where superscripts *n* and *n-1* refer to fluxes on the current and previous timesteps, respectively. The rate coefficient :math:`{r}_{xfer\_off}` varies with time to produce a linearly increasing litterfall rate throughout the offset period. The :math:`biofuel\_harvfrac` (:numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) is the harvested fraction of aboveground biomass (leaf & livestem) for bioenergy crops. The special case for fluxes in the final litterfall timestep (:math:`{t}_{offset}` = :math:`\Delta t`\ ) ensures that all of the displayed growth is sent to the litter pools or biofuel feedstock pools. The fraction (:math:`biofuel\_harvfrac`) of leaf biomass going to the biofuel feedstock pools (Equation :eq:`25.9`) is defined in Table 26.3 and is only non-zero for prognostic crops. The remaining fraction of leaf biomass (:math:`1-biofuel\_harvfrac`) for deciduous plant types is sent to the litter pools. Similar modifications made for livestem carbon pools for prognostic crops can be found in section :numref:`Harvest to food and seed` in Equations :eq:`25.9`-:eq:`25.14`. -Corresponding nitrogen fluxes during litterfall take into account retranslocation of nitrogen out of the displayed leaf pool prior to -litterfall (:math:`{NF}_{leaf,retrans}`, gN m\ :sup:`-2` s\ :sup:`-1`). Retranslocation of nitrogen out of fine roots is -assumed to be negligible. The fluxes are: +Corresponding nitrogen fluxes during litterfall take into account retranslocation of nitrogen out of the displayed leaf pool prior to litterfall (:math:`{NF}_{leaf,retrans}`, gN m\ :sup:`-2` s\ :sup:`-1`). Retranslocation of nitrogen out of fine roots is assumed to be negligible. The fluxes are: .. math:: :label: 20.17) @@ -182,17 +142,7 @@ where CN is C:N. 14.1.3 Background Onset Growth ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The stress-deciduous phenology algorithm includes a provision for the -case when stress signals are absent, and the vegetation shifts from a -deciduous habit to an evergreen habit, until the next occurrence of an -offset stress trigger . In that case, the regular onset flux mechanism -is switched off and a background onset growth algorithm is invoked -(:math:`{r}_{bgtr} > 0`). During this period, small fluxes -of carbon and nitrogen from the storage pools into the associated -transfer pools are calculated on each time step, and the entire contents -of the transfer pool are added to the associated displayed growth pool -on each time step. The carbon fluxes from transfer to display pools -under these conditions are: +The stress-deciduous phenology algorithm includes a provision for the case when stress signals are absent, and the vegetation shifts from a deciduous habit to an evergreen habit, until the next occurrence of an offset stress trigger. In that case, the regular onset flux mechanism is switched off and a background onset growth algorithm is invoked (:math:`{r}_{bgtr} > 0`). During this period, small fluxes of carbon and nitrogen from the storage pools into the associated transfer pools are calculated on each time step, and the entire contents of the transfer pool are added to the associated displayed growth pool on each time step. The carbon fluxes from transfer to display pools under these conditions are: .. math:: :label: 20.20) @@ -259,14 +209,7 @@ and the corresponding nitrogen fluxes are: 14.1.4 Background Litterfall ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Both evergreen and stress-deciduous phenology algorithms can specify a -litterfall flux that is not associated with a specific offset period, -but which occurs instead at a slow rate over an extended period of time, -referred to as background litterfall. For evergreen types the background -litterfall is the only litterfall flux. For stress-deciduous types -either the offset period litterfall or the background litterfall -mechanism may be active, but not both at once. Given a specification of -the background litterfall rate (:math:`{r}_{bglf}`, s\ :sup:`-1`), litterfall carbon fluxes are calculated as +Both evergreen and stress-deciduous phenology algorithms can specify a litterfall flux that is not associated with a specific offset period, but which occurs instead at a slow rate over an extended period of time, referred to as background litterfall. For evergreen types the background litterfall is the only litterfall flux. For stress-deciduous types either the offset period litterfall or the background litterfall mechanism may be active, but not both at once. Given a specification of the background litterfall rate (:math:`{r}_{bglf}`, s\ :sup:`-1`), litterfall carbon fluxes are calculated as .. math:: :label: 20.32) @@ -298,27 +241,16 @@ with corresponding nitrogen litterfall and retranslocation fluxes: 14.1.5 Livewood Turnover ^^^^^^^^^^^^^^^^^^^^^^^^ -The conceptualization of live wood vs. dead wood fractions for stem and -coarse root pools is intended to capture the difference in maintenance -respiration rates between these two physiologically distinct tissue -types. Unlike displayed pools for leaf and fine root, which are lost to -litterfall, live wood cells reaching the end of their lifespan are -retained as a part of the dead woody structure of stems and coarse -roots. A mechanism is therefore included in the phenology routine to -effect the transfer of live wood to dead wood pools, which also takes -into account the different nitrogen concentrations typical of these -tissue types. +The conceptualization of live wood vs. dead wood fractions for stem and coarse root pools is intended to capture the difference in maintenance respiration rates between these two physiologically distinct tissue types. Unlike displayed pools for leaf and fine root, which are lost to litterfall, live wood cells reaching the end of their lifespan are retained as a part of the dead woody structure of stems and coarse roots. A mechanism is therefore included in the phenology routine to effect the transfer of live wood to dead wood pools, which also takes into account the different nitrogen concentrations typical of these tissue types. -A live wood turnover rate (:math:`{r}_{lwt}`, s\ :sup:`-1`) is -defined as +A live wood turnover rate (:math:`{r}_{lwt}`, s\ :sup:`-1`) is defined as .. math:: :label: 20.37) r_{lwt} ={p_{lwt} \mathord{\left/ {\vphantom {p_{lwt} \left(365\cdot 86400\right)}} \right.} \left(365\cdot 86400\right)} -where :math:`{p}_{lwt} = 0.7` is the assumed annual live wood -turnover fraction. Carbon fluxes from live to dead wood pools are: +where :math:`{p}_{lwt} = 0.7` is the assumed annual live wood turnover fraction. Carbon fluxes from live to dead wood pools are: .. math:: :label: 20.38) @@ -330,8 +262,7 @@ turnover fraction. Carbon fluxes from live to dead wood pools are: CF_{livecroot,deadcroot} =CS_{livecroot} r_{lwt} , -and the associated nitrogen fluxes, including retranslocation of -nitrogen out of live wood during turnover, are: +and the associated nitrogen fluxes, including retranslocation of nitrogen out of live wood during turnover, are: .. math:: :label: 20.40) @@ -356,22 +287,7 @@ nitrogen out of live wood during turnover, are: Evergreen Phenology ------------------------ -The evergreen phenology algorithm is by far the simplest of the three -possible types. It is assumed for all evergreen types that all carbon -and nitrogen allocated for new growth in the current timestep goes -immediately to the displayed growth pools (i.e. f\ :math:`{f}_{cur} = 1.0` -(Chapter 13)). As such, there is never an accumulation of carbon or -nitrogen in the storage or transfer pools, and so the onset growth and -background onset growth mechanisms are never invoked for this type. -Litterfall is specified to occur only through the background litterfall -mechanism – there are no distinct periods of litterfall for evergreen -types, but rather a continuous (slow) shedding of foliage and fine -roots. This is an obvious area for potential improvements in the model, -since it is known, at least for evergreen needleleaf trees in the -temperate and boreal zones, that there are distinct periods of higher -and lower leaf litterfall (Ferrari, 1999; Gholz et al., 1985). The rate -of background litterfall (:math:`{r}_{bglf}`, section 14.1.4) -depends on the specified leaf longevity (:math:`\tau_{leaf}`\ , y), as +The evergreen phenology algorithm is by far the simplest of the three possible types. It is assumed for all evergreen types that all carbon and nitrogen allocated for new growth in the current timestep goes immediately to the displayed growth pools (i.e. f\ :math:`{f}_{cur} = 1.0` (Chapter 13)). As such, there is never an accumulation of carbon or nitrogen in the storage or transfer pools, and so the onset growth and background onset growth mechanisms are never invoked for this type. Litterfall is specified to occur only through the background litterfall mechanism – there are no distinct periods of litterfall for evergreen types, but rather a continuous (slow) shedding of foliage and fine roots. This is an obvious area for potential improvements in the model, since it is known, at least for evergreen needleleaf trees in the temperate and boreal zones, that there are distinct periods of higher and lower leaf litterfall (Ferrari, 1999; Gholz et al., 1985). The rate of background litterfall (:math:`{r}_{bglf}`, section 14.1.4) depends on the specified leaf longevity (:math:`\tau_{leaf}`\, y), as .. math:: :label: 20.44) @@ -381,65 +297,35 @@ depends on the specified leaf longevity (:math:`\tau_{leaf}`\ , y), as Seasonal-Deciduous Phenology --------------------------------- -The seasonal-deciduous phenology algorithm derives directly from the -treatment used in the offline model Biome-BGC v. 4.1.2, (Thornton et -al., 2002), which in turn is based on the parameterizations for leaf -onset and offset for temperate deciduous broadleaf forest from White et -al. (1997). Initiation of leaf onset is triggered when a common -degree-day summation exceeds a critical value, and leaf litterfall is -initiated when daylength is shorter than a critical value. Because of -the dependence on daylength, the seasonal deciduous phenology algorithm -is only valid for latitudes outside of the tropical zone, defined here -as :math:`\left|{\rm latitude}\right|>19.5{\rm {}^\circ }`. Neither the -background onset nor background litterfall mechanism is invoked for the -seasonal-deciduous phenology algorithm. The algorithm allows a maximum -of one onset period and one offset period each year. - -The algorithms for initiation of onset and offset periods use the winter -and summer solstices as coordination signals. The period between winter -and summer solstice is identified as :math:`{dayl}_{n} > {dayl}_{n-1}`, -and the period between summer and winter -solstice is identified as :math:`{dayl}_{n} < {dayl}_{n-1}`, -where :math:`{dayl}_{n}` and :math:`{dayl}_{n-1}` are the day length(s) calculated for the -current and previous timesteps, respectively, using +The seasonal-deciduous phenology algorithm derives directly from the treatment used in the offline model Biome-BGC v. 4.1.2, (Thornton et al., 2002), which in turn is based on the parameterizations for leaf onset and offset for temperate deciduous broadleaf forest from White et al. (1997). Initiation of leaf onset is triggered when a common degree-day summation exceeds a critical value, and leaf litterfall is initiated when daylength is shorter than a critical value. Because of the dependence on daylength, the seasonal deciduous phenology algorithm is only valid for latitudes outside of the tropical zone, defined here as :math:`\left|{\rm latitude}\right|>19.5{\rm {}^\circ }`. Neither the background onset nor background litterfall mechanism is invoked for the seasonal-deciduous phenology algorithm. The algorithm allows a maximum of one onset period and one offset period each year. + +The algorithms for initiation of onset and offset periods use the winter and summer solstices as coordination signals. The period between winter and summer solstice is identified as :math:`{dayl}_{n} > {dayl}_{n-1}`, and the period between summer and winter solstice is identified as :math:`{dayl}_{n} < {dayl}_{n-1}`, where :math:`{dayl}_{n}` and :math:`{dayl}_{n-1}` are the day length(s) calculated for the current and previous timesteps, respectively, using .. math:: :label: 20.45) dayl=2\cdot 13750.9871\cdot acos\left(\frac{-\sin (lat)\sin (decl)}{\cos (lat)\cos (decl)} \right), -where *lat* and *decl* are the latitude and solar declination (radians), -respectively, and the factor 13750.9871 is the number of seconds per -radian of hour-angle. +where *lat* and *decl* are the latitude and solar declination (radians), respectively, and the factor 13750.9871 is the number of seconds per radian of hour-angle. 14.3.1 Seasonal-Deciduous Onset Trigger ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -The onset trigger for the seasonal-deciduous phenology algorithm is -based on an accumulated growing-degree-day approach (White et al., -1997). The growing-degree-day summation (:math:`{GDD}_{sum}`) is -initiated ( :math:`{GDD}_{sum} = 0`) when the phenological state is -dormant and the model timestep crosses the winter solstice. Once these -conditions are met, :math:`{GDD}_{sum}` is updated on each timestep as +The onset trigger for the seasonal-deciduous phenology algorithm is based on an accumulated growing-degree-day approach (White et al., 1997). The growing-degree-day summation (:math:`{GDD}_{sum}`) is initiated ( :math:`{GDD}_{sum} = 0`) when the phenological state is dormant and the model timestep crosses the winter solstice. Once these conditions are met, :math:`{GDD}_{sum}` is updated on each timestep as .. math:: :label: ZEqnNum510730 GDD_{sum}^{n} =\left\{\begin{array}{l} {GDD_{sum}^{n-1} +\left(T_{s,3} -TKFRZ\right)f_{day} \qquad {\rm for\; }T_{s,3} >TKFRZ} \\ {GDD_{sum}^{n-1} \qquad \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \end{array}\right. -where :math:`{T}_{s,3}` (K) is the temperature of the third soil layer, and -:math:`f_{day} ={\Delta t\mathord{\left/ {\vphantom {\Delta t 86400}} \right.} 86400}` . -The onset period is initiated if :math:`GDD_{sum} >GDD_{sum\_ crit}` , -where +where :math:`{T}_{s,3}` (K) is the temperature of the third soil layer, and :math:`f_{day} ={\Delta t\mathord{\left/ {\vphantom {\Delta t 86400}} \right.} 86400}`. The onset period is initiated if :math:`GDD_{sum} >GDD_{sum\_ crit}`, where .. math:: :label: ZEqnNum598907 GDD_{sum\_ crit} =\exp \left(4.8+0.13{\kern 1pt} \left(T_{2m,ann\_ avg} -TKFRZ\right)\right) -and where :math:`{T}_{2m,ann\_avg}` (K) is the annual average of -the 2m air temperature, and TKFRZ is the freezing point of water (273.15 K). The following control variables are set when a new onset growth -period is initiated: +and where :math:`{T}_{2m,ann\_avg}` (K) is the annual average of the 2m air temperature, and TKFRZ is the freezing point of water (273.15 K). The following control variables are set when a new onset growth period is initiated: .. math:: :label: 20.48) @@ -451,9 +337,7 @@ period is initiated: t_{onset} =86400\cdot n_{days\_ on} , -where :math:`{n}_{days\_on}` is set to a constant value of 30 days. -Fluxes from storage into transfer pools occur in the timestep when a new -onset growth period is initiated. Carbon fluxes are: +where :math:`{n}_{days\_on}` is set to a constant value of 30 days. Fluxes from storage into transfer pools occur in the timestep when a new onset growth period is initiated. Carbon fluxes are: .. math:: :label: ZEqnNum904388 @@ -522,20 +406,9 @@ and the associated nitrogen fluxes are: NF_{deadcroot\_ stor,deadcroot\_ xfer} ={f_{stor,xfer} NS_{deadcroot\_ stor} \mathord{\left/ {\vphantom {f_{stor,xfer} NS_{deadcroot\_ stor} \Delta t}} \right.} \Delta t} -where :math:`{f}_{stor,xfer}` is the fraction of current storage -pool moved into the transfer pool for display over the incipient onset -period. This fraction is set to 0.5, based on the observation that -seasonal deciduous trees are capable of replacing their canopies from -storage reserves in the event of a severe early-season disturbance such -as frost damage or defoliation due to insect herbivory. +where :math:`{f}_{stor,xfer}` is the fraction of current storage pool moved into the transfer pool for display over the incipient onset period. This fraction is set to 0.5, based on the observation that seasonal deciduous trees are capable of replacing their canopies from storage reserves in the event of a severe early-season disturbance such as frost damage or defoliation due to insect herbivory. -If the onset criterion (:math:`{GDD}_{sum} > {GDD}_{sum\_crit}`) is not met before the summer solstice, -then :math:`{GDD}_{sum}` is set to 0.0 and the growing-degree-day -accumulation will not start again until the following winter solstice. -This mechanism prevents the initiation of very short growing seasons -late in the summer in cold climates. The onset counter is decremented on -each time step after initiation of the onset period, until it reaches -zero, signaling the end of the onset period: +If the onset criterion (:math:`{GDD}_{sum} > {GDD}_{sum\_crit}`) is not met before the summer solstice, then :math:`{GDD}_{sum}` is set to 0.0 and the growing-degree-day accumulation will not start again until the following winter solstice. This mechanism prevents the initiation of very short growing seasons late in the summer in cold climates. The onset counter is decremented on each time step after initiation of the onset period, until it reaches zero, signaling the end of the onset period: .. math:: :label: 20.63) @@ -545,14 +418,7 @@ zero, signaling the end of the onset period: 14.3.2 Seasonal-Deciduous Offset Trigger ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -After the completion of an onset period, and once past the summer -solstice, the offset (litterfall) period is triggered when daylength is -shorter than 39300 s. The offset counter is set at the initiation of the -offset period: :math:`t_{offset} =86400\cdot n_{days\_ off}` , where -:math:`{n}_{days\_off}` is set to a constant value of 15 days. The -offset counter is decremented on each time step after initiation of the -offset period, until it reaches zero, signaling the end of the offset -period: +After the completion of an onset period, and once past the summer solstice, the offset (litterfall) period is triggered when daylength is shorter than 39300 s. The offset counter is set at the initiation of the offset period: :math:`t_{offset} =86400\cdot n_{days\_ off}`, where :math:`{n}_{days\_off}` is set to a constant value of 15 days. The offset counter is decremented on each time step after initiation of the offset period, until it reaches zero, signaling the end of the offset period: .. math:: :label: 20.64) @@ -562,70 +428,30 @@ period: Stress-Deciduous Phenology ------------------------------- -The stress-deciduous phenology algorithm was developed specifically for -the CLM based in part on the grass phenology model proposed by White et -al. (1997). The algorithm handles phenology for vegetation types such as -grasses and tropical drought-deciduous trees that respond to both cold -and drought-stress signals, and that can have multiple growing seasons -per year. The algorithm also allows for the possibility that leaves -might persist year-round in the absence of a suitable stress trigger. In -that case the phenology switches to an evergreen habit, maintaining a -marginally-deciduous leaf longevity (one year) until the occurrence of -the next stress trigger. +The stress-deciduous phenology algorithm was developed specifically for the CLM based in part on the grass phenology model proposed by White et al. (1997). The algorithm handles phenology for vegetation types such as grasses and tropical drought-deciduous trees that respond to both cold and drought-stress signals, and that can have multiple growing seasons per year. The algorithm also allows for the possibility that leaves might persist year-round in the absence of a suitable stress trigger. In that case the phenology switches to an evergreen habit, maintaining a marginally-deciduous leaf longevity (one year) until the occurrence of the next stress trigger. 14.4.1 Stress-Deciduous Onset Triggers ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -In climates that are warm year-round, onset triggering depends on soil -water availability. At the beginning of a dormant period (end of -previous offset period), an accumulated soil water index -(:math:`{SWI}_{sum}`, d) is initialized (:math:`{SWI}_{sum} = 0`), with subsequent accumulation calculated as: +In climates that are warm year-round, onset triggering depends on soil water availability. At the beginning of a dormant period (end of previous offset period), an accumulated soil water index (:math:`{SWI}_{sum}`, d) is initialized (:math:`{SWI}_{sum} = 0`), with subsequent accumulation calculated as: .. math:: :label: ZEqnNum503826 SWI_{sum}^{n} =\left\{\begin{array}{l} {SWI_{sum}^{n-1} +f_{day} \qquad {\rm for\; }\Psi _{s,3} \ge \Psi _{onset} } \\ {SWI_{sum}^{n-1} \qquad \qquad {\rm for\; }\Psi _{s,3} <\Psi _{onset} } \end{array}\right. -where :math:`\Psi`\ :sub:`s,3` is the soil water potential (MPa) -in the third soil layer and :math:`{\Psi}_{onset} = -0.6 MPa` -is the onset soil water potential threshold. Onset triggering is -possible once :math:`{SWI}_{sum} > 15`. To avoid spurious onset triggering due to -soil moisture in the third soil layer exceeding the threshold due only to -soil water suction of water from deeper in the soil column, an additional precipitation trigger is included which requires -at least 20 mm of rain over the previous 10 days :ref:`(Dahlin et al., 2015) `. If the cold climate -growing degree-day accumulator is not active at the time when the soil moisture and precipitation -thresholds are reached (see below), and if the daylength is greater than 6 -hours, then onset is triggered. Except as noted below, -:math:`{SWI}_{sum}` continues to accumulate according to Eq. :eq:`ZEqnNum503826` during -the dormant period if the daylength criterion prevents onset triggering, -and onset is then triggered at the timestep when daylength exceeds 6 -hours. - -In climates with a cold season, onset triggering depends on both -accumulated soil temperature summation and adequate soil moisture. At -the beginning of a dormant period a freezing day accumulator -(:math:`{FD}_{sum}`, d) is initialized (:math:`{FD}_{sum} = 0`), -with subsequent accumulation calculated as: +where :math:`\Psi`\ :sub:`s,3` is the soil water potential (MPa) in the third soil layer and :math:`{\Psi}_{onset} = -0.6 MPa` is the onset soil water potential threshold. Onset triggering is possible once :math:`{SWI}_{sum} > 15`. To avoid spurious onset triggering due to soil moisture in the third soil layer exceeding the threshold due only to soil water suction of water from deeper in the soil column, an additional precipitation trigger is included which requires at least 20 mm of rain over the previous 10 days :ref:`(Dahlin et al., 2015) `. If the cold climate growing degree-day accumulator is not active at the time when the soil moisture and precipitation thresholds are reached (see below), and if the daylength is greater than 6 hours, then onset is triggered. Except as noted below, :math:`{SWI}_{sum}` continues to accumulate according to Eq. :eq:`ZEqnNum503826` during the dormant period if the daylength criterion prevents onset triggering, and onset is then triggered at the timestep when daylength exceeds 6 hours. + +In climates with a cold season, onset triggering depends on both accumulated soil temperature summation and adequate soil moisture. At the beginning of a dormant period a freezing day accumulator (:math:`{FD}_{sum}`, d) is initialized (:math:`{FD}_{sum} = 0`), with subsequent accumulation calculated as: .. math:: :label: 20.66) FD_{sum}^{n} =\left\{\begin{array}{l} {FD_{sum}^{n-1} +f_{day} \qquad {\rm for\; }T_{s,3} >TKFRZ} \\ {FD_{sum}^{n-1} \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \end{array}\right. . -If :math:`{FD}_{sum} > 15` during the dormant period, then a -cold-climate onset triggering criterion is introduced, following exactly -the growing degree-day summation (:math:`{GDD}_{sum}`) logic of Eqs. :eq:`ZEqnNum510730` -and :eq:`ZEqnNum598907`. At that time :math:`{SWI}_{sum}` is reset -(:math:`{SWI}_{sum} = 0`). Onset triggering under these conditions -depends on meeting all three of the following criteria: -:math:`{SWI}_{sum} > 15`, :math:`{GDD}_{sum} > {GDD}_{sum\_crit}`, and daylength greater than 6 hrs. +If :math:`{FD}_{sum} > 15` during the dormant period, then a cold-climate onset triggering criterion is introduced, following exactly the growing degree-day summation (:math:`{GDD}_{sum}`) logic of Eqs. :eq:`ZEqnNum510730` and :eq:`ZEqnNum598907`. At that time :math:`{SWI}_{sum}` is reset (:math:`{SWI}_{sum} = 0`). Onset triggering under these conditions depends on meeting all three of the following criteria: :math:`{SWI}_{sum} > 15`, :math:`{GDD}_{sum} > {GDD}_{sum\_crit}`, and daylength greater than 6 hrs. -The following control variables are set when a new onset growth period -is initiated: :math:`{SWI}_{sum} = 0`, :math:`{FD}_{sum} = 0`, :math:`{GDD}_{sum} = 0`, :math:`{n}_{days\_active} = 0`, and -:math:`t_{onset} = 86400\cdot n_{days\_ on}` , where :math:`{n}_{days\_on}` is set to a constant value of 30 days. Fluxes -from storage into transfer pools occur in the timestep when a new onset growth period is initiated, and are handled identically to Eqs. :eq:`ZEqnNum904388` -:eq:`ZEqnNum195642` for -carbon fluxes, and to Eqs. :eq:`ZEqnNum812152` - :eq:`ZEqnNum605338` for nitrogen fluxes. The onset counter is decremented on each time step after initiation of the onset period, -until it reaches zero, signaling the end of the onset period: +The following control variables are set when a new onset growth period is initiated: :math:`{SWI}_{sum} = 0`, :math:`{FD}_{sum} = 0`, :math:`{GDD}_{sum} = 0`, :math:`{n}_{days\_active} = 0`, and :math:`t_{onset} = 86400\cdot n_{days\_ on}`, where :math:`{n}_{days\_on}` is set to a constant value of 30 days. Fluxes from storage into transfer pools occur in the timestep when a new onset growth period is initiated, and are handled identically to Eqs. :eq:`ZEqnNum904388` -:eq:`ZEqnNum195642` for carbon fluxes, and to Eqs. :eq:`ZEqnNum812152` - :eq:`ZEqnNum605338` for nitrogen fluxes. The onset counter is decremented on each time step after initiation of the onset period, until it reaches zero, signaling the end of the onset period: .. math:: :label: 20.67) @@ -635,45 +461,25 @@ until it reaches zero, signaling the end of the onset period: 14.4.2 Stress-Deciduous Offset Triggers ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Any one of the following three conditions is sufficient to initiate an -offset period for the stress-deciduous phenology algorithm: sustained -period of dry soil, sustained period of cold temperature, or daylength -shorter than 6 hours. Offset triggering due to dry soil or cold -temperature conditions is only allowed once the most recent onset period -is complete. Dry soil condition is evaluated with an offset soil water -index accumulator (:math:`{OSWI}_{sum}`, d). To test for a sustained -period of dry soils, this control variable can increase or decrease, as -follows: +Any one of the following three conditions is sufficient to initiate an offset period for the stress-deciduous phenology algorithm: sustained period of dry soil, sustained period of cold temperature, or daylength shorter than 6 hours. Offset triggering due to dry soil or cold temperature conditions is only allowed once the most recent onset period is complete. Dry soil condition is evaluated with an offset soil water index accumulator (:math:`{OSWI}_{sum}`, d). To test for a sustained period of dry soils, this control variable can increase or decrease, as follows: .. math:: :label: 20.68) OSWI_{sum}^{n} =\left\{\begin{array}{l} {OSWI_{sum}^{n-1} +f_{day} \qquad \qquad \qquad {\rm for\; }\Psi _{s,3} \le \Psi _{offset} } \\ {{\rm max}\left(OSWI_{sum}^{n-1} -f_{day} ,0\right)\qquad {\rm for\; }\Psi _{s,3} >\Psi _{onset} } \end{array}\right. -where :math:`{\Psi}_{offset} = -0.8 MPa` is the offset soil -water potential threshold. An offset period is triggered if the previous -onset period is complete and :math:`{OSWI}_{sum}` -:math:`\mathrm{\ge}` :math:`{OSWI}_{sum\_crit}`, where :math:`{OSWI}_{sum\_crit} = 15`. +where :math:`{\Psi}_{offset} = -0.8 MPa` is the offset soil water potential threshold. An offset period is triggered if the previous onset period is complete and :math:`{OSWI}_{sum}` :math:`\mathrm{\ge}` :math:`{OSWI}_{sum\_crit}`, where :math:`{OSWI}_{sum\_crit} = 15`. -The cold temperature trigger is calculated with an offset freezing day -accumulator (:math:`{OFD}_{sum}`, d). To test for a sustained period -of cold temperature, this variable can increase or decrease, as follows: +The cold temperature trigger is calculated with an offset freezing day accumulator (:math:`{OFD}_{sum}`, d). To test for a sustained period of cold temperature, this variable can increase or decrease, as follows: .. math:: :label: 20.69) OFD_{sum}^{n} =\left\{\begin{array}{l} {OFD_{sum}^{n-1} +f_{day} \qquad \qquad \qquad {\rm for\; }T_{s,3} \le TKFRZ} \\ {{\rm max}\left(OFD_{sum}^{n-1} -f_{day} ,0\right)\qquad \qquad {\rm for\; }T_{s,3} >TKFRZ} \end{array}\right. -An offset period is triggered if the previous onset period is complete -and :math:`{OFD}_{sum} > {OFD}_{sum\_crit}`, -where :math:`{OFD}_{sum\_crit} = 15`. +An offset period is triggered if the previous onset period is complete and :math:`{OFD}_{sum} > {OFD}_{sum\_crit}`, where :math:`{OFD}_{sum\_crit} = 15`. -The offset counter is set at the initiation of the offset period: -:math:`t_{offset} =86400\cdot n_{days\_ off}` , where -:math:`{n}_{days\_off}` is set to a constant value of 15 days. The -offset counter is decremented on each time step after initiation of the -offset period, until it reaches zero, signaling the end of the offset -period: +The offset counter is set at the initiation of the offset period: :math:`t_{offset} =86400\cdot n_{days\_ off}`, where :math:`{n}_{days\_off}` is set to a constant value of 15 days. The offset counter is decremented on each time step after initiation of the offset period, until it reaches zero, signaling the end of the offset period: .. math:: :label: 20.70) @@ -683,15 +489,7 @@ period: 14.4.3 Stress-Deciduous: Long Growing Season ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -Under conditions when the stress-deciduous conditions triggering offset -are not met for one year or longer, the stress-deciduous algorithm -shifts toward the evergreen behavior. This can happen in cases where a -stress-deciduous vegetation type is assigned in a climate where suitably -strong stresses occur less frequently than once per year. This condition -is evaluated by tracking the number of days since the beginning of the -most recent onset period (:math:`{n}_{days\_active}`, d). At the end -of an offset period :math:`{n}_{days\_active}` is reset to 0. A long -growing season control variable (*LGS*, range 0 to 1) is calculated as: +Under conditions when the stress-deciduous conditions triggering offset are not met for one year or longer, the stress-deciduous algorithm shifts toward the evergreen behavior. This can happen in cases where a stress-deciduous vegetation type is assigned in a climate where suitably strong stresses occur less frequently than once per year. This condition is evaluated by tracking the number of days since the beginning of the most recent onset period (:math:`{n}_{days\_active}`, d). At the end of an offset period :math:`{n}_{days\_active}` is reset to 0. A long growing season control variable (*LGS*, range 0 to 1) is calculated as: .. math:: :label: 20.71) @@ -705,8 +503,7 @@ The rate coefficient for background litterfall (:math:`{r}_{bglf}`, s\ :sup:`-1` r_{bglf} =\frac{LGS}{\tau _{leaf} \cdot 365\cdot 86400} -where :math:`{\tau}_{leaf}` is the leaf longevity. The result is a shift to continuous litterfall as -:math:`{n}_{days\_active}` increases from 365 to 730. When a new offset period is triggered :math:`{r}_{bglf}` is set to 0. +where :math:`{\tau}_{leaf}` is the leaf longevity. The result is a shift to continuous litterfall as :math:`{n}_{days\_active}` increases from 365 to 730. When a new offset period is triggered :math:`{r}_{bglf}` is set to 0. The rate coefficient for background onset growth from the transfer pools ( :math:`{r}_{bgtr}`, s\ :sup:`-1`) also depends on *LGS*, as: @@ -779,27 +576,12 @@ with corresponding nitrogen fluxes: NF_{deadcroot\_ stor,deadcroot\_ xfer} =NS_{deadcroot\_ stor} r_{bgtr} . -The result, in conjunction with the treatment of background onset -growth, is a shift to continuous transfer from storage to display pools -at a rate that would result in complete turnover of the storage pools in -one year at steady state, once *LGS* reaches 1 (i.e. after two years -without stress-deciduous offset conditions). If and when conditions -cause stress-deciduous triggering again, :math:`{r}_{bgtr}` is rest -to 0. +The result, in conjunction with the treatment of background onset growth, is a shift to continuous transfer from storage to display pools at a rate that would result in complete turnover of the storage pools in one year at steady state, once *LGS* reaches 1 (i.e. after two years without stress-deciduous offset conditions). If and when conditions cause stress-deciduous triggering again, :math:`{r}_{bgtr}` is rest to 0. Litterfall Fluxes Merged to the Column Level ------------------------------------------------- -CLM uses three litter pools, defined on the basis of commonly measured -chemical fractionation of fresh litter into labile (LIT1 = hot water and -alcohol soluble fraction), cellulose/hemicellulose (LIT2 = acid soluble -fraction) and remaining material, referred to here for convenience as -lignin (LIT3 = acid insoluble fraction) (Aber et al., 1990; Taylor et -al., 1989). While multiple plant functional types can coexist on a -single CLM soil column, each soil column includes a single instance of -the litter pools. Fluxes entering the litter pools due to litterfall are -calculated using a weighted average of the fluxes originating at the PFT -level. Carbon fluxes are calculated as: +CLM uses three litter pools, defined on the basis of commonly measured chemical fractionation of fresh litter into labile (LIT1 = hot water and alcohol soluble fraction), cellulose/hemicellulose (LIT2 = acid soluble fraction) and remaining material, referred to here for convenience as lignin (LIT3 = acid insoluble fraction) (Aber et al., 1990; Taylor et al., 1989). While multiple plant functional types can coexist on a single CLM soil column, each soil column includes a single instance of the litter pools. Fluxes entering the litter pools due to litterfall are calculated using a weighted average of the fluxes originating at the PFT level. Carbon fluxes are calculated as: .. math:: :label: 20.86) @@ -831,17 +613,7 @@ level. Carbon fluxes are calculated as: CF_{froot,lit3} =\sum _{p=0}^{npfts}CF_{froot,litter} f_{lig\_ froot,p} wcol_{p} , -where :math:`{f}_{lab\_leaf,p}`, :math:`{f}_{cel\_leaf,p}`, and -:math:`{f}_{lig\_leaf,p}` are the labile, cellulose/hemicellulose, -and lignin fractions of leaf litter for PFT *p*, -:math:`{f}_{lab\_froot,p}`, :math:`{f}_{cel\_froot,p}`, and -:math:`{f}_{lig\_froot,p}` are the labile, cellulose/hemicellulose, -and lignin fractions of fine root litter for PFT *p*, -:math:`{wtcol}_{p}` is the weight relative to the column for PFT -*p*, and *p* is an index through the plant functional types occurring on -a column. Nitrogen fluxes to the litter pools are assumed to follow the -C:N of the senescent tissue, and so are distributed using the same -fractions used for carbon fluxes: +where :math:`{f}_{lab\_leaf,p}`, :math:`{f}_{cel\_leaf,p}`, and :math:`{f}_{lig\_leaf,p}` are the labile, cellulose/hemicellulose, and lignin fractions of leaf litter for PFT *p*, :math:`{f}_{lab\_froot,p}`, :math:`{f}_{cel\_froot,p}`, and :math:`{f}_{lig\_froot,p}` are the labile, cellulose/hemicellulose, and lignin fractions of fine root litter for PFT *p*, :math:`{wtcol}_{p}` is the weight relative to the column for PFT *p*, and *p* is an index through the plant functional types occurring on a column. Nitrogen fluxes to the litter pools are assumed to follow the C:N of the senescent tissue, and so are distributed using the same fractions used for carbon fluxes: .. math:: :label: 20.92) diff --git a/doc/source/tech_note/index.rst b/doc/source/tech_note/index.rst index a3475c7589..429788240f 100644 --- a/doc/source/tech_note/index.rst +++ b/doc/source/tech_note/index.rst @@ -11,10 +11,7 @@ CLM Technical Note .. important:: - **You are viewing the documentation for** |version_label_bold|. **There are separate - versions of this documentation for each maintained CTSM release (e.g., CLM5.0) and for - the latest development code. Use the menu at the top left to select the version of CTSM - you are using.** + **You are viewing the documentation for** |version_label_bold|. **There are separate versions of this documentation for each maintained CTSM release (e.g., CLM5.0) and for the latest development code. Use the menu at the top left to select the version of CTSM you are using.** .. toctree:: :maxdepth: 2 From 80ac17b600add9f68a5f5cea49fcda6a36c41790 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 18 Oct 2023 22:26:09 -0600 Subject: [PATCH 1664/2067] Unwrap User's Guide. --- ...w-Files-to-the-build-namelist-Database.rst | 17 +- .../Adding-Resolution-Names.rst | 11 +- .../Adding-or-Changing-Default-Filenames.rst | 15 +- doc/source/users_guide/index.rst | 5 +- .../users_guide/overview/getting-help.rst | 13 +- .../users_guide/overview/introduction.rst | 199 ++++-------------- .../users_guide/overview/quickstart.rst | 6 +- .../overview/scientific_validation.rst | 7 +- .../running-PTCLM/adding-ptclm-site-data.rst | 31 +-- .../running-PTCLM/introduction-to-ptclm.rst | 6 +- .../users_guide/running-PTCLM/using-ptclm.rst | 52 ++--- .../running-pts_mode-configurations.rst | 12 +- .../running-single-point-configurations.rst | 18 +- ...point-and-regional-grid-configurations.rst | 26 +-- ...transient-historical-CO2-concentration.rst | 21 +- ...tmospheric-forcing-to-spinup-the-model.rst | 6 +- ...tmospheric-forcing-to-spinup-the-model.rst | 3 +- ...Satellite-Phenology-Model-CLMSP-spinup.rst | 14 +- ...ning-up-the-biogeochemistry-BGC-spinup.rst | 23 +- .../running-the-prognostic-crop-model.rst | 5 +- .../running-with-irrigation.rst | 7 +- .../what-is-a-special-case.rst | 4 +- .../choosing-a-compset.rst | 16 +- .../customizing-the-clm-configuration.rst | 50 ++--- .../customizing-the-clm-namelist.rst | 58 +---- .../customizing-the-datm-namelist.rst | 55 +---- doc/source/users_guide/testing/testing.rst | 16 +- .../trouble-shooting/trouble-shooting.rst | 13 +- .../building-the-clm-tools.rst | 15 +- .../users_guide/using-clm-tools/cprnc.rst | 8 +- .../using-clm-tools/creating-domain-files.rst | 3 +- ...g-input-for-surface-dataset-generation.rst | 11 +- .../datasts-for-observational-sites.rst | 13 +- .../observational-sites-datasets.rst | 13 +- .../what-are-the-clm-tools.rst | 40 +--- 35 files changed, 170 insertions(+), 642 deletions(-) diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst index b8722c3508..ccd196baf6 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst @@ -6,20 +6,9 @@ Adding New Resolutions ======================== -In the last chapter we gave the details on how to create new files for input into CLM. -These files could be either global resolutions, regional-grids or even a single grid point. -If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. -You can deal with them, just by putting the settings in the ``user_nl_clm namelist`` file, or by using ``CLM_USRDAT_NAME``. -Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. -This keeps one central database for all your files, rather than having multiple locations to keep track of files. -If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. -If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above. +In the last chapter we gave the details on how to create new files for input into CLM. These files could be either global resolutions, regional-grids or even a single grid point. If you want to easily have these files available for continued use in your development you will then want to include them in the build-namelist database so that build-namelist can easily find them for you. You can deal with them, just by putting the settings in the ``user_nl_clm namelist`` file, or by using ``CLM_USRDAT_NAME``. Another way to deal with them is to enter them into the database for build-namelist, so that build-namelist can find them for you. This keeps one central database for all your files, rather than having multiple locations to keep track of files. If you have a LOT of files to keep track of it also might be easier than keeping track by hand, especially if you have to periodically update your files. If you just have a few quick experiments to try, for a short time period you might be best off using the other methods mentioned above. -There are two parts to adding files to the build-namelist database. -The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. -You can then use the new resolution by using ``CLM_USRDAT_NAME``. -If you also want to be able to give the resolution into **create_newcase** -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file. +There are two parts to adding files to the build-namelist database. The first part is adding new resolution names which is done in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You can then use the new resolution by using ``CLM_USRDAT_NAME``. If you also want to be able to give the resolution into **create_newcase** -- you'll need to add the grid to the ``$CIMEROOT/config/cesm/config_grid.xml`` file. -The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). -If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file. +The second part is actually adding the new filenames which is done in the ``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml`` file (``$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5_tools.xml`` file for CLM tools). If you aren't adding any new resolutions, and you are just changing the files for existing resolutions, you don't need to edit the namelist_definition file. diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst index 2a7f079d5b..4511116344 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst @@ -6,16 +6,7 @@ Adding Resolution Names ========================= -If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. -The list of valid resolutions is in the id="res" entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. -You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the id="res" entry. -The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. -The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. -The convention for unstructured HOMME grids is nenp4, where corresponds to the resolution. -The higher is the higher the resolution. -So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. -For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. -The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file: +If you are adding files for new resolutions which aren't covered in the namelist_definition file -- you'll need to add them in. The list of valid resolutions is in the id="res" entry in the ``$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml`` file. You need to choose a name for your new resolution and simply add it to the comma delimited list of valid_values for the id="res" entry. The convention for global Gaussian grids is number_of_latitudes x number_of_longitudes. The convention for global finite volume grids is latitude_grid_size x longitude_grid_size where latitude and longitude is measured in degrees. The convention for unstructured HOMME grids is nenp4, where corresponds to the resolution. The higher is the higher the resolution. So for example, ne60np4 is roughly half-degree while ne240np4 is roughly a eighth degree. For regional or single-point datasets the names have a grid size number_of_latitudes x number_of_longitudes followed by an underscore and then a descriptive name such as a City name followed by an abbreviation for the Country in caps. The only hard requirement is that names be unique for different grid files. Here's what the entry for resolutions looks like in the file: :: @@ -19,19 +16,15 @@ lnd/clm2/surfdata_map/surfdata_0.9x1.25_78pfts_CMIP6_simyr1850_c170824.nc Other ``fsurdat`` files are distinguished from this one by their resolution (hgrid), simulation year (sim_year) and prognostic crop (use_crop) attributes. -To add or change the default filenames for CLM tools edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. -Editing this file is similar to the ``namelist_defaults_clm4_5.xml`` talked about above. +To add or change the default filenames for CLM tools edit the ``$CTSMROOT/bld/namelist_files/namelist_defaults_|version|_tools.xml`` and either change an existing filename or add a new one. Editing this file is similar to the ``namelist_defaults_clm4_5.xml`` talked about above. ---------------------------- What are the required files? ---------------------------- -Different types of simulations and different types of configurations for CLM require different lists of files. -The |version|-BGC or Carbon Nitrogen (cn) Biogeochemistry model for example requires ``stream_fldfilename_ndep`` files, which are NOT required by CLMSP. -Transient simulations also require transient datasets, and the names of these datasets are sometimes different from the static versions (sometimes both are required as in the dynamic PFT cases). +Different types of simulations and different types of configurations for CLM require different lists of files. The |version|-BGC or Carbon Nitrogen (cn) Biogeochemistry model for example requires ``stream_fldfilename_ndep`` files, which are NOT required by CLMSP. Transient simulations also require transient datasets, and the names of these datasets are sometimes different from the static versions (sometimes both are required as in the dynamic PFT cases). -In the following table we list the different files used by CLM, they are listed in order of importance, dependencies, and customizing. -So the required files are all near the top, and the files used only under different conditions are listed later, and files with the fewest dependencies are near the top, as are the files that are least likely to be customized. +In the following table we list the different files used by CLM, they are listed in order of importance, dependencies, and customizing. So the required files are all near the top, and the files used only under different conditions are listed later, and files with the fewest dependencies are near the top, as are the files that are least likely to be customized. Table 3-1. Required Files for Different Configurations and Simulation Types --------------------------------------------------------------------------- diff --git a/doc/source/users_guide/index.rst b/doc/source/users_guide/index.rst index 45afc39c72..75a2949bec 100644 --- a/doc/source/users_guide/index.rst +++ b/doc/source/users_guide/index.rst @@ -13,10 +13,7 @@ .. important:: - **You are viewing the documentation for** |version_label_bold|. **There are separate - versions of this documentation for each maintained CTSM release (e.g., CLM5.0) and for - the latest development code. Use the menu at the top left to select the version of CTSM - you are using.** + **You are viewing the documentation for** |version_label_bold|. **There are separate versions of this documentation for each maintained CTSM release (e.g., CLM5.0) and for the latest development code. Use the menu at the top left to select the version of CTSM you are using.** .. toctree:: :maxdepth: 2 diff --git a/doc/source/users_guide/overview/getting-help.rst b/doc/source/users_guide/overview/getting-help.rst index 6f8887b8d1..3a1c2b4d8f 100644 --- a/doc/source/users_guide/overview/getting-help.rst +++ b/doc/source/users_guide/overview/getting-help.rst @@ -5,9 +5,7 @@ ============== Getting Help ============== -In addition to this users-guide there are several other resources that are available to help you use |version|. The first one is the |cesmrelease| User's-Guide, which documents the entire process of creating cases with |cesmrelease|. -And next is the CIME User's Guide which goes over the scripts and infrastructure used for running |version| in |cesmrelease|. -The CESM bulletin board which is a web-site for exchanging information between users of CESM. There are also CLM web-pages specific for CLM, and finally there is an email address to report bugs that you find in |cesmrelease|. +In addition to this users-guide there are several other resources that are available to help you use |version|. The first one is the |cesmrelease| User's-Guide, which documents the entire process of creating cases with |cesmrelease|. And next is the CIME User's Guide which goes over the scripts and infrastructure used for running |version| in |cesmrelease|. The CESM bulletin board which is a web-site for exchanging information between users of CESM. There are also CLM web-pages specific for CLM, and finally there is an email address to report bugs that you find in |cesmrelease|. --------------------------- The CESM User's-Guide @@ -21,8 +19,7 @@ The CESM User's-Guide The CIME User's-Guide --------------------------- -The CIME Users'-Guide goes into the how to use the scripts and infrastructure of the CESM. -`CIME Users Guide `_ +The CIME Users'-Guide goes into the how to use the scripts and infrastructure of the CESM. `CIME Users Guide `_ ----------------------- The CESM Bulletin Board @@ -59,11 +56,7 @@ Also note that several of the XML database files can be viewed in a web browser Reporting bugs in |version| ---------------------------- -If you have any problems, additional questions, bug reports, or any other feedback, please report it as an issue -on GitHub https://github.com/ESCOMP/ctsm/issues or for CIME scripts and infrastructure to https://github.com/ESMCI/CIME/issues. -Or send an email to -<`cesmhelp@cgd.ucar.edu `_> or <`ctsm-software@ucar.edu `_>. -If you find bad, wrong, or misleading information in this users guide report it as an issue on CTSM. +If you have any problems, additional questions, bug reports, or any other feedback, please report it as an issue on GitHub https://github.com/ESCOMP/ctsm/issues or for CIME scripts and infrastructure to https://github.com/ESMCI/CIME/issues. Or send an email to <`cesmhelp@cgd.ucar.edu `_> or <`ctsm-software@ucar.edu `_>. If you find bad, wrong, or misleading information in this users guide report it as an issue on CTSM. --------------------------------------- Some Acronym's and Terms We'll be Using diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index a7a9ef434c..f7add659a7 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -6,12 +6,7 @@ **Authors: Benjamin Andre, Erik Kluzek, William Sacks** -The National Center for Atmospheric Research (NCAR) is operated by the -nonprofit University Corporation for Atmospheric Research (UCAR) under -the sponsorship of the National Science Foundation. Any opinions, -findings, conclusions, or recommendations expressed in this publication -are those of the author(s) and do not necessarily reflect the views of -the National Science Foundation. +The National Center for Atmospheric Research (NCAR) is operated by the nonprofit University Corporation for Atmospheric Research (UCAR) under the sponsorship of the National Science Foundation. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. National Center for Atmospheric Research P. O. Box 3000, Boulder, Colorado 80307-3000 @@ -22,65 +17,15 @@ P. O. Box 3000, Boulder, Colorado 80307-3000 Introduction ============== -The Community Land Model (|release| in |cesmrelease|) is the latest in a -series of global land models developed by the CESM Land Model Working -Group (LMWG) and maintained at the National Center for Atmospheric -Research (NCAR). This guide is intended to instruct both the novice -and experienced user on running CLM. This guide pertains to the latest -version |version| in |cesmrelease| available for download from the public -release subversion repository as a part of |cesmrelease|. Documentation -may be different if you are using an older version, you should either -use the documentation for that release version, update to the latest -version, or use the documentation inside your own source tree. There -is information in the ChangeLog file and in the `What is new with -|version| in |cesmrelease| since previous public releases? `_ -regarding the changes from previous versions of CESM. - -.. note:: This release of |version| in |cesmrelease| includes BOTH CLM4.0 - physics and CLM4.5 physics used in previous releases as well as the updated |version| - physics. CLM allow you to trigger between the three physics modes. Most often when we refer to CLM4.0 we - are referring to the CLM4.0 physics in |version| in |cesmrelease| rather - than to a specific version of CLM4.0 (where we would give the exact - version). And when we refer to CLM4.5 we are referring to the CLM4.5 - physics in |version| in |cesmrelease| rather - than to a specific version of CLM4.5. Likewise, when referring to |version| we are referring to the - |version| physics in |version| in |cesmrelease|. - -The novice user should read `Chapter 1 `_ in detail before -beginning work, while the expert user should read `What is new with -|version| in |cesmrelease| since previous public releases? `_ and -`Quickstart to using |version| `_ chapters, and then use the -more detailed chapters as reference. Before novice users go onto more -technical problems covered in `Chapter 2 `_, `Chapter 3 -`_, `Chapter 4 `_, or `Chapter 5 `_ they -should know the material covered in `Chapter 1 `_ and be able -to replicate some of the examples given there. - -All users should read the `How to Use This Document `_ and -`Other resources to get help from `_ sections to understand -the document conventions and the various ways of getting help on using -|version|. Users should also read the `What is scientifically validated -and functional in |version| in |cesmrelease|? `_ section to see if -their planned use of the model is something that has been -scientifically validated and well tested. Users that are NOT using -NCAR machines or our list of well tested machines should also read the -What are the UNIX utilities required to use |version|? section to make -sure they have all the required UNIX utilities on the system they want -to do their work. - -Developers that are making changes to CLM either for their own -development or for development that they hope will eventually become a -part of the main CLM should read the `Chapter 8 `_ -chapter. We have a suite of test scripts that automatically test many -different model configurations and namelist options, as well as -ensuring things like restarts are bit-for-bit and the like. It's -helpful to use these scripts to ensure your changes are working -correctly. As well as being a required part of the process to bring in -new code developments. And it's far easier to use the automated -scripts rather than having to figure out, what to test, how to do it, -and then finally do it by hand. If you are using non supported -machines you may also want to use the test scripts to make sure your -machine is working correctly. +The Community Land Model (|release| in |cesmrelease|) is the latest in a series of global land models developed by the CESM Land Model Working Group (LMWG) and maintained at the National Center for Atmospheric Research (NCAR). This guide is intended to instruct both the novice and experienced user on running CLM. This guide pertains to the latest version |version| in |cesmrelease| available for download from the public release subversion repository as a part of |cesmrelease|. Documentation may be different if you are using an older version, you should either use the documentation for that release version, update to the latest version, or use the documentation inside your own source tree. There is information in the ChangeLog file and in the `What is new with |version| in |cesmrelease| since previous public releases? `_ regarding the changes from previous versions of CESM. + +.. note:: This release of |version| in |cesmrelease| includes BOTH CLM4.0 physics and CLM4.5 physics used in previous releases as well as the updated |version| physics. CLM allow you to trigger between the three physics modes. Most often when we refer to CLM4.0 we are referring to the CLM4.0 physics in |version| in |cesmrelease| rather than to a specific version of CLM4.0 (where we would give the exact version). And when we refer to CLM4.5 we are referring to the CLM4.5 physics in |version| in |cesmrelease| rather than to a specific version of CLM4.5. Likewise, when referring to |version| we are referring to the |version| physics in |version| in |cesmrelease|. + +The novice user should read `Chapter 1 `_ in detail before beginning work, while the expert user should read `What is new with |version| in |cesmrelease| since previous public releases? `_ and `Quickstart to using |version| `_ chapters, and then use the more detailed chapters as reference. Before novice users go onto more technical problems covered in `Chapter 2 `_, `Chapter 3 `_, `Chapter 4 `_, or `Chapter 5 `_ they should know the material covered in `Chapter 1 `_ and be able to replicate some of the examples given there. + +All users should read the `How to Use This Document `_ and `Other resources to get help from `_ sections to understand the document conventions and the various ways of getting help on using |version|. Users should also read the `What is scientifically validated and functional in |version| in |cesmrelease|? `_ section to see if their planned use of the model is something that has been scientifically validated and well tested. Users that are NOT using NCAR machines or our list of well tested machines should also read the What are the UNIX utilities required to use |version|? section to make sure they have all the required UNIX utilities on the system they want to do their work. + +Developers that are making changes to CLM either for their own development or for development that they hope will eventually become a part of the main CLM should read the `Chapter 8 `_ chapter. We have a suite of test scripts that automatically test many different model configurations and namelist options, as well as ensuring things like restarts are bit-for-bit and the like. It's helpful to use these scripts to ensure your changes are working correctly. As well as being a required part of the process to bring in new code developments. And it's far easier to use the automated scripts rather than having to figure out, what to test, how to do it, and then finally do it by hand. If you are using non supported machines you may also want to use the test scripts to make sure your machine is working correctly. .. _what-is-new-with-clm5_0: @@ -88,9 +33,7 @@ machine is working correctly. What is New with |version| ============================ -`What's new with |version| science `_ -gives a synopsis of the changes to CLM since the CLM4.5 release. -More details are given in the `CLM ChangeLog file `_. +`What's new with |version| science `_ gives a synopsis of the changes to CLM since the CLM4.5 release. More details are given in the `CLM ChangeLog file `_. Previous release pages give similar list of changes for previous versions of the model. @@ -100,52 +43,27 @@ Previous release pages give similar list of changes for previous versions of the Overview of User's Guide ========================== -In this introduction we first give a simple guide to understand the document conventions in `How to Use This Document `_. -The next section `What is new with |version| in |cesmrelease| since previous public releases? `_ gives references to describe the differences between |version| in |cesmrelease| and previous CESM releases both from a scientific as well as a software engineering point of view. -For information on previous releases of |version| before |version| in |cesmrelease| see the CESM1.2.2 documentation. -The next section `Quickstart to using |version| `_ is for users that are already experts in using CLM and gives a quickstart guide to the bare details on how to use |version|. -The next `What is scientifically validated and functional in |version| in |cesmrelease|? `_ tells you about what has been extensively tested and scientifically validated (and maybe more importantly) what has NOT. -`What are the UNIX utilities required to use |version|? `_ lists the UNIX utilities required to use |version| and is important if you are running on non-NCAR machines, generic local machines, or machines NOT as well tested by us at NCAR. -Next we have `Important Notes and Best Practices for Usage of |version| `_ to detail some of the best practices for using |version| for science. -The last introductory section is `Other resources `_ to get help from which lists different resources for getting help with |version| and |cesmrelease|. - -`Chapter 1 `_ goes into detail on how to setup and run simulations with |version| and especially how to customize cases. -Details of cesm_setup modes and build-namelist options as well as namelist options are given in this chapter. - -`Chapter 2 `_ gives instructions on the CLM tools for either CLM4.5 or |version| physics for creating input datasets for use by CLM, for the expert user. -There's an overview of what each tool does, and some general notes on how to build the FORTRAN tools. -Then each tool is described in detail along with different ways in which the tool might be used. -A final section on how to customize datasets for observational sites for very savvy expert users is given as the last section of this chapter. - -As a followup to the tools chapter, `Chapter 3 `_ tells how to add files to the XML database for build-namelist to use. -This is important if you want to use the XML database to automatically select user-created input files that you have created when you setup new cases with CLM (CLM4.0, CLM4.5 and |version| physics). - -In `Chapter 4 `_, again for the expert user, we give details on how to do some particularly difficult special cases. -For example, we give the protocol for spinning up the |version|-BGC and CLMCN models as well as CLM with dynamic vegetation active (CNDV). -We give instructions to do a spinup case from a previous case with Coupler history output for atmospheric forcing. -We also give instructions on running both the prognostic crop and irrigation models. -Lastly we tell the user how to use the DATM model to send historical CO2 data to CLM. - -`Chapter 5 `_ outlines how to do single-point or regional simulations using |version|. -This is useful to either compare |version| simulations with point observational stations, such as tower sites (which might include your own atmospheric forcing), or to do quick simulations with CLM for example to test a new parameterization. -There are several different ways given on how to perform single-point simulations which range from simple PTS_MODE to more complex where you create all your own datasets, tying into `Chapter 2 `_ and also `Chapter 3 `_ to add the files into the build-namelist XML database. -The PTCLM python script to run single-point simulations was added back in for this release (but it has bugs that don't allow it to work out of the box). -CLM4 in CESM1.0.5 has a fully working versions of PTCLM. +In this introduction we first give a simple guide to understand the document conventions in `How to Use This Document `_. The next section `What is new with |version| in |cesmrelease| since previous public releases? `_ gives references to describe the differences between |version| in |cesmrelease| and previous CESM releases both from a scientific as well as a software engineering point of view. For information on previous releases of |version| before |version| in |cesmrelease| see the CESM1.2.2 documentation. The next section `Quickstart to using |version| `_ is for users that are already experts in using CLM and gives a quickstart guide to the bare details on how to use |version|. The next `What is scientifically validated and functional in |version| in |cesmrelease|? `_ tells you about what has been extensively tested and scientifically validated (and maybe more importantly) what has NOT. `What are the UNIX utilities required to use |version|? `_ lists the UNIX utilities required to use |version| and is important if you are running on non-NCAR machines, generic local machines, or machines NOT as well tested by us at NCAR. Next we have `Important Notes and Best Practices for Usage of |version| `_ to detail some of the best practices for using |version| for science. The last introductory section is `Other resources `_ to get help from which lists different resources for getting help with |version| and |cesmrelease|. + +`Chapter 1 `_ goes into detail on how to setup and run simulations with |version| and especially how to customize cases. Details of cesm_setup modes and build-namelist options as well as namelist options are given in this chapter. + +`Chapter 2 `_ gives instructions on the CLM tools for either CLM4.5 or |version| physics for creating input datasets for use by CLM, for the expert user. There's an overview of what each tool does, and some general notes on how to build the FORTRAN tools. Then each tool is described in detail along with different ways in which the tool might be used. A final section on how to customize datasets for observational sites for very savvy expert users is given as the last section of this chapter. + +As a followup to the tools chapter, `Chapter 3 `_ tells how to add files to the XML database for build-namelist to use. This is important if you want to use the XML database to automatically select user-created input files that you have created when you setup new cases with CLM (CLM4.0, CLM4.5 and |version| physics). + +In `Chapter 4 `_, again for the expert user, we give details on how to do some particularly difficult special cases. For example, we give the protocol for spinning up the |version|-BGC and CLMCN models as well as CLM with dynamic vegetation active (CNDV). We give instructions to do a spinup case from a previous case with Coupler history output for atmospheric forcing. We also give instructions on running both the prognostic crop and irrigation models. Lastly we tell the user how to use the DATM model to send historical CO2 data to CLM. + +`Chapter 5 `_ outlines how to do single-point or regional simulations using |version|. This is useful to either compare |version| simulations with point observational stations, such as tower sites (which might include your own atmospheric forcing), or to do quick simulations with CLM for example to test a new parameterization. There are several different ways given on how to perform single-point simulations which range from simple PTS_MODE to more complex where you create all your own datasets, tying into `Chapter 2 `_ and also `Chapter 3 `_ to add the files into the build-namelist XML database. The PTCLM python script to run single-point simulations was added back in for this release (but it has bugs that don't allow it to work out of the box). CLM4 in CESM1.0.5 has a fully working versions of PTCLM. Need `Chapter 6 `_ blurb... -`Chapter 7 `_ gives some guidance on trouble-shooting problems when using |version|. -It doesn't cover all possible problems with CLM, but gives you some guidelines for things that can be done for some common problems. +`Chapter 7 `_ gives some guidance on trouble-shooting problems when using |version|. It doesn't cover all possible problems with CLM, but gives you some guidelines for things that can be done for some common problems. -`Chapter 8 `_ goes over the automated testing scripts for validating that the CLM is working correctly. -The test scripts run many different configurations and options with CLM4.0 physics as well and |version| physics making sure that they work, as well as doing automated testing to verify restarts are working correctly, and testing at many different resolutions. -In general this is an activity important only for a developer of |version|, but could also be used by users who are doing extensive code modifications and want to ensure that the model continues to work correctly. +`Chapter 8 `_ goes over the automated testing scripts for validating that the CLM is working correctly. The test scripts run many different configurations and options with CLM4.0 physics as well and |version| physics making sure that they work, as well as doing automated testing to verify restarts are working correctly, and testing at many different resolutions. In general this is an activity important only for a developer of |version|, but could also be used by users who are doing extensive code modifications and want to ensure that the model continues to work correctly. In the appendices we talk about some issues that are useful for advanced users and developers of |version|. -Finally in `Appendix A `_ we give instructions on how to build the documentation associated with |version| (i.e. how to build this document). -This document is included in every CLM distribution and can be built so that you can view a local copy rather than having to go to the CESM website. -This also could be useful for developers who need to update the documentation due to changes they have made. +Finally in `Appendix A `_ we give instructions on how to build the documentation associated with |version| (i.e. how to build this document). This document is included in every CLM distribution and can be built so that you can view a local copy rather than having to go to the CESM website. This also could be useful for developers who need to update the documentation due to changes they have made. ================================ README file describing |version| @@ -162,43 +80,19 @@ The README (which can be found in ``$CTSMROOT/doc``) is repeated here. Best Practices ================ -- |version| includes BOTH the old CLM4.0, CLM4.5 physics AND the new |version| physics and you can toggle between those three. - The "standard" practice for CLM4.0 is to run with CN on, and with Qian atmospheric forcing. - While the "standard" practice for CLM4.5 is to run with BGC on, and CRUNCEP atmospheric forcing. - And finally the "standard" practice for |version| is to run with BGC and Prognostic Crop on, with the MOSART model for river routing, as well as the CISM - ice sheet model, and using GSWP3 atmospheric forcing. - "BGC" is the new |version| biogeochemistry and include CENTURY-like pools, vertical resolved carbon, as well as Nitrification and de-Nitrification (see `the Section called Some Acronym's and Terms We'll be Using in Other resources to get help from `_ ). - -- When running with CLMCN (either CLM4.0 or |version| physics) or |version|-BGC, it is critical to begin with initial conditions that are provided with the release or to spin the model up following the CN spinup procedure before conducting scientific runs (see `the Section called Spinning up the |version| biogeochemistry (CLMBGC spinup) in Chapter 4 `_ for |version| or `the Section called Spinning up the CLM4.0 biogeochemistry Carbon-Nitrogen Model (CN spinup) in Chapter 4 `_ for CLM4.0). - Simulations without a proper spinup will effectively be starting from an unvegetated world. - See `the Section called Setting Your Initial Conditions File in Chapter 1 `_ for information on how to provide initial conditions for your simulation. - -- Initial condition files are provided for CLM4.0-CN as before, for fully coupled BCN and offline ICN cases for 1850 and 2000 at finite volume grids: 1deg (0.9x1.25), 2deg (1.9x2.5), and T31 resolutions. - We also have interpolated initial conditions for BCN for 1850 and 2000 for two finite volume grids: 10x15, 4x5 and two HOMME grids (ne30np4 and ne120np4). - There's also an initial condition file for ICN with the prognostic crop model for 2000 at 2deg resolution, and one with CLMSP for 2000 at 2deg resolution. - We also have initial conditions for offline CNDV for 1850. - The 1850 initial condition files are in 'reasonable' equilibrium. - The 2000 initial condition files represent the model state for the year 2000, and have been taken from transient simulations. - Therefore, by design the year 2000 initial condition files do not represent an equilibrium state. - Note also that spinning the 2000 initial conditions out to equilibrium will not reflect the best estimate of the real carbon/nitrogen state for the year 2000. - -- Initial condition files are also provided for |version| for several configurations and resolutions. - For CLM4.5-SP and CLM4.5-BGC with both CRUNCEP and GSWP3 forcing we have initial conditions at 1deg resolution for 1850. - For |version|-SP and |version|-BGC-Crop with both CRUNCEP and GSWP3 forcing we have initial conditions at 1deg resolution for 1850. - Normally, these files are interpolated to any other resolution that you run at. - -- Users can interpolate initial condition files at different resolutions at startup of a CLM4.5 or |version| simulation. And the file created can be stored for later use. - Interpolated initial condition files may no longer be in 'reasonable' equilibrium. - -- In |version| for both |version|-CN, |version|-BGC, and |version|-BGC-Crop the new fire model requires lightning frequency data, and human population density (both are read inside of CLM). - By default we have provided a climatology dataset for lightning frequency and a dataset with coverage from 1850 to 2014 for population density. - Both of these datasets are interpolated from the native resolution of the datasets to the resolution you are running the model on. - If you are running with an atmosphere model or forcing that is significantly different than present day -- the lightning frequency may NOT appropriately correspond to your atmosphere forcing and fire initiation would be inappropriate. - -- Aerosol deposition is a required field to both CLM4.0, CLM4.5 and |version| physics, sent from the atmosphere model. - Simulations without aerosol deposition will exhibit unreasonably high snow albedos. - The model sends aerosol deposition from the atmospheric model (either CAM or DATM). - When running with prescribed aerosol the atmosphere model will interpolate the aerosols from 2-degree resolution to the resolution the atmosphere model is running at. +- |version| includes BOTH the old CLM4.0, CLM4.5 physics AND the new |version| physics and you can toggle between those three. The "standard" practice for CLM4.0 is to run with CN on, and with Qian atmospheric forcing. While the "standard" practice for CLM4.5 is to run with BGC on, and CRUNCEP atmospheric forcing. And finally the "standard" practice for |version| is to run with BGC and Prognostic Crop on, with the MOSART model for river routing, as well as the CISM ice sheet model, and using GSWP3 atmospheric forcing. "BGC" is the new |version| biogeochemistry and include CENTURY-like pools, vertical resolved carbon, as well as Nitrification and de-Nitrification (see `the Section called Some Acronym's and Terms We'll be Using in Other resources to get help from `_ ). + +- When running with CLMCN (either CLM4.0 or |version| physics) or |version|-BGC, it is critical to begin with initial conditions that are provided with the release or to spin the model up following the CN spinup procedure before conducting scientific runs (see `the Section called Spinning up the |version| biogeochemistry (CLMBGC spinup) in Chapter 4 `_ for |version| or `the Section called Spinning up the CLM4.0 biogeochemistry Carbon-Nitrogen Model (CN spinup) in Chapter 4 `_ for CLM4.0). Simulations without a proper spinup will effectively be starting from an unvegetated world. See `the Section called Setting Your Initial Conditions File in Chapter 1 `_ for information on how to provide initial conditions for your simulation. + +- Initial condition files are provided for CLM4.0-CN as before, for fully coupled BCN and offline ICN cases for 1850 and 2000 at finite volume grids: 1deg (0.9x1.25), 2deg (1.9x2.5), and T31 resolutions. We also have interpolated initial conditions for BCN for 1850 and 2000 for two finite volume grids: 10x15, 4x5 and two HOMME grids (ne30np4 and ne120np4). There's also an initial condition file for ICN with the prognostic crop model for 2000 at 2deg resolution, and one with CLMSP for 2000 at 2deg resolution. We also have initial conditions for offline CNDV for 1850. The 1850 initial condition files are in 'reasonable' equilibrium. The 2000 initial condition files represent the model state for the year 2000, and have been taken from transient simulations. Therefore, by design the year 2000 initial condition files do not represent an equilibrium state. Note also that spinning the 2000 initial conditions out to equilibrium will not reflect the best estimate of the real carbon/nitrogen state for the year 2000. + +- Initial condition files are also provided for |version| for several configurations and resolutions. For CLM4.5-SP and CLM4.5-BGC with both CRUNCEP and GSWP3 forcing we have initial conditions at 1deg resolution for 1850. For |version|-SP and |version|-BGC-Crop with both CRUNCEP and GSWP3 forcing we have initial conditions at 1deg resolution for 1850. Normally, these files are interpolated to any other resolution that you run at. + +- Users can interpolate initial condition files at different resolutions at startup of a CLM4.5 or |version| simulation. And the file created can be stored for later use. Interpolated initial condition files may no longer be in 'reasonable' equilibrium. + +- In |version| for both |version|-CN, |version|-BGC, and |version|-BGC-Crop the new fire model requires lightning frequency data, and human population density (both are read inside of CLM). By default we have provided a climatology dataset for lightning frequency and a dataset with coverage from 1850 to 2014 for population density. Both of these datasets are interpolated from the native resolution of the datasets to the resolution you are running the model on. If you are running with an atmosphere model or forcing that is significantly different than present day -- the lightning frequency may NOT appropriately correspond to your atmosphere forcing and fire initiation would be inappropriate. + +- Aerosol deposition is a required field to both CLM4.0, CLM4.5 and |version| physics, sent from the atmosphere model. Simulations without aerosol deposition will exhibit unreasonably high snow albedos. The model sends aerosol deposition from the atmospheric model (either CAM or DATM). When running with prescribed aerosol the atmosphere model will interpolate the aerosols from 2-degree resolution to the resolution the atmosphere model is running at. .. _ctsm_vs_cesm_checkout: @@ -206,10 +100,7 @@ The README (which can be found in ``$CTSMROOT/doc``) is repeated here. A CTSM versus a CESM checkout ============================= -The directory structure for |version| is different depending on if it's checked out from |release| or |cesmrelease|. -If |version| is checked out from |ctsm_gh| the CLM source code is directly under the top level directory. If |cesmrelease| -is checkout out from |cesm_gh| then the CLM source directories are under "components/clm" from the top level directory. We -will refer to this directory for the CLM source directories in the User's Guide as "$CTSMROOT". +The directory structure for |version| is different depending on if it's checked out from |release| or |cesmrelease|. If |version| is checked out from |ctsm_gh| the CLM source code is directly under the top level directory. If |cesmrelease| is checkout out from |cesm_gh| then the CLM source directories are under "components/clm" from the top level directory. We will refer to this directory for the CLM source directories in the User's Guide as "$CTSMROOT". .. _how-to-use-this-document: @@ -221,17 +112,7 @@ Links to descriptions and definitions have been provided in the code below. We u :: - Throughout the document this style is used to indicate shell - commands and options, fragments of code, namelist variables, etc. - Where examples from an interactive shell session are presented, lines - starting with > indicate the shell prompt. A backslash "\" at the end - of a line means the line continues onto the next one (as it does in - standard UNIX shell). Note that $EDITOR" is used to refer to the - text editor of your choice. $EDITOR is a standard UNIX environment - variable and should be set on most UNIX systems. Comment lines are - signaled with a "#" sign, which is the standard UNIX comment sign as well. - $CSMDATA is used to denote the path to the inputdata directory for - your CESM data. + Throughout the document this style is used to indicate shell commands and options, fragments of code, namelist variables, etc. Where examples from an interactive shell session are presented, lines starting with > indicate the shell prompt. A backslash "\" at the end of a line means the line continues onto the next one (as it does in standard UNIX shell). Note that $EDITOR" is used to refer to the text editor of your choice. $EDITOR is a standard UNIX environment variable and should be set on most UNIX systems. Comment lines are signaled with a "#" sign, which is the standard UNIX comment sign as well. $CSMDATA is used to denote the path to the inputdata directory for your CESM data. > This is a shell prompt with commands \ that continues to the following line. diff --git a/doc/source/users_guide/overview/quickstart.rst b/doc/source/users_guide/overview/quickstart.rst index ec581b2ec4..f8b810cc0d 100644 --- a/doc/source/users_guide/overview/quickstart.rst +++ b/doc/source/users_guide/overview/quickstart.rst @@ -6,8 +6,7 @@ Quickstart ============ -Running the CLM requires a suite of UNIX utilities and programs and you should make sure you have all of these available before trying to go forward with using it. -If you are missing one of these you should contact the systems administrator for the machine you wish to run on and make sure they are installed. +Running the CLM requires a suite of UNIX utilities and programs and you should make sure you have all of these available before trying to go forward with using it. If you are missing one of these you should contact the systems administrator for the machine you wish to run on and make sure they are installed. List of utilities required for CESM in the "|cesmrelease| Software/Operating System Prerequisites" section in `http://www.cesm.ucar.edu/models/cesm1.2//cesm/doc/usersguide/book1.html `_ - UNIX bash shell (for some of the CLM tools scripts) @@ -24,8 +23,7 @@ The IMPORTANT_NOTES file talks about important things for users to know about us The ChangeLog/ChangeSum talk about advances in different versions of CLM. The content of these files is largely explained in the previous chapter on `"What is new with |version| in |cesmrelease| since previous public releases?" `_. -The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that -culimated in that given version of the CLM. +The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that culimated in that given version of the CLM. Note other directories have README files that explain different components and tools used when running CLM and are useful in understanding how those parts of the model work and should be consulted when using tools in those directories. For more details on configuring and customizing a case with CLM see `Chapter 1 `_. diff --git a/doc/source/users_guide/overview/scientific_validation.rst b/doc/source/users_guide/overview/scientific_validation.rst index 5f83457033..3110cbd81f 100644 --- a/doc/source/users_guide/overview/scientific_validation.rst +++ b/doc/source/users_guide/overview/scientific_validation.rst @@ -12,8 +12,7 @@ In this section we go over what has been extensively tested and scientifically v Standard Configuration and Namelist Options that are Validated -------------------------------------------------------------- -See -`http://www.cesm.ucar.edu/models/cesm1.2/clm/CLM_configurations_CESM1.2.pdf `_ for an explanation of what configurations are scientifically validated for |version|. For CLM4.0 changes to the science of the model are minimal since CESM1.1.1 so we expect answers to be very similar to using it. +See `http://www.cesm.ucar.edu/models/cesm1.2/clm/CLM_configurations_CESM1.2.pdf `_ for an explanation of what configurations are scientifically validated for |version|. For CLM4.0 changes to the science of the model are minimal since CESM1.1.1 so we expect answers to be very similar to using it. In the sections below we go through configuration and/or namelist options or modes that the user should be especially wary of using. You are of course free to use these options, and you may find that they work functionally. Although in some cases you will find issues even with functionality of using them. If so you will need to test, debug and find solutions for these issues on your own. But in every case you will need to go through more extensive work to validate these options from a scientific standpoint. Some of these options are only for |version| while others are for both CLM4.0 AND |version| we explicitly say which they apply to. @@ -21,9 +20,7 @@ In the sections below we go through configuration and/or namelist options or mod Configurations that should be used with caution ----------------------------------------------- -There are some options in |version| that are available but either not tested extensively, or not scientifically evaluated. These -options should be used with caution. And any options that deviate from the scientifically supported configurations can have issues. -The IMPORTANT_NODES file goes into more details on this. +There are some options in |version| that are available but either not tested extensively, or not scientifically evaluated. These options should be used with caution. And any options that deviate from the scientifically supported configurations can have issues. The IMPORTANT_NODES file goes into more details on this. The IMPORTANT_NOTES (which can be found in ``$CTSMROOT/doc``) is repeated here. diff --git a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst index a349efd5f4..9492b9ce59 100644 --- a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst +++ b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst @@ -6,14 +6,7 @@ Adding PTCLMmkdata Site Data ============================ -The "sitegroupname" option to PTCLMmkdata looks for groups of sites in the files in the ``PTCLM_sitedata`` directory under the PTCLMmkdata directory. -You can add new names available for this option including your own lists of sites, by adding more files in this directory. -There are three files for each "sitegroupname": ``$SITEGROUP_sitedata.txt``, ``$SITEGROUP_soildata.txt`` and ``$SITEGROUP_pftdata.txt`` (where ``$SITEGROUP`` is the name that would be entered as "sitegroupname" to PTCLMmkdata). -Each file needs to have the same list of sites, but gives different information: site data, PFT data, and soil data respectively. -Although the site codes need to be the same between the three files, the files do NOT have to be in the same order. -Each file has a one-line header that lists the contents of each column which are separated by commas. -The first column for each of the files is the "site_code" which must be consistent between the three files. -The site code can be any unique character string, but in general we use the AmeriFlux site code. +The "sitegroupname" option to PTCLMmkdata looks for groups of sites in the files in the ``PTCLM_sitedata`` directory under the PTCLMmkdata directory. You can add new names available for this option including your own lists of sites, by adding more files in this directory. There are three files for each "sitegroupname": ``$SITEGROUP_sitedata.txt``, ``$SITEGROUP_soildata.txt`` and ``$SITEGROUP_pftdata.txt`` (where ``$SITEGROUP`` is the name that would be entered as "sitegroupname" to PTCLMmkdata). Each file needs to have the same list of sites, but gives different information: site data, PFT data, and soil data respectively. Although the site codes need to be the same between the three files, the files do NOT have to be in the same order. Each file has a one-line header that lists the contents of each column which are separated by commas. The first column for each of the files is the "site_code" which must be consistent between the three files. The site code can be any unique character string, but in general we use the AmeriFlux site code. Site data file:`` $SITEGROUP_sitedata.txt``): The header for this file is: :: @@ -51,35 +44,21 @@ This file only requires a line for each year where a transition or harvest happe Converting AmeriFlux Data for use by PTCLMmkdata ------------------------------------------------ -AmeriFlux data comes in comma separated format and is available from: -`http://public.ornl.gov/ameriflux/dataproducts.shtml `_. Before you download the data you need to agree to the usage terms. +AmeriFlux data comes in comma separated format and is available from: `http://public.ornl.gov/ameriflux/dataproducts.shtml `_. Before you download the data you need to agree to the usage terms. Here is a copy of the usage terms from the web-site on June/13/2011. -"The AmeriFlux data provided on this site are freely available and were furnished by individual AmeriFlux scientists who encourage their use. -Please kindly inform the appropriate AmeriFlux scientist(s) of how you are using the data and of any publication plans. -Please acknowledge the data source as a citation or in the acknowledgments if the data are not yet published. -If the AmeriFlux Principal Investigators (PIs) feel that they should be acknowledged or offered participation as authors, they will let you know and we assume that an agreement on such matters will be reached before publishing and/or use of the data for publication. -If your work directly competes with the PI's analysis they may ask that they have the opportunity to submit a manuscript before you submit one that uses unpublished data. -In addition, when publishing, please acknowledge the agency that supported the research. -Lastly, we kindly request that those publishing papers using AmeriFlux data provide preprints to the PIs providing the data and to the data archive at the Carbon Dioxide Information Analysis Center (CDIAC)." +"The AmeriFlux data provided on this site are freely available and were furnished by individual AmeriFlux scientists who encourage their use. Please kindly inform the appropriate AmeriFlux scientist(s) of how you are using the data and of any publication plans. Please acknowledge the data source as a citation or in the acknowledgments if the data are not yet published. If the AmeriFlux Principal Investigators (PIs) feel that they should be acknowledged or offered participation as authors, they will let you know and we assume that an agreement on such matters will be reached before publishing and/or use of the data for publication. If your work directly competes with the PI's analysis they may ask that they have the opportunity to submit a manuscript before you submit one that uses unpublished data. In addition, when publishing, please acknowledge the agency that supported the research. Lastly, we kindly request that those publishing papers using AmeriFlux data provide preprints to the PIs providing the data and to the data archive at the Carbon Dioxide Information Analysis Center (CDIAC)." The above agreement applies to the "US-UMB" dataset imported into our repository as well, and Gil Bohrer is the PI on record for that dataset. -The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap filled datasets. -The fields will also need to be renamed. -The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes "FLDS", "PRESS" becomes "PSRF". -"ZBOT" can just be set to the constant of "30" (m). -The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the value in ``SHR_CONST_TKFRZ`` in the file ``models/csm_share/shr/shr_const.F90`` of ``273.15``. -The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and LONGXY should also be set to the latitude and longitude of the site. +The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap filled datasets. The fields will also need to be renamed. The "WS" column becomes "WIND", "PREC" becomes "PRECmms", "RH" stays as "RH", "TA" becomes "TBOT", "Rg" becomes "FSDS", "Rgl" becomes "FLDS", "PRESS" becomes "PSRF". "ZBOT" can just be set to the constant of "30" (m). The units of Temperature need to be converted from "Celsius" to "Kelvin" (use the value in ``SHR_CONST_TKFRZ`` in the file ``models/csm_share/shr/shr_const.F90`` of ``273.15``. The units of Pressure also need to be converted from "kPa" to "Pa". LATIXY, and LONGXY should also be set to the latitude and longitude of the site. ----------------------------------------------------------------- Example: PTCLMmkdata transient example over a shorter time period ----------------------------------------------------------------- -This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. -In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as show in the `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ section above. -Also note that this site has a site-specific dynamic land-use change file for it ``PTCLM_sitedata/US-Ha1_dynpftdata.txt`` in the PTCLMmkdata directory and this file will be used for land-use change and harvesting rather than the global dataset. +This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as show in the `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ section above. Also note that this site has a site-specific dynamic land-use change file for it ``PTCLM_sitedata/US-Ha1_dynpftdata.txt`` in the PTCLMmkdata directory and this file will be used for land-use change and harvesting rather than the global dataset. :: diff --git a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst index 56b0a7ad51..a94d62d1b5 100644 --- a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst @@ -10,8 +10,7 @@ PTCLMmkdata (pronounced Pee-Tee Cee-L-M make data is a Python script to help you set up PoinT CLM simulations. -It runs the CLM tools for you to get datasets set up, and copies them to a location you can use them including the changes -needed for a case to use the dataset with namelist and XML changes. +It runs the CLM tools for you to get datasets set up, and copies them to a location you can use them including the changes needed for a case to use the dataset with namelist and XML changes. Then you run **create_newcase** and point to the directory so that the namelist and XML changes are automatically applied. @@ -106,8 +105,7 @@ The output to the above command is as follows: Main Script Version Id: $Id: PTCLM.py 47576 2013-05-29 19:11:16Z erik $ Scripts URL: $HeadURL: https://svn-ccsm-models.cgd.ucar.edu/PTCLM/trunk_tags/PTCLM1_130529/PTCLM.py $: -Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. -Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ for permission information to use this data. +Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ for permission information to use this data. Example 6-1. Example of running PTCLMmkdata for US-UMB on cheyenne ------------------------------------------------------------------ diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst index 9085ac19d6..c69e2cdd91 100644 --- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/using-ptclm.rst @@ -6,17 +6,13 @@ Using PTCLMmkdata ************************** -There are two types of options to PTCLMmkdata: required and optional. -The three required options are the three settings that MUST be specified for PTCLMmkdata to work at all. The other settings have default values that will default to something useful. Most options use a double dash "--" "longname" such as "--list", but the most common options also have a short-name with a single dash. +There are two types of options to PTCLMmkdata: required and optional. The three required options are the three settings that MUST be specified for PTCLMmkdata to work at all. The other settings have default values that will default to something useful. Most options use a double dash "--" "longname" such as "--list", but the most common options also have a short-name with a single dash. -The required options to PTCLMmkdata are: inputdata directory (-d) and site-name (-s). -Inputdata directory is the directory where you have the CESM inputdata files. Finally site-name is the name of the site that you want to run for. Site-name is a Fluxnet site name from the list of sites you are running on (see the --sitegroupname for more information about the site lists). +The required options to PTCLMmkdata are: inputdata directory (-d) and site-name (-s). Inputdata directory is the directory where you have the CESM inputdata files. Finally site-name is the name of the site that you want to run for. Site-name is a Fluxnet site name from the list of sites you are running on (see the --sitegroupname for more information about the site lists). -After PTCLMmkdata is run you can run **create_newcase** to setup a case to use the datasets created. -It also creates a ``README.PTCLM`` in that directory that documents the commandline options to PTCLMmkdata that were used to create it. +After PTCLMmkdata is run you can run **create_newcase** to setup a case to use the datasets created. It also creates a ``README.PTCLM`` in that directory that documents the commandline options to PTCLMmkdata that were used to create it. -After "help" the "list" option is one of the most useful options for getting help on using PTCLMmkdata. -This option gives you information about some of the other options to PTCLMmkdata. To get a list of the sites that can be used for PTCLMmkdata use the "--list" option as follows. +After "help" the "list" option is one of the most useful options for getting help on using PTCLMmkdata. This option gives you information about some of the other options to PTCLMmkdata. To get a list of the sites that can be used for PTCLMmkdata use the "--list" option as follows. :: > cd $CTSMROOT/tools/PTCLM @@ -30,16 +26,14 @@ The output to the above command is as follows: Steps in running PTCLMmkdata ============================ -1. Build the CLM tools - Next you need to make sure all the CLM FORTRAN tools are built. +1. Build the CLM tools Next you need to make sure all the CLM FORTRAN tools are built. :: > cd $CTSMROOT/tools/PTCLM > ./buildtools > gmake clean -2. Run PTCLMmkdata - Next you actually run PTCLMmkdata which does the different things listed below: +2. Run PTCLMmkdata Next you actually run PTCLMmkdata which does the different things listed below: a. PTCLMmkdata names your output file directory based on your input :: @@ -57,26 +51,17 @@ Steps in running PTCLMmkdata > cd scripts > ./PTCLMmkdata -s US-UMB -d $MYCSMDATA - b. PTCLMmkdata creates datasets for you - It will populate $MYCSMDATA with new datasets it creates using the CLM tools. + b. PTCLMmkdata creates datasets for you It will populate $MYCSMDATA with new datasets it creates using the CLM tools. - c. If a transient compset and PTCLMmkdata finds a _dynpftdata.txt file - If you are running a transient compset (such as the "I_1850-2000_CN" compset) AND you there is a file in the PTCLM_sitedata directory under the PTCLMmkdata directory called $SITE_dynpftdata.txt it will use this file for the land-use changes. - Otherwise it will leave land-use constant, unless you use the pftgrid option so it uses the global dataset for landuse changes. - See the Section called Dynamic Land-Use Change Files for use by PTCLMmkdata for more information on this. - There is a sample transient dataset called US-Ha1_dynpftdata.txt. - Transient compsets, are compsets that create transient land-use change and forcing conditions such as: 'I_1850-2000', 'I_1850-2000_CN', 'I_RCP8.5_CN', 'I_RCP6.0_CN', 'I_RCP4.5_CN', or 'I_RCP2.6_CN'. + c. If a transient compset and PTCLMmkdata finds a _dynpftdata.txt file If you are running a transient compset (such as the "I_1850-2000_CN" compset) AND you there is a file in the PTCLM_sitedata directory under the PTCLMmkdata directory called $SITE_dynpftdata.txt it will use this file for the land-use changes. Otherwise it will leave land-use constant, unless you use the pftgrid option so it uses the global dataset for landuse changes. See the Section called Dynamic Land-Use Change Files for use by PTCLMmkdata for more information on this. There is a sample transient dataset called US-Ha1_dynpftdata.txt. Transient compsets, are compsets that create transient land-use change and forcing conditions such as: 'I_1850-2000', 'I_1850-2000_CN', 'I_RCP8.5_CN', 'I_RCP6.0_CN', 'I_RCP4.5_CN', or 'I_RCP2.6_CN'. - d. PTCLMmkdata creates a pft-physiology for you - PTCLMmkdata will create a local copy of the pft-physiology specific for your site that you could then customize with changes specific for that site. + d. PTCLMmkdata creates a pft-physiology for you PTCLMmkdata will create a local copy of the pft-physiology specific for your site that you could then customize with changes specific for that site. - e. PTCLMmkdata creates a README.PTCLM for you - PTCLMmkdata will create a simple text file with the command line for it in a file called README.PTCLM in the case directory it creates for you. + e. PTCLMmkdata creates a README.PTCLM for you PTCLMmkdata will create a simple text file with the command line for it in a file called README.PTCLM in the case directory it creates for you. 3. Run create_newcase pointing to the directory created -4. Customize, setup, build and run case as normal - You then customize your case as you would normally. See the Chapter 1 chapter for more information on doing this. +4. Customize, setup, build and run case as normal You then customize your case as you would normally. See the Chapter 1 chapter for more information on doing this. PTCLMmkdata options ========================= @@ -93,8 +78,7 @@ Configure options include: This option is for running PTCLMmkdata with a different root directory to CESM than the version PTCLMmkdata exists in. Normally you do NOT need to use this option. ``--sitegroupname`` - In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. - These site groups are all separate ASCII files with the same prefix followed by a "_*data.txt" name. See `the Section called PTCLMmkdata Group Site Lists `_ for more information on these files. By default we have provided three different valid group names: + In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. These site groups are all separate ASCII files with the same prefix followed by a "_*data.txt" name. See `the Section called PTCLMmkdata Group Site Lists `_ for more information on these files. By default we have provided three different valid group names: EXAMPLE ------- @@ -102,11 +86,7 @@ AmeriFlux Fluxnet-Canada -The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. -The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. -You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. -Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. -Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ with permission information to use the US-UMB data. +The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ with permission information to use the US-UMB data. ``--donot_use_tower_yrs`` This option is used with the "useQIAN" option to set the years to cycle over for the Qian data. In this case Qian atmospheric forcing will be used, but the simulation will run over the same years that tower site is available for this site. @@ -127,10 +107,8 @@ The options that with a "grid" suffix all mean to create datasets using the glob Because supported single-point datasets already have the data created for them, you MUST use the "nopointdata" and "ndepgrid" options when you are using a supported single-point site. You must use "ndepgrid" even for a compset without CN. You also can NOT use the options: "soilgrid", "pftgrid", "aerdepgrid", or "owritesrfaer". ``--pftgrid`` - This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_pftdata.txt file when creating the surface dataset. - This option must NOT be used when you you are using a site that is a supported single point dataset. + This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_pftdata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. ``--soilgrid`` - This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_soildata.txt file when creating the surface dataset. - This option must NOT be used when you you are using a site that is a supported single point dataset. + This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_soildata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. diff --git a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst index 9dcdd51ac4..9362e93fe8 100644 --- a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst @@ -6,8 +6,7 @@ Running a single point using global data - PTS_MODE **************************************************** -``PTS_MODE`` enables you to run the model using global datasets, but just picking a single point from those datasets and operating on it. -It can be a very quick way to do fast simulations and get a quick turnaround. +``PTS_MODE`` enables you to run the model using global datasets, but just picking a single point from those datasets and operating on it. It can be a very quick way to do fast simulations and get a quick turnaround. To setup a ``PTS_MODE`` simulation you use the "-pts_lat" and "-pts_lon" arguments to **create_newcase** to give the latitude and longitude of the point you want to simulate for (the code will pick the point on the global grid nearest to the point you give. Here's an example to setup a simulation for the nearest point at 2-degree resolution to Boulder Colorado. :: @@ -29,11 +28,6 @@ Then setup, build and run as normal. We make sure initial conditions are NOT use Running in a single processor ============================== -Note, that when running with ``PTS_MODE`` the number of processors is automatically set to one. -When running a single grid point you can only use a single processor. -You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to ``TRUE`` so that you can also run interactively without having to use MPI to start up your job. +Note, that when running with ``PTS_MODE`` the number of processors is automatically set to one. When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to ``TRUE`` so that you can also run interactively without having to use MPI to start up your job. -On many machines, batch queues have a minimum number of nodes or processors that can be used. -On these machines you may have to change the queue and possibly the time-limits of the job, to get it to run in the batch queue. -On the NCAR machine, cheyenne, this is done for you automatically, and the "share" or "caldera" queue is used for such single-processor simulations. -For single point mode you also may want to consider using a smaller workstation or cluster, rather than a super-computer, because you can't take advantage of the multi-processing power of the super-computer anyway. +On many machines, batch queues have a minimum number of nodes or processors that can be used. On these machines you may have to change the queue and possibly the time-limits of the job, to get it to run in the batch queue. On the NCAR machine, cheyenne, this is done for you automatically, and the "share" or "caldera" queue is used for such single-processor simulations. For single point mode you also may want to consider using a smaller workstation or cluster, rather than a super-computer, because you can't take advantage of the multi-processing power of the super-computer anyway. diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index ab3954599f..778deb3220 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -6,9 +6,7 @@ Running Single Point Configurations ****************************************** -In addition to ``PTS_MODE``, CLM supports running using single-point or regional datasets that are customized to a particular region. -CLM supports a a small number of out-of-the-box single-point and regional datasets. -However, users can create their own dataset. +In addition to ``PTS_MODE``, CLM supports running using single-point or regional datasets that are customized to a particular region. CLM supports a a small number of out-of-the-box single-point and regional datasets. However, users can create their own dataset. To get the list of supported dataset resolutions do this: :: @@ -67,16 +65,9 @@ Then setup, build and run normally. Using Supported Single-point Datasets that have their own Atmospheric Forcing ================================================================================ -Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). -Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. -To turn on the atmospheric forcing for these datasets, you set the ``env_run.xml DATM_MODE`` variable to ``CLM1PT``, and then the atmospheric forcing datasets will be used for the point picked. -If you use one of the compsets that has "I1Pt" in the name that will be set automatically. +Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. To turn on the atmospheric forcing for these datasets, you set the ``env_run.xml DATM_MODE`` variable to ``CLM1PT``, and then the atmospheric forcing datasets will be used for the point picked. If you use one of the compsets that has "I1Pt" in the name that will be set automatically. -When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. -If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. -However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. -In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. -For the supported data points, these values are in the XML database and you can use the **queryDefaultNamelist.pl** script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha). +When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. For the supported data points, these values are in the XML database and you can use the **queryDefaultNamelist.pl** script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha). In the example below we will show how to do this for the Vancouver, Canada point. @@ -120,8 +111,7 @@ Example: Running CLM over the single-point of Vancouver Canada with supplied atm Creating your own single-point dataset =================================================== -The following provides an example of setting up a case using ``CLM_USRDAT_NAME`` where you rename the files according to the ``CLM_USRDAT_NAME`` convention. -We have an example of such datafiles in the repository for a specific region over Alaska (actually just a sub-set of the global f19 grid). +The following provides an example of setting up a case using ``CLM_USRDAT_NAME`` where you rename the files according to the ``CLM_USRDAT_NAME`` convention. We have an example of such datafiles in the repository for a specific region over Alaska (actually just a sub-set of the global f19 grid). Example: Using CLM_USRDAT_NAME to run a simulation using user datasets for a specific region over Alaska ----------------------------------------------------------------------------------------------------------------------- diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst index f0adaa0e0c..a927bed53e 100644 --- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst +++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst @@ -6,8 +6,7 @@ Single and Regional Grid Configurations ***************************************** -CLM allows you to set up and run cases with a single-point or a local region as well as global resolutions. -This is often useful for running quick cases for testing, evaluating specific vegetation types, or land-units, or running with observed data for a specific site. +CLM allows you to set up and run cases with a single-point or a local region as well as global resolutions. This is often useful for running quick cases for testing, evaluating specific vegetation types, or land-units, or running with observed data for a specific site. There are three different ways to do this for normal-supported site @@ -28,26 +27,13 @@ There are three different ways to do this for normal-supported site Choosing the right single point options ========================================= -Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see `the Section called Running Supported Single-point/Regional Datasets `_). -All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. -The problem is that there is a very limited set of supported datasets. -You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region. +Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see `the Section called Running Supported Single-point/Regional Datasets `_). All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region. -In general `the Section called Running PTS_MODE configurations `_ is the quick and dirty method that gets you started without having to create datasets -- but has limitations. -It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. -It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts. +In general `the Section called Running PTS_MODE configurations `_ is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts. -Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see `the Section called Creating your own single-point/regional surface datasets `_). -With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. -However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. -This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method. +Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see `the Section called Creating your own single-point/regional surface datasets `_). With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method. -Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. -It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. -A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter `Chapter 6 `_. +Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter `Chapter 6 `_. -Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. -You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. -You may also need to modify DATM to use your forcing data. -And you'll need to change your forcing data to be in a format that DATM can use. In the PTCLMmkdata chapter `the Section called Converting AmeriFlux Data for use by PTCLMmkdata in Chapter 6 `_ section tells you how to use AmeriFlux data for atmospheric forcing. +Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. In the PTCLMmkdata chapter `the Section called Converting AmeriFlux Data for use by PTCLMmkdata in Chapter 6 `_ section tells you how to use AmeriFlux data for atmospheric forcing. diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst index 9c216b5c7b..9e9bacaf1e 100644 --- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst +++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst @@ -6,30 +6,17 @@ Running with historical CO2 forcing ===================================== -In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. -For this example, we will start with the "I_1850-2000_CN" compset that has transient: land-use, Nitrogen and Aerosol deposition already. -You could also use another compset if you didn't want these other features to be transient. -In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the user_nl_datm file. -You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file. +In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the "I_1850-2000_CN" compset that has transient: land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the user_nl_datm file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file. .. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide `_ especially as it pertains to the datm. .. warning:: This section documents the process for doing something that is non-standard. There may be errors with the documentation and process, and you may have to do some work before all of this works for you. If that is the case, we recommend that you do further research into understanding the process and the files, as well as understanding the datm and how it works. You may have to read documentation found in the code for datm as well as "csm_share". -The datm has "streams" files that have rough XML-like syntax and specify the location and file to get data from, as well as information on the variable names and the data locations of the grid points. -The datm expects specific variable names and the datm "maps" the expected variable names from the file to the names expected by datm. -The file we are working with here is a file with a single-point, that covers the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 degrees in longitude). -Since it's a single point it's a little easier to work with than datasets that may be at a given horizontal resolution. -The datm also expects that variables will be in certain units, and only expects a limited number of variables so arbitrary fields can NOT be exchanged this way. -However, the process would be similar for datasets that do contain more than one point. +The datm has "streams" files that have rough XML-like syntax and specify the location and file to get data from, as well as information on the variable names and the data locations of the grid points. The datm expects specific variable names and the datm "maps" the expected variable names from the file to the names expected by datm. The file we are working with here is a file with a single-point, that covers the entire globe (so the vertices go from -90 to 90 degrees in latitude and 0 to 360 degrees in longitude). Since it's a single point it's a little easier to work with than datasets that may be at a given horizontal resolution. The datm also expects that variables will be in certain units, and only expects a limited number of variables so arbitrary fields can NOT be exchanged this way. However, the process would be similar for datasets that do contain more than one point. -The three things that are needed: a domain file, a data file, and a streams text file. -The domain file is a CF-compliant NetCDF file that has information on the grid points (latitudes and longitudes for cell-centers and vertices, mask , fraction, and areas). -The datafile is a CF-compliant NetCDF file with the data that will be mapped. -The streams text file is the XML-like file that tells datm how to find the files and how to map the variables datm knows about to the variable names on the NetCDF files. Note, that in our case the domain file and the data file are the same file. In other cases, the domain file may be separate from the data file. +The three things that are needed: a domain file, a data file, and a streams text file. The domain file is a CF-compliant NetCDF file that has information on the grid points (latitudes and longitudes for cell-centers and vertices, mask, fraction, and areas). The datafile is a CF-compliant NetCDF file with the data that will be mapped. The streams text file is the XML-like file that tells datm how to find the files and how to map the variables datm knows about to the variable names on the NetCDF files. Note, that in our case the domain file and the data file are the same file. In other cases, the domain file may be separate from the data file. -First we are going to create a case, and we will edit the ``user_nl_datm`` so that we add a CO2 data stream in. -There is a streams text file available in ``$CTSMROOT/doc/UsersGuide/co2_streams.txt``, that includes file with a CO2 time-series from 1765 to 2007. +First we are going to create a case, and we will edit the ``user_nl_datm`` so that we add a CO2 data stream in. There is a streams text file available in ``$CTSMROOT/doc/UsersGuide/co2_streams.txt``, that includes file with a CO2 time-series from 1765 to 2007. Example: Transient Simulation with Historical CO2 -------------------------------------------------------------- diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst index 17e2e11d5c..7f210ba151 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst @@ -6,11 +6,9 @@ Running with MOAR data ======================== -Because it takes so long to spinup the CN model (as we just saw previously), if you are doing fully coupled simulations with active atmosphere and ocean, you will want to do the spinup portion of this "offline". -So instead of doing expensive fully coupled simulations for the spinup duration, you run CLM in a very cheap "I" compset using atmospheric forcing from a shorter fully coupled simulation (or a simulation run previously by someone else). +Because it takes so long to spinup the CN model (as we just saw previously), if you are doing fully coupled simulations with active atmosphere and ocean, you will want to do the spinup portion of this "offline". So instead of doing expensive fully coupled simulations for the spinup duration, you run CLM in a very cheap "I" compset using atmospheric forcing from a shorter fully coupled simulation (or a simulation run previously by someone else). -In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on cheyenne. -There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to `Example 4-11 `_. +In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on cheyenne. There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to `Example 4-11 `_. Example: Simulation with MOAR Data on cheyenne ------------------------------------------------------------- diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst index e812576b99..af98005840 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst @@ -6,8 +6,7 @@ Running with atmospheric forcing from a previous simulation ============================================================= -Another way that you might want to spinup the model is to run your own simulation for a relatively short period (either a B, E, or F compset) and then use it as forcing for your "I" case later. -By only running 20 to 50 years for the fully coupled case, you'll save a substantial amount of computer time rather than running the entire spinup period with a fully coupled model. +Another way that you might want to spinup the model is to run your own simulation for a relatively short period (either a B, E, or F compset) and then use it as forcing for your "I" case later. By only running 20 to 50 years for the fully coupled case, you'll save a substantial amount of computer time rather than running the entire spinup period with a fully coupled model. The first thing we need to do is to run a fully coupled case and save the atmospheric coupling fields on a three hourly basis. In this example, we will run on cheyenne and archive the data to a local disk that we can then use in the next simulation. diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst index 806535fa91..3292a2bbf6 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst @@ -6,16 +6,9 @@ Spinning up the Satellite Phenology Model =========================================== -To spin-up the CLMSP model you merely need to run CLMSP for about 50 simulation years starting from arbitrary initial conditions. -You then use the final restart file for initial conditions in other simulations. -Because, this is a straight forward operation we will NOT give the details on how to do that here, but leave it as an exercise for the reader. -See the `Example 4-7 `_ as an example of doing this as the last step for CLMCN. +To spin-up the CLMSP model you merely need to run CLMSP for about 50 simulation years starting from arbitrary initial conditions. You then use the final restart file for initial conditions in other simulations. Because, this is a straight forward operation we will NOT give the details on how to do that here, but leave it as an exercise for the reader. See the `Example 4-7 `_ as an example of doing this as the last step for CLMCN. -You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure SP spinup plot for 1850` shows -spinup behavior for an 1850 SP case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), -initialized with an initial file generated from a GSWP3 atmospheric forcing case. Note that it takes less than 10 years for state variables -such as FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), H2OSOI (soil water), and TSOI (soil temperature) to reach -a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. TWS (total water storage) may take a bit longer. +You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure SP spinup plot for 1850` shows spinup behavior for an 1850 SP case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with an initial file generated from a GSWP3 atmospheric forcing case. Note that it takes less than 10 years for state variables such as FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), H2OSOI (soil water), and TSOI (soil temperature) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. TWS (total water storage) may take a bit longer. .. _Figure SP spinup plot for 1850: @@ -23,8 +16,7 @@ a specified equilibrium state (denoted by the dotted lines) due to the different SP spinup plot for year 1850. Variables examined are FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), TWS (total water storage), H2OSOI (volumetric soil water in layer 8) and TSOI (soil temperature in layer 10). Generated using .../tools/contrib/SpinupStability_SP.ncl. -:numref:`Figure SP spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). -Again, it takes about 10 years to reach equilibrium. +:numref:`Figure SP spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). Again, it takes about 10 years to reach equilibrium. .. _Figure SP spinup plot for 2000 CO2: diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index c289464019..20cbdae1e5 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -6,9 +6,7 @@ Spinup of |version|-BGC-Crop ========================== -To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM **configure**, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 -BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in -total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. +To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM **configure**, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. .. _Figure BGC AD spinup plot for 1850 GSWP3: @@ -16,11 +14,7 @@ total ecosystem carbon disequilibrium takes the longest to satisfy due to slow s BGC AD spinup plot for a year 1850 case with GSWP3 atmospheric forcing. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. -After this you branch from this mode in the "final spinup" (-bgc_spinup off in CLM **configure**, see example below), and run for several hundred simulation years. -:numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 -BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in -total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this -criteria depending on their application. +After this you branch from this mode in the "final spinup" (-bgc_spinup off in CLM **configure**, see example below), and run for several hundred simulation years. :numref:`Figure BGC pAD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC post accelerated decomposition (pAD) case using GSWP3 atmospheric forcing. As before, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy. It can be difficult to meet this strict criteria in less than 1000 years and users may want to relax this criteria depending on their application. .. _Figure BGC pAD spinup plot for 1850 GSWP3: @@ -28,10 +22,7 @@ criteria depending on their application. BGC pAD spinup plot for a year 1850 case with GSWP3 atmospheric forcing and initialization from the end of the BGC AD spinup case. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. -You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows -spinup behavior for an 1850 pAD BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), -initialized with a BGC initial file generated from a GSWP3 atmospheric forcing case. Note that it takes about 10 years for variables -such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. +You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure BGC initialized spinup plot for 1850` shows spinup behavior for an 1850 pAD BGC case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with a BGC initial file generated from a GSWP3 atmospheric forcing case. Note that it takes about 10 years for variables such as TLAI (total leaf area index), GPP (gross primary production), and TWS (total water storage) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. .. _Figure BGC initialized spinup plot for 1850: @@ -39,8 +30,7 @@ such as TLAI (total leaf area index), GPP (gross primary production), and TWS (t BGC initialized spinup plot for year 1850. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. -:numref:`Figure BGC initialized spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). -Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. +:numref:`Figure BGC initialized spinup plot for 2000 CO2` shows spinup behavior for the same case but also changes CO2 to present-day conditions (379ppmv). Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. .. _Figure BGC initialized spinup plot for 2000 CO2: @@ -48,10 +38,7 @@ Again, it takes about 10 years to reach equilibrium for TLAI, GPP, and TWS. BGC initialized spinup plot for year 2000 CO2. Variables examined are TOTECOSYSC (total ecosystem carbon), TOTSOMC (total soil organic matter carbon), TOTVEGC (total vegetation carbon), TLAI (total leaf area index), GPP (gross primary production) and TWS (total water storage). Generated using .../tools/contrib/SpinupStability.ncl. -If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon -equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to -reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a -bit of leaf carbon to give those plant functional types another chance to grow under the new atmospheric forcing or model conditions. +If you use the default initial file and you signficantly change model behavior or atmospheric forcing, and you are concerned about the carbon equilibrium (e.g., TOTECOSYSC, TOTSOMC, TOTVEGC), particularly at high latitudes, then we recommend you put the model back into AD mode to reach a new equilibrium. In this configuration, this will also automatically reseed "dead" plant functional types in the initial file with a bit of leaf carbon to give those plant functional types another chance to grow under the new atmospheric forcing or model conditions. **1. |version| accelerated-decomposition (AD) spinup** For the first step of running 200+ years in "-bgc_spinup on" mode, you will setup a case, and then edit the values in env_build.xml and env_run.xml so that the right configuration is turned on and the simulation is setup to run for the required length of simulation time. So do the following: diff --git a/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst b/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst index db5fcdd793..caa7b86552 100644 --- a/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst +++ b/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst @@ -6,10 +6,7 @@ Running the prognostic crop model =================================== -The prognostic crop model is setup to work with CLM4.0, CLM4.5 or |version| with either BGC or CN (with or without DV). -In order to use the initial condition file, we need to set the ``RUN_TYPE`` to startup rather than ``hybrid`` since the compset for f19 sets up to use an initial condition file without crop active. -To activate the crop model you can choose a compset that has "Crop" in the name such as "I1850Clm50BgcCropCru" or simply add -"-crop" to ``CLM_BLDNML_OPTS`` (or for CLM4.0 add "-crop on" to ``CLM_CONFIG_OPTS``). +The prognostic crop model is setup to work with CLM4.0, CLM4.5 or |version| with either BGC or CN (with or without DV). In order to use the initial condition file, we need to set the ``RUN_TYPE`` to startup rather than ``hybrid`` since the compset for f19 sets up to use an initial condition file without crop active. To activate the crop model you can choose a compset that has "Crop" in the name such as "I1850Clm50BgcCropCru" or simply add "-crop" to ``CLM_BLDNML_OPTS`` (or for CLM4.0 add "-crop on" to ``CLM_CONFIG_OPTS``). Example: Crop Simulation ------------------------------------ diff --git a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst index 33c853a1b5..f4b04c5b59 100644 --- a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst +++ b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst @@ -6,12 +6,7 @@ Running with irrigation =================================== -In CLM4.0 irrigation isn't an allowed option. -In CLM4.5 irrigation can ONLY be used WITH crop. With CLM5.0 irrigation can be used whether crop is on or not -- **BUT** -if crop is off, your surface datasets **HAVE** to have irrigation defined appropriately. Right now *ALL* surface -datasets without crop enabled have irrigation hard-wired on. In order to create datasets with irrigation off, you'd need -to make changes to ``mksurfdata_map`` in order to have all generic crops to be non-irrigated. -To turn on irrigation in |version| we simply add "-irrig on" to ``CLM_BLDNML_OPTS``. +In CLM4.0 irrigation isn't an allowed option. In CLM4.5 irrigation can ONLY be used WITH crop. With CLM5.0 irrigation can be used whether crop is on or not -- **BUT** if crop is off, your surface datasets **HAVE** to have irrigation defined appropriately. Right now *ALL* surface datasets without crop enabled have irrigation hard-wired on. In order to create datasets with irrigation off, you'd need to make changes to ``mksurfdata_map`` in order to have all generic crops to be non-irrigated. To turn on irrigation in |version| we simply add "-irrig on" to ``CLM_BLDNML_OPTS``. Example: Irrigation Simulation ------------------------------------------ diff --git a/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst b/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst index 63423e211a..4f6a46a7d5 100644 --- a/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst +++ b/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst @@ -6,9 +6,7 @@ What is a special case? ========================= -All of the following special cases cases that take more than one step to do. -The straightforward cases have compsets and/or build-namelist use-cases setup for them or require simple editing of a single-case. -All of the cases here require you to do at least two simulations with different configurations, or require more complex editing of the case (changing the streams files). +All of the following special cases cases that take more than one step to do. The straightforward cases have compsets and/or build-namelist use-cases setup for them or require simple editing of a single-case. All of the cases here require you to do at least two simulations with different configurations, or require more complex editing of the case (changing the streams files). .. note:: The cases in this chapter are more sophisticated and require more technical knowledge and skill than cases in previous chapters. The user should be very familiar with doing simple cases before moving onto the cases described here. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index dc289d00d6..a081f9e869 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -6,16 +6,11 @@ Choosing a compset ==================== -When setting up a new case one of the first choices to make is which "component set" (or compset) to use. -The compset refers to which component models are used as well as specific settings for them. -We label the different types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). -The compsets of interest when working with CLM are the "I" compsets (which contain CLM with a data atmosphere model and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain CLM with the active atmosphere model (CAM), prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. -Below we go into details on the "I" compsets which emphasize CLM as the only active model, and just mention the two other categories. +When setting up a new case one of the first choices to make is which "component set" (or compset) to use. The compset refers to which component models are used as well as specific settings for them. We label the different types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). The compsets of interest when working with CLM are the "I" compsets (which contain CLM with a data atmosphere model and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain CLM with the active atmosphere model (CAM), prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. Below we go into details on the "I" compsets which emphasize CLM as the only active model, and just mention the two other categories. To run CLM coupled to CAM ("E" or "F" compsets) or fully coupled ("B compsets) you need to be running CLM from a CESM checkout rather than a CTSM checkout (see :ref:`ctsm_vs_cesm_checkout`). -When working with CLM you usually want to start with a relevant "I" compset before moving to the more complex cases that involve other active model components. -The "I" compsets can exercise CLM in a way that is similar to the coupled modes, but with much lower computational cost and faster turnaround times. +When working with CLM you usually want to start with a relevant "I" compset before moving to the more complex cases that involve other active model components. The "I" compsets can exercise CLM in a way that is similar to the coupled modes, but with much lower computational cost and faster turnaround times. Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) ------------------------------------------------------------------------- @@ -26,8 +21,7 @@ Here is the entire list of compsets available. `CESM compsets `_ -Note that using the "-user_compset" option even more combinations are possible. To get a list of the compsets use the "query_config" -command as follows: +Note that using the "-user_compset" option even more combinations are possible. To get a list of the compsets use the "query_config" command as follows: :: $CTSMROOT/cime/scripts/query_config --compsets clm @@ -42,6 +36,4 @@ Fully coupled compsets are compsets that start with "B" in the name. They are de Conclusion to choosing a compset -------------------------------- -We've introduced the basic type of compsets that use CLM and given some further details for the "standalone CLM" (or "I" compsets). -The `$CTSMROOT/cime_config/config_compsets.xml `_ lists all of the compsets and gives a full description of each of them. -In the next section we look into customizing the setup time options for compsets using CLM. +We've introduced the basic type of compsets that use CLM and given some further details for the "standalone CLM" (or "I" compsets). The `$CTSMROOT/cime_config/config_compsets.xml `_ lists all of the compsets and gives a full description of each of them. In the next section we look into customizing the setup time options for compsets using CLM. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index 3f11fffa89..5321e471c2 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -6,9 +6,7 @@ Customizing CLM's Configuration ******************************** -The section of the |cesmrelease| Quickstart `CESM Create a Case `_ gives instructions on creating a case. -Also see a similar section in the CIME User's-Guide `CIME Create a case `_. -What is of interest here is how to customize your use of CLM for the case that you created. +The section of the |cesmrelease| Quickstart `CESM Create a Case `_ gives instructions on creating a case. Also see a similar section in the CIME User's-Guide `CIME Create a case `_. What is of interest here is how to customize your use of CLM for the case that you created. For CLM when **preview_namelist**, **case.build**, or **case.run** are called there are two steps that take place: @@ -20,8 +18,7 @@ When customizing your case at the **case.setup** step you are able to modify the There are five different types of customization for the configuration that we will discuss: |version| in |cesmrelease| build-time options, |version| in |cesmrelease| run-time options, User Namelist, other noteworthy |cesmrelease| configuration items, the CLM **configure** script options, and the CLM **build-namelist** script options. -Information on all of the CLM script, configuration, build and run items is found under ``$CTSMROOT/cime_config/config_component.xml``. -See `CLM CASEROOT Variable Definitions `_. +Information on all of the CLM script, configuration, build and run items is found under ``$CTSMROOT/cime_config/config_component.xml``. See `CLM CASEROOT Variable Definitions `_. ================================ CLM Script configuration items @@ -46,14 +43,7 @@ For the precedence of the different options to **build-namelist** see the sectio The first item ``CLM_CONFIG_OPTS`` has to do with customizing the CLM build-time options for your case, the rest all have to do with generating the namelist. CLM_CONFIG_OPTS - The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. - It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. - You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. - Hence, we recommend using the "-append" option to the xmlchange script. - In `the Section called More information on the CLM configure script `_ below we will go into more details on options that can be customized in the CLM "**configure**" script. - It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). - The options to CLM **configure** are given with the "-help" option which is given in `the Section called More information on the CLM configure script `_. - .. note:: ``CLM_CONFIG_OPTS`` is locked after the **case.build** script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun **case.build**. The other env variables can be changed at run-time so are never locked. + The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. Hence, we recommend using the "-append" option to the xmlchange script. In `the Section called More information on the CLM configure script `_ below we will go into more details on options that can be customized in the CLM "**configure**" script. It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). The options to CLM **configure** are given with the "-help" option which is given in `the Section called More information on the CLM configure script `_... note:: ``CLM_CONFIG_OPTS`` is locked after the **case.build** script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun **case.build**. The other env variables can be changed at run-time so are never locked. CLM_NML_USE_CASE ``CLM_NML_USE_CASE`` is used to set a particular set of conditions that set multiple namelist items, all centering around a particular usage of the model. To list the valid options do the following: @@ -113,8 +103,7 @@ CLM_NML_USE_CASE .. note::See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. CLM_BLDNML_OPTS - The option CLM_BLDNML_OPTS is for passing options to the CLM "build-namelist" script. - As with the CLM "configure" script the CLM $CTSMROOT/cime_config/buildnml may already invoke certain options and as such those options will NOT be available to be set here. The best way to see what options can be sent to the "build-namelist" script is to do + The option CLM_BLDNML_OPTS is for passing options to the CLM "build-namelist" script. As with the CLM "configure" script the CLM $CTSMROOT/cime_config/buildnml may already invoke certain options and as such those options will NOT be available to be set here. The best way to see what options can be sent to the "build-namelist" script is to do :: > cd $CTSMROOT/bld @@ -260,8 +249,7 @@ CLM_BLDNML_OPTS (i.e. CLM_NML_USE_CASE env_run variable) 5. values from the namelist defaults file. -The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. -Hence only the following different options can be set: +The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set: 1. -bgc_spinup @@ -311,9 +299,7 @@ To see a list of valid variables that you could set do this: "-ignore_ic_year" ignores the Initial Conditions (IC) year for finding initial condition files to startup from. The date is used, but the year is ignored. Without this option or the "-ignore_ic_date" option below, the date and year of the file comes into play. -When "-irrig on" is used **build-namelist** will try to find surface datasets that have the irrigation model enabled (when running -with Sattellitte Phenology). When running with the prognostic crop model on, "-irrig on" will turn irrigate crops on, while "-irrig off" -will manage all crop areas as rain-fed without irrigation. +When "-irrig on" is used **build-namelist** will try to find surface datasets that have the irrigation model enabled (when running with Sattellitte Phenology). When running with the prognostic crop model on, "-irrig on" will turn irrigate crops on, while "-irrig off" will manage all crop areas as rain-fed without irrigation. "no-megan" means do NOT add the MEGAN model Biogenic Volatile Organic Compounds (BVOC) namelist to the driver. This namelist is created by default, so normally this WILL be done. This is a driver namelist, so unless "no-megan" is specified the CLM **build-namelist** will create the ``drv_flds_in`` file that the driver will copy over and use (if you are running with CAM and CAM produces this file as well, it's file will have precedence). @@ -354,10 +340,7 @@ will manage all crop areas as rain-fed without irrigation. when set to on, *requires* that your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it will use an initial condition file if it can find an appropriate one, and otherwise do a cold start. ``CLM_FORCE_COLDSTART`` is a good way to ensure that you are doing a cold start if that is what you want to do. ``CLM_USRDAT_NAME`` - Provides a way to enter your own datasets into the namelist. - The files you create must be named with specific naming conventions outlined in: `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. - To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. - For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be: + Provides a way to enter your own datasets into the namelist. The files you create must be named with specific naming conventions outlined in: `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be: :: > cd $CTSMROOT/bld @@ -368,10 +351,7 @@ will manage all crop areas as rain-fed without irrigation. .. note: See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. ``CLM_CO2_TYPE`` - sets the type of input CO2 for either "constant", "diagnostic" or prognostic". - If "constant" the value from ``CCSM_CO2_PPMV`` will be used. - If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. - For more information on how to send CO2 from the data atmosphere model see `the Section called Running stand-alone CLM with transient historical CO2 concentration in Chapter 4 `_. + sets the type of input CO2 for either "constant", "diagnostic" or prognostic". If "constant" the value from ``CCSM_CO2_PPMV`` will be used. If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. For more information on how to send CO2 from the data atmosphere model see `the Section called Running stand-alone CLM with transient historical CO2 concentration in Chapter 4 `_. =============== User Namelist @@ -501,10 +481,7 @@ Like other datasets, if you want to use a given initial condition file to be use Other noteworthy configuration items ------------------------------------ -For running "I" cases there are several other noteworthy configuration items that you may want to work with. -Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM -settings is `here `_. -If you are running an B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files +For running "I" cases there are several other noteworthy configuration items that you may want to work with. Most of these involve settings for the DATM, but one ``CCSM_CO2_PPMV`` applies to all models. The list of DATM settings is `here `_. If you are running an B, E, or F case that doesn't use the DATM obviously the DATM_* settings will not be used. All of the settings below are in your ``env_build.xml`` and ``env_run.xml`` files :: CCSM_CO2_PPMV @@ -534,12 +511,10 @@ If you are running an B, E, or F case that doesn't use the DATM obviously the DA CPLHISTForcing ``CLMCRUNCEP`` - The standard mode for CLM4.5 of using global atmospheric data that was developed by CRU using NCEP data from 1901 to 2010 (version 4 of this series). - See `the Section called CLMCRUNCEP mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. + The standard mode for CLM4.5 of using global atmospheric data that was developed by CRU using NCEP data from 1901 to 2010 (version 4 of this series). See `the Section called CLMCRUNCEP mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. ``CLMCRUNCEPv7`` - Version 7 of the CRUNCEP data from 1901 to 2016. - See `the Section called CLMCRUNCEPv7 mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. + Version 7 of the CRUNCEP data from 1901 to 2016. See `the Section called CLMCRUNCEPv7 mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. ``CLMGSWP3v1`` GSWP3 version 1 forcing data based on NCEP reanalysis with bias corrections by GSWP3 from 1901 to 2010. @@ -694,5 +669,4 @@ The output to the above command is as follows: no-nitrif Turn the Nitrification/denitrification off [no-vert,no-cent,no-nitrif,no-vert:no-cent] -We've given details on how to use the options in env_build.xml and env_run.xml to interact with the CLM "configure" and "build-namelist" scripts, as well as giving a good understanding of how these scripts work and the options to them. -In the next section we give further details on the CLM namelist. You could customize the namelist for these options after "case.setup" is run. +We've given details on how to use the options in env_build.xml and env_run.xml to interact with the CLM "configure" and "build-namelist" scripts, as well as giving a good understanding of how these scripts work and the options to them. In the next section we give further details on the CLM namelist. You could customize the namelist for these options after "case.setup" is run. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst index 017317ad6e..afd850d458 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst @@ -8,9 +8,7 @@ Once a case has run **case.setup**, we can then customize the case further, by editing the run-time namelist for CLM. First let's list the definition of each namelist item and their valid values, and then we'll list the default values for them. Next for some of the most used or tricky namelist items we'll give examples of their use, and give you example namelists that highlight these features. -In the following, various examples of namelists are provided that feature the use of different namelist options to customize a case for particular uses. -Most the examples revolve around how to customize the output history fields. -This should give you a good basis for setting up your own CLM namelist. +In the following, various examples of namelists are provided that feature the use of different namelist options to customize a case for particular uses. Most the examples revolve around how to customize the output history fields. This should give you a good basis for setting up your own CLM namelist. ----------------------------------------------------- Definition of Namelist items and their default values @@ -111,8 +109,7 @@ Example 1-2. Default CLM Namelist Adding/removing fields on your primary history file --------------------------------------------------- -The primary history files are output monthly, and contain an extensive list of fieldnames, but the list of fieldnames can be added to using ``hist_fincl1`` or removed from by adding fieldnames to ``hist_fexcl1``. -A sample user namelist ``user_nl_clm`` adding few new fields (cosine of solar zenith angle, and solar declination) and excluding a few standard fields is (ground temperature, vegetation temperature, soil temperature and soil water).: +The primary history files are output monthly, and contain an extensive list of fieldnames, but the list of fieldnames can be added to using ``hist_fincl1`` or removed from by adding fieldnames to ``hist_fexcl1``. A sample user namelist ``user_nl_clm`` adding few new fields (cosine of solar zenith angle, and solar declination) and excluding a few standard fields is (ground temperature, vegetation temperature, soil temperature and soil water).: Example 1-3. Example user_nl_clm namelist adding and removing fields on primary history file -------------------------------------------------------------------------------------------- @@ -124,18 +121,11 @@ Example 1-3. Example user_nl_clm namelist adding and removing fields on primary Adding auxiliary history files and changing output frequency ------------------------------------------------------------ -The ``hist_fincl2`` through ``hist_fincl6`` set of namelist variables add given history fieldnames to auxiliary history file "streams", and ``hist_fexcl2`` through ``hist_fexcl6`` set of namelist variables remove given history fieldnames from history file auxiliary "streams". -A history "stream" is a set of history files that are produced at a given frequency. -By default there is only one stream of monthly data files. -To add more streams you add history fieldnames to ``hist_fincl2`` through ``hist_fincl6``. -The output frequency and the way averaging is done can be different for each history file stream. -By default the primary history files are monthly and any others are daily. You can have up to six active history streams, but you need to activate them in order. So if you activate stream "6" by setting ``hist_fincl6``, but if any of ``hist_fincl2`` through ``hist_fincl5`` are unset, only the history streams up to the first blank one will be activated. +The ``hist_fincl2`` through ``hist_fincl6`` set of namelist variables add given history fieldnames to auxiliary history file "streams", and ``hist_fexcl2`` through ``hist_fexcl6`` set of namelist variables remove given history fieldnames from history file auxiliary "streams". A history "stream" is a set of history files that are produced at a given frequency. By default there is only one stream of monthly data files. To add more streams you add history fieldnames to ``hist_fincl2`` through ``hist_fincl6``. The output frequency and the way averaging is done can be different for each history file stream. By default the primary history files are monthly and any others are daily. You can have up to six active history streams, but you need to activate them in order. So if you activate stream "6" by setting ``hist_fincl6``, but if any of ``hist_fincl2`` through ``hist_fincl5`` are unset, only the history streams up to the first blank one will be activated. The frequency of the history file streams is given by the namelist variable ``hist_nhtfrq`` which is an array of rank six for each history stream. The values of the array ``hist_nhtfrq`` must be integers, where the following values have the given meaning: -*Positive value* means the output frequency is the number of model steps between output. -*Negative value* means the output frequency is the absolute value in hours given (i.e -1 would mean an hour and -24 would mean a full day). Daily (-24) is the default value for all auxiliary files. -*Zero* means the output frequency is monthly. This is the default for the primary history files. +*Positive value* means the output frequency is the number of model steps between output. *Negative value* means the output frequency is the absolute value in hours given (i.e -1 would mean an hour and -24 would mean a full day). Daily (-24) is the default value for all auxiliary files. *Zero* means the output frequency is monthly. This is the default for the primary history files. The number of samples on each history file stream is given by the namelist variable ``hist_mfilt`` which is an array of rank six for each history stream. The values of the array ``hist_mfilt`` must be positive integers. By default the primary history file stream has one time sample on it (i.e. output is to separate monthly files), and all other streams have thirty time samples on them. @@ -155,12 +145,7 @@ Example: user_nl_clm namelist adding auxiliary history files and changing output Removing all history fields --------------------------- -Sometimes for various reasons you want to remove all the history fields either because you want to do testing without any output, or you only want a very small custom list of output fields rather than the default extensive list of fields. -By default only the primary history files are active, so technically using ``hist_fexcl1`` explained in the first example, you could list ALL of the history fields that are output in ``hist_fexcl1`` and then you wouldn't get any output. -However, as the list is very extensive this would be a cumbersome thing to do. -So to facilitate this ``hist_empty_htapes`` allows you to turn off all default output. -You can still use ``hist_fincl1`` to turn your own list of fields on, but you then start from a clean slate. -A sample user namelist ``user_nl_clm`` turning off all history fields and then activating just a few selected fields (ground and vegetation temperatures and absorbed solar radiation) is: +Sometimes for various reasons you want to remove all the history fields either because you want to do testing without any output, or you only want a very small custom list of output fields rather than the default extensive list of fields. By default only the primary history files are active, so technically using ``hist_fexcl1`` explained in the first example, you could list ALL of the history fields that are output in ``hist_fexcl1`` and then you wouldn't get any output. However, as the list is very extensive this would be a cumbersome thing to do. So to facilitate this ``hist_empty_htapes`` allows you to turn off all default output. You can still use ``hist_fincl1`` to turn your own list of fields on, but you then start from a clean slate. A sample user namelist ``user_nl_clm`` turning off all history fields and then activating just a few selected fields (ground and vegetation temperatures and absorbed solar radiation) is: Example 1-5. Example user_nl_clm namelist removing all history fields --------------------------------------------------------------------- @@ -172,18 +157,14 @@ Example 1-5. Example user_nl_clm namelist removing all history fields Various ways to change history output averaging flags ----------------------------------------------------- -There are two ways to change the averaging of output history fields. -The first is using ``hist_avgflag_pertape`` which gives a default value for each history stream, the second is when you add fields using ``hist_fincl*``, you add an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would output the maximum of TSOI). -The types of averaging that can be done are: +There are two ways to change the averaging of output history fields. The first is using ``hist_avgflag_pertape`` which gives a default value for each history stream, the second is when you add fields using ``hist_fincl*``, you add an averaging flag to the end of the field name after a colon (for example 'TSOI:X', would output the maximum of TSOI). The types of averaging that can be done are: - *A* Average, over the output interval. - *I* Instantaneous, output the value at the output interval. - *X* Maximum, over the output interval. - *M* Minimum, over the output interval. -The default averaging depends on the specific fields, but for most fields is an average. -A sample user namelist ``user_nl_clm`` making the monthly output fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), and adding auxiliary file streams for instantaneous (6-hourly), maximum (daily), minimum (daily), and average (daily). -For some of the fields we diverge from the per-tape value given and customize to some different type of optimization. +The default averaging depends on the specific fields, but for most fields is an average. A sample user namelist ``user_nl_clm`` making the monthly output fields all averages (except TSOI for the first two streams and FIRE for the 5th stream), and adding auxiliary file streams for instantaneous (6-hourly), maximum (daily), minimum (daily), and average (daily). For some of the fields we diverge from the per-tape value given and customize to some different type of optimization. Example: user_nl_clm namelist with various ways to average history fields ------------------------------------------------------------------------------------- @@ -203,27 +184,16 @@ Example: user_nl_clm namelist with various ways to average history fields hist_avgflag_pertape = 'A', 'I', 'X', 'M', 'A' hist_nhtfrq = 0, -6, -24, -24, -24 -In the example we put the same list of fields on each of the tapes: soil-temperature, ground temperature, vegetation temperature, emitted longwave radiation, reflected solar radiation, sensible heat, total latent-heat, and total water storage. -We also modify the soil-temperature for the primary and secondary auxiliary tapes by outputting them for a maximum instead of the prescribed per-tape of average and instantaneous respectively. -For the tertiary auxiliary tape we output ground temperature instantaneous instead of as a maximum, and for the fourth auxiliary tape we output vegetation temperature instantaneous instead of as a minimum. -Finally, for the fifth auxiliary tapes we output ``FIRE`` instantaneously instead of as an average. +In the example we put the same list of fields on each of the tapes: soil-temperature, ground temperature, vegetation temperature, emitted longwave radiation, reflected solar radiation, sensible heat, total latent-heat, and total water storage. We also modify the soil-temperature for the primary and secondary auxiliary tapes by outputting them for a maximum instead of the prescribed per-tape of average and instantaneous respectively. For the tertiary auxiliary tape we output ground temperature instantaneous instead of as a maximum, and for the fourth auxiliary tape we output vegetation temperature instantaneous instead of as a minimum. Finally, for the fifth auxiliary tapes we output ``FIRE`` instantaneously instead of as an average. .. note:: We also use ``hist_empty_htapes`` as in the previous example, so we can list ONLY the fields that we want on the primary history tapes. Outputting history files as a vector in order to analyze the plant function types within gridcells -------------------------------------------------------------------------------------------------- -By default the output to history files are the grid-cell average of all land-units, and vegetation types within that grid-cell, and output is on the full 2D latitude/longitude grid with ocean masked out. -Sometimes it's important to understand how different land-units or vegetation types are acting within a grid-cell. -The way to do this is to output history files as a 1D-vector of all land-units and vegetation types. -In order to display this, you'll need to do extensive post-processing to make sense of the output. -Often you may only be interested in a few points, so once you figure out the 1D indices for the grid-cells of interest, you can easily view that data. -1D vector output can also be useful for single point datasets, since it's then obvious that all data is for the same grid cell. +By default the output to history files are the grid-cell average of all land-units, and vegetation types within that grid-cell, and output is on the full 2D latitude/longitude grid with ocean masked out. Sometimes it's important to understand how different land-units or vegetation types are acting within a grid-cell. The way to do this is to output history files as a 1D-vector of all land-units and vegetation types. In order to display this, you'll need to do extensive post-processing to make sense of the output. Often you may only be interested in a few points, so once you figure out the 1D indices for the grid-cells of interest, you can easily view that data. 1D vector output can also be useful for single point datasets, since it's then obvious that all data is for the same grid cell. -To do this you use ``hist_dov2xy`` which is an array of rank six for each history stream. -Set it to ``.false.`` if you want one of the history streams to be a 1D vector. -You can also use ``hist_type1d_pertape`` if you want to average over all the: Plant-Function-Types, columns, land-units, or grid-cells. -A sample user namelist ``user_nl_clm`` leaving the primary monthly files as 2D, and then doing grid-cell (GRID), column (COLS), and no averaging over auxiliary tapes output daily for a single field (ground temperature) is: +To do this you use ``hist_dov2xy`` which is an array of rank six for each history stream. Set it to ``.false.`` if you want one of the history streams to be a 1D vector. You can also use ``hist_type1d_pertape`` if you want to average over all the: Plant-Function-Types, columns, land-units, or grid-cells. A sample user namelist ``user_nl_clm`` leaving the primary monthly files as 2D, and then doing grid-cell (GRID), column (COLS), and no averaging over auxiliary tapes output daily for a single field (ground temperature) is: Example: user_nl_clm namelist outputting some files in 1D Vector format ----------------------------------------------------------------------- @@ -242,10 +212,4 @@ Example: user_nl_clm namelist outputting some files in 1D Vector format .. note:: Technically the default for hist_nhtfrq is for primary files output monthly and the other auxiliary tapes for daily, so we don't actually have to include hist_nhtfrq, we could use the default for it. Here we specify it for clarity. -Visualizing global 1D vector files will take effort. -You'll probably want to do some post-processing and possibly just extract out single points of interest to see what is going on. -Since, the output is a 1D vector, of only land-points traditional plots won't be helpful. -The number of points per grid-cell will also vary for anything, but grid-cell averaging. -You'll need to use the output fields pfts1d_ixy, and pfts1d_jxy, to get the mapping of the fields to the global 2D array. -pfts1d_itype_veg gives you the PFT number for each PFT. -Most likely you'll want to do this analysis in a data processing tool (such as NCL, Matlab, Mathmatica, IDL, etcetera that is able to read and process NetCDF data files). +Visualizing global 1D vector files will take effort. You'll probably want to do some post-processing and possibly just extract out single points of interest to see what is going on. Since, the output is a 1D vector, of only land-points traditional plots won't be helpful. The number of points per grid-cell will also vary for anything, but grid-cell averaging. You'll need to use the output fields pfts1d_ixy, and pfts1d_jxy, to get the mapping of the fields to the global 2D array. pfts1d_itype_veg gives you the PFT number for each PFT. Most likely you'll want to do this analysis in a data processing tool (such as NCL, Matlab, Mathmatica, IDL, etcetera that is able to read and process NetCDF data files). diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst index 68c1180370..df55e46b22 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst @@ -11,11 +11,7 @@ When running "I" compsets with CLM you use the DATM model to give atmospheric fo 1. **DATM Main Namelist and Stream Namlist gorup** (``datm_in``) 2. **DATM stream files** -The `Data Model Documentation `_ gives the details of all the options for the data models and for DATM specifically. -It goes into detail on all namelist items both for DATM and for DATM streams. -So here we won't list ALL of the DATM namelist options, nor go into great details about stream files. -But, we will talk about a few of the different options that are relevant for running with CLM. -All of the options for changing the namelists or stream files is done by editing the ``user_nl_datm`` file. +The `Data Model Documentation `_ gives the details of all the options for the data models and for DATM specifically. It goes into detail on all namelist items both for DATM and for DATM streams. So here we won't list ALL of the DATM namelist options, nor go into great details about stream files. But, we will talk about a few of the different options that are relevant for running with CLM. All of the options for changing the namelists or stream files is done by editing the ``user_nl_datm`` file. Because, they aren't useful for work with CLM we will NOT discuss any of the options for the main DATM namelist. Use the DATM Users Guide at the link above to find details of that. For the streams namelist we will discuss three items: @@ -32,9 +28,7 @@ mapalgo ``mapalgo`` sets the spatial interpolation method to go from the DATM input data to the output DATM model grid. The default is ``bilinear``. For ``CLM1PT`` we set it to ``nn`` to just select the nearest neighbor. This saves time and we also had problems running the interpolation for single-point mode. taxmode - ``taxmode`` is the time axis mode. - For CLM we usually have it set to ``cycle`` which means that once the end of the data is reached it will start over at the beginning. - The extend modes is used have it use the last time-step of the forcing data once it reaches the end of forcing data (or use the first time-step before it reaches where the forcing data starts). See the warning below about the extend mode. + ``taxmode`` is the time axis mode. For CLM we usually have it set to ``cycle`` which means that once the end of the data is reached it will start over at the beginning. The extend modes is used have it use the last time-step of the forcing data once it reaches the end of forcing data (or use the first time-step before it reaches where the forcing data starts). See the warning below about the extend mode. .. warning:: *THE extend OPTION NEEDS TO BE USED WITH CAUTION!* It is only invoked by default for the CLM1PT mode and is only intended for the supported urban datasets to extend the data for a single time-step. If you have the model *run extensively through periods in this mode you will effectively be repeating that last time-step over that entire period*. This means the output of your simulation will be worthless. @@ -54,23 +48,13 @@ In the sections below we go over each of the relevant ``DATM_MODE`` options and CLMGSWP3v1 mode and it's DATM settings -------------------------------------- -In ``CLMGSWP3v1`` mode the GSWP3 NCEP forcing dataset is used and all of it's data is on a 3-hourly interval. -Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity, Long-Wave down and wind). -The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. -``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution). +In ``CLMGSWP3v1`` mode the GSWP3 NCEP forcing dataset is used and all of it's data is on a 3-hourly interval. Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity, Long-Wave down and wind). The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution). ---------------------------------------- CLMCRUNCEPv7 mode and it's DATM settings ---------------------------------------- -In ``CLMCRUNCEPv7`` mode the CRUNCEP dataset is used and all of it's data is on a 6-hourly interval. -Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). -The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. -``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution). - -.. note:: The "everything else" data stream (of temperature, pressure, humidity and wind) also includes the data for longwave downward forcing as well. Our simulations showed sensitivity to this field, so we backed off in using it, and let DATM calculate longwave down from the other fields. +In ``CLMCRUNCEPv7`` mode the CRUNCEP dataset is used and all of it's data is on a 6-hourly interval. Like ``CLM_QIAN`` the dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input exact half degree grid to the grid the atmosphere model is being run at (to run at this same model resolution use the 360x720cru_360x720cru resolution)... note:: The "everything else" data stream (of temperature, pressure, humidity and wind) also includes the data for longwave downward forcing as well. Our simulations showed sensitivity to this field, so we backed off in using it, and let DATM calculate longwave down from the other fields. For more information on CRUNCEP forcing see `http://dods.extra.cea.fr/data/p529viov/cruncep/ `_. @@ -84,11 +68,7 @@ CLMCRUNCEP mode and it's DATM settings CLM_QIAN mode and it's DATM settings ------------------------------------ -In ``CLM_QIAN`` mode the Qian dataset is used which has 6-hourly solar and precipitation data, and 3-hourly for everything else. -The dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). -The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. -``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input T62 grid to the grid the atmosphere model is being run at. +In ``CLM_QIAN`` mode the Qian dataset is used which has 6-hourly solar and precipitation data, and 3-hourly for everything else. The dataset is divided into those three data streams: solar, precipitation, and everything else (temperature, pressure, humidity and wind). The time-stamps of the data were also adjusted so that they are the beginning of the interval for solar, and the middle for the other two. Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is: ``coszen``, ``nearest``, and ``linear`` for the solar, precipitation and other data respectively. ``taxmode`` is set to ``cycle`` and ``mapalgo`` is set to ``bilinear`` so that the data is spatially interpolated from the input T62 grid to the grid the atmosphere model is being run at. Normally you wouldn't customize the ``CLM_QIAN`` settings, but you might replicate it's use for your own global data that had similar temporal characteristics. @@ -96,15 +76,7 @@ Normally you wouldn't customize the ``CLM_QIAN`` settings, but you might replica CLM1PT mode and it's DATM settings ---------------------------------- -In ``CLM1PT`` mode the model is assumed to have half-hourly or hourly data for a single-point. -For the supported datasets that is exactly what it has. -But, if you add your own data you may need to make adjustments accordingly. -Using the ``CLM_USRDAT_NAME`` resolution you can easily extend this mode for your own datasets that may be regional or even global and could be at different temporal frequencies. -If you do so you'll need to make adjustments to your DATM settings. -The dataset has all data in a single stream file. -The time-stamps of the data were also adjusted so that they are at the middle of the interval. -Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is set to ``nearest``. -``taxmode`` is set to ``extend`` and ``mapalgo`` is set to ``nn`` so that simply the nearest point is used. +In ``CLM1PT`` mode the model is assumed to have half-hourly or hourly data for a single-point. For the supported datasets that is exactly what it has. But, if you add your own data you may need to make adjustments accordingly. Using the ``CLM_USRDAT_NAME`` resolution you can easily extend this mode for your own datasets that may be regional or even global and could be at different temporal frequencies. If you do so you'll need to make adjustments to your DATM settings. The dataset has all data in a single stream file. The time-stamps of the data were also adjusted so that they are at the middle of the interval. Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is set to ``nearest``. ``taxmode`` is set to ``extend`` and ``mapalgo`` is set to ``nn`` so that simply the nearest point is used. If you are using your own data for this mode and it's not at least hourly you'll want to adjust the DATM settings for it. If the data is three or six hourly, you'll need to divide it up into separate streams like in ``CLM_QIAN`` mode which will require fairly extensive changes to the DATM namelist and streams files. For an example of doing this see `Example 5-8 `_. @@ -112,15 +84,6 @@ If you are using your own data for this mode and it's not at least hourly you'll CPLHISTForcing mode and it's DATM settings ------------------------------------------ -In ``CPLHISTForcing`` mode the model is assumed to have 3-hourly for a global grid from a previous CESM simulation. -Like ``CLM_QIAN`` mode the data is divided into three streams: one for precipitation, one for solar, and one for everything else. -The time-stamps for Coupler history files for CESM is at the end of the interval, so the ``offset`` needs to be set in order to adjust the time-stamps to what it needs to be for the ``tintalgo`` settings. -For precipitation ``taxmode`` is set to ``nearest`` so the ``offset`` is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. -For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` seconds so that the ending time-step is adjust by three hours to the beginning of the interval. -For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. -For an example of such a case see `the Section called Running with MOAR data as atmospheric forcing to spinup the model in Chapter 4 `_. - -Normally you wouldn't modify the DATM settings for this mode. -However, if you had data at a different frequency than 3-hours you would need to modify the ``offset`` and possibly the ``taxmode``. -The other two things that you might modify would be the path to the data or the domain file for the resolution (which is currently hardwired to f09). -For data at a different input resolution you would need to change the domain file in the streams file to use a domain file to the resolution that the data comes in on. +In ``CPLHISTForcing`` mode the model is assumed to have 3-hourly for a global grid from a previous CESM simulation. Like ``CLM_QIAN`` mode the data is divided into three streams: one for precipitation, one for solar, and one for everything else. The time-stamps for Coupler history files for CESM is at the end of the interval, so the ``offset`` needs to be set in order to adjust the time-stamps to what it needs to be for the ``tintalgo`` settings. For precipitation ``taxmode`` is set to ``nearest`` so the ``offset`` is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` seconds so that the ending time-step is adjust by three hours to the beginning of the interval. For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For an example of such a case see `the Section called Running with MOAR data as atmospheric forcing to spinup the model in Chapter 4 `_. + +Normally you wouldn't modify the DATM settings for this mode. However, if you had data at a different frequency than 3-hours you would need to modify the ``offset`` and possibly the ``taxmode``. The other two things that you might modify would be the path to the data or the domain file for the resolution (which is currently hardwired to f09). For data at a different input resolution you would need to change the domain file in the streams file to use a domain file to the resolution that the data comes in on. diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index d5e93de728..c821ba19e7 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -6,24 +6,12 @@ Testing ******* -Technically, you could use the customization we gave in `Chapter 1 `_ to test various configuration and namelist options for CLM. -Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. -It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. -To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. -There are two types of testing scripts for CLM. -The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. -The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. -Below we will go into further details of how to use both methods. +Technically, you could use the customization we gave in `Chapter 1 `_ to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods. CIME Testing scripts ==================== -We first introduce the test scripts that work for all CESM components. -The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. -See `CIME Chapter on Testing `_ for how to use it to run single -tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as -well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also -see the `CTSM Wiki on Testing `_. +We first introduce the test scripts that work for all CESM components. The CIME script **create_test** runs a specific type of test, at a given resolution, for a given compset using a given machine. See `CIME Chapter on Testing `_ for how to use it to run single tests as well as lists of tests. The standard testname for CLM is "aux_clm" for cheyenne with intel and gnu compilers as well as the CGD machine hobart for intel, nag, and pgi compilers. There's also a shorter test list called "clm_short". Also see the `CTSM Wiki on Testing `_. CTSM Tools Testing ================== diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst index e45ba2f362..6fc53c3a89 100644 --- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst +++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst @@ -110,17 +110,14 @@ The second method is to use the local index along with the processor number:: write(iulog,*)'CNCStateUpdate1Mod +leafc_xfer_to_leafc: ',cf_veg%leafc_xfer_to_leafc_patch(p)*dt end if -By placing these write statements in the code, one can get a sense of how leafc is evolving toward a negative state and why. -This is a very complex example of troubleshooting. To make a long story short, as described `here `_, the error turned out to be caused by a few lines in the phenology code that weren't handling a 20 minute time step properly, thus an actual bug in the code. This was also a good example of where a much less computationally expensive land-only simulation was able to be used for debugging instead of the orginal expensive fully-coupled simulation. +By placing these write statements in the code, one can get a sense of how leafc is evolving toward a negative state and why. This is a very complex example of troubleshooting. To make a long story short, as described `here `_, the error turned out to be caused by a few lines in the phenology code that weren't handling a 20 minute time step properly, thus an actual bug in the code. This was also a good example of where a much less computationally expensive land-only simulation was able to be used for debugging instead of the orginal expensive fully-coupled simulation. Another method of troubleshooting is to use the **point_of_interest** module. Use the point_of_interest module -------------------------------- -It is common, when debugging, to want to print the values of various variables for all patches or columns of certain landunit types within a certain grid cell of interest. For example, one might be able to identify a certain grid cell with an erroneous value for a particular history field variable (e.g., GPP) using for example ncview. Once the latitude and longitude of this grid cell has been determined, the point_of_interest module (**src/utils/point_of_interest.F90**) helps create the logical functions needed to do this. -This module is compiled into every CTSM build, but is not invoked by default. -To use it +It is common, when debugging, to want to print the values of various variables for all patches or columns of certain landunit types within a certain grid cell of interest. For example, one might be able to identify a certain grid cell with an erroneous value for a particular history field variable (e.g., GPP) using for example ncview. Once the latitude and longitude of this grid cell has been determined, the point_of_interest module (**src/utils/point_of_interest.F90**) helps create the logical functions needed to do this. This module is compiled into every CTSM build, but is not invoked by default. To use it (1) Enter in the latitude/longitude of the point of interest in the function **at_poi** in **point_of_interest.F90** by setting the variables **poi_lat** and **poi_lon**. @@ -196,9 +193,5 @@ Along the same lines, you might try running a simpler case, trying another comps Run with a debugger ------------------- -Another suggestion is to run the model with a debugger such as: **ddt**, **dbx**, **gdb**, or **totalview**. -Often to run with a debugger you will need to reduce the number of processors as outlined above. -Some debuggers such as **dbx** will only work with one processor, while more advanced debuggers such as **totalview** can work with both MPI tasks and OMP threads. -Even simple debuggers though can be used to query core files, to see where the code was at when it died (for example using the **where** in **dbx** for a core file can be very helpful. -For help in running with a debugger you will need to contact your system administrators for the machine you are running on. +Another suggestion is to run the model with a debugger such as: **ddt**, **dbx**, **gdb**, or **totalview**. Often to run with a debugger you will need to reduce the number of processors as outlined above. Some debuggers such as **dbx** will only work with one processor, while more advanced debuggers such as **totalview** can work with both MPI tasks and OMP threads. Even simple debuggers though can be used to query core files, to see where the code was at when it died (for example using the **where** in **dbx** for a core file can be very helpful. For help in running with a debugger you will need to contact your system administrators for the machine you are running on. diff --git a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst index b41c574b14..09725c8afc 100644 --- a/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/building-the-clm-tools.rst @@ -4,16 +4,9 @@ .. include:: ../substitutions.rst -The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools -**cprnc** and **gen_domain** use the CIME configure/build system which is described in the next section. +The CLM FORTRAN tools all have similar makefiles, and similar options for building. The tools **cprnc** and **gen_domain** use the CIME configure/build system which is described in the next section. -The Makefiles (for **mksurfdata_map** and **mkprocdata_map**) use GNU Make extensions and thus require that you use GNU make to use them. -They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. -There are also environment variables that can be set to set things that must be customized. -All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. -On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. -The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. -Finally the tools allow you to turn optimization on (which is off by default but on for **mksurfdata_map**) with the OPT flag so that the tool will run faster. +The Makefiles (for **mksurfdata_map** and **mkprocdata_map**) use GNU Make extensions and thus require that you use GNU make to use them. They also auto detect the type of platform you are on, using "uname -s" and set the compiler, compiler flags and such accordingly. There are also environment variables that can be set to set things that must be customized. All the tools use NetCDF and hence require the path to the NetCDF libraries and include files. On some platforms (such as Linux) multiple compilers can be used, and hence there are env variables that can be set to change the FORTRAN and/or "C" compilers used. The tools also allow finer control, by also allowing the user to add compiler flags they choose, for both FORTRAN and "C", as well as picking the compiler, linker and and add linker options. Finally the tools allow you to turn optimization on (which is off by default but on for **mksurfdata_map**) with the OPT flag so that the tool will run faster. Options used by all: **mksurfdata_map** @@ -108,7 +101,5 @@ The *README.filecopies* (which can be found in ``$CTSMROOT/tools``) is repeated **cprnc** and *gen_domain** both use the CIME configure/build system rather than the CLM specific version described above. -See `CIME documentation on adding grids `_ for -more information on adding grids, creating mapping files, and running **gen_domain**. Also see the CIME file: -``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build **gen_domain**. +See `CIME documentation on adding grids `_ for more information on adding grids, creating mapping files, and running **gen_domain**. Also see the CIME file: ``$CTSMROOT/tools/mapping/gen_domain_files/INSTALL`` for how to build **gen_domain**. diff --git a/doc/source/users_guide/using-clm-tools/cprnc.rst b/doc/source/users_guide/using-clm-tools/cprnc.rst index 5076bc296b..67ea63e638 100644 --- a/doc/source/users_guide/using-clm-tools/cprnc.rst +++ b/doc/source/users_guide/using-clm-tools/cprnc.rst @@ -6,13 +6,7 @@ Comparing History Files ========================= -**cprnc** is a tool shared by |cesmrelease| to compare two NetCDF history files. -It differences every field that is shared on both files, and reports a summary of the difference. -The summary includes the three largest differences, as well as the root mean square (RMS) difference. -It also gives some summary information on the field as well. -You have to enter at least one file, and up to two files. -With one file it gives you summary information on the file, and with two it gives you information on the differences between the two. -At the end it will give you a summary of the fields compared and how many fields were different and how many were identical. +**cprnc** is a tool shared by |cesmrelease| to compare two NetCDF history files. It differences every field that is shared on both files, and reports a summary of the difference. The summary includes the three largest differences, as well as the root mean square (RMS) difference. It also gives some summary information on the field as well. You have to enter at least one file, and up to two files. With one file it gives you summary information on the file, and with two it gives you information on the differences between the two. At the end it will give you a summary of the fields compared and how many fields were different and how many were identical. Options: diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst index 85458b3707..202881bf20 100644 --- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst +++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst @@ -6,8 +6,7 @@ Creating CLM domain files ***************************** -*gen_domain* to create a domain file for datm from a mapping file. **gen_domain** is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of **mknoocnmap.pl** (see `the Section called Using mknocnmap.pl to create grid and maps for single-point regional grids `_) to create a regional or single-point map file that is then run through **gen_domain** to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the -$CIMEROOT/tools/mapping/gen_domain_files/README `_ file for more help on **gen_domain**. +*gen_domain* to create a domain file for datm from a mapping file. **gen_domain** is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of **mknoocnmap.pl** (see `the Section called Using mknocnmap.pl to create grid and maps for single-point regional grids `_) to create a regional or single-point map file that is then run through **gen_domain** to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README `_ file for more help on **gen_domain**. Here we create domain files for a regular global domain. diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 07967cd60e..9c6e8a1f20 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -9,8 +9,7 @@ Creating input for surface dataset generation 1. Generating SCRIP grid files ================================== -The utility ``mkmapdata.sh`` requires SCRIP format input files to describe the input and output grids that maps are generated for. CLM provides a utility, ``mkmapgrids`` that generates those files. -The program converts old formats of CAM or CLM grid files to SCRIP grid format. There is also a NCL script (``mkscripgrid.ncl``) to create regular latitude longitude regional or single-point grids at the resolution the user desires. +The utility ``mkmapdata.sh`` requires SCRIP format input files to describe the input and output grids that maps are generated for. CLM provides a utility, ``mkmapgrids`` that generates those files. The program converts old formats of CAM or CLM grid files to SCRIP grid format. There is also a NCL script (``mkscripgrid.ncl``) to create regular latitude longitude regional or single-point grids at the resolution the user desires. SCRIP grid files for all the standard model resolutions and the raw surface datasets have already been done and the files are in the XML database. Hence, this step doesn't need to be done -- EXCEPT WHEN YOU ARE CREATING YOUR OWN GRIDS. @@ -44,13 +43,7 @@ See :numref:`Figure mknoocnmap.pl` for a visual representation of this process. ``mkmapdata.sh`` uses the above SCRIP grid input files to create SCRIP mapping data files (uses ESMF). -The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. -Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. -Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. -See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. -The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. -You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map** (see `the Section called Running mksurfdata.pl `_ below). -mkmapdata.sh has a help option with the following +The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map** (see `the Section called Running mksurfdata.pl `_ below). mkmapdata.sh has a help option with the following :: ../../tools/mkmapdata/mkmapdata.sh diff --git a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst index 02efb2492d..4ddd738b5d 100644 --- a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst +++ b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst @@ -4,15 +4,6 @@ Datasets for Observational Sites ================================== -There are two ways to customize datasets for a particular observational site. -The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. -Depending on the tool it might be easier to do it one way or the other. -In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. -Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. -Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. -For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. -And PTCLM uses these methods to customize datasets see `Chapter 6 `_. +There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. -Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. -See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. -Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. +Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. diff --git a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst index 29a0b96326..8fafca1df0 100644 --- a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst @@ -6,15 +6,6 @@ Observational Sites Datasets ******************************* -There are two ways to customize datasets for a particular observational site. -The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. -Depending on the tool it might be easier to do it one way or the other. -In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. -Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. -Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. -For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. -And PTCLM uses these methods to customize datasets see `Chapter 6 `_. +There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. -Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. -See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. -Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. +Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst index 30cb1d9e1d..dd650a79e9 100644 --- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst @@ -6,14 +6,9 @@ What are the CLM tools ======================== -There are several tools provided with CLM that allow you to create your own input datasets at resolutions you choose, or to interpolate initial conditions to a different resolution, or used to compare CLM history files between different cases. -The tools are all available in the ``$CTSMROOT/tools`` directory. -Most of the tools are FORTRAN stand-alone programs in their own directory, but there is also a suite of NCL scripts in the ``$CTSMROOT/tools//ncl_scripts`` directory, and some of the tools are scripts that may also call the ESMF regridding program. -Some of the NCL scripts are very specialized and not meant for general use, and we won't document them here. -They still contain documentation in the script itself and the README file in the tools directory. +There are several tools provided with CLM that allow you to create your own input datasets at resolutions you choose, or to interpolate initial conditions to a different resolution, or used to compare CLM history files between different cases. The tools are all available in the ``$CTSMROOT/tools`` directory. Most of the tools are FORTRAN stand-alone programs in their own directory, but there is also a suite of NCL scripts in the ``$CTSMROOT/tools//ncl_scripts`` directory, and some of the tools are scripts that may also call the ESMF regridding program. Some of the NCL scripts are very specialized and not meant for general use, and we won't document them here. They still contain documentation in the script itself and the README file in the tools directory. -The tools produce files that can be used for CLM4.5 and |version|. They do **NOT** produce files that can be used for CLM4.0. -If you need files for CLM4.0, you'll need to use a previous version of CLM. +The tools produce files that can be used for CLM4.5 and |version|. They do **NOT** produce files that can be used for CLM4.0. If you need files for CLM4.0, you'll need to use a previous version of CLM. The list of generally important scripts and programs are as follows. @@ -29,30 +24,22 @@ The list of generally important scripts and programs are as follows. #. *$CIMEROOT/tools/cprnc* to compare two NetCDF files. -In the sections to come we will go into detailed description of how to use each of these tools in turn. -First, however we will discuss the common environment variables and options that are used by all of the FORTRAN tools. -Second, we go over the outline of the entire file creation process for all input files needed by CLM for a new resolution, then we turn to each tool. -In the last section we will discuss how to customize files for particular observational sites. +In the sections to come we will go into detailed description of how to use each of these tools in turn. First, however we will discuss the common environment variables and options that are used by all of the FORTRAN tools. Second, we go over the outline of the entire file creation process for all input files needed by CLM for a new resolution, then we turn to each tool. In the last section we will discuss how to customize files for particular observational sites. The FORTRAN tools (mksurfdata_map and mkprocdata_map) run, with a namelist (mksurfdata_map) to provide options, or with command line arguments (mkprocdata_map). -In the following sections, we will outline how to make these files available for build-namelist so that you can easily create simulations that include them. -In the chapter on single-point and regional datasets we also give an alternative way to enter new datasets without having to edit files. +In the following sections, we will outline how to make these files available for build-namelist so that you can easily create simulations that include them. In the chapter on single-point and regional datasets we also give an alternative way to enter new datasets without having to edit files. ------------------------------------ Running FORTRAN tools with namelists ------------------------------------ -**mksurfdata_map** runs with a namelist that is read from standard input. -Hence, you create a namelist and then run them by redirecting the namelist file into standard input as follows: +**mksurfdata_map** runs with a namelist that is read from standard input. Hence, you create a namelist and then run them by redirecting the namelist file into standard input as follows: :: ./program < namelist -There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_map/mksurfdata_map.namleist`` that shows you what the -namelist should look like. **mksurfdata_map** also has a script that creates the namelist and runs the program for you. -Namelists that you create should be similar to the example namelist. -The namelist values are also documented along with the other namelists in the: +There is a sample namelist called ``$CTSMROOT/tools/mksurfdata_map/mksurfdata_map.namleist`` that shows you what the namelist should look like. **mksurfdata_map** also has a script that creates the namelist and runs the program for you. Namelists that you create should be similar to the example namelist. The namelist values are also documented along with the other namelists in the: :: $CTSMROOT/bld/namelist_files/namelist_definition.xml`` file @@ -63,25 +50,16 @@ The namelist values are also documented along with the other namelists in the: Running FORTRAN tools with command line options ----------------------------------------------- -**gen_domain**, mkprocdata_map, and **cprnc** run with command line arguments. -The detailed sections below will give you more information on the command line arguments specific to each tool. -Also running the tool without any arguments will give you a general synopsis on how to run the tool. +**gen_domain**, mkprocdata_map, and **cprnc** run with command line arguments. The detailed sections below will give you more information on the command line arguments specific to each tool. Also running the tool without any arguments will give you a general synopsis on how to run the tool. ----------------------------------------- Running FORTRAN tools built with SMP=TRUE ----------------------------------------- -When you enable ``SMP=TRUE`` on your build of one of the tools that make use of it, you are using OpenMP for shared memory parallelism (SMP). -In SMP loops are run in parallel with different threads run on different processors all of which access the same memory (called on-node). -Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. -For example, on the NCAR machine cheyenne there are 36 processors per node, so you can use up to 36 processors. +When you enable ``SMP=TRUE`` on your build of one of the tools that make use of it, you are using OpenMP for shared memory parallelism (SMP). In SMP loops are run in parallel with different threads run on different processors all of which access the same memory (called on-node). Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. For example, on the NCAR machine cheyenne there are 36 processors per node, so you can use up to 36 processors. --------- Using NCL --------- -In the tools directory ``$CTSMROOT/tools/ncl_scripts`` and in a few other locations there are scripts that use NCAR Command Language (NCL). -Unlike the FORTRAN tools, you will need to get a copy of NCL in order to use them. -You also won't have to build an executable in order to use them, hence no Makefile is provided. -NCL is provided for free download as either binaries or source code from: `http://www.ncl.ucar.edu/ `_. -The NCL web-site also contains documentation on NCL and it's use. These scripts are stand-alone and at most use environment variables to control how to use them. In some cases there are perl scripts with command line arguments that call the NCL scripts to control what they do. +In the tools directory ``$CTSMROOT/tools/ncl_scripts`` and in a few other locations there are scripts that use NCAR Command Language (NCL). Unlike the FORTRAN tools, you will need to get a copy of NCL in order to use them. You also won't have to build an executable in order to use them, hence no Makefile is provided. NCL is provided for free download as either binaries or source code from: `http://www.ncl.ucar.edu/ `_. The NCL web-site also contains documentation on NCL and it's use. These scripts are stand-alone and at most use environment variables to control how to use them. In some cases there are perl scripts with command line arguments that call the NCL scripts to control what they do. From 189086595734910995067e54eb7948b64eb19f9a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 19 Oct 2023 11:13:25 -0600 Subject: [PATCH 1665/2067] Removing duplicate lines of code #2129 #2107 --- src/biogeochem/CNVegCarbonStateType.F90 | 1 - src/biogeophys/BareGroundFluxesMod.F90 | 4 ---- 2 files changed, 5 deletions(-) diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index 7515051d38..8ce278c166 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -1612,7 +1612,6 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c3_r2 else this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c4_r2 - this%leafc_storage_patch(i) = c12_cnveg_carbonstate_inst%leafc_storage_patch(i) * c4_r2 endif end do end if diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 645b908157..7dfa83820d 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -306,10 +306,6 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & ulrad(p) = 0._r8 dhsdt_canopy(p) = 0._r8 eflx_sh_stem(p) = 0._r8 - z0mv(p) = 0._r8 - z0hv(p) = 0._r8 - z0qv(p) = 0._r8 - ur(p) = max(params_inst%wind_min,sqrt(forc_u(g)*forc_u(g)+forc_v(g)*forc_v(g))) dth(p) = thm(p)-t_grnd(c) From c3d0b0f1e55405c49caa5fa782396412571b5b55 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 11:30:01 -0600 Subject: [PATCH 1666/2067] Replace \* with * to fix VSCode rendering. --- doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst | 4 ++-- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 2 +- .../CLM50_Tech_Note_External_Nitrogen_Cycle.rst | 2 +- .../tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst | 6 +++--- doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst | 14 +++++++------- .../CLM50_Tech_Note_Photosynthesis.rst | 8 ++++---- .../CLM50_Tech_Note_Surface_Albedos.rst | 2 +- .../users_guide/running-PTCLM/using-ptclm.rst | 4 ++-- 8 files changed, 21 insertions(+), 21 deletions(-) diff --git a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst index 3e8dab983f..f1dd139cb5 100644 --- a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst +++ b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst @@ -97,9 +97,9 @@ In :eq:`29.5`, :math:`u_{*s}` is defined as the wind friction speed (m s\ :sup:` .. math:: :label: 29.12 - u_{\*s} = \left\{ + u_{*s} = \left\{ \begin{array}{lr} - u_{\*} & \quad {\rm \; for \;} U_{10} `). These parameters are all calculated separately at each layer to define a profile of anoxic porespace fraction in the soil. -The nitrification/denitrification models used here also predict fluxes of N\ :sub:`2`\ O via a "hole-in-the-pipe" approach (:ref:`Firestone and Davidson, 1989 `). A constant fraction (6 \* 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction of denitrification going to N\ :sub:`2`\ O, \ :math:`{P}_{N2:N2O}`, is variable, following the Century (:ref:`del Grosso et al. 2000 `) approach: +The nitrification/denitrification models used here also predict fluxes of N\ :sub:`2`\ O via a "hole-in-the-pipe" approach (:ref:`Firestone and Davidson, 1989 `). A constant fraction (6 * 10\ :math:`{}^{-4}`, :ref:`Li et al. 2000 `) of the nitrification flux is assumed to be N\ :sub:`2`\ O, while the fraction of denitrification going to N\ :sub:`2`\ O, \ :math:`{P}_{N2:N2O}`, is variable, following the Century (:ref:`del Grosso et al. 2000 `) approach: .. math:: :label: 22.5) diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index 01f609b0a1..38daab9774 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -80,7 +80,7 @@ The surface vertical kinematic fluxes of momentum :math:`\overline{u'w'}` and :m \frac{k\left(z-d\right)}{q_{*} } \frac{\partial q}{\partial z} =\phi _{w} \left(\zeta \right) -where :math:`z` is height in the surface layer (m), :math:`d` is the displacement height (m), :math:`L` is the Monin-Obukhov length scale (m) that accounts for buoyancy effects resulting from vertical density gradients (i.e., the atmospheric stability), k is the von Karman constant (:numref:`Table Physical constants`), and :math:`\left|{\it u}\right|` is the atmospheric wind speed (m s\ :sup:`-1`). :math:`\phi _{m}`, :math:`\phi _{h}`, and :math:`\phi _{w}` are universal (over any surface) similarity functions of :math:`\zeta` that relate the constant fluxes of momentum, sensible heat, and latent heat to the mean profile gradients of :math:`\left|{\it u}\right|`, :math:`\theta`, and :math:`q` in the surface layer. In neutral conditions, :math:`\phi _{m} =\phi _{h} =\phi _{w} =1`. The velocity (i.e., friction velocity) :math:`u_{\*}` (m s\ :sup:`-1`), temperature :math:`\theta _{\*}` (K), and moisture :math:`q_{\*}` (kg kg\ :sup:`-1`) scales are +where :math:`z` is height in the surface layer (m), :math:`d` is the displacement height (m), :math:`L` is the Monin-Obukhov length scale (m) that accounts for buoyancy effects resulting from vertical density gradients (i.e., the atmospheric stability), k is the von Karman constant (:numref:`Table Physical constants`), and :math:`\left|{\it u}\right|` is the atmospheric wind speed (m s\ :sup:`-1`). :math:`\phi _{m}`, :math:`\phi _{h}`, and :math:`\phi _{w}` are universal (over any surface) similarity functions of :math:`\zeta` that relate the constant fluxes of momentum, sensible heat, and latent heat to the mean profile gradients of :math:`\left|{\it u}\right|`, :math:`\theta`, and :math:`q` in the surface layer. In neutral conditions, :math:`\phi _{m} =\phi _{h} =\phi _{w} =1`. The velocity (i.e., friction velocity) :math:`u_{*}` (m s\ :sup:`-1`), temperature :math:`\theta _{*}` (K), and moisture :math:`q_{*}` (kg kg\ :sup:`-1`) scales are .. math:: :label: 5.13 @@ -203,7 +203,7 @@ where :math:`w_{*}` is the convective velocity scale .. math:: :label: 5.29 - w_{*} =\left(\frac{-gu_{\*} \theta _{v*} z_{i} }{\overline{\theta _{v,\, atm} }} \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } , + w_{*} =\left(\frac{-gu_{*} \theta _{v*} z_{i} }{\overline{\theta _{v,\, atm} }} \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } , :math:`z_{i} =1000` is the convective boundary layer height (m), and :math:`\beta =1`. @@ -610,7 +610,7 @@ The roughness lengths used to calculate :math:`r_{am}`, :math:`r_{ah}`, and :mat z_{0h,\, g} =z_{0w,\, g} =z_{0m,\, g} e^{-a\left({u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon } \right)^{0.45} } -where the quantity :math:`{u_{\*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. +where the quantity :math:`{u_{*} z_{0m,\, g} \mathord{\left/ {\vphantom {u_{*} z_{0m,\, g} \upsilon }} \right.} \upsilon }` is the roughness Reynolds number (and may be interpreted as the Reynolds number of the smallest turbulent eddy in the flow) with the kinematic viscosity of air :math:`\upsilon =1.5\times 10^{-5}` m\ :sup:`2` s\ :sup:`-1` and :math:`a=0.13`. The numerical solution for the fluxes of momentum, sensible heat, and water vapor flux from non-vegetated surfaces proceeds as follows: diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index e84947265f..c1654074be 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -63,7 +63,7 @@ The surface roughnesses are functions of the lake state and atmospheric forcing. \begin{array}{l} {R_{0} =\frac{z_{0m} u_{*} }{\nu } ,} \\ {z_{0h} =z_{0q} =z_{0m} \exp \left\{-0.13R_{0} ^{0.45} \right\}} \end{array} -where :math:`R_{0}` is the near-surface atmospheric roughness Reynolds number, :math:`z_{0h}` is the roughness length for sensible heat, :math:`z_{0q}` is the roughness length for latent heat, :math:`\nu` (m\ :sup:`2` s\ :sup:`-1`) is the kinematic viscosity of air, and :math:`u_{\*}` (m s\ :sup:`-1`) is the friction velocity in the atmospheric surface layer. For frozen lakes without resolved snow layers, :math:`z_{0m} =1\times 10^{-3} {\rm m}` (:ref:`Subin et al. (2012a) `), and the scalar roughness lengths are given by. +where :math:`R_{0}` is the near-surface atmospheric roughness Reynolds number, :math:`z_{0h}` is the roughness length for sensible heat, :math:`z_{0q}` is the roughness length for latent heat, :math:`\nu` (m\ :sup:`2` s\ :sup:`-1`) is the kinematic viscosity of air, and :math:`u_{*}` (m s\ :sup:`-1`) is the friction velocity in the atmospheric surface layer. For frozen lakes without resolved snow layers, :math:`z_{0m} =1\times 10^{-3} {\rm m}` (:ref:`Subin et al. (2012a) `), and the scalar roughness lengths are given by. For unfrozen lakes, *z*\ :sub:`0m` is given by (:ref:`Subin et al. (2012a) `) @@ -88,7 +88,7 @@ where .. math:: :label: 12.6 - \begin{array}{l} {C=C_{\min } +(C_{\max } -C_{\min } )\exp \left\{-\min \left(A,B\right)\right\}} \\ {A={\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } \mathord{\left/ {\vphantom {\left(\frac{Fg}{u_{\*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } f_{c} }} \right.} f_{c} } } \\ {B=\varepsilon \frac{\sqrt{dg} }{u} } \end{array} + \begin{array}{l} {C=C_{\min } +(C_{\max } -C_{\min } )\exp \left\{-\min \left(A,B\right)\right\}} \\ {A={\left(\frac{Fg}{u_{*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } \mathord{\left/ {\vphantom {\left(\frac{Fg}{u_{*} ^{2} } \right)^{{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} } f_{c} }} \right.} f_{c} } } \\ {B=\varepsilon \frac{\sqrt{dg} }{u} } \end{array} where *A* and *B* define the fetch- and depth-limitation, respectively; :math:`C_{\min } =0.01` , :math:`C_{\max } =0.01`, @@ -231,7 +231,7 @@ where the partial derivatives are \frac{\partial G}{\partial T_{g} } =\frac{2\lambda _{T} }{\Delta z_{T} } . -The fluxes of momentum, sensible heat, and water vapor are solved for simultaneously with lake surface temperature as follows. The stability-related equations are the same as for non-vegetated surfaces (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), except that the surface roughnesses are here (weakly varying) functions of the friction velocity :math:`u_{\*}`. To begin, *z*\ :sub:`0m` is set based on the value calculated for the last timestep (for :math:`T_{g} >T_{f}` ) or based on the values in section :numref:`Surface Properties Lake` (otherwise), and the scalar roughness lengths are set based on the relationships in section :numref:`Surface Properties Lake`. +The fluxes of momentum, sensible heat, and water vapor are solved for simultaneously with lake surface temperature as follows. The stability-related equations are the same as for non-vegetated surfaces (section :numref:`Sensible and Latent Heat Fluxes for Non-Vegetated Surfaces`), except that the surface roughnesses are here (weakly varying) functions of the friction velocity :math:`u_{*}`. To begin, *z*\ :sub:`0m` is set based on the value calculated for the last timestep (for :math:`T_{g} >T_{f}` ) or based on the values in section :numref:`Surface Properties Lake` (otherwise), and the scalar roughness lengths are set based on the relationships in section :numref:`Surface Properties Lake`. #. An initial guess for the wind speed :math:`V_{a}` including the convective velocity :math:`U_{c}` is obtained from :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m s\ :sup:`-1` for stable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` as evaluated from :eq:`5.50`) and :math:`U_{c} =0.5` for unstable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). @@ -243,11 +243,11 @@ The fluxes of momentum, sensible heat, and water vapor are solved for simultaneo #. Thermal conductivity :math:`\lambda _{T}` \ (above) -#. Friction velocity :math:`u_{\*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) +#. Friction velocity :math:`u_{*}` (:eq:`5.32`, :eq:`5.33`, :eq:`5.34`, :eq:`5.35`) -#. Potential temperature scale :math:`\theta _{\*}` (:eq:`5.37`, :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) +#. Potential temperature scale :math:`\theta _{*}` (:eq:`5.37`, :eq:`5.38`, :eq:`5.39`, :eq:`5.40`) -#. Humidity scale :math:`q_{\*}` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) +#. Humidity scale :math:`q_{*}` (:eq:`5.41`, :eq:`5.42`, :eq:`5.43`, :eq:`5.44`) #. Aerodynamic resistances :math:`r_{am}`, :math:`r_{ah}`, and :math:`r_{aw}` (:eq:`5.55`, :eq:`5.56`, :eq:`5.57`) @@ -268,7 +268,7 @@ where the last term on the right side of equation is the change in saturated spe #. Saturated specific humidity :math:`q_{sat}^{T_{g} }` and its derivative :math:`\frac{dq_{sat}^{T_{g} } }{dT_{g} }` are updated for :math:`T_{g}^{n+1}` (section :numref:`Monin-Obukhov Similarity Theory`). -#. Virtual potential temperature scale :math:`\theta _{v\*}` (:eq:`5.17`) +#. Virtual potential temperature scale :math:`\theta _{v*}` (:eq:`5.17`) #. Wind speed including the convective velocity, :math:`V_{a}` (:eq:`5.24`) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 0648a039da..dd65058532 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -114,14 +114,14 @@ The RuBP carboxylase (Rubisco) limited rate of carboxylation :math:`A_{c}` (:mat .. math:: :label: 9.3 - A_{c} =\left\{\begin{array}{l} {\frac{V_{c\max } \left(c_{i} -\Gamma _{\*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{\*} \ge 0. + A_{c} =\left\{\begin{array}{l} {\frac{V_{c\max } \left(c_{i} -\Gamma _{*} \right)}{c_{i} +K_{c} \left(1+{o_{i} \mathord{\left/ {\vphantom {o_{i} K_{o} }} \right.} K_{o} } \right)} \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {V_{c\max } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{*} \ge 0. The maximum rate of carboxylation allowed by the capacity to regenerate RuBP (i.e., the light-limited rate) :math:`A_{j}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is .. math:: :label: 9.4 - A_{j} =\left\{\begin{array}{l} {\frac{J_{x}\left(c_{i} -\Gamma _{\*} \right)}{4c_{i} +8\Gamma _{\*} } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {\alpha (4.6\phi )\qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{\*} \ge 0. + A_{j} =\left\{\begin{array}{l} {\frac{J_{x}\left(c_{i} -\Gamma _{*} \right)}{4c_{i} +8\Gamma _{*} } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {\alpha (4.6\phi )\qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}\qquad \qquad c_{i} -\Gamma _{*} \ge 0. The product-limited rate of carboxylation for C\ :sub:`3` plants and the PEP carboxylase-limited rate of carboxylation for C\ :sub:`4` plants :math:`A_{p}` (:math:`\mu` \ mol CO\ :sub:`2` m\ :sup:`-2` s\ :sup:`-1`) is @@ -130,7 +130,7 @@ The product-limited rate of carboxylation for C\ :sub:`3` plants and the PEP car A_{p} =\left\{\begin{array}{l} {3T_{p\qquad } \qquad \qquad {\rm for\; C}_{{\rm 3}} {\rm \; plants}} \\ {k_{p} \frac{c_{i} }{P_{atm} } \qquad \qquad \qquad {\rm for\; C}_{{\rm 4}} {\rm \; plants}} \end{array}\right\}. -In these equations, :math:`c_{i}` is the internal leaf CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{\*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), taken as :math:`T_{p} =0.167V_{c\max }` so that :math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in :ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` mol\ :sup:`-1` photon). :math:`\phi` is the absorbed photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`), which is converted to photosynthetic photon flux assuming 4.6 :math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope of C\ :sub:`4` CO\ :sub:`2` response curve. +In these equations, :math:`c_{i}` is the internal leaf CO\ :sub:`2` partial pressure (Pa) and :math:`o_{i} =0.20P_{atm}` is the O\ :sub:`2` partial pressure (Pa). :math:`K_{c}` and :math:`K_{o}` are the Michaelis-Menten constants (Pa) for CO\ :sub:`2` and O\ :sub:`2`. :math:`\Gamma _{*}` (Pa) is the CO\ :sub:`2` compensation point. :math:`V_{c\max }` is the maximum rate of carboxylation (µmol m\ :sup:`-2` s\ :sup:`-1`, Chapter :numref:`rst_Photosynthetic Capacity`) and :math:`J_{x}` is the electron transport rate (µmol m\ :sup:`-2` s\ :sup:`-1`). :math:`T_{p}` is the triose phosphate utilization rate (µmol m\ :sup:`-2` s\ :sup:`-1`), taken as :math:`T_{p} =0.167V_{c\max }` so that :math:`A_{p} =0.5V_{c\max }` for C\ :sub:`3` plants (as in :ref:`Collatz et al. 1992 `). For C\ :sub:`4` plants, the light-limited rate :math:`A_{j}` varies with :math:`\phi` in relation to the quantum efficiency (:math:`\alpha =0.05` mol CO\ :sub:`2` mol\ :sup:`-1` photon). :math:`\phi` is the absorbed photosynthetically active radiation (W m\ :sup:`-2`) (section :numref:`Solar Fluxes`), which is converted to photosynthetic photon flux assuming 4.6 :math:`\mu` \ mol photons per joule. :math:`k_{p}` is the initial slope of C\ :sub:`4` CO\ :sub:`2` response curve. For C\ :sub:`3` plants, the electron transport rate depends on the photosynthetically active radiation absorbed by the leaf. A common expression is the smaller of the two roots of the equation @@ -236,7 +236,7 @@ with :math:`Q_{10} =2`. +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ | :math:`K_{o}` | 36380 | – | +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ - | :math:`\Gamma _{\*}` | 37830 | – | + | :math:`\Gamma _{*}` | 37830 | – | +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ In the model, acclimation is implemented as in :ref:`Kattge and Knorr (2007) `. In this parameterization, :math:`V_{c\max }` and :math:`J_{\max }` vary with the plant growth temperature. This is achieved by allowing :math:`\Delta S`\ to vary with growth temperature according to diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index d4670c2389..54c50486f1 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -530,7 +530,7 @@ For each constituent (ice, two black carbon species, two organic carbon species, \tau _{k} =\psi _{k} w_{k} -The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri-diagonal matrix solution to produce upward and downward radiative fluxes at each layer interface, from which net radiation, layer absorption, and surface albedo are easily derived. Solar fluxes are computed in five spectral bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. Because snow albedo varies strongly across the solar spectrum, it was determined that four bands were needed to accurately represent the near-infrared (NIR) characteristics of snow, whereas only one band was needed for the visible spectrum. Boundaries of the NIR bands were selected to capture broad radiative features and maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 :math:`\mu` m) surface downwelling flux from CLM according to the weights listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`, which are unique for diffuse and direct incident flux. These fixed weights were determined with offline hyperspectral radiative transfer calculations for an atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). The tri-diagonal solution includes intermediate terms that allow for easy interchange of two-stream techniques. We apply the Eddington solution for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the hemispheric mean solution ((:ref:`Toon et al. (1989) `) for NIR bands. These choices were made because the Eddington scheme works well for highly scattering media, but can produce negative albedo for absorptive NIR bands with diffuse incident flux. Delta scalings are applied to :math:`\tau`, :math:`\omega`, and :math:`g` (:ref:`Wiscombe and Warren 1980 `) in all spectral bands, producing effective values (denoted with \*) that are applied in the two-stream solution +The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri-diagonal matrix solution to produce upward and downward radiative fluxes at each layer interface, from which net radiation, layer absorption, and surface albedo are easily derived. Solar fluxes are computed in five spectral bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. Because snow albedo varies strongly across the solar spectrum, it was determined that four bands were needed to accurately represent the near-infrared (NIR) characteristics of snow, whereas only one band was needed for the visible spectrum. Boundaries of the NIR bands were selected to capture broad radiative features and maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 :math:`\mu` m) surface downwelling flux from CLM according to the weights listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`, which are unique for diffuse and direct incident flux. These fixed weights were determined with offline hyperspectral radiative transfer calculations for an atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). The tri-diagonal solution includes intermediate terms that allow for easy interchange of two-stream techniques. We apply the Eddington solution for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the hemispheric mean solution ((:ref:`Toon et al. (1989) `) for NIR bands. These choices were made because the Eddington scheme works well for highly scattering media, but can produce negative albedo for absorptive NIR bands with diffuse incident flux. Delta scalings are applied to :math:`\tau`, :math:`\omega`, and :math:`g` (:ref:`Wiscombe and Warren 1980 `) in all spectral bands, producing effective values (denoted with *) that are applied in the two-stream solution .. math:: :label: 3.66 diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst index c69e2cdd91..c161d2df39 100644 --- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/using-ptclm.rst @@ -107,8 +107,8 @@ The options that with a "grid" suffix all mean to create datasets using the glob Because supported single-point datasets already have the data created for them, you MUST use the "nopointdata" and "ndepgrid" options when you are using a supported single-point site. You must use "ndepgrid" even for a compset without CN. You also can NOT use the options: "soilgrid", "pftgrid", "aerdepgrid", or "owritesrfaer". ``--pftgrid`` - This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_pftdata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. + This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/*_pftdata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. ``--soilgrid`` - This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_soildata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. + This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/*_soildata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. From 6e15b4c72fe32debf4ae40ce19e2ed49a17099c5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 11:40:20 -0600 Subject: [PATCH 1667/2067] Automatically assign high priority items to project 25. --- .github/workflows/assign-to-project.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 .github/workflows/assign-to-project.yml diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml new file mode 100644 index 0000000000..5b3814488f --- /dev/null +++ b/.github/workflows/assign-to-project.yml @@ -0,0 +1,23 @@ +name: Auto Assign to Project(s) + +on: + issues: + types: [opened, labeled] + pull_request: + types: [opened, labeled] + issue_comment: + types: [created] + +jobs: + assign_high_priority: + runs-on: ubuntu-latest + name: Assign to High Priority project + steps: + - name: Assign issues and pull requests with `priority:high` label to project 25 + uses: srggrs/assign-one-project-github-action@1.3.1 + if: | + contains(github.event.issue.labels.*.name, 'priority:high') || + contains(github.event.pull_request.labels.*.name, 'priority:high') + with: + project: 'https://github.com/ESCOMP/CTSM/projects/25' + column_name: 'Needs triage' From 804c281fb8e91afcdad023d827238501d9757e08 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 12:00:16 -0600 Subject: [PATCH 1668/2067] Correct label. --- .github/workflows/assign-to-project.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml index 5b3814488f..8c6c259c33 100644 --- a/.github/workflows/assign-to-project.yml +++ b/.github/workflows/assign-to-project.yml @@ -13,11 +13,11 @@ jobs: runs-on: ubuntu-latest name: Assign to High Priority project steps: - - name: Assign issues and pull requests with `priority:high` label to project 25 + - name: Assign issues and pull requests with `priority: high` label to project 25 uses: srggrs/assign-one-project-github-action@1.3.1 if: | - contains(github.event.issue.labels.*.name, 'priority:high') || - contains(github.event.pull_request.labels.*.name, 'priority:high') + contains(github.event.issue.labels.*.name, 'priority: high') || + contains(github.event.pull_request.labels.*.name, 'priority: high') with: project: 'https://github.com/ESCOMP/CTSM/projects/25' column_name: 'Needs triage' From 732d3b9757faa236e8bda44aa4dc3685895f07d1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 19 Oct 2023 12:03:09 -0600 Subject: [PATCH 1669/2067] add threaded region check to seed dispersal call --- src/utils/clmfates_interfaceMod.F90 | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 1d7be0d813..1f00ece45f 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2669,8 +2669,21 @@ subroutine WrapGlobalSeedDispersal(this,is_restart_flag) logical :: set_restart_flag ! local logical variable to pass to IsItDispersalTime ! if optional is_restart_flag is true +#ifdef _OPENMP + logical, external :: omp_in_parallel +#endif type (neighbor_type), pointer :: neighbor + + ! Check to see if we are not in a threaded region. Fail the run if this returns true. +#ifdef _OPENMP + write(iulog,*) 'omp check: ', omp_in_parallel() + if (omp_in_parallel()) then + call endrun(msg='clmfates interface error: MPI routine called within threaded region'//& + errMsg(sourcefile, __LINE__)) + end if +#endif + ! This should only be run once per day if(is_beg_curr_day()) then From 6953572e48668542e4f4baaf73c2e2ec589fdf09 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 19 Oct 2023 12:04:35 -0600 Subject: [PATCH 1670/2067] remove temporary write statement --- src/utils/clmfates_interfaceMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 1f00ece45f..c9b1c9a5e7 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2677,7 +2677,6 @@ subroutine WrapGlobalSeedDispersal(this,is_restart_flag) ! Check to see if we are not in a threaded region. Fail the run if this returns true. #ifdef _OPENMP - write(iulog,*) 'omp check: ', omp_in_parallel() if (omp_in_parallel()) then call endrun(msg='clmfates interface error: MPI routine called within threaded region'//& errMsg(sourcefile, __LINE__)) From 15d3207f29b818296f75f2d8f281098003a1d22d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 11:46:12 -0600 Subject: [PATCH 1671/2067] =?UTF-8?q?Use=20=C2=B0=20instead=20of=20=C2=BA?= =?UTF-8?q?=20or=20superscript-o.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 14 +++--- .../Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 46 +++++++++---------- .../tech_note/Fire/CLM50_Tech_Note_Fire.rst | 2 +- .../Fluxes/CLM50_Tech_Note_Fluxes.rst | 4 +- .../Hydrology/CLM50_Tech_Note_Hydrology.rst | 2 +- .../Isotopes/CLM50_Tech_Note_Isotopes.rst | 2 +- .../tech_note/Lake/CLM50_Tech_Note_Lake.rst | 2 +- .../CLM50_Tech_Note_Land-Only_Mode.rst | 6 +-- .../MOSART/CLM50_Tech_Note_MOSART.rst | 4 +- .../Methane/CLM50_Tech_Note_Methane.rst | 6 +-- .../CLM50_Tech_Note_Photosynthesis.rst | 6 +-- ...LM50_Tech_Note_Photosynthetic_Capacity.rst | 8 ++-- .../CLM50_Tech_Note_Plant_Respiration.rst | 2 +- .../References/CLM50_Tech_Note_References.rst | 2 +- .../tech_note/Urban/CLM50_Tech_Note_Urban.rst | 2 +- 15 files changed, 54 insertions(+), 54 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 9ed603ad89..6a9b551ecd 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -163,7 +163,7 @@ All crops must meet the following requirements between the minimum planting date {GDD_{8} \ge GDD_{\min } } \end{array} -where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are degree-days or :sup:`o` days) tracked from April through September (NH) above 8\ :sup:`o` C with maximum daily increments of 30\ :sup:`o` days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. +where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are degree-days or ° days) tracked from April through September (NH) above 8° C with maximum daily increments of 30° days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, :math:`{GDD}_{mat}`, according to the following AgroIBIS rules: @@ -178,7 +178,7 @@ At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain pr GDD_{{\rm mat}}^{{\rm trop.soy}} =GDD_{{\rm 10}} & {\rm \; \; \; and\; \; \; } & GDD_{{\rm mat}}^{{\rm trop.soy}} <2100{}^\circ {\rm days} \end{array} -where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0\ :sup:`o`\C, 8\ :sup:`o`\C, and 10\ :sup:`o`\C, respectively, with maximum daily increments of 26\ :sup:`o`\days (for :math:`{GDD}_{0}`) or 30\ :sup:`o`\days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: +where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0°C, 8°C, and 10°C, respectively, with maximum daily increments of 26°days (for :math:`{GDD}_{0}`) or 30°days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: .. math:: :label: 25.3 @@ -189,7 +189,7 @@ where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-ye GDD_{{\rm 10}} =GDD_{10} +T_{2{\rm m}} -T_{f} -10 & \quad {\rm \; \; \; where\; \; \; } & 0 \le T_{2{\rm m}} -T_{f} -10\le 30{}^\circ {\rm days} \end{array} -where, if :math:`{T}_{2m}` - :math:`{T}_{f}` takes on values outside the above ranges within a day, then it equals the minimum or maximum value in the range for that day. :math:`{T}_{f}` is the freezing temperature of water and equals 273.15 K, :math:`{T}_{2m}` is the 2-m air temperature in units of K, and *GDD* is in units of ºdays. +where, if :math:`{T}_{2m}` - :math:`{T}_{f}` takes on values outside the above ranges within a day, then it equals the minimum or maximum value in the range for that day. :math:`{T}_{f}` is the freezing temperature of water and equals 273.15 K, :math:`{T}_{2m}` is the 2-m air temperature in units of K, and *GDD* is in units of °days. .. _Leaf emergence: @@ -224,9 +224,9 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD :math:`Date_{planting}^{max}` June 15 June 15 June 15 May 31 Feburary 28 March 31 April 15 June 31 June 15 June 15 :math:`T_{p}`\(K) 283.15 280.15 286.15 294.15 294.15 294.15 294.15 294.15 283.15 283.15 :math:`T_{p}^{ min }`\(K) 279.15 272.15 279.15 283.15 283.15 283.15 283.15 283.15 279.15 279.15 - :math:`{GDD}_{min}`\(ºdays) 50 50 50 50 50 50 50 50 50 50 - base temperature for GDD (ºC) 8 0 10 10 10 10 10 10 8 8 - :math:`{GDD}_{mat}`\(ºdays) 950-1850 :math:`\mathrm{\le}`\ 1700 :math:`\mathrm{\le}`\ 1900 :math:`\mathrm{\le}`\ 1700 :math:`\mathrm{\le}`\ 2100 950-1850 950-1850 :math:`\mathrm{\le}`\ 2100 950-1850 950-1850 + :math:`{GDD}_{min}`\(°days) 50 50 50 50 50 50 50 50 50 50 + base temperature for GDD (°C) 8 0 10 10 10 10 10 10 8 8 + :math:`{GDD}_{mat}`\(°days) 950-1850 :math:`\mathrm{\le}`\ 1700 :math:`\mathrm{\le}`\ 1900 :math:`\mathrm{\le}`\ 1700 :math:`\mathrm{\le}`\ 2100 950-1850 950-1850 :math:`\mathrm{\le}`\ 2100 950-1850 950-1850 Phase 2 % :math:`{GDD}_{mat}` 0.03 0.05 0.03 0.03 0.01 0.03 0.03 0.03 0.03 0.03 Phase 3 % :math:`{GDD}_{mat}` 0.65 0.6 0.5 0.5 0.4 0.65 0.5 0.5 0.4 0.4 Harvest: days past planting :math:`\mathrm{\le}`\ 165 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 160 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 300 :math:`\mathrm{\le}`\ 160 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 210 :math:`\mathrm{\le}`\ 210 @@ -507,7 +507,7 @@ For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) baset +12 + 0.4 \times latitude &\qquad -30 \le latitude \le 0 \end{array} \right\} -where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. Such latitudinal variation in base growth temperature could increase the base temperature, slow down :math:`GDD_{T_{{\rm 2m}} }` accumulation, and extend the growing season for regions within 30ºS to 30ºN for spring wheat and sugarcane. +where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. Such latitudinal variation in base growth temperature could increase the base temperature, slow down :math:`GDD_{T_{{\rm 2m}} }` accumulation, and extend the growing season for regions within 30°S to 30°N for spring wheat and sugarcane. .. _Separate reproductive pool: diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst index a3e6aa98a1..6425c20efd 100644 --- a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst +++ b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst @@ -294,7 +294,7 @@ The current state of the atmosphere (:numref:`Table Atmospheric input to land mo :sup:`4`\ The nitrogen deposition rate is required by the biogeochemistry model when active and represents the total deposition of mineral nitrogen onto the land surface, combining deposition of NO\ :sub:`y` and NH\ :sub:`x`. The rate is supplied either as a time-invariant spatially-varying annual mean rate or time-varying for a transient simulation. Nitrogen deposition rates were calculated from the same CAM chemistry simulation that generated the aerosol deposition rates. -:sup:`5`\ Climatological 3-hourly lightning frequency at :math:`\sim`\ 1.8\ :sup:`o` resolution is provided, which was calculated via bilinear interpolation from 1995-2011 NASA LIS/OTD grid product v2.2 (http://ghrc.msfc.nasa.gov) 2-hourly, 2.5\ :sup:`o` lightning frequency data. In future versions of the model, lightning data may be obtained directly from the atmosphere model. +:sup:`5`\ Climatological 3-hourly lightning frequency at :math:`\sim`\ 1.8° resolution is provided, which was calculated via bilinear interpolation from 1995-2011 NASA LIS/OTD grid product v2.2 (http://ghrc.msfc.nasa.gov) 2-hourly, 2.5° lightning frequency data. In future versions of the model, lightning data may be obtained directly from the atmosphere model. Density of air (:math:`\rho _{atm}` ) (kg m\ :sup:`-3`) is also required but is calculated directly from :math:`\rho _{atm} =\frac{P_{atm} -0.378e_{atm} }{R_{da} T_{atm} }` where :math:`P_{atm}` is atmospheric pressure (Pa), :math:`e_{atm}` is atmospheric vapor pressure (Pa), :math:`R_{da}` is the gas constant for dry air (J kg\ :sup:`-1` K\ :sup:`-1`) (:numref:`Table Physical constants`), and :math:`T_{atm}` is the atmospheric temperature (K). The atmospheric vapor pressure :math:`e_{atm}` is derived from atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`) as :math:`e_{atm} =\frac{q_{atm} P_{atm} }{0.622+0.378q_{atm} }`. @@ -377,60 +377,60 @@ Required surface data for each land grid cell are listed in :numref:`Table Surfa +--------------------------------------------+---------------------------+ | Surface Field | Resolution | +============================================+===========================+ - | Percent glacier | 0.05\ :sup:`o` | + | Percent glacier | 0.05° | +--------------------------------------------+---------------------------+ - | Percent lake and lake depth | 0.05\ :sup:`o` | + | Percent lake and lake depth | 0.05° | +--------------------------------------------+---------------------------+ - | Percent urban | 0.05\ :sup:`o` | + | Percent urban | 0.05° | +--------------------------------------------+---------------------------+ - | Percent plant functional types (PFTs) | 0.05\ :sup:`o` | + | Percent plant functional types (PFTs) | 0.05° | +--------------------------------------------+---------------------------+ - | Monthly leaf and stem area index | 0.5\ :sup:`o` | + | Monthly leaf and stem area index | 0.5° | +--------------------------------------------+---------------------------+ - | Canopy height (top, bottom) | 0.5\ :sup:`o` | + | Canopy height (top, bottom) | 0.5° | +--------------------------------------------+---------------------------+ - | Soil color | 0.5\ :sup:`o` | + | Soil color | 0.5° | +--------------------------------------------+---------------------------+ - | Percent sand, percent clay | 0.083\ :sup:`o` | + | Percent sand, percent clay | 0.083° | +--------------------------------------------+---------------------------+ - | Soil organic matter density | 0.083\ :sup:`o` | + | Soil organic matter density | 0.083° | +--------------------------------------------+---------------------------+ - | Maximum fractional saturated area | 0.125\ :sup:`o` | + | Maximum fractional saturated area | 0.125° | +--------------------------------------------+---------------------------+ | Elevation | 1km | +--------------------------------------------+---------------------------+ | Slope | 1km | +--------------------------------------------+---------------------------+ - | Biogenic Volatile Organic Compounds | 0.5\ :sup:`o` | + | Biogenic Volatile Organic Compounds | 0.5° | +--------------------------------------------+---------------------------+ - | Crop Irrigation | 0.083\ :sup:`o` | + | Crop Irrigation | 0.083° | +--------------------------------------------+---------------------------+ - | Managed crops | 0.5\ :sup:`o` | + | Managed crops | 0.5° | +--------------------------------------------+---------------------------+ - | Population density | 0.5\ :sup:`o` | + | Population density | 0.5° | +--------------------------------------------+---------------------------+ - | Gross domestic production | 0.5\ :sup:`o` | + | Gross domestic production | 0.5° | +--------------------------------------------+---------------------------+ - | Peat area fraction | 0.5\ :sup:`o` | + | Peat area fraction | 0.5° | +--------------------------------------------+---------------------------+ - | Peak month of agricultural waste burning | 0.5\ :sup:`o` | + | Peak month of agricultural waste burning | 0.5° | +--------------------------------------------+---------------------------+ -At the base spatial resolution of 0.05\ :sup:`o`, the percentage of each PFT is defined with respect to the vegetated portion of the grid cell and the sum of the PFTs is 100%. The percent lake, glacier, and urban at their base resolution are specified with respect to the entire grid cell. The surface dataset creation routines re-adjust the PFT percentages to ensure that the sum of all land cover types in the grid cell sum to 100%. A minimum threshold of 0.1% of the grid cell by area is required for urban areas. +At the base spatial resolution of 0.05°, the percentage of each PFT is defined with respect to the vegetated portion of the grid cell and the sum of the PFTs is 100%. The percent lake, glacier, and urban at their base resolution are specified with respect to the entire grid cell. The surface dataset creation routines re-adjust the PFT percentages to ensure that the sum of all land cover types in the grid cell sum to 100%. A minimum threshold of 0.1% of the grid cell by area is required for urban areas. The percentage glacier mask was derived from vector data of global glacier and ice sheet spatial coverage. Vector data for glaciers (ice caps, icefields and mountain glaciers) were taken from the first globally complete glacier inventory, the Randolph Glacier Inventory version 1.0 (RGIv1.0: :ref:`Arendt et al. 2012 `). Vector data for the Greenland Ice Sheet were provided by Frank Paul and Tobias Bolch (University of Zurich: :ref:`Rastner et al. 2012 `). Antarctic Ice Sheet data were provided by Andrew Bliss (University of Alaska) and were extracted from the Scientific Committee on Antarctic Research (SCAR) Antarctic Digital Database version 5.0. Floating ice is only provided for the Antarctic and does not include the small area of Arctic ice shelves. High spatial resolution vector data were then processed to determine the area of glacier, ice sheet and floating ice within 30-second grid cells globally. The 30-second glacier, ice sheet and Antarctic ice shelf masks were subsequently draped over equivalent-resolution GLOBE topography (Global Land One-km Base Elevation Project, Hastings et al. 1999) to extract approximate ice-covered elevations of ice-covered regions. Grid cells flagged as land-ice in the mask but ocean in GLOBE (typically, around ice sheets at high latitudes) were designated land-ice with an elevation of 0 meters. Finally, the high-resolution mask/topography datasets were aggregated and processed into three 3-minute datasets: 3-minute fractional areal land ice coverage (including both glaciers and ice sheets); 3-minute distributions of areal glacier fractional coverage by elevation and areal ice sheet fractional coverage by elevation. Ice fractions were binned at 100 meter intervals, with bin edges defined from 0 to 6000 meters (plus one top bin encompassing all remaining high-elevation ice, primarily in the Himalaya). These distributions by elevation are used to divide each glacier land unit into columns based on elevation class. When running with the CISM ice sheet model, CISM dictates glacier areas and elevations in its domain, overriding the values specified by CLM's datasets. In typical CLM5 configurations, this means that CISM dictates glacier areas and elevations over Greenland. -Percent lake and lake depth are area-averaged from the 90-second resolution data of :ref:`Kourzeneva (2009, 2010) ` to the 0.05\ :sup:`o` resolution using the MODIS land-mask. Percent urban is derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity and slope (:ref:`Dobson et al. 2000 `) as described by :ref:`Jackson et al. (2010) ` at 1km resolution and aggregated to 0.05\ :sup:`o`. A number of urban radiative, thermal, and morphological fields are also required and are obtained from :ref:`Jackson et al. (2010) `. Their description can be found in Table 3 of the Community Land Model Urban (CLMU) technical note (:ref:`Oleson et al. 2010b `). +Percent lake and lake depth are area-averaged from the 90-second resolution data of :ref:`Kourzeneva (2009, 2010) ` to the 0.05° resolution using the MODIS land-mask. Percent urban is derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity and slope (:ref:`Dobson et al. 2000 `) as described by :ref:`Jackson et al. (2010) ` at 1km resolution and aggregated to 0.05°. A number of urban radiative, thermal, and morphological fields are also required and are obtained from :ref:`Jackson et al. (2010) `. Their description can be found in Table 3 of the Community Land Model Urban (CLMU) technical note (:ref:`Oleson et al. 2010b `). Percent PFTs are derived from MODIS satellite data as described in :ref:`Lawrence and Chase (2007) ` (section 21.3.3). Prescribed PFT leaf area index is derived from the MODIS satellite data of :ref:`Myneni et al. (2002) ` using the de-aggregation methods described in :ref:`Lawrence and Chase (2007) ` (section 2.2.3). Prescribed PFT stem area index is derived from PFT leaf area index phenology combined with the methods of :ref:`Zeng et al. (2002) `. Prescribed canopy top and bottom heights are from :ref:`Bonan (1996) ` as described in :ref:`Bonan et al. (2002b) `. If the biogeochemistry model is active, it supplies the leaf and stem area index and canopy top and bottom heights dynamically, and the prescribed values are ignored. Soil color determines dry and saturated soil albedo (section :numref:`Ground Albedos`). Soil colors are from :ref:`Lawrence and Chase (2007) `. -The soil texture and organic matter content determine soil thermal and hydrologic properties (sections 6.3 and 7.4.1). The International Geosphere-Biosphere Programme (IGBP) soil dataset (Global Soil Data Task 2000) of 4931 soil mapping units and their sand and clay content for each soil layer were used to create a mineral soil texture dataset :ref:`(Bonan et al. 2002b) `. Soil organic matter data is merged from two sources. The majority of the globe is from ISRIC-WISE (:ref:`Batjes, 2006 `). The high latitudes come from the 0.25\ :sup:`o` version of the Northern Circumpolar Soil Carbon Database (:ref:`Hugelius et al. 2012 `). Both datasets report carbon down to 1m depth. Carbon is partitioned across the top seven CLM4 layers (:math:`\sim`\ 1m depth) as in :ref:`Lawrence and Slater (2008) `. +The soil texture and organic matter content determine soil thermal and hydrologic properties (sections 6.3 and 7.4.1). The International Geosphere-Biosphere Programme (IGBP) soil dataset (Global Soil Data Task 2000) of 4931 soil mapping units and their sand and clay content for each soil layer were used to create a mineral soil texture dataset :ref:`(Bonan et al. 2002b) `. Soil organic matter data is merged from two sources. The majority of the globe is from ISRIC-WISE (:ref:`Batjes, 2006 `). The high latitudes come from the 0.25° version of the Northern Circumpolar Soil Carbon Database (:ref:`Hugelius et al. 2012 `). Both datasets report carbon down to 1m depth. Carbon is partitioned across the top seven CLM4 layers (:math:`\sim`\ 1m depth) as in :ref:`Lawrence and Slater (2008) `. -The maximum fractional saturated area (:math:`f_{\max }` ) is used in determining surface runoff and infiltration (section 7.3). Maximum fractional saturated area at 0.125\ :sup:`o` resolution is calculated from 1-km compound topographic indices (CTIs) based on the USGS HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) following the algorithm in :ref:`Niu et al. (2005) `. :math:`f_{\max }` is the ratio between the number of 1-km pixels with CTIs equal to or larger than the mean CTI and the total number of pixels in a 0.125\ :sup:`o` grid cell. See section 7.3.1 and :ref:`Li et al. (2013b) ` for further details. Slope and elevation are also obtained from the USGS HYDRO1K 1-km dataset (:ref:`Verdin and Greenlee 1996 `). Slope is used in the surface water parameterization (section :numref:`Surface Water Storage`), and elevation is used to calculate the grid cell standard deviation of topography for the snow cover fraction parameterization (section :numref:`Snow Covered Area Fraction`). +The maximum fractional saturated area (:math:`f_{\max }` ) is used in determining surface runoff and infiltration (section 7.3). Maximum fractional saturated area at 0.125° resolution is calculated from 1-km compound topographic indices (CTIs) based on the USGS HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) following the algorithm in :ref:`Niu et al. (2005) `. :math:`f_{\max }` is the ratio between the number of 1-km pixels with CTIs equal to or larger than the mean CTI and the total number of pixels in a 0.125° grid cell. See section 7.3.1 and :ref:`Li et al. (2013b) ` for further details. Slope and elevation are also obtained from the USGS HYDRO1K 1-km dataset (:ref:`Verdin and Greenlee 1996 `). Slope is used in the surface water parameterization (section :numref:`Surface Water Storage`), and elevation is used to calculate the grid cell standard deviation of topography for the snow cover fraction parameterization (section :numref:`Snow Covered Area Fraction`). Biogenic Volatile Organic Compounds emissions factors are from the Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1; :ref:`Guenther et al. 2012 `). @@ -440,7 +440,7 @@ To allow crops to coexist with natural vegetation in a grid cell and be treated CLM includes the option to irrigate cropland areas that are equipped for irrigation. The application of irrigation responds dynamically to climate (see Chapter :numref:`rst_Crops and Irrigation`). In CLM, irrigation is implemented for the C3 generic crop only. When irrigation is enabled, the cropland area of each grid cell is divided into an irrigated and unirrigated fraction according to a dataset of areas equipped for irrigation (:ref:`Siebert et al. (2005) `). The area of irrigated cropland in each grid cell is given by the smaller of the grid cell's total cropland area, according to the default CLM4 dataset, and the grid cell's area equipped for irrigation. The remainder of the grid cell's cropland area (if any) is then assigned to unirrigated cropland. Irrigated and unirrigated crops are placed on separate soil columns, so that irrigation is only applied to the soil beneath irrigated crops. -Several input datasets are required for the fire model (:ref:`Li et al. 2013a `) including population density, gross domestic production, peat area fraction, and peak month of agricultural waste burning. Population density at 0.5\ :sup:`o` resolution for 1850-2100 combines 5-min resolution decadal population density data for 1850–1980 from the Database of the Global Environment version 3.1 (HYDEv3.1) with 0.5\ :sup:`o` resolution population density data for 1990, 1995, 2000, and 2005 from the Gridded Population of the World version 3 dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per capita in 2000 at 0.5\ :sup:`o` is from :ref:`Van Vuuren et al. (2006) `, which is the base-year GDP data for IPCC-SRES and derived from country-level World Bank's World Development Indicators (WDI) measured in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database (:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5\ :sup:`o` resolution is derived from three vector datasets: peatland data in Indonesia and Malaysian Borneo (:ref:`Olson et al. 2001 `); peatland data in Canada (:ref:`Tarnocai et al. 2011 `); and bog, fen and mire data in boreal regions (north of 45\ :sup:`o`\ N) outside Canada provided by the Global Lakes and Wetlands Database (GLWD) (:ref:`Lehner and Döll, 2004 `). The climatological peak month for agricultural waste burning is from :ref:`van der Werf et al. (2010) `. +Several input datasets are required for the fire model (:ref:`Li et al. 2013a `) including population density, gross domestic production, peat area fraction, and peak month of agricultural waste burning. Population density at 0.5° resolution for 1850-2100 combines 5-min resolution decadal population density data for 1850–1980 from the Database of the Global Environment version 3.1 (HYDEv3.1) with 0.5° resolution population density data for 1990, 1995, 2000, and 2005 from the Gridded Population of the World version 3 dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per capita in 2000 at 0.5° is from :ref:`Van Vuuren et al. (2006) `, which is the base-year GDP data for IPCC-SRES and derived from country-level World Bank's World Development Indicators (WDI) measured in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database (:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5° resolution is derived from three vector datasets: peatland data in Indonesia and Malaysian Borneo (:ref:`Olson et al. 2001 `); peatland data in Canada (:ref:`Tarnocai et al. 2011 `); and bog, fen and mire data in boreal regions (north of 45° N) outside Canada provided by the Global Lakes and Wetlands Database (GLWD) (:ref:`Lehner and Döll, 2004 `). The climatological peak month for agricultural waste burning is from :ref:`van der Werf et al. (2010) `. .. _Adjustable Parameters and Physical Constants: diff --git a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst index e0230ba6d2..e10c969d17 100644 --- a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst +++ b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst @@ -320,7 +320,7 @@ CLM focuses on deforestation fires in tropical closed forests. Tropical closed f where :math:`b` (s\ :sup:`-1`) is a global constant; :math:`f_{lu}` (fraction) represents the effect of decreasing fractional coverage of tree PFTs derived from land use data; :math:`f_{cli,d}` (fraction) represents the effect of climate conditions on the burned area. -Constants :math:`b` and :math:`{f}_{lu}` are calibrated based on observations and reanalysis datasets in the Amazon rainforest (tropical closed forests within 15.5 :sup:`o` S :math:`\text{-}` 10.5 :sup:`o` N, 30.5 :sup:`o` W :math:`\text{-}` 91 :sup:`o` W). :math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as +Constants :math:`b` and :math:`{f}_{lu}` are calibrated based on observations and reanalysis datasets in the Amazon rainforest (tropical closed forests within 15.5 ° S :math:`\text{-}` 10.5 ° N, 30.5 ° W :math:`\text{-}` 91 ° W). :math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as .. math:: :label: 23.35 diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index 38daab9774..b05f8b2307 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -1154,7 +1154,7 @@ The numerical solution for vegetation temperature and the fluxes of momentum, se #. If the latent heat flux has changed sign from the latent heat flux computed at the previous iteration (:math:`\lambda E_{v} ^{n+1} \times \lambda E_{v} ^{n} <0`), the latent heat flux is constrained to be 10% of the computed value. The difference between the constrained and computed value (:math:`\Delta _{1} =0.1\lambda E_{v} ^{n+1} -\lambda E_{v} ^{n+1}` ) is added to the sensible heat flux later. -#. Change in vegetation temperature :math:`\Delta T_{v}` (:eq:`5.129` ) and update the vegetation temperature as :math:`T_{v}^{n+1} =T_{v}^{n} +\Delta T_{v}`. :math:`T_{v}` is constrained to change by no more than 1ºK in one iteration. If this limit is exceeded, the energy error is +#. Change in vegetation temperature :math:`\Delta T_{v}` (:eq:`5.129` ) and update the vegetation temperature as :math:`T_{v}^{n+1} =T_{v}^{n} +\Delta T_{v}`. :math:`T_{v}` is constrained to change by no more than 1°K in one iteration. If this limit is exceeded, the energy error is .. math:: :label: 5.138 @@ -1310,7 +1310,7 @@ The system balances energy as Saturation Vapor Pressure ----------------------------- -Saturation vapor pressure :math:`e_{sat}^{T}` (Pa) and its derivative :math:`\frac{de_{sat}^{T} }{dT}`, as a function of temperature :math:`T` (ºC), are calculated from the eighth-order polynomial fits of :ref:`Flatau et al. (1992) ` +Saturation vapor pressure :math:`e_{sat}^{T}` (Pa) and its derivative :math:`\frac{de_{sat}^{T} }{dT}`, as a function of temperature :math:`T` (°C), are calculated from the eighth-order polynomial fits of :ref:`Flatau et al. (1992) ` .. math:: :label: 5.154 diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index dd8d0a7276..5599eeedd8 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -233,7 +233,7 @@ The fractional saturated area is a function of soil moisture f_{sat} =f_{\max } \ \exp \left(-0.5f_{over} z_{\nabla } \right) -where :math:`f_{\max }` is the potential or maximum value of :math:`f_{sat}`, :math:`f_{over}` is a decay factor (m\ :sup:`-1`), and :math:`z_{\nabla}` is the water table depth (m) (section :numref:`Lateral Sub-surface Runoff`). The maximum saturated fraction, :math:`f_{\max }`, is defined as the value of the discrete cumulative distribution function (CDF) of the topographic index when the grid cell mean water table depth is zero. Thus, :math:`f_{\max }` is the percent of pixels in a grid cell whose topographic index is larger than or equal to the grid cell mean topographic index. It should be calculated explicitly from the CDF at each grid cell at the resolution that the model is run. However, because this is a computationally intensive task for global applications, :math:`f_{\max }` is calculated once at 0.125\ :sup:`o` resolution using the 1-km compound topographic indices (CTIs) based on the HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) from USGS following the algorithm in :ref:`Niu et al. (2005) ` and then area-averaged to the desired model resolution (section :numref:`Surface Data`). Pixels with CTIs exceeding the 95 percentile threshold in each 0.125\ :sup:`o` grid cell are excluded from the calculation to eliminate biased estimation of statistics due to large CTI values at pixels on stream networks. For grid cells over regions without CTIs such as Australia, the global mean :math:`f_{\max }` is used to fill the gaps. See :ref:`Li et al. (2013b) ` for additional details. The decay factor :math:`f_{over}` for global simulations was determined through sensitivity analysis and comparison with observed runoff to be 0.5 m\ :sup:`-1`. +where :math:`f_{\max }` is the potential or maximum value of :math:`f_{sat}`, :math:`f_{over}` is a decay factor (m\ :sup:`-1`), and :math:`z_{\nabla}` is the water table depth (m) (section :numref:`Lateral Sub-surface Runoff`). The maximum saturated fraction, :math:`f_{\max }`, is defined as the value of the discrete cumulative distribution function (CDF) of the topographic index when the grid cell mean water table depth is zero. Thus, :math:`f_{\max }` is the percent of pixels in a grid cell whose topographic index is larger than or equal to the grid cell mean topographic index. It should be calculated explicitly from the CDF at each grid cell at the resolution that the model is run. However, because this is a computationally intensive task for global applications, :math:`f_{\max }` is calculated once at 0.125° resolution using the 1-km compound topographic indices (CTIs) based on the HYDRO1K dataset (:ref:`Verdin and Greenlee 1996 `) from USGS following the algorithm in :ref:`Niu et al. (2005) ` and then area-averaged to the desired model resolution (section :numref:`Surface Data`). Pixels with CTIs exceeding the 95 percentile threshold in each 0.125° grid cell are excluded from the calculation to eliminate biased estimation of statistics due to large CTI values at pixels on stream networks. For grid cells over regions without CTIs such as Australia, the global mean :math:`f_{\max }` is used to fill the gaps. See :ref:`Li et al. (2013b) ` for additional details. The decay factor :math:`f_{over}` for global simulations was determined through sensitivity analysis and comparison with observed runoff to be 0.5 m\ :sup:`-1`. .. _Surface Water Storage: diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index d9eb6d1213..3bd8700a06 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -109,5 +109,5 @@ In the preindustrial biosphere, radioactive decay of :sup:`14`\ C in carbon pool For radioactive decay, at each timestep all :sup:`14`\ C pools are reduced at a rate of –log/:math:`\tau`, where :math:`\tau` is the half-life (Libby half-life value of 5568 years). In order to rapidly equilibrate the long-lived pools during accelerated decomposition spinup, the radioactive decay of the accelerated pools is also accelerated by the same degree as the decomposition, such that the :sup:`14`\ C value of these pools is in equilibrium when taken out of the spinup mode. -For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 :sup:`o`\ N-90 :sup:`o`\ N, 30 :sup:`o`\ S-30 :sup:`o`\ N, and 30 :sup:`o`\ S-90 :sup:`o`\ S). +For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 ° N-90 ° N, 30 ° S-30 ° N, and 30 ° S-90 ° S). diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index c1654074be..0a7f2dda63 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -283,7 +283,7 @@ Once the four iterations for lake surface temperature have been yielded a tentat \begin{array}{l} {{\rm 1)\; }T_{T} \le T_{f} T_{g} ^{{'} } >T_{m} \Rightarrow T_{g} =T_{T} ,} \\ {{\rm 3)\; }T_{m} >T_{g} ^{{'} } >T_{T} >T_{f} \Rightarrow T_{g} =T_{T} } \end{array} -where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85\ :sup:`o` C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. +where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85° C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. If eq. XXX is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance eq. XXX in order to precisely conserve energy. XXX This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). An energy balance check is included at each timestep to insure that eq. XXX is obeyed to within 0.1 W m\ :sup:`-2`. diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index 6d08d7df6a..5ee0087fec 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -3,11 +3,11 @@ Land-Only Mode ================ -In land-only mode (uncoupled to an atmospheric model), the atmospheric forcing required by CLM (:numref:`Table Atmospheric input to land model`) is supplied by observed datasets. The standard forcing provided with the model is a 110-year (1901-2010) dataset provided by the Global Soil Wetness Project (GSWP3; NEED A REFERENCE). The GSWP3 dataset has a spatial resolution of 0.5\ :sup:`o` X 0.5\ :sup:`o` and a temporal resolution of three hours. +In land-only mode (uncoupled to an atmospheric model), the atmospheric forcing required by CLM (:numref:`Table Atmospheric input to land model`) is supplied by observed datasets. The standard forcing provided with the model is a 110-year (1901-2010) dataset provided by the Global Soil Wetness Project (GSWP3; NEED A REFERENCE). The GSWP3 dataset has a spatial resolution of 0.5° X 0.5° and a temporal resolution of three hours. -An alternative forcing dataset is also available, CRUNCEP, a 110-year (1901-2010) dataset (CRUNCEP; :ref:`Viovy 2011 `) that is a combination of two existing datasets; the CRU TS3.2 0.5\ :sup:`o` X 0.5\ :sup:`o` monthly data covering the period 1901 to 2002 (:ref:`Mitchell and Jones 2005 `) and the NCEP reanalysis 2.5\ :sup:`o` X 2.5\ :sup:`o` 6-hourly data covering the period 1948 to 2010. The CRUNCEP dataset has been used to force CLM for studies of vegetation growth, evapotranspiration, and gross primary production (:ref:`Mao et al. 2012 `, :ref:`Mao et al. 2013 `, :ref:`Shi et al. 2013 `) and for the TRENDY (trends in net land-atmosphere carbon exchange over the period 1980-2010) project (:ref:`Piao et al. 2012 `). Version 7 is available here (:ref:`Viovy 2011 `). +An alternative forcing dataset is also available, CRUNCEP, a 110-year (1901-2010) dataset (CRUNCEP; :ref:`Viovy 2011 `) that is a combination of two existing datasets; the CRU TS3.2 0.5° X 0.5° monthly data covering the period 1901 to 2002 (:ref:`Mitchell and Jones 2005 `) and the NCEP reanalysis 2.5° X 2.5° 6-hourly data covering the period 1948 to 2010. The CRUNCEP dataset has been used to force CLM for studies of vegetation growth, evapotranspiration, and gross primary production (:ref:`Mao et al. 2012 `, :ref:`Mao et al. 2013 `, :ref:`Shi et al. 2013 `) and for the TRENDY (trends in net land-atmosphere carbon exchange over the period 1980-2010) project (:ref:`Piao et al. 2012 `). Version 7 is available here (:ref:`Viovy 2011 `). -Here, the GSWP3 dataset, which does not include data for particular fields over oceans, lakes, and Antarctica is modified. This missing data is filled with :ref:`Qian et al. (2006) ` data from 1948 that is interpolated by the data atmosphere model to the 0.5\ :sup:`o` GSWP3 grid. This allows the model to be run over Antarctica and ensures data is available along coastlines regardless of model resolution. +Here, the GSWP3 dataset, which does not include data for particular fields over oceans, lakes, and Antarctica is modified. This missing data is filled with :ref:`Qian et al. (2006) ` data from 1948 that is interpolated by the data atmosphere model to the 0.5° GSWP3 grid. This allows the model to be run over Antarctica and ensures data is available along coastlines regardless of model resolution. The forcing data is ingested into a data atmosphere model in three "streams"; precipitation (:math:`P`) (mm s\ :sup:`-1`), solar radiation (:math:`S_{atm}` ) (W m\ :sup:`-2`), and four other fields [atmospheric pressure :math:`P_{atm}` (Pa), atmospheric specific humidity :math:`q_{atm}` (kg kg\ :sup:`-1`), atmospheric temperature :math:`T_{atm}` (K), and atmospheric wind :math:`W_{atm}` (m s\ :sup:`-1`)]. These are separate streams because they are handled differently according to the type of field. In the GSWP3 dataset, the precipitation stream is provided at three hour intervals and the data atmosphere model prescribes the same precipitation rate for each model time step within the three hour period. The four fields that are grouped together in another stream (pressure, humidity, temperature, and wind) are provided at three hour intervals and the data atmosphere model linearly interpolates these fields to the time step of the model. diff --git a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst index 7d35991a62..3c10cd4507 100644 --- a/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst +++ b/doc/source/tech_note/MOSART/CLM50_Tech_Note_MOSART.rst @@ -76,7 +76,7 @@ The numerical implementation of MOSART is mainly based on a subcycling scheme an Parameters and Input Data --------------------------------- -MOSART is supported by a comprehensive, global hydrography dataset at 0.5 :sup:`o` resolution. As such, the fundamental spatial unit of MOSART is a 0.5 :sup:`o` lat/lon grid. The topographic parameters (such as flow direction, channel length, topographic and channel slopes, etc.) were derived using the Dominant River Tracing (DRT) algorithm (:ref:`Wu et al., 2011`; :ref:`Wu et al. 2012 `). The DRT algorithm produces the topographic parameters in a scale-consistent way to preserve/upscale the key features of a baseline high-resolution hydrography dataset at multiple coarser spatial resolutions. Here the baseline high-resolution hydrography dataset is the 1km resolution Hydrological data and maps based on SHuttle Elevation Derivatives at multiple Scales (HydroSHEDS) (:ref:`Lehner and Döll, 2004 `; :ref:`Lehner et al., 2008 `). The channel geometry parameters, e.g., bankfull width and depth, were estimated from empirical hydraulic geometry relationships as functions of the mean annual discharge. The Manning roughness coefficients for overland and channel flow were calculated as functions of landcover and water depth. For more details on the methodology to derive channel geometry and the Manning's roughness coefficients, please refer to :ref:`Getirana et al. (2012) `. The full list of parameters included in this global hydrography dataset is provided in :numref:`Table MOSART Parameters`. Evaluation of global simulations by MOSART using the aforementioned parameters is described in :ref:`Li et al. (2015b) `. +MOSART is supported by a comprehensive, global hydrography dataset at 0.5 ° resolution. As such, the fundamental spatial unit of MOSART is a 0.5 ° lat/lon grid. The topographic parameters (such as flow direction, channel length, topographic and channel slopes, etc.) were derived using the Dominant River Tracing (DRT) algorithm (:ref:`Wu et al., 2011`; :ref:`Wu et al. 2012 `). The DRT algorithm produces the topographic parameters in a scale-consistent way to preserve/upscale the key features of a baseline high-resolution hydrography dataset at multiple coarser spatial resolutions. Here the baseline high-resolution hydrography dataset is the 1km resolution Hydrological data and maps based on SHuttle Elevation Derivatives at multiple Scales (HydroSHEDS) (:ref:`Lehner and Döll, 2004 `; :ref:`Lehner et al., 2008 `). The channel geometry parameters, e.g., bankfull width and depth, were estimated from empirical hydraulic geometry relationships as functions of the mean annual discharge. The Manning roughness coefficients for overland and channel flow were calculated as functions of landcover and water depth. For more details on the methodology to derive channel geometry and the Manning's roughness coefficients, please refer to :ref:`Getirana et al. (2012) `. The full list of parameters included in this global hydrography dataset is provided in :numref:`Table MOSART Parameters`. Evaluation of global simulations by MOSART using the aforementioned parameters is described in :ref:`Li et al. (2015b) `. .. _Table MOSART Parameters: @@ -119,7 +119,7 @@ Difference between CLM5.0 and CLM4.5 2. Runoff treatment: In RTM runoff is routed regardless of its sign so negative streamflow can be simulated at times. MOSART routes only non-negative runoff and always produces positive streamflow, which is important for future extensions to model riverine heat and biogeochemical fluxes. -3. Input parameters: RTM in CLM4.5 only requires one layer of a spatially varying variable of channel velocity, whilst MOSART in CLM5.0 requires 13 parameters that are all available globally at 0.5 :sup:`o` resolution. +3. Input parameters: RTM in CLM4.5 only requires one layer of a spatially varying variable of channel velocity, whilst MOSART in CLM5.0 requires 13 parameters that are all available globally at 0.5 ° resolution. 4. Outputs: RTM only produces streamflow simulation, whilst MOSART additionally simulates the time-varying channel velocities, channel water depth, and channel surface water variations. diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index e0fe0def4e..a904a899a2 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -54,7 +54,7 @@ Because CLM does not currently specifically represent wetland plant functional t Here, :math:`f_{CH_{4} }` is the baseline ratio between CO\ :sub:`2` and CH\ :sub:`4` production (all parameters values are given in :numref:`Table Methane Parameter descriptions`). Currently, :math:`f_{CH_{4} }` is modified to account for our assumptions that methanogens may have a higher Q\ :math:`{}_{10}` than aerobic decomposers; are not N limited; and do not have a low-moisture limitation. -When the single BGC soil level is used in CLM (Chapter :numref:`rst_Decomposition`), the temperature factor, :math:`f_{T}`, is set to 0 for temperatures equal to or below freezing, even though CLM allows heterotrophic respiration below freezing. However, if the vertically resolved BGC soil column is used, CH\ :sub:`4` production continues below freezing because liquid water stress limits decomposition. The base temperature for the :math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22\ :sup:`o` C and effectively modified the base :math:`f_{CH_{4}}` value. +When the single BGC soil level is used in CLM (Chapter :numref:`rst_Decomposition`), the temperature factor, :math:`f_{T}`, is set to 0 for temperatures equal to or below freezing, even though CLM allows heterotrophic respiration below freezing. However, if the vertically resolved BGC soil column is used, CH\ :sub:`4` production continues below freezing because liquid water stress limits decomposition. The base temperature for the :math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22° C and effectively modified the base :math:`f_{CH_{4}}` value. For the single-layer BGC version, :math:`{R}_{H}` is distributed among soil levels by assuming that 50% is associated with the roots (using the CLM PFT-specific rooting distribution) and the rest is evenly divided among the top 0.28 m of soil (to be consistent with CLM's soil decomposition algorithm). For the vertically resolved BGC version, the prognosed distribution of :math:`{R}_{H}` is used to estimate CH\ :sub:`4` production. @@ -186,7 +186,7 @@ CLM represents CH\ :sub:`4` oxidation with double Michaelis-Menten kinetics (:re R_{oxic} =R_{o,\max } \left[\frac{C_{CH_{4} } }{K_{CH_{4} } +C_{CH_{4} } } \right]\left[\frac{C_{O_{2} } }{K_{O_{2} } +C_{O_{2} } } \right]Q_{10} F_{\vartheta } -where :math:`K_{CH_{4} }` and :math:`K_{O_{2} }` \ are the half saturation coefficients (mol m\ :sup:`-3`) with respect to CH\ :sub:`4` and O\ :sub:`2` concentrations, respectively; :math:`R_{o,\max }` is the maximum oxidation rate (mol m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` specifies the temperature dependence of the reaction with a base temperature set to 12 :sup:`o` C. The soil moisture limitation factor :math:`F_{\theta }` is applied above the water table to represent water stress for methanotrophs. Based on the data in :ref:`Schnell and King (1996)`, we take :math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. +where :math:`K_{CH_{4} }` and :math:`K_{O_{2} }` \ are the half saturation coefficients (mol m\ :sup:`-3`) with respect to CH\ :sub:`4` and O\ :sub:`2` concentrations, respectively; :math:`R_{o,\max }` is the maximum oxidation rate (mol m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` specifies the temperature dependence of the reaction with a base temperature set to 12 ° C. The soil moisture limitation factor :math:`F_{\theta }` is applied above the water table to represent water stress for methanotrophs. Based on the data in :ref:`Schnell and King (1996)`, we take :math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. .. _Reactive Transport Solution: @@ -329,7 +329,7 @@ A simplified dynamic representation of spatial inundation based on recent work b f_{s} =fws_{slope} TWS + fws_{intercept} . -These parameters were evaluated at the 0.5\ :sup:`o` resolution, and aggregated for coarser simulations. Ongoing work in the hydrology submodel of CLM may alleviate the need for this crude simplification of inundated fraction in future model versions. +These parameters were evaluated at the 0.5° resolution, and aggregated for coarser simulations. Ongoing work in the hydrology submodel of CLM may alleviate the need for this crude simplification of inundated fraction in future model versions. .. _Seasonal Inundation: diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index dd65058532..f1e573a98e 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -157,7 +157,7 @@ The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) < Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. :math:`A_{n} =A-R_{d}`. -The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 :sup:`o` \ C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. +The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 ° C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. :math:`J_{\max 25}` at 25 :sup:`\o`\ C: is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) @@ -246,14 +246,14 @@ In the model, acclimation is implemented as in :ref:`Kattge and Knorr (2007) `) based on an optimality hypothesis to nitrogen allocation among light capture, electron transport, carboxylation, respiration and storage. Specifically, the model allocates the nitrogen by maximizing the daily net photosynthetic carbon gain under following two key assumptions: +The photosynthetic capacity is represented by two key parameters: 1) the maximum rate of carboxylation at 25 ° C, :math:`V_{\text{c,max25}}`; and 2) the maximum rate of electron transport at 25 ° C, :math:`J_{\text{max25}}`. They are predicted by a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) (:ref:`Ali et al. 2016`) based on an optimality hypothesis to nitrogen allocation among light capture, electron transport, carboxylation, respiration and storage. Specifically, the model allocates the nitrogen by maximizing the daily net photosynthetic carbon gain under following two key assumptions: - nitrogen allocated for light capture, electron transport and carboxylation are co-limiting; @@ -183,14 +183,14 @@ where :math:`\text{PAR}_{\text{{max}}}` ( :math:`\mu mol`/m :sup:`2`/s) is the m Maximum rate of carboxylation '''''''''''''''''''''''''''''' -The maximum rate of carboxylation at 25\ :sup:`o`\ C varies with foliage nitrogen concentration and specific leaf area and is calculated as in :ref:`Thornton and Zimmermann (2007)`. At 25ºC, +The maximum rate of carboxylation at 25° C varies with foliage nitrogen concentration and specific leaf area and is calculated as in :ref:`Thornton and Zimmermann (2007)`. At 25°C, .. math:: :label: 10.11) V_{c\max 25} = N_{cb} NUE_{V_{c\max 25}} -where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, :numref:`Table Plant functional type (PFT) leaf N parameters`), and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) measured at 25\ :sup:`o`\ C, and the constant 6.25 is the nitrogen binding factor for Rubisco (g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). +where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, :numref:`Table Plant functional type (PFT) leaf N parameters`), and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) measured at 25° C, and the constant 6.25 is the nitrogen binding factor for Rubisco (g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). :math:`V_{c\max 25}` additionally varies with daylength (:math:`DYL`) using the function :math:`f(DYL)`, which introduces seasonal variation to :math:`V_{c\max }` @@ -206,7 +206,7 @@ with :math:`0.01\le f\left(DYL\right)\le 1`. Daylength (seconds) is given by DYL=2\times 13750.9871\cos ^{-1} \left[\frac{-\sin \left(lat\right)\sin \left(decl\right)}{\cos \left(lat\right)\cos \left(decl\right)} \right] -where :math:`lat` (latitude) and :math:`decl` (declination angle) are from section :numref:`Solar Zenith Angle`. Maximum daylength (:math:`DYL_{\max }` ) is calculated similarly but using the maximum declination angle for present-day orbital geometry (:math:`\pm`\ 23.4667º [:math:`\pm`\ 0.409571 radians], positive for Northern Hemisphere latitudes and negative for Southern Hemisphere). +where :math:`lat` (latitude) and :math:`decl` (declination angle) are from section :numref:`Solar Zenith Angle`. Maximum daylength (:math:`DYL_{\max }` ) is calculated similarly but using the maximum declination angle for present-day orbital geometry (:math:`\pm`\ 23.4667° [:math:`\pm`\ 0.409571 radians], positive for Northern Hemisphere latitudes and negative for Southern Hemisphere). Implementation of Photosynthetic Capacity '''''''''''''''''''''''''''''''''''''''''' diff --git a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst index 7a996f2c8e..0269454042 100644 --- a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst +++ b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst @@ -38,7 +38,7 @@ The temperature dependance of leaf maintenance (dark) respiration is described i CF_{mr\_ froot} \_ =\sum _{j=1}^{nlevsoi}NS_{froot} rootfr_{j} MR_{base} MR_{Q10} ^{(Ts_{j} -20)/10} -where :math:`MR_{q10}` (= 2.0) is the temperature sensitivity for maintenance respiration, :math:`T_{2m}` (:sup:`o`\ C) is the air temperature at 2m height, :math:`Ts_{j}`* (:sup:`o`\ C) is the soil temperature at level *j*, and :math:`rootfr_{j}` is the fraction of fine roots distributed in soil level *j*. +where :math:`MR_{q10}` (= 2.0) is the temperature sensitivity for maintenance respiration, :math:`T_{2m}` (° C) is the air temperature at 2m height, :math:`Ts_{j}`* (° C) is the soil temperature at level *j*, and :math:`rootfr_{j}` is the fraction of fine roots distributed in soil level *j*. .. table:: Atkin leaf respiration model intercept values. diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index d3c81b243e..917b084d1f 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -461,7 +461,7 @@ Gotangco Castillo C., Levis S., and Thornton P. 2012. Evaluation of the new CNDV .. _Grahametal1999: -Graham, S.T., Famiglietti, J.S., and Maidment, D.R. 1999. Five-minute, 1/2º, and 1º data sets of continental watersheds and river networks for use in regional and global hydrologic and climate system modeling studies. Water Resour. Res. 35:583-587. +Graham, S.T., Famiglietti, J.S., and Maidment, D.R. 1999. Five-minute, 1/2°, and 1° data sets of continental watersheds and river networks for use in regional and global hydrologic and climate system modeling studies. Water Resour. Res. 35:583-587. .. _Gravenetal2017: diff --git a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst index 7336bc7266..e9bfb5eb57 100644 --- a/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst +++ b/doc/source/tech_note/Urban/CLM50_Tech_Note_Urban.rst @@ -15,7 +15,7 @@ Turbulent [sensible heat (:math:`Q_{H,\, u}` ) and latent heat (:math:`Q_{E,\, u The heat and moisture fluxes from each surface interact with each other through a bulk air mass that represents air in the urban canopy layer for which specific humidity (:math:`q_{ac}` ) and temperature (:math:`T_{ac}` ) are prognosed (:numref:`Figure schematic of urban and atmospheric model coupling`). The air temperature can be compared with that from surrounding vegetated/soil (rural) surfaces in the model to ascertain heat island characteristics. As with other landunits, the CLMU is forced either with output from a host atmospheric model (e.g., the Community Atmosphere Model (CAM)) or observed forcing (e.g., reanalysis or field observations). The urban model produces sensible, latent heat, and momentum fluxes, emitted longwave, and reflected solar radiation, which are area-averaged with fluxes from non-urban "landunits" (e.g., vegetation, lakes) to supply grid cell averaged fluxes to the atmospheric model. -Present day global urban extent and urban properties were developed by :ref:`Jackson et al. (2010) `. Urban extent, defined for four classes [tall building district (TBD), and high, medium, and low density (HD, MD, LD)], was derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity, and slope (:ref:`Dobson et al. 2000 `). The urban extent data for TBD, HD, and MD classes are aggregated from the original 1 km resolution to both a 0.05\ :sup:`o` by 0.05\ :sup:`o` global grid for high-resolution studies or a 0.5\ :sup:`o` by 0.5\ :sup:`o` grid. For the current implementation, the LD class is not used because it is highly rural and better modeled as a vegetated/soil surface. Although the TBD, HD, and MD classes are represented as individual urban landunits, urban model history output is currently a weighted average of the output for individual classes. +Present day global urban extent and urban properties were developed by :ref:`Jackson et al. (2010) `. Urban extent, defined for four classes [tall building district (TBD), and high, medium, and low density (HD, MD, LD)], was derived from LandScan 2004, a population density dataset derived from census data, nighttime lights satellite observations, road proximity, and slope (:ref:`Dobson et al. 2000 `). The urban extent data for TBD, HD, and MD classes are aggregated from the original 1 km resolution to both a 0.05° by 0.05° global grid for high-resolution studies or a 0.5° by 0.5° grid. For the current implementation, the LD class is not used because it is highly rural and better modeled as a vegetated/soil surface. Although the TBD, HD, and MD classes are represented as individual urban landunits, urban model history output is currently a weighted average of the output for individual classes. For each of 33 distinct regions across the globe, thermal (e.g., heat capacity and thermal conductivity), radiative (e.g., albedo and emissivity) and morphological (e.g., height to width ratio, roof fraction, average building height, and pervious fraction of the canyon floor) properties are provided for each of the density classes. Building interior minimum and maximum temperatures are prescribed based on climate and socioeconomic considerations. The surface dataset creation routines (see CLM5.0 User's Guide) aggregate the data to the desired resolution. From a7c95a4d7fc4845ca2f0145b875f351e4cf7e9ce Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 11:59:01 -0600 Subject: [PATCH 1672/2067] =?UTF-8?q?Use=20=E2=89=A4=20instead=20of=20math?= =?UTF-8?q?=20symbol.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 6a9b551ecd..658271a003 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -226,10 +226,10 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD :math:`T_{p}^{ min }`\(K) 279.15 272.15 279.15 283.15 283.15 283.15 283.15 283.15 279.15 279.15 :math:`{GDD}_{min}`\(°days) 50 50 50 50 50 50 50 50 50 50 base temperature for GDD (°C) 8 0 10 10 10 10 10 10 8 8 - :math:`{GDD}_{mat}`\(°days) 950-1850 :math:`\mathrm{\le}`\ 1700 :math:`\mathrm{\le}`\ 1900 :math:`\mathrm{\le}`\ 1700 :math:`\mathrm{\le}`\ 2100 950-1850 950-1850 :math:`\mathrm{\le}`\ 2100 950-1850 950-1850 + :math:`{GDD}_{mat}`\(°days) 950-1850 ≤ 1700 ≤ 1900 ≤ 1700 ≤ 2100 950-1850 950-1850 ≤ 2100 950-1850 950-1850 Phase 2 % :math:`{GDD}_{mat}` 0.03 0.05 0.03 0.03 0.01 0.03 0.03 0.03 0.03 0.03 Phase 3 % :math:`{GDD}_{mat}` 0.65 0.6 0.5 0.5 0.4 0.65 0.5 0.5 0.4 0.4 - Harvest: days past planting :math:`\mathrm{\le}`\ 165 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 160 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 300 :math:`\mathrm{\le}`\ 160 :math:`\mathrm{\le}`\ 150 :math:`\mathrm{\le}`\ 210 :math:`\mathrm{\le}`\ 210 + Harvest: days past planting ≤ 165 ≤ 150 ≤ 150 ≤ 160 ≤ 150 ≤ 300 ≤ 160 ≤ 150 ≤ 210 ≤ 210 :math:`z_{top}^{\max }` (m) 2.5 1.2 0.75 1.5 1.8 4 2.5 1 2.5 2.5 SLA (m :sup:`2` leaf g :sup:`-1` C) 0.05 0.035 0.035 0.035 0.035 0.05 0.05 0.035 0.057 0.049 :math:`\chi _{L}` index -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 From a0902b22d3f2b400f02301924ae37cd55d07bb19 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 12:10:43 -0600 Subject: [PATCH 1673/2067] =?UTF-8?q?No=20space=20in=20=C2=B0C,=20=C2=B0N,?= =?UTF-8?q?=20or=20=C2=B0S.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- .../tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst | 2 +- doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst | 2 +- doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst | 2 +- doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst | 2 +- doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst | 4 ++-- .../Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 6 +++--- .../CLM50_Tech_Note_Photosynthetic_Capacity.rst | 6 +++--- .../Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst | 2 +- 9 files changed, 14 insertions(+), 14 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 658271a003..593e30cb4d 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -163,7 +163,7 @@ All crops must meet the following requirements between the minimum planting date {GDD_{8} \ge GDD_{\min } } \end{array} -where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are degree-days or ° days) tracked from April through September (NH) above 8° C with maximum daily increments of 30° days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. +where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are degree-days or ° days) tracked from April through September (NH) above 8°C with maximum daily increments of 30° days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, :math:`{GDD}_{mat}`, according to the following AgroIBIS rules: diff --git a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst index 6425c20efd..33c035f282 100644 --- a/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst +++ b/doc/source/tech_note/Ecosystem/CLM50_Tech_Note_Ecosystem.rst @@ -440,7 +440,7 @@ To allow crops to coexist with natural vegetation in a grid cell and be treated CLM includes the option to irrigate cropland areas that are equipped for irrigation. The application of irrigation responds dynamically to climate (see Chapter :numref:`rst_Crops and Irrigation`). In CLM, irrigation is implemented for the C3 generic crop only. When irrigation is enabled, the cropland area of each grid cell is divided into an irrigated and unirrigated fraction according to a dataset of areas equipped for irrigation (:ref:`Siebert et al. (2005) `). The area of irrigated cropland in each grid cell is given by the smaller of the grid cell's total cropland area, according to the default CLM4 dataset, and the grid cell's area equipped for irrigation. The remainder of the grid cell's cropland area (if any) is then assigned to unirrigated cropland. Irrigated and unirrigated crops are placed on separate soil columns, so that irrigation is only applied to the soil beneath irrigated crops. -Several input datasets are required for the fire model (:ref:`Li et al. 2013a `) including population density, gross domestic production, peat area fraction, and peak month of agricultural waste burning. Population density at 0.5° resolution for 1850-2100 combines 5-min resolution decadal population density data for 1850–1980 from the Database of the Global Environment version 3.1 (HYDEv3.1) with 0.5° resolution population density data for 1990, 1995, 2000, and 2005 from the Gridded Population of the World version 3 dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per capita in 2000 at 0.5° is from :ref:`Van Vuuren et al. (2006) `, which is the base-year GDP data for IPCC-SRES and derived from country-level World Bank's World Development Indicators (WDI) measured in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database (:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5° resolution is derived from three vector datasets: peatland data in Indonesia and Malaysian Borneo (:ref:`Olson et al. 2001 `); peatland data in Canada (:ref:`Tarnocai et al. 2011 `); and bog, fen and mire data in boreal regions (north of 45° N) outside Canada provided by the Global Lakes and Wetlands Database (GLWD) (:ref:`Lehner and Döll, 2004 `). The climatological peak month for agricultural waste burning is from :ref:`van der Werf et al. (2010) `. +Several input datasets are required for the fire model (:ref:`Li et al. 2013a `) including population density, gross domestic production, peat area fraction, and peak month of agricultural waste burning. Population density at 0.5° resolution for 1850-2100 combines 5-min resolution decadal population density data for 1850–1980 from the Database of the Global Environment version 3.1 (HYDEv3.1) with 0.5° resolution population density data for 1990, 1995, 2000, and 2005 from the Gridded Population of the World version 3 dataset (GPWv3) (CIESIN, 2005). Gross Domestic Production (GDP) per capita in 2000 at 0.5° is from :ref:`Van Vuuren et al. (2006) `, which is the base-year GDP data for IPCC-SRES and derived from country-level World Bank's World Development Indicators (WDI) measured in constant 1995 US$ (:ref:`World Bank, 2004 `) and the UN Statistics Database (:ref:`UNSTAT, 2005 `). The peatland area fraction at 0.5° resolution is derived from three vector datasets: peatland data in Indonesia and Malaysian Borneo (:ref:`Olson et al. 2001 `); peatland data in Canada (:ref:`Tarnocai et al. 2011 `); and bog, fen and mire data in boreal regions (north of 45°N) outside Canada provided by the Global Lakes and Wetlands Database (GLWD) (:ref:`Lehner and Döll, 2004 `). The climatological peak month for agricultural waste burning is from :ref:`van der Werf et al. (2010) `. .. _Adjustable Parameters and Physical Constants: diff --git a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst index e10c969d17..1adcb03cf1 100644 --- a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst +++ b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst @@ -320,7 +320,7 @@ CLM focuses on deforestation fires in tropical closed forests. Tropical closed f where :math:`b` (s\ :sup:`-1`) is a global constant; :math:`f_{lu}` (fraction) represents the effect of decreasing fractional coverage of tree PFTs derived from land use data; :math:`f_{cli,d}` (fraction) represents the effect of climate conditions on the burned area. -Constants :math:`b` and :math:`{f}_{lu}` are calibrated based on observations and reanalysis datasets in the Amazon rainforest (tropical closed forests within 15.5 ° S :math:`\text{-}` 10.5 ° N, 30.5 ° W :math:`\text{-}` 91 ° W). :math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as +Constants :math:`b` and :math:`{f}_{lu}` are calibrated based on observations and reanalysis datasets in the Amazon rainforest (tropical closed forests within 15.5 °S :math:`\text{-}` 10.5 °N, 30.5 ° W :math:`\text{-}` 91 ° W). :math:`b` = 0.033 d\ :sup:`-1` and :math:`f_{lu}` is defined as .. math:: :label: 23.35 diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 3bd8700a06..4222faf0e6 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -109,5 +109,5 @@ In the preindustrial biosphere, radioactive decay of :sup:`14`\ C in carbon pool For radioactive decay, at each timestep all :sup:`14`\ C pools are reduced at a rate of –log/:math:`\tau`, where :math:`\tau` is the half-life (Libby half-life value of 5568 years). In order to rapidly equilibrate the long-lived pools during accelerated decomposition spinup, the radioactive decay of the accelerated pools is also accelerated by the same degree as the decomposition, such that the :sup:`14`\ C value of these pools is in equilibrium when taken out of the spinup mode. -For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 ° N-90 ° N, 30 ° S-30 ° N, and 30 ° S-90 ° S). +For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 °N-90 °N, 30 °S-30 °N, and 30 °S-90 °S). diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 0a7f2dda63..e002d8100b 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -283,7 +283,7 @@ Once the four iterations for lake surface temperature have been yielded a tentat \begin{array}{l} {{\rm 1)\; }T_{T} \le T_{f} T_{g} ^{{'} } >T_{m} \Rightarrow T_{g} =T_{T} ,} \\ {{\rm 3)\; }T_{m} >T_{g} ^{{'} } >T_{T} >T_{f} \Rightarrow T_{g} =T_{T} } \end{array} -where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85° C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. +where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85°C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. If eq. XXX is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance eq. XXX in order to precisely conserve energy. XXX This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). An energy balance check is included at each timestep to insure that eq. XXX is obeyed to within 0.1 W m\ :sup:`-2`. diff --git a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst index a904a899a2..1b3228e6dc 100644 --- a/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst +++ b/doc/source/tech_note/Methane/CLM50_Tech_Note_Methane.rst @@ -54,7 +54,7 @@ Because CLM does not currently specifically represent wetland plant functional t Here, :math:`f_{CH_{4} }` is the baseline ratio between CO\ :sub:`2` and CH\ :sub:`4` production (all parameters values are given in :numref:`Table Methane Parameter descriptions`). Currently, :math:`f_{CH_{4} }` is modified to account for our assumptions that methanogens may have a higher Q\ :math:`{}_{10}` than aerobic decomposers; are not N limited; and do not have a low-moisture limitation. -When the single BGC soil level is used in CLM (Chapter :numref:`rst_Decomposition`), the temperature factor, :math:`f_{T}`, is set to 0 for temperatures equal to or below freezing, even though CLM allows heterotrophic respiration below freezing. However, if the vertically resolved BGC soil column is used, CH\ :sub:`4` production continues below freezing because liquid water stress limits decomposition. The base temperature for the :math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22° C and effectively modified the base :math:`f_{CH_{4}}` value. +When the single BGC soil level is used in CLM (Chapter :numref:`rst_Decomposition`), the temperature factor, :math:`f_{T}`, is set to 0 for temperatures equal to or below freezing, even though CLM allows heterotrophic respiration below freezing. However, if the vertically resolved BGC soil column is used, CH\ :sub:`4` production continues below freezing because liquid water stress limits decomposition. The base temperature for the :math:`{Q}_{10}` factor, :math:`{T}_{B}`, is 22°C and effectively modified the base :math:`f_{CH_{4}}` value. For the single-layer BGC version, :math:`{R}_{H}` is distributed among soil levels by assuming that 50% is associated with the roots (using the CLM PFT-specific rooting distribution) and the rest is evenly divided among the top 0.28 m of soil (to be consistent with CLM's soil decomposition algorithm). For the vertically resolved BGC version, the prognosed distribution of :math:`{R}_{H}` is used to estimate CH\ :sub:`4` production. @@ -186,7 +186,7 @@ CLM represents CH\ :sub:`4` oxidation with double Michaelis-Menten kinetics (:re R_{oxic} =R_{o,\max } \left[\frac{C_{CH_{4} } }{K_{CH_{4} } +C_{CH_{4} } } \right]\left[\frac{C_{O_{2} } }{K_{O_{2} } +C_{O_{2} } } \right]Q_{10} F_{\vartheta } -where :math:`K_{CH_{4} }` and :math:`K_{O_{2} }` \ are the half saturation coefficients (mol m\ :sup:`-3`) with respect to CH\ :sub:`4` and O\ :sub:`2` concentrations, respectively; :math:`R_{o,\max }` is the maximum oxidation rate (mol m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` specifies the temperature dependence of the reaction with a base temperature set to 12 ° C. The soil moisture limitation factor :math:`F_{\theta }` is applied above the water table to represent water stress for methanotrophs. Based on the data in :ref:`Schnell and King (1996)`, we take :math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. +where :math:`K_{CH_{4} }` and :math:`K_{O_{2} }` \ are the half saturation coefficients (mol m\ :sup:`-3`) with respect to CH\ :sub:`4` and O\ :sub:`2` concentrations, respectively; :math:`R_{o,\max }` is the maximum oxidation rate (mol m\ :sup:`-3` s\ :sup:`-1`); and :math:`{Q}_{10}` specifies the temperature dependence of the reaction with a base temperature set to 12 °C. The soil moisture limitation factor :math:`F_{\theta }` is applied above the water table to represent water stress for methanotrophs. Based on the data in :ref:`Schnell and King (1996)`, we take :math:`F_{\theta } = {e}^{-P/{P}_{c}}`, where *P* is the soil moisture potential and :math:`{P}_{c} = -2.4 \times {10}^{5}` mm. .. _Reactive Transport Solution: diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index f1e573a98e..5ae6735906 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -157,7 +157,7 @@ The model uses co-limitation as described by :ref:`Collatz et al. (1991, 1992) < Values are :math:`\Theta _{cj} =0.98` and :math:`\Theta _{ip} =0.95` for C\ :sub:`3` plants; and :math:`\Theta _{cj} =0.80`\ and :math:`\Theta _{ip} =0.95` for C\ :sub:`4` plants. :math:`A_{i}` is the intermediate co-limited photosynthesis. :math:`A_{n} =A-R_{d}`. -The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 ° C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. +The parameters :math:`K_{c}`, :math:`K_{o}`, and :math:`\Gamma` depend on temperature. Values at 25 °C are :math:`K_{c25} ={\rm 4}0{\rm 4}.{\rm 9}\times 10^{-6} P_{atm}`, :math:`K_{o25} =278.4\times 10^{-3} P_{atm}`, and :math:`\Gamma _{25} {\rm =42}.75\times 10^{-6} P_{atm}`. :math:`V_{c\max }`, :math:`J_{\max }`, :math:`T_{p}`, :math:`k_{p}`, and :math:`R_{d}` also vary with temperature. :math:`J_{\max 25}` at 25 :sup:`\o`\ C: is calculated by the LUNA model (Chapter :numref:`rst_Photosynthetic Capacity`) @@ -246,14 +246,14 @@ In the model, acclimation is implemented as in :ref:`Kattge and Knorr (2007) `) based on an optimality hypothesis to nitrogen allocation among light capture, electron transport, carboxylation, respiration and storage. Specifically, the model allocates the nitrogen by maximizing the daily net photosynthetic carbon gain under following two key assumptions: +The photosynthetic capacity is represented by two key parameters: 1) the maximum rate of carboxylation at 25 °C, :math:`V_{\text{c,max25}}`; and 2) the maximum rate of electron transport at 25 °C, :math:`J_{\text{max25}}`. They are predicted by a mechanistic model of leaf utilization of nitrogen for assimilation (LUNA V1.0) (:ref:`Ali et al. 2016`) based on an optimality hypothesis to nitrogen allocation among light capture, electron transport, carboxylation, respiration and storage. Specifically, the model allocates the nitrogen by maximizing the daily net photosynthetic carbon gain under following two key assumptions: - nitrogen allocated for light capture, electron transport and carboxylation are co-limiting; @@ -183,14 +183,14 @@ where :math:`\text{PAR}_{\text{{max}}}` ( :math:`\mu mol`/m :sup:`2`/s) is the m Maximum rate of carboxylation '''''''''''''''''''''''''''''' -The maximum rate of carboxylation at 25° C varies with foliage nitrogen concentration and specific leaf area and is calculated as in :ref:`Thornton and Zimmermann (2007)`. At 25°C, +The maximum rate of carboxylation at 25°C varies with foliage nitrogen concentration and specific leaf area and is calculated as in :ref:`Thornton and Zimmermann (2007)`. At 25°C, .. math:: :label: 10.11) V_{c\max 25} = N_{cb} NUE_{V_{c\max 25}} -where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, :numref:`Table Plant functional type (PFT) leaf N parameters`), and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) measured at 25° C, and the constant 6.25 is the nitrogen binding factor for Rubisco (g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). +where :math:`N_{cb}` is nitrogen for carboxylation (g N m\ :sup:`-2` leaf, :numref:`Table Plant functional type (PFT) leaf N parameters`), and :math:`NUE_{V_{c\max 25}}` = 47.3 x 6.25 and is the nitrogen use efficiency for :math:`V_{c\max 25}`. The constant 47.3 is the specific Rubisco activity ( :math:`\mu` mol CO\ :sub:`2` g\ :sup:`-1` Rubisco s\ :sup:`-1`) measured at 25°C, and the constant 6.25 is the nitrogen binding factor for Rubisco (g Rubisco g\ :sup:`-1` N; :ref:`Rogers 2014`). :math:`V_{c\max 25}` additionally varies with daylength (:math:`DYL`) using the function :math:`f(DYL)`, which introduces seasonal variation to :math:`V_{c\max }` diff --git a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst index 0269454042..a9b7650bc4 100644 --- a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst +++ b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst @@ -38,7 +38,7 @@ The temperature dependance of leaf maintenance (dark) respiration is described i CF_{mr\_ froot} \_ =\sum _{j=1}^{nlevsoi}NS_{froot} rootfr_{j} MR_{base} MR_{Q10} ^{(Ts_{j} -20)/10} -where :math:`MR_{q10}` (= 2.0) is the temperature sensitivity for maintenance respiration, :math:`T_{2m}` (° C) is the air temperature at 2m height, :math:`Ts_{j}`* (° C) is the soil temperature at level *j*, and :math:`rootfr_{j}` is the fraction of fine roots distributed in soil level *j*. +where :math:`MR_{q10}` (= 2.0) is the temperature sensitivity for maintenance respiration, :math:`T_{2m}` (°C) is the air temperature at 2m height, :math:`Ts_{j}`* (°C) is the soil temperature at level *j*, and :math:`rootfr_{j}` is the fraction of fine roots distributed in soil level *j*. .. table:: Atkin leaf respiration model intercept values. From a90850ceff03a8abc30d02c75827ac52554e29e5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 12:18:23 -0600 Subject: [PATCH 1674/2067] Standardize use of "degree-days". --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 48 +++++++++---------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 593e30cb4d..ecffe65660 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -163,7 +163,7 @@ All crops must meet the following requirements between the minimum planting date {GDD_{8} \ge GDD_{\min } } \end{array} -where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are degree-days or ° days) tracked from April through September (NH) above 8°C with maximum daily increments of 30° days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. +where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are °C day) tracked from April through September (NH) above 8°C with maximum daily increments of 30 degree-days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, :math:`{GDD}_{mat}`, according to the following AgroIBIS rules: @@ -178,7 +178,7 @@ At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain pr GDD_{{\rm mat}}^{{\rm trop.soy}} =GDD_{{\rm 10}} & {\rm \; \; \; and\; \; \; } & GDD_{{\rm mat}}^{{\rm trop.soy}} <2100{}^\circ {\rm days} \end{array} -where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0°C, 8°C, and 10°C, respectively, with maximum daily increments of 26°days (for :math:`{GDD}_{0}`) or 30°days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: +where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0°C, 8°C, and 10°C, respectively, with maximum daily increments of 26degree-days (for :math:`{GDD}_{0}`) or 30degree-days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: .. math:: :label: 25.3 @@ -189,7 +189,7 @@ where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-ye GDD_{{\rm 10}} =GDD_{10} +T_{2{\rm m}} -T_{f} -10 & \quad {\rm \; \; \; where\; \; \; } & 0 \le T_{2{\rm m}} -T_{f} -10\le 30{}^\circ {\rm days} \end{array} -where, if :math:`{T}_{2m}` - :math:`{T}_{f}` takes on values outside the above ranges within a day, then it equals the minimum or maximum value in the range for that day. :math:`{T}_{f}` is the freezing temperature of water and equals 273.15 K, :math:`{T}_{2m}` is the 2-m air temperature in units of K, and *GDD* is in units of °days. +where, if :math:`{T}_{2m}` - :math:`{T}_{f}` takes on values outside the above ranges within a day, then it equals the minimum or maximum value in the range for that day. :math:`{T}_{f}` is the freezing temperature of water and equals 273.15 K, :math:`{T}_{2m}` is the 2-m air temperature in units of K, and *GDD* is in units of degree-days. .. _Leaf emergence: @@ -216,27 +216,27 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD .. table:: Crop phenology and morphology parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. - =================================== ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== - \ temperate corn spring wheat temperate soybean cotton rice sugarcane tropical corn tropical soybean miscanthus switchgrass - =================================== ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== - IVT 17, 18 19, 20 23, 24 41, 42 61, 62 67, 68 75, 76 77, 78 71, 72 73, 74 - :math:`Date_{planting}^{min}` April 1 April 1 May 1 April 1 Janurary 1 Janurary 1 March 20 April 15 April 1 April 1 - :math:`Date_{planting}^{max}` June 15 June 15 June 15 May 31 Feburary 28 March 31 April 15 June 31 June 15 June 15 - :math:`T_{p}`\(K) 283.15 280.15 286.15 294.15 294.15 294.15 294.15 294.15 283.15 283.15 - :math:`T_{p}^{ min }`\(K) 279.15 272.15 279.15 283.15 283.15 283.15 283.15 283.15 279.15 279.15 - :math:`{GDD}_{min}`\(°days) 50 50 50 50 50 50 50 50 50 50 - base temperature for GDD (°C) 8 0 10 10 10 10 10 10 8 8 - :math:`{GDD}_{mat}`\(°days) 950-1850 ≤ 1700 ≤ 1900 ≤ 1700 ≤ 2100 950-1850 950-1850 ≤ 2100 950-1850 950-1850 - Phase 2 % :math:`{GDD}_{mat}` 0.03 0.05 0.03 0.03 0.01 0.03 0.03 0.03 0.03 0.03 - Phase 3 % :math:`{GDD}_{mat}` 0.65 0.6 0.5 0.5 0.4 0.65 0.5 0.5 0.4 0.4 - Harvest: days past planting ≤ 165 ≤ 150 ≤ 150 ≤ 160 ≤ 150 ≤ 300 ≤ 160 ≤ 150 ≤ 210 ≤ 210 - :math:`z_{top}^{\max }` (m) 2.5 1.2 0.75 1.5 1.8 4 2.5 1 2.5 2.5 - SLA (m :sup:`2` leaf g :sup:`-1` C) 0.05 0.035 0.035 0.035 0.035 0.05 0.05 0.035 0.057 0.049 - :math:`\chi _{L}` index -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 - grperc 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 - flnr 0.293 0.41 0.41 0.41 0.41 0.293 0.293 0.41 0.293 0.293 - fcur 1 1 1 1 1 1 1 1 1 1 - =================================== ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== + ========================================= ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== + \ temperate corn spring wheat temperate soybean cotton rice sugarcane tropical corn tropical soybean miscanthus switchgrass + ========================================= ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== + IVT 17, 18 19, 20 23, 24 41, 42 61, 62 67, 68 75, 76 77, 78 71, 72 73, 74 + :math:`Date_{planting}^{min}` April 1 April 1 May 1 April 1 Janurary 1 Janurary 1 March 20 April 15 April 1 April 1 + :math:`Date_{planting}^{max}` June 15 June 15 June 15 May 31 Feburary 28 March 31 April 15 June 31 June 15 June 15 + :math:`T_{p}`\(K) 283.15 280.15 286.15 294.15 294.15 294.15 294.15 294.15 283.15 283.15 + :math:`T_{p}^{ min }`\(K) 279.15 272.15 279.15 283.15 283.15 283.15 283.15 283.15 279.15 279.15 + :math:`{GDD}_{min}` (degree-days) 50 50 50 50 50 50 50 50 50 50 + base temperature for GDD (°C) 8 0 10 10 10 10 10 10 8 8 + :math:`{GDD}_{mat}` (degree-days) 950-1850 ≤ 1700 ≤ 1900 ≤ 1700 ≤ 2100 950-1850 950-1850 ≤ 2100 950-1850 950-1850 + Phase 2 % :math:`{GDD}_{mat}` 0.03 0.05 0.03 0.03 0.01 0.03 0.03 0.03 0.03 0.03 + Phase 3 % :math:`{GDD}_{mat}` 0.65 0.6 0.5 0.5 0.4 0.65 0.5 0.5 0.4 0.4 + Harvest: days past planting ≤ 165 ≤ 150 ≤ 150 ≤ 160 ≤ 150 ≤ 300 ≤ 160 ≤ 150 ≤ 210 ≤ 210 + :math:`z_{top}^{\max }` (m) 2.5 1.2 0.75 1.5 1.8 4 2.5 1 2.5 2.5 + SLA (m :sup:`2` leaf g :sup:`-1` C) 0.05 0.035 0.035 0.035 0.035 0.05 0.05 0.035 0.057 0.049 + :math:`\chi _{L}` index -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 + grperc 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 + flnr 0.293 0.41 0.41 0.41 0.41 0.293 0.293 0.41 0.293 0.293 + fcur 1 1 1 1 1 1 1 1 1 1 + ========================================= ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== Notes: :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates in the Southern Hemisphere apply 6 months later. :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. Crop growth phases are described in the text. :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop, *SLA* is specific leaf area. :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. grperc is the growth respiration factor. flnr is the fraction of leaf N in the Rubisco enzyme. fcur is the fraction of allocation that goes to currently displayed growth. From ea4305377f7f42bf53aee73fe846fd5827b7ba5f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 12:20:53 -0600 Subject: [PATCH 1675/2067] Clean up some latitude ranges. --- doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst index 4222faf0e6..45689d613c 100644 --- a/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst +++ b/doc/source/tech_note/Isotopes/CLM50_Tech_Note_Isotopes.rst @@ -109,5 +109,5 @@ In the preindustrial biosphere, radioactive decay of :sup:`14`\ C in carbon pool For radioactive decay, at each timestep all :sup:`14`\ C pools are reduced at a rate of –log/:math:`\tau`, where :math:`\tau` is the half-life (Libby half-life value of 5568 years). In order to rapidly equilibrate the long-lived pools during accelerated decomposition spinup, the radioactive decay of the accelerated pools is also accelerated by the same degree as the decomposition, such that the :sup:`14`\ C value of these pools is in equilibrium when taken out of the spinup mode. -For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30 °N-90 °N, 30 °S-30 °N, and 30 °S-90 °S). +For variation of atmospheric :sup:`14`\ C and :sup:`13`\ C over the historical period, :math:`\mathrm{\Delta}`\ :sup:`14`\ C and :math:`\mathrm{\Delta}`\ :sup:`13`\ C values can be set to either fixed concentrations or time-varying concentrations read in from a file. A default file is provided that spans the historical period (:ref:`Graven et al., 2017 `). For :math:`\mathrm{\Delta}`\ :sup:`14`\ C, values are provided and read in for three latitude bands (30°N--90°N, 30°S--30°N, and 30°S--90°S). From 2da69a6d5791c4758f39cca57bb63968e8e6c516 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 12:25:41 -0600 Subject: [PATCH 1676/2067] Fix an equation rendering in VSCode. --- doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst index 1adcb03cf1..84dd2bcaaf 100644 --- a/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst +++ b/doc/source/tech_note/Fire/CLM50_Tech_Note_Fire.rst @@ -73,7 +73,7 @@ Fuel combustibility :math:`f_{m}` is estimated by .. math:: :label: 23.7 - f_{m} = {f_{RH} f_{\beta}}, &\qquad T_{17cm} > T_{f} + f_{m} = {f_{RH} f_{\beta}}, \qquad T_{17cm} > T_{f} where :math:`f_{RH}` and :math:`f_{\beta }` represent the dependence of fuel combustibility on relative humidity :math:`RH` (%) and root-zone soil moisture limitation :math:`\beta` (fraction); :math:`T_{17cm}` is the temperature of the top 17 cm of soil (K) and :math:`T_{f}` is the freezing temperature. :math:`f_{RH}` is a weighted average of real time :math:`RH` (:math:`RH_{0}`) and 30-day running mean :math:`RH` (:math:`RH_{30d}`): From 7e106c464f2cfb03999f9e626b012a3685d304d9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 12:31:31 -0600 Subject: [PATCH 1677/2067] Tiny fixes. --- .../CLM50_Tech_Note_External_Nitrogen_Cycle.rst | 5 ++--- .../Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 2 +- doc/source/users_guide/running-PTCLM/using-ptclm.rst | 4 ++-- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst index 1fb6da7e16..f594778562 100644 --- a/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst +++ b/doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst @@ -72,8 +72,7 @@ CLM includes a detailed representation of nitrification and denitrification base where :math:`{f}_{nitr,p}` is the potential nitrification rate (prior to competition for NH\ :sub:`4`\ :sup:`+` by plant uptake and N immobilization), :math:`{k}_{nitr}` is the maximum nitrification rate (10 % day\ :math:`\mathrm{-}`\ 1, (:ref:`Parton et al. 2001 `), and *f(T)* and *f(H\)*\ :sub:`2`\ O) are rate modifiers for temperature and moisture content. CLM uses the same rate modifiers as are used in the decomposition routine. *f(pH)* is a rate modifier for pH; however, because CLM does not calculate pH, instead a fixed pH value of 6.5 is used in the pH function of :ref:`Parton et al. (1996) `. -The potential denitrification rate is co-limited by -NO\ :sup:`-3` concentration and C consumption rates, and occurs only in the anoxic fraction of soils: +The potential denitrification rate is co-limited by NO\ :sup:`-3` concentration and C consumption rates, and occurs only in the anoxic fraction of soils: .. math:: :label: 22.3) @@ -137,5 +136,5 @@ where :math:`{WS}_{tot\_soil}` (kgH\ :sub:`2`\ O m\ :sup:`-2`) is the total mass Losses of Nitrogen Due to Fire ----------------------------------- -The final pathway for nitrogen loss is through combustion, also known as pyrodenitrification. Detailed equations are provided, together with the effects of fire on the carbon budget, in Chapter :numref:`rst_Fire`). It is assumed in CLM-CN that losses of N due to fire are restricted to vegetation and litter pools (including coarse woody debris). Loss rates of N are determined by the fraction of biomass lost to combustion, assuming that most of the nitrogen in the burned biomass is lost to the atmosphere (:ref:`Schlesinger, 1997 `; :ref:`Smith et al. 2005 `). It is assumed that soil organic matter pools of carbon and nitrogen are not directly affected by fire (:ref:`Neff et al. 2005 `). +The final pathway for nitrogen loss is through combustion, also known as pyrodenitrification. Detailed equations are provided, together with the effects of fire on the carbon budget, in Chapter :numref:`rst_Fire`. It is assumed in CLM-CN that losses of N due to fire are restricted to vegetation and litter pools (including coarse woody debris). Loss rates of N are determined by the fraction of biomass lost to combustion, assuming that most of the nitrogen in the burned biomass is lost to the atmosphere (:ref:`Schlesinger, 1997 `; :ref:`Smith et al. 2005 `). It is assumed that soil organic matter pools of carbon and nitrogen are not directly affected by fire (:ref:`Neff et al. 2005 `). diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index 5ae6735906..a86b945384 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -236,7 +236,7 @@ with :math:`Q_{10} =2`. +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ | :math:`K_{o}` | 36380 | – | +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ - | :math:`\Gamma _{*}` | 37830 | – | + | :math:`\Gamma _{*}` | 37830 | – | +------------------------+-----------------------------------------------------------------+-----------------------------------------------------------------+ In the model, acclimation is implemented as in :ref:`Kattge and Knorr (2007) `. In this parameterization, :math:`V_{c\max }` and :math:`J_{\max }` vary with the plant growth temperature. This is achieved by allowing :math:`\Delta S`\ to vary with growth temperature according to diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst index c161d2df39..c69e2cdd91 100644 --- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/using-ptclm.rst @@ -107,8 +107,8 @@ The options that with a "grid" suffix all mean to create datasets using the glob Because supported single-point datasets already have the data created for them, you MUST use the "nopointdata" and "ndepgrid" options when you are using a supported single-point site. You must use "ndepgrid" even for a compset without CN. You also can NOT use the options: "soilgrid", "pftgrid", "aerdepgrid", or "owritesrfaer". ``--pftgrid`` - This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/*_pftdata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. + This option says to use the PFT values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_pftdata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. ``--soilgrid`` - This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/*_soildata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. + This option says to use the soil values provided on the global dataset rather than using the specific site based values from the PTCLM_sitedata/\*_soildata.txt file when creating the surface dataset. This option must NOT be used when you you are using a site that is a supported single point dataset. From 995e775185d3e6db7561d591c42c1f90370f1337 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 19 Oct 2023 13:50:38 -0600 Subject: [PATCH 1678/2067] Update ChangeLog/ChangeSum with tag ctsm5.1.dev144. --- doc/ChangeLog | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 58 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index a01469e0c2..f5ee2785f8 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,61 @@ =============================================================== +Tag name: ctsm5.1.dev144 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Thu Oct 19 13:30:02 MDT 2023 +One-line Summary: Remove a deprecated shr_mpi_bcast call + +Purpose and description of changes +---------------------------------- + +Removes a use of the deprecated shr_mpi_mod, replacing with ESMF_VMBroadcast. In addition, since the last tag, some minor documentation changes have been made. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + +If the tag used for baseline comparisons was NOT the previous tag, note that here: Compared ctsm5.1.dev142 to a version of this branch (1f39800e1) with ctsm5.1.dev142 merged in. + + +Answer changes +-------------- + +Changes answers relative to baseline: No + +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +* #1991 (https://github.com/ESCOMP/CTSM/pull/1991) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev143 Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-) Date: Fri Oct 13 08:53:38 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index b6a5cdd29c..e1a1462981 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev144 samrabin 10/19/2023 Remove a deprecated shr_mpi_bcast call ctsm5.1.dev143 rgknox 10/13/2023 Zeroing of wood product fluxes on fates columns ctsm5.1.dev142 samrabin 09/19/2023 Merge 5 bit-for-bit pull requests ctsm5.1.dev141 slevis 09/13/2023 Change small snocan to zero From b338b2668b006b1cefdf7298c1659639731d2781 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 19 Oct 2023 13:28:00 -0700 Subject: [PATCH 1679/2067] Update fates external --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 6030bfea95..ea5a15eefb 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.68.0_api.27.0.0 +tag = sci.1.68.0_api.28.0.0 required = True [externals_description] From 5a2e0ff6b3309d6850c4cfadff3c37c069e331d0 Mon Sep 17 00:00:00 2001 From: glemieux Date: Mon, 23 Oct 2023 15:52:25 -0700 Subject: [PATCH 1680/2067] update changelog and changesum for ctsm5.1.dev145 --- doc/ChangeLog | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 95 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 537febda2c..58599534be 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,98 @@ =============================================================== +Tag name: ctsm5.1.dev146 +Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) +Date: Mon Oct 23 15:22:00 PM MDT 2023 +One-line Summary: FATES cross-grid seed dispersal + +Purpose and description of changes +---------------------------------- + +This PR enables FATES to disperse seeds across neighboring grid cells using MPI. +The API update includes calls to new fates dispersal procedures. There are +four parameters that are utilized to control the dispersal kernel, although +these were introduced in ctsm5.1.dev130 so no new default FATES parameter file +is necessary with this update. A new namelist parameter has been added to +enable the use of the seed dispersal mode. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +Known bugs introduced in this tag (include issue #): +- ESCOMP/CTSM#1089 (Cross-grid seed dispersal mechanism is not b4b for PE layout changes) + +Notes of particular relevance for users +--------------------------------------- +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- New namelist option, fates_seeddisp_cadence, added. This option Setting the switch +value to zero turns off dispersal. Setting the switch to 1, 2, or 3 sets the dispersal +cadence to daily, monthly or yearly. + +Substantial timing or memory changes: +- Users should be careful to limit the maximum dispersal distance parameter, +fates_seed_dispersal_max_dist, to a reasonable value based on the gridcell +resolution used. Using a very large value will increase the memory requirements +to store the gridcell neighborhood information. + +Notes of particular relevance for developers: +--------------------------------------------- +Caveats for developers (e.g., code that is duplicated that requires double maintenance): +- This PR introduces MPI calls to subroutines that are called by clm_driver. +Comments have been provided in code to make future developers aware of these +calls so as to avoid moving them into OpenMP threaded regions. + +Changes to tests or testing: +- Two new testmods have been added into the fates suite to test seed +dispersal. One of the tests is to track issue CTSM#1089 which was introduced +with this PR. + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- PASS + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: Only fates testmods in aux_clm are +answer changing due to science updates associated with externals update. + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +- fates: sci.1.67.2_api.27.0.0 -> sci.1.68.0_api.28.0.0 + +Pull Requests that document the changes (include PR ids): +https://github.com/ESCOMP/CTSM/pull/2077 +https://github.com/NGEET/fates/pull/1005 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev145 Originator(s): @cenlinhe (Cenlin He,UCAR/RAL), slevis (Samuel Levis,UCAR/TSS,303-665-1310) Date: Thu Oct 19 14:34:25 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index d53fd26b54..222d608adb 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev146 glemieux 10/23/2023 FATES cross-grid seed dispersal ctsm5.1.dev145 slevis 10/19/2023 SNICAR snow albedo scheme updates ctsm5.1.dev144 samrabin 10/19/2023 Remove a deprecated shr_mpi_bcast call ctsm5.1.dev143 rgknox 10/13/2023 Zeroing of wood product fluxes on fates columns From 528fc5c3079f853fc4debe9438de219d4fb0b9e9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 12:56:43 -0600 Subject: [PATCH 1681/2067] Convert crop phenology parameters table to list-table. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 224 ++++++++++++++++-- 1 file changed, 201 insertions(+), 23 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index ecffe65660..b29b943ff7 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -214,29 +214,207 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD .. _Table Crop phenology parameters: -.. table:: Crop phenology and morphology parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. - - ========================================= ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== - \ temperate corn spring wheat temperate soybean cotton rice sugarcane tropical corn tropical soybean miscanthus switchgrass - ========================================= ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== - IVT 17, 18 19, 20 23, 24 41, 42 61, 62 67, 68 75, 76 77, 78 71, 72 73, 74 - :math:`Date_{planting}^{min}` April 1 April 1 May 1 April 1 Janurary 1 Janurary 1 March 20 April 15 April 1 April 1 - :math:`Date_{planting}^{max}` June 15 June 15 June 15 May 31 Feburary 28 March 31 April 15 June 31 June 15 June 15 - :math:`T_{p}`\(K) 283.15 280.15 286.15 294.15 294.15 294.15 294.15 294.15 283.15 283.15 - :math:`T_{p}^{ min }`\(K) 279.15 272.15 279.15 283.15 283.15 283.15 283.15 283.15 279.15 279.15 - :math:`{GDD}_{min}` (degree-days) 50 50 50 50 50 50 50 50 50 50 - base temperature for GDD (°C) 8 0 10 10 10 10 10 10 8 8 - :math:`{GDD}_{mat}` (degree-days) 950-1850 ≤ 1700 ≤ 1900 ≤ 1700 ≤ 2100 950-1850 950-1850 ≤ 2100 950-1850 950-1850 - Phase 2 % :math:`{GDD}_{mat}` 0.03 0.05 0.03 0.03 0.01 0.03 0.03 0.03 0.03 0.03 - Phase 3 % :math:`{GDD}_{mat}` 0.65 0.6 0.5 0.5 0.4 0.65 0.5 0.5 0.4 0.4 - Harvest: days past planting ≤ 165 ≤ 150 ≤ 150 ≤ 160 ≤ 150 ≤ 300 ≤ 160 ≤ 150 ≤ 210 ≤ 210 - :math:`z_{top}^{\max }` (m) 2.5 1.2 0.75 1.5 1.8 4 2.5 1 2.5 2.5 - SLA (m :sup:`2` leaf g :sup:`-1` C) 0.05 0.035 0.035 0.035 0.035 0.05 0.05 0.035 0.057 0.049 - :math:`\chi _{L}` index -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 - grperc 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 - flnr 0.293 0.41 0.41 0.41 0.41 0.293 0.293 0.41 0.293 0.293 - fcur 1 1 1 1 1 1 1 1 1 1 - ========================================= ========================= ========================== ========================== ========================== ========================== ========================= ========================= ========================== ========================== ========================== +.. list-table:: Crop phenology and morphology parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. + :header-rows: 1 + + * - \ + - temperate corn + - spring wheat + - temperate soybean + - cotton + - rice + - sugarcane + - tropical corn + - tropical soybean + - miscanthus + - switchgrass + * - IVT + - 17, 18 + - 19, 20 + - 23, 24 + - 41, 42 + - 61, 62 + - 67, 68 + - 75, 76 + - 77, 78 + - 71, 72 + - 73, 74 + * - :math:`Date_{planting}^{min}` + - April 1 + - April 1 + - May 1 + - April 1 + - Janurary 1 + - Janurary 1 + - March 20 + - April 15 + - April 1 + - April 1 + * - :math:`Date_{planting}^{max}` + - June 15 + - June 15 + - June 15 + - May 31 + - Feburary 28 + - March 31 + - April 15 + - June 31 + - June 15 + - June 15 + * - :math:`T_{p}`\(K) + - 283.15 + - 280.15 + - 286.15 + - 294.15 + - 294.15 + - 294.15 + - 294.15 + - 294.15 + - 283.15 + - 283.15 + * - :math:`T_{p}^{ min }`\(K) + - 279.15 + - 272.15 + - 279.15 + - 283.15 + - 283.15 + - 283.15 + - 283.15 + - 283.15 + - 279.15 + - 279.15 + * - :math:`{GDD}_{min}` (degree-days) + - 50 + - 50 + - 50 + - 50 + - 50 + - 50 + - 50 + - 50 + - 50 + - 50 + * - base temperature for GDD (°C) + - 8 + - 0 + - 10 + - 10 + - 10 + - 10 + - 10 + - 10 + - 8 + - 8 + * - :math:`{GDD}_{mat}` (degree-days) + - 950-1850 + - ≤ 1700 + - ≤ 1900 + - ≤ 1700 + - ≤ 2100 + - 950-1850 + - 950-1850 + - ≤ 2100 + - 950-1850 + - 950-1850 + * - Phase 2 % :math:`{GDD}_{mat}` + - 0.03 + - 0.05 + - 0.03 + - 0.03 + - 0.01 + - 0.03 + - 0.03 + - 0.03 + - 0.03 + - 0.03 + * - Phase 3 % :math:`{GDD}_{mat}` + - 0.65 + - 0.6 + - 0.5 + - 0.5 + - 0.4 + - 0.65 + - 0.5 + - 0.5 + - 0.4 + - 0.4 + * - Harvest: days past planting + - ≤ 165 + - ≤ 150 + - ≤ 150 + - ≤ 160 + - ≤ 150 + - ≤ 300 + - ≤ 160 + - ≤ 150 + - ≤ 210 + - ≤ 210 + * - :math:`z_{top}^{\max }` (m) + - 2.5 + - 1.2 + - 0.75 + - 1.5 + - 1.8 + - 4 + - 2.5 + - 1 + - 2.5 + - 2.5 + * - SLA (m :sup:`2` leaf g :sup:`-1` C) + - 0.05 + - 0.035 + - 0.035 + - 0.035 + - 0.035 + - 0.05 + - 0.05 + - 0.035 + - 0.057 + - 0.049 + * - :math:`\chi _{L}` index + - -0.5 + - -0.5 + - -0.5 + - -0.5 + - -0.5 + - -0.5 + - -0.5 + - -0.5 + - -0.5 + - -0.5 + * - grperc + - 0.11 + - 0.11 + - 0.11 + - 0.11 + - 0.11 + - 0.11 + - 0.11 + - 0.11 + - 0.11 + - 0.11 + * - flnr + - 0.293 + - 0.41 + - 0.41 + - 0.41 + - 0.41 + - 0.293 + - 0.293 + - 0.41 + - 0.293 + - 0.293 + * - fcur + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 + - 1 Notes: :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates in the Southern Hemisphere apply 6 months later. :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. Crop growth phases are described in the text. :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop, *SLA* is specific leaf area. :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. grperc is the growth respiration factor. flnr is the fraction of leaf N in the Rubisco enzyme. fcur is the fraction of allocation that goes to currently displayed growth. From 54e71e8e77d1c587e9fb3c71289f7d70f83d48f0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:04:30 -0600 Subject: [PATCH 1682/2067] Improve some elements of crop phenology parameters table. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 62 +++++++++---------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index b29b943ff7..4642a3b0f0 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -317,38 +317,38 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD - 950-1850 - 950-1850 * - Phase 2 % :math:`{GDD}_{mat}` - - 0.03 - - 0.05 - - 0.03 - - 0.03 - - 0.01 - - 0.03 - - 0.03 - - 0.03 - - 0.03 - - 0.03 + - 3% + - 5% + - 3% + - 3% + - 1% + - 3% + - 3% + - 3% + - 3% + - 3% * - Phase 3 % :math:`{GDD}_{mat}` - - 0.65 - - 0.6 - - 0.5 - - 0.5 - - 0.4 - - 0.65 - - 0.5 - - 0.5 - - 0.4 - - 0.4 - * - Harvest: days past planting - - ≤ 165 - - ≤ 150 - - ≤ 150 - - ≤ 160 - - ≤ 150 - - ≤ 300 - - ≤ 160 - - ≤ 150 - - ≤ 210 - - ≤ 210 + - 65% + - 60% + - 50% + - 50% + - 40% + - 65% + - 50% + - 50% + - 40% + - 40% + * - Max. growing season length (:math:`mxmat`) + - 165 + - 150 + - 150 + - 160 + - 150 + - 300 + - 160 + - 150 + - 210 + - 210 * - :math:`z_{top}^{\max }` (m) - 2.5 - 1.2 From ebffd102e500a15c79f5a42fdda2094511f1821c Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 19:05:53 +0000 Subject: [PATCH 1683/2067] Resolve documentation problems in issue #2136 --- doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst | 6 +++--- doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst | 6 +++--- .../tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst | 4 ++-- doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst | 6 +++--- .../Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst | 4 ++-- .../Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst | 6 +++--- .../Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst | 6 +++--- 7 files changed, 19 insertions(+), 19 deletions(-) diff --git a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst index f1dd139cb5..ad593b6060 100644 --- a/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst +++ b/doc/source/tech_note/Dust/CLM50_Tech_Note_Dust.rst @@ -28,7 +28,7 @@ where :math:`f_{lake}` and :math:`f_{sno}` are the CLM grid cell fractions of la 0\le f_{v} =\frac{L+S}{\left(L+S\right)_{t} } \le 1{\rm \; \; \; \; where\; }\left(L+S\right)_{t} =0.3{\rm \; m}^{2} {\rm m}^{-2} -where equation applies only for dust mobilization and is not related to the plant functional type fractions prescribed from the CLM input data or simulated by the CLM dynamic vegetation model (Chapter 22). :math:`L` and :math:`S` are the CLM leaf and stem area index values (m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so as to include all the pfts and the bare ground present in a vegetated land unit. :math:`L` and :math:`S` may be prescribed from the CLM input data (section :numref:`Phenology and vegetation burial by snow`) or simulated by the CLM biogeochemistry model (Chapter :numref:`rst_Vegetation Phenology and Turnover`). +where equation :eq:`29.3` applies only for dust mobilization and is not related to the plant functional type fractions prescribed from the CLM input data or simulated by the CLM dynamic vegetation model (Chapter 22). :math:`L` and :math:`S` are the CLM leaf and stem area index values (m :sup:`2` m\ :sup:`-2`) averaged at the land unit level so as to include all the pfts and the bare ground present in a vegetated land unit. :math:`L` and :math:`S` may be prescribed from the CLM input data (section :numref:`Phenology and vegetation burial by snow`) or simulated by the CLM biogeochemistry model (Chapter :numref:`rst_Vegetation Phenology and Turnover`). The sandblasting mass efficiency :math:`\alpha` (m :sup:`-1`) is calculated as @@ -78,7 +78,7 @@ and w=\frac{\theta _{1} \rho _{liq} }{\rho _{d,1} } -where :math:`a=M_{clay}^{-1}` for tuning purposes, :math:`\theta _{1}` is the volumetric soil moisture in the top soil layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), :math:`\rho _{liq}` is the density of liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) defined as in section :numref:`Soil and Snow Thermal Properties` rather than as in :ref:`Zender et al. (2003)`. :math:`Re_{*t}^{f}` from equation is the threshold friction Reynolds factor +where :math:`a=M_{clay}^{-1}` for tuning purposes, :math:`\theta _{1}` is the volumetric soil moisture in the top soil layer (m :math:`{}^{3 }`\ m\ :sup:`-3`) (section :numref:`Soil Water`), :math:`\rho _{liq}` is the density of liquid water (kg m\ :sup:`-3`) (:numref:`Table Physical constants`), and :math:`\rho _{d,\, 1}` is the bulk density of soil in the top soil layer (kg m\ :sup:`-3`) defined as in section :numref:`Soil and Snow Thermal Properties` rather than as in :ref:`Zender et al. (2003)`. :math:`Re_{*t}^{f}` from equation :eq:`29.6` is the threshold friction Reynolds factor .. math:: :label: 29.10 @@ -110,7 +110,7 @@ where :math:`u_{*}` is the CLM wind friction speed (m s\ :sup:`-1`), also known U_{10,t} =u_{*t} \frac{U_{10} }{u_{*} } -In equation we sum :math:`M_{i,\, j}` over :math:`I=3` source modes :math:`i` where :math:`M_{i,\, j}` is the mass fraction of each source mode :math:`i` carried in each of *:math:`J=4`* transport bins :math:`j` +In equation :eq:`29.1` we sum :math:`M_{i,\, j}` over :math:`I=3` source modes :math:`i` where :math:`M_{i,\, j}` is the mass fraction of each source mode :math:`i` carried in each of *:math:`J=4`* transport bins :math:`j` .. math:: :label: 29.14 diff --git a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst index f70ca7c35a..c759d11f92 100644 --- a/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst +++ b/doc/source/tech_note/Fluxes/CLM50_Tech_Note_Fluxes.rst @@ -803,7 +803,7 @@ When the expression for :math:`T_{s}` is substituted into equation :eq:`5.88`, t H_{v} = -\rho _{atm} C_{p} \left[c_{a}^{h} \theta _{atm} +c_{g}^{h} T_{g} -\left(c_{a}^{h} +c_{g}^{h} \right)T_{v} \right]\frac{c_{v}^{h} }{c_{a}^{h} +c_{v}^{h} +c_{g}^{h} } . -Similarly, the expression for :math:`T_{s}` can be substituted into equation to obtain the sensible heat flux from ground :math:`H_{g}` +Similarly, the expression for :math:`T_{s}` can be substituted into equations :eq:`5.89`, :eq:`5.90`, :eq:`5.91`, and :eq:`5.92` to obtain the sensible heat flux from ground :math:`H_{g}` .. math:: :label: 5.98 @@ -1199,7 +1199,7 @@ The numerical solution for vegetation temperature and the fluxes of momentum, se #. An initial guess for the wind speed :math:`V_{a}` is obtained from :eq:`5.24` assuming an initial convective velocity :math:`U_{c} =0` m s\ :sup:`-1` for stable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} \ge 0` as evaluated from :eq:`5.50` ) and :math:`U_{c} =0.5` for unstable conditions (:math:`\theta _{v,\, atm} -\theta _{v,\, s} <0`). -#. An initial guess for the Monin-Obukhov length :math:`L` is obtained from the bulk Richardson number using equation and :eq:`5.46` and :eq:`5.48`. +#. An initial guess for the Monin-Obukhov length :math:`L` is obtained from the bulk Richardson number using equations :eq:`5.46` and :eq:`5.48`. #. Iteration proceeds on the following system of equations: @@ -1296,7 +1296,7 @@ The sensible and water vapor heat fluxes derived above for bare soil and soil be E'_{g} =E_{g} +\left(T_{g}^{n+1} -T_{g}^{n} \right)\frac{\partial E_{g} }{\partial T_{g} } -where :math:`H_{g}` and :math:`E_{g}` are the sensible heat and water vapor fluxes derived from equations and for non-vegetated surfaces and equations and for vegetated surfaces using :math:`T_{g}^{n}`. One further adjustment is made to :math:`H'_{g}` and :math:`E'_{g}`. If the soil moisture in the top snow/soil layer is not sufficient to support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and :math:`f_{evap} < 1` where +where :math:`H_{g}`, :math:`E_{g}`, :math:`\frac{\partial H_{g} }{\partial T_{g} }`, and :math:`\frac{\partial E_{g} }{\partial T_{g} }` are the sensible heat and water vapor fluxes and their partial derivatives derived from equations :eq:`5.62`, :eq:`5.66`, :eq:`5.83`, and :eq:`5.84` for non-vegetated surfaces and equations :eq:`5.89`, :eq:`5.102`, :eq:`5.123`, and :eq:`5.124` for vegetated surfaces using :math:`T_{g}^{n}`. One further adjustment is made to :math:`H'_{g}` and :math:`E'_{g}`. If the soil moisture in the top snow/soil layer is not sufficient to support the updated ground evaporation, i.e., if :math:`E'_{g} > 0` and :math:`f_{evap} < 1` where .. math:: :label: 5.142 diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 5599eeedd8..02188d5e25 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -358,7 +358,7 @@ For one-dimensional vertical water flow in soils, the conservation of mass is st where :math:`\theta` is the volumetric soil water content (mm\ :sup:`3` of water / mm\ :sup:`-3` of soil), :math:`t` is time (s), :math:`z` is height above some datum in the soil column (mm) (positive upwards), :math:`q` is soil water flux (kg m\ :sup:`-2` s\ :sup:`-1` or mm s\ :sup:`-1`) (positive upwards), and :math:`e` is a soil moisture sink term (mm of water mm\ :sup:`-1` of soil s\ :sup:`-1`) (ET loss). This equation is solved numerically by dividing the soil column into multiple layers in the vertical and integrating downward over each layer with an upper boundary condition of the infiltration flux into the top soil layer :math:`q_{infl}` and a zero-flux lower boundary condition at the bottom of the soil column (sub-surface runoff is removed later in the timestep, section :numref:`Lateral Sub-surface Runoff`). -The soil water flux :math:`q` in equation can be described by Darcy's law :ref:`(Dingman 2002) ` +The soil water flux :math:`q` in equation :eq:`7.79` can be described by Darcy's law :ref:`(Dingman 2002) ` .. math:: :label: 7.80 @@ -641,7 +641,7 @@ where The tridiagonal equation set is solved over :math:`i=1,\ldots,N_{levsoi}`. -The finite-difference forms of the fluxes and partial derivatives in equations :eq:`7.111` - :eq:`7.114` can be obtained from equation as +The finite-difference forms of the fluxes and partial derivatives in equations :eq:`7.111` - :eq:`7.114` can be obtained from equation :eq:`7.82` as .. math:: :label: 7.115 diff --git a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst index 18f6e1e8f4..88cb77d737 100644 --- a/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst +++ b/doc/source/tech_note/Lake/CLM50_Tech_Note_Lake.rst @@ -316,7 +316,7 @@ The fluxes of momentum, sensible heat, and water vapor are solved for simultaneo E_{g} =-\frac{\rho _{atm} }{r_{aw} } \left[q_{atm} -q_{sat}^{T_{g} } -\frac{\partial q_{sat}^{T_{g} } }{\partial T_{g} } \left(T_{g}^{n+1} -T_{g}^{n} \right)\right] -where the last term on the right side of equation is the change in saturated specific humidity due to the change in :math:`T_{g}` between iterations. +where the last term on the right side of equation :eq:`12.23` is the change in saturated specific humidity due to the change in :math:`T_{g}` between iterations. #. Saturated specific humidity :math:`q_{sat}^{T_{g} }` and its derivative :math:`\frac{dq_{sat}^{T_{g} } }{dT_{g} }` are updated for :math:`T_{g}^{n+1}` (section :numref:`Monin-Obukhov Similarity Theory`). @@ -337,7 +337,7 @@ Once the four iterations for lake surface temperature have been yielded a tentat where :math:`T_{m}` \ is the temperature of maximum liquid water density, 3.85°C (:ref:`Hostetler and Bartlein (1990) `). The first condition requires that, if there is any snow or ice present, the surface temperature is restricted to be less than or equal to freezing. The second and third conditions maintain convective stability in the top lake layer. -If eq. XXX is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance eq. XXX in order to precisely conserve energy. XXX This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). An energy balance check is included at each timestep to insure that eq. XXX is obeyed to within 0.1 W m\ :sup:`-2`. +If equation :eq:`12.24` is applied, the turbulent fluxes :math:`H_{g}` and :math:`E_{g}` are re-evaluated. The emitted longwave radiation and the momentum fluxes are re-evaluated in any case. The final ground heat flux :math:`G` is calculated from the residual of the energy balance (equation :eq:`12.7`) in order to precisely conserve energy. This ground heat flux is taken as a prescribed flux boundary condition for the lake temperature solution (section :numref:`Boundary Conditions Lake`). A check is included at each timestep to insure that energy balance is obeyed to within 0.1 W m\ :sup:`-2` (see :numref:`Energy Conservation Lake`). .. _Lake Temperature: @@ -678,7 +678,7 @@ The ice is lumped together at the top. For each lake layer *j* from 1 to *i* + 1 Energy Conservation ^^^^^^^^^^^^^^^^^^^^^^^^^^ -To check energy conservation, the left-hand side of eq. XXX is re-written to yield the total enthalpy of the lake system (J m\ :sup:`-2`) :math:`H_{tot}` : +To check energy conservation, the left-hand side of equation :eq:`12.27` is re-written to yield the total enthalpy of the lake system (J m\ :sup:`-2`) :math:`H_{tot}` : .. math:: :label: 12.57 diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index 5ee0087fec..baa05dff59 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -1,4 +1,4 @@ -.. _rst_Land-only Mode: + _rst_Land-only Mode: Land-Only Mode ================ @@ -21,7 +21,7 @@ The total solar radiation is also provided at three hour intervals. The data is S_{atm} \left(t_{M} \right)=0 & \qquad {\rm for\; }\mu \left(t_{M} \right)\le 0.001 \end{array} -where :math:`\Delta t_{FD}` is the time step of the forcing data (3 hours :math:`\times` 3600 seconds hour\ :sup:`-1` = 10800 seconds), :math:`\Delta t_{M}` is the model time step (seconds), :math:`S_{atm} \left(t_{FD} \right)` is the three-hourly solar radiation from the forcing data (W m\ :sup:`-2`), and :math:`\mu \left(t_{M} \right)` is the cosine of the solar zenith angle at model time step :math:`t_{M}` (section :numref:`Solar Zenith Angle`). The term in the denominator of equation (1) is the sum of the cosine of the solar zenith angle for each model time step falling within the three hour period. For numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. +where :math:`\Delta t_{FD}` is the time step of the forcing data (3 hours :math:`\times` 3600 seconds hour\ :sup:`-1` = 10800 seconds), :math:`\Delta t_{M}` is the model time step (seconds), :math:`S_{atm} \left(t_{FD} \right)` is the three-hourly solar radiation from the forcing data (W m\ :sup:`-2`), and :math:`\mu \left(t_{M} \right)` is the cosine of the solar zenith angle at model time step :math:`t_{M}` (section :numref:`Solar Zenith Angle`). The term in the denominator of equation :eq:`31.1` is the sum of the cosine of the solar zenith angle for each model time step falling within the three hour period. For numerical purposes, :math:`\mu \left(t_{M_{i} } \right)\ge 0.001`. The total incident solar radiation :math:`S_{atm}` at the model time step :math:`t_{M}` is then split into near-infrared and visible radiation and partitioned into direct and diffuse according to factors derived from one year's worth of hourly CAM output from CAM version cam3\_5\_55 as diff --git a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst index 5668af1a0b..fdc559e1c2 100644 --- a/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst +++ b/doc/source/tech_note/Snow_Hydrology/CLM50_Tech_Note_Snow_Hydrology.rst @@ -143,7 +143,7 @@ In the second step, after surface fluxes and snow/soil temperatures have been de w_{ice,\, snl+1}^{n+1} =w_{ice,\, snl+1}^{n} +f_{sno} \left(q_{frost} -q_{subl} \right)\Delta t. -If :math:`w_{ice,\, snl+1}^{n+1} <0` upon solution of equation, the ice content is reset to zero and the liquid water content :math:`w_{liq,\, snl+1}` is reduced by the amount required to bring :math:`w_{ice,\, snl+1}^{n+1}` up to zero. +If :math:`w_{ice,\, snl+1}^{n+1} <0` upon solution of equation :eq:`8.25`, the ice content is reset to zero and the liquid water content :math:`w_{liq,\, snl+1}` is reduced by the amount required to bring :math:`w_{ice,\, snl+1}^{n+1}` up to zero. The snow water equivalent :math:`W_{sno}` is capped to not exceed 10,000 kg m\ :sup:`-2`. If the addition of :math:`q_{frost}` were to result in :math:`W_{sno} > 10,000` kg m\ :sup:`-2`, the frost term :math:`q_{frost}` is instead added to the ice runoff term :math:`q_{snwcp,\, ice}` (section :numref:`Runoff from glaciers and snow-capped surfaces`). @@ -192,7 +192,7 @@ where the volumetric liquid water :math:`\theta _{liq,\, i}` and ice :math:`\the \theta _{liq,\, i} =\frac{w_{liq,\, i} }{f_{sno} \Delta z_{i} \rho _{liq} } \le 1-\theta _{ice,\, i} , -and :math:`S_{r} =0.033` is the irreducible water saturation (snow holds a certain amount of liquid water due to capillary retention after drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the underlying layer limits the flow of water :math:`q_{liq,\, i}` calculated in equation, unless the underlying layer is the surface soil layer, as +and :math:`S_{r} =0.033` is the irreducible water saturation (snow holds a certain amount of liquid water due to capillary retention after drainage has ceased (:ref:`Anderson (1976) `)). The water holding capacity of the underlying layer limits the flow of water :math:`q_{liq,\, i}` calculated in equation :eq:`8.29`, unless the underlying layer is the surface soil layer, as .. math:: :label: 8.32 @@ -206,7 +206,7 @@ The liquid water content :math:`w_{liq,\, i}` is updated as w_{liq,\, i}^{n+1} =w_{liq,\, i}^{n} +\left(q_{i-1} -q_{i} \right)\Delta t. -Equations - are solved sequentially from top (:math:`i=snl+1`) to bottom (:math:`i=0`) snow layer in each time step. The total flow of liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` which is used in the calculation of surface runoff and infiltration (sections :numref:`Surface Runoff` and :numref:`Infiltration`). +Equations :eq:`8.29` - :eq:`8.33` are solved sequentially from top (:math:`i=snl+1`) to bottom (:math:`i=0`) snow layer in each time step. The total flow of liquid water reaching the soil surface is then :math:`q_{liq,\, 0}` which is used in the calculation of surface runoff and infiltration (sections :numref:`Surface Runoff` and :numref:`Infiltration`). .. _Black and organic carbon and mineral dust within snow: diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index 54c50486f1..405a0bd014 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -105,7 +105,7 @@ where :math:`\bar{\theta }` is the mean leaf inclination angle relative to the h \cos \bar{\theta }=\frac{1+\chi _{L} }{2} -Using this approximation, for vertical leaves (:math:`\chi _{L} =-1`, :math:`\bar{\theta }=90^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =0.5\left(\alpha _{\Lambda } +\tau _{\Lambda } \right)`, and for horizontal leaves (:math:`\chi _{L} =1`, :math:`\bar{\theta }=0^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\alpha _{\Lambda }`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }`. This discrepancy arises from the fact that a spherical leaf angle distribution has a true mean leaf inclination :math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation, while :math:`\bar{\theta }=60` in equation. The upscatter for direct beam radiation is +Using this approximation, for vertical leaves (:math:`\chi _{L} =-1`, :math:`\bar{\theta }=90^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =0.5\left(\alpha _{\Lambda } +\tau _{\Lambda } \right)`, and for horizontal leaves (:math:`\chi _{L} =1`, :math:`\bar{\theta }=0^{{\rm o}}` ), :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} =\alpha _{\Lambda }`, which agree with both :ref:`Dickinson (1983) ` and :ref:`Sellers (1985) `. For random (spherically distributed) leaves (:math:`\chi _{L} =0`, :math:`\bar{\theta }=60^{{\rm o}}` ), the approximation yields :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={5\mathord{\left/ {\vphantom {5 8}} \right.} 8} \alpha _{\Lambda } +{3\mathord{\left/ {\vphantom {3 8}} \right.} 8} \tau _{\Lambda }` whereas the approximate solution of :ref:`Dickinson (1983) ` is :math:`\omega _{\Lambda }^{veg} \beta _{\Lambda }^{veg} ={2\mathord{\left/ {\vphantom {2 3}} \right.} 3} \alpha _{\Lambda } +{1\mathord{\left/ {\vphantom {1 3}} \right.} 3} \tau _{\Lambda }`. This discrepancy arises from the fact that a spherical leaf angle distribution has a true mean leaf inclination :math:`\bar{\theta }\approx 57` :ref:`(Campbell and Norman 1998) ` in equation :eq:`3.13`, while :math:`\bar{\theta }=60` in equation :eq:`3.14`. The upscatter for direct beam radiation is .. math:: :label: 3.15 @@ -572,7 +572,7 @@ Soil albedo (or underlying substrate albedo), which is defined for visible and N The radiative transfer calculation is performed twice for each column containing a mass of snow greater than :math:`1 \times 10^{-30}` kg\ m\ :sup:`-2` (excluding lake and urban columns); once each for direct-beam and diffuse incident flux. Absorption in each layer :math:`i` of pure snow is initially recorded as absorbed flux per unit incident flux on the ground (:math:`S_{sno,\, i}` ), as albedos must be calculated for the next timestep with unknown incident flux. The snow absorption fluxes that are used for column temperature calculations are .. math:: - :label: ZEqnNum275338 + :label: 3.69 S_{g,\, i} =S_{sno,\, i} \left(1-\alpha _{sno} \right) @@ -599,7 +599,7 @@ Broadband single-scatter albedo (:math:`\bar{\omega }`) is additionally weighted Inclusion of this additional albedo weight was found to improve accuracy of the five-band albedo solutions (relative to 470-band solutions) because of the strong dependence of optically-thick snowpack albedo on ice grain single-scatter albedo (:ref:`Flanner et al. (2007) `). The lookup tables contain optical properties for lognormal distributions of ice particles over the range of effective radii: 30\ :math:`\mu`\ m :math:`< r _{e} < \text{1500} \mu \text{m}`, at 1 :math:`\mu` m resolution. Single-scatter albedos for the end-members of this size range are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`. -Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. Single-scatter albedo, mass extinction cross-section, and asymmetry parameter values for all snowpack species, in the five spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, :numref:`Table Mass extinction values`, and :numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. These properties were also derived with Mie Theory, using various published sources of indices of refraction and assumptions about particle size distribution. Weighting into the five CLM spectral bands was determined only with incident solar flux, as in equation. +Optical properties for black carbon are described in :ref:`Flanner et al. (2007) `. Single-scatter albedo, mass extinction cross-section, and asymmetry parameter values for all snowpack species, in the five spectral bands used, are listed in :numref:`Table Single-scatter albedo values used for snowpack impurities and ice`, :numref:`Table Mass extinction values`, and :numref:`Table Asymmetry scattering parameters used for snowpack impurities and ice`. These properties were also derived with Mie Theory, using various published sources of indices of refraction and assumptions about particle size distribution. Weighting into the five CLM spectral bands was determined only with incident solar flux, as in equation :eq:`3.69`. .. _Table Single-scatter albedo values used for snowpack impurities and ice: From bf7825d91caf123866653af3a90f74c2a7fd471c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:21:51 -0600 Subject: [PATCH 1684/2067] Convert crop phenology parameters table notes to bulleted list. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 4642a3b0f0..c8401fdb46 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -416,7 +416,19 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD - 1 - 1 -Notes: :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates in the Southern Hemisphere apply 6 months later. :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. Crop growth phases are described in the text. :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop, *SLA* is specific leaf area. :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. grperc is the growth respiration factor. flnr is the fraction of leaf N in the Rubisco enzyme. fcur is the fraction of allocation that goes to currently displayed growth. +Notes: + +- :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates in the Southern Hemisphere apply 6 months later. +- :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. +- :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). +- :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. +- Crop growth phases are described in the text. +- :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop. +- *SLA* is specific leaf area. +- :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. +- grperc is the growth respiration factor. +- flnr is the fraction of leaf N in the Rubisco enzyme. +- fcur is the fraction of allocation that goes to currently displayed growth. .. _Allocation: From 6604c49644a9ee9b9f453cb9ddcfa9f464316753 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:23:21 -0600 Subject: [PATCH 1685/2067] Crop phen. params table notes: Improve min/max planting dates. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index c8401fdb46..35fe650d89 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -418,7 +418,7 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD Notes: -- :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting date in the Northern Hemisphere, the corresponding dates in the Southern Hemisphere apply 6 months later. +- :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) - :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. - :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). - :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. From fc5896339bbb61cad6e7f4e0dcfa1567271901f8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:24:31 -0600 Subject: [PATCH 1686/2067] Crop phen. params table notes: Add ref. for Tp variables. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 35fe650d89..e8d9146e16 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -419,7 +419,7 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD Notes: - :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) -- :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. +- :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. (See Sect. :numref:`Planting`.) - :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). - :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. - Crop growth phases are described in the text. From eb34902b395ad22eb5c839f66715f9a31bc4693b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:25:08 -0600 Subject: [PATCH 1687/2067] Crop phen. params table notes: Improve GDDmin. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index e8d9146e16..13f22023a8 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -420,7 +420,7 @@ Notes: - :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) - :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. (See Sect. :numref:`Planting`.) -- :math:`{GDD}_{min}` is the lowest (for planting) 20-year running mean growing degree-days based on the base temperature threshold in the 7\ :sup:`th` row, tracked from April to September (NH). +- :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. - :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. - Crop growth phases are described in the text. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop. From b939a67359d2f04e66aaadc1f0153f7b40ca7ede Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:25:48 -0600 Subject: [PATCH 1688/2067] Crop phen. params table notes: Improve GDDmat. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 13f22023a8..cd43afa479 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -421,7 +421,7 @@ Notes: - :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) - :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. (See Sect. :numref:`Planting`.) - :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. -- :math:`{GDD}_{mat}` is a crop's 20-year running mean growing degree-days needed for vegetative and physiological maturity. Harvest occurs at 100%\ :math:`{GDD}_{mat}` or when the days past planting reach the number in the 11\ :sup:`th` row. +- :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. Heat unit index can be "boosted" to the Phase 3 (grain fill) threshold value if it is below that threshold but maximum leaf area index has been reached; see Sect. :numref:`Grain fill`. - Crop growth phases are described in the text. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop. - *SLA* is specific leaf area. From ee4e4042df21afc54c3719b30b2522e44699393e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:27:04 -0600 Subject: [PATCH 1689/2067] Crop phen. params table notes: Add mxmat. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index cd43afa479..17ed13806d 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -422,6 +422,7 @@ Notes: - :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. (See Sect. :numref:`Planting`.) - :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. - :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. Heat unit index can be "boosted" to the Phase 3 (grain fill) threshold value if it is below that threshold but maximum leaf area index has been reached; see Sect. :numref:`Grain fill`. +- :math:`mxmat` is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached :math:`GDD_{mat}`. - Crop growth phases are described in the text. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop. - *SLA* is specific leaf area. From 3fb56ee90e60d847b4d1e596eef20da707ef5190 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:27:17 -0600 Subject: [PATCH 1690/2067] Crop phen. params table notes: Remove unneeded line. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 17ed13806d..1488fdb42c 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -423,7 +423,6 @@ Notes: - :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. - :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. Heat unit index can be "boosted" to the Phase 3 (grain fill) threshold value if it is below that threshold but maximum leaf area index has been reached; see Sect. :numref:`Grain fill`. - :math:`mxmat` is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached :math:`GDD_{mat}`. -- Crop growth phases are described in the text. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop. - *SLA* is specific leaf area. - :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. From ebe37e53bb1c19feb04a627b72e972f511e0fcc5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:27:44 -0600 Subject: [PATCH 1691/2067] Crop phen. params table notes: Add z-top-max ref. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 1488fdb42c..830c92496e 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -423,7 +423,7 @@ Notes: - :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. - :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. Heat unit index can be "boosted" to the Phase 3 (grain fill) threshold value if it is below that threshold but maximum leaf area index has been reached; see Sect. :numref:`Grain fill`. - :math:`mxmat` is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached :math:`GDD_{mat}`. -- :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop. +- :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop (see Sect. :numref:`Vegetation Structure`). - *SLA* is specific leaf area. - :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. - grperc is the growth respiration factor. From 978e5f99515b7798203c9ed23a8cb6aac891f6fc Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:28:00 -0600 Subject: [PATCH 1692/2067] Crop phen. params table notes: Add SLA ref. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 830c92496e..a88a9aef6b 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -424,7 +424,7 @@ Notes: - :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. Heat unit index can be "boosted" to the Phase 3 (grain fill) threshold value if it is below that threshold but maximum leaf area index has been reached; see Sect. :numref:`Grain fill`. - :math:`mxmat` is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached :math:`GDD_{mat}`. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop (see Sect. :numref:`Vegetation Structure`). -- *SLA* is specific leaf area. +- SLA is specific leaf area (see Chapter :numref:`rst_Photosynthetic Capacity`). - :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. - grperc is the growth respiration factor. - flnr is the fraction of leaf N in the Rubisco enzyme. From 86f59698d4d88c0a18327bfafdb78d3c5066687a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:28:41 -0600 Subject: [PATCH 1693/2067] Crop phen. params table notes: Add grperc ref. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- .../Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index a88a9aef6b..58c86e0c01 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -426,7 +426,7 @@ Notes: - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop (see Sect. :numref:`Vegetation Structure`). - SLA is specific leaf area (see Chapter :numref:`rst_Photosynthetic Capacity`). - :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. -- grperc is the growth respiration factor. +- grperc is the growth respiration factor (see Sect. :numref:`Growth Respiration`). - flnr is the fraction of leaf N in the Rubisco enzyme. - fcur is the fraction of allocation that goes to currently displayed growth. diff --git a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst index a9b7650bc4..588e7e0060 100644 --- a/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst +++ b/doc/source/tech_note/Plant_Respiration/CLM50_Tech_Note_Plant_Respiration.rst @@ -70,6 +70,8 @@ The total maintenance respiration cost is then given as: CF_{mr} =CF_{mr\_ leaf} +CF_{mr\_ froot} +CF_{mr\_ livestem} +CF_{mr\_ livecroot} . +.. _Growth Respiration: + Growth Respiration ^^^^^^^^^^^^^^^^^^^^^^^^^ From 0639596619c441fe4bf928a9b5fd00ace1c95303 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:33:36 -0600 Subject: [PATCH 1694/2067] Crop phen. params table notes: Add chi_L ref. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 58c86e0c01..3b6049d571 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -425,7 +425,7 @@ Notes: - :math:`mxmat` is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached :math:`GDD_{mat}`. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop (see Sect. :numref:`Vegetation Structure`). - SLA is specific leaf area (see Chapter :numref:`rst_Photosynthetic Capacity`). -- :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. +- :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. (See Sect. :numref:`Canopy Radiative Transfer`.) - grperc is the growth respiration factor (see Sect. :numref:`Growth Respiration`). - flnr is the fraction of leaf N in the Rubisco enzyme. - fcur is the fraction of allocation that goes to currently displayed growth. From e582db78ae8ad91d539f3805e8271f02be022598 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:45:55 -0600 Subject: [PATCH 1695/2067] Crop phen. params table notes: Added flnr ref. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- .../CLM50_Tech_Note_Photosynthetic_Capacity.rst | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 3b6049d571..4734b077cb 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -427,8 +427,8 @@ Notes: - SLA is specific leaf area (see Chapter :numref:`rst_Photosynthetic Capacity`). - :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. (See Sect. :numref:`Canopy Radiative Transfer`.) - grperc is the growth respiration factor (see Sect. :numref:`Growth Respiration`). -- flnr is the fraction of leaf N in the Rubisco enzyme. - fcur is the fraction of allocation that goes to currently displayed growth. +- flnr is the fraction of leaf N in the Rubisco enzyme (a.k.a. :math:`N_{cb}` in Sect. :numref:`Plant Nitrogen`). .. _Allocation: diff --git a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst index 68b2853bda..0701685061 100755 --- a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst +++ b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst @@ -29,6 +29,8 @@ The above four parameters are estimated by fitting the LUNA model to a global co Model structure ---------------------------------------------------------- +.. _Plant Nitrogen: + Plant Nitrogen '''''''''''''''''''''''''' From 7852eaac143fa126d41866b009131db3ca5dfd23 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:46:09 -0600 Subject: [PATCH 1696/2067] Crop phen. params table notes: Added fcur ref. --- .../tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst | 2 ++ .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst index 7cf6ec6fc8..1c0e5dee57 100644 --- a/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst +++ b/doc/source/tech_note/CN_Allocation/CLM50_Tech_Note_CN_Allocation.rst @@ -172,6 +172,8 @@ Since the C:N stoichiometry for new growth allocation is defined, from Eq., as : NF_{plant\_ demand} =CF_{avail\_ alloc} \frac{N_{allom} }{C_{allom} } . +.. _Carbon Allocation to New Growth: + Carbon Allocation to New Growth ----------------------------------------- diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 4734b077cb..3bd0eda3e6 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -427,8 +427,8 @@ Notes: - SLA is specific leaf area (see Chapter :numref:`rst_Photosynthetic Capacity`). - :math:`\chi _{L}` is the leaf orientation index, equals -1 for vertical, 0 for random, and 1 for horizontal leaf orientation. (See Sect. :numref:`Canopy Radiative Transfer`.) - grperc is the growth respiration factor (see Sect. :numref:`Growth Respiration`). -- fcur is the fraction of allocation that goes to currently displayed growth. - flnr is the fraction of leaf N in the Rubisco enzyme (a.k.a. :math:`N_{cb}` in Sect. :numref:`Plant Nitrogen`). +- fcur is the fraction of allocation that goes to currently displayed growth (i.e., that is not sent to storage). See Sect. :numref:`Carbon Allocation to New Growth`. .. _Allocation: From 45a3f7efc53c07d5805f336da866bb3d00fd05e4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 13:48:10 -0600 Subject: [PATCH 1697/2067] Crop phen. params table notes: Improve GDDmat clarity, reduce redundancy. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 3bd0eda3e6..2e6aa7e44a 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -421,7 +421,7 @@ Notes: - :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) - :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. (See Sect. :numref:`Planting`.) - :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. -- :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. Heat unit index can be "boosted" to the Phase 3 (grain fill) threshold value if it is below that threshold but maximum leaf area index has been reached; see Sect. :numref:`Grain fill`. +- :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. - :math:`mxmat` is the maximum growing season length (days past planting), at which harvest occurs even if heat unit index has not reached :math:`GDD_{mat}`. - :math:`z_{top}^{\max }` is the maximum top-of-canopy height of a crop (see Sect. :numref:`Vegetation Structure`). - SLA is specific leaf area (see Chapter :numref:`rst_Photosynthetic Capacity`). From 88d8fa16cfa47d4e7c823bf6046de99ce97c18da Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 20:02:37 +0000 Subject: [PATCH 1698/2067] Resolve documentation issues identified in issue #872 --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index ecffe65660..0b87314361 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -533,25 +533,25 @@ The soil moisture deficit :math:`D_{irrig}` is D_{irrig} = \left\{ \begin{array}{lr} - w_{thresh} - w_{avail} &\qquad w_{thresh} > w_{avail} \\ + w_{target} - w_{avail} &\qquad w_{thresh} > w_{avail} \\ 0 &\qquad w_{thresh} \le w_{avail} \end{array} \right\} -where :math:`w_{thresh}` is the irrigation moisture threshold (mm) and :math:`w_{avail}` is the available moisture (mm). The moisture threshold is +where :math:`w_{target}` is the irrigation target soil moisture (mm) .. math:: :label: 25.62 - w_{thresh} = f_{thresh} \left(w_{target} - w_{wilt}\right) + w_{wilt} + w_{target} = \sum_{j=1}^{N_{irr}} \theta_{target} \Delta z_{j} \ . -where :math:`w_{target}` is the irrigation target soil moisture (mm) +The irrigation moisture threshold (mm) is .. math:: :label: 25.63 - w_{target} = \sum_{j=1}^{N_{irr}} \theta_{target} \Delta z_{j} \ , + w_{thresh} = f_{thresh} \left(w_{target} - w_{wilt}\right) + w_{wilt} -:math:`w_{wilt}` is the wilting point soil moisture (mm) +where :math:`w_{wilt}` is the wilting point soil moisture (mm) .. math:: :label: 25.64 @@ -559,13 +559,15 @@ where :math:`w_{target}` is the irrigation target soil moisture (mm) w_{wilt} = \sum_{j=1}^{N_{irr}} \theta_{wilt} \Delta z_{j} \ , and :math:`f_{thresh}` is a tuning parameter. The available moisture in -the soil is +the soil (mm) is .. math:: :label: 25.65 w_{avail} = \sum_{j=1}^{N_{irr}} \theta_{j} \Delta z_{j} \ , +Note that :math:`w_{target}` is truly supposed to give the target soil moisture value that we're shooting for whenever irrigation happens; then the soil moisture deficit :math:`D_{irrig}` gives the difference between this target value and the current soil moisture. The irrigation moisture threshold :math:`w_{thresh}`, on the other hand, gives a threshold at which we decide to do any irrigation at all. The way this is written allows for the possibility that one may not want to irrigate every time there becomes even a tiny soil moisture deficit. Instead, one may want to wait until the deficit is larger before initiating irrigation; at that point, one doesn't want to just irrigate up to the "threshold" but instead up to the higher "target". The target should always be greater than or equal to the threshold. + :math:`N_{irr}` is the index of the soil layer corresponding to a specified depth :math:`z_{irrig}` (:numref:`Table Irrigation parameters`) and :math:`\Delta z_{j}` is the thickness of the soil layer in layer :math:`j` (section :numref:`Vertical Discretization`). :math:`\theta_{j}` is the volumetric soil moisture in layer :math:`j` (section :numref:`Soil Water`). :math:`\theta_{target}` and :math:`\theta_{wilt}` are the target and wilting point volumetric soil moisture values, respectively, and are determined by inverting :eq:`7.94` using soil matric potential parameters :math:`\Psi_{target}` and :math:`\Psi_{wilt}` (:numref:`Table Irrigation parameters`). After the soil moisture deficit :math:`D_{irrig}` is calculated, irrigation in an amount equal to :math:`\frac{D_{irrig}}{T_{irrig}}` (mm/s) is applied uniformly over the irrigation period :math:`T_{irrig}` (s). Irrigation water is applied directly to the ground surface, bypassing canopy interception (i.e., added to :math:`{q}_{grnd,liq}`: section :numref:`Canopy Water`). To conserve mass, irrigation is removed from river water storage (Chapter :numref:`rst_River Transport Model (RTM)`). When river water storage is inadequate to meet irrigation demand, there are two options: 1) the additional water can be removed from the ocean model, or 2) the irrigation demand can be reduced such that river water storage is maintained above a specified threshold. From 5de0b2a3379b4ac660bea351dfb98cf58fc83583 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 14:14:56 -0600 Subject: [PATCH 1699/2067] Crops & irrigation: Capitalize PFT. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 2e6aa7e44a..588e83bd4f 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -59,15 +59,15 @@ With interactive crop management and, therefore, a more accurate representation Crop plant functional types ^^^^^^^^^^^^^^^^^^^^^^^^^^^ -To allow crops to coexist with natural vegetation in a grid cell, the vegetated land unit is separated into a naturally vegetated land unit and a managed crop land unit. Unlike the plant functional types (pfts) in the naturally vegetated land unit, the managed crop pfts in the managed crop land unit do not share soil columns and thus permit for differences in the land management between crops. Each crop type has a rainfed and an irrigated pft that are on independent soil columns. Crop grid cell coverage is assigned from satellite data (similar to all natural pfts), and the managed crop type proportions within the crop area is based on the dataset created by :ref:`Portmann et al. (2010)` for present day. New in CLM5, crop area is extrapolated through time using the dataset provided by Land Use Model Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries (:ref:`Lawrence et al. 2016 `). For more details about how crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. +To allow crops to coexist with natural vegetation in a grid cell, the vegetated land unit is separated into a naturally vegetated land unit and a managed crop land unit. Unlike the plant functional types (PFTs) in the naturally vegetated land unit, the managed crop PFTs in the managed crop land unit do not share soil columns and thus permit for differences in the land management between crops. Each crop type has a rainfed and an irrigated PFT that are on independent soil columns. Crop grid cell coverage is assigned from satellite data (similar to all natural PFTs), and the managed crop type proportions within the crop area is based on the dataset created by :ref:`Portmann et al. (2010)` for present day. New in CLM5, crop area is extrapolated through time using the dataset provided by Land Use Model Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries (:ref:`Lawrence et al. 2016 `). For more details about how crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. CLM5 includes ten actively managed crop types (temperate soybean, tropical soybean, temperate corn, tropical corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen based on the availability of corresponding algorithms in AgroIBIS and as developed by :ref:`Badger and Dirmeyer (2015)` and described by :ref:`Levis et al. (2016)`, or from available observations as described by :ref:`Cheng et al. (2019)`. The representations of sugarcane, rice, cotton, tropical corn, and tropical soy are new in CLM5. Miscanthus and switchgrass are added after the CLM5 release. Sugarcane and tropical corn are both C4 plants and are therefore represented using the temperate corn functional form. Tropical soybean uses the temperate soybean functional form, while rice and cotton use the wheat functional form. In tropical regions, parameter values were developed for the Amazon Basin, and planting date window is shifted by six months relative to the Northern Hemisphere. Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and have quite different physiological traits and land management practices than annual crops, such as longer growing seasons, higher productivity, and lower demands for nutrients and water. About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using observation data collected at the University of Illinois Energy Farm located in Central Midwestern United States (:ref:`Cheng et al., 2019`). -In addition, CLM's default list of plant functional types (pfts) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. The unmanaged C3 crop is only used when the crop model is not active and has grid cell coverage assigned from satellite data, and the unmanaged C3 irrigated crop type is currently not used since irrigation requires the crop model to be active. The default list of pfts also includes twenty-one inactive crop pfts that do not yet have associated parameters required for active management. Each of the inactive crop types is simulated using the parameters of the spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), which is required to maintain similar phenological parameters based on temperature thresholds. Information detailing which parameters are used for each crop type is included in :numref:`Table Crop plant functional types`. It should be noted that pft-level history output merges all crop types into the actively managed crop type, so analysis of crop-specific output will require use of the land surface dataset to remap the yields of each actively and inactively managed crop type. Otherwise, the actively managed crop type will include yields for that crop type and all inactively managed crop types that are using the same parameter set. +In addition, CLM's default list of plant functional types (PFTs) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. The unmanaged C3 crop is only used when the crop model is not active and has grid cell coverage assigned from satellite data, and the unmanaged C3 irrigated crop type is currently not used since irrigation requires the crop model to be active. The default list of PFTs also includes twenty-one inactive crop PFTs that do not yet have associated parameters required for active management. Each of the inactive crop types is simulated using the parameters of the spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), which is required to maintain similar phenological parameters based on temperature thresholds. Information detailing which parameters are used for each crop type is included in :numref:`Table Crop plant functional types`. It should be noted that PFT-level history output merges all crop types into the actively managed crop type, so analysis of crop-specific output will require use of the land surface dataset to remap the yields of each actively and inactively managed crop type. Otherwise, the actively managed crop type will include yields for that crop type and all inactively managed crop types that are using the same parameter set. .. _Table Crop plant functional types: -.. table:: Crop plant functional types (pfts) included in CLM5BGCCROP. +.. table:: Crop plant functional types (PFTs) included in CLM5BGCCROP. === =========================== ================ =========================== IVT Plant function types (PFTs) Management Class Crop Parameters Used @@ -165,7 +165,7 @@ All crops must meet the following requirements between the minimum planting date where :math:`{T}_{10d}` is the 10-day running mean of :math:`{T}_{2m}`, (the simulated 2-m air temperature during each model time step) and :math:`T_{10d}^{\min}` is the 10-day running mean of :math:`T_{2m}^{\min }` (the daily minimum of :math:`{T}_{2m}`). :math:`{T}_{p}` and :math:`T_{p}^{\min }` are crop-specific coldest planting temperatures (:numref:`Table Crop phenology parameters`), :math:`{GDD}_{8}` is the 20-year running mean growing degree-days (units are °C day) tracked from April through September (NH) above 8°C with maximum daily increments of 30 degree-days (see equation :eq:`25.3`), and :math:`{GDD}_{min }`\ is the minimum growing degree day requirement (:numref:`Table Crop phenology parameters`). :math:`{GDD}_{8}` does not change as quickly as :math:`{T}_{10d}` and :math:`T_{10d}^{\min }`, so it determines whether it is warm enough for the crop to be planted in a grid cell, while the 2-m air temperature variables determine the day when the crop may be planted if the :math:`{GDD}_{8}` threshold is met. If the requirements in equation :eq:`25.1` are not met by the maximum planting date, crops are still planted on the maximum planting date as long as :math:`{GDD}_{8} > 0`. In the southern hemisphere (SH) the NH requirements apply 6 months later. -At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the pft's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, :math:`{GDD}_{mat}`, according to the following AgroIBIS rules: +At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain product pool. The seed carbon is transferred to the leaves upon leaf emergence. An equivalent amount of seed leaf N is assigned given the PFT's C to N ratio for leaves (:math:`{CN}_{leaf}` in :numref:`Table Crop allocation parameters`; this differs from AgroIBIS, which uses a seed leaf area index instead of seed C). The model updates the average growing degree-days necessary for the crop to reach vegetative and physiological maturity, :math:`{GDD}_{mat}`, according to the following AgroIBIS rules: .. math:: :label: 25.2 @@ -203,7 +203,7 @@ According to AgroIBIS, leaves may emerge when the growing degree-days of soil te Grain fill '''''''''' -The grain fill phase (phase 3) begins in one of two ways. The first potential trigger is based on temperature, similar to phase 2. A variable tracked since planting, similar to :math:`GDD_{T_{soi} }` but for 2-m air temperature, :math:`GDD_{T_{{\rm 2m}} }`, must reach a heat unit threshold, *h*, of of 40 to 65% of :math:`{GDD}_{mat}` (see Phase 3 % :math:`{GDD}_{mat}` in :numref:`Table Crop phenology parameters`). For crops with the C4 photosynthetic pathway (temperate and tropical corn, sugarcane), the :math:`{GDD}_{mat}` is based on an empirical function and ranges between 950 and 1850. The second potential trigger for phase 3 is based on leaf area index. When the maximum value of leaf area index is reached in phase 2 (:numref:`Table Crop allocation parameters`), phase 3 begins. In phase 3, the leaf area index begins to decline in response to a background litterfall rate calculated as the inverse of leaf longevity for the pft as done in the BGC part of the model. +The grain fill phase (phase 3) begins in one of two ways. The first potential trigger is based on temperature, similar to phase 2. A variable tracked since planting, similar to :math:`GDD_{T_{soi} }` but for 2-m air temperature, :math:`GDD_{T_{{\rm 2m}} }`, must reach a heat unit threshold, *h*, of of 40 to 65% of :math:`{GDD}_{mat}` (see Phase 3 % :math:`{GDD}_{mat}` in :numref:`Table Crop phenology parameters`). For crops with the C4 photosynthetic pathway (temperate and tropical corn, sugarcane), the :math:`{GDD}_{mat}` is based on an empirical function and ranges between 950 and 1850. The second potential trigger for phase 3 is based on leaf area index. When the maximum value of leaf area index is reached in phase 2 (:numref:`Table Crop allocation parameters`), phase 3 begins. In phase 3, the leaf area index begins to decline in response to a background litterfall rate calculated as the inverse of leaf longevity for the PFT as done in the BGC part of the model. .. _Harvest: @@ -214,7 +214,7 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD .. _Table Crop phenology parameters: -.. list-table:: Crop phenology and morphology parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. +.. list-table:: Crop phenology and morphology parameters for the active crop plant functional types (PFTs) in CLM5BGCCROP. Numbers in the first row correspond to the list of PFTs in :numref:`Table Crop plant functional types`. :header-rows: 1 * - \ @@ -614,7 +614,7 @@ Whereas food C and N was formerly transferred to the litter pool, CLM5 routes fo .. _Table Crop allocation parameters: -.. table:: Crop allocation parameters for the active crop plant functional types (pfts) in CLM5BGCCROP. Numbers in the first row correspond to the list of pfts in :numref:`Table Crop plant functional types`. +.. table:: Crop allocation parameters for the active crop plant functional types (PFTs) in CLM5BGCCROP. Numbers in the first row correspond to the list of PFTs in :numref:`Table Crop plant functional types`. =========================================== ============== ============ ================== ====== ====== ========= ============= ================ ================ ================ \ temperate corn spring wheat temperate soybean cotton rice sugarcane tropical corn tropical soybean miscanthus switchgrass @@ -680,7 +680,7 @@ where *n* is set to 20 fertilizer application days and 86400 is the number of se Biological nitrogen fixation for soybeans ''''''''''''''''''''''''''''''''''''''''' -Biological N fixation for soybeans is calculated by the fixation and uptake of nitrogen module (Chapter :numref:`rst_FUN`) and is the same as N fixation in natural vegetation. Unlike natural vegetation, where a fraction of each pft are N fixers, all soybeans are treated as N fixers. +Biological N fixation for soybeans is calculated by the fixation and uptake of nitrogen module (Chapter :numref:`rst_FUN`) and is the same as N fixation in natural vegetation. Unlike natural vegetation, where a fraction of each PFT are N fixers, all soybeans are treated as N fixers. .. _Latitude vary base tempereature for growing degree days: From 790bfdd8cc2541d11c91e1c49ef4ff6c0cf1a168 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 14:23:49 -0600 Subject: [PATCH 1700/2067] Crop & irrigation: Typo/formatting fixes. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 588e83bd4f..9de4830623 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -52,7 +52,7 @@ Groups developing Earth System Models generally account for the human footprint AgroIBIS is a state-of-the-art land surface model with options to simulate dynamic vegetation (:ref:`Kucharik et al. 2000 `) and interactive crop management (:ref:`Kucharik and Brye 2003 `). The interactive crop management parameterizations from AgroIBIS (March 2003 version) were coupled as a proof-of-concept to the Community Land Model version 3 [CLM3.0, :ref:`Oleson et al. (2004) ` ] (not published), then coupled to the CLM3.5 (:ref:`Levis et al. 2009 `) and later released to the community with CLM4CN (:ref:`Levis et al. 2012 `), and CLM4.5BGC. Additional updates after the release of CLM4.5 were available by request (:ref:`Levis et al. 2016 `), and those are now incorporated into CLM5. -With interactive crop management and, therefore, a more accurate representation of agricultural landscapes, we hope to improve the CLM's simulated biogeophysics and biogeochemistry. These advances may improve fully coupled simulations with the Community Earth System Model (CESM), while helping human societies answer questions about changing food, energy, and water resources in response to climate, environmental, land use, and land management change (e.g., :ref:`Kucharik and Brye 2003 `; :ref:`Lobell et al. 2006 `). As implemented here, the crop model uses the same physiology as the natural vegetation, though uses different crop-specific parameter values, phenology, and allocation, as well as fertilizer and irrigation management. +With interactive crop management and, therefore, a more accurate representation of agricultural landscapes, we hope to improve the CLM's simulated biogeophysics and biogeochemistry. These advances may improve fully coupled simulations with the Community Earth System Model (CESM), while helping human societies answer questions about changing food, energy, and water resources in response to climate, environmental, land use, and land management change (e.g., :ref:`Kucharik and Brye 2003 `; :ref:`Lobell et al. 2006 `). As implemented here, the crop model uses the same physiology as the natural vegetation but with uses different crop-specific parameter values, phenology, and allocation, as well as fertilizer and irrigation management. .. _Crop plant functional types: @@ -61,7 +61,7 @@ Crop plant functional types To allow crops to coexist with natural vegetation in a grid cell, the vegetated land unit is separated into a naturally vegetated land unit and a managed crop land unit. Unlike the plant functional types (PFTs) in the naturally vegetated land unit, the managed crop PFTs in the managed crop land unit do not share soil columns and thus permit for differences in the land management between crops. Each crop type has a rainfed and an irrigated PFT that are on independent soil columns. Crop grid cell coverage is assigned from satellite data (similar to all natural PFTs), and the managed crop type proportions within the crop area is based on the dataset created by :ref:`Portmann et al. (2010)` for present day. New in CLM5, crop area is extrapolated through time using the dataset provided by Land Use Model Intercomparison Project (LUMIP), which is part of CMIP6 Land use timeseries (:ref:`Lawrence et al. 2016 `). For more details about how crop distributions are determined, see Chapter :numref:`rst_Transient Landcover Change`. -CLM5 includes ten actively managed crop types (temperate soybean, tropical soybean, temperate corn, tropical corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen based on the availability of corresponding algorithms in AgroIBIS and as developed by :ref:`Badger and Dirmeyer (2015)` and described by :ref:`Levis et al. (2016)`, or from available observations as described by :ref:`Cheng et al. (2019)`. The representations of sugarcane, rice, cotton, tropical corn, and tropical soy are new in CLM5. Miscanthus and switchgrass are added after the CLM5 release. Sugarcane and tropical corn are both C4 plants and are therefore represented using the temperate corn functional form. Tropical soybean uses the temperate soybean functional form, while rice and cotton use the wheat functional form. In tropical regions, parameter values were developed for the Amazon Basin, and planting date window is shifted by six months relative to the Northern Hemisphere. Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and have quite different physiological traits and land management practices than annual crops, such as longer growing seasons, higher productivity, and lower demands for nutrients and water. About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using observation data collected at the University of Illinois Energy Farm located in Central Midwestern United States (:ref:`Cheng et al., 2019`). +CLM5 includes ten actively managed crop types (temperate soybean, tropical soybean, temperate corn, tropical corn, spring wheat, cotton, rice, sugarcane, miscanthus, and switchgrass) that are chosen based on the availability of corresponding algorithms in AgroIBIS and as developed by :ref:`Badger and Dirmeyer (2015)` and described by :ref:`Levis et al. (2016)`, or from available observations as described by :ref:`Cheng et al. (2019)`. The representations of sugarcane, rice, cotton, tropical corn, and tropical soy were new in CLM5; miscanthus and switchgrass were added after the CLM5 release. Sugarcane and tropical corn are both C4 plants and are therefore represented using the temperate corn functional form. Tropical soybean uses the temperate soybean functional form, while rice and cotton use the wheat functional form. In tropical regions, parameter values were developed for the Amazon Basin, and planting date window is shifted by six months relative to the Northern Hemisphere. Plantation areas of bioenergy crops are projected to expand throughout the 21st century as a major energy source to replace fossil fuels and mitigate climate change. Miscanthus and switchgrass are perennial bioenergy crops and have quite different physiological traits and land management practices than annual crops, such as longer growing seasons, higher productivity, and lower demands for nutrients and water. About 70% of biofuel aboveground biomass (leaf & livestem) is removed at harvest. Parameter values were developed by using observation data collected at the University of Illinois Energy Farm located in Central Midwestern United States (:ref:`Cheng et al., 2019`). In addition, CLM's default list of plant functional types (PFTs) includes an irrigated and unirrigated unmanaged C3 crop (:numref:`Table Crop plant functional types`) treated as a second C3 grass. The unmanaged C3 crop is only used when the crop model is not active and has grid cell coverage assigned from satellite data, and the unmanaged C3 irrigated crop type is currently not used since irrigation requires the crop model to be active. The default list of PFTs also includes twenty-one inactive crop PFTs that do not yet have associated parameters required for active management. Each of the inactive crop types is simulated using the parameters of the spatially closest associated crop type that is most similar to the functional type (e.g., C3 or C4), which is required to maintain similar phenological parameters based on temperature thresholds. Information detailing which parameters are used for each crop type is included in :numref:`Table Crop plant functional types`. It should be noted that PFT-level history output merges all crop types into the actively managed crop type, so analysis of crop-specific output will require use of the land surface dataset to remap the yields of each actively and inactively managed crop type. Otherwise, the actively managed crop type will include yields for that crop type and all inactively managed crop types that are using the same parameter set. @@ -178,7 +178,7 @@ At planting, each crop seed pool is assigned 3 gC m\ :sup:`-2` from its grain pr GDD_{{\rm mat}}^{{\rm trop.soy}} =GDD_{{\rm 10}} & {\rm \; \; \; and\; \; \; } & GDD_{{\rm mat}}^{{\rm trop.soy}} <2100{}^\circ {\rm days} \end{array} -where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0°C, 8°C, and 10°C, respectively, with maximum daily increments of 26degree-days (for :math:`{GDD}_{0}`) or 30degree-days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: +where :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` are the 20-year running mean growing degree-days tracked from April through September (NH) over 0°C, 8°C, and 10°C, respectively, with maximum daily increments of 26 degree-days (for :math:`{GDD}_{0}`) or 30 degree-days (for :math:`{GDD}_{8}` and :math:`{GDD}_{10}`). Equation :eq:`25.3` shows how we calculate :math:`{GDD}_{0}`, :math:`{GDD}_{8}`, and :math:`{GDD}_{10}` for each model timestep: .. math:: :label: 25.3 @@ -483,7 +483,7 @@ where :math:`a_{leaf}^{i,3}` and :math:`a_{livestem}^{i,3}` (initial values) equ Nitrogen retranslocation for crops '''''''''''''''''''''''''''''''''' -Nitrogen retranslocation in crops occurs when nitrogen that was used for tissue growth of leaves, stems, and fine roots during the early growth season is remobilized and used for grain development (:ref:`Pollmer et al. 1979 `, :ref:`Crawford et al. 1982 `, :ref:`Simpson et al. 1983 `, :ref:`Ta and Weiland 1992 `, :ref:`Barbottin et al. 2005 `, :ref:`Gallais et al. 2006 `, :ref:`Gallais et al. 2007 `). Nitrogen allocation for crops follows that of natural vegetation, is supplied in CLM by the soil mineral nitrogen pool, and depends on C:N ratios for leaves, stems, roots, and organs. Nitrogen demand during organ development is fulfilled through retranslocation from leaves, stems, and roots. Nitrogen retranslocation is initiated at the beginning of the grain fill stage for all crops except soybean, for which retranslocation is after LAI decline. Nitrogen stored in the leaf and stem is moved into a storage retranslocation pool for all crops, and for wheat and rice, nitrogen in roots is also released into the retranslocation storage pool. The quantity of nitrogen mobilized depends on the C:N ratio of the plant tissue, and is calculated as +Nitrogen retranslocation in crops occurs when nitrogen that was used for tissue growth of leaves, stems, and fine roots during the early growth season is remobilized and used for grain development (:ref:`Pollmer et al. 1979 `, :ref:`Crawford et al. 1982 `, :ref:`Simpson et al. 1983 `, :ref:`Ta and Weiland 1992 `, :ref:`Barbottin et al. 2005 `, :ref:`Gallais et al. 2006 `, :ref:`Gallais et al. 2007 `). Nitrogen allocation for crops follows that of natural vegetation, is supplied in CLM by the soil mineral nitrogen pool, and depends on C:N ratios for leaves, stems, roots, and organs. Nitrogen demand during organ development is fulfilled through retranslocation from leaves, stems, and roots. Nitrogen retranslocation is initiated at the beginning of the grain fill stage for all crops except soybean, for which retranslocation is after LAI decline. Nitrogen stored in the leaf and stem is moved into a storage retranslocation pool for all crops, and for wheat and rice, nitrogen in roots is also released into the retranslocation storage pool. The quantity of nitrogen mobilized depends on the C:N ratio of the plant tissue and is calculated as .. math:: :label: 25.6 @@ -667,7 +667,7 @@ where :math:`z_{top}^{\max }` is the maximum top-of-canopy height of the crop (: Interactive Fertilization ''''''''''''''''''''''''' -CLM simulates fertilization by adding nitrogen directly to the soil mineral nitrogen pool to meet crop nitrogen demands using both industrial fertilizer and manure application. CLM's separate crop land unit ensures that natural vegetation will not access the fertilizer applied to crops. Fertilizer in CLM5BGCCROP is prescribed by crop functional types and varies spatially for each year based on the LUMIP land use and land cover change time series (LUH2 for historical and SSPs for future) (:ref:`Lawrence et al. 2016 `). One of two fields is used to prescribe industrial fertilizer based on the type of simulation. For non-transient simulations, annual fertilizer application in g N/m\ :sup:`2`/yr is specified on the land surface data set by the field CONST_FERTNITRO_CFT. In transient simulations, annual fertilizer application is specified on the land use time series file by the field FERTNITRO_CFT, which is also in g N/m\ :sup:`2`/yr. The values for both of these fields come from the LUMIP time series for each year. In addition to the industrial fertilizer, background manure fertilizer is specified on the parameter file by the field 'manunitro'. For perennial bioenergy crops, little fertilizer (56kg/ha/yr) is applied to switchgrass, no fertilizer is applied to Miscanthus. Note these rates are only based on local land management practices at the University of Illinois Energy Farm located in Central Midwestern United States :ref:`(Cheng et al., 2019)` rather than the LUMIP timeseries. For the current CLM5BGCCROP, manure N is applied at a rate of 0.002 kg N/m\ :sup:`2`/yr. Because previous versions of CLM (e.g., CLM4) had rapid denitrification rates, fertilizer is applied slowly to minimize N loss (primarily through denitrification) and maximize plant uptake. The current implementation of CLM5 inherits this legacy, although denitrification rates are slower in the current version of the model (:ref:`Koven et al. 2013 `). As such, fertilizer application begins during the leaf emergence phase of crop development (phase 2) and continues for 20 days, which helps reduce large losses of nitrogen from leaching and denitrification during the early stage of crop development. The 20-day period is chosen as an optimization to limit fertilizer application to the emergence stage. A fertilizer counter in seconds, *f*, is set as soon as the leaf emergence phase for crops initiates: +CLM simulates fertilization by adding nitrogen directly to the soil mineral nitrogen pool to meet crop nitrogen demands using both industrial fertilizer and manure application. CLM's separate crop land unit ensures that natural vegetation will not access the fertilizer applied to crops. Fertilizer in CLM5BGCCROP is prescribed by crop functional types and varies spatially for each year based on the LUMIP land use and land cover change time series (LUH2 for historical and SSPs for future) (:ref:`Lawrence et al. 2016 `). One of two fields is used to prescribe industrial fertilizer based on the type of simulation. For non-transient simulations, annual fertilizer application in g N/m\ :sup:`2`/yr is specified on the land surface data set by the field CONST_FERTNITRO_CFT. In transient simulations, annual fertilizer application is specified on the land use time series file by the field FERTNITRO_CFT, which is also in g N/m\ :sup:`2`/yr. The values for both of these fields come from the LUMIP time series for each year. In addition to the industrial fertilizer, background manure fertilizer is specified on the parameter file by the field ``manunitro``. For perennial bioenergy crops, little fertilizer (56kg/ha/yr) is applied to switchgrass and no fertilizer is applied to Miscanthus. Note these rates are only based on local land management practices at the University of Illinois Energy Farm located in Central Midwestern United States :ref:`(Cheng et al., 2019)` rather than the LUMIP timeseries. For the current CLM5BGCCROP, manure N is applied at a rate of 0.002 kg N/m\ :sup:`2`/yr. Because previous versions of CLM (e.g., CLM4) had rapid denitrification rates, fertilizer is applied slowly to minimize N loss (primarily through denitrification) and maximize plant uptake. The current implementation of CLM5 inherits this legacy, although denitrification rates are slower in the current version of the model (:ref:`Koven et al. 2013 `). As such, fertilizer application begins during the leaf emergence phase of crop development (phase 2) and continues for 20 days, which helps reduce large losses of nitrogen from leaching and denitrification during the early stage of crop development. The 20-day period is chosen as an optimization to limit fertilizer application to the emergence stage. A fertilizer counter in seconds, *f*, is set as soon as the leaf emergence phase for crops initiates: .. math:: :label: 25.17 @@ -686,7 +686,7 @@ Biological N fixation for soybeans is calculated by the fixation and uptake of n Latitudinal variation in base growth tempereature ''''''''''''''''''''''''''''''''''''''''''''''''' -For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) is the same in all locations. However, the for both rainfed and irrigated spring wheat and sugarcane, the calculation of :math:`GDD_{T_{{\rm 2m}} }` allows for latitudinal variation: +For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) is the same in all locations. However, for both rainfed and irrigated spring wheat and sugarcane, the calculation of :math:`GDD_{T_{{\rm 2m}} }` allows for latitudinal variation: .. math:: :label: 25.18 @@ -697,7 +697,7 @@ For most crops, :math:`GDD_{T_{{\rm 2m}} }` (growing degree days since planting) baset +12 + 0.4 \times latitude &\qquad -30 \le latitude \le 0 \end{array} \right\} -where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. Such latitudinal variation in base growth temperature could increase the base temperature, slow down :math:`GDD_{T_{{\rm 2m}} }` accumulation, and extend the growing season for regions within 30°S to 30°N for spring wheat and sugarcane. +where :math:`baset` is the *base temperature for GDD* (7\ :sup:`th` row) in :numref:`Table Crop phenology parameters`. Such latitudinal variation in base temperature could slow :math:`GDD_{T_{{\rm 2m}} }` accumulation extend the growing season for regions within 30°S to 30°N for spring wheat and sugarcane. .. _Separate reproductive pool: @@ -748,8 +748,7 @@ where :math:`w_{target}` is the irrigation target soil moisture (mm) w_{wilt} = \sum_{j=1}^{N_{irr}} \theta_{wilt} \Delta z_{j} \ , -and :math:`f_{thresh}` is a tuning parameter. The available moisture in -the soil is +and :math:`f_{thresh}` is a tuning parameter. The available moisture in the soil is .. math:: :label: 25.65 From 4dbd9686702098acf8876f2a0d824fc376bbdfa2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 14:30:23 -0600 Subject: [PATCH 1701/2067] Crop & irrigation Tech Note: mention sowing window start/end date input files. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 9de4830623..9bb1be0f43 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -418,7 +418,7 @@ Harvest is assumed to occur as soon as the crop reaches maturity. When :math:`GD Notes: -- :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) +- :math:`Date_{planting}^{min}` and :math:`Date_{planting}^{max}` are the minimum and maximum planting dates (defining the "sowing window") in the Northern Hemisphere; the corresponding dates in the Southern Hemisphere are shifted by 6 months. (See Sect. :numref:`Planting`.) These parameters can also be set with more geographic variation via input map stream files ``stream_fldFileName_swindow_start`` and ``stream_fldFileName_swindow_end``. - :math:`T_{p}` and :math:`T_{p}^{ min }` are crop-specific average and coldest planting temperatures, respectively. (See Sect. :numref:`Planting`.) - :math:`GDD_{min}` is a threshold describing the coolest historical climate a patch can have had in order for a crop to be sown there; see Sect. :numref:`Planting` for details. - :math:`GDD_{mat}` is the heat unit index, in units of accumulated growing degree-days, a crop needs to reach maturity. From cda9d1988c3b025a28e7159ea04e4a166d78d271 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 15:49:51 -0600 Subject: [PATCH 1702/2067] User's Guide: Add instructions for running w/ custom crop calendars. --- .../running-special-cases/index.rst | 1 + .../running-with-custom-crop-calendars.rst | 96 +++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 doc/source/users_guide/running-special-cases/running-with-custom-crop-calendars.rst diff --git a/doc/source/users_guide/running-special-cases/index.rst b/doc/source/users_guide/running-special-cases/index.rst index f84b7706fb..896eafef34 100644 --- a/doc/source/users_guide/running-special-cases/index.rst +++ b/doc/source/users_guide/running-special-cases/index.rst @@ -17,6 +17,7 @@ Running Special Cases what-is-a-special-case.rst running-the-prognostic-crop-model.rst running-with-irrigation.rst + running-with-custom-crop-calendars.rst Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst Spinning-up-the-biogeochemistry-BGC-spinup.rst Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst diff --git a/doc/source/users_guide/running-special-cases/running-with-custom-crop-calendars.rst b/doc/source/users_guide/running-special-cases/running-with-custom-crop-calendars.rst new file mode 100644 index 0000000000..b19ebcdb09 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/running-with-custom-crop-calendars.rst @@ -0,0 +1,96 @@ +.. running-with-custom-crop-calendars: + +.. include:: ../substitutions.rst + +======================================= + Running with custom crop calendars +======================================= + +Since CLM5.1, functionality has been added to enable the customization of crop sowing window and maturity requirements. + +Sowing window +------------- +Crops are allowed to be sown only within certain date windows. By default, these are static in time and specific to each crop in each hemisphere. These values can be inspected by looking at (and changed by modifying) the following variables on the parameter file: + +- ``min_NH_planting_date`` (start of sowing window, northern hemisphere) +- ``max_NH_planting_date`` (end of sowing window, northern hemisphere) +- ``min_SH_planting_date`` (start of sowing window, southern hemisphere) +- ``max_SH_planting_date`` (end of sowing window, southern hemisphere) + +However, geographically- and temporally-varying maps can also be used to prescribe sowing window like so (in ``user_nl_clm``): +:: + + ! Input files with maps of the start and end date (1-365) of every crop + stream_fldFileName_swindow_start = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' + stream_fldFileName_swindow_end = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' + + ! A mesh file matching the resolution of the sowing window datasets + stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc' + + ! First and last years on the sowing window datasets + stream_year_first_cropcal = 2000 + stream_year_last_cropcal = 2000 + +Sowing date +----------- +Specific sowing *dates* can be prescribed for any crop in any gridcell by setting the start and end dates of its sowing windows to the same value. The simplest way to do this for all crops in all gridcells is to specify the same file for both ``stream_fldFileName_swindow_start`` and ``stream_fldFileName_swindow_end``. + +.. note:: In cells with prescribed sowing dates, the usual weather- and climate-based criteria for determining whether planting is allowed are ignored. The crop will be planted on the prescribed day no matter what. + +Maturity requirements +--------------------- +The heat unit accumulation required for a crop to reach maturity (and thus be harvested) is typically determined by a formula with crop-specific parameters that are specified on the parameter file. However, geographically- and temporally-varying maps of maturity requirement (in units of degree-days) can also be specified using the ``user_nl_clm`` input variable ``stream_fldFileName_cultivar_gdds``. (Note that ``stream_meshfile_cropcal``, ``stream_year_first_cropcal``, and ``stream_year_last_cropcal``---see above---are all also required.) + +Generating maturity requirements +-------------------------------- +For phase 3 of the Global Gridded Crop Model Intercomparison (GGCMI), maturity requirements should be the average (over the 1980--2009 growing seasons) growing degree-days accumulated between specified observation-derived sowing and harvest dates. In CLM, this requires the use of a special "GDD-generating" run and some postprocessing. + +In a GDD-generating run, crops are planted on the specified sowing dates and are then left in the field---regardless of when they reach maturity and ignoring maximum growing season length---for 364 days. This is set up like so in ``user_nl_clm``: +:: + + ! Variables that we introduced above + stream_fldFileName_swindow_start = '/path/to/sowing_date_file.nc' + stream_fldFileName_swindow_end = '/path/to/sowing_date_file.nc' + stream_meshfile_cropcal = '/path/to/mesh_file.nc' + stream_year_first_cropcal = YEAR + stream_year_last_cropcal = YEAR + + ! Special settings for "GDD-generating" run + generate_crop_gdds = .true. + use_mxmat = .false. + + ! (h0) Save default variables monthly instead of daily to save space + hist_nhtfrq = 0 + hist_mfilt = 12 + + ! (h1) Annual outputs for GDD generation + hist_fincl2 = 'GRAINC_TO_FOOD_PERHARV', 'GRAINC_TO_FOOD_ANN', 'SDATES', 'SDATES_PERHARV', 'SYEARS_PERHARV', 'HDATES', 'GDDHARV_PERHARV', 'GDDACCUM_PERHARV', 'HUI_PERHARV', 'SOWING_REASON_PERHARV', 'HARVEST_REASON_PERHARV' + hist_nhtfrq(2) = 17520 + hist_mfilt(2) = 999 + hist_type1d_pertape(2) = 'PFTS' + hist_dov2xy(2) = .false. + + ! (h2) Daily outputs for GDD generation + hist_fincl3 = 'GDDACCUM', 'GDDHARV' + hist_nhtfrq(3) = -24 + hist_mfilt(3) = 365 + hist_type1d_pertape(3) = 'PFTS' + hist_dov2xy(3) = .false. + +Once the GDD-generating run completes, calling the following Python script will generate a file that can serve as ``stream_fldFileName_cultivar_gdds`` in subsequent runs (along with maps illustrating the results): +:: + + python3 python/ctsm/crop_calendars/generate_gdds.py \ + --input-dir /path/to/output/dir/from/gdd-generating-run \ + --first-season 1980 \ + --last-season 2009 \ + --sdates-file '/path/to/sowing_date_file.nc' \ + --hdates-file '/path/to/harvest_date_file.nc' \ + --output-dir '/path/where/you/want/results/saved' \ + --skip-crops miscanthus,irrigated_miscanthus + +The entire process can be illustrated with the RXCROPMATURITY system test. E.g.: + +:: + + run_sys_tests -t RXCROPMATURITY_Lm61.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-cropMonthOutput --skip-generate --skip-compare \ No newline at end of file From fd4a2623c64ddca056712b7e68a1b15d79469c04 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 15:59:10 -0600 Subject: [PATCH 1703/2067] Crop & irrigation Tech Note: Use GRAINC_TO_FOOD_ANN. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 9bb1be0f43..a7362c7bd0 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -605,12 +605,14 @@ where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is | Switchgrass | 0.70 | +----------------------------------+----------------------------+ -Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. Calcuating the crop yields (Equation :eq:`25.15`) requires that you sum the GRAINC_TO_FOOD variable for each year, and must account for the proportion of C in the dry crop weight. Here, we assume that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so analysis needs to assume that harvest efficiency is less. We assume a harvest efficiency of 85%. +Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. + +Annual food crop yields (g dry matter m\ :sup:`-2`) can be calculated by saving the GRAINC_TO_FOOD_ANN variable once per year, then postprocessing with Equation :eq:`25.15`. This calculation assumes that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so analysis needs to assume that harvest efficiency is less---we use 85%. .. math:: :label: 25.15 - Grain\ yield(g.m^{-2})=\frac{\sum(GRAINC\_ TO\_ FOOD)*0.85}{0.45} + \text{Grain yield} = \frac{GRAINC\_TO\_FOOD\_ANN)*0.85}{0.45} .. _Table Crop allocation parameters: From f54d15cf7453597fb0ac8857fa81352c9b043898 Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 22:00:50 +0000 Subject: [PATCH 1704/2067] Resolve documentation problems identified in issue #993 --- ...LM50_Tech_Note_Photosynthetic_Capacity.rst | 110 +++++++++--------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst index 68b2853bda..2250139c01 100755 --- a/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst +++ b/doc/source/tech_note/Photosynthetic_Capacity/CLM50_Tech_Note_Photosynthetic_Capacity.rst @@ -22,7 +22,7 @@ The LUNA model includes the following four unitless parameters: - :math:`t_{c,j0}` , which defines the baseline ratio of Rubisco-limited rate to light-limited rate; - :math:`H` , which determines the response of electron transport rate to relative humidity. -The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. The estimated values in CLM5 for the listed parameters are 0.0311, 0.1745, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist between crops and natural vegetations due to human selection and genetic modifications, in CLM5, the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for :math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. +The above four parameters are estimated by fitting the LUNA model to a global compilation of >800 obervations located at different biomes, canopy locations, and time of the year from 1993-2013 (Ali et al. 2015). The model inputs are area-based leaf nitrogen content, leaf mass per unit leaf area and the driving environmental conditions (average of past 10 days) including temperature, CO :sub:`2` concentrations, daily mean and maximum radiation, relative humidity and day length. The estimated values in CLM5 for the listed parameters are 0.0311, 0.17, 0.8054, and 6.0999, repectively. In LUNA V1.0, the estimated parameter values are for C3 natural vegetations. In view that potentially large differences in photosythetic capacity could exist between crops and natural vegetations due to human selection and genetic modifications, in CLM5, the LUNA model are used only for C3 natural vegetations. The photosynthetic capacity for crops and C4 plants are thus still kept the same as CLM4.5. Namely, it is estimated based on the leaf nitrogen content, fixed RUBISCO allocations for :math:`V_{c\max 25}` and an adjusting factor to account for the impact of day length. In CLM5, the model simulates both sun-lit and shaded leaves; however, because the sun-lit and shaded leaves can changes through the day based on the sun angles, we do not differentiate the photosynthetic capacity difference for sun-lit or shaded leaves. .. _Model structure: @@ -53,65 +53,65 @@ The structural nitrogen, :math:`N_{\text{str}}`, is calculated as the multiplica N_{\text{str}} = \text{SNC} \cdot \text{LMA} -where :math:`\text{SNC}` is set to be fixed at 0.002 (gN/g biomass), based on data on C:N ratio from dead wood (White etal.,2000), and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (:math:`SLA_{\text{0}}`), a PFT-level parameter (:numref:`Table Plant functional type (PFT) leaf N parameters`). +where :math:`\text{SNC}` is set to be fixed at 0.004 (gN/g biomass), based on data on C:N ratio from dead wood (White etal.,2000), and :math:`\text{LMA}` is the inverse of specific leaf area at the canopy top (:math:`SLA_{\text{0}}`), a PFT-level parameter (:numref:`Table Plant functional type (PFT) leaf N parameters`). .. _Table Plant functional type (PFT) leaf N parameters: .. table:: Plant functional type (PFT) leaf N parameters. - +----------------------------------+--------------------------+--------------------------+ - | PFT | :math:`SLA_{\text{0}}` | :math:`N_{\text{cb}}` | - +==================================+==========================+==========================+ - | NET Temperate | 0.0100 | 0.0509 | - +----------------------------------+--------------------------+--------------------------+ - | NET Boreal | 0.0100 | 0.0466 | - +----------------------------------+--------------------------+--------------------------+ - | NDT Boreal | 0.0202 | 0.0546 | - +----------------------------------+--------------------------+--------------------------+ - | BET Tropical | 0.0190 | 0.0461 | - +----------------------------------+--------------------------+--------------------------+ - | BET temperate | 0.0190 | 0.0515 | - +----------------------------------+--------------------------+--------------------------+ - | BDT tropical | 0.0308 | 0.0716 | - +----------------------------------+--------------------------+--------------------------+ - | BDT temperate | 0.0308 | 0.1007 | - +----------------------------------+--------------------------+--------------------------+ - | BDT boreal | 0.0308 | 0.1007 | - +----------------------------------+--------------------------+--------------------------+ - | BES temperate | 0.0180 | 0.0517 | - +----------------------------------+--------------------------+--------------------------+ - | BDS temperate | 0.0307 | 0.0943 | - +----------------------------------+--------------------------+--------------------------+ - | BDS boreal | 0.0307 | 0.0943 | - +----------------------------------+--------------------------+--------------------------+ - | C\ :sub:`3` arctic grass | 0.0402 | 0.1365 | - +----------------------------------+--------------------------+--------------------------+ - | C\ :sub:`3` grass | 0.0402 | 0.1365 | - +----------------------------------+--------------------------+--------------------------+ - | C\ :sub:`4` grass | 0.0385 | 0.0900 | - +----------------------------------+--------------------------+--------------------------+ - | Temperate Corn | 0.0500 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Spring Wheat | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Temperate Soybean | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Cotton | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Rice | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Sugarcane | 0.0500 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Tropical Corn | 0.0500 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Tropical Soybean | 0.0350 | 0.4102 | - +----------------------------------+--------------------------+--------------------------+ - | Miscanthus | 0.0570 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - | Switchgrass | 0.0490 | 0.2930 | - +----------------------------------+--------------------------+--------------------------+ - -Notes: :math:`SLA_{\text{0}}` is the specific leaf area at the canopy top (m :sup:`2` leaf/g biomass), and :math:`N_{\text{cb}}` is the fraction of leaf nitrogen in Rubisco (g N in Rubisco g :sup:`-1` N) + +----------------------------------+--------------------------+ + | PFT | :math:`SLA_{\text{0}}` | + +==================================+==========================+ + | NET Temperate | 0.01000 | + +----------------------------------+--------------------------+ + | NET Boreal | 0.01000 | + +----------------------------------+--------------------------+ + | NDT Boreal | 0.02018 | + +----------------------------------+--------------------------+ + | BET Tropical | 0.01900 | + +----------------------------------+--------------------------+ + | BET temperate | 0.01900 | + +----------------------------------+--------------------------+ + | BDT tropical | 0.03080 | + +----------------------------------+--------------------------+ + | BDT temperate | 0.03080 | + +----------------------------------+--------------------------+ + | BDT boreal | 0.03080 | + +----------------------------------+--------------------------+ + | BES temperate | 0.01798 | + +----------------------------------+--------------------------+ + | BDS temperate | 0.03072 | + +----------------------------------+--------------------------+ + | BDS boreal | 0.02800 | + +----------------------------------+--------------------------+ + | C\ :sub:`3` arctic grass | 0.02100 | + +----------------------------------+--------------------------+ + | C\ :sub:`3` grass | 0.04024 | + +----------------------------------+--------------------------+ + | C\ :sub:`4` grass | 0.03846 | + +----------------------------------+--------------------------+ + | Temperate Corn | 0.05000 | + +----------------------------------+--------------------------+ + | Spring Wheat | 0.03500 | + +----------------------------------+--------------------------+ + | Temperate Soybean | 0.03500 | + +----------------------------------+--------------------------+ + | Cotton | 0.03500 | + +----------------------------------+--------------------------+ + | Rice | 0.03500 | + +----------------------------------+--------------------------+ + | Sugarcane | 0.05000 | + +----------------------------------+--------------------------+ + | Tropical Corn | 0.05000 | + +----------------------------------+--------------------------+ + | Tropical Soybean | 0.03500 | + +----------------------------------+--------------------------+ + | Miscanthus | 0.03500 | + +----------------------------------+--------------------------+ + | Switchgrass | 0.03500 | + +----------------------------------+--------------------------+ + +Notes: :math:`SLA_{\text{0}}` is the specific leaf area at the canopy top (m :sup:`2` leaf/g biomass) We assume that plants optimize their nitrogen allocations (i.e., :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}`) to maximize the photosynthetic carbon gain, defined as the gross photosynthesis ( :math:`A` ) minus the maintenance respiration for photosynthetic enzymes ( :math:`R_{\text{psn}}` ), under specific environmental conditions and given plant's strategy of leaf nitrogen use. Namely, the solutions of nitrogen allocations \{ :math:`N_{\text{store}}`, :math:`N_{\text{resp}}`, :math:`N_{\text{lc}}`, :math:`N_{\text{et}}`, :math:`N_{\text{cb}}` \} can be estimated as follows, From 81c3a4a425fb08214a10af8f406326bb9279d241 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 24 Oct 2023 16:14:53 -0600 Subject: [PATCH 1705/2067] Crops/irrigation Tech Note: Crop calendars in "features since 5.0" --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index a7362c7bd0..2e5fc2fd74 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -39,7 +39,7 @@ These updates appear in detail in the sections below. Many also appear in :ref:` Available new features since the CLM5 release ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Addition of bioenergy crops - +- Ablity to customize crop calendars (sowing windows/dates, maturity requirements) using stream files .. _The crop model: The crop model: cash and bioenergy crops From f8c2c71c46c7259e55c018a333e6843361d1033f Mon Sep 17 00:00:00 2001 From: olyson Date: Tue, 24 Oct 2023 22:23:44 +0000 Subject: [PATCH 1706/2067] Resolve documentation problems identified in issue #2194 --- doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst index 02188d5e25..130629f0eb 100644 --- a/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst +++ b/doc/source/tech_note/Hydrology/CLM50_Tech_Note_Hydrology.rst @@ -895,7 +895,7 @@ The specific yield, :math:`S_{y}`, which depends on the soil properties and the where B is the Clapp-Hornberger exponent. Because :math:`S_{y}` is a function of the soil properties, it results in water table dynamics that are consistent with the soil water fluxes described in section :numref:`Soil Water`. -After the above calculations, two numerical adjustments are implemented to keep the liquid water content of each soil layer (:math:`w_{liq,\, i}` ) within physical constraints of :math:`w_{liq}^{\min } \le w_{liq,\, i} \le \left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i}` where :math:`w_{liq}^{\min } =0.01` (mm). First, beginning with the bottom soil layer :math:`i=N_{levsoi}`, any excess liquid water in each soil layer (:math:`w_{liq,\, i}^{excess} =w_{liq,\, i} -\left(\theta_{sat,\, i} -\theta_{ice,\, i} \right)\Delta z_{i} \ge 0`) is successively added to the layer above. Any excess liquid water that remains after saturating the entire soil column (plus a maximum surface ponding depth :math:`w_{liq}^{pond} =10` kg m\ :sup:`-2`), is added to drainage :math:`q_{drai}`. Second, to prevent negative :math:`w_{liq,\, i}`, each layer is successively brought up to :math:`w_{liq,\, i} =w_{liq}^{\min }` by taking the required amount of water from the layer below. If this results in :math:`w_{liq,\, N_{levsoi} } Date: Tue, 24 Oct 2023 20:14:01 -0600 Subject: [PATCH 1707/2067] Update date --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 58599534be..c9192e4ffa 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev146 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) -Date: Mon Oct 23 15:22:00 PM MDT 2023 +Date: Tue Oct 24 20:13:17 MDT 2023 One-line Summary: FATES cross-grid seed dispersal Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index 222d608adb..f530ef9f7a 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev146 glemieux 10/23/2023 FATES cross-grid seed dispersal + ctsm5.1.dev146 glemieux 10/24/2023 FATES cross-grid seed dispersal ctsm5.1.dev145 slevis 10/19/2023 SNICAR snow albedo scheme updates ctsm5.1.dev144 samrabin 10/19/2023 Remove a deprecated shr_mpi_bcast call ctsm5.1.dev143 rgknox 10/13/2023 Zeroing of wood product fluxes on fates columns From b95b986e3c5df0c622c8a9fd1bde197cf8a155d0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 10:14:34 -0600 Subject: [PATCH 1708/2067] Fix in-progress attempt to add note to N_TO_FOOD longnames. --- src/biogeochem/CNVegNitrogenFluxType.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index 5de48e4284..dec8237d86 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -1054,7 +1054,7 @@ subroutine InitHistory(this, bounds) data1dptr => this%repr_grainn_to_food_patch(:,k) call hist_addfld1d ( & ! e.g., GRAINN_TO_FOOD - fname=get_repr_hist_fname(k)//'N_TO_FOOD (not scientifically)', & + fname=get_repr_hist_fname(k)//'N_TO_FOOD', & units='gN/m^2/s', & avgflag='A', & long_name=get_repr_longname(k)//' N to food', & From 205848bca27a5172e169225c7d4dda63ed5e7ddd Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 10:15:09 -0600 Subject: [PATCH 1709/2067] Add "not scientifically supported" to reproductive N hist field longnames. --- src/biogeochem/CNVegNitrogenFluxType.F90 | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CNVegNitrogenFluxType.F90 b/src/biogeochem/CNVegNitrogenFluxType.F90 index dec8237d86..cdfab748f3 100644 --- a/src/biogeochem/CNVegNitrogenFluxType.F90 +++ b/src/biogeochem/CNVegNitrogenFluxType.F90 @@ -1057,7 +1057,7 @@ subroutine InitHistory(this, bounds) fname=get_repr_hist_fname(k)//'N_TO_FOOD', & units='gN/m^2/s', & avgflag='A', & - long_name=get_repr_longname(k)//' N to food', & + long_name=get_repr_longname(k)//' N to food (not scientifically supported)', & ptr_patch=data1dptr, & default='inactive') data1dptr => this%repr_grainn_to_seed_patch(:,k) @@ -1066,7 +1066,7 @@ subroutine InitHistory(this, bounds) fname=get_repr_hist_fname(k)//'N_TO_SEED', & units='gN/m^2/s', & avgflag='A', & - long_name=get_repr_longname(k)//' N to seed', & + long_name=get_repr_longname(k)//' N to seed (not scientifically supported)', & ptr_patch=data1dptr, & default='inactive') data2dptr => this%repr_grainn_to_food_perharv_patch(:,:,k) @@ -1076,7 +1076,7 @@ subroutine InitHistory(this, bounds) units='gN/m^2', & type2d='mxharvests', & avgflag='I', & - long_name=get_repr_longname(k)//' N to food per harvest; should only be output annually', & + long_name=get_repr_longname(k)//' N to food per harvest; should only be output annually (not scientifically supported)', & ptr_patch=data2dptr, & default='inactive') data1dptr => this%repr_grainn_to_food_thisyr_patch(:,k) @@ -1085,7 +1085,7 @@ subroutine InitHistory(this, bounds) fname=get_repr_hist_fname(k)//'N_TO_FOOD_ANN', & units='gN/m^2', & avgflag='I', & - long_name=get_repr_longname(k)//' N to food harvested per calendar year; should only be output annually', & + long_name=get_repr_longname(k)//' N to food harvested per calendar year; should only be output annually (not scientifically supported)', & ptr_patch=data1dptr, & default='inactive') data2dptr => this%repr_grainn_to_seed_perharv_patch(:,:,k) @@ -1095,7 +1095,7 @@ subroutine InitHistory(this, bounds) units='gN/m^2', & type2d='mxharvests', & avgflag='I', & - long_name=get_repr_longname(k)//' N to seed per harvest; should only be output annually', & + long_name=get_repr_longname(k)//' N to seed per harvest; should only be output annually (not scientifically supported)', & ptr_patch=data2dptr, & default='inactive') data1dptr => this%repr_grainn_to_seed_thisyr_patch(:,k) @@ -1104,7 +1104,7 @@ subroutine InitHistory(this, bounds) fname=get_repr_hist_fname(k)//'N_TO_SEED_ANN', & units='gN/m^2', & avgflag='I', & - long_name=get_repr_longname(k)//' N to seed harvested per calendar year; should only be output annually', & + long_name=get_repr_longname(k)//' N to seed harvested per calendar year; should only be output annually (not scientifically supported)', & ptr_patch=data1dptr, & default='inactive') end do From 509bba32bad6c2ca4bad527cf711d4f0e346748c Mon Sep 17 00:00:00 2001 From: John Alex Date: Wed, 25 Oct 2023 09:58:05 -0600 Subject: [PATCH 1710/2067] Remove is_host_file param from fates_param_reader_type::Read implementation --- src/utils/clmfates_paraminterfaceMod.F90 | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90 index 8f63c68965..95b1e428da 100644 --- a/src/utils/clmfates_paraminterfaceMod.F90 +++ b/src/utils/clmfates_paraminterfaceMod.F90 @@ -252,25 +252,20 @@ subroutine ParametersFromNetCDF(filename, is_host_file, fates_params) end subroutine ParametersFromNetCDF !----------------------------------------------------------------------- - subroutine Read(this, is_host_file, fates_params ) + subroutine Read(this, fates_params ) ! ! !DESCRIPTION: - ! Read 'fates_params' parameters from appropriate filename given 'is_host_file'. + ! Read 'fates_params' parameters from storage. ! ! USES use clm_varctl, only : fname_len, paramfile, fates_paramfile ! !ARGUMENTS: class(fates_param_reader_ctsm_impl) :: this - logical, intent(in) :: is_host_file class(fates_parameters_type), intent(inout) :: fates_params !----------------------------------------------------------------------- - character(len=fname_len) :: filename ! file to read + logical :: is_host_file = .false. - filename = fates_paramfile - if (is_host_file) then - filename = paramfile - endif - call ParametersFromNetCDF(filename, is_host_file, fates_params) + call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params) end subroutine Read From ae8f46a22d853f4daa952651af2119bcafd4cef2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 12:00:41 -0600 Subject: [PATCH 1711/2067] Move GRAINC_TO_SEED_ANN to same place as GRAINC_TO_SEED. --- src/biogeochem/CNVegCarbonFluxType.F90 | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index bd8765db00..d6f5375b5d 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -958,7 +958,6 @@ subroutine InitHistory(this, bounds, carbon_type) end do this%repr_grainc_to_food_thisyr_patch(begp:endp,:) = spval - this%repr_grainc_to_seed_thisyr_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainc_to_food_thisyr_patch(:,k) call hist_addfld1d ( & @@ -969,15 +968,6 @@ subroutine InitHistory(this, bounds, carbon_type) long_name=get_repr_longname(k)//' C to food harvested per calendar year; should only be output annually', & ptr_patch=data1dptr, & default='inactive') - data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) - call hist_addfld1d ( & - ! e.g., GRAINC_TO_SEED_ANN - fname=get_repr_hist_fname(k)//'C_TO_SEED_ANN', & - units='gC/m^2', & - avgflag='I', & - long_name=get_repr_longname(k)//' C to seed harvested per calendar year; should only be output annually', & - ptr_patch=data1dptr, & - default='inactive') end do this%leafc_to_biofuelc_patch(begp:endp) = spval @@ -991,6 +981,7 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=this%livestemc_to_biofuelc_patch) this%repr_grainc_to_seed_patch(begp:endp,:) = spval + this%repr_grainc_to_seed_thisyr_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainc_to_seed_patch(:,k) call hist_addfld1d ( & @@ -1000,6 +991,15 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', & long_name=get_repr_longname(k)//' C to seed', & ptr_patch=data1dptr) + data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) + call hist_addfld1d ( & + ! e.g., GRAINC_TO_SEED_ANN + fname=get_repr_hist_fname(k)//'C_TO_SEED_ANN', & + units='gC/m^2', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to seed harvested per calendar year; should only be output annually', & + ptr_patch=data1dptr, & + default='inactive') end do end if From af4a6889c36f9759a7637b0cd57050eed341a28a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 12:02:56 -0600 Subject: [PATCH 1712/2067] Added *C_TO_SEED_PERHARV hist fields. --- src/biogeochem/CNVegCarbonFluxType.F90 | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index d6f5375b5d..c7aa3469e2 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -981,6 +981,7 @@ subroutine InitHistory(this, bounds, carbon_type) ptr_patch=this%livestemc_to_biofuelc_patch) this%repr_grainc_to_seed_patch(begp:endp,:) = spval + this%repr_grainc_to_seed_perharv_patch(begp:endp,:,:) = spval this%repr_grainc_to_seed_thisyr_patch(begp:endp,:) = spval do k = repr_grain_min, repr_grain_max data1dptr => this%repr_grainc_to_seed_patch(:,k) @@ -991,6 +992,16 @@ subroutine InitHistory(this, bounds, carbon_type) avgflag='A', & long_name=get_repr_longname(k)//' C to seed', & ptr_patch=data1dptr) + data2dptr => this%repr_grainc_to_seed_perharv_patch(:,:,k) + call hist_addfld2d ( & + ! e.g., GRAINC_TO_SEED_PERHARV + fname=get_repr_hist_fname(k)//'C_TO_SEED_PERHARV', & + units='gC/m^2', & + type2d='mxharvests', & + avgflag='I', & + long_name=get_repr_longname(k)//' C to seed per harvest; should only be output annually', & + ptr_patch=data2dptr, & + default='inactive') data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) call hist_addfld1d ( & ! e.g., GRAINC_TO_SEED_ANN From 0d9dd113c32e16efbe9910f7cc4ba94970d2c076 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 12:42:04 -0600 Subject: [PATCH 1713/2067] Move some section labels to fix rendering (maybe just in VSCode). --- doc/source/users_guide/adding-new-resolutions/index.rst | 4 ++-- doc/source/users_guide/overview/getting-help.rst | 4 ++-- doc/source/users_guide/overview/index.rst | 4 ++-- doc/source/users_guide/overview/introduction.rst | 2 +- doc/source/users_guide/overview/quickstart.rst | 4 ++-- doc/source/users_guide/overview/scientific_validation.rst | 4 ++-- doc/source/users_guide/running-single-points/index.rst | 4 ++-- doc/source/users_guide/running-special-cases/index.rst | 4 ++-- .../users_guide/setting-up-and-running-a-case/index.rst | 4 ++-- doc/source/users_guide/testing/index.rst | 4 ++-- doc/source/users_guide/using-clm-tools/index.rst | 4 ++-- 11 files changed, 21 insertions(+), 21 deletions(-) diff --git a/doc/source/users_guide/adding-new-resolutions/index.rst b/doc/source/users_guide/adding-new-resolutions/index.rst index 88bbda3f5b..f524461395 100644 --- a/doc/source/users_guide/adding-new-resolutions/index.rst +++ b/doc/source/users_guide/adding-new-resolutions/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _adding-new-resolutions-section: - .. include:: ../substitutions.rst +.. _adding-new-resolutions-section: + ##################################### Adding New Resolutions ##################################### diff --git a/doc/source/users_guide/overview/getting-help.rst b/doc/source/users_guide/overview/getting-help.rst index 3a1c2b4d8f..07ee972c30 100644 --- a/doc/source/users_guide/overview/getting-help.rst +++ b/doc/source/users_guide/overview/getting-help.rst @@ -1,7 +1,7 @@ -.. _getting-help: - .. include:: ../substitutions.rst +.. _getting-help: + ============== Getting Help ============== diff --git a/doc/source/users_guide/overview/index.rst b/doc/source/users_guide/overview/index.rst index b03eae4034..b0dcfcdd96 100644 --- a/doc/source/users_guide/overview/index.rst +++ b/doc/source/users_guide/overview/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _overview_section: - .. include:: ../substitutions.rst +.. _overview_section: + ##################################### Overview ##################################### diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index 5117aca429..d8c7630710 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -21,7 +21,7 @@ The Community Land Model (|release| in |cesmrelease|) is the latest in a series .. note:: This release of |version| in |cesmrelease| includes BOTH CLM4.0 physics and CLM4.5 physics used in previous releases as well as the updated |version| physics. CLM allow you to trigger between the three physics modes. Most often when we refer to CLM4.0 we are referring to the CLM4.0 physics in |version| in |cesmrelease| rather than to a specific version of CLM4.0 (where we would give the exact version). And when we refer to CLM4.5 we are referring to the CLM4.5 physics in |version| in |cesmrelease| rather than to a specific version of CLM4.5. Likewise, when referring to |version| we are referring to the |version| physics in |version| in |cesmrelease|. -The novice user should read :ref:`overview_section` in detail before beginning work, while the expert user should read :ref:`what-is-new-with-clm5_0` and :ref:`quickstart`, and then use the more detailed sections as reference. Before novice users go onto more technical problems covered in :ref:`customizing_section`, :ref:`using-clm-tools-section`, :ref:`adding-new-resolutions-section`, :ref:`running-special-cases-section` or :ref:`running-single-points`, they should know the material covered in :ref:`overview_section` and be able to replicate some of the examples given there. +The novice user should read the :ref:`overview_section` chapter in detail before beginning work, while the expert user should read :ref:`what-is-new-with-clm5_0` and :ref:`quickstart`, and then use the more detailed sections as reference. Before novice users go onto more technical problems covered in :ref:`customizing_section`, :ref:`using-clm-tools-section`, :ref:`adding-new-resolutions-section`, :ref:`running-special-cases-section` or :ref:`running-single-points`, they should know the material covered in :ref:`overview_section` and be able to replicate some of the examples given there. All users should read :ref:`how-to-use-this-document` and :ref:`getting-help` to understand the document conventions and the various ways of getting help on using |version|. Users should also read the :ref:`scientific-validiation` section to see if their planned use of the model is something that has been scientifically validated and well tested. Users that are NOT using NCAR machines or our list of well tested machines should also read the What are the UNIX utilities required to use |version|? section to make sure they have all the required UNIX utilities on the system they want to do their work. diff --git a/doc/source/users_guide/overview/quickstart.rst b/doc/source/users_guide/overview/quickstart.rst index f8b810cc0d..d9bf51538a 100644 --- a/doc/source/users_guide/overview/quickstart.rst +++ b/doc/source/users_guide/overview/quickstart.rst @@ -1,7 +1,7 @@ -.. _quickstart: - .. include:: ../substitutions.rst +.. _quickstart: + ============ Quickstart ============ diff --git a/doc/source/users_guide/overview/scientific_validation.rst b/doc/source/users_guide/overview/scientific_validation.rst index 3110cbd81f..348bd97250 100644 --- a/doc/source/users_guide/overview/scientific_validation.rst +++ b/doc/source/users_guide/overview/scientific_validation.rst @@ -1,7 +1,7 @@ -.. _scientific-validiation: - .. include:: ../substitutions.rst +.. _scientific-validiation: + ======================== Scientific Validation ======================== diff --git a/doc/source/users_guide/running-single-points/index.rst b/doc/source/users_guide/running-single-points/index.rst index e1d955ac0a..ba342d0ba9 100644 --- a/doc/source/users_guide/running-single-points/index.rst +++ b/doc/source/users_guide/running-single-points/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _running-single-points: - .. include:: ../substitutions.rst +.. _running-single-points: + ##################################### Running Single Point Regional Cases ##################################### diff --git a/doc/source/users_guide/running-special-cases/index.rst b/doc/source/users_guide/running-special-cases/index.rst index f84b7706fb..5aeb0a466a 100644 --- a/doc/source/users_guide/running-special-cases/index.rst +++ b/doc/source/users_guide/running-special-cases/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _running-special-cases-section: - .. include:: ../substitutions.rst +.. _running-special-cases-section: + ##################################### Running Special Cases ##################################### diff --git a/doc/source/users_guide/setting-up-and-running-a-case/index.rst b/doc/source/users_guide/setting-up-and-running-a-case/index.rst index b11587ee21..40988c303e 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/index.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _customizing_section: - .. include:: ../substitutions.rst +.. _customizing_section: + ##################################### Setting Up and Running a Case ##################################### diff --git a/doc/source/users_guide/testing/index.rst b/doc/source/users_guide/testing/index.rst index 7d1370dec6..b7baedc04f 100644 --- a/doc/source/users_guide/testing/index.rst +++ b/doc/source/users_guide/testing/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _testing_section: - .. include:: ../substitutions.rst +.. _testing_section: + ##################################### Testing ##################################### diff --git a/doc/source/users_guide/using-clm-tools/index.rst b/doc/source/users_guide/using-clm-tools/index.rst index 58435f92aa..c09653706b 100644 --- a/doc/source/users_guide/using-clm-tools/index.rst +++ b/doc/source/users_guide/using-clm-tools/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _using-clm-tools-section: - .. include:: ../substitutions.rst +.. _using-clm-tools-section: + ##################################### Using CLM tools ##################################### From 3c72ff0c4ed79f3f6855b95b13f9707b529e15b3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 12:47:41 -0600 Subject: [PATCH 1714/2067] UG Introduction: Fix link(s) to ChangeLog file(s). --- doc/source/users_guide/overview/introduction.rst | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index d8c7630710..62274f165e 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -33,7 +33,14 @@ Developers that are making changes to CLM either for their own development or fo What is New with |version| ============================ -`What's new with |version| science `_ gives a synopsis of the changes to CLM since the CLM4.5 release. More details are given in the `CLM ChangeLog file `_. +`What's new with |version| science `_ gives a synopsis of the changes to CLM since the CLM4.5 release. More details are given in the CLM ChangeLog files: + +- `CLM 3.0 ChangeLog file `_ +- `CLM 4.0 ChangeLog file `_ +- `CLM 4.5 ChangeLog file `_ +- `CLM 5.0 ChangeLog file `_ +- `CTSM 1.0 ChangeLog file `_ +- `Latest ChangeLog file `_ Previous release pages give similar list of changes for previous versions of the model. From f885f56c7617cca146507eae758e28eb5248cbbb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 12:52:19 -0600 Subject: [PATCH 1715/2067] Remove version number from what-is-new-with-clm5_0 label. --- doc/source/users_guide/overview/introduction.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index 62274f165e..809165eb50 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -17,17 +17,17 @@ P. O. Box 3000, Boulder, Colorado 80307-3000 Introduction ============== -The Community Land Model (|release| in |cesmrelease|) is the latest in a series of global land models developed by the CESM Land Model Working Group (LMWG) and maintained at the National Center for Atmospheric Research (NCAR). This guide is intended to instruct both the novice and experienced user on running CLM. This guide pertains to the latest version |version| in |cesmrelease| available for download from the public release subversion repository as a part of |cesmrelease|. Documentation may be different if you are using an older version, you should either use the documentation for that release version, update to the latest version, or use the documentation inside your own source tree. There is information in the ChangeLog file and in :ref:`what-is-new-with-clm5_0` regarding the changes from previous versions of CESM. +The Community Land Model (|release| in |cesmrelease|) is the latest in a series of global land models developed by the CESM Land Model Working Group (LMWG) and maintained at the National Center for Atmospheric Research (NCAR). This guide is intended to instruct both the novice and experienced user on running CLM. This guide pertains to the latest version |version| in |cesmrelease| available for download from the public release subversion repository as a part of |cesmrelease|. Documentation may be different if you are using an older version, you should either use the documentation for that release version, update to the latest version, or use the documentation inside your own source tree. There is information in the ChangeLog file and in :ref:`what-is-new-with-clm` regarding the changes from previous versions of CESM. .. note:: This release of |version| in |cesmrelease| includes BOTH CLM4.0 physics and CLM4.5 physics used in previous releases as well as the updated |version| physics. CLM allow you to trigger between the three physics modes. Most often when we refer to CLM4.0 we are referring to the CLM4.0 physics in |version| in |cesmrelease| rather than to a specific version of CLM4.0 (where we would give the exact version). And when we refer to CLM4.5 we are referring to the CLM4.5 physics in |version| in |cesmrelease| rather than to a specific version of CLM4.5. Likewise, when referring to |version| we are referring to the |version| physics in |version| in |cesmrelease|. -The novice user should read the :ref:`overview_section` chapter in detail before beginning work, while the expert user should read :ref:`what-is-new-with-clm5_0` and :ref:`quickstart`, and then use the more detailed sections as reference. Before novice users go onto more technical problems covered in :ref:`customizing_section`, :ref:`using-clm-tools-section`, :ref:`adding-new-resolutions-section`, :ref:`running-special-cases-section` or :ref:`running-single-points`, they should know the material covered in :ref:`overview_section` and be able to replicate some of the examples given there. +The novice user should read the :ref:`overview_section` chapter in detail before beginning work, while the expert user should read :ref:`what-is-new-with-clm` and :ref:`quickstart`, and then use the more detailed sections as reference. Before novice users go onto more technical problems covered in :ref:`customizing_section`, :ref:`using-clm-tools-section`, :ref:`adding-new-resolutions-section`, :ref:`running-special-cases-section` or :ref:`running-single-points`, they should know the material covered in :ref:`overview_section` and be able to replicate some of the examples given there. All users should read :ref:`how-to-use-this-document` and :ref:`getting-help` to understand the document conventions and the various ways of getting help on using |version|. Users should also read the :ref:`scientific-validiation` section to see if their planned use of the model is something that has been scientifically validated and well tested. Users that are NOT using NCAR machines or our list of well tested machines should also read the What are the UNIX utilities required to use |version|? section to make sure they have all the required UNIX utilities on the system they want to do their work. Developers that are making changes to CLM either for their own development or for development that they hope will eventually become a part of the main CLM should read :ref:`testing_section`. We have a suite of test scripts that automatically test many different model configurations and namelist options, as well as ensuring things like restarts are bit-for-bit and the like. It's helpful to use these scripts to ensure your changes are working correctly. As well as being a required part of the process to bring in new code developments. And it's far easier to use the automated scripts rather than having to figure out, what to test, how to do it, and then finally do it by hand. If you are using non supported machines you may also want to use the test scripts to make sure your machine is working correctly. -.. _what-is-new-with-clm5_0: +.. _what-is-new-with-clm: ============================ What is New with |version| From a83168ecbcbf8c25e85c299055c388210a6441ad Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 12:56:29 -0600 Subject: [PATCH 1716/2067] UG Quickstart: Fix rendering of a list. --- doc/source/users_guide/overview/quickstart.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/users_guide/overview/quickstart.rst b/doc/source/users_guide/overview/quickstart.rst index d9bf51538a..ee2ffb22fb 100644 --- a/doc/source/users_guide/overview/quickstart.rst +++ b/doc/source/users_guide/overview/quickstart.rst @@ -9,6 +9,7 @@ Running the CLM requires a suite of UNIX utilities and programs and you should make sure you have all of these available before trying to go forward with using it. If you are missing one of these you should contact the systems administrator for the machine you wish to run on and make sure they are installed. List of utilities required for CESM in the "|cesmrelease| Software/Operating System Prerequisites" section in `http://www.cesm.ucar.edu/models/cesm1.2//cesm/doc/usersguide/book1.html `_ + - UNIX bash shell (for some of the CLM tools scripts) - NCL (for some of the offline tools for creating/modifying CLM input datasets see `Chapter 2 `_ for more information on NCL) - Python From 0db5e4d97df0cf4d2f74b0f6378ab8e2ae1e0619 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 13:14:24 -0600 Subject: [PATCH 1717/2067] UG Overview: Fix CLM-URL links in 1.1.3. --- .../users_guide/overview/getting-help.rst | 2 ++ .../users_guide/overview/introduction.rst | 22 +++++++++---------- .../users_guide/running-PTCLM/index.rst | 4 ++-- .../users_guide/trouble-shooting/index.rst | 4 ++-- .../trouble-shooting/trouble-shooting.rst | 4 ++-- 5 files changed, 19 insertions(+), 17 deletions(-) diff --git a/doc/source/users_guide/overview/getting-help.rst b/doc/source/users_guide/overview/getting-help.rst index 07ee972c30..7899b81626 100644 --- a/doc/source/users_guide/overview/getting-help.rst +++ b/doc/source/users_guide/overview/getting-help.rst @@ -58,6 +58,8 @@ Reporting bugs in |version| If you have any problems, additional questions, bug reports, or any other feedback, please report it as an issue on GitHub https://github.com/ESCOMP/ctsm/issues or for CIME scripts and infrastructure to https://github.com/ESMCI/CIME/issues. Or send an email to <`cesmhelp@cgd.ucar.edu `_> or <`ctsm-software@ucar.edu `_>. If you find bad, wrong, or misleading information in this users guide report it as an issue on CTSM. +.. _acronyms-and-terms: + --------------------------------------- Some Acronym's and Terms We'll be Using --------------------------------------- diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index 809165eb50..a4e9b727ff 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -50,27 +50,27 @@ Previous release pages give similar list of changes for previous versions of the Overview of User's Guide ========================== -In this introduction we first give a simple guide to understand the document conventions in `How to Use This Document `_. The next section `What is new with |version| in |cesmrelease| since previous public releases? `_ gives references to describe the differences between |version| in |cesmrelease| and previous CESM releases both from a scientific as well as a software engineering point of view. For information on previous releases of |version| before |version| in |cesmrelease| see the CESM1.2.2 documentation. The next section `Quickstart to using |version| `_ is for users that are already experts in using CLM and gives a quickstart guide to the bare details on how to use |version|. The next `What is scientifically validated and functional in |version| in |cesmrelease|? `_ tells you about what has been extensively tested and scientifically validated (and maybe more importantly) what has NOT. `What are the UNIX utilities required to use |version|? `_ lists the UNIX utilities required to use |version| and is important if you are running on non-NCAR machines, generic local machines, or machines NOT as well tested by us at NCAR. Next we have `Important Notes and Best Practices for Usage of |version| `_ to detail some of the best practices for using |version| for science. The last introductory section is `Other resources `_ to get help from which lists different resources for getting help with |version| and |cesmrelease|. +In this introduction we first give a simple guide to understand the document conventions in :ref:`how-to-use-this-document`. The next section, :ref:`what-is-new-with-clm`, gives references to describe the differences between |version| in |cesmrelease| and previous CESM releases both from a scientific as well as a software engineering point of view. For information on previous releases of |version| before |version| in |cesmrelease| see the CESM1.2.2 documentation. The :ref:`quickstart` section is for users that are already experts in using CLM and gives a quickstart guide to the bare details on how to use |version|. It also lists the UNIX utilities required to use |version| and is important if you are running on non-NCAR machines, generic local machines, or machines NOT as well tested by us at NCAR. The :ref:`scientific-validiation` section tells you about what has been extensively tested and scientifically validated (and maybe more importantly) what has NOT. Next we have :ref:`best-practices-for-usage` to detail some of the best practices for using |version| for science. The last introductory section is :ref:`getting-help`, which lists different resources for getting help with |version| and |cesmrelease|. -`Chapter 1 `_ goes into detail on how to setup and run simulations with |version| and especially how to customize cases. Details of cesm_setup modes and build-namelist options as well as namelist options are given in this chapter. +:ref:`customizing_section` goes into detail on how to setup and run simulations with |version| and especially how to customize cases. Details of cesm_setup modes and build-namelist options as well as namelist options are given in this chapter. -`Chapter 2 `_ gives instructions on the CLM tools for either CLM4.5 or |version| physics for creating input datasets for use by CLM, for the expert user. There's an overview of what each tool does, and some general notes on how to build the FORTRAN tools. Then each tool is described in detail along with different ways in which the tool might be used. A final section on how to customize datasets for observational sites for very savvy expert users is given as the last section of this chapter. +:ref:`using-clm-tools-section` gives instructions on the CLM tools for either CLM4.5 or |version| physics for creating input datasets for use by CLM, for the expert user. There's an overview of what each tool does, and some general notes on how to build the FORTRAN tools. Then each tool is described in detail along with different ways in which the tool might be used. A final section on how to customize datasets for observational sites for very savvy expert users is given as the last section of this chapter. -As a followup to the tools chapter, `Chapter 3 `_ tells how to add files to the XML database for build-namelist to use. This is important if you want to use the XML database to automatically select user-created input files that you have created when you setup new cases with CLM (CLM4.0, CLM4.5 and |version| physics). +As a followup to the tools chapter, :ref:`adding-new-resolutions-section` tells how to add files to the XML database for build-namelist to use. This is important if you want to use the XML database to automatically select user-created input files that you have created when you setup new cases with CLM (CLM4.0, CLM4.5 and |version| physics). -In `Chapter 4 `_, again for the expert user, we give details on how to do some particularly difficult special cases. For example, we give the protocol for spinning up the |version|-BGC and CLMCN models as well as CLM with dynamic vegetation active (CNDV). We give instructions to do a spinup case from a previous case with Coupler history output for atmospheric forcing. We also give instructions on running both the prognostic crop and irrigation models. Lastly we tell the user how to use the DATM model to send historical CO2 data to CLM. +In :ref:`running-special-cases-section`, again for the expert user, we give details on how to do some particularly difficult special cases. For example, we give the protocol for spinning up the |version|-BGC and CLMCN models as well as CLM with dynamic vegetation active (CNDV). We give instructions to do a spinup case from a previous case with Coupler history output for atmospheric forcing. We also give instructions on running both the prognostic crop and irrigation models. Lastly we tell the user how to use the DATM model to send historical CO2 data to CLM. -`Chapter 5 `_ outlines how to do single-point or regional simulations using |version|. This is useful to either compare |version| simulations with point observational stations, such as tower sites (which might include your own atmospheric forcing), or to do quick simulations with CLM for example to test a new parameterization. There are several different ways given on how to perform single-point simulations which range from simple PTS_MODE to more complex where you create all your own datasets, tying into `Chapter 2 `_ and also `Chapter 3 `_ to add the files into the build-namelist XML database. The PTCLM python script to run single-point simulations was added back in for this release (but it has bugs that don't allow it to work out of the box). CLM4 in CESM1.0.5 has a fully working versions of PTCLM. +:ref:`running-single-points` outlines how to do single-point or regional simulations using |version|. This is useful to either compare |version| simulations with point observational stations, such as tower sites (which might include your own atmospheric forcing), or to do quick simulations with CLM for example to test a new parameterization. There are several different ways given on how to perform single-point simulations which range from simple PTS_MODE to more complex where you create all your own datasets, tying into :ref:`using-clm-tools-section` and also :ref:`adding-new-resolutions-section` to add the files into the build-namelist XML database. The PTCLM python script to run single-point simulations was added back in for this release (but it has bugs that don't allow it to work out of the box). CLM4 in CESM1.0.5 has a fully working versions of PTCLM. -Need `Chapter 6 `_ blurb... +Need :ref:`running-PTCLM` blurb... -`Chapter 7 `_ gives some guidance on trouble-shooting problems when using |version|. It doesn't cover all possible problems with CLM, but gives you some guidelines for things that can be done for some common problems. +:ref:`troubleshooting-index` gives some guidance on trouble-shooting problems when using |version|. It doesn't cover all possible problems with CLM, but gives you some guidelines for things that can be done for some common problems. -`Chapter 8 `_ goes over the automated testing scripts for validating that the CLM is working correctly. The test scripts run many different configurations and options with CLM4.0 physics as well and |version| physics making sure that they work, as well as doing automated testing to verify restarts are working correctly, and testing at many different resolutions. In general this is an activity important only for a developer of |version|, but could also be used by users who are doing extensive code modifications and want to ensure that the model continues to work correctly. +:ref:`testing_section` goes over the automated testing scripts for validating that the CLM is working correctly. The test scripts run many different configurations and options with CLM4.0 physics as well and |version| physics making sure that they work, as well as doing automated testing to verify restarts are working correctly, and testing at many different resolutions. In general this is an activity important only for a developer of |version|, but could also be used by users who are doing extensive code modifications and want to ensure that the model continues to work correctly. In the appendices we talk about some issues that are useful for advanced users and developers of |version|. -Finally in `Appendix A `_ we give instructions on how to build the documentation associated with |version| (i.e. how to build this document). This document is included in every CLM distribution and can be built so that you can view a local copy rather than having to go to the CESM website. This also could be useful for developers who need to update the documentation due to changes they have made. +Finally on Github we give `instructions `_ on how to build the documentation associated with |version| (i.e. how to build this document). This document is included in every CLM distribution and can be built so that you can view a local copy rather than having to go to the CESM website. This also could be useful for developers who need to update the documentation due to changes they have made. ================================ README file describing |version| @@ -87,7 +87,7 @@ The README (which can be found in ``$CTSMROOT/doc``) is repeated here. Best Practices ================ -- |version| includes BOTH the old CLM4.0, CLM4.5 physics AND the new |version| physics and you can toggle between those three. The "standard" practice for CLM4.0 is to run with CN on, and with Qian atmospheric forcing. While the "standard" practice for CLM4.5 is to run with BGC on, and CRUNCEP atmospheric forcing. And finally the "standard" practice for |version| is to run with BGC and Prognostic Crop on, with the MOSART model for river routing, as well as the CISM ice sheet model, and using GSWP3 atmospheric forcing. "BGC" is the new |version| biogeochemistry and include CENTURY-like pools, vertical resolved carbon, as well as Nitrification and de-Nitrification (see `the Section called Some Acronym's and Terms We'll be Using in Other resources to get help from `_ ). +- |version| includes BOTH the old CLM4.0, CLM4.5 physics AND the new |version| physics and you can toggle between those three. The "standard" practice for CLM4.0 is to run with CN on, and with Qian atmospheric forcing. While the "standard" practice for CLM4.5 is to run with BGC on, and CRUNCEP atmospheric forcing. And finally the "standard" practice for |version| is to run with BGC and Prognostic Crop on, with the MOSART model for river routing, as well as the CISM ice sheet model, and using GSWP3 atmospheric forcing. "BGC" is the new |version| biogeochemistry and include CENTURY-like pools, vertical resolved carbon, as well as Nitrification and de-Nitrification (see :ref:`acronyms-and-terms`). - When running with CLMCN (either CLM4.0 or |version| physics) or |version|-BGC, it is critical to begin with initial conditions that are provided with the release or to spin the model up following the CN spinup procedure before conducting scientific runs (see `the Section called Spinning up the |version| biogeochemistry (CLMBGC spinup) in Chapter 4 `_ for |version| or `the Section called Spinning up the CLM4.0 biogeochemistry Carbon-Nitrogen Model (CN spinup) in Chapter 4 `_ for CLM4.0). Simulations without a proper spinup will effectively be starting from an unvegetated world. See `the Section called Setting Your Initial Conditions File in Chapter 1 `_ for information on how to provide initial conditions for your simulation. diff --git a/doc/source/users_guide/running-PTCLM/index.rst b/doc/source/users_guide/running-PTCLM/index.rst index 26e18d3a73..0b44c01b49 100644 --- a/doc/source/users_guide/running-PTCLM/index.rst +++ b/doc/source/users_guide/running-PTCLM/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _running-PTCLM: - .. include:: ../substitutions.rst +.. _running-PTCLM: + ##################################### Running PTCLM ##################################### diff --git a/doc/source/users_guide/trouble-shooting/index.rst b/doc/source/users_guide/trouble-shooting/index.rst index 64b0cecee3..de6b0c053a 100644 --- a/doc/source/users_guide/trouble-shooting/index.rst +++ b/doc/source/users_guide/trouble-shooting/index.rst @@ -3,10 +3,10 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -.. _troubleshooting: - .. include:: ../substitutions.rst +.. _troubleshooting-index: + ##################################### Troubleshooting ##################################### diff --git a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst index 6fc53c3a89..e139796f71 100644 --- a/doc/source/users_guide/trouble-shooting/trouble-shooting.rst +++ b/doc/source/users_guide/trouble-shooting/trouble-shooting.rst @@ -1,7 +1,7 @@ -.. _trouble-shooting: - .. include:: ../substitutions.rst +.. _trouble-shooting: + *************** Troubleshooting *************** From 90802f5e7a738ad03859417d7cdff45271cde4f8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 13:44:57 -0600 Subject: [PATCH 1718/2067] UG Introduction: Fixed links re: spinup/initial conditions. Replaced link for CLM4.0 spinup (can't find it) with SP spinup (wasn't mentioned). --- doc/source/users_guide/overview/introduction.rst | 2 +- ...Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst | 4 ++-- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 4 ++-- .../customizing-the-clm-configuration.rst | 2 ++ 4 files changed, 7 insertions(+), 5 deletions(-) diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index a4e9b727ff..bd46116e9e 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -89,7 +89,7 @@ The README (which can be found in ``$CTSMROOT/doc``) is repeated here. - |version| includes BOTH the old CLM4.0, CLM4.5 physics AND the new |version| physics and you can toggle between those three. The "standard" practice for CLM4.0 is to run with CN on, and with Qian atmospheric forcing. While the "standard" practice for CLM4.5 is to run with BGC on, and CRUNCEP atmospheric forcing. And finally the "standard" practice for |version| is to run with BGC and Prognostic Crop on, with the MOSART model for river routing, as well as the CISM ice sheet model, and using GSWP3 atmospheric forcing. "BGC" is the new |version| biogeochemistry and include CENTURY-like pools, vertical resolved carbon, as well as Nitrification and de-Nitrification (see :ref:`acronyms-and-terms`). -- When running with CLMCN (either CLM4.0 or |version| physics) or |version|-BGC, it is critical to begin with initial conditions that are provided with the release or to spin the model up following the CN spinup procedure before conducting scientific runs (see `the Section called Spinning up the |version| biogeochemistry (CLMBGC spinup) in Chapter 4 `_ for |version| or `the Section called Spinning up the CLM4.0 biogeochemistry Carbon-Nitrogen Model (CN spinup) in Chapter 4 `_ for CLM4.0). Simulations without a proper spinup will effectively be starting from an unvegetated world. See `the Section called Setting Your Initial Conditions File in Chapter 1 `_ for information on how to provide initial conditions for your simulation. +- When running with CLMCN (either CLM4.0 or |version| physics) or |version|-BGC, it is critical to begin with initial conditions that are provided with the release or to spin the model up following the CN spinup procedure before conducting scientific runs (see :ref:`spinning-up-clm-bgc` or :ref:`spinning-up-sp`). Simulations without a proper spinup will effectively be starting from an unvegetated world. See :ref:`setting-initial-conditions` for information on how to provide initial conditions for your simulation. - Initial condition files are provided for CLM4.0-CN as before, for fully coupled BCN and offline ICN cases for 1850 and 2000 at finite volume grids: 1deg (0.9x1.25), 2deg (1.9x2.5), and T31 resolutions. We also have interpolated initial conditions for BCN for 1850 and 2000 for two finite volume grids: 10x15, 4x5 and two HOMME grids (ne30np4 and ne120np4). There's also an initial condition file for ICN with the prognostic crop model for 2000 at 2deg resolution, and one with CLMSP for 2000 at 2deg resolution. We also have initial conditions for offline CNDV for 1850. The 1850 initial condition files are in 'reasonable' equilibrium. The 2000 initial condition files represent the model state for the year 2000, and have been taken from transient simulations. Therefore, by design the year 2000 initial condition files do not represent an equilibrium state. Note also that spinning the 2000 initial conditions out to equilibrium will not reflect the best estimate of the real carbon/nitrogen state for the year 2000. diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst index 3292a2bbf6..be67998ec1 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst @@ -1,7 +1,7 @@ -.. _spinning-up-sp: - .. include:: ../substitutions.rst +.. _spinning-up-sp: + =========================================== Spinning up the Satellite Phenology Model =========================================== diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 20cbdae1e5..c5cfc971f1 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -1,7 +1,7 @@ -.. _spinning-up-clm50-bgc: - .. include:: ../substitutions.rst +.. _spinning-up-clm-bgc: + ========================== Spinup of |version|-BGC-Crop ========================== diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index 5321e471c2..5687f9c13d 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -431,6 +431,8 @@ Note: The precedence for setting the values of namelist variables with the diffe Thus a setting in ``CLM_BLDNML_OPTS`` will override a setting for the same thing given in a use case with ``CLM_NML_USE_CASE``. Likewise, a setting in ``CLM_NAMELIST_OPTS`` will override a setting in ``user_nl_clm``. +.. _setting-initial-conditions: + ------------------------------------ Setting Your Initial Conditions File ------------------------------------ From 5fa5d2fe3affe9e9c1111c5d6dc52ae7422bfd24 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 13:53:14 -0600 Subject: [PATCH 1719/2067] UG Getting Help: Fix CLM-URL links. --- .../users_guide/overview/getting-help.rst | 32 +++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/doc/source/users_guide/overview/getting-help.rst b/doc/source/users_guide/overview/getting-help.rst index 7899b81626..74765d1ad0 100644 --- a/doc/source/users_guide/overview/getting-help.rst +++ b/doc/source/users_guide/overview/getting-help.rst @@ -35,22 +35,22 @@ There is a rich and diverse set of people that use the CESM, and often it is use The CLM web pages ----------------- -The main CLM web page contains information on the CLM, it's history, developers, as well as downloads for previous model versions. There are also documentation text files in the $CTSMROOT/doc directory that give some quick information on using CLM. - -`CLM web page `_ -`|cesmrelease| |version| web page `_ -`CLM Documentation Text Files `_ - -Also note that several of the XML database files can be viewed in a web browser to get a nice table of namelist options, namelist defaults, or compsets. Simply view them as a local file and bring up one of the following files: - -- `$CTSMROOT/bld/namelist_files/namelist_definition_clm4_0.xml `_ -- definition of CLM4.0 namelist items. -- `$CTSMROOT/bld/namelist_files/namelist_definition_clm4_5.xml `_ -- definition of CLM4.5/CLM5.0 namelist items. -- `$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_0.xml `_ -- default values for CLM4.0 namelist items. -- `$CTSMROOT/bld/namelist_files/namelist_defaults_clm4_5.xml `_ -- default values for CLM4.5/CLM5.0 namelist items. -- `$CTSMROOT/cime_config/config_component.xml `_ -- definition of all the CLM specific XML variables. -- `$CTSMROOT/cime_config/config_compsets.xml `_ -- definition of all the CLM compsets. -- `$CTSMROOT/bld/namelist_files/history_fields_clm4_0.xml `_ -- definition of CLM4.0 history fields. -- `$CTSMROOT/bld/namelist_files/history_fields_clm4_5.xml `_ -- definition of CLM4.5/CLM5.0 history fields. +The main `CLM web page `_ contains information on the CLM, its history, developers, as well as downloads for previous model versions. Some other links are available at the `CESM2 land component webpage `. There are also documentation text files in the `$CTSMROOT/doc directory `_ that give some quick information on using CLM. + +Also note that several of the XML database files can help with namelist options, namelist defaults, or compsets. For the most recent release: + +- `$CTSMROOT/bld/namelist_files/namelist_definition_ctsm.xml `_ -- definition of latest CTSM namelist items. +- `$CTSMROOT/bld/namelist_files/namelist_defaults_ctsm.xml `_ -- default values for latest CTSM namelist items. +- `$CTSMROOT/cime_config/config_component.xml `_ -- definition of all the CLM specific XML variables. +- `$CTSMROOT/cime_config/config_compsets.xml `_ -- definition of all the CLM compsets. + +Some archives are available for previous versions: + +- `Archive of namelist_definition_clm4_0.xml `_ -- definition of CLM4.0 namelist items. +- `Archive of namelist_definition_clm4_5.xml `_ -- definition of CLM4.5/CLM5.0 namelist items. +- `Archive of namelist_defaults_clm4_0.xml `_ -- default values for CLM4.0 namelist items. +- `Archive of namelist_defaults_clm4_5.xml `_ -- default values for CLM4.5/CLM5.0 namelist items. + ---------------------------- Reporting bugs in |version| From 4751e20e889c4fd6f389da533927edf96acc973b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 25 Oct 2023 16:01:30 -0600 Subject: [PATCH 1720/2067] UG Quickstart: Make a bulleted list. --- doc/source/users_guide/overview/quickstart.rst | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/doc/source/users_guide/overview/quickstart.rst b/doc/source/users_guide/overview/quickstart.rst index ee2ffb22fb..1a78d1f61d 100644 --- a/doc/source/users_guide/overview/quickstart.rst +++ b/doc/source/users_guide/overview/quickstart.rst @@ -16,15 +16,12 @@ List of utilities required for CESM in the "|cesmrelease| Software/Operating Sys Before working with |version| read the QuickStart Guide in the `|cesmrelease| Scripts User's Guide `_. Once you are familiar with how to setup cases for any type of simulation with CESM you will want to direct your attention to the specifics of using CLM. -For some of the details of setting up cases for |version| read the README and text files available from the "$CTSMROOT/doc" directory (see the "CLM Web pages" section for a link to the list of these files). Here are the important ones that you should be familiar with. +For some of the details of setting up cases for |version| read the README and text files available from the "$CTSMROOT/doc" directory (see the "CLM Web pages" section for a link to the list of these files). Here are the important ones that you should be familiar with: -`README file `_ describing the directory structure. - -The IMPORTANT_NOTES file talks about important things for users to know about using the model scientifically. It content is given in the next chapter on `"What is scientifically validated and functional in |version| in |cesmrelease|?" `_. - -The ChangeLog/ChangeSum talk about advances in different versions of CLM. The content of these files is largely explained in the previous chapter on `"What is new with |version| in |cesmrelease| since previous public releases?" `_. - -The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that culimated in that given version of the CLM. +- `README file `_ describing the directory structure. +- The IMPORTANT_NOTES file talks about important things for users to know about using the model scientifically. It content is given in the next chapter on `"What is scientifically validated and functional in |version| in |cesmrelease|?" `_. +- The ChangeLog/ChangeSum talk about advances in different versions of CLM. The content of these files is largely explained in the previous chapter on `"What is new with |version| in |cesmrelease| since previous public releases?" `_. +- The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that culimated in that given version of the CLM. Note other directories have README files that explain different components and tools used when running CLM and are useful in understanding how those parts of the model work and should be consulted when using tools in those directories. For more details on configuring and customizing a case with CLM see `Chapter 1 `_. From f39a0d8348d6eb3f97c98cbc41b98ad354745999 Mon Sep 17 00:00:00 2001 From: olyson Date: Thu, 26 Oct 2023 15:48:22 +0000 Subject: [PATCH 1721/2067] Changes in response to review. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 3 +-- .../Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 0b87314361..013efdca08 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -558,8 +558,7 @@ where :math:`w_{wilt}` is the wilting point soil moisture (mm) w_{wilt} = \sum_{j=1}^{N_{irr}} \theta_{wilt} \Delta z_{j} \ , -and :math:`f_{thresh}` is a tuning parameter. The available moisture in -the soil (mm) is +and :math:`f_{thresh}` is a tuning parameter. The available moisture in the soil (mm) is .. math:: :label: 25.65 diff --git a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst index baa05dff59..c233a0cb4b 100644 --- a/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst +++ b/doc/source/tech_note/Land-Only_Mode/CLM50_Tech_Note_Land-Only_Mode.rst @@ -1,4 +1,4 @@ - _rst_Land-only Mode: +.. _rst_Land-only Mode: Land-Only Mode ================ From 68539c5b1367491419c321e242e12a2cc7f8b818 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 10:25:51 -0600 Subject: [PATCH 1722/2067] UG Quickstart: Fix CLM-URL links. --- doc/source/users_guide/overview/introduction.rst | 2 ++ doc/source/users_guide/overview/quickstart.rst | 14 +++++++------- .../using-clm-tools/what-are-the-clm-tools.rst | 2 ++ 3 files changed, 11 insertions(+), 7 deletions(-) diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index bd46116e9e..3dcdda1cf0 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -72,6 +72,8 @@ In the appendices we talk about some issues that are useful for advanced users a Finally on Github we give `instructions `_ on how to build the documentation associated with |version| (i.e. how to build this document). This document is included in every CLM distribution and can be built so that you can view a local copy rather than having to go to the CESM website. This also could be useful for developers who need to update the documentation due to changes they have made. +.. _readme: + ================================ README file describing |version| ================================ diff --git a/doc/source/users_guide/overview/quickstart.rst b/doc/source/users_guide/overview/quickstart.rst index 1a78d1f61d..5414963c4d 100644 --- a/doc/source/users_guide/overview/quickstart.rst +++ b/doc/source/users_guide/overview/quickstart.rst @@ -8,22 +8,22 @@ Running the CLM requires a suite of UNIX utilities and programs and you should make sure you have all of these available before trying to go forward with using it. If you are missing one of these you should contact the systems administrator for the machine you wish to run on and make sure they are installed. -List of utilities required for CESM in the "|cesmrelease| Software/Operating System Prerequisites" section in `http://www.cesm.ucar.edu/models/cesm1.2//cesm/doc/usersguide/book1.html `_ +List of utilities required for CESM in the `Software/OS Prerequisites `_ section of the CESM User's Guide. - UNIX bash shell (for some of the CLM tools scripts) -- NCL (for some of the offline tools for creating/modifying CLM input datasets see `Chapter 2 `_ for more information on NCL) +- NCL (for some of the offline tools for creating/modifying CLM input datasets; see :ref:`using-ncl` for more information) - Python -Before working with |version| read the QuickStart Guide in the `|cesmrelease| Scripts User's Guide `_. Once you are familiar with how to setup cases for any type of simulation with CESM you will want to direct your attention to the specifics of using CLM. +Before working with |version| read the `CESM QuickStart Guide `_. Once you are familiar with how to setup cases for any type of simulation with CESM you will want to direct your attention to the specifics of using CLM. For some of the details of setting up cases for |version| read the README and text files available from the "$CTSMROOT/doc" directory (see the "CLM Web pages" section for a link to the list of these files). Here are the important ones that you should be familiar with: -- `README file `_ describing the directory structure. -- The IMPORTANT_NOTES file talks about important things for users to know about using the model scientifically. It content is given in the next chapter on `"What is scientifically validated and functional in |version| in |cesmrelease|?" `_. -- The ChangeLog/ChangeSum talk about advances in different versions of CLM. The content of these files is largely explained in the previous chapter on `"What is new with |version| in |cesmrelease| since previous public releases?" `_. +- :ref:`readme` describing the directory structure. +- The IMPORTANT_NOTES file talks about important things for users to know about using the model scientifically. It content is given in the next chapter on :ref:`scientific-validiation`. +- The ChangeLog/ChangeSum talk about advances in different versions of CLM. The content of these files is largely explained in the previous chapter on :ref:`what-is-new-with-clm`. - The release-clm5.0.ChangeLog gives the specific changes that have gone on the release-clm5.0 branch. clm3_0_ChangeLog, clm4_0_ChangeLog, clm4_5_ChangeLog gives the changes that culimated in that given version of the CLM. -Note other directories have README files that explain different components and tools used when running CLM and are useful in understanding how those parts of the model work and should be consulted when using tools in those directories. For more details on configuring and customizing a case with CLM see `Chapter 1 `_. +Note other directories have README files that explain different components and tools used when running CLM and are useful in understanding how those parts of the model work and should be consulted when using tools in those directories. For more details on configuring and customizing a case with CLM see :ref:`customizing_section`. The Quickstart.GUIDE (which can be found in ``$CTSMROOT/doc``) is repeated here. diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst index dd650a79e9..a0d426672d 100644 --- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst @@ -58,6 +58,8 @@ Running FORTRAN tools built with SMP=TRUE When you enable ``SMP=TRUE`` on your build of one of the tools that make use of it, you are using OpenMP for shared memory parallelism (SMP). In SMP loops are run in parallel with different threads run on different processors all of which access the same memory (called on-node). Thus you can only usefully run up to the number of processors that are available on a single-node of the machine you are running on. For example, on the NCAR machine cheyenne there are 36 processors per node, so you can use up to 36 processors. +.. _using-ncl: + --------- Using NCL --------- From 1bbe5fa912ac5d6c9ffe918ce838f0ecc4b5efe6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 10:42:18 -0600 Subject: [PATCH 1723/2067] UG running-PTCLM: Fix CLM-URL links. --- .../users_guide/running-PTCLM/adding-ptclm-site-data.rst | 8 +++++--- .../users_guide/running-PTCLM/introduction-to-ptclm.rst | 2 +- doc/source/users_guide/running-PTCLM/using-ptclm.rst | 4 ++-- 3 files changed, 8 insertions(+), 6 deletions(-) diff --git a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst index 9492b9ce59..d085c2f689 100644 --- a/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst +++ b/doc/source/users_guide/running-PTCLM/adding-ptclm-site-data.rst @@ -1,7 +1,7 @@ -.. _adding-ptclm-site-data: - .. include:: ../substitutions.rst +.. _adding-ptclm-site-data: + ============================ Adding PTCLMmkdata Site Data ============================ @@ -40,6 +40,8 @@ There is a mechanism for giving site-specific land-use change in PTCLMmkdata. Ad This file only requires a line for each year where a transition or harvest happens. As in the "pftdata" file above "pft_f" refers to the fraction and "pft_c" refers to the PFT index, and only up to five vegetation types are allowed to co-exist. The last eight columns have to do with harvesting and grazing. The last two columns are whether to hold harvesting and/or grazing constant until the next transition year and will just be either 1 or 0. This file will be converted by the **PTCLM_sitedata/cnvrt_trnsyrs2_pftdyntxtfile.pl** script in the PTCLMmkdata directory to a format that **mksurfdata_map** can read that has an entry for each year for the range of years valid for the compset in question. +.. _converting-ameriflux-for-ptclmmkdata: + ------------------------------------------------ Converting AmeriFlux Data for use by PTCLMmkdata ------------------------------------------------ @@ -58,7 +60,7 @@ The CESM can NOT handle missing data, so we recommend using the "Level 4" Gap fi Example: PTCLMmkdata transient example over a shorter time period ----------------------------------------------------------------- -This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as show in the `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ section above. Also note that this site has a site-specific dynamic land-use change file for it ``PTCLM_sitedata/US-Ha1_dynpftdata.txt`` in the PTCLMmkdata directory and this file will be used for land-use change and harvesting rather than the global dataset. +This is an example of using PTCLMmkdata for Harvard Forest (AmeriFlux site code US-Ha1) for transient land use 1991-2006. In order to do this we would've needed to have converted the AmeriFlux data into NetCDF format as shown in :ref:`converting-ameriflux-for-ptclmmkdata` section above. Also note that this site has a site-specific dynamic land-use change file for it ``PTCLM_sitedata/US-Ha1_dynpftdata.txt`` in the PTCLMmkdata directory and this file will be used for land-use change and harvesting rather than the global dataset. :: diff --git a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst index a94d62d1b5..9ae4186d2c 100644 --- a/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/introduction-to-ptclm.rst @@ -105,7 +105,7 @@ The output to the above command is as follows: Main Script Version Id: $Id: PTCLM.py 47576 2013-05-29 19:11:16Z erik $ Scripts URL: $HeadURL: https://svn-ccsm-models.cgd.ucar.edu/PTCLM/trunk_tags/PTCLM1_130529/PTCLM.py $: -Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ for permission information to use this data. +Here we give a simple example of using PTCLMmkdata for a straightforward case of running at the US-UMB Fluxnet site on cheyenne where we already have the meteorology data on the machine. Note, see :ref:`converting-ameriflux-for-ptclmmkdata` for permission information to use this data. Example 6-1. Example of running PTCLMmkdata for US-UMB on cheyenne ------------------------------------------------------------------ diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst index c69e2cdd91..e1e69be88d 100644 --- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/using-ptclm.rst @@ -78,7 +78,7 @@ Configure options include: This option is for running PTCLMmkdata with a different root directory to CESM than the version PTCLMmkdata exists in. Normally you do NOT need to use this option. ``--sitegroupname`` - In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. These site groups are all separate ASCII files with the same prefix followed by a "_*data.txt" name. See `the Section called PTCLMmkdata Group Site Lists `_ for more information on these files. By default we have provided three different valid group names: + In the PTCLMmkdata directory there is a subdirectory "PTCLM_sitedata" that contains files with the site, PFT and soil data information for groups of sites. These site groups are all separate ASCII files with the same prefix followed by a "_*data.txt" name. See :ref:`adding-ptclm-site-data` for more information on these files. By default we have provided three different valid group names: EXAMPLE ------- @@ -86,7 +86,7 @@ AmeriFlux Fluxnet-Canada -The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. Note, see `the Section called Converting AmeriFlux Data for use by PTCLMmkdata `_ with permission information to use the US-UMB data. +The EXAMPLE is the group used by default and ONLY includes the US-UMB site as that is the only site we have data provided for. The other two site groups include the site information for all of both the AmeriFlux and Fluxnet-Canada sites. You can use the "sitegroupname" option to use one of the other lists, or you can create your own lists using the EXAMPLE file as an example. Your list of sites could be real world locations or could be theoretical "virtual" sites given to exercise CLM on differing biomes for example. Note, see :ref:`converting-ameriflux-for-ptclmmkdata` with permission information to use the US-UMB data. ``--donot_use_tower_yrs`` This option is used with the "useQIAN" option to set the years to cycle over for the Qian data. In this case Qian atmospheric forcing will be used, but the simulation will run over the same years that tower site is available for this site. From c8b3e2a76e627158caa013dcea765cdb040fb6f0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 12:37:16 -0600 Subject: [PATCH 1724/2067] UG running-single-points: Fix CLM-URL links. --- .../running-pts_mode-configurations.rst | 4 ++-- .../running-single-point-configurations.rst | 19 ++++++++++++------- ...point-and-regional-grid-configurations.rst | 8 ++++---- 3 files changed, 18 insertions(+), 13 deletions(-) diff --git a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst index 9362e93fe8..d3b14e6184 100644 --- a/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-pts_mode-configurations.rst @@ -1,7 +1,7 @@ -.. _pts_mode: - .. include:: ../substitutions.rst +.. _pts_mode: + **************************************************** Running a single point using global data - PTS_MODE **************************************************** diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index 778deb3220..a282e2f11b 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -1,7 +1,7 @@ -.. _running-single-point-datasets: - .. include:: ../substitutions.rst +.. _running-single-point-datasets: + ****************************************** Running Single Point Configurations ****************************************** @@ -29,7 +29,12 @@ Which results in the following: The resolution names that have an underscore in them ("_") are all single-point or regional resolutions. -To run for the Brazil test site do the following: +.. _warning-singleproc-on-batch: + +Warning about Running with a Single Processor on a Batch Machine +---------------------------------------------------------------- + +When running a single point, the number of processors is automatically set to one. When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to TRUE so that you can also run interactively without having to use mpi to start up your job. Example: Running CLM over a single-point test site in Brazil ------------------------------------------------------------ @@ -58,9 +63,9 @@ Then setup, build and run normally. **Important:** Just like PTS_MODE above, By default it sets up to run with ``MPILIB=mpi-serial`` (in the ``env_build.xml`` file) turned on, which allows you to run the model interactively. On some machines this mode is NOT supported and you may need to change it to FALSE before you are able to build. -.. warning:: See `the Section called Warning about Running with a Single-Processor on a Batch Machine `_ for a warning about running single-point jobs on batch machines. +.. warning:: See :ref:`warning-singleproc-on-batch` for a warning about running single-point jobs on batch machines. -.. note:: When running a ``pt1_pt1`` resolution the number of processors is automatically set to one. When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to TRUE so that you can also run interactively without having to use mpi to start up your job. +.. note:: Using Supported Single-point Datasets that have their own Atmospheric Forcing ================================================================================ @@ -106,7 +111,7 @@ Example: Running CLM over the single-point of Vancouver Canada with supplied atm .. note:: Just like ``PTS_MODE`` above, By default it sets up to run with ``MPILIB=mpi-serial`` (in the env_build.xml file) turned on, which allows you to run the model interactively. -.. note:: When running a ``pt1_pt1`` resolution the number of processors is automatically set to one. When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to ``TRUE`` so that you can also run interactively without having to use mpi to start up your job. +.. warning:: See :ref:`warning-singleproc-on-batch` for a warning about running single-point jobs on batch machines. Creating your own single-point dataset =================================================== @@ -134,7 +139,7 @@ Example: Using CLM_USRDAT_NAME to run a simulation using user datasets for a spe #> svn export $SVN_INP_URL/lnd/clm2/surfdata_map/surfdata_${GRIDNAME}_simyr2000.nc $CSMDATA/lnd/clm2/surfdata_map/surfdata_${GRIDNAME}_simyr2000.nc > ./case.setup -The first step is to create the domain and surface datasets using the process outlined in `the Section called The File Creation Process in Chapter 2 `_. Below we show an example of the process. +The first step is to create the domain and surface datasets using the process outlined in :ref:`using-clm-tools-section`. Below we show an example of the process. Example: Creating a surface dataset for a single point --------------------------------------------------------------------- diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst index a927bed53e..d64a687f69 100644 --- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst +++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst @@ -29,11 +29,11 @@ There are three different ways to do this for normal-supported site Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see `the Section called Running Supported Single-point/Regional Datasets `_). All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region. -In general `the Section called Running PTS_MODE configurations `_ is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts. +In general :ref:`pts_mode` is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts. -Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see `the Section called Creating your own single-point/regional surface datasets `_). With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method. +Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have to create your own datasets (see :ref:`running-single-point-datasets`). With this method you don't have to change DATM or add files to the XML database -- but you have to follow a strict naming convention for files. However, once the files are named and in the proper location, you can easily setup new cases that use these datasets. This is good for treating all the required datasets as a "group" and for a particular model version. For advanced CLM developers who need to track dataset changes with different model versions you would be best off adding these datasets as supported datasets with the "normal supported datasets" method. -Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter `Chapter 6 `_. +Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter, :ref:`running-PTCLM`. -Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. In the PTCLMmkdata chapter `the Section called Converting AmeriFlux Data for use by PTCLMmkdata in Chapter 6 `_ section tells you how to use AmeriFlux data for atmospheric forcing. +Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. :ref:`converting-ameriflux-for-ptclmmkdata` tells you how to use AmeriFlux data for atmospheric forcing. From 5cb70af593d6732d09e89bbd52c947f9275e63a0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 12:50:45 -0600 Subject: [PATCH 1725/2067] Removed a TODO. --- src/biogeochem/CNPhenologyMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 60931fb13b..60ab4f6dba 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -2039,7 +2039,6 @@ subroutine CropPhenology(num_pcropp, filter_pcropp , & is_end_sowing_window = jday == sowing_window_enddate ! We only want to plant on a specific day if the prescribed sowing window starts AND ends on the same day. Also make sure we haven't planted yet today. - ! TODO: ¿Allow use of NON-prescribed sowing with one-day-long windows? has_rx_sowing_date = sowing_window_startdate == sowing_window_enddate do_plant_prescribed = has_rx_sowing_date .and. & sowing_window_startdate == jday .and. & From 85610b5d3b005acfd2d3a86f8946551ba43fb3ee Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 26 Oct 2023 14:10:27 -0600 Subject: [PATCH 1726/2067] include temporary system test files that still need adapting. Update unit tests to have more clearly invalid site names --- python/ctsm/site_and_regional/run_neon.py | 8 +- .../test_sys_modify_singlept_site_neon.py | 72 ++++++++++++++++ python/ctsm/test/test_sys_run_neon.py | 86 +++++++++++++++++++ .../test_unit_modify_singlept_site_neon.py | 8 +- python/ctsm/test/test_unit_run_neon.py | 11 +-- 5 files changed, 168 insertions(+), 17 deletions(-) create mode 100755 python/ctsm/test/test_sys_modify_singlept_site_neon.py create mode 100755 python/ctsm/test/test_sys_run_neon.py diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 987883fe93..e8706e4cce 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -415,12 +415,12 @@ def build_base_case( if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( match is None, - "Existing base case is a historical type and should not be -- rerun with the --orverwrite option", + "Existing base case is a historical type and should not be -- rerun with the --overwrite option", ) else: expect( match is not None, - "Existing base case should be a historical type and is not -- rerun with the --orverwrite option", + "Existing base case should be a historical type and is not -- rerun with the --overwrite option", ) # reset the case case.case_setup(reset=True) @@ -534,12 +534,12 @@ def run_case( if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( match is None, - "Existing base case is a historical type and should not be -- rerun with the --orverwrite option", + "Existing base case is a historical type and should not be -- rerun with the --overwrite option", ) else: expect( match is not None, - "Existing base case should be a historical type and is not -- rerun with the --orverwrite option", + "Existing base case should be a historical type and is not -- rerun with the --overwrite option", ) if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): print("Case {} appears to be complete, not rerunning.".format(case_root)) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py new file mode 100755 index 0000000000..9eb9ed9256 --- /dev/null +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python3 + +""" +System tests for modify_singlept_site_neon.py +""" + +import os +import re + +import unittest +import tempfile +import shutil +import sys + +import xarray as xr +import numpy as np + +# THESE LINES ARE JUST HERE FOR TESTING +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.path_utils import path_to_ctsm_root +from ctsm import unit_testing +from ctsm.site_and_regional import modify_singlept_site_neon +from ctsm.site_and_regional.modify_singlept_site_neon import main, get_parser + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + + +class TestSysModifySingleptSiteNeon(unittest.TestCase): + """System tests for modify_singlept_site_neon""" + + def setUp(self): + """ + Make /_tempdir for use by these tests. + Check tempdir for history files + """ + self._tempdir = tempfile.mkdtemp() + testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") + self._cfg_file_path = os.path.join( + testinputs_path, "modify_singlept_site_neon_opt_sections.cfg" + ) + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_modify_site(self): + """ + Test modifying a singple point site + The primary items to test here are the following: + 1) Fields are overwritten with site-specific data for neon sites + 2) Downloaded data is used in surface dataset + 3) Check specific fields listed in update_metadata for correct output + 4) Check that a netcdf with correct formatting is created + """ + sys.argv = ["--neon_site", ["ABBY"]] # self._cfg_file_path] #, "ABBY"] + print("sys.argv:") + print(sys.argv) + parser = get_parser() + print("parser:") + print(parser) + main() # running into error here because main doesn't take in any arguments and doesn't know what arguments are needed. + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py new file mode 100755 index 0000000000..f654c03111 --- /dev/null +++ b/python/ctsm/test/test_sys_run_neon.py @@ -0,0 +1,86 @@ +#!/usr/bin/env python3 + +"""System tests for run_neon + +""" + +import os +import re + +import unittest +import tempfile +import shutil +import sys + +import xarray as xr +import numpy as np + +# THESE LINES ARE JUST HERE FOR TESTING +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.path_utils import path_to_ctsm_root, path_to_cime +from ctsm import unit_testing +from ctsm.site_and_regional import run_neon +from ctsm.site_and_regional.run_neon import main, get_parser + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + + +class TestSysRunNeon(unittest.TestCase): + """System tests for run_neon""" + + def setUp(self): + """ + Make /_tempdir for use by these tests. + Check tempdir for history files + """ + self._tempdir = tempfile.mkdtemp() + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_one_site(self): + """ + This test specifies a site to run + Run the tool, check history file output exists + Could also check log files? Although this functionally doesn't change output, + it might be good to ensure the log files are working as expected? + Test running transient, ad and post ad cases. + Test use of base case root. + Test for using prism? + Test setup_only? This should be encapsulated within the full run? + """ + + # run the run_neon tool + # sys.argv = ["run_neon", "--neon_sites 'ABBY'"] + # sys.argv = ["--neon_sites", ["ABBY"]] + sys.argv = ["--neon-sites 'ABBY'"] + print("sys.argv:") + print(sys.argv) + valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] + parser = get_parser(sys.argv, "description_for_parser", valid_neon_sites) + print("parser:") + print(parser) + main("") + # this seems to run OSBS (default site, instead of ABBY), + # but does create files! It takes a while though, should we do setup-only? + # Could assert that dir is created with files; we should also move this into a tempdir? + + # the critical piece of this test is that the above command + # doesn't generate errors; however, we also do some assertions below + + # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) + # fsurdat_out_data = xr.open_dataset(self._fsurdat_out) + # assert that fsurdat_out equals fsurdat_in + # self.assertTrue(fsurdat_out_data.equals(fsurdat_in_data)) + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index b8315c7bae..21f7c839c2 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -18,6 +18,8 @@ _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) +from ctsm.path_utils import path_to_ctsm_root + # pylint: disable=wrong-import-position from ctsm import unit_testing from ctsm.site_and_regional.modify_singlept_site_neon import ( @@ -62,7 +64,7 @@ def test_get_neon_false_site(self): """ Test to see if neon data for invalid site name is found """ - site_name = "ABY" + site_name = "INVALID_SITE" neon_dir = self._tempdir with self.assertRaises(SystemExit): get_neon(neon_dir, site_name) @@ -83,7 +85,7 @@ def test_find_soil_structure(self): soil_texture_raw_data_file_name should be found, and test should go through sysexit. """ surf_file = ( - "testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" + os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc") ) f1 = xr.open_dataset(surf_file) self.assertEqual( @@ -99,7 +101,7 @@ def test_update_metadata(self): surf_file = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" neon_file = "dummy_neon_file.nc" zb_flag = True - f1 = xr.open_dataset("testinputs/" + surf_file) + f1 = xr.open_dataset(os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs/") + surf_file) f2 = update_metadata(f1, surf_file, neon_file, zb_flag) today = date.today() today_string = today.strftime("%Y-%m-%d") diff --git a/python/ctsm/test/test_unit_run_neon.py b/python/ctsm/test/test_unit_run_neon.py index a8031fff1d..72c1b67a31 100755 --- a/python/ctsm/test/test_unit_run_neon.py +++ b/python/ctsm/test/test_unit_run_neon.py @@ -29,15 +29,6 @@ class TestRunNeon(unittest.TestCase): Basic class for testing run_neon.py. """ - # def setUp(self): - # sys.argv = ["subset_data", "point", "--create-surface"] - # DEFAULTS_FILE = os.path.join(os.getcwd(), "ctsm/test/testinputs/default_data.cfg") - # self.parser = get_parser() - # self.args = self.parser.parse_args() - # self.cesmroot = path_to_ctsm_root() - # self.defaults = configparser.ConfigParser() - # self.defaults.read(os.path.join(self.cesmroot, "tools/site_and_regional", DEFAULTS_FILE)) - def test_check_neon_listing(self): """ Test that neon listing is available for valid sites @@ -55,7 +46,7 @@ def test_check_neon_listing_misspelled(self): """ Test that neon listing is not available for invalid sites """ - valid_neon_sites = ["ABY", "BRT"] + valid_neon_sites = ["INVALID_SITE1", "INVALID_SITE2"] available_list = check_neon_listing(valid_neon_sites) self.assertEqual( available_list, [], "available list of incorrect dummy site not as expected" From 5714ffb8eb16382aefa7d0f9ab327784e2888026 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 26 Oct 2023 14:26:49 -0600 Subject: [PATCH 1727/2067] sys test assertion and formatting modify singlept site neon --- python/ctsm/test/test_sys_run_neon.py | 19 ++++++------------- .../test_unit_modify_singlept_site_neon.py | 9 ++++++--- 2 files changed, 12 insertions(+), 16 deletions(-) diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index f654c03111..c2599d782d 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -4,6 +4,7 @@ """ +import glob import os import re @@ -60,26 +61,18 @@ def test_one_site(self): # run the run_neon tool # sys.argv = ["run_neon", "--neon_sites 'ABBY'"] # sys.argv = ["--neon_sites", ["ABBY"]] + sys.argv = ["--neon-sites 'ABBY'"] - print("sys.argv:") - print(sys.argv) valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] parser = get_parser(sys.argv, "description_for_parser", valid_neon_sites) - print("parser:") - print(parser) main("") + # this seems to run OSBS (default site, instead of ABBY), # but does create files! It takes a while though, should we do setup-only? - # Could assert that dir is created with files; we should also move this into a tempdir? - - # the critical piece of this test is that the above command - # doesn't generate errors; however, we also do some assertions below - - # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) - # fsurdat_out_data = xr.open_dataset(self._fsurdat_out) - # assert that fsurdat_out equals fsurdat_in - # self.assertTrue(fsurdat_out_data.equals(fsurdat_in_data)) + # Could assert that dir is created with files + #we should also move this into a tempdir and delete files after running (and cancel queue?) + self.assertTrue("OSBS" in glob.glob("*")) if __name__ == "__main__": unit_testing.setup_for_tests() diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index 21f7c839c2..7817dd535e 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -84,8 +84,9 @@ def test_find_soil_structure(self): Test to ensure that correct attributes are found for find_soil_structure. soil_texture_raw_data_file_name should be found, and test should go through sysexit. """ - surf_file = ( - os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc") + surf_file = os.path.join( + path_to_ctsm_root(), + "python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc", ) f1 = xr.open_dataset(surf_file) self.assertEqual( @@ -101,7 +102,9 @@ def test_update_metadata(self): surf_file = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" neon_file = "dummy_neon_file.nc" zb_flag = True - f1 = xr.open_dataset(os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs/") + surf_file) + f1 = xr.open_dataset( + os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs/") + surf_file + ) f2 = update_metadata(f1, surf_file, neon_file, zb_flag) today = date.today() today_string = today.strftime("%Y-%m-%d") From 2a1e40ef8791af67516716a38b757e37bb0926b0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 15:32:13 -0600 Subject: [PATCH 1728/2067] UG Running Single Point Configurations: Cleanup and removal of an outdated note. The outdated note concerned a suggestion to set MPILIB=mpi-serial to TRUE, which is unnecessary because that's automatically set now for single-point cases. --- .../running-single-point-configurations.rst | 48 +++++++++---------- 1 file changed, 23 insertions(+), 25 deletions(-) diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index a282e2f11b..631ee410bf 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -6,7 +6,7 @@ Running Single Point Configurations ****************************************** -In addition to ``PTS_MODE``, CLM supports running using single-point or regional datasets that are customized to a particular region. CLM supports a a small number of out-of-the-box single-point and regional datasets. However, users can create their own dataset. +In addition to ``PTS_MODE`` (Sect. :numref:`pts_mode`), CLM supports running using single-point or regional datasets that are customized to a particular region. CLM supports a a small number of out-of-the-box single-point and regional datasets. However, users can create their own dataset. To get the list of supported dataset resolutions do this: :: @@ -29,15 +29,20 @@ Which results in the following: The resolution names that have an underscore in them ("_") are all single-point or regional resolutions. -.. _warning-singleproc-on-batch: +.. note:: When running a single point, the number of processors is automatically set to one, which is the only value allowed. -Warning about Running with a Single Processor on a Batch Machine ----------------------------------------------------------------- +.. warning:: + Just like ``PTS_MODE`` (Sect. :numref:`pts_mode`), by default these setups run with ``MPILIB=mpi-serial`` (in the ``env_build.xml`` file) turned on, which allows you to run the model interactively. On some machines this mode is NOT supported and you may need to change it to FALSE before you are able to build. -When running a single point, the number of processors is automatically set to one. When running a single grid point you can only use a single processor. You might also want to set the ``env_build.xml`` variable: ``MPILIB=mpi-serial`` to TRUE so that you can also run interactively without having to use mpi to start up your job. +.. _single-point-global-climate: -Example: Running CLM over a single-point test site in Brazil ------------------------------------------------------------- +Single-point runs with global climate forcings +============================================== + +Example: Use global forcings at a site without its own special forcings +----------------------------------------------------------------------- + +This example uses the single-point site in Brazil. :: > cd scripts @@ -47,10 +52,11 @@ Example: Running CLM over a single-point test site in Brazil Then setup, build and run normally. -Then to run for the urban Mexico City Mexico test site that also has atmosphere forcing data, but to run it with the Qian forcing data, but over the period for which it's own forcing data is provided do the following: +Example: Use global forcings at a site WITH its own special forcings +-------------------------------------------------------------------- + +The urban Mexico City test site has its own atmosphere forcing data (see Sect. :numref:`single-point-with-own-forcing`). To ignore that and run it with the default global forcing data, but over the period for which its own forcing data is provided, do the following: -Example: Running CLM over the single-point of Mexicocity Mexico with the default Qian atmosphere data forcing. -------------------------------------------------------------------------------------------------------------------------- :: > cd scripts @@ -59,25 +65,20 @@ Example: Running CLM over the single-point of Mexicocity Mexico with the default > ./create_newcase -case testSPDATASET -res $SITE -compset I1PtClm50SpGs > cd testSPDATASET -Then setup, build and run normally. - -**Important:** Just like PTS_MODE above, By default it sets up to run with ``MPILIB=mpi-serial`` (in the ``env_build.xml`` file) turned on, which allows you to run the model interactively. On some machines this mode is NOT supported and you may need to change it to FALSE before you are able to build. - -.. warning:: See :ref:`warning-singleproc-on-batch` for a warning about running single-point jobs on batch machines. +(Note the use of ``I1Pt`` instead of ``I2000`` as in the example above.) Then setup, build and run normally. -.. note:: +.. _single-point-with-own-forcing: -Using Supported Single-point Datasets that have their own Atmospheric Forcing -================================================================================ +Supported single-point runs for sites with their own atmospheric forcing +======================================================================== Of the supported single-point datasets we have three that also have atmospheric forcing data that go with them: Mexico City (Mexico), Vancouver, (Canada, British Columbia), and ``urbanc_alpha`` (test data for an Urban inter-comparison project). Mexico city and Vancouver also have namelist options in the source code for them to work with modified urban data parameters that are particular to these locations. To turn on the atmospheric forcing for these datasets, you set the ``env_run.xml DATM_MODE`` variable to ``CLM1PT``, and then the atmospheric forcing datasets will be used for the point picked. If you use one of the compsets that has "I1Pt" in the name that will be set automatically. When running with datasets that have their own atmospheric forcing you need to be careful to run over the period that data is available. If you have at least one year of forcing it will cycle over the available data over and over again no matter how long of a simulation you run. However, if you have less than a years worth of data (or if the start date doesn't start at the beginning of the year, or the end date doesn't end at the end of the year) then you won't be able to run over anything but the data extent. In this case you will need to carefully set the ``RUN_STARTDATE``, ``START_TOD`` and ``STOP_N/STOP_OPTION`` variables for your case to run over the entire time extent of your data. For the supported data points, these values are in the XML database and you can use the **queryDefaultNamelist.pl** script to query the values and set them for your case (they are set for the three urban test cases: Mexicocity, Vancouver, and urbanc_alpha). -In the example below we will show how to do this for the Vancouver, Canada point. - -Example: Running CLM over the single-point of Vancouver Canada with supplied atmospheric forcing data for Vancouver. -------------------------------------------------------------------------------------------------------------------------- +Example: Use site-specific atmospheric forcings +----------------------------------------------- +In this example, we show how to use the atmospheric forcings specific to the Vancouver, Canada point. :: > cd scripts @@ -109,9 +110,6 @@ Example: Running CLM over the single-point of Vancouver Canada with supplied atm .. warning:: If you don't set the start-year and run-length carefully as shown above the model will abort with a "dtlimit error" in the atmosphere model. Since, the forcing data for this site (and the MexicoCity site) is less than a year, the model won't be able to run for a full year. The ``1x1_urbanc_alpha`` site has data for more than a full year, but neither year is complete hence, it has the same problem (see the problem for this site above). -.. note:: Just like ``PTS_MODE`` above, By default it sets up to run with ``MPILIB=mpi-serial`` (in the env_build.xml file) turned on, which allows you to run the model interactively. - -.. warning:: See :ref:`warning-singleproc-on-batch` for a warning about running single-point jobs on batch machines. Creating your own single-point dataset =================================================== From db78563f06264ef00fd74f6d67f8f0c5ef8214c0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 15:35:22 -0600 Subject: [PATCH 1729/2067] UG running-single-points: Fix remaining CLM-URL links. --- .../running-single-point-configurations.rst | 1 + .../single-point-and-regional-grid-configurations.rst | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index 631ee410bf..c5d19cc115 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -110,6 +110,7 @@ In this example, we show how to use the atmospheric forcings specific to the Van .. warning:: If you don't set the start-year and run-length carefully as shown above the model will abort with a "dtlimit error" in the atmosphere model. Since, the forcing data for this site (and the MexicoCity site) is less than a year, the model won't be able to run for a full year. The ``1x1_urbanc_alpha`` site has data for more than a full year, but neither year is complete hence, it has the same problem (see the problem for this site above). +.. _creating-your-own-singlepoint-dataset: Creating your own single-point dataset =================================================== diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst index d64a687f69..3220f16352 100644 --- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst +++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst @@ -27,7 +27,7 @@ There are three different ways to do this for normal-supported site Choosing the right single point options ========================================= -Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see `the Section called Running Supported Single-point/Regional Datasets `_). All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region. +Running for a *normal supported site* is a great solution, if one of the supported single-point/regional datasets, is your region of interest (see :ref:`running-single-point-datasets`). All the datasets are created for you, and you can easily select one and run, out of the box with it using a supported resolution from the top level of the CESM scripts. The problem is that there is a very limited set of supported datasets. You can also use this method for your own datasets, but you have to create the datasets, and add them to the XML database in scripts, CLM and to the DATM. This is worthwhile if you want to repeat many multiple cases for a given point or region. In general :ref:`pts_mode` is the quick and dirty method that gets you started without having to create datasets -- but has limitations. It's good for an initial attempt at seeing results for a point of interest, but since you can NOT restart with it, it's usage is limited. It is the quickest method as you can create a case for it directly from **create_newcase**. Although you can't restart, running a single point is very fast, and you can run for long simulation times even without restarts. @@ -35,5 +35,5 @@ Next, ``CLM_USRDAT_NAME`` is the best way to setup cases quickly where you have Lastly *PTCLMmkdata* is a great way to easily create datasets, setup simulations and run simulations for tower sites. It takes advantage of both normal supported site functionality and CLM_USRDAT_NAME internally. A big advantage to it, is that it's one-stop shopping, it runs tools to create datasets, and runs **create_newcase** and sets the appropriate env variables for you. So you only have to learn how to run one tool, rather than work with many different ones. PTCLMmkdata is described in the next chapter, :ref:`running-PTCLM`. -Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in `the Section called Running with your own atmosphere forcing `_. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. :ref:`converting-ameriflux-for-ptclmmkdata` tells you how to use AmeriFlux data for atmospheric forcing. +Finally, if you also have meteorology data that you want to force your CLM simulations with you'll need to setup cases as described in :ref:`creating-your-own-singlepoint-dataset`. You'll need to create CLM datasets either according to ``CLM_USRDAT_NAME``. You may also need to modify DATM to use your forcing data. And you'll need to change your forcing data to be in a format that DATM can use. :ref:`converting-ameriflux-for-ptclmmkdata` tells you how to use AmeriFlux data for atmospheric forcing. From 0bc8c04c60a1af06210c89d4d7dd575397085d15 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 26 Oct 2023 16:07:02 -0600 Subject: [PATCH 1730/2067] cleanup modify_singlept_site_neon.py --- .../ctsm/site_and_regional/modify_singlept_site_neon.py | 8 -------- python/ctsm/test/test_sys_run_neon.py | 3 ++- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index fc4964c0b4..a7838bedac 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -524,12 +524,6 @@ def main(): # better suggestion by WW to write dzsoi to neon surface dataset # This todo needs to go to the subset_data - # TODO Will: if I sum them up , are they 3.5? (m) YES - print("soil_top:", soil_top) - print("soil_bot:", soil_bot) - print("Sum of soil top depths :", sum(soil_top)) - print("Sum of soil bottom depths :", sum(soil_bot)) - soil_top = np.cumsum(soil_top) soil_bot = np.cumsum(soil_bot) soil_mid = 0.5 * (soil_bot - soil_top) + soil_top @@ -656,9 +650,7 @@ def main(): print("Updated : ", f2.PCT_CROP.values) print("Updating PCT_NAT_PFT") - # print (f2.PCT_NAT_PFT) print(f2.PCT_NAT_PFT.values[0]) - # f2.PCT_NAT_PFT.values[0] = [[100.0]] print(f2.PCT_NAT_PFT[0].values) out_dir = args.out_dir diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index c2599d782d..db90dc8bb0 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -70,10 +70,11 @@ def test_one_site(self): # this seems to run OSBS (default site, instead of ABBY), # but does create files! It takes a while though, should we do setup-only? # Could assert that dir is created with files - #we should also move this into a tempdir and delete files after running (and cancel queue?) + # we should also move this into a tempdir and delete files after running (and cancel queue?) self.assertTrue("OSBS" in glob.glob("*")) + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() From d783396e659d90ddb30ec2ff2dc09e2724e891ac Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 16:48:18 -0600 Subject: [PATCH 1731/2067] Fix bug in was_sown_in_this_window() for windows w/ start==end. --- src/biogeochem/CNPhenologyMod.F90 | 6 +-- .../test/CNPhenology_test/test_CNPhenology.pf | 49 +++++++++++++++++++ 2 files changed, 52 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90 index 60ab4f6dba..5a3f02a1ee 100644 --- a/src/biogeochem/CNPhenologyMod.F90 +++ b/src/biogeochem/CNPhenologyMod.F90 @@ -1812,10 +1812,10 @@ function was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, return end if - ! Sometimes we're in an active sowing window, and the patch was sown between the start and end dates of the window, but not *the currently active* window. - if (sowing_window_startdate <= sowing_window_enddate .and. idop > jday) then + ! Sometimes we're in an active sowing window, and the patch was sown between the start and end dates of the window, but not *the currently active* window. Note that windows with start==end are not checked here; we always trust the input value of sown_in_this_window in such cases. + if (sowing_window_startdate < sowing_window_enddate .and. idop > jday) then was_sown_in_this_window = .false. - else if (sowing_window_startdate >= sowing_window_enddate) then + else if (sowing_window_startdate > sowing_window_enddate) then if (jday <= sowing_window_enddate .and. idop <= sowing_window_enddate .and. idop > jday) then was_sown_in_this_window = .false. else if (jday >= sowing_window_startdate .and. (idop > jday .or. idop <= sowing_window_enddate)) then diff --git a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf index 9a3701d68c..9e06bc74e2 100644 --- a/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf +++ b/src/biogeochem/test/CNPhenology_test/test_CNPhenology.pf @@ -452,4 +452,53 @@ contains end subroutine test_was_sown_in_this_window_endstart + @Test + subroutine test_was_sown_in_this_window_sameday(this) + use clm_time_manager , only : is_doy_in_interval + class(TestCNPhenology), intent(inout) :: this + integer, parameter :: sowing_window_startdate = 205 + integer, parameter :: sowing_window_enddate = 205 + integer :: jday, idop + + ! If today == start == end, we trust whatever the current value of sown_in_this_window is. + jday = 205 + idop = 205 + ! If it's false, then even if idop == jday, it that idop value must be left over from planting in a PREVIOUS year. + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + ! The ONLY way was_sown_in_this_window() should return true is if today == start == end == idop AND the current value is true. + @assertTrue(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + ! There is no other situation where was_sown_in_this_window() should return true. + + jday = 300 + idop = 60 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 205 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 300 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 301 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + jday = 70 + + idop = 60 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + idop = 75 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + + idop = 301 + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .true.)) + @assertFalse(was_sown_in_this_window(sowing_window_startdate, sowing_window_enddate, jday, idop, .false.)) + + end subroutine test_was_sown_in_this_window_sameday + end module test_CNPhenology From b459eeff9c6eb1d82ea130f813d4928097074f74 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 22:04:59 -0600 Subject: [PATCH 1732/2067] UG running-special-cases: Fix CLM-URL links. --- ...-alone-CLM-with-transient-historical-CO2-concentration.rst | 2 +- ...h-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst | 2 +- ...-simulation-as-atmospheric-forcing-to-spinup-the-model.rst | 4 +++- ...Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst | 2 +- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 2 ++ .../customizing-the-datm-namelist.rst | 2 ++ 6 files changed, 10 insertions(+), 4 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst index 9e9bacaf1e..b323082619 100644 --- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst +++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst @@ -8,7 +8,7 @@ In this case you want to run a simulation with stand-alone CLM responding to changes in CO2 for a historical period. For this example, we will start with the "I_1850-2000_CN" compset that has transient: land-use, Nitrogen and Aerosol deposition already. You could also use another compset if you didn't want these other features to be transient. In order to get CO2 to be transient we need to add a new streams file and add it to the list of streams in the user_nl_datm file. You also need a NetCDF datafile that datm can read that gives the variation. You could supply your own file, but we have a standard file that is used by CAM for this and our example will make use of this file. -.. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide `_ especially as it pertains to the datm. +.. note:: Most everything here has to do with changing datm rather than CLM to allow this to happen. As such the user that wishes to do this should first become more familiar with datm and read the `CESM Data Model User's Guide `_ especially as it pertains to the datm. .. warning:: This section documents the process for doing something that is non-standard. There may be errors with the documentation and process, and you may have to do some work before all of this works for you. If that is the case, we recommend that you do further research into understanding the process and the files, as well as understanding the datm and how it works. You may have to read documentation found in the code for datm as well as "csm_share". diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst index 7f210ba151..f2d5248ec8 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst @@ -8,7 +8,7 @@ Because it takes so long to spinup the CN model (as we just saw previously), if you are doing fully coupled simulations with active atmosphere and ocean, you will want to do the spinup portion of this "offline". So instead of doing expensive fully coupled simulations for the spinup duration, you run CLM in a very cheap "I" compset using atmospheric forcing from a shorter fully coupled simulation (or a simulation run previously by someone else). -In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on cheyenne. There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to `Example 4-11 `_. +In this example we will use the ``I1850Clm50BgcSpinup compset`` to setup CLM to run with atmospheric forcing from a previous fully coupled simulation with data that is already stored on disk on Cheyenne. There are several simulations that have high frequency data for which we can do this. You can also do this on a machine other than Cheyenne, but would need to download the data from the Earth System Grid and change the datapath similar to Example :numref:`eg-sim-data-from-prev-sim`. Example: Simulation with MOAR Data on cheyenne ------------------------------------------------------------- diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst index af98005840..988e1fe029 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst @@ -36,7 +36,9 @@ Example: Fully Coupled Simulation to Create Data to Force Next Example Simulatio # Now run as normal > ./case.submit -Now we run an I compset forced with the data from the previous simulation using the CPLHISTForcing`` option to DATM_MODE. See `the Section called CPLHISTForcing mode and it's DATM settings in Chapter 1 `_ for more information on the DATM settings for ``CPLHISTForcing`` mode. +Now we run an I compset forced with the data from the previous simulation using the ``CPLHISTForcing`` option to DATM_MODE. See :ref:`cplhistforcing` for more information. + +.. _eg-sim-data-from-prev-sim: Example: Simulation Forced with Data from the Previous Simulation ------------------------------------------------------------------------------ diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst index be67998ec1..eb482efdd6 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-Satellite-Phenology-Model-CLMSP-spinup.rst @@ -6,7 +6,7 @@ Spinning up the Satellite Phenology Model =========================================== -To spin-up the CLMSP model you merely need to run CLMSP for about 50 simulation years starting from arbitrary initial conditions. You then use the final restart file for initial conditions in other simulations. Because, this is a straight forward operation we will NOT give the details on how to do that here, but leave it as an exercise for the reader. See the `Example 4-7 `_ as an example of doing this as the last step for CLMCN. +To spin-up the CLMSP model you merely need to run CLMSP for about 50 simulation years starting from arbitrary initial conditions. You then use the final restart file for initial conditions in other simulations. Because this is a straight forward operation we will NOT give the details on how to do that here, but leave it as an exercise for the reader. See the Example :numref:`eg-final-clmbgc-spinup` as an example of doing this as the last step for CLMCN. You can also start from a default initial file that is setup as part of the selected compset. :numref:`Figure SP spinup plot for 1850` shows spinup behavior for an 1850 SP case that loops over one year of coupler history output for atmospheric forcing (generated from the fully coupled model), initialized with an initial file generated from a GSWP3 atmospheric forcing case. Note that it takes less than 10 years for state variables such as FSH (sensible heat flux), EFLX_LH_TOT (latent heat flux), GPP (photosynthesis), H2OSOI (soil water), and TSOI (soil temperature) to reach a specified equilibrium state (denoted by the dotted lines) due to the different atmospheric forcing. TWS (total water storage) may take a bit longer. diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index c5cfc971f1..772bba1243 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -69,6 +69,8 @@ Afterwards save the last restart file from this simulation to use in the next st **2. Final spinup for |version|-BGC** Next save the last restart file from this step and use it as the "finidat" file to use for one more spinup for at least 400+ years in normal mode. So do the following: +.. _eg-final-clmbgc-spinup: + Example: Final CLMBGC Spinup Simulation for |version|-BGC ------------------------------------------------------------------ :: diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst index df55e46b22..121964db66 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst @@ -80,6 +80,8 @@ In ``CLM1PT`` mode the model is assumed to have half-hourly or hourly data for a If you are using your own data for this mode and it's not at least hourly you'll want to adjust the DATM settings for it. If the data is three or six hourly, you'll need to divide it up into separate streams like in ``CLM_QIAN`` mode which will require fairly extensive changes to the DATM namelist and streams files. For an example of doing this see `Example 5-8 `_. +.. _cplhistforcing: + ------------------------------------------ CPLHISTForcing mode and it's DATM settings ------------------------------------------ From 89f24958de48049a9f8b7b0b7e413c1f8d2d1873 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 22:09:17 -0600 Subject: [PATCH 1733/2067] UG: Deleted references to tables that no longer exist in the docs. Old versions of the tables are here: https://www2.cesm.ucar.edu/models/cesm1.2/clm/models/lnd/clm/doc/UsersGuide/c720.html --- .../setting-up-and-running-a-case/choosing-a-compset.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index a081f9e869..aa4024f735 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -15,8 +15,6 @@ When working with CLM you usually want to start with a relevant "I" compset befo Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) ------------------------------------------------------------------------- -`Supported CLM Configurations `_ are listed in `Table 1-1 `_ for the Scientifically Supported compsets (have been scientifically validated with long simulations) and in `Table 1-2 `_ for the Functionally Supported compsets (we've only checked that they function). - Here is the entire list of compsets available. `CESM compsets `_ From a3a051409b9caf3a26cf8cb21c2982cafac6afe3 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 22:15:57 -0600 Subject: [PATCH 1734/2067] UG choosing a compset: Replace outdated ref to -user_compset with link to longnames. --- .../setting-up-and-running-a-case/choosing-a-compset.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index aa4024f735..27fed2de4c 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -19,7 +19,7 @@ Here is the entire list of compsets available. `CESM compsets `_ -Note that using the "-user_compset" option even more combinations are possible. To get a list of the compsets use the "query_config" command as follows: +Note that using the `compset longnames `_ even more combinations are possible. To get a list of the compsets use the ``query_config`` command as follows: :: $CTSMROOT/cime/scripts/query_config --compsets clm From be1d64657e6ac99f30301ffe0cb704494fffc21e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 22:53:57 -0600 Subject: [PATCH 1735/2067] UG setting-up-and-running-a-case: Fix CLM-URL links. --- ...transient-historical-CO2-concentration.rst | 4 +- ...tmospheric-forcing-to-spinup-the-model.rst | 4 +- .../choosing-a-compset.rst | 6 +- .../customizing-the-clm-configuration.rst | 74 +++++++++++-------- .../customizing-the-clm-namelist.rst | 29 ++------ .../customizing-the-datm-namelist.rst | 10 ++- 6 files changed, 61 insertions(+), 66 deletions(-) diff --git a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst index b323082619..f93bcca2f0 100644 --- a/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst +++ b/doc/source/users_guide/running-special-cases/Running-stand-alone-CLM-with-transient-historical-CO2-concentration.rst @@ -1,7 +1,7 @@ -.. _running-with-historical-co2-forcing: - .. include:: ../substitutions.rst +.. _running-with-historical-co2-forcing: + ===================================== Running with historical CO2 forcing ===================================== diff --git a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst index f2d5248ec8..dbe01c497c 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-MOAR-data-as-atmospheric-forcing-to-spinup-the-model.rst @@ -1,7 +1,7 @@ -.. _running-with-moar-data: - .. include:: ../substitutions.rst +.. _running-with-moar-data: + ======================== Running with MOAR data ======================== diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index 27fed2de4c..5eca296cc5 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -15,9 +15,7 @@ When working with CLM you usually want to start with a relevant "I" compset befo Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) ------------------------------------------------------------------------- -Here is the entire list of compsets available. - -`CESM compsets `_ +Here is the entire list of compsets available: `CESM compsets `_ Note that using the `compset longnames `_ even more combinations are possible. To get a list of the compsets use the ``query_config`` command as follows: :: @@ -34,4 +32,4 @@ Fully coupled compsets are compsets that start with "B" in the name. They are de Conclusion to choosing a compset -------------------------------- -We've introduced the basic type of compsets that use CLM and given some further details for the "standalone CLM" (or "I" compsets). The `$CTSMROOT/cime_config/config_compsets.xml `_ lists all of the compsets and gives a full description of each of them. In the next section we look into customizing the setup time options for compsets using CLM. +We've introduced the basic type of compsets that use CLM and given some further details for the "standalone CLM" (or "I" compsets). `$CTSMROOT/cime_config/config_compsets.xml `_ lists all of the compsets and gives a full description of each of them. In the next section we look into customizing the setup time options for compsets using CLM. diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index 5687f9c13d..c3e25e790d 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -10,9 +10,9 @@ The section of the |cesmrelease| Quickstart `CESM Create a Case `_). The env variables for **configure** are locked after the **case.build** step. So the results of the CLM **configure** are locked after the build has taken place. +1. The CLM "**configure**" script is called to setup the build-time configuration for CLM (see :ref:`more-info-clm-config-script`). The env variables for **configure** are locked after the **case.build** step. So the results of the CLM **configure** are locked after the build has taken place. -2. The CLM "**build-namelist**" script is called to generate the run-time namelist for CLM (more information on **build-namelist** is given below in `the Section called Definition of Namelist items and their default values `_. +2. The CLM "**build-namelist**" script is called to generate the run-time namelist for CLM (more information on **build-namelist** is given below in :ref:`def-nl-items-and-defaults`). When customizing your case at the **case.setup** step you are able to modify the process by effecting either one or both of these steps. The CLM "**configure**" and "**build-namelist**" scripts are both available in the "$CTSMROOT/bld" directory in the distribution. Both of these scripts have a "-help" option that is useful to examine to see what types of options you can give either of them. @@ -43,10 +43,10 @@ For the precedence of the different options to **build-namelist** see the sectio The first item ``CLM_CONFIG_OPTS`` has to do with customizing the CLM build-time options for your case, the rest all have to do with generating the namelist. CLM_CONFIG_OPTS - The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. Hence, we recommend using the "-append" option to the xmlchange script. In `the Section called More information on the CLM configure script `_ below we will go into more details on options that can be customized in the CLM "**configure**" script. It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). The options to CLM **configure** are given with the "-help" option which is given in `the Section called More information on the CLM configure script `_... note:: ``CLM_CONFIG_OPTS`` is locked after the **case.build** script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun **case.build**. The other env variables can be changed at run-time so are never locked. + The option ``CLM_CONFIG_OPTS`` is all about passing command line arguments to the CLM **configure** script. It is important to note that some compsets, may already put a value into the ``CLM_CONFIG_OPTS`` variable. You can still add more options to your ``CLM_CONFIG_OPTS`` but make sure you add to what is already there rather than replacing it. Hence, we recommend using the "-append" option to the xmlchange script. In :ref:`more-info-clm-config-script` below we will go into more details on options that can be customized in the CLM "**configure**" script. It's also important to note that the **$CTSMROOT/cime_config/buildnml** script may already invoke certain CLM **configure** options and as such those command line options are NOT going to be available to change at this step (nor would you want to change them). The options to CLM **configure** are given with the "-help" option which is given in :ref:`more-info-clm-config-script`... note:: ``CLM_CONFIG_OPTS`` is locked after the **case.build** script is run. If you want to change something in ``CLM_CONFIG_OPTS`` you'll need to clean the build and rerun **case.build**. The other env variables can be changed at run-time so are never locked. CLM_NML_USE_CASE - ``CLM_NML_USE_CASE`` is used to set a particular set of conditions that set multiple namelist items, all centering around a particular usage of the model. To list the valid options do the following: + ``CLM_NML_USE_CASE`` is used to set a particular set of conditions that set multiple namelist items, all centering around a particular usage of the model. (See :ref:`precedence-of-opts` for the precedence of this option relative to the others.) To list the valid options do the following: :: > cd $CTSMROOT @@ -100,8 +100,6 @@ CLM_NML_USE_CASE glacierMEC_pd = Running an IG case with the ice sheet model glimmer stdurbpt_pd = Standard Urban Point Namelist Settings - .. note::See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. - CLM_BLDNML_OPTS The option CLM_BLDNML_OPTS is for passing options to the CLM "build-namelist" script. As with the CLM "configure" script the CLM $CTSMROOT/cime_config/buildnml may already invoke certain options and as such those options will NOT be available to be set here. The best way to see what options can be sent to the "build-namelist" script is to do :: @@ -237,17 +235,17 @@ CLM_BLDNML_OPTS -version Echo the SVN tag name used to check out this CLM distribution. Note: The precedence for setting the values of namelist variables is (highest to lowest): - 0. namelist values set by specific command-line options, like, -d, -sim_year + 1. namelist values set by specific command-line options, like, -d, -sim_year (i.e. CLM_BLDNML_OPTS env_run variable) - 1. values set on the command-line using the -namelist option, + 2. values set on the command-line using the -namelist option, (i.e. CLM_NAMELIST_OPTS env_run variable) - 2. values read from the file(s) specified by -infile, + 3. values read from the file(s) specified by -infile, (i.e. user_nl_clm files) - 3. datasets from the -clm_usr_name option, + 4. datasets from the -clm_usr_name option, (i.e. CLM_USRDAT_NAME env_run variable) - 4. values set from a use-case scenario, e.g., -use_case + 5. values set from a use-case scenario, e.g., -use_case (i.e. CLM_NML_USE_CASE env_run variable) - 5. values from the namelist defaults file. + 6. values from the namelist defaults file. The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and mask as well as the CLM **configure** file, and defines an input namelist and namelist input file, and the output namelist directory, and sets the start-type (from ``RUN_TYPE``), namelist options (from ``CLM_NAMELIST_OPTS``), co2_ppmv (from ``CCSM_CO2_PPMV``, co2_type (from ``CLM_CO2_TYPE``), lnd_frac (from ``LND_DOMAIN_PATH`` and ``LND_DOMAIN_FILE``), l_ncpl (from ``LND_NCPL``, glc_grid, glc_smb, glc_nec (from ``GLC_GRID``, ``GLC_SMB``, and ``GLC_NEC``), and "clm_usr_name" is set (to ``CLM_USRDAT_NAME >``when the grid is set to ``CLM_USRDAT_NAME``. Hence only the following different options can be set: @@ -276,7 +274,7 @@ The **$CTSMROOT/cime_config/buildnml** script already sets the resolution and ma #. -verbose -"-bgc_spinup" is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See `the Section called Spinning up the |version| biogeochemistry (CLMBGC spinup) in Chapter 4 `_ for an example using this option. +"-bgc_spinup" is an option only available for |version| for any configuration when CN is turned on (so either CLMCN or CLMBGC). It can be set to "on" or "off". If "on" the model will go into Accelerated Decomposition mode, while for "off" (the default) it will have standard decomposition rates. If you are starting up from initial condition files the model will check what mode the initial condition file is in and do the appropriate action on the first time-step to change the Carbon pools to the appropriate spinup setting. See :ref:`spinning-up-clm-bgc` for an example using this option. "-chk_res" ensures that the resolution chosen is supported by CLM. If the resolution is NOT supported it will cause the CLM **build-namelist** to abort when run. So when either **preview_namelist**, **case.build** or **case.run** is executed it will abort early. Since, the CESM scripts only support certain resolutions anyway, in general this option is NOT needed in the context of running CESM cases. @@ -318,7 +316,7 @@ When "-irrig on" is used **build-namelist** will try to find surface datasets th > ../bld/build-namelist -sim_year list ``CLM_NAMELIST_OPTS`` - passes namelist items into one of the CLM namelists. + passes namelist items into one of the CLM namelists. (See :ref:`precedence-of-opts` for the precedence of this option relative to the others.) .. note:: For character namelist items you need to use "'" as quotes for strings so that the scripts don't get confused with other quotes they use. @@ -332,26 +330,22 @@ When "-irrig on" is used **build-namelist** will try to find surface datasets th > ./xmlchange CLM_NAMELIST_OPTS="hist_fincl1='HK'" - For a list of the history fields available see `CLM History Fields `_. - - .. note::See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. + For lists of the history fields available see :ref:`customizing_section`. ``CLM_FORCE_COLDSTART`` when set to on, *requires* that your simulation do a cold start from arbitrary initial conditions. If this is NOT set, it will use an initial condition file if it can find an appropriate one, and otherwise do a cold start. ``CLM_FORCE_COLDSTART`` is a good way to ensure that you are doing a cold start if that is what you want to do. ``CLM_USRDAT_NAME`` - Provides a way to enter your own datasets into the namelist. The files you create must be named with specific naming conventions outlined in: `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be: + Provides a way to enter your own datasets into the namelist. The files you create must be named with specific naming conventions outlined in :ref:`creating-your-own-singlepoint-dataset`. To see what the expected names of the files are, use the **queryDefaultNamelist.pl** to see what the names will need to be. For example if your ``CLM_USRDAT_NAME`` will be "1x1_boulderCO", with a "navy" land-mask, constant simulation year range, for 1850, the following will list what your filenames should be: :: > cd $CTSMROOT/bld > queryDefaultNamelist.pl -usrname "1x1_boulderCO" -options mask=navy,sim_year=1850,sim_year_range="constant" -csmdata $CSMDATA - An example of using ``CLM_USRDAT_NAME`` for a simulation is given in `Example 5-4 `_. - - .. note: See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. + An example of using ``CLM_USRDAT_NAME`` for a simulation is given in Example :numref:`creating-your-own-singlepoint-dataset`. ``CLM_CO2_TYPE`` - sets the type of input CO2 for either "constant", "diagnostic" or prognostic". If "constant" the value from ``CCSM_CO2_PPMV`` will be used. If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. For more information on how to send CO2 from the data atmosphere model see `the Section called Running stand-alone CLM with transient historical CO2 concentration in Chapter 4 `_. + sets the type of input CO2 for either "constant", "diagnostic" or prognostic". If "constant" the value from ``CCSM_CO2_PPMV`` will be used. If "diagnostic" or "prognostic" the values MUST be sent from the atmosphere model. See :ref:`running-with-historical-co2-forcing` for more information on how to send CO2 from the data atmosphere model. =============== User Namelist @@ -405,12 +399,12 @@ Example: user_nl_clm namelist file **Note:** The comments at the top are some guidance given in the default user_nl_clm and just give some guidance on how to set variables and use the file. -**Note:** See `the Section called Precedence of Options `_ section for the precedence of this option relative to the others. - **Note:** You do NOT need to specify the namelist group that the variables are in because the CLM **build-namelist** knows the namelist that specific variable names belong to, and it puts them there. Obviously, all of this would be difficult to put in the CLM_NAMELIST_OPTS variable, especially having to put ' around all the character strings. For more information on the namelist variables being set here and what they mean, see the section on CLM namelists below, as well as the namelist definition that gives details on each variable. +.. _precedence-of-opts: + --------------------- Precedence of Options --------------------- @@ -439,13 +433,15 @@ Setting Your Initial Conditions File Especially with CLMBGC and CLMCN starting from initial conditions is very important. Even with CLMSP it takes many simulation years to get the model fully spunup. There are a couple different ways to provide an initial condition file. -- `the Section called Doing a hybrid simulation to provide initial conditions `_ -- `the Section called Doing a branch simulation to provide initial conditions `_ -- `the Section called Providing a finidat file in your user_nl_clm file `_ -- `the Section called Adding a finidat file to the XML database `_ +- :ref:`doing-a-hybrid-sim-for-init-conds` +- :ref:`doing-a-branch-sim-for-init-conds` +- :ref:`providing-finidat-in-usernlclm` +- :ref:`adding-finidat-to-xml` **Note:** Your initial condition file MUST agree with the surface dataset you are using to run the simulation. If the two files do NOT agree you will get a run-time about a mis-match in PFT weights, or in the number of PFT's or columns. To get around this you'll need to add the "use_init_interp=T" namelist flag in your namelist so that the initial conditions will be interpolated on startup.** +.. _doing-a-hybrid-sim-for-init-conds: + ------------------------------------------------------- Doing a hybrid simulation to provide initial conditions ------------------------------------------------------- @@ -456,12 +452,16 @@ The first option is to setup a hybrid simulation and give a ``RUN_REFCASE`` and Setting the ``GET_REFCASE`` option to ``TRUE means`` it will copy the files from the RUN_REFDIR usually under: ``$DIN_LOC_ROOT/cesm2_init/$RUN_REFCASE/$RUN_REFDATE`` directory. Note, that the ``RUN_REFCASE`` and ``RUN_REFDATE`` variables are expanded to get the directory name above. If you do NOT set ``GET_REFCASE`` to ``TRUE`` then you will need to have placed the file in your run directory yourself. In either case, the file is expected to be named: ``$RUN_REFCASE.clm2.r.$RUN_REFDATE-00000.nc`` with the variables expanded of course. +.. _doing-a-branch-sim-for-init-conds: + ------------------------------------------------------- Doing a branch simulation to provide initial conditions ------------------------------------------------------- The setup for running a branch simulation is essentially the same as for a hybrid. With the exception of setting ``RUN_TYPE`` to branch rather than hybrid. A branch simulation runs the case essentially as restarting from it's place before to exactly reproduce it (but possibly output more or different fields on the history files). While a hybrid simulation allows you to change the configuration or run-time options, as well as use a different code base than the original case that may have fewer fields on it than a full restart file. The ``GET_REFCASE`` option works similarly for a branch case as for a hybrid. +.. _providing-finidat-in-usernlclm: + ------------------------------------------------- Providing a finidat file in your user_nl_clm file ------------------------------------------------- @@ -473,6 +473,8 @@ Setting up a branch or hybrid simulation requires the initial condition file to Note, if you provide an initial condition file -- you can NOT set ``CLM_FORCE_COLDSTART`` to ``TRUE``. +.. _adding-finidat-to-xml: + ------------------------------------------- Adding a finidat file to the XML database ------------------------------------------- @@ -513,16 +515,22 @@ For running "I" cases there are several other noteworthy configuration items tha CPLHISTForcing ``CLMCRUNCEP`` - The standard mode for CLM4.5 of using global atmospheric data that was developed by CRU using NCEP data from 1901 to 2010 (version 4 of this series). See `the Section called CLMCRUNCEP mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. + The standard mode for CLM4.5 of using global atmospheric data that was developed by CRU using NCEP data from 1901 to 2010 (version 4 of this series). See :ref:`clmcruncep-and-its-datm` for more information. ``CLMCRUNCEPv7`` - Version 7 of the CRUNCEP data from 1901 to 2016. See `the Section called CLMCRUNCEPv7 mode and it's DATM settings `_ for more information on the DATM settings for ``CLMCRUNCEP`` mode. + Version 7 of the CRUNCEP data from 1901 to 2016. See :ref:`clmcruncep-and-its-datm` for more information. ``CLMGSWP3v1`` GSWP3 version 1 forcing data based on NCEP reanalysis with bias corrections by GSWP3 from 1901 to 2010. ``CLM_QIAN`` - The standard mode for CLM4.0 of using global atmospheric data that was developed by Qian et. al. for CLM using NCEP data from 1948 to 2004. See the `Section called CLM_QIAN mode and it's DATM settings `_ for more information on the DATM settings for ``CLM_QIAN`` mode. ``CLM1PT`` is for the special cases where we have single-point tower data for particular sites. Right now we only have data for three urban locations: MexicoCity Mexico, Vancouver Canada, and the urban-c alpha site. And we have data for the US-UMB AmeriFlux tower site for University of Michigan Biological Station. See `the Section called CLM1PT mode and it's DATM settings `_ for more information on the DATM settings for ``CLM1PT`` mode. ``CPLHISTForcing`` is for running with atmospheric forcing from a previous CESM simulation. See `the Section called CPLHISTForcing mode and it's DATM settings `_ for more information on the DATM settings for ``CPLHISTForcing`` mode. + The standard mode for CLM4.0 of using global atmospheric data that was developed by Qian et. al. for CLM using NCEP data from 1948 to 2004. See :ref:`clmqian-and-its-datm` for more information. + +``CLM1PT`` + This is for the special cases where we have single-point tower data for particular sites. Right now we only have data for three urban locations: MexicoCity Mexico, Vancouver Canada, and the urban-c alpha site. And we have data for the US-UMB AmeriFlux tower site for University of Michigan Biological Station. See :ref:`clm1pt-and-its-datm` for more information. + +``CPLHISTForcing`` + This is for running with atmospheric forcing from a previous CESM simulation. See :ref:`cplhistforcing` for more information. ``DATM_PRESAERO`` sets the prescribed aerosol mode for the data atmosphere model. The list of valid options include: @@ -585,11 +593,13 @@ The final thing that the user may wish to do before **case.setup** is run is to **datm.buildexe.csh** **datm.buildnml.csh** +.. _more-info-clm-config-script: + -------------------------------------------- More information on the CLM configure script -------------------------------------------- -The CLM **configure** script defines the details of a clm configuration and summarizes it into a ``config_cache.xml`` file. The ``config_cache.xml`` will be placed in your case directory under ``Buildconf/clmconf``. The `config_definition.xml `_ in ``$CTSMROOT/bld/config_files`` gives a definition of each CLM configuration item, it is viewable in a web-browser. Many of these items are things that you would NOT change, but looking through the list gives you the valid options, and a good description of each. Below we repeat the ``config_definition.xml`` files contents: +The CLM ``configure`` script defines the details of a clm configuration and summarizes it into a ``config_cache.xml`` file. The ``config_cache.xml`` will be placed in your case directory under ``Buildconf/clmconf``. The `config_definition_ctsm.xml `_ in ``$CTSMROOT/bld/config_files`` gives a definition of each CLM configuration item, it is viewable in a web-browser. Many of these items are things that you would NOT change, but looking through the list gives you the valid options, and a good description of each. Help on CLM configure --------------------- diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst index afd850d458..d753f19104 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst @@ -10,41 +10,22 @@ Once a case has run **case.setup**, we can then customize the case further, by e In the following, various examples of namelists are provided that feature the use of different namelist options to customize a case for particular uses. Most the examples revolve around how to customize the output history fields. This should give you a good basis for setting up your own CLM namelist. +.. _def-nl-items-and-defaults: + ----------------------------------------------------- Definition of Namelist items and their default values ----------------------------------------------------- Here we point to you where you can find the definition of each namelist item and separately the default values for them. The default values may change depending on the resolution, land-mask, simulation-year and other attributes. Both of these files are viewable in your web browser, and then expand each in turn. -1. `Definition of Namelists Relevant for |version| `_ - -2. `Default values of each CLM4.0 Namelist Item `_ +1. `Definition of Namelists `_ -3. `Default values of each |version| Namelist Item `_ +2. `Default values of each Namelist Item `_ List of fields that can be added to your output history files by namelist ------------------------------------------------------------------------- -One set of the namelist items allows you to add fields to the output history files: ``hist_fincl1``, ``hist_fincl2``, ``hist_fincl3``, ``hist_fincl4``, ``hist_fincl5``, and ``hist_fincl6``. The following links for `CLM4.0 History Fields `_ and `|version| History Fields `_ documents all of the history fields available and gives the long-name and units for each. The table below lists all the |version| history fields. - -Definition of CLM history variables ------------------------------------ - -Included in the table are the following pieces of information: - -- Variable name. - -- Long name description. - -- units - -Table 1-3. CLM History Fields from a BgcCrop case -------------------------------------------------- -For Table from a BgcCrop case, please see :doc:`history_fields_nofates`. - -Table 1-4. CLM History Fields from a Fates case ------------------------------------------------ -For Table from a Fates case, please see :doc:`history_fields_fates`. +One set of the namelist items allows you to add fields to the output history files: ``hist_fincl1``, ``hist_fincl2``, ``hist_fincl3``, ``hist_fincl4``, ``hist_fincl5``, and ``hist_fincl6``. The :doc:`history_fields_nofates` and :doc:`history_fields_fates` files list all of the history fields available and gives the long-name and units for each. --------------------------------------------- Examples of using different namelist features diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst index 121964db66..2c5ddacbc6 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst @@ -58,12 +58,16 @@ In ``CLMCRUNCEPv7`` mode the CRUNCEP dataset is used and all of it's data is on For more information on CRUNCEP forcing see `http://dods.extra.cea.fr/data/p529viov/cruncep/ `_. +.. _clmcruncep-and-its-datm: + -------------------------------------- CLMCRUNCEP mode and it's DATM settings -------------------------------------- ``CLMCRUNCEP`` is similar to the ``CLMCRUNCEPv7`` mode above, except it uses Version 4 of the CRUNCEP data rather than version 7. +.. _clmqian-and-its-datm: + ------------------------------------ CLM_QIAN mode and it's DATM settings ------------------------------------ @@ -72,13 +76,15 @@ In ``CLM_QIAN`` mode the Qian dataset is used which has 6-hourly solar and preci Normally you wouldn't customize the ``CLM_QIAN`` settings, but you might replicate it's use for your own global data that had similar temporal characteristics. +.. _clm1pt-and-its-datm: + ---------------------------------- CLM1PT mode and it's DATM settings ---------------------------------- In ``CLM1PT`` mode the model is assumed to have half-hourly or hourly data for a single-point. For the supported datasets that is exactly what it has. But, if you add your own data you may need to make adjustments accordingly. Using the ``CLM_USRDAT_NAME`` resolution you can easily extend this mode for your own datasets that may be regional or even global and could be at different temporal frequencies. If you do so you'll need to make adjustments to your DATM settings. The dataset has all data in a single stream file. The time-stamps of the data were also adjusted so that they are at the middle of the interval. Because, of this the ``offset`` is set to zero, and the ``tintalgo`` is set to ``nearest``. ``taxmode`` is set to ``extend`` and ``mapalgo`` is set to ``nn`` so that simply the nearest point is used. -If you are using your own data for this mode and it's not at least hourly you'll want to adjust the DATM settings for it. If the data is three or six hourly, you'll need to divide it up into separate streams like in ``CLM_QIAN`` mode which will require fairly extensive changes to the DATM namelist and streams files. For an example of doing this see `Example 5-8 `_. +If you are using your own data for this mode and it's not at least hourly you'll want to adjust the DATM settings for it. If the data is three or six hourly, you'll need to divide it up into separate streams like in ``CLM_QIAN`` mode which will require fairly extensive changes to the DATM namelist and streams files. For an example of doing this see :ref:`eg-sim-data-from-prev-sim`. .. _cplhistforcing: @@ -86,6 +92,6 @@ If you are using your own data for this mode and it's not at least hourly you'll CPLHISTForcing mode and it's DATM settings ------------------------------------------ -In ``CPLHISTForcing`` mode the model is assumed to have 3-hourly for a global grid from a previous CESM simulation. Like ``CLM_QIAN`` mode the data is divided into three streams: one for precipitation, one for solar, and one for everything else. The time-stamps for Coupler history files for CESM is at the end of the interval, so the ``offset`` needs to be set in order to adjust the time-stamps to what it needs to be for the ``tintalgo`` settings. For precipitation ``taxmode`` is set to ``nearest`` so the ``offset`` is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` seconds so that the ending time-step is adjust by three hours to the beginning of the interval. For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For an example of such a case see `the Section called Running with MOAR data as atmospheric forcing to spinup the model in Chapter 4 `_. +In ``CPLHISTForcing`` mode the model is assumed to have 3-hourly for a global grid from a previous CESM simulation. Like ``CLM_QIAN`` mode the data is divided into three streams: one for precipitation, one for solar, and one for everything else. The time-stamps for Coupler history files for CESM is at the end of the interval, so the ``offset`` needs to be set in order to adjust the time-stamps to what it needs to be for the ``tintalgo`` settings. For precipitation ``taxmode`` is set to ``nearest`` so the ``offset`` is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For solar ``taxmode`` is set to ``coszen`` so the offset is set to ``-10800`` seconds so that the ending time-step is adjust by three hours to the beginning of the interval. For everything else ``taxmode`` is set to ``linear`` so the offset is set to ``-5400`` seconds so that the ending time-step is adjusted by an hour and half to the middle of the interval. For an example of such a case see :ref:`running-with-moar-data`. Normally you wouldn't modify the DATM settings for this mode. However, if you had data at a different frequency than 3-hours you would need to modify the ``offset`` and possibly the ``taxmode``. The other two things that you might modify would be the path to the data or the domain file for the resolution (which is currently hardwired to f09). For data at a different input resolution you would need to change the domain file in the streams file to use a domain file to the resolution that the data comes in on. From bebfb13fa5f8a03f3d15613bed1f8dcac7c1c3c8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 26 Oct 2023 22:59:17 -0600 Subject: [PATCH 1736/2067] UG: Ensure all labels come after include of substitutions.rst. --- ...esolutions-or-New-Files-to-the-build-namelist-Database.rst | 4 ++-- .../Adding-or-Changing-Default-Filenames.rst | 4 ++-- doc/source/users_guide/overview/introduction.rst | 4 ++-- doc/source/users_guide/running-PTCLM/ptclm-examples.rst | 4 ++-- doc/source/users_guide/running-PTCLM/using-ptclm.rst | 4 ++-- .../single-point-and-regional-grid-configurations.rst | 4 ++-- .../running-special-cases/Running-with-anomaly-forcing.rst | 4 ++-- ...-simulation-as-atmospheric-forcing-to-spinup-the-model.rst | 4 ++-- .../running-the-prognostic-crop-model.rst | 4 ++-- .../running-special-cases/running-with-irrigation.rst | 4 ++-- .../running-special-cases/what-is-a-special-case.rst | 4 ++-- .../setting-up-and-running-a-case/choosing-a-compset.rst | 4 ++-- .../customizing-the-clm-configuration.rst | 4 ++-- .../customizing-the-clm-namelist.rst | 4 ++-- .../customizing-the-datm-namelist.rst | 4 ++-- doc/source/users_guide/testing/testing.rst | 4 ++-- doc/source/users_guide/using-clm-tools/cprnc.rst | 4 ++-- .../users_guide/using-clm-tools/creating-domain-files.rst | 4 ++-- .../creating-input-for-surface-dataset-generation.rst | 4 ++-- .../users_guide/using-clm-tools/creating-surface-datasets.rst | 4 ++-- .../using-clm-tools/observational-sites-datasets.rst | 4 ++-- .../users_guide/using-clm-tools/what-are-the-clm-tools.rst | 4 ++-- 22 files changed, 44 insertions(+), 44 deletions(-) diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst index ccd196baf6..78edaaf629 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-New-Resolutions-or-New-Files-to-the-build-namelist-Database.rst @@ -1,7 +1,7 @@ -.. _adding-resolutions: - .. include:: ../substitutions.rst +.. _adding-resolutions: + ======================== Adding New Resolutions ======================== diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst index 16ed81f679..97e81eb754 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst @@ -1,7 +1,7 @@ -.. _changing-default-filenames: - .. include:: ../substitutions.rst +.. _changing-default-filenames: + ============================ Changing Default Filenames ============================ diff --git a/doc/source/users_guide/overview/introduction.rst b/doc/source/users_guide/overview/introduction.rst index 3dcdda1cf0..bc7c1fd82c 100644 --- a/doc/source/users_guide/overview/introduction.rst +++ b/doc/source/users_guide/overview/introduction.rst @@ -1,7 +1,7 @@ -.. _introduction: - .. include:: ../substitutions.rst +.. _introduction: + **User's Guide to version |version| of the Community Land Model (CLM)** **Authors: Benjamin Andre, Erik Kluzek, William Sacks** diff --git a/doc/source/users_guide/running-PTCLM/ptclm-examples.rst b/doc/source/users_guide/running-PTCLM/ptclm-examples.rst index 8b341c89ae..6801c5f3d8 100644 --- a/doc/source/users_guide/running-PTCLM/ptclm-examples.rst +++ b/doc/source/users_guide/running-PTCLM/ptclm-examples.rst @@ -1,7 +1,7 @@ -.. _ptclm-examples: - .. include:: ../substitutions.rst +.. _ptclm-examples: + ============================== Examples of using PTCLMmkdata ============================== diff --git a/doc/source/users_guide/running-PTCLM/using-ptclm.rst b/doc/source/users_guide/running-PTCLM/using-ptclm.rst index e1e69be88d..e7be79bee6 100644 --- a/doc/source/users_guide/running-PTCLM/using-ptclm.rst +++ b/doc/source/users_guide/running-PTCLM/using-ptclm.rst @@ -1,7 +1,7 @@ -.. _using-ptclm.rst: - .. include:: ../substitutions.rst +.. _using-ptclm.rst: + ************************** Using PTCLMmkdata ************************** diff --git a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst index 3220f16352..34a199ebe8 100644 --- a/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst +++ b/doc/source/users_guide/running-single-points/single-point-and-regional-grid-configurations.rst @@ -1,7 +1,7 @@ -.. _single-point-configurations: - .. include:: ../substitutions.rst +.. _single-point-configurations: + ***************************************** Single and Regional Grid Configurations ***************************************** diff --git a/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst b/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst index 06429688d4..0c6009f3fe 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-anomaly-forcing.rst @@ -1,7 +1,7 @@ -.. _running-with-anomaly-forcing: - .. include:: ../substitutions.rst +.. _running-with-anomaly-forcing: + ============================== Running with anomaly forcing ============================== diff --git a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst index 988e1fe029..ff05836f6e 100644 --- a/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst +++ b/doc/source/users_guide/running-special-cases/Running-with-your-own-previous-simulation-as-atmospheric-forcing-to-spinup-the-model.rst @@ -1,7 +1,7 @@ -.. _running-with-previous-simulation-forcing: - .. include:: ../substitutions.rst +.. _running-with-previous-simulation-forcing: + ============================================================= Running with atmospheric forcing from a previous simulation ============================================================= diff --git a/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst b/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst index caa7b86552..7e19af8678 100644 --- a/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst +++ b/doc/source/users_guide/running-special-cases/running-the-prognostic-crop-model.rst @@ -1,7 +1,7 @@ -.. running-prognostic-crop-model: - .. include:: ../substitutions.rst +.. _running-prognostic-crop-model: + =================================== Running the prognostic crop model =================================== diff --git a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst index f4b04c5b59..12fa76af5b 100644 --- a/doc/source/users_guide/running-special-cases/running-with-irrigation.rst +++ b/doc/source/users_guide/running-special-cases/running-with-irrigation.rst @@ -1,7 +1,7 @@ -.. running-with-irrigation: - .. include:: ../substitutions.rst +.. _running-with-irrigation: + =================================== Running with irrigation =================================== diff --git a/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst b/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst index 4f6a46a7d5..eece6aab51 100644 --- a/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst +++ b/doc/source/users_guide/running-special-cases/what-is-a-special-case.rst @@ -1,7 +1,7 @@ -.. _what is a special case: - .. include:: ../substitutions.rst +.. _what is a special case: + ========================= What is a special case? ========================= diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index 5eca296cc5..a7cd1251a0 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -1,7 +1,7 @@ -.. _choosing-a-compset: - .. include:: ../substitutions.rst +.. _choosing-a-compset: + ==================== Choosing a compset ==================== diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst index c3e25e790d..f8b5fee002 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-configuration.rst @@ -1,7 +1,7 @@ -.. _configuring-clm: - .. include:: ../substitutions.rst +.. _configuring-clm: + ******************************** Customizing CLM's Configuration ******************************** diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst index d753f19104..ff76a841c9 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-clm-namelist.rst @@ -1,7 +1,7 @@ -.. _customizing-a-case: - .. include:: ../substitutions.rst +.. _customizing-a-case: + ============================ Customizing CLM's namelist ============================ diff --git a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst index 2c5ddacbc6..92aa8b4aaa 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/customizing-the-datm-namelist.rst @@ -1,7 +1,7 @@ -.. customizing-the-datm-namelist: - .. include:: ../substitutions.rst +.. _customizing-the-datm-namelist: + =============================== Customizing the DATM namelist =============================== diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index c821ba19e7..54dc748646 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -1,7 +1,7 @@ -.. _testing: - .. include:: ../substitutions.rst +.. _testing: + ******* Testing ******* diff --git a/doc/source/users_guide/using-clm-tools/cprnc.rst b/doc/source/users_guide/using-clm-tools/cprnc.rst index 67ea63e638..0b4ff2ac9f 100644 --- a/doc/source/users_guide/using-clm-tools/cprnc.rst +++ b/doc/source/users_guide/using-clm-tools/cprnc.rst @@ -1,7 +1,7 @@ -.. comparing-history-files: - .. include:: ../substitutions.rst +.. _comparing-history-files: + ========================= Comparing History Files ========================= diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst index 202881bf20..e7105a36d3 100644 --- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst +++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst @@ -1,7 +1,7 @@ -.. _creating-domain-files: - .. include:: ../substitutions.rst +.. _creating-domain-files: + ***************************** Creating CLM domain files ***************************** diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 9c6e8a1f20..122e637e72 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -1,7 +1,7 @@ -.. _creating-maps-for-mksurfdata: - .. include:: ../substitutions.rst +.. _creating-maps-for-mksurfdata: + ********************************************* Creating input for surface dataset generation ********************************************* diff --git a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst index c974b9c886..7a0ad522fa 100644 --- a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst @@ -1,7 +1,7 @@ -.. _creating-surface-datasets: - .. include:: ../substitutions.rst +.. _creating-surface-datasets: + =========================== Creating Surface Datasets =========================== diff --git a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst index 8fafca1df0..ff03106fd4 100644 --- a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst @@ -1,7 +1,7 @@ -.. _observational-sites-datasets: - .. include:: ../substitutions.rst +.. _observational-sites-datasets: + ******************************* Observational Sites Datasets ******************************* diff --git a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst index a0d426672d..6921e4dafd 100644 --- a/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst +++ b/doc/source/users_guide/using-clm-tools/what-are-the-clm-tools.rst @@ -1,7 +1,7 @@ -.. _what-are-the-clm-tools: - .. include:: ../substitutions.rst +.. _what-are-the-clm-tools: + ======================== What are the CLM tools ======================== From c40d288b562f7479632b46a75d2309cbcd2d4303 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 09:15:00 -0600 Subject: [PATCH 1737/2067] UG input for surface data gen: Removed manual section numbering. --- .../creating-input-for-surface-dataset-generation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 122e637e72..8fd6d74adf 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -6,7 +6,7 @@ Creating input for surface dataset generation ********************************************* -1. Generating SCRIP grid files +Generating SCRIP grid files ================================== The utility ``mkmapdata.sh`` requires SCRIP format input files to describe the input and output grids that maps are generated for. CLM provides a utility, ``mkmapgrids`` that generates those files. The program converts old formats of CAM or CLM grid files to SCRIP grid format. There is also a NCL script (``mkscripgrid.ncl``) to create regular latitude longitude regional or single-point grids at the resolution the user desires. @@ -38,7 +38,7 @@ If you want to create a regular latitude/longitude single-point or regional grid See :numref:`Figure mknoocnmap.pl` for a visual representation of this process. -2. Creating mapping files for mksurfdata_map +Creating mapping files for mksurfdata_map ============================================== ``mkmapdata.sh`` uses the above SCRIP grid input files to create SCRIP mapping data files (uses ESMF). From 7f81b3eef87c97284cced2fe1e08a49f0d53ff63 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 09:20:52 -0600 Subject: [PATCH 1738/2067] UG: Removed ref to nonexistent "Running mksurfdata.pl" section. --- .../creating-input-for-surface-dataset-generation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 8fd6d74adf..980a4ac5ef 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -43,7 +43,7 @@ Creating mapping files for mksurfdata_map ``mkmapdata.sh`` uses the above SCRIP grid input files to create SCRIP mapping data files (uses ESMF). -The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map** (see `the Section called Running mksurfdata.pl `_ below). mkmapdata.sh has a help option with the following +The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map**. mkmapdata.sh has a help option with the following :: ../../tools/mkmapdata/mkmapdata.sh From 4fdc8451b19db4ccf7251556b64f315e0e312d92 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 09:32:05 -0600 Subject: [PATCH 1739/2067] UG: Deleted a duplicate file. datasts-for-observational-sites.rst deleted; was duplicative of observational-sites-datasets.rst. --- .../using-clm-tools/datasts-for-observational-sites.rst | 9 --------- 1 file changed, 9 deletions(-) delete mode 100644 doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst diff --git a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst b/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst deleted file mode 100644 index 4ddd738b5d..0000000000 --- a/doc/source/users_guide/using-clm-tools/datasts-for-observational-sites.rst +++ /dev/null @@ -1,9 +0,0 @@ -.. include:: ../substitutions.rst - -================================== - Datasets for Observational Sites -================================== - -There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. - -Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. From 8e775436027a5e9cf3b657f56fc0434c60b71bf6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 09:32:44 -0600 Subject: [PATCH 1740/2067] UG testing and using-clm-tools: Fix CLM-URL links. --- .../adding-new-resolutions/Adding-Resolution-Names.rst | 4 ++-- .../Adding-or-Changing-Default-Filenames.rst | 2 ++ doc/source/users_guide/testing/testing.rst | 2 +- doc/source/users_guide/using-clm-tools/cprnc.rst | 2 +- .../users_guide/using-clm-tools/creating-domain-files.rst | 4 ++-- .../creating-input-for-surface-dataset-generation.rst | 6 ++++-- .../using-clm-tools/creating-surface-datasets.rst | 2 +- .../using-clm-tools/observational-sites-datasets.rst | 4 ++-- 8 files changed, 15 insertions(+), 11 deletions(-) diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst index 4511116344..216de19f54 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-Resolution-Names.rst @@ -1,7 +1,7 @@ -.. _adding-resolution-names: - .. include:: ../substitutions.rst +.. _adding-resolution-names: + ========================= Adding Resolution Names ========================= diff --git a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst index 97e81eb754..a2e7fcfc4e 100644 --- a/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst +++ b/doc/source/users_guide/adding-new-resolutions/Adding-or-Changing-Default-Filenames.rst @@ -26,6 +26,8 @@ Different types of simulations and different types of configurations for CLM req In the following table we list the different files used by CLM, they are listed in order of importance, dependencies, and customizing. So the required files are all near the top, and the files used only under different conditions are listed later, and files with the fewest dependencies are near the top, as are the files that are least likely to be customized. +.. _reqd-files-table: + Table 3-1. Required Files for Different Configurations and Simulation Types --------------------------------------------------------------------------- Insert table 3-1 diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index 54dc748646..b270455946 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -6,7 +6,7 @@ Testing ******* -Technically, you could use the customization we gave in `Chapter 1 `_ to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods. +Technically, you could use the customization we gave in :ref:`customizing_section` to test various configuration and namelist options for CLM. Sometimes, it's also useful to have automated tests though to test that restarts give exactly the same results as without a restart. It's also useful to have automated tests to run over a wide variety of configurations, resolutions, and namelist options. To do that we have several different types of scripts set up to make running comprehensive testing of CLM easy. There are two types of testing scripts for CLM. The first are the CESM test scripts, which utilize the **create_newcase** scripts that we shown how to use in this User's Guide. The second are a set of stand-alone scripts that use the CLM **configure** and **build-namelist** scripts to build and test the model as well as testing the CLM tools as well. Below we will go into further details of how to use both methods. CIME Testing scripts ==================== diff --git a/doc/source/users_guide/using-clm-tools/cprnc.rst b/doc/source/users_guide/using-clm-tools/cprnc.rst index 0b4ff2ac9f..05a2ca8279 100644 --- a/doc/source/users_guide/using-clm-tools/cprnc.rst +++ b/doc/source/users_guide/using-clm-tools/cprnc.rst @@ -20,5 +20,5 @@ Options: -kpr -See the **cprnc** `README `_ file for more details. +See the ``cprnc`` `README `_ file for more details. diff --git a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst index e7105a36d3..d4ebd6c4e7 100644 --- a/doc/source/users_guide/using-clm-tools/creating-domain-files.rst +++ b/doc/source/users_guide/using-clm-tools/creating-domain-files.rst @@ -6,7 +6,7 @@ Creating CLM domain files ***************************** -*gen_domain* to create a domain file for datm from a mapping file. **gen_domain** is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of **mknoocnmap.pl** (see `the Section called Using mknocnmap.pl to create grid and maps for single-point regional grids `_) to create a regional or single-point map file that is then run through **gen_domain** to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README `_ file for more help on **gen_domain**. +*gen_domain* to create a domain file for datm from a mapping file. ``gen_domain`` is a tool that is a part of CIME. The domain file is then used by BOTH DATM AND CLM to define the grid and land-mask. The general data flow is shown in two figures. :numref:`Figure mkmapdata.sh` shows the general flow for a general global case (or for a regional grid that DOES include ocean). :numref:`Figure mknoocnmap.pl` shows the use of ``mknoocnmap.pl`` (see :ref:`using-mkocnmap`) to create a regional or single-point map file that is then run through ``gen_domain`` to create the domain file for it. As stated before :numref:`Figure Data_Flow_Legend` is the legend for both of these figures. See `the $CIMEROOT/tools/mapping/gen_domain_files/README `_ file for more help on ``gen_domain``. Here we create domain files for a regular global domain. @@ -21,7 +21,7 @@ Global Domain file creation Starting from SCRIP grid files for both your atmosphere and ocean, you use **$CIMEROOT/tools/mapping/gen_mapping_files/gen_cesm_maps.sh** to create a mapping file between the atmosphere and ocean. That mapping file is then used as input to **gen_domain** to create output domain files for both atmosphere and ocean. The atmosphere domain file is then used by both CLM and DATM for I compsets, while the ocean domain file is ignored. For this process you have to define your SCRIP grid files on your own. For a regional or single-point case that doesn't include ocean see :numref:`Figure mknoocnmap.pl`. (See :numref:`Figure Global-Domain` for the legend for this figure.) -Note, that the SCRIP grid file used to start this process, is also used in **mkmapdata.sh** (see `the Section called Creating mapping files that mksurfdata_map will use `_). Next we create domain files for a single-point or regional domain. +Note that the SCRIP grid file used to start this process is also used in ``mkmapdata.sh`` (see :ref:`using-mkocnmap`). Next we create domain files for a single-point or regional domain. Domain file creation using mknoocnmap.pl ======================================== diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 980a4ac5ef..3cd0767bf4 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -13,6 +13,8 @@ The utility ``mkmapdata.sh`` requires SCRIP format input files to describe the i SCRIP grid files for all the standard model resolutions and the raw surface datasets have already been done and the files are in the XML database. Hence, this step doesn't need to be done -- EXCEPT WHEN YOU ARE CREATING YOUR OWN GRIDS. +.. _using-mkocnmap: + Using mknocnmap.pl to create grid and maps for single-point regional grids -------------------------------------------------------------------------- @@ -43,13 +45,13 @@ Creating mapping files for mksurfdata_map ``mkmapdata.sh`` uses the above SCRIP grid input files to create SCRIP mapping data files (uses ESMF). -The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses **ESMF_RegridWeightGen** to create a list of maps from the raw datasets that are input to **mksurfdata_map**. Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. Hence, there doesn't need to be a different mapping file for EACH raw dataset -- just for each raw dataset that has a DIFFERENT grid or land-mask.. See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. The bash script figures out which mapping files it needs to create and then runs **ESMF_RegridWeightGen** for each one. You can then either enter the datasets into the XML database (see `Chapter 3 `_ or leave the files in place, and use the "-res usrspec -usr_gname -usr_gdate" options to **mksurfdata_map**. mkmapdata.sh has a help option with the following +The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses ``ESMF_RegridWeightGen`` to create a list of maps from the raw datasets that are input to ``mksurfdata_map``. Each dataset that has a different grid, or land-mask needs a different mapping file for it, but many different raw datasets share the same grid/land-mask as other files. Hence, there doesn't need to be a different mapping file for EACH raw dataset---just for each raw dataset that has a DIFFERENT grid or land-mask. See :numref:`Figure mkmapdata.sh` for a visual representation of how this works. The bash script figures out which mapping files it needs to create and then runs ``ESMF_RegridWeightGen`` for each one. You can then either enter the datasets into the XML database (see Chapter :numref:`adding-new-resolutions-section`), or leave the files in place and use the ``-res usrspec -usr_gname -usr_gdate`` options to ``mksurfdata_map``. ``mkmapdata.sh`` has a help option with the following :: ../../tools/mkmapdata/mkmapdata.sh ********************** - usage on cheyenne: + usage on cheyenne:Figure mkmapdata.sh ./mkmapdata.sh valid arguments: diff --git a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst index 7a0ad522fa..57b09e1e91 100644 --- a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst @@ -6,7 +6,7 @@ Creating Surface Datasets =========================== -When just creating a replacement file for an existing one, the relevant tool should be used directly to create the file. When you are creating a set of files for a new resolution there are some dependencies between the tools that you need to keep in mind when creating them. The main dependency is that you MUST create a SCRIP grid file first as the SCRIP grid dataset is then input into the other tools. Also look at `Table 3-1 `_ which gives information on the files required and when. :numref:`Figure Data_Flow` shows an overview of the general data-flow for creation of the fsurdat datasets. +When just creating a replacement file for an existing one, the relevant tool should be used directly to create the file. When you are creating a set of files for a new resolution there are some dependencies between the tools that you need to keep in mind when creating them. The main dependency is that you MUST create a SCRIP grid file first as the SCRIP grid dataset is then input into the other tools. Also look at Table :numref:`reqd-files-table` which gives information on the files required and when. :numref:`Figure Data_Flow` shows an overview of the general data-flow for creation of the fsurdat datasets. .. _Figure Data_Flow: diff --git a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst index ff03106fd4..385ec159aa 100644 --- a/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/observational-sites-datasets.rst @@ -6,6 +6,6 @@ Observational Sites Datasets ******************************* -There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to over-write the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In `Table 3-1 `_ we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: fatmlndfrc, fsurdat, faerdep (for DATM), and stream_fldfilename_ndep. Note **mksurfdata_map** as documented previously has options to overwrite the vegetation and soil types. For more information on this also see `the Section called Creating your own single-point/regional surface datasets in Chapter 5 `_. And PTCLM uses these methods to customize datasets see `Chapter 6 `_. +There are two ways to customize datasets for a particular observational site. The first is to customize the input to the tools that create the dataset, and the second is to overwrite the default data after you've created a given dataset. Depending on the tool it might be easier to do it one way or the other. In Table :numref:`reqd-files-table` we list the files that are most likely to be customized and the way they might be customized. Of those files, the ones you are most likely to customize are: ``fatmlndfrc``, ``fsurdat``, ``faerdep`` (for DATM), and ``stream_fldfilename_ndep``. Note ``mksurfdata_map`` as documented previously has options to overwrite the vegetation and soil types. For more information on this also see :ref:`creating-your-own-singlepoint-dataset`. ``PTCLM`` uses these methods to customize datasets; see Chapter :numref:`running-PTCLM`. -Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets. See `the Section called Running with your own atmosphere forcing in Chapter 5 `_ for more information on this. Also the chapter on PTCLM in `the Section called Converting AmeriFlux Data for use by PTCLM in Chapter 6 `_ has information on using the AmeriFlux tower site data as atmospheric forcing. +Another aspect of customizing your input datasets is customizing the input atmospheric forcing datasets; see :ref:`creating-your-own-singlepoint-dataset` for more information on this. :ref:`converting-ameriflux-for-ptclmmkdata` has information on using the AmeriFlux tower site data as atmospheric forcing. From 0b6a94abdcdf9fe30632b9840e77f35709a70ae6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 09:53:39 -0600 Subject: [PATCH 1741/2067] Fix various issues in docs identified during HTML build. --- .../tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst | 2 +- .../Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst | 2 +- .../Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst | 2 +- .../Spinning-up-the-biogeochemistry-BGC-spinup.rst | 4 ++-- .../creating-input-for-surface-dataset-generation.rst | 2 +- .../users_guide/using-clm-tools/creating-surface-datasets.rst | 4 ++-- doc/source/users_guide/using-clm-tools/index.rst | 1 - 7 files changed, 8 insertions(+), 9 deletions(-) diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index 7bfd1bebdb..c0970d2bd5 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -336,7 +336,7 @@ where If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t* :math:`<` :math:`{N where :math:`{f}_{immob\_demand,j}` is the fraction of potential immobilization demand that can be met given current supply of mineral nitrogen in this layer. We also set the actual nitrification flux to be the same as the potential flux (:math:`NF_{nit}` = :math:`NF_{nit\_ demand}`). -If :math:`{NF}_{total\_demand,j}`\ :math:`\Delta`\ *t :math:`\mathrm{\ge}` :math:`{NS}_{sminn,j}`, then there is not enough mineral nitrogen to meet the combined demands for plant growth and heterotrophic immobilization, immobilization is reduced proportional to the discrepancy, by :math:`f_{immob\_ demand,j}`, where +If :math:`{NF}_{total\_demand,j} \Delta t \mathrm{\ge} {NS}_{sminn,j}`, then there is not enough mineral nitrogen to meet the combined demands for plant growth and heterotrophic immobilization, immobilization is reduced proportional to the discrepancy, by :math:`f_{immob\_ demand,j}`, where .. math:: :label: 21.30) diff --git a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst index a86b945384..8c0899cc17 100644 --- a/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst +++ b/doc/source/tech_note/Photosynthesis/CLM50_Tech_Note_Photosynthesis.rst @@ -253,7 +253,7 @@ The effect is to cause the temperature optimum of :math:`V_{c\max }` and :math:` J_{\max 25} /V_{c\max 25} =2.59-0.035(T_{10} -T_{f} ). -In these acclimation functions, :math:`T_{10}` is the 10-day mean air temperature (K) and :math:`T_{f}` is the freezing point of water (K). For lack of data, :math:`T_{p}` acclimates similar to :math:`V_{c\max }`. Acclimation is restricted over the temperature range :math:`T_{10} -T_{f} \ge 11`°C and :math:`T_{10} -T_{f} \le 35`°C. +In these acclimation functions, :math:`T_{10}` is the 10-day mean air temperature (K) and :math:`T_{f}` is the freezing point of water (K). For lack of data, :math:`T_{p}` acclimates similar to :math:`V_{c\max }`. Acclimation is restricted over the temperature range :math:`T_{10} -T_{f} \ge` 11°C and :math:`T_{10} -T_{f} \le` 35°C. .. _Canopy scaling: diff --git a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst index 54c50486f1..2bc42bfaeb 100644 --- a/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst +++ b/doc/source/tech_note/Surface_Albedos/CLM50_Tech_Note_Surface_Albedos.rst @@ -530,7 +530,7 @@ For each constituent (ice, two black carbon species, two organic carbon species, \tau _{k} =\psi _{k} w_{k} -The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri-diagonal matrix solution to produce upward and downward radiative fluxes at each layer interface, from which net radiation, layer absorption, and surface albedo are easily derived. Solar fluxes are computed in five spectral bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. Because snow albedo varies strongly across the solar spectrum, it was determined that four bands were needed to accurately represent the near-infrared (NIR) characteristics of snow, whereas only one band was needed for the visible spectrum. Boundaries of the NIR bands were selected to capture broad radiative features and maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 :math:`\mu` m) surface downwelling flux from CLM according to the weights listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`, which are unique for diffuse and direct incident flux. These fixed weights were determined with offline hyperspectral radiative transfer calculations for an atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). The tri-diagonal solution includes intermediate terms that allow for easy interchange of two-stream techniques. We apply the Eddington solution for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the hemispheric mean solution ((:ref:`Toon et al. (1989) `) for NIR bands. These choices were made because the Eddington scheme works well for highly scattering media, but can produce negative albedo for absorptive NIR bands with diffuse incident flux. Delta scalings are applied to :math:`\tau`, :math:`\omega`, and :math:`g` (:ref:`Wiscombe and Warren 1980 `) in all spectral bands, producing effective values (denoted with *) that are applied in the two-stream solution +The two-stream solution (:ref:`Toon et al. (1989) `) applies a tri-diagonal matrix solution to produce upward and downward radiative fluxes at each layer interface, from which net radiation, layer absorption, and surface albedo are easily derived. Solar fluxes are computed in five spectral bands, listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`. Because snow albedo varies strongly across the solar spectrum, it was determined that four bands were needed to accurately represent the near-infrared (NIR) characteristics of snow, whereas only one band was needed for the visible spectrum. Boundaries of the NIR bands were selected to capture broad radiative features and maximize accuracy and computational efficiency. We partition NIR (0.7-5.0 :math:`\mu` m) surface downwelling flux from CLM according to the weights listed in :numref:`Table Spectral bands and weights used for snow radiative transfer`, which are unique for diffuse and direct incident flux. These fixed weights were determined with offline hyperspectral radiative transfer calculations for an atmosphere typical of mid-latitude winter (:ref:`Flanner et al. (2007) `). The tri-diagonal solution includes intermediate terms that allow for easy interchange of two-stream techniques. We apply the Eddington solution for the visible band (following :ref:`Wiscombe and Warren 1980 `) and the hemispheric mean solution ((:ref:`Toon et al. (1989) `) for NIR bands. These choices were made because the Eddington scheme works well for highly scattering media, but can produce negative albedo for absorptive NIR bands with diffuse incident flux. Delta scalings are applied to :math:`\tau`, :math:`\omega`, and :math:`g` (:ref:`Wiscombe and Warren 1980 `) in all spectral bands, producing effective values (denoted with :math:`*`) that are applied in the two-stream solution .. math:: :label: 3.66 diff --git a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst index 772bba1243..cc266506a8 100644 --- a/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst +++ b/doc/source/users_guide/running-special-cases/Spinning-up-the-biogeochemistry-BGC-spinup.rst @@ -2,9 +2,9 @@ .. _spinning-up-clm-bgc: -========================== +============================= Spinup of |version|-BGC-Crop -========================== +============================= To get the |version|-BGC model to a steady state, you first run it from arbitrary initial conditions using the "accelerated decomposition spinup" (-bgc_spinup on in CLM **configure**, see example below) mode for about 200 simulation years. :numref:`Figure BGC AD spinup plot for 1850 GSWP3` shows spinup behavior for an 1850 BGC accelerated decomposition (AD) case using GSWP3 atmospheric forcing. Generally, the criteria that less than 3% of the land surface be in total ecosystem carbon disequilibrium takes the longest to satisfy due to slow soil carbon (TOTSOMC) turnover times in the Arctic. diff --git a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst index 3cd0767bf4..276394e2b9 100644 --- a/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst +++ b/doc/source/users_guide/using-clm-tools/creating-input-for-surface-dataset-generation.rst @@ -104,4 +104,4 @@ The bash shell script ``$CTSMROOT/tools/mkmapgrids/mkmapdata.sh`` uses ``ESMF_Re Details of running mkmapdata.sh -Each of the raw datasets for **mksurfdata_map** needs a mapping file to map from the output grid you are running on to the grid and land-mask for that dataset. This is what **mkmapdata.sh** does. To create the mapping files you need a SCRIP grid file to correspond with each resolution and land mask that you have a raw data file in **mksurfdata_map**. Some raw datasets share the same grid and land mask -- hence they can share the same SCRIP grid file. The output maps created here go into **mksurfdata_map** see :numref:`Figure mksurfdatamap`. +Each of the raw datasets for ``mksurfdata_map`` needs a mapping file to map from the output grid you are running on to the grid and land-mask for that dataset. This is what ``mkmapdata.sh`` does. To create the mapping files you need a SCRIP grid file to correspond with each resolution and land mask that you have a raw data file in ``mksurfdata_map``. Some raw datasets share the same grid and land mask -- hence they can share the same SCRIP grid file. The output maps created here go into ``mksurfdata_map`` see :numref:`Figure Workflow of CLM5 Land Use Data Tool and Mksurfdata_map Tool`. diff --git a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst index 57b09e1e91..cfaa8527cd 100644 --- a/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst +++ b/doc/source/users_guide/using-clm-tools/creating-surface-datasets.rst @@ -14,9 +14,9 @@ When just creating a replacement file for an existing one, the relevant tool sho Data Flow for Creation of Surface Datasets from Raw SCRIP Grid Files -Starting from a SCRIP grid file that describes the grid you will run the model on, you first run **mkmapdata.sh** to create a list of mapping files. See :numref:`Figure mkmapdata.sh` for a more detailed view of how **mkmapdata.sh** works. The mapping files tell **mksurfdata_map** how to map between the output grid and the raw datasets that it uses as input. The output of **mksurfdata_map** is a surface dataset that you then use for running the model. See `Figure :numref:`Figure mksurfdatamap` for a more detailed view of how **mksurfdata_map** works. +Starting from a SCRIP grid file that describes the grid you will run the model on, you first run ```mkmapdata.sh`` to create a list of mapping files. See :numref:`Figure mkmapdata.sh` for a more detailed view of how ``mkmapdata.sh`` works. The mapping files tell ``mksurfdata_map`` how to map between the output grid and the raw datasets that it uses as input. The output of ``mksurfdata_map`` is a surface dataset that you then use for running the model. See :numref:`Figure Workflow of CLM5 Land Use Data Tool and Mksurfdata_map Tool` for a more detailed view of how ``mksurfdata_map`` works. -:numref:`Figure Data_Flow_Legend` is the legend for this figure (:numref:`Figure Data_Flow`) and other figures in this chapter (:numref:`Figure Global_Domain`, :numref:`Figure mknoocnmap.pl` and :numref:`Figure mksurfdatamap`). +:numref:`Figure Data_Flow_Legend` is the legend for this figure (:numref:`Figure Data_Flow`) and other figures in this chapter (:numref:`Figure Global-Domain` and :numref:`Figure mknoocnmap.pl`). .. _Figure Data_Flow_Legend: diff --git a/doc/source/users_guide/using-clm-tools/index.rst b/doc/source/users_guide/using-clm-tools/index.rst index c09653706b..e9a1dd5238 100644 --- a/doc/source/users_guide/using-clm-tools/index.rst +++ b/doc/source/users_guide/using-clm-tools/index.rst @@ -18,7 +18,6 @@ Using CLM tools building-the-clm-tools.rst creating-input-for-surface-dataset-generation.rst creating-surface-datasets.rst - datasts-for-observational-sites.rst creating-domain-files.rst observational-sites-datasets.rst cprnc.rst From 5dd89d8e09fe3b09c5e536167a35bc95d27c1930 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 10:02:35 -0600 Subject: [PATCH 1742/2067] Add a blank line after a list. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 2e5fc2fd74..708a2cf3d4 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -40,6 +40,7 @@ Available new features since the CLM5 release ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Addition of bioenergy crops - Ablity to customize crop calendars (sowing windows/dates, maturity requirements) using stream files + .. _The crop model: The crop model: cash and bioenergy crops From b3dcbfa12a1615c56c737d1144be8a2a0d2becbb Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Fri, 27 Oct 2023 11:34:57 -0600 Subject: [PATCH 1743/2067] Fix misplaced if statement and end model run if no-isotope to isotope with user_init_interp=.false. --- src/biogeochem/CNVegCarbonStateType.F90 | 173 +++++++++++++----------- 1 file changed, 94 insertions(+), 79 deletions(-) diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index 8ce278c166..076c96ec27 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -1139,8 +1139,12 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, real(r8), pointer :: data1dptr(:) ! temp. pointer for slicing larger arrays real(r8), parameter:: totvegcthresh = 1.0_r8 ! Total vegetation carbon threshold to reseed dead vegetation + logical :: missing_ciso ! whether C isotope fields are missing from the input file, despite the run containing C isotopes + !------------------------------------------------------------------------ + missing_ciso = .false. + if (carbon_type == 'c13' .or. carbon_type == 'c14') then if (.not. present(c12_cnveg_carbonstate_inst)) then call endrun(msg=' ERROR: for C14 must pass in c12_cnveg_carbonstate_inst as argument' //& @@ -1332,86 +1336,14 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, end if end if end if - !-------------------------------- - ! C12 carbon state variables - !-------------------------------- - - if (carbon_type == 'c12') then - call restartvar(ncid=ncid, flag=flag, varname='totvegc', xtype=ncd_double, & - dim1name='pft', long_name='', units='', & - interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) - ! totvegc_col needed for resetting soil carbon stocks during AD spinup exit - call restartvar(ncid=ncid, flag=flag, varname='totvegc_col', xtype=ncd_double, & - dim1name='column', long_name='', units='', & - interpinic_flag='interp', readvar=readvar, data=this%totvegc_col) - end if - - !-------------------------------- - ! C13 carbon state variables - !-------------------------------- - - if ( carbon_type == 'c13') then - call restartvar(ncid=ncid, flag=flag, varname='totvegc_13', xtype=ncd_double, & - dim1name='pft', long_name='', units='', & - interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) - if (flag=='read' .and. .not. readvar) then - if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c13 value' - do i = bounds%begp,bounds%endp - if (pftcon%c3psn(patch%itype(i)) == 1._r8) then - this%totvegc_patch(i) = c12_cnveg_carbonstate_inst%totvegc_patch(i) * c3_r2 - else - this%totvegc_patch(i) = c12_cnveg_carbonstate_inst%totvegc_patch(i) * c4_r2 - endif - end do - end if - - call restartvar(ncid=ncid, flag=flag, varname='totvegc_col_13', xtype=ncd_double, & - dim1name='column', long_name='', units='', & - interpinic_flag='interp', readvar=readvar, data=this%totvegc_col) - if (flag=='read' .and. .not. readvar) then - if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c13 value' - do i = bounds%begc,bounds%endc - if (pftcon%c3psn(patch%itype(i)) == 1._r8) then - this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c3_r2 - else - this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c4_r2 - endif - end do - end if - - end if - !-------------------------------- - ! C14 patch carbon state variables - !-------------------------------- - - if ( carbon_type == 'c14') then - call restartvar(ncid=ncid, flag=flag, varname='totvegc_14', xtype=ncd_double, & - dim1name='pft', long_name='', units='', & - interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) - if (flag=='read' .and. .not. readvar) then - if ( masterproc ) write(iulog,*) 'initializing this%totvegc_patch with atmospheric c14 value' - do i = bounds%begp,bounds%endp - if (this%totvegc_patch(i) /= spval .and. & - .not. isnan(this%totvegc_patch(i)) ) then - this%totvegc_patch(i) = c12_cnveg_carbonstate_inst%totvegc_patch(i) * c14ratio - endif - end do - endif - - call restartvar(ncid=ncid, flag=flag, varname='totvegc_col_14', xtype=ncd_double, & - dim1name='column', long_name='', units='', & - interpinic_flag='interp', readvar=readvar, data=this%totvegc_col) - if (flag=='read' .and. .not. readvar) then - if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c14 value' - do i = bounds%begc,bounds%endc - if (this%totvegc_col(i) /= spval .and. & - .not. isnan(this%totvegc_col(i)) ) then - this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c14ratio - endif - end do - end if - end if + call restartvar(ncid=ncid, flag=flag, varname='totvegc', xtype=ncd_double, & + dim1name='pft', long_name='', units='', & + interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) + ! totvegc_col needed for resetting soil carbon stocks during AD spinup exit + call restartvar(ncid=ncid, flag=flag, varname='totvegc_col', xtype=ncd_double, & + dim1name='column', long_name='', units='', & + interpinic_flag='interp', readvar=readvar, data=this%totvegc_col) if ( flag == 'read' .and. (enter_spinup .or. (reseed_dead_plants .and. .not. is_restart())) .and. .not. use_cndv) then @@ -1588,6 +1520,75 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, !-------------------------------- if ( carbon_type == 'c13') then + + call restartvar(ncid=ncid, flag=flag, varname='totvegc_13', xtype=ncd_double, & + dim1name='pft', long_name='', units='', & + interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) + if (flag=='read' .and. .not. readvar) then + ! BUG(kwo, 2023-10-19, ESCOMP/ctsm#2119) There is a bug that causes incorrect values for + ! C isotopes if running from a case without C isotopes (an initial file) to a case with C + ! isotopes (https://github.com/ESCOMP/ctsm/issues/2119). Here we check if the user + ! the user is doing this and abort if they are. This particular check is covering the case + ! when use_init_interp=.false. There is a similar check (but for the purpose of working around + ! a different bug) in initInterp.F90. This check here should be removed once bug #2119 is resolved + ! and replaced by the logic shown below for .e.g, totvegc_col, where totvegc_cl is initialized with + ! atmospheric c13 values. + ! We arbitrarily check totvegc_13 (we could pick any c13 restart field). + if (masterproc) then + write(iulog,*) 'Cannot initialize from a run without c13 to a run with c13,' + write(iulog,*) 'due to .' + write(iulog,*) 'Either use an input initial conditions file with c13 information,' + write(iulog,*) 'or re-spinup from cold start.' + end if + missing_ciso = .true. + end if + + end if + + if ( carbon_type == 'c14') then + call restartvar(ncid=ncid, flag=flag, varname='totvegc_14', xtype=ncd_double, & + dim1name='pft', long_name='', units='', & + interpinic_flag='interp', readvar=readvar, data=this%totvegc_patch) + if (flag=='read' .and. .not. readvar) then + ! BUG(kwo, 2023-10-19, ESCOMP/ctsm#2119) There is a bug that causes incorrect values for + ! C isotopes if running from a case without C isotopes (an initial file) to a case with C + ! isotopes (https://github.com/ESCOMP/ctsm/issues/2119). Here we check if the user + ! the user is doing this and abort if they are. This particular check is covering the case + ! when use_init_interp=.false. There is a similar check (but for the purpose of working around + ! a different bug) in initInterp.F90. This check here should be removed once bug #2119 is resolved + ! and replaced by the logic shown below for .e.g, totvegc_col, where totvegc_cl is initialized with + ! atmospheric c14 values. + ! We arbitrarily check totvegc_14 (we could pick any c14 restart field). + if (masterproc) then + write(iulog,*) 'Cannot interpolate from a run without c14 to a run with c14,' + write(iulog,*) 'due to .' + write(iulog,*) 'Either use an input initial conditions file with c14 information,' + write(iulog,*) 'or re-spinup from cold start.' + end if + missing_ciso = .true. + endif + end if + + if (missing_ciso) then + call endrun(msg='Cannot initialize from a run without c13/c14 to a run with c13/c14', & + additional_msg=errMsg(sourcefile, __LINE__)) + end if + + if ( carbon_type == 'c13') then + + call restartvar(ncid=ncid, flag=flag, varname='totvegc_col_13', xtype=ncd_double, & + dim1name='column', long_name='', units='', & + interpinic_flag='interp', readvar=readvar, data=this%totvegc_col) + if (flag=='read' .and. .not. readvar) then + if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c13 value' + do i = bounds%begc,bounds%endc + if (this%totvegc_col(i) /= spval .and. & + .not. isnan(this%totvegc_col(i)) ) then + this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c13ratio + endif + end do + end if + call restartvar(ncid=ncid, flag=flag, varname='leafc_13', xtype=ncd_double, & dim1name='pft', long_name='', units='', & interpinic_flag='interp', readvar=readvar, data=this%leafc_patch) @@ -1942,6 +1943,20 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, !-------------------------------- if ( carbon_type == 'c14') then + + call restartvar(ncid=ncid, flag=flag, varname='totvegc_col_14', xtype=ncd_double, & + dim1name='column', long_name='', units='', & + interpinic_flag='interp', readvar=readvar, data=this%totvegc_col) + if (flag=='read' .and. .not. readvar) then + if ( masterproc ) write(iulog,*) 'initializing cnveg_carbonstate_inst%totvegc with atmospheric c14 value' + do i = bounds%begc,bounds%endc + if (this%totvegc_col(i) /= spval .and. & + .not. isnan(this%totvegc_col(i)) ) then + this%totvegc_col(i) = c12_cnveg_carbonstate_inst%totvegc_col(i) * c14ratio + endif + end do + end if + call restartvar(ncid=ncid, flag=flag, varname='leafc_14', xtype=ncd_double, & dim1name='pft', long_name='', units='', & interpinic_flag='interp', readvar=readvar, data=this%leafc_patch) From 2bf01c969656dc41cc3a1a32decdb76d1baeecc1 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 27 Oct 2023 11:43:22 -0600 Subject: [PATCH 1744/2067] minor updates to clean up modify_singlept_site_neon.py --- python/ctsm/site_and_regional/modify_singlept_site_neon.py | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index a7838bedac..1013ba944c 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -529,7 +529,6 @@ def main(): soil_mid = 0.5 * (soil_bot - soil_top) + soil_top # print ("Cumulative sum of soil bottom depths :", sum(soil_bot)) - # obs_top = df["biogeoTopDepth"] / 100 obs_bot = df["biogeoBottomDepth"] / 100 # -- Mapping surface dataset and neon soil levels From fa2be089322bf24d4d59b447c45eeedcc63c5602 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 13:30:28 -0600 Subject: [PATCH 1745/2067] UG: single-point setups don't always have MPILIB=mpi-serial by default. --- .../running-single-point-configurations.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst index c5d19cc115..8588da8b99 100644 --- a/doc/source/users_guide/running-single-points/running-single-point-configurations.rst +++ b/doc/source/users_guide/running-single-points/running-single-point-configurations.rst @@ -32,7 +32,7 @@ The resolution names that have an underscore in them ("_") are all single-point .. note:: When running a single point, the number of processors is automatically set to one, which is the only value allowed. .. warning:: - Just like ``PTS_MODE`` (Sect. :numref:`pts_mode`), by default these setups run with ``MPILIB=mpi-serial`` (in the ``env_build.xml`` file) turned on, which allows you to run the model interactively. On some machines this mode is NOT supported and you may need to change it to FALSE before you are able to build. + Just like ``PTS_MODE`` (Sect. :numref:`pts_mode`), by default these setups sometimes run with ``MPILIB=mpi-serial`` (in the ``env_build.xml`` file) turned on, which allows you to run the model interactively. On some machines this mode is NOT supported and you may need to change it to FALSE before you are able to build. .. _single-point-global-climate: From 0ac8b3a987ee08527d0dbb669407d8d7ed0275de Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 13:37:00 -0600 Subject: [PATCH 1746/2067] UG: Mention compset testing/validation info. --- .../setting-up-and-running-a-case/choosing-a-compset.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst index a7cd1251a0..a3fb4770f7 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/choosing-a-compset.rst @@ -8,16 +8,16 @@ Choosing a compset When setting up a new case one of the first choices to make is which "component set" (or compset) to use. The compset refers to which component models are used as well as specific settings for them. We label the different types of compsets with a different letter of the alphabet from "A" (for all data model) to "X" (for all dead model). The compsets of interest when working with CLM are the "I" compsets (which contain CLM with a data atmosphere model and a stub ocean, and stub sea-ice models), "E" and "F" compsets (which contain CLM with the active atmosphere model (CAM), prescribed sea-ice model, and a data ocean model), and "B" compsets which have all active components. Below we go into details on the "I" compsets which emphasize CLM as the only active model, and just mention the two other categories. -To run CLM coupled to CAM ("E" or "F" compsets) or fully coupled ("B compsets) you need to be running CLM from a CESM checkout rather than a CTSM checkout (see :ref:`ctsm_vs_cesm_checkout`). +To run CLM coupled to CAM ("E" or "F" compsets) or fully coupled ("B" compsets) you need to be running CLM from a CESM checkout rather than a CTSM checkout (see :ref:`ctsm_vs_cesm_checkout`). When working with CLM you usually want to start with a relevant "I" compset before moving to the more complex cases that involve other active model components. The "I" compsets can exercise CLM in a way that is similar to the coupled modes, but with much lower computational cost and faster turnaround times. Compsets coupled to data atmosphere and stub ocean/sea-ice ("I" compsets) ------------------------------------------------------------------------- -Here is the entire list of compsets available: `CESM compsets `_ +The entire list of compsets available out-of-the-box can be browsed at the `CESM Component Set Definitions `_ page. Note that using the compset longnames, even more combinations are possible than those listed. That webpage also includes information on whether each compset has been tested and/or scientifically validated. -Note that using the `compset longnames `_ even more combinations are possible. To get a list of the compsets use the ``query_config`` command as follows: +To get a list of the compsets use the ``query_config`` command as follows: :: $CTSMROOT/cime/scripts/query_config --compsets clm From 54e5f247031210f5e082bdfb978d692c83483b2a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 13:45:36 -0600 Subject: [PATCH 1747/2067] More precise error check in get_doy_tomorrow(). --- src/utils/clm_time_manager.F90 | 2 +- src/utils/test/clm_time_manager_test/test_clm_time_manager.pf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 35abbfc6bf..11b05a171a 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -1284,7 +1284,7 @@ function get_doy_tomorrow(doy_today) result(doy_tomorrow) integer :: doy_tomorrow character(len=*), parameter :: sub = 'clm::get_doy_tomorrow' - if ( doy_today < 1 .or. doy_today > 367 )then + if ( doy_today < 1 .or. doy_today > get_curr_days_per_year() )then write(iulog,*) sub, ' = ', doy_today call shr_sys_abort( sub//': error doy_today out of range' ) end if diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index 736d745e3a..c28b87fb2c 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -672,7 +672,7 @@ contains @assertEqual(get_doy_tomorrow(150), 151) @assertEqual(get_doy_tomorrow(get_curr_days_per_year()), 1) - doy_tomorrow = get_doy_tomorrow(400) + doy_tomorrow = get_doy_tomorrow(get_curr_days_per_year() + 1) expected_msg = endrun_msg("clm::get_doy_tomorrow: error doy_today out of range" ) @assertExceptionRaised(expected_msg) From 99e0b916651ccb4ffc72540bbfc043d5ff51ce6d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 15:43:46 -0600 Subject: [PATCH 1748/2067] Added entries in ChangeLog and ChangeSum. --- doc/ChangeLog | 94 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 95 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index c9192e4ffa..657f78cca1 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,98 @@ =============================================================== +Tag name: ctsm5.1.dev147 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Fri Oct 27 15:32:54 MDT 2023 +One-line Summary: Add sowing window input files + +Purpose and description of changes +---------------------------------- + +Previously, one could run crops with either (a) sowing windows defined by the hemisphere-specific start and end dates on the paramfile or (b) prescribed sowing dates specified by input file stream_fldFileName_sdate. This PR replaces the latter with two new input files, stream_fldFileName_swindow_start and stream_fldFileName_swindow_end. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +* Replaces input file stream_fldfilename_sdate (prescribed sowing date) with stream_fldFileName_swindow_start (start of sowing window) and stream_fldFileName_swindow_end (end of sowing window). +* Any gridcell with sowing window start == end will experience prescribed sowing, matching previous behavior with stream_fldfilename_sdate. +* Setting new parameter allow_invalid_swindow_inputs to .true. makes it so that gridcell-crops without values in provided sowing window files will fall back to paramfile sowing windows. Otherwise, such cells will cause an error. + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + any other testing (give details below): + * RXCROPMATURITY test passes. + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: + + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] + + Summarize any changes to answers, i.e., + - what code configurations: + - what platforms/compilers: + - nature of change (roundoff; larger than roundoff/same climate; new climate): + + If bitwise differences were observed, how did you show they were no worse + than roundoff? Roundoff differences means one or more lines of code change results + only by roundoff level (because order of operation changes for example). Roundoff + changes to state fields usually grow to greater than roundoff as the simulation progresses. + + If this tag changes climate describe the run(s) done to evaluate the new + climate (put details of the simulations in the experiment database) + - casename: + + URL for LMWG diagnostics output used to validate new climate: + + +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): +* #2193 (https://github.com/ESCOMP/CTSM/pull/2193) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev146 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) Date: Tue Oct 24 20:13:17 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index f530ef9f7a..b6fc5f0214 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev147 samrabin 10/27/2023 Add sowing window input files ctsm5.1.dev146 glemieux 10/24/2023 FATES cross-grid seed dispersal ctsm5.1.dev145 slevis 10/19/2023 SNICAR snow albedo scheme updates ctsm5.1.dev144 samrabin 10/19/2023 Remove a deprecated shr_mpi_bcast call From e212bc9b1750884e0d05b76b8775da1a05342c3b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 27 Oct 2023 16:01:19 -0600 Subject: [PATCH 1749/2067] Fix formatting in a write() call. --- src/cpl/share_esmf/cropcalStreamMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index d07359ce81..46696eeba9 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -139,7 +139,7 @@ subroutine cropcal_init(bounds) write(iulog,'(a,i8)') ' stream_year_first_cropcal = ',stream_year_first_cropcal write(iulog,'(a,i8)') ' stream_year_last_cropcal = ',stream_year_last_cropcal write(iulog,'(a,i8)') ' model_year_align_cropcal = ',model_year_align_cropcal - write(iulog,'(a,i8)') ' allow_invalid_swindow_inputs = ',allow_invalid_swindow_inputs + write(iulog,'(a,l1)') ' allow_invalid_swindow_inputs = ',allow_invalid_swindow_inputs write(iulog,'(a,a)' ) ' stream_fldFileName_swindow_start = ',trim(stream_fldFileName_swindow_start) write(iulog,'(a,a)' ) ' stream_fldFileName_swindow_end = ',trim(stream_fldFileName_swindow_end) write(iulog,'(a,a)' ) ' stream_fldFileName_cultivar_gdds = ',trim(stream_fldFileName_cultivar_gdds) From 80a01b07c6a1ae57d19c0cc89f6fb6952a1684fa Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 10:53:12 -0600 Subject: [PATCH 1750/2067] Centralize defs of secs_in_day & dtime in test_clm_time_manager. --- .../test_clm_time_manager.pf | 111 +++++++++--------- 1 file changed, 55 insertions(+), 56 deletions(-) diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index c28b87fb2c..4ac3613164 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -15,7 +15,10 @@ module test_clm_time_manager save real(r8), parameter :: tol = 1.e-13_r8 - integer, parameter :: dtime = 1800 + integer, parameter :: secs_in_day_int = 86400 + real(r8), parameter :: secs_in_day_r8 = 86400._r8 + integer, parameter :: dtime_int = 1800 + real(r8), parameter :: dtime_r8 = 1800._r8 @TestCase type, extends(TestCase) :: TestTimeManager @@ -42,11 +45,11 @@ contains class(TestTimeManager), intent(inout) :: this integer :: step_size - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) step_size = get_step_size() - @assertEqual(dtime, step_size) + @assertEqual(dtime_int, step_size) end subroutine getStepSize_returnsCorrectValue @Test @@ -54,7 +57,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: calday - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) calday = get_calday(101, 0) @@ -66,7 +69,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: calday - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) calday = get_calday(41231, 43200) @@ -78,7 +81,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: calday - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) calday = get_calday(41231, 43200, reuse_day_365_for_day_366=.true.) @@ -90,7 +93,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: calday - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2000, mon=1, day=1, tod=0) @@ -104,7 +107,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: calday - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) call set_date(yr=2000, mon=12, day=31, tod=43200) @@ -118,7 +121,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: calday - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) call set_date(yr=2000, mon=12, day=31, tod=43200) @@ -133,12 +136,12 @@ contains real(r8) :: calday real(r8) :: calday_expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2000, mon=1, day=1, tod=0) calday = get_prev_calday() - calday_expected = 366._r8 - dtime/86400._r8 + calday_expected = 366._r8 - dtime_int/secs_in_day_r8 @assertEqual(calday_expected, calday, tolerance=tol) end subroutine getPrevCalday_jan1Time0_returnsCorrectValue @@ -149,12 +152,12 @@ contains real(r8) :: calday real(r8) :: calday_expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2000, mon=1, day=2, tod=0) calday = get_prev_calday() - calday_expected = 2._r8 - dtime/86400._r8 + calday_expected = 2._r8 - dtime_int/secs_in_day_r8 @assertEqual(calday_expected, calday, tolerance=tol) end subroutine getPrevCalday_jan2Time0_returnsCorrectValue @@ -164,7 +167,7 @@ contains class(TestTimeManager), intent(inout) :: this real(r8) :: yearfrac - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2, mon=1, day=1, tod=0) @@ -179,7 +182,7 @@ contains real(r8) :: yearfrac real(r8) :: yearfrac_expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2, mon=3, day=1, tod=43200) @@ -195,7 +198,7 @@ contains real(r8) :: yearfrac real(r8) :: yearfrac_expected - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) call set_date(yr=2000, mon=12, day=31, tod=43200) @@ -209,16 +212,15 @@ contains subroutine getPrevYearfrac_atYearBoundary_returnsLargeValue(this) class(TestTimeManager), intent(inout) :: this real(r8) :: yearfrac - integer, parameter :: secs_in_day = 86400 real(r8) :: yearfrac_expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2, mon=1, day=1, tod=0) yearfrac = get_prev_yearfrac() - yearfrac_expected = (365._r8 - real(dtime, r8) / real(secs_in_day, r8)) / 365._r8 + yearfrac_expected = (365._r8 - dtime_r8 / secs_in_day_r8) / 365._r8 @assertEqual(yearfrac_expected, yearfrac) end subroutine getPrevYearfrac_atYearBoundary_returnsLargeValue @@ -226,16 +228,15 @@ contains subroutine getPrevYearfrac_inMiddleOfYear_returnsCorrectValue(this) class(TestTimeManager), intent(inout) :: this real(r8) :: yearfrac - integer, parameter :: secs_in_day = 86400 real(r8) :: yearfrac_expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2, mon=3, day=1, tod=43200) yearfrac = get_prev_yearfrac() - yearfrac_expected = (59.5_r8 - real(dtime, r8) / real(secs_in_day, r8)) / 365._r8 + yearfrac_expected = (59.5_r8 - dtime_r8 / secs_in_day_r8) / 365._r8 @assertEqual(yearfrac_expected, yearfrac) end subroutine getPrevYearfrac_inMiddleOfYear_returnsCorrectValue @@ -243,16 +244,15 @@ contains subroutine getPrevYearfrac_leapYearInMiddleOfYear_returnsCorrectValue(this) class(TestTimeManager), intent(inout) :: this real(r8) :: yearfrac - integer, parameter :: secs_in_day = 86400 real(r8) :: yearfrac_expected - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar = .true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar = .true.) call set_date(yr=2000, mon=3, day=1, tod=43200) yearfrac = get_prev_yearfrac() - yearfrac_expected = (60.5_r8 - real(dtime, r8) / real(secs_in_day, r8)) / 366._r8 + yearfrac_expected = (60.5_r8 - dtime_r8 / secs_in_day_r8) / 366._r8 @assertEqual(yearfrac_expected, yearfrac) end subroutine getPrevYearfrac_leapYearInMiddleOfYear_returnsCorrectValue @@ -261,10 +261,9 @@ contains ! This ensures that the correct year is used in determining the number of days in the year class(TestTimeManager), intent(inout) :: this real(r8) :: yearfrac - integer, parameter :: secs_in_day = 86400 real(r8) :: yearfrac_expected - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar = .true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar = .true.) call set_date(yr=2000, mon=1, day=1, tod=0) @@ -272,7 +271,7 @@ contains ! In the following, note that we have 365 and not 366, because the prev_yearfrac uses ! year 1999, which is not a leap year: - yearfrac_expected = (365._r8 - real(dtime, r8) / real(secs_in_day, r8)) / 365._r8 + yearfrac_expected = (365._r8 - dtime_r8 / secs_in_day_r8) / 365._r8 @assertEqual(yearfrac_expected, yearfrac) end subroutine getPrevYearfrac_leapYearAtYearBoundary_returnsCorrectValue @@ -281,7 +280,7 @@ contains class(TestTimeManager), intent(inout) :: this integer :: nstep - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) nstep = get_nstep() @@ -294,7 +293,7 @@ contains integer, parameter :: expected_nstep = 3 integer :: nstep - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_nstep(expected_nstep) @@ -308,9 +307,9 @@ contains class(TestTimeManager), intent(inout) :: this logical :: is_beg - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) - call set_date(yr=2, mon=1, day=1, tod=dtime) + call set_date(yr=2, mon=1, day=1, tod=dtime_int) is_beg = is_beg_curr_year() @@ -322,9 +321,9 @@ contains class(TestTimeManager), intent(inout) :: this logical :: is_beg - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) - call set_date(yr=2, mon=1, day=2, tod=dtime) + call set_date(yr=2, mon=1, day=2, tod=dtime_int) is_beg = is_beg_curr_year() @@ -336,7 +335,7 @@ contains class(TestTimeManager), intent(inout) :: this logical :: is_end - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2, mon=1, day=1, tod=0) @@ -350,7 +349,7 @@ contains class(TestTimeManager), intent(inout) :: this logical :: is_end - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_date(yr=2, mon=1, day=2, tod=0) @@ -364,7 +363,7 @@ contains class(TestTimeManager), intent(inout) :: this logical :: is_first - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) is_first = is_first_step() @@ -376,7 +375,7 @@ contains class(TestTimeManager), intent(inout) :: this logical :: is_first - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) call set_nstep(1) @@ -390,7 +389,7 @@ contains class(TestTimeManager), intent(inout) :: this integer :: nstep - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) nstep = 100 call set_nstep(nstep) @@ -419,7 +418,7 @@ contains real(r8) :: londeg integer :: expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) ! Check for local noon at Greenich londeg = 0.0_r8 @@ -446,7 +445,7 @@ contains integer :: secs real(r8) :: londeg - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) londeg = 0.0_r8 do while ( londeg <= 360.0_r8 ) @@ -470,16 +469,16 @@ contains real(r8) :: londeg integer :: expected - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) ! Check for local noon at Greenich for 1 time step ahead londeg = 0.0_r8 - secs = 3600*12 + dtime + secs = 3600*12 + dtime_int call set_date(yr=2018, mon=9, day=3, tod=secs) - expected = secs - dtime - @assertEqual( expected, get_local_time( londeg, offset=-dtime ) ) + expected = secs - dtime_int + @assertEqual( expected, get_local_time( londeg, offset=-dtime_int ) ) londeg = 360.0_r8 - @assertEqual( expected, get_local_time( londeg, offset=-dtime ) ) + @assertEqual( expected, get_local_time( londeg, offset=-dtime_int ) ) end subroutine check_local_time_woffset @@ -490,7 +489,7 @@ contains integer :: secs real(r8) :: londeg - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) ! Check for local noon at Greenich will be true from 11 to 1pm londeg = 0.0_r8 @@ -528,7 +527,7 @@ contains integer :: secs logical :: check - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) londeg = 0.0_r8 secs = get_local_time( londeg ) @@ -549,7 +548,7 @@ contains real(r8) :: londeg integer :: secs - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) londeg = -200.0_r8 secs = get_local_time( londeg ) @@ -567,7 +566,7 @@ contains real(r8) :: londeg integer :: secs - call unittest_timemgr_setup(dtime=dtime) + call unittest_timemgr_setup(dtime=dtime_int) londeg = 400.0_r8 secs = get_local_time( londeg ) @@ -627,7 +626,7 @@ contains integer :: start, end - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) start = 100 ! April 10 end = 300 ! October 27 @@ -641,7 +640,7 @@ contains @assertFalse(is_today_in_doy_interval(start, end)) ! Test first timestep of interval - call set_date(yr=2009, mon=4, day=10, tod=dtime) + call set_date(yr=2009, mon=4, day=10, tod=dtime_int) @assertTrue(is_today_in_doy_interval(start, end)) ! Test well within interval @@ -653,7 +652,7 @@ contains @assertTrue(is_today_in_doy_interval(start, end)) ! Test first timestep after interval - call set_date(yr=2009, mon=10, day=28, tod=dtime) + call set_date(yr=2009, mon=10, day=28, tod=dtime_int) @assertFalse(is_today_in_doy_interval(start, end)) end subroutine check_is_today_in_doy_interval @@ -662,11 +661,11 @@ contains subroutine check_get_doy_tomorrow(this) class(TestTimeManager), intent(inout) :: this character(len=256) :: expected_msg - integer :: doy_tomorrow + integer :: doy_tomorrow ! Dummy needed for exception tests ! We don't care about the actual date here; we just want to enable get_curr_days_per_year() - call unittest_timemgr_setup(dtime=dtime, use_gregorian_calendar=.true.) - call set_date(yr=2009, mon=10, day=28, tod=dtime) + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) + call set_date(yr=2009, mon=10, day=28, tod=dtime_int) @assertEqual(get_doy_tomorrow(1), 2) @assertEqual(get_doy_tomorrow(150), 151) From 31d84925d80bcbb4818f53f4b0f38a24e4b9bc0d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 11:34:24 -0600 Subject: [PATCH 1751/2067] Better handling of days in year. --- src/utils/clm_time_manager.F90 | 10 +++++++--- .../clm_time_manager_test/test_clm_time_manager.pf | 7 +++++-- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 11b05a171a..783493d528 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -1282,14 +1282,18 @@ function get_doy_tomorrow(doy_today) result(doy_tomorrow) integer, intent(in) :: doy_today integer :: doy_tomorrow + integer :: days_in_year character(len=*), parameter :: sub = 'clm::get_doy_tomorrow' - if ( doy_today < 1 .or. doy_today > get_curr_days_per_year() )then - write(iulog,*) sub, ' = ', doy_today + days_in_year = get_curr_days_per_year() + + if ( doy_today < 1 .or. doy_today > days_in_year )then + write(iulog,*) 'doy_today = ', doy_today + write(iulog,*) 'days_in_year = ', days_in_year call shr_sys_abort( sub//': error doy_today out of range' ) end if - if (doy_today == get_curr_days_per_year()) then + if (doy_today == days_in_year) then doy_tomorrow = 1 else doy_tomorrow = doy_today + 1 diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index 4ac3613164..fa05b904ca 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -662,16 +662,19 @@ contains class(TestTimeManager), intent(inout) :: this character(len=256) :: expected_msg integer :: doy_tomorrow ! Dummy needed for exception tests + integer :: days_in_year ! We don't care about the actual date here; we just want to enable get_curr_days_per_year() call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) call set_date(yr=2009, mon=10, day=28, tod=dtime_int) + days_in_year = get_curr_days_per_year() + @assertEqual(get_doy_tomorrow(1), 2) @assertEqual(get_doy_tomorrow(150), 151) - @assertEqual(get_doy_tomorrow(get_curr_days_per_year()), 1) + @assertEqual(get_doy_tomorrow(days_in_year), 1) - doy_tomorrow = get_doy_tomorrow(get_curr_days_per_year() + 1) + doy_tomorrow = get_doy_tomorrow(days_in_year + 1) expected_msg = endrun_msg("clm::get_doy_tomorrow: error doy_today out of range" ) @assertExceptionRaised(expected_msg) From 818f3ce6aff9f13eee9508cccad17a073ae68316 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 11:40:28 -0600 Subject: [PATCH 1752/2067] Add leap-year test of get_doy_tomorrow(). --- .../test_clm_time_manager.pf | 27 +++++++++++++++++-- 1 file changed, 25 insertions(+), 2 deletions(-) diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index fa05b904ca..fafe7c0f09 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -658,7 +658,7 @@ contains end subroutine check_is_today_in_doy_interval @Test - subroutine check_get_doy_tomorrow(this) + subroutine check_get_doy_tomorrow_noleap(this) class(TestTimeManager), intent(inout) :: this character(len=256) :: expected_msg integer :: doy_tomorrow ! Dummy needed for exception tests @@ -678,6 +678,29 @@ contains expected_msg = endrun_msg("clm::get_doy_tomorrow: error doy_today out of range" ) @assertExceptionRaised(expected_msg) - end subroutine check_get_doy_tomorrow + end subroutine check_get_doy_tomorrow_noleap + + @Test + subroutine check_get_doy_tomorrow_leap(this) + class(TestTimeManager), intent(inout) :: this + character(len=256) :: expected_msg + integer :: doy_tomorrow ! Dummy needed for exception tests + integer :: days_in_year + + call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) + + ! Ensure that things work even in the last timestep of a leap year... + call set_date(yr=2008, mon=12, day=31, tod=secs_in_day_int - dtime_int) + days_in_year = get_curr_days_per_year() + @assertEqual(get_doy_tomorrow(days_in_year), 1) + doy_tomorrow = get_doy_tomorrow(days_in_year + 1) + @assertExceptionRaised(expected_msg) + + ! ... as well as in the first timestep after a leap year + call set_date(yr=2009, mon=1, day=1, tod=0) + @assertEqual(get_doy_tomorrow(1), 2) + + end subroutine check_get_doy_tomorrow_leap + end module test_clm_time_manager From c803feac091dd3ef3d1138d8207780fe1869892d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 11:57:54 -0600 Subject: [PATCH 1753/2067] get_doy_tomorrow(): Use get_prev_days_per_year() instead of _curr_. --- src/utils/clm_time_manager.F90 | 2 +- .../test/clm_time_manager_test/test_clm_time_manager.pf | 7 ++++--- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 783493d528..5f535b7126 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -1285,7 +1285,7 @@ function get_doy_tomorrow(doy_today) result(doy_tomorrow) integer :: days_in_year character(len=*), parameter :: sub = 'clm::get_doy_tomorrow' - days_in_year = get_curr_days_per_year() + days_in_year = get_prev_days_per_year() if ( doy_today < 1 .or. doy_today > days_in_year )then write(iulog,*) 'doy_today = ', doy_today diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index fafe7c0f09..14d244f65c 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -664,11 +664,11 @@ contains integer :: doy_tomorrow ! Dummy needed for exception tests integer :: days_in_year - ! We don't care about the actual date here; we just want to enable get_curr_days_per_year() + ! We don't care about the actual date here; we just want to enable get_prev_days_per_year() call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) call set_date(yr=2009, mon=10, day=28, tod=dtime_int) - days_in_year = get_curr_days_per_year() + days_in_year = get_prev_days_per_year() @assertEqual(get_doy_tomorrow(1), 2) @assertEqual(get_doy_tomorrow(150), 151) @@ -691,9 +691,10 @@ contains ! Ensure that things work even in the last timestep of a leap year... call set_date(yr=2008, mon=12, day=31, tod=secs_in_day_int - dtime_int) - days_in_year = get_curr_days_per_year() + days_in_year = get_prev_days_per_year() @assertEqual(get_doy_tomorrow(days_in_year), 1) doy_tomorrow = get_doy_tomorrow(days_in_year + 1) + expected_msg = endrun_msg("clm::get_doy_tomorrow: error doy_today out of range") @assertExceptionRaised(expected_msg) ! ... as well as in the first timestep after a leap year From f80250971819f9b1e2c3e09e132232401ab16311 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 30 Oct 2023 12:05:56 -0600 Subject: [PATCH 1754/2067] added longish fates f10 test, added is_restarting arguments to ed_site_type call --- cime_config/testdefs/testlist_clm.xml | 13 +++++++++++++ src/utils/clmfates_interfaceMod.F90 | 16 +++++++++++++--- 2 files changed, 26 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 6cef2f35f1..392c769ab3 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1562,6 +1562,19 @@ + + + + + + + + + + + + + diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index 63f08675d7..66fb846f66 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -1054,7 +1054,8 @@ subroutine dynamics_driv(this, nc, bounds_clump, & call ed_update_site(this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s),.false.) + this%fates(nc)%bc_out(s), & + is_restarting = .false.) enddo @@ -1714,9 +1715,17 @@ subroutine restart( this, bounds_proc, ncid, flag, waterdiagnosticbulk_inst, & this%fates(nc)%bc_in(s)%max_rooting_depth_index_col = & min(this%fates(nc)%bc_in(s)%nlevsoil, active_layer_inst%altmax_lastyear_indx_col(c)) + ! When restarting the model, this subroutine has several + ! procedures that are incremental or don't need to be performed for + ! during the restart sequence. For the prior, we don't want the restarted + ! run to call these routines more than would had been called during + ! a continuous simulation period, as it would change results. So + ! we pass in the "is_restarting=.true." flag so we can bypass those procedures + call ed_update_site( this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s),.true. ) + this%fates(nc)%bc_out(s), & + is_restarting = .true. ) end do @@ -1940,7 +1949,8 @@ subroutine init_coldstart(this, waterstatebulk_inst, waterdiagnosticbulk_inst, & call ed_update_site(this%fates(nc)%sites(s), & this%fates(nc)%bc_in(s), & - this%fates(nc)%bc_out(s),.false.) + this%fates(nc)%bc_out(s), & + is_restarting = .false.) end do From 0bcec665702da6ba44c527b74ec9fac9fc580d18 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 13:17:23 -0600 Subject: [PATCH 1755/2067] Explain use of get_prev_days_per_year(). --- src/utils/clm_time_manager.F90 | 1 + src/utils/test/clm_time_manager_test/test_clm_time_manager.pf | 2 ++ 2 files changed, 3 insertions(+) diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 5f535b7126..955d98057a 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -1285,6 +1285,7 @@ function get_doy_tomorrow(doy_today) result(doy_tomorrow) integer :: days_in_year character(len=*), parameter :: sub = 'clm::get_doy_tomorrow' + ! Use get_prev_days_per_year() instead of get_curr_days_per_year() because the latter, in the last timestep of a year, actually returns the number of days in the NEXT year. days_in_year = get_prev_days_per_year() if ( doy_today < 1 .or. doy_today > days_in_year )then diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf index 14d244f65c..df8a59de4b 100644 --- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf +++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf @@ -668,6 +668,7 @@ contains call unittest_timemgr_setup(dtime=dtime_int, use_gregorian_calendar=.true.) call set_date(yr=2009, mon=10, day=28, tod=dtime_int) + ! Use get_prev_days_per_year() instead of get_curr_days_per_year() because the latter, in the last timestep of a year, actually returns the number of days in the NEXT year. days_in_year = get_prev_days_per_year() @assertEqual(get_doy_tomorrow(1), 2) @@ -691,6 +692,7 @@ contains ! Ensure that things work even in the last timestep of a leap year... call set_date(yr=2008, mon=12, day=31, tod=secs_in_day_int - dtime_int) + ! Use get_prev_days_per_year() instead of get_curr_days_per_year() because the latter, in the last timestep of a year, actually returns the number of days in the NEXT year. days_in_year = get_prev_days_per_year() @assertEqual(get_doy_tomorrow(days_in_year), 1) doy_tomorrow = get_doy_tomorrow(days_in_year + 1) From 806f12414bc15ade6b204dfe6254e89e9a7d8d18 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 16:53:29 -0600 Subject: [PATCH 1756/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 39 ++++----------------------------------- doc/ChangeSum | 2 +- 2 files changed, 5 insertions(+), 36 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 657f78cca1..76286ce770 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev147 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) -Date: Fri Oct 27 15:32:54 MDT 2023 +Date: Mon Oct 30 16:53:20 MDT 2023 One-line Summary: Add sowing window input files Purpose and description of changes @@ -43,50 +43,19 @@ Testing summary: build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - + cheyenne - PASS regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- - izumi ------- + cheyenne ---- OK (some diffs in field lists) + izumi ------- OK (some diffs in field lists) any other testing (give details below): * RXCROPMATURITY test passes. -If the tag used for baseline comparisons was NOT the previous tag, note that here: - - -Answer changes --------------- - -Changes answers relative to baseline: - - [ If a tag changes answers relative to baseline comparison the - following should be filled in (otherwise remove this section). - And always remove these three lines and parts that don't apply. ] - - Summarize any changes to answers, i.e., - - what code configurations: - - what platforms/compilers: - - nature of change (roundoff; larger than roundoff/same climate; new climate): - - If bitwise differences were observed, how did you show they were no worse - than roundoff? Roundoff differences means one or more lines of code change results - only by roundoff level (because order of operation changes for example). Roundoff - changes to state fields usually grow to greater than roundoff as the simulation progresses. - - If this tag changes climate describe the run(s) done to evaluate the new - climate (put details of the simulations in the experiment database) - - casename: - - URL for LMWG diagnostics output used to validate new climate: - Other details ------------- -[Remove any lines that don't apply. Remove entire section if nothing applies.] - -List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): Pull Requests that document the changes (include PR ids): * #2193 (https://github.com/ESCOMP/CTSM/pull/2193) diff --git a/doc/ChangeSum b/doc/ChangeSum index b6fc5f0214..5e4f816f64 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev147 samrabin 10/27/2023 Add sowing window input files + ctsm5.1.dev147 samrabin 10/30/2023 Add sowing window input files ctsm5.1.dev146 glemieux 10/24/2023 FATES cross-grid seed dispersal ctsm5.1.dev145 slevis 10/19/2023 SNICAR snow albedo scheme updates ctsm5.1.dev144 samrabin 10/19/2023 Remove a deprecated shr_mpi_bcast call From fe6385bba8370bfd4787e59f0f50be04b6a821a2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 30 Oct 2023 17:05:46 -0600 Subject: [PATCH 1757/2067] User's Guide, testing: Fix/fill Build-namelist section. --- doc/source/users_guide/testing/testing.rst | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/doc/source/users_guide/testing/testing.rst b/doc/source/users_guide/testing/testing.rst index c821ba19e7..6ccbecadfe 100644 --- a/doc/source/users_guide/testing/testing.rst +++ b/doc/source/users_guide/testing/testing.rst @@ -28,11 +28,20 @@ CTSM Fortran Unit Tests CTSM Build-namelist Tests ========================= -Run the following perl tester that +Test the namelist build script by running the following: :: + > cd bld/unit_testers - > ./build-namelist_test.pl + > ./build-namelist_test.pl 1>namelist_test.log 2>&1 + +When that's complete, inspect ``namelist_test.log`` (e.g., with ``less namelist_test.log``). If you see ``Successfully ran all testing for build-namelist`` but nothing like ``# Looks like you failed 4 tests of 1999.``, then everything went fine. + +If something went wrong, you can find the failing tests like so: + +:: + + > grep -E "^[0-9]+/[0-9]+ < [a-zA-Z]+" namelist_test.log | grep -v "PASS" Testing PTCLM ============= From 37db306904dbc8649a76c0b5b7d04eb022013116 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 30 Oct 2023 17:56:15 -0600 Subject: [PATCH 1758/2067] Update comments, add placeholder for thermal_cond_snow option --- src/biogeophys/SoilTemperatureMod.F90 | 36 +++++++++++++++++++-------- 1 file changed, 25 insertions(+), 11 deletions(-) diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index caeedd1603..d3e797631b 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -47,7 +47,7 @@ module SoilTemperatureMod ! o The thermal conductivity of soil is computed from ! the algorithm of Johansen (as reported by Farouki 1981), and the ! conductivity of snow is from the formulation used in - ! Sturm (1997). + ! Sturm (1997) or Jordan (1991) p. 18 depending on namelist option. ! o Boundary conditions: ! F = Rnet - Hg - LEg (top), F= 0 (base of the soil column). ! o Soil / snow temperature is predicted from heat conduction @@ -100,7 +100,7 @@ subroutine SoilTemperature(bounds, num_urbanl, filter_urbanl, num_urbanc, filter ! o The thermal conductivity of soil is computed from ! the algorithm of Johansen (as reported by Farouki 1981), and the ! conductivity of snow is from the formulation used in - ! Sturm (1997). + ! Sturm (1997) or Jordan (1991) p. 18 depending on namelist option. ! o Boundary conditions: ! F = Rnet - Hg - LEg (top), F= 0 (base of the soil column). ! o Soil / snow temperature is predicted from heat conduction @@ -611,7 +611,8 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter ! ! (2) The thermal conductivity of soil is computed from the algorithm of ! Johansen (as reported by Farouki 1981), and of snow is from the - ! formulation used in Sturm (1997). + ! formulation used in Sturm (1997) or Jordan (1991) p. 18 depending on + ! namelist option. ! The thermal conductivities at the interfaces between two neighboring ! layers (j, j+1) are derived from an assumption that the flux across ! the interface is equal to that from the node j to the interface and the @@ -734,16 +735,29 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter endif endif - ! Thermal conductivity of snow, which from Sturm (1997) + ! Thermal conductivity of snow ! Only examine levels from snl(c)+1 -> 0 where snl(c) < 1 if (snl(c)+1 < 1 .AND. (j >= snl(c)+1) .AND. (j <= 0)) then - bw(c,j) = ((h2osoi_ice(c,j)*1)+h2osoi_liq(c,j))/(frac_sno(c)*dz(c,j)) ! ==RHOS - ! thk(c,j) = tkair + (7.75e-5_r8 *bw(c,j) + 1.105e-6_r8*bw(c,j)*bw(c,j))*(tkice-tkair) ! Original (Jordan) Parameterisation - if (bw(c,j) <= 156) then !LMW or 0.156 ? - thk(c,j) = 0.023 + 0.234*(bw(c,j)/1000) !LMW - units changed by VRD - else !LMW - thk(c,j) = 0.138 - 1.01*(bw(c,j)/1000) +(3.233*((bw(c,j)/1000)*(bw(c,j)/1000))) ! LMW Sturm I think - end if + bw(c,j) = (h2osoi_ice(c,j)+h2osoi_liq(c,j))/(frac_sno(c)*dz(c,j)) +! TODO slevis: Add namelist option thermal_cond_snow and then +! uncomment relevant lines below +! select case (thermal_cond_snow) +! case ('Jordan1991') +! thk(c,j) = tkair + (7.75e-5_r8 *bw(c,j) + 1.105e-6_r8*bw(c,j)*bw(c,j))*(tkice-tkair) +! case ('Sturm1997') + ! Implemented by Vicky Dutch (VRD), Nick Rutter, and + ! Leanne Wake (LMW) + ! https://tc.copernicus.org/articles/16/4201/2022/ + ! Code provided by Adrien Dams to Will Wieder + if (bw(c,j) <= 156) then !LMW or 0.156 ? + thk(c,j) = 0.023 + 0.234*(bw(c,j)/1000) !LMW - units changed by VRD + else !LMW + thk(c,j) = 0.138 - 1.01*(bw(c,j)/1000) +(3.233*((bw(c,j)/1000)*(bw(c,j)/1000))) ! LMW Sturm I think + end if +! case default +! write(iulog,*) subname//' ERROR: unknown thermal_cond_snow value: ', thermal_cond_snow +! call endrun(msg=errMsg(sourcefile, __LINE__)) +! end select end if end do From 1bc6e7205fa9b33b608d26c4460b68386c275edf Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 31 Oct 2023 09:37:35 -0600 Subject: [PATCH 1759/2067] functional (but simple) sys tests --- .../test_sys_modify_singlept_site_neon.py | 17 ++++++------- python/ctsm/test/test_sys_run_neon.py | 25 +++++++------------ 2 files changed, 17 insertions(+), 25 deletions(-) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index 9eb9ed9256..eb0575789d 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -51,21 +51,20 @@ def tearDown(self): def test_modify_site(self): """ - Test modifying a singple point site - The primary items to test here are the following: + Test modifying a singple point site. This test currently checks that the run fails due to dir structure + + TODO: The primary items to test here are the following: 1) Fields are overwritten with site-specific data for neon sites 2) Downloaded data is used in surface dataset 3) Check specific fields listed in update_metadata for correct output 4) Check that a netcdf with correct formatting is created """ - sys.argv = ["--neon_site", ["ABBY"]] # self._cfg_file_path] #, "ABBY"] - print("sys.argv:") - print(sys.argv) + sys.argv = ["modify_singlept_site_neon", "--neon_site", "/glade/work/tking/ctsm/cime_config/usermods_dirs/NEON/ABBY"] + # TODO: the above requires a full path instead of site name because of how run_neon is configured... This needs to be fixed/generalized. parser = get_parser() - print("parser:") - print(parser) - main() # running into error here because main doesn't take in any arguments and doesn't know what arguments are needed. - + with self.assertRaises(SystemExit): + print("This should currently fail due to directory structure in run_neon and the directory structure listed in sys.argv") + main() if __name__ == "__main__": unit_testing.setup_for_tests() diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index db90dc8bb0..7f83eb6453 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -49,30 +49,23 @@ def tearDown(self): def test_one_site(self): """ This test specifies a site to run - Run the tool, check history file output exists - Could also check log files? Although this functionally doesn't change output, - it might be good to ensure the log files are working as expected? - Test running transient, ad and post ad cases. - Test use of base case root. - Test for using prism? - Test setup_only? This should be encapsulated within the full run? + Run the tool, check that file structure is set up correctly """ # run the run_neon tool - # sys.argv = ["run_neon", "--neon_sites 'ABBY'"] - # sys.argv = ["--neon_sites", ["ABBY"]] - - sys.argv = ["--neon-sites 'ABBY'"] + sys.argv = ["run_neon", "--neon-sites", "BART", "--setup-only", "--output-root", self._tempdir] valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] parser = get_parser(sys.argv, "description_for_parser", valid_neon_sites) main("") - # this seems to run OSBS (default site, instead of ABBY), - # but does create files! It takes a while though, should we do setup-only? - # Could assert that dir is created with files - # we should also move this into a tempdir and delete files after running (and cancel queue?) + # assert that BART directories were created during setup + self.assertTrue("BART" in glob.glob(self._tempdir+"/*")) - self.assertTrue("OSBS" in glob.glob("*")) + # TODO: Would also be useful to test the following items: + # It might be good to ensure the log files are working as expected? + # Test running transient, ad and post ad cases. + # Test use of base case root. + # Test for using prism? if __name__ == "__main__": From 6be5dae9f83b6172da6a33676e71a6cb60c5054d Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 31 Oct 2023 09:46:03 -0600 Subject: [PATCH 1760/2067] minor reformatting --- .../test_sys_modify_singlept_site_neon.py | 24 +++++++++++-------- python/ctsm/test/test_sys_run_neon.py | 18 +++++++------- 2 files changed, 23 insertions(+), 19 deletions(-) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index eb0575789d..d6d4acce74 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -5,23 +5,17 @@ """ import os -import re - import unittest import tempfile import shutil import sys -import xarray as xr -import numpy as np - # THESE LINES ARE JUST HERE FOR TESTING _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing -from ctsm.site_and_regional import modify_singlept_site_neon from ctsm.site_and_regional.modify_singlept_site_neon import main, get_parser # Allow test names that pylint doesn't like; otherwise hard to make them @@ -51,7 +45,8 @@ def tearDown(self): def test_modify_site(self): """ - Test modifying a singple point site. This test currently checks that the run fails due to dir structure + Test modifying a singple point site. + This test currently checks that the run fails due to dir structure TODO: The primary items to test here are the following: 1) Fields are overwritten with site-specific data for neon sites @@ -59,13 +54,22 @@ def test_modify_site(self): 3) Check specific fields listed in update_metadata for correct output 4) Check that a netcdf with correct formatting is created """ - sys.argv = ["modify_singlept_site_neon", "--neon_site", "/glade/work/tking/ctsm/cime_config/usermods_dirs/NEON/ABBY"] - # TODO: the above requires a full path instead of site name because of how run_neon is configured... This needs to be fixed/generalized. + sys.argv = [ + "modify_singlept_site_neon", + "--neon_site", + "/glade/work/tking/ctsm/cime_config/usermods_dirs/NEON/ABBY", + ] + # TODO: the above requires a full path instead of site name because of how run_neon is configured. + # This needs to be fixed/generalized. parser = get_parser() with self.assertRaises(SystemExit): - print("This should currently fail due to directory structure in run_neon and the directory structure listed in sys.argv") + print( + """This should currently fail due to directory structure in run_neon + and the directory structure listed in sys.argv""" + ) main() + if __name__ == "__main__": unit_testing.setup_for_tests() unittest.main() diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index 7f83eb6453..d19c18002c 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -6,23 +6,16 @@ import glob import os -import re - import unittest import tempfile import shutil import sys -import xarray as xr -import numpy as np - # THESE LINES ARE JUST HERE FOR TESTING _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) -from ctsm.path_utils import path_to_ctsm_root, path_to_cime from ctsm import unit_testing -from ctsm.site_and_regional import run_neon from ctsm.site_and_regional.run_neon import main, get_parser # Allow test names that pylint doesn't like; otherwise hard to make them @@ -53,13 +46,20 @@ def test_one_site(self): """ # run the run_neon tool - sys.argv = ["run_neon", "--neon-sites", "BART", "--setup-only", "--output-root", self._tempdir] + sys.argv = [ + "run_neon", + "--neon-sites", + "BART", + "--setup-only", + "--output-root", + self._tempdir, + ] valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] parser = get_parser(sys.argv, "description_for_parser", valid_neon_sites) main("") # assert that BART directories were created during setup - self.assertTrue("BART" in glob.glob(self._tempdir+"/*")) + self.assertTrue("BART" in glob.glob(self._tempdir + "/*")) # TODO: Would also be useful to test the following items: # It might be good to ensure the log files are working as expected? From 4dc31b1a47c45e856d8489c116d32a84b3af541a Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 31 Oct 2023 13:24:10 -0600 Subject: [PATCH 1761/2067] update path --- python/ctsm/test/test_sys_modify_singlept_site_neon.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index d6d4acce74..9ea1322141 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -57,7 +57,7 @@ def test_modify_site(self): sys.argv = [ "modify_singlept_site_neon", "--neon_site", - "/glade/work/tking/ctsm/cime_config/usermods_dirs/NEON/ABBY", + path_to_ctsm_root()+"/ctsm/cime_config/usermods_dirs/NEON/ABBY", ] # TODO: the above requires a full path instead of site name because of how run_neon is configured. # This needs to be fixed/generalized. From a83784b177dcf3dfb15344fa64802f9d3c6c8aaf Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 31 Oct 2023 13:45:31 -0600 Subject: [PATCH 1762/2067] reformat --- python/ctsm/test/test_sys_modify_singlept_site_neon.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index 9ea1322141..ab285f1a8b 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -57,7 +57,7 @@ def test_modify_site(self): sys.argv = [ "modify_singlept_site_neon", "--neon_site", - path_to_ctsm_root()+"/ctsm/cime_config/usermods_dirs/NEON/ABBY", + path_to_ctsm_root() + "/ctsm/cime_config/usermods_dirs/NEON/ABBY", ] # TODO: the above requires a full path instead of site name because of how run_neon is configured. # This needs to be fixed/generalized. From d708fb3aa0f72391affedbe63f5fdee2e25a2e38 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 1 Nov 2023 11:31:44 -0600 Subject: [PATCH 1763/2067] minor fix --- python/ctsm/test/test_sys_run_neon.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index d19c18002c..eb22ac45d5 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -59,7 +59,8 @@ def test_one_site(self): main("") # assert that BART directories were created during setup - self.assertTrue("BART" in glob.glob(self._tempdir + "/*")) + print(glob.glob(self._tempdir + "/BART*")) + self.assertTrue("BART" in glob.glob(self._tempdir + "/BART*")[0]) # TODO: Would also be useful to test the following items: # It might be good to ensure the log files are working as expected? From 338b1800ac73dc6015b82dae40b20ef24314456c Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 1 Nov 2023 11:44:59 -0600 Subject: [PATCH 1764/2067] remove print statement --- python/ctsm/test/test_sys_run_neon.py | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index eb22ac45d5..d14b2ce312 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -59,7 +59,6 @@ def test_one_site(self): main("") # assert that BART directories were created during setup - print(glob.glob(self._tempdir + "/BART*")) self.assertTrue("BART" in glob.glob(self._tempdir + "/BART*")[0]) # TODO: Would also be useful to test the following items: From 07d1ec326b69d61a01eee883670a8d2e2796e5f5 Mon Sep 17 00:00:00 2001 From: John Alex Date: Wed, 1 Nov 2023 12:24:12 -0600 Subject: [PATCH 1765/2067] Remove CLM-side FatesReadParameters (The FATES repo will be updated to define this method within FATES) --- src/utils/clmfates_paraminterfaceMod.F90 | 39 ------------------------ 1 file changed, 39 deletions(-) diff --git a/src/utils/clmfates_paraminterfaceMod.F90 b/src/utils/clmfates_paraminterfaceMod.F90 index 95b1e428da..ea27f563bf 100644 --- a/src/utils/clmfates_paraminterfaceMod.F90 +++ b/src/utils/clmfates_paraminterfaceMod.F90 @@ -29,7 +29,6 @@ module CLMFatesParamInterfaceMod ! NOTE(bja, 2017-01) these methods can NOT be part of the clm-fates ! interface type because they are called before the instance is ! initialized. - public :: FatesReadParameters public :: FatesReadPFTs private :: ParametersFromNetCDF private :: SetParameterDimensions @@ -42,44 +41,6 @@ module CLMFatesParamInterfaceMod contains - !----------------------------------------------------------------------- - subroutine FatesReadParameters() - use clm_varctl, only : use_fates, paramfile, fates_paramfile - use spmdMod, only : masterproc - - implicit none - - character(len=32) :: subname = 'FatesReadParameters' - class(fates_parameters_type), allocatable :: fates_params - logical :: is_host_file - - if (masterproc) then - write(fates_log(), *) 'clmfates_interfaceMod.F90::'//trim(subname)//' :: CLM reading ED/FATES '//' parameters ' - end if - - allocate(fates_params) - call fates_params%Init() ! fates_params class, in FatesParameterInterfaceMod - call FatesRegisterParams(fates_params) !EDParamsMod, only operates on fates_params class - call SpitFireRegisterParams(fates_params) !SpitFire Mod, only operates of fates_params class - call PRTRegisterParams(fates_params) ! PRT mod, only operates on fates_params class - call FatesSynchronizedParamsInst%RegisterParams(fates_params) !Synchronized params class in Synchronized params mod, only operates on fates_params class - - is_host_file = .false. - call ParametersFromNetCDF(fates_paramfile, is_host_file, fates_params) - - is_host_file = .true. - call ParametersFromNetCDF(paramfile, is_host_file, fates_params) - - call FatesReceiveParams(fates_params) - call SpitFireReceiveParams(fates_params) - call PRTReceiveParams(fates_params) - call FatesSynchronizedParamsInst%ReceiveParams(fates_params) - - call fates_params%Destroy() - deallocate(fates_params) - - end subroutine FatesReadParameters - !----------------------------------------------------------------------- subroutine FatesReadPFTs() From 800e85aec79c6f91b954300e2c1bc1341ab870c5 Mon Sep 17 00:00:00 2001 From: Keith Oleson Date: Wed, 1 Nov 2023 14:15:33 -0600 Subject: [PATCH 1766/2067] Changes to comments --- src/biogeochem/CNVegCarbonStateType.F90 | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/src/biogeochem/CNVegCarbonStateType.F90 b/src/biogeochem/CNVegCarbonStateType.F90 index 076c96ec27..c7e21da1d6 100644 --- a/src/biogeochem/CNVegCarbonStateType.F90 +++ b/src/biogeochem/CNVegCarbonStateType.F90 @@ -1528,11 +1528,12 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, ! BUG(kwo, 2023-10-19, ESCOMP/ctsm#2119) There is a bug that causes incorrect values for ! C isotopes if running from a case without C isotopes (an initial file) to a case with C ! isotopes (https://github.com/ESCOMP/ctsm/issues/2119). Here we check if the user - ! the user is doing this and abort if they are. This particular check is covering the case + ! is doing this and abort if they are. This particular check is covering the case ! when use_init_interp=.false. There is a similar check (but for the purpose of working around - ! a different bug) in initInterp.F90. This check here should be removed once bug #2119 is resolved - ! and replaced by the logic shown below for .e.g, totvegc_col, where totvegc_cl is initialized with - ! atmospheric c13 values. + ! a different bug) in initInterp.F90. This check below should be removed if bug #2119 is ever + ! fully resolved (i.e., we decide we need to support going from a case without C isotopes (an + ! initial file) to a case with C isotopes), and replaced by the logic shown below for .e.g, + ! totvegc_col_13, where totvegc_col_13 is initialized with atmospheric c13 values. ! We arbitrarily check totvegc_13 (we could pick any c13 restart field). if (masterproc) then write(iulog,*) 'Cannot initialize from a run without c13 to a run with c13,' @@ -1553,11 +1554,12 @@ subroutine Restart ( this, bounds, ncid, flag, carbon_type, reseed_dead_plants, ! BUG(kwo, 2023-10-19, ESCOMP/ctsm#2119) There is a bug that causes incorrect values for ! C isotopes if running from a case without C isotopes (an initial file) to a case with C ! isotopes (https://github.com/ESCOMP/ctsm/issues/2119). Here we check if the user - ! the user is doing this and abort if they are. This particular check is covering the case + ! is doing this and abort if they are. This particular check is covering the case ! when use_init_interp=.false. There is a similar check (but for the purpose of working around - ! a different bug) in initInterp.F90. This check here should be removed once bug #2119 is resolved - ! and replaced by the logic shown below for .e.g, totvegc_col, where totvegc_cl is initialized with - ! atmospheric c14 values. + ! a different bug) in initInterp.F90. This check below should be removed if bug #2119 is ever + ! fully resolved (i.e., we decide we need to support going from a case without C isotopes (an + ! initial file) to a case with C isotopes), and replaced by the logic shown below for .e.g, + ! totvegc_col_14, where totvegc_col_l4 is initialized with atmospheric c14 values. ! We arbitrarily check totvegc_14 (we could pick any c14 restart field). if (masterproc) then write(iulog,*) 'Cannot interpolate from a run without c14 to a run with c14,' From 75d5f10f09fd7b9ef3e2cb535a5e4d30976d28a1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 1 Nov 2023 16:53:23 -0600 Subject: [PATCH 1767/2067] Add new namelist variable snow_thermal_cond_method (not tested) --- bld/CLMBuildNamelist.pm | 7 +++++++ bld/namelist_files/namelist_defaults_ctsm.xml | 1 + .../namelist_definition_ctsm.xml | 5 +++++ src/biogeophys/SoilTemperatureMod.F90 | 21 +++++++++---------- src/main/clm_varctl.F90 | 2 ++ src/main/controlMod.F90 | 4 +++- 6 files changed, 28 insertions(+), 12 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index c12c54645f..5afaaab40d 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2031,6 +2031,13 @@ sub setup_logic_snicar_methods { sub setup_logic_snow { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_thermal_cond_method' ); + + my $var = $nl->get_value('snow_thermal_cond_method'); + if ( $var ne 'Jordan1991' && $var ne 'Sturm1997' ) { + $log->fatal_error("$var is incorrect entry for the namelist variable snow_thermal_cond_method; expected Jordan1991 or Sturm1997"); + } + my $numrad_snw = $nl->get_value('snicar_numrad_snw'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fsnowoptics', 'snicar_numrad_snw' => $numrad_snw); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2e57391df7..b23e67ed6b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -445,6 +445,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 1.e9 SwensonLawrence2012 +Jordan1991 diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index d3e797631b..69f9958efa 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -623,7 +623,8 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter use clm_varcon , only : denh2o, denice, tfrz, tkwat, tkice, tkair, cpice, cpliq, thk_bedrock, csol_bedrock use landunit_varcon , only : istice, istwet use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv - use clm_varctl , only : iulog + use clm_varctl , only : iulog, snow_thermal_cond_method + ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds @@ -739,12 +740,10 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter ! Only examine levels from snl(c)+1 -> 0 where snl(c) < 1 if (snl(c)+1 < 1 .AND. (j >= snl(c)+1) .AND. (j <= 0)) then bw(c,j) = (h2osoi_ice(c,j)+h2osoi_liq(c,j))/(frac_sno(c)*dz(c,j)) -! TODO slevis: Add namelist option thermal_cond_snow and then -! uncomment relevant lines below -! select case (thermal_cond_snow) -! case ('Jordan1991') -! thk(c,j) = tkair + (7.75e-5_r8 *bw(c,j) + 1.105e-6_r8*bw(c,j)*bw(c,j))*(tkice-tkair) -! case ('Sturm1997') + select case (snow_thermal_cond_method) + case ('Jordan1991') + thk(c,j) = tkair + (7.75e-5_r8 *bw(c,j) + 1.105e-6_r8*bw(c,j)*bw(c,j))*(tkice-tkair) + case ('Sturm1997') ! Implemented by Vicky Dutch (VRD), Nick Rutter, and ! Leanne Wake (LMW) ! https://tc.copernicus.org/articles/16/4201/2022/ @@ -754,10 +753,10 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter else !LMW thk(c,j) = 0.138 - 1.01*(bw(c,j)/1000) +(3.233*((bw(c,j)/1000)*(bw(c,j)/1000))) ! LMW Sturm I think end if -! case default -! write(iulog,*) subname//' ERROR: unknown thermal_cond_snow value: ', thermal_cond_snow -! call endrun(msg=errMsg(sourcefile, __LINE__)) -! end select + case default + write(iulog,*) subname//' ERROR: unknown snow_thermal_cond_method value: ', snow_thermal_cond_method + call endrun(msg=errMsg(sourcefile, __LINE__)) + end select end if end do diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 95c800504b..a5201a53cf 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -221,6 +221,8 @@ module clm_varctl ! which snow cover fraction parameterization to use character(len=64), public :: snow_cover_fraction_method + ! which snow thermal conductivity parameterization to use + character(len=25), public :: snow_thermal_cond_method ! atmospheric CO2 molar ratio (by volume) (umol/mol) real(r8), public :: co2_ppmv = 355._r8 ! diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 5937e55b04..deb8c044d8 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -199,7 +199,8 @@ subroutine control_init(dtime) clump_pproc, & create_crop_landunit, nsegspc, co2_ppmv, & albice, soil_layerstruct_predefined, soil_layerstruct_userdefined, & - soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, snow_cover_fraction_method, & + soil_layerstruct_userdefined_nlevsoi, use_subgrid_fluxes, & + snow_thermal_cond_method, snow_cover_fraction_method, & irrigate, run_zero_weight_urban, all_active, & crop_fsat_equals_zero, for_testing_run_ncdiopio_tests, & for_testing_use_second_grain_pool, for_testing_use_repr_structure_pool, & @@ -850,6 +851,7 @@ subroutine control_spmd() ! physics variables call mpi_bcast (nsegspc, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (use_subgrid_fluxes , 1, MPI_LOGICAL, 0, mpicom, ier) + call mpi_bcast (snow_thermal_cond_method, len(snow_thermal_cond_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (snow_cover_fraction_method , len(snow_cover_fraction_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (z0param_method , len(z0param_method), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (use_z0m_snowmelt, 1, MPI_LOGICAL, 0, mpicom, ier) From 0b066bee71e80cbc7b7d164c0d862ed5cb9b9af1 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 2 Nov 2023 12:28:15 -0600 Subject: [PATCH 1768/2067] cleaning up tests and implementing path fix with chdir to tempdir --- python/ctsm/test/test_sys_modify_singlept_site_neon.py | 7 ++----- python/ctsm/test/test_sys_run_neon.py | 7 +++---- python/ctsm/test/test_unit_neon_surf_wrapper.py | 3 --- python/ctsm/test/test_unit_run_neon.py | 3 --- 4 files changed, 5 insertions(+), 15 deletions(-) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index ab285f1a8b..3f2dc6d7f2 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -10,10 +10,6 @@ import shutil import sys -# THESE LINES ARE JUST HERE FOR TESTING -_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) -sys.path.insert(1, _CTSM_PYTHON) - from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing from ctsm.site_and_regional.modify_singlept_site_neon import main, get_parser @@ -59,7 +55,8 @@ def test_modify_site(self): "--neon_site", path_to_ctsm_root() + "/ctsm/cime_config/usermods_dirs/NEON/ABBY", ] - # TODO: the above requires a full path instead of site name because of how run_neon is configured. + # TODO: the above requires a full path instead of site name + # because of how run_neon is configured. # This needs to be fixed/generalized. parser = get_parser() with self.assertRaises(SystemExit): diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index d14b2ce312..74bee17b35 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -11,10 +11,6 @@ import shutil import sys -# THESE LINES ARE JUST HERE FOR TESTING -_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) -sys.path.insert(1, _CTSM_PYTHON) - from ctsm import unit_testing from ctsm.site_and_regional.run_neon import main, get_parser @@ -32,6 +28,7 @@ def setUp(self): Check tempdir for history files """ self._tempdir = tempfile.mkdtemp() + os.chdir(self._tempdir) # cd to tempdir def tearDown(self): """ @@ -52,6 +49,7 @@ def test_one_site(self): "BART", "--setup-only", "--output-root", + #"FAKE_DIR" self._tempdir, ] valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] @@ -60,6 +58,7 @@ def test_one_site(self): # assert that BART directories were created during setup self.assertTrue("BART" in glob.glob(self._tempdir + "/BART*")[0]) + #self.assertTrue("BART" in glob.glob("BART*")[0]) # TODO: Would also be useful to test the following items: # It might be good to ensure the log files are working as expected? diff --git a/python/ctsm/test/test_unit_neon_surf_wrapper.py b/python/ctsm/test/test_unit_neon_surf_wrapper.py index 0092bdb91c..443af2079b 100755 --- a/python/ctsm/test/test_unit_neon_surf_wrapper.py +++ b/python/ctsm/test/test_unit_neon_surf_wrapper.py @@ -7,8 +7,6 @@ """ import unittest -import configparser -import argparse import os import sys @@ -19,7 +17,6 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing from ctsm.site_and_regional.neon_surf_wrapper import get_parser -from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name diff --git a/python/ctsm/test/test_unit_run_neon.py b/python/ctsm/test/test_unit_run_neon.py index 72c1b67a31..314b1e8b89 100755 --- a/python/ctsm/test/test_unit_run_neon.py +++ b/python/ctsm/test/test_unit_run_neon.py @@ -7,8 +7,6 @@ """ import unittest -import configparser -import argparse import os import sys @@ -19,7 +17,6 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing from ctsm.site_and_regional.run_neon import check_neon_listing -from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name From f477d610887b793f32dfd6bb91da7bab4451e959 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 2 Nov 2023 13:29:57 -0600 Subject: [PATCH 1769/2067] fix for listing.csv file generated in python dir --- python/ctsm/test/test_sys_run_neon.py | 4 ++-- .../test_unit_modify_singlept_site_neon.py | 4 ++++ python/ctsm/test/test_unit_run_neon.py | 22 +++++++++++++++++++ 3 files changed, 28 insertions(+), 2 deletions(-) diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index 74bee17b35..4dd5aca896 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -49,7 +49,7 @@ def test_one_site(self): "BART", "--setup-only", "--output-root", - #"FAKE_DIR" + # "FAKE_DIR" self._tempdir, ] valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] @@ -58,7 +58,7 @@ def test_one_site(self): # assert that BART directories were created during setup self.assertTrue("BART" in glob.glob(self._tempdir + "/BART*")[0]) - #self.assertTrue("BART" in glob.glob("BART*")[0]) + # self.assertTrue("BART" in glob.glob("BART*")[0]) # TODO: Would also be useful to test the following items: # It might be good to ensure the log files are working as expected? diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index 7817dd535e..4c3a473394 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -124,6 +124,8 @@ def test_check_neon_time(self): """ Test that dictionary containing last modified information is correctly downloaded """ + previous_dir = os.getcwd() + os.chdir(self._tempdir) # cd to tempdir last_abby_download = check_neon_time()[ "https://storage.neonscience.org/neon-ncar/NEON/surf_files/v1/ABBY_surfaceData.csv" ] @@ -138,6 +140,8 @@ def test_check_neon_time(self): self.assertGreater( int(last_abby_download[:4]), 2021, "ABBY download is older than expected" ) + # change back to previous dir once listing.csv file has been created in tempdir and test complete + os.chdir(previous_dir) if __name__ == "__main__": diff --git a/python/ctsm/test/test_unit_run_neon.py b/python/ctsm/test/test_unit_run_neon.py index 314b1e8b89..2cdcc915ad 100755 --- a/python/ctsm/test/test_unit_run_neon.py +++ b/python/ctsm/test/test_unit_run_neon.py @@ -7,6 +7,8 @@ """ import unittest +import tempfile +import shutil import os import sys @@ -26,11 +28,25 @@ class TestRunNeon(unittest.TestCase): Basic class for testing run_neon.py. """ + def setUp(self): + """ + Make /_tempdir for use by these tests. + """ + self._tempdir = tempfile.mkdtemp() + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + def test_check_neon_listing(self): """ Test that neon listing is available for valid sites """ valid_neon_sites = ["ABBY", "BART"] + previous_dir = os.getcwd() + os.chdir(self._tempdir) # cd to tempdir available_list = check_neon_listing(valid_neon_sites) self.assertEqual( available_list[0].name, "ABBY", "available list of actual sites not as expected" @@ -38,16 +54,22 @@ def test_check_neon_listing(self): self.assertEqual( available_list[1].name, "BART", "available list of actual sites not as expected" ) + # change back to previous dir once listing.csv file has been created in tempdir and test complete + os.chdir(previous_dir) def test_check_neon_listing_misspelled(self): """ Test that neon listing is not available for invalid sites """ valid_neon_sites = ["INVALID_SITE1", "INVALID_SITE2"] + previous_dir = os.getcwd() + os.chdir(self._tempdir) # cd to tempdir available_list = check_neon_listing(valid_neon_sites) self.assertEqual( available_list, [], "available list of incorrect dummy site not as expected" ) + # change back to previous dir once listing.csv file has been created in tempdir and test complete + os.chdir(previous_dir) if __name__ == "__main__": From f2312244149b37694f87a73be2012ca9fbccd734 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 2 Nov 2023 16:16:15 -0600 Subject: [PATCH 1770/2067] cleanup; changelog; some pylint fixes --- doc/ChangeLog | 138 ++++++++++++++++++ doc/ChangeSum | 1 + python/README.md | 3 +- python/ctsm/run_ctsm_py_tests.py | 5 +- .../site_and_regional/neon_surf_wrapper.py | 10 +- python/ctsm/site_and_regional/run_neon.py | 2 + .../test_sys_modify_singlept_site_neon.py | 2 +- python/ctsm/test/test_sys_run_neon.py | 7 +- .../test_unit_modify_singlept_site_neon.py | 5 +- python/ctsm/test/test_unit_run_neon.py | 4 +- 10 files changed, 160 insertions(+), 17 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 955f071933..d787c8d36c 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,142 @@ =============================================================== +Tag name: ctsm5.1.dev151 +Originator(s): tking (Teagan King,UCAR/CCR) +Date: Thu Nov 2 16:03:44 MDT 2023 +One-line Summary: Move tools to python directory and add tests + +Purpose and description of changes +---------------------------------- + +Move the following scripts to /python/ctsm/site_and_regional +and make wrapper scripts for them in /tools/site_and_regional: +- run_neon.py +- neon_surf_wrapper.py +- modify_singlept_site_neon.py + +Add unit testing for: +- iso_utils +- modify_singlept_site_neon +- neon_surf_wrapper +- run_neon + +Add system testing for: +- modify_singlept_site_neon +- run_neon + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +#1441 + +Known Issues: +There were some previous pylint errors that still remain in this tag. + +Notes of particular relevance for users +--------------------------------------- +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +wrapper scripts don't have .py suffixes + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +Numerous changes were made to include new tests. +README.md for testing was also updated to clarify that arguments should be used. + +Testing summary: +---------------- +[... Remove before making master tag. + +Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. +However, it occasionally makes sense to do more or less system testing; +here is guidance on different available levels of system testing: + a) no system testing (for use when the only changes are ones that + have absolutely no impact on system runs; this + includes documentation-only tags, tags that + just change the tools or some python code that + does not impact system runs, etc.) + b) minimal (for use in rare cases where only a small change with + known behavior is added ... eg. a minor bug fix. This + might be to just run the "short" test list, or to run + a single test. Whatever makes sense for the particular case.) + c) python only (for use where the only changes are in the python directory: + run the python testing listed below) + d) regular (regular tests on normal machines if CTSM source is modified) + e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists + and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) + would be run as well) + +In addition, various other tests of the tools, python and perl +infrastructure should be run when appropriate, as described below. + +...] + +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + cheyenne - + + tools-tests (test/tools) (if tools have been changed): + + cheyenne - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - + + [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python + code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system + tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in + either model output or namelists, is: create sym links pointing to the last tag's baseline directory, + named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT + doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to + separately run the clm_pymods test suite, and you can remove the following line.] + + clm_pymods test suite on cheyenne - + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + +Answer changes +-------------- +Changes answers relative to baseline: None + +Other details +------------- +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull/2156) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev140 Originator(s): afoster (Adrianna Foster) Date: Tue Sep 12 14:47:06 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 5ca9ceab70..b5d5170267 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev151 tking 11/02/2023 Move tools to python directory and add tests ctsm5.1.dev140 afoster 09/12/2023 add lai_streams capability for FATES ctsm5.1.dev139 slevis 08/28/2023 Fix problems uncovered by nag -nan tests ctsm5.1.dev138 slevis 08/25/2023 Refactor max_patch_per_col and maxsoil_patches loops diff --git a/python/README.md b/python/README.md index cf3b893084..c40f55c6c7 100644 --- a/python/README.md +++ b/python/README.md @@ -47,7 +47,8 @@ thing, but support different options: 2. via `./run_ctsm_py_tests` You can specify various arguments to this; run `./run_ctsm_py_tests - -h` for details + -h` for details. Please specify either --unit or --sys rather than + not including any arguments. In any configuration where you run the system tests, you need to first execute `module load nco`. diff --git a/python/ctsm/run_ctsm_py_tests.py b/python/ctsm/run_ctsm_py_tests.py index 0542dc41cb..8b39d69afa 100644 --- a/python/ctsm/run_ctsm_py_tests.py +++ b/python/ctsm/run_ctsm_py_tests.py @@ -45,7 +45,10 @@ def main(description): def _commandline_args(description): - """Parse and return command-line arguments""" + """Parse and return command-line arguments + Note that run_ctsm_py_tests is not intended to be + used without argument specifications + """ parser = argparse.ArgumentParser( description=description, formatter_class=argparse.RawTextHelpFormatter ) diff --git a/python/ctsm/site_and_regional/neon_surf_wrapper.py b/python/ctsm/site_and_regional/neon_surf_wrapper.py index c2e5ac61b8..a2cc619a29 100755 --- a/python/ctsm/site_and_regional/neon_surf_wrapper.py +++ b/python/ctsm/site_and_regional/neon_surf_wrapper.py @@ -26,12 +26,10 @@ from __future__ import print_function import os -import sys -import tqdm import logging import argparse import subprocess - +import tqdm import pandas as pd @@ -89,13 +87,13 @@ def execute(command): subprocess.check_call(command, stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT) except subprocess.CalledProcessError as e: - # raise RuntimeError("command '{}' return with error (code {}): {}".format(e.cmd, e.returncode, e.output)) - # print (e.ouput) print(e) def main(): - + """ + Loop through neon sites and execute subset and modify commands + """ args = get_parser().parse_args() if args.verbose: diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index e8706e4cce..104e325617 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -74,6 +74,8 @@ from ctsm.utils import parse_isoduration from ctsm.download_utils import download_file +from ctsm import add_cime_to_path + from standard_script_setup import * logger = logging.getLogger(__name__) diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index 3f2dc6d7f2..b5ded30399 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -57,7 +57,7 @@ def test_modify_site(self): ] # TODO: the above requires a full path instead of site name # because of how run_neon is configured. - # This needs to be fixed/generalized. + # This needs to be fixed in run_neon. parser = get_parser() with self.assertRaises(SystemExit): print( diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index 4dd5aca896..30d996b817 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -13,6 +13,7 @@ from ctsm import unit_testing from ctsm.site_and_regional.run_neon import main, get_parser +from ctsm.path_utils import path_to_ctsm_root # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -44,21 +45,19 @@ def test_one_site(self): # run the run_neon tool sys.argv = [ - "run_neon", + os.path.join( path_to_ctsm_root(), "tools", "site_and_regional", "run_neon" ), "--neon-sites", "BART", "--setup-only", "--output-root", - # "FAKE_DIR" self._tempdir, ] - valid_neon_sites = ["ABBY", "OSBS", "BART"] # ["all"] + valid_neon_sites = ["ABBY", "OSBS", "BART"] parser = get_parser(sys.argv, "description_for_parser", valid_neon_sites) main("") # assert that BART directories were created during setup self.assertTrue("BART" in glob.glob(self._tempdir + "/BART*")[0]) - # self.assertTrue("BART" in glob.glob("BART*")[0]) # TODO: Would also be useful to test the following items: # It might be good to ensure the log files are working as expected? diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index 4c3a473394..98d630447e 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -84,9 +84,10 @@ def test_find_soil_structure(self): Test to ensure that correct attributes are found for find_soil_structure. soil_texture_raw_data_file_name should be found, and test should go through sysexit. """ + surf_file_name = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" surf_file = os.path.join( path_to_ctsm_root(), - "python/ctsm/test/testinputs/surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc", + "python/ctsm/test/testinputs/", surf_file_name, ) f1 = xr.open_dataset(surf_file) self.assertEqual( @@ -140,7 +141,7 @@ def test_check_neon_time(self): self.assertGreater( int(last_abby_download[:4]), 2021, "ABBY download is older than expected" ) - # change back to previous dir once listing.csv file has been created in tempdir and test complete + # change back to previous dir once listing.csv file is created in tempdir and test complete os.chdir(previous_dir) diff --git a/python/ctsm/test/test_unit_run_neon.py b/python/ctsm/test/test_unit_run_neon.py index 2cdcc915ad..a35608e249 100755 --- a/python/ctsm/test/test_unit_run_neon.py +++ b/python/ctsm/test/test_unit_run_neon.py @@ -54,7 +54,7 @@ def test_check_neon_listing(self): self.assertEqual( available_list[1].name, "BART", "available list of actual sites not as expected" ) - # change back to previous dir once listing.csv file has been created in tempdir and test complete + # change to previous dir once listing.csv file is created in tempdir and test complete os.chdir(previous_dir) def test_check_neon_listing_misspelled(self): @@ -68,7 +68,7 @@ def test_check_neon_listing_misspelled(self): self.assertEqual( available_list, [], "available list of incorrect dummy site not as expected" ) - # change back to previous dir once listing.csv file has been created in tempdir and test complete + # change to previous dir once listing.csv file is created in tempdir and test complete os.chdir(previous_dir) From e4d38681df23ccca0ae29581a45f8362574e0630 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 2 Nov 2023 16:18:12 -0600 Subject: [PATCH 1771/2067] black reformat --- python/ctsm/test/test_sys_run_neon.py | 2 +- python/ctsm/test/test_unit_modify_singlept_site_neon.py | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index 30d996b817..b6814ee2bc 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -45,7 +45,7 @@ def test_one_site(self): # run the run_neon tool sys.argv = [ - os.path.join( path_to_ctsm_root(), "tools", "site_and_regional", "run_neon" ), + os.path.join(path_to_ctsm_root(), "tools", "site_and_regional", "run_neon"), "--neon-sites", "BART", "--setup-only", diff --git a/python/ctsm/test/test_unit_modify_singlept_site_neon.py b/python/ctsm/test/test_unit_modify_singlept_site_neon.py index 98d630447e..ecd96357b3 100755 --- a/python/ctsm/test/test_unit_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_unit_modify_singlept_site_neon.py @@ -87,7 +87,8 @@ def test_find_soil_structure(self): surf_file_name = "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc" surf_file = os.path.join( path_to_ctsm_root(), - "python/ctsm/test/testinputs/", surf_file_name, + "python/ctsm/test/testinputs/", + surf_file_name, ) f1 = xr.open_dataset(surf_file) self.assertEqual( From 1d5297e74273efb61fb9362d137a119645e2da2e Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 2 Nov 2023 16:52:59 -0700 Subject: [PATCH 1772/2067] update duration to 25 months and increase wall time to avoid hitting limit --- cime_config/testdefs/testlist_clm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 392c769ab3..e5a930d7a6 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1563,14 +1563,14 @@ - + - + From 1e2c520fe41e4f4f36d0c79d97b7168a14a1ea01 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 07:48:18 -0600 Subject: [PATCH 1773/2067] Updated history_fields*.rst files. --- .../history_fields_fates.rst | 2 ++ .../history_fields_nofates.rst | 20 ++++++++++++------- 2 files changed, 15 insertions(+), 7 deletions(-) diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst index 32f1a353d9..ec10de5080 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_fates.rst @@ -739,6 +739,8 @@ FATES_NPLANT_SEC_PF fates_levpft total PFT-level number of i FATES_NPP_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second kg m-2 s-1 T FATES_NPP_SE_PF fates_levpft total PFT-level NPP in kg carbon per m2 land area per second, secondary patches kg m-2 s-1 T FATES_RECRUITMENT_PF fates_levpft PFT-level recruitment rate in number of individuals per m2 land area per year m-2 yr-1 T +FATES_SEEDS_IN_GRIDCELL_PF fates_levpft Site-level seed mass input from neighboring gridcells per pft kg F +FATES_SEEDS_OUT_GRIDCELL_PF fates_levpft Site-level seed mass output to neighboring gridcells per pft kg F FATES_STOREC_PF fates_levpft total PFT-level stored biomass in kg carbon per m2 land area kg m-2 T FATES_VEGC_PF fates_levpft total PFT-level biomass in kg of carbon per land area kg m-2 T FATES_VEGC_SE_PF fates_levpft total PFT-level biomass in kg of carbon per land area, secondary patches kg m-2 T diff --git a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst index ee2548b6c5..b1ff4d70bd 100644 --- a/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst +++ b/doc/source/users_guide/setting-up-and-running-a-case/history_fields_nofates.rst @@ -4,9 +4,9 @@ CTSM History Fields (nofates) CAUTION: Not all variables are relevant / present for all CTSM cases. Key flags used in this CTSM case: -use_cn = T -use_crop = T -use_fates = F +use_cn = T +use_crop = T +use_fates = F =================================== ================ ============================================================================================== ================================================================= ======= CTSM History Fields @@ -359,10 +359,12 @@ GRAINC - grain C (does not equal yie GRAINC_TO_FOOD - grain C to food gC/m^2/s T GRAINC_TO_FOOD_ANN - grain C to food harvested per calendar year; should only be output annually gC/m^2 F GRAINC_TO_SEED - grain C to seed gC/m^2/s T +GRAINC_TO_SEED_ANN - grain C to seed harvested per calendar year; should only be output annually gC/m^2 F GRAINN - grain N gN/m^2 T -GRAINN_TO_FOOD - grain N to food gN/m^2/s F -GRAINN_TO_FOOD_ANN - grain N to food harvested per calendar year; should only be output annually gN/m^2 F -GRAINN_TO_SEED - grain N to seed gN/m^2/s F +GRAINN_TO_FOOD - grain N to food (not scientifically supported) gN/m^2/s F +GRAINN_TO_FOOD_ANN - grain N to food harvested per calendar year; should only be output annually (not scientificall gN/m^2 F +GRAINN_TO_SEED - grain N to seed (not scientifically supported) gN/m^2/s F +GRAINN_TO_SEED_ANN - grain N to seed harvested per calendar year; should only be output annually (not scientificall gN/m^2 F GRESP_STORAGE - growth respiration storage gC/m^2 F GRESP_STORAGE_TO_XFER - growth respiration shift storage to transfer gC/m^2/s F GRESP_XFER - growth respiration transfer gC/m^2 F @@ -1330,7 +1332,9 @@ W_SCALAR levsoi Moisture (dryness) inhibiti GDDACCUM_PERHARV mxharvests At-harvest accumulated growing degree days past planting date for crop; should only be output ddays F GDDHARV_PERHARV mxharvests Growing degree days (gdd) needed to harvest; should only be output annually ddays F GRAINC_TO_FOOD_PERHARV mxharvests grain C to food per harvest; should only be output annually gC/m^2 F -GRAINN_TO_FOOD_PERHARV mxharvests grain N to food per harvest; should only be output annually gN/m^2 F +GRAINC_TO_SEED_PERHARV mxharvests grain C to seed per harvest; should only be output annually gC/m^2 F +GRAINN_TO_FOOD_PERHARV mxharvests grain N to food per harvest; should only be output annually (not scientifically supported) gN/m^2 F +GRAINN_TO_SEED_PERHARV mxharvests grain N to seed per harvest; should only be output annually (not scientifically supported) gN/m^2 F HARVEST_REASON_PERHARV mxharvests Reason for each crop harvest; should only be output annually 1 = mature; 2 = max season length; 3 = incorrect Dec. 31 sowing; F HDATES mxharvests actual crop harvest dates; should only be output annually day of year F HUI_PERHARV mxharvests At-harvest accumulated heat unit index for crop; should only be output annually ddays F @@ -1339,6 +1343,8 @@ SOWING_REASON_PERHARV mxharvests Reason for sowing of each c SYEARS_PERHARV mxharvests actual sowing years for crops harvested this year; should only be output annually year F SDATES mxsowings actual crop sowing dates; should only be output annually day of year F SOWING_REASON mxsowings Reason for each crop sowing; should only be output annually unitless F +SWINDOW_ENDS mxsowings crop sowing window end dates; should only be output annually day of year F +SWINDOW_STARTS mxsowings crop sowing window start dates; should only be output annually day of year F ALBD numrad surface albedo (direct) proportion T ALBDSF numrad diagnostic snow-free surface albedo (direct) proportion T ALBGRD numrad ground albedo (direct) proportion F From 333c0d64ded98e8e0510f658fb60a9c893ae3a65 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 07:57:28 -0600 Subject: [PATCH 1774/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 45 +++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 46 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 76286ce770..b3f1644af7 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,49 @@ =============================================================== +Tag name: ctsm5.1.dev148 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Fri Nov 3 07:56:43 MDT 2023 +One-line Summary: Add GRAINN outputs + +Purpose and description of changes +---------------------------------- + +In response to a user request for GRAINN_TO_FOOD outputs, this adds *_N_TO_FOOD(_ANN) and *_N_TO_SEED(_ANN) outputs for reproductive N pools. These are off by default, unlike their C counterparts. Note that the results are not scientifically supported, and tests have revealed unrealistic values. (Also adds GRAINC_TO_SEED_ANN output.) + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK (with some fieldlist diffs) + izumi ------- PASS (with some fieldlist diffs) + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +* #2074 (https://github.com/ESCOMP/CTSM/pull/2074) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev147 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Mon Oct 30 16:53:20 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 5e4f816f64..40dc6a2b6a 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev148 samrabin 11/03/2023 Add GRAINN outputs ctsm5.1.dev147 samrabin 10/30/2023 Add sowing window input files ctsm5.1.dev146 glemieux 10/24/2023 FATES cross-grid seed dispersal ctsm5.1.dev145 slevis 10/19/2023 SNICAR snow albedo scheme updates From 239a5524e697e2274f10d206f79c2b91e8d4cdcc Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 3 Nov 2023 10:59:00 -0600 Subject: [PATCH 1775/2067] Change snow_thermal_cond_method to char*25 --- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- src/biogeophys/SoilTemperatureMod.F90 | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 23f6063a97..58c1980232 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2835,7 +2835,7 @@ NiuYang2007: Niu and Yang 2007 SwensonLawrence2012: Swenson and Lawrence 2012 - Parameterization to use for snow thermal conductivity diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index 69f9958efa..bd7efc0788 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -624,7 +624,6 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter use landunit_varcon , only : istice, istwet use column_varcon , only : icol_roof, icol_sunwall, icol_shadewall, icol_road_perv, icol_road_imperv use clm_varctl , only : iulog, snow_thermal_cond_method - ! ! !ARGUMENTS: type(bounds_type) , intent(in) :: bounds From 1f5e0428692434b5b3cc9838e992ed3cd0dc5d1c Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 3 Nov 2023 11:27:49 -0600 Subject: [PATCH 1776/2067] ignore black revision --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index c520df4357..e15f21d8ca 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -12,6 +12,7 @@ b771971e3299c4fa56534b93421f7a2b9c7282fd 8bc4688e52ea23ef688e283698f70a44388373eb 4ee49e3e516ca7dee5df378f65664f93a7db4415 0207bc98dd5c75cd69a0e788bc53e41093712f5c +e4d38681df23ccca0ae29581a45f8362574e0630 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From aa7f32b99d0526ad07656bab73112374f6f368aa Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 3 Nov 2023 12:35:53 -0600 Subject: [PATCH 1777/2067] updated coupling with fates wrap running means --- src/utils/clmfates_interfaceMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c9b1c9a5e7..6f6b2cb6fd 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -3042,7 +3042,7 @@ subroutine WrapUpdateFatesRmean(this, nc, temperature_inst) end do end do - call UpdateFatesRMeansTStep(this%fates(nc)%sites,this%fates(nc)%bc_in) + call UpdateFatesRMeansTStep(this%fates(nc)%sites,this%fates(nc)%bc_in,this%fates(nc)%bc_out) end subroutine WrapUpdateFatesRmean From c4faeab430991cfa3f9111f1f1d13a7759d7bbe8 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 3 Nov 2023 12:40:11 -0600 Subject: [PATCH 1778/2067] Temporarily pointing to fates test branch --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index ea5a15eefb..c9cf9b52e1 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/NGEET/fates -tag = sci.1.68.0_api.28.0.0 +repo_url = https://github.com/rgknox/fates +branch = hetresp_restart_v2 required = True [externals_description] From 389bca9186bb852b11b18ce9df7736f6cb90272c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 2 Nov 2023 14:52:19 -0600 Subject: [PATCH 1779/2067] Make output_dir if needed. --- tools/contrib/ssp_anomaly_forcing_smooth | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index a0b6419744..7bfb0bd384 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -120,10 +120,9 @@ if os.path.exists(datapath): print("Input data directory:" + datapath) else: sys.exit("Could not find input directory: " + datapath) -if os.path.exists(args.output_dir): - print("Output data directory:" + args.output_dir) -else: - sys.exit("Could not find output directory: " + args.output_dir) +if not os.path.exists(args.output_dir): + os.makedirs(args.output_dir) +print("Output data directory:" + args.output_dir) # Settings to run with today = datetime.date.today() From 247305996c17dabdf150fd8d771e9108882aeeb6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 2 Nov 2023 16:27:07 -0600 Subject: [PATCH 1780/2067] Refactor output file setup. --- tools/contrib/ssp_anomaly_forcing_smooth | 183 +++++++++++++---------- 1 file changed, 104 insertions(+), 79 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 7bfb0bd384..774d4e5b78 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -21,6 +21,104 @@ import numpy as np import netCDF4 as netcdf4 +# Adds global attributes, returning hdir and fdir +def add_global_attributes(ds, historydate, histdir, sspdir, num_ens, climo_year, climo_base_nyrs, dpath, dfile, hist_yrstart, hist_yrend, ssp_yrstart, ssp_yrend, timetag): + ds.Created_on = timetag + + ds.title = "anomaly forcing data" + ds.note1 = ( + "Anomaly/scale factors calculated relative to " + + str(climo_year - (climo_base_nyrs - 1) / 2) + + "-" + + str(climo_year + (climo_base_nyrs - 1) / 2) + ) + ds.history = historydate + ": created by " + sys.argv[0] + stdout = os.popen("git describe") + ds.gitdescribe = stdout.read().rstrip() + ds.Source = "CMIP6 CESM simulations" + ds.Conventions = "CF-1.0" + ds.comment = ( + "Monthly scale factors for given SSP scenario compared to a climatology based on" + + " data centered on " + + str(climo_year) + + " over the range given in note1" + ) + ds.number_of_ensemble_members = str(num_ens) + ds.Created_by = getuser() + + for nens in range(num_ens): + hdir = dpath + histdir[nens] + dfile + fdir = dpath + sspdir[nens] + dfile + if nens == 0: + ds.Created_from_historical_dirs = hdir + ds.Created_from_scenario_dirs = fdir + else: + ds.Created_from_historical_dirs += ", " + hdir + ds.Created_from_scenario_dirs += ", " + fdir + + ds.History_years = str(hist_yrstart) + "," + str(hist_yrend) + ds.Scenario_years = str(ssp_yrstart) + "," + str(ssp_yrend) + ds.institution = "National Center for Atmospheric Research" + return hdir,fdir + + +def create_fill_dims(ds, nlat, nlon, ssp_time_units, ssp_time_longname, lon, lat, ssp_time): + ds.createDimension("lat", size=int(nlat)) + ds.createDimension("lon", size=int(nlon)) + ds.createDimension("time", None) + + wtime = ds.createVariable("time", np.float64, ("time",)) + wlat = ds.createVariable("lat", np.float64, ("lat",)) + wlon = ds.createVariable("lon", np.float64, ("lon",)) + + wtime.units = ssp_time_units + wlon.units = "degrees_east" + wlat.units = "degrees_north" + + wtime.long_name = ssp_time_longname + wlon.long_name = "Longitude" + wlat.long_name = "Latitude" + + wlon.mode = "time-invariant" + wlat.mode = "time-invariant" + + # adjust time to middle of month + wtime_offset = 15 - ssp_time[0] + wtime[:] = ssp_time + wtime_offset + + wtime.calendar = "noleap" + wlon[:] = lon + wlat[:] = lat + + return ds + + +def create_fill_ancillary_vars(ds, landfrac, landmask, area): + + wmask = ds.createVariable("landmask", np.int32, ("lat", "lon")) + warea = ds.createVariable("area", np.float64, ("lat", "lon")) + wfrac = ds.createVariable("landfrac", np.float64, ("lat", "lon")) + + warea.units = "km2" + wfrac.units = "unitless" + wmask.units = "unitless" + + warea.long_name = "Grid cell area" + wfrac.long_name = "Grid cell land fraction" + wmask.long_name = "Grid cell land mask" + + warea.mode = "time-invariant" + wfrac.mode = "time-invariant" + wmask.mode = "time-invariant" + + # write to file -------------------------------------------- + wmask[:, :] = landmask + wfrac[:, :] = landfrac + warea[:, :] = area + + return ds + + parser = argparse.ArgumentParser(description="Create anomaly forcing") parser.add_argument( "sspnum", @@ -560,87 +658,14 @@ for f in range(nfields): x = x2.communicate() timetag = x[0].decode("utf-8").strip() - outfile.Created_on = timetag + # Add global attributes and get hdir/fdir + hdir, fdir = add_global_attributes(outfile, historydate, histdir, sspdir, num_ens, climo_year, climo_base_nyrs, dpath, dfile, hist_yrstart, hist_yrend, ssp_yrstart, ssp_yrend, timetag) - outfile.title = "anomaly forcing data" - outfile.note1 = ( - "Anomaly/scale factors calculated relative to " - + str(climo_year - (climo_base_nyrs - 1) / 2) - + "-" - + str(climo_year + (climo_base_nyrs - 1) / 2) - ) - outfile.history = historydate + ": created by " + sys.argv[0] - stdout = os.popen("git describe") - outfile.gitdescribe = stdout.read().rstrip() - outfile.Source = "CMIP6 CESM simulations" - outfile.Conventions = "CF-1.0" - outfile.comment = ( - "Monthly scale factors for given SSP scenario compared to a climatology based on" - + " data centered on " - + str(climo_year) - + " over the range given in note1" - ) - outfile.number_of_ensemble_members = str(num_ens) - outfile.Created_by = getuser() - - for nens in range(num_ens): - hdir = dpath + histdir[nens] + dfile - fdir = dpath + sspdir[nens] + dfile - if nens == 0: - outfile.Created_from_historical_dirs = hdir - outfile.Created_from_scenario_dirs = fdir - else: - outfile.Created_from_historical_dirs += ", " + hdir - outfile.Created_from_scenario_dirs += ", " + fdir - - outfile.History_years = str(hist_yrstart) + "," + str(hist_yrend) - outfile.Scenario_years = str(ssp_yrstart) + "," + str(ssp_yrend) - outfile.institution = "National Center for Atmospheric Research" - - outfile.createDimension("lat", size=int(nlat)) - outfile.createDimension("lon", size=int(nlon)) - outfile.createDimension("time", None) - - wtime = outfile.createVariable("time", np.float64, ("time",)) - wlat = outfile.createVariable("lat", np.float64, ("lat",)) - wlon = outfile.createVariable("lon", np.float64, ("lon",)) - wmask = outfile.createVariable("landmask", np.int32, ("lat", "lon")) - warea = outfile.createVariable("area", np.float64, ("lat", "lon")) - wfrac = outfile.createVariable("landfrac", np.float64, ("lat", "lon")) - wtime.units = ssp_time_units - wlon.units = "degrees_east" - wlat.units = "degrees_north" - warea.units = "km2" - wfrac.units = "unitless" - wmask.units = "unitless" - - # wtime.long_name = 'Months since January '+str(fut_yrstart) - wtime.long_name = ssp_time_longname - wlon.long_name = "Longitude" - wlat.long_name = "Latitude" - warea.long_name = "Grid cell area" - wfrac.long_name = "Grid cell land fraction" - wmask.long_name = "Grid cell land mask" - wlon.mode = "time-invariant" - wlat.mode = "time-invariant" - warea.mode = "time-invariant" - wfrac.mode = "time-invariant" - wmask.mode = "time-invariant" - - wtime.calendar = "noleap" + # Create dimensions + outfile = create_fill_dims(outfile, nlat, nlon, ssp_time_units, ssp_time_longname, lon, lat, ssp_time) - # write to file -------------------------------------------- - # wtime_offset = 0 - # adjust time to middle of month - # wtime_offset = -15 - wtime_offset = 15 - ssp_time[0] - wtime[:] = ssp_time + wtime_offset - wtime.calendar = "noleap" - wlon[:] = lon - wlat[:] = lat - wmask[:, :] = landmask - wfrac[:, :] = landfrac - warea[:, :] = area + # Create and fill ancillary variables () + outfile = create_fill_ancillary_vars(outfile, landfrac, landmask, area) # -- End if on open file if field_out[f] == "sfcWind": From dda9163d52e7930ce863ff4bfd76bd05741f6048 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 13:59:47 -0600 Subject: [PATCH 1781/2067] Refactor creation and filling of forcing variables. --- tools/contrib/ssp_anomaly_forcing_smooth | 112 ++++++++++++----------- 1 file changed, 59 insertions(+), 53 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 774d4e5b78..ae92020981 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -119,6 +119,61 @@ def create_fill_ancillary_vars(ds, landfrac, landmask, area): return ds +def create_fill_forcing(ds, field_out, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld): + if field_out[f] == "sfcWind": + wvar = ds.createVariable( + field_out_wind[0], + np.float64, + ("time", "lat", "lon"), + fill_value=np.float64(1.0e36), + ) + else: + wvar = ds.createVariable( + field_out[f], + np.float64, + ("time", "lat", "lon"), + fill_value=np.float64(1.0e36), + ) + wvar.units = units[f] + wvar.mode = "time-dependent" + if field_out[f] == "sfcWind": + wvar.long_name = str(long_name) + " U component " + anomsf[f] + else: + wvar.long_name = str(long_name) + " " + anomsf[f] + # List of source files + wvar.historical_source_files = "".join(histfiles).replace(hdir, "") + wvar.scenario_source_files = "".join(sspfiles).replace(fdir, "") + + # write to file -------------------------------------------- + if field_out[f] == "sfcWind": + wvar[:, :, :] = anom_fld / np.sqrt(2) + else: + wvar[:, :, :] = anom_fld + + return ds + + +def create_fill_windv(ds, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld): + + wvar = ds.createVariable( + field_out_wind[1], + np.float64, + ("time", "lat", "lon"), + fill_value=np.float64(1.0e36), + ) + wvar.units = units[f] + wvar.cell_methods = "time: mean" + wvar.long_name = str(long_name) + " V component " + anomsf[f] + # List of source files + wvar.historical_source_files = "".join(histfiles).replace(hdir, "") + wvar.scenario_source_files = "".join(sspfiles).replace(fdir, "") + + # write to file -------------------------------------------- + wvar[:, :, :] = anom_fld / np.sqrt(2) + + return ds + + parser = argparse.ArgumentParser(description="Create anomaly forcing") parser.add_argument( "sspnum", @@ -668,63 +723,14 @@ for f in range(nfields): outfile = create_fill_ancillary_vars(outfile, landfrac, landmask, area) # -- End if on open file - if field_out[f] == "sfcWind": - wvar = outfile.createVariable( - field_out_wind[0], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - else: - wvar = outfile.createVariable( - field_out[f], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar.units = units[f] - wvar.mode = "time-dependent" - - # write to file -------------------------------------------- - if field_out[f] == "sfcWind": - wvar.long_name = str(long_name) + " U component " + anomsf[f] - else: - wvar.long_name = str(long_name) + " " + anomsf[f] - - if field_out[f] == "sfcWind": - wvar[:, :, :] = anom_fld / np.sqrt(2) - else: - wvar[:, :, :] = anom_fld + outfile = create_fill_forcing(outfile, field_out, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld) - # List of source files - wvar.historical_source_files = "".join(histfiles).replace(hdir, "") - wvar.scenario_source_files = "".join(sspfiles).replace(fdir, "") - - # create second wind field for V component + # create second wind field for V component if field_out[f] == "sfcWind": - command = 'date "+%y%m%d"' - x2 = subprocess.Popen(command, stdout=subprocess.PIPE, shell="True") - x = x2.communicate() - timetag = x[0].decode("utf-8").strip() - - wvar = outfile.createVariable( - field_out_wind[1], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar.units = units[f] - wvar.cell_methods = "time: mean" - wvar.long_name = str(long_name) + " V component " + anomsf[f] - - # write to file -------------------------------------------- - wvar[:, :, :] = anom_fld / np.sqrt(2) - - # List of source files - wvar.historical_source_files = "".join(histfiles).replace(hdir, "") - wvar.scenario_source_files = "".join(sspfiles).replace(fdir, "") + create_fill_windv(outfile, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld) # -- end if statement for write for V field -------- + break # -- End Loop over forcing fields ------------------------------------ outfile.close() From ca394867da41ed3159eb5e70569062d456969d5c Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 3 Nov 2023 14:37:51 -0600 Subject: [PATCH 1782/2067] bug fix --- src/cpl/share_esmf/cropcalStreamMod.F90 | 59 ++++++++++++++----------- 1 file changed, 32 insertions(+), 27 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 46696eeba9..19fc11d136 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -7,7 +7,8 @@ module cropcalStreamMod ! Read crop calendars from streams ! ! !USES: - use ESMF + use ESMF , only : ESMF_LogFoundError, ESMF_LOGERR_PASSTHRU, ESMF_Finalize + use ESMF , only : ESMF_END_ABORT use shr_kind_mod , only : r8 => shr_kind_r8, CL => shr_kind_CL, CS => shr_kind_CS use dshr_strdata_mod , only : shr_strdata_type use decompMod , only : bounds_type @@ -54,7 +55,7 @@ subroutine cropcal_init(bounds) ! ! Initialize data stream information for crop calendars. ! - ! !USES: + !USES: use shr_mpi_mod , only : shr_mpi_bcast use clm_nlUtilsMod , only : find_nlgroup_name use lnd_comp_shr , only : mesh, model_clock @@ -62,7 +63,7 @@ subroutine cropcal_init(bounds) use controlMod , only : NLFilename ! ! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds ! bounds + type(bounds_type), intent(in) :: bounds ! bounds ! ! !LOCAL VARIABLES: integer :: i,n,ivt ! index @@ -248,12 +249,12 @@ subroutine cropcal_advance( bounds ) ! ! Advance crop calendar streams ! - ! !USES: + !USES: use clm_time_manager , only : get_curr_date use dshr_strdata_mod , only : shr_strdata_advance ! ! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: g, ig ! Indices @@ -298,22 +299,22 @@ end subroutine cropcal_advance !================================================================ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) - ! - ! Interpolate data stream information for crop calendars. - ! - ! !USES: - use CropType , only : crop_type - use PatchType , only : patch - use clm_time_manager, only : get_curr_days_per_year - use pftconMod , only : pftname - use dshr_methods_mod , only : dshr_fldbun_getfldptr - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter - integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches - type(crop_type) , intent(inout) :: crop_inst + ! + ! Interpolate data stream information for crop calendars. + ! + ! !USES: + use CropType , only : crop_type + use PatchType , only : patch + use clm_time_manager, only : get_curr_days_per_year + use pftconMod , only : pftname + use dshr_methods_mod , only : dshr_fldbun_getfldptr + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter + integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches + type(crop_type) , intent(inout) :: crop_inst ! ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig @@ -322,6 +323,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) integer :: n, g integer :: lsize integer :: rc + integer :: begp, endp real(r8), pointer :: dataptr1d_swindow_start(:) real(r8), pointer :: dataptr1d_swindow_end (:) real(r8), pointer :: dataptr1d_cultivar_gdds(:) @@ -342,6 +344,9 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Place all data from each type into a temporary 2d array lsize = bounds%endg - bounds%begg + 1 + begp = bounds%begp + endp= bounds%endp + dayspyr = get_curr_days_per_year() ! Read prescribed sowing window start dates from input files @@ -397,17 +402,17 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) ! Ensure that, if mxsowings > 1, sowing windows are ordered such that ENDS are monotonically increasing. This is necessary because of how get_swindow() works. if (mxsowings > 1) then - if (any(ends(:,2:mxsowings) <= ends(:,1:mxsowings-1) .and. & - ends(:,2:mxsowings) >= 1)) then + if (any(ends(begp:endp,2:mxsowings) <= ends(begp:endp,1:mxsowings-1) .and. & + ends(begp:endp,2:mxsowings) >= 1)) then write(iulog, *) 'Sowing window inputs must be ordered such that end dates are monotonically increasing.' call ESMF_Finalize(endflag=ESMF_END_ABORT) end if end if ! Handle invalid sowing window values - if (any(starts < 1 .or. ends < 1)) then + if (any(starts(begp:endp,:) < 1 .or. ends(begp:endp,:) < 1)) then ! Fail if not allowing fallback to paramfile sowing windows - if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then + if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts(begp:endp,:) < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.' write(iulog, *) 'Affected crops:' do ivt = npcropmin, mxpft @@ -422,11 +427,11 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) call ESMF_Finalize(endflag=ESMF_END_ABORT) ! Fail if a sowing window start date is prescribed without an end date (or vice versa) - else if (any((starts >= 1 .and. ends < 1) .or. (starts < 1 .and. ends >= 1))) then + else if (any((starts(begp:endp,:) >= 1 .and. ends(begp:endp,:) < 1) .or. (starts(begp:endp,:) < 1 .and. ends(begp:endp,:) >= 1))) then write(iulog, *) 'Every prescribed sowing window start date must have a corresponding end date.' call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - end if + end if end if ! use_cropcal_rx_swindows deallocate(dataptr2d_swindow_start) From 8b55281d1b1ee54df621a40cf749f317c8fcdded Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 14:24:51 -0600 Subject: [PATCH 1783/2067] Refactor creation and filling of time. --- tools/contrib/ssp_anomaly_forcing_smooth | 83 ++++++++++-------------- 1 file changed, 36 insertions(+), 47 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index ae92020981..f7acd6a13b 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -62,37 +62,48 @@ def add_global_attributes(ds, historydate, histdir, sspdir, num_ens, climo_year, return hdir,fdir -def create_fill_dims(ds, nlat, nlon, ssp_time_units, ssp_time_longname, lon, lat, ssp_time): - ds.createDimension("lat", size=int(nlat)) - ds.createDimension("lon", size=int(nlon)) - ds.createDimension("time", None) - - wtime = ds.createVariable("time", np.float64, ("time",)) +def create_fill_latlon(ds, lon, lat): + ds.createDimension("lat", int(lat.size)) + ds.createDimension("lon", int(lon.size)) wlat = ds.createVariable("lat", np.float64, ("lat",)) wlon = ds.createVariable("lon", np.float64, ("lon",)) - wtime.units = ssp_time_units wlon.units = "degrees_east" wlat.units = "degrees_north" - - wtime.long_name = ssp_time_longname wlon.long_name = "Longitude" wlat.long_name = "Latitude" - wlon.mode = "time-invariant" wlat.mode = "time-invariant" - # adjust time to middle of month - wtime_offset = 15 - ssp_time[0] - wtime[:] = ssp_time + wtime_offset - - wtime.calendar = "noleap" wlon[:] = lon wlat[:] = lat return ds +def create_fill_time(ds, time, ntime, ssp_time_units=None, ssp_time_longname=None, adj_time=False): + if ntime is not None: + ntime = int(ntime) + ds.createDimension("time", ntime) + + wtime = ds.createVariable("time", np.float64, ("time",)) + + if ssp_time_units is not None: + wtime.units = ssp_time_units + if ssp_time_longname is not None: + wtime.long_name = ssp_time_longname + wtime.calendar = "noleap" + + # adjust time to middle of month + if adj_time: + wtime_offset = 15 - time[0] + wtime[:] = time + wtime_offset + else: + wtime[:] = time + + return ds + + def create_fill_ancillary_vars(ds, landfrac, landmask, area): wmask = ds.createVariable("landmask", np.int32, ("lat", "lon")) @@ -392,6 +403,8 @@ nfields = len(field_in) output_format = "NETCDF3_64BIT_DATA" # -- Loop over forcing fields ------------------------------------ + + for f in range(nfields): # -- Loop over ensemble members ------------------------------ @@ -633,28 +646,15 @@ for f in range(nfields): "w", format=output_format, ) - w.createDimension("lat", int(nlat)) - w.createDimension("lon", int(nlon)) - w.createDimension("time", int(nmo)) - - wtime = w.createVariable("time", np.float64, ("time",)) - wlat = w.createVariable("lat", np.float64, ("lat",)) - wlon = w.createVariable("lon", np.float64, ("lon",)) + w = create_fill_latlon(w, lon, lat) + w = create_fill_time(w, time[0:12], nmo) + wvar = w.createVariable( field_out[f], np.float64, ("time", "lat", "lon"), fill_value=np.float64(1.0e36), ) - wtime[ - :, - ] = time[0:12] - wlon[ - :, - ] = lon - wlat[ - :, - ] = lat wvar[:, :, :] = climo w.close() @@ -664,13 +664,9 @@ for f in range(nfields): "w", format=output_format, ) - w.createDimension("lat", int(nlat)) - w.createDimension("lon", int(nlon)) - w.createDimension("time", int(tm)) - - wtime = w.createVariable("time", np.float64, ("time",)) - wlat = w.createVariable("lat", np.float64, ("lat",)) - wlon = w.createVariable("lon", np.float64, ("lon",)) + w = create_fill_latlon(w, lon, lat) + w = create_fill_time(w, time, tm) + wvar = w.createVariable( field_out[f], np.float64, @@ -683,14 +679,6 @@ for f in range(nfields): ("time", "lat", "lon"), fill_value=np.float64(1.0e36), ) - - wtime[:] = time - wlon[ - :, - ] = lon - wlat[ - :, - ] = lat wvar[:, :, :] = temp_fld wvar2[:, :, :] = stemp_fld w.close() @@ -717,7 +705,8 @@ for f in range(nfields): hdir, fdir = add_global_attributes(outfile, historydate, histdir, sspdir, num_ens, climo_year, climo_base_nyrs, dpath, dfile, hist_yrstart, hist_yrend, ssp_yrstart, ssp_yrend, timetag) # Create dimensions - outfile = create_fill_dims(outfile, nlat, nlon, ssp_time_units, ssp_time_longname, lon, lat, ssp_time) + outfile = create_fill_latlon(outfile, lon, lat) + outfile = create_fill_time(outfile, ssp_time, None, ssp_time_units=ssp_time_units, ssp_time_longname=ssp_time_longname, adj_time=True) # Create and fill ancillary variables () outfile = create_fill_ancillary_vars(outfile, landfrac, landmask, area) From 8c994b32a4d8fce59c7cfa95bb1078dabbd75133 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 15:11:00 -0600 Subject: [PATCH 1784/2067] Allow alternate flags with hyphens instead of underscores. --- tools/contrib/ssp_anomaly_forcing_smooth | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index f7acd6a13b..647f96bf4f 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -195,12 +195,14 @@ parser.add_argument( ) parser.add_argument( "--write_climo", + "--write-climo", help="write out climatology files and exit", action="store_true", default=False, ) parser.add_argument( "--print_ssps", + "--print-ssps", help="Just print out directory names and exit", action="store_true", default=False, From 904266ad28a957ef93a829f0e195f949f1f67ea5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 15:26:19 -0600 Subject: [PATCH 1785/2067] Create and fill lat/lon in separate calls of function. --- tools/contrib/ssp_anomaly_forcing_smooth | 34 +++++++++++++----------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index 647f96bf4f..fadebbf89a 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -62,22 +62,21 @@ def add_global_attributes(ds, historydate, histdir, sspdir, num_ens, climo_year, return hdir,fdir -def create_fill_latlon(ds, lon, lat): - ds.createDimension("lat", int(lat.size)) - ds.createDimension("lon", int(lon.size)) - wlat = ds.createVariable("lat", np.float64, ("lat",)) - wlon = ds.createVariable("lon", np.float64, ("lon",)) +def create_fill_latlon(ds, data, var_name): - wlon.units = "degrees_east" - wlat.units = "degrees_north" - wlon.long_name = "Longitude" - wlat.long_name = "Latitude" - wlon.mode = "time-invariant" - wlat.mode = "time-invariant" + ds.createDimension(var_name, int(data.size)) + wl = ds.createVariable(var_name, np.float64, (var_name,)) - wlon[:] = lon - wlat[:] = lat + if var_name == "lat": + wl.units = "degrees_north" + wl.long_name = "Latitude" + elif var_name == "lon": + wl.units = "degrees_east" + wl.long_name = "Longitude" + wl.mode = "time-invariant" + wl[:] = data + return ds @@ -648,7 +647,8 @@ for f in range(nfields): "w", format=output_format, ) - w = create_fill_latlon(w, lon, lat) + w = create_fill_latlon(w, lat, "lat") + w = create_fill_latlon(w, lon, "lon") w = create_fill_time(w, time[0:12], nmo) wvar = w.createVariable( @@ -666,7 +666,8 @@ for f in range(nfields): "w", format=output_format, ) - w = create_fill_latlon(w, lon, lat) + w = create_fill_latlon(w, lat, "lat") + w = create_fill_latlon(w, lon, "lon") w = create_fill_time(w, time, tm) wvar = w.createVariable( @@ -707,7 +708,8 @@ for f in range(nfields): hdir, fdir = add_global_attributes(outfile, historydate, histdir, sspdir, num_ens, climo_year, climo_base_nyrs, dpath, dfile, hist_yrstart, hist_yrend, ssp_yrstart, ssp_yrend, timetag) # Create dimensions - outfile = create_fill_latlon(outfile, lon, lat) + outfile = create_fill_latlon(outfile, lat, "lat") + outfile = create_fill_latlon(outfile, lon, "lon") outfile = create_fill_time(outfile, ssp_time, None, ssp_time_units=ssp_time_units, ssp_time_longname=ssp_time_longname, adj_time=True) # Create and fill ancillary variables () From b626e88a2e930e61e440783cbbadaccae06ed81a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 3 Nov 2023 15:36:01 -0600 Subject: [PATCH 1786/2067] Small corrections for tests to run --- bld/CLMBuildNamelist.pm | 2 +- src/biogeophys/SoilTemperatureMod.F90 | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 9a039b1cfc..116a585270 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2034,7 +2034,7 @@ sub setup_logic_snow { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_thermal_cond_method' ); my $var = $nl->get_value('snow_thermal_cond_method'); - if ( $var ne 'Jordan1991' && $var ne 'Sturm1997' ) { + if ( $var ne "'Jordan1991'" && $var ne "'Sturm1997'" ) { $log->fatal_error("$var is incorrect entry for the namelist variable snow_thermal_cond_method; expected Jordan1991 or Sturm1997"); } diff --git a/src/biogeophys/SoilTemperatureMod.F90 b/src/biogeophys/SoilTemperatureMod.F90 index bd7efc0788..0dc8876d24 100644 --- a/src/biogeophys/SoilTemperatureMod.F90 +++ b/src/biogeophys/SoilTemperatureMod.F90 @@ -619,6 +619,7 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter ! flux from the interface to the node j+1. ! ! !USES: + use shr_log_mod , only : errMsg => shr_log_errMsg use clm_varpar , only : nlevsno, nlevgrnd, nlevurb, nlevsoi, nlevmaxurbgrnd use clm_varcon , only : denh2o, denice, tfrz, tkwat, tkice, tkair, cpice, cpliq, thk_bedrock, csol_bedrock use landunit_varcon , only : istice, istwet @@ -648,6 +649,8 @@ subroutine SoilThermProp (bounds, num_urbanc, filter_urbanc, num_nolakec, filter real(r8) :: fl ! volume fraction of liquid or unfrozen water to total water real(r8) :: satw ! relative total water content of soil. real(r8) :: zh2osfc + + character(len=*),parameter :: subname = 'SoilThermProp' !----------------------------------------------------------------------- call t_startf( 'SoilThermProp' ) From 37c2de9635917ccfcff72322f93a06846f121b48 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 3 Nov 2023 19:53:46 -0600 Subject: [PATCH 1787/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 73 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index b3f1644af7..f82a6c17b8 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,76 @@ =============================================================== +Tag name: ctsm5.1.dev149 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Fri Nov 3 19:52:44 MDT 2023 +One-line Summary: Rearrange leaf/stem "harvest" and fix soil gas diffusivity + +Purpose and description of changes +---------------------------------- + +1. Rearranges the calculation of how much leaf and livestem C and N goes to biofuels vs. litter, in anticipation of adding crop residue removal. Also makes the affected subroutine easier to read. +2. Resolves two bugs in the calculation of diffusion in SoilBiogeochemNitrifDenitrif(). Also does some rearranging and renaming to improve clarity. +3. Includes unrelated documentation updates from Documentation Week Oct. 2023. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[X] clm5_1 + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): +* Resolves #1990: Problems about the soil gas diffusivity in methane code and nitrification-denitrification mod (https://github.com/ESCOMP/CTSM/issues/1990) + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- DIFF + izumi ------- DIFF + + +Answer changes +-------------- + +Changes answers relative to baseline: + + Summarize any changes to answers, i.e., + - what code configurations: virtually all + - what platforms/compilers: cheyenne and izumi; intel, gnu, and nag + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff/same climate + + If bitwise differences were observed, how did you show they were no worse + than roundoff? Roundoff differences means one or more lines of code change results + only by roundoff level (because order of operation changes for example). Roundoff + changes to state fields usually grow to greater than roundoff as the simulation progresses. + + * Roundoff-level differences were observed for the rearrangement of leaf/stem "harvest" code. + * Notable differences were observed for the soil gas diffusivity bugfix, but only for output variable diffus. + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +* #2154: Rearrange calculation of leaf/livestem C and N to biofuels/litter (https://github.com/ESCOMP/CTSM/pull/2154) +* #2157: Soil gas diffusivity bugfix (https://github.com/ESCOMP/CTSM/pull/2157) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev148 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Fri Nov 3 07:56:43 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 40dc6a2b6a..31b5572594 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev149 samrabin 11/03/2023 Rearrange leaf/stem "harvest" and fix soil gas diffusivity ctsm5.1.dev148 samrabin 11/03/2023 Add GRAINN outputs ctsm5.1.dev147 samrabin 10/30/2023 Add sowing window input files ctsm5.1.dev146 glemieux 10/24/2023 FATES cross-grid seed dispersal From 2b45ef4bd559a2d76ab15ff66cbbfc9021523a3f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 5 Nov 2023 20:57:24 -0700 Subject: [PATCH 1788/2067] Refactor add_to_dataset() out of create_fill_forcing(). --- tools/contrib/ssp_anomaly_forcing_smooth | 128 +++++++++-------------- 1 file changed, 52 insertions(+), 76 deletions(-) diff --git a/tools/contrib/ssp_anomaly_forcing_smooth b/tools/contrib/ssp_anomaly_forcing_smooth index fadebbf89a..362e47c67d 100755 --- a/tools/contrib/ssp_anomaly_forcing_smooth +++ b/tools/contrib/ssp_anomaly_forcing_smooth @@ -129,58 +129,58 @@ def create_fill_ancillary_vars(ds, landfrac, landmask, area): return ds -def create_fill_forcing(ds, field_out, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld): - if field_out[f] == "sfcWind": - wvar = ds.createVariable( - field_out_wind[0], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - else: - wvar = ds.createVariable( - field_out[f], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar.units = units[f] - wvar.mode = "time-dependent" - if field_out[f] == "sfcWind": - wvar.long_name = str(long_name) + " U component " + anomsf[f] - else: - wvar.long_name = str(long_name) + " " + anomsf[f] - # List of source files - wvar.historical_source_files = "".join(histfiles).replace(hdir, "") - wvar.scenario_source_files = "".join(sspfiles).replace(fdir, "") - - # write to file -------------------------------------------- - if field_out[f] == "sfcWind": - wvar[:, :, :] = anom_fld / np.sqrt(2) - else: - wvar[:, :, :] = anom_fld +def add_to_dataset(ds, var_name, data, units=None, mode=None, historical_source_files=None, scenario_source_files=None, long_name=None, cell_methods=None): + dims = ("time", "lat", "lon") + data_type = np.float64 + + wvar = ds.createVariable( + var_name, + data_type, + dims, + fill_value=data_type(1.0e36), + ) + + wvar[:, :, :] = data + + if units is not None: + wvar.units = units + if mode is not None: + wvar.mode = mode + if historical_source_files is not None: + wvar.historical_source_files = historical_source_files + if scenario_source_files is not None: + wvar.scenario_source_files = scenario_source_files + if long_name is not None: + wvar.long_name = long_name + if cell_methods is not None: + wvar.cell_methods = cell_methods return ds -def create_fill_windv(ds, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld): - - wvar = ds.createVariable( - field_out_wind[1], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar.units = units[f] - wvar.cell_methods = "time: mean" - wvar.long_name = str(long_name) + " V component " + anomsf[f] - # List of source files - wvar.historical_source_files = "".join(histfiles).replace(hdir, "") - wvar.scenario_source_files = "".join(sspfiles).replace(fdir, "") - - # write to file -------------------------------------------- - wvar[:, :, :] = anom_fld / np.sqrt(2) +def create_fill_forcing(ds, field_out, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld): + + historical_source_files = "".join(histfiles).replace(hdir, "") + scenario_source_files = "".join(sspfiles).replace(fdir, "") + mode = "time-dependent" + + if field_out[f] == "sfcWind": + long_name = str(long_name) + " U component " + anomsf[f] + var_name = field_out_wind[0] + data = anom_fld / np.sqrt(2) + else: + long_name = str(long_name) + " " + anomsf[f] + var_name = field_out[f] + data = anom_fld + # Was missing cell_methods attribute in original + ds = add_to_dataset(ds, var_name, data, units=units[f], mode=mode, historical_source_files=historical_source_files, scenario_source_files=scenario_source_files, long_name=long_name) + if field_out[f] == "sfcWind": + long_name = long_name.replace("U component", "V component") + var_name = field_out_wind[1] + # Was missing mode attribute in original + ds = add_to_dataset(ds, var_name, data, units=units[f], historical_source_files=historical_source_files, scenario_source_files=scenario_source_files, long_name=long_name, cell_methods="time: mean") + return ds @@ -651,13 +651,7 @@ for f in range(nfields): w = create_fill_latlon(w, lon, "lon") w = create_fill_time(w, time[0:12], nmo) - wvar = w.createVariable( - field_out[f], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar[:, :, :] = climo + add_to_dataset(w, field_out[f], climo) w.close() # Use NetCDF4 format, because using older NetCDF formats are too slow @@ -670,21 +664,10 @@ for f in range(nfields): w = create_fill_latlon(w, lon, "lon") w = create_fill_time(w, time, tm) - wvar = w.createVariable( - field_out[f], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar2 = w.createVariable( - "smooth_" + field_out[f], - np.float64, - ("time", "lat", "lon"), - fill_value=np.float64(1.0e36), - ) - wvar[:, :, :] = temp_fld - wvar2[:, :, :] = stemp_fld + add_to_dataset(w, field_out[f], temp_fld) + add_to_dataset(w, "smooth_" + field_out[f], stemp_fld) w.close() + print("Exit early after writing out climatology\n\n") sys.exit() @@ -712,19 +695,12 @@ for f in range(nfields): outfile = create_fill_latlon(outfile, lon, "lon") outfile = create_fill_time(outfile, ssp_time, None, ssp_time_units=ssp_time_units, ssp_time_longname=ssp_time_longname, adj_time=True) - # Create and fill ancillary variables () + # Create and fill ancillary variables outfile = create_fill_ancillary_vars(outfile, landfrac, landmask, area) # -- End if on open file outfile = create_fill_forcing(outfile, field_out, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld) - # create second wind field for V component - if field_out[f] == "sfcWind": - create_fill_windv(outfile, units, anomsf, field_out_wind, f, hdir, fdir, histfiles, sspfiles, long_name, anom_fld) - - # -- end if statement for write for V field -------- - break - # -- End Loop over forcing fields ------------------------------------ outfile.close() From 61d746faf51a855dbd7ef46d41a4f85d4757d892 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 6 Nov 2023 11:04:48 -0700 Subject: [PATCH 1789/2067] Move comments and add whitespace. --- src/biogeochem/CNVegCarbonFluxType.F90 | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index c7aa3469e2..1c5fb60d31 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -3729,8 +3729,8 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) ! BACKWARDS_COMPATIBILITY(wjs/ssr, 2022-06-10) See note in CallRestartvarDimOK() if (CallRestartvarDimOK(ncid, flag, 'mxharvests')) then do k = repr_grain_min, repr_grain_max - data2dptr => this%repr_grainc_to_food_perharv_patch(:,:,k) ! e.g., grainc_to_food_perharv + data2dptr => this%repr_grainc_to_food_perharv_patch(:,:,k) varname = get_repr_rest_fname(k)//'c_to_food_perharv' call restartvar(ncid=ncid, flag=flag, varname=varname, & xtype=ncd_double, & @@ -3746,8 +3746,8 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) end if do k = repr_grain_min, repr_grain_max - data1dptr => this%repr_grainc_to_food_thisyr_patch(:,k) ! e.g., grainc_to_food_thisyr + data1dptr => this%repr_grainc_to_food_thisyr_patch(:,k) varname = get_repr_rest_fname(k)//'c_to_food_thisyr' call restartvar(ncid=ncid, flag=flag, varname=varname, & xtype=ncd_double, & @@ -3755,8 +3755,9 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) long_name=get_repr_longname(k)//' C to food per calendar year; should only be output annually', & units='gC/m2', & interpinic_flag='interp', readvar=readvar, data=data1dptr) - data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) + ! e.g., grainc_to_seed_thisyr + data1dptr => this%repr_grainc_to_seed_thisyr_patch(:,k) varname = get_repr_rest_fname(k)//'c_to_seed_thisyr' call restartvar(ncid=ncid, flag=flag, varname=varname, & xtype=ncd_double, & From 32f2907e6de8d4870623b2e75235420802f67688 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 6 Nov 2023 11:08:29 -0700 Subject: [PATCH 1790/2067] Save repr_grainc_to_seed_perharv_patch for restart. --- src/biogeochem/CNVegCarbonFluxType.F90 | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 1c5fb60d31..298e7b3053 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -3742,6 +3742,20 @@ subroutine RestartBulkOnly ( this, bounds, ncid, flag ) readvar=readvar, & scale_by_thickness=.false., & interpinic_flag='interp', data=data2dptr) + + ! e.g., grainc_to_seed_perharv + data2dptr => this%repr_grainc_to_seed_perharv_patch(:,:,k) + varname = get_repr_rest_fname(k)//'c_to_seed_perharv' + call restartvar(ncid=ncid, flag=flag, varname=varname, & + xtype=ncd_double, & + dim1name='pft', & + dim2name='mxharvests', & + switchdim=.true., & + long_name=get_repr_longname(k)//' C to seed per harvest; should only be output annually', & + units='gC/m2', & + readvar=readvar, & + scale_by_thickness=.false., & + interpinic_flag='interp', data=data2dptr) end do end if From cc43a1a73bf8dd12995bfdd28f137ac09e9680d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 6 Nov 2023 11:12:01 -0700 Subject: [PATCH 1791/2067] Save sowing window dates for restart. --- src/biogeochem/CropType.F90 | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 29c4717ab3..e8de7059c0 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -655,6 +655,16 @@ subroutine Restart(this, bounds, ncid, cnveg_state_inst, flag) long_name='crop sowing dates for this patch this year', units='day of year', & scale_by_thickness=.false., & interpinic_flag='interp', readvar=readvar, data=this%sdates_thisyr_patch) + call restartvar(ncid=ncid, flag=flag, varname='swindow_starts_thisyr_patch', xtype=ncd_double, & + dim1name='pft', dim2name='mxsowings', switchdim=.true., & + long_name='sowing window start dates for this patch this year', units='day of year', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%swindow_starts_thisyr_patch) + call restartvar(ncid=ncid, flag=flag, varname='swindow_ends_thisyr_patch', xtype=ncd_double, & + dim1name='pft', dim2name='mxsowings', switchdim=.true., & + long_name='sowing window end dates for this patch this year', units='day of year', & + scale_by_thickness=.false., & + interpinic_flag='interp', readvar=readvar, data=this%swindow_ends_thisyr_patch) ! Fill variable(s) derived from read-in variable(s) if (flag == 'read' .and. readvar) then do p = bounds%begp,bounds%endp From 1851b5d4ceec3ad9339058ac66dbdb8bc9ba8bf4 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 6 Nov 2023 14:09:26 -0700 Subject: [PATCH 1792/2067] Updated fates tag --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index c9cf9b52e1..61e2a29f85 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -branch = hetresp_restart_v2 +repo_url = https://github.com/NGEET/fates +tag = sci.1.68.1_api.29.0.0 required = True [externals_description] From 82ac5d64cab397043bc4dd320b7d00c4e4cdb263 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Mon, 6 Nov 2023 14:16:40 -0700 Subject: [PATCH 1793/2067] remove extraneous ws --- src/cpl/share_esmf/cropcalStreamMod.F90 | 44 ++++++++++++------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/src/cpl/share_esmf/cropcalStreamMod.F90 b/src/cpl/share_esmf/cropcalStreamMod.F90 index 19fc11d136..0ea63f2c6d 100644 --- a/src/cpl/share_esmf/cropcalStreamMod.F90 +++ b/src/cpl/share_esmf/cropcalStreamMod.F90 @@ -55,7 +55,7 @@ subroutine cropcal_init(bounds) ! ! Initialize data stream information for crop calendars. ! - !USES: + ! !USES: use shr_mpi_mod , only : shr_mpi_bcast use clm_nlUtilsMod , only : find_nlgroup_name use lnd_comp_shr , only : mesh, model_clock @@ -63,7 +63,7 @@ subroutine cropcal_init(bounds) use controlMod , only : NLFilename ! ! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds ! bounds + type(bounds_type), intent(in) :: bounds ! bounds ! ! !LOCAL VARIABLES: integer :: i,n,ivt ! index @@ -249,12 +249,12 @@ subroutine cropcal_advance( bounds ) ! ! Advance crop calendar streams ! - !USES: + ! !USES: use clm_time_manager , only : get_curr_date use dshr_strdata_mod , only : shr_strdata_advance ! ! !ARGUMENTS: - type(bounds_type), intent(in) :: bounds + type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: integer :: g, ig ! Indices @@ -299,22 +299,22 @@ end subroutine cropcal_advance !================================================================ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) - ! - ! Interpolate data stream information for crop calendars. - ! - ! !USES: - use CropType , only : crop_type - use PatchType , only : patch - use clm_time_manager, only : get_curr_days_per_year - use pftconMod , only : pftname - use dshr_methods_mod , only : dshr_fldbun_getfldptr - ! - ! !ARGUMENTS: - implicit none - type(bounds_type) , intent(in) :: bounds - integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter - integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches - type(crop_type) , intent(inout) :: crop_inst + ! + ! Interpolate data stream information for crop calendars. + ! + ! !USES: + use CropType , only : crop_type + use PatchType , only : patch + use clm_time_manager, only : get_curr_days_per_year + use pftconMod , only : pftname + use dshr_methods_mod , only : dshr_fldbun_getfldptr + ! + ! !ARGUMENTS: + implicit none + type(bounds_type) , intent(in) :: bounds + integer , intent(in) :: num_pcropp ! number of prog. crop patches in filter + integer , intent(in) :: filter_pcropp(:) ! filter for prognostic crop patches + type(crop_type) , intent(inout) :: crop_inst ! ! !LOCAL VARIABLES: integer :: ivt, p, ip, ig @@ -410,7 +410,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) end if ! Handle invalid sowing window values - if (any(starts(begp:endp,:) < 1 .or. ends(begp:endp,:) < 1)) then + if (any(starts(begp:endp,:) < 1 .or. ends(begp:endp,:) < 1)) then ! Fail if not allowing fallback to paramfile sowing windows if ((.not. allow_invalid_swindow_inputs) .and. any(all(starts(begp:endp,:) < 1, dim=2) .and. patch%wtgcell > 0._r8 .and. patch%itype >= npcropmin)) then write(iulog, *) 'At least one crop in one gridcell has invalid prescribed sowing window start date(s). To ignore and fall back to paramfile sowing windows, set allow_invalid_swindow_inputs to .true.' @@ -431,7 +431,7 @@ subroutine cropcal_interp(bounds, num_pcropp, filter_pcropp, crop_inst) write(iulog, *) 'Every prescribed sowing window start date must have a corresponding end date.' call ESMF_Finalize(endflag=ESMF_END_ABORT) end if - end if + end if end if ! use_cropcal_rx_swindows deallocate(dataptr2d_swindow_start) From 9c3ea99041b5369ba2326ad405090732ea58c3c2 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 6 Nov 2023 14:21:52 -0700 Subject: [PATCH 1794/2067] Update changelogs for fates npp fix --- doc/ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 75 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index f82a6c17b8..a5eba5e49e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,78 @@ =============================================================== +Tag name: ctsm5.1.dev150 +Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153) +Date: Mon Nov 6 14:12:37 MST 2023 +One-line Summary: FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM. + +Purpose and description of changes +---------------------------------- + +This set of changes accomodates an API change on the FATES side of the code. Those changes are needed +to accomodate a bug-fix in E3SM. These changes will also accomodate correct coupling with free-living nitrogen +fixation when it is enabled in clm-fates. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +none + +Bugs fixed or introduced +------------------------ + +Supports fixes FATES issues: +https://github.com/NGEET/fates/issues/1113 +https://github.com/NGEET/fates/issues/1106 + +CTSM issues fixed (include CTSM Issue #): none + +Known bugs introduced in this tag (include issue #): + +Notes of particular relevance for users +--------------------------------------- + +none + +Notes of particular relevance for developers: +--------------------------------------------- + +This set of changes is introduced, while there is a known test failure in: +ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial + +This is documented in issue: 2236 and a fix is slated for integration. The nature of the changes +in this PR where obviously orthogonal to the issue. + +Changes to tests or testing: none + + +Testing summary: +---------------- + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- ok + izumi ------- ok + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- ok + + +Answer changes +-------------- + +no answer changes + +Other details +------------- + +none + +Pull Requests that document the changes (include PR ids): + +https://github.com/ESCOMP/CTSM/pull/2231 + + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev149 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Fri Nov 3 19:52:44 MDT 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 31b5572594..ecaa21c598 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev150 rgknox 11/06/2023 FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM. ctsm5.1.dev149 samrabin 11/03/2023 Rearrange leaf/stem "harvest" and fix soil gas diffusivity ctsm5.1.dev148 samrabin 11/03/2023 Add GRAINN outputs ctsm5.1.dev147 samrabin 10/30/2023 Add sowing window input files From d1b7b018f5be4ad6a0239060b90ca7d145ee4d4e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 1 Nov 2023 16:26:40 -0600 Subject: [PATCH 1795/2067] Add optional -c/--crop-list arg to regrid_ggcmi_shdates. --- .../crop_calendars/regrid_ggcmi_shdates.py | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index d864328e2e..70ce3953c8 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -72,7 +72,7 @@ def import_coord_2d(ds, coordName, varName): def main( - regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory, extension + regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory, extension, crop_list ): print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") @@ -89,6 +89,10 @@ def main( os.remove(templatefile) template_ds_in = xr.open_dataset(regrid_template_file_in) + + # Process crop list + if crop_list is not None: + crop_list = crop_list.split(",") # Import and format latitude if "lat" in template_ds_in: @@ -135,7 +139,11 @@ def main( raise FileNotFoundError(f"No files found matching {os.path.join(os.getcwd(), pattern)}") input_files.sort() for f in input_files: - print(" " + f[0:6]) + this_crop = f[0:6] + if crop_list is not None and this_crop not in crop_list: + continue + + print(" " + this_crop) f2 = os.path.join(regrid_output_directory, f) f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") @@ -189,6 +197,12 @@ def main( help=f"File extension of raw GGCMI sowing/harvest date files (default {default}).", default=default, ) + parser.add_argument( + "-c", + "--crop-list", + help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", + default=None, + ) # Get arguments args = parser.parse_args(sys.argv[1:]) @@ -202,4 +216,5 @@ def main( os.path.realpath(args.regrid_input_directory), os.path.realpath(args.regrid_output_directory), args.extension, + args.crop_list, ) From da6f274e939a93c876bbbda9d04cb23a6134e03a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 1 Nov 2023 16:32:50 -0600 Subject: [PATCH 1796/2067] regrid_ggcmi_shdates: Add leading . to extension if needed. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 70ce3953c8..177237cfb3 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -93,6 +93,8 @@ def main( # Process crop list if crop_list is not None: crop_list = crop_list.split(",") + if extension[0] != ".": + extension = "." + extension # Import and format latitude if "lat" in template_ds_in: From 3840c780636a1fbce654d277064421cb64237a35 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 09:35:47 -0700 Subject: [PATCH 1797/2067] Start files for system/unit testing regrid_ggcmi_shdates. --- .../test/test_sys_regrid_ggcmi_shdates.py | 525 ++++++++++++++++++ .../test/test_unit_regrid_ggcmi_shdates.py | 97 ++++ ...wh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 | Bin 0 -> 139563 bytes 3 files changed, 622 insertions(+) create mode 100755 python/ctsm/test/test_sys_regrid_ggcmi_shdates.py create mode 100755 python/ctsm/test/test_unit_regrid_ggcmi_shdates.py create mode 100644 python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py new file mode 100755 index 0000000000..765ec5023b --- /dev/null +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -0,0 +1,525 @@ +#!/usr/bin/env python3 + +"""System tests for fsurdat_modifier + +""" + +import os +import re + +import unittest +import tempfile +import shutil +import sys + +import xarray as xr +import numpy as np + +from ctsm.path_utils import path_to_ctsm_root +from ctsm import unit_testing +from ctsm.crop_calendars.regrid_ggcmi_shdates import main as regrid_ggcmi_shdates + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + + +class TestRegridGgcmiShdates(unittest.TestCase): + """System tests for regrid_ggcmi_shdates""" + + def setUp(self): + # Where in the /testinputs directory are the raw crop calendar file(s)? + testinputs_cc_path = os.path.join(path_to_ctsm_root(), "python", "ctsm", "test", "testinputs", "cropcals") + self._testinputs_cc_path = testinputs_cc_path + + # Make /_tempdir for use by these tests. + self._tempdir = tempfile.mkdtemp() + + # Obtain path for the directory being created in /_tempdir + self._regridded_cropcals = os.path.join(self._tempdir, "regridded_cropcals") + + # What extension do the raw crop calendar file(s) have? + self._extension = ".nc4" + + # Which crop(s) should we test? (comma-separated string) + self._crop_list = "swh_rf" + + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + # def test_no_files_given_fail(self): + # """ + # Test that if no input or output files are given that it will gracefully fail + # """ + # self._cfg_file_path = os.path.join( + # self._testinputs_cc_path, "modify_fsurdat_short_nofiles.cfg" + # ) + # sys.argv = ["fsurdat_modifier", self._cfg_file_path] + # parser = fsurdat_modifier_arg_process() + # with self.assertRaisesRegex(SystemExit, "must contain item 'fsurdat_in'"): + # fsurdat_modifier(parser) + + # def test_short_config(self): + # """ + # Test that a short config file works + # """ + # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_short.cfg") + # sys.argv = ["fsurdat_modifier", self._cfg_file_path] + # parser = fsurdat_modifier_arg_process() + # fsurdat_out = ( + # "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" + # ) + # if os.path.exists(fsurdat_out): + # os.remove(fsurdat_out) + # fsurdat_modifier(parser) + # # Run it again with the overwrite option so that it will overwrite the file just created + # sys.argv = ["fsurdat_modifier", self._cfg_file_path, "--overwrite"] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + # # Cleanup + # os.remove(fsurdat_out) + + # def test_short_infile_both_cmdline_and_cfg(self): + # """ + # Test that a graceful fail happens when the infile + # is given both in the command line and the config file + # """ + # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_short.cfg") + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # "-i", + # "specify_fsurdat_in_on_cmd_line.nc", + # ] + # parser = fsurdat_modifier_arg_process() + # with self.assertRaisesRegex( + # SystemExit, + # "fsurdat_in is specified in both the command line and the config file, pick one", + # ): + # fsurdat_modifier(parser) + + # def test_short_outfile_both_cmdline_and_cfg(self): + # """ + # Test that a graceful fail happens when the outfile is given + # both in the command line and the config file + # """ + # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_short.cfg") + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # "-o", + # "specify_fsurdat_out_on_cmd_line.nc", + # ] + # parser = fsurdat_modifier_arg_process() + # with self.assertRaisesRegex( + # SystemExit, + # "fsurdat_out is specified in both the command line and the config file, pick one", + # ): + # fsurdat_modifier(parser) + + # def test_opt_sections(self): + # """ + # Test that a simple file with the optional sections works + # """ + # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_opt_sections.cfg") + # outfile = os.path.join( + # self._tempdir, + # "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_output_urban.nc", + # ) + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # "-i", + # os.path.join( + # self._testinputs_cc_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" + # ), + # "-o", + # outfile, + # ] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + # # Read the resultant output file and make sure the fields are changed as expected + # fsurdat_out_data = xr.open_dataset(outfile) + # zero0d = np.zeros((5, 5)) + # one0d = np.ones((5, 5)) + # pct_urban = np.array( + # [ + # [ + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # ], + # [ + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # ], + # [ + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # [0.0, 0.0, 0.0, 0.0, 0.0], + # ], + # ] + # ) + # lev2_two = np.empty((2, 3, 5, 5)) + # lev2_two[0, :, :, :] = 200.0 + # lev2_two[1, :, :, :] = 100.0 + # lev2_five = np.empty((5, 3, 5, 5)) + # lev2_five[0, :, :, :] = 1.0 + # lev2_five[1, :, :, :] = 2.0 + # lev2_five[2, :, :, :] = 3.0 + # lev2_five[3, :, :, :] = 4.0 + # lev2_five[4, :, :, :] = 5.0 + # lev1 = np.array( + # [ + # [ + # [200.0, 200.0, 200.0, 200.0, 200.0], + # [200.0, 200.0, 200.0, 200.0, 200.0], + # [200.0, 200.0, 200.0, 200.0, 200.0], + # [200.0, 200.0, 200.0, 200.0, 200.0], + # [200.0, 200.0, 200.0, 200.0, 200.0], + # ], + # [ + # [150.0, 150.0, 150.0, 150.0, 150.0], + # [150.0, 150.0, 150.0, 150.0, 150.0], + # [150.0, 150.0, 150.0, 150.0, 150.0], + # [150.0, 150.0, 150.0, 150.0, 150.0], + # [150.0, 150.0, 150.0, 150.0, 150.0], + # ], + # [ + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # [100.0, 100.0, 100.0, 100.0, 100.0], + # ], + # ] + # ) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, zero0d) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, pct_urban) + # np.testing.assert_array_equal(fsurdat_out_data.LAKEDEPTH, one0d * 200.0) + # np.testing.assert_array_equal(fsurdat_out_data.T_BUILDING_MIN, lev1) + # np.testing.assert_array_equal(fsurdat_out_data.ALB_ROOF_DIR, lev2_two) + # np.testing.assert_array_equal(fsurdat_out_data.TK_ROOF, lev2_five) + + # def test_evenly_split_cropland(self): + # """ + # Test that evenly splitting cropland works + # """ + # self._create_config_file_evenlysplitcrop() + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # ] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + # # Read the resultant output file and make sure the fields are changed as expected + # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) + # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) + # Ncrops = fsurdat_out_data.dims["cft"] + # pct_cft = np.full_like(fsurdat_out_data.PCT_CFT, 100 / Ncrops) + # np.testing.assert_array_equal(fsurdat_in_data.PCT_NATVEG, fsurdat_out_data.PCT_NATVEG) + # np.testing.assert_array_equal(fsurdat_in_data.PCT_CROP, fsurdat_out_data.PCT_CROP) + # np.testing.assert_array_equal(fsurdat_in_data.PCT_LAKE, fsurdat_out_data.PCT_LAKE) + # np.testing.assert_array_equal(fsurdat_in_data.PCT_WETLAND, fsurdat_out_data.PCT_WETLAND) + # np.testing.assert_array_equal(fsurdat_in_data.PCT_GLACIER, fsurdat_out_data.PCT_GLACIER) + # np.testing.assert_array_equal(fsurdat_in_data.PCT_URBAN, fsurdat_out_data.PCT_URBAN) + # np.testing.assert_array_equal(fsurdat_out_data.PCT_CFT, pct_cft) + + # def test_1x1_mexicocity(self): + # """ + # Test that the mexicocity file is handled correctly + # """ + # self._cfg_file_path = os.path.join( + # self._testinputs_cc_path, "modify_fsurdat_1x1mexicocity.cfg" + # ) + # expectfile = os.path.join( + # self._testinputs_cc_path, + # "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc", + # ) + # outfile = os.path.join( + # self._tempdir, + # "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc", + # ) + # infile = os.path.join( + # self._testinputs_cc_path, + # "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc", + # ) + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # "-i", + # infile, + # "-o", + # outfile, + # ] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + + # # Read the resultant output file and make sure the fields are changed as expected + # fsurdat_out_data = xr.open_dataset(outfile) + # fsurdat_inp_data = xr.open_dataset(infile) + # fsurdat_exp_data = xr.open_dataset(expectfile) + + # self.assertFalse(fsurdat_out_data.equals(fsurdat_inp_data)) + # # assert that fsurdat_out equals fsurdat_out_baseline + # self.assertTrue(fsurdat_out_data.equals(fsurdat_exp_data)) + + # def test_cfg_file_DNE_fail(self): + # """ + # Test that if the config file does not exist that it gracefully fails + # """ + # self._cfg_file_path = os.path.join(self._tempdir, "FILE_DOES_NOT_EXIST.cfg") + # sys.argv = ["fsurdat_modifier", self._cfg_file_path] + # with self.assertRaisesRegex(SystemExit, "Config file does NOT exist"): + # fsurdat_modifier_arg_process() + + # def test_input_fsurdat_DNE_fail(self): + # """ + # Test that if the input fsurdat file does not exist that it gracefully fails + # """ + # self._cfg_file_path = os.path.join( + # self._testinputs_cc_path, "modify_fsurdat_short_nofiles.cfg" + # ) + # sys.argv = ["fsurdat_modifier", self._cfg_file_path, "-i", "FILE_DOES_NOT_EXIST.nc"] + # parser = fsurdat_modifier_arg_process() + # with self.assertRaisesRegex(SystemExit, "Input fsurdat_in file does NOT exist"): + # fsurdat_modifier(parser) + + # def test_output_fsurdat_EXISTS_fail(self): + # """ + # Test that if the output fsurdat file does exist that it gracefully fails + # without --overwrite option + # """ + # self._cfg_file_path = os.path.join( + # self._testinputs_cc_path, "modify_fsurdat_short_nofiles.cfg" + # ) + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # "-i", + # self._cfg_file_path, + # "-o", + # self._cfg_file_path, + # ] + # parser = fsurdat_modifier_arg_process() + # with self.assertRaisesRegex(SystemExit, "Output file already exists"): + # fsurdat_modifier(parser) + + # def test_cfg_file_empty_fail(self): + # """ + # Test that if the config file is empty it gracefully fails + # """ + # self._cfg_file_path = os.path.join(self._tempdir, "EMPTY_FILE.cfg") + # fil = open(self._cfg_file_path, "w") + # fil.close() + # sys.argv = ["fsurdat_modifier", self._cfg_file_path] + # parser = fsurdat_modifier_arg_process() + # with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): + # fsurdat_modifier(parser) + + # def test_minimalInfo(self): + # """ + # This test specifies a minimal amount of information + # Create .cfg file, run the tool, compare fsurdat_in to fsurdat_out + # """ + + # self._create_config_file_minimal() + + # # run the fsurdat_modifier tool + # sys.argv = ["fsurdat_modifier", self._cfg_file_path] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + # # the critical piece of this test is that the above command + # # doesn't generate errors; however, we also do some assertions below + + # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) + # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) + # # assert that fsurdat_out equals fsurdat_in + # self.assertTrue(fsurdat_out_data.equals(fsurdat_in_data)) + + # def test_crop(self): + # """ + # This version replaces the vegetation with a crop + # Create .cfg file, run the tool, compare fsurdat_in to fsurdat_out + # """ + + # self._create_config_file_crop() + + # # run the fsurdat_modifier tool + # sys.argv = ["fsurdat_modifier", self._cfg_file_path] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + # # the critical piece of this test is that the above command + # # doesn't generate errors; however, we also do some assertions below + + # # compare fsurdat_out to fsurdat_in + # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) + # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) + # # assert that fsurdat_out does not equal fsurdat_in + # self.assertFalse(fsurdat_out_data.equals(fsurdat_in_data)) + + # # compare fsurdat_out to fsurdat_out_baseline located in /testinputs + # fsurdat_out_baseline = self._fsurdat_in[:-3] + "_modified_with_crop" + self._fsurdat_in[-3:] + # fsurdat_out_base_data = xr.open_dataset(fsurdat_out_baseline) + # # assert that fsurdat_out equals fsurdat_out_baseline + # self.assertTrue(fsurdat_out_data.equals(fsurdat_out_base_data)) + + # def test_allInfo(self): + # """ + # This version specifies all possible information + # Create .cfg file, run the tool, compare fsurdat_in to fsurdat_out + # """ + + # self._create_config_file_complete() + + # # run the fsurdat_modifier tool + # sys.argv = [ + # "fsurdat_modifier", + # self._cfg_file_path, + # ] + # parser = fsurdat_modifier_arg_process() + # fsurdat_modifier(parser) + # # the critical piece of this test is that the above command + # # doesn't generate errors; however, we also do some assertions below + + # # compare fsurdat_out to fsurdat_in + # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) + # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) + # # assert that fsurdat_out does not equal fsurdat_in + # self.assertFalse(fsurdat_out_data.equals(fsurdat_in_data)) + + # # compare fsurdat_out to fsurdat_out_baseline located in /testinputs + # fsurdat_out_baseline = self._fsurdat_in[:-3] + "_modified" + self._fsurdat_in[-3:] + # fsurdat_out_base_data = xr.open_dataset(fsurdat_out_baseline) + # # assert that fsurdat_out equals fsurdat_out_baseline + # self.assertTrue(fsurdat_out_data.equals(fsurdat_out_base_data)) + + # def _create_config_file_minimal(self): + # """ + # Open the new and the template .cfg files + # Loop line by line through the template .cfg file + # When string matches, replace that line's content + # """ + # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: + # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: + # for line in cfg_in: + # if re.match(r" *fsurdat_in *=", line): + # line = f"fsurdat_in = {self._fsurdat_in}" + # elif re.match(r" *fsurdat_out *=", line): + # line = f"fsurdat_out = {self._regridded_cropcals}" + # cfg_out.write(line) + + # def _create_config_file_evenlysplitcrop(self): + # """ + # Open the new and the template .cfg files + # Loop line by line through the template .cfg file + # When string matches, replace that line's content + # """ + # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: + # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: + # for line in cfg_in: + # if re.match(r" *evenly_split_cropland *=", line): + # line = "evenly_split_cropland = True" + # elif re.match(r" *fsurdat_in *=", line): + # line = f"fsurdat_in = {self._fsurdat_in}" + # elif re.match(r" *fsurdat_out *=", line): + # line = f"fsurdat_out = {self._regridded_cropcals}" + # cfg_out.write(line) + + # def _create_config_file_crop(self): + # """ + # Open the new and the template .cfg files + # Loop line by line through the template .cfg file + # When string matches, replace that line's content + # """ + # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: + # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: + # for line in cfg_in: + # if re.match(r" *fsurdat_in *=", line): + # line = f"fsurdat_in = {self._fsurdat_in}" + # elif re.match(r" *fsurdat_out *=", line): + # line = f"fsurdat_out = {self._regridded_cropcals}" + # elif re.match(r" *lnd_lat_1 *=", line): + # line = "lnd_lat_1 = -10\n" + # elif re.match(r" *lnd_lat_2 *=", line): + # line = "lnd_lat_2 = -7\n" + # elif re.match(r" *lnd_lon_1 *=", line): + # line = "lnd_lon_1 = 295\n" + # elif re.match(r" *lnd_lon_2 *=", line): + # line = "lnd_lon_2 = 300\n" + # elif re.match(r" *dom_pft *=", line): + # line = "dom_pft = 15" + # elif re.match(r" *evenly_split_cropland *=", line): + # line = "evenly_split_cropland = False" + # elif re.match(r" *lai *=", line): + # line = "lai = 0 1 2 3 4 5 5 4 3 2 1 0\n" + # elif re.match(r" *sai *=", line): + # line = "sai = 1 1 1 1 1 1 1 1 1 1 1 1\n" + # elif re.match(r" *hgt_top *=", line): + # line = "hgt_top = 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5\n" + # elif re.match(r" *hgt_bot *=", line): + # line = "hgt_bot = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1\n" + # cfg_out.write(line) + + # def _create_config_file_complete(self): + # """ + # Open the new and the template .cfg files + # Loop line by line through the template .cfg file + # When string matches, replace that line's content + # """ + # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: + # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: + # for line in cfg_in: + # if re.match(r" *fsurdat_in *=", line): + # line = f"fsurdat_in = {self._fsurdat_in}" + # elif re.match(r" *fsurdat_out *=", line): + # line = f"fsurdat_out = {self._regridded_cropcals}" + # elif re.match(r" *idealized *=", line): + # line = "idealized = True" + # elif re.match(r" *lnd_lat_1 *=", line): + # line = "lnd_lat_1 = -10\n" + # elif re.match(r" *lnd_lat_2 *=", line): + # line = "lnd_lat_2 = -7\n" + # elif re.match(r" *lnd_lon_1 *=", line): + # line = "lnd_lon_1 = 295\n" + # elif re.match(r" *lnd_lon_2 *=", line): + # line = "lnd_lon_2 = 300\n" + # elif re.match(r" *dom_pft *=", line): + # line = "dom_pft = 1" + # elif re.match(r" *evenly_split_cropland *=", line): + # line = "evenly_split_cropland = False" + # elif re.match(r" *lai *=", line): + # line = "lai = 0 1 2 3 4 5 5 4 3 2 1 0\n" + # elif re.match(r" *sai *=", line): + # line = "sai = 1 1 1 1 1 1 1 1 1 1 1 1\n" + # elif re.match(r" *hgt_top *=", line): + # line = "hgt_top = 5 5 5 5 5 5 5 5 5 5 5 5\n" + # elif re.match(r" *hgt_bot *=", line): + # line = "hgt_bot = 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5\n" + # elif re.match(r" *soil_color *=", line): + # line = "soil_color = 5" + # elif re.match(r" *std_elev *=", line): + # line = "std_elev = 0.1" + # elif re.match(r" *max_sat_area *=", line): + # line = "max_sat_area = 0.2" + # cfg_out.write(line) + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py new file mode 100755 index 0000000000..199fc85816 --- /dev/null +++ b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py @@ -0,0 +1,97 @@ +#!/usr/bin/env python3 + +""" +Unit tests for regrid_ggcmi_shdates subroutines: +""" + +import unittest +import os +import sys +import shutil + +import tempfile +from configparser import ConfigParser +import xarray as xr + +from ctsm import unit_testing +from ctsm.path_utils import path_to_ctsm_root +from ctsm.crop_calendars.regrid_ggcmi_shdates import import_coord_1d +from ctsm.crop_calendars.regrid_ggcmi_shdates import import_coord_2d + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + +# pylint: disable=protected-access + + +# Allow as many public methods as needed... +# pylint: disable=too-many-public-methods +# Allow all the instance attributes that we need +# pylint: disable=too-many-instance-attributes +class TestRegridGgcmiShdates(unittest.TestCase): + # Tests the regrid_ggcmi_shdates subroutines + + def setUp(self): + """Setup for trying out the methods""" + testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") + self._cfg_file_path = os.path.join(testinputs_path, "modify_fsurdat_opt_sections.cfg") + self._testinputs_path = testinputs_path + self._fsurdat_in = os.path.join( + testinputs_path, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", + ) + self._tempdir = tempfile.mkdtemp() + self._fsurdat_in = os.path.join( + testinputs_path, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", + ) + self._fsurdat_out = os.path.join(self._tempdir, "fsurdat_out.nc") + sys.argv = [ + "fsurdat_modifier", + self._cfg_file_path, + "-i", + self._fsurdat_in, + "-o", + self._fsurdat_out, + ] + parser = fsurdat_modifier_arg_process() + self.cfg_path = str(parser.cfg_path) + self.config = ConfigParser() + self.config.read(self.cfg_path) + my_data = xr.open_dataset(self._fsurdat_in) + self.modify_fsurdat = ModifyFsurdat( + my_data=my_data, + lon_1=0.0, + lon_2=360.0, + lat_1=90.0, + lat_2=90.0, + landmask_file=None, + lat_dimname=None, + lon_dimname=None, + ) + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + # def test_subgrid_and_idealized_fails(self): + # # Test that + # section = "modify_fsurdat_basic_options" + # self.config.set(section, "idealized", "True") + # self.config.set(section, "include_nonveg", "False") + # self.config.set(section, "process_subgrid_section", "True") + # self.config.set(section, "dom_pft", "UNSET") + # with self.assertRaisesRegex( + # SystemExit, + # "idealized AND process_subgrid_section can NOT both be on, pick one or the other", + # ): + # read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 b/python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 new file mode 100644 index 0000000000000000000000000000000000000000..985210eaeaee7d1d6c4a047bbb2ed06353d2f9ef GIT binary patch literal 139563 zcmeF(2Uru^x-fne1yq`{rAUhv3%y7uC?YB?ii$`VLqIyAm!Pu6MiZ3|0Z~9fsvsR~ zbP|*`i`oXU$qOd1p-4T9YUD&zw5VvVG5X zI_kp2M7M>G{r6Ma!x}8d_HO>YiWbw#&1g^lfx2f-UD(Xrw|U?1a(V{XjMmKGyL~g= zCh8{azmFnv&-&)4p%&fm>g#owO{pt4(XrAoQT{X4QA0U9IHH|htkGD?dJf8;?C)~Q z17&eTJ7cXK?3E>a?9nb3*DY7;kiNw3kd0vtwXnknY#V@w$xSe8ce&W(rC!H&N0^&6%3k2|YbZOwAQF-Rs9oM|bM1wz`hqSzR4dJ+%{B>U7KpsAZez zw*IcAb3$94vhnX))ZNi)Q8GivEKNs8J%Oxr%#>|Sb$+K>`joYu^>xaY?35QltwBeJ z`29$$NeyhvmK%Ss^sub>trd6$JOj#she2+T37kh)&{3CRupO)h3&2z`61)d`fL7oY z@C+yi9tOEVCUE{b>>q3gtHA;=6^sP$fgYe0cm+HI%7KSLZjcF_w}AbF?O-)n0H%VG 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z&mm2=L59$id9+Qzvq&Rfzfa)p&zOYGD%xh<#sEmJg?p8{4*mLGa0dRM5Ny2$dsiGnM8{otwKqOtF z{xAg|Njz!Ns!Tkxk<**$a}2Ia*T}s4bAswV5^7fXdRDbP3z!Bt%dVQNGnB_ z`@TlxKfN{sk>rr_a=?pE4w*Nf*POLJ{Nn`ZHwIX3M&ULbChvpu_%i$NUnMuy3B(v`T!Hj|Y$?=G;#1_jEy4&&f@g9qu z=Sb6^9i^TE#d^Z3AK`>dUSjXqjBOr=dX8zdL29QtWLWIv=-Jj!y19U{ZaB&vy$ty@ z5jnp25j6@$C=1&Q6g|h{C(Z2t*`K0=Q*>EMSIbIAXN~^?XG^5V;*$=YGm44sKvbA+ zRq2q^qJPZfDCswG&p3|+I;9Bgl2mqAZBp=>?VTobItdYE4(ZoZe&tY0d|2{~vfb7;HsmGUd(nD&Y|4fn_8Oc)ih_7IADFFUD^ zM_B=Zv~(7@W7|iaR|wKzC=E$jcOi4N!8!;;&H$W-nJO?aW^^#Urb0H7v7k#H8LOzhFlQQAXpbdc zLMN_(Tz#GJfxcixkt3Na?if$UdnvZZ6JC4hA~gqUM5Jc<7z08bj|js6*C~RpKS5d_ z7|?5-5%Ls8(+Y0$UNm%DVCqRdUHnGvnC+ncp>F&``;M}<=#@WYoC&Z<5yEJt#p={3 zu)#652h}hasZ(QqNe`KA(BP|dz3KUcqSh)tiT|rEG%xq2EgfoYs%fgXgFsqua3479 z=~jY#^?k*R|C5WR0)wrT6`=rOaUwcOUsu9qrCsN*S3~1#rFV3JzufGJHi0lJHvfDl zEPiM?$_1Af@@sE`RpzWi8-455%|row?V%R;VloD2pKRi;)0r-A`y+E@>zSG)XgpIP zt@B2o)m;?w&7a^gaSYUE{3sLzVllIEg3l--#}Npf^FQAiaq-O5$zW%;V?9{gVh*nO z{RI!wsnfC!rRjG4vt?shS#>KQOLnaXSnPK7w%=V=6?F4HIUng<|KnOr=J$O7*paWh zO)&q%$9pSo&4JB|ZMUI64$k%d&&P zDU~S%5>o>+SqpJlHclE6BvKyp?z;Y{Iekcx{qZFJ4?!;EDmpxK^^Y(A|L6a!2$c0` K^%@tq<^Ml&ww|c~ literal 0 HcmV?d00001 From 51cc972d37dc060ab3cc983c1e5b41426f23504e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 10:14:01 -0700 Subject: [PATCH 1798/2067] Move import_coord_[12]d to python/ctsm/utils.py. --- python/ctsm/crop_calendars/__init__.py | 0 .../crop_calendars/regrid_ggcmi_shdates.py | 37 +++---------------- python/ctsm/utils.py | 32 ++++++++++++++++ 3 files changed, 38 insertions(+), 31 deletions(-) create mode 100644 python/ctsm/crop_calendars/__init__.py diff --git a/python/ctsm/crop_calendars/__init__.py b/python/ctsm/crop_calendars/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 177237cfb3..b7ce09492c 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -6,6 +6,12 @@ import xarray as xr import numpy as np +# -- add python/ctsm to path (needed if we want to run regrid_ggcmi_shdates stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.utils import import_coord_1d, import_coord_2d + def run_and_check(cmd): result = run( @@ -40,37 +46,6 @@ def define_arguments(parser): return parser -# lat or lon -def import_coord_1d(ds, coordName): - da = ds[coordName] - if len(da.dims) != 1: - raise RuntimeError(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") - return da, len(da) - - -# LATIXY or LONGXY -def import_coord_2d(ds, coordName, varName): - da = ds[varName] - thisDim = [x for x in da.dims if coordName in x] - if len(thisDim) != 1: - raise RuntimeError( - f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}" - ) - thisDim = thisDim[0] - otherDim = [x for x in da.dims if coordName not in x] - if len(otherDim) != 1: - raise RuntimeError( - f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" - ) - otherDim = otherDim[0] - da = da.astype(np.float32) - da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) - da = da.assign_coords({coordName: da.values}) - da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] - da.attrs["units"] = da.attrs["units"].replace(" ", "_") - return da, len(da) - - def main( regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory, extension, crop_list ): diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 42444e32c5..3a2f5fc300 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -6,6 +6,7 @@ import string import re import pdb +import numpy as np from datetime import date from getpass import getuser @@ -189,3 +190,34 @@ def write_output(file, file_in, file_out, file_type): file.to_netcdf(path=file_out, mode="w", format="NETCDF3_64BIT") logger.info("Successfully created: %s", file_out) file.close() + + +# Import 1-d latitude or longitude variable from a CESM history file (e.g., name lat or lon) and return it as a DataArray that can be used for writing CESM input files +def import_coord_1d(ds, coordName): + da = ds[coordName] + if len(da.dims) != 1: + raise RuntimeError(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") + return da, len(da) + + +# Import 1-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files +def import_coord_2d(ds, coordName, varName): + da = ds[varName] + thisDim = [x for x in da.dims if coordName in x] + if len(thisDim) != 1: + raise RuntimeError( + f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}" + ) + thisDim = thisDim[0] + otherDim = [x for x in da.dims if coordName not in x] + if len(otherDim) != 1: + raise RuntimeError( + f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" + ) + otherDim = otherDim[0] + da = da.astype(np.float32) + da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) + da = da.assign_coords({coordName: da.values}) + da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] + da.attrs["units"] = da.attrs["units"].replace(" ", "_") + return da, len(da) \ No newline at end of file From 40768c3cc4c33b92f4770a9468c0fef8f21b7988 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 10:44:44 -0700 Subject: [PATCH 1799/2067] Use abort() instead of raise RuntimeError(). --- python/ctsm/utils.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 3a2f5fc300..bcf871eacc 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -196,7 +196,7 @@ def write_output(file, file_in, file_out, file_type): def import_coord_1d(ds, coordName): da = ds[coordName] if len(da.dims) != 1: - raise RuntimeError(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") + abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") return da, len(da) @@ -205,13 +205,13 @@ def import_coord_2d(ds, coordName, varName): da = ds[varName] thisDim = [x for x in da.dims if coordName in x] if len(thisDim) != 1: - raise RuntimeError( + abort( f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}" ) thisDim = thisDim[0] otherDim = [x for x in da.dims if coordName not in x] if len(otherDim) != 1: - raise RuntimeError( + abort( f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" ) otherDim = otherDim[0] From 96b88aa038486f6b6130f025fbc3c23dccac856d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 10:46:41 -0700 Subject: [PATCH 1800/2067] Add unit tests for importing 2-d latitude. --- .../test/test_unit_regrid_ggcmi_shdates.py | 102 +++++++++--------- 1 file changed, 54 insertions(+), 48 deletions(-) diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py index 199fc85816..b4ef544c9b 100755 --- a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py @@ -10,13 +10,16 @@ import shutil import tempfile -from configparser import ConfigParser import xarray as xr +import numpy as np + +# -- add python/ctsm to path (needed if we want to run test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) from ctsm import unit_testing from ctsm.path_utils import path_to_ctsm_root -from ctsm.crop_calendars.regrid_ggcmi_shdates import import_coord_1d -from ctsm.crop_calendars.regrid_ggcmi_shdates import import_coord_2d +from ctsm.utils import import_coord_1d, import_coord_2d # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -35,41 +38,11 @@ class TestRegridGgcmiShdates(unittest.TestCase): def setUp(self): """Setup for trying out the methods""" testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") - self._cfg_file_path = os.path.join(testinputs_path, "modify_fsurdat_opt_sections.cfg") self._testinputs_path = testinputs_path - self._fsurdat_in = os.path.join( - testinputs_path, - "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", - ) self._tempdir = tempfile.mkdtemp() - self._fsurdat_in = os.path.join( - testinputs_path, - "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc", - ) - self._fsurdat_out = os.path.join(self._tempdir, "fsurdat_out.nc") - sys.argv = [ - "fsurdat_modifier", - self._cfg_file_path, - "-i", - self._fsurdat_in, - "-o", - self._fsurdat_out, - ] - parser = fsurdat_modifier_arg_process() - self.cfg_path = str(parser.cfg_path) - self.config = ConfigParser() - self.config.read(self.cfg_path) - my_data = xr.open_dataset(self._fsurdat_in) - self.modify_fsurdat = ModifyFsurdat( - my_data=my_data, - lon_1=0.0, - lon_2=360.0, - lat_1=90.0, - lat_2=90.0, - landmask_file=None, - lat_dimname=None, - lon_dimname=None, - ) + + self._1d_lonlat_file = os.path.join(self._testinputs_path, "cropcals", "swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4") + self._2d_lonlat_file = os.path.join(self._testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_modified.nc") def tearDown(self): """ @@ -77,19 +50,52 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) - # def test_subgrid_and_idealized_fails(self): - # # Test that - # section = "modify_fsurdat_basic_options" - # self.config.set(section, "idealized", "True") - # self.config.set(section, "include_nonveg", "False") - # self.config.set(section, "process_subgrid_section", "True") - # self.config.set(section, "dom_pft", "UNSET") - # with self.assertRaisesRegex( - # SystemExit, - # "idealized AND process_subgrid_section can NOT both be on, pick one or the other", - # ): - # read_cfg_option_control(self.modify_fsurdat, self.config, section, self.cfg_path) + def test_importcoord1d_too_many_dims(self): + ds = xr.open_dataset(self._2d_lonlat_file) + with self.assertRaisesRegex( + SystemExit, + "Expected 1 dimension for LATIXY; found 2: \('lsmlat', 'lsmlon'\)", + ): + import_coord_1d(ds, "LATIXY") + + def test_importcoord2d(self): + ds = xr.open_dataset(self._2d_lonlat_file) + lat, _ = import_coord_2d(ds, "lat", "LATIXY") + expected_values = np.array([-13.9, -11.7, -9.5, -7.3, -5.1]).astype(np.float32) + np.testing.assert_array_equal(lat.values, expected_values) + + def test_importcoord2d_attrs(self): + ds = xr.open_dataset(self._2d_lonlat_file) + lat, _ = import_coord_2d(ds, "lat", "LATIXY") + expected_attributes = { + "long_name": "coordinate latitude", + "units": "degrees_north", + } + self.assertDictEqual(lat.attrs, expected_attributes) + + def test_importcoord2d_rename_dim(self): + ds = xr.open_dataset(self._2d_lonlat_file) + lat, _ = import_coord_2d(ds, "lat", "LATIXY") + self.assertTupleEqual(lat.dims, ("lat",)) + + def test_importcoord2d_no_dim_contains_coordName(self): + ds = xr.open_dataset(self._2d_lonlat_file) + ds = ds.rename({"lsmlat": "abc"}) + with self.assertRaisesRegex( + SystemExit, + "ERROR: Expected 1 dimension name containing lat; found 0: \[\]", + ): + import_coord_2d(ds, "lat", "LATIXY") + + def test_importcoord2d_1_dim_containing(self): + ds = xr.open_dataset(self._2d_lonlat_file) + ds = ds.rename({"lsmlon": "lsmlat2"}) + with self.assertRaisesRegex( + SystemExit, + "Expected 1 dimension name containing lat; found 2: \['lsmlat', 'lsmlat2'\]", + ): + import_coord_2d(ds, "lat", "LATIXY") if __name__ == "__main__": From fdd36b3fb8207d6554bf18c297f7374c6434803b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 11:00:49 -0700 Subject: [PATCH 1801/2067] Fix "Expected 1 dimension name containing" in import_coord_2d. --- python/ctsm/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index bcf871eacc..1ea0717f2d 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -206,7 +206,7 @@ def import_coord_2d(ds, coordName, varName): thisDim = [x for x in da.dims if coordName in x] if len(thisDim) != 1: abort( - f"Expected 1 dimension name containing {coordName}; found {len(otherDim)}: {otherDim}" + f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}" ) thisDim = thisDim[0] otherDim = [x for x in da.dims if coordName not in x] From 04d2d73aec5ac866c9a6eba213dd0abd8126a19b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 11:09:21 -0700 Subject: [PATCH 1802/2067] Add unit tests for importing 1-d latitude. --- .../test/test_unit_regrid_ggcmi_shdates.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py index b4ef544c9b..be39766e93 100755 --- a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py @@ -51,6 +51,24 @@ def tearDown(self): shutil.rmtree(self._tempdir, ignore_errors=True) + def test_importcoord1d(self): + ds = xr.open_dataset(self._1d_lonlat_file) + lat, Nlat = import_coord_1d(ds, "lat") + print(lat) + np.testing.assert_equal(Nlat, 360) + np.testing.assert_array_equal(lat.values[:4], [89.75, 89.25, 88.75, 88.25]) + np.testing.assert_array_equal(lat.values[-4:], [-88.25, -88.75, -89.25, -89.75]) + + def test_importcoord1d_attrs(self): + ds = xr.open_dataset(self._1d_lonlat_file) + lat, _ = import_coord_1d(ds, "lat") + # Unlike import_coord_2d, import_coord_1d doesn't rename the long name. + expected_attributes = { + "long_name": ds["lat"].attrs["long_name"], + "units": "degrees_north", + } + self.assertDictEqual(lat.attrs, expected_attributes) + def test_importcoord1d_too_many_dims(self): ds = xr.open_dataset(self._2d_lonlat_file) with self.assertRaisesRegex( From 4d2d497c61216bffe86b33737992f6bbaa7ea7da Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 11:23:52 -0700 Subject: [PATCH 1803/2067] Functionize processing of regrid_ggcmi_shdates input args. --- .../crop_calendars/regrid_ggcmi_shdates.py | 27 ++++++++++++++----- 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index b7ce09492c..eef898b580 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -11,6 +11,11 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm.utils import import_coord_1d, import_coord_2d +from ctsm.ctsm_logging import ( + setup_logging_pre_config, + add_logging_args, + process_logging_args, +) def run_and_check(cmd): @@ -65,7 +70,7 @@ def main( template_ds_in = xr.open_dataset(regrid_template_file_in) - # Process crop list + # Process inputs if crop_list is not None: crop_list = crop_list.split(",") if extension[0] != ".": @@ -142,11 +147,12 @@ def main( # Delete template file, which is no longer needed os.remove(templatefile) - -if __name__ == "__main__": - ############################### - ### Process input arguments ### - ############################### +# Process input arguments +def regrid_ggcmi_shdates_arg_process(): + + # set up logging allowing user control + setup_logging_pre_config() + parser = argparse.ArgumentParser( description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." ) @@ -183,6 +189,15 @@ def main( # Get arguments args = parser.parse_args(sys.argv[1:]) + + return args + + +if __name__ == "__main__": + ############################### + ### Process input arguments ### + ############################### + args = regrid_ggcmi_shdates_arg_process() ########### ### Run ### From 4f59927958f77dc30c9e0182fb36e8fb00417b7b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 11:24:41 -0700 Subject: [PATCH 1804/2067] regrid_ggcmi_shdates: Use abort() instead of raise RuntimeError(). --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index eef898b580..6c3431064f 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -10,7 +10,7 @@ _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) -from ctsm.utils import import_coord_1d, import_coord_2d +from ctsm.utils import abort, import_coord_1d, import_coord_2d from ctsm.ctsm_logging import ( setup_logging_pre_config, add_logging_args, @@ -26,7 +26,7 @@ def run_and_check(cmd): text=True, ) if result.returncode != 0: - raise RuntimeError( + abort( f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}" ) @@ -83,7 +83,7 @@ def main( lat, Nlat = import_coord_2d(template_ds_in, "lat", "LATIXY") lat.attrs["axis"] = "Y" else: - raise RuntimeError("No latitude variable found in regrid template file") + abort("No latitude variable found in regrid template file") # Flip latitude, if needed if lat.values[0] < lat.values[1]: @@ -96,7 +96,7 @@ def main( lon, Nlon = import_coord_2d(template_ds_in, "lon", "LONGXY") lon.attrs["axis"] = "Y" else: - raise RuntimeError("No longitude variable found in regrid template file") + abort("No longitude variable found in regrid template file") template_da_out = xr.DataArray( data=np.full((Nlat, Nlon), 0.0), dims={"lat": lat, "lon": lon}, @@ -118,7 +118,7 @@ def main( pattern = "*" + extension input_files = glob.glob(pattern) if len(input_files) == 0: - raise FileNotFoundError(f"No files found matching {os.path.join(os.getcwd(), pattern)}") + abort(f"No files found matching {os.path.join(os.getcwd(), pattern)}") input_files.sort() for f in input_files: this_crop = f[0:6] From 2a6b4acf60717f805ed8ed887112b8d3c5edb63a Mon Sep 17 00:00:00 2001 From: Teagan King <98482480+TeaganKing@users.noreply.github.com> Date: Tue, 7 Nov 2023 12:03:50 -0700 Subject: [PATCH 1805/2067] Update ChangeSum --- doc/ChangeSum | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeSum b/doc/ChangeSum index b5d5170267..66d064f72e 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev151 tking 11/02/2023 Move tools to python directory and add tests + ctsm5.1.dev153 tking 11/02/2023 Move tools to python directory and add tests ctsm5.1.dev140 afoster 09/12/2023 add lai_streams capability for FATES ctsm5.1.dev139 slevis 08/28/2023 Fix problems uncovered by nag -nan tests ctsm5.1.dev138 slevis 08/25/2023 Refactor max_patch_per_col and maxsoil_patches loops From eaf488d3bd882f2ed42e14243dd710752df9beb4 Mon Sep 17 00:00:00 2001 From: Teagan King <98482480+TeaganKing@users.noreply.github.com> Date: Tue, 7 Nov 2023 12:04:14 -0700 Subject: [PATCH 1806/2067] Update ChangeLog --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index d787c8d36c..40fd18a89c 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,5 +1,5 @@ =============================================================== -Tag name: ctsm5.1.dev151 +Tag name: ctsm5.1.dev153 Originator(s): tking (Teagan King,UCAR/CCR) Date: Thu Nov 2 16:03:44 MDT 2023 One-line Summary: Move tools to python directory and add tests From 414ad550f97bccbf5cacae2525130ccd153c931c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 12:04:21 -0700 Subject: [PATCH 1807/2067] Add system test for regrid_ggcmi_shdates. --- .../crop_calendars/regrid_ggcmi_shdates.py | 11 +- .../test/test_sys_regrid_ggcmi_shdates.py | 535 +++--------------- 2 files changed, 74 insertions(+), 472 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 6c3431064f..75874a0c02 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -190,6 +190,11 @@ def regrid_ggcmi_shdates_arg_process(): # Get arguments args = parser.parse_args(sys.argv[1:]) + # Process arguments + args.regrid_template_file = os.path.realpath(args.regrid_template_file) + args.regrid_input_directory = os.path.realpath(args.regrid_input_directory) + args.regrid_output_directory = os.path.realpath(args.regrid_output_directory) + return args @@ -204,9 +209,9 @@ def regrid_ggcmi_shdates_arg_process(): ########### main( args.regrid_resolution, - os.path.realpath(args.regrid_template_file), - os.path.realpath(args.regrid_input_directory), - os.path.realpath(args.regrid_output_directory), + args.regrid_template_file, + args.regrid_input_directory, + args.regrid_output_directory, args.extension, args.crop_list, ) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py index 765ec5023b..d4a2e2c1c3 100755 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -15,9 +15,15 @@ import xarray as xr import numpy as np +# -- add python/ctsm to path (needed if we want to run test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + + from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing from ctsm.crop_calendars.regrid_ggcmi_shdates import main as regrid_ggcmi_shdates +from ctsm.crop_calendars.regrid_ggcmi_shdates import regrid_ggcmi_shdates_arg_process # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -29,7 +35,8 @@ class TestRegridGgcmiShdates(unittest.TestCase): def setUp(self): # Where in the /testinputs directory are the raw crop calendar file(s)? - testinputs_cc_path = os.path.join(path_to_ctsm_root(), "python", "ctsm", "test", "testinputs", "cropcals") + testinputs_path = os.path.join(path_to_ctsm_root(), "python", "ctsm", "test", "testinputs") + testinputs_cc_path = os.path.join(testinputs_path, "cropcals") self._testinputs_cc_path = testinputs_cc_path # Make /_tempdir for use by these tests. @@ -44,480 +51,70 @@ def setUp(self): # Which crop(s) should we test? (comma-separated string) self._crop_list = "swh_rf" + # What is the complete set of input arguments (including script name)? + regrid_template_file = os.path.join(testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc") + self._function_call_list = [ + "regrid_ggcmi_shdates", + "-i", + testinputs_cc_path, + "-x", + ".nc4", + "-o", + self._regridded_cropcals, + "-rr", + "5x5amazon", + "-rt", + regrid_template_file, + "--crop-list", + "swh_rf", + ] def tearDown(self): """ Remove temporary directory """ shutil.rmtree(self._tempdir, ignore_errors=True) - - # def test_no_files_given_fail(self): - # """ - # Test that if no input or output files are given that it will gracefully fail - # """ - # self._cfg_file_path = os.path.join( - # self._testinputs_cc_path, "modify_fsurdat_short_nofiles.cfg" - # ) - # sys.argv = ["fsurdat_modifier", self._cfg_file_path] - # parser = fsurdat_modifier_arg_process() - # with self.assertRaisesRegex(SystemExit, "must contain item 'fsurdat_in'"): - # fsurdat_modifier(parser) - - # def test_short_config(self): - # """ - # Test that a short config file works - # """ - # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_short.cfg") - # sys.argv = ["fsurdat_modifier", self._cfg_file_path] - # parser = fsurdat_modifier_arg_process() - # fsurdat_out = ( - # "ctsm/test/testinputs/surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_out.nc" - # ) - # if os.path.exists(fsurdat_out): - # os.remove(fsurdat_out) - # fsurdat_modifier(parser) - # # Run it again with the overwrite option so that it will overwrite the file just created - # sys.argv = ["fsurdat_modifier", self._cfg_file_path, "--overwrite"] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - # # Cleanup - # os.remove(fsurdat_out) - - # def test_short_infile_both_cmdline_and_cfg(self): - # """ - # Test that a graceful fail happens when the infile - # is given both in the command line and the config file - # """ - # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_short.cfg") - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # "-i", - # "specify_fsurdat_in_on_cmd_line.nc", - # ] - # parser = fsurdat_modifier_arg_process() - # with self.assertRaisesRegex( - # SystemExit, - # "fsurdat_in is specified in both the command line and the config file, pick one", - # ): - # fsurdat_modifier(parser) - - # def test_short_outfile_both_cmdline_and_cfg(self): - # """ - # Test that a graceful fail happens when the outfile is given - # both in the command line and the config file - # """ - # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_short.cfg") - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # "-o", - # "specify_fsurdat_out_on_cmd_line.nc", - # ] - # parser = fsurdat_modifier_arg_process() - # with self.assertRaisesRegex( - # SystemExit, - # "fsurdat_out is specified in both the command line and the config file, pick one", - # ): - # fsurdat_modifier(parser) - - # def test_opt_sections(self): - # """ - # Test that a simple file with the optional sections works - # """ - # self._cfg_file_path = os.path.join(self._testinputs_cc_path, "modify_fsurdat_opt_sections.cfg") - # outfile = os.path.join( - # self._tempdir, - # "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_output_urban.nc", - # ) - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # "-i", - # os.path.join( - # self._testinputs_cc_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" - # ), - # "-o", - # outfile, - # ] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - # # Read the resultant output file and make sure the fields are changed as expected - # fsurdat_out_data = xr.open_dataset(outfile) - # zero0d = np.zeros((5, 5)) - # one0d = np.ones((5, 5)) - # pct_urban = np.array( - # [ - # [ - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # ], - # [ - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # ], - # [ - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # [0.0, 0.0, 0.0, 0.0, 0.0], - # ], - # ] - # ) - # lev2_two = np.empty((2, 3, 5, 5)) - # lev2_two[0, :, :, :] = 200.0 - # lev2_two[1, :, :, :] = 100.0 - # lev2_five = np.empty((5, 3, 5, 5)) - # lev2_five[0, :, :, :] = 1.0 - # lev2_five[1, :, :, :] = 2.0 - # lev2_five[2, :, :, :] = 3.0 - # lev2_five[3, :, :, :] = 4.0 - # lev2_five[4, :, :, :] = 5.0 - # lev1 = np.array( - # [ - # [ - # [200.0, 200.0, 200.0, 200.0, 200.0], - # [200.0, 200.0, 200.0, 200.0, 200.0], - # [200.0, 200.0, 200.0, 200.0, 200.0], - # [200.0, 200.0, 200.0, 200.0, 200.0], - # [200.0, 200.0, 200.0, 200.0, 200.0], - # ], - # [ - # [150.0, 150.0, 150.0, 150.0, 150.0], - # [150.0, 150.0, 150.0, 150.0, 150.0], - # [150.0, 150.0, 150.0, 150.0, 150.0], - # [150.0, 150.0, 150.0, 150.0, 150.0], - # [150.0, 150.0, 150.0, 150.0, 150.0], - # ], - # [ - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # [100.0, 100.0, 100.0, 100.0, 100.0], - # ], - # ] - # ) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_NATVEG, zero0d) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_CROP, zero0d) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_LAKE, zero0d) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_WETLAND, zero0d) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_GLACIER, zero0d) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_URBAN, pct_urban) - # np.testing.assert_array_equal(fsurdat_out_data.LAKEDEPTH, one0d * 200.0) - # np.testing.assert_array_equal(fsurdat_out_data.T_BUILDING_MIN, lev1) - # np.testing.assert_array_equal(fsurdat_out_data.ALB_ROOF_DIR, lev2_two) - # np.testing.assert_array_equal(fsurdat_out_data.TK_ROOF, lev2_five) - - # def test_evenly_split_cropland(self): - # """ - # Test that evenly splitting cropland works - # """ - # self._create_config_file_evenlysplitcrop() - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # ] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - # # Read the resultant output file and make sure the fields are changed as expected - # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) - # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) - # Ncrops = fsurdat_out_data.dims["cft"] - # pct_cft = np.full_like(fsurdat_out_data.PCT_CFT, 100 / Ncrops) - # np.testing.assert_array_equal(fsurdat_in_data.PCT_NATVEG, fsurdat_out_data.PCT_NATVEG) - # np.testing.assert_array_equal(fsurdat_in_data.PCT_CROP, fsurdat_out_data.PCT_CROP) - # np.testing.assert_array_equal(fsurdat_in_data.PCT_LAKE, fsurdat_out_data.PCT_LAKE) - # np.testing.assert_array_equal(fsurdat_in_data.PCT_WETLAND, fsurdat_out_data.PCT_WETLAND) - # np.testing.assert_array_equal(fsurdat_in_data.PCT_GLACIER, fsurdat_out_data.PCT_GLACIER) - # np.testing.assert_array_equal(fsurdat_in_data.PCT_URBAN, fsurdat_out_data.PCT_URBAN) - # np.testing.assert_array_equal(fsurdat_out_data.PCT_CFT, pct_cft) - - # def test_1x1_mexicocity(self): - # """ - # Test that the mexicocity file is handled correctly - # """ - # self._cfg_file_path = os.path.join( - # self._testinputs_cc_path, "modify_fsurdat_1x1mexicocity.cfg" - # ) - # expectfile = os.path.join( - # self._testinputs_cc_path, - # "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc", - # ) - # outfile = os.path.join( - # self._tempdir, - # "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206_modified.nc", - # ) - # infile = os.path.join( - # self._testinputs_cc_path, - # "surfdata_1x1_mexicocityMEX_hist_16pfts_Irrig_CMIP6_simyr2000_c221206.nc", - # ) - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # "-i", - # infile, - # "-o", - # outfile, - # ] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - - # # Read the resultant output file and make sure the fields are changed as expected - # fsurdat_out_data = xr.open_dataset(outfile) - # fsurdat_inp_data = xr.open_dataset(infile) - # fsurdat_exp_data = xr.open_dataset(expectfile) - - # self.assertFalse(fsurdat_out_data.equals(fsurdat_inp_data)) - # # assert that fsurdat_out equals fsurdat_out_baseline - # self.assertTrue(fsurdat_out_data.equals(fsurdat_exp_data)) - - # def test_cfg_file_DNE_fail(self): - # """ - # Test that if the config file does not exist that it gracefully fails - # """ - # self._cfg_file_path = os.path.join(self._tempdir, "FILE_DOES_NOT_EXIST.cfg") - # sys.argv = ["fsurdat_modifier", self._cfg_file_path] - # with self.assertRaisesRegex(SystemExit, "Config file does NOT exist"): - # fsurdat_modifier_arg_process() - - # def test_input_fsurdat_DNE_fail(self): - # """ - # Test that if the input fsurdat file does not exist that it gracefully fails - # """ - # self._cfg_file_path = os.path.join( - # self._testinputs_cc_path, "modify_fsurdat_short_nofiles.cfg" - # ) - # sys.argv = ["fsurdat_modifier", self._cfg_file_path, "-i", "FILE_DOES_NOT_EXIST.nc"] - # parser = fsurdat_modifier_arg_process() - # with self.assertRaisesRegex(SystemExit, "Input fsurdat_in file does NOT exist"): - # fsurdat_modifier(parser) - - # def test_output_fsurdat_EXISTS_fail(self): - # """ - # Test that if the output fsurdat file does exist that it gracefully fails - # without --overwrite option - # """ - # self._cfg_file_path = os.path.join( - # self._testinputs_cc_path, "modify_fsurdat_short_nofiles.cfg" - # ) - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # "-i", - # self._cfg_file_path, - # "-o", - # self._cfg_file_path, - # ] - # parser = fsurdat_modifier_arg_process() - # with self.assertRaisesRegex(SystemExit, "Output file already exists"): - # fsurdat_modifier(parser) - - # def test_cfg_file_empty_fail(self): - # """ - # Test that if the config file is empty it gracefully fails - # """ - # self._cfg_file_path = os.path.join(self._tempdir, "EMPTY_FILE.cfg") - # fil = open(self._cfg_file_path, "w") - # fil.close() - # sys.argv = ["fsurdat_modifier", self._cfg_file_path] - # parser = fsurdat_modifier_arg_process() - # with self.assertRaisesRegex(SystemExit, "Config file does not have the expected section"): - # fsurdat_modifier(parser) - - # def test_minimalInfo(self): - # """ - # This test specifies a minimal amount of information - # Create .cfg file, run the tool, compare fsurdat_in to fsurdat_out - # """ - - # self._create_config_file_minimal() - - # # run the fsurdat_modifier tool - # sys.argv = ["fsurdat_modifier", self._cfg_file_path] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - # # the critical piece of this test is that the above command - # # doesn't generate errors; however, we also do some assertions below - - # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) - # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) - # # assert that fsurdat_out equals fsurdat_in - # self.assertTrue(fsurdat_out_data.equals(fsurdat_in_data)) - - # def test_crop(self): - # """ - # This version replaces the vegetation with a crop - # Create .cfg file, run the tool, compare fsurdat_in to fsurdat_out - # """ - - # self._create_config_file_crop() - - # # run the fsurdat_modifier tool - # sys.argv = ["fsurdat_modifier", self._cfg_file_path] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - # # the critical piece of this test is that the above command - # # doesn't generate errors; however, we also do some assertions below - - # # compare fsurdat_out to fsurdat_in - # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) - # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) - # # assert that fsurdat_out does not equal fsurdat_in - # self.assertFalse(fsurdat_out_data.equals(fsurdat_in_data)) - - # # compare fsurdat_out to fsurdat_out_baseline located in /testinputs - # fsurdat_out_baseline = self._fsurdat_in[:-3] + "_modified_with_crop" + self._fsurdat_in[-3:] - # fsurdat_out_base_data = xr.open_dataset(fsurdat_out_baseline) - # # assert that fsurdat_out equals fsurdat_out_baseline - # self.assertTrue(fsurdat_out_data.equals(fsurdat_out_base_data)) - - # def test_allInfo(self): - # """ - # This version specifies all possible information - # Create .cfg file, run the tool, compare fsurdat_in to fsurdat_out - # """ - - # self._create_config_file_complete() - - # # run the fsurdat_modifier tool - # sys.argv = [ - # "fsurdat_modifier", - # self._cfg_file_path, - # ] - # parser = fsurdat_modifier_arg_process() - # fsurdat_modifier(parser) - # # the critical piece of this test is that the above command - # # doesn't generate errors; however, we also do some assertions below - - # # compare fsurdat_out to fsurdat_in - # fsurdat_in_data = xr.open_dataset(self._fsurdat_in) - # fsurdat_out_data = xr.open_dataset(self._regridded_cropcals) - # # assert that fsurdat_out does not equal fsurdat_in - # self.assertFalse(fsurdat_out_data.equals(fsurdat_in_data)) - - # # compare fsurdat_out to fsurdat_out_baseline located in /testinputs - # fsurdat_out_baseline = self._fsurdat_in[:-3] + "_modified" + self._fsurdat_in[-3:] - # fsurdat_out_base_data = xr.open_dataset(fsurdat_out_baseline) - # # assert that fsurdat_out equals fsurdat_out_baseline - # self.assertTrue(fsurdat_out_data.equals(fsurdat_out_base_data)) - - # def _create_config_file_minimal(self): - # """ - # Open the new and the template .cfg files - # Loop line by line through the template .cfg file - # When string matches, replace that line's content - # """ - # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: - # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: - # for line in cfg_in: - # if re.match(r" *fsurdat_in *=", line): - # line = f"fsurdat_in = {self._fsurdat_in}" - # elif re.match(r" *fsurdat_out *=", line): - # line = f"fsurdat_out = {self._regridded_cropcals}" - # cfg_out.write(line) - - # def _create_config_file_evenlysplitcrop(self): - # """ - # Open the new and the template .cfg files - # Loop line by line through the template .cfg file - # When string matches, replace that line's content - # """ - # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: - # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: - # for line in cfg_in: - # if re.match(r" *evenly_split_cropland *=", line): - # line = "evenly_split_cropland = True" - # elif re.match(r" *fsurdat_in *=", line): - # line = f"fsurdat_in = {self._fsurdat_in}" - # elif re.match(r" *fsurdat_out *=", line): - # line = f"fsurdat_out = {self._regridded_cropcals}" - # cfg_out.write(line) - - # def _create_config_file_crop(self): - # """ - # Open the new and the template .cfg files - # Loop line by line through the template .cfg file - # When string matches, replace that line's content - # """ - # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: - # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: - # for line in cfg_in: - # if re.match(r" *fsurdat_in *=", line): - # line = f"fsurdat_in = {self._fsurdat_in}" - # elif re.match(r" *fsurdat_out *=", line): - # line = f"fsurdat_out = {self._regridded_cropcals}" - # elif re.match(r" *lnd_lat_1 *=", line): - # line = "lnd_lat_1 = -10\n" - # elif re.match(r" *lnd_lat_2 *=", line): - # line = "lnd_lat_2 = -7\n" - # elif re.match(r" *lnd_lon_1 *=", line): - # line = "lnd_lon_1 = 295\n" - # elif re.match(r" *lnd_lon_2 *=", line): - # line = "lnd_lon_2 = 300\n" - # elif re.match(r" *dom_pft *=", line): - # line = "dom_pft = 15" - # elif re.match(r" *evenly_split_cropland *=", line): - # line = "evenly_split_cropland = False" - # elif re.match(r" *lai *=", line): - # line = "lai = 0 1 2 3 4 5 5 4 3 2 1 0\n" - # elif re.match(r" *sai *=", line): - # line = "sai = 1 1 1 1 1 1 1 1 1 1 1 1\n" - # elif re.match(r" *hgt_top *=", line): - # line = "hgt_top = 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5\n" - # elif re.match(r" *hgt_bot *=", line): - # line = "hgt_bot = 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1\n" - # cfg_out.write(line) - - # def _create_config_file_complete(self): - # """ - # Open the new and the template .cfg files - # Loop line by line through the template .cfg file - # When string matches, replace that line's content - # """ - # with open(self._cfg_file_path, "w", encoding="utf-8") as cfg_out: - # with open(self._cfg_template_path, "r", encoding="utf-8") as cfg_in: - # for line in cfg_in: - # if re.match(r" *fsurdat_in *=", line): - # line = f"fsurdat_in = {self._fsurdat_in}" - # elif re.match(r" *fsurdat_out *=", line): - # line = f"fsurdat_out = {self._regridded_cropcals}" - # elif re.match(r" *idealized *=", line): - # line = "idealized = True" - # elif re.match(r" *lnd_lat_1 *=", line): - # line = "lnd_lat_1 = -10\n" - # elif re.match(r" *lnd_lat_2 *=", line): - # line = "lnd_lat_2 = -7\n" - # elif re.match(r" *lnd_lon_1 *=", line): - # line = "lnd_lon_1 = 295\n" - # elif re.match(r" *lnd_lon_2 *=", line): - # line = "lnd_lon_2 = 300\n" - # elif re.match(r" *dom_pft *=", line): - # line = "dom_pft = 1" - # elif re.match(r" *evenly_split_cropland *=", line): - # line = "evenly_split_cropland = False" - # elif re.match(r" *lai *=", line): - # line = "lai = 0 1 2 3 4 5 5 4 3 2 1 0\n" - # elif re.match(r" *sai *=", line): - # line = "sai = 1 1 1 1 1 1 1 1 1 1 1 1\n" - # elif re.match(r" *hgt_top *=", line): - # line = "hgt_top = 5 5 5 5 5 5 5 5 5 5 5 5\n" - # elif re.match(r" *hgt_bot *=", line): - # line = "hgt_bot = 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5\n" - # elif re.match(r" *soil_color *=", line): - # line = "soil_color = 5" - # elif re.match(r" *std_elev *=", line): - # line = "std_elev = 0.1" - # elif re.match(r" *max_sat_area *=", line): - # line = "max_sat_area = 0.2" - # cfg_out.write(line) + + def test_regrid_ggcmi_shdates(self): + + # Call script + sys.argv = self._function_call_list + args = regrid_ggcmi_shdates_arg_process() + regrid_ggcmi_shdates( + args.regrid_resolution, + args.regrid_template_file, + args.regrid_input_directory, + args.regrid_output_directory, + args.extension, + args.crop_list, + ) + + # Read output file + regrid_out_file = os.path.join( + self._regridded_cropcals, + "swh_rf_ggcmi_crop_calendar_phase3_v1.01_nninterp-5x5amazon.nc4", + ) + regrid_out_ds = xr.open_dataset(regrid_out_file) + + # Check sowing dates + expected_sow_dates = np.array( + [[120, 120, 120, 120, 120], + [120, 120, 120, 120, 120], + [120, 120, 120, 120, 120], + [330, 335, 335, 120, 120], + [325, 335, 335, 335, 120]] + ) + np.testing.assert_array_equal(expected_sow_dates, regrid_out_ds["planting_day"].values) + + # Check maturity dates + expected_mat_dates = np.array( + [[221, 221, 221, 221, 221], + [221, 221, 221, 221, 221], + [221, 221, 221, 221, 221], + [153, 128, 128, 221, 221], + [163, 128, 128, 128, 221]] + ) + np.testing.assert_array_equal(expected_mat_dates, regrid_out_ds["maturity_day"].values) if __name__ == "__main__": From 183fc26a6691bbdf87f515dc47924a64be3ced9b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 12:15:54 -0700 Subject: [PATCH 1808/2067] Format regrid_ggcmi_shdates tests with black. --- .../test/test_sys_regrid_ggcmi_shdates.py | 52 +++++++++++-------- .../test/test_unit_regrid_ggcmi_shdates.py | 20 ++++--- 2 files changed, 41 insertions(+), 31 deletions(-) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py index d4a2e2c1c3..6c06493160 100755 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -38,21 +38,23 @@ def setUp(self): testinputs_path = os.path.join(path_to_ctsm_root(), "python", "ctsm", "test", "testinputs") testinputs_cc_path = os.path.join(testinputs_path, "cropcals") self._testinputs_cc_path = testinputs_cc_path - + # Make /_tempdir for use by these tests. self._tempdir = tempfile.mkdtemp() - + # Obtain path for the directory being created in /_tempdir self._regridded_cropcals = os.path.join(self._tempdir, "regridded_cropcals") - + # What extension do the raw crop calendar file(s) have? self._extension = ".nc4" - + # Which crop(s) should we test? (comma-separated string) self._crop_list = "swh_rf" - + # What is the complete set of input arguments (including script name)? - regrid_template_file = os.path.join(testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc") + regrid_template_file = os.path.join( + testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" + ) self._function_call_list = [ "regrid_ggcmi_shdates", "-i", @@ -74,9 +76,9 @@ def tearDown(self): Remove temporary directory """ shutil.rmtree(self._tempdir, ignore_errors=True) - + def test_regrid_ggcmi_shdates(self): - + # Call script sys.argv = self._function_call_list args = regrid_ggcmi_shdates_arg_process() @@ -88,32 +90,36 @@ def test_regrid_ggcmi_shdates(self): args.extension, args.crop_list, ) - + # Read output file regrid_out_file = os.path.join( self._regridded_cropcals, "swh_rf_ggcmi_crop_calendar_phase3_v1.01_nninterp-5x5amazon.nc4", ) regrid_out_ds = xr.open_dataset(regrid_out_file) - + # Check sowing dates expected_sow_dates = np.array( - [[120, 120, 120, 120, 120], - [120, 120, 120, 120, 120], - [120, 120, 120, 120, 120], - [330, 335, 335, 120, 120], - [325, 335, 335, 335, 120]] - ) + [ + [120, 120, 120, 120, 120], + [120, 120, 120, 120, 120], + [120, 120, 120, 120, 120], + [330, 335, 335, 120, 120], + [325, 335, 335, 335, 120], + ] + ) np.testing.assert_array_equal(expected_sow_dates, regrid_out_ds["planting_day"].values) - + # Check maturity dates expected_mat_dates = np.array( - [[221, 221, 221, 221, 221], - [221, 221, 221, 221, 221], - [221, 221, 221, 221, 221], - [153, 128, 128, 221, 221], - [163, 128, 128, 128, 221]] - ) + [ + [221, 221, 221, 221, 221], + [221, 221, 221, 221, 221], + [221, 221, 221, 221, 221], + [153, 128, 128, 221, 221], + [163, 128, 128, 128, 221], + ] + ) np.testing.assert_array_equal(expected_mat_dates, regrid_out_ds["maturity_day"].values) diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py index be39766e93..c47e81ac15 100755 --- a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py @@ -40,9 +40,14 @@ def setUp(self): testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") self._testinputs_path = testinputs_path self._tempdir = tempfile.mkdtemp() - - self._1d_lonlat_file = os.path.join(self._testinputs_path, "cropcals", "swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4") - self._2d_lonlat_file = os.path.join(self._testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_modified.nc") + + self._1d_lonlat_file = os.path.join( + self._testinputs_path, "cropcals", "swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4" + ) + self._2d_lonlat_file = os.path.join( + self._testinputs_path, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_modified.nc", + ) def tearDown(self): """ @@ -50,7 +55,6 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) - def test_importcoord1d(self): ds = xr.open_dataset(self._1d_lonlat_file) lat, Nlat = import_coord_1d(ds, "lat") @@ -58,7 +62,7 @@ def test_importcoord1d(self): np.testing.assert_equal(Nlat, 360) np.testing.assert_array_equal(lat.values[:4], [89.75, 89.25, 88.75, 88.25]) np.testing.assert_array_equal(lat.values[-4:], [-88.25, -88.75, -89.25, -89.75]) - + def test_importcoord1d_attrs(self): ds = xr.open_dataset(self._1d_lonlat_file) lat, _ = import_coord_1d(ds, "lat") @@ -91,12 +95,12 @@ def test_importcoord2d_attrs(self): "units": "degrees_north", } self.assertDictEqual(lat.attrs, expected_attributes) - + def test_importcoord2d_rename_dim(self): ds = xr.open_dataset(self._2d_lonlat_file) lat, _ = import_coord_2d(ds, "lat", "LATIXY") self.assertTupleEqual(lat.dims, ("lat",)) - + def test_importcoord2d_no_dim_contains_coordName(self): ds = xr.open_dataset(self._2d_lonlat_file) ds = ds.rename({"lsmlat": "abc"}) @@ -105,7 +109,7 @@ def test_importcoord2d_no_dim_contains_coordName(self): "ERROR: Expected 1 dimension name containing lat; found 0: \[\]", ): import_coord_2d(ds, "lat", "LATIXY") - + def test_importcoord2d_1_dim_containing(self): ds = xr.open_dataset(self._2d_lonlat_file) ds = ds.rename({"lsmlon": "lsmlat2"}) From 1bebd5e8000c1cd8362e254f7d641d4414ebf9bf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 12:16:36 -0700 Subject: [PATCH 1809/2067] Add previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 6a0bf3d280..960bc254c3 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -20,3 +20,4 @@ c8bd4c6f98c0b411391b4355da449507db3aab4e 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 540b256d1f3382f4619d7b0877c32d54ce5c40b6 8a168bb0895f4f2421608dd2589398e13a6663e6 +183fc26a6691bbdf87f515dc47924a64be3ced9b From 025d5e7c2e80263717fb029101d65cbbf261c3c4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 12:19:16 -0700 Subject: [PATCH 1810/2067] More black reformatting. --- .../crop_calendars/regrid_ggcmi_shdates.py | 24 +++++++++++-------- python/ctsm/utils.py | 6 ++--- 2 files changed, 16 insertions(+), 14 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 75874a0c02..02abbf99f9 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -26,9 +26,7 @@ def run_and_check(cmd): text=True, ) if result.returncode != 0: - abort( - f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}" - ) + abort(f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}") # Functionized because these are shared by process_ggcmi_shdates @@ -52,7 +50,12 @@ def define_arguments(parser): def main( - regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory, extension, crop_list + regrid_resolution, + regrid_template_file_in, + regrid_input_directory, + regrid_output_directory, + extension, + crop_list, ): print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") @@ -69,7 +72,7 @@ def main( os.remove(templatefile) template_ds_in = xr.open_dataset(regrid_template_file_in) - + # Process inputs if crop_list is not None: crop_list = crop_list.split(",") @@ -124,7 +127,7 @@ def main( this_crop = f[0:6] if crop_list is not None and this_crop not in crop_list: continue - + print(" " + this_crop) f2 = os.path.join(regrid_output_directory, f) f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") @@ -147,12 +150,13 @@ def main( # Delete template file, which is no longer needed os.remove(templatefile) + # Process input arguments def regrid_ggcmi_shdates_arg_process(): - + # set up logging allowing user control setup_logging_pre_config() - + parser = argparse.ArgumentParser( description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." ) @@ -189,12 +193,12 @@ def regrid_ggcmi_shdates_arg_process(): # Get arguments args = parser.parse_args(sys.argv[1:]) - + # Process arguments args.regrid_template_file = os.path.realpath(args.regrid_template_file) args.regrid_input_directory = os.path.realpath(args.regrid_input_directory) args.regrid_output_directory = os.path.realpath(args.regrid_output_directory) - + return args diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 1ea0717f2d..e5885aae7e 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -205,9 +205,7 @@ def import_coord_2d(ds, coordName, varName): da = ds[varName] thisDim = [x for x in da.dims if coordName in x] if len(thisDim) != 1: - abort( - f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}" - ) + abort(f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}") thisDim = thisDim[0] otherDim = [x for x in da.dims if coordName not in x] if len(otherDim) != 1: @@ -220,4 +218,4 @@ def import_coord_2d(ds, coordName, varName): da = da.assign_coords({coordName: da.values}) da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] da.attrs["units"] = da.attrs["units"].replace(" ", "_") - return da, len(da) \ No newline at end of file + return da, len(da) From d0df9122471cc6aac042cb95ee8ef1c17513543c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 7 Nov 2023 12:19:47 -0700 Subject: [PATCH 1811/2067] Add previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 960bc254c3..7c0b2f9b47 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -15,6 +15,7 @@ c8bd4c6f98c0b411391b4355da449507db3aab4e 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 810cb346f05ac1aabfff931ab1a2b7b584add241 5933b0018f8e29413e30dda9b906370d147bad45 +025d5e7c2e80263717fb029101d65cbbf261c3c4 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From 19a97fb364c9db8727dbc7007eaf824c06fb2039 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 Nov 2023 10:40:25 -0700 Subject: [PATCH 1812/2067] Add comment in LakeHydrology() pointing to issue #2227. Closes #2227 (wontfix). --- src/biogeophys/LakeHydrologyMod.F90 | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/biogeophys/LakeHydrologyMod.F90 b/src/biogeophys/LakeHydrologyMod.F90 index f6f83d8956..c1e69cbb13 100644 --- a/src/biogeophys/LakeHydrologyMod.F90 +++ b/src/biogeophys/LakeHydrologyMod.F90 @@ -351,6 +351,10 @@ subroutine LakeHydrology(bounds, & end if if (h2osno_temp > 0._r8) then ! Assume that snow bulk density remains the same as before + ! NOTE (SSR, 2023-11-08): Small h2osno_temp can cause unrealistically high snow depths: see https://github.com/ESCOMP/CTSM/issues/2227. Suggested fix there is to replace this line with + ! snow_depth(c) = h2osno_no_layers(c) * min (snow_depth(c)/h2osno_temp, 1._r8/50._r8) + ! where 50 kg/m3 is suggested as a lower limit for snow density. + ! As this bug seemingly has never been encountered in CTSM, we are not yet implementing the fix. snow_depth(c) = snow_depth(c) * h2osno_no_layers(c) / h2osno_temp else ! Assume a constant snow bulk density = 250. From 80d47d0c2d15dd0ec7e4b5be0722b0e9866184ce Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 Nov 2023 11:58:30 -0700 Subject: [PATCH 1813/2067] Functionize and unit-test latbaset calculation. --- src/biogeochem/CropType.F90 | 25 ++-- src/biogeochem/test/CMakeLists.txt | 1 + .../test/Latbaset_test/CMakeLists.txt | 6 + .../test/Latbaset_test/test_Latbaset.pf | 112 ++++++++++++++++++ 4 files changed, 137 insertions(+), 7 deletions(-) create mode 100644 src/biogeochem/test/Latbaset_test/CMakeLists.txt create mode 100644 src/biogeochem/test/Latbaset_test/test_Latbaset.pf diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 29c4717ab3..7e4dec6c1f 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -23,6 +23,7 @@ module CropType private ! ! !PUBLIC DATA TYPES: + public :: latbaset ! ! Possible values of cphase @@ -383,13 +384,7 @@ subroutine InitCold(this, bounds) this%nyrs_crop_active_patch(p) = 0 - if ( grc%latdeg(g) >= 0.0_r8 .and. grc%latdeg(g) <= 30.0_r8) then - this%latbaset_patch(p)=pftcon%baset(ivt)+12._r8-0.4_r8*grc%latdeg(g) - else if (grc%latdeg(g) < 0.0_r8 .and. grc%latdeg(g) >= -30.0_r8) then - this%latbaset_patch(p)=pftcon%baset(ivt)+12._r8+0.4_r8*grc%latdeg(g) - else - this%latbaset_patch(p)=pftcon%baset(ivt) - end if + this%latbaset_patch(p) = latbaset(pftcon%baset(ivt), grc%latdeg(g), this%baset_latvary_intercept, this%baset_latvary_slope) if ( trim(this%baset_mapping) == baset_map_constant ) then this%latbaset_patch(p) = nan end if @@ -972,4 +967,20 @@ subroutine checkDates( ) end subroutine checkDates + real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope) + ! !ARGUMENTS: + real(r8), intent(in) :: baset + real(r8), intent(in) :: latdeg + real(r8), intent(in) :: baset_latvary_intercept + real(r8), intent(in) :: baset_latvary_slope + + if ( latdeg >= 0.0_r8 .and. latdeg <= 30.0_r8) then + latbaset = baset + 12._r8 - 0.4_r8*latdeg + else if (latdeg < 0.0_r8 .and. latdeg >= -30.0_r8) then + latbaset = baset + 12._r8 + 0.4_r8*latdeg + else + latbaset = baset + end if + end function latbaset + end module CropType diff --git a/src/biogeochem/test/CMakeLists.txt b/src/biogeochem/test/CMakeLists.txt index ad91c7c995..81fe9bbaf0 100644 --- a/src/biogeochem/test/CMakeLists.txt +++ b/src/biogeochem/test/CMakeLists.txt @@ -1,3 +1,4 @@ add_subdirectory(Species_test) add_subdirectory(CNVegComputeSeed_test) add_subdirectory(CNPhenology_test) +add_subdirectory(Latbaset_test) diff --git a/src/biogeochem/test/Latbaset_test/CMakeLists.txt b/src/biogeochem/test/Latbaset_test/CMakeLists.txt new file mode 100644 index 0000000000..217fc7233c --- /dev/null +++ b/src/biogeochem/test/Latbaset_test/CMakeLists.txt @@ -0,0 +1,6 @@ +set (pfunit_sources + test_Latbaset.pf) + +add_pfunit_ctest(CropTypeLatbaset + TEST_SOURCES "${pfunit_sources}" + LINK_LIBRARIES clm csm_share esmf_wrf_timemgr) diff --git a/src/biogeochem/test/Latbaset_test/test_Latbaset.pf b/src/biogeochem/test/Latbaset_test/test_Latbaset.pf new file mode 100644 index 0000000000..1b164d5d69 --- /dev/null +++ b/src/biogeochem/test/Latbaset_test/test_Latbaset.pf @@ -0,0 +1,112 @@ +module test_Latbaset + + ! Tests of CropType module: latbaset + + use funit + use shr_kind_mod , only : r8 => shr_kind_r8 + use unittestSubgridMod + use unittestSimpleSubgridSetupsMod + use unittestFilterBuilderMod + use CropType, only : latbaset + + implicit none + + @TestCase + type, extends(TestCase) :: TestLatbaset + contains + procedure :: setUp + procedure :: tearDown + end type TestLatbaset + + real(r8) :: baset + real(r8) :: latdeg + real(r8) :: baset_latvary_intercept + real(r8) :: baset_latvary_slope + real(r8) :: expected + +contains + + subroutine setUp(this) + class(TestLatbaset), intent(inout) :: this + end subroutine setUp + + subroutine tearDown(this) + class(TestLatbaset), intent(inout) :: this + + call unittest_subgrid_teardown() + end subroutine tearDown + + @Test + subroutine too_far_north(this) + class(TestLatbaset), intent(inout) :: this + + baset = 5._r8 + latdeg = 80._r8 + baset_latvary_intercept = 8.7_r8 + baset_latvary_slope = 0.5_r8 + + @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) + end subroutine too_far_north + + @Test + subroutine too_far_south(this) + class(TestLatbaset), intent(inout) :: this + + baset = 5._r8 + latdeg = -80._r8 + baset_latvary_intercept = 8.7_r8 + baset_latvary_slope = 0.5_r8 + + @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) + end subroutine too_far_south + + @Test + subroutine at_northern_limit(this) + class(TestLatbaset), intent(inout) :: this + + baset = 5._r8 + latdeg = 30._r8 + baset_latvary_intercept = 12._r8 + baset_latvary_slope = 0.4_r8 + + @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) + end subroutine at_northern_limit + + @Test + subroutine at_southern_limit(this) + class(TestLatbaset), intent(inout) :: this + + baset = 5._r8 + latdeg = -30._r8 + baset_latvary_intercept = 12._r8 + baset_latvary_slope = 0.4_r8 + + @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) + end subroutine at_southern_limit + + @Test + subroutine in_nh(this) + class(TestLatbaset), intent(inout) :: this + + baset = 5._r8 + latdeg = 10._r8 + baset_latvary_intercept = 13._r8 + baset_latvary_slope = 0.3_r8 + + @assertEqual(15._r8, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) + end subroutine in_nh + + @Test + subroutine in_sh(this) + class(TestLatbaset), intent(inout) :: this + + baset = 5._r8 + latdeg = -10._r8 + baset_latvary_intercept = 13._r8 + baset_latvary_slope = 0.3_r8 + + @assertEqual(15._r8, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) + end subroutine in_sh + +end module test_Latbaset + From 151cf482e3a31f548916c4fd794825aec0f3cc84 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 Nov 2023 12:21:46 -0700 Subject: [PATCH 1814/2067] latbaset() now uses baset_latvary_intercept and _slope. --- src/biogeochem/CropType.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 7e4dec6c1f..b3e09b3adf 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -975,9 +975,9 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary real(r8), intent(in) :: baset_latvary_slope if ( latdeg >= 0.0_r8 .and. latdeg <= 30.0_r8) then - latbaset = baset + 12._r8 - 0.4_r8*latdeg + latbaset = baset + baset_latvary_intercept - baset_latvary_slope*latdeg else if (latdeg < 0.0_r8 .and. latdeg >= -30.0_r8) then - latbaset = baset + 12._r8 + 0.4_r8*latdeg + latbaset = baset + baset_latvary_intercept + baset_latvary_slope*latdeg else latbaset = baset end if From 054f2a6f3d81f008ac21a5a885a708494862d2f9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 Nov 2023 12:27:44 -0700 Subject: [PATCH 1815/2067] Simplify latbaset(). --- src/biogeochem/CropType.F90 | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index b3e09b3adf..8068fed4d9 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -973,14 +973,18 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary real(r8), intent(in) :: latdeg real(r8), intent(in) :: baset_latvary_intercept real(r8), intent(in) :: baset_latvary_slope + ! + ! !LOCAL VARIABLES + real(r8) :: maxlat ! Outside latitude range defined by ±maxlat, use baset - if ( latdeg >= 0.0_r8 .and. latdeg <= 30.0_r8) then - latbaset = baset + baset_latvary_intercept - baset_latvary_slope*latdeg - else if (latdeg < 0.0_r8 .and. latdeg >= -30.0_r8) then - latbaset = baset + baset_latvary_intercept + baset_latvary_slope*latdeg - else + maxlat = 30._r8 + + if (abs(latdeg) > maxlat) then latbaset = baset + else + latbaset = baset + baset_latvary_intercept - baset_latvary_slope*abs(latdeg) end if + end function latbaset end module CropType From f2d30ed3da8129921be56e7897d39acbb57be5b9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 Nov 2023 13:23:06 -0700 Subject: [PATCH 1816/2067] Do not hard-code maxlat. --- src/biogeochem/CropType.F90 | 10 +++++++++- src/biogeochem/test/Latbaset_test/test_Latbaset.pf | 10 +++++----- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 8068fed4d9..7e80d4a9ea 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -24,6 +24,7 @@ module CropType ! ! !PUBLIC DATA TYPES: public :: latbaset + public :: latbaset_max_lat ! ! Possible values of cphase @@ -977,7 +978,7 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary ! !LOCAL VARIABLES real(r8) :: maxlat ! Outside latitude range defined by ±maxlat, use baset - maxlat = 30._r8 + maxlat = latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) if (abs(latdeg) > maxlat) then latbaset = baset @@ -987,4 +988,11 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary end function latbaset + real(r8) function latbaset_max_lat(intercept, slope) + real(r8), intent(in) :: intercept + real(r8), intent(in) :: slope + + latbaset_max_lat = intercept / slope + end function latbaset_max_lat + end module CropType diff --git a/src/biogeochem/test/Latbaset_test/test_Latbaset.pf b/src/biogeochem/test/Latbaset_test/test_Latbaset.pf index 1b164d5d69..8fcc4de1bb 100644 --- a/src/biogeochem/test/Latbaset_test/test_Latbaset.pf +++ b/src/biogeochem/test/Latbaset_test/test_Latbaset.pf @@ -7,7 +7,7 @@ module test_Latbaset use unittestSubgridMod use unittestSimpleSubgridSetupsMod use unittestFilterBuilderMod - use CropType, only : latbaset + use CropType, only : latbaset, latbaset_max_lat implicit none @@ -41,9 +41,9 @@ contains class(TestLatbaset), intent(inout) :: this baset = 5._r8 - latdeg = 80._r8 baset_latvary_intercept = 8.7_r8 baset_latvary_slope = 0.5_r8 + latdeg = 10._r8 + latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) end subroutine too_far_north @@ -53,9 +53,9 @@ contains class(TestLatbaset), intent(inout) :: this baset = 5._r8 - latdeg = -80._r8 baset_latvary_intercept = 8.7_r8 baset_latvary_slope = 0.5_r8 + latdeg = -10._r8 - latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) end subroutine too_far_south @@ -65,9 +65,9 @@ contains class(TestLatbaset), intent(inout) :: this baset = 5._r8 - latdeg = 30._r8 baset_latvary_intercept = 12._r8 baset_latvary_slope = 0.4_r8 + latdeg = latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) end subroutine at_northern_limit @@ -77,9 +77,9 @@ contains class(TestLatbaset), intent(inout) :: this baset = 5._r8 - latdeg = -30._r8 baset_latvary_intercept = 12._r8 baset_latvary_slope = 0.4_r8 + latdeg = -latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) @assertEqual(baset, latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary_slope)) end subroutine at_southern_limit From aa61010e2700854ab01feec060870c5358f26e45 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 8 Nov 2023 13:40:47 -0700 Subject: [PATCH 1817/2067] Convert latbaset() to a one-liner. --- src/biogeochem/CropType.F90 | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 7e80d4a9ea..11972d3286 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -974,17 +974,17 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary real(r8), intent(in) :: latdeg real(r8), intent(in) :: baset_latvary_intercept real(r8), intent(in) :: baset_latvary_slope - ! - ! !LOCAL VARIABLES - real(r8) :: maxlat ! Outside latitude range defined by ±maxlat, use baset - maxlat = latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) + ! Was originally + ! maxlat = latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) + ! if (abs(latdeg) > maxlat) then + ! latbaset = baset + ! else + ! latbaset = baset + baset_latvary_intercept - baset_latvary_slope*abs(latdeg) + ! end if + ! But the one-liner below should improve efficiency, at least marginally. - if (abs(latdeg) > maxlat) then - latbaset = baset - else - latbaset = baset + baset_latvary_intercept - baset_latvary_slope*abs(latdeg) - end if + latbaset = baset + baset_latvary_intercept - min(baset_latvary_intercept, baset_latvary_slope * abs(latdeg)) end function latbaset From e421959a3a506023e688a3f72dbbe5b3d101364f Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 8 Nov 2023 19:26:07 -0700 Subject: [PATCH 1818/2067] Changed fates long test to be FatesColdNoComp, increased wall time too --- cime_config/testdefs/testlist_clm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 8c928e1bd6..34c2cc33f9 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1563,14 +1563,14 @@ - + - + From 35478a38d5e5448444cf7486d3c82cdf2c769240 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 9 Nov 2023 13:23:37 -0700 Subject: [PATCH 1819/2067] Improve CropType%InitCold() efficiency. --- src/biogeochem/CropType.F90 | 35 +++++++++++++++-------------------- 1 file changed, 15 insertions(+), 20 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 11972d3286..03e25135e6 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -373,37 +373,32 @@ subroutine InitCold(this, bounds) type(bounds_type), intent(in) :: bounds ! ! !LOCAL VARIABLES: - integer :: c, l, g, p, m, ivt ! indices + integer :: l, g, p, ivt ! indices + logical :: latvary_baset character(len=*), parameter :: subname = 'InitCold' !----------------------------------------------------------------------- -!DLL - added wheat & sugarcane restrictions to base T vary by lat + latvary_baset = trim(this%baset_mapping) == baset_map_latvary + if (.not. latvary_baset) then + this%latbaset_patch(bounds%begp:bounds%endp) = nan + end if + do p= bounds%begp,bounds%endp - g = patch%gridcell(p) - ivt = patch%itype(p) + l = patch%landunit(p) this%nyrs_crop_active_patch(p) = 0 - this%latbaset_patch(p) = latbaset(pftcon%baset(ivt), grc%latdeg(g), this%baset_latvary_intercept, this%baset_latvary_slope) - if ( trim(this%baset_mapping) == baset_map_constant ) then - this%latbaset_patch(p) = nan - end if - end do -!DLL -- end of mods - - if (use_crop) then - do p= bounds%begp,bounds%endp + if (lun%itype(l) == istcrop) then g = patch%gridcell(p) - l = patch%landunit(p) - c = patch%column(p) + ivt = patch%itype(p) + this%fertnitro_patch(p) = fert_cft(g,ivt) - if (lun%itype(l) == istcrop) then - m = patch%itype(p) - this%fertnitro_patch(p) = fert_cft(g,m) + if (latvary_baset) then + this%latbaset_patch(p) = latbaset(pftcon%baset(ivt), grc%latdeg(g), this%baset_latvary_intercept, this%baset_latvary_slope) end if - end do - end if + end if + end do end subroutine InitCold From 901656a5d8e67a84982c80044709d27d8f9def4f Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 10 Nov 2023 15:31:03 -0700 Subject: [PATCH 1820/2067] Updating fates external to api30 --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 38ecd0dd3e..cab31b6b7f 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -branch = nocomp-fix-tests +repo_url = https://github.com/NGEET/fates +tag = sci.1.68.2_api.30.0.0 required = True [externals_description] From 1e190bb58b25ffd4320f5747727fcd1c31a92561 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Fri, 10 Nov 2023 15:49:10 -0700 Subject: [PATCH 1821/2067] Added changelogs --- doc/ChangeLog | 74 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 75 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index a5eba5e49e..067fb4ed98 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,78 @@ =============================================================== +Tag name: ctsm5.1.dev151 +Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153) +Date: Fri Nov 10 15:33:37 MST 2023 +One-line Summary: Fixes to FATES long run restarts + +Purpose and description of changes +---------------------------------- + +This is a set of changes that enables exact restart tests to pass with FATES, for + longer periods, particularly those that have elapsed over a year. + We removed calls that were incrementing, uncecessary calls, and added key new + variables to the restart file (such as the leaf layer carbon balance vector). + +Collaborators: @mvdebolskiy, @mvertens, @glemieux, @ekluzek, @ckoven, @rosiealice + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +No changes to scientifically-supported configurations. + +Bugs fixed or introduced +------------------------ + +Fixes: FATES#1051 https://github.com/NGEET/fates/issues/1051 + +Notes of particular relevance for users +--------------------------------------- + +This set of changes is introduced, while there is a known test failure in: +ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial + +This is documented in issue: 2236 and a fix is slated for integration. The nature of the changes + in this PR where obviously orthogonal to the issue. + +Substantial timing or memory changes: None + + +Notes of particular relevance for developers: +--------------------------------------------- + +A new test was added to aux_clm and fates test suites. The walltime for this test + was 29 minutes. This is an important new test for FATES because it is the + first gridded test that spans significantly over a year (and passes). Various test + configurations were explored to find a gridded test that completed 25 months + with some attempt at expedience in walltime. A walltime + allowance of 60 minutes is set in the test. Here is the test: + ERS_P144x1_Lm25.f10_f10_mg37.I2000Clm51Fates clm-FatesColdNoComp + + +Testing summary: +---------------- + regular tests: + + cheyenne ---- ok + izumi ------- ok + +Answer changes +-------------- + +No answer changes + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates API30 + +Pull Requests that document the changes (include PR ids): + +https://github.com/ESCOMP/CTSM/pull/2199 +https://github.com/NGEET/fates/pull/1098 + + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev150 Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153) Date: Mon Nov 6 14:12:37 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index ecaa21c598..de15031e69 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev151 rgknox 11/10/2023 Fixes to FATES long run restarts ctsm5.1.dev150 rgknox 11/06/2023 FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM. ctsm5.1.dev149 samrabin 11/03/2023 Rearrange leaf/stem "harvest" and fix soil gas diffusivity ctsm5.1.dev148 samrabin 11/03/2023 Add GRAINN outputs From 808c947ffdb83e0252bff6c18095092eefee8bc5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 11 Nov 2023 16:52:50 -0700 Subject: [PATCH 1822/2067] Add #2236 to expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 8e72abb8eb..b696fadcf2 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -57,6 +57,13 @@ + + + FAIL + #2236 + + + From 2b186d2519082529d3bccbb47cf7dcc5b2d9801c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 11 Nov 2023 16:53:49 -0700 Subject: [PATCH 1823/2067] Update changelog --- doc/ChangeLog | 2 +- doc/ChangeSum | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 067fb4ed98..66fc04a752 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev151 Originator(s): rgknox (Ryan Knox,LAWRENCE BERKELEY NATIONAL LABORATORY,510-495-2153) -Date: Fri Nov 10 15:33:37 MST 2023 +Date: Sat Nov 11 16:53:01 MST 2023 One-line Summary: Fixes to FATES long run restarts Purpose and description of changes diff --git a/doc/ChangeSum b/doc/ChangeSum index de15031e69..9ef20790d9 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev151 rgknox 11/10/2023 Fixes to FATES long run restarts + ctsm5.1.dev151 rgknox 11/11/2023 Fixes to FATES long run restarts ctsm5.1.dev150 rgknox 11/06/2023 FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM. ctsm5.1.dev149 samrabin 11/03/2023 Rearrange leaf/stem "harvest" and fix soil gas diffusivity ctsm5.1.dev148 samrabin 11/03/2023 Add GRAINN outputs From 239aa8715b278c8a1925d157cb0facbee5bc34b0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 12 Nov 2023 13:01:11 -0700 Subject: [PATCH 1824/2067] Move latbaset_max_lat() to test_Latbaset. --- src/biogeochem/CropType.F90 | 10 +--------- src/biogeochem/test/Latbaset_test/test_Latbaset.pf | 9 ++++++++- 2 files changed, 9 insertions(+), 10 deletions(-) diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90 index 03e25135e6..2e059c5ac1 100644 --- a/src/biogeochem/CropType.F90 +++ b/src/biogeochem/CropType.F90 @@ -24,7 +24,6 @@ module CropType ! ! !PUBLIC DATA TYPES: public :: latbaset - public :: latbaset_max_lat ! ! Possible values of cphase @@ -971,7 +970,7 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary real(r8), intent(in) :: baset_latvary_slope ! Was originally - ! maxlat = latbaset_max_lat(baset_latvary_intercept, baset_latvary_slope) + ! maxlat = baset_latvary_intercept / baset_latvary_slope ! if (abs(latdeg) > maxlat) then ! latbaset = baset ! else @@ -983,11 +982,4 @@ real(r8) function latbaset(baset, latdeg, baset_latvary_intercept, baset_latvary end function latbaset - real(r8) function latbaset_max_lat(intercept, slope) - real(r8), intent(in) :: intercept - real(r8), intent(in) :: slope - - latbaset_max_lat = intercept / slope - end function latbaset_max_lat - end module CropType diff --git a/src/biogeochem/test/Latbaset_test/test_Latbaset.pf b/src/biogeochem/test/Latbaset_test/test_Latbaset.pf index 8fcc4de1bb..ebb5bfa5e4 100644 --- a/src/biogeochem/test/Latbaset_test/test_Latbaset.pf +++ b/src/biogeochem/test/Latbaset_test/test_Latbaset.pf @@ -7,7 +7,7 @@ module test_Latbaset use unittestSubgridMod use unittestSimpleSubgridSetupsMod use unittestFilterBuilderMod - use CropType, only : latbaset, latbaset_max_lat + use CropType, only : latbaset implicit none @@ -36,6 +36,13 @@ contains call unittest_subgrid_teardown() end subroutine tearDown + real(r8) function latbaset_max_lat(intercept, slope) + real(r8), intent(in) :: intercept + real(r8), intent(in) :: slope + + latbaset_max_lat = intercept / slope + end function latbaset_max_lat + @Test subroutine too_far_north(this) class(TestLatbaset), intent(inout) :: this From 60d99ba2f738d178af4365baa7c7d0304260af3e Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Mon, 13 Nov 2023 10:15:19 +0100 Subject: [PATCH 1825/2067] update ccs_config and add 10x15 default pes betzy --- Externals.cfg | 2 +- cime_config/config_pes.xml | 40 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 41 insertions(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index edee8c8d13..4a41895631 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_noresm0.0.8 +tag = ccs_config_noresm0.0.22 protocol = git repo_url = https://github.com/NorESMhub/ccs_config_noresm.git local_path = ccs_config diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 4513b28728..d6f90167e1 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -1485,4 +1485,44 @@ + + + + + none + + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + + From df110db54f2fdea4ae2a314dd65c48b716ac1ce3 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 14 Nov 2023 12:51:09 -0700 Subject: [PATCH 1826/2067] Update ChangeLog/ChangeSum --- doc/ChangeLog | 108 ++++++++++++++++++++++++++++---------------------- doc/ChangeSum | 2 +- 2 files changed, 61 insertions(+), 49 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 374793cd34..50636efe5a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,12 +1,13 @@ =============================================================== Tag name: ctsm5.1.dev152 -Originator(s): multiple (Teagan King,UCAR/CCR; slevis TSS) -Date: Thu Nov 2 16:03:44 MDT 2023 -One-line Summary: Move tools to python directory and add tests; also... +Originator(s): multiple (tking (Teagan King); slevis (Sam Levis); AdrienDams (Adrien Damseaux); afoster (Adrianna Foster); samrabin (Sam Rabin); ekluzek (Erik Kluzek); wwieder (Will Wieder); sacks (Bill Sacks); a few others listed below) +Date: Tue Nov 14 10:54:43 MST 2023 +One-line Summary: Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors Purpose and description of changes ---------------------------------- +#2156 tking, slevis Move the following scripts to /python/ctsm/site_and_regional and make wrapper scripts for them in /tools/site_and_regional: - run_neon.py @@ -23,6 +24,30 @@ Add system testing for: - modify_singlept_site_neon - run_neon +#2148 Adrien Damseaux, Victoria Dutch, Leanne Wake +Add namelist option snow_thermal_cond_method to select between Jordan (1991) (default) and +Sturm et al. (1997). Sturm option described for single point runs by Dutch et al. (2022). + +#2233 afoster, sacks +Fix a compiler error (for GNU 13.2) within cropcalStreamMod. +Simple fix was to change whole-array assignments/references for the starts and ends arrays to specifically +reference bounds (begp and endp). + +#2235 srabin, wwieder +Refactor ssp_anomaly_forcing script to make it easier to read and more amenable to future development. +- Adds --output-dir option; default ./anomaly_forcing reproduces previous behavior +- Makes synonyms for options with hyphens replacing underscores + +#2237 srabin +Add the following fields to restart files: +- repr_grainc_to_seed_perharv_patch +- swindow_starts_thisyr_patch +- swindow_ends_thisyr_patch + +#2044 ekluzek +More confined regular expression for NEON and a few simple fixes. + + Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -43,50 +68,35 @@ Does this tag change answers significantly for any of the following physics conf Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): -#1441 +Closes #2156 Fixes #1441 +Closes #2148 +Closes #2233 Fixes #2232 +Closes #2235 +Closes #2237 Fixes #2236 +Closes #2044 Fixes #2039 Fixes #2103 Fixes #2028 Fixes #1506 Fixes #1499 Known Issues: -There were some previous pylint errors that still remain in this tag. +pylint errors from previous work remain in this tag. Notes of particular relevance for users --------------------------------------- Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): -wrapper scripts don't have .py suffixes +#2156 New wrapper scripts don't have .py suffixes. +#2148 New namelist option snow_thermal_cond_method as described above. +#2133 None +#2135 New --output-dir option; default ./anomaly_forcing reproduces previous behavior. +Also makes synonyms for options with hyphens replacing underscores. +#2137 None +#2044 None Notes of particular relevance for developers: --------------------------------------------- Changes to tests or testing: -Numerous changes were made to include new tests. -README.md for testing was also updated to clarify that arguments should be used. +#2156 Numerous changes were made to include new tests. +README.md for testing was updated to clarify that arguments should be used. Testing summary: ---------------- -[... Remove before making master tag. - -Nearly all CTSM tags should undergo 'regular' (aux_clm) testing. -However, it occasionally makes sense to do more or less system testing; -here is guidance on different available levels of system testing: - a) no system testing (for use when the only changes are ones that - have absolutely no impact on system runs; this - includes documentation-only tags, tags that - just change the tools or some python code that - does not impact system runs, etc.) - b) minimal (for use in rare cases where only a small change with - known behavior is added ... eg. a minor bug fix. This - might be to just run the "short" test list, or to run - a single test. Whatever makes sense for the particular case.) - c) python only (for use where the only changes are in the python directory: - run the python testing listed below) - d) regular (regular tests on normal machines if CTSM source is modified) - e) release (regular tests plus the fates, ctsm_sci, mosart and rtm test lists - and normally all of the ancillary tests (build-namelist, python, ptclm, etc.) - would be run as well) - -In addition, various other tests of the tools, python and perl -infrastructure should be run when appropriate, as described below. - -...] - [Remove any lines that don't apply.] [PASS means all tests PASS; OK means tests PASS other than expected fails.] @@ -101,21 +111,11 @@ infrastructure should be run when appropriate, as described below. python testing (if python code has changed; see instructions in python/README.md; document testing done): - (any machine) - - - [If python code has changed and you are NOT running aux_clm (e.g., because the only changes are in python - code) then also run the clm_pymods test suite; this is a small subset of aux_clm that runs the system - tests impacted by python changes. The best way to do this, if you expect no changes from the last tag in - either model output or namelists, is: create sym links pointing to the last tag's baseline directory, - named with the upcoming tag; then run the clm_pymods test suite comparing against these baselines but NOT - doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to - separately run the clm_pymods test suite, and you can remove the following line.] - - clm_pymods test suite on cheyenne - + (any machine) - cheyenne OK (pylint suggestions from previous work remain) regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- + cheyenne ---- IN PROGRESS izumi ------- fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) @@ -128,12 +128,24 @@ If the tag used for baseline comparisons was NOT the previous tag, note that her Answer changes -------------- -Changes answers relative to baseline: None +Changes answers relative to baseline: +#2156 NO +#2148 NO +#2233 NO +#2235 Adds attributes to write_climo files' dimension variables +#2237 ONLY Smallville "no initial" restarts; specifically, this previously failing (COMPARE_base_rest) +aux_clm test ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial +#2044 For NEON cases? Other details ------------- Pull Requests that document the changes (include PR ids): -(https://github.com/ESCOMP/ctsm/pull/2156) + https://github.com/ESCOMP/ctsm/pull/2156 + https://github.com/ESCOMP/ctsm/pull/2148 + https://github.com/ESCOMP/ctsm/pull/2233 + https://github.com/ESCOMP/ctsm/pull/2235 + https://github.com/ESCOMP/ctsm/pull/2237 + https://github.com/ESCOMP/ctsm/pull/2044 =============================================================== =============================================================== diff --git a/doc/ChangeSum b/doc/ChangeSum index 8668cd240a..6af88be0e4 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev152 multiple 11/13/2023 Move tools to python directory and add tests and... + ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors ctsm5.1.dev151 rgknox 11/11/2023 Fixes to FATES long run restarts ctsm5.1.dev150 rgknox 11/06/2023 FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM. ctsm5.1.dev149 samrabin 11/03/2023 Rearrange leaf/stem "harvest" and fix soil gas diffusivity From ed57371cb5d6d9f9461472c747d6ab02030e4893 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 14 Nov 2023 13:09:03 -0700 Subject: [PATCH 1827/2067] Minor update to ChangeLog --- doc/ChangeLog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 50636efe5a..c198863971 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -24,7 +24,7 @@ Add system testing for: - modify_singlept_site_neon - run_neon -#2148 Adrien Damseaux, Victoria Dutch, Leanne Wake +#2148 Adrien Damseaux (AWI, Germany), Victoria Dutch, Leanne Wake Add namelist option snow_thermal_cond_method to select between Jordan (1991) (default) and Sturm et al. (1997). Sturm option described for single point runs by Dutch et al. (2022). From db5806ab4cfebfc104e71eb3804e7d5c91631a89 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 14 Nov 2023 17:15:04 -0700 Subject: [PATCH 1828/2067] Remove test from ExpectedTestFails.xml and update ChangeLog --- cime_config/testdefs/ExpectedTestFails.xml | 7 ------ doc/ChangeLog | 28 ++++++++++++++++------ 2 files changed, 21 insertions(+), 14 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index b696fadcf2..8e72abb8eb 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -57,13 +57,6 @@ - - - FAIL - #2236 - - - diff --git a/doc/ChangeLog b/doc/ChangeLog index c198863971..9405e19922 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev152 Originator(s): multiple (tking (Teagan King); slevis (Sam Levis); AdrienDams (Adrien Damseaux); afoster (Adrianna Foster); samrabin (Sam Rabin); ekluzek (Erik Kluzek); wwieder (Will Wieder); sacks (Bill Sacks); a few others listed below) -Date: Tue Nov 14 10:54:43 MST 2023 +Date: Tue Nov 14 17:09:43 MST 2023 One-line Summary: Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors Purpose and description of changes @@ -115,8 +115,14 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- IN PROGRESS - izumi ------- + cheyenne ---- OK + izumi ------- OK, the following PASS/FAILs are expected: + +PASS ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial COMPARE_base_rest (UNEXPECTED: expected FAIL) +FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial BASELINE ctsm5.1.dev151: DIFF + +FAIL SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-default--clm-NEON-NIWO BASELINE ctsm5.1.dev151: DIFF +FAIL SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM BASELINE ctsm5.1.dev151: DIFF fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) cheyenne ---- @@ -132,10 +138,18 @@ Changes answers relative to baseline: #2156 NO #2148 NO #2233 NO -#2235 Adds attributes to write_climo files' dimension variables -#2237 ONLY Smallville "no initial" restarts; specifically, this previously failing (COMPARE_base_rest) -aux_clm test ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial -#2044 For NEON cases? +#2235 NO, adds attributes to write_climo files' dimension variables +#2237 ONLY Smallville "no initial" restarts; specifically, this previously +failing (COMPARE_base_rest) aux_clm test +ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial +now differs from the baseline as follows: + SUMMARY of cprnc: + A total number of 76 fields were compared + and 3 had differences in fill patterns + A total number of 2 fields could not be analyzed + diff_test: the two files seem to be DIFFERENT +#2044 ONLY the NEON tests listed above due to the one-line change in +cime_config/usermods_dirs/NEON/defaults/shell_commands in #2044 Other details ------------- From 9e0f81c1a531786844a17005af6c86ae0fcf867b Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 15 Nov 2023 08:05:47 -0700 Subject: [PATCH 1829/2067] Fix subset_data error 'no attribute evenly_split_cropland' --- python/ctsm/subset_data.py | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/python/ctsm/subset_data.py b/python/ctsm/subset_data.py index a99d42cc14..030cea2247 100644 --- a/python/ctsm/subset_data.py +++ b/python/ctsm/subset_data.py @@ -149,6 +149,13 @@ def get_parser(): dest="cap_saturation", required=False, ) + pt_parser.add_argument( + "--evenly_split_cropland", + help="Introduce equal areas of all crops", + action="store_true", + dest="evenly_split_cropland", + required=False, + ) pt_parser.add_argument( "--dompft", help="Dominant PFT(s): if we set the grid to 100%% one or multiple PFTs \ From d895c6eecbbc943a0cfd1a775cc53e0952199c8e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 15 Nov 2023 13:10:26 -0700 Subject: [PATCH 1830/2067] Updates recommended by pylint while keeping black passing --- .../modify_singlept_site_neon.py | 132 +++++++++--------- .../site_and_regional/neon_surf_wrapper.py | 6 +- python/ctsm/site_and_regional/run_neon.py | 123 ++++++++-------- .../test_sys_modify_singlept_site_neon.py | 3 +- python/ctsm/test/test_sys_run_neon.py | 4 +- 5 files changed, 132 insertions(+), 136 deletions(-) diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py index 1013ba944c..ae1318e2f8 100755 --- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py +++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py @@ -178,8 +178,8 @@ def get_neon(neon_dir, site_name): ) response = requests.get(url) - with open(neon_file, "wb") as f: - f.write(response.content) + with open(neon_file, "wb") as a_file: + a_file.write(response.content) # -- Check if download status_code if response.status_code == 200: @@ -274,12 +274,12 @@ def find_soil_structure(args, surf_file): print("------------") print("surf_file : ", surf_file) - f1 = xr.open_dataset(surf_file) + f_1 = xr.open_dataset(surf_file) print("------------") - # print (f1.attrs["Soil_texture_raw_data_file_name"]) + # print (f_1.attrs["Soil_texture_raw_data_file_name"]) clm_input_dir = os.path.join(args.inputdatadir, "lnd/clm2/rawdata/") - surf_soildepth_file = os.path.join(clm_input_dir, f1.attrs["Soil_texture_raw_data_file_name"]) + surf_soildepth_file = os.path.join(clm_input_dir, f_1.attrs["Soil_texture_raw_data_file_name"]) if os.path.exists(surf_soildepth_file): print( @@ -287,9 +287,9 @@ def find_soil_structure(args, surf_file): surf_soildepth_file, "for surface data soil structure information:", ) - f1_soildepth = xr.open_dataset(surf_soildepth_file) - print(f1_soildepth["DZSOI"]) - soil_bot = f1_soildepth["DZSOI"].values + f_1_soildepth = xr.open_dataset(surf_soildepth_file) + print(f_1_soildepth["DZSOI"]) + soil_bot = f_1_soildepth["DZSOI"].values # -- soil layer top soil_top = soil_bot[:-1] @@ -303,34 +303,34 @@ def find_soil_structure(args, surf_file): return soil_bot, soil_top -def update_metadata(nc, surf_file, neon_file, zb_flag): +def update_metadata(nc_file, surf_file, neon_file, zb_flag): """ Function for updating modified surface dataset metadata for neon sites. Args: - nc (xr Dataset): netcdf file including updated neon surface data + nc_file (xr Dataset): netcdf file including updated neon surface data surf_file (str): single point surface data filename neon_file (str): filename of neon downloaded surface dataset zb_flag (bool): update bedrock Returns: - nc (xr Dataset): netcdf file including updated neon surface data + nc_file (xr Dataset): netcdf file including updated neon surface data """ today = date.today() today_string = today.strftime("%Y-%m-%d") - nc.attrs["Updated_on"] = today_string - nc.attrs["Updated_by"] = myname - nc.attrs["Updated_with"] = os.path.abspath(__file__) - nc.attrs["Updated_from"] = surf_file - nc.attrs["Updated_using"] = neon_file + nc_file.attrs["Updated_on"] = today_string + nc_file.attrs["Updated_by"] = myname + nc_file.attrs["Updated_with"] = os.path.abspath(__file__) + nc_file.attrs["Updated_from"] = surf_file + nc_file.attrs["Updated_using"] = neon_file if zb_flag: - nc.attrs["Updated_fields"] = "PCT_CLAY, PCT_SAND, ORGANIC, zbedrock" + nc_file.attrs["Updated_fields"] = "PCT_CLAY, PCT_SAND, ORGANIC, zbedrock" else: - nc.attrs["Updated_fields"] = "PCT_CLAY, PCT_SAND, ORGANIC" + nc_file.attrs["Updated_fields"] = "PCT_CLAY, PCT_SAND, ORGANIC" - return nc + return nc_file def update_time_tag(fname_in): @@ -387,7 +387,7 @@ def sort_print_soil_layers(obs_bot, soil_bot): print("================================", "================================") - for index, row in depth_df.iterrows(): + for _, row in depth_df.iterrows(): if row["type"] == "obs": print("-------------", "{0:.3f}".format(row["depth"]), "------------") else: @@ -413,10 +413,9 @@ def check_neon_time(): download_file(url, listing_file) - df = pd.read_csv(listing_file) - df = df[df["object"].str.contains("_surfaceData.csv")] - # df=df.join(df['object'].str.split("/", expand=True)) - dict_out = dict(zip(df["object"], df["last_modified"])) + d_f = pd.read_csv(listing_file) + d_f = d_f[d_f["object"].str.contains("_surfaceData.csv")] + dict_out = dict(zip(d_f["object"], d_f["last_modified"])) print(dict_out) return dict_out @@ -433,8 +432,8 @@ def download_file(url, fname): try: response = requests.get(url) - with open(fname, "wb") as f: - f.write(response.content) + with open(fname, "wb") as a_file: + a_file.write(response.content) # -- Check if download status_code if response.status_code == 200: @@ -447,7 +446,7 @@ def download_file(url, fname): print("Error code:", err.code) -def fill_interpolate(f2, var, method): +def fill_interpolate(f_2, var, method): """ Function to interpolate a variable in a xarray dataset a specific method @@ -456,26 +455,25 @@ def fill_interpolate(f2, var, method): print("Filling in ", var, "with interpolation (method =" + method + ").") print("Variable before filling : ") - print(f2[var]) + print(f_2[var]) - tmp_df = pd.DataFrame(f2[var].values.ravel()) + tmp_df = pd.DataFrame(f_2[var].values.ravel()) tmp_df = tmp_df.interpolate(method=method, limit_direction="both") - # tmp_df = tmp_df.interpolate(method ='spline',order = 2, limit_direction ='both') - # tmp_df = tmp_df.interpolate(method="pad", limit=5, limit_direction = 'forward') tmp = tmp_df.to_numpy() - soil_levels = f2[var].size + soil_levels = f_2[var].size for soil_lev in range(soil_levels): - f2[var][soil_lev] = tmp[soil_lev].reshape(1, 1) + f_2[var][soil_lev] = tmp[soil_lev].reshape(1, 1) print("Variable after filling : ") - print(f2[var]) + print(f_2[var]) print("=====================================") def main(): + """modify_singlept_site_neon main function""" args = get_parser().parse_args() # -- debugging option @@ -501,7 +499,6 @@ def main(): surf_file = find_surffile(surf_dir, site_name, args.pft_16) # -- directory structure - current_dir = os.getcwd() clone_dir = os.path.abspath(os.path.join(__file__, "../../../..")) neon_dir = os.path.join(clone_dir, "neon_surffiles") @@ -509,11 +506,11 @@ def main(): neon_file = get_neon(neon_dir, site_name) # -- Read neon data - df = pd.read_csv(neon_file) + d_f = pd.read_csv(neon_file) # -- Read surface dataset files print("surf_file:", surf_file) - f1 = xr.open_dataset(surf_file) + f_1 = xr.open_dataset(surf_file) # -- Find surface dataset soil depth information soil_bot, soil_top = find_soil_structure(args, surf_file) @@ -529,10 +526,10 @@ def main(): soil_mid = 0.5 * (soil_bot - soil_top) + soil_top # print ("Cumulative sum of soil bottom depths :", sum(soil_bot)) - obs_bot = df["biogeoBottomDepth"] / 100 + obs_bot = d_f["biogeoBottomDepth"] / 100 # -- Mapping surface dataset and neon soil levels - bins = df["biogeoTopDepth"] / 100 + bins = d_f["biogeoTopDepth"] / 100 bin_index = np.digitize(soil_mid, bins) - 1 """ @@ -560,18 +557,18 @@ def main(): """ # -- update fields with neon - f2 = f1 - soil_levels = f2["PCT_CLAY"].size + f_2 = f_1 + soil_levels = f_2["PCT_CLAY"].size for soil_lev in range(soil_levels): print("--------------------------") print("soil_lev:", soil_lev) - print(df["clayTotal"][bin_index[soil_lev]]) - f2["PCT_CLAY"][soil_lev] = df["clayTotal"][bin_index[soil_lev]] - f2["PCT_SAND"][soil_lev] = df["sandTotal"][bin_index[soil_lev]] + print(d_f["clayTotal"][bin_index[soil_lev]]) + f_2["PCT_CLAY"][soil_lev] = d_f["clayTotal"][bin_index[soil_lev]] + f_2["PCT_SAND"][soil_lev] = d_f["sandTotal"][bin_index[soil_lev]] - bulk_den = df["bulkDensExclCoarseFrag"][bin_index[soil_lev]] - carbon_tot = df["carbonTot"][bin_index[soil_lev]] - estimated_oc = df["estimatedOC"][bin_index[soil_lev]] + bulk_den = d_f["bulkDensExclCoarseFrag"][bin_index[soil_lev]] + carbon_tot = d_f["carbonTot"][bin_index[soil_lev]] + estimated_oc = d_f["estimatedOC"][bin_index[soil_lev]] # -- estimated_oc in neon data is rounded to the nearest integer. # -- Check to make sure the rounded oc is not higher than carbon_tot. @@ -580,10 +577,11 @@ def main(): estimated_oc = min(estimated_oc, carbon_tot) layer_depth = ( - df["biogeoBottomDepth"][bin_index[soil_lev]] - df["biogeoTopDepth"][bin_index[soil_lev]] + d_f["biogeoBottomDepth"][bin_index[soil_lev]] + - d_f["biogeoTopDepth"][bin_index[soil_lev]] ) - # f2["ORGANIC"][soil_lev] = estimated_oc * bulk_den / 0.58 + # f_2["ORGANIC"][soil_lev] = estimated_oc * bulk_den / 0.58 # -- after adding caco3 by NEON: # -- if caco3 exists: @@ -592,7 +590,7 @@ def main(): # -- else: # -- organic = estimated_oc * bulk_den /0.58 - caco3 = df["caco3Conc"][bin_index[soil_lev]] + caco3 = d_f["caco3Conc"][bin_index[soil_lev]] inorganic = caco3 / 100.0869 * 12.0107 print("inorganic:", inorganic) @@ -601,7 +599,7 @@ def main(): else: actual_oc = estimated_oc - f2["ORGANIC"][soil_lev] = actual_oc * bulk_den / 0.58 + f_2["ORGANIC"][soil_lev] = actual_oc * bulk_den / 0.58 print("~~~~~~~~~~~~~~~~~~~~~~~~") print("inorganic:") @@ -614,14 +612,14 @@ def main(): print("carbon_tot : ", carbon_tot) print("estimated_oc : ", estimated_oc) print("bulk_den : ", bulk_den) - print("organic :", f2["ORGANIC"][soil_lev].values) + print("organic :", f_2["ORGANIC"][soil_lev].values) print("--------------------------") # -- Interpolate missing values method = "linear" - fill_interpolate(f2, "PCT_CLAY", method) - fill_interpolate(f2, "PCT_SAND", method) - fill_interpolate(f2, "ORGANIC", method) + fill_interpolate(f_2, "PCT_CLAY", method) + fill_interpolate(f_2, "PCT_SAND", method) + fill_interpolate(f_2, "ORGANIC", method) # -- Update zbedrock if neon observation does not make it down to 2m depth rock_thresh = 2 @@ -630,7 +628,7 @@ def main(): if obs_bot.iloc[-1] < rock_thresh: print("zbedrock is updated.") - f2["zbedrock"].values[:, :] = obs_bot.iloc[-1] + f_2["zbedrock"].values[:, :] = obs_bot.iloc[-1] zb_flag = True sort_print_soil_layers(obs_bot, soil_bot) @@ -639,18 +637,18 @@ def main(): ag_sites = ["KONA", "STER"] if site_name in ag_sites: print("Updating PCT_NATVEG") - print("Original : ", f2.PCT_NATVEG.values) - f2.PCT_NATVEG.values = [[0.0]] - print("Updated : ", f2.PCT_NATVEG.values) + print("Original : ", f_2.PCT_NATVEG.values) + f_2.PCT_NATVEG.values = [[0.0]] + print("Updated : ", f_2.PCT_NATVEG.values) print("Updating PCT_CROP") - print("Original : ", f2.PCT_CROP.values) - f2.PCT_CROP.values = [[100.0]] - print("Updated : ", f2.PCT_CROP.values) + print("Original : ", f_2.PCT_CROP.values) + f_2.PCT_CROP.values = [[100.0]] + print("Updated : ", f_2.PCT_CROP.values) print("Updating PCT_NAT_PFT") - print(f2.PCT_NAT_PFT.values[0]) - print(f2.PCT_NAT_PFT[0].values) + print(f_2.PCT_NAT_PFT.values[0]) + print(f_2.PCT_NAT_PFT[0].values) out_dir = args.out_dir @@ -662,9 +660,9 @@ def main(): wfile = out_dir + update_time_tag(surf_file) # -- update netcdf metadata - f2 = update_metadata(f2, surf_file, neon_file, zb_flag) + f_2 = update_metadata(f_2, surf_file, neon_file, zb_flag) - print(f2.attrs) - f2.to_netcdf(path=wfile, mode="w", format="NETCDF3_64BIT") + print(f_2.attrs) + f_2.to_netcdf(path=wfile, mode="w", format="NETCDF3_64BIT") print("Successfully updated surface data file for neon site(" + site_name + "):\n - " + wfile) diff --git a/python/ctsm/site_and_regional/neon_surf_wrapper.py b/python/ctsm/site_and_regional/neon_surf_wrapper.py index a2cc619a29..5ec6183801 100755 --- a/python/ctsm/site_and_regional/neon_surf_wrapper.py +++ b/python/ctsm/site_and_regional/neon_surf_wrapper.py @@ -86,8 +86,8 @@ def execute(command): try: subprocess.check_call(command, stdout=open(os.devnull, "w"), stderr=subprocess.STDOUT) - except subprocess.CalledProcessError as e: - print(e) + except subprocess.CalledProcessError as err: + print(err) def main(): @@ -101,7 +101,7 @@ def main(): neon_sites = pd.read_csv("neon_sites_dompft.csv") - for i, row in tqdm.tqdm(neon_sites.iterrows()): + for _, row in tqdm.tqdm(neon_sites.iterrows()): lat = row["Lat"] lon = row["Lon"] site = row["Site"] diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 104e325617..f0c9084936 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -62,6 +62,8 @@ import time import pandas as pd +from standard_script_setup import * + # Get the ctsm util tools and then the cime tools. _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) @@ -74,10 +76,6 @@ from ctsm.utils import parse_isoduration from ctsm.download_utils import download_file -from ctsm import add_cime_to_path - -from standard_script_setup import * - logger = logging.getLogger(__name__) @@ -350,9 +348,7 @@ def __init__(self, name, start_year, end_year, start_month, end_month, finidat): self.finidat = finidat def __str__(self): - return ( - str(self.__class__) + "\n" + "\n".join((str(item) + " = " for item in (self.__dict__))) - ) + return str(self.__class__) + "\n" + "\n".join((str(item) + " = " for item in self.__dict__)) def build_base_case( self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False @@ -381,8 +377,8 @@ def build_base_case( output_root = os.getcwd() case_path = os.path.join(output_root, self.name) - logger.info("base_case_name : {}".format(self.name)) - logger.info("user_mods_dir : {}".format(user_mods_dirs[0])) + logger.info("base_case_name : %s", self.name) + logger.info("user_mods_dir : %s", user_mods_dirs[0]) if overwrite and os.path.isdir(case_path): print("Removing the existing case at: {}".format(case_path)) @@ -417,12 +413,14 @@ def build_base_case( if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( match is None, - "Existing base case is a historical type and should not be -- rerun with the --overwrite option", + "Existing base case is a historical type and should " + + "not be -- rerun with the --overwrite option", ) else: expect( match is not None, - "Existing base case should be a historical type and is not -- rerun with the --overwrite option", + "Existing base case should be a historical type and " + + "is not -- rerun with the --overwrite option", ) # reset the case case.case_setup(reset=True) @@ -434,10 +432,10 @@ def build_base_case( print("---- base case build ------") print("--- This may take a while and you may see WARNING messages ---") # always walk through the build process to make sure it's up to date. - t0 = time.time() + t_0 = time.time() build.case_build(case_path, case=case) - t1 = time.time() - total = t1 - t0 + t_1 = time.time() + total = t_1 - t_0 print("Time required to building the base case: {} s.".format(total)) # update case_path to be the full path to the base case return case_path @@ -446,23 +444,9 @@ def diff_month(self): """ Determine difference between two dates in months """ - d1 = datetime.datetime(self.end_year, self.end_month, 1) - d2 = datetime.datetime(self.start_year, self.start_month, 1) - return (d1.year - d2.year) * 12 + d1.month - d2.month - - def get_batch_query(self, case): - """ - Function for querying the batch queue query command for a case, depending on the - user's batch system. - - Args: - case: - case object - """ - - if case.get_value("BATCH_SYSTEM") == "none": - return "none" - return case.get_value("batch_query") + d_1 = datetime.datetime(self.end_year, self.end_month, 1) + d_2 = datetime.datetime(self.start_year, self.start_month, 1) + return (d_1.year - d_2.year) * 12 + d_1.month - d_2.month def run_case( self, @@ -536,12 +520,14 @@ def run_case( if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( match is None, - "Existing base case is a historical type and should not be -- rerun with the --overwrite option", + "Existing base case is a historical type and " + + "should not be -- rerun with the --overwrite option", ) else: expect( match is not None, - "Existing base case should be a historical type and is not -- rerun with the --overwrite option", + "Existing base case should be a historical type " + + "and is not -- rerun with the --overwrite option", ) if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): print("Case {} appears to be complete, not rerunning.".format(case_root)) @@ -555,13 +541,13 @@ def run_case( print(f"Use {batch_query} to check its run status") return else: - logger.warning("Case already exists in {}, not overwritting.".format(case_root)) + logger.warning("Case already exists in %s, not overwritting.", case_root) return if run_type == "postad": adcase_root = case_root.replace(".postad", ".ad") if not os.path.isdir(adcase_root): - logger.warning("postad requested but no ad case found in {}".format(adcase_root)) + logger.warning("postad requested but no ad case found in %s", adcase_root) return if not os.path.isdir(case_root): @@ -645,9 +631,7 @@ def set_ref_case(self, case): root = ".postad" if not os.path.isdir(ref_case_root): logger.warning( - "ERROR: spinup must be completed first, could not find directory {}".format( - ref_case_root - ) + "ERROR: spinup must be completed first, could not find directory %s", ref_case_root ) return False @@ -657,13 +641,13 @@ def set_ref_case(self, case): case.set_value("RUN_REFCASE", os.path.basename(ref_case_root)) refdate = None for reffile in glob.iglob(refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root)): - m = re.search("(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile) - if m: - refdate = m.group(1) + mon = re.search(r"(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile) + if mon: + refdate = mon.group(1) symlink_force(reffile, os.path.join(rundir, os.path.basename(reffile))) - logger.info("Found refdate of {}".format(refdate)) + logger.info("Found refdate of %s", refdate) if not refdate: - logger.warning("Could not find refcase for {}".format(case_root)) + logger.warning("Could not find refcase for %s", case_root) return False for rpfile in glob.iglob(refrundir + "/rpointer*"): @@ -697,13 +681,30 @@ def modify_user_nl(self, case_root, run_type, rundir): "hist_mfilt = 20", "hist_nhtfrq = -8760", "hist_empty_htapes = .true.", - "hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC', 'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO'", + "hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', " + + "'TOTSOMN', 'TOTVEGC', 'TOTVEGN', 'TLAI', " + + "'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO'", ] if user_nl_lines: - with open(user_nl_fname, "a") as fd: + with open(user_nl_fname, "a") as f_d: for line in user_nl_lines: - fd.write("{}\n".format(line)) + f_d.write("{}\n".format(line)) + + +def get_batch_query(case): + """ + Function for querying the batch queue query command for a case, depending on the + user's batch system. + + Args: + case: + case object + """ + + if case.get_value("BATCH_SYSTEM") == "none": + return "none" + return case.get_value("batch_query") def check_neon_listing(valid_neon_sites): @@ -737,27 +738,27 @@ def parse_neon_listing(listing_file, valid_neon_sites): available_list = [] - df = pd.read_csv(listing_file) + d_f = pd.read_csv(listing_file) # check for finidat files for transient run - finidatlist = df[df["object"].str.contains("lnd/ctsm")] + finidatlist = d_f[d_f["object"].str.contains("lnd/ctsm")] # -- filter lines with atm/cdep - df = df[df["object"].str.contains("atm/cdeps/")] + d_f = d_f[d_f["object"].str.contains("atm/cdeps/")] # -- split the object str to extract site name - df = df["object"].str.split("/", expand=True) + d_f = d_f["object"].str.split("/", expand=True) # -- groupby site name - grouped_df = df.groupby(8) - for key, item in grouped_df: + grouped_df = d_f.groupby(8) + for key, _ in grouped_df: # -- check if it is a valid neon site if any(key in x for x in valid_neon_sites): site_name = key tmp_df = grouped_df.get_group(key) # -- filter files only ending with YYYY-MM.nc - tmp_df = tmp_df[tmp_df[9].str.contains("\d\d\d\d-\d\d.nc")] + tmp_df = tmp_df[tmp_df[9].str.contains(r"\d\d\d\d-\d\d.nc")] # -- find all the data versions # versions = tmp_df[7].unique() @@ -782,12 +783,12 @@ def parse_neon_listing(listing_file, valid_neon_sites): start_month = tmp_df2[1].iloc[0] end_month = tmp_df2[1].iloc[-1] - logger.debug("Valid neon site " + site_name + " found!") - logger.debug("File version {}".format(latest_version)) - logger.debug("start_year={}".format(start_year)) - logger.debug("end_year={}".format(end_year)) - logger.debug("start_month={}".format(start_month)) - logger.debug("end_month={}".format(end_month)) + logger.debug("Valid neon site found: %s", site_name) + logger.debug("File version %s", latest_version) + logger.debug("start_year=%s", start_year) + logger.debug("end_year=%s", end_year) + logger.debug("start_month=%s", start_month) + logger.debug("end_month=%s", end_month) finidat = None for line in finidatlist["object"]: if site_name in line: @@ -829,7 +830,7 @@ def main(description): ) = get_parser(sys.argv, description, valid_neon_sites) if output_root: - logger.debug("output_root : " + output_root) + logger.debug("output_root : %s", output_root) if not os.path.exists(output_root): os.makedirs(output_root) @@ -857,7 +858,7 @@ def main(description): cesmroot, output_root, res, compset, overwrite, setup_only ) logger.info("-----------------------------------") - logger.info("Running CTSM for neon site : {}".format(neon_site.name)) + logger.info("Running CTSM for neon site : %s", neon_site.name) neon_site.run_case( base_case_root, run_type, diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py index b5ded30399..74362be4cd 100755 --- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py +++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py @@ -12,7 +12,7 @@ from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing -from ctsm.site_and_regional.modify_singlept_site_neon import main, get_parser +from ctsm.site_and_regional.modify_singlept_site_neon import main # Allow test names that pylint doesn't like; otherwise hard to make them # readable @@ -58,7 +58,6 @@ def test_modify_site(self): # TODO: the above requires a full path instead of site name # because of how run_neon is configured. # This needs to be fixed in run_neon. - parser = get_parser() with self.assertRaises(SystemExit): print( """This should currently fail due to directory structure in run_neon diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index b6814ee2bc..707e3dc366 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -12,7 +12,7 @@ import sys from ctsm import unit_testing -from ctsm.site_and_regional.run_neon import main, get_parser +from ctsm.site_and_regional.run_neon import main from ctsm.path_utils import path_to_ctsm_root # Allow test names that pylint doesn't like; otherwise hard to make them @@ -52,8 +52,6 @@ def test_one_site(self): "--output-root", self._tempdir, ] - valid_neon_sites = ["ABBY", "OSBS", "BART"] - parser = get_parser(sys.argv, "description_for_parser", valid_neon_sites) main("") # assert that BART directories were created during setup From 3bbbc53590a480a73c541d4454818102a591d255 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 Nov 2023 12:40:59 -0800 Subject: [PATCH 1831/2067] update fates setup loging to use remove_leading_and_trailing_quotes function --- bld/CLMBuildNamelist.pm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 3dec1dffbc..bc9f443399 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4406,7 +4406,7 @@ sub setup_logic_fates { if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { $var = "fates_inventory_ctrl_filename"; - my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_inventory_init is set" ); } elsif ( ! -f "$fname" ) { @@ -4418,7 +4418,7 @@ sub setup_logic_fates { if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { $var = "fluh_timeseries"; - my $fname = substr $nl->get_value($var), 1, -1; # ignore first and last positions of string because those are quote characters + my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_luh is set" ); } elsif ( ! -f "$fname" ) { From 96b827c90568af10f420530f31b1d765d16c061c Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 Nov 2023 12:41:58 -0800 Subject: [PATCH 1832/2067] add test to check for namelist build error conditions --- bld/unit_testers/build-namelist_test.pl | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 4c717a58bf..13b6cd879e 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1061,6 +1061,16 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, + "useinventorybutnotfile" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_luh=.true.", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, + "inventoryfileDNE" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + namelst=>"use_fates_luh=.true., fluh_timeseries='zztop'", + GLC_TWO_WAY_COUPLING=>"FALSE", + phys=>"clm4_5", + }, "useMEGANwithFATES" =>{ options=>"-bgc fates -envxml_dir . -megan", namelst=>"", GLC_TWO_WAY_COUPLING=>"FALSE", From f795147d6d1c61df54e88bd603cf5f818200013a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 Nov 2023 12:48:12 -0800 Subject: [PATCH 1833/2067] define LUH acronym --- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 4d82faa658..4f63e98fd4 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -780,7 +780,7 @@ Full pathname to the inventory initialization control file. -If TRUE, enable use of land use state and transition data from luh_timeseries file. +If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file. (Only valid for fates land use change runs, where there is a luh_timeseries file.) (Also, only valid for use_fates = true and is incompatible with transient runs currently.) @@ -788,7 +788,7 @@ If TRUE, enable use of land use state and transition data from luh_timeseries fi -Full pathname of unified land use harmonization data file. This causes the land-use +Full pathname of unified land use harmonization (LUH) data file. This causes the land-use types to vary over time. (Required, if use_fates_luh=T) (Only relevant if FATES is on). From 042b7ef27d660a9b6e544c99bb4a44a6e5ac69e5 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 Nov 2023 12:50:33 -0800 Subject: [PATCH 1834/2067] remove erroneous comment in use_fates_luh namelist option --- bld/namelist_files/namelist_definition_ctsm.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 4f63e98fd4..8f854a674e 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -781,7 +781,6 @@ Full pathname to the inventory initialization control file. If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file. -(Only valid for fates land use change runs, where there is a luh_timeseries file.) (Also, only valid for use_fates = true and is incompatible with transient runs currently.) From 87b149f86fe87a0e07ef627d64febb304306fd7a Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 Nov 2023 13:48:30 -0800 Subject: [PATCH 1835/2067] add clarifying comments for the fates landuse timeseries module --- src/dyn_subgrid/dynFATESLandUseChangeMod.F90 | 36 ++++++++++++++------ 1 file changed, 25 insertions(+), 11 deletions(-) diff --git a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 index 2180572c0a..45f4340d6a 100644 --- a/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 +++ b/src/dyn_subgrid/dynFATESLandUseChangeMod.F90 @@ -20,12 +20,17 @@ module dynFATESLandUseChangeMod private + ! Yearly landuse transition rate (fraction of gridcell), landuse transition name x gridcell real(r8), allocatable, public :: landuse_transitions(:,:) + + ! Landuse state at beginning of year (fraction of gridcell), landuse state name x gridcell real(r8), allocatable, public :: landuse_states(:,:) + ! Number of landuse transition and state names integer, public, parameter :: num_landuse_transition_vars = 108 integer, public, parameter :: num_landuse_state_vars = 12 + ! landuse filename type(dyn_file_type), target :: dynFatesLandUse_file ! Land use name arrays @@ -112,9 +117,8 @@ subroutine dynFatesLandUseInit(bounds, landuse_filename) if (use_fates_luh) then - ! Generate the dyn_file_type object - ! TO DO: check whether to initialize with start or end - ! dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_START_OF_TIMESTEP) + ! Generate the dyn_file_type object. Note that the land use data being read in is for the + ! transitions occuring within the current year dynFatesLandUse_file = dyn_file_type(landuse_filename, YEAR_POSITION_END_OF_TIMESTEP) ! Get initial land use data @@ -144,6 +148,16 @@ end subroutine dynFatesLandUseInit !----------------------------------------------------------------------- subroutine dynFatesLandUseInterp(bounds, init_state) + + ! !DESCRIPTION: + ! Get landuse state and transition rate data + ! + ! Note that the landuse state and transition rates are stored as fractions + ! of a gridcell for a given year, which is constant throughout the year. + ! This routine does not interpolate the rate at this time; any interpolation + ! is handled by FATES. + + ! !USES: use dynTimeInfoMod , only : time_info_type use clm_varctl , only : use_cn @@ -152,17 +166,16 @@ subroutine dynFatesLandUseInterp(bounds, init_state) logical, optional, intent(in) :: init_state ! fates needs state for initialization ! !LOCAL VARIABLES: - integer :: varnum - integer :: i - logical :: init_flag - real(r8), allocatable :: this_data(:) + integer :: varnum ! variable number index + logical :: init_flag ! local variable to take optional argument value + real(r8), allocatable :: this_data(:) ! temporary array to take get_current_date results + character(len=*), parameter :: subname = 'dynFatesLandUseInterp' !----------------------------------------------------------------------- SHR_ASSERT_ALL(bounds%level == BOUNDS_LEVEL_PROC, subname // ': argument must be PROC-level bounds') - ! This shouldn't be called by cn currently, but return if it is - if (use_cn) return ! Use this as a protection in lieu of build namelist check? - + ! Determine if the optional initialization state flag is present and if so + ! set the init_flag to that optional input value init_flag = .false. if (present(init_state)) then init_flag = init_state @@ -176,7 +189,8 @@ subroutine dynFatesLandUseInterp(bounds, init_state) landuse_transitions(1:num_landuse_transition_vars,bounds%begg:bounds%endg) = 0._r8 landuse_states(1:num_landuse_state_vars,bounds%begg:bounds%endg) = 0._r8 else - ! Right now we don't account for the topounits + ! Loop through all variables on the data file and put data into the temporary array + ! then update the global state and transitions array. allocate(this_data(bounds%begg:bounds%endg)) do varnum = 1, num_landuse_transition_vars call landuse_transition_vars(varnum)%get_current_data(this_data) From f9978db4a7cbc924bf1bc8a848ecbccee1be5236 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 1 Nov 2023 20:59:53 -0600 Subject: [PATCH 1836/2067] Changes to fix #2219 --- src/biogeophys/BareGroundFluxesMod.F90 | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 7dfa83820d..dcc2b8f5b5 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -190,8 +190,12 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & forc_th => atm2lnd_inst%forc_th_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric potential temperature (Kelvin) forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric temperature (Kelvin) forc_pbot => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric pressure (Pa) - forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] density (kg/m**3) - forc_q => wateratm2lndbulk_inst%forc_q_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric specific humidity (kg/kg) + forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] density (kg/m**3) + forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] + forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] + forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] + + forc_q => wateratm2lndbulk_inst%forc_q_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric specific humidity (kg/kg) watsat => soilstate_inst%watsat_col , & ! Input: [real(r8) (:,:) ] volumetric soil water at saturation (porosity) soilbeta => soilstate_inst%soilbeta_col , & ! Input: [real(r8) (:) ] soil wetness relative to field capacity @@ -362,9 +366,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & ! Update the forcing heights for new roughness lengths ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 if (z0param_method == 'Meier2022') then - forc_hgt_u_patch(p) = forc_hgt_u_patch(g) + z0mg_patch(p) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t_patch(g) + z0hg_patch(p) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q_patch(g) + z0qg_patch(p) + displa(p) + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg_patch(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg_patch(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg_patch(p) + displa(p) end if thvstar = tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar zeta(p) = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) From b8c71fa58119b5ef164746660123b3f9cbaaadc2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 15 Nov 2023 16:09:22 -0700 Subject: [PATCH 1837/2067] Change namelist_defaults_ctsm.xml to use ctsm51_params.RMz0.c231011.nc --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ec3bc2f2b4..21746f5411 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -488,7 +488,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/ctsm51_params.c211112.nc +lnd/clm2/paramdata/ctsm51_params.RMz0.c231011.nc lnd/clm2/paramdata/clm50_params.c211112.nc lnd/clm2/paramdata/clm45_params.c211112.nc From 626f520a0c90d3fa5d11273591cdbf87a9d776d7 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 15 Nov 2023 16:10:52 -0700 Subject: [PATCH 1838/2067] Update forcing heights per #2071 --- src/biogeophys/BareGroundFluxesMod.F90 | 10 ++++------ src/biogeophys/CanopyFluxesMod.F90 | 9 +++------ src/biogeophys/LakeFluxesMod.F90 | 22 ++++++---------------- 3 files changed, 13 insertions(+), 28 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index dcc2b8f5b5..2ad943f1ca 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -364,12 +364,10 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & z0qg_patch(p) = z0hg_patch(p) ! Update the forcing heights for new roughness lengths - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg_patch(p) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg_patch(p) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg_patch(p) + displa(p) - end if + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg_patch(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg_patch(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg_patch(p) + displa(p) + thvstar = tstar*(1._r8+0.61_r8*forc_q(c)) + 0.61_r8*forc_th(c)*qstar zeta(p) = zldis(p)*vkc*grav*thvstar/(ustar(p)**2*thv(c)) diff --git a/src/biogeophys/CanopyFluxesMod.F90 b/src/biogeophys/CanopyFluxesMod.F90 index ae0832a2b2..f152e761eb 100644 --- a/src/biogeophys/CanopyFluxesMod.F90 +++ b/src/biogeophys/CanopyFluxesMod.F90 @@ -927,12 +927,9 @@ subroutine CanopyFluxes(bounds, num_exposedvegp, filter_exposedvegp, z0qv(p) = z0mv(p) ! Update the forcing heights - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mv(p) + displa(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hv(p) + displa(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qv(p) + displa(p) - end if + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mv(p) + displa(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hv(p) + displa(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qv(p) + displa(p) end do diff --git a/src/biogeophys/LakeFluxesMod.F90 b/src/biogeophys/LakeFluxesMod.F90 index fdd105ad8f..fb5f723839 100644 --- a/src/biogeophys/LakeFluxesMod.F90 +++ b/src/biogeophys/LakeFluxesMod.F90 @@ -373,16 +373,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, ! Surface temperature and fluxes ! Update forcing heights for updated roughness lengths - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(p) - else - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0mg(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0mg(p) - end if + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(p) ! Find top layer jtop(c) = snl(c) + 1 @@ -626,12 +619,9 @@ subroutine LakeFluxes(bounds, num_lakec, filter_lakec, num_lakep, filter_lakep, end if ! Update forcing heights for updated roughness lengths - ! TODO(KWO, 2022-03-15) Only for Meier2022 for now to maintain bfb with ZengWang2007 - if (z0param_method == 'Meier2022') then - forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) - forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(p) - forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(p) - end if + forc_hgt_u_patch(p) = forc_hgt_u(g) + z0mg(p) + forc_hgt_t_patch(p) = forc_hgt_t(g) + z0hg(p) + forc_hgt_q_patch(p) = forc_hgt_q(g) + z0qg(p) end do ! end of filtered pft loop From b06181632f3e7609d6a71fd3b55fa0b4fe5fc800 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 15 Nov 2023 15:20:03 -0800 Subject: [PATCH 1839/2067] trim filename strings in control mod diagnostic output --- src/main/controlMod.F90 | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 1e20b8b6f2..eeb1e6847d 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -1157,10 +1157,10 @@ subroutine control_print () write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp write(iulog, *) ' use_fates_luh= ', use_fates_sp - write(iulog, *) ' fluh_timeseries = ',fluh_timeseries + write(iulog, *) ' fluh_timeseries = ', trim(fluh_timeseries) write(iulog, *) ' fates_seeddisp_cadence = ', fates_seeddisp_cadence write(iulog, *) ' fates_seeddisp_cadence: 0, 1, 2, 3 => off, daily, monthly, or yearly dispersal' - write(iulog, *) ' fates_inventory_ctrl_filename = ',fates_inventory_ctrl_filename + write(iulog, *) ' fates_inventory_ctrl_filename = ', trim(fates_inventory_ctrl_filename) end if end subroutine control_print From 319d194d6962ec7fc4496b4e2d90e64d3277ffef Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 15 Nov 2023 17:57:52 -0700 Subject: [PATCH 1840/2067] Update code and params file with MIMICS changes per #1845 --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- .../SoilBiogeochemDecompCascadeMIMICSMod.F90 | 13 +++++-------- 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 21746f5411..7d8a3e0342 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -488,7 +488,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/ctsm51_params.RMz0.c231011.nc +/glade/u/home/slevis/paramfiles/ctsm51_params.c231115.nc lnd/clm2/paramdata/clm50_params.c211112.nc lnd/clm2/paramdata/clm45_params.c211112.nc diff --git a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 index b8e7137a32..7185febca6 100644 --- a/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 +++ b/src/soilbiogeochem/SoilBiogeochemDecompCascadeMIMICSMod.F90 @@ -251,12 +251,12 @@ subroutine readParams ( ncid ) call ncd_io(trim(tString), params_inst%mimics_fmet(:), 'read', ncid, readvar=readv) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - allocate(params_inst%mimics_fchem_r(4)) + allocate(params_inst%mimics_fchem_r(2)) tString='mimics_fchem_r' call ncd_io(trim(tString), params_inst%mimics_fchem_r(:), 'read', ncid, readvar=readv) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) - allocate(params_inst%mimics_fchem_k(4)) + allocate(params_inst%mimics_fchem_k(2)) tString='mimics_fchem_k' call ncd_io(trim(tString), params_inst%mimics_fchem_k(:), 'read', ncid, readvar=readv) if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__)) @@ -828,10 +828,8 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & real(r8):: mimics_fmet_p4 real(r8):: mimics_fchem_r_p1 real(r8):: mimics_fchem_r_p2 - real(r8):: mimics_fchem_r_p3 real(r8):: mimics_fchem_k_p1 real(r8):: mimics_fchem_k_p2 - real(r8):: mimics_fchem_k_p3 real(r8):: mimics_tau_mod_min real(r8):: mimics_tau_mod_max real(r8):: mimics_tau_mod_factor @@ -1092,10 +1090,8 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & mimics_fmet_p4 = params_inst%mimics_fmet(4) mimics_fchem_r_p1 = params_inst%mimics_fchem_r(1) mimics_fchem_r_p2 = params_inst%mimics_fchem_r(2) - mimics_fchem_r_p3 = params_inst%mimics_fchem_r(3) mimics_fchem_k_p1 = params_inst%mimics_fchem_k(1) mimics_fchem_k_p2 = params_inst%mimics_fchem_k(2) - mimics_fchem_k_p3 = params_inst%mimics_fchem_k(3) mimics_tau_mod_min = params_inst%mimics_tau_mod_min mimics_tau_mod_max = params_inst%mimics_tau_mod_max mimics_tau_mod_factor = params_inst%mimics_tau_mod_factor @@ -1186,9 +1182,9 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & ! Used in the update of certain pathfrac terms that vary with time ! in the next loop fchem_m1 = min(1._r8, max(0._r8, mimics_fchem_r_p1 * & - exp(mimics_fchem_r_p2 * fmet) * mimics_fchem_r_p3)) + exp(mimics_fchem_r_p2 * fmet))) fchem_m2 = min(1._r8, max(0._r8, mimics_fchem_k_p1 * & - exp(mimics_fchem_k_p2 * fmet) * mimics_fchem_k_p3)) + exp(mimics_fchem_k_p2 * fmet))) do j = 1,nlevdecomp ! vmax ends up in units of per hour but is expected @@ -1283,6 +1279,7 @@ subroutine decomp_rates_mimics(bounds, num_bgc_soilc, filter_bgc_soilc, & ! The right hand side is OXIDAT in the testbed (line 1145) decomp_k(c,j,i_chem_som) = (term_1 + term_2) * w_d_o_scalars + ! Currently, mimics_densdep = 1 so as to have no effect decomp_k(c,j,i_cop_mic) = tau_m1 * & m1_conc**(mimics_densdep - 1.0_r8) * w_d_o_scalars favl = min(1.0_r8, max(0.0_r8, 1.0_r8 - fphys_m1(c,j) - fchem_m1)) From 28ebdd4668afe27ddb4615b624b4cee9ea0e5938 Mon Sep 17 00:00:00 2001 From: Adrianna Foster Date: Fri, 17 Nov 2023 07:52:17 -0700 Subject: [PATCH 1841/2067] remove expected fails, update neon testdef to use v2 data --- cime_config/testdefs/ExpectedTestFails.xml | 20 ------------------- .../NEON/FATES/defaults/shell_commands | 2 ++ .../NEON/defaults/shell_commands | 2 ++ 3 files changed, 4 insertions(+), 20 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 8e72abb8eb..047d8ee952 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -59,26 +59,6 @@ - - - FAIL - #667 - - - - - - FAIL - FATES#897 - - - - - - FAIL - FATES#897 - - diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands index 798abcae84..5bec7332b0 100644 --- a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands @@ -39,3 +39,5 @@ fi # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) ./xmlchange PIO_TYPENAME=netcdf + +./xmlchange NEONVERSION="v2" diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/NEON/defaults/shell_commands index 1f5427ca98..39810dbc70 100644 --- a/cime_config/usermods_dirs/NEON/defaults/shell_commands +++ b/cime_config/usermods_dirs/NEON/defaults/shell_commands @@ -43,3 +43,5 @@ fi # Explicitly set PIO Type to NETCDF since this is a single processor case (should already be set this way) ./xmlchange PIO_TYPENAME=netcdf + +./xmlchange NEONVERSION="v2" From af5c36c5ac116b27b3613a394275f76cf5cf90af Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 17 Nov 2023 11:53:29 -0700 Subject: [PATCH 1842/2067] update externals, update changelog --- Externals_CLM.cfg | 2 +- doc/ChangeLog | 62 +++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 3 files changed, 64 insertions(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index cab31b6b7f..5f8e8d2441 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.68.2_api.30.0.0 +tag = sci.1.68.2_api.31.0.0 required = True [externals_description] diff --git a/doc/ChangeLog b/doc/ChangeLog index 9405e19922..65926f9164 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,66 @@ =============================================================== +Tag name: ctsm5.1.dev153 +Originator(s): afoster (Adrianna Foster) and johnpaulalex (John Paul Alex) +Date: Fri Nov 17 11:53:14 MST 2023 +One-line Summary: Call new FATES-side FatesReadParameters + +Purpose and description of changes +---------------------------------- + +Have CTSM use the new code path in FATES that allows passing in a `fates_param_reader_type`, which does the actual work reading the parameter files, in lieu of calling CTSM methods. + +Also updated NEON usermods to use version 2 data by default, rather than latest. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + cheyenne ---- OK + izumi ------- OK + + fates baseline: `fates-sci.1.68.2_api.31.0.0-ctsm5.1.dev153` + + +Answer changes +-------------- + +None + + +Other details +-------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates + +Pull Requests that document the changes (include PR ids): +https://github.com/NGEET/fates/pull/1096 +https://github.com/ESCOMP/CTSM/pull/2198 + + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev152 Originator(s): multiple (tking (Teagan King); slevis (Sam Levis); AdrienDams (Adrien Damseaux); afoster (Adrianna Foster); samrabin (Sam Rabin); ekluzek (Erik Kluzek); wwieder (Will Wieder); sacks (Bill Sacks); a few others listed below) Date: Tue Nov 14 17:09:43 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 6af88be0e4..953884bab1 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev153 afoster 11/17/2023 Call new FATES-side FatesReadParameters ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors ctsm5.1.dev151 rgknox 11/11/2023 Fixes to FATES long run restarts ctsm5.1.dev150 rgknox 11/06/2023 FATES API fix to support future fates npp-fixation coupling, and urgent coupling fixes with E3SM. From 2ee6943d11f72919d2550e1f1760090465683257 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 17 Nov 2023 12:13:28 -0700 Subject: [PATCH 1843/2067] Change namelist_defaults_ctsm.xml to use ctsm51_params.c231115b.nc --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 7d8a3e0342..f3c8728294 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -488,7 +488,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -/glade/u/home/slevis/paramfiles/ctsm51_params.c231115.nc +/glade/u/home/slevis/paramfiles/ctsm51_params.c231115b.nc lnd/clm2/paramdata/clm50_params.c211112.nc lnd/clm2/paramdata/clm45_params.c211112.nc From f185a31aa7d9b5bcf4744f722de7c99523307226 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 17 Nov 2023 12:16:33 -0700 Subject: [PATCH 1844/2067] Revised indentation based on code review --- src/biogeophys/BareGroundFluxesMod.F90 | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/BareGroundFluxesMod.F90 b/src/biogeophys/BareGroundFluxesMod.F90 index 2ad943f1ca..7db214065d 100644 --- a/src/biogeophys/BareGroundFluxesMod.F90 +++ b/src/biogeophys/BareGroundFluxesMod.F90 @@ -191,9 +191,9 @@ subroutine BareGroundFluxes(bounds, num_noexposedvegp, filter_noexposedvegp, & forc_t => atm2lnd_inst%forc_t_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric temperature (Kelvin) forc_pbot => atm2lnd_inst%forc_pbot_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric pressure (Pa) forc_rho => atm2lnd_inst%forc_rho_downscaled_col , & ! Input: [real(r8) (:) ] density (kg/m**3) - forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] - forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] - forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] + forc_hgt_t => atm2lnd_inst%forc_hgt_t_grc , & ! Input: [real(r8) (:) ] observational height of temperature [m] + forc_hgt_u => atm2lnd_inst%forc_hgt_u_grc , & ! Input: [real(r8) (:) ] observational height of wind [m] + forc_hgt_q => atm2lnd_inst%forc_hgt_q_grc , & ! Input: [real(r8) (:) ] observational height of specific humidity [m] forc_q => wateratm2lndbulk_inst%forc_q_downscaled_col , & ! Input: [real(r8) (:) ] atmospheric specific humidity (kg/kg) From bd08985459befa7070b40ae903f75ec32192ab6c Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 17 Nov 2023 13:24:42 -0700 Subject: [PATCH 1845/2067] add issues to changelog --- doc/ChangeLog | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 65926f9164..af74421906 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -26,7 +26,10 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 +Bugs fixed or introduced +------------------------ +Some progress towards CTSM#2006 and FATES#1076 Testing summary: ---------------- From b8d1508286afe7963357b0b12bf0481d01df5dc6 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Fri, 17 Nov 2023 13:31:31 -0700 Subject: [PATCH 1846/2067] update to pend --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 047d8ee952..44876ba818 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -83,7 +83,7 @@ - FAIL + PEND FATES#983 This job should time out on izumi, seems to be hanging on history output. From 29ca5ada72b03d374b93c0a06e21af2c8e977a3a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 17 Nov 2023 18:45:07 -0700 Subject: [PATCH 1847/2067] Move SNICAR params to params files per #2247 --- bld/CLMBuildNamelist.pm | 1 - bld/namelist_files/namelist_defaults_ctsm.xml | 10 +--- .../namelist_definition_ctsm.xml | 5 -- src/biogeophys/AerosolMod.F90 | 57 ------------------- src/biogeophys/SnowHydrologyMod.F90 | 44 +++++++++----- src/biogeophys/SnowSnicarMod.F90 | 31 +++++----- src/biogeophys/WaterDiagnosticBulkType.F90 | 14 ++--- 7 files changed, 57 insertions(+), 105 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 5769af0ea2..17d64cd59f 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4212,7 +4212,6 @@ sub setup_logic_snowpack { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph'); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fresh_snw_rds_max'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc'); add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela'); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index f3c8728294..07b440c37b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -431,10 +431,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). 175.d00 175.d00 -54.526d00 -204.526d00 -204.526d00 - 0.08d00 .false. @@ -488,9 +484,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -/glade/u/home/slevis/paramfiles/ctsm51_params.c231115b.nc -lnd/clm2/paramdata/clm50_params.c211112.nc -lnd/clm2/paramdata/clm45_params.c211112.nc +/glade/u/home/slevis/paramfiles/ctsm51_params.c231117.nc +/glade/u/home/slevis/paramfiles/clm50_params.c231117.nc +/glade/u/home/slevis/paramfiles/clm45_params.c231117.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 93306b32d5..2cb95d5c68 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2783,11 +2783,6 @@ Snow compaction overburden exponential factor (1/K) Not used for snow_overburden_compaction_method=Vionnet2012 - -maximum warm (at freezing) fresh snow effective radius [microns] - - If set to .true., then reset the snow pack over non-glacier columns to a small value. diff --git a/src/biogeophys/AerosolMod.F90 b/src/biogeophys/AerosolMod.F90 index bce2b6f9ab..39ade89fb0 100644 --- a/src/biogeophys/AerosolMod.F90 +++ b/src/biogeophys/AerosolMod.F90 @@ -26,9 +26,6 @@ module AerosolMod public :: AerosolFluxes ! ! !PUBLIC DATA MEMBERS: - real(r8), public, parameter :: snw_rds_min = 54.526_r8 ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] - real(r8), public :: fresh_snw_rds_max = 204.526_r8 ! maximum warm fresh snow effective radius [microns] - ! type, public :: aerosol_type real(r8), pointer, public :: mss_bcpho_col(:,:) ! mass of hydrophobic BC in snow (col,lyr) [kg] real(r8), pointer, public :: mss_bcphi_col(:,:) ! mass of hydrophillic BC in snow (col,lyr) [kg] @@ -93,7 +90,6 @@ module AerosolMod procedure, private :: InitAllocate procedure, private :: InitHistory procedure, private :: InitCold - procedure, private :: InitReadNML end type aerosol_type @@ -113,7 +109,6 @@ subroutine Init(this, bounds, NLFilename) call this%InitAllocate(bounds) call this%InitHistory(bounds) call this%InitCold(bounds) - call this%InitReadNML(NLFilename) end subroutine Init @@ -294,58 +289,6 @@ subroutine InitCold(this, bounds) end subroutine InitCold !----------------------------------------------------------------------- - subroutine InitReadNML(this, NLFilename) - ! - ! !USES: - ! !USES: - use fileutils , only : getavu, relavu, opnfil - use shr_nl_mod , only : shr_nl_find_group_name - use spmdMod , only : masterproc, mpicom - use shr_mpi_mod , only : shr_mpi_bcast - use clm_varctl , only : iulog - ! - ! !ARGUMENTS: - class(aerosol_type) :: this - character(len=*), intent(in) :: NLFilename ! Input namelist filename - ! - ! !LOCAL VARIABLES: - !----------------------------------------------------------------------- - integer :: ierr ! error code - integer :: unitn ! unit for namelist file - - character(len=*), parameter :: subname = 'Aerosol::InitReadNML' - character(len=*), parameter :: nmlname = 'aerosol' - !----------------------------------------------------------------------- - namelist/aerosol/ fresh_snw_rds_max - - if (masterproc) then - unitn = getavu() - write(iulog,*) 'Read in '//nmlname//' namelist' - call opnfil (NLFilename, unitn, 'F') - call shr_nl_find_group_name(unitn, nmlname, status=ierr) - if (ierr == 0) then - read(unitn, nml=aerosol, iostat=ierr) - if (ierr /= 0) then - call endrun(msg="ERROR reading "//nmlname//" namelist "//errmsg(sourcefile, __LINE__)) - end if - else - call endrun(msg="ERROR could NOT find "//nmlname//" namelist "//errmsg(sourcefile, __LINE__)) - end if - call relavu( unitn ) - end if - - call shr_mpi_bcast (fresh_snw_rds_max , mpicom) - - if (masterproc) then - write(iulog,*) ' ' - write(iulog,*) nmlname//' settings:' - write(iulog,nml=aerosol) - write(iulog,*) ' ' - end if - - end subroutine InitReadNML - - !------------------------------------------------------------------------ subroutine Restart(this, bounds, ncid, flag, & h2osoi_ice_col, h2osoi_liq_col) ! diff --git a/src/biogeophys/SnowHydrologyMod.F90 b/src/biogeophys/SnowHydrologyMod.F90 index 4698e1136d..9fb1a52dbc 100644 --- a/src/biogeophys/SnowHydrologyMod.F90 +++ b/src/biogeophys/SnowHydrologyMod.F90 @@ -79,7 +79,14 @@ module SnowHydrologyMod real(r8) :: rho_max ! Wind drift compaction / maximum density (kg/m3) real(r8) :: tau_ref ! Wind drift compaction / reference time (48*3600) (s) real(r8) :: scvng_fct_mlt_sf ! Scaling factor modifying scavenging factors for BC, OC, and dust species inclusion in meltwater (-) + real(r8) :: scvng_fct_mlt_bcphi ! scavenging factor for hydrophillic BC inclusion in meltwater [frc] + real(r8) :: scvng_fct_mlt_bcpho ! scavenging factor for hydrophobic BC inclusion in meltwater [frc] + real(r8) :: scvng_fct_mlt_dst1 ! scavenging factor for dust species 1 inclusion in meltwater [frc] + real(r8) :: scvng_fct_mlt_dst2 ! scavenging factor for dust species 2 inclusion in meltwater [frc] + real(r8) :: scvng_fct_mlt_dst3 ! scavenging factor for dust species 3 inclusion in meltwater [frc] + real(r8) :: scvng_fct_mlt_dst4 ! scavenging factor for dust species 4 inclusion in meltwater [frc] real(r8) :: ceta ! Overburden compaction constant (kg/m3) + real(r8) :: snw_rds_min ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] end type params_type type(params_type), private :: params_inst @@ -120,14 +127,8 @@ module SnowHydrologyMod ! 7= dust species 3 ! 8= dust species 4 ! - real(r8), public, parameter :: scvng_fct_mlt_bcphi = 0.20_r8 ! scavenging factor for hydrophillic BC inclusion in meltwater [frc] - real(r8), public, parameter :: scvng_fct_mlt_bcpho = 0.03_r8 ! scavenging factor for hydrophobic BC inclusion in meltwater [frc] real(r8), public, parameter :: scvng_fct_mlt_ocphi = 0.20_r8 ! scavenging factor for hydrophillic OC inclusion in meltwater [frc] real(r8), public, parameter :: scvng_fct_mlt_ocpho = 0.03_r8 ! scavenging factor for hydrophobic OC inclusion in meltwater [frc] - real(r8), public, parameter :: scvng_fct_mlt_dst1 = 0.02_r8 ! scavenging factor for dust species 1 inclusion in meltwater [frc] - real(r8), public, parameter :: scvng_fct_mlt_dst2 = 0.02_r8 ! scavenging factor for dust species 2 inclusion in meltwater [frc] - real(r8), public, parameter :: scvng_fct_mlt_dst3 = 0.01_r8 ! scavenging factor for dust species 3 inclusion in meltwater [frc] - real(r8), public, parameter :: scvng_fct_mlt_dst4 = 0.01_r8 ! scavenging factor for dust species 4 inclusion in meltwater [frc] ! The following are public for the sake of unit testing integer, parameter, public :: LoTmpDnsSlater2017 = 2 ! For temperature below -15C use equation from Slater 2017 @@ -316,8 +317,22 @@ subroutine readParams( ncid ) call readNcdioScalar(ncid, 'tau_ref', subname, params_inst%tau_ref) ! Scaling factor modifying scavenging factors for BC, OC, and dust species inclusion in meltwater (-) call readNcdioScalar(ncid, 'scvng_fct_mlt_sf', subname, params_inst%scvng_fct_mlt_sf) + ! scavenging factor for hydrophillic BC inclusion in meltwater [frc] + call readNcdioScalar(ncid, 'scvng_fct_mlt_bcphi', subname, params_inst%scvng_fct_mlt_bcphi) + ! scavenging factor for hydrophobic BC inclusion in meltwater [frc] + call readNcdioScalar(ncid, 'scvng_fct_mlt_bcpho', subname, params_inst%scvng_fct_mlt_bcpho) + ! scavenging factor for dust species 1 inclusion in meltwater [frc] + call readNcdioScalar(ncid, 'scvng_fct_mlt_dst1', subname, params_inst%scvng_fct_mlt_dst1) + ! scavenging factor for dust species 2 inclusion in meltwater [frc] + call readNcdioScalar(ncid, 'scvng_fct_mlt_dst2', subname, params_inst%scvng_fct_mlt_dst2) + ! scavenging factor for dust species 3 inclusion in meltwater [frc] + call readNcdioScalar(ncid, 'scvng_fct_mlt_dst3', subname, params_inst%scvng_fct_mlt_dst3) + ! scavenging factor for dust species 4 inclusion in meltwater [frc] + call readNcdioScalar(ncid, 'scvng_fct_mlt_dst4', subname, params_inst%scvng_fct_mlt_dst4) ! Overburden compaction constant (kg/m3) call readNcdioScalar(ncid, 'ceta', subname, params_inst%ceta) + ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] + call readNcdioScalar(ncid, 'snw_rds_min', subname, params_inst%snw_rds_min) end subroutine readParams @@ -1586,7 +1601,7 @@ subroutine CalcAndApplyAerosolFluxes(bounds, num_snowc, filter_snowc, & ! BCPHI: ! 1. flux with meltwater: qout_bc_phi(c) = qflx_snow_percolation(c,j)*params_inst%scvng_fct_mlt_sf* & - scvng_fct_mlt_bcphi*(mss_bcphi(c,j)/mss_liqice) + params_inst%scvng_fct_mlt_bcphi*(mss_bcphi(c,j)/mss_liqice) if (qout_bc_phi(c)*dtime > mss_bcphi(c,j)) then qout_bc_phi(c) = mss_bcphi(c,j)/dtime mss_bcphi(c,j) = 0._r8 @@ -1598,7 +1613,7 @@ subroutine CalcAndApplyAerosolFluxes(bounds, num_snowc, filter_snowc, & ! BCPHO: ! 1. flux with meltwater: qout_bc_pho(c) = qflx_snow_percolation(c,j)*params_inst%scvng_fct_mlt_sf* & - scvng_fct_mlt_bcpho*(mss_bcpho(c,j)/mss_liqice) + params_inst%scvng_fct_mlt_bcpho*(mss_bcpho(c,j)/mss_liqice) if (qout_bc_pho(c)*dtime > mss_bcpho(c,j)) then qout_bc_pho(c) = mss_bcpho(c,j)/dtime mss_bcpho(c,j) = 0._r8 @@ -1634,7 +1649,7 @@ subroutine CalcAndApplyAerosolFluxes(bounds, num_snowc, filter_snowc, & ! DUST 1: ! 1. flux with meltwater: qout_dst1(c) = qflx_snow_percolation(c,j)*params_inst%scvng_fct_mlt_sf* & - scvng_fct_mlt_dst1*(mss_dst1(c,j)/mss_liqice) + params_inst%scvng_fct_mlt_dst1*(mss_dst1(c,j)/mss_liqice) if (qout_dst1(c)*dtime > mss_dst1(c,j)) then qout_dst1(c) = mss_dst1(c,j)/dtime mss_dst1(c,j) = 0._r8 @@ -1646,7 +1661,7 @@ subroutine CalcAndApplyAerosolFluxes(bounds, num_snowc, filter_snowc, & ! DUST 2: ! 1. flux with meltwater: qout_dst2(c) = qflx_snow_percolation(c,j)*params_inst%scvng_fct_mlt_sf* & - scvng_fct_mlt_dst2*(mss_dst2(c,j)/mss_liqice) + params_inst%scvng_fct_mlt_dst2*(mss_dst2(c,j)/mss_liqice) if (qout_dst2(c)*dtime > mss_dst2(c,j)) then qout_dst2(c) = mss_dst2(c,j)/dtime mss_dst2(c,j) = 0._r8 @@ -1658,7 +1673,7 @@ subroutine CalcAndApplyAerosolFluxes(bounds, num_snowc, filter_snowc, & ! DUST 3: ! 1. flux with meltwater: qout_dst3(c) = qflx_snow_percolation(c,j)*params_inst%scvng_fct_mlt_sf* & - scvng_fct_mlt_dst3*(mss_dst3(c,j)/mss_liqice) + params_inst%scvng_fct_mlt_dst3*(mss_dst3(c,j)/mss_liqice) if (qout_dst3(c)*dtime > mss_dst3(c,j)) then qout_dst3(c) = mss_dst3(c,j)/dtime mss_dst3(c,j) = 0._r8 @@ -1670,7 +1685,7 @@ subroutine CalcAndApplyAerosolFluxes(bounds, num_snowc, filter_snowc, & ! DUST 4: ! 1. flux with meltwater: qout_dst4(c) = qflx_snow_percolation(c,j)*params_inst%scvng_fct_mlt_sf* & - scvng_fct_mlt_dst4*(mss_dst4(c,j)/mss_liqice) + params_inst%scvng_fct_mlt_dst4*(mss_dst4(c,j)/mss_liqice) if (qout_dst4(c)*dtime > mss_dst4(c,j)) then qout_dst4(c) = mss_dst4(c,j)/dtime mss_dst4(c,j) = 0._r8 @@ -3936,7 +3951,6 @@ function MassWeightedSnowRadius( rds1, rds2, swtot, zwtot ) result(mass_weighted ! Calculate the mass weighted snow radius when two layers are combined ! ! !USES: - use AerosolMod , only : snw_rds_min use SnowSnicarMod, only : snw_rds_max implicit none ! !ARGUMENTS: @@ -3951,8 +3965,8 @@ function MassWeightedSnowRadius( rds1, rds2, swtot, zwtot ) result(mass_weighted if ( mass_weighted_snowradius > snw_rds_max ) then mass_weighted_snowradius = snw_rds_max - else if ( mass_weighted_snowradius < snw_rds_min ) then - mass_weighted_snowradius = snw_rds_min + else if ( mass_weighted_snowradius < params_inst%snw_rds_min ) then + mass_weighted_snowradius = params_inst%snw_rds_min end if end function MassWeightedSnowRadius diff --git a/src/biogeophys/SnowSnicarMod.F90 b/src/biogeophys/SnowSnicarMod.F90 index 9a95188232..5bc1c61edb 100644 --- a/src/biogeophys/SnowSnicarMod.F90 +++ b/src/biogeophys/SnowSnicarMod.F90 @@ -18,7 +18,6 @@ module SnowSnicarMod use shr_const_mod , only : SHR_CONST_RHOICE use abortutils , only : endrun use decompMod , only : bounds_type, subgrid_level_column - use AerosolMod , only : snw_rds_min use atm2lndType , only : atm2lnd_type use WaterStateBulkType , only : waterstatebulk_type use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type @@ -42,6 +41,8 @@ module SnowSnicarMod real(r8) :: snw_rds_refrz ! Effective radius of re-frozen snow (microns) real(r8) :: C2_liq_Brun89 ! Constant for liquid water grain growth [m3 s-1], ! from Brun89: corrected for LWC in units of percent + real(r8) :: fresh_snw_rds_max ! maximum warm fresh snow effective radius [microns] + real(r8) :: snw_rds_min ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] end type params_type type(params_type), private :: params_inst ! @@ -66,7 +67,6 @@ module SnowSnicarMod integer, parameter :: snw_rds_max_tbl = 1500 ! maximum effective radius defined in Mie lookup table [microns] integer, parameter :: snw_rds_min_tbl = 30 ! minimium effective radius defined in Mie lookup table [microns] - integer, parameter :: snw_rds_min_int = nint(snw_rds_min) ! minimum allowed snow effective radius as integer [microns] real(r8), parameter :: snw_rds_max = 1500._r8 ! maximum allowed snow effective radius [microns] real(r8), parameter :: min_snw = 1.0E-30_r8 ! minimum snow mass required for SNICAR RT calculation [kg m-2] @@ -182,6 +182,10 @@ subroutine readParams( ncid ) call readNcdioScalar(ncid, 'snw_rds_refrz', subname, params_inst%snw_rds_refrz) ! constant for liquid water grain growth [m3 s-1], from Brun89: corrected for LWC in units of percent call readNcdioScalar(ncid, 'C2_liq_Brun89', subname, params_inst%C2_liq_Brun89) + ! maximum warm fresh snow effective radius [microns] + call readNcdioScalar(ncid, 'fresh_snw_rds_max', subname, params_inst%fresh_snw_rds_max) + ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] + call readNcdioScalar(ncid, 'snw_rds_min', subname, params_inst%snw_rds_min) end subroutine readParams @@ -677,7 +681,7 @@ subroutine SNICAR_RT (bounds, num_nourbanc, filter_nourbanc, & snl_lcl = -1 h2osno_ice_lcl(0) = h2osno_lcl h2osno_liq_lcl(0) = 0._r8 - snw_rds_lcl(0) = snw_rds_min_int + snw_rds_lcl(0) = nint(params_inst%snw_rds_min) else flg_nosnl = 0 snl_lcl = snl(c_idx) @@ -1628,10 +1632,10 @@ subroutine SnowAge_grain(bounds, & !LvK extra boundary check, to prevent when using old restart file with lower snw_rds_min than current run - snw_rds(c_idx,i) = max(snw_rds(c_idx,i), snw_rds_min) + snw_rds(c_idx,i) = max(snw_rds(c_idx,i), params_inst%snw_rds_min) ! change in snow effective radius, using best-fit parameters - dr_fresh = snw_rds(c_idx,i)-snw_rds_min + dr_fresh = snw_rds(c_idx,i) - params_inst%snw_rds_min dr = (bst_drdt0 * (bst_tau / (dr_fresh + bst_tau))**(1._r8 / bst_kappa)) * (dtime / secsphr) ! @@ -1701,7 +1705,7 @@ subroutine SnowAge_grain(bounds, & !********** 5. CHECK BOUNDARIES *********** ! ! boundary check - snw_rds(c_idx,i) = max(snw_rds(c_idx,i), snw_rds_min) + snw_rds(c_idx,i) = max(snw_rds(c_idx,i), params_inst%snw_rds_min) snw_rds(c_idx,i) = min(snw_rds(c_idx,i), snw_rds_max) ! set top layer variables for history files @@ -1720,7 +1724,7 @@ subroutine SnowAge_grain(bounds, & do fc = 1, num_nosnowc c_idx = filter_nosnowc(fc) if (h2osno_no_layers(c_idx) > 0._r8) then - snw_rds(c_idx,0) = snw_rds_min + snw_rds(c_idx,0) = params_inst%snw_rds_min endif enddo @@ -1744,7 +1748,7 @@ real(r8) function FreshSnowRadius(c_idx, atm2lnd_inst) ! Author: Leo VanKampenhout ! ! !USES: - use AerosolMod , only : fresh_snw_rds_max + ! ! !ARGUMENTS: integer, intent(in) :: c_idx ! column index type(atm2lnd_type) , intent(in) :: atm2lnd_inst ! Forcing from atmosphere @@ -1753,16 +1757,17 @@ real(r8) function FreshSnowRadius(c_idx, atm2lnd_inst) !----------------------------------------------------------------------- real(r8), parameter :: tmin = tfrz - 30._r8 ! start of linear ramp real(r8), parameter :: tmax = tfrz - 0._r8 ! end of linear ramp - real(r8), parameter :: gs_min = snw_rds_min ! minimum value - real(r8) :: gs_max ! maximum value + real(r8) :: gs_min ! minimum value + real(r8) :: gs_max ! maximum value associate( & forc_t => atm2lnd_inst%forc_t_downscaled_col & ! Input: [real(r8) (:) ] atmospheric temperature (Kelvin) ) - if ( fresh_snw_rds_max <= snw_rds_min )then - FreshSnowRadius = snw_rds_min + if ( params_inst%fresh_snw_rds_max <= params_inst%snw_rds_min )then + FreshSnowRadius = params_inst%snw_rds_min else - gs_max = fresh_snw_rds_max + gs_max = params_inst%fresh_snw_rds_max + gs_min = params_inst%snw_rds_min if (forc_t(c_idx) < tmin) then FreshSnowRadius = gs_min diff --git a/src/biogeophys/WaterDiagnosticBulkType.F90 b/src/biogeophys/WaterDiagnosticBulkType.F90 index 426ddb464c..057062777f 100644 --- a/src/biogeophys/WaterDiagnosticBulkType.F90 +++ b/src/biogeophys/WaterDiagnosticBulkType.F90 @@ -108,12 +108,10 @@ module WaterDiagnosticBulkType type, private :: params_type real(r8) :: zlnd ! Momentum roughness length for soil, glacier, wetland (m) + real(r8) :: snw_rds_min ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] end type params_type type(params_type), private :: params_inst - ! minimum allowed snow effective radius (also "fresh snow" value) [microns] - real(r8), public, parameter :: snw_rds_min = 54.526_r8 - character(len=*), parameter, private :: sourcefile = & __FILE__ !------------------------------------------------------------------------ @@ -136,6 +134,8 @@ subroutine readParams( ncid ) ! Momentum roughness length for soil, glacier, wetland (m) call readNcdioScalar(ncid, 'zlnd', subname, params_inst%zlnd) + ! minimum allowed snow effective radius (also cold "fresh snow" value) [microns] + call readNcdioScalar(ncid, 'snw_rds_min', subname, params_inst%snw_rds_min) end subroutine readParams @@ -750,11 +750,11 @@ subroutine InitBulkCold(this, bounds, & do c = bounds%begc,bounds%endc if (snl(c) < 0) then - this%snw_rds_col(c,snl(c)+1:0) = snw_rds_min + this%snw_rds_col(c,snl(c)+1:0) = params_inst%snw_rds_min this%snw_rds_col(c,-nlevsno+1:snl(c)) = 0._r8 - this%snw_rds_top_col(c) = snw_rds_min + this%snw_rds_top_col(c) = params_inst%snw_rds_min elseif (h2osno_input_col(c) > 0._r8) then - this%snw_rds_col(c,0) = snw_rds_min + this%snw_rds_col(c,0) = params_inst%snw_rds_min this%snw_rds_col(c,-nlevsno+1:-1) = 0._r8 this%snw_rds_top_col(c) = spval this%sno_liq_top_col(c) = spval @@ -1236,7 +1236,7 @@ subroutine ResetBulk(this, column) integer , intent(in) :: column ! column index !----------------------------------------------------------------------- - this%snw_rds_col(column,0) = snw_rds_min + this%snw_rds_col(column,0) = params_inst%snw_rds_min end subroutine ResetBulk From 71e174fa81170451cc5dd99098a89c0f1960dca9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 11:09:18 -0700 Subject: [PATCH 1848/2067] Upd. paramfile / z0param_method in namelist_defaults_ctsm and two /testmod dirs --- bld/namelist_files/namelist_defaults_ctsm.xml | 10 ++++++---- .../testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm | 2 -- .../testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 07b440c37b..9fcea25784 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -484,9 +484,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -/glade/u/home/slevis/paramfiles/ctsm51_params.c231117.nc -/glade/u/home/slevis/paramfiles/clm50_params.c231117.nc -/glade/u/home/slevis/paramfiles/clm45_params.c231117.nc +lnd/clm2/paramdata/ctsm51_params.c231117.nc +lnd/clm2/paramdata/clm50_params.c231117.nc +lnd/clm2/paramdata/clm45_params.c231117.nc @@ -498,7 +498,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -ZengWang2007 +ZengWang2007 +ZengWang2007 +Meier2022 .true. .false. diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm index 01df79ecba..6fa686b403 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm @@ -1,4 +1,2 @@ z0param_method = 'Meier2022' use_z0m_snowmelt = .true. -paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_params.RMz0.c220304.nc' - diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm index 7ae4a69aad..57ac8a6461 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm @@ -1,2 +1,2 @@ -paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c211112.nc' +paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c231117.nc' hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr' From 13ef0cd2e58a7a375cc0d3265cc6845a28d583c6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 11:48:43 -0700 Subject: [PATCH 1849/2067] Draft ChangeLog/Sum --- doc/ChangeLog | 109 ++++++++++++++++++++++++++++++++++++++++++-------- doc/ChangeSum | 1 + 2 files changed, 94 insertions(+), 16 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index af74421906..62837f1f0a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,97 @@ =============================================================== +Tag name: ctsm5.1.dev154 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) +Date: Mon Nov 20 11:09:45 MST 2023 +One-line Summary: New params files: Changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc + +Purpose and description of changes +---------------------------------- + +This PR (#2258) addresses several issues: +1) Start using existing new params file for Meier roughness: +/glade/campaign/cesm/cesmdata/inputdata/lnd/clm2/paramdata/ctsm51_params.RMz0.c231011.nc +and include bug-fix #2219. +2) Update forcing heights per #2071. +3) Update params file for MIMICS per #1845. +4) Make leafcn for pfts 15 and 16 the same per #2184. +5) Switch the values of params kc_nonmyc and kn_nonmyc per #2120. +6) Move SNICAR parameters to ctsm51, clm50, and clm45 params files per #2247. + +See #2258 and the above issues for a list of contributors. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[x] clm5_1 + +[x] clm5_0 + +[x] ctsm5_0-nwp + +[x] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +Fixes #2219 +Fixes #2071 +Fixes #1845 +Fixes #2184 +Fixes #2120 +Fixes #2247 + + +Notes of particular relevance for users +--------------------------------------- +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + SNICAR namelist variable fresh_snw_rds_max moved to the params file. + +Changes made to namelist defaults (e.g., changed parameter values): + SNICAR namelist variable fresh_snw_rds_max moved to the params file. + Pointing to new params files for clm4_5, clm5_0, clm5_1. + +Changes to the datasets (e.g., parameter, surface or initial files): + New clm5_1 params file with new parameters and with modified values of existing parameters. + New clm5_0 and clm4_5 params files with new parameters for SNICAR. + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- + izumi ------- + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change: larger than roundoff/same climate? + I will post this tag on the Answer changing tags wiki page as "SIGNIFICANT" + and will run a simulation and diagnostics to compare against dev145. + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2258 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev153 Originator(s): afoster (Adrianna Foster) and johnpaulalex (John Paul Alex) Date: Fri Nov 17 11:53:14 MST 2023 @@ -162,18 +255,9 @@ README.md for testing was updated to clarify that arguments should be used. Testing summary: ---------------- -[Remove any lines that don't apply.] [PASS means all tests PASS; OK means tests PASS other than expected fails.] - build-namelist tests (if CLMBuildNamelist.pm has changed): - - cheyenne - - - tools-tests (test/tools) (if tools have been changed): - - cheyenne - - python testing (if python code has changed; see instructions in python/README.md; document testing done): (any machine) - cheyenne OK (pylint suggestions from previous work remain) @@ -189,13 +273,6 @@ FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm FAIL SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-default--clm-NEON-NIWO BASELINE ctsm5.1.dev151: DIFF FAIL SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM BASELINE ctsm5.1.dev151: DIFF - fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) - cheyenne ---- - izumi ------- - - any other testing (give details below): - -If the tag used for baseline comparisons was NOT the previous tag, note that here: Answer changes -------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index 953884bab1..d86a084cd9 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev154 slevis 11/20/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc ctsm5.1.dev153 afoster 11/17/2023 Call new FATES-side FatesReadParameters ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors ctsm5.1.dev151 rgknox 11/11/2023 Fixes to FATES long run restarts From 4792efce2a8cf0e7db0217e0ae89ad2f7b4c954a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 13:55:22 -0700 Subject: [PATCH 1850/2067] Remove Meier2022 testmods directory; update testlist accordingly --- cime_config/testdefs/testlist_clm.xml | 16 ++++++++-------- .../clm/Meier2022_surf_rough/include_user_mods | 1 - .../clm/Meier2022_surf_rough/user_nl_clm | 2 -- 3 files changed, 8 insertions(+), 11 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 34c2cc33f9..d0e2418b56 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -17,13 +17,13 @@ - + - + @@ -1163,16 +1163,16 @@ - + - + - + @@ -1182,16 +1182,16 @@ - + - + - + diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods deleted file mode 100644 index fe0e18cf88..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../default diff --git a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm deleted file mode 100644 index 6fa686b403..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/Meier2022_surf_rough/user_nl_clm +++ /dev/null @@ -1,2 +0,0 @@ -z0param_method = 'Meier2022' -use_z0m_snowmelt = .true. From 6b231bfd278886085d47ff6017b0794f4ceb8608 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 13:56:59 -0700 Subject: [PATCH 1851/2067] Small revision based on code review --- bld/namelist_files/namelist_defaults_ctsm.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 9fcea25784..0516ecbc22 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -498,8 +498,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -ZengWang2007 -ZengWang2007 +ZengWang2007 Meier2022 .true. From 939bea766ee176b9e4b1a485c04cfba3972744cc Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 16:07:33 -0700 Subject: [PATCH 1852/2067] For Meier IHist...Crop tests to pass, permit htop < 1e-10 for istcrop --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 11842560ee..62643d680c 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -138,7 +138,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & type(canopystate_type) , intent(inout) :: canopystate_inst ! ! !LOCAL VARIABLES: - integer :: fp, p + integer :: fp, p, l character(len=*), parameter :: subname = 'SetZ0mDisp' real(r8) :: U_ustar ! wind at canopy height divided by friction velocity (unitless) @@ -164,6 +164,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & do fp = 1, num_nolakep p = filter_nolakep(fp) + l = patch%landunit(p) if( .not.(patch%is_fates(p))) then select case (z0param_method) @@ -199,8 +200,13 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) if ( htop(p) <= 1.e-10_r8 )then - write(iulog,*) ' nstep = ', get_nstep(), ' htop = ', htop(p) - call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__)) + if (lun%itype(l) == istcrop) then + z0m(p) = 0._r8 + displa(p) = 0._r8 + else + write(iulog,*) ' nstep = ', get_nstep(), ' htop = ', htop(p) + call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__)) + end if else z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) From ae8d808e9c33ab6153cd9d83f0dcc9430054fc6d Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 17:18:05 -0700 Subject: [PATCH 1853/2067] Update testlists: mimics tests to clm51 and remove obsolete Meier2022 test --- cime_config/testdefs/testlist_clm.xml | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index d0e2418b56..5f9d86c7ff 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -17,15 +17,6 @@ - - - - - - - - - @@ -532,7 +523,7 @@ - + @@ -2039,7 +2030,7 @@ - + From 5ed438fee20418f61ec015ce8ce0f9db89c809ed Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 20 Nov 2023 17:51:44 -0700 Subject: [PATCH 1854/2067] Update ChangeLog --- doc/ChangeLog | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 62837f1f0a..648c27e556 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -61,6 +61,11 @@ Changes to the datasets (e.g., parameter, surface or initial files): New clm5_1 params file with new parameters and with modified values of existing parameters. New clm5_0 and clm4_5 params files with new parameters for SNICAR. +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +- Remove clm50 Meier test. Should be clm51 but the compset I1850Clm51BgcNoAnthro does not exist. +- Remove Meier testmod directory. Remove from corresponding tests. Testing summary: ---------------- @@ -69,8 +74,8 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- - izumi ------- + cheyenne ---- OK + izumi ------- OK Answer changes From fc631f4392ced2bad4206dab45e30d65c9db4ddf Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 Nov 2023 13:11:18 -0700 Subject: [PATCH 1855/2067] Update ExpectedTestFails and testlist --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- cime_config/testdefs/testlist_clm.xml | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 44876ba818..0f8062da0a 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -74,7 +74,7 @@ - + PEND #1045 diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 5f9d86c7ff..85fdd0bb9c 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1167,9 +1167,6 @@ - - - @@ -1408,10 +1405,11 @@ - + + From e8aa4ebbf49b5966310b1b44daf6fbfce38bdf28 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 21 Nov 2023 13:20:38 -0700 Subject: [PATCH 1856/2067] Update ChangeLog/ChangeSum --- doc/ChangeLog | 6 ++++-- doc/ChangeSum | 2 +- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 648c27e556..d9fd062d0d 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev154 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Mon Nov 20 11:09:45 MST 2023 +Date: Tue Nov 21 13:13:57 MST 2023 One-line Summary: New params files: Changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc Purpose and description of changes @@ -65,7 +65,9 @@ Notes of particular relevance for developers: --------------------------------------------- Changes to tests or testing: - Remove clm50 Meier test. Should be clm51 but the compset I1850Clm51BgcNoAnthro does not exist. -- Remove Meier testmod directory. Remove from corresponding tests. +- Remove Meier testmod directory and remove such reference from corresponding tests. +- Change mimics tests from clm50 to clm51. +- For details, see the updated testlist_clm.xml file. Testing summary: ---------------- diff --git a/doc/ChangeSum b/doc/ChangeSum index d86a084cd9..a057281dc5 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev154 slevis 11/20/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc + ctsm5.1.dev154 slevis 11/21/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc ctsm5.1.dev153 afoster 11/17/2023 Call new FATES-side FatesReadParameters ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors ctsm5.1.dev151 rgknox 11/11/2023 Fixes to FATES long run restarts From d5785876d773fb63fadd13b2c26399b3df37053a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 22 Nov 2023 12:46:42 -0700 Subject: [PATCH 1857/2067] Update ChangeLog/ChangeSum --- doc/ChangeLog | 22 ++++++++++++++++++++-- doc/ChangeSum | 2 +- 2 files changed, 21 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index d9fd062d0d..a1626a9022 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev154 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) -Date: Tue Nov 21 13:13:57 MST 2023 +Date: Wed Nov 22 09:53:01 MST 2023 One-line Summary: New params files: Changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc Purpose and description of changes @@ -60,6 +60,8 @@ Changes made to namelist defaults (e.g., changed parameter values): Changes to the datasets (e.g., parameter, surface or initial files): New clm5_1 params file with new parameters and with modified values of existing parameters. New clm5_0 and clm4_5 params files with new parameters for SNICAR. + ./rimport on the new params files fails with "No space left on device" but the 4 files are safe here: + /glade/u/home/slevis/paramfiles/*_params.c231117.nc Notes of particular relevance for developers: --------------------------------------------- @@ -88,10 +90,26 @@ Changes answers relative to baseline: YES Summarize any changes to answers, i.e., - what code configurations: ALL - what platforms/compilers: ALL - - nature of change: larger than roundoff/same climate? + - nature of change: + Larger than roundoff/same climate? I will post this tag on the Answer changing tags wiki page as "SIGNIFICANT" and will run a simulation and diagnostics to compare against dev145. + I used the izumi test-suite to perform one bfb sanity test: + I backed up my branch to 6dc1966 (before the snicar mods), then I put back the changes of the + commit right after snicar (71e174f). Comparing to dev154 (this tag's new baseline), + the izumi test-suite passed bfb (12 gnu, 18 intel, and 32 nag tests). + Other mods are quite confined and clear, so I will not pursue other sanity tests. + + Changes to answers commit-by-commit in this PR: + f9978db and b8c71fa: These two change answers for Meier2022 and, therefore, clm51 only + 626f520: Takes out if (z0param_method == 'Meier2022'), so changes answers for all three CLMs + 319d194: Changes answers for mimics and, therefore clm51 only (order of ops, so roundoff) + 2ee6943: Changes clm51 params file, so affects clm51 only (expect more than roundoff) + f185a31: bfb + 6dc1966: This git merge escomp/master probably does change answers from previous commit + 29ca5ad and 71e174f: Puts snicar params on the params files for all three CLMs; sanity test gave bfb + Other details ------------- Pull Requests that document the changes (include PR ids): diff --git a/doc/ChangeSum b/doc/ChangeSum index a057281dc5..2d2e82b420 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev154 slevis 11/21/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc + ctsm5.1.dev154 slevis 11/22/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc ctsm5.1.dev153 afoster 11/17/2023 Call new FATES-side FatesReadParameters ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors ctsm5.1.dev151 rgknox 11/11/2023 Fixes to FATES long run restarts From 1d432db7d623da66101a9380a0476a710e796df7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 16 Oct 2023 18:19:34 -0600 Subject: [PATCH 1858/2067] turn excess ice and meier roughness on by default, add LND_TUNING_MODE for clm5_1_cam6.0, fix a syntax issue from the earlier merge (cherry picked from commit 2746a0d21289dd2a0226ff9727f8c5441f0fe7ee) Conflicts: bld/namelist_files/namelist_defaults_ctsm.xml --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++-- bld/namelist_files/namelist_definition_ctsm.xml | 2 +- cime_config/config_component.xml | 3 ++- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0516ecbc22..a3b8c093c6 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -502,7 +502,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Meier2022 .true. -.false. +.true. @@ -2763,7 +2763,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -.false. +.true. lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 2cb95d5c68..97310ebe80 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -2156,7 +2156,7 @@ Land mask description + valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_0_cam6.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_cam6.0"> General configuration of model version and atmospheric forcing to tune the model to run under. This sets the model to run with constants and initial conditions that were set to run well under the configuration of model version and atmospheric forcing. To run well constants would need to be changed diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml index 743e9229b9..281a94a0b2 100644 --- a/cime_config/config_component.xml +++ b/cime_config/config_component.xml @@ -63,7 +63,7 @@ Tuning parameters and initial conditions should be optimized for what CLM model version and what meteorlogical forcing combination? UNSET - clm5_0_cam6.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_1_GSWP3v1 + clm5_0_cam6.0,clm5_0_GSWP3v1,clm5_0_CRUv7,clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_1_GSWP3v1,clm5_1_cam6.0 clm4_5_CRUv7 clm4_5_CRUv7 @@ -76,6 +76,7 @@ clm5_0_cam6.0 clm5_0_cam6.0 clm5_1_GSWP3v1 + clm5_1_cam6.0 From 34368e0c3d03eeac7e002f1656aa6055996dae02 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 19 Oct 2023 00:51:09 -0600 Subject: [PATCH 1859/2067] Update externals to cesm2_3_beta16 (cherry picked from commit aba49b6f5373d998c1821bb101707d4d31a9ed27) --- Externals.cfg | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index e683f199ac..9e7b4acc31 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -8,7 +8,7 @@ required = True local_path = components/cism protocol = git repo_url = https://github.com/ESCOMP/CISM-wrapper -tag = cismwrap_2_1_95 +tag = cismwrap_2_1_96 externals = Externals_CISM.cfg required = True @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_cesm0.0.65 +tag = ccs_config_cesm0.0.82 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config @@ -44,18 +44,18 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.125 +tag = cime6.0.175 required = True [cmeps] -tag = cmeps0.14.21 +tag = cmeps0.14.43 protocol = git repo_url = https://github.com/ESCOMP/CMEPS.git local_path = components/cmeps required = True [cdeps] -tag = cdeps1.0.13 +tag = cdeps1.0.23 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps @@ -63,7 +63,7 @@ externals = Externals_CDEPS.cfg required = True [cpl7] -tag = cpl77.0.5 +tag = cpl77.0.7 protocol = git repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps local_path = components/cpl7 @@ -84,7 +84,7 @@ local_path = libraries/mct required = True [parallelio] -tag = pio2_5_10 +tag = pio2_6_2 protocol = git repo_url = https://github.com/NCAR/ParallelIO local_path = libraries/parallelio From 53524623e4d114af4f4bc42fea4599a42e23ddc4 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 19 Oct 2023 00:56:14 -0600 Subject: [PATCH 1860/2067] Add finidat for ne30np4.pg3 from @olyson /glade/p/cgd/tss/people/oleson/CLM5_restarts/ctsm51_cesm23a14a_ne30pg3ne30pg3mg17_CPLHIST_1850pAD.clm2.r.0561-01-01-00000.nc (cherry picked from commit b80808fc123ac5d623db0d4288f40e2aa0c46df8) --- bld/namelist_files/namelist_defaults_ctsm.xml | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a3b8c093c6..d1ab3fe8dc 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -678,6 +678,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). set up. If more finidat files are added you may need to add more of these. Or one specific file will be chosen over another. --> + hgrid=0.9x1.25 maxpft=17 mask=gx1v7 use_cn=.true. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. @@ -722,6 +723,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. + +hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. + + hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. @@ -878,7 +885,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). hgrid="ne0np4.ARCTICGRIS.ne30x8" use_cn=".false." maxpft="17" >hgrid=ne0np4.ARCTICGRIS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. -p + lnd/clm2/initdata_map/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c200428.nc + +lnd/clm2/initdata_map/clmi.I1850Clm51CplhistBgcCrop-ciso.0561-01-01.ne30np4.pg3_gx1v7_simyr1850_c230717.nc + + hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. @@ -1283,6 +1282,8 @@ lnd/clm2/surfdata_map/ctsm5.1.dev120/surfdata_ne16np4.pg3_hist_78pfts_CMIP6_simy lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4.pg2_hist_78pfts_CMIP6_simyr1850_c200426.nc + +lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4.pg3_hist_78pfts_CMIP6_simyr1850_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4.pg3_hist_78pfts_CMIP6_simyr1850_c200426.nc From e40ca1c4d4b6708389eb5a0753e0782f67f58cf1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 20 Oct 2023 17:48:08 -0600 Subject: [PATCH 1871/2067] Add PE layout for ne30 on Cheyenne (cherry picked from commit da5beb8003c72eed6684edfaf1f783f2d8cadd15) --- cime_config/config_pes.xml | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 03cea52e7b..90b3fe9efe 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -631,6 +631,43 @@ + + + + none + + -1 + -20 + -20 + -20 + -20 + -20 + -20 + -20 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + From 01abaeea43313fd33ea5e73cc71f8658f26c2eba Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 21 Oct 2023 15:01:31 -0600 Subject: [PATCH 1872/2067] Add more tests to deal with issue #2219, add a test that turns excess ice off, add tests to expected fails (cherry picked from commit c1cadb377c0458350691eba1426a3a56ae13aed6) --- cime_config/testdefs/ExpectedTestFails.xml | 15 +++++++++++ cime_config/testdefs/testlist_clm.xml | 27 +++++++++++++++++++ .../include_user_mods | 1 + .../clm51cam6LndTuningModeNoExIce/user_nl_clm | 3 +++ 4 files changed, 46 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 0f8062da0a..47c6ade336 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -28,6 +28,21 @@ --> + + + + FAIL + #2210 + + + + + FAIL + #2210 + + + + diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index f2a95596c3..5db428361a 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -53,6 +53,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods new file mode 100644 index 0000000000..a102434d88 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods @@ -0,0 +1 @@ +../clm51cam6LndTuningMode/ diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm new file mode 100644 index 0000000000..918670a060 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm @@ -0,0 +1,3 @@ +! Turn off excess ice +use_exice = .true. +use_exice_streams = .true. From 071cf722585be6a8e9989171b206316dfa2cc977 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 5 Nov 2023 01:48:13 -0600 Subject: [PATCH 1873/2067] Add an LII test using the spunup 1850 ne30pg3_g17 file (cherry picked from commit d6994f733f0bfe004e50a45e9d25ff7cb9a1b15e) --- cime_config/testdefs/testlist_clm.xml | 10 ++++++++++ .../clm/clm51cam6LndTuningModeCiso/include_user_mods | 1 + .../clm/clm51cam6LndTuningModeCiso/user_nl_clm | 5 +++++ 3 files changed, 16 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 5db428361a..984a439dd3 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1265,6 +1265,16 @@ + + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/include_user_mods new file mode 100644 index 0000000000..aa76c52034 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/include_user_mods @@ -0,0 +1 @@ +../clm51cam6LndTuningMode diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/user_nl_clm new file mode 100644 index 0000000000..e7627dea50 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeCiso/user_nl_clm @@ -0,0 +1,5 @@ +! Turn on Carbon isotopes +use_c13 = .true. +use_c14 = .true. +use_c13_timeseries = .true. +use_c14_bombspike = .true. From ab597dd271ca1d99ce3860c9899458043177ae76 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 7 Nov 2023 02:47:16 -0700 Subject: [PATCH 1874/2067] Adjust tests with tests expected to pass (cherry picked from commit 9882289b28b3876d96d826989e09c9e31b8aa4fa) --- cime_config/testdefs/testlist_clm.xml | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 984a439dd3..9d958d0d76 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -524,6 +524,15 @@ + + + + + + + + + @@ -1265,7 +1274,7 @@ - + @@ -1275,7 +1284,7 @@ - + From 6a7c0e7b23f893d589776dc0d64e9d6fedd4c040 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 27 Nov 2023 21:17:43 -0700 Subject: [PATCH 1875/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 46 ++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 47 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index a1626a9022..0b181a1543 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,50 @@ =============================================================== +Tag name: ctsm5.1.dev155 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Mon Nov 27 21:16:51 MST 2023 +One-line Summary: Use baset_latvary parameters + +Purpose and description of changes +---------------------------------- + +Namelist parameters baset_latvary_slope and baset_latvary_intercept were never actually used, with values of 0.4 and 12 being hard-coded in the relevant subroutine instead. This PR fixes that, and also adds unit testing of a refactored function that uses them. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- PASS + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +* #2240: Use baset_latvary parameters (https://github.com/ESCOMP/CTSM/pull/2240) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev154 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310) Date: Wed Nov 22 09:53:01 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 2d2e82b420..65173a9cc1 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev155 samrabin 11/27/2023 Use baset_latvary parameters ctsm5.1.dev154 slevis 11/22/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc ctsm5.1.dev153 afoster 11/17/2023 Call new FATES-side FatesReadParameters ctsm5.1.dev152 multiple 11/14/2023 Mv tools to /python and add tests; add snow_thermal_cond_method; a few fixes / refactors From 16ba2019d8003b21a26d22e544d008eb4dad5485 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 9 Nov 2023 00:47:31 -0700 Subject: [PATCH 1876/2067] Fix some of the filepaths (cherry picked from commit a4eff78bd07be1895176d13efecc99ff23a6624d) Conflicts: bld/namelist_files/namelist_defaults_ctsm.xml --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2893784dac..67d934345d 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1282,8 +1282,6 @@ lnd/clm2/surfdata_map/ctsm5.1.dev120/surfdata_ne16np4.pg3_hist_78pfts_CMIP6_simy lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4_hist_78pfts_CMIP6_simyr1850_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4.pg2_hist_78pfts_CMIP6_simyr1850_c200426.nc - -lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4.pg3_hist_78pfts_CMIP6_simyr1850_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_ne30np4.pg3_hist_78pfts_CMIP6_simyr1850_c200426.nc @@ -1431,9 +1429,9 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4.pg2_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc + >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne30np4_SSP5-8.5_78_CMIP6_1850-2100_c230530.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc + >lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP5-8.5_78_CMIP6_1850-2100_c230530.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc Date: Thu, 9 Nov 2023 00:49:15 -0700 Subject: [PATCH 1877/2067] Add issue number to expected fails (cherry picked from commit 4e091304e60250c8f9415619cbb04797162df2c0) Conflicts: cime_config/testdefs/ExpectedTestFails.xml --- cime_config/testdefs/ExpectedTestFails.xml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 47c6ade336..d30088c125 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -38,11 +38,10 @@ FAIL - #2210 + #2234 - From c48a334b7f6f63fca05062ce94f33402bb88cd87 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 9 Nov 2023 15:16:29 -0700 Subject: [PATCH 1878/2067] Update baseline directory for Derecho (cherry picked from commit b916d3875da71ca48b8099133dbdfe358eec67d6) --- python/ctsm/machine_defaults.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/machine_defaults.py b/python/ctsm/machine_defaults.py index 305c86e03c..ea1a4db45b 100644 --- a/python/ctsm/machine_defaults.py +++ b/python/ctsm/machine_defaults.py @@ -69,7 +69,7 @@ "derecho": MachineDefaults( job_launcher_type=JOB_LAUNCHER_QSUB, scratch_dir=os.path.join(os.path.sep, "glade", "derecho", "scratch", get_user()), - baseline_dir=os.path.join(os.path.sep, "glade", "p", "cgd", "tss", "ctsm_baselines"), + baseline_dir=os.path.join(os.path.sep, "glade", "campaign", "cgd", "tss", "ctsm_baselines"), account_required=True, create_test_retry=0, create_test_queue="regular", From 79f64df1f02cf5f5aeb8562269799e8f68e80325 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 9 Nov 2023 17:31:18 -0700 Subject: [PATCH 1879/2067] Change queue and wallclock limit for Derecho (cherry picked from commit 863ed22b5a490bc63b83adf03b8f5bb788fa0e76) --- python/ctsm/machine_defaults.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/machine_defaults.py b/python/ctsm/machine_defaults.py index ea1a4db45b..18f4ff4752 100644 --- a/python/ctsm/machine_defaults.py +++ b/python/ctsm/machine_defaults.py @@ -75,8 +75,8 @@ create_test_queue="regular", job_launcher_defaults={ JOB_LAUNCHER_QSUB: QsubDefaults( - queue="regular", - walltime="11:50:00", + queue="main", + walltime="03:50:00", extra_args="", # The following assumes a single node, with a single mpi proc; we may want # to add more flexibility in the future, making the node / proc counts From 0e8caee16565eaf2d4e610b65a582ed0b79ddeec Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 9 Nov 2023 21:19:22 -0700 Subject: [PATCH 1880/2067] Add 2000 and HIST tests for ne30np4.pg3 to cesm3_dev testlist, remove the PEM test that is no longer needed and doesn't have a testmod for it (cherry picked from commit 04853a83c55ec77d954149555923a3c0dd5dcd77) --- cime_config/testdefs/testlist_clm.xml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 9d958d0d76..876c834d1e 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -53,22 +53,22 @@ - + - + - + - + @@ -98,6 +98,15 @@ + + + + + + + + + From 0fa6ebcb150bec66464e7100bf3c85c7583508a9 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 9 Nov 2023 23:30:28 -0700 Subject: [PATCH 1881/2067] Get finidat file working for 2000 ne30np4.pg3 clm5_1_cam6.0 working (cherry picked from commit 88ac3ae9a7e01515bc202b9efc91ed7e6d515df8) --- bld/namelist_files/namelist_defaults_ctsm.xml | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 67d934345d..a8e1f20221 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -826,6 +826,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc +lnd/clm2/initdata_map/clmi.BHIST.2000-01-01.0.9x1.25_gx1v7_simyr2000_c200728.nc + + Date: Fri, 10 Nov 2023 00:20:22 -0700 Subject: [PATCH 1882/2067] Update ne30np4.pg3 1850 finidat file so LII tests work, and add in ne30np4.pg3 landuse.timeseries file (cherry picked from commit d3a82a568dded619a2ed2012a33048fbbe7372df) Conflicts: bld/namelist_files/namelist_defaults_ctsm.xml --- bld/namelist_files/namelist_defaults_ctsm.xml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a8e1f20221..ac80b1b336 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -988,7 +988,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false." ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false." lnd_tuning_mode="clm5_1_cam6.0" ->lnd/clm2/initdata_map/clmi.I1850Clm51CplhistBgcCrop-ciso.0561-01-01.ne30np4.pg3_gx1v7_simyr1850_c230717.nc +>lnd/clm2/initdata_map/clmi.I1850Clm51CplhistBgcCrop-ciso.0561-01-01.ne30np4.pg3_gx1v7_simyr1850_c231109.nc @@ -1442,7 +1444,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4.pg2_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne30np4_SSP5-8.5_78_CMIP6_1850-2100_c230530.nc + >lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pft_c231026.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP5-8.5_78_CMIP6_1850-2100_c230530.nc Date: Fri, 10 Nov 2023 09:29:42 -0700 Subject: [PATCH 1883/2067] Actually turn Meier off (cherry picked from commit 1a09d07801e05c48aab90a30b1b1fe679fad8184) Conflicts: cime_config/testdefs/testmods_dirs/clm/ciso_decStartNoMeier/user_nl_clm --- cime_config/testdefs/testlist_clm.xml | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 876c834d1e..03a4d0c91b 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -533,7 +533,7 @@ - + @@ -1283,17 +1283,25 @@ - + - - + - + + + + + + + + + + From f1f1a91599e7cbbf38beddd1acdde3b6bf836260 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 28 Nov 2023 09:16:40 -0500 Subject: [PATCH 1884/2067] Updating spacing for fates radiation path join --- cime_config/buildlib | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/buildlib b/cime_config/buildlib index a0a56d2702..0e253c9d98 100755 --- a/cime_config/buildlib +++ b/cime_config/buildlib @@ -140,7 +140,7 @@ def _main_func(): os.path.join(lnd_root, "src", "fates", "biogeochem"), os.path.join(lnd_root, "src", "fates", "fire"), os.path.join(lnd_root, "src", "fates", "parteh"), - os.path.join(lnd_root, "src", "fates", "radiation"), + os.path.join(lnd_root, "src", "fates", "radiation"), os.path.join(lnd_root, "src", "utils"), os.path.join(lnd_root, "src", "cpl"), os.path.join(lnd_root, "src", "cpl", "utils"), From 82800f05e04b8e61722fd7b3eb728a2b65019c54 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 09:15:54 -0700 Subject: [PATCH 1885/2067] Correct some namelist settings --- bld/namelist_files/namelist_defaults_ctsm.xml | 8 ++++---- .../clm/clm51cam6LndTuningModeNoExIce/include_user_mods | 1 - .../clm/clm51cam6LndTuningModeNoExIce/user_nl_clm | 3 --- 3 files changed, 4 insertions(+), 8 deletions(-) delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods delete mode 100644 cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ac80b1b336..7c5d19eeaa 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -502,7 +502,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). Meier2022 .true. -.true. +.false. @@ -1444,9 +1444,9 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4.pg2_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc lnd/clm2/surfdata_esmf/ctsm5.2.0/landuse.timeseries_ne30np4.pg3_SSP2-4.5_1850-2100_78pft_c231026.nc + >lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne30np4.pg3_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP5-8.5_78_CMIP6_1850-2100_c230530.nc + >lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTICGRIS.ne30x8_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc lnd/clm2/surfdata_map/release-clm5.0.30/landuse.timeseries_ne0np4.ARCTIC.ne30x4_SSP5-8.5_78pfts_CMIP6_simyr1850-2100_c200426.nc lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -.true. +.false. lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods deleted file mode 100644 index a102434d88..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/include_user_mods +++ /dev/null @@ -1 +0,0 @@ -../clm51cam6LndTuningMode/ diff --git a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm deleted file mode 100644 index 918670a060..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/clm51cam6LndTuningModeNoExIce/user_nl_clm +++ /dev/null @@ -1,3 +0,0 @@ -! Turn off excess ice -use_exice = .true. -use_exice_streams = .true. From 8f3327cd5bc1c3d8a05d30c6477c9d8bf3ceb2db Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 10:20:15 -0700 Subject: [PATCH 1886/2067] The ne30pg3 finidat file needs to do interpolation to get started since it was created with ctsm5.2 datasets --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 7c5d19eeaa..60366149c0 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -987,7 +987,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/initdata_map/clmi.I1850Clm51CplhistBgcCrop-ciso.0561-01-01.ne30np4.pg3_gx1v7_simyr1850_c231109.nc From 18c2a501379553c08560543ccd57fc77c0b62d97 Mon Sep 17 00:00:00 2001 From: adrifoster Date: Tue, 28 Nov 2023 11:11:57 -0700 Subject: [PATCH 1887/2067] move add_cime_to_path import --- python/ctsm/site_and_regional/run_neon.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 104e325617..f8d55fa6f2 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -66,6 +66,8 @@ _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) +from ctsm import add_cime_to_path + from CIME import build from CIME.case import Case from CIME.utils import safe_copy, expect, symlink_force @@ -74,8 +76,6 @@ from ctsm.utils import parse_isoduration from ctsm.download_utils import download_file -from ctsm import add_cime_to_path - from standard_script_setup import * logger = logging.getLogger(__name__) From 30361835aaed1d6c6a828797d42f8b55af9efc1d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 11:54:16 -0700 Subject: [PATCH 1888/2067] Remove the ne30pg3 LII tests because they will fail as use_init_interp is required because the finidat file is based on ctsm5.2 datasets --- cime_config/testdefs/testlist_clm.xml | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 03a4d0c91b..cbef667b93 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1283,15 +1283,6 @@ - - - - - - - - - @@ -1301,15 +1292,6 @@ - - - - - - - - - From ebb3e64e389c2d407147034070b7456879d327b2 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 11:55:08 -0700 Subject: [PATCH 1889/2067] Add use_init_interp to the ne30pg3 finidat file, because it's needed for non ctsm5.2 surface datasets --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 60366149c0..7c5d19eeaa 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -987,7 +987,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). lnd/clm2/initdata_map/clmi.I1850Clm51CplhistBgcCrop-ciso.0561-01-01.ne30np4.pg3_gx1v7_simyr1850_c231109.nc From 98cb379df0d6bb53f41455f11a74ee7ce70fb86c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 12:33:15 -0700 Subject: [PATCH 1890/2067] Set init_interp_fill_missing_with_natveg for the ne30np4.pg3 grid --- bld/CLMBuildNamelist.pm | 5 +++++ bld/namelist_files/namelist_defaults_ctsm.xml | 2 ++ 2 files changed, 7 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 17d64cd59f..9a4dadfd6c 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4356,6 +4356,11 @@ sub setup_logic_initinterp { $log->fatal_error("$var can only be set if use_init_interp is true"); } } + # This only seems to be important for this one grid... + if ( $nl_flags->{'res'} eq "ne30np4.pg3" ) { + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_fill_missing_with_natveg", + 'hgrid'=>$nl_flags->{'res'} ); + } } #------------------------------------------------------------------------------- diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 7c5d19eeaa..e6b35380f9 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -903,6 +903,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + +.true. - - - FAIL - #2210 - - - - + + FAIL - #2234 + #2268 From 9f457dbadc6a01d6b8ee98c9fa7c995941ad0585 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 16:10:31 -0700 Subject: [PATCH 1892/2067] Add a couple cesm3_dev tests to aux_clm --- cime_config/testdefs/testlist_clm.xml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index cbef667b93..8ffae44d6d 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -47,6 +47,7 @@ + @@ -77,12 +78,13 @@ - + + From 3a3a97eec36cd82d7b30c0e1ea17e35a8d69beb8 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 16:27:15 -0700 Subject: [PATCH 1893/2067] PE layouts for f45 and f10 for Derecho --- cime_config/config_pes.xml | 75 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 90b3fe9efe..60c7355825 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -113,6 +113,43 @@ + + + + none + + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + @@ -1336,6 +1373,44 @@ + + + + none + + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + From 651ff5c7b3c5426bb3cc2fc3b14445ef606c0463 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 19:14:57 -0700 Subject: [PATCH 1894/2067] Lengthen test time --- cime_config/testdefs/testlist_clm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 8ffae44d6d..bb073be374 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2032,7 +2032,7 @@ - + From a8c535a976daf87832ba4b72b91f0f67deea9ba5 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Tue, 28 Nov 2023 19:28:24 -0700 Subject: [PATCH 1895/2067] Remove the nvhpc tests that are now passing --- cime_config/testdefs/ExpectedTestFails.xml | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 067f54b8c0..f4b4ff6f5d 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -50,24 +50,9 @@ #1733 - - - - FAIL - #1733 - - - - - - FAIL - #1733 - - - + - FAIL From 10b3985ec55e07495c13a25692cbb86fa6529f66 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 29 Nov 2023 11:21:41 -0700 Subject: [PATCH 1896/2067] Update Externals.cfg to version from CESM3_dev aba49b6. --- Externals.cfg | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index e683f199ac..f5243f9166 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -8,7 +8,7 @@ required = True local_path = components/cism protocol = git repo_url = https://github.com/ESCOMP/CISM-wrapper -tag = cismwrap_2_1_95 +tag = cismwrap_2_1_96 externals = Externals_CISM.cfg required = True @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_cesm0.0.65 +tag = ccs_config_cesm0.0.82 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config @@ -44,18 +44,18 @@ required = True local_path = cime protocol = git repo_url = https://github.com/ESMCI/cime -tag = cime6.0.125 +tag = cime6.0.175 required = True [cmeps] -tag = cmeps0.14.21 +tag = cmeps0.14.43 protocol = git repo_url = https://github.com/ESCOMP/CMEPS.git local_path = components/cmeps required = True [cdeps] -tag = cdeps1.0.13 +tag = cdeps1.0.23 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps @@ -63,7 +63,7 @@ externals = Externals_CDEPS.cfg required = True [cpl7] -tag = cpl77.0.5 +tag = cpl77.0.7 protocol = git repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps local_path = components/cpl7 @@ -84,7 +84,7 @@ local_path = libraries/mct required = True [parallelio] -tag = pio2_5_10 +tag = pio2_6_2 protocol = git repo_url = https://github.com/NCAR/ParallelIO local_path = libraries/parallelio @@ -98,4 +98,4 @@ tag = v1.0.8 required = False [externals_description] -schema_version = 1.0.0 +schema_version = 1.0.0 \ No newline at end of file From 242974bcdcac5c8ce1ac730fc13697a55e71b29a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 29 Nov 2023 16:17:08 -0700 Subject: [PATCH 1897/2067] Remove endrun for Meier2022 case to work --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 62643d680c..defd1ff144 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -200,16 +200,11 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) if ( htop(p) <= 1.e-10_r8 )then - if (lun%itype(l) == istcrop) then - z0m(p) = 0._r8 - displa(p) = 0._r8 - else - write(iulog,*) ' nstep = ', get_nstep(), ' htop = ', htop(p) - call endrun(subgrid_index=p, subgrid_level=subgrid_level_patch, msg=errMsg(sourcefile, __LINE__)) - end if + z0m(p) = 0._r8 + displa(p) = 0._r8 else - z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & - log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) + z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & + log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) end if end if From f2ad0487eaf8101520fc3d3535bb2a737f971de9 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 29 Nov 2023 20:51:05 -0700 Subject: [PATCH 1898/2067] fates external pointer --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 5f8e8d2441..ec0028a880 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.68.2_api.31.0.0 +tag = sci.1.69.0_api.31.0.0 required = True [externals_description] From 1f44adf93e0a61d15e3dd83db6af6c832924f777 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 29 Nov 2023 23:23:12 -0700 Subject: [PATCH 1899/2067] update fates parameter file name in defaults --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index ced8e15d13..5053a481df 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -492,7 +492,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc +lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231130.nc From f85fea88f5ee68cf628640ad37592f472206e9bc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 30 Nov 2023 00:22:59 -0700 Subject: [PATCH 1900/2067] First pass at adding derecho tests, also change the syntax for ones with options per machine to options after machine lists, and add intel-oneapi and nvhpc tests to test lists with clm_short --- cime_config/testdefs/testlist_clm.xml | 931 ++++++++++++++++++++++---- 1 file changed, 807 insertions(+), 124 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index bb073be374..33e1f000fa 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3,6 +3,7 @@ + @@ -12,14 +13,18 @@ + + + + @@ -29,6 +34,7 @@ + @@ -39,6 +45,8 @@ + + @@ -112,6 +120,7 @@ + @@ -121,6 +130,7 @@ + @@ -130,6 +140,7 @@ + @@ -146,6 +157,7 @@ + @@ -155,6 +167,7 @@ + @@ -164,6 +177,7 @@ + @@ -173,6 +187,7 @@ + @@ -182,6 +197,7 @@ + @@ -192,6 +208,8 @@ + + @@ -235,6 +253,7 @@ + @@ -250,6 +269,15 @@ + + + + + + + + + @@ -259,6 +287,15 @@ + + + + + + + + + @@ -267,6 +304,14 @@ + + + + + + + + @@ -275,9 +320,18 @@ + + + + + + + + + @@ -287,6 +341,8 @@ + + @@ -295,6 +351,7 @@ + @@ -303,6 +360,7 @@ + @@ -312,6 +370,7 @@ + @@ -320,6 +379,7 @@ + @@ -328,6 +388,7 @@ + @@ -337,6 +398,8 @@ + + @@ -351,9 +414,19 @@ + + + + + + + + + + @@ -363,6 +436,7 @@ + @@ -372,6 +446,7 @@ + @@ -395,9 +470,19 @@ + + + + + + + + + + @@ -407,6 +492,7 @@ + @@ -416,6 +502,7 @@ + @@ -425,6 +512,7 @@ + @@ -434,6 +522,7 @@ + @@ -443,6 +532,8 @@ + + @@ -451,6 +542,7 @@ + @@ -461,6 +553,8 @@ + + @@ -469,6 +563,7 @@ + @@ -477,6 +572,7 @@ + @@ -486,6 +582,8 @@ + + @@ -494,6 +592,7 @@ + @@ -503,6 +602,7 @@ + @@ -512,6 +612,7 @@ + @@ -535,6 +636,15 @@ + + + + + + + + + @@ -544,9 +654,19 @@ + + + + + + + + + + @@ -573,6 +693,8 @@ + + @@ -580,6 +702,19 @@ + + + + + + + + + + + + + @@ -588,6 +723,14 @@ + + + + + + + + @@ -597,6 +740,15 @@ + + + + + + + + + @@ -623,6 +775,14 @@ + + + + + + + + @@ -631,6 +791,14 @@ + + + + + + + + @@ -639,6 +807,14 @@ + + + + + + + + @@ -648,6 +824,15 @@ + + + + + + + + + @@ -657,6 +842,15 @@ + + + + + + + + + @@ -666,6 +860,15 @@ + + + + + + + + + @@ -675,10 +878,21 @@ + + + + + + + + + + + @@ -697,6 +911,7 @@ + @@ -706,6 +921,8 @@ + + @@ -714,6 +931,7 @@ + @@ -722,6 +940,7 @@ + @@ -738,6 +957,7 @@ + @@ -747,6 +967,7 @@ + @@ -786,9 +1007,19 @@ + + + + + + + + + + @@ -798,6 +1029,7 @@ + @@ -807,6 +1039,7 @@ + @@ -822,6 +1055,15 @@ + + + + + + + + + @@ -830,6 +1072,14 @@ + + + + + + + + @@ -839,6 +1089,15 @@ + + + + + + + + + @@ -848,9 +1107,19 @@ + + + + + + + + + + @@ -860,6 +1129,7 @@ + @@ -869,6 +1139,7 @@ + @@ -878,6 +1149,7 @@ + @@ -887,6 +1159,7 @@ + @@ -895,6 +1168,7 @@ + @@ -904,6 +1178,7 @@ + @@ -920,6 +1195,16 @@ + + + + + + + + + + @@ -930,6 +1215,16 @@ + + + + + + + + + + @@ -940,6 +1235,16 @@ + + + + + + + + + + @@ -949,6 +1254,15 @@ + + + + + + + + + @@ -957,6 +1271,14 @@ + + + + + + + + @@ -966,6 +1288,15 @@ + + + + + + + + + @@ -976,6 +1307,16 @@ + + + + + + + + + + @@ -984,6 +1325,14 @@ + + + + + + + + @@ -993,6 +1342,15 @@ + + + + + + + + + @@ -1003,6 +1361,16 @@ + + + + + + + + + + @@ -1013,9 +1381,20 @@ + + + + + + + + + + + @@ -1030,9 +1409,19 @@ + + + + + + + + + + @@ -1042,6 +1431,7 @@ + @@ -1051,6 +1441,7 @@ + @@ -1060,6 +1451,7 @@ + @@ -1075,12 +1467,27 @@ + + + + + + + + + + + + + + + @@ -1089,6 +1496,7 @@ + @@ -1098,6 +1506,7 @@ + @@ -1106,6 +1515,7 @@ + @@ -1115,6 +1525,8 @@ + + @@ -1132,6 +1544,7 @@ + @@ -1186,6 +1599,7 @@ + @@ -1210,6 +1624,15 @@ + + + + + + + + + @@ -1219,6 +1642,15 @@ + + + + + + + + + @@ -1228,9 +1660,19 @@ + + + + + + + + + + @@ -1241,6 +1683,8 @@ + + @@ -1250,6 +1694,7 @@ + @@ -1279,6 +1724,7 @@ + @@ -1294,9 +1740,19 @@ + + + + + + + + + + @@ -1307,6 +1763,8 @@ + + @@ -1317,6 +1775,8 @@ + + @@ -1326,6 +1786,8 @@ + + @@ -1350,10 +1812,21 @@ + + + + + + + + + + + @@ -1363,6 +1836,7 @@ + @@ -1373,6 +1847,8 @@ + + @@ -1381,6 +1857,7 @@ + @@ -1389,6 +1866,7 @@ + @@ -1399,6 +1877,7 @@ + @@ -1408,6 +1887,7 @@ + @@ -1417,6 +1897,7 @@ + @@ -1426,6 +1907,7 @@ + @@ -1435,6 +1917,7 @@ + @@ -1444,6 +1927,7 @@ + @@ -1453,6 +1937,7 @@ + @@ -1462,6 +1947,7 @@ + @@ -1471,6 +1957,7 @@ + @@ -1481,6 +1968,8 @@ + + @@ -1501,9 +1990,13 @@ + + + + @@ -1519,9 +2012,19 @@ - + + + + + + + + + + + - + @@ -1543,6 +2046,12 @@ + + + + + + @@ -1553,6 +2062,9 @@ + + + @@ -1561,6 +2073,7 @@ + @@ -1570,6 +2083,8 @@ + + @@ -1588,11 +2103,13 @@ + + - + @@ -1637,6 +2154,17 @@ + + + + + + + + + + + @@ -1663,6 +2191,7 @@ + @@ -1673,6 +2202,7 @@ + @@ -1690,23 +2220,23 @@ - - - - - - + + + + + + - - - - - - + + + + + + @@ -1721,6 +2251,7 @@ + @@ -1729,9 +2260,11 @@ + + @@ -1746,6 +2279,8 @@ + + @@ -1755,6 +2290,7 @@ + @@ -1781,6 +2317,8 @@ + + @@ -1790,6 +2328,7 @@ + @@ -1799,6 +2338,7 @@ + @@ -1808,6 +2348,7 @@ + @@ -1827,6 +2368,7 @@ + @@ -1837,6 +2379,8 @@ + + @@ -1863,6 +2407,7 @@ + @@ -1872,6 +2417,7 @@ + @@ -1880,6 +2426,7 @@ + @@ -1889,6 +2436,8 @@ + + @@ -1897,6 +2446,7 @@ + @@ -1906,6 +2456,7 @@ + @@ -1914,6 +2465,7 @@ + @@ -1923,6 +2475,7 @@ + @@ -1932,6 +2485,7 @@ + @@ -1941,6 +2495,7 @@ + @@ -1960,6 +2515,8 @@ + + @@ -1969,6 +2526,7 @@ + @@ -1977,6 +2535,7 @@ + @@ -1986,6 +2545,7 @@ + @@ -1995,6 +2555,8 @@ + + @@ -2012,6 +2574,7 @@ + @@ -2022,6 +2585,8 @@ + + @@ -2035,12 +2600,23 @@ + + + + + + + + + + + @@ -2049,6 +2625,7 @@ + @@ -2057,6 +2634,7 @@ + @@ -2066,6 +2644,7 @@ + @@ -2076,6 +2655,7 @@ + @@ -2086,6 +2666,7 @@ + @@ -2096,6 +2677,7 @@ + @@ -2112,6 +2694,16 @@ + + + + + + + + + + @@ -2146,15 +2738,24 @@ + + + + + + + + + - - - - - - + + + + + + @@ -2168,33 +2769,40 @@ - + + + + + + + - - - - - - - + + + + + + + + + - - - - - - - - + + + + + + + @@ -2210,9 +2818,19 @@ + + + + + + + + + + @@ -2223,6 +2841,7 @@ + @@ -2233,6 +2852,7 @@ + @@ -2244,6 +2864,7 @@ + @@ -2255,6 +2876,8 @@ + + @@ -2265,6 +2888,7 @@ + @@ -2275,6 +2899,7 @@ + @@ -2286,8 +2911,10 @@ + + @@ -2298,6 +2925,7 @@ + @@ -2308,6 +2936,7 @@ + @@ -2319,6 +2948,7 @@ + @@ -2329,6 +2959,7 @@ + @@ -2339,6 +2970,7 @@ + @@ -2349,6 +2981,7 @@ + @@ -2359,6 +2992,7 @@ + @@ -2368,6 +3002,7 @@ + @@ -2377,6 +3012,7 @@ + @@ -2386,6 +3022,7 @@ + @@ -2394,6 +3031,7 @@ + @@ -2403,6 +3041,7 @@ + @@ -2412,6 +3051,7 @@ + @@ -2422,6 +3062,7 @@ + @@ -2431,6 +3072,7 @@ + @@ -2440,6 +3082,7 @@ + @@ -2457,9 +3100,20 @@ + + + + + + + + + + + @@ -2469,6 +3123,7 @@ + @@ -2479,6 +3134,7 @@ + @@ -2490,6 +3146,8 @@ + + @@ -2499,6 +3157,7 @@ + @@ -2510,6 +3169,9 @@ + + + @@ -2519,6 +3181,7 @@ + @@ -2528,97 +3191,82 @@ - - - - - - + + + + + + - - - - - - - - - - - + + + + + + + - - - - - - + + + + + + - - - - - - - - + + + + + + + + - - - - - - - - - - - - + + + + + + + - - - - - - - - - - - - + + + + + + + + + - - - - - - - - + + + + + @@ -2631,6 +3279,15 @@ + + + + + + + + + @@ -2641,6 +3298,15 @@ + + + + + + + + + @@ -2651,47 +3317,64 @@ + + + + + + + + + - - - - - - + + + + + + + + + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + - - - - - - + + + + + + From 5c8f17b1a3badc4699882cae3c408c100a0e6a3f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 30 Nov 2023 00:29:36 -0700 Subject: [PATCH 1901/2067] Work on f09 f19 and nldas pe-layouts for Derecho --- cime_config/config_pes.xml | 233 +++++++++++++++++++++++++++++++++---- 1 file changed, 209 insertions(+), 24 deletions(-) diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 60c7355825..34fd593425 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -298,6 +298,80 @@ + + + + none + + -1 + -12 + -12 + -12 + -12 + -12 + -12 + -12 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + Much lower core count f19 layout, mainly for testing + + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + @@ -340,34 +414,34 @@ none - -4 - -4 - -4 - -4 - -4 - -4 - -4 - -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 + -4 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 @@ -413,6 +487,43 @@ none + + -1 + -14 + -14 + -14 + -14 + -14 + -14 + -14 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + Much lower core count f09 layout, mainly for testing -1 -5 @@ -1560,5 +1671,79 @@ + + + + none + + -1 + -14 + -14 + -14 + -14 + -14 + -14 + -14 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + + + + + + Much lower core count nldas2 layout, mainly for testing + + -1 + -1 + -1 + -1 + -1 + -1 + -1 + -1 + + + 1 + 1 + 1 + 1 + 1 + 1 + 1 + 1 + + + 0 + 0 + 0 + 0 + 0 + 0 + 0 + 0 + + + + From fd7373d2b7387023756716197ca2f4abb390b7fa Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 30 Nov 2023 09:29:10 -0700 Subject: [PATCH 1902/2067] remove obsolete disturbance variables from base fates testmod --- cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index 03ed340cbb..f7b62048ef 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -16,10 +16,8 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_SAPWOODC', 'FATES_LEAFC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR', -'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', -'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE', +'FATES_HARVEST_CARBON_FLUX', 'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL', -'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX', 'FATES_STOMATAL_COND', 'FATES_LBLAYER_COND', 'FATES_NPP', 'FATES_GPP', 'FATES_AUTORESP', 'FATES_GROWTH_RESP', 'FATES_MAINT_RESP', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', From 97a93b7b5953e177d4f04cb4d55c139cb7f80b59 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 30 Nov 2023 09:38:29 -0700 Subject: [PATCH 1903/2067] add landuse site level variables to default fates testmod --- cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm index f7b62048ef..406fb598f6 100644 --- a/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm @@ -26,4 +26,5 @@ hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS', 'FATES_NEP', 'FATES_HET_RESP', 'FATES_FIRE_CLOSS', 'FATES_FIRE_FLUX_EL', 'FATES_CBALANCE_ERROR', 'FATES_ERROR_EL', 'FATES_LEAF_ALLOC', 'FATES_SEED_ALLOC', 'FATES_STEM_ALLOC', 'FATES_FROOT_ALLOC', -'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC' +'FATES_CROOT_ALLOC', 'FATES_STORE_ALLOC', +'FATES_PATCHAREA_LU', 'FATES_DISTURBANCE_RATE_MATRIX_LULU' From b24e5f512ef85a63b0151b2fd8d511017b5d13b4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 30 Nov 2023 12:32:29 -0700 Subject: [PATCH 1904/2067] Do not use Meier roughness by default, even with 5.1. --- bld/namelist_files/namelist_defaults_ctsm.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 0516ecbc22..1be3827d1b 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -499,7 +499,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). ZengWang2007 -Meier2022 .true. .false. From c2455923458f2c788d373c0ba7117c4d15264518 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 30 Nov 2023 15:10:40 -0700 Subject: [PATCH 1905/2067] remove obsolete disturbance variables from excluded output of fates_sp usersmod --- cime_config/usermods_dirs/fates_sp/user_nl_clm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/fates_sp/user_nl_clm index 0df139403d..093ecd7eda 100644 --- a/cime_config/usermods_dirs/fates_sp/user_nl_clm +++ b/cime_config/usermods_dirs/fates_sp/user_nl_clm @@ -21,9 +21,8 @@ hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLD 'FATES_SEEDS_IN_EXTERN_EL', 'FATES_SEED_GERM_EL', 'FATES_SEED_DECAY_EL', 'FATES_STOREC', 'FATES_VEGC', 'FATES_SAPWOODC', 'FATES_FROOTC', 'FATES_REPROC', 'FATES_STRUCTC', 'FATES_NONSTRUCTC', 'FATES_VEGC_ABOVEGROUND', 'FATES_CANOPY_VEGC', 'FATES_USTORY_VEGC', 'FATES_PRIMARY_PATCHFUSION_ERR', - 'FATES_DISTURBANCE_RATE_P2P', 'FATES_DISTURBANCE_RATE_P2S', 'FATES_DISTURBANCE_RATE_S2S', 'FATES_DISTURBANCE_RATE_FIRE', 'FATES_DISTURBANCE_RATE_LOGGING', 'FATES_DISTURBANCE_RATE_TREEFALL', - 'FATES_DISTURBANCE_RATE_POTENTIAL', 'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY', + 'FATES_HARVEST_CARBON_FLUX', 'FATES_GPP_CANOPY', 'FATES_AUTORESP_CANOPY', 'FATES_GPP_USTORY', 'FATES_AUTORESP_USTORY', 'FATES_CROWNAREA_CL', 'FATES_DEMOTION_CARBONFLUX', 'FATES_PROMOTION_CARBONFLUX', 'FATES_MORTALITY_CFLUX_CANOPY', 'FATES_MORTALITY_CFLUX_USTORY', 'FATES_DDBH_CANOPY_SZ', 'FATES_DDBH_USTORY_SZ', 'FATES_BASALAREA_SZ', From da4af8ed95522d589693b2974f79e499f1ce923c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 30 Nov 2023 15:27:55 -0700 Subject: [PATCH 1906/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 65 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 0b181a1543..aabefea0fe 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,68 @@ =============================================================== +Tag name: ctsm5.1.dev156 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Thu Nov 30 15:27:18 MST 2023 +One-line Summary: Do not use Meier roughness by default + +Purpose and description of changes +---------------------------------- + +ctsm5.1.dev155 had turned on Meier2022 surface roughness calculation by default for 5.1 compsets. Several bugs have recently emerged that were not caught by pre-merge testing, so this tag reverts that change. Thus, the ZengWang2007 method is default for all compsets again. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Notes of particular relevance for users +--------------------------------------- + +Changes made to namelist defaults (e.g., changed parameter values): 5.1 compsets now use ZengWang2007 method (instead of Meier2022) for roughness calculation. + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- PASS + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: 5.1 compsets + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): new climate + + No climate-evaluating run performed, as this change is reverting part of a commit thats barely a week old. + + +Other details +------------- +Pull Requests that document the changes (include PR ids): +(https://github.com/ESCOMP/ctsm/pull) +* #2273: Do not use Meier roughness by default, even with 5.1. (https://github.com/ESCOMP/CTSM/pull/2273) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev155 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Mon Nov 27 21:16:51 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 65173a9cc1..d891a68d87 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev156 samrabin 11/30/2023 Do not use Meier roughness by default. ctsm5.1.dev155 samrabin 11/27/2023 Use baset_latvary parameters ctsm5.1.dev154 slevis 11/22/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc ctsm5.1.dev153 afoster 11/17/2023 Call new FATES-side FatesReadParameters From 8c0b078de072713d038b229febea83d1b06a2bb7 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 30 Nov 2023 15:54:04 -0700 Subject: [PATCH 1907/2067] add luh2 testmod --- cime_config/testdefs/testlist_clm.xml | 9 +++++++++ .../testmods_dirs/clm/FatesColdLUH2/include_user_mods | 1 + .../testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm | 1 + 3 files changed, 11 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 85fdd0bb9c..88d9fbbc88 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2177,6 +2177,15 @@ + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm new file mode 100644 index 0000000000..854c21407f --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdLUH2/user_nl_clm @@ -0,0 +1 @@ +use_fates_luh = .true. From 7222bb6b3ef1f9d6ee55cd322b2f4ac67d9aa927 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 Nov 2023 16:10:00 -0700 Subject: [PATCH 1908/2067] Try z0m(p) = z0mg(c) instead of zero as the bug-fix --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index defd1ff144..66feb049f9 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -92,7 +92,7 @@ subroutine BiogeophysPreFluxCalcs(bounds, & !----------------------------------------------------------------------- call SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & - clm_fates, canopystate_inst) + clm_fates, frictionvel_inst, canopystate_inst) call frictionvel_inst%SetRoughnessLengthsAndForcHeightsNonLake(bounds, & num_nolakec, filter_nolakec, & @@ -120,7 +120,7 @@ end subroutine BiogeophysPreFluxCalcs !----------------------------------------------------------------------- subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & - clm_fates, canopystate_inst) + clm_fates, frictionvel_inst, canopystate_inst) ! ! !DESCRIPTION: ! Set z0m and displa @@ -135,10 +135,11 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & integer , intent(in) :: num_nolakep ! number of column non-lake points in patch filter integer , intent(in) :: filter_nolakep(:) ! patch filter for non-lake points type(hlm_fates_interface_type) , intent(in) :: clm_fates + type(frictionvel_type) , intent(in) :: frictionvel_inst type(canopystate_type) , intent(inout) :: canopystate_inst ! ! !LOCAL VARIABLES: - integer :: fp, p, l + integer :: fp, p, c character(len=*), parameter :: subname = 'SetZ0mDisp' real(r8) :: U_ustar ! wind at canopy height divided by friction velocity (unitless) @@ -146,6 +147,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & !----------------------------------------------------------------------- associate( & + z0mg => frictionvel_inst%z0mg_col , & ! Input: [real(r8) (:) ] roughness length of ground, momentum [m] htop => canopystate_inst%htop_patch , & ! Input: [real(r8) (:) ] canopy top (m) z0m => canopystate_inst%z0m_patch , & ! Output: [real(r8) (:) ] momentum roughness length (m) displa => canopystate_inst%displa_patch & ! Output: [real(r8) (:) ] displacement height (m) @@ -164,7 +166,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & do fp = 1, num_nolakep p = filter_nolakep(fp) - l = patch%landunit(p) + c = patch%column(p) if( .not.(patch%is_fates(p))) then select case (z0param_method) @@ -200,8 +202,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & / 2._r8)**(-0.5_r8) / (pftcon%z0v_LAImax(patch%itype(p))) / pftcon%z0v_c(patch%itype(p)) if ( htop(p) <= 1.e-10_r8 )then - z0m(p) = 0._r8 - displa(p) = 0._r8 + z0m(p) = z0mg(c) else z0m(p) = htop(p) * (1._r8 - displa(p) / htop(p)) * exp(-0.4_r8 * U_ustar + & log(pftcon%z0v_cw(patch%itype(p))) - 1._r8 + pftcon%z0v_cw(patch%itype(p))**(-1._r8)) From bdf616c3aa2904bfc66f8585471c80dafe8a988c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 30 Nov 2023 16:16:22 -0700 Subject: [PATCH 1909/2067] Correct ChangeLog description of aux_clm results for ctsm5.1.dev156. --- doc/ChangeLog | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index aabefea0fe..80ddf5be12 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -38,8 +38,8 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- OK - izumi ------- PASS + cheyenne ---- DIFF + izumi ------- DIFF Answer changes From ced34c3e63464ce327431cc89c79b604be7fee83 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 30 Nov 2023 16:17:05 -0700 Subject: [PATCH 1910/2067] Fix comment alignment --- src/biogeophys/BiogeophysPreFluxCalcsMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 index 66feb049f9..574af6f782 100644 --- a/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 +++ b/src/biogeophys/BiogeophysPreFluxCalcsMod.F90 @@ -147,7 +147,7 @@ subroutine SetZ0mDisp(bounds, num_nolakep, filter_nolakep, & !----------------------------------------------------------------------- associate( & - z0mg => frictionvel_inst%z0mg_col , & ! Input: [real(r8) (:) ] roughness length of ground, momentum [m] + z0mg => frictionvel_inst%z0mg_col , & ! Input: [real(r8) (:) ] roughness length of ground, momentum [m] htop => canopystate_inst%htop_patch , & ! Input: [real(r8) (:) ] canopy top (m) z0m => canopystate_inst%z0m_patch , & ! Output: [real(r8) (:) ] momentum roughness length (m) displa => canopystate_inst%displa_patch & ! Output: [real(r8) (:) ] displacement height (m) From f65c99ca079726e62c84ca040f0f38f25228ab2a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 00:14:00 -0700 Subject: [PATCH 1911/2067] Update externals for ccs_config which is needed for mpi-serial tests --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index 9e7b4acc31..cf2ff73498 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_cesm0.0.82 +tag = ccs_config_cesm0.0.84 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config From 4ce2a9d98fccbe38664659a026c5c1a64194429a Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 00:15:29 -0700 Subject: [PATCH 1912/2067] The same intel tests are failing on Derecho as were on Cheyenne --- cime_config/testdefs/ExpectedTestFails.xml | 29 +++++++++++++++++++++- 1 file changed, 28 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index f4b4ff6f5d..55b47dc4c9 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -50,10 +50,17 @@ #1733 + + + + FAIL + #1733 + + - + FAIL FATES#701 @@ -67,6 +74,13 @@ + + + FAIL + FATES#701 + + + PEND @@ -74,6 +88,13 @@ + + + PEND + #1045 + + + PEND @@ -89,5 +110,11 @@ + + + FAIL + FATES#1089 + + From 14d666e4b8120c4491ca19ac3d8f67f8fdbc4f45 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 00:34:46 -0700 Subject: [PATCH 1913/2067] Fix pe-layouts for Derecho, remove new nvhpc tests on Derecho that weren't in Cheyenne, and remove the intel-oneapi tests since they fail --- cime_config/testdefs/testlist_clm.xml | 94 ++++++++++++--------------- 1 file changed, 43 insertions(+), 51 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 33e1f000fa..1a1bfed7e3 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -304,7 +304,7 @@ - + @@ -320,7 +320,7 @@ - + @@ -414,7 +414,7 @@ - + @@ -636,7 +636,7 @@ - + @@ -654,7 +654,7 @@ - + @@ -693,7 +693,6 @@ - @@ -702,11 +701,10 @@ - + - @@ -723,7 +721,7 @@ - + @@ -740,7 +738,7 @@ - + @@ -775,7 +773,7 @@ - + @@ -791,7 +789,7 @@ - + @@ -807,7 +805,7 @@ - + @@ -824,7 +822,7 @@ - + @@ -842,7 +840,7 @@ - + @@ -860,7 +858,7 @@ - + @@ -878,7 +876,7 @@ - + @@ -1007,7 +1005,7 @@ - + @@ -1055,7 +1053,7 @@ - + @@ -1072,7 +1070,7 @@ - + @@ -1089,7 +1087,7 @@ - + @@ -1107,7 +1105,7 @@ - + @@ -1195,7 +1193,7 @@ - + @@ -1215,7 +1213,7 @@ - + @@ -1254,7 +1252,7 @@ - + @@ -1288,7 +1286,7 @@ - + @@ -1307,7 +1305,7 @@ - + @@ -1325,7 +1323,7 @@ - + @@ -1342,7 +1340,7 @@ - + @@ -1361,7 +1359,7 @@ - + @@ -1381,7 +1379,7 @@ - + @@ -1409,7 +1407,7 @@ - + @@ -1467,7 +1465,7 @@ - + @@ -1483,8 +1481,6 @@ - - @@ -1624,7 +1620,7 @@ - + @@ -1642,7 +1638,7 @@ - + @@ -1660,7 +1656,7 @@ - + @@ -1812,7 +1808,7 @@ - + @@ -1991,8 +1987,6 @@ - - @@ -2022,7 +2016,7 @@ - + @@ -2047,8 +2041,6 @@ - - @@ -2154,7 +2146,7 @@ - + @@ -2162,7 +2154,7 @@ - + @@ -2738,7 +2730,7 @@ - + @@ -2769,7 +2761,7 @@ - + @@ -3279,7 +3271,7 @@ - + @@ -3298,7 +3290,7 @@ - + @@ -3317,7 +3309,7 @@ - + From 84bab54dcd6d7e93fc0323cd5b48c7f5b824a7bf Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 09:25:59 -0700 Subject: [PATCH 1914/2067] Correct expected fail --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 55b47dc4c9..9a14b7e8da 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -88,7 +88,7 @@ - + PEND #1045 From 15c9527f5ab79acdfc41606a59c8d293b483feac Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 09:55:41 -0700 Subject: [PATCH 1915/2067] Add two expected fails because of a build issue presumably in ccs_config --- cime_config/testdefs/ExpectedTestFails.xml | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 9a14b7e8da..1d83bb2e7a 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -95,6 +95,20 @@ + + + FAIL + ESMCI/ccs_config_cesm#130 + + + + + + FAIL + ESMCI/ccs_config_cesm#130 + + + PEND From 11e706cc617750609b06759f9fd19aaabf649294 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 10:04:40 -0700 Subject: [PATCH 1916/2067] Add more mpi-serial intel debug failed tests --- cime_config/testdefs/ExpectedTestFails.xml | 28 ++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 1d83bb2e7a..bfd87c2fd9 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -57,6 +57,34 @@ #1733 + + + + FAIL + ESMCI/ccs_config_cesm#130 + + + + + + FAIL + ESMCI/ccs_config_cesm#130 + + + + + + FAIL + ESMCI/ccs_config_cesm#130 + + + + + + FAIL + ESMCI/ccs_config_cesm#130 + + From 24c088c8e9103bd639d0fece4674c4ea44b03393 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 10:38:31 -0700 Subject: [PATCH 1917/2067] Remove two nvhpc tests that fail, one from Cheyenne that wasn't there before and the other from Derecho --- cime_config/testdefs/testlist_clm.xml | 2 -- 1 file changed, 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 1a1bfed7e3..86dde5bebd 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -693,7 +693,6 @@ - @@ -705,7 +704,6 @@ - From a0f8ff9d43f88776c877861154ac878e9b6f7753 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 11:45:08 -0700 Subject: [PATCH 1918/2067] change location of luh2 fates data and make sure default is available --- bld/CLMBuildNamelist.pm | 1 + bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index b2178f1ca1..26e132d4fb 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4368,6 +4368,7 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fluh_timeseries', 'phys'=>$nl_flags->{'phys'}); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 5053a481df..f16b04988c 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1548,7 +1548,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/luh/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c230415.nc + use_crop=".false." >lnd/clm2/surfdata_map/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc .true. From bb23a70ca53ce36be9f8acbbaaf5324ae3ba92af Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 12:54:30 -0800 Subject: [PATCH 1919/2067] replace use statements from the fluh_timeseries default setting --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index f16b04988c..614873dc2c 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1547,8 +1547,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -lnd/clm2/surfdata_map/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc +lnd/clm2/surfdata_map/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc .true. From e2716ca65a7e4f6c5614ea077e24c40c110f67cf Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 12:55:55 -0800 Subject: [PATCH 1920/2067] add build subdirectory for fates landuse timeseries default file --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 614873dc2c..32ce121845 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1548,7 +1548,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc + >lnd/clm2/surfdata_map/sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc .true. From ffac03f29f4765dfa1916d61cccc6a24d0151f93 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 12:57:41 -0800 Subject: [PATCH 1921/2067] add fates to the build tag subdirectory name --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 32ce121845..d7301197e2 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1548,7 +1548,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 lnd/clm2/surfdata_map/sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc + >lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc .true. From 6c5c24d193f714321a02e8296b563dbef6652442 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 14:11:35 -0700 Subject: [PATCH 1922/2067] Add NEON tests to Derecho --- cime_config/testdefs/testlist_clm.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 86dde5bebd..8247236db2 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2104,6 +2104,7 @@ + @@ -2115,6 +2116,7 @@ + @@ -2125,6 +2127,7 @@ + @@ -2158,6 +2161,8 @@ + + @@ -2171,6 +2176,8 @@ + + From 7ccd479e9f89b9dd755448037fa77b7c5db68c13 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Fri, 1 Dec 2023 14:12:25 -0700 Subject: [PATCH 1923/2067] Change some of the comments about Cheyenne to also include Derecho --- python/conda_env_ctsm_py.txt | 5 +++-- python/conda_env_ctsm_py_cgd.txt | 1 - python/ctsm/test/testinputs/README.md | 1 + 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index 0ac4656e73..0306a9ca06 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -1,7 +1,8 @@ # -# NOTE: Changes here should be coordinated with the cgd python environment file +# NOTE: Changes here should be coordinated with the cgd python environment file +# +# NOTE: Derecho already has conda installed for you, so you just need to do the following... # -# To install this on cheyenne with conda loaded in modules # use the top level bash script: # ../py_env_create # Do this each time you update your CTSM Version # conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script diff --git a/python/conda_env_ctsm_py_cgd.txt b/python/conda_env_ctsm_py_cgd.txt index 8312dc328a..3afcf4bba2 100644 --- a/python/conda_env_ctsm_py_cgd.txt +++ b/python/conda_env_ctsm_py_cgd.txt @@ -3,7 +3,6 @@ # # This should be coordinated with the main python environment file! # -# To install this on cheyenne with conda loaded in modules # use the top level bash script: # ../py_env_create # Do this each time you update your CTSM Version # conda activate ctsm_pylib # Do this anytime you want to run a CTSM python script diff --git a/python/ctsm/test/testinputs/README.md b/python/ctsm/test/testinputs/README.md index 1775de48b7..ef8953d20e 100644 --- a/python/ctsm/test/testinputs/README.md +++ b/python/ctsm/test/testinputs/README.md @@ -6,6 +6,7 @@ Installing Git LFS on your machine is a two-step process; step (1) needs to be done once per machine, and step (2) needs to be done once per user: 1. Install the Git LFS tool: Follow the instructions on the [Git LFS page](https://git-lfs.github.com/) for installing Git LFS on your platform. + - On derecho the system default version of git already has Git LFS installed. - On cheyenne and casper, Git LFS is already available as long as you are using a git module rather than the default system-level git. So just make sure that you are always using git via a git module (`module load git`). From be78a0bbec8ad11c8012f2d0b75ac40f056ff8a3 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 14:43:45 -0800 Subject: [PATCH 1924/2067] add resolution to the add_default call for the fates landuse timeseries --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 26e132d4fb..bb6be82bea 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4368,7 +4368,7 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fluh_timeseries', 'phys'=>$nl_flags->{'phys'}); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fluh_timeseries', 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>"4x5"); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); From 3def7e304610fee86ad704158e54228cd4c1e0ec Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 15:42:22 -0800 Subject: [PATCH 1925/2067] correct descriptions and diagnostic write --- src/main/clm_varctl.F90 | 4 ++-- src/main/controlMod.F90 | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90 index 7498597b34..e0d142bffd 100644 --- a/src/main/clm_varctl.F90 +++ b/src/main/clm_varctl.F90 @@ -310,8 +310,8 @@ module clm_varctl logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode - logical, public :: use_fates_luh = .false. ! true => use FATES satellite phenology mode - character(len=256), public :: fluh_timeseries = '' ! filename for inventory control + logical, public :: use_fates_luh = .false. ! true => use FATES landuse data mode + character(len=256), public :: fluh_timeseries = '' ! filename for fates landuse timeseries data character(len=256), public :: fates_inventory_ctrl_filename = '' ! filename for inventory control ! FATES SP AND FATES BGC are MUTUTALLY EXCLUSIVE, THEY CAN'T BOTH BE ON diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index eeb1e6847d..44efec4eeb 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -1156,7 +1156,7 @@ subroutine control_print () write(iulog, *) ' use_fates_fixed_biogeog = ', use_fates_fixed_biogeog write(iulog, *) ' use_fates_nocomp = ', use_fates_nocomp write(iulog, *) ' use_fates_sp = ', use_fates_sp - write(iulog, *) ' use_fates_luh= ', use_fates_sp + write(iulog, *) ' use_fates_luh= ', use_fates_luh write(iulog, *) ' fluh_timeseries = ', trim(fluh_timeseries) write(iulog, *) ' fates_seeddisp_cadence = ', fates_seeddisp_cadence write(iulog, *) ' fates_seeddisp_cadence: 0, 1, 2, 3 => off, daily, monthly, or yearly dispersal' From e8b0508890d5c4be573e00f4e3e9b48d0e02a4cf Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 1 Dec 2023 16:08:11 -0800 Subject: [PATCH 1926/2067] correct hlm group name in namelist definition --- bld/namelist_files/namelist_definition_ctsm.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml index 4f26dc5dff..408a037737 100644 --- a/bld/namelist_files/namelist_definition_ctsm.xml +++ b/bld/namelist_files/namelist_definition_ctsm.xml @@ -779,14 +779,14 @@ Full pathname to the inventory initialization control file. + group="clm_inparm" valid_values="" > If TRUE, enable use of land use harmonization (LUH) state and transition data from luh_timeseries file. (Also, only valid for use_fates = true and is incompatible with transient runs currently.) + input_pathname="abs" group="clm_inparm" valid_values="" > Full pathname of unified land use harmonization (LUH) data file. This causes the land-use types to vary over time. (Required, if use_fates_luh=T) From 1a2f5e8a1a20796953fa4b16d348fd4c25d28e0f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 2 Dec 2023 19:49:20 -0700 Subject: [PATCH 1927/2067] Move the Derecho intel/DEBUG tests to gnu keeping only one that's expected to fail --- cime_config/testdefs/testlist_clm.xml | 40 ++++++++++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 8247236db2..2e76ca5d66 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1984,11 +1984,15 @@ + + + - @@ -2104,7 +2108,10 @@ + + @@ -2116,7 +2123,10 @@ + + @@ -2127,7 +2137,10 @@ + + @@ -2161,8 +2174,12 @@ + + + @@ -2176,8 +2193,12 @@ + + + @@ -2188,7 +2209,10 @@ + + + @@ -2552,8 +2576,12 @@ + + + @@ -2571,7 +2599,10 @@ + + @@ -2896,7 +2927,10 @@ + + @@ -2922,7 +2956,10 @@ + + @@ -3201,6 +3238,7 @@ + From a6e3db81f791e99a95e6c3793c2e9fbaa9ca6f4c Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 2 Dec 2023 22:46:04 -0700 Subject: [PATCH 1928/2067] Add FUNITCTSM to the list of expected fails --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index bfd87c2fd9..f5053a7843 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -58,6 +58,13 @@ + + + FAIL + ESMCI/ccs_config_cesm#131 + + + FAIL From ad5c0768be91778b8298f30fa602bd7eabcb8f45 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sun, 3 Dec 2023 17:52:34 -0700 Subject: [PATCH 1929/2067] Remove references to Cheyenne and make it more explicit what to do on different systems, as well as adding Derecho --- tools/modify_input_files/README.fsurdat_modifier | 9 ++++++++- tools/modify_input_files/README.mesh_mask_modifier | 9 ++++++++- tools/site_and_regional/README | 4 ++-- 3 files changed, 18 insertions(+), 4 deletions(-) diff --git a/tools/modify_input_files/README.fsurdat_modifier b/tools/modify_input_files/README.fsurdat_modifier index 58dbadb902..885227c928 100644 --- a/tools/modify_input_files/README.fsurdat_modifier +++ b/tools/modify_input_files/README.fsurdat_modifier @@ -27,10 +27,17 @@ tools/modify_input_files/modify_fsurdat_template.cfg Instructions ------------ -To run on Cheyenne/Casper/Izumi +To run on various machines: 1) (Un)load, execute, and activate the following: +1a) First step to activate conda on your system +1a) Casper: module unload python module load conda +1a) Izumi: +module load python +1a) Derecho (nothing needs to be done for this step) +1a) Elsewhere (do what's needed to activate conda) +1b) On all systems ./py_env_create conda activate ctsm_pylib (Use "deactivate" to reverse the latter.) diff --git a/tools/modify_input_files/README.mesh_mask_modifier b/tools/modify_input_files/README.mesh_mask_modifier index 13d98b9e7f..9484058ffd 100644 --- a/tools/modify_input_files/README.mesh_mask_modifier +++ b/tools/modify_input_files/README.mesh_mask_modifier @@ -10,10 +10,17 @@ tools/modify_input_files/modify_mesh_template.cfg Instructions ------------ -To run on Cheyenne/Casper/Izumi +To run on various machines: 1) (Un)load, execute, and activate the following: +1a) First step to activate conda on your system +1a) Casper: module unload python module load conda +1a) Izumi: +module load python +1a) Derecho (nothing needs to be done +1a) Elsewhere (do what's needed to activate conda) +1b) On all systems ./py_env_create conda activate ctsm_py (Use "deactivate" to reverse the latter.) diff --git a/tools/site_and_regional/README b/tools/site_and_regional/README index 723ddb4a97..7b36b7d2b9 100644 --- a/tools/site_and_regional/README +++ b/tools/site_and_regional/README @@ -3,9 +3,9 @@ $CTSMROOT/tools/site_and_regional/README The purpose of this directory is to contain all of the scripts that involve creating CTSM input data files for single site as well as regional cases. -The python scripts require the following settings before running on cheyenne: +The python scripts require the following settings before running: -module load conda +(Do what's needed to make conda available on your system) ../../py_env_create conda activate ctsm_pylib From 9c4d186b0fd666c79112b17ba352aee6a8563235 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 4 Dec 2023 01:47:47 -0700 Subject: [PATCH 1930/2067] Update /glade/p references --- bld/namelist_files/createMapEntry.pl | 2 +- bld/unit_testers/build-namelist_test.pl | 2 +- bld/unit_testers/xFail/expectedClmTestFails.xml | 13 ------------- 3 files changed, 2 insertions(+), 15 deletions(-) diff --git a/bld/namelist_files/createMapEntry.pl b/bld/namelist_files/createMapEntry.pl index 561683bb05..f9009ba86f 100755 --- a/bld/namelist_files/createMapEntry.pl +++ b/bld/namelist_files/createMapEntry.pl @@ -23,7 +23,7 @@ my $scriptName; ($scriptName = $0) =~ s!(.*)/!!; # get name of script my $cwd = getcwd(); - my $CSMDATA = "/glade/p/cesm/cseg/inputdata"; + my $CSMDATA = "/glade/campaign/cesm/cesmdata/cseg/inputdata"; if ($#ARGV != 0 ) { usage(); diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 4c717a58bf..4d03124116 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -139,7 +139,7 @@ sub cat_and_create_namelistinfile { $inputdata_rootdir = $ENV{'CSMDATA'}; } else { # use yellowstone location as default - $inputdata_rootdir="/glade/p/cesm/cseg/inputdata"; + $inputdata_rootdir="/glade/campaign/cesm/cesmdata/cseg/inputdata"; print("WARNING: -csmdata nor CSMDATA are set, using default yellowstone location: $inputdata_rootdir\n"); } diff --git a/bld/unit_testers/xFail/expectedClmTestFails.xml b/bld/unit_testers/xFail/expectedClmTestFails.xml index 12c954d38b..c7cbfee488 100644 --- a/bld/unit_testers/xFail/expectedClmTestFails.xml +++ b/bld/unit_testers/xFail/expectedClmTestFails.xml @@ -34,19 +34,6 @@ - - - - Doesn't check for valid values - - - - - - - - From fe97097f561b2dfb8cb9c47e5b1a5142ffe6f5d7 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 4 Dec 2023 01:48:21 -0700 Subject: [PATCH 1931/2067] Update /glade/p path references --- tools/modify_input_files/README.mesh_mask_modifier | 2 +- tools/site_and_regional/default_data.cfg | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/modify_input_files/README.mesh_mask_modifier b/tools/modify_input_files/README.mesh_mask_modifier index 9484058ffd..4e25e73826 100644 --- a/tools/modify_input_files/README.mesh_mask_modifier +++ b/tools/modify_input_files/README.mesh_mask_modifier @@ -56,7 +56,7 @@ In your copy of the CTSM (say, ~user/ctsm), go to the appropriate tool: Enter the following (or similar) selections in modify_fill_indianocean.cfg: -mesh_mask_in = /glade/p/cesmdata/cseg/inputdata/share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc +mesh_mask_in = /glade/campaign/cesm/cesmdata/cseg/inputdata/share/meshes/fv0.9x1.25_141008_polemod_ESMFmesh.nc mesh_mask_out = fv0.9x1.25_141008_polemod_ESMFmesh_modified.nc landmask_file = .../path_to_your_copy_of/fill_indianocean.nc diff --git a/tools/site_and_regional/default_data.cfg b/tools/site_and_regional/default_data.cfg index 7e841dca54..0425aba133 100644 --- a/tools/site_and_regional/default_data.cfg +++ b/tools/site_and_regional/default_data.cfg @@ -1,5 +1,5 @@ [main] -clmforcingindir = /glade/p/cesmdata/inputdata +clmforcingindir = /glade/campaign/cesm/cesmdata/cseg/inputdata [datm_gswp3] dir = atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516 From 12057ea300fe7590ecd96ec8669df22377356dbf Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 4 Dec 2023 02:08:16 -0700 Subject: [PATCH 1932/2067] Update /glade/p paths --- python/ctsm/crop_calendars/generate_gdds.py | 2 +- python/ctsm/machine_defaults.py | 2 +- python/ctsm/test/test_unit_subset_data.py | 2 +- python/ctsm/test/testinputs/default_data.cfg | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/python/ctsm/crop_calendars/generate_gdds.py b/python/ctsm/crop_calendars/generate_gdds.py index b54e7df40f..16e3e130da 100644 --- a/python/ctsm/crop_calendars/generate_gdds.py +++ b/python/ctsm/crop_calendars/generate_gdds.py @@ -1,4 +1,4 @@ -paramfile_dir = "/glade/p/cesmdata/cseg/inputdata/lnd/clm2/paramdata" +paramfile_dir = "/glade/campaign/cesm/cesmdata/cseg/inputdata/lnd/clm2/paramdata" # Import other shared functions import os diff --git a/python/ctsm/machine_defaults.py b/python/ctsm/machine_defaults.py index 18f4ff4752..e30881c474 100644 --- a/python/ctsm/machine_defaults.py +++ b/python/ctsm/machine_defaults.py @@ -47,7 +47,7 @@ "cheyenne": MachineDefaults( job_launcher_type=JOB_LAUNCHER_QSUB, scratch_dir=os.path.join(os.path.sep, "glade", "scratch", get_user()), - baseline_dir=os.path.join(os.path.sep, "glade", "p", "cgd", "tss", "ctsm_baselines"), + baseline_dir=os.path.join(os.path.sep, "glade", "p", "cgd", "tss", "To_Be_Safely_Deleted", "ctsm_baselines"), account_required=True, create_test_retry=0, # NOTE(wjs, 2022-02-23) By default, use the regular queue, even for diff --git a/python/ctsm/test/test_unit_subset_data.py b/python/ctsm/test/test_unit_subset_data.py index fd9aef631d..b8ea5b06f2 100755 --- a/python/ctsm/test/test_unit_subset_data.py +++ b/python/ctsm/test/test_unit_subset_data.py @@ -56,7 +56,7 @@ def test_inputdata_setup_files_basic(self): ) self.assertEqual( files["main_dir"], - "/glade/p/cesmdata/inputdata", + "/glade/campaign/cesm/cesmdata/cseg/inputdata", "main_dir directory not whats expected", ) diff --git a/python/ctsm/test/testinputs/default_data.cfg b/python/ctsm/test/testinputs/default_data.cfg index 7e841dca54..0425aba133 100644 --- a/python/ctsm/test/testinputs/default_data.cfg +++ b/python/ctsm/test/testinputs/default_data.cfg @@ -1,5 +1,5 @@ [main] -clmforcingindir = /glade/p/cesmdata/inputdata +clmforcingindir = /glade/campaign/cesm/cesmdata/cseg/inputdata [datm_gswp3] dir = atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516 From 8b249d532f7dd39c56867ea93a92fbf6dad6fac1 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 4 Dec 2023 02:47:08 -0700 Subject: [PATCH 1933/2067] First stab at getting the test/tools framework to work on Derecho, isn't working as conda and module is not available in my default shell --- test/tools/README | 4 +- test/tools/test_driver.sh | 71 ++++++++++++++++++++++++--- test/tools/tests_pretag_derecho_nompi | 9 ++++ 3 files changed, 76 insertions(+), 8 deletions(-) create mode 100644 test/tools/tests_pretag_derecho_nompi diff --git a/test/tools/README b/test/tools/README index a2acbcae40..c545f625b8 100644 --- a/test/tools/README +++ b/test/tools/README @@ -11,7 +11,7 @@ To use... ./test_driver.sh -i -on cheyenne +on Derecho qcmd -l walltime=08:00:00 -- ./test_driver.sh -i >& run.out & @@ -33,7 +33,7 @@ To run neon-specific tests, please use login nodes: env CLM_INPUT_TESTS=`pwd`/tests_pretag_nompi_neon ./test_driver.sh -i > & run_neon.out & -Intended for use on NCAR machines cheyenne, geyser (DAV) and hobart. +Intended for use on NCAR machines Derecho, Casper (DAV) and izumi. II. RUNNING test_driver.sh TOOLS TESTING: diff --git a/test/tools/test_driver.sh b/test/tools/test_driver.sh index d4676cca69..6b1811c8ab 100755 --- a/test/tools/test_driver.sh +++ b/test/tools/test_driver.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/sh # # test_driver.sh: driver script for the offline testing of CLM of tools # @@ -26,15 +26,74 @@ hostname=`hostname` echo $hostname case $hostname in - ##cheyenne - cheyenne* | r*i*n*) - submit_script="test_driver_cheyenne${cur_time}.sh" + ##Derecho + derecho* | dec*) + submit_script="test_driver_derecho${cur_time}.sh" ##vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv cat > ./${submit_script} << EOF #!/bin/sh # +interactive="YES" +input_file="tests_pretag_derecho_nompi" +c_threads=128 + +export INITMODULES="/glade/u/apps/derecho/23.06/spack/opt/spack/lmod/8.7.20/gcc/7.5.0/pdxb/lmod/lmod/init/sh" +. \$INITMODULES + +module --force purge +module load ncarenv +module load craype +module load intel +module load mkl +module load ncarcompilers +module load netcdf +module load nco +module load ncl + +#omp threads +if [ -z "\$CLM_THREADS" ]; then #threads NOT set on command line + export CLM_THREADS=\$c_threads +fi + +# Stop on first failed test +if [ -z "\$CLM_SOFF" ]; then #CLM_SOFF NOT set + export CLM_SOFF=FALSE +fi + +export CESM_MACH="derecho" +export CESM_COMP="intel" + +export NETCDF_DIR=\$NETCDF +export INC_NETCDF=\$NETCDF/include +export LIB_NETCDF=\$NETCDF/lib +export MAKE_CMD="gmake -j " +export CFG_STRING="" +export TOOLS_MAKE_STRING="USER_FC=ifort USER_LINKER=ifort USER_CPPDEFS=-DLINUX" +export MACH_WORKSPACE=\$SCRATCH +export CPRNC_EXE="$CESMDATAROOT/cprnc/cprnc" +dataroot="$CESMDATAROOT/inputdata" +export TOOLSLIBS="" +export REGRID_PROC=1 +export TOOLS_CONF_STRING="--mpilib mpi-serial" + + +echo_arg="" + +EOF +#^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ writing to batch script ^^^^^^^^^^^^^^^^^^^ + ;; + + ##cheyenne + cheyenne* | r*i*n*) + submit_script="test_driver_cheyenne${cur_time}.sh" + +#vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv writing to batch script vvvvvvvvvvvvvvvvvvv +at > ./${submit_script} << EOF +!/bin/sh + + interactive="YES" input_file="tests_pretag_cheyenne_nompi" c_threads=36 @@ -314,7 +373,7 @@ EOF ;; * ) - echo "Only setup to work on: cheyenne, hobart and izumi" + echo "Only setup to work on: derecho, cheyenne, hobart and izumi" exit @@ -633,7 +692,7 @@ case $arg1 in * ) echo "" echo "**********************" - echo "usage on cheyenne, hobart, and izumi: " + echo "usage on derecho, cheyenne, hobart, and izumi: " echo "./test_driver.sh -i" echo "" echo "valid arguments: " diff --git a/test/tools/tests_pretag_derecho_nompi b/test/tools/tests_pretag_derecho_nompi new file mode 100644 index 0000000000..5fdaf335ae --- /dev/null +++ b/test/tools/tests_pretag_derecho_nompi @@ -0,0 +1,9 @@ +smba1 blba1 +smbd1 blbd1 +sm0a1 bl0a1 +sm0c1 bl0c1 +smaa2 blaa2 +smba1 blba1 +smb81 blb81 +smbc1 blbc1 +smbd1 blbd1 From 8085fa344c0119e2eeb299b521082a0e74636158 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Mon, 4 Dec 2023 03:10:02 -0700 Subject: [PATCH 1934/2067] Update paths to use /glade/campaign/cesm/cesmdata/cseg/inputdata resolving most of #2196 --- .../testmods_dirs/clm/DA_multidrv/user_nl_clm_0001 | 1 + .../testmods_dirs/clm/DA_multidrv/user_nl_clm_0002 | 1 + .../testdefs/testmods_dirs/clm/USUMB_mct/shell_commands | 7 +++---- .../testdefs/testmods_dirs/clm/USUMB_mct/user_nl_clm | 5 ++--- .../testdefs/testmods_dirs/clm/USUMB_nuopc/shell_commands | 3 +-- .../testdefs/testmods_dirs/clm/USUMB_nuopc/user_nl_clm | 5 ++--- .../testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm | 2 +- .../clm/collapse_pfts_78_to_16_decStart_f10/README | 4 ++-- .../clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm | 4 ++-- .../testdefs/testmods_dirs/clm/cplhist/shell_commands | 2 +- .../modify_smallville_with_dynurban.ncl | 1 + .../testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm | 6 +++--- 12 files changed, 20 insertions(+), 21 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0001 b/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0001 index 719785e25d..96b8d387db 100644 --- a/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0001 +++ b/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0001 @@ -10,4 +10,5 @@ hist_type1d_pertape = ' ',' ',' ' use_init_interp = .true. + ! IMPORTANT: The path for this file NEEDS to be updated for the removal of Cheyenne and /glade/p finidat = '/glade/p/cisl/dares/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0001.r.2001-01-01-00000.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0002 b/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0002 index 37d5b2b24e..6a606720d5 100644 --- a/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0002 +++ b/cime_config/testdefs/testmods_dirs/clm/DA_multidrv/user_nl_clm_0002 @@ -10,4 +10,5 @@ hist_type1d_pertape = ' ',' ',' ' use_init_interp = .true. + ! IMPORTANT: The path for this file NEEDS to be updated for the removal of Cheyenne and /glade/p finidat = '/glade/p/cisl/dares/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0002.r.2001-01-01-00000.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/shell_commands b/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/shell_commands index 446125abf9..4fb282d511 100755 --- a/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/shell_commands @@ -5,8 +5,8 @@ ./xmlchange DATM_CLMNCEP_YR_END=2006 # Comment this out if NINST_LND is greater than 1 (see: http://bugs.cgd.ucar.edu/show_bug.cgi?id=2521) ./xmlchange MPILIB=mpi-serial -./xmlchange ATM_DOMAIN_PATH=/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB -./xmlchange LND_DOMAIN_PATH=/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB +./xmlchange ATM_DOMAIN_PATH='$DIN_LOC_ROOT/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB' +./xmlchange LND_DOMAIN_PATH='$DIN_LOC_ROOT/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB' ./xmlchange ATM_DOMAIN_FILE=domain.lnd.1x1pt_US-UMB_navy.171024.nc ./xmlchange LND_DOMAIN_FILE=domain.lnd.1x1pt_US-UMB_navy.171024.nc ./xmlchange --append CLM_BLDNML_OPTS='-mask navy -no-crop' @@ -15,5 +15,4 @@ ./xmlchange ATM_NCPL=24 ./xmlchange RUN_STARTDATE=1999-01-01 ./xmlchange DATM_CLMNCEP_YR_ALIGN=1999 -./xmlchange DIN_LOC_ROOT=/glade/p/cesm/cseg/inputdata -./xmlchange DIN_LOC_ROOT_CLMFORC=/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024 +./xmlchange DIN_LOC_ROOT_CLMFORC='$DIN_LOC_ROOT/lnd/clm2/PTCLMmydatafiles.c171024' diff --git a/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/user_nl_clm index 38ce400297..8bb7848d49 100644 --- a/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/USUMB_mct/user_nl_clm @@ -1,5 +1,4 @@ -! user_nl_clm namelist options written by PTCLMmkdata: -! ./PTCLMmkdata --cesm_root ../../../.. -s US-UMB -d /glade/p/cesm/cseg/inputdata --mydatadir=/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024 - fsurdat = '/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB/surfdata_1x1pt_US-UMB_16pfts_Irrig_CMIP6_simyr2000_c171024.nc' +! user_nl_clm namelist options written by PTCLMmkdata, which is no longer available + fsurdat = '$DIN_LOC_ROOT/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB/surfdata_1x1pt_US-UMB_16pfts_Irrig_CMIP6_simyr2000_c171024.nc' hist_nhtfrq = 0 hist_mfilt = 1200 diff --git a/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/shell_commands b/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/shell_commands index 08a9014abe..ec6eb898d7 100755 --- a/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/shell_commands @@ -11,7 +11,6 @@ ./xmlchange ATM_NCPL=24 ./xmlchange RUN_STARTDATE=1999-01-01 ./xmlchange DATM_YR_ALIGN=1999 -./xmlchange DIN_LOC_ROOT=/glade/p/cesm/cseg/inputdata -./xmlchange DIN_LOC_ROOT_CLMFORC=/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024 +./xmlchange DIN_LOC_ROOT_CLMFORC='$DIN_LOC_ROOT/lnd/clm2/PTCLMmydatafiles.c171024' ./xmlchange PTS_LON=275.2862 ./xmlchange PTS_LAT=45.5598 diff --git a/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/user_nl_clm index 38ce400297..8bb7848d49 100644 --- a/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/USUMB_nuopc/user_nl_clm @@ -1,5 +1,4 @@ -! user_nl_clm namelist options written by PTCLMmkdata: -! ./PTCLMmkdata --cesm_root ../../../.. -s US-UMB -d /glade/p/cesm/cseg/inputdata --mydatadir=/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024 - fsurdat = '/glade/p/cesm/cseg/inputdata/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB/surfdata_1x1pt_US-UMB_16pfts_Irrig_CMIP6_simyr2000_c171024.nc' +! user_nl_clm namelist options written by PTCLMmkdata, which is no longer available + fsurdat = '$DIN_LOC_ROOT/lnd/clm2/PTCLMmydatafiles.c171024/1x1pt_US-UMB/surfdata_1x1pt_US-UMB_16pfts_Irrig_CMIP6_simyr2000_c171024.nc' hist_nhtfrq = 0 hist_mfilt = 1200 diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm index 57ac8a6461..534cbb84b8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm @@ -1,2 +1,2 @@ -paramfile = '/glade/p/cesm/cseg/inputdata/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c231117.nc' +paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c231117.nc' hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr' diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README index 81fb991ed0..af5d819ffc 100644 --- a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README +++ b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/README @@ -9,10 +9,10 @@ According to the file the following two files used in this test are default files for the following options: -fsurdat = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc' +fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc' hgrid="10x15" sim_year="1850" use_crop=".true." -flanduse_timeseries = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc' +flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc' hgrid="10x15" sim_year_range="1850-2000" use_crop=".true." hgrid="10x15" rcp="8.5" sim_year_range="1850-2100" use_crop=".true." hgrid="10x15" rcp="6" sim_year_range="1850-2100" use_crop=".true." diff --git a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm index ff78e0122c..8c4fed6873 100644 --- a/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/collapse_pfts_78_to_16_decStart_f10/user_nl_clm @@ -1,2 +1,2 @@ -fsurdat = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc' -flanduse_timeseries = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc' +fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_10x15_78pfts_CMIP6_simyr1850_c170824.nc' +flanduse_timeseries = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/landuse.timeseries_10x15_hist_78pfts_CMIP6_simyr1850-2015_c170824.nc' diff --git a/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands b/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands index a284aefcb9..f0eb85010b 100755 --- a/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/cplhist/shell_commands @@ -1,5 +1,5 @@ ./xmlchange DATM_CPLHIST_CASE=cam6ctsm51_cesm23a12c_ne30pg3g17_CPLHIST_1850 -./xmlchange DATM_CPLHIST_DIR=/glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.cdeps_datm.CPLHIST_cam6ctsm51_cesm23a12c_ne30pg3g17_1850 +./xmlchange DATM_CPLHIST_DIR='$DIN_LOC_ROOT/atm/datm7/atm_forcing.cdeps_datm.CPLHIST_cam6ctsm51_cesm23a12c_ne30pg3g17_1850' ./xmlchange DATM_YR_START=1 ./xmlchange DATM_YR_END=1 ./xmlchange DATM_YR_ALIGN=1 diff --git a/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/modify_smallville_with_dynurban.ncl b/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/modify_smallville_with_dynurban.ncl index 15ec0469be..30e73535a4 100644 --- a/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/modify_smallville_with_dynurban.ncl +++ b/cime_config/testdefs/testmods_dirs/clm/smallville_dynurban_monthly/modify_smallville_with_dynurban.ncl @@ -18,6 +18,7 @@ begin print ("Start Time: "+systemfunc("date") ) print ("=========================================") + ; IMPORTANT NOTE: The path for these files needs to be updated with the removal of Cheyenne and /glade/p (See history note below as well) infile = "/glade/p/cgd/tss/people/oleson/modify_surfdata/landuse.timeseries_1x1_smallvilleIA_hist_78pfts_simyr1850-1855_c160127.nc" outfile = "/glade/p/cgd/tss/people/oleson/modify_surfdata/landuse.timeseries_1x1_smallvilleIA_hist_78pfts_simyr1850-1855_dynUrban_c220223.nc" diff --git a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm index d3d922f721..03165bb306 100644 --- a/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/sowingWindows/user_nl_clm @@ -1,5 +1,5 @@ -stream_fldFileName_swindow_start = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' -stream_fldFileName_swindow_end = '/glade/p/cesmdata/cseg/inputdata/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' -stream_meshfile_cropcal = '/glade/p/cesmdata/cseg/inputdata/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc' +stream_fldFileName_swindow_start = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_starts_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' +stream_fldFileName_swindow_end = '$DIN_LOC_ROOT/lnd/clm2/cropdata/calendars/processed/swindow_ends_ggcmi_crop_calendar_phase3_v1.01.2000-2000.20231005_145103.nc' +stream_meshfile_cropcal = '$DIN_LOC_ROOT/share/meshes/360x720_120830_ESMFmesh_c20210507_cdf5.nc' stream_year_first_cropcal = 2000 stream_year_last_cropcal = 2000 From 662ab292788661335ce68354d1ee2ef3fb1910a8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 4 Dec 2023 11:19:05 -0700 Subject: [PATCH 1935/2067] Update ccs_config to version from ekluzek:derecho1#8085fa3. --- Externals.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals.cfg b/Externals.cfg index f5243f9166..cf2ff73498 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -34,7 +34,7 @@ hash = 34723c2 required = True [ccs_config] -tag = ccs_config_cesm0.0.82 +tag = ccs_config_cesm0.0.84 protocol = git repo_url = https://github.com/ESMCI/ccs_config_cesm.git local_path = ccs_config @@ -98,4 +98,4 @@ tag = v1.0.8 required = False [externals_description] -schema_version = 1.0.0 \ No newline at end of file +schema_version = 1.0.0 From c5b409d0f4bdd93d9315ccb3bd31725de4bb0f78 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Tue, 5 Dec 2023 09:48:43 -0700 Subject: [PATCH 1936/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 72 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 73 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index aabefea0fe..ca67adff02 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,76 @@ =============================================================== +Tag name: ctsm5.1.dev157 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Tue Dec 5 09:48:26 MST 2023 +One-line Summary: Update Externals to work on Derecho + +Purpose and description of changes +---------------------------------- + +Updates Externals.cfg to work on Derecho. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): +* Resolves #2217 ("Tags for building CTSM library on Derecho [WRF-CTSM]", https://github.com/ESCOMP/CTSM/issues/2217) +* Resolves #2090 ("Update to cesm2_3_beta16 externals.", https://github.com/ESCOMP/CTSM/issues/2090) + +Known bugs introduced in this tag (include issue #): +* #2280: Updating Externals for Derecho causes Izumi nag tests to fail (https://github.com/ESCOMP/CTSM/issues/2280) + + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: +* All Izumi nag tests fail early in the run phase. This should be fixed in the next tag, which will be a more comprehensive Derecho-focused update. + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + izumi ------- PASS (except nag) + + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): +* cime: cime6.0.125 -> cime6.0.175 +* cmeps: cmeps0.14.21 -> cmeps0.14.43 +* cdeps: cdeps1.0.13 -> cdeps1.0.23 +* cpl7: cpl77.0.5 -> cpl77.0.7 +* parallelio: pio2_5_10 -> pio2_6_2 + +Pull Requests that document the changes (include PR ids): +* #2270: Update Externals.cfg to work on Derecho (https://github.com/ESCOMP/CTSM/pull/2270) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev156 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Thu Nov 30 15:27:18 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index d891a68d87..4c8c356a41 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho ctsm5.1.dev156 samrabin 11/30/2023 Do not use Meier roughness by default. ctsm5.1.dev155 samrabin 11/27/2023 Use baset_latvary parameters ctsm5.1.dev154 slevis 11/22/2023 New params files with changes for Meier roughness, MIMICS, and SNICAR, and changes to leafcn and k*_nonmyc From 7efee20795948f3474ed3e8b813f1859bb099284 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 6 Dec 2023 00:07:41 -0700 Subject: [PATCH 1937/2067] Update cdeps version to fix #2280 so NAG compiler can run --- Externals.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals.cfg b/Externals.cfg index cf2ff73498..a17f8e2ec6 100644 --- a/Externals.cfg +++ b/Externals.cfg @@ -55,7 +55,7 @@ local_path = components/cmeps required = True [cdeps] -tag = cdeps1.0.23 +tag = cdeps1.0.24 protocol = git repo_url = https://github.com/ESCOMP/CDEPS.git local_path = components/cdeps From 6fccf682eaf718615407d9bacdd3903b8786a03d Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 6 Dec 2023 09:42:56 -0700 Subject: [PATCH 1938/2067] Run through black --- python/ctsm/machine_defaults.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/python/ctsm/machine_defaults.py b/python/ctsm/machine_defaults.py index e30881c474..0f3900c152 100644 --- a/python/ctsm/machine_defaults.py +++ b/python/ctsm/machine_defaults.py @@ -47,7 +47,9 @@ "cheyenne": MachineDefaults( job_launcher_type=JOB_LAUNCHER_QSUB, scratch_dir=os.path.join(os.path.sep, "glade", "scratch", get_user()), - baseline_dir=os.path.join(os.path.sep, "glade", "p", "cgd", "tss", "To_Be_Safely_Deleted", "ctsm_baselines"), + baseline_dir=os.path.join( + os.path.sep, "glade", "p", "cgd", "tss", "To_Be_Safely_Deleted", "ctsm_baselines" + ), account_required=True, create_test_retry=0, # NOTE(wjs, 2022-02-23) By default, use the regular queue, even for From 90541f66ec23ec7e8de9db8e7bbd167fa22b1afb Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 6 Dec 2023 09:44:06 -0700 Subject: [PATCH 1939/2067] ignore black format --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index b093c298e9..f2a9d2da8d 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -23,3 +23,4 @@ e4d38681df23ccca0ae29581a45f8362574e0630 0bc3f00115d86d026a977918661c93779b3b19f9 540b256d1f3382f4619d7b0877c32d54ce5c40b6 8a168bb0895f4f2421608dd2589398e13a6663e6 +6fccf682eaf718615407d9bacdd3903b8786a03d From d7cd648a620d3d874dfc757365bf6747d818a4ed Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 6 Dec 2023 09:52:02 -0700 Subject: [PATCH 1940/2067] Remove new ne30np4.pg3 finidat file from CTSM5.2 as incompatible with CTSM5.1 --- bld/namelist_files/namelist_defaults_ctsm.xml | 22 ------------------- 1 file changed, 22 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e9b9b7c54d..e03ad755ae 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -722,11 +722,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. - -hgrid=ne30np4.pg3 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. - - hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. @@ -825,12 +820,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. - -hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. - - hgrid=ne0np4CONUS.ne30x8 maxpft=17 mask=tx0.1v2 use_cn=.false. use_crop=.false. irrigate=.true. glc_nec=10 do_transient_pfts=.false. - -.true. - -lnd/clm2/initdata_map/clmi.I1850Clm51CplhistBgcCrop-ciso.0561-01-01.ne30np4.pg3_gx1v7_simyr1850_c231109.nc - - - + From 7be29765f622ddfbe20aff6f8b5a655cd3155177 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 7 Dec 2023 12:24:41 -0700 Subject: [PATCH 1947/2067] Correct the finidat file settings for clm5_1_cam6 to point to the clm5_0_cam6 f09 files --- bld/namelist_files/namelist_defaults_ctsm.xml | 21 ++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e03ad755ae..b5ae57e5ae 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -722,6 +722,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.false. glc_nec=10 do_transient_pfts=.false. + + hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. @@ -820,6 +825,12 @@ attributes from the config_cache.xml file (with keys converted to upper-case). >hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + +hgrid=0.9x1.25 maxpft=79 mask=gx1v7 use_cn=.true. use_crop=.true. irrigate=.true. glc_nec=10 do_transient_pfts=.false. + + lnd/clm2/initdata_map/clmi.I1850Clm50BgcCrop-ciso.1366-01-01.0.9x1.25_gx1v7_simyr1850_c200428.nc +>lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc + + + +lnd/clm2/initdata_map/clmi.B1850Clm50BgcCrop.0161-01-01.0.9x1.25_gx1v7_simyr1850_c200729.nc From aaf740cdfcba1fe884107794d8244fc74d0f9384 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 7 Dec 2023 22:16:13 -0700 Subject: [PATCH 1949/2067] Update Change files --- doc/.ChangeLog_template | 10 ++-- doc/ChangeLog | 107 ++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 3 files changed, 113 insertions(+), 5 deletions(-) diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index 9f4f64c587..bbd65c8c83 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -96,11 +96,11 @@ infrastructure should be run when appropriate, as described below. build-namelist tests (if CLMBuildNamelist.pm has changed): - cheyenne - + derecho - tools-tests (test/tools) (if tools have been changed): - cheyenne - + derecho - python testing (if python code has changed; see instructions in python/README.md; document testing done): @@ -114,15 +114,15 @@ infrastructure should be run when appropriate, as described below. doing their own baseline generation. If you are already running the full aux_clm then you do NOT need to separately run the clm_pymods test suite, and you can remove the following line.] - clm_pymods test suite on cheyenne - + clm_pymods test suite on derecho - regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - cheyenne ---- + derecho ----- izumi ------- fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) - cheyenne ---- + derecho ----- izumi ------- any other testing (give details below): diff --git a/doc/ChangeLog b/doc/ChangeLog index 168183cee7..961ccab675 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,111 @@ =============================================================== +Tag name: ctsm5.1.dev158 +Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) +Date: Thu 07 Dec 2023 10:15:56 PM MST +One-line Summary: First tag with testing moved to Derecho and working PE-layouts for Derecho + +Purpose and description of changes +---------------------------------- + +First tag for CTSM working and tested on Derecho. Update CDEPS so that we can run with the NAG compiler. +Working PE layouts. Changes from CESM3_dev over to main-dev. Testing added for Derecho. +Do some work to get tools testing working on Derecho, not completed. +Add Derecho to the README files under tools/modify_input_files and tools/site_and_regional +Make sure there are no /glade/p references in the code (other than in the doc directory). + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): + Resolves Derecho transition: Tests and test infrastructure #1995 + Resolves Updating Externals for Derecho causes Izumi nag tests to fail #2280 + Resolves Transient simulation with ne30np4.pg3 fails due to floating point error #2268 + Resolves Need to move location of DA_multidrv finidat files from /glade/p to /glade/campaign #2282 + Works on Add support to test/tools/test_driver.sh for Derecho for NEON tools #2276 + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): + Added clm5_1_cam6 option to LND_TUNING_MODE + This is important in order to enable using latest clm5_1 physics with fully coupled cases + +Changes made to namelist defaults (e.g., changed parameter values): + Make sure there are finidat files for clm5_1 with CAM6 for 1850 and 2000 (from clm5_0 version at f09 + Make sure ne30np4.pg3 is setup + Some adjustments for ne30np4 and ne30np4.pg3 to make sure landuse.timeseries files are correct + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: + Add cesm3_dev test list from the CESM3_dev branch + Make sure ne30np4.pg3 + + Unit tests fail on Derecho because of ESMCI/ccs_config_cesm#131 + Derecho tests with DEBUG=T, intel compiler, and mpi-serial fail because of ESMCI/ccs_config_cesm#130 + + +Testing summary: regular + fates + ctsm_sci + cesm3_dev +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + cheyenne ---- OK + derecho ----- OK + izumi ------- OK + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + derecho ----- OK + izumi ------- OK + + + +Answer changes +-------------- + +Changes answers relative to baseline: No, bit-for-bit + +Other details +------------- +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): cdeps + cdeps -> cdeps1.0.24 (allows to run with NAG compiler) + +Pull Requests that document the changes (include PR ids): + #2269 -- First tag with testing moved to Derecho and working PE layouts +(https://github.com/ESCOMP/ctsm/pull) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev157 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Tue Dec 5 09:48:26 MST 2023 diff --git a/doc/ChangeSum b/doc/ChangeSum index 4c8c356a41..abf4401013 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev158 erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho ctsm5.1.dev156 samrabin 11/30/2023 Do not use Meier roughness by default. ctsm5.1.dev155 samrabin 11/27/2023 Use baset_latvary parameters From 10d05382fb8e43fc1527d692e26a596f418cbfb3 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Thu, 7 Dec 2023 22:22:58 -0700 Subject: [PATCH 1950/2067] Update changelog --- doc/ChangeLog | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 961ccab675..04694b5c07 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev158 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) -Date: Thu 07 Dec 2023 10:15:56 PM MST +Date: Thu 07 Dec 2023 10:22:46 PM MST One-line Summary: First tag with testing moved to Derecho and working PE-layouts for Derecho Purpose and description of changes @@ -11,7 +11,8 @@ First tag for CTSM working and tested on Derecho. Update CDEPS so that we can r Working PE layouts. Changes from CESM3_dev over to main-dev. Testing added for Derecho. Do some work to get tools testing working on Derecho, not completed. Add Derecho to the README files under tools/modify_input_files and tools/site_and_regional -Make sure there are no /glade/p references in the code (other than in the doc directory). +Remove some /glade/p references in the code. This is still an issue in the: doc, lilac, tools/mksurfdata_map, +tools/contrib, tools/mkmapdata directories, and the namelist_defaults_ctsm_tools file. Significant changes to scientifically-supported configurations From ff02badf4a8e8c21ed4c79134e9acfea5a7ff08e Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 8 Dec 2023 13:05:56 -0700 Subject: [PATCH 1951/2067] Add module load cdo to regrid_ggcmi_shdates.py for sys test to pass --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 02abbf99f9..6c2d9b52c8 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -61,7 +61,7 @@ def main( # Ensure we can call necessary shell script(s) for cmd in ["cdo"]: - run_and_check(f"{cmd} --help") + run_and_check(f"module load {cmd}; {cmd} --help") os.chdir(regrid_input_directory) if not os.path.exists(regrid_output_directory): @@ -137,15 +137,15 @@ def main( # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") # Delete template file, which is no longer needed os.remove(templatefile) From bb536ed8621d68955ae000079f571fb9f40f2d4c Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 8 Dec 2023 13:09:48 -0700 Subject: [PATCH 1952/2067] Minor reformat --- .../ctsm/crop_calendars/regrid_ggcmi_shdates.py | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 6c2d9b52c8..4d1a457821 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -137,15 +137,23 @@ def main( # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) except: try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) except: try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) except: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) # Delete template file, which is no longer needed os.remove(templatefile) From 1aa54e627eb7c3fd71440b579a9a3d1dbfa7aae1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 8 Dec 2023 15:30:18 -0700 Subject: [PATCH 1953/2067] Revert "Minor reformat" This reverts commit bb536ed8621d68955ae000079f571fb9f40f2d4c. First of 3 expected reverts. --- .../ctsm/crop_calendars/regrid_ggcmi_shdates.py | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 4d1a457821..6c2d9b52c8 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -137,23 +137,15 @@ def main( # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: - run_and_check( - f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" - ) + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check( - f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" - ) + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check( - f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" - ) + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: - run_and_check( - f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" - ) + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") # Delete template file, which is no longer needed os.remove(templatefile) From 868c8af76c56255aaf6aa6faedf5229f26d731ee Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 8 Dec 2023 15:31:12 -0700 Subject: [PATCH 1954/2067] Revert "Add module load cdo to regrid_ggcmi_shdates.py for sys test to pass" This reverts commit ff02badf4a8e8c21ed4c79134e9acfea5a7ff08e. Second of 3 expected reverts. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 6c2d9b52c8..02abbf99f9 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -61,7 +61,7 @@ def main( # Ensure we can call necessary shell script(s) for cmd in ["cdo"]: - run_and_check(f"module load {cmd}; {cmd} --help") + run_and_check(f"{cmd} --help") os.chdir(regrid_input_directory) if not os.path.exists(regrid_output_directory): @@ -137,15 +137,15 @@ def main( # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") # Delete template file, which is no longer needed os.remove(templatefile) From a0594453e6e7161f78c2a7fee771b23ae8ac6cd5 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 8 Dec 2023 15:37:41 -0700 Subject: [PATCH 1955/2067] Revert "Merge remote-tracking branch 'samsrabin/regrid-shdate-dev' into subset_data_fix" This reverts commit f47de1d2cef6b1a300a085abbbd7f0c7e2b10bda, reversing changes made to f335221b5a0095985ce51c258bb5b56d5ace6612. Resolve conflicts: .git-blame-ignore-revs --- .git-blame-ignore-revs | 3 - python/ctsm/crop_calendars/__init__.py | 0 .../crop_calendars/process_ggcmi_shdates.py | 8 +- .../crop_calendars/regrid_ggcmi_shdates.py | 150 ++++-------------- .../test/test_sys_regrid_ggcmi_shdates.py | 128 --------------- .../test/test_unit_regrid_ggcmi_shdates.py | 125 --------------- ...wh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 | Bin 139563 -> 0 bytes python/ctsm/utils.py | 30 ---- 8 files changed, 34 insertions(+), 410 deletions(-) delete mode 100644 python/ctsm/crop_calendars/__init__.py delete mode 100755 python/ctsm/test/test_sys_regrid_ggcmi_shdates.py delete mode 100755 python/ctsm/test/test_unit_regrid_ggcmi_shdates.py delete mode 100644 python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 790a472142..f2a9d2da8d 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -11,19 +11,16 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb -c8bd4c6f98c0b411391b4355da449507db3aab4e 4ee49e3e516ca7dee5df378f65664f93a7db4415 0207bc98dd5c75cd69a0e788bc53e41093712f5c e4d38681df23ccca0ae29581a45f8362574e0630 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 810cb346f05ac1aabfff931ab1a2b7b584add241 5933b0018f8e29413e30dda9b906370d147bad45 -025d5e7c2e80263717fb029101d65cbbf261c3c4 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 0bc3f00115d86d026a977918661c93779b3b19f9 540b256d1f3382f4619d7b0877c32d54ce5c40b6 8a168bb0895f4f2421608dd2589398e13a6663e6 -183fc26a6691bbdf87f515dc47924a64be3ced9b 6fccf682eaf718615407d9bacdd3903b8786a03d diff --git a/python/ctsm/crop_calendars/__init__.py b/python/ctsm/crop_calendars/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 30ab006ab4..b2ffcfe1f8 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -1,5 +1,6 @@ import numpy as np import xarray as xr +import shutil import os import datetime as dt import cftime @@ -169,11 +170,9 @@ def set_var_dict(name_ggcmi, outfile): # Create output files datetime_string = dt.datetime.now().strftime("%Y%m%d_%H%M%S") - nninterp_suffix = "nninterp-" + regrid_resolution for v in variable_dict: outfile = os.path.join( - output_directory, - f"{v}s_{file_specifier}_{nninterp_suffix}.{first_year}-{last_year}.{datetime_string}.nc", + output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc" ) variable_dict[v]["outfile"] = outfile template_ds.to_netcdf( @@ -213,8 +212,7 @@ def set_var_dict(name_ggcmi, outfile): ) file_ggcmi = os.path.join( - regridded_ggcmi_files_dir, - f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4", + regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}.nc4" ) if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 02abbf99f9..85e9ddeb4d 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -1,21 +1,9 @@ from subprocess import run import os +import shutil import glob import argparse import sys -import xarray as xr -import numpy as np - -# -- add python/ctsm to path (needed if we want to run regrid_ggcmi_shdates stand-alone) -_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) -sys.path.insert(1, _CTSM_PYTHON) - -from ctsm.utils import abort, import_coord_1d, import_coord_2d -from ctsm.ctsm_logging import ( - setup_logging_pre_config, - add_logging_args, - process_logging_args, -) def run_and_check(cmd): @@ -26,7 +14,9 @@ def run_and_check(cmd): text=True, ) if result.returncode != 0: - abort(f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}") + raise RuntimeError( + f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}" + ) # Functionized because these are shared by process_ggcmi_shdates @@ -42,7 +32,7 @@ def define_arguments(parser): parser.add_argument( "-rt", "--regrid-template-file", - help="Template netCDF file to be used in regridding of inputs. This can be a CLM output file (i.e., something with 1-d lat and lon variables) or a CLM surface dataset (i.e., something with 2-d LATIXY and LONGXY variables).", + help="Template file to be used in regridding of inputs.", type=str, required=True, ) @@ -50,17 +40,11 @@ def define_arguments(parser): def main( - regrid_resolution, - regrid_template_file_in, - regrid_input_directory, - regrid_output_directory, - extension, - crop_list, + regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory ): - print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") - # Ensure we can call necessary shell script(s) - for cmd in ["cdo"]: + # Ensure we can call necessary shell scripts + for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: run_and_check(f"{cmd} --help") os.chdir(regrid_input_directory) @@ -68,69 +52,29 @@ def main( os.makedirs(regrid_output_directory) templatefile = os.path.join(regrid_output_directory, "template.nc") - if os.path.exists(templatefile): - os.remove(templatefile) - template_ds_in = xr.open_dataset(regrid_template_file_in) - - # Process inputs - if crop_list is not None: - crop_list = crop_list.split(",") - if extension[0] != ".": - extension = "." + extension - - # Import and format latitude - if "lat" in template_ds_in: - lat, Nlat = import_coord_1d(template_ds_in, "lat") - elif "LATIXY" in template_ds_in: - lat, Nlat = import_coord_2d(template_ds_in, "lat", "LATIXY") - lat.attrs["axis"] = "Y" - else: - abort("No latitude variable found in regrid template file") - - # Flip latitude, if needed - if lat.values[0] < lat.values[1]: - lat = lat.reindex(lat=list(reversed(lat["lat"]))) - - # Import and format longitude - if "lon" in template_ds_in: - lon, Nlon = import_coord_1d(template_ds_in, "lon") - elif "LONGXY" in template_ds_in: - lon, Nlon = import_coord_2d(template_ds_in, "lon", "LONGXY") - lon.attrs["axis"] = "Y" - else: - abort("No longitude variable found in regrid template file") - template_da_out = xr.DataArray( - data=np.full((Nlat, Nlon), 0.0), - dims={"lat": lat, "lon": lon}, - name="area", + # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. + regrid_template_file = os.path.join( + regrid_output_directory, + os.path.basename(regrid_template_file_in), ) + shutil.copyfile(regrid_template_file_in, regrid_template_file) - # Save template Dataset for use by cdo - template_ds_out = xr.Dataset( - data_vars={ - "planting_day": template_da_out, - "maturity_day": template_da_out, - "growing_season_length": template_da_out, - }, - coords={"lat": lat, "lon": lon}, - ) - template_ds_out.to_netcdf(templatefile, mode="w") + if os.path.exists(templatefile): + os.remove(templatefile) - # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor - pattern = "*" + extension - input_files = glob.glob(pattern) - if len(input_files) == 0: - abort(f"No files found matching {os.path.join(os.getcwd(), pattern)}") + for v in ["planting_day", "maturity_day", "growing_season_length"]: + run_and_check(f"ncks -A -v area '{regrid_template_file}' '{templatefile}'") + run_and_check(f"ncrename -v area,{v} '{templatefile}'") + os.remove(regrid_template_file) + run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") + + input_files = glob.glob("*nc4") input_files.sort() for f in input_files: - this_crop = f[0:6] - if crop_list is not None and this_crop not in crop_list: - continue - - print(" " + this_crop) + print(f[0:6]) f2 = os.path.join(regrid_output_directory, f) - f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") + f3 = f2.replace(".nc4", f"_nninterp-{regrid_resolution}.nc4") if os.path.exists(f3): os.remove(f3) @@ -147,16 +91,13 @@ def main( except: run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") - # Delete template file, which is no longer needed os.remove(templatefile) -# Process input arguments -def regrid_ggcmi_shdates_arg_process(): - - # set up logging allowing user control - setup_logging_pre_config() - +if __name__ == "__main__": + ############################### + ### Process input arguments ### + ############################### parser = argparse.ArgumentParser( description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." ) @@ -177,45 +118,16 @@ def regrid_ggcmi_shdates_arg_process(): type=str, required=True, ) - default = ".nc" - parser.add_argument( - "-x", - "--extension", - help=f"File extension of raw GGCMI sowing/harvest date files (default {default}).", - default=default, - ) - parser.add_argument( - "-c", - "--crop-list", - help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", - default=None, - ) # Get arguments args = parser.parse_args(sys.argv[1:]) - # Process arguments - args.regrid_template_file = os.path.realpath(args.regrid_template_file) - args.regrid_input_directory = os.path.realpath(args.regrid_input_directory) - args.regrid_output_directory = os.path.realpath(args.regrid_output_directory) - - return args - - -if __name__ == "__main__": - ############################### - ### Process input arguments ### - ############################### - args = regrid_ggcmi_shdates_arg_process() - ########### ### Run ### ########### main( args.regrid_resolution, - args.regrid_template_file, - args.regrid_input_directory, - args.regrid_output_directory, - args.extension, - args.crop_list, + os.path.realpath(args.regrid_template_file), + os.path.realpath(args.regrid_input_directory), + os.path.realpath(args.regrid_output_directory), ) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py deleted file mode 100755 index 6c06493160..0000000000 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ /dev/null @@ -1,128 +0,0 @@ -#!/usr/bin/env python3 - -"""System tests for fsurdat_modifier - -""" - -import os -import re - -import unittest -import tempfile -import shutil -import sys - -import xarray as xr -import numpy as np - -# -- add python/ctsm to path (needed if we want to run test stand-alone) -_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) -sys.path.insert(1, _CTSM_PYTHON) - - -from ctsm.path_utils import path_to_ctsm_root -from ctsm import unit_testing -from ctsm.crop_calendars.regrid_ggcmi_shdates import main as regrid_ggcmi_shdates -from ctsm.crop_calendars.regrid_ggcmi_shdates import regrid_ggcmi_shdates_arg_process - -# Allow test names that pylint doesn't like; otherwise hard to make them -# readable -# pylint: disable=invalid-name - - -class TestRegridGgcmiShdates(unittest.TestCase): - """System tests for regrid_ggcmi_shdates""" - - def setUp(self): - # Where in the /testinputs directory are the raw crop calendar file(s)? - testinputs_path = os.path.join(path_to_ctsm_root(), "python", "ctsm", "test", "testinputs") - testinputs_cc_path = os.path.join(testinputs_path, "cropcals") - self._testinputs_cc_path = testinputs_cc_path - - # Make /_tempdir for use by these tests. - self._tempdir = tempfile.mkdtemp() - - # Obtain path for the directory being created in /_tempdir - self._regridded_cropcals = os.path.join(self._tempdir, "regridded_cropcals") - - # What extension do the raw crop calendar file(s) have? - self._extension = ".nc4" - - # Which crop(s) should we test? (comma-separated string) - self._crop_list = "swh_rf" - - # What is the complete set of input arguments (including script name)? - regrid_template_file = os.path.join( - testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" - ) - self._function_call_list = [ - "regrid_ggcmi_shdates", - "-i", - testinputs_cc_path, - "-x", - ".nc4", - "-o", - self._regridded_cropcals, - "-rr", - "5x5amazon", - "-rt", - regrid_template_file, - "--crop-list", - "swh_rf", - ] - - def tearDown(self): - """ - Remove temporary directory - """ - shutil.rmtree(self._tempdir, ignore_errors=True) - - def test_regrid_ggcmi_shdates(self): - - # Call script - sys.argv = self._function_call_list - args = regrid_ggcmi_shdates_arg_process() - regrid_ggcmi_shdates( - args.regrid_resolution, - args.regrid_template_file, - args.regrid_input_directory, - args.regrid_output_directory, - args.extension, - args.crop_list, - ) - - # Read output file - regrid_out_file = os.path.join( - self._regridded_cropcals, - "swh_rf_ggcmi_crop_calendar_phase3_v1.01_nninterp-5x5amazon.nc4", - ) - regrid_out_ds = xr.open_dataset(regrid_out_file) - - # Check sowing dates - expected_sow_dates = np.array( - [ - [120, 120, 120, 120, 120], - [120, 120, 120, 120, 120], - [120, 120, 120, 120, 120], - [330, 335, 335, 120, 120], - [325, 335, 335, 335, 120], - ] - ) - np.testing.assert_array_equal(expected_sow_dates, regrid_out_ds["planting_day"].values) - - # Check maturity dates - expected_mat_dates = np.array( - [ - [221, 221, 221, 221, 221], - [221, 221, 221, 221, 221], - [221, 221, 221, 221, 221], - [153, 128, 128, 221, 221], - [163, 128, 128, 128, 221], - ] - ) - np.testing.assert_array_equal(expected_mat_dates, regrid_out_ds["maturity_day"].values) - - -if __name__ == "__main__": - unit_testing.setup_for_tests() - unittest.main() diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py deleted file mode 100755 index c47e81ac15..0000000000 --- a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py +++ /dev/null @@ -1,125 +0,0 @@ -#!/usr/bin/env python3 - -""" -Unit tests for regrid_ggcmi_shdates subroutines: -""" - -import unittest -import os -import sys -import shutil - -import tempfile -import xarray as xr -import numpy as np - -# -- add python/ctsm to path (needed if we want to run test stand-alone) -_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) -sys.path.insert(1, _CTSM_PYTHON) - -from ctsm import unit_testing -from ctsm.path_utils import path_to_ctsm_root -from ctsm.utils import import_coord_1d, import_coord_2d - -# Allow test names that pylint doesn't like; otherwise hard to make them -# readable -# pylint: disable=invalid-name - -# pylint: disable=protected-access - - -# Allow as many public methods as needed... -# pylint: disable=too-many-public-methods -# Allow all the instance attributes that we need -# pylint: disable=too-many-instance-attributes -class TestRegridGgcmiShdates(unittest.TestCase): - # Tests the regrid_ggcmi_shdates subroutines - - def setUp(self): - """Setup for trying out the methods""" - testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") - self._testinputs_path = testinputs_path - self._tempdir = tempfile.mkdtemp() - - self._1d_lonlat_file = os.path.join( - self._testinputs_path, "cropcals", "swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4" - ) - self._2d_lonlat_file = os.path.join( - self._testinputs_path, - "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_modified.nc", - ) - - def tearDown(self): - """ - Remove temporary directory - """ - shutil.rmtree(self._tempdir, ignore_errors=True) - - def test_importcoord1d(self): - ds = xr.open_dataset(self._1d_lonlat_file) - lat, Nlat = import_coord_1d(ds, "lat") - print(lat) - np.testing.assert_equal(Nlat, 360) - np.testing.assert_array_equal(lat.values[:4], [89.75, 89.25, 88.75, 88.25]) - np.testing.assert_array_equal(lat.values[-4:], [-88.25, -88.75, -89.25, -89.75]) - - def test_importcoord1d_attrs(self): - ds = xr.open_dataset(self._1d_lonlat_file) - lat, _ = import_coord_1d(ds, "lat") - # Unlike import_coord_2d, import_coord_1d doesn't rename the long name. - expected_attributes = { - "long_name": ds["lat"].attrs["long_name"], - "units": "degrees_north", - } - self.assertDictEqual(lat.attrs, expected_attributes) - - def test_importcoord1d_too_many_dims(self): - ds = xr.open_dataset(self._2d_lonlat_file) - with self.assertRaisesRegex( - SystemExit, - "Expected 1 dimension for LATIXY; found 2: \('lsmlat', 'lsmlon'\)", - ): - import_coord_1d(ds, "LATIXY") - - def test_importcoord2d(self): - ds = xr.open_dataset(self._2d_lonlat_file) - lat, _ = import_coord_2d(ds, "lat", "LATIXY") - expected_values = np.array([-13.9, -11.7, -9.5, -7.3, -5.1]).astype(np.float32) - np.testing.assert_array_equal(lat.values, expected_values) - - def test_importcoord2d_attrs(self): - ds = xr.open_dataset(self._2d_lonlat_file) - lat, _ = import_coord_2d(ds, "lat", "LATIXY") - expected_attributes = { - "long_name": "coordinate latitude", - "units": "degrees_north", - } - self.assertDictEqual(lat.attrs, expected_attributes) - - def test_importcoord2d_rename_dim(self): - ds = xr.open_dataset(self._2d_lonlat_file) - lat, _ = import_coord_2d(ds, "lat", "LATIXY") - self.assertTupleEqual(lat.dims, ("lat",)) - - def test_importcoord2d_no_dim_contains_coordName(self): - ds = xr.open_dataset(self._2d_lonlat_file) - ds = ds.rename({"lsmlat": "abc"}) - with self.assertRaisesRegex( - SystemExit, - "ERROR: Expected 1 dimension name containing lat; found 0: \[\]", - ): - import_coord_2d(ds, "lat", "LATIXY") - - def test_importcoord2d_1_dim_containing(self): - ds = xr.open_dataset(self._2d_lonlat_file) - ds = ds.rename({"lsmlon": "lsmlat2"}) - with self.assertRaisesRegex( - SystemExit, - "Expected 1 dimension name containing lat; found 2: \['lsmlat', 'lsmlat2'\]", - ): - import_coord_2d(ds, "lat", "LATIXY") - - -if __name__ == "__main__": - unit_testing.setup_for_tests() - unittest.main() diff --git a/python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 b/python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 deleted file mode 100644 index 985210eaeaee7d1d6c4a047bbb2ed06353d2f9ef..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 139563 zcmeF(2Uru^x-fne1yq`{rAUhv3%y7uC?YB?ii$`VLqIyAm!Pu6MiZ3|0Z~9fsvsR~ zbP|*`i`oXU$qOd1p-4T9YUD&zw5VvVG5X zI_kp2M7M>G{r6Ma!x}8d_HO>YiWbw#&1g^lfx2f-UD(Xrw|U?1a(V{XjMmKGyL~g= zCh8{azmFnv&-&)4p%&fm>g#owO{pt4(XrAoQT{X4QA0U9IHH|htkGD?dJf8;?C)~Q z17&eTJ7cXK?3E>a?9nb3*DY7;kiNw3kd0vtwXnknY#V@w$xSe8ce&W(rC!H&N0^&6%3k2|YbZOwAQF-Rs9oM|bM1wz`hqSzR4dJ+%{B>U7KpsAZez zw*IcAb3$94vhnX))ZNi)Q8GivEKNs8J%Oxr%#>|Sb$+K>`joYu^>xaY?35QltwBeJ z`29$$NeyhvmK%Ss^sub>trd6$JOj#she2+T37kh)&{3CRupO)h3&2z`61)d`fL7oY 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z{RI!wsnfC!rRjG4vt?shS#>KQOLnaXSnPK7w%=V=6?F4HIUng<|KnOr=J$O7*paWh zO)&q%$9pSo&4JB|ZMUI64$k%d&&P zDU~S%5>o>+SqpJlHclE6BvKyp?z;Y{Iekcx{qZFJ4?!;EDmpxK^^Y(A|L6a!2$c0` K^%@tq<^Ml&ww|c~ diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 9b398a7791..8578ea860c 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -6,7 +6,6 @@ import string import re import pdb -import numpy as np from datetime import date, timedelta from getpass import getuser @@ -192,35 +191,6 @@ def write_output(file, file_in, file_out, file_type): file.close() -# Import 1-d latitude or longitude variable from a CESM history file (e.g., name lat or lon) and return it as a DataArray that can be used for writing CESM input files -def import_coord_1d(ds, coordName): - da = ds[coordName] - if len(da.dims) != 1: - abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") - return da, len(da) - - -# Import 1-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files -def import_coord_2d(ds, coordName, varName): - da = ds[varName] - thisDim = [x for x in da.dims if coordName in x] - if len(thisDim) != 1: - abort(f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}") - thisDim = thisDim[0] - otherDim = [x for x in da.dims if coordName not in x] - if len(otherDim) != 1: - abort( - f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" - ) - otherDim = otherDim[0] - da = da.astype(np.float32) - da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) - da = da.assign_coords({coordName: da.values}) - da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] - da.attrs["units"] = da.attrs["units"].replace(" ", "_") - return da, len(da) - - def get_isosplit(iso_string, split): """ Split a string (iso_string) by the character sent in from split From 1fbf551c00d3604c311543be1cb057395e8173f9 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 8 Dec 2023 17:35:19 -0700 Subject: [PATCH 1956/2067] Draft ChangeLog/ChangeSum --- doc/ChangeLog | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 106 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 04694b5c07..0f38f3157a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,109 @@ =============================================================== +Tag name: ctsm5.1.dev159 +Originator(s): multiple (slevis (Sam Levis), afoster (Adrianna Foster), erik (Erik Kluzek), wwieder (Will Wieder), glemieux (Greg Lemieux), oleson (Keith Oleson), sacks (Bill Sacks), samrabin (Sam Rabin), santos (Sean Patrick Santos)) +Date: Fri Dec 8 16:36:37 MST 2023 +One-line Summary: Various BFB fixes and updates + +Purpose and description of changes +---------------------------------- + +#2253 Fix subset_data error (slevis) +#2271 bfb bug-fix allowing us to make Meier2022 the default; making it +the default comes in a later tag (slevis) +#2267 Fix run_neon CIME path import (afoster, erik, wwieder) +#2075 Add xesmf to the standard python env (glemieux) +#2229 Fix misplaced if statement and end model run if no-isotope to isotope run with user_init_interp=.false. (oleson, sacks, wwieder) +#2239 Add comment in LakeHydrology (samrabin, santos) + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): +Fixes #2253 +Fixes #2271 +Fixes #2267 +Fixes #2075 +Fixes #2229 +Fixes #2239 + +Known bugs introduced in this tag (include issue #): + +Notes of particular relevance for users +--------------------------------------- +None + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: +Follow up with Erik about "does not exist" failures + +Testing summary: +---------------- +[Remove any lines that don't apply.] + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - + + tools-tests (test/tools) (if tools have been changed): + + derecho - + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- 2 FAILs that already appear in dev158, follow up w Erik, else OK + izumi ------- 1 FAIL, follow up w Erik, else PASS + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + derecho ----- + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +Changes answers relative to baseline: NO + +Other details +------------- +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2253 + https://github.com/ESCOMP/ctsm/pull/2271 + https://github.com/ESCOMP/ctsm/pull/2267 + https://github.com/ESCOMP/ctsm/pull/2075 + https://github.com/ESCOMP/ctsm/pull/2229 + https://github.com/ESCOMP/ctsm/pull/2239 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev158 Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326) Date: Thu 07 Dec 2023 10:22:46 PM MST diff --git a/doc/ChangeSum b/doc/ChangeSum index abf4401013..bdf0fd5e59 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev159 multiple 12/11/2023 Various BFB fixes and updates ctsm5.1.dev158 erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho ctsm5.1.dev156 samrabin 11/30/2023 Do not use Meier roughness by default. From 14ea4c3b57eb9119390b6be38d20b0c81784d9de Mon Sep 17 00:00:00 2001 From: mvdebolskiy Date: Mon, 11 Dec 2023 17:02:45 +0100 Subject: [PATCH 1957/2067] fix pes --- cime_config/config_pes.xml | 100 +------------------------------------ 1 file changed, 1 insertion(+), 99 deletions(-) diff --git a/cime_config/config_pes.xml b/cime_config/config_pes.xml index 7bccfd96df..a77ea8ff1f 100644 --- a/cime_config/config_pes.xml +++ b/cime_config/config_pes.xml @@ -1857,7 +1857,7 @@ - + none @@ -1895,102 +1895,4 @@ - - - - Need at least 4 nodes to default to normal queue - - -1 - -3 - -3 - -3 - -3 - -3 - -3 - -3 - - - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - - - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 - - - - - - - - none - - -1 - -7 - -7 - -7 - -7 - -7 - -7 - -7 - - - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - - - 0 - -1 - -1 - -1 - -1 - -1 - -1 - -1 - - - - - - 1 - 1 - 1 - 1 - 1 - 1 - 1 - 1 - - - 0 - 0 - 0 - 0 - 0 - 0 - 0 - 0 - - - - - From 7dba40216fe536be211ac8cc4f76b7930c2950d0 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Mon, 11 Dec 2023 10:29:29 -0700 Subject: [PATCH 1958/2067] Fates pointer --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 5f8e8d2441..ec0028a880 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.68.2_api.31.0.0 +tag = sci.1.69.0_api.31.0.0 required = True [externals_description] From fb5dd43fc96e83b07a7d29109d80ae24b39a9103 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Mon, 11 Dec 2023 16:14:28 -0700 Subject: [PATCH 1959/2067] Correction for one test in ExpectedTestFails.xml --- cime_config/testdefs/ExpectedTestFails.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index f5053a7843..bea4300aeb 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -52,7 +52,7 @@ - + FAIL #1733 From 5cd5758fe7708d2584b174e6b8e8021e3ae7aae6 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 12 Dec 2023 11:18:14 -0700 Subject: [PATCH 1960/2067] Updated ChangeLog/ChangeSum --- doc/ChangeLog | 40 +++------------------------------------- doc/ChangeSum | 2 +- 2 files changed, 4 insertions(+), 38 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 0f38f3157a..67564b6dd0 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,12 +1,11 @@ =============================================================== Tag name: ctsm5.1.dev159 Originator(s): multiple (slevis (Sam Levis), afoster (Adrianna Foster), erik (Erik Kluzek), wwieder (Will Wieder), glemieux (Greg Lemieux), oleson (Keith Oleson), sacks (Bill Sacks), samrabin (Sam Rabin), santos (Sean Patrick Santos)) -Date: Fri Dec 8 16:36:37 MST 2023 +Date: Tue 12 Dec 2023 11:10:26 AM MST One-line Summary: Various BFB fixes and updates Purpose and description of changes ---------------------------------- - #2253 Fix subset_data error (slevis) #2271 bfb bug-fix allowing us to make Meier2022 the default; making it the default comes in a later tag (slevis) @@ -17,7 +16,6 @@ the default comes in a later tag (slevis) Significant changes to scientifically-supported configurations -------------------------------------------------------------- - Does this tag change answers significantly for any of the following physics configurations? (Details of any changes will be given in the "Answer changes" section below.) @@ -31,7 +29,6 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 - Bugs fixed or introduced ------------------------ CTSM issues fixed (include CTSM Issue #): @@ -42,52 +39,21 @@ Fixes #2075 Fixes #2229 Fixes #2239 -Known bugs introduced in this tag (include issue #): - -Notes of particular relevance for users ---------------------------------------- -None - -Notes of particular relevance for developers: ---------------------------------------------- -Changes to tests or testing: -Follow up with Erik about "does not exist" failures - Testing summary: ---------------- -[Remove any lines that don't apply.] - [PASS means all tests PASS; OK means tests PASS other than expected fails.] - build-namelist tests (if CLMBuildNamelist.pm has changed): - - derecho - - - tools-tests (test/tools) (if tools have been changed): - - derecho - - python testing (if python code has changed; see instructions in python/README.md; document testing done): derecho - PASS regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- 2 FAILs that already appear in dev158, follow up w Erik, else OK - izumi ------- 1 FAIL, follow up w Erik, else PASS - - fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) - derecho ----- - izumi ------- - - any other testing (give details below): - -If the tag used for baseline comparisons was NOT the previous tag, note that here: - + derecho ----- OK + izumi ------- PASS Answer changes -------------- - Changes answers relative to baseline: NO Other details diff --git a/doc/ChangeSum b/doc/ChangeSum index bdf0fd5e59..4b82850d85 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev159 multiple 12/11/2023 Various BFB fixes and updates + ctsm5.1.dev159 multiple 12/12/2023 Various BFB fixes and updates ctsm5.1.dev158 erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho ctsm5.1.dev156 samrabin 11/30/2023 Do not use Meier roughness by default. From 1a1ec94c71ce67eb3ba490d06643dbed4325a661 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Tue, 12 Dec 2023 15:06:22 -0700 Subject: [PATCH 1961/2067] remove wood product flux from fates carbon balance check --- src/biogeochem/CNBalanceCheckMod.F90 | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/biogeochem/CNBalanceCheckMod.F90 b/src/biogeochem/CNBalanceCheckMod.F90 index 35efd2e9aa..8801efdf72 100644 --- a/src/biogeochem/CNBalanceCheckMod.F90 +++ b/src/biogeochem/CNBalanceCheckMod.F90 @@ -258,7 +258,6 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & real(r8) :: hrv_xsmrpool_amount_left_to_dribble(bounds%begg:bounds%endg) real(r8) :: gru_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) real(r8) :: dwt_conv_cflux_amount_left_to_dribble(bounds%begg:bounds%endg) - real(r8) :: fates_woodproduct_flux ! Total carbon wood products flux from FATES to CLM [gC/m2/s] !----------------------------------------------------------------------- @@ -309,11 +308,7 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & s = clm_fates%f2hmap(ic)%hsites(c) - - fates_woodproduct_flux = clm_fates%fates(ic)%bc_out(s)%hrv_deadstemc_to_prod10c + & - clm_fates%fates(ic)%bc_out(s)%hrv_deadstemc_to_prod100c - - col_cinputs = fates_litter_flux(c) + fates_woodproduct_flux + col_cinputs = fates_litter_flux(c) ! calculate total column-level outputs ! fates has already exported burn losses and fluxes to the atm @@ -372,7 +367,6 @@ subroutine CBalanceCheck(this, bounds, num_soilc, filter_soilc, & write(iulog,*)'--- Inputs ---' if( col%is_fates(c) ) then write(iulog,*)'fates litter_flux = ',fates_litter_flux(c)*dt - write(iulog,*)'fates wood product flux = ',fates_woodproduct_flux*dt else write(iulog,*)'gpp = ',gpp(c)*dt end if From 67426be73889944e2df64bd83b911d700efcd167 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Thu, 14 Dec 2023 11:36:37 -0700 Subject: [PATCH 1962/2067] update externals with fates landuse tag --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 5f8e8d2441..dc1bc3f0e7 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.68.2_api.31.0.0 +tag = sci.1.70.0_api.32.0.0 required = True [externals_description] From 131308f74c0f8c6dc2aa89f8511e1e1e53db1b82 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 14 Dec 2023 12:15:10 -0700 Subject: [PATCH 1963/2067] update external --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 5f8e8d2441..ec0028a880 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/NGEET/fates -tag = sci.1.68.2_api.31.0.0 +tag = sci.1.69.0_api.31.0.0 required = True [externals_description] From 3425f4d647df03f76295c661585b60ea3d804a33 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Dec 2023 14:52:43 -0800 Subject: [PATCH 1964/2067] Revert "Revert "Merge remote-tracking branch 'samsrabin/regrid-shdate-dev' into subset_data_fix"" This reverts commit a0594453e6e7161f78c2a7fee771b23ae8ac6cd5. --- .git-blame-ignore-revs | 3 + python/ctsm/crop_calendars/__init__.py | 0 .../crop_calendars/process_ggcmi_shdates.py | 8 +- .../crop_calendars/regrid_ggcmi_shdates.py | 150 ++++++++++++++---- .../test/test_sys_regrid_ggcmi_shdates.py | 128 +++++++++++++++ .../test/test_unit_regrid_ggcmi_shdates.py | 125 +++++++++++++++ ...wh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 | Bin 0 -> 139563 bytes python/ctsm/utils.py | 30 ++++ 8 files changed, 410 insertions(+), 34 deletions(-) create mode 100644 python/ctsm/crop_calendars/__init__.py create mode 100755 python/ctsm/test/test_sys_regrid_ggcmi_shdates.py create mode 100755 python/ctsm/test/test_unit_regrid_ggcmi_shdates.py create mode 100644 python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index f2a9d2da8d..790a472142 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -11,16 +11,19 @@ b88e1cd1b28e3609684c79a2ec0e88f26cfc362b b771971e3299c4fa56534b93421f7a2b9c7282fd 9de88bb57ea9855da408cbec1dc8acb9079eda47 8bc4688e52ea23ef688e283698f70a44388373eb +c8bd4c6f98c0b411391b4355da449507db3aab4e 4ee49e3e516ca7dee5df378f65664f93a7db4415 0207bc98dd5c75cd69a0e788bc53e41093712f5c e4d38681df23ccca0ae29581a45f8362574e0630 0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7 810cb346f05ac1aabfff931ab1a2b7b584add241 5933b0018f8e29413e30dda9b906370d147bad45 +025d5e7c2e80263717fb029101d65cbbf261c3c4 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 0bc3f00115d86d026a977918661c93779b3b19f9 540b256d1f3382f4619d7b0877c32d54ce5c40b6 8a168bb0895f4f2421608dd2589398e13a6663e6 +183fc26a6691bbdf87f515dc47924a64be3ced9b 6fccf682eaf718615407d9bacdd3903b8786a03d diff --git a/python/ctsm/crop_calendars/__init__.py b/python/ctsm/crop_calendars/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b2ffcfe1f8..30ab006ab4 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -1,6 +1,5 @@ import numpy as np import xarray as xr -import shutil import os import datetime as dt import cftime @@ -170,9 +169,11 @@ def set_var_dict(name_ggcmi, outfile): # Create output files datetime_string = dt.datetime.now().strftime("%Y%m%d_%H%M%S") + nninterp_suffix = "nninterp-" + regrid_resolution for v in variable_dict: outfile = os.path.join( - output_directory, f"{v}s_{file_specifier}.{first_year}-{last_year}.{datetime_string}.nc" + output_directory, + f"{v}s_{file_specifier}_{nninterp_suffix}.{first_year}-{last_year}.{datetime_string}.nc", ) variable_dict[v]["outfile"] = outfile template_ds.to_netcdf( @@ -212,7 +213,8 @@ def set_var_dict(name_ggcmi, outfile): ) file_ggcmi = os.path.join( - regridded_ggcmi_files_dir, f"{thiscrop_ggcmi}_{file_specifier}.nc4" + regridded_ggcmi_files_dir, + f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4", ) if not os.path.exists(file_ggcmi): raise Exception("Input file not found: " + file_ggcmi) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 85e9ddeb4d..02abbf99f9 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -1,9 +1,21 @@ from subprocess import run import os -import shutil import glob import argparse import sys +import xarray as xr +import numpy as np + +# -- add python/ctsm to path (needed if we want to run regrid_ggcmi_shdates stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.utils import abort, import_coord_1d, import_coord_2d +from ctsm.ctsm_logging import ( + setup_logging_pre_config, + add_logging_args, + process_logging_args, +) def run_and_check(cmd): @@ -14,9 +26,7 @@ def run_and_check(cmd): text=True, ) if result.returncode != 0: - raise RuntimeError( - f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}" - ) + abort(f"Trouble running `{result.args}` in shell:\n{result.stdout}\n{result.stderr}") # Functionized because these are shared by process_ggcmi_shdates @@ -32,7 +42,7 @@ def define_arguments(parser): parser.add_argument( "-rt", "--regrid-template-file", - help="Template file to be used in regridding of inputs.", + help="Template netCDF file to be used in regridding of inputs. This can be a CLM output file (i.e., something with 1-d lat and lon variables) or a CLM surface dataset (i.e., something with 2-d LATIXY and LONGXY variables).", type=str, required=True, ) @@ -40,11 +50,17 @@ def define_arguments(parser): def main( - regrid_resolution, regrid_template_file_in, regrid_input_directory, regrid_output_directory + regrid_resolution, + regrid_template_file_in, + regrid_input_directory, + regrid_output_directory, + extension, + crop_list, ): + print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") - # Ensure we can call necessary shell scripts - for cmd in ["ncks", "ncrename", "ncpdq", "cdo"]: + # Ensure we can call necessary shell script(s) + for cmd in ["cdo"]: run_and_check(f"{cmd} --help") os.chdir(regrid_input_directory) @@ -52,29 +68,69 @@ def main( os.makedirs(regrid_output_directory) templatefile = os.path.join(regrid_output_directory, "template.nc") - - # For some reason, doing ncks -v directly doesn't work. Have to copy it over first. - regrid_template_file = os.path.join( - regrid_output_directory, - os.path.basename(regrid_template_file_in), - ) - shutil.copyfile(regrid_template_file_in, regrid_template_file) - if os.path.exists(templatefile): os.remove(templatefile) - for v in ["planting_day", "maturity_day", "growing_season_length"]: - run_and_check(f"ncks -A -v area '{regrid_template_file}' '{templatefile}'") - run_and_check(f"ncrename -v area,{v} '{templatefile}'") - os.remove(regrid_template_file) - run_and_check(f"ncpdq -O -h -a -lat '{templatefile}' '{templatefile}'") + template_ds_in = xr.open_dataset(regrid_template_file_in) + + # Process inputs + if crop_list is not None: + crop_list = crop_list.split(",") + if extension[0] != ".": + extension = "." + extension + + # Import and format latitude + if "lat" in template_ds_in: + lat, Nlat = import_coord_1d(template_ds_in, "lat") + elif "LATIXY" in template_ds_in: + lat, Nlat = import_coord_2d(template_ds_in, "lat", "LATIXY") + lat.attrs["axis"] = "Y" + else: + abort("No latitude variable found in regrid template file") + + # Flip latitude, if needed + if lat.values[0] < lat.values[1]: + lat = lat.reindex(lat=list(reversed(lat["lat"]))) + + # Import and format longitude + if "lon" in template_ds_in: + lon, Nlon = import_coord_1d(template_ds_in, "lon") + elif "LONGXY" in template_ds_in: + lon, Nlon = import_coord_2d(template_ds_in, "lon", "LONGXY") + lon.attrs["axis"] = "Y" + else: + abort("No longitude variable found in regrid template file") + template_da_out = xr.DataArray( + data=np.full((Nlat, Nlon), 0.0), + dims={"lat": lat, "lon": lon}, + name="area", + ) + + # Save template Dataset for use by cdo + template_ds_out = xr.Dataset( + data_vars={ + "planting_day": template_da_out, + "maturity_day": template_da_out, + "growing_season_length": template_da_out, + }, + coords={"lat": lat, "lon": lon}, + ) + template_ds_out.to_netcdf(templatefile, mode="w") - input_files = glob.glob("*nc4") + # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor + pattern = "*" + extension + input_files = glob.glob(pattern) + if len(input_files) == 0: + abort(f"No files found matching {os.path.join(os.getcwd(), pattern)}") input_files.sort() for f in input_files: - print(f[0:6]) + this_crop = f[0:6] + if crop_list is not None and this_crop not in crop_list: + continue + + print(" " + this_crop) f2 = os.path.join(regrid_output_directory, f) - f3 = f2.replace(".nc4", f"_nninterp-{regrid_resolution}.nc4") + f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") if os.path.exists(f3): os.remove(f3) @@ -91,13 +147,16 @@ def main( except: run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + # Delete template file, which is no longer needed os.remove(templatefile) -if __name__ == "__main__": - ############################### - ### Process input arguments ### - ############################### +# Process input arguments +def regrid_ggcmi_shdates_arg_process(): + + # set up logging allowing user control + setup_logging_pre_config() + parser = argparse.ArgumentParser( description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." ) @@ -118,16 +177,45 @@ def main( type=str, required=True, ) + default = ".nc" + parser.add_argument( + "-x", + "--extension", + help=f"File extension of raw GGCMI sowing/harvest date files (default {default}).", + default=default, + ) + parser.add_argument( + "-c", + "--crop-list", + help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", + default=None, + ) # Get arguments args = parser.parse_args(sys.argv[1:]) + # Process arguments + args.regrid_template_file = os.path.realpath(args.regrid_template_file) + args.regrid_input_directory = os.path.realpath(args.regrid_input_directory) + args.regrid_output_directory = os.path.realpath(args.regrid_output_directory) + + return args + + +if __name__ == "__main__": + ############################### + ### Process input arguments ### + ############################### + args = regrid_ggcmi_shdates_arg_process() + ########### ### Run ### ########### main( args.regrid_resolution, - os.path.realpath(args.regrid_template_file), - os.path.realpath(args.regrid_input_directory), - os.path.realpath(args.regrid_output_directory), + args.regrid_template_file, + args.regrid_input_directory, + args.regrid_output_directory, + args.extension, + args.crop_list, ) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py new file mode 100755 index 0000000000..6c06493160 --- /dev/null +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -0,0 +1,128 @@ +#!/usr/bin/env python3 + +"""System tests for fsurdat_modifier + +""" + +import os +import re + +import unittest +import tempfile +import shutil +import sys + +import xarray as xr +import numpy as np + +# -- add python/ctsm to path (needed if we want to run test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + + +from ctsm.path_utils import path_to_ctsm_root +from ctsm import unit_testing +from ctsm.crop_calendars.regrid_ggcmi_shdates import main as regrid_ggcmi_shdates +from ctsm.crop_calendars.regrid_ggcmi_shdates import regrid_ggcmi_shdates_arg_process + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + + +class TestRegridGgcmiShdates(unittest.TestCase): + """System tests for regrid_ggcmi_shdates""" + + def setUp(self): + # Where in the /testinputs directory are the raw crop calendar file(s)? + testinputs_path = os.path.join(path_to_ctsm_root(), "python", "ctsm", "test", "testinputs") + testinputs_cc_path = os.path.join(testinputs_path, "cropcals") + self._testinputs_cc_path = testinputs_cc_path + + # Make /_tempdir for use by these tests. + self._tempdir = tempfile.mkdtemp() + + # Obtain path for the directory being created in /_tempdir + self._regridded_cropcals = os.path.join(self._tempdir, "regridded_cropcals") + + # What extension do the raw crop calendar file(s) have? + self._extension = ".nc4" + + # Which crop(s) should we test? (comma-separated string) + self._crop_list = "swh_rf" + + # What is the complete set of input arguments (including script name)? + regrid_template_file = os.path.join( + testinputs_path, "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214.nc" + ) + self._function_call_list = [ + "regrid_ggcmi_shdates", + "-i", + testinputs_cc_path, + "-x", + ".nc4", + "-o", + self._regridded_cropcals, + "-rr", + "5x5amazon", + "-rt", + regrid_template_file, + "--crop-list", + "swh_rf", + ] + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_regrid_ggcmi_shdates(self): + + # Call script + sys.argv = self._function_call_list + args = regrid_ggcmi_shdates_arg_process() + regrid_ggcmi_shdates( + args.regrid_resolution, + args.regrid_template_file, + args.regrid_input_directory, + args.regrid_output_directory, + args.extension, + args.crop_list, + ) + + # Read output file + regrid_out_file = os.path.join( + self._regridded_cropcals, + "swh_rf_ggcmi_crop_calendar_phase3_v1.01_nninterp-5x5amazon.nc4", + ) + regrid_out_ds = xr.open_dataset(regrid_out_file) + + # Check sowing dates + expected_sow_dates = np.array( + [ + [120, 120, 120, 120, 120], + [120, 120, 120, 120, 120], + [120, 120, 120, 120, 120], + [330, 335, 335, 120, 120], + [325, 335, 335, 335, 120], + ] + ) + np.testing.assert_array_equal(expected_sow_dates, regrid_out_ds["planting_day"].values) + + # Check maturity dates + expected_mat_dates = np.array( + [ + [221, 221, 221, 221, 221], + [221, 221, 221, 221, 221], + [221, 221, 221, 221, 221], + [153, 128, 128, 221, 221], + [163, 128, 128, 128, 221], + ] + ) + np.testing.assert_array_equal(expected_mat_dates, regrid_out_ds["maturity_day"].values) + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py new file mode 100755 index 0000000000..c47e81ac15 --- /dev/null +++ b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py @@ -0,0 +1,125 @@ +#!/usr/bin/env python3 + +""" +Unit tests for regrid_ggcmi_shdates subroutines: +""" + +import unittest +import os +import sys +import shutil + +import tempfile +import xarray as xr +import numpy as np + +# -- add python/ctsm to path (needed if we want to run test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm import unit_testing +from ctsm.path_utils import path_to_ctsm_root +from ctsm.utils import import_coord_1d, import_coord_2d + +# Allow test names that pylint doesn't like; otherwise hard to make them +# readable +# pylint: disable=invalid-name + +# pylint: disable=protected-access + + +# Allow as many public methods as needed... +# pylint: disable=too-many-public-methods +# Allow all the instance attributes that we need +# pylint: disable=too-many-instance-attributes +class TestRegridGgcmiShdates(unittest.TestCase): + # Tests the regrid_ggcmi_shdates subroutines + + def setUp(self): + """Setup for trying out the methods""" + testinputs_path = os.path.join(path_to_ctsm_root(), "python/ctsm/test/testinputs") + self._testinputs_path = testinputs_path + self._tempdir = tempfile.mkdtemp() + + self._1d_lonlat_file = os.path.join( + self._testinputs_path, "cropcals", "swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4" + ) + self._2d_lonlat_file = os.path.join( + self._testinputs_path, + "surfdata_5x5_amazon_16pfts_Irrig_CMIP6_simyr2000_c171214_modified.nc", + ) + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_importcoord1d(self): + ds = xr.open_dataset(self._1d_lonlat_file) + lat, Nlat = import_coord_1d(ds, "lat") + print(lat) + np.testing.assert_equal(Nlat, 360) + np.testing.assert_array_equal(lat.values[:4], [89.75, 89.25, 88.75, 88.25]) + np.testing.assert_array_equal(lat.values[-4:], [-88.25, -88.75, -89.25, -89.75]) + + def test_importcoord1d_attrs(self): + ds = xr.open_dataset(self._1d_lonlat_file) + lat, _ = import_coord_1d(ds, "lat") + # Unlike import_coord_2d, import_coord_1d doesn't rename the long name. + expected_attributes = { + "long_name": ds["lat"].attrs["long_name"], + "units": "degrees_north", + } + self.assertDictEqual(lat.attrs, expected_attributes) + + def test_importcoord1d_too_many_dims(self): + ds = xr.open_dataset(self._2d_lonlat_file) + with self.assertRaisesRegex( + SystemExit, + "Expected 1 dimension for LATIXY; found 2: \('lsmlat', 'lsmlon'\)", + ): + import_coord_1d(ds, "LATIXY") + + def test_importcoord2d(self): + ds = xr.open_dataset(self._2d_lonlat_file) + lat, _ = import_coord_2d(ds, "lat", "LATIXY") + expected_values = np.array([-13.9, -11.7, -9.5, -7.3, -5.1]).astype(np.float32) + np.testing.assert_array_equal(lat.values, expected_values) + + def test_importcoord2d_attrs(self): + ds = xr.open_dataset(self._2d_lonlat_file) + lat, _ = import_coord_2d(ds, "lat", "LATIXY") + expected_attributes = { + "long_name": "coordinate latitude", + "units": "degrees_north", + } + self.assertDictEqual(lat.attrs, expected_attributes) + + def test_importcoord2d_rename_dim(self): + ds = xr.open_dataset(self._2d_lonlat_file) + lat, _ = import_coord_2d(ds, "lat", "LATIXY") + self.assertTupleEqual(lat.dims, ("lat",)) + + def test_importcoord2d_no_dim_contains_coordName(self): + ds = xr.open_dataset(self._2d_lonlat_file) + ds = ds.rename({"lsmlat": "abc"}) + with self.assertRaisesRegex( + SystemExit, + "ERROR: Expected 1 dimension name containing lat; found 0: \[\]", + ): + import_coord_2d(ds, "lat", "LATIXY") + + def test_importcoord2d_1_dim_containing(self): + ds = xr.open_dataset(self._2d_lonlat_file) + ds = ds.rename({"lsmlon": "lsmlat2"}) + with self.assertRaisesRegex( + SystemExit, + "Expected 1 dimension name containing lat; found 2: \['lsmlat', 'lsmlat2'\]", + ): + import_coord_2d(ds, "lat", "LATIXY") + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 b/python/ctsm/test/testinputs/cropcals/swh_rf_ggcmi_crop_calendar_phase3_v1.01.nc4 new file mode 100644 index 0000000000000000000000000000000000000000..985210eaeaee7d1d6c4a047bbb2ed06353d2f9ef GIT binary patch literal 139563 zcmeF(2Uru^x-fne1yq`{rAUhv3%y7uC?YB?ii$`VLqIyAm!Pu6MiZ3|0Z~9fsvsR~ zbP|*`i`oXU$qOd1p-4T9YUD&zw5VvVG5X zI_kp2M7M>G{r6Ma!x}8d_HO>YiWbw#&1g^lfx2f-UD(Xrw|U?1a(V{XjMmKGyL~g= zCh8{azmFnv&-&)4p%&fm>g#owO{pt4(XrAoQT{X4QA0U9IHH|htkGD?dJf8;?C)~Q z17&eTJ7cXK?3E>a?9nb3*DY7;kiNw3kd0vtwXnknY#V@w$xSe8ce&W(rC!H&N0^&6%3k2|YbZOwAQF-Rs9oM|bM1wz`hqSzR4dJ+%{B>U7KpsAZez zw*IcAb3$94vhnX))ZNi)Q8GivEKNs8J%Oxr%#>|Sb$+K>`joYu^>xaY?35QltwBeJ z`29$$NeyhvmK%Ss^sub>trd6$JOj#she2+T37kh)&{3CRupO)h3&2z`61)d`fL7oY z@C+yi9tOEVCUE{b>>q3gtHA;=6^sP$fgYe0cm+HI%7KSLZjcF_w}AbF?O-)n0H%VG 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z{RI!wsnfC!rRjG4vt?shS#>KQOLnaXSnPK7w%=V=6?F4HIUng<|KnOr=J$O7*paWh zO)&q%$9pSo&4JB|ZMUI64$k%d&&P zDU~S%5>o>+SqpJlHclE6BvKyp?z;Y{Iekcx{qZFJ4?!;EDmpxK^^Y(A|L6a!2$c0` K^%@tq<^Ml&ww|c~ literal 0 HcmV?d00001 diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 8578ea860c..9b398a7791 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -6,6 +6,7 @@ import string import re import pdb +import numpy as np from datetime import date, timedelta from getpass import getuser @@ -191,6 +192,35 @@ def write_output(file, file_in, file_out, file_type): file.close() +# Import 1-d latitude or longitude variable from a CESM history file (e.g., name lat or lon) and return it as a DataArray that can be used for writing CESM input files +def import_coord_1d(ds, coordName): + da = ds[coordName] + if len(da.dims) != 1: + abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") + return da, len(da) + + +# Import 1-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files +def import_coord_2d(ds, coordName, varName): + da = ds[varName] + thisDim = [x for x in da.dims if coordName in x] + if len(thisDim) != 1: + abort(f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}") + thisDim = thisDim[0] + otherDim = [x for x in da.dims if coordName not in x] + if len(otherDim) != 1: + abort( + f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" + ) + otherDim = otherDim[0] + da = da.astype(np.float32) + da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) + da = da.assign_coords({coordName: da.values}) + da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] + da.attrs["units"] = da.attrs["units"].replace(" ", "_") + return da, len(da) + + def get_isosplit(iso_string, split): """ Split a string (iso_string) by the character sent in from split From 197e53a2253b5bd18babb3cff0172df6c8617a15 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Dec 2023 15:15:07 -0800 Subject: [PATCH 1965/2067] Improve comments/docstrings. --- .../test/test_sys_regrid_ggcmi_shdates.py | 2 +- .../test/test_unit_regrid_ggcmi_shdates.py | 2 +- python/ctsm/utils.py | 24 ++++++++++++++++--- 3 files changed, 23 insertions(+), 5 deletions(-) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py index 6c06493160..86a6338d5a 100755 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -1,6 +1,6 @@ #!/usr/bin/env python3 -"""System tests for fsurdat_modifier +"""System tests for regrid_ggcmi_shdates.py """ diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py index c47e81ac15..44889a62ac 100755 --- a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py @@ -1,7 +1,7 @@ #!/usr/bin/env python3 """ -Unit tests for regrid_ggcmi_shdates subroutines: +Unit tests for utils.py functions related to importing coordinate variables """ import unittest diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 9b398a7791..53a3eda8f1 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -192,16 +192,34 @@ def write_output(file, file_in, file_out, file_type): file.close() -# Import 1-d latitude or longitude variable from a CESM history file (e.g., name lat or lon) and return it as a DataArray that can be used for writing CESM input files def import_coord_1d(ds, coordName): + """Import 1-d coordinate variable + + Args: + ds (xarray Dataset): Dataset whose coordinate you want to import. + coordName (str): Name of coordinate to import + + Returns: + xarray DataArray: DataArray corresponding to the requested coordinate. + """ da = ds[coordName] if len(da.dims) != 1: abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") return da, len(da) - -# Import 1-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files +# def import_coord_2d(ds, coordName, varName): + """Import 2-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files + + Args: + ds (xarray Dataset): Dataset whose coordinate you want to import. + coordName (str): Name of coordinate to import + varName (str): Name of variable with dimension coordName + + Returns: + xarray DataArray: 1-d variable that can be used as a coordinate for writing CESM input files + int: Length of that variable + """ da = ds[varName] thisDim = [x for x in da.dims if coordName in x] if len(thisDim) != 1: From 0224c2a8ba6310cfd81478084df8d5c625e3ccd9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Dec 2023 15:20:10 -0800 Subject: [PATCH 1966/2067] Another comment/docstring improvement. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 02abbf99f9..880b32ee0e 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -151,8 +151,12 @@ def main( os.remove(templatefile) -# Process input arguments def regrid_ggcmi_shdates_arg_process(): + """Process input arguments + + Returns: + argparse.ArgumentParser: Arguments/options + """ # set up logging allowing user control setup_logging_pre_config() From 4bf2384d245e12e7d25ba255b8feb1931188a98d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Dec 2023 15:25:15 -0800 Subject: [PATCH 1967/2067] Rename TestRegridGgcmiShdates to TestUtilsImportCoord. Similarly rename its file. --- ...egrid_ggcmi_shdates.py => test_unit_utils_import_coord.py} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename python/ctsm/test/{test_unit_regrid_ggcmi_shdates.py => test_unit_utils_import_coord.py} (97%) diff --git a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py b/python/ctsm/test/test_unit_utils_import_coord.py similarity index 97% rename from python/ctsm/test/test_unit_regrid_ggcmi_shdates.py rename to python/ctsm/test/test_unit_utils_import_coord.py index 44889a62ac..31d6e4697d 100755 --- a/python/ctsm/test/test_unit_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_unit_utils_import_coord.py @@ -32,8 +32,8 @@ # pylint: disable=too-many-public-methods # Allow all the instance attributes that we need # pylint: disable=too-many-instance-attributes -class TestRegridGgcmiShdates(unittest.TestCase): - # Tests the regrid_ggcmi_shdates subroutines +class TestUtilsImportCoord(unittest.TestCase): + # Tests the importcoord* subroutines from utils.py def setUp(self): """Setup for trying out the methods""" From 164357eeb945b4f8a91a6448d205a2b2e4ad2b5e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 14 Dec 2023 15:55:38 -0800 Subject: [PATCH 1968/2067] regrid_ggcmi_shdates now loads cdo module. --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 880b32ee0e..a0a42a7442 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -60,7 +60,7 @@ def main( print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") # Ensure we can call necessary shell script(s) - for cmd in ["cdo"]: + for cmd in ["module load cdo; cdo"]: run_and_check(f"{cmd} --help") os.chdir(regrid_input_directory) @@ -137,15 +137,15 @@ def main( # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: try: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") except: - run_and_check(f"cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") # Delete template file, which is no longer needed os.remove(templatefile) From 225f0926866be7b26ff9fde438529784f91d17ab Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 15 Dec 2023 15:09:25 -0700 Subject: [PATCH 1969/2067] Update the default fates paramfile A newer parameter file was generated that reduces the maximum number of fates patches for the default configuration. This avoids misalignment between the default surface datasets. --- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 2dfde24737..d8b33ab579 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -492,7 +492,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231130.nc +lnd/clm2/paramdata/fates_params_api.32.0.0_12pft_c231215.nc From 809ef0893c7d6b9f065188c18e1495e8f3368ede Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Fri, 15 Dec 2023 13:16:05 -0700 Subject: [PATCH 1970/2067] Pass surfpft bounds as input argumment The wt_nat_patch array is allocated using surfpft bounds. While surfpft and natpft will typically match, this isn't the case for fates currently. As such the nag compiler will complain if the input array has lower bounds for its dimensions than the dummy argument bounds. --- src/main/surfrdMod.F90 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90 index 78c9d8492e..23e96e7c1a 100644 --- a/src/main/surfrdMod.F90 +++ b/src/main/surfrdMod.F90 @@ -723,6 +723,7 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns, actual_numcft) ! !USES: use clm_varctl , only : create_crop_landunit, use_fates, n_dom_pfts use clm_varpar , only : natpft_lb, natpft_ub, natpft_size, cft_size, cft_lb, cft_ub + use clm_varpar , only : surfpft_lb, surfpft_ub use clm_instur , only : wt_lunit, wt_nat_patch, wt_cft, fert_cft use landunit_varcon , only : istsoil, istcrop use surfrdUtilsMod , only : convert_cft_to_pft @@ -851,7 +852,7 @@ subroutine surfrd_veg_all(begg, endg, ncid, ns, actual_numcft) ! - Pfts could be up to 16 before collapsing if create_crop_landunit = .F. ! TODO Add the same call to subroutine dynpft_interp for transient runs - call collapse_to_dominant(wt_nat_patch(begg:endg,:), natpft_lb, natpft_ub, & + call collapse_to_dominant(wt_nat_patch(begg:endg,:), surfpft_lb, surfpft_ub, & begg, endg, n_dom_pfts) end subroutine surfrd_veg_all From 27b26071597da617b57907b7725cc8444e6dde3d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 13:26:06 -0700 Subject: [PATCH 1971/2067] Delete a print(lat). --- python/ctsm/test/test_unit_utils_import_coord.py | 1 - 1 file changed, 1 deletion(-) diff --git a/python/ctsm/test/test_unit_utils_import_coord.py b/python/ctsm/test/test_unit_utils_import_coord.py index 31d6e4697d..2844e2dec1 100755 --- a/python/ctsm/test/test_unit_utils_import_coord.py +++ b/python/ctsm/test/test_unit_utils_import_coord.py @@ -58,7 +58,6 @@ def tearDown(self): def test_importcoord1d(self): ds = xr.open_dataset(self._1d_lonlat_file) lat, Nlat = import_coord_1d(ds, "lat") - print(lat) np.testing.assert_equal(Nlat, 360) np.testing.assert_array_equal(lat.values[:4], [89.75, 89.25, 88.75, 88.25]) np.testing.assert_array_equal(lat.values[-4:], [-88.25, -88.75, -89.25, -89.75]) From f39f7b445b0ced08bd550d1f236e8099b2fd043d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 13:38:57 -0700 Subject: [PATCH 1972/2067] Use logging infra for *_ggcmi_shdates.py scripts. --- .../crop_calendars/process_ggcmi_shdates.py | 41 +++++++++++-------- .../crop_calendars/regrid_ggcmi_shdates.py | 17 ++++---- 2 files changed, 32 insertions(+), 26 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 30ab006ab4..8d3577deb8 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -5,10 +5,19 @@ import cftime import sys import argparse +import logging import cropcal_utils as utils import regrid_ggcmi_shdates +# -- add python/ctsm to path (needed if we want to run regrid_ggcmi_shdates stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm import ctsm_logging + +logger = logging.getLogger(__name__) + def get_cft(y): return cftime.DatetimeNoLeap(y, 1, 1, 0, 0, 0, 0, has_year_zero=True) @@ -200,17 +209,16 @@ def set_var_dict(name_ggcmi, outfile): if thiscrop_ggcmi == None: if c == 1: raise ValueError(f"First crop ({thiscrop_clm}) must have a GGCMI type") - print( + logger.info( "Filling %s with dummy data (%d of %d)..." % (str(thiscrop_clm), c, len(crop_dict)) ) # Otherwise, import crop calendar file else: - if verbose: - print( - "Importing %s -> %s (%d of %d)..." - % (str(thiscrop_ggcmi), str(thiscrop_clm), c, len(crop_dict)) - ) + logger.info( + "Importing %s -> %s (%d of %d)..." + % (str(thiscrop_ggcmi), str(thiscrop_clm), c, len(crop_dict)) + ) file_ggcmi = os.path.join( regridded_ggcmi_files_dir, @@ -227,8 +235,7 @@ def set_var_dict(name_ggcmi, outfile): for thisvar_clm in variable_dict: # Get GGCMI netCDF info varname_ggcmi = variable_dict[thisvar_clm]["name_ggcmi"] - if verbose: - print(" Processing %s..." % varname_ggcmi) + logger.info(" Processing %s..." % varname_ggcmi) # Get CLM netCDF info varname_clm = thisvar_clm + "1_" + str(thiscrop_int) @@ -299,19 +306,22 @@ def set_var_attrs( ) # Save - if verbose: - print(" Saving %s..." % varname_ggcmi) + logger.info(" Saving %s..." % varname_ggcmi) thisvar_da.to_netcdf(file_clm, mode="a", format="NETCDF3_CLASSIC") cropcal_ds.close() - print("Done!") + logger.info("Done!") if __name__ == "__main__": ############################### ### Process input arguments ### ############################### + + # set up logging allowing user control + ctsm_logging.setup_logging_pre_config() + parser = argparse.ArgumentParser( description="Converts raw sowing and harvest date files provided by GGCMI into a format that CLM can read, optionally at a target resolution." ) @@ -360,25 +370,20 @@ def set_var_attrs( type=int, default=2000, ) - parser.add_argument( - "-v", - "--verbose", - help="Whether to print verbose messages", - type=bool, - default=True, - ) parser.add_argument( "--ggcmi-author", help="Author of original GGCMI files", type=str, default="Jonas Jägermeyr (jonas.jaegermeyr@columbia.edu)", ) + ctsm_logging.add_logging_args(parser) # Arguments for regridding parser = regrid_ggcmi_shdates.define_arguments(parser) # Get arguments args = parser.parse_args(sys.argv[1:]) + ctsm_logging.process_logging_args(args) ########### ### Run ### diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index a0a42a7442..9c3cf100ff 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -5,17 +5,16 @@ import sys import xarray as xr import numpy as np +import logging # -- add python/ctsm to path (needed if we want to run regrid_ggcmi_shdates stand-alone) _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) from ctsm.utils import abort, import_coord_1d, import_coord_2d -from ctsm.ctsm_logging import ( - setup_logging_pre_config, - add_logging_args, - process_logging_args, -) +from ctsm import ctsm_logging + +logger = logging.getLogger(__name__) def run_and_check(cmd): @@ -57,7 +56,7 @@ def main( extension, crop_list, ): - print(f"Regridding GGCMI crop calendars to {regrid_resolution}:") + logger.info(f"Regridding GGCMI crop calendars to {regrid_resolution}:") # Ensure we can call necessary shell script(s) for cmd in ["module load cdo; cdo"]: @@ -128,7 +127,7 @@ def main( if crop_list is not None and this_crop not in crop_list: continue - print(" " + this_crop) + logger.info(" " + this_crop) f2 = os.path.join(regrid_output_directory, f) f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") @@ -159,7 +158,7 @@ def regrid_ggcmi_shdates_arg_process(): """ # set up logging allowing user control - setup_logging_pre_config() + ctsm_logging.setup_logging_pre_config() parser = argparse.ArgumentParser( description="Regrids raw sowing and harvest date files provided by GGCMI to a target CLM resolution." @@ -194,9 +193,11 @@ def regrid_ggcmi_shdates_arg_process(): help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", default=None, ) + ctsm_logging.add_logging_args(parser) # Get arguments args = parser.parse_args(sys.argv[1:]) + ctsm_logging.process_logging_args(args) # Process arguments args.regrid_template_file = os.path.realpath(args.regrid_template_file) From 747eda6755d4738b1555e010a145a9bbad3e69cb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 14:10:40 -0700 Subject: [PATCH 1973/2067] chdir out of tempdir in tests and regrid_ggcmi_shdates. Resolves #2167. Affected scripts: * test_sys_mesh_modifier * test_sys_run_neon * regrid_ggcmi_shdates --- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 2 ++ python/ctsm/test/test_sys_mesh_modifier.py | 3 ++- python/ctsm/test/test_sys_run_neon.py | 2 ++ 3 files changed, 6 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 9c3cf100ff..66a8f51390 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -62,6 +62,7 @@ def main( for cmd in ["module load cdo; cdo"]: run_and_check(f"{cmd} --help") + previous_dir = os.getcwd() os.chdir(regrid_input_directory) if not os.path.exists(regrid_output_directory): os.makedirs(regrid_output_directory) @@ -148,6 +149,7 @@ def main( # Delete template file, which is no longer needed os.remove(templatefile) + os.chdir(previous_dir) def regrid_ggcmi_shdates_arg_process(): diff --git a/python/ctsm/test/test_sys_mesh_modifier.py b/python/ctsm/test/test_sys_mesh_modifier.py index 0889a505ba..da59368391 100755 --- a/python/ctsm/test/test_sys_mesh_modifier.py +++ b/python/ctsm/test/test_sys_mesh_modifier.py @@ -57,6 +57,7 @@ def setUp(self): metadata_file = os.path.join(self._tempdir, "metadata.nc") configure_path = os.path.join(path_to_cime(), "CIME/scripts/configure") + self._previous_dir = os.getcwd() os.chdir(self._tempdir) # cd to tempdir # Run configure to generate .env_mach_specific.sh @@ -111,7 +112,7 @@ def tearDown(self): """ Remove temporary directory """ - os.getcwd() # cd back to the original working directory + os.chdir(self._previous_dir) # cd back to the original working directory shutil.rmtree(self._tempdir, ignore_errors=True) def test_allInfo(self): diff --git a/python/ctsm/test/test_sys_run_neon.py b/python/ctsm/test/test_sys_run_neon.py index 707e3dc366..f4c417ea51 100755 --- a/python/ctsm/test/test_sys_run_neon.py +++ b/python/ctsm/test/test_sys_run_neon.py @@ -28,6 +28,7 @@ def setUp(self): Make /_tempdir for use by these tests. Check tempdir for history files """ + self._previous_dir = os.getcwd() self._tempdir = tempfile.mkdtemp() os.chdir(self._tempdir) # cd to tempdir @@ -35,6 +36,7 @@ def tearDown(self): """ Remove temporary directory """ + os.chdir(self._previous_dir) shutil.rmtree(self._tempdir, ignore_errors=True) def test_one_site(self): From 3f3f40c18d58a258762f340b299fac5ab7b836ba Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 15:04:19 -0700 Subject: [PATCH 1974/2067] Call regrid_ggcmi_shdates from tools/crop_calendars. --- .../crop_calendars/regrid_ggcmi_shdates.py | 38 +++++++++---------- .../test/test_sys_regrid_ggcmi_shdates.py | 2 +- tools/README | 2 + tools/crop_calendars/regrid_ggcmi_shdates | 19 ++++++++++ 4 files changed, 41 insertions(+), 20 deletions(-) create mode 100755 tools/crop_calendars/regrid_ggcmi_shdates diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 66a8f51390..69b5b398a9 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -17,6 +17,24 @@ logger = logging.getLogger(__name__) +def main(): + """ + Description + ----------- + Calls function that regrids GGCMI sowing and harvest dates. + """ + + args = regrid_ggcmi_shdates_arg_process() + regrid_ggcmi_shdates( + args.regrid_resolution, + args.regrid_template_file, + args.regrid_input_directory, + args.regrid_output_directory, + args.extension, + args.crop_list, + ) + + def run_and_check(cmd): result = run( cmd, @@ -48,7 +66,7 @@ def define_arguments(parser): return parser -def main( +def regrid_ggcmi_shdates( regrid_resolution, regrid_template_file_in, regrid_input_directory, @@ -208,21 +226,3 @@ def regrid_ggcmi_shdates_arg_process(): return args - -if __name__ == "__main__": - ############################### - ### Process input arguments ### - ############################### - args = regrid_ggcmi_shdates_arg_process() - - ########### - ### Run ### - ########### - main( - args.regrid_resolution, - args.regrid_template_file, - args.regrid_input_directory, - args.regrid_output_directory, - args.extension, - args.crop_list, - ) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py index 86a6338d5a..815a4bccf6 100755 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -22,7 +22,7 @@ from ctsm.path_utils import path_to_ctsm_root from ctsm import unit_testing -from ctsm.crop_calendars.regrid_ggcmi_shdates import main as regrid_ggcmi_shdates +from ctsm.crop_calendars.regrid_ggcmi_shdates import regrid_ggcmi_shdates from ctsm.crop_calendars.regrid_ggcmi_shdates import regrid_ggcmi_shdates_arg_process # Allow test names that pylint doesn't like; otherwise hard to make them diff --git a/tools/README b/tools/README index a35cff8b7c..2aaecc3bd8 100644 --- a/tools/README +++ b/tools/README @@ -8,6 +8,8 @@ I. General directory structure: $CTSMROOT/tools mksurfdata_map --- Create surface datasets. + crop_calendars --- Regrid and process GGCMI sowing and harvest date files for use in CTSM. + mkmapgrids ------- Create regular lat/lon SCRIP grid files needed by mkmapdata mkmapdata -------- Create SCRIP mapping data from SCRIP grid files (uses ESMF) mkprocdata_map --- Convert output unstructured grids into a 2D format that diff --git a/tools/crop_calendars/regrid_ggcmi_shdates b/tools/crop_calendars/regrid_ggcmi_shdates new file mode 100755 index 0000000000..50ef2636bb --- /dev/null +++ b/tools/crop_calendars/regrid_ggcmi_shdates @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 +""" +For description and instructions, please see README. +""" + +import os +import sys + +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), + os.pardir, + os.pardir, + 'python') +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.crop_calendars.regrid_ggcmi_shdates import main + +if __name__ == "__main__": + main() + From c6bd82961df7d0621e71bcffdf5834e0a13068b1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 15:41:26 -0700 Subject: [PATCH 1975/2067] Update process_ggcmi_shdates to work with reworked regrid_ggcmi_shdates. --- .../crop_calendars/process_ggcmi_shdates.py | 8 ++- .../crop_calendars/regrid_ggcmi_shdates.py | 49 ++++++++++--------- .../test/test_sys_regrid_ggcmi_shdates.py | 6 +-- 3 files changed, 34 insertions(+), 29 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 8d3577deb8..60e075f728 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -42,6 +42,8 @@ def main( ggcmi_author, regrid_resolution, regrid_template_file, + regrid_extension, + regrid_crop_list, ): ############################################################ @@ -52,8 +54,8 @@ def main( output_directory, f"regridded_ggcmi_files-{regrid_resolution}" ) - regrid_ggcmi_shdates.main( - regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir + regrid_ggcmi_shdates.regrid_ggcmi_shdates( + regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir, regrid_extension, regrid_crop_list ) ########################### @@ -399,4 +401,6 @@ def set_var_attrs( args.ggcmi_author, args.regrid_resolution, args.regrid_template_file, + args.regrid_extension, + args.regrid_crop_list, ) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 69b5b398a9..badb5fb281 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -30,8 +30,8 @@ def main(): args.regrid_template_file, args.regrid_input_directory, args.regrid_output_directory, - args.extension, - args.crop_list, + args.regrid_extension, + args.regrid_crop_list, ) @@ -63,6 +63,20 @@ def define_arguments(parser): type=str, required=True, ) + + default = ".nc" + parser.add_argument( + "-x", + "--regrid-extension", + help=f"File regrid_extension of raw GGCMI sowing/harvest date files (default {default}).", + default=default, + ) + parser.add_argument( + "-c", + "--regrid-crop-list", + help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", + default=None, + ) return parser @@ -71,8 +85,8 @@ def regrid_ggcmi_shdates( regrid_template_file_in, regrid_input_directory, regrid_output_directory, - extension, - crop_list, + regrid_extension, + regrid_crop_list, ): logger.info(f"Regridding GGCMI crop calendars to {regrid_resolution}:") @@ -92,10 +106,10 @@ def regrid_ggcmi_shdates( template_ds_in = xr.open_dataset(regrid_template_file_in) # Process inputs - if crop_list is not None: - crop_list = crop_list.split(",") - if extension[0] != ".": - extension = "." + extension + if regrid_crop_list is not None: + regrid_crop_list = regrid_crop_list.split(",") + if regrid_extension[0] != ".": + regrid_extension = "." + regrid_extension # Import and format latitude if "lat" in template_ds_in: @@ -136,19 +150,19 @@ def regrid_ggcmi_shdates( template_ds_out.to_netcdf(templatefile, mode="w") # Loop through original crop calendar files, interpolating using cdo with nearest-neighbor - pattern = "*" + extension + pattern = "*" + regrid_extension input_files = glob.glob(pattern) if len(input_files) == 0: abort(f"No files found matching {os.path.join(os.getcwd(), pattern)}") input_files.sort() for f in input_files: this_crop = f[0:6] - if crop_list is not None and this_crop not in crop_list: + if regrid_crop_list is not None and this_crop not in regrid_crop_list: continue logger.info(" " + this_crop) f2 = os.path.join(regrid_output_directory, f) - f3 = f2.replace(extension, f"_nninterp-{regrid_resolution}{extension}") + f3 = f2.replace(regrid_extension, f"_nninterp-{regrid_resolution}{regrid_extension}") if os.path.exists(f3): os.remove(f3) @@ -200,19 +214,6 @@ def regrid_ggcmi_shdates_arg_process(): type=str, required=True, ) - default = ".nc" - parser.add_argument( - "-x", - "--extension", - help=f"File extension of raw GGCMI sowing/harvest date files (default {default}).", - default=default, - ) - parser.add_argument( - "-c", - "--crop-list", - help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", - default=None, - ) ctsm_logging.add_logging_args(parser) # Get arguments diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py index 815a4bccf6..2032a67364 100755 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -67,7 +67,7 @@ def setUp(self): "5x5amazon", "-rt", regrid_template_file, - "--crop-list", + "--regrid-crop-list", "swh_rf", ] @@ -87,8 +87,8 @@ def test_regrid_ggcmi_shdates(self): args.regrid_template_file, args.regrid_input_directory, args.regrid_output_directory, - args.extension, - args.crop_list, + args.regrid_extension, + args.regrid_crop_list, ) # Read output file From 9fd3237bda0ee2e84cfbac5ab752f8dcee75fbf1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 15:46:30 -0700 Subject: [PATCH 1976/2067] Warn instead of failing if process_ggcmi_shdates is missing an input file. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 60e075f728..902772bfcd 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -227,7 +227,8 @@ def set_var_dict(name_ggcmi, outfile): f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4", ) if not os.path.exists(file_ggcmi): - raise Exception("Input file not found: " + file_ggcmi) + logger.warning(f"Skipping {thiscrop_ggcmi} because input file not found: {file_ggcmi}") + continue cropcal_ds = xr.open_dataset(file_ggcmi) # Flip latitude to match destination cropcal_ds = cropcal_ds.reindex(lat=cropcal_ds.lat[::-1]) From 9c59d40cfe7247a8e2d524c6f2bac64a66baf927 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 18:27:23 -0700 Subject: [PATCH 1977/2067] process_ggcmi_sdates now respects --crop-list. --- python/ctsm/crop_calendars/process_ggcmi_shdates.py | 10 +++++++--- python/ctsm/crop_calendars/regrid_ggcmi_shdates.py | 12 ++++++------ python/ctsm/test/test_sys_regrid_ggcmi_shdates.py | 4 ++-- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 902772bfcd..b439ebc1f6 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -43,7 +43,7 @@ def main( regrid_resolution, regrid_template_file, regrid_extension, - regrid_crop_list, + crop_list, ): ############################################################ @@ -55,7 +55,7 @@ def main( ) regrid_ggcmi_shdates.regrid_ggcmi_shdates( - regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir, regrid_extension, regrid_crop_list + regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir, regrid_extension, crop_list ) ########################### @@ -206,6 +206,10 @@ def set_var_dict(name_ggcmi, outfile): thiscrop_int = this_dict["clm_num"] thiscrop_ggcmi = this_dict["thiscrop_ggcmi"] + # If --regrid-crop-list specified, only process crops from that list + if crop_list is not None and thiscrop_ggcmi is not None and thiscrop_ggcmi not in crop_list: + continue + # If no corresponding GGCMI crop, skip opening dataset. # Will use previous cropcal_ds as a template. if thiscrop_ggcmi == None: @@ -403,5 +407,5 @@ def set_var_attrs( args.regrid_resolution, args.regrid_template_file, args.regrid_extension, - args.regrid_crop_list, + args.crop_list, ) diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index badb5fb281..fbefa7b6b3 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -31,7 +31,7 @@ def main(): args.regrid_input_directory, args.regrid_output_directory, args.regrid_extension, - args.regrid_crop_list, + args.crop_list, ) @@ -73,7 +73,7 @@ def define_arguments(parser): ) parser.add_argument( "-c", - "--regrid-crop-list", + "--crop-list", help="List of GGCMI crops to process; e.g., '--crop-list mai_rf,mai_ir'. If not provided, will process all GGCMI crops.", default=None, ) @@ -86,7 +86,7 @@ def regrid_ggcmi_shdates( regrid_input_directory, regrid_output_directory, regrid_extension, - regrid_crop_list, + crop_list, ): logger.info(f"Regridding GGCMI crop calendars to {regrid_resolution}:") @@ -106,8 +106,8 @@ def regrid_ggcmi_shdates( template_ds_in = xr.open_dataset(regrid_template_file_in) # Process inputs - if regrid_crop_list is not None: - regrid_crop_list = regrid_crop_list.split(",") + if crop_list is not None: + crop_list = crop_list.split(",") if regrid_extension[0] != ".": regrid_extension = "." + regrid_extension @@ -157,7 +157,7 @@ def regrid_ggcmi_shdates( input_files.sort() for f in input_files: this_crop = f[0:6] - if regrid_crop_list is not None and this_crop not in regrid_crop_list: + if crop_list is not None and this_crop not in crop_list: continue logger.info(" " + this_crop) diff --git a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py index 2032a67364..7521ef09a5 100755 --- a/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py +++ b/python/ctsm/test/test_sys_regrid_ggcmi_shdates.py @@ -67,7 +67,7 @@ def setUp(self): "5x5amazon", "-rt", regrid_template_file, - "--regrid-crop-list", + "--crop-list", "swh_rf", ] @@ -88,7 +88,7 @@ def test_regrid_ggcmi_shdates(self): args.regrid_input_directory, args.regrid_output_directory, args.regrid_extension, - args.regrid_crop_list, + args.crop_list, ) # Read output file From e4b4def38c0a807504df2cbbf2ce94060fedb33c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 18:43:38 -0700 Subject: [PATCH 1978/2067] Call process_ggcmi_shdates from tools/crop_calendars. --- .../crop_calendars/process_ggcmi_shdates.py | 190 +++++++++--------- tools/crop_calendars/process_ggcmi_shdates | 19 ++ 2 files changed, 114 insertions(+), 95 deletions(-) create mode 100755 tools/crop_calendars/process_ggcmi_shdates diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index b439ebc1f6..2d603dba06 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -7,14 +7,13 @@ import argparse import logging -import cropcal_utils as utils -import regrid_ggcmi_shdates - -# -- add python/ctsm to path (needed if we want to run regrid_ggcmi_shdates stand-alone) +# -- add python/ctsm to path (needed if we want to run process_ggcmi_shdates stand-alone) _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) from ctsm import ctsm_logging +import ctsm.crop_calendars.cropcal_utils as utils +import ctsm.crop_calendars.regrid_ggcmi_shdates as regrid logger = logging.getLogger(__name__) @@ -31,7 +30,94 @@ def get_dayssince_jan1y1(y1, y): return time_delta_secs / (60 * 60 * 24) -def main( +def main(): + ctsm_logging.setup_logging_pre_config() + args = process_ggcmi_shdates_args() + process_ggcmi_shdates( + args.input_directory, + args.output_directory, + args.author, + args.file_specifier, + args.first_year, + args.last_year, + args.verbose, + args.ggcmi_author, + args.regrid_resolution, + args.regrid_template_file, + args.regrid_extension, + args.crop_list, + ) + + +def process_ggcmi_shdates_args(): + parser = argparse.ArgumentParser( + description="Converts raw sowing and harvest date files provided by GGCMI into a format that CLM can read, optionally at a target resolution." + ) + + # Required + parser.add_argument( + "-i", + "--input-directory", + help="Directory containing the raw GGCMI sowing/harvest date files", + type=str, + required=True, + ) + parser.add_argument( + "-o", + "--output-directory", + help="Where to save the CLM-compatible sowing and harvest date files", + type=str, + required=True, + ) + parser.add_argument( + "-a", + "--author", + help="String to be saved in author_thisfile attribute of output files. E.g., 'Author Name (authorname@ucar.edu)'", + type=str, + required=True, + ) + + # Optional + parser.add_argument( + "--file-specifier", + help="String following CROP_IRR_ in input filenames. E.g., mai_ir_FILESPECIFIER.nc4. Will also be saved to output filenames.", + type=str, + default="ggcmi_crop_calendar_phase3_v1.01", + ) + parser.add_argument( + "-y1", + "--first-year", + help="First year in output files. Must be present in template file, unless it's the same as the last year.", + type=int, + default=2000, + ) + parser.add_argument( + "-yN", + "--last-year", + help="Last year in output files. Must be present in template file, unless it's the same as the first year.", + type=int, + default=2000, + ) + parser.add_argument( + "--ggcmi-author", + help="Author of original GGCMI files", + type=str, + default="Jonas Jägermeyr (jonas.jaegermeyr@columbia.edu)", + ) + + ctsm_logging.add_logging_args(parser) + + # Arguments for regridding + parser = regrid.define_arguments(parser) + + # Get arguments + args = parser.parse_args(sys.argv[1:]) + ctsm_logging.process_logging_args(args) + + return args + + +def process_ggcmi_shdates( input_directory, output_directory, author, @@ -46,6 +132,9 @@ def main( crop_list, ): + input_directory = os.path.realpath(input_directory) + output_directory = os.path.realpath(output_directory) + ############################################################ ### Regrid original GGCMI files to target CLM resolution ### ############################################################ @@ -54,7 +143,7 @@ def main( output_directory, f"regridded_ggcmi_files-{regrid_resolution}" ) - regrid_ggcmi_shdates.regrid_ggcmi_shdates( + regrid.regrid_ggcmi_shdates( regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir, regrid_extension, crop_list ) @@ -320,92 +409,3 @@ def set_var_attrs( logger.info("Done!") - -if __name__ == "__main__": - ############################### - ### Process input arguments ### - ############################### - - # set up logging allowing user control - ctsm_logging.setup_logging_pre_config() - - parser = argparse.ArgumentParser( - description="Converts raw sowing and harvest date files provided by GGCMI into a format that CLM can read, optionally at a target resolution." - ) - - # Required - parser.add_argument( - "-i", - "--input-directory", - help="Directory containing the raw GGCMI sowing/harvest date files", - type=str, - required=True, - ) - parser.add_argument( - "-o", - "--output-directory", - help="Where to save the CLM-compatible sowing and harvest date files", - type=str, - required=True, - ) - parser.add_argument( - "-a", - "--author", - help="String to be saved in author_thisfile attribute of output files. E.g., 'Author Name (authorname@ucar.edu)'", - type=str, - required=True, - ) - - # Optional - parser.add_argument( - "--file-specifier", - help="String following CROP_IRR_ in input filenames. E.g., mai_ir_FILESPECIFIER.nc4. Will also be saved to output filenames.", - type=str, - default="ggcmi_crop_calendar_phase3_v1.01", - ) - parser.add_argument( - "-y1", - "--first-year", - help="First year in output files. Must be present in template file, unless it's the same as the last year.", - type=int, - default=2000, - ) - parser.add_argument( - "-yN", - "--last-year", - help="Last year in output files. Must be present in template file, unless it's the same as the first year.", - type=int, - default=2000, - ) - parser.add_argument( - "--ggcmi-author", - help="Author of original GGCMI files", - type=str, - default="Jonas Jägermeyr (jonas.jaegermeyr@columbia.edu)", - ) - ctsm_logging.add_logging_args(parser) - - # Arguments for regridding - parser = regrid_ggcmi_shdates.define_arguments(parser) - - # Get arguments - args = parser.parse_args(sys.argv[1:]) - ctsm_logging.process_logging_args(args) - - ########### - ### Run ### - ########### - main( - os.path.realpath(args.input_directory), - os.path.realpath(args.output_directory), - args.author, - args.file_specifier, - args.first_year, - args.last_year, - args.verbose, - args.ggcmi_author, - args.regrid_resolution, - args.regrid_template_file, - args.regrid_extension, - args.crop_list, - ) diff --git a/tools/crop_calendars/process_ggcmi_shdates b/tools/crop_calendars/process_ggcmi_shdates new file mode 100755 index 0000000000..82d7660651 --- /dev/null +++ b/tools/crop_calendars/process_ggcmi_shdates @@ -0,0 +1,19 @@ +#!/usr/bin/env python3 +""" +For description and instructions, please see README. +""" + +import os +import sys + +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), + os.pardir, + os.pardir, + 'python') +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm.crop_calendars.process_ggcmi_shdates import main + +if __name__ == "__main__": + main() + From 35a2f98e53ce3dce1bd0061514c2ea9fc300daf0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 18:45:45 -0700 Subject: [PATCH 1979/2067] Remove an extraneous #. --- python/ctsm/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index 53a3eda8f1..e83e4bc888 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -207,7 +207,7 @@ def import_coord_1d(ds, coordName): abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") return da, len(da) -# + def import_coord_2d(ds, coordName, varName): """Import 2-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files From a9d96219902cf609636886c7073a84407f450d9a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 18:46:28 -0700 Subject: [PATCH 1980/2067] Reformatting with black. --- .../crop_calendars/process_ggcmi_shdates.py | 12 +++++++++--- .../crop_calendars/regrid_ggcmi_shdates.py | 19 +++++++++++++------ python/ctsm/utils.py | 2 +- 3 files changed, 23 insertions(+), 10 deletions(-) diff --git a/python/ctsm/crop_calendars/process_ggcmi_shdates.py b/python/ctsm/crop_calendars/process_ggcmi_shdates.py index 2d603dba06..835f91cb22 100644 --- a/python/ctsm/crop_calendars/process_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/process_ggcmi_shdates.py @@ -144,7 +144,12 @@ def process_ggcmi_shdates( ) regrid.regrid_ggcmi_shdates( - regrid_resolution, regrid_template_file, input_directory, regridded_ggcmi_files_dir, regrid_extension, crop_list + regrid_resolution, + regrid_template_file, + input_directory, + regridded_ggcmi_files_dir, + regrid_extension, + crop_list, ) ########################### @@ -320,7 +325,9 @@ def set_var_dict(name_ggcmi, outfile): f"{thiscrop_ggcmi}_{file_specifier}_{nninterp_suffix}.nc4", ) if not os.path.exists(file_ggcmi): - logger.warning(f"Skipping {thiscrop_ggcmi} because input file not found: {file_ggcmi}") + logger.warning( + f"Skipping {thiscrop_ggcmi} because input file not found: {file_ggcmi}" + ) continue cropcal_ds = xr.open_dataset(file_ggcmi) # Flip latitude to match destination @@ -408,4 +415,3 @@ def set_var_attrs( cropcal_ds.close() logger.info("Done!") - diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index fbefa7b6b3..87ba3fb00a 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -63,7 +63,7 @@ def define_arguments(parser): type=str, required=True, ) - + default = ".nc" parser.add_argument( "-x", @@ -169,15 +169,23 @@ def regrid_ggcmi_shdates( # Sometimes cdo fails for no apparent reason. In testing this never happened more than 3x in a row. try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) except: try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) except: try: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) except: - run_and_check(f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'") + run_and_check( + f"module load cdo; cdo -L -remapnn,'{templatefile}' -setmisstonn '{f}' '{f3}'" + ) # Delete template file, which is no longer needed os.remove(templatefile) @@ -226,4 +234,3 @@ def regrid_ggcmi_shdates_arg_process(): args.regrid_output_directory = os.path.realpath(args.regrid_output_directory) return args - diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index e83e4bc888..d7a8b2f57e 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -207,7 +207,7 @@ def import_coord_1d(ds, coordName): abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") return da, len(da) - + def import_coord_2d(ds, coordName, varName): """Import 2-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files From d19abd1ec1777c9ce1ad6f50a71ba44dd18b6d1c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Sun, 17 Dec 2023 18:47:06 -0700 Subject: [PATCH 1981/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 790a472142..3370a2fe7c 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -19,6 +19,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630 810cb346f05ac1aabfff931ab1a2b7b584add241 5933b0018f8e29413e30dda9b906370d147bad45 025d5e7c2e80263717fb029101d65cbbf261c3c4 +a9d96219902cf609636886c7073a84407f450d9a # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From aa463cf2b36886e624996b1a3a9fd534246d5078 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 18 Dec 2023 15:43:24 -0700 Subject: [PATCH 1982/2067] add fates luh2 test to derecho --- cime_config/testdefs/testlist_clm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 7e4adb7df1..dec8cf49d8 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2903,6 +2903,7 @@ + From 8bd8bfeac7207c891dec28c61292bc7c0a598321 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Mon, 18 Dec 2023 18:35:23 -0800 Subject: [PATCH 1983/2067] update changelog --- doc/ChangeLog | 96 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 97 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 67564b6dd0..e515165dc0 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,100 @@ =============================================================== +Tag name: ctsm5.1.dev160 +Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) +Date: Mon Dec 18 18:32:23 MST 2023 +One-line Summary: FATES landuse version 1 + +Purpose and description of changes +---------------------------------- + +This tag enables FATES to utilize the state and transitions data +from the Land Use Harmonization (https://luh.umd.edu/) data sets. +This data has been preprocessed using tooling provided by FATES via +a separate pull request (FATES#1032). A new module has been added +to the dyn_subgrid directory that largely adapts the dynHarvest +module to import and read this minimially processed data, which is +data is passed to fates. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ +CTSM issues fixed (include CTSM Issue #): + #1077 -- Read in full LUH2 dataset for use by FATES + #2283 -- fates wood product flux not being correctly reported during CBalanceCheck endrun diagnostic output + +Notes of particular relevance for users +--------------------------------------- +Changes made to namelist defaults (e.g., changed parameter values): + New namelist item: fluh_timeseries and use_fates_luh + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + FATES landuse testmod, FatesColdLUH2, added + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + build-namelist tests (if CLMBuildNamelist.pm has changed): + + derecho - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- PASS + + fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates--) + derecho ----- OK + izumi ------- OK + + +Answer changes +-------------- + +Changes answers relative to baseline: yes, for FATES only + + Summarize any changes to answers, i.e., + - what code configurations: FATES + - what platforms/compilers: ALL + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff + + The fates tag update incorporates bug fixes and hydraulic mortality fixes, as well as the + restructured disturbance code necessary to accomodate the new landuse transitions capability. + As such, small differences were observed in testmods that engaged specific disturbance modes + or were long enough to trigger other default disturbances (e.g. fire) + +Other details +------------- + +List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): + fates: sci.1.69.0_api.31.0.0 -> fates-sci.1.70.0_api.32.0.0 + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2076 + https://github.com/NGEET/fates/pull/1040 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev159 Originator(s): multiple (slevis (Sam Levis), afoster (Adrianna Foster), erik (Erik Kluzek), wwieder (Will Wieder), glemieux (Greg Lemieux), oleson (Keith Oleson), sacks (Bill Sacks), samrabin (Sam Rabin), santos (Sean Patrick Santos)) Date: Tue 12 Dec 2023 11:10:26 AM MST diff --git a/doc/ChangeSum b/doc/ChangeSum index 4b82850d85..97d4c2269c 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev160 glemieux 12/18/2023 FATES landuse version 1 ctsm5.1.dev159 multiple 12/12/2023 Various BFB fixes and updates ctsm5.1.dev158 erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho From cdf1bf933a3f3a3485710ee2f5285b216384e57b Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 20 Dec 2023 10:47:06 -0700 Subject: [PATCH 1984/2067] updated fates externals to two-stream b4b test branch --- Externals_CLM.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index fba501ee60..61436bf7ba 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -2,7 +2,7 @@ local_path = src/fates protocol = git repo_url = https://github.com/rgknox/fates -branch = two-stream-clean-b4b2 +branch = two-stream-clean-b4b-nohist required = True [externals_description] From 877493fc73969b77cd738bfba97935d3c4d8c504 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 20 Dec 2023 10:50:17 -0700 Subject: [PATCH 1985/2067] Updated call to fates history --- src/utils/clmfates_interfaceMod.F90 | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index a7cf4967f3..176af43923 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2838,14 +2838,7 @@ subroutine wrap_update_hifrq_hist(this, bounds_clump, & dtime = get_step_size_real() ! Update history variables that track these variables - call fates_hist%update_history_hifrq_simple(nc, & - this%fates(nc)%nsites, & - this%fates(nc)%sites, & - this%fates(nc)%bc_in, & - this%fates(nc)%bc_out, & - dtime) - - call fates_hist%update_history_hifrq_multi(nc, & + call fates_hist%update_history_hifrq(nc, & this%fates(nc)%nsites, & this%fates(nc)%sites, & this%fates(nc)%bc_in, & From 8607b250596df72daf965d64902b4acacf5748e3 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Thu, 21 Dec 2023 12:50:35 -0700 Subject: [PATCH 1986/2067] update argument to fates hifrq hist --- src/utils/clmfates_interfaceMod.F90 | 1 - 1 file changed, 1 deletion(-) diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90 index c9a70f0e44..7039884847 100644 --- a/src/utils/clmfates_interfaceMod.F90 +++ b/src/utils/clmfates_interfaceMod.F90 @@ -2885,7 +2885,6 @@ subroutine wrap_update_hifrq_hist(this, bounds_clump, & this%fates(nc)%nsites, & this%fates(nc)%sites, & this%fates(nc)%bc_in, & - this%fates(nc)%bc_out, & dtime) end associate From 554a6ece2f17bd15b28127e7a4cfd2f65fee6860 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 22 Dec 2023 17:18:26 -0700 Subject: [PATCH 1987/2067] Crop tech note: Biofuel stems are also routed to biofuel pools. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 2addbd2507..c4f56542f9 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -508,7 +508,7 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. .. math:: :label: 25.9 From 3d23110fce3d78c4f1e7718b1dd503fbc417e51d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 22 Dec 2023 17:29:59 -0700 Subject: [PATCH 1988/2067] Crop tech note: Add info about residue removal. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 32 ++++++++++++++++--- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index c4f56542f9..92097ccbfb 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -508,7 +508,7 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which put leaf C and N into litter pools only. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. .. math:: :label: 25.9 @@ -516,17 +516,29 @@ Variables track the flow of grain C and N to food and of all other plant pools, CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac +.. math:: + :label: harv_leafc_to_removed_residue + + CF_{leaf,removed\_residue} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} + \right) * (1 - biofuel\_harvfrac) * crop\_residue\_removal\_frac + .. math:: :label: 25.10 CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac +.. math:: + :label: harv_stemc_to_removed_residue + + CF_{livestem,removed\_residue} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} + \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac + .. math:: :label: 25.11 CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem} \Delta t}} \right.} \Delta t} - \right) * \left( 1-biofuel\_harvfrac \right) +CF_{alloc,livestem} + \right) * \left( 1-biofuel\_harvfrac \right) * \left( 1-crop\_residue\_removal\_frac \right) +CF_{alloc,livestem} with corresponding nitrogen fluxes: @@ -536,17 +548,29 @@ with corresponding nitrogen fluxes: NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac +.. math:: + :label: harv_leafn_to_removed_residue + + NF_{leaf,removed\_residue} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} + \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac + .. math:: :label: 25.13 NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac +.. math:: + :label: harv_stemn_to_removed_residue + + NF_{livestem,removed\_residue} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} + \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac + .. math:: :label: 25.14 NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} - \right) * \left( 1-biofuel\_harvfrac \right) + \right) * \left( 1-biofuel\_harvfrac \right) * \left( 1-crop\_residue\_removal\_frac \right) where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction of leaf/livestem for biofuel feedstocks. @@ -606,7 +630,7 @@ where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is | Switchgrass | 0.70 | +----------------------------------+----------------------------+ -Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. The biofuel C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. +Whereas food C and N was formerly transferred to the litter pool, CLM5 routes food C and N to a grain product pool where the C and N decay to the atmosphere over one year, similar in structure to the wood product pools. Biofuel and removed-residue C and N is also routed to the grain product pool and decays to the atmosphere over one year. Additionally, CLM5 accounts for the C and N required for crop seeding by removing the seed C and N from the grain product pool during harvest. The crop seed pool is then used to seed crops in the subsequent year. Annual food crop yields (g dry matter m\ :sup:`-2`) can be calculated by saving the GRAINC_TO_FOOD_ANN variable once per year, then postprocessing with Equation :eq:`25.15`. This calculation assumes that grain C is 45% of the total dry weight. Additionally, harvest is not typically 100% efficient, so analysis needs to assume that harvest efficiency is less---we use 85%. From a4c37415aac3f9d4a96f8aba859d80089facf9ca Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 22 Dec 2023 17:48:58 -0700 Subject: [PATCH 1989/2067] Crop tech note: Don't show separate eqs for livestem and leaf removal. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 42 +++++-------------- 1 file changed, 10 insertions(+), 32 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 92097ccbfb..67c49685e9 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -508,68 +508,46 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`, :eq:`25.10`, :eq:`25.12`, and :eq:`25.13`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9` and :eq:`25.12`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. + +In the equations below, subscript :math:`p` refers to either the leaf or live stem biomass pool. .. math:: :label: 25.9 - CF_{leaf,biofuel} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} + CF_{p,biofuel} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac .. math:: :label: harv_leafc_to_removed_residue - CF_{leaf,removed\_residue} = \left({CS_{leaf} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} + CF_{p,removed\_residue} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p} \Delta t}} \right.} \Delta t} \right) * (1 - biofuel\_harvfrac) * crop\_residue\_removal\_frac -.. math:: - :label: 25.10 - - CF_{livestem,biofuel} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} - \right) * biofuel\_harvfrac - -.. math:: - :label: harv_stemc_to_removed_residue - - CF_{livestem,removed\_residue} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{leaf} \Delta t}} \right.} \Delta t} - \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac - .. math:: :label: 25.11 - CF_{livestem,litter} = \left({CS_{livestem} \mathord{\left/ {\vphantom {CS_{livestem} \Delta t}} \right.} \Delta t} - \right) * \left( 1-biofuel\_harvfrac \right) * \left( 1-crop\_residue\_removal\_frac \right) +CF_{alloc,livestem} + CF_{p,litter} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p} \Delta t}} \right.} \Delta t} + \right) * \left( 1-biofuel\_harvfrac \right) * \left( 1-crop\_residue\_removal\_frac \right) +CF_{p,alloc} with corresponding nitrogen fluxes: .. math:: :label: 25.12 - NF_{leaf,biofuel} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} + NF_{p,biofuel} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p} \Delta t}} \right.} \Delta t} \right) * biofuel\_harvfrac .. math:: :label: harv_leafn_to_removed_residue - NF_{leaf,removed\_residue} = \left({NS_{leaf} \mathord{\left/ {\vphantom {NS_{leaf} \Delta t}} \right.} \Delta t} - \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac - -.. math:: - :label: 25.13 - - NF_{livestem,biofuel} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} - \right) * biofuel\_harvfrac - -.. math:: - :label: harv_stemn_to_removed_residue - - NF_{livestem,removed\_residue} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} + NF_{p,removed\_residue} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p} \Delta t}} \right.} \Delta t} \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac .. math:: :label: 25.14 - NF_{livestem,litter} = \left({NS_{livestem} \mathord{\left/ {\vphantom {NS_{livestem} \Delta t}} \right.} \Delta t} + NF_{p,litter} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p} \Delta t}} \right.} \Delta t} \right) * \left( 1-biofuel\_harvfrac \right) * \left( 1-crop\_residue\_removal\_frac \right) where CF is the carbon flux, CS is stored carbon, NF is the nitrogen flux, NS is stored nitrogen, and :math:`biofuel\_harvfrac` is the harvested fraction of leaf/livestem for biofuel feedstocks. From c05f7284feba11a887c2a364e7072cf5d03a2042 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 22 Dec 2023 18:00:02 -0700 Subject: [PATCH 1990/2067] Crop tech note: Refer to residue removal equations. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 67c49685e9..cefa4b5ccb 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -508,7 +508,7 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9` and :eq:`25.12`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`. :eq:`harv_leafc_to_removed_residue`, :eq:`25.12`, and :eq:`harv_leafn_to_removed_residue`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. In the equations below, subscript :math:`p` refers to either the leaf or live stem biomass pool. From 6d78b7f40a209a8e83b4e0a01007315b76cb8c1e Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 22 Dec 2023 18:01:24 -0700 Subject: [PATCH 1991/2067] Crop tech note: Remove "leaf" from residue removal eq labels. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index cefa4b5ccb..feedd86130 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -508,7 +508,7 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`. :eq:`harv_leafc_to_removed_residue`, :eq:`25.12`, and :eq:`harv_leafn_to_removed_residue`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`. :eq:`harv_c_to_removed_residue`, :eq:`25.12`, and :eq:`harv_n_to_removed_residue`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. In the equations below, subscript :math:`p` refers to either the leaf or live stem biomass pool. @@ -519,7 +519,7 @@ In the equations below, subscript :math:`p` refers to either the leaf or live st \right) * biofuel\_harvfrac .. math:: - :label: harv_leafc_to_removed_residue + :label: harv_c_to_removed_residue CF_{p,removed\_residue} = \left({CS_{p} \mathord{\left/ {\vphantom {CS_{p} \Delta t}} \right.} \Delta t} \right) * (1 - biofuel\_harvfrac) * crop\_residue\_removal\_frac @@ -539,7 +539,7 @@ with corresponding nitrogen fluxes: \right) * biofuel\_harvfrac .. math:: - :label: harv_leafn_to_removed_residue + :label: harv_n_to_removed_residue NF_{p,removed\_residue} = \left({NS_{p} \mathord{\left/ {\vphantom {NS_{p} \Delta t}} \right.} \Delta t} \right) * \left( 1 - biofuel\_harvfrac \right) * crop\_residue\_removal\_frac From 1740a97fb27ae5c53e989397a26ce78942ad41ac Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 22 Dec 2023 18:03:56 -0700 Subject: [PATCH 1992/2067] Crop tech note: Remove "wholly or partially." --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index feedd86130..200e9606d9 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -508,7 +508,7 @@ where :math:`{C}_{leaf}`, :math:`{C}_{stem}`, and :math:`{C}_{froot}` is the car Harvest ''''''' -Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`. :eq:`harv_c_to_removed_residue`, :eq:`25.12`, and :eq:`harv_n_to_removed_residue`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed, wholly or partially, to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. +Variables track the flow of grain C and N to food and of all other plant pools, including live stem C and N, to litter, and to biofuel feedstock. A fraction (determined by the :math:`biofuel\_harvfrac`, defined in :numref:`Table Plant functional type (PFT) parameters for harvested fraction of leaf/livestem for bioenergy production`) of leaf/livestem C and N from bioenergy crops is removed at harvest for biofuels (Equations :eq:`25.9`. :eq:`harv_c_to_removed_residue`, :eq:`25.12`, and :eq:`harv_n_to_removed_residue`), with the remaining portions going to the litter pools (Equations :eq:`20.14)`, :eq:`25.11`, and :eq:`25.14`). Putting live stem C and N into the litter and biofuel pools is in contrast to the approach for unmanaged PFTs which puts live stem C and N into dead stem pools first. Biofuel crop leaf and stem C and N pools are routed to the litter and biofuel pools, in contrast to that of unmanaged PFTs and non-biofuel crops, which under default settings put leaf C and N into litter pools only. All crops can have their leaf and stem pools routed to a "removed residue" pool by setting namelist parameter :math:`crop\_residue\_removal\_frac` to something greater than its default zero. Root C and N pools are routed to the litter pools in the same manner as natural vegetation. In the equations below, subscript :math:`p` refers to either the leaf or live stem biomass pool. From 84182bdb6d0bed0088f905cb756578fe9b0aeb32 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 27 Dec 2023 12:45:17 -0700 Subject: [PATCH 1993/2067] Updated test nl with updated fates history --- .../testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm index e3d311efd4..7f5ece27c8 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm @@ -17,7 +17,7 @@ hist_fincl1 = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF', 'FATES_FABI_SUN_CLLLPF', 'FATES_FABI_SHA_CLLLPF', 'FATES_FABD_SUN_CLLL', 'FATES_FABD_SHA_CLLL', 'FATES_FABI_SUN_CLLL', 'FATES_FABI_SHA_CLLL', 'FATES_PARPROF_DIR_CLLLPF', 'FATES_PARPROF_DIF_CLLLPF', -'FATES_PARPROF_DIR_CLLL', 'FATES_PARPROF_DIF_CLLL', 'FATES_FABD_SUN_TOPLF_CL', +'FATES_FABD_SUN_TOPLF_CL', 'FATES_FABD_SHA_TOPLF_CL', 'FATES_FABI_SUN_TOPLF_CL', 'FATES_FABI_SHA_TOPLF_CL', 'FATES_NET_C_UPTAKE_CLLL', 'FATES_CROWNAREA_CLLL', 'FATES_NPLANT_CANOPY_SZAP', 'FATES_NPLANT_USTORY_SZAP', 'FATES_DDBH_CANOPY_SZAP', 'FATES_DDBH_USTORY_SZAP', From d1f08a7a6cc8707309c102d32eded942816698f7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Dec 2023 11:58:00 -0700 Subject: [PATCH 1994/2067] Add script used to add tillage to paramfile. --- tools/contrib/add_tillage_to_paramsfile.py | 171 +++++++++++++++++++++ 1 file changed, 171 insertions(+) create mode 100644 tools/contrib/add_tillage_to_paramsfile.py diff --git a/tools/contrib/add_tillage_to_paramsfile.py b/tools/contrib/add_tillage_to_paramsfile.py new file mode 100644 index 0000000000..ebea329ef6 --- /dev/null +++ b/tools/contrib/add_tillage_to_paramsfile.py @@ -0,0 +1,171 @@ +import xarray as xr +import numpy as np +import os +import subprocess +import argparse +import sys + +def make_dataarray(np_array, decomp_model, ntill_intensities_max, ndecomp_pools_max, ntill_stages_max): + intensities_dim = xr.IndexVariable( + dims = "ntill_intensities_max", + data = np.arange(ntill_intensities_max), + ) + pools_dim = xr.IndexVariable( + dims = "ndecomp_pools_max", + data = np.arange(ndecomp_pools_max), + ) + stages_dim = xr.IndexVariable( + dims = "ntill_stages_max", + data = np.arange(ntill_stages_max), + ) + + # Name DataArray + if decomp_model.lower() == "mimics": + da_name = "mimics" + elif decomp_model.lower() == "century": + da_name = "bgc" + da_name += "_till_decompk_multipliers" + + da = xr.DataArray( + data = np_array, + dims = { + "ntill_intensities_max": intensities_dim, + "ndecomp_pools_max": pools_dim, + "ntill_stages_max": stages_dim + }, + name = da_name, + attrs = { + "long_name": f"Value by which decomp_k should be multiplied during tillage with {decomp_model} soil", + "units": "unitless", + } + ) + + # netCDF variable needs dimensions reversed from how they're specified in code + da = da.transpose() + + return da + +def main(file_in, + file_out): + # Get git info + thisDir = os.path.dirname(__file__) + git_status = subprocess.run( + ["git", "status"], + capture_output=True, + ) + git_status = git_status.stdout.decode() + repo_is_clean = "working tree clean" in git_status + if not repo_is_clean: + print("WARNING: Repo not clean; will not save params file.") + print(git_status) + git_log = subprocess.run( + ["git", "log", "-1"], + capture_output=True, + ) + git_log = git_log.stdout.decode() + + + # Set up dimensions + ds0 = xr.open_dataset(file_in) + ntill_intensities_max = 2 + ndecomp_pools_max = ds0.dims["ndecomp_pools_max"] + ntill_stages_max = 3 + tillage_shape_ips = (ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) + tillage_shape_ps = (ndecomp_pools_max, ntill_stages_max) + + + # Fill CENTURY array + # Define pool indices + i_litr_min = 0 # 1 in FORTRAN, but Python is 0-indexed + i_met_lit = i_litr_min + i_cel_lit = i_met_lit + 1 + i_lig_lit = i_cel_lit + 1 + i_act_som = i_lig_lit + 1 + i_slo_som = i_act_som + 1 + i_pas_som = i_slo_som + 1 + tillage_century = np.full(tillage_shape_ips, 1.0) + tillage_century_lo = np.full(tillage_shape_ps, 1.0) + tillage_century_lo[i_act_som,:] = np.array([1.0, 1.0, 1.0]) + tillage_century_lo[i_slo_som,:] = np.array([3.0, 1.6, 1.3]) + tillage_century_lo[i_pas_som,:] = np.array([3.0, 1.6, 1.3]) + tillage_century_lo[i_cel_lit,:] = np.array([1.5, 1.5, 1.1]) + tillage_century_lo[i_lig_lit,:] = np.array([1.5, 1.5, 1.1]) + tillage_century[0,:,:] = tillage_century_lo + tillage_century_hi = np.full(tillage_shape_ps, 1.0) + tillage_century_hi[i_act_som,:] = np.array([1.2, 1.0, 1.0]) + tillage_century_hi[i_slo_som,:] = np.array([4.8, 3.5, 2.5]) + tillage_century_hi[i_pas_som,:] = np.array([4.8, 3.5, 2.5]) + tillage_century_hi[i_cel_lit,:] = np.array([1.8, 1.5, 1.1]) + tillage_century_hi[i_lig_lit,:] = np.array([1.8, 1.5, 1.1]) + tillage_century[1,:,:] = tillage_century_hi + + + # Fill MIMICS array + i_litr_min = 1 + i_met_lit = i_litr_min + i_str_lit = i_met_lit + 1 + i_avl_som = i_str_lit + 1 + i_chem_som = i_avl_som + 1 + i_phys_som = i_chem_som + 1 + tillage_mimics = np.full(tillage_shape_ips, 1.0) + tillage_mimics[:,i_avl_som,:] = tillage_century[:,i_act_som,:] + tillage_mimics[:,i_chem_som,:] = tillage_century[:,i_slo_som,:] + tillage_mimics[:,i_phys_som,:] = tillage_century[:,i_pas_som,:] + if not np.array_equal(tillage_century[:,i_cel_lit,:], tillage_century[:,i_lig_lit,:]): + raise RuntimeError("How to combine 2 CENTURY litter pools into 1 MIMICS litter pool?") + tillage_mimics[:,i_str_lit,:] = tillage_century[:,i_cel_lit,:] + + # Make DataArrays + tillage_century_da = make_dataarray( + tillage_century, "CENTURY", + ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) + tillage_mimics_da = make_dataarray( + tillage_mimics, "MIMICS", + ntill_intensities_max, ndecomp_pools_max, ntill_stages_max) + + if not repo_is_clean: + raise RuntimeError("Clean up git repo before trying to save!") + + ds1 = ds0.copy() + ds0.close() + + ds1[tillage_century_da.name] = tillage_century_da + ds1[tillage_mimics_da.name] = tillage_mimics_da + ds1.attrs['latest_git_log'] = git_log + + ds1.to_netcdf(file_out, format="NETCDF3_CLASSIC") + + +if __name__ == "__main__": + ############################### + ### Process input arguments ### + ############################### + parser = argparse.ArgumentParser( + description="Adds tillage parameters to a CLM parameter file (netCDF)." + ) + + # Define arguments + parser.add_argument( + "-i", + "--input-file", + help="Parameter file (netCDF) to which you wish to add tillage parameters.", + type=str, + required=True, + ) + parser.add_argument( + "-o", + "--output-file", + help="Output parameter file.", + type=str, + required=True, + ) + + # Get arguments + args = parser.parse_args(sys.argv[1:]) + + ########### + ### Run ### + ########### + main(os.path.realpath(args.input_file), + os.path.realpath(args.output_file), + ) \ No newline at end of file From d566b6ddd9aa16a87c2a4c6dd5e93da0b9be55bb Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 27 Dec 2023 13:17:40 -0700 Subject: [PATCH 1995/2067] Specify posNOTonfile=.true. in call of ncd_io() for till_decompk_multipliers. --- src/soilbiogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index 60afe52e14..b82b277419 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -146,7 +146,7 @@ subroutine readParams_netcdf(ncid) ! Read off of netcdf file allocate(tempr(ntill_stages_max,ndecomp_pools_max,ntill_stages_max)) - call ncd_io(trim(tString), tempr, 'read', ncid, readvar = readv) + call ncd_io(trim(tString), tempr, 'read', ncid, readvar = readv, posNOTonfile = .true.) if (.not. readv) then call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__)) end if From 693750c828b924234e98a0603d8ec2b2a8ba93ed Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Dec 2023 12:01:43 -0700 Subject: [PATCH 1996/2067] Replace a ntill_stages_max with ntill_intensities_max. --- src/soilbiogeochem/TillageMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/soilbiogeochem/TillageMod.F90 b/src/soilbiogeochem/TillageMod.F90 index b82b277419..4a24daf4c2 100644 --- a/src/soilbiogeochem/TillageMod.F90 +++ b/src/soilbiogeochem/TillageMod.F90 @@ -145,7 +145,7 @@ subroutine readParams_netcdf(ncid) end select ! Read off of netcdf file - allocate(tempr(ntill_stages_max,ndecomp_pools_max,ntill_stages_max)) + allocate(tempr(ntill_intensities_max,ndecomp_pools_max,ntill_stages_max)) call ncd_io(trim(tString), tempr, 'read', ncid, readvar = readv, posNOTonfile = .true.) if (.not. readv) then call endrun(msg=trim(errCode)//trim(tString)//errMsg(__FILE__, __LINE__)) From fffa8515ad78c41010b46afaa9a956544008f3d1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Dec 2023 14:06:45 -0700 Subject: [PATCH 1997/2067] Typo fix in crop Tech Note. --- .../Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index 2addbd2507..accea5e524 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -39,7 +39,7 @@ These updates appear in detail in the sections below. Many also appear in :ref:` Available new features since the CLM5 release ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Addition of bioenergy crops -- Ablity to customize crop calendars (sowing windows/dates, maturity requirements) using stream files +- Ability to customize crop calendars (sowing windows/dates, maturity requirements) using stream files .. _The crop model: From ff610b4441c28845eb0aebe54fab43d43530e45a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Dec 2023 14:54:27 -0700 Subject: [PATCH 1998/2067] Add tillage documentation to Tech Note. --- .../CLM50_Tech_Note_Crop_Irrigation.rst | 7 +++++ .../CLM50_Tech_Note_Decomposition.rst | 29 +++++++++++++++++++ .../References/CLM50_Tech_Note_References.rst | 4 +++ 3 files changed, 40 insertions(+) diff --git a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst index accea5e524..6ac4bc85c6 100755 --- a/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst +++ b/doc/source/tech_note/Crop_Irrigation/CLM50_Tech_Note_Crop_Irrigation.rst @@ -40,6 +40,7 @@ Available new features since the CLM5 release ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - Addition of bioenergy crops - Ability to customize crop calendars (sowing windows/dates, maturity requirements) using stream files +- Cropland soil tillage .. _The crop model: @@ -708,6 +709,12 @@ Separate reproductive pool '''''''''''''''''''''''''' One notable difference between natural vegetation and crops is the presence of reproductive carbon and nitrogen pools. Accounting for the reproductive pools helps determine whether crops are performing reasonably through yield calculations. The reproductive pool is maintained similarly to the leaf, stem, and fine root pools, but allocation of carbon and nitrogen does not begin until the grain fill stage of crop development. Equation :eq:`25.5` describes the carbon and nitrogen allocation coefficients to the reproductive pool. In CLM5BGCCROP, as allocation declines in stem, leaf, and root pools (see section :numref:`Grain fill to harvest`) during the grain fill stage of growth, increasing amounts of carbon and nitrogen are available for grain development. +.. _Tillage: + +Tillage +''''''' +Tillage is represented as an enhancement of the decomposition rate coefficient; see section :numref:`decomp_mgmt_modifiers`. + .. _The irrigation model: The irrigation model diff --git a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst index c0970d2bd5..bf6d52ee45 100644 --- a/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst +++ b/doc/source/tech_note/Decomposition/CLM50_Tech_Note_Decomposition.rst @@ -209,6 +209,35 @@ The combined decomposition rate scalar (:math:`{r}_{total}`,unitless) is: r_{total} =r_{tsoil} r_{water} r_{oxygen} r_{depth} . +.. _decomp_mgmt_modifiers: + +Management modifiers on decomposition rate +-------------------------------------------------- + +Tillage of cropland soil is represented as an additional rate scalar that depends on tillage intensity (default off), soil pool, and time since planting :ref:`(Graham et al., 2021) `. The tillage enhancement is strongest in the first 14 days after planting (idpp < 15), weaker in the next 30 days (15 ≤ idpp < 45), weaker still in the next 30 days (45 ≤ idpp < 75), and nonexistent after that (idpp ≥ 75). + +.. list-table:: Tillage decomposition rate scalars. Values in each cell represent enhancement in different periods of days past planting: [0, 14], [15, 44], [45, 74]. + :header-rows: 1 + + * - \ + - low + - high + * - Litter 2 (cel_lit) + - 1.5, 1.5, 1.1 + - 1.8, 1.5, 1.1 + * - Litter 3 (lig_lit) + - 1.5, 1.5, 1.1 + - 1.8, 1.5, 1.1 + * - SOM 1 (act_som) + - 1.0, 1.0, 1.0 + - 1.2, 1.0, 1.0 + * - SOM 2 (slo_som) + - 3.0, 1.6, 1.3 + - 4.8, 3.5, 2.5 + * - SOM 3 (pas_som) + - 3.0, 1.6, 1.3 + - 4.8, 3.5, 2.5 + N-limitation of Decomposition Fluxes ----------------------------------------- diff --git a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst index a1f84e055b..b824f705bd 100644 --- a/doc/source/tech_note/References/CLM50_Tech_Note_References.rst +++ b/doc/source/tech_note/References/CLM50_Tech_Note_References.rst @@ -463,6 +463,10 @@ Gotangco Castillo C., Levis S., and Thornton P. 2012. Evaluation of the new CNDV Graham, S.T., Famiglietti, J.S., and Maidment, D.R. 1999. Five-minute, 1/2°, and 1° data sets of continental watersheds and river networks for use in regional and global hydrologic and climate system modeling studies. Water Resour. Res. 35:583-587. +.. _Grahametal2021: + +Graham, M. W., Thomas, R. Q., Lombardozzi, D. L., & O'Rourke, M. E. (2021). Modest capacity of no-till farming to offset emissions over 21st century. Environmental Research Letters, 16(5), 054055. doi: 10.1088/1748-9326/abe6c6 + .. _Gravenetal2017: Graven, H., C. E. Allison, D. M. Etheridge, S. Hammer, R. F. Keeling, I. Levin, H. A. J. Meijer, M. Rubino, P. P. Tans, C. M. Trudinger, B. H. Vaughn and J. W. C. White, 2017. Compiled records of carbon isotopes in atmospheric CO2 for historical simulations in CMIP6, Geoscientific Model Development, in review. doi: 10.5194/gmd-2017-166. From c86e1b6c3cd774812982ba8d1d5dfa9c77c55ab0 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Dec 2023 15:16:26 -0700 Subject: [PATCH 1999/2067] Add "Running with tillage" section to User's Guide. --- .../Running-with-tillage.rst | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 doc/source/users_guide/running-special-cases/Running-with-tillage.rst diff --git a/doc/source/users_guide/running-special-cases/Running-with-tillage.rst b/doc/source/users_guide/running-special-cases/Running-with-tillage.rst new file mode 100644 index 0000000000..77309aea07 --- /dev/null +++ b/doc/source/users_guide/running-special-cases/Running-with-tillage.rst @@ -0,0 +1,38 @@ +.. _running-with-tillage: + +.. include:: ../substitutions.rst + +===================== + Running with tillage +===================== + + +Cropland tillage (Sect. :numref:`decomp_mgmt_modifiers`) can be toggled by specifying a value of ``'low'`` (low intensity) or ``'high'`` (high intensity) for the ``tillage_mode`` namelist option. By default this option is ``'off'``. + +Depth of tillage can be changed with the ``max_tillage_depth`` parameter (meters; default 0.26). + +Tillage multipliers for different soil pools and time since planting are defined on the parameter file, in variables ``bgc_till_decompk_multipliers`` (for CENTURY soil) and ``mimics_till_decompk_multipliers`` (for MIMICS soil). These variables were originally added with the script at ``tools/contrib/add_tillage_to_paramsfile.py``, which can be modified as needed to change tillage multipliers. + + +Example: Crop simulation with tillage +------------------------------------- +:: + + > cime/scripts/create_newcase -case IHistClm51BgcCrop_till -res f19_g17_gl4 -compset IHistClm51BgcCrop + + + > cd IHistClm51BgcCrop_till + > ./case.setup + + # turn on tillage ('low' or 'high'; default 'off') + > echo "tillage_mode = 'high'" >> user_nl_clm + +Reverting fixes relative to original tillage implementation +----------------------------------------------------------- + +The current implementation of tillage in CTSM is based on work by :ref:`Graham et al. (2021) `, but with fixes to how days after planting is calculated and to default tillage depth. To run without those changes: + +:: + + > echo "use_original_tillage_phases = .true." >> user_nl_clm + > echo "max_tillage_depth = 0.32" >> user_nl_clm From f344ff1c4446627e82c78ab07ceb444d3d90d277 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 29 Dec 2023 15:37:09 -0700 Subject: [PATCH 2000/2067] Add 'till' testdef. --- cime_config/testdefs/testmods_dirs/clm/till/include_user_mods | 1 + cime_config/testdefs/testmods_dirs/clm/till/shell_commands | 2 ++ cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm | 3 +++ 3 files changed, 6 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/till/include_user_mods create mode 100755 cime_config/testdefs/testmods_dirs/clm/till/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm diff --git a/cime_config/testdefs/testmods_dirs/clm/till/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/till/include_user_mods new file mode 100644 index 0000000000..23ea3745e6 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/till/include_user_mods @@ -0,0 +1 @@ +../crop diff --git a/cime_config/testdefs/testmods_dirs/clm/till/shell_commands b/cime_config/testdefs/testmods_dirs/clm/till/shell_commands new file mode 100755 index 0000000000..6bcde2a588 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/till/shell_commands @@ -0,0 +1,2 @@ +./xmlchange CLM_BLDNML_OPTS="-bgc bgc -crop -ignore_warnings" + diff --git a/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm new file mode 100644 index 0000000000..3e3aff75ef --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm @@ -0,0 +1,3 @@ +tillage_mode = 'high' +paramfile = '/glade/work/samrabin/paramdata/ctsm51_params.c231117.tillage.nc' + From 225a510c2a328380b5bf965e9ed5d832d03905bc Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 30 Dec 2023 18:08:16 -0700 Subject: [PATCH 2001/2067] Change LUH2 test to f09 so there won't be a LUH2 timeseries file for it --- bld/unit_testers/build-namelist_test.pl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 0c7a49d8b5..9b579dd9ce 100755 --- a/bld/unit_testers/build-namelist_test.pl +++ b/bld/unit_testers/build-namelist_test.pl @@ -1061,7 +1061,7 @@ sub cat_and_create_namelistinfile { GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", }, - "useinventorybutnotfile" =>{ options=>"-bgc fates -envxml_dir . -no-megan", + "useinventorybutnotfile" =>{ options=>"--res 0.9x1.25 --bgc fates --envxml_dir . --no-megan", namelst=>"use_fates_luh=.true.", GLC_TWO_WAY_COUPLING=>"FALSE", phys=>"clm4_5", From 6747e8c30652bee5ebb7922c3e653aefad0b5bfa Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 30 Dec 2023 18:09:39 -0700 Subject: [PATCH 2002/2067] Only get a default luh timeseries file if you need one, and ask for one at the model resolution and sim_year_range --- bld/CLMBuildNamelist.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index bb6be82bea..4df42d5e74 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -4368,7 +4368,6 @@ sub setup_logic_fates { if (&value_is_true( $nl_flags->{'use_fates'}) ) { add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'}); - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fluh_timeseries', 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>"4x5"); my @list = ( "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", "use_fates_inventory_init","use_fates_fixed_biogeog","use_fates_nocomp","fates_seeddisp_cadence", "use_fates_logging","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_luh" ); @@ -4418,6 +4417,7 @@ sub setup_logic_fates { if ( defined($nl->get_value($var)) ) { if ( &value_is_true($nl->get_value($var)) ) { $var = "fluh_timeseries"; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'phys'=>$nl_flags->{'phys'}, 'hgrid'=>$nl_flags->{'res'}, 'sim_year_range'=>$nl_flags->{'sim_year_range'}, nofail=>1 ); my $fname = remove_leading_and_trailing_quotes( $nl->get_value($var) ); if ( ! defined($nl->get_value($var)) ) { $log->fatal_error("$var is required when use_fates_luh is set" ); From 4e059c794e7781fb232372f304e539b33f872242 Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 30 Dec 2023 23:22:47 -0700 Subject: [PATCH 2003/2067] LUH file should be for 1850-2000, and add a case for constant until issue #2304 is resolved --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index d8b33ab579..7891361238 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -1574,7 +1574,11 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 -lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc + + +lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc From ebc5cd8806691b1a8930ebe09bdaf3d84acfd49f Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Sat, 30 Dec 2023 23:30:03 -0700 Subject: [PATCH 2004/2067] Update change files --- doc/.ChangeLog_template | 4 ++-- doc/ChangeLog | 12 ++++++++---- doc/ChangeSum | 2 +- 3 files changed, 11 insertions(+), 7 deletions(-) diff --git a/doc/.ChangeLog_template b/doc/.ChangeLog_template index bbd65c8c83..a1170a61cf 100644 --- a/doc/.ChangeLog_template +++ b/doc/.ChangeLog_template @@ -27,8 +27,8 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 -Bugs fixed or introduced ------------------------- +Bugs fixed +---------- [Remove any lines that don't apply. Remove entire section if nothing applies.] CTSM issues fixed (include CTSM Issue #): diff --git a/doc/ChangeLog b/doc/ChangeLog index e515165dc0..925141f310 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev160 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) -Date: Mon Dec 18 18:32:23 MST 2023 +Date: Sat 30 Dec 2023 11:23:47 PM MST One-line Summary: FATES landuse version 1 Purpose and description of changes @@ -33,8 +33,8 @@ Does this tag change answers significantly for any of the following physics conf [ ] clm4_5 -Bugs fixed or introduced ------------------------- +Bugs fixed +---------- CTSM issues fixed (include CTSM Issue #): #1077 -- Read in full LUH2 dataset for use by FATES #2283 -- fates wood product flux not being correctly reported during CBalanceCheck endrun diagnostic output @@ -49,6 +49,10 @@ Notes of particular relevance for developers: Changes to tests or testing: FATES landuse testmod, FatesColdLUH2, added +IMPORTANT NOTE ON BASELINES: + FATES baseline tests have a change in namelists because the fluh_timeseries file is listed in the baselines + but was removed in a last minute change. Compare to baseline other than that change are exact though. + Testing summary: ---------------- @@ -56,7 +60,7 @@ Testing summary: build-namelist tests (if CLMBuildNamelist.pm has changed): - derecho - PASS + derecho - PASS (66 FATES tests differ because of new fates param file) regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): diff --git a/doc/ChangeSum b/doc/ChangeSum index 97d4c2269c..d9da687477 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev160 glemieux 12/18/2023 FATES landuse version 1 + ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1 ctsm5.1.dev159 multiple 12/12/2023 Various BFB fixes and updates ctsm5.1.dev158 erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho ctsm5.1.dev157 samrabin 12/05/2023 Update Externals to work on Derecho From 0d8dc9842097ffd2a2c24f8962b9b764088c90ea Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 4 Jan 2024 09:01:10 -0700 Subject: [PATCH 2005/2067] Update ChangeLog/ChangeSum. --- doc/ChangeLog | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 64 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 925141f310..8e5f54a97f 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,67 @@ =============================================================== +Tag name: ctsm5.1.dev161 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Thu Jan 4 09:00:28 MST 2024 +One-line Summary: Refactor 20-year running means of crop GDD accumulation + +Purpose and description of changes +---------------------------------- + +Three variables track the 20-year running mean of GDD accumulation (base temperatures 0, 8, and 10°C) during the "growing season" (April through September in the Northern Hemisphere, October through March in the Southern Hemisphere). This PR refactors those to use accumulMod, resolving overly-strong weighting of the first few years after a crop becomes active. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[X] clm5_1 + +[X] clm5_0 + +[X] ctsm5_0-nwp + +[X] clm4_5 + + +Bugs fixed +---------- +CTSM issues fixed (include CTSM Issue #): +* Fixes #75. + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- DIFF + izumi ------- DIFF + + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + Summarize any changes to answers, i.e., + - what code configurations: All crop configurations + - what platforms/compilers: All + - nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff/same climate + +GDD020, GDD820, and GDD1020 will differ, most strongly in the first few years after a crop becomes active. This will have downstream effects on lots of variables, since those are used in determining sowing date and maturity requirements. + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +* #2060: Refactor 20-year running means of crop GDD accumulation (https://github.com/ESCOMP/CTSM/pull/2060) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev160 Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov) Date: Sat 30 Dec 2023 11:23:47 PM MST diff --git a/doc/ChangeSum b/doc/ChangeSum index d9da687477..dcd9cdb571 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1 ctsm5.1.dev159 multiple 12/12/2023 Various BFB fixes and updates ctsm5.1.dev158 erik 12/07/2023 First tag with testing moved to Derecho and working PE-layouts for Derecho From 0665754292969721406dce1e25d3bd85bca018f9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 11:53:51 -0700 Subject: [PATCH 2006/2067] Use parameter files with tillage multipliers (*.c240105.nc). --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++--- .../testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm | 2 +- cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm | 1 - 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index a2aeab8562..6206391794 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -484,9 +484,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/ctsm51_params.c231117.nc -lnd/clm2/paramdata/clm50_params.c231117.nc -lnd/clm2/paramdata/clm45_params.c231117.nc +lnd/clm2/paramdata/ctsm51_params.c240105.nc +lnd/clm2/paramdata/clm50_params.c240105.nc +lnd/clm2/paramdata/clm45_params.c240105.nc diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm index 534cbb84b8..4e073859be 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm @@ -1,2 +1,2 @@ -paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c231117.nc' +paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240105.nc' hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr' diff --git a/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm index 3e3aff75ef..f94c6df309 100644 --- a/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/till/user_nl_clm @@ -1,3 +1,2 @@ tillage_mode = 'high' -paramfile = '/glade/work/samrabin/paramdata/ctsm51_params.c231117.tillage.nc' From 2f694738e39a6ba0a25acd62b9c8cc8c6482a5b8 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 12:38:41 -0700 Subject: [PATCH 2007/2067] Remove warning about tillage not being scientifically tested. --- bld/CLMBuildNamelist.pm | 3 --- cime_config/testdefs/testmods_dirs/clm/till/shell_commands | 2 -- 2 files changed, 5 deletions(-) delete mode 100755 cime_config/testdefs/testmods_dirs/clm/till/shell_commands diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 1a8c423652..cdfceb7ccb 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2252,9 +2252,6 @@ sub setup_logic_tillage { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); - if ( $tillage_mode ne "" && $tillage_mode ne "off") { - $log->warning( "Tillage has not yet been scientifically tested." ); - } if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." ); } diff --git a/cime_config/testdefs/testmods_dirs/clm/till/shell_commands b/cime_config/testdefs/testmods_dirs/clm/till/shell_commands deleted file mode 100755 index 6bcde2a588..0000000000 --- a/cime_config/testdefs/testmods_dirs/clm/till/shell_commands +++ /dev/null @@ -1,2 +0,0 @@ -./xmlchange CLM_BLDNML_OPTS="-bgc bgc -crop -ignore_warnings" - From 1e1f2e44ef4df6c7013b7d50da61ae6c50553a5b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 14:08:59 -0700 Subject: [PATCH 2008/2067] Point to raw GGCMI calendar files in *ggcmi_shdates scripts. --- tools/crop_calendars/process_ggcmi_shdates | 2 +- tools/crop_calendars/regrid_ggcmi_shdates | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tools/crop_calendars/process_ggcmi_shdates b/tools/crop_calendars/process_ggcmi_shdates index 82d7660651..587d790e32 100755 --- a/tools/crop_calendars/process_ggcmi_shdates +++ b/tools/crop_calendars/process_ggcmi_shdates @@ -1,6 +1,6 @@ #!/usr/bin/env python3 """ -For description and instructions, please see README. +For description and instructions, please see README. Raw GGCMI sowing and harvest dates are on Derecho and Casper at /glade/campaign/cgd/tss/people/samrabin/raw_ggcmi3_v1.01_nc4/ """ import os diff --git a/tools/crop_calendars/regrid_ggcmi_shdates b/tools/crop_calendars/regrid_ggcmi_shdates index 50ef2636bb..33dafa12c2 100755 --- a/tools/crop_calendars/regrid_ggcmi_shdates +++ b/tools/crop_calendars/regrid_ggcmi_shdates @@ -1,6 +1,6 @@ #!/usr/bin/env python3 """ -For description and instructions, please see README. +For description and instructions, please see README. Raw GGCMI sowing and harvest dates are on Derecho and Casper at /glade/campaign/cgd/tss/people/samrabin/raw_ggcmi3_v1.01_nc4/ """ import os From 675205fc0561c0a2224f3469737e048b09e5d7f2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 15:57:57 -0700 Subject: [PATCH 2009/2067] Update ChangeLog/ChangeSum. --- doc/ChangeLog | 69 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 70 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 8e5f54a97f..6ce0b524b7 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,73 @@ =============================================================== +Tag name: ctsm5.1.dev162 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Fri Jan 5 15:57:23 MST 2024 +One-line Summary: Improvements to processing of crop calendar files + +Purpose and description of changes +---------------------------------- + +In python/ctsm/crop_calendars/, process_ggcmi_shdates.py and regrid_ggcmi_shdates.py are used to convert the raw GGCMI crop calendar files into CTSM-compatible versions. This update fixes some bugs, removes dependencies on the nco utilities, enables the use of surface datasets as template files (in addition to the existing ability to use CTSM output files), and standardizes things for consistency with other CTSM Python tools. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed or introduced +------------------------ + +CTSM issues fixed (include CTSM Issue #): +* Fixes #2167: run_ctsm_py_tests failures at os.getcwd() (https://github.com/ESCOMP/CTSM/issues/2167) + + +Notes of particular relevance for users +--------------------------------------- + +These scripts can now be called using the wrapper scripts in tools/crop_calendars/. + + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: +* Adds test_sys_regrid_ggcmi_shdates and test_unit_utils_import_coord +* Fixes bugs that were causing failures using `python/run_ctsm_py_tests` even when `make all` was fine. + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (derecho) - PASS + + clm_pymods test suite on derecho - PASS + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +* #2292: Improvements to processing of crop calendar files (v2) (https://github.com/ESCOMP/CTSM/pull/2292) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev161 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Thu Jan 4 09:00:28 MST 2024 diff --git a/doc/ChangeSum b/doc/ChangeSum index dcd9cdb571..6a18630673 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev162 samrabin 01/05/2024 Improvements to processing of crop calendar files ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1 ctsm5.1.dev159 multiple 12/12/2023 Various BFB fixes and updates From 336f848ab77e8fa173263f99fcd5cc5aea8c1cd1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 16:22:04 -0700 Subject: [PATCH 2010/2067] *_TO_REMOVEDRESIDUEC outputs now off by default. --- src/biogeochem/CNVegCarbonFluxType.F90 | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/biogeochem/CNVegCarbonFluxType.F90 b/src/biogeochem/CNVegCarbonFluxType.F90 index 3206892ff0..8210bafc97 100644 --- a/src/biogeochem/CNVegCarbonFluxType.F90 +++ b/src/biogeochem/CNVegCarbonFluxType.F90 @@ -987,12 +987,14 @@ subroutine InitHistory(this, bounds, carbon_type) this%leafc_to_removedresiduec_patch(begp:endp) = spval call hist_addfld1d (fname='LEAFC_TO_REMOVEDRESIDUEC', units='gC/m^2/s', & avgflag='A', long_name='leaf C to removed residue C', & - ptr_patch=this%leafc_to_removedresiduec_patch) + ptr_patch=this%leafc_to_removedresiduec_patch, & + default='inactive') this%livestemc_to_removedresiduec_patch(begp:endp) = spval call hist_addfld1d (fname='LIVESTEMC_TO_REMOVEDRESIDUEC', units='gC/m^2/s', & avgflag='A', long_name='livestem C to removed residue C', & - ptr_patch=this%livestemc_to_removedresiduec_patch) + ptr_patch=this%livestemc_to_removedresiduec_patch, & + default='inactive') this%repr_grainc_to_seed_patch(begp:endp,:) = spval this%repr_grainc_to_seed_perharv_patch(begp:endp,:,:) = spval From 142c2c1f01be7e21c1b879d010d3529a016481a1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 16:32:17 -0700 Subject: [PATCH 2011/2067] Enable tillage in two aux_clm tests. --- cime_config/testdefs/testlist_clm.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 5e15eba958..3b51a596b9 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1787,7 +1787,7 @@ - + @@ -2296,7 +2296,7 @@ - + @@ -2305,7 +2305,7 @@ - + From 88519c035b1b9e377d9661cd3fb57f033f6ea186 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 8 Jan 2024 11:39:18 -0700 Subject: [PATCH 2012/2067] Move numpy-dependent Python functions out of utils.py. --- .../crop_calendars/regrid_ggcmi_shdates.py | 3 +- python/ctsm/ctsm_pylib_dependent_utils.py | 48 +++++++++++++++++++ .../ctsm/test/test_unit_utils_import_coord.py | 2 +- python/ctsm/utils.py | 48 ------------------- 4 files changed, 51 insertions(+), 50 deletions(-) create mode 100644 python/ctsm/ctsm_pylib_dependent_utils.py diff --git a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py index 87ba3fb00a..911b2f93a1 100644 --- a/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py +++ b/python/ctsm/crop_calendars/regrid_ggcmi_shdates.py @@ -11,7 +11,8 @@ _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) sys.path.insert(1, _CTSM_PYTHON) -from ctsm.utils import abort, import_coord_1d, import_coord_2d +from ctsm.utils import abort +from ctsm.ctsm_pylib_dependent_utils import import_coord_1d, import_coord_2d from ctsm import ctsm_logging logger = logging.getLogger(__name__) diff --git a/python/ctsm/ctsm_pylib_dependent_utils.py b/python/ctsm/ctsm_pylib_dependent_utils.py new file mode 100644 index 0000000000..82ffa53fe1 --- /dev/null +++ b/python/ctsm/ctsm_pylib_dependent_utils.py @@ -0,0 +1,48 @@ +import numpy as np + +def import_coord_1d(ds, coordName): + """Import 1-d coordinate variable + + Args: + ds (xarray Dataset): Dataset whose coordinate you want to import. + coordName (str): Name of coordinate to import + + Returns: + xarray DataArray: DataArray corresponding to the requested coordinate. + """ + da = ds[coordName] + if len(da.dims) != 1: + abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") + return da, len(da) + + +def import_coord_2d(ds, coordName, varName): + """Import 2-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files + + Args: + ds (xarray Dataset): Dataset whose coordinate you want to import. + coordName (str): Name of coordinate to import + varName (str): Name of variable with dimension coordName + + Returns: + xarray DataArray: 1-d variable that can be used as a coordinate for writing CESM input files + int: Length of that variable + """ + da = ds[varName] + thisDim = [x for x in da.dims if coordName in x] + if len(thisDim) != 1: + abort(f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}") + thisDim = thisDim[0] + otherDim = [x for x in da.dims if coordName not in x] + if len(otherDim) != 1: + abort( + f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" + ) + otherDim = otherDim[0] + da = da.astype(np.float32) + da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) + da = da.assign_coords({coordName: da.values}) + da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] + da.attrs["units"] = da.attrs["units"].replace(" ", "_") + return da, len(da) + diff --git a/python/ctsm/test/test_unit_utils_import_coord.py b/python/ctsm/test/test_unit_utils_import_coord.py index 2844e2dec1..b7ec8f90ec 100755 --- a/python/ctsm/test/test_unit_utils_import_coord.py +++ b/python/ctsm/test/test_unit_utils_import_coord.py @@ -19,7 +19,7 @@ from ctsm import unit_testing from ctsm.path_utils import path_to_ctsm_root -from ctsm.utils import import_coord_1d, import_coord_2d +from ctsm.ctsm_pylib_dependent_utils import import_coord_1d, import_coord_2d # Allow test names that pylint doesn't like; otherwise hard to make them # readable diff --git a/python/ctsm/utils.py b/python/ctsm/utils.py index d7a8b2f57e..8578ea860c 100644 --- a/python/ctsm/utils.py +++ b/python/ctsm/utils.py @@ -6,7 +6,6 @@ import string import re import pdb -import numpy as np from datetime import date, timedelta from getpass import getuser @@ -192,53 +191,6 @@ def write_output(file, file_in, file_out, file_type): file.close() -def import_coord_1d(ds, coordName): - """Import 1-d coordinate variable - - Args: - ds (xarray Dataset): Dataset whose coordinate you want to import. - coordName (str): Name of coordinate to import - - Returns: - xarray DataArray: DataArray corresponding to the requested coordinate. - """ - da = ds[coordName] - if len(da.dims) != 1: - abort(f"Expected 1 dimension for {coordName}; found {len(da.dims)}: {da.dims}") - return da, len(da) - - -def import_coord_2d(ds, coordName, varName): - """Import 2-d latitude or longitude variable from a CESM history file (e.g., name LATIXY or LONGXY) and return it as a 1-d DataArray that can be used as a coordinate for writing CESM input files - - Args: - ds (xarray Dataset): Dataset whose coordinate you want to import. - coordName (str): Name of coordinate to import - varName (str): Name of variable with dimension coordName - - Returns: - xarray DataArray: 1-d variable that can be used as a coordinate for writing CESM input files - int: Length of that variable - """ - da = ds[varName] - thisDim = [x for x in da.dims if coordName in x] - if len(thisDim) != 1: - abort(f"Expected 1 dimension name containing {coordName}; found {len(thisDim)}: {thisDim}") - thisDim = thisDim[0] - otherDim = [x for x in da.dims if coordName not in x] - if len(otherDim) != 1: - abort( - f"Expected 1 dimension name not containing {coordName}; found {len(otherDim)}: {otherDim}" - ) - otherDim = otherDim[0] - da = da.astype(np.float32) - da = da.isel({otherDim: [0]}).squeeze().rename({thisDim: coordName}).rename(coordName) - da = da.assign_coords({coordName: da.values}) - da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] - da.attrs["units"] = da.attrs["units"].replace(" ", "_") - return da, len(da) - - def get_isosplit(iso_string, split): """ Split a string (iso_string) by the character sent in from split From b991db32d8eff61602d04063d9cb9b4eedd037d4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 8 Jan 2024 12:03:33 -0700 Subject: [PATCH 2013/2067] Import abort() in ctsm_pylib_dependent_utils.py. --- python/ctsm/ctsm_pylib_dependent_utils.py | 1 + 1 file changed, 1 insertion(+) diff --git a/python/ctsm/ctsm_pylib_dependent_utils.py b/python/ctsm/ctsm_pylib_dependent_utils.py index 82ffa53fe1..9a04ab4f47 100644 --- a/python/ctsm/ctsm_pylib_dependent_utils.py +++ b/python/ctsm/ctsm_pylib_dependent_utils.py @@ -1,3 +1,4 @@ +from ctsm.utils import abort import numpy as np def import_coord_1d(ds, coordName): From d866510188d26d51bcd6d37239283db690af7e82 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 8 Jan 2024 12:05:05 -0700 Subject: [PATCH 2014/2067] Formatting with black. --- python/ctsm/ctsm_pylib_dependent_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/ctsm_pylib_dependent_utils.py b/python/ctsm/ctsm_pylib_dependent_utils.py index 9a04ab4f47..13ccf7a969 100644 --- a/python/ctsm/ctsm_pylib_dependent_utils.py +++ b/python/ctsm/ctsm_pylib_dependent_utils.py @@ -1,6 +1,7 @@ from ctsm.utils import abort import numpy as np + def import_coord_1d(ds, coordName): """Import 1-d coordinate variable @@ -46,4 +47,3 @@ def import_coord_2d(ds, coordName, varName): da.attrs["long_name"] = "coordinate " + da.attrs["long_name"] da.attrs["units"] = da.attrs["units"].replace(" ", "_") return da, len(da) - From be081997af0ecf9b8780f4e7e80d0c5d9470e21f Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 8 Jan 2024 12:05:39 -0700 Subject: [PATCH 2015/2067] Add previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index 3370a2fe7c..e63de8e099 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -20,6 +20,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630 5933b0018f8e29413e30dda9b906370d147bad45 025d5e7c2e80263717fb029101d65cbbf261c3c4 a9d96219902cf609636886c7073a84407f450d9a +d866510188d26d51bcd6d37239283db690af7e82 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From 1e2fa2264ff19808674f27ebdefa45cc43076ff7 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 10 Jan 2024 09:34:05 -0700 Subject: [PATCH 2016/2067] Added fates two-stream test --- cime_config/testdefs/testlist_clm.xml | 12 ++++++++++++ .../testmods_dirs/clm/FatesColdTwoStream/README | 15 +++++++++++++++ .../clm/FatesColdTwoStream/include_user_mods | 1 + .../clm/FatesColdTwoStream/shell_commands | 8 ++++++++ .../clm/FatesColdTwoStream/user_nl_clm | 1 + 5 files changed, 37 insertions(+) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/README create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index dec8cf49d8..4d5fa6d0ff 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2513,6 +2513,18 @@ + + + + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/README new file mode 100644 index 0000000000..295f8125f3 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/README @@ -0,0 +1,15 @@ +Testing FATES two-stream radiation scheme is activated by switching the fates_rad_model +parameter from 1 to 2. This is all that is needed, both radiation schemes +1) Norman and 2) two-stream use the same optical parameters. + +fates_rad_model + +Note that to avoid exceeding the filename string length maximum, the parameter +file generated on the fly is placed in the $SRCROOT/src/fates/parameter_files +directory. This may still run into problems is the $SRCROOT string is too long. + +Like the test with seed dispersal activation, the main downside of this method is +that this file will require a custom update for every fates parameter file API update. +Addressing CTSM issue #2126 will alleviate +this issue as it will provide the capability to build the fates parameter file on +the fly which with the appropriate values for this test. diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/include_user_mods new file mode 100644 index 0000000000..14f7591b72 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/include_user_mods @@ -0,0 +1 @@ +../FatesCold diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands new file mode 100644 index 0000000000..5d94e5f659 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/shell_commands @@ -0,0 +1,8 @@ +SRCDIR=`./xmlquery SRCROOT --value` +CASEDIR=`./xmlquery CASEROOT --value` +FATESDIR=$SRCDIR/src/fates +FATESPARAMFILE=$CASEDIR/fates_params_twostream.nc + +ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl + +$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm new file mode 100644 index 0000000000..cae5fc2112 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStream/user_nl_clm @@ -0,0 +1 @@ +fates_paramfile = '$CASEROOT/fates_params_twostream.nc' From 6a9af1517523060cf7a76f5299e9c68e7a629d1d Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 10 Jan 2024 09:23:44 -0800 Subject: [PATCH 2017/2067] fix len error for fates landuse timeseries --- src/main/controlMod.F90 | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90 index 44efec4eeb..783c93a473 100644 --- a/src/main/controlMod.F90 +++ b/src/main/controlMod.F90 @@ -786,7 +786,7 @@ subroutine control_spmd() call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier) call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) - call mpi_bcast (fluh_timeseries, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier) + call mpi_bcast (fluh_timeseries, len(fluh_timeseries) , MPI_CHARACTER, 0, mpicom, ier) call mpi_bcast (fates_parteh_mode, 1, MPI_INTEGER, 0, mpicom, ier) call mpi_bcast (fates_seeddisp_cadence, 1, MPI_INTEGER, 0, mpicom, ier) From f9f38b61dd89ed8e79f61f6f6dbe24206303753e Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 10 Jan 2024 10:33:03 -0700 Subject: [PATCH 2018/2067] initial refactoring from refactoring branch --- python/ctsm/site_and_regional/arg_parse.py | 267 +++++++++ python/ctsm/site_and_regional/neon_site.py | 393 ++++++++++++ python/ctsm/site_and_regional/run_neon.py | 658 +-------------------- python/ctsm/test/test_unit_NeonSite.py | 64 ++ python/ctsm/test/test_unit_arg_parse.py | 64 ++ tools/site_and_regional/run_neon | 4 + 6 files changed, 804 insertions(+), 646 deletions(-) create mode 100644 python/ctsm/site_and_regional/arg_parse.py create mode 100755 python/ctsm/site_and_regional/neon_site.py create mode 100755 python/ctsm/test/test_unit_NeonSite.py create mode 100755 python/ctsm/test/test_unit_arg_parse.py diff --git a/python/ctsm/site_and_regional/arg_parse.py b/python/ctsm/site_and_regional/arg_parse.py new file mode 100644 index 0000000000..9025f5dde8 --- /dev/null +++ b/python/ctsm/site_and_regional/arg_parse.py @@ -0,0 +1,267 @@ +""" +Argument parser to use throughout run_neon.py +""" + +import argparse +import datetime +import logging +import os +import sys + +# Get the ctsm util tools and then the cime tools. +_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm import add_cime_to_path + +from CIME import build +from CIME.case import Case +from CIME.utils import safe_copy, expect, parse_args_and_handle_standard_logging_options, setup_standard_logging_options, symlink_force + +from ctsm.utils import parse_isoduration + + +def get_parser(args, description, valid_neon_sites): + """ + Get parser object for this script. + """ + parser = argparse.ArgumentParser( + description=description, formatter_class=argparse.RawDescriptionHelpFormatter + ) + + setup_standard_logging_options(parser) + + parser.print_usage = parser.print_help + + parser.add_argument( + "--neon-sites", + help="4-letter neon site code.", + action="store", + required=False, + choices=valid_neon_sites + ["all"], + dest="neon_sites", + default=["OSBS"], + nargs="+", + ) + + parser.add_argument( + "--base-case", + help=""" + Root Directory of base case build + [default: %(default)s] + """, + action="store", + dest="base_case_root", + type=str, + required=False, + default=None, + ) + + parser.add_argument( + "--output-root", + help=""" + Root output directory of cases + [default: %(default)s] + """, + action="store", + dest="output_root", + type=str, + required=False, + default="CIME_OUTPUT_ROOT as defined in cime", + ) + + parser.add_argument( + "--overwrite", + help=""" + overwrite existing case directories + [default: %(default)s] + """, + action="store_true", + dest="overwrite", + required=False, + default=False, + ) + + parser.add_argument( + "--setup-only", + help=""" + Only setup the requested cases, do not build or run + [default: %(default)s] + """, + action="store_true", + dest="setup_only", + required=False, + default=False, + ) + + parser.add_argument( + "--rerun", + help=""" + If the case exists but does not appear to be complete, restart it. + [default: %(default)s] + """, + action="store_true", + dest="rerun", + required=False, + default=False, + ) + + parser.add_argument( + "--no-batch", + help=""" + Run locally, do not use batch queueing system (if defined for Machine) + [default: %(default)s] + """, + action="store_true", + dest="no_batch", + required=False, + default=False, + ) + + parser.add_argument( + "--run-type", + help=""" + Type of run to do + [default: %(default)s] + """, + choices=["ad", "postad", "transient"], #, "sasu"], + default="transient", + ) + + parser.add_argument( + "--prism", + help=""" + Uses the PRISM reanaylsis precipitation data for the site instead of the NEON data + (only available over Continental US) + """, + action="store_true", + dest="prism", + required=False, + default=False, + ) + + parser.add_argument( + "--experiment", + help=""" + Appends the case name with string for model experiment + """, + action="store", + dest="experiment", + type=str, + required=False, + default=None, + ) + + parser.add_argument( + "--run-length", + help=""" + How long to run (modified ISO 8601 duration) + [default: %(default)s] + """, + required=False, + type=str, + default="0Y", + ) + + #parser.add_argument( + # "--start-date", + # help=""" + # Start date for running CTSM simulation in ISO format. + # [default: %(default)s] + # (currently non-functional) + # """, + # action="store", + # dest="start_date", + # required=False, + # type=datetime.date.fromisoformat, + # default=datetime.datetime.strptime("2018-01-01", "%Y-%m-%d"), + #) + + #parser.add_argument( + # "--end-date", + # help=""" + # End date for running CTSM simulation in ISO format. + # [default: %(default)s] + # """, + # action="store", + # dest="end_date", + # required=False, + # type=datetime.date.fromisoformat, + # default=datetime.datetime.strptime("2021-01-01", "%Y-%m-%d"), + #) + + parser.add_argument( + "--run-from-postad", + help=""" + For transient runs only - should we start from the postad spinup or finidat? + By default start from finidat, if this flag is used the postad run must be available. + """, + action="store_true", + required=False, + default=False, + ) + parser.add_argument( + "--neon-version", + help=""" + Neon data version to use for this simulation. + [default: use the latest data available] + """, + action="store", + dest="user_version", + required=False, + type=str, + choices=["v1", "v2", "v3"], + ) + + args = parse_args_and_handle_standard_logging_options(args, parser) + + if "all" in args.neon_sites: + neon_sites = valid_neon_sites + else: + neon_sites = args.neon_sites + for site in neon_sites: + if site not in valid_neon_sites: + raise ValueError("Invalid site name {}".format(site)) + + if "CIME_OUTPUT_ROOT" in args.output_root: + args.output_root = None + + if args.run_length == "0Y": + if args.run_type == "ad": + run_length = "100Y" + elif args.run_type == "postad": + run_length = "100Y" + else: + # The transient run length is set by cdeps atm buildnml to + # the last date of the available tower data + # this value is not used + run_length = "4Y" + else: + run_length = args.run_length + + run_length = parse_isoduration(run_length) + base_case_root = None + if args.base_case_root: + base_case_root = os.path.abspath(args.base_case_root) + + # Reduce output level for this script unless --debug or + # --verbose is provided on the command line + if not args.debug and not args.verbose: + root_logger = logging.getLogger() + root_logger.setLevel(logging.WARN) + + return ( + neon_sites, + args.output_root, + args.run_type, + args.experiment, + args.prism, + args.overwrite, + run_length, + base_case_root, + args.run_from_postad, + args.setup_only, + args.no_batch, + args.rerun, + args.user_version, + ) diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py new file mode 100755 index 0000000000..873d02fec7 --- /dev/null +++ b/python/ctsm/site_and_regional/neon_site.py @@ -0,0 +1,393 @@ +""" +This module contains the NeonSite class and class functions which are used in run_neon.py +""" + +# Import libraries +import datetime +import glob +import logging +import os +import re +import shutil +import sys +import time + +# Get the ctsm util tools and then the cime tools. +_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) +sys.path.insert(1, _CTSM_PYTHON) + +from ctsm import add_cime_to_path + +from CIME import build +from CIME.case import Case +from CIME.utils import safe_copy, expect, symlink_force + +from ctsm.path_utils import path_to_ctsm_root + +logger = logging.getLogger(__name__) + + +class NeonSite: + """ + A class for encapsulating neon sites. + """ + + def __init__(self, name, start_year, end_year, start_month, end_month, finidat): + self.name = name + self.start_year = int(start_year) + self.end_year = int(end_year) + self.start_month = int(start_month) + self.end_month = int(end_month) + self.cesmroot = path_to_ctsm_root() + self.finidat = finidat + + def __str__(self): + return ( + str(self.__class__) + "\n" + "\n".join((str(item) + " = " for item in (self.__dict__))) + ) + + def build_base_case( + self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False + ): + """ + Function for building a base_case to clone. + To spend less time on building ctsm for the neon cases, + all the other cases are cloned from this case + + Args: + self: + The NeonSite object + base_root (str): + root of the base_case CIME + res (str): + base_case resolution or gridname + compset (str): + base case compset + overwrite (bool) : + Flag to overwrite the case if exists + """ + print("---- building a base case -------") + self.base_case_root = output_root + user_mods_dirs = [os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)] + if not output_root: + output_root = os.getcwd() + case_path = os.path.join(output_root, self.name) + + logger.info("base_case_name : %s", self.name) + logger.info("user_mods_dir : %s", user_mods_dirs[0]) + + if overwrite and os.path.isdir(case_path): + print("Removing the existing case at: {}".format(case_path)) + shutil.rmtree(case_path) + + with Case(case_path, read_only=False) as case: + if not os.path.isdir(case_path): + print("---- creating a base case -------") + + case.create( + case_path, + cesmroot, + compset, + res, + run_unsupported=True, + answer="r", + output_root=output_root, + user_mods_dirs=user_mods_dirs, + driver="nuopc", + ) + + print("---- base case created ------") + + # --change any config for base_case: + # case.set_value("RUN_TYPE","startup") + print("---- base case setup ------") + case.case_setup() + else: + # For existing case check that the compset name is correct + existingcompname = case.get_value("COMPSET") + match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) + if re.search("^HIST", compset, flags=re.IGNORECASE) is None: + expect( + match is None, + """Existing base case is a historical type and should not be + --rerun with the --overwrite option""", + ) + else: + expect( + match is not None, + """Existing base case should be a historical type and is not + --rerun with the --overwrite option""", + ) + # reset the case + case.case_setup(reset=True) + case_path = case.get_value("CASEROOT") + + if setup_only: + return case_path + + print("---- base case build ------") + print("--- This may take a while and you may see WARNING messages ---") + # always walk through the build process to make sure it's up to date. + initial_time = time.time() + build.case_build(case_path, case=case) + end_time = time.time() + total = end_time - initial_time + print("Time required to building the base case: {} s.".format(total)) + # update case_path to be the full path to the base case + return case_path + + def get_batch_query(self, case): + """ + Function for querying the batch queue query command for a case, depending on the + user's batch system. + + Args: + case: + case object + """ + + if case.get_value("BATCH_SYSTEM") == "none": + return "none" + return case.get_value("batch_query") + + def run_case( + self, + base_case_root, + run_type, + prism, + run_length, + user_version, + overwrite=False, + setup_only=False, + no_batch=False, + rerun=False, + experiment=False, + ): + """ + Run case. + + Args: + self + base_case_root: str, opt + file path of base case + run_type: str, opt + transient, post_ad, or ad case, default transient + prism: bool, opt + if True, use PRISM precipitation, default False + run_length: str, opt + length of run, default '4Y' + user_version: str, opt + default 'latest' + overwrite: bool, opt + default False + setup_only: bool, opt + default False; if True, set up but do not run case + no_batch: bool, opt + default False + rerun: bool, opt + default False + experiment: str, opt + name of experiment, default False + """ + user_mods_dirs = [ + os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name) + ] + expect( + os.path.isdir(base_case_root), + "Error base case does not exist in {}".format(base_case_root), + ) + # -- if user gives a version: + if user_version: + version = user_version + else: + version = "latest" + + print("using this version:", version) + + if experiment is not None: + self.name = self.name + "." + experiment + case_root = os.path.abspath(os.path.join(base_case_root, "..", self.name + "." + run_type)) + + rundir = None + if os.path.isdir(case_root): + if overwrite: + print("---- removing the existing case -------") + shutil.rmtree(case_root) + elif rerun: + with Case(case_root, read_only=False) as case: + rundir = case.get_value("RUNDIR") + # For existing case check that the compset name is correct + existingcompname = case.get_value("COMPSET") + match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) + if re.search("^HIST", compset, flags=re.IGNORECASE) is None: + expect( + match is None, + """Existing base case is a historical type and should not be + --rerun with the --overwrite option""", + ) + else: + expect( + match is not None, + """Existing base case should be a historical type and is not + --rerun with the --overwrite option""", + ) + if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): + print("Case {} appears to be complete, not rerunning.".format(case_root)) + elif not setup_only: + print("Resubmitting case {}".format(case_root)) + case.submit(no_batch=no_batch) + print("-----------------------------------") + print("Successfully submitted case!") + batch_query = self.get_batch_query(case) + if batch_query != "none": + print(f"Use {batch_query} to check its run status") + return + else: + logger.warning("Case already exists in %s, not overwritting", case_root) + return + + if run_type == "postad": + adcase_root = case_root.replace(".postad", ".ad") + if not os.path.isdir(adcase_root): + logger.warning("postad requested but no ad case found in %s", adcase_root) + return + + if not os.path.isdir(case_root): + # read_only = False should not be required here + with Case(base_case_root, read_only=False) as basecase: + print("---- cloning the base case in {}".format(case_root)) + # + # EBK: 11/05/2022 -- Note keeping the user_mods_dirs argument is important. Although + # it causes some of the user_nl_* files to have duplicated inputs. It also ensures + # that the shell_commands file is copied, as well as taking care of the DATM inputs. + # See https://github.com/ESCOMP/CTSM/pull/1872#pullrequestreview-1169407493 + # + basecase.create_clone(case_root, keepexe=True, user_mods_dirs=user_mods_dirs) + + with Case(case_root, read_only=False) as case: + if run_type != "transient": + # in order to avoid the complication of leap years, + # we always set the run_length in units of days. + case.set_value("STOP_OPTION", "ndays") + case.set_value("REST_OPTION", "end") + case.set_value("CONTINUE_RUN", False) + case.set_value("NEONVERSION", version) + if prism: + case.set_value("CLM_USRDAT_NAME", "NEON.PRISM") + + if run_type == "ad": + case.set_value("CLM_FORCE_COLDSTART", "on") + case.set_value("CLM_ACCELERATED_SPINUP", "on") + case.set_value("RUN_REFDATE", "0018-01-01") + case.set_value("RUN_STARTDATE", "0018-01-01") + case.set_value("RESUBMIT", 1) + case.set_value("STOP_N", run_length) + + else: + case.set_value("CLM_FORCE_COLDSTART", "off") + case.set_value("CLM_ACCELERATED_SPINUP", "off") + case.set_value("RUN_TYPE", "hybrid") + + if run_type == "postad": + self.set_ref_case(case) + case.set_value("STOP_N", run_length) + + # For transient cases STOP will be set in the user_mod_directory + if run_type == "transient": + if self.finidat: + case.set_value("RUN_TYPE", "startup") + else: + if not self.set_ref_case(case): + return + case.set_value("CALENDAR", "GREGORIAN") + case.set_value("RESUBMIT", 0) + case.set_value("STOP_OPTION", "nmonths") + + if not rundir: + rundir = case.get_value("RUNDIR") + + self.modify_user_nl(case_root, run_type, rundir) + + case.create_namelists() + # explicitly run check_input_data + case.check_all_input_data() + if not setup_only: + case.submit(no_batch=no_batch) + print("-----------------------------------") + print("Successfully submitted case!") + batch_query = self.get_batch_query(case) + if batch_query != "none": + print(f"Use {batch_query} to check its run status") + + def set_ref_case(self, case): + """ + Set an existing case as the reference case, eg for use with spinup. + """ + rundir = case.get_value("RUNDIR") + case_root = case.get_value("CASEROOT") + if case_root.endswith(".postad"): + ref_case_root = case_root.replace(".postad", ".ad") + root = ".ad" + else: + ref_case_root = case_root.replace(".transient", ".postad") + root = ".postad" + if not os.path.isdir(ref_case_root): + logger.warning( + "ERROR: spinup must be completed first, could not find directory %s", ref_case_root + ) + return False + + with Case(ref_case_root) as refcase: + refrundir = refcase.get_value("RUNDIR") + case.set_value("RUN_REFDIR", refrundir) + case.set_value("RUN_REFCASE", os.path.basename(ref_case_root)) + refdate = None + for reffile in glob.iglob(refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root)): + m_searched = re.search(r"(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile) + if m_searched: + refdate = m_searched.group(1) + symlink_force(reffile, os.path.join(rundir, os.path.basename(reffile))) + logger.info("Found refdate of %s", refdate) + if not refdate: + logger.warning("Could not find refcase for %s", case_root) + return False + + for rpfile in glob.iglob(refrundir + "/rpointer*"): + safe_copy(rpfile, rundir) + if not os.path.isdir(os.path.join(rundir, "inputdata")) and os.path.isdir( + os.path.join(refrundir, "inputdata") + ): + symlink_force(os.path.join(refrundir, "inputdata"), os.path.join(rundir, "inputdata")) + + case.set_value("RUN_REFDATE", refdate) + if case_root.endswith(".postad"): + case.set_value("RUN_STARTDATE", refdate) + # NOTE: if start options are set, RUN_STARTDATE should be modified here + return True + + def modify_user_nl(self, case_root, run_type, rundir): + """ + Modify user namelist. If transient, include finidat in user_nl; + Otherwise, adjust user_nl to include different mfilt, nhtfrq, and variables in hist_fincl1. + """ + user_nl_fname = os.path.join(case_root, "user_nl_clm") + user_nl_lines = None + if run_type == "transient": + if self.finidat: + user_nl_lines = [ + "finidat = '{}/inputdata/lnd/ctsm/initdata/{}'".format(rundir, self.finidat) + ] + else: + user_nl_lines = [ + "hist_fincl2 = ''", + "hist_mfilt = 20", + "hist_nhtfrq = -8760", + "hist_empty_htapes = .true.", + """hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC', + 'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO'""", + ] + + if user_nl_lines: + with open(user_nl_fname, "a") as nl_file: + for line in user_nl_lines: + nl_file.write("{}\n".format(line)) diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index a69dc0bdb0..f7ed477cf1 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -47,670 +47,36 @@ # - [ ] Matrix spin-up if (SASU) Eric merged it in # - [ ] Make sure both AD and SASU are not on at the same time -# - [ ] Make sure CIME and other dependencies is checked out. +# - [ ] Make sure CIME and other dependencies are checked out. # Import libraries -import argparse -import datetime import glob import logging import os -import re -import shutil import sys -import time import pandas as pd -from standard_script_setup import * - # Get the ctsm util tools and then the cime tools. _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) +from ctsm.path_utils import path_to_ctsm_root +from ctsm.download_utils import download_file +from ctsm.site_and_regional.arg_parse import get_parser +from ctsm.site_and_regional.neon_site import NeonSite + from ctsm import add_cime_to_path from CIME import build from CIME.case import Case from CIME.utils import safe_copy, expect, symlink_force -from ctsm.path_utils import path_to_ctsm_root -from ctsm.utils import parse_isoduration -from ctsm.download_utils import download_file - from standard_script_setup import * logger = logging.getLogger(__name__) -def get_parser(args, description, valid_neon_sites): - """ - Get parser object for this script. - """ - parser = argparse.ArgumentParser( - description=description, formatter_class=argparse.RawDescriptionHelpFormatter - ) - - CIME.utils.setup_standard_logging_options(parser) - - parser.print_usage = parser.print_help - - parser.add_argument( - "--neon-sites", - help="4-letter neon site code.", - action="store", - required=False, - choices=valid_neon_sites + ["all"], - dest="neon_sites", - default=["OSBS"], - nargs="+", - ) - - parser.add_argument( - "--base-case", - help=""" - Root Directory of base case build - [default: %(default)s] - """, - action="store", - dest="base_case_root", - type=str, - required=False, - default=None, - ) - - parser.add_argument( - "--output-root", - help=""" - Root output directory of cases - [default: %(default)s] - """, - action="store", - dest="output_root", - type=str, - required=False, - default="CIME_OUTPUT_ROOT as defined in cime", - ) - - parser.add_argument( - "--overwrite", - help=""" - overwrite existing case directories - [default: %(default)s] - """, - action="store_true", - dest="overwrite", - required=False, - default=False, - ) - - parser.add_argument( - "--setup-only", - help=""" - Only setup the requested cases, do not build or run - [default: %(default)s] - """, - action="store_true", - dest="setup_only", - required=False, - default=False, - ) - - parser.add_argument( - "--rerun", - help=""" - If the case exists but does not appear to be complete, restart it. - [default: %(default)s] - """, - action="store_true", - dest="rerun", - required=False, - default=False, - ) - - parser.add_argument( - "--no-batch", - help=""" - Run locally, do not use batch queueing system (if defined for Machine) - [default: %(default)s] - """, - action="store_true", - dest="no_batch", - required=False, - default=False, - ) - - parser.add_argument( - "--run-type", - help=""" - Type of run to do - [default: %(default)s] - """, - choices=["ad", "postad", "transient", "sasu"], - default="transient", - ) - - parser.add_argument( - "--prism", - help=""" - Uses the PRISM reanaylsis precipitation data for the site instead of the NEON data - (only available over Continental US) - """, - action="store_true", - dest="prism", - required=False, - default=False, - ) - - parser.add_argument( - "--experiment", - help=""" - Appends the case name with string for model experiment - """, - action="store", - dest="experiment", - type=str, - required=False, - default=None, - ) - - parser.add_argument( - "--run-length", - help=""" - How long to run (modified ISO 8601 duration) - [default: %(default)s] - """, - required=False, - type=str, - default="0Y", - ) - - parser.add_argument( - "--start-date", - help=""" - Start date for running CTSM simulation in ISO format. - [default: %(default)s] - (currently non-functional) - """, - action="store", - dest="start_date", - required=False, - type=datetime.date.fromisoformat, - default=datetime.datetime.strptime("2018-01-01", "%Y-%m-%d"), - ) - - parser.add_argument( - "--end-date", - help=""" - End date for running CTSM simulation in ISO format. - [default: %(default)s] - """, - action="store", - dest="end_date", - required=False, - type=datetime.date.fromisoformat, - default=datetime.datetime.strptime("2021-01-01", "%Y-%m-%d"), - ) - - parser.add_argument( - "--run-from-postad", - help=""" - For transient runs only - should we start from the postad spinup or finidat? - By default start from finidat, if this flag is used the postad run must be available. - """, - action="store_true", - required=False, - default=False, - ) - parser.add_argument( - "--neon-version", - help=""" - Neon data version to use for this simulation. - [default: use the latest data available] - """, - action="store", - dest="user_version", - required=False, - type=str, - choices=["v1", "v2", "v3"], - ) - - args = CIME.utils.parse_args_and_handle_standard_logging_options(args, parser) - - if "all" in args.neon_sites: - neon_sites = valid_neon_sites - else: - neon_sites = args.neon_sites - for site in neon_sites: - if site not in valid_neon_sites: - raise ValueError("Invalid site name {}".format(site)) - - if "CIME_OUTPUT_ROOT" in args.output_root: - args.output_root = None - - if args.run_length == "0Y": - if args.run_type == "ad": - run_length = "100Y" - elif args.run_type == "postad": - run_length = "100Y" - else: - # The transient run length is set by cdeps atm buildnml to - # the last date of the available tower data - # this value is not used - run_length = "4Y" - else: - run_length = args.run_length - - run_length = parse_isoduration(run_length) - base_case_root = None - if args.base_case_root: - base_case_root = os.path.abspath(args.base_case_root) - - # Reduce output level for this script unless --debug or - # --verbose is provided on the command line - if not args.debug and not args.verbose: - root_logger = logging.getLogger() - root_logger.setLevel(logging.WARN) - - return ( - neon_sites, - args.output_root, - args.run_type, - args.experiment, - args.prism, - args.overwrite, - run_length, - base_case_root, - args.run_from_postad, - args.setup_only, - args.no_batch, - args.rerun, - args.user_version, - ) - - -class NeonSite: - """ - A class for encapsulating neon sites. - - ... - - Attributes - ---------- - - Methods - ------- - """ - - def __init__(self, name, start_year, end_year, start_month, end_month, finidat): - self.name = name - self.start_year = int(start_year) - self.end_year = int(end_year) - self.start_month = int(start_month) - self.end_month = int(end_month) - self.cesmroot = path_to_ctsm_root() - self.finidat = finidat - - def __str__(self): - return str(self.__class__) + "\n" + "\n".join((str(item) + " = " for item in self.__dict__)) - - def build_base_case( - self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False - ): - """ - Function for building a base_case to clone. - To spend less time on building ctsm for the neon cases, - all the other cases are cloned from this case - - Args: - self: - The NeonSite object - base_root (str): - root of the base_case CIME - res (str): - base_case resolution or gridname - compset (str): - base case compset - overwrite (bool) : - Flag to overwrite the case if exists - """ - print("---- building a base case -------") - self.base_case_root = output_root - user_mods_dirs = [os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)] - if not output_root: - output_root = os.getcwd() - case_path = os.path.join(output_root, self.name) - - logger.info("base_case_name : %s", self.name) - logger.info("user_mods_dir : %s", user_mods_dirs[0]) - - if overwrite and os.path.isdir(case_path): - print("Removing the existing case at: {}".format(case_path)) - shutil.rmtree(case_path) - - with Case(case_path, read_only=False) as case: - if not os.path.isdir(case_path): - print("---- creating a base case -------") - - case.create( - case_path, - cesmroot, - compset, - res, - run_unsupported=True, - answer="r", - output_root=output_root, - user_mods_dirs=user_mods_dirs, - driver="nuopc", - ) - - print("---- base case created ------") - - # --change any config for base_case: - # case.set_value("RUN_TYPE","startup") - print("---- base case setup ------") - case.case_setup() - else: - # For existing case check that the compset name is correct - existingcompname = case.get_value("COMPSET") - match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) - if re.search("^HIST", compset, flags=re.IGNORECASE) is None: - expect( - match is None, - "Existing base case is a historical type and should " - + "not be -- rerun with the --overwrite option", - ) - else: - expect( - match is not None, - "Existing base case should be a historical type and " - + "is not -- rerun with the --overwrite option", - ) - # reset the case - case.case_setup(reset=True) - case_path = case.get_value("CASEROOT") - - if setup_only: - return case_path - - print("---- base case build ------") - print("--- This may take a while and you may see WARNING messages ---") - # always walk through the build process to make sure it's up to date. - t_0 = time.time() - build.case_build(case_path, case=case) - t_1 = time.time() - total = t_1 - t_0 - print("Time required to building the base case: {} s.".format(total)) - # update case_path to be the full path to the base case - return case_path - - def diff_month(self): - """ - Determine difference between two dates in months - """ - d_1 = datetime.datetime(self.end_year, self.end_month, 1) - d_2 = datetime.datetime(self.start_year, self.start_month, 1) - return (d_1.year - d_2.year) * 12 + d_1.month - d_2.month - - def run_case( - self, - base_case_root, - run_type, - prism, - run_length, - user_version, - overwrite=False, - setup_only=False, - no_batch=False, - rerun=False, - experiment=False, - ): - """ - Run case. - - Args: - self - base_case_root: str, opt - file path of base case - run_type: str, opt - transient, post_ad, or ad case, default transient - prism: bool, opt - if True, use PRISM precipitation, default False - run_length: str, opt - length of run, default '4Y' - user_version: str, opt - default 'latest' - overwrite: bool, opt - default False - setup_only: bool, opt - default False; if True, set up but do not run case - no_batch: bool, opt - default False - rerun: bool, opt - default False - experiment: str, opt - name of experiment, default False - """ - user_mods_dirs = [ - os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name) - ] - expect( - os.path.isdir(base_case_root), - "Error base case does not exist in {}".format(base_case_root), - ) - # -- if user gives a version: - if user_version: - version = user_version - else: - version = "latest" - - print("using this version:", version) - - if experiment is not None: - self.name = self.name + "." + experiment - case_root = os.path.abspath(os.path.join(base_case_root, "..", self.name + "." + run_type)) - - rundir = None - if os.path.isdir(case_root): - if overwrite: - print("---- removing the existing case -------") - shutil.rmtree(case_root) - elif rerun: - with Case(case_root, read_only=False) as case: - rundir = case.get_value("RUNDIR") - # For existing case check that the compset name is correct - existingcompname = case.get_value("COMPSET") - match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) - if re.search("^HIST", compset, flags=re.IGNORECASE) is None: - expect( - match is None, - "Existing base case is a historical type and " - + "should not be -- rerun with the --overwrite option", - ) - else: - expect( - match is not None, - "Existing base case should be a historical type " - + "and is not -- rerun with the --overwrite option", - ) - if os.path.isfile(os.path.join(rundir, "ESMF_Profile.summary")): - print("Case {} appears to be complete, not rerunning.".format(case_root)) - elif not setup_only: - print("Resubmitting case {}".format(case_root)) - case.submit(no_batch=no_batch) - print("-----------------------------------") - print("Successfully submitted case!") - batch_query = self.get_batch_query(case) - if batch_query != "none": - print(f"Use {batch_query} to check its run status") - return - else: - logger.warning("Case already exists in %s, not overwritting.", case_root) - return - - if run_type == "postad": - adcase_root = case_root.replace(".postad", ".ad") - if not os.path.isdir(adcase_root): - logger.warning("postad requested but no ad case found in %s", adcase_root) - return - - if not os.path.isdir(case_root): - # read_only = False should not be required here - with Case(base_case_root, read_only=False) as basecase: - print("---- cloning the base case in {}".format(case_root)) - # - # EBK: 11/05/2022 -- Note keeping the user_mods_dirs argument is important. Although - # it causes some of the user_nl_* files to have duplicated inputs. It also ensures - # that the shell_commands file is copied, as well as taking care of the DATM inputs. - # See https://github.com/ESCOMP/CTSM/pull/1872#pullrequestreview-1169407493 - # - basecase.create_clone(case_root, keepexe=True, user_mods_dirs=user_mods_dirs) - - with Case(case_root, read_only=False) as case: - if run_type != "transient": - # in order to avoid the complication of leap years, - # we always set the run_length in units of days. - case.set_value("STOP_OPTION", "ndays") - case.set_value("REST_OPTION", "end") - case.set_value("CONTINUE_RUN", False) - case.set_value("NEONVERSION", version) - if prism: - case.set_value("CLM_USRDAT_NAME", "NEON.PRISM") - - if run_type == "ad": - case.set_value("CLM_FORCE_COLDSTART", "on") - case.set_value("CLM_ACCELERATED_SPINUP", "on") - case.set_value("RUN_REFDATE", "0018-01-01") - case.set_value("RUN_STARTDATE", "0018-01-01") - case.set_value("RESUBMIT", 1) - case.set_value("STOP_N", run_length) - - else: - case.set_value("CLM_FORCE_COLDSTART", "off") - case.set_value("CLM_ACCELERATED_SPINUP", "off") - case.set_value("RUN_TYPE", "hybrid") - - if run_type == "postad": - self.set_ref_case(case) - case.set_value("STOP_N", run_length) - - # For transient cases STOP will be set in the user_mod_directory - if run_type == "transient": - if self.finidat: - case.set_value("RUN_TYPE", "startup") - else: - if not self.set_ref_case(case): - return - case.set_value("CALENDAR", "GREGORIAN") - case.set_value("RESUBMIT", 0) - case.set_value("STOP_OPTION", "nmonths") - - if not rundir: - rundir = case.get_value("RUNDIR") - - self.modify_user_nl(case_root, run_type, rundir) - - case.create_namelists() - # explicitly run check_input_data - case.check_all_input_data() - if not setup_only: - case.submit(no_batch=no_batch) - print("-----------------------------------") - print("Successfully submitted case!") - batch_query = self.get_batch_query(case) - if batch_query != "none": - print(f"Use {batch_query} to check its run status") - - def set_ref_case(self, case): - """ - Set an existing case as the reference case, eg for use with spinup. - """ - rundir = case.get_value("RUNDIR") - case_root = case.get_value("CASEROOT") - if case_root.endswith(".postad"): - ref_case_root = case_root.replace(".postad", ".ad") - root = ".ad" - else: - ref_case_root = case_root.replace(".transient", ".postad") - root = ".postad" - if not os.path.isdir(ref_case_root): - logger.warning( - "ERROR: spinup must be completed first, could not find directory %s", ref_case_root - ) - return False - - with Case(ref_case_root) as refcase: - refrundir = refcase.get_value("RUNDIR") - case.set_value("RUN_REFDIR", refrundir) - case.set_value("RUN_REFCASE", os.path.basename(ref_case_root)) - refdate = None - for reffile in glob.iglob(refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root)): - mon = re.search(r"(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile) - if mon: - refdate = mon.group(1) - symlink_force(reffile, os.path.join(rundir, os.path.basename(reffile))) - logger.info("Found refdate of %s", refdate) - if not refdate: - logger.warning("Could not find refcase for %s", case_root) - return False - - for rpfile in glob.iglob(refrundir + "/rpointer*"): - safe_copy(rpfile, rundir) - if not os.path.isdir(os.path.join(rundir, "inputdata")) and os.path.isdir( - os.path.join(refrundir, "inputdata") - ): - symlink_force(os.path.join(refrundir, "inputdata"), os.path.join(rundir, "inputdata")) - - case.set_value("RUN_REFDATE", refdate) - if case_root.endswith(".postad"): - case.set_value("RUN_STARTDATE", refdate) - # NOTE: if start options are set, RUN_STARTDATE should be modified here - return True - - def modify_user_nl(self, case_root, run_type, rundir): - """ - Modify user namelist. If transient, include finidat in user_nl; - Otherwise, adjust user_nl to include different mfilt, nhtfrq, and variables in hist_fincl1. - """ - user_nl_fname = os.path.join(case_root, "user_nl_clm") - user_nl_lines = None - if run_type == "transient": - if self.finidat: - user_nl_lines = [ - "finidat = '{}/inputdata/lnd/ctsm/initdata/{}'".format(rundir, self.finidat) - ] - else: - user_nl_lines = [ - "hist_fincl2 = ''", - "hist_mfilt = 20", - "hist_nhtfrq = -8760", - "hist_empty_htapes = .true.", - "hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', " - + "'TOTSOMN', 'TOTVEGC', 'TOTVEGN', 'TLAI', " - + "'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO'", - ] - - if user_nl_lines: - with open(user_nl_fname, "a") as f_d: - for line in user_nl_lines: - f_d.write("{}\n".format(line)) - - -def get_batch_query(case): - """ - Function for querying the batch queue query command for a case, depending on the - user's batch system. - - Args: - case: - case object - """ - - if case.get_value("BATCH_SYSTEM") == "none": - return "none" - return case.get_value("batch_query") - - def check_neon_listing(valid_neon_sites): """ A function to download and parse neon listing file. @@ -742,19 +108,19 @@ def parse_neon_listing(listing_file, valid_neon_sites): available_list = [] - d_f = pd.read_csv(listing_file) + listing_df = pd.read_csv(listing_file) # check for finidat files for transient run - finidatlist = d_f[d_f["object"].str.contains("lnd/ctsm")] + finidatlist = listing_df[listing_df["object"].str.contains("lnd/ctsm")] # -- filter lines with atm/cdep - d_f = d_f[d_f["object"].str.contains("atm/cdeps/")] + listing_df = listing_df[listing_df["object"].str.contains("atm/cdeps/")] # -- split the object str to extract site name - d_f = d_f["object"].str.split("/", expand=True) + listing_df = listing_df["object"].str.split("/", expand=True) # -- groupby site name - grouped_df = d_f.groupby(8) + grouped_df = listing_df.groupby(8) for key, _ in grouped_df: # -- check if it is a valid neon site if any(key in x for x in valid_neon_sites): @@ -787,7 +153,7 @@ def parse_neon_listing(listing_file, valid_neon_sites): start_month = tmp_df2[1].iloc[0] end_month = tmp_df2[1].iloc[-1] - logger.debug("Valid neon site found: %s", site_name) + logger.debug("Valid neon site %s found!", site_name) logger.debug("File version %s", latest_version) logger.debug("start_year=%s", start_year) logger.debug("end_year=%s", end_year) diff --git a/python/ctsm/test/test_unit_NeonSite.py b/python/ctsm/test/test_unit_NeonSite.py new file mode 100755 index 0000000000..2e6c2650e5 --- /dev/null +++ b/python/ctsm/test/test_unit_NeonSite.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python3 +""" +Unit tests for NeonSite + +You can run this by: + python -m unittest test_unit_NeonSite.py +""" + +import unittest +import tempfile +import shutil +import os +import sys + +# -- add python/ctsm to path (needed if we want to run the test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +# pylint: disable=wrong-import-position +from ctsm import unit_testing +from ctsm.site_and_regional.NeonSite import FUNCTION_NAME + +# pylint: disable=invalid-name + + +class TestNeonSite(unittest.TestCase): + """ + Basic class for testing NeonSite.py. + """ + + def setUp(self): + """ + Make /_tempdir for use by these tests. + """ + self._tempdir = tempfile.mkdtemp() + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_function(self): + """ + Test that NeonSite class is working properly... + """ + #valid_neon_sites = ["ABBY", "BART"] + #previous_dir = os.getcwd() + #os.chdir(self._tempdir) # cd to tempdir + #available_list = check_neon_listing(valid_neon_sites) + #self.assertEqual( + # available_list[0].name, "ABBY", "available list of actual sites not as expected" + #) + #self.assertEqual( + # available_list[1].name, "BART", "available list of actual sites not as expected" + #) + # change to previous dir once listing.csv file is created in tempdir and test complete + #os.chdir(previous_dir) + continue + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/python/ctsm/test/test_unit_arg_parse.py b/python/ctsm/test/test_unit_arg_parse.py new file mode 100755 index 0000000000..ab4fc2adb8 --- /dev/null +++ b/python/ctsm/test/test_unit_arg_parse.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python3 +""" +Unit tests for arg_parse + +You can run this by: + python -m unittest test_unit_arg_parse.py +""" + +import unittest +import tempfile +import shutil +import os +import sys + +# -- add python/ctsm to path (needed if we want to run the test stand-alone) +_CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) +sys.path.insert(1, _CTSM_PYTHON) + +# pylint: disable=wrong-import-position +from ctsm import unit_testing +from ctsm.site_and_regional.arg_parse import FUNCTION_NAME + +# pylint: disable=invalid-name + + +class Testarg_parse(unittest.TestCase): + """ + Basic class for testing arg_parse.py. + """ + + def setUp(self): + """ + Make /_tempdir for use by these tests. + """ + self._tempdir = tempfile.mkdtemp() + + def tearDown(self): + """ + Remove temporary directory + """ + shutil.rmtree(self._tempdir, ignore_errors=True) + + def test_function(self): + """ + Test that arg_parse is working properly... + """ + #valid_neon_sites = ["ABBY", "BART"] + #previous_dir = os.getcwd() + #os.chdir(self._tempdir) # cd to tempdir + #available_list = check_neon_listing(valid_neon_sites) + #self.assertEqual( + # available_list[0].name, "ABBY", "available list of actual sites not as expected" + #) + #self.assertEqual( + # available_list[1].name, "BART", "available list of actual sites not as expected" + #) + # change to previous dir once listing.csv file is created in tempdir and test complete + #os.chdir(previous_dir) + continue + + +if __name__ == "__main__": + unit_testing.setup_for_tests() + unittest.main() diff --git a/tools/site_and_regional/run_neon b/tools/site_and_regional/run_neon index ad930f50e3..d2bdfbe786 100755 --- a/tools/site_and_regional/run_neon +++ b/tools/site_and_regional/run_neon @@ -34,6 +34,7 @@ conda activate ctsm_pylib import os import sys +import argparse # -- add python/ctsm to path _CTSM_PYTHON = os.path.join( @@ -41,6 +42,9 @@ _CTSM_PYTHON = os.path.join( ) sys.path.insert(1, _CTSM_PYTHON) +from ctsm.site_and_regional.neon_site import NeonSite +from ctsm.site_and_regional.arg_parse import get_parser + from ctsm.site_and_regional.run_neon import main if __name__ == "__main__": From db2aa54fa3f002e8e302390b1db8040de1f906e2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 10 Jan 2024 10:57:22 -0700 Subject: [PATCH 2019/2067] Add NEON tests to expected fail list. See #2310: NEON tests sometimes fail (https://github.com/ESCOMP/CTSM/issues/2310) --- cime_config/testdefs/ExpectedTestFails.xml | 35 ++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index bea4300aeb..d1f7baf9a2 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -93,6 +93,41 @@ + + + FAIL + #2310 + + + + + + FAIL + #2310 + + + + + + FAIL + #2310 + + + + + + FAIL + #2310 + + + + + + FAIL + #2310 + + + From 77610f18b7e4d184c49dc7f5e60193dc8890dc8b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 10 Jan 2024 11:20:58 -0700 Subject: [PATCH 2020/2067] NEON tests can also fail during RUN. See #2310: NEON tests sometimes fail (https://github.com/ESCOMP/CTSM/issues/2310) --- cime_config/testdefs/ExpectedTestFails.xml | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index d1f7baf9a2..a24299855e 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -98,6 +98,10 @@ FAIL #2310 + + FAIL + #2310 + @@ -105,6 +109,10 @@ FAIL #2310 + + FAIL + #2310 + @@ -112,6 +120,10 @@ FAIL #2310 + + FAIL + #2310 + @@ -119,6 +131,10 @@ FAIL #2310 + + FAIL + #2310 + @@ -126,6 +142,10 @@ FAIL #2310 + + FAIL + #2310 + From c7d7cfc05bfd9464dea2f4977a99a94f39c28cc6 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 5 Jan 2024 16:32:17 -0700 Subject: [PATCH 2021/2067] Enable tillage in two aux_clm tests. (cherry picked from commit 142c2c1f01be7e21c1b879d010d3529a016481a1) --- cime_config/testdefs/testlist_clm.xml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index dec8cf49d8..a3da1e5860 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1787,7 +1787,7 @@ - + @@ -2296,7 +2296,7 @@ - + @@ -2305,7 +2305,7 @@ - + From 3cb6a6ad5fd9218146132b03ab2b9c1e6bae69d9 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 10 Jan 2024 11:50:04 -0700 Subject: [PATCH 2022/2067] Remove tillage from CLM4.5 Intel test. --- cime_config/testdefs/testlist_clm.xml | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index a3da1e5860..9e916b0b58 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2299,15 +2299,23 @@ - - + + + + + + + + + + From 537a422fbaa606c3001fd52fa9be8f7925021a7a Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 10 Jan 2024 11:55:40 -0700 Subject: [PATCH 2023/2067] Add residue removal test. --- cime_config/testdefs/testlist_clm.xml | 2 +- .../testmods_dirs/clm/remove_residues/include_user_mods | 1 + .../testdefs/testmods_dirs/clm/remove_residues/user_nl_clm | 2 ++ 3 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/remove_residues/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/remove_residues/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 9e916b0b58..d6b8d7966b 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2296,7 +2296,7 @@ - + diff --git a/cime_config/testdefs/testmods_dirs/clm/remove_residues/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/remove_residues/include_user_mods new file mode 100644 index 0000000000..23ea3745e6 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/remove_residues/include_user_mods @@ -0,0 +1 @@ +../crop diff --git a/cime_config/testdefs/testmods_dirs/clm/remove_residues/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/remove_residues/user_nl_clm new file mode 100644 index 0000000000..cea306136b --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/remove_residues/user_nl_clm @@ -0,0 +1,2 @@ +crop_residue_removal_frac = 1.0 + From 682072031f6a280e189e62ecce8a94d33342874b Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 10 Jan 2024 11:10:01 -0800 Subject: [PATCH 2024/2067] update seed dispersal test mod to place temp parameter file in case dir --- .../clm/FatesColdSeedDisp/shell_commands | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands index 5d230dc5e9..db5a1f8672 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands @@ -1,11 +1,11 @@ SRCDIR=`./xmlquery SRCROOT --value` CASEDIR=`./xmlquery CASEROOT --value` -FATESROOT=$SRCDIR/src/fates/ -FATESPARAMFILE=$FATESROOT/parameter_files/fates_params_seeddisp_4x5.nc +FATESDIR=$SRCDIR/src/fates/ +FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc -ncgen -o $FATESPARAMFILE $FATESROOT/parameter_files/fates_params_default.cdl +ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl -$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts -$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts -$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_scale --val 1e-05 --allpfts -$FATESROOT/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_shape --val 0.1 --allpfts +$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_fraction --val 0.2 --allpfts +$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_max_dist --val 2500000 --allpfts +$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_scale --val 1e-05 --allpfts +$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_seed_dispersal_pdf_shape --val 0.1 --allpfts From 65d5f8edb4339bdee5bc4104851cfead180830d1 Mon Sep 17 00:00:00 2001 From: Gregory Lemieux Date: Wed, 10 Jan 2024 11:14:11 -0800 Subject: [PATCH 2025/2067] update seed dispersal clm user namelist to look in case dir for temp paramfile --- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index 8e60c6a2e0..ecd1dc8b57 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,3 +1,3 @@ -fates_paramfile = '$SRCROOT/src/fates/parameter_files/fates_params_seeddisp_4x5.nc' +fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc' fates_seeddisp_cadence = 1 hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From 0f321ffc3549f63fce07df3380d31f4e5e659b6c Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 10 Jan 2024 13:04:06 -0700 Subject: [PATCH 2026/2067] Update ChangeLog and ChangeSum --- doc/ChangeLog | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 86 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 6ce0b524b7..05888b353a 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,89 @@ =============================================================== +Tag name: ctsm5.1.dev163 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Wed Jan 10 13:03:34 MST 2024 +One-line Summary: Add tillage and residue removal + +Purpose and description of changes +---------------------------------- + +Adds capability for cropland soil tillage and post-harvest residue removal. + +Tillage: This PR brings in the tillage code written by Sam Levis and Michael Graham and used in Graham et al. (2021, ERL, doi:10.1088/1748-9326/abe6c6). Low- and high-intensity tillage here work by increasing the decomposition rate of different soil carbon pools. These "decomposition multipliers" vary based on soil pool and how long it's been since the crop was planted; they are set with new paramfile variables till_decompk_multipliers and mimics_till_decompk_multipliers. Note that tillage is off by default. + +Residue removal: Adds a parameter hat represents what fraction of post-harvest crop residues (stems and leaves) should be removed to the crop product pool rather than being transferred to litter. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +CTSM issues fixed (include CTSM Issue #): +- Resolves #112 (https://github.com/ESCOMP/CTSM/issues/112) +- Contributes to #2310 (https://github.com/ESCOMP/CTSM/issues/2310) by adding NEON tests to expected failure list) +- run_sys_tests no longer fails on Izumi + + +Notes of particular relevance for users +--------------------------------------- + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): +- Adds parameter tillage_mode with options off (default), low, and high. +- Adds parameter use_original_tillage_phases (false by default; see Add soil tillage for crops #2040). +- Adds parameter max_tillage_depth (cm). +- Adds parameter crop_residue_removal_frac (default 0) + + +Notes of particular relevance for developers: +--------------------------------------------- + +Changes to tests or testing: +- Changes SMS_Ld5.f10_f10_mg37.I1850Clm45BgcCrop.derecho_gnu.clm-crop to use tillage and residue removal; now SMS_Ld5.f10_f10_mg37.I1850Clm45BgcCrop.derecho_gnu.clm-till--clm-remove_residues +- Changes PEM_Ld1.f10_f10_mg37.I2000Clm51BgcCrop.izumi_intel.clm-crop to use tilllage; now PEM_Ld1.f10_f10_mg37.I2000Clm51BgcCrop.izumi_intel.clm-till + + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + (any machine) - PASS + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- PASS + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +- #2311: Add tillage and residue removal (https://github.com/ESCOMP/CTSM/pull/2311) +which is a combination of: +- #2040: Add soil tillage for crops (https://github.com/ESCOMP/CTSM/pull/2040) +- #2297: Add crop residue removal (https://github.com/ESCOMP/CTSM/pull/2297) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev162 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Fri Jan 5 15:57:23 MST 2024 diff --git a/doc/ChangeSum b/doc/ChangeSum index 6a18630673..50bc77377f 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev163 sam 01/10/2024 Add tillage and residue removal ctsm5.1.dev162 samrabin 01/05/2024 Improvements to processing of crop calendar files ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1 From 4a8c4995c7578c82a680b52f54fc785d4138212d Mon Sep 17 00:00:00 2001 From: Teagan King Date: Wed, 10 Jan 2024 14:10:33 -0700 Subject: [PATCH 2027/2067] a few more refactoring updates, formatting & testing --- python/ctsm/site_and_regional/arg_parse.py | 3 +- python/ctsm/site_and_regional/neon_site.py | 3 +- python/ctsm/test/test_unit_NeonSite.py | 16 +++++++++-- python/ctsm/test/test_unit_arg_parse.py | 33 +++++++++++++--------- tools/site_and_regional/run_neon | 3 -- 5 files changed, 35 insertions(+), 23 deletions(-) diff --git a/python/ctsm/site_and_regional/arg_parse.py b/python/ctsm/site_and_regional/arg_parse.py index 9025f5dde8..f61a262911 100644 --- a/python/ctsm/site_and_regional/arg_parse.py +++ b/python/ctsm/site_and_regional/arg_parse.py @@ -13,13 +13,12 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm import add_cime_to_path +from ctsm.utils import parse_isoduration from CIME import build from CIME.case import Case from CIME.utils import safe_copy, expect, parse_args_and_handle_standard_logging_options, setup_standard_logging_options, symlink_force -from ctsm.utils import parse_isoduration - def get_parser(args, description, valid_neon_sites): """ diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py index 873d02fec7..c3fe6e2c68 100755 --- a/python/ctsm/site_and_regional/neon_site.py +++ b/python/ctsm/site_and_regional/neon_site.py @@ -17,13 +17,12 @@ sys.path.insert(1, _CTSM_PYTHON) from ctsm import add_cime_to_path +from ctsm.path_utils import path_to_ctsm_root from CIME import build from CIME.case import Case from CIME.utils import safe_copy, expect, symlink_force -from ctsm.path_utils import path_to_ctsm_root - logger = logging.getLogger(__name__) diff --git a/python/ctsm/test/test_unit_NeonSite.py b/python/ctsm/test/test_unit_NeonSite.py index 2e6c2650e5..3832bf8537 100755 --- a/python/ctsm/test/test_unit_NeonSite.py +++ b/python/ctsm/test/test_unit_NeonSite.py @@ -18,7 +18,7 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing -from ctsm.site_and_regional.NeonSite import FUNCTION_NAME +from ctsm.site_and_regional.neon_site import NeonSite # pylint: disable=invalid-name @@ -40,7 +40,7 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) - def test_function(self): + def test_build_base_case(self): """ Test that NeonSite class is working properly... """ @@ -57,6 +57,18 @@ def test_function(self): # change to previous dir once listing.csv file is created in tempdir and test complete #os.chdir(previous_dir) continue + def test_get_batch_query(self): + """ + """ + continue + def test_run_case(self): + """ + """ + continue + def test_modify_user_nl(self): + """ + """ + continue if __name__ == "__main__": diff --git a/python/ctsm/test/test_unit_arg_parse.py b/python/ctsm/test/test_unit_arg_parse.py index ab4fc2adb8..f7cf7a97ff 100755 --- a/python/ctsm/test/test_unit_arg_parse.py +++ b/python/ctsm/test/test_unit_arg_parse.py @@ -11,6 +11,7 @@ import shutil import os import sys +import glob # -- add python/ctsm to path (needed if we want to run the test stand-alone) _CTSM_PYTHON = os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir) @@ -18,7 +19,8 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing -from ctsm.site_and_regional.arg_parse import FUNCTION_NAME +from ctsm.site_and_regional.arg_parse import get_parser +from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name @@ -44,19 +46,22 @@ def test_function(self): """ Test that arg_parse is working properly... """ - #valid_neon_sites = ["ABBY", "BART"] - #previous_dir = os.getcwd() - #os.chdir(self._tempdir) # cd to tempdir - #available_list = check_neon_listing(valid_neon_sites) - #self.assertEqual( - # available_list[0].name, "ABBY", "available list of actual sites not as expected" - #) - #self.assertEqual( - # available_list[1].name, "BART", "available list of actual sites not as expected" - #) - # change to previous dir once listing.csv file is created in tempdir and test complete - #os.chdir(previous_dir) - continue + sys.argv = ["--neon-sites ['ABBY']"] + #arguments= ["--neon-sites", "ABBY"] #, "--experiment 'test'", '--overwrite False', '--setup-only True', '--rerun False', '--run-type ad', '--experiment test'] + description='' + cesmroot = path_to_ctsm_root() + valid_neon_sites = glob.glob( + os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", "[!d]*") + ) + valid_neon_sites = sorted([v.split("/")[-1] for v in valid_neon_sites]) + parsed_arguments = get_parser(sys.argv, description, valid_neon_sites) + + print(parsed_arguments) + self.assertEqual( + parsed_arguments[0], "ABBY", "arguments not processed as expected" + ) + # TODO: Still need to figure out correct formatting to get argument recognized properly! + # TODO: Also it might be useful to add in a number of fake arguments to check that they all work... if __name__ == "__main__": diff --git a/tools/site_and_regional/run_neon b/tools/site_and_regional/run_neon index d2bdfbe786..e20189a374 100755 --- a/tools/site_and_regional/run_neon +++ b/tools/site_and_regional/run_neon @@ -42,9 +42,6 @@ _CTSM_PYTHON = os.path.join( ) sys.path.insert(1, _CTSM_PYTHON) -from ctsm.site_and_regional.neon_site import NeonSite -from ctsm.site_and_regional.arg_parse import get_parser - from ctsm.site_and_regional.run_neon import main if __name__ == "__main__": From 9413b6225372cc89ff33c7ba823244b0d511e549 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Wed, 10 Jan 2024 14:12:06 -0700 Subject: [PATCH 2028/2067] Added two-stream nocomp test --- cime_config/testdefs/testlist_clm.xml | 10 +++++++++- .../clm/FatesColdTwoStreamNoCompFixedBioGeo/README | 3 +++ .../include_user_mods | 1 + .../FatesColdTwoStreamNoCompFixedBioGeo/shell_commands | 8 ++++++++ .../FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm | 2 ++ 5 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/README create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/include_user_mods create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands create mode 100644 cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 486611981c..2d4dd17b75 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -2532,7 +2532,15 @@ - + + + + + + + + + diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/README b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/README new file mode 100644 index 0000000000..d2c2269fae --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/README @@ -0,0 +1,3 @@ +This tests two-stream radiation crossed with fixed biogeography and nocomp, for +a description of how two-stream is turned on for tests see +FatesColdTwoStream/README diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/include_user_mods new file mode 100644 index 0000000000..17d5840e8c --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/include_user_mods @@ -0,0 +1 @@ +../FatesColdNoComp diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands new file mode 100644 index 0000000000..5d94e5f659 --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/shell_commands @@ -0,0 +1,8 @@ +SRCDIR=`./xmlquery SRCROOT --value` +CASEDIR=`./xmlquery CASEROOT --value` +FATESDIR=$SRCDIR/src/fates +FATESPARAMFILE=$CASEDIR/fates_params_twostream.nc + +ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl + +$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_rad_model --val 2 --allpfts diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm new file mode 100644 index 0000000000..362dfa4a5e --- /dev/null +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdTwoStreamNoCompFixedBioGeo/user_nl_clm @@ -0,0 +1,2 @@ +fates_paramfile = '$CASEROOT/fates_params_twostream.nc' +use_fates_fixed_biogeog=.true. \ No newline at end of file From d3bffbe824c05ff919f80b1ece6d3e641696ff12 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 11 Jan 2024 11:12:56 -0700 Subject: [PATCH 2029/2067] included new tests for NeonSite class --- python/ctsm/site_and_regional/neon_site.py | 1 + python/ctsm/test/test_unit_NeonSite.py | 95 ++++++++++++++++++---- tools/site_and_regional/run_neon | 1 - 3 files changed, 78 insertions(+), 19 deletions(-) diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py index c3fe6e2c68..2e92e7f04b 100755 --- a/python/ctsm/site_and_regional/neon_site.py +++ b/python/ctsm/site_and_regional/neon_site.py @@ -390,3 +390,4 @@ def modify_user_nl(self, case_root, run_type, rundir): with open(user_nl_fname, "a") as nl_file: for line in user_nl_lines: nl_file.write("{}\n".format(line)) + diff --git a/python/ctsm/test/test_unit_NeonSite.py b/python/ctsm/test/test_unit_NeonSite.py index 3832bf8537..1520a58426 100755 --- a/python/ctsm/test/test_unit_NeonSite.py +++ b/python/ctsm/test/test_unit_NeonSite.py @@ -10,6 +10,7 @@ import tempfile import shutil import os +import glob import sys # -- add python/ctsm to path (needed if we want to run the test stand-alone) @@ -42,33 +43,91 @@ def tearDown(self): def test_build_base_case(self): """ - Test that NeonSite class is working properly... + Test that NeonSite class' build_base_case is working properly... """ - #valid_neon_sites = ["ABBY", "BART"] - #previous_dir = os.getcwd() - #os.chdir(self._tempdir) # cd to tempdir - #available_list = check_neon_listing(valid_neon_sites) - #self.assertEqual( - # available_list[0].name, "ABBY", "available list of actual sites not as expected" - #) - #self.assertEqual( - # available_list[1].name, "BART", "available list of actual sites not as expected" - #) - # change to previous dir once listing.csv file is created in tempdir and test complete - #os.chdir(previous_dir) - continue + #neonsite = NeonSite(ADD SOME PARAMETERS) + #neonsite.build_base_case(ARGUMENTS) # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? + #CHECK IF ACTS AS EXPECTED + #continue + def test_get_batch_query(self): """ + Test that NeonSite class' get_batch_query is working properly... """ - continue + #neonsite = NeonSite(ADD SOME PARAMETERS) + #neonsite.get_batch_query(ARGUMENTS) + #CHECK IF ACTS AS EXPECTED + #continue + # ALSO DOESN'T SEEM THE MOST REASONABLE TO TEST + def test_run_case(self): """ + Test that NeonSite class' run_case is working properly... """ - continue - def test_modify_user_nl(self): + #neonsite = NeonSite(ADD SOME PARAMETERS) + #neonsite.run_case(ARGUMENTS) # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? + #CHECK IF ACTS AS EXPECTED + #continue + + def test_modify_user_nl_transient(self): """ + Test that NeonSite class' modify_user_nl is correctly adding lines to namelist for transient cases """ - continue + # NeonSite parameters: + name = 'ABBY' + start_year = 2020 + end_year = 2021 + start_month = 1 + end_month = 12 + #finidat = None + finidat = 'dummy_finidat' + + # modify_user_nl parameters: + case_root = self._tempdir + run_type = 'transient' + rundir = '' + + # update namelist + neonsite = NeonSite(name, start_year, end_year, start_month, end_month, finidat) + modified_neonsite = neonsite.modify_user_nl(case_root, run_type, rundir) + + # gather file contents for test + new_nl_file = open(glob.glob(case_root+'/*')[0], "r") + lines_read = new_nl_file.readlines()[0] + new_nl_file.close() + + # assertion + self.assertEqual(lines_read, "finidat = '/inputdata/lnd/ctsm/initdata/dummy_finidat'\n", 'transient case has unexpected nl') + + def test_modify_user_nl_ad(self): + """ + Test that NeonSite class' modify_user_nl is correctly adding lines to namelist for ad cases + """ + # NeonSite parameters: + name = 'ABBY' + start_year = 2020 + end_year = 2021 + start_month = 1 + end_month = 12 + #finidat = None + finidat = 'dummy_finidat' + + # modify_user_nl parameters: + case_root = self._tempdir + run_type = 'ad' + rundir = '' + + # update namelist + neonsite = NeonSite(name, start_year, end_year, start_month, end_month, finidat) + modified_neonsite = neonsite.modify_user_nl(case_root, run_type, rundir) + + # gather file contents for test + new_nl_file = open(glob.glob(case_root+'/*')[0], "r") + lines_read = new_nl_file.readlines()[1] + new_nl_file.close() + + # assertion + self.assertEqual(lines_read, "hist_mfilt = 20\n", 'ad case has unexpected nl') if __name__ == "__main__": diff --git a/tools/site_and_regional/run_neon b/tools/site_and_regional/run_neon index e20189a374..ad930f50e3 100755 --- a/tools/site_and_regional/run_neon +++ b/tools/site_and_regional/run_neon @@ -34,7 +34,6 @@ conda activate ctsm_pylib import os import sys -import argparse # -- add python/ctsm to path _CTSM_PYTHON = os.path.join( From 88372f2b9fc1a3947f0b743268f93f51f6aff4d4 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Thu, 11 Jan 2024 13:39:06 -0700 Subject: [PATCH 2030/2067] black/pylint --- python/ctsm/site_and_regional/arg_parse.py | 38 +-------- python/ctsm/site_and_regional/neon_site.py | 3 +- python/ctsm/site_and_regional/run_neon.py | 10 +-- python/ctsm/test/test_unit_arg_parse.py | 11 ++- ...nit_NeonSite.py => test_unit_neon_site.py} | 80 ++++++++++--------- tools/site_and_regional/run_neon | 1 + 6 files changed, 59 insertions(+), 84 deletions(-) rename python/ctsm/test/{test_unit_NeonSite.py => test_unit_neon_site.py} (54%) diff --git a/python/ctsm/site_and_regional/arg_parse.py b/python/ctsm/site_and_regional/arg_parse.py index f61a262911..f45fef041c 100644 --- a/python/ctsm/site_and_regional/arg_parse.py +++ b/python/ctsm/site_and_regional/arg_parse.py @@ -3,7 +3,6 @@ """ import argparse -import datetime import logging import os import sys @@ -12,13 +11,11 @@ _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) +#pylint: disable=wrong-import-position, import-error, unused-import from ctsm import add_cime_to_path from ctsm.utils import parse_isoduration - -from CIME import build -from CIME.case import Case -from CIME.utils import safe_copy, expect, parse_args_and_handle_standard_logging_options, setup_standard_logging_options, symlink_force - +from CIME.utils import parse_args_and_handle_standard_logging_options +from CIME.utils import setup_standard_logging_options def get_parser(args, description, valid_neon_sites): """ @@ -123,7 +120,7 @@ def get_parser(args, description, valid_neon_sites): Type of run to do [default: %(default)s] """, - choices=["ad", "postad", "transient"], #, "sasu"], + choices=["ad", "postad", "transient"], # , "sasu"], default="transient", ) @@ -162,33 +159,6 @@ def get_parser(args, description, valid_neon_sites): default="0Y", ) - #parser.add_argument( - # "--start-date", - # help=""" - # Start date for running CTSM simulation in ISO format. - # [default: %(default)s] - # (currently non-functional) - # """, - # action="store", - # dest="start_date", - # required=False, - # type=datetime.date.fromisoformat, - # default=datetime.datetime.strptime("2018-01-01", "%Y-%m-%d"), - #) - - #parser.add_argument( - # "--end-date", - # help=""" - # End date for running CTSM simulation in ISO format. - # [default: %(default)s] - # """, - # action="store", - # dest="end_date", - # required=False, - # type=datetime.date.fromisoformat, - # default=datetime.datetime.strptime("2021-01-01", "%Y-%m-%d"), - #) - parser.add_argument( "--run-from-postad", help=""" diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py index 2e92e7f04b..8881ef5867 100755 --- a/python/ctsm/site_and_regional/neon_site.py +++ b/python/ctsm/site_and_regional/neon_site.py @@ -3,7 +3,6 @@ """ # Import libraries -import datetime import glob import logging import os @@ -16,6 +15,7 @@ _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) +#pylint: disable=wrong-import-position, import-error, unused-import from ctsm import add_cime_to_path from ctsm.path_utils import path_to_ctsm_root @@ -390,4 +390,3 @@ def modify_user_nl(self, case_root, run_type, rundir): with open(user_nl_fname, "a") as nl_file: for line in user_nl_lines: nl_file.write("{}\n".format(line)) - diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index f7ed477cf1..3802133a64 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -61,18 +61,16 @@ _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) +# pylint: disable=wrong-import-position from ctsm.path_utils import path_to_ctsm_root from ctsm.download_utils import download_file from ctsm.site_and_regional.arg_parse import get_parser from ctsm.site_and_regional.neon_site import NeonSite -from ctsm import add_cime_to_path - -from CIME import build -from CIME.case import Case -from CIME.utils import safe_copy, expect, symlink_force - +# pylint: disable=import-error from standard_script_setup import * +# the above import is need to set CIMEROOT environment variable +# TODO: figure out what specifically needs to be imported (not '*') logger = logging.getLogger(__name__) diff --git a/python/ctsm/test/test_unit_arg_parse.py b/python/ctsm/test/test_unit_arg_parse.py index f7cf7a97ff..1da6b63f77 100755 --- a/python/ctsm/test/test_unit_arg_parse.py +++ b/python/ctsm/test/test_unit_arg_parse.py @@ -47,8 +47,9 @@ def test_function(self): Test that arg_parse is working properly... """ sys.argv = ["--neon-sites ['ABBY']"] - #arguments= ["--neon-sites", "ABBY"] #, "--experiment 'test'", '--overwrite False', '--setup-only True', '--rerun False', '--run-type ad', '--experiment test'] - description='' + # arguments= ["--neon-sites", "ABBY"] #, "--experiment 'test'", '--overwrite False', + # '--setup-only True', '--rerun False', '--run-type ad', '--experiment test'] + description = "" cesmroot = path_to_ctsm_root() valid_neon_sites = glob.glob( os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", "[!d]*") @@ -57,11 +58,9 @@ def test_function(self): parsed_arguments = get_parser(sys.argv, description, valid_neon_sites) print(parsed_arguments) - self.assertEqual( - parsed_arguments[0], "ABBY", "arguments not processed as expected" - ) + self.assertEqual(parsed_arguments[0], "ABBY", "arguments not processed as expected") # TODO: Still need to figure out correct formatting to get argument recognized properly! - # TODO: Also it might be useful to add in a number of fake arguments to check that they all work... + # TODO: It might be useful to add a number of arguments to check that they all work... if __name__ == "__main__": diff --git a/python/ctsm/test/test_unit_NeonSite.py b/python/ctsm/test/test_unit_neon_site.py similarity index 54% rename from python/ctsm/test/test_unit_NeonSite.py rename to python/ctsm/test/test_unit_neon_site.py index 1520a58426..a75326e185 100755 --- a/python/ctsm/test/test_unit_NeonSite.py +++ b/python/ctsm/test/test_unit_neon_site.py @@ -3,7 +3,7 @@ Unit tests for NeonSite You can run this by: - python -m unittest test_unit_NeonSite.py + python -m unittest test_unit_neon_site.py """ import unittest @@ -45,89 +45,97 @@ def test_build_base_case(self): """ Test that NeonSite class' build_base_case is working properly... """ - #neonsite = NeonSite(ADD SOME PARAMETERS) - #neonsite.build_base_case(ARGUMENTS) # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? - #CHECK IF ACTS AS EXPECTED - #continue + # neonsite = NeonSite(ADD SOME PARAMETERS) + # neonsite.build_base_case(ARGUMENTS) + # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? + # CHECK IF ACTS AS EXPECTED + # continue def test_get_batch_query(self): """ Test that NeonSite class' get_batch_query is working properly... """ - #neonsite = NeonSite(ADD SOME PARAMETERS) - #neonsite.get_batch_query(ARGUMENTS) - #CHECK IF ACTS AS EXPECTED - #continue + # neonsite = NeonSite(ADD SOME PARAMETERS) + # neonsite.get_batch_query(ARGUMENTS) + # CHECK IF ACTS AS EXPECTED + # continue # ALSO DOESN'T SEEM THE MOST REASONABLE TO TEST def test_run_case(self): """ Test that NeonSite class' run_case is working properly... """ - #neonsite = NeonSite(ADD SOME PARAMETERS) - #neonsite.run_case(ARGUMENTS) # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? - #CHECK IF ACTS AS EXPECTED - #continue + # neonsite = NeonSite(ADD SOME PARAMETERS) + # neonsite.run_case(ARGUMENTS) + # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? + # CHECK IF ACTS AS EXPECTED + # continue def test_modify_user_nl_transient(self): """ - Test that NeonSite class' modify_user_nl is correctly adding lines to namelist for transient cases + Test that modify_user_nl is correctly adding lines to namelist for transient cases """ # NeonSite parameters: - name = 'ABBY' + name = "ABBY" start_year = 2020 end_year = 2021 start_month = 1 end_month = 12 - #finidat = None - finidat = 'dummy_finidat' + # finidat = None + finidat = "dummy_finidat" # modify_user_nl parameters: case_root = self._tempdir - run_type = 'transient' - rundir = '' + run_type = "transient" + rundir = "" - # update namelist - neonsite = NeonSite(name, start_year, end_year, start_month, end_month, finidat) - modified_neonsite = neonsite.modify_user_nl(case_root, run_type, rundir) + # create NeonSite object and update namelist + NeonSite(name, start_year, end_year, start_month, end_month, finidat).modify_user_nl( + case_root, run_type, rundir + ) # gather file contents for test - new_nl_file = open(glob.glob(case_root+'/*')[0], "r") + new_nl_file = open(glob.glob(case_root + "/*")[0], "r") lines_read = new_nl_file.readlines()[0] new_nl_file.close() - + # assertion - self.assertEqual(lines_read, "finidat = '/inputdata/lnd/ctsm/initdata/dummy_finidat'\n", 'transient case has unexpected nl') + self.assertEqual( + lines_read, + "finidat = '/inputdata/lnd/ctsm/initdata/dummy_finidat'\n", + "transient case has unexpected nl", + ) def test_modify_user_nl_ad(self): """ - Test that NeonSite class' modify_user_nl is correctly adding lines to namelist for ad cases + Test that modify_user_nl is correctly adding lines to namelist for ad cases """ # NeonSite parameters: - name = 'ABBY' + name = "ABBY" start_year = 2020 end_year = 2021 start_month = 1 end_month = 12 - #finidat = None - finidat = 'dummy_finidat' + # finidat = None + finidat = "dummy_finidat" # modify_user_nl parameters: case_root = self._tempdir - run_type = 'ad' - rundir = '' + run_type = "ad" + rundir = "" - # update namelist - neonsite = NeonSite(name, start_year, end_year, start_month, end_month, finidat) - modified_neonsite = neonsite.modify_user_nl(case_root, run_type, rundir) + # create NeonSite object and update namelist + NeonSite(name, start_year, end_year, start_month, end_month, finidat).modify_user_nl( + case_root, run_type, rundir + ) # gather file contents for test - new_nl_file = open(glob.glob(case_root+'/*')[0], "r") + new_nl_file = open(glob.glob(case_root + "/*")[0], "r") lines_read = new_nl_file.readlines()[1] new_nl_file.close() # assertion - self.assertEqual(lines_read, "hist_mfilt = 20\n", 'ad case has unexpected nl') + self.assertEqual(lines_read, "hist_mfilt = 20\n", "ad case has unexpected nl") if __name__ == "__main__": diff --git a/tools/site_and_regional/run_neon b/tools/site_and_regional/run_neon index ad930f50e3..2a3091f6a6 100755 --- a/tools/site_and_regional/run_neon +++ b/tools/site_and_regional/run_neon @@ -41,6 +41,7 @@ _CTSM_PYTHON = os.path.join( ) sys.path.insert(1, _CTSM_PYTHON) +#pylint: disable=import-error, wrong-import-position from ctsm.site_and_regional.run_neon import main if __name__ == "__main__": From 1c12818024c2d9dfe79481364775e87984646bf0 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Fri, 12 Jan 2024 13:35:49 -0700 Subject: [PATCH 2031/2067] mostly testing updates --- python/ctsm/site_and_regional/arg_parse.py | 6 ++++- python/ctsm/site_and_regional/neon_site.py | 14 +++++----- python/ctsm/site_and_regional/run_neon.py | 4 +-- python/ctsm/test/test_unit_arg_parse.py | 12 ++++----- python/ctsm/test/test_unit_neon_site.py | 30 ---------------------- tools/site_and_regional/run_neon | 2 +- 6 files changed, 20 insertions(+), 48 deletions(-) diff --git a/python/ctsm/site_and_regional/arg_parse.py b/python/ctsm/site_and_regional/arg_parse.py index f45fef041c..99f184dd62 100644 --- a/python/ctsm/site_and_regional/arg_parse.py +++ b/python/ctsm/site_and_regional/arg_parse.py @@ -11,12 +11,13 @@ _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) -#pylint: disable=wrong-import-position, import-error, unused-import +# pylint: disable=wrong-import-position, import-error, unused-import, wrong-import-order from ctsm import add_cime_to_path from ctsm.utils import parse_isoduration from CIME.utils import parse_args_and_handle_standard_logging_options from CIME.utils import setup_standard_logging_options + def get_parser(args, description, valid_neon_sites): """ Get parser object for this script. @@ -209,9 +210,12 @@ def get_parser(args, description, valid_neon_sites): run_length = args.run_length run_length = parse_isoduration(run_length) + base_case_root = None if args.base_case_root: base_case_root = os.path.abspath(args.base_case_root) + if not os.path.exists(base_case_root): + raise ValueError("Base case root does not exist: {}".format(base_case_root)) # Reduce output level for this script unless --debug or # --verbose is provided on the command line diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py index 8881ef5867..31ae78f5ad 100755 --- a/python/ctsm/site_and_regional/neon_site.py +++ b/python/ctsm/site_and_regional/neon_site.py @@ -15,7 +15,7 @@ _CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python")) sys.path.insert(1, _CTSM_PYTHON) -#pylint: disable=wrong-import-position, import-error, unused-import +# pylint: disable=wrong-import-position, import-error, unused-import, wrong-import-order from ctsm import add_cime_to_path from ctsm.path_utils import path_to_ctsm_root @@ -26,6 +26,7 @@ logger = logging.getLogger(__name__) +# pylint: disable=too-many-instance-attributes class NeonSite: """ A class for encapsulating neon sites. @@ -40,11 +41,6 @@ def __init__(self, name, start_year, end_year, start_month, end_month, finidat): self.cesmroot = path_to_ctsm_root() self.finidat = finidat - def __str__(self): - return ( - str(self.__class__) + "\n" + "\n".join((str(item) + " = " for item in (self.__dict__))) - ) - def build_base_case( self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False ): @@ -66,7 +62,9 @@ def build_base_case( Flag to overwrite the case if exists """ print("---- building a base case -------") + # pylint: disable=attribute-defined-outside-init self.base_case_root = output_root + # pylint: enable=attribute-defined-outside-init user_mods_dirs = [os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)] if not output_root: output_root = os.getcwd() @@ -135,6 +133,7 @@ def build_base_case( # update case_path to be the full path to the base case return case_path + # pylint: disable=no-self-use def get_batch_query(self, case): """ Function for querying the batch queue query command for a case, depending on the @@ -149,6 +148,7 @@ def get_batch_query(self, case): return "none" return case.get_value("batch_query") + # pylint: disable=too-many-statements def run_case( self, base_case_root, @@ -218,12 +218,14 @@ def run_case( # For existing case check that the compset name is correct existingcompname = case.get_value("COMPSET") match = re.search("^HIST", existingcompname, flags=re.IGNORECASE) + # pylint: disable=undefined-variable if re.search("^HIST", compset, flags=re.IGNORECASE) is None: expect( match is None, """Existing base case is a historical type and should not be --rerun with the --overwrite option""", ) + # pylint: enable=undefined-variable else: expect( match is not None, diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 3802133a64..31c5bbafb4 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -67,10 +67,8 @@ from ctsm.site_and_regional.arg_parse import get_parser from ctsm.site_and_regional.neon_site import NeonSite -# pylint: disable=import-error +# pylint: disable=import-error, wildcard-import, wrong-import-order from standard_script_setup import * -# the above import is need to set CIMEROOT environment variable -# TODO: figure out what specifically needs to be imported (not '*') logger = logging.getLogger(__name__) diff --git a/python/ctsm/test/test_unit_arg_parse.py b/python/ctsm/test/test_unit_arg_parse.py index 1da6b63f77..71254eee60 100755 --- a/python/ctsm/test/test_unit_arg_parse.py +++ b/python/ctsm/test/test_unit_arg_parse.py @@ -46,9 +46,7 @@ def test_function(self): """ Test that arg_parse is working properly... """ - sys.argv = ["--neon-sites ['ABBY']"] - # arguments= ["--neon-sites", "ABBY"] #, "--experiment 'test'", '--overwrite False', - # '--setup-only True', '--rerun False', '--run-type ad', '--experiment test'] + sys.argv = ["arg_parse", "--neon-sites", "ABBY", "--experiment", "test", "--run-type", "ad"] description = "" cesmroot = path_to_ctsm_root() valid_neon_sites = glob.glob( @@ -57,10 +55,10 @@ def test_function(self): valid_neon_sites = sorted([v.split("/")[-1] for v in valid_neon_sites]) parsed_arguments = get_parser(sys.argv, description, valid_neon_sites) - print(parsed_arguments) - self.assertEqual(parsed_arguments[0], "ABBY", "arguments not processed as expected") - # TODO: Still need to figure out correct formatting to get argument recognized properly! - # TODO: It might be useful to add a number of arguments to check that they all work... + self.assertEqual(parsed_arguments[0][0], "ABBY", "arguments not processed as expected") + self.assertEqual(parsed_arguments[3], "test", "arguments not processed as expected") + self.assertEqual(parsed_arguments[4], False, "arguments not processed as expected") + self.assertEqual(parsed_arguments[2], "ad", "arguments not processed as expected") if __name__ == "__main__": diff --git a/python/ctsm/test/test_unit_neon_site.py b/python/ctsm/test/test_unit_neon_site.py index a75326e185..4828718272 100755 --- a/python/ctsm/test/test_unit_neon_site.py +++ b/python/ctsm/test/test_unit_neon_site.py @@ -41,36 +41,6 @@ def tearDown(self): """ shutil.rmtree(self._tempdir, ignore_errors=True) - def test_build_base_case(self): - """ - Test that NeonSite class' build_base_case is working properly... - """ - # neonsite = NeonSite(ADD SOME PARAMETERS) - # neonsite.build_base_case(ARGUMENTS) - # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? - # CHECK IF ACTS AS EXPECTED - # continue - - def test_get_batch_query(self): - """ - Test that NeonSite class' get_batch_query is working properly... - """ - # neonsite = NeonSite(ADD SOME PARAMETERS) - # neonsite.get_batch_query(ARGUMENTS) - # CHECK IF ACTS AS EXPECTED - # continue - # ALSO DOESN'T SEEM THE MOST REASONABLE TO TEST - - def test_run_case(self): - """ - Test that NeonSite class' run_case is working properly... - """ - # neonsite = NeonSite(ADD SOME PARAMETERS) - # neonsite.run_case(ARGUMENTS) - # NOT SURE WE ACTUALLY WANT TO DO THIS DUE TO TIME CONSTRAINTS? - # CHECK IF ACTS AS EXPECTED - # continue - def test_modify_user_nl_transient(self): """ Test that modify_user_nl is correctly adding lines to namelist for transient cases diff --git a/tools/site_and_regional/run_neon b/tools/site_and_regional/run_neon index 2a3091f6a6..ffc3be2af7 100755 --- a/tools/site_and_regional/run_neon +++ b/tools/site_and_regional/run_neon @@ -41,7 +41,7 @@ _CTSM_PYTHON = os.path.join( ) sys.path.insert(1, _CTSM_PYTHON) -#pylint: disable=import-error, wrong-import-position +# pylint: disable=import-error, wrong-import-position from ctsm.site_and_regional.run_neon import main if __name__ == "__main__": From 674715e8939ced6b038c54ec5dd905fade142c7b Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 16 Jan 2024 11:14:43 -0700 Subject: [PATCH 2032/2067] Changed test configuration to be gnu and debug to trigger errors --- cime_config/testdefs/ExpectedTestFails.xml | 7 +++++++ cime_config/testdefs/testlist_clm.xml | 8 ++++---- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index a24299855e..16fff0e71e 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -150,6 +150,13 @@ + + + FAIL + #2321 + + + FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 2d4dd17b75..c915552748 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3131,13 +3131,13 @@ - + - - + + - + From 2d2df94cdc536ca80a925c3dde517516bea9d7c0 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 16 Jan 2024 12:20:31 -0700 Subject: [PATCH 2033/2067] rename arg_parse --- .../{arg_parse.py => neon_arg_parse.py} | 0 python/ctsm/site_and_regional/run_neon.py | 2 +- ...it_arg_parse.py => test_unit_neon_arg_parse.py} | 14 +++++++------- 3 files changed, 8 insertions(+), 8 deletions(-) rename python/ctsm/site_and_regional/{arg_parse.py => neon_arg_parse.py} (100%) rename python/ctsm/test/{test_unit_arg_parse.py => test_unit_neon_arg_parse.py} (80%) diff --git a/python/ctsm/site_and_regional/arg_parse.py b/python/ctsm/site_and_regional/neon_arg_parse.py similarity index 100% rename from python/ctsm/site_and_regional/arg_parse.py rename to python/ctsm/site_and_regional/neon_arg_parse.py diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py index 31c5bbafb4..72bf3fdfb4 100755 --- a/python/ctsm/site_and_regional/run_neon.py +++ b/python/ctsm/site_and_regional/run_neon.py @@ -64,7 +64,7 @@ # pylint: disable=wrong-import-position from ctsm.path_utils import path_to_ctsm_root from ctsm.download_utils import download_file -from ctsm.site_and_regional.arg_parse import get_parser +from ctsm.site_and_regional.neon_arg_parse import get_parser from ctsm.site_and_regional.neon_site import NeonSite # pylint: disable=import-error, wildcard-import, wrong-import-order diff --git a/python/ctsm/test/test_unit_arg_parse.py b/python/ctsm/test/test_unit_neon_arg_parse.py similarity index 80% rename from python/ctsm/test/test_unit_arg_parse.py rename to python/ctsm/test/test_unit_neon_arg_parse.py index 71254eee60..863c7e3e5a 100755 --- a/python/ctsm/test/test_unit_arg_parse.py +++ b/python/ctsm/test/test_unit_neon_arg_parse.py @@ -1,9 +1,9 @@ #!/usr/bin/env python3 """ -Unit tests for arg_parse +Unit tests for neon_arg_parse You can run this by: - python -m unittest test_unit_arg_parse.py + python -m unittest test_unit_neon_arg_parse.py """ import unittest @@ -19,15 +19,15 @@ # pylint: disable=wrong-import-position from ctsm import unit_testing -from ctsm.site_and_regional.arg_parse import get_parser +from ctsm.site_and_regional.neon_arg_parse import get_parser from ctsm.path_utils import path_to_ctsm_root # pylint: disable=invalid-name -class Testarg_parse(unittest.TestCase): +class Test_neon_arg_parse(unittest.TestCase): """ - Basic class for testing arg_parse.py. + Basic class for testing neon_arg_parse.py. """ def setUp(self): @@ -44,9 +44,9 @@ def tearDown(self): def test_function(self): """ - Test that arg_parse is working properly... + Test that neon_arg_parse is properly reading arguments... """ - sys.argv = ["arg_parse", "--neon-sites", "ABBY", "--experiment", "test", "--run-type", "ad"] + sys.argv = ["neon_arg_parse", "--neon-sites", "ABBY", "--experiment", "test", "--run-type", "ad"] description = "" cesmroot = path_to_ctsm_root() valid_neon_sites = glob.glob( From a59c6e12d5d7cb2bd438bda5f536a9e668e022e4 Mon Sep 17 00:00:00 2001 From: Teagan King Date: Tue, 16 Jan 2024 12:32:19 -0700 Subject: [PATCH 2034/2067] black arg_parse unit test --- python/ctsm/test/test_unit_neon_arg_parse.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/python/ctsm/test/test_unit_neon_arg_parse.py b/python/ctsm/test/test_unit_neon_arg_parse.py index 863c7e3e5a..7bae337709 100755 --- a/python/ctsm/test/test_unit_neon_arg_parse.py +++ b/python/ctsm/test/test_unit_neon_arg_parse.py @@ -46,7 +46,15 @@ def test_function(self): """ Test that neon_arg_parse is properly reading arguments... """ - sys.argv = ["neon_arg_parse", "--neon-sites", "ABBY", "--experiment", "test", "--run-type", "ad"] + sys.argv = [ + "neon_arg_parse", + "--neon-sites", + "ABBY", + "--experiment", + "test", + "--run-type", + "ad", + ] description = "" cesmroot = path_to_ctsm_root() valid_neon_sites = glob.glob( From a32174ec7fd37030351d59d41ad8d1c82d52d094 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 16 Jan 2024 13:33:34 -0700 Subject: [PATCH 2035/2067] reverting PEM seed dispersal test (fates) to use srcdir --- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands | 2 +- .../testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands index db5a1f8672..94a832af25 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/shell_commands @@ -1,7 +1,7 @@ SRCDIR=`./xmlquery SRCROOT --value` CASEDIR=`./xmlquery CASEROOT --value` FATESDIR=$SRCDIR/src/fates/ -FATESPARAMFILE=$CASEDIR/fates_params_seeddisp_4x5.nc +FATESPARAMFILE=$SRCDIR/fates_params_seeddisp_4x5.nc ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm index ecd1dc8b57..e8d24253c1 100644 --- a/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdSeedDisp/user_nl_clm @@ -1,3 +1,3 @@ -fates_paramfile = '$CASEROOT/fates_params_seeddisp_4x5.nc' +fates_paramfile = '$SRCROOT/fates_params_seeddisp_4x5.nc' fates_seeddisp_cadence = 1 hist_fincl1 = 'FATES_SEEDS_IN_GRIDCELL_PF', 'FATES_SEEDS_OUT_GRIDCELL_PF' From 38d505b00785180279e03679da6f1bc681e3f528 Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 16 Jan 2024 15:19:31 -0700 Subject: [PATCH 2036/2067] Updated fates external to new tag --- Externals_CLM.cfg | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg index 61436bf7ba..a6fae66356 100644 --- a/Externals_CLM.cfg +++ b/Externals_CLM.cfg @@ -1,8 +1,8 @@ [fates] local_path = src/fates protocol = git -repo_url = https://github.com/rgknox/fates -branch = two-stream-clean-b4b-nohist +repo_url = https://github.com/NGEET/fates +tag = sci.1.71.0_api.33.0.0 required = True [externals_description] From f81961a73d35d0e5240f28634ad0d38b6e86712b Mon Sep 17 00:00:00 2001 From: Ryan Knox Date: Tue, 16 Jan 2024 17:41:24 -0500 Subject: [PATCH 2037/2067] update change logs --- doc/ChangeLog | 95 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 96 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index 05888b353a..37df88efc2 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,99 @@ =============================================================== +Tag name: ctsm5.1.dev164 +Originator(s): rgknox (Ryan Knox) +Date: Tue Jan 16 05:28:37 PM EST 2024 +One-line Summary: Compatibility and tests for FATES 2-Stream + +Purpose and description of changes +---------------------------------- + +This set of changes enables compatibility and testing for FATES two-stream radiation scattering. Two stream radiation is selected by setting the FATES parameter file variable fates_rad_mod = 2. This is an alternative to Norman radiation. The FATES default radiation model will continue to be Norman for the time being, but is expected to transition to two-stream in the near future. + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +CTSM issues fixed (include CTSM Issue #): 2305 + +Known bugs introduced in this tag (include issue #): none, but testing was modified to catch a pre-existing bug via test: SMS_D_Ld3.f09_g17.I2000Clm51FatesSpCruRsGs.derecho_gnu.clm-FatesColdSatPhen_prescribed. This has been documented in CTSM issue #2321 + +Notes of particular relevance for users +--------------------------------------- + +Caveats for users (e.g., need to interpolate initial conditions): none + +Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): none + +Changes made to namelist defaults (e.g., changed parameter values): none + +Changes to the datasets (e.g., parameter, surface or initial files): none + +Substantial timing or memory changes: +[e.g., check PFS test in the test suite and look at timings, if you +expect possible significant timing changes] + +If a fates user does opt to use two-stream radiation, they should expect changes in simulation time compared with norman radiation. This difference varies and is somewhere between equal or 20% slower at a maximum. Most tests seemed to be about 10-15% slower for regions with high vegetation demographic diversity. + +Notes of particular relevance for developers: +--------------------------------------------- +NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide +[Remove any lines that don't apply. Remove entire section if nothing applies.] + +Caveats for developers (e.g., code that is duplicated that requires double maintenance): + +Changes to tests or testing: + +New tests were added to the fates and aux_clm regression suites, with suffix clm-FatesColdTwoStream. One of them uses fixed giogeography and no cross-pft competition. + +Testing summary: +---------------- + + regular tests, baseline: ctsm5.1.dev163 + + derecho ----- OK + izumi ------- OK + + fates tests: baseline: fates-sci.1.70.0_api.32.0.0-ctsm5.1.dev163 + derecho ----- OK + izumi ------- + + any other testing (give details below): + +If the tag used for baseline comparisons was NOT the previous tag, note that here: + + +Answer changes +-------------- + +All answers are B4B with baselines mentioned above, except for one fates variable: FATES_RAD_ERROR. This variable was changed to report the maximum of VIS and NIR, instead of just VIS. A follow up set of changes will change the dimension of this variable. This change was expected. + + +Other details +------------- + +This set of changes is synchronized with the new FATES tag: sci.1.71.0_api.33.0.0 +PR: https://github.com/NGEET/fates/pull/1141 + + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev163 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) Date: Wed Jan 10 13:03:34 MST 2024 diff --git a/doc/ChangeSum b/doc/ChangeSum index 50bc77377f..214c9535bd 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev164 rgknox 01/16/2024 Compatibility and tests for FATES 2-Stream ctsm5.1.dev163 sam 01/10/2024 Add tillage and residue removal ctsm5.1.dev162 samrabin 01/05/2024 Improvements to processing of crop calendar files ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation From f0d80175b973f6b322acab7df1e7c994e84c5a5e Mon Sep 17 00:00:00 2001 From: Erik Kluzek Date: Wed, 17 Jan 2024 12:39:39 -0700 Subject: [PATCH 2038/2067] Update change files --- doc/ChangeLog | 4 ++-- doc/ChangeSum | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 37df88efc2..5b4a214880 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev164 Originator(s): rgknox (Ryan Knox) -Date: Tue Jan 16 05:28:37 PM EST 2024 +Date: Wed 17 Jan 2024 12:38:18 PM MST One-line Summary: Compatibility and tests for FATES 2-Stream Purpose and description of changes @@ -72,7 +72,7 @@ Testing summary: fates tests: baseline: fates-sci.1.70.0_api.32.0.0-ctsm5.1.dev163 derecho ----- OK - izumi ------- + izumi ------- (being run after tag was made) any other testing (give details below): diff --git a/doc/ChangeSum b/doc/ChangeSum index 214c9535bd..dee25d848c 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev164 rgknox 01/16/2024 Compatibility and tests for FATES 2-Stream + ctsm5.1.dev164 rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream ctsm5.1.dev163 sam 01/10/2024 Add tillage and residue removal ctsm5.1.dev162 samrabin 01/05/2024 Improvements to processing of crop calendar files ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation From a5e8382425e98ce888958b562102185d98eed2d2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 17 Jan 2024 15:27:36 -0700 Subject: [PATCH 2039/2067] Answer-changing merge tag: turn Meier2022 on and bring in #2212 --- bld/namelist_files/namelist_defaults_ctsm.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 456d99ac2a..fcb9bc2074 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -498,7 +498,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case). + +Meier2022 .true. .false. From 96466e868cd3a674c81a5fdeb929dc99664155a1 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 18 Jan 2024 11:44:23 -0700 Subject: [PATCH 2040/2067] Making Meier2022 the default for ctsm5.1 --- bld/namelist_files/namelist_defaults_ctsm.xml | 3 --- 1 file changed, 3 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index fcb9bc2074..fd5b18f132 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -498,11 +498,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case). - -Meier2022 .true. .false. From 1ca0860e63db55f5a75e5089d6da6b3a6ae37fdf Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 18 Jan 2024 13:20:28 -0700 Subject: [PATCH 2041/2067] Add subr. setup_logic_roughness_methods to CLMBuildNamelist.pm --- bld/CLMBuildNamelist.pm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 17c46f9bef..14a3a2ddb5 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1571,6 +1571,7 @@ sub process_namelist_inline_logic { setup_logic_irrigate($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_start_type($opts, $nl_flags, $nl); setup_logic_decomp_performance($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_roughness_methods($opts, $nl_flags, $definition, $defaults, $nl, $physv); setup_logic_snicar_methods($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_snow($opts, $nl_flags, $definition, $defaults, $nl); setup_logic_glacier($opts, $nl_flags, $definition, $defaults, $nl, $envxml_ref); @@ -2002,6 +2003,25 @@ sub setup_logic_decomp_performance { #------------------------------------------------------------------------------- +sub setup_logic_roughness_methods { + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; + + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'z0param_method', + 'phys'=>$nl_flags->{'phys'} ); + + my $var = remove_leading_and_trailing_quotes( $nl->get_value("z0param_method") ); + if ( $var ne "Meier2022" && $var ne "ZengWang2007" ) { + $log->fatal_error("$var is incorrect entry for the namelist variable z0param_method; expected Meier2022 or ZengWang2007"); + } + my $phys = $physv->as_string(); + if ( $phys eq "clm4_5" || $phys eq "clm5_0" ) { + if ( $var eq "Meier2022" ) { + $log->fatal_error("z0param_method = $var and phys = $phys, but this method has been tested only with clm5_1 and later versions; to use with earlier versions, disable this error, and add Meier2022 parameters to the corresponding params file"); + } + } +} +#------------------------------------------------------------------------------- + sub setup_logic_snicar_methods { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; From b3a05fae812fff71fbab3e23eca5c51a10b5914a Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Thu, 18 Jan 2024 14:55:40 -0700 Subject: [PATCH 2042/2067] Add clm51 namelist defaults for crop_residue_removal_frac and tillage_mode --- bld/CLMBuildNamelist.pm | 3 +++ bld/namelist_files/namelist_defaults_ctsm.xml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 14a3a2ddb5..555f0d5f98 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -2262,6 +2262,7 @@ sub setup_logic_crop_inparm { 'use_crop'=>$nl->get_value('use_crop') ); my $crop_residue_removal_frac = $nl->get_value('crop_residue_removal_frac'); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'crop_residue_removal_frac' ); if ( $crop_residue_removal_frac < 0.0 or $crop_residue_removal_frac > 1.0 ) { $log->fatal_error("crop_residue_removal_frac must be in range [0, 1]"); } @@ -2276,6 +2277,8 @@ sub setup_logic_crop_inparm { sub setup_logic_tillage { my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'tillage_mode' ); + my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." ); diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index fd5b18f132..5ae01ef2ae 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -555,6 +555,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case). .true. 0.d+0 +0.5d00 constant @@ -2814,6 +2815,8 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 off +low + .false. 0.26d00 From 7b14631ef2f7fc5ab02e00669f8580c11f842a86 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 19 Jan 2024 09:32:26 -0700 Subject: [PATCH 2043/2067] Add new expected failures to ExpectedTestFails.xml --- cime_config/testdefs/ExpectedTestFails.xml | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index 16fff0e71e..55d1363e6b 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -228,4 +228,25 @@ + + + FAIL + #2325 + + + + + + FAIL + #2325 + + + + + + FAIL + #2325 + + + From ed885061bd9b98ebfcb0aa1286cfbea9ade71325 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 Jan 2024 09:42:07 -0700 Subject: [PATCH 2044/2067] run_sys_tests: Check Python environment for FatesColdTwoStream tests. --- python/ctsm/run_sys_tests.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index e4a0bcf009..959d9e52ae 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -249,7 +249,7 @@ def run_sys_tests( else: raise RuntimeError("None of suite_name, testfile or testlist were provided") if not running_ctsm_py_tests: - _try_systemtests(testname_list) + _check_py_env(testname_list) _run_create_test( cime_path=cime_path, test_args=test_args, @@ -708,7 +708,7 @@ def _run_test_suite( ) -def _try_systemtests(testname_list): +def _check_py_env(test_attributes): err_msg = " can't be loaded. Do you need to activate the ctsm_pylib conda environment?" # Suppress pylint import-outside-toplevel warning because (a) we only want to import # this when certain tests are requested, and (b) the import needs to be in a try-except @@ -716,11 +716,21 @@ def _try_systemtests(testname_list): # pylint: disable=import-outside-toplevel disable # Suppress pylint unused-import warning because the import itself IS the use. # pylint: disable=unused-import disable - if any("FSURDATMODIFYCTSM" in t for t in testname_list): + if any("FSURDATMODIFYCTSM" in t for t in test_attributes): try: import ctsm.modify_input_files.modify_fsurdat except ModuleNotFoundError as err: raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err + if any("FatesColdTwoStream" in t for t in test_attributes): + # This bit is needed because it's outside the top-level python/ directory. + _FATES_DIR = os.path.join( + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir,"src", "fates" + ) + sys.path.insert(1, _FATES_DIR) + try: + import tools.modify_fates_paramfile + except ModuleNotFoundError as err: + raise ModuleNotFoundError("modify_fates_paramfile" + err_msg) from err def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests): @@ -730,7 +740,8 @@ def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests): "No tests found for suite {} on machine {}".format(suite_name, machine_name) ) if not running_ctsm_py_tests: - _try_systemtests([t["testname"] for t in test_data]) + _check_py_env([t["testname"] for t in test_data]) + _check_py_env([t["testmods"] for t in test_data]) compilers = sorted({one_test["compiler"] for one_test in test_data}) logger.info("Running with compilers: %s", compilers) return compilers From 4f65f39b2baf856150f8ade9268205da385866b2 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 Jan 2024 10:36:33 -0700 Subject: [PATCH 2045/2067] run_sys_tests: Check exact name of testmods. --- python/ctsm/run_sys_tests.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 959d9e52ae..c996f3fdaa 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -716,12 +716,25 @@ def _check_py_env(test_attributes): # pylint: disable=import-outside-toplevel disable # Suppress pylint unused-import warning because the import itself IS the use. # pylint: disable=unused-import disable + + # Check requirements for FSURDATMODIFYCTSM, if needed if any("FSURDATMODIFYCTSM" in t for t in test_attributes): try: import ctsm.modify_input_files.modify_fsurdat except ModuleNotFoundError as err: raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err - if any("FatesColdTwoStream" in t for t in test_attributes): + + # Isolate testmods, producing a list like ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] + test_attributes_split = [] + for t in test_attributes: + for x in t.split("."): + y = x.replace("/", "-") + for z in y.split("--"): + test_attributes_split.append(z) + + # Check that list for any testmods that use modify_fates_paramfile.py + testmods_to_check = ["clm-FatesColdTwoStream", "clm-FatesColdTwoStreamNoCompFixedBioGeo"] + if any(t in testmods_to_check for t in test_attributes_split): # This bit is needed because it's outside the top-level python/ directory. _FATES_DIR = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir,"src", "fates" From 33be9f67aab9b0db6fa46014e6aa0297024300c4 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 Jan 2024 10:56:09 -0700 Subject: [PATCH 2046/2067] run_sys_tests: Handle tests without testmods. --- python/ctsm/run_sys_tests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index c996f3fdaa..7dcafd059f 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -754,7 +754,7 @@ def _get_compilers_for_suite(suite_name, machine_name, running_ctsm_py_tests): ) if not running_ctsm_py_tests: _check_py_env([t["testname"] for t in test_data]) - _check_py_env([t["testmods"] for t in test_data]) + _check_py_env([t["testmods"] for t in test_data if "testmods" in t.keys()]) compilers = sorted({one_test["compiler"] for one_test in test_data}) logger.info("Running with compilers: %s", compilers) return compilers From c5966a4a77b908f673a0738ab94dd4b4638af410 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 Jan 2024 10:57:21 -0700 Subject: [PATCH 2047/2067] run_sys_tests: Changes to satisfy pylint. --- python/ctsm/run_sys_tests.py | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 7dcafd059f..0d6cf9dcd5 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -716,6 +716,9 @@ def _check_py_env(test_attributes): # pylint: disable=import-outside-toplevel disable # Suppress pylint unused-import warning because the import itself IS the use. # pylint: disable=unused-import disable + # Suppress pylint import-error warning because the whole point here is to check + # whether import is possible. + # pylint: disable=import-error disable # Check requirements for FSURDATMODIFYCTSM, if needed if any("FSURDATMODIFYCTSM" in t for t in test_attributes): @@ -724,22 +727,23 @@ def _check_py_env(test_attributes): except ModuleNotFoundError as err: raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err - # Isolate testmods, producing a list like ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] + # Isolate testmods, producing a list like\ + # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] test_attributes_split = [] - for t in test_attributes: - for x in t.split("."): - y = x.replace("/", "-") - for z in y.split("--"): - test_attributes_split.append(z) + for test_attribute in test_attributes: + for dot_split in test_attribute.split("."): + slash_replaced = dot_split.replace("/", "-") + for ddash_split in slash_replaced.split("--"): + test_attributes_split.append(ddash_split) # Check that list for any testmods that use modify_fates_paramfile.py testmods_to_check = ["clm-FatesColdTwoStream", "clm-FatesColdTwoStreamNoCompFixedBioGeo"] if any(t in testmods_to_check for t in test_attributes_split): # This bit is needed because it's outside the top-level python/ directory. - _FATES_DIR = os.path.join( + fates_dir = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir,"src", "fates" ) - sys.path.insert(1, _FATES_DIR) + sys.path.insert(1, fates_dir) try: import tools.modify_fates_paramfile except ModuleNotFoundError as err: From 0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 Jan 2024 10:57:57 -0700 Subject: [PATCH 2048/2067] run_sys_tests: Reformatting with black. --- python/ctsm/run_sys_tests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 0d6cf9dcd5..033edf918d 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -741,7 +741,7 @@ def _check_py_env(test_attributes): if any(t in testmods_to_check for t in test_attributes_split): # This bit is needed because it's outside the top-level python/ directory. fates_dir = os.path.join( - os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir,"src", "fates" + os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "src", "fates" ) sys.path.insert(1, fates_dir) try: From 41e7db5ba74f0a0a4673c9f81fb0cf94ca75eda1 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Fri, 19 Jan 2024 10:58:46 -0700 Subject: [PATCH 2049/2067] Added previous commit to .git-blame-ignore-revs. --- .git-blame-ignore-revs | 1 + 1 file changed, 1 insertion(+) diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index e63de8e099..8708f8e0c2 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -21,6 +21,7 @@ e4d38681df23ccca0ae29581a45f8362574e0630 025d5e7c2e80263717fb029101d65cbbf261c3c4 a9d96219902cf609636886c7073a84407f450d9a d866510188d26d51bcd6d37239283db690af7e82 +0dcd0a3c1abcaffe5529f8d79a6bc34734b195c7 # Ran SystemTests and python/ctsm through black python formatter 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c 8056ae649c1b37f5e10aaaac79005d6e3a8b2380 From 0244d13a6ce2e87f5bd38947dfb573d58e89e4cd Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 19 Jan 2024 10:59:39 -0700 Subject: [PATCH 2050/2067] Making sure tillage stays off when use_crop = .false. --- bld/CLMBuildNamelist.pm | 9 +++++---- bld/namelist_files/namelist_defaults_ctsm.xml | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm index 555f0d5f98..dae7b5f7f0 100755 --- a/bld/CLMBuildNamelist.pm +++ b/bld/CLMBuildNamelist.pm @@ -1637,7 +1637,7 @@ sub process_namelist_inline_logic { ############################### # namelist group: tillage # ############################### - setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl); + setup_logic_tillage($opts, $nl_flags, $definition, $defaults, $nl, $physv); ############################### # namelist group: ch4par_in # @@ -2275,12 +2275,13 @@ sub setup_logic_crop_inparm { #------------------------------------------------------------------------------- sub setup_logic_tillage { - my ($opts, $nl_flags, $definition, $defaults, $nl) = @_; + my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_; - add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'tillage_mode' ); + add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'tillage_mode', + 'use_crop'=>$nl_flags->{'use_crop'}, 'phys'=>$physv->as_string() ); my $tillage_mode = remove_leading_and_trailing_quotes( $nl->get_value( "tillage_mode" ) ); - if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl->get_value('use_crop')) ) { + if ( $tillage_mode ne "off" && $tillage_mode ne "" && not &value_is_true($nl_flags->{'use_crop'}) ) { $log->fatal_error( "Tillage only works on crop columns, so use_crop must be true if tillage is enabled." ); } } diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index 5ae01ef2ae..d5d8bc08eb 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -2815,7 +2815,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1 off -low +low .false. 0.26d00 From 9a54faf4b8ebd908bdf21acc6fe73d14bba8bb69 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Fri, 19 Jan 2024 18:57:31 -0700 Subject: [PATCH 2051/2067] Updated ChangeLog/ChangeSum --- doc/ChangeLog | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 3 +- 2 files changed, 78 insertions(+), 1 deletion(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 5b4a214880..ee6314d1cc 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,80 @@ =============================================================== +Tag name: ctsm5.1.dev165 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), oleson (Keith Oleson), samrabin (Sam Rabin) +Date: Fri 19 Jan 2024 06:40:36 PM MST +One-line Summary: Turn Meier2022, tillage, and residue removal on for ctsm5.1, fix #2212 + +Purpose and description of changes +---------------------------------- + +Answer-changing merge-tag: +- Turn Meier2022 on for ctsm5.1. Had turned off temporarily while fixing a bug. +- Bring in Urban answer fix #2212. +- Turn tillage and residue removal on for ctsm5.1. + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[x] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- +CTSM issues fixed (include CTSM Issue #): +Fixes #2212 + +Notes of particular relevance for users +--------------------------------------- +Changes made to namelist defaults (e.g., changed parameter values): +- Making Meier2022 the default for ctsm5.1 again. +- Making tillage low by default for ctsm5.1. +- Making residue removal 0.5 by default for ctsm5.1. + +Testing summary: +---------------- + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + +Answer changes +-------------- + +Changes answers relative to baseline: YES + + [ If a tag changes answers relative to baseline comparison the + following should be filled in (otherwise remove this section). + And always remove these three lines and parts that don't apply. ] + + Summarize any changes to answers, i.e., + - what code configurations: ALL + - what platforms/compilers: ALL + - nature of change:i + clm45 and clm50: larger than roundoff + clm51: possibly climate changing + Effect of Meier2022 was documented here: https://github.com/NCAR/LMWG_dev/issues/38 + Effect of tillage and residue removal may require an Answer Changing Tag simulation + +Other details +------------- +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2323 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev164 Originator(s): rgknox (Ryan Knox) Date: Wed 17 Jan 2024 12:38:18 PM MST diff --git a/doc/ChangeSum b/doc/ChangeSum index dee25d848c..0d563ec2bb 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,7 +1,8 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev165 slevis 01/19/2024 Turn Meier2022, tillage, residue removal on for ctsm5.1, fix #2212 ctsm5.1.dev164 rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream - ctsm5.1.dev163 sam 01/10/2024 Add tillage and residue removal + ctsm5.1.dev163 samrabin 01/10/2024 Add tillage and residue removal ctsm5.1.dev162 samrabin 01/05/2024 Improvements to processing of crop calendar files ctsm5.1.dev161 samrabin 01/04/2024 Refactor 20-year running means of crop GDD accumulation ctsm5.1.dev160 glemieux 12/30/2023 FATES landuse version 1 From 975e628b10ce49990cc60846079f2f735508caaf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Jan 2024 10:07:07 -0700 Subject: [PATCH 2052/2067] Fix typo in comment. --- python/ctsm/run_sys_tests.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 033edf918d..33ff158f27 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -727,7 +727,7 @@ def _check_py_env(test_attributes): except ModuleNotFoundError as err: raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err - # Isolate testmods, producing a list like\ + # Isolate testmods, producing a list like # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] test_attributes_split = [] for test_attribute in test_attributes: From 473a581de75ceead7c690938b5cfb8fafc9a2001 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Jan 2024 11:06:41 -0700 Subject: [PATCH 2053/2067] run_sys_tests: Functionize _get_testmod_list(). --- python/ctsm/run_sys_tests.py | 26 ++++++++++++++++---------- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 33ff158f27..a386598766 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -708,6 +708,20 @@ def _run_test_suite( ) +def _get_testmod_list(test_attributes): + # Isolate testmods, producing a list like + # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] + # Handles test attributes passed in from run_sys_tests calls using -t, -f, or -s + + testmods = [] + for test_attribute in test_attributes: + for dot_split in test_attribute.split("."): + slash_replaced = dot_split.replace("/", "-") + for ddash_split in slash_replaced.split("--"): + testmods.append(ddash_split) + return testmods + + def _check_py_env(test_attributes): err_msg = " can't be loaded. Do you need to activate the ctsm_pylib conda environment?" # Suppress pylint import-outside-toplevel warning because (a) we only want to import @@ -727,18 +741,10 @@ def _check_py_env(test_attributes): except ModuleNotFoundError as err: raise ModuleNotFoundError("modify_fsurdat" + err_msg) from err - # Isolate testmods, producing a list like - # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] - test_attributes_split = [] - for test_attribute in test_attributes: - for dot_split in test_attribute.split("."): - slash_replaced = dot_split.replace("/", "-") - for ddash_split in slash_replaced.split("--"): - test_attributes_split.append(ddash_split) - # Check that list for any testmods that use modify_fates_paramfile.py testmods_to_check = ["clm-FatesColdTwoStream", "clm-FatesColdTwoStreamNoCompFixedBioGeo"] - if any(t in testmods_to_check for t in test_attributes_split): + testmods = _get_testmod_list(test_attributes) + if any(t in testmods_to_check for t in testmods): # This bit is needed because it's outside the top-level python/ directory. fates_dir = os.path.join( os.path.dirname(os.path.realpath(__file__)), os.pardir, os.pardir, "src", "fates" From 039a243f52d6a1f565ebed513fe90084e14fbd8b Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Jan 2024 11:12:34 -0700 Subject: [PATCH 2054/2067] Add 'unique' option to _get_testmod_list(), default True. --- python/ctsm/run_sys_tests.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index a386598766..7e232d8efe 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -708,7 +708,7 @@ def _run_test_suite( ) -def _get_testmod_list(test_attributes): +def _get_testmod_list(test_attributes, unique=True): # Isolate testmods, producing a list like # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] # Handles test attributes passed in from run_sys_tests calls using -t, -f, or -s @@ -718,7 +718,9 @@ def _get_testmod_list(test_attributes): for dot_split in test_attribute.split("."): slash_replaced = dot_split.replace("/", "-") for ddash_split in slash_replaced.split("--"): - testmods.append(ddash_split) + if ddash_split not in testmods or not unique: + testmods.append(ddash_split) + return testmods From a7dbc378cf88f2e0befdd34e83bca5902995fa89 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Jan 2024 11:45:03 -0700 Subject: [PATCH 2055/2067] _get_testmod_list(): Only include strings with 'clm-'. --- python/ctsm/run_sys_tests.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/python/ctsm/run_sys_tests.py b/python/ctsm/run_sys_tests.py index 7e232d8efe..de93081504 100644 --- a/python/ctsm/run_sys_tests.py +++ b/python/ctsm/run_sys_tests.py @@ -708,7 +708,7 @@ def _run_test_suite( ) -def _get_testmod_list(test_attributes, unique=True): +def _get_testmod_list(test_attributes, unique=False): # Isolate testmods, producing a list like # ["clm-test1mod1", "clm-test2mod1", "clm-test2mod2", ...] # Handles test attributes passed in from run_sys_tests calls using -t, -f, or -s @@ -718,7 +718,7 @@ def _get_testmod_list(test_attributes, unique=True): for dot_split in test_attribute.split("."): slash_replaced = dot_split.replace("/", "-") for ddash_split in slash_replaced.split("--"): - if ddash_split not in testmods or not unique: + if "clm-" in ddash_split and (ddash_split not in testmods or not unique): testmods.append(ddash_split) return testmods From 8d7d88a245b7f0e7fc4d10a060a5fee567ada2de Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Jan 2024 11:45:42 -0700 Subject: [PATCH 2056/2067] Add unit tests for _get_testmod_list(). --- python/ctsm/test/test_unit_run_sys_tests.py | 53 ++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/python/ctsm/test/test_unit_run_sys_tests.py b/python/ctsm/test/test_unit_run_sys_tests.py index ee5197d76f..65ec1df5a5 100755 --- a/python/ctsm/test/test_unit_run_sys_tests.py +++ b/python/ctsm/test/test_unit_run_sys_tests.py @@ -16,7 +16,7 @@ from ctsm import add_cime_to_path # pylint: disable=unused-import from ctsm import unit_testing -from ctsm.run_sys_tests import run_sys_tests +from ctsm.run_sys_tests import run_sys_tests, _get_testmod_list from ctsm.machine_defaults import MACHINE_DEFAULTS from ctsm.machine import create_machine from ctsm.joblauncher.job_launcher_factory import JOB_LAUNCHER_FAKE @@ -269,6 +269,57 @@ def test_withDryRun_nothingDone(self): self.assertEqual(os.listdir(self._scratch), []) self.assertEqual(machine.job_launcher.get_commands(), []) + def test_getTestmodList_suite(self): + """Ensure that _get_testmod_list() works correctly with suite-style input""" + input = [ + "clm/default", + "clm/default", + "clm/crop", + "clm/cropMonthlyOutput", + ] + target = [ + "clm-default", + "clm-default", + "clm-crop", + "clm-cropMonthlyOutput", + ] + output = _get_testmod_list(input, unique=False) + self.assertEqual(output, target) + + def test_getTestmodList_suite_unique(self): + """Ensure that _get_testmod_list() works correctly with unique=True""" + input = [ + "clm/default", + "clm/default", + "clm/crop", + "clm/cropMonthlyOutput", + ] + target = [ + "clm-default", + "clm-crop", + "clm-cropMonthlyOutput", + ] + + output = _get_testmod_list(input, unique=True) + self.assertEqual(output, target) + + def test_getTestmodList_testname(self): + """Ensure that _get_testmod_list() works correctly with full test name(s) specified""" + input = [ + "ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-crop", + "ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-default", + ] + target = ["clm-crop", "clm-default"] + output = _get_testmod_list(input) + self.assertEqual(output, target) + + def test_getTestmodList_twomods(self): + """Ensure that _get_testmod_list() works correctly with full test name(s) specified and two mods in one test""" + input = ["ERS_D_Ld15.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-default--clm-crop"] + target = ["clm-default", "clm-crop"] + output = _get_testmod_list(input) + self.assertEqual(output, target) + if __name__ == "__main__": unit_testing.setup_for_tests() From 4ae91064cf476e1b6ce76d98f7ec668befedaa1d Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Mon, 22 Jan 2024 12:58:51 -0700 Subject: [PATCH 2057/2067] Add Izumi version of the aux_clm unit testing. --- cime_config/testdefs/testlist_clm.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index c915552748..4761a2111f 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -3433,6 +3433,7 @@ + From 02950989606c1c772303fe21ab3a1fc3dca6c076 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Tue, 23 Jan 2024 18:09:59 -0700 Subject: [PATCH 2058/2067] First drafts of ChangeLog/ChangeSum --- doc/ChangeLog | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 82 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index ee6314d1cc..34af74d42d 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,85 @@ =============================================================== +Tag name: ctsm5.1.dev166 +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), tking (Teagan King), afoster (Adrianna Foster), samrabin (Sam Rabin) +Date: Tue 23 Jan 2024 05:48:34 PM MST +One-line Summary: BFB merge tag + +Purpose and description of changes +---------------------------------- + + #2315 @TeaganKing Refactoring run_neon for PLUMBER2 part1 + #2213 @samsrabin Automatically assign high priority items to project 25 + #2330 @samsrabin Add Izumi version of the aux_clm unit testing + #2326 @samsrabin run_sys_tests: Check Python environment for FatesColdTwoStream tests +KEEP? #2124 @adrifoster Create helper function for interpMontlyVeg to improve readability + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + + [Put an [X] in the box for any configuration with significant answer changes.] + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +CTSM issues fixed (include CTSM Issue #): + Fixes #2315 + Fixes #2213 + Fixes #2330 + Fixes #2326 +KEEP? Fixes #2124 + +Known bugs introduced in this tag (include issue #): + New feature coming in with #2213 where user will receive email from + github when pushing to their remote: + "Run failed: .github/workflows/assign-to-project.yml" + +Notes of particular relevance for developers: +--------------------------------------------- +Changes to tests or testing: + #2315 New unit tests for arg_parse and NeonSite + #2330 New test in aux_clm that does unit testing on izumi because unit + testing does not work on derecho, yet + +Testing summary: +---------------- + + [PASS means all tests PASS; OK means tests PASS other than expected fails.] + + python testing (if python code has changed; see instructions in python/README.md; document testing done): + + derecho - OK, pylint gives long list of warnings (expected) + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- + izumi ------- + + +Answer changes +-------------- + +Changes answers relative to baseline: No + +Other details +------------- + +Pull Requests that document the changes (include PR ids): + https://github.com/ESCOMP/ctsm/pull/2334 + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev165 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), oleson (Keith Oleson), samrabin (Sam Rabin) Date: Fri 19 Jan 2024 06:40:36 PM MST diff --git a/doc/ChangeSum b/doc/ChangeSum index 0d563ec2bb..a796d1b09f 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev166 multiple 01/23/2024 BFB merge tag ctsm5.1.dev165 slevis 01/19/2024 Turn Meier2022, tillage, residue removal on for ctsm5.1, fix #2212 ctsm5.1.dev164 rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream ctsm5.1.dev163 samrabin 01/10/2024 Add tillage and residue removal From 8b262bdc0ec4972ec786ea8659ea8d300e2322d2 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 24 Jan 2024 11:40:54 -0700 Subject: [PATCH 2059/2067] Revert "Merge remote-tracking branch 'adrifoster/interpMonthlyVeg_helper_function' into bfb_merge_tag_2315_et_al" This reverts commit d327ec5cfa4ce4eab53a66fc71cc1c3c8395fe61, reversing changes made to 8189178f49574c46990694024444dac7153e175e. --- src/biogeochem/SatellitePhenologyMod.F90 | 50 ------------------------ src/main/clm_driver.F90 | 37 +++++++++++++++++- 2 files changed, 35 insertions(+), 52 deletions(-) diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90 index 7714af02eb..3e9341f430 100644 --- a/src/biogeochem/SatellitePhenologyMod.F90 +++ b/src/biogeochem/SatellitePhenologyMod.F90 @@ -28,7 +28,6 @@ module SatellitePhenologyMod public :: SatellitePhenologyInit ! Dynamically allocate memory public :: interpMonthlyVeg ! interpolate monthly vegetation data public :: readAnnualVegetation ! Read in annual vegetation (needed for Dry-deposition) - public :: do_interpMonthlyVeg ! whether or not to call interpMonthlyVeg ! ! !PRIVATE MEMBER FUNCTIONS: private :: readMonthlyVegetation ! read monthly vegetation data for two months @@ -258,55 +257,6 @@ subroutine interpMonthlyVeg (bounds, canopystate_inst) end subroutine interpMonthlyVeg !============================================================================== - - logical function do_interpMonthlyVeg(use_cn, use_fates, use_fates_sp, doalb, n_drydep) - ! - ! !DESCRIPTION: - ! returns whether or not to conduct interpMonthlyVeg subroutine - ! - ! !ARGUMENTS: - logical, intent(in) :: use_cn ! are we using the big-leaf, BGC version of model? - logical, intent(in) :: use_fates ! are we running FATES? - logical, intent(in) :: use_fates_sp ! are we running FATES-SP? - logical, intent(in) :: doalb ! true if time for surface albedo calc - integer, intent(in) :: n_drydep ! number in drypdep list - - if (use_cn .and. n_drydep > 0) then - - ! For dry-deposition need to call CLMSP so that mlaidiff is obtained - ! NOTE: This is also true of FATES below - do_interpMonthlyVeg = .true. - - else if (use_fates .and. use_fates_sp) then - - ! For FATES-Specified phenology mode interpolate the weights for - ! time-interpolation of monthly vegetation data (as in SP mode below) - ! Also for FATES with dry-deposition as above need to call CLMSP so that mlaidiff is obtained - !if ( use_fates_sp .or. (n_drydep > 0 ) ) then ! Replace with this when we have dry-deposition working - ! For now don't allow for dry-deposition because of issues in #1044 EBK Jun/17/2022 - do_interpMonthlyVeg = .true. - - else if (doalb .or. n_drydep > 0) then - - ! Determine weights for time interpolation of monthly vegetation data. - ! This also determines whether it is time to read new monthly vegetation and - ! obtain updated leaf area index [mlai1,mlai2], stem area index [msai1,msai2], - ! vegetation top [mhvt1,mhvt2] and vegetation bottom [mhvb1,mhvb2]. The - ! weights obtained here are used in subroutine SatellitePhenology to obtain time - ! interpolated values. - ! This is also done for FATES-SP mode above - do_interpMonthlyVeg = .true. - - else - - do_interpMonthlyVeg = .false. - - end if - - end function do_interpMonthlyVeg - - !============================================================================== - subroutine readAnnualVegetation (bounds, canopystate_inst) ! ! !DESCRIPTION: diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90 index 47dcf37cf0..33e9412ba9 100644 --- a/src/main/clm_driver.F90 +++ b/src/main/clm_driver.F90 @@ -58,7 +58,7 @@ module clm_driver use UrbanRadiationMod , only : UrbanRadiation ! use SoilBiogeochemVerticalProfileMod , only : SoilBiogeochemVerticalProfile - use SatellitePhenologyMod , only : SatellitePhenology, interpMonthlyVeg, do_interpMonthlyVeg + use SatellitePhenologyMod , only : SatellitePhenology, interpMonthlyVeg use ndepStreamMod , only : ndep_interp use cropcalStreamMod , only : cropcal_advance, cropcal_interp use ch4Mod , only : ch4, ch4_init_gridcell_balance_check, ch4_init_column_balance_check @@ -227,11 +227,44 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro ! Specified phenology ! Done in SP mode, FATES-SP mode and also when dry-deposition is active ! ============================================================================ + + if (use_cn) then + ! For dry-deposition need to call CLMSP so that mlaidiff is obtained + ! NOTE: This is also true of FATES below + if ( n_drydep > 0 ) then + call t_startf('interpMonthlyVeg') + call interpMonthlyVeg(bounds_proc, canopystate_inst) + call t_stopf('interpMonthlyVeg') + endif - if (do_interpMonthlyVeg(use_cn, use_fates, use_fates_sp, doalb, n_drydep)) then + elseif(use_fates) then + + ! For FATES-Specified phenology mode interpolate the weights for + ! time-interpolation of monthly vegetation data (as in SP mode below) + ! Also for FATES with dry-deposition as above need to call CLMSP so that mlaidiff is obtained + !if ( use_fates_sp .or. (n_drydep > 0 ) ) then ! Replace with this when we have dry-deposition working + ! For now don't allow for dry-deposition because of issues in #1044 EBK Jun/17/2022 + if ( use_fates_sp ) then call t_startf('interpMonthlyVeg') call interpMonthlyVeg(bounds_proc, canopystate_inst) call t_stopf('interpMonthlyVeg') + end if + + else + + ! Determine weights for time interpolation of monthly vegetation data. + ! This also determines whether it is time to read new monthly vegetation and + ! obtain updated leaf area index [mlai1,mlai2], stem area index [msai1,msai2], + ! vegetation top [mhvt1,mhvt2] and vegetation bottom [mhvb1,mhvb2]. The + ! weights obtained here are used in subroutine SatellitePhenology to obtain time + ! interpolated values. + ! This is also done for FATES-SP mode above + if ( doalb .or. ( n_drydep > 0 ) )then + call t_startf('interpMonthlyVeg') + call interpMonthlyVeg(bounds_proc, canopystate_inst) + call t_stopf('interpMonthlyVeg') + end if + end if ! ================================================================================== From 6a27557ff72c615359f457f2459a668a762a4c12 Mon Sep 17 00:00:00 2001 From: Samuel Levis Date: Wed, 24 Jan 2024 17:41:02 -0700 Subject: [PATCH 2060/2067] Updated ChangeLog/ChangeSum --- doc/ChangeLog | 19 ++++++++++--------- doc/ChangeSum | 2 +- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/doc/ChangeLog b/doc/ChangeLog index 34af74d42d..dbb9b05c84 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,7 +1,7 @@ =============================================================== Tag name: ctsm5.1.dev166 -Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), tking (Teagan King), afoster (Adrianna Foster), samrabin (Sam Rabin) -Date: Tue 23 Jan 2024 05:48:34 PM MST +Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), tking (Teagan King), samrabin (Sam Rabin) +Date: Wed 24 Jan 2024 05:39:41 PM MST One-line Summary: BFB merge tag Purpose and description of changes @@ -11,7 +11,6 @@ Purpose and description of changes #2213 @samsrabin Automatically assign high priority items to project 25 #2330 @samsrabin Add Izumi version of the aux_clm unit testing #2326 @samsrabin run_sys_tests: Check Python environment for FatesColdTwoStream tests -KEEP? #2124 @adrifoster Create helper function for interpMontlyVeg to improve readability Significant changes to scientifically-supported configurations -------------------------------------------------------------- @@ -38,12 +37,16 @@ CTSM issues fixed (include CTSM Issue #): Fixes #2213 Fixes #2330 Fixes #2326 -KEEP? Fixes #2124 Known bugs introduced in this tag (include issue #): - New feature coming in with #2213 where user will receive email from + - New feature coming in with #2213 where user will receive email from github when pushing to their remote: "Run failed: .github/workflows/assign-to-project.yml" + - New feature that also affects older tags: The izumi FatesColdTwoStream + test submitted from ./run_sys_tests will fail at CREATE_NEWCASE unless users + introduce "module load lang/python/3.7.0" in their .bash_profile. + Longterm solution discussed in #2335. The test also works when submitted + manually with ./create_test. Notes of particular relevance for developers: --------------------------------------------- @@ -63,18 +66,16 @@ Testing summary: regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): - derecho ----- - izumi ------- + derecho ----- OK + izumi ------- OK Answer changes -------------- - Changes answers relative to baseline: No Other details ------------- - Pull Requests that document the changes (include PR ids): https://github.com/ESCOMP/ctsm/pull/2334 diff --git a/doc/ChangeSum b/doc/ChangeSum index a796d1b09f..bfc8b86174 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,6 +1,6 @@ Tag Who Date Summary ============================================================================================================================ - ctsm5.1.dev166 multiple 01/23/2024 BFB merge tag + ctsm5.1.dev166 multiple 01/24/2024 BFB merge tag ctsm5.1.dev165 slevis 01/19/2024 Turn Meier2022, tillage, residue removal on for ctsm5.1, fix #2212 ctsm5.1.dev164 rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream ctsm5.1.dev163 samrabin 01/10/2024 Add tillage and residue removal From 99bd6018268a0cf75f09d6106fdd3200d66fc2bf Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 31 Jan 2024 14:55:46 -0700 Subject: [PATCH 2061/2067] Remove backticks from assign-to-project.yml --- .github/workflows/assign-to-project.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml index 8c6c259c33..c51a4a6cba 100644 --- a/.github/workflows/assign-to-project.yml +++ b/.github/workflows/assign-to-project.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest name: Assign to High Priority project steps: - - name: Assign issues and pull requests with `priority: high` label to project 25 + - name: Assign issues and pull requests with priority: high label to project 25 uses: srggrs/assign-one-project-github-action@1.3.1 if: | contains(github.event.issue.labels.*.name, 'priority: high') || From 829da767707b8e8576563411e38f5691aa9d10e5 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 1 Feb 2024 08:31:43 -0700 Subject: [PATCH 2062/2067] Remove a colon from assign-to-project.yml --- .github/workflows/assign-to-project.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/assign-to-project.yml b/.github/workflows/assign-to-project.yml index c51a4a6cba..225c223bde 100644 --- a/.github/workflows/assign-to-project.yml +++ b/.github/workflows/assign-to-project.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest name: Assign to High Priority project steps: - - name: Assign issues and pull requests with priority: high label to project 25 + - name: Assign issues and pull requests with priority-high label to project 25 uses: srggrs/assign-one-project-github-action@1.3.1 if: | contains(github.event.issue.labels.*.name, 'priority: high') || From 1949f5c76897016d8d2d6de9ce93eb75cb7a1a51 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 7 Feb 2024 16:32:39 -0700 Subject: [PATCH 2063/2067] Update parameter files to 240207 (delete _FillValue and history). --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++--- .../testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm | 2 +- py_env_create | 2 +- python/conda_env_ctsm_py.txt | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index d5d8bc08eb..e065807741 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -484,9 +484,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/ctsm51_params.c240105.nc -lnd/clm2/paramdata/clm50_params.c240105.nc -lnd/clm2/paramdata/clm45_params.c240105.nc +lnd/clm2/paramdata/ctsm51_params.c240207.nc +lnd/clm2/paramdata/clm50_params.c240207.nc +lnd/clm2/paramdata/clm45_params.c240207.nc diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm index 4e073859be..8135bddf3b 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm @@ -1,2 +1,2 @@ -paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240105.nc' +paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240207.nc' hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr' diff --git a/py_env_create b/py_env_create index c323a374df..a2a2bbbcb7 100755 --- a/py_env_create +++ b/py_env_create @@ -23,7 +23,7 @@ if [ $error != 0 ]; then exit -1 fi rm condahelp.txt -ctsm_python=ctsm_pylib +ctsm_python=ctsm_pylib3 condadir="$dir/python" diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index e621081591..e469c3e37a 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -18,9 +18,9 @@ scipy netcdf4 requests packaging -numpy=1.18.5 +numpy xarray=0.17.0 xesmf -numba=0.55.2 # Avoid 0.56 until numpy>=1.20. This is the minimum for xesmf +numba # Avoid 0.56 until numpy>=1.20. This is the minimum for xesmf pylint=2.8.3 black=22.3.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows From 9511108ad5b5939a4b0b9f4f42946140f97800ca Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Wed, 7 Feb 2024 16:48:10 -0700 Subject: [PATCH 2064/2067] Revert accidental changes re: ctsm_pylib --- py_env_create | 2 +- python/conda_env_ctsm_py.txt | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/py_env_create b/py_env_create index a2a2bbbcb7..c323a374df 100755 --- a/py_env_create +++ b/py_env_create @@ -23,7 +23,7 @@ if [ $error != 0 ]; then exit -1 fi rm condahelp.txt -ctsm_python=ctsm_pylib3 +ctsm_python=ctsm_pylib condadir="$dir/python" diff --git a/python/conda_env_ctsm_py.txt b/python/conda_env_ctsm_py.txt index e469c3e37a..e621081591 100644 --- a/python/conda_env_ctsm_py.txt +++ b/python/conda_env_ctsm_py.txt @@ -18,9 +18,9 @@ scipy netcdf4 requests packaging -numpy +numpy=1.18.5 xarray=0.17.0 xesmf -numba # Avoid 0.56 until numpy>=1.20. This is the minimum for xesmf +numba=0.55.2 # Avoid 0.56 until numpy>=1.20. This is the minimum for xesmf pylint=2.8.3 black=22.3.0 # NOTE: The version here needs to be coordinated with the black github action under ../.github/workflows From dca964c2cb939ac30e10eca11fb1310f1a5aed21 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 8 Feb 2024 11:28:28 -0700 Subject: [PATCH 2065/2067] Update ChangeLog and ChangeSum. --- doc/ChangeLog | 52 +++++++++++++++++++++++++++++++++++++++++++++++++++ doc/ChangeSum | 1 + 2 files changed, 53 insertions(+) diff --git a/doc/ChangeLog b/doc/ChangeLog index dbb9b05c84..84787d3087 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,56 @@ =============================================================== +Tag name: ctsm5.1.dev167 +Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) +Date: Thu Feb 8 11:24:15 MST 2024 +One-line Summary: Delete _FillValue and history from parameter files + +Purpose and description of changes +---------------------------------- + +Updates parameter files to c240207. These are the same as c240105 except: +- Attribute _FillValue has been removed from all variables +- Global attributes history, history_of_appended_files, and latest_git_log have been removed + + +Significant changes to scientifically-supported configurations +-------------------------------------------------------------- + +Does this tag change answers significantly for any of the following physics configurations? +(Details of any changes will be given in the "Answer changes" section below.) + +[ ] clm5_1 + +[ ] clm5_0 + +[ ] ctsm5_0-nwp + +[ ] clm4_5 + + +Bugs fixed +---------- + +CTSM issues fixed (include CTSM Issue #): +- Fixes #2347 + + +Testing summary: +---------------- + + regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing): + + derecho ----- OK + izumi ------- OK + + +Other details +------------- + +Pull Requests that document the changes (include PR ids): +- #2350: Delete _FillValue and history from parameter files (https://github.com/ESCOMP/CTSM/pull/2350) + +=============================================================== +=============================================================== Tag name: ctsm5.1.dev166 Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310), tking (Teagan King), samrabin (Sam Rabin) Date: Wed 24 Jan 2024 05:39:41 PM MST diff --git a/doc/ChangeSum b/doc/ChangeSum index bfc8b86174..d644cff144 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + ctsm5.1.dev167 samrabin 02/08/2024 Delete _FillValue and history from parameter files ctsm5.1.dev166 multiple 01/24/2024 BFB merge tag ctsm5.1.dev165 slevis 01/19/2024 Turn Meier2022, tillage, residue removal on for ctsm5.1, fix #2212 ctsm5.1.dev164 rgknox 01/17/2024 Compatibility and tests for FATES 2-Stream From 4d7493afd7a7a382b7eccc3b75221d28df6f4c81 Mon Sep 17 00:00:00 2001 From: Sam Rabin Date: Thu, 8 Feb 2024 13:55:30 -0700 Subject: [PATCH 2066/2067] Use c240207b parameter files. --- bld/namelist_files/namelist_defaults_ctsm.xml | 6 +++--- .../testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm | 2 +- doc/ChangeLog | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml index e065807741..d3b3cc9715 100644 --- a/bld/namelist_files/namelist_defaults_ctsm.xml +++ b/bld/namelist_files/namelist_defaults_ctsm.xml @@ -484,9 +484,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case). -lnd/clm2/paramdata/ctsm51_params.c240207.nc -lnd/clm2/paramdata/clm50_params.c240207.nc -lnd/clm2/paramdata/clm45_params.c240207.nc +lnd/clm2/paramdata/ctsm51_params.c240207b.nc +lnd/clm2/paramdata/clm50_params.c240207b.nc +lnd/clm2/paramdata/clm45_params.c240207b.nc diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm index 8135bddf3b..c235d72df1 100644 --- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm +++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm @@ -1,2 +1,2 @@ -paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240207.nc' +paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c240207b.nc' hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr' diff --git a/doc/ChangeLog b/doc/ChangeLog index 84787d3087..084516e23e 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,13 +1,13 @@ =============================================================== Tag name: ctsm5.1.dev167 Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu) -Date: Thu Feb 8 11:24:15 MST 2024 +Date: Thu 08 Feb 2024 01:56:05 PM MST One-line Summary: Delete _FillValue and history from parameter files Purpose and description of changes ---------------------------------- -Updates parameter files to c240207. These are the same as c240105 except: +Updates parameter files to c240207b. These are the same as c240105 except: - Attribute _FillValue has been removed from all variables - Global attributes history, history_of_appended_files, and latest_git_log have been removed From 29bb217d70aaf570482e287adf09c6baf4c4054f Mon Sep 17 00:00:00 2001 From: Mariana Vertenstein Date: Mon, 1 Apr 2024 02:41:01 -0600 Subject: [PATCH 2067/2067] put in changes needed for addition of new dglc component --- cime_config/buildnml | 33 ++++++++++++++++++++++----------- 1 file changed, 22 insertions(+), 11 deletions(-) diff --git a/cime_config/buildnml b/cime_config/buildnml index 84e1581406..d2e7ddc886 100755 --- a/cime_config/buildnml +++ b/cime_config/buildnml @@ -60,6 +60,7 @@ def buildnml(case, caseroot, compname): run_reftod = case.get_value("RUN_REFTOD") glc_nec = case.get_value("GLC_NEC") cism_use_antarctica = case.get_value("CISM_USE_ANTARCTICA") + dglc_use_antarctica = case.get_value("DGLC_USE_ANTARCTICA") mask = case.get_value("MASK_GRID") driver = case.get_value("COMP_INTERFACE").lower() @@ -144,8 +145,8 @@ def buildnml(case, caseroot, compname): or clm_usrdat_name is "NEON.PRISM" ): logger.warning( - "WARNING: Do you have approriprate initial conditions for this simulation?" - + " Check that the finidat file used in the lnd_in namelist is apprporiately spunup for your case" + "WARNING: Do you have appropriate initial conditions for this simulation?" + + " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case" ) if comp_atm != "datm": @@ -153,20 +154,30 @@ def buildnml(case, caseroot, compname): else: nomeg = "" - if cism_use_antarctica is None: - # This is the case for compsets without CISM, where the CISM_USE_ANTARCTICA xml - # variable isn't defined + + glc_use_antarctica = cism_use_antarctica + if glc_use_antarctica is None: + glc_use_antarctica = dglc_use_antarctica + if glc_use_antarctica is None: + # This is the case for compsets without CISM or DGLC, where the + # CISM_USE_ANTARCTICA and DGLC_USE_ANTARCTICA xml variables are not defined glc_use_antarctica_flag = "" - elif isinstance(cism_use_antarctica, bool): - if cism_use_antarctica: + elif isinstance(glc_use_antarctica, bool): + if glc_use_antarctica: glc_use_antarctica_flag = "-glc_use_antarctica" else: glc_use_antarctica_flag = "" else: - expect( - False, - "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica), - ) + if cism_use_antarctia: + expect( + False, + "Unexpected value for CISM_USE_ANTARCTICA: {}".format(cism_use_antarctica), + ) + else: + expect( + False, + "Unexpected value for DGLC_USE_ANTARCTICA: {}".format(dglc_use_antarctica), + ) if clm_nml_use_case != "UNSET": usecase = "-use_case %s" % clm_nml_use_case